https://launchpad.net/ubuntu/+source/apbs/3.4.1-5build5/+build/27660352 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos01-arm64-034 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:53:38 UTC 2023 aarch64 Buildd toolchain package versions: launchpad-buildd_235~645~ubuntu20.04.1 python3-lpbuildd_235~645~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 19 Jan 18:59:44 ntpdate[1896]: adjust time server 10.211.37.1 offset -0.004184 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27660352 --image-type chroot /home/buildd/filecache-default/59612f0fc5bae33f6226b6e60c2e882b82c04bd0 Creating target for build PACKAGEBUILD-27660352 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27660352 Starting target for build PACKAGEBUILD-27660352 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27660352 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27660352 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27660352 Updating target for build PACKAGEBUILD-27660352 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [256 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main armhf Packages [1333 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe armhf Packages [14.2 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6019 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [170 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [68.9 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [798 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [338 kB] Fetched 24.0 MB in 4s (6620 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.36 libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.38 libunistring5 perl-modules-5.38 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-arm-linux-gnueabihf binutils-common bsdextrautils bsdutils coreutils cpp cpp-13 debconf debconf-i18n debianutils diffutils dpkg dpkg-dev fakeroot g++ g++-13 gcc gcc-13 gcc-13-base grep init init-system-helpers krb5-locales libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgssapi-krb5-2 libidn2-0 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libpng16-16 libproc2-0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libssl3 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base perl-modules-5.36 pinentry-curses procps psmisc readline-common sed systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring usrmerge util-linux uuid-runtime xz-utils zlib1g 144 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 100 MB of archives. After this operation, 40.7 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main armhf libnsl-dev armhf 1.3.0-3 [65.8 kB] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcrypt-dev armhf 1:4.4.36-4 [136 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main armhf libc6-dev armhf 2.38-3ubuntu1 [1347 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main armhf libc-dev-bin armhf 2.38-3ubuntu1 [18.9 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main armhf libtirpc-common all 1.3.4+ds-1build1 [8566 B] Get:6 http://ftpmaster.internal/ubuntu noble/main armhf libtirpc-dev armhf 1.3.4+ds-1build1 [207 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main armhf libgssapi-krb5-2 armhf 1.20.1-5build1 [118 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main armhf libkrb5-3 armhf 1.20.1-5build1 [320 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main armhf libk5crypto3 armhf 1.20.1-5build1 [78.6 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main armhf libkrb5support0 armhf 1.20.1-5build1 [31.3 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main armhf libssl3 armhf 3.0.10-1ubuntu3 [1560 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main armhf libtirpc3 armhf 1.3.4+ds-1build1 [81.0 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main armhf libnsl2 armhf 1.3.0-3 [35.9 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcrypt1 armhf 1:4.4.36-4 [104 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main armhf linux-libc-dev armhf 6.6.0-14.14 [1539 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcc1-0 armhf 13.2.0-10ubuntu1 [43.8 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libctf0 armhf 2.41.90.20240115-1ubuntu1 [87.7 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libctf-nobfd0 armhf 2.41.90.20240115-1ubuntu1 [87.7 kB] Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils-arm-linux-gnueabihf armhf 2.41.90.20240115-1ubuntu1 [2932 kB] Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbinutils armhf 2.41.90.20240115-1ubuntu1 [459 kB] Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils-common armhf 2.41.90.20240115-1ubuntu1 [216 kB] Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main armhf binutils armhf 2.41.90.20240115-1ubuntu1 [3086 B] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13-base armhf 13.2.0-10ubuntu1 [46.1 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcc-s1 armhf 13.2.0-10ubuntu1 [41.0 kB] Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgomp1 armhf 13.2.0-10ubuntu1 [120 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libatomic1 armhf 13.2.0-10ubuntu1 [7798 B] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libasan8 armhf 13.2.0-10ubuntu1 [2749 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libubsan1 armhf 13.2.0-10ubuntu1 [1072 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main armhf g++-13 armhf 13.2.0-10ubuntu1 [9437 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libstdc++-13-dev armhf 13.2.0-10ubuntu1 [2401 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcc-13-dev armhf 13.2.0-10ubuntu1 [901 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13 armhf 13.2.0-10ubuntu1 [16.5 MB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main armhf cpp-13 armhf 13.2.0-10ubuntu1 [8249 kB] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libstdc++6 armhf 13.2.0-10ubuntu1 [698 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main armhf zlib1g armhf 1:1.3.dfsg-3ubuntu1 [50.6 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsframe1 armhf 2.41.90.20240115-1ubuntu1 [12.8 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main armhf libzstd1 armhf 1.5.5+dfsg2-2 [265 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main armhf libc6 armhf 2.38-3ubuntu1 [2818 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main armhf base-files armhf 13ubuntu6 [84.0 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main armhf debianutils armhf 5.16 [93.1 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main armhf bash armhf 5.2.21-2ubuntu1 [673 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main armhf bsdutils armhf 1:2.39.2-6ubuntu1 [99.5 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main armhf coreutils armhf 9.4-2ubuntu2 [1489 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main armhf diffutils armhf 1:3.10-1 [167 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main armhf libgpg-error-l10n all 1.47-3build1 [8024 B] Get:46 http://ftpmaster.internal/ubuntu noble/main armhf libgpg-error0 armhf 1.47-3build1 [61.6 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcrypt20 armhf 1.10.3-2 [454 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main armhf liblzma5 armhf 5.4.5-0.3 [120 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main armhf libacl1 armhf 2.3.1-4ubuntu1 [16.2 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main armhf libapparmor1 armhf 4.0.0~alpha2-0ubuntu7 [43.8 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main armhf libaudit-common all 1:3.1.2-1 [5512 B] Get:52 http://ftpmaster.internal/ubuntu noble/main armhf libcap-ng0 armhf 0.8.4-1 [14.5 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main armhf libaudit1 armhf 1:3.1.2-1 [44.2 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main armhf libblkid1 armhf 2.39.2-6ubuntu1 [159 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main armhf libkmod2 armhf 30+20230601-2ubuntu1 [43.9 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main armhf libpcre2-8-0 armhf 10.42-4ubuntu1 [198 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main armhf libselinux1 armhf 3.5-1build2 [69.6 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main armhf libmount1 armhf 2.39.2-6ubuntu1 [171 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-iconv-perl armhf 1.7-8build1 [12.6 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-charwidth-perl armhf 0.04-11build1 [8894 B] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-modules-5.38 all 5.38.2-3 [3110 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libperl5.38 armhf 5.38.2-3 [4105 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl armhf 5.38.2-3 [231 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-base armhf 5.38.2-3 [1670 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblocale-gettext-perl armhf 1.07-6build1 [14.8 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main armhf perl-modules-5.36 all 5.36.0-10ubuntu1 [2984 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main armhf libperl5.36 armhf 5.36.0-10ubuntu1 [4019 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main armhf libdb5.3 armhf 5.3.28+dfsg2-4 [652 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main armhf libgdbm6 armhf 1.23-5 [29.8 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main armhf libgdbm-compat4 armhf 1.23-5 [5970 B] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main armhf debconf-i18n all 1.5.83 [238 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main armhf debconf all 1.5.83 [147 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam0g armhf 1.5.2-9.1ubuntu2 [60.2 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libseccomp2 armhf 2.5.4-2ubuntu1 [48.9 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-sysv armhf 255.2-3ubuntu1 [12.5 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-dev all 255.2-3ubuntu1 [107 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd armhf 255.2-3ubuntu1 [3985 kB] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd-shared armhf 255.2-3ubuntu1 [2356 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main armhf libargon2-1 armhf 0~20190702+dfsg-4 [22.3 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main armhf libuuid1 armhf 2.39.2-6ubuntu1 [33.4 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main armhf libcryptsetup12 armhf 2:2.6.1-6ubuntu1 [216 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main armhf libfdisk1 armhf 2.39.2-6ubuntu1 [195 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main armhf mount armhf 2.39.2-6ubuntu1 [132 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd0 armhf 255.2-3ubuntu1 [454 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libudev1 armhf 255.2-3ubuntu1 [176 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main armhf libxxhash0 armhf 0.8.2-2 [31.3 kB] Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapt-pkg6.0 armhf 2.7.10 [984 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main armhf tar armhf 1.35+dfsg-3 [236 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main armhf dpkg armhf 1.22.2ubuntu2 [1253 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main armhf grep armhf 3.11-4 [166 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main armhf login armhf 1:4.13+dfsg1-3ubuntu1 [200 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ncurses-bin armhf 6.4+20240113-1 [178 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main armhf sed armhf 4.9-2 [198 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main armhf util-linux armhf 2.39.2-6ubuntu1 [1211 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main armhf libdebconfclient0 armhf 0.271ubuntu1 [10.8 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main armhf base-passwd armhf 3.6.3 [51.0 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main armhf init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main armhf libc-bin armhf 2.38-3ubuntu1 [532 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ncurses-base all 6.4+20240113-1 [25.4 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main armhf sysvinit-utils armhf 3.08-3ubuntu1 [33.4 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt armhf 2.7.10 [1362 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt-utils armhf 2.7.10 [211 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main armhf ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main armhf libffi8 armhf 3.4.4-2 [20.8 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main armhf libp11-kit0 armhf 0.25.3-2ubuntu2 [261 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main armhf libunistring5 armhf 1.1-2 [512 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main armhf libidn2-0 armhf 2.3.4-1build1 [94.2 kB] Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgnutls30 armhf 3.8.1-4ubuntu7 [942 kB] Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules-bin armhf 1.5.2-9.1ubuntu2 [43.6 kB] Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules armhf 1.5.2-9.1ubuntu2 [265 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main armhf init armhf 1.66ubuntu1 [6186 B] Get:112 http://ftpmaster.internal/ubuntu noble/main armhf libsmartcols1 armhf 2.39.2-6ubuntu1 [116 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main armhf uuid-runtime armhf 2.39.2-6ubuntu1 [40.7 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main armhf libattr1 armhf 1:2.5.1-5 [11.5 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main armhf libmd0 armhf 1.1.0-2 [23.1 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-runtime all 1.5.2-9.1ubuntu2 [40.6 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main armhf libsemanage-common all 3.5-1build1 [9982 B] Get:118 http://ftpmaster.internal/ubuntu noble/main armhf libsepol2 armhf 3.5-2 [262 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main armhf libsemanage2 armhf 3.5-1build1 [84.1 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libncursesw6 armhf 6.4+20240113-1 [118 kB] Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtinfo6 armhf 6.4+20240113-1 [90.6 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main armhf passwd armhf 1:4.13+dfsg1-3ubuntu1 [817 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main armhf libproc2-0 armhf 2:4.0.4-2ubuntu1 [49.6 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main armhf mawk armhf 1.3.4.20231126-1 [115 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main armhf procps armhf 2:4.0.4-2ubuntu1 [699 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main armhf usrmerge all 38ubuntu1 [58.8 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main armhf krb5-locales all 1.20.1-5build1 [13.7 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main armhf readline-common all 8.2-3 [56.2 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main armhf libreadline8 armhf 8.2-3 [129 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main armhf libsqlite3-0 armhf 3.44.2-1 [593 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main armhf openssl armhf 3.0.10-1ubuntu3 [1158 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main armhf tzdata all 2023d-1ubuntu2 [321 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main armhf bash-completion all 1:2.11-8 [180 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main armhf bsdextrautils armhf 2.39.2-6ubuntu1 [77.7 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main armhf libpng16-16 armhf 1.6.40-3 [176 kB] Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main armhf psmisc armhf 23.6-2 [176 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main armhf xz-utils armhf 5.4.5-0.3 [274 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main armhf g++ armhf 4:13.2.0-2ubuntu1 [1108 B] Get:139 http://ftpmaster.internal/ubuntu noble/main armhf gcc armhf 4:13.2.0-2ubuntu1 [5196 B] Get:140 http://ftpmaster.internal/ubuntu noble/main armhf cpp armhf 4:13.2.0-2ubuntu1 [29.0 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main armhf dpkg-dev all 1.22.2ubuntu2 [1168 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main armhf libdpkg-perl all 1.22.2ubuntu2 [321 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main armhf lto-disabled-list all 45 [12.4 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main armhf libfakeroot armhf 1.32.2-1 [28.0 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main armhf fakeroot armhf 1.32.2-1 [68.8 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main armhf optipng armhf 0.7.7-3 [82.2 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main armhf pinentry-curses armhf 1.2.1-3ubuntu1 [36.4 kB] Preconfiguring packages ... 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Setting up dpkg-dev (1.22.2ubuntu2) ... Setting up libnsl-dev:armhf (1.3.0-3) ... Setting up libc6-dev:armhf (2.38-3ubuntu1) ... Setting up libstdc++-13-dev:armhf (13.2.0-10ubuntu1) ... Setting up g++-13 (13.2.0-10ubuntu1) ... Setting up g++ (4:13.2.0-2ubuntu1) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... Processing triggers for debianutils (5.16) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27660352 armhf noble-proposed -c chroot:build-PACKAGEBUILD-27660352 --arch=armhf --dist=noble-proposed --nolog apbs_3.4.1-5build5.dsc Initiating build PACKAGEBUILD-27660352 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:53:38 UTC 2023 armv7l sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos01-arm64-034.buildd +==============================================================================+ | apbs 3.4.1-5build5 (armhf) Fri, 19 Jan 2024 19:00:12 +0000 | +==============================================================================+ Package: apbs Version: 3.4.1-5build5 Source Version: 3.4.1-5build5 Distribution: noble-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27660352/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/apbs-Sxaa0b/resolver-qyehWH' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- apbs_3.4.1-5build5.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/apbs-Sxaa0b/apbs-3.4.1' with '<>' I: NOTICE: Log filtering will replace 'build/apbs-Sxaa0b' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, pkg-config, libarpack2-dev, libmaloc-dev, libsuitesparse-dev, libsuperlu-dev, libtirpc-dev, mpi-default-dev, python3, python3-dev, python3-pybind11, python3-setuptools, python3-sphinx | sphinx, swig, zlib1g-dev, build-essential, fakeroot Filtered Build-Depends: cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, pkg-config, libarpack2-dev, libmaloc-dev, libsuitesparse-dev, libsuperlu-dev, libtirpc-dev, mpi-default-dev, python3, python3-dev, python3-pybind11, python3-setuptools, python3-sphinx | sphinx, swig, zlib1g-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [492 B] Get:5 copy:/<>/apt_archive ./ Packages [574 B] Fetched 2023 B in 0s (92.0 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libunistring2 perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev cmake cmake-data debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file gettext gettext-base gfortran-13 groff-base ibverbs-providers intltool-debian libamd3 libarchive-zip-perl libarchive13 libarpack2 libarpack2-dev libblas-dev libblas3 libbrotli1 libbsd0 libbtf2 libcamd3 libcbor0.10 libccolamd3 libcholmod5 libcolamd3 libcurl4 libcxsparse4 libdebhelper-perl libdw1 libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libexpat1-dev libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu74 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl libjsoncpp25 libklu2 liblapack-dev liblapack3 libldap2 libldl3 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmaloc-dev libmaloc1 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libparu0 libpciaccess0 libpipeline1 libpkgconf3 libpmix-dev libpmix2 libpsl5 libpython3-dev libpython3-stdlib libpython3.12 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib librbio4 librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libspex2 libspqr4 libssh-4 libsub-override-perl libsuitesparse-dev libsuitesparse-mongoose3 libsuitesparseconfig7 libsuperlu-dev libsuperlu6 libtool libuchardet0 libumfpack6 libuv1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db media-types mpi-default-dev netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config pkgconf pkgconf-bin po-debconf pybind11-dev pybuild-plugin-pyproject python-babel-localedata python3 python3-alabaster python3-babel python3-build python3-certifi python3-chardet python3-dev python3-distutils python3-docutils python3-idna python3-imagesize python3-installer python3-jinja2 python3-lib2to3 python3-markupsafe python3-minimal python3-packaging python3-pkg-resources python3-pybind11 python3-pygments python3-pyproject-hooks python3-requests python3-roman python3-setuptools python3-snowballstemmer python3-sphinx python3-toml python3-tz python3-urllib3 python3-wheel python3.12 python3.12-dev python3.12-minimal sgml-base sphinx-common swig swig4.0 xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format elpa-cmake-mode ninja-build dh-make flit gettext-doc libasprintf-dev libgettextpo-dev gfortran-13-doc libcoarrays-dev groff lrzip liblapack-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils libsuperlu-doc gcj-jdk m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl pybind11-doc python3-doc python3-tk python3-venv python3-pip docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base texlive-latex-recommended python-installer-doc python-jinja2-doc python-pygments-doc ttf-bitstream-vera python3-cryptography python3-openssl python3-socks python-requests-doc python-setuptools-doc python3-stemmer dvipng fonts-freefont-otf imagemagick-6.q16 latexmk libjs-mathjax python3-sphinx-rtd-theme sphinx-doc tex-gyre texlive-fonts-recommended texlive-latex-extra texlive-plain-generic python3-brotli python3.12-venv python3.12-doc binfmt-support sgml-base-doc swig-doc swig-examples swig4.0-examples swig4.0-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libjson-xs-perl libldap-common libcoarrays-openmpi-dev publicsuffix libsasl2-modules libgraphblas-dev xauth libmail-sendmail-perl libeigen3-dev libpaper-utils python3-pil python3-numpy The following NEW packages will be installed: autoconf automake autopoint autotools-dev cmake cmake-data debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file gettext gettext-base gfortran-13 groff-base ibverbs-providers intltool-debian libamd3 libarchive-zip-perl libarchive13 libarpack2 libarpack2-dev libblas-dev libblas3 libbrotli1 libbsd0 libbtf2 libcamd3 libcbor0.10 libccolamd3 libcholmod5 libcolamd3 libcurl4 libcxsparse4 libdebhelper-perl libdw1 libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libexpat1-dev libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu74 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl libjsoncpp25 libklu2 liblapack-dev liblapack3 libldap2 libldl3 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmaloc-dev libmaloc1 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libparu0 libpciaccess0 libpipeline1 libpkgconf3 libpmix-dev libpmix2 libpsl5 libpython3-dev libpython3-stdlib libpython3.12 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib librbio4 librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libspex2 libspqr4 libssh-4 libsub-override-perl libsuitesparse-dev libsuitesparse-mongoose3 libsuitesparseconfig7 libsuperlu-dev libsuperlu6 libtool libuchardet0 libumfpack6 libuv1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db media-types mpi-default-dev netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config pkgconf pkgconf-bin po-debconf pybind11-dev pybuild-plugin-pyproject python-babel-localedata python3 python3-alabaster python3-babel python3-build python3-certifi python3-chardet python3-dev python3-distutils python3-docutils python3-idna python3-imagesize python3-installer python3-jinja2 python3-lib2to3 python3-markupsafe python3-minimal python3-packaging python3-pkg-resources python3-pybind11 python3-pygments python3-pyproject-hooks python3-requests python3-roman python3-setuptools python3-snowballstemmer python3-sphinx python3-toml python3-tz python3-urllib3 python3-wheel python3.12 python3.12-dev python3.12-minimal sbuild-build-depends-main-dummy sgml-base sphinx-common swig swig4.0 xml-core zlib1g-dev 0 upgraded, 183 newly installed, 0 to remove and 0 not upgraded. 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armhf python3-tz all 2023.3.post1-2 [31.4 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main armhf python3-babel all 2.10.3-3build1 [87.5 kB] Get:162 http://ftpmaster.internal/ubuntu noble/main armhf python3-certifi all 2023.11.17-1 [165 kB] Get:163 http://ftpmaster.internal/ubuntu noble/main armhf python3-chardet all 5.2.0+dfsg-1 [117 kB] Get:164 http://ftpmaster.internal/ubuntu noble/main armhf python3.12-dev armhf 3.12.1-2 [507 kB] Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-dev armhf 3.12.1-0ubuntu1 [26.7 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main armhf python3-roman all 3.3-3 [9632 B] Get:167 http://ftpmaster.internal/ubuntu noble/main armhf python3-docutils all 0.20.1+dfsg-3 [393 kB] Get:168 http://ftpmaster.internal/ubuntu noble/main armhf python3-idna all 3.3-2 [45.4 kB] Get:169 http://ftpmaster.internal/ubuntu noble/main armhf python3-imagesize all 1.4.1-1 [6844 B] Get:170 http://ftpmaster.internal/ubuntu noble/main armhf python3-markupsafe armhf 2.1.3-1build1 [13.2 kB] Get:171 http://ftpmaster.internal/ubuntu noble/main armhf python3-jinja2 all 3.1.2-1 [107 kB] Get:172 http://ftpmaster.internal/ubuntu noble/universe armhf python3-pybind11 all 2.11.1-2 [167 kB] Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main armhf python3-urllib3 all 2.0.7-1 [113 kB] Get:174 http://ftpmaster.internal/ubuntu noble/main armhf python3-requests all 2.31.0+dfsg-1ubuntu1 [50.7 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main armhf python3-snowballstemmer all 2.2.0-4 [59.7 kB] Get:176 http://ftpmaster.internal/ubuntu noble/main armhf sphinx-common all 7.2.6-3 [741 kB] Get:177 http://ftpmaster.internal/ubuntu noble/main armhf python3-alabaster all 0.7.12-1 [17.8 kB] Get:178 http://ftpmaster.internal/ubuntu noble/main armhf python3-sphinx all 7.2.6-3 [557 kB] Get:179 http://ftpmaster.internal/ubuntu noble/universe armhf swig4.0 armhf 4.1.0-0.3 [1086 kB] Get:180 http://ftpmaster.internal/ubuntu noble/universe armhf swig all 4.1.0-0.3 [5990 B] Get:181 http://ftpmaster.internal/ubuntu noble/main armhf libibverbs-dev armhf 48.0-1 [201 kB] Get:182 http://ftpmaster.internal/ubuntu noble/universe armhf libopenmpi-dev armhf 4.1.6-5ubuntu1 [1564 kB] Get:183 http://ftpmaster.internal/ubuntu noble/universe armhf mpi-default-dev armhf 1.15 [3116 B] Preconfiguring packages ... Fetched 92.5 MB in 21s (4335 kB/s) Selecting previously unselected package libpython3.12-minimal:armhf. (Reading database ... 15490 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.1-2_armhf.deb ... Unpacking libpython3.12-minimal:armhf (3.12.1-2) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.5.0-2_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-2) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.1-2_armhf.deb ... Unpacking python3.12-minimal (3.12.1-2) ... Setting up libpython3.12-minimal:armhf (3.12.1-2) ... Setting up libexpat1:armhf (2.5.0-2) ... Setting up python3.12-minimal (3.12.1-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 15808 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.1-0ubuntu1_armhf.deb ... 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Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libmaloc1 (1.5-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:armhf (1.5.7-1) ... Setting up libpciaccess0:armhf (0.17-3) ... Setting up libxau6:armhf (1:1.0.9-1build5) ... Setting up libpsl5:armhf (0.21.2-1build1) ... Setting up libmagic-mgc (1:5.45-2) ... Setting up libcbor0.10:armhf (0.10.2-1.1ubuntu1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.9ubuntu1) ... Setting up libbrotli1:armhf (1.1.0-2) ... Setting up libcxsparse4:armhf (1:7.5.1+dfsg-1) ... Setting up libnghttp2-14:armhf (1.58.0-1) ... Setting up libmagic1:armhf (1:5.45-2) ... Setting up gettext-base (0.21-14) ... Setting up m4 (1.4.19-4) ... Setting up libldl3:armhf (1:7.5.1+dfsg-1) ... Setting up file (1:5.45-2) ... Setting up python-babel-localedata (2.10.3-3build1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-4) ... Setting up libbtf2:armhf (1:7.5.1+dfsg-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.11.0-2build1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libpkgconf3:armhf (1.8.1-2) ... Setting up libuv1:armhf (1.46.0-3) ... Setting up libmunge2:armhf (0.5.15-3ubuntu1) ... Setting up libexpat1-dev:armhf (2.5.0-2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libhwloc15:armhf (2.10.0-1) ... Setting up libevent-core-2.1-7:armhf (2.1.12-stable-9) ... Setting up libevent-2.1-7:armhf (2.1.12-stable-9) ... Setting up autopoint (0.21-14) ... Setting up libjsoncpp25:armhf (1.9.5-6) ... Setting up pkgconf-bin (1.8.1-2) ... Setting up libltdl7:armhf (2.4.7-7) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-4) ... Setting up libssh-4:armhf (0.10.6-2) ... Setting up libgfortran5:armhf (13.2.0-10ubuntu1) ... 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Setting up libldap2:armhf (2.6.6+dfsg-1~exp1ubuntu2) ... Setting up libblas-dev:armhf (3.11.0-2build1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-9) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libdw1:armhf (0.190-1) ... Setting up libxdmcp6:armhf (1:1.1.3-0ubuntu5) ... Setting up libevent-extra-2.1-7:armhf (2.1.12-stable-9) ... Setting up liblapack3:armhf (3.11.0-2build1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libxcb1:armhf (1.15-1) ... Setting up gettext (0.21-14) ... Setting up swig (4.1.0-0.3) ... Setting up libamd3:armhf (1:7.5.1+dfsg-1) ... Setting up libpython3.12-stdlib:armhf (3.12.1-2) ... Setting up libtool (2.4.7-7) ... Setting up libcolamd3:armhf (1:7.5.1+dfsg-1) ... Setting up libarchive13:armhf (3.7.2-1ubuntu2) ... Setting up libsuitesparse-mongoose3:armhf (1:7.5.1+dfsg-1) ... Setting up python3.12 (3.12.1-2) ... Setting up libedit2:armhf (3.1-20230828-1) ... Setting up libarpack2:armhf (3.9.1-1) ... Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-9) ... Setting up libsuperlu6:armhf (6.0.1+dfsg1-1) ... Setting up libcamd3:armhf (1:7.5.1+dfsg-1) ... Setting up pkgconf:armhf (1.8.1-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:armhf (2.0.16-1) ... Setting up libnl-route-3-200:armhf (3.7.0-0.3) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:armhf (2.4.7-7) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up gfortran-13 (13.2.0-10ubuntu1) ... Setting up librbio4:armhf (1:7.5.1+dfsg-1) ... Setting up libevent-dev (2.1.12-stable-9) ... Setting up liblapack-dev:armhf (3.11.0-2build1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode Setting up pkg-config:armhf (1.8.1-2) ... Setting up libjs-sphinxdoc (7.2.6-3) ... Setting up libccolamd3:armhf (1:7.5.1+dfsg-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libnl-3-dev:armhf (3.7.0-0.3) ... Setting up groff-base (1.23.0-3) ... Setting up xml-core (0.19) ... Setting up debugedit (1:5.0-5) ... Setting up libcurl4:armhf (8.5.0-2ubuntu1) ... Setting up libx11-6:armhf (2:1.8.7-1) ... Setting up libhwloc-dev:armhf (2.10.0-1) ... Setting up libsuperlu-dev:armhf (6.0.1+dfsg1-1) ... Setting up libpython3.12:armhf (3.12.1-2) ... Setting up libpython3-stdlib:armhf (3.12.1-0ubuntu1) ... Setting up libibverbs1:armhf (48.0-1) ... Setting up libcholmod5:armhf (1:7.5.1+dfsg-1) ... Setting up libarpack2-dev:armhf (3.9.1-1) ... Setting up libspex2:armhf (1:7.5.1+dfsg-1) ... Setting up ibverbs-providers:armhf (48.0-1) ... Setting up libspqr4:armhf (1:7.5.1+dfsg-1) ... Setting up openssh-client (1:9.4p1-1ubuntu2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:armhf (2:1.3.4-1build1) ... Setting up python3 (3.12.1-0ubuntu1) ... Setting up libpython3.12-dev:armhf (3.12.1-2) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up python3-markupsafe (2.1.3-1build1) ... Setting up python3-tz (2023.3.post1-2) ... Setting up libxnvctrl0:armhf (510.47.03-0ubuntu1) ... Setting up libnl-route-3-dev:armhf (3.7.0-0.3) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.2-1) ... Setting up python3-packaging (23.2-1) ... Setting up python3-pyproject-hooks (1.0.0-2) ... Setting up python3-certifi (2023.11.17-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up libklu2:armhf (1:7.5.1+dfsg-1) ... Setting up sphinx-common (7.2.6-3) ... Setting up python3-idna (3.3-2) ... Setting up python3.12-dev (3.12.1-2) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.7.0+dfsg1-2) ... Setting up python3-urllib3 (2.0.7-1) ... Setting up libumfpack6:armhf (1:7.5.1+dfsg-1) ... Setting up cmake (3.28.1-1) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.11.5-1) ... python3.12: can't get files for byte-compilation Setting up librdmacm1:armhf (48.0-1) ... Setting up libpython3-dev:armhf (3.12.1-0ubuntu1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-babel (2.10.3-3build1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-alabaster (0.7.12-1) ... Setting up debhelper (13.11.9ubuntu1) ... Setting up libparu0:armhf (1:7.5.1+dfsg-1) ... Setting up libibverbs-dev:armhf (48.0-1) ... Setting up libhwloc-plugins:armhf (2.10.0-1) ... Setting up python3-wheel (0.42.0-1) ... Setting up pybind11-dev (2.11.1-2) ... Setting up python3-pygments (2.15.1+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-dev (3.12.1-0ubuntu1) ... Setting up python3-requests (2.31.0+dfsg-1ubuntu1) ... Setting up python3-build (0.10.0-1) ... Setting up python3-pybind11 (2.11.1-2) ... Setting up dh-python (6.20231223) ... Setting up libfabric1:armhf (1.17.0-3) ... Setting up libsuitesparse-dev:armhf (1:7.5.1+dfsg-1) ... Setting up libpmix2:armhf (5.0.1-4) ... Setting up pybuild-plugin-pyproject (6.20231223) ... Setting up libopenmpi3:armhf (4.1.6-5ubuntu1) ... Setting up libpmix-dev:armhf (5.0.1-4) ... Setting up openmpi-bin (4.1.6-5ubuntu1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:armhf (4.1.6-5ubuntu1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode Setting up mpi-default-dev (1.15) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... Processing triggers for systemd (255.2-3ubuntu1) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.20.1+dfsg-3) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.20.1+dfsg-3) ... Setting up python3-sphinx (7.2.6-3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:53:38 UTC 2023 arm64 (armv7l) Toolchain package versions: binutils_2.41.90.20240115-1ubuntu1 dpkg-dev_1.22.2ubuntu2 g++-13_13.2.0-10ubuntu1 gcc-13_13.2.0-10ubuntu1 libc6-dev_2.38-3ubuntu1 libstdc++-13-dev_13.2.0-10ubuntu1 libstdc++6_13.2.0-10ubuntu1 linux-libc-dev_6.6.0-14.14 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.10 apt-utils_2.7.10 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13ubuntu6 base-passwd_3.6.3 bash_5.2.21-2ubuntu1 bash-completion_1:2.11-8 binutils_2.41.90.20240115-1ubuntu1 binutils-arm-linux-gnueabihf_2.41.90.20240115-1ubuntu1 binutils-common_2.41.90.20240115-1ubuntu1 bsdextrautils_2.39.2-6ubuntu1 bsdutils_1:2.39.2-6ubuntu1 build-essential_12.10ubuntu1 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 cmake_3.28.1-1 cmake-data_3.28.1-1 coreutils_9.4-2ubuntu2 cpp_4:13.2.0-2ubuntu1 cpp-13_13.2.0-10ubuntu1 dash_0.5.12-6ubuntu1 debconf_1.5.83 debconf-i18n_1.5.83 debhelper_13.11.9ubuntu1 debianutils_5.16 debugedit_1:5.0-5 dh-autoreconf_20 dh-python_6.20231223 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 docutils-common_0.20.1+dfsg-3 dpkg_1.22.2ubuntu2 dpkg-dev_1.22.2ubuntu2 dwz_0.15-1 e2fsprogs_1.47.0-2ubuntu1 fakeroot_1.32.2-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-2ubuntu1 g++-13_13.2.0-10ubuntu1 gcc_4:13.2.0-2ubuntu1 gcc-13_13.2.0-10ubuntu1 gcc-13-base_13.2.0-10ubuntu1 gettext_0.21-14 gettext-base_0.21-14 gfortran-13_13.2.0-10ubuntu1 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linux-libc-dev_6.6.0-14.14 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-3ubuntu1 logsave_1.47.0-2ubuntu1 lto-disabled-list_45 m4_1.4.19-4 make_4.3-4.1build1 man-db_2.12.0-3 mawk_1.3.4.20231126-1 media-types_10.1.0 mount_2.39.2-6ubuntu1 mpi-default-dev_1.15 ncurses-base_6.4+20240113-1 ncurses-bin_6.4+20240113-1 netbase_6.4 ocl-icd-libopencl1_2.3.2-1 openmpi-bin_4.1.6-5ubuntu1 openmpi-common_4.1.6-5ubuntu1 openssh-client_1:9.4p1-1ubuntu2 openssl_3.0.10-1ubuntu3 optipng_0.7.7-3 passwd_1:4.13+dfsg1-3ubuntu1 patch_2.7.6-7build2 perl_5.38.2-3 perl-base_5.38.2-3 perl-modules-5.36_5.36.0-10ubuntu1 perl-modules-5.38_5.38.2-3 pinentry-curses_1.2.1-3ubuntu1 pkg-config_1.8.1-2 pkgbinarymangler_154 pkgconf_1.8.1-2 pkgconf-bin_1.8.1-2 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-2ubuntu1 psmisc_23.6-2 pybind11-dev_2.11.1-2 pybuild-plugin-pyproject_6.20231223 python-babel-localedata_2.10.3-3build1 python3_3.12.1-0ubuntu1 python3-alabaster_0.7.12-1 python3-babel_2.10.3-3build1 python3-build_0.10.0-1 python3-certifi_2023.11.17-1 python3-chardet_5.2.0+dfsg-1 python3-dev_3.12.1-0ubuntu1 python3-distutils_3.11.5-1 python3-docutils_0.20.1+dfsg-3 python3-idna_3.3-2 python3-imagesize_1.4.1-1 python3-installer_0.7.0+dfsg1-2 python3-jinja2_3.1.2-1 python3-lib2to3_3.11.5-1 python3-markupsafe_2.1.3-1build1 python3-minimal_3.12.1-0ubuntu1 python3-packaging_23.2-1 python3-pkg-resources_68.1.2-2 python3-pybind11_2.11.1-2 python3-pygments_2.15.1+dfsg-1 python3-pyproject-hooks_1.0.0-2 python3-requests_2.31.0+dfsg-1ubuntu1 python3-roman_3.3-3 python3-setuptools_68.1.2-2 python3-snowballstemmer_2.2.0-4 python3-sphinx_7.2.6-3 python3-toml_0.10.2-1 python3-tz_2023.3.post1-2 python3-urllib3_2.0.7-1 python3-wheel_0.42.0-1 python3.12_3.12.1-2 python3.12-dev_3.12.1-2 python3.12-minimal_3.12.1-2 readline-common_8.2-3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.20 sgml-base_1.31 sphinx-common_7.2.6-3 swig_4.1.0-0.3 swig4.0_4.1.0-0.3 systemd_255.2-3ubuntu1 systemd-dev_255.2-3ubuntu1 systemd-sysv_255.2-3ubuntu1 sysvinit-utils_3.08-3ubuntu1 tar_1.35+dfsg-3 tzdata_2023d-1ubuntu2 ubuntu-keyring_2023.11.28.1 usrmerge_38ubuntu1 util-linux_2.39.2-6ubuntu1 uuid-runtime_2.39.2-6ubuntu1 xml-core_0.19 xz-utils_5.4.5-0.3 zlib1g_1:1.3.dfsg-3ubuntu1 zlib1g-dev_1:1.3.dfsg-3ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: apbs Binary: apbs, python3-apbslib, libapbs-dev, libapbs3, apbs-data, apbs-doc, libfetk-dev, libfetk1.9 Architecture: any all Version: 3.4.1-5build5 Maintainer: Ubuntu Developers Uploaders: Michael Banck Homepage: http://www.poissonboltzmann.org/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/debichem-team/apbs Vcs-Git: https://salsa.debian.org/debichem-team/apbs.git Testsuite: autopkgtest Testsuite-Triggers: python3 Build-Depends: cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, pkg-config, libarpack2-dev, libmaloc-dev, libsuitesparse-dev, libsuperlu-dev, libtirpc-dev, mpi-default-dev, python3, python3-dev, python3-pybind11, python3-setuptools, python3-sphinx | sphinx, swig, zlib1g-dev Build-Depends-Indep: libjs-mathjax, python3-sphinx-rtd-theme, python3-yaml Package-List: apbs deb science optional arch=any apbs-data deb science optional arch=all apbs-doc deb science optional arch=all libapbs-dev deb libdevel optional arch=any libapbs3 deb libs optional arch=any libfetk-dev deb libdevel optional arch=any libfetk1.9 deb libs optional arch=any python3-apbslib deb python optional arch=any Checksums-Sha1: 584fd36dc1424cb22fd8846f1cf2c7ead60ce0c6 85806314 apbs_3.4.1.orig.tar.gz 81bc54c4edbbc84f99b0e5632b757207a2556967 20305776 apbs_3.4.1-5build5.debian.tar.xz Checksums-Sha256: 644e6246fd37c9dd4172fc7be1763337082ab8584dbcd53e738c831b62c89bb2 85806314 apbs_3.4.1.orig.tar.gz f4dd15bcf97fcb4d1f903bacc574a8dde158dfc6226a103516dead35b4bca0eb 20305776 apbs_3.4.1-5build5.debian.tar.xz Files: 5d2af7c3592f8c410a5df39887361520 85806314 apbs_3.4.1.orig.tar.gz e49396706c404b9a38190a966e7d4551 20305776 apbs_3.4.1-5build5.debian.tar.xz Original-Maintainer: Debichem Team -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEJeP/LX9Gnb59DU5Qr8/sjmac4cIFAmWqxfoACgkQr8/sjmac 4cKNIA/7B08ovSFROpLeN9nzFcj/f3VflUMypqmQj5nHig0EmYkN6dPTWqFuaKeT KuCk5eJLtzo0b0fhtVa+INWfXrwS7zHRm6RY6FAwrH8qnTcm1znHxCcHTvAfdrwU YmWGGRLHd8fxzVkRT/ohXkPYAkA1OrC3U4bsvKwd3e3Y9y8Sag0zsrt2itT579RS Mxs22wxt9vmxtEi2QEl8P01LksrFVCstY4IK4VPtrsrRR4Rb+ahNfzLlMHyLGB/M 5zX4y/Gfbco71sssmdoaj6Db3LlEHn1rLvr9rT8bkzqJdph6rbT7nfqy1z83NxhW m1npm6IwhZyXT0sSdmFApO/tMckrh9VEvuYTxqFPoTgkGgLAr6kwFrUngVqdQoSF 9LD+wx73dtUMWreQcs0JFB4DsX+jrepW7p9QV+ySbwmnVo3pz+3+W1phBzJ3ikln 4skBKxBDchGd/ZqGLx28P2PFM6f4L/Cbj7Mo7OVtLWmXp4tO+2Leph+pbDhScJoe pFp96qH/gttJfuAUn60SLrdy0WoC3XGna4zieYCMIuWhuvn7e36gKtnVwGO+7yQI FE93bluMOIjFOO2saHmBO97HVquEfvC3Z4Gq0QT3HpwSKL2YygL4cMKjutfFVdlQ bBJpaiV43ue1nsKref4gd3MuV9U9bIiAOO2w4FhikVqX4mu7n48= =Fi87 -----END PGP SIGNATURE----- gpgv: Signature made Fri Jan 19 18:56:58 2024 UTC gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./apbs_3.4.1-5build5.dsc: no acceptable signature found dpkg-source: info: extracting apbs in /<> dpkg-source: info: unpacking apbs_3.4.1.orig.tar.gz dpkg-source: info: unpacking apbs_3.4.1-5build5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying wrong-path-for-interpreter.patch dpkg-source: info: applying debian_testfiles.patch dpkg-source: info: applying fix_spelling_errors.patch dpkg-source: info: applying shared_library_soname.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying cmake.patch dpkg-source: info: applying docs.patch dpkg-source: info: applying open-U-obsolete.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-27660352 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27660352 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27660352 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package apbs dpkg-buildpackage: info: source version 3.4.1-5build5 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=cmake dh_auto_clean -O--buildsystem=cmake dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules build-arch dh build-arch --with python3,sphinxdoc --buildsystem=cmake dh_update_autotools_config -a -O--buildsystem=cmake dh_autoreconf -a -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- \ -DCMAKE_BUILD_TYPE=None \ -DAPBS_STATIC_BUILD=Off \ -DBUILD_DOC=Off -DBUILD_TOOLS=On \ -DENABLE_OPENMP=On -DENABLE_MPI=On \ -DENABLE_PYTHON=On -DBUILD_SHARED_LIBS=On \ -DENABLE_READLINE=Off -DENABLE_ZLIB=On \ -DFETCHCONTENT_SOURCE_DIR_FETK=/<>/debian/external_deps/fetk \ -DRPC_CFLAGS=-I/usr/include/tirpc \ -DBUILD_MALOC=Off cd obj-arm-linux-gnueabihf && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DCMAKE_BUILD_TYPE=None -DAPBS_STATIC_BUILD=Off -DBUILD_DOC=Off -DBUILD_TOOLS=On -DENABLE_OPENMP=On -DENABLE_MPI=On -DENABLE_PYTHON=On -DBUILD_SHARED_LIBS=On -DENABLE_READLINE=Off -DENABLE_ZLIB=On -DFETCHCONTENT_SOURCE_DIR_FETK=/<>/debian/external_deps/fetk -DRPC_CFLAGS=-I/usr/include/tirpc -DBUILD_MALOC=Off .. -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Install prefix: /usr -- -- APBS Static build: Off -- Building shared libs: ON -- Find-library suffixes: .so;.so;.a -- -- Building FETK from commit 57195e55351e04ce6ee0ef56a143c996a9aee7e2 -- FETK set_basic_vars_and_paths: FALSE, FETK -- Setting project paths -- Install prefix: /usr -- FETK static build: OFF -- Building shared libs: ON -- Find-library suffixes: .so;.so;.so;.a Configuring build for PUNC -- FETK set_basic_vars_and_paths: FALSE, punc -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of mode_t -- Check size of mode_t - done -- Check size of pid_t -- Check size of pid_t - done -- Check size of size_t -- Check size of size_t - done -- Looking for 4 include files stdlib.h, ..., float.h -- Looking for 4 include files stdlib.h, ..., float.h - found -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file sys/socket.h -- Looking for include file sys/socket.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file sys/un.h -- Looking for include file sys/un.h - found -- Looking for include file sys/wait.h -- Looking for include file sys/wait.h - found -- Looking for include file netinet/in.h -- Looking for include file netinet/in.h - found -- Looking for include file arpa/inet.h -- Looking for include file arpa/inet.h - found -- Looking for include file netdb.h -- Looking for include file netdb.h - found -- Looking for include file sys/stat.h -- Looking for include file sys/stat.h - found -- Looking for include file fcntl.h -- Looking for include file fcntl.h - found -- Looking for include file rpc/rpc.h -- Looking for include file rpc/rpc.h - found -- Looking for getcwd -- Looking for getcwd - found -- Looking for O_NONBLOCK -- Looking for O_NONBLOCK - found -- Will build vf2c -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so -- Performing Test SUPERLU_HAS_GLOBAL_MEM_USAGE_T -- Performing Test SUPERLU_HAS_GLOBAL_MEM_USAGE_T - Success -- Performing Test SUPERLU_HAS_CLEAN_ENUMS -- Performing Test SUPERLU_HAS_CLEAN_ENUMS - Success -- Performing Test SUPERLU_HAS_GLOBALLU_T -- Performing Test SUPERLU_HAS_GLOBALLU_T - Success -- Found SuperLU: /usr/include/superlu (found version "5.0") -- Found ARPACK: libraries at /usr/lib/arm-linux-gnueabihf/libarpack.so -- Will build CGCODE -- Building vf2c -- Type: EXTERNAL_HEADERS -- Items: punc/varpack.h;punc/vblas.h;punc/vcgcode.h;punc/vlapack.h;punc/vpmg.h;punc/vf2c.h -- Type: INTERNAL_HEADERS -- Items: f2c.h;fio.h;fmt.h;fp.h;lio.h;rawio.h;signal1.h;sysdep1.h -- Type: SOURCES -- Items: f77vers.c;i77vers.c;s_rnge.c;abort_.c;exit_.c;getarg_.c;iargc_.c;getenv_.c;signal_.c;s_stop.c;s_paus.c;system_.c;cabs.c;derf_.c;derfc_.c;erf_.c;erfc_.c;sig_die.c;uninit.c;pow_ci.c;pow_dd.c;pow_di.c;pow_hh.c;pow_ii.c;pow_ri.c;pow_zi.c;pow_zz.c;c_abs.c;c_cos.c;c_div.c;c_exp.c;c_log.c;c_sin.c;c_sqrt.c;z_abs.c;z_cos.c;z_div.c;z_exp.c;z_log.c;z_sin.c;z_sqrt.c;r_abs.c;r_acos.c;r_asin.c;r_atan.c;r_atn2.c;r_cnjg.c;r_cos.c;r_cosh.c;r_dim.c;r_exp.c;r_imag.c;r_int.c;r_lg10.c;r_log.c;r_mod.c;r_nint.c;r_sign.c;r_sin.c;r_sinh.c;r_sqrt.c;r_tan.c;r_tanh.c;d_abs.c;d_acos.c;d_asin.c;d_atan.c;d_atn2.c;d_cnjg.c;d_cos.c;d_cosh.c;d_dim.c;d_exp.c;d_imag.c;d_int.c;d_lg10.c;d_log.c;d_mod.c;d_nint.c;d_prod.c;d_sign.c;d_sin.c;d_sinh.c;d_sqrt.c;d_tan.c;d_tanh.c;i_abs.c;i_dim.c;i_dnnt.c;i_indx.c;i_len.c;i_mod.c;i_nint.c;i_sign.c;lbitbits.c;lbitshft.c;h_abs.c;h_dim.c;h_dnnt.c;h_indx.c;h_len.c;h_mod.c;h_nint.c;h_sign.c;l_ge.c;l_gt.c;l_le.c;l_lt.c;hl_ge.c;hl_gt.c;hl_le.c;hl_lt.c;ef1asc_.c;ef1cmc_.c;f77_aloc.c;s_cat.c;s_cmp.c;s_copy.c;dtime_.c;etime_.c;backspac.c;close.c;dfe.c;dolio.c;due.c;endfile.c;err.c;fmt.c;fmtlib.c;ftell_.c;iio.c;ilnw.c;inquire.c;lread.c;lwrite.c;open.c;rdfmt.c;rewind.c;rsfe.c;rsli.c;rsne.c;sfe.c;sue.c;typesize.c;uio.c;util.c;wref.c;wrtfmt.c;wsfe.c;wsle.c;wsne.c;xwsne.c;main.c -- Building cgcode -- Type: INTERNAL_HEADERS -- Items: vcgcode.h -- Type: SOURCES -- Items: scgdrv.c;scg.c;scr.c;scrind.c;spcg.c;scgnr.c;scgne.c;spcgnr.c;spcgne.c;sppcg.c;spcgca.c;sdpchb.c;scbfix.c;sckchb.c;scgchk.c;sonest.c;msstop.c;r1mach.c;sratqr.c;dcgdrv.c;dcg.c;dcr.c;dcrind.c;dpcg.c;dcgnr.c;dcgne.c;dpcgnr.c;dpcgne.c;dppcg.c;dpcgca.c;ddpchb.c;dcbfix.c;dckchb.c;dcgchk.c;donest.c;mdstop.c;d1mach.c;dratqr.c;depsln.c -- Type: INTERNAL_HEADERS -- Items: /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/punccf.h -- Type: SOURCES -- Items: punc_base.c -- Type: EXTERNAL_HEADERS -- Items: punc/punc.h;punc/punc_base.h -- Type: INTERNAL_HEADERS -- Items: punc_base_p.h Configuring build for GAMER -- FETK set_basic_vars_and_paths: FALSE, gamer -- Type: INTERNAL_HEADERS -- Items: /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src/gamercf.h -- Type: SOURCES -- Items: gamer_base.c -- Type: EXTERNAL_HEADERS -- Items: gamer/gamer.h;gamer/gamer_base.h -- Type: INTERNAL_HEADERS -- Items: gamer_base_p.h -- Type: SOURCES -- Items: triangle.c -- Type: EXTERNAL_HEADERS -- Items: gamer/triangle.h -- Type: INTERNAL_HEADERS -- Items: triangle_p.h -- Type: SOURCES -- Items: predicates.cpp;tetgen.cpp -- Type: EXTERNAL_HEADERS -- Items: gamer/tetgen.h -- Type: INTERNAL_HEADERS -- Items: tetgen_p.h -- Type: SOURCES -- Items: CorrectNormals.C;GenerateSphereMesh.C;MarchingCube.C;PDB2Mesh.C;PDB2Volume.C;ReadLattice.C;ReadPDB.C;ReadWriteMesh.C;RegionGrowing.C;SurfaceMesh.C;SurfExtract.C;SurfRefine.C;SurfSmooth.C -- Type: EXTERNAL_HEADERS -- Items: gamer/biom.h -- Type: INTERNAL_HEADERS -- Items: MarchingCube.h;PDB2Volume.h Configuring build for MC -- FETK set_basic_vars_and_paths: FALSE, mc -- Found UMFPACK: /usr/include/suitesparse -- @@@@ finding blas -- @@@@ finding lapack -- %%%%% list of libraries: -- Testing libraries: TRUE -- CMAKE_REQUIRED_LIBRARIES: /usr/lib/arm-linux-gnueabihf/libblas.so;-lm;-ldl -- checking for function cheev_ -- result: TRUE -- Found LAPACK: /usr/lib/arm-linux-gnueabihf/libblas.so;-lm;-ldl -- @@@@ finding amd -- Found AMD headers in: /usr/include/suitesparse -- Found AMD library: /usr/lib/arm-linux-gnueabihf/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/arm-linux-gnueabihf/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/arm-linux-gnueabihf/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/arm-linux-gnueabihf/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/arm-linux-gnueabihf/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/arm-linux-gnueabihf/libspqr.so -- Did not find Intel TBB library, assuming SuiteSparseQR was not compiled with TBB. -- @@@@ finding config -- Found SUITESPARSE_CONFIG headers in: /usr/include/suitesparse -- Found SUITESPARSE_CONFIG library: /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/arm-linux-gnueabihf/librt.a -- Adding librt: /usr/lib/arm-linux-gnueabihf/librt.a to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing). -- @@@@ finding metis -- Did not find METIS library (optional SuiteSparse dependency) -- Found SuiteSparse: TRUE (found version "..") -- Type: INTERNAL_HEADERS -- Items: /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src/mccf.h -- Type: SOURCES -- Items: mc_base.c -- Type: EXTERNAL_HEADERS -- Items: mc/mc_base.h;mc/mc.h -- Type: INTERNAL_HEADERS -- Items: mc_base_p.h -- Type: SOURCES -- Items: bmat.c;bsolv.c;bvec.c;mat.c;matcopy.c;matln.c;mtool.c;slu.c;vec.c;vec3.c;zslu.c -- Type: EXTERNAL_HEADERS -- Items: mc/bam.h;mc/bmat.h;mc/bvec.h;mc/mat.h;mc/mtool.h;mc/slu.h;mc/vec.h;mc/vec3.h;mc/zslu.h -- Type: INTERNAL_HEADERS -- Items: bam_p.h;bmat_p.h;bvec_p.h;mat_p.h;mtool_p.h;slu_p.h;vec_p.h;vec3_p.h;zslu_p.h -- Type: SOURCES -- Items: whb.c;bvechb.c;hbtools.c;rcmat.c;brcmat.c;subopt.c -- Type: EXTERNAL_HEADERS -- Items: mc/whb.h -- Type: INTERNAL_HEADERS -- Items: brcmat_p.h;bvechb_p.h;cholesky_p.h;hbtools_p.h;rcmat_p.h;subopt_p.h;whb_p.h -- Type: SOURCES -- Items: aprx.c;assem.c;bnode.c;estim.c;eval.c;io.c;node.c;parti.c;re.c -- Type: EXTERNAL_HEADERS -- Items: mc/aprx.h;mc/bnode.h;mc/node.h;mc/re.h -- Type: INTERNAL_HEADERS -- Items: aprx_p.h;bnode_p.h;node_p.h;re_p.h -- Type: SOURCES -- Items: vel.c;ves.c;gem.c;gemchk.c;gemdisp.c;gemg.c;gemgen.c;gemio.c;gemref.c;gemunref.c;gemcube.c -- Type: EXTERNAL_HEADERS -- Items: mc/gem.h;mc/vel.h;mc/ves.h -- Type: INTERNAL_HEADERS -- Items: gem_p.h;vel_p.h;ves_p.h -- Type: SOURCES -- Items: pde.c -- Type: EXTERNAL_HEADERS -- Items: mc/pde.h -- Type: INTERNAL_HEADERS -- Items: pde_p.h -- Type: SOURCES -- Items: am.c;lsolv.c;nsolv.c -- Type: EXTERNAL_HEADERS -- Items: mc/am.h;mc/nam.h -- Type: INTERNAL_HEADERS -- Items: am_p.h;nam_p.h -- Type: SOURCES -- Items: dyn.c;svio.c -- Type: EXTERNAL_HEADERS -- Items: mc/dyn.h -- Type: INTERNAL_HEADERS -- Items: dyn_p.h;svio_p.h -- Type: SOURCES -- Items: mcsh.c -- Type: EXTERNAL_HEADERS -- Items: mc/mcsh.h -- Type: INTERNAL_HEADERS -- Items: mcsh_p.h -- ############################################################# -- ** PROJECT NAME: APBS -- ** PROJECT DESC: Adaptive Poisson-Boltzmann Solver -- ** PROJECT URL: http://www.poissonboltzmann.org/ -- ** VERSION_DATA: 3.4.1 -- ** CURRENT_TIME: 2024-01-19T18:56:34 -- ** CURRENT_YEAR: 2024 -- Setting project paths -- Setting lookup paths for headers and libraries -- Computing machine epsilon values -- Floating point epsilon is 2.220446e-16 -- Double precision epsilon is 2.220446e-16 -- Looking for time -- Looking for time - found -- Looking for rand -- Looking for rand - found -- Looking for srand -- Looking for srand - found -- Found Intl: built in to C library -- Performing Test Iconv_IS_BUILT_IN -- Performing Test Iconv_IS_BUILT_IN - Success -- Found Iconv: built in to C library -- @@@@ finding blas -- @@@@ finding lapack -- %%%%% list of libraries: -- Testing libraries: TRUE -- CMAKE_REQUIRED_LIBRARIES: /usr/lib/arm-linux-gnueabihf/libblas.so;-lm;-ldl -- checking for function cheev_ -- result: TRUE -- @@@@ finding amd -- Found AMD headers in: /usr/include/suitesparse -- Found AMD library: /usr/lib/arm-linux-gnueabihf/libamd.so -- @@@@ finding camd -- Found CAMD headers in: /usr/include/suitesparse -- Found CAMD library: /usr/lib/arm-linux-gnueabihf/libcamd.so -- @@@@ finding colamd -- Found COLAMD headers in: /usr/include/suitesparse -- Found COLAMD library: /usr/lib/arm-linux-gnueabihf/libcolamd.so -- @@@@ finding ccolamd -- Found CCOLAMD headers in: /usr/include/suitesparse -- Found CCOLAMD library: /usr/lib/arm-linux-gnueabihf/libccolamd.so -- @@@@ finding cholmod -- Found CHOLMOD headers in: /usr/include/suitesparse -- Found CHOLMOD library: /usr/lib/arm-linux-gnueabihf/libcholmod.so -- @@@@ finding parseqr -- Found SUITESPARSEQR headers in: /usr/include/suitesparse -- Found SUITESPARSEQR library: /usr/lib/arm-linux-gnueabihf/libspqr.so -- Did not find Intel TBB library, assuming SuiteSparseQR was not compiled with TBB. -- @@@@ finding config -- Found SUITESPARSE_CONFIG headers in: /usr/include/suitesparse -- Found SUITESPARSE_CONFIG library: /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so -- Found LIBRT library: /usr/lib/arm-linux-gnueabihf/librt.a -- Adding librt: /usr/lib/arm-linux-gnueabihf/librt.a to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing). -- @@@@ finding metis -- Did not find METIS library (optional SuiteSparse dependency) -- UMFPack libraries: /usr/lib/arm-linux-gnueabihf/libumfpack.so -- SUITESPARSE_INCLUDE_DIRS: /usr/include/suitesparse -- SUITESPARSE_LIBRARIES: /usr/lib/arm-linux-gnueabihf/libspqr.so;/usr/lib/arm-linux-gnueabihf/libcholmod.so;/usr/lib/arm-linux-gnueabihf/libccolamd.so;/usr/lib/arm-linux-gnueabihf/libcamd.so;/usr/lib/arm-linux-gnueabihf/libcolamd.so;/usr/lib/arm-linux-gnueabihf/libamd.so;/usr/lib/arm-linux-gnueabihf/libblas.so;-lm;-ldl;/usr/lib/arm-linux-gnueabihf/libblas.so;/usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so;/usr/lib/arm-linux-gnueabihf/librt.a -- Checking for MPI -- Found MPI_C: /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- MPI support enabled -- Inline functions enabled -- Verbose debugging mode enabled -- Checking for OpenMP -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- OpenMP support enabled -- Building of iAPBS interface disabled -- Adding apbs_generic -- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c -- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/arm-linux-gnueabihf/libumfpack.so;/usr/lib/arm-linux-gnueabihf/libspqr.so;/usr/lib/arm-linux-gnueabihf/libcholmod.so;/usr/lib/arm-linux-gnueabihf/libccolamd.so;/usr/lib/arm-linux-gnueabihf/libcamd.so;/usr/lib/arm-linux-gnueabihf/libcolamd.so;/usr/lib/arm-linux-gnueabihf/libamd.so;/usr/lib/arm-linux-gnueabihf/libblas.so;-lm;-ldl;/usr/lib/arm-linux-gnueabihf/libblas.so;/usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so;/usr/lib/arm-linux-gnueabihf/librt.a;/usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so;-fopenmp -- Added apbs_generic -- Adding apbs_pmgc -- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c -- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/arm-linux-gnueabihf/libumfpack.so;/usr/lib/arm-linux-gnueabihf/libspqr.so;/usr/lib/arm-linux-gnueabihf/libcholmod.so;/usr/lib/arm-linux-gnueabihf/libccolamd.so;/usr/lib/arm-linux-gnueabihf/libcamd.so;/usr/lib/arm-linux-gnueabihf/libcolamd.so;/usr/lib/arm-linux-gnueabihf/libamd.so;/usr/lib/arm-linux-gnueabihf/libblas.so;-lm;-ldl;/usr/lib/arm-linux-gnueabihf/libblas.so;/usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so;/usr/lib/arm-linux-gnueabihf/librt.a;/usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so;-fopenmp -- Added apbs_pmgc -- Adding apbs_mg -- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c -- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/arm-linux-gnueabihf/libumfpack.so;/usr/lib/arm-linux-gnueabihf/libspqr.so;/usr/lib/arm-linux-gnueabihf/libcholmod.so;/usr/lib/arm-linux-gnueabihf/libccolamd.so;/usr/lib/arm-linux-gnueabihf/libcamd.so;/usr/lib/arm-linux-gnueabihf/libcolamd.so;/usr/lib/arm-linux-gnueabihf/libamd.so;/usr/lib/arm-linux-gnueabihf/libblas.so;-lm;-ldl;/usr/lib/arm-linux-gnueabihf/libblas.so;/usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so;/usr/lib/arm-linux-gnueabihf/librt.a;/usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so;-fopenmp;apbs_generic;apbs_pmgc -- Added apbs_mg -- Adding apbs_fem -- With source files vcsm.c;vfetk.c;vpee.c -- With external header files vcsm.h;vfetk.h;vpee.h -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/arm-linux-gnueabihf/libumfpack.so;/usr/lib/arm-linux-gnueabihf/libspqr.so;/usr/lib/arm-linux-gnueabihf/libcholmod.so;/usr/lib/arm-linux-gnueabihf/libccolamd.so;/usr/lib/arm-linux-gnueabihf/libcamd.so;/usr/lib/arm-linux-gnueabihf/libcolamd.so;/usr/lib/arm-linux-gnueabihf/libamd.so;/usr/lib/arm-linux-gnueabihf/libblas.so;-lm;-ldl;/usr/lib/arm-linux-gnueabihf/libblas.so;/usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so;/usr/lib/arm-linux-gnueabihf/librt.a;/usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so;-fopenmp;apbs_generic -- Added apbs_fem -- Adding apbs_routines -- With source files routines.c -- With external header files -- With internal header files -- With library dependencies mc;util;dl;m;stdc++;/usr/lib/arm-linux-gnueabihf/libumfpack.so;/usr/lib/arm-linux-gnueabihf/libspqr.so;/usr/lib/arm-linux-gnueabihf/libcholmod.so;/usr/lib/arm-linux-gnueabihf/libccolamd.so;/usr/lib/arm-linux-gnueabihf/libcamd.so;/usr/lib/arm-linux-gnueabihf/libcolamd.so;/usr/lib/arm-linux-gnueabihf/libamd.so;/usr/lib/arm-linux-gnueabihf/libblas.so;-lm;-ldl;/usr/lib/arm-linux-gnueabihf/libblas.so;/usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so;/usr/lib/arm-linux-gnueabihf/librt.a;/usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so;-fopenmp;mc;util;dl;m;stdc++;/usr/lib/arm-linux-gnueabihf/libumfpack.so;/usr/lib/arm-linux-gnueabihf/libspqr.so;/usr/lib/arm-linux-gnueabihf/libcholmod.so;/usr/lib/arm-linux-gnueabihf/libccolamd.so;/usr/lib/arm-linux-gnueabihf/libcamd.so;/usr/lib/arm-linux-gnueabihf/libcolamd.so;/usr/lib/arm-linux-gnueabihf/libamd.so;/usr/lib/arm-linux-gnueabihf/libblas.so;-lm;-ldl;/usr/lib/arm-linux-gnueabihf/libblas.so;/usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so;/usr/lib/arm-linux-gnueabihf/librt.a;/usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so;-fopenmp;apbs_generic;apbs_pmgc;apbs_mg;apbs_fem -- Added apbs_routines -- External Headers: -- -- APBS Libraries: mc;util;dl;m;stdc++;/usr/lib/arm-linux-gnueabihf/libumfpack.so;/usr/lib/arm-linux-gnueabihf/libspqr.so;/usr/lib/arm-linux-gnueabihf/libcholmod.so;/usr/lib/arm-linux-gnueabihf/libccolamd.so;/usr/lib/arm-linux-gnueabihf/libcamd.so;/usr/lib/arm-linux-gnueabihf/libcolamd.so;/usr/lib/arm-linux-gnueabihf/libamd.so;/usr/lib/arm-linux-gnueabihf/libblas.so;-lm;-ldl;/usr/lib/arm-linux-gnueabihf/libblas.so;/usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so;/usr/lib/arm-linux-gnueabihf/librt.a;/usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so;-fopenmp -- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_routines -- -- -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -- Supplemental tools enabled -- Building mesh -- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines -- Building manip -- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem;apbs_routines CMake Deprecation Warning at tools/python/CMakeLists.txt:2 (CMAKE_POLICY): The OLD behavior for policy CMP0078 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. CMake Deprecation Warning at tools/python/CMakeLists.txt:3 (CMAKE_POLICY): The OLD behavior for policy CMP0086 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- Found SWIG: /usr/bin/swig4.0 (found version "4.1.0") -- Found Python3: /usr/bin/python3 (found suitable version "3.12.1", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- ***** Python3 include path is: /usr/include/python3.12 -- ***** Python3 library path is: /usr/lib/arm-linux-gnueabihf/libpython3.12.so -- ***** Python3 library dir is: /usr/lib/arm-linux-gnueabihf CMake Warning at /usr/lib/cmake/pybind11/pybind11Tools.cmake:24 (message): Set PYBIND11_PYTHON_VERSION to search for a specific version, not PYTHON_VERSION (which is an output). Assuming that is what you meant to do and continuing anyway. Call Stack (most recent call first): /usr/lib/cmake/pybind11/pybind11Common.cmake:188 (include) /usr/lib/cmake/pybind11/pybind11Config.cmake:250 (include) tools/python-pybind/CMakeLists.txt:2 (find_package) CMake Warning (dev) at /usr/lib/cmake/pybind11/FindPythonLibsNew.cmake:98 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): /usr/lib/cmake/pybind11/pybind11Tools.cmake:50 (find_package) /usr/lib/cmake/pybind11/pybind11Common.cmake:188 (include) /usr/lib/cmake/pybind11/pybind11Config.cmake:250 (include) tools/python-pybind/CMakeLists.txt:2 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.12.1", minimum required is "3.6") -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.12.so -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/include (found version "2.11.1") -- LIBS mc;util;dl;m;stdc++;/usr/lib/arm-linux-gnueabihf/libumfpack.so;/usr/lib/arm-linux-gnueabihf/libspqr.so;/usr/lib/arm-linux-gnueabihf/libcholmod.so;/usr/lib/arm-linux-gnueabihf/libccolamd.so;/usr/lib/arm-linux-gnueabihf/libcamd.so;/usr/lib/arm-linux-gnueabihf/libcolamd.so;/usr/lib/arm-linux-gnueabihf/libamd.so;/usr/lib/arm-linux-gnueabihf/libblas.so;-lm;-ldl;/usr/lib/arm-linux-gnueabihf/libblas.so;/usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so;/usr/lib/arm-linux-gnueabihf/librt.a;/usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so;-fopenmp -- INTERNAL_LIBS apbs_generic;apbs_pmgc;apbs_mg;apbs_fem;apbs_routines -- ******* TESTING ADDED ***************** -- Found Python3: /usr/bin/python3 (found suitable exact version "3.12.1") found components: Interpreter -- ******* FOUND TEST CASE born, born -- TEST born_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t born -- ******* FOUND TEST CASE actin, actin-dimer-auto -- TEST actin-dimer-auto_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t actin-dimer-auto -- ******* FOUND TEST CASE alkanes, alkanes -- TEST alkanes_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t alkanes -- ******* FOUND TEST CASE FKBP, FKBP -- TEST FKBP_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t FKBP -- ******* FOUND TEST CASE hca, hca-bind -- TEST hca-bind_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t hca-bind -- ******* FOUND TEST CASE ionize, ionize -- TEST ionize_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t ionize -- ******* FOUND TEST CASE ion, ion-pmf -- TEST ion-pmf_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t ion-pmf -- ******* FOUND TEST CASE pka, pka-lig -- TEST pka-lig_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t pka-lig -- ******* FOUND TEST CASE point, point-pmf -- TEST point-pmf_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t point-pmf -- ******* FOUND TEST CASE solv, solv -- TEST solv_test WORKING_DIRECTORY /<>/tests COMMAND /usr/bin/python3 /<>/tests/apbs_tester.py -e apbs -t solv -- Configuring done (8.2s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY ENABLE_READLINE ENABLE_ZLIB -- Build files have been written to: /<>/obj-arm-linux-gnueabihf make[1]: Leaving directory '/<>' dh_auto_build -a -O--buildsystem=cmake cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/<> -B/<>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabihf/CMakeFiles /<>/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-arm-linux-gnueabihf' make -f _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build.make _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depend make -f _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build.make _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/depend make -f _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build.make _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/debian/external_deps/fetk/punc/src/cgcode /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/DependInfo.cmake "--color=" make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/python /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/tools/python /<>/obj-arm-linux-gnueabihf/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/debian/external_deps/fetk/gamer/src /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/debian/external_deps/fetk/punc/src/vf2c /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build.make _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/build make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build.make _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' Dependee "/<>/obj-arm-linux-gnueabihf/tools/python/CMakeFiles/apbslib_swig_compilation.dir/DependInfo.cmake" is newer than depender "/<>/obj-arm-linux-gnueabihf/tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend.internal". Dependee "/<>/obj-arm-linux-gnueabihf/tools/python/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/obj-arm-linux-gnueabihf/tools/python/CMakeFiles/apbslib_swig_compilation.dir/depend.internal". Scanning dependencies of target apbslib_swig_compilation make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build.make _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/build make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f tools/python/CMakeFiles/apbslib_swig_compilation.dir/build.make tools/python/CMakeFiles/apbslib_swig_compilation.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 1%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/base/gamer_base.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/base/gamer_base.c.o -MF CMakeFiles/gamer.dir/base/gamer_base.c.o.d -o CMakeFiles/gamer.dir/base/gamer_base.c.o -c /<>/debian/external_deps/fetk/gamer/src/base/gamer_base.c make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 1%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgdrv.c.o [ 1%] Swig compile apbslib.i for python cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgdrv.c.o -MF CMakeFiles/cgcode.dir/scgdrv.c.o.d -o CMakeFiles/cgcode.dir/scgdrv.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/scgdrv.c cd /<>/obj-arm-linux-gnueabihf/tools/python && /usr/bin/cmake -E make_directory /<>/obj-arm-linux-gnueabihf/tools/python/CMakeFiles/_apbslib.dir /<>/obj-arm-linux-gnueabihf/tools/python /<>/obj-arm-linux-gnueabihf/tools/python/CMakeFiles/_apbslib.dir [ 1%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77vers.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77vers.c.o -MF CMakeFiles/vf2c.dir/f77vers.c.o.d -o CMakeFiles/vf2c.dir/f77vers.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/f77vers.c cd /<>/obj-arm-linux-gnueabihf/tools/python && /usr/bin/cmake -E touch /<>/obj-arm-linux-gnueabihf/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON.stamp cd /<>/obj-arm-linux-gnueabihf/tools/python && /usr/bin/cmake -E env SWIG_LIB=/usr/share/swig4.0 /usr/bin/swig4.0 -python -outdir /<>/obj-arm-linux-gnueabihf/tools/python -interface _apbslib -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/python3.12 -I/<>/tools/python -o /<>/obj-arm-linux-gnueabihf/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c /<>/tools/python/apbslib.i [ 2%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i77vers.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i77vers.c.o -MF CMakeFiles/vf2c.dir/i77vers.c.o.d -o CMakeFiles/vf2c.dir/i77vers.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i77vers.c [ 2%] Building C object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/triangle/triangle.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/cc -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/triangle/triangle.c.o -MF CMakeFiles/gamer.dir/triangle/triangle.c.o.d -o CMakeFiles/gamer.dir/triangle/triangle.c.o -c /<>/debian/external_deps/fetk/gamer/src/triangle/triangle.c [ 2%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_rnge.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_rnge.c.o -MF CMakeFiles/vf2c.dir/s_rnge.c.o.d -o CMakeFiles/vf2c.dir/s_rnge.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/s_rnge.c [ 3%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scg.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scg.c.o -MF CMakeFiles/cgcode.dir/scg.c.o.d -o CMakeFiles/cgcode.dir/scg.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/scg.c [ 3%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/abort_.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/abort_.c.o -MF CMakeFiles/vf2c.dir/abort_.c.o.d -o CMakeFiles/vf2c.dir/abort_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/abort_.c [ 3%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/exit_.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/exit_.c.o -MF CMakeFiles/vf2c.dir/exit_.c.o.d -o CMakeFiles/vf2c.dir/exit_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/exit_.c [ 3%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scr.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scr.c.o -MF CMakeFiles/cgcode.dir/scr.c.o.d -o CMakeFiles/cgcode.dir/scr.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/scr.c [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getarg_.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getarg_.c.o -MF CMakeFiles/vf2c.dir/getarg_.c.o.d -o CMakeFiles/vf2c.dir/getarg_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/getarg_.c [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iargc_.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iargc_.c.o -MF CMakeFiles/vf2c.dir/iargc_.c.o.d -o CMakeFiles/vf2c.dir/iargc_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/iargc_.c [ 4%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scrind.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scrind.c.o -MF CMakeFiles/cgcode.dir/scrind.c.o.d -o CMakeFiles/cgcode.dir/scrind.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/scrind.c [ 4%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getenv_.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/getenv_.c.o -MF CMakeFiles/vf2c.dir/getenv_.c.o.d -o CMakeFiles/vf2c.dir/getenv_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/getenv_.c make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 4%] Built target apbslib_swig_compilation [ 5%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/signal_.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/signal_.c.o -MF CMakeFiles/vf2c.dir/signal_.c.o.d -o CMakeFiles/vf2c.dir/signal_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/signal_.c [ 5%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_stop.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_stop.c.o -MF CMakeFiles/vf2c.dir/s_stop.c.o.d -o CMakeFiles/vf2c.dir/s_stop.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/s_stop.c [ 5%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_paus.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_paus.c.o -MF CMakeFiles/vf2c.dir/s_paus.c.o.d -o CMakeFiles/vf2c.dir/s_paus.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/s_paus.c [ 5%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/system_.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/system_.c.o -MF CMakeFiles/vf2c.dir/system_.c.o.d -o CMakeFiles/vf2c.dir/system_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/system_.c [ 6%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcg.c.o [ 7%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/cabs.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcg.c.o -MF CMakeFiles/cgcode.dir/spcg.c.o.d -o CMakeFiles/cgcode.dir/spcg.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/spcg.c cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/cabs.c.o -MF CMakeFiles/vf2c.dir/cabs.c.o.d -o CMakeFiles/vf2c.dir/cabs.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/cabs.c [ 7%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derf_.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derf_.c.o -MF CMakeFiles/vf2c.dir/derf_.c.o.d -o CMakeFiles/vf2c.dir/derf_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/derf_.c [ 7%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derfc_.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/derfc_.c.o -MF CMakeFiles/vf2c.dir/derfc_.c.o.d -o CMakeFiles/vf2c.dir/derfc_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/derfc_.c [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erf_.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erf_.c.o -MF CMakeFiles/vf2c.dir/erf_.c.o.d -o CMakeFiles/vf2c.dir/erf_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/erf_.c [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erfc_.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/erfc_.c.o -MF CMakeFiles/vf2c.dir/erfc_.c.o.d -o CMakeFiles/vf2c.dir/erfc_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/erfc_.c [ 8%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgnr.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgnr.c.o -MF CMakeFiles/cgcode.dir/scgnr.c.o.d -o CMakeFiles/cgcode.dir/scgnr.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/scgnr.c [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sig_die.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sig_die.c.o -MF CMakeFiles/vf2c.dir/sig_die.c.o.d -o CMakeFiles/vf2c.dir/sig_die.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/sig_die.c [ 8%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uninit.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uninit.c.o -MF CMakeFiles/vf2c.dir/uninit.c.o.d -o CMakeFiles/vf2c.dir/uninit.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/uninit.c [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ci.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ci.c.o -MF CMakeFiles/vf2c.dir/pow_ci.c.o.d -o CMakeFiles/vf2c.dir/pow_ci.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/pow_ci.c [ 9%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgne.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgne.c.o -MF CMakeFiles/cgcode.dir/scgne.c.o.d -o CMakeFiles/cgcode.dir/scgne.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/scgne.c [ 9%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgnr.c.o [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_dd.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgnr.c.o -MF CMakeFiles/cgcode.dir/spcgnr.c.o.d -o CMakeFiles/cgcode.dir/spcgnr.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/spcgnr.c cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_dd.c.o -MF CMakeFiles/vf2c.dir/pow_dd.c.o.d -o CMakeFiles/vf2c.dir/pow_dd.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/pow_dd.c [ 9%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_di.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_di.c.o -MF CMakeFiles/vf2c.dir/pow_di.c.o.d -o CMakeFiles/vf2c.dir/pow_di.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/pow_di.c [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgne.c.o [ 10%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_hh.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgne.c.o -MF CMakeFiles/cgcode.dir/spcgne.c.o.d -o CMakeFiles/cgcode.dir/spcgne.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/spcgne.c cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_hh.c.o -MF CMakeFiles/vf2c.dir/pow_hh.c.o.d -o CMakeFiles/vf2c.dir/pow_hh.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/pow_hh.c [ 10%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sppcg.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sppcg.c.o -MF CMakeFiles/cgcode.dir/sppcg.c.o.d -o CMakeFiles/cgcode.dir/sppcg.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/sppcg.c [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ii.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ii.c.o -MF CMakeFiles/vf2c.dir/pow_ii.c.o.d -o CMakeFiles/vf2c.dir/pow_ii.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/pow_ii.c [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ri.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_ri.c.o -MF CMakeFiles/vf2c.dir/pow_ri.c.o.d -o CMakeFiles/vf2c.dir/pow_ri.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/pow_ri.c [ 11%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zi.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zi.c.o -MF CMakeFiles/vf2c.dir/pow_zi.c.o.d -o CMakeFiles/vf2c.dir/pow_zi.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/pow_zi.c [ 11%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/predicates.cpp.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/predicates.cpp.o -MF CMakeFiles/gamer.dir/tetgen/predicates.cpp.o.d -o CMakeFiles/gamer.dir/tetgen/predicates.cpp.o -c /<>/debian/external_deps/fetk/gamer/src/tetgen/predicates.cpp [ 11%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgca.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/spcgca.c.o -MF CMakeFiles/cgcode.dir/spcgca.c.o.d -o CMakeFiles/cgcode.dir/spcgca.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/spcgca.c [ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zz.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/pow_zz.c.o -MF CMakeFiles/vf2c.dir/pow_zz.c.o.d -o CMakeFiles/vf2c.dir/pow_zz.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/pow_zz.c [ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_abs.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_abs.c.o -MF CMakeFiles/vf2c.dir/c_abs.c.o.d -o CMakeFiles/vf2c.dir/c_abs.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/c_abs.c [ 12%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_cos.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_cos.c.o -MF CMakeFiles/vf2c.dir/c_cos.c.o.d -o CMakeFiles/vf2c.dir/c_cos.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/c_cos.c [ 13%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sdpchb.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sdpchb.c.o -MF CMakeFiles/cgcode.dir/sdpchb.c.o.d -o CMakeFiles/cgcode.dir/sdpchb.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/sdpchb.c [ 13%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_div.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_div.c.o -MF CMakeFiles/vf2c.dir/c_div.c.o.d -o CMakeFiles/vf2c.dir/c_div.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/c_div.c [ 14%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_exp.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_exp.c.o -MF CMakeFiles/vf2c.dir/c_exp.c.o.d -o CMakeFiles/vf2c.dir/c_exp.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/c_exp.c [ 14%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scbfix.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scbfix.c.o -MF CMakeFiles/cgcode.dir/scbfix.c.o.d -o CMakeFiles/cgcode.dir/scbfix.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/scbfix.c [ 14%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_log.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_log.c.o -MF CMakeFiles/vf2c.dir/c_log.c.o.d -o CMakeFiles/vf2c.dir/c_log.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/c_log.c [ 14%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sckchb.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sckchb.c.o -MF CMakeFiles/cgcode.dir/sckchb.c.o.d -o CMakeFiles/cgcode.dir/sckchb.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/sckchb.c [ 14%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sin.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sin.c.o -MF CMakeFiles/vf2c.dir/c_sin.c.o.d -o CMakeFiles/vf2c.dir/c_sin.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/c_sin.c [ 15%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sqrt.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/c_sqrt.c.o -MF CMakeFiles/vf2c.dir/c_sqrt.c.o.d -o CMakeFiles/vf2c.dir/c_sqrt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/c_sqrt.c [ 15%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/scgchk.c.o -MF CMakeFiles/cgcode.dir/scgchk.c.o.d -o CMakeFiles/cgcode.dir/scgchk.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/scgchk.c [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_abs.c.o [ 16%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sonest.c.o -MF CMakeFiles/cgcode.dir/sonest.c.o.d -o CMakeFiles/cgcode.dir/sonest.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/sonest.c cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_abs.c.o -MF CMakeFiles/vf2c.dir/z_abs.c.o.d -o CMakeFiles/vf2c.dir/z_abs.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/z_abs.c [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o [ 16%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/msstop.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/msstop.c.o -MF CMakeFiles/cgcode.dir/msstop.c.o.d -o CMakeFiles/cgcode.dir/msstop.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/msstop.c cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_cos.c.o -MF CMakeFiles/vf2c.dir/z_cos.c.o.d -o CMakeFiles/vf2c.dir/z_cos.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/z_cos.c [ 16%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/r1mach.c.o [ 16%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_div.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_div.c.o -MF CMakeFiles/vf2c.dir/z_div.c.o.d -o CMakeFiles/vf2c.dir/z_div.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/z_div.c cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/r1mach.c.o -MF CMakeFiles/cgcode.dir/r1mach.c.o.d -o CMakeFiles/cgcode.dir/r1mach.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/r1mach.c [ 17%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/sratqr.c.o -MF CMakeFiles/cgcode.dir/sratqr.c.o.d -o CMakeFiles/cgcode.dir/sratqr.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/sratqr.c [ 18%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_exp.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_exp.c.o -MF CMakeFiles/vf2c.dir/z_exp.c.o.d -o CMakeFiles/vf2c.dir/z_exp.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/z_exp.c [ 18%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_log.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_log.c.o -MF CMakeFiles/vf2c.dir/z_log.c.o.d -o CMakeFiles/vf2c.dir/z_log.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/z_log.c [ 18%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sin.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sin.c.o -MF CMakeFiles/vf2c.dir/z_sin.c.o.d -o CMakeFiles/vf2c.dir/z_sin.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/z_sin.c [ 18%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgdrv.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgdrv.c.o -MF CMakeFiles/cgcode.dir/dcgdrv.c.o.d -o CMakeFiles/cgcode.dir/dcgdrv.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dcgdrv.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/z_sqrt.c.o -MF CMakeFiles/vf2c.dir/z_sqrt.c.o.d -o CMakeFiles/vf2c.dir/z_sqrt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/z_sqrt.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_abs.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_abs.c.o -MF CMakeFiles/vf2c.dir/r_abs.c.o.d -o CMakeFiles/vf2c.dir/r_abs.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_abs.c [ 19%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcg.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcg.c.o -MF CMakeFiles/cgcode.dir/dcg.c.o.d -o CMakeFiles/cgcode.dir/dcg.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dcg.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_acos.c.o -MF CMakeFiles/vf2c.dir/r_acos.c.o.d -o CMakeFiles/vf2c.dir/r_acos.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_acos.c [ 19%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_asin.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_asin.c.o -MF CMakeFiles/vf2c.dir/r_asin.c.o.d -o CMakeFiles/vf2c.dir/r_asin.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_asin.c [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atan.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atan.c.o -MF CMakeFiles/vf2c.dir/r_atan.c.o.d -o CMakeFiles/vf2c.dir/r_atan.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_atan.c [ 20%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcr.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcr.c.o -MF CMakeFiles/cgcode.dir/dcr.c.o.d -o CMakeFiles/cgcode.dir/dcr.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dcr.c [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atn2.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_atn2.c.o -MF CMakeFiles/vf2c.dir/r_atn2.c.o.d -o CMakeFiles/vf2c.dir/r_atn2.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_atn2.c [ 20%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cnjg.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cnjg.c.o -MF CMakeFiles/vf2c.dir/r_cnjg.c.o.d -o CMakeFiles/vf2c.dir/r_cnjg.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_cnjg.c [ 21%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cos.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cos.c.o -MF CMakeFiles/vf2c.dir/r_cos.c.o.d -o CMakeFiles/vf2c.dir/r_cos.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_cos.c [ 22%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcrind.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcrind.c.o -MF CMakeFiles/cgcode.dir/dcrind.c.o.d -o CMakeFiles/cgcode.dir/dcrind.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dcrind.c [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cosh.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_cosh.c.o -MF CMakeFiles/vf2c.dir/r_cosh.c.o.d -o CMakeFiles/vf2c.dir/r_cosh.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_cosh.c [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_dim.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_dim.c.o -MF CMakeFiles/vf2c.dir/r_dim.c.o.d -o CMakeFiles/vf2c.dir/r_dim.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_dim.c [ 22%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_exp.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_exp.c.o -MF CMakeFiles/vf2c.dir/r_exp.c.o.d -o CMakeFiles/vf2c.dir/r_exp.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_exp.c [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_imag.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_imag.c.o -MF CMakeFiles/vf2c.dir/r_imag.c.o.d -o CMakeFiles/vf2c.dir/r_imag.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_imag.c [ 23%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcg.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcg.c.o -MF CMakeFiles/cgcode.dir/dpcg.c.o.d -o CMakeFiles/cgcode.dir/dpcg.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dpcg.c [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_int.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_int.c.o -MF CMakeFiles/vf2c.dir/r_int.c.o.d -o CMakeFiles/vf2c.dir/r_int.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_int.c [ 23%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_lg10.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_lg10.c.o -MF CMakeFiles/vf2c.dir/r_lg10.c.o.d -o CMakeFiles/vf2c.dir/r_lg10.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_lg10.c [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_log.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_log.c.o -MF CMakeFiles/vf2c.dir/r_log.c.o.d -o CMakeFiles/vf2c.dir/r_log.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_log.c [ 24%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgnr.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgnr.c.o -MF CMakeFiles/cgcode.dir/dcgnr.c.o.d -o CMakeFiles/cgcode.dir/dcgnr.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dcgnr.c [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_mod.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_mod.c.o -MF CMakeFiles/vf2c.dir/r_mod.c.o.d -o CMakeFiles/vf2c.dir/r_mod.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_mod.c [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_nint.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_nint.c.o -MF CMakeFiles/vf2c.dir/r_nint.c.o.d -o CMakeFiles/vf2c.dir/r_nint.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_nint.c [ 24%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgne.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgne.c.o -MF CMakeFiles/cgcode.dir/dcgne.c.o.d -o CMakeFiles/cgcode.dir/dcgne.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dcgne.c [ 24%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sign.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sign.c.o -MF CMakeFiles/vf2c.dir/r_sign.c.o.d -o CMakeFiles/vf2c.dir/r_sign.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_sign.c [ 25%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sin.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sin.c.o -MF CMakeFiles/vf2c.dir/r_sin.c.o.d -o CMakeFiles/vf2c.dir/r_sin.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_sin.c [ 25%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sinh.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sinh.c.o -MF CMakeFiles/vf2c.dir/r_sinh.c.o.d -o CMakeFiles/vf2c.dir/r_sinh.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_sinh.c [ 26%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgnr.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgnr.c.o -MF CMakeFiles/cgcode.dir/dpcgnr.c.o.d -o CMakeFiles/cgcode.dir/dpcgnr.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dpcgnr.c [ 26%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sqrt.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_sqrt.c.o -MF CMakeFiles/vf2c.dir/r_sqrt.c.o.d -o CMakeFiles/vf2c.dir/r_sqrt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_sqrt.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tan.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tan.c.o -MF CMakeFiles/vf2c.dir/r_tan.c.o.d -o CMakeFiles/vf2c.dir/r_tan.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_tan.c [ 27%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgne.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgne.c.o -MF CMakeFiles/cgcode.dir/dpcgne.c.o.d -o CMakeFiles/cgcode.dir/dpcgne.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dpcgne.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tanh.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/r_tanh.c.o -MF CMakeFiles/vf2c.dir/r_tanh.c.o.d -o CMakeFiles/vf2c.dir/r_tanh.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/r_tanh.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_abs.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_abs.c.o -MF CMakeFiles/vf2c.dir/d_abs.c.o.d -o CMakeFiles/vf2c.dir/d_abs.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_abs.c [ 27%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_acos.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_acos.c.o -MF CMakeFiles/vf2c.dir/d_acos.c.o.d -o CMakeFiles/vf2c.dir/d_acos.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_acos.c [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_asin.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_asin.c.o -MF CMakeFiles/vf2c.dir/d_asin.c.o.d -o CMakeFiles/vf2c.dir/d_asin.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_asin.c [ 28%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dppcg.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dppcg.c.o -MF CMakeFiles/cgcode.dir/dppcg.c.o.d -o CMakeFiles/cgcode.dir/dppcg.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dppcg.c [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atan.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atan.c.o -MF CMakeFiles/vf2c.dir/d_atan.c.o.d -o CMakeFiles/vf2c.dir/d_atan.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_atan.c [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atn2.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_atn2.c.o -MF CMakeFiles/vf2c.dir/d_atn2.c.o.d -o CMakeFiles/vf2c.dir/d_atn2.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_atn2.c [ 28%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cnjg.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cnjg.c.o -MF CMakeFiles/vf2c.dir/d_cnjg.c.o.d -o CMakeFiles/vf2c.dir/d_cnjg.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_cnjg.c [ 29%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cos.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cos.c.o -MF CMakeFiles/vf2c.dir/d_cos.c.o.d -o CMakeFiles/vf2c.dir/d_cos.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_cos.c [ 30%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgca.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dpcgca.c.o -MF CMakeFiles/cgcode.dir/dpcgca.c.o.d -o CMakeFiles/cgcode.dir/dpcgca.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dpcgca.c [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cosh.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_cosh.c.o -MF CMakeFiles/vf2c.dir/d_cosh.c.o.d -o CMakeFiles/vf2c.dir/d_cosh.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_cosh.c [ 30%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_dim.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_dim.c.o -MF CMakeFiles/vf2c.dir/d_dim.c.o.d -o CMakeFiles/vf2c.dir/d_dim.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_dim.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_exp.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_exp.c.o -MF CMakeFiles/vf2c.dir/d_exp.c.o.d -o CMakeFiles/vf2c.dir/d_exp.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_exp.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_imag.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_imag.c.o -MF CMakeFiles/vf2c.dir/d_imag.c.o.d -o CMakeFiles/vf2c.dir/d_imag.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_imag.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_int.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_int.c.o -MF CMakeFiles/vf2c.dir/d_int.c.o.d -o CMakeFiles/vf2c.dir/d_int.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_int.c [ 31%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/ddpchb.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/ddpchb.c.o -MF CMakeFiles/cgcode.dir/ddpchb.c.o.d -o CMakeFiles/cgcode.dir/ddpchb.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/ddpchb.c [ 31%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_lg10.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_lg10.c.o -MF CMakeFiles/vf2c.dir/d_lg10.c.o.d -o CMakeFiles/vf2c.dir/d_lg10.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_lg10.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_log.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_log.c.o -MF CMakeFiles/vf2c.dir/d_log.c.o.d -o CMakeFiles/vf2c.dir/d_log.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_log.c [ 32%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcbfix.c.o -MF CMakeFiles/cgcode.dir/dcbfix.c.o.d -o CMakeFiles/cgcode.dir/dcbfix.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dcbfix.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_mod.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_mod.c.o -MF CMakeFiles/vf2c.dir/d_mod.c.o.d -o CMakeFiles/vf2c.dir/d_mod.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_mod.c [ 32%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dckchb.c.o -MF CMakeFiles/cgcode.dir/dckchb.c.o.d -o CMakeFiles/cgcode.dir/dckchb.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dckchb.c [ 32%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_nint.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_nint.c.o -MF CMakeFiles/vf2c.dir/d_nint.c.o.d -o CMakeFiles/vf2c.dir/d_nint.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_nint.c [ 33%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgchk.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dcgchk.c.o -MF CMakeFiles/cgcode.dir/dcgchk.c.o.d -o CMakeFiles/cgcode.dir/dcgchk.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dcgchk.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_prod.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_prod.c.o -MF CMakeFiles/vf2c.dir/d_prod.c.o.d -o CMakeFiles/vf2c.dir/d_prod.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_prod.c [ 34%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/donest.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/donest.c.o -MF CMakeFiles/cgcode.dir/donest.c.o.d -o CMakeFiles/cgcode.dir/donest.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/donest.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sign.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sign.c.o -MF CMakeFiles/vf2c.dir/d_sign.c.o.d -o CMakeFiles/vf2c.dir/d_sign.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_sign.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sin.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sin.c.o -MF CMakeFiles/vf2c.dir/d_sin.c.o.d -o CMakeFiles/vf2c.dir/d_sin.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_sin.c [ 34%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/mdstop.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/mdstop.c.o -MF CMakeFiles/cgcode.dir/mdstop.c.o.d -o CMakeFiles/cgcode.dir/mdstop.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/mdstop.c [ 34%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sinh.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sinh.c.o -MF CMakeFiles/vf2c.dir/d_sinh.c.o.d -o CMakeFiles/vf2c.dir/d_sinh.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_sinh.c [ 35%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/d1mach.c.o -MF CMakeFiles/cgcode.dir/d1mach.c.o.d -o CMakeFiles/cgcode.dir/d1mach.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/d1mach.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sqrt.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_sqrt.c.o -MF CMakeFiles/vf2c.dir/d_sqrt.c.o.d -o CMakeFiles/vf2c.dir/d_sqrt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_sqrt.c [ 36%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dratqr.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/dratqr.c.o -MF CMakeFiles/cgcode.dir/dratqr.c.o.d -o CMakeFiles/cgcode.dir/dratqr.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/dratqr.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tan.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tan.c.o -MF CMakeFiles/vf2c.dir/d_tan.c.o.d -o CMakeFiles/vf2c.dir/d_tan.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_tan.c [ 36%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tanh.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/d_tanh.c.o -MF CMakeFiles/vf2c.dir/d_tanh.c.o.d -o CMakeFiles/vf2c.dir/d_tanh.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/d_tanh.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_abs.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_abs.c.o -MF CMakeFiles/vf2c.dir/i_abs.c.o.d -o CMakeFiles/vf2c.dir/i_abs.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i_abs.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dim.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dim.c.o -MF CMakeFiles/vf2c.dir/i_dim.c.o.d -o CMakeFiles/vf2c.dir/i_dim.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i_dim.c [ 37%] Building C object _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depsln.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cc -Dcgcode_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/cgcode/CMakeFiles/cgcode.dir/depsln.c.o -MF CMakeFiles/cgcode.dir/depsln.c.o.d -o CMakeFiles/cgcode.dir/depsln.c.o -c /<>/debian/external_deps/fetk/punc/src/cgcode/depsln.c [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dnnt.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_dnnt.c.o -MF CMakeFiles/vf2c.dir/i_dnnt.c.o.d -o CMakeFiles/vf2c.dir/i_dnnt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i_dnnt.c [ 37%] Linking C shared library libcgcode.so cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cmake -E cmake_link_script CMakeFiles/cgcode.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libcgcode.so.1.9 -o libcgcode.so.1.9.3 CMakeFiles/cgcode.dir/scgdrv.c.o CMakeFiles/cgcode.dir/scg.c.o CMakeFiles/cgcode.dir/scr.c.o CMakeFiles/cgcode.dir/scrind.c.o CMakeFiles/cgcode.dir/spcg.c.o CMakeFiles/cgcode.dir/scgnr.c.o CMakeFiles/cgcode.dir/scgne.c.o CMakeFiles/cgcode.dir/spcgnr.c.o CMakeFiles/cgcode.dir/spcgne.c.o CMakeFiles/cgcode.dir/sppcg.c.o CMakeFiles/cgcode.dir/spcgca.c.o CMakeFiles/cgcode.dir/sdpchb.c.o CMakeFiles/cgcode.dir/scbfix.c.o CMakeFiles/cgcode.dir/sckchb.c.o CMakeFiles/cgcode.dir/scgchk.c.o CMakeFiles/cgcode.dir/sonest.c.o CMakeFiles/cgcode.dir/msstop.c.o CMakeFiles/cgcode.dir/r1mach.c.o CMakeFiles/cgcode.dir/sratqr.c.o CMakeFiles/cgcode.dir/dcgdrv.c.o CMakeFiles/cgcode.dir/dcg.c.o CMakeFiles/cgcode.dir/dcr.c.o CMakeFiles/cgcode.dir/dcrind.c.o CMakeFiles/cgcode.dir/dpcg.c.o CMakeFiles/cgcode.dir/dcgnr.c.o CMakeFiles/cgcode.dir/dcgne.c.o CMakeFiles/cgcode.dir/dpcgnr.c.o CMakeFiles/cgcode.dir/dpcgne.c.o CMakeFiles/cgcode.dir/dppcg.c.o CMakeFiles/cgcode.dir/dpcgca.c.o CMakeFiles/cgcode.dir/ddpchb.c.o CMakeFiles/cgcode.dir/dcbfix.c.o CMakeFiles/cgcode.dir/dckchb.c.o CMakeFiles/cgcode.dir/dcgchk.c.o CMakeFiles/cgcode.dir/donest.c.o CMakeFiles/cgcode.dir/mdstop.c.o CMakeFiles/cgcode.dir/d1mach.c.o CMakeFiles/cgcode.dir/dratqr.c.o CMakeFiles/cgcode.dir/depsln.c.o [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_indx.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_indx.c.o -MF CMakeFiles/vf2c.dir/i_indx.c.o.d -o CMakeFiles/vf2c.dir/i_indx.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i_indx.c cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/cgcode && /usr/bin/cmake -E cmake_symlink_library libcgcode.so.1.9.3 libcgcode.so.1.9 libcgcode.so make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 37%] Built target cgcode [ 37%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_mod.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_mod.c.o -MF CMakeFiles/vf2c.dir/i_mod.c.o.d -o CMakeFiles/vf2c.dir/i_mod.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i_mod.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_len.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_len.c.o -MF CMakeFiles/vf2c.dir/i_len.c.o.d -o CMakeFiles/vf2c.dir/i_len.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i_len.c [ 38%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_nint.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_nint.c.o -MF CMakeFiles/vf2c.dir/i_nint.c.o.d -o CMakeFiles/vf2c.dir/i_nint.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i_nint.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_sign.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/i_sign.c.o -MF CMakeFiles/vf2c.dir/i_sign.c.o.d -o CMakeFiles/vf2c.dir/i_sign.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/i_sign.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitbits.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitbits.c.o -MF CMakeFiles/vf2c.dir/lbitbits.c.o.d -o CMakeFiles/vf2c.dir/lbitbits.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/lbitbits.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitshft.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lbitshft.c.o -MF CMakeFiles/vf2c.dir/lbitshft.c.o.d -o CMakeFiles/vf2c.dir/lbitshft.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/lbitshft.c [ 39%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_abs.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_abs.c.o -MF CMakeFiles/vf2c.dir/h_abs.c.o.d -o CMakeFiles/vf2c.dir/h_abs.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/h_abs.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dim.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dim.c.o -MF CMakeFiles/vf2c.dir/h_dim.c.o.d -o CMakeFiles/vf2c.dir/h_dim.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/h_dim.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dnnt.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_dnnt.c.o -MF CMakeFiles/vf2c.dir/h_dnnt.c.o.d -o CMakeFiles/vf2c.dir/h_dnnt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/h_dnnt.c [ 40%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_indx.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_indx.c.o -MF CMakeFiles/vf2c.dir/h_indx.c.o.d -o CMakeFiles/vf2c.dir/h_indx.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/h_indx.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_len.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_len.c.o -MF CMakeFiles/vf2c.dir/h_len.c.o.d -o CMakeFiles/vf2c.dir/h_len.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/h_len.c [ 41%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o -MF CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o.d -o CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o -c /<>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_mod.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_mod.c.o -MF CMakeFiles/vf2c.dir/h_mod.c.o.d -o CMakeFiles/vf2c.dir/h_mod.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/h_mod.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_nint.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_nint.c.o -MF CMakeFiles/vf2c.dir/h_nint.c.o.d -o CMakeFiles/vf2c.dir/h_nint.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/h_nint.c [ 41%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_sign.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/h_sign.c.o -MF CMakeFiles/vf2c.dir/h_sign.c.o.d -o CMakeFiles/vf2c.dir/h_sign.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/h_sign.c [ 42%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/CorrectNormals.C.o -MF CMakeFiles/gamer.dir/biom/CorrectNormals.C.o.d -o CMakeFiles/gamer.dir/biom/CorrectNormals.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/CorrectNormals.C [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_ge.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_ge.c.o -MF CMakeFiles/vf2c.dir/l_ge.c.o.d -o CMakeFiles/vf2c.dir/l_ge.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/l_ge.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_gt.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_gt.c.o -MF CMakeFiles/vf2c.dir/l_gt.c.o.d -o CMakeFiles/vf2c.dir/l_gt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/l_gt.c [ 43%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_le.c.o -MF CMakeFiles/vf2c.dir/l_le.c.o.d -o CMakeFiles/vf2c.dir/l_le.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/l_le.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_lt.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/l_lt.c.o -MF CMakeFiles/vf2c.dir/l_lt.c.o.d -o CMakeFiles/vf2c.dir/l_lt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/l_lt.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_ge.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_ge.c.o -MF CMakeFiles/vf2c.dir/hl_ge.c.o.d -o CMakeFiles/vf2c.dir/hl_ge.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/hl_ge.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_gt.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_gt.c.o -MF CMakeFiles/vf2c.dir/hl_gt.c.o.d -o CMakeFiles/vf2c.dir/hl_gt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/hl_gt.c [ 44%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_le.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_le.c.o -MF CMakeFiles/vf2c.dir/hl_le.c.o.d -o CMakeFiles/vf2c.dir/hl_le.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/hl_le.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_lt.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/hl_lt.c.o -MF CMakeFiles/vf2c.dir/hl_lt.c.o.d -o CMakeFiles/vf2c.dir/hl_lt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/hl_lt.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1asc_.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1asc_.c.o -MF CMakeFiles/vf2c.dir/ef1asc_.c.o.d -o CMakeFiles/vf2c.dir/ef1asc_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/ef1asc_.c /<>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function ‘void tetgenmesh::constrainedfacets()’: /<>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20804:26: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 20804 | equatptlist = new list("point *"); | ^~~~~~~~~ /<>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20809:26: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 20809 | horizptlist = new list("point *"); | ^~~~~~~~~ /<>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20810:26: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 20810 | belowptlist = new list("point *"); | ^~~~~~~~~ /<>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:20811:26: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 20811 | aboveptlist = new list("point *"); | ^~~~~~~~~ [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1cmc_.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ef1cmc_.c.o -MF CMakeFiles/vf2c.dir/ef1cmc_.c.o.d -o CMakeFiles/vf2c.dir/ef1cmc_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/ef1cmc_.c [ 45%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77_aloc.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/f77_aloc.c.o -MF CMakeFiles/vf2c.dir/f77_aloc.c.o.d -o CMakeFiles/vf2c.dir/f77_aloc.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/f77_aloc.c /<>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp: In member function ‘long int tetgenmesh::reconstructmesh()’: /<>/debian/external_deps/fetk/gamer/src/tetgen/tetgen.cpp:24383:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 24383 | markerlist = new list("int"); | ^~~~~ [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cat.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cat.c.o -MF CMakeFiles/vf2c.dir/s_cat.c.o.d -o CMakeFiles/vf2c.dir/s_cat.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/s_cat.c [ 46%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o -MF CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o.d -o CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/GenerateSphereMesh.C [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cmp.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_cmp.c.o -MF CMakeFiles/vf2c.dir/s_cmp.c.o.d -o CMakeFiles/vf2c.dir/s_cmp.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/s_cmp.c [ 46%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_copy.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/s_copy.c.o -MF CMakeFiles/vf2c.dir/s_copy.c.o.d -o CMakeFiles/vf2c.dir/s_copy.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/s_copy.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dtime_.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dtime_.c.o -MF CMakeFiles/vf2c.dir/dtime_.c.o.d -o CMakeFiles/vf2c.dir/dtime_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/dtime_.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/etime_.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/etime_.c.o -MF CMakeFiles/vf2c.dir/etime_.c.o.d -o CMakeFiles/vf2c.dir/etime_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/etime_.c [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/backspac.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/backspac.c.o -MF CMakeFiles/vf2c.dir/backspac.c.o.d -o CMakeFiles/vf2c.dir/backspac.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/backspac.c /<>/debian/external_deps/fetk/punc/src/vf2c/backspac.c: In function ‘f_back’: /<>/debian/external_deps/fetk/punc/src/vf2c/backspac.c:47:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 47 | fread((char *)&n,sizeof(uiolen),1,f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 47%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/close.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/close.c.o -MF CMakeFiles/vf2c.dir/close.c.o.d -o CMakeFiles/vf2c.dir/close.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/close.c [ 47%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/MarchingCube.C.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/MarchingCube.C.o -MF CMakeFiles/gamer.dir/biom/MarchingCube.C.o.d -o CMakeFiles/gamer.dir/biom/MarchingCube.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/MarchingCube.C [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dfe.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dfe.c.o -MF CMakeFiles/vf2c.dir/dfe.c.o.d -o CMakeFiles/vf2c.dir/dfe.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/dfe.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dolio.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/dolio.c.o -MF CMakeFiles/vf2c.dir/dolio.c.o.d -o CMakeFiles/vf2c.dir/dolio.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/dolio.c [ 48%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/due.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/due.c.o -MF CMakeFiles/vf2c.dir/due.c.o.d -o CMakeFiles/vf2c.dir/due.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/due.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/endfile.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/endfile.c.o -MF CMakeFiles/vf2c.dir/endfile.c.o.d -o CMakeFiles/vf2c.dir/endfile.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/endfile.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/err.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/err.c.o -MF CMakeFiles/vf2c.dir/err.c.o.d -o CMakeFiles/vf2c.dir/err.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/err.c [ 49%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmt.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmt.c.o -MF CMakeFiles/vf2c.dir/fmt.c.o.d -o CMakeFiles/vf2c.dir/fmt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/fmt.c [ 50%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o -MF CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o.d -o CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/PDB2Mesh.C [ 50%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmtlib.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/fmtlib.c.o -MF CMakeFiles/vf2c.dir/fmtlib.c.o.d -o CMakeFiles/vf2c.dir/fmtlib.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/fmtlib.c [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ftell_.c.o [ 51%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Volume.C.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/PDB2Volume.C.o -MF CMakeFiles/gamer.dir/biom/PDB2Volume.C.o.d -o CMakeFiles/gamer.dir/biom/PDB2Volume.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ftell_.c.o -MF CMakeFiles/vf2c.dir/ftell_.c.o.d -o CMakeFiles/vf2c.dir/ftell_.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/ftell_.c [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iio.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/iio.c.o -MF CMakeFiles/vf2c.dir/iio.c.o.d -o CMakeFiles/vf2c.dir/iio.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/iio.c [ 51%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ilnw.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/ilnw.c.o -MF CMakeFiles/vf2c.dir/ilnw.c.o.d -o CMakeFiles/vf2c.dir/ilnw.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/ilnw.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/inquire.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/inquire.c.o -MF CMakeFiles/vf2c.dir/inquire.c.o.d -o CMakeFiles/vf2c.dir/inquire.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/inquire.c /<>/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C: In function ‘float PDB2Volume(char*, float**, int*, int*, int*, float*, float*, ATOM**, int*, char)’: /<>/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C:85:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85 | fscanf(fp,"%d\n",&m); | ~~~~~~^~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/gamer/src/biom/PDB2Volume.C:88:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | fscanf(fp,"%f %f %f %f\n",&x,&y,&z,&radius); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lread.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lread.c.o -MF CMakeFiles/vf2c.dir/lread.c.o.d -o CMakeFiles/vf2c.dir/lread.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/lread.c [ 52%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadLattice.C.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadLattice.C.o -MF CMakeFiles/gamer.dir/biom/ReadLattice.C.o.d -o CMakeFiles/gamer.dir/biom/ReadLattice.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/ReadLattice.C [ 52%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadPDB.C.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadPDB.C.o -MF CMakeFiles/gamer.dir/biom/ReadPDB.C.o.d -o CMakeFiles/gamer.dir/biom/ReadPDB.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/ReadPDB.C [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lwrite.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/lwrite.c.o -MF CMakeFiles/vf2c.dir/lwrite.c.o.d -o CMakeFiles/vf2c.dir/lwrite.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/lwrite.c [ 52%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/open.c.o [ 53%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o -MF CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o.d -o CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/open.c.o -MF CMakeFiles/vf2c.dir/open.c.o.d -o CMakeFiles/vf2c.dir/open.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/open.c [ 53%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/RegionGrowing.C.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/RegionGrowing.C.o -MF CMakeFiles/gamer.dir/biom/RegionGrowing.C.o.d -o CMakeFiles/gamer.dir/biom/RegionGrowing.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/RegionGrowing.C [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rdfmt.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rdfmt.c.o -MF CMakeFiles/vf2c.dir/rdfmt.c.o.d -o CMakeFiles/vf2c.dir/rdfmt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/rdfmt.c /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function ‘SurfaceMesh* SurfaceMesh_readOFF(char*)’: /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:401:14: warning: too many arguments for format [-Wformat-extra-args] 401 | printf("Read error. Expected 3 integers for the first simplex.\n", n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:494:14: warning: too many arguments for format [-Wformat-extra-args] 494 | printf("Read error. Expected 4 integers for the first simplex.\n", n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C: In function ‘GemMesh* GemMesh_fromSurfaceMesh(SurfaceMesh*, char*)’: /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:754:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 754 | in.save_nodes("plc"); | ^~~~~ /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:755:16: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 755 | in.save_poly("plc"); | ^~~~~ /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:761:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 761 | out.save_nodes("result"); | ^~~~~~~~ /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:762:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 762 | out.save_elements("result"); | ^~~~~~~~ /<>/debian/external_deps/fetk/gamer/src/biom/ReadWriteMesh.C:763:18: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 763 | out.save_faces("result"); | ^~~~~~~~ [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rewind.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rewind.c.o -MF CMakeFiles/vf2c.dir/rewind.c.o.d -o CMakeFiles/vf2c.dir/rewind.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/rewind.c [ 54%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsfe.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsfe.c.o -MF CMakeFiles/vf2c.dir/rsfe.c.o.d -o CMakeFiles/vf2c.dir/rsfe.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/rsfe.c [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsli.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsli.c.o -MF CMakeFiles/vf2c.dir/rsli.c.o.d -o CMakeFiles/vf2c.dir/rsli.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/rsli.c [ 55%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o -MF CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o.d -o CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/SurfaceMesh.C [ 55%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsne.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/rsne.c.o -MF CMakeFiles/vf2c.dir/rsne.c.o.d -o CMakeFiles/vf2c.dir/rsne.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/rsne.c [ 56%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfExtract.C.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfExtract.C.o -MF CMakeFiles/gamer.dir/biom/SurfExtract.C.o.d -o CMakeFiles/gamer.dir/biom/SurfExtract.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/SurfExtract.C [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sfe.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sfe.c.o -MF CMakeFiles/vf2c.dir/sfe.c.o.d -o CMakeFiles/vf2c.dir/sfe.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/sfe.c [ 56%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfRefine.C.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfRefine.C.o -MF CMakeFiles/gamer.dir/biom/SurfRefine.C.o.d -o CMakeFiles/gamer.dir/biom/SurfRefine.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/SurfRefine.C [ 56%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sue.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/sue.c.o -MF CMakeFiles/vf2c.dir/sue.c.o.d -o CMakeFiles/vf2c.dir/sue.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/sue.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/typesize.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/typesize.c.o -MF CMakeFiles/vf2c.dir/typesize.c.o.d -o CMakeFiles/vf2c.dir/typesize.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/typesize.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uio.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/uio.c.o -MF CMakeFiles/vf2c.dir/uio.c.o.d -o CMakeFiles/vf2c.dir/uio.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/uio.c [ 57%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/util.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/util.c.o -MF CMakeFiles/vf2c.dir/util.c.o.d -o CMakeFiles/vf2c.dir/util.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/util.c [ 57%] Building CXX object _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfSmooth.C.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/c++ -Dgamer_EXPORTS -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src -I/<>/debian/external_deps/fetk/gamer/src/base -I/<>/debian/external_deps/fetk/gamer/src/triangle -I/<>/debian/external_deps/fetk/gamer/src/tetgen -I/<>/debian/external_deps/fetk/gamer/src/biom -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/gamer/src/CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -MF CMakeFiles/gamer.dir/biom/SurfSmooth.C.o.d -o CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -c /<>/debian/external_deps/fetk/gamer/src/biom/SurfSmooth.C [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wref.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wref.c.o -MF CMakeFiles/vf2c.dir/wref.c.o.d -o CMakeFiles/vf2c.dir/wref.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/wref.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wrtfmt.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wrtfmt.c.o -MF CMakeFiles/vf2c.dir/wrtfmt.c.o.d -o CMakeFiles/vf2c.dir/wrtfmt.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/wrtfmt.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsfe.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsfe.c.o -MF CMakeFiles/vf2c.dir/wsfe.c.o.d -o CMakeFiles/vf2c.dir/wsfe.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/wsfe.c [ 58%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsle.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsle.c.o -MF CMakeFiles/vf2c.dir/wsle.c.o.d -o CMakeFiles/vf2c.dir/wsle.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/wsle.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsne.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/wsne.c.o -MF CMakeFiles/vf2c.dir/wsne.c.o.d -o CMakeFiles/vf2c.dir/wsne.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/wsne.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/xwsne.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/xwsne.c.o -MF CMakeFiles/vf2c.dir/xwsne.c.o.d -o CMakeFiles/vf2c.dir/xwsne.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/xwsne.c [ 59%] Building C object _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/main.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cc -Dvf2c_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/vf2c/CMakeFiles/vf2c.dir/main.c.o -MF CMakeFiles/vf2c.dir/main.c.o.d -o CMakeFiles/vf2c.dir/main.c.o -c /<>/debian/external_deps/fetk/punc/src/vf2c/main.c /<>/debian/external_deps/fetk/punc/src/vf2c/main.c:115:1: warning: return type defaults to ‘int’ [-Wimplicit-int] 115 | main(int argc, char **argv) | ^~~~ [ 60%] Linking C shared library libvf2c.so cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cmake -E cmake_link_script CMakeFiles/vf2c.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libvf2c.so.1.9 -o libvf2c.so.1.9.3 CMakeFiles/vf2c.dir/f77vers.c.o CMakeFiles/vf2c.dir/i77vers.c.o CMakeFiles/vf2c.dir/s_rnge.c.o CMakeFiles/vf2c.dir/abort_.c.o CMakeFiles/vf2c.dir/exit_.c.o CMakeFiles/vf2c.dir/getarg_.c.o CMakeFiles/vf2c.dir/iargc_.c.o CMakeFiles/vf2c.dir/getenv_.c.o CMakeFiles/vf2c.dir/signal_.c.o CMakeFiles/vf2c.dir/s_stop.c.o CMakeFiles/vf2c.dir/s_paus.c.o CMakeFiles/vf2c.dir/system_.c.o CMakeFiles/vf2c.dir/cabs.c.o CMakeFiles/vf2c.dir/derf_.c.o CMakeFiles/vf2c.dir/derfc_.c.o CMakeFiles/vf2c.dir/erf_.c.o CMakeFiles/vf2c.dir/erfc_.c.o CMakeFiles/vf2c.dir/sig_die.c.o CMakeFiles/vf2c.dir/uninit.c.o CMakeFiles/vf2c.dir/pow_ci.c.o CMakeFiles/vf2c.dir/pow_dd.c.o CMakeFiles/vf2c.dir/pow_di.c.o CMakeFiles/vf2c.dir/pow_hh.c.o CMakeFiles/vf2c.dir/pow_ii.c.o CMakeFiles/vf2c.dir/pow_ri.c.o CMakeFiles/vf2c.dir/pow_zi.c.o CMakeFiles/vf2c.dir/pow_zz.c.o CMakeFiles/vf2c.dir/c_abs.c.o CMakeFiles/vf2c.dir/c_cos.c.o CMakeFiles/vf2c.dir/c_div.c.o CMakeFiles/vf2c.dir/c_exp.c.o CMakeFiles/vf2c.dir/c_log.c.o CMakeFiles/vf2c.dir/c_sin.c.o CMakeFiles/vf2c.dir/c_sqrt.c.o CMakeFiles/vf2c.dir/z_abs.c.o CMakeFiles/vf2c.dir/z_cos.c.o CMakeFiles/vf2c.dir/z_div.c.o CMakeFiles/vf2c.dir/z_exp.c.o CMakeFiles/vf2c.dir/z_log.c.o CMakeFiles/vf2c.dir/z_sin.c.o CMakeFiles/vf2c.dir/z_sqrt.c.o CMakeFiles/vf2c.dir/r_abs.c.o CMakeFiles/vf2c.dir/r_acos.c.o CMakeFiles/vf2c.dir/r_asin.c.o CMakeFiles/vf2c.dir/r_atan.c.o CMakeFiles/vf2c.dir/r_atn2.c.o CMakeFiles/vf2c.dir/r_cnjg.c.o CMakeFiles/vf2c.dir/r_cos.c.o CMakeFiles/vf2c.dir/r_cosh.c.o CMakeFiles/vf2c.dir/r_dim.c.o CMakeFiles/vf2c.dir/r_exp.c.o CMakeFiles/vf2c.dir/r_imag.c.o CMakeFiles/vf2c.dir/r_int.c.o CMakeFiles/vf2c.dir/r_lg10.c.o CMakeFiles/vf2c.dir/r_log.c.o CMakeFiles/vf2c.dir/r_mod.c.o CMakeFiles/vf2c.dir/r_nint.c.o CMakeFiles/vf2c.dir/r_sign.c.o CMakeFiles/vf2c.dir/r_sin.c.o CMakeFiles/vf2c.dir/r_sinh.c.o CMakeFiles/vf2c.dir/r_sqrt.c.o CMakeFiles/vf2c.dir/r_tan.c.o CMakeFiles/vf2c.dir/r_tanh.c.o CMakeFiles/vf2c.dir/d_abs.c.o CMakeFiles/vf2c.dir/d_acos.c.o CMakeFiles/vf2c.dir/d_asin.c.o CMakeFiles/vf2c.dir/d_atan.c.o CMakeFiles/vf2c.dir/d_atn2.c.o CMakeFiles/vf2c.dir/d_cnjg.c.o CMakeFiles/vf2c.dir/d_cos.c.o CMakeFiles/vf2c.dir/d_cosh.c.o CMakeFiles/vf2c.dir/d_dim.c.o CMakeFiles/vf2c.dir/d_exp.c.o CMakeFiles/vf2c.dir/d_imag.c.o CMakeFiles/vf2c.dir/d_int.c.o CMakeFiles/vf2c.dir/d_lg10.c.o CMakeFiles/vf2c.dir/d_log.c.o CMakeFiles/vf2c.dir/d_mod.c.o CMakeFiles/vf2c.dir/d_nint.c.o CMakeFiles/vf2c.dir/d_prod.c.o CMakeFiles/vf2c.dir/d_sign.c.o CMakeFiles/vf2c.dir/d_sin.c.o CMakeFiles/vf2c.dir/d_sinh.c.o CMakeFiles/vf2c.dir/d_sqrt.c.o CMakeFiles/vf2c.dir/d_tan.c.o CMakeFiles/vf2c.dir/d_tanh.c.o CMakeFiles/vf2c.dir/i_abs.c.o CMakeFiles/vf2c.dir/i_dim.c.o CMakeFiles/vf2c.dir/i_dnnt.c.o CMakeFiles/vf2c.dir/i_indx.c.o CMakeFiles/vf2c.dir/i_len.c.o CMakeFiles/vf2c.dir/i_mod.c.o CMakeFiles/vf2c.dir/i_nint.c.o CMakeFiles/vf2c.dir/i_sign.c.o CMakeFiles/vf2c.dir/lbitbits.c.o CMakeFiles/vf2c.dir/lbitshft.c.o CMakeFiles/vf2c.dir/h_abs.c.o CMakeFiles/vf2c.dir/h_dim.c.o CMakeFiles/vf2c.dir/h_dnnt.c.o CMakeFiles/vf2c.dir/h_indx.c.o CMakeFiles/vf2c.dir/h_len.c.o CMakeFiles/vf2c.dir/h_mod.c.o CMakeFiles/vf2c.dir/h_nint.c.o CMakeFiles/vf2c.dir/h_sign.c.o CMakeFiles/vf2c.dir/l_ge.c.o CMakeFiles/vf2c.dir/l_gt.c.o CMakeFiles/vf2c.dir/l_le.c.o CMakeFiles/vf2c.dir/l_lt.c.o CMakeFiles/vf2c.dir/hl_ge.c.o CMakeFiles/vf2c.dir/hl_gt.c.o CMakeFiles/vf2c.dir/hl_le.c.o CMakeFiles/vf2c.dir/hl_lt.c.o CMakeFiles/vf2c.dir/ef1asc_.c.o CMakeFiles/vf2c.dir/ef1cmc_.c.o CMakeFiles/vf2c.dir/f77_aloc.c.o CMakeFiles/vf2c.dir/s_cat.c.o CMakeFiles/vf2c.dir/s_cmp.c.o CMakeFiles/vf2c.dir/s_copy.c.o CMakeFiles/vf2c.dir/dtime_.c.o CMakeFiles/vf2c.dir/etime_.c.o CMakeFiles/vf2c.dir/backspac.c.o CMakeFiles/vf2c.dir/close.c.o CMakeFiles/vf2c.dir/dfe.c.o CMakeFiles/vf2c.dir/dolio.c.o CMakeFiles/vf2c.dir/due.c.o CMakeFiles/vf2c.dir/endfile.c.o CMakeFiles/vf2c.dir/err.c.o CMakeFiles/vf2c.dir/fmt.c.o CMakeFiles/vf2c.dir/fmtlib.c.o CMakeFiles/vf2c.dir/ftell_.c.o CMakeFiles/vf2c.dir/iio.c.o CMakeFiles/vf2c.dir/ilnw.c.o CMakeFiles/vf2c.dir/inquire.c.o CMakeFiles/vf2c.dir/lread.c.o CMakeFiles/vf2c.dir/lwrite.c.o CMakeFiles/vf2c.dir/open.c.o CMakeFiles/vf2c.dir/rdfmt.c.o CMakeFiles/vf2c.dir/rewind.c.o CMakeFiles/vf2c.dir/rsfe.c.o CMakeFiles/vf2c.dir/rsli.c.o CMakeFiles/vf2c.dir/rsne.c.o CMakeFiles/vf2c.dir/sfe.c.o CMakeFiles/vf2c.dir/sue.c.o CMakeFiles/vf2c.dir/typesize.c.o CMakeFiles/vf2c.dir/uio.c.o CMakeFiles/vf2c.dir/util.c.o CMakeFiles/vf2c.dir/wref.c.o CMakeFiles/vf2c.dir/wrtfmt.c.o CMakeFiles/vf2c.dir/wsfe.c.o CMakeFiles/vf2c.dir/wsle.c.o CMakeFiles/vf2c.dir/wsne.c.o CMakeFiles/vf2c.dir/xwsne.c.o CMakeFiles/vf2c.dir/main.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/vf2c && /usr/bin/cmake -E cmake_symlink_library libvf2c.so.1.9.3 libvf2c.so.1.9 libvf2c.so make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 60%] Built target vf2c make -f _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build.make _deps/fetk-build/punc/src/CMakeFiles/punc.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/debian/external_deps/fetk/punc/src /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src/CMakeFiles/punc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build.make _deps/fetk-build/punc/src/CMakeFiles/punc.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 60%] Building C object _deps/fetk-build/punc/src/CMakeFiles/punc.dir/base/punc_base.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src && /usr/bin/cc -Dpunc_EXPORTS -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/punc/src/CMakeFiles/punc.dir/base/punc_base.c.o -MF CMakeFiles/punc.dir/base/punc_base.c.o.d -o CMakeFiles/punc.dir/base/punc_base.c.o -c /<>/debian/external_deps/fetk/punc/src/base/punc_base.c [ 60%] Linking C shared library libpunc.so cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/punc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libpunc.so.1.9 -o libpunc.so.1.9.3 CMakeFiles/punc.dir/base/punc_base.c.o -lmaloc /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so vf2c/libvf2c.so.1.9.3 cgcode/libcgcode.so.1.9.3 cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src && /usr/bin/cmake -E cmake_symlink_library libpunc.so.1.9.3 libpunc.so.1.9 libpunc.so make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 60%] Built target punc make -f _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build.make _deps/fetk-build/mc/src/CMakeFiles/mc.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/debian/external_deps/fetk/mc/src /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src/CMakeFiles/mc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build.make _deps/fetk-build/mc/src/CMakeFiles/mc.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 60%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bmat.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bmat.c.o -MF CMakeFiles/mc.dir/bam/bmat.c.o.d -o CMakeFiles/mc.dir/bam/bmat.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/bmat.c [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/base/mc_base.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/base/mc_base.c.o -MF CMakeFiles/mc.dir/base/mc_base.c.o.d -o CMakeFiles/mc.dir/base/mc_base.c.o -c /<>/debian/external_deps/fetk/mc/src/base/mc_base.c [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bsolv.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bsolv.c.o -MF CMakeFiles/mc.dir/bam/bsolv.c.o.d -o CMakeFiles/mc.dir/bam/bsolv.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c /<>/debian/external_deps/fetk/mc/src/bam/bmat.c: In function ‘Bmat_ctor’: /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:104:36: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 104 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~ /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:104:32: note: directive argument in the range [0, 2147483646] 104 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:104:32: note: directive argument in the range [0, 3] In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /<>/debian/external_deps/fetk/mc/src/bam/mc/bmat.h:121, from /<>/debian/external_deps/fetk/mc/src/bam/bmat_p.h:37, from /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:34: In function ‘sprintf’, inlined from ‘Bmat_ctor’ at /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:104:17: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 4 and 22 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_bcg’: /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:922:29: warning: ‘%s’ directive writing up to 79 bytes into a region of size 72 [-Wformat-overflow=] 922 | sprintf(rn,"Bvec_bcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /<>/debian/external_deps/fetk/mc/src/bam/mc/bvec.h:41, from /<>/debian/external_deps/fetk/mc/src/bam/bvec_p.h:37, from /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:34: In function ‘sprintf’, inlined from ‘Bvec_bcg’ at /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:922:9: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 9 and 88 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_bcg’: /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:919:33: warning: ‘%s’ directive writing up to 79 bytes into a region of size 68 [-Wformat-overflow=] 919 | sprintf(rn,"--->Bvec_bcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_bcg’ at /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:919:9: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 13 and 92 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 61%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bvec.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/bvec.c.o -MF CMakeFiles/mc.dir/bam/bvec.c.o.d -o CMakeFiles/mc.dir/bam/bvec.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/bvec.c /<>/debian/external_deps/fetk/mc/src/bam/bmat.c: In function ‘Bmat_galerkin’: /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:36: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 1018 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~ /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:32: note: directive argument in the range [0, 2147483646] 1018 | sprintf(bname, "%s_%d%d", thee->name, p, q); | ^~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:32: note: directive argument in the range [0, 2147483646] In function ‘sprintf’, inlined from ‘Bmat_galerkin’ at /<>/debian/external_deps/fetk/mc/src/bam/bmat.c:1018:17: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 4 and 31 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cg’: /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:631:28: warning: ‘%s’ directive writing up to 79 bytes into a region of size 73 [-Wformat-overflow=] 631 | sprintf(rn,"Bvec_cg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_cg’ at /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:631:9: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 8 and 87 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cg’: /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:628:32: warning: ‘%s’ directive writing up to 79 bytes into a region of size 69 [-Wformat-overflow=] 628 | sprintf(rn,"--->Bvec_cg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_cg’ at /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:628:9: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 12 and 91 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mat.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mat.c.o -MF CMakeFiles/mc.dir/bam/mat.c.o.d -o CMakeFiles/mc.dir/bam/mat.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/mat.c /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cgnr’: /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:1422:30: warning: ‘%s’ directive writing up to 79 bytes into a region of size 71 [-Wformat-overflow=] 1422 | sprintf(rn,"Bvec_cgnr%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_cgnr’ at /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:1422:9: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 10 and 89 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c: In function ‘Bvec_cgnr’: /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:1419:34: warning: ‘%s’ directive writing up to 79 bytes into a region of size 67 [-Wformat-overflow=] 1419 | sprintf(rn,"--->Bvec_cgnr%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_cgnr’ at /<>/debian/external_deps/fetk/mc/src/bam/bsolv.c:1419:9: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 14 and 93 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matcopy.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matcopy.c.o -MF CMakeFiles/mc.dir/bam/matcopy.c.o.d -o CMakeFiles/mc.dir/bam/matcopy.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/matcopy.c [ 62%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matln.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/matln.c.o -MF CMakeFiles/mc.dir/bam/matln.c.o.d -o CMakeFiles/mc.dir/bam/matln.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/matln.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mtool.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/mtool.c.o -MF CMakeFiles/mc.dir/bam/mtool.c.o.d -o CMakeFiles/mc.dir/bam/mtool.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/mtool.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/slu.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/slu.c.o -MF CMakeFiles/mc.dir/bam/slu.c.o.d -o CMakeFiles/mc.dir/bam/slu.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/slu.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec.c.o -MF CMakeFiles/mc.dir/bam/vec.c.o.d -o CMakeFiles/mc.dir/bam/vec.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/vec.c [ 63%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec3.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/vec3.c.o -MF CMakeFiles/mc.dir/bam/vec3.c.o.d -o CMakeFiles/mc.dir/bam/vec3.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/vec3.c [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/zslu.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/bam/zslu.c.o -MF CMakeFiles/mc.dir/bam/zslu.c.o.d -o CMakeFiles/mc.dir/bam/zslu.c.o -c /<>/debian/external_deps/fetk/mc/src/bam/zslu.c [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/whb.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/whb.c.o -MF CMakeFiles/mc.dir/whb/whb.c.o.d -o CMakeFiles/mc.dir/whb/whb.c.o -c /<>/debian/external_deps/fetk/mc/src/whb/whb.c [ 64%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/bvechb.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/bvechb.c.o -MF CMakeFiles/mc.dir/whb/bvechb.c.o.d -o CMakeFiles/mc.dir/whb/bvechb.c.o -c /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/hbtools.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/hbtools.c.o -MF CMakeFiles/mc.dir/whb/hbtools.c.o.d -o CMakeFiles/mc.dir/whb/hbtools.c.o -c /<>/debian/external_deps/fetk/mc/src/whb/hbtools.c /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hcg’: /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:267:29: warning: ‘%s’ directive writing up to 79 bytes into a region of size 72 [-Wformat-overflow=] 267 | sprintf(rn,"Bvec_hcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /<>/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /<>/debian/external_deps/fetk/mc/src/whb/bvechb_p.h:37, from /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:34: In function ‘sprintf’, inlined from ‘Bvec_hcg’ at /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:267:9: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 9 and 88 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hcg’: /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:264:33: warning: ‘%s’ directive writing up to 79 bytes into a region of size 68 [-Wformat-overflow=] 264 | sprintf(rn,"--->Bvec_hcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_hcg’ at /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:264:9: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 13 and 92 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/whb/hbtools.c: In function ‘Bvec_ctorPoint’: /<>/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:28: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 5 and 14 [-Wformat-overflow=] 291 | sprintf(bname, "%s_%d", thee->name, p); | ^~ /<>/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:24: note: directive argument in the range [0, 1073741823] 291 | sprintf(bname, "%s_%d", thee->name, p); | ^~~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /<>/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /<>/debian/external_deps/fetk/mc/src/whb/hbtools_p.h:37, from /<>/debian/external_deps/fetk/mc/src/whb/hbtools.c:34: In function ‘sprintf’, inlined from ‘Bvec_ctorPoint’ at /<>/debian/external_deps/fetk/mc/src/whb/hbtools.c:291:9: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 3 and 21 bytes into a destination of size 15 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/rcmat.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/rcmat.c.o -MF CMakeFiles/mc.dir/whb/rcmat.c.o.d -o CMakeFiles/mc.dir/whb/rcmat.c.o -c /<>/debian/external_deps/fetk/mc/src/whb/rcmat.c /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hbcg’: /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:474:30: warning: ‘%s’ directive writing up to 79 bytes into a region of size 71 [-Wformat-overflow=] 474 | sprintf(rn,"Bvec_hbcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_hbcg’ at /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:474:9: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 10 and 89 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c: In function ‘Bvec_hbcg’: /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:471:34: warning: ‘%s’ directive writing up to 79 bytes into a region of size 67 [-Wformat-overflow=] 471 | sprintf(rn,"--->Bvec_hbcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_hbcg’ at /<>/debian/external_deps/fetk/mc/src/whb/bvechb.c:471:9: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 14 and 93 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/brcmat.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/brcmat.c.o -MF CMakeFiles/mc.dir/whb/brcmat.c.o.d -o CMakeFiles/mc.dir/whb/brcmat.c.o -c /<>/debian/external_deps/fetk/mc/src/whb/brcmat.c [ 65%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/subopt.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/whb/subopt.c.o -MF CMakeFiles/mc.dir/whb/subopt.c.o.d -o CMakeFiles/mc.dir/whb/subopt.c.o -c /<>/debian/external_deps/fetk/mc/src/whb/subopt.c [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/aprx.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/aprx.c.o -MF CMakeFiles/mc.dir/aprx/aprx.c.o.d -o CMakeFiles/mc.dir/aprx/aprx.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/aprx.c /<>/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’: /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:776:32: warning: ‘%s’ directive writing up to 79 bytes into a region of size 69 [-Wformat-overflow=] 776 | sprintf(rn,"Bvec_sfpbcg%s",rmeth); | ^~ ~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /<>/debian/external_deps/fetk/mc/src/whb/mc/whb.h:50, from /<>/debian/external_deps/fetk/mc/src/whb/subopt_p.h:37, from /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:39: In function ‘sprintf’, inlined from ‘Bvec_sfpbcg’ at /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:776:9, inlined from ‘Bvec_submethod’ at /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:102:18: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 12 and 91 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’: /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:773:36: warning: ‘%s’ directive writing up to 79 bytes into a region of size 65 [-Wformat-overflow=] 773 | sprintf(rn,"--->Bvec_sfpbcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_sfpbcg’ at /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:773:9, inlined from ‘Bvec_submethod’ at /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:102:18: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 16 and 95 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’: /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:495:31: warning: ‘%s’ directive writing up to 79 bytes into a region of size 70 [-Wformat-overflow=] 495 | sprintf(rn,"Bvec_sfpcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_sfpcg’ at /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:495:9, inlined from ‘Bvec_submethod’ at /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:93:18: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 11 and 90 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/whb/subopt.c: In function ‘Bvec_submethod’: /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:492:35: warning: ‘%s’ directive writing up to 79 bytes into a region of size 66 [-Wformat-overflow=] 492 | sprintf(rn,"--->Bvec_sfpcg%s",rmeth); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘Bvec_sfpcg’ at /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:492:9, inlined from ‘Bvec_submethod’ at /<>/debian/external_deps/fetk/mc/src/whb/subopt.c:93:18: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 15 and 94 bytes into a destination of size 80 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/assem.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/assem.c.o -MF CMakeFiles/mc.dir/aprx/assem.c.o.d -o CMakeFiles/mc.dir/aprx/assem.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/assem.c [ 66%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/bnode.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/bnode.c.o -MF CMakeFiles/mc.dir/aprx/bnode.c.o.d -o CMakeFiles/mc.dir/aprx/bnode.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/bnode.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/estim.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/estim.c.o -MF CMakeFiles/mc.dir/aprx/estim.c.o.d -o CMakeFiles/mc.dir/aprx/estim.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/estim.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/eval.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/eval.c.o -MF CMakeFiles/mc.dir/aprx/eval.c.o.d -o CMakeFiles/mc.dir/aprx/eval.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/eval.c /<>/debian/external_deps/fetk/mc/src/aprx/eval.c: In function ‘Aprx_fe2fd’: /<>/debian/external_deps/fetk/mc/src/aprx/eval.c:368:40: warning: ‘__builtin___sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 368 | sprintf(filename, "f%dz.dat", block); | ^ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /<>/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:40, from /<>/debian/external_deps/fetk/mc/src/aprx/aprx_p.h:37, from /<>/debian/external_deps/fetk/mc/src/aprx/eval.c:34: In function ‘sprintf’, inlined from ‘Aprx_fe2fd’ at /<>/debian/external_deps/fetk/mc/src/aprx/eval.c:368:13: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/aprx/eval.c: In function ‘Aprx_fe2fd’: /<>/debian/external_deps/fetk/mc/src/aprx/eval.c:366:40: warning: ‘__builtin___sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 366 | sprintf(filename, "f%dy.dat", block); | ^ In function ‘sprintf’, inlined from ‘Aprx_fe2fd’ at /<>/debian/external_deps/fetk/mc/src/aprx/eval.c:366:13: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/aprx/eval.c: In function ‘Aprx_fe2fd’: /<>/debian/external_deps/fetk/mc/src/aprx/eval.c:364:40: warning: ‘__builtin___sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 364 | sprintf(filename, "f%dx.dat", block); | ^ In function ‘sprintf’, inlined from ‘Aprx_fe2fd’ at /<>/debian/external_deps/fetk/mc/src/aprx/eval.c:364:13: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 8 and 18 bytes into a destination of size 7 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/io.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/io.c.o -MF CMakeFiles/mc.dir/aprx/io.c.o.d -o CMakeFiles/mc.dir/aprx/io.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/io.c [ 67%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/node.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/node.c.o -MF CMakeFiles/mc.dir/aprx/node.c.o.d -o CMakeFiles/mc.dir/aprx/node.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/node.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/parti.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/parti.c.o -MF CMakeFiles/mc.dir/aprx/parti.c.o.d -o CMakeFiles/mc.dir/aprx/parti.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/parti.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/re.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/aprx/re.c.o -MF CMakeFiles/mc.dir/aprx/re.c.o.d -o CMakeFiles/mc.dir/aprx/re.c.o -c /<>/debian/external_deps/fetk/mc/src/aprx/re.c [ 68%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/vel.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/vel.c.o -MF CMakeFiles/mc.dir/gem/vel.c.o.d -o CMakeFiles/mc.dir/gem/vel.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/vel.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/ves.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/ves.c.o -MF CMakeFiles/mc.dir/gem/ves.c.o.d -o CMakeFiles/mc.dir/gem/ves.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/ves.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gem.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gem.c.o -MF CMakeFiles/mc.dir/gem/gem.c.o.d -o CMakeFiles/mc.dir/gem/gem.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gem.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemchk.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemchk.c.o -MF CMakeFiles/mc.dir/gem/gemchk.c.o.d -o CMakeFiles/mc.dir/gem/gemchk.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gemchk.c [ 69%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemdisp.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemdisp.c.o -MF CMakeFiles/mc.dir/gem/gemdisp.c.o.d -o CMakeFiles/mc.dir/gem/gemdisp.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gemdisp.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemg.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemg.c.o -MF CMakeFiles/mc.dir/gem/gemg.c.o.d -o CMakeFiles/mc.dir/gem/gemg.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gemg.c [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemgen.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemgen.c.o -MF CMakeFiles/mc.dir/gem/gemgen.c.o.d -o CMakeFiles/mc.dir/gem/gemgen.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c: In function ‘Gem_delaunay’: /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: warning: ‘Gem_writeGV’ accessing 16 bytes in a region of size 12 [-Wstringop-overflow=] 522 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c:522:5: note: referencing argument 8 of type ‘double *[4]’ In file included from /<>/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c:34: /<>/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function ‘Gem_writeGV’ 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: warning: ‘Gem_writeGV’ accessing 16 bytes in a region of size 12 [-Wstringop-overflow=] 659 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c:659:13: note: referencing argument 8 of type ‘double *[4]’ /<>/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function ‘Gem_writeGV’ 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: warning: ‘Gem_writeGV’ accessing 16 bytes in a region of size 12 [-Wstringop-overflow=] 743 | Gem_writeGV(thee,sock,0,0,0,1.0,0,defX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/gem/gemgen.c:743:5: note: referencing argument 8 of type ‘double *[4]’ /<>/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3117:15: note: in a call to function ‘Gem_writeGV’ 3117 | VEXTERNC void Gem_writeGV(Gem *thee, Vio *sock, | ^~~~~~~~~~~ [ 70%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemio.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemio.c.o -MF CMakeFiles/mc.dir/gem/gemio.c.o.d -o CMakeFiles/mc.dir/gem/gemio.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gemio.c /<>/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function ‘Gem_writeTEC’: /<>/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1656:33: warning: ‘__builtin___sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 1656 | sprintf(str1,"TETRAHEDRA"); | ^ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/debian/external_deps/fetk/mc/src/base/mc/mc_base.h:40, from /<>/debian/external_deps/fetk/mc/src/gem/mc/gem.h:41, from /<>/debian/external_deps/fetk/mc/src/gem/gem_p.h:37, from /<>/debian/external_deps/fetk/mc/src/gem/gemdisp.c:34: In function ‘sprintf’, inlined from ‘Gem_writeTEC’ at /<>/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1656:9: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/gem/gemdisp.c: In function ‘Gem_writeTEC’: /<>/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1657:33: warning: ‘TETRAHEDRON’ directive writing 11 bytes into a region of size 10 [-Wformat-overflow=] 1657 | sprintf(str2,"TETRAHEDRON"); | ~~~~~~~~~~^ In function ‘sprintf’, inlined from ‘Gem_writeTEC’ at /<>/debian/external_deps/fetk/mc/src/gem/gemdisp.c:1657:9: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 12 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemref.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemref.c.o -MF CMakeFiles/mc.dir/gem/gemref.c.o.d -o CMakeFiles/mc.dir/gem/gemref.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gemref.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemunref.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemunref.c.o -MF CMakeFiles/mc.dir/gem/gemunref.c.o.d -o CMakeFiles/mc.dir/gem/gemunref.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gemunref.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemcube.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/gem/gemcube.c.o -MF CMakeFiles/mc.dir/gem/gemcube.c.o.d -o CMakeFiles/mc.dir/gem/gemcube.c.o -c /<>/debian/external_deps/fetk/mc/src/gem/gemcube.c [ 71%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/pde/pde.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/pde/pde.c.o -MF CMakeFiles/mc.dir/pde/pde.c.o.d -o CMakeFiles/mc.dir/pde/pde.c.o -c /<>/debian/external_deps/fetk/mc/src/pde/pde.c [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/am.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/am.c.o -MF CMakeFiles/mc.dir/nam/am.c.o.d -o CMakeFiles/mc.dir/nam/am.c.o -c /<>/debian/external_deps/fetk/mc/src/nam/am.c [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/lsolv.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/lsolv.c.o -MF CMakeFiles/mc.dir/nam/lsolv.c.o.d -o CMakeFiles/mc.dir/nam/lsolv.c.o -c /<>/debian/external_deps/fetk/mc/src/nam/lsolv.c [ 72%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/nsolv.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/nam/nsolv.c.o -MF CMakeFiles/mc.dir/nam/nsolv.c.o.d -o CMakeFiles/mc.dir/nam/nsolv.c.o -c /<>/debian/external_deps/fetk/mc/src/nam/nsolv.c [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/dyn.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/dyn.c.o -MF CMakeFiles/mc.dir/dyn/dyn.c.o.d -o CMakeFiles/mc.dir/dyn/dyn.c.o -c /<>/debian/external_deps/fetk/mc/src/dyn/dyn.c [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/svio.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/dyn/svio.c.o -MF CMakeFiles/mc.dir/dyn/svio.c.o.d -o CMakeFiles/mc.dir/dyn/svio.c.o -c /<>/debian/external_deps/fetk/mc/src/dyn/svio.c [ 73%] Building C object _deps/fetk-build/mc/src/CMakeFiles/mc.dir/mcsh/mcsh.c.o cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cc -Dmc_EXPORTS -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -fPIC -fPIC -MD -MT _deps/fetk-build/mc/src/CMakeFiles/mc.dir/mcsh/mcsh.c.o -MF CMakeFiles/mc.dir/mcsh/mcsh.c.o.d -o CMakeFiles/mc.dir/mcsh/mcsh.c.o -c /<>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c /<>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c: In function ‘MCsh_builtIn’: /<>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: warning: ‘Gem_writeGEOM’ accessing 16 bytes in a region of size 12 [-Wstringop-overflow=] 765 | Gem_writeGEOM(thee->gm, | ^~~~~~~~~~~~~~~~~~~~~~~ 766 | sock, | ~~~~~ 767 | defKey, | ~~~~~~~ 768 | Vsh_getenvInt(thee->vsh,"CKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 769 | Vsh_getenvInt(thee->vsh,"DKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 770 | Vsh_getenvReal(thee->vsh,"GVAL"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 771 | Vsh_getenvInt(thee->vsh,"FKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 772 | defX, | ~~~~~ 773 | "GV"); | ~~~~~ /<>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:765:9: note: referencing argument 8 of type ‘double *[4]’ In file included from /<>/debian/external_deps/fetk/mc/src/aprx/mc/aprx.h:42, from /<>/debian/external_deps/fetk/mc/src/nam/mc/am.h:43, from /<>/debian/external_deps/fetk/mc/src/nam/mc/nam.h:36, from /<>/debian/external_deps/fetk/mc/src/mcsh/mc/mcsh.h:42, from /<>/debian/external_deps/fetk/mc/src/mcsh/mcsh_p.h:37, from /<>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:34: /<>/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3036:15: note: in a call to function ‘Gem_writeGEOM’ 3036 | VEXTERNC void Gem_writeGEOM(Gem *thee, Vio *sock, | ^~~~~~~~~~~~~ /<>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: warning: ‘Gem_writeGEOM’ accessing 16 bytes in a region of size 12 [-Wstringop-overflow=] 810 | Gem_writeGEOM(thee->gm, | ^~~~~~~~~~~~~~~~~~~~~~~ 811 | sock, | ~~~~~ 812 | defKey, | ~~~~~~~ 813 | Vsh_getenvInt(thee->vsh,"CKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 814 | Vsh_getenvInt(thee->vsh,"DKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 815 | Vsh_getenvReal(thee->vsh,"GVAL"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 816 | Vsh_getenvInt(thee->vsh,"FKEY"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 817 | defX, | ~~~~~ 818 | "MATH"); | ~~~~~~~ /<>/debian/external_deps/fetk/mc/src/mcsh/mcsh.c:810:9: note: referencing argument 8 of type ‘double *[4]’ /<>/debian/external_deps/fetk/mc/src/gem/mc/gem.h:3036:15: note: in a call to function ‘Gem_writeGEOM’ 3036 | VEXTERNC void Gem_writeGEOM(Gem *thee, Vio *sock, | ^~~~~~~~~~~~~ [ 73%] Linking C shared library libmc.so cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/mc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libmc.so.1.9 -o libmc.so.1.9.3 CMakeFiles/mc.dir/base/mc_base.c.o CMakeFiles/mc.dir/bam/bmat.c.o CMakeFiles/mc.dir/bam/bsolv.c.o CMakeFiles/mc.dir/bam/bvec.c.o CMakeFiles/mc.dir/bam/mat.c.o CMakeFiles/mc.dir/bam/matcopy.c.o CMakeFiles/mc.dir/bam/matln.c.o CMakeFiles/mc.dir/bam/mtool.c.o CMakeFiles/mc.dir/bam/slu.c.o CMakeFiles/mc.dir/bam/vec.c.o CMakeFiles/mc.dir/bam/vec3.c.o CMakeFiles/mc.dir/bam/zslu.c.o CMakeFiles/mc.dir/whb/whb.c.o CMakeFiles/mc.dir/whb/bvechb.c.o CMakeFiles/mc.dir/whb/hbtools.c.o CMakeFiles/mc.dir/whb/rcmat.c.o CMakeFiles/mc.dir/whb/brcmat.c.o CMakeFiles/mc.dir/whb/subopt.c.o CMakeFiles/mc.dir/aprx/aprx.c.o CMakeFiles/mc.dir/aprx/assem.c.o CMakeFiles/mc.dir/aprx/bnode.c.o CMakeFiles/mc.dir/aprx/estim.c.o CMakeFiles/mc.dir/aprx/eval.c.o CMakeFiles/mc.dir/aprx/io.c.o CMakeFiles/mc.dir/aprx/node.c.o CMakeFiles/mc.dir/aprx/parti.c.o CMakeFiles/mc.dir/aprx/re.c.o CMakeFiles/mc.dir/gem/vel.c.o CMakeFiles/mc.dir/gem/ves.c.o CMakeFiles/mc.dir/gem/gem.c.o CMakeFiles/mc.dir/gem/gemchk.c.o CMakeFiles/mc.dir/gem/gemdisp.c.o CMakeFiles/mc.dir/gem/gemg.c.o CMakeFiles/mc.dir/gem/gemgen.c.o CMakeFiles/mc.dir/gem/gemio.c.o CMakeFiles/mc.dir/gem/gemref.c.o CMakeFiles/mc.dir/gem/gemunref.c.o CMakeFiles/mc.dir/gem/gemcube.c.o CMakeFiles/mc.dir/pde/pde.c.o CMakeFiles/mc.dir/nam/am.c.o CMakeFiles/mc.dir/nam/lsolv.c.o CMakeFiles/mc.dir/nam/nsolv.c.o CMakeFiles/mc.dir/dyn/dyn.c.o CMakeFiles/mc.dir/dyn/svio.c.o CMakeFiles/mc.dir/mcsh/mcsh.c.o /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so /usr/lib/arm-linux-gnueabihf/libblas.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a -lmaloc ../../punc/src/libpunc.so.1.9.3 /usr/lib/arm-linux-gnueabihf/libblas.so -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../punc/src/vf2c/libvf2c.so.1.9.3 ../../punc/src/cgcode/libcgcode.so.1.9.3 cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src && /usr/bin/cmake -E cmake_symlink_library libmc.so.1.9.3 libmc.so.1.9 libmc.so make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 73%] Built target mc make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/depend make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/generic /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/generic /<>/obj-arm-linux-gnueabihf/src/generic/CMakeFiles/apbs_generic.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/pmgc /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/pmgc /<>/obj-arm-linux-gnueabihf/src/pmgc/CMakeFiles/apbs_pmgc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/pmgc/CMakeFiles/apbs_pmgc.dir/build.make src/pmgc/CMakeFiles/apbs_pmgc.dir/build make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/generic/CMakeFiles/apbs_generic.dir/build.make src/generic/CMakeFiles/apbs_generic.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 74%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildAd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildAd.c.o -c /<>/src/pmgc/buildAd.c [ 75%] Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o [ 75%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o -MF CMakeFiles/apbs_generic.dir/nosh.c.o.d -o CMakeFiles/apbs_generic.dir/nosh.c.o -c /<>/src/generic/nosh.c cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildBd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildBd.c.o -c /<>/src/pmgc/buildBd.c [ 75%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildGd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildGd.c.o -c /<>/src/pmgc/buildGd.c [ 76%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o -MF CMakeFiles/apbs_pmgc.dir/buildPd.c.o.d -o CMakeFiles/apbs_pmgc.dir/buildPd.c.o -c /<>/src/pmgc/buildPd.c [ 76%] Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o -MF CMakeFiles/apbs_generic.dir/mgparm.c.o.d -o CMakeFiles/apbs_generic.dir/mgparm.c.o -c /<>/src/generic/mgparm.c [ 76%] Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o -MF CMakeFiles/apbs_generic.dir/femparm.c.o.d -o CMakeFiles/apbs_generic.dir/femparm.c.o -c /<>/src/generic/femparm.c [ 76%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o -MF CMakeFiles/apbs_pmgc.dir/cgd.c.o.d -o CMakeFiles/apbs_pmgc.dir/cgd.c.o -c /<>/src/pmgc/cgd.c [ 76%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o -MF CMakeFiles/apbs_generic.dir/pbamparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbamparm.c.o -c /<>/src/generic/pbamparm.c [ 76%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o -MF CMakeFiles/apbs_pmgc.dir/gsd.c.o.d -o CMakeFiles/apbs_pmgc.dir/gsd.c.o -c /<>/src/pmgc/gsd.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o -MF CMakeFiles/apbs_generic.dir/pbsamparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbsamparm.c.o -c /<>/src/generic/pbsamparm.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o -MF CMakeFiles/apbs_generic.dir/pbeparm.c.o.d -o CMakeFiles/apbs_generic.dir/pbeparm.c.o -c /<>/src/generic/pbeparm.c [ 77%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o -MF CMakeFiles/apbs_pmgc.dir/matvecd.c.o.d -o CMakeFiles/apbs_pmgc.dir/matvecd.c.o -c /<>/src/pmgc/matvecd.c [ 77%] Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o -MF CMakeFiles/apbs_generic.dir/bemparm.c.o.d -o CMakeFiles/apbs_generic.dir/bemparm.c.o -c /<>/src/generic/bemparm.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o -MF CMakeFiles/apbs_generic.dir/geoflowparm.c.o.d -o CMakeFiles/apbs_generic.dir/geoflowparm.c.o -c /<>/src/generic/geoflowparm.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o -MF CMakeFiles/apbs_generic.dir/apolparm.c.o.d -o CMakeFiles/apbs_generic.dir/apolparm.c.o -c /<>/src/generic/apolparm.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o -MF CMakeFiles/apbs_generic.dir/vacc.c.o.d -o CMakeFiles/apbs_generic.dir/vacc.c.o -c /<>/src/generic/vacc.c [ 78%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/valist.c.o -MF CMakeFiles/apbs_generic.dir/valist.c.o.d -o CMakeFiles/apbs_generic.dir/valist.c.o -c /<>/src/generic/valist.c [ 79%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o -MF CMakeFiles/apbs_generic.dir/vatom.c.o.d -o CMakeFiles/apbs_generic.dir/vatom.c.o -c /<>/src/generic/vatom.c [ 80%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgcsd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o -c /<>/src/pmgc/mgcsd.c [ 80%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o -MF CMakeFiles/apbs_generic.dir/vpbe.c.o.d -o CMakeFiles/apbs_generic.dir/vpbe.c.o -c /<>/src/generic/vpbe.c [ 80%] Linking CXX shared library libgamer.so cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gamer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgamer.so.1.9 -o libgamer.so.1.9.3 CMakeFiles/gamer.dir/base/gamer_base.c.o CMakeFiles/gamer.dir/triangle/triangle.c.o CMakeFiles/gamer.dir/tetgen/predicates.cpp.o CMakeFiles/gamer.dir/tetgen/tetgen.cpp.o CMakeFiles/gamer.dir/biom/CorrectNormals.C.o CMakeFiles/gamer.dir/biom/GenerateSphereMesh.C.o CMakeFiles/gamer.dir/biom/MarchingCube.C.o CMakeFiles/gamer.dir/biom/PDB2Mesh.C.o CMakeFiles/gamer.dir/biom/PDB2Volume.C.o CMakeFiles/gamer.dir/biom/ReadLattice.C.o CMakeFiles/gamer.dir/biom/ReadPDB.C.o CMakeFiles/gamer.dir/biom/ReadWriteMesh.C.o CMakeFiles/gamer.dir/biom/RegionGrowing.C.o CMakeFiles/gamer.dir/biom/SurfaceMesh.C.o CMakeFiles/gamer.dir/biom/SurfExtract.C.o CMakeFiles/gamer.dir/biom/SurfRefine.C.o CMakeFiles/gamer.dir/biom/SurfSmooth.C.o -lmaloc cd /<>/obj-arm-linux-gnueabihf/_deps/fetk-build/gamer/src && /usr/bin/cmake -E cmake_symlink_library libgamer.so.1.9.3 libgamer.so.1.9 libgamer.so make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 80%] Built target gamer [ 80%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o -MF CMakeFiles/apbs_generic.dir/vcap.c.o.d -o CMakeFiles/apbs_generic.dir/vcap.c.o -c /<>/src/generic/vcap.c [ 81%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o -MF CMakeFiles/apbs_generic.dir/vclist.c.o.d -o CMakeFiles/apbs_generic.dir/vclist.c.o -c /<>/src/generic/vclist.c [ 81%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o -MF CMakeFiles/apbs_generic.dir/vstring.c.o.d -o CMakeFiles/apbs_generic.dir/vstring.c.o -c /<>/src/generic/vstring.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -c /<>/src/pmgc/mgdrvd.c [ 81%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o -MF CMakeFiles/apbs_generic.dir/vparam.c.o.d -o CMakeFiles/apbs_generic.dir/vparam.c.o -c /<>/src/generic/vparam.c [ 81%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cc -Dapbs_generic_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o -MF CMakeFiles/apbs_generic.dir/vgreen.c.o.d -o CMakeFiles/apbs_generic.dir/vgreen.c.o -c /<>/src/generic/vgreen.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgsubd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -c /<>/src/pmgc/mgsubd.c [ 81%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -MF CMakeFiles/apbs_pmgc.dir/mikpckd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -c /<>/src/pmgc/mikpckd.c [ 82%] Linking C shared library libapbs_generic.so cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_generic.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_generic.so.3 -o libapbs_generic.so.3 CMakeFiles/apbs_generic.dir/nosh.c.o CMakeFiles/apbs_generic.dir/mgparm.c.o CMakeFiles/apbs_generic.dir/femparm.c.o CMakeFiles/apbs_generic.dir/pbamparm.c.o CMakeFiles/apbs_generic.dir/pbsamparm.c.o CMakeFiles/apbs_generic.dir/pbeparm.c.o CMakeFiles/apbs_generic.dir/bemparm.c.o CMakeFiles/apbs_generic.dir/geoflowparm.c.o CMakeFiles/apbs_generic.dir/apolparm.c.o CMakeFiles/apbs_generic.dir/vacc.c.o CMakeFiles/apbs_generic.dir/valist.c.o CMakeFiles/apbs_generic.dir/vatom.c.o CMakeFiles/apbs_generic.dir/vpbe.c.o CMakeFiles/apbs_generic.dir/vcap.c.o CMakeFiles/apbs_generic.dir/vclist.c.o CMakeFiles/apbs_generic.dir/vstring.c.o CMakeFiles/apbs_generic.dir/vparam.c.o CMakeFiles/apbs_generic.dir/vgreen.c.o ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so /usr/lib/arm-linux-gnueabihf/libblas.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 /usr/lib/arm-linux-gnueabihf/libblas.so cd /<>/obj-arm-linux-gnueabihf/src/generic && /usr/bin/cmake -E cmake_symlink_library libapbs_generic.so.3 libapbs_generic.so.3 libapbs_generic.so make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 82%] Built target apbs_generic make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/fem /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/fem /<>/obj-arm-linux-gnueabihf/src/fem/CMakeFiles/apbs_fem.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/fem/CMakeFiles/apbs_fem.dir/build.make src/fem/CMakeFiles/apbs_fem.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 82%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vcsm.c.o cd /<>/obj-arm-linux-gnueabihf/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vcsm.c.o -MF CMakeFiles/apbs_fem.dir/vcsm.c.o.d -o CMakeFiles/apbs_fem.dir/vcsm.c.o -c /<>/src/fem/vcsm.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o -MF CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o -c /<>/src/pmgc/mlinpckd.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o -MF CMakeFiles/apbs_pmgc.dir/mypdec.c.o.d -o CMakeFiles/apbs_pmgc.dir/mypdec.c.o -c /<>/src/pmgc/mypdec.c [ 83%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o -MF CMakeFiles/apbs_pmgc.dir/newtond.c.o.d -o CMakeFiles/apbs_pmgc.dir/newtond.c.o -c /<>/src/pmgc/newtond.c [ 84%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vfetk.c.o cd /<>/obj-arm-linux-gnueabihf/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vfetk.c.o -MF CMakeFiles/apbs_fem.dir/vfetk.c.o.d -o CMakeFiles/apbs_fem.dir/vfetk.c.o -c /<>/src/fem/vfetk.c /<>/src/fem/vfetk.c: In function ‘Vfetk_PDE_ctor2’: /<>/src/fem/vfetk.c:1211:24: warning: assignment to ‘void (*)(struct sPDE *, int, int, double *, double *, double (*)[3])’ from incompatible pointer type ‘void (*)(PDE *, int, int, double *, double *)’ {aka ‘void (*)(struct sPDE *, int, int, double *, double *)’} [-Wincompatible-pointer-types] 1211 | thee->u_T = Vfetk_PDE_u_T; | ^ [ 85%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -MF CMakeFiles/apbs_pmgc.dir/newdrvd.c.o.d -o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -c /<>/src/pmgc/newdrvd.c [ 85%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o -MF CMakeFiles/apbs_pmgc.dir/powerd.c.o.d -o CMakeFiles/apbs_pmgc.dir/powerd.c.o -c /<>/src/pmgc/powerd.c [ 85%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o -MF CMakeFiles/apbs_pmgc.dir/smoothd.c.o.d -o CMakeFiles/apbs_pmgc.dir/smoothd.c.o -c /<>/src/pmgc/smoothd.c [ 85%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cc -Dapbs_pmgc_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -MF CMakeFiles/apbs_pmgc.dir/mgfasd.c.o.d -o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -c /<>/src/pmgc/mgfasd.c [ 85%] Building C object src/fem/CMakeFiles/apbs_fem.dir/vpee.c.o cd /<>/obj-arm-linux-gnueabihf/src/fem && /usr/bin/cc -Dapbs_fem_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/fem/CMakeFiles/apbs_fem.dir/vpee.c.o -MF CMakeFiles/apbs_fem.dir/vpee.c.o.d -o CMakeFiles/apbs_fem.dir/vpee.c.o -c /<>/src/fem/vpee.c /<>/src/fem/vfetk.c: In function ‘Bmat_printHB’: /<>/src/fem/vfetk.c:1073:28: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1073 | sprintf(ptrfmt,"(%dI%d)",nptrline,numZdigits+1); | ^ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/src/fem/vfetk.h:67, from /<>/src/fem/vfetk.c:57: In function ‘sprintf’, inlined from ‘Bmat_printHB’ at /<>/src/fem/vfetk.c:1073:5: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 6 and 18 bytes into a destination of size 17 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/fem/vfetk.c: In function ‘Bmat_printHB’: /<>/src/fem/vfetk.c:1074:26: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 1074 | sprintf(ptrfmtstr,"%%%dd",numZdigits+1); | ^~ /<>/src/fem/vfetk.c:1074:23: note: directive argument in the range [-2147483646, 2147483647] 1074 | sprintf(ptrfmtstr,"%%%dd",numZdigits+1); | ^~~~~~~ In function ‘sprintf’, inlined from ‘Bmat_printHB’ at /<>/src/fem/vfetk.c:1074:5: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 4 and 14 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/fem/vfetk.c: In function ‘Bmat_printHB’: /<>/src/fem/vfetk.c:1075:28: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1075 | sprintf(indfmt,"(%dI%d)",nindline,nrowdigits+1); | ^ In function ‘sprintf’, inlined from ‘Bmat_printHB’ at /<>/src/fem/vfetk.c:1075:5: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 6 and 18 bytes into a destination of size 17 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/fem/vfetk.c: In function ‘Bmat_printHB’: /<>/src/fem/vfetk.c:1076:26: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 1076 | sprintf(indfmtstr,"%%%dd",nrowdigits+1); | ^~ /<>/src/fem/vfetk.c:1076:23: note: directive argument in the range [-2147483646, 2147483647] 1076 | sprintf(indfmtstr,"%%%dd",nrowdigits+1); | ^~~~~~~ In function ‘sprintf’, inlined from ‘Bmat_printHB’ at /<>/src/fem/vfetk.c:1076:5: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 4 and 14 bytes into a destination of size 5 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 85%] Linking C shared library libapbs_fem.so cd /<>/obj-arm-linux-gnueabihf/src/fem && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_fem.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_fem.so.3 -o libapbs_fem.so.3 CMakeFiles/apbs_fem.dir/vcsm.c.o CMakeFiles/apbs_fem.dir/vfetk.c.o CMakeFiles/apbs_fem.dir/vpee.c.o -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so /usr/lib/arm-linux-gnueabihf/libblas.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp ../generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp cd /<>/obj-arm-linux-gnueabihf/src/fem && /usr/bin/cmake -E cmake_symlink_library libapbs_fem.so.3 libapbs_fem.so.3 libapbs_fem.so make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 85%] Built target apbs_fem [ 86%] Linking C shared library libapbs_pmgc.so cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_pmgc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_pmgc.so.3 -o libapbs_pmgc.so.3 CMakeFiles/apbs_pmgc.dir/buildAd.c.o CMakeFiles/apbs_pmgc.dir/buildBd.c.o CMakeFiles/apbs_pmgc.dir/buildGd.c.o CMakeFiles/apbs_pmgc.dir/buildPd.c.o CMakeFiles/apbs_pmgc.dir/cgd.c.o CMakeFiles/apbs_pmgc.dir/gsd.c.o CMakeFiles/apbs_pmgc.dir/matvecd.c.o CMakeFiles/apbs_pmgc.dir/mgcsd.c.o CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o CMakeFiles/apbs_pmgc.dir/mgsubd.c.o CMakeFiles/apbs_pmgc.dir/mikpckd.c.o CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o CMakeFiles/apbs_pmgc.dir/mypdec.c.o CMakeFiles/apbs_pmgc.dir/newtond.c.o CMakeFiles/apbs_pmgc.dir/newdrvd.c.o CMakeFiles/apbs_pmgc.dir/powerd.c.o CMakeFiles/apbs_pmgc.dir/smoothd.c.o CMakeFiles/apbs_pmgc.dir/mgfasd.c.o ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so /usr/lib/arm-linux-gnueabihf/libblas.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 /usr/lib/arm-linux-gnueabihf/libblas.so cd /<>/obj-arm-linux-gnueabihf/src/pmgc && /usr/bin/cmake -E cmake_symlink_library libapbs_pmgc.so.3 libapbs_pmgc.so.3 libapbs_pmgc.so make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 86%] Built target apbs_pmgc make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/mg /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src/mg /<>/obj-arm-linux-gnueabihf/src/mg/CMakeFiles/apbs_mg.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/mg/CMakeFiles/apbs_mg.dir/build.make src/mg/CMakeFiles/apbs_mg.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 86%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o cd /<>/obj-arm-linux-gnueabihf/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o -MF CMakeFiles/apbs_mg.dir/vgrid.c.o.d -o CMakeFiles/apbs_mg.dir/vgrid.c.o -c /<>/src/mg/vgrid.c cd /<>/obj-arm-linux-gnueabihf/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o -MF CMakeFiles/apbs_mg.dir/vopot.c.o.d -o CMakeFiles/apbs_mg.dir/vopot.c.o -c /<>/src/mg/vopot.c [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o cd /<>/obj-arm-linux-gnueabihf/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o -MF CMakeFiles/apbs_mg.dir/vmgrid.c.o.d -o CMakeFiles/apbs_mg.dir/vmgrid.c.o -c /<>/src/mg/vmgrid.c [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o cd /<>/obj-arm-linux-gnueabihf/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o -MF CMakeFiles/apbs_mg.dir/vpmg.c.o.d -o CMakeFiles/apbs_mg.dir/vpmg.c.o -c /<>/src/mg/vpmg.c /<>/src/mg/vgrid.c: In function ‘Vgrid_readDXBIN’: /<>/src/mg/vgrid.c:853:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 853 | fgets(tok, VMAX_BUFSIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o cd /<>/obj-arm-linux-gnueabihf/src/mg && /usr/bin/cc -Dapbs_mg_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o -MF CMakeFiles/apbs_mg.dir/vpmgp.c.o.d -o CMakeFiles/apbs_mg.dir/vpmgp.c.o -c /<>/src/mg/vpmgp.c /<>/src/mg/vgrid.c:831:7: warning: argument 1 null where non-null expected [-Wnonnull] 831 | fclose(fd); | ^~~~~~~~~~ In file included from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/src/mg/vgrid.h:67, from /<>/src/mg/vgrid.c:57: /usr/include/stdio.h:183:12: note: in a call to function ‘fclose’ declared ‘nonnull’ 183 | extern int fclose (FILE *__stream) __nonnull ((1)); | ^~~~~~ [ 87%] Linking C shared library libapbs_mg.so cd /<>/obj-arm-linux-gnueabihf/src/mg && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_mg.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_mg.so.3 -o libapbs_mg.so.3 CMakeFiles/apbs_mg.dir/vgrid.c.o CMakeFiles/apbs_mg.dir/vmgrid.c.o CMakeFiles/apbs_mg.dir/vopot.c.o CMakeFiles/apbs_mg.dir/vpmg.c.o CMakeFiles/apbs_mg.dir/vpmgp.c.o -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so /usr/lib/arm-linux-gnueabihf/libblas.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp ../generic/libapbs_generic.so.3 ../pmgc/libapbs_pmgc.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp cd /<>/obj-arm-linux-gnueabihf/src/mg && /usr/bin/cmake -E cmake_symlink_library libapbs_mg.so.3 libapbs_mg.so.3 libapbs_mg.so make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 87%] Built target apbs_mg make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src /<>/obj-arm-linux-gnueabihf/src/CMakeFiles/apbs_routines.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/apbs_routines.dir/build.make src/CMakeFiles/apbs_routines.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 87%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/cc -Dapbs_routines_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT src/CMakeFiles/apbs_routines.dir/routines.c.o -MF CMakeFiles/apbs_routines.dir/routines.c.o.d -o CMakeFiles/apbs_routines.dir/routines.c.o -c /<>/src/routines.c /<>/src/routines.c: In function ‘initAPOL’: /<>/src/routines.c:5046:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 5046 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/routines.c:5046:20: note: referencing argument 2 of type ‘char[1024]’ /<>/src/routines.c:5046:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /<>/src/routines.c:5046:20: note: referencing argument 3 of type ‘char[1024]’ In file included from /<>/src/generic/apolparm.h:73, from /<>/src/generic/nosh.h:73, from /<>/src/apbs.h:70, from /<>/src/routines.h:64, from /<>/src/routines.c:54: /<>/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’ 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /<>/src/routines.c:5048:24: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 5048 | atomData = Vparam_getAtomData(param, "WAT", "O"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/routines.c:5048:24: note: referencing argument 2 of type ‘char[1024]’ /<>/src/routines.c:5048:24: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /<>/src/routines.c:5048:24: note: referencing argument 3 of type ‘char[1024]’ /<>/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’ 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writematMG’: /<>/src/routines.c:2020:30: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2020 | sprintf(outpath, "%s.%s", writematstem, "mat"); | ^~ ~~~~~ In file included from /usr/include/stdio.h:964, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /<>/src/apbs.h:67: In function ‘sprintf’, inlined from ‘writematMG’ at /<>/src/routines.c:2020:9: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataMG’: /<>/src/routines.c:2919:34: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2919 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /<>/src/routines.c:2919:13: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataMG’: /<>/src/routines.c:2963:34: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2963 | sprintf(outpath, "%s.%s", writestem, "txt"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /<>/src/routines.c:2963:13: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataMG’: /<>/src/routines.c:2954:34: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2954 | sprintf(outpath, "%s.%s", writestem, "dx.gz"); | ^~ ~~~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /<>/src/routines.c:2954:13: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataMG’: /<>/src/routines.c:2937:34: warning: ‘%s’ directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2937 | sprintf(outpath, "%s.%s", writestem, "mcsf"); | ^~ ~~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /<>/src/routines.c:2937:13: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 6 and 1029 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataMG’: /<>/src/routines.c:2930:34: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2930 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /<>/src/routines.c:2930:13: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataMG’: /<>/src/routines.c:2944:34: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2944 | sprintf(outpath, "%s.%s", writestem, "grd"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /<>/src/routines.c:2944:13: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataMG’: /<>/src/routines.c:2909:34: warning: ‘%s’ directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2909 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In function ‘sprintf’, inlined from ‘writedataMG’ at /<>/src/routines.c:2909:13: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataFE’: /<>/src/routines.c:4887:34: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4887 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In function ‘sprintf’, inlined from ‘writedataFE’ at /<>/src/routines.c:4887:13: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataFE’: /<>/src/routines.c:4893:34: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4893 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In function ‘sprintf’, inlined from ‘writedataFE’ at /<>/src/routines.c:4893:13: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /<>/src/routines.c: In function ‘writedataFE’: /<>/src/routines.c:4880:34: warning: ‘%s’ directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 4880 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In function ‘sprintf’, inlined from ‘writedataFE’ at /<>/src/routines.c:4880:13: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 88%] Linking C shared library libapbs_routines.so cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_routines.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libapbs_routines.so.3 -o libapbs_routines.so.3 CMakeFiles/apbs_routines.dir/routines.c.o -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so /usr/lib/arm-linux-gnueabihf/libblas.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so /usr/lib/arm-linux-gnueabihf/libblas.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp mg/libapbs_mg.so.3 fem/libapbs_fem.so.3 pmgc/libapbs_pmgc.so.3 generic/libapbs_generic.so.3 ../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_symlink_library libapbs_routines.so.3 libapbs_routines.so.3 libapbs_routines.so make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 88%] Built target apbs_routines make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/depend make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/depend make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/depend make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/tools/mesh /<>/obj-arm-linux-gnueabihf/tools/mesh/CMakeFiles/mgmesh.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/tools/mesh /<>/obj-arm-linux-gnueabihf/tools/mesh/CMakeFiles/smooth.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src /<>/obj-arm-linux-gnueabihf/src/CMakeFiles/apbs.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/tools/mesh /<>/obj-arm-linux-gnueabihf/tools/mesh/CMakeFiles/dxmath.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/apbs.dir/build.make src/CMakeFiles/apbs.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f tools/mesh/CMakeFiles/smooth.dir/build.make tools/mesh/CMakeFiles/smooth.dir/build make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f tools/mesh/CMakeFiles/mgmesh.dir/build.make tools/mesh/CMakeFiles/mgmesh.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f tools/mesh/CMakeFiles/dxmath.dir/build.make tools/mesh/CMakeFiles/dxmath.dir/build [ 88%] Building C object src/CMakeFiles/apbs.dir/main.c.o make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/cc -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIE -fopenmp -MD -MT src/CMakeFiles/apbs.dir/main.c.o -MF CMakeFiles/apbs.dir/main.c.o.d -o CMakeFiles/apbs.dir/main.c.o -c /<>/src/main.c [ 89%] Building C object tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o [ 89%] Building C object tools/mesh/CMakeFiles/smooth.dir/smooth.c.o cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cc -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/smooth.dir/smooth.c.o -MF CMakeFiles/smooth.dir/smooth.c.o.d -o CMakeFiles/smooth.dir/smooth.c.o -c /<>/tools/mesh/smooth.c cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cc -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o -MF CMakeFiles/mgmesh.dir/mgmesh.c.o.d -o CMakeFiles/mgmesh.dir/mgmesh.c.o -c /<>/tools/mesh/mgmesh.c [ 89%] Building C object tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cc -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o -MF CMakeFiles/dxmath.dir/dxmath.c.o.d -o CMakeFiles/dxmath.dir/dxmath.c.o -c /<>/tools/mesh/dxmath.c /<>/src/main.c: In function ‘main’: /<>/src/main.c:319:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 319 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ /<>/src/main.c:319:74: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 319 | Vnm_tprint( 1, "This executable compiled on %s at %s\n\n", __DATE__, __TIME__); | ^~~~~~~~ [ 89%] Linking C executable ../bin/mgmesh cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mgmesh.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mgmesh.dir/mgmesh.c.o -o ../bin/mgmesh ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp [ 89%] Linking C executable ../bin/smooth cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/smooth.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/smooth.dir/smooth.c.o -o ../bin/smooth ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 89%] Linking C executable ../bin/dxmath cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dxmath.dir/link.txt --verbose=1 [ 89%] Built target mgmesh make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/depend /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/dxmath.dir/dxmath.c.o -o ../bin/dxmath ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/tools/mesh /<>/obj-arm-linux-gnueabihf/tools/mesh/CMakeFiles/mergedx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f tools/mesh/CMakeFiles/mergedx.dir/build.make tools/mesh/CMakeFiles/mergedx.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 90%] Building C object tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cc -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o -MF CMakeFiles/mergedx.dir/mergedx.c.o.d -o CMakeFiles/mergedx.dir/mergedx.c.o -c /<>/tools/mesh/mergedx.c [ 90%] Linking C executable apbs cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/apbs.dir/main.c.o -o apbs -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so /usr/lib/arm-linux-gnueabihf/libblas.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp libapbs_routines.so.3 mg/libapbs_mg.so.3 pmgc/libapbs_pmgc.so.3 fem/libapbs_fem.so.3 generic/libapbs_generic.so.3 ../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 90%] Built target smooth make -f tools/mesh/CMakeFiles/mergedx2.dir/build.make tools/mesh/CMakeFiles/mergedx2.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/tools/mesh /<>/obj-arm-linux-gnueabihf/tools/mesh/CMakeFiles/mergedx2.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f 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tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o -MF CMakeFiles/multivalue.dir/multivalue.c.o.d -o CMakeFiles/multivalue.dir/multivalue.c.o -c /<>/tools/mesh/multivalue.c [ 91%] Linking C executable ../bin/value cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/value.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/value.dir/value.c.o -o ../bin/value ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp [ 92%] Linking C executable ../bin/multivalue cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/multivalue.dir/link.txt --verbose=1 [ 92%] Linking C executable ../bin/mergedx cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/multivalue.dir/multivalue.c.o -o ../bin/multivalue ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mergedx.dir/mergedx.c.o -o ../bin/mergedx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 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tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o -MF CMakeFiles/benchmark.dir/benchmark.c.o.d -o CMakeFiles/benchmark.dir/benchmark.c.o -c /<>/tools/mesh/benchmark.c [ 92%] Linking C executable ../bin/mergedx2 cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/mergedx2.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/mergedx2.dir/mergedx2.c.o -o ../bin/mergedx2 ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 92%] Built target multivalue [ 92%] Built target mergedx make -f tools/mesh/CMakeFiles/similarity.dir/build.make 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-I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/similarity.dir/similarity.c.o -MF CMakeFiles/similarity.dir/similarity.c.o.d -o CMakeFiles/similarity.dir/similarity.c.o -c /<>/tools/mesh/similarity.c [ 92%] Building C object tools/mesh/CMakeFiles/analysis.dir/analysis.c.o cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cc -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src 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-D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/analysis.dir/analysis.c.o -MF CMakeFiles/analysis.dir/analysis.c.o.d -o CMakeFiles/analysis.dir/analysis.c.o -c /<>/tools/mesh/analysis.c [ 93%] Linking C executable ../bin/benchmark cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/benchmark.dir/benchmark.c.o -o ../bin/benchmark ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 93%] Built target mergedx2 make -f tools/mesh/CMakeFiles/dx2mol.dir/build.make 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-I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o -MF 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-I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -MF CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o.d -o CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -c /<>/tools/mesh/dx2uhbd.c [ 94%] Linking C executable ../bin/analysis cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysis.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/analysis.dir/analysis.c.o -o ../bin/analysis ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp [ 94%] Linking C executable ../bin/dx2mol cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2mol.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/dx2mol.dir/dx2mol.c.o -o ../bin/dx2mol ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp [ 95%] Linking C executable ../bin/similarity cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/similarity.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/similarity.dir/similarity.c.o -o ../bin/similarity ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp [ 96%] Linking C executable ../bin/dx2uhbd cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/dx2uhbd.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -o ../bin/dx2uhbd ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 96%] Built target analysis make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/tools/mesh /<>/obj-arm-linux-gnueabihf/tools/mesh/CMakeFiles/del2dx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f tools/mesh/CMakeFiles/del2dx.dir/build.make tools/mesh/CMakeFiles/del2dx.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 96%] Building C object tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cc -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o -MF CMakeFiles/del2dx.dir/del2dx.c.o.d -o CMakeFiles/del2dx.dir/del2dx.c.o -c /<>/tools/mesh/del2dx.c make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 96%] Built target dx2mol make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/tools/mesh /<>/obj-arm-linux-gnueabihf/tools/mesh/CMakeFiles/tensor2dx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f tools/mesh/CMakeFiles/tensor2dx.dir/build.make tools/mesh/CMakeFiles/tensor2dx.dir/build [ 96%] Built target similarity make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/mesh /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/tools/mesh /<>/obj-arm-linux-gnueabihf/tools/mesh/CMakeFiles/uhbd_asc2bin.dir/DependInfo.cmake "--color=" [ 97%] Building C object tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cc -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o -MF CMakeFiles/tensor2dx.dir/tensor2dx.c.o.d -o CMakeFiles/tensor2dx.dir/tensor2dx.c.o -c /<>/tools/mesh/tensor2dx.c /<>/tools/mesh/del2dx.c: In function ‘main’: /<>/tools/mesh/del2dx.c:76:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | fread(&igrid, 1, sizeof(int), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/del2dx.c:89:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 89 | fread(buffer, 1, sizeof(char) * 10, pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/del2dx.c:97:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fread(data, tot_grid, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/del2dx.c:103:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 103 | fread(&scale, 1, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/del2dx.c:106:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 106 | fread(oldmid, 3, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build.make tools/mesh/CMakeFiles/uhbd_asc2bin.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 97%] Building C object tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cc -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -MF CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o.d -o CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -c /<>/tools/mesh/uhbd_asc2bin.c make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 97%] Built target dx2uhbd make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/manip /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/tools/manip /<>/obj-arm-linux-gnueabihf/tools/manip/CMakeFiles/coulomb.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f tools/manip/CMakeFiles/coulomb.dir/build.make tools/manip/CMakeFiles/coulomb.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 98%] Building C object tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o cd /<>/obj-arm-linux-gnueabihf/tools/manip && /usr/bin/cc -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o -MF CMakeFiles/coulomb.dir/coulomb.c.o.d -o CMakeFiles/coulomb.dir/coulomb.c.o -c /<>/tools/manip/coulomb.c [ 99%] Linking C executable ../bin/del2dx cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/del2dx.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/del2dx.dir/del2dx.c.o -o ../bin/del2dx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp /<>/tools/mesh/tensor2dx.c: In function ‘main’: /<>/tools/mesh/tensor2dx.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf(pfile1,"%lf %lf %lf",&origin_xyz[0],&origin_xyz[1],&origin_xyz[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:98:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 98 | fscanf(pfile1,"%lf %lf %lf",&gspace[0],&gspace[1],&gspace[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:137:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 137 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:138:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:139:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 139 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:140:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 140 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:155:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:156:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 156 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:157:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/tensor2dx.c:158:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 158 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c: In function ‘main’: /<>/tools/mesh/uhbd_asc2bin.c:30:5: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 30 | scanf("%s", flnm); | ^~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:42:5: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 42 | scanf("%s", newfile); | ^~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:54:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 54 | fscanf(inFile, "%s", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:57:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | fscanf(inFile, "%lf", &scale); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:60:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | fscanf(inFile, "%lf", &dum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:63:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 63 | fscanf(inFile, "%d", &grdflg); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:66:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | fscanf(inFile, "%d", &idum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:69:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:72:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | fscanf(inFile, "%d", &one); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:75:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 75 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:78:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:81:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:84:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 84 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:87:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | fscanf(inFile, "%lf", &h); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:90:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 90 | fscanf(inFile, "%lf", &ox); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:93:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 93 | fscanf(inFile, "%lf", &oy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:96:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | fscanf(inFile, "%lf", &oz); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:99:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | fscanf(inFile, "%lf", &dum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:102:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 102 | fscanf(inFile, "%lf", &dum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:105:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 105 | fscanf(inFile, "%lf", &dum5); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:108:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 108 | fscanf(inFile, "%lf", &dum6); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:111:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | fscanf(inFile, "%lf", &dum7); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:114:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 114 | fscanf(inFile, "%lf", &dum8); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:117:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 117 | fscanf(inFile, "%d", &idum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:120:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 120 | fscanf(inFile, "%d", &idum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:125:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 125 | fscanf(inFile, "%d", &kk); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:128:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 128 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:131:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/tools/mesh/uhbd_asc2bin.c:138:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | fscanf(inFile, "%lf", RAT3(grid, i, j, k)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 99%] Linking C executable ../bin/tensor2dx cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/tensor2dx.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/tensor2dx.dir/tensor2dx.c.o -o ../bin/tensor2dx ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp [ 99%] Linking C executable ../bin/uhbd_asc2bin cd /<>/obj-arm-linux-gnueabihf/tools/mesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/uhbd_asc2bin.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -o ../bin/uhbd_asc2bin ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 99%] Linking C executable ../bin/coulomb cd /<>/obj-arm-linux-gnueabihf/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/coulomb.dir/link.txt --verbose=1 [ 99%] Built target del2dx /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/coulomb.dir/coulomb.c.o -o ../bin/coulomb ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/manip /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/tools/manip /<>/obj-arm-linux-gnueabihf/tools/manip/CMakeFiles/born.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f tools/manip/CMakeFiles/born.dir/build.make tools/manip/CMakeFiles/born.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 99%] Building C object tools/manip/CMakeFiles/born.dir/born.c.o cd /<>/obj-arm-linux-gnueabihf/tools/manip && /usr/bin/cc -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fopenmp -MD -MT tools/manip/CMakeFiles/born.dir/born.c.o -MF CMakeFiles/born.dir/born.c.o.d -o CMakeFiles/born.dir/born.c.o -c /<>/tools/manip/born.c make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 99%] Built target tensor2dx make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/python /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/tools/python /<>/obj-arm-linux-gnueabihf/tools/python/CMakeFiles/_apbslib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f tools/python/CMakeFiles/_apbslib.dir/build.make tools/python/CMakeFiles/_apbslib.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 99%] Building C object tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o cd /<>/obj-arm-linux-gnueabihf/tools/python && /usr/bin/cc -D_apbslib_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/python3.12 -I/<>/tools/python -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -fPIC -fopenmp -MD -MT tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -MF CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o.d -o CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -c /<>/obj-arm-linux-gnueabihf/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 99%] Built target uhbd_asc2bin make -f tools/python-pybind/CMakeFiles/apbs_pybind.dir/build.make tools/python-pybind/CMakeFiles/apbs_pybind.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/python-pybind /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/tools/python-pybind /<>/obj-arm-linux-gnueabihf/tools/python-pybind/CMakeFiles/apbs_pybind.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f tools/python-pybind/CMakeFiles/apbs_pybind.dir/build.make tools/python-pybind/CMakeFiles/apbs_pybind.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 99%] Built target coulomb [ 99%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o cd /<>/obj-arm-linux-gnueabihf/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o -c /<>/tools/python-pybind/bind_nosh.cpp [ 99%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/module.cpp.o cd /<>/obj-arm-linux-gnueabihf/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/module.cpp.o -MF CMakeFiles/apbs_pybind.dir/module.cpp.o.d -o CMakeFiles/apbs_pybind.dir/module.cpp.o -c /<>/tools/python-pybind/module.cpp [ 99%] Linking C executable ../bin/born cd /<>/obj-arm-linux-gnueabihf/tools/manip && /usr/bin/cmake -E cmake_link_script CMakeFiles/born.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -Wl,--no-as-needed CMakeFiles/born.dir/born.c.o -o ../bin/born ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [ 99%] Built target born [100%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o cd /<>/obj-arm-linux-gnueabihf/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o -c /<>/tools/python-pybind/bind_vatom.cpp [100%] Linking C shared library _apbslib.so cd /<>/obj-arm-linux-gnueabihf/tools/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/_apbslib.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -fcommon -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/tirpc -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,_apbslib.so -o _apbslib.so CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so /usr/lib/arm-linux-gnueabihf/libblas.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp ../../src/libapbs_routines.so.3 /usr/lib/arm-linux-gnueabihf/libpython3.12.so ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [100%] Built target _apbslib [100%] Building CXX object tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o cd /<>/obj-arm-linux-gnueabihf/tools/python-pybind && /usr/bin/c++ -Dapbs_pybind_EXPORTS -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/<>/src -I/<>/obj-arm-linux-gnueabihf/src -I/<>/include -I/usr/include/suitesparse -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/mc/src -I/<>/debian/external_deps/fetk/mc/src/base -I/<>/debian/external_deps/fetk/mc/src/bam -I/<>/debian/external_deps/fetk/mc/src/whb -I/<>/debian/external_deps/fetk/mc/src/aprx -I/<>/debian/external_deps/fetk/mc/src/gem -I/<>/debian/external_deps/fetk/mc/src/pde -I/<>/debian/external_deps/fetk/mc/src/nam -I/<>/debian/external_deps/fetk/mc/src/dyn -I/<>/debian/external_deps/fetk/mc/src/mcsh -I/<>/debian/external_deps/fetk/punc/src/vf2c -I/<>/debian/external_deps/fetk/punc/src/vf2c/punc -I/<>/debian/external_deps/fetk/punc/src/cgcode -I/usr/include/superlu -I/<>/obj-arm-linux-gnueabihf/_deps/fetk-build/punc/src -I/<>/debian/external_deps/fetk/punc/src -I/<>/debian/external_deps/fetk/punc/src/base -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -std=gnu++17 -fPIC -fopenmp -MD -MT tools/python-pybind/CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -MF CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o.d -o CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -c /<>/tools/python-pybind/bind_valist.cpp In file included from /usr/include/c++/13/vector:72, from /<>/tools/python-pybind/bind_valist.hpp:3, from /<>/tools/python-pybind/bind_valist.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const sVatom&}; _Tp = sVatom; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = sVatom; _Alloc = std::allocator]’, inlined from ‘bool pybind11::detail::list_caster::load(pybind11::handle, bool) [with Type = std::vector; Value = sVatom]’ at /usr/include/pybind11/stl.h:180:28: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘bool pybind11::detail::list_caster::load(pybind11::handle, bool) [with Type = std::vector; Value = double]’ at /usr/include/pybind11/stl.h:180:28: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [100%] Linking CXX shared module apbs.cpython-312-arm-linux-gnueabihf.so cd /<>/obj-arm-linux-gnueabihf/tools/python-pybind && /usr/bin/cmake -E cmake_link_script CMakeFiles/apbs_pybind.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/apbs-3.4.1-5build5 -Wdate-time -D_FORTIFY_SOURCE=3 -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wpedantic -fpermissive -fPIC -O2 -g -DNDEBUG -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -o apbs.cpython-312-arm-linux-gnueabihf.so CMakeFiles/apbs_pybind.dir/module.cpp.o CMakeFiles/apbs_pybind.dir/bind_nosh.cpp.o CMakeFiles/apbs_pybind.dir/bind_vatom.cpp.o CMakeFiles/apbs_pybind.dir/bind_valist.cpp.o -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so /usr/lib/arm-linux-gnueabihf/libblas.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp ../../src/libapbs_routines.so.3 ../../src/mg/libapbs_mg.so.3 ../../src/pmgc/libapbs_pmgc.so.3 ../../src/fem/libapbs_fem.so.3 ../../src/generic/libapbs_generic.so.3 ../../_deps/fetk-build/mc/src/libmc.so.1.9.3 ../../_deps/fetk-build/punc/src/libpunc.so.1.9.3 -lmaloc /usr/lib/arm-linux-gnueabihf/libarpack.so /usr/lib/arm-linux-gnueabihf/libsuperlu.so ../../_deps/fetk-build/punc/src/vf2c/libvf2c.so.1.9.3 ../../_deps/fetk-build/punc/src/cgcode/libcgcode.so.1.9.3 -lutil -ldl -lm -lstdc++ /usr/lib/arm-linux-gnueabihf/libumfpack.so /usr/lib/arm-linux-gnueabihf/libspqr.so /usr/lib/arm-linux-gnueabihf/libcholmod.so /usr/lib/arm-linux-gnueabihf/libccolamd.so /usr/lib/arm-linux-gnueabihf/libcamd.so /usr/lib/arm-linux-gnueabihf/libcolamd.so /usr/lib/arm-linux-gnueabihf/libamd.so -lm -ldl /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/libsuitesparseconfig.so /usr/lib/arm-linux-gnueabihf/librt.a /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -fopenmp make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [100%] Built target apbs_pybind make[2]: Leaving directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-arm-linux-gnueabihf' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python3,sphinxdoc --buildsystem=cmake dh_testroot -a -O--buildsystem=cmake dh_prep -a -O--buildsystem=cmake dh_auto_install -a -O--buildsystem=cmake cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/<> -B/<>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "RELWITHDEBINFO" -- Installing: /<>/debian/tmp/usr/share/apbs/cmake -- Installing: /<>/debian/tmp/usr/share/apbs/cmake/FindUMFPACK.cmake -- Installing: /<>/debian/tmp/usr/share/apbs/cmake/FindARPACK.cmake -- Installing: /<>/debian/tmp/usr/share/apbs/cmake/FindSuiteSparse.cmake -- Installing: /<>/debian/tmp/usr/share/apbs/cmake/FindSuperLU.cmake -- Installing: /<>/debian/tmp/usr/share/apbs/cmake/FindAMD.cmake -- Installing: /<>/debian/tmp/usr/share/apbs/cmake/FindLAPACK.cmake -- Installing: /<>/debian/tmp/usr/include/punc/punc.h -- Installing: /<>/debian/tmp/usr/include/punc/punc_base.h -- Installing: /<>/debian/tmp/usr/include/punc/punccf.h -- Installing: /<>/debian/tmp/usr/include/punc/punc_base_p.h -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libpunc.so.1.9.3 -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libpunc.so.1.9 -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libpunc.so -- Installing: /<>/debian/tmp/usr/include/punc/varpack.h -- Installing: /<>/debian/tmp/usr/include/punc/vblas.h -- Installing: /<>/debian/tmp/usr/include/punc/vcgcode.h -- Installing: /<>/debian/tmp/usr/include/punc/vlapack.h -- Installing: /<>/debian/tmp/usr/include/punc/vpmg.h -- Installing: /<>/debian/tmp/usr/include/punc/vf2c.h -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libvf2c.so.1.9.3 -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libvf2c.so.1.9 -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libvf2c.so -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libcgcode.so.1.9.3 -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libcgcode.so.1.9 -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libcgcode.so -- Installing: /<>/debian/tmp/usr/include/gamer/gamer.h -- Installing: /<>/debian/tmp/usr/include/gamer/gamer_base.h -- Installing: /<>/debian/tmp/usr/include/gamer/triangle.h -- Installing: /<>/debian/tmp/usr/include/gamer/tetgen.h -- Installing: /<>/debian/tmp/usr/include/gamer/biom.h -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libgamer.so.1.9.3 -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libgamer.so.1.9 -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libgamer.so -- Installing: /<>/debian/tmp/usr/include/mc/mc_base.h -- Installing: /<>/debian/tmp/usr/include/mc/mc.h -- Installing: /<>/debian/tmp/usr/include/mc/bam.h -- Installing: /<>/debian/tmp/usr/include/mc/bmat.h -- Installing: /<>/debian/tmp/usr/include/mc/bvec.h -- Installing: /<>/debian/tmp/usr/include/mc/mat.h -- Installing: /<>/debian/tmp/usr/include/mc/mtool.h -- Installing: /<>/debian/tmp/usr/include/mc/slu.h -- Installing: /<>/debian/tmp/usr/include/mc/vec.h -- Installing: /<>/debian/tmp/usr/include/mc/vec3.h -- Installing: /<>/debian/tmp/usr/include/mc/zslu.h -- Installing: /<>/debian/tmp/usr/include/mc/whb.h -- Installing: /<>/debian/tmp/usr/include/mc/aprx.h -- Installing: /<>/debian/tmp/usr/include/mc/bnode.h -- Installing: /<>/debian/tmp/usr/include/mc/node.h -- Installing: /<>/debian/tmp/usr/include/mc/re.h -- Installing: /<>/debian/tmp/usr/include/mc/gem.h -- Installing: /<>/debian/tmp/usr/include/mc/vel.h -- Installing: /<>/debian/tmp/usr/include/mc/ves.h -- Installing: /<>/debian/tmp/usr/include/mc/pde.h -- Installing: /<>/debian/tmp/usr/include/mc/am.h -- Installing: /<>/debian/tmp/usr/include/mc/nam.h -- Installing: /<>/debian/tmp/usr/include/mc/dyn.h -- Installing: /<>/debian/tmp/usr/include/mc/mcsh.h -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libmc.so.1.9.3 -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libmc.so.1.9 -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libmc.so -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libapbs_routines.so.3 -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libapbs_routines.so -- Installing: /<>/debian/tmp/usr/include/apbs/apbs.h -- Installing: /<>/debian/tmp/usr/include/apbs/routines.h -- Installing: /<>/debian/tmp/usr/bin/apbs -- Installing: /<>/debian/tmp/usr/include/generic/nosh.h -- Installing: /<>/debian/tmp/usr/include/generic/mgparm.h -- Installing: /<>/debian/tmp/usr/include/generic/femparm.h -- Installing: /<>/debian/tmp/usr/include/generic/pbamparm.h -- Installing: /<>/debian/tmp/usr/include/generic/pbsamparm.h -- Installing: /<>/debian/tmp/usr/include/generic/pbeparm.h -- Installing: /<>/debian/tmp/usr/include/generic/bemparm.h -- Installing: /<>/debian/tmp/usr/include/generic/geoflowparm.h -- Installing: /<>/debian/tmp/usr/include/generic/apolparm.h -- Installing: /<>/debian/tmp/usr/include/generic/vacc.h -- Installing: /<>/debian/tmp/usr/include/generic/valist.h -- Installing: /<>/debian/tmp/usr/include/generic/vatom.h -- Installing: /<>/debian/tmp/usr/include/generic/vpbe.h -- Installing: /<>/debian/tmp/usr/include/generic/vcap.h -- Installing: /<>/debian/tmp/usr/include/generic/vclist.h -- Installing: /<>/debian/tmp/usr/include/generic/vstring.h -- Installing: /<>/debian/tmp/usr/include/generic/vparam.h -- Installing: /<>/debian/tmp/usr/include/generic/vgreen.h -- Installing: /<>/debian/tmp/usr/include/generic/vmatrix.h -- Installing: /<>/debian/tmp/usr/include/generic/vhal.h -- Installing: /<>/debian/tmp/usr/include/generic/vunit.h -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libapbs_generic.so.3 -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libapbs_generic.so -- Installing: /<>/debian/tmp/usr/include/pmgc/buildAd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/buildBd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/buildGd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/buildPd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/cgd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/gsd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/matvecd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/mgcsd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/mgdrvd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/mgsubd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/mikpckd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/mlinpckd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/mypdec.h -- Installing: /<>/debian/tmp/usr/include/pmgc/newtond.h -- Installing: /<>/debian/tmp/usr/include/pmgc/newdrvd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/powerd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/smoothd.h -- Installing: /<>/debian/tmp/usr/include/pmgc/mgfasd.h -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libapbs_pmgc.so.3 -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libapbs_pmgc.so -- Installing: /<>/debian/tmp/usr/include/mg/vgrid.h -- Installing: /<>/debian/tmp/usr/include/mg/vmgrid.h -- Installing: /<>/debian/tmp/usr/include/mg/vopot.h -- Installing: /<>/debian/tmp/usr/include/mg/vpmg.h -- Installing: /<>/debian/tmp/usr/include/mg/vpmgp.h -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libapbs_mg.so.3 -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libapbs_mg.so -- Installing: /<>/debian/tmp/usr/include/fem/vcsm.h -- Installing: /<>/debian/tmp/usr/include/fem/vfetk.h -- Installing: /<>/debian/tmp/usr/include/fem/vpee.h -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libapbs_fem.so.3 -- Installing: /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libapbs_fem.so -- Installing: /<>/debian/tmp/usr/lib/apbs.cpython-312-arm-linux-gnueabihf.so -- Installing: /<>/debian/tmp/usr/share/apbs/examples -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_apo_apbs.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_bin_apbs.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/bx6_7_lig_apbs.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-lig.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-apo.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-bin.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-lig.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd2-bin.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/README -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/UHBD/uhbd1-apo.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-vdw.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-surf.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-smol-vdw.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pka-lig/apbs-mol-surf.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer1.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/test_proteins/1d30_monomer2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30_monomer2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/1d30_monomer1.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-binding-energy/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/run_examples.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/1a63_NanoShaper_SES.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/451c_order1.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/1a63_NanoShaper_Skin.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/451c_order5.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1a63.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/twob.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/oneb.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1ajj.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/twob2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/451c.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/test_proteins/1bbl.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/cyclohexane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/ethane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/mol.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/methane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/apbs-forces.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/propane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/butane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/parm.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/hexane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/neopentane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/pentane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/cyclopentane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/isobutane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/alkanes.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/2-methylbutane.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/alkanes/force.result -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/neg_1.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/neg_2.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/pos_1.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/1a63.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/pos_3.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/pos_2.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/toy_electrostatic.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/pos_charge.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/neg_3.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/neg_charge.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/toy_energyforce.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/1a63.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/toy_dynamics.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbam/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/ASH66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-ASP66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-ASH66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASH66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/ASP66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASP66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-noASP66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/ASH66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/test_proteins/2LZT-ASH66.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-noASP66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/2LZT-noASH66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/ASP66.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/bem-pKa/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/model_outNpep.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/postprocess.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/apbs_dx.py -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/PDB -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outNB.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outNpep.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/PDB/model_outBoxB19.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/run_apdx_files.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/dxmath.txt -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/template.txt -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/test.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/model_outNB.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/model_outBoxB19.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/fit.py -- Installing: /<>/debian/tmp/usr/share/apbs/examples/protein-rna/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-auto.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apolarforces -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-parallel.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-fem.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-apolar.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-forces.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/polarforces -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-fem-extmesh.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/parm.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/mesh.m -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-parallel.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/ion.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-mol-fem.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/apbs-smol-auto.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/pmf.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/born/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/apolarforces -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/runme.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/polarforces -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/complex.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/ion-pmf.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/parm.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-pmf/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/1d7h-min.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/dmso-min.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/bindf.oldlog -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso/UHBD/pqr2qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/1d7i-min.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/dss-min.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-dss/UHBD/bindf.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-min.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/dss-min.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7i-min.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/dmso-min.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/FKBP/1d7h-dmso-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys.config -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys.param -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_3.face -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_stern.face -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_1.vert -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_3.vert -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1.vert -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_stern.vert -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_2.face -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1.face -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_2.vert -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/geometry/Lys1_1.face -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pygbe/lys/lys1_charges.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/apbs-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/acetate.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/acetic-acid.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.dat.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.pdb.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.inp.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/UHBD/elec.out.orig.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/apbs-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/proton.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ionize/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/hca.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.err -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf2.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf1.qcd -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf2.err -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.out -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/bindf-nmap.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/UHBD/srsrf.dot -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/apbs-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/mesh.m -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/acet.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/hca-bind/complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_3.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/runme.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/point-pmf-0.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_1.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_4.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol0.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol3.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/energy.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol4.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_3.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol1.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/apbs.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/mol2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_1.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/complex-0_4.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/point-pmf/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/param.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/apbs-PDB.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/mache.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/achbp.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/apbs.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/fas2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/misc/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/1a63.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/gly.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/imidazole.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/glycerol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/imidazole_zap.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/gly.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/1a63.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/geoflow/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-auto.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-mol-parallel.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.full.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/single.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/prot4.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/nuc.3-4.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/prot3.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/aheall-atom.charmm.dat -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/UHBD/srsrf.dot -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/mesh.m -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-parallel.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/mol1.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/apbs-smol-auto.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/mol2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/actin-dimer/complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barnase.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barstar.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-barn_bars/barn_bars_electro.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/small491.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/491.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.pdb -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.e2.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.log -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/UHBD/small491.inp -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-smol-pdiel12.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/491.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-mol-pdiel12.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-smol-pdiel2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/apbs-mol-pdiel2.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/ion-protein/complex.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Apbs_solv-TEMPLATE.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy-TEMPLATE.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-16.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-0.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Apbs_dummy.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Run_membrane-helix.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-12.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-4.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/Membrane-helix-8.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/helix/draw_membrane2.c -- Installing: /<>/debian/tmp/usr/share/apbs/examples/run_selected_examples.sh -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_1_2.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms/gly_electrostatic.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/msms/gly_msms.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_dynamics.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_2_1.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_2_2.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_electrostatic.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_energyforce.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_cg2.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly.vert -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/gly_cg.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/traj_1_1.xyz -- Installing: /<>/debian/tmp/usr/share/apbs/examples/pbsam-gly/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/apbs-smol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/UHBD -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.out.orig.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.inp.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/UHBD/solv.dat.exam -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/apbs-mol.in -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/methanol.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/methoxide.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/examples/solv/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/examples/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/tests -- Installing: /<>/debian/tmp/usr/share/apbs/tests/test_cases.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_check_intermediate_energies.py -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_check_results.py -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_tester.py -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_check_forces.py -- Installing: /<>/debian/tmp/usr/share/apbs/tests/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/tests/apbs_logger.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/WHATIF2AMBER.sed -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/amber2charmm.sh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/vparam -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/vparam/vparam-amber-parm94.xml -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/vparam/vparam-amber-parm94.dat -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/c-alpha.dat -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/amber2uhbd.sh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/amber-param.dat -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/param/pdb2pqr/weiner86-param.dat -- Installing: /<>/debian/tmp/usr/share/apbs/tools/conversion/qcd2pqr.awk -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/mergedx2.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/similarity.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/dx2mol.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/uhbd_asc2bin.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/multivalue.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/mgmesh.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/benchmark.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/dx2uhbd.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/smooth.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/analysis.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/mergedx.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/del2dx.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/tensor2dx.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/value.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/mesh/dxmath.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/Makefile.in -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/Makefile -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/Makefile.am -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/apbslib.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/apbslib_wrap.doc -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/noinput.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/main.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/ion.pqr -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/apbs.in -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile.in -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/Makefile.am -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/average.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/mergedx.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/vgrid.i -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/read.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/vgridlib.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/vgrid.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/vgrid/README -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/apbslib.i -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python/README -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.net -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/surface.net -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/surface.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/pot.cm -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/multipot.cfg -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/multipot.net -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.cm -- Installing: /<>/debian/tmp/usr/share/apbs/tools/visualization/opendx/potacc.net -- Installing: /<>/debian/tmp/usr/share/apbs/tools/github -- Installing: /<>/debian/tmp/usr/share/apbs/tools/github/release-data.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/github/getReleases.sh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_vatom.cpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/module.cpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_valist.cpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_constants.hpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_nosh.cpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_vatom.hpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_nosh.hpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/python-pybind/bind_valist.hpp -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/born.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/coulomb.c -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/CMakeLists.txt -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/inputgen.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/manip/psize.py -- Installing: /<>/debian/tmp/usr/share/apbs/tools/README.md -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/dx2uhbd -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/born -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/mergedx2 -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/uhbd_asc2bin -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/mergedx -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/tensor2dx -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/mgmesh -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/similarity -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/smooth -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/benchmark -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/dxmath -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/multivalue -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/del2dx -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/dx2mol -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/coulomb -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/analysis -- Installing: /<>/debian/tmp/usr/share/apbs/tools/bin/value make[1]: Leaving directory '/<>/obj-arm-linux-gnueabihf' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/<>' (cd tests; PATH=/<>/debian/tmp/usr/bin:${PATH} LD_LIBRARY_PATH=/<>/debian/tmp/usr/lib/arm-linux-gnueabihf:${LD_LIBRARY_PATH} PYTHONPATH=${PYTHONPATH}:/<>/tools/manip python3 apbs_tester.py -c test_cases.cfg; rm -rf __pycache__) TESTING WITH BINARY_NAME:apbs START_DIR:/<>/build -------------------------------------------------------------------------------- Testing forces from apbs-forces.in Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.004512 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in CHECKING:/<>/debian/tmp/usr/bin/apbs NOTE: Using apbs binary:/<>/debian/tmp/usr/bin/apbs Testing all sections The following sections will be tested: born, actin-dimer-auto, alkanes, FKBP, hca-bind, ionize, ion-pmf, pka-lig, point-pmf, solv ================================================================================ Running tests for born section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol-auto.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 61.262 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.607073836227E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.200266567971E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to potential.dx.gz Total electrostatic energy = 4.732245131587E+03 kJ/mol Calculating forces... Writing potential to potential-PE0.dx.gz ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.297735526282E+02 kJ/mol Global net ELEC energy = -2.297735526282E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.067 MB high water Thanks for using APBS! Testing computed result against expected result (9.607073836227e+02, 9.607073836227e+02) *** PASSED *** Testing computed result against expected result (2.200266567971e+03, 2.200266567971e+03) *** PASSED *** Testing computed result against expected result (4.732245131587e+03, 4.732245131587e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) *** PASSED *** Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) *** PASSED *** Testing computed result against expected result (-2.297735526282e+02, -2.297735411962e+02) *** PASSED *** Elapsed time: 3.101455 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in Checking for intermediate energies in input file apbs-mol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [960.7073836227, 2200.266567971, 4732.245131587, 1190.871482831, 2430.874049735, 4962.018684215, -229.7735526282] EXPECTED: ['9.607073836227E+02', '2.2002665679710E+03', '4.732245131587E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.297735411962E+02'] COMPUTED RESULT 960.7073836227 COMPUTED RESULT 2200.266567971 COMPUTED RESULT 4732.245131587 COMPUTED RESULT 1190.871482831 COMPUTED RESULT 2430.874049735 COMPUTED RESULT 4962.018684215 COMPUTED RESULT -229.7735526282 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-auto.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 61.262 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.532928767450E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.201243880085E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.733006258977E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.290124252387E+02 kJ/mol Global net ELEC energy = -2.290124252387E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.067 MB high water Thanks for using APBS! Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) *** PASSED *** Testing computed result against expected result (2.201243880085e+03, 2.201243880085e+03) *** PASSED *** Testing computed result against expected result (4.733006258977e+03, 4.733006258977e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (2.430874049735e+03, 2.430874049735e+03) *** PASSED *** Testing computed result against expected result (4.962018684215e+03, 4.962018684215e+03) *** PASSED *** Testing computed result against expected result (-2.290124252387e+02, -2.290124171992e+02) *** PASSED *** Elapsed time: 2.282255 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 4 separate files using the inputgen utility Checking for intermediate energies in input file apbs-smol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [953.292876745, 2201.243880085, 4733.006258977, 1190.871482831, 2430.874049735, 4962.018684215, -229.0124252387] EXPECTED: ['9.532928767450E+02', '2.2012438800850E+03', '4.733006258977E+03', '1.190871482831E+03', '2.4308740497350E+03', '4.962018684215E+03', '-2.290124171992E+02'] COMPUTED RESULT 953.292876745 COMPUTED RESULT 2201.243880085 COMPUTED RESULT 4733.006258977 COMPUTED RESULT 1190.871482831 COMPUTED RESULT 2430.874049735 COMPUTED RESULT 4962.018684215 COMPUTED RESULT -229.0124252387 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE0.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE0.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 61.262 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935592471E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255308186E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864094552E+01 kJ/mol Global net ELEC energy = -5.761864094552E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.067 MB high water Thanks for using APBS! Processor 0 results: 2.401768459022e+02 8.142935592471e+02 1.485255308186e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.761864094552e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE0.out BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE1.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 61.262 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778312125E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246667424E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728170718E+01 kJ/mol Global net ELEC energy = -5.762728170718E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.067 MB high water Thanks for using APBS! Processor 1 results: 2.401768459022e+02 8.142778312125e+02 1.485246667424e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.762728170718e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE1.out BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE2.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 61.262 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935605696E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255306569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864257239E+01 kJ/mol Global net ELEC energy = -5.761864257239E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.067 MB high water Thanks for using APBS! Processor 2 results: 2.401768459091e+02 8.142935605696e+02 1.485255306569e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.761864257239e+01 Checking for intermediate energies in input file apbs-mol-parallel-PE2.out BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol-parallel-PE3.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol-parallel-PE3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 61.262 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778325440E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246665692E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728344954E+01 kJ/mol Global net ELEC energy = -5.762728344954E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.067 MB high water Thanks for using APBS! Processor 3 results: 2.401768459091e+02 8.142778325440e+02 1.485246665692e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.762728344954e+01 Testing computed result against expected result (9.607073836226e+02, 9.607073836226e+02) *** PASSED *** Testing computed result against expected result (3.257142783573e+03, 3.257142783573e+03) *** PASSED *** Testing computed result against expected result (5.941003947871e+03, 5.941003947871e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) *** PASSED *** Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) *** PASSED *** Testing computed result against expected result (-2.304918486746e+02, -2.304918086635e+02) *** PASSED *** Elapsed time: 11.789694 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 4 separate files using the inputgen utility Checking for intermediate energies in input file apbs-mol-parallel-PE3.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [960.7073836226, 3257.1427835731997, 5941.0039478710005, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -230.49184867463003] EXPECTED: ['9.607073836226E+02', '3.2571427835732E+03', '5.941003947871E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.304918086635E+02'] COMPUTED RESULT 960.7073836226 COMPUTED RESULT 3257.1427835731997 COMPUTED RESULT 5941.0039478710005 COMPUTED RESULT 1190.8714828309999 COMPUTED RESULT 3519.7218230368003 COMPUTED RESULT 6171.495796544 COMPUTED RESULT -230.49184867463003 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE0.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE0.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 61.262 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369591602E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524998001E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895113069E+01 kJ/mol Global net ELEC energy = -5.734895113069E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.067 MB high water Thanks for using APBS! Processor 0 results: 2.383232191816e+02 8.145369591602e+02 1.485524998001e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.734895113069e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE0.out BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE1.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 61.262 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419898332E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328612E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462051928E+01 kJ/mol Global net ELEC energy = -5.734462051928E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.067 MB high water Thanks for using APBS! Processor 1 results: 2.383232191816e+02 8.145419898332e+02 1.485529328612e+03 2.977178707009e+02 8.799304557588e+02 1.542873949131e+03 -5.734462051928e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE1.out BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE2.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 61.262 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369593489E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524997676E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895146550E+01 kJ/mol Global net ELEC energy = -5.734895146550E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.067 MB high water Thanks for using APBS! Processor 2 results: 2.383232191909e+02 8.145369593489e+02 1.485524997676e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.734895146550e+01 Checking for intermediate energies in input file apbs-smol-parallel-PE2.out BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-parallel-PE3.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-parallel-PE3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from ion.pqr. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 61.262 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419900310E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.262 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328301E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.189 MB total, 122.067 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462084052E+01 kJ/mol Global net ELEC energy = -5.734462084052E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.067 MB high water Thanks for using APBS! Processor 3 results: 2.383232191909e+02 8.145419900310e+02 1.485529328301e+03 2.977178707146e+02 8.799304557596e+02 1.542873949141e+03 -5.734462084052e+01 Testing computed result against expected result (9.532928767450e+02, 9.532928767450e+02) *** PASSED *** Testing computed result against expected result (3.258157898373e+03, 3.258157898373e+03) *** PASSED *** Testing computed result against expected result (5.942108652590e+03, 5.942108652590e+03) *** PASSED *** Testing computed result against expected result (1.190871482831e+03, 1.190871482831e+03) *** PASSED *** Testing computed result against expected result (3.519721823037e+03, 3.519721823037e+03) *** PASSED *** Testing computed result against expected result (6.171495796544e+03, 6.171495796544e+03) *** PASSED *** Testing computed result against expected result (-2.293871439560e+02, -2.293871354771e+02) *** PASSED *** Elapsed time: 11.511078 seconds -------------------------------------------------------------------------------- Total elapsed time: 28.688994 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in Checking for intermediate energies in input file apbs-smol-parallel-PE3.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [953.292876745, 3258.1578983732998, 5942.108652589999, 1190.8714828309999, 3519.7218230368003, 6171.495796544, -229.38714395599] EXPECTED: ['9.532928767450E+02', '3.2581578983733E+03', '5.942108652590E+03', '1.190871482831E+03', '3.5197218230368E+03', '6.171495796544E+03', '-2.293871354771E+02'] COMPUTED RESULT 953.292876745 COMPUTED RESULT 3258.1578983732998 COMPUTED RESULT 5942.108652589999 COMPUTED RESULT 1190.8714828309999 COMPUTED RESULT 3519.7218230368003 COMPUTED RESULT 6171.495796544 COMPUTED RESULT -229.38714395599 Running tests for actin-dimer-auto section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol-auto.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1004.896 MB total, 1004.896 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527617850342E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1004.896 MB total, 1995.284 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.919510754196E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1005.881 MB total, 1995.284 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527671844880E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1005.881 MB total, 1997.252 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.915468859278E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1018.381 MB total, 1997.252 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.056317807611E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1018.381 MB total, 2013.407 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.836028296532E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.048683058628E+02 kJ/mol Global net ELEC energy = 1.048683058628E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2013.407 MB high water Thanks for using APBS! Testing computed result against expected result (1.527617850342e+05, 1.527617850342e+05) *** PASSED *** Testing computed result against expected result (2.919510754196e+05, 2.919510754196e+05) *** PASSED *** Testing computed result against expected result (1.527671844880e+05, 1.527671844880e+05) *** PASSED *** Testing computed result against expected result (2.915468859278e+05, 2.915468859278e+05) *** PASSED *** Testing computed result against expected result (3.056317807611e+05, 3.056317807611e+05) *** PASSED *** Testing computed result against expected result (5.836028296532e+05, 5.836028296532e+05) *** PASSED *** Testing computed result against expected result (1.048683058628e+02, 1.048683060915e+02) *** PASSED *** Elapsed time: 119.839005 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in Checking for intermediate energies in input file apbs-mol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [152761.7850342, 291951.0754196, 152767.184488, 291546.8859278, 305631.7807611, 583602.8296532, 104.8683058628] EXPECTED: ['1.52761785034200E+05', '2.91951075419600E+05', '1.52767184488000E+05', '2.91546885927800E+05', '3.0563178076110E+05', '5.8360282965320E+05', '1.048683060915E+02'] COMPUTED RESULT 152761.7850342 COMPUTED RESULT 291951.0754196 COMPUTED RESULT 152767.184488 COMPUTED RESULT 291546.8859278 COMPUTED RESULT 305631.7807611 COMPUTED RESULT 583602.8296532 COMPUTED RESULT 104.8683058628 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-auto.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-auto.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1004.896 MB total, 1004.896 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.528632421825E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1004.896 MB total, 1995.284 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.920618662320E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1005.881 MB total, 1995.284 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.529297900572E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1005.881 MB total, 1997.252 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.916592202835E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1018.381 MB total, 1997.252 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.059244262535E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1018.381 MB total, 2013.407 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.838306706232E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.095841077691E+02 kJ/mol Global net ELEC energy = 1.095841077691E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2013.407 MB high water Thanks for using APBS! Testing computed result against expected result (1.528632421825e+05, 1.528632421825e+05) *** PASSED *** Testing computed result against expected result (2.920618662320e+05, 2.920618662320e+05) *** PASSED *** Testing computed result against expected result (1.529297900572e+05, 1.529297900572e+05) *** PASSED *** Testing computed result against expected result (2.916592202835e+05, 2.916592202835e+05) *** PASSED *** Testing computed result against expected result (3.059244262535e+05, 3.059244262535e+05) *** PASSED *** Testing computed result against expected result (5.838306706232e+05, 5.838306706232e+05) *** PASSED *** Testing computed result against expected result (1.095841077691e+02, 1.095841074454e+02) *** PASSED *** Elapsed time: 87.376608 seconds -------------------------------------------------------------------------------- Total elapsed time: 207.215613 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file alkanes.in Checking for intermediate energies in input file apbs-smol-auto.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [152863.2421825, 292061.866232, 152929.7900572, 291659.2202835, 305924.4262535, 583830.6706232, 109.5841077691] EXPECTED: ['1.52863242182500E+05', '2.92061866232000E+05', '1.52929790057200E+05', '2.91659220283500E+05', '3.0592442625350E+05', '5.8383067062320E+05', '1.095841074454E+02'] COMPUTED RESULT 152863.2421825 COMPUTED RESULT 292061.866232 COMPUTED RESULT 152929.7900572 COMPUTED RESULT 291659.2202835 COMPUTED RESULT 305924.4262535 COMPUTED RESULT 583830.6706232 COMPUTED RESULT 109.5841077691 Running tests for alkanes section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: alkanes.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'alkanes.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file alkanes.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 11 molecules Reading PDB-format atom data from 2-methylbutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 4.33e+00 e Reading PDB-format atom data from butane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (3.917e+00, 7.025e-01, -8.575e+00) Net charge 3.51e+00 e Reading PDB-format atom data from cyclohexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (1.123e+00, 5.880e-01, 7.680e-01) Net charge 4.93e+00 e Reading PDB-format atom data from cyclopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 13 atoms Centered at (1.320e+00, 5.255e-01, 1.289e+00) Net charge 3.88e+00 e Reading PDB-format atom data from ethane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (2.210e-01, -2.100e-02, 7.650e-01) Net charge 1.87e+00 e Reading PDB-format atom data from hexane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 20 atoms Centered at (4.951e+00, -9.500e-03, -8.406e+00) Net charge 5.16e+00 e Reading PDB-format atom data from isobutane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.859e+01, 1.864e+01, 1.921e+01) Net charge 3.51e+00 e Reading PDB-format atom data from methane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5 atoms Centered at (1.803e+01, 1.779e+01, 1.782e+01) Net charge 1.05e+00 e Reading PDB-format atom data from neopentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (1.867e+01, 1.894e+01, 1.920e+01) Net charge 4.33e+00 e Reading PDB-format atom data from pentane.pdb. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (4.460e+00, 1.615e-01, -8.566e+00) Net charge 4.33e+00 e Reading PDB-format atom data from propane.pdb. 11 atoms Centered at (1.836e+01, 1.896e+01, 1.861e+01) Net charge 2.69e+00 e Preparing to run 11 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated-2-methylbutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.815624614267E+00 SASA for atom 1: 0.000000000000E+00 SASA for atom 2: 6.122920124655E-01 SASA for atom 3: 3.957497153740E+00 SASA for atom 4: 4.308445014544E+00 SASA for atom 5: 1.843264951960E+01 SASA for atom 6: 1.837011296483E+01 SASA for atom 7: 1.666599184724E+01 SASA for atom 8: 1.480031796315E+01 SASA for atom 9: 1.603020354037E+01 SASA for atom 10: 1.473778140838E+01 SASA for atom 11: 1.611879699297E+01 SASA for atom 12: 1.810954398660E+01 SASA for atom 13: 1.420100931324E+01 SASA for atom 14: 1.437298483886E+01 SASA for atom 15: 1.814081226399E+01 SASA for atom 16: 2.152820898091E+01 Total solvent accessible surface area: 214.202 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.243280922127E-02 Surface tension*area energy for atom 1: 0.000000000000E+00 Surface tension*area energy for atom 2: 5.204482105957E-03 Surface tension*area energy for atom 3: 3.363872580679E-02 Surface tension*area energy for atom 4: 3.662178262362E-02 Surface tension*area energy for atom 5: 1.566775209166E-01 Surface tension*area energy for atom 6: 1.561459602010E-01 Surface tension*area energy for atom 7: 1.416609307015E-01 Surface tension*area energy for atom 8: 1.258027026868E-01 Surface tension*area energy for atom 9: 1.362567300932E-01 Surface tension*area energy for atom 10: 1.252711419712E-01 Surface tension*area energy for atom 11: 1.370097744402E-01 Surface tension*area energy for atom 12: 1.539311238861E-01 Surface tension*area energy for atom 13: 1.207085791625E-01 Surface tension*area energy for atom 14: 1.221703711303E-01 Surface tension*area energy for atom 15: 1.541969042439E-01 Surface tension*area energy for atom 16: 1.829897763377E-01 Total surface tension energy: 1.82072 kJ/mol Total solvent accessible volume: 253.665 A^3 Total pressure*volume energy: 60.7274 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.271287875274E+00 WCA energy for atom 1: -5.600872869478E+00 WCA energy for atom 2: -5.773775123943E+00 WCA energy for atom 3: -6.072801488986E+00 WCA energy for atom 4: -6.378470721845E+00 WCA energy for atom 5: -1.573474558351E+00 WCA energy for atom 6: -1.582338715648E+00 WCA energy for atom 7: -1.504044838266E+00 WCA energy for atom 8: -1.351002262819E+00 WCA energy for atom 9: -1.437367175239E+00 WCA energy for atom 10: -1.384626257493E+00 WCA energy for atom 11: -1.468867560891E+00 WCA energy for atom 12: -1.557005662832E+00 WCA energy for atom 13: -1.473759654043E+00 WCA energy for atom 14: -1.502261431335E+00 WCA energy for atom 15: -1.550940901474E+00 WCA energy for atom 16: -1.667828659696E+00 Total WCA energy: -48.1507 kJ/mol Total non-polar energy = 1.439739455792E+01 kJ/mol ---------------------------------------- CALCULATION #2 (solvated-butane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 8.064333822716E-01 SASA for atom 3: 4.375647796400E+00 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.660345529247E+01 SASA for atom 8: 1.658782115377E+01 SASA for atom 9: 1.658260977421E+01 SASA for atom 10: 1.658260977421E+01 SASA for atom 11: 2.145003828744E+01 SASA for atom 12: 1.852124297220E+01 SASA for atom 13: 1.856293400871E+01 Total solvent accessible surface area: 193.855 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 6.854683749309E-03 Surface tension*area energy for atom 3: 3.719300626940E-02 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.411293699860E-01 Surface tension*area energy for atom 8: 1.409964798071E-01 Surface tension*area energy for atom 9: 1.409521830808E-01 Surface tension*area energy for atom 10: 1.409521830808E-01 Surface tension*area energy for atom 11: 1.823253254433E-01 Surface tension*area energy for atom 12: 1.574305652637E-01 Surface tension*area energy for atom 13: 1.577849390741E-01 Total surface tension energy: 1.64777 kJ/mol Total solvent accessible volume: 217.863 A^3 Total pressure*volume energy: 52.1564 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.728858147814E+00 WCA energy for atom 1: -6.204037472587E+00 WCA energy for atom 2: -6.202937735018E+00 WCA energy for atom 3: -6.728762249931E+00 WCA energy for atom 4: -1.623549989062E+00 WCA energy for atom 5: -1.709092300778E+00 WCA energy for atom 6: -1.625196457114E+00 WCA energy for atom 7: -1.484289341167E+00 WCA energy for atom 8: -1.485410538626E+00 WCA energy for atom 9: -1.485593139015E+00 WCA energy for atom 10: -1.484878734279E+00 WCA energy for atom 11: -1.708585062695E+00 WCA energy for atom 12: -1.625094916482E+00 WCA energy for atom 13: -1.624416805392E+00 Total WCA energy: -41.7207 kJ/mol Total non-polar energy = 1.208346456826E+01 kJ/mol ---------------------------------------- CALCULATION #3 (solvated-cyclohexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 7.840324549863E-01 SASA for atom 1: 8.064333822716E-01 SASA for atom 2: 8.288343095569E-01 SASA for atom 3: 7.840324549863E-01 SASA for atom 4: 7.989664065098E-01 SASA for atom 5: 8.363012853187E-01 SASA for atom 6: 2.001169752764E+01 SASA for atom 7: 1.616048802948E+01 SASA for atom 8: 2.001169752764E+01 SASA for atom 9: 1.619175630687E+01 SASA for atom 10: 1.616048802948E+01 SASA for atom 11: 1.993352683418E+01 SASA for atom 12: 2.001169752764E+01 SASA for atom 13: 1.618133354774E+01 SASA for atom 14: 1.617091078861E+01 SASA for atom 15: 2.001690890721E+01 SASA for atom 16: 1.993873821374E+01 SASA for atom 17: 1.617091078861E+01 Total solvent accessible surface area: 221.799 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 6.664275867383E-03 Surface tension*area energy for atom 1: 6.854683749309E-03 Surface tension*area energy for atom 2: 7.045091631234E-03 Surface tension*area energy for atom 3: 6.664275867383E-03 Surface tension*area energy for atom 4: 6.791214455333E-03 Surface tension*area energy for atom 5: 7.108560925209E-03 Surface tension*area energy for atom 6: 1.700994289850E-01 Surface tension*area energy for atom 7: 1.373641482506E-01 Surface tension*area energy for atom 8: 1.700994289850E-01 Surface tension*area energy for atom 9: 1.376299286084E-01 Surface tension*area energy for atom 10: 1.373641482506E-01 Surface tension*area energy for atom 11: 1.694349780905E-01 Surface tension*area energy for atom 12: 1.700994289850E-01 Surface tension*area energy for atom 13: 1.375413351558E-01 Surface tension*area energy for atom 14: 1.374527417032E-01 Surface tension*area energy for atom 15: 1.701437257113E-01 Surface tension*area energy for atom 16: 1.694792748168E-01 Surface tension*area energy for atom 17: 1.374527417032E-01 Total surface tension energy: 1.88529 kJ/mol Total solvent accessible volume: 267.435 A^3 Total pressure*volume energy: 64.0239 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -5.793234697241E+00 WCA energy for atom 1: -5.784370526583E+00 WCA energy for atom 2: -5.791799130412E+00 WCA energy for atom 3: -5.788504399087E+00 WCA energy for atom 4: -5.797319672490E+00 WCA energy for atom 5: -5.787358035342E+00 WCA energy for atom 6: -1.523887929614E+00 WCA energy for atom 7: -1.413678912317E+00 WCA energy for atom 8: -1.521751604392E+00 WCA energy for atom 9: -1.414741802525E+00 WCA energy for atom 10: -1.413367854344E+00 WCA energy for atom 11: -1.523407238081E+00 WCA energy for atom 12: -1.523000623583E+00 WCA energy for atom 13: -1.413922068538E+00 WCA energy for atom 14: -1.416316744211E+00 WCA energy for atom 15: -1.524577474659E+00 WCA energy for atom 16: -1.523300410052E+00 WCA energy for atom 17: -1.414522566061E+00 Total WCA energy: -52.3691 kJ/mol Total non-polar energy = 1.354016672221E+01 kJ/mol ---------------------------------------- CALCULATION #4 (solvated-cyclopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 9.490526193215E+00 SASA for atom 1: 9.512927120500E+00 SASA for atom 2: 2.299828534626E+00 SASA for atom 3: 1.919012770776E+00 SASA for atom 4: 2.307295510388E+00 SASA for atom 5: 2.325838699632E+01 SASA for atom 6: 2.325838699632E+01 SASA for atom 7: 2.045987617019E+01 SASA for atom 8: 2.067875411190E+01 SASA for atom 9: 2.028790064456E+01 SASA for atom 10: 1.897463299431E+01 SASA for atom 11: 2.048593306801E+01 SASA for atom 12: 2.070481100972E+01 Total solvent accessible surface area: 193.638 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.066947264233E-02 Surface tension*area energy for atom 1: 8.085988052425E-02 Surface tension*area energy for atom 2: 1.954854254432E-02 Surface tension*area energy for atom 3: 1.631160855160E-02 Surface tension*area energy for atom 4: 1.961201183830E-02 Surface tension*area energy for atom 5: 1.976962894687E-01 Surface tension*area energy for atom 6: 1.976962894687E-01 Surface tension*area energy for atom 7: 1.739089474466E-01 Surface tension*area energy for atom 8: 1.757694099511E-01 Surface tension*area energy for atom 9: 1.724471554788E-01 Surface tension*area energy for atom 10: 1.612843804516E-01 Surface tension*area energy for atom 11: 1.741304310781E-01 Surface tension*area energy for atom 12: 1.759908935826E-01 Total surface tension energy: 1.64593 kJ/mol Total solvent accessible volume: 217.998 A^3 Total pressure*volume energy: 52.1887 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.343496616804E+00 WCA energy for atom 1: -6.327869601807E+00 WCA energy for atom 2: -6.334858040579E+00 WCA energy for atom 3: -6.296075406417E+00 WCA energy for atom 4: -6.345600816761E+00 WCA energy for atom 5: -1.663697465126E+00 WCA energy for atom 6: -1.662444032853E+00 WCA energy for atom 7: -1.572325104493E+00 WCA energy for atom 8: -1.604626551065E+00 WCA energy for atom 9: -1.586431484963E+00 WCA energy for atom 10: -1.554291291374E+00 WCA energy for atom 11: -1.574315220751E+00 WCA energy for atom 12: -1.604941679892E+00 Total WCA energy: -44.471 kJ/mol Total non-polar energy = 9.363673200142E+00 kJ/mol ---------------------------------------- CALCULATION #5 (solvated-ethane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 5.995981536705E+00 SASA for atom 1: 5.966113633657E+00 SASA for atom 2: 2.121552620704E+01 SASA for atom 3: 2.124158310486E+01 SASA for atom 4: 2.125200586399E+01 SASA for atom 5: 2.123116034573E+01 SASA for atom 6: 2.125200586399E+01 SASA for atom 7: 2.127285138225E+01 Total solvent accessible surface area: 139.427 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 5.096584306199E-02 Surface tension*area energy for atom 1: 5.071196588609E-02 Surface tension*area energy for atom 2: 1.803319727598E-01 Surface tension*area energy for atom 3: 1.805534563913E-01 Surface tension*area energy for atom 4: 1.806420498439E-01 Surface tension*area energy for atom 5: 1.804648629387E-01 Surface tension*area energy for atom 6: 1.806420498439E-01 Surface tension*area energy for atom 7: 1.808192367491E-01 Total surface tension energy: 1.18513 kJ/mol Total solvent accessible volume: 140.346 A^3 Total pressure*volume energy: 33.5988 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -7.360066353115E+00 WCA energy for atom 1: -7.355483516201E+00 WCA energy for atom 2: -1.776106201066E+00 WCA energy for atom 3: -1.773973940651E+00 WCA energy for atom 4: -1.775401936843E+00 WCA energy for atom 5: -1.773464835521E+00 WCA energy for atom 6: -1.774382856097E+00 WCA energy for atom 7: -1.772366599434E+00 Total WCA energy: -25.3612 kJ/mol Total non-polar energy = 9.422717598546E+00 kJ/mol ---------------------------------------- CALCULATION #6 (solvated-hexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 2.986790304710E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.381536722546E+01 SASA for atom 12: 1.384142412329E+01 SASA for atom 13: 7.765654792245E-01 SASA for atom 14: 1.684839013200E+01 SASA for atom 15: 1.682233323417E+01 SASA for atom 16: 4.166572475070E+00 SASA for atom 17: 2.179398933870E+01 SASA for atom 18: 1.877660057086E+01 SASA for atom 19: 1.876096643216E+01 Total solvent accessible surface area: 250.291 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 2.538771759003E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.174306214164E-01 Surface tension*area energy for atom 12: 1.176521050479E-01 Surface tension*area energy for atom 13: 6.600806573408E-03 Surface tension*area energy for atom 14: 1.432113161220E-01 Surface tension*area energy for atom 15: 1.429898324905E-01 Surface tension*area energy for atom 16: 3.541586603809E-02 Surface tension*area energy for atom 17: 1.852489093789E-01 Surface tension*area energy for atom 18: 1.596011048523E-01 Surface tension*area energy for atom 19: 1.594682146734E-01 Total surface tension energy: 2.12748 kJ/mol Total solvent accessible volume: 298.053 A^3 Total pressure*volume energy: 71.3539 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.635406071935E+00 WCA energy for atom 1: -5.957247427848E+00 WCA energy for atom 2: -5.524801144538E+00 WCA energy for atom 3: -5.522294168859E+00 WCA energy for atom 4: -1.605314409440E+00 WCA energy for atom 5: -1.701051761776E+00 WCA energy for atom 6: -1.606669162773E+00 WCA energy for atom 7: -1.442505934938E+00 WCA energy for atom 8: -1.443059002759E+00 WCA energy for atom 9: -1.328947132810E+00 WCA energy for atom 10: -1.328906972440E+00 WCA energy for atom 11: -1.331566344214E+00 WCA energy for atom 12: -1.328041776815E+00 WCA energy for atom 13: -5.937562025661E+00 WCA energy for atom 14: -1.442277774427E+00 WCA energy for atom 15: -1.442777091510E+00 WCA energy for atom 16: -6.602262542378E+00 WCA energy for atom 17: -1.698172146664E+00 WCA energy for atom 18: -1.600970858835E+00 WCA energy for atom 19: -1.600841970217E+00 Total WCA energy: -57.0807 kJ/mol Total non-polar energy = 1.640068943201E+01 kJ/mol ---------------------------------------- CALCULATION #7 (solvated-isobutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.464676753463E+00 SASA for atom 1: 1.984493338158E+01 SASA for atom 2: 1.778643845361E+01 SASA for atom 3: 1.671289426332E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 3.531879535319E+00 SASA for atom 6: 1.673895116114E+01 SASA for atom 7: 1.793756846098E+01 SASA for atom 8: 1.973549441072E+01 SASA for atom 9: 1.710895911022E+01 SASA for atom 10: 4.599657069253E+00 SASA for atom 11: 1.937069784121E+01 SASA for atom 12: 1.654613011726E+01 SASA for atom 13: 1.936548646165E+01 Total solvent accessible surface area: 192.744 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.944975240444E-02 Surface tension*area energy for atom 1: 1.686819337434E-01 Surface tension*area energy for atom 2: 1.511847268556E-01 Surface tension*area energy for atom 3: 1.420596012382E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 3.002097605021E-02 Surface tension*area energy for atom 6: 1.422810848697E-01 Surface tension*area energy for atom 7: 1.524693319183E-01 Surface tension*area energy for atom 8: 1.677517024912E-01 Surface tension*area energy for atom 9: 1.454261524369E-01 Surface tension*area energy for atom 10: 3.909708508865E-02 Surface tension*area energy for atom 11: 1.646509316503E-01 Surface tension*area energy for atom 12: 1.406421059967E-01 Surface tension*area energy for atom 13: 1.646066349240E-01 Total surface tension energy: 1.63832 kJ/mol Total solvent accessible volume: 218.943 A^3 Total pressure*volume energy: 52.415 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.381016335247E+00 WCA energy for atom 1: -1.612317964554E+00 WCA energy for atom 2: -1.588013719598E+00 WCA energy for atom 3: -1.532162371190E+00 WCA energy for atom 4: -5.987950445279E+00 WCA energy for atom 5: -6.393089030861E+00 WCA energy for atom 6: -1.533454887042E+00 WCA energy for atom 7: -1.587650918485E+00 WCA energy for atom 8: -1.614083521570E+00 WCA energy for atom 9: -1.442402031577E+00 WCA energy for atom 10: -6.408813541353E+00 WCA energy for atom 11: -1.605830214390E+00 WCA energy for atom 12: -1.529385873788E+00 WCA energy for atom 13: -1.605662490385E+00 Total WCA energy: -40.8218 kJ/mol Total non-polar energy = 1.323144287435E+01 kJ/mol ---------------------------------------- CALCULATION #8 (solvated-methane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.231304303117E+01 SASA for atom 1: 2.323233009850E+01 SASA for atom 2: 2.345641941977E+01 SASA for atom 3: 2.377431357320E+01 SASA for atom 4: 2.264344420771E+01 Total solvent accessible surface area: 105.42 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 1.046608657649E-01 Surface tension*area energy for atom 1: 1.974748058372E-01 Surface tension*area energy for atom 2: 1.993795650680E-01 Surface tension*area energy for atom 3: 2.020816653722E-01 Surface tension*area energy for atom 4: 1.924692757655E-01 Total surface tension energy: 0.896066 kJ/mol Total solvent accessible volume: 95.985 A^3 Total pressure*volume energy: 22.9788 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -8.133807570805E+00 WCA energy for atom 1: -1.962181541765E+00 WCA energy for atom 2: -1.964078319162E+00 WCA energy for atom 3: -1.963015006647E+00 WCA energy for atom 4: -1.957425549100E+00 Total WCA energy: -15.9805 kJ/mol Total non-polar energy = 7.894367190329E+00 kJ/mol ---------------------------------------- CALCULATION #9 (solvated-neopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 2.441701074100E+00 SASA for atom 1: 1.663993494942E+01 SASA for atom 2: 1.715586152630E+01 SASA for atom 3: 1.645753666466E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 2.389432243768E+00 SASA for atom 6: 1.638457735076E+01 SASA for atom 7: 1.667641460637E+01 SASA for atom 8: 1.721839808108E+01 SASA for atom 9: 2.419300146815E+00 SASA for atom 10: 1.640021148945E+01 SASA for atom 11: 1.666599184724E+01 SASA for atom 12: 1.719234118325E+01 SASA for atom 13: 2.449168049862E+00 SASA for atom 14: 1.723403221977E+01 SASA for atom 15: 1.639500010989E+01 SASA for atom 16: 1.663472356985E+01 Total solvent accessible surface area: 210.755 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.075445912985E-02 Surface tension*area energy for atom 1: 1.414394470700E-01 Surface tension*area energy for atom 2: 1.458248229736E-01 Surface tension*area energy for atom 3: 1.398890616496E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 2.031017407203E-02 Surface tension*area energy for atom 6: 1.392689074814E-01 Surface tension*area energy for atom 7: 1.417495241541E-01 Surface tension*area energy for atom 8: 1.463563836891E-01 Surface tension*area energy for atom 9: 2.056405124793E-02 Surface tension*area energy for atom 10: 1.394017976603E-01 Surface tension*area energy for atom 11: 1.416609307015E-01 Surface tension*area energy for atom 12: 1.461349000577E-01 Surface tension*area energy for atom 13: 2.081792842383E-02 Surface tension*area energy for atom 14: 1.464892738680E-01 Surface tension*area energy for atom 15: 1.393575009340E-01 Surface tension*area energy for atom 16: 1.413951503437E-01 Total surface tension energy: 1.79141 kJ/mol Total solvent accessible volume: 251.127 A^3 Total pressure*volume energy: 60.1198 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.011082520236E+00 WCA energy for atom 1: -1.497367782613E+00 WCA energy for atom 2: -1.498546483218E+00 WCA energy for atom 3: -1.492562171495E+00 WCA energy for atom 4: -5.447325863939E+00 WCA energy for atom 5: -6.004516149175E+00 WCA energy for atom 6: -1.492776531092E+00 WCA energy for atom 7: -1.496078170066E+00 WCA energy for atom 8: -1.501529655270E+00 WCA energy for atom 9: -5.996267554365E+00 WCA energy for atom 10: -1.492194267752E+00 WCA energy for atom 11: -1.496027211216E+00 WCA energy for atom 12: -1.500561393960E+00 WCA energy for atom 13: -6.000218612907E+00 WCA energy for atom 14: -1.500859921426E+00 WCA energy for atom 15: -1.492908499790E+00 WCA energy for atom 16: -1.494057174414E+00 Total WCA energy: -47.4149 kJ/mol Total non-polar energy = 1.449633815052E+01 kJ/mol ---------------------------------------- CALCULATION #10 (solvated-pentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 7.466975761774E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.685881289113E+01 SASA for atom 12: 1.687444702982E+01 SASA for atom 13: 4.196440378117E+00 SASA for atom 14: 1.881308022781E+01 SASA for atom 15: 1.882350298694E+01 SASA for atom 16: 2.182004623652E+01 Total solvent accessible surface area: 222.524 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 6.346929397508E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.432999095746E-01 Surface tension*area energy for atom 12: 1.434327997535E-01 Surface tension*area energy for atom 13: 3.566974321399E-02 Surface tension*area energy for atom 14: 1.599111819364E-01 Surface tension*area energy for atom 15: 1.599997753890E-01 Surface tension*area energy for atom 16: 1.854703930104E-01 Total surface tension energy: 1.89145 kJ/mol Total solvent accessible volume: 258.93 A^3 Total pressure*volume energy: 61.9878 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.655804319869E+00 WCA energy for atom 1: -6.027315962813E+00 WCA energy for atom 2: -5.696430965386E+00 WCA energy for atom 3: -6.016749084714E+00 WCA energy for atom 4: -1.608595384643E+00 WCA energy for atom 5: -1.703300955380E+00 WCA energy for atom 6: -1.609931495887E+00 WCA energy for atom 7: -1.457107525189E+00 WCA energy for atom 8: -1.457741620594E+00 WCA energy for atom 9: -1.354235498709E+00 WCA energy for atom 10: -1.354106470090E+00 WCA energy for atom 11: -1.456736412636E+00 WCA energy for atom 12: -1.455995435596E+00 WCA energy for atom 13: -6.633650611186E+00 WCA energy for atom 14: -1.605996088477E+00 WCA energy for atom 15: -1.606549890103E+00 WCA energy for atom 16: -1.700042300035E+00 Total WCA energy: -49.4003 kJ/mol Total non-polar energy = 1.447900211546E+01 kJ/mol ---------------------------------------- CALCULATION #11 (solvated-propane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.173464698754E+00 SASA for atom 1: 1.931858404557E+01 SASA for atom 2: 2.014198201675E+01 SASA for atom 3: 2.149694070352E+01 SASA for atom 4: 1.904078819252E+00 SASA for atom 5: 2.067354273233E+01 SASA for atom 6: 1.937590922077E+01 SASA for atom 7: 3.098794941136E+00 SASA for atom 8: 1.942802301642E+01 SASA for atom 9: 1.973028303116E+01 SASA for atom 10: 2.204934693736E+01 Total solvent accessible surface area: 170.391 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.697444993941E-02 Surface tension*area energy for atom 1: 1.642079643873E-01 Surface tension*area energy for atom 2: 1.712068471424E-01 Surface tension*area energy for atom 3: 1.827239959799E-01 Surface tension*area energy for atom 4: 1.618466996365E-02 Surface tension*area energy for atom 5: 1.757251132248E-01 Surface tension*area energy for atom 6: 1.646952283766E-01 Surface tension*area energy for atom 7: 2.633975699966E-02 Surface tension*area energy for atom 8: 1.651381956396E-01 Surface tension*area energy for atom 9: 1.677074057649E-01 Surface tension*area energy for atom 10: 1.874194489675E-01 Total surface tension energy: 1.44832 kJ/mol Total solvent accessible volume: 183.573 A^3 Total pressure*volume energy: 43.9474 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.818670105515E+00 WCA energy for atom 1: -1.641297645338E+00 WCA energy for atom 2: -1.649584120441E+00 WCA energy for atom 3: -1.711408141255E+00 WCA energy for atom 4: -6.624720142882E+00 WCA energy for atom 5: -1.610117050515E+00 WCA energy for atom 6: -1.596858009746E+00 WCA energy for atom 7: -6.816460624835E+00 WCA energy for atom 8: -1.642782751806E+00 WCA energy for atom 9: -1.645779566650E+00 WCA energy for atom 10: -1.714436154542E+00 Total WCA energy: -33.4721 kJ/mol Total non-polar energy = 1.192358496286E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print APOL energy 1 (solvated-2-methylbutane) end Global net APOL energy = 1.439739455792E+01 kJ/mol print APOL energy 2 (solvated-butane) end Global net APOL energy = 1.208346456826E+01 kJ/mol print APOL energy 3 (solvated-cyclohexane) end Global net APOL energy = 1.354016672221E+01 kJ/mol print APOL energy 4 (solvated-cyclopentane) end Global net APOL energy = 9.363673200142E+00 kJ/mol print APOL energy 5 (solvated-ethane) end Global net APOL energy = 9.422717598546E+00 kJ/mol print APOL energy 6 (solvated-hexane) end Global net APOL energy = 1.640068943201E+01 kJ/mol print APOL energy 7 (solvated-isobutane) end Global net APOL energy = 1.323144287435E+01 kJ/mol print APOL energy 8 (solvated-methane) end Global net APOL energy = 7.894367190329E+00 kJ/mol print APOL energy 9 (solvated-neopentane) end Global net APOL energy = 1.449633815052E+01 kJ/mol print APOL energy 10 (solvated-pentane) end Global net APOL energy = 1.447900211546E+01 kJ/mol print APOL energy 11 (solvated-propane) end Global net APOL energy = 1.192358496286E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 11 molecules Final memory usage: 0.001 MB total, 2.204 MB high water Thanks for using APBS! Testing computed result against expected result (1.439739455792e+01, 1.439739455792e+01) *** PASSED *** Testing computed result against expected result (1.208346456826e+01, 1.208346456826e+01) *** PASSED *** Testing computed result against expected result (1.354016672221e+01, 1.354016672221e+01) *** PASSED *** Testing computed result against expected result (9.363673200142e+00, 9.363673200142e+00) *** PASSED *** Testing computed result against expected result (9.422717598546e+00, 9.422717598546e+00) *** PASSED *** Testing computed result against expected result (1.640068943201e+01, 1.640068943201e+01) *** PASSED *** Testing computed result against expected result (1.323144287435e+01, 1.323144287435e+01) *** PASSED *** Testing computed result against expected result (7.894367190329e+00, 7.894367190329e+00) *** PASSED *** Testing computed result against expected result (1.449633815052e+01, 1.449633815052e+01) *** PASSED *** Testing computed result against expected result (1.447900211546e+01, 1.447900211546e+01) *** PASSED *** Testing computed result against expected result (1.192358496286e+01, 1.192358496286e+01) *** PASSED *** Elapsed time: 13.007023 seconds -------------------------------------------------------------------------------- Total elapsed time: 13.007023 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-mol.in Checking for intermediate energies in input file alkanes.out EXPECTED COMPUTED: 11 EXPECTED EXPECTED: 11 COMPUTED: [14.39739455792, 12.08346456826, 13.54016672221, 9.363673200142, 9.422717598546, 16.40068943201, 13.23144287435, 7.894367190329, 14.49633815052, 14.47900211546, 11.92358496286] EXPECTED: ['1.439739455792E+01', '1.208346456826E+01', '1.354016672221E+01', '9.363673200142E+00', '9.422717598546E+00', '1.640068943201E+01', '1.323144287435E+01', '7.894367190329E+00', '1.449633815052E+01', '1.447900211546E+01', '1.192358496286E+01'] COMPUTED RESULT 14.39739455792 COMPUTED RESULT 12.08346456826 COMPUTED RESULT 13.54016672221 COMPUTED RESULT 9.363673200142 COMPUTED RESULT 9.422717598546 COMPUTED RESULT 16.40068943201 COMPUTED RESULT 13.23144287435 COMPUTED RESULT 7.894367190329 COMPUTED RESULT 14.49633815052 COMPUTED RESULT 14.47900211546 COMPUTED RESULT 11.92358496286 Running tests for FKBP section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: 1d7h-dmso-mol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', '1d7h-dmso-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file 1d7h-dmso-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 102.625 MB total, 102.625 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.060899690259E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 102.625 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.276523673491E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 102.625 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 102.625 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.396 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.961107503213E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.396 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.121048606059E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.396 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.396 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 102.404 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.058410584089E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 102.404 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.205385249581E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 102.404 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 102.404 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.335429017008E+03 kJ/mol Global net ELEC energy = -3.335429017008E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.180527370616E+01 kJ/mol Global net ELEC energy = -2.180527370616E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.328631844166E+03 kJ/mol Global net ELEC energy = -3.328631844166E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.500810086371E+01 kJ/mol Global net ELEC energy = 1.500810086371E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 182.834 MB high water Thanks for using APBS! Testing computed result against expected result (1.060899690259e+04, 1.060899690259e+04) *** PASSED *** Testing computed result against expected result (4.276523673491e+04, 4.276523673491e+04) *** PASSED *** Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) *** PASSED *** Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) *** PASSED *** Testing computed result against expected result (3.961107503213e+01, 3.961107503213e+01) *** PASSED *** Testing computed result against expected result (7.121048606059e+02, 7.121048606059e+02) *** PASSED *** Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) *** PASSED *** Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) *** PASSED *** Testing computed result against expected result (1.058410584089e+04, 1.058410584089e+04) *** PASSED *** Testing computed result against expected result (4.205385249581e+04, 4.205385249581e+04) *** PASSED *** Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) *** PASSED *** Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) *** PASSED *** Testing computed result against expected result (1.500810086371e+01, 1.500810086371e+01) *** PASSED *** Elapsed time: 12.896824 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-smol.in Checking for intermediate energies in input file 1d7h-dmso-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [10608.99690259, 42765.23673491, 13992.34956777, 46100.66575192, 39.61107503213, 712.1048606059, 67.51571424823, 733.9101343121, 10584.10584089, 42053.85249581, 13959.61902233, 45382.48433997, -3335.429017008, -21.80527370616, -3328.631844166, 15.00810086371] EXPECTED: ['1.060899690259E+04', '4.276523673491E+04', '1.399234956777E+04', '4.610066575192E+04', '3.961107503213E+01', '7.121048606059E+02', '6.751571424823E+01', '7.339101343121E+02', '1.058410584089E+04', '4.205385249581E+04', '1.395961902233E+04', '4.538248433997E+04', '*', '*', '*', '1.500810086371E+01'] COMPUTED RESULT 10608.99690259 COMPUTED RESULT 42765.23673491 COMPUTED RESULT 13992.34956777 COMPUTED RESULT 46100.66575192 COMPUTED RESULT 39.61107503213 COMPUTED RESULT 712.1048606059 COMPUTED RESULT 67.51571424823 COMPUTED RESULT 733.9101343121 COMPUTED RESULT 10584.10584089 COMPUTED RESULT 42053.85249581 COMPUTED RESULT 13959.61902233 COMPUTED RESULT 45382.48433997 COMPUTED RESULT -3335.429017008 COMPUTED RESULT -21.80527370616 COMPUTED RESULT -3328.631844166 COMPUTED RESULT 15.00810086371 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: 1d7h-dmso-smol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', '1d7h-dmso-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file 1d7h-dmso-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 102.625 MB total, 102.625 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.074948704824E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 102.625 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.289487256481E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 102.625 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 102.625 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.396 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.719709905887E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.396 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.125747080979E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.396 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.396 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 102.404 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.071654753674E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 102.404 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.218178203716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 102.404 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 102.404 MB total, 182.834 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.205793187109E+03 kJ/mol Global net ELEC energy = -3.205793187109E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.133542621421E+01 kJ/mol Global net ELEC energy = -2.133542621421E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.200702302816E+03 kJ/mol Global net ELEC energy = -3.200702302816E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.624454192073E+01 kJ/mol Global net ELEC energy = 1.624454192073E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 182.834 MB high water Thanks for using APBS! Testing computed result against expected result (1.074948704824e+04, 1.074948704824e+04) *** PASSED *** Testing computed result against expected result (4.289487256481e+04, 4.289487256481e+04) *** PASSED *** Testing computed result against expected result (1.399234956777e+04, 1.399234956777e+04) *** PASSED *** Testing computed result against expected result (4.610066575192e+04, 4.610066575192e+04) *** PASSED *** Testing computed result against expected result (3.719709905887e+01, 3.719709905887e+01) *** PASSED *** Testing computed result against expected result (7.125747080979e+02, 7.125747080979e+02) *** PASSED *** Testing computed result against expected result (6.751571424823e+01, 6.751571424823e+01) *** PASSED *** Testing computed result against expected result (7.339101343121e+02, 7.339101343121e+02) *** PASSED *** Testing computed result against expected result (1.071654753674e+04, 1.071654753674e+04) *** PASSED *** Testing computed result against expected result (4.218178203716e+04, 4.218178203716e+04) *** PASSED *** Testing computed result against expected result (1.395961902233e+04, 1.395961902233e+04) *** PASSED *** Testing computed result against expected result (4.538248433997e+04, 4.538248433997e+04) *** PASSED *** Testing computed result against expected result (1.624454192073e+01, 1.624454192072e+01) *** PASSED *** Elapsed time: 11.457171 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-mol.in Checking for intermediate energies in input file 1d7h-dmso-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [10749.48704824, 42894.87256481, 13992.34956777, 46100.66575192, 37.19709905887, 712.5747080979, 67.51571424823, 733.9101343121, 10716.54753674, 42181.78203716, 13959.61902233, 45382.48433997, -3205.793187109, -21.33542621421, -3200.702302816, 16.24454192073] EXPECTED: ['1.074948704824E+04', '4.289487256481E+04', '1.399234956777E+04', '4.610066575192E+04', '3.719709905887E+01', '7.125747080979E+02', '6.751571424823E+01', '7.339101343121E+02', '1.071654753674E+04', '4.218178203716E+04', '1.395961902233E+04', '4.538248433997E+04', '*', '*', '*', '1.624454192072E+01'] COMPUTED RESULT 10749.48704824 COMPUTED RESULT 42894.87256481 COMPUTED RESULT 13992.34956777 COMPUTED RESULT 46100.66575192 COMPUTED RESULT 37.19709905887 COMPUTED RESULT 712.5747080979 COMPUTED RESULT 67.51571424823 COMPUTED RESULT 733.9101343121 COMPUTED RESULT 10716.54753674 COMPUTED RESULT 42181.78203716 COMPUTED RESULT 13959.61902233 COMPUTED RESULT 45382.48433997 COMPUTED RESULT -3205.793187109 COMPUTED RESULT -21.33542621421 COMPUTED RESULT -3200.702302816 COMPUTED RESULT 16.24454192073 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-mol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', '1d7i-dss-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file 1d7i-dss-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 102.869 MB total, 102.869 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.160578033846E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 102.869 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.955701871716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 102.869 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 102.869 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.482 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.431133325426E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.482 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677348113184E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.482 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.482 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 102.566 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.040108332204E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 102.566 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.787747796627E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 102.566 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 102.566 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.460997931137E+03 kJ/mol Global net ELEC energy = -3.460997931137E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.052167100108E+01 kJ/mol Global net ELEC energy = -2.052167100108E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -3.454901259473E+03 kJ/mol Global net ELEC energy = -3.454901259473E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.442499933668E+01 kJ/mol Global net ELEC energy = 1.442499933668E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 183.200 MB high water Thanks for using APBS! Testing computed result against expected result (9.160578033846e+03, 9.160578033846e+03) *** PASSED *** Testing computed result against expected result (3.955701871716e+04, 3.955701871716e+04) *** PASSED *** Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) *** PASSED *** Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) *** PASSED *** Testing computed result against expected result (9.431133325426e+01, 9.431133325426e+01) *** PASSED *** Testing computed result against expected result (1.677348113184e+03, 1.677348113184e+03) *** PASSED *** Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) *** PASSED *** Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) *** PASSED *** Testing computed result against expected result (9.040108332204e+03, 9.040108332204e+03) *** PASSED *** Testing computed result against expected result (3.787747796627e+04, 3.787747796627e+04) *** PASSED *** Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) *** PASSED *** Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) *** PASSED *** Testing computed result against expected result (1.442499933668e+01, 1.442500529301e+01) *** PASSED *** Elapsed time: 13.679568 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-smol.in Checking for intermediate energies in input file 1d7i-dss-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [9160.578033846, 39557.01871716, 12649.65939588, 43018.01664829, 94.31133325426, 1677.348113184, 117.1079106781, 1697.869784185, 9040.108332204, 37877.47796627, 12524.95566243, 41332.37922574, -3460.997931137, -20.52167100108, -3454.901259473, 14.42499933668] EXPECTED: ['9.160578033846E+03', '3.955701871716E+04', '1.264965939588E+04', '4.301801664829E+04', '9.431133325426E+01', '1.677348113184E+03', '1.171079106781E+02', '1.697869784185E+03', '9.040108332204E+03', '3.787747796627E+04', '1.252495566243E+04', '4.133237922574E+04', '*', '*', '*', '1.442500529301E+01'] COMPUTED RESULT 9160.578033846 COMPUTED RESULT 39557.01871716 COMPUTED RESULT 12649.65939588 COMPUTED RESULT 43018.01664829 COMPUTED RESULT 94.31133325426 COMPUTED RESULT 1677.348113184 COMPUTED RESULT 117.1079106781 COMPUTED RESULT 1697.869784185 COMPUTED RESULT 9040.108332204 COMPUTED RESULT 37877.47796627 COMPUTED RESULT 12524.95566243 COMPUTED RESULT 41332.37922574 COMPUTED RESULT -3460.997931137 COMPUTED RESULT -20.52167100108 COMPUTED RESULT -3454.901259473 COMPUTED RESULT 14.42499933668 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: 1d7i-dss-smol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', '1d7i-dss-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file 1d7i-dss-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 102.869 MB total, 102.869 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.634884642408E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 102.869 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.003177540425E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 102.869 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 102.869 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.482 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.942232645345E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.482 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677798535473E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.482 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.482 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 102.566 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.507068451372E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 102.566 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.835075772299E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 102.566 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 102.566 MB total, 183.200 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -2.986241244040E+03 kJ/mol Global net ELEC energy = -2.986241244040E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.007124871262E+01 kJ/mol Global net ELEC energy = -2.007124871262E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -2.981621502756E+03 kJ/mol Global net ELEC energy = -2.981621502756E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.545150742844E+01 kJ/mol Global net ELEC energy = 1.545150742844E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 183.200 MB high water Thanks for using APBS! Testing computed result against expected result (9.634884642408e+03, 9.634884642408e+03) *** PASSED *** Testing computed result against expected result (4.003177540425e+04, 4.003177540425e+04) *** PASSED *** Testing computed result against expected result (1.264965939588e+04, 1.264965939588e+04) *** PASSED *** Testing computed result against expected result (4.301801664829e+04, 4.301801664829e+04) *** PASSED *** Testing computed result against expected result (7.942232645345e+01, 7.942232645345e+01) *** PASSED *** Testing computed result against expected result (1.677798535473e+03, 1.677798535473e+03) *** PASSED *** Testing computed result against expected result (1.171079106781e+02, 1.171079106781e+02) *** PASSED *** Testing computed result against expected result (1.697869784185e+03, 1.697869784185e+03) *** PASSED *** Testing computed result against expected result (9.507068451372e+03, 9.507068451372e+03) *** PASSED *** Testing computed result against expected result (3.835075772299e+04, 3.835075772299e+04) *** PASSED *** Testing computed result against expected result (1.252495566243e+04, 1.252495566243e+04) *** PASSED *** Testing computed result against expected result (4.133237922574e+04, 4.133237922574e+04) *** PASSED *** Testing computed result against expected result (1.545150742844e+01, 1.545150009785e+01) *** PASSED *** Elapsed time: 11.229069 seconds -------------------------------------------------------------------------------- Total elapsed time: 49.262631999999996 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file 1d7i-dss-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [9634.884642408, 40031.77540425, 12649.65939588, 43018.01664829, 79.42232645345, 1677.798535473, 117.1079106781, 1697.869784185, 9507.068451372, 38350.75772299, 12524.95566243, 41332.37922574, -2986.24124404, -20.07124871262, -2981.621502756, 15.45150742844] EXPECTED: ['9.634884642408E+03', '4.003177540425E+04', '1.264965939588E+04', '4.301801664829E+04', '7.942232645345E+01', '1.677798535473E+03', '1.171079106781E+02', '1.697869784185E+03', '9.507068451372E+03', '3.835075772299E+04', '1.252495566243E+04', '4.133237922574E+04', '*', '*', '*', '1.545150009785E+01'] COMPUTED RESULT 9634.884642408 COMPUTED RESULT 40031.77540425 COMPUTED RESULT 12649.65939588 COMPUTED RESULT 43018.01664829 COMPUTED RESULT 79.42232645345 COMPUTED RESULT 1677.798535473 COMPUTED RESULT 117.1079106781 COMPUTED RESULT 1697.869784185 COMPUTED RESULT 9507.068451372 COMPUTED RESULT 38350.75772299 COMPUTED RESULT 12524.95566243 COMPUTED RESULT 41332.37922574 COMPUTED RESULT -2986.24124404 COMPUTED RESULT -20.07124871262 COMPUTED RESULT -2981.621502756 COMPUTED RESULT 15.45150742844 Running tests for hca-bind section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.632 MB total, 62.632 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.213600726771E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.632 MB total, 123.513 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.825764811255E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.632 MB total, 123.513 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.458471211905E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 127.616 MB total, 127.616 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.093606095527E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 127.616 MB total, 207.303 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.515433544464E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 127.616 MB total, 207.303 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.786369323561E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 127.915 MB total, 207.303 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.105322784838E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 127.915 MB total, 207.713 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.533304996252E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 127.915 MB total, 207.713 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850429388099E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.246475812665E+01 kJ/mol Global net ELEC energy = -5.246475812665E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 207.713 MB high water Thanks for using APBS! Testing computed result against expected result (2.213600726771e+02, 2.213600726771e+02) *** PASSED *** Testing computed result against expected result (1.825764811255e+03, 1.825764811255e+03) *** PASSED *** Testing computed result against expected result (6.458471211905e+03, 6.458471211905e+03) *** PASSED *** Testing computed result against expected result (2.093606095527e+04, 2.093606095527e+04) *** PASSED *** Testing computed result against expected result (1.515433544464e+05, 1.515433544464e+05) *** PASSED *** Testing computed result against expected result (1.786369323561e+05, 1.786369323561e+05) *** PASSED *** Testing computed result against expected result (2.105322784838e+04, 2.105322784838e+04) *** PASSED *** Testing computed result against expected result (1.533304996252e+05, 1.533304996252e+05) *** PASSED *** Testing computed result against expected result (1.850429388099e+05, 1.850429388099e+05) *** PASSED *** Testing computed result against expected result (-5.246475812665e+01, -5.246475812665e+01) *** PASSED *** Elapsed time: 12.033843 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 10 EXPECTED EXPECTED: 10 COMPUTED: [221.3600726771, 1825.764811255, 6458.471211905, 20936.06095527, 151543.3544464, 178636.9323561, 21053.22784838, 153330.4996252, 185042.9388099, -52.46475812665] EXPECTED: ['2.213600726771E+02', '1.825764811255E+03', '6.458471211905E+03', '2.093606095527E+04', '1.515433544464E+05', '1.786369323561E+05', '2.105322784838E+04', '1.533304996252E+05', '1.850429388099E+05', '-5.246475812665E+01'] COMPUTED RESULT 221.3600726771 COMPUTED RESULT 1825.764811255 COMPUTED RESULT 6458.471211905 COMPUTED RESULT 20936.06095527 COMPUTED RESULT 151543.3544464 COMPUTED RESULT 178636.9323561 COMPUTED RESULT 21053.22784838 COMPUTED RESULT 153330.4996252 COMPUTED RESULT 185042.9388099 COMPUTED RESULT -52.46475812665 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.632 MB total, 62.632 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.884888131017E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.632 MB total, 123.513 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.820045922544E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.632 MB total, 123.513 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.460002606908E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 127.616 MB total, 127.616 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.189161497021E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 127.616 MB total, 207.303 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.520000494925E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 127.616 MB total, 207.303 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.790436191580E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 127.915 MB total, 207.303 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.195842512312E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 127.915 MB total, 207.713 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.537771604355E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 127.915 MB total, 207.713 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.854495619747E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.405979017066E+01 kJ/mol Global net ELEC energy = -5.405979017066E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 207.713 MB high water Thanks for using APBS! Testing computed result against expected result (1.884888131017e+02, 1.884888131017e+02) *** PASSED *** Testing computed result against expected result (1.820045922544e+03, 1.820045922544e+03) *** PASSED *** Testing computed result against expected result (6.460002606908e+03, 6.460002606908e+03) *** PASSED *** Testing computed result against expected result (2.189161497021e+04, 2.189161497021e+04) *** PASSED *** Testing computed result against expected result (1.520000494925e+05, 1.520000494925e+05) *** PASSED *** Testing computed result against expected result (1.790436191580e+05, 1.790436191580e+05) *** PASSED *** Testing computed result against expected result (2.195842512312e+04, 2.195842512312e+04) *** PASSED *** Testing computed result against expected result (1.537771604355e+05, 1.537771604355e+05) *** PASSED *** Testing computed result against expected result (1.854495619747e+05, 1.854495619747e+05) *** PASSED *** Testing computed result against expected result (-5.405979017066e+01, -5.405977880082e+01) *** PASSED *** Elapsed time: 9.635587 seconds -------------------------------------------------------------------------------- Total elapsed time: 21.66943 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 10 EXPECTED EXPECTED: 10 COMPUTED: [188.4888131017, 1820.045922544, 6460.002606908, 21891.61497021, 152000.0494925, 179043.619158, 21958.42512312, 153777.1604355, 185449.5619747, -54.05979017066] EXPECTED: ['1.884888131017E+02', '1.820045922544E+03', '6.460002606908E+03', '2.189161497021E+04', '1.520000494925E+05', '1.790436191580E+05', '2.195842512312E+04', '1.537771604355E+05', '1.854495619747E+05', '-5.405977880082E+01'] COMPUTED RESULT 188.4888131017 COMPUTED RESULT 1820.045922544 COMPUTED RESULT 6460.002606908 COMPUTED RESULT 21891.61497021 COMPUTED RESULT 152000.0494925 COMPUTED RESULT 179043.619158 COMPUTED RESULT 21958.42512312 COMPUTED RESULT 153777.1604355 COMPUTED RESULT 185449.5619747 COMPUTED RESULT -54.05979017066 Running tests for ionize section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acetic-acid.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading PQR-format atom data from acetate.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading PQR-format atom data from proton.pqr. 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.581 MB total, 61.581 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.823898055191E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.581 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793274462353E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.405 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.405 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.581 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.219846763777E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.581 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392741988698E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.405 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.405 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.410 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.862359524598E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.410 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.288156251610E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.371 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.371 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.267882018629E+01 kJ/mol Global net ELEC energy = -2.267882018629E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.997462636633E+02 kJ/mol Global net ELEC energy = -1.997462636633E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.974598403628E+02 kJ/mol Global net ELEC energy = -2.974598403628E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.745272838398E+02 kJ/mol Global net ELEC energy = -4.745272838398E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.371 MB high water Thanks for using APBS! Testing computed result against expected result (5.823898055191e+03, 5.823898055191e+03) *** PASSED *** Testing computed result against expected result (9.793274462353e+03, 9.793274462353e+03) *** PASSED *** Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) *** PASSED *** Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) *** PASSED *** Testing computed result against expected result (8.219846763777e+03, 8.219846763777e+03) *** PASSED *** Testing computed result against expected result (1.392741988698e+04, 1.392741988698e+04) *** PASSED *** Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) *** PASSED *** Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) *** PASSED *** Testing computed result against expected result (3.862359524598e+03, 3.862359524598e+03) *** PASSED *** Testing computed result against expected result (6.288156251610e+03, 6.288156251610e+03) *** PASSED *** Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) *** PASSED *** Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) *** PASSED *** Testing computed result against expected result (-2.267882018629e+01, -2.267881997628e+01) *** PASSED *** Testing computed result against expected result (-1.997462636633e+02, -1.997462580204e+02) *** PASSED *** Testing computed result against expected result (-2.974598403628e+02, -2.974598331751e+02) *** PASSED *** Testing computed result against expected result (-4.745272838398e+02, -4.745272868358e+02) *** PASSED *** Elapsed time: 6.292585 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [5823.898055191, 9793.274462353, 5846.917564309, 9815.953282539, 8219.846763777, 13927.41988698, 8420.373979905, 14127.16615065, 3862.359524598, 6288.15625161, 4162.533113906, 6585.616091973, -22.67882018629, -199.7462636633, -297.4598403628, -474.5272838398] EXPECTED: ['5.823898055191E+03', '9.793274462353E+03', '5.846917564309E+03', '9.815953282539E+03', '8.219846763777E+03', '1.392741988698E+04', '8.420373979905E+03', '1.412716615065E+04', '3.862359524598E+03', '6.288156251610E+03', '4.162533113906E+03', '6.585616091973E+03', '-2.267881997628E+01', '-1.997462580204E+02', '-2.974598331751E+02', '-4.745272868358E+02'] COMPUTED RESULT 5823.898055191 COMPUTED RESULT 9793.274462353 COMPUTED RESULT 5846.917564309 COMPUTED RESULT 9815.953282539 COMPUTED RESULT 8219.846763777 COMPUTED RESULT 13927.41988698 COMPUTED RESULT 8420.373979905 COMPUTED RESULT 14127.16615065 COMPUTED RESULT 3862.359524598 COMPUTED RESULT 6288.15625161 COMPUTED RESULT 4162.533113906 COMPUTED RESULT 6585.616091973 COMPUTED RESULT -22.67882018629 COMPUTED RESULT -199.7462636633 COMPUTED RESULT -297.4598403628 COMPUTED RESULT -474.5272838398 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acetic-acid.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading PQR-format atom data from acetate.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading PQR-format atom data from proton.pqr. 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.581 MB total, 61.581 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.824172730822E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.581 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793622759239E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.405 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.405 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.581 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.221328580569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.581 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392867783119E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.405 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.405 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.410 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.863066835285E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.410 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.289649216644E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.371 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.371 MB total, 122.371 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.233052329981E+01 kJ/mol Global net ELEC energy = -2.233052329981E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.984883194538E+02 kJ/mol Global net ELEC energy = -1.984883194538E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.959668753288E+02 kJ/mol Global net ELEC energy = -2.959668753288E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.721246714828E+02 kJ/mol Global net ELEC energy = -4.721246714828E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.371 MB high water Thanks for using APBS! Testing computed result against expected result (5.824172730822e+03, 5.824172730822e+03) *** PASSED *** Testing computed result against expected result (9.793622759239e+03, 9.793622759239e+03) *** PASSED *** Testing computed result against expected result (5.846917564309e+03, 5.846917564309e+03) *** PASSED *** Testing computed result against expected result (9.815953282539e+03, 9.815953282539e+03) *** PASSED *** Testing computed result against expected result (8.221328580569e+03, 8.221328580569e+03) *** PASSED *** Testing computed result against expected result (1.392867783119e+04, 1.392867783119e+04) *** PASSED *** Testing computed result against expected result (8.420373979905e+03, 8.420373979905e+03) *** PASSED *** Testing computed result against expected result (1.412716615065e+04, 1.412716615065e+04) *** PASSED *** Testing computed result against expected result (3.863066835285e+03, 3.863066835285e+03) *** PASSED *** Testing computed result against expected result (6.289649216644e+03, 6.289649216644e+03) *** PASSED *** Testing computed result against expected result (4.162533113906e+03, 4.162533113906e+03) *** PASSED *** Testing computed result against expected result (6.585616091973e+03, 6.585616091973e+03) *** PASSED *** Testing computed result against expected result (-2.233052329981e+01, -2.233050451129e+01) *** PASSED *** Testing computed result against expected result (-1.984883194538e+02, -1.984883191396e+02) *** PASSED *** Testing computed result against expected result (-2.959668753288e+02, -2.959668653531e+02) *** PASSED *** Testing computed result against expected result (-4.721246714828e+02, -4.721247084138e+02) *** PASSED *** Elapsed time: 5.093847 seconds -------------------------------------------------------------------------------- Total elapsed time: 11.386432 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file ion-pmf.in Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 16 EXPECTED EXPECTED: 16 COMPUTED: [5824.172730822, 9793.622759239, 5846.917564309, 9815.953282539, 8221.328580569, 13928.67783119, 8420.373979905, 14127.16615065, 3863.066835285, 6289.649216644, 4162.533113906, 6585.616091973, -22.33052329981, -198.4883194538, -295.9668753288, -472.1246714828] EXPECTED: ['5.824172730822E+03', '9.793622759239E+03', '5.846917564309E+03', '9.815953282539E+03', '8.221328580569E+03', '1.392867783119E+04', '8.420373979905E+03', '1.412716615065E+04', '3.863066835285E+03', '6.289649216644E+03', '4.162533113906E+03', '6.585616091973E+03', '-2.233050451129E+01', '-1.984883191396E+02', '-2.959668653531E+02', '-4.721247084138E+02'] COMPUTED RESULT 5824.172730822 COMPUTED RESULT 9793.622759239 COMPUTED RESULT 5846.917564309 COMPUTED RESULT 9815.953282539 COMPUTED RESULT 8221.328580569 COMPUTED RESULT 13928.67783119 COMPUTED RESULT 8420.373979905 COMPUTED RESULT 14127.16615065 COMPUTED RESULT 3863.066835285 COMPUTED RESULT 6289.649216644 COMPUTED RESULT 4162.533113906 COMPUTED RESULT 6585.616091973 COMPUTED RESULT -22.33052329981 COMPUTED RESULT -198.4883194538 COMPUTED RESULT -295.9668753288 COMPUTED RESULT -472.1246714828 Running tests for ion-pmf section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: ion-pmf.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'ion-pmf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file ion-pmf.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 1 molecules Reading PDB-format atom data from ion-pmf.pdb. Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.094 MB total, 61.094 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 7.839535983197E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! ---------------------------------------- CALCULATION #2 (ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.095 MB total, 61.134 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 8.964727588811E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 0.000e+00 0.000e+00 0.000e+00 mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 0.000e+00 0.000e+00 0.000e+00 ---------------------------------------- CALCULATION #3 (asolv): APOLAR Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n gamma 0.000720 pressure 0.000000 bconc 0.033000 tot 0 2.715e-02 9.130e-07 9.130e-07 sasa 0 -1.100e+01 0.000e+00 0.000e+00 sav 0 0.000e+00 0.000e+00 0.000e+00 wca 0 -5.827e-01 -2.767e-05 -2.767e-05 tot 1 -2.723e-02 9.133e-07 9.133e-07 sasa 1 1.112e+01 0.000e+00 0.000e+00 sav 1 0.000e+00 0.000e+00 0.000e+00 wca 1 5.827e-01 -2.767e-05 -2.767e-05 Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.153275282828E+02 SASA for atom 1: 1.153114143344E+02 Total solvent accessible surface area: 230.639 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.303582036361E-02 Surface tension*area energy for atom 1: 8.302421832080E-02 Total surface tension energy: 0.16606 kJ/mol Total solvent accessible volume: 0 A^3 Total pressure*volume energy: 0 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.909718359932E+00 WCA energy for atom 1: -6.909422551724E+00 Total WCA energy: -13.8191 kJ/mol Total non-polar energy = -1.365308087297E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print energy 1 (solv) - 2 (ref) end Local net energy (PE 0) = -1.125191605614E+03 kJ/mol Global net ELEC energy = -1.125191605614E+03 kJ/mol print force 1 (solv) - 2 (ref) end Printing per-atom forces (kJ/mol/A). Legend: tot n -- Total force for atom n qf n -- Fixed charge force for atom n db n -- Dielectric boundary force for atom n ib n -- Ionic boundary force for atom n tot all -- Total force for system qf 0 8.398642197666E+01 -1.324564548552E-05 -1.613435632529E-05 ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 0 6.148357059184E+00 -2.667517425897E-05 -5.378919678211E-05 tot 0 9.013477903584E+01 -3.992081974449E-05 -6.992355310740E-05 qf 1 -8.466423642736E+01 -1.836748045969E-05 -3.062224428458E-05 ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 1 2.882739230548E+00 -3.149946357588E-05 -6.291495506459E-05 tot 1 -8.178149719681E+01 -4.986694403557E-05 -9.353719934917E-05 tot all 8.353281839029E+00 -8.978776378007E-05 -1.634607524566E-04 print APOL energy 1 (asolv) end Global net APOL energy = -1.365308087297E+01 kJ/mol print APOL force 1 (asolv) end Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n tot all -- Total force for system sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 0 -5.826577086437E-01 -2.766670515801E-05 -2.766670515838E-05 tot 0 -1.158042745197E+01 -2.766670515801E-05 -2.766670515838E-05 sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 1 5.826560767576E-01 -2.767485007141E-05 -2.767485007183E-05 tot 1 1.170128043265E+01 -2.767485007141E-05 -2.767485007183E-05 tot all 1.208529806779E-01 -5.534155522943E-05 -5.534155523021E-05 ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 1 molecules Final memory usage: 60.711 MB total, 62.228 MB high water Thanks for using APBS! Testing computed result against expected result (7.839535983197e+03, 7.839535983197e+03) *** PASSED *** Testing computed result against expected result (8.964727588811e+03, 8.964727588811e+03) *** PASSED *** Testing computed result against expected result (-1.125191605614e+03, -1.125192402906e+03) *** PASSED *** Elapsed time: 8.113223 seconds -------------------------------------------------------------------------------- Total elapsed time: 8.113223 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-vdw.in Checking for intermediate energies in input file ion-pmf.out EXPECTED COMPUTED: 4 EXPECTED EXPECTED: 4 COMPUTED: [7839.535983197, 8964.727588811, -1125.191605614, -13.65308087297] EXPECTED: ['7.839535983197E+03', '8.964727588811E+03', '-1.125192402906E+03', '*'] COMPUTED RESULT 7839.535983197 COMPUTED RESULT 8964.727588811 COMPUTED RESULT -1125.191605614 COMPUTED RESULT -13.65308087297 Running tests for pka-lig section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol-vdw.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol-vdw.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.811 MB total, 203.811 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.224988750664E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.811 MB total, 405.040 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.049695084686E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 270.381 MB total, 405.040 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.818450789522E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 270.381 MB total, 491.899 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.008254338259E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 271.059 MB total, 491.899 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.840918409896E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 271.059 MB total, 492.811 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.113304681884E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 8.083515648730E+00 kJ/mol Global net ELEC energy = 8.083515648730E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 492.811 MB high water Thanks for using APBS! Testing computed result against expected result (2.224988750664e+03, 2.224988750664e+03) *** PASSED *** Testing computed result against expected result (1.049695084686e+04, 1.049695084686e+04) *** PASSED *** Testing computed result against expected result (1.818450789522e+05, 1.818450789522e+05) *** PASSED *** Testing computed result against expected result (3.008254338259e+05, 3.008254338259e+05) *** PASSED *** Testing computed result against expected result (1.840918409896e+05, 1.840918409896e+05) *** PASSED *** Testing computed result against expected result (3.113304681884e+05, 3.113304681884e+05) *** PASSED *** Testing computed result against expected result (8.083515648730e+00, 8.083515648730e+00) *** PASSED *** Elapsed time: 22.008779 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-vdw.in Checking for intermediate energies in input file apbs-mol-vdw.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2224.988750664, 10496.95084686, 181845.0789522, 300825.4338259, 184091.8409896, 311330.4681884, 8.08351564873] EXPECTED: ['2.224988750664E+03', '1.049695084686E+04', '1.818450789522E+05', '3.008254338259E+05', '1.840918409896E+05', '3.113304681884E+05', '8.083515648730E+00'] COMPUTED RESULT 2224.988750664 COMPUTED RESULT 10496.95084686 COMPUTED RESULT 181845.0789522 COMPUTED RESULT 300825.4338259 COMPUTED RESULT 184091.8409896 COMPUTED RESULT 311330.4681884 COMPUTED RESULT 8.08351564873 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-vdw.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-vdw.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.811 MB total, 203.811 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.226793167046E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.811 MB total, 405.040 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.050504485887E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 270.381 MB total, 405.040 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.827976621645E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 270.381 MB total, 491.899 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.017228546773E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 271.059 MB total, 491.899 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850819075387E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 271.059 MB total, 492.811 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.122488625388E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 2.096300255723E+01 kJ/mol Global net ELEC energy = 2.096300255723E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 492.811 MB high water Thanks for using APBS! Testing computed result against expected result (2.226793167046e+03, 2.226793167046e+03) *** PASSED *** Testing computed result against expected result (1.050504485887e+04, 1.050504485887e+04) *** PASSED *** Testing computed result against expected result (1.827976621645e+05, 1.827976621645e+05) *** PASSED *** Testing computed result against expected result (3.017228546773e+05, 3.017228546773e+05) *** PASSED *** Testing computed result against expected result (1.850819075387e+05, 1.850819075387e+05) *** PASSED *** Testing computed result against expected result (3.122488625388e+05, 3.122488625388e+05) *** PASSED *** Testing computed result against expected result (2.096300255723e+01, 2.096296139195e+01) *** PASSED *** Elapsed time: 16.142405 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-surf.in Checking for intermediate energies in input file apbs-smol-vdw.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2226.793167046, 10505.04485887, 182797.6621645, 301722.8546773, 185081.9075387, 312248.8625388, 20.96300255723] EXPECTED: ['2.226793167046E+03', '1.050504485887E+04', '1.827976621645E+05', '3.017228546773E+05', '1.850819075387E+05', '3.122488625388E+05', '2.096296139195E+01'] COMPUTED RESULT 2226.793167046 COMPUTED RESULT 10505.04485887 COMPUTED RESULT 182797.6621645 COMPUTED RESULT 301722.8546773 COMPUTED RESULT 185081.9075387 COMPUTED RESULT 312248.8625388 COMPUTED RESULT 20.96300255723 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol-surf.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol-surf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.396 MB total, 203.396 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.244350164274E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.396 MB total, 404.625 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052149475373E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 230.750 MB total, 404.625 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.862615690066E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 230.750 MB total, 452.268 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.051810884053E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 230.854 MB total, 452.268 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.886625455219E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 230.854 MB total, 452.606 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.158218439277E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.192607686581E+02 kJ/mol Global net ELEC energy = 1.192607686581E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 452.606 MB high water Thanks for using APBS! Testing computed result against expected result (2.244350164274e+03, 2.244350164274e+03) *** PASSED *** Testing computed result against expected result (1.052149475373e+04, 1.052149475373e+04) *** PASSED *** Testing computed result against expected result (1.862615690066e+05, 1.862615690066e+05) *** PASSED *** Testing computed result against expected result (3.051810884053e+05, 3.051810884053e+05) *** PASSED *** Testing computed result against expected result (1.886625455219e+05, 1.886625455219e+05) *** PASSED *** Testing computed result against expected result (3.158218439277e+05, 3.158218439277e+05) *** PASSED *** Testing computed result against expected result (1.192607686581e+02, 1.192608095265e+02) *** PASSED *** Elapsed time: 17.316264 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-surf.in Checking for intermediate energies in input file apbs-mol-surf.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2244.350164274, 10521.49475373, 186261.5690066, 305181.0884053, 188662.5455219, 315821.8439277, 119.2607686581] EXPECTED: ['2.244350164274E+03', '1.052149475373E+04', '1.862615690066E+05', '3.051810884053E+05', '1.886625455219E+05', '3.158218439277E+05', '1.192608095265E+02'] COMPUTED RESULT 2244.350164274 COMPUTED RESULT 10521.49475373 COMPUTED RESULT 186261.5690066 COMPUTED RESULT 305181.0884053 COMPUTED RESULT 188662.5455219 COMPUTED RESULT 315821.8439277 COMPUTED RESULT 119.2607686581 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol-surf.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol-surf.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.396 MB total, 203.396 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.251466789420E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.396 MB total, 404.625 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052814502873E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 230.750 MB total, 404.625 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.864071689626E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 230.750 MB total, 452.268 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.053319953673E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 230.854 MB total, 452.268 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.888027142979E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 230.854 MB total, 452.606 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.159690177241E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.088773280806E+02 kJ/mol Global net ELEC energy = 1.088773280806E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 452.606 MB high water Thanks for using APBS! Testing computed result against expected result (2.251466789420e+03, 2.251466789420e+03) *** PASSED *** Testing computed result against expected result (1.052814502873e+04, 1.052814502873e+04) *** PASSED *** Testing computed result against expected result (1.864071689626e+05, 1.864071689626e+05) *** PASSED *** Testing computed result against expected result (3.053319953673e+05, 3.053319953673e+05) *** PASSED *** Testing computed result against expected result (1.888027142979e+05, 1.888027142979e+05) *** PASSED *** Testing computed result against expected result (3.159690177241e+05, 3.159690177241e+05) *** PASSED *** Testing computed result against expected result (1.088773280806e+02, 1.088773280806e+02) *** PASSED *** Elapsed time: 14.269039 seconds -------------------------------------------------------------------------------- Total elapsed time: 69.736487 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_1.in Checking for intermediate energies in input file apbs-smol-surf.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [2251.46678942, 10528.14502873, 186407.1689626, 305331.9953673, 188802.7142979, 315969.0177241, 108.8773280806] EXPECTED: ['2.251466789420E+03', '1.052814502873E+04', '1.864071689626E+05', '3.053319953673E+05', '1.888027142979E+05', '3.159690177241E+05', '1.088773280806E+02'] COMPUTED RESULT 2251.46678942 COMPUTED RESULT 10528.14502873 COMPUTED RESULT 186407.1689626 COMPUTED RESULT 305331.9953673 COMPUTED RESULT 188802.7142979 COMPUTED RESULT 315969.0177241 COMPUTED RESULT 108.8773280806 Running tests for point-pmf section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: complex-0_1.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'complex-0_1.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file complex-0_1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol1.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_1.pqr. 2 atoms Centered at (-2.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.059 MB total, 61.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.059 MB total, 61.066 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.975920687031E+01 kJ/mol Fixed charge energy = 89.7592 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 88.6151 kJ/mol Per-atom energies: Atom 0: 8.975920687031E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.059 MB total, 61.066 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.058277719334E+02 kJ/mol Fixed charge energy = 205.828 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 201.106 kJ/mol Per-atom energies: Atom 0: 1.069144350786E+02 kJ/mol Atom 1: 9.891333685475E+01 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 1.830820799027E+01 kJ/mol Global net ELEC energy = 1.830820799027E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.066 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (8.975920687031e+01, 8.975920687031e+01) *** PASSED *** Testing computed result against expected result (2.058277719334e+02, 2.058277719334e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (8.975920000000e+01, 8.975920000000e+01) *** PASSED *** Testing computed result against expected result (2.058280000000e+02, 2.058280000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (8.861510000000e+01, 8.861510000000e+01) *** PASSED *** Testing computed result against expected result (2.011060000000e+02, 2.011060000000e+02) *** PASSED *** Testing computed result against expected result (1.830820799027e+01, 1.830820799027e+01) *** PASSED *** Elapsed time: 0.9519 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_2.in Checking for intermediate energies in input file complex-0_1.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 89.75920687031, 205.8277719334, 0.0, 0.0, 0.0, 97.7604, 89.7592, 205.828, 96.5336, 88.6151, 201.106, 18.30820799027] EXPECTED: ['9.776035707281E+01', '8.975920687031E+01', '2.058277719334E+02', '*', '*', '*', '97.7604', '89.7592', '205.828', '96.5336', '88.6151', '201.106', '1.830820799027E+01'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 89.75920687031 COMPUTED RESULT 205.8277719334 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 89.7592 COMPUTED RESULT 205.828 COMPUTED RESULT 96.5336 COMPUTED RESULT 88.6151 COMPUTED RESULT 201.106 COMPUTED RESULT 18.30820799027 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: complex-0_2.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'complex-0_2.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file complex-0_2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol2.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_2.pqr. 2 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.059 MB total, 61.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.059 MB total, 61.066 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.656 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.059 MB total, 61.066 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.084282010393E+02 kJ/mol Fixed charge energy = 208.428 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 203.83 kJ/mol Per-atom energies: Atom 0: 1.022136878480E+02 kJ/mol Atom 1: 1.062145131913E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 8.906694086750E+00 kJ/mol Global net ELEC energy = 8.906694086750E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.066 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) *** PASSED *** Testing computed result against expected result (2.084282010393e+02, 2.084282010393e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) *** PASSED *** Testing computed result against expected result (2.084280000000e+02, 2.084280000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.006560000000e+02, 1.006560000000e+02) *** PASSED *** Testing computed result against expected result (2.038300000000e+02, 2.038300000000e+02) *** PASSED *** Testing computed result against expected result (8.906694086750e+00, 8.906694086750e+00) *** PASSED *** Elapsed time: 0.97656 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_3.in Checking for intermediate energies in input file complex-0_2.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 101.7611498797, 208.4282010393, 0.0, 0.0, 0.0, 97.7604, 101.761, 208.428, 96.5336, 100.656, 203.83, 8.90669408675] EXPECTED: ['9.776035707281E+01', '1.017611498797E+02', '2.084282010393E+02', '*', '*', '*', '97.7604', '101.761', '208.428', '96.5336', '100.656', '203.83', '8.906694086750E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 101.7611498797 COMPUTED RESULT 208.4282010393 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 101.761 COMPUTED RESULT 208.428 COMPUTED RESULT 96.5336 COMPUTED RESULT 100.656 COMPUTED RESULT 203.83 COMPUTED RESULT 8.90669408675 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: complex-0_3.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'complex-0_3.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file complex-0_3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol3.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_3.pqr. 2 atoms Centered at (-1.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.059 MB total, 61.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.059 MB total, 61.066 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.337661883222E+02 kJ/mol Fixed charge energy = 133.766 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 132.672 kJ/mol Per-atom energies: Atom 0: 1.337661883222E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.059 MB total, 61.066 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.374361452120E+02 kJ/mol Fixed charge energy = 237.436 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 232.924 kJ/mol Per-atom energies: Atom 0: 1.007151570480E+02 kJ/mol Atom 1: 1.367209881640E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 5.909599816984E+00 kJ/mol Global net ELEC energy = 5.909599816984E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.066 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.337661883222e+02, 1.337661883222e+02) *** PASSED *** Testing computed result against expected result (2.374361452120e+02, 2.374361452120e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.337660000000e+02, 1.337660000000e+02) *** PASSED *** Testing computed result against expected result (2.374360000000e+02, 2.374360000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.326720000000e+02, 1.326720000000e+02) *** PASSED *** Testing computed result against expected result (2.329240000000e+02, 2.329240000000e+02) *** PASSED *** Testing computed result against expected result (5.909599816984e+00, 5.909599816984e+00) *** PASSED *** Elapsed time: 0.969195 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_4.in Checking for intermediate energies in input file complex-0_3.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 133.7661883222, 237.436145212, 0.0, 0.0, 0.0, 97.7604, 133.766, 237.436, 96.5336, 132.672, 232.924, 5.909599816984] EXPECTED: ['9.776035707281E+01', '1.337661883222E+02', '2.374361452120E+02', '*', '*', '*', '97.7604', '133.766', '237.436', '96.5336', '132.672', '232.924', '5.909599816984E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 133.7661883222 COMPUTED RESULT 237.436145212 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 133.766 COMPUTED RESULT 237.436 COMPUTED RESULT 96.5336 COMPUTED RESULT 132.672 COMPUTED RESULT 232.924 COMPUTED RESULT 5.909599816984 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: complex-0_4.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'complex-0_4.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file complex-0_4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol4.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_4.pqr. 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.059 MB total, 61.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.059 MB total, 61.066 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.654 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.059 MB total, 61.066 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.039516519000E+02 kJ/mol Fixed charge energy = 203.952 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 199.493 kJ/mol Per-atom energies: Atom 0: 9.997541697022E+01 kJ/mol Atom 1: 1.039762349297E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 4.430144947418E+00 kJ/mol Global net ELEC energy = 4.430144947418E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.066 MB high water Thanks for using APBS! Testing computed result against expected result (9.776035707281e+01, 9.776035707281e+01) *** PASSED *** Testing computed result against expected result (1.017611498797e+02, 1.017611498797e+02) *** PASSED *** Testing computed result against expected result (2.039516519000e+02, 2.039516519000e+02) *** PASSED *** Testing computed result against expected result (9.776040000000e+01, 9.776040000000e+01) *** PASSED *** Testing computed result against expected result (1.017610000000e+02, 1.017610000000e+02) *** PASSED *** Testing computed result against expected result (2.039520000000e+02, 2.039520000000e+02) *** PASSED *** Testing computed result against expected result (9.653360000000e+01, 9.653360000000e+01) *** PASSED *** Testing computed result against expected result (1.006540000000e+02, 1.006540000000e+02) *** PASSED *** Testing computed result against expected result (1.994930000000e+02, 1.994930000000e+02) *** PASSED *** Testing computed result against expected result (4.430144947418e+00, 4.430144947418e+00) *** PASSED *** Elapsed time: 0.920179 seconds -------------------------------------------------------------------------------- Total elapsed time: 3.817834 seconds Test results have been logged -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol.in Checking for intermediate energies in input file complex-0_4.out EXPECTED COMPUTED: 13 EXPECTED EXPECTED: 13 COMPUTED: [97.76035707281, 101.7611498797, 203.9516519, 0.0, 0.0, 0.0, 97.7604, 101.761, 203.952, 96.5336, 100.654, 199.493, 4.430144947418] EXPECTED: ['9.776035707281E+01', '1.017611498797E+02', '2.039516519000E+02', '*', '*', '*', '97.7604', '101.761', '203.952', '96.5336', '100.654', '199.493', '4.430144947418E+00'] COMPUTED RESULT 97.76035707281 COMPUTED RESULT 101.7611498797 COMPUTED RESULT 203.9516519 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 0.0 COMPUTED RESULT 97.7604 COMPUTED RESULT 101.761 COMPUTED RESULT 203.952 COMPUTED RESULT 96.5336 COMPUTED RESULT 100.654 COMPUTED RESULT 199.493 COMPUTED RESULT 4.430144947418 Running tests for solv section BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-mol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-mol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.247 MB total, 61.247 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847663548071E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.247 MB total, 61.316 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.883912182952E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.243 MB total, 61.316 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.732623683321E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.243 MB total, 61.316 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.123035854133E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.624863488074E+01 kJ/mol Global net ELEC energy = -3.624863488074E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.904121708125E+02 kJ/mol Global net ELEC energy = -3.904121708125E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.541635359318E+02 kJ/mol Global net ELEC energy = -3.541635359318E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.316 MB high water Thanks for using APBS! Testing computed result against expected result (1.847663548071e+03, 1.847663548071e+03) *** PASSED *** Testing computed result against expected result (1.883912182952e+03, 1.883912182952e+03) *** PASSED *** Testing computed result against expected result (2.732623683321e+03, 2.732623683321e+03) *** PASSED *** Testing computed result against expected result (3.123035854133e+03, 3.123035854133e+03) *** PASSED *** Testing computed result against expected result (-3.624863488074e+01, -3.624863445503e+01) *** PASSED *** Testing computed result against expected result (-3.904121708125e+02, -3.904121297757e+02) *** PASSED *** Testing computed result against expected result (-3.541635359318e+02, -3.541635359318e+02) *** PASSED *** Elapsed time: 1.554059 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in Checking for intermediate energies in input file apbs-mol.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [1847.663548071, 1883.912182952, 2732.623683321, 3123.035854133, -36.24863488074, -390.4121708125, -354.1635359318] EXPECTED: ['1.847663548071E+03', '1.883912182952E+03', '2.732623683321E+03', '3.123035854133E+03', '-3.624863445503E+01', '-3.904121297757E+02', '-3.541635359318E+02'] COMPUTED RESULT 1847.663548071 COMPUTED RESULT 1883.912182952 COMPUTED RESULT 2732.623683321 COMPUTED RESULT 3123.035854133 COMPUTED RESULT -36.24863488074 COMPUTED RESULT -390.4121708125 COMPUTED RESULT -354.1635359318 BINARY: /<>/debian/tmp/usr/bin/apbs INPUT: apbs-smol.in COMMAND: ['/<>/debian/tmp/usr/bin/apbs', 'apbs-smol.in'] asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version APBS 3.4.1 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jan 19 2024 at 18:56:34 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.247 MB total, 61.247 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847860440020E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.247 MB total, 61.316 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.885436377745E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.243 MB total, 61.316 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.734040568569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.243 MB total, 61.316 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.125279428954E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.757593772493E+01 kJ/mol Global net ELEC energy = -3.757593772493E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.912388603848E+02 kJ/mol Global net ELEC energy = -3.912388603848E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.536629226599E+02 kJ/mol Global net ELEC energy = -3.536629226599E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying finite element structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.316 MB high water Thanks for using APBS! Testing computed result against expected result (1.847860440020e+03, 1.847860440020e+03) *** PASSED *** Testing computed result against expected result (1.885436377745e+03, 1.885436377745e+03) *** PASSED *** Testing computed result against expected result (2.734040568569e+03, 2.734040568569e+03) *** PASSED *** Testing computed result against expected result (3.125279428954e+03, 3.125279428954e+03) *** PASSED *** Testing computed result against expected result (-3.757593772493e+01, -3.757593797629e+01) *** PASSED *** Testing computed result against expected result (-3.912388603848e+02, -3.912388198513e+02) *** PASSED *** Testing computed result against expected result (-3.536629226599e+02, -3.536628818750e+02) *** PASSED *** Elapsed time: 1.383057 seconds -------------------------------------------------------------------------------- Total elapsed time: 2.937116 seconds Test results have been logged -------------------------------------------------------------------------------- Checking for intermediate energies in input file apbs-smol.out EXPECTED COMPUTED: 7 EXPECTED EXPECTED: 7 COMPUTED: [1847.86044002, 1885.436377745, 2734.040568569, 3125.279428954, -37.57593772493, -391.2388603848, -353.6629226599] EXPECTED: ['1.847860440020E+03', '1.885436377745E+03', '2.734040568569E+03', '3.125279428954E+03', '-3.757593797629E+01', '-3.912388198513E+02', '-3.536628818750E+02'] COMPUTED RESULT 1847.86044002 COMPUTED RESULT 1885.436377745 COMPUTED RESULT 2734.040568569 COMPUTED RESULT 3125.279428954 COMPUTED RESULT -37.57593772493 COMPUTED RESULT -391.2388603848 COMPUTED RESULT -353.6629226599 make[1]: Leaving directory '/<>' dh_install -a -O--buildsystem=cmake dh_installdocs -a -O--buildsystem=cmake dh_sphinxdoc -a -O--buildsystem=cmake dh_sphinxdoc: warning: Sphinx documentation not found dh_installchangelogs -a -O--buildsystem=cmake dh_installman -a -O--buildsystem=cmake dh_python3 -a -O--buildsystem=cmake I: dh_python3 fs:431: renaming _apbslib.so to _apbslib.cpython-312-arm-linux-gnueabihf.so dh_installsystemduser -a -O--buildsystem=cmake dh_lintian -a -O--buildsystem=cmake dh_perl -a -O--buildsystem=cmake dh_link -a -O--buildsystem=cmake dh_strip_nondeterminism -a -O--buildsystem=cmake dh_compress -a -O--buildsystem=cmake dh_fixperms -a -O--buildsystem=cmake dh_missing -a -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dwz: debian/libapbs3/usr/lib/arm-linux-gnueabihf/libapbs_pmgc.so.3: DWARF compression not beneficial - old size 150035 new size 150726 dwz: debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libmc.so.1.9.3: DWARF compression not beneficial - old size 363459 new size 371217 dwz: debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libvf2c.so.1.9.3: DWARF compression not beneficial - old size 96259 new size 99093 dwz: debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libgamer.so.1.9.3: DWARF compression not beneficial - old size 829468 new size 831987 dwz: debian/python3-apbslib/usr/lib/python3/dist-packages/apbs.cpython-312-arm-linux-gnueabihf.so: DWARF compression not beneficial - old size 5863541 new size 5867466 dh_strip -a -O--buildsystem=cmake debugedit: debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd: Unknown DWARF DW_FORM_0x1f21 f38ac2b97fcb170085f6b37832086d3d6dc3eb66 b3d6650830c75286944542234dce7204b3e2d2e6 debugedit: debian/libapbs3/usr/lib/arm-linux-gnueabihf/libapbs_routines.so.3: Unknown DWARF DW_FORM_0x1f21 6d3b5be3e4f7dc4bfb2631c1f8d26f8739335977 debugedit: debian/apbs/usr/lib/apbs/tools/bin/born: Unknown DWARF DW_FORM_0x1f21 9fbb9d0cb3eebc8f45a40b7ae80dad4bde41ae65 debugedit: debian/libapbs3/usr/lib/arm-linux-gnueabihf/libapbs_generic.so.3: Unknown DWARF DW_FORM_0x1f21 9aa24832f3a1f23f62f87a1e3eb8520354a3319f 83d2f0937ed4e45c367b4a1d2d37a5379a208782 debugedit: debian/apbs/usr/lib/apbs/tools/bin/mergedx2: Unknown DWARF DW_FORM_0x1f20 60b118fef1b59cf9f54b920e2b6f161741b74e5c debugedit: debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin: Unknown DWARF DW_FORM_0x1f21 856e516c6b12cd026a12cc085f274c9e9982a9a1 debugedit: debian/libapbs3/usr/lib/arm-linux-gnueabihf/libapbs_mg.so.3: Unknown DWARF DW_FORM_0x1f21 385058407698821346254949cd72d2adf455d753 debugedit: debian/apbs/usr/lib/apbs/tools/bin/mergedx: Unknown DWARF DW_FORM_0x1f21 57fc95cccb651584bb3590509de44f54cec0ddd7 debugedit: debian/apbs/usr/lib/apbs/tools/bin/tensor2dx: Unknown DWARF DW_FORM_0x1f20 d1d26c5bff205d77fa4afe1a4347f2a17fa86c11 5125b06180f3b772c82be1138485ddcd589436ed debugedit: debian/apbs/usr/lib/apbs/tools/bin/mgmesh: Unknown DWARF DW_FORM_0x1f21 9cd9c1f6d3d0e91287a1fc368cf08588f0eeb050 debugedit: debian/apbs/usr/lib/apbs/tools/bin/similarity: Unknown DWARF DW_FORM_0x1f21 d7730ff82e9236fbbad14b8b414aa09a829dc1bc debugedit: debian/libapbs3/usr/lib/arm-linux-gnueabihf/libapbs_fem.so.3: Unknown DWARF DW_FORM_0x1f21 801ae30751ff20303b5874fc395bf744d9f834d9 debugedit: debian/apbs/usr/lib/apbs/tools/bin/smooth: Unknown DWARF DW_FORM_0x1f21 e1c9d0ba7dd930cdd987d33c71b6c324e773ea75 debugedit: debian/apbs/usr/lib/apbs/tools/bin/benchmark: Unknown DWARF DW_FORM_0x1f20 99cb35096466cf0b8c9880590e02c1461b776439 7c10161483789d214f7bad97142c5fb8b71de3ad debugedit: debian/apbs/usr/lib/apbs/tools/bin/dxmath: Unknown DWARF DW_FORM_0x1f21 3c2b917d2bd43c8b43649af60f0a46aacb801c38 debugedit: debian/apbs/usr/lib/apbs/tools/bin/multivalue: Unknown DWARF DW_FORM_0x1f21 1400fa71a05805cf0a1272fafc17f6c72265ada2 debugedit: debian/apbs/usr/lib/apbs/tools/bin/del2dx: Unknown DWARF DW_FORM_0x1f21 17ba36c0fe80ba29df29f0e6f1704d4bb1fb0fb8 debugedit: debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libcgcode.so.1.9.3: Unknown DWARF DW_FORM_0x1f20 7e16c4a2825645adc7715876109ef0962cddc0d6 debugedit: debian/apbs/usr/lib/apbs/tools/bin/dx2mol: Unknown DWARF DW_FORM_0x1f21 4eab1692bf61a2005980fb0bd139b8f7504b6735 debugedit: debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libpunc.so.1.9.3: Unknown DWARF DW_FORM_0x1f21 425473a471c054aea2fb5a3a858f981a30d32a5f debugedit: debian/apbs/usr/lib/apbs/tools/bin/coulomb: Unknown DWARF DW_FORM_0x1f20 6b93d5e9177cbb44f9bbd35ebdb272af2c5e8b55 debugedit: debian/apbs/usr/lib/apbs/tools/bin/analysis: Unknown DWARF DW_FORM_0x1f20 f6095021ee126c0024925ef29833aac37638cb1e debugedit: debian/apbs/usr/lib/apbs/tools/bin/value: Unknown DWARF DW_FORM_0x1f21 ef81675940aaf0e70fdcdc46ee969e64bcaf1e87 debugedit: debian/apbs/usr/bin/apbs: Unknown DWARF DW_FORM_0x1f20 985967cee432348a87785d574ac39dbc94dd9426 c61c4735f36745e12e4a5097a58355f96b86ca38 debugedit: debian/python3-apbslib/usr/lib/python3/dist-packages/apbslib/_apbslib.cpython-312-arm-linux-gnueabihf.so: Unknown DWARF DW_FORM_0x1f21 7d437b43e2cb4f88a451418c364a99126c45eeff dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: symbol scopy_ used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol snrm2_ used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol log used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sqrt used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol ddot_ used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol daxpy_ used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol do_fio used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol s_wsfe used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol e_wsfe used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sdot_ used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libcgcode.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: symbol tanh used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol erfc used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol floor used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol acos used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol atan2 used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol exp used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol pow used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sinh used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol cos used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: symbol sqrt used by debian/libfetk1.9/usr/lib/arm-linux-gnueabihf/libvf2c.so.1.9.3 found in none of the libraries dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libapbs_pmgc.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libvf2c.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libblas.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libmpi.so.40 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libgomp.so.1 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libsuperlu.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libcgcode.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libapbs_fem.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libmc.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libarpack.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libcholmod.so.5 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libpunc.so.1.9 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libcamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libsuitesparseconfig.so.7 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libspqr.so.4 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libstdc++.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libumfpack.so.6 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libcolamd.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/apbs/usr/lib/apbs/tools/bin/analysis debian/apbs/usr/lib/apbs/tools/bin/value debian/apbs/usr/lib/apbs/tools/bin/benchmark debian/apbs/usr/lib/apbs/tools/bin/dx2uhbd debian/apbs/usr/bin/apbs debian/apbs/usr/lib/apbs/tools/bin/dx2mol debian/apbs/usr/lib/apbs/tools/bin/del2dx debian/apbs/usr/lib/apbs/tools/bin/tensor2dx debian/apbs/usr/lib/apbs/tools/bin/mgmesh debian/apbs/usr/lib/apbs/tools/bin/mergedx2 debian/apbs/usr/lib/apbs/tools/bin/smooth debian/apbs/usr/lib/apbs/tools/bin/multivalue debian/apbs/usr/lib/apbs/tools/bin/uhbd_asc2bin debian/apbs/usr/lib/apbs/tools/bin/coulomb debian/apbs/usr/lib/apbs/tools/bin/mergedx debian/apbs/usr/lib/apbs/tools/bin/born debian/apbs/usr/lib/apbs/tools/bin/similarity debian/apbs/usr/lib/apbs/tools/bin/dxmath were not linked against libccolamd.so.3 (they use none of the library's symbols) dh_installdeb -a -O--buildsystem=cmake dh_gencontrol -a -O--buildsystem=cmake dpkg-gencontrol: warning: Depends field of package libfetk-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libapbs-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package apbs: substitution variable ${sphinxdoc:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package apbs: substitution variable ${sphinxdoc:Depends} used, but is not defined dh_md5sums -a -O--buildsystem=cmake dh_builddeb -a -O--buildsystem=cmake INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing apbs (in debian/apbs); do_strip: , oemstrip: pkgstriptranslations: processing libfetk1.9-dbgsym (in debian/.debhelper/libfetk1.9/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing libapbs3-dbgsym (in debian/.debhelper/libapbs3/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing python3-apbslib-dbgsym (in debian/.debhelper/python3-apbslib/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/apbs/DEBIAN/control, package apbs, directory debian/apbs .. removing usr/share/doc/apbs/ChangeLog.md Searching for duplicated docs in dependency libapbs3... pkgstripfiles: processing control file: debian/.debhelper/libapbs3/dbgsym-root/DEBIAN/control, package libapbs3-dbgsym, directory debian/.debhelper/libapbs3/dbgsym-root symlinking changelog.Debian.gz in apbs to file in libapbs3 pkgstripfiles: processing control file: debian/.debhelper/python3-apbslib/dbgsym-root/DEBIAN/control, package python3-apbslib-dbgsym, directory debian/.debhelper/python3-apbslib/dbgsym-root dpkg-deb: building package 'libapbs3-dbgsym' in 'debian/.debhelper/scratch-space/build-libapbs3/libapbs3-dbgsym_3.4.1-5build5_armhf.deb'. dpkg-deb: building package 'python3-apbslib-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-apbslib/python3-apbslib-dbgsym_3.4.1-5build5_armhf.deb'. Searching for duplicated docs in dependency libfetk1.9... pkgstripfiles: Running PNG optimization (using 4 cpus) for package apbs ... pkgstripfiles: No PNG files. dpkg-deb: building package 'apbs' in '../apbs_3.4.1-5build5_armhf.deb'. Renaming libapbs3-dbgsym_3.4.1-5build5_armhf.deb to libapbs3-dbgsym_3.4.1-5build5_armhf.ddeb INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing apbs-dbgsym (in debian/.debhelper/apbs/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing libfetk-dev (in debian/libfetk-dev); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/.debhelper/apbs/dbgsym-root/DEBIAN/control, package apbs-dbgsym, directory debian/.debhelper/apbs/dbgsym-root dpkg-deb: building package 'apbs-dbgsym' in 'debian/.debhelper/scratch-space/build-apbs/apbs-dbgsym_3.4.1-5build5_armhf.deb'. pkgstripfiles: processing control file: debian/libfetk-dev/DEBIAN/control, package libfetk-dev, directory debian/libfetk-dev INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... Renaming python3-apbslib-dbgsym_3.4.1-5build5_armhf.deb to python3-apbslib-dbgsym_3.4.1-5build5_armhf.ddeb Renaming apbs-dbgsym_3.4.1-5build5_armhf.deb to apbs-dbgsym_3.4.1-5build5_armhf.ddeb INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libapbs-dev (in debian/libapbs-dev); do_strip: , oemstrip: pkgstriptranslations: processing python3-apbslib (in debian/python3-apbslib); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/libapbs-dev/DEBIAN/control, package libapbs-dev, directory debian/libapbs-dev .. removing usr/share/doc/libapbs-dev/ChangeLog.md INFO: pkgstripfiles: waiting for lock (libapbs-dev) ... pkgstripfiles: processing control file: debian/python3-apbslib/DEBIAN/control, package python3-apbslib, directory debian/python3-apbslib Searching for duplicated docs in dependency libapbs3... symlinking changelog.Debian.gz in python3-apbslib to file in libapbs3 pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-apbslib ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-apbslib' in '../python3-apbslib_3.4.1-5build5_armhf.deb'. INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... Searching for duplicated docs in dependency libapbs3... symlinking changelog.Debian.gz in libapbs-dev to file in libapbs3 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libapbs-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libapbs-dev' in '../libapbs-dev_3.4.1-5build5_armhf.deb'. INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libapbs3 (in debian/libapbs3); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com INFO: pkgstripfiles: waiting for lock (libfetk-dev) ... pkgstripfiles: processing control file: debian/libapbs3/DEBIAN/control, package libapbs3, directory debian/libapbs3 Searching for duplicated docs in dependency libfetk1.9... symlinking changelog.Debian.gz in libapbs3 to file in libfetk1.9 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libapbs3 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libapbs3' in '../libapbs3_3.4.1-5build5_armhf.deb'. pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com Searching for duplicated docs in dependency libfetk1.9... symlinking changelog.Debian.gz in libfetk-dev to file in libfetk1.9 pkgstripfiles: processing control file: debian/.debhelper/libfetk1.9/dbgsym-root/DEBIAN/control, package libfetk1.9-dbgsym, directory debian/.debhelper/libfetk1.9/dbgsym-root dpkg-deb: building package 'libfetk1.9-dbgsym' in 'debian/.debhelper/scratch-space/build-libfetk1.9/libfetk1.9-dbgsym_3.4.1-5build5_armhf.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package libfetk-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libfetk-dev' in '../libfetk-dev_3.4.1-5build5_armhf.deb'. Renaming libfetk1.9-dbgsym_3.4.1-5build5_armhf.deb to libfetk1.9-dbgsym_3.4.1-5build5_armhf.ddeb INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libfetk1.9 (in debian/libfetk1.9); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/libfetk1.9/DEBIAN/control, package libfetk1.9, directory debian/libfetk1.9 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libfetk1.9 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libfetk1.9' in '../libfetk1.9_3.4.1-5build5_armhf.deb'. dpkg-genbuildinfo --build=any -O../apbs_3.4.1-5build5_armhf.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../apbs_3.4.1-5build5_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-01-19T19:09:20Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ apbs_3.4.1-5build5_armhf.changes: --------------------------------- Format: 1.8 Date: Fri, 19 Jan 2024 18:56:34 +0000 Source: apbs Binary: apbs libapbs-dev libapbs3 libfetk-dev libfetk1.9 python3-apbslib Built-For-Profiles: noudeb Architecture: armhf Version: 3.4.1-5build5 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Graham Inggs Description: apbs - Adaptive Poisson Boltzmann Solver libapbs-dev - Adaptive Poisson Boltzmann Solver libapbs3 - Adaptive Poisson Boltzmann Solver libfetk-dev - FETK libraries for APBS (development headers) libfetk1.9 - FETK libraries for APBS (shared libraries) python3-apbslib - Adaptive Poisson Boltzmann Solver Changes: apbs (3.4.1-5build5) noble; urgency=medium . * No-change rebuild with Python 3.12 as default Checksums-Sha1: b98a9371a79fbac410cd24165bb9a8dcaf56f113 107126 apbs-dbgsym_3.4.1-5build5_armhf.ddeb 502bec09f26bf56ff9e54a96d5fb12cc7697b778 13260 apbs_3.4.1-5build5_armhf.buildinfo 8703e3708796fd9dc44a1b5a8f03fabd8ec32a03 73624 apbs_3.4.1-5build5_armhf.deb 9dd08a08f77ac5e50052a8bfbc581e50b2182294 99452 libapbs-dev_3.4.1-5build5_armhf.deb 241e0db11aa72af67d8e2fd895ce9e4bc2149243 560940 libapbs3-dbgsym_3.4.1-5build5_armhf.ddeb ef4b8a8fe86bda2cc90e9e2e623b6a8d8dde6e3d 254246 libapbs3_3.4.1-5build5_armhf.deb 4b64716aebbb8736f96e0d056caf40c091b6b39b 144482 libfetk-dev_3.4.1-5build5_armhf.deb 06efa03edb710c09706223276501bfafbd93a29d 1692296 libfetk1.9-dbgsym_3.4.1-5build5_armhf.ddeb a28e28a318b35d5eb6c399a1a57384aaca202f48 535432 libfetk1.9_3.4.1-5build5_armhf.deb 8a5f85f25b174142280afcc20373e22cdd507b92 3240886 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Installed-Build-Depends: adduser (= 3.137ubuntu1), autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-14), autotools-dev (= 20220109.1), base-files (= 13ubuntu6), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu1), binutils (= 2.41.90.20240115-1ubuntu1), binutils-arm-linux-gnueabihf (= 2.41.90.20240115-1ubuntu1), binutils-common (= 2.41.90.20240115-1ubuntu1), bsdextrautils (= 2.39.2-6ubuntu1), bsdutils (= 1:2.39.2-6ubuntu1), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5build1), ca-certificates (= 20230311ubuntu1), cmake (= 3.28.1-1), cmake-data (= 3.28.1-1), coreutils (= 9.4-2ubuntu2), cpp (= 4:13.2.0-2ubuntu1), cpp-13 (= 13.2.0-10ubuntu1), dash (= 0.5.12-6ubuntu1), debconf (= 1.5.83), debhelper (= 13.11.9ubuntu1), debianutils (= 5.16), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-python (= 6.20231223), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), docutils-common (= 0.20.1+dfsg-3), dpkg (= 1.22.2ubuntu2), dpkg-dev (= 1.22.2ubuntu2), dwz (= 0.15-1), 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libuv1 (= 1.46.0-3), libx11-6 (= 2:1.8.7-1), libx11-data (= 2:1.8.7-1), libxau6 (= 1:1.0.9-1build5), libxcb1 (= 1.15-1), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxml2 (= 2.9.14+dfsg-1.3build3), libxnvctrl0 (= 510.47.03-0ubuntu1), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.6.0-14.14), login (= 1:4.13+dfsg1-3ubuntu1), lto-disabled-list (= 45), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-3), mawk (= 1.3.4.20231126-1), media-types (= 10.1.0), mpi-default-dev (= 1.15), ncurses-base (= 6.4+20240113-1), ncurses-bin (= 6.4+20240113-1), netbase (= 6.4), ocl-icd-libopencl1 (= 2.3.2-1), openmpi-bin (= 4.1.6-5ubuntu1), openmpi-common (= 4.1.6-5ubuntu1), openssh-client (= 1:9.4p1-1ubuntu2), openssl (= 3.0.10-1ubuntu3), passwd (= 1:4.13+dfsg1-3ubuntu1), patch (= 2.7.6-7build2), perl (= 5.38.2-3), perl-base (= 5.38.2-3), perl-modules-5.38 (= 5.38.2-3), pkg-config (= 1.8.1-2), pkgconf (= 1.8.1-2), pkgconf-bin (= 1.8.1-2), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-2ubuntu1), pybind11-dev (= 2.11.1-2), pybuild-plugin-pyproject (= 6.20231223), python-babel-localedata (= 2.10.3-3build1), python3 (= 3.12.1-0ubuntu1), python3-alabaster (= 0.7.12-1), python3-babel (= 2.10.3-3build1), python3-build (= 0.10.0-1), python3-certifi (= 2023.11.17-1), python3-chardet (= 5.2.0+dfsg-1), python3-dev (= 3.12.1-0ubuntu1), python3-distutils (= 3.11.5-1), python3-docutils (= 0.20.1+dfsg-3), python3-idna (= 3.3-2), python3-imagesize (= 1.4.1-1), python3-installer (= 0.7.0+dfsg1-2), python3-jinja2 (= 3.1.2-1), python3-lib2to3 (= 3.11.5-1), python3-markupsafe (= 2.1.3-1build1), python3-minimal (= 3.12.1-0ubuntu1), python3-packaging (= 23.2-1), python3-pkg-resources (= 68.1.2-2), python3-pybind11 (= 2.11.1-2), python3-pygments (= 2.15.1+dfsg-1), python3-pyproject-hooks (= 1.0.0-2), python3-requests (= 2.31.0+dfsg-1ubuntu1), python3-roman (= 3.3-3), python3-setuptools (= 68.1.2-2), python3-snowballstemmer (= 2.2.0-4), python3-sphinx (= 7.2.6-3), python3-toml (= 0.10.2-1), python3-tz (= 2023.3.post1-2), python3-urllib3 (= 2.0.7-1), python3-wheel (= 0.42.0-1), python3.12 (= 3.12.1-2), python3.12-dev (= 3.12.1-2), python3.12-minimal (= 3.12.1-2), readline-common (= 8.2-3), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-2), sensible-utils (= 0.0.20), sgml-base (= 1.31), sphinx-common (= 7.2.6-3), swig (= 4.1.0-0.3), swig4.0 (= 4.1.0-0.3), sysvinit-utils (= 3.08-3ubuntu1), tar (= 1.35+dfsg-3), tzdata (= 2023d-1ubuntu2), util-linux (= 2.39.2-6ubuntu1), xml-core (= 0.19), xz-utils (= 5.4.5-0.3), zlib1g (= 1:1.3.dfsg-3ubuntu1), zlib1g-dev (= 1:1.3.dfsg-3ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1705690594" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ apbs_3.4.1-5build5_armhf.deb ---------------------------- new Debian package, version 2.0. size 73624 bytes: control archive=1740 bytes. 1829 bytes, 30 lines control 1479 bytes, 23 lines md5sums Package: apbs Version: 3.4.1-5build5 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 264 Depends: apbs-data (= 3.4.1-5build5), libapbs3 (= 3.4.1-5build5), libjs-mathjax, libamd3 (>= 1:7.0.1), libarpack2 (>= 2.1), libblas3 | libblas.so.3, libc6 (>= 2.34), libcamd3 (>= 1:7.0.1), libccolamd3 (>= 1:7.0.1), libcholmod5 (>= 1:7.3.1), libcolamd3 (>= 1:7.0.1), libfetk1.9 (>= 3.4.1), libgomp1 (>= 4.2.1), libmaloc1 (>= 0.2-1), libopenmpi3 (>= 4.1.6), libspqr4 (>= 1:7.5.1+dfsg), libstdc++6 (>= 4.1.1), libsuitesparseconfig7 (>= 1:7.0.1), libsuperlu6 (>= 6.0.1+dfsg1), libumfpack6 (>= 1:7.0.1) Section: science Priority: optional Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including: . * simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, * implicit solvent molecular dynamics of biomolecules , * solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, * and biomolecular titration studies. . APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. . This package contains the apbs program and utilities. Original-Maintainer: Debichem Team drwxr-xr-x root/root 0 2024-01-19 18:56 ./ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/bin/ -rwxr-xr-x root/root 22056 2024-01-19 18:56 ./usr/bin/apbs drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/apbs/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/apbs/tools/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/ -rwxr-xr-x root/root 9768 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/analysis -rwxr-xr-x root/root 9768 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/benchmark -rwxr-xr-x root/root 9768 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/born -rwxr-xr-x root/root 9768 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/coulomb -rwxr-xr-x root/root 9772 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/del2dx -rwxr-xr-x root/root 9768 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/dx2mol -rwxr-xr-x root/root 9768 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/dx2uhbd -rwxr-xr-x root/root 13864 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/dxmath -rwxr-xr-x root/root 13864 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/mergedx -rwxr-xr-x root/root 17960 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/mergedx2 -rwxr-xr-x root/root 5672 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/mgmesh -rwxr-xr-x root/root 9768 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/multivalue -rwxr-xr-x root/root 17960 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/similarity -rwxr-xr-x root/root 13864 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/smooth -rwxr-xr-x root/root 9772 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/tensor2dx -rwxr-xr-x root/root 9768 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/uhbd_asc2bin -rwxr-xr-x root/root 9768 2024-01-19 18:56 ./usr/lib/apbs/tools/bin/value drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/ -rw-r--r-- root/root 78 2022-04-29 18:53 ./usr/share/doc/apbs/README -rw-r--r-- root/root 294 2021-01-10 13:57 ./usr/share/doc/apbs/README.test lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/apbs/changelog.Debian.gz -> ../libapbs3/changelog.Debian.gz -rw-r--r-- root/root 6898 2023-01-10 18:37 ./usr/share/doc/apbs/copyright -rw-r--r-- root/root 17248 2022-04-29 18:53 ./usr/share/doc/apbs/releases.rst.gz drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/man/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/man/man1/ -rw-r--r-- root/root 835 2024-01-19 18:56 ./usr/share/man/man1/apbs.1.gz libapbs-dev_3.4.1-5build5_armhf.deb ----------------------------------- new Debian package, version 2.0. size 99452 bytes: control archive=2157 bytes. 752 bytes, 20 lines control 3873 bytes, 58 lines md5sums Package: libapbs-dev Source: apbs Version: 3.4.1-5build5 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 713 Depends: libapbs3 (= 3.4.1-5build5) Section: libdevel Priority: optional Multi-Arch: same Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package contains the development headers to build against libapbs_* shared libraries. Original-Maintainer: Debichem Team drwxr-xr-x root/root 0 2024-01-19 18:56 ./ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/apbs/ -rw-r--r-- root/root 3281 2022-04-29 18:53 ./usr/include/apbs/apbs.h drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/apbs/fem/ -rw-r--r-- root/root 11331 2022-04-29 18:53 ./usr/include/apbs/fem/vcsm.h -rw-r--r-- root/root 37852 2022-04-29 18:53 ./usr/include/apbs/fem/vfetk.h -rw-r--r-- root/root 10184 2022-04-29 18:53 ./usr/include/apbs/fem/vpee.h drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/apbs/generic/ -rw-r--r-- root/root 8229 2022-04-29 18:53 ./usr/include/apbs/generic/apolparm.h -rw-r--r-- root/root 6395 2022-04-29 18:53 ./usr/include/apbs/generic/bemparm.h -rw-r--r-- root/root 8873 2022-04-29 18:53 ./usr/include/apbs/generic/femparm.h -rw-r--r-- root/root 6121 2022-04-29 18:53 ./usr/include/apbs/generic/geoflowparm.h -rw-r--r-- 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./usr/include/apbs/generic/vmatrix.h -rw-r--r-- root/root 12145 2022-04-29 18:53 ./usr/include/apbs/generic/vparam.h -rw-r--r-- root/root 19880 2022-04-29 18:53 ./usr/include/apbs/generic/vpbe.h -rw-r--r-- root/root 5171 2022-04-29 18:53 ./usr/include/apbs/generic/vstring.h -rw-r--r-- root/root 3958 2022-04-29 18:53 ./usr/include/apbs/generic/vunit.h drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/apbs/mg/ -rw-r--r-- root/root 14945 2022-04-29 18:53 ./usr/include/apbs/mg/vgrid.h -rw-r--r-- root/root 6887 2022-04-29 18:53 ./usr/include/apbs/mg/vmgrid.h -rw-r--r-- root/root 6160 2022-04-29 18:53 ./usr/include/apbs/mg/vopot.h -rw-r--r-- root/root 52888 2022-04-29 18:53 ./usr/include/apbs/mg/vpmg.h -rw-r--r-- root/root 11010 2022-04-29 18:53 ./usr/include/apbs/mg/vpmgp.h drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/apbs/pmgc/ -rw-r--r-- root/root 12319 2022-04-29 18:53 ./usr/include/apbs/pmgc/buildAd.h -rw-r--r-- root/root 5305 2022-04-29 18:53 ./usr/include/apbs/pmgc/buildBd.h -rw-r--r-- root/root 16972 2022-04-29 18:53 ./usr/include/apbs/pmgc/buildGd.h -rw-r--r-- root/root 10038 2022-04-29 18:53 ./usr/include/apbs/pmgc/buildPd.h -rw-r--r-- root/root 3475 2022-04-29 18:53 ./usr/include/apbs/pmgc/cgd.h -rw-r--r-- root/root 5776 2022-04-29 18:53 ./usr/include/apbs/pmgc/gsd.h -rw-r--r-- root/root 19097 2022-04-29 18:53 ./usr/include/apbs/pmgc/matvecd.h -rw-r--r-- root/root 5762 2022-04-29 18:53 ./usr/include/apbs/pmgc/mgcsd.h -rw-r--r-- root/root 9284 2022-04-29 18:53 ./usr/include/apbs/pmgc/mgdrvd.h -rw-r--r-- root/root 7729 2022-04-29 18:53 ./usr/include/apbs/pmgc/mgfasd.h -rw-r--r-- root/root 14987 2022-04-29 18:53 ./usr/include/apbs/pmgc/mgsubd.h -rw-r--r-- root/root 12104 2022-04-29 18:53 ./usr/include/apbs/pmgc/mikpckd.h -rw-r--r-- root/root 4008 2022-04-29 18:53 ./usr/include/apbs/pmgc/mlinpckd.h -rw-r--r-- root/root 7781 2022-04-29 18:53 ./usr/include/apbs/pmgc/mypdec.h -rw-r--r-- root/root 5950 2022-04-29 18:53 ./usr/include/apbs/pmgc/newdrvd.h -rw-r--r-- root/root 6700 2022-04-29 18:53 ./usr/include/apbs/pmgc/newtond.h -rw-r--r-- root/root 8220 2022-04-29 18:53 ./usr/include/apbs/pmgc/powerd.h -rw-r--r-- root/root 4685 2022-04-29 18:53 ./usr/include/apbs/pmgc/smoothd.h -rw-r--r-- root/root 33482 2022-04-29 18:53 ./usr/include/apbs/routines.h drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/ lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libapbs_fem.so -> libapbs_fem.so.3 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libapbs_generic.so -> libapbs_generic.so.3 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libapbs_mg.so -> libapbs_mg.so.3 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libapbs_pmgc.so -> libapbs_pmgc.so.3 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libapbs_routines.so -> libapbs_routines.so.3 drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/cmake/ -rw-r--r-- root/root 949 2023-01-10 18:37 ./usr/share/apbs/cmake/FindAMD.cmake -rw-r--r-- root/root 2501 2023-01-10 18:37 ./usr/share/apbs/cmake/FindARPACK.cmake -rw-r--r-- root/root 22563 2023-01-10 18:37 ./usr/share/apbs/cmake/FindLAPACK.cmake -rw-r--r-- root/root 23393 2023-01-10 18:37 ./usr/share/apbs/cmake/FindSuiteSparse.cmake -rw-r--r-- root/root 2578 2023-01-10 18:37 ./usr/share/apbs/cmake/FindSuperLU.cmake -rw-r--r-- root/root 1153 2023-01-10 18:37 ./usr/share/apbs/cmake/FindUMFPACK.cmake drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/libapbs-dev/ -rw-r--r-- root/root 78 2022-04-29 18:53 ./usr/share/doc/libapbs-dev/README lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/libapbs-dev/changelog.Debian.gz -> ../libapbs3/changelog.Debian.gz -rw-r--r-- root/root 6898 2023-01-10 18:37 ./usr/share/doc/libapbs-dev/copyright -rw-r--r-- root/root 17248 2022-04-29 18:53 ./usr/share/doc/libapbs-dev/releases.rst.gz libapbs3_3.4.1-5build5_armhf.deb -------------------------------- new Debian package, version 2.0. size 254246 bytes: control archive=1006 bytes. 760 bytes, 19 lines control 542 bytes, 7 lines md5sums 179 bytes, 5 lines shlibs 75 bytes, 2 lines triggers Package: libapbs3 Source: apbs Version: 3.4.1-5build5 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 524 Depends: libc6 (>= 2.29), libfetk1.9 (>= 3.4.1), libgomp1 (>= 4.9), libmaloc1 (>= 0.2-1) Section: libs Priority: optional Multi-Arch: same Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package contains the libapbs_* shared libraries. Original-Maintainer: Debichem Team drwxr-xr-x root/root 0 2024-01-19 18:56 ./ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/ -rw-r--r-- root/root 44376 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libapbs_fem.so.3 -rw-r--r-- root/root 144776 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libapbs_generic.so.3 -rw-r--r-- root/root 112008 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libapbs_mg.so.3 -rw-r--r-- root/root 136456 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libapbs_pmgc.so.3 -rw-r--r-- root/root 71048 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libapbs_routines.so.3 drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/libapbs3/ lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/libapbs3/changelog.Debian.gz -> ../libfetk1.9/changelog.Debian.gz -rw-r--r-- root/root 6898 2023-01-10 18:37 ./usr/share/doc/libapbs3/copyright drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 108 2023-01-10 18:37 ./usr/share/lintian/overrides/libapbs3 libfetk-dev_3.4.1-5build5_armhf.deb ----------------------------------- new Debian package, version 2.0. size 144482 bytes: control archive=1987 bytes. 1344 bytes, 32 lines control 2509 bytes, 40 lines md5sums Package: libfetk-dev Source: apbs Version: 3.4.1-5build5 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 1505 Depends: libfetk1.9 (= 3.4.1-5build5), libmaloc-dev Section: libdevel Priority: optional Multi-Arch: same Homepage: http://www.poissonboltzmann.org/ Description: FETK libraries for APBS (development headers) The Finite Element ToolKit (FETK) is a collection of adaptive finite element method (AFEM) software libraries and tools for solving coupled systems of nonlinear geometric partial differential equations (PDE). The FETK libraries and tools are written in an object-oriented form of ANSI-C and in C++, and include a collection of standard numerical libraries (PUNC), a stand-alone high-quality surface and volume simplex mesh generator (GAMer), a stand-alone networked polygon display tool (SG), a general nonlinear finite element modeling kernel (MC) . This package provides a fork of FETK intended for use by APBS (Adaptive Poisson Boltzmann Solver). . The FETK component MALOC (Minimal Abstraction Layer for Object-oriented C/C++ programs) is provided separately by libmaloc-dev. . This package contains the development headers to build against libapbs_* shared libraries. Original-Maintainer: Debichem Team drwxr-xr-x root/root 0 2024-01-19 18:56 ./ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/fetk/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/fetk/gamer/ -rw-r--r-- root/root 11439 2023-01-10 18:37 ./usr/include/fetk/gamer/biom.h -rw-r--r-- root/root 1459 2023-01-10 18:37 ./usr/include/fetk/gamer/gamer.h -rw-r--r-- root/root 2282 2023-01-10 18:37 ./usr/include/fetk/gamer/gamer_base.h -rw-r--r-- root/root 106910 2023-01-10 18:37 ./usr/include/fetk/gamer/tetgen.h -rw-r--r-- root/root 22024 2023-01-10 18:37 ./usr/include/fetk/gamer/triangle.h drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/fetk/mc/ -rw-r--r-- root/root 27753 2023-01-10 18:37 ./usr/include/fetk/mc/am.h -rw-r--r-- root/root 49795 2023-01-10 18:37 ./usr/include/fetk/mc/aprx.h -rw-r--r-- root/root 1297 2023-01-10 18:37 ./usr/include/fetk/mc/bam.h -rw-r--r-- root/root 29085 2023-01-10 18:37 ./usr/include/fetk/mc/bmat.h -rw-r--r-- root/root 5029 2023-01-10 18:37 ./usr/include/fetk/mc/bnode.h -rw-r--r-- root/root 32284 2023-01-10 18:37 ./usr/include/fetk/mc/bvec.h -rw-r--r-- root/root 13191 2023-01-10 18:37 ./usr/include/fetk/mc/dyn.h -rw-r--r-- root/root 130602 2023-01-10 18:37 ./usr/include/fetk/mc/gem.h -rw-r--r-- root/root 47965 2023-01-10 18:37 ./usr/include/fetk/mc/mat.h -rw-r--r-- root/root 1457 2023-01-10 18:37 ./usr/include/fetk/mc/mc.h -rw-r--r-- root/root 5705 2023-01-10 18:37 ./usr/include/fetk/mc/mc_base.h -rw-r--r-- root/root 4665 2023-01-10 18:37 ./usr/include/fetk/mc/mcsh.h -rw-r--r-- root/root 14987 2023-01-10 18:37 ./usr/include/fetk/mc/mtool.h -rw-r--r-- root/root 1189 2023-01-10 18:37 ./usr/include/fetk/mc/nam.h -rw-r--r-- root/root 4772 2023-01-10 18:37 ./usr/include/fetk/mc/node.h -rw-r--r-- root/root 17885 2023-01-10 18:37 ./usr/include/fetk/mc/pde.h -rw-r--r-- root/root 17026 2023-01-10 18:37 ./usr/include/fetk/mc/re.h -rw-r--r-- root/root 4823 2023-01-10 18:37 ./usr/include/fetk/mc/slu.h -rw-r--r-- root/root 12682 2023-01-10 18:37 ./usr/include/fetk/mc/vec.h -rw-r--r-- root/root 14016 2023-01-10 18:37 ./usr/include/fetk/mc/vec3.h -rw-r--r-- root/root 26120 2023-01-10 18:37 ./usr/include/fetk/mc/vel.h -rw-r--r-- root/root 68269 2023-01-10 18:37 ./usr/include/fetk/mc/ves.h -rw-r--r-- root/root 50938 2023-01-10 18:37 ./usr/include/fetk/mc/whb.h -rw-r--r-- root/root 7767 2023-01-10 18:37 ./usr/include/fetk/mc/zslu.h drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/include/fetk/punc/ -rw-r--r-- root/root 1569 2023-01-10 18:37 ./usr/include/fetk/punc/punc.h -rw-r--r-- root/root 1272 2023-01-10 18:37 ./usr/include/fetk/punc/punc_base.h -rw-r--r-- root/root 1455 2023-01-10 18:37 ./usr/include/fetk/punc/punc_base_p.h -rw-r--r-- root/root 3987 2024-01-19 18:56 ./usr/include/fetk/punc/punccf.h -rw-r--r-- root/root 46865 2023-01-10 18:37 ./usr/include/fetk/punc/varpack.h -rw-r--r-- root/root 39886 2023-01-10 18:37 ./usr/include/fetk/punc/vblas.h -rw-r--r-- root/root 17098 2023-01-10 18:37 ./usr/include/fetk/punc/vcgcode.h -rw-r--r-- root/root 13077 2023-01-10 18:37 ./usr/include/fetk/punc/vf2c.h -rw-r--r-- root/root 552778 2023-01-10 18:37 ./usr/include/fetk/punc/vlapack.h -rw-r--r-- root/root 82089 2023-01-10 18:37 ./usr/include/fetk/punc/vpmg.h drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/ lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libcgcode.so -> libcgcode.so.1.9 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libgamer.so -> libgamer.so.1.9 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libmc.so -> libmc.so.1.9 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libpunc.so -> libpunc.so.1.9 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libvf2c.so -> libvf2c.so.1.9 drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/libfetk-dev/ lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/libfetk-dev/changelog.Debian.gz -> ../libfetk1.9/changelog.Debian.gz -rw-r--r-- root/root 6898 2023-01-10 18:37 ./usr/share/doc/libfetk-dev/copyright libfetk1.9_3.4.1-5build5_armhf.deb ---------------------------------- new Debian package, version 2.0. size 535432 bytes: control archive=1395 bytes. 1429 bytes, 32 lines control 617 bytes, 8 lines md5sums 171 bytes, 5 lines shlibs 75 bytes, 2 lines triggers Package: libfetk1.9 Source: apbs Version: 3.4.1-5build5 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 992 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.5), libmaloc1 (>= 0.2-1), libstdc++6 (>= 5), libsuperlu6 (>= 6.0.1+dfsg1), libumfpack6 (>= 1:7.0.1) Section: libs Priority: optional Multi-Arch: same Homepage: http://www.poissonboltzmann.org/ Description: FETK libraries for APBS (shared libraries) The Finite Element ToolKit (FETK) is a collection of adaptive finite element method (AFEM) software libraries and tools for solving coupled systems of nonlinear geometric partial differential equations (PDE). The FETK libraries and tools are written in an object-oriented form of ANSI-C and in C++, and include a collection of standard numerical libraries (PUNC), a stand-alone high-quality surface and volume simplex mesh generator (GAMer), a stand-alone networked polygon display tool (SG), a general nonlinear finite element modeling kernel (MC) . This package provides a fork of FETK intended for use by APBS (Adaptive Poisson Boltzmann Solver). . The FETK component MALOC (Minimal Abstraction Layer for Object-oriented C/C++ programs) is provided separately via libmaloc-dev. . This package contains the libgamer, libmc, libpunc (and libcgcode, libvf2c) shared libraries. Original-Maintainer: Debichem Team drwxr-xr-x root/root 0 2024-01-19 18:56 ./ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/ lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libcgcode.so.1.9 -> libcgcode.so.1.9.3 -rw-r--r-- root/root 71440 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libcgcode.so.1.9.3 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libgamer.so.1.9 -> libgamer.so.1.9.3 -rw-r--r-- root/root 510956 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libgamer.so.1.9.3 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libmc.so.1.9 -> libmc.so.1.9.3 -rw-r--r-- root/root 328968 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libmc.so.1.9.3 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libpunc.so.1.9 -> libpunc.so.1.9.3 -rw-r--r-- root/root 5408 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libpunc.so.1.9.3 lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libvf2c.so.1.9 -> libvf2c.so.1.9.3 -rw-r--r-- root/root 67420 2024-01-19 18:56 ./usr/lib/arm-linux-gnueabihf/libvf2c.so.1.9.3 drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/libfetk1.9/ -rw-r--r-- root/root 3605 2024-01-19 18:56 ./usr/share/doc/libfetk1.9/changelog.Debian.gz -rw-r--r-- root/root 6898 2023-01-10 18:37 ./usr/share/doc/libfetk1.9/copyright drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 80 2023-01-10 18:37 ./usr/share/lintian/overrides/libfetk1.9 python3-apbslib_3.4.1-5build5_armhf.deb --------------------------------------- new Debian package, version 2.0. size 211544 bytes: control archive=2037 bytes. 917 bytes, 19 lines control 2866 bytes, 36 lines md5sums 277 bytes, 12 lines * postinst #!/bin/sh 390 bytes, 12 lines * prerm #!/bin/sh Package: python3-apbslib Source: apbs Version: 3.4.1-5build5 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 924 Depends: libapbs3 (= 3.4.1-5build5), python3 (<< 3.13), python3 (>= 3.12~), python3:any, libc6 (>= 2.32), libgcc-s1 (>= 3.5), libmaloc1 (>= 0.2-1), libpython3.12 (>= 3.12.1), libstdc++6 (>= 11) Section: python Priority: optional Homepage: http://www.poissonboltzmann.org/ Description: Adaptive Poisson Boltzmann Solver APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. . This package provides both the apbs and apbslib modules for Python3 enabling Python applications to access apbs. Original-Maintainer: Debichem Team drwxr-xr-x root/root 0 2024-01-19 18:56 ./ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/python3/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/python3/dist-packages/ -rw-r--r-- root/root 255436 2024-01-19 18:56 ./usr/lib/python3/dist-packages/apbs.cpython-312-arm-linux-gnueabihf.so drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/lib/python3/dist-packages/apbslib/ -rw-r--r-- root/root 23 2021-01-10 13:57 ./usr/lib/python3/dist-packages/apbslib/__init__.py -rw-r--r-- root/root 83876 2024-01-19 18:56 ./usr/lib/python3/dist-packages/apbslib/_apbslib.cpython-312-arm-linux-gnueabihf.so -rw-r--r-- root/root 14524 2024-01-19 18:56 ./usr/lib/python3/dist-packages/apbslib/apbslib.py drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/python-pybind/ -rw-r--r-- root/root 551 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/CMakeLists.txt -rw-r--r-- root/root 812 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_constants.hpp -rw-r--r-- root/root 4224 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_nosh.cpp -rw-r--r-- root/root 1906 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_nosh.hpp -rw-r--r-- root/root 3131 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_valist.cpp -rw-r--r-- root/root 1018 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_valist.hpp -rw-r--r-- root/root 1601 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_vatom.cpp -rw-r--r-- root/root 702 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/bind_vatom.hpp -rw-r--r-- root/root 988 2022-04-29 18:53 ./usr/share/apbs/tools/python-pybind/module.cpp drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/python/ -rw-r--r-- root/root 1896 2024-01-19 18:56 ./usr/share/apbs/tools/python/CMakeLists.txt -rw-r--r-- root/root 20999 2022-04-29 18:53 ./usr/share/apbs/tools/python/Makefile -rw-r--r-- root/root 898 2022-04-29 18:53 ./usr/share/apbs/tools/python/Makefile.am -rw-r--r-- root/root 20457 2022-04-29 18:53 ./usr/share/apbs/tools/python/Makefile.in -rw-r--r-- root/root 1834 2022-04-29 18:53 ./usr/share/apbs/tools/python/README -rw-r--r-- root/root 6111 2022-04-29 18:53 ./usr/share/apbs/tools/python/apbs.in -rw-r--r-- root/root 260435 2022-04-29 18:53 ./usr/share/apbs/tools/python/apbslib.c -rw-r--r-- root/root 14676 2022-04-29 18:53 ./usr/share/apbs/tools/python/apbslib.i -rw-r--r-- root/root 11686 2022-04-29 18:53 ./usr/share/apbs/tools/python/apbslib_wrap.doc -rw-r--r-- root/root 66 2022-04-29 18:53 ./usr/share/apbs/tools/python/ion.pqr -rw-r--r-- root/root 15725 2022-04-29 18:53 ./usr/share/apbs/tools/python/main.py -rw-r--r-- root/root 19499 2024-01-19 18:56 ./usr/share/apbs/tools/python/noinput.py drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/apbs/tools/python/vgrid/ -rw-r--r-- root/root 15551 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/Makefile -rw-r--r-- root/root 845 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/Makefile.am -rw-r--r-- root/root 15036 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/Makefile.in -rw-r--r-- root/root 1638 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/README -rw-r--r-- root/root 3134 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/average.py -rw-r--r-- root/root 14146 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/mergedx.py -rw-r--r-- root/root 2514 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/read.py -rw-r--r-- root/root 3038 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/vgrid.i -rw-r--r-- root/root 4711 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/vgrid.py -rw-r--r-- root/root 97354 2022-04-29 18:53 ./usr/share/apbs/tools/python/vgrid/vgridlib.c drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 18:56 ./usr/share/doc/python3-apbslib/ lrwxrwxrwx root/root 0 2024-01-19 18:56 ./usr/share/doc/python3-apbslib/changelog.Debian.gz -> ../libapbs3/changelog.Debian.gz -rw-r--r-- root/root 6898 2023-01-10 18:37 ./usr/share/doc/python3-apbslib/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: 314000 Build-Time: 502 Distribution: noble-proposed Host Architecture: armhf Install-Time: 41 Job: apbs_3.4.1-5build5.dsc Machine Architecture: arm64 Package: apbs Package-Time: 548 Source-Version: 3.4.1-5build5 Space: 314000 Status: successful Version: 3.4.1-5build5 -------------------------------------------------------------------------------- Finished at 2024-01-19T19:09:20Z Build needed 00:09:08, 314000k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27660352 Scanning for processes to kill in build PACKAGEBUILD-27660352