https://launchpad.net/ubuntu/+archive/test-rebuild-20201216-hirsute-gcc11/+build/20625810 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-029 4.15.0-135-generic #139-Ubuntu SMP Mon Jan 18 17:40:29 UTC 2021 aarch64 Buildd toolchain package versions: launchpad-buildd_194~476~ubuntu18.04.1 python3-lpbuildd_194~476~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.7 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 6 Feb 08:49:20 ntpdate[1659]: adjust time server 10.211.37.1 offset 0.001370 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=armhf PACKAGEBUILD-20625810 --image-type chroot /home/buildd/filecache-default/6663ab897c1b9684e4da3138ea2f806b3d40e7b1 Creating target for build PACKAGEBUILD-20625810 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=armhf PACKAGEBUILD-20625810 Starting target for build PACKAGEBUILD-20625810 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=armhf PACKAGEBUILD-20625810 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu hirsute main' 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute main' 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu hirsute main' 'deb http://ftpmaster.internal/ubuntu hirsute main universe' Overriding sources.list in build-PACKAGEBUILD-20625810 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=hirsute --arch=armhf PACKAGEBUILD-20625810 Adding trusted keys to build-PACKAGEBUILD-20625810 Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)). OK Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)). /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2018-archive.gpg ------------------------------------------------------ pub rsa4096 2018-09-17 [SC] F6EC B376 2474 EDA9 D21B 7022 8719 20D1 991B C93C uid [ unknown] Ubuntu Archive Automatic Signing Key (2018) RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=armhf PACKAGEBUILD-20625810 Updating target for build PACKAGEBUILD-20625810 Get:1 http://ftpmaster.internal/ubuntu hirsute InRelease [269 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu hirsute InRelease [23.8 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute InRelease [17.6 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu hirsute InRelease [17.6 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main armhf Packages [1344 kB] Get:6 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu hirsute/main armhf Packages [15.1 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [510 kB] Get:8 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu hirsute/main Translation-en [10.0 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/universe armhf Packages [12.5 MB] Get:10 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main armhf Packages [11.7 kB] Get:11 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main Translation-en [6856 B] Get:12 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu hirsute/main armhf Packages [14.9 kB] Get:13 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu hirsute/main Translation-en [11.0 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/universe Translation-en [5434 kB] Fetched 20.2 MB in 7s (2858 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: g++-10 libisl22 libperl5.30 libstdc++-10-dev perl-modules-5.30 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: cpp-11 g++-11 gcc-11 gcc-11-base libgcc-11-dev libisl23 libperl5.32 libstdc++-11-dev libxxhash0 lto-disabled-list perl-modules-5.32 The following packages will be upgraded: adduser apt base-files base-passwd bash binutils binutils-arm-linux-gnueabihf binutils-common bsdutils coreutils cpp cpp-10 dash dpkg dpkg-dev fakeroot g++ g++-10 gcc gcc-10 gcc-10-base gpg gpg-agent gpgconf gpgv grep gzip init init-system-helpers libacl1 libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libgcc-10-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgssapi-krb5-2 libhogweed6 libidn2-0 libip4tc2 libjson-c5 libk5crypto3 libkrb5-3 libkrb5support0 liblockfile-bin liblockfile1 liblz4-1 libmount1 libmpc3 libncurses6 libncursesw6 libnettle8 libnpth0 libp11-kit0 libpcre2-8-0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.1 libstdc++-10-dev libstdc++6 libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login mount ncurses-base ncurses-bin openssl passwd patch perl perl-base readline-common sensible-utils systemd systemd-sysv systemd-timesyncd sysvinit-utils tar tzdata util-linux 119 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. Need to get 238 MB of archives. After this operation, 549 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute/main armhf libcrypt-dev armhf 1:4.4.17-1ubuntu1 [113 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main armhf gcc-11-base armhf 11-20210123-1ubuntu1 [19.0 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main armhf libgcc-s1 armhf 11-20210123-1ubuntu1 [36.3 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main armhf libc6-dev armhf 2.32-0ubuntu6 [1582 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main armhf libstdc++6 armhf 11-20210123-1ubuntu1 [499 kB] Get:6 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main armhf libgomp1 armhf 11-20210123-1ubuntu1 [91.0 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main armhf libatomic1 armhf 11-20210123-1ubuntu1 [7232 B] Get:8 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main armhf libasan6 armhf 11-20210123-1ubuntu1 [2004 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main armhf libc-dev-bin armhf 2.32-0ubuntu6 [29.6 kB] Get:10 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main armhf libubsan1 armhf 11-20210123-1ubuntu1 [807 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main armhf libcrypt1 armhf 1:4.4.17-1ubuntu1 [86.7 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main armhf linux-libc-dev armhf 5.8.0-36.40+21.04.1 [1108 kB] Get:13 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main armhf libcc1-0 armhf 11-20210123-1ubuntu1 [41.2 kB] Get:14 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main armhf cpp-11 armhf 11-20210123-1ubuntu1 [49.7 MB] Get:15 http://ftpmaster.internal/ubuntu hirsute/main armhf libtirpc-common all 1.3.1-1 [7452 B] Get:16 http://ftpmaster.internal/ubuntu hirsute/main armhf libk5crypto3 armhf 1.18.3-4 [74.1 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute/main armhf libgssapi-krb5-2 armhf 1.18.3-4 [107 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute/main armhf libkrb5-3 armhf 1.18.3-4 [282 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main armhf libkrb5support0 armhf 1.18.3-4 [27.9 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main armhf libssl1.1 armhf 1.1.1f-1ubuntu5 [1079 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main armhf libtirpc-dev armhf 1.3.1-1 [174 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute/main armhf libtirpc3 armhf 1.3.1-1 [65.6 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main armhf libc6 armhf 2.32-0ubuntu6 [2124 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main armhf base-files armhf 11ubuntu16 [60.2 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute/main armhf bash armhf 5.1-1ubuntu1 [606 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main armhf bsdutils armhf 1:2.36.1-1ubuntu2 [78.6 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main armhf coreutils armhf 8.32-4ubuntu2 [1207 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute/main armhf tar armhf 1.32+dfsg-1 [249 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute/main armhf dpkg armhf 1.20.7.1ubuntu2 [1212 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute/main armhf dash armhf 0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1 [78.9 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute/main armhf grep armhf 3.6-1 [143 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute/main armhf gzip armhf 1.10-2ubuntu3 [90.9 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute/main armhf login armhf 1:4.8.1-1ubuntu8 [217 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute/main armhf libncurses6 armhf 6.2+20201114-2 [79.9 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute/main armhf libncursesw6 armhf 6.2+20201114-2 [106 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute/main armhf libtinfo6 armhf 6.2+20201114-2 [74.0 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute/main armhf ncurses-bin armhf 6.2+20201114-2 [165 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main armhf perl-modules-5.32 all 5.32.0-6 [2754 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main armhf libperl5.32 armhf 5.32.0-6 [3357 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute/main armhf perl armhf 5.32.0-6 [225 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main armhf perl-base armhf 5.32.0-6 [1423 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main armhf libgdbm6 armhf 1.19-2 [24.6 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main armhf libgdbm-compat4 armhf 1.19-2 [5896 B] Get:44 http://ftpmaster.internal/ubuntu hirsute/main armhf util-linux armhf 2.36.1-1ubuntu2 [1005 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main armhf libdebconfclient0 armhf 0.256ubuntu1 [5712 B] Get:46 http://ftpmaster.internal/ubuntu hirsute/main armhf base-passwd armhf 3.5.48 [46.0 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main armhf init-system-helpers all 1.60 [37.8 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main armhf libc-bin armhf 2.32-0ubuntu6 [505 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main armhf ncurses-base all 6.2+20201114-2 [18.4 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main armhf sysvinit-utils armhf 2.96-5ubuntu1 [19.2 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main armhf libxxhash0 armhf 0.8.0-2 [21.8 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main armhf libgcrypt20 armhf 1.8.7-2ubuntu1 [364 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main armhf liblz4-1 armhf 1.9.3-0ubuntu1 [49.4 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/main armhf systemd-sysv armhf 247.1-4ubuntu1 [10.3 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/main armhf libaudit-common all 1:2.8.5-3ubuntu3 [4048 B] Get:56 http://ftpmaster.internal/ubuntu hirsute/main armhf libcap-ng0 armhf 0.7.9-2.2build1 [9672 B] Get:57 http://ftpmaster.internal/ubuntu hirsute/main armhf libaudit1 armhf 1:2.8.5-3ubuntu3 [36.1 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main armhf libpcre2-8-0 armhf 10.35-2ubuntu1 [169 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main armhf libselinux1 armhf 3.1-2build2 [61.0 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/main armhf libsemanage-common all 3.1-1build2 [10.0 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute/main armhf libsemanage1 armhf 3.1-1build2 [75.6 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute/main armhf passwd armhf 1:4.8.1-1ubuntu8 [751 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/main armhf adduser all 3.118ubuntu5 [156 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/main armhf systemd-timesyncd armhf 247.1-4ubuntu1 [27.7 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute/main armhf libapparmor1 armhf 3.0.0-0ubuntu5 [30.4 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute/main armhf libblkid1 armhf 2.36.1-1ubuntu2 [117 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute/main armhf libudev1 armhf 247.1-4ubuntu1 [61.5 kB] Get:68 http://ftpmaster.internal/ubuntu hirsute/main armhf libdevmapper1.02.1 armhf 2:1.02.167-1ubuntu4 [120 kB] Get:69 http://ftpmaster.internal/ubuntu hirsute/main armhf libjson-c5 armhf 0.15-2 [27.2 kB] Get:70 http://ftpmaster.internal/ubuntu hirsute/main armhf libuuid1 armhf 2.36.1-1ubuntu2 [20.4 kB] Get:71 http://ftpmaster.internal/ubuntu hirsute/main armhf libcryptsetup12 armhf 2:2.3.4-1ubuntu1 [174 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute/main armhf libnettle8 armhf 3.7-2 [158 kB] Get:73 http://ftpmaster.internal/ubuntu hirsute/main armhf libhogweed6 armhf 3.7-2 [183 kB] Get:74 http://ftpmaster.internal/ubuntu hirsute/main armhf libidn2-0 armhf 2.3.0-5 [49.6 kB] Get:75 http://ftpmaster.internal/ubuntu hirsute/main armhf libp11-kit0 armhf 0.23.22-1 [170 kB] Get:76 http://ftpmaster.internal/ubuntu hirsute/main armhf libgnutls30 armhf 3.7.0-5ubuntu1 [860 kB] Get:77 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main armhf libgcc-11-dev armhf 11-20210123-1ubuntu1 [739 kB] Get:78 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main armhf gcc-11 armhf 11-20210123-1ubuntu1 [56.8 MB] Get:79 http://ftpmaster.internal/ubuntu hirsute/main armhf libip4tc2 armhf 1.8.5-3ubuntu4 [16.7 kB] Get:80 http://ftpmaster.internal/ubuntu hirsute/main armhf libseccomp2 armhf 2.4.3-1ubuntu6 [32.5 kB] Get:81 http://ftpmaster.internal/ubuntu hirsute/main armhf mount armhf 2.36.1-1ubuntu2 [113 kB] Get:82 http://ftpmaster.internal/ubuntu hirsute/main armhf systemd armhf 247.1-4ubuntu1 [3806 kB] Get:83 http://ftpmaster.internal/ubuntu hirsute/main armhf libsystemd0 armhf 247.1-4ubuntu1 [250 kB] Get:84 http://ftpmaster.internal/ubuntu hirsute/main armhf libzstd1 armhf 1.4.8+dfsg-1 [258 kB] Get:85 http://ftpmaster.internal/ubuntu hirsute/main armhf libapt-pkg6.0 armhf 2.1.18 [819 kB] Get:86 http://ftpmaster.internal/ubuntu hirsute/main armhf gpgv armhf 2.2.20-1ubuntu2 [172 kB] Get:87 http://ftpmaster.internal/ubuntu hirsute/main armhf apt armhf 2.1.18 [1275 kB] Get:88 http://ftpmaster.internal/ubuntu hirsute/main armhf init armhf 1.60 [6040 B] Get:89 http://ftpmaster.internal/ubuntu hirsute/main armhf libacl1 armhf 2.2.53-9 [14.9 kB] Get:90 http://ftpmaster.internal/ubuntu hirsute/main armhf libattr1 armhf 1:2.4.48-6 [11.7 kB] Get:91 http://ftpmaster.internal/ubuntu hirsute/main armhf libmount1 armhf 2.36.1-1ubuntu2 [131 kB] Get:92 http://ftpmaster.internal/ubuntu hirsute/main armhf libsmartcols1 armhf 2.36.1-1ubuntu2 [82.3 kB] Get:93 http://ftpmaster.internal/ubuntu hirsute/main armhf g++-10 armhf 10.2.1-6ubuntu1 [7613 kB] Get:94 http://ftpmaster.internal/ubuntu hirsute/main armhf gcc-10 armhf 10.2.1-6ubuntu1 [13.6 MB] Get:95 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main armhf libstdc++-11-dev armhf 11-20210123-1ubuntu1 [1846 kB] Get:96 http://ftpmaster.internal/ubuntu hirsute/main armhf libstdc++-10-dev armhf 10.2.1-6ubuntu1 [1815 kB] Get:97 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main armhf g++-11 armhf 11-20210123-1ubuntu1 [55.9 MB] Get:98 http://ftpmaster.internal/ubuntu hirsute/main armhf libgcc-10-dev armhf 10.2.1-6ubuntu1 [717 kB] Get:99 http://ftpmaster.internal/ubuntu hirsute/main armhf libisl23 armhf 0.23-1 [513 kB] Get:100 http://ftpmaster.internal/ubuntu hirsute/main armhf libmpc3 armhf 1.2.0-1 [36.1 kB] Get:101 http://ftpmaster.internal/ubuntu hirsute/main armhf libctf0 armhf 2.36-2ubuntu1 [82.2 kB] Get:102 http://ftpmaster.internal/ubuntu hirsute/main armhf libctf-nobfd0 armhf 2.36-2ubuntu1 [81.2 kB] Get:103 http://ftpmaster.internal/ubuntu hirsute/main armhf binutils-arm-linux-gnueabihf armhf 2.36-2ubuntu1 [2481 kB] Get:104 http://ftpmaster.internal/ubuntu hirsute/main armhf libbinutils armhf 2.36-2ubuntu1 [420 kB] Get:105 http://ftpmaster.internal/ubuntu hirsute/main armhf binutils armhf 2.36-2ubuntu1 [3372 B] Get:106 http://ftpmaster.internal/ubuntu hirsute/main armhf binutils-common armhf 2.36-2ubuntu1 [216 kB] Get:107 http://ftpmaster.internal/ubuntu hirsute/main armhf cpp-10 armhf 10.2.1-6ubuntu1 [6637 kB] Get:108 http://ftpmaster.internal/ubuntu hirsute/main armhf gcc-10-base armhf 10.2.1-6ubuntu1 [19.7 kB] Get:109 http://ftpmaster.internal/ubuntu hirsute/main armhf sensible-utils all 0.0.14 [13.5 kB] Get:110 http://ftpmaster.internal/ubuntu hirsute/main armhf libcap2 armhf 1:2.44-1 [14.7 kB] Get:111 http://ftpmaster.internal/ubuntu hirsute/main armhf readline-common all 8.1-1 [54.1 kB] Get:112 http://ftpmaster.internal/ubuntu hirsute/main armhf libreadline8 armhf 8.1-1 [115 kB] Get:113 http://ftpmaster.internal/ubuntu hirsute/main armhf libsqlite3-0 armhf 3.34.0-1 [504 kB] Get:114 http://ftpmaster.internal/ubuntu hirsute/main armhf openssl armhf 1.1.1f-1ubuntu5 [597 kB] Get:115 http://ftpmaster.internal/ubuntu hirsute/main armhf tzdata all 2021a-1ubuntu1 [294 kB] Get:116 http://ftpmaster.internal/ubuntu hirsute/main armhf dpkg-dev all 1.20.7.1ubuntu2 [935 kB] Get:117 http://ftpmaster.internal/ubuntu hirsute/main armhf libdpkg-perl all 1.20.7.1ubuntu2 [233 kB] Get:118 http://ftpmaster.internal/ubuntu hirsute/main armhf patch armhf 2.7.6-7 [102 kB] Get:119 http://ftpmaster.internal/ubuntu hirsute/main armhf lto-disabled-list all 1 [1996 B] Get:120 http://ftpmaster.internal/ubuntu hirsute/main armhf libfakeroot armhf 1.25.3-1.1 [23.2 kB] Get:121 http://ftpmaster.internal/ubuntu hirsute/main armhf fakeroot armhf 1.25.3-1.1 [60.9 kB] Get:122 http://ftpmaster.internal/ubuntu hirsute/main armhf libnpth0 armhf 1.6-3 [6980 B] Get:123 http://ftpmaster.internal/ubuntu hirsute/main armhf gpg armhf 2.2.20-1ubuntu2 [429 kB] Get:124 http://ftpmaster.internal/ubuntu hirsute/main armhf gpgconf armhf 2.2.20-1ubuntu2 [108 kB] Get:125 http://ftpmaster.internal/ubuntu hirsute/main armhf gpg-agent armhf 2.2.20-1ubuntu2 [196 kB] Get:126 http://ftpmaster.internal/ubuntu hirsute/main armhf liblockfile-bin armhf 1.17-1 [10.8 kB] Get:127 http://ftpmaster.internal/ubuntu hirsute/main armhf liblockfile1 armhf 1.17-1 [5616 B] Get:128 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu hirsute/main armhf g++ armhf 4:11-20201114-1ubuntu1 [1620 B] Get:129 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu hirsute/main armhf gcc armhf 4:11-20201114-1ubuntu1 [5236 B] Get:130 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu hirsute/main armhf cpp armhf 4:11-20201114-1ubuntu1 [27.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 238 MB in 5s (47.7 MB/s) (Reading database ... 12723 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.17-1ubuntu1_armhf.deb ... Unpacking libcrypt-dev:armhf (1:4.4.17-1ubuntu1) over (1:4.4.16-1ubuntu1) ... Preparing to unpack .../libc6-dev_2.32-0ubuntu6_armhf.deb ... Unpacking libc6-dev:armhf (2.32-0ubuntu6) over (2.32-0ubuntu3) ... Preparing to unpack .../libc-dev-bin_2.32-0ubuntu6_armhf.deb ... Unpacking libc-dev-bin (2.32-0ubuntu6) over (2.32-0ubuntu3) ... Preparing to unpack .../libcrypt1_1%3a4.4.17-1ubuntu1_armhf.deb ... Unpacking libcrypt1:armhf (1:4.4.17-1ubuntu1) over (1:4.4.16-1ubuntu1) ... Setting up libcrypt1:armhf (1:4.4.17-1ubuntu1) ... (Reading database ... 12722 files and directories currently installed.) Preparing to unpack .../0-linux-libc-dev_5.8.0-36.40+21.04.1_armhf.deb ... Unpacking linux-libc-dev:armhf (5.8.0-36.40+21.04.1) over (5.8.0-25.26) ... Preparing to unpack .../1-libtirpc-common_1.3.1-1_all.deb ... Unpacking libtirpc-common (1.3.1-1) over (1.2.6-1build1) ... 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Setting up init (1.60) ... Setting up libtirpc-common (1.3.1-1) ... Setting up perl-modules-5.32 (5.32.0-6) ... Setting up libsqlite3-0:armhf (3.34.0-1) ... Setting up binutils-common:armhf (2.36-2ubuntu1) ... Setting up linux-libc-dev:armhf (5.8.0-36.40+21.04.1) ... Setting up libctf-nobfd0:armhf (2.36-2ubuntu1) ... Setting up libnpth0:armhf (1.6-3) ... Setting up libgomp1:armhf (11-20210123-1ubuntu1) ... Setting up libcap2:armhf (1:2.44-1) ... Setting up libfakeroot:armhf (1.25.3-1.1) ... Setting up libasan6:armhf (11-20210123-1ubuntu1) ... Setting up libkrb5support0:armhf (1.18.3-4) ... Setting up tzdata (2021a-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Feb 6 08:50:57 UTC 2021. Universal Time is now: Sat Feb 6 08:50:57 UTC 2021. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.25.3-1.1) ... Setting up gcc-10-base:armhf (10.2.1-6ubuntu1) ... Setting up libncurses6:armhf (6.2+20201114-2) ... 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Setting up g++-11 (11-20210123-1ubuntu1) ... Setting up g++ (4:11-20201114-1ubuntu1) ... Processing triggers for libc-bin (2.32-0ubuntu6) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-20625810 armhf hirsute -c chroot:build-PACKAGEBUILD-20625810 --arch=armhf --dist=hirsute --nolog gromacs_2020.4-2.dsc Initiating build PACKAGEBUILD-20625810 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-135-generic #139-Ubuntu SMP Mon Jan 18 17:40:29 UTC 2021 armv7l sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-029.buildd +==============================================================================+ | gromacs 2020.4-2 (armhf) Sat, 06 Feb 2021 08:51:02 +0000 | +==============================================================================+ Package: gromacs Version: 2020.4-2 Source Version: 2020.4-2 Distribution: hirsute Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20625810/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- gromacs_2020.4-2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/gromacs-omYQrr/gromacs-2020.4' with '<>' I: NOTICE: Log filtering will replace 'build/gromacs-omYQrr' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-HyYpQ5/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-HyYpQ5/apt_archive ./ InRelease Get:2 copy:/<>/resolver-HyYpQ5/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-HyYpQ5/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-HyYpQ5/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-HyYpQ5/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (41.7 kB/s) Reading package lists... Reading package lists... Install core 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: cpp-10 g++-10 gcc-10 libgcc-10-dev libisl22 libperl5.30 libstdc++-10-dev perl-modules-5.30 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-HyYpQ5/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (57.2 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 15693 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: chrpath, cmake, debhelper-compat (= 13), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.10.2-7), libx11-dev, lsb-release, mpich, openmpi-bin, zlib1g-dev Filtered Build-Depends: chrpath, cmake, debhelper-compat (= 13), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.10.2-7), libx11-dev, lsb-release, mpich, openmpi-bin, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-gromacs-dummy' in '/<>/resolver-HyYpQ5/apt_archive/sbuild-build-depends-gromacs-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gromacs-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-HyYpQ5/apt_archive ./ InRelease Get:2 copy:/<>/resolver-HyYpQ5/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-HyYpQ5/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-HyYpQ5/apt_archive ./ Sources [586 B] Get:5 copy:/<>/resolver-HyYpQ5/apt_archive ./ Packages [667 B] Fetched 2216 B in 0s (40.8 kB/s) Reading package lists... Reading package lists... Install gromacs 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: g++-10 libisl22 libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils chrpath cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism distro-info-data dwz file gettext gettext-base gfortran gfortran-11 groff-base hwloc-nox ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libblas-dev libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libcbor0.6 libcurl4 libdebhelper-perl 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 libfabric1 libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-single3 libfido2-1 libfile-stripnondeterminism-perl libgfortran-11-dev libgfortran5 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhwloc-dev libhwloc-plugins libhwloc15 libhx509-5-heimdal libibverbs-dev libibverbs1 libicu67 libjs-jquery libjs-jquery-ui libjsoncpp24 libkrb5-26-heimdal liblapack-dev liblapack3 libldap-2.4-2 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmpdec3 libmpich-dev libmpich12 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librdmacm1 librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libuv1 libwind0-heimdal libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext6 libxml2 libxnvctrl0 lsb-release m4 mailcap man-db media-types mime-support mpich ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf python3 python3-minimal python3.9 python3.9-minimal x11proto-core-dev x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-multilib gfortran-doc gfortran-11-multilib gfortran-11-doc libcoarrays-dev groff lrzip liblapack-doc libboost-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev libfftw3-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils gcj-jdk libx11-doc libxcb-doc m4-doc apparmor less www-browser mpich-doc opencl-icd keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl python3-doc python3-tk python3-venv python3.9-venv python3.9-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libldap-common libcoarrays-openmpi-dev publicsuffix libsasl2-modules xauth libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils chrpath cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism distro-info-data dwz file gettext gettext-base gfortran gfortran-11 groff-base hwloc-nox ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libblas-dev libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libcbor0.6 libcurl4 libdebhelper-perl 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 libfabric1 libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-single3 libfido2-1 libfile-stripnondeterminism-perl libgfortran-11-dev libgfortran5 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhwloc-dev libhwloc-plugins libhwloc15 libhx509-5-heimdal libibverbs-dev libibverbs1 libicu67 libjs-jquery libjs-jquery-ui libjsoncpp24 libkrb5-26-heimdal liblapack-dev liblapack3 libldap-2.4-2 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmpdec3 libmpich-dev libmpich12 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librdmacm1 librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libuv1 libwind0-heimdal libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext6 libxml2 libxnvctrl0 lsb-release m4 mailcap man-db media-types mime-support mpich ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf python3 python3-minimal python3.9 python3.9-minimal sbuild-build-depends-gromacs-dummy x11proto-core-dev x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev 0 upgraded, 142 newly installed, 0 to remove and 0 not upgraded. Need to get 107 MB of archives. After this operation, 480 MB of additional disk space will be used. 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http://ftpmaster.internal/ubuntu hirsute/universe armhf chrpath armhf 0.16-2 [11.9 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main armhf cmake-data all 3.18.4-1ubuntu3 [1705 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main armhf libarchive13 armhf 3.4.3-2 [294 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/main armhf libbrotli1 armhf 1.0.9-2build2 [259 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/main armhf libroken18-heimdal armhf 7.7.0+dfsg-2 [34.5 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/main armhf libasn1-8-heimdal armhf 7.7.0+dfsg-2 [140 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main armhf libheimbase1-heimdal armhf 7.7.0+dfsg-2 [24.3 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main armhf libhcrypto4-heimdal armhf 7.7.0+dfsg-2 [78.5 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main armhf libwind0-heimdal armhf 7.7.0+dfsg-2 [47.2 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/main armhf libhx509-5-heimdal armhf 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http://ftpmaster.internal/ubuntu hirsute/main armhf libxdmcp-dev armhf 1:1.1.3-0ubuntu1 [24.0 kB] Get:129 http://ftpmaster.internal/ubuntu hirsute/main armhf xtrans-dev all 1.4.0-1 [68.9 kB] Get:130 http://ftpmaster.internal/ubuntu hirsute/main armhf libxcb1-dev armhf 1.14-2.1 [79.3 kB] Get:131 http://ftpmaster.internal/ubuntu hirsute/main armhf libx11-dev armhf 2:1.7.0-2 [589 kB] Get:132 http://ftpmaster.internal/ubuntu hirsute/universe armhf openmpi-common all 4.1.0-7ubuntu2 [158 kB] Get:133 http://ftpmaster.internal/ubuntu hirsute/universe armhf openmpi-bin armhf 4.1.0-7ubuntu2 [79.0 kB] Get:134 http://ftpmaster.internal/ubuntu hirsute/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2ubuntu4 [149 kB] Get:135 http://ftpmaster.internal/ubuntu hirsute/universe armhf hwloc-nox armhf 2.4.1~rc2+dfsg-1 [165 kB] Get:136 http://ftpmaster.internal/ubuntu hirsute/main armhf libnuma-dev armhf 2.0.12-1build1 [30.4 kB] Get:137 http://ftpmaster.internal/ubuntu hirsute/universe armhf libhwloc-dev armhf 2.4.1~rc2+dfsg-1 [200 kB] Get:138 http://ftpmaster.internal/ubuntu hirsute/main armhf libibverbs-dev armhf 33.1-1 [180 kB] Get:139 http://ftpmaster.internal/ubuntu hirsute/universe armhf libmpich12 armhf 3.4~a2+really3.3.2-2 [1047 kB] Get:140 http://ftpmaster.internal/ubuntu hirsute/universe armhf mpich armhf 3.4~a2+really3.3.2-2 [337 kB] Get:141 http://ftpmaster.internal/ubuntu hirsute/universe armhf libmpich-dev armhf 3.4~a2+really3.3.2-2 [1626 kB] Get:142 http://ftpmaster.internal/ubuntu hirsute/universe armhf libopenmpi-dev armhf 4.1.0-7ubuntu2 [1000 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 107 MB in 3s (30.9 MB/s) Selecting previously unselected package libpython3.9-minimal:armhf. (Reading database ... 15693 files and directories currently installed.) Preparing to unpack .../libpython3.9-minimal_3.9.1-3_armhf.deb ... Unpacking libpython3.9-minimal:armhf (3.9.1-3) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.2.10-1_armhf.deb ... Unpacking libexpat1:armhf (2.2.10-1) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../python3.9-minimal_3.9.1-3_armhf.deb ... Unpacking python3.9-minimal (3.9.1-3) ... Setting up libpython3.9-minimal:armhf (3.9.1-3) ... Setting up libexpat1:armhf (2.2.10-1) ... Setting up python3.9-minimal (3.9.1-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 15986 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.0-3ubuntu1_armhf.deb ... Unpacking python3-minimal (3.9.0-3ubuntu1) ... Selecting previously unselected package media-types. 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Setting up bsdextrautils (2.36.1-1ubuntu2) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:armhf (67.1-5) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up distro-info-data (0.46) ... Setting up libdebhelper-perl (13.3.1ubuntu1) ... Setting up libbrotli1:armhf (1.0.9-2build2) ... Setting up libnghttp2-14:armhf (1.42.0-1) ... Setting up libmagic1:armhf (1:5.39-3) ... Setting up gettext-base (0.21-3ubuntu2) ... Setting up file (1:5.39-3) ... Setting up libcbor0.6:armhf (0.6.0-0ubuntu3) ... Setting up libpthread-stubs0-dev:armhf (0.4-1) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-2ubuntu1) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:armhf (3.9.0-3ubuntu1) ... 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 libuv1:armhf (1.40.0-1) ... Setting up libx11-data (2:1.7.0-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build2) ... Setting up libsigsegv2:armhf (2.13-1) ... Setting up libhwloc15:armhf (2.4.1~rc2+dfsg-1) ... Setting up libevent-core-2.1-7:armhf (2.1.12-stable-1) ... Setting up libevent-2.1-7:armhf (2.1.12-stable-1) ... Setting up autopoint (0.21-3ubuntu2) ... Setting up libltdl7:armhf (2.4.6-15) ... Setting up libfftw3-double3:armhf (3.3.8-2ubuntu6) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-2ubuntu1) ... Setting up libssh-4:armhf (0.9.5-1) ... Setting up libgfortran5:armhf (11-20210123-1ubuntu1) ... Setting up libroken18-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libjsoncpp24:armhf (1.9.4-4) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2ubuntu4) ... Setting up libnuma1:armhf (2.0.12-1build1) ... Setting up libmpich12:armhf (3.4~a2+really3.3.2-2) ... Setting up ocl-icd-libopencl1:armhf (2.2.14-2) ... Setting up librhash0:armhf (1.4.1-1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libnl-3-200:armhf (3.4.0-1) ... Setting up libmpdec3:armhf (2.5.1-1) ... Setting up openmpi-common (4.1.0-7ubuntu2) ... Setting up libsub-override-perl (0.09-2) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up cmake-data (3.18.4-1ubuntu3) ... Setting up libboost-dev:armhf (1.74.0.3ubuntu2) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up libfido2-1:armhf (1.6.0-2) ... Setting up libbsd0:armhf (0.10.0-1) ... Setting up mailcap (3.68ubuntu1) ... Setting up libelf1:armhf (0.182-3) ... Setting up libxml2:armhf (2.9.10+dfsg-6.3build1) ... Setting up chrpath (0.16-2) ... Setting up libblas-dev:armhf (3.9.0-3ubuntu1) ... 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 libpython3.9-stdlib:armhf (3.9.1-3) ... Setting up libpython3-stdlib:armhf (3.9.0-3ubuntu1) ... Setting up libheimbase1-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-1) ... Setting up x11proto-dev (2020.1-1) ... Setting up libfile-stripnondeterminism-perl (1.10.0-1) ... Setting up libxdmcp6:armhf (1:1.1.3-0ubuntu1) ... Setting up libevent-extra-2.1-7:armhf (2.1.12-stable-1) ... Setting up liblapack3:armhf (3.9.0-3ubuntu1) ... 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 (1.14-2.1) ... Setting up gettext (0.21-3ubuntu2) ... Setting up mime-support (3.66) ... Setting up libxau-dev:armhf (1:1.0.9-0ubuntu1) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:armhf (3.4.3-2) ... Setting up libfftw3-bin (3.3.8-2ubuntu6) ... Setting up libgfortran-11-dev:armhf (11-20210123-1ubuntu1) ... Setting up libasn1-8-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libedit2:armhf (3.1-20191231-2) ... Setting up hwloc-nox (2.4.1~rc2+dfsg-1) ... Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-1) ... Setting up m4 (1.4.18-5) ... Setting up libhcrypto4-heimdal:armhf (7.7.0+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnuma-dev:armhf (2.0.12-1build1) ... Setting up libnl-route-3-200:armhf (3.4.0-1) ... Setting up libxdmcp-dev:armhf (1:1.1.3-0ubuntu1) ... Setting up libwind0-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libjs-jquery-ui (1.12.1+dfsg-8) ... Setting up x11proto-core-dev (2020.1-1) ... Setting up libevent-dev (2.1.12-stable-1) ... Setting up liblapack-dev:armhf (3.9.0-3ubuntu1) ... 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 gfortran-11 (11-20210123-1ubuntu1) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.10.0-1) ... Setting up dwz (0.13+20210126-1) ... Setting up libnl-3-dev:armhf (3.4.0-1) ... Setting up groff-base (1.22.4-6) ... Setting up libx11-6:armhf (2:1.7.0-2) ... Setting up libfftw3-dev:armhf (3.3.8-2ubuntu6) ... Setting up python3.9 (3.9.1-3) ... Setting up automake (1:1.16.3-2ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libibverbs1:armhf (33.1-1) ... Setting up libxcb1-dev:armhf (1.14-2.1) ... Setting up ibverbs-providers:armhf (33.1-1) ... Setting up mpich (3.4~a2+really3.3.2-2) ... update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode Setting up openssh-client (1:8.4p1-3) ... Setting up libhx509-5-heimdal:armhf (7.7.0+dfsg-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libx11-dev:armhf (2:1.7.0-2) ... Setting up libxext6:armhf (2:1.3.4-0ubuntu1) ... Setting up python3 (3.9.0-3ubuntu1) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up gfortran (4:11-20201114-1ubuntu1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libxnvctrl0:armhf (440.82-0ubuntu1) ... Setting up libnl-route-3-dev:armhf (3.4.0-1) ... Setting up libltdl-dev:armhf (2.4.6-15) ... Setting up libmpich-dev:armhf (3.4~a2+really3.3.2-2) ... update-alternatives: using /usr/include/arm-linux-gnueabihf/mpich to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode Setting up libhwloc-dev:armhf (2.4.1~rc2+dfsg-1) ... Setting up lsb-release (11.1.0ubuntu2) ... Setting up libkrb5-26-heimdal:armhf (7.7.0+dfsg-2) ... Setting up librdmacm1:armhf (33.1-1) ... Setting up libibverbs-dev:armhf (33.1-1) ... Setting up libhwloc-plugins:armhf (2.4.1~rc2+dfsg-1) ... Setting up libheimntlm0-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libfabric1 (1.11.0-2) ... Setting up libpmix2:armhf (4.0.0-4ubuntu1) ... Setting up libopenmpi3:armhf (4.1.0-7ubuntu2) ... Setting up libldap-2.4-2:armhf (2.4.56+dfsg-1ubuntu2) ... Setting up libcurl4:armhf (7.74.0-1ubuntu1) ... Setting up libpmix-dev:armhf (4.0.0-4ubuntu1) ... Setting up openmpi-bin (4.1.0-7ubuntu2) ... 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 cmake (3.18.4-1ubuntu3) ... Setting up libopenmpi-dev:armhf (4.1.0-7ubuntu2) ... 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 debhelper (13.3.1ubuntu1) ... Setting up sbuild-build-depends-gromacs-dummy (0.invalid.0) ... Setting up dh-autoreconf (19) ... Processing triggers for libc-bin (2.32-0ubuntu6) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-135-generic arm64 (armv7l) Toolchain package versions: binutils_2.36-2ubuntu1 dpkg-dev_1.20.7.1ubuntu2 g++-10_10.2.1-6ubuntu1 g++-11_11-20210123-1ubuntu1 gcc-10_10.2.1-6ubuntu1 gcc-11_11-20210123-1ubuntu1 libc6-dev_2.32-0ubuntu6 libstdc++-10-dev_10.2.1-6ubuntu1 libstdc++-11-dev_11-20210123-1ubuntu1 libstdc++6_11-20210123-1ubuntu1 linux-libc-dev_5.8.0-36.40+21.04.1 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1build1 apt_2.1.18 autoconf_2.69-14 automake_1:1.16.3-2ubuntu1 autopoint_0.21-3ubuntu2 autotools-dev_20180224.1+nmu1 base-files_11ubuntu16 base-passwd_3.5.48 bash_5.1-1ubuntu1 binutils_2.36-2ubuntu1 binutils-arm-linux-gnueabihf_2.36-2ubuntu1 binutils-common_2.36-2ubuntu1 bsdextrautils_2.36.1-1ubuntu2 bsdutils_1:2.36.1-1ubuntu2 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 ca-certificates_20200601 chrpath_0.16-2 cmake_3.18.4-1ubuntu3 cmake-data_3.18.4-1ubuntu3 coreutils_8.32-4ubuntu2 cpp_4:11-20201114-1ubuntu1 cpp-10_10.2.1-6ubuntu1 cpp-11_11-20210123-1ubuntu1 dash_0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1 debconf_1.5.74 debhelper_13.3.1ubuntu1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.10.0-1 diffutils_1:3.7-3ubuntu1 distro-info-data_0.46 dpkg_1.20.7.1ubuntu2 dpkg-dev_1.20.7.1ubuntu2 dwz_0.13+20210126-1 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.7.0-1ubuntu2 g++_4:11-20201114-1ubuntu1 g++-10_10.2.1-6ubuntu1 g++-11_11-20210123-1ubuntu1 gcc_4:11-20201114-1ubuntu1 gcc-10_10.2.1-6ubuntu1 gcc-10-base_10.2.1-6ubuntu1 gcc-11_11-20210123-1ubuntu1 gcc-11-base_11-20210123-1ubuntu1 gettext_0.21-3ubuntu2 gettext-base_0.21-3ubuntu2 gfortran_4:11-20201114-1ubuntu1 gfortran-11_11-20210123-1ubuntu1 gpg_2.2.20-1ubuntu2 gpg-agent_2.2.20-1ubuntu2 gpgconf_2.2.20-1ubuntu2 gpgv_2.2.20-1ubuntu2 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-2ubuntu3 hostname_3.23 hwloc-nox_2.4.1~rc2+dfsg-1 ibverbs-providers_33.1-1 init_1.60 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-9 libapparmor1_3.0.0-0ubuntu5 libapt-pkg6.0_2.1.18 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libargon2-1_0~20171227-0.2build20.10.0 libasan6_11-20210123-1ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-2 libassuan0_2.5.3-7.1 libatomic1_11-20210123-1ubuntu1 libattr1_1:2.4.48-6 libaudit-common_1:2.8.5-3ubuntu3 libaudit1_1:2.8.5-3ubuntu3 libbinutils_2.36-2ubuntu1 libblas-dev_3.9.0-3ubuntu1 libblas3_3.9.0-3ubuntu1 libblkid1_2.36.1-1ubuntu2 libboost-dev_1.74.0.3ubuntu2 libboost1.74-dev_1.74.0-3ubuntu2 libbrotli1_1.0.9-2build2 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-4ubuntu2 libc-bin_2.32-0ubuntu6 libc-dev-bin_2.32-0ubuntu6 libc6_2.32-0ubuntu6 libc6-dev_2.32-0ubuntu6 libcap-ng0_0.7.9-2.2build1 libcap2_1:2.44-1 libcbor0.6_0.6.0-0ubuntu3 libcc1-0_11-20210123-1ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcrypt-dev_1:4.4.17-1ubuntu1 libcrypt1_1:4.4.17-1ubuntu1 libcryptsetup12_2:2.3.4-1ubuntu1 libctf-nobfd0_2.36-2ubuntu1 libctf0_2.36-2ubuntu1 libcurl4_7.74.0-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu3 libdebconfclient0_0.256ubuntu1 libdebhelper-perl_13.3.1ubuntu1 libdevmapper1.02.1_2:1.02.167-1ubuntu4 libdpkg-perl_1.20.7.1ubuntu2 libedit2_3.1-20191231-2 libelf1_0.182-3 libevent-2.1-7_2.1.12-stable-1 libevent-core-2.1-7_2.1.12-stable-1 libevent-dev_2.1.12-stable-1 libevent-extra-2.1-7_2.1.12-stable-1 libevent-openssl-2.1-7_2.1.12-stable-1 libevent-pthreads-2.1-7_2.1.12-stable-1 libexpat1_2.2.10-1 libext2fs2_1.45.6-1ubuntu1 libfabric1_1.11.0-2 libfakeroot_1.25.3-1.1 libffi8ubuntu1_3.4~20200819gead65ca871-0ubuntu3 libfftw3-bin_3.3.8-2ubuntu6 libfftw3-dev_3.3.8-2ubuntu6 libfftw3-double3_3.3.8-2ubuntu6 libfftw3-single3_3.3.8-2ubuntu6 libfido2-1_1.6.0-2 libfile-stripnondeterminism-perl_1.10.0-1 libgcc-10-dev_10.2.1-6ubuntu1 libgcc-11-dev_11-20210123-1ubuntu1 libgcc-s1_11-20210123-1ubuntu1 libgcrypt20_1.8.7-2ubuntu1 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgfortran-11-dev_11-20210123-1ubuntu1 libgfortran5_11-20210123-1ubuntu1 libgmp10_2:6.2.0+dfsg-6ubuntu1 libgnutls30_3.7.0-5ubuntu1 libgomp1_11-20210123-1ubuntu1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-4 libgssapi3-heimdal_7.7.0+dfsg-2 libhcrypto4-heimdal_7.7.0+dfsg-2 libheimbase1-heimdal_7.7.0+dfsg-2 libheimntlm0-heimdal_7.7.0+dfsg-2 libhogweed6_3.7-2 libhwloc-dev_2.4.1~rc2+dfsg-1 libhwloc-plugins_2.4.1~rc2+dfsg-1 libhwloc15_2.4.1~rc2+dfsg-1 libhx509-5-heimdal_7.7.0+dfsg-2 libibverbs-dev_33.1-1 libibverbs1_33.1-1 libicu67_67.1-5 libidn2-0_2.3.0-5 libip4tc2_1.8.5-3ubuntu4 libisl22_0.22.1-1 libisl23_0.23-1 libjs-jquery_3.5.1+dfsg+~3.5.5-7 libjs-jquery-ui_1.12.1+dfsg-8 libjson-c5_0.15-2 libjsoncpp24_1.9.4-4 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27+20200310-2ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 liblapack-dev_3.9.0-3ubuntu1 liblapack3_3.9.0-3ubuntu1 libldap-2.4-2_2.4.56+dfsg-1ubuntu2 liblockfile-bin_1.17-1 liblockfile1_1.17-1 libltdl-dev_2.4.6-15 libltdl7_2.4.6-15 liblz4-1_1.9.3-0ubuntu1 liblzma5_5.2.4-1ubuntu1 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-1ubuntu2 libmpc3_1.2.0-1 libmpdec3_2.5.1-1 libmpfr6_4.1.0-3 libmpich-dev_3.4~a2+really3.3.2-2 libmpich12_3.4~a2+really3.3.2-2 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 libnettle8_3.7-2 libnghttp2-14_1.42.0-1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-0ubuntu3 libnsl2_1.3.0-0ubuntu3 libnss-nis_3.1-0ubuntu4 libnss-nisplus_1.3-0ubuntu4 libnuma-dev_2.0.12-1build1 libnuma1_2.0.12-1build1 libopenmpi-dev_4.1.0-7ubuntu2 libopenmpi3_4.1.0-7ubuntu2 libp11-kit0_0.23.22-1 libpam-modules_1.3.1-5ubuntu6 libpam-modules-bin_1.3.1-5ubuntu6 libpam-runtime_1.3.1-5ubuntu6 libpam0g_1.3.1-5ubuntu6 libpciaccess0_0.16-1 libpcre2-8-0_10.35-2ubuntu1 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libperl5.32_5.32.0-6 libpipeline1_1.5.3-1 libpmix-dev_4.0.0-4ubuntu1 libpmix2_4.0.0-4ubuntu1 libpng16-16_1.6.37-3 libprocps8_2:3.3.16-5ubuntu2 libpsl5_0.21.0-1.1ubuntu1 libpthread-stubs0-dev_0.4-1 libpython3-stdlib_3.9.0-3ubuntu1 libpython3.9-minimal_3.9.1-3 libpython3.9-stdlib_3.9.1-3 librdmacm1_33.1-1 libreadline8_8.1-1 librhash0_1.4.1-1 libroken18-heimdal_7.7.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2build2 libsasl2-2_2.1.27+dfsg-2ubuntu1 libsasl2-modules-db_2.1.27+dfsg-2ubuntu1 libseccomp2_2.4.3-1ubuntu6 libselinux1_3.1-2build2 libsemanage-common_3.1-1build2 libsemanage1_3.1-1build2 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.36.1-1ubuntu2 libsqlite3-0_3.34.0-1 libss2_1.45.6-1ubuntu1 libssh-4_0.9.5-1 libssl1.1_1.1.1f-1ubuntu5 libstdc++-10-dev_10.2.1-6ubuntu1 libstdc++-11-dev_11-20210123-1ubuntu1 libstdc++6_11-20210123-1ubuntu1 libsub-override-perl_0.09-2 libsystemd0_247.1-4ubuntu1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_11-20210123-1ubuntu1 libuchardet0_0.0.7-1 libudev1_247.1-4ubuntu1 libunistring2_0.9.10-4 libuuid1_2.36.1-1ubuntu2 libuv1_1.40.0-1 libwind0-heimdal_7.7.0+dfsg-2 libx11-6_2:1.7.0-2 libx11-data_2:1.7.0-2 libx11-dev_2:1.7.0-2 libxau-dev_1:1.0.9-0ubuntu1 libxau6_1:1.0.9-0ubuntu1 libxcb1_1.14-2.1 libxcb1-dev_1.14-2.1 libxdmcp-dev_1:1.1.3-0ubuntu1 libxdmcp6_1:1.1.3-0ubuntu1 libxext6_2:1.3.4-0ubuntu1 libxml2_2.9.10+dfsg-6.3build1 libxnvctrl0_440.82-0ubuntu1 libxxhash0_0.8.0-2 libzstd1_1.4.8+dfsg-1 linux-libc-dev_5.8.0-36.40+21.04.1 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu8 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 lsb-release_11.1.0ubuntu2 lto-disabled-list_1 m4_1.4.18-5 mailcap_3.68ubuntu1 make_4.3-4ubuntu1 man-db_2.9.3-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mime-support_3.66 mount_2.36.1-1ubuntu2 mpich_3.4~a2+really3.3.2-2 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 ocl-icd-libopencl1_2.2.14-2 openmpi-bin_4.1.0-7ubuntu2 openmpi-common_4.1.0-7ubuntu2 openssh-client_1:8.4p1-3 openssl_1.1.1f-1ubuntu5 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu8 patch_2.7.6-7 perl_5.32.0-6 perl-base_5.32.0-6 perl-modules-5.30_5.30.3-4 perl-modules-5.32_5.32.0-6 pinentry-curses_1.1.0-4build1 pkgbinarymangler_146 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-5ubuntu2 python3_3.9.0-3ubuntu1 python3-minimal_3.9.0-3ubuntu1 python3.9_3.9.1-3 python3.9-minimal_3.9.1-3 readline-common_8.1-1 rpcsvc-proto_1.4.2-0ubuntu4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gromacs-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.14 systemd_247.1-4ubuntu1 systemd-sysv_247.1-4ubuntu1 systemd-timesyncd_247.1-4ubuntu1 sysvinit-utils_2.96-5ubuntu1 tar_1.32+dfsg-1 tzdata_2021a-1ubuntu1 ubuntu-keyring_2020.06.17.1 util-linux_2.36.1-1ubuntu2 x11proto-core-dev_2020.1-1 x11proto-dev_2020.1-1 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.2.4-1ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu4 zlib1g-dev_1:1.2.11.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Oct 22 02:13:15 2020 UTC gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F gpgv: issuer "nbreen@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gromacs_2020.4-2.dsc dpkg-source: info: extracting gromacs in /<> dpkg-source: info: unpacking gromacs_2020.4.orig.tar.gz dpkg-source: info: unpacking gromacs_2020.4-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable-listed-forces-test.patch dpkg-source: info: applying arm64-disable-numa-test.patch dpkg-source: info: applying readme.patch dpkg-source: info: applying copyright-file.patch dpkg-source: info: applying disable-cpuinfotest.patch dpkg-source: info: applying mdrun-test-timeout.patch dpkg-source: info: applying local-mathjax.patch dpkg-source: info: applying mpi-tests-localhost.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym 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-20625810 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20625810 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20625810 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2020.4-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh_testdir dh_testroot rm -rf build docs/doxygen/*.pyc dh_clean build-basic build-mpich build-openmpi build-manual configure-stamp \ debian/gromacs-mpich.README.Debian debian/gromacs-openmpi.README.Debian debian/rules binary-arch dh_testdir (mkdir -p build/basic; cd build/basic; cmake /<> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Ubuntu-2020.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_INSTALL_LEGACY_API=ON) -- The C compiler identification is GNU 11.0.0 -- The CXX compiler identification is GNU 11.0.0 -- 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 -- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- 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 unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1rc2", minimum required is "1.5") -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so -- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - ARMv8 Processor rev 1 (v8l) -- Detected build CPU family - 8 -- Detected build CPU model - 0 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64 -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Using dynamic plugins (e.g VMD-supported file formats) -- Checking for suitable VMD version -- VMD plugins not found. Path to VMD can be set with VMDDIR. -- Using default binary suffix: "" -- Using default library suffix: "" -- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized Traceback (most recent call last): File "", line 1, in ModuleNotFoundError: No module named 'pygments' -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1") -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Doxygen not found. Documentation targets will not be generated. -- Configuring done -- Generating done -- Build files have been written to: /<>/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake /<> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Ubuntu-2020.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 11.0.0 -- The CXX compiler identification is GNU 11.0.0 -- 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 CMake Warning at cmake/gmxManageGPU.cmake:53 (message): GPU acceleration is not available in double precision, disabled! Call Stack (most recent call first): CMakeLists.txt:217 (include) -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- 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 unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1rc2", minimum required is "1.5") -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so -- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - ARMv8 Processor rev 1 (v8l) -- Detected build CPU family - 8 -- Detected build CPU model - 0 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64 -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3, trying generic detection -- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Using dynamic plugins (e.g VMD-supported file formats) -- Checking for suitable VMD version -- VMD plugins not found. Path to VMD can be set with VMDDIR. -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized Traceback (most recent call last): File "", line 1, in ModuleNotFoundError: No module named 'pygments' -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1") -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Doxygen not found. Documentation targets will not be generated. -- Configuring done -- Generating done -- Build files have been written to: /<>/build/basic-dp (mkdir -p build/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \ /<> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Ubuntu-2020.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich") -- The C compiler identification is GNU 11.0.0 -- The CXX compiler identification is GNU 11.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc.mpich - 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/mpicxx.mpich - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- 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 unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1rc2", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - ARMv8 Processor rev 1 (v8l) -- Detected build CPU family - 8 -- Detected build CPU model - 0 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64 -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi.mpich" -- Using manually set library suffix: "_mpi.mpich" -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /<>/build/mpich (mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \ /<> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Ubuntu-2020.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich") -- The C compiler identification is GNU 11.0.0 -- The CXX compiler identification is GNU 11.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc.mpich - 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/mpicxx.mpich - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning at cmake/gmxManageGPU.cmake:53 (message): GPU acceleration is not available in double precision, disabled! Call Stack (most recent call first): CMakeLists.txt:217 (include) -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- 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 unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1rc2", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - ARMv8 Processor rev 1 (v8l) -- Detected build CPU family - 8 -- Detected build CPU model - 0 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64 -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3, trying generic detection -- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi_d.mpich" -- Using manually set library suffix: "_mpi_d.mpich" -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /<>/build/mpich-dp (mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \ /<> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Ubuntu-2020.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi") -- The C compiler identification is GNU 11.0.0 -- The CXX compiler identification is GNU 11.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc.openmpi - 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/mpicxx.openmpi - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- 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 unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1rc2", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - ARMv8 Processor rev 1 (v8l) -- Detected build CPU family - 8 -- Detected build CPU model - 0 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64 -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Looking for fftwf_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so -- Looking for fftwf_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi.openmpi" -- Using manually set library suffix: "_mpi.openmpi" -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /<>/build/openmpi (mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \ /<> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Ubuntu-2020.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi") -- The C compiler identification is GNU 11.0.0 -- The CXX compiler identification is GNU 11.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc.openmpi - 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/mpicxx.openmpi - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Warning at cmake/gmxManageGPU.cmake:53 (message): GPU acceleration is not available in double precision, disabled! Call Stack (most recent call first): CMakeLists.txt:217 (include) -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- 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 unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1rc2", minimum required is "1.5") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so -- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - ARMv8 Processor rev 1 (v8l) -- Detected build CPU family - 8 -- Detected build CPU model - 0 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon -- Disabling RDTSCP support -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64 -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- pkg-config could not detect fftw3, trying generic detection -- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi_d.openmpi" -- Using manually set library suffix: "_mpi_d.openmpi" -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Performing Test HAS_NO_CLASS_MEMACCESS -- Performing Test HAS_NO_CLASS_MEMACCESS - Success -- Check if the system is big endian -- Searching 16 bit integer -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /<>/build/openmpi-dp touch configure-stamp dh_testdir /usr/bin/make -j4 -C build/basic make[1]: Entering directory '/<>/build/basic' /usr/bin/cmake -S/<> -B/<>/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/build/basic/CMakeFiles /<>/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/gromacs/selection /<>/build/basic /<>/build/basic/src/gromacs/selection /<>/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/build/basic /<>/build/basic /<>/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/gromacs /<>/build/basic /<>/build/basic/src/gromacs /<>/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/gromacs /<>/build/basic /<>/build/basic/src/gromacs /<>/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= Scanning dependencies of target release-version-info make[3]: Leaving directory '/<>/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/<>/build/basic' cd /<> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.4-Ubuntu-2020.4-2 -D PROJECT_SOURCE_DIR=/<> -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/<>/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<>/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Ubuntu-2020.4-2 -P /<>/cmake/gmxGenerateVersionInfoRelease.cmake Scanning dependencies of target scanner make[3]: Leaving directory '/<>/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<>/src/gromacs/selection/parser.cpp Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/<>/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Leaving directory '/<>/build/basic' make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<>/src/external/tng_io/src/compression/bwlzh.c Scanning dependencies of target thread_mpi make[3]: Leaving directory '/<>/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build [ 0%] Built target release-version-info /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<>/src/external/thread_mpi/src/errhandler.cpp make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/gromacs /<>/build/basic /<>/build/basic/src/gromacs /<>/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/<>/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<>/src/external/lmfit/lmmin.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<>/src/external/thread_mpi/src/tmpi_malloc.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<>/src/external/thread_mpi/src/atomic.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<>/src/external/thread_mpi/src/lock.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<>/src/external/thread_mpi/src/pthreads.cpp cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<>/src/external/tng_io/src/compression/bwt.c cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<>/src/external/thread_mpi/src/system_error.cpp cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<>/src/external/tng_io/src/compression/coder.c cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /<>/src/external/thread_mpi/src/alltoall.cpp make[3]: Leaving directory '/<>/build/basic' [ 0%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/gromacs/linearalgebra /<>/build/basic /<>/build/basic/src/gromacs/linearalgebra /<>/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= Scanning dependencies of target linearalgebra make[3]: Leaving directory '/<>/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<>/src/gromacs/linearalgebra/eigensolver.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<>/src/external/thread_mpi/src/p2p_protocol.cpp cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<>/src/external/tng_io/src/compression/dict.c cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<>/src/external/tng_io/src/compression/fixpoint.c cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<>/src/external/tng_io/src/compression/huffman.c cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<>/src/external/thread_mpi/src/barrier.cpp cd /<>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<>/src/gromacs/linearalgebra/gmx_arpack.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<>/src/external/thread_mpi/src/p2p_send_recv.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<>/src/external/thread_mpi/src/bcast.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /<>/src/external/thread_mpi/src/p2p_wait.cpp cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<>/src/external/tng_io/src/compression/huffmem.c cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /<>/src/external/thread_mpi/src/collective.cpp cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<>/src/external/tng_io/src/compression/lz77.c cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /<>/src/external/thread_mpi/src/profile.cpp cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<>/src/external/tng_io/src/compression/merge_sort.c cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /<>/src/external/thread_mpi/src/comm.cpp cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<>/src/external/tng_io/src/compression/mtf.c cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<>/src/external/tng_io/src/compression/rle.c cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /<>/src/external/thread_mpi/src/reduce.cpp cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<>/src/external/tng_io/src/compression/tng_compress.c cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /<>/src/external/thread_mpi/src/event.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /<>/src/external/thread_mpi/src/reduce_fast.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /<>/src/external/thread_mpi/src/gather.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<>/src/external/thread_mpi/src/scatter.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /<>/src/external/thread_mpi/src/group.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<>/src/external/thread_mpi/src/tmpi_init.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /<>/src/external/thread_mpi/src/topology.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /<>/src/external/thread_mpi/src/list.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /<>/src/external/thread_mpi/src/type.cpp cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<>/src/external/tng_io/src/compression/vals16.c cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<>/src/external/tng_io/src/compression/warnmalloc.c cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<>/src/external/tng_io/src/compression/widemuldiv.c cd /<>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<>/src/gromacs/linearalgebra/matrix.cpp cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<>/src/external/tng_io/src/compression/xtc2.c cd /<>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<>/src/gromacs/linearalgebra/nrjac.cpp cd /<>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<>/src/gromacs/linearalgebra/sparsematrix.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /<>/src/external/thread_mpi/src/scan.cpp cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<>/src/external/tng_io/src/compression/xtc3.c cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<>/src/external/thread_mpi/src/numa_malloc.cpp cd /<>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<>/src/external/thread_mpi/src/once.cpp make[3]: Leaving directory '/<>/build/basic' [ 0%] Built target linearalgebra /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/gromacs/modularsimulator /<>/build/basic /<>/build/basic/src/gromacs/modularsimulator /<>/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/build/basic' [ 3%] Built target thread_mpi /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend Scanning dependencies of target modularsimulator make[3]: Leaving directory '/<>/build/basic' make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/gromacs/fileio /<>/build/basic /<>/build/basic/src/gromacs/fileio /<>/build/basic/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<>/src/gromacs/modularsimulator/checkpointhelper.cpp Scanning dependencies of target vmddlopen make[3]: Leaving directory '/<>/build/basic' /usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic/src/gromacs/fileio && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/vmddlopen.dir/__/__/external/vmd_molfile/vmddlopen.cpp.o -c /<>/src/external/vmd_molfile/vmddlopen.cpp make[3]: Leaving directory '/<>/build/basic' [ 3%] Built target vmddlopen /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/programs /<>/build/basic /<>/build/basic/src/programs /<>/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/<>/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<>/src/programs/mdrun/mdrun.cpp cd /<>/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<>/src/gromacs/selection/scanner.cpp cd /<>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<>/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<>/src/external/tng_io/src/lib/tng_io.c make[3]: Leaving directory '/<>/build/basic' [ 4%] Built target scanner /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/programs /<>/build/basic /<>/build/basic/src/programs /<>/build/basic/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target view_objlib make[3]: Leaving directory '/<>/build/basic' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[3]: Entering directory '/<>/build/basic' cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /<>/src/programs/view/3dview.cpp cd /<>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<>/src/gromacs/modularsimulator/computeglobalselement.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<>/src/programs/mdrun/nonbonded_bench.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<>/src/programs/view/buttons.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<>/src/programs/view/dialogs.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<>/src/programs/view/fgrid.cpp make[3]: Leaving directory '/<>/build/basic' [ 4%] Built target mdrun_objlib cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /<>/src/programs/view/filter.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /<>/src/programs/view/logo.cpp cd /<>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<>/src/gromacs/modularsimulator/constraintelement.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<>/src/programs/view/manager.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<>/src/programs/view/molps.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<>/src/programs/view/nleg.cpp cd /<>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<>/src/gromacs/modularsimulator/domdechelper.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<>/src/programs/view/nmol.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<>/src/programs/view/popup.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<>/src/programs/view/pulldown.cpp cd /<>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<>/src/gromacs/modularsimulator/energyelement.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<>/src/programs/view/view.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<>/src/programs/view/x11.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<>/src/programs/view/xdlg.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<>/src/programs/view/xdlghi.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<>/src/programs/view/xdlgitem.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<>/src/programs/view/xmb.cpp cd /<>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<>/src/programs/view/xutil.cpp cd /<>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<>/src/gromacs/modularsimulator/forceelement.cpp cd /<>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp make[3]: Leaving directory '/<>/build/basic' [ 7%] Built target view_objlib cd /<>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<>/src/gromacs/modularsimulator/modularsimulator.cpp cd /<>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp In file included from /<>/src/gromacs/modularsimulator/modularsimulator.cpp:44: /<>/src/gromacs/modularsimulator/modularsimulator.h:269:31: error: ‘numeric_limits’ is not a member of ‘std’ 269 | Step lastStep_ = std::numeric_limits::max(); | ^~~~~~~~~~~~~~ /<>/src/gromacs/modularsimulator/modularsimulator.h:269:50: error: expected primary-expression before ‘>’ token 269 | Step lastStep_ = std::numeric_limits::max(); | ^ /<>/src/gromacs/modularsimulator/modularsimulator.h:269:53: error: ‘::max’ has not been declared; did you mean ‘std::max’? 269 | Step lastStep_ = std::numeric_limits::max(); | ^~~ | std::max cd /<>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp In file included from /usr/include/c++/11/algorithm:62, from /<>/src/gromacs/math/vectypes.h:42, from /<>/src/gromacs/mdlib/vcm.h:44, from /<>/src/gromacs/mdlib/md_support.h:40, from /<>/src/gromacs/modularsimulator/modularsimulator.h:46, from /<>/src/gromacs/modularsimulator/modularsimulator.cpp:44: /usr/include/c++/11/bits/stl_algo.h:3467:5: note: ‘std::max’ declared here 3467 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ cd /<>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<>/build/basic/src -I/<>/src -I/<>/src/external/tng_io/include -I/<>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<>/src/external/tng_io/src/lib/md5.c make[3]: Leaving directory '/<>/build/basic' [ 9%] Built target tng_io_obj cd /<>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<>/src/gromacs/modularsimulator/propagator.cpp cd /<>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<>/src/gromacs/modularsimulator/shellfcelement.cpp cd /<>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<>/src/gromacs/modularsimulator/signallers.cpp cd /<>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<>/src/gromacs/modularsimulator/statepropagatordata.cpp cd /<>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<>/build/basic/src -I/<>/src -isystem /<>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<>/src/gromacs/modularsimulator/topologyholder.cpp make[3]: *** [src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make:177: src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o] Error 1 make[3]: *** Waiting for unfinished jobs.... make[3]: Leaving directory '/<>/build/basic' make[2]: *** [CMakeFiles/Makefile2:5197: src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/all] Error 2 make[2]: Leaving directory '/<>/build/basic' make[1]: *** [Makefile:185: all] Error 2 make[1]: Leaving directory '/<>/build/basic' make: *** [debian/rules:126: build-basic] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2021-02-06T09:00:22Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: n/a Build-Time: 486 Distribution: hirsute Fail-Stage: build Host Architecture: armhf Install-Time: 68 Job: gromacs_2020.4-2.dsc Machine Architecture: arm64 Package: gromacs Package-Time: 560 Source-Version: 2020.4-2 Space: n/a Status: attempted Version: 2020.4-2 -------------------------------------------------------------------------------- Finished at 2021-02-06T09:00:22Z Build needed 00:09:20, no disk space E: Build failure (dpkg-buildpackage died) RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=hirsute --arch=armhf PACKAGEBUILD-20625810 Scanning for processes to kill in build PACKAGEBUILD-20625810