Ghemical Doesn't run under Ubuntu 11.10 (undefined symbol: _ZTIN2sc7RefBaseE)

I get the same error message when attempting to run ghemical on Ubuntu 11.10.

I tried installing libghemical v 3 from the ghemical site in /usr/lib and changing the libghemical.so.5 link to point to it and the errors stays the same.

I compiled ghemical 3.00 from source, starting with mopac, mpqc, libghemical (must compile liboglappth 1.0 from ghemical website for version 3.00, not use liboglappth 0.98-2 package), and finally ghemical. I was ultimately successful, but discovered many missing dependencies (not well-documented or undocumented) along the way. With the missing dependencies in place, ghemical 2.99 from the package still fails with the same error message, Could libghemical 2.99-1 in the package have been compiled without a needed library? In any case, the current version of ghemical is 3.00, not 2.99-2 in the package. Perhaps upgrade to the new version?

I have exactly the same problem as above.

I tried to compile Ghemical 3.0 from the tar files in the Ghemical sites, with cfortran installed (sudo apt-get install cfortran) I succeeded in building all the modules except ghemical 3 it self which fails due to some gtk dependencies that are missing. Thus far I have been unable to figure out which versions of the missing libraries are and where to find them. I keep trying. Incidentally, the problem is same with Linux Mint 12rc, so it seems that the problem is Gnome 3 related.

It can't be related to Gnome 3, Ghemical is based on gtk2. More, I can build ghemical-3.0.0 from sources on debian sid and it runs like a charm.

The symbol name points to libsc7 (mpqc). However atm I have no idea, what the problem exactly is. Is libsc7 installed? Is ghemical linked to it (ldd)?

This is a bug in libsc-dev, its sc-config tool does not list the SC libraries in the "sc-config --libs" output, which libghemical uses for linking.

"This is a bug in libsc-dev, its sc-config tool does not list the SC libraries in the "sc-config --libs" output, which libghemical uses for linking"

My attempts to compile ghemical 3 under Mint 12 fail when including mpqc in the libgemical library, I have not been able to satisfy the sc dependency, my guess was that I was using the wrong version of the package but perhaps this is not the case and in fact the sc library has a bug, as suggested in the comment above.

The Debian/Ubuntu libsc-dev packages certainly have bugs which make it impossible to build ghemical. Ubuntu 11.10 is suffering from Debian Bug #642668 (fixed in mpqc_2.3.1-9), and the current LP bug #885740, to be fixed in mpqc_2.3.1-10 in Debian shortly.

After a bug fix for this has been uploaded to Debian, a stable update for Ubuntu 11.10 should be issued, followed by a rebuild of libghemical and possibly ghemical as well. After this, ghemical should hopefully work again in Ubuntu 11.10.

mpqc_2.3.1-10 has been published in Debian unstable fixing this bug.

I quit, ghemical is crucial to me. But fixing all dependencies and getting it to work under Ubuntu 11.10 is beyond my time and patience. I'll quit Ubuntu 11/10.

Carlos,
Michael and Daniel have been working hard on getting updated packages for Ghemical and friends uploaded to Debian. At this point I think most everything should be in. If I were you I'd grab the updated mpqc (2.3.1-10) [0], liboglappth (1.0.0-1) [1], libghemical (3.0.0-1) [2], and ghemical (3.0.0-1) [3] when they're all done building.

At this point I'm not sure how quickly fixed can be pushed through official Ubuntu channels, but grabbing the packages from Debian should work in the interim.

[0] http://packages.debian.org/source/unstable/mpqc
[1] http://packages.debian.org/source/unstable/liboglappth
[2] http://packages.debian.org/source/unstable/libghemical
[3] http://packages.debian.org/source/unstable/ghemical

Thanks Jordan, I'll try once again following your suggestion and path.

Hi Jordan,

Compiling and installing

[0] http://packages.debian.org/source/unstable/mpqc
[1] http://packages.debian.org/source/unstable/liboglappth

was easy. I also compiled and installed mopac7. But the configuration of

[2] http://packages.debian.org/source/unstable/libghemical

fails with the following message:

checking for main in -llapack... yes
checking for sc-config... /usr/bin/sc-config
checking SC - version... no
*** Could not run SC test program, checking why...
*** The test program failed to compile or link. See the file config.log for the
*** exact error that occured. This usually means SC was incorrectly installed
*** or that you have moved SC since it was installed. In the latter case, you
*** may want to edit the sc-config script: /usr/bin/sc-config
configure: error: Cannot find proper SC version

Any idea about how to overcome this without breaking a lot of system dependencies?

Thanks

Carlos

please quote the relevant part of config.log leading to the error; it is not possible to figure out what went wrong from just looking at the configure output.

This bug was fixed in the package mpqc - 2.3.1-10

---------------
mpqc (2.3.1-10) unstable; urgency=low

  * debian/rules.old: Removed.
  * debian/rules (override_dh_auto_configure): Added --with-include flag for
    mpi-default-dev.
  * debian/control (libsc-dev/Depends): Added mpi-default-dev.
  * debian/patches/14_sc-config_sclibs.patch: New patch, fixes the output of
    "sc-config --libs" to include the SC libraries. LP: #885740.
 -- Ubuntu Archive Auto-Sync <email address hidden> Mon, 05 Dec 2011 11:02:04 +0000

This forum is frustrating, 3 month after the bug was "solved" I still cannot break through the maze of broken dependecies one finds when trying to install the "solution".

Carlos,

You should be able to install the binary .deb files and not worry about building from source. Are you on 32-bit or 64-bit Ubuntu? I could point you to the specific .deb files to download. This particular fix has been included in what will be the upcoming Ubuntu 12.04 release.

ghemical

OpenGL extension version - 1.4
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/builder/amino.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/builder/nucleic.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/default/atomtypes.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/default/parameters1.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/default/parameters2.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/default/parameters3.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/default/parameters4.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/tripos52/atomtypes.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/tripos52/parameters1.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/tripos52/parameters2.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/tripos52/parameters3.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/tripos52/parameters4.txt
DEBUG ; preparing to open file /usr/share/libghemical/3.0.0/param_mm/tripos52/parameters5.txt
Added local light.

OpenGL visual configurations :

gdk_gl_config_is_rgba (glconfig) = TRUE
gdk_gl_config_is_double_buffered (glconfig) = TRUE
gdk_gl_config_is_stereo (glconfig) = FALSE
gdk_gl_config_has_alpha (glconfig) = FALSE
gdk_gl_config_has_depth_buffer (glconfig) = TRUE
gdk_gl_config_has_stencil_buffer (glconfig) = TRUE
gdk_gl_config_has_accum_buffer (glconfig) = FALSE

(ghemical:2303): GdkGLExt-WARNING **: cannot load PangoFont
*** ERROR : Can't load font 'courier 12'