[gmx-users] problems when installing gromacs 4.5.3 or 4.5.4 with GPU's

[Szilárd Páll]

Hi Jordi,

I've never seen this error or anything similar, but I can give you hints.

The CMake build system first generates binaries in the build directory
which are also runnable from there (are linked against libs located in
the build three). When you do a "make install[-mdrun]", howerver,
these binaries get relinked to rewrite the library dependencies. lt
seems that in your case this last step fails.

What you can do is to try to run
$ make install-mdrun VERBOSE=1 ,
maybe you can see something on the verbose output. For reference I've
attached a verbose output of the above command I just generated.

Otherwise, you could set BUILD_SHARED_LIBS=OFF, case in which internal
Gromacs libraries will be linked statically.

Cheers,
--
Szilárd



2011/3/28 Jordi Inglés <jordi.ingles at qi.ub.es>:
> Hi,
>
> I'm compiling gromacs with gcc compiler (v 4.3.2), cmake (2.8.3) and OpenMM
> 2.0 in a SLES 11.0 Linux.
>
> I follow the instructions in the page and it seems that the compilation goes
> fine.
>
> gpu01:/scratch/jingles/gcc/gromacs-4.5.3 # ls -ltra src/kernel/mdrun-gpu
> -rwxr-xr-x 1 root root 518294 Mar 28 10:16 src/kernel/mdrun-gpu
>
> But when I try to install the application I obtain this error:
>
> make install-mdrun
>
> -- Using default binary suffix: "-gpu"
> -- Using default library suffix: "_gpu"
> -- Using internal FFT library - fftpack
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /scratch/jingles/gcc/gromacs-4.5.3
> Linking CXX static library libgmx_gpu_utils.a
> [  0%] Built target gmx_gpu_utils
> [ 78%] Built target gmx
> [ 92%] Built target md
> [ 98%] Built target gmxpreprocess
> [ 98%] Built target openmm_api_wrapper
> Linking CXX executable mdrun-gpu
> [100%] Built target mdrun
> Scanning dependencies of target install-mdrun
> [100%] Installing mdrun
> -- Install configuration: "Release"
> -- Install component: "libraries"
> CMake Error at
> /scratch/jingles/gcc/gromacs-4.5.3/src/gmxlib/cmake_install.cmake:38 (FILE):
>  file INSTALL cannot find
>  "/scratch/jingles/gcc/gromacs-4.5.3/src/gmxlib/CMakeFiles/CMakeRelink.dir/libgmx_gpu.so.6".
> Call Stack (most recent call first):
>  /scratch/jingles/gcc/gromacs-4.5.3/src/cmake_install.cmake:37 (INCLUDE)
>  /scratch/jingles/gcc/gromacs-4.5.3/cmake_install.cmake:40 (INCLUDE)
>
>
> make[3]: *** [src/kernel/CMakeFiles/install-mdrun] Error 1
> make[2]: *** [src/kernel/CMakeFiles/install-mdrun.dir/all] Error 2
> make[1]: *** [src/kernel/CMakeFiles/install-mdrun.dir/rule] Error 2
> make: *** [install-mdrun] Error 2
>
> It seems that CMakeRelink.dir it's empty (I supose that the own compilation
> cleans it). the libgmx_gpu.so.6 exist in her source directory:
>
> gpu01:/scratch/jingles/gcc/gromacs-4.5.3 # ls -ltra
> src/gmxlib/libgmx_gpu.so*
> -rwxr-xr-x 1 root root 3378435 Mar 28 10:11 src/gmxlib/libgmx_gpu.so.6
> lrwxrwxrwx 1 root root      15 Mar 28 10:11 src/gmxlib/libgmx_gpu.so ->
> libgmx_gpu.so.6
>
>
> Have you got any idea about the problem? I tried to compile with the
> --debut-output --debug-trycompile options of cmake that don't clean the
> compilation after finishing for checking that CMakeRelink.dir is empty or
> not, but it seems that still continues empty.
>
> Thanks for any advise.
>
> Jordi Inglés Camats
>
> --
>
> __________________________________
> Jordi Inglés Camats
> Institut de Química Teòrica Computacional (IQTCUB)
> Facultat de Física i Química
> Despatx 766
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: make-install-VERBOSE.out
Type: application/octet-stream
Size: 12718 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110328/e8553196/attachment.obj>