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

[Jordi Inglés]

Thanks Szilárd for your fast mail,

but it seems that is still failing and don't appears any new error. With 
BUILD_SHARED_LIBS flag it seems that it pass the library error but I 
receive a similar error with the executable (see attached file) 
mdrun-gpu, but this executable exist in other directory:

-rwxr-xr-x  1 root   root  3433307 Mar 29 08:31 mdrun-gpu

I attach also the CMakeCache list if it can help.

Thanks for any advise!

jordi inglés

El 28/03/11 21:50, Szilárd Páll escribió:
> 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
>>
>>
>> --
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-- 

__________________________________
Jordi Inglés Camats
Institut de Química Teòrica Computacional (IQTCUB)
Facultat de Física i Química
Despatx 766


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