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

[Szilárd Páll]

Hi,

I've diff-ed the cache file you sent me against the one I generated
and I couldn't see anything relevant. Neither does the verbose CMake
output suggest anything useful, but that it tries to copy the
mdrun-gpu binary from a location where it obviously does not exist. I
don't even have this "CMakeRelink.dir" directory in my build tree.

I googled around a found the same issue being mentioned in a few
places, but couldn't figure out what the reason/solution is.

A few more things you could try if you haven't tried yet:
1) 4.5.4 (does it produce the same error?);
2) Run cmake in a _clean_ build directory;
3) Try a different (possibly earlier) CMake version, for me it works
fine with 2.8.0 and actually the latest version I used was AFAIR
2.8.2.

Cheers,
--
Szilárd



On Tue, Mar 29, 2011 at 8:52 AM, Jordi Inglés <jordi.ingles at qi.ub.es> wrote:
> 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
>
>
>