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

[Jordi Inglés]

Hi!

tried with cmake 2.8.0 and it seems that is working!!!!

Thanks for all Szilárd :)

Jordi Inglés

El 29/03/11 13:00, Szilárd Páll escribió:
> 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
>>
>>
>>

-- 

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