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

[Szilárd Páll]

Great! I would really appreciate if you could file a bug on
redmine.gromacs.org against the build system.

Thanks,
--
Szilárd



On Tue, Mar 29, 2011 at 2:27 PM, Jordi Inglés <jordi.ingles at qi.ub.es> wrote:
> 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
>
>
>