[gmx-developers] Gromacs 2018 detects NVML but doesn't link to it unless set explicitly

[Christoph Junghans]

Jernej,

read the full story here: https://redmine.gromacs.org/issues/2311

Christoph

On Mon, Jan 15, 2018 at 2:08 AM, Jernej Zidar <jernej.zidar at gmail.com> wrote:
> Dear Erik,
>
> I can imagine. Nvidia changing the location of the library (between CUDA 8
> and CUDA 9) didn't help either.
>
> Thanks for explaining!
>
> Jernej
>
> On Mon, Jan 15, 2018 at 4:06 PM, Erik Lindahl <erik.lindahl at gmail.com>
> wrote:
>>
>> Hi Jernej,
>>
>> Unfortunately we had too many issues with NVML libraries not working in
>> the beta, and this is not detected until people actually run mdrun, so for
>> that reason we've had to disable it by default.
>>
>> Cheers,
>>
>> Erik
>>
>> On Mon, Jan 15, 2018 at 4:03 AM, Jernej Zidar <jernej.zidar at gmail.com>
>> wrote:
>>>
>>> Hi,
>>>
>>> I want to report a bug that I encountered when compiling the final
>>> version of Gromacs 2018.
>>>
>>> The cmake command I issue is this:
>>>
>>> CMAKE_PREFIX_PATH=/home/zidar/utils/fftw-3.3.6-gcc/ cmake ../gromacs-2018
>>> -DGMX_GPU=on -DGMX_MPI=off -DGMX_FFT_LIBRARY=fftw3
>>> -DCMAKE_INSTALL_PREFIX=/home/zidar/utils/gromacs-2018-gcc
>>> -DGMX_SIMD=AVX2_256
>>>
>>>
>>> And the NVML library is found:
>>>
>>> - Found NVML: /usr/lib/x86_64-linux-gnu/libnvidia-ml.so
>>>
>>>
>>> When I compile mdrun, the process completes without a problem, yet the
>>> support is not there with mdrun complaining mdrun was compiled without NVML.
>>>
>>> After the checking the various cmake-generated files, it appears the
>>> problem is in the CMakeCache.txt file, where the relevant options is set to
>>> OFF (line 698) despite being detected and presumably enabled.
>>>
>>> //Use NVML support for better CUDA performance
>>>
>>> GMX_USE_NVML:BOOL=OFF
>>>
>>>
>>> After manually editing the file, the support is there.
>>>
>>> I was able to replicate this behaviour on two different workstations with
>>> the following configurations:
>>> - Debian, GCC 6.3, CUDA 9.1
>>> - Ubuntu, GCC 6.4, CUDA 9.0
>>>
>>> I've also found that setting the NVML support on explicity using the
>>> switch "-DGMX_USE_NVML=ON" makes everything work as advertised. Perhaps this
>>> behaviour should be mentioned in the documentation.
>>>
>>> Cheers,
>>> Jernej
>>>
>>> --
>>> Gromacs Developers mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>>> or send a mail to gmx-developers-request at gromacs.org.
>>
>>
>>
>>
>> --
>> Erik Lindahl <erik.lindahl at dbb.su.se>
>> Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
>> University
>> Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
>>
>> --
>> Gromacs Developers mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers or
>> send a mail to gmx-developers-request at gromacs.org.
>
>
>
> --
> Gromacs Developers mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers or
> send a mail to gmx-developers-request at gromacs.org.



-- 
Christoph Junghans
Web: http://www.compphys.de