[gmx-users] gmx 2019 running problems

[Mark Abraham]

Hi,

On Mon, Jan 14, 2019 at 9:06 PM Tamas Hegedus <tamas at hegelab.org> wrote:

> Hi,
>
> I tried to install and use gmx 2019 on a single node computer with 4 GPUs.
>
> I think that the build was ok, but the running is...
> There is only workload on 4 cores (-nt 16) and
> there is no workload on the GPUs at all.
>

Sounds like your driver might be incompatible with either the GPUs or the
CUDA version found. Check out the log file written by mdrun, and probably
plan to reinstall CUDA 10 and get the latest drivers.

Mark


> gmx 2018 was deployed on the same computer with the same tools and
> libraries.
>
> CPU 16cores + 16threads
> GPU 1080Ti
>
> cmake -j 16 -DCMAKE_C_COMPILER=gcc-6 -DCMAKE_CXX_COMPILER=g++-6
> -DCMAKE_INSTALL_PREFIX=$HOME/opt/gromacs-2019-gpu -DGMX_GPU=ON
> -DCMAKE_PREFIX_PATH=$HOME/opt/OpenBLAS-0.2.20
> -DFFTWF_LIBRARY=$HOME/opt/fftw-3.3.7/lib/libfftw3f.so
> -DFFTWF_INCLUDE_DIR=$HOME/opt/fftw-3.3.7/include ../ | tee out.cmake
>
> -- Looking for NVIDIA GPUs present in the system
> -- Number of NVIDIA GPUs detected: 4
> -- Found CUDA: /usr (found suitable version "9.1", minimum required is
> "7.0")
>
> make -j16
> make -j16 install # note: a lot of building happened also in this step
>
> **********************
> gmx mdrun -nt 16 -ntmpi 4 -gputasks 0123 -nb gpu -bonded gpu -pme gpu
> -npme 1 -pin on -v -deffnm md_2 -s md_2_500ns.tpr -cpi md_2.1.cpt -noappend
>
>
> +-----------------------------------------------------------------------------+
> | NVIDIA-SMI 390.48                 Driver Version: 390.48
>       |
>
> |-------------------------------+----------------------+----------------------+
> | GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile
> Uncorr. ECC |
> | Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util
> Compute M. |
>
> |===============================+======================+======================|
> |   0  GeForce GTX 108...  Off  | 00000000:02:00.0 Off |
>   N/A |
> |  0%   28C    P8    19W / 250W |    179MiB / 11178MiB |      0%
> Default |
>
> +-------------------------------+----------------------+----------------------+
> |   1  GeForce GTX 108...  Off  | 00000000:03:00.0 Off |
>   N/A |
> |  0%   28C    P8     8W / 250W |    179MiB / 11178MiB |      0%
> Default |
>
> +-------------------------------+----------------------+----------------------+
> |   2  GeForce GTX 108...  Off  | 00000000:83:00.0 Off |
>   N/A |
> |  0%   28C    P8     9W / 250W |    179MiB / 11178MiB |      0%
> Default |
>
> +-------------------------------+----------------------+----------------------+
> |   3  GeForce GTX 108...  Off  | 00000000:84:00.0 Off |
>   N/A |
> |  0%   27C    P8     9W / 250W |    237MiB / 11178MiB |      0%
> Default |
>
> +-------------------------------+----------------------+----------------------+
>
>
>
> +-----------------------------------------------------------------------------+
> | Processes:                                                       GPU
> Memory |
> |  GPU       PID   Type   Process name                             Usage
>       |
>
> |=============================================================================|
> |    0     20243      C   gmx
> 161MiB |
> |    1     20243      C   gmx
> 161MiB |
> |    2     20243      C   gmx
> 161MiB |
> |    3     20243      C   gmx
> 219MiB |
>
> +-----------------------------------------------------------------------------+
>
> Thanks for your suggestions,
> Tamas
>
> --
> Tamas Hegedus, PhD
> Senior Research Fellow
> MTA-SE Molecular Biophysics Research Group
> Hungarian Academy of Sciences  | phone: (36) 1-459 1500/60233
> Semmelweis University          | fax:   (36) 1-266 6656
> Tuzolto utca 37-47             | mailto:tamas at hegelab.org
> Budapest, 1094, Hungary        | http://www.hegelab.org
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_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-users or
> send a mail to gmx-users-request at gromacs.org.
>