[gmx-users] gmx 2019 running problems

[paul buscemi]

Tamas

I’ve the same build as you (almost… 2 gpus )  I found good  results  using one change :   from  -nt 16   to    -ntomp 4  which should map the GPU’s and tasks in the same manner, but may be handled differently by mdrun.  These two versions run with different efficiency on my rig.

Paul

> On Jan 14, 2019, at 2:06 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.
> 
> 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.