[gmx-users] gmx 2019 running problems
paul buscemi
pbuscemi at q.com
Tue Jan 15 04:07:47 CET 2019
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.
More information about the gromacs.org_gmx-users
mailing list