[gmx-users] gmx 2019 running problems
Tamas Hegedus
tamas at hegelab.org
Tue Jan 15 12:49:53 CET 2019
Hi,
Thanks for the feed-backs.
Yes, I could build gmx 2019 on a hosts running with nvidia driver 4.10
Tamas
On 01/14/2019 09:06 PM, Tamas Hegedus 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
Department of Biophysics and Radiation Biology
Semmelweis University | phone: (36) 1-459 1500/60233
Tuzolto utca 37-47 | mailto:tamas at hegelab.org
Budapest, 1094, Hungary | http://www.hegelab.org
More information about the gromacs.org_gmx-users
mailing list