[gmx-users] gmx 2019 running problems

[paul buscemi]

One  other  suggestion:

 from the PPA repository, install the Nvidia 410 driver.   Your Cuda 9 install  may work with the 410 driver but more likely you will  need to reinstall. cuda

 If so, install the CUDA 10 toolkit, but DO NOT use the toolkit to install the driver when asked,  it will revert to the Nvidia  v384 driver

Hope it works out for your monster 

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
> -- 
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