[gmx-users] gmx 2019 running problems

[Tamas Hegedus]

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