Problem running with GPU

User discussions
1

GROMACS version: 2020
GROMACS modification: No
Here post your question

Dear All,

I am trying to run GROMACS with GPU, however when I try to run it with the following command:

gmx_mpi mdrun -v -cpi state.cpt -nb gpu -pme gpu

the simulation just stall.

I tried to use the older gromacs version 2018,

similar thing occurred and the file stop writing anything. The error file is not showing anything (see as below), thus I do not know how to make sure it run on GPU. (The stall system did not crash).

GROMACS: gmx mdrun, version 2018.6
Executable: /share/apps/gromacs/2018.6-ompi-4.0.0-cuda9/gcc/6.5.0/bin/gmx_mpi
Data prefix: /share/apps/gromacs/2018.6-ompi-4.0.0-cuda9/gcc/6.5.0
Working dir: /home/benjamintam/Coral/gromacs/AMBER03/TP53/Pathogenic/SPCE/2OCJ/2OCJ-fix-ion-single3
Command line:
gmx_mpi mdrun -v -cpi state.cpt -nb gpu -pme gpu

Back Off! I just backed up md.log to ./#md.log.2#

The system did not crash with CPU just to clarify. Thank you very much.

Best regards,

Benjamin Tam

2

Hi Benjamin,

This sounds like an issue for gitlab to me - could you help us fix this, by creating an issue at https://gitlab.com/gromacs/gromacs/-/issues and providing the .tpr and the .cpt file, together with all the input / output you had?

Sorry that I cannot help you further, maybe this sounds already familiar to @pszilard or @zhmurov?

3

Hi, because it didn’t run. It didn’t have any .cpt file. However I still post my system to the link that you have provided.

Best,

Ben