[gmx-users] Run mdrun in parallel

Husen R hus3nr at gmail.com
Tue Apr 12 16:44:10 CEST 2016

Hi all,

Currently, I'm trying to run mdrun command in parallel.
the following is my batch script using Slurm as a resource manager:

=====================Batch Script==================
#SBATCH -o eq1-%j.out
#SBATCH -A pro
#SBATCH -n 16

gmx mdrun -deffnm tpr
=======================End Batch Script===============

As we can see from the batch script above, I tried to run mdrun with 2
Nodes and 16 processors.
After the batch job is submitted, I tried to see running process in the
background in each node using htop command and I found that only one node
that run 'gmx mdrun -deffnm tpr' command, there was no running process
called 'gmx mdrun -deffnm tpr' in the other one.

Please, anyone tell me how to run mdrun (or gromacs in general) in parallel

note : If I run mpi application, I always able to see it running in every
allocated nodes using htop.

thank you in advance.



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