[gmx-users] Running gromacs in parallel

Savio James saviojam at gmail.com
Tue Aug 23 02:49:03 CEST 2016

Hi All,

I am trying to run gromacs in parallel on 2 nodes. Each node is 16 physical
cores/32 logical cores and job scheduler is slurm. I installed version
5.1.3 with DGMX_MPI=on.

When I run a slurm script like srun -n 64 gmx_mpi mdrun -ntomp 1,

it runs 64 independent simulations. I get 64 log files, energy files and
trajectory files. The cluster support at my university has also not been
able to figure out why this happens. Any help would be appreciated.

I am able to run the simulation on a single node. If i run, gmx_mpi mdrun
-ntomp 32, I am able to run my simulations.It is an issue only when I use
multiple nodes.


Savio James Poovathingal
Graduate Student
University of Minnesota
107 Akerman Hall
110 Union St SE
Minneapolis, MN 55455*-*0153

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