[gmx-users] OpenMP multithreading mdrun

Smith, Iris smithi4 at ccf.org
Wed Jul 25 16:27:31 CEST 2018

Good Morning Gromacs Users,

Gromacs 2018.2 was recently installed on our intel-based HPC cluster using OpenMP (without MPI).

Can I still utilize multiple threads within one node when utilizing mdrun? If so, do I need to call openmp and export OMP_NUM_THREADS in my script?

For example when using 20 threads:

module load openmpi/gcc/64/3.1.1
module load gromacs/2018.2

gmx mdrun -ntomp 20 -s wt.tpr -deffnm wt -v

Thank you,


Iris Nira Smith  |  Postdoctoral Fellow |  Genomic Medicine Institute
Cleveland Clinic  |  9500 Euclid Ave. / NE5-255  |  Cleveland, OH 44195  | (216) 445-7885


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