[gmx-users] OpenMP multithreading mdrun

[Smith, Iris]

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
export OMP_NUM_THREADS=2

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

Thank you,
Iris

[/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1326358176]

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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