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Load the necessary modulefiles. Note that Intel MPI module file should be loaded first

module load impi/20182019.5 gromacs/2018.4

This provides access to the binary gmx_mpi wich can be used to run simulations with sub-commands as gmx_mpi mdrun

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mpirun gmx_mpi mdrun MDRUNARGUMENTS

Job Script Examples

For Intel Cascade Lake compute nodes – A simple case of a GROMACS job using a total of 960 640 CPU cores distributed over 10 nodes running 96 tasks each for 12 hours

Code Block
languagebash
linenumberstrue
#!/bin/bash
#SBATCH -t 12:00:00
#SBATCH -p standard96
#SBATCH -N 10
#SBATCH --tasks-per-node 96n 640

export SLURM_CPU_BIND=none

module load impi/2019.5
module load gromacs/2019.6

mpirun gmx_mpi mdrun MDRUNARGUMENTS

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