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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
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#!/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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