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A simple case of a GROMACS job using a total of 640 CPU cores for 12 hours. The requested amount of Cores in the example does not include all cores on the allocated nodes. The job will execute 92 ranks on 3 nodes + 91 ranks on 4 nodes. You can use this example if you know the exact amount of required ranks you want to use.
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#!/bin/bash
#SBATCH -t 12:00:00
#SBATCH -p standard96
#SBATCH -n 640
export SLURM_CPU_BIND=none
module load impi/2019.5
module load gromacs/2019.6
mpirun gmx_mpi mdrun MDRUNARGUMENTS |
In case you want to use all cores on the allocated nodes, there are another options of the batch system to request the amount of nodes and number of tasks. The example below will result in running 672 ranks.
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#!/bin/bash
#SBATCH -t 12:00:00
#SBATCH -p standard96
#SBATCH -N 7
#SBATCH --tasks-per-node 96
export SLURM_CPU_BIND=none
module load impi/2019.5
module load gromacs/2019.6
mpirun gmx_mpi mdrun MDRUNARGUMENTS |
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