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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.

Code Block
languagebash
linenumberstrue
#!/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. 

Code Block
languagebash
linenumberstrue
#!/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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