...
mpirun gmx_mpi mdrun MDRUNARGUMENTS
Job Script Examples
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 available 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.
Codeblock language bash linenumbers true #!/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 MDRUNARGUMENTSIn 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.
Codeblock language bash linenumbers true #!/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