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| software:gromacs:darwin [2023-09-06 18:31] – [Batch job] anita | software:gromacs:darwin [2023-09-07 11:17] (current) – [Batch job] anita |
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| | ====== Gromacs on DARWIN ====== |
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| | Templates for Slurm job submission scripts are available for batch GROMACS jobs in ''/opt/shared/templates/slurm/applications''. Copy and edit the template based on your job by following the usage described in ''gromacs.qs''. |
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| | <note tip>It is always a good idea to periodically check ''/opt/shared/templates/slurm/applications'' for changes in existing templates, or the addition of new templates, designed to provide the best performance for a particular version of GROMACS on that cluster.</note> |
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| | ===== Batch job ===== |
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| | On DARWIN, the template (''/opt/shared/templates/slurm/applications/gromacs.qs'') provides a number of options to provide the best performance, but you must read the comments and set the options accordingly for your job. By default the template uses double-precision, however changing ''GROMACS_PRECISION=single'' will specify the single-precision version instead. By default the ''gromacs.sh'' script executed as part of the GROMACS environment setup in the job script template will choose ''mpi'' or ''thread'' based on the node count in the Slurm runtime environment unless explicitly setting the environment variable ''GROMACS_PARALLELISM'', and will load the particular version of GROMACS via VALET to satisfy single vs double, and mpi vs threads. |