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| software:gromacs:caviness [2019-08-29 17:34] – created anita | software:gromacs:caviness [2021-04-27 16:21] (current) – external edit 127.0.0.1 |
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| ====== Gromacs on Caviness ====== | ====== Gromacs on Caviness ====== |
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| Templates for Slurm job submission scripts are available for batch GROMACS jobs in ''/opt/templates/slurm/applications/gromacs''. Copy and edit the template based on your job by following the usage described in ''gromacs.qs''. | Templates for Slurm job submission scripts are available for batch GROMACS jobs in ''/opt/shared/templates/slurm/applications/gromacs''. 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 a good idea to periodically check in ''/opt/templates/slurm/applications/gromacs'' 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> | <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 ===== | ===== Batch job ===== |
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| On Caviness, the template (''/opt/templates/gridengine/gromacs.qs'' specifies a number of resource options to provide the best performance, but you must read the comments and set the options according to your job. By default the template uses double-precision (''md_rund''), however commenting out ''GROMACS_DOUBLE_PRECISION=YES'' will specify the single-precision version (''md_run'') instead. | On Caviness, 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 (''md_rund''), however commenting out ''GROMACS_DOUBLE_PRECISION=YES'' will specify the single-precision version (''md_run'') instead. |