Difference between revisions of "NAMD/Batch"
From ScientificComputing
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| − | + | You need to submit your NAMD calculations in batch mode, through the batch system. To run a simulation with an input file <tt>input.in</tt> use the following command: | |
| + | |||
bsub [LSF options] "namd2 input.in" | bsub [LSF options] "namd2 input.in" | ||
| − | By default the output | + | |
| + | By default you can find the output in the <tt>lsf.oXXXXXXX</tt> output file where XXXXXXX corresponds to the job ID of the job. You need to replace ''[LSF options]'' with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of <tt>bsub</tt> on the wiki page about the [[Using_the_batch_system|batch system]]. For example, | ||
| + | |||
bsub -W 12:00 -R "rusage[mem=500]" "namd2 input.in" | bsub -W 12:00 -R "rusage[mem=500]" "namd2 input.in" | ||
| + | |||
will request a runtime of up to 12 hours and only 500 MB of RAM. | will request a runtime of up to 12 hours and only 500 MB of RAM. | ||
Jobs that can run on a single node (24 cores) can be submitted in a similar way: | Jobs that can run on a single node (24 cores) can be submitted in a similar way: | ||
| + | |||
bsub [LSF options] -n N "charmrun +p N +isomalloc_sync namd2 input.in" | bsub [LSF options] -n N "charmrun +p N +isomalloc_sync namd2 input.in" | ||
Revision as of 12:19, 29 August 2016
You need to submit your NAMD calculations in batch mode, through the batch system. To run a simulation with an input file input.in use the following command:
bsub [LSF options] "namd2 input.in"
By default you can find the output in the lsf.oXXXXXXX output file where XXXXXXX corresponds to the job ID of the job. You need to replace [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub on the wiki page about the batch system. For example,
bsub -W 12:00 -R "rusage[mem=500]" "namd2 input.in"
will request a runtime of up to 12 hours and only 500 MB of RAM.
Jobs that can run on a single node (24 cores) can be submitted in a similar way:
bsub [LSF options] -n N "charmrun +p N +isomalloc_sync namd2 input.in"
