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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 use the following command:

bsub [LSF options] "namd2"

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"

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"