View source for NAMD/Batch

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"

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"

will request a runtime of up to 12 hours and only 500&nbsp;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"