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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:

sbatch [Slurm options] --wrap="namd2"

By default you can find the output in the Slurm-XXXXXXX output file where XXXXXXX corresponds to the job ID of the job. You need to replace [Slurm options] with Slurm parameters for the resource requirements of the job. Please find a documentation about the parameters of Slurm on the wiki page about the batch system. For example,

sbatch --time=12:00:00 --mem-per-core=500 --wrap="namd2"

will request a runtime of up to 12 hours and only 500 MB of RAM.

Jobs that can run on a single node (up to 128 cores) can be submitted in a similar way:

sbatch [Slurm options] --ntasks=N --wrap="charmrun +p N +isomalloc_sync namd2"