NAMD/Batch

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:

sbatch [Slurm options] --wrap="namd2 input.in"

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 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 (up to 128 cores) can be submitted in a similar way:

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