NAMD/Parallel

You can run NAMD on a single node (for example, up to 36 cores on Euler) or over multiple nodes.

To run on a single node, request a number of processors, N from the batch system and tell NAMD2 to use the same number of threads:

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

where [Slurm options] are the Slurm parameters for the resource requirements of the job.

You can also run NAMD calculations on more than one node. Since multiple nodes will be used in this case, you must load an MPI module (such as MVAPICH2) before loading the NAMD module. Then use the following command to submit such a job to the batch system:

sbatch [Slurm parameters] --ntasks=N --wrap="mpirun namd2 input.in"

where [Slurm options] are the Slurm parameters for the resource requirements of the job.