This is the NAMD version 2.12 Scalable Molecular Dynamics package.
It was built directly on top of ibverbs, so it will run on InfiniBand nodes. Here is a sample run script:
#!/bin/bash # #SBATCH --nodes=2 #SBATCH --ntasks-per-node=40 #SBATCH --time=11:00:00 #SBATCH --job-name namdtest # Note that the module will likely be taken out of experimental mode at some point. module load namd/.experimental-2.12-ibverbs-smp # DIRECTORY TO RUN - $SLURM_SUBMIT_DIR is directory job was submitted from cd $SLURM_SUBMIT_DIR # EXECUTION COMMAND; -np = nodes*ppn charmrun ++p 80 namd2 +idlepoll input.namd
The above script requests 2 nodes and runs namd on 80 processors.
Full documentation for NAMD is available on their website: http://www.ks.uiuc.edu/Research/namd/