NAMD

The NAMD version 2.8 molecular mechanics package.

Sample script:

<source lang="bash">

1. !/bin/bash
2. MOAB/Torque submission script for SciNet GPC (ethernet)
4. PBS -l nodes=2:ppn=8:ib,walltime=1:00:00
5. PBS -N namdtest

module purge module load use.experimental gcc openmpi/1.4.3-gcc-v4.4.0-ofed namd/2.8-ibverbs

1. DIRECTORY TO RUN - $PBS_O_WORKDIR is directory job was submitted from

cd $PBS_O_WORKDIR

1. EXECUTION COMMAND; ++p = nodes*ppn

$SCINET_NAMD_HOME/charmrun ++verbose ++p 16 ++mpiexec ++remote-shell $SCINET_NAMD_HOME/namdmpiexec $SCINET_NAMD_HOME/namd2 somejob.conf >& somejob.log

</source>

This script, which resides in the submission directory, requests 2 nodes with InfiniBand. It then requests to run 16 processes, and uses another script, namdmpiexec, to start the job. The set of modules to load depends on the specific versions that we have available on the machine.