NAMD Wiki: NamdOnPBS
If your NAMD binary was built using an MPI build of Charm++ then you should ignore the following and run NAMD like any other MPI program on your cluster. The following only applies to NAMD binaries that are not built on MPI and require the charmrun program to launch parallel runs. If your charmrun is a script that calls mpirun then you may ignore it.
Portable Batch System
Here is an example batch job and pbsrun script I used to test network versions of NAMD at NCSA. The batch job looked like this:
#PBS -l walltime=00:30:00 #PBS -m be cat $PBS_NODEFILE cd NAMD_2.5b1_Linux-i686 pbsrun ./charmrun ./namd2 $HOME/apoa1/apoa1.namd
And this was the "pbsrun" script:
#!/bin/csh set nodefile = $TMPDIR/$PBS_JOBID.nodelist echo group main >! $nodefile set nodes = `cat $PBS_NODEFILE` foreach node ( $nodes ) echo host $node >> $nodefile end echo $nodefile echo $#nodes nodes set charmrun = $1 shift argv setenv CONV_RSH ssh $charmrun +p$#nodes ++nodelist $nodefile $*