NAMD Wiki: NamdOnPBS

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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

Either OpenPBS ( or PBS Pro ( ).

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


cd NAMD_2.5b1_Linux-i686

pbsrun ./charmrun ./namd2 $HOME/apoa1/apoa1.namd

And this was the "pbsrun" script:


set nodefile = $TMPDIR/$PBS_JOBID.nodelist
echo group main >! $nodefile
set nodes = `cat $PBS_NODEFILE`
foreach node ( $nodes )
  echo host $node >> $nodefile

echo $nodefile

echo $#nodes nodes

set charmrun = $1
shift argv

setenv CONV_RSH ssh

$charmrun +p$#nodes ++nodelist $nodefile $*