How do I submit a VSW job to run on only one cluster compute node with PBS?

Sometimes clusters are configured so that entire nodes are assigned to jobs, on the assumption that jobs are parallelized. In this case it is useful to ensure that VSW keeps all of its subjobs within these bounds. This cannot be done via Job Control: the parent job normally submits subjobs back into the queue, where they could end up on any other node, and the scheduler may need a long time before a full node is free for each subjob.

To keep a VSW job packed into one node when submitting it to PBS, we recommends that you set up and submit your own batch script. For example:

#!/bin/sh
#PBS -l nodes=1:ppn=8

cd input-file-dir
$SCHRODINGER/vsw -WAIT -HOST localhost:8 -NJOBS 32 ...

# End script

Then submit this script to the PBS queue with qsub after ensuring that the nodes have access to all the input files that VSW requires. The output is written to the same directory as the input, so you must collect it from that location if necessary.

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