I usually set up simulated annealing composite omit map calculations via the Phenix GUI and set the number of processors equal to 2 to take advantage of my Mac's dual core processor in order to shorten the calculation time somewhat.

My department does have a high performance cluster, however, and I would like to start using that multi-node system to shorten the calculation time substantially.  The problem for me is that the high performance cluster requires jobs to be submitted and managed via a PBS queue.  I know how to specify in the PBS shell script the computing resources I want to use (say, for example, 8 dual core processors for a total of 16 nodes).

My question is, do I need to specify any additional settings in the actual Phenix command line execution statement?  For example, nproc = 16?  Anything else?

The entire shell script containing the PBS setup statements and the actual Phenix execution statements is submitted by the qsub command.  In essence, I am wondering how to get Phenix to "play nicely" with the queueing system such that the composite omit calculations will be distributed box by box over the resources I reserve via the PBS statements.

Thanks in advance for any advice.  Also, if anybody has experience running Phenix jobs via a shell script submitted to a batch queueing system, I would very much appreciate the chance to look at the shell script.  

Thanks,

Matthew