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Hi Matthew, I use an SGE queue and for this the command is simply "group_run_command=qsub" along with "nproc=16" or whatever number of processors to use. Basically you put into group_run_command all the commands that you need to submit a job, then autobuild submits up to nproc of these at a time. I hope that helps! -Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Matthew J. Whitley [[email protected]] Sent: Tuesday, February 07, 2012 10:58 AM To: [email protected] Subject: [phenixbb] Composite Omit Map Calculations - Batch Que Hello all, 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 --- Matthew J. Whitley, Ph.D. Postdoctoral Research Fellow Angela Gronenborn Lab Department of Structural Biology University of Pittsburgh School of Medicine