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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Matthew,
<div>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. </div>
<div>I hope that helps!</div>
<div>-Tom T</div>
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<div id="divRpF352720" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><b>From:</b> phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Matthew J. Whitley [mwhitley@structbio.pitt.edu]<br>
<b>Sent:</b> Tuesday, February 07, 2012 10:58 AM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> [phenixbb] Composite Omit Map Calculations - Batch Que<br>
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<div>Hello all,
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<div>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.</div>
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<div>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).</div>
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<div>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?</div>
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<div>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.</div>
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<div>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. </div>
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<div>Thanks,</div>
<div>Matthew</div>
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<div>---</div>
Matthew J. Whitley, Ph.D.<br>
Postdoctoral Research Fellow<br>
Angela Gronenborn Lab<br>
Department of Structural Biology<br>
University of Pittsburgh School of Medicine<br>
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