<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Mark,<div><br><div>Hmmm...I hadn't thought of that situation. Right now you can only specify one type of "run_command", either specifying a submitted job or a subprocess, but not both in one run, I'm afraid. In your case I'd suggest two options:</div><div><br></div><div>1. Set nproc= the smaller of ( the number of nodes on your cluster, the number of omit regions in your composit omit job)</div><div>2. Run a separate job for each omit region with omit_box_start and omit_box_end ,specify run-command="csh -f" and nproc=8:</div><div><div> omit_box_start = 0</div><div> .help = " To only carry out omit in some of the omit boxes, use"</div><div> "omit_box_start and omit_box_end "</div><div> .type = int</div><div> omit_box_end = 0</div><div> .help = " To only carry out omit in some of the omit boxes, use"</div><div> "omit_box_start and omit_box_end "</div><div> .type = int</div><div><br></div><div>I hope that helps!</div><div>All the best,</div><div>Tom T</div><div><br></div><div><br></div><div><div>On May 26, 2010, at 10:06 AM, Mark A Saper wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Tom and colleagues,<div><br><div>We're running Autobuild composite omit on a large cluster, each node has 8 processors. Autobuild submits jobs with the "run_command". And it appears that each of those jobs submit other jobs. Are the latter jobs necessary? That is, are there situtations where they wouldn't be submitted as separate jobs but run as subprocesses? Currently nodes in our cluster don't have capability of qsubing new jobs, but we are in the process of changing this.</div><div><br></div><div>Thanks, Mark<br><div> <span class="Apple-style-span" style="color: rgb(0, 0, 0); "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; 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widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; 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font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; 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"><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">_________________________________</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; "><span class="Apple-style-span" style="color: rgb(0, 64, 128); font-weight: bold; "><font class="Apple-style-span" color="#BB623F"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 13px; ">Mark A. Saper, Ph.D.</span></font></font><span class="Apple-tab-span" style="white-space: pre; "> </span></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" color="#000000">Associate Professor of Biological Chemistry</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" color="#000000">University of Michigan</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font style="font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">Biophysics, 3040 Chemistry Building</font></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font style="font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">930 N University Ave</font></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font style="font: normal normal normal 12px/normal Helvetica; "><font class="Apple-style-span" color="#000000">Ann Arbor MI 48109-1055 U.S.A.</font></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-style-span" style="font-size: medium; "><div apple-content-edited="true"><a href="mailto:saper@umich.edu">saper@umich.edu</a> phone (734) 764-3353 fax (734) 764-3323</div><div apple-content-edited="true"><span class="Apple-tab-span" style="white-space: pre; "><a href="http://www.biochem.med.umich.edu/?q=saper">http://www.biochem.med.umich.edu/?q=saper</a> </span><a href="http://www.strucbio.umich.edu/">http://www.strucbio.umich.edu/</a></div><div><br></div></span></div></span></font></div></span></span></font></span></div></span></div></div></span></span></span></span></span></span></span></span></span></span></div></span></span></span></span></div></span></div></span></div></span></div></span><br class="Apple-interchange-newline"> </div> <br></div></div></div>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br></blockquote></div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><div><div><div><br>Thomas C. 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