<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Donnie,<div><br><div>Thanks for the note; I'll check into it. The SGE mechanism is very simple and perhaps it will be applicable to other queueing systems without modification.</div><div><br></div><div>For example if you queue jobs with:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>queue_command_here -flags -etcetc myjob.sh</div><div><br></div><div>then you just give the GUI/autobuild/ligandfit the command</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>run_command="queue_command_here -flags -etcetc"</div><div><br></div><div>and then it runs the jobs as above.</div><div><br></div><div>All the best,</div><div>Tom T</div><div><br><div><div>On Nov 3, 2010, at 8:21 AM, Donnie Berkholz wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>On 18:12 Tue 02 Nov , Nathaniel Echols wrote:<br><blockquote type="cite">On Tue, Nov 2, 2010 at 6:02 PM, <<a href="mailto:zhangh1@umbc.edu">zhangh1@umbc.edu</a>> wrote:<br></blockquote><blockquote type="cite"><blockquote type="cite">I tried a dimer of 4000aa at 3.2A using the following script:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">phenix.autobuild data=2VZ8.mtz model=${f}.pdb composite_omit_type=simple_omit<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> It took hours and ended up with nothing (probably due to memory leaking).<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Is there anyway to make it faster?<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">This is what the 'nproc' argument does - you should use as many<br></blockquote><blockquote type="cite">processors as you have available. If you can distribute it across a<br></blockquote><blockquote type="cite">queuing system, even better. (The GUI can set this up for you<br></blockquote><blockquote type="cite">semi-automatically if you have Sun Grid Engine, but it's possible on<br></blockquote><blockquote type="cite">the command line too - check the documentation for details.) <br></blockquote><br>Now that new versions of SGE will no longer be free thanks to Oracle's <br>purchase, have you considered adding support for a queueing system that <br>is free and open-source, such as Torque?<br><br>-- <br>Thanks,<br>Donnie<br><br>Donald S. Berkholz, Ph.D.<br>Research Fellow<br>James R. Thompson lab, Physiology & Biomedical Engineering<br>Grazia Isaya lab, Pediatric & Adolescent Medicine<br>Medical Sciences 2-66<br>Mayo Clinic College of Medicine<br>200 First Street SW<br>Rochester, MN 55905<br>office: 507-538-6924<br>cell: 612-991-1321<br>_______________________________________________<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></div></blockquote></div><br><div>
<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><div><div><div><div><br>Thomas C. Terwilliger<br>Mail Stop M888<br>Los Alamos National Laboratory<br>Los Alamos, NM 87545<br><br>Tel: 505-667-0072 email: <a href="mailto:terwilliger@LANL.gov">terwilliger@LANL.gov</a><br>Fax: 505-665-3024 SOLVE web site: <a href="http://solve.lanl.gov">http://solve.lanl.gov</a><br>PHENIX web site: http:www.phenix-online.org<br>ISFI Integrated Center for Structure and Function Innovation web site: <a href="http://techcenter.mbi.ucla.edu">http://techcenter.mbi.ucla.edu</a><br>TB Structural Genomics Consortium web site: <a href="http://www.doe-mbi.ucla.edu/TB">http://www.doe-mbi.ucla.edu/TB</a></div><div>CBSS Center for Bio-Security Science web site: <a href="http://www.lanl.gov/cbss">http://www.lanl.gov/cbss</a><br><br></div></div></div></div><br></div></span><br class="Apple-interchange-newline">
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