<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi,</div><div><br></div><div>This is a technical question for cluster experts.</div><div><br></div>I tried to run phenix.composite-omit-map which can divide the calculations into separate jobs, on a very large cluster controlled by the PBS system. I used this command of which the first 2 lines specify to divide the work up into 16 processes, and each process will use 1 of the CPU's in the cluster. <div><br></div><div>phenix.composite_omit_map nproc=16 background=False technology=pbs \<br> qsub_command="qsub -V -l procs=1,walltime=00:30:00,mem=2000mb,qos=flux -j oe -M <a href="mailto:saper@umich.edu">saper@umich.edu</a> -q flux -m abe " \<br> omit_type=anneal map_type=2mFo-Dfc output.file_name=composite_omit_map9.mtz \<br> reflections3_5percent.mtz Refine_122.pdb<br><br>This is the end of the log file before it aborted:</div><div><br></div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><div> ----------Calculating individual omit maps---------- </div><div><br></div><div>|-----------------------------------------------------------------------------|</div><div>| target_work(ml) = 4.65539 r_work = 0.1750 r_free = 0.2066 |</div><div>|-----------------------------------------------------------------------------|</div></blockquote><div><br></div><div>And this is the error log:</div><div><br></div><div><div>Traceback (most recent call last):</div><div> File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/composite_omit_map.py", line 238, in <module></div><div> run(sys.argv[1:])</div><div> File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/composite_omit_map.py", line 166, in run</div><div> out=out)</div><div> File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/phenix/phenix/automation/composite_omit_map.py", line 395, in __init__</div><div> preserve_exception_message=True)</div><div> File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/cctbx_project/libtbx/easy_mp.py", line 502, in parallel_map</div><div> display_stderr = not preserve_exception_message,</div><div> File "/usr/cac/rhel6/lsa/phenix/phenix-dev-1624/cctbx_project/libtbx/queuing_system_utils/processing/__init__.py", line 405, in PBS</div><div> raise RuntimeError, "PBS does not support synchronous submission"</div><div>RuntimeError: PBS does not support synchronous submission</div><div><br></div><div>I know that PBS doesn't support synchronous submission. Perhaps each job (or map region) requires more than one processor?</div><br></div><div>Thanks,</div><div>Mark</div><div><br></div><div><div>
<div style="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-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; 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-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-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; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-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; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-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; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-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; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-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; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-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; "><div style="font-family: Helvetica; font-size: medium; font-weight: normal; font-style: normal; margin: 0px; "><font face="Helvetica" size="3" style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: Helvetica; ">_________________________________</font></div><div style="margin: 0px; "><font face="Helvetica" style="font-variant: normal; line-height: normal; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="font-family: Helvetica; font-size: 12px; font-weight: normal; font-style: normal; margin: 0px; "><font face="Helvetica" size="3" style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: 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="font-family: Helvetica; font-size: 12px; font-weight: normal; font-style: normal; margin: 0px; "><font class="Apple-style-span" color="#000000">Associate Professor of Biological Chemistry, </font>University of Michigan</div><div style="font-family: Helvetica; font-size: 12px; font-weight: normal; font-style: normal; margin: 0px; ">c/o Biophysics, Chem 3040</div><div style="font-family: Helvetica; font-size: 12px; font-weight: normal; font-style: normal; margin: 0px; ">930 N University Ave</div><div style="font-family: Helvetica; font-size: 12px; font-weight: normal; font-style: normal; margin: 0px; "><font style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-family: Helvetica; "><font class="Apple-style-span" color="#000000">Ann Arbor MI 48109-1055 U.S.A.</font></font></div><div style="margin: 0px; "><div apple-content-edited="true"><span style="font-size: 12px; "><a href="mailto:saper@umich.edu">saper@umich.edu</a> phone (734) 764-3353 fax (734) 764-3323</span></div></div></span></font></div></div></span></div></span></div></span></div></span></div></span></div></span></div>
</div>
<br></div></body></html>