<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<style id="owaParaStyle" type="text/css">P {margin-top:0;margin-bottom:0;}</style>
</head>
<body ocsi="0" fpstyle="1" style="word-wrap: break-word;">
<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;"><font style="font-family: Tahoma;" size="3">Hi Dr<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); 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;">
<font size="3">Terwilliger, <br>
I see. Thank you so much!<br>
<br>
Best,<br>
Wei<br>
</font></span></font>
<div style="font-family: Times New Roman; color: rgb(0, 0, 0); font-size: 16px;">
<hr tabindex="-1">
<div style="direction: ltr;" id="divRpF479617"><font color="#000000" face="Tahoma" size="2"><b>From:</b> phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Tom Terwilliger [terwilliger@lanl.gov]<br>
<b>Sent:</b> Thursday, November 17, 2011 2:57 PM<br>
<b>To:</b> PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] MR_ROSETTA<br>
</font><br>
</div>
<div></div>
<div>Hi Wei,
<div><br>
</div>
<div>I think that you may not have "qsub" as a command on your machine. In that case, then you can use "group_run_command=sh" and then it should work.</div>
<div><br>
</div>
<div>Note that if it takes "forever" with 1 processor, it will still take a long time with 4... It may be useful to run your job on a cluster with more processors.</div>
<div><br>
</div>
<div>All the best,</div>
<div>Tom T</div>
<div><br>
<div>
<div>On Nov 17, 2011, at 12:49 PM, Wei Shi wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; 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; font-size: medium;">
<div>
<div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt;">
<p class="MsoNormal" style="margin: 0cm 0cm 10pt; font-size: 12pt; font-family: 'Times New Roman';">
Hi all,<br>
</p>
<p class="MsoNormal" style="margin: 0cm 0cm 10pt; font-size: 12pt; font-family: 'Times New Roman';">
I am trying to run phenix.mr_rosetta using the following script for rebuilding the model with Rosetta before MR from phenix website except omitting specifying ncs_copies number. Following is the script I am using:</p>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
<span style="font-size: 10pt; font-family: Courier;">phenix.mr_rosetta \</span></div>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
<span style="font-size: 10pt; font-family: Courier;">seq_file = seq.dat \</span></div>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
<span style="font-size: 10pt; font-family: Courier;">data=coords1.mtz \<span> </span></span></div>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
<span style="font-size: 10pt; font-family: Courier;">search_models=coords1.pdb \<span> </span></span></div>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
<span style="font-size: 10pt; font-family: Courier;">run_prerefine=True \<span> </span></span></div>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
<span style="font-size: 10pt; font-family: Courier;">number_of_prerefine_models=1000 \<span> </span></span></div>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
<span style="font-size: 10pt; font-family: Courier;">fragment_files = test3.gz \<span> </span></span></div>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
<span style="font-size: 10pt; font-family: Courier;">fragment_files = test9.gz \<span> </span></span></div>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
<span style="font-size: 10pt; font-family: Courier;">rescore_mr.relax=False \<span> </span></span></div>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
<span style="font-size: 10pt; font-family: Courier;">rosetta_models=20 \<span> </span></span></div>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
<span style="font-size: 10pt; font-family: Courier;">space_group=p222<span> <span class="Apple-converted-space"> </span></span>\<span> </span></span></div>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
<span style="font-size: 10pt; font-family: Courier;">use_all_plausible_sg=False \<span> </span></span></div>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
<span style="font-size: 10pt; font-family: Courier;">nproc=4 \<span> </span></span></div>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
<span style="font-size: 10pt; font-family: Courier;">group_run_command=qsub\</span></div>
<p class="MsoNormal" style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
<span style="font-size: 10pt; font-family: Courier;"> </span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 10pt; font-size: 12pt; font-family: 'Times New Roman';">
When I run the above script, it gives the following error message:</p>
<p class="MsoNormal" style="margin: 0cm 0cm 10pt; font-size: 12pt; font-family: 'Times New Roman';">
child process stderr output:</p>
<p class="MsoNormal" style="margin: 0cm 0cm 10pt; font-size: 12pt; font-family: 'Times New Roman';">
<span> <span class="Apple-converted-space"> </span></span>command: 'qsub /home/wei/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1'</p>
<p class="MsoNormal" style="margin: 0cm 0cm 10pt; font-size: 12pt; font-family: 'Times New Roman';">
<span> <span class="Apple-converted-space"> </span></span>/bin/sh: qsub: not found</p>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
Then, I omit the last line in the command �<span style="font-size: 10pt; font-family: Courier;">group_run_command=qsub\</span>�. MR_ROSETTA seems to be running.<span> <span class="Apple-converted-space"> </span></span>But, it takes forever to run.</div>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
<br>
</div>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
My questions is:</div>
<div style="margin: 0.1pt 0cm 0.1pt 36pt; font-size: 12pt; font-family: 'Times New Roman'; text-indent: -18pt;">
<span><span>1.<span style="font: 7pt 'Times New Roman';"> <span class="Apple-converted-space"> </span></span></span></span>Does anyone happen to know why it tells me �qsub: not found� when I include<span class="Apple-converted-space"> </span><span> </span>�group_run_command=qsub�
in my script?</div>
<div style="margin: 0.1pt 0cm 0.1pt 36pt; font-size: 12pt; font-family: 'Times New Roman'; text-indent: -18pt;">
<span><span>2.<span style="font: 7pt 'Times New Roman';"> <span class="Apple-converted-space"> </span></span></span></span>When I omit �group_run_command=qsub� in the script, mr_rosetta seems to be running.<span> But<span class="Apple-converted-space"> </span></span>it
just gives me the following message and it takes forever to run. Almost 10h later, no job is finished. I don�t know whether this is normal. If not, any idea about why it�s so slow and any suggestions about how to speed up the run? Thank you so much!<br>
</div>
<p class="MsoNormal" style="margin: 0.1pt 0cm 0.1pt 36pt; font-size: 12pt; font-family: 'Times New Roman';">
</p>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
Splitting work into 1 jobs and running with 4 processors using sh</div>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
background=True in /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1</div>
<p class="MsoNormal" style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
</p>
<div style="margin: 0.1pt 0cm; font-size: 12pt; font-family: 'Times New Roman';">
Starting job 1...Log will be: /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log</div>
</div>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
</div>
</span></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-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">
<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" target="_blank">
terwilliger@LANL.gov</a><br>
Fax: 505-665-3024 SOLVE web site: <a href="http://solve.lanl.gov" target="_blank">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" target="_blank">http://techcenter.mbi.ucla.edu</a><br>
TB Structural Genomics Consortium web site: <a href="http://www.doe-mbi.ucla.edu/TB" target="_blank">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" target="_blank">
http://www.lanl.gov/cbss</a><br>
<br>
</div>
</div>
</div>
</div>
<br>
</div>
</span><br class="Apple-interchange-newline">
</div>
<br>
</div>
</div>
</div>
</div>
</body>
</html>