<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 12 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
        {font-family:"Cambria Math";
        panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
        {font-family:Calibri;
        panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
        {font-family:Tahoma;
        panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
        {font-family:Consolas;
        panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
        {margin-top:0in;
        margin-right:0in;
        margin-bottom:10.0pt;
        margin-left:0in;
        font-size:11.0pt;
        font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
        {color:blue;
        text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
        {color:purple;
        text-decoration:underline;}
span.EmailStyle17
        {mso-style-type:personal;
        font-family:"Arial","sans-serif";
        color:windowtext;
        letter-spacing:0pt;}
span.EmailStyle18
        {mso-style-type:personal-reply;
        font-family:"Calibri","sans-serif";
        color:#1F497D;}
.MsoChpDefault
        {mso-style-type:export-only;
        font-size:10.0pt;}
@page WordSection1
        {size:8.5in 11.0in;
        margin:1.0in 1.25in 1.0in 1.25in;}
div.WordSection1
        {page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='color:#1F497D'>Dave,<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>&nbsp; Welcome to Torque. I switched from NQS some time ago, and Torque/PBS has been a good replacement for me.<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>Things to check:<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>&nbsp; What does the error output say? ( Probably in file </span><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>dn_test.txt.e[0-9]* )</span><span style='color:#1F497D'><o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>&nbsp; Permissions on &nbsp;</span><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>/home/zarnocda/torque/scripts_test/dn_test.sh , is it executable?&nbsp; <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>You may need:</span><span style='color:#1F497D'>&nbsp;&nbsp; &nbsp;chmod u+x </span><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>/home/zarnocda/torque/scripts_test/dn_test.sh<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'> <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>&nbsp;&nbsp;I&#8217;d also check if /home/zarnocda/torque/scripts_test/dn_test.sh <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>even exists on the compute node.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>e.g.&nbsp; ls /home/zarnocda/torque/scripts_test/dn_test.sh&nbsp; executable<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>&nbsp; I usually use the interactive opion ( qsub &#8211;I ) to debug these kinds of problems.<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>You could issue:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>qsub -V &#8211;I &nbsp;-l nodes=1 -q dn</span><span style='color:#1F497D'><o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>which will start an interactive jobs and log you into the mother superior node for that job<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'>where you can then try issuing the commands within your job that is not working.<o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:16.0pt;font-family:Consolas;color:#1F497D'>James Coyle, PhD<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:16.0pt;font-family:Consolas;color:#1F497D'> High Performance Computing Group&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:16.0pt;font-family:Consolas;color:#1F497D'>&nbsp;Iowa State Univ.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:16.0pt;font-family:Consolas;color:#1F497D'>web: <a href="http://www.public.iastate.edu/~jjc"><span style='color:blue'>http://jjc.public.iastate.edu/</span></a><o:p></o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span style='color:#1F497D'><o:p>&nbsp;</o:p></span></p><div style='border:none;border-left:solid blue 1.5pt;padding:0in 0in 0in 4.0pt'><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> torqueusers-bounces@supercluster.org [mailto:torqueusers-bounces@supercluster.org] <b>On Behalf Of </b>Zarnoch, Dave<br><b>Sent:</b> Wednesday, September 14, 2011 8:42 AM<br><b>To:</b> torqueusers@supercluster.org<br><b>Subject:</b> [torqueusers] Batch not running<br><b>Importance:</b> High<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p>&nbsp;</o:p></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Hello folks,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>New to Torque, used to run NQS&#8230;.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Concerning Torque&#8230;<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>I have a small script:<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>$ more dn_test.sh<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>#!/bin/sh<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>#<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>PATH=/bin:/usr/bin:/usr/local/bin:/etc:/usr/sbin:/usr/ucb:$HOME/bin:/usr/bin/X11<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>:/sbin:.<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>export PATH<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>DATE=`date +%H%M`<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>echo &quot;Hello&quot;<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>touch /tmp/dn_test_${DATE}<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>sleep 90<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>When I submit the script:<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>qsub -V -l nodes=1 -q dn dn_test.sh<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>It runs fine.<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>But I need to run batch&#8230;<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>I created a text file &#8220;dn_test.txt&#8221;<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>That contains:<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>/home/zarnocda/torque/scripts_test/dn_test.sh<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>When I run:<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>qsub -V -l nodes=1 &#8211;q dn dn_test.txt<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>It appears to process the file:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>qstat &#8211;s<o:p></o:p></span></p><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:red'>Job id&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Name&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; User&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Time Use S Queue<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:red'>------------------------- ---------------- --------------- -------- - -----<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:red'>7592.usphl1ora002.amer&nbsp;&nbsp;&nbsp; dn_test.txt&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; zarnocda&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 R dn&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <o:p></o:p></span></b></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>But it doesn&#8217;t excute the script within:<o:p></o:p></span></p><p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><span style='font-size:10.0pt;font-family:"Arial","sans-serif"'>/home/zarnocda/torque/scripts_test/dn_test.sh<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>Any help!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>Thanks!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>Dave<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>Dave Zarnoch<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>UNIX Systems Administration<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>(215)200-0911<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy'>Dave.Zarnoch@sykes.com</span><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p></o:p></span></p><p class=MsoNormal><o:p>&nbsp;</o:p></p></div></div></body></html>