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</o:shapelayout></xml><![endif]--></head><body lang=EN-AU link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi Ryan,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Unset queue </span><span style='font-family:"Times","serif"'>batch resources_default.nodes – you don’t need that.<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Times","serif"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-family:"Times","serif"'>The nodes resource is fighting with the procs resource. You need to only set one or the other for a given job (neither is OK for serial tasks).<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Times","serif"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-family:"Times","serif"'>Gareth</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt'><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Ryan Golhar [mailto:ngsbioinformatics@gmail.com] <br><b>Sent:</b> Saturday, 14 January 2012 4:31 AM<br><b>To:</b> Torque Users Mailing List<br><b>Subject:</b> Re: [torqueusers] Do I have to define the ncpus for a compute node?<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>So that's what's throwing me off. I already configured the queue using:<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-family:"Times","serif"'>[root@bic database]# qmgr -c 'create queue batch'</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-family:"Times","serif"'>[root@bic database]# qmgr -c 'set queue batch queue_type = execution'</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-family:"Times","serif"'>[root@bic database]# qmgr -c 'set queue batch started = true'</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-family:"Times","serif"'>[root@bic database]# qmgr -c 'set queue batch enabled = true'</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-family:"Times","serif"'>[root@bic database]# qmgr -c 'set queue batch resources_default.nodes=1:ppn=1'</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-family:"Times","serif"'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-family:"Times","serif"'>[root@bic database]# qmgr -c "set queue batch keep_completed=120"</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-family:"Times","serif"'>[root@bic database]# qmgr -c "set server default_queue=batch" </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-family:"Times","serif"'>[root@bic database]# qmgr -c "set server query_other_jobs = true"</span><o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I assumed, by default, if the user doesn't specify any resources, a job would consume 1 core on 1 node. My nodes file shows:<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>[root@bic hg19]# cat /var/spool/torque/server_priv/nodes <o:p></o:p></p></div><div><p class=MsoNormal>compute-0-0 np=8<o:p></o:p></p></div><div><p class=MsoNormal>compute-0-1 np=8<o:p></o:p></p></div><div><p class=MsoNormal>compute-0-2 np=8<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>So Torque knows there are 8 cpus per node, and I haven't set a maximum limit to how many resources a job could use. To me, requesting 2 cpus on 1 node should have succeeded. <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><div><p class=MsoNormal>On Fri, Jan 13, 2012 at 11:18 AM, Axel Kohlmeyer <<a href="mailto:akohlmey@cmm.chem.upenn.edu">akohlmey@cmm.chem.upenn.edu</a>> wrote:<o:p></o:p></p><div><div><p class=MsoNormal style='margin-bottom:12.0pt'>On Fri, Jan 13, 2012 at 10:59 AM, Ryan Golhar<br><<a href="mailto:ngsbioinformatics@gmail.com">ngsbioinformatics@gmail.com</a>> wrote:<br>> Hi - I have a ROCKS cluster running and installed Torque. I'm able to<br>> submit 1 core, 1 cpu jobs without problem. I tried submitting a job that<br>> requested 4 cpus on 1 node using<br>><br>> #PBS -l nodes=1:ppn=4<br>><br>> in my job submission script. When I submit the job however, I get the<br>> error:<br>><br>> qsub: Job exceeds queue resource limits MSG=cannot locate feasible nodes<br>> (nodes file is empty or requested nodes exceed all systems)<br>><br>> If I run anodes, I see:<br>><br>> compute-0-0<br>> state = free<br>> np = 8<br>> ntype = cluster<br>> status =<br>> rectime=1326469800,varattr=,jobs=,state=free,netload=1720539412488,gres=,loadave=0.01,ncpus=8,physmem=16431248kb,availmem=17311704kb,totmem=17451364kb,idletime=339141,nusers=0,nsessions=?<br>> 15201,sessions=? 15201,uname=Linux compute-0-0.local 2.6.18-238.19.1.el5 #1<br>> SMP Fri Jul 15 07:31:24 EDT 2011 x86_64,opsys=linux<br>> gpus = 0<br>><br>><br>> All my compute nodes have 8 cpus. Do I need to tell Torque this? I thought<br>> Torque could figure this out from np=8 or ncpus=8.<o:p></o:p></p></div></div><p class=MsoNormal>the error message says that the request exceeds the queue configuration.<br>that is being checked before it looks at any nodes. thus you probably have<br>to adjust the queue configuration.<br><br>axel.<br><br><br>><br>> Ryan<br>><br>> _______________________________________________<br>> torqueusers mailing list<br>> <a href="mailto:torqueusers@supercluster.org">torqueusers@supercluster.org</a><br>> <a href="http://www.supercluster.org/mailman/listinfo/torqueusers" target="_blank">http://www.supercluster.org/mailman/listinfo/torqueusers</a><br>><br><span style='color:#888888'><br><br><br><span class=hoenzb>--</span><br><span class=hoenzb>Dr. Axel Kohlmeyer <a href="mailto:akohlmey@gmail.com">akohlmey@gmail.com</a></span><br><span class=hoenzb><a href="http://sites.google.com/site/akohlmey/" target="_blank">http://sites.google.com/site/akohlmey/</a></span><br><br><span class=hoenzb>Institute for Computational Molecular Science</span><br><span class=hoenzb>Temple University, Philadelphia PA, USA.</span><br><span class=hoenzb>_______________________________________________</span><br><span class=hoenzb>torqueusers mailing list</span><br><span class=hoenzb><a href="mailto:torqueusers@supercluster.org">torqueusers@supercluster.org</a></span><br><span class=hoenzb><a href="http://www.supercluster.org/mailman/listinfo/torqueusers" target="_blank">http://www.supercluster.org/mailman/listinfo/torqueusers</a></span></span><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p></div></div></div></div></body></html>