Thanks Gareth. I removed that setting, using <div><br></div><div>qmgr -c 'unset queue batch resources_default.nodes'</div><div><br></div><div>but I'm still getting the same error. I can submit jobs that request 1-3 ppn, but not 4 ppn.<div>
<br></div><div><br><div><br><div class="gmail_quote">On Sat, Jan 14, 2012 at 5:08 AM, <span dir="ltr"><Gareth.Williams@csiro.au></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-AU" link="blue" vlink="purple"><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hi Ryan,<u></u><u></u></span></p><p class="MsoNormal">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></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.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times","serif""><u></u> <u></u></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).<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Times","serif""><u></u> <u></u></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"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></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:<a href="mailto:ngsbioinformatics@gmail.com" target="_blank">ngsbioinformatics@gmail.com</a>] <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?<u></u><u></u></span></p></div></div><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">So that's what's throwing me off. I already configured the queue using:<u></u><u></u></p><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">
<span style="font-family:"Times","serif"">[root@bic database]# qmgr -c 'create queue batch'</span><u></u><u></u></p><p class="MsoNormal"><span style="font-family:"Times","serif"">[root@bic database]# qmgr -c 'set queue batch queue_type = execution'</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-family:"Times","serif"">[root@bic database]# qmgr -c 'set queue batch started = true'</span><u></u><u></u></p><p class="MsoNormal"><span style="font-family:"Times","serif"">[root@bic database]# qmgr -c 'set queue batch enabled = true'</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-family:"Times","serif"">[root@bic database]# qmgr -c 'set queue batch resources_default.nodes=1:ppn=1'</span><u></u><u></u></p><p class="MsoNormal"><span style="font-family:"Times","serif""> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-family:"Times","serif"">[root@bic database]# qmgr -c "set queue batch keep_completed=120"</span><u></u><u></u></p><p class="MsoNormal"><span style="font-family:"Times","serif"">[root@bic database]# qmgr -c "set server default_queue=batch" </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-family:"Times","serif"">[root@bic database]# qmgr -c "set server query_other_jobs = true"</span><u></u><u></u></p><div><p class="MsoNormal"><u></u> <u></u></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:<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p>
</div><div><p class="MsoNormal">[root@bic hg19]# cat /var/spool/torque/server_priv/nodes <u></u><u></u></p></div><div><p class="MsoNormal">compute-0-0 np=8<u></u><u></u></p></div><div><p class="MsoNormal">compute-0-1 np=8<u></u><u></u></p>
</div><div><p class="MsoNormal">compute-0-2 np=8<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></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. <u></u><u></u></p>
</div><div><p class="MsoNormal"><u></u> <u></u></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" target="_blank">akohlmey@cmm.chem.upenn.edu</a>> wrote:<u></u><u></u></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" target="_blank">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.<u></u><u></u></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" target="_blank">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>--</span><br><span>Dr. Axel Kohlmeyer <a href="mailto:akohlmey@gmail.com" target="_blank">akohlmey@gmail.com</a></span><br>
<span><a href="http://sites.google.com/site/akohlmey/" target="_blank">http://sites.google.com/site/akohlmey/</a></span><br><br><span>Institute for Computational Molecular Science</span><br><span>Temple University, Philadelphia PA, USA.</span><br>
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<br></blockquote></div><br></div></div></div>