<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><a href="http://markmail.org/message/zdj5ebfrzhnadglf">This</a> finally solved my problem. Thank you Rayson and Justin!<div><br></div><div>Amir<br><div><br><div><div>On Dec 5, 2011, at 3:14 PM, Justin Riley wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>-----BEGIN PGP SIGNED MESSAGE-----<br>Hash: SHA1<br><br>Also, just for drill, try running:<br><br>$ source /etc/profile<br><br>before trying qconf in case your environment was altered at some point<br>in your SSH session.<br><br>~Justin<br><br>On 12/05/2011 06:13 PM, Justin Riley wrote:<br><blockquote type="cite">Amir,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">qconf is included in the StarCluster AMIs so there must be some<br></blockquote><blockquote type="cite">other issue you're facing. Also, I wouldn't recommend installing<br></blockquote><blockquote type="cite">the gridengine packages from ubuntu as they're most likely not<br></blockquote><blockquote type="cite">compatible with StarCluster's bundled version in /opt/sge6 as<br></blockquote><blockquote type="cite">you're seeing.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">With that said which AMI are you using and what does "echo $PATH"<br></blockquote><blockquote type="cite">look like when you login as root (via sshmaster)?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">~Justin<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On 12/05/2011 06:07 PM, Amirhossein Kiani wrote:<br></blockquote><blockquote type="cite"><blockquote type="cite">So I tried this and couldn't run qconf because it was not <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">installed. I then tried installing it using apt-get and<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">specified default for the cell name and "master" for the master<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">name which is the default for the SGE created using StarCluster.<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">However now when I want to use qconf, it says:<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">root@master:/data/stanford/aligned# qconf -msconf error: commlib <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">error: got select error (Connection refused) unable to send <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">message to qmaster using port 6444 on host "master": got send <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">error<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Any idea how i could configure it to work?<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Many thanks, Amir<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">On Dec 5, 2011, at 1:52 PM, Rayson Ho wrote:<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi Amirhossein,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I was working on a few other things, and I just saw your<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">message -- I have to spend less time on mailing list<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">discussions these days due to the number of things that I<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">needed to develop and/or fix, and I am also working on a new<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">patch release of OGS/Grid Engine 2011.11. Luckily, I just found<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">the mail that exactly solves the issue you are encountering:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="http://markmail.org/message/zdj5ebfrzhnadglf">http://markmail.org/message/zdj5ebfrzhnadglf</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">For more info, see the "job_load_adjustments" and <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">"load_adjustment_decay_time" parameters in the Grid Engine <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">manpage:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="http://gridscheduler.sourceforge.net/htmlman/htmlman5/sched_conf.html">http://gridscheduler.sourceforge.net/htmlman/htmlman5/sched_conf.html</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote>Rayson<br><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">================================= Grid Engine / Open Grid <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Scheduler <a href="http://gridscheduler.sourceforge.net/">http://gridscheduler.sourceforge.net/</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Scalable Grid Engine Support Program <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="http://www.scalablelogic.com/">http://www.scalablelogic.com/</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">________________________________ From: Amirhossein Kiani <br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><<a href="mailto:amirhkiani@gmail.com">amirhkiani@gmail.com</a>> To: Rayson Ho <<a href="mailto:raysonlogin@yahoo.com">raysonlogin@yahoo.com</a>><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Cc: Justin Riley <<a href="mailto:justin.t.riley@gmail.com">justin.t.riley@gmail.com</a>>;<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">"<a href="mailto:starcluster@mit.edu">starcluster@mit.edu</a>" <<a href="mailto:starcluster@mit.edu">starcluster@mit.edu</a>> Sent: Friday,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">December 2, 2011 6:36 PM Subject: Re: [StarCluster] AWS<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">instance runs out of memory and swaps<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Dear Rayson,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Did you have a chance to test your solution on this?<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Basically, all I want is to prevent a job from running on an<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">instance if it does not have the memory required for the job.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I would very much appreciate your help!<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Many thanks, Amir<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">On Nov 21, 2011, at 10:29 AM, Rayson Ho wrote:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Amir,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">You can use qhost to list all the node and resources that<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">each node has.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I have an answer to the memory issue, but I have not have<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">time to properly type up a response and test it.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Rayson<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">________________________________ From: Amirhossein Kiani <br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><<a href="mailto:amirhkiani@gmail.com">amirhkiani@gmail.com</a>> To: Justin Riley <br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><<a href="mailto:justin.t.riley@gmail.com">justin.t.riley@gmail.com</a>> Cc: Rayson Ho <br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><<a href="mailto:rayrayson@gmail.com">rayrayson@gmail.com</a>>; "<a href="mailto:starcluster@mit.edu">starcluster@mit.edu</a>" <br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><<a href="mailto:starcluster@mit.edu">starcluster@mit.edu</a>> Sent: Monday, November 21, 2011 1:26<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">PM Subject: Re: [StarCluster] AWS instance runs out of memory<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">and swaps<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi Justin,<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Many thanks for your reply. I don't have any issue with <br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">multiple jobs running per node if there is enough memory for <br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">them. But since I know about the nature of my jobs, I can <br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">predict that only one per node should be running. How can I <br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">see how much memory does SGE think each node have? Is there<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">a way to list that?<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Regards, Amir<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">On Nov 21, 2011, at 8:18 AM, Justin Riley wrote:<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi Amir,<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Sorry to hear you're still having issues. This is really <br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">more of an SGE issue more than anything but perhaps Rayson <br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">can give a better insight as to what's going on. It seems <br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">you're using 23G nodes and 12GB jobs. Just for drill does <br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">'qhost' show each node having 23GB? Definitely seems like <br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">there's a boundary issue here given that two of your jobs <br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">together approaches the total memory of the machine<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">(23GB). Is it your goal only to have one job per<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">node?<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">~Justin<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">On 11/16/2011 09:00 PM, Amirhossein Kiani wrote:<br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Dear all,<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I even wrote the queue submission script myself, adding <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">the mem_free=MEM_NEEDED,h_vmem=MEM_MAX parameter but <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">sometimes two jobs are randomly sent to one node that<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">does not have enough memory for two jobs and they start<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">running. I think the SGE should check on the instance<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">memory and not run multiple jobs on a machine when the<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">memory requirement for the jobs in total is above the<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">memory available in the node (or maybe there is a bug in<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">the current check)<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Amir<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">On Nov 8, 2011, at 5:37 PM, Amirhossein Kiani wrote:<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi Justin,<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I'm using a third-party tool to submit the jobs but I<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">am setting the hard<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">limit.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">For all my jobs I have something like this for the job <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">description:<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">[root@master test]# qstat -j 1 <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">==============================================================<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote>job_number: 1<br><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">exec_file: job_scripts/1 <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">submission_time: Tue Nov 8 17:31:39 2011 <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">owner: root uid: 0 group: root<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">gid: 0<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">sge_o_home: /root<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">sge_o_log_name: root sge_o_path: <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">/home/apps/bin:/home/apps/vcftools_0.1.7/bin:/home/apps/tabix-0.2.5:/home/apps/BEDTools-Version-2.14.2/bin:/home/apps/samtools/bcftools:/home/apps/samtools:/home/apps/bwa-0.5.9:/home/apps/Python-2.7.2:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/bin:/home/apps/sjm-1.0/bin:/home/apps/hugeseq/bin:/usr/lib64/openmpi/1.4-gcc/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/cuda/bin:/usr/local/cuda/computeprof/bin:/usr/local/cuda/open64/bin:/opt/sge6/bin/lx24-amd64:/root/bin<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote>sge_o_shell: /bin/bash<br><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">sge_o_workdir:<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">/data/test<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">sge_o_host: master account: sge <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">stderr_path_list: <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">NONE:master:/data/log/SAMPLE.bin_aln-chr1_e111108173139.txt<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote>*hard resource_list: h_vmem=12000M*<br><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">mail_list: root@master notify: FALSE <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">job_name: SAMPLE.bin_aln-chr1 <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">stdout_path_list: <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">NONE:master:/data/log/SAMPLE.bin_aln-chr1_o111108173139.txt<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote>jobshare:<br><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">0<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">hard_queue_list: all.q env_list: job_args: <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">-c,/home/apps/hugeseq/bin/hugeseq_mod.sh bin_sam.sh<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">chr1 /data/chr1.bam /data/bwa_small.bam && <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">/home/apps/hugeseq/bin/hugeseq_mod.sh sam_index.sh <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">/data/chr1.bam script_file: /bin/sh <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">verify_suitable_queues: 2 scheduling info: <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">(Collecting of scheduler job information is turned<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">off)<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">And I'm using the Cluster GPU Quadruple Extra Large <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">instances which<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">think has about 23G memory. The issue that I see is<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">too many of the jobs are submitted. I guess I need to<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">set the mem_free too? (the problem is the tool im using<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">does not seem to have a way tot set that...)<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Many thanks, Amir<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">On Nov 8, 2011, at 5:47 AM, Justin Riley wrote:<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi Amirhossein,<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Did you specify the memory usage in your job script or<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">at command line and what parameters did you use exactly?<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Doing a quick search I believe that the following will <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">solve the problem although I haven't tested myself:<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">$ qsub -l mem_free=MEM_NEEDED,h_vmem=MEM_MAX yourjob.sh<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Here, MEM_NEEDED and MEM_MAX are the lower and<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">upper bounds for your<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">job's memory requirements.<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">HTH,<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">~Justin<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">On 7/22/64 2:59 PM, Amirhossein Kiani wrote:<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Dear Star Cluster users,<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I'm using Star Cluster to set up an SGE and when I ran <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">my job list,<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">although I had specified the memory usage for each job,<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">it submitted too many jobs on my instance and my<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">instance started going out of memory and swapping.<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I wonder if anyone knows how I could tell the SGE the <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">max memory to<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">consider when submitting jobs to each node so that it <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">doesn't run the jobs if there is not enough memory <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">available on a node.<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I'm using the Cluster GPU Quadruple Extra Large <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">instances.<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Many thanks, Amirhossein Kiani<br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">_______________________________________________ <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">StarCluster mailing list <a href="mailto:StarCluster@mit.edu">StarCluster@mit.edu</a> <br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="http://mailman.mit.edu/mailman/listinfo/starcluster">http://mailman.mit.edu/mailman/listinfo/starcluster</a><br></blockquote></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">_______________________________________________ StarCluster <br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">mailing list <a href="mailto:StarCluster@mit.edu">StarCluster@mit.edu</a> <br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="http://mailman.mit.edu/mailman/listinfo/starcluster">http://mailman.mit.edu/mailman/listinfo/starcluster</a><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">_______________________________________________ StarCluster <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">mailing list <a href="mailto:StarCluster@mit.edu">StarCluster@mit.edu</a> <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="http://mailman.mit.edu/mailman/listinfo/starcluster">http://mailman.mit.edu/mailman/listinfo/starcluster</a><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________ StarCluster mailing<br></blockquote><blockquote type="cite">list <a href="mailto:StarCluster@mit.edu">StarCluster@mit.edu</a> <br></blockquote><blockquote type="cite"><a href="http://mailman.mit.edu/mailman/listinfo/starcluster">http://mailman.mit.edu/mailman/listinfo/starcluster</a><br></blockquote><br>-----BEGIN PGP SIGNATURE-----<br>Version: GnuPG v2.0.17 (GNU/Linux)<br>Comment: Using GnuPG with Mozilla - <a 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