<p dir="ltr">Thanks Lyn, Thanks Rayson, </p>
<p dir="ltr">For those who may be reading this in the future looking for a solution, here is a partial solution. </p>
<p dir="ltr">It does not reduce the time for deleting many jobs, yet it prevents the system from crushing multiple times in the attempt to delete the jobs. </p>
<p dir="ltr">Here is what I did: <br>
while sleep 600; do timeout 480 qdel -u UserName ; done</p>
<p dir="ltr">Just replace 600 with a safe period for the system to recover and 480 with approxinate time that the system runs before memory being exhausted, and replace UserName with your user. Those numbers will change from system to system. </p>
<p dir="ltr">This will delete a chunk at a time without crushing the system. I am still waiting after about 9 hours, yet I did not need to restart the server due to SGE crushing. </p>
<p dir="ltr">I hope this solution will help others. </p>
<p dir="ltr"> Jacob</p>
<div class="gmail_quote">On Feb 23, 2015 2:03 AM, "Rayson Ho" <<a href="mailto:raysonlogin@gmail.com">raysonlogin@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Is your local cluster using classic or BerkeleyDB spooling? If it is classic over NFS, then qdel can be very slow.<div><br></div><div>One quick workaround is to hide the job spooling files manually, just move the spooled jobs from <span style="font-size:12.8000001907349px">$</span><span style="font-size:12.8000001907349px;background-color:rgb(255,255,255)">SGE_ROOT</span><span style="font-size:12.8000001907349px">/$</span><span style="font-size:12.8000001907349px;background-color:rgb(255,255,255)">SGE_CELL</span><span style="font-size:12.8000001907349px">/</span><span style="font-size:12.8000001907349px;background-color:rgb(255,255,255)">spool</span><span style="font-size:12.8000001907349px">/</span><span style="font-size:12.8000001907349px;background-color:rgb(255,255,255)">qmaster</span><span style="font-size:12.8000001907349px">/</span><span style="font-size:12.8000001907349px;background-color:rgb(255,255,255)">jobs to a private backup directory.</span><br><div class="gmail_extra"><br clear="all"><div><div>Rayson<br><br>==================================================<br>Open Grid Scheduler - The Official Open Source Grid Engine<br><a href="http://gridscheduler.sourceforge.net/" target="_blank">http://gridscheduler.sourceforge.net/</a><br><a href="http://gridscheduler.sourceforge.net/GridEngine/GridEngineCloud.html" target="_blank">http://gridscheduler.sourceforge.net/GridEngine/GridEngineCloud.html</a></div></div>
<div class="gmail_extra"><br></div><div class="gmail_extra"><br></div><br><div class="gmail_quote">On Sun, Feb 22, 2015 at 8:31 PM, Jacob Barhak <span dir="ltr"><<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><p dir="ltr">Hi to SGE experts, </p>
<p dir="ltr">This is an SGE question rather than StarCluster related. I am actually having this issue on a local clyster. And I did raise thulis issue a while ago. So sorry for repetition. And if you know of another list that can help, please direct me there. </p>
<p dir="ltr">The qdel command does not respond well with a large number of jobs. More than 100k jobs makes things intollerable. </p>
<p dir="ltr">It takes a long time and consumes too much memory if trying to delete all jobs. </p>
<p dir="ltr">Is there a shortcut someone is aware of to clear the enite queue without waiting for many hours or the server running out of memory? </p>
<p dir="ltr">Will removing the StarCluser server and reinstalling it work? If so, how to bypass long configuration? Are there several files that can do the trick if handled properly? </p>
<p dir="ltr">I hope someone has a quick solution. </p><span><font color="#888888">
<p dir="ltr"> Jacob</p>
</font></span><br>_______________________________________________<br>
StarCluster mailing list<br>
<a href="mailto:StarCluster@mit.edu" target="_blank">StarCluster@mit.edu</a><br>
<a href="http://mailman.mit.edu/mailman/listinfo/starcluster" target="_blank">http://mailman.mit.edu/mailman/listinfo/starcluster</a><br>
<br></blockquote></div><br></div></div></div>
</blockquote></div>