<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
<title></title>
</head>
<body>
<p style="margin: 0px;"><span></span></p>
<div style="margin: 5px 0px 5px 0px;">
<br />
On October 28, 2010 at 4:11 AM TJ Mustard <mustardt@onid.orst.edu> wrote:<br />
<br />
<blockquote type="cite" style="margin-left: 0px; padding-left: 10px; border-left: solid 1px blue;">
<p style="margin: 0px;"><span></span></p>
<div style="margin: 5px 0px 5px 0px;">
<br />
On October 28, 2010 at 4:05 AM fancy2012 <fancy2012@yeah.net> wrote:<br />
<br />
<blockquote type="cite" style="margin-left: 0px; padding-left: 10px; border-left: solid 1px blue;">
<div>
Dear GMX users,
</div>
<div>
 
</div>
<div>
I have a problem when I run gromacs-4.5.1 on a cluster, I can only do paralleled running using 1 node, which is 8-cpu, but when I use more nodes, it will abort abnormally. Could someone help me figure it out? Thanks very much!
</div>
<div>
 
</div>
</blockquote>
</div>
<p style="margin: 0px;">Gromacs 4.5.1 is somewhat viral on cpu (takes all of them if not told otherwise). I you submit multiple jobs to a node without telling gromacs (ie. mdrun) how many cpus to use, all the jobs will use all the cpus simultaneously. This can cause job failure.</p>
</blockquote>
</div>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">If you use SGE, you may want to use SMP or MPI.</p>
<p style="margin: 0px;"> </p>
<div style="margin: 5px 0px 5px 0px;">
<blockquote type="cite" style="margin-left: 0px; padding-left: 10px; border-left: solid 1px blue;">
<div style="margin: 5px 0px 5px 0px;">
<blockquote type="cite" style="margin-left: 0px; padding-left: 10px; border-left: solid 1px blue;">
<div>
All the best,
</div>
<div>
fancy
</div>
<div>
 
</div>
</blockquote>
</div>
<p style="margin: 0px;"> </p>
<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
</blockquote>
</div>
<p style="margin: 0px;"> </p>
<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
</body>
</html>