<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Candara, sans-serif;">
<div>
<div>Thanks Justin. Will give that a go and let you know if I get something to work.</div>
<div>
<p style="font-size: 12px; margin: 0px; font-family: Verdana;">---</p>
<p style="margin: 0px; font-family: Verdana;"><span style="font-size: 10px;"><b>Timothy Stitt PhD</b> / Head of Scientific Computing</span></p>
<p style="margin: 0px; font-family: Verdana;"><span style="font-size: 10px;">The Genome Analysis Centre (TGAC)</span></p>
<p style="margin: 0px; font-family: Verdana; color: rgb(4, 46, 238);"><span style="text-decoration: underline; font-size: 10px;"><a href="http://www.tgac.ac.uk/">http://www.tgac.ac.uk/</a></span></p>
<p style="margin: 0px; font-family: Cambria; min-height: 19px;"><span style="font-size: 10px;"><br>
</span></p>
<p style="margin: 0px; font-family: Verdana;"><span style="font-size: 10px;">p: +44 1603 450378</span></p>
<p style="margin: 0px; font-family: Verdana; color: rgb(13, 102, 213);"><span style="color: rgb(0, 0, 0); font-size: 10px;">e: <a href="mailto:timothy.stitt@tgac.ac.uk">timothy.stitt@tgac.ac.uk</a></span></p>
</div>
</div>
<div><br>
</div>
<span id="OLK_SRC_BODY_SECTION">
<div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt">
<span style="font-weight:bold">From: </span>Justin M Wozniak <<a href="mailto:wozniak@mcs.anl.gov">wozniak@mcs.anl.gov</a>><br>
<span style="font-weight:bold">Date: </span>Monday, 16 March 2015 21:27<br>
<span style="font-weight:bold">To: </span>Timothy Stitt <<a href="mailto:timothy.stitt@tgac.ac.uk">timothy.stitt@tgac.ac.uk</a>>, "<a href="mailto:exm-user@lists.mcs.anl.gov">exm-user@lists.mcs.anl.gov</a>" <<a href="mailto:exm-user@lists.mcs.anl.gov">exm-user@lists.mcs.anl.gov</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ExM Users] LSF Job Launcher?<br>
</div>
<div><br>
</div>
<div>
<div text="#000000" bgcolor="#FFFFFF">
<div class="moz-cite-prefix">Hi<br>
No, and I don't have access to any LSF systems. <br>
The way to get started is to check the information here: <a class="moz-txt-link-freetext" href="http://swift-lang.org/Swift-T/turbine-sites.html#_turbine_as_mpi_program">
http://swift-lang.org/Swift-T/turbine-sites.html#_turbine_as_mpi_program</a><br>
Turbine runs as an MPI program. <br>
Then, take a look at some other scheduler script that you have used before. In PBS, the turbine-pbs-run.zsh script is in control. It substitutes variables into a template named turbine.pbs.m4, creating turbine.pbs, and qsubs that. In turbine.pbs.m4, the
key line is: <br>
<br>
${TURBINE_LAUNCHER} ${TCLSH} ${PROGRAM} ${ARGS}<br>
<br>
which will run as something like: <br>
<br>
mpiexec /path/to/tclsh myprogram.tic args...<br>
<br>
Everything else is just setting up environment variables, most of which are optional. The key Turbine settings are set by this command (line 54):
<br>
<br>
source ${TURBINE_HOME}/scripts/turbine-config.sh<br>
<br>
You should be able to construct an ad hoc solution with those two key lines. <br>
<br>
Alternatively, you could copy turbine/scripts/submit/pbs to turbine/scripts/submit/lsf and edit the shell scripts until it works. Then you could send us a patch!
<br>
<br>
Justin<br>
<br>
On 03/16/2015 04:08 PM, Timothy Stitt (TGAC) wrote:<br>
</div>
<blockquote cite="mid:D12CF6CE.11F58%25timothy.stitt@tgac.ac.uk" type="cite">
<div>
<div>
<div>Hi all,</div>
<div><br>
</div>
<div>Has anyone developed a Turbine job launcher script for the LSF batch system? If so, could you kindly pass on some assistance on how to set it up with my local LSF cluster.</div>
<div><br>
</div>
<div>Thanks in advance,</div>
<div><br>
</div>
<div>Tim.</div>
<div>
<p style="font-size: 12px; margin: 0px; font-family:
Verdana;">---</p>
<p style="margin: 0px; font-family: Verdana;"><span style="font-size: 10px;"><b>Timothy Stitt PhD</b> / Head of Scientific Computing</span></p>
<p style="margin: 0px; font-family: Verdana;"><span style="font-size: 10px;">The Genome Analysis Centre (TGAC)</span></p>
<p style="margin: 0px; font-family: Verdana; color: rgb(4,
46, 238);">
<span style="text-decoration: underline;
font-size: 10px;"><a moz-do-not-send="true" href="http://www.tgac.ac.uk/">http://www.tgac.ac.uk/</a></span></p>
<p style="margin: 0px; font-family: Cambria; min-height:
19px;"><span style="font-size: 10px;"><br>
</span></p>
<p style="margin: 0px; font-family: Verdana;"><span style="font-size: 10px;">p: +44 1603 450378</span></p>
<p style="margin: 0px; font-family: Verdana; color: rgb(13,
102, 213);">
<span style="color: rgb(0, 0, 0); font-size:
10px;">e: <a moz-do-not-send="true" href="mailto:timothy.stitt@tgac.ac.uk">timothy.stitt@tgac.ac.uk</a></span></p>
</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset> <br>
<pre wrap="">_______________________________________________
ExM-user mailing list
<a class="moz-txt-link-abbreviated" href="mailto:ExM-user@lists.mcs.anl.gov">ExM-user@lists.mcs.anl.gov</a><a class="moz-txt-link-freetext" href="https://lists.mcs.anl.gov/mailman/listinfo/exm-user">https://lists.mcs.anl.gov/mailman/listinfo/exm-user</a></pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Justin M Wozniak</pre>
</div>
</div>
</span>
</body>
</html>