<html><body bgcolor="#FFFFFF"><div>I just recently finished working on a project called WATERS (Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences), and it also runs jobs on a Rocks cluster. It uses the Comad framework (so data is managed as a stream that passes sequentially through all the actors, each actor choosing what to add or remove), so it might be a bit unfamiliar, but it could be worth a look.</div><div><br></div><div>I handled the Rocks cluster submission and monitoring through qsub etc., but I do it in the Java code rather than at the actor level, so that it can be abstracted away and hidden from the user.</div><div><br></div><div>A zip intended for end users can be found at <a href="http://daks.ucdavis.edu/waters.zip">daks.ucdavis.edu/waters.zip</a>. I believe the source is included. Hope it helps.</div><div><br></div><div>- Sean<br><br>Sent from my iPhone</div><div><br>On Dec 2, 2009, at 9:26 AM, Jianwu Wang <<a href="mailto:jianwu@sdsc.edu">jianwu@sdsc.edu</a>> wrote:<br><br></div><div></div><br><blockquote type="cite"><div>
Arthur Goldberg wrote:
<blockquote cite="mid:4B14A50D.9020804@cs.nyu.edu" type="cite">Hello<br>
<br>
I've a bio-informatics workflow, that I'm considering running in
Kepler. The workflow analyzes about a dozen genomes, and will take a
few hundred hours of computing, which I'll run on our 64 node Rocks
cluster. <br>
<br>
Several Perl programs retrieve the data and analyze it, inputting and
outputting results from and to both files and a MySQL database. Each
program needs to be instantiated multiple times with different input.<br>
<br>
It appears that Kepler might be able to execute these computations with
its PN scheduler and ExternalExecution Actor, but 1) we typically
manage jobs on the cluster via the SGE (qsub) and 2) Kepler's
documentation says that "to use the ExternalExecution actor, the
invoked application must be on the local computer", which implies that
Kepler must be installed on all nodes of the cluster.<br>
<br>
How would one approach this problem with Kepler?<br>
<br>
If Kepler isn't the right tool for this problem, what would you
recommend?<br>
<br>
Thanks<br>
Arthur<br>
<br>
<br>
Arthur P. Goldberg, PhD<br>
<br>
Research Scientist in Bioinformatics Group<br>
Plant Systems Biology Laboratory<br>
<a moz-do-not-send="true" href="http://www.virtualplant.org" target="_blank"><a href="http://www.virtualplant.org">www.virtualplant.org</a></a><br>
<br>
Visiting Academic<br>
Computer Science Department<br>
Courant Institute of Mathematical Sciences<br>
<a moz-do-not-send="true" href="http://www.cs.nyu.edu/artg" target="_blank"><a href="http://www.cs.nyu.edu/artg">www.cs.nyu.edu/artg</a></a><br>
<br>
<a moz-do-not-send="true" href="mailto:artg@cs.nyu.edu" target="_blank"><a href="mailto:artg@cs.nyu.edu">artg@cs.nyu.edu</a></a><br>
New York University<br>
212 995-4918<br>
100 Washington Sq East<br>
8th Floor Silver Building
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