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Hi Arthur,<br>
<br>
Kepler has Job related actors which could submit jobs to SGE, PBS,
and other job scheduler. You can have a look at this workflow
<a class="moz-txt-link-freetext" href="https://code.kepler-project.org/code/kepler/trunk/workflows/SC06-Tutorial/JobSubmission.xml">https://code.kepler-project.org/code/kepler/trunk/workflows/SC06-Tutorial/JobSubmission.xml</a>,
which submit jobs to SGE, and wait until the job is finished. This
workflow can be easily extended to submit a job sequence. <br>
<pre class="moz-signature" cols="72">Best wishes
Sincerely yours
Jianwu Wang
<a class="moz-txt-link-abbreviated" href="mailto:jianwu@sdsc.edu">jianwu@sdsc.edu</a>
<a class="moz-txt-link-freetext" href="http://users.sdsc.edu/~jianwu/">http://users.sdsc.edu/~jianwu/</a>
Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center
University of California, San Diego
San Diego, CA, U.S.A. </pre>
<br>
<br>
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">www.virtualplant.org</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">www.cs.nyu.edu/artg</a><br>
<br>
<a moz-do-not-send="true" href="mailto:artg@cs.nyu.edu"
target="_blank">artg@cs.nyu.edu</a><br>
New York University<br>
212 995-4918<br>
100 Washington Sq East<br>
8th Floor Silver Building
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</blockquote>
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