[kepler-users] Using Kepler on a Rocks cluster

[Arthur Goldberg]

Hello

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.

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.

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.

How would one approach this problem with Kepler?

If Kepler isn't the right tool for this problem, what would you recommend?

Thanks
Arthur


Arthur P. Goldberg, PhD

Research Scientist in Bioinformatics Group
Plant Systems Biology Laboratory
www.virtualplant.org <http://www.virtualplant.org>

Visiting Academic
Computer Science Department
Courant Institute of Mathematical Sciences
www.cs.nyu.edu/artg <http://www.cs.nyu.edu/artg>

artg at cs.nyu.edu <mailto:artg at cs.nyu.edu>
New York University
212 995-4918
100 Washington Sq East
8th Floor Silver Building
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