[kepler-users] Using Kepler on a Rocks cluster

[Jianwu Wang]

Hi Arthur,

    Kepler has Job related actors which could submit jobs to SGE, PBS, 
and other job scheduler. You can have a look at this workflow 
https://code.kepler-project.org/code/kepler/trunk/workflows/SC06-Tutorial/JobSubmission.xml, 
which submit jobs to SGE, and wait until the job is finished. This 
workflow can be easily extended to submit a job sequence.

Best wishes

Sincerely yours

Jianwu Wang
jianwu at sdsc.edu
http://users.sdsc.edu/~jianwu/

Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center 
University of California, San Diego
San Diego, CA, U.S.A. 



Arthur Goldberg wrote:
> 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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