[Iplant-api-dev] Job Arrays via Agave or fAPI?

[Barthelson, Roger A - (rogerab)]

If it is an mpi version of Blast, it could use the same approach that we use for GeneSeqer. Input files in that case are split across separate jobs on half nodes to maximize efficiency of threading. At the end the separate job outputs are combined to a final output file. If that sounds like something that could work I could send a wrapper script that runs it all. I don't know if that is the same as a job array or not.

Roger

Sent from my iPhone

On Feb 27, 2014, at 4:55 PM, "Matthew Vaughn" <vaughn at tacc.utexas.edu<mailto:vaughn at tacc.utexas.edu>> wrote:

TACC doesn’t allow job arrays for performance reasons. However, take a peek at this repo:

https://github.com/mwvaughn/blast-2.2.26/tree/master/stampede

for how to use our Parametric Launcher. Also, ping Nirav as he’s working through the same problem right now.

Matt

On Feb 27, 2014, at 3:41 PM, Jennewein, Douglas M <Doug.Jennewein at usd.edu<mailto:Doug.Jennewein at usd.edu>> wrote:

I am attempting to create some embarrassingly parallel blast jobs.  One approach is to split the input file into several fasta files and run each in its own blast job task by creating a Job Array<http://slurm.schedmd.com/job_array.html>.

Is there a way to specify a Job Array through fAPI or Agave?

On a related note, is it possible to specify job dependencies?

Doug Jennewein
Research Computing Manager
Information Technology Services
The University of South Dakota

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