launching openmpi tool with Galaxy

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launching openmpi tool with Galaxy

Olivia Doppelt
Dear developers,

I'm trying to launch a mpi version of test tool.

To do so, I have a test xml called sleep.xml but all he does is write
the hostname of the machine in an output file.

(command:  /usr/lib64/openmpi/bin/mpirun  hostname > $output)

When I launch this tool as a local job (we use son of grid engine as the
job scheduler), everything is ok.

When i specify the following line in the universe_wsgi.xml:

sleep = drmaa://-q galaxy -pe openmpi 8/

The program is launched but it is lost somewhere and juste doesn't do
anything. It is just running and never ends.

Does someone has an explanation for that ?

Thanks in advance,

Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur

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