This is just a guess, which may help you troubleshoot.
It could be a that python is reaching a stack limit: run ulimit -s and set it
to a higher value if required
I’m completely guessing here but is it possible that the DRMAA is missing a
linked library on the redhat system – check with ldd?
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[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of I Kozin
Sent: Tuesday, June 10, 2014 12:42 PM
Subject: [galaxy-dev] troubleshooting Galaxy with LSF
This is largely a repost from the biostar forum following the suggestion there
to post here.
I'm doing my first steps in setting up a Galaxy server with an LSF job
scheduler. Recently LSF started supporting DRMAA again so I decided to give it
I have two setups. The one that works is a stand along server (OpenSuse 12.1,
python 2.7.2, LSF 9.1.2). By "works" I mean that when I login into Galaxy using
a browser and upload a file, a job gets submitted and run and everything seems
The second setup does not work (RH 6.4, python 2.6.6, LSF 9.1.2). It's a server
running Galaxy which is meant to submit jobs to an LSF cluster. When I
similarly pick and download a file I get
Job <72266> is submitted to queue <short>.
./run.sh: line 79: 99087 Segmentation fault python ./scripts/paster.py
serve universe_wsgi.ini $@
For the moment, I'm not bothered with the full server setup, I'm just testing
whether Galaxy works with LSF and therefore run ./run.sh as a user.
The job configuration job_conf.xml is identical in both cases:
<plugin id="lsf" type="runner"
<destination id="lsf_default" runner="lsf">
<param id="nativeSpecification">-W 24:00</param>
run.sh is only changed to allow remote access.
Most recently I tried replacing python with 2.7.5 to no avail. Still the same
kind of error. I also updated Galaxy.
Any hints would be much appreciated. Thank you
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