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?

Iyad Kandalaft

Iyad Kandalaft
Microbial Biodiversity Bioinformatics
Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
960 Carling Ave.| 960 Ave. Carling
Ottawa, ON| Ottawa (ON) K1A 0C6
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[] 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 
a go.

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>.
./ line 79: 99087 Segmentation fault      python ./scripts/ 
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 ./ as a user.

The job configuration job_conf.xml is identical in both cases:

<?xml version="1.0"?>
        <plugin id="lsf" type="runner" 
        <handler id="main"/>
    <destinations default="lsf_default">
        <destination id="lsf_default" runner="lsf">
            <param id="nativeSpecification">-W 24:00</param>
</job_conf> 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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