Hello, 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. First of all, I should point out at the error on the wiki which is rather confusing when you follow the steps and they do not work.
It has to be
runner="sge" rather than
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 browser and download a file, a job gets submitted and run and everything seems fine.
The second setup does not work. 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 is identical in both cases:
<plugin id="lsf" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
<destination id="lsf_default" runner="lsf">
<param id="nativeSpecification">-W 24:00</param>
Any hints would be much appreciated. Thank you