Question: troubleshooting Galaxy with LSF
0
gravatar for ink
4.3 years ago by
ink0
United Kingdom
ink0 wrote:

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.

https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#DRMAA

It has to be runner="sge" rather than runner="drmaa"

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:

<?xml version="1.0"?>
<job_conf>
    <plugins>
        <plugin id="lsf" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
            <param id="drmaa_library_path">/opt/gridware/lsf/9.1/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so</param>
        </plugin>
    </plugins>
    <handlers>
        <handler id="main"/>
    </handlers>
    <destinations default="lsf_default">
        <destination id="lsf_default" runner="lsf">
            <param id="nativeSpecification">-W 24:00</param>
        </destination>
    </destinations>
</job_conf>

Any hints would be much appreciated. Thank you

 

admin jobs lsf • 1.8k views
ADD COMMENTlink modified 4.3 years ago by Jennifer Hillman Jackson25k • written 4.3 years ago by ink0
1
gravatar for Jennifer Hillman Jackson
4.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

We just added more documentation for this functionality and it was included in the recent News Brief. Perhaps the sample configuration file or other items will be of help?

New docs are under the section "Jobs" here:

http://wiki.galaxyproject.org/DevNewsBriefs/2014_06_02#Core

And be sure you are running the latest build for best results and following these instructions:

http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
http://wiki.galaxyproject.org/Admin/Config/Jobs

Posting to the galaxy-dev@bx.psu.edu mailing list will provide better exposure to the development community, if you continue to have problems. I didn't find a post there already, but may have missed it.

Best, Jen, Galaxy team

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Jennifer Hillman Jackson25k
1

I just wanted to chime in that I agree with Jen - the galaxy-dev list might be a better place to get advice on this for now. I have never used LSF myself - so I don't know if there are any tricks to get these interactions right but I know other people have gotten it to work and I know some of these people read galaxy-dev.

Also - I have fixed the confusing and incorrect example on the wiki you pointed out, thanks for reporting the problem! 

ADD REPLYlink written 4.3 years ago by jmchilton1.1k
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