Il 04.08.2015 07:57 Hakeem Almabrazi ha scritto:
Hello everyone,

I was able to setup galaxy to work with our HPC cluster using the LSF
scheduler. So far so good except with few exceptions:

...

3. Finally, how do I control the resources (i.e cores for a job ) given
to a submitted job on Galaxy?

Hi Hakeem,
you need to specify new destinations in config/job_conf.xml, for example if you want to submit jobs asking for 4 cores on the same cluster node, use:

        <destination id="queue_name_4t" runner="drmaa">
<param id="nativeSpecification">-q queue_name -n 4 -R "span[hosts=1]"</param>
        </destination>

Then in the <tools> section of config/job_conf.xml add

        <tool id="tool_id" destination="queue_name_4t"/>

for each tool that should use 4 cores.

More info at:

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

Ciao,
Nicola


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