Nicola,

 

I have added your suggestion and seems to work J.  Is there a way to control these parameters based on a tool?  For example, lets say I want to require more cores for certain tools such as bwa.  How can I do that?

 

Here is my job_conf.xml.  Please let me know if you have better suggestion to it. 

 

<job_conf>

    <plugins>

        <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>

    </plugins>

    <handlers default="handlers">

        <!--handler id="main" /-->

        <handler id="handler0" tags="handlers"/>

        <!--handler id="handler1" tags="handlers"/-->

    </handlers>

    <destinations default="lsf">

        <!--destination id="lsf" runner="drmaa"/-->

        <!-- suggested by Nicola-->

        <destination id="lsf" runner="drmaa">

             <param id="nativeSpecification">-n 32 -R "span[hosts=1]"</param>

        </destination>

    </destinations>

</job_conf>

 

Regards,

Hak

 

 

 

Yes, I'm using LSF with Galaxy at TGAC.

Unfortunately I don't have suggestions for your other problems.

Ciao,
Nicola

Il 04.08.2015 13:27 Hakeem Almabrazi ha scritto:

Thank you Nicola,

I will play with these options and see how it works.

Have you played with LSF and Galaxy setup?

Thank you,

-----Original Message-----

From: Nicola Soranzo [mailto:nsoranzo@tiscali.it]

Sent: Tuesday, August 04, 2015 2:23 PM

To: Hakeem Almabrazi

Cc: galaxy-dev@lists.galaxyproject.orgSubject: Re: [galaxy-dev] LSF cluster wierd behaviours!

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:-q queue_name -n 4 -R "span[hosts=1]"

Then in the  section of config/job_conf.xml add

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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