Hi Hakeem,
you have to _add_ a destination for each number of cores you need, and then specify this destination in the corresponding tools as I said in the previous email, i.e.:


<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"/>
        <destination id="lsf_4t" runner="drmaa">
<param id="nativeSpecification">-n 4 -R "span[hosts=1]"</param>
        </destination>
        <destination id="lsf_32t" runner="drmaa">
<param id="nativeSpecification">-n 32 -R "span[hosts=1]"</param>
        </destination>
    </destinations>
    <tools>
        <tool id="spades" destination="lsf_4t"/>
        <tool id="bwa" destination="lsf_32t"/>
    </tools>
</job_conf>

Cheers,
Nicola

Il 04.08.2015 14:12 Hakeem Almabrazi ha scritto:
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

FROM: Nicola Soranzo [mailto:nsora...@tiscali.it]
SENT: Tuesday, August 04, 2015 2:37 PM
TO: Hakeem Almabrazi
CC: galaxy-dev@lists.galaxyproject.org
SUBJECT: RE: [galaxy-dev] LSF cluster wierd behaviours!

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:nsora...@tiscali.it [1]]

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

To: Hakeem Almabrazi

Cc: galaxy-dev@lists.galaxyproject.org [2]Subject: 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 [3]

https://wiki.galaxyproject.org/Admin/Config/Jobs [4]

Ciao,

Nicola

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Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate,
le video chiamate e persino le chiamate di gruppo.
E chiami gratis anche i numeri fissi e mobili nel mondo!
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Links:
------
[1] mailto:nsora...@tiscali.it
[2] mailto:galaxy-dev@lists.galaxyproject.org
[3] https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
[4] https://wiki.galaxyproject.org/Admin/Config/Jobs
[5] https://www.indoona.com/
[6] https://www.indoona.com/



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