Nicola,
I have added your suggestion and seems to work ☺. 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<mailto:nsora...@tiscali.it>]
Sent: Tuesday, August 04, 2015 2:23 PM
To: Hakeem Almabrazi
Cc:
galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>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
https://wiki.galaxyproject.org/Admin/Config/Jobs
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!
Scarica subito l’app Vai su https://www.indoona.com/
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solely for the use of the individual to whom it is addressed. If you are not
the intended recipient, any reading, printing, storage, disclosure, copying or
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