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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