Thank you Nicola,
I will play with
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: 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 [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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