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:[email protected]]
SENT: Tuesday, August 04, 2015 2:37 PM
TO: Hakeem Almabrazi
CC: [email protected]
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:[email protected] [1]]
Sent: Tuesday, August 04, 2015 2:23 PM
To: Hakeem Almabrazi
Cc: [email protected] [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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[6] https://www.indoona.com/
Connetti gratis il mondo con la nuova indoona: hai la chat, le
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