On Jul 29, 2011, at 4:13 PM, Ka Ming Nip wrote:
Hi Shantanu,
I am also using a SGE cluster and the DRMAA runner for my Galaxy install. I am
also having the same issue for jobs that were killed.
How did you define the run-time or memory/runtime configurations in your DRMAA
URLs?
I had to add "-w n" in the DRMAA URLs in order for my jobs to be dispatched to
the cluster. However, someone said (on another thread) that doing so might hide
the errors. I am not sure if this is the cause since my jobs won't be
dispatched at all if "-w n" was not in the DRMAA URLs.
Ka Ming
The drmaa/SGE URL in our configuration looks something like this:
{{{
drmaa:// -V -m be -M <email.address.for.notification> -l
vf=<memory>,h_rt=<hard-run-time>,s_rt=<soft-run-time>,h_vmem=<memory> /
}}}
We don't use "-w n" option in our configuration. The "-w n" will turn off
validation of your job script. Refer to qsub manual for details. The -l
options (complex configuration options) can be found here:
http://linux.die.net/man/5/sge_complex .
Hope this helps you.
--
Shantanu.
________________________________________
From:
galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu>
[galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Shantanu Pavgi
[pa...@uab.edu]
Sent: July 29, 2011 1:56 PM
To: galaxydev psu
Subject: [galaxy-dev] job status when SGE kills/aborts job
We are using SGE cluster with our galaxy install. We have specified resource
and run-time limits for certain tools using tool specific drmaa URL
configuration, e.g.:
- run-time (h_rt, s_rt)
- memory (vf, h_vmem).
This helps scheduler in submitting jobs to an appropriate node and also prevent
node from crashing because of excessive memory consumption. However, sometimes
a job needs more resources and/or run-time than specified in the drmaa URL
configuration. In such cases SGE kills particular job and we get email
notification with appropriate job summary. However, the galaxy web interface
doesn't show any error for such failures. The job table doesn't contain any
related state/info as well. The jobs are shown in green-boxes meaning they
completed without any failure. In reality these jobs have been killed/aborted
by the scheduler. This is really confusing as there is inconsistency between
job status indicated by the galaxy and SGE/drmaa. Has anyone else experienced
and/or addressed this issue? Any comments or suggestions will be really helpful.
Thanks,
Shantanu.
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