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.


From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Shantanu Pavgi [pavgi@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.

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