With Regards, ---------------- Ambarish Biswas, University of Otago Department of Biochemistry, Dunedin, New Zealand, Tel: +64(22)0855647 Fax: +64(0)3 479 7866
Hi have u tested the option *drmaa://-q galaxy -V/ *option yet? Here as it suggests, -q galaxy creats a queue name with galaxy, not sure what V stands for, but could be verbose On Sat, Jul 30, 2011 at 9:13 AM, Ka Ming Nip <km...@bcgsc.ca> 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 > ________________________________________ > From: 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. > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ >
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
