Hi Matthias, I can't speak for GridEngine's specific behavior because I haven't used it in a long time, but it's not surprising that jobs "disappear" as soon as they've exited. Unfortunately, Galaxy uses periodic polling rather than waiting on completion. We'd need to create a thread-per-submitted job unless you can still get job exit details by looping over jobs with a timeout wait.
You can gain some control over how Galaxy handles InvalidJobException exceptions with drmaa job runner plugin params, see here: https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L9 However, if normally finished jobs also result in InvalidJobException, that probably won't help. Alternatively, you could create a DRMAAJobRunner subclass for GridEngine like we've done for Slurm that does some digging to learn more about terminal jobs. --nate On Thu, Jun 15, 2017 at 10:27 AM, Matthias Bernt <m.be...@ufz.de> wrote: > Dear list, > > I have two question for all DRMAA users. Here is the first one. > > I was checking how our queuing system (univa GridEngine) and Galaxy react > if jobs are submitted that exceed run time or memory limits. > > I found out that the python drmaa library cannot query the job status > after the job is finished (for both successful and unsuccessful jobs). > > In lib/galaxy/jobs/runners/drmaa.py the call gives an exception > self.ds.job_status( external_job_id ) > > Is this always the case? Or might this be a problem with our GridEngine? > > I have attached some code for testing. Here the first call to > s.jobStatus(jobid) works, but the second after s.wait(...) doesn't. > But I get "drmaa.errors.InvalidJobException: code 18: The job specified > by the 'jobid' does not exist." > > The same error pops up in the Galaxy logs. The consequence is that jobs > that reached the limits are shown as completed successfully in Galaxy. > > Interestingly, quite a bit of information can be obtained from the return > value of s.wait. I was wondering if this can be used to differentiate > successful from failed jobs. In particular hasExited, hasSignal, and > terminateSignal are different in the two cases. > > Cheers, > Matthias > > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ >
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