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_...
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.bernt@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
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