Matthias, We have had this problem on our SGE based installation for years. We referred to it as the "green screen of death" - as it would allow a biologist to continue analysis using output that was partial, at best, often resulting in seemingly successful completion of the entire analysis, but completely bogus results (say, cuffdiff killed half way through the genome, but it's green in galaxy, so no transcripts on the smaller chromosomes, but no error, either).
We ended up implementing an external reaper that detected these killed jobs from SGE, and notified the user and galaxy post-hoc. It was not a very satisfactory solution. We are currently moving to SLURM for other reasons and hope the problem will not be present there. Regards, Curtis -----Original Message----- From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf Of Matthias Bernt Sent: Thursday, June 15, 2017 9:27 AM To: email@example.com Subject: [galaxy-dev] drmaa job status 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/