So I was able to simulate a torque environment with https://github.com/aiidateam/torquessh_base-docker and that seemed to have worked fine.
I did have to install the torque headers, activate galaxy's virtualenv and install https://github.com/ehiggs/pbs-python. You should be seeing something like: ``` galaxy.jobs.runners.pbs DEBUG 2018-06-14 09:23:31,549 [p:1944,w:1,m:0] [PBSRunner.work_thread-2] (2) submitting file /home/app/galaxy/database/pbs/2.sh galaxy.jobs.runners.pbs DEBUG 2018-06-14 09:23:31,551 [p:1944,w:1,m:0] [PBSRunner.work_thread-2] (2) queued in default queue as 3.605046c8289c galaxy.jobs DEBUG 2018-06-14 09:23:31,552 [p:1944,w:1,m:0] [PBSRunner.work_thread-2] (2) Persisting job destination (destination id: local) galaxy.jobs.runners.pbs DEBUG 2018-06-14 09:23:31,855 [p:1944,w:1,m:0] [Dummy-5] (2/3.605046c8289c) PBS job state changed from N to R galaxy.jobs.runners.pbs DEBUG 2018-06-14 09:23:33,994 [p:1944,w:1,m:0] [Dummy-5] (2/3.605046c8289c) PBS job has left queue galaxy.model.metadata DEBUG 2018-06-14 09:23:34,110 [p:1944,w:1,m:0] [PBSRunner.work_thread-3] loading metadata from file for: HistoryDatasetAssociation 2 galaxy.jobs INFO 2018-06-14 09:23:34,218 [p:1944,w:1,m:0] [PBSRunner.work_thread-3] Collecting metrics for Job 2 galaxy.jobs DEBUG 2018-06-14 09:23:34,234 [p:1944,w:1,m:0] [PBSRunner.work_thread-3] job 2 ended (finish() executed in (189.200 ms)) ``` in your logs. Let me know how this goes. Best, Marius On 14 June 2018 at 10:15, Marius van den Beek <[email protected]> wrote: > Hi Sheldon, > > I'm not sure what the issue could be, the PBS runner hasn't been updated > in ~3 years, > but of course many things around it have been. > Could you set galaxy's logging level to debug if it isn't already and > check the logs ? > (https://github.com/galaxyproject/galaxy/blob/release_18.05/config/galaxy. > yml.sample#L895) > When you are submitting a job in galaxy what messages are you seeing in > the logs ? > > Best, > Marius > > On 13 June 2018 at 22:07, Briand, Sheldon (NRC/CNRC) < > [email protected]> wrote: > >> Hi Marius, >> >> >> >> The PBS runner and the user is the galaxy user. I do not use the run as >> real user option. I haven’t been using drmaa_external_runjob_script. >> This setup worked for my old 17.05 and previous versions of galaxy. >> >> >> >> Thanks, >> >> -Sheldon >> >> >> >> *From:* Marius van den Beek [mailto:[email protected]] >> *Sent:* Wednesday, June 13, 2018 4:58 PM >> *To:* Briand, Sheldon (NRC/CNRC) <[email protected]> >> *Cc:* [email protected] >> *Subject:* Re: [galaxy-dev] pbs/torque jobs >> >> >> >> Hi Sheldon, >> >> >> >> is there anything particular about your job configuration, e.g. >> >> are you you using the run as real user option or are you using >> >> the drmaa_external_runjob_script option ? >> >> Are you using the drmaa or the PBS runner ? >> >> >> >> Best, >> >> Marius >> >> >> >> On 13 June 2018 at 21:13, Briand, Sheldon (NRC/CNRC) < >> [email protected]> wrote: >> >> Hi, >> >> >> >> I have upgraded to Galaxy 18.05 (from 17.05). I am running a torque job >> scheduler (version 6.02). >> >> >> >> When I submit a job through galaxy and I look in the admin/manage jobs >> section I see that the job has been submitted successfully. It shows that >> the job is queued and waiting to run. On the cluster I see that the job >> runs and goes to completion. However, the status in galaxy continue to >> show that the job is waiting to run and the status never gets updated. I’m >> using postgres as my database and I am running through a nginx proxy. >> >> >> >> I see no errors in my galaxy.log file. >> >> >> >> I switched from galaxy.ini to galaxy.yml and from paste to uwsgi. Is >> this a configuration problem on my end? Where should I be looking? >> >> >> >> Thanks, >> >> -Sheldon >> >> >> >> Sheldon Briand >> >> Computer Systems and Applications Analyst >> >> National Research Council/Government of Canada >> >> [email protected]/ Tel: (902) 426-1677 >> >> >> >> >> ___________________________________________________________ >> 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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