Dear list, I have implemented a new DRMAA job runner allows to detect runtime and memory violations. This is done by using the drmaa library functions job_info + wait or as fallback the commandline tools qstat + qacct. This has the additional advantage that the runner works also in setups using the external runner scripts to start jobs as real user (the original DRMAAJobRunner can not query these jobs at all). You may have a look here: https://github.com/galaxyproject/galaxy/pull/4275 I have successfully tested the but settings: galaxy user/real user submits the jobs. Also the resubmission in case of memory and time violations seems to work. Would be great to get some comments. One problem that I encountered is that upload jobs do not work in the real user setting (for the original and the new runner): The permissions of the uploaded file in /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/ are not changed. Any idea what needs to be changed to get this running? Best, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------
Code looks interesting. This is for Univa Grid Engine? In terms of the upload jobs, are those not designed to be run as 'local' jobs and not with the 'real user' setting? On Fri, 7 Jul 2017 at 17:32 Matthias Bernt <m.bernt@ufz.de> wrote:
Dear list,
I have implemented a new DRMAA job runner allows to detect runtime and memory violations. This is done by using the drmaa library functions job_info + wait or as fallback the commandline tools qstat + qacct. This has the additional advantage that the runner works also in setups using the external runner scripts to start jobs as real user (the original DRMAAJobRunner can not query these jobs at all).
You may have a look here:
https://github.com/galaxyproject/galaxy/pull/4275
I have successfully tested the but settings: galaxy user/real user submits the jobs. Also the resubmission in case of memory and time violations seems to work.
Would be great to get some comments.
One problem that I encountered is that upload jobs do not work in the real user setting (for the original and the new runner): The permissions of the uploaded file in /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/ are not changed. Any idea what needs to be changed to get this running?
Best, Matthias
--
------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296 <+49%20341%20235482296>, m.bernt@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann ------------------------------------------- ___________________________________________________________ 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/
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participants (2)
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Matthias Bernt -
Peter van Heusden