Hi there all, Has anyone had success setting up job_conf.xml for slurm based clusters? I am having trouble getting the GALAXY_SLOTS env var set for any jobs. I've tried looking at destinations in the job_conf.xml but can't get SLURM_NTASKS to be set correctly so the slurm run script can translate that into GALAXY_SLOTS.. Does anyone have a toy example of a job_conf.xml for slurm that they wouldn't mind sharing? Cheers, Simon. -- Simon Gladman | Bioinformatician Victorian Life Sciences Computation Initiative - LSCC 700 Swanston Street, The University of Melbourne | Victoria 3010 Australia T +61 3 9035 5822 | M 0418 421 077 Mail: simon.gladman@unimelb.edu.au Web: http://www.vlsci.org.au
Hi Simon, the Galaxy Docker Image is using Slurm you can look at it here: https://github.com/bgruening/docker-galaxy-stable Hope this helps, Bjoern Am 15.10.2015 um 06:38 schrieb Simon Gladman:
Hi there all,
Has anyone had success setting up job_conf.xml for slurm based clusters? I am having trouble getting the GALAXY_SLOTS env var set for any jobs. I've tried looking at destinations in the job_conf.xml but can't get SLURM_NTASKS to be set correctly so the slurm run script can translate that into GALAXY_SLOTS..
Does anyone have a toy example of a job_conf.xml for slurm that they wouldn't mind sharing?
Cheers,
Simon.
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Hi Simon, we use slurm via drmaa. Find configurations here: https://github.com/mpg-age-bioinformatics/galaxy-admin/tree/master/server/co... https://github.com/mpg-age-bioinformatics/galaxy-admin/tree/master/system Best, Sven
On 15 Oct 2015, at 08:38, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Simon,
the Galaxy Docker Image is using Slurm you can look at it here:
https://github.com/bgruening/docker-galaxy-stable
Hope this helps, Bjoern
Am 15.10.2015 um 06:38 schrieb Simon Gladman:
Hi there all,
Has anyone had success setting up job_conf.xml for slurm based clusters? I am having trouble getting the GALAXY_SLOTS env var set for any jobs. I've tried looking at destinations in the job_conf.xml but can't get SLURM_NTASKS to be set correctly so the slurm run script can translate that into GALAXY_SLOTS..
Does anyone have a toy example of a job_conf.xml for slurm that they wouldn't mind sharing?
Cheers,
Simon.
___________________________________________________________ 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/mailinglists/
___________________________________________________________ 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 (3)
-
Björn Grüning -
Simon Gladman -
Sven E Templer