Galaxy Slurm job_conf.xml

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Galaxy Slurm job_conf.xml

Simon Gladman-2
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 


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Re: Galaxy Slurm job_conf.xml

Björn Grüning-3
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/
>
___________________________________________________________
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Re: Galaxy Slurm job_conf.xml

Sven E. Templer
Hi Simon,

we use slurm via drmaa. Find configurations here:

https://github.com/mpg-age-bioinformatics/galaxy-admin/tree/master/server/config
https://github.com/mpg-age-bioinformatics/galaxy-admin/tree/master/system

Best,
Sven

> On 15 Oct 2015, at 08:38, Björn Grüning <[hidden email]> 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/
>
> 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:
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