slurm drmaaa

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slurm drmaaa

Jillian Rowe
Hello all,

I would like to get galaxy to submit jobs to slurm using the drmaa.
Galaxy exists on its own machine, and slurm is run on a cluster.

I am at a bit of a lose as to how to do this. I have galaxy installed
and working fine, and slurm works fine on its own. I saw a blog post
detailing how to get the two connected, but it seems like maybe it was
outdated.

Any tips?

Best,
Jillian
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Re: slurm drmaaa

Brian Claywell
Jillian,

We've connected our Galaxy instance to a slurm cluster via slurm-drmaa
[1], and use the DRMAAJobRunner plugin configured according to the
Galaxy admin wiki [2]. It works pretty well, but it should be noted
that the nativeSpecification options slurm-drmaa makes available to
you (that is, options like those you'd pass to sbatch) are *not*
complete. For example, one of our IT guys just patched slurm-drmaa to
add support for the --cpus-per-task option, which wasn't present in
slurm-drmaa 1.0.7.

[1] http://apps.man.poznan.pl/trac/slurm-drmaa
[2] https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#DRMAA


On Mon, Mar 10, 2014 at 5:33 AM, Jillian Rowe
<[hidden email]> wrote:

> Hello all,
>
> I would like to get galaxy to submit jobs to slurm using the drmaa. Galaxy
> exists on its own machine, and slurm is run on a cluster.
>
> I am at a bit of a lose as to how to do this. I have galaxy installed and
> working fine, and slurm works fine on its own. I saw a blog post detailing
> how to get the two connected, but it seems like maybe it was outdated.
>
> Any tips?
>
> Best,
> Jillian
> ___________________________________________________________
> 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:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/



--
Brian Claywell, Systems Analyst/Programmer
Fred Hutchinson Cancer Research Center
[hidden email]
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