Many thanks to all of you!!

Definitely Nate's approach is a better choice. We are running Slurm 14.03, but Nate's manual is exhaustive enough to recompile even the existing version. (I don't know how we can do this on a running cluster though :) I will most probably go for this solution.

There is a sentence in Nate's answer  I don't really understand :

"... using `--clusters` means you have to have your controllers integrated using slurmdbd, ..."

what do you mean by this, Nate?

Carie, I don't actually get how you implemented the hack : did you reduplicate the

class DRMAAJobRunner

under a different name in drmaa.py? And where do you define every next cluster (controller machines)?

Can you give me some more detalis?

Thank you

Nikolay

===============
Nikolay Vazov, PhD
Department for Research Computing, University of Oslo

---

From: Nate Coraor <nate@bx.psu.edu>
Sent: 01 February 2016 17:28
To: Ganote, Carrie L
Cc: John Chilton; Nikolay Aleksandrov Vazov; dannon.baker@gmail.com; galaxy-dev@lists.galaxyproject.org

Subject: Re: Galaxy sending jobs to multiple clusters

 

Hi Nikolay,

It's worth noting that using `--clusters` means you have to have your controllers integrated using slurmdbd, and they must share munge keys. You can set up separate destinations as in Carrie's example without having to "integrate" your controllers at the slurm level. The downside of this approach is that you can't have slurm automatically "balance" across clusters, although Slurm's algorithm for doing this with `--clusters` is fairly primitive. If you don't use `--clusters` you can attempt to do the balancing with a dynamic job destination.

If you're not using slurmdbd, you may still need to share the same munge key across clusters to allow the slurm client lib on the Galaxy server to talk to both clusters. There could be ways around this if it's a problem, though.

--nate

On Mon, Feb 1, 2016 at 11:10 AM, Ganote, Carrie L <cganote@iu.edu> wrote:

Hi Nikolay,

The slurm branch that John mentioned sounds great! That might be your best bet.

I didn't get drmaa to run with multiple clusters with flags, but I did 'assign' different job handlers to different destinations in the drmaa.py runner in Galaxy - but that is a bit of a hacky way to do it.

-Carrie

From: John Chilton <jmchilton@gmail.com>
Date: Monday, February 1, 2016 at 11:02 AM
To: Nikolay Aleksandrov Vazov <n.a.vazov@usit.uio.no>
Cc: "dannon.baker@gmail.com" <dannon.baker@gmail.com>, "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org>, Carrie Ganote <cganote@iu.edu>, Nate Coraor <nate@bx.psu.edu>
Subject: Re: Galaxy sending jobs to multiple clusters

Nate has a branch of slurm drmaa that allows specifying a --clusters

argument in the native specification this can be used to target

multiple hosts.

More information can be found here:

https://github.com/natefoo/slurm-drmaa

Here is how Nate uses it to configure usegalaxy.org:

https://github.com/galaxyproject/usegalaxy-playbook/blob/master/templates/galaxy/usegalaxy.org/config/job_conf.xml.j2

I guess instead of installing slurm-drmaa for a package manager or the

default source - you will just need to install Nate's version.

-John

On Wed, Jan 20, 2016 at 1:18 PM, Nikolay Aleksandrov Vazov

<n.a.vazov@usit.uio.no> wrote:

Hi, John, Dan, Carrie and all others,

I am considering a task of setting up a Galaxy instance which shall send

jobs to more than on cluster at a time. In my case I am using drmaa-python

and I was wondering if it was possible to configure multiple drmaa runners

each "pointing" at a different (slurm) control host, e.g.

local

drmaa1

drmaa2

Thanks a lot for your advice

Nikolay

===============

Nikolay Vazov, PhD

Department for Research Computing, University of Oslo