[Bio-Linux] Biolinux8 - Best job scheduler for small cluster?

[James Mategko]

Hi Xavier,

 If you are running metagenomics with Qiime version 1.9 adds a new script
called "start parallel jobs with slurm". I'm not familiar with its inner
workings since I'm still using the default Qiime 1.8 in Bio-linux 8, but it
looks promising.

http://qiime.org/scripts/start_parallel_jobs_slurm.html

Best Regards,
- James

On Thu, Feb 5, 2015 at 3:18 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi Xavi,
>
> To be honest I don't really know.  Hopefully someone on the list will
> have some practical experience to share.  We use Torqe on a cluster here
> at CEH but it's not actually running Bio-Linux and I had no part in
> setting it up so I don't know how easy it is to configure.
>
> I have experience with Condor and I don't think it is what you need at
> all.  SGE used to be good but Oracle have not looked after it well.
>
> My guess would be that Slurm is the best answer for you.  The latest
> version of QIIME recommends it, which is a good sign, and I'm told that
> set-up for a small cluster is "very simple".  You might well have issues
> with running a cluster of Bio-Linux 7 and 8 machines, though, because
> the packaged versions of Slurm and of the bioinformatics software will
> be different on the different nodes.  I'd strongly recommend  upgrading
> everything to the same version.
>
> Also, you really should set up a fast shared NFS drive that all the
> machines can see.  Running a cluster without a shared filesystem is
> possible but for most bioinformatics tasks it's highly impractical.
>
> Cheers,
>
> TIM
>
>
>
>
> On Thu, 2015-02-05 at 07:16 +0000, Xavier Martínez Serrano wrote:
> > Hi,
> >
> > We have 4 computers with ~20CPU each in a hospital research group  and
> > we would like to set a cluster with them. Which is the best suitable
> > job scheduler for us if we are running Biolinux7 in three of them and
> > Biolinux8 in the other?
> >
> > We have been looking at common job schedulers like: Slurm, SGE,
> > Condor, Torque, ... but we wonder which best suits for our small
> > resources, to make it as easy as possible.
> >
> > What can you recommend us?
> >
> > Many thanks in advance,
> > Xavi
> >
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://environmentalomics.org/bio-linux
> +44 1491 69 2297
>
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