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

[Tim Booth]

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
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