[BioC] Bioconductor on a Rocks cluster

[Patrick Durham]

Thanks Seth,

The more I thought about this the more I came to the same conclusions.
Basically we are trying to most efficiently utilize our hardware
resources for our R/Bioconductor users.  My current plan is to deploy
R/Bioconductor on multiple Citrix servers and do load balancing via the
Citrix software.  This will at least make sure that each new
R/Bioconductor user connection will be launched on the least busy
server.  Crude but it will probably server our needs (plus it will be
much easier than administering a cluster).

Thanks again.

Pat

-----Original Message-----
From: Seth Falcon [mailto:sfalcon at fhcrc.org] 
Sent: Friday, April 20, 2007 7:11 AM
To: Patrick Durham
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Bioconductor on a Rocks cluster

Hi Patrick,

"Patrick Durham" <patrickd at crab.org> writes:
> Hello,
>
> I'm trying to find information about running Bioconductor in a 
> clustered environment (specifically Rocks).  I've searched Google and 
> the mailing list and I haven't found much at all.  I am interested in 
> hearing from anyone who is successfully running Bioconductor on a 
> cluster.  My first question is whether or not it will actually run on 
> a cluster.  If so I'd would appreciate any links or documents you 
> could forward to me on a clustered implementation.

I'm not sure Bioconductor is enough of a coehesive whole ask a question
like "does Bioconductor run on a cluster"?

But in general, R and Bioconductor packages will run on a cluster --
meaning you should be able to launch an R process that makes use of
Bioconductor packages on a given cluster node.  How much this helps you
will depend on what you are trying to do.

There are a few packages that help you do parallel computations (a good
example is MLInterfaces, I believe).  But at present, most BioC packages
won't parallelize without some custom coding effort.

+ seth

--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research
Center http://bioconductor.org