[Bioclusters] mrbayes + lam-mpi/mpich + grid engine integration

Nick Brockner bioclusters@bioinformatics.org
Thu, 23 Sep 2004 08:32:45 -0400

Hi Tony,

We are using the Bioteam iNquiry product for our web-based access.  So 
far, so good.  What type of COTS cluster have you built (number of 
nodes, OS, hardware)?  We are running an 8 node Apple Xserve G5 cluster 
with Gig ethernet.

I am in the process of implementing mrbayes on our cluster.  I have not 
gotten into the parallel implementation of mrbayes yet, but may do so 
in the near future.  If you want to access my nexus files, let me know 
and I will send you the access info directly.  You may have to tweak 
the files a little bit for mrbayes, as I have seen some issues with 
these particular nexus files (which were originally made to be used by 
PAUP).  You may have to add some information about the dimensions 
before mybayes will happily read them.

Nick Brockner
Systems Administrator, Biology Computing Facility
Hamilton College

On Sep 22, 2004, at 6:54 AM, Tony Travis wrote:

> Nick Brockner wrote:
>> Hi There Chris,
>> I have been testing the limits of clustalw_mpi, and making sure the 
>> nexus data was good (for paup), so I have a few nexus files that are 
>> BIG (from 10-30 MB).  Let me know if you want some of these.
> Hello, Nick.
> I'm interested in what you are doing with your bioinformatics portal 
> for a number of reasons. First of all, I've built a COTS cluster here 
> for bioinformatics and I want to provide web-based access. I'd be 
> interested in any general advice you have about setting this up?
> Second, I've been benchmarking MrBayes on our cluster and I'm 
> interested in clustalw_mpi. I found that MrBayes was optimal with only 
> 4-8 nodes on a 100Base-T network fabric. I would be interested to run 
> your nexus files here, and compare them with the performance of your 
> G5 cluster.
> 	Tony.
> -- 
> Dr. A.J.Travis,                     |  mailto:ajt@rri.sari.ac.uk
> Rowett Research Institute,          |    http://www.rri.sari.ac.uk/~ajt
> Greenburn Road, Bucksburn,          |   phone:+44 (0)1224 712751
> Aberdeen AB21 9SB, Scotland, UK.    |     fax:+44 (0)1224 716687
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