[Bioclusters] SMP system for bioinformatics apps

David Adelson david.adelson at tamu.edu
Sun Sep 21 07:12:23 EDT 2008


I have an Altix310 (2x8 cores in one chassis, 2GB/core RAM) running  
Red Hat Enterprise 5.  I don't use Arb, but do use both versions of  
blast and RAxML (among other applications).  I don't think you can go  
wrong with any multicore box running RHE or Centos, just make sure you  
have enough RAM; if I was buying another server now, I would probably  
go with 4GB/core.  For big jobs I have access to a supercluster made  
up of Altix310 (544 cores total).



David Adelson

formerly Texas A&M University,
currently Adjunct Faculty, Dept. of Veterinary Integrative Biosciences.

currently Professor and Chair of Bioinformatics and Computational  
The University of Adelaide

On 2008/09/20, at 2:09 AM, Chuck Pepe-Ranney wrote:

> Hello Biocluster Community,
> My lab is interested in purchasing a SMP system to run various
> bioinformatics applications.  At the moment we heavily use Arb,
> NCBI-BLAST/WU-BLAST, and RAxML.  We also sparingly use ClustalW and
> MrBayes.  We will have access to a cluster at our institution in the  
> near
> future so we're not interested in purchasing a traditional cluster  
> of our
> own.  We're hoping that a multi-socket multi-core system in its  
> simplicity
> will be easier to maintain and administer than a cluster.  Obviously  
> we'd
> like to make sure that our hardware meshes as best as possible with  
> the
> structure of the programs we plan on using.  RAxML and Arb would be  
> our
> highest priorities at the moment.  BLASTing against large databases
> hopefully will be done on the institution's cluster using mpiBLAST.   
> We will
> be running NCBI-BLAST or WU-BLAST jobs on our system with smaller  
> databases,
> however.  We're hoping to to gain some insight by studying some  
> existing
> systems and are wondering if any members of the bioclusters group  
> had some
> relevant experience or expertise to share?
> At the moment we're invetigating CPUs.  A collaborator is heavily  
> endorsing
> the Intel Xeons but RAxML scales better on AMD Opterons.  Has Intel  
> come up
> with any recent innovation to compete with the Opteron memory  
> organization?
> Also, any help with subsequent steps involved would be appreciated.   
> We're
> considering building this system ourselves but would welcome advice  
> as to a
> particular vendor to contact if we decide to go with a pre-built  
> solution.
> Thanks,
> - Chuck
> -- 
> Chuck Pepe-Ranney
> Graduate Student
> Environmental Science and Engineering Division
> Colorado School of Mines
> Golden, CO 80401
> Email: cpepera at mines.edu
> office: (303)384-2218
> cell: (575)313-0993
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