[Bioclusters] SMP system for bioinformatics apps
David Adelson
david.adelson at tamu.edu
Sun Sep 21 07:12:23 EDT 2008
Chuck,
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).
Cheers,
Dave
David Adelson
formerly Texas A&M University,
currently Adjunct Faculty, Dept. of Veterinary Integrative Biosciences.
currently Professor and Chair of Bioinformatics and Computational
Genetics
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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