[Bioclusters] SMP system for bioinformatics apps

Chuck Pepe-Ranney cpepera at mines.edu
Fri Sep 19 12:39:16 EDT 2008

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.


- 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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