[Bioclusters] SMP system for bioinformatics apps

John Van Workum john at tticluster.com
Sat Sep 20 10:25:16 EDT 2008

The new Harpertown Xeons, when used in conjunction with the 5300 or
5400 chipset, vs. new Opterons are showing better overall performance
comparing to earlier generation Xeon vs. Opteron. Our file storage
server vendor went from using Opterons to using the Harpertown Xeon
because of cost and performance. If you build yourself, I recommend
Supermicro motherboards. We have a number of Supermicro dual socket,
quad core Xeon machines available if you wish to run some benchmarks.
Email me offline. If you are looking for a vendor, Scalable
Informatics is a good place to start.


John Van Workum
Tsunamic Technologies Inc.
john at tticluster.com

On Fri, Sep 19, 2008 at 12:39 PM, Chuck Pepe-Ranney <cpepera at mines.edu> 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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