[Bioclusters] SMP system for bioinformatics apps

steve slitster at rcn.com
Sat Sep 20 09:40:58 EDT 2008

This is certainly not meant to be an endorsement of any technology, but 
we have recently (within the last 6 months) had a number updates from 

The latest chip from Intel is supposed to surpass the AMD offering and 
I'm sure they'd be more than willing to give you an update as to why. We 
are actually waiting until early next year before upgrading our current 
clusters, so we can benchmark the latest offerings from both companies.

In addition we had an interesting demo from Dell yesterday on their 
scaleMP offering, I'd drop them a line and checkout the benchmarks they 
have for Blast on this system (sorry I can't distribute the benchmarks)

I'd also be very interested in hearing from anyone running 
bioinformatics  apps  on the Cell processor?



> 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
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