Re: SMP system for bioinformatics apps

Chuck Pepe-Ranney wrote:
> Hello Biocluster Community,

[...]

> 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?

The forthcoming Nehalem CPU uses on-board memory controllers and NUMA 
designs similar to Opteron.  It should be available Feb/March time frame 
for purchase.  Assuming Arb and RAxML require higher non-blocking memory 
access, current Opteron or future Nehalem will likely be good choices.

This said, some of the units we have built based upon Harpertown (Xeon 
54xx) have been quite fast with BLAST and other codes.  Not as good with 
HMMer.

> 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.

Nehalems will be out soon, if you can wait, you may be able to get this. 
      If you bug your favorite vendor, they may have a unit they can 
provide some access to.

Joe

> 
> Thanks,
> 
> - Chuck
> 


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Joseph Landman, Ph.D
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