[Bioclusters] bio/life science cluster switch

Joe Landman bioclusters@bioinformatics.org
Fri, 06 Aug 2004 07:58:46 -0400

Hi Steve:

   The choice of switch fabric is largely determined by the application 
and use case mix.  For codes requiring low latency network fabric such 
as electronic structure codes, various molecular dynamics, and whatnot 
else, you would be looking at one of the low latency high bandwidth 
systems.  For more general applications, and trivial/embarrassingly 
parallel work, you could go with a higher latency fabric.

  Fabric topology is also important, though for this size, most folks 
aim towards fat trees or simple switch connected with no hierarchies.

   Since you will be going pure gigabit, I might recommend you look at 
some of the switches with better backplane bandwidth and latency 
characteristics.  The HP Procurve 4108gl are modular, and you can add 
the J4908A 20 port gigabit module (6 to cover your needs).  It wont be 
cheap, but it will work nicely.  The Foundry's are good choices as 
well.  I would avoid putting a Cisco in a cluster.

  One of the nicer aspects of the low latency gigabit connections is the 
ability to use TCP offload cards.  If you really need low latency 
interconnects over all or a portion of your system, the offload adapters 
may benefit some workloads.  As always, it is a cost-benefit analysis.

  (disclosure:  my company designs/integrates clusters like this, so my 
comments reflect our biases)


Steve wrote:

> I'm putting together a general lifescience based cluster (software 
> ranging from docking apps. to blast). Its going to consist of 
> approximately 100 nodes, including 2 head nodes. All nodes will be 
> connected through GIGE, and we will not be using high speed 
> interconnects.
> In the past I've used Cisco switches (4000 and 6000 series), stable, 
> reliable and costly.
> Does anyone have any recommendations? I've had mixed reviews about 
> Extreme, so I'd be interested in Foundy, Procurve or any systems 
> people may have had success with.
> Cheers,
> Steve

Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 612 4615