[Bioclusters] FPGA in bioinformatics clusters (again?)

Joe Landman landman at scalableinformatics.com
Sat Feb 11 08:42:24 EST 2006

Acceleration systems make sense in specific situations.  They are rarely 
general purpose.  Most FPGA implementations are non-trivial to program. 
  FPGA's are not the only form of accelerator, but they have received 
the most attention in recent months.

That said, when they are applicable, and you have intensive processing 
needs, there is nothing quite like a custom CPU or a custom processing 
circuit to speed through your calculation.  Getting 20-100x the 
performance is possible and reasonable as an expectation, per CPU/FPGA. 
  If your application needs this, then there is little that is 
comparible.  You can put multiple boards into multiple elements in your 
cluster, and provided your application is parallelizable at the process 
level (blast, hmmer, much of bioinformatics, ...) you ought to be able 
to realize multiple orders of magnitude acceleration without paying huge 
sums of money.  Basically, if you are building a cluster for speed, then 
likely you need something like this for at least one of your applications.

If you don't need speed, and you just need lots of apps, there are 
solutions to that, and accelerators won't help much there.  If you run a 
few critical apps which are performance bottlenecked, and the bottleneck 
are CPU cycles (and not data motion), then accelerators will likely help.

Accelerators make lots of sense in analysis pipelines, where specific 
calculations may bottleneck the entire workflow.  They can be built/sold 
for reasonable cost in a number of cases, and the performance in these 
cases can be excellent.

George Magklaras wrote:
> The Linux Journal issue 142 (February 2006) talks about FPGA's in an 
> article with title 'Heterogeneous Processing: a Strategy for Augmenting 
> Moore's Law', written by a chap from Cray. Apart from the ehmm indirect 
> XD1 product marketing, the article makes the case for FPGA's outlining 
> alternative approaches to traditional commodity HPC clusters, as well as 
> the obstacles of turning scalar proc code to FPGA code.
> Best Regards,
> GM

Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 786 8423
fax  : +1 734 786 8452
cell : +1 734 612 4615

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