[Bioclusters] FPGA in bioinformatics clusters (again?)

Kathleen kathleen at massivelyparallel.com
Sat Feb 11 10:18:44 EST 2006

There are alternatives to FPGAs that provide similar speedup and
scalability.  If you can utilize your existing infrastructure, but increase
performance by several orders of magnititude (extending Moore's Law) with
software, that may provide the best price/performance ratio and lowest
impact of MTBF.  Better yet, if you just have one or two commonly used apps
like BLAST and HMMer that are causing you problems on your existing
hardware, why not outsource to a service that plugs into your existing
workflow? Just a thought.

-----Original Message-----
From: Joe Landman [mailto:landman at scalableinformatics.com] 
Sent: Saturday, February 11, 2006 6:42 AM
To: Clustering, compute farming & distributed computing in life science
Subject: Re: [Bioclusters] FPGA in bioinformatics clusters (again?)

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
Bioclusters maillist  -  Bioclusters at bioinformatics.org

More information about the Bioclusters mailing list