[Bioclusters] FPGA in bioinformatics clusters (again?)

Joe Landman landman at scalableinformatics.com
Fri Jan 13 20:33:43 EST 2006

Kathleen wrote:
> TIA:
> One thing to consider when using FPGAs for bioinformatics or any complex
> computational life science application is whether or not the FPGA supports
> cross coupled communication.

... which is needed in which algorithms?

> I believe FPGAs do not, therefore, FPGAs will
> be limited in scalability, performance and very expensive.  

FPGA performance on various algorithms is already 1 to 2 orders of 
magnitude (e.g. 10 to 100 times) faster than single CPUs.  The price 
points of modern FPGA boards with modern algorithms is about 2-4x single 
node pricing.

As FPGAs improve (and they are), expect to achieve significantly more 


> almost have HMMR and GROMACS parallelized and will be parallelizing AMBER or
> some other MD code next.

Hmmm.... HMMer was parallelized using PVM quite some time ago, and using 
MPI quite recently (with excellent results reported).  GROMACS also has 
been parallel for a while.

Gromacs: http://www.gromacs.org/benchmarks/scaling.php
HMMer: http://hmmer.wustl.edu

Amber and many other MD codes have been parallelized for a while now...

> Kathleen Erickson
> Senior Marcom Strategist , Massively Parallel Technologies, Inc.

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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