[Beowulf] [landman at scalableinformatics.com: Re: [Bioclusters] FPGA in bioinformatics clusters (again?)]

Eugen Leitl eugen at leitl.org
Sat Jan 14 02:18:48 PST 2006

----- Forwarded message from Joe Landman <landman at scalableinformatics.com> -----

From: Joe Landman <landman at scalableinformatics.com>
Date: Fri, 13 Jan 2006 20:33:43 -0500
To: "Clustering,  compute farming & distributed computing in life science informatics" <bioclusters at bioinformatics.org>
Subject: Re: [Bioclusters] FPGA in bioinformatics clusters (again?)
User-Agent: Thunderbird 1.5 (Windows/20051201)
Reply-To: "Clustering,  compute farming & distributed computing in life science informatics" <bioclusters at bioinformatics.org>

Kathleen wrote:
>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
Bioclusters maillist  -  Bioclusters at bioinformatics.org

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