[Beowulf] [landman at scalableinformatics.com: Re: [Bioclusters] FPGA in bioinformatics clusters (again?)]
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>
>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
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.
Amber and many other MD codes have been parallelized for a while now...
>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
----- End forwarded message -----
Eugen* Leitl <a href="http://leitl.org">leitl</a> http://leitl.org
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