[Bioclusters] FPGA in bioinformatics clusters (again?)

Kathleen kathleen at massivelyparallel.com
Fri Jan 13 15:12:05 EST 2006


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.  I believe FPGAs do not, therefore, FPGAs will
be limited in scalability, performance and very expensive.  I'd like to
invite you to give us a try.  We have a highly scalable, high performance
supercomputing methodology that runs on COTS hardware and is OS agnostic.
In fact, you can try BLAST right now at www.mptbiotech.com for free. We
almost have HMMR and GROMACS parallelized and will be parallelizing AMBER or
some other MD code next.  If you are a MatLab user, you can even use MatLab
to access your account with us.  Please contact me to discuss what you want
to do in more detail as we would be very interested in helping you achieve
your goals.

Kind Regards,


Kathleen Erickson
Senior Marcom Strategist , Massively Parallel Technologies, Inc.
kathleen at massivelyparallel.com
W: (303)468-1179
M: (303)601-0057

-----Original Message-----
From: William Harman [mailto:wharman at prism.net] 
Sent: Friday, January 13, 2006 12:32 PM
To: 'Clustering, compute farming & distributed computing in life science
Subject: RE: [Bioclusters] FPGA in bioinformatics clusters (again?)

Starbridge Systems did an FPGA implementation for NIH, white paper at

Solentas has an R&D project, that stills needs some funding, that will
convert code, and put it into the FPGA core without having to have a logic
programmer on staff.  Their box will just attach to the network, so it is
also less invasive.  http://www.solentas.com

Bill Harman,
P - (801) 572-9252
wharman at prism.net

-----Original Message-----
From: bioclusters-bounces+wharman=prism.net at bioinformatics.org
[mailto:bioclusters-bounces+wharman=prism.net at bioinformatics.org] On Behalf
Of Farul Mohd. Ghazali
Sent: Friday, January 13, 2006 7:46 AM
To: bioclusters at bioinformatics.org
Subject: [Bioclusters] FPGA in bioinformatics clusters (again?)

Some years back when Timelogic and Paracel were popular there were some
discussions on FPGA based computing for Linux clusters. I can't recall if
there was a general conclusion but one of the limitations was that you're
stuck with the algorithms the manufacturer provided.

SGI approached me recently to talk about their reconfigurable FPGA systems
and I was intrigued. The new RASC allows a user to remap the FPGA according
to your own algorithms instead of being limited to one set of libraries.
They also link it with GNU tools for debugging etc.

Has anyone looked at the SGI RASC or any other equivalent system out there?
Any ideas if it makes sense in today's clusters? The workload I'm supporting
has very few custom written algorithms and is mostly BLAST, phred/phrap,
hmmer with some heavy Amber and Gromacs thrown in as well.

Bioclusters maillist  -  Bioclusters at bioinformatics.org

Bioclusters maillist  -  Bioclusters at bioinformatics.org

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