[Bioclusters] FPGA in bioinformatics clusters (again?)

William Harman wharman at prism.net
Fri Jan 13 14:31:42 EST 2006

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

More information about the Bioclusters mailing list