[Bioclusters] FPGA in bioinformatics clusters (again?)

Farul Mohd. Ghazali farul at aldrix.net
Fri Jan 13 09:46:04 EST 2006

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.


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