[Bioclusters] FPGA in bioinformatics clusters (again?)

George Magklaras georgios at ulrik.uio.no
Sat Feb 11 06:30:46 EST 2006

The Linux Journal issue 142 (February 2006) talks about FPGA's in an 
article with title 'Heterogeneous Processing: a Strategy for Augmenting 
Moore's Law', written by a chap from Cray. Apart from the ehmm indirect 
XD1 product marketing, the article makes the case for FPGA's outlining 
alternative approaches to traditional commodity HPC clusters, as well as 
the obstacles of turning scalar proc code to FPGA code.

Best Regards,

George B. Magklaras

Senior Computer Systems Engineer/UNIX Systems Administrator
The Biotechnology Centre of Oslo,
University of Oslo

EMBnet Norway: http://www.biotek.uio.no/EMBNET/

Farul Mohd. Ghazali wrote:
> 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.
> TIA.
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