[Bioclusters] FPGA in bioinformatics clusters (again?)

Amar Shan shan at cray.com
Sat Feb 11 11:39:28 EST 2006

You weren't supposed to notice the "indirect XD1 marketing ..." :-)  I tried
to keep the article reasonably factual.

My take on FPGAs in bioinformatics is really this:  given the amount of
compute intensive processing in your pipelines, the FPGAs should be a
no-brainer.  What I've found, though, is that people dislike being locked
into a proprietary implementation, and as a result a lot of commodity
processor cycles wind up being used to implement the pipeline.

To counter the proprietary argument, we've released the source for the XD1
implementation of FPGAs to quite a number of people, and I'm trying to find
the best way to put it into the open source community.  I'll probably
release the source through OpenFPGA.org -- good source of FPGA information
and free implementations.  They're trying to build a critical mass of
applications so that adoption of FPGAs becomes ubiquitous.

Joe Landman's comment about the complexity of programming FPGAs is fair, but
there are a lot of good tools coming on the market which simplify the task.
We have a few bioinformatics customers that are building FPGA
implementations of their own algorithms with good success.  



Amar Shan
t. 604-484-2253
f. 604-484-2221

-----Original Message-----
From: bioclusters-bounces+shan=octigabay.com at bioinformatics.org
[mailto:bioclusters-bounces+shan=octigabay.com at bioinformatics.org] On Behalf
Of George Magklaras
Sent: Saturday, February 11, 2006 3:31 AM
To: Clustering, compute farming & distributed computing in life science
Subject: Re: [Bioclusters] FPGA in bioinformatics clusters (again?)

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.
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
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