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FPGA in bioinformatics clusters (again?)

Hi all,

On 12/02/2006, at 12:39 AM, Amar Shan wrote:

<...>

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.

Furthermore, comparing the development of an FPGA-based processing solution to *installation and configuration* of software solutions may not be very fair. Developing scientific software tools is generally hard too.

But my thinking is this: if the FPGAs (and support hardware like RAM) are already there and the interconnects are there, then it stands to reason that off-the-shelf cores would proliferate in strategic application domains -- and the bioinformatics community would be the first to benefit from the emergence of such a development and distribution model... well, maybe second after the "black helicopter brigade's" crypto departments ;-).

These cores could then be downloaded and installed with minimal end- user mucking around, and certainly almost NO hardware design. Take this for example:

http://wiki.ittc.ku.edu/rcblast/Download

Of course there's compatibility sludge to wade through right now... but that's sortable.

Hypothesis: FPGA core == "a different kind of software, for a different kind of computer".

Comments? [Should probably be sent off-list since this is stretching the mandate of Bioclusters.]

-tirath


We have a few bioinformatics customers that are building FPGA
implementations of their own algorithms with good success.

Cheers,

Amar

---------------
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
informatics
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,
GM

--
--
George B. Magklaras

Senior Computer Systems Engineer/UNIX Systems Administrator
The Biotechnology Centre of Oslo,
University of Oslo
http://www.biotek.uio.no/

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
https://bioinformatics.org/mailman/listinfo/bioclusters


_______________________________________________
Bioclusters maillist  -  Bioclusters (at) bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bioclusters

_______________________________________________
Bioclusters maillist  -  Bioclusters (at) bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bioclusters


_______________________________________________
Bioclusters maillist  -  Bioclusters (at) bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bioclusters