[Bioclusters] FPGA in bioinformatics clusters (again?)

[Tirath Ramdas]

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
>>
>
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