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