Starbridge Systems did an FPGA implementation for NIH, white paper at http://www.starbridgesystems.com/whitepapers.htm Solentas has an R&D project, that stills needs some funding, that will convert code, and put it into the FPGA core without having to have a logic programmer on staff. Their box will just attach to the network, so it is also less invasive. http://www.solentas.com Bill Harman, P - (801) 572-9252 wharman at prism.net -----Original Message----- From: bioclusters-bounces+wharman=prism.net at bioinformatics.org [mailto:bioclusters-bounces+wharman=prism.net at bioinformatics.org] On Behalf Of Farul Mohd. Ghazali Sent: Friday, January 13, 2006 7:46 AM To: bioclusters at bioinformatics.org Subject: [Bioclusters] FPGA in bioinformatics clusters (again?) 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