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FPGA in bioinformatics clusters (again?)

Hi Joe and all,

Please excuse the ridiculous latency of this response... been on holiday :)

On 13/02/2006, at 4:33 PM, Joe Landman wrote:
I/we strongly support their use. Not as replacements for clusters, but as tools to significantly augment desktop and cluster level supercomputing in Life sciences and related fields. 

Noted, and agreed.


The issue is that you have some design work to do to interface the core to the rest of the board. Now if the boards were somehow standardized (cough cough) this would be a "good thing". [anyone want to talk about standard boards?]

I see your point. There's some irony here... the problem is in ``glue logic''. That's exactly what FPGAs were considered good for in the early days! But yes, I appreciate the significance of the integration headache, especially considering where we want to take this: i.e. making FPGAs available to end users. You might want to pop by over to the OpenFPGA list; I recall seeing some discussion of integration related matters, even to the Operating System level, though to be frank right now that isn't really a core technical interest of mine.


I would argue the opposite, that bioclusters is all about providing scalable platforms for bio-computing tasks, and that acceleration systems, as people need them require a platform to host them. What better platform for a bio-accelerator than a bio-cluster ? (note:

Yep, fair enough. My concern was that we were getting a bit away from the bio side of things, but you pulled it back, so it's all good - believe me, I'm quite happy to go on and on about FPGAs and application specific processors :)

Actually, I have a question for folks who actually have access to FPGA equipped systems (I have a bunch of FPGAs lying around, but the very BEST system comms available is USB - and there's a Spartan sitting on that one!!); sorry for dragging vendor names into this, but I think it's probably the best way to illustrate the nature of the system I have in mind - I'm speaking of systems of the ilk of the Cray XD-1, Altix, and SRC's boxen. How much of a "multiple-use" attitude is there with these systems?

Bioinformatics is great, but other tasks - e.g. network intrusion detection, molecular dynamics, dense linear algebra - are also at home on FPGAs. The issue is multiplexing of the resources for shared access in a multi-user system, and this actually builds on top of the need for standardized integration, which presumably is already somewhat sorted on the systems mentioned. In a real world "production" environment, what actually happens?





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