[Bioclusters] FPGA in bioinformatics clusters (again?)

Alan Kilian kilian at bobodyne.com
Sun Feb 12 21:22:19 EST 2006

On Sat, 2006-02-11 at 08:18 -0700, Kathleen wrote:
> There are alternatives to FPGAs that provide similar speedup and
> scalability.  

    I am very interested in hearing how to get a speedup of 700
    on a HMM search similar to what can be achieved with a single
    $30,000 FPGA card. I'm not sure what a 700 CPU cluster costs,
    but my feeling is that it will be somewhat larger than adding
    an FPGA card to an existing server.

> If you can utilize your existing infrastructure, but increase
> performance by several orders of magnititude ... with software ...

    I am also interested in how I can increase my performance 
    several orders of magnitude using my existing infrastructure.

    These sound like very impressive improvements.


- Alan Kilian <kilian(at)bobodyne.com>

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