David spoel at xray.bmc.uu.se
Fri Apr 22 22:00:57 CEST 2005

On Fri, 2005-04-22 at 09:20 -0700, Brendan Moran wrote:
> Hi,
> I saw that there was a discussion of a hardware accellerator for gmx a 
> while back.  I would be interested in contributing to such a project and 
> I have access to a PCI FPGA platform that I can experiment with.
> If there are still people who are interested in a gmx hardware 
> accellerator, I'd like to help out.  If someone could point me at the 
> more processor intensive sections of the gmx algorithm (I don't know the 
> gmx code at all yet), I could have a look and see if FPGA based 
> optimization looks practical.
Check the equations in the manual at chapter 4.

Do you think you can achieve much more than 2 GFlop/s on your chip? This
is the performance I get in the best case on a single 2 GHz Opteron. It
seems that would be hard to beat even with special hardware, but I'm
ready to be surprised. As you may (or may not) know, the GROMACS project
started out as a hardware project, and we succeeded doing a 1/sqrt(x)
computation in hardware at 5 MHz (in 1990 or so). Then we gave up and
bought 40 MHz i860 chips that were programmable...

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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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