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GPU Computing Case Study Molecular Modeling Applications Ks Uiuc Form

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you're looking for cases where you can where you can have reuse or where the arithmetic cost is a large multiple of the data set size so one simple ratio drops uh one to four oh no no no you would you would want probably 40 flops per bite to make it worth your time at least maybe more because uh the time it takes you to get the data there from the host in the first place so to give you an example so barry who's maybe over there barry has been working on a really interesting analysis tool for bmd called timeline and what it does is it basically performs a bunch of standard molecular dynamics uh analyses on every frame of a trajectory now a lot of these turn out to be very if you look at them in isolation each one is a very trivial number of floating point operations relative to the size of the data so if i just wrote one cuda kernel to for example calculate the rmsd in between two structures or something like that that's barely enough floating point to be worth e

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