[gmx-developers] Posit-enablement of GROMACS

Erik Lindahl erik.lindahl at gmail.com
Sat Aug 4 21:54:37 CEST 2018


On Sat, Aug 4, 2018 at 8:12 PM Theodore Omtzigt <theo at stillwater-sc.com>

> It doesn't need to be low hanging fruit. We are building a custom
> supercomputer for this,
> so we are interested how to speed up this workload.

What Mark is saying is that MD codes are almost entirely floating-point
limited, and the last few years we have been pretty good at improving
algorithms to the point where we reach a decent fraction of the max
theoretical FLOP-rate, including single-precision SIMD instructions. Using
modern Skylake-EP x86 cores (dual avx512 FMA SIMD units) as an example,
that means the theoretical FLOP-rate of each core is 2*16*2=64 flops per
cycle, and our inner kernels can get quite close to that rate.

For any new floating-point format to be competitive, it would need to
provide similar performance per core. I haven't studied the details of
posits, but unless you can execute them e.g. with single integer
instructions, you will need a new custom chip architecture rather than just
building a computer :-)

> In broad strokes, posits improve on IEEE float in reduced complexity,
> higher accuracy,
> and adherence to associative and distributive laws of arithmetic. The
> latter is where
> the reproducibility comes from.

... and I predict none of that is going to be relevant at all to users if
it comes at the cost of 10x lower performance :-)

> If we need some education on how best to apply this to MM-style MDs, we
> are eager
> to learn how best to apply this from GROMACS SMEs.

While I think innovation is great in general, the caveat for us is that I
think we have experience with 5-10 esoteric/new/special architectures that
never made it into the market for various reasons ;-) So, the one thing
that would be interesting is benchmarks showing posits provide higher
absolute performance for a highly optimized floating-point limited
algorithm that already used single precision on a broadly available



Erik Lindahl <erik.lindahl at dbb.su.se>
Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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