Re: [AMBER-Developers] weird behavior for pmemd.cuda on Volta cards

From: David Cerutti <dscerutti.gmail.com>
Date: Fri, 8 Dec 2017 12:17:58 -0500

OK that then confirms some odd things I had been seeing. With systems
larger than JAC, and probably longer overall run times, I was also seeing
dramatic performance decreases, to the point where our Volta was giving the
performance of a GP100. It's good to know, then, that our Volta in Case
lab is not unique (uniquely broken).

Dave


On Fri, Dec 8, 2017 at 9:11 AM, David A Case <david.case.rutgers.edu> wrote:

> Hi folks:
>
> The few developers that have Volta cards have reported markedly different
> speedups vs. Pascal for different benchmarks.
>
> I think these may be related to the following observation: jobs seem to
> slow
> down the longer they run. You can check this on the JAC_production_NVE_4fs
> benchmark: make nstlim ten times large, and re-run; (you can increase ntwx
> and ntwr if you like--doesn't seem to make much difference).
>
> For me, the default run (250000 steps) clocks at 923 ns/day (total time is
> 95 sec.) This is in line with what others are getting
>
> The 10x longer run returns 824 ns/day; if I also increase ntwx by a
> factor of
> 10, I get up to 847 ns/day. (total time of 0.28 hours).
>
> A 100x run kind of plateaus at 830 ns/day (total time of 2.9 hours).
>
> For larger systems, the difference between the "short run" timings (which
> I suspect are typical of the official benchmarks) and "real" production
> runs can be larger. For at 391000 atom system, 10000 steps (82 seconds)
> runs at 51 ns/day, whereas 50000 steps (450 sec.) runs at 40 ns/day,
> and 100000 steps (900 seconds) is at 39 ns/day. These are jobs with
> ntwx=ntwr=100000, so there is no dumping of coordinates to disk, etc.
>
> So:
>
> 1. Be careful with benchmarks: the official JAC benchmark, at 250000
> steps,
> is not long enough for this platform. (!?) Same is probably true for other
> benchmarks.
>
> 2. If we can figure out what is causing the slowdown, we might see a way
> to
> get performance improvements in legacy mode.
>
> ...dac
>
>
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Received on Fri Dec 08 2017 - 09:30:02 PST
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