[gmx-users] possible configuration for gromacs gpu node

[Szilárd Páll]

On Wed, May 7, 2014 at 2:13 PM, Harry Mark Greenblatt
<harry.greenblatt at weizmann.ac.il> wrote:
> BS"D
>
>    So a job should run the same or faster on 10 cores at 2.5GHz relative to 6 cores at 3.5GHz?
> Thanks for letting me know....

Well, the "guesstimation" is not bulletproof, so if you want to be
sure, please do measurement, preferably on the actual CPUs in
question.

However, if you assume perfect multi-threaded scaling and core
frequencies locked at the base frequency, you get a ratio of 10*2.5 /
6*3.5 > 1. Again, you can make such sloppy estimates for GROMACS
because MD runs in L1/L2 cache at the scales of interest. Now, in
practice, the fact that you need a higher number of threads on the
10-core processor means that multi-threaded scaling could diminish the
gain, but if your main workload will be GROMACS (especially if you'll
run mostly single GPU/without DD), this should not be a big concern. I
just did a quick check of extrapolated vs actual measured performance
between a 6-core 3.2 Ghz and a 12-core 2.7 Ghz Sandy Bridge and the
numbers roughly match up.

Note that the single- and poorly threaded application performance on
the 6-core CPUs will be a bit better (15% higher turbo clock).

--
Szilárd


>
> Harry
>
>
> Btw, the 10-core 2.5 Ghz Xeon (2670?) will be a better
> price/performance - for the same price - as the  E5-2643V2, at least
> for GROMACS and in general codes that scale well.
>
>
>
> -------------------------------------------------------------------------
>
> Harry M. Greenblatt
>
> Associate Staff Scientist
>
> Dept of Structural Biology           Harry.Greenblatt at weizmann.ac.il<mailto:arry.Greenblatt at weizmann.ac.il>
>
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