[gmx-developers] Gromacs benchmark set

Szilárd Páll pall.szilard at gmail.com
Tue Jul 1 17:03:26 CEST 2014

Hi Alexey,

There is no official benchmark set yet.

The right benchmark set will greatly depend on what your goal is.
There is a wide range of possible ways to set up benchmarks and there
is no single right way to do it. Most importantly, unless the goal is
to i) show off hardware ii) benchmark algorithms, the input systems
should be representative of the production simulations that are/will
be running on the hardware.

More concretely, for instance if you want to show decent performance
with Xeon Phi (especially strong scaling), you will probably need huge
input systems, preferably homogeneous and even better without PME
(which  - 3D FFT-s across multiple Phi-s will probably run very
poorly). In contrast, if you use an input system like a 50-70k
membrane protein simulated with PME, you will probably find it hard to
show good performance compared to to an IVB Xeon let alone scaling.

IMHO the STFC benchmarks are very disadvantageous for GROMACS (all
inputs use CHARMM FF and related peculiar settings) and therefore they
are not very representative. Moreover they are outdated too.


On Mon, Jun 30, 2014 at 3:50 PM, Alexey Shvetsov
<alexxy at omrb.pnpi.spb.ru> wrote:
> Hi all!
> We're going to run a series of benchmarks on RSC PetaStream system. Its
> based on Xeon Phi and designed to run native mode codes. Are there some kind
> of representative benchmark set? I'm currently found
> http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx this one. May be
> there are some other sets?
> --
> Best Regards,
> Alexey 'Alexxy' Shvetsov, PhD
> Department of Molecular and Radiation Biophysics
> FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
> Leningrad region, Gatchina, Russia
> mailto:alexxyum at gmail.com
> mailto:alexxy at omrb.pnpi.spb.ru
> --
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