[gmx-developers] Gromacs benchmark set

[Alexey Shvetsov]

Hi Szilárd,

There are actualy few goals related to such benchmarking:

1. Check if this hardware suitable to run GROMACS (I already did some tests on 
my systems such as RecA protein filaments, nucleosomes etc all have sizes ca 
~800k - 1.4M atoms). Check scaling and compare it to existing systems (thats 
why I ask about some kind of standart benchmark set)

2. Another thing is to check scalability of algorithms (PME, RF)

RSC PetaStream is a special systems (it has very similar design to next gen 
Xeon Phi KNL systems). It uses Xeon Phi as regular compute nodes connected 
with multiple InfiniBand links so Xeon Phi to Xeon Phi bandwith is ~6GB/s on 
medium and large size MPI messages.

As I see on some systems GMX 5.0 on Xeon Phi scales quite well (up to ~100-200 
atoms per Xeon Phi thread)

В письме от 1 июля 2014 17:03:23 пользователь Szilárd Páll написал:
> 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 Moreover they are outdated too.
> 
> Cheers,
> --
> Szilárd
> 
> 
> 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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-- 
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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