[gmx-developers] Gromacs benchmark set

David van der Spoel spoel at xray.bmc.uu.se
Thu Jul 3 09:27:04 CEST 2014

On 02/07/14 09:28, Alexey Shvetsov wrote:
> 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)

However a benchmark should not be all about 1M atom systems (nothing 
against those) but should also cover smaller systems, such that we can 
show scaling versus system size too. I could contribute some relatively 
simple liquids.

We should also focus on accuracy. In 5.0 we now have LJ-PME and we 
should push that we can achieve higher accuracy in our calculations with 
this (I'm about to submit a force field paper on this). Hence we should 
not waste (too much) time on low accuracy solutions that are of limited 
practical use - read Reaction Fields.

> 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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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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