[gmx-developers] reproducability of md sims

[Mark Abraham]

Hi,

Indeed. I missed this email when Michael wrote it, but I have added a
little more flesh on the bones of a provably reproducible build type at
http://redmine.gromacs.org/issues/1587#note-6

Mark

On Tue, Dec 2, 2014 at 6:20 AM, Shirts, Michael R. (mrs5pt) <
mrs5pt at eservices.virginia.edu> wrote:

>   > So one can have fully deterministic forces in MD by simply paying a
> couple of flops per force component in each inner loop.
>
>  If there was a way to overload functions in such a way as to make this a
> compile time option, it might be pretty useful for validation . . .
>
>  ~~~~~~~~~~~~
> Michael Shirts
> Associate Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434) 243-1821
>
>   From: Mark Abraham <mark.j.abraham at gmail.com>
> Reply-To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
> Date: Sunday, November 30, 2014 at 5:40 AM
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] reproducability of md sims
>
>
>
> On Sun, Nov 30, 2014 at 12:03 PM, Carsten Kutzner <ckutzne at gwdg.de> wrote:
>
>> Hi,
>>
>> On 30 Nov 2014, at 11:17, Berk Hess <hess at kth.se> wrote:
>>
>> > Hi,
>> >
>> > There is documentation on this somewhere.
>> > Even when running with MPI and/or OpenMP simulations should be
>> reproducible when ran on an identical run
>> But reductions of several summands into a sum do not yield a
>> bit-identical result across runs.
>> Therefore I think at least with MPI and/or OpenMP we will never get
>> bit-identical
>> trajectories unless the order of summation is fixed somehow for such
>> operations.
>>
>
>  True, but not the whole story. You can leave the order free if you
> pre-round the operands such that the result is provably insensitive to the
> order of the operations. See
> http://htor.inf.ethz.ch/publications/img/arteaga-fuhrer-hoefler-reproducible-apps-ipdps14.pdf.
> So one can have fully deterministic forces in MD by simply paying a couple
> of flops per force component in each inner loop.
>
>  Mark
>
>  Best,
>>   Carsten
>>
>>
>> > setup. The only things that usually matter, and which -reprod should
>> turn off, are dynamic load balancing and FFTW kernel choice by timing.
>> > You can mail me your tpr and I can have a look.
>> >
>> > Cheers,
>> >
>> > BerkOn Nov 30, 2014 9:05 AM, David van der Spoel <spoel at xray.bmc.uu.se>
>> wrote:
>> >>
>> >> Hi,
>> >>
>> >> I'm trying to test reproducibility of simulations of liquids. The
>> >> simulation systems are flexible (no constraints) and run with the
>> >> -reprod flag, starting from the same tpr, on a single core. However
>> >> after a few hundred fs the energy starts to diverge.
>> >>
>> >> Are there factors impacting the reproducibility that are not controlled
>> >> by the -reprod flag?
>> >>
>> >> --
>> >> David van der Spoel, Ph.D., Professor of Biology
>> >> Dept. of Cell & Molec. Biol., Uppsala University.
>> >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>> >> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>> >> --
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