[gmx-developers] reproducability of md sims

[Berk Hess]

Hi,

What I tried to say is that running on the same number of MPI ranks and OpenMP threads should, at least currently, give identical results, unless MPI_Allreduce does not have a defined summation order. Currently our OpenMP reduction order is defined. Indeed changing the rank or thread count does affect the results. We would need to use fixed precision reduction to avoid this.

BerkOn Nov 30, 2014 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. 
>
> 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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