[gmx-users] same initial velocities vs. -reprod

[Mala L Radhakrishnan]

Hi Mark,

Thanks so much -- good to know that it's basically equivalent to different
starting velocities and I should expect them to be different.

I found this page that sort of explains it:
http://www.gromacs.org/Documentation/Terminology/Reproducibility

Out of curiosity, I was wondering if someone can point me to something that
explains why (a+b)+c != a+(b+c) sometimes for computations across multiple
processors.  Is it a finite precision issue?

thanks again,
M

On Fri, Mar 22, 2019 at 1:21 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> The dynamic load balancing on by default for domain decomposition means
> divergence happens by default. After a few ps it's logically equivalent to
> starting from different velocities. See the GROMACS user guide for more
> details on reproducibility questions!
>
> Mark
>
> On Fri., 22 Mar. 2019, 18:15 Mala L Radhakrishnan, <mradhakr at wellesley.edu
> >
> wrote:
>
> > Hi all,
> >
> > We set up replicate simulations (same starting mdp files and structures)
> > that ran across GPUs WITHOUT using the -reprod flag, but we set gen-vel
> to
> > no and used the same ld-seed value for both with the v-rescale
> thermostat.
> > They also ran on the same machine -- so from a deterministic point of
> view,
> > I would expect them to be "exactly" the same.
> >
> > The simulations, while having similar average energetics throughout,
> sample
> > different conformations and they start to differ pretty much right after
> > the simulation starts.
> >
> > I understand that I could have gotten results to be more reproducible by
> > using the -reprod flag, but in the case I describe (and I don't think I
> > have any other stochastic things going on unless I'm not understanding
> > ld-seed or gen-vel = no, or am forgetting something?),  what is causing
> the
> > difference?   Online, I see something about domain decomposition and
> > optimization, but I'd like to understand that better.
> >
> > My major question, though, is -- are the differences due to domain
> > decomposition optimization enough to basically equal what you might get
> > from "replicates" starting with different starting velocities, especially
> > once equilibration (as measure by RMSD) is reached? That's what I'm
> seeing,
> > so I wanted to make sure that these differences can actually be this big.
> > Or is there some other source of stochasticity I'm forgetting?
> >
> > Thanks so much, and I hope my question makes sense.
> >
> > M
> >
> > --
> > Mala L. Radhakrishnan
> > Whitehead Associate Professor of Critical Thought
> > Associate Professor of Chemistry
> > Wellesley College
> > 106 Central Street
> > Wellesley, MA 02481
> > (781)283-2981
> > --
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-- 
Mala L. Radhakrishnan
Whitehead Associate Professor of Critical Thought
Associate Professor of Chemistry
Wellesley College
106 Central Street
Wellesley, MA 02481
(781)283-2981