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

[Mala L Radhakrishnan]

Thanks.

It's interesting how such small differences can compound to totally
different conformations within a few ps (the energies are close though,
which one would expect at equilibration).

M

On Fri, Mar 22, 2019 at 4:29 PM Benson Muite <benson_muite at emailplus.org>
wrote:

> Hi,
>
> Yes, finite precision and order of computations may not be respected by
> the compiler. In most cases, they should be close, however much
> analytical work remains in this area. A  relevant paper (though there
> are many others) is:
>
> Collange, Defour, Grailaat and Iakymchuk
>
> Numerical Reproducibility for the Parallel Reduction on Multi- and
> Many-Core Architectures
>
> https://hal.archives-ouvertes.fr/hal-00949355v4/document
>
> It is unclear if it would be too expensive to implement such methods in
> GROMACs though.
>
> Benson
>
> On 3/22/19 10:11 PM, Mala L Radhakrishnan wrote:
> > 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