[gmx-users] At what point is the random seed generated?

[Mark Abraham]

On Jan 29, 2014 4:59 AM, "Trayder Thomas" <trayder.thomas at monash.edu> wrote:
>
> Curses! Kinda seemed intuitive that way. I assume the philosophy being
> worked towards is that every unique run should have a unique .tpr file
that
> it is reproducible from?

It has that effect, which is very useful for debugging. I think of the
design more like that the tpr should describe the physics, and command line
options to mdrun should relate to its implementation (though this divide is
not perfectly implemented, either). Setting up the initial velocities is
considered part of setting up the model physics. Whether you want to
simulate copies of the same or different systems is your business.

> Curiously, I ran and checked a first batch on a different cluster and the
> simulations rapidly diverged (even between simulations run one after the
> other on the same node), while the second cluster managed to create 50
> identical simulations across 50 different nodes. The most obvious
> difference being that the diverging simulations used GPUs.

This kind of thing is expected - see
http://www.gromacs.org/Documentation/Terminology/Reproducibility

> I suspect I never would have noticed if I had of stuck to the one cluster.
> Might be worth stating explicitly in the manual for gen-seed, with
> reproducibility being what it is.

True, but http://manual.gromacs.org/online/mdp_opt.html#vel specifies "in
grompp" for gen-vel. We can't repeat ourselves everywhere, unfortunately,
lest one copy falls out of date! :-(

Mark

> Oh well, Thanks guys.
>
> -Trayder
>
>
>
>
> On Tue, Jan 28, 2014 at 10:55 PM, Mark Abraham <mark.j.abraham at gmail.com
>wrote:
>
> > Indeed. grompp does report the seed it uses to stderr.
> >
> > Mark
> >
> >
> > On Tue, Jan 28, 2014 at 8:51 AM, David van der Spoel
> > <spoel at xray.bmc.uu.se>wrote:
> >
> > > On 2014-01-28 08:37, Trayder Thomas wrote:
> > >
> > >> Hi,
> > >> When using 'gen-seed = -1' at what point is the random seed assigned?
> > >>
> > >> e.g. Does it use the process ID of grompp and embed the seed number
in
> > the
> > >> tpr file, or does it use the process ID of mdrun?
> > >>
> > >> I ask because I have 50 identical simulations started from the same
tpr
> > >> file :(
> > >>
> > >> Thanks,
> > >> -Trayder
> > >>
> > >>  I guess you found out. Sorry about that. It is done in grompp and
same
> > > tpr should give reproducible results. So you want to generate 50
> > different
> > > tpr files.
> > >
> > > --
> > > 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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