[gmx-users] Changing number of processors after a job restart

[Nash, Anthony]

Fantastic! I figured it would all fall under the dominion of floating point arithmetic reproducibility.

Thanks
Anthony 

Dr Anthony Nash
Department of Chemistry
University College London
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: 09 January 2015 12:49
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Changing number of processors after a job restart

On 1/9/15 7:46 AM, Nash, Anthony wrote:
> Hi Justin,
>
> I thought I would just give it a try at the risk of then being dropped back down on the queue. Turns out I end up with warnings rather than system-halting errors:
>
> -------------
>    #nodes mismatch,
>      current program: 32
>      checkpoint file: 64
>
>    #PME-nodes mismatch,
>      current program: -1
>      checkpoint file: 16
>
> Gromacs binary or parallel settings not identical to previous run.
> Continuation is exact, but is not guaranteed to be binary identical.
>
> --------------
>
> I am now weighing up the pros and cons of this simulation.
>

Any possible differences are unlikely to be more significant than the normal
chaos of MD, I would think.  See, for instance:

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation

http://www.gromacs.org/Documentation/Terminology/Reproducibility

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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