[gmx-developers] parallelization and accuracy

[David van der Spoel]

On Mon, 2003-02-10 at 11:06, Anton Feenstra wrote:
> Frauke Meyer wrote:
> > 
> > Dear all, dear Justin,
> > 
> > I tried to change the pull code of the 3.1.4 version to enable it to
> > run in parallel. In principle it works, but the force I obtain starts to
> > differ (by 10^-3 kJ/mol/nm) from a sequential run from the 5th integration
> > step on. The force profiles of the seq. and parallel run finally diverge
> > after several 100 steps.
> > Any hint, what the reason might be for that? The only things I changed are
> > to add the stuff for parallel runs to the list of variables the procedures
> > of the pull code are called with (start, homenr, cr) and to restrict I/O
> > to the master node (actually I just transferred all changes for parallel
> > pulling of the cvs version into my code).
> 
> Guessing from my intuition, without much factual basis, I might
> suggest this is simply the result of rounding. It seems likely
> that in paralell, some calculations are performed in different
> order w/r to a sequential run, which would lead to different rounding
> and hence to divergence in the results. IMHO, nothing to worry about,
> as long as the first steps are, with execption of the last decimal, 
> identical.
This is true in principle, but you still get the same averages.
Different trajectories, but the same average. If you use double
precision it should be much more similar. If it is not in double, you
may have an error somewhere still.
> 
> 
> -- 
> Groetjes,
> 
> Anton
>  ________ ___________________________________________________________
> |        | Anton Feenstra                                            |
> | .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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> | ' __   | Feenstra at chem.vu.nl - http://www.few.vu.nl/~feenstra/     |
> |  /  \  |-----------------------------------------------------------|
> | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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