[gmx-developers] Alternate Parallelization scheme

David spoel at xray.bmc.uu.se
Sat Jun 18 22:48:59 CEST 2005

On Sat, 2005-06-18 at 15:41 -0500, Nathan Moore wrote:
> >> (2) Which particles does each node control?  I assume that the grompp
> >> options -sort and -shuffle destroy the easy mapping, rank=0 gets the
> >> first
> >> 10 atoms, rank=1 gets the second 10 atoms etc.
> > This doesn't matter once you're in mdrun. All this stuff is done in the
> > preprocessor. As a matter of fact mdrun prints in md0.log how the
> > division over processors is done.
> How is the division of labor coded into mdrun?  Is there an array that
> maps the control of atoms to each processor?  I'm imagining an array,
>      int control[num_atoms];
> where the value of control[i] is the rank of the processor assigned to
> update force and position of atom i.
(Neighbor Search Border)

We have a project going to include dynamics load balancing in the code,
but it is not completely trivial, and the main developers (Erik, Berk,
me) have not enough time...
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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