[gmx-users] grompp -np option
spoel at xray.bmc.uu.se
Fri Jun 10 19:07:17 CEST 2005
On Fri, 2005-06-10 at 10:42 -0500, Nathan Moore wrote:
> So MAXNODES is defined in
> #define MAXNODES 256
> Can this definition be changed without code failure/corruption?
yes, but you need to recompile and toss all your old tpr files. We'll
make this dynamic. In fact, I've implemented a change where this
information is taken out of the tpr file altogether and all
parallellization is done in mdrun. One tpr file to rule them all.
> > Is the limit of -np to no more that 256 hard-coded into grompp for a
> > specific reason? Is it a simple change to the code (I havn't looked)?
> > More generally, is there much understanding of the "optimum" number of
> > atoms each node should have for peak performance in a parallel job? eg if
> > I have two systems, one with 5,000 atoms, and another with 500,000 atoms,
> > would they both be split up into blocks of 1000 atoms/compute node for
> > optimum (minimum real time) performace?
> > regards,
> > NT Moore
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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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