[gmx-users] default -rdd with distance restraints seems too large
x.periole at rug.nl
Thu Oct 17 15:30:39 CEST 2013
Yes it is a pity!
But particle decomposition helps :)) well helped!
> It's a shame that long distance restraints limit the parallalization so much, but it is understandable. Thanks for helping me with this.
> -- original message --
> Initializing Domain Decomposition on 8 nodes
> Dynamic load balancing: auto
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
> two-body bonded interactions: 2.636 nm, Dis. Rest., atoms 1701 4425
> multi-body bonded interactions: 0.479 nm, CMAP Dih., atoms 1062 1081
> Minimum cell size due to bonded interactions: 2.899 nm
> Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.172 nm
> Estimated maximum distance required for P-LINCS: 1.172 nm
> Using 0 separate PME nodes, as there are too few total
> nodes for efficient splitting
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 8 cells with a minimum initial size of 3.624 nm
> The maximum allowed number of cells is: X 1 Y 1 Z 2
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