[gmx-users] Domain Decomposition

[Mark Abraham]

Hi,

You have a bonded interaction at a distance of 10 nm. I assume that's not
your intention. Perhaps you should give a configuration to grompp that has
whole molecules. IIRC less ancient versions of GROMACS do a better job of
this.

Mark

On Thu, Feb 15, 2018 at 5:39 PM Iman Ahmadabadi <imanahmadabadi75 at gmail.com>
wrote:

> Dear Gromacs Users,
>
> In one job, I always get in (any number of nodes) the domain decomposition
> error as following and I don't know what should I do. I have to use the
> -dds or -rdd setting for my problem?
>
> Sincerely
> Iman
>
> Initializing Domain Decomposition on 56 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: 9.579 nm, LJ-14, atoms 1663 1728
>   multi-body bonded interactions: 9.579 nm, Angle, atoms 1727 1728
> Minimum cell size due to bonded interactions: 10.537 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.700 nm
> Estimated maximum distance required for P-LINCS: 0.700 nm
> Guess for relative PME load: 0.87
> Using 0 separate PME nodes, as guessed by mdrun
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 56 cells with a minimum initial size of 13.171
> nm
> The maximum allowed number of cells is: X 0 Y 0 Z 0
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.6
> Source code file: /share/apps/gromacs/gromacs-4.6/src/mdlib/domdec.c, line:
> 6767
>
> Fatal error:
> There is no domain decomposition for 56 nodes that is compatible with the
> given box and a minimum cell size of 13.1712 nm
> Change the number of nodes or mdrun option -rdd or -dds
> Look in the log file for details on the domain decomposition
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
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