[gmx-users] No compatible domain decomposition

[Mark Abraham]

Hi,

If you express those as [intermolecular_interactions] then perhaps DD will
cope better because it understands that they are intended to be handled
separately. It doesn't matter that they are actually intramolecular!

Mark

On Tue., 2 Jul. 2019, 14:27 Daniel Bauer, <bauer at cbs.tu-darmstadt.de> wrote:

> Hello,
>
> I am trying to run a protein simulation consisting of ~100.000 atoms
> (box dimensions: 8.8x8.8x9.4nm) on multiple mpi threads. For the
> protein, I need to define a few distance restraints. Right now, these
> are defined with harmonic bonds in the  [ bond ] section of the protein:
>
> [ bonds ]
>
> ...
>
>    53  1952     6  2.437  1000.0
>  1952  3851     6  2.437  1000.0
>  3851  5750     6  2.437  1000.0
>  5750    53     6  2.438  1000.0
>    53  3851     6  3.447  1000.0
>  1952  5750     6  3.447  1000.0
>
> Unfortunately, when I try to run this system with more than 1 mpi
> thread, it fails. Apparently,  the high distance for the bond does not
> allow proper domain decomposition (which makes sense because the bond
> cannot go over multiple domains). What are my options here? Is there no
> way to run this across multiple computation nodes except using something
> like plumed?
>
>
> Initializing Domain Decomposition on 32 ranks
> Dynamic load balancing: locked
> Minimum cell size due to atom displacement: 1.301 nm
> Initial maximum distances in bonded interactions:
>     two-body bonded interactions: 3.444 nm, Harmonic Pot., atoms 53 3851
>   multi-body bonded interactions: 0.424 nm, Proper Dih., atoms 5136 5145
> Minimum cell size due to bonded interactions: 3.789 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.855 nm
> Estimated maximum distance required for P-LINCS: 0.855 nm
> Using 0 separate PME ranks
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 32 cells with a minimum initial size of 4.736 nm
> The maximum allowed number of cells is: X 1 Y 1 Z 1
>
> -------------------------------------------------------
> Program:     gmx mdrun, version 2019.1
> Source file: src/gromacs/domdec/domdec.cpp (line 2403)
> MPI rank:    0 (out of 32)
>
> Fatal error:
> There is no domain decomposition for 32 ranks that is compatible with the
> given box and a minimum cell size of 4.73566 nm
> Change the number of ranks 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
> -------------------------------------------------------
>
>
> Best regards,
>
> Daniel
>
>
> --
> Daniel Bauer, M.Sc.
>
> TU Darmstadt
> Computational Biology & Simulation
> Schnittspahnstr. 2
> 64287 Darmstadt
> bauer at cbs.tu-darmstadt.de
>
> Don't trust atoms, they make up everything.
>
>
> --
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