[gmx-users] No compatible domain decomposition

[Daniel Bauer]

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.