[gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3

Mark Abraham Mark.Abraham at anu.edu.au
Sat Aug 22 04:18:12 CEST 2009

YH wrote:
> Dear Dr.  Saavedra,
> I would like to ask your help for my use of Gromacs.
> Now I run the Gromacs 4.05 on 16 node computer, but always meet the problems like the following.
> Would you please tell me how to sovle it. 
> Thank you very much in advanc,
> James, Wang(Dr.)
> Dalian university of Technology, 
> China
> -------------------------------------
> 	Back Off! I just backed up pr1.log to ./#pr1.log.5#
> Reading file pr1.tpr, VERSION 4.0.5 (single precision)
> Will use 10 particle-particle and 6 PME only nodes
> This is a guess, check the performance at the end of the log file
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.0.5
> Source code file: domdec.c, line: 5873
> Fatal error:
> There is no domain decomposition for 10 nodes that is compatible with the given box and a minimum cell size of 0.96025 nm
> Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings
> Look in the log file for details on the domain decomposition
> -------------------------------------------------------

You should read about the domain decomposition algorithm in the manual.
Probably your system is too small to make effective use of this many
processors with this algorithm.


More information about the gromacs.org_gmx-users mailing list