[gmx-users] Shake block crossing node boundaries

Suman Chakrabarty suman at sscu.iisc.ernet.in
Sun Apr 12 09:50:55 CEST 2009


I am trying brownian dynamics simulation of a single polymer chain
consisting of 100 atoms in vacuum. All bonds are constrained by LINCS.
I am trying to use the particle decomposition scheme for parallel run
since for a molecule in vacuum domain decomposition seems to be a
waste. I am using the 4.0.4 version.

But for whatever number of nodes I choose (> 1), I am getting the
following error (in this case the number of nodes was 4):

The number of constraints is 99
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest
There are: 100 Atoms
splitting topology...
There are 100 charge group borders and 1 shake borders
There are 100 total borders
Division over nodes in atoms:
      25      25      25      25
Walking down the molecule graph to make constraint-blocks

Program mdrun_mpi_d, VERSION 4.0.4
Source code file: splitter.c, line: 130

Fatal error:
Shake block crossing node boundaries
constraint between atoms (75,76)

So is there any way to avoid such an error and still have a particle
decomposed parallel run or I am forced to use single processor always?


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