[gmx-users] domain decomposition error

[Justin A. Lemkul]

nikhil damle wrote:
> Hi,
> 
> I am trying to run a vacuum simulation of a system associated with ATP 
> and peptide. Being vacuum MD i removed pressure coupling and included 
> plain electrostatic cut-offs while calculating potential. Energy 
> minimisation converged to machine precesion even though not upto the 
> specified cut-off limits.
> 
> Now when i am running production MD on multiple processors it gives 
> following error.
> 
> There were 96 inconsistent shifts. Check your topology
> There were 96 inconsistent shifts. Check your topology
> There were 4 inconsistent shifts. Check your topology
> There were 4 inconsistent shifts. Check your topology
> There were 6 inconsistent shifts. Check your topology
> There were 6 inconsistent shifts. Check your topology
> 

These are related to periodic boundary conditions.  Search the list archive.

> -------------------------------------------------------
> Program mdrun, VERSION 4.0.5
> Source code file: domdec.c, line: 5873
> 
> Fatal error:
> There is no domain decomposition for 8 nodes that is compatible with the 
> given box and a minimum cell size of 1.025 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
> 
> Why in the very first place, it is considering box and cell size for a 
> vacuum MD when no related parameters are input ? This error is not given 

If you are running MD, then you most certainly have a box.  How could you have 
periodicity if your unit cell was not defined?

The simple fact is that DD cannot split such a small system over 8 processors. 
Either try fewer processors, or switch to particle decomposition with mdrun -pd.

-Justin

> if i run on single processor. What could be the possible reason ? I have 
> checked my topology and it is proper. How should i proceed. Fast reply 
> will be appreciated.
> 
> Regards,
> Nikhil
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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