[gmx-users] Error There is no domain decomposition for 6 nodes that is compatible

Justin Lemkul jalemkul at vt.edu
Fri Oct 5 12:09:00 CEST 2012

On 10/5/12 5:35 AM, lloyd riggs wrote:
> you have to play with the ratio usually of domain decompositions Vs. Grid size, I had that error some time ago though, if you look at the generated .mdp from the one you show (-o xxx.mdp), then look at the set FFT or xyz grid spacing and play with it.  It dosent like odd numbers or non-whole decompositions which are based on the cpu's versus total size.
> fourierspacing           = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx               = 0
> fourier_ny               = 0
> fourier_nz               = 0
> I might have remembered the answer wrong though, but someone will correct me if I am wrong I hope.

Tweaking these settings may have a minor impact (and moreso on performance, I 
would think).  Decoupling an entire protein with explicit pair interactions and 
exclusions is going to dominate DD cell size, as there are very long-range 
interactions that are considered that normally are not.  There is no really easy 
way to get around a DD cell requirement upwards of 7 nm without changing 
methodology entirely.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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