[gmx-users] Error There is no domain decomposition for 6 nodes that is compatible
lloyd.riggs at gmx.ch
Fri Oct 5 11:35:18 CEST 2012
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.
PS, are you from LA. Just asking I used to know someone with the exact same name, but I also vaguely remember seeing your name here and asking that once before...
> I am performing a free energy calculation based on Justin Lemkul's
> My system is a protein in water and dodecane and I'm coupling the protein
> considering none to only vdw interactions for my lambda 0 and 1 states.
> However, I get this error when trying to minimize the system:
> Fatal error:
> There is no domain decomposition for 6 nodes that is compatible with the
> given box and a minimum cell size of 7.55833 nm min1.0.mdp
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition
> I know I can fix easily this problem by using -nt 1 option. But I still
> to use all available cores. I suspect the error is in the mdp file because
> if I use the following mdp file for the minimization it works.
> title = cpeptide
> cpp = /usr/bin/cpp
> define = -DFLEX_SPC
> constraints = none
> integrator = steep
> dt = 0.002 ; ps !
> nsteps = 1000
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> rcoulomb = 1.0
> rvdw = 1.0
> ; Energy minimizing stuff
> emtol = 1000.0
> emstep = 0.01
> Obviously this mdp file does not work for free energy calculations. I
> want to use the attached one, but I don´t know what to change to make it
> This is the link for my log and mdp file.
> Thank you in advance,
> Sonia Aguilera
> Graduate Assistant
> Universidad de los Andes-Colombia
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