[gmx-users] Domain decomposition configuration

[Denny Frost]

I'm using version 4.5.3

Here's the output from the log file from DD initiation to the error:

Initializing Domain Decomposition on 8 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
    two-body bonded interactions: 4.893 nm, Bond, atoms 8994 8996
  multi-body bonded interactions: 4.893 nm, Angle, atoms 8994 8997
Minimum cell size due to bonded interactions: 5.382 nm
Using 0 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size of 6.728 nm
The maximum allowed number of cells is: X 0 Y 0 Z 1

-------------------------------------------------------
Program mdrun_mpi, VERSION 4.5.3
Source code file: domdec.c, line: 6428

Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the
given box and a minimum cell size of 6.72787 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

And here is my mdp file

title               =  BMIM+PF6
cpp                 =  /lib/cpp
constraints         =  hbonds
integrator          =  md
dt                  =  0.002   ; ps !
nsteps              =  75000   ; total 150 ps
nstcomm             =  10
nstxout             =  50000
nstvout             =  50000
nstfout             =  0
nstlog              =  5000
nstenergy           =  5000
nstxtcout           =  25000
nstlist             =  10
ns_type             =  grid
pbc                 =  xyz
coulombtype         =  PME
vdwtype             =  Cut-off
rlist               =  1.2
rcoulomb            =  1.2
rvdw                =  1.2
fourierspacing      =  0.12
pme_order           =  4
ewald_rtol          =  1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc_grps             =  BMI      PF6     SOL
tau_t               =  0.2  0.2  0.2
ref_t               =  300  300  300
nsttcouple          =  1
; Energy monitoring
energygrps          =  BMI      PF6     SOL
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
pcoupltype          =  isotropic
;pc-grps             =  BMI      PFF
tau_p               =  2.0
ref_p               =  1.0
compressibility     =  4.5e-5

; Generate velocites is off at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  100000


On Wed, Feb 9, 2011 at 1:39 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Denny Frost wrote:
>
>> I am trying to start a run using domain decomposition on a 5x5x10 nm box
>> with about 26,000 atoms in it.  I've tried running 8-16 pp nodes, but
>> gromacs always throws an error saying that there is no domain decomposition
>> compatible with this box and a minimum cell size of 6.728 nm.  I've tried
>> many values for -dds and a few dd vectors, but with no luck.  Does anyone
>> know to get domain decomposition working on a rectangular system like this?
>>
>>
> Not without significantly more information.  Please post:
>
> 1. Your Gromacs version
> 2. Any DD-related information that is printed to either the log file or
> stdout
> 3. Your .mdp file
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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