[gmx-users] Domain decomposition configuration

[Justin A. Lemkul]

Denny Frost wrote:
> 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

Bonded interactions should normally not occur over such a length.  The 
information printed here points to the culprits.  What are these atoms, and why 
are they bonded if they are so far away?

-Justin

> 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 
> <mailto: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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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-- 
========================================

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

========================================