[gmx-users] No domain decomposition

[Tsjerk Wassenaar]

Hi Soumadwip,

The output says:

The maximum allowed number of cells is: X 2 Y 2 Z 8

That means you can't go beyond -nt 8
Your system is too small for more.

Hope it helps,

Tsjerk

On Thu, Sep 24, 2015 at 12:28 PM, soumadwip ghosh <soumadwipghosh at gmail.com>
wrote:

> Please ignore the previous mail.
>
> Hi all,
>        I am simulating a swCNT-ssDNA hybrid ( dna encapsulated in CNT) in
> the presence of some organic fillers. I made the topologies using pdb2gmx
> and until the energy minimization mdrun step everything was fine. I used
> the following command to for energy minimization
>
> mdrun -deffnm em and I was stuck with the following error
>
> There is no domain decomposition for 56 nodes that is compatible with the
> given box and a minimum cell size of 3.60353 nm
> Change the number of nodes or mdrun option -rdd
>
> Although I have seen a lot of discussions on this topic in the forum I did
> not get the probable solution. I am using GROMACS 4.5.6 and the water model
> employed is SPCE. Is there a possibility that my system topology is bad and
> that is getting reflected here or by changing the no. of nodes or the -rdd
> option the error can be tackled?
>
> I am attaching my minim.mdp file here followed by the em.log file created.
>
> minim.mdp
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator      = steep         ; Algorithm (steep = steepest descent
> minimization)
> emtol           = 1000.0        ; Stop minimization when the maximum force
> < 1000.0 kJ/mol/nm
> emstep          = 0.001          ; Energy step size
> nsteps          = 50000         ; Maximum number of (minimization) steps to
> perform
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist         = 1             ; Frequency to update the neighbor list and
> long range forces
> ns_type         = grid          ; Method to determine neighbor list
> (simple, grid)
> rlist           = 1.0           ; Cut-off for making neighbor list (short
> range forces)
> coulombtype     = PME           ; Treatment of long range electrostatic
> interactions
> rcoulomb        = 1.0           ; Short-range electrostatic cut-off
> rvdw            = 1.0           ; Short-range Van der Waals cut-off
> pbc             = xyz           ; Periodic Boundary Conditions (yes/no)
>
>
> and the em.log file (last few lines) as follows-
>
> Initializing Domain Decomposition on 80 nodes
> Dynamic load balancing: no
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
>     two-body bonded interactions: 3.276 nm, LJ-14, atoms 1550 1554
>   multi-body bonded interactions: 3.276 nm, Proper Dih., atoms 1550 1554
> Minimum cell size due to bonded interactions: 3.604 nm
> Guess for relative PME load: 0.31
> Will use 56 particle-particle and 24 PME only nodes
> This is a guess, check the performance at the end of the log file
> Using 24 separate PME nodes, as guessed by mdrun
> Optimizing the DD grid for 56 cells with a minimum initial size of 3.604 nm
> The maximum allowed number of cells is: X 2 Y 2 Z 2
>
> I would appreciate any kind of help. In these cases do switching to a
> higher version of GROMACS or take the help of MPI be helpful? I am sorry if
> I am saying something stupid. I tried playing around with options such as
> -nt, -npme and all but this error is still popping up.
> Thanks for your time in advance.
>
> Soumadwip Ghosh
> Research Fellow
> IITB
> Mumbai
> India
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-- 
Tsjerk A. Wassenaar, Ph.D.