[gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group

Mark Abraham Mark.Abraham at anu.edu.au
Mon Dec 27 00:17:33 CET 2010


On 27/12/2010 9:22 AM, WU Yanbin wrote:
> Hi, Mark,
>
> Thanks for the reply.
>
> As suggested, I tried a "water in vacuum" case. Initially the water 
> droplet is a cubic 4nm-by-4nm-by-4nm water box, located in the middle 
> of the simulation box. Everywhere else is just vacuum. The simulation 
> box size is 8nm by 8nm by 8nm. SPC/E model is used to describe 
> interaction between water molecules.
>
> Such system is first equilibrated with "steep" option.
>
> The "mdrun" simulation goes with no problem with parallel running on 
> 32 cpus, even though there are occasionaly one or two water molecules 
> move very fast (Mean square displacement being 200 times fast than 
> bulk water) in the vacuum.

OK, that sounds like behaviour that might be expected... some molecules 
evaporate. Check the trajectory to be confident this is the situation.

>
> When I switch to 64 cpus, the error "X particles communicated to PME 
> node Y are more than a cell length out of the domain decomposition 
> cell of their charge group" appears.

The most plausible reason for this is that the above evaporated 
molecules are moving so fast that they're doing what the error message 
says - travelling more than width of a box in one integration step. The 
DD implementation is predicated on that being impossible.

You might succeed by arranging for the largest possible internal DD cell 
diameter, i.e. a 4x4x4 DD. mdrun -npme 0 might choose this, otherwise 
use the hidden options to mdrun (use mdrun -hidden) to use that DD with 
-npme 0.

Otherwise, you'll need to accept the fact that there are "engineering" 
constraints on efficient parallelization algorithms, and not every 
situation can be catered for. For example, a simulation of a bulk LJ 
fluid would fail if you used so many processors that the cell diameter 
was too small with respect to the distribution of particle speeds.

Mark

>
> Below is the parameter file I'm using.
>
> ------------------------------------
> integrator               = md
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 5000000
>
> comm-mode                = Linear
> nstcomm                  = 1
> comm-grps                =
>
> energygrps               =
>
> nstlist                  = 1
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.5
>
> coulombtype              = PME
> rcoulomb-switch          = 0
> rcoulomb                 = 1.5
> epsilon-r                = 1
>
> vdw-type                 = Cut-off ;Switch
> rvdw-switch              = 1.0
> rvdw                     = 1.5
>
> fourierspacing           = 0.12
> fourier_nx               = 0
> fourier_ny               = 0
> fourier_nz               = 0
> pme_order                = 4
> ewald_rtol               = 1e-05
> ewald_geometry           = 3d
> epsilon_surface          = 0
> optimize_fft             = no
>
> Tcoupl                   = nose-hoover
> tc-grps                  = System
> tau_t                    = 1.0
> ref_t                    = 300
>
> Pcoupl                   = no ;Parrinello-Rahman ;no ;berendsen
> Pcoupltype               = isotropic
> tau_p                    = 1.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
>
> gen_vel                  = no
> gen_temp                 = 300
> gen_seed                 = 2008
>
> constraints              = none
> constraint-algorithm     = Lincs
> Shake-SOR                = no
> shake-tol                = 1e-04
> lincs-order              = 4
> lincs-warnangle          = 30
>
> energygrp_excl           =
> ------------------------------------
>
> Is there any parameters configuration wrong with the simulation? Or is 
> there any way to go around this error?
>
> Any tip is appreciated.
> Thank you.
>
> Best,
> Yanbin
>
>
>
>
>
>     ----------------------------------------------------------------------
>
>     Message: 1
>     Date: Thu, 02 Dec 2010 17:24:18 +1100
>     From: Mark Abraham <Mark.Abraham at anu.edu.au
>     <mailto:Mark.Abraham at anu.edu.au>>
>     Subject: Re: [gmx-users] How to suppress the error "X particles
>            communicated    to PME node Y are more than a cell length
>     out of the
>            domain  decomposition cell of their charge group"
>     To: Discussion list for GROMACS users <gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>>
>     Message-ID: <4CF73B92.40003 at anu.edu.au
>     <mailto:4CF73B92.40003 at anu.edu.au>>
>     Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>     On 2/12/2010 4:16 PM, WU Yanbin wrote:
>     > Dear GMXers,
>     >
>     > I'm running a simulation of water contact angle measurement on
>     top of
>     > graphite surface.
>     > Initially a water cubic box is placed on two-layer graphite surface
>     > with the rest of the box being vacuum. The water droplet is relaxed
>     > during the simulation to develop a spherical shape.
>     >
>     > An error of "X particles communicated to PME node Y are more than a
>     > cell length out of the domain decomposition cell of their charge
>     > group" was encountered.
>     > And I have read the suggested solutions at the link below
>     >
>     http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group.
>     >
>     > I guess the reason for this error in my case is because of the
>     vacuum
>     > such that the water molecules at the boundary of the droplet can
>     move
>     > fast. I have check the trajectory and the simulation is OK.
>
>     I doubt the simulation is OK. This error message is one of several
>     that
>     can happen when the system is not well-enough conditioned for the
>     MD to
>     be stable. See
>     www.gromacs.org/Documentation/Terminology/Blowing_Up
>     <http://www.gromacs.org/Documentation/Terminology/Blowing_Up>.
>     Here, you have atoms moving much faster than GROMACS was engineered to
>     expect.
>
>     You should be confident that a water drop in a vacuum, and your
>     graphite
>     surface are both stable on their own before you try the wetting
>     simulation.
>
>     >
>     > For this situation, is there a way of suppressing this error? Or
>     what
>     > else can I do?
>
>     Work out why it's poorly conditioned.
>
>     Mark
>

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