[gmx-users] RE: shake block problem

[Jianhui Tian]

> Hi GMX-Users,
>
> Does anyone have any idea about the problem? Thanks a lot in advance.
>
> I got an error message when using gromacs on 2 processors on the same
> computer.
> The error message is like this:
> _________________________________________________________________
> splitting topology...
> Walking down the molecule graph to make shake-blocks
> There are 24390 charge group borders and 26054 shake borders
> There are 24390 total borders
> Division over nodes in atoms:
>   21234   21234
> -------------------------------------------------------
> Program grompp_d, VERSION 3.3
> Source code file: splitter.c, line: 121
>
> Fatal error:
> Shake block crossing node boundaries
> constraint between atoms (21226,21234)
> -------------------------------------------------------
> ________________________________________________________________
> I used h-bonds constraints.  I tried not
> to without constraints and the system can be ran on 2 processors well,
> but the time-step is small then.
>
please submit a bugzilla and upload your input files (top, gro, mdp).

Hi David,

There are the mdp file and the errors in the following:
The mdp file:
_________________________________________________________________
title                    = ps md at 300 K, 1 bar
cpp                      = /lib/cpp
include                  = -I../top
define                   =
integrator               = md
tinit                    = 0.0
dt                       = 0.001
nsteps                   = 50000
nstxout                  = 500
nstvout                  = 500
nstlog                   = 500
nstenergy                = 500
energygrps               = AOTs Cores ICTs
nstlist                  = 1
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.0
coulombtype              = pme
rcoulomb                 = 1.0
vdwtype                  = Cut-off
rvdw                     = 1.0
DispCorr                 = no
tcoupl                   = Berendsen
tc_grps                  = AOTs Cores ICTs
tau_t                    = 0.5  0.5  0.5
ref_t                    = 300.0   300.0 300.0
pcoupl                   = berendsen
pcoupltype               = isotropic
tau_p                    = 0.5
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = no
constraints              = h-bonds
constraint_algorithm     = shake
____________________________________________________
Errors:
_________________________________________________________________
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 72x72x72, spacing 0.119 0.119 0.119
splitting topology...
Walking down the molecule graph to make shake-blocks
There are 24210 charge group borders and 25874 shake borders
There are 24210 total borders
Division over nodes in atoms:
   21078   21078
-------------------------------------------------------
Program grompp_d, VERSION 3.3
Source code file: splitter.c, line: 121

Fatal error:
Shake block crossing node boundaries
constraint between atoms (21070,21078)
-------------------------------------------------------

"You Think That You're Bigger When You Fill the Void" (Urban Dance Squad)

NNODES=2, MYRANK=0, HOSTNAME=compute-3-15.local
NNODES=2, MYRANK=1, HOSTNAME=compute-3-15.local
NODEID=1 argc=11
NODEID=0 argc=11
_____________
_________________________________________________________________