Hi ,
I am getting the following error when I try to run in parallel (I've
tried with 8 and 2 nodes and get the same).
Not all bonded interactions have been properly assigned to the domain
decomposition cells
But my simulation works when I run in serial.
I'm using gromacs 4.0.5. I am working on a mesoprous silica which I
define as a single residue (each atom is assigned to a single charge
group).
I've tried changing table_ext in the .mdp file (I first increased it
to 2.5 and then 30) following advice on previous forum posts but I
still get the same thing.
Does anyone know why this is happening and how I can fix this? I could
run in serial but it would take too long.
I also get a NOTE: Periodic molecules: can not easily determine the
required minimum bonded cut-off, using half the non-bonded cut-off
Is this part of the same problem or a different thing altogether?
I've pasted my md.log file below
Thanks
010/AP_ready> more md.log
Log file opened on Tue Oct 27 13:31:44 2009
Host: vlxbig20.see.ed.ac.uk pid: 6930 nodeid: 0 nnodes: 8
The Gromacs distribution was built Tue Jul 21 13:18:34 BST 2009 by
parameters of the run:
integrator = md
nsteps = 5000000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 0
comm_mode = None
nstlog = 1000
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstenergy = 1000
nstxtcout = 1000
init_t = 0
delta_t = 0.001
xtcprec = 1000
nkx = 39
nky = 39
nkz = 64
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols = TRUE
bContinuation = FALSE
bShakeSOR = FALSE
etc = Nose-Hoover
epc = No
epctype = Isotropic
tau_p = 1
ref_p (3x3):
ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress (3x3):
compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.00000e+00
posres_com[1]= 0.00000e+00
posres_com[2]= 0.00000e+00
posres_comB (3):
posres_comB[0]= 0.00000e+00
posres_comB[1]= 0.00000e+00
posres_comB[2]= 0.00000e+00
andersen_seed = 815131
rlist = 1.5
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.5
vdwtype = Shift
rvdw_switch = 1.2
rvdw = 1.5
epsilon_r = 1
epsilon_rf = 1
tabext = 2.5
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = EnerPres
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall = 0
wall_type = 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre = No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 5392
ref_t: 300
tau_t: 0.1
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: Y Y Y N
N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Initializing Domain Decomposition on 8 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
NOTE: Periodic molecules: can not easily determine the required
minimum bonded cut-off, using half the non-bonded cut-off
Minimum cell size due to bonded interactions: 0.750 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.376 nm
Estimated maximum distance required for P-LINCS: 0.376 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 0.938 nm
The maximum allowed number of cells is: X 4 Y 4 Z 8
Domain decomposition grid 2 x 1 x 4, separate PME nodes 0
Domain decomposition nodeid 0, coordinates 0 0 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw: TRUE
Will do PME sum in reciprocal space.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------
Using a Gaussian width (1/beta) of 0.480244 nm for Ewald
Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
Cut-off's: NS: 1.5 Coulomb: 1.5 LJ: 1.2
System total charge: 0.000
Generated table with 2000 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 2000 data points for LJ6Shift.
Tabscale = 500 points/nm
Generated table with 2000 data points for LJ12Shift.
Tabscale = 500 points/nm
Generated table with 2000 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 2000 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 2000 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Configuring nonbonded kernels...
Testing x86_64 SSE support... present.
Initializing Parallel LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 116-122
-------- -------- --- Thank You --- -------- --------
The number of constraints is 800
There are inter charge-group constraints,
will communicate selected coordinates each lincs iteration
Linking all bonded interactions to atoms
There are 3236 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME
The initial number of communication pulses is: X 1 Z 1
The initial domain decomposition cell size is: X 2.01 nm Z 1.90 nm
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.500 nm
two-body bonded interactions (-rdd) 1.500 nm
multi-body bonded interactions (-rdd) 1.500 nm
atoms separated by up to 5 constraints (-rcon) 1.896 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Z 1
The minimum size for domain decomposition cells is 1.500 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.75 Z 0.79
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.500 nm
two-body bonded interactions (-rdd) 1.500 nm
multi-body bonded interactions (-rdd) 1.500 nm
atoms separated by up to 5 constraints (-rcon) 1.500 nm
Making 2D domain decomposition grid 2 x 1 x 4, home cell index 0 0 0
There are: 5244 Atoms
There are: 476 VSites
Charge group distribution at step 0: 583 565 583 565 666 684 666 684
Grid: 9 x 6 x 6 cells
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
Not all bonded interactions have been properly assigned to the domain
decomposition cells
Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
Sanderson Building
The King's Buildings
Mayfield Road
Edinburgh, EH9 3JL, United Kingdom
Phone: ++44 (0)131 650 4 861
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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