Jennifer Williams wrote:
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).
How many atoms in what size simulation cell? What are your v-sites?
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?
My random guess is that there's a single problem with the interaction
of parallel DD, PBC, vsites, periodic molecules and/or constraints. Berk did
fix a bug earlier this month whose git commit description is
"fixed v-site pbc bug with charge groups consisting ofonly multiple v-sites"
but I do not know if this is at all applicable.
Compiling the git release-4-0-patches branch and trying to run with that
may help.
See bottom of text also.
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
More output should follow here, to wit, a list of missing bonded
interactions. It might also be in the stderr from the calculation. Is there any?
Mark
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