[gmx-developers] Zero cell size
Roland Schulz
schulzr at ornl.gov
Mon Jul 21 16:48:34 CEST 2008
Hi,
I get the error:
Fatal error:
Step 0: The X-size (0.000000) times the triclinic skew factor (1.000000) is
smaller than the smallest allowed cell size (1.200000) for domain
decomposition grid cell 0 0 0
I don't quite understand the initialization of cell_x1, cell_x0, thus have
problems to find out the cause.
This is with RF and mdrun options -nosum -dlb
I tested both revision 1.145 and 1.148 of domdec.c. (all other files today
version) Thus it is not the recent fatal-fix or 2d PME preparation.
The simulation runs find without dlb.
Where should I start looking why the size is 0?
The below md.log file is for 1M atoms and 256 cores but it crashes the same
with a subsystem of 4200 atoms and 16 cores.
Thanks
Roland
the md.log:
parameters of the run:
integrator = md
nsteps = 1000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 0
comm_mode = Linear
nstcheckpoint = 1000
nstlog = 0
nstxout = 0
nstvout = 0
nstfout = 0
nstenergy = 0
nstxtcout = 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 72
nky = 72
nkz = 72
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = No
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 = 1.2
rtpi = 0.05
coulombtype = Reaction-Field
rcoulomb_switch = 0
rcoulomb = 1.2
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.2
epsilon_r = 1
epsilon_rf = 78
tabext = 1
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 = No
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_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 0
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 100
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 1e-04
lincs_order = 8
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: 2.16e+06
ref_t: 0
tau_t: 0
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0 0
energygrp_flags[ 1]: 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 256 nodes
Will use dynamic load balancing
Will sort the charge groups at every domain (re)decomposition
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 256 cells with a minimum initial size of 0.750 nm
The maximum allowed number of cells is: X 24 Y 24 Z 37
Domain decomposition grid 8 x 4 x 8, separate PME nodes 0
Domain decomposition nodeid 0, coordinates 0 0 0
Using two step summing over 64 groups of on average 4.0 processes
There are 0 dihedral restraints
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
Reaction-Field:
epsRF = 78, rc = 1.2, krf = 0.283823, crf = 1.24204, epsfac = 138.935
The electrostatics potential has its minimum at r = 1.20774
System total charge: -0.000
Generated table with 1100 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Enabling SPC water optimization for 240000 molecules.
Configuring nonbonded kernels...
Testing x86_64 SSE support... present.
Removing pbc first time
Done rmpbc
Initializing LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------
The number of constraints is 144000
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
Linking all bonded interactions to atoms
There are 1092000 inter charge-group exclusions,
will use an extra communication step for exclusion forces for Reaction-Field
The maximum number of communication pulses is: X 1 Y 1 Z 1
The minimum size for domain decomposition cells is 1.200 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.52 Y 0.26 Z 0.34
The maximum allowed distance for atoms involved in interactions is:
two-body bonded interactions (-rdd) 1.200 nm
multi-body bonded interactions (-rdd) 1.200 nm
Making 3D domain decomposition grid 8 x 4 x 8, home cell index 0 0 0
Will not sum the energies at every step,
therefore the energy file does not contain exact averages and fluctuations.
WARNING:
Because of the no energy summing option setting nstcomm (was 0) to nstlist
(10)
There are: 1008000 Atoms
Charge group distribution at step 0: 1262 1274 1251 1282 1277 1242 1289 1260
1264 1271 1277 1274 1249 1285 1263 1263 1261 1274 1250 1281 1277 1240 1289
1259 1265 1271 1278 1275 1249 1287 1263 1264 1292 1267 1299 1275 1277 1301
1265 1284 1251 1283 1269 1272 1280 1270 1265 1289 1292 1267 1299 1275 1277
1301 1265 1284 1251 1283 1269 1272 1280 1270 1265 1289 1239 1263 1266 1234
1250 1265 1240 1257 1282 1252 1277 1264 1266 1281 1260 1255 1239 1263 1266
1234 1250 1265 1240 1257 1282 1252 1277 1264 1266 1281 1260 1255 1249 1279
1263 1254 1275 1255 1272 1272 1254 1252 1246 1245 1263 1236 1252 1260 1249
1279 1262 1254 1275 1254 1272 1271 1254 1252 1247 1245 1263 1237 1252 1261
1262 1274 1251 1282 1277 1242 1289 1260 1264 1271 1277 1274 1249 1285 1263
1263 1261 1274 1250 1281 1277 1240 1289 1259 1265 1271 1278 1275 1249 1287
1263 1264 1291 1267 1299 1274 1277 1301 1264 1284 1251 1283 1269 1272 1280
1270 1265 1289 1291 1267 1299 1274 1277 1301 1264 1284 1251 1283 1269 1272
1280 1270 1265 1289 1240 1263 1266 1235 1250 1265 1241 1257 1282 1252 1277
1264 1266 1281 1260 1255 1240 1263 1266 1235 1250 1265 1241 1257 1282 1252
1277 1264 1266 1281 1260 1255 1249 1279 1263 1254 1275 1255 1272 1272 1254
1252 1246 1245 1263 1236 1252 1260 1249 1279 1262 1254 1275 1254 1272 1271
1254 1252 1247 1245 1263 1237 1252 1261
-------------------------------------------------------
Program mdrun, VERSION 3.3.99_development_20080718
Source code file: domdec.c, line: 2220
Fatal error:
Step 0: The X-size (0.000000) times the triclinic skew factor (1.000000) is
smaller than the smallest allowed cell size (1.200000) for domain
decomposition grid cell 0 0 0
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
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