[gmx-developers] Zero cell size
Berk Hess
hessb at mpip-mainz.mpg.de
Mon Jul 21 17:50:43 CEST 2008
Hi,
There has been a bug like this about two weeks ago.
It has been fixed for some time.
But today I did a partial commit, which I only noticed now.
With the current CVS I can run a system similar to yours
with the same options.
Could you try CVS update and recompile and run again?
Berk.
Roland Schulz wrote:
> 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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