[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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