[gmx-developers] Zero cell size
Roland Schulz
schulzr at ornl.gov
Mon Jul 21 23:23:27 CEST 2008
Hi,
now I get:
The maximum allowed number of cells is: X 0 Y 0 Z 5
Both with or without dlb. The system dimensions are the same in all three
dimensions.
With the old binary it still works without dlb.
I was using an old version of grompp but also with a current grompp I get
this error.
Could you send me your working tpr file? I would like to check whether it is
the input system our the different compilation/platform.
Because this is not only with this input
When I run the standard water tutor (without specifying -dd). I get
Optimizing the DD grid for 4 cells with a minimum initial size of 0.000 nm
Domain decomposition grid 4 x 0 x 0, separate PME nodes 0
with -dd 2 2 1
Making 2D domain decomposition 2 x 2 x 1
starting mdrun 'Pure Water'
10000 steps, 20.0 ps.
_pmii_daemon(SIGCHLD): PE 2 exit signal Segmentation fault
Roland
On Mon, Jul 21, 2008 at 11:50 AM, Berk Hess <hessb at mpip-mainz.mpg.de> wrote:
> 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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