very early blowing_up

[zhouchaojie]

here are the output ,I have checked the depth, there are no 0 or negative value, I am a new user of the roms, it makes me confused now.....
Resolution, Grid 01: 0198x0098x020, Parallel Threads: 1, Tiling: 001x001


Physical Parameters, Grid: 01
=============================

1235520 ntimes Number of timesteps for 3-D equations.
100.000 dt Timestep size (s) for 3-D equations.
30 ndtfast Number of timesteps for 2-D equations between
each 3D timestep.
1 ERstr Starting ensemble/perturbation run number.
1 ERend Ending ensemble/perturbation run number.
0 nrrec Number of restart records to read from disk.
T LcycleRST Switch to recycle time-records in restart file.
155520 nRST Number of timesteps between the writing of data
into restart fields.
1 ninfo Number of timesteps between print of information
to standard output.
T ldefout Switch to create a new output NetCDF file(s).
8640 nHIS Number of timesteps between the writing fields
into history file.
311040 ndefHIS Number of timesteps between creation of new
history files.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
25920 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
311040 ndefAVG Number of timesteps between creation of new
time-averaged file.
1 ntsDIA Starting timestep for the accumulation of output
time-averaged diagnostics data.
25920 nDIA Number of timesteps between the writing of
time-averaged data into diagnostics file.
311040 ndefDIA Number of timesteps between creation of new
diagnostic file.
1.0000E+01 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
1.0000E+01 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
1.0000E+01 nl_visc2 NLM Horizontal, harmonic mixing coefficient
(m2/s) for momentum.
F LuvSponge Turning OFF sponge on horizontal momentum.
F LtracerSponge(01) Turning OFF sponge on tracer 01: temp
F LtracerSponge(02) Turning OFF sponge on tracer 02: salt
1.0000E-06 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
1.0000E-06 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: salt
1.0000E-05 Akv_bak Background vertical mixing coefficient (m2/s)
for momentum.
3.0000E-04 rdrg Linear bottom drag coefficient (m/s).
3.0000E-03 rdrg2 Quadratic bottom drag coefficient.
2.0000E-02 Zob Bottom roughness (m).
2 Vtransform S-coordinate transformation equation.
2 Vstretching S-coordinate stretching function.
5.0000E+00 theta_s S-coordinate surface control parameter.
4.0000E-01 theta_b S-coordinate bottom control parameter.
5.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1025.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
0.000 dstart Time-stamp assigned to model initialization (days).
20050101.00 time_ref Reference time for units attribute (yyyymmdd.dd)
0.0000E+00 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
0.0000E+00 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
0.0000E+00 Znudg Nudging/relaxation time scale (days)
for free-surface.
0.0000E+00 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
0.0000E+00 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
0.0000E+00 obcfac Factor between passive and active
open boundary conditions.
F VolCons(1) NLM western edge boundary volume conservation.
F VolCons(2) NLM southern edge boundary volume conservation.
F VolCons(3) NLM eastern edge boundary volume conservation.
F VolCons(4) NLM northern edge boundary volume conservation.
14.000 T0 Background potential temperature (C) constant.
35.000 S0 Background salinity (PSU) constant.
1027.000 R0 Background density (kg/m3) used in linear Equation
of State.
1.7000E-04 Tcoef Thermal expansion coefficient (1/Celsius).
0.0000E+00 Scoef Saline contraction coefficient (1/PSU).
1.000 gamma2 Slipperiness variable: free-slip (1.0) or
no-slip (-1.0).
F LuvSrc Turning OFF momentum point Sources/Sinks.
F LwSrc Turning OFF volume influx point Sources/Sinks.
F LtracerSrc(01) Turning OFF point Sources/Sinks on tracer 01: temp
F LtracerSrc(02) Turning OFF point Sources/Sinks on tracer 02: salt
F LsshCLM Turning OFF processing of SSH climatology.
F Lm2CLM Turning OFF processing of 2D momentum climatology.
F Lm3CLM Turning OFF processing of 3D momentum climatology.
F LtracerCLM(01) Turning OFF processing of climatology tracer 01: temp
F LtracerCLM(02) Turning OFF processing of climatology tracer 02: salt
F LnudgeM2CLM Turning OFF nudging of 2D momentum climatology.
F LnudgeM3CLM Turning OFF nudging of 3D momentum climatology.
F LnudgeTCLM(01) Turning OFF nudging of climatology tracer 01: temp
F LnudgeTCLM(02) Turning OFF nudging of climatology tracer 02: salt
T Hout(idFsur) Write out free-surface.
T Hout(idUbar) Write out 2D U-momentum component.
T Hout(idVbar) Write out 2D V-momentum component.
T Hout(idUvel) Write out 3D U-momentum component.
T Hout(idVvel) Write out 3D V-momentum component.
T Hout(idWvel) Write out W-momentum component.
T Hout(idOvel) Write out omega vertical velocity.
T Hout(idTvar) Write out tracer 01: temp
T Hout(idTvar) Write out tracer 02: salt

T Aout(idFsur) Write out averaged free-surface.
T Aout(idUbar) Write out averaged 2D U-momentum component.
T Aout(idVbar) Write out averaged 2D V-momentum component.
T Aout(idUvel) Write out averaged 3D U-momentum component.
T Aout(idVvel) Write out averaged 3D V-momentum component.
T Aout(idWvel) Write out averaged W-momentum component.
T Aout(idOvel) Write out averaged omega vertical velocity.
T Aout(idTvar) Write out averaged tracer 01: temp
T Aout(idTvar) Write out averaged tracer 02: salt

T Dout(M2rate) Write out 2D momentum acceleration.
T Dout(M2pgrd) Write out 2D momentum pressure gradient.
T Dout(M2fcor) Write out 2D momentum Coriolis force.
T Dout(M2hadv) Write out 2D momentum horizontal advection.
T Dout(M2xadv) Write out 2D momentum horizontal X-advection.
T Dout(M2yadv) Write out 2D momentum horizontal Y-advection.
T Dout(M2hvis) Write out 2D momentum horizontal viscosity.
T Dout(M2xvis) Write out 2D momentum horizontal X-viscosity.
T Dout(M2yvis) Write out 2D momentum horizontal Y-viscosity.
T Dout(M2sstr) Write out 2D momentum surface stress.
T Dout(M2bstr) Write out 2D momentum bottom stress.

T Dout(M3rate) Write out 3D momentum acceleration.
T Dout(M3pgrd) Write out 3D momentum pressure gradient.
T Dout(M3fcor) Write out 3D momentum Coriolis force.
T Dout(M3hadv) Write out 3D momentum horizontal advection.
T Dout(M3xadv) Write out 3D momentum horizontal X-advection.
T Dout(M3yadv) Write out 3D momentum horizontal Y-advection.
T Dout(M3vadv) Write out 3D momentum vertical advection.
T Dout(M3hvis) Write out 3D momentum horizontal viscosity.
T Dout(M3xvis) Write out 3D momentum horizontal X-viscosity.
T Dout(M3yvis) Write out 3D momentum horizontal Y-viscosity.
T Dout(M3vvis) Write out 3D momentum vertical viscosity.

T Dout(iTrate) Write out rate of change of tracer 01: temp
T Dout(iTrate) Write out rate of change of tracer 02: salt
T Dout(iThadv) Write out horizontal advection, tracer 01: temp
T Dout(iThadv) Write out horizontal advection, tracer 02: salt
T Dout(iTxadv) Write out horizontal X-advection, tracer 01: temp
T Dout(iTxadv) Write out horizontal X-advection, tracer 02: salt
T Dout(iTyadv) Write out horizontal Y-advection, tracer 01: temp
T Dout(iTyadv) Write out horizontal Y-advection, tracer 02: salt
T Dout(iTvadv) Write out vertical advection, tracer 01: temp
T Dout(iTvadv) Write out vertical advection, tracer 02: salt
T Dout(iThdif) Write out horizontal diffusion, tracer 01: temp
T Dout(iThdif) Write out horizontal diffusion, tracer 02: salt
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 01: temp
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 02: salt
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 01: temp
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 02: salt
T Dout(iTvdif) Write out vertical diffusion, tracer 01: temp
T Dout(iTvdif) Write out vertical diffusion, tracer 02: salt

Output/Input Files:

Output Restart File: /public/home/wanglong/Projects/CHS/test/result/CHS_rst.nc
Prefix for History Files: /public/home/wanglong/Projects/CHS/test/result/CHS_his
Prefix for Averages Files: /public/home/wanglong/Projects/CHS/test/result/CHS_avg
Prefix for Diagnostics Files: /public/home/wanglong/Projects/CHS/test/result/CHS_dia
Input Grid File: /public/home/wanglong/Projects/CHS/test/chsouth_grid.nc
Input Nonlinear Initial File: /public/home/wanglong/Projects/CHS/test/chsouth_initial.nc
Input Boundary File: /public/home/wanglong/Projects/CHS/test/chsouth_boundary.nc

Tile partition information for Grid 01: 0198x0098x0020 tiling: 001x001

tile Istr Iend Jstr Jend Npts

0 1 198 1 98 388080

Tile minimum and maximum fractional coordinates for Grid 01:
(interior points only)

tile Xmin Xmax Ymin Ymax grid

0 0.50 199.50 0.50 99.50 RHO-points

0 0.00 199.00 0.50 99.50 U-points

0 0.50 199.50 0.00 99.00 V-points

Lateral Boundary Conditions: NLM
============================

Variable Grid West Edge South Edge East Edge North Edge
--------- ---- ---------- ---------- ---------- ----------

zeta 1 Closed Chapman Imp Chapman Imp Closed

ubar 1 Closed Flather Flather Closed

vbar 1 Closed Flather Flather Closed

u 1 Closed Rad + Nud Rad + Nud Closed

v 1 Closed Rad + Nud Rad + Nud Closed

temp 1 Closed Rad + Nud Rad + Nud Closed

salt 1 Closed Rad + Nud Rad + Nud Closed

Activated C-preprocessing Options:

CHS China-South Sea Simulation
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_FSOBC Analytical free-surface boundary conditions.
ANA_M2OBC Analytical 2D momentum boundary conditions.
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_SSFLUX Analytical kinematic surface salinity flux.
ANA_STFLUX Analytical kinematic surface temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged nonlinear model fields.
DIAGNOSTICS_TS Computing and writing tracer diagnostic terms.
DIAGNOSTICS_UV Computing and writing momentum diagnostic terms.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
MIX_S_TS Mixing of tracers along constant S-surfaces.
MIX_S_UV Mixing of momentum along constant S-surfaces.
NONLINEAR Nonlinear Model.
!NONLIN_EOS Linear Equation of State for seawater.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
RADIATION_2D Use tangential phase speed in radiation conditions.
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SOLVE3D Solving 3D Primitive Equations.
SPLINES Conservative parabolic spline reconstruction.
TS_U3HADVECTION Third-order upstream horizontal advection of tracers.
TS_C4VADVECTION Fourth-order centered vertical advection of tracers.
TS_DIF2 Harmonic mixing of tracers.
UV_ADV Advection of momentum.
UV_COR Coriolis term.
UV_U3HADVECTION Third-order upstream horizontal advection of 3D momentum.
UV_C4VADVECTION Fourth-order centered vertical advection of momentum.
UV_LDRAG Linear bottom stress.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.

Process Information:

Thread # 0 (pid= 23154) is active.

INITIAL: Configuring and initializing forward nonlinear model ...
*******

Vertical S-coordinate System, Grid 01:

level S-coord Cs-curve Z at hmin at hc half way at hmax

20 0.0000000 0.0000000 0.000 0.000 0.000 0.000
19 -0.0500000 -0.0005591 -0.126 -0.126 -0.806 -1.365
18 -0.1000000 -0.0027709 -0.257 -0.257 -3.262 -6.027
17 -0.1500000 -0.0074493 -0.394 -0.394 -8.177 -15.610
16 -0.2000000 -0.0154245 -0.539 -0.539 -16.381 -31.770
15 -0.2500000 -0.0275411 -0.694 -0.694 -28.717 -56.192
14 -0.3000000 -0.0446548 -0.862 -0.862 -46.037 -90.583
13 -0.3500000 -0.0676257 -1.044 -1.044 -69.200 -136.660
12 -0.4000000 -0.0973060 -1.243 -1.243 -99.055 -196.122
11 -0.4500000 -0.1345207 -1.461 -1.461 -136.427 -270.615
10 -0.5000000 -0.1800368 -1.700 -1.700 -182.079 -361.669
9 -0.5500000 -0.2345153 -1.961 -1.961 -236.671 -470.604
8 -0.6000000 -0.2984398 -2.246 -2.246 -300.686 -598.384
7 -0.6500000 -0.3720103 -2.555 -2.555 -374.323 -745.407
6 -0.7000000 -0.4549887 -2.887 -2.887 -457.345 -911.199
5 -0.7500000 -0.5464743 -3.241 -3.241 -548.853 -1093.964
4 -0.8000000 -0.6445848 -3.611 -3.611 -646.970 -1289.945
3 -0.8500000 -0.7460014 -3.990 -3.990 -748.384 -1492.521
2 -0.9000000 -0.8453281 -4.363 -4.363 -847.713 -1690.929
1 -0.9500000 -0.9341941 -4.710 -4.710 -936.608 -1868.467
0 -1.0000000 -1.0000000 -5.000 -5.000 -1002.500 -2000.000

Time Splitting Weights for Grid 01: ndtfast = 30 nfast = 42
==================================

Primary Secondary Accumulated to Current Step

1-0.0008094437383769 0.0333333333333333-0.0008094437383769 0.0333333333333333
2-0.0014053566728197 0.0333603147912792-0.0022148004111966 0.0666936481246126
3-0.0017877524645903 0.0334071600137066-0.0040025528757869 0.1001008081383191
4-0.0019566842408176 0.0334667517625262-0.0059592371166046 0.1335675599008453
5-0.0019122901320372 0.0335319745705535-0.0078715272486418 0.1670995344713988
6-0.0016548570247459 0.0335957175749547-0.0095263842733877 0.2006952520463536
7-0.0011849025289723 0.0336508794757796-0.0107112868023600 0.2343461315221331
8-0.0005032751608631 0.0336903762267453-0.0112145619632232 0.2680365077488784
9 0.0003887272597151 0.0337071520654408-0.0108258347035081 0.3017436598143192
10 0.0014892209965583 0.0336941944901169-0.0093366137069498 0.3354378543044362
11 0.0027955815694920 0.0336445537902317-0.0065410321374578 0.3690824080946679
12 0.0043042707117221 0.0335513677379153-0.0022367614257356 0.4026337758325831
13 0.0060106451121704 0.0334078920475245 0.0037738836864348 0.4360416678801076
14 0.0079087469427945 0.0332075372104522 0.0116826306292293 0.4692492050905598
15 0.0099910761708920 0.0329439123123590 0.0216737068001213 0.5021931174029188
16 0.0122483446563884 0.0326108764399960 0.0339220514565097 0.5348039938429148
17 0.0146692120341107 0.0322025982847830 0.0485912634906204 0.5670065921276978
18 0.0172400033810439 0.0317136245503127 0.0658312668716643 0.5987202166780105
19 0.0199444086685725 0.0311389577709445 0.0857756755402368 0.6298591744489550
20 0.0227631639997064 0.0304741441486588 0.1085388395399432 0.6603333185976138
21 0.0256737146312911 0.0297153720153352 0.1342125541712342 0.6900486906129490
22 0.0286498597812016 0.0288595815276255 0.1628624139524359 0.7189082721405746
23 0.0316613792205220 0.0279045862015855 0.1945237931729578 0.7468128583421600
24 0.0346736416507075 0.0268492068942347 0.2291974348236653 0.7736620652363948
25 0.0376471948657328 0.0256934188392112 0.2668446296893981 0.7993554840756060
26 0.0405373376992232 0.0244385123436867 0.3073819673886213 0.8237939964192927
27 0.0432936737565710 0.0230872677537126 0.3506756411451924 0.8468812641730054
28 0.0458596469320356 0.0216441452951603 0.3965352880772280 0.8685254094681656
29 0.0481720587108284 0.0201154903974257 0.4447073467880565 0.8886408998655914
30 0.0501605672561820 0.0185097551070648 0.4948679140442384 0.9071506549726561
31 0.0517471682814030 0.0168377361985254 0.5466150823256415 0.9239883911711815
32 0.0528456577069106 0.0151128305891453 0.5994607400325521 0.9391012217603267
33 0.0533610761022577 0.0133513086655816 0.6528218161348098 0.9524525304259084
34 0.0531891349131379 0.0115726061288397 0.7060109510479478 0.9640251365547481
35 0.0522156244733761 0.0097996349650684 0.7582265755213239 0.9738247715198165
36 0.0503158038019030 0.0080591141492892 0.8085423793232269 0.9818838856691057
37 0.0473537721847153 0.0063819206892258 0.8558961515079423 0.9882658063583315
38 0.0431818225418188 0.0048034616164019 0.8990779740497611 0.9930692679747334
39 0.0376397765791564 0.0033640675316746 0.9367177506289175 0.9964333355064080
40 0.0305543017255206 0.0021094083123694 0.9672720523544381 0.9985427438187774
41 0.0217382098544504 0.0010909315881854 0.9890102622088885 0.9996336754069628
42 0.0109897377911118 0.0003663245930371 1.0000000000000004 0.9999999999999999

ndtfast, nfast = 30 42 nfast/ndtfast = 1.40000

Centers of gravity and integrals (values must be 1, 1, approx 1/2, 1, 1):

1.000000000000 1.047601458608 0.523800729304 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.18933

Metrics information for Grid 01:
===============================

Minimum X-grid spacing, DXmin = 1.93936657E+00 km
Maximum X-grid spacing, DXmax = 1.79412067E+01 km
Minimum Y-grid spacing, DYmin = 8.82198551E+00 km
Maximum Y-grid spacing, DYmax = 4.51487239E+01 km
Minimum Z-grid spacing, DZmin = 1.26397788E-01 m
Maximum Z-grid spacing, DZmax = 2.02576586E+02 m

Minimum barotropic Courant Number = 2.36319705E-03
Maximum barotropic Courant Number = 1.50161474E-01
Maximum Coriolis Courant Number = 6.00466551E-03


NLM: GET_STATE - Read state initial conditions, t = 0 00:00:00
(Grid 01, File: chsouth_initial.nc, Rec=0001, Index=1)
- free-surface
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- vertically integrated u-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- vertically integrated v-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- u-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- v-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- potential temperature
(Min = 2.14800000E+00 Max = 2.55639992E+01)
- salinity
(Min = 3.32639999E+01 Max = 3.47130013E+01)
GET_NGFLD - 3D u-momentum eastern boundary condition, t = 0 00:00:00
(Rec=0000001, Index=2, File: chsouth_boundary.nc)
(Tmin= 0.0000 Tmax= 1430.0000)
(Min = -1.91762894E-01 Max = 3.29111695E-01)
GET_NGFLD - 3D v-momentum eastern boundary condition, t = 0 00:00:00
(Rec=0000001, Index=2, File: chsouth_boundary.nc)
(Tmin= 0.0000 Tmax= 1430.0000)
(Min = -1.63401559E-01 Max = 3.10286045E-01)
GET_NGFLD - 3D u-momentum southern boundary condition, t = 0 00:00:00
(Rec=0000001, Index=2, File: chsouth_boundary.nc)
(Tmin= 0.0000 Tmax= 1430.0000)
(Min = -2.80825829E-04 Max = 2.94956088E-01)
GET_NGFLD - 3D v-momentum southern boundary condition, t = 0 00:00:00
(Rec=0000001, Index=2, File: chsouth_boundary.nc)
(Tmin= 0.0000 Tmax= 1430.0000)
(Min = -1.93699211E-01 Max = 7.04723597E-03)
GET_NGFLD - temperature eastern boundary condition, t = 0 00:00:00
(Rec=0000001, Index=2, File: chsouth_boundary.nc)
(Tmin= 0.0000 Tmax= 1430.0000)
(Min = 1.04921162E+00 Max = 2.58121376E+01)
GET_NGFLD - salinity eastern boundary condition, t = 0 00:00:00
(Rec=0000001, Index=2, File: chsouth_boundary.nc)
(Tmin= 0.0000 Tmax= 1430.0000)
(Min = 1.38241091E+01 Max = 3.46544914E+01)
GET_NGFLD - temperature southern boundary condition, t = 0 00:00:00
(Rec=0000001, Index=2, File: chsouth_boundary.nc)
(Tmin= 0.0000 Tmax= 1430.0000)
(Min = 0.00000000E+00 Max = 2.48827629E+01)
GET_NGFLD - salinity southern boundary condition, t = 0 00:00:00
(Rec=0000001, Index=2, File: chsouth_boundary.nc)
(Tmin= 0.0000 Tmax= 1430.0000)
(Min = 0.00000000E+00 Max = 3.45693321E+01)

Basin information for Grid 01:

Maximum grid stiffness ratios: rx0 = 8.101426E-01 (Beckmann and Haidvogel)
rx1 = 2.460969E+01 (Haney)

Initial basin volumes: TotVolume = 8.8292239712E+14 m3
MinVolume = 3.0220893296E+06 m3
MaxVolume = 2.6485366717E+10 m3
Max/Min = 8.7639258238E+03

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 01235520)

GET_NGFLD - 3D u-momentum eastern boundary condition, t = 31 00:00:00
(Rec=0000002, Index=1, File: chsouth_boundary.nc)
(Tmin= 0.0000 Tmax= 1430.0000)
(Min = -1.84981614E-01 Max = 1.40755355E-01)
GET_NGFLD - 3D v-momentum eastern boundary condition, t = 31 00:00:00
(Rec=0000002, Index=1, File: chsouth_boundary.nc)
(Tmin= 0.0000 Tmax= 1430.0000)
(Min = -1.15769587E-01 Max = 3.85912329E-01)
GET_NGFLD - 3D u-momentum southern boundary condition, t = 31 00:00:00
(Rec=0000002, Index=1, File: chsouth_boundary.nc)
(Tmin= 0.0000 Tmax= 1430.0000)
(Min = -1.98467728E-02 Max = 4.95366976E-02)
GET_NGFLD - 3D v-momentum southern boundary condition, t = 31 00:00:00
(Rec=0000002, Index=1, File: chsouth_boundary.nc)
(Tmin= 0.0000 Tmax= 1430.0000)
(Min = -1.76414698E-02 Max = 5.85185885E-02)
GET_NGFLD - temperature eastern boundary condition, t = 31 00:00:00
(Rec=0000002, Index=1, File: chsouth_boundary.nc)
(Tmin= 0.0000 Tmax= 1430.0000)
(Min = 1.05293703E+00 Max = 2.67493687E+01)
GET_NGFLD - salinity eastern boundary condition, t = 31 00:00:00
(Rec=0000002, Index=1, File: chsouth_boundary.nc)
(Tmin= 0.0000 Tmax= 1430.0000)
(Min = 1.38240118E+01 Max = 3.46413422E+01)
GET_NGFLD - temperature southern boundary condition, t = 31 00:00:00
(Rec=0000002, Index=1, File: chsouth_boundary.nc)
(Tmin= 0.0000 Tmax= 1430.0000)
(Min = 0.00000000E+00 Max = 2.58873386E+01)
GET_NGFLD - salinity southern boundary condition, t = 31 00:00:00
(Rec=0000002, Index=1, File: chsouth_boundary.nc)
(Tmin= 0.0000 Tmax= 1430.0000)
(Min = 0.00000000E+00 Max = 3.45682297E+01)

STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
C => (i,j,k) Cu Cv Cw Max Speed

0 0 00:00:00 0.000000E+00 8.478125E+03 8.478125E+03 8.829224E+14
(000,00,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS - creating history file, Grid 01: /public/home/wanglong/Projects/CHS/test/result/CHS_his_0001.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001
DEF_AVG - creating average file, Grid 01: /public/home/wanglong/Projects/CHS/test/result/CHS_avg_0001.nc
DEF_DIAGS - creating diagnostics file, Grid 01: /public/home/wanglong/Projects/CHS/test/result/CHS_dia_0001.nc
1 0 00:01:40 1.789299E-04 8.478029E+03 8.478029E+03 8.829224E+14
(100,96,01) 5.613402E-03 2.621833E-04 0.000000E+00 2.584277E-01
2 0 00:03:20 6.163918E-04 8.477838E+03 8.477839E+03 8.829227E+14
(184,51,20) 3.356748E-04 7.004853E-05 1.475031E+00 4.639972E-01
3 0 00:05:00 1.258552E-03 8.477614E+03 8.477615E+03 8.829237E+14
(185,48,20) 6.803756E-04 1.405660E-05 1.563733E+00 6.647432E-01
4 0 00:06:40 2.089459E-03 8.477373E+03 8.477375E+03 8.829252E+14
(186,48,20) 2.235542E-03 1.093114E-06 1.944758E+00 8.599670E-01
5 0 00:08:20 3.111652E-03 8.477134E+03 8.477138E+03 8.829271E+14
(187,48,20) 4.374491E-03 1.008752E-05 2.328212E+00 1.053392E+00
6 0 00:10:00 4.330676E-03 8.476909E+03 8.476914E+03 8.829294E+14
(190,46,20) 1.044480E-03 1.391924E-03 2.925310E+00 1.251163E+00
7 0 00:11:40 5.750702E-03 8.476699E+03 8.476704E+03 8.829320E+14
(189,49,20) 5.948986E-04 1.354592E-03 3.334080E+00 1.449143E+00
8 0 00:13:20 7.382219E-03 8.476502E+03 8.476510E+03 8.829346E+14
(190,47,20) 2.150543E-03 1.197780E-03 4.213287E+00 1.645868E+00
9 0 00:15:00 9.240417E-03 8.476318E+03 8.476328E+03 8.829374E+14
(189,48,20) 2.945573E-04 6.267164E-04 4.075286E+00 1.840354E+00
10 0 00:16:40 1.133784E-02 8.476147E+03 8.476158E+03 8.829402E+14
(082,98,20) 2.080882E-02 9.826687E-05 2.380251E+00 2.033919E+00
11 0 00:18:20 1.368169E-02 8.475987E+03 8.476001E+03 8.829432E+14
(081,98,20) 2.284108E-02 9.116569E-05 2.356497E+00 2.223963E+00
12 0 00:20:00 1.628796E-02 8.475840E+03 8.475856E+03 8.829461E+14
(081,98,20) 2.838376E-02 1.823538E-04 2.530111E+00 2.413136E+00
13 0 00:21:40 1.917915E-02 8.475704E+03 8.475723E+03 8.829490E+14
(080,98,20) 3.184099E-02 1.099705E-04 2.698820E+00 2.605837E+00
14 0 00:23:20 2.237130E-02 8.475579E+03 8.475601E+03 8.829518E+14
(188,48,20) 2.720186E-03 1.014868E-03 3.684499E+00 2.810083E+00
15 0 00:25:00 2.587583E-02 8.475462E+03 8.475488E+03 8.829546E+14
(187,48,20) 6.961907E-03 3.853289E-04 3.725498E+00 3.032715E+00
16 0 00:26:40 2.970996E-02 8.475351E+03 8.475381E+03 8.829574E+14
(187,48,20) 6.664531E-03 1.245864E-05 3.761336E+00 3.270852E+00
17 0 00:28:20 3.389597E-02 8.475242E+03 8.475276E+03 8.829602E+14
(189,48,20) 1.514998E-03 2.657766E-04 2.711070E+00 3.517918E+00
18 0 00:30:00 3.845877E-02 8.475131E+03 8.475169E+03 8.829631E+14
(077,98,20) 4.985909E-02 5.605878E-04 3.008470E+00 3.764849E+00
19 0 00:31:40 4.342550E-02 8.475018E+03 8.475061E+03 8.829659E+14
(076,98,20) 4.361423E-02 8.600033E-04 2.550401E+00 3.999212E+00
20 0 00:33:20 4.882572E-02 8.474906E+03 8.474955E+03 8.829688E+14
(076,98,20) 5.809759E-02 1.029236E-03 3.081947E+00 4.219616E+00
21 0 00:35:00 5.469145E-02 8.474800E+03 8.474855E+03 8.829720E+14
(076,98,20) 6.795970E-02 1.014750E-03 2.773882E+00 4.488508E+00
22 0 00:36:40 6.105677E-02 8.474700E+03 8.474761E+03 8.829755E+14
(075,98,20) 6.234720E-02 1.586861E-03 3.063894E+00 4.812606E+00
23 0 00:38:20 6.795814E-02 8.474604E+03 8.474672E+03 8.829794E+14
(075,98,20) 7.574510E-02 1.635204E-03 3.063914E+00 5.113439E+00
24 0 00:40:00 7.543802E-02 8.474508E+03 8.474584E+03 8.829837E+14
(074,98,20) 6.222094E-02 2.157962E-03 2.929051E+00 5.378895E+00
25 0 00:41:40 8.354390E-02 8.474409E+03 8.474493E+03 8.829886E+14
(074,98,20) 7.963354E-02 2.330817E-03 3.276937E+00 5.597764E+00
26 0 00:43:20 9.232835E-02 8.474306E+03 8.474398E+03 8.829939E+14
(074,98,20) 9.121120E-02 2.138314E-03 2.789197E+00 5.843395E+00
27 0 00:45:00 1.018468E-01 8.474199E+03 8.474301E+03 8.829998E+14
(073,98,20) 7.880304E-02 3.033585E-03 3.228117E+00 6.063732E+00
28 0 00:46:40 1.121592E-01 8.474093E+03 8.474206E+03 8.830062E+14
(073,98,20) 9.619793E-02 2.991791E-03 3.243239E+00 6.230914E+00
29 0 00:48:20 1.233324E-01 8.473992E+03 8.474116E+03 8.830132E+14
(071,97,20) 6.941703E-02 3.625552E-03 2.906709E+00 6.457778E+00
30 0 00:50:00 1.354417E-01 8.473898E+03 8.474034E+03 8.830207E+14
(072,98,20) 9.267275E-02 3.762039E-03 3.273025E+00 6.855489E+00
31 0 00:51:40 1.485587E-01 8.473810E+03 8.473959E+03 8.830287E+14
(072,98,20) 1.089115E-01 3.502214E-03 3.007492E+00 7.195881E+00
32 0 00:53:20 1.627721E-01 8.473727E+03 8.473889E+03 8.830371E+14
(071,98,20) 8.139794E-02 4.291825E-03 3.038932E+00 7.463352E+00
33 0 00:55:00 1.781643E-01 8.473644E+03 8.473823E+03 8.830457E+14
(071,98,20) 1.023752E-01 4.319977E-03 3.276868E+00 7.646356E+00
34 0 00:56:40 1.948384E-01 8.473563E+03 8.473758E+03 8.830544E+14
(071,98,20) 1.160307E-01 3.865038E-03 2.701805E+00 7.737092E+00
35 0 00:58:20 2.128781E-01 8.473481E+03 8.473694E+03 8.830634E+14
(070,98,20) 9.149097E-02 4.611385E-03 3.243355E+00 8.012538E+00
36 0 01:00:00 2.323620E-01 8.473400E+03 8.473632E+03 8.830725E+14
(070,98,20) 1.104856E-01 4.422625E-03 3.195967E+00 8.361815E+00
37 0 01:01:40 2.533687E-01 8.473319E+03 8.473572E+03 8.830819E+14
(069,98,20) 7.876480E-02 4.183685E-03 2.987151E+00 8.632169E+00
38 0 01:03:20 2.759588E-01 8.473237E+03 8.473513E+03 8.830914E+14
(069,98,20) 1.013995E-01 4.279415E-03 3.373946E+00 8.813875E+00
39 0 01:05:00 3.001408E-01 8.473156E+03 8.473456E+03 8.831011E+14
(069,98,20) 1.170150E-01 3.860999E-03 2.928909E+00 8.901033E+00
40 0 01:06:40 3.259519E-01 8.473075E+03 8.473401E+03 8.831110E+14
(068,98,20) 8.985717E-02 4.002488E-03 3.282169E+00 8.893317E+00
41 0 01:08:20 3.533475E-01 8.472996E+03 8.473349E+03 8.831211E+14
(068,98,20) 1.096720E-01 3.825629E-03 3.304661E+00 8.798172E+00
42 0 01:10:00 3.823576E-01 8.472918E+03 8.473300E+03 8.831315E+14
(067,98,20) 7.776326E-02 3.634346E-03 3.058456E+00 8.811698E+00
43 0 01:11:40 4.129811E-01 8.472841E+03 8.473254E+03 8.831420E+14
(067,98,20) 1.001394E-01 3.676213E-03 3.451956E+00 9.009731E+00
44 0 01:13:20 4.454346E-01 8.472763E+03 8.473208E+03 8.831524E+14
(074,33,20) 3.177135E-02 4.228970E-03 3.383427E+00 9.114218E+00
45 0 01:15:00 4.809424E-01 8.472683E+03 8.473164E+03 8.831627E+14
(066,98,20) 9.071340E-02 3.431107E-03 3.442409E+00 1.180460E+01
46 0 01:16:40 5.249684E-01 8.472602E+03 8.473127E+03 8.831729E+14
(066,98,20) 1.084213E-01 3.130223E-03 3.268604E+00 2.405290E+01

Blowing-up: Saving latest model state into RESTART file

WRT_RST - wrote re-start fields (Index=1,1) into time record = 0000001

Elapsed CPU time (seconds):

Thread # 0 CPU: 1266.517
Total: 1266.517

Nonlinear model elapsed time profile:

Allocation and array initialization .............. 4.169 ( 0.3292 %)
Ocean state initialization ....................... 1.059 ( 0.0836 %)
Reading of input data ............................ 0.030 ( 0.0024 %)
Processing of input data ......................... 0.168 ( 0.0133 %)
Processing of output time averaged data .......... 167.136 (13.1965 %)
Computation of vertical boundary conditions ...... 0.233 ( 0.0184 %)
Computation of global information integrals ...... 11.849 ( 0.9356 %)
Writing of output data ........................... 0.246 ( 0.0194 %)
Model 2D kernel .................................. 610.615 (48.2121 %)
2D/3D coupling, vertical metrics ................. 6.817 ( 0.5382 %)
Omega vertical velocity .......................... 6.685 ( 0.5278 %)
Equation of state for seawater ................... 6.485 ( 0.5120 %)
3D equations right-side terms .................... 55.380 ( 4.3726 %)
3D equations predictor step ...................... 84.623 ( 6.6816 %)
Pressure gradient ................................ 31.771 ( 2.5085 %)
Harmonic mixing of tracers, S-surfaces ........... 18.521 ( 1.4624 %)
Harmonic stress tensor, S-surfaces ............... 29.093 ( 2.2971 %)
Corrector time-step for 3D momentum .............. 129.143 (10.1967 %)
Corrector time-step for tracers .................. 92.967 ( 7.3404 %)
Total: 1256.990 99.2477

All percentages are with respect to total time = 1266.517

ROMS/TOMS - Output NetCDF summary for Grid 01:
number of time records written in HISTORY file = 00000001
number of time records written in RESTART file = 00000001

Analytical header files used:

ROMS/Functionals/ana_btflux.h
ROMS/Functionals/ana_fsobc.h
ROMS/Functionals/ana_m2obc.h
ROMS/Functionals/ana_smflux.h
ROMS/Functionals/ana_stflux.h

ROMS/TOMS: DONE... Thursday - May 21, 2015 - 1:23:29 AM

[rtopper]

Smoothing your bathymetry will probably solve your problem.
Your current rx0 and rx1 values are too high:

Maximum grid stiffness ratios:
rx0 = 8.101426E-01 (Beckmann and Haidvogel)
rx1 = 2.460969E+01 (Haney)

If you search this forum you'll find that rx0 values are usually recommended to be < 0.2 and rx1 ~ 5-8 (although Kate will tell you she runs her model with much higher rx1 values).

[jcwarner]

if it blows up after 46 time steps, you could set NHIS = 5 (or so) and look at the output to see where things are going strange.