model blowing up

[asujrpv]

Hello,

I created a grid using seagrid with some small islands and tried to run my test case. As soon as it starts running it blows up. The information that I got is below, I would be grateful for your guidance, since I am new ROMS user.

thanks!
Rafael


rpacheco@mexico~/SRC/MyTest/cdw/CDW > oceanG < ocean_cdw.in

Model Input Parameters: ROMS/TOMS version 3.5
Saturday - July 2, 2011 - 12:17:46 PM
-----------------------------------------------------------------------------

CDW modeling

Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran
Compiler command : /usr/bin/gfortran
Compiler flags : -frepack-arrays -g -fbounds-check -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none

SVN Root URL : https:://myroms.org/svn/src
SVN Revision : 564M

Local Root : /home/rpacheco/SRC
Header Dir : /home/rpacheco/SRC/MyTest/cdw/CDW
Header file : cdw.h
Analytical Dir: /home/rpacheco/SRC/MyTest/cdw/CDW

Resolution, Grid 01: 0028x0058x012, Parallel Threads: 1, Tiling: 001x002


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

450000 ntimes Number of timesteps for 3-D equations.
360.000 dt Timestep size (s) for 3-D equations.
10 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.
1080 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).
1080 nHIS Number of timesteps between the writing fields
into history file.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
1080 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
1 ntsDIA Starting timestep for the accumulation of output
time-averaged diagnostics data.
1080 nDIA Number of timesteps between the writing of
time-averaged data into diagnostics file.
5.0000E+00 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
5.0000E+00 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
5.0000E+00 nl_visc2 NLM Horizontal, harmonic mixing coefficient
(m2/s) for momentum.
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.
2.6500E-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.
4 Vstretching S-coordinate stretching function.
3.3000E+00 theta_s S-coordinate surface control parameter.
0.0000E+00 theta_b S-coordinate bottom control parameter.
1400.000 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).
0.00 time_ref Reference time for units attribute (yyyymmdd.dd)
5.0000E+01 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
5.0000E+01 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.
5.000 T0 Background potential temperature (C) constant.
35.000 S0 Background salinity (PSU) constant.
1028.000 R0 Background density (kg/m3) used in linear Equation
of State.
1.0000E-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).
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 Hout(idDano) Write out density anomaly.

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 Dout(M2rate) Write out 2D momentun 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 momentun 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: ocean_rst.nc
Output History File: ocean_his.nc
Output Averages File: ocean_avg.nc
Output Diagnostics File: ocean_dia.nc
Input Grid File: ../Data/roms_grdJRP.nc

Tile partition information for Grid 01: 0028x0058x0012 tiling: 001x002

tile Istr Iend Jstr Jend Npts

0 1 28 1 29 9744
1 1 28 30 58 9744

Tile minimum and maximum fractional grid coordinates:
(interior points only)

tile Xmin Xmax Ymin Ymax grid

0 0.50 29.50 0.50 60.50 RHO-points
1 0.50 29.50 -0.50 59.50 RHO-points

0 0.00 29.00 0.50 60.50 U-points
1 0.00 29.00 -0.50 59.50 U-points

0 0.50 29.50 0.00 60.50 V-points
1 0.50 29.50 -0.50 59.00 V-points

Activated C-preprocessing Options:

CDW CDW modeling
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_INITIAL Analytical initial 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.
DOUBLE_PRECISION Double precision arithmetic.
EAST_VOLCONS Eastern edge, enforce mass conservation.
MASKING Land/Sea masking.
MIX_S_TS Mixing of tracers along constant S-surfaces.
MIX_GEO_UV Mixing of momentum along geopotential surfaces.
NONLINEAR Nonlinear Model.
!NONLIN_EOS Linear Equation of State for seawater.
NORTH_VOLCONS Northern edge, enforce mass conservation.
POWER_LAW Power-law shape time-averaging barotropic filter.
PRSGRD31 Standard density Jacobian formulation (Song, 1998).
PROFILE Time profiling activated .
RHO_SURF Include difference between rho0 and surface density.
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SOLVE3D Solving 3D Primitive Equations.
SOUTH_VOLCONS Southern edge, enforce mass conservation.
TS_A4HADVECTION Fourth-order Akima horizontal advection of tracers.
TS_A4VADVECTION Fourth-order Akima 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_LOGDRAG Logarithmic bottom stress.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.
WEST_VOLCONS Western edge, enforce mass conservation.

Process Information:

Thread # 0 (pid= 14077) is active.

INITIAL: Configuring and initializing forward nonlinear model ...


Vertical S-coordinate System:

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

12 0.0000000 0.0000000 0.000 0.000 0.000 0.000
11 -0.0833333 -0.0030260 -0.000 -5.608 -2.871 -5.608
10 -0.1666667 -0.0123343 -0.000 -11.238 -5.747 -11.238
9 -0.2500000 -0.0286334 -0.000 -16.892 -8.629 -16.892
8 -0.3333333 -0.0531635 -0.000 -22.573 -11.518 -22.573
7 -0.4166667 -0.0877916 -0.000 -28.288 -14.416 -28.288
6 -0.5000000 -0.1351529 -0.000 -34.047 -17.325 -34.047
5 -0.5833333 -0.1988517 -0.000 -39.861 -20.248 -39.861
4 -0.6666667 -0.2837357 -0.000 -45.747 -23.190 -45.747
3 -0.7500000 -0.3962648 -0.000 -51.726 -26.155 -51.726
2 -0.8333333 -0.5450028 -0.000 -57.828 -29.152 -57.828
1 -0.9166667 -0.7412691 -0.000 -64.091 -32.190 -64.091
0 -1.0000000 -1.0000000 -0.000 -70.565 -35.282 -70.565

Time Splitting Weights: ndtfast = 10 nfast = 15

Primary Secondary Accumulated to Current Step

1 0.0014850648765542 0.1000000000000000 0.0014850648765542 0.1000000000000000
2 0.0059386031399402 0.0998514935123446 0.0074236680164944 0.1998514935123445
3 0.0133457074936657 0.0992576331983506 0.0207693755101601 0.2991091267106951
4 0.0236484051180389 0.0979230624489840 0.0444177806281990 0.3970321891596791
5 0.0366959666818608 0.0955582219371801 0.0811137473100598 0.4925904110968592
6 0.0521753389587947 0.0918886252689940 0.1332890862688545 0.5844790363658532
7 0.0695217010484137 0.0866710913731145 0.2028107873172682 0.6711501277389678
8 0.0878091442019233 0.0797189212682732 0.2906199315191915 0.7508690490072409
9 0.1056214752525633 0.0709380068480808 0.3962414067717548 0.8218070558553218
10 0.1209031436506851 0.0603758593228245 0.5171445504224399 0.8821829151781463
11 0.1307902921035067 0.0482855449577560 0.6479348425259466 0.9304684601359023
12 0.1314219308195445 0.0352065157474053 0.7793567733454911 0.9656749758833076
13 0.1177312353577226 0.0220643226654509 0.8970880087032138 0.9877392985487585
14 0.0832169680811588 0.0102911991296786 0.9803049767843727 0.9980304976784371
15 0.0196950232156274 0.0019695023215627 1.0000000000000000 0.9999999999999999

ndtfast, nfast = 10 15 nfast/ndtfast = 1.50000

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

1.000000000000 1.083803072626 0.541901536313 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.00000

Minimum X-grid spacing, DXmin = 1.84859141E+00 km
Maximum X-grid spacing, DXmax = 1.85789243E+00 km
Minimum Y-grid spacing, DYmin = 1.58868269E+00 km
Maximum Y-grid spacing, DYmax = 1.59667601E+00 km
Minimum Z-grid spacing, DZmin = 0.00000000E+00 m
Maximum Z-grid spacing, DZmax = 6.47431687E+00 m

Minimum barotropic Courant Number = 2.43753255E-01
Maximum barotropic Courant Number = 7.82187629E-01
Maximum Coriolis Courant Number = 2.70267912E-02


Maximum grid stiffness ratios: rx0 = 1.701259E-01 (Beckmann and Haidvogel)
rx1 = 3.839680E+00 (Haney)


Initial basin volumes: TotVolume = 1.9240017367E+11 m3
MinVolume = 1.7514841182E+06 m3
MaxVolume = 1.8246743887E+07 m3
Max/Min = 1.0417875730E+01


NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00450000)


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 2.222067E+02 2.222067E+02 1.924002E+11
(00,00,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS - creating history file: ocean_his.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001
DEF_AVG - creating average file: ocean_avg.nc
DEF_DIAGS - creating diagnostics file: ocean_dia.nc
1 0 00:06:00 NaN NaN NaN NaN
(00,00,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00

Blowing-up: Saving latest model state into RESTART file

WRT_RST - wrote re-start fields (Index=2,2) into time record = 0000001

Elapsed CPU time (seconds):

Thread # 0 CPU: 1.490
Total: 1.490

Nonlinear model elapsed time profile:

Allocation and array initialization .............. 0.370 (24.8322 %)
Ocean state initialization ....................... 0.030 ( 2.0134 %)
Computation of global information integrals ...... 0.040 ( 2.6846 %)
Writing of output data ........................... 0.080 ( 5.3691 %)
Model 2D kernel .................................. 0.400 (26.8456 %)
2D/3D coupling, vertical metrics ................. 0.020 ( 1.3423 %)
Equation of state for seawater ................... 0.020 ( 1.3423 %)
3D equations right-side terms .................... 0.060 ( 4.0268 %)
3D equations predictor step ...................... 0.070 ( 4.6980 %)
Harmonic mixing of tracers, S-surfaces ........... 0.020 ( 1.3423 %)
Harmonic stress tensor, geopotentials ............ 0.120 ( 8.0537 %)
Corrector time-step for 3D momentum .............. 0.130 ( 8.7248 %)
Corrector time-step for tracers .................. 0.080 ( 5.3691 %)
Total: 1.440 96.6443

All percentages are with respect to total time = 1.490

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
/home/rpacheco/SRC/MyTest/cdw/CDW/ana_initial.h
ROMS/Functionals/ana_smflux.h
ROMS/Functionals/ana_stflux.h

ROMS/TOMS: DONE... Saturday - July 2, 2011 - 12:17:47 PM

[nganju]

If you look at the output for vertical stretching, it looks like your shallowest depth is zero in your grid file.
All cells must be greater than zero unless using wetting/drying.

[nganju]

and your courant number is 0.8.
I would also reduce the timestep by half.

[asujrpv]

I am most grateful for the advice, it is running now after I set the minimum depth to a numerical value.

However, I have a question. I have several small islands located at near the top in the middle of the attached contour plot png-file, that I thought I was simulating using masking. So even if I use masking I need to set the minimum depth to a positive value?

How could I use the option wetting/drying?

Thank you!
Rafael

[nganju]

Yes, even with masking the minimum depth must be greater than zero, even in masked cells.
With wetting and drying, you activate "WET_DRY", and specify your mask as cells which should never become wet. You then have the option of making any wet cell a negative depth. When zeta exceeds that depth+dcrit (critical water depth specified in input file) the cell will become wet and active for computations. You can search the forum for wet_dry and you will find advice on using those options.