online nesting test problem

[simion1232006]

I am working on testing the newest nesting scheme for my application. It seems that the model start to ran, while stop at the initialization and configuration step. Does any of you have experiences on that? Also I found a problem to run the nesting model:The tiles specified for the coarse grid should be the same as the refined grid, otherwise the model will stop. Any comments are appreciated.
The log file is attached as follow:




Model Input Parameters: ROMS/TOMS version 3.7
Tuesday - February 18, 2014 - 9:34:50 AM
-----------------------------------------------------------------------------

Wind-Driven Upwelling/Downwelling : nesting test

Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran
Compiler command : /usr/local/MPI/bin/mpif90
Compiler flags : -frepack-arrays -O3 -ffast-math -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none

Input Script :

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 714

Local Root : /home/tao/Desktop/ROMS4
Header Dir : /home/tao/Nesting_model_test
Header file : ningaloo.h
Analytical Dir: /home/tao/Nesting_model_test

Resolution, Grid 01: 0536x0228x040, Parallel Nodes: 4, Tiling: 002x002


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

3600 ntimes Number of timesteps for 3-D equations.
120.000 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.
720 nRST Number of timesteps between the writing of data
into restart fields.
10 ninfo Number of timesteps between print of information
to standard output.
T ldefout Switch to create a new output NetCDF file(s).
720 nHIS Number of timesteps between the writing fields
into history file.
14400 ndefHIS Number of timesteps between creation of new
history files.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
720 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
14400 ndefAVG Number of timesteps between creation of new
time-averaged file.
1.0000E-05 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
1.0000E-05 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
1.0000E-05 nl_visc2 NLM Horizontal, harmonic mixing coefficient
(m2/s) for momentum.
1.0000E-05 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
1.0000E-05 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.
1.0000E-05 Akk_bak Background vertical mixing coefficient (m2/s)
for turbulent energy.
1.0000E-05 Akp_bak Background vertical mixing coefficient (m2/s)
for turbulent generic statistical field.
2.000 gls_p GLS stability exponent.
1.000 gls_m GLS turbulent kinetic energy exponent.
-0.670 gls_n GLS turbulent length scale exponent.
1.0000E-08 gls_Kmin GLS minimum value of turbulent kinetic energy.
1.0000E-08 gls_Pmin GLS minimum value of dissipation.
5.5440E-01 gls_cmu0 GLS stability coefficient.
1.0000E+00 gls_c1 GLS shear production coefficient.
1.2200E+00 gls_c2 GLS dissipation coefficient.
1.0000E-01 gls_c3m GLS stable buoyancy production coefficient.
1.0000E+00 gls_c3p GLS unstable buoyancy production coefficient.
8.0000E-01 gls_sigk GLS constant Schmidt number for TKE.
1.0700E+00 gls_sigp GLS constant Schmidt number for PSI.
1400.000 charnok_alpha Charnok factor for Zos calculation.
0.500 zos_hsig_alpha Factor for Zos calculation using Hsig(Awave).
0.250 sz_alpha Factor for Wave dissipation surface tke flux .
100.000 crgban_cw Factor for Craig/Banner surface tke flux.
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).
2.0000E-03 Zos Surface roughness (m).
1.0000E+01 blk_ZQ Height (m) of surface air humidity measurement.
2.0000E+00 blk_ZT Height (m) of surface air temperature measurement.
1.0000E+01 blk_ZW Height (m) of surface winds measurement.
2 Vtransform S-coordinate transformation equation.
4 Vstretching S-coordinate stretching function.
3.0000E+00 theta_s S-coordinate surface control parameter.
4.0000E-01 theta_b S-coordinate bottom control parameter.
10.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1024.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
40116.000 dstart Time-stamp assigned to model initialization (days).
19000101.00 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
1.0000E+02 Znudg Nudging/relaxation time scale (days)
for free-surface.
1.0000E+02 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
1.0000E+02 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
1.0000E+02 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.
10.000 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).
7.6000E-04 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
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(idTvar) Write out tracer 01: temp
T Hout(idTvar) Write out tracer 02: salt
T Hout(idBott) Write out bottom property 01: grain_diameter
T Hout(idBott) Write out bottom property 02: grain_density
T Hout(idBott) Write out bottom property 03: settling_vel
T Hout(idBott) Write out bottom property 04: erosion_stress
T Hout(idBott) Write out bottom property 05: ripple_length
T Hout(idBott) Write out bottom property 06: ripple_height
T Hout(idBott) Write out bottom property 07: bed_wave_amp
T Hout(idBott) Write out bottom property 08: Zo_def
T Hout(idBott) Write out bottom property 09: Zo_app
T Hout(idBott) Write out bottom property 17: ero_flux
T Hout(idBott) Write out bottom property 18: dep_net

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(idTvar) Write out averaged tracer 01: temp
T Aout(idTvar) Write out averaged tracer 02: salt

Output/Input Files:

Output Restart File: ocean_rst.nc
Prefix for History Files: Ningaloo_WAC_2009_his
Prefix for Averages Files: Ningaloo_WAC_2009_avg
Input Grid File: Ningaloo_WAC_grid.nc
Nesting grid connectivity File: Ningaloo_WAC_ngc.nc
Input Nonlinear Initial File: Ningaloo_WAC_2009_INI.nc
Input Forcing File 01: Ningaloo_WAC_2009_heat.nc
Input Forcing File 02: Ningaloo_WAC_2009_wind.nc
Input Forcing File 03: Ningaloo_NF_2009_heat.nc
Input Forcing File 04: Ningaloo_NF_2009_wind.nc
Input Boundary File: Ningaloo_WAC_2009_BC.nc

Resolution, Grid 02: 0177x0084x040, Parallel Nodes: 4, Tiling: 002x002


Physical Parameters, Grid: 02
=============================

7200 ntimes Number of timesteps for 3-D equations.
60.000 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.
1440 nRST Number of timesteps between the writing of data
into restart fields.
10 ninfo Number of timesteps between print of information
to standard output.
T ldefout Switch to create a new output NetCDF file(s).
1440 nHIS Number of timesteps between the writing fields
into history file.
28800 ndefHIS Number of timesteps between creation of new
history files.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
720 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
14400 ndefAVG Number of timesteps between creation of new
time-averaged file.
1.0000E-05 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
1.0000E-05 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
1.0000E-05 nl_visc2 NLM Horizontal, harmonic mixing coefficient
(m2/s) for momentum.
1.0000E-05 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
1.0000E-05 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.
1.0000E-05 Akk_bak Background vertical mixing coefficient (m2/s)
for turbulent energy.
1.0000E-05 Akp_bak Background vertical mixing coefficient (m2/s)
for turbulent generic statistical field.
2.000 gls_p GLS stability exponent.
1.000 gls_m GLS turbulent kinetic energy exponent.
-0.670 gls_n GLS turbulent length scale exponent.
1.0000E-08 gls_Kmin GLS minimum value of turbulent kinetic energy.
1.0000E-08 gls_Pmin GLS minimum value of dissipation.
5.5440E-01 gls_cmu0 GLS stability coefficient.
1.0000E+00 gls_c1 GLS shear production coefficient.
1.2200E+00 gls_c2 GLS dissipation coefficient.
1.0000E-01 gls_c3m GLS stable buoyancy production coefficient.
1.0000E+00 gls_c3p GLS unstable buoyancy production coefficient.
8.0000E-01 gls_sigk GLS constant Schmidt number for TKE.
1.0700E+00 gls_sigp GLS constant Schmidt number for PSI.
1400.000 charnok_alpha Charnok factor for Zos calculation.
0.500 zos_hsig_alpha Factor for Zos calculation using Hsig(Awave).
0.250 sz_alpha Factor for Wave dissipation surface tke flux .
100.000 crgban_cw Factor for Craig/Banner surface tke flux.
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).
2.0000E-03 Zos Surface roughness (m).
1.0000E+01 blk_ZQ Height (m) of surface air humidity measurement.
2.0000E+00 blk_ZT Height (m) of surface air temperature measurement.
1.0000E+01 blk_ZW Height (m) of surface winds measurement.
2 Vtransform S-coordinate transformation equation.
4 Vstretching S-coordinate stretching function.
3.0000E+00 theta_s S-coordinate surface control parameter.
4.0000E-01 theta_b S-coordinate bottom control parameter.
10.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1024.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
40116.000 dstart Time-stamp assigned to model initialization (days).
19000101.00 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
1.0000E+02 Znudg Nudging/relaxation time scale (days)
for free-surface.
1.0000E+02 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
1.0000E+02 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
1.0000E+02 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.
10.000 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).
7.6000E-04 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
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(idTvar) Write out tracer 01: temp
T Hout(idTvar) Write out tracer 02: salt
T Hout(idBott) Write out bottom property 01: grain_diameter
T Hout(idBott) Write out bottom property 02: grain_density
T Hout(idBott) Write out bottom property 03: settling_vel
T Hout(idBott) Write out bottom property 04: erosion_stress
T Hout(idBott) Write out bottom property 05: ripple_length
T Hout(idBott) Write out bottom property 06: ripple_height
T Hout(idBott) Write out bottom property 07: bed_wave_amp

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(idTvar) Write out averaged tracer 01: temp
T Aout(idTvar) Write out averaged tracer 02: salt

Output/Input Files:

Output Restart File: ocean_rst.nc
Prefix for History Files: Ningaloo_NF_2009_his
Prefix for Averages Files: Ningaloo_NF_2009_avg
Input Grid File: Ningaloo_NF_grid2.nc
Nesting grid connectivity File: Ningaloo_WAC_ngc.nc
Input Nonlinear Initial File: Ningaloo_NF_2009_INI.nc
Input Forcing File 01: Ningaloo_WAC_2009_heat.nc
Input Forcing File 02: Ningaloo_WAC_2009_wind.nc
Input Forcing File 03: Ningaloo_NF_2009_heat.nc
Input Forcing File 04: Ningaloo_NF_2009_wind.nc

Tile partition information for Grid 01: 0536x0228x0040 tiling: 002x002

tile Istr Iend Jstr Jend Npts

0 1 268 1 114 1222080
1 269 536 1 114 1222080
2 1 268 115 228 1222080
3 269 536 115 228 1222080

Tile partition information for Grid 02: 0177x0084x0040 tiling: 002x002

tile Istr Iend Jstr Jend Npts

0 1 89 1 42 149520
1 90 177 1 42 147840
2 1 89 43 84 149520
3 90 177 43 84 147840

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 268.50 0.50 114.50 RHO-points
1 268.50 536.50 0.50 114.50 RHO-points
2 0.50 268.50 114.50 228.50 RHO-points
3 268.50 536.50 114.50 228.50 RHO-points

0 1.00 268.50 0.50 114.50 U-points
1 268.50 536.00 0.50 114.50 U-points
2 1.00 268.50 114.50 228.50 U-points
3 268.50 536.00 114.50 228.50 U-points

0 0.50 268.50 1.00 114.50 V-points
1 268.50 536.50 1.00 114.50 V-points
2 0.50 268.50 114.50 228.00 V-points
3 268.50 536.50 114.50 228.00 V-points

Tile minimum and maximum fractional coordinates for Grid 02:
(interior points only)

tile Xmin Xmax Ymin Ymax grid

0 0.50 89.50 0.50 42.50 RHO-points
1 89.50 177.50 0.50 42.50 RHO-points
2 0.50 89.50 42.50 84.50 RHO-points
3 89.50 177.50 42.50 84.50 RHO-points

0 1.00 89.50 0.50 42.50 U-points
1 89.50 177.00 0.50 42.50 U-points
2 1.00 89.50 42.50 84.50 U-points
3 89.50 177.00 42.50 84.50 U-points

0 0.50 89.50 1.00 42.50 V-points
1 89.50 177.50 1.00 42.50 V-points
2 0.50 89.50 42.50 84.00 V-points
3 89.50 177.50 42.50 84.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 843
HaloSizeJ(1) = 381
TileSide(1) = 275
TileSize(1) = 33275


Maximum halo size in XI and ETA directions:

HaloSizeI(2) = 312
HaloSizeJ(2) = 171
TileSide(2) = 98
TileSize(2) = 4998


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

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

zeta 1 Chapman Imp Closed Chapman Imp Chapman Imp
2 Nested Nested Nested Nested

ubar 1 Flather Closed Flather Flather
2 Nested Nested Nested Nested

vbar 1 Flather Closed Flather Flather
2 Nested Nested Nested Nested

u 1 Rad + Nud Closed Rad + Nud Rad + Nud
2 Nested Nested Nested Nested

v 1 Rad + Nud Closed Rad + Nud Rad + Nud
2 Nested Nested Nested Nested

temp 1 Rad + Nud Closed Rad + Nud Rad + Nud
2 Nested Nested Nested Nested

salt 1 Rad + Nud Closed Rad + Nud Rad + Nud
2 Nested Nested Nested Nested

tke 1 Rad + Nud Closed Rad + Nud Rad + Nud
2 Nested Nested Nested Nested

Activated C-preprocessing Options:

NINGALOO Wind-Driven Upwelling/Downwelling : nesting test
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_SSFLUX Analytical kinematic surface salinity flux.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged nonlinear model fields.
BULK_FLUXES Surface bulk fluxes parameterization.
CURVGRID Orthogonal curvilinear grid.
DIURNAL_SRFLUX Modulate shortwave radiation by the local diurnal cycle.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
GLS_MIXING Generic Length-Scale turbulence closure.
KANTHA_CLAYSON Kantha and Clayson stability function formulation.
LONGWAVE_OUT Compute outgoing longwave radiation internally.
MASKING Land/Sea masking.
MB_BBL Blaas Bottom Boundary Layer.
MIX_GEO_TS Mixing of tracers along geopotential surfaces.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
NESTING Nesting grids: Composite and Refinement.
NONLINEAR Nonlinear Model.
!NONLIN_EOS Linear Equation of State for seawater.
N2S2_HORAVG Horizontal smoothing of buoyancy and shear.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
K_GSCHEME Third-order upstream advection of TKE fields.
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.
SPHERICAL Spherical grid configuration.
SPONGE Enhanced horizontal mixing in the sponge areas.
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.

CHECKDEFS - only one bottom stress formulation is allowed.

Elapsed CPU time (seconds):


ROMS/TOMS - Output NetCDF summary for Grid 01:

ROMS/TOMS - Output NetCDF summary for Grid 02:

ROMS/TOMS - Configuration error ..... exit_flag: 5


ERROR: Illegal model configuration.

[simion1232006]

Problem solved. I should not define the uv_logdrag and MB_BBL at the same time.

[kee]

hi simion,

which tools did you use to create your datasets to start your 2-way nesting model?
I want to use it. Could you tell me about it?
thanks.

Cheer!