Problem about yellow_sea case

[chenzhen2181]

I try to learn pyroms tools to generate grid ,initial and boundary file .
I download yellow_sea case files from http://www.people.arsc.edu/~kate/ROMS/HK/Yellow_Sea/.
I compile it well, but I get some error when I run it. Could someone give me some help?

run log
Process Information:

Node # 0 (pid= 19125) is active.

Model Input Parameters: ROMS/TOMS version 3.4
Wednesday - June 18, 2014 - 8:15:16 PM
-----------------------------------------------------------------------------
Node # 1 (pid= 19126) is active.

Yellow Sea

Operating system : Linux
CPU/hardware : i686
Compiler system : gfortran
Compiler command : /home/chenzhen/install/mpich2-1.5/bin/mpif90
Compiler flags : -frepack-arrays -O3 -ffast-math -ffree-form -ffree-line-length-none

Input Script : cal/ocean_yellow.in

SVN Root URL : https://www.myroms.org/svn/omlab/branches/jcwarner
SVN Revision : 已导出

Local Root : /home/chenzhen/COAWST
Header Dir : /home/chenzhen/COAWST/Projects/chenzhen/Yellow/ROMS/Include
Header file : yellow.h
Analytical Dir: /home/chenzhen/COAWST/Projects/chenzhen/Yellow/ROMS/Functionals

Resolution, Grid 01: 0080x0080x040, Parallel Nodes: 2, Tiling: 001x002


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

1080 ntimes Number of timesteps for 3-D equations.
800.000 dt Timestep size (s) for 3-D equations.
20 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.
108 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).
108 nHIS Number of timesteps between the writing fields
into history file.
0.0000E+00 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-04 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.
0.0000E+00 Zob Bottom roughness (m).
1.0000E+01 blk_ZQ Height (m) of surface air humidity measurement.
1.0000E+01 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.
1 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.
1000.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
0.000 dstart Time-stamp assigned to model initialization (days).
0.000 tide_start Reference time origin for tidal forcing (days).
0.00 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.
0.000 T0 Background potential temperature (C) constant.
0.000 S0 Background salinity (PSU) constant.
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

Output/Input Files:

Output Restart File: result/ocean_rst.nc
Output History File: result/ocean_his.nc
Input Grid File: Data/yellow_sea_grid.nc
Input Nonlinear Initial File: Data/Yellow_Sea_ini_SODA.nc
Input Forcing File 01: Data/tides_yellow_sea.nc
Input Boundary File: Data/Yellow_Sea_bdry_SODA.nc

Tile partition information for Grid 01: 0080x0080x0040 tiling: 001x002

tile Istr Iend Jstr Jend Npts

0 1 80 1 40 128000
1 1 80 41 80 128000

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 80.50 0.50 40.50 RHO-points
1 0.50 80.50 40.50 80.50 RHO-points

0 1.00 80.00 0.50 40.50 U-points
1 1.00 80.00 40.50 80.50 U-points

0 0.50 80.50 1.00 40.50 V-points
1 0.50 80.50 40.50 80.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 182
HaloSizeJ(1) = 104
TileSide(1) = 85
TileSize(1) = 3910


Activated C-preprocessing Options:

YELLOW_SEA Yellow Sea
ADD_FSOBC Adding tidal elevation to proccesed OBC data.
ADD_M2OBC Adding tidal currents to proccesed OBC data.
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
BULK_FLUXES Surface bulk fluxes parametererization.
CURVGRID Orthogonal curvilinear grid.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
EMINUSP Compute Salt Flux using E-P.
LONGWAVE_OUT Compute outgoing longwave radiation internally.
MASKING Land/Sea masking.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SOLVE3D Solving 3D Primitive Equations.
SOUTH_FSCHAPMAN Southern edge, free-surface, Chapman condition.
SOUTH_M2FLATHER Southern edge, 2D momentum, Flather condition.
SOUTH_M3NUDGING Southern edge, 3D momentum, passive/active outflow/inflow.
SOUTH_M3RADIATION Southern edge, 3D momentum, radiation condition.
SOUTH_TNUDGING Southern edge, tracers, passive/active outflow/inflow.
SOUTH_TRADIATION Southern edge, tracers, radiation condition.
SSH_TIDES Add tidal elevation to SSH climatology.
TS_U3HADVECTION Third-order upstream horizontal advection of tracers.
TS_C4VADVECTION Fourth-order centered vertical advection 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_TIDES Add tidal currents to 2D momentum climatologies.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions

yellow_sea.h
#define ROMS_MODEL

#undef STATIONS
#undef FLOATS
#undef DIAGNOSTICS_UV
#define MASKING
#define SOLVE3D

#define UV_ADV
#define UV_COR
#define UV_VIS2
#define UV_LDRAG
#define DJ_GRADPS
#define CURVGRID
#define MIX_S_UV

#define TS_U3HADVECTION
#define TS_C4VADVECTION
#define SALINITY
#define NONLIN_EOS

#undef MY25_MIXING
# if defined GLS_MIXING || defined MY25_MIXING
# define KANTHA_CLAYSON
# define N2S2_HORAVG
# endif

#undef LMD_MIXING
#ifdef LMD_MIXING
# define LMD_CONVEC
# define LMD_NONLOCAL
# define LMD_RIMIX
# define LMD_SKPP
#endif

#define ANA_BTFLUX
#define ANA_BSFLUX
#undef ANA_SMFLUX
#undef ANA_STFLUX
#undef ANA_SSFLUX
#define BULK_FLUXES
#define LONGWAVE_OUT
#define EMINUSP

#define SOUTH_FSCHAPMAN
#define SOUTH_M2FLATHER
#define SOUTH_M3RADIATION
#define SOUTH_M3NUDGING
#define SOUTH_TRADIATION
#define SOUTH_TNUDGING
#undef ANA_FSOBC
#undef ANA_M2OBC
#define UV_TIDES
#define SSH_TIDES
#define ADD_FSOBC
#define ADD_M2OBC

[kate]

I wrote this with what I know of segmentation faults. In your case, you should carefully compare the ocean_yellow.in from my site with an ocean.in from COAWST. Each ROMS version needs to be run with a compatible ocean.in. Ditto the list of cppdefs.

[chenzhen2181]

I wrote this with what I know of segmentation faults. In your case, you should carefully compare the ocean_yellow.in from my site with an ocean.in from COAWST. Each ROMS version needs to be run with a compatible ocean.in. Ditto the list of cppdefs.

Hi kate
I set wrong MyAppCPP in ocean.in, so it shows an error .
I changed it, and get another error.It seems I didn't have wind components in the forcing file.
Does this case need wind condition ?
--chenzhen

run log
Process Information:

Node # 0 (pid= 3374) is active.
Node # 1 (pid= 3375) is active.

Model Input Parameters: ROMS/TOMS version 3.4
Thursday - June 19, 2014 - 7:33:15 AM
-----------------------------------------------------------------------------

Yellow Sea

Operating system : Linux
CPU/hardware : i686
Compiler system : gfortran
Compiler command : /home/chenzhen/install/mpich2-1.5/bin/mpif90
Compiler flags : -frepack-arrays -O3 -ffast-math -ffree-form -ffree-line-length-none

Input Script : cal/ocean_yellow.in

SVN Root URL : https://www.myroms.org/svn/omlab/branches/jcwarner
SVN Revision : 已导出

Local Root : /home/chenzhen/COAWST
Header Dir : /home/chenzhen/COAWST/Projects/chenzhen/Yellow/ROMS/Include
Header file : yellow.h
Analytical Dir: /home/chenzhen/COAWST/Projects/chenzhen/Yellow/ROMS/Functionals

Resolution, Grid 01: 0080x0080x040, Parallel Nodes: 2, Tiling: 001x002


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

1080 ntimes Number of timesteps for 3-D equations.
800.000 dt Timestep size (s) for 3-D equations.
20 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.
108 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).
108 nHIS Number of timesteps between the writing fields
into history file.
0.0000E+00 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-04 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.
0.0000E+00 Zob Bottom roughness (m).
1.0000E+01 blk_ZQ Height (m) of surface air humidity measurement.
1.0000E+01 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.
1 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.
1000.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
0.000 dstart Time-stamp assigned to model initialization (days).
0.000 tide_start Reference time origin for tidal forcing (days).
0.00 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.
0.000 T0 Background potential temperature (C) constant.
0.000 S0 Background salinity (PSU) constant.
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

Output/Input Files:

Output Restart File: result/ocean_rst.nc
Output History File: result/ocean_his.nc
Input Grid File: Data/yellow_sea_grid.nc
Input Nonlinear Initial File: Data/Yellow_Sea_ini_SODA.nc
Input Forcing File 01: Data/tides_yellow_sea.nc
Input Boundary File: Data/Yellow_Sea_bdry_SODA.nc

Tile partition information for Grid 01: 0080x0080x0040 tiling: 001x002

tile Istr Iend Jstr Jend Npts

0 1 80 1 40 128000
1 1 80 41 80 128000

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 80.50 0.50 40.50 RHO-points
1 0.50 80.50 40.50 80.50 RHO-points

0 1.00 80.00 0.50 40.50 U-points
1 1.00 80.00 40.50 80.50 U-points

0 0.50 80.50 1.00 40.50 V-points
1 0.50 80.50 40.50 80.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 182
HaloSizeJ(1) = 104
TileSide(1) = 85
TileSize(1) = 3910


Activated C-preprocessing Options:

YELLOW Yellow Sea
ADD_FSOBC Adding tidal elevation to proccesed OBC data.
ADD_M2OBC Adding tidal currents to proccesed OBC data.
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
BULK_FLUXES Surface bulk fluxes parametererization.
CURVGRID Orthogonal curvilinear grid.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
EMINUSP Compute Salt Flux using E-P.
LONGWAVE_OUT Compute outgoing longwave radiation internally.
MASKING Land/Sea masking.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SOLVE3D Solving 3D Primitive Equations.
SOUTH_FSCHAPMAN Southern edge, free-surface, Chapman condition.
SOUTH_M2FLATHER Southern edge, 2D momentum, Flather condition.
SOUTH_M3NUDGING Southern edge, 3D momentum, passive/active outflow/inflow.
SOUTH_M3RADIATION Southern edge, 3D momentum, radiation condition.
SOUTH_TNUDGING Southern edge, tracers, passive/active outflow/inflow.
SOUTH_TRADIATION Southern edge, tracers, radiation condition.
SSH_TIDES Add tidal elevation to SSH climatology.
TS_U3HADVECTION Third-order upstream horizontal advection of tracers.
TS_C4VADVECTION Fourth-order centered vertical advection 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_TIDES Add tidal currents to 2D momentum climatologies.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.

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

40 0.0000000 0.0000000 0.000 0.000 0.000 0.000
39 -0.0250000 -0.0017775 -0.067 -0.067 -0.108 -0.132
38 -0.0500000 -0.0037835 -0.134 -0.134 -0.217 -0.268
37 -0.0750000 -0.0060921 -0.203 -0.203 -0.330 -0.409
36 -0.1000000 -0.0087922 -0.272 -0.272 -0.446 -0.557
35 -0.1250000 -0.0119914 -0.342 -0.342 -0.568 -0.714
34 -0.1500000 -0.0158197 -0.415 -0.415 -0.695 -0.882
33 -0.1750000 -0.0204330 -0.489 -0.489 -0.830 -1.063
32 -0.2000000 -0.0260168 -0.565 -0.565 -0.974 -1.261
31 -0.2250000 -0.0327879 -0.644 -0.644 -1.129 -1.479
30 -0.2500000 -0.0409944 -0.727 -0.727 -1.298 -1.722
29 -0.2750000 -0.0509117 -0.815 -0.815 -1.483 -1.995
28 -0.3000000 -0.0628318 -0.907 -0.907 -1.688 -2.303
27 -0.3250000 -0.0770446 -1.005 -1.005 -1.914 -2.650
26 -0.3500000 -0.0938098 -1.110 -1.110 -2.165 -3.042
25 -0.3750000 -0.1133185 -1.221 -1.221 -2.442 -3.481
24 -0.4000000 -0.1356491 -1.339 -1.339 -2.746 -3.968
23 -0.4250000 -0.1607245 -1.464 -1.464 -3.076 -4.504
22 -0.4500000 -0.1882840 -1.596 -1.596 -3.430 -5.082
21 -0.4750000 -0.2178817 -1.732 -1.732 -3.804 -5.695
20 -0.5000000 -0.2489214 -1.872 -1.872 -4.191 -6.334
19 -0.5250000 -0.2807264 -2.014 -2.014 -4.585 -6.986
18 -0.5500000 -0.3126323 -2.157 -2.157 -4.981 -7.639
17 -0.5750000 -0.3440788 -2.298 -2.298 -5.372 -8.285
16 -0.6000000 -0.3746809 -2.437 -2.437 -5.755 -8.916
15 -0.6250000 -0.4042644 -2.573 -2.573 -6.128 -9.529
14 -0.6500000 -0.4328656 -2.707 -2.707 -6.492 -10.125
13 -0.6750000 -0.4607052 -2.839 -2.839 -6.849 -10.708
12 -0.7000000 -0.4881475 -2.970 -2.970 -7.201 -11.285
11 -0.7250000 -0.5156591 -3.102 -3.102 -7.555 -11.862
10 -0.7500000 -0.5437741 -3.234 -3.234 -7.914 -12.450
9 -0.7750000 -0.5730691 -3.370 -3.370 -8.285 -13.058
8 -0.8000000 -0.6041494 -3.510 -3.510 -8.672 -13.697
7 -0.8250000 -0.6376434 -3.657 -3.657 -9.083 -14.378
6 -0.8500000 -0.6742046 -3.811 -3.811 -9.523 -15.112
5 -0.8750000 -0.7145184 -3.974 -3.974 -9.999 -15.911
4 -0.9000000 -0.7593114 -4.148 -4.148 -10.517 -16.788
3 -0.9250000 -0.8093643 -4.336 -4.336 -11.086 -17.756
2 -0.9500000 -0.8655258 -4.539 -4.539 -11.713 -18.829
1 -0.9750000 -0.9287272 -4.759 -4.759 -12.408 -20.024
0 -1.0000000 -1.0000000 -5.000 -5.000 -13.179 -21.359

Time Splitting Weights: ndtfast = 20 nfast = 29

Primary Secondary Accumulated to Current Step

1-0.0009651193358779 0.0500000000000000-0.0009651193358779 0.0500000000000000
2-0.0013488780126037 0.0500482559667939-0.0023139973484816 0.1000482559667939
3-0.0011514592651645 0.0501156998674241-0.0034654566136461 0.1501639558342180
4-0.0003735756740661 0.0501732728306823-0.0038390322877122 0.2003372286649003
5 0.0009829200513762 0.0501919516143856-0.0028561122363360 0.2505291802792859
6 0.0029141799764308 0.0501428056118168 0.0000580677400948 0.3006719858911027
7 0.0054132615310267 0.0499970966129953 0.0054713292711215 0.3506690825040980
8 0.0084687837865132 0.0497264335364439 0.0139401130576347 0.4003955160405419
9 0.0120633394191050 0.0493029943471183 0.0260034524767397 0.4496985103876602
10 0.0161716623600090 0.0486998273761630 0.0421751148367487 0.4983983377638232
11 0.0207585511322367 0.0478912442581626 0.0629336659689854 0.5462895820219857
12 0.0257765478740990 0.0468533167015507 0.0887102138430844 0.5931428987235364
13 0.0311633730493853 0.0455644893078458 0.1198735868924698 0.6387073880313822
14 0.0368391158442262 0.0440063206553765 0.1567127027366960 0.6827137086867586
15 0.0427031802506397 0.0421643648631652 0.1994158829873357 0.7248780735499238
16 0.0486309868367616 0.0400292058506332 0.2480468698240973 0.7649072794005570
17 0.0544704302037592 0.0375976565087951 0.3025173000278565 0.8025049359093521
18 0.0600380921294286 0.0348741349986072 0.3625553921572851 0.8373790709079593
19 0.0651152103984763 0.0318722303921357 0.4276706025557614 0.8692513013000950
20 0.0694434033194840 0.0286164698722119 0.4971140058752453 0.8978677711723069
21 0.0727201499285570 0.0251442997062377 0.5698341558038024 0.9230120708785446
22 0.0745940258796570 0.0215082922098099 0.6444281816834594 0.9445203630883545
23 0.0746596950216180 0.0177785909158270 0.7190878767050775 0.9622989540041815
24 0.0724526566618460 0.0140456061647461 0.7915405333669234 0.9763445601689277
25 0.0674437485167025 0.0104229733316538 0.8589842818836260 0.9867675335005816
26 0.0590334053485720 0.0070507859058187 0.9180176872321980 0.9938183194064003
27 0.0465456732896125 0.0040991156383901 0.9645633605218105 0.9979174350447904
28 0.0292219798521905 0.0017718319739095 0.9937853403740009 0.9996892670186999
29 0.0062146596259991 0.0003107329813000 1.0000000000000000 0.9999999999999998

ndtfast, nfast = 20 29 nfast/ndtfast = 1.45000

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

1.000000000000 1.060707743385 0.530353871693 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.14200

Minimum X-grid spacing, DXmin = 8.88372172E+00 km
Maximum X-grid spacing, DXmax = 1.16654601E+01 km
Minimum Y-grid spacing, DYmin = 7.65876935E+00 km
Maximum Y-grid spacing, DYmax = 1.00685906E+01 km
Minimum Z-grid spacing, DZmin = 6.69436342E-02 m
Maximum Z-grid spacing, DZmax = 1.33482535E+00 m

Minimum barotropic Courant Number = 3.67539224E-02
Maximum barotropic Courant Number = 8.79350377E-02
Maximum Coriolis Courant Number = 7.65944146E-02


NLM: GET_STATE - Read state initial conditions, t = 39451 12:00:00
(File: Yellow_Sea_ini_SODA.nc, Rec=0001, Index=1)
- free-surface
(Min = 8.77033105E-02 Max = 2.54816829E-01)
- vertically integrated u-momentum component
(Min = -6.69384175E+33 Max = 1.03453879E-01)
- vertically integrated v-momentum component
(Min = -1.45373899E+33 Max = 6.30954578E-02)
- u-momentum component
(Min = -9.98603466E+33 Max = 1.03502824E-01)
- v-momentum component
(Min = -4.06589696E+33 Max = 7.96828220E-02)
- potential temperature
(Min = -8.20340958E+33 Max = 1.87979098E+01)
- salinity
(Min = -8.20340958E+33 Max = 3.38521819E+01)
GET_NGFLD - tidal period
(Min = 4.30820446E+04 Max = 9.67260841E+04)
GET_2DFLD - tidal elevation amplitude
(Min = 0.00000000E+00 Max = 6.20000029E+00)
GET_2DFLD - tidal elevation phase angle
(Min = 0.00000000E+00 Max = 6.26344809E+00)
GET_2DFLD - tidal current inclination angle
(Min = -1.53817380E+00 Max = 3.14159265E+00)
GET_2DFLD - tidal current phase angle
(Min = 0.00000000E+00 Max = 6.24788031E+00)
GET_2DFLD - maximum tidal current, ellipse major axis
(Min = 0.00000000E+00 Max = 7.62899017E+00)
GET_2DFLD - minimum tidal current, ellipse minor axis
(Min = -6.62547231E-01 Max = 1.86996365E+00)

GET_2DFLD - unable to find requested variable: Uwind

GET_2DFLD - unable to find requested variable: Uwind
in file:
Data/tides_yellow_sea.nc
in file:
Data/tides_yellow_sea.nc

Elapsed CPU time (seconds):

Node # 0 CPU: 0.912
Node # 1 CPU: 1.108
Total: 2.020

Nonlinear model elapsed time profile:

Reading of input data ............................ 0.220 (10.8911 %)
2D/3D coupling, vertical metrics ................. 0.024 ( 1.1881 %)
Omega vertical velocity .......................... 0.020 ( 0.9901 %)
Equation of state for seawater ................... 0.224 (11.0891 %)
Total: 0.488 24.1584

Nonlinear model message Passage profile:

Message Passage: 2D halo exchanges ............... 0.004 ( 0.1980 %)
Message Passage: 3D halo exchanges ............... 0.028 ( 1.3862 %)
Message Passage: data broadcast .................. 0.400 (19.8020 %)
Message Passage: data scattering.................. 0.268 (13.2672 %)
Total: 0.700 34.6534

All percentages are with respect to total time = 2.020

ROMS/TOMS - Output NetCDF summary for Grid 01:

Analytical header files used:

ROMS/Functionals/ana_nudgcoef.h

ROMS/TOMS - Input error ............. exit_flag: 2


ERROR: Abnormal termination: NetCDF INPUT.
REASON: No error

[kate]

Yes, you have selected BULK_FLUXES which needs winds. Here are your choices:
https://www.myroms.org/wiki/index.php/F ... forcing.3F

[simion1232006]

#define ANA_SMFLUX and #undef BULK_FLUX. Otherwise it needs to read in the heat flux and wind forcing.

[chenzhen2181]

#define ANA_SMFLUX and #undef BULK_FLUX. Otherwise it needs to read in the heat flux and wind forcing.

Thank you for your reply !
I #define ANA_SMFLUX and ANA_STFLUX.h ,#undef BULK_FLUX . Still get an error !
I couldn't find zeta_time in Yellow_Sea_bdry_SODA.nc. I also check make_bdry_file.py , also couldn't find some aboult 'zeta_time'.

RUN LOG
Process Information:

Node # 0 (pid= 14858) is active.
Node # 1 (pid= 14859) is active.

Model Input Parameters: ROMS/TOMS version 3.4
Saturday - June 21, 2014 - 10:14:49 AM
-----------------------------------------------------------------------------

Yellow Sea

Operating system : Linux
CPU/hardware : i686
Compiler system : gfortran
Compiler command : /home/chenzhen/install/mpich2-1.5/bin/mpif90
Compiler flags : -frepack-arrays -O3 -ffast-math -ffree-form -ffree-line-length-none

Input Script : cal/ocean_yellow.in

SVN Root URL : https://www.myroms.org/svn/omlab/branches/jcwarner
SVN Revision : 已导出

Local Root : /home/chenzhen/COAWST
Header Dir : /home/chenzhen/COAWST/Projects/chenzhen/Yellow/ROMS/Include
Header file : yellow.h
Analytical Dir: /home/chenzhen/COAWST/Projects/chenzhen/Yellow/ROMS/Functionals

Resolution, Grid 01: 0080x0080x040, Parallel Nodes: 2, Tiling: 001x002


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

1080 ntimes Number of timesteps for 3-D equations.
800.000 dt Timestep size (s) for 3-D equations.
20 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.
108 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).
108 nHIS Number of timesteps between the writing fields
into history file.
0.0000E+00 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-04 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.
0.0000E+00 Zob Bottom roughness (m).
2 Vtransform S-coordinate transformation equation.
1 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.
1000.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
0.000 dstart Time-stamp assigned to model initialization (days).
0.000 tide_start Reference time origin for tidal forcing (days).
0.00 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.
0.000 T0 Background potential temperature (C) constant.
0.000 S0 Background salinity (PSU) constant.
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

Output/Input Files:

Output Restart File: result/ocean_rst.nc
Output History File: result/ocean_his.nc
Input Grid File: Data/yellow_sea_grid.nc
Input Nonlinear Initial File: Data/Yellow_Sea_ini_SODA.nc
Input Forcing File 01: Data/tides_yellow_sea.nc
Input Boundary File: Data/Yellow_Sea_bdry_SODA.nc

Tile partition information for Grid 01: 0080x0080x0040 tiling: 001x002

tile Istr Iend Jstr Jend Npts

0 1 80 1 40 128000
1 1 80 41 80 128000

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 80.50 0.50 40.50 RHO-points
1 0.50 80.50 40.50 80.50 RHO-points

0 1.00 80.00 0.50 40.50 U-points
1 1.00 80.00 40.50 80.50 U-points

0 0.50 80.50 1.00 40.50 V-points
1 0.50 80.50 40.50 80.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 182
HaloSizeJ(1) = 104
TileSide(1) = 85
TileSize(1) = 3910


Activated C-preprocessing Options:

YELLOW Yellow Sea
ADD_FSOBC Adding tidal elevation to proccesed OBC data.
ADD_M2OBC Adding tidal currents to proccesed OBC data.
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_STFLUX Analytical kinematic surface temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
CURVGRID Orthogonal curvilinear grid.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
MASKING Land/Sea masking.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SOLVE3D Solving 3D Primitive Equations.
SOUTH_FSCHAPMAN Southern edge, free-surface, Chapman condition.
SOUTH_M2FLATHER Southern edge, 2D momentum, Flather condition.
SOUTH_M3NUDGING Southern edge, 3D momentum, passive/active outflow/inflow.
SOUTH_M3RADIATION Southern edge, 3D momentum, radiation condition.
SOUTH_TNUDGING Southern edge, tracers, passive/active outflow/inflow.
SOUTH_TRADIATION Southern edge, tracers, radiation condition.
SSH_TIDES Add tidal elevation to SSH climatology.
TS_U3HADVECTION Third-order upstream horizontal advection of tracers.
TS_C4VADVECTION Fourth-order centered vertical advection 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_TIDES Add tidal currents to 2D momentum climatologies.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.

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

40 0.0000000 0.0000000 0.000 0.000 0.000 0.000
39 -0.0250000 -0.0017775 -0.067 -0.067 -0.108 -0.132
38 -0.0500000 -0.0037835 -0.134 -0.134 -0.217 -0.268
37 -0.0750000 -0.0060921 -0.203 -0.203 -0.330 -0.409
36 -0.1000000 -0.0087922 -0.272 -0.272 -0.446 -0.557
35 -0.1250000 -0.0119914 -0.342 -0.342 -0.568 -0.714
34 -0.1500000 -0.0158197 -0.415 -0.415 -0.695 -0.882
33 -0.1750000 -0.0204330 -0.489 -0.489 -0.830 -1.063
32 -0.2000000 -0.0260168 -0.565 -0.565 -0.974 -1.261
31 -0.2250000 -0.0327879 -0.644 -0.644 -1.129 -1.479
30 -0.2500000 -0.0409944 -0.727 -0.727 -1.298 -1.722
29 -0.2750000 -0.0509117 -0.815 -0.815 -1.483 -1.995
28 -0.3000000 -0.0628318 -0.907 -0.907 -1.688 -2.303
27 -0.3250000 -0.0770446 -1.005 -1.005 -1.914 -2.650
26 -0.3500000 -0.0938098 -1.110 -1.110 -2.165 -3.042
25 -0.3750000 -0.1133185 -1.221 -1.221 -2.442 -3.481
24 -0.4000000 -0.1356491 -1.339 -1.339 -2.746 -3.968
23 -0.4250000 -0.1607245 -1.464 -1.464 -3.076 -4.504
22 -0.4500000 -0.1882840 -1.596 -1.596 -3.430 -5.082
21 -0.4750000 -0.2178817 -1.732 -1.732 -3.804 -5.695
20 -0.5000000 -0.2489214 -1.872 -1.872 -4.191 -6.334
19 -0.5250000 -0.2807264 -2.014 -2.014 -4.585 -6.986
18 -0.5500000 -0.3126323 -2.157 -2.157 -4.981 -7.639
17 -0.5750000 -0.3440788 -2.298 -2.298 -5.372 -8.285
16 -0.6000000 -0.3746809 -2.437 -2.437 -5.755 -8.916
15 -0.6250000 -0.4042644 -2.573 -2.573 -6.128 -9.529
14 -0.6500000 -0.4328656 -2.707 -2.707 -6.492 -10.125
13 -0.6750000 -0.4607052 -2.839 -2.839 -6.849 -10.708
12 -0.7000000 -0.4881475 -2.970 -2.970 -7.201 -11.285
11 -0.7250000 -0.5156591 -3.102 -3.102 -7.555 -11.862
10 -0.7500000 -0.5437741 -3.234 -3.234 -7.914 -12.450
9 -0.7750000 -0.5730691 -3.370 -3.370 -8.285 -13.058
8 -0.8000000 -0.6041494 -3.510 -3.510 -8.672 -13.697
7 -0.8250000 -0.6376434 -3.657 -3.657 -9.083 -14.378
6 -0.8500000 -0.6742046 -3.811 -3.811 -9.523 -15.112
5 -0.8750000 -0.7145184 -3.974 -3.974 -9.999 -15.911
4 -0.9000000 -0.7593114 -4.148 -4.148 -10.517 -16.788
3 -0.9250000 -0.8093643 -4.336 -4.336 -11.086 -17.756
2 -0.9500000 -0.8655258 -4.539 -4.539 -11.713 -18.829
1 -0.9750000 -0.9287272 -4.759 -4.759 -12.408 -20.024
0 -1.0000000 -1.0000000 -5.000 -5.000 -13.179 -21.359

Time Splitting Weights: ndtfast = 20 nfast = 29

Primary Secondary Accumulated to Current Step

1-0.0009651193358779 0.0500000000000000-0.0009651193358779 0.0500000000000000
2-0.0013488780126037 0.0500482559667939-0.0023139973484816 0.1000482559667939
3-0.0011514592651645 0.0501156998674241-0.0034654566136461 0.1501639558342180
4-0.0003735756740661 0.0501732728306823-0.0038390322877122 0.2003372286649003
5 0.0009829200513762 0.0501919516143856-0.0028561122363360 0.2505291802792859
6 0.0029141799764308 0.0501428056118168 0.0000580677400948 0.3006719858911027
7 0.0054132615310267 0.0499970966129953 0.0054713292711215 0.3506690825040980
8 0.0084687837865132 0.0497264335364439 0.0139401130576347 0.4003955160405419
9 0.0120633394191050 0.0493029943471183 0.0260034524767397 0.4496985103876602
10 0.0161716623600090 0.0486998273761630 0.0421751148367487 0.4983983377638232
11 0.0207585511322367 0.0478912442581626 0.0629336659689854 0.5462895820219857
12 0.0257765478740990 0.0468533167015507 0.0887102138430844 0.5931428987235364
13 0.0311633730493853 0.0455644893078458 0.1198735868924698 0.6387073880313822
14 0.0368391158442262 0.0440063206553765 0.1567127027366960 0.6827137086867586
15 0.0427031802506397 0.0421643648631652 0.1994158829873357 0.7248780735499238
16 0.0486309868367616 0.0400292058506332 0.2480468698240973 0.7649072794005570
17 0.0544704302037592 0.0375976565087951 0.3025173000278565 0.8025049359093521
18 0.0600380921294286 0.0348741349986072 0.3625553921572851 0.8373790709079593
19 0.0651152103984763 0.0318722303921357 0.4276706025557614 0.8692513013000950
20 0.0694434033194840 0.0286164698722119 0.4971140058752453 0.8978677711723069
21 0.0727201499285570 0.0251442997062377 0.5698341558038024 0.9230120708785446
22 0.0745940258796570 0.0215082922098099 0.6444281816834594 0.9445203630883545
23 0.0746596950216180 0.0177785909158270 0.7190878767050775 0.9622989540041815
24 0.0724526566618460 0.0140456061647461 0.7915405333669234 0.9763445601689277
25 0.0674437485167025 0.0104229733316538 0.8589842818836260 0.9867675335005816
26 0.0590334053485720 0.0070507859058187 0.9180176872321980 0.9938183194064003
27 0.0465456732896125 0.0040991156383901 0.9645633605218105 0.9979174350447904
28 0.0292219798521905 0.0017718319739095 0.9937853403740009 0.9996892670186999
29 0.0062146596259991 0.0003107329813000 1.0000000000000000 0.9999999999999998

ndtfast, nfast = 20 29 nfast/ndtfast = 1.45000

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

1.000000000000 1.060707743385 0.530353871693 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.14200

Minimum X-grid spacing, DXmin = 8.88372172E+00 km
Maximum X-grid spacing, DXmax = 1.16654601E+01 km
Minimum Y-grid spacing, DYmin = 7.65876935E+00 km
Maximum Y-grid spacing, DYmax = 1.00685906E+01 km
Minimum Z-grid spacing, DZmin = 6.69436342E-02 m
Maximum Z-grid spacing, DZmax = 1.33482535E+00 m

Minimum barotropic Courant Number = 3.67539224E-02
Maximum barotropic Courant Number = 8.79350377E-02
Maximum Coriolis Courant Number = 7.65944146E-02


NLM: GET_STATE - Read state initial conditions, t = 39451 12:00:00
(File: Yellow_Sea_ini_SODA.nc, Rec=0001, Index=1)
- free-surface
(Min = 8.77033105E-02 Max = 2.54816829E-01)
- vertically integrated u-momentum component
(Min = -6.69384175E+33 Max = 1.03453879E-01)
- vertically integrated v-momentum component
(Min = -1.45373899E+33 Max = 6.30954578E-02)
- u-momentum component
(Min = -9.98603466E+33 Max = 1.03502824E-01)
- v-momentum component
(Min = -4.06589696E+33 Max = 7.96828220E-02)
- potential temperature
(Min = -8.20340958E+33 Max = 1.87979098E+01)
- salinity
(Min = -8.20340958E+33 Max = 3.38521819E+01)
GET_NGFLD - tidal period
(Min = 4.30820446E+04 Max = 9.67260841E+04)
GET_2DFLD - tidal elevation amplitude
(Min = 0.00000000E+00 Max = 6.20000029E+00)
GET_2DFLD - tidal elevation phase angle
(Min = 0.00000000E+00 Max = 6.26344809E+00)
GET_2DFLD - tidal current inclination angle
(Min = -1.53817380E+00 Max = 3.14159265E+00)
GET_2DFLD - tidal current phase angle
(Min = 0.00000000E+00 Max = 6.24788031E+00)
GET_2DFLD - maximum tidal current, ellipse major axis
(Min = 0.00000000E+00 Max = 7.62899017E+00)
GET_2DFLD - minimum tidal current, ellipse minor axis
(Min = -6.62547231E-01 Max = 1.86996365E+00)

NETCDF_GET_FVAR_1D - error while inquiring ID for variable: zeta_time
in input file: Data/Yellow_Sea_bdry_SODA.nc
call from: get_cycle.F

Elapsed CPU time (seconds):

Node # 0 CPU: 0.848
Node # 1 CPU: 0.844
Total: 1.692

Nonlinear model elapsed time profile:

Reading of input data ............................ 0.212 (12.5295 %)
2D/3D coupling, vertical metrics ................. 0.020 ( 1.1821 %)
Omega vertical velocity .......................... 0.020 ( 1.1820 %)
Equation of state for seawater ................... 0.136 ( 8.0378 %)
Total: 0.388 22.9314

Nonlinear model message Passage profile:

Message Passage: 2D halo exchanges ............... 0.020 ( 1.1820 %)
Message Passage: 3D halo exchanges ............... 0.020 ( 1.1820 %)
Message Passage: data broadcast .................. 0.180 (10.6384 %)
Message Passage: data scattering.................. 0.288 (17.0210 %)
Total: 0.508 30.0234

All percentages are with respect to total time = 1.692

ROMS/TOMS - Output NetCDF summary for Grid 01:

Analytical header files used:

ROMS/Functionals/ana_nudgcoef.h

ROMS/TOMS - Input error ............. exit_flag: 2


ERROR: Abnormal termination: NetCDF INPUT.
REASON: NetCDF: Variable not found

[kate]

That python script probably called it "ocean_time" instead of "zeta_time". One choice is to modify the appropriate entries in the varinfo.dat file. Another choice is to modify the python script so that the "time" attribute gets added to fields like "zeta_south", set to "ocean_time". A third choice is to run ncatted to do the same thing.

[simion1232006]

Best choice would be using the ROMS official input file generating scripts (Matlab). You can modified it for your own purpose. Those scripts guarantee an standard input and usually would not make any mistake. I personally don't recommend change anything in varinfo.dat, as it might cause confusion later.

[kate]

Varinfo.dat is the way it is to allow users the freedom to modify it for our particular needs (even naming variables in French if so desired). You can also have a different varinfo.dat for each domain, for instance when changing forcing fields requires a change of scaling. Those using pyroms must be bold enough to do a little customization.

[chenzhen2181]

That python script probably called it "ocean_time" instead of "zeta_time". One choice is to modify the appropriate entries in the varinfo.dat file. Another choice is to modify the python script so that the "time" attribute gets added to fields like "zeta_south", set to "ocean_time". A third choice is to run ncatted to do the same thing.

Thank you for your suggestion !
I am a newer in python and ROMS model. I have a try to change the dimensions 'ocean_time' to 'zeta_time'.
Scrip:
import netCDF4
fname='/home/chenzhen/COAWST/Projects/chenzhen/Yellow/Data/Yellow_Sea_bdry_SODA.nc'
f=netCDF4.Dataset(fname,'r+')
f.renameDimension('ocean_time','zeta_time')
I can find the dimensions is changed from 'ocean_time' to 'zeta_time'.
But when I run it ,it still show a same error .
NETCDF_GET_FVAR_1D - error while inquiring ID for variable: zeta_time
in input file: Data/Yellow_Sea_bdry_SODA.nc
call from: get_cycle.F
Could you give me some help ? You can find Yellow_Sea_bdry_SODA.nc in attachment.

[kate]

Code: Select all

	double ocean_time(zeta_time) ;
		ocean_time:long_name = "time" ;
		ocean_time:units = "days since 1900-01-01 00:00:00" ;
		ocean_time:field = " " ;

Next time, please just include the "ncdump -h" from the file, not the entire binary file.

OK, so you changed the dimension name from ocean_time to zeta_time, but you didn't change the variable name. The reason I didn't suggest changing the variable/dimension names is that varinfo.dat points to zeta_time for zeta, v2d_time for ubar/vbar, v3d_time for u/v, and so on. You would need to duplicate the ocean_time variable, renaming it to each of these things.

Better would be to add the time attributes, to get:

Code: Select all

	double v_west(zeta_time, s_rho, eta_v) ;
		v_west:_FillValue = -9.98999971057742e+33 ;
		v_west:long_name = "3D v-momentum west boundary condition" ;
		v_west:units = "meter second-1" ;
		v_west:field = "v_east, scalar, series" ;
		v_west:time = "ocean_time" ;

[chenzhen2181]

Code: Select all

	double ocean_time(zeta_time) ;
		ocean_time:long_name = "time" ;
		ocean_time:units = "days since 1900-01-01 00:00:00" ;
		ocean_time:field = " " ;

Next time, please just include the "ncdump -h" from the file, not the entire binary file.

OK, so you changed the dimension name from ocean_time to zeta_time, but you didn't change the variable name. The reason I didn't suggest changing the variable/dimension names is that varinfo.dat points to zeta_time for zeta, v2d_time for ubar/vbar, v3d_time for u/v, and so on. You would need to duplicate the ocean_time variable, renaming it to each of these things.

Better would be to add the time attributes, to get:

Code: Select all

	double v_west(zeta_time, s_rho, eta_v) ;
		v_west:_FillValue = -9.98999971057742e+33 ;
		v_west:long_name = "3D v-momentum west boundary condition" ;
		v_west:units = "meter second-1" ;
		v_west:field = "v_east, scalar, series" ;
		v_west:time = "ocean_time" ;

Thank you kate !
I modified varinfo.dat file. The error about "zeta_time" disappered. But I get another error ,when I run it. And I couldn't find any infomation about it. Could you give me some advice?
--chenzhen
run log
Process Information:

Node # 0 (pid= 3851) is active.
Node # 1 (pid= 3852) is active.

Model Input Parameters: ROMS/TOMS version 3.4
Sunday - June 29, 2014 - 11:51:58 PM
-----------------------------------------------------------------------------

Yellow Sea

Operating system : Linux
CPU/hardware : i686
Compiler system : gfortran
Compiler command : /home/chenzhen/install/mpich2-1.5/bin/mpif90
Compiler flags : -frepack-arrays -O3 -ffast-math -ffree-form -ffree-line-length-none

Input Script : cal/ocean_yellow.in

SVN Root URL : https://www.myroms.org/svn/omlab/branches/jcwarner
SVN Revision : 已导出

Local Root : /home/chenzhen/COAWST
Header Dir : /home/chenzhen/COAWST/Projects/chenzhen/Yellow/ROMS/Include
Header file : yellow.h
Analytical Dir: /home/chenzhen/COAWST/Projects/chenzhen/Yellow/ROMS/Functionals

Resolution, Grid 01: 0080x0080x040, Parallel Nodes: 2, Tiling: 001x002


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

1080 ntimes Number of timesteps for 3-D equations.
800.000 dt Timestep size (s) for 3-D equations.
20 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.
108 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).
108 nHIS Number of timesteps between the writing fields
into history file.
0.0000E+00 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-04 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.
0.0000E+00 Zob Bottom roughness (m).
2 Vtransform S-coordinate transformation equation.
1 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.
1000.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
0.000 dstart Time-stamp assigned to model initialization (days).
0.000 tide_start Reference time origin for tidal forcing (days).
0.00 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.
0.000 T0 Background potential temperature (C) constant.
0.000 S0 Background salinity (PSU) constant.
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

Output/Input Files:

Output Restart File: result/ocean_rst.nc
Output History File: result/ocean_his.nc
Input Grid File: Data/yellow_sea_grid.nc
Input Nonlinear Initial File: Data/Yellow_Sea_ini_SODA.nc
Input Forcing File 01: Data/tides_yellow_sea.nc
Input Boundary File: Data/Yellow_Sea_bdry_SODA.nc

Tile partition information for Grid 01: 0080x0080x0040 tiling: 001x002

tile Istr Iend Jstr Jend Npts

0 1 80 1 40 128000
1 1 80 41 80 128000

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 80.50 0.50 40.50 RHO-points
1 0.50 80.50 40.50 80.50 RHO-points

0 1.00 80.00 0.50 40.50 U-points
1 1.00 80.00 40.50 80.50 U-points

0 0.50 80.50 1.00 40.50 V-points
1 0.50 80.50 40.50 80.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 182
HaloSizeJ(1) = 104
TileSide(1) = 85
TileSize(1) = 3910


Activated C-preprocessing Options:

YELLOW Yellow Sea
ADD_FSOBC Adding tidal elevation to proccesed OBC data.
ADD_M2OBC Adding tidal currents to proccesed OBC data.
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_STFLUX Analytical kinematic surface temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
CURVGRID Orthogonal curvilinear grid.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
MASKING Land/Sea masking.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SOLVE3D Solving 3D Primitive Equations.
SOUTH_FSCHAPMAN Southern edge, free-surface, Chapman condition.
SOUTH_M2FLATHER Southern edge, 2D momentum, Flather condition.
SOUTH_M3NUDGING Southern edge, 3D momentum, passive/active outflow/inflow.
SOUTH_M3RADIATION Southern edge, 3D momentum, radiation condition.
SOUTH_TNUDGING Southern edge, tracers, passive/active outflow/inflow.
SOUTH_TRADIATION Southern edge, tracers, radiation condition.
SSH_TIDES Add tidal elevation to SSH climatology.
TS_U3HADVECTION Third-order upstream horizontal advection of tracers.
TS_C4VADVECTION Fourth-order centered vertical advection 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_TIDES Add tidal currents to 2D momentum climatologies.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.

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

40 0.0000000 0.0000000 0.000 0.000 0.000 0.000
39 -0.0250000 -0.0017775 -0.067 -0.067 -0.108 -0.132
38 -0.0500000 -0.0037835 -0.134 -0.134 -0.217 -0.268
37 -0.0750000 -0.0060921 -0.203 -0.203 -0.330 -0.409
36 -0.1000000 -0.0087922 -0.272 -0.272 -0.446 -0.557
35 -0.1250000 -0.0119914 -0.342 -0.342 -0.568 -0.714
34 -0.1500000 -0.0158197 -0.415 -0.415 -0.695 -0.882
33 -0.1750000 -0.0204330 -0.489 -0.489 -0.830 -1.063
32 -0.2000000 -0.0260168 -0.565 -0.565 -0.974 -1.261
31 -0.2250000 -0.0327879 -0.644 -0.644 -1.129 -1.479
30 -0.2500000 -0.0409944 -0.727 -0.727 -1.298 -1.722
29 -0.2750000 -0.0509117 -0.815 -0.815 -1.483 -1.995
28 -0.3000000 -0.0628318 -0.907 -0.907 -1.688 -2.303
27 -0.3250000 -0.0770446 -1.005 -1.005 -1.914 -2.650
26 -0.3500000 -0.0938098 -1.110 -1.110 -2.165 -3.042
25 -0.3750000 -0.1133185 -1.221 -1.221 -2.442 -3.481
24 -0.4000000 -0.1356491 -1.339 -1.339 -2.746 -3.968
23 -0.4250000 -0.1607245 -1.464 -1.464 -3.076 -4.504
22 -0.4500000 -0.1882840 -1.596 -1.596 -3.430 -5.082
21 -0.4750000 -0.2178817 -1.732 -1.732 -3.804 -5.695
20 -0.5000000 -0.2489214 -1.872 -1.872 -4.191 -6.334
19 -0.5250000 -0.2807264 -2.014 -2.014 -4.585 -6.986
18 -0.5500000 -0.3126323 -2.157 -2.157 -4.981 -7.639
17 -0.5750000 -0.3440788 -2.298 -2.298 -5.372 -8.285
16 -0.6000000 -0.3746809 -2.437 -2.437 -5.755 -8.916
15 -0.6250000 -0.4042644 -2.573 -2.573 -6.128 -9.529
14 -0.6500000 -0.4328656 -2.707 -2.707 -6.492 -10.125
13 -0.6750000 -0.4607052 -2.839 -2.839 -6.849 -10.708
12 -0.7000000 -0.4881475 -2.970 -2.970 -7.201 -11.285
11 -0.7250000 -0.5156591 -3.102 -3.102 -7.555 -11.862
10 -0.7500000 -0.5437741 -3.234 -3.234 -7.914 -12.450
9 -0.7750000 -0.5730691 -3.370 -3.370 -8.285 -13.058
8 -0.8000000 -0.6041494 -3.510 -3.510 -8.672 -13.697
7 -0.8250000 -0.6376434 -3.657 -3.657 -9.083 -14.378
6 -0.8500000 -0.6742046 -3.811 -3.811 -9.523 -15.112
5 -0.8750000 -0.7145184 -3.974 -3.974 -9.999 -15.911
4 -0.9000000 -0.7593114 -4.148 -4.148 -10.517 -16.788
3 -0.9250000 -0.8093643 -4.336 -4.336 -11.086 -17.756
2 -0.9500000 -0.8655258 -4.539 -4.539 -11.713 -18.829
1 -0.9750000 -0.9287272 -4.759 -4.759 -12.408 -20.024
0 -1.0000000 -1.0000000 -5.000 -5.000 -13.179 -21.359

Time Splitting Weights: ndtfast = 20 nfast = 29

Primary Secondary Accumulated to Current Step

1-0.0009651193358779 0.0500000000000000-0.0009651193358779 0.0500000000000000
2-0.0013488780126037 0.0500482559667939-0.0023139973484816 0.1000482559667939
3-0.0011514592651645 0.0501156998674241-0.0034654566136461 0.1501639558342180
4-0.0003735756740661 0.0501732728306823-0.0038390322877122 0.2003372286649003
5 0.0009829200513762 0.0501919516143856-0.0028561122363360 0.2505291802792859
6 0.0029141799764308 0.0501428056118168 0.0000580677400948 0.3006719858911027
7 0.0054132615310267 0.0499970966129953 0.0054713292711215 0.3506690825040980
8 0.0084687837865132 0.0497264335364439 0.0139401130576347 0.4003955160405419
9 0.0120633394191050 0.0493029943471183 0.0260034524767397 0.4496985103876602
10 0.0161716623600090 0.0486998273761630 0.0421751148367487 0.4983983377638232
11 0.0207585511322367 0.0478912442581626 0.0629336659689854 0.5462895820219857
12 0.0257765478740990 0.0468533167015507 0.0887102138430844 0.5931428987235364
13 0.0311633730493853 0.0455644893078458 0.1198735868924698 0.6387073880313822
14 0.0368391158442262 0.0440063206553765 0.1567127027366960 0.6827137086867586
15 0.0427031802506397 0.0421643648631652 0.1994158829873357 0.7248780735499238
16 0.0486309868367616 0.0400292058506332 0.2480468698240973 0.7649072794005570
17 0.0544704302037592 0.0375976565087951 0.3025173000278565 0.8025049359093521
18 0.0600380921294286 0.0348741349986072 0.3625553921572851 0.8373790709079593
19 0.0651152103984763 0.0318722303921357 0.4276706025557614 0.8692513013000950
20 0.0694434033194840 0.0286164698722119 0.4971140058752453 0.8978677711723069
21 0.0727201499285570 0.0251442997062377 0.5698341558038024 0.9230120708785446
22 0.0745940258796570 0.0215082922098099 0.6444281816834594 0.9445203630883545
23 0.0746596950216180 0.0177785909158270 0.7190878767050775 0.9622989540041815
24 0.0724526566618460 0.0140456061647461 0.7915405333669234 0.9763445601689277
25 0.0674437485167025 0.0104229733316538 0.8589842818836260 0.9867675335005816
26 0.0590334053485720 0.0070507859058187 0.9180176872321980 0.9938183194064003
27 0.0465456732896125 0.0040991156383901 0.9645633605218105 0.9979174350447904
28 0.0292219798521905 0.0017718319739095 0.9937853403740009 0.9996892670186999
29 0.0062146596259991 0.0003107329813000 1.0000000000000000 0.9999999999999998

ndtfast, nfast = 20 29 nfast/ndtfast = 1.45000

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

1.000000000000 1.060707743385 0.530353871693 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.14200

Minimum X-grid spacing, DXmin = 8.88372172E+00 km
Maximum X-grid spacing, DXmax = 1.16654601E+01 km
Minimum Y-grid spacing, DYmin = 7.65876935E+00 km
Maximum Y-grid spacing, DYmax = 1.00685906E+01 km
Minimum Z-grid spacing, DZmin = 6.69436342E-02 m
Maximum Z-grid spacing, DZmax = 1.33482535E+00 m

Minimum barotropic Courant Number = 3.67539224E-02
Maximum barotropic Courant Number = 8.79350377E-02
Maximum Coriolis Courant Number = 7.65944146E-02


NLM: GET_STATE - Read state initial conditions, t = 39451 12:00:00
(File: Yellow_Sea_ini_SODA.nc, Rec=0001, Index=1)
- free-surface
(Min = 8.77033105E-02 Max = 2.54816829E-01)
- vertically integrated u-momentum component
(Min = -6.69384175E+33 Max = 1.03453879E-01)
- vertically integrated v-momentum component
(Min = -1.45373899E+33 Max = 6.30954578E-02)
- u-momentum component
(Min = -9.98603466E+33 Max = 1.03502824E-01)
- v-momentum component
(Min = -4.06589696E+33 Max = 7.96828220E-02)
- potential temperature
(Min = -8.20340958E+33 Max = 1.87979098E+01)
- salinity
(Min = -8.20340958E+33 Max = 3.38521819E+01)
GET_NGFLD - tidal period
(Min = 4.30820446E+04 Max = 9.67260841E+04)
GET_2DFLD - tidal elevation amplitude
(Min = 0.00000000E+00 Max = 6.20000029E+00)
GET_2DFLD - tidal elevation phase angle
(Min = 0.00000000E+00 Max = 6.26344809E+00)
GET_2DFLD - tidal current inclination angle
(Min = -1.53817380E+00 Max = 3.14159265E+00)
GET_2DFLD - tidal current phase angle
(Min = 0.00000000E+00 Max = 6.24788031E+00)
GET_2DFLD - maximum tidal current, ellipse major axis
(Min = 0.00000000E+00 Max = 7.62899017E+00)
GET_2DFLD - minimum tidal current, ellipse minor axis
(Min = -6.62547231E-01 Max = 1.86996365E+00)
GET_NGFLD - free-surface southern boundary condition, t = 39451 12:00:00
(Rec=0001, Index=2, File: Yellow_Sea_bdry_SODA.nc)
(Tmin= 39451.5000 Tmax= 39501.5000)
(Min = 0.00000000E+00 Max = 2.46359504E-01)
GET_NGFLD - 2D u-momentum southern boundary condition, t = 39451 12:00:00
(Rec=0001, Index=2, File: Yellow_Sea_bdry_SODA.nc)
(Tmin= 39451.5000 Tmax= 39501.5000)
(Min = -4.58702028E-02 Max = 1.06274266E-01)
GET_NGFLD - 2D v-momentum southern boundary condition, t = 39451 12:00:00
(Rec=0001, Index=2, File: Yellow_Sea_bdry_SODA.nc)
(Tmin= 39451.5000 Tmax= 39501.5000)
(Min = -9.42163486E-02 Max = 3.96214616E-02)
GET_NGFLD - 3D u-momentum southern boundary condition, t = 39451 12:00:00
(Rec=0001, Index=2, File: Yellow_Sea_bdry_SODA.nc)
(Tmin= 39451.5000 Tmax= 39501.5000)
(Min = -4.67661370E-02 Max = 1.02964423E-01)
GET_NGFLD - 3D v-momentum southern boundary condition, t = 39451 12:00:00
(Rec=0001, Index=2, File: Yellow_Sea_bdry_SODA.nc)
(Tmin= 39451.5000 Tmax= 39501.5000)
(Min = -1.00452846E-01 Max = 6.09981780E-02)
GET_NGFLD - temperature southern boundary condition, t = 39451 12:00:00
(Rec=0001, Index=2, File: Yellow_Sea_bdry_SODA.nc)
(Tmin= 39451.5000 Tmax= 39501.5000)
(Min = 0.00000000E+00 Max = 1.88157837E+01)
GET_NGFLD - salinity southern boundary condition, t = 39451 12:00:00
(Rec=0001, Index=2, File: Yellow_Sea_bdry_SODA.nc)
(Tmin= 39451.5000 Tmax= 39501.5000)
(Min = 0.00000000E+00 Max = 3.41110077E+01)

Maximum grid stiffness ratios: rx0 = 3.500000E-01 (Beckmann and Haidvogel)
rx1 = 1.504617E+01 (Haney)


Initial basin volumes: TotVolume = 1.2341359223E+12 m3
MinVolume = 4.8927290410E+06 m3
MaxVolume = 1.1700882170E+08 m3
Max/Min = 2.3914837859E+01

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 04260763 - 00001080)

Elapsed CPU time (seconds):

Node # 0 CPU: 0.876
Node # 1 CPU: 0.892
Total: 1.768

Nonlinear model elapsed time profile:

Initialization ................................... 1.172 (66.2896 %)
OI data assimilation ............................. 0.004 ( 0.2262 %)
Reading of input data ............................ 0.300 (16.9684 %)
2D/3D coupling, vertical metrics ................. 0.024 ( 1.3574 %)
Omega vertical velocity .......................... 0.020 ( 1.1312 %)
Equation of state for seawater ................... 0.140 ( 7.9186 %)
Total: 1.660 93.8914

Nonlinear model message Passage profile:

Message Passage: 2D halo exchanges ............... 0.012 ( 0.6787 %)
Message Passage: 3D halo exchanges ............... 0.012 ( 0.6788 %)
Message Passage: data broadcast .................. 0.260 (14.7060 %)
Message Passage: data reduction .................. 0.004 ( 0.2263 %)
Message Passage: data scattering.................. 0.256 (14.4795 %)
Total: 0.544 30.7693

All percentages are with respect to total time = 1.768

ROMS/TOMS - Output NetCDF summary for Grid 01:

Analytical header files used:

ROMS/Functionals/ana_nudgcoef.h

ROMS/TOMS: DONE... Sunday - June 29, 2014 - 11:51:59 PM

[kate]

NLM: GET_STATE - Read state initial conditions, t = 39451 12:00:00
(File: Yellow_Sea_ini_SODA.nc, Rec=0001, Index=1)
- free-surface
(Min = 8.77033105E-02 Max = 2.54816829E-01)
- vertically integrated u-momentum component
(Min = -6.69384175E+33 Max = 1.03453879E-01)
- vertically integrated v-momentum component
(Min = -1.45373899E+33 Max = 6.30954578E-02)
- u-momentum component
(Min = -9.98603466E+33 Max = 1.03502824E-01)
- v-momentum component
(Min = -4.06589696E+33 Max = 7.96828220E-02)
- potential temperature
(Min = -8.20340958E+33 Max = 1.87979098E+01)
- salinity
(Min = -8.20340958E+33 Max = 3.38521819E+01)

These minimum values are worrisome. I'd look into where they are coming from.