Model Run

General scientific issues regarding ROMS

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surja
Posts: 12
Joined: Thu Jan 12, 2012 5:19 pm
Location: Jadavpur university,INCOIS

Model Run

#1 Unread post by surja »

Dear all,
Today I tried to run Indian ocean Model in Matlab version of Roms.
I take model domain as 40S- 25N, 30E-120E and gird size 1/3 deg.When I am trying to run this model I have got the following output


INDIAN OCEAN MODEL
720 ntimes Total number of timesteps for 3D equations.
3600.00 dt Timestep [sec] for 3D equations
60 ndtfast Number of 2D timesteps within each 3D step.
1 ninfo Number of timesteps between runtime diagnostics.

6.000E+00 theta_s S-coordinate surface control parameter.
0.000E+00 theta_b S-coordinate bottom control parameter.
1.000E+01 Tcline S-coordinate surface/bottom layer width used in
vertical coordinate stretching, meters.
Grid File: ROMS_FILES/roms_grd_ind_2.nc
Forcing Data File: ROMS_FILES/roms_frc_ind_2.nc

WARNING: Unrecognized keyword: bulk_forcing --> DISREGARDED.

Climatology File: ROMS_FILES/roms_clm_ind_2.nc

WARNING: Unrecognized keyword: boundary --> DISREGARDED.

Initial State File: ROMS_FILES/roms_ini_ind_2.nc Record: 1
Restart File: ROMS_FILES/roms_rst_ind_2.nc nrst = 720 rec/file: -1
History File: ROMS_FILES/roms_his_ind_2.nc Create new: T nwrt = 72 rec/file = 0
1 ntsavg Starting timestep for the accumulation of output
time-averaged data.
72 navg Number of timesteps between writing of time-averaged
data into averages file.
Averages File: ROMS_FILES/roms_avg_ind_2.nc rec/file = 0

Fields to be saved in history file: (T/F)
T write zeta free-surface.
T write UBAR 2D U-momentum component.
T write VBAR 2D V-momentum component.
T write U 3D U-momentum component.
T write V 3D V-momentum component.
T write T( 1) Tracer of index 1.
T write T( 2) Tracer of index 2.

F write RHO Density anomaly.
F write Omega Omega vertical velocity.
T write W True vertical velocity.
F write Akv Vertical viscosity.
T write Akt Vertical diffusivity for temperature.
F write Aks Vertical diffusivity for salinity.
T write Hbl Depth of KPP-model boundary layer.
T write Hbbl Depth of bottom planetary boundary layer.

T write Bostr Bottom Stress.
T write Wstress Wind Stress.
T write U-Wstress comp. U-Wind Stress.
T write V-Wstress comp. V-Wind Stress.


Fields to be saved in averages file: (T/F)
T write zeta free-surface.
T write UBAR 2D U-momentum component.
T write VBAR 2D V-momentum component.
T write U 3D U-momentum component.
T write V 3D V-momentum component.
T write T( 1) Tracer of index 1.
T write T( 2) Tracer of index 2.

F write RHO Density anomaly
T write Omega Omega vertical velocity.
T write W True vertical velocity.
F write Akv Vertical viscosity
T write Akt Vertical diffusivity for temperature.
F write Aks Vertical diffusivity for salinity.
T write Hbl Depth of KPP-model boundary layer
T write Hbbl Depth of the bottom planetary boundary layer

T write Bostr Bottom Stress.
T write Wstr Wind Stress.
T write U-Wstress comp. U-Wind Stress.
T write V-Wstress comp. V-Wind Stress.

1025.0000 rho0 Boussinesq approximation mean density, kg/m3.
0.000E+00 visc2 Horizontal Laplacian mixing coefficient [m2/s]
for momentum.
0.000E+00 tnu2( 1) Horizontal Laplacian mixing coefficient (m2/s)
for tracer 1.
0.000E+00 tnu2( 2) Horizontal Laplacian mixing coefficient (m2/s)
for tracer 2.

WARNING: Unrecognized keyword: tracer_diff4 --> DISREGARDED.


WARNING: Unrecognized keyword: vertical_mixing --> DISREGARDED.

3.000E-04 rdrg Linear bottom drag coefficient (m/si).
0.000E+00 rdrg2 Quadratic bottom drag coefficient.
0.000E+00 Zob Bottom roughness for logarithmic law (m).
1.000E-04 Cdb_min Minimum bottom drag coefficient.
1.000E-01 Cdb_max Maximum bottom drag coefficient.

1.00 gamma2 Slipperiness parameter: free-slip +1, or no-slip -1.
1.50E+05 x_sponge Thickness of sponge and/or nudging layer (m)
1000.00 v_sponge Viscosity in sponge layer (m2/s)
1.157E-05 tauT_in Nudging coefficients [sec^-1]
3.215E-08 tauT_out Nudging coefficients [sec^-1]
3.858E-06 tauM_in Nudging coefficients [sec^-1]
3.215E-08 tauM_out Nudging coefficients [sec^-1]


WARNING: Unrecognized keyword: diagnostics --> DISREGARDED.


WARNING: Unrecognized keyword: diag_avg --> DISREGARDED.


WARNING: Unrecognized keyword: diag3D_history_fields --> DISREGARDED.


WARNING: Unrecognized keyword: diag2D_history_fields --> DISREGARDED.


WARNING: Unrecognized keyword: diag3D_average_fields --> DISREGARDED.


WARNING: Unrecognized keyword: diag2D_average_fields --> DISREGARDED.


WARNING: Unrecognized keyword: diagnosticsM --> DISREGARDED.


WARNING: Unrecognized keyword: diagM_avg --> DISREGARDED.


WARNING: Unrecognized keyword: diagM_history_fields --> DISREGARDED.


WARNING: Unrecognized keyword: diagM_average_fields --> DISREGARDED.


WARNING: Unrecognized keyword: diagnostics_bio --> DISREGARDED.


WARNING: Unrecognized keyword: diagbio_avg --> DISREGARDED.


WARNING: Unrecognized keyword: biology --> DISREGARDED.


WARNING: Unrecognized keyword: sediments --> DISREGARDED.


WARNING: Unrecognized keyword: sediment_history_fields --> DISREGARDED.


WARNING: Unrecognized keyword: bbl_history_fields --> DISREGARDED.


WARNING: Unrecognized keyword: floats --> DISREGARDED.


WARNING: Unrecognized keyword: float_fields --> DISREGARDED.


WARNING: Unrecognized keyword: stations --> DISREGARDED.


WARNING: Unrecognized keyword: station_fields --> DISREGARDED.


WARNING: Unrecognized keyword: psource --> DISREGARDED.


Activated C-preprocessing Options:

REGIONAL
IO
OBC_EAST
OBC_WEST
OBC_NORTH
OBC_SOUTH
SOLVE3D
UV_COR
UV_ADV
CURVGRID
SPHERICAL
MASKING
UV_VIS2
MIX_GP_UV
MIX_GP_TS
TS_DIF2
LMD_MIXING
LMD_SKPP
LMD_BKPP
LMD_RIMIX
LMD_CONVEC
SALINITY
NONLIN_EOS
SPLIT_EOS
QCORRECTION
SFLX_CORR
DIURNAL_SRFLUX
SPONGE
CLIMATOLOGY
ZCLIMATOLOGY
M2CLIMATOLOGY
M3CLIMATOLOGY
TCLIMATOLOGY
ZNUDGING
M2NUDGING
M3NUDGING
TNUDGING
ANA_BSFLUX
ANA_BTFLUX
OBC_M2CHARACT
OBC_M3ORLANSKI
OBC_TORLANSKI
AVERAGES
AVERAGES_K
VAR_RHO_2D
M2FILTER_POWER
CLIMAT_UV_MIXH
VADV_SPLINES_UV
HADV_UPSTREAM_TS
CLIMAT_TS_MIXH
VADV_AKIMA_TS
DBLEPREC
Linux
QUAD
QuadZero
GLOBAL_2D_ARRAY
GLOBAL_1D_ARRAYXI
GLOBAL_1D_ARRAYETA
START_2D_ARRAY
START_1D_ARRAYXI
START_1D_ARRAYETA
PRIVATE_1D_SCRATCH_ARRAY
PRIVATE_2D_SCRATCH_ARRAY
PRIVATE_1DXI_SCRATCH_ARRAY
PRIVATE_1DETA_SCRATCH_ARRAY
WESTERN_EDGE
EASTERN_EDGE
SOUTHERN_EDGE
NORTHERN_EDGE
MYID
MPI_master_only
ZEROTH_TILE
SINGLE_TILE_MODE
LF_AM_STEP
FIRST_TIME_STEP
FIRST_2D_STEP
NOT_LAST_2D_STEP
PUT_GRID_INTO_RESTART
PUT_GRID_INTO_HISTORY
PUT_GRID_INTO_AVERAGES
NF_FTYPE
nf_get_att_FTYPE
nf_put_att_FTYPE
nf_get_var1_FTYPE
nf_put_var1_FTYPE
nf_get_vara_FTYPE
nf_put_vara_FTYPE
NF_FOUT
fast_indx_out
AGRIF_UPDATE_MIX_LOW
AGRIF_UPDATE_DECAL
AGRIF_SPONGE


NUMBER OF THREADS: 1 BLOCKING: 1 x 1.

Spherical grid detected.


hmin hmax grdmin grdmax Cu_min Cu_max
200.000000 5000.000000 .284040041E+05 .370440172E+05 0.10146066 0.66161686
volume=1.799780226185132480000E+17 open_cross=4.730308662844495391846E+10


Vertical S-coordinate System:

level S-coord Cs-curve at_hmin over_slope at_hmax

50 0.0000000 0.0000000 0.000 0.000 0.000
49 -0.0200000 -0.0005963 -0.313 -1.745 -3.176
48 -0.0400000 -0.0012013 -0.628 -3.511 -6.394
47 -0.0600000 -0.0018235 -0.946 -5.323 -9.699
46 -0.0800000 -0.0024721 -1.270 -7.203 -13.136
45 -0.1000000 -0.0031562 -1.600 -9.175 -16.750
44 -0.1200000 -0.0038859 -1.938 -11.265 -20.591
43 -0.1400000 -0.0046716 -2.288 -13.500 -24.711
42 -0.1600000 -0.0055247 -2.650 -15.909 -29.168
41 -0.1800000 -0.0064574 -3.027 -18.525 -34.022
40 -0.2000000 -0.0074832 -3.422 -21.382 -39.341
39 -0.2200000 -0.0086169 -3.837 -24.518 -45.198
38 -0.2400000 -0.0098748 -4.276 -27.976 -51.675
37 -0.2600000 -0.0112751 -4.742 -31.803 -58.863
36 -0.2800000 -0.0128380 -5.239 -36.050 -66.862
35 -0.3000000 -0.0145859 -5.771 -40.778 -75.784
34 -0.3200000 -0.0165442 -6.343 -46.049 -85.755
33 -0.3400000 -0.0187409 -6.961 -51.939 -96.917
32 -0.3600000 -0.0212079 -7.629 -58.528 -109.427
31 -0.3800000 -0.0239806 -8.356 -65.910 -123.463
30 -0.4000000 -0.0270990 -9.149 -74.186 -139.224
29 -0.4200000 -0.0306082 -10.016 -83.475 -156.935
28 -0.4400000 -0.0345586 -10.966 -93.907 -176.847
27 -0.4600000 -0.0390073 -12.011 -105.629 -199.246
26 -0.4800000 -0.0440183 -13.163 -118.807 -224.451
25 -0.5000000 -0.0496640 -14.436 -133.630 -252.823
24 -0.5200000 -0.0560257 -15.845 -150.306 -284.768
23 -0.5400000 -0.0631951 -17.407 -169.075 -320.743
22 -0.5600000 -0.0712756 -19.142 -190.204 -361.265
21 -0.5800000 -0.0803837 -21.073 -213.994 -406.915
20 -0.6000000 -0.0906508 -23.224 -240.786 -458.347
19 -0.6200000 -0.1022248 -25.623 -270.962 -516.302
18 -0.6400000 -0.1152726 -28.302 -304.956 -581.610
17 -0.6600000 -0.1299823 -31.297 -343.254 -655.211
16 -0.6800000 -0.1465660 -34.648 -386.406 -738.164
15 -0.7000000 -0.1652627 -38.400 -435.030 -831.661
14 -0.7200000 -0.1863422 -42.605 -489.826 -937.047
13 -0.7400000 -0.2101081 -47.321 -551.580 -1055.840
12 -0.7600000 -0.2369033 -52.612 -621.179 -1189.747
11 -0.7800000 -0.2671139 -58.552 -699.625 -1340.699
10 -0.8000000 -0.3011757 -65.223 -788.045 -1510.867
9 -0.8200000 -0.3395795 -72.720 -887.711 -1702.702
8 -0.8400000 -0.3828792 -81.147 -1000.057 -1918.967
7 -0.8600000 -0.4316989 -90.623 -1126.700 -2162.778
6 -0.8800000 -0.4867426 -101.281 -1269.463 -2437.646
5 -0.9000000 -0.5488038 -113.273 -1430.402 -2747.531
4 -0.9200000 -0.6187773 -126.768 -1611.833 -3096.899
3 -0.9400000 -0.6976718 -141.958 -1816.370 -3490.782
2 -0.9600000 -0.7866249 -159.059 -2046.958 -3934.858
1 -0.9800000 -0.8869190 -178.315 -2306.920 -4435.526
0 -1.0000000 -1.0000000 -200.000 -2600.000 -5000.000

Time splitting: ndtfast = 60 nfast = 82


Maximum grid stiffness ratios: rx0 =0.2373559629 rx1 = 4.0012505454

GET_INITIAL -- Processing data for time = 0.000 record = 1
GET_TCLIMA -- Read climatology of tracer 1 for time = 345.0
GET_TCLIMA -- Read climatology of tracer 1 for time = 15.00
GET_TCLIMA -- Read climatology of tracer 2 for time = 345.0
GET_TCLIMA -- Read climatology of tracer 2 for time = 15.00
GET_UCLIMA -- Read momentum climatology for time = 345.0
GET_UCLIMA -- Read momentum climatology for time = 15.00
GET_SSH - Read SSH climatology for time = 345.0
GET_SSH - Read SSH climatology for time = 15.00
GET_SMFLUX -- Read surface momentum stresses for time = 345.0
GET_SMFLUX -- Read surface momentum stresses for time = 15.00
GET_STFLUX -- Read surface flux of tracer 1 for time = 345.0
GET_STFLUX -- Read surface flux of tracer 1 for time = 15.00
GET_SST -- Read SST and dQdSST fields for time = 345.0
GET_SST -- Read SST and dQdSST fields for time = 15.00
GET_STFLUX -- Read surface flux of tracer 2 for time = 345.0
GET_STFLUX -- Read surface flux of tracer 2 for time = 15.00
GET_SSS -- Read SSS fields for time = 345.0
GET_SSS -- Read SSS fields for time = 15.00
GET_SRFLUX -- Read solar shortwave radiation for time = 345.0
GET_SRFLUX -- Read solar shortwave radiation for time = 15.00
DEF_HIS/AVG - Created new netCDF file 'ROMS_FILES/roms_his_ind_2.nc'.
WRT_GRID -- wrote grid data into file 'ROMS_FILES/roms_his_ind_2.nc'.
WRT_HIS -- wrote history fields into time record = 1 / 1

MAIN: started time-steping.

STEP time[DAYS] KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME trd
0 0.00000 0.000000000E+00 2.1844945E+01 2.1844945E+01 1.7997802E+17 0
1 0.04167 1.577126495E-04 2.1845419E+01 2.1845577E+01 1.7997756E+17 0
2 0.08333 1.931486057E-04 2.1845918E+01 2.1846111E+01 1.7997713E+17 0
3 0.12500 2.555911007E-04 2.1846458E+01 2.1846713E+01 1.7997706E+17 0
4 0.16667 3.083925051E-04 2.1847033E+01 2.1847341E+01 1.7997729E+17 0
5 0.20833 3.691629186E-04 2.1847614E+01 2.1847983E+01 1.7997718E+17 0
6 0.25000 4.306341498E-04 2.1848177E+01 2.1848607E+01 1.7997685E+17 0
7 0.29167 4.948640495E-04 2.1848540E+01 2.1849035E+01 1.7997660E+17 0
8 0.33333 5.578971845E-04 2.1848481E+01 2.1849039E+01 1.7997646E+17 0
9 0.37500 6.192035752E-04 2.1847989E+01 2.1848608E+01 1.7997635E+17 0
10 0.41667 6.747949900E-04 2.1847118E+01 2.1847793E+01 1.7997631E+17 0
11 0.45833 7.246149546E-04 2.1845949E+01 2.1846673E+01 1.7997633E+17 0
12 0.50000 7.659485652E-04 2.1844584E+01 2.1845350E+01 1.7997636E+17 0
13 0.54167 8.029952594E-04 2.1843138E+01 2.1843941E+01 1.7997644E+17 0
14 0.58333 8.378857559E-04 2.1841741E+01 2.1842579E+01 1.7997654E+17 0
15 0.62500 8.666076120E-04 2.1840513E+01 2.1841379E+01 1.7997662E+17 0
16 0.66667 8.931843882E-04 2.1839548E+01 2.1840441E+01 1.7997665E+17 0
17 0.70833 9.171618449E-04 2.1838935E+01 2.1839852E+01 1.7997662E+17 0
18 0.75000 9.405173393E-04 2.1838743E+01 2.1839683E+01 1.7997661E+17 0
19 0.79167 9.659097280E-04 2.1838976E+01 2.1839942E+01 1.7997662E+17 0
20 0.83333 9.939986921E-04 2.1839415E+01 2.1840409E+01 1.7997658E+17 0
21 0.87500 1.023260481E-03 2.1839890E+01 2.1840914E+01 1.7997651E+17 0
22 0.91667 1.053519353E-03 2.1840392E+01 2.1841446E+01 1.7997649E+17 0
23 0.95833 1.086478940E-03 2.1840911E+01 2.1841998E+01 1.7997650E+17 0
24 1.00000 1.121357870E-03 2.1841432E+01 2.1842553E+01 1.7997653E+17 0
25 1.04167 1.155410697E-03 2.1841945E+01 2.1843100E+01 1.7997656E+17 0
26 1.08333 1.190033255E-03 2.1842444E+01 2.1843634E+01 1.7997660E+17 0
27 1.12500 1.243348347E-03 2.1842926E+01 2.1844169E+01 1.7997658E+17 0
28 1.16667 1.633633748E-03 2.1843385E+01 2.1845018E+01 1.7997652E+17 0
29 1.20833 3.158684129E-01 3.3219772E+01 3.3535641E+01 1.7997649E+17 0


=======================================
= =
= STEP2D: ABNORMAL JOB END =
= BLOW UP =
= =
=======================================

VMAX (M/S) =32462.88
IMAX JMAX = 268 151
IINT IEXT = 30 1




but I have successfully run this model with same domain with grid (1 1)deg.
I want to know what is the problem and how will I solve it.
Please help me.
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User avatar
kate
Posts: 4091
Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA

Re: Model Run

#2 Unread post by kate »

You will need a shorter timestep for 1/3 degree than for 1 degree, perhaps 1/3 the value you had before.
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surja
Posts: 12
Joined: Thu Jan 12, 2012 5:19 pm
Location: Jadavpur university,INCOIS

Re: Model Run

#3 Unread post by surja »

Thank you Kate as your suggestion today I have run this model for 24 time step without any problem.I want to know what is the problem for running large number of time step? how can I run this model for one month ( for 720 time step).
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surja
Posts: 12
Joined: Thu Jan 12, 2012 5:19 pm
Location: Jadavpur university,INCOIS

Re: Model Run

#4 Unread post by surja »

Another problem comes in my model with same domain (30E-120E,40S-25N) but different grid size.When I tried to generate climatology file in this domain with grid size 1/5 deg I got the following error.

>> make_clim
mkdir: cannot create directory `/ocean/ROMS/Roms_tools/Run/ROMS_FILES/': File exists

Making the clim: /ocean/ROMS/Roms_tools/Run/ROMS_FILES/roms_clm_ind_5.nc

Title: Indian Ocean Model

Read in the grid...

Create the climatology file...

Creating the file : /ocean/ROMS/Roms_tools/Run/ROMS_FILES/roms_clm_ind_5.nc

Warning: ## close failed:
/ocean/ROMS/Roms_tools/Run/ROMS_FILES/roms_clm_ind_5.nc
> In netcdf.close at 20
In create_climfile at 338
In make_clim at 95

Create the OA file...

Creating the file : /ocean/ROMS/Roms_tools/Run/ROMS_FILES/roms_oa_ind_5.nc


Horizontal extrapolations

Temperature...

Ext tracers: Roa = 0 km - default value = NaN
Ext tracers: horizontal interpolation of the annual data
Ext tracers: horizontal interpolation of the seasonal data
time index: 1 of total: 12
time index: 2 of total: 12
time index: 3 of total: 12
time index: 4 of total: 12
time index: 5 of total: 12
time index: 6 of total: 12
time index: 7 of total: 12
time index: 8 of total: 12
time index: 9 of total: 12
time index: 10 of total: 12
time index: 11 of total: 12
time index: 12 of total: 12

Salinity...

Ext tracers: Roa = 0 km - default value = NaN
Ext tracers: horizontal interpolation of the annual data
Ext tracers: horizontal interpolation of the seasonal data
time index: 1 of total: 12
salinity test
time index: 2 of total: 12
salinity test
time index: 3 of total: 12
salinity test
time index: 4 of total: 12
salinity test
time index: 5 of total: 12
salinity test
time index: 6 of total: 12
salinity test
time index: 7 of total: 12
salinity test
time index: 8 of total: 12
salinity test
time index: 9 of total: 12
salinity test
time index: 10 of total: 12
salinity test
time index: 11 of total: 12
salinity test
time index: 12 of total: 12
salinity test

Vertical interpolations

Temperature...
## NetCDF file not opened: /ocean/ROMS/Roms_tools/Run/ROMS_FILES/roms_clm_ind_5.nc
Cell contents reference from a non-cell array object.

Error in vinterp_clm (line 43)
theta_s = nc{'theta_s'}(:);

Error in make_clim (line 134)
vinterp_clm(clmname,grdname,oaname,'temp','tclm_time','Z',0,'r');

>>

Please help me for which I can generate climatology file for 1/5 deg grid.
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User avatar
kate
Posts: 4091
Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA

Re: Model Run

#5 Unread post by kate »

Having it run for 20+ steps then die is consistent with using too long a timestep, having some instability which grows to kill the run.

For your other problems, you would be better served by asking on a forum dedicated to the tools you are using. This is the forum at myroms.org, set up to serve the myroms branch of ROMS.
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surja
Posts: 12
Joined: Thu Jan 12, 2012 5:19 pm
Location: Jadavpur university,INCOIS

Re: Model Run

#6 Unread post by surja »

Thank you Kata .
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nmhuan61

Re: Model Run

#7 Unread post by nmhuan61 »

Do you used ROMS AGRIF?
the warning message
"mkdir: cannot create directory `/ocean/ROMS/Roms_tools/Run/ROMS_FILES/': File exists"
because there is old file of previuos run exists, you have delete it first
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surja
Posts: 12
Joined: Thu Jan 12, 2012 5:19 pm
Location: Jadavpur university,INCOIS

Re: Model Run

#8 Unread post by surja »

Yes, I know this .
I use ROMS AGRIF.
Actually my problem is

## NetCDF file not opened: /ocean/ROMS/Roms_tools/Run/ROMS_FILES/roms_clm_ind_5.nc
Cell contents reference from a non-cell array object.

Error in vinterp_clm (line 43)
theta_s = nc{'theta_s'}(:);

Error in make_clim (line 134)
vinterp_clm(clmname,grdname,oaname,'temp','tclm_time','Z',0,'r');
Top
nmhuan61

Re: Model Run

#9 Unread post by nmhuan61 »

the problem is make_clim do not create roms_clm_ind_5.nc

## NetCDF file not opened: /ocean/ROMS/Roms_tools/Run/ROMS_FILES/roms_clm_ind_5.nc
Cell contents reference from a non-cell array object.

Then when it interpolates vertically will be error because there is not roms_clm_ind_5.nc

Error in vinterp_clm (line 43)
theta_s = nc{'theta_s'}(:);

Error in make_clim (line 134)
vinterp_clm(clmname,grdname,oaname,'temp','tclm_time','Z',0,'r');

You have to check param.h and add elseif with name of your case and LLm0 = xx MMm0=xx N = xx

you only run make_clim with number of layer <=32 I don't know why?

hope it helps
Best regards
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