unable to find variable: sand in input NetCDF

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IMRAN5379
Posts: 18
Joined: Fri Sep 08, 2017 11:59 pm
Location: Indian Institute of Technology Kharagpur

unable to find variable: sand in input NetCDF

#1 Post by IMRAN5379 »

Hi
I am a new user of ROMS, working on sediment transport modelling in Odisha coast of Northern Bay of Bengal. I have made all the initial file including grid, forcing, bulk, clim, boundary files. when I am running the model by giving command ./roms roms.in I am getting the error in roms_ini.nc file. my query is about to provide user defined values for sand,silt,bed_thick,bed_poros,bed_frac_sand,bed_frac_silt.
GET_INITIAL - unable to find variable: sand
in input NetCDF file: ROMS_FILES/roms_ini.nc -> analytical value

jcwarner
Posts: 1095
Joined: Wed Dec 31, 2003 6:16 pm
Location: USGS, USA

Re: unable to find variable: sand in input NetCDF

#2 Post by jcwarner »

have you been able to work on this?
If you activate SEDIMENT, then the model needs some initial fields of bed thickness, porosity, etc.
you can provide this information in ANA_SEDIMENT, or you need to include that information in the roms init nc file. we have some m files to create roms init with sediment if you would like.

IMRAN5379
Posts: 18
Joined: Fri Sep 08, 2017 11:59 pm
Location: Indian Institute of Technology Kharagpur

Re: unable to find variable: sand in input NetCDF

#3 Post by IMRAN5379 »

Thank you so much for your vital response, I am new in sediment transport modelling using ROMS.

IMRAN5379
Posts: 18
Joined: Fri Sep 08, 2017 11:59 pm
Location: Indian Institute of Technology Kharagpur

Re: unable to find variable: sand in input NetCDF

#4 Post by IMRAN5379 »

After adding the required variables in roms_ini.nc (ie. sand, silt, bed_thick, bed_poros..........etc) I am getting this error.

Maximum grid stiffness ratios: rx0 =0.2368669301 rx1 = 2.3216424860

GET_INITIAL -- Processing data for time = 0.000 record = 1

NF_FREAD ERROR: nf_get_vara netCDF error code = -57

GET_INITIAL - error while reading variable: bed_thick at time record = 1
in input NetCDF file: ROMS_FILES/roms_ini.nc


MAIN - number of records written into history file(s): 0
number of records written into restart file(s): 0
number of records written into averages file(s): 0


ERROR: Abnormal termination: netCDF INPUT

jcwarner
Posts: 1095
Joined: Wed Dec 31, 2003 6:16 pm
Location: USGS, USA

Re: unable to find variable: sand in input NetCDF

#5 Post by jcwarner »

not sure. if you ncview the ini file, does bed thick look ok? do you have bed_thick defined with the correct dimensions
bed_thickness(1:xi_rho,1:eta_rho,1:Nbed,1:length(init_time))
-j

IMRAN5379
Posts: 18
Joined: Fri Sep 08, 2017 11:59 pm
Location: Indian Institute of Technology Kharagpur

Re: unable to find variable: sand in input NetCDF

#6 Post by IMRAN5379 »

thank you sir for your valuable and quick response.
I checked the dimension of bed_thick which is ok but did not chek the NLAY = 2 (default in the model package) in param.h. I have defined Nbed=1 in nc file and I changed it to NLAY=1 in param.h file, after that the model is running properly.

IMRAN5379
Posts: 18
Joined: Fri Sep 08, 2017 11:59 pm
Location: Indian Institute of Technology Kharagpur

Re: unable to find variable: sand in input NetCDF

#7 Post by IMRAN5379 »

I am trying to run inter annual simulation for my area of study by coupling ROMS-CSTMS. I Have completed a climatology run for the same area but got the error when performing inter annual run.


NUMBER OF THREADS: 1 BLOCKING: 1 x 1.

sediment inputfile sediment.in
not found sediment initialization from restart file

Number of size classes in sediment computation:**

Spherical grid detected.


hmin hmax grdmin grdmax Cu_min Cu_max
75.000000 3399.893102 .854055350E+04 .898518398E+04 0.02134633 0.14416417
volume=1.820513185074921750000E+15 open_cross=3.942450174542450428009E+09

lonmin= 80.0000 lonmax= 98.0000latmin= 14.0000 latmax= 26.0330

Vertical S-coordinate System:

level S-coord Cs-curve at_hmin over_slope at_hmax

32 0.0000000 -0.0000000 -0.000 -0.000 -0.000
31 -0.0312500 -0.0004119 -0.339 -1.024 -1.709
30 -0.0625000 -0.0008686 -0.681 -2.126 -3.570
29 -0.0937500 -0.0014032 -1.029 -3.361 -5.694
28 -0.1250000 -0.0020583 -1.384 -4.806 -8.227
27 -0.1562500 -0.0028916 -1.750 -6.558 -11.365
26 -0.1875000 -0.0039825 -2.134 -8.755 -15.375
25 -0.2187500 -0.0054420 -2.541 -11.588 -20.635
24 -0.2500000 -0.0074255 -2.983 -15.327 -27.672
23 -0.2812500 -0.0101480 -3.472 -20.343 -37.213
22 -0.3125000 -0.0138984 -4.028 -27.134 -50.239
21 -0.3437500 -0.0190444 -4.675 -36.336 -67.996
20 -0.3750000 -0.0260104 -5.441 -48.682 -91.922
19 -0.4062500 -0.0352061 -6.351 -64.879 -123.408
18 -0.4375000 -0.0468928 -7.423 -85.380 -163.336
17 -0.4687500 -0.0610211 -8.654 -110.098 -211.542
16 -0.5000000 -0.0771529 -10.015 -138.277 -266.540
15 -0.5312500 -0.0945892 -11.461 -168.710 -325.960
14 -0.5625000 -0.1126937 -12.950 -200.297 -387.644
13 -0.5937500 -0.1312191 -14.467 -232.612 -450.756
12 -0.6250000 -0.1504450 -16.029 -266.136 -516.243
11 -0.6562500 -0.1711142 -17.685 -302.153 -586.621
10 -0.6875000 -0.1942949 -19.504 -342.509 -665.514
9 -0.7187500 -0.2212779 -21.571 -389.433 -757.296
8 -0.7500000 -0.2535471 -23.981 -445.489 -866.997
7 -0.7812500 -0.2928107 -26.845 -513.627 -1000.410
6 -0.8125000 -0.3410750 -30.295 -597.314 -1164.333
5 -0.8437500 -0.4007439 -34.486 -700.701 -1366.916
4 -0.8750000 -0.4747426 -39.608 -828.843 -1618.077
3 -0.9062500 -0.5666658 -45.896 -987.947 -1929.999
2 -0.9375000 -0.6809556 -53.637 -1185.689 -2317.742
1 -0.9687500 -0.8231200 -63.190 -1431.583 -2799.976
0 -1.0000000 -1.0000000 -75.000 -1737.447 -3399.893

Time splitting: ndtfast = 60 nfast = 82


Maximum grid stiffness ratios: rx0 =0.1938366915 rx1 = 3.0443284027

GET_INITIAL -- Processing data for time = 0.000 record = 1
GET_TCLIMA -- Read climatology of tracer 1 for time = -15.00
GET_TCLIMA -- Read climatology of tracer 1 for time = 15.00
GET_TCLIMA -- Read climatology of tracer 2 for time = -15.00
GET_TCLIMA -- Read climatology of tracer 2 for time = 15.00
GET_UCLIMA -- Read momentum climatology for time = -15.00
GET_UCLIMA -- Read momentum climatology for time = 15.00
GET_SSH - Read SSH climatology for time = -15.00
GET_SSH - Read SSH climatology for time = 15.00
GET_BRY -- Read all boundary data for time = -15.00
GET_BRY -- Read all boundary data for time = 15.00
GET_PSOURCE -- Read Run-off flow fields for time = 345.0
GET_PSOURCE -- Read Run-off flow fields for time = 15.00

GET_PSOURCE_TS - unable to find forcing variable: temp_src_time
in runoff NetCDF file: roms_runoff.nc--> analytical value (in analytical.F)

GET_PSOURCE_TS - unable to find forcing variable: salt_src_time
in runoff NetCDF file: roms_runoff.nc--> analytical value (in analytical.F)

SET_CYCLE ERROR: non-cycling regime, but model time exeeds
time of the last available data record for variable: bulk_time
TDAYS = 0.000 TLAST = 0.3656E+05


MAIN - number of records written into history file(s): 0
number of records written into restart file(s): 0
number of records written into averages file(s): 0


ERROR: Abnormal termination: netCDF INPUT

jcwarner
Posts: 1095
Joined: Wed Dec 31, 2003 6:16 pm
Location: USGS, USA

Re: unable to find variable: sand in input NetCDF

#8 Post by jcwarner »

not exactly sure what is going on from that information. but it looks like you are doing a restart, and the model is looking for fields in that restart file.
did you do a run with sediment and now restarting that? or did the first run not have sediment? if the first run did not have sediment, then you need to add those initial sediment fields to the ini file, or use ana_sediment to start them.
-j

IMRAN5379
Posts: 18
Joined: Fri Sep 08, 2017 11:59 pm
Location: Indian Institute of Technology Kharagpur

Re: unable to find variable: sand in input NetCDF

#9 Post by IMRAN5379 »

I was also thinking after getting the error that I should add the sediment parameters into the restart file because those parameters were added in the initial file. it is an inter-annual simulation for which I am looking. I have run a climatological simulation with those parameters already added into roms_ini.nc file. but when I am giving a long-term inter-annual simulation model gives the error with abnormal termination, probably due to the missing of those sediments fields in the restart file.

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