CDO

I am trying to regrid a file that depends on nCell dimensional variable into latitude and longitude dimensions. But it is giving an error of


Warning (cdfScanVarAttr): NetCDF: Variable not found - >lons<
Warning (cdfScanVarAttr): NetCDF: Variable not found - >lats<


If I understand correctly, above error only occurs when there is a variable that depends on 'lons' or 'lats'. But my data nor the grid file depends on any of those dimensional variables.

Below are the commands that I am using

1. for creating weights

cdo gendis,od.grid.nc -setgrid,mpas.grid.nc pr_15mn_MPAS-3km_DW-ATM_r1i1p1f1_2d_gn_20200121000000-20200121234500.nc mpas.wgt.nc

-> I get the above error messages for this command

2. remapping data file in to 1 degree latitude longitude grid

cdo -remap,od.grid.nc,mpas.wgt.nc pr_15mn_MPAS-3km_DW-ATM_r1i1p1f1_2d_gn_20200121000000-20200121234500.nc pr_15mn_MPAS-3km_DW-ATM_r1i1p1f1_2d_gn_20200121000000-20200121234500.od.nc

-> I not only get the above error messages for this command, but also the remapping does not work.

Why is this happening?

Below are the headers of the grid description file, grid file, and data sample file.

1. Grid description file

@# gridID 1 #
gridtype = lonlat
gridsize = 64800
xsize = 360
ysize = 180
xname = lon
xlongname = "longitude"
xunits = "degrees_east"
yname = lat
ylongname = "latitude"
yunits = "degrees_north"
xfirst = -179.95
xinc = 1
yfirst = -89.95
yinc = 1@

2. Grid file

netcdf mpas.grid {
dimensions:
nCells = 41943042 ;
nEdges = 125829120 ;
nVertices = 83886080 ;
maxEdges = 6 ;
maxEdges2 = 12 ;
TWO = 2 ;
vertexDegree = 3 ;
variables:
float latCell(nCells) ;
latCell:units = "radian" ;
latCell:bounds = "latCell_bnds" ;
latCell:standard_name = "latitude" ;
float lonCell(nCells) ;
lonCell:units = "radian" ;
lonCell:bounds = "lonCell_bnds" ;
lonCell:standard_name = "longitude" ;
float latVertex(nVertices) ;
latVertex:units = "radian" ;
latVertex:bounds = "latVertex_bnds" ;
latVertex:standard_name = "latitude" ;
float lonVertex(nVertices) ;
lonVertex:units = "radian" ;
lonVertex:bounds = "lonVertex_bnds" ;
lonVertex:standard_name = "longitude" ;
float areaCell(nCells) ;
areaCell:coordinates = "lonCell latCell" ;
float areaTriangle(nVertices) ;
areaTriangle:coordinates = "lonVertex latVertex" ;
float lonCell_bnds(nCells, maxEdges) ;
float latCell_bnds(nCells, maxEdges) ;
float lonVertex_bnds(nVertices, vertexDegree) ;
float latVertex_bnds(nVertices, vertexDegree) ;
}

3. Sample data file

@netcdf pr_15mn_MPAS-3km_DW-ATM_r1i1p1f1_2d_gn_20200121000000-20200121234500 {
dimensions:
xtime = UNLIMITED ; // (96 currently)
nCells = 41943042 ;
variables:
double xtime(xtime) ;
xtime:standard_name = "time" ;
xtime:long_name = "Model valid time" ;
xtime:units = "minutes since 2020-1-21 00:00:00" ;
xtime:calendar = "proleptic_gregorian" ;
xtime:axis = "T" ;
float pr(xtime, nCells) ;
pr:long_name = "accumulated total grid-scale precipitation" ;
pr:units = "mm" ;
pr:cell_methods = "Time: mean" ;
pr:standard_name = "precipitation_flux" ;
pr:origin = "rainnc" ;
pr:coordinates = "lons lats" ;

// global attributes:
:CDI = "Climate Data Interface version 2.0.4 (https://mpimet.mpg.de/cdi)" ;
:source = "MPAS" ;
:Conventions = "MPAS" ;
:model_name = "mpas" ;
:core_name = "atmosphere" ;
:git_version = "v6.1-502-gcded7e32-dirty" ;
:on_a_sphere = "YES" ;
:sphere_radius = 6371229.f ;
:is_periodic = "NO" ;
:x_period = 0.f ;
:y_period = 0.f ;
:history = "Sat Jun 18 16:09:23 2022: cdo -s -P 2 -f nc4 -z zip -r -splitname,swap -settaxis,2020-01-21,00:00:00,15min -setattribute,grid_file_path=/work/ka1081/DYAMOND_WINTER/NCAR/MPAS-3.7km/DW-ATM/atmos/fx/gn/grid.nc,pr@standard_name=precipitation_flux,pr@origin=rainnc,pr@coordinates=lons lats -chvar,rainnc,pr [ -cat /work/bk1040/DYAMOND/.input_winter_data/MPAS_3.75km/2d/rainnc.2020-01-21.nc ] _15mn_MPAS-3km_DW-ATM_r1i1p1f1_2d_gn_20200121000000-20200121234500\nmpirun -n 18432 ./atmosphere_model" ;
:parent_id = "59nuhuiy1s\nrwws7w16u3\n" ;
:mesh_spec = "0.0" ;
:config_time_integration = "SRK3" ;
:config_time_integration_order = 2 ;
:config_dt = 20.f ;
:config_calendar_type = "gregorian" ;
:config_start_time = "2020-01-20_00:00:00" ;
:config_stop_time = "none" ;
:config_run_duration = "1_00:00:00" ;
:config_split_dynamics_transport = "YES" ;
:config_number_of_sub_steps = 2 ;
:config_dynamics_split_steps = 3 ;
:config_h_mom_eddy_visc2 = 0.f ;
:config_h_mom_eddy_visc4 = 0.f ;
:config_v_mom_eddy_visc2 = 0.f ;
:config_h_theta_eddy_visc2 = 0.f ;
:config_h_theta_eddy_visc4 = 0.f ;
:config_v_theta_eddy_visc2 = 0.f ;
:config_horiz_mixing = "2d_smagorinsky" ;
:config_len_disp = 3750.f ;
:config_visc4_2dsmag = 0.05f ;
:config_del4u_div_factor = 10.f ;
:config_w_adv_order = 3 ;
:config_theta_adv_order = 3 ;
:config_scalar_adv_order = 3 ;
:config_u_vadv_order = 3 ;
:config_w_vadv_order = 3 ;
:config_theta_vadv_order = 3 ;
:config_scalar_vadv_order = 3 ;
:config_scalar_advection = "YES" ;
:config_positive_definite = "NO" ;
:config_monotonic = "YES" ;
:config_coef_3rd_order = 0.25f ;
:config_smagorinsky_coef = 0.125f ;
:config_mix_full = "YES" ;
:config_epssm = 0.1f ;
:config_smdiv = 0.1f ;
:config_apvm_upwinding = 0.f ;
:config_h_ScaleWithMesh = "YES" ;
:config_num_halos = 2 ;
:config_zd = 22000.f ;
:config_xnutr = 0.2f ;
:config_mpas_cam_coef = 0.f ;
:config_rayleigh_damp_u = "NO" ;
:config_rayleigh_damp_u_timescale_days = 2.f ;
:config_number_rayleigh_damp_u_levels = 6 ;
:config_apply_lbcs = "NO" ;
:config_restart_timestamp_name = "restart_timestamp" ;
:config_pio_num_iotasks = 512 ;
:config_pio_stride = 36 ;
:config_block_decomp_file_prefix = "x1.41943042.graph.info.part." ;
:config_number_of_blocks = 0 ;
:config_explicit_proc_decomp = "NO" ;
:config_proc_decomp_file_prefix = "graph.info.part." ;
:config_do_restart = "NO" ;
:config_do_DAcycling = "NO" ;
:config_print_global_minmax_vel = "YES" ;
:config_print_detailed_minmax_vel = "YES" ;
:config_print_global_minmax_sca = "NO" ;
:config_IAU_option = "off" ;
:config_IAU_window_length_s = 21600.f ;
:config_jedi_da = "NO" ;
:input_soil_data = "STAS" ;
:input_soil_temperature_lag = 140 ;
:num_soil_layers = 4 ;
:months = 12 ;
:noznlev = 59 ;
:config_frac_seaice = "YES" ;
:config_sfc_albedo = "YES" ;
:config_sfc_snowalbedo = "YES" ;
:config_sst_update = "NO" ;
:config_sstdiurn_update = "YES" ;
:config_deepsoiltemp_update = "NO" ;
:config_o3climatology = "YES" ;
:config_microp_re = "YES" ;
:config_ysu_pblmix = "NO" ;
:config_n_microp = 1 ;
:config_radtlw_interval = "00:15:00" ;
:config_radtsw_interval = "00:15:00" ;
:config_conv_interval = "none" ;
:config_pbl_interval = "none" ;
:config_greeness_update = "24:00:00" ;
:config_bucket_update = "none" ;
:config_physics_suite = "convection_permitting" ;
:config_microp_scheme = "mp_thompson" ;
:config_convection_scheme = "cu_ntiedtke" ;
:config_lsm_scheme = "noah" ;
:config_pbl_scheme = "bl_mynn" ;
:config_gwdo_scheme = "bl_ysu_gwdo" ;
:config_radt_cld_scheme = "cld_fraction_thompson" ;
:config_radt_lw_scheme = "rrtmg_lw" ;
:config_radt_sw_scheme = "rrtmg_sw" ;
:config_sfclayer_scheme = "sf_mynn" ;
:config_gfconv_deepc = "YES" ;
:config_gfconv_midlc = "YES" ;
:config_gfconv_shalc = "YES" ;
:config_gfconv_closure_deepc = 0 ;
:config_gfconv_closure_midlc = 0 ;
:config_gfconv_closure_shalc = 0 ;
:config_gfconv_closure_deep = 0 ;
:config_gfconv_closure_shallow = 8 ;
:config_mynn_closure = 2 ;
:config_mynn_cloudpdf = 2 ;
:config_mynn_edmf = 1 ;
:config_mynn_mixscalars = 1 ;
:config_bucket_radt = 1.e+09f ;
:config_bucket_rainc = 100.f ;
:config_bucket_rainnc = 100.f ;
:config_oml1d = "YES" ;
:config_oml_hml0 = 0.f ;
:config_oml_gamma = 0.14f ;
:config_oml_relaxation_time = 432000.f ;
:config_lightning_flash = "NO" ;
:config_sounding_interval = "01:00:00" ;
:file_id = "6t10t3cr4b" ;
:grid_file_path = "/work/ka1081/DYAMOND_WINTER/NCAR/MPAS-3.7km/DW-ATM/atmos/fx/gn/grid.nc" ;
:CDO = "Climate Data Operators version 2.0.4 (https://mpimet.mpg.de/cdo)" ;
:cdo_openmp_thread_number = 2 ;
}@