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Variable not assigned and variable not found when getting mean across time

Added by Najeen Rula 8 months ago

Hi. I am new to modelling and working with environmental layers. I am trying to merge several netcdf files of a variable (dissolved inorganic carbon) into one, getting a mean value of the variable at the same time. I used cdo to do this and made the following call:
cdo timmean -cat '*.nc' mean.nc
However, I get the following warning:
cdo(1) cat: Process started Warning (cdfScanVarAttr): NetCDF: Variable not found - >lat< Warning (cdfInqContents): Coordinates variable zc can't be assigned! cdo(1) cat: 0%Warning (cdfScanVarAttr): NetCDF: Variable not found - >lat< Warning (cdfInqContents): Coordinates variable zc can't be assigned! 100%Warning (cdfScanVarAttr): NetCDF: Variable not found - >lat< Warning (cdfInqContents): Coordinates variable zc can't be assigned! 100%cdo(1) cat: Processed 24306975 values from 3 variables over 305 timesteps. cdo timmean: Processed 24306975 values from 1 variable over 305 timesteps [0.53s 49MB].

I still get the output. But should I worry about the warnings?

The following is the ncdump output for one of the source files.
ncdump -h DIC_1.nc netcdf DIC_1 { dimensions: time = 64 ; k = 1 ; j = 253 ; i = 315 ; variables: float DIC ; DIC:puv__parameter = "http://vocab.nerc.ac.uk/collection/P01/current/CINCMOD1/" ; DIC:coordinates = "time zc latitude longitude lat lon" ; DIC:units = "mg C m-3" ; DIC:long_name = "Dissolved Inorganic Carbon" ; DIC:valid_range = 0.f, 1.e+35f ; DIC:missing_value = 1.e+35f ; DIC:_ChunkSizes = 1, 11, 598, 128 ; double time(time) ; time:units = "days since 1990-01-01 00:00:00 +10" ; time:long_name = "Time" ; time:standard_name = "time" ; time:coordinate_type = "time" ; time:puv__uom = "http://vocab.nerc.ac.uk/collection/P06/current/UTAA/" ; time:_ChunkSizes = 512 ; time:calendar = "gregorian" ; time:_CoordinateAxisType = "Time" ; double zc(k) ; zc:units = "m" ; zc:positive = "up" ; zc:long_name = "Z coordinate" ; zc:axis = "Z" ; zc:coordinate_type = "Z" ; zc:_CoordinateAxisType = "Height" ; zc:_CoordinateZisPositive = "up" ; double latitude(j, i) ; latitude:units = "degrees_north" ; latitude:long_name = "Latitude" ; latitude:standard_name = "latitude" ; latitude:coordinate_type = "latitude" ; latitude:projection = "geographic" ; latitude:puv__ofProperty = "http://vocab.nerc.ac.uk/collection/S06/current/S0600045/" ; latitude:puv__uom = "http://vocab.nerc.ac.uk/collection/P06/current/DEGN/" ; latitude:_CoordinateAxisType = "Lat" ; double longitude(j, i) ; longitude:puv__uom = "http://vocab.nerc.ac.uk/collection/P06/current/DEGE/" ; longitude:units = "degrees_east" ; longitude:long_name = "Longitude" ; longitude:standard_name = "longitude" ; longitude:coordinate_type = "longitude" ; longitude:projection = "geographic" ; longitude:_CoordinateAxisType = "Lon" ; // global attributes: :title = "GBR1_H2p0_B3p2_Cfur_Dnrt" ; :description = "eReefs GBR 1k grid with rivers. Uses JCU bathy (www.deepreef.org). Created by JA 08.05.2012. hydrodynamic 2.0 BGC 3.2 cathment constant concentrations." ; :paramhead = "eReefs 1 km grid. Mile Furnas Catchment constant concentrations. More details of naming protocol at: eReefs.info." ; :paramfile = "./tran/gbr1_bgc_nrt.tran" ; :ems_version = "v1.4.0 rev(7358)" ; :date_created = "Thu Jun 22 15:14:52 2023" ; :Conventions = "CF-1.0" ; :Run_ID = "2.0" ; :Run_code = "GBR1_H2p0_B3p2_Cfur_Dnrt|G0.00|H0.00|S0.0|B2.0" ; :Parameter_File_Revision = "$Revision: 1945 $" ; :bald__isPrefixedBy = "prefix_list" ; :prefix_list_puv__ = "https://w3id.org/env/puv#" ; :prefix_list_qudt__ = "http://qudt.org/vocab/unit/" ; :History = "Translated to CF-1.0 Conventions by Netcdf-Java CDM (CFGridWriter2)\n", "Original Dataset = file:fx3/GBR1_H2p0_B3p2_Cfur_Dnrt.ncml; Translation Date = 2023-06-28T06:23:38.428Z" ; :geospatial_lat_min = -25.168796 ; :geospatial_lat_max = -22.15316 ; :geospatial_lon_min = 150.22234 ; :geospatial_lon_max = 153.761098 ; }


Replies (2)

RE: Variable not assigned and variable not found when getting mean across time - Added by Estanislao Gavilan 8 months ago

Hi Najeen,

welcome to our lovely community. You should not be worried by that. That warning is saying that cdo cannot find the variable lat and zc that are included in your attributes "DIC:coordinates = "time zc latitude longitude lat lon". Your are only performing a time series mean which only requires the time axis.

Kind regards,

Estanislao

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