wiki:Documentation/UserGuide/CDO

How to use cdo to change the resolution of a file?

Author: J.Barichivich & S.Luyssaert
Last revision: 2020/03/19, J. Lathière

Similar to Ferret (see also https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/Ferret), CDO can also be used to regrid NetCDF files. It is very straight and fast. Contrary to Ferret, I [SL] did not find how to increase the memory allocation for CDO. Thus for very large files Ferret seems to be the software of your choice.

The call has the following structure:

cdo -f nc -regriddingMethod,gridTemplate.nc input.nc output.nc

There are three regridding methods: remapbil (bilinear interpolation), remapbic (bicubic interpolation), remapnn (nearest neighbour), remapcon (conservative regridding). Use remapnn and remapcon to avoid weird values if your variable is heterogeneous.

For the template file with your target grid, it can be any netcdf with regular lat/lon. A trick here is to use "full paths" and not relative paths to the files in order to work.

Some examples:

cdo -f nc -remapbil,/gpfs/cru/rst08auu/code/target.0.5degree.gpp.grid.45N.nc esa.ecv.smo.0.25deg.grid.monthly.1979.2010.nc esa.ecv.smo.0.25deg.grid.monthly.1979.2010.cdo.remapped.0.5deg.remapbil.45N.nc
cdo -f nc -remapnn,/gpfs/cru/rst08auu/code/target.0.5degree.gpp.grid.45N.nc esa.ecv.smo.0.25deg.grid.monthly.1979.2010.nc esa.ecv.smo.0.25deg.grid.monthly.1979.2010.cdo.remapped.0.5deg.remapnn.45N.nc

General info regarding nco and cdo

ncap2

The most powerful and quickly evolving tool from the nco set of functions

See also the website where you can search what you are looking on this growing list of answers forum nco

A simple exemple showing different capacities (creation of a variable, use of a mask, call to an attribute, count the total and the size of the field (we can restrict this operation to a dimension as shown on the second line)

<code>

ncap2 -O -s 'missing_flag[$y,$x]=0;where(t2m_daily!=t2m_daily@missing_value) missing_flag=1;missing_count=float(missing_flag.total())/missing_flag.size();print(missing_count)' stomate_restart.nc ~/foo.nc ncap2 -O -s 'missing_flag[$y,$x]=0;where(t2m_daily!=t2m_daily@missing_value) missing_flag=1;missing_count=float(missing_flag.total($x))/missing_flag.size($x);print(missing_count)' stomate_restart.nc ~/foo.nc

</code>

cdo

A command that handle many operations one would like to do when working on outputs of models of the Earth System :

  • changing of time axis
  • regridding (many grid are already implemented and it is an even more versatile tool)
  • complex operations...

See the website of the project {{https://code.zmaw.de/projects/cdo/wiki}} or the doc : {{:reunions_orchidee:cdo-manual.pdf| CDO Manual}} and the {{:reunions_orchidee:cdo_refcard.pdf | quickref}}

<code>

cdo -v # print list of available operators
cdo -V # version (if very old, think of downloading the source and install a new version, as it is a tool that is evolving quickly
cdo -h remapcon # informations about a command
cdo remapcon,my_grid my_climatology.nc my_regridded_climatology.nc # conservative regridding to an other resolution

</code>

my_grid could be a file like :

<code>

gridtype = lonlat gridsize = 220 xname = longitude xunits = degrees_east yname = latitude yunits = degrees_north xsize = 20 ysize = 11 xfirst = -18.75 xinc = 3.75 yfirst = 20

</code>

<code>

cdo sinfov my_file.nc #most info on the file cdo griddes my_file.nc #grid description (check that the type is not generic (which means unrecognised and thus not useable for mapping

</code>

Sometimes, one just need to add the attribute coordinates (linking to the variables defining the longitude and latitude positions) to enable the recognition of the grid that is used (see https://code.zmaw.de/boards/1/topics/55) <code>

ncatted -a coordinates,my_var,o,c,"nav_lon nav_lat" sst_data.nc

</code>

or to correct a wrong spelling of an attribute

<code>

ncatted -a units,latitude,m,c,"degrees_north" force2002.nc

</code>

Operator chaining

It is one of the main features of CDO. Use it as often as possible. But Note: Operatos with a arbitrary list of input files cannot be combined with other operators

# Simple combination: <code>

cdo sub -dayavg ifile2 -timavg ifile1 ofile

</code>

instead of :

<code>

cdo timavg ifile1 tmp1

cdo dayavg ifile2 tmp2

cdo sub tmp2 tmp1 ofile

rm tmp1 tmp2

</code>

To install a newer version than the default one on asterix/obelix

<code>

get files from https://code.zmaw.de/projects/cdo/files ./configure --prefix=/home/users/your_ACCOUNT/ --with-netcdf=/usr

make clean make make install

</code>

If you installed proj and hdf5 libraries somewhere, their can also be support for these file formats :

<code>

./configure --prefix=/home/users/your_ACCOUNT/ --with-netcdf=/usr --with-proj=/path/to/install --with-hdf5=/path/where/installed

</code>

Last modified 10 months ago Last modified on 03/19/20 16:46:32