CDO CMOR Operator for CDO version lower equal 1.8.1¶

Installation¶

Download source¶

git clone https://github.com/PCMDI/cmip6-cmor-tables.git
git clone https://github.com/PCMDI/cmor.git
git clone git@git.mpimet.mpg.de:cdo.git
cd cdo
git submodule init
git submodule update
git checkout develop

Configure (Mistral)¶

module load gcc
cd cmor
./configure --prefix=$HOME/local --with-uuid --with-udunits2=/sw/rhel6-x64/util/udunits-2.2.17-gcc48 --with-netcdf=/sw/rhel6-x64/netcdf/netcdf_c-4.4.0-gcc48 LIBS=-lossp-uuid
make install
cd ..
mkdir build-cdo
cd build-cdo
../cdo/configure --with-cmor=$HOME/local --with-hdf5=/sw/rhel6-x64/hdf5/hdf5-1.8.14-threadsafe-gcc48 --with-netcdf=/sw/rhel6-x64/netcdf/netcdf_c-4.4.0-gcc48 --with-udunits2=/sw/rhel6-x64/util/udunits-2.2.17-gcc48 CPPFLAGS="-I$HOME/local/include/cdTime -I$HOME/local/include/json-c" LIBS=-lossp-uuid
make -j8
ln -s ../cmip6-cmor-tables/Tables .

Configure (Ubuntu)¶

apt-get install libossp-uuid-dev libnetcdf-dev
# maybe more prerequisites needed
cd ../cmor
./configure --prefix=$HOME/local --with-uuid --with-udunits2 --with-netcdf CFLAGS="-I/usr/include/ossp" LDFLAGS=-L/usr/lib/x86_64-linux-gnu/hdf5/serial LIBS=-lossp-uuid
make install
cd ../build-cdo
../cdo/configure --with-cmor=$HOME/local --with-hdf5 --with-netcdf --with-udunits2 CPPFLAGS="-I/usr/include/hdf5/serial -I$HOME/local/include/cdTime -I$HOME/src/cmor/include/json-c" LIBS=-lossp-uuid LDFLAGS=-L/usr/lib/x86_64-linux-gnu/hdf5/serial
make -j8
ln -s ../cmip6-cmor-tables/Tables .

Running¶

Preprocess¶

Select two variables from GRIB file and prepare for cmor. Variable selection could also be done with the cmor operator but doing it early is obviously more efficient.

partab.txt:

&parameter
  param = 130.128
  out_name = ta
  cell_methods = "time: mean" 
  units = "K" 
/
&parameter
  param = 131.128
  out_name = ua
  units = "m s-1" 
/

src/cdo --cmor -r -f nc selcode,130,131 -setpartabp,partab.txt -invertlat -setreftime,1850-01-01,00:00:00,days -settbounds,month /work/mh0469/m221078/prj/cmip6/piControl_r1i1p1-MR_echam6_ATM_mm_1850-1899.grb tmp.nc

Cmorize¶

Some requested pressure levels are missing in GRIB data. CMIP6_Amon.json table was changed to compensate for that.
You have to edit the levels for the dimension belonging to your variable. For plev17 this would be:

--- a/Tables/CMIP6_Amon.json
+++ b/Tables/CMIP6_Amon.json
@@ -228,8 +228,6 @@
                 "7000.", 
                 "5000.", 
                 "3000.", 
-                "2000.", 
-                "1000." 
             ], 
             "stored_direction": "decreasing", 
             "z_factors": "", 

cmor.rc contains settings for cmor_dataset_json() and special entries used by the cmor operator. Entries with two leading underscores are used for cdo/cmor internal purposes. All other key-value pairs are dumped to a JSON file and fed to cmor_dataset_json(). CMOR itself uses entries with one leading underscore internally. The remaining k-v pairs are used to create the nc files. Unknown (to CMOR) keys are simply copied as global attributes.

Now run cdo with cmor3 operator

src/cdo cmor,Tables/CMIP6_Amon.json,__info=cmor.rc tmp.nc

Produces output files

CMIP6/ua_Amon_piControl_MPI-ESM_r1i1p1f1_gn_185001-189912.nc
CMIP6/ta_Amon_piControl_MPI-ESM_r1i1p1f1_gn_185001-189912.nc

These can be compared to "official" files in /work/ik0555/cmip5/archive/CMIP5/output/MPI-M/MPI-ESM-MR/piControl/mon/atmos/<var>/r1i1p1/...

Grid mappings¶

Basic support for grid mappings has been added. This was only tested with a rotated lon/lat grid. In order to handle grids, CMOR must load a grid table in addition to the normal table. The __grid_table keyword is used to tell cdo cmor which table to load as grid table.

src/cdo cmor,Tables/CMIP6_day.json,__info=cmor.rc /work/mh0287/users/uwe/grid_mapping/CNRM-CERFACS_rllc.nc