Blue beam: Explanation slides

Red beam: Contains instructions and executable code

# Get the strucutre of header of a example raw model output:
ncdump -h example_interface.nc 
# results:
netcdf example_interface {
dimensions:
	time = UNLIMITED ; // (12 currently)
	lon = 384 ;
	lat = 192 ;
	height_2 = 1 ;
	height = 1 ;
variables:
	double time(time) ;
		time:standard_name = "time" ;
		time:units = "day as %Y%m%d.%f" ;
		time:calendar = "proleptic_gregorian" ;
		time:axis = "T" ;
	float lon(lon) ;
		lon:standard_name = "longitude" ;
		lon:long_name = "longitude" ;
		lon:units = "degrees_east" ;
		lon:axis = "X" ;
	float lat(lat) ;
		lat:standard_name = "latitude" ;
		lat:long_name = "latitude" ;
		lat:units = "degrees_north" ;
		lat:axis = "Y" ;
	double height_2(height_2) ;
		height_2:standard_name = "height" ;
		height_2:long_name = "height" ;
		height_2:units = "m" ;
		height_2:positive = "up" ;
		height_2:axis = "Z" ;
	double height(height) ;
		height:standard_name = "height" ;
		height:long_name = "height" ;
		height:units = "m" ;
		height:positive = "up" ;
		height:axis = "Z" ;
	float uas(time, height_2, lat, lon) ;
		uas:units = "m s-1" ;
		uas:code = 1 ;
		uas:table = 255 ;
	float tas(time, height, lat, lon) ;
		tas:units = "K" ;
		tas:code = 1 ;
		tas:table = 255 ;

// global attributes:
		:CDI = "Climate Data Interface version 1.9.0 (http://mpimet.mpg.de/cdi)" ;
		:Conventions = "CF-1.6" ;
		:history = "Tue Sep 12 10:30:24 2017: cdo_recent_cmor2 merge testuas.nc testtas.nc test.nc\n",
			"Tue Sep 12 10:30:01 2017: cdo_recent_cmor2 -setunit,m s-1 -selname,uas example_interface.nc testuas.nc\n",
			"Tue Sep 12 10:03:02 2017: cdo_recent_cmor2 merge test.nc test2.nc test3.nc\n",
			"Tue Sep 12 10:02:45 2017: cdo_recent_cmor2 -f nc setname,tas test.grb test.nc" ;
		:institution = "Max-Planck-Institute for Meteorology" ;
		:CDO = "Climate Data Operators version 1.9.1rc1 (http://mpimet.mpg.de/cdo)" ;
}

#CMIP5
institute_id="MPI-M"
institution="Max Planck Institute for Meteorology"
#member=r1i1p1

#CMIP6
institution_id="MPI-M"
institution="Max Planck Institute for Meteorology, Hamburg 20146, Germany"
variant_label=r1i1p1f1

cmor_setup();
cmor_dataset_json();
cmor_load_table();
cmor_set_table();
cmor_axis();
cmor_grid();
cmor_set_grid_mapping();
cmor_time_varying_grid_coordinate();
cmor_zfactor();
cmor_variable();
cmor_set_deflate();
cmor_set_variable_attribute();
cmor_create_output_path();
cmor_write();
cmor_close();

cdo cmor,Amon,\
         i=info_table.txt,\
        gi=grid_info.nc,\
        mt=mapping_table.txt\
                             infile

"variable_entry":{
  "ccb":  {
    "frequency": "mon",
    "modeling_realm":"atmos"
    }
  }

ncdump -h mrsofc_fx_MPIESM-1-2-HR_historical_r1i1p1f1_gn.nc
#stdout:
netcdf test {
dimensions:
	lat = 192 ;
	lon = 384 ;
	bnds = 2 ;
variables:
        double lat(lat);
        double lat_bnds(lat,bnds);
        double lon(lon);
        double lon_bnds(lon,bnds);

activity_id="CMIP"
experiment="AMIP"
experiment_id="amip"
forcing_index="1"
grid="All grid attributes are set for the native grid and based on information from attribute source."
grid_label="gn"
initialization_index="1"
institution="Max Planck Institute for Meteorology, Hamburg 20146, Germany"
institution_id="MPI-M"
license="CMIP6 model data produced by REQUIRED is licensed under a Creative Commons Attribution ShareAlike 4.0 International License (https://creativecommons.org/licenses). Consult https://pcmdi.llnl.gov/CMIP6/TermsOfUse for terms of use governing CMIP6 output, including citation requirements and proper acknowledgment. Further information about this data, including some limitations, can be found via the further_info_url (recorded as a global attribute in this file) and. The data producers and data providers make no warranty, either express or implied, including, but not limited to, warranties of merchantability and fitness for a particular purpose. All liabilities arising from the supply of the information (including any liability arising in negligence) are excluded to the fullest extent permitted by law."
mip_era="CMIP6"
nominal_resolution="100 km"
physics_index="1"
realization_index="1"
source="MPIESM1.2-HR (2017): \naerosol: none, prescribed MACv2-SP\natmos: ECHAM6.3 (spectral T127; 384 x 192 longitude/latitude; 95 levels; top level 0.01 hPa)\natmosChem: none\nland: JSBACH3.2\nlandIce: none/prescribed\nocean: MPIOM1.63 (tripolar TP04, approximately 0.4deg; 900 x 450 longitude/latitude; 40 levels; top grid cell 0-12 m)\nocnBgchem: HAMOCC\nseaIce: unnamed (thermodynamic (Semtner zero-layer) dynamic (Hibler 79) sea ice model)"
source_id="MPIESM-1-2-HR"
source_type="AGCM"
sub_experiment="none"
sub_experiment_id="none"
parent_activity_id="no parent"
parent_experiment_id="no parent"
calendar="proleptic_gregorian"
required_time_units="days since REQUIRED"

ls -1 /work/bm0021/cdo_incl_cmor/
..
cdo_2018-08-03_cmor2_gcc
cdo_2019-09-01_cmor3_gcc
cdo_recent_cmor2 -> cdo_2018-08-03_cmor2_gcc/src/cdo
cdo_recent_cmor3 -> /work/bm0021/cdo_incl_cmor/cdo_2019-09-01_cmor3_gcc/src/cdo

sudo apt-get install cdo

#update conda
conda update conda
#name the environment for cdo with cmor
cdoenv=cdocmor
#install develop-cdo which contains CMOR "conda-forge/label/dev::cdo"
#use conda-forge channel with "-c conda-forge"
#set $cdoenv as environment with --name
conda create --name ${cdoenv} conda-forge/label/dev::cdo -c conda-forge
#then activate it
source activate ${cdoenv}

#update cdo cmor:
conda install --name ${cdoenv} conda-forge/label/dev::cdo -c conda-forge

#!/bin/sh
# INSTALL SCRIPT FOR CDO WITH SUPPORT FOR NETCDF, GRIB2, HDF5 AND CMOR on a LINUX platform
# based on the instructions by Mithil Shah (http://www.studytrails.com/blog/install-climate-data-operator-cdo-with-netcdf-grib2-and-hdf5-support/)
# Author: Fabian Wachsmann
#
#You might need to install a fortran compiler, C compiler and a macro environment:
#sudo apt-get install gfortran
#sudo apt-get install gcc
#sudo apt-get install m4
#
cd ../libs/
INSTALLDIR=$(pwd)

#Install CDO with support:
#ZLIB, HDF5, EXPAT, UDUNITS, UUID, NETCDF, JASPER, GRIB_API, CMOR
zlib=N
szlib=N
hdf5=N
expat=N
udunits=N
uuid=N
netcdf=N
jasper=N
gribapi=N
eccodes=N
unixuuid=Y
jsonc=Y
cmor=N
cdo=N

#ZLIB 1.2.8:
#for unzip and zipping:
zlib_link="http://www.zlib.net/fossils/zlib-1.2.8.tar.gz"
#szlib 0.3.4:
szlib_link="https://gitlab.dkrz.de/k202009/libaec/uploads/e3a951204308ba1f623b529cf9e5f574/libaec-0.3.4.tar.gz"
#HDF5 1.8.12
#data model used by netCDF allowing infinity file sizes
hdf5_link="https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.13/src/hdf5-1.8.13.tar.gz"
#EXPAT 2.2.2
#xml parser (used by cmor2)
expat_link="https://github.com/libexpat/libexpat/releases/download/R_2_2_2/expat-2.2.2.tar.bz2"
#UDUNITS 2.2.25
#changes units of variables
udunits_link="ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.2.25.tar.gz"
#UUID 1.6.2
#creates universal unique identifier
uuid_link="https://launchpad.net/ubuntu/+archive/primary/+files/ossp-uuid_1.6.2.orig.tar.gz"
#NETCDF 4.4.1
#data format of climate data
netcdf_link="https://github.com/Unidata/netcdf-c/archive/v4.4.1.tar.gz"
#JASPER 1.9.1
#jpeg compressor
jasper_link="http://www.ece.uvic.ca/~mdadams/jasper/software/jasper-1.900.1.zip"
#GRIB_API 1.14.4
#data format of climate data
gribapi_link="https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-1.14.4-Source.tar.gz?api=v2"
#ECCODES 2.3.0
#recent version of GRIB_API
eccodes_link="https://confluence.ecmwf.int/download/attachments/45757960/eccodes-2.3.0-Source.tar.gz?api=v2"
#JSON-C 0.13.1
jsonc_link="https://github.com/json-c/json-c/archive/json-c-0.13.1-20180305.tar.gz"

if [ "$zlib" = "Y" ]; then
#ZLIB 1.2.8
#wget ${zlib_link} &&
tar xf zlib* || exit 1
cd zlib* || exit 1
./configure --prefix=${INSTALLDIR} || exit 1
make && make check && make install || exit 1
cd ..
fi

if [ "$szlib" = "Y" ]; then
#SZLIB 0.3.4
wget ${szlib_link} &&
tar -xzf libaec-0.3.4.tar.gz || exit 1
cd libaec* || exit 1
./configure --prefix=${INSTALLDIR} || exit 1
make && make check && make install || exit 1
cd ..
fi

if [ "$hdf5" = "Y" ]; then
#HDF5 1.8.12
#wget --no-check-certificate ${hdf5_link} &&
tar xf hdf5* || exit 1
cd hdf5* || exit 1
./configure --with-zlib=${INSTALLDIR} --prefix=${INSTALLDIR} --enable-hl CFLAGS=-fPIC || exit 1
make && make check || exit 1
make install || exit 1
cd ..
fi

if [ "$expat" = "Y" ]; then
#EXPAT 2.2.2
#wget --no-check-certificate ${expat_link} && 
tar xf expat* || exit 1
cd expat* || exit 1
./configure --prefix=${INSTALLDIR} CFLAGS=-fPIC || exit 1
make && make check && make install || exit 1
cd ..
fi

if [ "$udunits" = "Y" ]; then
#UDUNITS 2.2.25
#wget ${udunits_link} && 
tar xf udunits* || exit 1
cd udunits* || exit 1
CPPFLAGS=-I${INSTALLDIR}/include LDFLAGS=-L${INSTALLDIR}/lib ./configure --prefix=${INSTALLDIR} CFLAGS=-fPIC || exit 1
make && make check && make install || exit 1
cd ..
fi

if [ "$uuid" = "Y" ]; then
#UUID 1.6.2
#wget --no-check-certificate ${uuid_link} && 
tar xf ossp-uuid* || exit 1
cd uuid*
./configure --prefix=${INSTALLDIR} CFLAGS=-fPIC || exit 1
make && make check && make install || exit 1
cd ..
fi

if [ "$netcdf" = "Y" ]; then
#NETCDF 4.4.1
#wget --no-check-certificate ${netcdf_link} && 
tar xf v4* || exit 1
cd net*
CPPFLAGS=-I${INSTALLDIR}/include LDFLAGS=-L${INSTALLDIR}/lib ./configure --prefix=${INSTALLDIR} --enable-netcdf-4 CFLAGS=-fPIC || exit 1
make && make check && make install || exit 1
cd ..
fi

if [ "$jasper" = "Y" ]; then
#JASPER 1.9.1
#wget ${jasper_link} && 
unzip jasper* || exit 1
cd jasper*
./configure --prefix=${INSTALLDIR} CFLAGS=-fPIC || exit 1
make && make check && make install || exit 1
cd ..
fi

if [ "$gribapi" = "Y" ]; then
#GRIB_API 1.14.4
#wget --no-check-certificate ${gribapi_link} && 
tar xf grib* || exit 1
cd grib*
./configure --prefix=${INSTALLDIR} CFLAGS=-fPIC --with-netcdf=${INSTALLDIR} --with-jasper=${INSTALLDIR} || exit 1
make && make install || exit 1
cd ..
fi

if [ "$eccodes" = "Y" ]; then
#ECCODES 2.3.0
#wget --no-check-certificate ${eccodes_link} && 
tar -xzf  eccodes-2.3.0-Source.tar.gz* || exit 1
mkdir eccodes-2.3.0-build
cd eccodes-2.3.0-build
cmake -DCMAKE_INSTALL_PREFIX=${INSTALLDIR} ../eccodes-2.3.0-Source
make
ctest
make install || exit 1
cd ..
fi

if [ "$unixuuid" = "Y" ]; then
#sudo apt-get install uuid-dev
mkdir -p ${INSTALLDIR}/libs4cmor/include/
cp /usr/include/uuid/uuid.h ${INSTALLDIR}/libs4cmor/include/ || exit 1
fi

if [ "$jsonc" = "Y" ]; then
#JSON-C 0.13.1
#wget ${jsonc_link} && 
#tar -xzf  json-c-0.13.1*.tar.gz || exit 1
cd json-c-json-c*
./configure --prefix=${INSTALLDIR}/libs4cmor/ || exit 1
make && make install || exit 1
cd ..
fi

#if [ "$cmor" = "Y" ]; then
#CMOR 3.3.1.
#cd cmor3_v331/ || exit 1
#CFLAGS=-fPIC CPPFLAGS=-I${INSTALLDIR}/include LDFLAGS=-L${INSTALLDIR}/lib ./configure --prefix=${INSTALLDIR} --with-udunits2=${INSTALLDIR} --with-uuid=${INSTALLDIR} --with-netcdf=${INSTALLDIR} || exit 1
#make && make install || exit 1
#cd ${INSTALLDIR}/../cdo/
#fi

if [ "$cmor" = "Y" ]; then
#CMOR 2.9.2
cd cmor2-lib/cmor2_v292/ || exit 1
F77=gcc CC=gcc CFLAGS=-fPIC CPPFLAGS=-I${INSTALLDIR}/include LDFLAGS=-L${INSTALLDIR}/lib ./configure --prefix=${INSTALLDIR} --with-uuid=${INSTALLDIR} --with-udunits2=${INSTALLDIR} --with-netcdf=${INSTALLDIR}
make install
cd ../../
fi

if [ "$cdo" = "Y" ]; then
cd ../cdo
cmor_support/branches/cdo_incl_cmor/cdo_2019-08-15/
echo "CDO 1.9.5rc1";
#CDO 1.9.5rc1
tar xf cdo-1.9.5rc1.tar.gz || exit 1
cd cdo-1.9.5rc1|| exit 1  
make distclean
CPPFLAGS="-I${INSTALLDIR}/include -I${INSTALLDIR}/local/include -I${INSTALLDIR}/local/include/json-c -I${INSTALLDIR}/local/include/cdTime" OPENMP=0 ./configure --prefix=$(pwd)/ --with-cmor=${INSTALLDIR} --with-hdf5=${INSTALLDIR} --with-netcdf=${INSTALLDIR} --with-udunits2=${INSTALLDIR} --with-grib_api=${INSTALLDIR} --with-ossp-uuid=${INSTALLDIR} || exit 1
                                                                                                                               
make -j8 && make install                                                                                                                                                                                                
cd ..
fi

#connect to mistral
ssh -X <usernr>@mistral.dkrz.de

#create workdir
mkdir cdocmor_handson
cd cdocmor_handson

#copy examples directory
cdoDir=/work/bm0021/cdo_incl_cmor/
cp -r ${cdoDir}examples ./
cd examples

#link cdo cmor installation
alias cdo=${cdoDir}cdo_recent_cmor3

#get examples directory from cloud
wget -r -H -N --cut-dirs=2 --content-disposition -I "/v1/" "https://swiftbrowser.dkrz.de/tcl_objects/2019-10-22T11:30:05Z/r_a86d66aead1ab64da2897925934f7b0aac981e74/w_/dkrz_5c667751-d212-48fd-96a1-6c02f7c7a919/examples/0/?show_all"
mv swift.dkrz.de/examples ./
cd examples

#Use the local installation for cdo:
alias cdo=${PathToLocalCdoCmor}

#**General usage:
#cdo cmor,MIP-table[,keyvaluelist] infile

#**The keyvaluelist is of format
#key=value[,value]

#**Some keywords only allow exactly one value.
#**Others allow a comma separated list (CSL) of values.

#**If the input file is of netCDF format and contains all required meta data,
#**it can be sufficient to call:
#cdo cmor,MIP-table infile

#**example:
cdo cmor,cmip6_tables/MIP_tables/Tables/CMIP6_Amon.json example_interface.nc

#**Parameter one MUST be the MIP table
#**It can be specified with a relative or absoulte path

#example:
cdo cmor,cmip6_tables/MIP_tables/Tables/CMIP6_Amon.json example_interface.nc

<variable_id>_<table_id>_
<source_id>_<experiment_id>_
<variant_label>_<grid_label>

<variable_id>_<table_id>_
<model_id>_<experiment_id>_
<member>

<activity_id>/<product>/<institute_id>/
<model_id>/<experiment_id>/<frequency>/
<realm>/<variable_id>/<member>

<mip_er>/<activity_id>/<institution_id>/<source_id>/
<experiment_id>/<variant_label>/<table_id>/
<variable_id>/<grid_label>/<version>

#example:
#select tas from infile
cdo cmor,cmip6_tables/MIP_tables/Tables/CMIP6_Amon.json,\
         cn=tas example_interface.nc
#select tas and uas from infile
cdo cmor,cmip6_tables/MIP_tables/Tables/CMIP6_Amon.json,\
         cn=tas,uas example_interface.nc

#example:
cdo cmor,cmip6_tables/MIP_tables/Tables/CMIP6_Amon.json example_interface.nc

#example:
cdo cmor,cmip6_tables/MIP_tables/Tables/CMIP6_Amon.json example_interface.nc

~/cdo-git/src/cdo cmor,Amon example_interface.nc
cdo cmor: MIP table file = 'cmip6_tables/MIP_tables/Tables/CMIP6_Amon.json'.
cdo cmor: Attribute 'time_units' = 'days since 1850-1-1 00:00:00'
cdo cmor: Since you set attribute 'parent_experiment_id'='piControl', further attributes are checked.
cdo cmor: Function 'all axes registration':
          You have not requested a particular variable via 'cmor_name'.
          There are several in infile and all will be processed.
          Notice that attributes specified in the cmdline will be used for all infile variables.
cdo cmor: Vertical axis is either default and scalar or not available.
cdo cmor: Vertical axis is either default and scalar or not available.
cdo cmor: Output mode: (R)eplace.
cdo cmor: Output mode: (R)eplace.
cdo cmor:      File stored in:  './/CMIP6/CMIP/MPI-M/MPI-ESM1-2-HR/historical/r1i1p1f1/Amon/uas/gn/v20191008/uas_Amon_MPI-ESM1-2-HR_historical_r1i1p1f1_gn_185001-185012.nc' with cmor!
cdo cmor:      File stored in:  './/CMIP6/CMIP/MPI-M/MPI-ESM1-2-HR/historical/r1i1p1f1/Amon/tas/gn/v20191008/tas_Amon_MPI-ESM1-2-HR_historical_r1i1p1f1_gn_185001-185012.nc' with cmor!
cdo cmor: Processed 10 variables over 12 timesteps [4.65s 452MB].

#The usual CDO options are valid for this operator as well:
#cdo cmor can be called in silent (-s) or verbose (-v) mode.
#The verbose mode is recommended if the processing is unclear:

cdo -v cmor,cmip6_tables/MIP_tables/Tables/CMIP6_Amon.json \
       example_interface.nc
cdo -s cmor,cmip6_tables/MIP_tables/Tables/CMIP6_Amon.json \
       example_interface.nc

#In many cases, operator chaining can be helpful:

cdo -cmor,cmip6_tables/MIP_tables/Tables/CMIP6_Amon.json \
    -addc,10 example_interface.nc

cdo cmor,cmip6_tables/MIP_tables/Tables/CMIP6_Amon.json example_interface.nc

CMIP6_3hr.json
CMIP6_6hrLev.json
CMIP6_6hrPlev.json
CMIP6_6hrPlevPt.json
CMIP6_AERday.json
CMIP6_AERhr.json
CMIP6_AERmon.json
CMIP6_AERmonZ.json
CMIP6_Amon.json
CMIP6_CF3hr.json
CMIP6_CFday.json
CMIP6_CFmon.json
CMIP6_CFsubhr.json
CMIP6_coordinate.json
CMIP6_CV.json
CMIP6_CV_test.json
CMIP6_day.json
CMIP6_E1hrClimMon.json
CMIP6_E1hr.json
CMIP6_E3hr.json
CMIP6_E3hrPt.json
CMIP6_E6hrZ.json
CMIP6_Eday.json
CMIP6_EdayZ.json
CMIP6_Efx.json
CMIP6_Emon.json
CMIP6_EmonZ.json
CMIP6_Esubhr.json
CMIP6_Eyr.json
CMIP6_formula_terms.json
CMIP6_fx.json
CMIP6_grids.json
CMIP6_IfxAnt.json
CMIP6_IfxGre.json
CMIP6_ImonAnt.json
CMIP6_ImonGre.json
CMIP6_IyrAnt.json
CMIP6_IyrGre.json
CMIP6_LImon.json
CMIP6_Lmon.json
CMIP6_Oclim.json
CMIP6_Oday.json
CMIP6_Odec.json
CMIP6_Ofx.json
CMIP6_Omon.json
CMIP6_Oyr.json
CMIP6_SIday.json
CMIP6_SImon.json

{
    "Header": {
        "data_specs_version": "01.00.13", 
        "table_id": "Table Amon", 
        "realm": "atmos atmosChem", 
        "cmor_version": "3.2", 
        "table_date": "12 July 2017", 
        "missing_value": "1e20", 
        "product": "model-output", 
        "approx_interval": "30.00000", 
        "generic_levels": "alevel alevhalf", 
        "mip_era": "CMIP6", 
        "Conventions": "CF-1.7 CMIP-6.0"
    }, 
    "variable_entry": {
        "ccb": {
            "frequency": "mon", 
            "modeling_realm": "atmos", 
            "standard_name": "air_pressure_at_convective_cloud_base", 
            "units": "Pa", 
            "cell_methods": "area: time: mean", 
            "cell_measures": "area: areacella", 
            "long_name": "Air Pressure at Convective Cloud Base", 
            "comment": "Where convective cloud is present in the grid cell, the instantaneous cloud base altitude should be that of the bottom of the lowest level containing convective cloud. Missing data should be reported in the absence of convective cloud. The time mean should be calculated from these quantities averaging over occasions when convective cloud is present only, and should contain missing data for occasions when no convective cloud is present during the meaning period.", 
            "dimensions": "longitude latitude time", 
            "out_name": "ccb", 
            "type": "real", 
            "positive": "", 
            "valid_min": "", 
            "valid_max": "", 
            "ok_min_mean_abs": "", 
            "ok_max_mean_abs": ""
        }, 
        "cct": {
            "frequency": "mon", 
            "modeling_realm": "atmos", 
            "standard_name": "air_pressure_at_convective_cloud_top", 
            "units": "Pa", 
            "cell_methods": "area: time: mean", 
            "cell_measures": "area: areacella", 
            "long_name": "Air Pressure at Convective Cloud Top", 
            "comment": "Where convective cloud is present in the grid cell, the instantaneous cloud top altitude should be that of the top of the highest level containing convective cloud. Missing data should be reported in the absence of convective cloud. The time mean should be calculated from these quantities averaging over occasions when convective cloud is present only, and should contain missing data for occasions when no convective cloud is present during the meaning period.", 
            "dimensions": "longitude latitude time", 
            "out_name": "cct", 
            "type": "real", 
            "positive": "", 
            "valid_min": "", 
            "valid_max": "", 
            "ok_min_mean_abs": "", 
            "ok_max_mean_abs": ""
        }, 
        "cfc113global": {
            "frequency": "mon", 
            "modeling_realm": "atmos atmosChem", 
            "standard_name": "mole_fraction_of_cfc113_in_air", 
            "units": "1e-12", 
            "cell_methods": "area: time: mean", 
            "cell_measures": "", 
            "long_name": "Global Mean Mole Fraction of CFC113", 
            "comment": "", 
            "dimensions": "time", 
            "out_name": "cfc113global", 
            "type": "real", 
            "positive": "", 
            "valid_min": "", 
            "valid_max": "", 
            "ok_min_mean_abs": "", 
            "ok_max_mean_abs": ""
        }, 
        "cfc11global": {
            "frequency": "mon", 
            "modeling_realm": "atmos atmosChem", 
            "standard_name": "mole_fraction_of_cfc11_in_air", 
            "units": "1e-12", 
            "cell_methods": "area: time: mean", 
            "cell_measures": "", 
            "long_name": "Global Mean Mole Fraction of CFC11", 
            "comment": "", 
            "dimensions": "time", 
            "out_name": "cfc11global", 
            "type": "real", 
            "positive": "", 
            "valid_min": "", 
            "valid_max": "", 
            "ok_min_mean_abs": "", 
            "ok_max_mean_abs": ""
        }
    }
}

cdo cmor,cmip6_tables/MIP_tables/Tables/CMIP6_Amon.json example_interface.nc

{
    "Header": {
        "data_specs_version": "01.00.13", 

{
    "Header": {
        "data_specs_version": "01.00.13", 

cdo cmor,cmip6_tables/MIP_tables/Tables/CMIP6_Amon.json,cn=tas example_interface.nc

cdo cmor,cmip6_tables/MIP_tables/Tables/CMIP6_Amon.json example_interface.nc

{
    "CV":{
        "required_global_attributes":[
            "Conventions",
            "activity_id",
            "creation_date",
            "data_specs_version",
            "experiment",
            "experiment_id",
            "forcing_index",
            "frequency",
            "further_info_url",
            "grid",
            "grid_label",
            "initialization_index",
            "institution",
            "institution_id",
            "license",
            "mip_era",
            "nominal_resolution",
            "physics_index",
            "product",
            "realization_index",
            "realm",
            "source",
            "source_id",
            "source_type",
            "sub_experiment",
            "sub_experiment_id",
            "table_id",
            "tracking_id",
            "variable_id",
            "variant_label"
        ],
        "version_metadata":{
            "author":"Paul J. Durack <durack1@llnl.gov>",
            "creation_date":"Wed Jul 5 10:30:00 2017 -0700",
            "institution_id":"PCMDI",
            "latest_tag_point":"3.2.4 (56; gcc9356e)",
            "note":"Revise source_id CNRM-CM6-1",
            "previous_commit":"f042b9339fd1cb3f5ee39bb2b5ccf958812bbd21"
        },
        "activity_id":[
            "AerChemMIP",
            "C4MIP",
            "CFMIP",
            "CMIP",
            "CORDEX",
            "DAMIP",
            "DCPP",
            "DynVarMIP",
            "FAFMIP",
            "GMMIP",
            "GeoMIP",
            "HighResMIP",
            "ISMIP6",
            "LS3MIP",
            "LUMIP",
            "OMIP",
            "PMIP",
            "RFMIP",
            "SIMIP",
            "ScenarioMIP",
            "VIACSAB",
            "VolMIP"
        ],
        "institution_id":{
            "AWI":"Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany",
            "BNU":"Beijing Normal University, Beijing 100875, China",
            "CAMS":"Chinese Academy of Meteorological Sciences, Beijing 100081, China",
            "CCCR-IITM":"Centre for Climate Change Research, Indian Institute of Tropical Meteorology Pune, Maharashtra 411 008, India",
            "CCCma":"Canadian Centre for Climate Modelling and Analysis, Victoria, BC V8P 5C2, Canada",
            "CMCC":"Fondazione Centro Euro-Mediterraneo sui Cambiamenti Climatici, Lecce 73100, Italy",
            "CNRM-CERFACS":"CNRM (Centre National de Recherches Meteorologiques, Toulouse 31057, France), CERFACS (Centre Europeen de Recherche et de Formation Avancee en Calcul Scientifique, Toulouse 31057, France)",
            "CSIR-CSIRO":"CSIR (Council for Scientific and Industrial Research - Natural Resources and the Environment, Pretoria, 0001, South Africa), CSIRO (Commonwealth Scientific and Industrial Research Organisation and Bureau of Meteorology, Melbourne, Victoria 3208, Australia)",
            "CSIRO-BOM":"Commonwealth Scientific and Industrial Research Organisation and Bureau of Meteorology, Melbourne, Victoria 3208, Australia",
            "EC-Earth-Consortium":"KNMI, The Netherlands; SMHI, Sweden; DMI, Denmark; AEMET, Spain; Met Eireann, Ireland; CNR-ISAC, Italy; Instituto de Meteorologia, Portugal; FMI, Finland; BSC, Spain; Centro de Geofisica, University of Lisbon, Portugal; ENEA, Italy; Geomar, Germany; Geophysical Institute, University of Bergen, Norway; ICHEC, Ireland; ICTP, Italy; IMAU, The Netherlands; IRV, Sweden;  Lund University, Sweden; Meteorologiska Institutionen, Stockholms University, Sweden; Niels Bohr Institute, University of Copenhagen, Denmark; NTNU, Norway; SARA, The Netherlands; Unite ASTR, Belgium; Universiteit Utrecht, The Netherlands; Universiteit Wageningen, The Netherlands; University College Dublin, Ireland; Vrije Universiteit Amsterdam, the Netherlands; University of Helsinki, Finland; KIT, Karlsruhe, Germany; USC, University of Santiago de Compostela, Spain; Uppsala Universitet, Sweden; NLeSC, Netherlands eScience Center, The Netherlands",
            "FIO-RONM":"FIO (First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, China), RONM (Laboratory for Regional Oceanography and Numerical Modeling, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China)",
            "INM":"Institute for Numerical Mathematics, Russian Academy of Science, Moscow 119991, Russia",
            "INPE":"National Institute for Space Research, Cachoeira Paulista, SP 12630-000, Brazil",
            "IPSL":"Institut Pierre Simon Laplace, Paris 75252, France",
            "MESSy-Consortium":"The Modular Earth Submodel System (MESSy) Consortium, represented by the Institute for Physics of the Atmosphere, Deutsches Zentrum fur Luft- und Raumfahrt (DLR), Wessling, Bavaria 82234, Germany",
            "MIROC":"JAMSTEC (Japan Agency for Marine-Earth Science and Technology, Kanagawa 236-0001, Japan), AORI (Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan), NIES (National Institute for Environmental Studies, Ibaraki 305-8506, Japan), and AICS (RIKEN Advanced Institute for Computational Science, Hyogo 650-0047, Japan)",
            "MOHC":"Met Office Hadley Centre, Fitzroy Road, Exeter, Devon, EX1 3PB, UK",
            "MPI-M":"Max Planck Institute for Meteorology, Hamburg 20146, Germany",
            "MRI":"Meteorological Research Institute, Tsukuba, Ibaraki 305-0052, Japan",
            "NASA-GISS":"Goddard Institute for Space Studies, New York, NY 10025, USA",
            "NCAR":"National Center for Atmospheric Research, Boulder, CO 80301, USA",
            "NCC":"NorESM Climate modeling Consortium consisting of CICERO (Center for International Climate and Environmental Research, Oslo 0349), MET-Norway (Norwegian Meteorological Institute, Oslo 0313), NERSC (Nansen Environmental and Remote Sensing Center, Bergen 5006), NILU (Norwegian Institute for Air Research, Kjeller 2027), UiB (University of Bergen, Bergen 5007), UiO (University of Oslo, Oslo 0313) and UNI (Uni Research, Bergen 5008), Norway",
            "NERC":"Natural Environment Research Council, STFC-RAL, Harwell, Oxford, OX11 0QX, UK",
            "NIMS-KMA":"National Institute of Meteorological Sciences/Korea Meteorological Administration, Climate Research Division, Seoho-bukro 33, Seogwipo-si, Jejudo 63568, Republic of Korea",
            "NOAA-GFDL":"National Oceanic and Atmospheric Administration, Geophysical Fluid Dynamics Laboratory, Princeton, NJ 08540, USA",
            "NUIST":"Nanjing University of Information Science and Technology, Nanjing, 210044, China",
            "PCMDI":"Program for Climate Model Diagnosis and Intercomparison, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA",
            "THU":"Department of Earth System Science, Tsinghua University, Beijing 100084, China"
        },
        "source_id":{
            "ACCESS-1-0":{
                "activity_participation":[
                    "CMIP"
                ],
                "cohort":[
                    "CMIP5"
                ],
                "institution_id":[
                    "CSIRO-BOM"
                ],
                "source_id":"ACCESS-1-0",
                "source":"ACCESS 1.0 (2011): \naerosol: CLASSIC (v1.0)\natmos: HadGAM2 (r1.1; N96, 192 x 145 longitude/latitude; 38 levels; top level 39255 m)\natmosChem: none\nland: MOSES2.2\nlandIce: none\nocean: ACCESS-OM (MOM4p1; tripolar primarily 1deg, 360 x 300 longitude/latitude; 50 levels; top grid cell 0-10 m)\nocnBgchem: none\nseaIce: CICE4.1"
            },
            "AWI-CM-1-0-HR":{
                "activity_participation":[
                    "CORDEX",
                    "HighResMIP",
                    "OMIP",
                    "SIMIP",
                    "VIACSAB"
                ],
                "cohort":[
                    "Registered"
                ],
                "institution_id":[
                    "AWI"
                ],
                "source_id":"AWI-CM-1-0-HR",
                "source":"AWI-CM 1.0 HR (2017): \naerosol: none\natmos: ECHAM6.3.02p4 (T127L95 native atmosphere T127 gaussian grid; 384 x 192 longitude/latitude; 95 levels; top level 80 km)\natmosChem: none\nland: JSBACH 3.10\nlandIce: none\nocean: FESOM 1.4 (unstructured grid in the horizontal with 1306775 wet nodes; 46 levels; top grid cell 0-5 m)\nocnBgchem: none\nseaIce: FESOM 1.4"
            },
            "AWI-CM-1-0-LR":{
                "activity_participation":[
                    "CMIP",
                    "CORDEX",
                    "HighResMIP",
                    "OMIP",
                    "PMIP",
                    "SIMIP",
                    "ScenarioMIP",
                    "VIACSAB"
                ],
                "cohort":[
                    "Registered"
                ],
                "institution_id":[
                    "AWI"
                ],
                "source_id":"AWI-CM-1-0-LR",
                "source":"AWI-CM 1.0 LR (2017): \naerosol: none\natmos: ECHAM6.3.02p4 (T63L47 native atmosphere T63 gaussian grid; 192 x 96 longitude/latitude; 47 levels; top level 80 km)\natmosChem: none\nland: JSBACH 3.10\nlandIce: none\nocean: FESOM 1.4 (unstructured grid in the horizontal with 126859 wet nodes; 46 levels; top grid cell 0-5 m)\nocnBgchem: none\nseaIce: FESOM 1.4"
            },

#Exercises:
#1. Create your own cdocmorinfo on 
#   c6dreq.dkrz.de/cdocmorinfo
#2. Copy that file to CWD/.cdocmorinfo
#3. Repeat
    cdo cmor,Amon example_interface.nc
#4. Adapt the infofile so that it finally works

# ways to configure the
# infile variable selector (ivs)
# and mapping table line selector (mtls)
#
# 1. ivs=cmor_name
cdo cmor,${MIP-table},cmor_name=${cn} ${infile}
# 2. ivs=name
cdo cmor,${MIP-table},cmor_name=${cn},name=${name} ${infile}
#
# with mapping table:

# 3. mtls=cmor_name, ivs=what is in corresponding mtl
cdo cmor,${MIP-table},mapping_table=${mt},cmor_name=${cn} ${infile}
# 4. mtls=cmor_name, ivs=name (overwrites mtl name)
cdo cmor,${MIP-table},mapping_table=${mt},cmor_name=${cn},name=${name} ${infile}
# 5. mtls=name/code  ivs=ALL
cdo cmor,${MIP-table},mapping_table=${mt} ${infile}

infile=example_mapping.grb

#1. Commandline mapping:
cdo cmor,Amon,cn=tas,c=167,u=K,cm=m ${infile}
#  Variable with code=167 from ${infile}.
#  is used. Its model units is Kelvin (u=K)
#  and its time cell method is mean (cm=m).

#2. Mapping table application:
#   create mapping table:
echo '&parameter cn=tas c=167 u=K cm=M' >>mt.txt
#   apply cdo cmor with mapping table:
cdo cmor,Amon,mapping_table=mt.txt ${infile}
#  Without additional information,
#  all variables from ${infile}
#  are taken and converted
cdo cmor,Amon,cmor_name=tas,mt=mt.txt ${infile}
#  If a cmor_name is provided, it is used
#  as a mapping table line selector.
#  The variable selector is taken
#  from the corresponding mapping table line.

"latitude": {
  "standard_name": "latitude", 
  "units": "degrees_north", 
  "axis": "Y", 
  "long_name": "latitude", 
  "climatology": "", 
  "formula": "", 
  "must_have_bounds": "yes", 
  "out_name": "lat", 
  "positive": "", 
  "requested": "", 
  "requested_bounds": "", 
  "stored_direction": "increasing", 
  "tolerance": "", 
  "type": "double", 
  "valid_max": "90.0", 
  "valid_min": "-90.0", 
  "value": "", 
  "z_bounds_factors": "", 
  "z_factors": "", 
  "bounds_values": ""
}

"tas": {
  "frequency": "mon", 
  "modeling_realm": "atmos", 
  "standard_name": "air_temperature", 
  "units": "K", 
  "cell_methods": "area: time: mean", 
  "cell_measures": "area: areacella", 
  "long_name": "Near-Surface Air Temperature", 
  "comment": "near-surface (usually, 2 meter) air temperature", 
  "dimensions": "longitude latitude time height2m", 
  "out_name": "tas", 
  "type": "real", 
  "positive": "", 
  "valid_min": "", 
  "valid_max": "", 
  "ok_min_mean_abs": "", 
  "ok_max_mean_abs": ""
}

bool is_lat_axis(const char *units, const char *stdname)
{
  bool status = false;
  char lc_units[16];

  memcpy(lc_units, units, 15);
  lc_units[15] = 0;
  str_tolower(lc_units);

  if ( (str_is_equal(lc_units, "degree") || str_is_equal(lc_units, "radian")) &&
        (str_is_equal(stdname, "grid_latitude") || str_is_equal(stdname, "latitude")) )
    {
      status = true;
    }
  else if ( str_is_equal(lc_units, "degree")
            && !str_is_equal(stdname, "grid_longitude")
            && !str_is_equal(stdname, "longitude") )
    {
      int ioff = 6;
      if ( lc_units[ioff] == 's' ) ioff++;
      if ( lc_units[ioff] == '_' ) ioff++;
      if ( lc_units[ioff] == 'n' || lc_units[ioff] == 's' ) status = true;
    }

  return status;
}

ncdump -h example_gridinfo_CCLM4-8-17.nc
netcdf example_gridinfo_CCLM4-8-17 {
dimensions:
	rlon = 424 ;
	rlat = 412 ;
	vertices = 4 ;
	time = UNLIMITED ; // (1 currently)
	bnds = 2 ;
variables:
	double lon(rlat, rlon) ;
		lon:standard_name = "longitude" ;
		lon:long_name = "longitude" ;
		lon:units = "degrees_east" ;
		lon:_CoordinateAxisType = "Lon" ;
		lon:bounds = "lon_bnds" ;
	double lon_bnds(rlat, rlon, vertices) ;
	double lat(rlat, rlon) ;
		lat:standard_name = "latitude" ;
		lat:long_name = "latitude" ;
		lat:units = "degrees_north" ;
		lat:_CoordinateAxisType = "Lat" ;
		lat:bounds = "lat_bnds" ;
	double lat_bnds(rlat, rlon, vertices) ;
	double rlon(rlon) ;
		rlon:standard_name = "grid_longitude" ;
		rlon:long_name = "longitude in rotated pole grid" ;
		rlon:units = "degrees" ;
		rlon:axis = "X" ;
	double rlat(rlat) ;
		rlat:standard_name = "grid_latitude" ;
		rlat:long_name = "latitude in rotated pole grid" ;
		rlat:units = "degrees" ;
		rlat:axis = "Y" ;
	int rotated_pole ;
		rotated_pole:grid_north_pole_latitude = 39.25 ;
		rotated_pole:grid_north_pole_longitude = -162. ;
		rotated_pole:grid_mapping_name = "rotated_latitude_longitude" ;
	double height ;
		height:standard_name = "height" ;
		height:long_name = "height" ;
		height:units = "m" ;
		height:positive = "up" ;
		height:axis = "Z" ;
	double time(time) ;
		time:standard_name = "time" ;
		time:long_name = "time" ;
		time:bounds = "time_bnds" ;
		time:units = "days since 1949-12-01 00:00:00" ;
		time:calendar = "365_day" ;
		time:axis = "T" ;
	double time_bnds(time, bnds) ;
	float tas(time, rlat, rlon) ;
		tas:standard_name = "air_temperature" ;
		tas:long_name = "Near-Surface Air Temperature" ;
		tas:units = "K" ;
		tas:grid_mapping = "rotated_pole" ;
		tas:coordinates = "height lat lon" ;
		tas:_FillValue = 1.e+20f ;
		tas:missing_value = 1.e+20f ;
		tas:cell_methods = "time: mean" ;
}

# MIP-Table request:
"cell_methods": "time: mean"
"dimensions": "time"
# Mapping attribute:
cm=m

# MIP-Table request:
"cell_methods": "time: point"
"dimensions": "time1"
# Mapping attribute:
cm=p

# MIP-Table request:
#  Climate:
"cell_methods": "time: mean within years time: mean over years"
"dimensions": "time2"
# Mapping attribute:
cm=c

#  Diurnal:
"cell_methods": "time: mean within days time: mean over days"
"dimensions": "time3"
# Mapping attribute:
cm=d

# MIP-Table request:
"cell_methods": "time: mean"
"dimensions": "time"
# Mapping attribute:
cm=m

# MIP-Table request:
"cell_methods": "time: point"
"dimensions": "time1"
# Mapping attribute:
cm=p

if ( ta == "cmip" )

# MIP-Table request:
#  Climate:
"cell_methods": "time: mean within years time: mean over years"
"dimensions": "time2"
# Mapping attribute:
cm=c

#  Diurnal:
"cell_methods": "time: mean within days time: mean over days"
"dimensions": "time3"
# Mapping attribute:
cm=d

# MIP-Table request:
#  Climate:
"cell_methods": "time: mean within years time: mean over years"
"dimensions": "time2"
# Mapping attribute:
cm=c

#  Diurnal:
"cell_methods": "time: mean within days time: mean over days"
"dimensions": "time3"
# Mapping attribute:
cm=d

# Get the strucutre of header of a example raw model output:
ncdump -h example_interface.nc 
# results:
netcdf example_interface {
dimensions:
	time = UNLIMITED ; // (12 currently)
	lon = 384 ;
	lat = 192 ;
	height = 1 ;

"height2m": {
  "valid_max": "10.0", 
  "valid_min": "1.0", 
  "value": "2.", 

"basin": { 
  "standard_name": "region",
  "requested": [
    "atlantic_arctic_ocean", 
    "indian_pacific_ocean", 
    "global_ocean"
   ], 
  "type": "character", 

"hfbasinpadv": {
  "dimensions": "latitude basin time", 

#From earlier examples, you should have created a tas-file 
#for year 2001. Now you want to append year 2002:
#
#Save the last chunk in a variable:
creationDate=v20171010
DRS=CMIP6/CMIP/MPI-M/MPIESM-1-2-HR/historical/ri1ip1f1/Amon/tas/gn/${creationDate}/
lc=${DRS}tas_Amon_MPIESM-1-2-HR_historical_r1i1p1f1_gn_200101-200112.nc

cdo cmor,Amon,mt=mapping_table.txt,last_chunk=${lc} example_append2002.grb


#The outfile path and filename is saved in
#„CHUNK_FILE_tas_Amon_MPI-ESM_amip_r1i1p1.txt“.
#This is the description for the default chunk in append mode.
#Now you can append the next year without defining lc:
cdo cmor,Amon,mt=mapping_table.txt example_append2003.grb