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_01_25_2018_cmor2
cdo_01_25_2018_cmor3
cdo_01_25_2018_cmor3_gcc
cdo_01_25_2018_cmor3_intel
cdo_03-31-2017
cdo_06_14_2017_cmor2
cdo_06_14_2017_cmor3
cdo_08_30_2017_cmor2
cdo_08_30_2017_cmor3
cdo_11_15_2017_cmor2
cdo_11_15_2017_cmor3

#!/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=Y
hdf5=Y
expat=Y
udunits=Y
uuid=Y
netcdf=Y
jasper=Y
gribapi=Y
cmor=Y

#ZLIB 1.2.8:
#for unzip and zipping:
zlib_link="http://www.zlib.net/fossils/zlib-1.2.8.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"

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 [ "$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 [ "$cmor" = "Y" ]; then
#CMOR 3.3.1.
#cd cmor3_v331/ || exit 1
#CFLAGS=-fPIC CPPFLAGS=-I${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 [ "$cmor" = "Y" ]; then
#CMOR 2.9.2
cd cmor2_v292/ || exit 1
F77=gcc CC=gcc CFLAGS=-fPIC CPPFLAGS=-I${INSTALLDIR}/include LDFLAGS=-L${INSTALLDIR}/lib ./configure --prefix=${INSTALLDIR} --with-uuid=${INSTALLDIR} --with-udunits2=${INSTALLDIR} --with-netcdf=${INSTALLDIR}
make install
cd ..
fi

cd ../cdo
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 ..

#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_handson_cmor2

#**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,cordex_mip_tables/CORDEX_mon example_interface.nc

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

#example:
cdo cmor,cordex_mip_tables/CORDEX_mon 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,cordex_mip_tables/CORDEX_mon,cn=tas example_interface.nc
#select tas and uas from infile
cdo cmor,cordex_mip_tables/CORDEX_mon,cn=tas,uas example_interface.nc

#example:
cdo cmor,cordex_mip_tables/CORDEX_mon example_interface.nc

#example:
cdo cmor,cordex_mip_tables/CORDEX_mon example_interface.nc

cdo cmor,cordex_mip_tables/CORDEX_mon,cn=tas,uas example_interface.nc 
cdo_handson_cmor2 cmor: 2.2. Start to find a MIP table file.
cdo_handson_cmor2 cmor: 2.2. MIP table file 'cordex_mip_tables/CORDEX_mon' exists in MIP table directory 'cordex_mip_tables/'.
cdo_handson_cmor2 cmor: Function 'attribute check, compare and set':
          Be aware of differences between infile and user specification.
          Attribute 'calendar' in input file: 'proleptic_gregorian' does not agree with user specification 'noleap'.
          Cmor library is called with 'noleap'.
cdo_handson_cmor2 cmor: Function 'attribute check, compare and set':
          Be aware of differences between infile and user specification.
          Attribute 'time_units' in input file: 'days since 1850-1-16 12:00:00' does not agree with user specification 'days since 1949-12-01T00:00:00Z'.
          Cmor library is called with 'days since 1949-12-01T00:00:00Z'.
cdo_handson_cmor2 cmor: Vertical axis is either default and scalar or not available.
cdo_handson_cmor2 cmor: Vertical axis is either default and scalar or not available.
cdo_handson_cmor2 cmor (Warning): Chunk description file 'CHUNK_FILE_uas_mon_historical_r1i1p1.txt' could not be opened.
Switched to replace mode.
cdo_handson_cmor2 cmor (Warning): In checking the last chunk:
          Chunk './/tas_mon_CLMcom-CCLM4-8-17_historical_r1i1p1_185001-185012.nc' configured via chunk description file does not exist.
          Switched to replace mode for this variable.

cdo_handson_cmor2 cmor:      File stored in:  './/CORDEX/output/EUR-11/CLMcom/CCCma-CanESM2/historical/r1i1p1/CLMcom-CCLM4-8-17/v1/mon/.//uas/.//uas_EUR-11_CCCma-CanESM2_historical_r1i1p1_CLMcom-CCLM4-8-17_v1_mon_185001-185012.nc' with cmor!
cdo_handson_cmor2 cmor:      File stored in:  './/CORDEX/output/EUR-11/CLMcom/CCCma-CanESM2/historical/r1i1p1/CLMcom-CCLM4-8-17/v1/mon/.//tas/.//tas_EUR-11_CCCma-CanESM2_historical_r1i1p1_CLMcom-CCLM4-8-17_v1_mon_185001-185012.nc' with cmor!
cdo_handson_cmor2 cmor: Processed 1769472 values from 10 variables over 12 timesteps [0.61s 441MB]

#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,cordex_mip_tables/CORDEX_mon example_interface.nc
cdo -s cmor,cordex_mip_tables/CORDEX_mon example_interface.nc

#In many cases, operator chaining can be helpful:

cdo -cmor,cordex_mip_tables/CORDEX_mon -addc,10 example_interface.nc

cdo cmor,cordex_mip_tables/CORDEX_mon example_interface.nc

ls cordex_mip_tables
CORDEX_3h
CORDEX_6h
CORDEX_day
CORDEX_fx
CORDEX_grids
CORDEX_mon
CORDEX_sem

table_id: Table mon
modeling_realm: atmos

frequency: mon

cmor_version: 2.6         ! version of CMOR that can read this table
cf_version:   1.4         ! version of CF that output conforms to
project_id:   CORDEX  ! project id
table_date:   Mar 2015 ! date this table was constructed

missing_value: 1.e20      ! value used to indicate a missing value
                          !   in arrays output by netCDF as 32-bit IEEE 
                          !   floating-point numbers (float or real)

product: output
! CMIP5's Table adapted for CORDEX
required_global_attributes: creation_date tracking_id model_id contact institute_id ! space separated required global attribute 

expt_id_ok: 'Evaluation run with reanalysis forcing' 'evaluation'
expt_id_ok: 'historical' 'historical'
expt_id_ok: 'RCP2.6' 'rcp26'
expt_id_ok: 'RCP4.5' 'rcp45'
expt_id_ok: 'RCP8.5' 'rcp85'
expt_id_ok: 'AMIP' 'amip'
expt_id_ok: '10- or 30-year run initialized in year XXXX' 'decadalXXXX'

approx_interval:  30.000000     ! approximate spacing between successive time
                               !   samples (in units of the output time 
                               !   coordinate.

!============
axis_entry: longitude
!============
!----------------------------------
! Axis attributes:
!----------------------------------
standard_name:    longitude
units:            degrees_east
axis:             X             ! X, Y, Z, T (default: undeclared)
long_name:        longitude
!----------------------------------
! Additional axis information:
!----------------------------------
out_name:         lon
stored_direction: increasing
type:             double
must_have_bounds: yes
!----------------------------------
!


!============
axis_entry: latitude
!============
!----------------------------------
! Axis attributes:
!----------------------------------
standard_name:    latitude
units:            degrees_north
axis:             Y             ! X, Y, Z, T (default: undeclared)
long_name:        latitude
!----------------------------------
! Additional axis information:
!----------------------------------
out_name:         lat
valid_min:        -90.0         
valid_max:        90.0 
stored_direction: increasing
type:             double
must_have_bounds: yes
!----------------------------------
!


!
!============
axis_entry: time
!============
!----------------------------------
! Axis attributes:
!----------------------------------
standard_name:    time
units:            days since ?
axis:             T             ! X, Y, Z, T (default: undeclared)
long_name:        time
!----------------------------------
! Additional axis information:
!----------------------------------
out_name:         time
stored_direction: increasing
type:             double
must_have_bounds: yes
!----------------------------------
!


!============
axis_entry: height2m
!============
!----------------------------------
! Axis attributes:
!----------------------------------
standard_name:    height
units:            m
axis:             Z             ! X, Y, Z, T (default: undeclared)
positive:         up         ! up or down (default: undeclared)
long_name:        height
!----------------------------------
! Additional axis information:
!----------------------------------
out_name:         height
valid_min:        1.0         
valid_max:        10.0 
stored_direction: increasing
type:             double
value:            2.            ! of scalar (singleton) dimension 
must_have_bounds: no
!----------------------------------
!


!============
axis_entry: height10m
!============
!----------------------------------
! Axis attributes:
!----------------------------------
standard_name:    height
units:            m
axis:             Z             ! X, Y, Z, T (default: undeclared)
positive:         up         ! up or down (default: undeclared)
long_name:        height
!----------------------------------
! Additional axis information:
!----------------------------------
out_name:         height
valid_min:        1.0         
valid_max:        30.0 
stored_direction: increasing
type:             double
value:            10.            ! of scalar (singleton) dimension 
must_have_bounds: no
!----------------------------------
!


!============
axis_entry: sdepth1 
!============
!----------------------------------
! Axis attributes:
!----------------------------------
standard_name:    depth
units:            m
axis:             Z             ! X, Y, Z, T (default: undeclared)
positive:         down         ! up or down (default: undeclared)
long_name:        depth
!----------------------------------
! Additional axis information:
!----------------------------------
out_name:         depth
valid_min:        0.0         
valid_max:        0.2 
stored_direction: increasing
type:             double
value:            0.05            ! of scalar (singleton) dimension 
bounds_values:    0.0 0.1    ! of scalar (singleton) dimension bounds
must_have_bounds: yes
!----------------------------------
!

!============
axis_entry: plev850
!============
!----------------------------------
! Axis attributes:
!----------------------------------
standard_name:    air_pressure
units:            Pa
axis:             Z             ! X, Y, Z, T (default: undeclared)
positive:         down         ! up or down (default: undeclared)
long_name:        pressure
!----------------------------------
! Additional axis information:
!----------------------------------
out_name:         plev
stored_direction: decreasing
valid_min:        85000.
valid_max:        85000.
type:             double
value:            85000.
must_have_bounds: no
!----------------------------------
!

!============
axis_entry: plev500
!============
!----------------------------------
! Axis attributes:
!----------------------------------
standard_name:    air_pressure
units:            Pa
axis:             Z             ! X, Y, Z, T (default: undeclared)
positive:         down         ! up or down (default: undeclared)
long_name:        pressure
!----------------------------------
! Additional axis information:
!----------------------------------
out_name:         plev
stored_direction: decreasing
valid_min:        50000.
valid_max:        50000.
type:             double
value:            50000.
must_have_bounds: no
!----------------------------------
!

!============
axis_entry: plev200
!============
!----------------------------------
! Axis attributes:
!----------------------------------
standard_name:    air_pressure
units:            Pa
axis:             Z             ! X, Y, Z, T (default: undeclared)
positive:         down         ! up or down (default: undeclared)
long_name:        pressure
!----------------------------------
! Additional axis information:
!----------------------------------
out_name:         plev
stored_direction: decreasing
valid_min:        20000.
valid_max:        20000.
type:             double
value:            20000.
must_have_bounds: no
!----------------------------------
!

!============
variable_entry:    tas
!============
deflate: 1
deflate_level: 1
shuffle: 1
modeling_realm:    atmos
!----------------------------------
! Variable attributes:
!----------------------------------
standard_name:     air_temperature
units:             K
cell_methods:      time: mean

long_name:         Near-Surface Air Temperature
comment:           daily-mean near-surface (usually, 2 meter) air temperature.
!----------------------------------
! Additional variable information:
!----------------------------------
dimensions:        longitude latitude time height2m
out_name:          tas
type:              real
!----------------------------------
!

!============
variable_entry:    tasmax
!============
deflate: 1
deflate_level: 1
shuffle: 1
modeling_realm:    atmos
!----------------------------------
! Variable attributes:
!----------------------------------
standard_name:     air_temperature
units:             K
cell_methods:      time: maximum within days time: mean over days

long_name:         Daily Maximum Near-Surface Air Temperature
comment:           daily-maximum near-surface (usually, 2 meter) air temperature.
!----------------------------------
! Additional variable information:
!----------------------------------
dimensions:        longitude latitude time height2m
out_name:          tasmax
type:              real
!----------------------------------
!



!============
variable_entry:    tasmin
!============
deflate: 1
deflate_level: 1
shuffle: 1
modeling_realm:    atmos
!----------------------------------
! Variable attributes:
!----------------------------------
standard_name:     air_temperature
units:             K
cell_methods:      time: minimum within days time: mean over days

long_name:         Daily Minimum Near-Surface Air Temperature
comment:           daily-minimum near-surface (usually, 2 meter) air temperature.  
!----------------------------------
! Additional variable information:
!----------------------------------
dimensions:        longitude latitude time height2m
out_name:          tasmin
type:              real
!----------------------------------
!

!============
variable_entry:    pr
!============
deflate: 1
deflate_level: 1
shuffle: 1
modeling_realm:    atmos
!----------------------------------
! Variable attributes:
!----------------------------------
standard_name:     precipitation_flux
units:             kg m-2 s-1
cell_methods:      time: mean

long_name:         Precipitation
comment:           at surface; includes both liquid and solid phases from all types of clouds (both large-scale and convective)
!----------------------------------
! Additional variable information:
!----------------------------------
dimensions:        longitude latitude time
out_name:          pr
type:              real
!----------------------------------
!

!============
variable_entry:    psl
!============
deflate: 1
deflate_level: 1
shuffle: 1
modeling_realm:    atmos
!----------------------------------
! Variable attributes:
!----------------------------------
standard_name:     air_pressure_at_sea_level
units:             Pa
cell_methods:      time: mean

long_name:         Sea Level Pressure
!----------------------------------
! Additional variable information:
!----------------------------------
dimensions:        longitude latitude time
out_name:          psl
type:              real
!----------------------------------
!

!============
variable_entry:    hurs
!============
modeling_realm:    atmos
!----------------------------------
! Variable attributes:
!----------------------------------
standard_name:     relative_humidity
units:             %
cell_methods:      time: mean
cell_measures:     area: areacella
long_name:         Near-Surface Relative Humidity
comment:           This is the relative humidity with respect to liquid water for T> 0 C, and with respect to ice for T<0 C.
!----------------------------------
! Additional variable information:
!----------------------------------
dimensions:        longitude latitude time height2m
out_name:          hurs
type:              real
!----------------------------------
!

!============
variable_entry:    huss
!============
deflate: 1
deflate_level: 1
shuffle: 1
modeling_realm:    atmos
!----------------------------------
! Variable attributes:
!----------------------------------
standard_name:     specific_humidity
units:             1
cell_methods:      time: mean

long_name:         Near-Surface Specific Humidity
comment:           near-surface (usually, 2 meter) specific humidity.
!----------------------------------
! Additional variable information:
!----------------------------------
dimensions:        longitude latitude time height2m
out_name:          huss
type:              real
!----------------------------------
!


!============
variable_entry:    sfcWind
!============
deflate: 1
deflate_level: 1
shuffle: 1
modeling_realm:    atmos
!----------------------------------
! Variable attributes:
!----------------------------------
standard_name:     wind_speed
units:             m s-1
cell_methods:      time: mean

long_name:         Near-Surface Wind Speed
comment:           near-surface (usually, 10 meters) wind speed.
!----------------------------------
! Additional variable information:
!----------------------------------
dimensions:        longitude latitude time height10m
out_name:          sfcWind
type:              real
!----------------------------------
!

cdo cmor,cordex_mip_tables/CORDEX_mon example_interface.nc

cdo cmor,cordex_mip_tables/CORDEX_mon,cn=tas 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"
            },

cdo cmor,cordex_mip_tables/CORDEX_mon,cn=tas example_interface.nc

#Exercises:
#1. Create your own cdocmorinfo
#2. Copy that file to CWD/.cdocmorinfo
#3. Repeat
    cdo cmor,Amon example_interface.nc
#4. Have a look at differences between the files with
    ncdump -h

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

infile=example_mapping.grb

#1. Commandline mapping:
cdo cmor,mon,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,mon,mapping_table=mt.txt ${infile}
#  Without additional information,
#  all variables from ${infile}
#  are taken and converted
cdo cmor,mon,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.

!============
axis_entry: latitude
!============
!----------------------------------
! Axis attributes:
!----------------------------------
standard_name:    latitude
units:            degrees_north
axis:             Y             ! X, Y, Z, T (default: undeclared)
long_name:        latitude
!----------------------------------
! Additional axis information:
!----------------------------------
out_name:         lat
valid_min:        -90.0         
valid_max:        90.0 
stored_direction: increasing
type:             double
must_have_bounds: yes
!----------------------------------
!

!============
variable_entry:    tas
!============
deflate: 1
deflate_level: 1
shuffle: 1
modeling_realm:    atmos
!----------------------------------
! Variable attributes:
!----------------------------------
standard_name:     air_temperature
units:             K
cell_methods:      time: mean

long_name:         Near-Surface Air Temperature
comment:           daily-mean near-surface (usually, 2 meter) air temperature.
!----------------------------------
! Additional variable information:
!----------------------------------
dimensions:        longitude latitude time height2m
out_name:          tas
type:              real
!----------------------------------

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

# 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:
DRS=CMIP6/CMIP/MPI-M/MPIESM-1-2-HR/historical/ri1ip1f1/Amon/tas/gn/v20171010/
lc=${DRS}tas_Amon_MPIESM-1-2-HR_historical_r1i1p1f1_gn_200101-200112.nc

cdo cmor,Amon,om=a,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,om=a,mt=mapping_table.txt example_append2003.grb