NetCDF Data Format and CF convention

A fundamental requirement for the exchange of scientific data is the ability to precisely describe the physical quantities being represented. Therefore, special attention needs to be paid to the representation of the model data in the output files. We require data in the ‘Network Common Data Form’ (netCDF) that adhere to the netCDF Climate and Forecast (CF) metadata convention (if
possible to version 1.6 from Dec. 2011 [2]). All netCDF files should have the file name extension ‘.nc’. We specify details of the netCDF requirements in Appendix F of the DCMIP test case document (see Overview of Test Cases) and will also provide help via NCO operators before the DCMIP event to make the data CF-compliant if necessary. Please communicate your output constraints or concerns (if any) to the DCMIP organizers as soon as possible. We will also ask for example data sets before the DCMIP event.

netCDF CF-Compliance Checker

A netCDF CF-compliance checker is installed on the NCAR machine mirage0.ucar.edu that has access to all /glade/... directories. The CF-compliance of the netCDF data set can be checked in the following way:

logon with your NCAR username and one-time password:

ssh -Y mirage0.ucar.edu

If your default shell is tcsh,execute:
   source /contrib/modules-3.2.8/Modules/3.2.8/init/tcsh
If your defaulkt shell is bash, execute
   source /contrib/modules-3.2.8/Modules/3.2.8/init/bash

Load the CF checker:
   module load cfchecks

Change to your directory on the glade server where the data are located. Check the netCDF file:
   cfchecks <filename>

This command checks the netCDF file for consistency and compliance with the CF standard.

INFO and WARNING messages are acceptable. ERROR messages require reformatting of the netCDF file via NCO operators (see below).

Examples of NCO operators to fix netCDF files:

The complete documentation is provided on the page: http://nco.sourceforge.net/nco.html

• Rename a variable name via ncrename
  Example: rename the variable (-v) 'temp' to the new name 'T' in file file.nc, the NCO command will not (-h) be appended as a global 'history' attribute:
  ncrename -h -v temp,T file.nc
  
  
• Rename a coordinate variable via ncrename
  Example: In order to rename a coordinate variable 'level' to 'lev' so that it remains a coordinate variable, you must separately rename both the dimension (-d) and the variable (-v):
  ncrename -h -d level,lev -v level,lev in.nc

• Changing or adding global attributes via ncatted
  Example: Add the global attributes 'horizontal_resolution' and 'grid' and set them to 'medium' and 'latlon'. If a global attribute with the same name is present is will be overwritten (o), if it is not present it will be created, the information 'medium' or 'latlon' is a character string (c)
  ncatted -h -a horizontal_resolution,global,o,c,"medium" -a grid,global,o,c,"latlon" file.nc
  Even more attributes can be added or changed at once.
  
   
• Delete all existing global attributes via ncatted 
  Example: Delete (d) all global attributes in file in.nc
  ncatted -h -a ,global,d,, in.nc
  
  
• Changing or adding attributes of a variable via ncatted
  Example: Change or add the 'long_name' attribute of the 'T' variable to 'Temperature' in file file.nc
  ncatted -h -a long_name,T,o,c,Temperature file.nc
  
  Example: Change or add the 'units' attribute of the coordinate variable 'lev' and set it to 'level', set the 'positive' indicator of the 'lev' variable 'lev' to 'down' which indicates that the 'lev' fields increases in the downward direction in file file.nc
  ncatted -h -a units,lev,o,c,level -a positive,lev,o,c,down file.nc

• Exclude variables from the netCDF file and create a new output file via ncks
  Example: Create the netCDF file out.nc containing all variables and any associated coordinates, except (-x) the listed variables (-v), from the netCDF in.nc
  ncks -h -x -v co2vmr,n2ovmr,isccp_prs,isccp_prstau,isccp_tau in.nc out.nc

• Extract variable from a netCDF file via ncks
  Example: Extract variables time and PS from netCDF in.nc. If out.nc does not exist it will be created. Otherwise you will be prompted whether to append to or to overwrite out.nc. All relevant coordinate information will be kept.
  ncks -h -v time,PS in.nc out.nc