A netCDF classic or 64-bit offset file is stored in three parts:

1. The header, containing information about dimensions, attributes, and variables (the schema
2. The fixed-size data, containing data values for variables that don't have an unlimited dimension
3. The record data, containing data values for variables that have an unlimited dimension

By default, the header has almost no extra space; it is just large enough to contain the dimensions, attributes (including all attribute values), and variable metadata, rounded up to a whole number of disk blocks.

• Advantage: netCDF files are compact, with little overhead
• Disadvantage: schema changes may require moving all the data:
  • defining new dimensions, variables, or attributes in an existing file
  • renaming existing dimensions, variables, or attributes with longer names
  • redefining an attribute to have values of a larger type or more values, such as a longer string value

To avoid copying data when the file schema changes

• Either create all necessary dimensions, variables, and attributes before writing data, or
• reserve extra space in the file header for later additions (using nc__enddef() in C, NF__ENDDEF() or NF90__ENDDEF() for Fortran, setExtraHeaderBytes() method of NetcdfFileWritable for Java)
• There is also an NCO program that adds extra space in a netCDF header, if you forget to do it when the file is created

NetCDF-4 note:  NetCDF-4 files do not have a contiguous header for schema, so none of this is necessary for netCDF-4! Schema additions are efficient.

2008 Unidata NetCDF Workshop for Developers and Data Providers > Formats and Performance