Two ways to implement a netCDF copy program for classic files:

1.     create empty target file
       add dimensions and global attributes to target
       for each variable in the source file
            add the variable definition to the target file
            copy the variable's attributes to target
            copy the variable's data to the target
     

2.     create empty target file
       add dimensions and global attributes to target
       add all the variable definitions to the target file
       copy all the variable attributes to target
       for each variable in the source file
            copy the variable's data to the target
     

Timings on a 44 MByte WRF model output, with about 100 variables:

Timing for Method 1

Timing for Method 2

NetCDF-4 note:  Since netCDF-4 files do not have a contiguous header, schema changes are efficient.

Timing for slower method copying to a netCDF-4 file

2010 Unidata NetCDF Workshop > Formats and Performance