ncgen has options to specify what kind of output to generate.
ncgen [-b] [-o file.nc] [-k kind] [-l c|f77|java]
[-x] file.cdl
[-b] binary output as a netCDF file (with ".nc" extension)
[-o file.nc] like -b except output netCDF to specified filename
[-k kind] kind of output netCDF file
omitted => simplest format that works
1 or 'classic' => classic file format
2 or '64-bit-offset' => 64-bit-offset format
3 or 'netCDF-4' => netcdf-4 format
4 or 'netCDF-4 classic model' => netCDF-4 classic model
[-l c|f77|java] language of program generated to standard output
file.cdl name of input CDL file