• The chunking may be set for each variable after it is defined.
• The default chunking in the 4.0 release was not good for very large variables.
• That problem is fixed in the 4.2 release, but you may not want to rely on the default, depending on expected access patterns.
• Explicitly set the chunking with the nc_def_var_chunking function:

  Usage
  
       int nc_def_var_chunking(int ncid, int varid, int storage, size_t *chunksizesp);
  
  ncid
    NetCDF ID, from a previous call to nc_open or nc_create. 
  
  varid
    Variable ID. 
  
  storage
    If NC_CONTIGUOUS, then contiguous storage is used for this
    variable. Variables with chunking, compression, checksums, or one or
    more unlimited dimensions cannot use contiguous storage.
    
    If NC_CHUNKED, then chunked storage is used for this variable. Chunk
    sizes may be specified with the chunksizes parameter or default
    sizes will be used if that parameter is NULL.
  
    By default contiguous storage is used for fix-sized variables when
    compression, chunking, and checksums are not used.
  
  *chunksizes
    A pointer to an array list of chunk sizes. The array must have one
    chunksize for each dimension of the variable. 
  

2012 Unidata NetCDF Workshop > Chunking and Deflating Data with NetCDF-4