For all netCDF formats:

• If data must be written in a different order than it is read, consider rewriting the data to the most efficient read order.
• If writing is a bottleneck and you write all data values for each variable, consider turning off default "fill mode", which pre-fills data with fill values.
  • Advantage: saves write time.
  • Disadvantage: eliminates possibility of detecting unwritten values.
• When writing from multiple processors, use parallel I/O.

2012 Unidata NetCDF Workshop > Formats and Performance