In general use with our data files, I don't see much of a performance hit. Here are some benchmark numbers . The other way of creating compressed netcdf files is to use the nczip utility routine. The size of the index in number of blocks that can be in the compressed netcdf file. This parameter effects the maximum file size.
Larger blocks allow better compression and larger total file size.
Smaller blocks allow more fine-grained access. Default is 8k. Allowable sizes are 4k, 8k, 16k and 32k. The number of buffers to keep in memory. Larger values for this parameter will increase memory usage but may speed up some types of netcdf file access.