The binary format option creates files in local machine binary format. These files are written as Fortran direct-access files so there are no record headers or footers and the file can be read by other applications as a pure binary stream. Typically, each record in the file contains a horizontal slice of a particular field (so the record length is the size of a horizontal slice of the global data). On parallel machines, fast parallel I/O is achieved by reading/writing each of these slices from a different processor with the number of processors reading/writing data specified in the I/O namelist.
Unlike netCDF, these binary files contain no information about themselves (not self-describing) and no information about the fields in the files. To remedy this, each binary file written by POP is accompanied by a 'header file' with the same name as the binary file and an additional suffix '.hdr'. This header file is an ASCII file which contains all the information you would find in a netCDF file, including file attributes, fields in the file and attributes of those fields. As part of the field attributes, the starting record of the field in the binary file is included. Such a header file provides some of the capability of a self-describing data format and also provides information for easy conversion to netCDF (or other self-describing format).
Because binary formats differ across machines, binary files are not typically portable across machines. To achieve portability, the user is encouraged to convert the binary files to a more portable data format like netCDF.