The I/O port arrangement which is used for input/output is differrent for each board.
e.g.) Physics port
PIO-32/32L(PCI)H: Input:+Port 0 - +Port 3, Output:+Port 4 - +Port 7
PIO-64/64L(PCI)H: Input:+Port 0 - +Port 7, Output:+Port 8 - +Port 15
Logic port is the number that I/O ports are numbered beginning from port 0, in order to program. It needn't to care about the I/O address arrangement is different for each board.
When input and ouput, use the logic port.
The above example is converted to logic port as follows.
e.g.) Logic port
PIO-32/32L(PCI)H: Input:Port 0 - Port 3, Output:Port 0 - Port 3
PIO-64/64L(PCI)H: Input:Port 0 - Port 7, Output:Port 0 - Port 7