An information processing system is operated by reference clock signals supplied to a plurality of units. High frequency clock signals are generated from the reference clock signals supplied. Shift-holding of the reference clock signals is performed based on the high frequency clock signals, and shift-hold data is stored. The reference clock signals and the high frequency clock signals are synchronized based on the shift-hold data, and synchronization information is stored. Data communication is carried out between the first unit and other units, based on the synchronization information.