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In this paper, the authors describe the design and development of the communication protocol for the customized data communication switch (FloSwitch). This protocol concentrates on the serial link interface between PCI-e add-on cards and the FloSwitch in the parallel computing system. The serial link is an optical interconnectivity with a bit rate of 6.25Gbps in full duplex mode. The protocol receives data from the PCI-Express (PCI-e) add-on cards through the optical link at the FloSwitch and does the necessary processing on the data (example: floating point addition), and the result is transmitted through the optical link to the destinations.