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This paper presents the porting of an RTOS Micro C/OS-II on a novel reconfigurable instruction cell based architecture which fills the gap between DSP, FPGA and ASIC with high performance, high flexibility and ANSI-C support. WiMAX physical layer program has been implemented on the target architecture with the RTOS support. A semaphore based synchronization scheme is used to improve the task independence. The research lays a foundation for further exploration of multithreading on multiple target architectures.