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Mobile platforms have started to employ FPGA based hardware accelerators to address the ever-increasing demand for computing performance. For many applications, the use of an operating system on the hardware platform proves beneficial for reasons of better resource management and more robust security. This paper evaluates the performance-power implications in a signal processing algorithm with respect to the introduction of Linux OS on two different architectures (a CPU-based and an FPGA-based hybrid architecture). The results reveal that there is a 22 times improvement in energy budget between the CPU-based implementation and the FPGA-based hybrid implementation, with a negligible performance degradation due to the introduction of Linux OS.