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On board computer (OBC) is an essential component of any On-Board Control System that involves several tasks that needs to be executed in precise order and for accurate periods of time. Most of the real time control systems require instantaneous execution of commands either through hardware or software. To ensure that these requirements are fulfilled, it is necessary to measure not only the execution time of individual tasks, but also establish the overall real time performance of the system as well. These measurements may then be used as a basis for accurate real time scheduling analysis and to identify timing problems or to spot which code segment needs to be optimized. The most common reasons for measuring execution times are to refine, estimates, optimize code, analyze real time performance, and to debug timing errors. Oscilloscope is one of the best tools for accurately measuring execution time with nano-second's result, especially when accurate timing is critical. This method requires extra hardware features, Oscilloscope analysis features, and additional software code segments. Depending on the real time operating system (RTOS) and hardware, it is possible that code is not executing at the proper rate or during the right period as specified by the designer. These drawbacks may result due to limitations in the operating system, the application software or the hardware used. This proposal presents hyper threads, a unifying programming model for specifying application threads running within a hybrid CPU/FPGA system that is used to control the real time operation of an auto-pilot control system.