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In recent years, magnetic random access memory (MRAM) based run-time system on programmable chip (SOPC) has been proposed as a solution to the critical drawbacks of current field programmable gate arrays (FPGAs), such as long (re)boot latency, high standby power, and limits for run time reconfiguration. However, the integration of MRAM in FPGA circuits brings its own problems, including large die area and high dynamic power for the switching circuit. In this paper, we present some solutions to overcome the power and area constraints and thereby improve the performance of MRAM based SOPC. We have done simulations and calculations based on the STMicroelectronics 90 nm design kit and a complete magnetic tunnel junction model.