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The article addresses the issue of reliability of complex embedded control systems in the safety-critical environment. In this article, we propose a novel approach to design controller that (i) guarantees the safety of nonlinear physical systems, (ii) enables safe system restart during runtime, and (iii) allows the use of complex, unverified controllers (e.g., neural networks) that drive the physical systems toward complex specifications. We use abstraction-based controller synthesis approach to design a formally verified controller that provides application and system-level fault tolerance along with safety guarantee. Moreover, our approach is implementable using a commercial-off-the-shelf (COTS) processing unit. To demonstrate the efficacy of our solution and to verify the safety of the system under various types of faults injected in applications and in the underlying real-time operating system (RTOS), we implemented the …