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The influence of the software, and its interaction and interdependency with the hardware in the creation and propagation of hardware failures, are usually neglected in reliability analyses of safety critical systems. The software operation is responsible for the usage of semiconductor devices along the system lifetime. This usage consists of voltage changes and current flows that steadily degrade the materials of circuit devices until the degradation becomes permanent, and the device can no longer perform its intended function. At the circuit level, these failures manifest as stuck-at values, signal delays, or circuit functional changes. These failures are permanent in nature. Due to the extremely high scaling of complementary metal-oxide-semiconductor (CMOS) technology into deep submicron regimes, permanent hardware failures are a key concern, and can no longer be neglected compared to transient failures in radiation-intense applications. Our work proposes a methodology for the reliability analysis of permanent failure manifestations of hardware devices due to the usage induced by the execution of embedded software applications. The methodology is illustrated with a case study based on a safety critical application.