The Advanced Logic System (ALS) is a complete control system architecture, based on a hardware platform rather than a software-based microprocessor system. It is significantly different from other PLC-type control system architectures, by implementing a FPGA in the central control unit. Standard FPGA logic circuits are used rather than a software-based microprocessor which eliminate problems with software based microprocessor systems, such as software common-mode failures. It provides a highly reliable system suitable for safety critical control systems, including nuclear plant protection systems. The system samples process inputs, provides for digital bus communications, applies a control logic function, and provides for controlled outputs. The architecture incorporates advanced features such as diagnostics, testability, and redundancy on multiple levels. It additionally provides significant improvements in failure detection, isolation, and mitigation for the highest level of integrity and reliability.