This paper describes the Blue GeneO((R))/L advanced diagnostics environment (ADE) used throughout all aspects of the Blue Gene/L project, including design, logic verification, bringup, diagnostics, and manufacturing test. The Blue Gene/L ADE consists of a lightweight multithreaded coherence-managed kernel, runtime libraries, device drivers, system progrannning interfaces, compilers, and host-based development tools. It provides complete and flexible access to all features of the Blue Gene/L hardware. Prior to the existence of hardware, ADE was used on Very highspeed integrated circuit Hardware Description Language (VHDL) models, not only for logic verification, but also for peformance measurements, code-path analysis, and evaluation of architectural tradeoff.. During early hardware bring-up, the ability, to run in a cycle-reprodueible manner on both hardware and VHDL proved invaluable in fault isolation and analysis. However, ADE is also capable of supporting high-performance applications and parallel test cases, thereby permitting us to stress the hardware to the limits of its capabilities. This paper also provides insights into system level and device-level programming of Blue Gene/L to assist dei;elopers of high-performance applications to more fully exploit the performance of the machine.