Tiwari, Ananta N.Auto-tuning has recently received significant attention from the High Performance Computing community. Most auto-tuning approaches are specialized to work either on specific domains such as dense linear algebra and stencil computations, or only at certain stages of program execution such as compile time and runtime. Real scientific applications, however, demand a cohesive environment that can efficiently provide auto-tuning solutions at all stages of application development and deployment. Towards that end, we describe a unified end-to-end approach to auto-tuning scientific applications. Our system, Active Harmony, takes a search-based collaborative approach to auto-tuning. Application programmers, library writers and compilers collaborate to describe and export a set of performance related tunable parameters to the Active Harmony system. These parameters define a tuning search-space. The auto-tuner monitors the program performance and suggests adaptation decisions. The decisions are made by a central controller using a parallel search algorithm. The algorithm leverages parallel architectures to search across a set of optimization parameter values. Different nodes of a parallel system evaluate different configurations at each timestep. Active Harmony supports runtime adaptive code-generation and tuning for parameters that require new code (e.g. unroll factors). Effectively, we merge traditional feedback directed optimization and just-in-time compilation. This feature also enables application developers to write applications once and have the auto-tuner adjust the application behavior automatically when run on new systems. We evaluated our system on multiple large-scale parallel applications and showed that our system can improve the execution time by up to 46% compared to the original version of the program. Finally, we believe that the success of any auto-tuning research depends on how effectively application developers, domain-experts and auto-tuners communicate and work together. To that end, we have developed and released a simple and extensible language that standardizes the parameter space representation. Using this language, developers and researchers can collaborate to export tunable parameters to the tuning frameworks. Relationships (e.g. ordering, dependencies, constraints, ranking) between tunable parameters and search-hints can also be expressed.DissertationComputer ScienceActive HarmonyAuto-tuningcompiler-based tuning