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We present NWPerf, a new system for analyzing fine granularity performance metric data on large-scale supercomputing clusters. This tool is able to measure application efficiency on a system wide basis from both a global system perspective as well as providing a detailed view of individual applications. NWPerf provides this service while minimizing the impact on the performance of user applications. We describe the type of information that can be derived from the system, and demonstrate how the system was used detect and eliminate a performance problem in an application application that improved performance by up to several thousand percent. The NWPerf architecture has proven to be a stable and scalable platform for gathering performance data on a large 1954-CPU production Linux cluster at PNNL.