This paper discusses high performance clustering from a series of critical topics: architectural design, system software infrastructure, and programming environment. This is accomplished through an overview of a large scale, high performance SuperCluster (Roadrunner). This SuperCluster is based almost entirely on freely available, vendor-independent software: for example, its operating system (Linux), job scheduler (PBS), compilers (GNU/EGCS), and parallel programming libraries (MPI). The Globus toolkit, also available for this platform allows high performance distributed computing applications to use geographical distributed resources such as this SuperCluster. In addition to describing the design and analysis of the Roadrunner SuperCluster we provide experimental analyses from grand challenge applications and future directions for SuperClusters.