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The modest I/O configurations and file system limitations of many current high-performance systems preclude solution of problems with large I/O needs. I/O hardware and file system parallelism is the key to achieving high performance. We analyze the I/O behavior of several versions of two scientific applications on the Intel Paragon XP/S. The versions involve incremental application code enhancements across multiple releases of the operating system. Studying the evolution of I/O access patterns underscores the interplay between application access patterns and file system features. Our results show that both small and large request sizes are common, that at present, application developers must manually aggregate small requests to obtain high disk transfer rates, that concurrent file accesses are frequent, and that appropriate matching of the application access pattern and the file system access mode can significantly increase application I/O performance. Based on these results, we describe a set of file system design principles.