CAREER: High-Performance Algorithms for Scientific Applications

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Parallel computing has long offered the promise of very high performance, but it has deliveredonly in a narrow range of applications. Exploiting parallelism at the level of large distributed-memorysystems is hampered by the cost of message-passing, while shared-memory systems remain mostlysmall-scale. With the advent of symmetric multiprocessors (SMPs), however, shared-memory on amodest scale is becoming an available commodity. High-performance gigabit networks allow scalable applications to run on large clusters of SMPs. Over the next five to ten years, clusters of SMPs will likely be the predominant architecture for scalable high-performance computing; however, little work has been done to date to support effective parallel computing on these SMP clusters.Preliminary work we have conducted indicates that it is possible to improve upon current programmingmethods for SMP clusters. In this career award the goal is to develop, implement, assess, andrefine algorithms for SMP clusters for irregular (e.g., string-, tree-, and graph-based) computations thatwill deliver significant speedups on typical configurations of SMP clusters and scale gracefully withthe number of processors. The research will investigate new algorithms and a library of basic routines tosupport irregular computations, mostly tree- and graph- based, along with new insights on how to leveragethe theoretical research in PRAM algorithms. Science-driven problems in genomics,bioinformatics, and computational ecology will provide the focus for this research.The education component of this project includes mentoring high school and minority students, diseminating research results through talks and papers, and presenting tutorials at key conferences andworkshops. Prior mentoring has produced several individual and group teams that have won first place in both local and national competitions and mentoring will continue activities with minority groups, such as the National Society of Black Engineers and Native American Pueblo student groups.