High-Performance Computing

The quest for greater computational power is never-ending, and exploiting parallelism is central to this quest. We are helping to design systems which will enable programmers to implement their applications not only on supercomputers and high-performance workstations, but on multiple architectures connected by networks. The development of algorithms, models, languages, compilers and tools for these systems are among the most compelling and difficult problems in computing.

Our faculty are Senior Fellows at the San Diego Supercomputer Center (SDSC), giving them access to a wide variety of machines at SDSC as well as to computational scientists and their challenging computing problems.

Scientific Computation

Scientific applications are becoming increasingly complex in part because they are relying more heavily on elaborate, dynamic numerical representations to capture irregular physical phenomena. Such applications are a challenge to implement on parallel computers since compilers presently cannot treat the requisite data decomposition and data motion at run time.

The Scientific Computation Group (SCG) investigates run-time software techniques aimed at reducing the development time of high-performance scientific applications. The group focuses on applications with special needs, including adaptive computations that employ elaborate, dynamic representations to enhance accuracy, improve running time, or both. The SCG has developed the KeLP software infrastructure to meet the needs of such applications. KeLP permits the programmer to exploit specific properties of an application in order to optimize data decompositions and data motion at run time. KeLP has been applied to a variety of scientific applications ranging from computational materials science to computational fluid dynamics.

More recently, the SCG is investigating multi-tier parallelism, in which multiple levels of parallelism exist within a single application. Multi-tier parallelism is appropriate for multicomputers comprising multiple symmetric multiprocessor nodes.

The programming abstractions explored by the SCG are vital not only in eliminating non-essential detail (e.g., load balancing and locality management), but also in protecting application software against inevitable changes in hardware.

Compiler Technology

Compiler technology provides the necessary interface between programming languages and architectures, and is intimately tied to new developments in both. The group's research focuses on the development of Compiler Technology, with particular interest in exploiting multiple levels of parallelism and optimizing data movement to achieve high performance.

Trends in both high level languages and machines have increased the gap between them, making the compiler's job of bridging this gap increasingly more challenging. For example, a major trend in machine architecture is towards a hierarchy of memory and parallelism.

We developed Hierarchical Tiling to simultaneously exploit such parallelism and locality. Hierarchical tiling extends traditional tiling to include optimization for storage and data movement. It has been used on perfectly nested loops with regular dependence structure to reduce cache misses, enhance interprocessor parallelism, and manage secondary storage, and to improve the use of superscalar pipelined and vector processors. Our current research will extend Hierarchical Tiling to obtain its advantages on a larger class of programs that include unstructured applications with less regular memory accesses. We are also looking at the compiler implications of multithreading and predicated execution capabilities on emerging architectures.

Scientific Computing also includes the development of parallel algorithms and software for use in computational molecular biology. Problems such as molecular structure prediction and protein-ligand docking require new methods and high performance computing. Such methods include a new global optimization algorithm which has been implemented on the SDSC CRAY T3E to compute global minimum energy conformations of small protein molecules.