Jarek Nieplocha

ChemIo: High Performance Parallel I/o for Computational Chemistry Applications

Recent developments in I/O systems on scalable parallel computers have sparked renewed interest in out-of-core methods for computational chemistry. These methods can improve execution time significantly relative to direct methods, which perform many redundant computations. However, the widespread use of such out-of-core methods requires efficient and portable implementations of often complex I/O patterns. The ChemlO project has addressed this problem by defining an I/O interface that captures the I/O patterns found in important computational chemistry applications and by providing high performance imple mentations of this interface on multiple platforms. This development broadens the user community for parallel I/O techniques and provides new insights into the functionality required in general purpose scalable I/O libraries and the techniques required to achieve high performance I/O on scalable parallel computers.

Characterizing Computation-Communication Overlap in Message-Passing Systems

Effective overlap of computation and communication is a well understood technique for latency hiding and can yield significant performance gains for applications on high-end computers. In this report, we describe an instrumentation framework developed for messagepassing systems to characterize the degree of overlap of communication with computation in the execution of parallel applications. The inability to obtain precise time-stamps for pertinent communication events is a significant problem, and is addressed by generation of minimum and maximum bounds on achieved overlap. The overlap measures can aid application developers and system designers in investigating scalability issues. The approach has been used to instrument two MPI implementations as well as the ARMCI system. The implementation resides entirely within the communication library and thus integrates well with existing approaches that operate outside the library. The utility of the framework is demonstrated by analyzing communication-computation overlap for micro-benchmarks and the NAS benchmarks, and the insights obtained are used to modify the NAS SP benchmark, resulting in improved overlap.