Large-Scale Normal Coordinate Analysis on Distributed Memory Parallel Systems
| Autor: | Chao Yang, Padma Raghavan, Robert E. Tuzun, Donald W. Noid, Lloyd F. Arrowood, Bobby G. Sumpter |
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| Rok vydání: | 2002 |
| Předmět: |
020203 distributed computing
Computer science Computation Lanczos algorithm Inversion (meteorology) 02 engineering and technology Parallel computing Solver Theoretical Computer Science Shared memory Hardware and Architecture Scalability 0202 electrical engineering electronic engineering information engineering Distributed memory Latency (engineering) Software |
| Zdroj: | The International Journal of High Performance Computing Applications. 16:409-424 |
| ISSN: | 1741-2846 1094-3420 |
| Popis: | Summary A parallel computational scheme for analyzing large-scale molecular vibration on distributed memory computing platforms is presented in this paper. This method combines the implicitly restarted Lanczos algorithm with a state-of-art parallel sparse direct solver to compute a set of low frequency vibrational modes for molecular systems containing tens of thousands of atoms. Although the original motivation for developing such a scheme was to overcome memory limitations on traditional sequential and shared memory machines, our computational experiments show that with a careful parallel design and data partitioning scheme one can achieve scalable performance on lightly coupled distributed memory parallel systems. In particular, we demonstrate performance enhancement achieved by using the latency tolerant “selective inversion” scheme in the sparse triangular substitution phase of the computation. |
| Databáze: | OpenAIRE |
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