| Автор | Kandaswamy, Meenakshi, A. |
| Автор | Kandemir, Mahmut, T. |
| Автор | Choudhary, Alok, N. |
| Автор | Bernholdt, David, E. |
| Дата выпуска | 1998 |
| dc.description | Many scientific applications tend to perform high-volume data storage, data retrieval, and data processing, all of which demand high performance from the I/O subsystem. The focus and contribution of this work is to study the I/O behavior of the Hartree-Fock (HF) method using PAS SION. HF's I/O phases can contribute up to 62.34% of the total execution time. The authors reduce the execution time and I/O time up to 54% and 6%, respectively, of that of the original case through PASSION and its optimiza tions. Additionally, the authors categorize the factors that affect the I/O performance of HF into key application- related parameters and key system-related parameters. Based on extensive empirical results and within the ex perimental space presented in this paper, the authors orderthe parameters according to the their impact on HF's I/O performance as follows: efficient interface, prefetching, buffering, number of I/O nodes, striping factor, and striping unit. The authors conclude that application-related factors have a more significant effect on HF's I/O performance than the system-related factors within the experimental space presented in this paper. |
| Издатель | Sage Publications |
| Название | An Experimental Study to Analyze and Optimize Hartree-Fock Application's I/O with Passion |
| Тип | Journal Article |
| DOI | 10.1177/109434209801200403 |
| Print ISSN | 1094-3420 |
| Журнал | International Journal of High Performance Computing Applications |
| Том | 12 |
| Первая страница | 411 |
| Последняя страница | 439 |
| Аффилиация | Kandaswamy, Meenakshi, A., ELECTRICAL ENGINEERING AND COMPUTER SCIENCE, SYRACUSE UNIVERSITY, SYRACUSE, NEW YORK, U.S.A. |
| Аффилиация | Kandemir, Mahmut, T., ELECTRICAL ENGINEERING AND COMPUTER SCIENCE, SYRACUSE UNIVERSITY, SYRACUSE, NEW YORK, U.S.A. |
| Аффилиация | Choudhary, Alok, N., DEPARTMENT OF ELECTRICAL AND COMPUTER ENGINEERING, NORTHWESTERN UNIVERSITY, EVANSTON, ILLINOIS, U.S.A. |
| Аффилиация | Bernholdt, David, E., NORTHEAST PARALLEL ARCHITECTURES CENTER, SYRACUSE UNIVERSITY, SYRACUSE, NEW YORK, U.S.A. |
| Выпуск | 4 |
| Библиографическая ссылка | Almlöf, J., Faegri, K., and Korsell, K.1982. Principles for a direct SCF approach to LCAO-MO ab initio calculations. J. Comput. Chem.3:385-399. |
| Библиографическая ссылка | Arunachalam, M., Choudhary, A., and Rullman, B.1996. Implementation and evaluation of prefetching in the Intel Paragon parallel file system. In Proceedings of International Parallel Processing Symposium, April, Maui, Hawaii. |
| Библиографическая ссылка | Bordawekar, R.1996. Techniques for compiling I/O intensive parallel programs. Ph.D. thesis, Department of Electrical and Computer Engineering , Syracuse University. |
| Библиографическая ссылка | Bordawekar, R., del Rosario, J.M., and Choudhary, A.1993. Design and implementation of primitives for parallel I/O . In Proceedings of Supercomputing '93, November, Portland, Oregon. |
| Библиографическая ссылка | Choudhary, A., Bordawekar, R., Harry, M., Krishnaiyer, R., Ponnusamy, R., Singh, T., and Thakur, R.1994. PASSION: Parallel and scalable software for input-output. NPAC Technical Report SCCS-636, Syracuse University. |
| Библиографическая ссылка | Choudhary, A., Bordawekar, R., More, S., Sivaram, K., and Thakur, R.1995. PASSION run-time library for the Intel Paragon . In Proceedings of the Intel Supercomputer User's Group Conference, June, Albuquerque, New Mexico. |
| Библиографическая ссылка | Crandall, P.E., Aydt, R.A., Chien, A.A., and Reed, D.A.1995. Input/output characterization of scalable parallel applications . In Proceedings of Supercomputing '95, San Diego, CA. |
| Библиографическая ссылка | del Rosario, J.M., and Choudhary, A.1994. High performance I/O for parallel computers: Problems and prospects. In IEEE Computer Magazine, March. |
| Библиографическая ссылка | Guest, M.F., Aprà, E., Bernholdt, D.E., Früchtl, H.A., Harrison, R.J., Kendall, R.A., Kutteh, R.A., Long, X., Nicholas, J.B., Nichols, J.A., Taylor, H.L., Wong, A.T., Fann, G.I., Littlefield, R.J., and Nieplocha, J.1995. High performance computational chemistry: NWChem and fully distributed parallel algorithms. In Advances in parallel computing: Volume 10. High performance computing: Technology, methods, and applications . Amsterdam: Elsevier, 1995, pp. 395-427. |
| Библиографическая ссылка | Guest, M.F., Aprà, E., Bernholdt, D.E., Früchtl, H.A., Harrison, R.J., Kendall, R.A., Kutteh, R.A., Long, X., Nicholas, J.B., Nichols, J.A., Taylor, H.L., Wong, A.T., Fann, G.I., Littlefield, R.J., and Nieplocha, J.1996. Advances in parallel distributed data software: Computational chemistry and NWChem. In Applied parallel computing: Computations in physics, chemistry and engineering science. Lecture Notes in Computer Science 1041. Heidelberg: Springer. |
| Библиографическая ссылка | Harrison, R.J., Guest, M.F., Kendall, R.A., Bernholdt, D.E., Wong, A.T., Stave, M., Anchell, J., Hess, A., Littlefield, R., Fann, G.I., Nieplocha, J., Thomas, G.S., Elwood, D., Tilson, J., Shepard, R.L., Wagner, A.F., Foster, I.T., Lusk, E., and Stevens, R.1995. High performance computational chemistry. II. A scalable SCF program. J. Comput. Chem.17:124. |
| Библиографическая ссылка | High Performance Computational Chemistry Group.1995. NWChem, a computational chemistry package for parallel computers, version 1.1. Available at Pacific Northwest Laboratory, Richland, WA 99352, U.S.A. |
| Библиографическая ссылка | Mowry, T.C., Demke, A.K., and Krieger, O.1996. Automatic compiler-inserted I/O prefetching for out-of-core applications. In Second Symposium on Operating Systems Design and Implementations (OSDI '96), October. |
| Библиографическая ссылка | Nieplocha, J., and Harrison, R.J.1998. Global array tools library. Available for anonymous FTP via URL ftp://ftp.pnl.gov/pub/permanent/global |
| Библиографическая ссылка | Nieplocha, J., Harrison, R.J., and Littlefield, R.J.1994. Global arrays: A portable "shared-memory" programming model for distributed memory computers. In Proceedings of Supercomputing '94. Los Alamitos, CA: Institute of Electrical and Electronics Engineers and Association for Computing Machinery, IEEE Computer Society Press . |
| Библиографическая ссылка | Nieplocha, J., Harrison, R.J., and Littlefield, R.J.1996. Global arrays: A nonuniform memory access programming model for high-performance computers. J. Supercomputing10:169-189. |
| Библиографическая ссылка | Reed, D.A., Aydt, R.A., Noe, R.J., Roth, P.C., Shields, K.A., Schwartz, B.W., and Tavera, L.F.1993. Scalable performance analysis: The Pablo performance analysis environment. In Proceedings of the Scalable Parallel Libraries Conference, edited by A. Skjellum. Los Alamitos, CA: IEEE Computer Society Press, pp. 104-113. |
| Библиографическая ссылка | Smimi, E., Elford, C.L., Lavery, A.J., and Chien, A.A.1997. Algorithmic influences on I/O access patterns and parallel file system performance. 1997International Conference on Parallel and Distributed Systems, December, Seoul, pp. 794-801. |
| Библиографическая ссылка | Szabo, A., and Ostlund, N.S.1989. Modern quantum chemistry: Introduction to advanced electronic structure theory. New York: McGraw-Hill . |
| Библиографическая ссылка | Thakur, R., Bordawekar, R., Choudhary, A., Ponnusamy, R., and Singh, T.1994. PASSION run-time library for parallel I/O. In Proceedings of the Scalable Parallel Libraries Conference, October |
| Библиографическая ссылка | Thakur, R., Choudhary, A., Bordawekar, R., More, S., and Kuditipudi, S.1996. PASSION: Optimized I/O for parallel applications . In IEEE Computer Magazine 29(6):70-78. |
| Библиографическая ссылка | Thakur, R., Gropp, W., and Lusk, E.1996. An experimental evaluation of the parallel I/O systems of the IBM SPand Intel Paragon using a production application. In Proceedings of the 3rd International Conference of the Austrian Center for Parallel Computation (ACPC) (with special emphasis on parallel databases and parallel I/O). Lecture Notes in Computer Science 1127. Springer-Verlag , pp. 24-35. |
