Constructing a performance database for large-scale quantum chemistry packages

Proceedings of the 2008 Spring Simulation Multiconference, SpringSim'08

Volumn , Issue , 2008, Pages 393-400

  Wu, Meng Shiou ^a   Mori, Hirotoshi ^b   Bentz, Jonathan ^c   Windus, Theresa ^b   Netzloff, Heather ^b   Sosonkina, Masha ^a   Gordon, Mark S ^a,b  

^a U S DEPARTMENT OF ENERGY   (United States)

^b IOWA STATE UNIVERSITY   (United States)

^c CRAY INC   (United States)

Author keywords

Common component architecture; Computational Quality of Service; Performance database; Quantum chemistry

Indexed keywords

BUILDING PROCESS; COMMON COMPONENT ARCHITECTURE; COMPLEX COMPUTATION; COMPUTATIONAL QUALITY; COMPUTATIONAL QUALITY OF SERVICE; DATABASE ENGINE; DEVELOPMENT COMMUNITY; DEVELOPMENT PROCESS; FAST PROTOTYPING; HISTORICAL PERFORMANCE DATA; PERFORMANCE DATABASE; PERFORMANCE TOOLS; ROBUST METHODS; TOOL TECHNOLOGY;

DATABASE SYSTEMS; DISTRIBUTED COMPUTER SYSTEMS; QUALITY CONTROL; QUALITY OF SERVICE; QUANTUM THEORY; SPRINGS (COMPONENTS);

QUANTUM CHEMISTRY;

EID: 70249084170     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1400549.1400609     Document Type: Conference Paper

References (23)

1. D. E. Bernholdt, B. A. Allan, R. Armstrong, F. Bertrand, K. Chiu, T. L. Dahlgren, K. Damevski, W.R. Elwasif, T. G. W. Epperly, M. Govindaraju, D. S. Katz, L. F. Diachin, J. A. Kohl, M. Krishnan, G. Kumfert, S. Lefantzi, M. J. Lewis, A. D. Malony, L. C. Mclnnes, J. Nieplocha, B. Norris, S. G. Parker, J. Ray, S. Shende, T. L. Windus, and Zhou. S., "A Component Architecture for High-Performance Scientific Computing," Intl. J. High-Perf. Computing Appl, 2004.
2. CCA-Forum. Common Component Architecture Forum. http://www.cca-forum.org
3. M. W. Schmidt, K. K. Baldridge, J. A. Boatz, S. T. Elbert, M. S. Cordon, J.H. Jensen, S. Koseki, N. Matsunaga, K. A. Nguyen, S. J. Su, T. L. Windus, M. Dupuis, J. A. Montgomery, "General Atomic and Molecular Electronic Structure System", J. Comput. Chem. 14, 1347-1363 (1993).
4. The Massively Parallel Quantum Chemistry Program (MPQC), Version 2.3.1, Curtis L. Janssen, Ida B. Nielsen, Matt L. Leininger, Edward F. Valeev, Edward T. Seidl, Sandia National Laboratories, Livermore, CA, USA, 2004.
5. Apra, E.; Windus, T.L.; Straatsma, T.P.; Bylaska, E.J.; de Jong, W.; Hirata, S.; Valiev, M.; Hackler, M.; Pollack, L.; Kowalski, K.; Harrison, R.; Dupuis, M.; Smith, D.M.A; Nieplocha, I.; Tipparaju V.; Krishnan, M.; Auer, A.A.; Brown, E.; Cisneros, G.; Farm, G.; Fruchtl, H.; Garza, J.; Hirao, K.; Kendall, R.; Nichols, J.; Tsemekhman, K.; Wolinski, K.; Anchell, J.; Bernholdt, D.; Borowski, P.; Clark, T.; Clerc, D.; Dachsel, H.; Deegan, M.; Dyall, K.; Elwood, D.; Glendening, E.; Gutowski, M.; Hess, A.; Jaffe, J.; Johnson, B.; Ju, J.; Kobayashi, R.; Kutteh, R.; Lin, Z.; Littlefield, R.; Long, X.; Meng, B.; Nakajima, T.; Niu, S.; Rosing, M.; Sandrone, G.; Stave, M.; Taylor, H.; Thomas, G.; van Lenthe, J.; Wong, A.; Zhang, Z.; "NWChem, A Computational Chemistry Package for Parallel Computers, Version 4.7" (2005), Pacific Northwest National Laboratory, Richland, Washington 99352-0999, USA
6. J. P. Kenny, S. J. Benson, Y. Alexeev, J. Sarich, C. L. Janssen, L. C. Mclnnes, M. Krishnan, J. Nieplocha, E. Jurrus, C. Fahlstrom and T. L. Windus, "Component-Based Integration of Chemistry and Optimization Software", Journal of Computational Chemistry, 24(14) 1717-1725 (2004).
7. F. Peng, M.-S. Wu, M. Sosonkina, R. A. Kendall, M. W. Schmidt, M. S. Gordon. "Coupling GAMESS via Standardized Interfaces", in the Workshop on Component and Framework Technology in High-Performance and Scientific Computing, held in conjunction with HPDC-15, Paris, France, June 19-20, 2006.
8. C. L. Janssen, J. P. Kenny, I. M. B. Nielsen, M. Krishnan, V. Gurumoorthi, E. F. Valeev, and T. L. Windus, "Enabling new capabilities and insights from quantum chemistry by using component architectures", Journal of Physics: Conference Series, 46 (2006) 220-228
9. F. Peng, M.-S. Wu, M. Sosonkina, J. Bentz, T. Windus, M.S. Gordon, J. Kenny, C. Janssen. "Tackling Component Interoperability in Quantum Chemistry Software," to appear in the Workshop on Component and Framework Technology in High-Performance anScientific Computing, held in conjunction with ooPLSA 2007, Montreal, Canada, October 21-22, 2007.
10. Boyana Norris, Jaideep Ray, Robert C. Armstrong, Lois C. Mclnnes, David E. Bernholdt, Wael R. Elwasif, Allen D. Malony, Sameer Shende: Computational Quality of Service for Scientific Components. CBSE 2004: 264-271
11. L. Mclnnes, J. Ray, R. Armstrong, T. Dahlgren, A. Malony, B. Norris, S. Shende, J. Kenny, and J. Steensland, Computational Quality of Service for Scientific CCA Applications: Composition, Substitution, and Reconfiguration, Argonne National Laboratory preprint ANL/MCS-P1326-0206, February, 2006.
12. Ryan M. Olson, Michael W. Schmidt, Mark S. Gordon, Alistair P. Rendell, "Enabling the Efficient Use of SMP Clusters: The GAMESS/DDI Model", SC'03, November 15-21, 2003, Phoenix, Arizona, USA
13. J. Nieplocha, J. Ju, T.P. Straatsma, A Multiprotocol Communication Support for the Global Address Space Programming Model on the IBM SP, Proceedings Euro-Par 2000, Munich, Germany, in A. Bode et al (Eds.). Euro-Par 2000 Parallel Processing, Springer Verlag LNCS 1900, pp. 718-728, 2000.
14. Jarek Nieplocha and Bryan Carpenter. ARMCI: A Portable Remote Memory Copy Library for Distributed Array Libraries and Compiler Run-time Systems. Proc. 3rd Workshop on Runtime Systems for Parallel Programming (RTSPP) of International Parallel Processing Symposium IPPS/SPDP '99, San Juan, Puerto Rico, April 1999, in (1) J. Rolim eat al. (eds.) Parallel and Distributed Processing, Springer Verlag LNCS 1586, and (2) IPPS/SDP'99 CDROM, 1999.
15. MPQC., The Massively Parallel Quantum Chemistry Program, http://www.mpqc.org
16. M.-S. Wu, R. A. Kendall, Z. Zhang, K. Wright, "Performance Modeling and Tuning Strategies of Mixed Mode Collective Communications", in the Proceedings of the ACM/IEEE Supercomputing Conference(SC|05) Seattle, Washington, November 12-18, 2005.
17. S. Shende and A. D. Malony, "The TAU Parallel Performance System," International Journal of High Performance Computing Applications, SAGE Publications, 20(2):287-331, Summer 2006
18. Browne, S., Deane, C., Ho, G., Mucci, P. "PAPI: A Portable Interface to Hardware Performance Counters," Proceedings of Department of Defense HPCMP Users Group Conference, June 1999.
19. Dynamic Program Instrumentation for Scalable Performance Tools Jeffrey K. Hollingsworth, Barton P. Miller, Jon Cargille Scalable High Performance Computing Conference (SHPCC), May 1994.
20. K. A. Huck, A. D. Malony, R. Bell, and A. Morris, "Design and Implementation of a Parallel Performance Data Management Framework," Proc. International Conference on Parallel Processing (ICPP 2005), IEEE Computer Society, 2005.
21. K. A. Huck, and A. D. Malony, "PerfExplorer: A Performance Data Mining Framework for Large-Scale Parallel Computing," in Proc. of SC 2005 Conference, ACM, 2005.
22. M.-S. Wu, J. Bentz, F. Peng, M. Sosonkina, M. S. Gordon, R. A. Kendall. "Integrating Performance Tools with Large-Scale Scientific Software," in The 8th IEEE International Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC-07), in conjunction with The 21st International Parallel and Distributed Processing Symposium (IPDPS-07), Long Beach, California, March 2007.
23. Dave Turner and Xuehua Chen, Protocol-Dependent Message-Passing Performance on Linux Clusters, Proceedings of the IEEE International Conference on Cluster Computing (Cluster 2002), Chicago, Illinois, September 23-26, 2002.