skip to main content
10.5555/1400549.1400609acmconferencesArticle/Chapter ViewAbstractPublication PagesspringsimConference Proceedingsconference-collections
research-article

Constructing a performance database for large-scale quantum chemistry packages

Published: 14 April 2008 Publication History

Abstract

When several large-scale quantum chemistry packages interoperate through components and some components provide similar functionality, we are faced with many challenges such as efficiently selecting the component with the best efficiency, finding compromises between efficiency and accuracy, or constructing new computations from available components with minimum overhead. These challenges are core questions in Computational Quality of Service (CQoS) research, and exploring robust methods for these questions requires a performance database as the foundation for referencing historical performance data. However, these large-scale packages have a long history of development, provide many complex computations, and involve a large number of chemists in the development process. Building a database for these packages is thus not as straightforward as simply selecting a database engine and uploading data. In this paper, we present our efforts in fast prototyping a system to construct a performance database for quantum chemistry packages. We discuss the requirements for such a system, delineate the tasks in each building stage, evaluate how current tool technologies can facilitate the building process, and discuss the support required from the performance tools development community for future CQoS research.

References

[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. McInnes, 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.orgm
[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]
Aprà, 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, J.; Tipparaju V.; Krishnan, M.; Auer, A. A.; Brown, E.; Cisneros, G.; Fann, 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. McInnes, 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. McInnes, David E. Bernholdt, Wael R. Elwasif, Allen D. Malony, Sameer Shende: Computational Quality of Service for Scientific Components. CBSE 2004: 264--271
[11]
L. McInnes, 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.

Recommendations

Comments

Information & Contributors

Information

Published In

cover image ACM Conferences
SpringSim '08: Proceedings of the 2008 Spring simulation multiconference
April 2008
880 pages
ISBN:1565553195

Sponsors

Publisher

Society for Computer Simulation International

San Diego, CA, United States

Publication History

Published: 14 April 2008

Check for updates

Author Tags

  1. common component architecture
  2. computational quality of service
  3. performance database
  4. quantum chemistry

Qualifiers

  • Research-article

Funding Sources

Conference

SCS SSM'08
Sponsor:
SCS SSM'08: Spring Simulation Multiconference
April 14 - 17, 2008
Ottawa, Canada

Contributors

Other Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

  • 0
    Total Citations
  • 125
    Total Downloads
  • Downloads (Last 12 months)3
  • Downloads (Last 6 weeks)0
Reflects downloads up to 16 Feb 2025

Other Metrics

Citations

View Options

Login options

View options

PDF

View or Download as a PDF file.

PDF

eReader

View online with eReader.

eReader

Figures

Tables

Media

Share

Share

Share this Publication link

Share on social media