Publications by David E. Bernholdt

1

Pratul K. Agarwal, Thomas Naughton, Sadaf R. Alam, Byung H. Park, David E. Bernholdt, Joshua J. Hursey, and Al Geist, Application Health Monitoring for Extreme-scale Resiliency using Cooperative Fault Management, Concurrency and Computing Practice and Experience (2012), submitted.

2

Ron Brightwell, Ron Oldfield, Arthur B. Maccabe, David E. Bernholdt, Eric Brewer, Patrick Bridges, Peter Dinda, Jack Dongarra, Costin Iancu, Michael Lang, Jack Lange, David Lowenthal, Frank Mueller, Karsten Schwan, Thomas Sterling, and Patricia Teller, Hobbes: Composition and Virtualization as the Foundations of an Extreme-scale OS/R, in International Workshop on Runtime and Operating Systems for Supercomputers ROSS 2013, 2013, (accepted).

3

Tiffany Mintz, Oscar Hernandez, Christos Kartsaklis, David E. Bernholdt, and Swaroop Pophale, Toward Abstracting the Communication Intent in Applications to Improve Portability and Productivity, in Proceedings of the International Parallel and Distributed Processing Symposium: IPDPS 2013 Workshops, 18th International Workshop on High-Level Parallel Programming Models and Supportive Environments (HIPS'13), 2013, (accepted).

4

Wael R. Elwasif, David E. Bernholdt, Sreekanth Pannala, Srikanth Allu, and Samantha S. Foley, Parameter Sweep Optimization of Loosely Coupled Simulations Using the DAKOTA Toolkit, in Computational Science and Engineering (CSE), 2012 IEEE 15th International Conference on, pages 102-110, 2012.

5

David E. Bernholdt, NEAMS Software Licensing, Release, and Distribution: Implications for FY2013 Work Package Planning, Technical Report ORNL/TM-2012/246, Oak Ridge National Laboratory, 2012.

6

David E. Bernholdt, Recommendations for NEAMS Engagement with the NRC: Preliminary Report, Technical Report ORNL/TM-2012/234, Oak Ridge National Laboratory, 2012.

7

David E. Bernholdt, Benjamin A. Allan, Robert C. Armstrong, Daniel Chavarria-Miranda, Tamara L. Dahlgren, Wael R. Elwasif, Tom Epperly, Samantha S. Foley, Geoffrey C. Hulette, Sriram Krishnamoorthy, Adrian Prantl, Ajay Panyala, and Matthew Sottile, COMPOSE-HPC: A Transformational Approach to Exascale, Technical Report ORNL/TM-2012/85, Oak Ridge National Laboratory, 2012.

8

Samantha S. Foley, Wael R. Elwasif, and David E. Bernholdt, The Integrated Plasma Simulator: A Flexible Python Framework for Coupled Multiphysics Simulation, Technical Report ORNL/TM-2012/57, Oak Ridge National Laboratory, 2012, originally appeared in PyHPC 2011: Python for High Performance and Scientific Computing, held 18 November 2011 in Seattle, WA.

9

Wael R. Elwasif, Samantha S. Foley, David E. Bernholdt, Lee A. Berry, Debasmita Samaddar, David E. Newman, and Raul Sanchez, A Dependency-Driven Formulation of Parareal: Parallel-in-Time Solution of PDEs as a Many-Task Application, in Proceedings of the 2011 ACM international workshop on Many task computing on grids and supercomputers, MTAGS '11, pages 15-24, New York, NY, USA, 2011, ACM.

10

David E. Bernholdt, A Roadmap for NEAMS Capability Transfer, Technical Report ORNL/TM-2011/485, Oak Ridge National Laboratory, 2011.

11

Wael R. Elwasif, David E. Bernholdt, Samantha S. Foley, Aniruddha G. Shet, and Randall Bramley, Multi-Level Concurrency in a Framework for Integrated Loosely Coupled Plasma Simulations, in Computer Systems and Applications (AICCSA), 2011. 9$^{th}$ IEEE/ACS International Conference on, 2011.

12

Byung H. Park, Thomas J. Naughton, Pratul Agarwal, David Bernholdt, Al Geist, and Jennifer L. Tippens, Realization of User-Level Fault Tolerance Policy Management through a Holistic Approach for Fault Correlation, in Policies for Distributed Systems and Networks (POLICY), 2011 IEEE International Symposium on, 2011.

13

Aniruddha G. Shet, Wael Elwasif, Samantha S. Foley, Byung H. Park, David E. Bernholdt, and Randall Bramley, Strategies for Fault Tolerance in Multicomponent Applications, Procedia Computer Science 4, 2287 (2011), Proceedings of the International Conference on Computational Science, ICCS 2011.

14

Samantha S. Foley, Wael Elwasif, David E. Bernholdt, Aniruddha G. Shet, and Randall Bramley, Many-Task Applications in the Integrated Plasma Simulator, in Many-Task Computing on Grids and Supercomputers (MTAGS), 2010 IEEE Workshop on, 2010.

15

Wael Elwasif, David E. Bernholdt, Aniruddha G. Shet, Samantha S. Foley, Randall Bramley, Donald B. Batchelor, and Lee A. Berry, The Design and Implementation of the SWIM Integrated Plasma Simulator, in Parallel, Distributed and Network-Based Processing (PDP), 2010 18th Euromicro International Conference on, pages 419-427, 2010.

16

Frank Siebenlist, Rachana Ananthakrishnan, David Bernholdt, Ian T. Foster, Neill Miller, Dean N. Williams, Luca Cinquini, and Don E. Middleton, Enhancing the Earth System Grid Authentication Infrastructure through Single Sign-On and Autoprovisioning, in GCE '09: Proceedings of the 5th Grid Computing Environments Workshop, pages 1-8, New York, NY, USA, 2009, ACM.

17

Jay J. Billings, Wael R. Elwasif, Lee M. Hively, David E. Bernholdt, John M. Hetrick, III, and Tim Bohn, Designing a Component-Based Architecture for the Modeling and Simulation of Nuclear Fuels and Reactors, in Proceedings of the 2009 Workshop on Component-Based High Performance Computing, pages 1-4, New York, NY, USA, 2009, ACM, (extended abstract).

18

Samantha S. Foley, Wael R. Elwasif, David E. Bernholdt, Aniruddha G. Shet, and Randall Bramley, Extending the Concept of Component Interfaces: Experience with the Integrated Plasma Simulator, in CBHPC '09: Proceedings of the 2009 Workshop on Component-Based High Performance Computing, pages 1-4, New York, NY, USA, 2009, ACM, (extended abstract).

19

Albert Hartono, Qingda Lu, Thomas Henretty, Sriram Krishnamoorthy, Huaijian Zhang, Gerald Baumgartner, David Bernholdt, Marcel Nooijen, Russell Pitzer, J Ramanujam, and P Sadayappan, Performance Optimization of Tensor Contraction Expressions for Many Body Methods in Quantum Chemistry, J. Phys. Chem. A 113, 12715 (2009), invited paper for Russell Pitzer Festschrift.

20

D Batchelor, G Abla, E D'Azevedo, G Bateman, DE Bernholdt, L Berry, P Bonoli, R Bramley, J Breslau, M Chance, J Chen, M Choi, W Elwasif, S Foley, G Fu, R Harvey, E Jaeger, S Jardin, T Jenkins, D Keyes, S Klasky, S Kruger, L Ku, V Lynch, D McCune, J Ramos, D Schissel, D Schnack, and J Wright, Advances in Simulation of Wave Interactions with Extended MHD Phenomena, in Horst Simon, editor, SciDAC 2009, 14-18 June 2009, San Diego, California, USA, volume 180 of Journal of Physics: Conference Series, page 012054, Institute of Physics, 2009, 6pp, invited paper.

21

Frank Siebenlist, Rachana Ananthakrishnan, Ian T. Foster, Neill Miller, David Bernholdt, Luca Cinquini, Don E. Middleton, and Dean N. Williams, The Earth System Grid Authentication Infrastructure: Integrating Local Authentication, OpenID and PKI, in TeraGrid '09 Technology Track, 2009.

22

D. N. Williams, R. Ananthakrishnan, D. E. Bernholdt, S. Bharathi, D. Brown, M. Chen, A. L. Chervenak, L. Cinquini, R. Drach, I. T. Foster, P. Fox, D. Fraser, J. Garcia, S. Hankin, P. Jones, D. E. Middleton, J. Schwidder, R. Schweitzer, R. Schuler, A. Shoshani, F. Siebenlist, A. Sim, W. G. Strand, M. Su, and N. Wilhelmi, The Earth System Grid: Enabling Access to Multimodel Climate Simulation Data, Bull. Amer. Meteor. Soc. 90, 195 (2009).

23

Samantha S. Foley, Wael R. Elwasif, Aniruddha G. Shet, David E. Bernholdt, and Randall Bramley, Incorporating Concurrent Component Execution in Loosely Coupled Integrated Fusion Plasma Simulation, in Component-Based High-Performance Computing (CBHPC) 2008, 2008, (extended abstract).

24

Tamara Dahlgren, David Bernholdt, and Lois Curfman McInnes, Gaining Confidence in Scientific Applications Through Executable Interface Contracts, in Rick Stevens, editor, SciDAC 2008, 13-17 July 2008, Washington, USA, volume 125 of Journal of Physics: Conference Series, page 012086, Institute of Physics, 2008, invited paper.

25

D. Batchelor, G. Abla, G. Bateman, D. Bernholdt, L. Berry, P. Bonoli, R. Bramley, J. Breslau, M. Chance, J. Chen, M. Choi, W. Elwasif, G. Fu, R. Harvey, E. Jaeger, S. Jardin, T. Jenkins, D. Keyes, S. Klasky, S. Kruger, L. Ku, V. Lynch, D. McCune, J. Ramos, D. Schissel, D. Schnack, and J. Wright, Simulation of Wave Interations with MHD, in Rick Stevens, editor, SciDAC 2008, 14-17 July 2008, Washington, USA, volume 125 of Journal of Physics: Conference Series, page 012039, Institute of Physics, 2008, invited paper.

26

D N Williams, R Ananthakrishnan, D E Bernholdt, S Bharathi, D Brown, M Chen, A L Chervenak, L Cinquini, R Drach, I T Foster, P Fox, S Hankin, V E Henson, P Jones, D E Middleton, J Schwidder, R Schweitzer, R Schuler, A Shoshani, F Siebenlist, A Sim, W G Strand, N Wilhelmi, and M Su, Data Management and Analysis for the Earth System Grid, in Rick Stevens, editor, SciDAC 2008, 14-17 July 2008, Washington, USA, volume 125 of Journal of Physics: Conference Series, page 012072, Institute of Physics, 2008, invited paper.

27

Richard F. Barrett, Sadaf R. Alam, Valmor de Almeida, David E. Bernholdt, Wael R. Elwasif, Jeffery A. Kuehn, Stephen W. Poole, and Aniruddha G. Shet, Exploring HPCS Languages in Scientific Computing, in Rick Stevens, editor, SciDAC 2008, 14-17 July 2008, Washington, USA, volume 125 of Journal of Physics: Conference Series, page 012034, Institute of Physics, 2008, invited paper.

28

Wesley Kendall, Markus Glatter, Jian Huang, Forrest Hoffman, and David E. Bernholdt, Web Enabled Collaborative Climate Visualization in the Earth System Grid, in The 2008 International Symposium on Collaborative Technologies and Systems (CTS 2008), pages 212-220, 2008, invited paper.

29

Aniruddha G. Shet, Wael R. Elwasif, Robert J. Harrison, and David E. Bernholdt, Programmability of the HPCS Languages: A Case Study with a Quantum Chemistry Kernel, in 2008 IEEE International Parallel and Distributed Processing Symposium, 2008.

30

Aniruddha G. Shet, Wael R. Elwasif, Robert J. Harrison, and David E. Bernholdt, Programmability of the HPCS Languages: A Case Study with a Quantum Chemistry Kernel (Extended Version), Technical Report ORNL/TM-2008/011, Oak Ridge National Laboratory, 2008, extended version of IPDPS 2008 paper.

31

Aniruddha G. Shet, P. Sadayappan, David E. Bernholdt, Jarek Nieplocha, and Vinod Tipparaju, A Performance Instrumentation Framework to Characterize Computation-Communication Overlap in Message-Passing Systems, Cluster Computing (2007), invited paper.

32

M. L. Chen, A. Geist, D. E. Bernholdt, K. Chanchio, and D. L. Million, The Design and Prototype of RUDA, A Distributed Grid Accounting System, Intl J. Critical Infrastructures 4, 296 (2008), invited paper.

33

Dean N. Williams, David E. Bernholdt, Ian T. Foster, and Don E. Middleton, The Earth System Grid Center for Enabling Technologies: Enabling Community Access to Petascale Climate Datasets, CTWatch Quarterly 3 (2007), invited paper.

34

Steven Parker, Rob Armstrong, David Bernholdt, Tamara Dahlgren, Tom Epperly, Joseph Kenny, Manoj Krishnan, Gary Kumfert, Jay Larson, Lois Curfman McInnes, Jarek Nieplocha, Jaideep Ray, and Sveta Shasharina, Enabling Advanced Scientific Computing Software, CTWatch Quarterly 3 (2007), invited paper.

35

David E. Bernholdt, Component Architectures in the Next Generation of Ultrascale Scientific Computing: Challenges and Opportunities, in HPC-GECO/CompFrame 2007, 21-22 October, Montreal, Quebec, Canada, 2007.

36

Wael R. Elwasif, David E. Bernholdt, Lee A. Berry, and Don B. Batchelor, Component Framework for Coupled Integrated Fusion Plasma Simulation, in HPC-GECO/CompFrame 2007, 21-22 October, Montreal, Quebec, Canada, 2007.

37

Lois Curfman McInnes, Tamara Dahlgren, Jarek Nieplocha, David Bernholdt, Ben Allan, Rob Armstrong, Daniel Chavarria, Wael Elwasif, Ian Gorton, Manoj Krishnan, Allen Malony, Boyana Norris, Jaideep Ray, and Sameer Shende, Research Initiatives for Plug-and-Play Scientific Computing, in David Keyes, editor, SciDAC 2007, 24-28 June 2007, Boston, Massachusetts, USA, volume 78 of Journal of Physics: Conference Series, page 012046, Institute of Physics, 2007, invited paper.

38

F M Hoffman, C C Covey, I Y Fung, J T Randerson, P E Thornton, Y-H Lee, N A Rosenbloom, R C Stöckli, S W Running, D E Bernholdt, and D N Williams, Results from the Carbon-Land Model Intercomparison Project (C-LAMP) and Availability of the Data on the Earth System Grid (ESG), in David Keyes, editor, SciDAC 2007, 24-28 June 2007, Boston, Massachusetts, USA, volume 78 of Journal of Physics: Conference Series, page 012026, Institute of Physics, 2007, invited paper.

39

R Ananthakrishnan, D E Bernholdt, S Bharathi, D Brown, M Chen, A L Chervenak, L Cinquini, R Drach, I T Foster, P Fox, D Fraser, K Halliday, S Hankin, P Jones, C Kesselman, D E Middleton, J Schwidder, R Schweitzer, R Schuler, A Shoshani, F Siebenlist, A Sim, W G Strand, N Wilhelmi, M Su, and D N Williams, Building a Global Federation System for Climate Change Research: The Earth System Grid Center for Enabling Technologies (ESG-CET), in David Keyes, editor, SciDAC 2007, 24-28 June 2007, Boston, Massachusetts, USA, volume 78 of Journal of Physics: Conference Series, page 012050, Institute of Physics, 2007, invited paper.

40

D. B. Batchelor, E. D'Azevedo, G. Bateman, D. E. Bernholdt, L. A. Berry, P. T. Bonoli, R. Bramley, J. Breslau, M. Chance, J. Chen, M. Choi, W. Elwasif, G-Y Fu, R.W. Harvey, W. A. Houlberg, E.F. Jaeger, S. C. Jardin, D. Keyes, S. Klasky, S. Kruger, L.P. Ku, D. McCune, J. Ramos, D. P. Schissel, D. Schnack, and J.C Wright, Integrated Physics Advances in Simulation of Wave Interactions with Extended MHD Phenomena, in David Keyes, editor, SciDAC 2007, 24-28 June 2007, Boston, Massachusetts, USA, volume 78 of Journal of Physics: Conference Series, page 012003, Institute of Physics, 2007, invited paper.

41

Ann Chervenak, Jennifer M. Schopf, Laura Pearlman, Mei-Hui Su, Shishir Bharathi, Luca Cinquini, Mike D'Arcy, Neill Miller, and David Bernholdt, Monitoring the Earth System Grid with MDS4, in Second IEEE International Conference on e-Science and Grid Computing (e-Science'06), page 69, Los Alamitos, CA, USA, 2006, IEEE Computer Society.

42

Felipe Bertrand, Randall Bramley, David E. Bernholdt, James A. Kohl, Alan Sussman, Jay W. Larson, and Kostadin B. Damevski, Data redistribution and remote method invocation for coupled components, J. Parallel Distrib. Comput. 66, 931 (2006).

43

G. Kumfert, D. E. Bernholdt, T. G. W. Epperly, J. A Kohl, L. C. McInnes, S. Parker, and J. Ray, How the Common Component Architecture Advances Computational Science, in William M Tang, editor, SciDAC 2006, Scientific Discovery through Advanced Computing, 25-29 June 2006, Denver, Colorado, USA, volume 46 of Journal of Physics: Conference Series, pages 479-493, Institute of Physics, 2006.

44

D. E. Middleton, D. E. Bernholdt, D. Brown, M. Chen, A. L. Chervenak, L. Cinquini, R. Drach, P. Fox, P. Jones, C. Kesselman, I. T. Foster, V. Nefedova, A. Shoshani, A. Sim, W. G. Strand, and D. Williams, Enabling Worldwide Access to Climate Simulation Data: the Earth System Grid (ESG), in William M Tang, editor, SciDAC 2006, Scientific Discovery through Advanced Computing, 25-29 June 2006, Denver, Colorado, USA, volume 46 of Journal of Physics: Conference Series, pages 510-514, Institute of Physics, 2006.

45

Aniruddha G. Shet, P. Sadayappan, David E. Bernholdt, Jarek Nieplocha, and Vinod Tipparaju, A Performance Instrumentation Framework to Characterize Computation-Communication Overlap in Message-Passing Systems, in Cluster 2006: 2006 IEEE International Conference on Cluster Computing, Barcelona, September 25th-28th, 2006, IEEE, 2006.

46

Christian Engelmann, Stephen L. Scott, David E. Bernholdt, Narasimha R. Gottumukkala, Chokchai Leangsuksun, Jyothish Varma, Chao Wang, Frank Mueller, Aniruddha G. Shet, and P. Sadayappan, MOLAR: Adaptive Runtime Support for High-End Computing Operating and Runtime Systems, ACM SIGOPS Operating Systems Review 40, 63 (2006).

47

Albert Hartono, Qingda Lu, Xiaoyang Gao, Sriram Krishnamoorthy, Marcel Nooijen, Gerald Baumgartner, David E. Bernholdt, Russell M. Pitzer, J. Ramanujam, Atanas Rountev, and P. Sadayappan, Identifying Cost-Effective Common Subexpressions to Reduce Operation Count in Tensor Contraction Evaluations, in V. N. Alexandrov, Geert Dick van Albada, Peter M. A. Sloot, and Jack J. Dongarra, editors, Computational Science - ICCS 2006 6th International Conference, Reading, UK, May 28-31, 2006, Part I, volume 3991 of Lecture Notes in Computer Science, pages 267-275, Reading, UK, 2006, Springer.

48

Benjamin A. Allan, Robert Armstrong, David E. Bernholdt, Felipe Bertrand, Kenneth Chiu, Tamara L. Dahlgren, Kostadin Damevski, Wael R. Elwasif, Thomas G. W. Epperly, Madhusudhan Govindaraju, Daniel S. Katz, James A. Kohl, Manoj Krishnan, Gary Kumfert, J. Walter Larson, Sophia Lefantzi, Michael J. Lewis, Allen D. Malony, Lois C. McInnes, Jarek Nieplocha, Boyana Norris, Steven G. Parker, Jaideep Ray, Sameer Shende, Theresa L. Windus, and Shujia Zhou, A Component Architecture for High-Performance Scientific Computing, Intl. J. High-Perf. Computing Appl. 20, 163 (2006).

49

James A. Kohl, Torsten Wilde, and David E. Bernholdt, CUMULVS: Interacting with High-Performance Scientific Simulations, for Visualization, Steering and Fault Tolerance, Intl. J. High-Perf. Computing Appl. 20, 255 (2006).

50

Alexander Auer, Gerald Baumgartner, David E. Bernholdt, Alina Bibireata, Venkatesh Choppella, Daniel Cociorva, Xiaoyang Gao, Robert Harrison, Sriram Krishnamoorthy, Sandhya Krishnan, Chi-Chung Lam, Marcel Nooijen, Russell Pitzer, J. Ramanujam, P. Sadayappan, and Alexander Sibiryakov, Automatic Code Generation for Many-Body Electronic Structure Methods: The Tensor Contraction Engine, Mol. Phys. 104, 211 (2006).

51

Lois Curfman McInnes, Benjamin A. Allan, Robert Armstrong, Steven J. Benson, David E. Bernholdt, Tamara L. Dahlgren, Lori Freitag Diachin, Manojkumar Krishnan, James A. Kohl, J. Walter Larson, Sophia Lefantzi, Jarek Nieplocha, Boyana Norris, Steven G. Parker, Jaideep Ray, and Shujia Zhou, Parallel PDE-Based Simulations Using the Common Component Architecture, in Are Magnus Bruaset and Aslak Tveito, editors, Numerical Solution of PDEs on Parallel Computers, volume 51 of Lecture Notes in Computational Science and Engineering (LNCSE), pages 327-384, Springer-Verlag, 2006, invited chapter, also Argonne National Laboratory technical report ANL/MCS-P1179-0704.

52

Yuri Alexeev, Benjamin A. Allan, Robert C. Armstrong, David E. Bernholdt, Tamara L. Dahlgren, Dennis Gannon, Curtis L. Janssen, Joseph P. Kenny, Manojkumar Krishnan, James A. Kohl, Gary Kumfert, Lois Curfman McInnes, Jarek Nieplocha, Steven G. Parker, Craig Rasmussen, and Theresa L. Windus, Component-Based Software for High-Performance Scientific Computing, in Anthony Mezzacappa, editor, SciDAC 2005, Scientific Discovery through Advanced Computing, 26-30 June 2005, San Francisco, CA, USA, volume 16 of Journal of Physics: Conference Series, pages 536-540, Institute of Physics, 2005.

53

Rob Armstrong, Benjamin A. Allan, David E. Bernholdt, and Wael R. Elwasif, On the Role of Self-Similarity in Component-Based Software, in CompFrame 2005 Workshop on Component Models and Frameworks in High Performance Computing, 22-23 June, Atlanta, Georgia, USA, 2005, (extended abstract).

54

Donald B. Batchelor, Lee A. Berry, Wayne A. Houlberg, E. F. Jaeger, David E. Bernholdt, Wael R. Elwasif, Ed F. D'Azevedo, James A. Kohl, and Shuihui Li, Applying Component Technology to Coupled Fusion Simulations, in CompFrame 2005 Workshop on Component Models and Frameworks in High Performance Computing, 22-23 June, Atlanta, Georgia, USA, 2005, (extended abstract).

55

Wael R. Elwasif, Donald B. Batchelor, David E. Bernholdt, Lee A. Berry, Ed F. D'Azevedo, Wayne A. Houlberg, E. F. Jaeger, James A. Kohl, and Shuhui Li, Coupled Fusion Simulation Using the Common Component Architecture, in Vaidy Sunderam, Geert Dick van Albada, Peter M. A. Sloot, and Jack J. Dongarra, editors, Computational Science - ICCS 2005 5th International Conference, Atlanta, USA, May 22-25, 2005, Proceedings, Part I, volume 3514 of Lecture Notes in Computer Science, pages 372-379, Atlanta, Georgia, USA, 2005, Springer.

56

A. Hartono, A. Sibiryakov, M. Nooijen, G. Baumgartner, D. E. Bernholdt, S. Hirata, C. Lam, R. Pitzer, J. Ramanujam, and P. Sadayappan, Automated Operation Minimization of Tensor Contraction Expressions in Electronic Structure Calculations, in Vaidy Sunderam, Geert Dick van Albada, Peter M. A. Sloot, and Jack J. Dongarra, editors, Computational Science - ICCS 2005 5th International Conference, Atlanta, USA, May 22-25, 2005, Proceedings, Part I, volume 3514 of Lecture Notes in Computer Science, pages 155-164, Atlanta, Georgia, USA, 2005, Springer.

57

M. L. Chen, A. Geist, D. E. Bernholdt, K. Chanchio, and D. L. Million, The Design and Prototype of RUDA, A Distributed Grid Accounting System, in Osvaldo Gervasi, Marina L. Gavrilova, Vipin Kumar, Kenneth Tan, Youngsong Mun, David Taniar, and Lee Heow Pueh, editors, Computational Science and Its Applications - ICCSA 2005: International Conference, Singapore, May 9-12, 2005, Proceedings, Part III, volume 3482 of Lecture Notes in Computer Science, page 29, Singapore, 2005, International Association for Mathematics and Computers in Simulation, Springer.

58

Felipe Bertrand, Randall Bramley, Kostadin B. Damevski, James A. Kohl, David E. Bernholdt, Jay W. Larson, and Alan Sussman, Data Redistribution and Remote Method Invocation in Parallel Component Architectures, in Proceedings of the 19th International Parallel and Distributed Processing Symposium: IPDPS 2005, 2005, Best Paper Award.

59

David Bernholdt, Shishir Bharathi, David Brown, Kasidit Chanchio, Meili Chen, Ann Chervenak, Luca Cinquini, Bob Drach, Ian Foster, Peter Fox, Jose Garcia, Carl Kesselman, Rob Markel, Don Middleton, Veronika Nefedova, Line Pouchard, Arie Shoshani, Alex Sim, Gary Strand, and Dean Williams, The Earth System Grid: Supporting the Next Generation of Climate Modeling Research, Proc. IEEE 93, 485 (2005), invited paper.

60

Line Pouchard, Andrew Woolf, and David Bernholdt, Data Grid Discovery and Semantic Web Technologies for the Earth Sciences, Int. J. Digit. Libr. 5, 72 (2005), invited paper.

61

Gerald Baumgartner, Alexander Auer, David E. Bernholdt, Alina Bibireata, Venkatesh Choppella, Daniel Cociorva, Xiaoyang Gao, Robert Harrison, So Hirata, Sriram Krishnamoorthy, Sandhya Krishnan, Chi-Chung Lam, Marcel Nooijen, Russell Pitzer, J. Ramanujam, P. Sadayappan, and Alexander Sibiryakov, Synthesis of High-Performance Parallel Programs for a Class of Ab Initio Quantum Chemistry Models, Proc. of the IEEE 93, 276 (2005), invited paper.

62

Boyana Norris, Jaideep Ray, Rob Armstrong, Lois C. McInnes, David E. Bernholdt, Wael R. Elwasif, Allen D. Malony, and Sameer Shende, Computational Quality of Service for Scientific Components, in Ivica Crnkovic, Judith A. Stafford, Heinz W. Schmidt, and Kurt Wallnau, editors, Proceedings of the International Symposium on Component-Based Software Engineering (CBSE7), volume 3054 of Lecture Notes in Computer Science, pages 264-271, Edinburgh, Scotland, 2004, Springer.

63

David E. Bernholdt, Jarek Nieplocha, and P. Sadayappan, Raising the Level of Programming Abstraction in Scalable Programming Models, in Proc. of HPCA Workshop on Productivity and Performance in High-End Computing (P-PHEC 2004), Madrid, Spain, IEEE Computer Society, 2004.

64

David E. Bernholdt, Robert C. Armstrong, and Benjamin A. Allan, Managing Complexity in Modern High End Scientific Computing through Component-Based Software Engineering, in Proc. of HPCA Workshop on Productivity and Performance in High-End Computing (P-PHEC 2004), Madrid, Spain, IEEE Computer Society, 2004.

65

J. Walter Larson, Boyana Norris, Everest T. Ong, David E. Bernholdt, John B. Drake, Wael R. Elwasif, Michael W. Ham, Craig E. Rasmussen, Gary Kumfert, Daniel S. Katz, Shujia Zhou, Cecelia DeLuca, and Nancy S. Collins, Components, the Common Component Architecture, and the Climate/Weather/Ocean Community, in 84th American Meteorological Society Annual Meeting, Seattle, Washington, 2004, American Meteorological Society.

66

Sandhya Krishnan, Sriram Krishnamoorthy, Gerald Baumgartner, Daniel Cociorva, Chi-Chung Lam, P. Sadayappan, J. Ramanujam, David E. Bernholdt, and Venkatesh Choppella, Data Locality Optimization for Synthesis of Efficient Out-Of-Core Algorithms, in 10th Annual International Conference on High-Performance Computing (HiPC-2003), volume 2913 of Lecture Notes in Computer Science, pages 406-417, Springer, 2003, Best paper award.

67

Alina Bibireata, Sandhya Krishnan, Gerald Baumgartner, Daniel Cociorva, Chi-Chung Lam, P. Sadayappan, J. Ramanujam, David E. Bernholdt, and Venkatesh Choppella, Memory-Constrained Data Locality Optimizations for Tensor Contractions, in 16th International Workshop on Languages and Compilers for Parallel Computing (LCPC'03), College Station, Texas, 2003.

68

Line Pouchard, Luca Cinquini, Bob Drach, Don Middleton, David Bernholdt, Kasidit Chanchio, Meili Chen, Ian Foster, Veronika Nefedova, David Brown, Peter Fox, Jose Garcia, Gary Strand, Dean Williams, Ann Chervenak, Carl Kesselman, Arie Shoshani, and Alex Sim, An Ontology for Scientific Information in a Grid Environment, in Proceedings of the Third International Workshop on Agent Based Cluster and Grid Computing, IEEE and ACM, 2003.

69

David E. Bernholdt, Wael R. Elwasif, James A. Kohl, and Thomas G. W. Epperly, A Component Architecture for High-Performance Computing, in Proceedings of the Workshop on Performance Optimization via High-Level Languages and Libraries (POHLL-02), 2002, invited paper.

70

G. Baumgartner, D.E. Bernholdt, D. Cociorva, R. Harrison, C. Lam, M. Nooijen, J. Ramanujam, and P. Sadayappan, Automatic Synthesis of High-Performance Codes for Quantum Chemistry Applications, in Proceedings of the Workshop on Performance Optimization via High-Level Languages and Libraries (POHLL-02), 2002, invited paper.

71

G. Baumgartner, D. Bernholdt, D. Cociorva, R. Harrison, C. Lam, M. Nooijen, R. Pitzer, J. Ramanujam, and P. Sadayappan, A High-Level Approach to Synthesis of High-Performance Codes for Quantum Chemistry, in SC002 Conference, Institute of Electrical and Electronics Engineers and Association for Computing Machinery, 2002.

72

David E. Bernholdt, Parallel Computational Chemistry: an Overview of NWChem, in The Sourcebook of Parallel Computing, pages 167-194, Morgan Kaufmann Publishers, 2002.

73

David E. Bernholdt, Wael R. Elwasif, and James A. Kohl, Communication Infrastructure in High-Performance Component-Based Scientific Computing, in Dieter Kranzlmüller, Peter Kacsuk, Jack Dongarra, and Jens Volkert, editors, Recent Advances in Parallel Virtual Machine and Message Passing Interface. 9th European PVM/MPI User's Group Meeting Linz, Austria, September/October 2002. Proceedings, volume 2474 of Lecture Notes in Computer Science, pages 260-270, Springer, 2002.

74

D. Cociorva, G. Baumgartner, C. Lam, P. Sadayappan, J. Ramanujam, M. Nooijen, D.E. Bernholdt, and R. Harrison, Space-Time Trade-Off Optimization for a Class of Electronic Structure Calculations, in Proceedings of the ACM SIGPLAN 2002 Conference on Programming Language Design and Implementation (PLDI '02), Berlin, Germany, June 2002, pages 177-186, ACM, 2002.

75

Benjamin A. Allan, Robert C. Armstrong, Alicia P. Wolfe, Jaideep Ray, David E. Bernholdt, and James A. Kohl, The CCA Core Specification In A Distributed Memory SPMD Framework, Concurrency and Computation: Practice and Experience 14, 323 (2002).

76

Gerald Baumgartner, David E. Bernholdt, Daniel Cociorva, Robert Harrison, Marcel Nooijen, J. Ramanujam, and P. Sadayappan, A Performance Optimization Framework for Compilation of Tensor Contraction Expressions into Parallel Programs, in Proceedings of the International Parallel and Distributed Processing Symposium: IPDPS 2002 Workshops, 7th International Workshop on High-Level Parallel Programming Models and Supportive Environments (HIPS'02), 2002.

77

Daniel Cociorva, John W. Wilkins, Gerald Baumgartner, P. Sadayappan, J. Ramanujam, Marcel Nooijen, David E. Bernholdt, and Robert Harrison, Towards Automatic Synthesis of High-Performance Codes for Electronic Structure Calculations: Data Locality Optimization, in High Performance Computing - HiPC 2001. 8th International Conference, Hyderabad, India, December, 17-20, 2001. Proceedings, volume 2228 of Lecture Notes in Computer Science, pages 237-248, Springer, 2001.

78

Daniel Cociorva, John W. Wilkins, Gerald Baumgartner, P. Sadayappan, J. Ramanujam, Marcel Nooijen, David E. Bernholdt, and Robert Harrison, Space-Time Trade-Off Optimization for a Class of Electronic Structure Calculations, Technical Report OSU-CISRC-11/01-TR24, Dept. of Computer and Information Science, Ohio State University, 2001, not peer reviewed.

79

Wael R. Elwasif, David E. Bernholdt, James A. Kohl, and G. A. Geist, An Architecture for a Multi-Threaded Harness Kernel, in Recent Advances in Parallel Virtual Machine and Message Passing Interface. 8th European PVM/MPI User's Group Meeting Santorini/Thera, Greece, September 2001. Proceedings, volume 2131 of Lecture Notes in Computer Science, pages 126-134, Springer, 2001.

80

G. Yu. Rudko, V. C. Long, J. L. Musfeldt, H.-J. Koo, M.-H. Whangbo, A. Revcolevschi, G. Dhalenne, and D. E. Bernholdt, Electronic Transitions in Doped and Undoped Copper Germanate, Chem. Mater. 13, 939 (2001).

81

Ricky A. Kendall, Edo Aprà, David E Bernholdt, Eric J. Bylaska, Michel Dupuis, George I. Fann, Robert J. Harrison, Jailin Ju, Jeffrey A. Nichols, Jarek Nieplocha, T. P. Straatsma, Theresa L. Windus, and Adrian T. Wong, High Performance Computational Chemistry; Overview of NWChem a Distributed Parallel Application, Comp. Physics Comm. 128, 260 (2000).

82

David E. Bernholdt, Scalability of Correlated Electronic Structure Calculations on Parallel Computers: A Case Study of the RI-MP2 Method, Parallel Computing 26, 945 (2000).

83

David E. Bernholdt and Rodney J. Bartlett, A Critical Assessment of Multireference Fock-Space CCSD and Perturbative Third-Order Triples Approximations for Photoelectron Spectra and Quasidegenerate Potential Energy Surfaces, Adv. Quantum Chem. 34, 271 (1999).

84

David E. Bernholdt, Geoffrey C. Fox, Roman Markowski, Nancy J. McCracken, Marek Podgorny, Thomas R. Scavo, Debasis Mitra, and Qutaibah Malluhi, Synchronous Learning at a Distance: Experiences with TANGO, in SC'98 Conference, Institute of Electrical and Electronics Engineers and Association for Computing Machinery, 1998.

85

David E. Bernholdt, Object Oriented Methods Without Object Oriented Languages, in Michael E. Henderson, Christopher R. Anderson, and Stephen L. Lyons, editors, Object Oriented Methods for Inter-operable Scientific and Engineering Computing, pages 40-49, Society for Industrial and Applied Mathematics, 1999.

86

Meenakshi A. Kandaswamy, Mahmut T. Kandemir, Alok N. Choudhary, and David E. Bernholdt, An Experimental Study to Analyze and Optimize Hartree-Fock Application's I/O with PASSION, Int. J. High Perf. Computing Appl. 12, 411 (1998).

87

Meenakshi A. Kandaswamy, Mahmut T. Kandemir, Alok N. Choudhary, and David E. Bernholdt, Performance Implications of Architectural and Software Techniques on I/O-Intensive Applications, in 1998 International Conference on Parallel Processing (ICPP'98), IEEE Computer Society Press, 1998.

88

David E. Bernholdt and Robert J. Harrison, Fitting Basis Sets for the RI-MP2 Approximate Second-Order Many-Body Perturbation Theory Method, J. Chem. Phys. 109, 1593 (1998).

89

Meenakshi A. Kandaswamy, Mahmut T. Kandemir, Alok N. Choudhary, and David E. Bernholdt, Optimization and Evaluation of Hartree-Fock Application's I/O with PASSION, in SC'97 Conference, Institute of Electrical and Electronics Engineers and Association for Computing Machinery, 1997.

90

David E. Bernholdt and Geoffrey C. Fox, Internet Resource Discovery for Chemistry - Where are Those Vast Untapped Resources?, Trends Anal. Chem. 16, 230 (1997).

91

M.F. Guest, E. Aprà, D.E. Bernholdt, H.A. Fruchtl, R.J. Harrison, R.A. Kendall, R.A. Kutteh, X. Long, J.B. Nicholas, J.A. Nichols, H.L. Taylor, A.T. Wong, G.I. Fann, R.J. Littlefield, and J. Nieplocha, High-performance Computing in Chemistry; NWChem, Future Generation Computer Systems 12, 273 (1996).

92

David Feller, Edoardo Aprà, Jeff A. Nichols, and David E. Bernholdt, The Structure and Binding Energy of K$^{+}$-Ether Complexes: A Comparison of MP2, RI-MP2 and Density Functional Methods, J. Chem. Phys. 105, 1940 (1996).

93

David E. Bernholdt and Robert J. Harrison, Large-Scale Correlated Electronic Structure Calculations: The RI-MP2 Method on Parallel Computers, Chem. Phys. Lett. 250, 477 (1996).

94

M. F. Guest, E. Aprà, D. E. Bernholdt, H. A. Früchtl, R. J. Harrison, R. A. Kendall, R. A. Kutteh, X. Long, J. B. Nicholas, J. A. Nichols, H. L. Taylor, A. T. Wong, G. I. Fann, R. J. Littlefield, and J. Nieplocha, Advances in Parallel Distributed Data Software; Computational Chemistry and NWChem, in Applied Parallel Computing. Computations in Physics, Chemistry and Engineering Science, volume 1041 of Lecture Notes in Computer Science, Springer, Heidelberg, 1996.

95

D. E. Bernholdt, E. Aprà, H. A. Früchtl, M. F. Guest, R. J. Harrison, R. A. Kendall, R. A. Kutteh, X. Long, J. B. Nicholas, J. A. Nichols, H. L. Taylor, A. T. Wong, G. I. Fann, R. J. Littlefield, and J. Nieplocha, Parallel Computational Chemistry Made Easier: The Development of NWChem, Int. J. Quantum Chemistry: Quantum Chem. Symposium 29, 475 (1995).

96

M. F. Guest, E. Aprà, D. E. Bernholdt, H. A. Früchtl, R. J. Harrison, R. A. Kendall, R. A. Kutteh, X. Long, J. B. Nicholas, J. A. Nichols, H. L. Taylor, A. T. Wong, G. I. Fann, R. J. Littlefield, and J. Nieplocha, High Performance Computational Chemistry: NWChem and Fully Distributed Parallel Algorithms, in High Performance Computing: Technology, Methods, and Applications, volume 10 of Advances in Parallel Computing, pages 395-427, Elsevier, Amsterdam, 1995.

97

David E. Bernholdt and Robert J. Harrison, Orbital Invariant Second-Order Many-Body Perturbation Theory on Parallel Computers: An Approach for Large Molecules, J. Chem. Phys. 102, 9582 (1995).

98

M. F. Guest, E. Aprà, D. E. Bernholdt, H. A. Früchtl, R. J. Harrison, R. A. Kendall, R. A. Kutteh, J. B. Nicholas, J. A. Nichols, M. S. Stave, A. T. Wong, R. J. Littlefield, and J. Nieplocha, High Performance Computational Chemistry: Towards Fully Distributed Parallel Algorithms, in A. M. Tentner, editor, High Performance Computing 1994: Grand Challenges in Computer Simulation, pages 511-521, San Diego, 1994, Society for Computer Simulation.

99

Robert J. Harrison, Martyn F. Guest, Rick A. Kendall, David E. Bernholdt, Adrian T. Wong, Mark Stave, James Anchell, Anthony Hess, Rik Littlefield, George I. Fann, Jarek Nieplocha, Greg S. Thomas, David Elwood, Jeff Tilson, Ron L. Shepard, Albert F. Wagner, Ian T. Foster, Ewing Lusk, and Rick Stevens, High Performance Computational Chemistry. II. A Scalable SCF Program, J. Computat. Chem. 17, 124 (1995).

100

S. Ajith Perera, David E. Bernholdt, and Rodney J. Bartlett, Localized Hartree Product Orbitals in Correlated Studies of Molecules, Int. J. Quantum Chem. 49, 559 (1994).

101

Rodney J. Bartlett, Magnus Rittby, John D. Watts, and David E. Bernholdt, Carbon Clusters: The Synergism Between Theory and Experiment, in P. J. Reynolds, editor, On Clusters and Clustering, From Atoms to Fractals, pages 23-31, Elsevier, 1993.

102

John F. Stanton and David E. Bernholdt, An Empirically Adjusted Newton-Raphson Algorithm for Finding Local Minima on Molecular Potential Energy Surfaces, J. Computat. Chem. 11, 58 (1990).

103

Joseph D. Augspurger, David E. Bernholdt, and Clifford E. Dykstra, Concise, Open-ended Implementation of Rys Polynomial Evaluation of Two-Electron Integrals, J. Computat. Chem. 11, 972 (1990).

104

Mark S. Gordon, Kim K. Baldridge, David E. Bernholdt, and Rodney J. Bartlett, The Transition State and Barrier Heights for the Reaction O($^3$P) + HCl $\longrightarrow$ OH + Cl, Chem. Phys. Lett. 158, 189 (1989).

105

David E. Bernholdt, David H. Magers, and Rodney J. Bartlett, Stability and Properties of C$_4$ Isomers, J. Chem. Phys. 89, 3612 (1988).

106

D. E. Bernholdt, J. D. Irwin, J. P. Lacosse, K. J. Mattson, J. B. Miers, K. D. Park, L. K. Tanaka, and C. E. Dykstra, The Structures and Stabilities of H$_4$C$_2$N$_2$ Isomers, J. Mol. Struct. (Theochem) 153, 175 (1987).

107

David E. Bernholdt, Shi-yi Liu, and Clifford E. Dykstra, A Theoretical Study of the Structure, Bonding, and Vibrational Frequency Shifts of the H$_2$-HF Complex, J. Chem. Phys. 85, 5120 (1986).

108

L. E. Snyder, C. E. Dykstra, and D. Bernholdt, Calculated Dipole Moments and Resulting Column Densities of Long Carbon Chain Molecules in TMC-1, in A. D. Haschick, editor, Masers, Molecules, and Mass Outflows in Star Forming Regions, pages 9-21, Westford, Massachussetts, 1986, Haystack Observatory Meeting, Haystack Observatory.