Advanced computational infrastructures for parallel and distributed adaptive applications /
edited by Manish Parashar, Xiaolin Li.
- xx, 518 pages: illustrations
- Wiley series on parallel and distributed computing .
- Wiley series on parallel and distributed computing. .
ABOUT THE AUTHOR
Manish Parashar, PhD, is Professor of Electrical and Computer Engineering at Rutgers University, where he is also the director of the Applied Software Systems Laboratory and director of the NSF Center for Autonomic Computing. He has received numerous awards, including the Rutgers Board of Trustees Award for Excellence in Research (2004-2005) and the NSF CAREER Award (1999).
Xiaolin Li, PhD, is Assistant Professor of Computer Science at Oklahoma State University.
Includes bibliographical references and index.
TABLE OF CONTENTS
Preface xi
Contributors xv
Biographies xix
1. Introduction: Enabling Large-Scale Computational Science—Motivations, Requirements, and
Challenges 1
Manish Parashar and Xiaolin Li
Part I Adaptive Applications in Science and Engineering
2. Adaptive Mesh Refinement MHD Simulations of Tokamak Refueling 11
Ravi Samtaney
3. Parallel Computing Engines for Subsurface Imaging Technologies 29
Tian-Chyi J. Yeh, Xing Cai, Hans P. Langtangen, Junfeng Zhu, and Chuen-Fa Ni
4. PlaneWave Seismic Data: Parallel and Adaptive Strategies for Velocity Analysis and Imaging 45
Paul L. Stoffa, Mrinal K. Sen, Roustam K. Seif, and Reynam C. Pestana
5. Data-Directed Importance Sampling for Climate Model Parameter Uncertainty Estimation 65
Charles S. Jackson, Mrinal K. Sen, Paul L. Stoffa, and Gabriel Huerta
6. Adaptive Cartesian Methods for Modeling Airborne Dispersion 79
Andrew Wissink, Branko Kosovic, Marsha Berger, Kyle Chand, and Fotini K. Chow
7. Parallel and Adaptive Simulation of Cardiac Fluid Dynamics 105
Boyce E. Griffith, Richard D. Hornung, David M. McQueen, and Charles S. Peskin
8. Quantum Chromodynamics on the BlueGene/L Supercomputer 131
Pavlos M. Vranas and Gyan Bhanot
Part II Adaptive Computational Infrastructures
9. The SCIJump Framework for Parallel and Distributed Scientific Computing 151
Steven G. Parker, Kostadin Damevski, Ayla Khan, Ashwin Swaminathan, and Christopher R. Johnson
10. Adaptive Computations in the Uintah Framework 171
Justin Luitjens, James Guilkey, Todd Harman, Bryan Worthen, and Steven G. Parker
11. Managing Complexity in Massively Parallel, Adaptive, Multiphysics Finite Element Applications 201
Harold C. Edwards
12. GrACE: Grid Adaptive Computational Engine for Parallel Structured AMR Applications 249
Manish Parashar and Xiaolin Li
13. Charm++ and AMPI: Adaptive Runtime Strategies via Migratable Objects 265
Laxmikant V. Kale and Gengbin Zheng
14. The Seine Data Coupling Framework for Parallel Scientific Applications 283
Li Zhang, Ciprian Docan, and Manish Parashar
Part III Dynamic Partitioning and Adaptive Runtime Management Frameworks
15. Hypergraph-Based Dynamic Partitioning and Load Balancing 313
Umit V. Catalyurek, Doruk Bozda¢g, Erik G. Boman, Karen D. Devine, Robert Heaphy, and Lee A. Riesen
16. Mesh Partitioning for Efficient Use of Distributed Systems 335
Jian Chen and Valerie E. Taylor
17. Variable Partition Inertia: Graph Repartitioning and Load Balancing for Adaptive Meshes 357
Chris Walshaw
18. A Hybrid and Flexible Data Partitioner for Parallel SAMR 381
Johan Steensland
19. Flexible Distributed Mesh Data Structure for Parallel Adaptive Analysis 407
Mark S. Shephard and Seegyoung Seol
20. HRMS: Hybrid Runtime Management Strategies for Large-Scale Parallel Adaptive Applications 437
Xiaolin Li and Manish Parashar
21. Physics-Aware Optimization Method 463
Yeliang Zhang and Salim Hariri
22. DistDLB: Improving Cosmology SAMR Simulations on Distributed Computing Systems Through Hierarchical Load Balancing 479
Zhiling Lan, Valerie E. Taylor, and Yawei Li
Index 503
A unique investigation of the state of the art in design, architectures, and implementations of advanced computational infrastructures and the applications they support
Emerging large-scale adaptive scientific and engineering applications are requiring an increasing amount of computing and storage resources to provide new insights into complex systems. Due to their runtime adaptivity, these applications exhibit complicated behaviors that are highly dynamic, heterogeneous, and unpredictable—and therefore require full-fledged computational infrastructure support for problem solving, runtime management, and dynamic partitioning/balancing. This book presents a comprehensive study of the design, architecture, and implementation of advanced computational infrastructures as well as the adaptive applications developed and deployed using these infrastructures from different perspectives, including system architects, software engineers, computational scientists, and application scientists. Providing insights into recent research efforts and projects, the authors include descriptions and experiences pertaining to the realistic modeling of adaptive applications on parallel and distributed systems.
The first part of the book focuses on high-performance adaptive scientific applications and includes chapters that describe high-impact, real-world application scenarios in order to motivate the need for advanced computational engines as well as to outline their requirements. The second part identifies popular and widely used adaptive computational infrastructures. The third part focuses on the more specific partitioning and runtime management schemes underlying these computational toolkits.
Presents representative problem-solving environments and infrastructures, runtime management strategies, partitioning and decomposition methods, and adaptive and dynamic applications
Provides a unique collection of selected solutions and infrastructures that have significant impact with sufficient introductory materials
Includes descriptions and experiences pertaining to the realistic modeling of adaptive applications on parallel and distributed systems
The cross-disciplinary approach of this reference delivers a comprehensive discussion of the requirements, design challenges, underlying design philosophies, architectures, and implementation/deployment details of advanced computational infrastructures. It makes it a valuable resource for advanced courses in computational science and software/systems engineering for senior undergraduate and graduate students, as well as for computational and computer scientists, software developers, and other industry professionals.
9780470072943 (cloth) 0470072946 (cloth) 9780470558027
2009031419
Parallel processing (Electronic computers)
Electronic data processing--Distributed processing.
Adaptive computing systems.
Electronic books.
QA76.58 / .A375 2010
004/.35
ABOUT THE AUTHOR
Manish Parashar, PhD, is Professor of Electrical and Computer Engineering at Rutgers University, where he is also the director of the Applied Software Systems Laboratory and director of the NSF Center for Autonomic Computing. He has received numerous awards, including the Rutgers Board of Trustees Award for Excellence in Research (2004-2005) and the NSF CAREER Award (1999).
Xiaolin Li, PhD, is Assistant Professor of Computer Science at Oklahoma State University.
Includes bibliographical references and index.
TABLE OF CONTENTS
Preface xi
Contributors xv
Biographies xix
1. Introduction: Enabling Large-Scale Computational Science—Motivations, Requirements, and
Challenges 1
Manish Parashar and Xiaolin Li
Part I Adaptive Applications in Science and Engineering
2. Adaptive Mesh Refinement MHD Simulations of Tokamak Refueling 11
Ravi Samtaney
3. Parallel Computing Engines for Subsurface Imaging Technologies 29
Tian-Chyi J. Yeh, Xing Cai, Hans P. Langtangen, Junfeng Zhu, and Chuen-Fa Ni
4. PlaneWave Seismic Data: Parallel and Adaptive Strategies for Velocity Analysis and Imaging 45
Paul L. Stoffa, Mrinal K. Sen, Roustam K. Seif, and Reynam C. Pestana
5. Data-Directed Importance Sampling for Climate Model Parameter Uncertainty Estimation 65
Charles S. Jackson, Mrinal K. Sen, Paul L. Stoffa, and Gabriel Huerta
6. Adaptive Cartesian Methods for Modeling Airborne Dispersion 79
Andrew Wissink, Branko Kosovic, Marsha Berger, Kyle Chand, and Fotini K. Chow
7. Parallel and Adaptive Simulation of Cardiac Fluid Dynamics 105
Boyce E. Griffith, Richard D. Hornung, David M. McQueen, and Charles S. Peskin
8. Quantum Chromodynamics on the BlueGene/L Supercomputer 131
Pavlos M. Vranas and Gyan Bhanot
Part II Adaptive Computational Infrastructures
9. The SCIJump Framework for Parallel and Distributed Scientific Computing 151
Steven G. Parker, Kostadin Damevski, Ayla Khan, Ashwin Swaminathan, and Christopher R. Johnson
10. Adaptive Computations in the Uintah Framework 171
Justin Luitjens, James Guilkey, Todd Harman, Bryan Worthen, and Steven G. Parker
11. Managing Complexity in Massively Parallel, Adaptive, Multiphysics Finite Element Applications 201
Harold C. Edwards
12. GrACE: Grid Adaptive Computational Engine for Parallel Structured AMR Applications 249
Manish Parashar and Xiaolin Li
13. Charm++ and AMPI: Adaptive Runtime Strategies via Migratable Objects 265
Laxmikant V. Kale and Gengbin Zheng
14. The Seine Data Coupling Framework for Parallel Scientific Applications 283
Li Zhang, Ciprian Docan, and Manish Parashar
Part III Dynamic Partitioning and Adaptive Runtime Management Frameworks
15. Hypergraph-Based Dynamic Partitioning and Load Balancing 313
Umit V. Catalyurek, Doruk Bozda¢g, Erik G. Boman, Karen D. Devine, Robert Heaphy, and Lee A. Riesen
16. Mesh Partitioning for Efficient Use of Distributed Systems 335
Jian Chen and Valerie E. Taylor
17. Variable Partition Inertia: Graph Repartitioning and Load Balancing for Adaptive Meshes 357
Chris Walshaw
18. A Hybrid and Flexible Data Partitioner for Parallel SAMR 381
Johan Steensland
19. Flexible Distributed Mesh Data Structure for Parallel Adaptive Analysis 407
Mark S. Shephard and Seegyoung Seol
20. HRMS: Hybrid Runtime Management Strategies for Large-Scale Parallel Adaptive Applications 437
Xiaolin Li and Manish Parashar
21. Physics-Aware Optimization Method 463
Yeliang Zhang and Salim Hariri
22. DistDLB: Improving Cosmology SAMR Simulations on Distributed Computing Systems Through Hierarchical Load Balancing 479
Zhiling Lan, Valerie E. Taylor, and Yawei Li
Index 503
A unique investigation of the state of the art in design, architectures, and implementations of advanced computational infrastructures and the applications they support
Emerging large-scale adaptive scientific and engineering applications are requiring an increasing amount of computing and storage resources to provide new insights into complex systems. Due to their runtime adaptivity, these applications exhibit complicated behaviors that are highly dynamic, heterogeneous, and unpredictable—and therefore require full-fledged computational infrastructure support for problem solving, runtime management, and dynamic partitioning/balancing. This book presents a comprehensive study of the design, architecture, and implementation of advanced computational infrastructures as well as the adaptive applications developed and deployed using these infrastructures from different perspectives, including system architects, software engineers, computational scientists, and application scientists. Providing insights into recent research efforts and projects, the authors include descriptions and experiences pertaining to the realistic modeling of adaptive applications on parallel and distributed systems.
The first part of the book focuses on high-performance adaptive scientific applications and includes chapters that describe high-impact, real-world application scenarios in order to motivate the need for advanced computational engines as well as to outline their requirements. The second part identifies popular and widely used adaptive computational infrastructures. The third part focuses on the more specific partitioning and runtime management schemes underlying these computational toolkits.
Presents representative problem-solving environments and infrastructures, runtime management strategies, partitioning and decomposition methods, and adaptive and dynamic applications
Provides a unique collection of selected solutions and infrastructures that have significant impact with sufficient introductory materials
Includes descriptions and experiences pertaining to the realistic modeling of adaptive applications on parallel and distributed systems
The cross-disciplinary approach of this reference delivers a comprehensive discussion of the requirements, design challenges, underlying design philosophies, architectures, and implementation/deployment details of advanced computational infrastructures. It makes it a valuable resource for advanced courses in computational science and software/systems engineering for senior undergraduate and graduate students, as well as for computational and computer scientists, software developers, and other industry professionals.
9780470072943 (cloth) 0470072946 (cloth) 9780470558027
2009031419
Parallel processing (Electronic computers)
Electronic data processing--Distributed processing.
Adaptive computing systems.
Electronic books.
QA76.58 / .A375 2010
004/.35