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.

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