Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications

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.

• Preface xiContributors xvBiographies xix1. Introduction: Enabling Large-Scale Computational Science—Motivations, Requirements, and Challenges 1Manish Parashar and Xiaolin LiPart I Adaptive Applications in Science and Engineering2. Adaptive Mesh Refinement MHD Simulations of Tokamak Refueling 11Ravi Samtaney3. Parallel Computing Engines for Subsurface Imaging Technologies 29Tian-Chyi J. Yeh, Xing Cai, Hans P. Langtangen, Junfeng Zhu, and Chuen-Fa Ni4. PlaneWave Seismic Data: Parallel and Adaptive Strategies for Velocity Analysis and Imaging 45Paul L. Stoffa, Mrinal K. Sen, Roustam K. Seif, and Reynam C. Pestana5. Data-Directed Importance Sampling for Climate Model Parameter Uncertainty Estimation 65Charles S. Jackson, Mrinal K. Sen, Paul L. Stoffa, and Gabriel Huerta6. Adaptive Cartesian Methods for Modeling Airborne Dispersion 79Andrew Wissink, Branko Kosovic, Marsha Berger, Kyle Chand, and Fotini K. Chow7. Parallel and Adaptive Simulation of Cardiac Fluid Dynamics 105Boyce E. Griffith, Richard D. Hornung, David M. McQueen, and Charles S. Peskin8. Quantum Chromodynamics on the BlueGene/L Supercomputer 131Pavlos M. Vranas and Gyan BhanotPart II Adaptive Computational Infrastructures9. The SCIJump Framework for Parallel and Distributed Scientific Computing 151Steven G. Parker, Kostadin Damevski, Ayla Khan, Ashwin Swaminathan, and Christopher R. Johnson10. Adaptive Computations in the Uintah Framework 171Justin Luitjens, James Guilkey, Todd Harman, Bryan Worthen, and Steven G. Parker11. Managing Complexity in Massively Parallel, Adaptive, Multiphysics Finite Element Applications 201Harold C. Edwards12. GrACE: Grid Adaptive Computational Engine for Parallel Structured AMR Applications 249Manish Parashar and Xiaolin Li13. Charm++ and AMPI: Adaptive Runtime Strategies via Migratable Objects 265Laxmikant V. Kale and Gengbin Zheng14. The Seine Data Coupling Framework for Parallel Scientific Applications 283Li Zhang, Ciprian Docan, and Manish ParasharPart III Dynamic Partitioning and Adaptive Runtime Management Frameworks15. Hypergraph-Based Dynamic Partitioning and Load Balancing 313Umit V. Catalyurek, Doruk Bozda¢g, Erik G. Boman, Karen D. Devine, Robert Heaphy, and Lee A. Riesen16. Mesh Partitioning for Efficient Use of Distributed Systems 335Jian Chen and Valerie E. Taylor17. Variable Partition Inertia: Graph Repartitioning and Load Balancing for Adaptive Meshes 357Chris Walshaw18. A Hybrid and Flexible Data Partitioner for Parallel SAMR 381Johan Steensland19. Flexible Distributed Mesh Data Structure for Parallel Adaptive Analysis 407Mark S. Shephard and Seegyoung Seol20. HRMS: Hybrid Runtime Management Strategies for Large-Scale Parallel Adaptive Applications 437Xiaolin Li and Manish Parashar21. Physics-Aware Optimization Method 463Yeliang Zhang and Salim Hariri22. DistDLB: Improving Cosmology SAMR Simulations on Distributed Computing Systems Through Hierarchical Load Balancing 479Zhiling Lan, Valerie E. Taylor, and Yawei LiIndex 503

"This edited volume brings together a high-powered list of experts mostly from leading research instates and universities in the US to deal, with the various aspects of parallel and distributed computing. It shall be valued greatly all over the world. Written in a reasoned and intelligible manner, it shall have an assured place in the parallel and distributed computing library where it should be accessible to any readerwith a solid background in the subject." (Current Engineering Practice, 1 November 2010)