Industrial Strength Parallel Computing

Today, parallel computing experts can solve problems previously deemed impossible and make the "merely difficult" problems economically feasible to solve. This book presents and synthesizes the recent experiences of reknown expert developers who design robust and complex parallel computing applications. They demonstrate how to adapt and implement today's most advanced, most effective parallel computing techniques.

The book begins with a highly focused introductory course designed to provide a working knowledge of all the relevant architectures, programming models, and performance issues, as well as the basic approaches to assessment, optimization, scheduling, and debugging.

Next comes a series of seventeen detailed case studies-all dealing with production-quality industrial and scientific applications, all presented firsthand by the actual code developers. Each chapter follows the same comparison-inviting format, presenting lessons learned and algorithms developed in the course of meeting real, non-academic challenges. A final section highlights the case studies' most important insights and turns an eye to the future of the discipline.

• Provides in-depth case studies of seventeen parallel computing applications, some built from scratch, others developed through parallelizing existing applications.

• Explains elements critical to all parallel programming environments, including:
  Terminology and architectures
  Programming models and methods
  Performance analysis and debugging tools

• Teaches primarily by example, showing how scientists in many fields have solved daunting problems using parallel computing.

• Covers a wide range of application areas-biology, aerospace, semiconductor design, environmental modeling, data imaging and analysis, fluid dynamics, and more.

• Summarizes the state of the art while looking to the future of parallel computing.

Presents technical animations and visualizations from many of the applications detailed in the case studies via a companion web site.

Inhalt

Chapter 1 - Parallel Computing Architectures
Alice E. Koniges, David C. Eder, Margaret Cahir

Chapter 2 - Parallel Application Performance
Alice E. Koniges

Chapter 3 - Programming Models and Methods
Margaret Cahir, Robert Moench, Alice E. Koniges

Chapter 4 - Parallel Programming Tools
Margaret Cahir, Robert Moench, Alice E. Koniges

Chapter 5 - Optimizing for Single-Processor Performance
Jeff Brooks, Sara Graffunder, Alice E. Koniges

Chapter 6 - Scheduling Issues
Morris A. Jette

Chapter 7 - Ocean Modeling and Visualization
Yi Chao, P. Peggy Li, Ping Wang, Daniel S. Katz, Benny N. Cheng, Scott Whitman

Chapter 8 - Impact of Aircraft on Global Atmospheric Chemistry
Douglas A. Rotman, John R. Tannahill, Steven L. Baughcum

Chapter 9 - Petroleum Reservoir Management
Michael DeLong, Allyson Gajraj, Wayne Joubert, Olaf Lubeck, James Sanderson, Robert E. Stephenson, Gautam S. Shiralkar, Bart van Bloemen Waanders

Chapter 10 - An Architecture-Independent Navier-Stokes Code
Johnson C. T. Wang, Stephen Taylor

Chapter 11 - Gaining Insights into the Flow in a Static Mixer
Olivier Byrde, Mark L. Sawley

Chapter 12 - Modeling Groundwater Flow and Contaminant Transport
William J. Bosil, Steven F. Ashby, Chuck Baldwin, Robert D. Falgout, Steven G. Smith, Andrew F. B. Tompson

Chapter 13 - Simulation of Plasma Reactors
Stephen Taylor, Marc Rieffel, Jerrell Watts, Sadasivan Shankar

Chapter 14 - Electron-Molecule Collisions for Plasma Modeling
Carl Winstead, Chuo-Han Lee, Vincent McKoy

Chapter 15 - Three-Dimensional Plasma Particle-in-Cell Calculations of Ion Thruster Backflow Contamination
Robie I. Samanta Roy, Daniel E. Hastings, Stephen Taylor

Chapter 16 - Advanced Atomic-Level Materials Design
Lin H. Yang

Chapter 17 - Solving Symmetric Eigenvalue Problems
David C. O'Neal, Raghurama Reddy

Chapter 18 - Nuclear Magnetic Resonance Simulations
Alan J. Benesi, Kenneth M. Merz, James J. Vincent, Ravi Subramanya

Chapter 19 - Molecular Dynamics Simulations Using Particle-Mesh Ewald Methods
Michael F. Crowley, David W. Deerfield II, Tom A. Darden, Thomas E. Cheatham III

Chapter 20 - Radar Scattering and Antenna Modeling
Tom Cwik, Cinzia Zuffada, Daniel S. Katz, Jay Parker

Chapter 21 - Functional Magnetic Resonance Imaging Dataset Analysis
Nigel H. Goddard, Greg Hood, Jonathan D. Cohen, Leigh E. Nystrom, William F. Eddy, Christopher R. Genovese, Douglas C. Noll

Chapter 22 - Selective and Sensitive Comparison of Genetic Sequence Data
Alexander J. Ropelewski, Hugh B. Nicholas, Jr., David W. Deerfield II

Chapter 23 - Interactive Optimization of Video Compression Algorithms
Henri Nicolas, Fred Jordan

Chapter 24 - Designing Industrial Parallel Applications
Alice E. Koniges, David C. Eder, Michael A. Heroux

Chapter 25 - The Future of Industrial Parallel Computing
Michael A. Heroux, Horst Simon, Alice E. Koniges