Provides the first collection of articles on petascale algorithms and applications for computational science and engineering Covers a breadth of topics in petascale computing, including architectures, software, programming methodologies, tools, scalable algorithms, performance evaluation, and application development Discusses expected breakthroughs in the field for computational science and engineering Includes contributions from international researchers who are pioneers in designing applications for petascale computing systems
Although the highly anticipated petascale computers of the near future will perform at an order of magnitude faster than today’s quickest supercomputer, the scaling up of algorithms and applications for this class of computers remains a tough challenge. From scalable algorithm design for massive concurrency toperformance analyses and scientific visualization, Petascale Computing: Algorithms and Applications
captures the state of the art in high-performance computing algorithms and applications. Featuring contributions from the world’s leading experts in computational science, this edited collection explores the use of petascale computers for solving the most difficult scientific and engineering problems of the current century.
Covering a wide range of important topics, the book illustrates how petascale computing can be applied to space and Earth science missions, biological systems, weather prediction, climate science, disasters, black holes, and gamma ray bursts. It details the simulation of multiphysics, cosmological evolution, molecular dynamics, and biomolecules. The book also discusses computational aspects that include the Uintah framework, Enzo code, multithreaded algorithms, petaflops, performance analysis tools, multilevel finite element solvers, finite element code development, Charm++, and the Cactus framework.
Supplying petascale tools, programming methodologies, and an eight-page color insert, this volume addresses the challenging problems of developing application codes that can take advantage of the architectural features of the new petascale systems in advance of their first deployment.
Table of Contents
Performance Characteristics of Potential Petascale Scientific Applications
John Shalf, Leonid Oliker, Michael Lijewski, Shoaib Kamil, Jonathan Carter, Andrew Canning, and Stéphane Ethier
Petascale Computing: Impact on Future NASA Missions
Rupak Biswas, Michael Aftosmis, Cetin Kiris, and Bo-Wen Shen
Multiphysics Simulations and Petascale Computing
Steven F. Ashby and John M. May
Scalable Parallel AMR for the Uintah Multi-Physics Code
Justin Luitjens, Bryan Worthen, Martin Berzins, and Thomas C. Henderson
Simulating Cosmological Evolution with Enzo
Michael L. Norman, James Bordner, Daniel Reynolds, Rick Wagner, Greg L. Bryan, Robert Harkness, and Brian O’Shea
Numerical Prediction of High-Impact Local Weather: A Driver for Petascale Computing
Ming Xue, Kelvin K. Droegemeier, and Daniel Weber
Software Design for Petascale Climate Science
John B. Drake, Philip W. Jones, Mariana Vertenstein, James B. White III, and Patrick H. Worley
Toward Distributed Petascale Computing
Alfons G. Hoekstra, Simon Portegies Zwart, Marian Bubak, and Peter M.A. Sloot
Biomolecular Modeling in the Era of Petascale Computing
Klaus Schulten, James C. Phillips, Laxmikant V. Kalé, and Abhinav Bhatele
Petascale Special-Purpose Computer for Molecular Dynamics Simulations
Makoto Taiji, Tetsu Narumi, and Yousuke Ohno
Simulating Biomolecules on the Petascale Supercomputers
Pratul K. Agarwal, Sadaf R. Alam, and Al Geist
Multithreaded Algorithms for Processing Massive Graphs
Kamesh Madduri, David A. Bader, Jonathan W. Berry, Joseph R. Crobak, and Bruce A. Hendrickson
Disaster Survival Guide in Petascale Computing: An Algorithmic Approach
Jack J. Dongarra, Zizhong Chen, George Bosilca, and Julien Langou
The Road to TSUBAME and Beyond
Petaflops Basics—Performance from SMP Building Blocks
Christian Bischof, Dieter an Mey, Christian Terboven, and Samuel Sarholz
Performance and Its Complexity on Petascale Systems
Highly Scalable Performance Analysis Tools
Michael Gerndt and Karl Fürlinger
Toward Petascale Multilevel Finite Element Solvers
Christoph Freundl, Tobias Gradl, Ulrich Rüde, and Benjamin Bergen
A Hybrid Approach to Efficient Finite Element Code Development
Anders Logg, Kent-Andre Mardal, Martin Sandve Alnæs, Hans Petter Langtangen, and Ola Skavhaug
Programming Petascale Applications with Charm++
Laxmikant V. Kalé, Eric Bohm, Celso L. Mendes, Terry Wilmarth, and Gengbin Zheng
Annotations for Productivity and Performance Portability
Boyana Norris, Albert Hartono, and William Gropp
Locality Awareness in a High-Productivity Programming Language
Roxana E. Diaconescu and Hans P. Zima
Architectural and Programming Issues for Sustained Petaflop Performance
Uwe Küster and Michael Resch
Cactus Framework: Black Holes to Gamma Ray Bursts
Erik Schnetter, Christian D. Ott, Gabrielle Allen, Peter Diener, Tom Goodale, Thomas Radke, Edward Seidel, and John Shalf
"…Bader has done an excellent job of creating a collection that holds together and covers a broad topic very well. At the same time, Petascale Computing remains accessible to anyone with HPC or scientific application experience. … The end result educates and informs our journey through petascale and into exascale, while serving to motivate us to travel as fast as we can toward the goal."
—John West, HPCwire
"This is an exciting period for HPC and a period which promises unprecedented discoveries ‘at scale’, which can provide tangible benefits for both science and society. This book provides a glimpse into the challenging work of petascale’s first wave of application and algorithm pioneers, and as such, provides an important context for both the present and the future."
—Francine Berman, Director, San Diego Supercomputer Center, La Jolla, California, USA
"This book provides a quick introduction on how the next generation of supercomputers will be used and a look into the future of large-scale scientific computing. The authors present many of the issues and challenges that face computational scientists in the effective use of the fastest computers."
—Jack Dongarra, University of Tennessee, Knoxville, USA
"The collection of articles in this book provides an excellent introduction to the state of the art in high-performance computing. Written by some of the best practitioners in the field and focused on real applications, it clearly illustrates the complex interplay between application characteristics, programming languages and libraries, and machine characteristics. Any person involved in the development of high-performance computing software will benefit from reading this timely book."
—Marc Snir, University of Illinois, Urbana-Champaign, USA
"A milestone book on petascale computing."
—Guojie Li, Chinese Academy of Sciences, Beijing
"There is a need for this book. Petascale systems are arriving in 2008 or so, and there will be a strong demand to demonstrate that these systems are useful. David Bader has collected an impressive list of topics and contributors. The content will be very relevant to the pursuit of effective petascale system use."
—Michael A. Heroux, Sandia National Laboratories, Albuquerque, New Mexico, USA
"A timely textbook for Japan’s next-generation supercomputer users in nanophysics, bioscience, and technology."
—Yoshio Oyanagi, Kogakuin University, Japan
"…this collection represents an academic milestone in the high-performance computing industry…"