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PETASCALE COMPUTING: Algorithms and Applications Edited by David A PETASCALE COMPUTING ALGORITHMS AND APPLICATIONS C9098_FM.indd 1 11/15/07 1:38:55 PM Chapman & Hall/CRC Computational Science Series SERIES EDITOR Horst Simon Associate Laboratory Director, Computing Sciences Lawrence Berkeley National Laboratory Berkeley, California, U.S.A. AIMS AND SCOPE This series aims to capture new developments and applications in the field of computational sci- ence through the publication of a broad range of textbooks, reference works, and handbooks. Books in this series will provide introductory as well as advanced material on mathematical, sta- tistical, and computational methods and techniques, and will present researchers with the latest theories and experimentation. The scope of the series includes, but is not limited to, titles in the areas of scientific computing, parallel and distributed computing, high performance computing, grid computing, cluster computing, heterogeneous computing, quantum computing, and their applications in scientific disciplines such as astrophysics, aeronautics, biology, chemistry, climate modeling, combustion, cosmology, earthquake prediction, imaging, materials, neuroscience, oil exploration, and weather forecasting. PUBLISHED TITLES PETASCALE COMPUTING: Algorithms and Applications Edited by David A. Bader C9098_FM.indd 2 11/15/07 1:38:55 PM PETASCALE COMPUTING ALGORITHMS AND APPLICATIONS EDITED BY DAVID A. BADER Georgia Institute of Technology Atlanta, U.S.A. C9098_FM.indd 3 11/15/07 1:38:56 PM Chapman & Hall/CRC Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2008 by Taylor & Francis Group, LLC Chapman & Hall/CRC is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Printed in the United States of America on acid-free paper 10 9 8 7 6 5 4 3 2 1 International Standard Book Number-13: 978-1-58488-909-0 (Hardcover) This book contains information obtained from authentic and highly regarded sources. Reprinted material is quoted with permission, and sources are indicated. A wide variety of references are listed. Reasonable efforts have been made to publish reliable data and information, but the author and the publisher cannot assume responsibility for the validity of all materials or for the conse- quences of their use. Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, please access www. copyright.com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC) 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and registration for a variety of users. For organizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged. Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe. Library of Congress Cataloging-in-Publication Data Petascale computing : algorithms and applications / editor, David A. Bader. p. cm. -- (Computational science series) Includes bibliographical references and index. ISBN 978-1-58488-909-0 (hardback : alk. paper) 1. High performance computing. 2. Petaflops computers. 3. Parallel processing (Electronic computers) I. Bader, David A. II. Title. III. Series. QA76.88.P475 2007 004’.35--dc22 2007044024 Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com C9098_FM.indd 4 11/15/07 1:38:56 PM To Sadie Rose v Chapman & Hall/CRC Computational Science Series Computational science, the scientific investigation of physical processes through modelling and simulation on computers, has become generally accepted as the third pillar of science, complementing and extending theory and experimen- tation. This view was probably first expressed in the mid-1980s. It grew out of an impressive list of accomplishments in such diverse areas as astrophysics, aeronautics, chemistry, climate modelling, combustion, cosmology, earthquake prediction, imaging, materials, neuroscience, oil exploration, and weather fore- casting. Today, in the middle of the first decade of the 21st century, the pace of innovation in information technology is accelerating, and consequently the opportunities for computational science and engineering abound. Computa- tional science and engineering (CSE) today serves to advance all of science and engineering, and many areas of research in the future will be only accessible to those with access to advanced computational technology and platforms. Progress in research using high performance computing platforms has been tightly linked to progress in computer hardware on one side and progress in software and algorithms on the other, with both sides generally acknowl- edged to contribute equally to the advances made by researchers using these technologies. With the arrival of highly parallel compute platforms in the mid- 1990s, several subtle changes occurred that changed the face of CSE in the last decade. Because of the complexities of large-scale hardware systems and the increasing sophistication of modelling software, including multi-physics and multiscale simulation, CSE increasingly became a team science. The most successful practitioners of CSE today are multidisciplinary teams that include mathematicians and computer scientists. These teams have set up a software infrastructure, including a support infrastructure, for large codes that are well maintained and extensible beyond the set of original developers. The importance of CSE for the future of research accomplishments and economic growth has been well established. “Computational science is now indispensable to the solution of complex problems in every sector, from tradi- tional science and engineering domains to such key areas as national security, public health, and economic innovation,” is the principal finding of the re- cent report of the President’s Information Technology Advisory Committee (PITAC) in the U.S. (President’s Information Technology Advisory Commit- tee, Computational Science: Ensuring America’s Competitiveness , Arlington, Virginia: National Coordination Office for Information Technology Research and Development, 2005, p. 2.) vii viii As advances in computational science and engineering continue to grow at a rapid pace, it becomes increasingly important to present the latest research and applications to professionals working in the field. Therefore I welcomed the invitation by Chapman & Hall/CRC Press to become series editor and start this new series of books on computational science and engineering. The series aims to capture new developments and applications in the field of com- putational science, through the publication of a broad range of textbooks, ref- erence works, and handbooks. By integrating mathematical, statistical, and computational methods and techniques, the titles included in the series are meant to appeal to students, researchers, and professionals, as well as interdis- ciplinary researchers and practitioners who are users of computing technology and practitioners of computational science. The inclusion of concrete exam- ples and applications is highly encouraged. The scope of the series includes, but is not limited to, titles in the areas of scientific computing, parallel and distributed computing, high performance computing, grid computing, cluster computing, heterogeneous computing, quantum computing, and their appli- cation in scientific areas such as astrophysics, aeronautics, biology, chemistry, climate modelling, combustion, cosmology, earthquake prediction, imaging, materials, neuroscience, oil exploration, and weather forecasting, and others. With this goal in mind I am very pleased to introduce the first book in the series, Petascale Computing: Algorithms and Applications, edited by my good colleague and friend David Bader. This book grew out of a workshop at Schloss Dagstuhl in February 2006, and is a perfect start for the series. It is probably the first book on real petascale computing. At the beginning of an exciting new phase in high performance computing, just as we are about to enter the age of petascale performance, the chapters in the book will form an ideal starting point for further investigations. They summarize the state of knowledge in algorithms and applications in 2007, just before the first peta- scale systems will become available. In the same way as petascale computing will open up new and unprecedented opportunities for research in computa- tional science, I expect this current book to lead the new series to a deeper understanding and appreciation of research in computational science and en- gineering. Berkeley, May 2007 Dr. Horst Simon Series Editor Associate Laboratory Director, Computing Sciences Lawrence Berkeley National Laboratory Foreword Over the last few decades, there have been innumerable science, engineering and societal breakthroughs enabled by the development of high performance computing (HPC) applications, algorithms, and architectures. These powerful tools have provided researchers, educators, and practitioners the ability to computationally
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