High Performance Computing Systems and Applications PDF
Preview High Performance Computing Systems and Applications
HIGH PERFORMANCE COMPUTING SYSTEMS AND APPLICATIONS THE KLUWER INTERNATIONAL SERIES IN ENGINEERING AND COMPUTER SCIENCE HIGH PERFORMANCE COMPUTING SYSTEMS AND APPLICATIONS edited by Nikitas J. Dimopoulos Kin F. Li Department of Electrical and Computer Engineering University of Victoria, Canada SPRINGER SCIENCE+BUSINESS MEDIA, LLC ISBN 978-1-4613-5269-3 ISBN 978-1-4615-0849-6 (eBook) DOI 10.1007/978-1-4615-0849-6 Library of Congress Cataloging-in-Publication Data A CLP. Catalogue record for this book is available from the Library of Congress. Copyright © 2002 by Springer Science+Business Media New York Originally published by Kluwer Academic Publishers in 2002 Softcover reprint of the hardcover 1st edition 2002 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, mechanical, photo-copying, recording, or otherwise, without the prior written permission of the publisher. Printed on acid-free paper. Contents Preface ix Part I Keynote Presentation 1 C3.ca: The State of Our Union 3 Andrew Pollard Part II Distributed Systems and Architecture 2 A Performance Evaluation of the ACORN Architecture 9 Virendra C. Bhavsar, Ali A. Ghorbani and Stephen Marsh 3 Towards a High Performance Extensible Grid Architecture 21 Klaus Krauter and Muthucumaru Maheswaran 4 On the Feasibility of Time-Parallel Discrete Event Simulations over 39 Local and WIde Area Networks loanis Nikolaidis 5 A Mobile Agent-based Approach to Web-based Distributed Computing 61 Qusay H. Mahmoud 6 A Qynamic Scheme in Support of Scalability in General Purpose 69 Distributed Virtual Environments Randy Fortier and Robert D. Kent Part III Numerical Methods and Simulation 7 Accuracy of Monte Carlo Method for Solution of Linear Algebraic 89 Equations Using PLFG and randO VI HIGH PERFORMANCE COMPUTING SYSTEMS AND APPLICATIONS Chih Jeng Kenneth Tan, Maria Isabel Casas Villalba and Vassil Alexandrov 8 Numerical Simulation of the Growth of GaxInl-xSb by the Trav- 103 elling Heater Method S. Dost, R. A. Meric, B. Lent and R. F. Redden 9 High Performance Computation for Time Domain Electromagnetic 123 Simulations E.Q. Hu, M. Fujii, P.P.M. So, W. Liu, J. W. Park and W.J.R. Hoefer Part IV Network Algorithms and Protocols 10 Modelling of Adaptive Wormhole-Routed Hypercubes in the Pres- 133 ence of Broadcast Traffic A. Shahmbi, L. M. Mackenzie and M. Ould-Khaoua 11 Frame-Based Fair Queueing: A Hardware Design for ATM Networks 149 Hossam Fattah, M. Watheq EI-Khamshi and Fayez Eiguibaly 12 Analysis of Frame-Based Fair Queueing under Self-Similar Traffic 161 Hossam Fattah and Fayez Elguibaly Part V Computer Architecture I 13 Reducing Cache Miss Penalty Using I-Fetch Instructions 177 Shusuke Okamoto and Takata K azuyoshi 14 Reducing Indirect Mispredictions of Two-STAGE Branch Predictors 187 Yul Chu and M. R. Ito 15 Data Prefetching Using Dual Processors 207 See-Mu Kim and S Manohamn Part VI Computer Architecture II 16 THOR: A Multi-purpose Commodity Component Supercomputer 223 James L. Pinfold 17 A New Methodology for Stack Operations Folding for Java Microprocessors 235 M. Watheq El-Khamshi, Fayez Eiguibaly and Kin F. Li Contents vii 18 Communication Prediction in Message-Passing Multiprocessors 253 Ahmad A/sahi and Nikitas J. Dimopoulos Part VII Distributed Memory 19 A Preliminary Study of Cache-Only Write Detection Technique for 275 Nautilus DSM Mario Donato Marino and Geraldo Lino de Campos 20 Analysis of?-Lightweight Transport Protocol for High-Performance 291 Computmg M. A. R. Dantas, M. V.G.R. Lima and M.R.A. Rodrigues 21 The GENESIS Cluster Operating System Supporting Parallel Processing 301 A. Goscinski, M. Hobbs and J. Silcock Part VIII High Performance Computing Applications I 22 UsiIlg a HPC System for the Simulation of the Trajectories of Solar 317 Wind Particles in the Ionosphere Gladimir V. G. Baranoski and Jon G. Rokne 23 Parallel MHD for Large-scale Plasma Simulation 331 Robert Rankin and Serguei Roupassov Part IX Parallel Algorithms 24 Parallel Broadcasting Scheme for Approximate String Matching 355 with K-Mismatches Jin Hwan Park and Keqin Li 25 Organization and Evaluation of Parallel Logic Simulator on a PC 375 Cluster Koichi Wada, Tetsuya Murakami and Yukari Hamada 26 Block Based Compression Storage Expected Performance 389 Stamatis Vassiliadis, Sorin Cotofana, and Pyrrhos Stathis 27 Distributing Fast Fourier Transform Algorithms for Grid Computing 407 Robert D. Kent, Neeta Majmudar, and Mordechay Schlesinger viii HIGH PERFORMANCE COMPUTING SYSTEMS AND APPLICATIONS Part X High Performance Computing Applications II 28 Netcaches on Engineering and Commercial Applications 427 Edward David Moreno 29 Monte Carlo and molecular dynamics studies of peptide-membrane 447 binding Craig M. Shepherd, Hans J. Vogel and Andre H. Juffer 30 An Analysis of Immediate Memory: The free-recall task 465 D. R. J. Franklin and D. J. K. Mewhort 31 Numerical Simulation of Unsteady Separated Flow and Convective 481 Heat Transfer N. Djilali and A. Suksangpanomrung Part XI Astrophysics Applications 32 High Performance Computational Astrophysics with PKDGRAV / 501 GASOLINE Joachim Stadel, James Wadsley and Derek C. Richardson Index 525 Preface This Volume includes a selection of papers presented at the 14th In ternational Conference on High Performance Computing Systems and Applications held at the University of Victoria campus June 14th to 17th 2000. It attracted 105 participants from around the world, including Japan, The Netherlands, U.S.A., Brazil, U.K. and Canada. The Symposium included a rich program of technical sessions inter mixed with plenary presentations and vendor demonstrations. The technical presentations spanned a number of topics at the state of the art in High Performance Computing Systems and Applications ranging from applications in astrophysics and space physics, to cluster computing, to numerical simulations for fluid dynamics, electromagnet ics and crystal growth, to networks and the Grid, to biology and monte carlo techniques, to distributed systems, and to computer architecture and performance analysis. Dr. Andrew Pollard, the Chair of the Board of Directors of C3.ca gave the keynote address on the status and future of High Performance Computing in Canada. In the plenary session that followed lunch in the first day, Mr. P. Tannenbaum of NEC HNSX presented the Earth Simu lator NEC is currently constructing. The plenary sessions of the second day included talks by Mr. Barry Crume of HP on "what is new on the Horizon for Technical Computing" and by Dr. Ken Jacobson from SGI on "Differentiated Super Computing in the Age of Commoditization" . The second day also included a morning session on the Grid project moderated by Dr. Brian Unger of iCORE who also gave an entertain ing address during lunch on "the Alberta Informatics Circle of Research Excellence (iCORE) and HPC" . The last day included two very informative plenary talks given by Bill Pulleyblank of IBM T.J. Watson Research Center on "Deep Computing: Proteins, petaflops and algorithms" and by Dr. G. Lake of University of Washington on "From Sir Isaac to Petafiop Computing-Calculating the Structure and-Chaos Owing to Gravity in the Universe" x HIGH PERFORMANCE COMPUTING SYSTEMS AND APPLICATIONS Breaking with tradition, the Conference Banquet was held on the first evening of the Conference at the Dunsmuir Lodge where the delegates were owed by the magnificent vistas of the Saanich Peninsula, the Gulf Islands, the straights of Georgia, and Mount Baker in the far reaches of the horizon. The Conference Reception was held in the evening of the second day in the eclectic surroundings of UVic's Maltwood Art Gallery. The papers included in this Volume have been fully refereed by an international panel of experts. We would like to thank them for the exceptional job they did in ensuring the high quality of contributions: • A. Afsahi • P. Agathoklis • A. Babul • A. Barak • G. Baranoski • M. Berg • V. Bhavsar • J. Bornemann • A. Calder • S. Cotofana • D. Dai • M. A. R. Dantas • F. Darema • V. Dimakopoulos • N. Djilali • R. Fujimoto • A. Goscinski • M. R. Ito • D. Kaeli • A. Karaivanova • R. Kent • K. Krauter • I. Nikolaidis • S. Manoharan • S. March • M. Marino • M. Mascagni • M. Mason • E. Moreno • S. Okamoto • Y. Pan • J. H. Park • A. Pollard
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