Algorithms and Data Structures for External Memory

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Algorithms and Data Structures for External Memory Jeffrey Scott Vitter Department of Computer Science Purdue University West Lafayette Indiana, 47907–2107 USA jsv@purdue.edu Boston – Delft
Foundations and Trends R○ in Theoretical Computer Science Published, sold and distributed by: now Publishers Inc. PO Box 1024 Hanover, MA 02339 USA Tel. +1-781-985-4510 www.nowpublishers.com sales@nowpublishers.com Outside North America: now Publishers Inc. PO Box 179 2600 AD Delft The Netherlands Tel. +31-6-51115274 The preferred citation for this publication is J. S. Vitter, Algorithms and Data Structures for External Memory, Foundation and Trends R○ in Theoretical Computer Science, vol 2, no 4, pp 305–474, 2006 ISBN: 978-1-60198-106-6 c○ 2008 J. S. Vitter 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, photocopying, recording or otherwise, without prior written permission of the publishers. Photocopying. In the USA: This journal is registered at the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923. Authorization to photocopy items for internal or personal use, or the internal or personal use of specific clients, is granted by now Publishers Inc. for users registered with the Copyright Clearance Center (CCC). The ‘services’ for users can be found on the internet at: www.copyright.com For those organizations that have been granted a photocopy license, a separate system of payment has been arranged. Authorization does not extend to other kinds of copying, such as that for general distribution, for advertising or promotional purposes, for creating new collective works, or for resale. In the rest of the world: Permission to photocopy must be obtained from the copyright owner. Please apply to now Publishers Inc., PO Box 1024, Hanover, MA 02339, USA; Tel. +1-781-871-0245; www.nowpublishers.com; sales@nowpublishers.com now Publishers Inc. has an exclusive license to publish this material worldwide. Permission to use this content must be obtained from the copyright license holder. Please apply to now Publishers, PO Box 179, 2600 AD Delft, The Netherlands, www.nowpublishers.com; e-mail: sales@nowpublishers.com
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Page 6 and 7: Foundations and Trends R○ in Theo
Page 8 and 9: Foundations and Trends R○ in Theo
Page 10 and 11: Preface I first became fascinated a
Page 12: Preface xi I would like to thank my
Page 15 and 16: xiv Contents 6 Lower Bounds on I/O
Page 18 and 19: 1 Introduction The world is drownin
Page 20 and 21: However, not all memory references
Page 22 and 23: 1.1 Overview 5 Our general goal is
Page 24: Table 1.1 Paradigms for I/O efficie
Page 27 and 28: 10 Parallel Disk Model (PDM) spindl
Page 29 and 30: 12 Parallel Disk Model (PDM) D = nu
Page 31 and 32: 14 Parallel Disk Model (PDM) The pr
Page 33 and 34: 16 Parallel Disk Model (PDM) 2.3 Re
Page 35 and 36: 18 Parallel Disk Model (PDM) archit
Page 38 and 39: 3 Fundamental I/O Operations and Bo
Page 40: As Table 3.1 indicates, the multipl
Page 43 and 44: 26 Exploiting Locality and Load Bal
Page 45 and 46: 28 Exploiting Locality and Load Bal
Page 47 and 48: 30 External Sorting and Related Pro
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36 External Sorting and Related Pro
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6 Lower Bounds on I/O In this chapt
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6.1 Permuting 59 in backwards order
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6.2 Lower Bounds for Sorting and Ot
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6.2 Lower Bounds for Sorting and Ot
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66 Matrix and Grid Computations the
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8 Batched Problems in Computational
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8.1 Distribution Sweep 71 Goodrich
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8.1 Distribution Sweep 73 the curre
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Time (seconds) Time (seconds) 7000
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9 Batched Problems on Graphs The pr
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Table 9.2 Best known I/O bounds for
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9.2 Special Cases 81 that contains
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10 External Hashing for Online Dict
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2 000 000 001 010 011 100 101 110 1
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10.2 Directoryless Methods 87 a tot
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11 Multiway Tree Data Structures In
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11.1 B-trees and Variants 91 “sha
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11.3 Parent Pointers and Level-Bala
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11.4 Buffer Trees 95 I/Os by follow
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11.4 Buffer Trees 97 between update
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100 Spatial Data Structures and Ran
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13 Dynamic and Kinetic Data Structu
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13.2 Continuously Moving Items 121
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14 String Processing In this chapte
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5 a b a 3 c a 0 b a 4 b 6 6 a b a b
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14.3 Suffix Trees and Suffix Arrays
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15 Compressed Data Structures The f
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15.1 Data Representations and Compr
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15.2 External Memory Compressed Dat
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140 Dynamic Memory Allocation For s
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142 External Memory Programming Env
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144 External Memory Programming Env
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146 Conclusions intriguing connecti
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148 Notations and Acronyms lowercas
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150 Notations and Acronyms � �
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152 References Proceedings of the A
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154 References [41] L. Arge, K. H.
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156 References Computer Science, pp
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158 References ACM Conference on In
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160 References [132] F. K. H. A. De
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162 References [165] R. W. Floyd,
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164 References [195] M. R. Henzinge
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166 References [228] K. Küspert,
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168 References [261] D. R. Morrison
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170 References [293] J. T. Robinson
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172 References [325] “TerraServer
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174 References [356] O. Wolfson, P.
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