Parallel Computing: Software Technology, Algorithms, Architectures & Applications (eBook)

Cover 1
Contents 12
Preface 6
Sponsors, Exhibitors / Participants in the industrial track 8
Committees 9
Part I: Invited Papers 22
Chapter 1. Parallel Machines and the "Digital Brain"- An Intricate Extrapolation on Occasion of JvN's 100-th Birthday 24
Chapter 2. So Much Data, So Little Time... 34
Part II: Software Technology 42
Chapter 3. On Compiler Support for Mixed Task and Data Parallelism 44
Chapter 4. Distributed Process Networks - Using Half FIFO Queues in CORBA 52
Chapter 5. An efficient data race detector backend for DIOTA 60
Chapter 6. Pipelined parallelism for multi-join queries on shared nothing machines 68
Chapter 7. Towards the Hierarchical Group Consistency for DSM systems : an efficient way to share data objects 76
Chapter 8. An operational semantics for skeletons 84
Chapter 9. A Programming Model for Tree Structured Parallel and Distributed Algorithms and its Implementation in a Java Environment 92
Chapter 10. A Rewriting Semantics for an Event-Oriented Functional Parallel Language 100
Chapter 11. RMI-like communication for migratable software components in HARNESS 108
Chapter 12. Semantics of a Functional BSP Language with Imperative Features 116
Chapter 13. The Use of Parallel Genetic Algorithms for Optimization in the Early Design Phases 124
Chapter 14. An Integrated Annotation and Compilation Framework for Task and Data Parallel Programming in Java 132
Chapter 15. On The Use of Java Arrays for Sparse Matrix Computations 140
Chapter 16. A Calculus of Functional BSP Programs with Explicit Substitution 148
Chapter 17. JToe: a Java API for Object Exchange 156
Chapter 18. A Modular Debugging Infrastructure for Parallel Programs 164
Chapter 19. Toward a Distributed Computational Steering Environment based on CORBA 172
Chapter 20. Parallel Decimation of 3D Meshes for Efficient Web-Based Isosurface Extraction 180
Part III: Parallel Programming 188
Chapter 21. MPI on a Virtual Shared Memory 190
Chapter 22. OpenMP vs. MPI on a Shared Memory Multiprocessor 198
Chapter 23. MPI and OpenMP implementations of Branch-and-Bound Skeletons 206
Chapter 24. Parallel Overlapped Block-Matching Motion Compensation Using MPI and OpenMP 214
Chapter 25. A comparison of OpenMP and MPI for neural network simulations on a SunFire 6800 222
Chapter 26. Comparison of Parallel Implementations of Runge-Kutta Solvers: Message Passing vs. Threads 230
Part IV: Scheduling 238
Chapter 27. Extending the Divisible Task Model for Workload Balancing in Clusters 240
Chapter 28. The generalized diffusion method for the load balancing problem 246
Chapter 29. Delivering High Performance to Parallel Applications Using Advanced Scheduling 254
Part V: Algorithms 262
Chapter 30. Multilevel Extended Algorithms in Structural Dynamics on Parallel Computers 264
Chapter 31. Parallel Model Reduction of Large-Scale Unstable Systems 272
Chapter 32. Parallel Decomposition Approaches for Training Support Vector Machines 280
Chapter 33. Fast parallel solvers for fourth-order boundary value problems 288
Chapter 34. Parallel Solution of Sparse Eigenproblems by Simultaneous Rayleigh Quotient Optimization with FSAI preconditioning 296
Chapter 35. An Accurate and Efficient Selfverifying Solver for Systems with Banded Coefficient Matrix 304
Chapter 36. 3D parallel calculations of dendritic growth with the lattice Boltzmann method 312
Chapter 37. Distributed Negative Cycle Detection Algorithms 318
Chapter 38. A Framework for Seamlesly Making Object Oriented Applications Distributed 326
Chapter 39. Performance Evaluation of Parallel Genetic Algorithms for Optimization Problems of Different Complexity 334
Chapter 40. Extensible and Customizable Just-In-Time Security (JITS) Management of Client- Server Communication in Java 342
Part VI: Applications & Simulation
Chapter 41. An Object-Oriented Parallel Multidisciplinary Simulation System„The SimServer 352
Chapter 42. Computer Simulation of Action Potential Propagation on Cardiac Tissues: An Efficient and Scalable Parallel Approach 360
Chapter 43. MoDySim- A parallel dynamical UMTS simulator 368
Chapter 44. apeNEXT: a Multi-TFlops Computer for Elementary Particle Physics 376
Chapter 45. The Parallel Model System LM-MUSCAT for Chemistry-Transport Simulations: Coupling Scheme, Parallelization and Applications 384
Chapter 46. Real-time Visualization of Smoke through Parallelizations 392
Chapter 47. Parallel Simulation of Cavitated Flows in High Pressure Systems 400
Chapter 48. Improvements in black hole detection using parallelism 408
Chapter 49. High Throughput Computing for Neural Network Simulation 416
Chapter 50. Parallel algorithms and data assimilation for hydraulic models 424
Part VII: Multimedia Applications 434
Chapter 51. Parallelization of VQ Codebook Generation using Lazy PNN Algorithm 436
Chapter 52. A Scalable Parallel Video Server Based on Autonomous Network-attached Storage 444
Chapter 53. Efficient Parallel Search in Video Databases with Dynamic Feature Extraction 452
Part VIII: Architectures 460
Chapter 54. Introspection in a Massively Parallel PIM-Based Architecture 462
Chapter 55. Time-Transparent Inter-Processor Connection Reconfiguration in Parallel Systems Based on Multiple Crossbar Switches 470
Chapter 56. SIMD design to solve partial differential equations 478
Part IX: Caches 486
Chapter 57. Trade-offs for Skewed-Associative Caches 488
Chapter 58. Cache Memory Behavior of Advanced PDE Solvers 496
Part X: Performance 504
Chapter 59. A Comparative Study of MPI Implementations on a Cluster of SMP Workstations 506
Chapter 60. MARMOT: An MPI Analysis and Checking Tool 514
Chapter 61. BenchIT„Performance Measurement and Comparison for Scientific Applications 522
Chapter 62. Performance Issues in the Implementation of the M-VIA Communication Software 530
Chapter 63. Performance and performance counters on the Itanium 2 „ A benchmarking case study 538
Chapter 64. On the parallel prediction of the RNA secondary structure 546
Part XI: Clusters 554
Chapter 65. MDICE– a MATLAB Toolbox for Efficient Cluster Computing 556
Chapter 66. Parallelization of Krylov Subspace Methods in Multiprocessor PC Clusters 564
Chapter 67. First Impressions of Different Parallel Cluster File Systems 572
Chapter 68. Fast Parallel I/O on ParaStation Clusters 580
Chapter 69. PRFX : a runtime library for high performance programming on clusters of SMP nodes 590
Part XII: Grids 598
Chapter 70. Experiences about Job Migration on a Dynamic Grid Environment 600
Chapter 71. Security in a Peer-to-Peer Distributed Virtual Environment 608
Chapter 72. A Grid Environment for Diesel Engine Chamber Optimization 620
Chapter 73. A Broker Architecture for Object-Oriented Master/Slave Computing in a Hierarchical Grid System 630
Chapter 74. A framework for experimenting with structured parallel programming environment design 638
Part XIII: Minisymposium - Grid Computing 646
Chapter 75. Considerations for Resource Brokerage and Scheduling in Grids 648
Chapter 76. Job Description Language and User Interface in a Grid context: The EU DataGrid experience 656
Chapter 77. On Pattern Oriented Software Architecture for the Grid 664
Part XIV: Minisymposium- Bioinformatics 672
Chapter 78. Green Destiny + mpiBLAST = Bioinfomagic 674
Chapter 79. Parallel Processing on Large Redundant Biological Data Sets: Protein Structures Classification with CEPAR 682
Chapter 80. MDGRAPE-3: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations 690
Chapter 81. Structural Protein Interactions: From Months to Minutes 698
Chapter 82. Spatially Realistic Computational Physiology: Past, Present and Future 706
Chapter 83. Cellular automaton modeling of pattern formation in interacting cell systems 716
Chapter 84. Numerical Simulation for eHealth: Grid-enabled Medical Simulation Services 726
Chapter 85. Parallel computing in biomedical research and the search for peta-scale biomedical applications 740
Part XV: Minisymposium- Performance Analysis 748
Chapter 86. Big Systems and Big Reliability Challenges 750
Chapter 87. Scalable Performance Analysis of Parallel Systems: Concepts and Experiences 758
Chapter 88. CrossWalk: A Tool for Performance Profiling Across the User-Kernel Boundary 766
Chapter 89. Hardware-Counter Based Automatic Performance Analysis of Parallel Programs 774
Chapter 90. Online Performance Observation of Large-Scale Parallel Applications 782
Chapter 91. Deriving analytical models from a limited number of runs 790
Chapter 92. Performance Modeling of HPC Applications 798
Part XVI: Minisymposium - OpenMP 806
Chapter 93. Thread based OpenMP for nested parallelization 808
Chapter 94. OpenMP on Distributed Memory via Global Arrays 816
Chapter 95. Performance Simulation of a Hybrid OpenMP/MPI Application with HeSSE 824
Chapter 96. An environment for OpenMP code parallelization 832
Chapter 97. Hindrances in OpenMP programming 840
Chapter 98. Wavelet-Based Still Image Coding Standards on SMPs using OpenMP 848
Part XVII: Minisymposium - Parallel Applications 856
Chapter 99. Parallel Solution of the Bidomain Equations with High Resolutions 858
Chapter 100. Balancing Domain Decomposition Applied to Structural Analysis Problems 866
Chapter 101. Multiperiod Portfolio Management Using Parallel Interior Point Method 874
Chapter 102. Performance of a parallel split operator method for the time dependent Schrödinger equation 882
Part XVIII: Minisymposium - Cluster Computing 890
Chapter 103. Design and implementation of a 512 CPU cluster for general purpose supercomputing 892
Chapter 104. Experiences Parallelizing, Configuring, Monitoring, and Visualizing Applications for Clusters and Multi-Clusters 900
Chapter 105. Cluster Computing as a Teaching Tool 908
Part XIX: Minisymposium- Mobile Agents 916
Chapter 106. Mobile Agents Principles of Operation 918
Chapter 107. Mobile Agent Application Fields 926
Chapter 108. Mobile Agents and Grid Computing 934
Chapter 109. Mobile Agents, Globus and Resource Discovery 940
Chapter 110. A Mobile Agent Tool for Resource Discovery 948
Chapter 111. Mobile Agents and Knowledge Discovery in Ubiquitous Computing 956
Author & Subject Index
Author Index 966
Subject Index 972