محاسبات موازی: معماری‌ها، الگوریتم‌ها و کاربردها: [مقالات کنفرانس بین‌المللی ParCo 2007]

ParCo2007 marks a quarter of a century of the international conferences on parallel computing that started in Berlin in 1983. The aim of the conference is to give an overview of the state-of-the-art of the developments, applications and future trends in high performance computing for all platforms. The conference addresses all aspects of parallel computing, including applications, hardware and software technologies as well as languages and development environments. Special emphasis was placed on the role of high performance processing to solve real-life problems in all areas, including scientific, engineering and multidisciplinary applications and strategies, experiences and conclusions made with respect to parallel computing. The book contains papers covering: 1) Applications; The application of parallel computers to solve computationally challenging problems in the physical and life sciences, engineering, industry and commerce. The treatment of complex multidisciplinary problems occurring in all application areas was discussed. 2) Algorithms; Design, analysis and implementation of generic parallel algorithms, including their scalability, in particular to a large number of processors (MPP), portability and adaptability and 3) Software and Architectures; Software engineering for developing and maintaining parallel software, including parallel programming models and paradigms, development environments, compile-time and run-time tools. A number of symposia on specialized topics formed part of the scientific program. The following topics were covered: Parallel Computing with FPGAs, The Future of OpenMP in the Multi-Core Era, Scalability and Usability of HPC Programming Tools, DEISA: Extreme Computing in an Advanced Supercomputing Environment and Scaling Science Applications on Blue Gene. The conference was organized by the renowned research and teaching institutions Forschungszentrum Julich and the RWTH Aachen University in Germany. IOS Press is an international science, technical and medical publisher of high-quality books for academics, scientists, and professionals in all fields. Some of the areas we publish in: -Biomedicine -Oncology -Artificial intelligence -Databases and information systems -Maritime engineering -Nanotechnology -Geoengineering -All aspects of physics -E-governance -E-commerce -The knowledge economy -Urban studies -Arms control -Understanding and responding to terrorism -Medical informatics -Computer Sciences Title page......Page 1 Preface......Page 5 Contents......Page 10 Invited Talks......Page 21 Enhancing OpenMP and Its Implementation for Programming Multicore Systems......Page 23 Efficient Parallel Simulations in Support of Medical Device Design......Page 39 Particle and Atomistic Simulation......Page 47 Domain Decomposition for Electronic Structure Computations......Page 49 Load Balanced Parallel Simulation of Particle-Fluid DEM-SPH Systems with Moving Boundaries......Page 57 Communication and Load Balancing of Force-Decomposition Algorithms for Parallel Molecular Dynamics......Page 65 Aspects of a Parallel Molecular Dynamics Software for Nano-Fluidics......Page 73 Massively Parallel Quantum Computer Simulations: Towards Realistic Systems......Page 81 Image Processing and Visualization......Page 89 Lessons Learned Using a Camera Cluster to Detect and Locate Objects......Page 91 Hybrid Parallelization for Interactive Exploration in Virtual Environments......Page 99 Performance Modeling and Tools......Page 107 Analysis of the Weather Research and Forecasting (WRF) Model on Large-Scale Systems......Page 109 Analytical Performance Models of Parallel Programs in Clusters......Page 119 Computational Force: A Unifying Concept for Scalability Analysis......Page 127 Distribution of Periscope Analysis Agents on ALTIX 4700......Page 133 Visualizing Parallel Functional Program Runs: Case Studies with the Eden Trace Viewer......Page 141 Automatic Phase Detection of MPI Applications......Page 149 Biomedical Applications......Page 157 Experimenting Grid Protocols to Improve Privacy Preservation in Efficient Distributed Image Processing......Page 159 A Parallel Workflow for the Reconstruction of Molecular Surfaces......Page 167 HPC Simulation of Magnetic Resonance Imaging......Page 175 A Load Balancing Framework in Multithreaded Tomographic Reconstruction......Page 185 Parallel Algorithms......Page 193 Parallelisation of Block-Recursive Matrix Multiplication in Prefix Computations......Page 195 Parallel Exact Inference......Page 205 Efficient Parallel String Comparison......Page 213 Parallel Programming Models......Page 221 Implementing Data-Parallel Patterns for Shared Memory with OpenMP......Page 223 Generic Locking and Deadlock-Prevention with C++......Page 231 Parallelizing a Real-Time Steering Simulation for Computer Games with OpenMP......Page 239 A Framework for Performance-Aware Composition of Explicitly Parallel Components......Page 247 A Framework for Prototyping and Reasoning about Distributed Systems......Page 255 Formal Semantics Applied to the Implementation of a Skeleton-Based Parallel Programming Library......Page 263 Numerical Algorithms and Automatic Differentiation......Page 273 Strategies for Parallelizing the Solution of Rational Matrix Equations......Page 275 A Heterogeneous Pipelined Parallel Algorithm for Minimum Mean Squared Error Estimation with Ordered Successive Interference Cancellation......Page 283 OpenMP Implementation of the Householder Reduction for Large Complex Hermitian Eigenvalue Problems......Page 291 Multigrid Smoothers on Multicore Architectures......Page 299 Parallelization of Multilevel Preconditioners Constructed from Inverse-Based ILUs on Shared-Memory Multiprocessors......Page 307 Parallelism in Structured Newton Computations......Page 315 Automatic Computation of Sensitivities for a Parallel Aerodynamic Simulation......Page 323 Parallel Jacobian Accumulation......Page 331 Scheduling......Page 339 Layer-Based Scheduling Algorithms for Multiprocessor-Tasks with Precedence Constraints......Page 341 Unified Scheduling of I/O- and Computation-Jobs for Climate Research Environments......Page 349 Fault Tolerance......Page 357 Towards Fault Resilient Global Arrays......Page 359 Using AOP to Automatically Provide Distribution, Fault Tolerance, and Load Balancing to the CORBA-LC Component Model......Page 367 VirtuaLinux: Virtualized High-Density Clusters with no Single Point of Failure......Page 375 Performance Analysis......Page 383 Analyzing Cache Bandwidth on the Intel Core 2 Architecture......Page 385 Analyzing Mutual Influences of High Performance Computing Programs on SGI Altix 3700 and 4700 Systems with PARbench......Page 393 Low-level Benchmarking of a New Cluster Architecture......Page 401 Comparative Study of Concurrency Control on Bulk-Synchronous Parallel Search Engines......Page 409 Gb Ethernet Protocols for Clusters: An OpenMPI, TIPC, GAMMA Case Study......Page 417 Performance Measurements and Analysis of the BlueGene/L MPI Implementation......Page 425 Potential Performance Improvement of Collective Operations in UPC......Page 433 Parallel Data Distribution and I/O......Page 443 Optimization Strategies for Data Distribution Schemes in a Parallel File System......Page 445 Parallel Redistribution of Multidimensional Data......Page 453 Parallel I/O Aspects in PIMA(GE)2 Lib......Page 461 Fluid and Magnetohydrodynamics Simulation......Page 469 Parallelisation of a Geothermal Simulation Package: A Case Study on Four Multicore Architectures......Page 471 A Lattice Gas Cellular Automata Simulator on the Cell Broadband EngineTM......Page 479 Massively Parallel Simulations of Solar Flares and Plasma Turbulence......Page 487 Object-Oriented Programming and Parallel Computing in Radiative Magnetohydrodynamics Simulations......Page 495 Parallel Simulation of Turbulent Magneto-hydrodynamic Flows......Page 503 Pseudo-Spectral Modeling in Geodynamo......Page 511 Parallel Tools and Middleware......Page 519 Design and Implementation of a General-Purpose API of Progress and Performance Indicators......Page 521 Efficient Object Placement including Node Selection in a Distributed Virtual Machine......Page 529 Memory Debugging of MPI-Parallel Applications in Open MPI......Page 537 Hyperscalable Applications......Page 545 Massively Parallel All Atom Protein Folding in a Single Day......Page 547 Simulations of QCD in the Era of Sustained Tflop/s Computing......Page 555 Optimizing Lattice QCD Simulations on BlueGene/L......Page 563 Parallel Computing with FPGAs......Page 571 IANUS: Scientific Computing on an FPGA-Based Architecture......Page 573 Optimizing Matrix Multiplication on Heterogeneous Reconfigurable Systems......Page 581 Mini-Symposium "The Future of OpenMP in the Multi-Core Era"......Page 589 The Future of OpenMP in the Multi-Core Era......Page 591 Towards an Implementation of the OpenMP Collector API......Page 593 Mini-Symposium "Scaling Science Applications on Blue Gene"......Page 601 Scaling Science Applications on Blue Gene......Page 603 Turbulence in Laterally Extended Systems......Page 605 Large Simulations of Shear Flow in Mixtures via the Lattice Boltzmann Equation......Page 613 Simulating Materials with Strong Correlations on BlueGene/L......Page 621 Massively Parallel Simulation of Cardiac Electrical Wave Propagation on Blue Gene......Page 629 Mini-Symposium "Scalability and Usability of HPC Programming Tools"......Page 637 Scalability and Usability of HPC Programming Tools......Page 639 Benchmarking the Stack Trace Analysis Tool for BlueGene/L......Page 641 Scalable, Automated Performance Analysis with TAU and PerfExplorer......Page 649 Developing Scalable Applications with Vampir, VampirServer and VampirTrace......Page 657 Scalable Collation and Presentation of Call-Path Profile Data with CUBE......Page 665 Coupling DDT and Marmot for Debugging of MPI Applications......Page 673 Compiler Support for Efficient Instrumentation......Page 681 Comparing Intel Thread Checker and Sun Thread Analyzer......Page 689 Continuous Runtime Profiling of OpenMP Applications......Page 697 Mini-Symposium "DEISA: Extreme Computing in an Advanced Supercomputing Environment"......Page 705 DEISA: Extreme Computing in an Advanced Supercomputing Environment......Page 707 DEISA: Enabling Cooperative Extreme Computing in Europe......Page 709 Development Strategies for Modern Predictive Simulation Codes......Page 717 Submission Scripts for Scientific Simulations on DEISA......Page 725 Application Enabling in DEISA: Petascaling of Plasma Turbulence Codes......Page 733 HEAVY: A High Resolution Numerical Experiment in Lagrangian Turbulence......Page 741 Atomistic Modeling of the Membrane-Embedded Synaptic Fusion Complex: a Grand Challenge Project on the DEISA HPC Infrastructure......Page 749 Mini-Symposium "Parallel Computing with FPGAs"......Page 757 Parallel Computing with FPGAs - Concepts and Applications......Page 759 Parallel Computing with Low-Cost FPGAs: A Framework for COPACOBANA......Page 761 Accelerating the Cube Cut Problem with an FPGA-Augmented Compute Cluster......Page 769 A Run-time Reconfigurable Cache Architecture......Page 777 Novel Brain-Derived Algorithms Scale Linearly with Number of Processing Elements......Page 787 Programmable Architectures for Realtime Music Decompression......Page 797 The HARWEST High Level Synthesis Flow to Design a Special-Purpose Architecture to Simulate the 3D Ising Model......Page 805 Towards an FPGA Solver for the PageRank Eigenvector Problem......Page 813 Author Index......Page 821