Parallel Computing: Architectures, Algorithms and Applications

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