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# Applied Parallel Computing: State of the Art in Scientific Computing

## byJack DongarraEditorKaj Madsen, Jerzy Wasniewski

### Paperback | March 3, 2006

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Introduction The PARA workshops in the past were devoted to parallel computing methods in science and technology. There have been seven PARA meetings to date: PARA'94, PARA'95 and PARA'96 in Lyngby, Denmark, PARA'98 in Umea, ? Sweden, PARA 2000 in Bergen, N- way, PARA 2002 in Espoo, Finland, and PARA 2004 again in Lyngby, Denmark. The ?rst six meetings featured lectures in modern numerical algorithms, computer science, en- neering, and industrial applications, all in the context of scienti?c parallel computing. This meeting in the series, the PARA 2004 Workshop with the title "State of the Art in Scienti?c Computing", was held in Lyngby, Denmark, June 20-23, 2004. The PARA 2004 Workshop was organized by Jack Dongarra from the University of Tennessee and Oak Ridge National Laboratory, and Kaj Madsen and Jerzy Was ´niewski from the Technical University of Denmark. The emphasis here was shifted to high-performance computing (HPC). The ongoing development of ever more advanced computers provides the potential for solving increasingly dif?cult computational problems. However, given the complexity of modern computer architectures, the task of realizing this potential needs careful attention. For example, the failure to exploit a computer's memory hi- archy can degrade performance badly. A main concern of HPC is the development of software that optimizes the performance of a given computer. The high cost of state-of-the-art computers can be prohibitive for many workplaces, especially if there is only an occasional need for HPC.

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Title:Applied Parallel Computing: State of the Art in Scientific ComputingFormat:PaperbackDimensions:1174 pages, 23.5 × 15.5 × 0.1 inPublished:March 3, 2006Publisher:Springer-Verlag/Sci-Tech/TradeLanguage:English

The following ISBNs are associated with this title:

ISBN - 10:3540290672

ISBN - 13:9783540290674

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Table of Contents

Invited Talks.- Fast and Reliable Random Number Generators for Scientific Computing.- New Generalized Data Structures for Matrices Lead to a Variety of High Performance Dense Linear Algebra Algorithms.- Management of Deep Memory Hierarchies - Recursive Blocked Algorithms and Hybrid Data Structures for Dense Matrix Computations.- Fortran Is Getting More and More Powerful.- Large-Scale Computations with the Unified Danish Eulerian Model.- Minisymposia.- Interval Methods: An Introduction.- A Chemical Engineering Challenge Problem That Can Benefit from Interval Methods.- Performance of Taylor Model Methods for Validated Integration of ODEs.- On the Use of Intervals in Scientific Computing: What Is the Best Transition from Linear to Quadratic Approximation?.- HPC-ICTM: The Interval Categorizer Tessellation-Based Model for High Performance Computing.- Counting the Number of Connected Components of a Set and Its Application to Robotics.- Interval-Based Markov Decision Processes for Regulating Interactions Between Two Agents in Multi-agent Systems.- A Domain Theoretic Account of Euler's Method for Solving Initial Value Problems.- Reliable Computation of Equilibrium States and Bifurcations in Nonlinear Dynamics.- A Verification Method for Solutions of Linear Programming Problems.- Compressing 3D Measurement Data Under Interval Uncertainty.- Computing Interval Bounds for Statistical Characteristics Under Expert-Provided Bounds on Probability Density Functions.- Interval Parallel Global Optimization with Charm++.- On the Approximation of Interval Functions.- The Distributed Interval Geometric Machine Model.- New Algorithms for Statistical Analysis of Interval Data.- On Efficiency of Tightening Bounds in Interval Global Optimization.- Trends in Large Scale Computing: An Introduction.- Ygdrasil: Aggregator Network Toolkit for Large Scale Systems and the Grid.- Enabling Coupled Scientific Simulations on the Grid.- High Performance Linear Algebra Algorithms: An Introduction.- Applying Software Testing Metrics to Lapack.- A Matrix-Type for Performance-Portability.- A New Array Format for Symmetric and Triangular Matrices.- A Family of High-Performance Matrix Multiplication Algorithms.- Substructuring, Dimension Reduction and Applications: An Introduction.- Parallel Algorithms for Balanced Truncation Model Reduction of Sparse Systems.- Towards an Optimal Substructuring Method for Model Reduction.- Model Reduction for RF MEMS Simulation.- A Model-Order Reduction Technique for Low Rank Rational Perturbations of Linear Eigenproblems.- Parallel Global Optimization of Foundation Schemes in Civil Engineering.- A Combined Linear and Nonlinear Preconditioning Technique for Incompressible Navier-Stokes Equations.- Structure-Preserving Model Reduction.- A Comparison of Parallel Preconditioners for the Sparse Generalized Eigenvalue Problems by Rayleigh-Quotient Minimization.- Theoretical Relations Between Domain Decomposition and Dynamic Substructuring.- Model Order Reduction for Large Scale Engineering Models Developed in ANSYS.- Rational Krylov for Large Nonlinear Eigenproblems.- Algebraic Sub-structuring for Electromagnetic Applications.- Parallel Processing in Science and Engineering: An Introduction.- Rapid Development of High-Performance Linear Algebra Libraries.- Automatic Derivation of Linear Algebra Algorithms with Application to Control Theory.- Cluster Computing for Financial Engineering.- Semi-automatic Generation of Grid Computing Interfaces for Numerical Software Libraries.- Rapid Development of High-Performance Out-of-Core Solvers.- ALPS: A Software Framework for Parallel Space-Time Adaptive Processing.- Hybrid Parallelization of CFD Applications with Dynamic Thread Balancing.- Distributed Computing: Tools, Paradigms and Infrastructures. An Introduction.- Parallelization of GSL: Performance of Case Studies.- Design of Policy-Based Security Mechanisms in a Distributed Web Services Architecture.- Supporting Location-Aware Distributed Applications on Mobile Devices.- Grid Application Development on the Basis of Web Portal Technology.- A Distributed Divide and Conquer Skeleton.- A Tool to Display Array Access Patterns in OpenMP Programs.- A Model Analysis of a Distributed Monitoring System Using a Multi-formalism Approach.- Performance Oriented Development and Tuning of GRID Applications.- Towards a Bulk-Synchronous Distributed Shared Memory Programming Environment for Grids.- High-Performance Computing in Earth- and Space-Science: An Introduction.- Applying High Performance Computing Techniques in Astrophysics.- Statistical Properties of Dissipative MHD Accelerators.- A Simulation Model for Forest Fires.- MHD Modeling of the Interaction Between the Solar Wind and Solar System Objects.- Implementing Applications with the Earth System Modeling Framework.- Parallel Discrete Event Simulations of Grid-Based Models: Asynchronous Electromagnetic Hybrid Code.- Electromagnetic Simulations of Dusty Plasmas.- Advanced Algorithms and Software Components for Scientific Computing: An Introduction.- Extending PSBLAS to Build Parallel Schwarz Preconditioners.- A Direct Orthogonal Sparse Static Methodology for a Finite Continuation Hybrid LP Solver.- Applying Parallel Direct Solver Techniques to Build Robust High Performance Preconditioners.- The Design of Trilinos.- Software Architecture Issues in Scientific Component Development.- Parallel Hybrid Sparse Solvers Through Flexible Incomplete Cholesky Preconditioning.- Parallel Heuristics for an On-Line Scientific Database for Efficient Function Approximation.- Software Engineering and Problem Solving Environments for Scientific Computing: An Introduction.- A General Architecture for Grid-Based PSE Toolkits.- An Expert Assistant for Computer Aided Parallelization.- Scalable Middleware Environment for Agent-Based Internet Applications.- Automatic Generation of Wrapper Code and Test Scripts for Problem Solving Environments.- Runtime Software Techniques for Enhancing High-Performance Applications: An introduction.- Efficient Execution of Scientific Computation on Geographically Distributed Clusters.- Improving the Performance of Large-Scale Unstructured PDE Applications.- A Runtime Adaptive Load Balancing Algorithm for Particle Simulations.- Evaluating Parallel Algorithms for Solving Sylvester-Type Matrix Equations: Direct Transformation-Based Versus Iterative Matrix-Sign-Function-Based Methods.- Performance Analysis for Parallel Adaptive FEM on SMP Clusters.- Performance Tuning of Matrix Triple Products Based on Matrix Structure.- Adapting Distributed Scientific Applications to Run-Time Network Conditions.- Sparse Direct Linear Solvers: An Introduction.- Oblio: Design and Performance.- Performance Analysis of Parallel Right-Looking Sparse LU Factorization on Two Dimensional Grids of Processors.- A Shared- and Distributed-Memory Parallel Sparse Direct Solver.- Simple and Efficient Modifications of Elimination Orderings.- Optimization of a Statically Partitioned Hypermatrix Sparse Cholesky Factorization.- Maximum-Weighted Matching Strategies and the Application to Symmetric Indefinite Systems.- An Evaluation of Sparse Direct Symmetric Solvers: An Introduction and Preliminary Findings.- Treatment of Large Scientific Problems: An Introduction.- Towards a Parallel Multilevel Preconditioned Maxwell Eigensolver.- On Improvement of the Volcano Search and Optimization Strategy.- Aggregation-Based Multilevel Preconditioning of Non-conforming FEM Elasticity Problems.- Efficient Solvers for 3-D Homogenized Elasticity Model.- Performance Evaluation of a Parallel Algorithm for a Radiative Transfer Problem.- Performance Evaluation and Design of Hardware-Aware PDE Solvers: An Introduction.- A Cache-Aware Algorithm for PDEs on Hierarchical Data Structures.- Constructing Flexible, Yet Run Time Efficient PDE Solvers.- Analyzing Advanced PDE Solvers Through Simulation.- Towards Cache-Optimized Multigrid Using Patch-Adaptive Relaxation.- Hierarchical Partitioning and Dynamic Load Balancing for Scientific Computation.- Cache Optimizations for Iterative Numerical Codes Aware of Hardware Prefetching.- Computationally Expensive Methods in Statistics: An Introduction.- Dimension Reduction vs. Variable Selection.- Reproducible Statistical Analysis in Microarray Profiling Studies.- Step-Down FDR Procedures for Large Numbers of Hypotheses.- Applying Security Engineering to Build Security Countermeasures: An Introduction.- CC-SEMS: A CC Based Information System Security Evaluation Management System.- A Secure Migration Mechanism of Mobile Agents Under Mobile Agent Environments.- A Flexible Privilege Management Scheme for Role Graph Model.- The System Modeling for Detections of New Malicious Codes.- Information Hiding Method Using CDMA on Wave Files.- Efficient Key Distribution Protocol for Electronic Commerce in Mobile Communications.- A Framework for Modeling Organization Structure in Role Engineering.- An Efficient Pointer Protection Scheme to Defend Buffer Overflow Attacks.- Contributed Talks.- Parallel Hierarchical Radiosity: The PIT Approach.- Optimizing Locationing of Multiple Masters for Master-Worker Grid Applications.- An OGSA-Based Bank Service for Grid Accounting Systems.- A Grid Resource Broker Supporting Advance Reservations and Benchmark-Based Resource Selection.- The Dragon Graph: A New Interconnection Network for High Speed Computing.- Speeding up Parallel Graph Coloring.- On the Efficient Generation of Taylor Expansions for DAE Solutions by Automatic Differentiation.- Edge-Disjoint Hamiltonian Cycles of WK-Recursive Networks.- Simulation-Based Analysis of Parallel Runge-Kutta Solvers.- A Novel Task Scheduling Algorithm for Distributed Heterogeneous Computing Systems.- Study of Load Balancing Strategies for Finite Element Computations on Heterogeneous Clusters.- Parallel Algorithms for the Determination of Lyapunov Characteristics of Large Nonlinear Dynamical Systems.- Online Task Scheduling on Heterogeneous Clusters: An Experimental Study.- A Parallel Method for Large Sparse Generalized Eigenvalue Problems by OmniRPC in a Grid Environment.- An Implementation of Parallel 3-D FFT Using Short Vector SIMD Instructions on Clusters of PCs.