ISBN: 3-540-65414-3
TITLE: Applied Parallel Computing. Large Scale Scientific and Industrial Problems
AUTHOR: Kagstrm, Bo; Dongarra, Jack; Elmroth, Erik; Wasniewski, Jerzy (Eds.)
TOC:

Speaker information
Communications Latency Hiding Techniques for a Reconfigurable Optical Interconnect: Benchmark Studies 1
A. Afsahi, N.J. Dimopoulos
Multifrontal Solvers Within the PARASOL Environment 7
P. Amestoy, I. Duff, J.-Y. L'Excellent
Parallelization of a 3D FD-TD Code for the Maxwell Equations Using MPI 12
U. Andersson
Advanced Calculations and Visualization of Enzymatic Reactions with the Combined Quantum Classical Molecular Dynamics Code 20
P. Bala, P. Grochowski, K. Nowinski, T. Clark, B. Lesyng, J.A. McCammon
Memory Access Profiling Tools for Alpha-based Architectures 28
S. M. Balle, S.C. Steely, Jr.
Parallelized BlockStructured NewtonType Methods in Dynamic Process Simulation 38
J. Borchardt
Tuning the Performance of Parallel Programs on NOWs Using Performance Analysis Tool 43
M. Bubak, W. Funika, J. Moscinski
Numerical Simulation of 3D Fully Nonlinear Water Waves on Parallel Computers 48
X. Cai Fluctuations in the Defect Creation by Ion Beam Irradiation 56
R. Chakarova, I. Pzsit
Parallelisation of an Industrial Hydrodynamics Application Using the PINEAPL Library 63
T. Christensen, A.R. Krommer, J. Larsen, L. Srensen
Hyper-Rectangle Selection Strategy for Parallel Adaptive Numerical Integration 71
R. Ciegis, R. ablinskas, J. Wasniewski
1 Bold style indicates the invited speaker. Underline indicates the speaker 
Parallelising Fuzzy Queries for Spatial Data Modelling on a Cray T3D 76
A. Clematis, A. Coda, M. Spagnuolo, S. Spinello, T. Sloan
Hyper-Systolic Implementation of BLAS-3 Routines on the APE100/Quadrics Machine 82
M. Coletta, T. Lippert, P. Palazzari
Resource Management for Ultra-scale Computational Grid Applications 88
K. Czajkowski, I. Foster, C. Kesselman
A ScaLAPACK-Style Algorithm for Reducing a Regular Matrix Pair to Block Hessenberg-Triangular Form 95
K. Dackland, B. Kgstrm
Parallel Tight-Binding Molecular Dynamics Code Based on Integration of HPF and Optimized Parallel Libraries 104
B. Di Martino, M. Celino, M. Briscolini, L. Colombo, S. Filippone, V. Rosato
Parallel Computation of Multidimensional Scattering Wavefunctions for Helmholtz/Schroedinger Equations 112
A. Edlund, I. Bar-On, U. Peskin
New Serial and Parallel Recursive QR Factorization Algorithms for SMP Systems 120
E. Elmroth, F. Gustavson
Visualization of CFD Computations 129
J. Engstrm
Improving the Performance of Scientific Parallel Applications in a Cluster of Workstations 134
A. Flores, J.M. Garca
On the Parallelisation of Non-linear Optimisation Algorithms for Ophthalmical Lens Design 142
E. Fontdecaba Baig, J.M. Cela Espn, J.C. Drsteler Lopez
Modelica - A Language for Equation-Based Physical Modeling and High Performance Simulation 149
P. Fritzson
Distributed Georeferring of Remotely Sensed Landsat-TM Imagery Using MPI 161
J.D. Garca-Consuegra, J.A. Gallud, G. Sebastin
Parallel Test Pattern Generation Using Circuit Partitioning in a Shared-Memory Multiprocessor 167
C. Gil, J. Ortega, J.L. Bernier, M.D. Gil
Parallel Adaptive Mesh Refinement for Large Eddy Simulation Using the Finite Element Method 172
D. Golden, N. Hurley, S. McGrath
WSSMP: A High-Performance Serial and Parallel Symmetric Sparse Linear Solver 182
A. Gupta, M. Joshi, V. Kumar
Recursive Blocked Data Formats and BLAS's for Dense Linear Algebra Algorithms 195
F. Gustavson, A. Henriksson, I. Jonsson, B. Kgstrm, P. Ling
Superscalar GEMM-based Level 3 BLAS  The On-going Evolution of a Portable and High-Performance Library 207
F. Gustavson, A. Henriksson, I. Jonsson, B. Kgstrm, P. Ling
Parallel Solution of Some Large-Scale Eigenvalue Problems Arising in Chemistry and Physics 216
D.L. Harrar II, M.R. Osborne
An Embarrassingly Parallel ab initio MD Method for Liquids 224
F. Hedman, A. Laaksonen
A New Parallel Preconditioner for the Euler Equations 230
L. Hemmingsson, A. Khri
Partitioning Sparse Rectangular Matrices for Parallel Computations of Ax and A^Tv 239
B. Hendrickson, T.G. Kolda
NetLink: A Modern Data Distribution Approach Applied to Transparent Access of High Performance Software Libraries 248
I. Holmqvist, E. Lindstrm
Modernization of Legacy Application Software 255
J. Howe, S.B. Baden, T. Grimmett, K. Nomura
Parallel Methods for Fluid-Structure Interaction 263
C.B. Jenssen, T. Kvamsdal, K.M. Okstad, J. Amundsen
Parallel Computing Tests on Large-Scale Convex Optimization 275
M. Kallio, S. Salo
Parallel Sparse Matrix Computations in the Industrial Strength PINEAPL Library 281
A.R. Krommer
Massively Parallel Linear Stability Analysis with P ARPACK for 3D Fluid Flow Modeled with MPSalsa 286
R.B. Lehoucq, A.G. Salinger
Parallel Molecular Dynamics Simulations of Biomolecular Systems 296
A. Lyubartsev, A. Laaksonen
A Parallel Solver for Animal Genetics 304
P. Madsen, M. Larsen
Scheduling of a Parallel Workload: Implementation and Use of the Argonne Easy Scheduler at PDC 309
L. Malinowsky, P. ster
An Algorithm to Evaluate Spectral Densities of High-Dimensional Stationary Diffusion Stochastic Processes with Non-linear Coefficients: The General Scheme and Issues on Implementation with PVM 315
Y.V. Mamontov, M. Willander
High-Performance Simulation of Evolutionary Aspects of Epidemics 322
W. Maniatty, B.K. Szymanski, T. Caraco
A Parallel Algorithm for Computing the Extremal Eigenvalues of Very Large Sparse Matrices 332
F. Manne
Technologies for Teracomputing: A European Option 337
A. Mathis
High Performance Fortran: Status and Prospects 345
P. Mehrotra, J. Van Rosendale, H. Zima
PAVOR - Parallel Adaptive Volume Rendering System 357
M. Meiner
Simulation Steering with SCIRun in a Distributed Environment 366
M. Miller, C.D. Hansen,, C.R. Johnson
Addressing the Requirements of ASCI-class Systems 377
J.H. Mirza
A Parallel Genetic Algorithm for the Graphs Mapping Problem 379
O.G. Monakhov, E.B. Grosbein
Parallel Wavelet Transforms 385
O. Mller Nielsen
Writing a Multigrid Solver Using Co-array Fortran 390
R.W. Numrich, J. Reid, K. Kim
Exploiting Visualization and Direct Manipulation to Make Parallel Tools More Communicative 400
C.M. Pancake
Deploying Fault-Tolerance and Task Migration with NetSolve 418
J.S. Plank, H. Casanova, M. Beck, J. Dongarra
Comparison of Implicit and Explicit Parallel Programming Models for a Finite Element Simulation Algorithm 433
J. Plazek, K. Banas, J. Kitowski
Parallel Algorithms for Triangular Sylvester Equations: Design, Scheduling and Scalability Issues 438
P. Poromaa
Fast and Quantitative Analysis of 4D Cardiac Images Using a SMP Architecture 447
V. Positano, M.F. Santarelli, L. Landini, A. Benassi
Ab Initio Electronic Structure Methods in Parallel Computers 452
S. Pykk
Iterative Solution of Dense Linear Systems Arising from Integral Equations 460
J. Rahola
Comparison of Partitioning Strategies for PDE Solvers on Multiblock Grids 468
J. Rantakokko
Ship Design Optimization 476
C. Risager, J.W. Perram
Parallelization Strategies for the VMEC Program 483
L.F. Romero, E.M. Ortigosa, E.L. Zapata, J.A. Jimnez
Rational Krylov Algorithms for Eigenvalue Computation and Model Reduction 491
A. Ruhe, D. Skoogh
Solution of Distributed Sparse Linear Systems Using PSPARSLIB 503
Y. Saad, M. Sosonkina
Parallelization of the DAO Atmospheric General Circulation Model 510
W. Sawyer, R. Lucchesi, P. Lyster, L. Takacs, J. Larson, A. Molod, S. Nebuda, C. Pabon-Ortiz
Dynamic Performance Callstack Sampling: Merging TAU and DAQV 515
S. Shende, A.D. Malony, S.T. Hackstadt
A Parallel Rational Krylov Algorithm for Eigenvalue Computations 521
D. Skoogh
Portable Implementation of Real-Time Signal Processing Benchmarks on HPC Platforms 527
J. Suh, V.K. Prasanna
Large Scale Active Networks Simulation 537
K. Swaminathan, R. Radhakrishnan, P.A. Wilsey, P. Alexander
Forward Dependence Folding as a Method of Communication Optimization in SPMD Programs 543
Z. Szczerbinski
A Parallel Genetic Clustering for Inverse Problems 551
H. Telega, R. Schaefer, E. Cabib
A Parallel Hierarchical Solver for Finite Element Applications 557
C.-A. Thole, A. Supalov, S. Mayer
Parallel Computation and Visualization of 3D, Time-Dependent, Thermal Convective Flows 565
P. Wang, P. Li
Recursive Formulation of Cholesky Algorithm in Fortran 90 574
J. Wasniewski, B.S. Andersen, F. Gustavson
High Performance Linear Algebra Package for FORTRAN 90 579
J. Wasniewski, J. Dongarra
Author Index 585
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