Parallel Computing: Software Technology, Algorithms, Architectures & Applications

Preface.
Sponsors, Exhibitors / Participants in the industrial track.
Committees.

Invited papers
Parallel Machines and the “Digital Brain” – An Intricate Extrapolation on Occasion
of JvN’s 100-th Birthday
F. Hossfeld
So Much Data, So Little Time...
C. Hansen, S. Parker, C. Gribble

Software Technology
On Compiler Support for Mixed Task and Data Parallelism
T. Rauber, R. Reilein, G. Rünger
Distributed Process Networks - Using Half FIFO Queues in CORBA
A. Amar, P. Boulet, J.-L. Dekeyser, F. Theeuwen
An efficient data race detector backend for DIOTA
M. Ronsse, B. Stougie, J. Maebe, F. Cornelis, K. De Bosschere
Pipelined parallelism for multi-join queries on shared nothing machines
M. Bamha, M. Exbrayat
Towards the Hierarchical Group Consistency for DSM systems : an efficient way to
share data objects
L. Lefèvre, A. Bonhomme
An operational semantics for skeletons
M. Aldinucci, M. Danelutto
A Programming Model for Tree Structured Parallel and Distributed Algorithms and
its Implementation in a Java Environment
H. Moritsch
A Rewriting Semantics for an Event-Oriented Functional Parallel Language
F. Loulergue
RMI-like communication for migratable software components in HARNESS
M. Migliardi, R. Podesta
Semantics of a Functional BSP Language with Imperative Features
F. Gava, F. Loulergue
The Use of Parallel Genetic Algorithms for Optimization in the Early Design Phases
E. Slaby, W. Funk
An Integrated Annotation and Compilation Framework for Task and Data Parallel
Programming in Java
H.J. Sips, K. van Reeuwijk
On The Use of Java Arrays for Sparse Matrix Computations
G. Gundersen, T. Steihaug
A Calculus of Functional BSP Programs with Explicit Substitution
F. Loulergue
JToe: a Java API for Object Exchange
S. Chaumette, P. Grange, B. Métrot, P. Vignéras
A Modular Debugging Infrastructure for Parallel Programs
D. Kranzlmüller, Ch. Schaubschläger, M. Scarpa, J. Volkert
Toward a Distributed Computational Steering Environment based on CORBA
O. Coulaud, M. Dussere, A. Esnard
Parallel Decimation of 3D Meshes for Efficient Web-Based Isosurface Extraction
A. Clematis, D. D’Agostino, M. Mancini, V. Gianuzzi

Parallel Programming
MPI on a Virtual Shared Memory
F. Baiardi, D. Guerri, P. Mori, L. Ricci, L. Vaglini
OpenMP vs. MPI on a Shared Memory Multiprocessor
J. Behrens, O. Haan, L. Kornblueh
MPI and OpenMP implementations of Branch-and-Bound Skeletons
I. Dorta, C. León, C. Rodríguez, A. Rojas
Parallel Overlapped Block-Matching Motion Compensation Using MPI and
OpenMP
E. Pschernig, A. Uhl
A comparison of OpenMP and MPI for neural network simulations on a SunFire

6800
A. Strey
Comparison of Parallel Implementations of Runge-Kutta Solvers: Message Passing
vs. Threads
M. Korch, T. Rauber

Scheduling
Extending the Divisible Task Model for Workload Balancing in Clusters
U. Rerrer, O. Kao, F. Drews
The generalized diffusion method for the load balancing problem
G. Karagiorgos, N. Missirlis, F. Tzaferis
Delivering High Performance to Parallel Applications Using Advanced Scheduling
N. Drosinos, G. Goumas, M. Athanasaki, N. Koziris

Algorithms
Multilevel Extended Algorithms in Structural Dynamics on Parallel Computers
K. Elssel, H. Voss
Parallel Model Reduction of Large-Scale Unstable Systems
P. Benner, M. Castillo, E.S. Quintana-Ortí, G. Quintana-Ortí
Parallel Decomposition Approaches for Training Support Vector Machines
T. Serafini, G. Zanghirati, L. Zanni
Fast parallel solvers for fourth-order boundary value problems
M. Jung
Parallel Solution of Sparse Eigenproblems by Simultaneous Rayleigh Quotient Optimization
with FSAI preconditioning
L. Bergamaschi, Á. Martínez, G. Pini
An Accurate and Efficient Selfverifying Solver for Systems with Banded Coefficient
Matrix
C. Hölbig, W. Krämer, T.A. Diverio

3D parallel calculations of dendritic growth with the lattice Boltzmann method
W. Miller, F. Pimentel, I. Rasin, U. Rehse
Distributed Negative Cycle Detection Algorithms
L. Brim, I. ¡ Cerná, L. Hejtmánek
A Framework for Seamlesly Making Object Oriented Applications Distributed
S. Chaumette, P. Vignéras
Performance Evaluation of Parallel Genetic Algorithms for Optimization Problems
of Different Complexity
P. Köchel, M. Riedel
Extensible and Customizable Just-In-Time Security (JITS) Management of Client-
Server Communication in Java
S. Chaumette, P. Vignéras

Applications & Simulation
An Object-Oriented Parallel Multidisciplinary Simulation System—The SimServer
U. Tremel, F. Deister, K.A. Sørensen, H. Rieger, N.P. Weatherill
Computer Simulation of Action Potential Propagation on Cardiac Tissues: An Effi-
cient and Scalable Parallel Approach
J.M. Alonso, J.M. Ferrero (Jr.), V. Hernández, G. Moltó, M. Monserrat, J. Saiz
MoDySim — A parallel dynamical UMTS simulator
M.J. Fleuren, H. Stüben, G.F. Zegwaard
apeNEXT: a Multi-TFlops Computer for Elementary Particle Physics
F. Bodin, Ph. Boucaud, N. Cabibbo, F. Di Carlo, R. De Pietri, F. Di Renzo,
H. Kaldass, A. Lonardo, M. Lukyanov, S. de Luca, J. Micheli, V. Morenas, O. Pene,
D. Pleiter, N. Paschedag, F. Rapuano, L. Sartori, F. Schifano, H. Simma,
R. Tripiccione, P. Vicini
The Parallel Model System LM-MUSCAT for Chemistry-Transport Simulations:
Coupling Scheme, Parallelization and Application
R. Wolke, O. Knoth, O. Hellmuth, W. Schröder, E. Renner
Real-time Visualization of Smoke through Parallelizations
T. Vik, A.C. Elster, T. Hallgren
Parallel Simulation of Cavitated Flows in High Pressure Systems
P.A. Adamidis, F. Wrona, U. Iben, R. Rabenseifner, C.-D. Munz
Improvements in black hole detection using parallelism
F. Almeida, E. Mediavilla, A. Oscoz, F. de Sande
High Throughput Computing for Neural Network Simulation
J. Culloty, P. Walsh
Parallel algorithms and data assimilation for hydraulic models
C. Mazauric, V.D. Tran, W. Castaings, D. Froehlich, F.X. Le Dimet

Multimedia Applications
Parallelization of VQ Codebook Generation using Lazy PNN Algorithm
A. Wakatani
A Scalable Parallel Video Server Based on Autonomous Network-attached Storage
G. Tan, S. Wu, H. Jin, F. Xian
Efficient Parallel Search in Video Databases with Dynamic Feature Extraction
S. Geisler

Architectures
Introspection in a Massively Parallel PIM-Based Architecture
H.P. Zima
Time-Transparent Inter-Processor Connection Reconfiguration in Parallel Systems
Based on Multiple Crossbar Switches
E. Laskowski, M. Tudruj
SIMD design to solve partial differential equations
R.W. Schulze

Caches
Trade-offs for Skewed-Associative Caches
H. Vandierendonck, K. De Bosschere
Cache Memory Behavior of Advanced PDE Solvers
D. Wallin, H. Johansson, S. Holmgren

Performance
A Comparative Study of MPI Implementations on a Cluster of SMP Workstations
G. Rünger, S. Trautmann
MARMOT: An MPI Analysis and Checking Tool
B. Krammer, K. Bidmon, M.S. Müller, M.M. Resch
BenchIT – Performance Measurement and Comparison for Scientific Applications
G. Juckeland, S. Börner, M. Kluge, S. Kölling, W.E. Nagel, S. Pflüger, H. Röding,
S. Seidl, T. William, R. Wloch
Performance Issues in the Implementation of the M-VIA Communication Software
Ch. Fearing, D. Hickey, P.A. Wilsey, K. Tomko
Performance and performance counters on the Itanium 2 — A benchmarking case
study
U. Andersson, P. Ekman, P. Öster
On the parallel prediction of the RNA secondary structure
F. Almeida, R. Andonov, L.M. Moreno, V. Poirriez, M. Pérez, C. Rodriguez

Clusters
MDICE – a MATLAB Toolbox for Efficient Cluster Computing
R. Pfarrhofer, P. Bachhiesl, M. Kelz, H. Stögner, A. Uhl
Parallelization of Krylov Subspace Methods in Multiprocessor PC Clusters
D. Picinin Jr., A.L. Martinotto, R.V. Dorneles, R.L. Rizzi, C. Hölbig, T.A. Diverio,
P.O.A. Navaux
First Impressions of Different Parallel Cluster File Systems
T.P. Boenisch, P.W. Haas, M. Hess, B. Krischok
Fast Parallel I/O on ParaStation Clusters
N. Eicker, F. Isaila, T. Lippert, T. Moschny, W.F. Tichy
PRFX : a runtime library for high performance programming on clusters of SMP
nodes
B. Cirou, M.C. Counilh, J. Roman

Grids
Experiences about Job Migration on a Dynamic Grid Environment
R.S. Montero, E. Huedo, I.M. Llorente
Security in a Peer-to-Peer Distributed Virtual Environment
J. Köhnlein
A Grid Environment for Diesel Engine Chamber Optimization
G. Aloisio, E. Blasi, M. Cafaro, I. Epicoco, S. Fiore, S. Mocavero
A Broker Architecture for Object-Oriented Master/Slave Computing in a Hierarchical
Grid System
M. Di Santo, N. Ranaldo, E. Zimeo
A framework for experimenting with structured parallel programming environment
design
M. Aldinucci, S. Campa, P. Ciullo, M. Coppola, M. Danelutto, P. Pesciullesi,
R. Ravazzolo, M. Torquati, M. Vanneschi, C. Zoccolo

Minisymposium - Grid Computing
Considerations for Resource Brokerage and Scheduling in Grids
R. Yahyapour
Job Description Language and User Interface in a Grid context: The EU DataGrid
experience
G. Avellino, S. Beco, F. Pacini, A. Maraschini, A. Terracina
On Pattern Oriented Software Architecture for the Grid
H. Prem, N.R. Srinivasa Raghavan

Minisymposium - Bioinformatics
Green Destiny + mpiBLAST = Bioinfomagic
W. Feng
Parallel Processing on Large Redundant Biological Data Sets: Protein Structures
Classification with CEPAR
D. Pekurovsky, I. Shindyalov, P. Bourneb
MDGRAPE-3: A Petaflops Special-Purpose Computer System for Molecular Dynamics
Simulations
M. Taiji, T. Narumi, Y. Ohno, A. Konagaya
Structural Protein Interactions: From Months to Minutes
P. Dafas, J. Gomoluch, A. Kozlenkov, M. Schroeder
Spatially Realistic Computational Physiology: Past, Present and Future
J.R. Stiles, W.C. Ford, J.M. Pattillo, T.E. Deerinck, M.H. Ellisman, T.M. Bartol,
T.J. Sejnowski
Cellular automaton modeling of pattern formation in interacting cell systems
A. Deutsch, U. Börner, M. Bär
Numerical Simulation for eHealth: Grid-enabled Medical Simulation Services
S. Benkner, W. Backfrieder, G. Berti, J. Fingberg, G. Kohring, J.G. Schmidt,
S.E. Middleton, D. Jones, J. Fenner
Parallel computing in biomedical research and the search for peta-scale biomedical
applications
C.A. Stewart, D. Hart, R.W. Sheppard, H. Li, R. Cruise, V. Moskvin, L. Papiez

Minisymposium - Performance Analysis
Big Systems and Big Reliability Challenges
D. A. Reed, C. Lu, C.L. Mendes
Scalable Performance Analysis of Parallel Systems: Concepts and Experiences
H. Brunst, W.E. Nagel
CrossWalk: A Tool for Performance Profiling Across the User-Kernel Boundary
A.V. Mirgorodskiy, B.P. Miller
Hardware-Counter Based Automatic Performance Analysis of Parallel Programs
F. Wolf, B. Mohr
Online Performance Observation of Large-Scale Parallel Applications
A.D. Malony, S. Shende, R. Bell
Deriving analytical models from a limited number of runs
R.M. Badia, G. Rodriguez, J. Labarta
Performance Modeling of HPC Applications
A. Snavely, X. Gao, C. Lee, L. Carrington, N. Wolter, J. Labarta, J. Gimenez,
P. Jones

Minisymposium - OpenMP
Thread based OpenMP for nested parallelization
R. Blikberg, T. Sørevik
OpenMP on Distributed Memory via Global Arrays
L. Huang, B. Chapman, R.A. Kendall
Performance Simulation of a Hybrid OpenMP/MPI Application with HeSSE
R. Aversa, B. Di Martino, M. Rak, S. Venticinque, U. Villano
An environment for OpenMP code parallelization
C.S. Ierotheou, H. Jin, G. Matthews, S.P. Johnson, R. Hood
Hindrances in OpenMP programming
F. Massaioli
Wavelet-Based Still Image Coding Standards on SMPs using OpenMP
R. Norcen, A. Uhl

Minisymposium - Parallel Applications
Parallel Solution of the Bidomain Equations with High Resolutions
X. Cai, G.T. Lines, A. Tveito
Balancing Domain Decomposition Applied to Structural Analysis Problems
P. E. Bjørstad, J. Koster
Multiperiod Portfolio Management Using Parallel Interior Point Method
L. Halada, M. Lucka, I. Melichercik
Performance of a parallel split operator method for the time dependent Schrödinger
equation
T. Matthey, T. Sørevik

Minisymposium - Cluster Computing
Design and implementation of a 512 CPU cluster for general purpose supercomputing
B. Vinter
Experiences Parallelizing, Configuring, Monitoring, and Visualizing Applications
for Clusters and Multi-Clusters
O.J. Anshus, J.M. Bjørndalen, L.A. Bongo
Cluster Computing as a Teaching Tool
O.J. Anshus, A.C. Elster, B. Vinter

Minisymposium - Mobile Agents
Mobile Agents Principles of Operation
A. Genco
Mobile Agent Application Fields
F. Agostaro, A. Genco, S. Sorce
Mobile Agent and Grid Computing
F. Agostaro, A. Ciello, A. Genco, S. Sorce
Mobile Agents, Globus and Resource Discovery
F. Agostaro, A. Genco, S. Sorce
A Mobile Agent Tool for Resource Discovery
F. Agostaro, A. Genco, S. Sorce
Mobile Agents and Knowledge Discovery in Ubiquitous Computing
A. Genco

Author & Subject Index
Author Index.
Subject Index.