|
NIC Series Volume 38:
Parallel Computing: Architectures, Algorithms and Applications
Proceedings
ParCo 2007 Conference 4. - 7. September 2007
C. Bischof, M. Bücker, P. Gibbon, G.R. Joubert, T. Lippert, B. Mohr, F. Peters (Eds.)
ISBN 978-3-9810843-4-4
December 2007, 830 pages
PDF
|
Preface
Christian Bischof, RWTH Aachen University, Germany
Martin Bücker, RWTH Aachen University, Germany
Paul Gibbon, Forschungszentrum J¨ulich, Germany
Gerhard Joubert, TU Clausthal, Germany
Thomas Lippert, Forschungszentrum Jülich, Germany
Bernd Mohr, Forschungszentrum Jülich, Germany
Frans Peters, Philips Research, The Netherlands

Invited Talks
Enhancing OpenMP and Its Implementation
for Programming Multicore Systems
Barbara Chapman, Lei Huang
Efficient Parallel Simulations in Support of Medical Device Design
Marek Behr, Mike Nicolai, Markus Probst

Particle and Atomistic Simulation
Domain Decomposition for Electronic Structure Computations
Maxime Barrault, Guy Bencteux, Eric Cancès, William W. Hager, Claude Le Bris
Load Balanced Parallel Simulation of Particle-Fluid DEM-SPH Systems
with Moving Boundaries
Florian Fleissner, Peter Eberhard
Communication and Load Balancing of Force-Decomposition Algorithms
for Parallel Molecular Dynamics
Godehard Sutmann, Florian Janoschek
Aspects of a Parallel Molecular Dynamics Software for Nano-Fluidics
Martin Bernreuther, Martin Buchholz, Hans-Joachim Bungartz
Massively Parallel Quantum Computer Simulations:
Towards Realistic Systems
Marcus Richter, Guido Arnold, Binh Trieu, Thomas Lippert

Image Processing and Visualization
Lessons Learned Using a Camera Cluster to Detect and Locate Objects
Daniel Stødle, Phuong Hoai Ha, John Markus Bjørndalen, Otto J. Anshus
Hybrid Parallelization for Interactive Exploration in Virtual Environments
Marc Wolter, Marc Schirski, Torsten Kuhlen

Performance Modeling and Tools
Analysis of the Weather Research and Forecasting (WRF) Model
on Large-Scale Systems
Darren J. Kerbyson, Kevin J. Barker, Kei Davis
Analytical Performance Models of Parallel Programs in Clusters
Diego R. Martínez, Vicente Blanco, Marcos Boullón, José Carlos Cabaleiro,
Tomás F. Pena
Computational Force: A Unifying Concept for Scalability Analysis
Robert W. Numrich
Distribution of Periscope Analysis Agents on ALTIX 4700
Michael Gerndt, Sebastian Strohhäcker
Visualizing Parallel Functional Program Runs:
Case Studies with the Eden Trace Viewer
Jost Berthold and Rita Loogen
Automatic Phase Detection of MPI Applications
Marc Casas, Rosa M. Badia, Jesús Labarta

Biomedical Applications
Experimenting Grid Protocols to Improve Privacy Preservation
in Efficient Distributed Image Processing
Antonella Galizia, Federica Viti, Daniele D'Agostino, Ivan Merelli, Luciano Milanesi,
Andrea Clematis
A Parallel Workflow for the Reconstruction of Molecular Surfaces
Daniele D'Agostino, Ivan Merelli, Andrea Clematis, Luciano Milanesi, Alessandro
Orro
HPC Simulation of Magnetic Resonance Imaging
Tony Stöcker, Kaveh Vahedipour, N. Jon Shah
A Load Balancing Framework in Multithreaded Tomographic Reconstruction
José Antonio Álvarez, Javier Roca Piera, José Jesús Fernández

Parallel Algorithms
Parallelisation of Block-Recursive Matrix Multiplication
in Prefix Computations
Michael Bader, Sebastian Hanigk, Thomas Huckle
Parallel Exact Inference
Yinglong Xia, Viktor K. Prasanna
Efficient Parallel String Comparison
Peter Krusche and Alexander Tiskin

Parallel Programming Models
Implementing Data-Parallel Patterns for Shared Memory with OpenMP
Michael Suess, Claudia Leopold
Generic Locking and Deadlock-Prevention with C++
Michael Suess, Claudia Leopold
Parallelizing a Real-Time Steering Simulation for Computer Games
with OpenMP
Bjoern Knafla, Claudia Leopold
A Framework for Performance-Aware Composition
of Explicitly Parallel Components
Christoph W. Kessler, Welf Löwe
A Framework for Prototyping and Reasoning about Distributed Systems
Marco Aldinucci, Marco Danelutto, Peter Kilpatrick
Formal Semantics Applied to the Implementation
of a Skeleton-Based Parallel Programming Library
Joel Falcou, Jocelyn Sérot

Numerical Algorithms and Automatic Differentiation
Strategies for Parallelizing the Solution of Rational Matrix Equations
José M. Badía, Peter Benner, Maribel Castillo, Heike Faßbender, Rafael Mayo,
Enrique S. Quintana-Ortí, Gregorio Quintana-Ortí
A Heterogeneous Pipelined Parallel Algorithm for Minimum Mean Squared
Error Estimation with Ordered Successive Interference Cancellation
Francisco-Jose Martínez-Zaldívar, Antonio M. Vidal-Maciá, Alberto González
OpenMP Implementation of the Householder Reduction
for Large Complex Hermitian Eigenvalue Problems
Andreas Honecker, Josef Schüle
Multigrid Smoothers on Multicore Architectures
Carlos García, Manuel Prieto, Fransisco Tirado
Parallelization of Multilevel Preconditioners Constructed from Inverse-Based
ILUs on Shared-Memory Multiprocessors
José I. Aliaga, Matthias Bollhöfer, Alberto F. Martín, Enrique S. Quintana-Ortí
Parallelism in Structured Newton Computations
Thomas F. Coleman, Wei Xu
Automatic Computation of Sensitivities for a Parallel Aerodynamic Simulation
Arno Rasch, H. Martin Bücker, Christian H. Bischof
Parallel Jacobian Accumulation
Ebadollah Varnik, Uwe Naumann

Scheduling
Layer-Based Scheduling Algorithms for Multiprocessor-Tasks
with Precedence Constraints
Jörg Dümmler, Raphael Kunis, Gudula Rünger
Unified Scheduling of I/O- and Computation-Jobs
for Climate Research Environments
N. Peter Drakenberg, Sven Trautmann

Fault Tolerance
Towards Fault Resilient Global Arrays
Vinod Tipparaju, Manoj Krishnan, Bruce Palmer, Fabrizio Petrini, Jarek Nieplocha
Using AOP to Automatically Provide Distribution, Fault Tolerance, and Load
Balancing to the CORBA-LC Component Model
Diego Sevilla, José M. García, Antonio Gómez
VirtuaLinux: Virtualized High-Density Clusters with no Single Point of Failure
Marco Aldinucci, Marco Danelutto, Massimo Torquati, Francesco Polzella, Gianmarco
Spinatelli, Marco Vanneschi, Alessandro Gervaso, Manuel Cacitti, Pierfrancesco
Zuccato

Performance Analysis
Analyzing Cache Bandwidth on the Intel Core 2 Architecture
Robert Schöne, Wolfgang E. Nagel, Stefan Pflüger
Analyzing Mutual Influences of High Performance Computing Programs
on SGI Altix 3700 and 4700 Systems with PARbench
Rick Janda, Matthias S. Müller, Wolfgang E. Nagel, Bernd Trenkler
Low-level Benchmarking of a New Cluster Architecture
Norbert Eicker, Thomas Lippert
Comparative Study of Concurrency Control
on Bulk-Synchronous Parallel Search Engines
Carolina Bonacic, Mauricio Marin
Gb Ethernet Protocols for Clusters: An OpenMPI, TIPC, GAMMA Case Study
Stylianos Bounanos, Martin Fleury
Performance Measurements and Analysis
of the BlueGene/L MPI Implementation
Michael Hofmann, Gudula Rünger
Potential Performance Improvement of Collective Operations in UPC
Rafik A. Salama, Ahmed Sameh

Parallel Data Distribution and I/O
Optimization Strategies for Data Distribution Schemes in a Parallel File System
Jan Seidel, Rudolf Berrendorf, Ace Crngarov, Marc-André Hermanns
Parallel Redistribution of Multidimensional Data
Tore Birkeland, Tor Sørevik
Parallel I/O Aspects in PIMA(GE)2 Lib
Andrea Clematis, Daniele D'Agostino, Antonella Galizia

Fluid and Magnetohydrodynamics Simulation
Parallelisation of a Geothermal Simulation Package:
A Case Study on Four Multicore Architectures
Andreas Wolf, Volker Rath, H. Martin Bücker
A Lattice Gas Cellular Automata Simulator on the Cell Broadband EngineTM
Yusuke Arai, Ryo Sawai, Yoshiki Yamaguchi, Tsutomu Maruyama, Moritoshi Yasunaga
Massively Parallel Simulations of Solar Flares and Plasma Turbulence
Lukas Arnold, Christoph Beetz, Jürgen Dreher, Holger Homann, Christian Schwarz,
Rainer Grauer
Object-Oriented Programming and Parallel Computing
in Radiative Magnetohydrodynamics Simulations
Vladimir Gasilov, Sergei D'yachenko, Olga Olkhovskaya, Alexei Boldarev, Elena
Kartasheva, Sergei Boldyrev
Parallel Simulation of Turbulent Magneto-hydrodynamic Flows
Axelle Viré, Dmitry Krasnov, Bernard Knaepen, Thomas Boeck
Pseudo-Spectral Modeling in Geodynamo
Maxim Reshetnyak, Bernhard Steffen

Parallel Tools and Middleware
Design and Implementation of a General-Purpose API
of Progress and Performance Indicators
Ivan Rodero, Francesc Guim, Julita Corbalan, Jesús Labarta
Efficient Object Placement including Node Selection in a Distributed Virtual Machine
Jose M. Velasco, David Atienza, Katzalin Olcoz, Francisco Tirado
Memory Debugging of MPI-Parallel Applications in Open MPI
Rainer Keller, Shiqing Fan, Michael Resch

Hyperscalable Applications
Massively Parallel All Atom Protein Folding in a Single Day
Abhinav Verma, Srinivasa M. Gopal, Alexander Schug, Jung S. Oh, Konstantin V.
Klenin, Kyu H. Lee, Wolfgang Wenzel
Simulations of QCD in the Era of Sustained Tflop/s Computing
Thomas Streuer, Hinnerk Stüben
Optimizing Lattice QCD Simulations on BlueGene/L
Stefan Krieg

Parallel Computing with FPGAs
IANUS: Scientific Computing on an FPGA-Based Architecture
Francesco Belletti, Maria Cotallo, Andres Cruz, Luis Antonio Fernández, Antonio
Gordillo, Andrea Maiorano, Filippo Mantovani, Enzo Marinari, Victor
Martín-Mayor, Antonio Munoz-Sudupe, Denis Navarro, Sergio Pérez-Gaviro,
Mauro Rossi, Juan Jesus Ruiz-Lorenzo, Sebastiano Fabio Schifano, Daniele Sciretti,
Alfonso Tarancón, Raffaele Tripiccione, Jose Luis Velasco
Optimizing Matrix Multiplication on Heterogeneous Reconfigurable Systems
Ling Zhuo, Viktor K. Prasanna

Mini-Symposium "The Future of OpenMP in the Multi-Core Era"
The Future of OpenMP in the Multi-Core Era
Barbara Chapman, Dieter an Mey
Towards an Implementation of the OpenMP Collector API
Van Bui, Oscar Hernandez, Barbara Chapman, Rick Kufrin, Danesh Tafti, Pradeep
Gopalkrishnan

Mini-Symposium "Scaling Science Applications on Blue Gene"
Scaling Science Applications on Blue Gene
William D. Gropp, Wolfgang Frings, Marc-André Hermanns, Ed Jedlicka,
Kirk E. Jordan, Fred Mintzer, Boris Orth
Turbulence in Laterally Extended Systems
Jörg Schumacher, Matthias Pütz
Large Simulations of Shear Flow in Mixtures
via the Lattice Boltzmann Equation
Kevin Stratford, Jean Christophe Desplat
Simulating Materials with Strong Correlations on BlueGene/L
Andreas Dolfen, Yuan Lung Luo, Erik Koch
Massively Parallel Simulation of Cardiac Electrical Wave Propagation
on Blue Gene
Jeffrey J. Fox, Gregery T. Buzzard, Robert Miller, Fernando Siso-Nadal

Mini-Symposium "Scalability and Usability
of HPC Programming Tools"
Scalability and Usability of HPC Programming Tools
Felix Wolf, Daniel Becker, Bettina Krammer, Dieter an Mey, Shirley Moore,
Matthias S. Müller
Benchmarking the Stack Trace Analysis Tool for BlueGene/L
Gregory L. Lee, Dong H. Ahn, Dorian C. Arnold, Bronis R. de Supinski, Barton P.
Miller, Martin Schulz
Scalable, Automated Performance Analysis with TAU and PerfExplorer
Kevin A. Huck, Allen D. Malony, Sameer Shende and Alan Morris
Developing Scalable Applications with Vampir, VampirServer
and VampirTrace
Matthias S. Müller, Andreas Knüpfer, Matthias Jurenz, Matthias Lieber, Holger
Brunst, Hartmut Mix, Wolfgang E. Nagel
Scalable Collation and Presentation of Call-Path Profile Data with CUBE
Markus Geimer, Björn Kuhlmann, Farzona Pulatova, Felix Wolf, Brian J. N. Wylie
Coupling DDT and Marmot for Debugging of MPI Applications
Bettina Krammer, Valentin Himmler, David Lecomber
Compiler Support for Efficient Instrumentation
Oscar Hernandez, Haoqiang Jin, Barbara Chapman
Comparing Intel Thread Checker and Sun Thread Analyzer
Christian Terboven
Continuous Runtime Profiling of OpenMP Applications
Karl Fürlinger, Shirley Moore

Mini-Symposium "DEISA: Extreme Computing in an
Advanced Supercomputing Environment"
DEISA: Extreme Computing in an Advanced Supercomputing Environment
Hermann Lederer, Gavin J. Pringle, Denis Girou, Marc-André Hermanns, Giovanni
Erbacci
DEISA: Enabling Cooperative Extreme Computing in Europe
Hermann Lederer, Victor Alessandrini
Development Strategies for Modern Predictive Simulation Codes
Alice E. Koniges, Brian T.N. Gunney, Robert W. Anderson, Aaron C. Fisher,
Nathan D. Masters
Submission Scripts for Scientific Simulations on DEISA
Gavin J. Pringle, Terence M. Sloan, Elena Breitmoser, Odysseas Bournas, Arthur S.
Trew
Application Enabling in DEISA: Petascaling of Plasma Turbulence Codes
Hermann Lederer, Reinhard Tisma, Roman Hatzky, Alberto Bottino, Frank Jenko
HEAVY: A High Resolution Numerical Experiment in Lagrangian Turbulence
Alessandra S. Lanotte, Federico Toschi
Atomistic Modeling of the Membrane-Embedded Synaptic Fusion Complex:
a Grand Challenge Project on the DEISA HPC Infrastructure
Elmar Krieger, Laurent Leger, Marie-Pierre Durrieu, Nada Taib, Peter Bond,
Michel Laguerre, Richard Lavery, Mark S. P. Sansom, Marc Baaden

Mini-Symposium "Parallel Computing with FPGAs"
Parallel Computing with FPGAs - Concepts and Applications
Erik H. D'Hollander, Dirk Stroobandt, Abdellah Touhafi
Parallel Computing with Low-Cost FPGAs: A Framework for COPACOBANA
Tim Güneysu, Christof Paar, Jan Pelzl, Gerd Pfeiffer, Manfred Schimmler, Christian
Schleiffer
Accelerating the Cube Cut Problem
with an FPGA-Augmented Compute Cluster
Tobias Schumacher, Enno Lübbers, Paul Kaufmann, Marco Platzner
A Run-time Reconfigurable Cache Architecture
Fabian Nowak, Rainer Buchty, Wolfgang Karl
Novel Brain-Derived Algorithms Scale Linearly
with Number of Processing Elements
Jeff Furlong, Andrew Felch, Jayram Moorkanikara Nageswaran, Nikil Dutt, Alex
Nicolau, Alex Veidenbaum, Ashok Chandrashekar, Richard Granger
Programmable Architectures for Realtime Music Decompression
Martin Botteck, Holger Blume, Jörg von Livonius, Martin Neuenhahn, Tobias G.
Noll
The HARWEST High Level Synthesis Flow to Design
a Special-Purpose Architecture to Simulate the 3D Ising Model
Alessandro Marongiu, Paolo Palazzari
Towards an FPGA Solver for the PageRank Eigenvector Problem
Séamas McGettrick, Dermot Geraghty, Ciarán McElroy

|