High Performance Computing In Science And Engineering, Munich 2004

by Wagner, Siegfried; Hanke, Werner; Bode, Arndt; Durst, Franz

• ISBN13: 9783540443261
• ISBN10: 3540443266
• Format: Hardcover
• Copyright: 2005-11-30
• Publisher: Springer-Verlag New York Inc

Summary

Leading-edge research groups in the field of scientific computing present their outstanding projects using the High Performance Computer in Bavaria (HLRB), Hitachi SR8000-F1, one of the top-level supercomputers for academic research in Germany. The projects address modelling and simulation in the disciplines Biosciences, Chemistry, Chemical Physics, Solid-State Physics, High-Energy Physics, Astrophysics, Geophysics, Computational Fluid Dynamics, and Computer Science. The authors describe their scientific background, their resource requirements with respect to top-level supercomputers, and their methods for efficient utilization of the costly high-performance computing power. Contributions of interdisciplinary research projects that have been supported by the Competence Network for Scientific High Performance Computing in Bavaria (KONWIHR) complete the broad range of supercomputer research and applications covered by this volume.

Table of Contents

Part I Performance and Tools
Performance of Scientific Applications on Modern Supercomputers
Frank Deserno, Georg Hager, Frank Brechtefeld, Gerhard Wellein	3	(24)
A Lightweight Dynamic Application Monitor for SMP Clusters
Karl Fürlinger, Michael Gerndt	27	(10)
gridlib - A Parallel, Object-oriented Framework for Hierarchical-hybrid Grid Structures in Technical Simulation and Scientific Visualization
Frank Hülsemann, Stefan Meinlschmidt, Ben Bergen, Günther Greiner, Ulrich Rüde	37	(14)
Part II Computational Fluid Dynamics
Preface
Rolf Rannacher	51	(2)
Fully Three-Dimensional Coupling of Fluid and Thin-Walled Structures
Dominik Scholz, Ernst Rank, Markus Glück, Michael Breuer, Franz Durst	53	(10)
Efficiency of Lattice Boltzmann Codes as Moderate Reynolds Number Turbulence Solvers
Kamen N. Beronov, Franz Durst	63	(14)
Testing of Closure Assumption for Fully Developed Turbulent Channel Flow with the Aid of a Lattice Boltzmann Simulation
Peter Lammers, Kamen N. Beronov, Thomas Zeiser, Franz Durst	77	(16)
High-Performance Computing in Turbulence Research: Separated Flow Past an Airfoil at High Angle of Attack
Nikola Jovicic, Michael Breuer	93	(14)
DNS of Passive Scalar Transport in Turbulent Supersonic Channel Flow
Holger Foysi, Rainer Friedrich	107	(12)
A Coupled DNS/Monte-Carlo Solver for Dilute Suspensions of Brownian Fibres in Turbulent Channel Flow
Michael Manhart	119	(14)
Large-Eddy-Simulation of an Airfoil at Re = 20000 Using Cartesian Grids
Gary Evans, Sven Eisenbach, Rainer Friedrich,	133	(12)
Interactive CFD Simulation by Coupling Supercomputers with Virtual Reality
Petra Hardt, Siegfried Kühner, Ernst Rank, Oliver Wenisch	145	(12)
Boundary Layer Separation Influenced by Free-Stream Disturbances
Jan Wissink, Wolfgang Rodi	157	(12)
parpp3d++- A Parallel HPC Code for the Incompressible Nonstationary Navier-Stokes Equations
Sven H.M. Buijssen, Stefan Turek	169	(10)
Flow Induced Noise Computation on Hitachi SR8000-F1
Max Escobar, Irfan Ali, Frank Hilsemann, Manfred Kaltenbacher, Stefan Becker	179	(8)
Part III Chemistry and Biosciences
Preface
Walter Thiel	187	(2)
Theoretical Studies of Vanadium Complexes: Reactivities and 51V NMR Chemical Shifts in Solution
Michael Bühl, Rachel Schurhammer, Petra Imhof	189	(10)
Ab-Initio Molecular Dynamics Simulations of Hydrous Silicate Systems
Markus Pöhlmann, Andreas Meyer, Magali Benoit, Walter Kob	199	(12)
Theoretical Studies of Ultrafast Electron Transfer Reactions in Condensed Phases
Ivan Kondov, Haobin Wang, Michael Thoss	211	(14)
Multi Dimensional Quantum Dynamics
Mauricio D. Coutinho-Neto, Alexandra Viel and Uwe Manthe	225	(12)
QM/MM Simulation of the First Step of Vision
Ute F. Röhrig, Stephan Grimm, Irrngard Frank, Leonardo Guidoni, Alessandro Laio, Ursula Röthlisberger	237	(8)
Computer Simulations of Enzyme Reaction Mechanisms: Simulation of Protein Spectra
Frank Beierlein, Timothy Clark	245	(16)
Computer Simulations of Enzyme Reaction Mechanisms: Application of a Hybrid Genetic Algorithm for the Superimposition of Three-Dimensional Chemical Structures
Alexander von Homeyer, Johann Gasteiger	261	(12)
A Fast Program for Phylogenetic Tree Inference with Maximum Likelihood
Alexandros P. Stamatakis, Thomas Ludwig, Harald Meier	273	(12)
Part IV Solid-State Physics
Preface
Werner Hanke	285	(4)
Phasediagram and Scaling Properties of the Projected SO(5) Model in Three Dimensions
Martin Jöstingmeier, Ansgar Dorneich, Enrico Arrigoni. Werner Hanke, Shou-Cheng Zhang	289	(12)
Electron-Spin Interaction in High-Tc Superconductors
Zhongbing Huang, Werner Hanke, Enrico Arrigoni	301	(8)
DCA for the 2D Hubbard Model at T -> 0
Thomas Pruschke, Robert Zitzler, Thomas A. Maier, Mark Jarrell	309	(10)
Density-functional Calculation of Structural Properties in Ionic and Semiconductor Crystals
Karin Schmalzl, Gernot Deinzer, Michael Malorny, Dieter Strauch	319	(10)
Planar Helium under Electromagnetic Driving
Javier Madroñero, Andreas Buchleitner	329	(10)
DMRG Investigation of Stripe Formation in Doped Hubbard Ladders
Georg Hager, Gerhard Wellein, Eric Jeckelmann, Holger Fehske	339	(10)
DNA Base Properties from First Principles Plane-Wave Calculations
Martin Preuß, Kaori Seino, Wolf G. Schmidt	349	(14)
Monte Carlo Studies of Connectivity Disorder
Wolfhard Janke, Martin Weigel	363	(12)
Structure, Energetics and Properties of Fe3O4(001) from First Principles
Rossitza Pentcheva, Frank Wagner, Wolfgang Moritz, Matthias Scheffler	375	(8)
Part V Fundamental Physics and Astrophysics
Preface
Bengt Petersson	383	(2)
Optimizing the Hybrid Monte Carlo Algorithm on the Hitachi SR8000
Gerrit Schierholz, Hinnerk Stüben	385	(10)
Towards a Converged 4He Scattering Calculation
Hartmut M. Hofmann, Gerald M. Hale	395	(6)
Heavy Quark Physics on Large Lattices
Arifa Ali Khan, Vladimir Braun, Tommy Burch, Meinulf Göckeler, Giuseppe Lacagnina, Andreas Schäfer, Gerrit Schierholz	401	(8)
Quantum Chromodynamics with Chiral Quarks
Vladimir Braun, Dirk Brömmel, Christof Gattringer, Meinulf Göckeler, Peter Hasenfratz, Simon Hauswirth, Dieter Hierl, Kieran Holland, Philipp Huber, Thomas Jörg, Keisuke Jimmy Juge, Christian B. Lang, Ferenc Niedermayer, Paul E.L. Rakow, Stefan Schaefer, Andreas Schäfer, Stefan Solbrig	409	(10)
Ultra-relativistic Plasma Shell Collisions in Pulsar Magnetospheres and γ-ray Bursts
Claus H. Jaroschek, Christoph Nodes, Rüdiger Schopper, Hartmut Ruhl, Harald Lesch	419	(12)
Simulation of Solar Magneto-Convection
Robert Cameron, Alexander Vögler, Manfred Schüssler	431	(12)
Part VI Geophysics
Preface
Heiner Igel	443	(2)
Computational Elastic Wave Propagation: Advances in Global and Regional Seismology
Gilbert Brietzke, Heiner Igel, Gunnar Jahnke, Markus Treml, Michael Ewald, Haijiang Wang, Alain Cochard, Guoquan Wang	445
Appendix
Colour Figures	459