High Performance Computing in Science and Engineering, Garching/Munich 2007

1. Front Matter

   Pages i-xii

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2. Astrophysics

   1. Front Matter

      Pages 1-1

      PDF

   2. Numerical Simulations of Compact Binary Systems

      • Bernd Brügmann, José A. González, Mark D. Hannam, Sascha Husa, Ulrich Sperhake

      Pages 3-18

   3. Ab Initio Vlasov Code Simulation of Micro-Turbulence, Phase Space Structure Formation and the Resulting Anomalous Transport and Particle Acceleration in Collisionless Astrophysical Plasmas, I: The 2D2V Code

      • Jörg Büchner, the TSSSP team

      Pages 19-28

   4. The ART of Cosmological Simulations

      • Stefan Gottlöber, Anatoly Klypin

      Pages 29-43

   5. Modeling of Turbulent Flows Applied to Numerical Simulations of Galaxy Clusters

      • Luigi Iapichino, Jens C. Niemeyer, Julian Adamek, Surajit Paul, Mario Scuderi

      Pages 45-56

   6. The Onset of Convection During the Core Helium Flash

      • Miroslav Mocák, Ewald Müller

      Pages 57-64

   7. Formation of the First Supermassive Black Holes in the Early Universe

      • Dominik Schleicher, Max Camenzind

      Pages 65-77

   8. Star Formation in the Turbulent Interstellar Medium and Its Implications on Galaxy Evolution

      • Wolfram Schmidt, Andreas Maier, Markus Hupp, Christoph Federrath, Jens Niemeyer

      Pages 79-91

   9. The Aquarius Project: Cold Dark Matter under a Numerical Microscope

      • Volker Springel, Simon D. M. White, Julio Navarro, Adrian Jenkins, Carlos S. Frenk, Amina Helmi et al.

      Pages 93-108

3. Biosciences

   1. Front Matter

      Pages 109-109

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   2. ParBaum: Large-Scale Maximum Likelihood-Based Phylogenetic Analyses

      • Michael Ott, Jaroslaw Zola, Srinivas Aluru, Alexandros Stamatakis

      Pages 111-125

4. Chemistry

   1. Front Matter

      Pages 127-127

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   2. A Theoretical Study of Polyoxometalates and Dendrizyme Model Compounds

      • Ralf Brodbeck, Dirk Andrae

      Pages 129-142

   3. Multi Dimensional Quantum Dynamics of Chemical Reaction Processes

      • Maurício D. Coutinho-Neto, Alexandra Viel, Uwe Manthe

      Pages 143-152

   4. Investigating Protein-Protein and Protein-Ligand Interactions by Molecular Dynamics Simulations

      • Florian Haberl, Olaf Othersen, Ute Seidel, Harald Lanig, Tim Clark

      Pages 153-164

   5. Probing the Mechanical Strength of Chemical Bonds by Stretching Single Molecules

      • Elizabeth M. Lupton, Irmgard Frank

      Pages 165-172

   6. Plane Wave Density Functional Model Studies of Chemistry at Surfaces

      • Notker Rösch, Sven Krüger

      Pages 173-186

   7. Oxidative Dehydrogenation of Simple Molecules over RuO2(110): Density Functional Theory Calculations

      • Ari P. Seitsonen, Herbert Over

      Pages 187-199

   8. Redox Catalysis and Reactivity of Metalloporphyrines

      • Tatyana E. Shubina, Timothy Clark

      Pages 201-212

For the fourth time, the Leibniz Supercomputing Centre (LRZ) and the Com- tence Network for Technical, Scienti c High Performance Computing in Bavaria (KONWIHR) publishes the results from scienti c projects conducted on the c- puter systems HLRB I and II (High Performance Computer in Bavaria). This book reports the research carried out on the HLRB systems within the last three years and compiles the proceedings of the Third Joint HLRB and KONWIHR Result and Reviewing Workshop (3rd and 4th December 2007) in Garching. In 2000, HLRB I was the rst system in Europe that was capable of performing more than one Tera op/s or one billion oating point operations per second. In 2006 it was replaced by HLRB II. After a substantial upgrade it now achieves a peak performance of more than 62 Tera op/s. To install and operate this powerful system, LRZ had to move to its new facilities in Garching. However, the situation regarding the need for more computation cycles has not changed much since 2000. The demand for higher performance is still present, a trend that is likely to continue for the foreseeable future. Other resources like memory and disk space are currently in suf cient abundance on this new system.

• Hochleistungsrechnen
• algorithms
• astrophysics
• computational fluid dynamics
• computational physics
• high performance computing
• material sciences
• optimization
• phylogenetic analyses
• fluid- and aerodynamics

• Institut für Aerodynamik und Gasdynamik, Universität Stuttgart, Stuttgart, Germany

  Siegfried Wagner

• Astrophysikalisches Institut Potsdam, Potsdam, Germany

  Matthias Steinmetz

• Lehrstuhl für Rechnertechnik und Rechnerorganisation, Technische Universität München, Garching b. München, Germany

  Arndt Bode

• Leibniz-Rechenzentrum, Garching b. München, Germany

  Matthias Brehm

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