High Performance Computing in Science and Engineering, Garching/Munich 2009
Transactions of the Fourth Joint HLRB and KONWIHR Review and Results Workshop, Dec. 8-9, 2009, Leibniz Supercomputing Centre, Garching/Munich, Germany Herausgegeben:Wagner, Siegfried; Steinmetz, Matthias; Bode, Arndt; Müller, Markus Michael
High Performance Computing in Science and Engineering, Garching/Munich 2009
Transactions of the Fourth Joint HLRB and KONWIHR Review and Results Workshop, Dec. 8-9, 2009, Leibniz Supercomputing Centre, Garching/Munich, Germany Herausgegeben:Wagner, Siegfried; Steinmetz, Matthias; Bode, Arndt; Müller, Markus Michael
The Leibniz Supercomputing Centre (LRZ) and the Bavarian Competence Network for Technical and Scienti?c High Performance Computing (KONWIHR) publish in the present book results of numerical simulations facilitated by the High P- formance Computer System in Bavaria (HLRB II) within the last two years. The papers were presented at the Fourth Joint HLRB and KONWIHR Review and - sult Workshop in Garching on 8th and 9th December 2009, and were selected from all progress reports of projects that use the HLRB II. Similar to the workshop two years ago, the majority of the contributed papers belong to…mehr
The Leibniz Supercomputing Centre (LRZ) and the Bavarian Competence Network for Technical and Scienti?c High Performance Computing (KONWIHR) publish in the present book results of numerical simulations facilitated by the High P- formance Computer System in Bavaria (HLRB II) within the last two years. The papers were presented at the Fourth Joint HLRB and KONWIHR Review and - sult Workshop in Garching on 8th and 9th December 2009, and were selected from all progress reports of projects that use the HLRB II. Similar to the workshop two years ago, the majority of the contributed papers belong to the area of computational ?uid dynamics (CFD), condensed matter physics, astrophysics, chemistry, computer sciences and high-energy physics. We note a considerable increase of the user c- munity in some areas: Compared to 2007, the number of papers increased from 6 to 12 in condensed matter physics and from 2 to 5 in high-energy physics. Bio s- ences contributed only one paper in 2007, but four papers in 2009. This indicates that the area of application of supercomputers is continuously growing and entering new ?elds of research. The year 2007 saw two major events of particular importance for the LRZ. First, after a substantial upgrade with dual-core processors the SGI Altix 4700 superc- puter reached a peak performance of more than 62 Tera?op/s. And second, the n- pro?t organization Gauss Centre for Supercomputing e. V. (GCS) was founded on April 13th.
Computer Science.- Complexities of Performance Prediction for Bandwidth-Limited Loop Kernels on Multi-Core Architectures.- Performance Limitations for Sparse Matrix-Vector Multiplications on Current Multi-Core Environments.- waLBerla: Optimization for Itanium-based Systems with Thousands of Processors.- Fast 3D Block Parallelisation for the Matrix Multiplication Prefix Problem.- OMI4papps: Optimisation, Modelling and Implementation for Highly Parallel Applications.- Computational Steering of Complex Flow Simulations.- Computational Fluid Dynamics.- Numerical Experiments for Quantification of Small-Scale Effects in Particle-Laden Turbulent Flow.- On the Turbulence Structure in a Supersonic Diffuser with Circular Cross-Section.- Numerical Simulation of Supersonic Jet Noise with Overset Grid Techniques for Highly Parallelized Computing.- Vorticity Statistics in Fully Developed Turbulence.- Assessment of CFD Predictive Capability for Aeronautical Applications.- Computational Aspects of Implicit LES of Complex Flows.- Numerical Investigation of the Micromechanical Behavior of DNA Immersed in a Hydrodynamic Flow.- Comparing Frequency-Based Flow Solutions to Traditional Unsteady Fluid Dynamics Analysis in Turbomachinery.- Capability of FDEM for Journal Bearings with Microstructured Surface.- Numerical Investigation of a Transonic Axial Compressor Stage with Inlet Distortions.- A Parallel CFD Solver Using the Discontinuous Galerkin Approach.- Characterization of the Aeroacoustic Properties of the SOFIA Cavity and its Passive Control.- Towards the Numerical Simulation of a Scram Jet Intake at High Mach Number.- Direct Numerical Simulations of Turbulent Mixed Convection in Enclosures with Heated Obstacles.- Determination of Acoustic Scattering Coefficients via Large EddySimulation and System Identification.- Identification of Flame Transfer Functions Using LES of Turbulent Reacting Flows.- Computational Modelling of the Respiratory System for Improvement of Mechanical Ventilation Strategies.- Geo Sciences.- SeisSol - A Software for Seismic Wave Propagation Simulations.- Advances in Modelling and Inversion of Seismic Wave Propagation.- Astrophysics.- Constrained Local UniversE Simulations (CLUES).- The Core Helium Flash: 3D Hydrodynamic Models.- 3D Simulations of Large-Scale Mixing in Core Collapse Supernova Explosions.- Relativistic Simulations of Neutron Star and Strange Star Mergers.- The Physics of Galactic Nuclei.- Numerical Models of Turbulence in Isothermal and Thermally Bistable Interstellar Gas.- Turbulence Modeling and the Physics of the Intra-Cluster Medium.- Project h1021: Dynamics of Binary Black Hole Systems.- Sheared Magnetic Field and Kelvin-Helmholtz Instability.- Solar Surface Flow Simulations at Ultra-High Resolution.- High-Energy Physics.- Lattice Investigation of Nucleon Structure: Towards the Physical Point.- Dynamical Lattice QCD with Ginsparg-Wilson-Type Fermions.- Continuum-Limit Scaling of Chirally Symmetric Fermions as Valence Quarks.- Quantum Boltzmann Equations in the Early Universe.- Topological Structure of the QCD Vacuum Revealed by Overlap Fermions.- Condendsed Matter Physics.- Gyrokinetic Turbulence Investigations Involving Ion and Electron Scales.- Quantum Monte Carlo Studies of Strongly Correlated Electron Systems.- Deacon Process over RuO2 and TiO2-Supported RuO2.- Charge-Carrier Transport Through Guanine Crystals and Stacks.- Nanomagnetism in Transition Metal Doped Si Nanocrystals.- High Performance Computing for the Simulation of Thin-Film Solar Cells.- Origin of Interface Magnetism inFe2O3/FeTiO3 Heterostructures.- Evaluation of Magnetic Spectra Using the Irreducible Tensor Operator Approach.- Simulating Strongly Coupled Plasmas on High-Performance Computers.- Material-Specific Investigations of Correlated Electron Systems.- Theoretical Study of Electron Transfer and Electron Transport Processes in Molecular Systems at Metal Substrates.- Fluctuations in the Photoionization Cross Sections of Highly Doubly Excited Two-Electron Atoms.- Chemistry.- Photophysics of the Trp-Gly Dipeptide: Role of Electron and Proton Transfer Processes for Efficient Excited-State Deactivation.- Grid Workflows for Molecular Simulations in Chemical Industry.- Global Chemistry-Climate Modelling with EMAC.- Ab Initio Path Integral Simulations of Floppy Molecular Systems.- Statistically Converged Properties of Water from Ab Initio Molecular Dynamics Simulations.- Ab Initio Molecular Dynamics Simulations of Aqueous Glycine Solutions: Solvation Structure and Vibrational Spectra.- Cyclodimerization of DNA and RNA Bases: Ab Initio Study of the Cyclodimerization of the Uracil Dimer Through a Butane-Like Conical Intersection.- Numerical Simulation of Electric Field Gradient Focusing and Separation of Analytes in Microchannels with Embedded Bipolar Electrode.- Bio Sciences.- Annotation of Entirely Sequenced Genomes.- Molecular Dynamics Simulation of the Nascent Peptide Chain in the Ribosomal Exit Tunnel.- Preparing RAxML for the SPEC MPI Benchmark Suite.- Parallel Computing with the R Language in a Supercomputing Environment.
Computer Science.- Complexities of Performance Prediction for Bandwidth-Limited Loop Kernels on Multi-Core Architectures.- Performance Limitations for Sparse Matrix-Vector Multiplications on Current Multi-Core Environments.- waLBerla: Optimization for Itanium-based Systems with Thousands of Processors.- Fast 3D Block Parallelisation for the Matrix Multiplication Prefix Problem.- OMI4papps: Optimisation, Modelling and Implementation for Highly Parallel Applications.- Computational Steering of Complex Flow Simulations.- Computational Fluid Dynamics.- Numerical Experiments for Quantification of Small-Scale Effects in Particle-Laden Turbulent Flow.- On the Turbulence Structure in a Supersonic Diffuser with Circular Cross-Section.- Numerical Simulation of Supersonic Jet Noise with Overset Grid Techniques for Highly Parallelized Computing.- Vorticity Statistics in Fully Developed Turbulence.- Assessment of CFD Predictive Capability for Aeronautical Applications.- Computational Aspects of Implicit LES of Complex Flows.- Numerical Investigation of the Micromechanical Behavior of DNA Immersed in a Hydrodynamic Flow.- Comparing Frequency-Based Flow Solutions to Traditional Unsteady Fluid Dynamics Analysis in Turbomachinery.- Capability of FDEM for Journal Bearings with Microstructured Surface.- Numerical Investigation of a Transonic Axial Compressor Stage with Inlet Distortions.- A Parallel CFD Solver Using the Discontinuous Galerkin Approach.- Characterization of the Aeroacoustic Properties of the SOFIA Cavity and its Passive Control.- Towards the Numerical Simulation of a Scram Jet Intake at High Mach Number.- Direct Numerical Simulations of Turbulent Mixed Convection in Enclosures with Heated Obstacles.- Determination of Acoustic Scattering Coefficients via Large EddySimulation and System Identification.- Identification of Flame Transfer Functions Using LES of Turbulent Reacting Flows.- Computational Modelling of the Respiratory System for Improvement of Mechanical Ventilation Strategies.- Geo Sciences.- SeisSol - A Software for Seismic Wave Propagation Simulations.- Advances in Modelling and Inversion of Seismic Wave Propagation.- Astrophysics.- Constrained Local UniversE Simulations (CLUES).- The Core Helium Flash: 3D Hydrodynamic Models.- 3D Simulations of Large-Scale Mixing in Core Collapse Supernova Explosions.- Relativistic Simulations of Neutron Star and Strange Star Mergers.- The Physics of Galactic Nuclei.- Numerical Models of Turbulence in Isothermal and Thermally Bistable Interstellar Gas.- Turbulence Modeling and the Physics of the Intra-Cluster Medium.- Project h1021: Dynamics of Binary Black Hole Systems.- Sheared Magnetic Field and Kelvin-Helmholtz Instability.- Solar Surface Flow Simulations at Ultra-High Resolution.- High-Energy Physics.- Lattice Investigation of Nucleon Structure: Towards the Physical Point.- Dynamical Lattice QCD with Ginsparg-Wilson-Type Fermions.- Continuum-Limit Scaling of Chirally Symmetric Fermions as Valence Quarks.- Quantum Boltzmann Equations in the Early Universe.- Topological Structure of the QCD Vacuum Revealed by Overlap Fermions.- Condendsed Matter Physics.- Gyrokinetic Turbulence Investigations Involving Ion and Electron Scales.- Quantum Monte Carlo Studies of Strongly Correlated Electron Systems.- Deacon Process over RuO2 and TiO2-Supported RuO2.- Charge-Carrier Transport Through Guanine Crystals and Stacks.- Nanomagnetism in Transition Metal Doped Si Nanocrystals.- High Performance Computing for the Simulation of Thin-Film Solar Cells.- Origin of Interface Magnetism inFe2O3/FeTiO3 Heterostructures.- Evaluation of Magnetic Spectra Using the Irreducible Tensor Operator Approach.- Simulating Strongly Coupled Plasmas on High-Performance Computers.- Material-Specific Investigations of Correlated Electron Systems.- Theoretical Study of Electron Transfer and Electron Transport Processes in Molecular Systems at Metal Substrates.- Fluctuations in the Photoionization Cross Sections of Highly Doubly Excited Two-Electron Atoms.- Chemistry.- Photophysics of the Trp-Gly Dipeptide: Role of Electron and Proton Transfer Processes for Efficient Excited-State Deactivation.- Grid Workflows for Molecular Simulations in Chemical Industry.- Global Chemistry-Climate Modelling with EMAC.- Ab Initio Path Integral Simulations of Floppy Molecular Systems.- Statistically Converged Properties of Water from Ab Initio Molecular Dynamics Simulations.- Ab Initio Molecular Dynamics Simulations of Aqueous Glycine Solutions: Solvation Structure and Vibrational Spectra.- Cyclodimerization of DNA and RNA Bases: Ab Initio Study of the Cyclodimerization of the Uracil Dimer Through a Butane-Like Conical Intersection.- Numerical Simulation of Electric Field Gradient Focusing and Separation of Analytes in Microchannels with Embedded Bipolar Electrode.- Bio Sciences.- Annotation of Entirely Sequenced Genomes.- Molecular Dynamics Simulation of the Nascent Peptide Chain in the Ribosomal Exit Tunnel.- Preparing RAxML for the SPEC MPI Benchmark Suite.- Parallel Computing with the R Language in a Supercomputing Environment.
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