Wagner / Steinmetz / Bode 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
1. Auflage 2010
ISBN: 978-3-642-13872-0
Verlag: Springer
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 780 Seiten

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.

Autoren/Hrsg.

Wagner, Siegfried

Steinmetz, Matthias

Bode, Arndt

Inhaltsverzeichnis

1;Preface;5
2;Contents;7
3;Part I Computer Science;13
3.1;Complexities of Performance Prediction for Bandwidth-Limited Loop Kernels on Multi-Core Architectures;14
3.1.1;Introduction;14
3.1.2;Experimental Test Bed;15
3.1.3;Bandwidth;16
3.1.3.1;Memory Bandwidth Balance Model;16
3.1.3.2;Limitations of the Memory Balance Model;16
3.1.3.3;Diagnostic Performance Model for Bandwidth-Limited Loop Kernels;18
3.1.4;Conclusion and Outlook;23
3.1.5;References;23
3.2;Performance Limitations for Sparse Matrix-Vector Multiplications on Current Multi-Core Environments;24
3.2.1;Introduction;24
3.2.2;Common Storage Schemes;26
3.2.3;Test Bed;27
3.2.4;Limitations of Serial Performance;28
3.2.4.1;Basic Sparse Vector Operations;28
3.2.4.2;Resulting Performance for SpMVM;32
3.2.5;Shared-Memory Parallel SpMVM;34
3.2.5.1;Intra-Socket Performance;34
3.2.5.2;Inter-Socket Performance;35
3.2.5.3;HLRB-II Scalability;36
3.2.6;Conclusion and Outlook;36
3.2.7;References;37
3.3;waLBerla: Optimization for Itanium-based Systems with Thousands of Processors;38
3.3.1;Introduction;38
3.3.2;The waLBerla Framework;39
3.3.3;Lattice Boltzmann Method;40
3.3.3.1;Single Phase Lattice Boltzmann Method;40
3.3.3.2;Free Surface Extension;41
3.3.4;Localized Bubble Merge Algorithm;42
3.3.5;Large-Scale Free Surface Applications;44
3.3.6;Itanium-Specific Optimizations;45
3.3.7;Conclusion;48
3.3.8;References;48
3.4;Fast 3D Block Parallelisation for the Matrix Multiplication Prefix Problem;50
3.4.1;Introduction: The Prefix Problem;50
3.4.1.1;Scope and Organisation of the Paper;51
3.4.1.2;Hardware and Software Setup;51
3.4.2;Parallelising the Prefix Problem;52
3.4.2.1;Coarse-Grain versus Fine-Grain Approach;52
3.4.2.2;3D Block-Oriented Parallel Matrix Multiplication;53
3.4.2.3;Numerical Results;55
3.4.3;Application: Optimal Quantum Control;56
3.4.3.1;Linear Algebra Tasks in the GRAPE Algorithm;58
3.4.3.2;Numerical Results;59
3.4.4;Conclusions;60
3.4.5;References;61
3.5;OMI4papps: Optimisation, Modelling and Implementation for Highly Parallel Applications;62
3.5.1;Performance Modelling Using the Apex-MAP Benchmark;62
3.5.1.1;The Apex-MAP Benchmark;63
3.5.1.2;Comparison of Apex-MAP with Real Application Performance;65
3.5.1.3;Modelling LRZ's Application Mix;66
3.5.2;Validation Using the EuroBen Mathematical Kernels;68
3.5.2.1;mod2am: Dense Matrix-Matrix Multiplication;69
3.5.2.2;mod2as: Sparse Matrix-Vector Multiplication;70
3.5.2.3;Validation of Apex-MAP;70
3.5.3;Conclusion and Outlook;71
3.5.4;References;73
3.6;Computational Steering of Complex Flow Simulations;74
3.6.1;Introduction;75
3.6.2;Computational Steering Environment;75
3.6.2.1;Hierarchical Approach;76
3.6.2.2;iFluids;76
3.6.2.3;Adaptive Load Balancing;77
3.6.2.4;Remote Visualisation and Steering Framework;78
3.6.3;Related Applications;80
3.6.3.1;Peano;81
3.6.3.2;Thermal Comfort Assessment;82
3.6.4;Summary and Outlook;84
3.6.5;References;85
4;Part II Computational Fluid Dynamics;86
4.1;Numerical Experiments for Quantification of Small-Scale Effects in Particle-Laden Turbulent Flow;87
4.1.1;Introduction;87
4.1.2;Numerical Simulation of the Carrier Flow;88
4.1.3;Discrete Particle Simulation;89
4.1.4;Validation of the Code;90
4.1.5;Effect of the SGS Turbulence on the Kinetic Energy Seen by the Particles;91
4.1.6;Effect of the SGS Turbulence on Preferential Concentration;94
4.1.7;Computational Requirements;95
4.1.8;Conclusions;96
4.1.9;References;97
4.2;On the Turbulence Structure in a Supersonic Diffuser with Circular Cross-Section;99
4.2.1;Introduction;99
4.2.2;Computational Details;100
4.2.3;Results;101
4.2.4;Conclusions;106
4.2.5;References;106
4.3;Numerical Simulation of Supersonic Jet Noise with Overset Grid Techniques for Highly Parallelized Computing;108
4.3.1;Introduction;108
4.3.2;Numerical Methods;110
4.3.2.1;Nozzle Geometry with Overset Grid Techniques;111
4.3.3;Results;114
4.3.3.1;Nozzle Geometry (Inlet 2);114
4.3.4;Conclusion;116
4.3.5;References;116
4.4;Vorticity Statistics in Fully Developed Turbulence;118
4.4.1;Introduction;118
4.4.2;Vorticity Statistics in Homogeneous Isotropic Turbulence;119
4.4.3;Theoretical Framework;121
4.4.3.1;The Lundgren-Monin-Novikov Hierarchy;121
4.4.3.2;Statistical Symmetries;123
4.4.4;Numerical Methods and Computations;123
4.4.4.1;Algorithm;123
4.4.4.2;Typical Runs;124
4.4.4.3;Scaling and Performance;125
4.4.5;Merging Theory and Direct Numerical Simulations;126
4.4.6;Conclusions and Outlook;128
4.4.7;References;129
4.5;Assessment of CFD Predictive Capability for Aeronautical Applications;130
4.5.1;Project Description;130
4.5.2;Theory;131
4.5.2.1;The k- SST Turbulence Model;131
4.5.2.2;The SAS-SST Turbulence Model;131
4.5.3;Verification of URANS Predictions;132
4.5.3.1;Fan-in-Wing;133
4.5.3.2;Flow Phenomena Around a Helicopter Fuselage;137
4.5.4;Conclusions;140
4.5.5;References;141
4.6;Computational Aspects of Implicit LES of Complex Flows;142
4.6.1;Project Description;142
4.6.2;Numerical Method;144
4.6.2.1;Underlying Finite-Volume Discretization and ALDM;144
4.6.2.2;Body-Fitted Grid Simulation Code LESOCC2;145
4.6.2.3;Cartesian Grid Simulation Code INCA;145
4.6.3;Test Case Round Cylinder;148
4.6.3.1;Computational Setup;148
4.6.3.2;Simulation Results;149
4.6.4;Computational Aspects;151
4.6.4.1;Parallelization;151
4.6.4.2;Computational Effort;152
4.6.4.3;Computational Performance of CIIM;153
4.6.5;Conclusions;154
4.6.6;References;154
4.7;Numerical Investigation of the Micromechanical Behavior of DNA Immersed in a Hydrodynamic Flow;156
4.7.1;Description of the Research Project;156
4.7.1.1;Stretching of DNA Molecules in a Hydrodynamic Flow;156
4.7.1.2;Numerical Methods for DNA in a Hydrodynamic Flow;157
4.7.2;Model;157
4.7.2.1;Mesoscopic Modeling of the Solvent;158
4.7.2.2;Mechanical Modeling of the Polymer Chain;159
4.7.2.3;Object-Oriented Package sph2000;159
4.7.2.4;A Client for Parallel Particle Mesh (PPM) Library;160
4.7.3;Visualization;161
4.7.4;Summary of Results;162
4.7.4.1;Transport Properties of the Solvent;162
4.7.4.2;Static Properties of Polymer;163
4.7.4.3;Dynamic Properties of the Polymer;165
4.7.4.4;Confined Polymer and Polymer in Complex Flows;166
4.7.5;Conclusions;167
4.7.6;References;167
4.8;Comparing Frequency-Based Flow Solutions to Traditional Unsteady Fluid Dynamics Analysis in Turbomachinery;170
4.8.1;Introduction;170
4.8.2;Investigated Compressor Stage;172
4.8.3;Numerical Model;172
4.8.3.1;Full-Annulus and NLH Coarse Grid;173
4.8.3.2;NLH Fine Grid;173
4.8.3.3;Boundary Conditions and Numerical Settings;174
4.8.4;Comparison of Numerical Effort;174
4.8.4.1;Convergence Behaviour;175
4.8.5;Numerical Results;175
4.8.5.1;Compressor Maps;175
4.8.5.2;Blade-to-Blade-Flow;177
4.8.5.3;Comparison with Fourier Analysis;179
4.8.6;Conclusion;182
4.8.7;References;183
4.9;Capability of FDEM for Journal Bearings with Microstructured Surface;184
4.9.1;Introduction;184
4.9.2;Topic;186
4.9.3;Numerical Results;186
4.9.3.1;Results for Journal Bearings with Microstructured Surface;187
4.9.3.2;Scalability Tests;190
4.9.4;Concluding Remarks;191
4.9.5;References;192
4.10;Numerical Investigation of a Transonic Axial Compressor Stage with Inlet Distortions;193
4.10.1;Introduction;193
4.10.2;Description of the Test Case;194
4.10.3;Flow Solver Information;195
4.10.4;Type of Simulation;196
4.10.5;Results of Steady and Unsteady Simulations;197
4.10.6;Outlook;201
4.10.7;References;202
4.11;A Parallel CFD Solver Using the Discontinuous Galerkin Approach;204
4.11.1;Introduction;204
4.11.2;Discontinuous Galerkin Schemes;205
4.11.2.1;Basic Equations;205
4.11.2.2;Turbulence Modeling;205
4.11.2.3;Detached Eddy Simulation;206
4.11.3;Computational Aspects;206
4.11.3.1;Parallelisation and Object-Oriented Design;206
4.11.3.2;Speedup and Performance;207
4.11.4;Results;209
4.11.4.1;Flat Plate Flow;209
4.11.4.2;Detached Eddy Investigation of the Flow Past a Sphere;210
4.11.5;Conclusion;211
4.11.6;References;211
4.12;Characterization of the Aeroacoustic Properties of the SOFIA Cavity and its Passive Control;213
4.12.1;Introduction;214
4.12.2;Numerical Methods;215
4.12.3;Impact of Cavity Door Position on the Aeroacoustic Characteristics;216
4.12.4;Shear-Layer Control by Means of a Porous Fence;217
4.12.5;Impact of TA/AA Misalignment on Aeroacoustics;218
4.12.6;Parametric Optimization of the Aperture-Ramp Geometry;221
4.12.7;Conclusions;223
4.12.8;References;223
4.13;Towards the Numerical Simulation of a Scram Jet Intake at High Mach Number;225
4.13.1;Introduction;225
4.13.2;Goals of the Project;226
4.13.3;Numerical Code;226
4.13.3.1;Space-Time Expansion;228
4.13.3.2;Local Time Stepping;229
4.13.4;Scale-up Efficiency;229
4.13.5;Preparatory Calculations;230
4.13.5.1;3D Flow Around a Sphere;230
4.13.5.2;3D Freestream Injector;230
4.13.5.3;3D Turbulent Flow Around a Cylinder;232
4.13.6;Code Performance;233
4.13.7;Outlook;235
4.13.8;References;235
4.14;Direct Numerical Simulations of Turbulent Mixed Convection in Enclosures with Heated Obstacles;236
4.14.1;Introduction;237
4.14.2;Governing Equations and Computational Domain;237
4.14.3;Numerical Method and Mesh Resolution Requirements;239
4.14.4;Results;240
4.14.5;Details on Performance on the HLRB System;246
4.14.6;Conclusions;246
4.14.7;References;247
4.15;Determination of Acoustic Scattering Coefficients via Large Eddy Simulation and System Identification;248
4.15.1;Introduction;248
4.15.2;Background;249
4.15.3;Method: LES/SI;250
4.15.4;Results;252
4.15.5;Numerical Methods and High Performance Computing;255
4.15.6;Summary;257
4.15.7;References;258
4.16;Identification of Flame Transfer Functions Using LES of Turbulent Reacting Flows;260
4.16.1;Introduction;260
4.16.2;Background;261
4.16.2.1;Large Eddy Simulations;261
4.16.2.2;Combustion Model;262
4.16.2.3;The Flame Transfer Function;262
4.16.2.4;LES/SI;262
4.16.3;Numerical Set Up;263
4.16.3.1;Boundary Conditions;265
4.16.4;Results and discussion;266
4.16.4.1;Identification of Flame Transfer Function;268
4.16.5;Summary;269
4.16.6;References;270
4.17;Computational Modelling of the Respiratory System for Improvement of Mechanical Ventilation Strategies;272
4.17.1;Introduction;273
4.17.2;Research Software Platform BACI;273
4.17.3;Computational Model of the Central Airways ;274
4.17.4;Computational Model of Lung Parenchyma ;277
4.17.5;Summary and Outlook;280
4.17.6;References;281
5;Part III Geo Sciences;283
5.1;SeisSol -- A Software for Seismic Wave Propagation Simulations;284
5.1.1;Introduction;285
5.1.2;The Numerical Approximation;285
5.1.3;Non-conforming Hybrid Meshes;286
5.1.4;Highly Heterogeneous Material;288
5.1.5;Large-Scale Basin Application;289
5.1.6;Scalability;292
5.1.7;Concluding Remarks;293
5.1.8;References;294
5.2;Advances in Modelling and Inversion of Seismic Wave Propagation;296
5.2.1;Introduction;296
5.2.2;Topographic Effects on Seismic Waves;298
5.2.3;Seismic Tomography Using Waveforms;300
5.2.4;Time Reversal of Seismic Waves;302
5.2.5;Scattering in the Earth's Crust;304
5.2.6;Conclusions;307
5.2.7;References;308
6;Part IV Astrophysics;310
6.1;Constrained Local UniversE Simulations (CLUES);311
6.1.1;Introduction;311
6.1.2;Constrained Simulations;313
6.1.2.1; Observational Data;313
6.1.2.2;Constrained Initial Conditions;313
6.1.2.3;Description of Simulations;314
6.1.2.4;An Ensemble of Constrained Simulations;317
6.1.3;Latest Results from CLUES Simulations;319
6.1.3.1;Warm Dark Matter in the Local Universe;319
6.1.3.2;Satellites in the Local Group;322
6.1.4;Summary;323
6.1.5;References;324
6.2;The Core Helium Flash: 3D Hydrodynamic Models;325
6.2.1;Introduction;325
6.2.2;Initial Model;326
6.2.3;Code;327
6.2.4;Results;328
6.2.5;Conclusions;333
6.2.6;References;335
6.3;3D Simulations of Large-Scale Mixing in Core Collapse Supernova Explosions;337
6.3.1;Introduction;338
6.3.2;Simulation Setup;339
6.3.3;Code Performance;340
6.3.4;Results;340
6.3.4.1;Dynamic Evolution;340
6.3.4.2;Radial Element Mixing;343
6.3.5;Conclusions;345
6.3.6;References;347
6.4;Relativistic Simulations of Neutron Star and Strange Star Mergers;349
6.4.1;Introduction;349
6.4.2;Mathematical Model and Numerical Implementation;350
6.4.3;Scalability of the Code;352
6.4.4;Simulations and Results;353
6.4.5;Summary, Conclusions and Outlook;359
6.4.6;References;359
6.5;The Physics of Galactic Nuclei;361
6.5.1;Introduction;361
6.5.2;Nuclear Disc Formation in Galactic Nuclei;362
6.5.2.1;Numerical Method and Model Setup;362
6.5.2.2;Density Evolution;364
6.5.2.3;Accretion;364
6.5.2.4;Disc Properties;365
6.5.3;Radiation Pressure Driven Dust Cloud Interactions;366
6.5.4;Multi-Phase Turbulence in the Tori of Active Galactic Nuclei;367
6.5.5;Feeding Supermassive Black Holes with Nuclear Star Clusters;369
6.5.5.1;Numerics and Code Performance;370
6.5.6;References;371
6.6;Numerical Models of Turbulence in Isothermal and Thermally Bistable Interstellar Gas;373
6.6.1;Introduction;373
6.6.2;Large Eddy Simulation;374
6.6.3;Supersonic Isothermal Turbulence;375
6.6.3.1;Turbulence Energy;376
6.6.3.2;Turbulent Viscosity;377
6.6.3.3;Turbulent Dissipation;379
6.6.4;Thermally Bistable Turbulence;380
6.6.5;Conclusion;382
6.6.6;References;383
6.7;Turbulence Modeling and the Physics of the Intra-Cluster Medium;385
6.7.1;Introduction;386
6.7.2;Numerical Tools for the Modeling of Turbulent Flows;387
6.7.3;Resolving the Turbulent Flow with AMR;388
6.7.4;FEARLESS Simulation of a Galaxy Cluster;391
6.7.5;Conclusions and Outlook;394
6.7.6;References;395
6.8;Project h1021: Dynamics of Binary Black Hole Systems;397
6.8.1;Goals and Motivation;397
6.8.2;Model and Methodology;398
6.8.3;Computational Infrastructure;399
6.8.4;Performance and Scaling;400
6.8.5;Resources Required for Typical Simulations;404
6.8.6;Status Report for h1021;405
6.8.7;Conclusion;408
6.8.8;References;408
6.9;Sheared Magnetic Field and Kelvin-Helmholtz Instability;410
6.9.1;Introduction;410
6.9.2;Model and Numerical Methods;411
6.9.2.1;The Model;411
6.9.2.2;Numerical Methods;411
6.9.3;Results;412
6.9.3.1;Single Layer Simulations;412
6.9.3.2;Slab-Jet Simulation;413
6.9.4;References;415
6.10;Solar Surface Flow Simulations at Ultra-High Resolution;416
6.10.1;Introduction;417
6.10.2;Current Status of the Simulations;418
6.10.3;Results;418
6.10.4;Applications and Interpretation;420
6.10.5;Visualization;423
6.10.6;Next Project Stages and Conclusions;424
6.10.7;References;425
7;Part V High-Energy Physics;427
7.1;Lattice Investigation of Nucleon Structure: Towards the Physical Point;428
7.1.1;Introduction;428
7.1.2;The Simulation;429
7.1.3;Nucleon Structure at Light Quark Masses;430
7.1.3.1;Electromagnetic Form Factors;431
7.1.3.2;Moments of Structure Functions;433
7.1.4;Conclusion and Outlook;435
7.1.5;References;436
7.2;Dynamical Lattice QCD with Ginsparg-Wilson-Type Fermions;438
7.2.1;The Research Field and Our Research Strategy;439
7.2.2;Investigations with Dynamical Chirally Improved Quarks;440
7.2.2.1;Generation of Ensembles;440
7.2.2.2;Ground State and Excited Hadron Masses;441
7.2.2.3;Filtering and Topological Charge Densities;442
7.2.3;2+1 Flavour QCD Results Obtained with the Fixed-Point Action;444
7.2.3.1; The -regime for Different Topological Sectors;444
7.2.4;References;447
7.3;Continuum-Limit Scaling of Chirally Symmetric Fermions as Valence Quarks;450
7.3.1;Introduction;450
7.3.2;A Brief Review of Overlap Fermions;451
7.3.2.1;The Need for Overlap Fermions;451
7.3.2.2;Techniques to Effectively Deal with Overlap Fermions;453
7.3.3;Simulation Setup;456
7.3.4;Computational Details;456
7.3.4.1;Parallelisation;456
7.3.4.2;Timings;457
7.3.5;Results;457
7.3.5.1;Tree-Level Test;457
7.3.5.2;The Interacting Case -- Matching the Pion Mass;457
7.3.5.3;Continuum-Limit Scaling of the Pion Decay Constant;459
7.3.6;Conclusion and Prospects;460
7.3.7;References;460
7.4;Quantum Boltzmann Equations in the Early Universe;462
7.4.1;Introduction;462
7.4.2;Kadanoff-Baym Equations;463
7.4.3;Numerical Results;465
7.4.4;Numerical Methods;467
7.4.4.1;Single-Host Algorithm;468
7.4.4.2;Parallel Distributed-Memory Algorithm;470
7.4.4.3;Memory Requirements;472
7.4.5;Conclusions and Outlook;472
7.4.6;References;473
7.5;Topological Structure of the QCD Vacuum Revealed by Overlap Fermions;474
7.5.1;Introduction: Overlap Fermions and Topological Charge;475
7.5.2;Topological Density with Different Resolution;476
7.5.3;Cluster Analysis;477
7.5.4;Fractal Dimensions;479
7.5.5;Smearing vs. Filtering;480
7.5.6;Selfduality;481
7.5.7;Localization and Local Chirality of Overlap Eigenmodes;483
7.5.8;Technical Details;483
7.5.9;Conclusions;484
7.5.10;References;485
8;Part VI Condensed Matter Physics;487
8.1;Gyrokinetic Turbulence Investigations Involving Ion and Electron Scales;488
8.1.1;Introduction;488
8.1.1.1;Magnetic Confinement Fusion and Plasma Turbulence;488
8.1.1.2;Plasma Turbulence Investigations Using Gyrokinetic Theory;489
8.1.2;The Plasma Turbulence Code Gene;490
8.1.3;Nonlinear Gyrokinetic Simulations Covering Multiple Spatio-Temporal Scales;491
8.1.3.1;Introduction and Context;491
8.1.3.2;Simulation Details;492
8.1.3.3;Simulation Results;493
8.1.4;ETG Turbulence in Edge Transport Barriers;495
8.1.5;High- Simulations and Microturbulence in Astrophysics;496
8.1.6;Conclusions;497
8.1.7;References;497
8.2;Quantum Monte Carlo Studies of Strongly Correlated Electron Systems;499
8.2.1;Magnetic Field Induced Semimetal-to-Canted-Antiferromagnet Transition on the Honeycomb Lattice;500
8.2.2;CTQMC Study of the Single Impurity and Periodic Anderson Models with s-Wave Superconducting Baths;504
8.2.2.1;Quantum Dot with Two Superconducting Baths;504
8.2.2.2;Periodic Anderson Model with Superconducting Conduction Band;507
8.2.3;Accessing the Thermodynamic Properties in the Hubbard Model;509
8.2.3.1;Method and Numerical Aspects;509
8.2.4;References;511
8.3;Deacon Process over RuO2 and TiO2-Supported RuO2;513
8.3.1;Introduction;514
8.3.2;Calculational Details;514
8.3.3;Reaction Mechanism for the Chlorination of RuO2(110) ;516
8.3.4;Reaction Mechanism of the HCl Oxidation over RuO2(110);518
8.3.5;Reaction Mechanism of the HCl Oxidation over RuO2(110) Supported on TiO2(110): DFT Predictions;520
8.3.6;Concluding Remarks;522
8.3.7;References;523
8.4;Charge-Carrier Transport Through Guanine Crystals and Stacks;525
8.4.1;Introduction;525
8.4.2;Theory, Computational Method, and Performance;528
8.4.3;Results and Discussion;530
8.4.4;Conclusions;534
8.4.5;References;535
8.5;Nanomagnetism in Transition Metal Doped Si Nanocrystals;537
8.5.1;Introduction;537
8.5.2;Computational Methods;538
8.5.2.1;DFT Framework;538
8.5.2.2;Numerical Simulations and Performance;539
8.5.3;Modeling and Methods;540
8.5.3.1;Nanocrystal Construction;540
8.5.3.2;Approaches Beyond GGA;542
8.5.4;Results and Discussion;542
8.5.4.1;Stability and Geometry;542
8.5.4.2;Self-purification Effect;545
8.5.4.3;Electronic and Magnetic Properties of Subsurface Doping Sites;546
8.5.5;Summary;547
8.5.6;References;547
8.6;High Performance Computing for the Simulation of Thin-Film Solar Cells;549
8.6.1;Introduction;549
8.6.2;Simulation of Thin-Film Solar Cells;550
8.6.2.1;Modeling Maxwell's Equations;551
8.6.2.2;Solar Cell Model;554
8.6.2.3;Integration of AFM Scans;555
8.6.2.4;Parallelization;556
8.6.3;Simulation Results;558
8.6.4;Conclusion;559
8.6.5;References;560
8.7;Origin of Interface Magnetism in Fe2O3/FeTiO3 Heterostructures;561
8.7.1;Introduction;561
8.7.2;Method and Details of the Calculations;563
8.7.3;Results and Discussion;563
8.7.3.1;Structural Relaxation;564
8.7.3.2;Energetic Stability;565
8.7.3.3;Electronic Properties;566
8.7.3.4;Influence of Epitaxial Strain;566
8.7.4;Summary;569
8.7.5;References;569
8.8;Evaluation of Magnetic Spectra Using the Irreducible Tensor Operator Approach;571
8.8.1;Introduction;571
8.8.2;Goals of the Project;572
8.8.3;Scientific Results from the HLRB Computations;573
8.8.3.1;Basic Background;573
8.8.3.2;General Point-Group Symmetries;573
8.8.3.3;Result I: Complete Energy Spectra of Frustrated Magnetic Molecules;575
8.8.3.4;Result II: Approximate Energy Spectra of Magnetic Molecules;577
8.8.4;Computations Run on the HLRB II;579
8.8.4.1;Technical and Algorithmic Methods;579
8.8.4.2;Programming Techniques;580
8.8.5;Technical Results from the HLRB Computations;580
8.8.5.1;Scaling of Calculations Using the Irreducible Tensor Operator Technique;580
8.8.5.2;Scaling of our Lanczos Diagonalization Routine;581
8.8.6;Technical and Numerical Issues for the Future;582
8.8.7;References;582
8.9;Simulating Strongly Coupled Plasmas on High-Performance Computers;585
8.9.1;Introduction to the Physics of Strongly Coupled Plasmas;585
8.9.2;Resolving Different Length Scales in the Simulation of Strongly Coupled OCPs;587
8.9.3;Resolving Different Time Scales in the Simulation of Strongly Coupled OCPs;587
8.9.4;Numerical Techniques used in Integrating the Equation of Motion;588
8.9.5;Recent Results on Stopping Highly Charged Ions in a Strongly Coupled Ion Plasma;590
8.9.6;Conclusion and Outlook;593
8.9.7;References;593
8.10;Material-Specific Investigations of Correlated Electron Systems;595
8.10.1;Introduction;595
8.10.2;Computational Method;596
8.10.2.1;The LDA+DMFT Approach;596
8.10.2.2;QMC Method;597
8.10.3;Results and Discussion;598
8.10.3.1;Pressure-Driven Metal-Insulator Transition in Hematite;598
8.10.3.2;Fluctuating Valence and Valence Transition of Yb Under Pressure;601
8.10.3.3;Metal-Insulator Transition in NiS2-xSex;602
8.10.3.4;Interaction Driven Insulator-to-Insulator Transition;604
8.10.4;Conclusions;605
8.10.5;References;606
8.11;Theoretical Study of Electron Transfer and Electron Transport Processes in Molecular Systems at Metal Substrates;609
8.11.1;Introduction;609
8.11.2;Photoinduced Electron Transfer of Molecules at Surfaces;610
8.11.2.1;Electron-Transfer Hamiltonian;610
8.11.2.2;Determination of Model Parameters;611
8.11.2.3;Electronic Structure Calculations;612
8.11.2.4;Electron Dynamics in Benzonitrilethiolate at Au(111);613
8.11.2.5;Computational Details;613
8.11.3;Electron Transport in Single-Molecule Junctions;614
8.11.3.1;Electron Transport Theory;614
8.11.3.2;Determination of Model Parameters;616
8.11.3.3;Vibrational Nonequilibrium Effects in Electron Transport Through Benzenedibutanethiolate;616
8.11.3.4;Photoinduced Switching of a Molecular Junction via Hydrogen Transfer;618
8.11.3.5;Computational Details;619
8.11.4;Concluding Remarks;620
8.11.5;References;621
8.12;Fluctuations in the Photoionization Cross Sections of Highly Doubly Excited Two-Electron Atoms;623
8.12.1;Introduction;623
8.12.2;Theory and Numerical Implementation;625
8.12.3;Results;627
8.12.4;Summary and Outlook;631
8.12.5;References;632
9;Part VII Chemistry;634
9.1;Photophysics of the Trp-Gly Dipeptide: Role of Electron and Proton Transfer Processes for Efficient Excited-State Deactivation;635
9.1.1;Introduction;635
9.1.2;Computational Methods;636
9.1.3;Scientific Results;637
9.1.3.1;Ground-State Equilibrium Structure;637
9.1.3.2;Excitation Energies and Molecular Orbitals;638
9.1.3.3;Proton-Transfer Reaction Path;638
9.1.4;Discussion of Reaction Mechanisms;640
9.1.5;Conclusions;640
9.1.6;Technical Results;641
9.1.7;References;642
9.2;Grid Workflows for Molecular Simulations in Chemical Industry;644
9.2.1;Introduction;644
9.2.2;Workflows for VLE Simulations;646
9.2.3;The GridSFEA Framework;647
9.2.4;Integration of GridSFEA with Workflow Management System;649
9.2.4.1;Workflow Management Systems Review;649
9.2.4.2;WS-VLAM Organisation and Properties;650
9.2.4.3;Integration of GridSFEA with WS-VLAM;651
9.2.5;Results;653
9.2.6;Concluding Remarks;654
9.2.7;References;655
9.3;Global Chemistry-Climate Modelling with EMAC;656
9.3.1;Introduction;656
9.3.2;Technical Information;658
9.3.3;Model Development;659
9.3.3.1;Upper-Boundary Parameterisation;659
9.3.3.2;Decoupling of Dynamics and Chemistry;660
9.3.3.3;Atmosphere-Ocean Feedbacks;661
9.3.3.4;Lagrangian Modelling;662
9.3.4;Production-Oriented Simulations;663
9.3.4.1;Atmospheric Ice Nuclei;663
9.3.4.2;Impact of Ship Emissions on Atmospheric Composition and Climate;665
9.3.5;Final Remarks;666
9.3.6;References;667
9.4;Ab Initio Path Integral Simulations of Floppy Molecular Systems;668
9.4.1;Introduction;668
9.4.2;Simulation Techniques and Technical Details;670
9.4.3;Results;671
9.4.3.1;Static Properties;671
9.4.3.2;Radii of Gyration;673
9.4.3.3;Analysis of CH5+;676
9.4.3.4;Performance and Scaling;676
9.4.4;Outlook and Planned Work;677
9.4.5;References;678
9.5;Statistically Converged Properties of Water from Ab Initio Molecular Dynamics Simulations;680
9.5.1;Introduction;680
9.5.2;Methods;684
9.5.3;Results;686
9.5.4;Discussion & Outlook;689
9.5.5;References;690
9.6;Ab Initio Molecular Dynamics Simulations of Aqueous Glycine Solutions: Solvation Structure and Vibrational Spectra;692
9.6.1;Introduction;692
9.6.2;Methods;693
9.6.3;Results and Discussion;695
9.6.4;Conclusions and Outlook;699
9.6.5;References;699
9.7;Cyclodimerization of DNA and RNA Bases: Ab Initio Study of the Cyclodimerization of the Uracil Dimer Through a Butane-Like Conical Intersection;702
9.7.1;Introduction;702
9.7.2;Computational Methods;704
9.7.3;Results and Discussion;705
9.7.3.1;Geometry Optimization;705
9.7.3.2;Vertical Excitation Energies;706
9.7.3.3;Reaction-Path Energy Profiles;707
9.7.4;Conclusions;709
9.7.5;Technical Support;709
9.7.6;References;710
9.8;Numerical Simulation of Electric Field Gradient Focusing and Separation of Analytes in Microchannels with Embedded Bipolar Electrode;712
9.8.1;Introduction;712
9.8.2;Experimental Section;713
9.8.3;Theoretical Background;715
9.8.4;Numerical Methods;718
9.8.5;Results and Discussion;719
9.8.6;Conclusion;722
9.8.7;References;723
10;Part VIII Bio Sciences;724
10.1;Annotation of Entirely Sequenced Genomes;725
10.1.1;Methods;726
10.1.1.1;Iterated Profile-Based Search (PSI-BLAST);726
10.1.1.2;Functional Sequence Motifs (ProSite);726
10.1.1.3;Low-Complexity Regions (SEG);726
10.1.1.4;Domain Assignment (ProDom);727
10.1.1.5;Secondary Structure (PHDsec);727
10.1.1.6;Solvent Accessibility (PHDacc);727
10.1.1.7;Globularity of Proteins (GLOBE);728
10.1.1.8;Transmembrane Helices (PHDhtm);728
10.1.1.9;Secondary Structure (PROFsec) and Solvent Accessibility (PROFacc);728
10.1.1.10;Coiled-Coil Regions (COILS);729
10.1.1.11;Disulphide Bridges (DISULFIND);729
10.1.1.12;Structural Switches (ASP);729
10.1.1.13;Localisation Classification (LOCtree);729
10.1.1.14;Prediction of Nuclear Localisation Signal (PredictNLS);730
10.1.1.15;Keyword Based Prediction of Cellular Localization (LOCkey);730
10.1.1.16;Prediction of Unstructured Loops (NORSnet);730
10.1.1.17;Prediction of Natively Unstructured Regions Through Contacts (Ucon);731
10.1.1.18;Meta-Disorder Predictor (MD);731
10.1.1.19;Prediction of Flexibility (PROFbval);731
10.1.1.20;Reflect;731
10.1.2;Results and Discussion;733
10.1.2.1;Parallelization Techniques;733
10.1.2.2;Number of Processors Used/Degree of Parallelization;734
10.1.2.3;Job Run Times;735
10.1.3;Conclusion;735
10.1.4;References;736
10.2;Molecular Dynamics Simulation of the Nascent Peptide Chain in the Ribosomal Exit Tunnel;738
10.2.1;Introduction;738
10.2.2;Methods;740
10.2.2.1;Principles of Molecular Dynamics;740
10.2.2.2;Periodic Boundary Condition;742
10.2.2.3;Temperature and Pressure Coupling;742
10.2.2.4;Parallelisation Techniques;743
10.2.2.5;Preparation of Simulation System;743
10.2.3;Results;744
10.2.3.1;Achieved Performance on the HLRB system;744
10.2.3.2;Conformations of Polypeptides Inside the Tunnel;744
10.2.4;References;746
10.3;Preparing RAxML for the SPEC MPI Benchmark Suite;747
10.3.1;Introduction;747
10.3.2;The Phylogenetic Likelihood Kernel;749
10.3.3;Sources of Parallelism in Phylogenetic Analyses and Related Work;750
10.3.4;Efficient Parallelization of the Phylogenetic Likelihood Kernel;751
10.3.4.1;Master/Worker Scheme;752
10.3.5;Experimental Setup and Results;754
10.3.6;Conclusion;756
10.3.7;References;757
10.4;Parallel Computing with the R Language in a Supercomputing Environment;759
10.4.1;Introduction;759
10.4.2;R and Parallel Computing;760
10.4.2.1;R at the HLRB2;761
10.4.2.2;Benchmark;763
10.4.3;Applications;764
10.4.3.1;Indirect Comparison of Interaction Graphs;764
10.4.3.2;Parallel Computing in Microarray Data;766
10.4.4;Conclusion;768
10.4.5;References;769