Nagel / Kröner / Resch High Performance Computing in Science and Engineering '10

Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2010
1. Auflage 2010
ISBN: 978-3-642-15748-6
Verlag: Springer
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 604 Seiten, eBook

This book presents the state-of-the-art in simulation on supercomputers. Leading researchers present results achieved on systems of the High Performance Computing Center Stuttgart (HLRS) for the year 2010. The reports cover all fields of computational science and engineering, ranging from CFD to computational physics and chemistry to computer science, with a special emphasis on industrially relevant applications. Presenting results for both vector systems and microprocessor-based systems, the book makes it possible to compare the performance levels and usability of various architectures. As HLRS operates the largest NEC SX-8 vector system in the world, this book gives an excellent insight into the potential of vector systems, covering the main methods in high performance computing. Its outstanding results in achieving the highest performance for production codes are of particular interest for both scientists and engineers. The book includes a wealth of color illustrations and tables .

Zielgruppe

Research

Autoren/Hrsg.

Nagel, Wolfgang E.

Kröner, Dietmar B.

Resch, Michael M.

Inhaltsverzeichnis

1;Preface;4
2;Contents;7
3;Physics;12
3.1;Spin-Liquid Phase in the Hubbard Model on the Honeycomb Lattice;15
3.1.1;Overview;15
3.1.2;Introduction;16
3.1.3;Model and Method;17
3.1.4;Results;19
3.1.5;Discussion;24
3.1.6;References;26
3.2;Massive and Massless Four-Loop Integrals;28
3.2.1;Introduction;28
3.2.2;Further Development of ParFORM;29
3.2.3;Massless Four-Loop Integrals;32
3.2.4;Massive Four-Loop Integrals;34
3.2.5;References;35
3.3;Ligand Protected Gold Alloy Clusters as Superatoms;38
3.3.1;Introduction;38
3.3.2;Methods;39
3.3.3;Doped Gold Clusters;39
3.3.4;Nickel-Carbonyl Protected Superatoms;43
3.3.5;Conclusions;48
3.3.6;References;48
3.4;The Chiral Critical Surface of QCD;51
3.4.1;Introduction;51
3.4.2;The Binder Cumulant and Universality;53
3.4.3;Chiral Critical Surface, Nf=3, Nt=4;55
3.4.4;Chiral Critical Surface, Nf=2+1, Nt=4;56
3.4.5;Results for Nf=3 and Nt=6;56
3.4.6;Simulation Details;57
3.4.7;Conclusions;58
3.4.8;References;58
3.5;Mesoscopic Simulations of Polyelectrolyte Electrophoresis in Nanochannels;60
3.5.1;Introduction;60
3.5.2;Dissipative Particle Dynamics;61
3.5.3;The Software Package ESPResSo;62
3.5.4;Polyelectrolyte Electrophoresis in Microchannels;63
3.5.4.1;General Theory;63
3.5.4.2;Simulation Details;65
3.5.4.3;Results;66
3.5.5;Summary;72
3.5.6;References;74
3.6;The SuperN-Project: An Update on Core-Collapse Supernova Simulations;75
3.6.1;Introduction;75
3.6.2;Numerical Models;76
3.6.2.1;History and Constraints;76
3.6.2.2;The Mathematical Model;78
3.6.2.3;``Ray-by-Ray Plus'' Method for the Neutrino Transport Problem;78
3.6.2.4;Parallelization;82
3.6.3;Recent Results and Ongoing Work;84
3.6.3.1;Relativistic Supernova Models;84
3.6.3.2;Simulations of Neutron Star Cooling;85
3.6.4;Conclusions and Outlook;87
3.6.5;References;88
3.7;Higgs Boson Mass Bounds from a Chirally Invariant Lattice Higgs-Yukawa Model;90
3.7.1;Introduction;90
3.7.2;The SU(2)LSU(2)R Invariant Higgs-Yukawa Model;91
3.7.3;Implementation, Performance, and Parallelization;94
3.7.4;Results;98
3.7.4.1;The Higgs Boson Mass Bounds;99
3.7.4.2;Preliminary Data on the Effects of a Heavy Fourth Generation;101
3.7.4.3;Resonance Parameters of the Higgs Boson;102
3.7.5;Summary and Outlook;104
3.7.6;References;105
3.8;Dust, Chemistry & Radiation Transport in MRI-Turbulent Protoplanetary Discs;108
3.8.1;Introduction;108
3.8.2;Numerical Code;110
3.8.3;Model Description;111
3.8.4;Simulation Results;112
3.8.4.1;Flow Structure;112
3.8.4.2;Time History ;113
3.8.4.3;Vertical Structure;115
3.8.4.4;Turbulent Saturation Level;117
3.8.5;Ressources Used;118
3.8.6;Conclusion & Outlook;119
3.8.7;References;120
4;Solid State Physics;122
4.1;Organic-Metal Interface: Adsorption of Cysteine on Au(110) from First Principles;124
4.1.1;Introduction;124
4.1.2;Computational Methods;125
4.1.3;Results and Discussion;126
4.1.3.1;The Thiolate-Gold Bond;126
4.1.3.2;The Amino-Gold Bond;133
4.1.4;Summary and Outlook;137
4.1.5;References;138
4.2;Ab-initio Characterization of Electronic Properties of PbTe Quantum Dots Embedded in a CdTe Matrix;140
4.2.1;Introduction;140
4.2.2;Computational Method;142
4.2.2.1;Theoretical Background;142
4.2.2.2;Computational Cost;143
4.2.3;Nanocrystal Construction Using Supercells;144
4.2.4;Results and Discussion;145
4.2.4.1;Induced Electrostatic Fields;145
4.2.4.2;Electronic Properties;145
4.2.4.3;Spatial Localization of Electrons and Holes: Quantum Confined Stark Effect (QCSE);149
4.2.5;Summary and Outlook;150
4.2.6;References;151
4.3;Si(111)-In Nanowire Optical Response from Large-scale Ab Initio Calculations;153
4.3.1;Introduction;153
4.3.2;Computational Method;155
4.3.3;Results;157
4.3.4;Summary;160
4.3.5;References;160
4.4;Laser Ablation of Metals;163
4.4.1;Introduction;163
4.4.1.1;Physical Challenge;163
4.4.2;Report;164
4.4.2.1;Interaction Parameters for Aluminium;164
4.4.2.2;Heat Propagation and Two-Temperature Model;165
4.4.2.3;Simulation of Laser Ablation in Aluminium;167
4.4.2.4;Active Boundary Conditions;168
4.4.2.5;Cluster Analysis of the Gas Phase;168
4.4.2.6;Anisotropic Materials;169
4.4.3;Performance;170
4.4.3.1;General Considerations;170
4.4.3.2;Benchmarks;170
4.4.4;Summary;172
4.4.5;References;172
4.5;Conductance and Noise Correlations of Correlated Nanostructures;173
4.5.1;Shot Noise in the Interacting Resonant Level Model;173
4.5.2;Transport in the Presence of Degenerate Levels;176
4.5.2.1;Kubo Approach for Degenerate Ground-States;177
4.5.2.2;Results;178
4.5.3;References;182
4.6;Cu Substitutionals and Defect Complexes in the Lead-Free Ferroelectric KNN;184
4.6.1;Introduction;184
4.6.2;Physical Approach;185
4.6.3;Computational Method;186
4.6.3.1;Details of the DFT Calculations;186
4.6.3.2;HPC Resources Used for the Present Study;187
4.6.4;Results;188
4.6.4.1;Energetically Preferred Lattice Sites for Cu Dopants;188
4.6.4.2;Stability of Defect Complexes of Cu Substitutionals and O Vacancies;189
4.6.5;Discussion;189
4.6.6;Summary and Outlook;190
4.6.7;References;190
5;Reacting Flows;192
5.1;Scalar Mixing in Droplet Arrays in Stagnant and Convective Environments;194
5.1.1;Introduction;194
5.1.2;Methodology;195
5.1.2.1;Code Parallelisation;198
5.1.3;Test Cases;199
5.1.4;Scalar Mixing in Droplet Arrays;201
5.1.5;Computational Resources;204
5.1.6;Conclusions;205
5.1.7;References;205
5.2;Euler-Lagrange Simulation of a LOX/H2 Model Combustor with Single Shear Coaxial Injector;206
5.2.1;Introduction;206
5.2.2;Governing Equations and Numerical Schemes;207
5.2.2.1;Gas Phase;207
5.2.2.2;Liquid Droplet Spray;208
5.2.2.3;Coupling;210
5.2.3;Boundary Conditions and Computational Procedure;210
5.2.4;Results and Discussion;213
5.2.5;Performance;215
5.2.6;References;216
5.3;Simulation of Triflux Heat Exchangers in Utility Boilers;219
5.3.1;Introduction;219
5.3.2;Models;220
5.3.2.1;The 3D-CFD-Code AIOLOS;220
5.3.2.2;The 1D Representation of Tubes;222
5.3.2.3;Interaction Between 3D CFD-Cells and 1D Tube Segments;223
5.3.2.4;Triflux Heatexchangers;223
5.3.2.5;Water and Steam Properties;224
5.3.3;Results;224
5.3.3.1;Triflux Heat Exchanger;226
5.3.3.2;Performance;228
5.3.4;Conclusions;228
5.3.5;References;229
6;Computational Fluid Dynamics;231
6.1;Direct Numerical Simulation of Swept-Wing Laminar Flow Control Using Pinpoint Suction;233
6.1.1;Introduction;233
6.1.2;Numerics;234
6.1.2.1;Incompressible Code N3D;234
6.1.2.2;Compressible Code NS3D;235
6.1.3;Results;236
6.1.3.1;Incompressible Test Case;237
6.1.3.2;Compressible Test Case;237
6.1.3.3;Comparison;239
6.1.3.4;Pinpoint Suction Results;242
6.1.3.5;Computational Aspects;247
6.1.4;References;250
6.2;A Numerical Study of Turbulent Stably-Stratified Plane Couette Flow;253
6.2.1;Introduction;253
6.2.2;Computational Setup;254
6.2.3;Computational Details;255
6.2.4;Results;256
6.2.5;Conclusions;260
6.2.6;References;261
6.3;DNS of Unsteady Heat Transfer Increase on a Curved Surface Due to Wake-Induced Turbulence;264
6.3.1;Introduction;264
6.3.2;Setup;265
6.3.2.1;Computational Grid;266
6.3.2.2;Reference Correlation;267
6.3.3;Flow Solver and Code Performance;268
6.3.4;Preliminary Results;269
6.3.4.1;Mean Heat Transfer;269
6.3.4.2;Instantaneous Temperature and Flow Field;270
6.3.5;Conclusions;271
6.3.6;References;272
6.4;Application of a Novel Turbulence Generator to Multiphase Flow Computations;273
6.4.1;Introduction;273
6.4.2;Numerical Method;274
6.4.2.1;Turbulent Inflow Generation;275
6.4.3;Applications;277
6.4.3.1;Turbulent Free Air Stream;277
6.4.3.2;Disintegration of Turbulent Liquid Jets;279
6.4.3.3;Drop Evaporation in a Turbulent Free Stream;282
6.4.4;Architecture and Performance;283
6.4.5;Conclusion;285
6.4.6;References;285
6.5;Numerical Investigation on the Deformation of Droplets in High-Pressure Homogenizers;287
6.5.1;Introduction;287
6.5.2;Characteristics of the Homogenizer;288
6.5.3;Governing Equations;288
6.5.4;Computational Domain, Grid and Boundary Conditions;290
6.5.5;Flow Field;290
6.5.6;Computational Effort;293
6.5.7;Summary;293
6.5.8;References;294
6.6;Direct Numerical Simulation of Sediment Transport in Turbulent Open Channel Flow;295
6.6.1;Introduction;295
6.6.2;Numerical Method;296
6.6.3;Setup of the Simulation;298
6.6.4;Computational Costs and Efficiency;300
6.6.5;Results and Discussion;300
6.6.6;Conclusions;304
6.6.7;References;305
6.7;Grid Sensitivity of LES Heat Transfer Results of a Turbulent Round Impinging Jet;307
6.7.1;Introduction;307
6.7.2;Numerical Procedure and Setup;310
6.7.3;Computational Details;310
6.7.3.1;Numerical Grid Resolution;310
6.7.3.2;Inflow Conditions;312
6.7.3.3;Outflow Conditions;312
6.7.4;Numerical Code & Its Performance;313
6.7.4.1;FASTEST;313
6.7.4.2;Code Performance & Solution Control;313
6.7.5;Results;314
6.7.5.1;Instabilities in an Axisymmetric Jet;314
6.7.5.2;Mean Flow Properties and Turbulent Flow Intensities;315
6.7.5.3;Heat Transfer and Coherent Structures;318
6.7.6;Conclusions;321
6.7.7;References;322
6.8;Large Eddy Simulations of a Jet in Crossflow;326
6.8.1;Introduction;326
6.8.2;Boundary Conditions;327
6.8.3;Simulation Aspects;328
6.8.4;Results;332
6.8.5;Conclusion;335
6.8.6;References;335
6.9;The Impact of Secondary Mean Vortices on Turbulent Separation in 3D Diffusers;337
6.9.1;Introduction;337
6.9.2;Computational Setup;339
6.9.2.1;Computational Domain and Boundary Conditions;339
6.9.2.2;Computational Grid and Averaging;341
6.9.2.3;Numerical Method and Turbulence Model;341
6.9.2.4;Methodology and Simulation Overview;341
6.9.3;Results;344
6.9.4;Conclusions;349
6.9.5;References;349
6.10;Time-Dependent Three-Dimensional Simulation of the Turbulent Flow and Heat Transfer in Czochralski Crystal Growth Including the Three-Phase Boundary Movement;351
6.10.1;Introduction;351
6.10.2;Mathematical Formulation;354
6.10.3;Numerical Method;356
6.10.3.1;General Solver Features;356
6.10.3.2;High-Performance Computing Approach;356
6.10.3.3;Problem-Specific Extensions;357
6.10.4;Problem Details;358
6.10.5;Results and Discussion;360
6.10.6;Conclusions;364
6.10.7;References;364
6.11;Numerical Investigation of Shock Wave Boundary-Layer Interaction Using a Zonal RANS-LES Ansatz;366
6.11.1;Introduction;366
6.11.2;Mathematical Formulation;367
6.11.2.1;Numerical Methods;367
6.11.2.2;Synthetic Turbulence Generation Methods (STGM);368
6.11.2.3;Reconstruction of Eddy Viscosity for Transition from LES to RANS;368
6.11.3;Results and Discussion;369
6.11.3.1;Validation of STGM;369
6.11.3.2;DRA2303 Transonic Profile;371
6.11.4;Computational Resources;377
6.11.5;Conclusion;378
6.11.6;References;379
6.12;Large Eddy Simulation of the Cyclic Variations in an Internal Combustion Engine;381
6.12.1;Introduction;381
6.12.2;Numerical Setup;382
6.12.3;Combustion Model;383
6.12.4;Mixing Model;385
6.12.5;Results;385
6.12.6;Computational Efficiency;387
6.12.7;Conclusions;387
6.12.8;References;388
6.13;CFD-CSD-Coupled Simulations of Helicopter Rotors Using an Unstructured Flow Solver;389
6.13.1;Introduction;389
6.13.2;Mathematical Formulation and Numerical Scheme;390
6.13.2.1;Flow and Structural Modeling;390
6.13.2.2;Weak Coupling Methodology and Trim Procedure;391
6.13.3;Results;392
6.13.3.1;Experiment and Test Case Setup;392
6.13.3.2;Trim Convergence;393
6.13.3.3;Blade Dynamics and Rotor aerodynamics;394
6.13.3.4;Computational Performance;397
6.13.4;Conclusions and Outlook;400
6.13.5;References;401
6.14;Wake Signature of Finite-Span Flapping Rigid Wings;403
6.14.1;Introduction;403
6.14.2;Solution Method;405
6.14.3;Computational Domain and Grid Dependence Study;408
6.14.4;Simulation Results;412
6.14.5;Conclusions and Future Perspectives;419
6.14.6;References;422
6.15;Computational Design Study of a 3D Hypersonic Intake for Scramjet Demonstrator Testing;424
6.15.1;Introduction;424
6.15.2;Physical Model;427
6.15.2.1;Conservation Equations;427
6.15.3;Numerical Method;428
6.15.3.1;Spatial Discretization;428
6.15.3.2;Time-Stepping Scheme;428
6.15.3.3;Reynolds Stress Model;429
6.15.3.4;Boundary Conditions;429
6.15.3.5;Numerical Accuracy;430
6.15.4;Results;431
6.15.5;Computational Considerations;434
6.15.6;Conclusions;434
6.15.7;References;435
6.16;Characterization of Mixing in Food Extrusion and Emulsification Processes by Using CFD;437
6.16.1;Introduction;437
6.16.2;Evaluation of Dispersive Mixing in the Fully Filled Zone of a Twin-Screw Extruder;438
6.16.2.1;Motivation;438
6.16.2.2;Fundamentals;439
6.16.2.3;Material and Methods;442
6.16.2.4;Results and Discussion;445
6.16.2.5;Conclusions;449
6.16.3;Evaluation of Local Mixing in SEM (Simultaneous Emulsification and Mixing) Nozzles for Melt Emulsification Purposes;449
6.16.3.1;Motivation;449
6.16.3.2;Materials and Methods;450
6.16.3.3;Results;451
6.16.3.4;Conclusion;453
6.16.4;References;454
7;Transport and Climate;457
7.1;Modelling Regional Climate Change in Germany;460
7.1.1;Introduction;460
7.1.2;The CCLM Model;461
7.1.3;Regional Climate Simulations Using the HLRS Facilities;461
7.1.3.1;Simulation Setup and Downscaling Chain;461
7.1.3.2;HPC Aspects;463
7.1.4;Results;464
7.1.4.1;Change of Number of Summer and Frost Daysin Baden-Württemberg;464
7.1.4.2;Future Changes of Strong Summer Precipitation Events;464
7.1.4.3;Validation Results for the CEDIM-Project Simulations;467
7.1.5;Future Work;469
7.1.6;References;469
7.2;Modelling the Extratropical Transition of Tropical Cyclones and Its Downstream Impact;472
7.2.1;Introduction;472
7.2.2;The COSMO Model;473
7.2.3;The Downstream Impact of Tropical Cyclones Undergoing Extratropical Transition;474
7.2.3.1;Operational COSMO-T-PARC Forecasts;474
7.2.3.2;Performance Tests and System Data;476
7.2.3.3;The Outflow-Jet Interaction During the Extratropical Transition of Typhoon Jangmi;477
7.2.4;Details of the Outflow-Jet Interaction of Typhoon Jangmi;481
7.2.4.1;PV Perspective;481
7.2.4.2;Quantification of the Impact of Jangmi on the Midlatitude Jet Using PV Surgery;484
7.2.5;Details of the COSMO Runs Used in the Case Study of Typhoon Jangmi;488
7.2.6;Summary and Outlook;490
7.2.7;References;490
7.3;Global Long-Term MIPAS Data Processing: Some Aspects of the Dynamics of the Atmosphere from Lower Stratosphere to Lower Thermosphere;493
7.3.1;The MIPAS/Envisat Mission;494
7.3.2;Data Analysis;494
7.3.3;Computational Considerations;495
7.3.3.1;Processing System Overview;495
7.3.3.2;Throughput;496
7.3.3.3;Processor Usage;496
7.3.4;Examples of Scientific Work with MIPAS Data;497
7.3.4.1;Carbon Monoxide Distributions from the Upper Troposphere to the Mesosphere;497
7.3.4.2;Temperature Distributions from the Stratosphere to the Lower Thermosphere During a Major Warming Event;502
7.3.5;Conclusions and Outlook;503
7.3.6;References;504
8;Miscellaneous Topics;506
8.1;Computer Simulation for Building Implosion Using LS-DYNA;509
8.1.1;Introduction;509
8.1.2;Aspects of Numerical Simulation;509
8.1.3;Simulation Models;510
8.1.3.1;Previous Models;510
8.1.3.2;Sparkasse Building in Hagen;510
8.1.3.3;Storehouse in Thueringen;514
8.1.4;References;517
8.2;Quaero Speech-to-Text and Text Translation Evaluation Systems;519
8.2.1;Introduction;519
8.2.2;Quaero;519
8.2.3;English Evaluation Recognition Systems;520
8.2.3.1;Front-End;521
8.2.3.2;Acoustic Model Training;521
8.2.4;Translation System;524
8.2.4.1;Data;524
8.2.4.2;Preprocessing;525
8.2.4.3;Language Model;525
8.2.4.4;Translation Model;526
8.2.4.5;Reordering Model;527
8.2.4.6;Decoder;528
8.2.4.7;Re-Ranking;528
8.2.5;Parallelization Utilized;529
8.2.5.1;Automatic Speech Recognition;529
8.2.5.2;Machine Translation;530
8.2.6;References;530
8.3;Molecular Modeling of Hydrogen Bonding Fluids: Transport Properties and Vapor-Liquid Coexistence;533
8.3.1;Introduction;533
8.3.2;Transport Properties of Ammonia;534
8.3.3;Vapor-Liquid Equilibria of Carbon Dioxide + Cyclohexane + Cyclohexanol and Its Subsystems;536
8.3.3.1;Carbon Dioxide + Cyclohexane ;537
8.3.3.2;Carbon Dioxide + Cyclohexanol ;537
8.3.3.3;Cyclohexane + Cyclohexanol ;539
8.3.3.4;Carbon Dioxide + Cyclohexane + Cyclohexanol ;539
8.3.4;Conclusion;540
8.3.5;References;541
8.4;Software Framework UG: Parallel Simulation of a Three-Dimensional Benchmark Problem for Thermohaline-Driven Flow;542
8.4.1;Introduction;542
8.4.2;Mathematical Model;543
8.4.3;Numerical Solution;543
8.4.4;Benchmark Description;544
8.4.5;Results and Discussion;545
8.4.6;References;549
8.5;Tailored Usage of the NEC SX-8 and SX-9 Systems in Satellite Geodesy;550
8.5.1;Introduction;550
8.5.2;Methodology;551
8.5.3;Tailored Implementation on NEC SX Systems;553
8.5.3.1;Data Input;553
8.5.3.2;Design Matrix Assembly;554
8.5.3.3;Setup of the Normal Equations System;555
8.5.3.4;Solution of the Normal Equations System;555
8.5.4;Results;556
8.5.4.1;Design Matrix Assembly;556
8.5.4.2;Parallelization Performance;556
8.5.5;Discussion and Conclusion;560
8.5.6;References;561
8.6;A Geodynamic Model of the Evolution of the Earth's Chemical Mantle Reservoirs;562
8.6.1;Introduction: Geochemical Mantle Reservoirs;562
8.6.2;Model;564
8.6.3;Solution of Numerical Problems Regarding the Tracers Representing the Incompatible Elements in the Earth's Mantle and Results;566
8.6.3.1;General Remarks;566
8.6.3.2;Thermal and Chemical Evolution Using a Pair of Reference Runs;566
8.6.3.3;Continents and Mantle Inhomogeneities;570
8.6.4;Numerical Method, Implementation, Scalability, and Performance;574
8.6.5;References;579
8.7;Three-Dimensional Simulation of Rarefied Plasma Flows Using a High Order Particle in Cell Method;582
8.7.1;Introduction;582
8.7.2;Maxwell Solver;583
8.7.2.1;The Discontinuous Galerkin Scheme;583
8.7.3;Particle-Grid Coupling;584
8.7.3.1;Deposition of Charges and Currents;584
8.7.3.2;Evaluation of Electromagnetic Fields at Particle Positions;585
8.7.4;Particle Pusher;586
8.7.4.1;Performance Analysis;586
8.7.5;Parallelization;587
8.7.6;Simulation Examples;589
8.7.6.1;Gyrotron Launcher;589
8.7.6.2;Plasma Wave 3D;590
8.7.6.3;Weibel Instability 3D;591
8.7.7;Summary and Outlook;592
8.7.8;References;592

Über Autor(innen)

Wolfgang E. Nagel: Chair of Computer Architecture at Technical University Dresden, Germany. Director of the Center for Information Services and High Performance Computing (ZIH) in Dresden; Chairman of the Advisory Board for the High Performance Computing Center Stuttgart (HLRS). Dietmar Kröner: Chair of Applied Mathematics at the University of Freiburg. Deputy Chairman of the Advisory Board for the High Performance Computing Center Stuttgart (HLRS). Michael Resch: Chair of high performance computing at the University of Stuttgart, Germany. Director of the High Performance Computing Center Stuttgart; Member of the board of the high performance computing competence center of the state of Baden-Württemberg, Winner of HPC Challenge 2003 at SC’2003, Invited Plenary Speaker at SC’07, Reno, USA