High Performance Computing in Science and Engineering ´16

Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2016

Wolfgang E. Nagel Dietmar H. Kröner Michael M. Resch(Herausgeber*in)

Springer (Verlag)

Erschienen am 11. Januar 2017

IX, 675 Seiten

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This book presents the state-of-the-art in supercomputer simulation. It includes the latest findings from leading researchers using systems from the High Performance Computing Center Stuttgart (HLRS) in 2016. The reports cover all fields of computational science and engineering ranging from CFD to computational physics and from chemistry to computer science with a special emphasis on industrially relevant applications. Presenting findings of one of Europe's leading systems, this volume covers a wide variety of applications that deliver a high level of sustained performance.

The book covers the main methods in high-performance computing. Its outstanding results in achieving the best performance for production codes are of particular interest for both scientists and engineers. The book comes with a wealth of color illustrations and tables of results.

Auflage

1st ed. 2016

Sprache

Englisch

Verlagsort

Cham

Schweiz

Verlagsgruppe

Springer International Publishing

Illustrationen

318 farbige Tabellen, 310 farbige Abbildungen, 58 s/w Abbildungen

IX, 675 p. 368 illus., 310 illus. in color.

Dateigröße

42,34 MB

ISBN-13

978-3-319-47066-5 (9783319470665)

DOI

10.1007/978-3-319-47066-5

Schlagworte

vector supercomputers Computational science and engineering Simulation Modelling high performance computing

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Informatik / Computer

Allgemein

Theoretische Informatik

Mathematik

Angewandte Mathematik

Mathematische Modellierung

Numerische Mathematik

Thema Klassifikation

EDV und Informationstechnologie

Informatik

Computermodellierung und -simulation

Theoretische Informatik

Mathematik und Naturwissenschaften

Chemie

Physikalische Chemie

Quanten- und theoretische Chemie

Mathematik

Mathematische Analysis, allgemein

Numerische Mathematik

Physik

Mathematische Physik

Technologie, Ingenieurswissenschaft, Landwirtschaft, Industrieprozesse

Technologie, allgemein

Mathematik für Ingenieure

DNB DDC Sachgruppen

Informatik

Mathematik

Naturwissenschaften

Dewey Decimal Classfication (DDC)

Computer science, information & general works

Computer science, knowledge & systems

Data processing & computer science

BIC 2 Klassifikation

Computing & information technology

Computer science

Computer modelling & simulation

Mathematics & science

Chemistry

Physical chemistry

Quantum & theoretical chemistry

Mathematics

Applied mathematics

Mathematical modelling

Physics

Mathematical physics

Science: general issues

Maths for scientists

Technology, engineering, agriculture

Technology: general issues

BISAC Klassifikation

Applied

Science

Chemistry / General

Physical & Theoretical

Physics / General

Mathematical & Computational

Technology & Engineering

Engineering (General)

Warengruppensystematik 2.0

Naturwissenschaften, Medizin, Informatik, Technik

Informatik, EDV

Allgemeines, Lexika

Andere Ausgaben

Wolfgang E. Nagel | Dietmar H. Kröner | Michael M. Resch

High Performance Computing in Science and Engineering ´16

Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2016

Versand in 10-15 Tagen

Intro
Contents
Part I Physics
The Illustris++ Project: The Next Generation of Cosmological Hydrodynamical Simulations of Galaxy Formation
1 Introduction
2 Physics and Code Developments for Illustris++
2.1 New Blackhole Physics Model
2.2 Hierarchical Time Integration
2.3 Chemical Enrichment Model
2.4 Hydrodynamical Accuracy Improvements
2.5 Elimination of All-to-All Communication Steps
3 Simulation Set and Production Runs
4 Selected Preliminary Results
5 Conclusions
References
Hydrangea: Simulating a Representative Population of Massive Galaxy Clusters
1 Introduction
2 Simulation Code
3 Galaxy Cluster Simulations
3.1 Simulations Performed at HLRS
4 Simulation Results
5 Summary
References
PAMOP Project: Computations in Support of Experiments and Astrophysical Applications
1 Introduction
2 R-Matrix Code Performance: Photoionization
3 X-Ray and Inner-Shell Processes
3.1 K-Shell Photoionization of Atomic Oxygen Ions: O4+ and O5+
3.2 L-Shell Photoionization: Ar+
3.3 Photoionization of Tungsten (W) Ions: W2+ and W3+
4 Single-Photon Double Ionization: He
5 Photodissociation: SH+
6 Summary
References
Estimation of Nucleation Barriers from Simulations of Crystal Nuclei Surrounded by Fluid in Equilibrium
1 Introduction and Overview
2 The Model and Its Bulk Properties
3 Simulation Analysis of the Nucleus-Fluid Equilibrium
4 Conclusions
References
The Internal Dynamics and Early Adsorption Stages of Fibrinogen Investigated by Molecular Dynamics Simulations
1 Introduction
2 Simulation Methods
3 Simulations of Fibrinogen Internal Dynamics
4 Simulations of Fibrinogen Adsorption
5 Conclusions
References
Vorticity, Variance, and the Vigor of Many-Body Phenomena in Ultracold Quantum Systems: MCTDHB and MCTDH-X
1 Introductory Remarks
2 Single Shots of Dynamically Created Quantum Many-Body Vortices
3 Many-Body Tunneling Dynamics of Bose-Einstein Condensates and Vortex States in 2D
4 Transition from Vortices to Solitonic Vortices in 2D Trapped Bose-Einstein Condensates
5 Variance as a Sensitive Probe of Correlations and Uncertainty Product of an Out-of-Equilibrium Many-Particle System
6 Beyond Structureless Bosons: Results Obtained with the MCTDH-X Package
6.1 Trapped Fermions Escape
6.2 Composite Fragmentation of Multi-component Bose-Einstein Condensates
7 Concluding Remarks and Future Plans
References
Nucleon Observables as Probes for Physics Beyond the Standard Model
1 Introduction
2 Lattice QCD Setup
3 Nucleon Mass and Lattice Spacing
4 Three-Point Functions
4.1 Nucleon s-Terms
4.2 Nucleon Charges and Moments of Generalized Parton Distributions
5 Conclusion
References
Numerical Evaluation of Multi-loop Feynman Integrals
1 Introduction
2 FIESTA
3 Anomalous Magnetic Moment of the Muon
4 Outlook
References
Part II Molecules, Interfaces, and Solids
Mechanochemistry of Ring-Opening Reactions: From Cyclopropane in the Gas Phase to Thiotic Acid on Gold in the Liquid Phase
1 Scientific Background
2 Results and Discussion
2.1 Mechanochemistry of Aliphatic and Aromatic Thiolates on Gold Surfaces
2.2 Mechanochemical Activation of Hydroxide Attack on the Anchoring Moiety of PEG-Thioctic Acid Adsorbed on a Gold Surface
3 Software and Computational Resources
References
Microscopic Insights into the Fluorite/Water Interfaces from Vibrational Sum Frequency Generation Spectroscopy
1 Introduction
2 Methodology
2.1 Simulation Setup
2.2 Method for VSFG
3 Results and Discussion
4 Conclusions
References
Growth, Structural and Electronic Properties of Functional Semiconductors Studied by First Principles
1 Introduction
2 Thermodynamic Properties of Hydrogen on Si(001) Under Chemical Vapor Deposition Conditions from Ab Initio Approaches
2.1 Methods
2.2 Results
3 Growth-Dependent Electronic and Optical Properties of Active Ga(NAsP) and Dilute Ga(AsBi) Materials
3.1 Strain Energy of Ga(NAsP) on Si and GaP Wegele2016
3.1.1 Methods
3.1.2 Results
3.2 Local Bi Ordering in Dilute Ga(AsBi) and Its Effect on Electronic Structure
3.2.1 Methods
3.2.2 Results: Local Ordering
3.2.3 Results: Effect on Electronic Structure
4 Electron-Phonon Coupling of NTCDA on Ag(111)
4.1 Methods
4.2 Results
References
Submonolayer Rare Earth Silicide Thin Films on the Si(111) Surface
1 Introduction
2 Methodology
3 Results
4 Conclusions
References
Computational Analysis of Li Diffusion in NZP-Type Materials by Atomistic Simulation and Compositional Screening
1 Introduction
2 Structure of NZP-Type Materials
3 Computational Methods
3.1 Ab-Initio Calculations
3.2 The Bond Valence Method
4 Results and Discussion
4.1 Energy Landscape Calculations
4.2 Activation Energies for NZP Materials
5 Computer Resources
6 Summary and Outlook
References
Molecular Dynamics Simulations of Silicon: The Influence of Electron-Temperature Dependent Interactions
1 Introduction
2 Continuum-Atomistic Modeling
3 Interatomic Potentials
4 Results
5 Benchmark Numbers
6 Conclusions
References
Non-linear Quantum Transport in Interacting Nanostructures
1 Introduction
2 Motivation of the Model System
3 Hamiltonian of the Model System
3.1 Interacting Ring Structure
3.2 Non-interacting Tight-Binding Leads
3.3 Coupling Between Ring Structure and Leads
4 Quenching of the System
5 Numerical Dynamics
6 Standard Parameters and Observables
7 Transient Dynamics of Currents in the Interacting System
7.1 Weak Interaction U=0.1J
7.2 Strong Interaction 0.1J& U =1.0J
7.3 Very Strong Interaction U & 1.0J
7.4 Transient Dynamics for Damped Boundary Conditions
8 Limit of Long Time
9 Study of the Uncoupled Interacting Structure
10 Calculation of the Reduced Density Matrix of the Interacting Structure
10.1 VSD=eT /e
10.2 VSD&eT /e
References
Part III Reactive Flows
A DNS Analysis of the Correlation of Heat Release Rate with Chemiluminescence Emissions in Turbulent Combustion
1 Introduction
2 Computational Methods
2.1 Governing Equations
2.2 Numerical Setups
3 Correlation of Heat Release with Chemiluminescent Species
3.1 Local Correlation in Laminar Planar Unstrained Flames
3.2 Integral Correlation in 3D Turbulent Flames
3.2.1 Simulation Setups
3.2.2 Performance
3.2.3 Results
3.2.4 Evaluation of Heat Release from Chemiluminescence Measurement
4 Conclusions
References
Direct Numerical Simulation of Non-premixed Syngas Combustion Using OpenFOAM
1 Introduction
2 Governing Equations
3 Computational Configuration and DNS Solvers
4 Results and Discussion
4.1 DNS Resolution Requirements
4.2 Flame Characteristics
5 Parallel Performance
6 Conclusions
References
Numerical Simulations of Rocket Combustion Chambers with Supercritical Injection
1 Introduction
2 Numerical Method
3 Non-ideal Fluids in Rocket Combustors
3.1 Non-ideal Thermodynamics
3.2 Non-ideal Molecular Transport Properties
3.3 Non-ideal Flow Phenomena
4 Simulation of Supercritical Nitrogen Jet
5 Simulation of Model Rocket Combustor
6 Performance Comparison of HERMIT and HORNET
7 Conclusion
References
Two-Zone Fluidized Bed Reactors for Butadiene Production: A Multiphysical Approach with Solver Coupling for Supercomputing Application
1 Introduction
2 The Engineering Problem and the Two-Zone Fluidized Bed Reactor
3 Models and Computer Codes
4 Calculation Procedure
5 Computer Specifications
6 Discussion of Current Limitations with Respect to the Efficient Use of the Targeted Parallel Computers
7 Results from the Strong Scaling
8 Conclusions
References
Part IV Computational Fluid Dynamics
High-Pressure Real-Gas Jet and Throttle Flow as a Simplified Gas Injector Model Using a Discontinuous Galerkin Method
1 Introduction
2 Modeling, Discretization, and Visualization
3 Simulation Strategy
4 Results and Discussion
4.1 Mass Flow
4.2 Shock Representation
4.3 HPC Assessment
5 Conclusion
References
Modeling of the Deformation Dynamics of Single and Twin Fluid Droplets Exposed to Aerodynamic Loads
1 Introduction
2 Methodology
2.1 SPH Formulation
2.2 SPH Formulation of the Navier-Stokes Equations
2.3 Treatment of Interfacial Tension
2.4 Boundary Conditions
3 Modeling of the Three Fluid Contact Line
4 Numerical Setup
5 Computational Performance
6 Results and Discussion
6.1 Single Fluid Droplet Simulations
6.1.1 Comparison of SPH Results to Empirical Findings
6.1.2 Temporal Evolution of the Initial Drop Deformation
6.2 Two Fluid Droplet Simulations
7 Conclusion
References
Smoothed Particle Hydrodynamics for Numerical Predictions of Primary Atomization
1 Introduction
2 Numerical Method
3 Reference Setup
4 Code Framework and Performance
5 Simulation of a Planar Prefilming Airblast Atomizer
5.1 Computation Details
5.2 Breakup Behavior and Spray Characteristics
6 Conclusion and Outlook
References
Towards Solving Fluid Flow Domain Identification Problems with Adjoint Lattice Boltzmann Methods
1 Introduction
2 Parameterised Fluid Flow Simulations with a Porous Media BGK-Boltzmann Model
2.1 Mesoscopic Modeling
2.2 Lattice Boltzmann Algorithm: Collide and Stream
2.3 Parallel Implementation
3 A Sensitivity-Based Strategy to Solve Fluid Flow Domain Identification Problems
3.1 Formulation of a General Fluid Flow Control Problem
3.2 Objective and Dual Problem Formulation for Domain Identification Problems
3.3 Adjoint Lattice Boltzmann Method: Collide and Stream
3.4 Adjoint Lattice Boltzmann Algorithm and Its Parallel Realisation
4 Numerical Experiments
4.1 Domain Identification Test Case
4.2 Single Core Performance Improvements
4.3 Parallel Efficiency and Scaling
4.3.1 Strong scaling
4.3.2 Weak Scaling
5 Conclusion
References
Investigation on Air Entrapment in Paint Drops Under Impact onto Dry Solid Surfaces
1 Introduction
2 Numerical Method
2.1 Governing Equations
2.2 Computational Domain, Mesh and Boundary Conditions
3 Simulation Results
3.1 Some Validation of Simulation Results
3.2 Newtonian Drop Impact on a Dry Solid Surface
3.2.1 Mechanism of Air Entrapment Under Droplet Impacting on a Solid Surface
3.2.2 Air Bubble Formation and Release Under Droplet Impactingon a Solid Surface
3.2.3 Effect of Liquid Property and Impact Velocity on the Air Entrapment
3.2.4 Effect of Liquid Property and Impact Velocity on the Spreading Factors
3.3 Yield-Stress Drop Impact onto a Dry Solid Surface
3.3.1 A Rheological Model of Yield-Stress Fluid
3.3.2 Simulation Results
4 Conclusions
References
Numerical Study of the Impact of Praestol® Droplets on Solid Walls
1 Introduction
2 Numerical Method
2.1 Simulation of Multiphase Flows with VOF and PLIC
2.2 Treatment of Non-Newtonian Shear-Thinning Liquids
3 Numerical Setup
4 Results
5 Computational Performance
6 Conclusions
References
Turbulent Skin-Friction Drag Reduction at High Reynolds Numbers
1 Introduction
2 Goals and Methods
3 Computational Details
4 Results
5 Conclusion
References
Control of Spatially Developing Turbulent Boundary Layers for Skin Friction Drag Reduction
1 Introduction
2 Description and Goals
3 Numerical Procedure
4 Computational Details
5 Results
5.1 Opposition Control in Spatially Developing Turbulent Boundary Layers
5.2 Downstream Behaviour of Locally Controlled Spatially Developing Turbulent Boundary Layers
6 Conclusions and Outlook
References
Scalability of OpenFOAM with Large Eddy Simulations and DNS on High-Performance Systems
1 Introduction
2 Turbulent Backward Facing Step
2.1 LES Principles and Modelling
2.2 Numerical Setup
2.3 Performance Results
3 Laminar Lid-Driven Cavity Flow
4 Conclusion
References
Numerical Simulation of Subsonic and Supersonic Impinging Jets II
1 Introduction
2 Numerical Method and Code Performance
3 Heat Transfer
3.1 Introduction
3.2 Results
3.2.1 Non-pulsed Impinging Jet
3.2.2 Pulsed Impinging Jet
3.3 Conclusion
4 Impinging Tone
4.1 Introduction
4.2 Results
4.2.1 Shock-Vortex-Interaction
4.2.2 Shock-Vortex-Shock-Interaction
4.2.3 Emanated Sound
4.3 Conclusion
References
Aeroacoustic Simulations of Ducted Axial Fan and Helicopter Engine Nozzle Flows
1 Introduction
2 Numerical Method
3 Effect of Tip-Gap Size on Fan Aeroacoustics
3.1 Effect of Tip-Gap Size on the Overall Flow Field
3.2 Effect of Tip-Gap Size on the Acoustic Field
4 Effect of the Interior Nozzle Geometry on Jet Aeroacoustics
4.1 Flow Field
4.2 Acoustic Field
5 Computational Specifications and Scalability Analysis
6 Conclusion
References
Adding Hybrid Mesh Capability to a CFD-Solver for Helicopter Flows
1 Introduction
2 Initial Numerical Code
3 Hybrid Mesh Implementation
3.1 High Performance Computing and Parallelization
4 Validation Case
5 HPC Simulation of a Hybrid-Meshed Helicopter
5.1 Mesh Generation
5.2 Evaluation
6 Advances in Code Optimization
7 Conclusions
References
Direct Numerical Simulation of Heated Pipe Flow with Strong Property Variation
1 Introduction
2 Computational Details
2.1 Governing Equations
2.2 Numerical Method
2.3 Inflow Turbulence
3 Results and Discussion
3.1 Bulk Properties
3.2 Average Flow Field and Secondary Flow
3.3 Turbulence Statistics
4 Computational Performance
5 Conclusions
References
CFD Analysis of Fast Transition from Pump Mode to Generating Mode in a Reversible Pump Turbine
1 Introduction
2 Computational Mesh
3 Numerical Setup and Methodology
4 Computational Resources
5 Simulation Results for the Transient
5.1 Results in the Guide Vanes
5.2 Results in the Runner
5.3 Results in the Draft Tube
6 Conclusion and Outlook
References
Scale Resolving Flow Simulations of a Francis Turbine Using Highly Parallel CFD Simulations
1 Introduction
2 Numerical Methods
2.1 Flow Solver
2.2 Turbulence Modelling
2.3 Temporal and Spatial Discretisation
3 Francis Turbine Case
3.1 Computational Setup
3.2 Global Machine Data
3.3 Flow Analysis
3.4 Vortex Rope Induced Pressure Pulsations
3.5 Turbulence Evaluation
4 Parallelisation and Computational Resources
5 Conclusion
References
CFD Simulations of Thermal-Hydraulic Flows in a Model Containment: Phase Change Model and Verification of Grid Convergence
1 Introduction
2 Computational Model
2.1 Mathematical Approach and Droplet Modeling
2.2 Grid Convergence Index
2.3 Parallelization
3 Phase Change Model
3.1 Consideration of Droplet Heating
3.2 Phase Change Model and Relevant Equations
4 Numerical Method
4.1 Geometry and Boundary Conditions
4.2 Numerical Setup
5 Results
5.1 Results of the Grid Convergence Index
5.2 Parallelization
6 Conclusions
References
Simulations of Unsteady Aerodynamic Effects on Innovative Wind Turbine Concepts
1 Introduction
2 Numerical Setup and Computational Details
2.1 Numerical Methods
2.2 Numerical Setups
2.2.1 Three-Bladed Turbine
2.2.2 Two-Bladed Turbine
3 FLOWer at HLRS
4 Grid Convergence Study
4.1 Approach
4.2 Results of the Grid Convergence Study
5 Results
5.1 Influence of Temporal Discretization on the Simulation of Coupled Leading and Trailing Edge Flaps
5.2 Influence of Yawed Inflow on a Two-Bladed Turbine
6 Conclusion
References
Part V Transport and Climate
Simulation of the Rain Belt of the West African Monsoon (WAM) in High Resolution CCLM Simulation
1 Introduction
2 Material and Methods
2.1 CCLM Model and Model Setup
2.2 Investigation Area
2.3 Observational Reference
3 Results
4 Conclusion
5 Details on the Computation Setup
References
Anthropogenic Aerosol Emissions and Rainfall Decline in South-West Australia
1 Introduction
2 Methods
2.1 Observational Rainfall, Temperature and Pressure Data
2.2 Aerosol-Aware Regional Climate Model
2.3 Aerosol-Aware Microphysics
3 Results and Discussion
3.1 Long-Term Rainfall Trends in South-West Australia
3.2 Aerosol Effects in High-Resolution Regional Climate Modelling
3.2.1 CCN and IN Number Concentrations
3.2.2 Precipitation
4 Summary and Conclusions
Appendix
References
High-Resolution Climate Projections Using the WRF Model on the HLRS
1 Introduction and Motivation
2 WRF Simulations at HLRS
2.1 Description of Forcing Data
2.2 Technical Description
3 Results
3.1 Comparison of GCM and WRF: Temperature
3.2 GCM-RCP and WRF-RCP Projections: Temperature
3.3 WRF-RCP Projections: Precipitation
4 Conclusion and Outlook
References
Biogeophysical Impacts of Land Surface on Regional Climate in Central Vietnam
1 Introduction
2 Data and Methods
3 Results
3.1 Temporal Modification of LULC Physical Properties
3.2 Spatial Modification of LULC Physical Properties
4 Impacts of Updated LULC on Climate Variables
4.1 Temporal Impacts of Updated LULC on Climate Variables
4.2 Spatial Impacts of Updated LULC on Climate Variables
5 CPU Usage and Storage Capacities for This Study
References
Reducing the Uncertainties of Climate Projections: High-Resolution Climate Modeling of Aerosol and Climate Interactions on the Regional Scale Using COSMO-ART: Interaction of Mineral Dust with Atmospheric Radiation over West-Africa
1 Motivation
2 The Model System COSMO-ART
3 Sensitivity Study
3.1 Model Set Up
3.2 Model Results
4 Resources
5 Summary
References
Part VI Miscellaneous Topics
Molecular Simulation Study of Transport Properties for 20 Binary Liquid Mixtures and New Force Fields for Benzene, Toluene and CCl4
1 Introduction
2 New Force Fields
3 Methodology
4 Simulation Results
4.1 Benzene+Toluene
4.2 Acetone+Benzene
4.3 Ethanol+Cyclohexane
5 Conclusion
References
Large-Scale Phase-Field Simulations of Directional Solidified Ternary Eutectics Using High-Performance Computing
1 Introduction
2 Methods
2.1 Phase-Field Method
2.2 Analysis the Second Moment of Inertia
3 Ternary Eutectic Directional Solidification
3.1 System S1
3.2 System S2
3.3 System S3
3.4 Comparison of the Three Systems with the Method of the Second Moment of Inertia
4 Conclusion
References
Seismic Applications of Full Waveform Inversion
1 Introduction
2 Methodology
2.1 Full Waveform Inversion
2.2 Parallel Implementation
3 Results Obtained on FORHLR Phase I
3.1 Application of FWI to Image Submarine Gas Hydrate Deposits
3.1.1 Motivation
3.1.2 FWI Setup and General Inversion Approach
3.1.3 Data Preparation
3.1.4 Results
3.1.5 Summary
3.2 Application of FWI to Marine Data Obtained in a River Delta
3.2.1 Motivation
3.2.2 Prerequisites for FWI and Inversion Strategy
3.2.3 Inversion Results
3.2.4 Summary
3.3 Subsalt Imaging with Acoustic and Elastic FWI
3.3.1 Motivation
3.3.2 Modeling
3.3.3 Results of Resolution Study
3.4 Viscoacoustic FWI for Spatially Uncorrelated Problems
3.4.1 Motivation
3.4.2 Methodology
3.4.3 Synthetic FWI Experiment
3.4.4 Summary
3.5 Joint-FWI of Rayleigh and Love Waves in Shallow Seismics
3.5.1 Motivation
3.5.2 FWI Test Setting
3.5.3 Results
3.5.4 Summary
4 Computational Efforts of FWI on FORHLR Phase I
References
A Massively Parallel Multigrid Method with Level Dependent Smoothers for Problems with High Anisotropies
1 Introduction
2 Problem Description
3 Solver Setup
4 Parallelization
5 Results
References

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