High Performance Computing on Vector Systems 2010 (eBook)

Preface 4
Contents 6
Operating System and Software for Large Scale Systems 12
Light-Weight Kernel with Portals 13
Introduction 13
Kitten 15
OFED 16
Benchmarks 17
Portals 17
Portals: A Brief Introduction 18
Optimizing Portals for LWK 19
A High-Performance Infiniband NAL 20
Benchmarks 21
MPI 22
ORTE Job Preparation and Startup 22
Job Start on the Light-Weight Kernel 24
Architecture of OOB/Portals 25
Conclusion and Future Work 25
References 26
Towards an Architecture for Management of Very Large Computing Systems 27
Introduction 27
Specific Challenges in HPC 28
Challenges 30
Jitter 31
Scalability 32
Data Correlation 33
Error Handling 33
Scheduler Awareness 34
Tool Integration 34
TIMaCS---The Project 35
Idea and Objectives 35
Issues---Addressed and Not Addressed 36
Architecture 37
Administrational Benefits 40
Security Constraints 40
Mission-Critical Constraints 40
Performance Tuning 41
Dynamic Changes 41
Hardware Management 41
Business-Benefits with Business-Policy Based Management 42
Need for Business-Policy Based Job-Scheduling in HPC 42
Approach 43
Conclusion and Future Outlook 44
References 44
Empirical Optimization of Collective Communications with ADCL 46
Introduction and Motivation 46
The Abstract Data and Communication Library (ADCL) 47
Semantics of the New ADCL Interfaces 49
The Vector-Map Object 49
Extension of the ADCL Interfaces 51
The New Function Sets 52
Performance Evaluation 53
Integration of ADCL 53
Setup 55
Results 55
Summary and Outlook 57
References 58
I/O Strategies 59
I/O Forwarding on NEC SX-9 60
IOFWD Implementation 60
Design of IOFWD 61
IOFWD Components 62
Implementation Status 63
Performance Results 64
IOFWD Usage 64
System Overview at HLRS 65
Application Workflow Example 66
Application Integration, Compilation, Building and Running 67
First Real Application Experiences 68
Conclusion 69
References 69
High-Speed Data Transmission Technology for the NEC SX-9 70
Introduction 70
LSI Technology 72
Serial Interface 72
Clocks 72
High-Speed Circuit Technology 73
Transmission Technology 74
Power Noise Countermeasures 76
Summary 78
References 78
Grid and Cloud Computing 79
The Vector Computing Cloud: Toward a Vector Meta-Computing Environment 80
Introduction 81
Basic Concept of the Vector Computing Clouds 82
Prototyping of the Vector Computing Cloud 83
Virtualizing Vector Supercomputers: GRID VM for SX 84
Job Scheduling on the Vector Computing Cloud 85
MPI Environment for Vector Computing Cloud 88
Feasibility Study and Early Performance Evaluations 88
Performance Evaluation of the Job Scheduling Mechanism 89
System Tests 90
Performance of HPL 93
Conclusions 95
References 95
Full-Scale 3D Vibration Simulator of an Entire Nuclear Power Plant on Simple Orchestration Application Framework 97
Introduction 98
Full-Scale 3D Vibration Simulator for an Entire Nuclear Power Plant 100
GDS Application of Full-Scale 3D Vibration Simulator 100
Needs of Pipelined Data-Transfer Scenario 101
Development of Simple Orchestration Application Framework 103
Functionalities 104
Implementation 104
Full-Scale Simulation of High Temperature Test Engineering Reactor 105
Summaries 108
References 109
Development of Simple Orchestration Application Framework and Its Application to Burning Plasma Simulation 111
Introduction 111
Simple Orchestration Application Framework (SOAF) 113
Overview of SOAF 113
Controller 114
Sentinel 115
Configuration File 116
Development of Simple Orchestration Application Framework 117
Burning Plasma Simulation 118
Experiment 120
Summaries 123
References 124
Acoustics and Structural Mechanic 125
On Sound Generated by a Globally Unstable Round Jet 126
Introduction 126
Numerical Setup 127
Round Jet Flow Simulation 127
Aeroacoustic Computation 129
Parallelization of the Acoustic Solver 131
Results 133
Jet Characteristics 133
Acoustic Results 135
Conclusion 137
References 137
Numerical Simulation of Sibilant [s] Using the Real Geometry of a Human Vocal Tract 140
Introduction 140
Signal Processing for Consonants 141
Sound Induced Flow 141
Sibiant [s] in Dental Treatments 141
Computational Analyses for Sibilant [s] 142
Complicated Morphology of Vocal Tracts 142
LES and Aeroacoustics 142
Materials and Methods 143
Result 145
Discussion 146
Validity of Real Morphological Geometry 147
Aeroacoustic Analyses 148
Requirements for High Performance Computing 149
Conclusion 150
References 150
Identification of Anisotropic Elastic Material Properties by Direct Mechanical Simulations: Estimation of Process Chain Resource Requirements 152
Introduction 152
Material and Methods 153
Theoretical Background---Standard Mechanics Approach 154
Process Chain Description 156
Results 158
Single Sub-Domain 158
Domain Count 159
Accumulation over Process 159
Summary & Conclusions
References 162
Computational Fluid Dynamics 163
Downscaling Climate Simulations for Use in Hydrological Modeling of Medium-Sized River Catchments 164
Introduction 164
The CCLM Model 165
Performance on the HLRS Systems 166
Results 167
Discussion 169
References 170
DNS of Rising Bubbles Using VOF and Balanced Force Surface Tension 172
Introduction 172
Governing Equations 174
Continuity and Navier-Stokes Equations 174
Interface Tracking by the VOF Method 174
Moving Frame of Reference 175
Surface Tension 176
The Continuum Surface Force (CSF) Model 176
Balanced-Force Algorithm 177
Curvature Estimation 178
Numerical Setup 179
Results: Rise Behavior of Bubbles 180
Reduction of Spurious Currents 180
Terminal Rise Velocity 183
Bubble Shape 183
Conclusion 184
References 185
Large-Eddy Simulation of Double-Row Compound-Angle Film-Cooling: Computational Aspects 186
Introduction 186
Simulation Methods 188
Code and Governing Equations 188
Integration and Flux Evaluation 189
Turbulence Modeling 189
Boundary Treatment 190
Computational Environment and Measuring Procedure 190
Performance Results and Flow Field Visualization 191
Sequential Performance of Individual Code Components 191
Overall Parallel Performance 192
Flow Field Visualization 195
Conclusions 195
References 196
Large Eddy Simulation of Wind Turbulence for Appropriate Urban Environment 198