High Performance Computing on Vector Systems 2011 (eBook)

High Performance Computing on Vector Systems 2011 
3 
Preface 5
Contents 7
Part I: Techniques and Tools for High Performance Systems 9
Performance and Scalability Analysisof a Chip Multi Vector Processor 10
1 Introduction 11
2 Chip Multi Vector Processor 12
2.1 Structure of a Chip Multi Vector Processor 12
2.2 Performance Model of a Chip Multi Vector Processor 13
3 Performance Tuning for a Chip Multi Vector Processor 15
3.1 Performance Analysis Using the Roofline Model 15
3.2 Program Optimization 16
3.2.1 Loop Unrolling 16
3.2.2 Cache Blocking 17
3.2.3 Performance Tuning Strategy Based on the Roofline Model 17
4 Performance and Scalability Analysis 18
4.1 Methodology 18
4.2 Benchmarks 19
4.3 Performance Evaluation of CMVP 20
4.4 Performance Evaluation of CMVP with Performance Tuning 22
5 Conclusions 25
References 26
I/O Forwarding for Quiet Clusters 28
1 Introduction 29
2 Operating System Noise 30
2.1 So …Who's the Noisy Neighbour? 31
2.2 Impact on Applications 31
2.3 Mitigation 32
2.3.1 Silence Your System 32
2.3.2 Embrace Noise 33
2.3.3 Synchronize Noise 33
2.3.4 Prioritize 33
2.3.5 Travel Light 33
3 Measuring Noise 34
3.1 Test System 34
3.2 Fixed Work Quanta Benchmark 35
3.3 Fixed Time Quanta Benchmark 36
4 I/O Induced Noise 36
5 I/O Forwarding 38
5.1 I/O Forwarding Architecture 39
5.2 System I/O Interceptors: Libsysio 40
5.3 I/O Forwarding Protocol: IOD Driver and Server 41
5.4 Communication Framework: Portals 41
5.5 Using the I/O Forwarding Framework 42
5.6 Noise 42
5.7 FUSE Driver 44
6 Conclusion 44
References 45
A Prototype Implementation of OpenCL for SX Vector Systems 47
1 Introduction 48
2 OpenCL 48
3 OpenCL for SX 49
4 Early Evaluation and Discussions 51
5 Conclusions 53
References 55
Distributed Parallelization of Semantic Web Java Applications by Means of the Message-Passing Interface 57
1 Introduction 57
2 Use Case Description: Random Indexing 59
3 Parallelization Strategy 60
4 Realization by Means of MPI 61
5 Implementation 63
6 Application Performance Evaluation 64
7 Performance Tailoring: Hybrid MPI-Java Threads Communication Pattern 66
8 Final Discussion and Conclusion 68
References 69
HPC Systems at JAIST and Development of Dynamic Loop Monitoring Tools Toward Runtime Parallelization 71
1 Introduction 71
2 Information Environment and HPC Systems at JAIST 72
3 Development of Dynamic Loop Monitoring Tools Toward Runtime Parallelization 74
3.1 Background and Objectives of Dynamic Loop Monitoring Tools 75
3.2 Parallelism and Loop Nest Structures 75
3.3 Loop Nest Detection and Loop-Call Context Tree Generation 76
3.4 Evaluation of Our L-CCT Generation 78
3.4.1 Experiment 78
3.4.2 Results 78
3.5 Run-Time Data Dependence Analysis 80
3.5.1 Motivations and Strategies 81
3.5.2 Details of Our Runtime Data Dependence Analysis 81
3.5.3 Preliminary Evaluation of Runtime Data Dependence Analysis 82
4 Conclusions 83
References 83
Part II: Methods and Technologies for Large-Scale Systems 85
Tree Based Voxelization of STL Data 86
1 Introduction 86
2 Octree Overview 88
3 Mesh Generation 89
3.1 Intersection Algorithm and Tree Generation 90
3.2 Flooding 92
3.3 Boundary Conditions 92
3.4 The File Format 94
4 Sample Mesh 95
5 Outlook 96
References 96
An Adaptable Simulation Framework Based on a Linearized Octree 98
1 Introduction and Overall Layout of the Apes Framework 98
1.1 Used Technologies 99
1.2 Components of the Apes Suite 99
1.3 Distributed Computing 101
2 Related Work 101
3 The Distributed Linearized Octree 102
3.1 Implementation of the Element Description 102
3.2 Element Properties 104
3.3 Acting on the Tree 106
4 Configuration of Simulation Runs 107
5 Usage in Solvers 107
5.1 Ateles 108
5.2 Musubi 109
6 Outlook 110
References 110
High Performance Computing for Analyzing PB-Scale Data in Nuclear Experiments and Simulations 111
1 Introduction 111
2 Large-Scale Data Integrated Analysis System 112
3 Heterogeneous Processors for Acceleration Large-Data Analyses 113
4 Distributed Parallel Computing Framework with Fault-Tolerance 116
5 Summary 120
References 121
Part III: Computational Fluid Dynamics, Physical Simulation and Engineering Application 122
TASCOM3D: A Scientific Code for Compressible Reactive Flows 123
1 Introduction 123
2 Governing Equations and Numerical Schemes 124
3 Numerical Investigations of NOx-Formation in Scramjet Combustors Using Wall and Strut Injectors 125
3.1 Configuration and Numerical Setup 126
3.2 Results 128
3.3 Conclusion and Further Reading 131
4 Steady and Unsteady RANS Simulations of a Cryogenic Rocket Combustor 131
4.1 Configuration and Numerical Setup 131
4.2 Results 133
4.3 Conclusion and Further Reading 136
5 Performance Analysis 136
5.1 Single CPU Performance 137
5.2 Scaling Performance 138
5.3 Conclusion and Further Reading 139
6 Conclusion 140
References 141
Investigations of Human Nasal Cavity Flows Based on a Lattice-Boltzmann Method 144
1 Introduction 144
2 Numerical Methods 146
2.1 The Lattice-Boltzmann Method with Local Grid Refinement 146
2.2 Computational Grid 149
3 Scalability and Performance Analysis 150
4 Nasal Cavity Flows 152
5 Discussion 156
6 Conflict of Interest 157
References 158
Influence of Adatoms on the Quantum Conductance and Metal-Insulator Transition of Atomic-Scale Nanowires 160
1 Introduction 160
2 Computational Method 161
3 Results 162
References 170
Current Status and Future Direction of Full-Scale Vibration Simulator for Entire Nuclear Power Plants 172
1 Introduction 172
2 Three-Dimensional Vibration Simulator for an Entire Nuclear Power Plant 174
2.1 Methodology of Assembled-Structure Analysis 174
2.2 Computation Platform for Large-Scale Simulation of an Entire Nuclear Plant 175
3 Current Status of Vibration Simulator 175
3.1 Development of Elastic Analysis of High Temperature Engineering Test Reactor 175
3.2 Development of a Feasible Design for the New Concept Tubesheet Structure in Fast Breeder Reactors 177
4 Future Direction of Vibration Simulator 177
4.1 Development of Algorithm in Numerical Calculation 177
4.2 Response Estimation Method for Elasto-Plastic Analysis 179
4.3 Analysis Capability for Seismic Fluid Phenomena 179
4.3.1 Installation of Open Source CFD Software on BX900 179
4.3.2 Development of Characteristic Simulation of Two-Phase Flow Turbulence 180
5 Conclusion 183
References 184