Computer performance issues

Cover Page\r......Page 1
Copyright Page\r......Page 2
Contributors......Page 3
Preface......Page 7
The UK HPC Integration Market: Commodity-Based Clusters......Page 9
Introduction......Page 12
The HPC Clusters of Today......Page 13
Hardware and HPC Cluster Performance......Page 15
The CPU......Page 16
System Packaging......Page 17
Connectivity......Page 18
Future Developments......Page 19
Custom and Commodity Clusters......Page 20
Operational Challenges with Large Systems......Page 23
Capacity Through Beowulf Clusters......Page 25
Power and Space......Page 26
The UK HPC Landscape......Page 27
HPCx......Page 29
HECToR......Page 30
SRIF3: 2006-2008......Page 31
Funding Research in the UK-Full-Economic Costing......Page 33
Challenges Faced by University HPC Facilities......Page 34
Brief Summary of the Clusters Deployed in 2007......Page 40
Tier-1 and System Integrators......Page 43
UK Integrators of Commodity Clusters......Page 44
HPC System Integrator Criteria......Page 45
ClusterVision......Page 46
Install Base......Page 47
Company Details and Size......Page 48
Company Expertise......Page 49
Relationship to Tier-1 Organizations......Page 50
OCF plc......Page 51
Company Details and Size......Page 52
Company Expertise......Page 53
Marketplace......Page 54
Relationship to Tier-1 Organizations......Page 56
Streamline Computing......Page 57
Install Base (During 2007)......Page 60
Marketplace......Page 61
Relationship to Tier-1 Organizations......Page 63
Other Cluster Suppliers in the UK......Page 64
Compusys......Page 65
Cambridge Online Systems Ltd......Page 67
Silicon Mechanics......Page 68
Linux Networx......Page 71
Western Scientific......Page 73
SCC......Page 74
Workstations UK......Page 75
Bull......Page 76
Comprehensive Services and Solutions......Page 77
Install Base......Page 78
Company Expertise......Page 79
Relationship to Tier-1 Organizations......Page 82
Relationship to Other System Integrators......Page 83
Install Base......Page 84
Company Details and Size......Page 85
International Presence......Page 86
Company Expertise......Page 87
Marketplace......Page 89
Relationship to Other Organizations......Page 90
Node Performance......Page 91
Evaluation Systems......Page 98
Interconnect Performance......Page 99
Molecular Simulation-DL_POLY......Page 101
Materials Simulation-CPMD......Page 104
Computational Engineering-PDNS3D......Page 108
Application Performance......Page 110
Summary and Conclusions......Page 112
Initial Integrator Discussion Points Around HPC Provision......Page 116
References......Page 117
Abstract......Page 120
Introduction......Page 122
Low-Level FPGA Models......Page 124
FPGA Computation Basics......Page 126
Sample Applications......Page 127
Multigrid for Electrostatic Computation......Page 128
Modeling Molecular Interactions (Docking)......Page 130
Sequence Alignment: BLAST......Page 131
Microarray Data Analysis Case Study: Finding Best Combinations......Page 132
Characteristics of Computations Amenable to FPGA Acceleration......Page 133
Methods for Avoiding Implementational Heat......Page 134
Overview......Page 135
Sequence Alignment Using BLAST......Page 136
Discrete Event-Based Molecular Dynamics (DMD)......Page 137
Example......Page 139
Flash Structure......Page 140
Finding Repetitive Structures in Biological Sequences......Page 142
Source Code Transformation Approach......Page 143
Example......Page 144
Example......Page 145
Examples......Page 146
Overview......Page 148
Example......Page 149
Example......Page 150
Example......Page 151
Scale Application for Maximal Use of Target Hardware......Page 153
Overview......Page 155
Data Path Structure......Page 156
Task Scheduling......Page 157
Comparison with HPRC......Page 158
Conclusion......Page 159
References......Page 161
Contents of Volumes in This Series......Page 165
Introduction......Page 166
Benchmarking Challenges......Page 168
Current Energy-Efficiency Metrics......Page 169
Component-Level Benchmarks and Metrics......Page 170
System-Level Benchmarks and Metrics......Page 171
Data Center-Level Benchmarks and Metrics......Page 172
Energy-Efficiency Benchmark Goals......Page 173
Workload......Page 174
Metric......Page 175
Energy Efficiency of Past Sort Benchmark Winners......Page 178
Design of the JouleSort Winner......Page 180
Other Energy-Efficiency Metrics......Page 182
Conclusions......Page 188
Power and Thermal Modeling Challenges......Page 189
Model Properties......Page 190
Simulation-Based Models......Page 191
Detailed Analytical Models......Page 193
Processor and Memory Models......Page 195
Server Models......Page 196
Overview......Page 197
Calibration Software Suite......Page 199
Portability and Limitations......Page 200
Model Inputs......Page 201
Models Studied......Page 202
Evaluation Setup......Page 203
Machines......Page 204
Benchmarks......Page 205
Results......Page 207
Summary......Page 209
Online Thermal Modeling and Management......Page 210
Location-Aware Infrastructure Properties......Page 214
Splice Architecture......Page 215
Implementation Results......Page 216
Temperature Modeling with ConSil......Page 217
Problem Statement......Page 219
Implementation......Page 221
Results......Page 223
Data Center Thermal Modeling: Weatherman......Page 225
Problem Statement......Page 226
Implementation......Page 227
Results......Page 228
Conclusions......Page 230
Metrics......Page 231
Power Models......Page 232
Summary......Page 233
References......Page 234
The Emerging Landscape of Computer Performance Evaluation......Page 240
User-Application Taxonomy......Page 241
Perspective......Page 245
Workload-Specific Processors......Page 250
Computer Architecture-General-Purpose Processors......Page 252
Real-Time Embedded Systems and Application-Specific Processors (ASPs)......Page 253
Workload-Specific Processors......Page 254
Personalized Architectures......Page 256
Architectures......Page 257
Experimental Results......Page 261
Workload Time Granularity......Page 263
Webpage Trends Analysis......Page 266
Experiments......Page 269
Discussion......Page 272
Spectroprocessing for Qualitative Computation......Page 273
A Universal Problem......Page 275
Enabling Constant Effort Access......Page 278
References......Page 281
Advances in Web Testing......Page 286
Introduction......Page 287
Heterogeneity and Distribution of Components......Page 289
Unpredictable Control Flow......Page 290
Development Factors, Adjusted Quality Requirements, and Novel Constructs......Page 291
Web Application Models......Page 292
Markov Models and Statecharts......Page 293
Object-Oriented Models......Page 295
Web Test Case Generation......Page 297
Markov Models and Statecharts......Page 298
Object-Oriented Models......Page 299
Portability Analysis......Page 300
Manual and Automated Execution-Based Approach......Page 301
Lookup-Based Approach......Page 304
Conclusion......Page 307
References......Page 308
Author Index\r......Page 312
Subject Index\r......Page 322
Contents of Volumes in This Series\r......Page 340