High performance computing: modern systems and practices
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| Language: | English |
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Amsterdam
Elsevier, Morgan Kaufmann Publishers
[2018]
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| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XXVIII, 689 Seiten Illustrationen, Diagramme |
| ISBN: | 9780124201583 |
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| 245 | 1 | 0 | |a High performance computing |b modern systems and practices |c Thomas Sterling, Matthew Anderson, Maciej Brodowicz (School of Infomatics, Computing, and Engineering, Indiana University, Bloomington) ; foreword by C. Gordon Bell |
| 264 | 1 | |a Amsterdam |b Elsevier, Morgan Kaufmann Publishers |c [2018] | |
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| 300 | |a XXVIII, 689 Seiten |b Illustrationen, Diagramme | ||
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Contents
Foreword.xix
Preface. xxi
Acknowledgments. xxvii
CHAPTER 1 Introduction.l
1.1 High Performance Computing Disciplines. 3
1.1.1 Definition.3
1.1.2 Application Programs.'.4
1.1.3 Performance and Metrics. 4
1.1.4 High Performance Computing Systems.5
1.1.5 Supercomputing Problems.7
1.1.6 Application Programming.8
1.2 Impact of Supercomputing on Science, Society, and Security.10
1.2.1 Catalyzing Fraud Detection and Market Data Analytics.10
1.2.2 Discovering, Managing, and Distributing Oil and Gas.10
1.2.3 Accelerating Innovation in Manufacturing.10
1.2.4 Personalized Medicine and Drug Discovery.11
1.2.5 Predicting Natural Disasters and Understanding Climate Change.12
1.3 Anatomy of a Supercomputer.14
1.4 Computer Performance. 16
1.4.1 Performance.16
1.4.2 Peak Performance.17
1.4.3 Sustained Performance.18
1.4.4 Scaling.18
1.4.5 Performance Degradation. 19
1.4.6 Performance Improvement.20
1.5 A Brief History of Supercomputing.21
1.5.1 Epoch 1—Automated Calculators Through Mechanical Technologies.22
1.5.2 Epoch II—von Neumann Architecture in Vacuum Tubes.24
1.5.3 Epoch III—Instruction-Level Parallelism. 29
1.5.4 Epoch IV—Vector Processing and Integration. 30
1.5.5 Epoch V—Single-Instruction Multiple Data Array.33
1.5.6 Epoch VI—Communicating Sequential Processors and Very Large
Scale Integration. 34
1.5.7 Epoch VII—Multicore Petaflops.37
1.5.8 Neodigital Age and Beyond Moore’s Law.37
1.6 This Textbook as a Guide and Tool for the Student.38
a •
VII
CONTENTS
■ ■ fl
VIII
1.7 Summary and Outcomes of Chapter 1.39
1.8 Questions and Problems.40
References.41
CHAPTER 2 HPC Architecture 1 : Systems and Technologies.43
2.1 Introduction.44
2.2 Key Properties of HPC Architecture.44
2.2.1 Speed.45
2.2.2 Parallelism.45
2.2.3 Efficiency.46
2.2.4 Power.46
2.2.5 Reliability.47
2.2.6 Programmability.48
2.3 Parallel Architecture Families—Flynn’s Taxonomy.48
2.4 Enabling Technology.51
2.4.1 Technology Epochs.51
2.4.2 Roles of Technologies.55
2.4.3 Digital Logic.55
2.4.4 Memory Technologies.58
2.5 von Neumann Sequential Processors.62
2.6 Vector and Pipelining.64
2.6.1 Pipeline Parallelism.65
2.6.2 Vector Processing.68
2.7 Single-Instruction, Multiple Data Array.69
2.7.1 Single-Instruction, Multiple Data Architecture.69
2.7.2 Amdahl’s Law.70
2.8 Multiprocessors.73
2.8.1 Shared-Memory Multiprocessors.74
2.8.2 Massively Parallel Processors.76
2.8.3 Commodity Clusters.77
2.9 Heterogeneous Computer Structures.78
2.10 Summary and Outcomes of Chapter 2.78
2.11 Questions and Problems.80
References. 82
CHAPTER 3 Commodity Clusters.83
3.1 Introduction.84
3.1.1 Definition of “Commodity Cluster”.84
3.1.2 Motivation and Justification for Clusters.84
3.1.3 Cluster Elements.85
CONTENTS ix
3.1.4 Impact on Top 500 List.86
3.1.5 Brief History.88
3.1.6 Chapter Guide.90
3.2 Beowulf Cluster Project. 91
3.3 Hardware Architecture.:.93
3.3.1 The Node.93
3.3.2 System Area Networks.94
3.3.3 Secondary Storage. 95
3.3.4 Commercial Systems Summary.95
3.4 Programming Interfaces. 97
3.4.1 High Performance Computing Programming Languages.;.97
3.4.2 Parallel Programming Modalities.97
3.5 Software Environment.98
3.5.1 Operating Systems.98
3.5.2 Resource Management.99
3.5.3 Debugger.101
3.5.4 Performance Profiling. 101
3.5.5 Visualization.101
3.6 Basic Methods of Use. 104
3.6.1 Logging On. .104
3.6.2 User Space and Directory System.105
3.6.3 Package Configuration and Building.110
3.6.4 Compilers and Compiling.112
3.6.5 Running Applications.113
3.7 Summary and Outcomes of Chapter 3. 113
3.8 Questions and Exercises. 114
References. 114
CHAPTER 4 Benchmarking. ns
4.1 Introduction. 115
4.2 Key Properties of an HPC Benchmark.117
4.3 Standard HPC Community Benchmarks.120
4.4 Highly Parallel Computing Linpack.120
4.5 HPC Challenge Benchmark Suite.123
4.6 High Performance Conjugate Gradients.126
4.7 NAS Parallel Benchmarks.130
4.8 Graph500. 132
4.9 Miniapplications as Benchmarks.'.135
4.10 Summary and Outcomes of Chapter 4.138
4.11 Exercises.139
References. .139
X
CONTENTS
CHAPTER 5 The Essential Resource Management. 141
5.1 Managing Resources.;.142
5.2 The Essential SLURM.146
5.2.1 Architecture Overview.147
5.2.2 Workload Organization. 148
5.2.3 SLURM Scheduling.149
5.2.4 Summary of Commands.151
5.2.5 SLURM Job Scripting.166
5.2.6 SLURM Cheat Sheet.171
5.3 The Essential Portable Batch System.172
5.3.1 Portable Batch System Overview.172
5.3.2 Portable Batch System Architecture.173
5.3.3 Summary of PBS Commands.174
5.3.4 PBS Job Scripting.184
5.3.5 PBS Cheat Sheet.186
5.4 Summary and Outcomes of Chapter 5. 187
5.5 Questions and Problems.189
References.190
CHAPTER 6 Symmetric Multiprocessor Architecture.191
6.1 Introduction.191
6.2 Architecture Overview.192
6.3 Amdahl’s Law Plus.196
6.4 Processor Core Architecture.199
6.4.1 Execution Pipeline.200
6.4.2 Instruction-Level Parallelism.201
6.4.3 Branch Prediction.201
6.4.4 Forwarding.202
6.4.5 Reservation Stations.202
6.4.6 Multithreading.203
6.5 Memory Hierarchy.204
6.5.1 Data Reuse and Locality.204
6.5.2 Memory Hierarchy.205
6.5.3 Memory System Performance.207
6.6 PCI Bus.209
6.7 External I/O Interfaces.213
6.7.1 Network Interface Controllers.213
6.7.2 Serial Advanced Technology Attachment.215
6.7.3 JTAG.218
6.7.4 Universal Serial Bus.220
6.8 Summary and Outcomes of Chapter 6.222
6.9 Questions and Exercises.223
References.224
CONTENTS xi
CHAPTER 7 The Essential OpenMP. 225
7.1 Introduction. 225
7.2 Overview of OpenMP Programming Model. 226
7.2.1 Thread Parallelism.226
7.2.2 Thread Variables. 228
7.2.3 Runtime Library and Environment Variables.228
7.3 Parallel Threads and Loops. 231
7.3.1 Parallel Threads. 231
7.3.2 Private.232
7.3.3 Parallel “For”. 233
7.3.4 Sections. 239
7.4 Synchronization.241
7.4.1 Critical Synchronization Directive.242
7.4.2 The Master Directive.242
7.4.3 The Barrier Directive.243
7.4.4 The Single Directive.243
7.5 Reduction.244
7.6 Summary and Outcomes of Chapter 7. 245
7.7 Questions and Problems. 246
Reference.247
CHAPTER 8 The Essential MPI.249
8.1 Introduction.250
8.2 Message-Passing Interface Standards.251
8.3 Message-Passing Interface Basics. 253
8.3.1 mpi.h.253
8.3.2 MPIJnit.253
8.3.3 MPLFinalize.254
8.3.4 Message-Passing Interface Example-Hello World.254
8.4 Communicators.255
8.4.1 Size. 256
8.4.2 Rank. 256
8.4.3 Example. 257
8.5 Point-to-Point Messages.258
8.5.1 MPI Send.259
\
8.5.2 Message-Passing Interface Data Types.'.259
8.5.3 MPIRecv.259
8.5.4 Example. 260
8.6 Synchronization Collectives. 262
8.6.1 Overview of Collective Calls.262
8.6.2 Barrier Synchronization. 263
8.6.3 Example. 264
xii CONTENTS
8.7 Communication Collectives.265
8.7.1 Collective Data Movement.265
8.7.2 Broadcast. 268
8.7.3 Scatter.269
8.7.4 Gather.271
8.7.5 Allgather.,.272
8.7.6 Reduction Operations.274
8.7.7 Alltoall.277
8.8 Nonblocking Point-to-Point Communication.279
8.9 User-Defined Data Types.281
8.10 Summary and Outcomes of Chapter 8.283
8.11 Exercises.283
References.284
CHAPTER 9 Parallel Algorithms.285
9.1 Introduction.285
9.2 Fork-Join.286
9.3 Divide and Conquer.287
9.4 Manager-Worker.291
9.5 Embarrassingly Parallel.292
9.6 Halo Exchange.294
9.6.1 The Advection Equation Using Finite Difference.295
9.6.2 Sparse Matrix Vector Multiplication.297
9.7 Permutation: Cannon’s Algorithm.301
9.8 Task Dataflow: Breadth First Search.306
9.9 Summary and Outcomes of Chapter 9.310
9.10 Exercises.311
References. 311
CHAPTER 10 Libraries.313
10.1 Introduction.313
10.2 Linear Algebra.315
10.2.1 Basic Linear Algebra Subprograms.317
10.2.2 Linear Algebra Package.324
10.2.3 Scalable Linear Algebra Package. 326
10.2.4 GNU Scientific Library. 326
10.2.5 Supemodal LU.326
10.2.6 Portable Extensible Toolkit for Scientific Computation.327
10.2.7 Scalable Library for Eigenvalue Problem Computations.328
10.2.8 Eigenvalue SoLvers for Petafiop-Applications.328
10.2.9 Hypre: Scalable Linear Solvers and Multigrid Methods.328
10.2.10 Domain-Specific Languages for Linear Algebra.329
CONTENTS xiii
10.3 Partial Differential Equations.329
10.4 Graph Algorithms.329
10.5 Parallel Input/Output.330
10.6 Mesh Decomposition.333
10.7 Visualization.334
10.8 Parallelization.334
10.9 Signal Processing.334
10.10 Performance Monitoring.341
10.11 Summary and Outcomes of Chapter 10.342
10.12 Exercises.343
References.344
CHAPTER 11 Operating Systems.347
11.1 Introduction.347
11.2 Operating System Structures and Services.349
11.2.1 System Components.349
11.2.2 Process Management.349
11.2.3 Memory Management. 350
11.2.4 File Management.350
11.2.5 I/O System Management.351
11.2.6 Secondary Storage Management.351
11.3 Process Management.351
11.3.1 Process States.352
11.3.2 Process Control Block.353
11.3.3 Process Management Activities.354
11.3.4 Scheduling.355
11.4 Threads.357
11.5 Memory Management.358
11.5.1 Virtual Memory. 359
11.5.2 Virtual Page Addresses.359
“■ 11.5.3 Virtual Address Translation.359
11.6 Summary and Outcomes of Chapter 11.361
11.7 Exercises. 362
CHAPTER 12 Visualization. 363
12.1 Introduction.363
12.2 Foundational Visualization Concepts.364
12.3 Gnuplot.365
12.4 Matplotlib. 369
12.5 The Visualization Toolkit.372
12.6 ParaView.379
12.7 Visit. 380
xiv CONTENTS
12.8 Summary and Outcomes of Chapter 12. 381
12.9 Exercises.381
References.382
CHAPTER 13 Performance Monitoring. 383
13.1 Introduction. 383
13.2 Time Measurement.385
13.3 Performance Profiling.390
13.3.1 Significance of Application Profiling.390
13.3.2 Essential gperftools.391
13.4 Monitoring Hardware Events.398
13.4.1 Perf.398
13.4.2 Performance Application Programming Interface.404
13.5 Integrated Performance Monitoring Toolkits.407
13.6 Profiling in Distributed Environments.411
13.7 Summary and Outcomes of Chapter 13.417
13.8 Questions and Problems.418
References.419
CHAPTER 14 Debugging.421
14.1 Introduction.421
14.2 Tools.423
14.2.1 The GNU Debugger.423
14.2.2 Valgrind.430
14.2.3 Commercial Parallel Debuggers.431
14.3 Debugging OpenMP Example: Accessing an Unprotected Shared Variable.433
14.4 Debugging MPI Example: Deadlock.434
14.5 Compiler Flags for Debugging.439
14.6 System Monitors to Aid Debugging.441
14.7 Summary and Outcomes of Chapter 14. 445
14.8 Exercises.446
References.450
CHAPTER 15 Accelerator Architecture.451
15.1 Introduction.451
15.2 A Historic Perspective.454
15.2.1 Coprocessors.456
15.2.2 Accelerators in Processor I/O Space.461
15.2.3 Accelerators with Industry-Standard Interfaces.462
15.3 Introduction to Graphics Processing Units. 464
15.4 Evolution of Graphics Processing Unit Functionality.466
15.5 Modern Graphics Processing Unit Architecture.471
CONTENTS xv
15.5.1 Compute Architecture.471
15.5.2 Memory Implementation. 474
15.5.3 Interconnects.475
15.5.4 Programming Environment.476
15.6 Heterogeneous System Architecture.477
15.7 Summary and Outcomes of Chapter 15.480
15.8 Problems and Questions.480
References.1.481
CHAPTER 16 The Essential OpenACC.483
16.1 Introduction.483
16.1.1 CUDA.485
16.1.2 OpenCL. 485
16.1.3 C++AMP.486
16.1.4 OpenACC.486
16.2 OpenACC Programming Concepts.487
16.3 OpenACC Library Calls.;.489
16.4 OpenACC Environment Variables.491
16.5 OpenACC Directives.492
16.5.1 Parallel Construct.493
16.5.2 Kernels Construct.495
16.5.3 Data Management. 497
16.5.4 Loop Scheduling.501
16.5.5 Variable Scope.504
16.5.6 Atomics.504
16.6 Summary and Outcomes of Chapter 16.506
16.7 Questions and Problems.506
References. 508
CHAPTER 17 Mass Storage.509
17.1 Introduction. 509
17.2 Brief History of Storage. 512
17.3 Storage Device Technology.514
17.3.1 Hard Disk Drives.514
17.3.2 Solid-State Drive Storage.520
17.3.3 Magnetic Tape. 524
17.3.4 Optical Storage.529
17.4 Aggregated Storage. 534
17.4.1 Redundant Array of Independent Disks.534
17.4.2 Storage Area Networks.541
17.4.3 Network Attached Storage. 543
17.4.4 Tertiary Storage.544
xvi CONTENTS
17.5 Summary and Outcomes of Chapter 17.545
.17.6 Questions and Problems.546
References.547
CHAPTER 18 File Systems.549
18.1 Role and Function of File Systems.549
18.2 The Essential POSIX File Interface.554
18.2.1 System Calls for File Access.554
18.2.2 Buffered File I/O.559
18.3 Network File System.562
18.4 General Parallel File System.565
18.5 Lustre File System.569
18.6 Summary and Outcomes of Chapter 18.575
18.7 Questions and Problems.576
References.577
CHAPTER 19 MapReduce.579
19.1 Introduction.579
19.2 Map and Reduce.579
19.2.1 Word Count.581
19.2.2 Shared Neighbors.581
19.2.3 K-Means Clustering.582
19.3 Distributed Computation.584
19.4 Hadoop.585
19.5 Summary and Outcomes of Chapter 19.588
19.6 Exercises.589
References.589
CHAPTER 20 Checkpointing.591
20.1 Introduction. 591
20.2 System-Level Checkpointing.592
20.3 Application-Level Checkpointing.598
20.4 Summary and Outcomes of Chapter 20.602
20.5 Exercises.602
References.603
CHAPTER 21 Next Steps and Beyond.605
21.1 Introduction. 606
21.2 Expanded Parallel Programming Models.606
21.2.1 Advance in Message-Passing Interface.606
21.2.2 Advances in OpenMP.607
21.2.3 MPI+X.607
CONTENTS xvii
21.3 Extended High Performance Computing Architecture.608
21.3.1 The World’s Fastest Machine.608
21.3.2 Lightweight Architectures.608
21.3.3 Field Programmable Gate Arrays. 609
21.4 Exascale Computing.610
21.4.1 Challenges to Exascale Computing.611
21.4.2 Doing the Math, How Big Is Exascale?.611
21.4.3 The Accelerated Approach.612
21.4.4 Lightweight Cores.612
21.5 Asynchronous Multitasking.613
21.5.1 Multithreaded. 613
21.5.2 Message-Driven Computation.613
21.5.3 Global Address Space.614
21.5.4 Actor Synchronization.615
21.5.5 Runtime System Software.615
21.6 The Neodigital Age.616
21.6.1 Dataflow. 617
21.6.2 Cellular Automata.618
21.6.3 Neuromorphic. 619
21.6.4 Quantum Computing.619
21.7 Exercises. 620
References.621
Appendix A: Essential C. 623
Appendix B: Essential Linux.639
Glossary.667
Index.677 |
| any_adam_object | 1 |
| author | Sterling, Thomas L. 1949- Anderson, Matthew Brodowicz, Maciej |
| author_GND | (DE-588)1089637063 (DE-588)1153741202 (DE-588)1153741385 (DE-588)141471018 |
| author_facet | Sterling, Thomas L. 1949- Anderson, Matthew Brodowicz, Maciej |
| author_role | aut aut aut |
| author_sort | Sterling, Thomas L. 1949- |
| author_variant | t l s tl tls m a ma m b mb |
| building | Verbundindex |
| bvnumber | BV044760484 |
| classification_rvk | ST 151 ST 150 QH 500 ST 155 |
| classification_tum | DAT 105f |
| ctrlnum | (OCoLC)1022286633 (DE-599)GBV896648141 |
| discipline | Informatik Wirtschaftswissenschaften |
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| id | DE-604.BV044760484 |
| illustrated | Illustrated |
| indexdate | 2025-02-20T06:41:07Z |
| institution | BVB |
| isbn | 9780124201583 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-030155893 |
| oclc_num | 1022286633 |
| open_access_boolean | |
| owner | DE-11 DE-739 DE-863 DE-BY-FWS DE-355 DE-BY-UBR DE-91G DE-BY-TUM DE-29T DE-706 DE-573 |
| owner_facet | DE-11 DE-739 DE-863 DE-BY-FWS DE-355 DE-BY-UBR DE-91G DE-BY-TUM DE-29T DE-706 DE-573 |
| physical | XXVIII, 689 Seiten Illustrationen, Diagramme |
| publishDate | 2018 |
| publishDateSearch | 2018 |
| publishDateSort | 2018 |
| publisher | Elsevier, Morgan Kaufmann Publishers |
| record_format | marc |
| spellingShingle | Sterling, Thomas L. 1949- Anderson, Matthew Brodowicz, Maciej High performance computing modern systems and practices Parallelrechner (DE-588)4173280-7 gnd Mehrprozessorsystem (DE-588)4038397-0 gnd Vektorrechner (DE-588)4062470-5 gnd |
| subject_GND | (DE-588)4173280-7 (DE-588)4038397-0 (DE-588)4062470-5 |
| title | High performance computing modern systems and practices |
| title_auth | High performance computing modern systems and practices |
| title_exact_search | High performance computing modern systems and practices |
| title_full | High performance computing modern systems and practices Thomas Sterling, Matthew Anderson, Maciej Brodowicz (School of Infomatics, Computing, and Engineering, Indiana University, Bloomington) ; foreword by C. Gordon Bell |
| title_fullStr | High performance computing modern systems and practices Thomas Sterling, Matthew Anderson, Maciej Brodowicz (School of Infomatics, Computing, and Engineering, Indiana University, Bloomington) ; foreword by C. Gordon Bell |
| title_full_unstemmed | High performance computing modern systems and practices Thomas Sterling, Matthew Anderson, Maciej Brodowicz (School of Infomatics, Computing, and Engineering, Indiana University, Bloomington) ; foreword by C. Gordon Bell |
| title_short | High performance computing |
| title_sort | high performance computing modern systems and practices |
| title_sub | modern systems and practices |
| topic | Parallelrechner (DE-588)4173280-7 gnd Mehrprozessorsystem (DE-588)4038397-0 gnd Vektorrechner (DE-588)4062470-5 gnd |
| topic_facet | Parallelrechner Mehrprozessorsystem Vektorrechner |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030155893&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT sterlingthomasl highperformancecomputingmodernsystemsandpractices AT andersonmatthew highperformancecomputingmodernsystemsandpractices AT brodowiczmaciej highperformancecomputingmodernsystemsandpractices AT bellcgordon highperformancecomputingmodernsystemsandpractices |
Indexes
THWS Würzburg Zentralbibliothek Lesesaal
| Call Number: |
1000 ST 150 S838 |
|---|---|
| Copy 1 | ausleihbar Available Place a Hold |