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Cluster Computing with Linux
BackCover
Beowulf Cluster Computing with Linux, Second Edition
Series Foreword
Foreword
Preface to the Second Edition
Acknowledgments for the Second Edition
Preface to the First Edition
Chapter 1: So You Want to Use a Cluster
1.1 What Is a Cluster?
1.2 Why Use a Cluster?
1.3 Understanding Application Requirements
1.4 Building and Using a Cluster
1.5 Another Way to Read This Book
Part I: Enabling Technologies
Chapter 2: Node Hardware
2.1 Node Hardware Overview
2.2 Microprocessor
2.3 Memory
2.4 I/O Channels
2.5 Motherboard
2.6 Persistent Storage
2.7 Video
2.8 Peripherals
2.9 Packaging
2.10 Node Choice and Cluster Construction
Chapter 3: Linux
3.2 The Linux Kernel
3.3 Pruning Your Beowulf Node
3.4 Scalable Services
3.5 Other Considerations
3.6 Final Tuning with /proc
3.7 Conclusions
Chapter 4: System Area Networks
4.1 Network Hardware
4.2 Example Networks
4.3 Network Software
4.4 Performance
4.5 Network Choice
Chapter 5: Configuring and Tuning Cluster Networks
5.1 Cluster Network Designs
5.2 Internet Protocol Stack
5.3 Networking Concepts and Services
5.4 Simple Cluster Configuration Walkthrough
5.5 Improving Performance
5.6 Protecting Your Cluster
5.7 Troubleshooting
Chapter 6: Setting up Clusters
6.1 Challenges
6.2 Hardware Provisioning Challenges and Best Practices
6.3 Different Types of Installation Management
6.4 The Basic Steps
6.5 NPACI Rocks
6.6 The OSCAR Toolkit
6.7 Other Important Toolkits
6.8 When Things go Wrong
6.9 Summary
Part II: Parallel Programming
Chapter 7: An Introduction to Writing Parallel Programs for Clusters
7.1 Creating Task Parallelism
7.2 Operating System Support for Parallelism
7.3 Parameter Studies
7.4 Sequence Matching in Computational Biology
7.5 Decomposing Programs Into Communicating Processes
Chapter 8: Parallel Programming with MPI
8.1 Hello World in MPI
8.2 Manager/Worker Example
8.3 Two-Dimensional Jacobi Example with One-Dimensional Decomposition
8.4 Collective Operations
8.5 Parallel Monte Carlo Computation
8.6 MPI Programming without MPI
8.7 Installing MPICH2 under Linux
8.8 Tools for MPI Programs
8.9 MPI Implementations for Clusters
Chapter 9: Advanced Topics in MPI Programming
9.2 Fault Tolerance
9.3 Revisiting Mesh Exchanges
9.4 Motivation for Communicators
9.5 More on Collective Operations
9.6 Parallel I/O
9.7 Remote Memory Access
9.8 Using C++ and Fortran 90
9.9 MPI, OpenMP, and Threads
9.10 Measuring MPI Performance
9.11 MPI-2 Status
Chapter 10: Parallel Virtual Machine
10.1 The PVM System
10.2 Writing PVM Applications
10.3 Installing PVM
Chapter 11: Fault-Tolerant and Adaptive Programs with PVM
11.1 Considerations for Fault Tolerance
11.2 Building Fault-Tolerant Parallel Applications
11.3 Adaptive Programs
Chapter 12: Numerical and Scientific Software for Clusters
12.1 Dense Linear System Solving
12.2 Sparse Linear System Solving
12.3 Eigenvalue Problems
12.4 FFTW
12.5 Load Balancing
12.6 Support Libraries
12.7 Scientific Applications
12.8 Freely Available Software for Linear Algebra on the Web
Part III: Managing Clusters
Chapter 13: Cluster Management
13.1 Logging
13.2 Monitoring, or Measuring Cluster Health
13.3 Hardware Failure and Recovery
13.4 Software Failure
13.5 File System Failure and Recovery
13.6 Account Management
13.7 Workload Management
13.8 Software upgrades
13.9 Configuration Management
13.10 Conclusion
Chapter 14: Cluster Workload Management
14.1 Goal of Workload Management Software
14.2 Workload Management Activities
14.3 Conclusions
Chapter 15: Condor: A Distributed Job Scheduler
15.1 Introduction to Condor
15.2 Using Condor
15.3 Condor Architecture
15.4 Configuring Condor
15.5 Administration Tools
15.6 Cluster Setup Scenarios
15.7 Conclusion
Chapter 16: Maui Scheduler: A High Performance Cluster Scheduler
16.2 Installation and Initial Configuration
16.3 Advanced Configuration
16.4 Steering Workload and Improving Quality of Information
16.5 Troubleshooting
16.6 Conclusions
Chapter 17: PBS: Portable Batch System
17.1 History of PBS
17.2 Using PBS
17.3 Installing PBS
17.4 Configuring PBS
17.5 Managing PBS
17.6 Troubleshooting
Chapter 18: Scyld Beowulf
18.2 Using Scyld Beowulf
18.3 Administration
18.4 Features in Upcoming Releases
18.5 Conclusion
Chapter 19: Parallel I/O and the Parallel Virtual File System
19.1 Parallel I/O Systems
19.2 Parallel File System Architectures
19.3 File System Access Semantics
19.4 Using PVFS
19.5 Parallel I/O in the Future
19.6 Conclusions
Chapter 20: A Tale of Two Clusters: Chiba City and Jazz
20.1 Chiba City
20.2 Jazz - A New Production Cluster
Chapter 21: Conclusions
21.2 Future Directions for Clusters
21.3 Learning More
Appendix A: Glossary of Terms
L-P
Q-W
Appendix B: Annotated Reading List
Appendix C: Annotated URLs
C.2 Node and Network Hardware
C.3 Network Security
C.4 Performance Tools
C.5 Parallel Programming and Software
C.6 Scheduling and Management
References
List of Figures
List of Tables
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