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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