High Performance Linux Clusters with OSCAR, Rocks, OpenMosix, and MPI

This new guide covers everything you need to plan, build, and deploy a high-performance Linux cluster. You'll learn about planning, hardware choices, bulk installation of Linux on multiple systems, and other basic considerations. Learn about the major free software projects and how to choose those that are most helpful to new cluster administrators and programmers. Guidelines for debugging, profiling, performance tuning, and managing jobs from multiple users round out this immensely useful book.

Table of Contents

Acknowledgments

Part I: An Introduction to Clusters

Chapter 1. Cluster Architecture

Section 1.1. Modern Computing and the Role of Clusters

Section 1.2. Types of Clusters

Section 1.3. Distributed Computing and Clusters

Section 1.4. Limitations

Section 1.5. My Biases

Chapter 2. Cluster Planning

Section 2.1. Design Steps

Section 2.2. Determining Your Cluster's Mission

Section 2.3. Architecture and Cluster Software

Section 2.4. Cluster Kits

Section 2.5. CD-ROM-Based Clusters

Section 2.6. Benchmarks

Chapter 3. Cluster Hardware

Section 3.1. Design Decisions

Section 3.2. Environment

Chapter 4. Linux for Clusters

Section 4.1. Installing Linux

Section 4.2. Configuring Services

Section 4.3. Cluster Security

Part II: Getting Started Quickly

Chapter 5. openMosix

Section 5.1. What Is openMosix?

Section 5.2. How openMosix Works

Section 5.3. Selecting an Installation Approach

Section 5.4. Installing a Precompiled Kernel

Section 5.5. Using openMosix

Section 5.6. Recompiling the Kernel

Section 5.7. Is openMosix Right for You?

Chapter 6. OSCAR

Section 6.1. Why OSCAR?

Section 6.2. What's in OSCAR

Section 6.3. Installing OSCAR

Section 6.4. Security and OSCAR

Section 6.5. Using switcher

Section 6.6. Using LAM/MPI with OSCAR

Chapter 7. Rocks

Section 7.1. Installing Rocks

Section 7.2. Managing Rocks

Section 7.3. Using MPICH with Rocks

Part III: Building Custom Clusters

Chapter 8. Cloning Systems

Section 8.1. Configuring Systems

Section 8.2. Automating Installations

Section 8.3. Notes for OSCAR and Rocks Users

Chapter 9. Programming Software

Section 9.1. Programming Languages

Section 9.2. Selecting a Library

Section 9.3. LAM/MPI

Section 9.4. MPICH

Section 9.5. Other Programming Software

Section 9.6. Notes for OSCAR Users

Section 9.7. Notes for Rocks Users

Chapter 10. Management Software

Section 10.1. C3

Section 10.2. Ganglia

Section 10.3. Notes for OSCAR and Rocks Users

Chapter 11. Scheduling Software

Section 11.1. OpenPBS

Section 11.2. Notes for OSCAR and Rocks Users

Chapter 12. Parallel Filesystems

Section 12.1. PVFS

Section 12.2. Using PVFS

Section 12.3. Notes for OSCAR and Rocks Users

Part IV: Cluster Programming

Chapter 13. Getting Started with MPI

Section 13.1. MPI

Section 13.2. A Simple Problem

Section 13.3. An MPI Solution

Section 13.4. I/O with MPI

Section 13.5. Broadcast Communications

Chapter 14. Additional MPI Features

Section 14.1. More on Point-to-Point Communication

Section 14.2. More on Collective Communication

Section 14.3. Managing Communicators

Section 14.4. Packaging Data

Chapter 15. Designing Parallel Programs

Section 15.1. Overview

Section 15.2. Problem Decomposition

Section 15.3. Mapping Tasks to Processors

Section 15.4. Other Considerations

Chapter 16. Debugging Parallel Programs

Section 16.1. Debugging and Parallel Programs

Section 16.2. Avoiding Problems

Section 16.3. Programming Tools

Section 16.4. Rereading Code

Section 16.5. Tracing with printf

Section 16.6. Symbolic Debuggers

Section 16.7. Using gdb and ddd with MPI

Section 16.8. Notes for OSCAR and Rocks Users

Chapter 17. Profiling Parallel Programs

Section 17.1. Why Profile?

Section 17.2. Writing and Optimizing Code

Section 17.3. Timing Complete Programs

Section 17.4. Timing C Code Segments

Section 17.5. Profilers

Section 17.6. MPE

Section 17.7. Customized MPE Logging

Section 17.8. Notes for OSCAR and Rocks Users

Part V: Appendix

Appendix A. References

Section A.1. Books

Section A.2. URLs