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IBM Parallel Environment (PE) Developer Edition

Book Description

This publication helps strengthen the position of IBM® software solutions and enables for High Performance Computing (hardware, software, and tools) with a well-defined and documented deployment model within an IBM environment. As a result, customers receive a planned foundation for dynamic infrastructure for parallel High Performance Computing (HPC) applications.

This IBM Redbooks® publication addresses topics to take advantage of the strengths of IBM PE Developers Edition for HPC applications. The objective is to solve customer's challenges and maximize systems' throughput, performance, and management. This publication examines the tools, utilities, documentation, and other resources available to help the IBM technical teams provide solutions and support for IBM HPC solutions in an IBM hardware environment.

This IBM Redbooks is targeted toward technical professionals (consultants, technical support staff, IT Architects, and IT Specialists) responsible for providing HPC solutions and support.

Table of Contents

  1. Front cover
  2. Notices
    1. Trademarks
  3. Preface
    1. The team who wrote this book
    2. Now you can become a published author, too!
    3. Comments welcome
    4. Stay connected to IBM Redbooks
  4. Chapter 1. Introduction
    1. 1.1 Overview
    2. 1.2 Features
    3. 1.3 Supported operating systems (software)
    4. 1.4 Supported hardware
    5. 1.5 Eclipse basics
      1. 1.5.1 What is Eclipse?
      2. 1.5.2 Eclipse architecture
      3. 1.5.3 Eclipse terms and concepts
    6. 1.6 Project types
  5. Chapter 2. Component tour
    1. 2.1 Parallel Environment Runtime Edition components
      1. 2.1.1 Parallel Operating Environment (POE)
      2. 2.1.2 IBM Message Passing Interface (IBM MPI)
      3. 2.1.3 IBM Parallel Active Messaging Interface (PAMI)
      4. 2.1.4 Low-level application programming interface (LAPI)
      5. 2.1.5 Command line parallel debugger (pdb)
    2. 2.2 Parallel Environment Developer Edition components
      1. 2.2.1 Eclipse, PTP, CDT and Photran
      2. 2.2.2 IBM specific add-ons in the IBM PE Developer Edition
  6. Chapter 3. Scenarios
    1. 3.1 Cluster design overview
      1. 3.1.1 HPC scenario based on IBM POWER Systems platform
      2. 3.1.2 HPC scenario based on x86 platform
      3. 3.1.3 IBM additional other software components for HPC solution
    2. 3.2 Developing parallel applications
      1. 3.2.1 Programming models
      2. 3.2.2 Most used frameworks and libraries
  7. Chapter 4. Server installation
    1. 4.1 Software requirements
    2. 4.2 PEDE packaging considerations
      1. 4.2.1 Package contents
      2. 4.2.2 Additional software
    3. 4.3 Installation
      1. 4.3.1 AIX 7.1
      2. 4.3.2 RHEL 6 (on IBM POWER)
      3. 4.3.3 SLES 11 SP2 or RHEL 6.2 (x86_64)
    4. 4.4 Post-installation set up
      1. 4.4.1 Quick Parallel Environment Runtime tuning
      2. 4.4.2 GPFS tunable parameters affecting HPC performance
      3. 4.4.3 HPC Cluster verifications
      4. 4.4.4 Customizing the environment
  8. Chapter 5. Managing projects using the Eclipse and PTP framework
    1. 5.1 Available project scenarios
      1. 5.1.1 Synchronized
      2. 5.1.2 Remote
      3. 5.1.3 Local
    2. 5.2 Creating a new parallel application
    3. 5.3 Importing an existing parallel application
    4. 5.4 Building and running an application
      1. 5.4.1 Building (using targets)
      2. 5.4.2 Running
    5. 5.5 Edit features of Eclipse
    6. 5.6 Debugging using Eclipse
    7. 5.7 Integrating external applications
  9. Chapter 6. Parallel Environment Developer Edition tools
    1. 6.1 Tuning tools
      1. 6.1.1 Preparing the application for profiling
      2. 6.1.2 Creating a profile launch configuration
      3. 6.1.3 Hardware Performance Monitoring
      4. 6.1.4 MPI profiling and trace
      5. 6.1.5 OpenMP profiling
      6. 6.1.6 I/O profiling
      7. 6.1.7 X Windows Performance Profiler
    2. 6.2 Debugging
      1. 6.2.1 Parallel Static Analysis
      2. 6.2.2 Eclipse PTP Parallel debugger
  10. Chapter 7. Application profiling and tuning
    1. 7.1 Profiling and tuning hints for sPPM
      1. 7.1.1 A glance at the application sPPM
      2. 7.1.2 Use gprof to view the profiling data
      3. 7.1.3 Using binary instrumentation for MPI profiling
      4. 7.1.4 Use OpenMP profiling to identify if the workload for threads
    2. 7.2 Profiling and analyzing Gadget 2
    3. 7.3 Analyzing a ScaLAPACK routine using the HPCT Toolkit
      1. 7.3.1 The Structure of ScaLAPACK
      2. 7.3.2 The build process
      3. 7.3.3 CPU profiling
      4. 7.3.4 HPM profiling
      5. 7.3.5 MPI profiling
  11. Appendix A. HPC Toolkit environment variables
    1. General environment variables
    2. Variables related to hardware performance counters
    3. Variables related to MPI profiling
    4. Variables related to I/O profiling
    5. Variables relating to OpenMP profiling
  12. Related publications
    1. Online resources
    2. Help from IBM
  13. Back cover