Document Outline

• User's Guide
• Table of Contents
• About This Document
  • Intended Audience
  • Document Organization
  • HP XC Information
    • For More Information
    • Supplementary Information
    • Manpages
  • Related Information
  • Typographic Conventions
  • HP Encourages Your Comments
• 1 Overview of the User Environment
  • System Architecture
    • HP XC System Software
    • Operating System
    • Node Platforms
    • Node Specialization
    • Storage and I/O
    • File System
    • System Interconnect Network
    • Network Address Translation (NAT)
  • Determining System Configuration Information
  • User Environment
    • LVS
    • Modules
    • Commands
  • Application Development Environment
    • Parallel Applications
    • Serial Applications
  • Run-Time Environment
    • SLURM
    • Load Sharing Facility (LSF-HPC)
    • Standard LSF
    • How LSF-HPC and SLURM Interact
    • HP-MPI
  • Components, Tools, Compilers, Libraries, and Debuggers
• 2 Using the System
  • Logging In to the System
    • LVS Login Routing
    • Using the Secure Shell to Log In
  • Overview of Launching and Managing Jobs
    • Introduction
    • Getting Information About Queues
    • Getting Information About Resources
    • Getting Information About System Partitions
    • Launching Jobs
    • Getting Information About Your Jobs
    • Stopping and Suspending Jobs
    • Resuming Suspended Jobs
  • Performing Other Common User Tasks
    • Determining the LSF Cluster Name and the LSF Execution Host
  • Getting System Help and Information
• 3 Configuring Your Environment with Modulefiles
  • Overview of Modules
  • Supplied Modulefiles
  • Modulefiles Automatically Loaded on the System
  • Viewing Available Modulefiles
  • Viewing Loaded Modulefiles
  • Loading a Modulefile
    • Loading a Modulefile for the Current Session
    • Automatically Loading a Modulefile at Login
  • Unloading a Modulefile
  • Modulefile Conflicts
  • Creating a Modulefile
  • Viewing Modulefile-Specific Help
• 4 Developing Applications
  • Application Development Environment Overview
  • Compilers
    • MPI Compiler
  • Examining Nodes and Partitions Before Running Jobs
  • Interrupting a Job
  • Setting Debugging Options
  • Developing Serial Applications
    • Serial Application Build Environment
    • Building Serial Applications
      • Compiling and Linking Serial Applications
  • Developing Parallel Applications
    • Parallel Application Build Environment
      • Modulefiles
      • HP-MPI
      • OpenMP
      • Pthreads
      • Quadrics SHMEM
      • MPI Library
      • Intel Fortran and C/C++Compilers
      • PGI Fortran and C/C++ Compilers
      • GNU C and C++ Compilers
      • Pathscale Compilers
      • GNU Parallel Make
      • MKL Library
      • ACML Library
      • Other Libraries
    • Building Parallel Applications
      • Compiling and Linking Non-MPI Applications
      • Compiling and Linking HP-MPI Applications
      • Examples of Compiling and Linking HP-MPI Applications
  • Developing Libraries
    • Designing Libraries for the CP4000 Platform
• 5 Submitting Jobs
  • Overview of Job Submission
  • Submitting a Serial Job Using Standard LSF
  • Submitting a Serial Job Using LSF-HPC
    • Submitting a Serial Job with the LSF bsub Command
    • Submitting a Serial Job Through SLURM only
  • Submitting a Non-MPI Parallel Job
  • Submitting a Parallel Job That Uses the HP-MPI Message Passing Interface
  • Submitting a Batch Job or Job Script
  • Running Preexecution Programs
• 6 Debugging Applications
  • Debugging Serial Applications
  • Debugging Parallel Applications
    • Debugging with TotalView
      • SSH and TotalView
      • Setting Up TotalView
      • Using TotalView with SLURM
      • Using TotalView with LSF-HPC
      • Setting TotalView Preferences
      • Debugging an Application
      • Debugging Running Applications
      • Exiting TotalView
• 7 Tuning Applications
  • Using the Intel Trace Collector and Intel Trace Analyzer
    • Building a Program — Intel Trace Collector and HP-MPI
    • Running a Program – Intel Trace Collector and HP-MPI
    • Visualizing Data – Intel Trace Analyzer and HP-MPI
• 8 Using SLURM
  • Introduction to SLURM
  • SLURM Utilities
  • Launching Jobs with the srun Command
    • The srun Roles and Modes
      • The srun Roles
      • The srun Modes
    • Using the srun Command with HP-MPI
    • Using the srun Command with LSF-HPC
  • Monitoring Jobs with the squeue Command
  • Terminating Jobs with the scancel Command
  • Getting System Information with the sinfo Command
  • Job Accounting
  • Fault Tolerance
  • Security
• 9 Using LSF
  • Using Standard LSF on an HP XC System
  • Using LSF-HPC
    • Introduction to LSF-HPC in the HP XC Environment
      • Overview of LSF-HPC
      • Differences Between LSF-HPC and Standard LSF
      • Job Terminology
      • HP XCCompute Node Resource Support
      • Notes on LSF-HPC
      • How LSF-HPC and SLURM Launch and Manage a Job
      • Notes About Using LSF-HPC in the HP XC Environment
        • Job Startup and Job Control
        • Preemption
    • Determining the LSF Execution Host
    • Determining Available LSF-HPC System Resources
      • Getting the Status of LSF-HPC
      • Getting Information About LSF Execution Host Node
      • Getting Host Load Information
      • Examining LSF-HPC System Queues
      • Getting Information About the lsf Partition
    • Submitting Jobs
      • Summary of the LSF bsub Command Format
      • LSF-SLURM External Scheduler
      • Submitting a Job from a Non-HP XC Host
    • Getting Information About Jobs
      • Getting Job Allocation Information
        • Job Allocation Information for a Running Job
        • Job Allocation Information for a Finished Job
      • Examining the Status of a Job
      • Viewing the Historical Information for a Job
    • Translating SLURM and LSF-HPC JOBIDs
    • Working Interactively Within an LSF-HPC Allocation
    • LSF-HPC Equivalents of SLURM srun Options
• 10 Advanced Topics
  • Enabling Remote Execution with OpenSSH
  • Running an X Terminal Session from a Remote Node
  • Using the GNU Parallel Make Capability
    • Example Procedure 1
    • Example Procedure 2
    • Example Procedure 3
  • Local Disks on Compute Nodes
  • I/O Performance Considerations
    • Shared File View
    • Private File View
  • Communication Between Nodes
• Appendix A Examples
  • Building and Running a Serial Application
  • Launching a Serial Interactive Shell Through LSF-HPC
  • Running LSF-HPC Jobs with a SLURM Allocation Request
    • Example 1. Two cores on Any Two Nodes
    • Example 2. Four cores on Two Specific Nodes
  • Launching a Parallel Interactive Shell Through LSF-HPC
  • Submitting a Simple Job Script with LSF-HPC
  • Submitting an Interactive Job with LSF-HPC
  • Submitting an HP-MPI Job with LSF-HPC
  • Using a Resource Requirements String in an LSF-HPC Command
• Glossary
• Index