HP XC System 2.x Software User Manual
Hp xc system software, User’s guide
Advertising
Table of contents
Document Outline
- HP XC System Software User's Guide
- Intended Audience
- Document Organization
- HP XC Information
- Related Information
- Typographical Conventions
- HP Encourages Your Comments
- 1 Overview of the User Environment
- 2 Using the System
- 2.1 Logging in to the System
- 2.2 Configuring Your Environment with Modulefiles
- 2.2.1 Notes on Modulefiles
- 2.2.2 Supplied Modulefiles
- 2.2.3 Modulefiles Automatically Loaded on the System
- 2.2.4 Viewing Available Modulefiles
- 2.2.5 Viewing Loaded Modulefiles
- 2.2.6 Loading a Modulefile
- 2.2.7 Unloading a Modulefile
- 2.2.8 Modulefile Conflicts
- Note
- 2.2.9 Creating a Modulefile
- 2.2.10 Viewing Modulefile-Specific Help
- 2.3 Launching and Managing Jobs Quick Start
- 2.3.1 Introduction
- 2.3.2 Getting Information About Queues
- 2.3.3 Getting Information About Resources
- 2.3.4 Getting Information About the System's Partitions
- 2.3.5 Launching Jobs
- 2.3.6 Getting Information About Your Jobs
- 2.3.7 Stopping and Suspending Jobs
- 2.3.8 Resuming Suspended Jobs
- 2.4 Performing Other Common User Tasks
- 2.5 Getting System Help and Information
- 3 Developing Applications
- 3.1 Overview
- 3.2 Using Compilers
- 3.3 Checking Nodes and Partitions Before Running Jobs
- 3.4 Interrupting a Job
- 3.5 Setting Debugging Options
- 3.6 Developing Serial Applications
- 3.7 Developing Parallel Applications
- 3.7.1 Parallel Application Build Environment
- 3.7.1.1 Modulefiles
- 3.7.1.2 HP-MPI
- 3.7.1.3 OpenMP
- 3.7.1.4 Pthreads
- 3.7.1.5 Quadrics SHMEM
- 3.7.1.6 MLIB Math Library
- 3.7.1.7 MPI Library
- 3.7.1.8 Intel Fortran and C/C++Compilers
- 3.7.1.9 PGI Fortran and C/C++ Compilers
- 3.7.1.10 GNU C and C++ Compilers
- 3.7.1.11 GNU Parallel Make
- 3.7.1.12 MKL Library
- 3.7.1.13 ACML Library
- 3.7.1.14 Other Libraries
- 3.7.1.15 Reserved Symbols and Names
- 3.7.2 Building Parallel Applications
- 3.7.1 Parallel Application Build Environment
- 3.8 Developing Libraries
- 3.9 Advanced Topics
- 4 Debugging Applications
- 4.1 Debugging Serial Applications
- 4.2 Debugging Parallel Applications
- Note
- 4.2.1 Debugging with TotalView
- 5 Tuning Applications
- 6 Using SLURM
- 6.1 Introduction
- 6.2 SLURM Commands
- 6.3 Accessing the SLURM Manpages
- 6.4 Launching Jobs with the srun Command
- Example 6-1: Simple Launch of a Serial Program
- 6.4.1 The srun Roles and Modes
- 6.4.2 srun Signal Handling
- 6.4.3 srun Run-Mode Options
- 6.4.4 srun Resource-Allocation Options
- 6.4.5 srun Control Options
- 6.4.6 srun I/O Options
- 6.4.7 srun Constraint Options
- 6.4.8 srun Environment Variables
- 6.4.9 Using srun with HP-MPI
- 6.4.10 Using srun with LSF
- 6.5 Monitoring Jobs with the squeue Command
- 6.6 Killing Jobs with the scancel Command
- 6.7 Getting System Information with the sinfo Command
- 6.8 Job Accounting
- 6.9 Fault Tolerance
- 6.10 Security
- 7 Using LSF
- 7.1 Introduction to LSF in the HP XC Environment
- 7.2 Determining Execution Host
- 7.3 Determining Available System Resources
- 7.4 Submitting Jobs
- 7.4.1 Summary of the LSF bsub Command Format
- 7.4.2 LSF-SLURM External Scheduler
- 7.4.3 Submitting a Serial Job
- 7.4.4 Submitting a Job in Parallel
- 7.4.5 Submitting an HP-MPI Job
- 7.4.6 Submitting a Batch Job or Job Script
- 7.4.6.1 Examples
- Example 7-8: Submitting a Batch Job Script
- Example 7-9: Submitting a Batch Script with a Specific Topologic
- Example 7-10: Submitting a Batch Job Script that uses a Subset o
- Example 7-11: Submitting a Batch job Script That Uses the srun -
- Example 7-12: Useful Environment Variables Available in a Batch
- 7.4.6.1 Examples
- 7.4.7 Submitting a Job from a Non- HP XC Host
- 7.5 Getting Information About Jobs
- 7.6 Working Interactively Within an LSF-HPC Allocation
- 7.7 LSF Equivalents of SLURM srun Options
- 8 Using HP-MPI
- 8.1 Overview
- 8.2 HP-MPI Directory Structure
- 8.3 Compiling and Running Applications
- 8.4 System Interconnect Support
- 8.5 32 Bit Builds on XC4000
- 8.6 Truncated Messages
- 8.7 Allowing Windows to Use Exclusive Locks
- 8.8 The mpirun Command Options
- 8.9 Environment Variables
- 8.10 MPICH Object Compatibility
- 8.11 HP-MPI Documentation and Manpages
- 8.12 Additional Information, Known Problems, and Work-arounds
- 9 Using HP MLIB
- 10 Advanced Topics
- A Examples
- A.1 Building and Running a Serial Application
- A.2 Launching a Serial Interactive Shell Through LSF
- A.3 Running LSF Jobs with a SLURM Allocation Request
- A.4 Launching a Parallel Interactive Shell Through LSF
- A.5 Submitting a Simple Job Script with LSF
- A.6 Submitting an Interactive Job with LSF
- A.7 Submitting an HP-MPI Job with LSF
- A.8 Using a Resource Requirements String in an LSF Command
- Glossary
- Index
- tables
- Table 2-1: Supplied Modulefiles
- Table 3-1: Intel Compiler Commands
- Table 3-2: PGI Compiler Commands
- Table 6-1: SLURM Commands
- Table 7-1: Output Provided by the bhist Command
- Table 7-2: LSF Equivalents of SLURM srun Options
- Table 8-1: Organization of the /opt/hpmpi Directory
- Table 8-2: HP-MPI Manpage Categories