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XC System 2.x Software manual
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154 pages, 1.21 Mb
Contents
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Page
Contents
About This Document
1 Overview of the User Environment
2 Using the System
3 Developing Applications
Debugging Applications
Tuning Applications
Using SLURM
7 Using LSF
8 Using HP-MPI
9 Using HP MLIB
Advanced Topics
Examples
Glossary
Index
Figures
Tables
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About This Document
Intended Audience
Document Organization
HP XC Information
For More Information
Supplementary Information
Manpages
Related Information
Typographical Conventions
HP Encourages Your Comments
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Overview of the User Environment
1.1System Architecture
1.1.1 Operating System
1.1.2 Node Specialization
1.1.3 Storage and I/O
1.1.4 File System
1.1.5 System Interconnect Network
1.1.6Network Address Translation (NAT)
1.2 User Environment
1.2.1 LVS
1.2.2 Modules
1.2.3 Commands
1.3 Application Development Environment
1.3.1 Parallel Applications
1.3.2 Serial Applications
1.4 Run-TimeEnvironment
1.4.1 SLURM
1.4.2 Load Sharing Facility (LSF-HPC)
1.4.3 How LSF-HPCand SLURM Interact
1.4.4 HP-MPI
1.5Components, Tools, Compilers, Libraries, and Debuggers
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Using the System
2.1Logging in to the System
2.1.1 LVS Login Routing
2.1.2 Using ssh to Log In
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
2.2.8Modulefile Conflicts
2.2.9 Creating a Modulefile
2.2.10 Viewing Modulefile-SpecificHelp
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
2.3.4Getting Information About the System’s Partitions
2.3.5 Launching Jobs
2.3.5.2 Submitting a Non-MPIParallel Job
Example 2-2:Submitting a Non-MPIParallel Job
Using SLURM Options with the LSF External Scheduler
Example 2-3:Submitting a Non-MPIParallel Job to Run One Task per Node
2.3.5.3 Submitting an MPI Job
Using SLURM Options in MPI Jobs with the LSF External Scheduler
Example 2-4:Running an MPI Job with LSF
Example 2-5:Running an MPI Job with LSF Using the External Scheduler Option
2.3.5.4 Submitting a Batch Job or Job Script
Example 2-6:Submitting a Job Script
2.3.6 Getting Information About Your Jobs
2.3.7 Stopping and Suspending Jobs
2.3.8Resuming Suspended Jobs
2.4 Performing Other Common User Tasks
2.4.1 Determining the LSF Cluster Name and LSF Execution Host
2.4.2 Installing Third-PartySoftware
2.5 Getting System Help and Information
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Developing Applications
3.1Overview
3.2 Using Compilers
3.2.1 Standard Linux Compilers
3.2.2 Intel Compilers
3.2.3PGI Compilers
3.2.4 Pathscale 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
3.6.1Serial Application Build Environment
3.7 Developing Parallel Applications
3.7.1Parallel Application Build Environment
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
3.7.2 Building Parallel Applications
3.8 Developing Libraries
3.8.1 Designing Libraries for XC4000
3.9 Advanced Topics
3.9.1 Using the GNU Parallel Make Capability
http://www.llnl.gov/asci/applications/SMG98README.html
3.9.1.1 Example Procedure
3.9.1.2 Example Procedure
3.9.1.3 Example Procedure
3.9.2 Local Disks on Compute Nodes
3.9.3 I/O Performance Considerations
3.9.4 Communication Between Nodes
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Debugging Applications
4.1 Debugging Serial Applications
4.2 Debugging Parallel Applications
4.2.1 Debugging with TotalView
______________________ Note:
4.2.1.3Using TotalView with SLURM
4.2.1.4 Using TotalView with LSF-HPC
4.2.1.5 Starting TotalView for the First Time
Figure 4-1:TotalView Root Window
Figure 4-2:TotalView Preferences Window
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4.2.1.6 Debugging an Application
Figure 4-3:TotalView Process Window Example
4.2.1.7 Debugging Running Applications
Figure 4-4:Unattached Window
Figure 4-5:Attached Window
4.2.1.8Exiting TotalView
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Tuning Applications
5.1 Using the Intel Trace Collector/Analyzer
5.1.1Building a Program — Intel Trace Collector and HP-MPI
5.1.2 Running a Program — Intel Trace Collector and HP-MPI
5.1.3 Visualizing Data — Intel Trace Analyzer and HP-MPI
Using SLURM
6.1 Introduction
6.2 SLURM Commands
6.3 Accessing the SLURM Manpages
6.4 Launching Jobs with the srun Command
6.4.1The srun Roles and Modes
6.4.1.1 srun Roles
6.4.1.2srun Modes
modes
6.4.2 srun Signal Handling
6.4.3srun Run-ModeOptions
6.4.4 srun Resource-AllocationOptions
-ccpt (--cpus-per-task=cpt)
-ppart (--partition=part)
-tminutes (--time=minutes)
-Tnthreads (--threads=nthreads)
6.4.5 srun Control Options
6.4.6 srun I/O Options
-omode (--output=mode)
-imode (--input=mode)
-emode (--error=mode)
-l (--label)
-u (--unbuffered)
6.4.7 srun Constraint Options
--contiguous=yes|no
--mem=size
--mincpus=n
--vmem=size
--tmp=size
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
Using LSF
7.1 Introduction to LSF in the HP XC Environment
7.1.1 Overview of LSF
7.1.2 Topology Support
7.1.3 Notes on LSF-HPC
7.1.4How LSF and SLURM Launch and Manage a Job
User
7.1.5 Differences Between LSF on HP XC and Standard LSF
7.1.6Notes About Using LSF in the HP XC Environment
7.2 Determining Execution Host
7.3 Determining Available System Resources
7.3.1 Getting Status of LSF
7.3.2Getting Information About LSF-HPCExecution Host Node
7.3.3Getting Host Load Information
7.3.4 Checking LSF System Queues
7.3.5 Getting Information About the lsf Partition
7.4 Submitting Jobs
7.4.1 Summary of the LSF bsub Command Format
7.4.2 LSF-SLURMExternal Scheduler
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7.4.3 Submitting a Serial Job
7.4.4 Submitting a Job in Parallel
7.4.5 Submitting an HP-MPIJob
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 Request
Example 7-10:Submitting a Batch Job Script that uses a Subset of the Allocation
7.4.7 Submitting a Job from a Non-HPXC Host
7.5 Getting Information About Jobs
7.5.1 Getting Job Allocation Information
7.5.2 Checking Status of a Job
7.5.3 Viewing a Job’s Historical Information
7.6 Working Interactively Within an LSF-HPCAllocation
7.6.1 Submitting an Interactive Job to Launch the xterm Program
Example 7-17:View Your Environment
Example 7-18:View Your Allocation in SLURM
Example 7-19:View Your Running Job in LSF
Example 7-20:View Job Details in LSF
7.6.2 Submitting an Interactive Job to Launch a Shell
7.7 LSF Equivalents of SLURM srun Options
Table 7-2:LSF Equivalents of SLURM srun Options (cont.)
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Using HP-MPI
8.1Overview
8.2 HP-MPIDirectory Structure
8.3 Compiling and Running Applications
8.3.1 Setting Environment Variables
8.3.2 Building and Running an Example Application
8.3.2.1 Example Application hello_world
8.3.2.2 Building and Running hello_world
8.3.3 Using srun with HP-MPI
8.3.3.2Creating Subshells and Launching Jobsteps
8.3.3.3System Interconnect Selection
8.3.4 Using LSF and HP-MPI
8.3.5 MPI Versioning
8.4 System Interconnect Support
8.4.1HP-MPIPerformance on HP XC with Multiple System Interconnects
8.4.2 Global Environment Variable Settings on the mpirun Command Line
8.5 32-BitBuilds on XC4000
8.6 Truncated Messages
8.7Allowing Windows to Use Exclusive Locks
8.8 The mpirun Command Options
8.9 Environment Variables
8.9.1 MPIRUN_OPTIONS
8.9.2MPIRUN_SYSTEM_OPTIONS
8.9.3 MPI_IC_ORDER
8.9.4MPI_PHYSICAL_MEMORY
8.9.5 MPI_PIN_PERCENTAGE
8.9.6 MPI_PAGE_ALIGN_MEM
8.9.7 MPI_MAX_WINDOW
8.9.8MPI_ELANLOCK
8.9.9MPI_USE_LIBELAN
8.10MPICH Object Compatibility
8.11 HP-MPIDocumentation and Manpages
8.12Additional Information, Known Problems, and Work-arounds
Using HP MLIB
9.1 Overview
9.1.1 Intel Compiler Notes
9.1.2 MLIB and Module Files
9.2 HP MLIB for the HP XC6000 Platform
9.2.1 Platform Support
9.2.2 Library Support
9.2.3 MPI Parallelism
9.2.4 Modulefiles and MLIB
9.2.5 Using Intel Compilers with HP MLIB
9.2.6 Compiling and Linking
9.2.7 Licensing
9.2.8 MLIB Manpages
9.3 HP MLIB for the HP XC4000 Platform
9.3.1 Platform Support
9.3.2 Library Support
9.3.3 MPI Parallelism
9.3.4 Modulefiles and MLIB
9.3.5 Compiling and Linking
9.3.6 Licensing
9.3.7 MLIB Manpages
Advanced Topics
10.1Enabling Remote Execution with OpenSSH
10.2 Running an X Terminal Session from a Remote Node
Step 2. Logging in to HP XC System
Step 3. Running an X terminal Session Using SLURM
Step 4. Running an X terminal Session Using LSF
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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.3.1 Example 1. Two Processors on Any Two Nodes
A.3.2 Example 2. Four Processors on Two Specific Nodes
A.4 Launching a Parallel Interactive Shell Through LSF
Note the output from the bjobs command:
Check the running job’s information:
A.5 Submitting a Simple Job Script with LSF
A.6 Submitting an Interactive Job with LSF
A.7 Submitting an HP-MPIJob with LSF
View the running job:
View the finished job:
A.8 Using a Resource Requirements String in an LSF Command
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Glossary
extensible firmware interface
external network node
fairshare
FCFS
first come first served
image server
Integrated Lights Out
interconnect
Internet address
I/O node
LSF master host
LVS
Management Processor
master host
module
parallel application
PXE
resource manager role
role
Root Administration Switch
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Index