HP XC System 3.x Software manual Determining System Configuration Information

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Be aware of the following information about the HP XC file system layout:

•Open source software that by default would be installed under the /usr/local directory is instead installed in the /opt/hptc directory.

•Software installed in the /opt/hptc directory is not intended to be updated by users.

•Software packages are installed in directories under the /opt/hptc directory under their own names. The exception to this is third-party software, which usually goes in /opt/r.

•Four directories under the /opt/hptc directory contain symbolic links to files included in the packages:

•/opt/hptc/bin

•/opt/hptc/sbin

•/opt/hptc/lib

•/opt/hptc/man

Each package directory should have a directory corresponding to each of these directories in which every file has a symbolic link created in the /opt/hptc/ directory.

System Interconnect Network

The HP XC system interconnect provides high-speed connectivity for parallel applications. The system interconnect network provides a high-speed communications path used primarily for user file service and for communications within user applications that are distributed among nodes of the system. The system interconnect network is a private network within the HP XC. Typically, every node in the HP XC is connected to the system interconnect.

Table 1-2indicates the types of system interconnects that are used on HP XC systems.

Table 1-2 HP XC System Interconnects

 

CP3000

CP4000

CP6000

Quadrics QSNet II®

 

X

X

Myrinet®

X

X

 

Gigabit Ethernet®

X

X

X

InfiniBand®

X

X

X

Additional information on supported system interconnects is provided in the HP XC Hardware Preparation Guide.

Network Address Translation (NAT)

The HP XC system uses Network Address Translation (NAT) to enable nodes in the HP XC system that do not have direct external network connections to open outbound network connections to external network resources.

Determining System Configuration Information

You can determine various system configuration parameters with a few commands:

HP XC System Software Version

Use the following command to display the version of the HP XC System

 

Software:

cat /etc/hptc-release

 

Kernel Version

Use the following command to display the version of the kernel:

uname -r

 

cat /proc/version

 

RPMs

Use the following command to display the RPMs:

rpm -qa

 

Memory

Use the following command to display the amount of free and used

 

memory in megabytes:

22 Overview of the User Environment

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Contents HP XC System Software Users Guide Page Table of Contents Developing Applications Configuring Your Environment with ModulefilesSubmitting Jobs Using LSF Tuning ApplicationsUsing Slurm Debugging ApplicationsExamples Advanced TopicsGlossary 109 Index 115 List of Figures Page List of Tables Determining the Node PlatformPage List of Examples Submitting a Job ScriptPage Document Organization About This DocumentIntended Audience This document is organized as followsHP XC Information For More Information $ man lsfcommandnameSupplementary Information $ man discover $ man 8 discover Related InformationManpages $ man -k keywordRelated Compiler Web Sites Related Linux Web SitesRelated MPI Web Sites Additional PublicationsEnvironment Variable Typographic ConventionsHP Encourages Your Comments User input HP XC System Software Overview of the User Environment System Architecture Operating SystemNode Specialization Storage and I/OLocal Storage File SystemSAN Storage File System LayoutSystem Interconnect Network Determining System Configuration InformationNetwork Address Translation NAT User Environment CommandsModules Parallel Applications Application Development EnvironmentRun-Time Environment Serial ApplicationsStandard LSF Load Sharing Facility LSF-HPCHow LSF-HPC and Slurm Interact Mpirun command Components, Tools, Compilers, Libraries, and DebuggersUsing the Secure Shell to Log Using the SystemLVS Login Routing Logging In to the SystemGetting Information About Queues IntroductionGetting Information About Resources Performing Other Common User Tasks Getting System Help and Information $ man sinfoConfiguring Your Environment with Modulefiles Overview of ModulesSupplied Modulefiles Viewing Loaded Modulefiles Modulefiles Automatically Loaded on the SystemViewing Available Modulefiles Loading a ModulefileModulefile Conflicts Automatically Loading a Modulefile at LoginUnloading a Modulefile Loading a Modulefile for the Current Session$ module load modules $ man modulefile Creating a ModulefileViewing Modulefile-Specific Help $ module help totalviewPage Application Development Environment Overview Developing ApplicationsCompilers MPI Compiler Examining Nodes and Partitions Before Running JobsInterrupting a Job Partition Avail Timelimit Nodes State NodelistSerial Application Build Environment Setting Debugging OptionsDeveloping Serial Applications Building Serial ApplicationsModulefiles Developing Parallel ApplicationsParallel Application Build Environment OpenMPMPI Library PthreadsQuadrics Shmem Intel Fortran and C/C++CompilersBuilding Parallel Applications Designing Libraries for the CP4000 Platform Developing LibrariesExamples of Compiling and Linking HP-MPI Applications Linkcommand 64-bit -L/opt/mypackage/lib/x8664 -lmystuff Linkcommand 32-bit -L/opt/mypackage/lib/i686 -lmystuffTo build a 64-bit application, you might enter Overview of Job Submission Submitting JobsExtSLURMslurm-arguments Submitting a Serial Job with the LSF bsub Command Submitting a Serial Job Using Standard LSFSubmitting a Serial Job Using LSF-HPC $ bsub hostnameSubmitting a Serial Job Through Slurm only Bsub -nnum-procsbsub-optionsmpijob Submitting a Non-MPI Parallel Job$ bsub -n4 -I srun hostname Mpirun mpirun--options-srunsrun-optionsmpi-jobname$ bsub -n4 -I mpirun -srun ./helloworld Submitting a Batch Job or Job ScriptBsub -nnum-procs bsub-optionsscript-name $ bsub -I -n4 Myscript.sh $ cat myscript.sh #!/bin/shSrun hostname mpirun -srun hellompi $ bsub -n4 -ext SLURMnodes=4 -I ./myscript.sh$ bsub -n4 -I ./myscript.sh Running Preexecution Programs$ cat ./envscript.sh #!/bin/sh name=`hostname` Opt/hptc/bin/srun Mypreexec Debugging Parallel Applications Debugging ApplicationsDebugging Serial Applications TotalViewSSH and TotalView Setting Up TotalViewUsing TotalView with Slurm Module load mpimodule load totalviewSetting TotalView Preferences Using TotalView with LSF-HPCDebugging an Application Directories in File ⇒ Search Path Sourcefile initfdte.f was not found, using assembler modeDebugging Running Applications $ mpirun -srun -n2 PsimpleExiting TotalView $ scancel --user username$ squeue Page Using the Intel Trace Collector and Intel Trace Analyzer Tuning ApplicationsBuilding a Program Intel Trace Collector and HP-MPI Libs Running a Program Intel Trace Collector and HP-MPIVisualizing Data Intel Trace Analyzer and HP-MPI CldflagsUsing the Intel Trace Collector and Intel Trace Analyzer Page Srun Squeue Scancel Sinfo Scontrol Using SlurmLaunching Jobs with the srun Command Introduction to SlurmUsing the srun Command with LSF-HPC Monitoring Jobs with the squeue CommandUsing the srun Command with HP-MPI Srun Roles and ModesGetting System Information with the sinfo Command Terminating Jobs with the scancel CommandJob Accounting Security Fault Tolerance# chmod a+r /hptccluster/slurm/job/jobacct.log Using Standard LSF on an HP XC System Using LSFUsing LSF-HPC Introduction to LSF-HPC in the HP XC Environment Overview of LSF-HPCResources Differences Between LSF-HPC and Standard LSFHostname Hostname Status JL/U MAX Njobs RUN Ssusp Ususp RSV$ ssh n15 lshosts Job TerminologyUnknown Unknown HP XCCompute Node Resource Support SLURMnodelist =nodelist if specified$ bsub -n 10 -ext SLURMnodes=10exclude=n16 -I srun hostname $ bsub -n 10 -I srun hostname$ bsub -n 10 -ext SLURMnodes=10 -I srun hostname $ bsub -n 10 -ext SLURMconstraint=dualcore -I srun hostnameHow LSF-HPC and Slurm Launch and Manage a Job $ bsub -n4 -ext SLURMnodes=4 -o output.out ./myscriptJob Startup and Job Control #!/bin/sh hostname srun hostname Mpirun -srun ./hellompiGetting the Status of LSF-HPC Determining the LSF Execution HostDetermining Available LSF-HPC System Resources Getting Information About LSF Execution Host NodeGetting Information About the lsf Partition Getting Host Load InformationExamining LSF-HPC System Queues SLINUX6$ sinfo -p lsf Summary of the LSF bsub Command Format$ sinfo -p lsf -lNe Bsub -n num-procs-ext SLURMslurm-arguments \ LSF-SLURM External SchedulerFor information about running scripts Bsub-options srun srun-optionsjobname job-optionsWaiting for dispatch ... Starting on lsfhost.localdomain n1 Submitting a Job from a Non-HP XC HostStarting on lsfhost.localdomain n6 Type=SLINUX64Slurmid=slurmjobidncpus=slurmnprocsslurmalloc=nodelist Getting Information About JobsGetting Job Allocation Information $ bjobs -lTime stamp Examining the Status of a Job$ bhist -l $ bjobsSummary of time in seconds spent Various States Viewing the Historical Information for a Job$ bhist Jobid User Jobname Pend Psusp RUN Ususp Ssusp Unkwn TotalTranslating Slurm and LSF-HPC JOBIDs $ bjobs -l 124 grep slurm Working Interactively Within an LSF-HPC Allocation$ bsub -I -n4 -ext SLURMnodes=4 /bin/bash $ srun --jobid=150 hostname$ export SLURMJOBID=150 $ export SLURMNPROCS=4 $ unset SlurmjobidAlternatively, you can use the following $ unset Slurmjobid $ unset Slurmnprocs$ srun --jobid=250 uptime Job 125 is submitted to the default queue normalLSF-HPC Equivalents of Slurm srun Options $ bsub -n4 -ext SLURMnodes=4 -o %J.out sleepBsub -iinputfile Mpi=mpitype Quit-on-interrupt Page Running an X Terminal Session from a Remote Node Advanced TopicsEnabling Remote Execution with OpenSSH Determining IP Address of Your Local MachineRunning an X terminal Session Using LSF-HPC Running an X terminal Session Using SlurmLogging in to HP XC System $ srun -n4 hostname n46 Using the GNU Parallel Make Capability$ bsub -n4 -Ip srun -n1 xterm -display $ srun -n2 hostname n46$ cd subdir srun -n1 -N1 $MAKE -j4 Example Procedure $ make PREFIX=’srun -n1 -N1 MAKEJ=-j4Modified Makefile is invoked as follows Local Disks on Compute NodesPerformance Considerations $ make PREFIX=srun -n1 -N1 MAKEJ=-j4Private File View Communication Between NodesShared File View Fp = fopen myfile, a+Page Launching a Serial Interactive Shell Through LSF-HPC Appendix a ExamplesBuilding and Running a Serial Application Examine the LSF execution host informationRunning LSF-HPC Jobs with a Slurm Allocation Request R15s r1m r15m It tmp swp mem LoadSched LoadStop Launching a Parallel Interactive Shell Through LSF-HPCExample 2. Four cores on Two Specific Nodes SLURMnodes=2$ hostname n16 $ srun hostname n5 $ bjobs Examine the the running jobs information124 Lsfad Show the environment Submitting a Simple Job Script with LSF-HPCExamine the the finished jobs information Display the scriptSubmit the job Run some commands from the pseudo-terminalSubmitting an Interactive Job with LSF-HPC Show the job allocationView the interactive jobs Submitting an HP-MPI Job with LSF-HPCExit the pseudo-terminal View the finished jobsView the finished job View the running jobLsfhost.localdomai States by date and time Using a Resource Requirements String in an LSF-HPC Command$ bsub -n 8 -R ALPHA5 SLINUX64 \ -ext SLURMnodes=4-4 myjob 108 Glossary As local storage To the queueFirst-come See Fcfs First-served Global storage Are not appropriate for replicationLinux Virtual See LVS Server Load file Single commandLogin requests and directs them to a node with a login role LSF master hostNotably to install and remove software packages Network See NIS Information ServicesRemotely. PXE booting is configured at the Bios level Slurm backupSsh Power available per unit of spaceSymmetric See SMP Multiprocessing 114 Index Index PGI Utilities, 63 Slurm commands
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