HP XC System 3.x Software specification

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Contents

HP XC System Software Users Guide Page Table of Contents Submitting Jobs Configuring Your Environment with ModulefilesDeveloping Applications Using LSF Tuning ApplicationsUsing Slurm Debugging Applications Glossary 109 Index 115 Advanced TopicsExamples 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 follows HP XC Information Supplementary Information $ man lsfcommandnameFor More Information $ man discover $ man 8 discover Related InformationManpages $ man -k keyword Related Compiler Web Sites Related Linux Web SitesRelated MPI Web Sites Additional Publications Environment Variable Typographic ConventionsHP Encourages Your Comments User input HP XC System Software Overview of the User EnvironmentSystem Architecture Operating System Node Specialization Storage and I/O Local Storage File SystemSAN Storage File System Layout Network Address Translation NAT Determining System Configuration InformationSystem Interconnect Network Modules CommandsUser Environment Parallel Applications Application Development EnvironmentRun-Time Environment Serial Applications How LSF-HPC and Slurm Interact Load Sharing Facility LSF-HPCStandard LSF Mpirun command Components, Tools, Compilers, Libraries, and Debuggers Using the Secure Shell to Log Using the SystemLVS Login Routing Logging In to the System Getting Information About Resources IntroductionGetting Information About Queues Performing Other Common User Tasks Getting System Help and Information $ man sinfo Configuring Your Environment with Modulefiles Overview of Modules Supplied Modulefiles Viewing Loaded Modulefiles Modulefiles Automatically Loaded on the SystemViewing Available Modulefiles Loading a Modulefile Modulefile 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 Compilers Developing ApplicationsApplication Development Environment Overview MPI Compiler Examining Nodes and Partitions Before Running JobsInterrupting a Job Partition Avail Timelimit Nodes State Nodelist Serial Application Build Environment Setting Debugging OptionsDeveloping Serial Applications Building Serial Applications Modulefiles Developing Parallel ApplicationsParallel Application Build Environment OpenMP MPI Library PthreadsQuadrics Shmem Intel Fortran and C/C++Compilers Building Parallel Applications Examples of Compiling and Linking HP-MPI Applications Developing LibrariesDesigning Libraries for the CP4000 Platform To build a 64-bit application, you might enter Linkcommand 32-bit -L/opt/mypackage/lib/i686 -lmystuffLinkcommand 64-bit -L/opt/mypackage/lib/x8664 -lmystuff ExtSLURMslurm-arguments Submitting JobsOverview of Job Submission Submitting a Serial Job with the LSF bsub Command Submitting a Serial Job Using Standard LSFSubmitting a Serial Job Using LSF-HPC $ bsub hostname Submitting 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 -nnum-procs bsub-optionsscript-name Submitting a Batch Job or Job Script$ bsub -n4 -I mpirun -srun ./helloworld $ bsub -I -n4 Myscript.sh $ cat myscript.sh #!/bin/shSrun hostname mpirun -srun hellompi $ bsub -n4 -ext SLURMnodes=4 -I ./myscript.sh $ cat ./envscript.sh #!/bin/sh name=`hostname` Running Preexecution Programs$ bsub -n4 -I ./myscript.sh Opt/hptc/bin/srun Mypreexec Debugging Parallel Applications Debugging ApplicationsDebugging Serial Applications TotalView SSH and TotalView Setting Up TotalViewUsing TotalView with Slurm Module load mpimodule load totalview Debugging an Application Using TotalView with LSF-HPCSetting TotalView Preferences Directories in File ⇒ Search Path Sourcefile initfdte.f was not found, using assembler modeDebugging Running Applications $ mpirun -srun -n2 Psimple $ squeue $ scancel --user usernameExiting TotalView Page Building a Program Intel Trace Collector and HP-MPI Tuning ApplicationsUsing the Intel Trace Collector and Intel Trace Analyzer Libs Running a Program Intel Trace Collector and HP-MPIVisualizing Data Intel Trace Analyzer and HP-MPI Cldflags Using the Intel Trace Collector and Intel Trace Analyzer Page Srun Squeue Scancel Sinfo Scontrol Using SlurmLaunching Jobs with the srun Command Introduction to Slurm Using the srun Command with LSF-HPC Monitoring Jobs with the squeue CommandUsing the srun Command with HP-MPI Srun Roles and Modes Job Accounting Terminating Jobs with the scancel CommandGetting System Information with the sinfo Command # chmod a+r /hptccluster/slurm/job/jobacct.log Fault ToleranceSecurity Using LSF-HPC Using LSFUsing Standard LSF on an HP XC System Introduction to LSF-HPC in the HP XC Environment Overview of LSF-HPC Resources Differences Between LSF-HPC and Standard LSFHostname Hostname Status JL/U MAX Njobs RUN Ssusp Ususp RSV Unknown Unknown Job Terminology$ ssh n15 lshosts 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 hostname How LSF-HPC and Slurm Launch and Manage a Job $ bsub -n4 -ext SLURMnodes=4 -o output.out ./myscript Job Startup and Job Control #!/bin/sh hostname srun hostname Mpirun -srun ./hellompi Getting the Status of LSF-HPC Determining the LSF Execution HostDetermining Available LSF-HPC System Resources Getting Information About LSF Execution Host Node Getting Information About the lsf Partition Getting Host Load InformationExamining LSF-HPC System Queues SLINUX6 $ sinfo -p lsf -lNe Summary of the LSF bsub Command Format$ sinfo -p lsf Bsub -n num-procs-ext SLURMslurm-arguments \ LSF-SLURM External SchedulerFor information about running scripts Bsub-options srun srun-optionsjobname job-options Waiting for dispatch ... Starting on lsfhost.localdomain n1 Submitting a Job from a Non-HP XC HostStarting on lsfhost.localdomain n6 Type=SLINUX64 Slurmid=slurmjobidncpus=slurmnprocsslurmalloc=nodelist Getting Information About JobsGetting Job Allocation Information $ bjobs -l Time stamp Examining the Status of a Job$ bhist -l $ bjobs Summary of time in seconds spent Various States Viewing the Historical Information for a Job$ bhist Jobid User Jobname Pend Psusp RUN Ususp Ssusp Unkwn Total Translating 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 sleep Bsub -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 Machine Logging in to HP XC System Running an X terminal Session Using SlurmRunning an X terminal Session Using LSF-HPC $ 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=-j4 Modified Makefile is invoked as follows Local Disks on Compute NodesPerformance Considerations $ make PREFIX=srun -n1 -N1 MAKEJ=-j4 Private 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 information Running 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=2 124 Lsfad Examine the the running jobs information$ hostname n16 $ srun hostname n5 $ bjobs Show the environment Submitting a Simple Job Script with LSF-HPCExamine the the finished jobs information Display the script Submit the job Run some commands from the pseudo-terminalSubmitting an Interactive Job with LSF-HPC Show the job allocation View the interactive jobs Submitting an HP-MPI Job with LSF-HPCExit the pseudo-terminal View the finished jobs Lsfhost.localdomai View the running jobView the finished job $ bsub -n 8 -R ALPHA5 SLINUX64 \ -ext SLURMnodes=4-4 myjob Using a Resource Requirements String in an LSF-HPC CommandStates by date and time 108 Glossary As local storage To the queueFirst-come See Fcfs First-served Global storage Are not appropriate for replication Linux Virtual See LVS Server Load file Single commandLogin requests and directs them to a node with a login role LSF master host Notably to install and remove software packages Network See NIS Information ServicesRemotely. PXE booting is configured at the Bios level Slurm backup Symmetric See SMP Multiprocessing Power available per unit of spaceSsh 114 Index Index PGI Utilities, 63 Slurm commands

HP XC System 3.x Software manual

Models: XC System 3.x Software