Power available per unit of space, Ssh | HP XC System 3.x Software

SMP	Symmetric multiprocessing. A system with two or more CPUs that share equal (symmetric) access
	to all of the facilities of a computer system, such as the memory and I/O subsystems. In an HP
	XC system, the use of SMP technology increases the number of CPUs (amount of computational
	power) available per unit of space.
ssh	Secure Shell. A shell program for logging in to and executing commands on a remote computer.
	It can provide secure encrypted communications between two untrusted hosts over an insecure
	network.
standard LSF	A workload manager for any kind of batch job. Standard LSF features comprehensive workload
	management policies in addition to simple first-come, first-serve scheduling (fairshare, preemption,
	backfill, advance reservation, service-level agreement, and so on). Standard LSF is suited for jobs
	that do not have complex parallel computational needs and is ideal for processing serial,
	single-process jobs. Standard LSF is not integrated with SLURM.
symmetric	See SMP.
multiprocessing

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HP XC System 3.x Software manual Power available per unit of space, Ssh, Symmetric See SMP Multiprocessing

Contents

HP XC System Software Users Guide Page Table of Contents Submitting Jobs Configuring Your Environment with ModulefilesDeveloping Applications Using Slurm Tuning ApplicationsUsing LSF Debugging Applications Glossary 109 Index 115 Advanced TopicsExamples List of Figures Page Determining the Node Platform List of TablesPage Submitting a Job Script List of ExamplesPage Intended Audience About This DocumentDocument Organization This document is organized as follows HP XC Information Supplementary Information $ man lsfcommandnameFor More Information Manpages Related Information$ man discover $ man 8 discover $ man -k keyword Related MPI Web Sites Related Linux Web SitesRelated Compiler Web Sites Additional Publications HP Encourages Your Comments Typographic ConventionsEnvironment Variable User input System Architecture Overview of the User EnvironmentHP XC System Software Operating System Storage and I/O Node Specialization SAN Storage File SystemLocal Storage File System Layout Network Address Translation NAT Determining System Configuration InformationSystem Interconnect Network Modules CommandsUser Environment Run-Time Environment Application Development EnvironmentParallel Applications Serial Applications How LSF-HPC and Slurm Interact Load Sharing Facility LSF-HPCStandard LSF Components, Tools, Compilers, Libraries, and Debuggers Mpirun command LVS Login Routing Using the SystemUsing the Secure Shell to Log Logging In to the System Getting Information About Resources IntroductionGetting Information About Queues Performing Other Common User Tasks $ man sinfo Getting System Help and Information Overview of Modules Configuring Your Environment with Modulefiles Supplied Modulefiles Viewing Available Modulefiles Modulefiles Automatically Loaded on the SystemViewing Loaded Modulefiles Loading a Modulefile Unloading a Modulefile Automatically Loading a Modulefile at LoginModulefile Conflicts Loading a Modulefile for the Current Session Viewing Modulefile-Specific Help Creating a Modulefile$ module load modules $ man modulefile $ module help totalviewPage Compilers Developing ApplicationsApplication Development Environment Overview Interrupting a Job Examining Nodes and Partitions Before Running JobsMPI Compiler Partition Avail Timelimit Nodes State Nodelist Developing Serial Applications Setting Debugging OptionsSerial Application Build Environment Building Serial Applications Parallel Application Build Environment Developing Parallel ApplicationsModulefiles OpenMP Quadrics Shmem PthreadsMPI Library 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 Using LSF-HPC Submitting a Serial Job Using Standard LSFSubmitting a Serial Job with the LSF bsub Command $ bsub hostname Submitting a Serial Job Through Slurm only $ bsub -n4 -I srun hostname Submitting a Non-MPI Parallel JobBsub -nnum-procsbsub-optionsmpijob 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 Srun hostname mpirun -srun hellompi $ cat myscript.sh #!/bin/sh$ bsub -I -n4 Myscript.sh $ 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 Serial Applications Debugging ApplicationsDebugging Parallel Applications TotalView Using TotalView with Slurm Setting Up TotalViewSSH and TotalView Module load mpimodule load totalview Debugging an Application Using TotalView with LSF-HPCSetting TotalView Preferences Debugging Running Applications Sourcefile initfdte.f was not found, using assembler modeDirectories in File ⇒ Search Path $ 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 Visualizing Data Intel Trace Analyzer and HP-MPI Running a Program Intel Trace Collector and HP-MPILibs Cldflags Using the Intel Trace Collector and Intel Trace Analyzer Page Launching Jobs with the srun Command Using SlurmSrun Squeue Scancel Sinfo Scontrol Introduction to Slurm Using the srun Command with HP-MPI Monitoring Jobs with the squeue CommandUsing the srun Command with LSF-HPC 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 Overview of LSF-HPC Introduction to LSF-HPC in the HP XC Environment Hostname Differences Between LSF-HPC and Standard LSFResources Hostname Status JL/U MAX Njobs RUN Ssusp Ususp RSV Unknown Unknown Job Terminology$ ssh n15 lshosts SLURMnodelist =nodelist if specified HP XCCompute Node Resource Support $ bsub -n 10 -ext SLURMnodes=10 -I srun hostname $ bsub -n 10 -I srun hostname$ bsub -n 10 -ext SLURMnodes=10exclude=n16 -I srun hostname $ bsub -n 10 -ext SLURMconstraint=dualcore -I srun hostname $ bsub -n4 -ext SLURMnodes=4 -o output.out ./myscript How LSF-HPC and Slurm Launch and Manage a Job #!/bin/sh hostname srun hostname Mpirun -srun ./hellompi Job Startup and Job Control Determining Available LSF-HPC System Resources Determining the LSF Execution HostGetting the Status of LSF-HPC Getting Information About LSF Execution Host Node Examining LSF-HPC System Queues Getting Host Load InformationGetting Information About the lsf Partition SLINUX6 $ sinfo -p lsf -lNe Summary of the LSF bsub Command Format$ sinfo -p lsf For information about running scripts LSF-SLURM External SchedulerBsub -n num-procs-ext SLURMslurm-arguments \ Bsub-options srun srun-optionsjobname job-options Starting on lsfhost.localdomain n6 Submitting a Job from a Non-HP XC HostWaiting for dispatch ... Starting on lsfhost.localdomain n1 Type=SLINUX64 Getting Job Allocation Information Getting Information About JobsSlurmid=slurmjobidncpus=slurmnprocsslurmalloc=nodelist $ bjobs -l $ bhist -l Examining the Status of a JobTime stamp $ bjobs $ bhist Viewing the Historical Information for a JobSummary of time in seconds spent Various States Jobid User Jobname Pend Psusp RUN Ususp Ssusp Unkwn Total Translating Slurm and LSF-HPC JOBIDs $ bsub -I -n4 -ext SLURMnodes=4 /bin/bash Working Interactively Within an LSF-HPC Allocation$ bjobs -l 124 grep slurm $ srun --jobid=150 hostname Alternatively, you can use the following $ unset Slurmjobid$ export SLURMJOBID=150 $ export SLURMNPROCS=4 $ unset Slurmjobid $ unset Slurmnprocs LSF-HPC Equivalents of Slurm srun Options Job 125 is submitted to the default queue normal$ srun --jobid=250 uptime $ bsub -n4 -ext SLURMnodes=4 -o %J.out sleep Bsub -iinputfile Mpi=mpitype Quit-on-interrupt Page Enabling Remote Execution with OpenSSH Advanced TopicsRunning an X Terminal Session from a Remote Node 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 $ bsub -n4 -Ip srun -n1 xterm -display Using the GNU Parallel Make Capability$ srun -n4 hostname n46 $ srun -n2 hostname n46 $ cd subdir srun -n1 -N1 $MAKE -j4 $ make PREFIX=’srun -n1 -N1 MAKEJ=-j4 Example Procedure Performance Considerations Local Disks on Compute NodesModified Makefile is invoked as follows $ make PREFIX=srun -n1 -N1 MAKEJ=-j4 Shared File View Communication Between NodesPrivate File View Fp = fopen myfile, a+Page Building and Running a Serial Application Appendix a ExamplesLaunching a Serial Interactive Shell Through LSF-HPC Examine the LSF execution host information Running LSF-HPC Jobs with a Slurm Allocation Request Example 2. Four cores on Two Specific Nodes Launching a Parallel Interactive Shell Through LSF-HPCR15s r1m r15m It tmp swp mem LoadSched LoadStop SLURMnodes=2 124 Lsfad Examine the the running jobs information$ hostname n16 $ srun hostname n5 $ bjobs Examine the the finished jobs information Submitting a Simple Job Script with LSF-HPCShow the environment Display the script Submitting an Interactive Job with LSF-HPC Run some commands from the pseudo-terminalSubmit the job Show the job allocation Exit the pseudo-terminal Submitting an HP-MPI Job with LSF-HPCView the interactive jobs 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 First-come See Fcfs First-served Global storage To the queueAs local storage Are not appropriate for replication Login requests and directs them to a node with a login role Single commandLinux Virtual See LVS Server Load file LSF master host Remotely. PXE booting is configured at the Bios level Network See NIS Information ServicesNotably to install and remove software packages Slurm backup Symmetric See SMP Multiprocessing Power available per unit of spaceSsh 114 Index Index PGI Utilities, 63 Slurm commands