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HP XC System 2.x Software manual

Models: XC System 2.x Software

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Contents

June Product Version Hewlett-Packard Company Palo Alto, CaliforniaPage Contents Developing Applications 5.4Tuning Applications Using SlurmDebugging Applications Using LSF Using HP-MPIUsing HP Mlib 6.4Advanced Topics ExamplesGlossary Index Examples Figures TablesPage About This Document Intended AudienceDocument Organization QuickSpecs for HP XC System Software Linux Administration HandbookHP XC Information HP XC Program Development EnvironmentHP Message Passing Interface For More InformationSupplementary Information HP Mathematical LibraryHttp//systemimager.org ManpagesHttp//supermon.sourceforge.net Http//sourceforge.net/projects/modulesRelated Information Http//linuxvirtualserver.orgHttp//www-unix.mcs.anl.gov/mpi # cd /opt/hptc/config/sbin Typographical ConventionsBold text HP Encourages Your Comments Ctrl/xPage Operating System Overview of the User EnvironmentSystem Architecture Node SpecializationSAN Storage Storage and I/OFile System Local StorageSystem Interconnect Network File System LayoutNetwork Address Translation NAT CommandsUser Environment 1 LVSApplication Development Environment Parallel ApplicationsSerial Applications Load Sharing Facility LSF-HPC Run-Time EnvironmentSlurm How LSF-HPC and Slurm InteractComponents, Tools, Compilers, Libraries, and Debuggers HP-MPI8Overview of the User Environment LVS Login Routing Using the SystemConfiguring Your Environment with Modulefiles Using ssh to Log2Using the System Supplied Modulefiles Supplied ModulefilesModulefile Sets the HP XC User Environment 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 totalviewGetting Information About Queues Launching and Managing Jobs Quick StartIntroduction Getting Information About ResourcesSubmitting a Serial Job Getting Information About the System’s PartitionsLaunching Jobs Example 2-1 Submitting a Serial JobExample 2-2 Submitting a Non-MPI Parallel Job Using Slurm Options with the LSF External SchedulerSubmitting a Non-MPI Parallel Job $ bsub -n4 -I srun hostnameSubmitting an MPI Job Example 2-4 Running an MPI Job with LSF$ bsub -n4 Mpirun -srun ./helloworld Submitting a Batch Job or Job Script Example 2-6 Submitting a Job Script$ bsub -I -n4 myjobscript.sh Performing Other Common User Tasks Getting System Help and Information$ man sinfo $ man -k keywordPage Developing Applications OverviewIntel Compilers Using CompilersStandard Linux Compilers PGI CompilersInterrupting a Job Setting Debugging OptionsChecking Nodes and Partitions Before Running Jobs Developing Serial ApplicationsSerial Application Build Environment Using Mlib in Serial ApplicationsDeveloping Parallel Applications Building Serial ApplicationsHP-MPI Parallel Application Build EnvironmentModulefiles OpenMPMPI Library Quadrics ShmemMlib Math Library $ mpicc object1.o ... -pthread -o myapp.exeGNU C and C++ Compilers Intel Fortran and C/C++CompilersPGI Fortran and C/C++ Compilers GNU Parallel MakeCompiling and Linking Non-MPI Applications Reserved Symbols and NamesBuilding Parallel Applications Compiling and Linking HP-MPI ApplicationsDeveloping Libraries Designing Libraries for XC4000$ mpicc -c -g foo.c Example 3-1 Directory Structure Using the GNU Parallel Make CapabilityAdvanced Topics Example 3-2 Recommended Directory Structure$ cd subdir srun $MAKE $ cd subdir srun -n1 -N1 $MAKE -j4Example Procedure $ make PREFIX=’srun -n1 -N1 MAKEJ=’-j4’ $ make PREFIX=’srun -n1 -N1’ MAKEJ=’-j4’Shared File View Local Disks on Compute Nodes3 I/O Performance Considerations Private File ViewCommunication Between Nodes Page Debugging Parallel Applications Debugging ApplicationsDebugging Serial Applications TotalViewSetting Up TotalView Debugging with TotalViewSSH and TotalView $ srun -Nx-A $ mpirun -tv -srun application Using TotalView with SlurmUsing TotalView with LSF-HPC $ bsub -nx-ext SLURMnodes=x \ -Is /usr/bin/xtermStarting TotalView for the First Time $ totalviewTotalView Preferences Window Preferences window, click on the Launch Strings tab Debugging Applications Debugging an Application $ mpicc -g -o Psimple simple.c -lm$ mpirun -tv -srun -n2 ./Psimple TotalView Process Window Example Debugging Running Applications $ mpirun -srun -n2 Psimple$ scancel --user username Exiting TotalView$ squeue Page Building a Program Intel Trace Collector and HP-MPI Tuning ApplicationsUsing the Intel Trace Collector/Analyzer ExampleRunning a Program Intel Trace Collector and HP-MPI Visualizing Data Intel Trace Analyzer and HP-MPIExample Running the vtjacobic Example Program Command Function Using SlurmSlurm Commands IntroductionSrun Roles and Modes Accessing the Slurm ManpagesLaunching Jobs with the srun Command Example 6-1 Simple Launch of a Serial ProgramSrun Roles Srun ModesBatch Srun Signal HandlingSrun Run-Mode Options AllocateSrun Resource-Allocation Options Minutes --time=minutes Cpt --cpus-per-task=cptPart --partition=part Nthreads --threads=nthreadsSrun Control Options Srun I/O Options Mode --error=mode Mode --output=modeMode --input=mode LabelSrun Constraint Options Clist --constraint=clistMincpus=n Contiguous=yesnoMem=size Vmem=sizeUsing srun with LSF Monitoring Jobs with the squeue CommandUsing srun with HP-MPI Srun Environment VariablesKilling Jobs with the scancel Command Getting System Information with the sinfo CommandSecurity Fault ToleranceJob Accounting $ sinfo -RUsing LSF Introduction to LSF in the HP XC EnvironmentOverview of LSF Topology Support Nodelist= list-of-nodes Exclude= list-of-nodes$ bsub -n 10 -ext SLURMnodes=10 srun myapp $ bsub -n 10 -ext SLURMnodes=10exclude=n16 srun myappHow LSF and Slurm Launch and Manage a Job $ bqueues -l normal grep Jobstarter$ bsub -Is hostname How LSF-HPC and Slurm Launch and Manage a Job $ bsub -n4 -ext SLURMnodes=4 -o output.out ./myscriptDifferences Between LSF on HP XC and Standard LSF Getting Status of LSF Determining Execution HostDetermining Available System Resources Job Startup and Job ControlGetting Information About LSF-HPC Execution Host Node Getting Host Load InformationGetting Information About the lsf Partition Submitting JobsChecking LSF System Queues $ sinfo -p lsfSummary of the LSF bsub Command Format Bsub bsuboptions jobname joboptionsLSF-SLURM External Scheduler Slurm Arguments FunctionStarting on lsfhost.localdomain n6 Submitting an HP-MPI Job Submitting a Serial JobSubmitting a Job in Parallel Example 7-5 Submitting an Interactive Serial JobSubmitting a Batch Job or Job Script Example 7-6 Submitting an HP-MPI Job$ bsub -n4 -I mpirun -srun ./helloworld $ bsub -n4 -I ./myscript.sh ExamplesExample 7-8 Submitting a Batch Job Script $ bsub -n4 -ext SLURMnodes=4 -I ./myscript.shSubmitting a Job from a Non-HP XC Host $ bsub -n4 -I ./myscript.sh -n8 -OType=SLINUX64 Job Allocation Information for a Running Job Getting Information About JobsGetting Job Allocation Information $ bsub -R type=SLINUX64 -n4 -I srun hostnameExample 7-13 Using the bjobs Command Short Output Checking Status of a JobJob Allocation Information for a Finished Job Output Provided by the bhist Command Example 7-14 Using the bjobs Command Long OutputExample 7-15 Using the bhist Command Short Output Viewing a Job’s Historical InformationExample 7-16 Using the bhist Command Long Output Working Interactively Within an LSF-HPC AllocationSubmitting an Interactive Job to Launch the xterm Program Example 7-19 View Your Running Job in LSF Example 7-17 View Your EnvironmentExample 7-18 View Your Allocation in Slurm Example 7-20 View Job Details in LSFExample 7-22 Submitting an Interactive Shell Program Submitting an Interactive Job to Launch a ShellExample 7-21 Running Jobs from an xterm Window $ hostname $ srun hostname $ srun -n2 hostname$ srun hostname n1 $ exit LSF Equivalents of Slurm srun OptionsLSF Equivalents of Slurm srun Options Srun Option Description LSF Equivalent24Using LSF Control the parallel job Page Using HP-MPI Compiling and Running Applications Setting Environment VariablesHP-MPI Directory Structure Building and Running an Example Application$ mpicc -o helloworld $MPIROOT/help/helloworld.c Example Application helloworldBuilding and Running helloworld $ $MPIROOT/bin/mpirun -srun -n4 helloworldLaunching MPI Jobs HP-MPI options allowed with -srun$ mpirun -srun -n6 -O -N2 -m cyclic ./a.out host1 rank1 Creating Subshells and Launching JobstepsSystem Interconnect Selection $ mpirun -srun -n4 -N2 -O -m cyclic ./a.out host1 rank1Using LSF and HP-MPI $ mpirun -subnet 192.168.1.1 -prot -srun -n4 ./a.outMPI Versioning $ /usr/sbin/ifconfig -aSystem Interconnect Support Example 8-5 Allocating 12 Processors on 6 Nodes32-Bit Builds on XC4000 Truncated MessagesAllowing Windows to Use Exclusive Locks Mpirun Command Options $ mpirun -TCP -srun -N8 ./a.outEnvironment Variables $MPIROOT/bin/mpirun -v -prot -np 2 /path/to/program.xExport MPIPAGEALIGNMEM=1 Export MPIPHYSICALMEMORY=1048576Export MPIPINPERCENTAGE=30 Export MPIMAXWINDOW=10Export MPIUSELIBELANUSE=5 Mpich Object CompatibilityExport MPIUSELIBELAN=0 $MPIROOT/bin/mpirun.mpich -np 2 ./prog.xHP-MPI Manpage Categories HP-MPI Documentation and ManpagesAt http//docs.hp.com Category Manpages DescriptionAdditional Information, Known Problems, and Work-arounds Version 8 Fortran Compiler Using HP MlibIntel Compiler Notes Version 7 Fortran CompilerPlatform Support HP Mlib for the HP XC6000 PlatformMlib and Module Files Library SupportUsing Intel Compilers with HP Mlib Modulefiles and MlibCompiling and Linking Mlib Manpages HP Mlib for the HP XC4000 PlatformLicensing Linking SuperLUDIST$ pgcc options file 6Using HP Mlib Running an X Terminal Session from a Remote Node Advanced TopicsEnabling Remote Execution with OpenSSH Determining IP Address of Your Local Machine$ hostname Running an X terminal Session Using SlurmLogging in to HP XC System $ host mymachineRunning an X terminal Session Using LSF $ bsub -n4 -Ip srun -n1 xterm -display$ bjobs Page Examples Building and Running a Serial ApplicationLaunching a Serial Interactive Shell Through LSF Running LSF Jobs with a Slurm Allocation Request Example 1. Two Processors on Any Two NodesLaunching a Parallel Interactive Shell Through LSF Example 2. Four Processors on Two Specific NodesView the job Check the running job’s information $ bsub -Is -n4 -ext SLURMnodes=4 /bin/bashShow the environment Submitting a Simple Job Script with LSFCheck the finished job’s information Display the scriptShow the Slurm job ID Submitting an Interactive Job with LSFShow the job allocation $ bsub -n8 -Ip /bin/shSubmitting an HP-MPI Job with LSF View the running job View the finished job$ bjobs -l Using a Resource Requirements String in an LSF Command $ bsub -n 8 -R ALPHA5 SLINUX64 \ -ext SLURMnodes=4-4 myjobPage Glossary Fairshare Extensible firmware interfaceExternal network node First come first servedInterconnect Image serverIntegrated Lights Out Internet addressManagement Processor Network Information ServicesLSF master host Master hostResource manager role Root Administration SwitchParallel application RoleSymmetric multiprocessing Glossary-6Index Index-1Gdb, 4-1 GNU Index-2Modulefile Index-3Resource manager, 7-1role Serial applications Index-4