HP XC System 3.x Software manual SAN Storage, Local Storage, File System Layout

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SAN Storage

The HP XC system uses the HP StorageWorks Scalable File Share (HP StorageWorks SFS), which is based on Lustre technology and uses the Lustre File System from Cluster File Systems, Inc. This is a turnkey Lustre system from HP. It supplies access to Lustre file systems through Lustre client/server protocols over various system interconnects. The HP XC system is a client to the HP StorageWorks SFS server.

Local Storage

Local storage for each node holds the operating system, a copy of the HP XC System Software, and temporary space that can be used by jobs running on the node.

HP XC file systems are described in detail in File System.

File System

Each node of the HP XC system has its own local copy of all the HP XC System Software files including the Linux distribution; it also has its own local user files. Every node can also import files from NFS or Lustre file servers. HP XC System Software uses NFS 3, including both client and server functionality. HP XC System Software also enables Lustre client services for high-performance and high-availability file I/O. These Lustre client services require the separate installation of Lustre software, provided with the HP Storage Works Scalable File Share (SFS).

NFS files can be shared exclusively among the nodes of the HP XC System or can be shared between the HP XC and external systems. External NFS files can be shared with any node having a direct external network connection. It is also possible to set up NFS to import external files to HP XC nodes without external network connections, by routing through a node with an external network connection. Your system administrator can choose to use either the HP XC administrative network or the HP XC system interconnect for NFS operations. The HP XC system interconnect can potentially offer higher performance, but only at the potential decrease in the performance of application communications.

For high-performance or high-availability file I/O, the Lustre file system is available on HP XC. The Lustre file system uses POSIX-compliant syntax and semantics. The HP XC System Software includes kernel modifications required for Lustre client services which enables the operation of the separately installable Lustre client software. The Lustre file server product used on HP XC is the HP StorageWorks Scalable File Share (SFS), which fully supports the HP XC System Software.

The SFS also includes HP XC Lustre client software. The SFS can be integrated with the HP XC so that Lustre I/O is performed over the same high-speed system interconnect fabric used by the HP XC. So, for example,

if the HP XC system interconnect is based on a Quadrics® QsNet II® switch, then the SFS will serve files over ports on that switch. The file operations are able to proceed at the full bandwidth of the HP XC system interconnect because these operations are implemented directly over the low-level communications libraries. Further optimizations of file I/O can be achieved at the application level using special file system commands

–implemented as ioctls – which allow a program to interrogate the attributes of the file system, modify the stripe size and other attributes of new (zero-length) files, and so on. Some of these optimizations are implicit in the HP-MPI I/O library, which implements the MPI-2 file I/O standard.

File System Layout

In an HP XC system, the basic file system layout is the same as that of the Red Hat Advanced Server 3.0 Linux file system.

The HP XC file system is structured to separate cluster-specific files, base operating system files, and user-installed software files. This allows for flexibility and ease of potential upgrades of the system software and keeps software from conflicting with user installed software. Files are segregated into the following types and locations:

•HP XC-specific software is located in /opt/hptc

•HP XC configuration data is located in /opt/hptc/etc

•Clusterwide directory structure (file system) is located in /hptc_cluster

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Contents HP XC System Software Users Guide Page Table of Contents Configuring Your Environment with Modulefiles Developing ApplicationsSubmitting Jobs Using Slurm Tuning ApplicationsUsing LSF Debugging ApplicationsAdvanced Topics ExamplesGlossary 109 Index 115 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 followsHP XC Information $ man lsfcommandname For More InformationSupplementary Information Manpages Related Information$ man discover $ man 8 discover $ man -k keywordRelated MPI Web Sites Related Linux Web SitesRelated Compiler Web Sites Additional Publications HP Encourages Your Comments Typographic Conventions Environment Variable User inputSystem Architecture Overview of the User EnvironmentHP XC System Software Operating SystemStorage and I/O Node SpecializationSAN Storage File SystemLocal Storage File System LayoutDetermining System Configuration Information System Interconnect NetworkNetwork Address Translation NAT Commands User EnvironmentModules Run-Time Environment Application Development EnvironmentParallel Applications Serial ApplicationsLoad Sharing Facility LSF-HPC Standard LSFHow LSF-HPC and Slurm Interact Components, Tools, Compilers, Libraries, and Debuggers Mpirun commandLVS Login Routing Using the SystemUsing the Secure Shell to Log Logging In to the SystemIntroduction Getting Information About QueuesGetting Information About Resources Performing Other Common User Tasks $ man sinfo Getting System Help and InformationOverview of Modules Configuring Your Environment with ModulefilesSupplied Modulefiles Viewing Available Modulefiles Modulefiles Automatically Loaded on the SystemViewing Loaded Modulefiles Loading a ModulefileUnloading a Modulefile Automatically Loading a Modulefile at LoginModulefile Conflicts Loading a Modulefile for the Current SessionViewing Modulefile-Specific Help Creating a Modulefile$ module load modules $ man modulefile $ module help totalviewPage Developing Applications Application Development Environment OverviewCompilers Interrupting a Job Examining Nodes and Partitions Before Running JobsMPI Compiler Partition Avail Timelimit Nodes State NodelistDeveloping Serial Applications Setting Debugging OptionsSerial Application Build Environment Building Serial ApplicationsParallel Application Build Environment Developing Parallel ApplicationsModulefiles OpenMPQuadrics Shmem PthreadsMPI Library Intel Fortran and C/C++CompilersBuilding Parallel Applications Developing Libraries Designing Libraries for the CP4000 PlatformExamples of Compiling and Linking HP-MPI Applications Linkcommand 32-bit -L/opt/mypackage/lib/i686 -lmystuff Linkcommand 64-bit -L/opt/mypackage/lib/x8664 -lmystuffTo build a 64-bit application, you might enter Submitting Jobs Overview of Job SubmissionExtSLURMslurm-arguments Submitting a Serial Job Using LSF-HPC Submitting a Serial Job Using Standard LSFSubmitting a Serial Job with the LSF bsub Command $ bsub hostnameSubmitting 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-jobnameSubmitting a Batch Job or Job Script $ bsub -n4 -I mpirun -srun ./helloworldBsub -nnum-procs bsub-optionsscript-name Srun hostname mpirun -srun hellompi $ cat myscript.sh #!/bin/sh$ bsub -I -n4 Myscript.sh $ bsub -n4 -ext SLURMnodes=4 -I ./myscript.shRunning Preexecution Programs $ bsub -n4 -I ./myscript.sh$ cat ./envscript.sh #!/bin/sh name=`hostname` Opt/hptc/bin/srun Mypreexec Debugging Serial Applications Debugging ApplicationsDebugging Parallel Applications TotalViewUsing TotalView with Slurm Setting Up TotalViewSSH and TotalView Module load mpimodule load totalviewUsing TotalView with LSF-HPC Setting TotalView PreferencesDebugging an Application Debugging Running Applications Sourcefile initfdte.f was not found, using assembler modeDirectories in File ⇒ Search Path $ mpirun -srun -n2 Psimple$ scancel --user username Exiting TotalView$ squeue Page Tuning Applications Using the Intel Trace Collector and Intel Trace AnalyzerBuilding a Program Intel Trace Collector and HP-MPI Visualizing Data Intel Trace Analyzer and HP-MPI Running a Program Intel Trace Collector and HP-MPILibs CldflagsUsing the Intel Trace Collector and Intel Trace Analyzer Page Launching Jobs with the srun Command Using SlurmSrun Squeue Scancel Sinfo Scontrol Introduction to SlurmUsing the srun Command with HP-MPI Monitoring Jobs with the squeue CommandUsing the srun Command with LSF-HPC Srun Roles and ModesTerminating Jobs with the scancel Command Getting System Information with the sinfo CommandJob Accounting Fault Tolerance Security# chmod a+r /hptccluster/slurm/job/jobacct.log Using LSF Using Standard LSF on an HP XC SystemUsing LSF-HPC Overview of LSF-HPC Introduction to LSF-HPC in the HP XC EnvironmentHostname Differences Between LSF-HPC and Standard LSFResources Hostname Status JL/U MAX Njobs RUN Ssusp Ususp RSVJob Terminology $ ssh n15 lshostsUnknown Unknown 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 ControlDetermining Available LSF-HPC System Resources Determining the LSF Execution HostGetting the Status of LSF-HPC Getting Information About LSF Execution Host NodeExamining LSF-HPC System Queues Getting Host Load InformationGetting Information About the lsf Partition SLINUX6Summary of the LSF bsub Command Format $ sinfo -p lsf$ sinfo -p lsf -lNe For information about running scripts LSF-SLURM External SchedulerBsub -n num-procs-ext SLURMslurm-arguments \ Bsub-options srun srun-optionsjobname job-optionsStarting on lsfhost.localdomain n6 Submitting a Job from a Non-HP XC HostWaiting for dispatch ... Starting on lsfhost.localdomain n1 Type=SLINUX64Getting 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 TotalTranslating 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 hostnameAlternatively, you can use the following $ unset Slurmjobid$ export SLURMJOBID=150 $ export SLURMNPROCS=4 $ unset Slurmjobid $ unset SlurmnprocsLSF-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 sleepBsub -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 MachineRunning an X terminal Session Using Slurm Running an X terminal Session Using LSF-HPCLogging in to HP XC System $ 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 ProcedurePerformance Considerations Local Disks on Compute NodesModified Makefile is invoked as follows $ make PREFIX=srun -n1 -N1 MAKEJ=-j4Shared 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 informationRunning 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=2Examine the the running jobs information $ hostname n16 $ srun hostname n5 $ bjobs124 Lsfad Examine the the finished jobs information Submitting a Simple Job Script with LSF-HPCShow the environment Display the scriptSubmitting an Interactive Job with LSF-HPC Run some commands from the pseudo-terminalSubmit the job Show the job allocationExit the pseudo-terminal Submitting an HP-MPI Job with LSF-HPCView the interactive jobs View the finished jobsView the running job View the finished jobLsfhost.localdomai Using a Resource Requirements String in an LSF-HPC Command States by date and time$ bsub -n 8 -R ALPHA5 SLINUX64 \ -ext SLURMnodes=4-4 myjob 108 Glossary First-come See Fcfs First-served Global storage To the queueAs local storage Are not appropriate for replicationLogin requests and directs them to a node with a login role Single commandLinux Virtual See LVS Server Load file LSF master hostRemotely. PXE booting is configured at the Bios level Network See NIS Information ServicesNotably to install and remove software packages Slurm backupPower available per unit of space SshSymmetric See SMP Multiprocessing 114 Index Index PGI Utilities, 63 Slurm commands
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