Creating a Modulefile | HP XC System 3.x Software manual

When a modulefile conflict occurs, unload the conflicting modulefile before loading the new modulefile. In the previous example, you should unload the ifort/8.0 modulefile before loading the ifort/8.1 modulefile. For information about unloading a modulefile, see Unloading a Modulefile (page 34).

Note

To avoid problems, HP recommends that you always unload one version of a modulefile before loading another version.

Creating a Modulefile

If you download or install a software package into a private directory, you can create your own (private) modulefile for products that you install by using the following general steps:

1.Create a private modulefiles directory.

2.Copy an existing modulefile (to use as a template), or copy the software's corresponding default modulefile from under /opt/modules/modulefiles, into the private modulefiles directory.

3.Edit and modify the modulefile accordingly.

4.Register the private directory with the module use command.

To install a variant of a product or package already on the system, copy the existing modulefile for that product to an appropriate name, and edit it accordingly to accommodate the newly-installed product variant.

To install a random product or package should look at the manpages for modulefiles, examine the existing modulefiles, and create a new modulefile for the product being installed using existing modulefiles as a template. To view modules manpages, load the modules modulefile and then display the modulefile manpage:

$ module load modules $ man modulefile

Read the manpages for modules so that you know how to create a directory for your private modulefiles and how to use the module use <dirname> module command to use your private modules.

Viewing Modulefile-Specific Help

You can view help information for any of the modulefiles on the HP XC system. For example, to access modulefile-specific help information for TotalView, issue the module help command as follows:

$ module help totalview

----------- Module Specific Help for 'totalview' -----------------

This loads the TotalView environment.

Version 6.0

Creating a Modulefile 35

Image 35

HP XC System 3.x Software Creating a Modulefile, Viewing Modulefile-Specific Help, $ module load modules $ man modulefile

Contents

HP XC System Software Users Guide Page Table of Contents Submitting Jobs Configuring Your Environment with ModulefilesDeveloping Applications Debugging Applications Tuning ApplicationsUsing Slurm Using LSF Glossary 109 Index 115 Advanced TopicsExamples List of Figures Page Determining the Node Platform List of TablesPage Submitting a Job Script List of ExamplesPage This document is organized as follows About This DocumentIntended Audience Document Organization HP XC Information Supplementary Information $ man lsfcommandnameFor More Information $ man -k keyword Related InformationManpages $ man discover $ man 8 discover Additional Publications Related Linux Web SitesRelated MPI Web Sites Related Compiler Web Sites User input Typographic ConventionsHP Encourages Your Comments Environment Variable Operating System Overview of the User EnvironmentSystem Architecture HP XC System Software Storage and I/O Node Specialization File System Layout File SystemSAN Storage Local Storage Network Address Translation NAT Determining System Configuration InformationSystem Interconnect Network Modules CommandsUser Environment Serial Applications Application Development EnvironmentRun-Time Environment Parallel Applications How LSF-HPC and Slurm Interact Load Sharing Facility LSF-HPCStandard LSF Components, Tools, Compilers, Libraries, and Debuggers Mpirun command Logging In to the System Using the SystemLVS Login Routing Using the Secure Shell to Log 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 Loading a Modulefile Modulefiles Automatically Loaded on the SystemViewing Available Modulefiles Viewing Loaded Modulefiles Loading a Modulefile for the Current Session Automatically Loading a Modulefile at LoginUnloading a Modulefile Modulefile Conflicts $ module help totalview Creating a ModulefileViewing Modulefile-Specific Help $ module load modules $ man modulefilePage Compilers Developing ApplicationsApplication Development Environment Overview Partition Avail Timelimit Nodes State Nodelist Examining Nodes and Partitions Before Running JobsInterrupting a Job MPI Compiler Building Serial Applications Setting Debugging OptionsDeveloping Serial Applications Serial Application Build Environment OpenMP Developing Parallel ApplicationsParallel Application Build Environment Modulefiles Intel Fortran and C/C++Compilers PthreadsQuadrics Shmem MPI Library 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 $ bsub hostname Submitting a Serial Job Using Standard LSFSubmitting a Serial Job Using LSF-HPC Submitting a Serial Job with the LSF bsub Command Submitting a Serial Job Through Slurm only Mpirun mpirun--options-srunsrun-optionsmpi-jobname Submitting a Non-MPI Parallel Job$ bsub -n4 -I srun hostname Bsub -nnum-procsbsub-optionsmpijob Bsub -nnum-procs bsub-optionsscript-name Submitting a Batch Job or Job Script$ bsub -n4 -I mpirun -srun ./helloworld $ bsub -n4 -ext SLURMnodes=4 -I ./myscript.sh $ cat myscript.sh #!/bin/shSrun hostname mpirun -srun hellompi $ bsub -I -n4 Myscript.sh $ cat ./envscript.sh #!/bin/sh name=`hostname` Running Preexecution Programs$ bsub -n4 -I ./myscript.sh Opt/hptc/bin/srun Mypreexec TotalView Debugging ApplicationsDebugging Serial Applications Debugging Parallel Applications Module load mpimodule load totalview Setting Up TotalViewUsing TotalView with Slurm SSH and TotalView Debugging an Application Using TotalView with LSF-HPCSetting TotalView Preferences $ mpirun -srun -n2 Psimple Sourcefile initfdte.f was not found, using assembler modeDebugging Running Applications Directories in File ⇒ Search Path $ 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 Cldflags Running a Program Intel Trace Collector and HP-MPIVisualizing Data Intel Trace Analyzer and HP-MPI Libs Using the Intel Trace Collector and Intel Trace Analyzer Page Introduction to Slurm Using SlurmLaunching Jobs with the srun Command Srun Squeue Scancel Sinfo Scontrol Srun Roles and Modes Monitoring Jobs with the squeue CommandUsing the srun Command with HP-MPI Using the srun Command with LSF-HPC 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 Status JL/U MAX Njobs RUN Ssusp Ususp RSV Differences Between LSF-HPC and Standard LSFHostname Resources Unknown Unknown Job Terminology$ ssh n15 lshosts SLURMnodelist =nodelist if specified HP XCCompute Node Resource Support $ bsub -n 10 -ext SLURMconstraint=dualcore -I srun hostname $ bsub -n 10 -I srun hostname$ bsub -n 10 -ext SLURMnodes=10 -I srun hostname $ bsub -n 10 -ext SLURMnodes=10exclude=n16 -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 Getting Information About LSF Execution Host Node Determining the LSF Execution HostDetermining Available LSF-HPC System Resources Getting the Status of LSF-HPC SLINUX6 Getting Host Load InformationExamining LSF-HPC System Queues Getting Information About the lsf Partition $ sinfo -p lsf -lNe Summary of the LSF bsub Command Format$ sinfo -p lsf Bsub-options srun srun-optionsjobname job-options LSF-SLURM External SchedulerFor information about running scripts Bsub -n num-procs-ext SLURMslurm-arguments \ Type=SLINUX64 Submitting a Job from a Non-HP XC HostStarting on lsfhost.localdomain n6 Waiting for dispatch ... Starting on lsfhost.localdomain n1 $ bjobs -l Getting Information About JobsGetting Job Allocation Information Slurmid=slurmjobidncpus=slurmnprocsslurmalloc=nodelist $ bjobs Examining the Status of a Job$ bhist -l Time stamp Jobid User Jobname Pend Psusp RUN Ususp Ssusp Unkwn Total Viewing the Historical Information for a Job$ bhist Summary of time in seconds spent Various States Translating Slurm and LSF-HPC JOBIDs $ srun --jobid=150 hostname Working Interactively Within an LSF-HPC Allocation$ bsub -I -n4 -ext SLURMnodes=4 /bin/bash $ bjobs -l 124 grep slurm $ unset Slurmjobid $ unset Slurmnprocs $ unset SlurmjobidAlternatively, you can use the following $ export SLURMJOBID=150 $ export SLURMNPROCS=4 $ bsub -n4 -ext SLURMnodes=4 -o %J.out sleep Job 125 is submitted to the default queue normalLSF-HPC Equivalents of Slurm srun Options $ srun --jobid=250 uptime Bsub -iinputfile Mpi=mpitype Quit-on-interrupt Page Determining IP Address of Your Local Machine Advanced TopicsEnabling Remote Execution with OpenSSH Running an X Terminal Session from a Remote Node Logging in to HP XC System Running an X terminal Session Using SlurmRunning an X terminal Session Using LSF-HPC $ srun -n2 hostname n46 Using the GNU Parallel Make Capability$ bsub -n4 -Ip srun -n1 xterm -display $ srun -n4 hostname n46 $ cd subdir srun -n1 -N1 $MAKE -j4 $ make PREFIX=’srun -n1 -N1 MAKEJ=-j4 Example Procedure $ make PREFIX=srun -n1 -N1 MAKEJ=-j4 Local Disks on Compute NodesPerformance Considerations Modified Makefile is invoked as follows Fp = fopen myfile, a+ Communication Between NodesShared File View Private File ViewPage Examine the LSF execution host information Appendix a ExamplesBuilding and Running a Serial Application Launching a Serial Interactive Shell Through LSF-HPC Running LSF-HPC Jobs with a Slurm Allocation Request SLURMnodes=2 Launching a Parallel Interactive Shell Through LSF-HPCExample 2. Four cores on Two Specific Nodes R15s r1m r15m It tmp swp mem LoadSched LoadStop 124 Lsfad Examine the the running jobs information$ hostname n16 $ srun hostname n5 $ bjobs Display the script Submitting a Simple Job Script with LSF-HPCExamine the the finished jobs information Show the environment Show the job allocation Run some commands from the pseudo-terminalSubmitting an Interactive Job with LSF-HPC Submit the job View the finished jobs Submitting an HP-MPI Job with LSF-HPCExit the pseudo-terminal View the interactive 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 Are not appropriate for replication To the queueFirst-come See Fcfs First-served Global storage As local storage LSF master host Single commandLogin requests and directs them to a node with a login role Linux Virtual See LVS Server Load file Slurm backup Network See NIS Information ServicesRemotely. PXE booting is configured at the Bios level Notably to install and remove software packages Symmetric See SMP Multiprocessing Power available per unit of spaceSsh 114 Index Index PGI Utilities, 63 Slurm commands