Using HP Mlib, Intel Compiler Notes | HP XC System 2.x Software

9

Using HP MLIB

The information in this section describes how to use HP MLIB Version 1.5 in the HP XC environment on HP XC4000 and HP XC6000 clusters. These are discussed in separate sections in this chapter.

9.1 Overview

HP MLIB is the mathematical library supported on the HP XC system. It is installed by default.

HP MLIB contains mathematical software and computational kernels for engineering and scientific applications including the following:

•Linear equations

•Least squares

•Eigenvalue problems

•Singular value decomposition

•Vector and matrix computations

•Convolutions

•Fourier Transforms

HP MLIB V1.5 for XC6000 supports 64-bit addressing and 64-bit address libraries with all integer values using 64 bits on XC6000 clusters.

HP MLIB for the HP XC4000 platform supports VECLIB, LAPACK, ScaLAPACK, SuperLU_DIST, and MPI parallelism. This release does not support quad precision sparse solver functionality on PGI/X86-64.

HP MLIB Version 1.5 is optimized for use on HP XC systems. HP MLIB Version 1.5 supports 64-bit addressing on XC6000 and XC4000 clusters.

9.1.1 Intel Compiler Notes

HP MLIB requires the Intel Fortran Compiler; the following provides information on Versions

8 and 7.1:

Version 8 Fortran Compiler

Command path name:

RPM:

tar file:

/opt/mlib/intel_8.0/hpmpi_2.0 intel-ifort8-8.0-57.ia64.rpm l_fc_pc_8[1].0.046.tar.gz

Version 7 Fortran Compiler
Command path name:	/opt/mlib/intel_7.1/hpmpi_2.0
RPM:	intel-efc7-7.1-41.ia64.rpm
tar file:	l_fc_pc_7[1].1.040.tar

After installation, MLIB directory information is located in the /opt/mlib/README file.

Using HP MLIB 9-1

Image 125

HP XC System 2.x Software Using HP Mlib, Intel Compiler Notes, Version 8 Fortran Compiler, Version 7 Fortran Compiler

Contents

Hewlett-Packard Company Palo Alto, California June Product VersionPage Contents 5.4 Developing Applications Debugging Applications Tuning ApplicationsUsing Slurm Using HP-MPI Using LSF 6.4 Using HP Mlib Glossary Index Examples Advanced TopicsExamples Tables FiguresPage Document Organization About This DocumentIntended Audience HP XC Information Linux Administration HandbookQuickSpecs for HP XC System Software HP XC Program Development Environment Supplementary Information For More InformationHP Message Passing Interface HP Mathematical Library Http//supermon.sourceforge.net ManpagesHttp//systemimager.org Http//sourceforge.net/projects/modules Http//www-unix.mcs.anl.gov/mpi Related InformationHttp//linuxvirtualserver.org Bold text # cd /opt/hptc/config/sbinTypographical Conventions Ctrl/x HP Encourages Your CommentsPage System Architecture Overview of the User EnvironmentOperating System Node Specialization File System Storage and I/OSAN Storage Local Storage File System Layout System Interconnect Network User Environment CommandsNetwork Address Translation NAT 1 LVS Serial Applications Application Development EnvironmentParallel Applications Slurm Run-Time EnvironmentLoad Sharing Facility LSF-HPC How LSF-HPC and Slurm Interact HP-MPI Components, Tools, Compilers, Libraries, and Debuggers 8Overview of the User Environment Configuring Your Environment with Modulefiles Using the SystemLVS Login Routing Using ssh to Log 2Using the System Modulefile Sets the HP XC User Environment Supplied ModulefilesSupplied 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 totalview Introduction Launching and Managing Jobs Quick StartGetting Information About Queues Getting Information About Resources Launching Jobs Getting Information About the System’s PartitionsSubmitting a Serial Job Example 2-1 Submitting a Serial Job Submitting a Non-MPI Parallel Job Using Slurm Options with the LSF External SchedulerExample 2-2 Submitting a Non-MPI Parallel Job $ bsub -n4 -I srun hostname $ bsub -n4 Mpirun -srun ./helloworld Submitting an MPI JobExample 2-4 Running an MPI Job with LSF $ bsub -I -n4 myjobscript.sh Submitting a Batch Job or Job ScriptExample 2-6 Submitting a Job Script Getting System Help and Information Performing Other Common User Tasks $ man -k keyword $ man sinfoPage Overview Developing Applications Standard Linux Compilers Using CompilersIntel Compilers PGI Compilers Checking Nodes and Partitions Before Running Jobs Setting Debugging OptionsInterrupting a Job Developing Serial Applications Developing Parallel Applications Using Mlib in Serial ApplicationsSerial Application Build Environment Building Serial Applications Modulefiles Parallel Application Build EnvironmentHP-MPI OpenMP Mlib Math Library Quadrics ShmemMPI Library $ mpicc object1.o ... -pthread -o myapp.exe PGI Fortran and C/C++ Compilers Intel Fortran and C/C++CompilersGNU C and C++ Compilers GNU Parallel Make Building Parallel Applications Reserved Symbols and NamesCompiling and Linking Non-MPI Applications Compiling and Linking HP-MPI Applications $ mpicc -c -g foo.c Developing LibrariesDesigning Libraries for XC4000 Advanced Topics Using the GNU Parallel Make CapabilityExample 3-1 Directory Structure Example 3-2 Recommended Directory Structure $ cd subdir srun -n1 -N1 $MAKE -j4 $ cd subdir srun $MAKE Example Procedure $ make PREFIX=’srun -n1 -N1’ MAKEJ=’-j4’ $ make PREFIX=’srun -n1 -N1 MAKEJ=’-j4’ 3 I/O Performance Considerations Local Disks on Compute NodesShared File View Private File View Communication Between Nodes Page Debugging Serial Applications Debugging ApplicationsDebugging Parallel Applications TotalView SSH and TotalView Setting Up TotalViewDebugging with TotalView Using TotalView with LSF-HPC Using TotalView with Slurm$ srun -Nx-A $ mpirun -tv -srun application $ bsub -nx-ext SLURMnodes=x \ -Is /usr/bin/xterm $ totalview Starting TotalView for the First Time TotalView Preferences Window Preferences window, click on the Launch Strings tab Debugging Applications $ mpirun -tv -srun -n2 ./Psimple Debugging an Application$ mpicc -g -o Psimple simple.c -lm TotalView Process Window Example $ mpirun -srun -n2 Psimple Debugging Running Applications $ squeue $ scancel --user usernameExiting TotalView Page Using the Intel Trace Collector/Analyzer Tuning ApplicationsBuilding a Program Intel Trace Collector and HP-MPI Example Example Running the vtjacobic Example Program Running a Program Intel Trace Collector and HP-MPIVisualizing Data Intel Trace Analyzer and HP-MPI Slurm Commands Using SlurmCommand Function Introduction Launching Jobs with the srun Command Accessing the Slurm ManpagesSrun Roles and Modes Example 6-1 Simple Launch of a Serial Program Srun Modes Srun Roles Srun Run-Mode Options Srun Signal HandlingBatch Allocate Srun Resource-Allocation Options Part --partition=part Cpt --cpus-per-task=cptMinutes --time=minutes Nthreads --threads=nthreads Srun Control Options Srun I/O Options Mode --input=mode Mode --output=modeMode --error=mode Label Clist --constraint=clist Srun Constraint Options Mem=size Contiguous=yesnoMincpus=n Vmem=size Using srun with HP-MPI Monitoring Jobs with the squeue CommandUsing srun with LSF Srun Environment Variables Getting System Information with the sinfo Command Killing Jobs with the scancel Command Job Accounting Fault ToleranceSecurity $ sinfo -R Overview of LSF Using LSFIntroduction to LSF in the HP XC Environment Nodelist= list-of-nodes Exclude= list-of-nodes Topology Support $ bsub -n 10 -ext SLURMnodes=10exclude=n16 srun myapp $ bsub -n 10 -ext SLURMnodes=10 srun myapp $ bsub -Is hostname How LSF and Slurm Launch and Manage a Job$ bqueues -l normal grep Jobstarter $ bsub -n4 -ext SLURMnodes=4 -o output.out ./myscript How LSF-HPC and Slurm Launch and Manage a Job Differences Between LSF on HP XC and Standard LSF Determining Available System Resources Determining Execution HostGetting Status of LSF Job Startup and Job Control Getting Host Load Information Getting Information About LSF-HPC Execution Host Node Checking LSF System Queues Submitting JobsGetting Information About the lsf Partition $ sinfo -p lsf Bsub bsuboptions jobname joboptions Summary of the LSF bsub Command Format Slurm Arguments Function LSF-SLURM External Scheduler Starting on lsfhost.localdomain n6 Submitting a Job in Parallel Submitting a Serial JobSubmitting an HP-MPI Job Example 7-5 Submitting an Interactive Serial Job $ bsub -n4 -I mpirun -srun ./helloworld Submitting a Batch Job or Job ScriptExample 7-6 Submitting an HP-MPI Job Example 7-8 Submitting a Batch Job Script Examples$ bsub -n4 -I ./myscript.sh $ bsub -n4 -ext SLURMnodes=4 -I ./myscript.sh Type=SLINUX64 Submitting a Job from a Non-HP XC Host$ bsub -n4 -I ./myscript.sh -n8 -O Getting Job Allocation Information Getting Information About JobsJob Allocation Information for a Running Job $ bsub -R type=SLINUX64 -n4 -I srun hostname Job Allocation Information for a Finished Job Example 7-13 Using the bjobs Command Short OutputChecking Status of a Job Example 7-15 Using the bhist Command Short Output Example 7-14 Using the bjobs Command Long OutputOutput Provided by the bhist Command Viewing a Job’s Historical Information Submitting an Interactive Job to Launch the xterm Program Example 7-16 Using the bhist Command Long OutputWorking Interactively Within an LSF-HPC Allocation Example 7-18 View Your Allocation in Slurm Example 7-17 View Your EnvironmentExample 7-19 View Your Running Job in LSF Example 7-20 View Job Details in LSF Example 7-21 Running Jobs from an xterm Window Submitting an Interactive Job to Launch a ShellExample 7-22 Submitting an Interactive Shell Program $ hostname $ srun hostname $ srun -n2 hostname LSF Equivalents of Slurm srun Options LSF Equivalents of Slurm srun Options$ srun hostname n1 $ exit Srun Option Description LSF Equivalent 24Using LSF Control the parallel job Page Using HP-MPI HP-MPI Directory Structure Setting Environment VariablesCompiling and Running Applications Building and Running an Example Application Building and Running helloworld Example Application helloworld$ mpicc -o helloworld $MPIROOT/help/helloworld.c $ $MPIROOT/bin/mpirun -srun -n4 helloworld HP-MPI options allowed with -srun Launching MPI Jobs System Interconnect Selection Creating Subshells and Launching Jobsteps$ mpirun -srun -n6 -O -N2 -m cyclic ./a.out host1 rank1 $ mpirun -srun -n4 -N2 -O -m cyclic ./a.out host1 rank1 $ mpirun -subnet 192.168.1.1 -prot -srun -n4 ./a.out Using LSF and HP-MPI System Interconnect Support $ /usr/sbin/ifconfig -aMPI Versioning Example 8-5 Allocating 12 Processors on 6 Nodes Allowing Windows to Use Exclusive Locks 32-Bit Builds on XC4000Truncated Messages $ mpirun -TCP -srun -N8 ./a.out Mpirun Command Options $MPIROOT/bin/mpirun -v -prot -np 2 /path/to/program.x Environment Variables Export MPIPINPERCENTAGE=30 Export MPIPHYSICALMEMORY=1048576Export MPIPAGEALIGNMEM=1 Export MPIMAXWINDOW=10 Export MPIUSELIBELAN=0 Mpich Object CompatibilityExport MPIUSELIBELANUSE=5 $MPIROOT/bin/mpirun.mpich -np 2 ./prog.x At http//docs.hp.com HP-MPI Documentation and ManpagesHP-MPI Manpage Categories Category Manpages Description Additional Information, Known Problems, and Work-arounds Intel Compiler Notes Using HP MlibVersion 8 Fortran Compiler Version 7 Fortran Compiler Mlib and Module Files HP Mlib for the HP XC6000 PlatformPlatform Support Library Support Compiling and Linking Using Intel Compilers with HP MlibModulefiles and Mlib Licensing HP Mlib for the HP XC4000 PlatformMlib Manpages Linking SuperLUDIST $ pgcc options file 6Using HP Mlib 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 Slurm$ hostname $ host mymachine $ bjobs Running an X terminal Session Using LSF$ bsub -n4 -Ip srun -n1 xterm -display Page Launching a Serial Interactive Shell Through LSF ExamplesBuilding and Running a Serial Application Example 1. Two Processors on Any Two Nodes Running LSF Jobs with a Slurm Allocation Request View the job Launching a Parallel Interactive Shell Through LSFExample 2. Four Processors on Two Specific Nodes $ bsub -Is -n4 -ext SLURMnodes=4 /bin/bash Check the running job’s information Check the finished job’s information Submitting a Simple Job Script with LSFShow the environment Display the script Show the job allocation Submitting an Interactive Job with LSFShow the Slurm job ID $ bsub -n8 -Ip /bin/sh Submitting an HP-MPI Job with LSF $ bjobs -l 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 CommandPage Glossary External network node Extensible firmware interfaceFairshare First come first served Integrated Lights Out Image serverInterconnect Internet address LSF master host Network Information ServicesManagement Processor Master host Parallel application Root Administration SwitchResource manager role Role Glossary-6 Symmetric multiprocessing Index-1 Index Index-2 Gdb, 4-1 GNU Index-3 Modulefile Index-4 Resource manager, 7-1role Serial applications