HP XC System 2.x Software 153

building parallel applications, 3-6 module commands

avail command, 2-4 list command, 2-4 load command, 2-4 unload command, 2-5

automatically loading at login, 2-5 configuring parallel build environment, 3-5 creating, 2-6

default modulefiles loaded, 2-4 gnu modulefile, 2-3

Intel modulefile, 2-3

loading for current session, 2-5modules modulefile, 2-1,2-3,2-4 mpi modulefile, 2-3

overview of loading, 2-4 setting shell variables, 2-1 supported modulefiles, 2-3 unloading, 2-5

viewing installed modulefiles, 2-4 viewing loaded modulefiles, 2-4 viewing modulefile-specific help, 2-6

modules modulefile

Modules software, 2-1

building parallel applications, 3-6

N

node specialization

introduction to, 1-1 types of roles, 1-1

P

parallel application

build environment, 3-5 building, 3-8 compiling and linking, 3-8 debugging, 4-1

debugging with TotalView, 4-2 developing, 3-1 environment for developing, 1-5 examples of, A-1

performance considerations, 3-14 pgdbg, 4-1

building parallel applications, 3-7

supported, 3-2 using, 3-2

PGI Fortran

( See Fortran )

plf command, 3-7 plf90 command, 3-7 private file view, 3-14 processor availability, 3-3 program development

building parallel applications, 3-8 checking processor availability before

launching jobs, 3-3 communication between nodes, 3-15 compiling and linking parallel applications,

compiling and linking serial applications, 3-4 debugging parallel applications, 4-1 debugging serial applications, 4-1 debugging with TotalView, 4-2 developing libraries, 3-9

developing parallel applications, 3-4 developing serial applications, 3-3 example parallel applications, A-1 example serial applications, A-1 I/O performance considerations, 3-14 introduction to, 3-1

introduction to building serial applications, 3-4

introduction to running serial applications, 3-4

linking with pthreads, 3-5

parallel application build environment, 3-5 parallel application programming model, 3-5 private file view, 3-14

serial application programming model, 3-4 shared file view, 3-14

using Fortran, 3-7 using GNU C/C++, 3-7using GNU make, 3-7,3-10 using libraries, 3-7

using MKL library, 3-7

using MLIB mathematical library, 3-6 using modulefiles, 3-5

using MPI library, 3-6 using PGI, 3-7 using pthreads, 3-5

using reserved symbol names, 3-8 programming environment

developing applications, 1-5 libraries, 1-5

linking requirements, 3-5 restrictions on using, 3-5

Q

checking availability, 7-9

Index-3

Contents

Page Page Contents About This Document 1 Overview of the User Environment 2 Using the System 3 Developing Applications Debugging Applications Tuning Applications Using SLURM 7 Using LSF 8 Using HP-MPI 9 Using HP MLIB Advanced Topics Examples Glossary Index Figures Tables Page About This Document Intended Audience Document Organization HP XC Information For More Information Supplementary Information Manpages Related Information Typographical Conventions HP Encourages Your Comments Page Overview of the User Environment 1.1System Architecture 1.1.1 Operating System 1.1.2 Node Specialization 1.1.3 Storage and I/O 1.1.4 File System 1.1.5 System Interconnect Network 1.1.6Network Address Translation (NAT) 1.2 User Environment 1.2.1 LVS 1.2.2 Modules 1.2.3 Commands 1.3 Application Development Environment 1.3.1 Parallel Applications 1.3.2 Serial Applications 1.4 Run-TimeEnvironment 1.4.1 SLURM 1.4.2 Load Sharing Facility (LSF-HPC) 1.4.3 How LSF-HPCand SLURM Interact 1.4.4 HP-MPI 1.5Components, Tools, Compilers, Libraries, and Debuggers Page Using the System 2.1Logging in to the System 2.1.1 LVS Login Routing 2.1.2 Using ssh to Log In 2.2 Configuring Your Environment with Modulefiles 2.2.1 Notes on Modulefiles 2.2.2 Supplied Modulefiles 2.2.3 Modulefiles Automatically Loaded on the System 2.2.4 Viewing Available Modulefiles 2.2.5 Viewing Loaded Modulefiles 2.2.6 Loading a Modulefile 2.2.7 Unloading a Modulefile 2.2.8Modulefile Conflicts 2.2.9 Creating a Modulefile 2.2.10 Viewing Modulefile-SpecificHelp 2.3 Launching and Managing Jobs Quick Start 2.3.1 Introduction 2.3.2 Getting Information About Queues 2.3.3 Getting Information About Resources 2.3.4Getting Information About the System’s Partitions 2.3.5 Launching Jobs 2.3.5.2 Submitting a Non-MPIParallel Job Example 2-2:Submitting a Non-MPIParallel Job Using SLURM Options with the LSF External Scheduler Example 2-3:Submitting a Non-MPIParallel Job to Run One Task per Node 2.3.5.3 Submitting an MPI Job Using SLURM Options in MPI Jobs with the LSF External Scheduler Example 2-4:Running an MPI Job with LSF Example 2-5:Running an MPI Job with LSF Using the External Scheduler Option 2.3.5.4 Submitting a Batch Job or Job Script Example 2-6:Submitting a Job Script 2.3.6 Getting Information About Your Jobs 2.3.7 Stopping and Suspending Jobs 2.3.8Resuming Suspended Jobs 2.4 Performing Other Common User Tasks 2.4.1 Determining the LSF Cluster Name and LSF Execution Host 2.4.2 Installing Third-PartySoftware 2.5 Getting System Help and Information Page Page Developing Applications 3.1Overview 3.2 Using Compilers 3.2.1 Standard Linux Compilers 3.2.2 Intel Compilers 3.2.3PGI Compilers 3.2.4 Pathscale Compilers 3.3 Checking Nodes and Partitions Before Running Jobs 3.4 Interrupting a Job 3.5 Setting Debugging Options 3.6 Developing Serial Applications 3.6.1Serial Application Build Environment 3.7 Developing Parallel Applications 3.7.1Parallel Application Build Environment 3.7.1.5 Quadrics SHMEM 3.7.1.6 MLIB Math Library 3.7.1.7 MPI Library 3.7.1.8 Intel Fortran and C/C++Compilers 3.7.1.9 PGI Fortran and C/C++ Compilers 3.7.1.10 GNU C and C++ Compilers 3.7.1.11 GNU Parallel Make 3.7.1.12 MKL Library 3.7.2 Building Parallel Applications 3.8 Developing Libraries 3.8.1 Designing Libraries for XC4000 3.9 Advanced Topics 3.9.1 Using the GNU Parallel Make Capability http://www.llnl.gov/asci/applications/SMG98README.html 3.9.1.1 Example Procedure 3.9.1.2 Example Procedure 3.9.1.3 Example Procedure 3.9.2 Local Disks on Compute Nodes 3.9.3 I/O Performance Considerations 3.9.4 Communication Between Nodes Page Debugging Applications 4.1 Debugging Serial Applications 4.2 Debugging Parallel Applications 4.2.1 Debugging with TotalView ______________________ Note: 4.2.1.3Using TotalView with SLURM 4.2.1.4 Using TotalView with LSF-HPC 4.2.1.5 Starting TotalView for the First Time Figure 4-1:TotalView Root Window Figure 4-2:TotalView Preferences Window Page Page 4.2.1.6 Debugging an Application Figure 4-3:TotalView Process Window Example 4.2.1.7 Debugging Running Applications Figure 4-4:Unattached Window Figure 4-5:Attached Window 4.2.1.8Exiting TotalView Page Tuning Applications 5.1 Using the Intel Trace Collector/Analyzer 5.1.1Building a Program — Intel Trace Collector and HP-MPI 5.1.2 Running a Program — Intel Trace Collector and HP-MPI 5.1.3 Visualizing Data — Intel Trace Analyzer and HP-MPI Using SLURM 6.1 Introduction 6.2 SLURM Commands 6.3 Accessing the SLURM Manpages 6.4 Launching Jobs with the srun Command 6.4.1The srun Roles and Modes 6.4.1.1 srun Roles 6.4.1.2srun Modes modes 6.4.2 srun Signal Handling 6.4.3srun Run-ModeOptions 6.4.4 srun Resource-AllocationOptions -ccpt (--cpus-per-task=cpt) -ppart (--partition=part) -tminutes (--time=minutes) -Tnthreads (--threads=nthreads) 6.4.5 srun Control Options 6.4.6 srun I/O Options -omode (--output=mode) -imode (--input=mode) -emode (--error=mode) -l (--label) -u (--unbuffered) 6.4.7 srun Constraint Options --contiguous=yes|no --mem=size --mincpus=n --vmem=size --tmp=size 6.5 Monitoring Jobs with the squeue Command 6.6 Killing Jobs with the scancel Command 6.7 Getting System Information with the sinfo Command 6.8 Job Accounting 6.9 Fault Tolerance 6.10 Security Using LSF 7.1 Introduction to LSF in the HP XC Environment 7.1.1 Overview of LSF 7.1.2 Topology Support 7.1.3 Notes on LSF-HPC 7.1.4How LSF and SLURM Launch and Manage a Job User 7.1.5 Differences Between LSF on HP XC and Standard LSF 7.1.6Notes About Using LSF in the HP XC Environment 7.2 Determining Execution Host 7.3 Determining Available System Resources 7.3.1 Getting Status of LSF 7.3.2Getting Information About LSF-HPCExecution Host Node 7.3.3Getting Host Load Information 7.3.4 Checking LSF System Queues 7.3.5 Getting Information About the lsf Partition 7.4 Submitting Jobs 7.4.1 Summary of the LSF bsub Command Format 7.4.2 LSF-SLURMExternal Scheduler Page 7.4.3 Submitting a Serial Job 7.4.4 Submitting a Job in Parallel 7.4.5 Submitting an HP-MPIJob 7.4.6 Submitting a Batch Job or Job Script 7.4.6.1 Examples Example 7-8:Submitting a Batch Job Script Example 7-9:Submitting a Batch Script with a Specific Topologic Request Example 7-10:Submitting a Batch Job Script that uses a Subset of the Allocation 7.4.7 Submitting a Job from a Non-HPXC Host 7.5 Getting Information About Jobs 7.5.1 Getting Job Allocation Information 7.5.2 Checking Status of a Job 7.5.3 Viewing a Job’s Historical Information 7.6 Working Interactively Within an LSF-HPCAllocation 7.6.1 Submitting an Interactive Job to Launch the xterm Program Example 7-17:View Your Environment Example 7-18:View Your Allocation in SLURM Example 7-19:View Your Running Job in LSF Example 7-20:View Job Details in LSF 7.6.2 Submitting an Interactive Job to Launch a Shell 7.7 LSF Equivalents of SLURM srun Options Table 7-2:LSF Equivalents of SLURM srun Options (cont.) Page Page Using HP-MPI 8.1Overview 8.2 HP-MPIDirectory Structure 8.3 Compiling and Running Applications 8.3.1 Setting Environment Variables 8.3.2 Building and Running an Example Application 8.3.2.1 Example Application hello_world 8.3.2.2 Building and Running hello_world 8.3.3 Using srun with HP-MPI 8.3.3.2Creating Subshells and Launching Jobsteps 8.3.3.3System Interconnect Selection 8.3.4 Using LSF and HP-MPI 8.3.5 MPI Versioning 8.4 System Interconnect Support 8.4.1HP-MPIPerformance on HP XC with Multiple System Interconnects 8.4.2 Global Environment Variable Settings on the mpirun Command Line 8.5 32-BitBuilds on XC4000 8.6 Truncated Messages 8.7Allowing Windows to Use Exclusive Locks 8.8 The mpirun Command Options 8.9 Environment Variables 8.9.1 MPIRUN_OPTIONS 8.9.2MPIRUN_SYSTEM_OPTIONS 8.9.3 MPI_IC_ORDER 8.9.4MPI_PHYSICAL_MEMORY 8.9.5 MPI_PIN_PERCENTAGE 8.9.6 MPI_PAGE_ALIGN_MEM 8.9.7 MPI_MAX_WINDOW 8.9.8MPI_ELANLOCK 8.9.9MPI_USE_LIBELAN 8.10MPICH Object Compatibility 8.11 HP-MPIDocumentation and Manpages 8.12Additional Information, Known Problems, and Work-arounds Using HP MLIB 9.1 Overview 9.1.1 Intel Compiler Notes 9.1.2 MLIB and Module Files 9.2 HP MLIB for the HP XC6000 Platform 9.2.1 Platform Support 9.2.2 Library Support 9.2.3 MPI Parallelism 9.2.4 Modulefiles and MLIB 9.2.5 Using Intel Compilers with HP MLIB 9.2.6 Compiling and Linking 9.2.7 Licensing 9.2.8 MLIB Manpages 9.3 HP MLIB for the HP XC4000 Platform 9.3.1 Platform Support 9.3.2 Library Support 9.3.3 MPI Parallelism 9.3.4 Modulefiles and MLIB 9.3.5 Compiling and Linking 9.3.6 Licensing 9.3.7 MLIB Manpages Advanced Topics 10.1Enabling Remote Execution with OpenSSH 10.2 Running an X Terminal Session from a Remote Node Step 2. Logging in to HP XC System Step 3. Running an X terminal Session Using SLURM Step 4. Running an X terminal Session Using LSF Page Examples A.1 Building and Running a Serial Application A.2 Launching a Serial Interactive Shell Through LSF A.3 Running LSF Jobs with a SLURM Allocation Request A.3.1 Example 1. Two Processors on Any Two Nodes A.3.2 Example 2. Four Processors on Two Specific Nodes A.4 Launching a Parallel Interactive Shell Through LSF Note the output from the bjobs command: Check the running job’s information: A.5 Submitting a Simple Job Script with LSF A.6 Submitting an Interactive Job with LSF A.7 Submitting an HP-MPIJob with LSF View the running job: View the finished job: A.8 Using a Resource Requirements String in an LSF Command Page Glossary extensible firmware interface external network node fairshare FCFS first come first served image server Integrated Lights Out interconnect Internet address I/O node LSF master host LVS Management Processor master host module parallel application PXE resource manager role role Root Administration Switch Page Index