HP XC System 4.x Software 134

developing, 39

environment for developing, 24 examples of, 115

partition

reporting state of, 83 PATH environment variable

setting with a module, 34 Pathscale

building parallel applications, 44 Pathscale compilers, 40 Pathscale Fortran (see Fortran) performance considerations, 113 performance health tests, 70–73pgdbg, 63

PGI

building parallel applications, 44 PGI compilers, 40

PGI Fortran (see Fortran) private file view, 113 /proc/cpuinfo, 19

program development (see application development) programming environment

compilers, 24

developing applications, 24 libraries, 24

pthreads

linking requirements, 43 MKL library, 45 restrictions on using, 43

Q

queue display, 82

examining availability, 96

R

remote execution, 107 reporting documentation errors

feedback e-mail address for, 17 resource manager, 81, 86 resources

determining available, 94 role, 19

routing login requests, 29 RPM, 23, 34, 69 run-time environment, 25

S

scancel command, 83 secure shell (see ssh) security, 107

SLURM, 84 serial applications

building, 42

compiling and linking, 42 debugging, 63 developing, 25, 39, 41 examples of, 115 programming model, 42

shared file view, 113 signal

sending to a job, 83

Simple Linux Utility for Resource Management (see

SLURM)

sinfo command, 83, 96 SLURM, 81

fault tolerance, 84 interaction with LSF, 92 job accounting, 84

lsf partition, 95 security model, 84

SLURM_JOBID environment variable, 97, 100 SLURM_NPROCS environment variable, 97 submitting a serial job, 50

utilities, 81 SLURM commands

sacct, 84 scancel, 83 sinfo, 83, 96 squeue, 82 srun, 41, 81 software RAID

documentation, 16 mdadm utility, 16 squeue command, 82

srun command, 81 interrupting jobs, 41 LSF equivalents, 103 used with HP-MPI, 82 used with LSF, 82

ssh, 29

ssh_create_shared_keys command, 29, 107 submitting a batch job, 56

submitting a job, 52 overview, 49

submitting a job script, 56 submitting a parallel job, 51 submitting a serial job, 49

through SLURM, 50

with the LSF bsub command, 49 submitting an HP-MPI job, 52 system, 29

developing applications on, 39 information, 83

logging in, 29 overview, 19

system architecture, 19

T

TotalView, 63, 64 debugging an application, 66 exiting, 67

setting preferences, 65 setting up, 64

tuning applications, 75

U

Unified Parallel C (see UPC)

134 Index

Contents

Version Page Table of Contents About This Document 1 Overview of the User Environment 2 Using the System 3 Configuring Your Environment with Modulefiles 4 Developing Applications 5 Submitting Jobs 6 Debugging Applications 7 Monitoring Node Activity 8 Tuning Applications 9 Using SLURM 10 Using LSF 11 Advanced Topics A Examples Glossary Index List of Figures List of Tables List of Examples About This Document Intended Audience New and Changed Information in This Edition Typographic Conventions HP XC and Related HP Products Information Related Information •http://www.platform.com —Administering Platform LSF —Administration Primer —Platform LSF Reference —Quick Reference Card •http://www.balabit.com/products/syslog_ng syslog-ng syslog •http://systemimager.org •http://linuxvirtualserver.org Manpages HP Encourages Your Comments Page 1.1.1 HP XC System Software 1.1.4 Node Specialization 1.1.5 Storage and I/O 1.1.6 File System 1.1.7 System Interconnect Network 1.1.8 Network Address Translation (NAT) 1.2 Determining System Configuration Information 1.3 User Environment 1.3.1 LVS 1.3.2 Modules 1.3.3 Commands 1.4 Application Development Environment 1.4.1 Parallel Applications 1.4.2 Serial Applications 1.5 Run-TimeEnvironment 1.5.1 SLURM 1.5.2 Load Sharing Facility (LSF) 1.5.3 Standard LSF 1.5.4 How LSF and SLURM Interact 1.5.5 HP-MPI 1.6 Components, Tools, Compilers, Libraries, and Debuggers Page 2 Using the System 2.1Logging In to the System 2.1.1 LVS Login Routing 2.1.2 Using the Secure Shell to Log In 2.2 Overview of Launching and Managing Jobs 2.2.1 Introduction 2.2.2 Getting Information About Queues 2.2.3 Getting Information About Resources 2.2.4Getting Information About System Partitions 2.2.5 Launching Jobs 2.3 Performing Other Common User Tasks 2.3.1 Determining the LSF Cluster Name and the LSF Execution Host 2.4 Getting System Help and Information 3 Configuring Your Environment with Modulefiles 3.1Overview of Modules 3.2 Supplied Modulefiles Table 3-1Supplied Modulefiles (continued) “Viewing Available Modulefiles” “Viewing Loaded Modulefiles” 3.3 Modulefiles Automatically Loaded on the System 3.4 Viewing Available Modulefiles 3.5 Viewing Loaded Modulefiles 3.6 Loading a Modulefile 3.6.1 Loading a Modulefile for the Current Session 3.7 Unloading a Modulefile 3.8Viewing Modulefile-SpecificHelp 3.9 Modulefile Conflicts 3.10 Creating a Modulefile 4 Developing Applications 4.1Application Development Environment Overview 4.2 Compilers 4.2.1 MPI Compiler 4.3 Examining Nodes and Partitions Before Running Jobs 4.4 Interrupting a Job 4.5 Setting Debugging Options 4.6 Developing Serial Applications 4.6.1 Serial Application Build Environment 4.7 Developing Parallel Applications 4.7.1Parallel Application Build Environment 4.7.1.1 Modulefiles 4.7.1.2 HP-MPI 4.7.1.3 OpenMP 4.7.1.4 Pthreads -pthread shmem.h 4.7.1.6 MPI Library MPI: A Message Passing Interface Standard mpi.h mpif.h 4.7.2 Building Parallel Applications 4.8 Developing Libraries 4.8.1 Designing Libraries for the CP4000 Platform Page Page 5 Submitting Jobs 5.1Overview of Job Submission 5.2 Submitting a Serial Job Using LSF 5.2.1 Submitting a Serial Job with the LSF bsub Command 5.2.2 Submitting a Serial Job Through SLURM Only 5.3 Submitting a Parallel Job 5.3.1Submitting a Non-MPIParallel Job 5.3.2 Submitting a Parallel Job That Uses the HP-MPIMessage Passing Interface 5.3.3 Submitting a Parallel Job Using the SLURM External Scheduler Page Example 5-10 shows one way to submit a parallel job to run one task per node n10 dualcore 5.4 Submitting a Batch Job or Job Script Example 5-16Submitting a Batch Job Script That Uses a Subset of the Allocation Example 5-17Submitting a Batch job Script That Uses the srun --overcommitOption SLURM Reference Manual 5.5 Submitting Multiple MPI Jobs Across the Same Set of Nodes 5.5.1 Using a Script to Submit Multiple Jobs 5.5.2 Using a Makefile to Submit Multiple Jobs mymake run1 run2 The following command line makes the program and executes it: 1This line attempts to submit a program that does not exist 5.6 Submitting a Job from a Host Other Than an HP XC Host 5.7 Running Preexecution Programs Page 6 Debugging Applications 6.1Debugging Serial Applications 6.2 Debugging Parallel Applications TotalView DDT 6.2.1 Debugging with TotalView 6.2.1.3 Using TotalView with SLURM These commands allocate nodes and run TotalView to debug the program named 6.2.1.4 Using TotalView with LSF You may need to verify the full path name of the xterm and mpirun commands: 6.2.1.6 Debugging an Application This section describes how to use TotalView to debug an application Compile the application to be debugged. For example: Use the -g option to enable debugging information 2.Run the application in TotalView: 6.2.1.7 Debugging Running Applications “Debugging an Application” Compile a long-running application as in Page 7 Monitoring Node Activity 7.1The Xtools Utilities 7.2 Running Performance Health Tests Page n11 n12 n14 n15 --keep Page Page 8 Tuning Applications 8.1 Using the Intel Trace Collector and Intel Trace Analyzer 8.1.1Building a Program — Intel Trace Collector and HP-MPI 8.1.2 Running a Program – Intel Trace Collector and HP-MPI 8.2 The Intel Trace Collector and Analyzer with HP-MPIon HP XC 8.2.1 Installation Kit 8.2.2 HP-MPIand the Intel Trace Collector Running a Program The following is a C example called vtjacobic: The following is a Fortran example called vtjacobif: 8.3 Visualizing Data – Intel Trace Analyzer and HP-MPI Page 9 Using SLURM 9.1Introduction to SLURM 9.2 SLURM Utilities 9.3 Launching Jobs with the srun Command 9.3.1 The srun Roles and Modes 9.4 Monitoring Jobs with the squeue Command 9.5 Terminating Jobs with the scancel Command 9.6 Getting System Information with the sinfo Command 9.7 Job Accounting 9.8 Fault Tolerance 9.9 Security 10 Using LSF 10.1Information for LSF 10.2Overview of LSF Integrated with SLURM describes the relationship between the and the LSF JOBID Example 10-1Examples of LSF Job Launch 10.3 Differences Between LSF and LSF Integrated with SLURM 10.4Job Terminology batch system scheduling policies Batch job submissions typically provide instructions on I/O management, such as files from which to read input and filenames to collect output batch jobs are submitted with the srun -b command. By 10.5 Using LSF Integrated with SLURM in the HP XC Environment 10.5.1 Useful Commands 10.5.2Job Startup and Job Control 10.5.3 Preemption 10.6 Submitting Jobs 10.7 LSF-SLURMExternal Scheduler 10.8 How LSF and SLURM Launch and Manage a Job Figure 10-1How LSF and SLURM Launch and Manage a Job User 1.A user logs in to login node n16 The user executes the following LSF command on login node 10.9 Determining the LSF Execution Host 10.10 Determining Available System Resources 10.10.1 Examining System Core Status 10.10.2Getting Information About the LSF Execution Host Node 10.10.3 Getting Host Load Information 10.10.4 Examining System Queues 10.10.5 Getting Information About the lsf Partition 10.11 Getting Information About Jobs 10.11.1 Getting Job Allocation Information 10.11.2 Examining the Status of a Job 10.11.3 Viewing the Historical Information for a Job 10.12 Translating SLURM and LSF JOBIDs 10.13Working Interactively Within an Allocation Section 5.3.2 (page 52) Example 10-9Launching an Interactive MPI Job Example 10-10 uses the -n8 option to launch on all cores in the allocation Example 10-10Launching an Interactive MPI Job on All Cores in the Allocation This example assumes 2 cores per node 10.14 LSF Equivalents of SLURM srun Options Table 10-3LSF Equivalents of SLURM srun Options (continued) Page Page 11 Advanced Topics 11.1Enabling Remote Execution with OpenSSH 11.2 Running an X Terminal Session from a Remote Node Step 1. Determining IP Address of Your Local Machine 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 11.3 Using the GNU Parallel Make Capability One way is to prefix the actual compilation line in the rule with an command. So, instead of executing it would execute . With concurrency, multiple command nodes would have multiple commands instead of multiple 11.3.1 Example Procedure 11.3.2 Example Procedure 11.3.3 Example Procedure 11.4 Local Disks on Compute Nodes 11.5 I/O Performance Considerations 11.5.1Shared File View 11.5.2 Private File View 11.6 Communication Between Nodes 11.7 Using MPICH on the HP XC System 11.7.1 Using MPICH with SLURM Allocation 11.7.2Using MPICH with LSF Allocation A Examples A.1 Building and Running a Serial Application A.2 Launching a Serial Interactive Shell Through LSF Examine the LSF execution host information: Examine the partition information: A.3 Running LSF Jobs with a SLURM Allocation Request A.3.1 Example 1. Two Cores on Any Two Nodes A.3.2 Example 2. Four Cores on Two Specific Nodes A.4 Launching a Parallel Interactive Shell Through LSF Note the output from the bjobs command: Examine the running job's information: Examine the finished job's information: A.5 Submitting a Simple Job Script with LSF Show the environment: Display the script: Run the job: A.6 Submitting an Interactive Job with LSF Submit the job: Show the job allocation: Show the SLURM job ID: Run some commands from the pseudo-terminal: Exit the pseudo-terminal: View the interactive jobs: View the finished jobs: 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 Page Page Page Page Page Index