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3 Configuring Your Environment with Modulefiles.......................................................31
3.1 Overview of Modules..........................................................................................................................31
3.2 Supplied Modulefiles..........................................................................................................................32
3.3 Modulefiles Automatically Loaded on the System.................................................................................33
3.4 Viewing Available Modulefiles.............................................................................................................33
3.5 Viewing Loaded Modulefiles...............................................................................................................34
3.6 Loading a Modulefile..........................................................................................................................34
3.6.1 Loading a Modulefile for the Current Session................................................................................34
3.6.2 Automatically Loading a Modulefile at Login...............................................................................34
3.7 Unloading a Modulefile.......................................................................................................................34
3.8 Viewing Modulefile-Specific Help........................................................................................................35
3.9 Modulefile Conflicts............................................................................................................................35
3.10 Creating a Modulefile........................................................................................................................35
4 Developing Applications.............................................................................................37
4.1 Application Development Environment Overview................................................................................37
4.2 Compilers...........................................................................................................................................37
4.2.1 MPI Compiler.............................................................................................................................38
4.3 Examining Nodes and Partitions Before Running Jobs...........................................................................38
4.4 Interrupting a Job................................................................................................................................38
4.5 Setting Debugging Options..................................................................................................................39
4.6 Developing Serial Applications............................................................................................................39
4.6.1 Serial Application Build Environment...........................................................................................39
4.6.2 Building Serial Applications.........................................................................................................39
4.6.2.1 Compiling and Linking Serial Applications...........................................................................39
4.7 Developing Parallel Applications.........................................................................................................39
4.7.1 Parallel Application Build Environment........................................................................................40
4.7.1.1 Modulefiles.........................................................................................................................40
4.7.1.2 HP-MPI..............................................................................................................................40
4.7.1.3 OpenMP.............................................................................................................................40
4.7.1.4 Pthreads.............................................................................................................................40
4.7.1.5 Quadrics SHMEM...............................................................................................................41
4.7.1.6 MPI Library........................................................................................................................41
4.7.1.7 Intel Fortran and C/C++Compilers........................................................................................41
4.7.1.8 PGI Fortran and C/C++ Compilers........................................................................................41
4.7.1.9 GNU C and C++ Compilers..................................................................................................41
4.7.1.10 Pathscale Compilers...........................................................................................................41
4.7.1.11 GNU Parallel Make............................................................................................................41
4.7.1.12 MKL Library.....................................................................................................................42
4.7.1.13 ACML Library...................................................................................................................42
4.7.1.14 Other Libraries..................................................................................................................42
4.7.2 Building Parallel Applications......................................................................................................42
4.7.2.1 Compiling and Linking Non-MPI Applications.....................................................................42
4.7.2.2 Compiling and Linking HP-MPI Applications.......................................................................42
4.7.2.3 Examples of Compiling and Linking HP-MPI Applications....................................................42
4.8 Developing Libraries...........................................................................................................................43
4.8.1 Designing Libraries for the CP4000 Platform.................................................................................43
5 Submitting Jobs............................................................................................................47
5.1 Overview of Job Submission................................................................................................................47
5.2 Submitting a Serial Job Using LSF-HPC................................................................................................47
5.2.1 Submitting a Serial Job with the LSF bsub Command.....................................................................47
5.2.2 Submitting a Serial Job Through SLURM Only..............................................................................48
5.3 Submitting a Parallel Job......................................................................................................................49
5.3.1 Submitting a Non-MPI Parallel Job...............................................................................................49
5.3.2 Submitting a Parallel Job That Uses the HP-MPI Message Passing Interface.....................................50
5.3.3 Submitting a Parallel Job Using the SLURM External Scheduler.....................................................51
4 Table of Contents
- HP XC System Software 1
- User's Guide 1
- Table of Contents 3
- 4 Table of Contents 4
- Table of Contents 5 5
- 6 Table of Contents 6
- List of Figures 7
- List of Examples 11
- About This Document 13
- 14 About This Document 14
- 5 Related information 15
- 16 About This Document 16
- Linux Web Sites 17 17
- 6 Manpages 18
- 7 HP Encourages Your Comments 18
- 1.1 System Architecture 19
- 1.1.4 Node Specialization 20
- 1.1.5 Storage and I/O 21
- 1.1.6 File System 21
- 1.3 User Environment 23
- 1.5 Run-Time Environment 24
- 1.5.3 Standard LSF 25
- 1.5.5 HP-MPI 26
- 2 Using the System 27
- 2.2.1 Introduction 28
- 30 Using the System 30
- 3.1 Overview of Modules 31
- 3.2 Supplied Modulefiles 32
- 3.6 Loading a Modulefile 34
- 3.7 Unloading a Modulefile 34
- 3.9 Modulefile Conflicts 35
- 3.10 Creating a Modulefile 35
- 4 Developing Applications 37
- 4.4 Interrupting a Job 38
- 4.5 Setting Debugging Options 39
- 4.7.1.1 Modulefiles 40
- 4.7.1.2 HP-MPI 40
- 4.7.1.3 OpenMP 40
- 4.7.1.4 Pthreads 40
- 42 Developing Applications 42
- 4.8 Developing Libraries 43
- 44 Developing Applications 44
- 4.8 Developing Libraries 45 45
- 5 Submitting Jobs 47
- 48 Submitting Jobs 48
- 5.3 Submitting a Parallel Job 49
- 50 Submitting Jobs 50
- 52 Submitting Jobs 52
- 54 Submitting Jobs 54
- 56 Submitting Jobs 56
- 6 Debugging Applications 57
- 6.2.1.1 SSH and TotalView 58
- 6.2.1.2 Setting Up TotalView 58
- 60 Debugging Applications 60
- 6.2.1.8 Exiting TotalView 61
- 7 Monitoring Node Activity 63
- 64 Monitoring Node Activity 64
- 66 Monitoring Node Activity 66
- 68 Monitoring Node Activity 68
- 70 Monitoring Node Activity 70
- 8 Tuning Applications 73
- 74 Tuning Applications 74
- 8.2.1 Installation Kit 75
- Running a Program 76
- 9 Using SLURM 79
- 9.3.1.1 The srun Roles 80
- 9.3.1.2 The srun Modes 80
- 9.7 Job Accounting 81
- 9.9 Security 82
- 9.8 Fault Tolerance 82
- 10 Using LSF-HPC 83
- 84 Using LSF-HPC 84
- 10.4 Job Terminology 86
- 10.5.1 Useful Commands 87
- 10.5.3 Preemption 87
- 10.6 Submitting Jobs 88
- SLURM_JOBID=53 89
- SLURM_NPROCS=4 89
- 90 Using LSF-HPC 90
- 92 Using LSF-HPC 92
- 94 Using LSF-HPC 94
- 96 Using LSF-HPC 96
- 98 Using LSF-HPC 98
- 100 Using LSF-HPC 100
- 102 Using LSF-HPC 102
- 11 Advanced Topics 103
- 104 Advanced Topics 104
- 106 Advanced Topics 106
- 11.3.1 Example Procedure 1 107
- 11.3.3 Example Procedure 3 108
- 11.3.2 Example Procedure 2 108
- 11.5.1 Shared File View 109
- 11.5.2 Private File View 109
- 110 Advanced Topics 110
- A Examples 113
- Submit the job: 114
- View the job: 115
- 116 Examples 116
- Exit from the shell: 117
- Show the environment: 117
- Display the script: 118
- Run the job: 118
- Submit the job: 119 119
- View the finished jobs: 120
- View the node state: 120
- View the running job: 121
- View the finished job: 121
- 122 Examples 122
- Glossary 123
- 124 Glossary 124
- 126 Glossary 126
- 130 Index 130
- 132 Index 132
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