Hp XC System 3.x Software Manuel d'utilisateur Page 6
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10.5 Using LSF-HPC Integrated with SLURM in the HP XC Environment....................................................87
10.5.1 Useful Commands.....................................................................................................................87
10.5.2 Job Startup and Job Control........................................................................................................87
10.5.3 Preemption...............................................................................................................................87
10.6 Submitting Jobs.................................................................................................................................88
10.7 LSF-SLURM External Scheduler.........................................................................................................88
10.8 How LSF-HPC and SLURM Launch and Manage a Job........................................................................88
10.9 Determining the LSF Execution Host..................................................................................................90
10.10 Determining Available System Resources..........................................................................................90
10.10.1 Examining System Core Status..................................................................................................90
10.10.2 Getting Information About the LSF Execution Host Node...........................................................91
10.10.3 Getting Host Load Information.................................................................................................91
10.10.4 Examining System Queues.......................................................................................................92
10.10.5 Getting Information About the lsf Partition................................................................................92
10.11 Getting Information About Jobs........................................................................................................92
10.11.1 Getting Job Allocation Information............................................................................................92
10.11.2 Examining the Status of a Job....................................................................................................94
10.11.3 Viewing the Historical Information for a Job..............................................................................95
10.12 Translating SLURM and LSF-HPC JOBIDs.........................................................................................96
10.13 Working Interactively Within an Allocation.......................................................................................97
10.14 LSF-HPC Equivalents of SLURM srun Options..................................................................................99
11 Advanced Topics......................................................................................................103
11.1 Enabling Remote Execution with OpenSSH.......................................................................................103
11.2 Running an X Terminal Session from a Remote Node.........................................................................103
11.3 Using the GNU Parallel Make Capability...........................................................................................105
11.3.1 Example Procedure 1...............................................................................................................107
11.3.2 Example Procedure 2...............................................................................................................108
11.3.3 Example Procedure 3...............................................................................................................108
11.4 Local Disks on Compute Nodes........................................................................................................109
11.5 I/O Performance Considerations.......................................................................................................109
11.5.1 Shared File View......................................................................................................................109
11.5.2 Private File View......................................................................................................................109
11.6 Communication Between Nodes.......................................................................................................109
11.7 Using MPICH on the HP XC System.................................................................................................109
11.7.1 Using MPICH with SLURM Allocation......................................................................................110
11.7.2 Using MPICH with LSF Allocation............................................................................................110
A Examples....................................................................................................................113
A.1 Building and Running a Serial Application.........................................................................................113
A.2 Launching a Serial Interactive Shell Through LSF-HPC.......................................................................113
A.3 Running LSF-HPC Jobs with a SLURM Allocation Request.................................................................114
A.3.1 Example 1. Two Cores on Any Two Nodes.................................................................................114
A.3.2 Example 2. Four Cores on Two Specific Nodes............................................................................115
A.4 Launching a Parallel Interactive Shell Through LSF-HPC....................................................................116
A.5 Submitting a Simple Job Script with LSF-HPC....................................................................................117
A.6 Submitting an Interactive Job with LSF-HPC......................................................................................118
A.7 Submitting an HP-MPI Job with LSF-HPC..........................................................................................120
A.8 Using a Resource Requirements String in an LSF-HPC Command.......................................................121
Glossary.........................................................................................................................123
Index...............................................................................................................................129
6 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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