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Table of Contents
About This Document.......................................................................................................15
Intended Audience................................................................................................................................15
New and Changed Information in This Edition...................................................................................15
Typographic Conventions.....................................................................................................................15
HP XC and Related HP Products Information.....................................................................................16
Related Information..............................................................................................................................17
Manpages..............................................................................................................................................20
HP Encourages Your Comments..........................................................................................................21
1 Overview of the User Environment.............................................................................23
1.1 System Architecture........................................................................................................................23
1.1.1 HP XC System Software..........................................................................................................23
1.1.2 Operating System....................................................................................................................23
1.1.3 Node Platforms.......................................................................................................................23
1.1.4 Node Specialization.................................................................................................................24
1.1.5 Storage and I/O........................................................................................................................25
1.1.6 File System...............................................................................................................................25
1.1.7 System Interconnect Network.................................................................................................26
1.1.8 Network Address Translation (NAT)......................................................................................27
1.2 Determining System Configuration Information............................................................................27
1.3 User Environment...........................................................................................................................27
1.3.1 LVS...........................................................................................................................................27
1.3.2 Modules...................................................................................................................................27
1.3.3 Commands..............................................................................................................................28
1.4 Application Development Environment.........................................................................................28
1.4.1 Parallel Applications...............................................................................................................28
1.4.2 Serial Applications..................................................................................................................29
1.5 Run-Time Environment...................................................................................................................29
1.5.1 SLURM....................................................................................................................................29
1.5.2 Load Sharing Facility (LSF-HPC)............................................................................................29
1.5.3 Standard LSF...........................................................................................................................30
1.5.4 How LSF-HPC and SLURM Interact.......................................................................................30
1.5.5 HP-MPI....................................................................................................................................30
1.6 Components, Tools, Compilers, Libraries, and Debuggers............................................................31
2 Using the System..........................................................................................................33
2.1 Logging In to the System.................................................................................................................33
2.1.1 LVS Login Routing..................................................................................................................33
2.1.2 Using the Secure Shell to Log In.............................................................................................33
2.2 Overview of Launching and Managing Jobs..................................................................................33
2.2.1 Introduction.............................................................................................................................34
2.2.2 Getting Information About Queues........................................................................................34
2.2.3 Getting Information About Resources....................................................................................34
2.2.4 Getting Information About System Partitions........................................................................35
2.2.5 Launching Jobs........................................................................................................................35
2.2.6 Getting Information About Your Jobs.....................................................................................35
2.2.7 Stopping and Suspending Jobs...............................................................................................35
2.2.8 Resuming Suspended Jobs......................................................................................................35
2.3 Performing Other Common User Tasks..........................................................................................35
Table of Contents 3
- 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
- Table of Contents 7 7
- List of Figures 9
- List of Tables 11
- List of Examples 13
- About This Document 15
- Related Information 17
- Linux Web Sites 19
- Manpages 20
- HP Encourages Your Comments 21
- 1.1 System Architecture 23
- 1.1.4 Node Specialization 24
- 1.1.5 Storage and I/O 25
- 1.1.6 File System 25
- File System Layout 26
- 1.3 User Environment 27
- 1.3.3 Commands 28
- 1.4.1 Parallel Applications 28
- 1.5 Run-Time Environment 29
- 1.5.3 Standard LSF 30
- 1.5.5 HP-MPI 30
- 2 Using the System 33
- 2.2.1 Introduction 34
- 2.2.5 Launching Jobs 35
- 2.2.8 Resuming Suspended Jobs 35
- 36 Using the System 36
- 3.1 Overview of Modules 37
- 3.2 Supplied Modulefiles 38
- 3.6 Loading a Modulefile 40
- 3.7 Unloading a Modulefile 41
- 3.9 Modulefile Conflicts 41
- 3.10 Creating a Modulefile 42
- 4 Developing Applications 43
- 4.2 Compilers 44
- 4.4 Interrupting a Job 45
- 4.5 Setting Debugging Options 45
- 46 Developing Applications 46
- 4.7.1.1 Modulefiles 47
- 4.7.1.2 HP-MPI 47
- 4.7.1.3 OpenMP 47
- 4.7.1.4 Pthreads 47
- 4.7.1.5 Quadrics SHMEM 47
- 48 Developing Applications 48
- $ module load mpi 49
- 4.8 Developing Libraries 50
- 4.8 Developing Libraries 51 51
- 52 Developing Applications 52
- 5 Submitting Jobs 53
- 54 Submitting Jobs 54
- 5.3 Submitting a Parallel Job 55
- 56 Submitting Jobs 56
- 60 Submitting Jobs 60
- 62 Submitting Jobs 62
- 64 Submitting Jobs 64
- -R "type=SLINUX64" 65
- 6 Debugging Applications 67
- 6.2.1.1 SSH and TotalView 68
- 6.2.1.2 Setting Up TotalView 68
- 70 Debugging Applications 70
- 6.2.1.8 Exiting TotalView 71
- 7 Monitoring Node Activity 73
- 74 Monitoring Node Activity 74
- $ xcxperf -node n6 78
- $ xcxperf -o test 78
- $ xcxperf test 78
- 80 Monitoring Node Activity 80
- 82 Monitoring Node Activity 82
- 8 Tuning Applications 85
- 86 Tuning Applications 86
- 8.2.1 Installation Kit 87
- Running a Program 88
- 9 Using SLURM 91
- 9.3.1.1 The srun Roles 92
- 9.3.1.2 The srun Modes 92
- 9.7 Job Accounting 94
- 9.8 Fault Tolerance 94
- 9.9 Security 94
- 10 Using LSF-HPC 95
- 96 Using LSF-HPC 96
- 10.4 Job Terminology 99
- 100 Using LSF-HPC 100
- 10.6 Submitting Jobs 101
- DescriptionExit Code 102
- Success0 102
- 102 Using LSF-HPC 102
- SLURM_JOBID=53 103
- SLURM_NPROCS=4 103
- $ sinfo -p lsf -lNe 106
- 106 Using LSF-HPC 106
- 108 Using LSF-HPC 108
- $ bjobs 24 109
- 112 Using LSF-HPC 112
- 11 Advanced Topics 117
- 118 Advanced Topics 118
- 120 Advanced Topics 120
- 11.3.1 Example Procedure 1 121
- 11.3.2 Example Procedure 2 121
- 11.3.3 Example Procedure 3 122
- 11.5.1 Shared File View 123
- 11.5.2 Private File View 123
- % srun -A options 124
- % ./wrapper 124
- % bsub -I options... wrapper 124
- A Examples 125
- Submit the job: 126
- View the job: 126
- 128 Examples 128
- Exit from the shell: 129
- Show the environment: 129
- Display the script: 129
- Run the job: 130
- Show the job allocation: 130
- Show the SLURM job ID: 131
- Exit the pseudo-terminal: 131
- View the interactive jobs: 131
- View the finished jobs: 131
- View the node state: 132
- View the running job: 132
- View the finished job: 133
- Glossary 135
- 136 Glossary 136
- 138 Glossary 138
- 140 Glossary 140
- 142 Index 142
- 144 Index 144
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