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3 Configuring Your Environment with Modulefiles
Overview of Modules............................................................................................................................31
Supplied Modulefiles.............................................................................................................................32
Modulefiles Automatically Loaded on the System.......................................................................................33
Viewing Available Modulefiles................................................................................................................33
Viewing Loaded Modulefiles...................................................................................................................33
Loading a Modulefile............................................................................................................................33
Loading a Modulefile for the Current Session.......................................................................................34
Automatically Loading a Modulefile at Login.......................................................................................34
Unloading a Modulefile.........................................................................................................................34
Modulefile Conflicts...............................................................................................................................34
Creating a Modulefile...........................................................................................................................35
Viewing Modulefile-Specific Help............................................................................................................35
4 Developing Applications
Application Development Environment Overview.......................................................................................37
Compilers............................................................................................................................................37
MPI Compiler..................................................................................................................................38
Examining Nodes and Partitions Before Running Jobs................................................................................38
Interrupting a Job..................................................................................................................................38
Setting Debugging Options....................................................................................................................39
Developing Serial Applications...............................................................................................................39
Serial Application Build Environment..................................................................................................39
Building Serial Applications..............................................................................................................39
Compiling and Linking Serial Applications.....................................................................................39
Developing Parallel Applications.............................................................................................................40
Parallel Application Build Environment................................................................................................40
Modulefiles................................................................................................................................40
HP-MPI......................................................................................................................................40
OpenMP...................................................................................................................................40
Pthreads....................................................................................................................................41
Quadrics SHMEM......................................................................................................................41
MPI Library................................................................................................................................41
Intel Fortran and C/C++Compilers...............................................................................................41
PGI Fortran and C/C++ Compilers...............................................................................................41
GNU C and C++ Compilers........................................................................................................41
Pathscale Compilers....................................................................................................................41
GNU Parallel Make....................................................................................................................42
MKL Library...............................................................................................................................42
ACML Library.............................................................................................................................42
Other Libraries...........................................................................................................................42
Building Parallel Applications............................................................................................................42
Compiling and Linking Non-MPI Applications.................................................................................42
Compiling and Linking HP-MPI Applications...................................................................................42
Examples of Compiling and Linking HP-MPI Applications.................................................................43
Developing Libraries..............................................................................................................................43
Designing Libraries for the CP4000 Platform........................................................................................43
5 Submitting Jobs
Overview of Job Submission...................................................................................................................45
Submitting a Serial Job Using Standard LSF..............................................................................................46
Submitting a Serial Job Using LSF-HPC.....................................................................................................46
Submitting a Serial Job with the LSF bsub Command............................................................................46
Submitting a Serial Job Through SLURM only.......................................................................................47
Submitting a Non-MPI Parallel Job...........................................................................................................48
Submitting a Parallel Job That Uses the HP-MPI Message Passing Interface....................................................48
Submitting a Batch Job or Job Script........................................................................................................49
4 Table of Contents
- HP XC System Software 1
- User's Guide 1
- Table of Contents 3
- 5 Submitting Jobs 4
- 6 Debugging Applications 5
- 7 Tuning Applications 5
- 8 Using SLURM 5
- 9 Using LSF 5
- 10 Advanced Topics 6
- List of Figures 7
- List of Tables 9
- List of Examples 11
- About This Document 13
- HP XC Information 14
- For More Information 15
- Supplementary Information 15
- Related Information 16
- Related Linux Web Sites 17
- Related MPI Web Sites 17
- Related Compiler Web Sites 17
- Additional Publications 17
- Typographic Conventions 18
- HP Encourages Your Comments 18
- System Architecture 19
- Node Specialization 20
- Storage and I/O 20
- File System 21
- System Interconnect Network 22
- User Environment 23
- Run-Time Environment 24
- Standard LSF 25
- 2 Using the System 27
- Introduction 28
- 30 Using the System 30
- Overview of Modules 31
- Supplied Modulefiles 32
- Viewing Available Modulefiles 33
- Viewing Loaded Modulefiles 33
- Loading a Modulefile 33
- Unloading a Modulefile 34
- Modulefile Conflicts 34
- Creating a Modulefile 35
- 4 Developing Applications 37
- Interrupting a Job 38
- Setting Debugging Options 39
- Modulefiles 40
- Standard 41
- 42 Developing Applications 42
- Developing Libraries 43
- 44 Developing Applications 44
- 46 Submitting Jobs 46
- 48 Submitting Jobs 48
- Compiling applications 49
- HP-MPI User's Guide 49
- 50 Submitting Jobs 50
- Running Preexecution Programs 51
- 52 Submitting Jobs 52
- SSH and TotalView 54
- Setting Up TotalView 54
- Using TotalView with SLURM 54
- Using TotalView with LSF-HPC 55
- Setting TotalView Preferences 55
- Debugging an Application 55
- TotalView process window 56
- Exiting TotalView 57
- 60 Tuning Applications 60
- The srun Roles and Modes 64
- Job Accounting 65
- Fault Tolerance 66
- Security 66
- Overview of LSF-HPC 68
- Using LSF-HPC 69 69
- Job Terminology 70
- Using LSF-HPC 71 71
- Notes on LSF-HPC 72
- Using LSF-HPC 73 73
- Job Startup and Job Control 74
- Preemption 75
- Getting Host Load Information 76
- Submitting Jobs 77
- LSF-SLURM External Scheduler 78
- Using LSF-HPC 79 79
- 80 Using LSF 80
- Examining the Status of a Job 81
- 82 Using LSF 82
- Using LSF-HPC 83 83
- 84 Using LSF 84
- Using LSF-HPC 85 85
- 86 Using LSF 86
- Using LSF-HPC 87 87
- 88 Using LSF 88
- Using LSF-HPC 89 89
- 92 Advanced Topics 92
- 94 Advanced Topics 94
- Example Procedure 1 95
- Example Procedure 2 95
- Local Disks on Compute Nodes 96
- Communication Between Nodes 97
- Appendix A Examples 99
- Submit the job: 100
- View the job: 100
- 102 Examples 102
- Show the environment: 103
- Display the script: 103
- Run the job: 103
- Show the SLURM job ID: 104
- Show the job allocation: 104
- Exit the pseudo-terminal: 105
- View the interactive jobs: 105
- View the finished jobs: 105
- View the node state: 105
- View the running job: 106
- View the finished job: 106
- Glossary 109
- 110 Glossary 110
- 112 Glossary 112
- 116 Index 116
- 118 Index 118
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