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Example 5-12 Submitting a Batch job Script That Uses the srun --overcommit Option
$ bsub -n4 -I ./myscript.sh
Job <81> is submitted to default queue <normal>.
<<Waiting for dispatch ...>>
<<Starting on lsfhost.localdomain>>
n1
n1
n1
n1
n2
n2
n2
n2
Hello world! I'm 0 of 8 on n1
Hello world! I'm 1 of 8 on n1
Hello world! I'm 2 of 8 on n1
Hello world! I'm 3 of 8 on n1
Hello world! I'm 4 of 8 on n2
Hello world! I'm 5 of 8 on n2
Hello world! I'm 6 of 8 on n2
Hello world! I'm 7 of 8 on n2
Example 5-13 shows some of the environment variables that are available in a batch script. The LSB_HOSTS
and LSB_MCPU_HOSTS environment variables are defined in
Platform LSF Reference
. The SLURM_JOBID
and SLURM_NPROCS environment variables are defined in the
SLURM Reference Manual
.
Example 5-13 Environment Variables Available in a Batch Job Script
$ cat ./envscript.sh
#!/bin/sh
name=`hostname`
echo "hostname = $name"
echo "LSB_HOSTS = '$LSB_HOSTS'"
echo "LSB_MCPU_HOSTS = '$LSB_MCPU_HOSTS'"
echo "SLURM_JOBID = $SLURM_JOBID"
echo "SLURM_NPROCS = $SLURM_NPROCS"
$ bsub -n4 -I ./envscript.sh
Job <82> is submitted to default queue <normal>.
<<Waiting for dispatch ...>>
<<Starting on lsfhost.localdomain>>
hostname = n1
LSB_HOSTS = 'n1 n1 n2 n2'
LSB_MCPU_HOSTS = 'n1 2 n2 2'
SLURM_JOBID = 176
SLURM_NPROCS = 4
Running Preexecution Programs
A
preexecution program
is a program that performs needed setup tasks that an application needs. It may
create directories, input files, and so on.
Though LSF-HPC daemons only run on a node with resource manager role, batch jobs can run on any
compute node that satisfies the scheduling and allocation requirements.
Where preexecution commands run depends on the type of job:
• For interactive jobs, preexecution commands run on the node where the sbatchd daemon runs,
typically, the resource manager node.
• For normal batch jobs, preexecution commands run on the first node of the SLURM allocation.
Before starting a preexecution program, LSF-HPC sets the SLURM_JOBID environment variable. To enable
srun to launch pre-execution on the first allocated node and other allocated nodes, your preexecution
Running Preexecution Programs 51
- 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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