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Example 2-3: Submitting a Non-MPI Parallel Job to Run One Task per Node
$ bsub -n4 -ext "SLURM[nodes=4]" -I srun hostname
Job <22> is submitted to default queue <normal>
<<Waiting for dispatch ...>>
<<Starting on lsfhost.localdomain>>
n1
n2
n3
n4
2.3.5.3 Submitting an M PI Job
Submitting MPI jobs is discussed in detail in S ection 7.4.5. T he bsub command format t o
submit a job to H P-MPI by m eans of mpirun command is:
bsub -n num-procs [bsub-options] mpirun [mpirun-options] [-srun
[srun-options]]mpi-jobname [job-options]
The -srun command is required by the mpirun command to run jobs in the LSF partition.
The -n nu m-p rocs parameter specifies the number o f processo rs the job requests. -n num-procs
is required for parallel jobs. A ny SLURM srun options that are included are jo b specific, not
allocation-specific.
Using SLURM Options in MPI Jobs with the LSF External Scheduler
An important option that can be included in subm itting HP-MPI jobs is LSF’s external scheduler
option. The L S F external scheduler provides addition a l capabilities at the job lev el and queue
level by allowing the inclusion of sev eral SLURM options in the LSF command line. For
example, it can be used to submit a job to run one task per node, or to submit a job to run
on specific nodes. This option is discussed in detail in Section 7.4.2. An example of its use
is provided in this secti on.
Consider an HP XC configuratio n where lsfhost.localdomain is the LSF execution host
and nodes n[1-10] are compute no des in the LSF partition. A ll nod es contain t wo processors,
providing 20 processors for use by LSF jobs.
Example2-4:RunninganMPIJobwithLSF
$ bsub -n4 -I mpirun -srun ./hello_world
Job <24> is submitted to default queue <normal>.
<<Waiting for dispatch ...>>
<<Starting on lsfhost.localdomain>>
Hello world!
Hello world! I’m 1 of 4 on host1
Hello world! I’m 3 of 4 on host2
Hello world! I’m 0 of 4 on host1
Hello world! I’m 2 of 4 on host2
Example 2-5: Running an MPI Job with LSF Using the External Scheduler Option
$ bsub -n4 -ext "SLURM [nodes=4]" -I mpirun -srun ./hello_world
Job <27> is submitted to default queue <normal>.
<<Waiting for dispatch ...>>
<<Starting on lsfhost.localdomain>>
Hello world!
Hello world! I’m 1 of 4 on host1
2-10 Using the System
- HP XC System Software 1
- Contents 3
- 3 Developing Applications 4
- 4 Debugging Applications 5
- 5 Tuning Applications 5
- 6UsingSLURM 5
- 8UsingHP-MPI 6
- 7 Using LSF 6
- 9UsingHPMLIB 7
- 10 Advanced Topics 8
- AExamples 8
- About This Document 11
- HP XC Inform ation 12
- For M ore Information 13
- Supplementary Information 13
- Manpages 14
- Related Information 15
- Typographical Conventions 16
- HP Encourages Your Comments 17
- 1.1 System Architecture 19
- 1.1.3 Storage and I/O 20
- 1.1.4 File System 20
- 1.2 User Environment 22
- 1.3.1 Parallel Applications 23
- 1.3.2 Serial Applications 23
- 1.4 Run-Time E nvironment 24
- 1.4.4 HP-MPI 25
- Using the System 27
- 2.2.1 Notes on Modulefiles 28
- 2.2.2 Supplied Modulefiles 29
- 2.2.6 Loading a Modulefile 30
- 2.2.7 Unloading a M odulefile 31
- 2.2.8 Modulefile Conflicts 31
- 2.2.9 Creating a Mod u lefile 32
- 2.3.1 Introduction 33
- 2.3.5 Launching Jobs 34
- $ man sinfo 39
- $ man -k keyword 39
- Using the System 2-13 39
- Developing Applications 41
- 3.2 Using Compilers 42
- 3.4 Interrupting a Job 43
- 3-4 Developing Applications 44
- Developing Applications 3-5 45
- 3-6 Developing Applications 46
- Developing Applications 3-7 47
- $ module load mpi 48
- $ mpicc -o mycode hello.c 48
- $ mpif90 -o mycode hello.f 48
- 3-8 Developing Applications 48
- 3.8 Developing Libraries 49
- 3.9 Advanced To pics 50
- 3-14 Deve loping Applications 54
- Developing Applications 3-15 55
- Debugging Applications 57
- 4-2 D ebugging Applications 58
- $ totalview 60
- 4-4 D ebugging Applications 60
- Debugging Applications 4-5 61
- 4-6 D ebugging Applications 62
- -verbosity %V %F" 63
- Debugging Applications 4-7 63
- 4-8 D ebugging Applications 64
- Etnus TotalView Version# 65
- Debugging Applications 4-9 65
- $ mpirun -srun -n2 Psimple 66
- 4-10 Debugging Applications 66
- $ squeue 67
- $ scancel --user username 67
- Debugging Applications 4-11 67
- Tuning Applications 69
- Using SLURM 71
- $ srun -N 16 -b myscript.sh 73
- $ srun -A -N 4 myscript.sh 73
- $ srun -a 6543 -j 73
- Using SLURM 6-3 73
- 6.4.2 srun Signal Handling 74
- 6.4.3 srun Run-Mode Options 74
- Using SLURM 6-5 75
- 6-6 Using SLURM 76
- 6.4.5 srun Control Options 77
- 6.4.6 srun I/O Options 78
- Using SLURM 6-9 79
- 6.4.7 srun Constraint Options 80
- Using SLURM 6-11 81
- 6.4.9 Using srun with HP-MPI 82
- 6.4.10 Using srun with LSF 82
- 6.8 Job Accounting 84
- 6.9 Fault Tolerance 84
- 6.10 Security 84
- Using LSF 85
- 7.1.2 Topology Support 86
- 7.1.3 Notes on LSF-HPC 87
- SLURM_JOBID=53 89
- SLURM_NPROCS=4 89
- 7-6 Using LSF 90
- 7.3.1 Getting Status of LSF 91
- $ bhosts 92
- 7-8 Using LSF 92
- 7.4 Submitting Jobs 93
- 7.4.3 Submitting a Serial Job 97
- Using LSF 7-17 101
- 7-18 Using LSF 102
- Using HP-MPI 111
- 8.3.3 Using srun with HP-MPI 114
- 8.3.4 Using LSF and HP-MPI 116
- 8.3.5 MPI Versioning 117
- 8.6 Truncated Messages 118
- 8.5 32-Bit B uilds on XC4000 118
- Using HP-MPI 8-9 119
- 8.9 Environment Variables 120
- 8.9.5 MPI_PIN_PERCENTAGE 121
- 8.9.6 MPI_PAGE_ALIGN_MEM 121
- 8.9.7 MPI_MAX_WINDOW 121
- 8.9.8 MPI_ELANLOCK 121
- 8.9.9 MPI_USE_LIBELAN 121
- 8.9.10 MPI_USE_LIBELAN_SUB 122
- Work-arounds 124
- Using HP MLIB 125
- 9.1.2 MLIB and Module Files 126
- 9.2.1 Platform Sup port 126
- 9.2.2 Library Support 126
- 9.2.3 MPI Parallelism 126
- 9.2.4 Modulefiles and MLIB 127
- 9.2.6 Compiling and Linking 127
- 9.2.7 Licensing 128
- 9.2.8 MLIB Man pages 128
- 9.3.1 Platform Sup port 128
- 9.3.2 Library Support 128
- 9.3.3 MPI Parallelism 129
- 9.3.4 Modulefiles and MLIB 129
- 9.3.5 Compiling and Linking 129
- 9.3.6 Licensing 130
- 9.3.7 MLIB Man pages 130
- Advanced Topics 131
- Examples 135
- $ lshosts 140
- Show the environment: 142
- Run the job: 142
- View the running job: 142
- View the finished job: 142
- Examples A-9 143
- Glossary 145
- Glossary-2 146
- Glossary-3 147
- Glossary-4 148
- Glossary-5 149
- Glossary-6 150
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