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The basic synopsis of the bsub command is:
bsub [ bsub_options] jobname [job_options]
The HP XC system has several features that make it o ptimal for running parallel applications,
particularly (but not exclusively) MPI applications. You can use the bsub command’s -n to
request more than one CPU for a job. This option, coupled with the external SLU R M scheduler,
discussedinSection7.4.2,givesyoumuchflexibility in selecting resources and shaping how
the job is executed on those resources.
LSF-HPC, like standard LSF, reserves the requested num ber of nodes and executes one instance
of the job on the first reserv ed n ode, w hen you request multiple no des. Use the srun command
or the mpirun comm and with the -srun option i n your jobs to launch p arallel applications.
The -srun can be set implicitly for the mpirun command; see Section 7.4.5 for more
information on using the mpirun -srun command.
Most parallel
applications rely on rsh or ssh to "launch" re mote tasks. The ssh utility is
installedont
he HP XC system by default. If you con fig ured the ssh keys to allow unprompted
access to othe
r nodes in the HP XC system , the parallel applications can u se ssh.
7.4.1 Summary of the LSF bsub Command Format
This section provides a summary of the fo rm at LSF bsub command on the HP XC system. The
bsub command can have the following formats:
bsub
When you invoke th e bsub command without any arguments, you are prompted for a
command from standard input.
bsub [bsub-options][srun ] jo bname [job-arguments]
This is the bsub command format t o submit a serial job. The srun command is required
to run parallel j obs on the allocated compute node. Refer to Section 7.4.3.
bsub -n num-procs [bsub-options] jobname [job-argu ments ]
This is the standard bsub comm and format to submit a par allel job to LSF execution host.
The jobname parameter can be name of an executable or a batch script. If jobname
is executable, job is launched on LSF execution host node. If jobname is batch script
(containing srun commands), job is launched on LSF node allocation (com pute nodes).
LSF n ode allocation is created by -n num-procs parameter, which specifies the number
of processors the job requests. Refer to Section 7.4.4 for information about running jobs.
Refer to Section 7.4.6 for information about running scripts.
bsub -n num-procs [bsub-op tions ] srun [srun-options] jo bname [job-arguments]
This is the bsub command format to subm it a parallel job to LSF node allocation (compute
nodes). LSF node allocation is created by -n num-procs parameter, which specifies the
number of processors the job requests. srun comm and is required to run jobs on LSF n ode
allocation. Refer to Section 7.4.4.
bsub -n num-procs [bsub-options] mpirun [mpirun-options] -srun
[srun-options] mpi-jobname [job-options]
This is the bsub command format to submit an HP-MPI job. The -srun option is
required. Refer to Section 7.4.5.
bsub -n num-procs -ext "SLURM[slurm-arguments]" [bsub-options]
[srun [srun-options]] jobname [job-options]
This is the bsub command format to subm it a parallel job to LSF node allocation (compute
nodes) using the external scheduler option. The external scheduler option provides
7-10 Using LSF
- 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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