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7
Using LSF
The Load Sharing Facility (LSF) from Platform Computing Corporation is a batch system
resource manager used on the HP XC system. LSF is included with HP XC, and is an integral
part of the HP XC environment. On an HP XC system, a job is s ubm itted to LSF, which
places the job in a queue and allows it to run when the necessary resources become available.
In addition to launching jobs, LSF provides extensive job m anagemen t and information
capabilities. LSF schedules, launches, controls, and tracks jobs that are submitted to it according
to the polic ies established by the HP XC s it e administrator.
This chapter describes the functionality ofLSFinanHPXCsystem,anddiscusseshow
to use some basic LSF commands to submit jobs, manage jobs, and access job information.
The following topics are discussed:
• Introduction to LSF on HP XC (Section 7.1)
• Determining the LSF execution host (Section 7.2)
• Determining available LSF resources (Section 7.3)
• SubmittingjobstoLSF(Section7.4)
• Getting information about LSF jobs (S ection 7.5)
• Working interactively within an LSF-HPC allocation (Section 7.6)
• LSF Equivalents of SLURM options (Section 7.7)
For full infor m a tio n about L SF, refer t o the stan dar d LSF docu m en tati on set, which is describ ed
in the Related Information section of this manual. LSF m anpages are also available online on
the HP XC system.
7.1 Introduction to LSF in the HP XC Environment
This section introd uces you to LSF in the HP XC environment. It provides an overview of how
LSF works, and discusses some of the features and differences of standard LSF compared to
LSFonanHPXCsystem.Thissectionalsocontains an important discussion of how LSF and
SLURM wo rk together to prov ide the HP XC job manageme nt environment. A description of
SLURM is provided in C hapter 6.
7.1.1 Overview of LSF
LSF is a batch system resource manager. In the HP XC environment, LSF manages just one
resource — the total number of HP XC processors designated for batch processing. The HP
XC system is based on dedicating processors to jobs, and LS F is implemented to use these
processors in the most efficient manner.
As jobs are submitted to LSF, LSF places the jobs in queues and determines an overall priority
for launching the jobs. W hen the required number of HP XC processors become available to
launch the next job, LSF reserves t hem and launch es t he job on these processors. When a job is
completed, LSF returns job output, job information, and any errors.
A standard LSF installation on an HP XC system would consist of LSF daemons running
on every node and providing activity and resource information for each node. LSF-HPC for
SLURM on an HP XC system consists of one node running LSF-HPC d aemo ns, and these
daemons commu nicate with SLURM for resou rce information about the other nodes. LSF-HPC
consolidates this resource information i nto one "virtual" n ode. Thus LSF-HPC integrated with
Using LSF 7-1
- 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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