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4. LSF-HPC prepares the user environment for the job on the LSF-HPC execution host
node and dispatches the job with the job_starter.sh script. This user environment
includes standard LSF environment variables and two SLURM-specific environment
variables: SLURM_JOBID and SLURM_NPROCS.
SLURM_JOBID is the SLURM job ID of the job. Note that this is no t the same as the
LSF jobID.
SLURM_NPROCS is the number of processors allocated.
These environment variables are intended for use by the user’s job, whether it is exp licitly
(user scripts may use these variables as necessary) or implicitly (any srun commands in
the user’s job can use these variables to d eterm ine its allocation of resources).
The value for SLURM_NPROCS is 4 and the SLURM_JOBID is 53 in t his example.
5. The user job myscript begins execution on com pu te node n1.
Thefirstlineinmyscript is the hostname command. It executes l ocally and returns
the name of node, n1.
6. The second line in the myscript script is the srun hostname command. The
srun command in myscript inherits SLURM_JOBID and SLURM_NPROCS from
the environment and executes the hostname command on each compute node in the
allocation.
7. The output of the hostname tasks (n1, n2, n3,andn4). is aggregated back to the srun
launch command (shown as dashed lines in Figure 7-1), and is ultimately returned to the
srun commandinthejobstarterscript, where it is collected by LSF-HPC.
Thelastlineinmyscript is the mpirun -srun ./hellompi command. The srun
command inside the mpirun command in myscript inherits the SLURM_JOBID and
SLURM_NPROCS environment variables from the environment and executes hellompi on
each compute node in the allocation.
The output of the hellompi tasks is aggregated back to the srun launch command where it
is collected by LSF-HPC.
The command executes on the allocated compute nodes n1, n2, n3,andn4.
When the job finishes, LSF-HPC cancels the SLURM allocation, which frees the compute
nodes for use by another job.
7.1.5 Differences Between LSF on HP XC and Stan dard LSF
LSF for the H P XC environment supports all the standard features and functions th at standard
LSF supports, except for those items described in this s ection, in S ection 7.1.6, and in the HP
XC release notes for LSF.
• The external scheduler option fo r HP XC provides additional capabilities at the job level and
queue level by allowing the inclusion of several S LURM opt ions in the LSF command lin e.
• LSF does not collect maxswap, ndisks, r15s, r1m, r15m, ut, pg, io, tmp, swp and
mem load indices from each application node. lshosts and lsload commands will
display "-" for all of these items.
• LSF-enforced job-level r un-time limits are not supported.
• Except run-time (wall clock ) and total number of CPUs, LSF cannot report any other job
accounting information.
• LSF does not support parallel or SLURM-based interactive j obs in PT Y mode (bsub -Is
and bsub -Ip).
• LSF does not support user-account mapping and system-account mapping.
7-6 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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