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request. LSF-HPC always tries to pack m ultiple serial jobs on the same node, with one CPU per
job. Parallel jobs and serial jobs cannot coexist on the same node.
After the LSF-HPC scheduler allocates the SLURM resources for a job, the SLU RM allocation
information is recorded with the job. You can view this information with the bjobs and
bhist commands.
When LSF-HPC starts a job, it sets the SLURM_JOBID and SLURM_NPROCS environment
variables in the job environment. SLURM_JOBID associates the LSF-HPC job with SLURM’s
allocated resources. The SLURM_NPROCS environm ent variable is set to the originally
requested number of processors. LSF-HPC dispatches the job from the LSF-HPC execution
host, which is the same node on which LSF-HPC daemons run. The LSF-HPC JOB_STARTER
script, which is configured for all queues, uses the srun command to launch a user job on the
first node in the allocation . You r job can contain additional srun or mpirun commands to
launch tasks to all no d es in the allocation.
While a job is running, all LSF-HPC-supported resource limits are e n forced, including co re
limit, cputime limit, data limit, file size limit, memory lim i t and stack limit. W hen you kill a
job, LSF-HPC uses the SLURM scancel command to propagate the signal to the entire job.
After a job finishes, LSF-HPC releases all allocated resources.
A detailed description, along with an example and illustration, of how LSF-HPC and SLURM
cooperate to launch and manage jobs is provided in Section 7.1.4. It is highly recom mended
that you review this information.
1.4.4 HP-MPI
HP-MPI is a high-perform a nce implementatio n of the Message Passing
Interface standard
and is included with the HP X C system. HP-MP I uses SLURM to launch jo
bs on an HP XC
system — however, it manages the global M PI exchange so that all pro
cesses can communicate
with each other.
HP-MPIcompliesfullywiththeMPI-1.2standard. HP-MPIalsocomplieswiththeMPI-2
standard, with some restrictions. HP-MPI provides an application programming interface and
software libraries to support parallel, message-passing applications that are efficient, portable,
and f lexible. HP-MPI version 2.1 is included in this release of HP XC.
HP-MPI 2.1 for HP XC is supported on XC4000 a nd XC6000 clusters, and includes support for
the following system interconnects:
• XC4000 Clusters — Myrinet, Gigabit Eth e rnet, TCP/IP, In fi niBand
• XC6000 Clusters — Q uadrics Elan4, Gigabit Ethernet, TCP/IP
1.5 Components, Tools, Compilers, Libraries, and Debuggers
This section provides a brief overview of the some of the common tools, compilers, librar ies,
and debuggers supported for use on HP XC.
An HP XC system is integrated with several open source software components. HP XC
incorporates the Linux operating system, and its standard commands and tools, and does not
diminish the Lin ux ABI in any way. In addition, H P XC incorporates LSF and SLURM to
launch and manag e jobs, and includes HP-MPI for high p erformance, parallel, message-passing
applications, and HP MLIB math library for intensive com putatio ns.
Most standard open source compilers an d tools can be used on an HP XC system, however
they must be purchased separately. Several open source and commercially available software
packages have been tested with the HP XC Software. The f ollowing list shows some of th e
software packages that have been tested for use with HP XC. This list provides an example
of what is available on HP XC and is not int ended as a complet e list. No te that some of the
packages listed are actually included as part of the HPC Lin ux distribution and as such are
Overview of the User Environment 1-7
- 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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