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8
Using HP-MPI
This chapter describes how to use HP-MPI in the HP X C environment. The main focus of
this chapter is to help you to quickly get started using HP -MPI on an HP XC syste m. In this
chapter, the basics of getting started are demonstrated. T he semantics o f building and running
a simple MPI program are described for single-host and mu ltiple-host systems. In add ition,
you are shown how to configure your env ironment before running your program. You will a lso
become familiar with the file str ucture in the HP -MPI directory.
This chapter discusses the following topics:
• AnoverviewofHP-MPI(Section8.1)
• HP-MPI Directory Structure (Section 8.2)
• Compiling and running programs (Section 8.3)
• System Interconnect Support (Section 8.4)
• Support for 32–bit builds on the XC4000 system (Section 8 .5 )
• Truncated messages (Section 8.6)
• Exclusive Locks (Section 8.7)
• Options for the mpirun command (Section 8.8)
• HP-MPI Environment Variables (Section 8.9)
• MPICH object com patibility (Section 8.10)
8.1 Overv
iew
HP-MPI is a high-performance implementation of the Message Passing Interface standard.
HP-MPI complies fully with the MPI-1.2 standard and provides full MPI-2 functionality.
HP-MPI provides an application programming interface and software libraries to support
parallel, message-passing applications that are efficient, portable, and flexible. HP MPI is
available as both archive and shared libraries.
Communication between MPI processes within an application is handled through the abstract
device interface of HP-MPI. HP-MPI provid es efficient support of different system interconnect
hardware. You can use only one type of system interconnect at a time on an HP XC system,
even though the library has support for multiple types of system intercon nects.
HP-MPI Version 2.1 is included in this release of HP XC. HP-MPI 2.1 is the fully functional
implementation of the HP Message Passing Interface standard for the HP XC system.
HP-MPI is available a s both archive and s hared libraries. Use of shared libraries is
recommended. In order to use shared libraries, HP-MPI must be installed on all m achines in
the same directory or accessible through NFS mount. HP-MPI strives to be compiler neutral.
HP-MPI 2.1 for HP XC systems was tested with the Intel, Portland, and GNU compilers.
HP-MPI 2.1 for H P XC is sup ported on HP XC4000 and HP XC6000 clusters, and includes
support for the following system interconnects:
• HP XC4000 Clusters — Myrinet, Gigabit Ethernet, InfiniBand
• HP XC6000 Clusters — Quadrics Elan4, Gigabit Ethernet,
For complete details about using HP-MPI, refer to the HP-MPI documentation, which is
included with your HP XC system documentation. For the latest informatio n about using
Using HP-MPI 8-1
- 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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