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9.3.3 MPI Parallelism
Internal parallelism in ScaLAPACK and SuperLU_DIST is implemented using MPI — a
portable, scalable programming model that gives distributed-memory parallel programmers a
simple and flexible interface for developing parallel applications.
9.3.4 Modulefiles and MLIB
When building or running an application built against MLIB, it is crucial th at the environment is
consistent.
Modulefiles can make it easier to access a package. Therefore if modulefiles are used, it is
necessary to use a consistent set of modulefiles.
In particular, modulefiles can be used to select a compiler, both making its comm and available
in $PATH as well as making its shared objects available in $LD_LIBRARY_PATH.
MLIB has a modulefile corresponding to each supported compiler, making its shared objects
available in $LD_LIBRARY_PATH. If m odulefiles are used to facilitate the user environment,
failure to use compan ion modulefiles will result in build and/or run-time errors.
If HP-MPI is used as well, it is important to make sure the mpi** comp iler scripts use the
intended co mp iler. Do this by set tin g the appropriate environment variables, such as, MPI_CC
and MPI_F90. Failure to do so may cause the compiler scripts to discover a compiler that is
not the intended compiler, and th us introduce an unintended inconsistency. It is importan t to
note that the MLIB modulefiles do not set any MPI environmen t variables.
For more information, refer to the MLIB User’s Guide.
9.3.5 Compiling and Linking
This section outlines compiling and linking information fo r HP XC ML I B libraries.
9.3.5.1 Linking VECLIB
For programs that link VECLIB, you can specify the entire path of the library file on the
compiler command line. Yo u can use the following comm a nds to link VECLIB:
$ pgf90 [options] file ...
/opt/mlib/pgi_5.1/hpmpi_2.1/lib/64/libveclib.a -mp
$ pgcc [options] file ...
/opt/mlib/pgi_5.1/hpmpi_2.1/lib/64/libveclib.a -mp -lpgf90
-lpgf90_rpml -lpgf902 -lpgf90rtl -lpgftnrtl
9.3.5.2 Linking LAPACK
For programs that l ink LAPACK , you can specify the entire path of the library f ile on the
compiler command line. You can use the following commands to l ink LAPACK:
$ pgf90 [options] file ...
/opt/mlib/pgi_5.1/hpmpi_2.1/lib/64/liblapack.a -mp
$ pgcc [options] file ...
/opt/mlib/pgi_5.1/hpmpi_2.1/lib/64/liblapack.a -mp -lpgf90
-lpgf90_rpml -lpgf902 -lpgf90rtl -lpgftnrtl
9.3.5.3 Linking ScaLAPACK
For programs that link ScaLAPA C K, you can specify the entire path of the library file on t he
compiler command line. You can use the following commands to link ScaLAPACK:
$ mpi90 [options] file ...
/opt/mlib/pgi_5.1/hpmpi_2.1/lib/64/libscalapack.a -mp
Using HP MLIB 9-5
- 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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