Hp XC System 2.x Software Manuel d'utilisateur Page 45
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- Table des matières
- MARQUE LIVRES
Noté. / 5. Basé sur avis des utilisateurs
• Launching applications w ith the srun command (Section 6.4)
• Advanced topics related to developing parallel applications (Section 3.9)
• Debugging parallel applications (Section 4.2)
3.7.1 Parallel A pplication Build Environment
This section discusses the parallel applicatio n build environm ent on an HP XC system.
The HP XC parallel application environment allows parallel application processes to be started
and stopped together on a large number of applicati on processors , alon g with the I/O and
process control structures to manage these kinds of applications.
HP XC supports the HP-MPI distrib uted memory programming model for bu ild ing and runn ing
parallel applications. In addition to using HP-MPI f or parallel application development, H P XC
supports the use of OpenMP and Pthreads. OpenMP and Pthreads can be used in conjunction
with HP-MPI or separatel y. The section discusses these development tools as they relate to
the HP XC system.
3.7.1.1 Modulefiles
The basics of yo ur working environ men t are set up autom atically by your system administrator
during the installation of HP XC. However, yo ur application developmen t environment can b e
modified by means of modulefiles, as described in Section 2.2.
There are modulef iles available that you can load yourself to further tailor your environment
to your specific application develo pm e nt requirements. For example, the TotalView module
is available for debugging applications. Section 2.2 provides instructions on how to list what
modulefiles are availab le for yo u to load, and h ow load a modulefile.
If you encounter problems accessing tools or comm ands (and associated m anpages), check to
ensure that required modules are loaded on your system. If necessary, load required m odules
yourself, as described in Section 2.2. Otherwise, contact your administrator.
3.7.1.2 HP-MPI
HP XC supports the HP-MPI distrib uted memory programming model for bu ild ing and runn ing
parallel applications. In this model, all data is private to each process. All interprocessor
communication within a parallel application is performed thr oug h calls to the HP-MPI message
passing library. Even t hou gh support for applications that use a shared-memory programming
model is not available at this time, individual processors within an application node can be
used in the same application as separate HP-MPI tasks. Applications that are MPI-based, and
currently run on Linux (or Linux compatible) systems, can be easily migrated to an HP XC
cluster. For information about using HP-MPI in the H P XC env iro nm ent, refer to Chapter 8.
3.7.1.3 OpenMP
The OpenMP specification is a set of compiler directives that can be used to specify
shared-memory parallelism in Fortran and C/C++ programs. Both Intel and Portland Group
Fortran and C/C++ compilers support OpenMP.
Although OpenMP is designed fo r use on shared-m em ory architectures, OpenMP can be used
on an HP XC system within a node.
OpenMP can be used alone, o r in conjunction w ith HP-MPI. For inform ation about compiling
programs using O pen M P, refer to OpenMP documentation.
3.7.1.4 Pthreads
POSIX Threads (Pthreads) is a standard library that programmers can use to develop portable
threaded applications. Pthreads can be used in conjunction w ith HP-MPI on the HP XC system.
Developing Applications 3-5
- 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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