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8.2
HP-MPI Directory Str
ucture .........................................................
8-2
8.3
Compiling and Runni
ng Applications ...............................................
8-2
8.3.1
Setting Environmen
t Variables .................................................
8-2
8.3.2
Building and Runnin
g an Example Application ..............................
8-2
8.3.2.1
Example Applicati
on hello_world ...................................
8-3
8.3.2.2
Building and Runni
ng hello_world ..................................
8-3
8.3.3
Using srun with HP-
MPI ......................................................
8-4
8.3.3.1
Launching MPI Jobs
.......................................................
8-4
8.3.3.2
Creating Subshel
ls and Launching Jobsteps ..............................
8-5
8.3.3.3
System Interconn
ect Selection ............................................
8-5
8.3.4
UsingLSFandHP-M
PI .........................................................
8-6
8.3.5
MPI Versioning .................................................................. 8-7
8.4
System Interconn
ect Support ........................................................
8-7
8.4.1
HP-MPI Performance on HP XC w ith Multiple S ystem Interconnects ..... 8-7
8.4.2
Global Environmen t Variable Settings on the mpirun Command Line ... 8-8
8.5
32-Bit Builds on XC4000 ............................................................ 8-8
8.6
Truncated Messages .................................................................. 8-8
8.7
Allowing Windows to Use Exclusive Locks ....................................... 8-8
8.8
The mpirun Command Options .................................................... 8-9
8.9
Environment Variables ............................................................... 8-10
8.9.1
MPIRUN_OPTIONS ............................................................ 8-10
8.9.2
MPIRUN_SYSTEM_OPTIONS ............................................... 8-10
8.9.3
MPI_IC_ORDE
R ................................................................
8-10
8.9.4
MPI_PHYSICAL_MEMORY .................................................. 8-10
8.9.5
MPI_PIN_PERCENTAGE ..................................................... 8-11
8.9.6
MPI_PAGE_A
LIGN_MEM ....................................................
8-11
8.9.7
MPI_MAX_WINDOW ......................................................... 8-11
8.9.8
MPI_ELANLOCK .............................................................. 8-11
8.9.9
MPI_USE_
LIBELAN ...........................................................
8-11
8.9.10
MPI_USE_LIBELAN_SUB .................................................... 8-12
8.10
MPICH Object Compatibility ........................................................ 8-12
8.11
HP-MPI Documentation and Manpages ............................................ 8-13
8.12
Additional Information, Known Problems, and Work-arounds ................... 8-14
9UsingHPMLIB
9.1
Overview .............................................................................. 9-1
9.1.1
Intel Compiler Notes ............................................................ 9-1
9.1.2
MLIB and Module Files ......................................................... 9-2
9.2
HP MLIB for the HP XC6000 Platform ............................................ 9-2
9.2.1
Platform Support ................................................................. 9-2
9.2.2
Library Support .................................................................. 9-2
9.2.3
MPI Parallelism .................................................................. 9-2
9.2.4
Modulefiles and MLIB .......................................................... 9-3
9.2.5
Using Intel Compilers with HP MLIB ......................................... 9-3
9.2.6
Compiling and Linking .......................................................... 9-3
9.2.6.1
Linking VECLIB ........................................................... 9-3
9.2.6.2
Linking LAPACK .......................................................... 9-3
9.2.6.3
Linking ScaLAPACK ...................................................... 9-3
9.2.6.4
Linking SuperLU_DIST ................................................... 9-4
9.2.7
Licensing ......................................................................... 9-4
9.2.8
MLIB Manpages ................................................................. 9-4
9.3
HP MLIB for the HP XC4000 Platform ............................................ 9-4
C
ontents vii
- 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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