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for the purpose of determining how much memory to pin for RDMA message transfers on
InfiniBand and Myrinet GM. The value determined by HP-MPI can be displayed using the -dd
option. If HP-MPI specifies an incorrect value for physical memory, this environ ment variable
can be used to specify the value explicitly:
% export MPI_PHYSICAL_MEMORY=1048576
The above example specifies that the system has 1GB of physical memory.
8.9.5 MPI_PIN_PERCENTAGE
MPI_PIN_PERCENTAGE communicates the maximum percentage of physical memory (see
MPI_PHYSICAL_MEMORY above) that can be pinned at any time. The defau lt is 20%.
% export MPI_PIN_PERCENTAGE=30
The above example permits the HP-MPI librarytopin(lockinmemory)upto30%of
physical mem ory. The pinned memory is shared between ranks of the host that were started
as part of the same mpirun invocation. Running multiple MPI applications on the same
host can cum ulatively cause more than one application’s MPI_PIN_PERCENTAGE to be
pinned. Increasing MPI_PIN_PERCENTAGE can improve communication performance for
communication intensive applications in which nodes send and receive multiple large messages
at a time, such as is comm on with collective operations. Increasing MPI_PIN_PERCENTAGE
allows more large messages to be progressed in parallel using RDMA transfers, however
pinning too much of physical memory may negatively impact computation performance.
MPI_PIN_PERCENTAGE and MPI_PHYSICAL_MEMORY are ign ored unless InfiniBand
or Myrinet G M is in use.
8.9.6 MPI_PAGE_ALIGN_MEM
MPI_PAGE_ALIGN_MEM causes the HP-MPI library to page align and page pad memory.
% export MPI_PAGE_ALIGN_MEM=1
For more information on when this setting should be used, refer to the “Work-arounds” section
of the HP-MPI V2.1 for XC4000 and XC6000 Clusters R elease Notes.
8.9.7 MPI_MAX_WINDOW
MPI_MAX_WINDOW is used for o ne-sided applications. It specifies the max imum number of
windows a rank can have at the same time. It tells HP-MPI to allocate enough table entries.
The default is 5.
% export MPI_MAX_WINDOW=10
8.9.8 MPI_ELANLOCK
By default, HP-MP
I only provides e xclusive window locks via Elan lock when using the Elan
system interconn
ect. In order to use HP-MPI shared windo w locks, you must turn off Elan lock
and use window loc
ks via shared memory. In this way, both exclusive and shared locks are
from shared mem o
ry. ToturnoffElanlocks:
% export MPI_ELANLOCK=0
8.9.9 MPI_USE_LIBELAN
By default when Elan is in u se, the HP-MPI library uses E lan’s native collective operations
for performing MPI_Bcast and MPI_Barrier operations on MPI_COMM_WORLD sized
communicators. This behavior can be changed by setting MPI_USE_LIBELAN to “false”or
“0”, in which case these operations will be im plemen ted using point-to-point Elan m essag e s.
Using HP-MPI 8-11
- 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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