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% export MPI_USE_LIBELAN=0
8.9.10 MPI_USE_LIBELAN_SUB
The use of Elan’s native collective op eration s may be extended to include communicators which
are sma ller than MPI_COMM_WORLD by setting the MPI_USE_LIBELAN_SUB environment
variable to “TRUE”. By default, t his functionality is d isabl ed due to the fact th at libelan
memory resources are consumed and may eventually cause run-time failures when too many
sub-communicators are created. When set to TRUE, the num ber of sub-com m unicators that can
be simultan e ously created is limited to 10. This limit can be changed to any desirable value by
setting the var iab le to a posi tive integer larger than 0.
% export MPI_USE_LIBELAN_USE=5
8.10 MPICH Object Compatibility
The MPI standard sp ecifies the function prototypes for the M PI functions, but does not specify
the types of the MPI opaque objects like communicators or the values of the MPI constants.
Hence an o bject file compiled using one vendor ’s MPI will generally not function correctly if
linked against another vendor’s MPI library.
There are some cases where such compatibility would be desirable. For instance a third-party
tool such as Vam pir might only be available using the MPICH interface.
To allow such compatibility, H P-MPI now in cludes a layer of MPICH w rappers which provides
an interface identical to MPICH 1.2.5, and translates th ese calls into the c or resp onding H P- M P I
interface. This MPICH compatibility interface is only provided for functions defined in MPICH
1.2.5 and cannot be used by an application which calls fu nctions outside the scope of MPICH
1.2.5.
HP-MPI can be used in MPICH mode by co mp iling using mpicc.mpich and running with
mpirun.mpich. The com piler script mpicc.mpich uses an include file which d efines the
interfaces the same as MPICH 1.2.5, and at link time it links against libmpich.so which is
the set of wrappers defining MPICH 1.2.5 compatible entry points for the MPI functions. The
mpirun.mpich takes the same arguments as the trad itional HP-MPI mpirun command, but
sets LD_LIBRARY_PATH so that libmpich.so is found.
An example of using a program with Vampir:
% $MPI_ROOT/bin/mpicc.mpich -o prog.x $MPI_ROOT/help
/communicator.c \ -L/path/to/vampir/lib -lVT -lpthread -lm
% $MPI_ROOT/bin/mpirun.mpich -np 2 ./prog.x
Here, the program communicator.c is being compiled with M PICH compatible interfaces
and is being linked against Vampir’s libVT first from the co mm and line option, followed
by HP-MPI’s libmpich.so then libmpi.so whichareaddedbythempicc.mpich
compiler wr a pper script. Thus libVT sees only the MPICH compatible interface to HP-MPI.
In general, object files built with HP-MPI’s MPICH mode can be used in an MPICH application,
and conversely object files built under MPICH can b e linked into an HP-MPI application using
MPICH mode. How ever using MPICH compatibility mode to produce a sing le executable to
run under both MPICH an d HP-MPI will be more problematic and is not advised.
communicator.c could be compiled under HP-MPI MPICH compatibility mode as:
% export MPI_ROOT=/opt/hpmpi%
$MPI_ROOT/bin/mpicc.mpich -o prog.x $MPI_ROOT
/help/communicator.c
8-12 Using HP-MPI
- 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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