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of shared objects. If you have multiple com pilers (perhaps with incompatible shared objects)
installed, it is probably wise to set MPI_CC ( and others) explicitly to the c ommands made
available by the compiler’s modulefile.
The c ontents of the modulefiles in the modulefiles_hptc RPM use th e vendor-intended
location of the installed software. In many cases, this is under the /opt directory, but in a few
cases (for exam ple, the PGI compilers and TotalView) this is under the /usr directory.
If you install a software package other than the intended place, you must create or edit an
appropriate modulefile un der the /opt/modules/modulefiles directory.
For the packages that install by default into the /usr directory (currently the PGI compilers and
TotalView), their correspo nding modulefiles w ill try their vendor-intended location under the
/usr directory. If they do not find that directory, the packages will also search under the /opt
directory. Therefore, no changes to the modulefiles are needed if you want to install third-party
software consistently as the vendor intended or consistently under the /opt directory,
If the package is the stable product intended to be used by the site, editing an existing modulefile
is appropriate. While each modulefile has its unique characteristics, they all set some v ariables
describing th e top-level directory, and editing to adjust the string should be sufficient. You may
need to repeat the adjustment if you update the modulefiles_hptc RPM or otherwise
rebuild your system .
If the package is a variant, for example, a beta version of a compiler, first copy the default
modulefile to a well-named copy, then edit the copy. You need root access to modify the
modulefiles, which is generally needed to install packages in either the /opt or /usr
directories.
If a user downloads a package into a private directory, the user can create a private modulefiles
directory. The user can then copy the corresponding defau lt modu lefile from under the
/opt/modules/modulefiles directory into a priv ate modulefiles dir ector y, edit the file,
and then register the directory w ith the module use command.
2.2.2 Supplied Modulefiles
The HP XC system p rov ides the Modules Package (not to be confused with Linux kernel
modules) to configure and modify the user environment. The Modules Package enables
dynamic modification of a user’s environment by means of modulefiles.
A modulefile contains inform a tion that alters or sets shell environm ent variables, such as PATH
and MANPATH. M odulefiles provide a convenient means for users to tailor their working
environment. Modulefiles can be loaded automatically when the user logs in to t he system or
any time a user needs to alter the environment.
The HP XC System S oftware provides a number of modulefiles. In addition, users can also
create and load their o wn modulefiles to modify their environment further.
The HP XC system supplies the modulefiles listed in Table 2-1.
Table 2-1: Supplied Modulefiles
Modulefile Sets the HP XC User Enviro nment:
icc/8.0
To use Intel C /C++ Version 8.0 compilers.
icc/8.1
To use Intel C /C++ Version 8.1 compilers.
ifort/8.0
To use Intel Fortran Version 8.0 compilers.
ifort/8.1
To use Intel Fortran Version 8.1 compilers.
intel/7.1
For Intel Version 7.1 compilers.
intel/8.0
For Intel Version 8.0 compilers.
Using the System 2-3
- 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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