HDF5 is a general purpose library and file format for storing scientific data. HDF5 can store two primary objects: datasets and groups. A dataset is essentially a multidimensional array of data elements, and a group is a structure for organizing objects in an HDF5 file. Using these two basic objects, one can create and store almost any kind of scientific data structure, such as images, arrays of vectors, and structured and unstructured grids.
For mpi-dependent codes, use the non-serial HDF5 module.
Availability and Restrictions
Versions
HDF5 is available for serial code on Pitzer and Owens Clusters. The versions currently available at OSC are:
| Version | Owens | Pitzer | Notes |
|---|---|---|---|
| 1.8.17 | X | ||
| 1.8.19 | |||
| 1.10.2 | X | X | |
| 1.10.4 | X | X | |
| 1.10.5 | X | X | |
| 1.12.0 | X* | X* | |
| 1.12.2 | X | X |
You can use module spider hdf5-serial to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.
Access
HDF5 is available to all OSC users. If you have any questions, please contact OSC Help.
Publisher/Vendor/Repository and License Type
The HDF Group, Open source (academic)
Usage
Usage on Owens
Set-up
Initalizing the system for use of the HDF5 library is dependent on the system you are using and the compiler you are using. To load the default serial HDF5 library, run the following command: module load hdf5-serial. To load a particular version, use module load hdf5-serial/version. For example, use module load hdf5-serial/1.10.5 to load HDF5 version 1.10.5. You can use module spider hdf5-serial to view available modules.
Building With HDF5
The HDF5 library provides the following variables for use at build time:
| Variable | Use |
|---|---|
$HDF5_C_INCLUDE |
Use during your compilation step for C programs |
$HDF5_CPP_INCLUDE |
Use during your compilation step for C++ programs (serial version only) |
$HDF5_F90_INCLUDE |
Use during your compilation step for FORTRAN programs |
$HDF5_C_LIBS |
Use during your linking step programs |
$HDF5_F90_LIBS |
Use during your linking step for FORTRAN programs |
For example, to build the code myprog.c or myprog.f90 with the hdf5 library you would use:
icc -c $HDF5_C_INCLUDE myprog.c icc -o myprog myprog.o $HDF5_C_LIBS ifort -c $HDF5_F90_INCLUDE myprog.f90 ifort -o myprog myprog.o $HDF5_F90_LIBS
Batch Usage
When you log into owens.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your job to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info.
Non-interactive Batch Job (Serial Run)
A batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice. Below is the example batch script that executes a program built with the HDF5 library:#PBS -N AppNameJob #PBS -l nodes=1:ppn=28 module load hdf5 cd $PBS_O_WORKDIR cp foo.dat $TMPDIR cd $TMPDIR appname cp foo_out.h5 $PBS_O_WORKDIR
Usage on Pitzer
Set-up
Initalizing the system for use of the HDF5 library is dependent on the system you are using and the compiler you are using. To load the default serial HDF5 library, run the following command: module load hdf5-serial. To load a particular version, use module load hdf5-serial/version. For example, use module load hdf5-serial/1.10.5 to load HDF5 version 1.10.5. You can use module spider hdf5-serial to view available modules.
Building With HDF5
The HDF5 library provides the following variables for use at build time:
| VARIABLE | USE |
|---|---|
$HDF5_C_INCLUDE |
Use during your compilation step for C programs |
$HDF5_CPP_INCLUDE |
Use during your compilation step for C++ programs (serial version only) |
$HDF5_F90_INCLUDE |
Use during your compilation step for FORTRAN programs |
$HDF5_C_LIBS |
Use during your linking step programs |
$HDF5_F90_LIBS |
Use during your linking step for FORTRAN programs |
For example, to build the code myprog.c or myprog.f90 with the hdf5 library you would use:
icc -c $HDF5_C_INCLUDE myprog.c icc -o myprog myprog.o $HDF5_C_LIBS ifort -c $HDF5_F90_INCLUDE myprog.f90 ifort -o myprog myprog.o $HDF5_F90_LIBS
Batch Usage
When you log into owens.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your job to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info.
Non-interactive Batch Job (Serial Run)
A batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice. Below is the example batch script that executes a program built with the HDF5 library:#PBS -N AppNameJob #PBS -l nodes=1:ppn=28 module load hdf5 cd $PBS_O_WORKDIR cp foo.dat $TMPDIR cd $TMPDIR appname cp foo_out.h5 $PBS_O_WORKDIR
