HDF5

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of data types, and is designed for flexible and efficient I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing applications t o evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.

Installations on NSC systems

Tetralith and Sigma

HDF5 is available via the module system on Tetralith and Sigma in a module named netCDF-HDF5-utils. For more information about available versions, please see the Tetralith and Sigma Software list.

How to run

Load the HDF5 module corresponding to the version you want to use, e.g.,

module load netCDF-HDF5-utils/4.9.2-1.12.2-hpc1-intel-2023a-eb

This will add the HDF5 commands to your search path and set the environment variable HDF5_DIR to point to the top directory.

You can build applications against the HDF5 library. In that case use the include files in ${HDF5_DIR}/include and libraries in ${HDF5_DIR}/lib. Example compiler options:

-I$HDF5_DIR/include -L$HDF5_DIR/lib -Wl,-rpath,$HDF5_DIR/lib