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. For more information about available versions, please see the Tetralith and Sigma Software list.

How to run

If all you want to do is run the HDF5 utilities:

h52gif   h5copy   h5diff  h5format_convert  h5jam  h5mkgrp  h5perf         h5redeploy  h5repart  h5unjam
h5clear  h5debug  h5dump  h5import          h5ls   h5pcc    h5perf_serial  h5repack    h5stat    h5watch

Simply directly load the utils module:

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

If you are compiling programs that require hdf5 libraries, first load an appropriate toolchain (e.g. buildenv-intel/2023a-eb), and then load the corresponding netCDF-HDF5 module (e.g. netCDF-HDF5/4.9.2-1.12.2-hpc1)

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

Loading the netCDF-HDF5 module sets an environment variable ${HDF5_DIR}. ${HDF5_DIR} points to the base folder containing the HDF5 installation. Sub-folders from ${HDF5_DIR}:

bin
include
lib
share

You can build applications against the HDF5 libraries using the include files in ${HDF5_DIR}/include and pre-built libraries in ${HDF5_DIR}/lib. e.g.

icc -I $HDF5_DIR/include -L $HDF5_DIR/lib -lhdf5