h5utils is a set of utilities for visualization and conversion of scientific data in the portable HDF5 format.

User instructions

The h5utils suite is available via the modules system. To add it to your environment run:

$ module load h5utils/1.13

Note that an hdf5 module must also be loaded.

The h5utils suite provides programs to convert data in the HDF5 format. See the h5utils wiki for more details. Not all programs are installed, as we don’t use (e.g.) Vis5d.


MIT License except h5tov5d (not installed) which is under GNU General Public License.

Admin notes

I didn’t install additional (and optional) prerequisites such as Vis5d because these weren’t needed and I left out the octave plug-in as that would have been installed to the NFS server directly (can octave plug-ins not go in arbitrary locations?). Users needing some of the functionality offered by Vis5d should be directed to mayavi2 instead. I compiled it for intel and gcc as it could be useful during development work with both compiler families and the convenience is nice. The rest was straightforward:

wget https://github.com/stevengj/h5utils/releases/download/1.13/h5utils-1.13.tar.gz
tar -xf h5utils-1.13.tar.gz
ml intel/2017.4.196 hdf5/1.8.19
mkdir build-1.13-intel2017-hdf51.8; cd build-1.13-intel2017-hdf51.8
../h5utils-1.13/configure --prefix=/common/debian/9.1/Compiler/intel/2017.4/h5utils/h5utils-1.13 --without-octave CC=icc
make && make install

cd ..
module load gcc/6.3.0
mkdir build-1.13-gcc6.3-hdf51.8; cd build-1.13-gcc6.3-hdf51.8
../h5utils-1.13/configure --prefix=/common/debian/9.1/Compiler/gcc/6.3/h5utils/h5utils-1.13 --without-octave
make && make install