Compressing field output files

When writing out field output files, sometimes called plot files or plt files, it is possible to output the files with HDF5 and compress these with ZFP. To enable this capability, AMR-Wind must be compiled with AMR_WIND_ENABLE_HDF5 and AMR_WIND_ENABLE_HDF5_ZFP. If using a spack installation of AMR-Wind, simply add +hdf5 to the spec to enable these compression features. The input file documentation documents the input options to output these files. The AMReX HDF5 documentation further documents valid options.

While generating the compressed files is straightforward, it takes a little work to read these into traditional visualization software (e.g., Paraview, Visit). However, the HDF5 files are easier to open with Python than traditional AMReX plotfiles.

ParaView

To read ZFP compressed HDF5 files into ParaView, ParaView must have the environment variable HDF5_PLUGIN_PATH populated and pointing to the HDF5 ZFP plugin location. Within a spack environment with the h5z-zfp package installed:

$ export HDF5_PLUGIN_PATH=$(spack location -i h5z-zfp)/plugin
$ paraview

Then the user can load the file as usual with the VisitChomboReader.

Convert to numpy files

To convert the HDF5 files to plain numpy data files, we have provided a script to do so in tools directory of this repository. It requires the h5py and hdf5plugin Python packages.

$ python convert_amrex_hdf5_plotfile.py -f plt117501-hdf5-zfp-0.0000001

The resulting file can then be opened in Python with numpy.

yt

To read HDF5 files into yt, the HDF5 file attributes need to be modified. We have provided a script to do so in tools directory of this repository. It requires the h5py and hdf5plugin Python packages.

$ python modify_hdf5_attributes.py -f plt00000 plt00010

The resulting file can then be opened in yt.