Reading HDF5 with dynamic filters

I am trying to read an HDF5 file that uses a zstd filter, and I am having trouble setting the HDF5_PLUGIN_PATH variable. Here is what I have tried:

>> !export HDF5_PLUGIN_PATH=/Users/bendichter/opt/miniconda3/lib/python3.9/site-packages/hdf5plugin/plugins

>> !echo $HDF5_PLUGIN_PATH

/Users/bendichter/opt/miniconda3/lib/python3.9/site-packages/hdf5plugin/plugins

>> setenv("HDF5_PLUGIN_PATH", "/Users/bendichter/opt/miniconda3/lib/python3.9/site-packages/hdf5plugin/plugins")

>> getenv("HDF5_PLUGIN_PATH")

'/Users/bendichter/opt/miniconda3/lib/python3.9/site-packages/hdf5plugin/plugins'

>> h5read("zstd.h5","/data")

Error using h5readc

The HDF5 library encountered an error and produced the following stack trace information:

H5PL__find_plugin_in_path can't open directory: /usr/local/hdf5/lib/plugin

Error in h5read (line 93)

[data,var_class] = h5readc(Filename,Dataset,start,count,stride);

Why is MATLAB looking in /usr/local/hdf5/lib/plugin? That directory does not exist, and I have tried two different ways to tell MATLAB to look an a different directory. What am I doing wrong?

[Ben Dichter]

update: it looks like this apprach does work on Windows, so it appears to be an OSX or unix-specific issue

[Benjamin Thompson]

HDF5 is also the MATLAB MAT file format. There may be some confusion there if you are attempting to use an alternative HDF5 library.

[Ben Dichter]

@Benjamin Thompson so do you have any ideas how I might fix this? I am not trying to read a .mat file

[Science Machine]

try loading path before starting matlab?

Answer 1

[Ninad]

Hi Ben,

As per my understanding you want to read an HDF5 file in MATLAB and you are unable to set HDF5_PLUGIN_PATH variable using the "setenv()" function.

Please go through the latest version of MATLAB documentation "Import HDF5 Files":

https://in.mathworks.com/help/matlab/import_export/import-hdf5-files.html

It clearly states that you need to set the HDF5_PLUGIN_PATH environment variable to the folder containing the installed plugin binary file before you start MATLAB.

On Windows® — Set the environment variable using System Properties > Advanced > Environment Variables, and then start MATLAB.

Hope this helps.

Regards

Ninad