Make a self contained hdf5 from an hdf5 with extenral files

HDF5 Library
1

I want to take an HDF5 file with a bunch of datasets with data in external files (created with H5Pset_external) and make a copy of the file with the same data stored inside the HDF5 file. I would absolutely love it if there is some invocation of h5copy or h5repack or similar that would do this for me.

So far, h5copy seems to just copy only the data already in the HDF5 file, it will resolve links to datasets, but wont resolve the external files, it just makes a new dataset pointing to the same external files.

h5repack seems to give errors on datasets that have external files.

Is there some existing tool that will do this form me? Or will I just have to write something?

2

Hello John,

h5repack cannot repack datasets with external storage. This is a known issue (HDFFV-10408). I hope we will address to in the next major release.

Thank you!

Elena