Google colab unable to work with hdf5 files

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I have 4 hdf5 files in my drive. While using colab, db=h5py.File(path_to_file, "r") works sometimes and doesn't rest of the time. While writing the hdf5 file, I have ensured that I closed it after writing. Say File1 works on notebook_#1, when I try to use it on notebook_#2 it works sometimes, and doesn't other times. When I run it again on notebook_#1 it may work or maynot.

Probably size is not a matter because my 4 files are 32GB and others 4GB and mostly the problem is with 4GB files.

The hdf5 files were generated using colab itself. The error that I get is:

OSError: Unable to open file (file read failed: time = Tue May 19 12:58:36 2020
, filename = '/content/drive/My Drive/Hrushi/dl4cv/hdf5_files/train.hdf5', file descriptor = 61, errno = 5, error message = 'Input/output error', buf = 0x7ffc437c4c20, total read size = 8, bytes this sub-read = 8, bytes actually read = 18446744073709551615, offset = 0

or

/usr/local/lib/python3.6/dist-packages/h5py/_hl/files.py in make_fid(name, mode, userblock_size, fapl, fcpl, swmr)
    171         if swmr and swmr_support:
    172             flags |= h5f.ACC_SWMR_READ
--> 173         fid = h5f.open(name, flags, fapl=fapl)
    174     elif mode == 'r+':
    175         fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/h5f.pyx in h5py.h5f.open()

OSError: Unable to open file (bad object header version number)

Would be grateful for any help, thanks in advance.

1 Answers

Reading directly from Google Drive can cause problems.

Try copying it to local directory e.g. /content/ first.

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