I suddenly started having troubles reading data from a relatively large HDF5 file (156 GB). In the past, I could read the file without issues but now I get the following error raised from h5py:
OSError: Can't read data (file read failed: time = Thu Jun 9 10:40:52 2022, filename = '../path/to/my_file.h5', file descriptor = 10, errno = 5, error message = 'Input/output error', buf = 0x7f77b1f422e0, total read size = 12139376, bytes this sub-read = 12139376, bytes actually read = 18446744073709551615, offset = 42224603136)
I’m only getting this error when I try to read certain datasets. Other datasets load fine.
I could find this thread where someone was facing a similar error but then they realised that it only affected them when they were trying to read a file from a network location. In my case, I have the file stored locally on an SSD (ext4 filesystem).
Is it possible that my file is corrupt? Do you have any suggestions on what I could check or try?
Thanks for help!