@dax.rodriguez Following up from our conversation at ISC19.
It is not immediately clear to me whether this problem is identical to the one my colleague @harryherold reported here: PHDF5: Inconsistent HDF5 file.. The end result of a HDF5-written file being reported as inconsistent when reopened is the same, and I believe what I have is the simplest reproducer of that problem, but there may be other factors at work in his reproducer.
If anyone is aware of a workaround that will allow us to call H5Iget_file_id safely at all times on versions 1.08/1.10, or can define what assumptions are safe to make about caching file IDs in these versions, that would also be helpful–as a tool developer, we don’t get to control our users’ use of the HDF5 API.