Interesting, I used HDF5 in a similar situation because we needed to save a lot ...

		radarsat1 on June 13, 2020 \| parent \| context \| favorite \| on: SQLite as an Application File Format (2014) Interesting, I used HDF5 in a similar situation because we needed to save a lot of same-sized rows of data (simulation time steps), so a matrix-oriented format seemed to make sense but it wasn't entirely without some need for cross-referencing between tables, so it does make me wonder now if sqlite would have been a comparable or better choice. Any reason for rejecting HDF5 in your case?

Is it cheap to insert/update/delete data in HDF5? If not, that should be the answer. I'm also curious if Parquet would fit your requirements.