I have the files, but can’t upload them (new user status - can that be removed? I promise I’ll behave 
)
I have put the callgrind files here:
https://nextcloud.marin.nl/index.php/s/r5GMFswRQAfmmKP
The refresco_new.callgrind file is the one with the bad performance. It took 84 seconds to run this, whereas refresco.callgrind (with HDF5 1.8.18) took about 9 seconds.
I notice that as the simulation progresses, it gets slower and slower.
When looking with qcachegrind I see marked differences. 85% of the time is spent in H5Fget_obj_count.
It is most likely related to this topic, as the code calls h5open_f/h5close_f a lot, as in each write.
I’ll take a look at the solution from https://github.com/HDFGroup/hdf5/pull/1657