issue_comments

Yeah that seems to be it. Dask's write neatly packs all the needed metadata at the beginning of the file, since we can scale this up to a many GB file with dozens of variables and still read in ~100ms. While xarray is doing a less well organized write of the metadata and we have to go seeking in the middle of the byte range. cache_type="first" does provide some improvement but still not as good as on the dask-written file.

FWIW, I inspected the actual bytes of the dask and xarray written files and they are identical for a single variable, but diverge when multiple variables are being written. So, the important differences are probably associated with this step:

It does set up the whole set of variables as a initialisation stage before writing any data - I don't know if xarray does this.

I do generally recommend cache_type="first" for reading HDF5 files, because they tend to have most of the metadata in the header area of the file, with short pieces of metadata "elsewhere"; so the default readahead doesn't perform very well.

As to what the two writers might be doing differently, I only have guesses. I imagine xarray leaves it entirely to HDF to make whatever choices it likes. Dask does not write in parallel, since HDF does not support that, but it may order the writes more logically. It does set up the whole set of variables as a initialisation stage before writing any data - I don't know if xarray does this.

The slow file:

And the fast file:

I did try many loops and different order of operations to make sure this isn't a caching or auth issue. You can see the std dev of the timeit calls above is pretty consistent.

For my actual use case, the difference is very apparent, with open_dataset taking about 9 seconds on the numpy-saved file and <1 second on the dask-saved one. I can also clearly see when monitoring network traffic that the slow version has to read in hundreds of MB of data to open the dataset, while the fast one only reads the tiny headers.

I also inspected the actual header bytes of these two files and see they are indeed different.