I've made the unfortunate mistake of failing to take compiler padding into account in the structures I've been using for HDF5 compound types. This has had the even more unfortunate result of making fill value elements not actually compare with the fill value (due to the pad bytes having different values, though this seems to occur only when a dataset has fill values explicitly written to disk as part of an output buffer).

My investigation has given indications that the pad bytes are being stored in the HDF5 file, which surprises me a bit. Is that the case? Should I pay rather more attention to optimizing my structures to mitigate padding?



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