[Hdf-forum] HDF lib incompatible with HDF file spec?

Krug, Markus markus.krug at hm.edu
Tue Sep 5 02:56:47 CDT 2017

Dear all,

I just came around an interesting issue.
I implemented the writing of HDF files on an embedded system. The amount of functionality I implemented is significant less than the HDF lib offers. So it is just tailored to my needs. I implemented everything on base of the HDF 3.0 file spec. One point of my tailoring was to optimize the file size. Therefore, I write every internal block in the HDF files aligned byte-by-byte to the next - or padded to the address alignment if it is requested by the HDF file specification. The HDF files generated by HDFview or Matlab have plenty of space in-between the internal blocks. Sometimes a few hundred bytes. As far as I read from the HDF file specification this 'extended padding' is not defined at all - not even recommended.
However, this 'extended padding' that is performed by the HDF lib leads to a behavior that I would consider as an incompatibility to itself. To demonstrate this I attached two HDF files to this email. The first (sizeoptimized.h5) is generated by my embedded software and is optimized concerning the file size. It contains three compounds with each of them has 2 elements. You should be able to open that file in HDFview or similar tools and read all its contents.
The second file (sizeoptimizedextended.h5) is generated by HDFview by adding a fourth compound after the sizeoptimized.h5 file was opened in HDFview. You can see that the file is partly corrupted. The reason for this is that HDFview (and therefore the HDF lib I guess) is not really taking care about the position of the internal blocks of a file that it is writing to. It seems to me it has some internal mapping of those blocks. This mapping gets applied even if it will collide, and therefore corrupt, the existing blocks.
If my observation is correct I think the HDF lib will need a bugfix or the HDF file spec will need a description of how the internal blocks are allowed to be positioned within a HDF file.
I forgot to mention that I tried to use the HDF lib sources and compile it to my system. However, I quit after a couple of days because the way the sources are written are not suitable at all to adopt them to an embedded system that runs a simplified file system and a real-time operating system - and all of it has to fit into a few hundred kilobytes.

Can anyone comment on my observation?

Best Regards
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