[Hdf-forum] Identical HDF5 files according to "h5diff" differ in comparison with "diff" Unix command

Ekin Akoglu ekin at ims.metu.edu.tr
Tue Aug 5 08:43:12 CDT 2014


Dear Alex,

Thank you for the reply. I think I need to make something clearer. I did
not make cross-comparison of HDF5 files between the Mac OS X and Debian
Linux systems. What I wanted to mean was that I tried the example I
depicted in my previous mail on both of those Unix-like systems and the
data files did differ. To me, this could be a bug, either in difftool or in
HDF5. But I remember that in the past I did not encounter such a problem
under GIT DVCS (I think for the releases before 1.8.12). If more
information is required, I can make trials with earlier HDF5 versions (<=
1.8.11) and report the results.

Thank you,

Ekin


On 5 August 2014 15:26, Stohr, Alexander <Alexander.Stohr at hdle.com> wrote:

>  Without any deep knowledge in the subject details…
>
>
>
> HDF5 is a container format that uses miscellaneous techniques
>
> for the purpose of storing those data.
>
> Some of them are e.g. binary trees, or chunking, or changing size of
> length values.
>
>
>
> Even if the data is the very same and even if any reader will see the same
> data
>
> there can still be many cases where the encapsulation might see
> differences.
>
>
>
> A binary tree can see different layouts.
>
> A chunking value can be tuned differently depending on platform, file
> system or even the used compiler.
>
> A size of a length value might be selected differently by default.
>
>
>
> A low level parsing of the container format will unveil what the origin is.
>
> This is not a bug – instead that is a feature.
>
>
>
> Maybe your invalid approach for the comparison is the real “bug”. ;-)
>
>
>
> regards, Alex.
>
>
>
>
> Managing Directors: Dr. Seok Cheol Kee, Andrea Weuffen, Wolfgang Vieweger
>
> *Von:* Hdf-forum [mailto:hdf-forum-bounces at lists.hdfgroup.org] *Im
> Auftrag von *Ekin Akoglu
> *Gesendet:* Dienstag, 5. August 2014 15:15
> *An:* HDF Users Discussion List
> *Betreff:* [Hdf-forum] Identical HDF5 files according to "h5diff" differ
> in comparison with "diff" Unix command
>
>
>
> Dear all,
>
>
>
> For the two versions of the same HDF5 file, h5diff comparison outputs "0
> differences found"; however, when compared with the Unix "diff" command,
> they differ. This is creating inconvenience under version control system.
> Do you have any suggestions why diff and h5diff conflicts? As far as I
> remember, this was not the case in the past and I remember managing HDF5
> data files without problems under GIT DVCS; however, I cannot recall which
> version of the HDF5 library.
>
>
>
> I tried this as below:
>
>
>
> I compiled my Fortran program (using GNU Fortran 4.8.2) and ran it so as
> to create the HDF5 datafile as output. I moved the datafile to some other
> directory. Then I re-ran my program (without recompiling) and then compared
> the newly created HDF5 data file with the old one using "diff" tool in Mac
> OS X (10.9.4) and Linux (Debian Wheezy 7.6 x64) and they did differ. Why?
>
>
>
> My HDF5 version is 1.8.12 and diff version is GNU diffutils 2.8.1.
>
>
>
> Thank you in advance,
>
>
>  Ekin
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum at lists.hdfgroup.org
>
> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> Twitter: https://twitter.com/hdf5
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/attachments/20140805/b1d7108e/attachment.html>


More information about the Hdf-forum mailing list