Hi, I think I also witnessed the difference. If you do a h5dump, you may see that some values are different. If you create twice the same file with the same procedure, it may also be different. I guess there is a timestamp or something like that in the file.
Cheers, Matthieu 2014-08-05 15:43 GMT+02:00 Ekin Akoglu <[email protected]>: > 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 <[email protected]> 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:[email protected]] 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. >> [email protected] >> >> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >> Twitter: https://twitter.com/hdf5 > > > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > Twitter: https://twitter.com/hdf5 -- Information System Engineer, Ph.D. Blog: http://matt.eifelle.com LinkedIn: http://www.linkedin.com/in/matthieubrucher Music band: http://liliejay.com/ _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
