Thank you all for the suggestions and brainstorming thus far. Like Rob, I would also expect that HDF5 binaries be equal. But suggestion by Werner is also a workaround for me for now.
In the meantime, I went from HDF5 release 1.8.12 down to as far back as HDF5 1.8.8 with Intel Fortran Compiler 14.0.3 on an Ubuntu 12.04.4 x64 using the h5ex_t_cmpd_F03.f90 <http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/hdf5-examples/1_8/FORTRAN/H5T/h5ex_t_cmpd_F03.f90> example and making trials; however, I could not manage to get binary equality out of "diff" command for HDF5 data files created by two identical runs. This shows that my memory of remembering managing h5 files under GIT is false, although I was almost sure that I could do manage a GIT repo with h5 files in the past. Anyway, thank you all for the fruitful discussion. It seems that the suggestion of Werner is the way to go. Regards, Ekin On 5 August 2014 17:32, Werner Benger <[email protected]> wrote: > HDF5, when using the newest version's library features, includes time > stamps in the file, as "h5ls -v" displays: > > h5ls -v LOD.f5 > Opened "LOD.f5" with sec2 driver. > Charts Group > Location: 1:70486 > Links: 1 > Modified: 2014-07-15 15:57:53 W. Europe Daylight Time > TableOfContents Group > Attribute: version {3} > Type: native int > Data: 0, 1, 5 > Location: 1:342 > Links: 1 > Modified: 2014-07-15 15:57:53 W. Europe Daylight Time > Comment: "All file objects in reverse order for easier browsing. " > t=000000000.0000000000 Group > Attribute: Time scalar > Type: native double > Data: 0 > Location: 1:195 > Links: 1 > Modified: 2014-07-15 15:57:53 W. Europe Daylight Time > > > However, you can control whether the newest library features are used or > not by calling > > H5Pset_libver_bounds(fapl_id, H5F_LIBVER_EARLIEST, H5F_LIBVER_LATEST); > > see > > http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetLibverBounds > > Thereby you should be able to disable timestamps to be put into the HDF5 > file by forcing it to *not* use the newest library features and binary > diffs should work again for such old-style files. > > > Cheers, > Werner > > > > On 05.08.2014 15:14, Ekin Akoglu wrote: > > 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 > [email protected]http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > Twitter: https://twitter.com/hdf5 > > > -- > ___________________________________________________________________________ > Dr. Werner Benger Visualization Research > Center for Computation & Technology at Louisiana State University (CCT/LSU) > 2019 Digital Media Center, Baton Rouge, Louisiana 70803 > Tel.: +1 225 578 4809 Fax.: +1 225 578-5362 > > > _______________________________________________ > 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 >
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