All, We investigated the problem reported by the H5Py maintainers. The issue goes back to the 1.8.2 release when an assertion was introduce to catch errors in the file format.
The https://github.com/PyTables/PyTables/raw/master/tables/tests/ex-noattr.h5 file is an example of such file - it contains a wrong version (1 instead of 2) of the array datatype in a header message. The symptom will be a failure of the HDF5 read utilities like h5dump or h5ls when HDF5 library is built in development mode or when --enable-strict-format-checks configure flag is used to configure the HDF5 library. h5dump (when used with the --enable-error-stack flag) shows the following errors at the bottom of the produced error stack: ./h5dump --enable-error-stack ex-noattr.h5 …… …. H5Odtype.c line 550 in H5O_dtype_decode_helper(): incorrect array datatype version major: Datatype minor: Wrong version number h5dump error: internal error (file h5dump.c:line 1615) The problem can be mitigated by repacking the file with h5repack. The tool has to be built using the HDF5 library in production mode (this is default for the official releases). The HDF5 library skips file format checks on read and writes the correct header to the new file. Elena ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Elena Pourmal The HDF Group http://hdfgroup.org 1800 So. Oak St., Suite 203, Champaign IL 61820 217.531.6112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Oct 23, 2013, at 10:26 PM, Elena Pourmal <epour...@hdfgroup.org> wrote: > Andrea, > > Thank you for report! We will take a look. > > Elena > > Sent from my iPhone > > On Oct 23, 2013, at 10:03 PM, "Andrea Bedini" <andrea.bed...@gmail.com> wrote: > >> Hi Elena, >> >> an user has reported some issues using PyTables with the rc1 and when I had >> a look I stumbled into this: >> >> $ ../hdf5-1.8.12-pre1/hdf5/bin/h5dump tables/tests/ex-noattr.h5 >> h5dump error: internal error (file h5dump.c:line 1471) >> >> ex-noattr.h5 is part of PyTables' test suite and it's available at the >> following link >> https://github.com/PyTables/PyTables/raw/master/tables/tests/ex-noattr.h5 >> >> The file works perfectly with 1.8.11. A backtrace (which I assume to be >> related to the issue but it might not be), is available here >> https://github.com/PyTables/PyTables/issues/290 >> >> Can anyone have a look? >> >> Thanks >> Andrea >> >> >> >> On 9 October 2013 12:15, Elena Pourmal <epour...@hdfgroup.org> wrote: >> Dear HDF5 users, >> >> A pre-release candidate of HDF5 1.8.12 is available for testing and can be >> downloaded from the following location: >> >> ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.12/pre1/ >> >> We will greatly appreciate if you test this pre-release on the platform(s) >> of your choice and report any problems found to this list as soon as >> possible. We have about three weeks to address the issues. >> >> The list of new features, bug fixes, and platforms tested by The HDF Group >> can be found in the >> ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.12/pre1/hdf5-1.8.12-pre1-RELEASE.txt >> file. >> >> The new release includes but is not limited to: >> >> - Support for Windows 8.1 >> - Support for OpenVMS on Itanium 64 >> - Fixes to gcc 4.8.x problems reported on FORUM >> - Enhancements to h5repack to support user-defined filters as described >> in section 6.2 of >> >> http://www.hdfgroup.org/HDF5/doc/Advanced/DynamicallyLoadedFilters/HDF5DynamicallyLoadedFilters.pdf >> - An option to specify default plugin directories at the HDF5 >> configuration time using >> --with-default-plugin=location (configure) >> -DH5_DEFAULT_PLUGINDIR:PATH=location (CMake) >> - New command-line options to h5dump >> + Print an object specified by its path >> + Exclude printing of attributes >> >> Happy testing and we look forward to hearing from you (hopefully no bugs :-)! >> >> Thank you! >> >> Elena >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> Elena Pourmal The HDF Group http://hdfgroup.org >> 1800 So. Oak St., Suite 203, Champaign IL 61820 >> 217.531.6112 >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> >> >> >> >> _______________________________________________ >> Hdf-forum is for HDF software users discussion. >> Hdf-forum@lists.hdfgroup.org >> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >> >> >> >> -- >> Andrea Bedini <andrea.bed...@gmail.com> >> _______________________________________________ >> Hdf-forum is for HDF software users discussion. >> Hdf-forum@lists.hdfgroup.org >> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > _______________________________________________ > Hdf-forum is for HDF software users discussion. > Hdf-forum@lists.hdfgroup.org > http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
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