I apologize for the error in my email below. It should read "PyTables maintainers" instead of "H5Py maintainers" :-)
Elena ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Elena Pourmal The HDF Group http://hdfgroup.org 1800 So. Oak St., Suite 203, Champaign IL 61820 217.531.6112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Oct 24, 2013, at 10:11 PM, Elena Pourmal <[email protected]> wrote: > 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 <[email protected]> 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" <[email protected]> >> 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 <[email protected]> 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. >>> [email protected] >>> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >>> >>> >>> >>> -- >>> Andrea Bedini <[email protected]> >>> _______________________________________________ >>> Hdf-forum is for HDF software users discussion. >>> [email protected] >>> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >> _______________________________________________ >> Hdf-forum is for HDF software users discussion. >> [email protected] >> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
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