[Octave-bug-tracker] [bug #38789] segfault on exit after failing to load HDF5 file

[Markus Appel]

URL:
  <http://savannah.gnu.org/bugs/?38789>

                 Summary: segfault on exit after failing to load HDF5 file
                 Project: GNU Octave
            Submitted by: mappel
            Submitted on: Sat 20 Apr 2013 06:52:04 PM GMT
                Category: None
                Severity: 3 - Normal
                Priority: 5 - Normal
              Item Group: Crash
                  Status: None
             Assigned to: None
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
         Discussion Lock: Any
                 Release: 3.6.4
        Operating System: GNU/Linux

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Details:

Trying to load the attached (3rd party) hdf5 file results in an error. Octave
remains functional, but closing the session ends in a segfault:


octave:1> a=load('-hdf5','dmc02.h5');
error: load: range error for insert
octave:1> exit

panic: Segmentation fault -- stopping myself...
attempting to save variables to 'octave-core'...
Segmentation fault (core dumped)


The resulting file octave-core has zero size.

Here is some complementary information of what I am trying to do, in case it
helps:

I want to read NeXus files ( nexusformat.org ) which is a format specification
built on top of HDF5. The attached file is a test data set also downloadable
from:

http://trac.nexusformat.org/code/browser/tags/4.3.0/test/data/dmc02.h5

It is a completely valid HDF5 file (at least h5check tells me so). I started
to remove data sets and groups from the file to figure out what prevents
octave from successfully reading it. My strong suspicion is that fields
containing strings cause the error. If I remove all string fields, the file
can be read without problems. It still works if I leave some string fields in
the file, but it seems not to be a certain string field that causes the
error.

Some strings which could be read are missing the last character, so it might
be connected to #35227
<http://savannah.gnu.org/bugs/?func=detailitem&item_id=35227> . An error upon
exit after reading hdf5 is also described in #37713
<https://savannah.gnu.org/bugs/?func=detailitem&item_id=37713> but I am not
sure whether it is related to this bug.

octave was built from 3.6.4 source on Ubuntu 12.04 with libhdf5-serial-dev
1.8.4-patch1-3ubuntu2 installed



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File Attachments:


-------------------------------------------------------
Date: Sat 20 Apr 2013 06:52:04 PM GMT  Name: dmc02.h5  Size: 29kB   By: mappel

<http://savannah.gnu.org/bugs/download.php?file_id=27913>

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