[Paraview] Fwd: Segfault reading polyhedral cells xdmf3 file

Thu Dec 15 16:39:50 EST 2016

Can confirm that it Alessangro's initial xdmf file fails on windows (crash
is in somewhere in the rendering stack - need a debug build to diagnose
further) but works OK on Linux.

Please submit an issue on the ParaView issue tracker.

David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Thu, Dec 1, 2016 at 4:07 PM, Alessandro De Maio <demaio.a at gmail.com>
wrote:

> Both the cases are ok on the Windows PC.
>
> On Thu, Dec 1, 2016 at 6:19 PM, Armin Wehrfritz <dkxls23 at gmail.com> wrote:
>
>> To follow up on this issue, I have done some more testing. From the link
>> below you can find two datasets with polyhedral cells, where one is
>> working just fine and the other one is crashing consistently when
>> opening it in ParaView 5.2.
>> The XDMF files are created form the respective .vtu files with ParaView
>> 5.2 (Kitware binaries, Linux 64bit) using the Xdmf3 writer.
>>
>> The strange thing is that the dataset leading to the seg fault is a
>> subset of the dataset that just works fine.
>>
>> Here the link:
>> https://drive.google.com/file/d/0B5CHY8CFeTf2V09NVUhTRkpYSE0
>> /view?usp=sharing
>>
>> Alessandro, can you test these files and report back which ones are
>> working on your PC?
>>
>> Thanks,
>> Armin
>>
>>
>>
>>
>>
>>
>>
>> On 11/30/2016 08:19 PM, Alessandro De Maio wrote:
>>
>>> You're right: the polyhedral cells of the cube.vtu example do not
>>> guarantee the planarity of faces, but this is a typical case of a
>>> polyhedral mesh automatically generated starting from a tetrahedral one
>>> (this example has been built using the Ansys-Fluent converter) and I
>>> think it's quite a usual situation.
>>> But I'm not sure this could generate a segfault as the problem could be
>>> in the algorythms applied by Paraview after the reading of the file that
>>> could consider this hypothesis (as you remarked), while the VTK
>>> topological description of a polyhedral cell doesn't seem to need it,
>>> and the reading phase should only build the data structure compliant
>>> with VTK data representation, as actually happens for vtu file format.
>>> But this is only my opinion and of course it could be wrong as I don't
>>> have a deep knowledge of all the involved procedures.
>>> My idea is that the problem could be due to a memory error, as it's only
>>> unfrequent with a small case (by the way the one cell mesh you attached
>>> can be read also on the windows machine although with a randomic
>>> connectivity error as the one I showed in the image attached to the
>>> previous message) but very frequent with a quite bigger case as the cube.
>>> Is it possible to use something like valgrind to check for memory errors
>>> in Paraview ?
>>>
>>> On Wed, Nov 30, 2016 at 6:35 PM, Armin Wehrfritz <dkxls23 at gmail.com
>>> <mailto:dkxls23 at gmail.com>> wrote:
>>>
>>>         In attach you can find the output of the saving of the
>>>         polyhedron.vtu
>>>         (saved.xmf and saved.h5) from the Windows machine.
>>>
>>>     OK, I tested the "saved.xmf" file and I can open it on my Linux
>>> machine
>>>     without issues. Also, I compared the files generated on windows and
>>>     linux machines, and the topology data is the same for both of them.
>>> The
>>>     datatype in the h5 file is different (H5T_STD_I32LE for the file from
>>>     the Windows machine vs. H5T_STD_I64LE for the file from the Linux
>>>     machine). The end of line in the xmf file is different, but I don't
>>>     think either one of them should cause an issue.
>>>
>>>         I've tried also to repeat the procedure (reading of your xmf
>>>         file) on a
>>>         Linux workstation and the behaviour is different: it seems that
>>>         randomically the crash happens again (once on about ten tries)
>>> and
>>>         sometimes it seems that the topology has a connectivity error
>>>         (see the
>>>         image in attachment), while for the most of the times it seems
>>>         to do the
>>>         right job.
>>>
>>>     As said, on my Linux machine it works consistently.
>>>
>>>         I've tried also another case, a little bit heavier: a polyhedral
>>>         mesh
>>>         read from the vtu in attach (cube.vtu) and saved with the Xdmf3
>>>         writer.
>>>         Trying to re-read the xmf version of this geometry always
>>>         produces a
>>>         crash also on the Linux machine.
>>>
>>>     I can confirm that the xmf file produce from the cube.vtu (using the
>>>     Xdmf3 writer in ParaView 5.2) leads consistently to seg fault.
>>>     However, even though the .vtu file works correctly, I'm not entirely
>>>     sure if this is xmf specific problem. To be more precise, the
>>>     implementation of polyhedral cells requires the face polygons to be
>>>     planar (see http://www.vtk.org/Wiki/VTK/Polyhedron_Support
>>>     <http://www.vtk.org/Wiki/VTK/Polyhedron_Support>). The example
>>>     file you send has a whole lot of faces that are not planar.
>>>
>>>     I extracted a single cell with several non-planar faces from your
>>>     example and saved it as .xmf file (attached). I can read this
>>> particular
>>>     file without issues on my Linux machine, whereas the original data
>>> file
>>>     leads to a seg fault. One reason why the cube.vtu file works and the
>>>     respective .xmf doesn't, could be related to the different approaches
>>>     polyhedral cells are stored in vtu and xdmf files, but debugging this
>>>     would require quite a bit of work...
>>>
>>>     Maybe somebody else has an idea here.
>>>
>>>     -Armin
>>>
>>>
>>>
>>>
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