[Paraview] Fwd: Segfault reading polyhedral cells xdmf3 file

[Alessandro De Maio]

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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