[Paraview] Fwd: Segfault reading polyhedral cells xdmf3 file

[Armin Wehrfritz]

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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