<div dir="ltr">Both the cases are ok on the Windows PC.<div class="gmail_extra"><br><div class="gmail_quote">On Thu, Dec 1, 2016 at 6:19 PM, Armin Wehrfritz <span dir="ltr"><<a href="mailto:dkxls23@gmail.com" target="_blank">dkxls23@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">To follow up on this issue, I have done some more testing. From the link<br>
below you can find two datasets with polyhedral cells, where one is<br>
working just fine and the other one is crashing consistently when<br>
opening it in ParaView 5.2.<br>
The XDMF files are created form the respective .vtu files with ParaView<br>
5.2 (Kitware binaries, Linux 64bit) using the Xdmf3 writer.<br>
<br>
The strange thing is that the dataset leading to the seg fault is a<br>
subset of the dataset that just works fine.<br>
<br>
Here the link:<br>
<a href="https://drive.google.com/file/d/0B5CHY8CFeTf2V09NVUhTRkpYSE0/view?usp=sharing" rel="noreferrer" target="_blank">https://drive.google.com/file/<wbr>d/0B5CHY8CFeTf2V09NVUhTRkpYSE0<wbr>/view?usp=sharing</a><br>
<br>
Alessandro, can you test these files and report back which ones are<br>
working on your PC?<br>
<br>
Thanks,<br>
Armin<span class=""><br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
On 11/30/2016 08:19 PM, Alessandro De Maio wrote:<br>
</span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">
You're right: the polyhedral cells of the cube.vtu example do not<br>
guarantee the planarity of faces, but this is a typical case of a<br>
polyhedral mesh automatically generated starting from a tetrahedral one<br>
(this example has been built using the Ansys-Fluent converter) and I<br>
think it's quite a usual situation.<br>
But I'm not sure this could generate a segfault as the problem could be<br>
in the algorythms applied by Paraview after the reading of the file that<br>
could consider this hypothesis (as you remarked), while the VTK<br>
topological description of a polyhedral cell doesn't seem to need it,<br>
and the reading phase should only build the data structure compliant<br>
with VTK data representation, as actually happens for vtu file format.<br>
But this is only my opinion and of course it could be wrong as I don't<br>
have a deep knowledge of all the involved procedures.<br>
My idea is that the problem could be due to a memory error, as it's only<br>
unfrequent with a small case (by the way the one cell mesh you attached<br>
can be read also on the windows machine although with a randomic<br>
connectivity error as the one I showed in the image attached to the<br>
previous message) but very frequent with a quite bigger case as the cube.<br>
Is it possible to use something like valgrind to check for memory errors<br>
in Paraview ?<br>
<br>
On Wed, Nov 30, 2016 at 6:35 PM, Armin Wehrfritz <<a href="mailto:dkxls23@gmail.com" target="_blank">dkxls23@gmail.com</a><br></span><div><div class="h5">
<mailto:<a href="mailto:dkxls23@gmail.com" target="_blank">dkxls23@gmail.com</a>>> wrote:<br>
<br>
In attach you can find the output of the saving of the<br>
polyhedron.vtu<br>
(saved.xmf and saved.h5) from the Windows machine.<br>
<br>
OK, I tested the "saved.xmf" file and I can open it on my Linux machine<br>
without issues. Also, I compared the files generated on windows and<br>
linux machines, and the topology data is the same for both of them. The<br>
datatype in the h5 file is different (H5T_STD_I32LE for the file from<br>
the Windows machine vs. H5T_STD_I64LE for the file from the Linux<br>
machine). The end of line in the xmf file is different, but I don't<br>
think either one of them should cause an issue.<br>
<br>
I've tried also to repeat the procedure (reading of your xmf<br>
file) on a<br>
Linux workstation and the behaviour is different: it seems that<br>
randomically the crash happens again (once on about ten tries) and<br>
sometimes it seems that the topology has a connectivity error<br>
(see the<br>
image in attachment), while for the most of the times it seems<br>
to do the<br>
right job.<br>
<br>
As said, on my Linux machine it works consistently.<br>
<br>
I've tried also another case, a little bit heavier: a polyhedral<br>
mesh<br>
read from the vtu in attach (cube.vtu) and saved with the Xdmf3<br>
writer.<br>
Trying to re-read the xmf version of this geometry always<br>
produces a<br>
crash also on the Linux machine.<br>
<br>
I can confirm that the xmf file produce from the cube.vtu (using the<br>
Xdmf3 writer in ParaView 5.2) leads consistently to seg fault.<br>
However, even though the .vtu file works correctly, I'm not entirely<br>
sure if this is xmf specific problem. To be more precise, the<br>
implementation of polyhedral cells requires the face polygons to be<br>
planar (see <a href="http://www.vtk.org/Wiki/VTK/Polyhedron_Support" rel="noreferrer" target="_blank">http://www.vtk.org/Wiki/VTK/Po<wbr>lyhedron_Support</a><br></div></div>
<<a href="http://www.vtk.org/Wiki/VTK/Polyhedron_Support" rel="noreferrer" target="_blank">http://www.vtk.org/Wiki/VTK/P<wbr>olyhedron_Support</a>>). The example<span class=""><br>
file you send has a whole lot of faces that are not planar.<br>
<br>
I extracted a single cell with several non-planar faces from your<br>
example and saved it as .xmf file (attached). I can read this particular<br>
file without issues on my Linux machine, whereas the original data file<br>
leads to a seg fault. One reason why the cube.vtu file works and the<br>
respective .xmf doesn't, could be related to the different approaches<br>
polyhedral cells are stored in vtu and xdmf files, but debugging this<br>
would require quite a bit of work...<br>
<br>
Maybe somebody else has an idea here.<br>
<br>
-Armin<br>
<br>
<br>
<br>
<br></span><span class="">
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