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 <[email protected] <mailto:[email protected]>> 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 _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Search the list archives at: http://markmail.org/search/?q=ParaView Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/paraview
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