Both the cases are ok on the Windows PC. On Thu, Dec 1, 2016 at 6:19 PM, Armin Wehrfritz <[email protected]> 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 <[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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