[MOAB-dev] read polygon mesh from vtk file

[Vijay S. Mahadevan]

Huayi,

Thanks for the bug report. We haven't been testing the read/write of
polygonal meshes rigorously. I was able to replicate your segfault
with my locally configured VTK and will try to find the exact cause of
the issue and push a fix. It is possible that the format expected
might be different or outdated in our reader.

Iulian, I'll send you the configuration commands for vtk 6.0/6.1 so
that you can add a check in buildbot too.

Vijay

On Sun, Jun 29, 2014 at 6:26 PM, Huayi Wei <huayiwei1984 at gmail.com> wrote:
> Hi, Lulian
>
> Thanks for your reply. The vtk file was generated by a simple matlab script
> wrote by myself . It is very simple, and just includes the points and the
> polygons.
>
> I think moab support such kind of vtk format, but maybe there exist some
> bugs in its reading code. Please see function
> `moab::ReadVtk::vtk_read_polygons` in `ReadVtk.cpp` file.
>
> Best
>
> Huayi
>
> ```
> # vtk DataFile Version 3.0
> MOAB 4.7.0pre
> ASCII
> DATASET POLYDATA
> POINTS 26 double
> 3.073901530231682e-06 2.977455744718462e-01 0.000000000000000e+00
> -7.071067811865476e-01 7.071067811865475e-01 0.000000000000000e+00
> -1.715691137876366e-01 3.536798274750831e-01 0.000000000000000e+00
> -4.719776146377113e-01 1.857355490854607e-01 0.000000000000000e+00
> -8.508854127205038e-01 3.599944589578263e-01 0.000000000000000e+00
> 2.775557561562891e-16 1.000000000000000e+00 0.000000000000000e+00
> -3.406715072241552e-01 8.588892413936710e-01 0.000000000000000e+00
> 1.715662369808998e-01 3.536768053562428e-01 0.000000000000000e+00
> 4.719754417201190e-01 1.857347459630188e-01 0.000000000000000e+00
> -4.719756118732749e-01 -1.857348097293946e-01 0.000000000000000e+00
> -1.000000000000000e+00 1.110223024625157e-16 0.000000000000000e+00
> -8.508847507623047e-01 -3.599960570662885e-01 0.000000000000000e+00
> 7.071067811865476e-01 7.071067811865476e-01 0.000000000000000e+00
> 3.406701269292776e-01 8.588898131305294e-01 0.000000000000000e+00
> 8.508845922027242e-01 3.599964398629780e-01 0.000000000000000e+00
> -7.071067811865476e-01 -7.071067811865476e-01 0.000000000000000e+00
> 4.719777412790575e-01 -1.857356073815120e-01 0.000000000000000e+00
> 7.071067811865472e-01 -7.071067811865477e-01 0.000000000000000e+00
> -3.051853356210140e-16 -1.000000000000000e+00 0.000000000000000e+00
> 1.715687253344436e-01 -3.536802010232855e-01 0.000000000000000e+00
> -3.319925237351595e-06 -2.977459818644166e-01 0.000000000000000e+00
> -1.715662714497118e-01 -3.536770586038507e-01 0.000000000000000e+00
> -3.406707216059742e-01 -8.588895668073767e-01 0.000000000000000e+00
> 3.406712167592965e-01 -8.588893617081550e-01 0.000000000000000e+00
> 1.000000000000000e+00 -2.775557561562891e-17 0.000000000000000e+00
> 8.508853951409249e-01 -3.599945013986841e-01 0.000000000000000e+00
> POLYGONS 10 64
> 6 21 22 18 23 19 20
> 6 20 0 7 8 16 19
> 5 10 4 3 9 11
> 5 12 13 7 8 14
> 5 24 14 8 16 25
> 5 21 9 11 15 22
> 6 7 0 2 6 5 13
> 5 19 23 17 25 16
> 5 3 4 1 6 2
> 6 21 9 3 2 0 20
> ```
>
> On 2014年06月29日 23:38, Grindeanu, Iulian R. wrote:
>>
>> Hi,
>> How was the file generated?
>> our vtk reader is very simple, it does not support all vtk formats, and
>> there is no plan to.
>> For general vtk files, you would need to configure with vtk , I think (I
>> am not sure, I would have to try).
>> Vijay
>>
>> What was your configure command?
>>
>> Iulian
>>
>> ________________________________________
>> From: moab-dev-bounces at mcs.anl.gov [moab-dev-bounces at mcs.anl.gov] on
>> behalf of Huayi Wei [huayiwei1984 at gmail.com]
>> Sent: Saturday, June 28, 2014 11:08 PM
>> To: MOAB Dev
>> Subject: [MOAB-dev] read polygon mesh from vtk file
>>
>> Hi, Moab Dev,
>>
>> I have a polygon mesh saved in vtk format, see attachment. I can show it
>> by paraview. But when loading it into moab, I meet `Segmentation fault
>> (core dumped)`
>> error. I don't know how to fixed it. Please help me, thanks very much.
>>
>> Here is the cpp file.
>> ```
>> #include "moab/Core.hpp"
>> #include <iostream>
>> #include <assert.h>
>>
>> using namespace moab;
>> using namespace std;
>>
>> int main(int argc, char ** argv)
>> {
>>       string file = s"/poly8-10.vtk";
>>       Interface * imesh = new Core;
>>
>>       ErrorCode rval =  imesh->load_mesh(file.c_str());
>>       assert(rval == MB_SUCCESS);
>>
>>       return 0;
>> }
>> ```
>>
>> And here is the information of core:
>> ```
>> Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
>> Core was generated by `./readpolygon_test'.
>> Program terminated with signal SIGSEGV, Segmentation fault.
>> #0  0x00007f3fee79cd3b in moab::Range::front (this=0xffffffffffffffe0)
>>       at ./moab/Range.hpp:824
>> 824      { return mHead.mNext->first; }
>> (gdb) list
>> 819    inline Range::const_iterator
>> Range::const_iterator::start_of_block() const
>> 820      { return Range::const_iterator( mNode, mNode->first ); }
>> 821
>> 822      //! get first entity in range
>> 823    inline const EntityHandle& Range::front() const
>> 824      { return mHead.mNext->first; }
>> 825      //! get last entity in range
>> 826    inline const EntityHandle& Range::back() const
>> 827      { return mHead.mPrev->second; }
>> 828
>> ```
>>
>> Best
>>
>> Huayi
>
>