[petsc-users] How to output VTK file with Vec associating with DMPLEX

Sun Dec 9 18:46:39 CST 2018

So I need to manually create a PetscSection by using DMPlexCreateSection().
Am I right?

Thanks,
Barry

Matthew Knepley <knepley at gmail.com> 於 2018年12月10日 週一 上午8:40寫道：

> On Sun, Dec 9, 2018 at 7:31 PM Tsung-Hsing Chen <barrydog505 at gmail.com>
> wrote:
>
>> Vertex-based is what I want.
>> Here I don't think I have created any PetscSection yet.
>> Do I need to create the PetscSection,
>>
>
> Yes. There is a manual chapter with this in it.
>
>
>> if I already have a mesh file from gmsh?
>>
>
> That is just topology and geometry. It says nothing about data layout.
>
>
>> or just I simply use DMPlexGetConeSection() to get vertex-based vector?
>>
>
> That is a Section which describes the layout of topology data.
>
>   Thanks,
>
>      Matt
>
>
>> Thanks,
>> Barry
>>
>>
>> Matthew Knepley <knepley at gmail.com> 於 2018年12月10日 週一 上午7:27寫道：
>>
>>> On Sun, Dec 9, 2018 at 5:47 PM Tsung-Hsing Chen via petsc-users <
>>> petsc-users at mcs.anl.gov> wrote:
>>>
>>>> Hi,
>>>> I want to output a VTK file containing Vec which associate with DMPLEX,
>>>> but I keep getting some errors.
>>>>
>>>
>>> The really easy way is to put
>>>
>>>   ierr = VecViewFromOptions(x, NULL, "-myvec_view");CHKERRQ(ierr);
>>>
>>> in your code and then give
>>>
>>>   -myvec_view vtk:sol.vtk
>>>
>>> on the command line.
>>>
>>>
>>>> I use PetscViewerVTKOpen() to create the vtk file.
>>>> Then I saw many examples just use DMCreateGlobalVector() to create the
>>>> Vec associate with DM.
>>>> However, almost all of them aren't DMPLEX but are DMDA.
>>>> I don't know whether it will cause some problems.
>>>> These is what I write:
>>>>
>>>
>>> 1) ALWAYS check return values. Your VecSetValue is failing.
>>>
>>> 2) VTK can only display two kinds of information, vertex-based and
>>> cell-based. DMDA only allows vertex based
>>>     information in Vecs. Since DMPLEX allows any kind of distribution,
>>> when we output VTK we need to determine
>>>     what kind of vector we have, vertex-based or cell-based. Here I
>>> cannot determine it, probably because your
>>>     PetscSection is not setup correctly. How is data supposed to be laid
>>> out on the Plex?
>>>
>>>   Thanks,
>>>
>>>      Matt
>>>
>>>
>>>>   PetscViewerCreate(PETSC_COMM_WORLD, &viewer);
>>>>   PetscViewerVTKOpen(PETSC_COMM_WORLD, "vtk_output_test.vtk",
>>>> FILE_MODE_WRITE, &viewer);
>>>>   DMCreateGlobalVector(dm, &x);
>>>>   VecSetValue();   //Set value for x
>>>>   VecView(x, viewer);
>>>>
>>>> Here is the error output:
>>>> [0]PETSC ERROR: --------------------- Error Message
>>>> --------------------------------------------------------------
>>>> [0]PETSC ERROR: Argument out of range
>>>> [0]PETSC ERROR: Out of range index value 1 maximum 0
>>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>>>> for trouble shooting.
>>>> [0]PETSC ERROR: Petsc Release Version 3.10.2, unknown
>>>> [0]PETSC ERROR: ./test3 on a arch-linux2-c-debug named barry-PhysioMech
>>>> by barry Mon Dec 10 05:52:19 2018
>>>> [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
>>>> --with-fc=gfortran --download-mpich --download-fblaslapack --download-mumps
>>>> --download-scalapack --download-ctetgen
>>>> [0]PETSC ERROR: #3 VecSetValues_Seq() line 726 in
>>>> /home/barry/petsc/src/vec/vec/impls/seq/bvec2.c
>>>> [0]PETSC ERROR: #4 VecSetValues() line 856 in
>>>> /home/barry/petsc/src/vec/vec/interface/rvector.c
>>>>
>>>> [0]PETSC ERROR: --------------------- Error Message
>>>> --------------------------------------------------------------
>>>> [0]PETSC ERROR: Invalid argument
>>>> [0]PETSC ERROR: Could not classify input Vec for VTK
>>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>>>> for trouble shooting.
>>>> [0]PETSC ERROR: Petsc Release Version 3.10.2, unknown
>>>> [0]PETSC ERROR: ./test3 on a arch-linux2-c-debug named barry-PhysioMech
>>>> by barry Mon Dec 10 05:52:19 2018
>>>> [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
>>>> --with-fc=gfortran --download-mpich --download-fblaslapack --download-mumps
>>>> --download-scalapack --download-ctetgen
>>>> [0]PETSC ERROR: #17 DMPlexGetFieldType_Internal() line 134 in
>>>> /home/barry/petsc/src/dm/impls/plex/plex.c
>>>> [0]PETSC ERROR: #18 VecView_Plex_Local_VTK() line 294 in
>>>> /home/barry/petsc/src/dm/impls/plex/plex.c
>>>> [0]PETSC ERROR: #19 VecView_Plex_Local() line 335 in
>>>> /home/barry/petsc/src/dm/impls/plex/plex.c
>>>> [0]PETSC ERROR: #20 VecView_Plex() line 382 in
>>>> /home/barry/petsc/src/dm/impls/plex/plex.c
>>>> [0]PETSC ERROR: #21 VecView() line 590 in
>>>> /home/barry/petsc/src/vec/vec/interface/vector.c
>>>>
>>>> I think the first part of the error comes from VecSetValue(), but I
>>>> don't know how to fix it.
>>>> And I totally don't know what its mean in the second part of the error.
>>>>
>>>> Thank you,
>>>> Barry
>>>>
>>>
>>>
>>> --
>>> What most experimenters take for granted before they begin their
>>> experiments is infinitely more interesting than any results to which their
>>> experiments lead.
>>> -- Norbert Wiener
>>>
>>> https://www.cse.buffalo.edu/~knepley/
>>> <http://www.cse.buffalo.edu/~knepley/>
>>>
>>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
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