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

[Matthew Knepley]

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/>
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