[petsc-users] object name overwritten in VecView

[Smith, Barry F.]

  It turns out the fix is really easy. Here is a patch.

  Apply it with

    patch -p1 < barry-vtk.patch

  then do

    make gnumake

  all in $PETSC_DIR



> On Feb 28, 2018, at 9:07 AM, Danyang Su <danyang.su at gmail.com> wrote:
>
> Hi Matt，
>
> Thanks for your suggestion and I will use xmf instead.
>
> Regards,
>
> Danyang
>
> On February 28, 2018 3:58:08 AM PST, Matthew Knepley <knepley at gmail.com> wrote:
> On Wed, Feb 28, 2018 at 12:39 AM, Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
>
>   Matt,
>
>   I have confirmed this is reproducible and a bug. The problem arises because
>
> frame #0: 0x000000010140625a libpetsc.3.8.dylib`PetscViewerVTKAddField_VTK(viewer=0x00007fe66760c750, dm=0x00007fe668810820, PetscViewerVTKWriteFunction=(libpetsc.3.8.dylib`DMPlexVTKWriteAll at plexvtk.c:633), fieldtype=PETSC_VTK_POINT_FIELD, vec=0x00007fe66880ee20) at vtkv.c:140
>     frame #1: 0x0000000101404e6e libpetsc.3.8.dylib`PetscViewerVTKAddField(viewer=0x00007fe66760c750, dm=0x00007fe668810820, PetscViewerVTKWriteFunction=(libpetsc.3.8.dylib`DMPlexVTKWriteAll at plexvtk.c:633), fieldtype=PETSC_VTK_POINT_FIELD, vec=0x00007fe66880ee20) at vtkv.c:46
>     frame #2: 0x0000000101e0b7c3 libpetsc.3.8.dylib`VecView_Plex_Local(v=0x00007fe66880ee20, viewer=0x00007fe66760c750) at plex.c:301
>     frame #3: 0x0000000101e0ead7 libpetsc.3.8.dylib`VecView_Plex(v=0x00007fe66880e820, viewer=0x00007fe66760c750) at plex.c:348
>
> keeps a linked list of vectors that are to be viewed and the vectors are the same Vec because they are obtained with DMGetLocalVector().
>
> The safest fix is to have PetscViewerVTKAddField_VTK() do a VecDuplicate() on the vector passed in and store that in the linked list instead of just storing a pointer to the passed in vector (which might and can be overwritten before all the linked vectors are actually stored).
>
> Danyang,
>
> Barry is right, and the bug can be fixed the way he says. However, this points out why VTK is bad format. I think a better choice is
> to use HDF5 and XDMF. For example, in my code now I always use
>
>   DMVIewFromOptions(dm, NULL, "-dm_view");
>
> and then later (perhaps several times)
>
>   VecViewFromOptions(u, NULL, "-u_vec_view")
>   VecViewFromOptions(v, NULL, "-v_vec_view")
>
> and then on the command line
>
>   -dm_view hdf5:test.h5 -u_vec_view hdf5:test.h5::append -v_vec_view hdf5:test.h5::append
>
> which produces a file
>
>   test.h5
>
> Then I run
>
>   $PETSC_DIR/bin/petsc_gen_xdmf.py test.h5
>
> which produces another file
>
>   test.xmf
>
> This can be loaded by Paraview for visualization.
>
>   Thanks,
>
>      Matt
>
>
>
>   Barry
>
>
>
> > On Feb 27, 2018, at 10:44 PM, Danyang Su <danyang.su at gmail.com> wrote:
> >
> > Hi All,
> >
> > How to set different object names when using multiple VecView? I try to use PetscObjectSetName with multiple output, but the object name is overwritten by the last one.
> >
> > As shown below, as well as the enclosed files as example, the vector name in sol.vtk is vec_v for both vector u and v.
> >
> >      call PetscViewerCreate(PETSC_COMM_WORLD, viewer, ierr);CHKERRA(ierr)
> >      call PetscViewerSetType(viewer, PETSCVIEWERVTK, ierr);CHKERRA(ierr)
> >      call PetscViewerPushFormat(viewer, PETSC_VIEWER_ASCII_VTK, ierr);CHKERRA(ierr)
> >      call PetscViewerFileSetName(viewer, 'sol.vtk', ierr);CHKERRA(ierr)
> >
> >      call PetscObjectSetName(u, 'vec_u', ierr);CHKERRA(ierr)
> >      call VecView(u, viewer, ierr);CHKERRA(ierr)
> >
> >      call PetscObjectSetName(v, 'vec_v', ierr);CHKERRA(ierr)
> >      call VecView(v, viewer, ierr);CHKERRA(ierr)
> >
> >      call PetscViewerDestroy(viewer, ierr);CHKERRA(ierr)
> >
> >      call DMRestoreGlobalVector(dm, u, ierr);CHKERRA(ierr)
> >      call DMRestoreGlobalVector(dm, v, ierr);CHKERRA(ierr)
> >
> > Thanks,
> >
> > Danyang
> >
> > <ex1f90.F90><makefile.txt><sol.vtk>
>
>
>
>
> --
> 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/
>
> --
> Sent from my Android device with K-9 Mail. Please excuse my brevity.

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