[petsc-users] object name overwritten in VecView

[Matthew Knepley]

On Wed, Feb 28, 2018 at 11:59 AM, Danyang Su <danyang.su at gmail.com> wrote:

> Hi Barry and Matt,
>
> Thanks for your quick response. Considering the output performance, as
> well as the long-term plan of PETSc development, which format would you
> suggest? I personally prefer the data format that can be post-processed by
> Paraview as our sequential code (written without PETSc) is also using
> Paraview compatible data format. XDMF sounds promising as suggested by Matt.
>
I definitely suggest the HDF5+XDMF route.

  Thanks,

    Matt


> Thanks,
>
> Danyang
> On 18-02-28 08:17 AM, Smith, Barry F. wrote:
>
>
>   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>
> <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>
> <knepley at gmail.com> wrote:
> > On Wed, Feb 28, 2018 at 12:39 AM, Smith, Barry F. <bsmith at mcs.anl.gov>
> <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>
> <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.
>
>
>


-- 
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.caam.rice.edu/~mk51/>
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