[petsc-users] binary vtk viewer DMDA

Wed Jan 9 15:36:49 CST 2013

On Jan 9, 2013, at 10:23 AM, Jed Brown <jedbrown at mcs.anl.gov<mailto:jedbrown at mcs.anl.gov>> wrote:

On Wed, Jan 9, 2013 at 10:20 AM, Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>> wrote:

On Wed, Jan 9, 2013 at 10:10 AM, Blaise A Bourdin <bourdin at lsu.edu<mailto:bourdin at lsu.edu>> wrote:
That's a good start indeed. Is there any way to save files defined on different DMDA (same grid but different number of dof). When I try to do that, I get the following error message:

Hmm, that would mean introducing a structural comparison rather than an identity.

Oh, good point. If someone implements a test for DM congruence, I can generalize the viewer.

Wouldn't it be trivial for a DMDA?
Blaise

  Matt

MacBook-Pro:VTK blaise$ ./TestVTK
[0]PETSC ERROR: --------------------- Error Message ------------------------------------
[0]PETSC ERROR: Arguments are incompatible!
[0]PETSC ERROR: Cannot write a field from more than one grid to the same VTK file!
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 5, unknown
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: ./TestVTK on a Darwin-gc named MacBook-Pro.local by blaise Wed Jan  9 10:09:37 2013
[0]PETSC ERROR: Libraries linked from /opt/HPC/petsc-3.3/Darwin-gcc4.2-mef90-g/lib
[0]PETSC ERROR: Configure run at Thu Jan  3 15:42:04 2013
[0]PETSC ERROR: Configure options --download-boost=1 --download-chaco=1 --download-exodusii=/opt/HPC/src/tarball/exodusii-5.22b.tgz --download-hdf5=1 --download-metis=1 --download-netcdf=1 --download-parmetis=1 --download-sowing=1 --download-triangle=1 --download-yaml=1 --with-clanguage=C++ --with-cmake=cmake --with-debugging=1 --with-fortran-datatypes --with-gnu-compilers=1 --with-mpi-dir=/opt/HPC/mpich2-1.4.1p1-gcc4.2 --with-pic --with-shared-libraries=1 --with-sieve --with-sieve-memory-logging --with-x11=1 PETSC_ARCH=Darwin-gcc4.2-mef90-g
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: PetscViewerVTKAddField_VTK() line 126 in /opt/HPC/petsc-3.3/src/sys/viewer/impls/vtk/vtkv.c
[0]PETSC ERROR: PetscViewerVTKAddField() line 32 in /opt/HPC/petsc-3.3/src/sys/viewer/impls/vtk/vtkv.c
[0]PETSC ERROR: VecView_MPI_DA() line 531 in /opt/HPC/petsc-3.3/src/dm/impls/da/gr2.c
[0]PETSC ERROR: VecView() line 776 in /opt/HPC/petsc-3.3/src/vec/vec/interface/vector.c
[0]PETSC ERROR: main() line 46 in TestVTK.c
application called MPI_Abort(MPI_COMM_WORLD, 75) - process 0
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 75) - process 0

Blaise

On Jan 9, 2013, at 9:51 AM, Jed Brown <jedbrown at mcs.anl.gov<mailto:jedbrown at mcs.anl.gov>>
 wrote:

None of that crazy "developer" nonsense is need for users. Just do this:

    PetscViewer viewer;
    /* file name extension sets format by default, see also PetscViewerSetFormat(viewer,PETSC_VIEWER_VTK_VTS) */
    ierr = PetscViewerVTKOpen(comm,"yourfile.vts",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
    ierr = VecView(X,viewer);CHKERRQ(ierr);
    ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);

When using TS, you can do -ts_monitor_draw_solution_vtk 'filename-%03D.vts' to save each time step to a numbered binary file (ready to animate in paraview or visit).

On Wed, Jan 9, 2013 at 9:37 AM, Blaise A Bourdin <bourdin at lsu.edu<mailto:bourdin at lsu.edu>> wrote:
Hi,

I am looking at the documentation and the examples looking for a simple illustration of how to use the new vtk binary viewers for structured data defined by a DMDA, but can't find any straightforward example. Is there a simple example that I am missing?

When I try
PetscViewerVTKAddField(VTKviewer,(PetscObject) dmda1,DMDAVTKWriteAll,PETSC_VTK_POINT_FIELD,(PetscObject) p);CHKERRQ(ierr);
I get a compilation time error:
TestVTK.c:53: error: ‘DMDAVTKWriteAll’ was not declared in this scope
indeed, DMDAVTKWriteAll is defined in a private header. Is this the way it is supposed to be?

Is the xml file describing the content of the binary files generated automatically or do I need to take care of it by myself?

I am using petsc-3.3, latest changeset.

Regards,
Blaise
--
Department of Mathematics and Center for Computation & Technology
Louisiana State University, Baton Rouge, LA 70803, USA
Tel. +1 (225) 578 1612<tel:%2B1%20%28225%29%20578%201612>, Fax  +1 (225) 578 4276<tel:%2B1%20%28225%29%20578%204276> http://www.math.lsu.edu/~bourdin

--
Department of Mathematics and Center for Computation & Technology
Louisiana State University, Baton Rouge, LA 70803, USA
Tel. +1 (225) 578 1612<tel:%2B1%20%28225%29%20578%201612>, Fax  +1 (225) 578 4276<tel:%2B1%20%28225%29%20578%204276> http://www.math.lsu.edu/~bourdin

--
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

--
Department of Mathematics and Center for Computation & Technology
Louisiana State University, Baton Rouge, LA 70803, USA
Tel. +1 (225) 578 1612, Fax  +1 (225) 578 4276 http://www.math.lsu.edu/~bourdin

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