[petsc-users] binary vtk viewer DMDA

[Jed Brown]

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

>
> On Wed, Jan 9, 2013 at 10:10 AM, Blaise A Bourdin <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.


>
>   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>
>>  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> 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, Fax  +1 (225) 578 4276
>>> 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, Fax  +1 (225) 578 4276
>> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20130109/58fcd9dc/attachment-0001.html>