[petsc-dev] getting ready for PETSc release

Matthew Knepley knepley at gmail.com
Tue Jun 10 09:50:23 CDT 2014 

On Mon, Jun 9, 2014 at 10:16 PM, Blaise A Bourdin <bourdin at lsu.edu> wrote:

>  Hi,
>
>    I agree with Barry that since this will not mean any interface
> changes, it can be done with patch releases.
>
>
>  Sounds like a plan
>
>
>
>>
>> I still can’t figure out how to deal with cell sets of different types
>> (say quads and tri).
>>
>
>  I have not tried this. I had been focusing getting higher order (Q2) and
> either quads or tris to work. This
> all seems to be working correctly now. I have been using it to
> visualize/restart a magma dynamics app
> with 3 fields all with different discretizations.
>
>
>  Nice.
>
>
>
>> All cell and vertex sets seem to be contained in the hdf5 file, but not
>> in a way that is usable by post processing tools (visit, paraview, ensight).
>>
>
>  For restarting, mixed meshes should work fine. They are stored in
>
>    /topology/cells
>                    /cones
>                    /order
>                    /orientation
>
>  and the field values are in
>
>    /fields/<name>
>
>
>  For visualization and most post-processing, there are separate arrays
>
>    /viz/topology
>         /geometry
>
>  which are exactly what I needed to make Paraview understand the xdmf.
> The fields
> sampled down to cells and vertices are in
>
>    /vertex_fields/<name>
>   /cell_fields/<name>
>
>
>  I saw that. Does it mean that all heavy data is duplicated in the hdf5
> file, i.e. that /fields contains values that petsc understands and /viz is
> for visualization?
>

Yes, this is controlled by the viewer format. I saw no way to get xmf to
look at scattered data, so duplication was inevitable.

>
>
>> The xdmf generation script bin/pythonscripts/petsc_gen_xdmf.py is quite
>> fragile.
>>
>
>  I have not had it fail for me, but would be happy to look at the failure
> you are getting.
>
>
>  Cool.
>
>  I am attaching a very simple code that reads an exo file and saves it,
> and two simple exodus meshes.
>

I have attached a cleaned up version.


> The xmf generation script fails on it, most likely because I don’t have a
> /time section in the file. My workaround is to replace l. 209 with time =
> [0,1].
>

The xmf script works on it now.


> When I read the xmf file in visit, I see only one cell set. In paraview, I
> see two blocks “domain” and “domain[1]", both of which contain the entire
> mesh.
>

The labels marking these sets are in the .h5 file, but I am not sure what
you want in the xmf. Can you show me
a simple example. Right now, I am using the xmf generation from PyLith.


> If I do not interpolate the mesh in DMPlexCreateExodusFromFile,
> petsc_gen_xdmf.py fails.
>

I just ran it and it worked here. See below.


> DMView fails in parallel. I must be doing something wrong.
>

There was a bug (overaggressive check) that caused this, but it has been
fixed. Are you using 'next'?


>  [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Argument out of range
> [0]PETSC ERROR: Point 8 has 0 constraints > -3 dof
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.4.4-4444-g8c25fe2  GIT
> Date: 2014-06-07 16:01:56 -0500
> [0]PETSC ERROR: ./testHDF5Plex on a Darwin-intel14.0-g named iMac.local by
> blaise Mon Jun  9 22:14:29 2014
> [0]PETSC ERROR: Configure options CFLAGS= CXXFLAGS= LDFLAGS=-Wl,-no_pie
> --download-chaco=1 --download-exodusii=1 --download-hdf5=1
> --download-metis=1 --download-netcdf=1 --download-parmetis=1
> --download-sowing=1 --download-triangle=1 --download-yaml=1
> --with-blas-lapack-dir=/opt/intel/composerxe/mkl --with-cmake=cmake
> --with-debugging=1 --with-mpi-dir=/opt/HPC/mpich-3.0.4-intel14.0 --with-pic
> --with-shared-libraries=1 --with-vendor-compilers=intel --with-x11=1
> [0]PETSC ERROR: #1 DMCreateDefaultSF() line 3065 in
> /opt/HPC/petsc-dev/src/dm/interface/dm.c
> [0]PETSC ERROR: #2 DMGetDefaultSF() line 2985 in
> /opt/HPC/petsc-dev/src/dm/interface/dm.c
> [0]PETSC ERROR: #3 DMLocalToGlobalBegin() line 1737 in
> /opt/HPC/petsc-dev/src/dm/interface/dm.c
> [0]PETSC ERROR: #4 VecView_Plex_Local_HDF5() line 122 in
> /opt/HPC/petsc-dev/src/dm/impls/plex/plexhdf5.c
> [0]PETSC ERROR: #5 VecView_Plex_Local() line 86 in
> /opt/HPC/petsc-dev/src/dm/impls/plex/plex.c
> [0]PETSC ERROR: #6 VecView() line 601 in
> /opt/HPC/petsc-dev/src/vec/vec/interface/vector.c
> [0]PETSC ERROR: #7 DMPlexWriteCoordinates_HDF5_Static() line 396 in
> /opt/HPC/petsc-dev/src/dm/impls/plex/plexhdf5.c
> [0]PETSC ERROR: #8 DMPlexView_HDF5() line 485 in
> /opt/HPC/petsc-dev/src/dm/impls/plex/plexhdf5.c
> [0]PETSC ERROR: #9 DMView_Plex() line 450 in
> /opt/HPC/petsc-dev/src/dm/impls/plex/plex.c
> [0]PETSC ERROR: #10 DMView() line 648 in
> /opt/HPC/petsc-dev/src/dm/interface/dm.c
> [0]PETSC ERROR: #11 main() line 79 in
> /Users/blaise/Development/DMComplex/testHDF5Plex.c
> [0]PETSC ERROR: ----------------End of Error Message -------send entire
> error message to petsc-maint at mcs.anl.gov----------
>
>
>  Finally, DMView fails with the mixed element type mesh with the
> following error message:
>  Writing to TwoSquaresMixed_seq.h5
>  *[0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------*
> [0]PETSC ERROR: No support for this operation for this object type
> [0]PETSC ERROR: Visualization topology currently only supports identical
> cell shapes
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Development GIT revision: v3.4.4-4444-g8c25fe2  GIT
> Date: 2014-06-07 16:01:56 -0500
> [0]PETSC ERROR: ./testHDF5Plex on a Darwin-intel14.0-g named iMac.local by
> blaise Mon Jun  9 22:11:48 2014
> [0]PETSC ERROR: Configure options CFLAGS= CXXFLAGS= LDFLAGS=-Wl,-no_pie
> --download-chaco=1 --download-exodusii=1 --download-hdf5=1
> --download-metis=1 --download-netcdf=1 --download-parmetis=1
> --download-sowing=1 --download-triangle=1 --download-yaml=1
> --with-blas-lapack-dir=/opt/intel/composerxe/mkl --with-cmake=cmake
> --with-debugging=1 --with-mpi-dir=/opt/HPC/mpich-3.0.4-intel14.0 --with-pic
> --with-shared-libraries=1 --with-vendor-compilers=intel --with-x11=1
> [0]PETSC ERROR: #1 DMPlexWriteTopology_Vertices_HDF5_Static() line 322 in
> /opt/HPC/petsc-dev/src/dm/impls/plex/plexhdf5.c
> [0]PETSC ERROR: #2 DMPlexView_HDF5() line 488 in
> /opt/HPC/petsc-dev/src/dm/impls/plex/plexhdf5.c
> [0]PETSC ERROR: #3 DMView_Plex() line 450 in
> /opt/HPC/petsc-dev/src/dm/impls/plex/plex.c
> [0]PETSC ERROR: #4 main() line 59 in
> /Users/blaise/Development/DMComplex/testHDF5Plex.c
>  *[0]PETSC ERROR: ----------------End of Error Message -------send entire
> error message to petsc-maint at mcs.anl.gov
> <petsc-maint at mcs.anl.gov>----------*
>

I need to understand how xmf treats these mixes meshes. This is where help
would be useful.
The checkpointing works with them however.

  Thanks,

     Matt

-- 
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
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