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<div>Hi,</div>
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<div>I agree with Barry that since this will not mean any interface changes, it can be done with patch releases.</div>
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<div>Sounds like a plan</div>
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<div> </div>
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I still can’t figure out how to deal with cell sets of different types (say quads and tri).<br>
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<div>I have not tried this. I had been focusing getting higher order (Q2) and either quads or tris to work. This</div>
<div>all seems to be working correctly now. I have been using it to visualize/restart a magma dynamics app</div>
<div>with 3 fields all with different discretizations.</div>
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<div>Nice.</div>
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<div> </div>
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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).<br>
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<div>For restarting, mixed meshes should work fine. They are stored in</div>
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<div> /topology/cells</div>
<div> /cones</div>
<div> /order</div>
<div> /orientation</div>
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<div>and the field values are in</div>
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<div> /fields/<name></div>
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<div>For visualization and most post-processing, there are separate arrays</div>
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<div> /viz/topology</div>
<div> /geometry</div>
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<div>which are exactly what I needed to make Paraview understand the xdmf. The fields</div>
<div>sampled down to cells and vertices are in</div>
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<div> /vertex_fields/<name></div>
<div> /cell_fields/<name></div>
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<div>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?</div>
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The xdmf generation script bin/pythonscripts/petsc_gen_xdmf.py is quite fragile.<br>
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<div>I have not had it fail for me, but would be happy to look at the failure you are getting.</div>
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<div>Cool.</div>
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<div>I am attaching a very simple code that reads an exo file and saves it, and two simple exodus meshes.</div>
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<div>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]. </div>
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<div>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.</div>
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<div>If I do not interpolate the mesh in DMPlexCreateExodusFromFile, petsc_gen_xdmf.py fails.</div>
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<div>DMView fails in parallel. I must be doing something wrong.</div>
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<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: Argument out of range</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: Point 8 has 0 constraints > -3 dof</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html">
http://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: Petsc Development GIT revision: v3.4.4-4444-g8c25fe2 GIT Date: 2014-06-07 16:01:56 -0500</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: ./testHDF5Plex on a Darwin-intel14.0-g named iMac.local by blaise Mon Jun 9 22:14:29 2014</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[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</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: #1 DMCreateDefaultSF() line 3065 in /opt/HPC/petsc-dev/src/dm/interface/dm.c</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: #2 DMGetDefaultSF() line 2985 in /opt/HPC/petsc-dev/src/dm/interface/dm.c</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: #3 DMLocalToGlobalBegin() line 1737 in /opt/HPC/petsc-dev/src/dm/interface/dm.c</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: #4 VecView_Plex_Local_HDF5() line 122 in /opt/HPC/petsc-dev/src/dm/impls/plex/plexhdf5.c</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: #5 VecView_Plex_Local() line 86 in /opt/HPC/petsc-dev/src/dm/impls/plex/plex.c</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: #6 VecView() line 601 in /opt/HPC/petsc-dev/src/vec/vec/interface/vector.c</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: #7 DMPlexWriteCoordinates_HDF5_Static() line 396 in /opt/HPC/petsc-dev/src/dm/impls/plex/plexhdf5.c</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: #8 DMPlexView_HDF5() line 485 in /opt/HPC/petsc-dev/src/dm/impls/plex/plexhdf5.c</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: #9 DMView_Plex() line 450 in /opt/HPC/petsc-dev/src/dm/impls/plex/plex.c</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: #10 DMView() line 648 in /opt/HPC/petsc-dev/src/dm/interface/dm.c</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: #11 main() line 79 in /Users/blaise/Development/DMComplex/testHDF5Plex.c</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: ----------------End of Error Message -------send entire error message to
<a href="mailto:petsc-maint@mcs.anl.gov">petsc-maint@mcs.anl.gov</a>----------</div>
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<div>Finally, DMView fails with the mixed element type mesh with the following error message:</div>
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<div style="margin: 0px; font-family: 'Source Code Pro';">Writing to TwoSquaresMixed_seq.h5</div>
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<b>[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</b></div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: No support for this operation for this object type</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: Visualization topology currently only supports identical cell shapes</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html">
http://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: Petsc Development GIT revision: v3.4.4-4444-g8c25fe2 GIT Date: 2014-06-07 16:01:56 -0500</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: ./testHDF5Plex on a Darwin-intel14.0-g named iMac.local by blaise Mon Jun 9 22:11:48 2014</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[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</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: #1 DMPlexWriteTopology_Vertices_HDF5_Static() line 322 in /opt/HPC/petsc-dev/src/dm/impls/plex/plexhdf5.c</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: #2 DMPlexView_HDF5() line 488 in /opt/HPC/petsc-dev/src/dm/impls/plex/plexhdf5.c</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: #3 DMView_Plex() line 450 in /opt/HPC/petsc-dev/src/dm/impls/plex/plex.c</div>
<div style="margin: 0px; font-family: 'Source Code Pro';">[0]PETSC ERROR: #4 main() line 59 in /Users/blaise/Development/DMComplex/testHDF5Plex.c</div>
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<b>[0]PETSC ERROR: ----------------End of Error Message -------send entire error message to
<a href="mailto:petsc-maint@mcs.anl.gov">petsc-maint@mcs.anl.gov</a>----------</b></div>
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