DMPlex: Guard for empty submesh in parallel during subSF creation

DMPlex: Make DMPlexCreateCohesiveSubmesh_Interpolated() also create PetscSF

DMPlex: Fix compiler warning in submesh creation

Merge branch 'barry/minor-draw-improvements' into jed/chem

DMPlex: Fixed hybrid cell creation in 3D with internal boundaries
- Fixed the support of hybrid edges introduced by unsplit vertices
- Look for unsplit vertices on a split edge
- Allow unsplit edges

DMPlex: Fixed hybrid cell creation in 3D with internal boundaries
- Fixed the support of hybrid edges introduced by unsplit vertices
- Look for unsplit vertices on a split edge
- Allow unsplit edges on a hybrid face
- Fixed labeling to split some edges on boundary split faces

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DMPlex: Small doc fix for DMPlexConstructCohesiveCells()

DMPlex: Protect another instance of empty IS

DMPlex: Protect submesh selection when some procs have empty labels

DMPlex: Turn off check for cells bordering a cohesive face
- In parallel, the negative side cell for a cohesive face can be on another process
- We might want to consider communicating these

Merge branch 'knepley/fix-plex-geometry-hex'

* knepley/fix-plex-geometry-hex:
DMPlex: If “vtk” label has no cells, do not use it
DMPlex: DMPlexCreateCohesiveSubmesh() must also extract orientati

Merge branch 'knepley/fix-plex-geometry-hex'

* knepley/fix-plex-geometry-hex:
DMPlex: If “vtk” label has no cells, do not use it
DMPlex: DMPlexCreateCohesiveSubmesh() must also extract orientations
DMPlex: Add 1D code for DMPlexCheckSkeleton()
DMPlex: Cleanup code for VTK output - Removed diagnostic print - Use DMLabel interface
DMPlex: Change geometry check to support interpolated meshes - This all has to be replaced anyway

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Merge branch 'master' into knepley/feature-dmda-section

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fi

Merge branch 'master' into knepley/feature-dmda-section

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fix for TSGetRHSMats_Private() in the creation of the Arhs and Brhs matrices
protect logging of objects (which uses global variables) with PETSC_USE_LOG
error handler API had been previously changed but this example was not updated to new API.
DMPlex: Fixed bug in coordinate permutation
PetscSection: Doc fix for permutation
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bugfix of MatCreateSeqAIJFromTriple() contributed by Nicolas Marsic <nicolas.marsic@montefiore.ulg.ac.be>
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
completed removing server code that was not removed in previous commit
removed PETSc webserver and configure package files that supported it
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
fix outdated PetscOptionsList
SNESQN: only monitor real part of dot product (fails with C++ complex)
Fix for multiple definitions in mat/color/interface/ custom fortran bindings
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/da/dageometry.c
src/dm/impls/plex/examples/tests/ex4.c
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexinterpolate.c

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DMPlex: DMPlexCreateCohesiveSubmesh() must also extract orientations

Merge branch 'master' into knepley/feature-fem-dgspace

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key

Merge branch 'master' into knepley/feature-fem-dgspace

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
SNESQN: only monitor real part of dot product (fails with C++ complex)
Corrected the #include statement in the man pages for the PetscObjectComposedDataSet/Getwhatever routines.
DMPlex: Added doc for DMPlexGetHybridBounds()
winzip: detect if winzip is used to extract petsc.tar.gz and error out.
configure: remove self.archIndependent as its not being used. [it is used to create externalpackages/package/arch dir which is unused]
configure: fix packages using package-dir/PETSC_ARCH as out-of-source-build location Perhaps this should be changed to package-dir/build?
configure: remove dead code previously used to download BuildSystem
configure: check if compilerDefines [and compilerFixes] exist in framework before using them
configure: save/restore reconfigure.py when --with-clean is used
configure: add --with-clean option to delete buildfiles/externalpackages in PETSC_DIR/PETSC_ARCH and potential externalpackages in --with-external-package-dir/PETSC_ARCH
configure: With --with-externalpackages-dir=dir store/build packages in dir/PETSC_ARCH
Add MatSeqSBAIJSetPreallocationCSR()
configure: switch to using PETSC_DIR/PETSC_ARCH/externalpackages by updating package.py to use externalpackages.py as the externalPackagesDirProvider
configure: move dead code configureExternalPackagesDir() from petscdir.py to externalpackagesdir.py Also set PETSC_DIR/PETSC_ARCH/externalpackages as the externalpackagesdir
...

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DMPlex: Fix setting of hybrid bounds for multiple faults

Merge branch 'master' into barry/saws

Conflicts:
src/ksp/pc/impls/gamg/gamg.c
src/sys/classes/viewer/impls/ams/ams.c
src/sys/objects/pinit.c

Merge branch 'knepley/feature-plex-refine-3d'

* knepley/feature-plex-refine-3d: (96 commits)
DMPlex: Fix label creation for 3D simplicial refinement
DMPlex ex4: Added another 2D simplex hybrid t

Merge branch 'knepley/feature-plex-refine-3d'

* knepley/feature-plex-refine-3d: (96 commits)
DMPlex: Fix label creation for 3D simplicial refinement
DMPlex ex4: Added another 2D simplex hybrid test
DMPlex ex4: Reworked 2D simplex hybrid test
DMPlex: Fixed bug for label creation in hex refinement
DMPlex: Fixed compiler warnings
DMPlex: Fix uniform refinement for empty mesh
DMPlex: Fixed creation of hybrid submesh - No more Lagrange flag, just check for proper prism hybrid cells
DMPlex ex5: Added test output for 2D quad test with fault ending in the domain
DMPlex: Major fix for hybrid cell creation - Faults that ended in the domain created inconsistent meshes - I now add a cohesive cell at the edge of a fault which may have some pieces "unsplit" - Unsplit points are connected by hybrid points, but are not replicated - This has only been tested in 2D
DMPlex: Fix bug with multiple point labels for cohesive completion
DMPlex: Allow an increase in support size for split points in hybrid construction
DMPlex: Fixed compiler warning
DMPlex ex5: Added a new quad test - Its broken for a good reason, need to deal with fault boundaries
DMPlex ex5: Added test output
DMPlex ex4 and ex5: Added new hexahedral test
DMPlex: Streamlined marking of points along a fault - Changed iteration strategy - Added comments
DMPlex ex4: Added hybrid hex tests
DMPlex ex4: Added test with 6 tets
DMPlex ex4: Now check initial mesh for consistency
DMPlex: Fix bug with DMPlexLabelCohesiveComplete() - Must mark point with correct dimension
...

Conflicts:
include/petscdmplex.h
src/dm/impls/plex/makefile
src/dm/impls/plex/plexinterpolate.c

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Merge branch 'knepley/fix-plex-ghost-cells'

* knepley/fix-plex-ghost-cells:
DMLabel: Fixed index for ranges with nonzero lower limit
DMPlex: Fixed DMPlexConstructGhostCells() to filter out non-f

Merge branch 'knepley/fix-plex-ghost-cells'

* knepley/fix-plex-ghost-cells:
DMLabel: Fixed index for ranges with nonzero lower limit
DMPlex: Fixed DMPlexConstructGhostCells() to filter out non-faces from the label
DMPlex: Added DMLabelFilter()

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DMPlex: Fixed compiler warnings

DMPlex: Fixed creation of hybrid submesh
- No more Lagrange flag, just check for proper prism hybrid cells

DMPlex: Major fix for hybrid cell creation
- Faults that ended in the domain created inconsistent meshes
- I now add a cohesive cell at the edge of a fault which may have some pieces "unsplit"
- Unsp

DMPlex: Major fix for hybrid cell creation
- Faults that ended in the domain created inconsistent meshes
- I now add a cohesive cell at the edge of a fault which may have some pieces "unsplit"
- Unsplit points are connected by hybrid points, but are not replicated
- This has only been tested in 2D

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Merge branch 'master' into prbrune/fas-gscolorsecant

There was a build error in master when I last merged.

DMPlex: Fixed DMPlexConstructGhostCells() to filter out non-faces from the label

DMPlex: Fix bug with multiple point labels for cohesive completion

DMPlex: Allow an increase in support size for split points in hybrid construction

DMPlex: Streamlined marking of points along a fault
- Changed iteration strategy
- Added comments