Merge branch 'master' into barry/reduce-dmsetup-da-memoryusage

Conflicts:
src/dm/examples/tests/ex15.c
src/dm/examples/tutorials/ex3.c
src/dm/impls/da/da2.c
src/dm/impls/da/da3.c

Merged master into barry/update-xxxviewfromoptions

Merge branch 'master' into barry/xcode

Merge branch 'barry/saws-push-header-body' into barry/saws-options

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

* knepley/feature-plex-hybrid-3d: (45 commits)
DMPlex ex5: Check faces on all meshes
DMPlex ex5: Fix consistency of original meshes - Fix orientatio

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

* knepley/feature-plex-hybrid-3d: (45 commits)
DMPlex ex5: Check faces on all meshes
DMPlex ex5: Fix consistency of original meshes - Fix orientations of tet meshes - Redo hex test to automatically interpolate - Replaced output
DMPlex ex5: Check original meshes for consistency
DMPlex: make non-namespaced CellRefiner functions static
DMPlex: Fix hybrid bounds in DMPlexCheckFaces()
DMPlex ex5: Now all test working - Two faults working correctly
DMPlex: Fix for hybrid meshes with multiple surfaces - Move the original hybrid cells to the end of the numbering, so that split+hybrid points are inserted as a block - Use DMPlexShiftPoint_Internal() uniformly
SNES ex4: Fix for DMCheckSkeleton()
DMPlex ex4: All non-hybrid refinement test pass (Fuck Yeah)
DMPlex: In tet refinement, fixed edge orientation in internal face
DMPlex ex4: Correct output after cross-tet edge orientation fix
DMPlex: In tet refinement, correct internal tet face orientations
DMPlex: In tet refinement, correct internal face cones
DMPlex: In tet refinement, correct check for cross-tet edge
DMPlex: Now DMPlexCheckFaces() also checks all subfaces
DMPlex: Added 1D stuff to DMPlexGetRawFaces_Internal()
DMPlex ex4: hex refinement now fixed
DMPlex: Fixed split face supports for tet refinement
DMPlex: Multiple refinement for hex now working - Fixed face orientations for hexes - Fixed split face orientations - Fixed split face supports - Fixed internal face orientations - Fixed internal edge supports
DMPlex: Added GetQuadEdgeInverse_Static() and GetQuadSubfaceInverse_Static() for refinement
...

Conflicts:
src/dm/impls/plex/examples/tests/ex4.c
src/dm/impls/plex/plexsubmesh.c

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Merge commit '58723a9' into knepley/feature-plex-hybrid-3d

* commit '58723a9':
DMPlex: Fix DMPlexCheckSkeleton() for submeshes
DMPlex ex5: Added second fault for quad test
DMPlex: Fix setting

Merge commit '58723a9' into knepley/feature-plex-hybrid-3d

* commit '58723a9':
DMPlex: Fix DMPlexCheckSkeleton() for submeshes
DMPlex ex5: Added second fault for quad test
DMPlex: Fix setting of hybrid bounds for multiple faults
DMPlex ex5: Turn on second fault in quad test
DMPlex: Removed compiler warnings
DMPlex ex5: Cleaned up 2D tensor tests to rely on interpolation
DMPlex ex5: Cleaned up 2D simplex tests to rely on interpolation

Conflicts:
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex4.c
src/dm/impls/plex/plexrefine.c

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DMPlex: Added Gmsh input

DMPlex: Added DMPlexCheckFaces() which checks the face closure against the cell closure
- Added DMPlexGetTransitiveClosure_Internal() which takes an initial orientation

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

DMDA+DMPlex: Fixed preallocation declarations

Merge branch 'knepley/fix-hash-scaling'

* knepley/fix-hash-scaling: (25 commits)
PetscSF: Register logging events
PetscSF: Added logging
DMPlex: Bug fix for interpolated adjacency formation

Merge branch 'knepley/fix-hash-scaling'

* knepley/fix-hash-scaling: (25 commits)
PetscSF: Register logging events
PetscSF: Added logging
DMPlex: Bug fix for interpolated adjacency formation
DMPlex: Fast adjacency graph construction for interpolated meshes
DMPlex: Fixed error in new events
DMPlex: More events for distribution
DMPlex: Fixed allocation bug in reordering
DMPlex: Fixed mismatched Malloc2 in reordering
DMLabel: Split Malloc3 into Malloc2 and Malloc
Hash+DMPlex: Changed PetscHashIPut() to eliminate pass-by-ref - Jed can sleep soundly tonight
DMPlex: Use PetscHashIHasKey() to check for membership
Hash; Added PetscHashIHasKey() - PetscHashIMap does not match the documentation
DMPlex: Added simple DMLabel test
DMPlex: Fix missing restore Reported-by: Jed Brown <jedbrown@mcs.anl.gov>
DMPlex: Use DMLabelDistribute() in DMPlexDistribute()
DMPlex: Use DMLabelGetStrautmBounds() in DMPlexGetDepth/HeightStratum()
DMPlex: Added DMLabelDistribute()
DMPlex: Added DMLabelGetStratumBounds()
DMPlex: Fixed quadratic behavior of DMLabel insert - Added hash table for each label value for insertion - Added arrayValid flag which says whether array data or hash table data is valid - Convert between representations using DMLabelMakeValid_Private() and DMLabelMakeInvalid_Private() - Split up allocation of stratumValues and stratumSize/Offsets - Most functions only use the array representation, but some can use both (should probably expand this with GetStratum) - Moved the DMLabelFIlter() function
Hash: Added PetscHashIPut() and PetscHashIDel() - Removed unused variable
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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: Fix DMPlexCheckSkeleton() for submeshes

DMPlex: Added DMLabelDistribute()

DMPlex: Added DMLabelGetStratumBounds()

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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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/feature-plex-reordering'

* knepley/feature-plex-reordering:
doc: update makefile with order.h -> ../../../include/petsc-private/matorderimpl.h rename
DMPlex: Fixed bug with

Merge branch 'knepley/feature-plex-reordering'

* knepley/feature-plex-reordering:
doc: update makefile with order.h -> ../../../include/petsc-private/matorderimpl.h rename
DMPlex: Fixed bug with DMPlexPermute - Fixed label permutation
DMPlex: Check whether default section exists to be reordered
DMPlex: Fixed compiler warning
DMPlex ex10: Fixed test output
DMPlex: Added missing declarations
DMPlex: Fixed misuse of PetscObjectSetName()
MatComputeBandwidth: use PetscInt instead of PetscMPIInt
Mat: Fixed declaration
Mat: Changed MatCalcBandwidth() to MatComputeBandwidth() - Added Fortran interface
DMPlex ex10: This tests reordering of meshes
DMPlex: Added DMPlexGetOrdering() and DMPlexPermute()
PetscSection: Added PetscSectionPermute()
DMLabel: Added DMLabelPermute()
DMPlex: Added DMPlexCreateDoublet()
DMPlex: Added DMPlexCopyLabels()
Mat: Added MatCalcBandwidth()
MatOrdering: Moved private header into petsc-private - Fix to pointer checks in sorder.c

Conflicts:
include/petscdmplex.h

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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: Added DMLabelFilter()

DM: Added DMGet/SetCoordinateSection()
- Removed obsolete DMPlexGetCoordinateSection()

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

* master: (397 commits)
PetscSynchronizedFGets: fix deadlock at EOF
Compiler: Fix warnings from MPI impls which do not initialize outputs

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

* master: (397 commits)
PetscSynchronizedFGets: fix deadlock at EOF
Compiler: Fix warnings from MPI impls which do not initialize outputs
Increase patchlevel to 3.4.3
SNES: Now work vectors come from the DM
SNES ex62: Remove code generation
SNES: Move setup involving snes->vec_sol from SNESSetUp() to SNESolve()
Compiler: Fix warnings from MPI impls which do not initialize outputs
DMPlex ex7: Added missing test output
SNES ex52: Removed old Jacobian stuff, and fixed call to DMPlexProjectFunction() - Fixed calls for new element handling
SNES ex12: Added a performance profiling mode
DMPlex ex8: Fixed leak
PetscSection: Must reset the section when changing the number of fields
DMPlex ex7: Fixed test output - Corrected orientations in interpolation
DMPlex ex1: Fixed test output - Uniform refinement for quads changed
DMPlex: Fix overagressive checks
PC: Removed support graph PC
configure: both downloadonWindows and worksonWindows refer to MS compilers. Also fix isWindows() -> isWindows(CC).
MatXAIJSetPreallocation: use array[] notation to help out Fortran
__float128: when blas/lapack is not found instruct using f2cblaslapack
Configure: Package.downloadonWindows is supposed to mean that Windows compilers work. not Cygwin - Also changed doc for Package.worksonWindows, which does refer to Cygwin
...

Conflicts:
src/dm/impls/da/dalocal.c

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DMPlex: Added DMPlexCreateHybridMesh()
- This was formerly done in a few steps by creating a submesh, making the label, and then constructing hybrid cells

Merge branch 'master' into prbrune/mat-matcolor

Conflicts:
src/snes/interface/snesj2.c