Merge remote-tracking branch 'origin/release' into master

Merge branch 'stefanozampini/fix-gamg-transposegencuda' into 'release'

Fix CUDA performance regression and KOKKOS bugfixes

See merge request petsc/petsc!3310

DMPlex: fix VecGetSubVector input

Merge branch 'knepley/fix-plex-exodus-surfaces' into 'master'

Knepley/fix plex exodus surfaces

See merge request petsc/petsc!2997

Plex+Exodus: Fix input
- Can have meshes with different embedding dimension
- Fixed handling of prisms
- Now read the cell type

Merge branch 'stefanozampini/feature-plexrefiner-boundarylayer' into 'master'

feature plexrefiner boundarylayer

See merge request petsc/petsc!2881

DMPlexExodus: use DMPlexInvertCell

Merge branch 'knepley/feature-dm-remove-hybrid' into 'master'

Knepley/feature dm remove hybrid

See merge request petsc/petsc!2614

DM+Plex: Removed the idea of hybrid and ghost cells, in favor of cell type
- Improved Plex tests to work for other cell types
- Plex creation, interpolation, submesh, and refinement routines now set

DM+Plex: Removed the idea of hybrid and ghost cells, in favor of cell type
- Improved Plex tests to work for other cell types
- Plex creation, interpolation, submesh, and refinement routines now set the cell type
- Distribution sorts strata by cell type
- Fixed orientation of prisms from input formats
- Added Plex ex40 to test regular refinement
- CellRefiner is a PetscObject
- dm_plex_cell_refiner chooses the refinement strategy
- Removed SimplexToTensor stuff in favor of ToHex refiner
- Most functions take DMPolytopeType instead of CellRefiner
- CellRefinerInCellTest_Internal()
- CellRefinerGetAffineTransforms_Internal()
- CellRefinerGetAffineFaceTransforms_Internal()
- DMForest now responds to DMPlexGetOverlap() and propagates its overlap to the underlying Plex
- Use DMPlexComputeCellType_Internal() to classify a cell based only on topology
- Added DMPlexGetSimplexOrBoxCells() to replace DMPlexGetInteriorCellStratum()
- Added DM_POLYTOPE_POINT_PRISM_TENSOR
- Added DMPolytopTypeGetDim() and DMPolyTopeTypeGetConeSize()
- Added DMLabelSetStratumBounds()
- Added DMPlexSetCellType()
- Added celltypes to DMView()
- Added DMPolytopeTypeGetNumVertices()
- Added DMPlexCreateReferenceCellByType()
- Added DMPolytopeTypeFromGmsh()
- Made DMPlexRefineUniform() public

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Merge branch 'haplav/fix-plexexodusii' into 'master'

Fix wrong copy-paste in plexexodusii.c

See merge request petsc/petsc!2537

Fix wrong copy-paste in plexexodusii.c

Merge branch 'knepley/feature-plex-exodusii-viewer' into 'master'

Knepley/feature plex exodusii viewer

See merge request petsc/petsc!2535

Plex: Added ExodusII viewer

Merge branch 'maint'

Merge branch 'jolivet/fix-double-semicolons' into 'maint'

Double semicolons

See merge request petsc/petsc!2150

Double semicolons

Merge branch 'knepley/feature-plex-hybrid-input' [PR #1922]

* knepley/feature-plex-hybrid-input:
Plex+GMsh: Allow hybrid meshes where wedges match cells at wedge sides
Plex+ExodusII: Order hybrid ce

Merge branch 'knepley/feature-plex-hybrid-input' [PR #1922]

* knepley/feature-plex-hybrid-input:
Plex+GMsh: Allow hybrid meshes where wedges match cells at wedge sides
Plex+ExodusII: Order hybrid cells last, and set hybrid bounds in DM
Plex ex1: Added more wedge tests

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Plex+ExodusII: Order hybrid cells last, and set hybrid bounds in DM

Merge remote-tracking branch 'origin/barry/add-petscarrayxxx-ops' [PR #1771]

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*()

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*() with PetscArraymove()

Commit-type: style-fix, feature

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Merged in barry/update-collective-on (pull request #1744)

Update the use of Collective on in the manual pages to reflect the new style

Update the use of Collective on in the manual pages to reflect the new style

Commit-type: style-fix, documentation
Thanks-to: Patrick Sanan <patrick.sanan@gmail.com>

Merged in psanan/man-pages-remove-keywords (pull request #1717)

Man pages: Remove .keywords fields

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be unif

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be uniformly used or maintained.

Thus, remove all .keywords: fields, and a following blank line, if present.

This is accomplished with GNU sed (gsed on OS X), with the following commands.
*Warning* that this type of command can corrupt a .git directory,
so be cautious in reusing or modifying these commands. They first look
for and delete matching lines with a following line consisting of only whitespace,
and then delete any remaining matching lines.

find src/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find src/ -type f -exec gsed -i '/keywords:/d' {} +
find include/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find include/ -type f -exec gsed -i '/keywords:/d' {} +

Hints on the sed command obtained from: https://unix.stackexchange.com/questions/100754/how-to-delete-a-specific-line-and-the-following-blank-line-using-gnu-sed

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Merged petsc/petsc into master