Merge branch 'barry/2022-08-21/clang-format-source' into 'main'

format repository with clang-format

See merge request petsc/petsc!5541

clang-format: convert PETSc sources to comply with clang-format

Merge branch 'jed/makefile-dirs' into 'main'

makefile: add missing DIRS (squash gmakegen.py --verbose warnings)

See merge request petsc/petsc!4677

DM: rename pforest.c to pforest.h since it's used as a header

Merge branch 'jacobf/2021-11-24/cupmblasinterface' into 'main'

Feature: CUPMBLASInterface

See merge request petsc/petsc!4592

apply new preprocessor macros

Merge branch 'knepley/feature-orientation-rethink' into 'main'

Plex: Rethink Plex orientation

See merge request petsc/petsc!4218

DM: New idea for cell orientations
- Add DMPolytopeTypeGetNumArrangments()
- Add DMPolytopeTypeGetArrangment()
- Add DMPolytopeTypeGetVertexArrangment()
- Add DMPolytopeTypeComposeOrientation()
- Add

DM: New idea for cell orientations
- Add DMPolytopeTypeGetNumArrangments()
- Add DMPolytopeTypeGetArrangment()
- Add DMPolytopeTypeGetVertexArrangment()
- Add DMPolytopeTypeComposeOrientation()
- Add DMPolytopeTypeComposeOrientationInv()
- Add DMPolytopeGetOrientation()
- Add DMPolytopeGetVertexOrientation()
- Inversion now uses just negation instead of face size
- Remove DMPlexOrientCell(), DMPlexReverseCell(), DMPlexCompareOrientations()
- Add DMPlexOrientPoint()
- Add MPIU_4INT and MPI_4INT
- Rewrote transitive closure
- DMPlexGetTransitiveClosure_Depth1_Static() now correctly handles ornt
- PetscDualSpaceLagrange and PetscSection use the number of arragnements and not the cone size
- Update examples

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Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax error with error message
SNES ex5: Correct Jacobian handling on patches
SNES ex5: Stupid complex fixes
DMP4est: fix transfer of labels to parents
petsc4py: update to latest snapshot. Fixes da example breakage in petsc4py test suite
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logging in interpolator creation
Plex: Correct use of tabs in ASCII viewer
DM: Shorten long event name
Plex ex12: Create boundary label automatically at all levels of mesh hierarchy
Plex ex12: Change PetscViewerSetFormat --> PetscViewerPushFormat - Fix order of SetMode and SetFilename
Plex ex12: Change all functions to static
Since DMDA with periodic boundary conditions does support P0 interpolation remove checks that error out under those conditions
ascem-io.py and amanzi.py need to handle self.hdf5.include being None correctly
fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests also fix check for location of python shared library on mac to check all cases each time
Switch back to Sherry's version since she accepted by pull request
PetscDraw: Update help messages for -draw_save* options
...

Conflicts:
src/dm/impls/plex/plexfem.c

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Merged petsc/petsc into master

Merge branch 'mlange/fix-plex-multi-level-overlap'

* mlange/fix-plex-multi-level-overlap: (259 commits)
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelG

Merge branch 'mlange/fix-plex-multi-level-overlap'

* mlange/fix-plex-multi-level-overlap: (259 commits)
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelGather()
Plex ex12: Fixed variable initialization and some output
Plex ex11: Added error checking
Plex ex14: Now boundary label does not have cells
Plex ex1: Now boundary label does not have cells
Plex ex1: Fix for VTK format
added some debugging code, getting ready to branch
added some print statements, should be an -info...
smome cleaning up
restructured ex11 to allow for problem specific BCs
DMPlex: Update test ex12_5 with correct level-2 overlap
DMPlex: Use global processSF in DMPlexPartitionInvert
DMPlex: Add remote leaf contributions to roots in DMLabelPropagate
DMPlex: Add DMLabelGather to migrate label values from leafs to roots
DMPlex: Refactor DMLabelDistribute to separate point stratum distribution
DMPlex: Add propagation of remote point donations for multi-level overlap
DMPlex: Fix DMLabelDistribute for all-to-all migrations
Plex: make extern exactly match prototype: semantic match is not enough.
DMP4est: typo fix
...

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Merge branch 'tisaac/dmforest' into mlange/fix-plex-multi-level-overlap

Conflicts:
src/dm/impls/plex/examples/tests/output/ex12_5.out
src/dm/label/dmlabel.c

DMP4est: fix P4estFaceToPetscFace

Was not the inverse permutation of PetscFaceToP4estFace before, now it
is.

DMP4est: implement hierarchical transfer SFs

Each cell creates a list of the points in its closure that have dofs in
the scheme, and a PetscSFNode is created for each point in that closure.
Then, th

DMP4est: implement hierarchical transfer SFs

Each cell creates a list of the points in its closure that have dofs in
the scheme, and a PetscSFNode is created for each point in that closure.
Then, the coarse mesh is transfered to overlap the first, so that cell
overlap from fine to coarse can be determined. Then, in looping over
the closure lists of the fine cells, we can match fine points to their
containing coarse points, which allows construction of a point-transer
SF, which can then be expanded into a dof transfer SF.

WIP DMP4est: repartitioning coarse to match fine

WIP DMP4est: factor out coarse/fine overlap code

WIP DMP4est: finally on the right track with the transfer PetscSF

DMP4est: finished DMPforetGetCellCoveringSF

WIP DMP4est: use the covering cells to compute the transfer SF

DMP4est: first completion of DMPforestGetTransferSF()

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DMForest: bring in p4est to plex convertino from p4est library

I think we still need to set up labels on the p4est side and transfer
them to the plex.

DMForest: p4est: make DMConvert lazily convert until the output is set up.

DMForet: First completion of DMPlexCreateConnectivity_{p4est,p8est}

Some information is lost in converting to p4est format: facets are
explicity enumerated in p4est's coarse mesh format.

I plan on

DMForet: First completion of DMPlexCreateConnectivity_{p4est,p8est}

Some information is lost in converting to p4est format: facets are
explicity enumerated in p4est's coarse mesh format.

I plan on writing the following two tests:

plex -> p4est (A) -> plex -> p4est (B), assert A ~ B
p4est -> plex (A) -> p4est -> plex (B), assert A ~ B

I think the type of equivalence that can be achieved is cone/orientation
equality, but supports may be permuted.

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WIP: p4est: DMPlex conversion

This orientation change seems right to me.

In DMPlex, there is an independent facet betweeen faces

+--+ | +--+
|A | | |B |
+--+ | +--+

And A and B each h

WIP: p4est: DMPlex conversion

This orientation change seems right to me.

In DMPlex, there is an independent facet betweeen faces

+--+ | +--+
|A | | |B |
+--+ | +--+

And A and B each have their orientation relative to each other in plex
conventions, orientA and orientB.

But, each quad/hex has numbering and orientations in p4est conventions,
and there is a conversion tranformation P that takes a facet in p4est
numbering and gives the permutation converts p4est cone numbering to
petsc cone numbering. We can compose these to get the permutation from
p4est cone numbering to the independent facet cone numbering, i.e.,
pA = orientA * P[k_A] and pB = orientB * P[k_B]. Then to get the p4est
cone numbering of k_B relative to k_A, we need pB^{-1} * pA. BUT, p4est
doesn't number cones, it numbers vertices, so we have to do a minor
conversion from cones to vertices, and then we get what we want.

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WIP: convert DMPlex to p4est

I have to convert dmplex orientations to p4est orientations.

DMForest: proper include files so CMake can determine dependencies

DMForest: test registering DMP4EST and DMP8EST