DMPlex: move DMPlexTransferVecTree() to public interface

Merge branch 'knepley/fix-dm-outputdm'

* knepley/fix-dm-outputdm:
Dammit
Plex: Remove DMPlexLoad() declaration
Plex: Fix package initializer in PlexPartitionCreate()
DM: Make check on DMGetO

Merge branch 'knepley/fix-dm-outputdm'

* knepley/fix-dm-outputdm:
Dammit
Plex: Remove DMPlexLoad() declaration
Plex: Fix package initializer in PlexPartitionCreate()
DM: Make check on DMGetOutputDM() collective

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Plex: Remove DMPlexLoad() declaration

Merge branch 'tisaac/dmp4est-fix-overlap'

This branch makes a lot of fixes that fix PetscFV and DMP4est for
parallel. At the root of the issues were discrepencies related to the
overlapping cells t

Merge branch 'tisaac/dmp4est-fix-overlap'

This branch makes a lot of fixes that fix PetscFV and DMP4est for
parallel. At the root of the issues were discrepencies related to the
overlapping cells that are currently required for finite volume
calculations.

* tisaac/dmp4est-fix-overlap: (23 commits)
TS tutorial ex11: make p4est example parallel
TS tutorial ex11: globalize maxspeed before cfl computation
DMPlexTransferVecTree_Inject(): sum child to parent contributions
DMP4est: do not cause error if overlap > 1 in serial run
TS tutorial ex11: fix memory leaks
DMPlexTSComputeRHSFunctionFVM: ADD_VALUES from locF to F instead of INSERT_VALUES
DMPlexComputeResidual_Internal: global/local function mismatch
DMPlexShiftLabels_Internal: not-a-ghost is indicated by -1, not 0
DMPlexComputeResidual_Internal(): do not add contributions of ghost cells
DMPlexTree: do proper vector assembly
DMPlexReconstructGradients_Internal(): clarify ternary operator terms
DMPlexConstructGhostCells_Internal(): correct error message communicator
DMPforestGetTransferSF_Point: only compute covers for owned quads
TS tutorial ex11: only read gradients from local vectors
DMPlex: fix point migration / hybrid point interaction
DMPlex: fix PetscPartitionerPartition() to deal with overlap
DMPlexComputeInterpolatorTree: fix loop variables from recent change
DMP4est: search _both_ directions of tree for match
DMP4est: update regression tests for parallel
DMP4est: remove unused cell sf loop
...

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DMPlex: fix PetscPartitionerPartition() to deal with overlap

It returned an IS that gave indices that had sf leaves filtered out, but the result is
used in DMPlexDistribute() as though the leaves ar

DMPlex: fix PetscPartitionerPartition() to deal with overlap

It returned an IS that gave indices that had sf leaves filtered out, but the result is
used in DMPlexDistribute() as though the leaves are present.

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DMPlex: fix PetscPartitionerPartition() to deal with overlap

It returned an IS that gave indices that had sf leaves filtered out, but the result is
used in DMPlexDistribute() as though the leaves ar

DMPlex: fix PetscPartitionerPartition() to deal with overlap

It returned an IS that gave indices that had sf leaves filtered out, but the result is
used in DMPlexDistribute() as though the leaves are present.

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Merge branch 'stefano_zampini/dmplex-matis-support-2'

Merge branch 'knepley/feature-plex-closure-reorder'

* knepley/feature-plex-closure-reorder:
IS+Plex: Changed interface to closure permutation to take an IS
IS+Plex: Changed interface to closure

Merge branch 'knepley/feature-plex-closure-reorder'

* knepley/feature-plex-closure-reorder:
IS+Plex: Changed interface to closure permutation to take an IS
IS+Plex: Changed interface to closure permutation to take an IS
Plex ex9: Can now test closure reordering - Also fixed some small bugs
Plex ex6: Example that shows how to set and retrieve values with the spectral element ordering
Plex: Allow closure permutation in PlexVecGet/SetClosure() - This supports spectral element ordering - This does not seem to introduce any performance degradation
Plex: Added DMPlexCreateSpectralClosurePermutation()
PetscSection: Added support for closure permutation - This supports entry in the spectral element ordering

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Plex: Added DMPlexCreateSpectralClosurePermutation()

Merge branch 'tisaac/ts-ex11-amr'

We now have an example (ts/examples/tutorials/ex11.c) where we can
use either DMPlex or DMP4est to handle adaptivity when time stepping.
We have tried to minimize t

Merge branch 'tisaac/ts-ex11-amr'

We now have an example (ts/examples/tutorials/ex11.c) where we can
use either DMPlex or DMP4est to handle adaptivity when time stepping.
We have tried to minimize the amount of code that is specialized to the
different DMs, and in the future more work can be done to improve this
interface.

* tisaac/ts-ex11-amr: (62 commits)
DMP4est: type fix
Plex: Fixes for analyzer
DMP4est: update snes ex12 regressions
DMPlex: fix parent/child interpolation with numFields > 0
DMP4est: also compute anyChange for uniformly refined/coarsened meshes
TS ex11: fix command line for AMR without computed gradients
TS ex11: remove gradient reconstruction from adaptivity requirements
DMPlexTree: some compilers want this var initialized
Plex: Changed Get/RestoreFaceFields() and Get/RestoreFaceGeometry() to return the number of active faces - This fixes a long-standing bad access in FV, although the values were never actually used.
DMPlexTS: removed unused variables
DMPlex/DMP4est: small fixes for next warnings and errors
SNES ex36 and ex52: These do not work anymore
DMPforestGetTransferSF_Point(): try to match parents
PetscViewerHDF5: destroy old file data if setting new filename
DMPlex + FV: remove leaky references in projection functions
Plex: Fixed incredibly stupid bug in Jacobian computation
PetscViewer HDF5: added get name method
DMPlexTree: do not skip out of child matrix loops early
PetscFV: correct field offsets when limiting gradients
DMP4estTree: ignore negative values when getting/setting vector values for transfer
...

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Merge branch 'knepley/feature-plex-projections'

* knepley/feature-plex-projections:
Plex: Expose projection routines

DMPlex: construct the correct l2gmap for MatIS using the subdomainSection (for local indexing) and the globalSection

Update ComputeJacobian to set the closure in the local matrix

Plex: Expose projection routines

Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary c

Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary commitid] - and dirname in tarball
Plex: Moved ReconstructGradients_Internal() and ApplyLimiter_Internal() to Plex from SNES
CUDA: Added external declaration for cuBLAS handle.
docs: fix reference to KSP_Create in parent commit
Add information on PETSC_EXTERN and PETSC_INTERN to developers manual
Plex: Symbol is shared between DM and SNES, so must be EXTERN
Plex: Remove unused variables
Configure: Fix check for spaces in PETSC_DIR
Plex: Updated examples to new DMPlexCreateBoxMesh()
sick of failure due to incorrect master branch
SNES ex12: Fixed unstructured GMG test
SNES ex12: Added another unstructured GMG test
petsc4py: use the snapshot with the fix for dmplex change
Examples that require Fortran to compile but were listed in tests that did not require Fortran
Plex ex19: Added DMSetFromOptions()
Plex: Store a flag indicating whether the boundary should change during remeshing - Set using -dm_plex_remesh_bd - Changed Remesh_Internal() signature
Always coarsen boundaries.
Plex: Fixed option name
Plex: Protect unused variables
...

Conflicts:
src/dm/impls/plex/makefile
src/snes/utils/dmplexsnes.c

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DMPlex: move FV methods out of DMPlexSNES and into their own file

DMPlex: cache FVM data

Merge branch 'pr478/knepley/feature-dmplex-adapt/master'

* pr478/knepley/feature-dmplex-adapt/master: (34 commits)
SNES ex12: Fixed unstructured GMG test
SNES ex12: Added another unstructured GM

Merge branch 'pr478/knepley/feature-dmplex-adapt/master'

* pr478/knepley/feature-dmplex-adapt/master: (34 commits)
SNES ex12: Fixed unstructured GMG test
SNES ex12: Added another unstructured GMG test
petsc4py: use the snapshot with the fix for dmplex change
Plex ex19: Added DMSetFromOptions()
Plex: Store a flag indicating whether the boundary should change during remeshing - Set using -dm_plex_remesh_bd - Changed Remesh_Internal() signature
Always coarsen boundaries.
Plex: Fixed option name
Plex: Protect unused variables
Plex: Fixes for c89
Plex: Fixes for complex
SNES ex12: Updated output for coarsening
Plex ex3: Updated output for coarsening
Plex ex19: Now working with refactored Adapt()
Plex: Refactored DMPlexAdapt() - Added DMPlexRemesh_Internal() - Use Remesh inside DMCoarsen_Plex() - Use Join() to set label on faces
Plex ex19: Simplified parallel construction of metric
Plex ex19: General cleanup
Plex: DMPlexCreateBoxMesh() now takes the number of faces
Add output files for tests
Fix previous memory fix
Fix memory problems
...

Conflicts:
config/BuildSystem/config/packages/petsc4py.py
config/builder.py

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Merge branch 'knepley/feature-parallel-mesh-load'

* knepley/feature-parallel-mesh-load:
Plex ex18: Small fixes - Use DMBOUNDARY_NONE correctly, document partition edges
Plex ex18: Added simplex

Merge branch 'knepley/feature-parallel-mesh-load'

* knepley/feature-parallel-mesh-load:
Plex ex18: Small fixes - Use DMBOUNDARY_NONE correctly, document partition edges
Plex ex18: Added simplex 3D tests
fix compile warnings
Plex: Removed unused variable
DMLabel: Fixed DMLabelGather() - The leaves are not compact, but rather follow the local numbering, so we need to allocate nroots space
Plex: Fix for parallel interpolation
Plex-ex18: Enabling 2D simplex tests with interpolation
Plex: Create pointSF for edge/facet points after interpolation
Plex-ex18: Add another test for 2D simplices on 3 ranks
Plex: Fix hash usage in DMPlexBuildFromCellList_Parallel_Private
Plex ex18: Added test for parallel mesh loads - Interpolation test is broken
Plex: Fixed static declaration of some functions
Plex: Added DMPlexCreateFromCellListParallel() - This directly creates a parallel mesh from pieces

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/mat/impls/aij/seq/mkl_pardiso/mkl_pardiso.c

Plex: DMPlexCreateBoxMesh() now takes the number of faces

Merge branch 'master' into barral/feature-dmplex-adapt

Merge branch 'knepley/fix-petscfe-kernels-ts'

* knepley/fix-petscfe-kernels-ts:
PetscFE+OpenCL: Fixed OpenCL residual eval for new interface
Plex+SNES: Fixed kernels for Jacobian action
Plex+S

Merge branch 'knepley/fix-petscfe-kernels-ts'

* knepley/fix-petscfe-kernels-ts:
PetscFE+OpenCL: Fixed OpenCL residual eval for new interface
Plex+SNES: Fixed kernels for Jacobian action
Plex+SNES+TS: Pass time and shift down into residual and Jacobian kernels, and the boundary kernels - Added time into ComputeRHS/IFunction
TS ex32: Added a heat equation example - Not yet working, but checking mass matrix now
Plex+SNES: Added DMPlexSNESComputeJacobianActionFEM() - And an internal version

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Merge branch 'knepley/feature-ts-mass-matrix' into knepley/fix-petscfe-kernels-ts

* knepley/feature-ts-mass-matrix:
TS ex32: Added a heat equation example - Not yet working, but checking mass matr

Merge branch 'knepley/feature-ts-mass-matrix' into knepley/fix-petscfe-kernels-ts

* knepley/feature-ts-mass-matrix:
TS ex32: Added a heat equation example - Not yet working, but checking mass matrix now
Plex+SNES: Added DMPlexSNESComputeJacobianActionFEM() - And an internal version

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Add docstring to DMPlexAdapt + clean

minor fixes