Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in m

Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in master (the introduction of MatFactorGetError()) therefor need
to merge in master and use the new construct before merging to next

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

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c

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

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcfetidp.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c
src/mat/impls/is/matis.h

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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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DMPlexTSComputeRHSFunctionFVM: ADD_VALUES from locF to F instead of INSERT_VALUES

We've actually designed it so that each cells contribution is only calculated once, but there are empty ghost cells

DMPlexTSComputeRHSFunctionFVM: ADD_VALUES from locF to F instead of INSERT_VALUES

We've actually designed it so that each cells contribution is only calculated once, but there are empty ghost cells on other processes with zero contributions. There's no version of INSERT_VALUES that just inserts the local values: it's essentially non-deterministic which value gets inserted. So we have to add all the zero contributions.

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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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DMPlexTS: removed unused variables

DMPlex/DMP4est: small fixes for next warnings and errors

DMPlexTS, DMPlexSNES: cache in the dm instead of the dmts, dmsnes objects

DMPlex: cache FVM data

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

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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Plex+SNES+TS: Pass time and shift down into residual and Jacobian kernels, and the boundary kernels
- Added time into ComputeRHS/IFunction

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 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/imp

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c

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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

Merge branch 'master' into barry/add-pcfieldsplit-logevent

DM+SNES/TS: Fixed caching of Plex

Plex+TS: Finally fixed BC function

Plex+TS: Condensing to one BC function

Merge branch 'tisaac/dmforest' of bitbucket.org:petsc/petsc into tisaac/dmforest

# By Toby Isaac (6) and Mark Adams (2)
# Via Mark Adams
* 'tisaac/dmforest' of bitbucket.org:petsc/petsc:
removed d

Merge branch 'tisaac/dmforest' of bitbucket.org:petsc/petsc into tisaac/dmforest

# By Toby Isaac (6) and Mark Adams (2)
# Via Mark Adams
* 'tisaac/dmforest' of bitbucket.org:petsc/petsc:
removed debugging print
DMP4est: regression test for ex11
Plex: correct memory management in DMProjectFunctionLocal_Plex()
Plex+FVM: correct counting of fluxes
trying to fix a BC bug
TS+Plex: provied face geometry for essential bcs
TS+Plex: added boundary routines for DMTSLocal, and PlexFEM/FVM implementations
SNES+Plex: added DMPlexSetSNESLocalFEM()

Conflicts:
include/petscdmplex.h
src/snes/examples/tutorials/ex62.c
src/ts/utils/dmlocalts.c
src/ts/utils/dmplexts.c

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Merge branch 'tisaac/dmforest' of bitbucket.org:petsc/petsc into tisaac/dmforest