Merged upstream/master to feature-dmmoab

Merge remote-tracking branch 'upstream/master'

PCFieldSplit: options bug fix.

PCFieldSplit/Schur: clarification of diag/off-diag Amat options in the docs and manual.

PCFieldSplit/Schur: a more consistent use of diag/off-diag Amat options.

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]
gfortran: remove 132 char limit from f90 free-form
SNES: Set up matrix-free *after* copying the user Jacobian to snes->pc
DMPlex-Gmsh: Use trueNumCells when building the coordinate section
Sys: Got guard logic reversed
Sys: The #define guard for PetscMalloc*() must match the one for PetscFree*()
PetscFV: I hate fucking complex
removed ltog scatter from DMDA since functionality can be obtained with gtol scatter and less memory
fix test of DMLocalToGlobalBegin/End and add actual test cases
improve object memory logging for DA, ISLocalToGlobal and ISBLOCK
lower high water mark of constructing parallel scatter by allocating only as much room in svalues as needed
owner in VecScatter construction is the rank, therefor can use PetscMPIInt to hold it do not PetscInt
another reuse of allocated array in 2d/3d DMDA create
improved high water mark of DMDASetups by implementing and using PETSC_USE_POINTER for ISCreateBlock()
PetscFV: Another complex fix
DMPlex+TS: Fixing types
ISIdentity() was wrong for block IS! Indices are NOT scaled by bs
PetscFV: Straighten out complex types
TS ex11: Fix casts and remove unused variable
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Merge branch 'master' into barry/saws-options

added MatFindOffBlockDiagonalEntries() for MPIAIJ so that -pc_fieldsplit_detect_coupling can be used in parallel
optimized fieldsplit for 2 splits with multiplicative, less expensive residual computa

added MatFindOffBlockDiagonalEntries() for MPIAIJ so that -pc_fieldsplit_detect_coupling can be used in parallel
optimized fieldsplit for 2 splits with multiplicative, less expensive residual computation and remove unneeded MatGetSubMatrix() for that case
optimized MatGetSubMatrix() for request of entire matrix

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Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

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

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

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

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Merge branch 'knepley/fix-pylith-parallel'

* knepley/fix-pylith-parallel: (22 commits)
DMPlex: In refinement, merge hybrid and non-hybrid SF creation (should be done for everything) - If missing,

Merge branch 'knepley/fix-pylith-parallel'

* knepley/fix-pylith-parallel: (22 commits)
DMPlex: In refinement, merge hybrid and non-hybrid SF creation (should be done for everything) - If missing, define *Max as *End - Fixed bound on hybrid 2D simplicial hybrid cell refinement - Fixes bug in which wrong remote point number was calculated if local process had no hybrid cells, but remote process did so refiners were mismatched
DMPlex: Fix for hybrid refinement - Must correct offsets when neighbor process has no hybrid points
DMPlex: Fix hex hybrid refinement SF - Fixed offset - Fixed number of cell faces - Fixed missing edge offset - Fixed number of cells faces - FIxed missing edge offset
PetscSection: Must initialize remoteOffsets
DMPlex: Fixed cohesive cell creation for clamped boundaries - Explicitly tag cross-edges (edges with two clamped endpoints) with 2 in boundary label - Add cross-edge to vertices when looking for things that need split points replaced - Remove extra check for boundary vertices
DMPlex: Fixes for marking cohesive submesh - Do not mark points as split which are in the boundary label - Mark boundary points from label as unsplit
DMPlex: Changing meaning of boundary label in DMPlexLabelCohesiveComplete() - Now it marks vertices already present in the original label - We mark these as unsplit, and ignore their stars - Remove old code
DMPlex: Fixed stupid typo
DMPlex: Fixed refinement to respect embedded manifolds
DMPlex: Fixed types in DMPlexOrient()
DMPlex: Fixed initialization in DMPlexLabelCohesiveComplete()
DMPlex: Fixed logic in hybrid cell tagging and added missing declaration
DMPlex Fixed huge error with last change set - Default cellHeight is 0
DMPlex: Allow cellHeight argument for DMPlexMarkBoundaryFaces()
DMPlex: Added blabel argument to DMPlexLabelCohesiveComplete() - Lets user designate the boundary of a dividing surface - Added GetSurfaceSize_Static()
DMPlex: Fix for DMPlexOrient() - I was not symmetrizing the orientation graph on processes
DMPlex: Added DMPlexAddConeSize()
DMPlex: Fixed memory overwrite at depth 0 for viewing
PC+Doc: Fixed FieldSplit doc
Sys: Replace Malloc1() in multiple mallocs (fix size)
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PC+Doc: Fixed FieldSplit doc

PCFieldSplit: use flags to optionally use Amat for (off)diag blocks.

Fixing merge conflicts in dmregall.

Merged petsc/petsc into master

Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c

Merge branch 'master' into shri/feature-dm-circuit

Conflicts:
src/dm/impls/makefile

Merge branch 'master' into prbrune/matcoloring-greedy

Merge branch 'jed/pcfieldsplit-getschurpre'

* jed/pcfieldsplit-getschurpre:
PCFieldSplit: fix PCFieldSplitSchurPrecondition name
PCFieldSplit: add accessor for Schur preconditioner configuration

Merge branch 'master' into barry/nonlinearsolvertable

Conflicts:
include/petscsnes.h

Merge branch 'master' into knepley/feature-plex-fas

* master: (863 commits)
Revert "mpich: use latest mpich tarball with gcov but use '--enable-coverage' mpich configure option."
MatCreateTransp

Merge branch 'master' into knepley/feature-plex-fas

* master: (863 commits)
Revert "mpich: use latest mpich tarball with gcov but use '--enable-coverage' mpich configure option."
MatCreateTranspose: fix for lazy block size
mpich: use latest mpich tarball with gcov but use '--enable-coverage' mpich configure option.
configure: add FC_DEFINE_FLAG to petscvariables
added a citation for pounders, Stefan finally came through
update to latest netcdf fixes bug that did not allow building on recent Mac OS X
DMPlex: Fixes for CGNS - Fixed loop bounds since CGNS uses closed intervals - Bug with mixed cell types - Typo with coordinates
final updates from nightly tests
fix for countcfunction
removed outdated docs and comments on MatStructure usage removed SAME_PRECONDITIONER since no longer used removed unneed use of MatStructure in Schur complement matrix
removed MatStructure arguments from Tao
fixes for Sundials and fun3d cannot use MPIU_SUM for integer arrays
inplace ILU factorization must update state of inplace matrix to prevent infinite recursion of updating PC
fixes for BDDC by the way not having BDDC always in the testing is going to lead to trouble
the compute Jacobian functions for SNES and TS now do not take a MatStructure flag
KSPSetOperators() no longer has the MatStructure argument. The Mat objects now track that information themselves. Use KPS/PCSetReusePreconditioner() to prevent the recomputation of the preconditioner if the operator changed in the way that SAME_PRECONDITIONER did with KSPSetOperators()
tracks when Mat's have a change in nonzero structure this information can be used by PC to determine how preconditioners must be rebuilt currently only does an error check if the user said same nonzero pattern but actually changed the pattern
completed cleanup of removal of matrix pointers to compute jacobian routines
makefile: Added 'make includegraph' to create an inclusion dependency graph.
Contrib: Updated include-graph.sh script to ignore *.hh files
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Conflicts:
src/dm/dt/interface/dt.c

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Merging master with feature-dmmoab. Only conflict was with SOURCECXX specification under impls/moab/makefile.

Merge branch 'barry/rm-matstructure-mat-pointer'

Conflicts:
include/petsctao.h

removed outdated docs and comments on MatStructure usage
removed SAME_PRECONDITIONER since no longer used
removed unneed use of MatStructure in Schur complement matrix

KSPSetOperators() no longer has the MatStructure argument. The Mat objects now track that information themselves. Use KPS/PCSetReusePreconditioner() to prevent the recomputation of the preconditioner

KSPSetOperators() no longer has the MatStructure argument. The Mat objects now track that information themselves. Use KPS/PCSetReusePreconditioner() to prevent the recomputation of the preconditioner if the operator changed in the way that SAME_PRECONDITIONER did with KSPSetOperators()

SNES/TS still need to be cleaned up to better utilize the new interfaces

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PCFieldSplit: fix PCFieldSplitSchurPrecondition name

Now symmetric with newly-added PCFieldSplitGetSchurPre.