Merged upstream/master to feature-dmmoab

Merge remote-tracking branch 'upstream/master'

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

Merge branch 'jed/dmda-memusage'

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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fixes for DA1d creation with scaled sizes of X direction logical coordinates

removed blocked versions of ISLocalToGlobalMapping in Vec and Mat
the single ISLocalToGlobalMapping supports ISLocalToGlobalMappingApply and ISLocalToGlobalMappingApplyBlock
still some fixes need for

removed blocked versions of ISLocalToGlobalMapping in Vec and Mat
the single ISLocalToGlobalMapping supports ISLocalToGlobalMappingApply and ISLocalToGlobalMappingApplyBlock
still some fixes need for these extensive changes

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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 '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
...

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.

Merged petsc/petsc into master

Merge branch 'master' into prbrune/snes-fascontinuation

Conflicts:
include/petscsnesfas.h

Merge branch 'barry/ts-rhsjacobian-only'

Merge branch 'master' into barry/ts-rhsjacobian-only

Merge branch 'shri/update-SuiteSparse' into shri/external-package-KLU

Conflicts:
conf/test
config/examples/arch-linux-pkgs-dbg-ftn-interfaces.py
config/examples/arch-linux-pkgs-opt.py

new version of fast matrix setter since old version was fundamentally broken

Merge branch 'master' into balay/tao-to-petsc

Conflicts:
src/dm/examples/tests/ex42.c
src/dm/examples/tutorials/ex65dm.c
src/ksp/ksp/examples/tutorials/ex42.c
src/snes/examples/tutorials/cahn-hi

Merge branch 'master' into balay/tao-to-petsc

Conflicts:
src/dm/examples/tests/ex42.c
src/dm/examples/tutorials/ex65dm.c
src/ksp/ksp/examples/tutorials/ex42.c
src/snes/examples/tutorials/cahn-hilliard-schemes/ex1.c
src/snes/examples/tutorials/ex54.c
src/snes/examples/tutorials/ex55.c
src/snes/examples/tutorials/ex60.c
src/snes/examples/tutorials/ex61.c
src/snes/examples/tutorials/ex63.c
src/snes/examples/tutorials/ex633d_db.c
src/snes/examples/tutorials/ex64.c
src/snes/examples/tutorials/ex65.c
src/snes/examples/tutorials/ex653d.c
src/ts/examples/tutorials/ex23.c

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Merge branch 'knepley/feature-periodic-mesh'

* knepley/feature-periodic-mesh:
Matt moved DMDA_BOUNDARY.. to DM_BOUNDARY... but did not fix ex2f.F includes
DM Fortran examples: fix petscdm.h -> f

Merge branch 'knepley/feature-periodic-mesh'

* knepley/feature-periodic-mesh:
Matt moved DMDA_BOUNDARY.. to DM_BOUNDARY... but did not fix ex2f.F includes
DM Fortran examples: fix petscdm.h -> finclude/petscdm.h
DMPlex: Fixed markers on periodic boundary
DM examples: include petscdm.h in examples that use DM_BOUNDARY_*
DMBoundary: fix line length for Fortran
DMPlex: Now DMPlexCreateHexBox() can have a Mobius topology using DM_BOUNDARY_TWIST
DM: Moved DMDABoundaryTypes to DMBoundaryTypes - Changed the enum values as well - Changed docs and updated Changes - Updated examples
DMPlex: DMPlexCreateHexBoxMesh() now allows periodicity - Changed declaration and uses - DMPlexCreateSquareMesh() now allows periodicity - Works with refinement

Conflicts:
src/dm/impls/plex/plexcreate.c
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

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Merge branch 'master' into balay/tao-to-petsc

Conflicts:
include/makefile

Merge branch 'master' into knepley/feature-mat-zerorowscols-baij

Merge branch 'master' into barry/remove-big-g

Merge branch 'master' into barry/ts-rhsjacobian-only