DM: Fixed pointer comparison

DM: Fix reference counting in DMSetField()

Merge branch 'knepley/feature-plex-fas'

* knepley/feature-plex-fas: (56 commits)
DMPlex: Removed unused variable
DMPlex: Fix for C++ build, small fix for PetscFE
DMPlex: Removed leak from Tria

Merge branch 'knepley/feature-plex-fas'

* knepley/feature-plex-fas: (56 commits)
DMPlex: Removed unused variable
DMPlex: Fix for C++ build, small fix for PetscFE
DMPlex: Removed leak from Triangle
SNES ex12: Two working unstructured FAS solves for the unregularized p-Laplacian
DMPlex: Cleaned up some memory issues
DMPlex: Implement injection - I don't think this should be required
DMPlex: DM interpolation requires the scaling vector for FAS
DMPlex: Can now create a map from coarse to fine vertices - This is currently necessary for FAS, which I think is wrong
DMPlex: Turn off Fortran stub
DMPlex: Fix DMPlexMatSetClosureRefined() - Reject duplicate fine points - Screen out point with dof = 0 - Fix the allocation for fine points
DMPlex: My brain did not work for several days - I have fixed the interpolation code - I think I can reuse that other code for something else
DMPlex: Fix setting Plex options on automatically refined meshed
SNES ex12/31/52/62/72: Use new SNESComputeJacobian() interface
DMPlex: Remove MatStructure from DMPlexComputeJacobianFEM() - Add missing declarations
Sys Logging: Fixes for log detail - Must preserve reduction count - Output objects and memory - Output stage summary
SNES ex12: Fixing things for multilevel - Need to set PetscFE on all coarse grids - Need application context for interpolator construction
SNES ex12: Use PetscFESetUp(), and fix quadrature ref handling
SNES ex52/62: Use PetscFESetUp(), and fix quadrature ref handling
DMPlex ex3: Uses automatic section creation, PetscFESetUp(), and fix quadrature ref handling
DMPlex: Fixing interpolator construction - Fixed definition of rectangular sizes - Use PetscFERefine() - Use special MatSet
...

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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 'prbrune/dm-destroylinkedlistfix'

* prbrune/dm-destroylinkedlistfix:
DM: Fix for recursive DMDestroy() causing valgrind issues

DM: If the local section is not present, it will be created automatically from PetscFE structures and boundary conditions
- Added createdefaultsection() to DM

DM: Change DM fields to PetscFE
- Really the DM should be split into topology and function space parts, and this would go in the later. Right now I can't
do it properly without circular dependencie

DM: Change DM fields to PetscFE
- Really the DM should be split into topology and function space parts, and this would go in the later. Right now I can't
do it properly without circular dependencies.
- This is setting up for automatic creation of Sections

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

DM: Fix for recursive DMDestroy() causing valgrind issues

runex26_2 in src/ts/examples/tutorials caused the following valgrind output:

> ==21447== Invalid read of size 8
> ==21447== at 0x599093E

DM: Fix for recursive DMDestroy() causing valgrind issues

runex26_2 in src/ts/examples/tutorials caused the following valgrind output:

> ==21447== Invalid read of size 8
> ==21447== at 0x599093E: DMDestroy (dm.c:401)
> ==21447== by 0x4F3F83F: PetscObjectDereference (inherit.c:612)
> ==21447== by 0x4F30C6A: PetscObjectListDestroy (olist.c:160)
> ==21447== by 0x4F3AA1F: PetscHeaderDestroy_Private (inherit.c:117)
> ==21447== by 0x5184D16: VecDestroy (vector.c:499)
> ==21447== by 0x5990EA5: DMDestroy (dm.c:425)
> ==21447== by 0x5B2833D: PCDestroy (precon.c:122)
> ==21447== by 0x5C0D6EF: KSPDestroy (itfunc.c:772)
> ==21447== by 0x5C93387: SNESDestroy (snes.c:2790)
> ==21447== by 0x5D35130: SNESReset_NASM (nasm.c:46)
> ==21447== by 0x5C92705: SNESReset (snes.c:2732)
> ==21447== by 0x5C92689: SNESReset (snes.c:2728)
> ==21447== by 0x5DA00E8: TSReset (ts.c:1872)
> ==21447== by 0x5DA09EB: TSDestroy (ts.c:1912)
> ==21447== by 0x402671: main (ex26.c:172)
> ==21447== Address 0x9b39778 is 24 bytes inside a block of size 32 free'd
> ==21447== at 0x4C2A82E: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
> ==21447== by 0x4F85AEB: PetscFreeAlign (mal.c:70)
> ==21447== by 0x5990F29: DMDestroy (dm.c:426)
> ==21447== by 0x5B2833D: PCDestroy (precon.c:122)
> ==21447== by 0x5C0D6EF: KSPDestroy (itfunc.c:772)
> ==21447== by 0x5C93387: SNESDestroy (snes.c:2790)
> ==21447== by 0x5D35130: SNESReset_NASM (nasm.c:46)
> ==21447== by 0x5C92705: SNESReset (snes.c:2732)
> ==21447== by 0x5C92689: SNESReset (snes.c:2728)
> ==21447== by 0x5DA00E8: TSReset (ts.c:1872)
> ==21447== by 0x5DA09EB: TSDestroy (ts.c:1912)
> ==21447== by 0x402671: main (ex26.c:172)

This was caused by recursive calls to DMDestroy(). When freeing the named local vector list, the linked list is freed
before being set to NULL. The recursive call of DMDestroy() by VecDestroy() then tries to access the value in the
structure. The fix to this is to zero out the DM member before the recursive call instead of after it.

Reported-by: Barry Smith <bsmith@mcs.anl.gov>

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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

Merge branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'knepley/fix-str-leak'

* knepley/fix-str-leak:
Sys: Have to check for all zero sizes in PetscMalloc*() - Produced a leak in optimized mode
DMPlex: Replaced a PetscMalloc3() with Pet

Merge branch 'knepley/fix-str-leak'

* knepley/fix-str-leak:
Sys: Have to check for all zero sizes in PetscMalloc*() - Produced a leak in optimized mode
DMPlex: Replaced a PetscMalloc3() with PetscMalloc1()s - Fieldsplit was freeing these individually
Sys: Fix memory leak in PetscStrreplace()

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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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DMPlex: Replaced a PetscMalloc3() with PetscMalloc1()s
- Fieldsplit was freeing these individually

DM: Barry missed a %G

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 remote-tracking branch 'origin/barry/remove-big-g'

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

completed some percentage of changes from %G format in prints

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

Conflicts:
src/ts/examples/tutorials/advection-dif

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

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Merged petsc/petsc into master