PetscSection: Added an optional permutation for the chart
- Removed the unnecessary atlasLayout
- This permutation will allow people to segregate ghost unknowns at the end of their numbering,
and

PetscSection: Added an optional permutation for the chart
- Removed the unnecessary atlasLayout
- This permutation will allow people to segregate ghost unknowns at the end of their numbering,
and also to get around the stratification of point numbering in Plex

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PetscSection: Added PetscSectionHasConstraints()

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 'master' into barry/google

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removed outdated docs and comments on MatStructure usage removed SAME_PRECONDITIONER since no longer used removed unneed use of MatStructure in Schur complement matrix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

removed unneeded includes in include files
added findvisibleprivatefunctions for finding symbols in libraries that might not belong
removed a couple of global symbols
named spaced a couple of Tao fun

removed unneeded includes in include files
added findvisibleprivatefunctions for finding symbols in libraries that might not belong
removed a couple of global symbols
named spaced a couple of Tao functions

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Merged petsc/petsc into master

Merge branch 'jed/lazy-blocksize'

* jed/lazy-blocksize:
Mat & Vec: make block sizes lazy
PetscLayoutSetBlockSize: allow PETSC_DECIDE for use when block size has already been set

Merge branch 'master' into prbrune/snes-fascontinuation

Conflicts:
include/petscsnesfas.h

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

Mat & Vec: make block sizes lazy

In the past, MatSetUp eagerly set the block sizes (to 1) if not already
set. This prevents use of the "convenience" constructors because they
call MatSetUp before r

Mat & Vec: make block sizes lazy

In the past, MatSetUp eagerly set the block sizes (to 1) if not already
set. This prevents use of the "convenience" constructors because they
call MatSetUp before returning. We could add bs as an explicit argument
to those constructors, but block size is an extraneous concept for most
users. The default value of the block size is -1, so now we use
PetscAbs(map->bs) anywhere it is not known in advance that bs has been
explicitly set. This allows block sizes to be lazy, and they can be set
arbitrarily late, so long as the new size is compatible with the
existing distribution. For (S)BAIJ matrices, the block size is
structural so it gets set explicitly and can thus be referenced directly
rather than via MatGetBlockSize or wrapped in PetscAbs.

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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' into balay/tao-to-petsc

Merge branch 'knepley/fix-plex-closure-index'

* knepley/fix-plex-closure-index:
DMPlex: work around -Wmaybe-uninitialized
DMPlex: Small fix
PetscSection: Added PetscSectionGetField()
DMPlex:

Merge branch 'knepley/fix-plex-closure-index'

* knepley/fix-plex-closure-index:
DMPlex: work around -Wmaybe-uninitialized
DMPlex: Small fix
PetscSection: Added PetscSectionGetField()
DMPlex: Reorganization of closure operations - Rename DMPlexVecGetClosure_Static() —> DMPlexVecGetClosure_Depth1_Static() - Added special cases with/out fields - Removed the need for field offsets by interchanging loops over points and fields - Fixed bug where field offsets were not calculated if an array was passed in - Made all local functions static - Using SNES ex62 to verify changes, and DMPlex ex9 to time them
DMPlex: Fixed object check
DMPlex ex9: Now test VecClosure with index - Made functions static
DMPlex: Optimization for Get/SetClosure - Only need field offsets if there is more than one field
PetscSection: Change clIndices member to clPoints - Added some docs
SNES ex12: Use ViewFromOptions correctly
DMPlex: Use closure index in DMPlexVecSetClosure() and DMPlexMatSetClosure() - Moved depth 1 optimization to static function
DMPlex: Reorgnized closure index - Now index stores points and orientations instead of offsets, so it can be used for updates as well - Moved index creation to plexindices.c - Moved optimization for depth 1 mesh to a static function
DMPlex: Fixed two bugs with DMPlexCreateClosureIndex() - Must make index for entire DM chart - Need to update cloff when no fields are present

Conflicts:
src/dm/impls/plex/makefile
src/dm/impls/plex/plex.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

PetscSection: Added PetscSectionGetField()

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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