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removed outdated docs and comments on MatStructure usage removed SAME_PRECONDITIONER since no longer used removed unneed use of MatStructure in Schur complement matrix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 'balay/split-sourcecxx'

build: split cxx [legacy] build target via SOURCECXX

Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

commit after merge

Hg-commit: d0f613618ca66a5aeb1aac97d210d2cc29755d3d

reemove OBJSC and OBJSF from invididual makefiles and auto-define in conf/variables

Hg-commit: 2f01c17f3c19dc4b89aaf306cfd60a12312c270d

committing after previous merge.

Hg-commit: 62ea3b3249ac52e1d599b51313301ac9e25ed491

Add basic Elemental interface

## Implemented
* MatMult and MatMultAdd
* MatSetValues for locally owner parts (no stash at this point)
* Use MatGetOwnershipIS() to determine which entries a process s

Add basic Elemental interface

## Implemented
* MatMult and MatMultAdd
* MatSetValues for locally owner parts (no stash at this point)
* Use MatGetOwnershipIS() to determine which entries a process should be responsible for assembling
* Viewing is currently in Elemental ordering, can use MatComputeExplicitOperator() for debugging

## Short-term priorities
* Grid needs to be shared between multiple Mats on the same communicator, implement by attribute caching on the MPI_Comm
* Stash for assembly of unowned entries, can cache locally and use Elemental's (collective) "axpy" interface
* MatMat operations, factorization, etc

Hg-commit: 9d1af7db82c9477605dc39b514d53db5a9855fc7

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