Merge remote-tracking branch 'origin/master' into feature-dmmoab

Merged petsc/petsc into master

Merge branch 'barry/rm-matstructure-leftover'

Removed some outdated use of MatStructure in users manuals
Removed TaoDM prototypes for DMLocal since the code does not exist

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removed outdated docs and comments on MatStructure usage removed SAME_PRECONDITIONER since no longer used removed unneed use of MatStructure in Schur complement matrix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

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

Conflicts:
include/petsctao.h

removed MatStructure arguments from Tao

completed cleanup of removal of matrix pointers to compute jacobian routines

update changes file

fixed tao examples to no longer use Mat* arguments for Jacobian/Hessian etc computations

Merged petsc/petsc into master

TaoSetHessianMat() does not exist but was listed in petsctao.h

Merge branch 'master' into prbrune/snes-fascontinuation

Conflicts:
include/petscsnesfas.h

Merge branch 'barry/tao-fixes-for-petsc4py'

tao: namespace TAO subvec and submat routines and make intern

Fix missing PETSC_EXTERN in TaoMonitor()

changed TaoTerminationReason TaoConvergedReason
changed TaoLineSearchTerminationReason to TaoLineSearchConvergedReason

reason: consistency with the rest of PETSc

updates to Tao per request of Lisandro for Petsc4py

* I would like to have TaoGetConstraintTolerances(), right now I'm
defining it in petsc4py as shown in the link below:
https://bitbucket.org/petsc

updates to Tao per request of Lisandro for Petsc4py

* I would like to have TaoGetConstraintTolerances(), right now I'm
defining it in petsc4py as shown in the link below:
https://bitbucket.org/petsc/petsc4py/commits/ab01ebe336491190a2db85c179c48b1c64fdc673?at=master#chg-src/include/custom.h

* Look at all these definitions, they should be exposed in the C API
to be able to call e.g. TaoSetType(tao,TAOLMVM);
https://bitbucket.org/petsc/petsc4py/commits/ab01ebe336491190a2db85c179c48b1c64fdc673?at=master#Lsrc/PETSc/petsctao.pxiT4

Also removed -tao_method, removed tao_ from names of tao methods and fixed some tao source code formatting

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