Merge branch 'master' into pr192/Fande-Kong/scalable-matincreaseoverlap/master

Needed to merge master to update to new calling sequence PetscCommBuildTwoSided

Merged petsc/petsc into master

Merge branch 'barry/fix-directory-layout'

do some refactoring of the scalable MatIncreaseOverlap() code for MPIAIJ to respect PETSc style
in particular not having an options database in the compute code; it should be handled in MatSetFromOpt

do some refactoring of the scalable MatIncreaseOverlap() code for MPIAIJ to respect PETSc style
in particular not having an options database in the compute code; it should be handled in MatSetFromOptions()
and use standard inheritence of replacing a method with a new derived method

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updated PETSc directory layout to match standard packaging strategies

include/petsc finclude,private,mpiuni
lib/petsc conf
bin/petsc*

Fixes in manpage of MatAssemblyEnd()

Merged petsc/petsc into master

Merge branch 'barry/fix-matsettype-cleanup/master'

MatSetType() when changing from a previously defined type needs to reset certain basic properties
of the matrix so they don't bleed into the new type

Contributed-by: Dmitry Karpeyev <karpeev@mcs.anl

MatSetType() when changing from a previously defined type needs to reset certain basic properties
of the matrix so they don't bleed into the new type

Contributed-by: Dmitry Karpeyev <karpeev@mcs.anl.gov>

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Merge branch 'tisaac/mat-get-submatrix-unordered'

Merge branch 'barry/optimize-matshift'

added an option description in MatIncreaseOverlap.
Use option -mat_increase_overlap_k when the problem
size is large

Resetting of inode information for SeqAIJ matrices did not always take place
when the matrix structured changed. Updated code to use nonzerostatus of matrix to
track when inode information needed to

Resetting of inode information for SeqAIJ matrices did not always take place
when the matrix structured changed. Updated code to use nonzerostatus of matrix to
track when inode information needed to be updated.

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Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
thi

Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
this branch. Matt's and my fixes in DMPlex will also be relevant.

* master: (1557 commits)
MatLoad_MPIDense() always allocated array space even if it was previously provided
Clarified lumping options for PCFieldSplitSchurPreType SELFP.
fixed up PetscInfo in GAMG
TSErrorWeightedNorm[2|Infinity]: API changes
MatLoad_SeqDense() always allocated new space for the data even if the user already provided it
Fixed DMCompositeGetAccessArray() to support readonly vectors
Fix obviously-wrong aspects of documentation on SNESVINEWTONRSLS and SNESVINEWTONSSLS.
fixed example to compile - demonstrates a bug
var name 'len' was F90 key word
For user provided Jacobian functions they should always assembly into the second matrix, the one from which the preconditioner is built because the first may be used as matrix-free with -snes_mf_operator
Suggest --with-64-bit-indices if users mistakenly use --with-64bit-indices
Fix configure logging of integer size.
missing underscore in #define of vecgetarrayread translation of fortran stub for VECGETARRAYREAD
updated test output files to reflect differences introduced previously in PCView output
-ksp_type preonly does not support -ksp_monitor_short so remove from test line to prevent extranious warning output
missing CHKERRQ; and ugly double declaration of ierr
Plex ex3: For want of a semicolon, the kingdom was lost
MatSetValuesMPISBAIJ will now print correct global indices when error generated due to new nonzero location
completed basic use of MatSetValuesBlocked_SeqBAIJ_Inlined() by MatSetValuesBlocked_MPIBAIJ() to allow proper global indices being printed when error generated by new nonzero locations.
Added inline version of MatSetValuesBlocked_SeqBAIJ() to be used by MatSetValuesBlocked_MPIBAIJ() to print error message for nonzero block with global indices
...

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Optimized MatShift() for a completely empty matrix since this is commonly used with SLEPc to produce diagonal matrices

Reported-by: Jose Roman <jroman@dsic.upv.es>

Merge branch 'master' into shri/ts-is-for-differential-variables

Conflicts:
include/petsc-private/tsimpl.h
src/ts/impls/eimex/eimex.c
src/ts/interface/ts.c

Merge branch 'barry/clean-gamg'

Conflicts:
src/ksp/pc/impls/gamg/gamg.c

Mat code cannot use MatGet/SetDM() since that is defined in the DM library

Merge branch 'master' into shri/adjoints-and-events

Need to update the branch to get the changes made by Hong to the adjoint code.

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

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

Merge branch 'hzhang/update-MUMPS_5.0.0'

MatMatSolve_MUMPS() works for parallel case

Merge branch 'barry/fix-matgetrowmax-fortran'

Mat: update documentation of MatGetSubmatrix() and MatGetSubMatrices()

Now state that index set restrictions are type specific.

Old doc stated that the row indices would be sorted, but that doesn't

Mat: update documentation of MatGetSubmatrix() and MatGetSubMatrices()

Now state that index set restrictions are type specific.

Old doc stated that the row indices would be sorted, but that doesn't
appear to be the case.

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