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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Viewer: PetscViewerRead() should return the number of items actually read
- This also applies to all its implementations

Merge branch 'knepley/feature-harmonic-advection'

* knepley/feature-harmonic-advection: (86 commits)
SNES: Some docs for NASM
TS: Added view for MIMEX
Plex: Silence compiler warnings
Builder

Merge branch 'knepley/feature-harmonic-advection'

* knepley/feature-harmonic-advection: (86 commits)
SNES: Some docs for NASM
TS: Added view for MIMEX
Plex: Silence compiler warnings
Builder: Check for missing numProcs was wrong
PetscFE: Turn off Fortran binding for PetscFECompositeGetMapping()
Plex: Fix big bug in DMPlexGetGlobalFieldOffset_Internal() - If offset is negative (dof is on another proc), then we must have end < start
Builder: Allow override of numProcs
Plex: Fix Fortran wrappers for DMLabelView() and DMPlexDistribute()
Plex+Label: Added Fortran wrapper for DMPlexCreateLabel()
Plex: Dammit, how did this not get checked in?
Plex: Refiner check for hybrid cells must use hybrid faces as well - Ghost cells in FV method are hybrid
TS: MIMEX now uses work vectors for correct grid
Plex: Adding support for FV in automatic interpolator construction - Notice that the injector cannot do the right thing until we scrap VecScatter
Plex+FEM: Using PetscFVGetDualSpace()
SNES+Doc: Added Options Database keys
PetscFV: Added PetscFVRefine() - This allows interpolation to finer grids needed for FAS
PetscFV: Added a dual space for calculating projections
DM: Better error checking in DMCoarsen()
DMDT+PetscFE: Added PetscQuadratureExpandComposite() - Replaces PetscFECompositeExpandQuadrature() - Added PetscFECompositeGetMapping()
Plex: Fixed complex type error
...

Conflicts:
src/dm/impls/plex/ftn-custom/makefile
src/ts/interface/ts.c

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DM: Better error checking in DMCoarsen()

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 '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

Removed unused variables

Merge branch 'pr270/knepley/dm-set-sf-options/master'

* pr270/knepley/dm-set-sf-options/master:
DM: call XXXSetFromOptions on SFs in DMSetFromOptions

DM: Now also save the DMBoundaryType for each dimension
- Should get rid of this in DMDA eventually

Merge branch 'master' into barry/clean-gamg

Need updates to KSPCHEBYSHEV since I will be adding to them

Merge branch 'knepley/fix-plex-submesh-section'

* knepley/fix-plex-submesh-section:
DM: Fix FUNCT
DM: Fixed naming of utility function
Plex: Fixed array reuse bug in PetscSectionCreateGlobalSe

Merge branch 'knepley/fix-plex-submesh-section'

* knepley/fix-plex-submesh-section:
DM: Fix FUNCT
DM: Fixed naming of utility function
Plex: Fixed array reuse bug in PetscSectionCreateGlobalSectionCensored()
DM+Plex: Added sanity checking for global sections received from user
Plex: Unified interpolated submesh creation - Now both versions create an SF - Moved DMPlexFilterPoint_Internal() - DMPlexMarkCohesiveSubmesh_Interpolated() now takes a DMLabel instead of a string
Plex: Allow NULL Label in DMPlexMarkSubmesh_Interpolated()

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DM: call XXXSetFromOptions on SFs in DMSetFromOptions

DM: Fix FUNCT

DM: Fixed naming of utility function

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c

DM+Plex: Added sanity checking for global sections received from user

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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Merge branch 'tisaac/simplify-register-all'

Removed the XXXRegisterAll() functions from the public interface. These should now only be handled by the package intialization functions.

Merge branch 'knepley/fix-veclock-fftw'

* knepley/fix-veclock-fftw:
DM: Fix more Vec lock issues
FFTW: Updated for vector locking

DM: Fix more Vec lock issues

Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Merge branch 'knepley/fix-dm-df-local-copy'

* knepley/fix-dm-df-local-copy:
Plex: Fix local to global section correspondence - This needs to go in the documentation somewhere
Plex+SF: Local copy

Merge branch 'knepley/fix-dm-df-local-copy'

* knepley/fix-dm-df-local-copy:
Plex: Fix local to global section correspondence - This needs to go in the documentation somewhere
Plex+SF: Local copy should ignore points with no global dogs

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Fixed errors in manual page documentation including formating.
Fixed rank argument for DMCreateRedundant() to be PetscMPIInt

Reported-by: Dave May <dave.mayhem23@gmail.com>

Merge branch 'barry/experiment'