Merge branch 'barry/clean-gamg'

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

PCGAMG did not respect MPIAIJ matrix type when passed in on one process
It used AIJ on one process in some cases causing crashes.
Now PCGAMG uses consistently the Seq or MPI nature of the input matri

PCGAMG did not respect MPIAIJ matrix type when passed in on one process
It used AIJ on one process in some cases causing crashes.
Now PCGAMG uses consistently the Seq or MPI nature of the input matrix to
create its new matrices and no longer crashes with input MPIAIJ matrix on
one process.

Reported-by: Randall Mackie <rlmackie862@gmail.com>

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Merge branch 'master' into barry/clean-gamg

Need updates to KSPCHEBYSHEV since I will be adding to them

MatLoad_ and VecLoad_ routines that use options database information from the binary file .info files need to PetscViewerSetUp() before accessing the options database because the "lazy" setup of bina

MatLoad_ and VecLoad_ routines that use options database information from the binary file .info files need to PetscViewerSetUp() before accessing the options database because the "lazy" setup of binary viewers defered the opening of the files until binary reading was first done which was after the calls to determine matrix and vector block sizes.

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

Merge branch 'master' into knepley/feature-harmonic-advection

* master: (205 commits)
Bib: Added bio refs
Don't print SAWs URL since it disturbs all the test output
missing (double) cast in pr

Merge branch 'master' into knepley/feature-harmonic-advection

* master: (205 commits)
Bib: Added bio refs
Don't print SAWs URL since it disturbs all the test output
missing (double) cast in print statement
don't output to test file all 12 digits of values
fixes and additions to SNESQM manual pages
PetscViewerBinaryGetDescriptor() is now a collective and must be treated as such fixed some calls to PetscViewerBinarySetUseMPIIO() removed some test runs that take too long
removed dead routine
ViennaCL: Added MCS download mirror URL for version 1.6.2
shift order of processing options for TS to be compatiable with SAWs Fix options handling for SAWs to duplicate array that previously was deleted too soon for SAWs processing
remove some dead code for AD and old AMS java and Matlab utilities
add missing PetscFunctionBegin; that messed up displaying of stack
Viewer: Fixed PetscViewerBinarySetUseMPIIO() in some examples
removed unused variables, removed dead code from AMS
git is so freaking annoying I accidently made a bunch of updates in next which I pushed lets see if this diff makes the same changes in my branch Why can't git just forbid me to make changes or next or set up some utility to prevent it!
moved saws directory to proper share directory location updated source to point to it.
rm checkboxes at top of pcoptions.html (ugly and not useful) and centered display of solver
PetscOptionsObject->prefix was freed before using in SAWs post processing hence SAWs was unable to change any type which had a prefix
display URL to point to to access SAWs server
missing break in case for handling string arguments better description for Options database option handling
removed extern PC_CLASSID and KSP_CLASSID that don't belong in petscoptions.h
...

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MatAssembly: move check for InsertMode consistency into MatStashScatter impls

The BTS implementation now encodes InsertMode in-band to avoid another
set of messages for MAT_SUBSET_OFF_PROC_ENTRIES.

MatAssembly: move check for InsertMode consistency into MatStashScatter impls

The BTS implementation now encodes InsertMode in-band to avoid another
set of messages for MAT_SUBSET_OFF_PROC_ENTRIES. It does the reduction
in debug mode for better error reporting.

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Merge branch 'knepley/fix-mpiio-flag'

PetscViewerBinaryGetDescriptor() is now a collective and must be treated as such
fixed some calls to PetscViewerBinarySetUseMPIIO()
removed some test runs that take too long

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

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

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

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

fix that was missed in manual merge for MPAIJ function pointer table

Merge branch 'xolotl'

Conflicts:
src/mat/impls/aij/mpi/mpiaij.c

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

Merge branch 'karpeev/fix-ksp-matgetschurcomplement-pmatreuse' into barry/experiment

Conflicts:
src/ksp/ksp/utils/schurm.c

Merge branch 'barry/update-sowing'

Conflicts:
tutorials/HandsOnExercise.html

Merge branch 'tisaac/feature-gamg-extensible' into barry/experiment

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

Merge branch 'knepley/feature-combined-tabulation' into knepley/feature-ts-fem+fvm-example

* knepley/feature-combined-tabulation: (41 commits)
Plex: Fix distribution of uninterpolated meshes - Doe

Merge branch 'knepley/feature-combined-tabulation' into knepley/feature-ts-fem+fvm-example

* knepley/feature-combined-tabulation: (41 commits)
Plex: Fix distribution of uninterpolated meshes - Does SF stratification by depth, not by dimension - The old code numbered cells after vertices
Plex+SNES: Fixes for nonzero cStart
cannot call PetscObjectGetName() on a subset of the MPI processes
MatView() with some matrix formats and ASCII_MATLAB did not print correct matrix name
Plex: Preserve periodicity when adding ghost cells
Plex: Fixed DMPlexGetGlobalFieldOffset_Private() in optimized mode
Plex+SNES: Offset should be into field components, not basis functions
Plex+SNES: Add guards for optional arrays
DS: Added PetscDSGetComponentOffset(), Added to petsc.h
Plex+TS: FVM RHS computation uses a global F
Plex+FV: Corrected accumulation of fluxes to cells and added time derivative term
Plex: Added DMPlexPointGlobalFieldRead/Ref()
Plex+SNES: Fixed DMPlexGetFaceFields() - It returns field values, not coefficients - FE evaluation is now done
FV: In PetscFVIntegrateRHSFunction(), the arguments are field values, not coefficients
FE: Added EvaluateFaceFields() to FE fields at face centroids
Plex: Added DMPlexPointLocalFieldRead()
FE: Have a standard tabulation at face centroids
Plex: Copy BC for hierarchical refinement
FE: Allow P0 over 1D cells
Plex+FV: Fixed BC with gradient calculation
...

Conflicts:
config/builder.py

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Merge branch 'knepley/fix-plex-distribute-uninterpolated' into knepley/feature-combined-tabulation

* knepley/fix-plex-distribute-uninterpolated:
Plex: Fix distribution of uninterpolated meshes - D

Merge branch 'knepley/fix-plex-distribute-uninterpolated' into knepley/feature-combined-tabulation

* knepley/fix-plex-distribute-uninterpolated:
Plex: Fix distribution of uninterpolated meshes - Does SF stratification by depth, not by dimension - The old code numbered cells after vertices
cannot call PetscObjectGetName() on a subset of the MPI processes
MatView() with some matrix formats and ASCII_MATLAB did not print correct matrix name

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Merge branch 'maint'

cannot call PetscObjectGetName() on a subset of the MPI processes

Merge branch 'maint'

MatView() with some matrix formats and ASCII_MATLAB did not print correct matrix name

Reported-by: Michael Souza <souza.michael@gmail.com>