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

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

Merge branch 'knepley/feature-combined-tabulation'

* knepley/feature-combined-tabulation: (38 commits)
Plex: Fix compiler warning
Plex+SNES: Fixes for nonzero cStart
Plex: Preserve periodicity

Merge branch 'knepley/feature-combined-tabulation'

* knepley/feature-combined-tabulation: (38 commits)
Plex: Fix compiler warning
Plex+SNES: Fixes for nonzero cStart
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
Plex ex1: Move overlap computation after SetFromOptions
Plex: DMPlexDistribute() no longer calls DMSetFromOptions() - Fixed examples
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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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Plex: Copy BC for hierarchical refinement

Merge branch 'master' into barry/ksp-converged-reason-viewer

Conflicts:
src/sys/objects/options.c

Plex: Fixed compiler warnings

Merge branch 'knepley/fix-plex-orient'

* knepley/fix-plex-orient:
Plex: Fix serial orientation
TetGen: Syntax fix
Plex: Fix MPI type for orientation
Plex: Small orientation fix
Plex ex13:

Merge branch 'knepley/fix-plex-orient'

* knepley/fix-plex-orient:
Plex: Fix serial orientation
TetGen: Syntax fix
Plex: Fix MPI type for orientation
Plex: Small orientation fix
Plex ex13: Orientation now working for flipped connected components
Plex: Reworked orientation to respect connected components on each process
Plex ex13: Check in initial output
Plex: Now mark initial cell as seen - Changes the outcome slightly
Plex: Added DMPlexCheckFace_Internal() - This checks a face in the mesh for orientation consistency
Plex: Fix orientation diagnostics
Plex: Added declaration for DMPlexReverseCell()
Plex ex13: Tests orientation - Only 2D triangle tests now - Last test shows problem for disconnected domains
Plex: Small example fixes
PetscBT: Do not overwrite a viewer passed to PetscBTView()
Plex: Remove unneeded headers
Plex: Added a file for orientation calculations - Moved DMPlexOrient()

Conflicts:
src/dm/impls/plex/plex.c

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TetGen: Syntax fix

Merge branch 'barry/remove-unneeded-paren-petscmalloc'

Conflicts:
src/mat/impls/baij/seq/baij.c

Merge branch 'master' into mlange/refactor-plex-distribute

Conflicts:
src/dm/impls/plex/examples/tests/output/ex12_1.out
src/dm/impls/plex/examples/tests/output/ex12_2.out

convert some PetscMalloc() to PetscMalloc1()
remove unneeded () in first argument to PetscMalloc/Calloc1()
fixes for MATLAB examples

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

Merge branch 'knepley/fix-plex-refinement-labels'

* knepley/fix-plex-refinement-labels:
Plex: No longer require the "marker" label for generation or refinement

Plex: No longer require the "marker" label for generation or refinement

Merge branch 'knepley/fix-plex-tetgen'

* knepley/fix-plex-tetgen:
Plex: Fix for TetGen wrapper

Plex: Fix for TetGen wrapper

Merge branch 'master' into knepley/fix-configure-petsc-dep

* master: (210 commits)
error out on special cases where DMLocalToGlobal_DA won't work
remove unneed uses of local DM vectors and DMLoc

Merge branch 'master' into knepley/fix-configure-petsc-dep

* master: (210 commits)
error out on special cases where DMLocalToGlobal_DA won't work
remove unneed uses of local DM vectors and DMLocalToGlobalBegin/End in examples removed to prevent cut and paste repeats of their use
openmpi: update to version 1.8.3
added more movies and pubs
more movies
MatGetDiagonalBlock() can be called before matrix is assembled
added a couple more movies/images
PetscLogEventGetId() was missing public prototype
simply output from make streams benchmark test
c2html: fixup so that C2HTML make variable is set [similar to cmake.py]
chaco: current blas test does'nt work with Cray CC [which automatically links with blas] and linux - where -lm needs to be listed explicitly. Switch the test to check if we are using PETSc modifled chaco
builddist: always install c2html/sowing
argonne logo for users manual cover
Remove PETSC_HAVE_CUSP_SMOOTHED_AGGREGATION, use PETSC_HAVE_CUSP instead.
mpich: use older tarball with cygwin/gnu compilers
updated information about packages PETSc can use in users manual
Updated users manual to latest ANL Report format requirements
mpich: update to mpich-3.1.3.tar.gz - remove -download-mpich-mpe [mpich no longer packages mpe] - remove -download-mpich-shared. It was added as a split from --with-mpi-shared to --known-mpi-shared and --download-mpich-shared in 50237a55163f90ac7341b723c6422dfa1dbce792 removing this gives back the control of shared=0/1 to package.py - remove download_solaris as the new tarball works with both gcov and on solaris - remove MPICHInstall() [and use GNUPackage.Install()] as the new tarball fixes 'make clean' requiring sudo
added more images and PETSc pubs
Doc: More refs
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Merge branch 'knepley/feature-plex-generator-args'

* knepley/feature-plex-generator-args:
Plex: Small fix
Plex: Fixed misspelling
Plex: Move generation to a separate source file, Can now speci

Merge branch 'knepley/feature-plex-generator-args'

* knepley/feature-plex-generator-args:
Plex: Small fix
Plex: Fixed misspelling
Plex: Move generation to a separate source file, Can now specify operator for mesh generators - Added DMPlexTriangleSetOptions() and DMPlexTetgenSetOptions()

Conflicts:
src/dm/impls/plex/makefile

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Plex: Small fix

Plex: Move generation to a separate source file, Can now specify operator for mesh generators
- Added DMPlexTriangleSetOptions() and DMPlexTetgenSetOptions()