PCGAMG_Classical: Leave diagonal of the graph intact.

This was causing VecAssemblyBegin() to hang in the MIS coarsening code.

Merge branch 'master' into knepley/feature-plex-gmsh

* master: (163 commits)
do not use C99 struct initialization code in PETSc
Nightly Summary: Added time taken to each of the tests in the dash

Merge branch 'master' into knepley/feature-plex-gmsh

* master: (163 commits)
do not use C99 struct initialization code in PETSc
Nightly Summary: Added time taken to each of the tests in the dashboard.
ASCII printing of floating point numbers must cast to (double) to support quad precision
configure: check fortranDatatypes only when fortran is enabled [this fixes configure crash with --with-fc=0]
don't use non-portable and also dependent on floating point precision system level math constants
picky compilers
fix a couple compiler warnings/errors (depending on compiler) for Matlab engine code
DMPlex: More fixup from bad rebase, moved to DMGet/SetCoordinateSection()
DM: Added DMGet/SetCoordinateSection()
Fuckup: Fix for merge that is still untangling bad rebase from Oct. 17th 2013 - Fixed const in declarations - Fixed merge from PetscFE - Fixed 2 mallocs
replace all echo in test/tutorial makefiles with printf since echo behaves differently on different systems
DMDA: Missing header - Damn rebase
DMPlex ex3: Added 2D Q_1 and 3D P_2 tests
DMDA: Added DMDAProjectFunction() and DMDAComputeL2Diff()
DMDA: Fixed 2D geometry - Should reuse DMPlex routines
DMDA: Fix bug in 2D closure operation for cells
DMDA: Make closure operations also return the size
DMDA: Changed DMDACreateSection() to emulate DMPlexCreateSection()
DMDA: Added functions which emulate DMPlex functionality
DMDA: Now DMDAGetNumCells() returns the cells in each direction as well
...

Conflicts:
config/builder.py

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PCGAMG_Classical: PetscOptionsList() -> PetscOptionsFList()

Merge branch 'madams/gamg-destroy' into prbrune/pcgamg-classicalinterpolationstrategies

Merge branch 'master' into madams/gamg-destroy

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

Merge branch 'master' into barry/reduce-dmsetup-da-memoryusage

Conflicts:
src/dm/examples/tests/ex15.c
src/dm/examples/tutorials/ex3.c
src/dm/impls/da/da2.c
src/dm/impls/da/da3.c

Merged master into barry/update-xxxviewfromoptions

Merge branch 'master' into barry/xcode

Merge branch 'barry/saws-push-header-body' into barry/saws-options

Merge branch 'jed/malloc-array'

Type arguments dropped from PetscMalloc[2-7], PetscNew, and PetscNewLog,
added PetscMalloc1 for allocating typed arrays, add PetscCalloc[1-7] for
allocating cleared (

Merge branch 'jed/malloc-array'

Type arguments dropped from PetscMalloc[2-7], PetscNew, and PetscNewLog,
added PetscMalloc1 for allocating typed arrays, add PetscCalloc[1-7] for
allocating cleared (zeroed) memory.

* jed/malloc-array:
Sys: Add pointer casts from (void **) in calls to PetscMalloc1()
Sys: drop explicit type arguments from PetscNew() and PetscNewLog()
Sys: add PetscCalloc[1-7]
Sys: add PetscMalloc1 macro, array allocation without redundant types
PetscMalloc[2-7]: remove type arguments, infer from pointer type
SNESComputeJacobianDefaultColor: fix uninitialized variable

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Sys: drop explicit type arguments from PetscNew() and PetscNewLog()

git grep -l 'PetscNew\(Log\)\?(' -- $1 | xargs perl -pi -e '
s@PetscNew\([^,;()]+ *, *@PetscNew(@;
s@PetscNewLog\(([^,;()]+) *,[^,

Sys: drop explicit type arguments from PetscNew() and PetscNewLog()

git grep -l 'PetscNew\(Log\)\?(' -- $1 | xargs perl -pi -e '
s@PetscNew\([^,;()]+ *, *@PetscNew(@;
s@PetscNewLog\(([^,;()]+) *,[^,;()]+, *@PetscNewLog($1,@'

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PCGAMG_Classical: Added Jacobi smoothing for the OptProl part

PCGAMG_Classical: Fixes for complex and 64-bit index builds in the new interp.

PCGAMG_Classical: Added PCGAMGClassicalSetType() and registration

PCGAMG_Classical: Add thresholding for the prolongator entries

PCGAMGClassical: Standard interpolation now works for scalar problems.

PCGAMG_Classical: Begin standard interpolation; match direct.

This matches the direct interpolation previously implemented as
a bug check. The next step is to add the indirect entries.

Merge branch 'madams/gamg-destroy' into prbrune/pcgamg-classicalinterpolationstrategies

PCGAMG_Classical Separate thresholding for graph coarsening and prolongator

Cleanup of PCGAMGClassical Prolongator creation.

Simplification of graph creation in PCGAMG_Classical

fixed incorrect sizeing in classical AMG

Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

Merge branch 'prbrune/dm-coordinaterestrict' into prbrune/snes-elasticityexample

Merge branch 'prbrune/pcgamg-classical'

* prbrune/pcgamg-classical:
PCGAMG Classical: no need to explicitly zero formkktprol
Fixed types for PCGAMGProlongator_Classical and PCGAMGGraph_Classical

Merge branch 'prbrune/pcgamg-classical'

* prbrune/pcgamg-classical:
PCGAMG Classical: no need to explicitly zero formkktprol
Fixed types for PCGAMGProlongator_Classical and PCGAMGGraph_Classical, strict C fix.
Complex fixes for classical
Added test examples for classical AMG
Fixed a number of bugs in Classical GAMG
Fix to the threshold calculation
Fixed PCGAMG_Classical so that thresholding decreases fill as bugs are fixed
Fixed one-processor memory corruption bug for classical GAMG.
Namespacing in gamg/classical.c
Added classical AMG to GAMG

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