Merge branch 'master' into barry/ts-rhsjacobian-only

Mat & Vec: make block sizes lazy

In the past, MatSetUp eagerly set the block sizes (to 1) if not already
set. This prevents use of the "convenience" constructors because they
call MatSetUp before r

Mat & Vec: make block sizes lazy

In the past, MatSetUp eagerly set the block sizes (to 1) if not already
set. This prevents use of the "convenience" constructors because they
call MatSetUp before returning. We could add bs as an explicit argument
to those constructors, but block size is an extraneous concept for most
users. The default value of the block size is -1, so now we use
PetscAbs(map->bs) anywhere it is not known in advance that bs has been
explicitly set. This allows block sizes to be lazy, and they can be set
arbitrarily late, so long as the new size is compatible with the
existing distribution. For (S)BAIJ matrices, the block size is
structural so it gets set explicitly and can thus be referenced directly
rather than via MatGetBlockSize or wrapped in PetscAbs.

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MatPermute_MPIAIJ: fix memory error repurposing arrays

The maximum row length is not known in advance, yet rowlen could be
larger than number of rows m or the number of local columns. This sums
in

MatPermute_MPIAIJ: fix memory error repurposing arrays

The maximum row length is not known in advance, yet rowlen could be
larger than number of rows m or the number of local columns. This sums
in batches to avoid potential allocating per-row.

Reported-by: Barry Smith <bsmith@mcs.anl.gov>

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Merge branch 'shri/update-SuiteSparse' into shri/external-package-KLU

Conflicts:
conf/test
config/examples/arch-linux-pkgs-dbg-ftn-interfaces.py
config/examples/arch-linux-pkgs-opt.py

Merge branch 'master' into balay/tao-to-petsc

Merge branch 'jose/mat-vec-fixes' into maint

* jose/mat-vec-fixes:
Correctly check input type of Mat argument in MatMPIAIJGetLocalMat
Fix Matlab viewer for parallel complex vectors

Merge branch 'knepley/feature-mat-zerorowscols-baij'

* knepley/feature-mat-zerorowscols-baij:
cannot printf a complex number nor use %d for a PetscInt
Mat ex18: Fixed type for norm result
Mat

Merge branch 'knepley/feature-mat-zerorowscols-baij'

* knepley/feature-mat-zerorowscols-baij:
cannot printf a complex number nor use %d for a PetscInt
Mat ex18: Fixed type for norm result
Mat ex18: Added to nightly builds
Mat ex18: Fixed var initialization and allow command line arguments
Mat ex18: Fixed bug with nonlocal boundary
Mat ex18: Changed to UNIX encoding
Mat: Fixed uninitialized variable Reported-by: Jed Brown <jedbrown@mcs.anl.gov>
Mat: Fixed uninitialized variable Reported-by: Jed Brown <jedbrown@mcs.anl.gov>
Mat: Added MatZeroRowsColumns_MPIBAIJ() - Added some tests for Mat ex18
Mat: Updated MatZeroRowsColumns_MPIAIJ() to use PetscSF
Mat ex18: Test for MatZeroRowsColumns() in parallel - Now works for MPIAIJ
Mat: Fixed bug in MatZeroRowsColumns() - In MPIAIJ, the scatter of rhs values was using ADD instead of INSERT

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Merge branch 'master' into balay/tao-to-petsc

Conflicts:
include/makefile

Merge branch 'master' into knepley/feature-mat-zerorowscols-baij

Mat: Fixed uninitialized variable
Reported-by: Jed Brown <jedbrown@mcs.anl.gov>

Mat: Updated MatZeroRowsColumns_MPIAIJ() to use PetscSF

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

Conflicts:
src/ts/examples/tutorials/advection-dif

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

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

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Merged petsc/petsc into master

Merge branch 'jose/mat-vec-fixes'

* jose/mat-vec-fixes:
Correctly check input type of Mat argument in MatMPIAIJGetLocalMat
Fix Matlab viewer for parallel complex vectors

Conflicts:
src/vec/vec

Merge branch 'jose/mat-vec-fixes'

* jose/mat-vec-fixes:
Correctly check input type of Mat argument in MatMPIAIJGetLocalMat
Fix Matlab viewer for parallel complex vectors

Conflicts:
src/vec/vec/impls/mpi/pdvec.c

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Correctly check input type of Mat argument in MatMPIAIJGetLocalMat

MatMPIAIJGetLocalMat requires MPIAIJ matrix as input, but it used
a explicit cast in the declaration of variables, before checking

Correctly check input type of Mat argument in MatMPIAIJGetLocalMat

MatMPIAIJGetLocalMat requires MPIAIJ matrix as input, but it used
a explicit cast in the declaration of variables, before checking that
the input Mat is actually of this type.

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Merge branch 'master' into knepley/feature-dmda-section

* master: (319 commits)
SNESGS: Fix for uninitialized variable warning in gssecant.c
DMPlex: Fix for orientation in Gmsh files - Fixed tes

Merge branch 'master' into knepley/feature-dmda-section

* master: (319 commits)
SNESGS: Fix for uninitialized variable warning in gssecant.c
DMPlex: Fix for orientation in Gmsh files - Fixed test output
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()
...

Conflicts:
config/builder.py
include/petscdmda.h
src/dm/dt/interface/dtfe.c
src/dm/impls/da/dageometry.c
src/dm/impls/da/dalocal.c
src/dm/impls/plex/plexgeometry.c

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Mat: Fixed bug in MatZeroRowsColumns()
- In MPIAIJ, the scatter of rhs values was using ADD instead of INSERT

Merged petsc/petsc into master

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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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 knepley/feature-plex-refine-hex

* master: (68 commits)
DMPlex: More fixup from bad rebase, moved to DMGet/SetCoordinateSection()
DM: Added DMGet/SetCoordinateSection()

Merge branch 'master' into knepley/feature-plex-refine-hex

* master: (68 commits)
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
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
PetscFE: Added support for tensor product cells in PetscDualSpace_Lagrange
PetscFE: Added tensor product polynomial spaces
example fix /sandbox/petsc/petsc.clone-3/include/petscmath.h(260): error: identifier "PETSC_CXX_STATIC_INLINE" is undefined PETSC_STATIC_INLINE PetscReal PetscAbsScalar(PetscScalar a) {return a < 0.0 ? -a : a;} ^
remove warning in fun3d example "user.F", line 1256: warning: In-place macro substitution leaves line truncated "user.F", line 1259: warning: In-place macro substitution leaves line truncated "user.F", line 1262: warning: In-place macro substitution leaves line truncated
/Users/petsc/petsc.clone-2/src/ksp/ksp/examples/tutorials/ex56.c:59: warning: comparison between signed and unsigned integer expressions
fix examples for portability
fixed to example outputs
fix output for a few examples changed due to changes to -mat_view and not using -snes_monitor_short
...

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

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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