Merge branch 'stefano_zampini/pcbddc-reusebddc'

* stefano_zampini/pcbddc-reusebddc:
PCBDDC: remove unneeded code to check nearnullspace
PCBDDC: remove trailing whitespaces from source
PCBDDC:

Merge branch 'stefano_zampini/pcbddc-reusebddc'

* stefano_zampini/pcbddc-reusebddc:
PCBDDC: remove unneeded code to check nearnullspace
PCBDDC: remove trailing whitespaces from source
PCBDDC: solved compilation error with complex build
PCBDDC: introduce a new variable in PCBDDC data stucture to store the actual number of current vertices (corners with constraints with basis changed)
PCBDDC: make BtoNmap a member of bddc data struct (created once after PCISSetUp)
PCBDDC: check of dirichlet and neumann solvers is not needed if pcbddc->NullSpace is not present
PCBDDC: improved reuse of coarse matrix
PCBDDC: better management of primal space. Now a coarse numbering is computed if and only if the primal space has been really changed
PCBDDC: allow different customization of dirichlet and neumann boundary indices among successive linear solves
PCBDDC: now PCBDDC reuses part of its private data if NearNullSpace customization is changed between different linear solves
PCBDDC: local work vectors should be created only if new constraints are created and the relevant sizes are different
PCBDDC/PCIS: make vec4_D a member of pcis, not pcbddc
PCBDDC: Prepare for different primal spaces customization among different linear solves
PCBDDC: demand object destruction to setup routines for BDDCGraph and constraints

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c (also update PetscMalloc[1-7])

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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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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

MATIS: solved memory leak when setting a new local to global mapping

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

Merge branch 'barry/fix-singleton-viewer'

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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Sys: add PetscMalloc1 macro, array allocation without redundant types

The type is inferred from the pointer return type. This patch is
automated via the following script:

git grep -l 'PetscMalloc(

Sys: add PetscMalloc1 macro, array allocation without redundant types

The type is inferred from the pointer return type. This patch is
automated via the following script:

git grep -l 'PetscMalloc(.*sizeof' src | xargs perl -pi -e 's@PetscMalloc\(([^,;]*[^,; ]) *\* *sizeof\([^,;()]+\),@PetscMalloc1($1,@'

This commit contains an additional bug-fix in csrperm.c, fixing pointer
arity. The code was introduced in 2006, but the allocation could not
have been correct at any time. This probably means that
MatDuplicate_SeqAIJPERM has never been tested.

a54129beb540034ba105796c682d589e7e1111f2
Richard Tran Mills <rmills@ornl.gov>

Added MATSEQCSRPERM support for MatDuplicate() and conversion to/from
MATSEQAIJ. Note that these changes are not quite debugged.

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fixed PetscViewerASCIIPrintf() for a single viewer so that the singletons ASCII output is actually preserved

PCBDDC: added reuse of coarse subassembling information

In order to do do, I had to change the MATIS class (I dont know why there was a guard for is->mapping in matis code)

Solved a couple of bugs

PCBDDC: added reuse of coarse subassembling information

In order to do do, I had to change the MATIS class (I dont know why there was a guard for is->mapping in matis code)

Solved a couple of bugs when doing multilevel and a dbg_viewer on a single level only

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Merge branch 'stefano_zampini/pcbddc-reusebddc' into stefano_zampini/pcbddc-multilevel-improvement

PCBDDC: improved reuse of coarse matrix

MatCovert_IS_AIJ renamed in MatISGetMPIXAIJ (MatConvert does not support out-of-place reuse of destination matrix)
Added some lines in MATIS code (commented).

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

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

Merged petsc/petsc into rmills/petsc master.

Merge branch 'stefano_zampini/pcbddc-development'

Conflict with 'jed/matnullspaceremove-inplace', resolved using:

$ git merge -X theirs --no-commit stefano_zampini/pcbddc-development
$ git grep

Merge branch 'stefano_zampini/pcbddc-development'

Conflict with 'jed/matnullspaceremove-inplace', resolved using:

$ git merge -X theirs --no-commit stefano_zampini/pcbddc-development
$ git grep -l MatNullSpaceRemove src/ksp | xargs perl -pi -e 's@(MatNullSpaceRemove\([^,]+,[^,]+),NULL\)@$1)@'
$ git commit -a

* stefano_zampini/pcbddc-development:
PCBDDC: add wrappers for PetscStackCallBLAS
PCBDDC: Final fix for locally periodic problems
PCNNCreateCoarseMatrix: fix allocation error
PCIS: consider myself as a neighbor when classifying interface nodes
PCBDDC: Remove misuses of neighbours_set in FETI-DP code
PCBDDC: Coarse solution lives in the span of phi (not psi)
MATIS: Add IsSymmetric and IsHermitian implementations
PCBDDC: More robust method to compute local boundary nodes
PCBDDC: Add partial support for periodic problems replacing Sort with RemoveDups
PCBDDC: Add support for non-symmetric linear systems
PCBDDC: Stiffness scaling should be rebuilt in any case (just to be safe)
PCBDDC: Remove trailing blanks
PCBDDC: Consistency of CSR graph passed in postponed to PCSetUp
PCBDDC: Preliminary work to split PCBDDCCoarseSetUp in simpler pieces
PCBDDC: allow compilation without metis header
PCBDDC: Optimal allocation in PCBDDCGetPrinalVerticesLocalIdx
PCBDDC: add verbosity level to graph view
PCBDDC: change boolean debug flag to integer -pc_bddc_check_level
PCBDDC: Workaround for BAIJ local matrices: convert to AIJ for coarse matrix
PCIS: Use PETSC_COMM_SELF instead of MPI_COMM_SELF
PCBDDC: many changes
ISG2LMapApply: fix __FUNCT__ and invalid access before globals are set up

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MATIS: Add IsSymmetric and IsHermitian implementations

Merged petsc/petsc into rmills/petsc master