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

show more ...

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

show more ...

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

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

show more ...

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,@'

show more ...

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.

show more ...

PetscMalloc[2-7]: remove type arguments, infer from pointer type

This change can be performed almost entirely by this script:

git grep -l PetscMalloc[2-7] $1 | xargs perl -pi \
-e '
s@PetscMalloc

PetscMalloc[2-7]: remove type arguments, infer from pointer type

This change can be performed almost entirely by this script:

git grep -l PetscMalloc[2-7] $1 | xargs perl -pi \
-e '
s@PetscMalloc2\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc2($1,$3,$4,$6)@;
s@PetscMalloc3\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc3($1,$3,$4,$6,$7,$9)@;
s@PetscMalloc4\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc4($1,$3,$4,$6,$7,$9,$10,$12)@;
s@PetscMalloc5\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc5($1,$3,$4,$6,$7,$9,$10,$12,$13,$15)@;
s@PetscMalloc6\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc6($1,$3,$4,$6,$7,$9,$10,$12,$13,$15,$16,$18)@;
s@PetscMalloc7\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc7($1,$3,$4,$6,$7,$9,$10,$12,$13,$15,$16,$18,$19,$21)@;
'

show more ...

Merge branch 'barry/minor-draw-improvements' into jed/chem

Merge branch 'barry/fix-hypre-superlu-64bitindex-casts'

another cast between PetscInt* and Hypre_Int* needed for 64 bit indices

since external packages use a variety of different types for 64 bit indices
(though all have the same bit values) casts are needed for some compilers to
prevent warning messages when using 64 bit ind

since external packages use a variety of different types for 64 bit indices
(though all have the same bit values) casts are needed for some compilers to
prevent warning messages when using 64 bit indices

show more ...

Merge branch 'barry/reduce-dmsetup-da-memoryusage' of bitbucket.org:petsc/petsc into barry/reduce-dmsetup-da-memoryusage

Hypre: Fix cast for DMDAGetGlobalIndices()

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 'jed/mat-restore-zeros'

* jed/mat-restore-zeros:
MatRestoreRowIJ/ColumnIJ: zero pointers to catch accidental misuse
MatRestoreRow: zero arguments after restore to catch accidental m

Merge branch 'jed/mat-restore-zeros'

* jed/mat-restore-zeros:
MatRestoreRowIJ/ColumnIJ: zero pointers to catch accidental misuse
MatRestoreRow: zero arguments after restore to catch accidental misuse

show more ...

MatRestoreRowIJ/ColumnIJ: zero pointers to catch accidental misuse

Only zero in case where the operation is "done" so that user's
uninitialized arguments are not overwritten. I don't know if it's
b

MatRestoreRowIJ/ColumnIJ: zero pointers to catch accidental misuse

Only zero in case where the operation is "done" so that user's
uninitialized arguments are not overwritten. I don't know if it's
best, but this is consistent with done=FALSE meaning that the arguments
are not changed.

Explicitly pass NULL when intentionally using the number of rows after
restoring.

show more ...

Merged petsc/petsc into rmills/petsc master