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

show more ...

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

show more ...

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 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: 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 ...

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 'madams/gamg-nokkt'

* madams/gamg-nokkt:
PCGAMG: remove dead function PCGAMGKKTProl_AGG
PCGAMG: remove dead KKT code

PCGAMG: remove dead KKT code

Merged petsc/petsc into rmills/petsc master.

Merge branch 'jed/stack-call-blas'

Fix performance bug that calling BLAS takes an amount of time dependent
on the number of memory allocations that the program has made.

* jed/stack-call-blas:
Pe

Merge branch 'jed/stack-call-blas'

Fix performance bug that calling BLAS takes an amount of time dependent
on the number of memory allocations that the program has made.

* jed/stack-call-blas:
PetscStackCallBLAS: new macro instead of PetscStackCall (skip CHKMEMQ)
Stack: consolidate handling of PetscStack

show more ...

PetscStackCallBLAS: new macro instead of PetscStackCall (skip CHKMEMQ)

When CHKMEMQ occurs on every call to BLAS or Lapack, we sometimes see
unacceptable performance degradation (orders of magnitude

PetscStackCallBLAS: new macro instead of PetscStackCall (skip CHKMEMQ)

When CHKMEMQ occurs on every call to BLAS or Lapack, we sometimes see
unacceptable performance degradation (orders of magnitude).
PetscStackCallBLAS is currently identical to PetscStackCall except for
skipping CHKMEMQ, but such checking could be made optional in the
future.

show more ...

Merge branch 'madams/gamg-aggoptions'

More delegation and less method-overriding.

* madams/gamg-aggoptions:
PCGAMG: call subtype destroy from PCDestroy_GAMG
PCGAMG: move subtype pointers to _PC

Merge branch 'madams/gamg-aggoptions'

More delegation and less method-overriding.

* madams/gamg-aggoptions:
PCGAMG: call subtype destroy from PCDestroy_GAMG
PCGAMG: move subtype pointers to _PCGAMGOps.
PCGAMG: set subtype in PCSetFromOptions_GAMG instead of PCCreate_GAMG

show more ...

PCGAMG: call subtype destroy from PCDestroy_GAMG

Having the subtype call the parent is more fragile because the
delineation of responsibilities is less clear and the call order could
be different fo

PCGAMG: call subtype destroy from PCDestroy_GAMG

Having the subtype call the parent is more fragile because the
delineation of responsibilities is less clear and the call order could
be different for different subtypes.

show more ...

PCGAMG: move subtype pointers to _PCGAMGOps.

Avoid stomping on user subtype preference in PCSetFromOptions_GAMG.

Subtype function pointers are now cleared by PCGAMGSetType to avoid
lingering from t

PCGAMG: move subtype pointers to _PCGAMGOps.

Avoid stomping on user subtype preference in PCSetFromOptions_GAMG.

Subtype function pointers are now cleared by PCGAMGSetType to avoid
lingering from the last type in cases where not all pointers get set.
Also store the type name to help with debugging and diagnostic output.

show more ...

PCGAMG: set subtype in PCSetFromOptions_GAMG instead of PCCreate_GAMG

Merged petsc/petsc into rmills/petsc master

Merge branch 'barry/rm-xxxregisterdynamic'

* barry/rm-xxxregisterdynamic:
Registration: remove stale 'XXRegisterDynamic)' entries in man pages
TS examples: fix use of PetscFunctionList and add t

Merge branch 'barry/rm-xxxregisterdynamic'

* barry/rm-xxxregisterdynamic:
Registration: remove stale 'XXRegisterDynamic)' entries in man pages
TS examples: fix use of PetscFunctionList and add to nightlies
Changes: Note updates to XRegisterDynamic/PetscObjectComposeFunctionDynamic
PetscObjectComposeFunctionDynamic: remove stale docs and usage
developers.tex: remove complications from function composition with dlls
removed string version of function name for XXXRegister(), PetscFunctionListAdd() and PetscObjectComposeFunction()
changes: document PetscFunctionListAdd() API change
developers.tex: update documentation of PetscObjectComposeFunction
removed path and MPI_Comm arguments from PetscFunctionListFind/Add()
removed path argument to XXXInitializePackage() and XXXRegister()
removed XXXRegisterDynamic() but kept the APIs for everything else underneath the same phase I of the update to handling registering function pointers

show more ...