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

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

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

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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 'barry/citations'

PCHypre: fix spelling

completed initial implementation of PetscCitationsRegister() and added proper cites for hypre, ml, mumps

-citations option causes the print out of approriate bibtex citation indices for all packages USED in the run
Most of the appropriate citations still need to be added

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

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Merge branch 'barry/rm-xxxregisterdynamic' into jed/ts-eimex

PetscObjectComposeFunctionDynamic() and TSRegisterDynamic() were
replaced by PetscObjectComposeFunction() and TSRegister(), both of which

Merge branch 'barry/rm-xxxregisterdynamic' into jed/ts-eimex

PetscObjectComposeFunctionDynamic() and TSRegisterDynamic() were
replaced by PetscObjectComposeFunction() and TSRegister(), both of which
drop the string name argument.

* barry/rm-xxxregisterdynamic: (82 commits)
...

Conflicts:
src/ts/interface/tsregall.c

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removed string version of function name for XXXRegister(), PetscFunctionListAdd() and PetscObjectComposeFunction()

Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

Automerge.

Hg-commit: b6659d546870fb013f3da5bcd5066d1dc0dc329c

Merge branch 'master' of gitifyhg::ssh://hg@bitbucket.org/BarryFSmith/petsc-dev-simp

Symbol visibility and namespacing.

C++ builds always set extern "C" and can be called from plain C. Most
users w

Merge branch 'master' of gitifyhg::ssh://hg@bitbucket.org/BarryFSmith/petsc-dev-simp

Symbol visibility and namespacing.

C++ builds always set extern "C" and can be called from plain C. Most
users will only want --with-clanguage=C++ for std::complex.


Hg-commit: f848d02318cae92d7b32037c7ee88f92dbe46347

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Change all PETSC_EXTERN_C to PETSC_EXTERN

Hg-commit: 8d2ebbb193fb583bccc64015e35640c4e08c3426

Change all PETSC_EXTERN_C to PETSC_EXTERN


Hg-commit: ba0cf153561ff2dc521f42e94b7164fbe7b5d798

completed removing unneeded EXTERN_C_BEGIN/END from Mat directories and converting to PETSC_EXTERN_C for constructors
tested with and without dynamic with and without C++

Hg-commit: 7d27d7f4d9ea3bfe

completed removing unneeded EXTERN_C_BEGIN/END from Mat directories and converting to PETSC_EXTERN_C for constructors
tested with and without dynamic with and without C++

Hg-commit: 7d27d7f4d9ea3bfe6616fafdfb32d046b5db53a1

show more ...

Automerge.

Hg-commit: 2a552fd584bf855b9dc42efec9e8ab778063a84f