Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (273 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (273 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

Conflicts:
include/petscdmplex.h

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

* master: (287 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib e

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

* master: (287 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

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Merge branch 'master' of bitbucket.org:petsc/petsc

Sys Logging: revert parent traversal

Traversing parents is dangerous because we can have dangling links.
The problem is explained in more detail on petsc-dev:

Subject: Memory corruption on 'maste

Sys Logging: revert parent traversal

Traversing parents is dangerous because we can have dangling links.
The problem is explained in more detail on petsc-dev:

Subject: Memory corruption on 'master' (barry/improve-memory-logging)
Message-ID: <87ob8snnht.fsf@mcs.anl.gov>

but the pattern of creating an inner solver with the outer PC is an
example that leaves a dangling parent.

KSPCreate(PETSC_COMM_WORLD,&eksp);
KSPGetPC(ksp,&pc);
KSPSetPC(eksp,pc);
// Use eksp for something, or not
KSPDestroy(&eksp); // pc->parent still points at eksp

In the general case, objects could have multiple parents and multiple
children. How would we avoid over-counting? How do we make the
addition or removal of parent-child relationships commutative in the
sense that the memory logging would be the same?

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Merge branch 'barry/improve-memory-logging'

Conflicts:
src/ksp/pc/impls/redundant/redundant.c
src/mat/interface/matnull.c

keep separate count of object memory and memory of all children

logging memory now credits to all ancestors

Merge branch 'master' of bitbucket.org:petsc/petsc

Merged petsc/petsc into rmills/petsc master

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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Merge branch 'barry/fix-petsctime'

Changed PetscTime(), PetscTimeSubtract(), PetscTimeAdd() to inline functions from macros
removed PetscGetTime()

Merge branch 'master' into jed/ts-eimex

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

Conflicts:
src/ts/interface/tsregall.c

mpe.h should never be exposed to all the PETSc code and certainly not to user code, fixed
logging code is still pretty ugly, could do with some cleanup

Hg-commit: d1a7c9a9194d1c3197bd4fe4054fef154d5

mpe.h should never be exposed to all the PETSc code and certainly not to user code, fixed
logging code is still pretty ugly, could do with some cleanup

Hg-commit: d1a7c9a9194d1c3197bd4fe4054fef154d5bc08e

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only compile utilities used by MPE if MPE is installed and make the utility intern

Hg-commit: 2f5f089601f3e09f100c5ff5643a47670a6717ae

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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PETSc interfaces are always extern "C"

PETSc can now be built using a C++ compiler (--with-clanguage=C++) and
then called from plain C code (compiled using a C compiler).

These configure options ha

PETSc interfaces are always extern "C"

PETSc can now be built using a C++ compiler (--with-clanguage=C++) and
then called from plain C code (compiled using a C compiler).

These configure options have been removed:

--with-c++-support : was not doing anything
--with-c-support : effectively always true now

PETSC_USE_EXTERN_CXX has been removed.

Hg-commit: df9678d34db91a29a55887d1193fea8e87ce32bf

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PETSc interfaces are always extern "C"

PETSc can now be built using a C++ compiler (--with-clanguage=C++) and
then called from plain C code (compiled using a C compiler).

These configure options ha

PETSc interfaces are always extern "C"

PETSc can now be built using a C++ compiler (--with-clanguage=C++) and
then called from plain C code (compiled using a C compiler).

These configure options have been removed:

--with-c++-support : was not doing anything
--with-c-support : effectively always true now

PETSC_USE_EXTERN_CXX has been removed.


Hg-commit: 51116dd5b11147ee16a9f551dec9723757fa740b

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Remove petscviewer.h from petscsys.h

Much of sys is independent of viewer. Viewer is used in so many other
places that it is now included by petscvec.h.

Hg-commit: 1d745f01618aa51d3043fb1f87b0546f6

Remove petscviewer.h from petscsys.h

Much of sys is independent of viewer. Viewer is used in so many other
places that it is now included by petscvec.h.

Hg-commit: 1d745f01618aa51d3043fb1f87b0546f60e6e730

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Merge branch 'private-impl-headers'

petsc-private/petscimpl.h and vecimpl.h are no longer included by
petscsys.h and petscvec.h. Some inline functions become normal functions
as a consequence of the

Merge branch 'private-impl-headers'

petsc-private/petscimpl.h and vecimpl.h are no longer included by
petscsys.h and petscvec.h. Some inline functions become normal functions
as a consequence of these changes.

Hg-commit: 5c59734726c7c41f493a5f5b9303cfab5c66ae21

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Make petscimpl.h private

Hg-commit: 910e8b03a54a915953944da6f75eb81c807d7428

added include stddef.h to petscsys.h
removed many duplicate includes of system includes

Hg-commit: 26ea335c035572bcbd495f9993b3270632d5d3c6

removed a bunch of duplicate unneeded includes of std include files

Hg-commit: b6c9f3e2b0eb8b7277fe131cc83beede5d495522

removed PETSC_NULL from C and Fortran (except declaration in C for backward compatibility). Kept PETSC_NULL_xxx for Fortran
Fixed a few bugs where PETSC_NULL had been used incorrectly.

Hg-commit: 05

removed PETSC_NULL from C and Fortran (except declaration in C for backward compatibility). Kept PETSC_NULL_xxx for Fortran
Fixed a few bugs where PETSC_NULL had been used incorrectly.

Hg-commit: 054705a517d7f4388a8a084415d7478cbe95dff4

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