Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
s

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
src/snes/impls/composite/snescomposite.c
src/snes/impls/gs/snesgs.c
src/snes/impls/nasm/nasm.c
src/snes/impls/ngmres/snesngmres.c

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Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

This option was mostly redundant because normal shared libraries satisfy
all the same needs. This commit adds the run-time option
-dynami

Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

This option was mostly redundant because normal shared libraries satisfy
all the same needs. This commit adds the run-time option
-dynamic_library_preload that can be used to load/initialize all the
packages in advance, as used to be done when --with-dynamic-loading.

The PetscDLLibraryRegister_petscxxx functions have been kept, but are
not called unless -dynamic_library_preload is used. The petsc-dev
discussion, "Why --with-dynamic-loading?" did not reach consensus about
whether this was ever useful, so it may also be removable.

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Merge branch 'master' into knepley/feature-dt-fem

* master: (211 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries

Merge branch 'master' into knepley/feature-dt-fem

* master: (211 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:
config/builder.py
src/dm/impls/plex/plexgeometry.c

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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

Merge branch 'barry/improve-memory-logging'

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

Merge branch 'barry/fix-PetscObjectPrintClassNamePrefixType'

* barry/fix-PetscObjectPrintClassNamePrefixType:
update tests of src/mat/examples/tests/ex136.c
Use classname in object for object na

Merge branch 'barry/fix-PetscObjectPrintClassNamePrefixType'

* barry/fix-PetscObjectPrintClassNamePrefixType:
update tests of src/mat/examples/tests/ex136.c
Use classname in object for object name when calling PetscObjectPrintClassNamePrefixType() instead of some string with less precise name passed in

Conflicts:
src/snes/interface/snes.c

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Merged petsc/petsc into rmills/petsc master.

Merge branch 'jed/matnullspaceremove-inplace'

* jed/matnullspaceremove-inplace:
Mat: remove 'vec' member of MatNullSpace
Mat: remove third argument to MatNullSpaceRemove

logging memory now credits to all ancestors

Use classname in object for object name when calling PetscObjectPrintClassNamePrefixType() instead of some string with less precise name passed in

Mat: remove 'vec' member of MatNullSpace

We no longer support out-of-place removal, so this field is only
relevant in MatNullSpaceTest. Might as well simplify the data structure
and free the memory

Mat: remove 'vec' member of MatNullSpace

We no longer support out-of-place removal, so this field is only
relevant in MatNullSpaceTest. Might as well simplify the data structure
and free the memory earlier.

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Mat: remove third argument to MatNullSpaceRemove

Out of place removals were dangerous because the MatNullSpace held the
only reference to the resulting Vec, which is dangerous. This use case
is rar

Mat: remove third argument to MatNullSpaceRemove

Out of place removals were dangerous because the MatNullSpace held the
only reference to the resulting Vec, which is dangerous. This use case
is rare (never used in PETSc itself) and can easily be accomplished:

VecDuplicate(x,&y);
VecCopy(x,y);
MatNullSpaceRemove(nullsp,y);

Suggested-by: Tobin Isaac <tisaac@ices.utexas.edu>

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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 path argument to XXXInitializePackage() and XXXRegister()

Merge branch 'master' into jed/ts-eimex

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

Conflicts:
src/ts/interface/tsregall.c

added PetscObjectComm() and used it to replace (((PetscObject)obj)->comm)

Hg-commit: 3da37c458124ad48ae939f4e9823e4430ee0b8be

removed typeid from PetscHeaderCreate() args since it is not know at create time anyway

Hg-commit: 368e928141e31cf1ff6cf108913006e5886dc6cc

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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commit after merge

Hg-commit: db805e8197486aa7db018c01793dec447b9e9cbb

Uncrustified src/mat/*.

Hg-commit: 5c6f04286a6cfcd98361b2479b884c0041d95b73

commit aftr merge

Hg-commit: 854807b200896ff0e3d6fb344a549ed1a2b93850