Merge branch 'master' into prbrune/removeunwrappedmathfunctions

Merge branch 'jed/fix-restrict-cxx' into maint

== PETSC_ARCH must be reconfigured ==

Fix C/C++ choice for PETSC_RESTRICT and PETSC_STATIC_INLINE.

* jed/fix-restrict-cxx:
config: define lang-spec

Merge branch 'jed/fix-restrict-cxx' into maint

== PETSC_ARCH must be reconfigured ==

Fix C/C++ choice for PETSC_RESTRICT and PETSC_STATIC_INLINE.

* jed/fix-restrict-cxx:
config: define lang-specific macros in petscconf.h, choose in petscsys.h

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Merge branch 'jed/fix-restrict-cxx'

* jed/fix-restrict-cxx:
config: define lang-specific macros in petscconf.h, choose in petscsys.h

config: define lang-specific macros in petscconf.h, choose in petscsys.h

C and C++ compilers can use different spellings for concepts like
"restrict", "static inline", and "__func__". Previously, t

config: define lang-specific macros in petscconf.h, choose in petscsys.h

C and C++ compilers can use different spellings for concepts like
"restrict", "static inline", and "__func__". Previously, these were
defined for the "C language", meaning that they could fail if when
clanguage=C PETSc headers are included by a file that is being compiled
by the C++ compiler. This happens outside of PETSc, but also with
third-party packages like Elemental (matelem.cxx).

Karl Rupp proposed an implementation that puts the __cplusplus dispatch
into petscconf.h, but I prefer that petscconf.h contain no logic.

Reported-by: Geoffrey Irving <irving@naml.us>
Reported-by: Geoff Oxberry <goxberry@mit.edu>

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

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Ste

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

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Stefano
fixed bug that has appeared recently of false positive errors when there are zero local equations on coarse grids in gamg-agg.
MatSchurComplement: Must initialize KSP package
bib: fix inbook citation
Bib: Updated some refs
SNES: fix copy/paste in man page
fortran: fix KSPCONVERGEDDEFAULT and SNESCONVERGEDSKIP in fortran includes
Mat SBAIJ: avoid invalid memory read in MatSOR_SBAIJ
Revert "MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values"
PCGAMG: fix corruption for multiple solves when MatSetNearNullSpace is used
PCGAMG: remove distracting comment
KSP ex49: restrict near-null space for elasticity example with sym BC
MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values was provided ordered by row within the block rows instead of by block as it was originally designed to be. Also added more discussion to the manual pages on the expected order of the values
Fix accidental creation of the matrices in SNESNCG used for linear analogue LS.
PCGAMG: add man page for PCGAMGType
fortran: fix snesconvergedskip_() kspconvergedskip_() kspconvergeddefault*_()
rm //
Sys: new_ir changed from PetscInt to PetscObjectState - so fix mallocs to use the new type
SNES: Fixed package init in SNESLineSearchCreate()
...

Conflicts:
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex5.c
src/dm/impls/plex/plex.c
src/dm/interface/dm.c

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Merge branch 'jed/remove-dynamic-loading-option'

Option --with-dynamic-loading has been removed. Similar functionality
is available via the run-time option -dynamic_library_preload.

* jed/remove-d

Merge branch 'jed/remove-dynamic-loading-option'

Option --with-dynamic-loading has been removed. Similar functionality
is available via the run-time option -dynamic_library_preload.

* jed/remove-dynamic-loading-option:
Sys: PetscContainerCreate must call PetscSysInitializePackage
Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

Conflicts:
src/dm/impls/mesh/mesh.c
src/dm/interface/dlregisdmdm.c
src/docs/website/documentation/changes/dev.html

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PetscObjectStateGet: fix stale comments about *StateQuery

Merge branch 'hzhang/snes-jacobiancoloropt' of bitbucket.org:petsc/petsc into hzhang/snes-jacobiancoloropt

Merge branch 'jed/object-id'

* jed/object-id:
Sys: mark PetscObjectState modification as logically collective
Sys: convert object ID to 64-bit and add PetscObjectGetId()
Sys: typedef PetscObje

Merge branch 'jed/object-id'

* jed/object-id:
Sys: mark PetscObjectState modification as logically collective
Sys: convert object ID to 64-bit and add PetscObjectGetId()
Sys: typedef PetscObjectState and change all accessors
unified PetscObjectStateXXX() commands. Fixed PetscObjectStateQuery() to PetscObjectStateGet()

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Merge branch 'hzhang/snes-jacobiancoloropt' of bitbucket.org:petsc/petsc into hzhang/snes-jacobiancoloropt

Merge branch 'barry/add-petscfopensetmachine'

* barry/add-petscfopensetmachine:
added PetscPOpenSetMachine() and command line form

Sys: convert object ID to 64-bit and add PetscObjectGetId()

Object Ids must never be reused. If objects are created in iterations
(e.g., due to sloppy coding or adaptivity), a 32-bit Id could overf

Sys: convert object ID to 64-bit and add PetscObjectGetId()

Object Ids must never be reused. If objects are created in iterations
(e.g., due to sloppy coding or adaptivity), a 32-bit Id could overflow
in a long simulation. Use a typedef for clarity.

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Sys: typedef PetscObjectState and change all accessors

State is used to manage caches of intermediate structures. If state
overflowed, it would allow a cached value to be reused incorrectly,
leadin

Sys: typedef PetscObjectState and change all accessors

State is used to manage caches of intermediate structures. If state
overflowed, it would allow a cached value to be reused incorrectly,
leading to wrong results or possibly corruption. In long runs, it is
conceivable for an object to undergo 2^32 state transitions between
encounters, thus it is important to use a 64-bit counter. The typedef
is just for clarity.

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Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

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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update to use SAWs _Block feature on PetscObjectSAWsBlock and -options_gui

Merge branch 'barry/petscdatatypefromstring' into maint

* barry/petscdatatypefromstring:
Sys: add PetscDataTypeFromString() and test code

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 'knepley/reordering'

* knepley/reordering:
Mat ex170: Comments
Mat ex170: Test for MatMult() using max instead of plus - Finds the number of connected components in parallel - Can s

Merge branch 'knepley/reordering'

* knepley/reordering:
Mat ex170: Comments
Mat ex170: Test for MatMult() using max instead of plus - Finds the number of connected components in parallel - Can still optimize better in parallel
Mat: Added stuff to let me do (max, mult) algebra things for reordering - Added MatMultMax_SeqAIJ() and MatMultAddMax_SeqAIJ() - Added PetscSparseDenseMaxDot()
Vec: Added VecUniqueEntries() - This is purely diagnostic, but I think its useful for tests
Sys: Added PetscSortRemoveDupsReal()

Conflicts:
config/builder.py

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Merge branch 'barry/petscdatatypefromstring'

Provide a way to determine type sizes dynamically from a shared
library, as requested by Julia developers.

* barry/petscdatatypefromstring:
Sys: add P

Merge branch 'barry/petscdatatypefromstring'

Provide a way to determine type sizes dynamically from a shared
library, as requested by Julia developers.

* barry/petscdatatypefromstring:
Sys: add PetscDataTypeFromString() and test code

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Sys: add PetscDataTypeFromString() and test code

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