Merge branch 'knepley/fix-section-clone'

* knepley/fix-section-clone:
Plex ex3: Test does not work with single precision
Section: Must also copy field symmetries when cloning
Section: Allow NU

Merge branch 'knepley/fix-section-clone'

* knepley/fix-section-clone:
Plex ex3: Test does not work with single precision
Section: Must also copy field symmetries when cloning
Section: Allow NULL argument to PetscSectionSetSym()
Plex ex3: Added tests for Q3
Plex: Added picture for 3D hex interpolation
Section: Copy symmetries when cloning

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fix build error %D -> %d
Reported-by: "Jose E. Roman" <jroman@dsic.upv.es>

Merge branch 'maint'

fix compile error on Mac with optimized build, with C++ and complex scalars

Reported-by: Jose E. Roman <jroman@dsic.upv.es>

/Users/jroman/soft/petsc-3.9/include/../src/vec/vscat/impls/vpscat.h:415:

fix compile error on Mac with optimized build, with C++ and complex scalars

Reported-by: Jose E. Roman <jroman@dsic.upv.es>

/Users/jroman/soft/petsc-3.9/include/../src/vec/vscat/impls/vpscat.h:415:133: error: cannot pass object of non-POD type 'PetscScalar' (aka 'complex<double>') through variadic function; call will abort at runtime [-Wnon-pod-varargs]
SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"[%D] statecnt %g > [%D] my_statecnt %g",i,sharedspace[-1],msrank,yv[-1]);
^
/Users/jroman/soft/petsc-3.9/include/../src/vec/vscat/impls/vpscat.h:459:110: error: cannot pass object of non-POD type 'PetscScalar' (aka 'complex<double>') through variadic function; call will abort at runtime [-Wnon-pod-varargs]
SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"[%D] statecnt %g > [%D] my_statecnt %g",i,sharedspace[-1],msrank,xv[-1]);

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fix fix-pr879-jczhang-optimize-vecscatter-multi-copy

- change VecScatterLocalOptimizeCopy back to VecScatterLocalOptimizeCopy_Private as this is not a public routine
- remove duplicate copy in vpsca

fix fix-pr879-jczhang-optimize-vecscatter-multi-copy

- change VecScatterLocalOptimizeCopy back to VecScatterLocalOptimizeCopy_Private as this is not a public routine
- remove duplicate copy in vpscat.c. This is protected by PETSC_HAVE_MPI_WIN_CREATE_FEATURE flag - and breaks uni build
- rename VecScatterLocalOptimizeCopy_Private_MPI1 to VecScatterLocalOptimizeCopy_Private
- move prototype to vecimpl.h and avoid duplicating it in vscat.c

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Merge branch 'jczhang/optimize-vecscatter-multi-copy' [PR #879]

* jczhang/optimize-vecscatter-multi-copy:
Optimize local scatter when it is made of multiple copies.

Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \(

Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \( -name "*.c" -or -name "*.h" -or -name "*.cxx" \) | xargs gsed -i 's/Notes\s*:\s*\(\w.*\)/Notes:\n \1/'

This adds a newline and 4 spaces whenever "Notes:" is followed by any "word" character, in any .c, .h, or .cxx file in src/ or include/

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Section: Must also copy field symmetries when cloning

Section: Allow NULL argument to PetscSectionSetSym()

Section: Copy symmetries when cloning

Merge remote-tracking branch 'origin/tisaac/feature-dmfield'

* origin/tisaac/feature-dmfield: (56 commits)
Plex: Updated test output for DMLabel change
DMLabel: make empty ISs strides
DMSwarm:

Merge remote-tracking branch 'origin/tisaac/feature-dmfield'

* origin/tisaac/feature-dmfield: (56 commits)
Plex: Updated test output for DMLabel change
DMLabel: make empty ISs strides
DMSwarm: silence static analyzer warning
PetscFECreateDefault: fix custom Fortran interface to use MPI_Comm
SNES ex69: Updated test output
SNES ex69: Removed all mantle stuff and change fields to constants - Also use dsymutil for executables
SNES ex69: Removed special partition
SNES ex69: Fixed null space creation - Null space locks its vectors
PetscFE: PetscFECreateDefault() now takes MPI_Comm instead of DM
DMField: default initialization of variable
PetscFE: fix integration for openCL
PetscFEGeomComplete(): correct normal vector in 2D.
DMField: c++/complex fixes
DMField: empty processor protections
DMField regression test fixes
DMLabel: try to keep stride IS as stride IS as much as possible
DMPlexRefine(): create depth before hybrid-bounded label
DMField: documentation of interface
DMField: implement shell
DMPlex: rename newly created label
...

Conflicts:
src/dm/dt/interface/dtfe.c
src/snes/examples/tutorials/ex69.c
src/snes/utils/dmplexsnes.c

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Section: Small fix

Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep us

Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep usage on solaris [use egrep]
opensolaris: fix errors
Update timer reporting and minor reporting fix
Remove redundant if statement. Found by @jedbrown
Fixed problem with order of developer photos on website.
superlu_dist: use correct flag in example [PETSC_HAVE_SUPERLU -> PETSC_HAVE_SUPERLU_DIST]
Bib: PERMON ref
fix for osx
doc: more author fixes
doc: more author fixes
Italicized "orderings" in MPI process placement discussion.
Added Richard to the user manual author list.
Added Richard to the list of active developers on the website.
add string check for MS-MPI and IMPI timeout errors
opensolaris does not have multiple grep utils - but default one does not support -F. So use fgrep instead
Standardizing timeout checks
Report wall clock time of total tests
Use time instead of date %s
...

Conflicts:
include/petscpc.h
src/ksp/ksp/interface/itfunc.c

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Merge remote-tracking branch 'origin/jczhang/fix-vecscatter-msg-logging'

Merge remote-tracking branch 'origin/dalcinl/fix-vecscatter-initpkg'

Replay the message size logging bug fix in vpscat_mpi1

Fix a bug in vecscatter message size logging when bs!=1

We multiplied bs in Irecv but forgot to do it in Isend. When bs != 1, old code
gave incorrect average message length in vecscatter with -log_v

Fix a bug in vecscatter message size logging when bs!=1

We multiplied bs in Irecv but forgot to do it in Isend. When bs != 1, old code
gave incorrect average message length in vecscatter with -log_view.

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Replay the vecscatter multi-copy optimization in vpscat_mpi1

We should remove the code duplication finally.

Do VecScatterLocalOptimizeCopy after VecScatterRemap

VecScatterRemap() is used to translate a DMGlobalToLocal vecscatter context to a
DMLocalToLocal vecscatter context. The remapping may invalidate

Do VecScatterLocalOptimizeCopy after VecScatterRemap

VecScatterRemap() is used to translate a DMGlobalToLocal vecscatter context to a
DMLocalToLocal vecscatter context. The remapping may invalidate old optimizaitons or
enable new optimizations. So we call VecScatterLocalOptimizeCopy after VecScatterRemap
to start optimizations from scratch

VecScatterLocalOptimizeCopy() was VecScatterLocalOptimizeCopy_Private(). This commit
made the function not private anymore so we changed its name.

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Style change: refactor VecScatterRemap to make it easier to read

Optimize local scatter when it is made of multiple copies

Old code optimized local scatter when it was actually a copy. We extend it to handle cases
when local scatter is made of multiple copies.

O

Optimize local scatter when it is made of multiple copies

Old code optimized local scatter when it was actually a copy. We extend it to handle cases
when local scatter is made of multiple copies.

One particular application of this optimzation is when we call DMGlobalToLocalBegin/End to
copy a global vector to a local vector created by DMCreateGlobalVector or DMCreateLocalVector
(see src/ts/examples/tutorials/advection-diffusion-reaction/ex5.c). The global vector is
contiguous in memory, but interior part of the local vector is only piece-wise contiguous in
memory. Therefore, multiple copies are needed.

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VecScatterDestroy: Error if in use AND refcount is one

VecScatterDestroy: Fix for type not set

VecScatterInitializePackage: Fix for -{info|log}_exclude cmdline options

Revert "VecScatterInitializePackage() must be called otherwise VEC_SCATTER_CLASSID is not set in ksp/ksp/examples/tutorials/ex100.c and Python fails with its uninitialized value of 0."

This reverts

Revert "VecScatterInitializePackage() must be called otherwise VEC_SCATTER_CLASSID is not set in ksp/ksp/examples/tutorials/ex100.c and Python fails with its uninitialized value of 0."

This reverts commit 856751a580fa99a94a1486bc222baa5a948e2b72.

Reverted as this fix should be in petsc4py - not petsc

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