Plex: Ghosted DM inherits setfromoptions state

Merge branch 'knepley/feature-label-object' [PR #1284]

* knepley/feature-label-object:
DMLabel: Make it a PetscObject

Merged petsc/petsc into master

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

Merge branch 'knepley/plexdoc-better-docs-for-dmplexcreatehybr-1545314385890' [PR #1286]

* knepley/plexdoc-better-docs-for-dmplexcreatehybr-1545314385890:
Plex+Doc: Better docs for DMPlexCreateHybri

Merge branch 'knepley/plexdoc-better-docs-for-dmplexcreatehybr-1545314385890' [PR #1286]

* knepley/plexdoc-better-docs-for-dmplexcreatehybr-1545314385890:
Plex+Doc: Better docs for DMPlexCreateHybridMesh()

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Merge remote-tracking branch 'origin/knepley/feature-label-object' into knepley/feature-section-label

* origin/knepley/feature-label-object:
DMLabel: When distributing, do not need a valid Label f

Merge remote-tracking branch 'origin/knepley/feature-label-object' into knepley/feature-section-label

* origin/knepley/feature-label-object:
DMLabel: When distributing, do not need a valid Label from processes which we are sending to
Plex: Cannot assume label "markers" exists
Forest ex2: Fixed DMLabelCreate()
DMLabel: Remove Fortran binding for DMLabelGetName()
TS ex11: Fixed interface for DMLabelCreate()
DMLabel: Make it a PetscObject - Add a CLASSID - Constructor takes an MPI_Comm - Remove interface that is in Object - Update interface in library - Fixed location of destruct in DMPlexCreateSubmeshGeneric_Interpolated() - Added DMLabelReset()

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Merge branch 'master' into knepley/fix-plex-partition-parallel

* master: (414 commits)
very small updates to users manual
syntax is define(XXX) in examples tests not defined(XXX)
Increase patc

Merge branch 'master' into knepley/fix-plex-partition-parallel

* master: (414 commits)
very small updates to users manual
syntax is define(XXX) in examples tests not defined(XXX)
Increase patchlevel to 3.10.3
petsc4py: updat to latest maint snapshot with SNESTEST updates
Fix link for CUDA example in PETSc from GPUs.html page Minor fixes to installation instructions
Mat: Fixed types in Pardiso interface
Converted example comment to latex
This example crashes (for unknown reasons, probably related to the handling of extended derived types passed as arguments) with the PGI Fortran compiler
Remove outdated requires: from top of several examples
remove outdated test requires: command from top of source file
Fix the documentation for -ksp_gmres_cgs_refinement_type
Commit f20c2d659b168217cb455989f28afe052d71a64c broke lex.py so the users manual was no longer being built. There reverted the changes to lex.py
Plex: Add PetscPartitioner to fort list Suggested-by: Jiaoyan Li <Jiaoyan.Li@inl.gov>
Doc: Fix spelling Suggested-by: Manuel Colera Rico <m.colera@upm.es>
Mat ex88: check in double or quad precision only
Fix error with PetscComplex when PETSc is compiled with C and used in C++
configure: fix typo endwith -> endswith
Sys ex23: Migrated to ts_max_time in yaml file as well.
AO ex5: Fixed missing CHKERRQ();
Mat test ex88: add tests for MatMultAdd and MatMultTranposeAdd
...

Conflicts:
src/dm/impls/plex/examples/tests/ex12.c

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Plex+Doc: Better docs for DMPlexCreateHybridMesh()

DMLabel: Make it a PetscObject
- Add a CLASSID
- Constructor takes an MPI_Comm
- Remove interface that is in Object
- Update interface in library
- Fixed location of destruct in DMPlexCreateSubmeshGe

DMLabel: Make it a PetscObject
- Add a CLASSID
- Constructor takes an MPI_Comm
- Remove interface that is in Object
- Update interface in library
- Fixed location of destruct in DMPlexCreateSubmeshGeneric_Interpolated()
- Added DMLabelReset()

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

Not sure if this has done the right thing because there are no tests
yet. Also, the fortran stubs break (it doesn't know what to do with
SNESCo

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

Not sure if this has done the right thing because there are no tests
yet. Also, the fortran stubs break (it doesn't know what to do with
SNESCompositeType), and I don't know how to fix it.

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Merged petsc/petsc into master

Merged petsc/petsc into master

Merge branch 'stefano_zampini/fix-p4est-squashed' [PR #1229]

* stefano_zampini/fix-p4est-squashed:
Few fixes to the p4est/p8est implementations of DMForest.

minor fixes

Merge from master

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (345 commits)
Update dev notes for the coming release
Increase patchlevel to 3.9.4
doc fixes
Added some AIJSELL tests t

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (345 commits)
Update dev notes for the coming release
Increase patchlevel to 3.9.4
doc fixes
Added some AIJSELL tests that mirror the SELL tests.
Bib: More refs
Removed use of hardwired -1 to represent PETSC_NULL_XXX object, since the null value is now 0.
fix memleaks flagged by valgrind
ex62: disable long running test and workaround differences in iteration counts on various builds.
Add FAQ we can point to when users get error messages such as: "PETSc was configured with one OpenMPI mpi.h version but now appears to be compiling using a different OpenMPI mpi.h version"
swith test from mpich to openmpi as mpich ch3:sock is unuserable per PetscShmCommGet()
DM: Forgot to move include statement
fix nightlybuild issues - disable hypre [for openmp] and fix uninitialized variables
tests: enable openmp and hwloc with one of the mumps tests
Default BoomerAMG smoothers
Configure: Revert changes from debb90c, so that we are back to the original Libmesh
Configure: Reverted change for Libmesh from 83cd5d7
Split vecimpl.h into vecimpl.h and vecscatterimpl.h
SNES ex62: Turned off some tests for other precisions and shortened output of sensitive tests
Use mmap to allocate the shared pthread barrier if available
Add configure test for functional mmap
...

Conflicts:
include/petscconvest.h
src/snes/examples/tutorials/ex13.c
src/snes/interface/snes.c
src/snes/utils/convest.c

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Merged petsc/petsc into master

Merge branch 'master' into knepley/fix-superdm-is

* master: (455 commits)
bib: spell out some names for format consistency with related refs
bib: two 2018 pubs now appeared
cleaning up analyze

Merge branch 'master' into knepley/fix-superdm-is

* master: (455 commits)
bib: spell out some names for format consistency with related refs
bib: two 2018 pubs now appeared
cleaning up analyzer warnings
compile fixes (workarround PGI bug?):
undoing the branch's changes to leastsquares outputs
more fixes for complex builds
compile error fix for complex builds
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix Pardiso code to only compile pardiso_init64 when needed, otherwise can generate warnings/errors
jenkins: run 'cleantest' before 'allgtest-tap' - an attempt to fix errors of type:
cuda: protect cuda includes
fix cuda warnings.
fix complex compile error
Revert "Improved polymorphism of interfaces for MatSetValuesBlocked()"
Bib: Updated ref
Doc: More function documentation
petscvec: move PetscSFCreateFromZero from vscat to vec sources
Fixed an uninitialized variable and got rid of an unused one.
memleak fixed and output files updated
fixing build errors on some archs
Mat: obey options prefix of Mat in MatNullSpaceTest
...

Conflicts:
include/petsc/private/dmpleximpl.h
src/dm/interface/dmi.c

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

* master: (281 commits)
compile fixes (workarround PGI bug?):
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix

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

* master: (281 commits)
compile fixes (workarround PGI bug?):
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix Pardiso code to only compile pardiso_init64 when needed, otherwise can generate warnings/errors
jenkins: run 'cleantest' before 'allgtest-tap' - an attempt to fix errors of type:
cuda: protect cuda includes
fix cuda warnings.
fix complex compile error
Revert "Improved polymorphism of interfaces for MatSetValuesBlocked()"
Bib: Updated ref
Doc: More function documentation
petscvec: move PetscSFCreateFromZero from vscat to vec sources
Mat: obey options prefix of Mat in MatNullSpaceTest
Plex+SNES: Must pass user context through
vscat: move ftn-custom to correct location remove custom vecscatterdestroy_()
vscat: move interface routines to correct location
vscat: delete dead code
fix compile error
FE: Correct coordinates in IntegrateBd
Bib: Added refs
SNES ex17: 3D tests must require a 3D grid generator
Plex+TS: We cannot run the check with the same vector that is the TS solution
...

Conflicts:
include/petsc/private/dmpleximpl.h
src/docs/website/documentation/changes/dev.html
src/snes/examples/tutorials/ex13.c
src/snes/utils/dmplexsnes.c

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Merge branch 'master' into knepley/feature-plex-bdjacobian-single

* master: (68 commits)
compile fixes (workarround PGI bug?):
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with

Merge branch 'master' into knepley/feature-plex-bdjacobian-single

* master: (68 commits)
compile fixes (workarround PGI bug?):
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix Pardiso code to only compile pardiso_init64 when needed, otherwise can generate warnings/errors
jenkins: run 'cleantest' before 'allgtest-tap' - an attempt to fix errors of type:
cuda: protect cuda includes
fix cuda warnings.
fix complex compile error
Revert "Improved polymorphism of interfaces for MatSetValuesBlocked()"
Bib: Updated ref
Doc: More function documentation
petscvec: move PetscSFCreateFromZero from vscat to vec sources
Mat: obey options prefix of Mat in MatNullSpaceTest
Plex+SNES: Must pass user context through
vscat: move ftn-custom to correct location remove custom vecscatterdestroy_()
vscat: move interface routines to correct location
vscat: delete dead code
fix compile error
FE: Correct coordinates in IntegrateBd
Bib: Added refs
SNES ex17: 3D tests must require a 3D grid generator
Plex+TS: We cannot run the check with the same vector that is the TS solution
...

Conflicts:
src/snes/utils/dmplexsnes.c

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Merged petsc/petsc into master

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (249 commits)
Bib: Added refs
Netcdf should always build netcdf-4 (needed for example by exodusii.
trivial fixes of incor

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (249 commits)
Bib: Added refs
Netcdf should always build netcdf-4 (needed for example by exodusii.
trivial fixes of incorrect formatting in SNES linesearch routines
ISSetBlockSize_General: removed blockwise contiguity check.
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out
config prefix: avoid ad-hoc path substitutions
config/install: no need to rename paths for installBinDir
rules: fix path in (evidently unimportant) uncrustify target
config pkgconfig: use ${prefix} in PETSc.pc and do not modify in install
fix gcov obj path
Improved polymorphism of interfaces for MatSetValuesBlocked()
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Dev manual: remove duplicate entry
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
...

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Merge remote-tracking branch 'origin/knepley/fix-plex-submesh-projection'

Merge branch 'master' into knepley/feature-plex-functionals

* master: (984 commits)
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out

Merge branch 'master' into knepley/feature-plex-functionals

* master: (984 commits)
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out
fix gcov obj path
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Dev manual: remove duplicate entry
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
...

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Merged petsc/petsc into master