Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead code.
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
...

Conflicts:
src/snes/examples/tutorials/ex13.c

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Merge branch 'master' into knepley/fix-plex-residual-loop
Warning: This merge includes real changes

* master: (188 commits)
Add JuMP citation
Copyedits and updates to developers manual
Add mor

Merge branch 'master' into knepley/fix-plex-residual-loop
Warning: This merge includes real changes

* master: (188 commits)
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
SNES ex62: Set name of solution vector - Update test output
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
move output file to the correct location. i.e fix 305862f9cd0dc399542ae11dd744508e4b6ad2e3
...

Conflicts:
src/snes/utils/dmplexsnes.c
src/ts/utils/dmplexts.c

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Merge remote-tracking branch 'origin/knepley/fix-dm-gmg'

* origin/knepley/fix-dm-gmg:
Plex+SNES: Fixed test output after naming vectors in solver loop
DM: Improved viewing
DM: DMCreateSubDM()

Merge remote-tracking branch 'origin/knepley/fix-dm-gmg'

* origin/knepley/fix-dm-gmg:
Plex+SNES: Fixed test output after naming vectors in solver loop
DM: Improved viewing
DM: DMCreateSubDM() should propagate the coarse mesh and DS properly
PetscDS: Dammit, these missed the other ChangeSet
PetscDS: Added flag for turning off Jacobian preconditioned - Added PetscDSUseJacobianPreconditioner
PetscDS: Fix viewing with a quadrature
DS: Fixes for ASCII viewer
PetscDS: Updated copy functions - Added PetscDSSelectEquations() which only copies a subset for a subDM - Added PetscDSCopyConstants() - Added docs
DM: Allow outputting residual/solution vectors at SNES iterates easily - I now think ViewFromOptions is way easier than monitors
DM: Do not allow a locked vector to be restored

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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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Deprecate DMSet/GetDefaultSection() for DMSet/GetSection()

Revert manual page change per Matt's preference

Commit-type: style-fix
Thanks-to: Matthew Knepley

Merge branch 'pr872/bourdin/dmplex-GlobalToNatural/master'

* pr872/bourdin/dmplex-GlobalToNatural/master:
Makes a subDM inherit the NaturalToGlobal SF from their parent upon creation.

dmplex: construct sfNaturalToGlobal in DMCreateSuperDM_Plex if any of the input DM has useNatural set

DM: DMCreateSubDM() should propagate the coarse mesh and DS properly

DM: make subDM inherit the GlobaltoNatural flag and SF

Merge branch 'barry/tao-to-new-test-harness' into barry/all-new-test-harness-branches

Merge branch 'jed/tests-cxx-linker' into barry/more-to-new-test-harness

Merge branch 'master' into knepley/feature-ts-plasma-example

* master: (22 commits)
Section: Fix CreateSupersection - Missing call to GetNumFields() for subsection
SNES ex13: Update test output

Merge branch 'master' into knepley/feature-ts-plasma-example

* master: (22 commits)
Section: Fix CreateSupersection - Missing call to GetNumFields() for subsection
SNES ex13: Update test output
PetscFE: Complex fixes for PetscFEIntegrate()
SNE ex13: Got adjoint solution and almost have a good error estimate
Section: Fix init in PetscSectionCreateSupersection()
DM: Remove debugging view
SNES ex13: Updated output after fix
Section: If global section allocates bc indices, must copy them
Section: Cleaned up PetscSectionCreateGlobalSection() - Used local variable and added input checks
Bib: Added pages
Section: Fix leaks in DMCreateSuperDM()
SNES ex13: Adding adjoint capability
DM: Use new PetscGlobalMinMaxInt()
DM: Added DMCreateSuperDM()
Plex: Refactor computation of integrals over the domain - Added DMPlexComputeCellwiseIntegral()
PetscFE: Fix PetscFEIntegrate() for multicomponent integrals
Adaptor: Use new PetscGlobalMinMaxInt()
Section: Added PetscSectionCreateSupersection() - This merges several sections together
Vec+Doc: Fix docs for VecISAXPY()
Vec: Added VecISCopy() - Use ScatterMode to determine direction of copying
...

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Merge branch 'knepley/feature-plex-adjoint-prelim'

* knepley/feature-plex-adjoint-prelim: (22 commits)
Section: Fix CreateSupersection - Missing call to GetNumFields() for subsection
SNES ex13:

Merge branch 'knepley/feature-plex-adjoint-prelim'

* knepley/feature-plex-adjoint-prelim: (22 commits)
Section: Fix CreateSupersection - Missing call to GetNumFields() for subsection
SNES ex13: Update test output
PetscFE: Complex fixes for PetscFEIntegrate()
SNE ex13: Got adjoint solution and almost have a good error estimate
Section: Fix init in PetscSectionCreateSupersection()
DM: Remove debugging view
SNES ex13: Updated output after fix
Section: If global section allocates bc indices, must copy them
Section: Cleaned up PetscSectionCreateGlobalSection() - Used local variable and added input checks
Bib: Added pages
Section: Fix leaks in DMCreateSuperDM()
SNES ex13: Adding adjoint capability
DM: Use new PetscGlobalMinMaxInt()
DM: Added DMCreateSuperDM()
Plex: Refactor computation of integrals over the domain - Added DMPlexComputeCellwiseIntegral()
PetscFE: Fix PetscFEIntegrate() for multicomponent integrals
Adaptor: Use new PetscGlobalMinMaxInt()
Section: Added PetscSectionCreateSupersection() - This merges several sections together
Vec+Doc: Fix docs for VecISAXPY()
Vec: Added VecISCopy() - Use ScatterMode to determine direction of copying
...

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Merge branch 'knepley/feature-plex-adjoint-prelim' into knepley/feature-plex-exodus-update

* knepley/feature-plex-adjoint-prelim:
SNE ex13: Got adjoint solution and almost have a good error estima

Merge branch 'knepley/feature-plex-adjoint-prelim' into knepley/feature-plex-exodus-update

* knepley/feature-plex-adjoint-prelim:
SNE ex13: Got adjoint solution and almost have a good error estimate
Section: Fix init in PetscSectionCreateSupersection()
DM: Remove debugging view
SNES ex13: Updated output after fix
Section: If global section allocates bc indices, must copy them
Section: Cleaned up PetscSectionCreateGlobalSection() - Used local variable and added input checks
Bib: Added pages
Section: Fix leaks in DMCreateSuperDM()
SNES ex13: Adding adjoint capability
DM: Use new PetscGlobalMinMaxInt()
DM: Added DMCreateSuperDM()
Plex: Refactor computation of integrals over the domain - Added DMPlexComputeCellwiseIntegral()
PetscFE: Fix PetscFEIntegrate() for multicomponent integrals
Adaptor: Use new PetscGlobalMinMaxInt()
Section: Added PetscSectionCreateSupersection() - This merges several sections together
Vec+Doc: Fix docs for VecISAXPY()
Vec: Added VecISCopy() - Use ScatterMode to determine direction of copying
Sys: Added PetscGlobalMinMaxReal/Int()
Plex: Make preallocation debugging work in serial

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Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (60 commits)
petsc4py: update to use latest 3.8 snapshot
petsc4py: update to snapshot that syncs with 276c550
fix warni

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (60 commits)
petsc4py: update to use latest 3.8 snapshot
petsc4py: update to snapshot that syncs with 276c550
fix warning
Plex ex26: Protect ExodusII stuff
DM: DMCreateSubDM() field argument should be const
TS ex46: Newlines and some numerical jitter
TS ex45: Newlines and some numerical jitter
TS ex11: Fixed indentation and time step numbering
SNES ex12: Update for DM view changes
Plex tests: Update to new DM output
Plex ex23: Use Nc not dim for vector fields
Plex: Default section now ignores cells hanging off boundary meshes
Plex: Viewer now reports the cell Height
Increase patchlevel to 3.8.3
Plex: Fixed DMPlexInterpolate() bugs - Do not copy associated data if we are not interpolating - Do not interpolate if we already have full depth
fix valgrind errors with using PetscObjectGetName()/SetName() with the same object - resulting in a free() before copy.
ex4: fix compile warning and update makefile
Minor fixes
Improving report_tests
PetscDS: Must initialize the default adjacency
...

Conflicts:
include/petsc/private/dmimpl.h
include/petscdm.h
include/petscis.h
src/dm/impls/plex/plexcreate.c

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Merge branch 'master' into knepley/feature-plex-exodus-update

* master:
petsc4py: update to use latest 3.8 snapshot
petsc4py: update to snapshot that syncs with 276c550
fix warning
Plex ex26

Merge branch 'master' into knepley/feature-plex-exodus-update

* master:
petsc4py: update to use latest 3.8 snapshot
petsc4py: update to snapshot that syncs with 276c550
fix warning
Plex ex26: Protect ExodusII stuff
DM: DMCreateSubDM() field argument should be const
TS ex46: Newlines and some numerical jitter
TS ex45: Newlines and some numerical jitter
TS ex11: Fixed indentation and time step numbering
SNES ex12: Update for DM view changes
Plex tests: Update to new DM output
Plex ex23: Use Nc not dim for vector fields
Plex: Default section now ignores cells hanging off boundary meshes
Plex: Viewer now reports the cell Height
DM: Check IS block size in DMCreateSubDM()
DM: DMCreateSubDM() should take a const array
Plex ex26: Test for FEM dof layout and DMCreateSubDM() Contributed-by: Blaise A Bourdin <bourdin@lsu.edu>

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Merge remote-tracking branch 'origin/knepley/feature-subdm-test'

DM: DMCreateSubDM() field argument should be const

DM: Remove debugging view

DM: Check IS block size in DMCreateSubDM()

Section: Fix leaks in DMCreateSuperDM()

DM: Use new PetscGlobalMinMaxInt()

DM: Added DMCreateSuperDM()

Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

Obtain changed (v3.5) handling of MatMPIBAIJSetPreallocationCSR to match
documentation.

Merge branch 'master' into knepley/fix-fe-default

* master: (297 commits)
Bib: Added refs and fixed one
Doc: Fixed formatting problems for MatCreateAIJ() manual page.
Add to PCSOR manual page

Merge branch 'master' into knepley/fix-fe-default

* master: (297 commits)
Bib: Added refs and fixed one
Doc: Fixed formatting problems for MatCreateAIJ() manual page.
Add to PCSOR manual page information about convergence testing when using KSPRICHARDSON
SNES ex5: Restore old output since this breaks an example I have
Noted that some Cray XC systems will use 'aprun' instead of 'srun'. Thanks to Herr Doktor Hong Zhang for this suggestion.
Added example configure script for Cray XC40 with KNL processors (e.g., NERSC Cori).
Fix possible sprintf -Wformat-overflow
PetscMalloc2-7: fix -Wint-in-bool-context for GCC 7
SNES ex5: make boundary condition handling consistent for symmetry
SNES ex5: use L2 norm and *_monitor_short for output
SNES ex5: the L^2 norm scales with the l^2 norm over sqrt(N)
SNES ex5: refactor MMS capability to avoid extreme code duplication
Documentation fix: typo in PetscLogStageRegister manual page.
nodes -> vertices
rename DMNetworkGetComponentTypeOffset -> DMNetworkGetComponentKeyOffset
rename DMNetworkGetConnectedNodes() -> DMNetworkGetConnectedVertices()
Jacobians for adjoints for explicit methods and constant Jacobians never got initialized
fix complex build error
fix build failure with fortran interface
fix compile error with cdc753b64c658d532d7813e942002e67025667a6
...

Conflicts:
src/snes/examples/tutorials/ex13.c
src/snes/examples/tutorials/ex62.c
src/snes/examples/tutorials/ex69.c

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