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

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

* knepley/feature-ts-plasma-example:
TS ex48: Turn off plotting by default since it fails for complex
TS ex48: c89 fixes
TS ex48: Protect HDF5

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

* knepley/feature-ts-plasma-example:
TS ex48: Turn off plotting by default since it fails for complex
TS ex48: c89 fixes
TS ex48: Protect HDF5
TS ex48: More complex fixes
TS ex48: Update to latest API
Plex: Fix return type of DMPlexComputeIntegralFEM()
TS ex48: Plasma physics example

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Plex: Fix return type of DMPlexComputeIntegralFEM()

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 remote-tracking branch 'origin/knepley/fix-plex-spectral-incomplete'

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

* master: (251 commits)
yaml: add a backup download URL
Fix documentation of MatSetRandom function
Ignore -malloc-hbw option if m

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

* master: (251 commits)
yaml: add a backup download URL
Fix documentation of MatSetRandom function
Ignore -malloc-hbw option if malloc is already set
Plex: Fixed array initialization
pgi: compile fix
knl: update test to use memkind and remove option that worked arround a bug with intel 17
Check the return value for memkind_posix_memalign
Change the default behavour for -malloc_hbw
Bib: More refs
test: remove runex13f90 as its now converted to new test suite
fix win32 crash. This test was previously run with '-n 4' - so restoring it
Fix petscsfgetgraph_ to work for all Fortran compilers by directly using array of PetscSFNodes
bugfix for MatDuplicate_MPIAIJ_PtAP Reported-by: Samuel Lanthaler <s.lanthaler@gmail.com>
strip out dead sundials usage code; change sundials test to only run 5 timesteps to prevent different number of steps on different systems.
Remove extra lines of output file
Example uses C99 constructs so must mark with requires: c99
fix const missmatch for DMDAVecRestoreArrayRead()
remove conflict between function name in example and new PETSc TS function
builds: attempt to do maint/master/next test builds in separate clones
ex62: it turned out that CHACO partioning is not deterministic. Use a prescribed partition instead
...

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

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Merge remote-tracking branch 'origin/knepley/feature-adaptor-plex' into next-tmp

Merge remote-tracking branch 'origin/knepley/fix-l2-projection-submesh' into next-tmp

Plex: DMPlexCreateSpectralClosurePermutation() now takes a point argument
- This allows the user to have the solution only partially supported in the domain
- Give PETSC_DETERMINE for the prior behav

Plex: DMPlexCreateSpectralClosurePermutation() now takes a point argument
- This allows the user to have the solution only partially supported in the domain
- Give PETSC_DETERMINE for the prior behavior
- Give an edge or cell which supports the field

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Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with

Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with updated 17.10 compilers
Fix for test dirs that are not tutorials/tests
fix use of double in PetscAbsReal() which produces compiler warnings with single precision build
elemental: remove info on conflict of -with-cxx-dialect=C++11 on osx - it works now.
Cleanup .bib files
Fix allfortranstubs rule to rm generated files from correct directory, not outdated location
ierr set but not checked
Remove initial refine so test runs faster and does not time out on some machines
Gail's copyedits for bibtex items
Docs: manual: add further description of 3 different current testing options
DM: check for ops->localtolocalbegin/end before calling
PetscSF: fix typo in tutorial ex1
Vec+HDF5: Fix output for complex - Need to check for empty group name
SNES: SNESDestroy() can be called with snes->dm == NULL
SNES: SNESDestroy() can be called with snes->dm == NULL
Vec+HDF5: Fix output for complex - Need to check for empty group name
Docs: Manual: Update tests section
gmakegentest: also exclude .#filenames created by emacs
DMPlex: Fix output of test ex1 after changes to Gmsh reader
...

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Plex: Refactor computation of integrals over the domain
- Added DMPlexComputeCellwiseIntegral()

Merge branch 'knepley/feature-rigid-bodies'

* knepley/feature-rigid-bodies:
Plex: Added declaration
Plex: Added DMPlexCreateRigidBodies() - Handles disconnected pieces, like sides of a fault
D

Merge branch 'knepley/feature-rigid-bodies'

* knepley/feature-rigid-bodies:
Plex: Added declaration
Plex: Added DMPlexCreateRigidBodies() - Handles disconnected pieces, like sides of a fault
DM: Added DMProjectFunctionLabel()

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Plex: Added DMPlexComputeL2DiffLocal()
- Fix docs to say that DM version uses global vectors

Plex: DMPlexCreateHybridMesh() now takes a boundary label and returns the submesh
- Added check that no cell has all vertices on the submesh

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

* knepley/feature-adaptor-plex: (38 commits)
SNES ex12: Fixed AMR tests - Cleaned up use of r Vec - Updated out

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

* knepley/feature-adaptor-plex: (38 commits)
SNES ex12: Fixed AMR tests - Cleaned up use of r Vec - Updated output
DMAdaptor: Fixes handling of original Vec and DM - Fix handling of input vector x - Only LABEL needs a Plex conversion
fixed uninitialized var
SNES ex12: Added adaptation test for p4est
DMAdaptor: Error indicator working for p4est on SNES ex12 - Changed DMAdaptor to a DM class - Added DMAdaptorComputeErrorIndicator_Private() - Added DMAdaptorSimpleErrorIndicator_Private() - Name projected solution vector
PetscFE: Added PetscFEInterpolateFieldAndGradient_Internal()
DMPlexComputeGradientClementInterpolant: fix debug statement for complex
SMAdaptor: Fix for complex ev decamp
compile fixes
DMAdaptor: Correct warnings and complex problems
Plex: Added versions of the Det functions that take Scalar data
DMAdaptor: Declare DMAdaptorSet/GetSequenceLength()
SNES+ex12: Added support for ascii_info_detail in -snes_converged_reason - It prints the L_2 error using the DS information - SNES ex12 output updated
DMAdaptor: Added options - Added options for N_adapt, refinement factor, h_min and h_max
SNES ex12: I finally think test output is correct
DMAdaptor: Refine viewing
SNES ex12: Updated adaptation tests - Added sequential adaptation
SNES: Added -snes_adapt_sequence - Eventually remove snes_grid_sequence
DMAdaptor: - Added sequential adaptation - Added DMAdaptorGet/SetSequenceLength() - Use AdaptationCriterion now - Added untested unstructured interpolation
DMAdaptor: Now I have AdaptationStrategy and AdaptationCriterion - Fixed some docs
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Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

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

Merge remote-tracking branch 'origin/knepley/feature-plex-l2-projection'

Plex: Added declarations

Merge remote-tracking branch 'origin/maint'

Merged in dalcinl/partitioner-ptscotch (pull request #770)

DMPLex: Implement PTScotch partitioner

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

* master: (56 commits)
test: Disable TS ex19 with single precision
PETSCVIEWERGLVIS: Support DMView_DA() out of VecView_GLVis()
test: Fi

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

* master: (56 commits)
test: Disable TS ex19 with single precision
PETSCVIEWERGLVIS: Support DMView_DA() out of VecView_GLVis()
test: Fix TS ex19 time drift issue with quad precision
testing
Minor edit to 3.8 changes log for AIJMKL/BAIJMKL.
Bib: Added ref
Plex: Change initializers for C89
small update as complained by nightly tests
doc: fix missing from 0e50f9e530a7b78427514d3e384f6941d4a9cc62
small fix for nightly tests
PetscDualSpaceApplyFVM(): Fix for change in dual space semantics
Plex: All tests now passing after DMPlexCreateBoxMesh() update
cleanup MatPtAP_MPIAIJ_MPIAIJ; rm MatPtAPXXX_MPIAIJ_MPIAIJ_ptap()
update MatView_MUMPS()
PFLOW: Bug-fix in parser.
PFLOW: Bug-fix in parser.
Plex: Small fix for box meshing
Plex: Unified box mesh creation to DMPlexCreateBoxMesh() - Makes simplices and tensor cells - Does not work for all combinations, but gives correct error
Plex: Added bounds and faces in each dim to DMPlexCreateBoxMesh()
Plex: Added domain bounds to HexBoxMesh()
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DMPlex: Implement PTScotch partitioner