Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/mat/impls/aij/seq/mkl_pardiso/mkl_pardiso.c

Merge branch 'master' into barral/feature-dmplex-adapt

Merge branch 'tisaac/dmp4est-set-periodic-domain' into knepley/fix-plex-mf-prec

* tisaac/dmp4est-set-periodic-domain:
Plex: fix line geometry for localized
Plex: fix section access to last commi

Merge branch 'tisaac/dmp4est-set-periodic-domain' into knepley/fix-plex-mf-prec

* tisaac/dmp4est-set-periodic-domain:
Plex: fix line geometry for localized
Plex: fix section access to last commit
DMPlex: fix rectanlge geometry for localized
DMConvert_p4est_plex: set projection height early, so it passes to coordinate dm
DMLocalizeCoordinates(): make more flexible and targeted
DMP4est: change order of setting projection height and localizing coordinates
DMP4est: prefer [0,L) for periodic coordinates
Plex: more descriptive debugging

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Merge branch 'master' into knepley/fix-plex-mf-prec

* master:
GAMG: Fix nearnullspace check
Plex: Must check block size in parallel from DMGetLocalToGlobalMapping() - Small format cleanup
Mov

Merge branch 'master' into knepley/fix-plex-mf-prec

* master:
GAMG: Fix nearnullspace check
Plex: Must check block size in parallel from DMGetLocalToGlobalMapping() - Small format cleanup
Move spinlocks definitions to pinit.c, where they don't depend on PETSC_HAVE_FORTRAN
Allow empty data
Update output files after change in PetscObjectPrintClassNamePrefixType
Deactivate tabs when printing several things in the same line

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Merge branch 'tisaac/dmplex-localize-targeted' into tisaac/dmp4est-set-periodic-domain

* tisaac/dmplex-localize-targeted:
DMLocalizeCoordinates(): make more flexible and targeted
GAMG: Fix nearn

Merge branch 'tisaac/dmplex-localize-targeted' into tisaac/dmp4est-set-periodic-domain

* tisaac/dmplex-localize-targeted:
DMLocalizeCoordinates(): make more flexible and targeted
GAMG: Fix nearnullspace check
Move spinlocks definitions to pinit.c, where they don't depend on PETSC_HAVE_FORTRAN
Allow empty data
Update output files after change in PetscObjectPrintClassNamePrefixType
Deactivate tabs when printing several things in the same line

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DMLocalizeCoordinates(): make more flexible and targeted

More flexible because methods that do calculations on facets might need
to localize them as well. This information can be passed to the
coor

DMLocalizeCoordinates(): make more flexible and targeted

More flexible because methods that do calculations on facets might need
to localize them as well. This information can be passed to the
coordinate DM with DMPlexSetMaxProjectionHeight().

More targeted by only localizing cells/points that are needed. If I'm
localizing cells _and_ facets, then that's a lot of indiscriminate
localizing, when I only need it for a lower dimensional manifold.

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Merge branch 'knepley/fix-plex-mat-bs'

* knepley/fix-plex-mat-bs:
Plex: Must check block size in parallel from DMGetLocalToGlobalMapping() - Small format cleanup

Plex: Must check block size in parallel from DMGetLocalToGlobalMapping()
- Small format cleanup

Merge branch 'knepley/fix-plex-bs'

* knepley/fix-plex-bs:
Plex: deal correctly with off-process dof when calculating block size
Plex: Fix default partition weighting
Plex: Fix support for ADD_

Merge branch 'knepley/fix-plex-bs'

* knepley/fix-plex-bs:
Plex: deal correctly with off-process dof when calculating block size
Plex: Fix default partition weighting
Plex: Fix support for ADD_BC_VALUES
Plex: Allow incoming blocksize in DMCreateMatrix()
Plex: Fix for blocksize in preallocation
Plex: Fix blocksizes determination in ltog mapping
Plex: Set block size regardless of whether the Mat has block storage

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Merge branch 'knepley/fix-plex-bs' into knepley/fix-plex-namespace

* knepley/fix-plex-bs:
Plex: Fix default partition weighting
Plex: Fix support for ADD_BC_VALUES
Plex: Allow incoming blocksi

Merge branch 'knepley/fix-plex-bs' into knepley/fix-plex-namespace

* knepley/fix-plex-bs:
Plex: Fix default partition weighting
Plex: Fix support for ADD_BC_VALUES
Plex: Allow incoming blocksize in DMCreateMatrix()
Plex: Fix for blocksize in preallocation
Plex: Fix blocksizes determination in ltog mapping
Plex: Set block size regardless of whether the Mat has block storage

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Plex: Fix support for ADD_BC_VALUES

Plex: Fix blocksizes determination in ltog mapping

Merge branch 'master' into knepley/feature-parallel-mesh-load

* master: (180 commits)
Bib: Added ref
-random_view caused error because PetscRandomView() was not provided in PetscRandomCreate()

Merge branch 'master' into knepley/feature-parallel-mesh-load

* master: (180 commits)
Bib: Added ref
-random_view caused error because PetscRandomView() was not provided in PetscRandomCreate()
Update the xSDKTrilinos test message to use interactive session and ctest
gcc6: fix comple warnings with -Wmisleading-indentation
fix compile warning
bugfix for MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable()
minor formatting cleanup of gamg.c
add ml example to tutorials page for xsdk
bugfix of MatDuplicate for mpiaij matrix product Reported-by: Miorelli, Federico <Federico.Miorelli@cgg.com>
The deprecated -log_summary_exclude was still being used when it should have been -log_exclude
cpardiso: requires mkl_blacs so check for that. Also common code to detect MKL for both pardiso and cpardiso
cpardiso: fix segv and memory leaks
resume MatGetSubMatrix_SeqSBAIJ() because it cannot share routine with BAIJ due to cast
fix bad relative links
replace MatSeqBAIJSetPreallocation_SeqBAIJ with MatSeqBAIJSetPreallocation to skip this call when input mat is sbaij type
fix a variety of set but not used variables in examples detected by clang static analyzer
removed declared but not used variable
ANL Report formatting requires listing authors by affiliation
DMP4est: uncrustify
DMP4est: remove memset()
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Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c

Merge branch 'knepley/fix-plex-blocksize'

* knepley/fix-plex-blocksize:
Plex ex12: Mark p4est requirements
Plex: Fix line geometry - There was a bad dependency
Plex: Fix FVM geometry - There w

Merge branch 'knepley/fix-plex-blocksize'

* knepley/fix-plex-blocksize:
Plex ex12: Mark p4est requirements
Plex: Fix line geometry - There was a bad dependency
Plex: Fix FVM geometry - There was a bad dependency
Plex: Fixed possibly bad access
PetscFE: Fixed missing initializations
PetscFE: PetscDualSpaceGetNumDof() can no longer return NULL - Had to implement it for Simple dual space
DM: Protect possibly NULL input
Plex: Fixed parallel block size for DM matrix
DM: Fixed block size for LocalToGlobal mapping with PetscSection

Conflicts:
config/builder.py

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DM: Protect possibly NULL input

DM: Fixed block size for LocalToGlobal mapping with PetscSection

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

Merge branch 'tisaac/dm-locate-points-sf'

* tisaac/dm-locate-points-sf:
Plex: missed in IS
DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

Merge branch 'tisaac/dmp4est-feature-injection'

* tisaac/dmp4est-feature-injection: (27 commits)
DMP4est: linear solve regression tests
DMP4est: regression tests for exact interpolation/injectio

Merge branch 'tisaac/dmp4est-feature-injection'

* tisaac/dmp4est-feature-injection: (27 commits)
DMP4est: linear solve regression tests
DMP4est: regression tests for exact interpolation/injection
PetscDualSpace: create height subspaces at setup.
DMClone(): get agreement on cloning coordinates
DMP4est: bump number of procs in regression test
DMP4est: fix memory leaks
DMP4est: added diagnostic views
DMP4est: adding regression tests
SNES tutorials ex12: added RUN_EXACT, solve from exact solution
DMPlex: memory clean up in Injector/InterpolatorTree routines
DMP4est: use DMCoarsen_Forest
DMPlexComputerInterpolatorTree(): restore another work array
DMPlexAnchorsModifyMat(): restore work arrays
DMPlexComputeInjectorTree(): fix local / off-process bounds
DMPlexComputeInjectorTree(): more fixes
DMPlexComputeInjectorTree(): fix coarse/fine char mixup
DMPlexComputeInjectorTree() compiles
WIP: DMPlexComputeInjectorTree()
Plex tests ex3: added regression tests for injectors
DMPlex tests ex3: fix viewing, creating injectors
...

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Merge branch 'tisaac/fix-static-analysis-warnings'

* tisaac/fix-static-analysis-warnings:
Add missing CHKERRQ
Address static analysis warnings

DMClone(): get agreement on cloning coordinates

Address static analysis warnings

Merge branch 'tisaac/sf-fix-multi-sf-leaves' into tisaac/dmp4est-feature-injection

* tisaac/sf-fix-multi-sf-leaves: (174 commits)
PetscSF: fix PetscSFGetMultiSF() for sparse leaves
PetscSF: make

Merge branch 'tisaac/sf-fix-multi-sf-leaves' into tisaac/dmp4est-feature-injection

* tisaac/sf-fix-multi-sf-leaves: (174 commits)
PetscSF: fix PetscSFGetMultiSF() for sparse leaves
PetscSF: make regression test that fails
few more clang static analyzer fixes
many issues detected by clang static analyzer
Update hypre to its release version
Updates for xSDKTrilinos builds
Added --download-xsdktrilinos
Communicator passed to VecCreateSeq should be PETSC_COMM_SELF
PCMG man page: fix typo in options name
Bib: Added refs
DMLabel: Removed unused variable
Metis tries to use backtrace which requires -lexecinfo on some systems such as freebsd Remove -lexecinfo from freebsd configure files since it is only needed by metis
add alternative output that occurs on some systems due to use of random number generator in partitioner
Plex: When creating cohesive submeshes, fix memory leak
Plex ex11: Updated output for new distribution algorithm
Plex: When explicitly distributing the depth label, we must recreate empty strata
Plex: When partitioning, the cell numbering should include hybrid points
Plex: Allow cell and vertex numberings to include hybrid points
need to show diffs of ex22 if it fails
Support two different output for test example, since due to roundoff this example can produce slightly different convergence history
...

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