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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Plex: Fixed possibly bad access

Plex: Fixed parallel block size for DM matrix

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

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

Plex: fix loop arguments

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

Address static analysis warnings

fix 'unused variable' compile warnings

DMPlexAnchorsModifyMat(): restore work arrays

There are still some out there...

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' into sanderarens/fix-plex-neumann-bc

* master: (28 commits)
few more clang static analyzer fixes
many issues detected by clang static analyzer
Update hypre to its release

Merge branch 'master' into sanderarens/fix-plex-neumann-bc

* master: (28 commits)
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
DMLabel: Removed unused variable
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
Plex ex1: Fixed output for empty strata
DMLabel: Added DMLabelHasStratum()
Minor changes and fix to bugs introduced in 82f73ecaa
Modified makefile to fix aijcusparse tests
Add missing code for the case PETSC_HAVE_VECCUDA
Fix bugs introduced in 82f73ecaa
Use VECCUDA with MATAIJCUSPARSE
CUDA: Fixed visibility and disabled Fortran bindings for VecScatters on GPU.
Replace kernels with thrust
...

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Merge branch 'knepley/fix-plex-examples'

* knepley/fix-plex-examples:
DMLabel: Removed unused variable
Plex: When creating cohesive submeshes, fix memory leak
Plex ex11: Updated output for new

Merge branch 'knepley/fix-plex-examples'

* knepley/fix-plex-examples:
DMLabel: Removed unused variable
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
Plex ex1: Fixed output for empty strata
DMLabel: Added DMLabelHasStratum()

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few more clang static analyzer fixes

Merge branch 'pr421/alex/feature-veccuda'

* pr421/alex/feature-veccuda
The rationale of this pull request is to have GPU-enabled vectors purely based on CUDA,
and with the possibility of placing a u

Merge branch 'pr421/alex/feature-veccuda'

* pr421/alex/feature-veccuda
The rationale of this pull request is to have GPU-enabled vectors purely based on CUDA,
and with the possibility of placing a user-provided array on the GPU side.

Conflicts:
src/vec/vec/impls/seq/seqcusp/cuspvecimpl.h
src/vec/vec/impls/seq/seqviennacl/viennaclvecimpl.h

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Plex: Allow cell and vertex numberings to include hybrid points

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

Toby used an MPIU_MAX with an MPIU_INT

Time: .2 hours
Reported-by: nightly builds

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax error with error message
SNES ex5: Correct Jacobian handling on patches
SNES ex5: Stupid complex fixes
DMP4est: fix transfer of labels to parents
petsc4py: update to latest snapshot. Fixes da example breakage in petsc4py test suite
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logging in interpolator creation
Plex: Correct use of tabs in ASCII viewer
DM: Shorten long event name
Plex ex12: Create boundary label automatically at all levels of mesh hierarchy
Plex ex12: Change PetscViewerSetFormat --> PetscViewerPushFormat - Fix order of SetMode and SetFilename
Plex ex12: Change all functions to static
Since DMDA with periodic boundary conditions does support P0 interpolation remove checks that error out under those conditions
ascem-io.py and amanzi.py need to handle self.hdf5.include being None correctly
fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests also fix check for location of python shared library on mac to check all cases each time
Switch back to Sherry's version since she accepted by pull request
PetscDraw: Update help messages for -draw_save* options
...

Conflicts:
src/dm/impls/plex/plexfem.c

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Merge branch 'knepley/fix-plex-point-location'

* knepley/fix-plex-point-location:
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logg

Merge branch 'knepley/fix-plex-point-location'

* knepley/fix-plex-point-location:
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logging in interpolator creation
Plex: Correct use of tabs in ASCII viewer
DM: Shorten long event name
Plex ex12: Create boundary label automatically at all levels of mesh hierarchy
Plex ex12: Change PetscViewerSetFormat --> PetscViewerPushFormat - Fix order of SetMode and SetFilename
Plex ex12: Change all functions to static

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Merge branch 'tisaac/dmforest'

* tisaac/dmforest: (36 commits)
DMP4est: fix transfer of labels to parents
DMPlexCreateInterpolatorTree: fix handling of global dofs (can be < 0)
DMPlexComputeIn

Merge branch 'tisaac/dmforest'

* tisaac/dmforest: (36 commits)
DMP4est: fix transfer of labels to parents
DMPlexCreateInterpolatorTree: fix handling of global dofs (can be < 0)
DMPlexComputeInterpolatorTree(): fix workspace size
DM: warn when no injection implemented
DMPlexComputeInterpolatorTree(): use row layout to preallocate
DMP4est: all processes agree on root type
DMPlexComputeInterpolatorTree(): valgrind fixes
DMP4est: reset childID if anctecedent is not parent
DMP4est: send labels from children to parents and bcast
DMForest: added DMForestGetAdaptivityPurpose()
DMP4est: enable caching of results of DMPforestGetTransferSF()
Plex: fix empty partition errors
DMPforestGetTransferSF_Internal(): handle different type roots on different processes
DMP4est: broadcast labels when transfering for agreement
PetscSFBasic: fix usage of MPI_Reduce_local
DMPforestLabelsInitialize(): search through parents when finding a point in the closure
DMP4est: try to connect high strata points when transfering
DMP4est: can't use PetscSFCreateSectionSF. It compresses when we don't want to
DMP4est: expand transfer sfs by the CellSF
DMP4est: add DMForestCreateCellSF_p4est
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Plex: Correct use of tabs in ASCII viewer

Merged petsc/petsc into master