Merge branch 'knepley/fix-cublas-init' into knepley/feature-plex-refine-3d

* knepley/fix-cublas-init:
Sys: Allow CUBLAS init to be turned off - This causes SEGV on my Air all the time
DMPlex: Re

Merge branch 'knepley/fix-cublas-init' into knepley/feature-plex-refine-3d

* knepley/fix-cublas-init:
Sys: Allow CUBLAS init to be turned off - This causes SEGV on my Air all the time
DMPlex: Removed dead declaration (thanks Lisandro)
added citation for superlu99

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DMPlex: Removed dead declaration (thanks Lisandro)

DMPlex: Updated ProjectFunction() to use PetscDualSpace for generic projection
- Has not been tested with moment dofs
- Accommodates vector functions

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (71 commits)
Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
SNESMonitorCancel: enable fort

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (71 commits)
Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
SNESMonitorCancel: enable fortran interface
PetscSection: Added docs for Fortran binding for VecSetValuesSection()
Vec: Removed old F90 binding for PetscSection
bgq: fix deadlock on bgq due to inconsistant values returned by getpwuid(getuid()) on runs with 256nodes [or 4096 cores]. This fix removes the reliance on PetscGetHomeDirectory() returning 'same' value across nodes. [using the fact that PetscOptionsInsertFile() uses HOMEDIR from node-0 only]
DMPlex: change order of assignment to appease -Wmaybe-initialized (gcc-4.8.1)
DMPlex: Fix 64-bit int problem in VTK
Mat: Fix for PetscSparseDenseMaxDot() for complex
Vec: Correct VecUniqueEntries() for 64-bit indices
MatSeqAIJGetArrayF90: add man pages and fix typo in MatDense version
SF docs: add link to summary page and fix title
Doc: Fixed DM code in manual
metis/parmetis: update to metis-5.1.0/parmetis-4.0.3 Also update the test output as the partitioning appears to have changed.
DMPlex: remove unused variables
blaslapack: update f,f2c tarballs to 3.4.2 version
DMPlex ex5: Added test for 2 face cohesive submesh - Fixed old tests for cohesive cell orientation
DMPlex: Put in depth label optimization
DMPlex: Fix flipping of fault normal
DMPlex: We label cells with only vertices on the fault, but they have no cone replacement
DMPlex: Fix translation to cohesive edges in 3D - They are labeled by the vertices they connect
...

Conflicts:
include/petscdmplex.h

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Merge branch 'master' into knepley/feature-dt-fem

* master: (51 commits)
Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
SNESMonitorCancel: enable fortran inte

Merge branch 'master' into knepley/feature-dt-fem

* master: (51 commits)
Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
SNESMonitorCancel: enable fortran interface
PetscSection: Added docs for Fortran binding for VecSetValuesSection()
Vec: Removed old F90 binding for PetscSection
bgq: fix deadlock on bgq due to inconsistant values returned by getpwuid(getuid()) on runs with 256nodes [or 4096 cores]. This fix removes the reliance on PetscGetHomeDirectory() returning 'same' value across nodes. [using the fact that PetscOptionsInsertFile() uses HOMEDIR from node-0 only]
DMPlex: change order of assignment to appease -Wmaybe-initialized (gcc-4.8.1)
metis/parmetis: update to metis-5.1.0/parmetis-4.0.3 Also update the test output as the partitioning appears to have changed.
DMPlex: remove unused variables
blaslapack: update f,f2c tarballs to 3.4.2 version
DMPlex ex5: Added test for 2 face cohesive submesh - Fixed old tests for cohesive cell orientation
DMPlex: Put in depth label optimization
DMPlex: Fix flipping of fault normal
DMPlex: We label cells with only vertices on the fault, but they have no cone replacement
DMPlex: Fix translation to cohesive edges in 3D - They are labeled by the vertices they connect
DMPlex: Added flip argument to DMPlexLabelCohesiveComplete() to reverse submesh normal - Fixed ex5 test
DMPlex ex5: Fixed existing tests and added two cohesive cell test - Fixed tests for new cohesive cell orientation
DMPlex: Propagate orientation information to the submesh properly
DMPlex: Orientation of cohesive cell should come from face to which it is attached
DMPlex: Added subdm argument to DMPlexLabelCohesiveComplete() - Use the subdm for orientation information so we replace vertices all on the same side
DMPlex: Fix DMPlexOrient() for submeshes - Need to also reverse cone orientation of cells attached to fault faces when we flip them
...

Conflicts:
config/builder.py
include/petsc-private/dmpleximpl.h
include/petscdm.h
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexfem.c
src/dm/interface/dlregisdmdm.c
src/snes/examples/tutorials/ex52.c
src/snes/examples/tutorials/output/ex12_10.out
src/snes/examples/tutorials/output/ex12_11.out
src/snes/examples/tutorials/output/ex12_5.out
src/snes/examples/tutorials/output/ex12_6.out
src/snes/examples/tutorials/output/ex12_7.out
src/snes/examples/tutorials/output/ex12_8.out
src/snes/examples/tutorials/output/ex12_9.out

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Merge branch 'knepley/fix-plex-orient'

* knepley/fix-plex-orient:
DMPlex: Fixed bug with mesh orientation - flipped marker must be a boolean for ^ operation - Final check needs a mismatch as well

Merge branch 'knepley/fix-plex-orient'

* knepley/fix-plex-orient:
DMPlex: Fixed bug with mesh orientation - flipped marker must be a boolean for ^ operation - Final check needs a mismatch as well
DMInterpolation: Fixed declarations
DMPlex: Added declaration

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Merge branch 'knepley/fix-plex-submesh-orient'

* knepley/fix-plex-submesh-orient:
DMPlex ex5: Added test for 2 face cohesive submesh - Fixed old tests for cohesive cell orientation
DMPlex: Put i

Merge branch 'knepley/fix-plex-submesh-orient'

* knepley/fix-plex-submesh-orient:
DMPlex ex5: Added test for 2 face cohesive submesh - Fixed old tests for cohesive cell orientation
DMPlex: Put in depth label optimization
DMPlex: Fix flipping of fault normal
DMPlex: We label cells with only vertices on the fault, but they have no cone replacement
DMPlex: Fix translation to cohesive edges in 3D - They are labeled by the vertices they connect
DMPlex: Added flip argument to DMPlexLabelCohesiveComplete() to reverse submesh normal - Fixed ex5 test
DMPlex ex5: Fixed existing tests and added two cohesive cell test - Fixed tests for new cohesive cell orientation
DMPlex: Propagate orientation information to the submesh properly
DMPlex: Orientation of cohesive cell should come from face to which it is attached
DMPlex: Added subdm argument to DMPlexLabelCohesiveComplete() - Use the subdm for orientation information so we replace vertices all on the same side
DMPlex: Fix DMPlexOrient() for submeshes - Need to also reverse cone orientation of cells attached to fault faces when we flip them
DMPlex: Propagate orientations in cohesive cell creation - Also fix hybrid bounds

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

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Merge branch 'knepley/plex-depth-label'

* knepley/plex-depth-label:
DMPlex: remove unused variables
DMPlex: Use BFS to calculate depth rather than crazy recursive scheme
DMPlex: Now use DMPlex

Merge branch 'knepley/plex-depth-label'

* knepley/plex-depth-label:
DMPlex: remove unused variables
DMPlex: Use BFS to calculate depth rather than crazy recursive scheme
DMPlex: Now use DMPlexGetDepthLabel() to interrogate point depths
DMPlex: Optimize depth retrieval by storing a pointer to the label - This is a little unsafe since someone could go in and create a new "depth" label out from under you

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DMPlex: Changed DMPlexCreatePartition() to take the partitioner name

Merge branch 'master' into knepley/feature-dt-fem

* master: (211 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries

Merge branch 'master' into knepley/feature-dt-fem

* master: (211 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

Conflicts:
config/builder.py
src/dm/impls/plex/plexgeometry.c

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Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (273 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (273 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

Conflicts:
include/petscdmplex.h

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Merge branch 'master' into knepley/feature-dmda-section

* master: (287 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib e

Merge branch 'master' into knepley/feature-dmda-section

* master: (287 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...

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Merge branch 'knepley/plex-submesh-cohesive'

* knepley/plex-submesh-cohesive:
DMPlex: Fix hybrid bounds for interpolated mesh with cohesive cells
DMPlex: Fixes for cohesive label reconstruction

Merge branch 'knepley/plex-submesh-cohesive'

* knepley/plex-submesh-cohesive:
DMPlex: Fix hybrid bounds for interpolated mesh with cohesive cells
DMPlex: Fixes for cohesive label reconstruction - Do not put cohesive edges in labels - Do not reconstruct "depth" label
DMPlex: Now a label can be used to restrict the points for a cohesive submesh - Added label and value arguments to DMPlexCreateCohesiveSubmesh()

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Merge branch 'knepley/fix-3d-orientation'

* knepley/fix-3d-orientation:
DMPlex: Fix initialization for DMPlexVecGetClosure()
DMPlex: fix argument to DMPlexVecRestoreClosure
DMPlex: Fix orienta

Merge branch 'knepley/fix-3d-orientation'

* knepley/fix-3d-orientation:
DMPlex: Fix initialization for DMPlexVecGetClosure()
DMPlex: fix argument to DMPlexVecRestoreClosure
DMPlex: Fix orientation for VTU output
plex: remove unused variable
DMPlex: Fixed orientation conversion for VTK
DMPlex: Fixed field interpolation in tetrahedra and hexahedra for new orientation
DMPlex: Fixed face definition in tetrahedra and hexahedra for new orientation
DMPlex: Fixed point location in hexahedrons for new orientation
DMPlex: Added generic DMPlexInvertCell() to aid in changing orientation to the internal convention

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DMPlex: Added DMPlexGetSupportSection()

DMPlex: Fix DMPlexComputeL2Diff() to take PetscFE

DMPlex: Added DMPlexEqual() and DMPlexUninterpolate()
- These will be needed for testing refined meshes

DMPlex: Moved refinement functions into new file
- Reorganized DMPlex header

PetscFE: FEM Jacobian computation working, and now cache default tabulation
- Added PetscFEIntegratJacobianChunk()
- Changed interface in DMPlexComputeJacobianFEM()
- Changed signature of integrateJa

PetscFE: FEM Jacobian computation working, and now cache default tabulation
- Added PetscFEIntegratJacobianChunk()
- Changed interface in DMPlexComputeJacobianFEM()
- Changed signature of integrateJacobianFEM in DMPlex
- Added DMPLEX_JacobianFEM event
- Now PetscFE caches default tabulation

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PetscFE: Large reorganization of FEM dispatch
- WARNING: Now DMPlex and PetscFE have a circular dependence. We need to move the FEM methods to PetscFE
- Changed FEMIntegrateResidualBatch() from to Pe

PetscFE: Large reorganization of FEM dispatch
- WARNING: Now DMPlex and PetscFE have a circular dependence. We need to move the FEM methods to PetscFE
- Changed FEMIntegrateResidualBatch() from to PetscFEIntegrateResidualChunk()
- Changed DMPlexComputeResidualFEM() to use new interface
- Changed signature of f_k and g_kl functions
- Added DMPlexResidualFEM event
- Put PetscQuadrature and PetscCellGeometry
- Moved and changed PetscFEM structure

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DMPlex: Added flip argument to DMPlexLabelCohesiveComplete() to reverse submesh normal
- Fixed ex5 test

DMPlex: Added subdm argument to DMPlexLabelCohesiveComplete()
- Use the subdm for orientation information so we replace vertices all on the same side

DMPlex: Now use DMPlexGetDepthLabel() to interrogate point depths

DMPlex: Now a label can be used to restrict the points for a cohesive submesh
- Added label and value arguments to DMPlexCreateCohesiveSubmesh()

Merged petsc/petsc into rmills/petsc master.