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-speed-tests' into knepley/feature-dt-fem

* knepley/plex-speed-tests:
DMPlex: Remove unused variables
DMPlex: Fixed bug in special case for DMPlexVecGetClosure() - Need

Merge branch 'knepley/plex-speed-tests' into knepley/feature-dt-fem

* knepley/plex-speed-tests:
DMPlex: Remove unused variables
DMPlex: Fixed bug in special case for DMPlexVecGetClosure() - Need to set outgoing size if array is passed in
DMPlex: Added special case for DMPlexVecSetClosure() - Could add more modes
DMPlex: Optimizations for DMPlexVecGetClosure() - Removed branch (seems to have little effect) - Removed calculation of size when array is provided (profiled for 20% effect)
DMPlex: Forgot one init for DMPlexVecGetClosure()
DMPlex: Must initialize argument to DMPlexVecGetClosure()
DMPlex ex9: Added ability to reuse array in VecGetClosure()
DMPlex: Allow DMPlexVecGetClosure() to take an input array
DMPlex: Fix bug in specialization of DMPlexVecGetClosure()
DMPlex: Bug fix for special case in DMPlexVecGetClosure()
DMPlex: Added optimization for depth 1 DMPlexVecGetClosure()
DMPlex ex9: Does not fail by default - Will turn back on failure once we calculate variance
SNES ex12: Cleaning up in preparation for speed testing
DMPlex: Added ex9 to test performance, put in depth 1 special case for TransitiveClosure

Conflicts:
config/builder.py
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_8.out
src/snes/examples/tutorials/output/ex12_9.out

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Merge branch 'knepley/feature-dm-clone'

* knepley/feature-dm-clone:
DMPlex: Removed unused variables
DM: Dammit, forgot declaration
DM: Small fix to DMClone for DMPlex
DM: Added specializati

Merge branch 'knepley/feature-dm-clone'

* knepley/feature-dm-clone:
DMPlex: Removed unused variables
DM: Dammit, forgot declaration
DM: Small fix to DMClone for DMPlex
DM: Added specialization for DMCreateSubDM() with a PetscSection - Replace DMPlex implementation - Is used by DMDA when a section is defined
DM: Fix DMDA clone - Made it work for all dimensions (which makes DMCreateSubDM() work) - Removed DMSetUp() which should be called by caller
DM: Added DMClone() which makes a shallow copy - This is very useful for DM since it can have a lot of associated data and is used as a building block for different problems - This replaces DMPlexClone()

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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: Fixed view

DMPlex: Now DMView_Plex() uses the DM name

DMPlex: Added DMPlexGetSupportSection()

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

Merge branch 'karlrupp/feature-snes-ex52-OpenCL' into knepley/feature-dt-fem

* karlrupp/feature-snes-ex52-OpenCL:
SNES ex52: OpenCL integration now natively supports double precision as well.
SN

Merge branch 'karlrupp/feature-snes-ex52-OpenCL' into knepley/feature-dt-fem

* karlrupp/feature-snes-ex52-OpenCL:
SNES ex52: OpenCL integration now natively supports double precision as well.
SNES ex52: Added option to switch between OpenCL and CUDA backends.
SNES ex52: Added test for multiple regular parallel refinements
SNES ex52: Fixed output flag for residual printing
SNES ex52: Added -refinement_rounds to allow multiple regular parallel refinements
SNES ex52: Added uniform parallel refinement - Added test
DMPlex: Uniform refinement does not work on uninterpolated meshes
SNES ex52: Changed output for 3D tests
SNES ex52: Fixed Makefile to support compilation of both the OpenCL and the CUDA version
SNES ex52: OpenCL version can now deal with multiple parallel blocks.
SNES ex52: Fixed OpenCL vector-type initialization for Laplacian as well.
SNES ex52: Fixed static initialization issue in OpenCL kernel for the AMD SDK.
SNES ex52: Fixed OpenCL test suite, added reference output
SNES ex52: Now builder runs for OpenCL are separate
SNES ex52: Unify dispatch function for CUDA and OpenCL - Now only one function works at a time (I think this is alright in the example) - Remove -opencl flag
SNES ex52: Added OpenCL profiling information.
SNES ex52: Now supporting elasticity in 2d via OpenCL.
SNES ex52: Updated OpenCL version such that spatial dimension is now a runtime parameter.
Added OpenCL version of SNES ex52 for the Laplacian.
Builder: Fixed problems for snes/ex52: "Cuda" -> "cuda", stripping "\r" from output for comparison with reference.

Conflicts:
src/snes/examples/tutorials/ex52.c

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

DMPlex: Fix memory leak with refinement

DMPlex: Fixed some function names to cleanup the refinement file move

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

DMPlex: remove unused variables

Merge branch 'knepley/opt-plex-depth' into knepley/plex-depth-label

Fixes build error due to missing depthLabel field in DM_Plex.

* knepley/opt-plex-depth:
DMPlex: Use BFS to calculate depth ra

Merge branch 'knepley/opt-plex-depth' into knepley/plex-depth-label

Fixes build error due to missing depthLabel field in DM_Plex.

* knepley/opt-plex-depth:
DMPlex: Use BFS to calculate depth rather than crazy recursive scheme
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

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

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DMPlex: Put in METIS support

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: Fix DMPlexOrient() for submeshes
- Need to also reverse cone orientation of cells attached to fault faces when we flip them

DMPlex: Use BFS to calculate depth rather than crazy recursive scheme

DMPlex: Now use DMPlexGetDepthLabel() to interrogate point depths

DMPlex: Added new events for distribution

DMPlex: Remove unused variables