Merge branch 'knepley/plex-profile-distribution'

* knepley/plex-profile-distribution:
DMPlex: Added new events for distribution

DM: Fixed initialization
- Sys because we use PetscContainer internally

Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

This option was mostly redundant because normal shared libraries satisfy
all the same needs. This commit adds the run-time option
-dynami

Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

This option was mostly redundant because normal shared libraries satisfy
all the same needs. This commit adds the run-time option
-dynamic_library_preload that can be used to load/initialize all the
packages in advance, as used to be done when --with-dynamic-loading.

The PetscDLLibraryRegister_petscxxx functions have been kept, but are
not called unless -dynamic_library_preload is used. The petsc-dev
discussion, "Why --with-dynamic-loading?" did not reach consensus about
whether this was ever useful, so it may also be removable.

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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 '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 'jed/is-view-from-options'

Fix SEGV on -ao_view, which was being called from AOCreate.

* jed/is-view-from-options:
AO: fix erroneous processing of -ao_view and factor into AOViewFrom

Merge branch 'jed/is-view-from-options'

Fix SEGV on -ao_view, which was being called from AOCreate.

* jed/is-view-from-options:
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions

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doc: fix named argument in {Vec,Mat,DM}ViewFromOptions

DM: Added a tolerance to DMPrintLocalVec()
- Also added member to DMPlex to store tolerance, use -dm_plex_print_tol to set

PetscFE: Added OpenCL implementation

Merge branch 'barry/improve-memory-logging'

Conflicts:
src/ksp/pc/impls/redundant/redundant.c
src/mat/interface/matnull.c

DMPlex+PetscFE: Moved integration functions from DMPlex to PetscFE
- Now PetscFE type indicates the integration method
- Added all machinery for PetscFE types

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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DM: Added DMPrintLocalVec()

PetscFE: Added package initialization to DM, register classes

Merge branch 'rmills/dm-localtolocal'

Introduces DMLocalToLocalxxx() (and deprecates DMDALocalToLocalxxx()) to
support local-to-local communication operations for any DM type, not just
DMDA. Adds D

Merge branch 'rmills/dm-localtolocal'

Introduces DMLocalToLocalxxx() (and deprecates DMDALocalToLocalxxx()) to
support local-to-local communication operations for any DM type, not just
DMDA. Adds DMShell routines to set up local-to-local operations.

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DMPlex: Added new events for distribution

converted uAMS usage to SAWs usage; starts server but cannot see any published directories

Removed unused variables.

DM: Added specialization for DMCreateSubDM() with a PetscSection
- Replace DMPlex implementation
- Is used by DMDA when a section is defined

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 DMPlexClo

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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Finished converting DMDALocalToLocalBegin()/End() to internal functions (DMLocalToLocalBegin()/End() should now be used) and deprecated this interface.

Cleaned out code copied from DMGlobalToLocalBegin()/End() that shouldn't be present in DMLocalToLocalBegin()/End().

Updated documentation for DMLocalToLocalBegin()/End().

DMSubDomainHook_Coordinates() for restricting user coordinates to subdomain DM