Merged in barry/update-collective-on (pull request #1744)

Update the use of Collective on in the manual pages to reflect the new style

Update the use of Collective on in the manual pages to reflect the new style

Commit-type: style-fix, documentation
Thanks-to: Patrick Sanan <patrick.sanan@gmail.com>

Merged in psanan/man-pages-remove-keywords (pull request #1717)

Man pages: Remove .keywords fields

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be unif

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be uniformly used or maintained.

Thus, remove all .keywords: fields, and a following blank line, if present.

This is accomplished with GNU sed (gsed on OS X), with the following commands.
*Warning* that this type of command can corrupt a .git directory,
so be cautious in reusing or modifying these commands. They first look
for and delete matching lines with a following line consisting of only whitespace,
and then delete any remaining matching lines.

find src/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find src/ -type f -exec gsed -i '/keywords:/d' {} +
find include/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find include/ -type f -exec gsed -i '/keywords:/d' {} +

Hints on the sed command obtained from: https://unix.stackexchange.com/questions/100754/how-to-delete-a-specific-line-and-the-following-blank-line-using-gnu-sed

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Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComp

Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex type is missing from fortran
initialize variables so that static analyzer doesn't mistakenly think they are used uninitialized.
Move access of prefix until it is actually used
Remove DMDASplitComm2d(), used in one example that was not tested
Functions that do not return PetscErrorCode should not use PetscFunctionBegin/End paradgm
remove unneeded reassignment of same value
Missing CHKERRQ(); Mostly in Tao code
Remove clang static analyser warning about passing NULL variable to strncat()
missing newline in -ts_monitor_extreme
minor fixes for integer counters
Configure: Deal with '__func__' in C89 builds with newer Clang and GCC.
Jenkinsfile: Increased timeout for tests to 5 minutes.
3.9 changes: further clarify removal of -pc_factor_mat_solver_package
Options deprecations: add "PETSc" to inline warning
removing unused variable
MatShift support added to MATSUBMAT. Mimics MATSHELL functionality. Needed for matrix-free Hessians in TAO Newton-Line-Search methods.
Add -ts_monitor_extreme
Dev manual: add note on deprecating options database keys
...

Conflicts:
src/dm/impls/plex/examples/tests/ex4.c

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Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead code.
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
...

Conflicts:
src/snes/examples/tutorials/ex13.c

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Merged in psanan/private-functions-rename (pull request #842)

Rename some private functions

Rename some private functions

Rename some private functions which start with XXX_, where XXX is the name of a main PETSc class,
and mark static if needbe.

more remove __FUNCT__

Merge remote-tracking branch 'origin/pr644/vijaysm/update-dmmoab-5/master'

Some fixes to get serial and parallel examples running correctly without malloc errors.

Fix several memory leaks and some inconsistencies in tests

Several key fixes for parallel computations

- A bug fix for parallel boundary vertex resolution (filter by interface
rather than shared entities); Other miscellaneous updates to the drivers.
- Upd

Several key fixes for parallel computations

- A bug fix for parallel boundary vertex resolution (filter by interface
rather than shared entities); Other miscellaneous updates to the drivers.
- Updating the nnz/onz allocation computation for the interpolation matrices

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Updating the interpolation matrix to use a consistent basis for FEM problems.

- This needs to be exposed as an option in the future (can allow us to compare
different types of interpolation operat

Updating the interpolation matrix to use a consistent basis for FEM problems.

- This needs to be exposed as an option in the future (can allow us to compare
different types of interpolation operators).
- Updates for Hex basis evaluation and other minor updates

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Adding a consolidated FEM helper class for evaluating basis functions for computations
- Updating the 2-D example to use the new interface for FEM assmebly
- Some warning fixes and making the formatt

Adding a consolidated FEM helper class for evaluating basis functions for computations
- Updating the 2-D example to use the new interface for FEM assmebly
- Some warning fixes and making the formatting consistent everywhere

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Several modifications to enable DMMoab to work consistently in serial
i.e., when MOAB is not configured with MPI.

** Important: Removing the SetParallelComm API routine since the user
never needs th

Several modifications to enable DMMoab to work consistently in serial
i.e., when MOAB is not configured with MPI.

** Important: Removing the SetParallelComm API routine since the user
never needs the MOAB internal PCOMM object anyway when using DMMoab.

Additionally, there are several minor fixes and cosmetic cleanups.

* fix inconsistencies for 1-D mesh generation
* minor bug in computation of max nnz for AIJ matrices
* fix convergence issues for 3-D example
* fix the DMMoab dependency on non-MPI enabled MOAB
* fixes for the TS Brusselator example

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Add new API functions to support mesh copies, view and modifications and
creation of sub-DM objects

* Adding new operations (DMView and DMClone) for DMMoab.
* Adding several public API functions to

Add new API functions to support mesh copies, view and modifications and
creation of sub-DM objects

* Adding new operations (DMView and DMClone) for DMMoab.
* Adding several public API functions to support mesh modifications
and creation of sub-DM objects
* Store the local/global min/max ID space in DMMoab object

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Enhancements to DMMoab driven through the 2-D and 3-D example use-cases.

* Updates to the FEM examples to verify convergence and use of GMG
preconditioners with arbitrary levels.
++ TODO: Handle

Enhancements to DMMoab driven through the 2-D and 3-D example use-cases.

* Updates to the FEM examples to verify convergence and use of GMG
preconditioners with arbitrary levels.
++ TODO: Handle mixed meshes in the future.
* Updates to the parallel structured grid mesh-generation which was failing
for non-divisible parallel square meshes.
* Fix a bug in boundary element computation through skinner.
- This was tricky to find and the ksp/tutorials/ex35.cxx helped when
the convergence order was not as expected. After verifying the bases,
the issue was found to be the B.C treatment which missed certain
elements that only had a node on the boundary and not any edges/faces,
which meant that Skinner did not acknowledge these as boundary elements.
* Some profiling monitors are now available during mesh generation.
* Added a new API to get the mesh hierarchy level.
* Fix the nnz computation routine for interpolation operators.
The allocation is still suboptimal in parallel.

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Memory allocation for vector and matrices, debugging through ex3.cxx.

1) Fixes for matrix allocation, especially for refined levels of the mesh.
2) Small fix for a bug when user provides Tag

Several key bug fixes to get the boundary data and UMR working correctly
for both the 2-D and 3-D scenarios.

* Do not use the skinner to get boundary data if we are on a refined level.
We should u

Several key bug fixes to get the boundary data and UMR working correctly
for both the 2-D and 3-D scenarios.

* Do not use the skinner to get boundary data if we are on a refined level.
We should use it only for coarsest levels and then just decipher based
on coarse level entity parent-child property inheritance.
* Updates to the ex35 and ex36 examples to make them verifiable through MMS
and modify tests to use the new API changes.
+ ex35 and ex36 can now compute the L2 discretization error wrt exact solution.
+ Update examples and tests to respect the new API change to accept ghost layers when
loading a mesh.
+ Added an exact solution for problem 2 (MMS) and fix forcing function
so that we can verify the solution convergence
* Several bug fixes and minor enhancements for RefineMesh with edges/faces
enabled. Also tested the computation of all the boundary vertices/faces/edges
to impose BC data for the operators.
* Fix a bug in the numbering and decomposition of HEX->TETS during mesh generation.
Now the numberings are consistent and nested refinement works cleanly for arbitrary levels.
Tested with impls/moab/tests/ex3 for dim=[1,2,3] with simplex=[on,off].
* Added code to exchange ghost layers for all hierarchically generated mesh levels
* Fix issues with boundary marker caching and querying
* Fixes for parallel ghosting for refined entities. Added flexibility to specify ghost
rings for both in-memory mesh and loaded from file.
* Bugfix for read options (mem corruption)
* Update the NNZ allocation an creation of interpolation matrices in parallel.

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The box mesh generation routine was ad-hoc. Complete revamp of the
implementation along with good verification of the generated mesh. The
GenLargeMesh example in MOAB has been useful here but in the

The box mesh generation routine was ad-hoc. Complete revamp of the
implementation along with good verification of the generated mesh. The
GenLargeMesh example in MOAB has been useful here but in the future,
need to expose this as an API in MOAB so that we can just make use of
that. This replication of code is stupid.

* Fix parallel generation and ghost layer creation
* Adding options to control refinement etc from command line.

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Updating the memory allocation for interpolation matrices to reduce number of unnecessary nonzero entries.

Potentially, this operation needs to be discretization-aware. Link to
PetscFe etc in the fu

Updating the memory allocation for interpolation matrices to reduce number of unnecessary nonzero entries.

Potentially, this operation needs to be discretization-aware. Link to
PetscFe etc in the future can be helpful here.

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Make use of the ParallelComm object and prepare it to generate the mesh
hierarchy in parallel

* Modifications to both examples and tests to conform to API changes
+ ex35: Refactoring to allow both

Make use of the ParallelComm object and prepare it to generate the mesh
hierarchy in parallel

* Modifications to both examples and tests to conform to API changes
+ ex35: Refactoring to allow both TRI and QUAD to be used for the problem of interest.
+ Several changes to clean up the MOAB based inhomogeneous Laplacian solver in
2-D (based on ATPESC 2014 version).
* Adding a new test for verifying the uniform mesh refinement capability exposed by DMMoab.
* Fix some memory corruption and leaks -- when user does not set fieldNames. Found through tests/ex3
* Reduction in memory footprint in DOF number storage. Can eventually remove usage of llmap,lgmap.
* Cleanup and more optimizations for DOF evaluations.

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Several clean ups and updates/fixes for GMG.
* Adding a new 3-D example - based on ex35 to test multigrid PC functionality with MOAB
- Sample runs converge to correct solution. Need to measure MG e

Several clean ups and updates/fixes for GMG.
* Adding a new 3-D example - based on ex35 to test multigrid PC functionality with MOAB
- Sample runs converge to correct solution. Need to measure MG efficiency with a DA example.
* Clean up the implementation for refine/coarsen hierarchy methods for DM.
* Fixing memory leaks and changing API for generate_mesh_hierarchy.
* Fix several warnings. Fix mattype to be consistent with DM.

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First consolidate changelist with several additions for enabling geometric multigrid with DMMoab

* Implement hooks to generate mesh hierarchy through MOAB NestedRefine functions
* Adding several pla

First consolidate changelist with several additions for enabling geometric multigrid with DMMoab

* Implement hooks to generate mesh hierarchy through MOAB NestedRefine functions
* Adding several placeholders and API functions to orchestrate the DMMoab + MG functionality.
* Add variable to store current level in the hierarchy. Also, no need to implement coarsen/refine hierarchy since this will internally use DMRefine/DMCoarsen anyway.
* Added an API for DMMoabSetBlockFills (needs proper implementation)
* Adding necessary implementation to enable DMRefine/DMCoarsen methods once the mesh hierarchy has already been generated. This is a pre-processing step and need to discuss to make sure it follows PETSc's option driven computation
* Rearrange the data structure to better document interaction between levels and level specific data.
* A pointer to the native MOAB NestedRefine hierarchy is also maintained to improve inter-level query efficiency. This is also used for adjacency and boundary entity data queries.
* The interpolator is full weighting based on inverse distance square (RBF?). Next, to provide semantics for discretization specific projections operators between levels.
* Prepped the 2-D example for verification of GMG solvers

TODO: Revisit SubDM concept based on subset ranges

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