Remove use of _ and __ in front of PETSc include guards. Reason: C99 Reserved Identifiers

Commit-type: portability-fix

Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

Obtain changed (v3.5) handling of MatMPIBAIJSetPreallocationCSR to match
documentation.

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

Verified solution accuracy and convergence of 2-D and 3-D problems

- Adding a physical to reference natural coordinate computation routine through
Newton iteration. Verified.

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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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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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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Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of git. I think it is not justified to ever have anything in next for more than a few weeks at most.
Either take it out of next if it is broken or put it in master if it is not broken. Hanging around in next but
not master for ever is not a good policy.

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Merge branch 'master' into knepley/solkx

* master: (6933 commits)
Bib: Added reference
Includegraph: Updated for compatibility with new folder layout.
Add SNESLineSearchReason to fortran inclu

Merge branch 'master' into knepley/solkx

* master: (6933 commits)
Bib: Added reference
Includegraph: Updated for compatibility with new folder layout.
Add SNESLineSearchReason to fortran includes Also truncate names to fit 32 char fortran limit
fix compile warnings /usr/home/balay/petsc.clone-2/src/vec/vec/interface/vector.c:1944: warning: division by zero in '1.0e+0 / 0.' /usr/home/balay/petsc.clone-2/src/ksp/ksp/interface/itfunc.c:508: warning: 'vec_rhs' may be used uninitialized in this function
updated output for new trust region initial size
initial size of the trust region is set as a percent of the norm of the initial guess, it should not be related to the initial norm of the function (which is kind of nuts).
The default bounds for SNESVISetVariableBounds() in the manual page were reversed from correct values
Bib: Added refs
Bib: Update MPICH webpage
Plex: Forgot to close file
removed nonexistent ex46f from makefile test rule
Revert "fixed bad merge into master"
fixed bad merge into master
fix memory leak in mkl_pardiso fix some formatting in mkl_pardiso code
mv runex111 from TESTEXAMPLES_C to TESTEXAMPLES_DATAFILESPATH
Mat+Doc: More Fortran docs
Plex ex3: Run tests with the correct number of field components
Bib: Added TetGen cite
parmetis: make sure 'ldd libparmetis.so' points to the correct libmetis.so that its linked with.
small fix as reported by the nightly test
...

Conflicts:
config/builder.py

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Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
thi

Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
this branch. Matt's and my fixes in DMPlex will also be relevant.

* master: (1557 commits)
MatLoad_MPIDense() always allocated array space even if it was previously provided
Clarified lumping options for PCFieldSplitSchurPreType SELFP.
fixed up PetscInfo in GAMG
TSErrorWeightedNorm[2|Infinity]: API changes
MatLoad_SeqDense() always allocated new space for the data even if the user already provided it
Fixed DMCompositeGetAccessArray() to support readonly vectors
Fix obviously-wrong aspects of documentation on SNESVINEWTONRSLS and SNESVINEWTONSSLS.
fixed example to compile - demonstrates a bug
var name 'len' was F90 key word
For user provided Jacobian functions they should always assembly into the second matrix, the one from which the preconditioner is built because the first may be used as matrix-free with -snes_mf_operator
Suggest --with-64-bit-indices if users mistakenly use --with-64bit-indices
Fix configure logging of integer size.
missing underscore in #define of vecgetarrayread translation of fortran stub for VECGETARRAYREAD
updated test output files to reflect differences introduced previously in PCView output
-ksp_type preonly does not support -ksp_monitor_short so remove from test line to prevent extranious warning output
missing CHKERRQ; and ugly double declaration of ierr
Plex ex3: For want of a semicolon, the kingdom was lost
MatSetValuesMPISBAIJ will now print correct global indices when error generated due to new nonzero location
completed basic use of MatSetValuesBlocked_SeqBAIJ_Inlined() by MatSetValuesBlocked_MPIBAIJ() to allow proper global indices being printed when error generated by new nonzero locations.
Added inline version of MatSetValuesBlocked_SeqBAIJ() to be used by MatSetValuesBlocked_MPIBAIJ() to print error message for nonzero block with global indices
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Merge branch 'master' into shri/ts-is-for-differential-variables

Conflicts:
include/petsc-private/tsimpl.h
src/ts/impls/eimex/eimex.c
src/ts/interface/ts.c

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Merge branch 'pr235/vijaysm/dmmoab-complex'
PR235

Coordinates do not have to be PetscScalar -> Failure for complex builds.

Merge branch 'stefano_zampini/pcbddc-maint' into stefano_zampini/pcbddc_deluxe

Merge branch 'barry/feature-dmmoab-hdf5-tests'

Conflicts:
src/dm/interface/dmregall.c
src/ts/examples/tutorials/makefile

Modifying the BoxMesh creation function to also generate simplices (triangles and tets) in a structured fashion. This complements the quad, hex generation. Now the createmesh function takes an option

Modifying the BoxMesh creation function to also generate simplices (triangles and tets) in a structured fashion. This complements the quad, hex generation. Now the createmesh function takes an optional isSimplex argument.

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Add the capability to access the block or material number for each entity.

Adding DMSetFromOptions_Moab to unify all options database retrieval from command line. Added appropriate storage fields in data-structures and made sure that they are universally used, consistently.

Adding DMSetFromOptions_Moab to unify all options database retrieval from command line. Added appropriate storage fields in data-structures and made sure that they are universally used, consistently. Still need to figure out: how to propagate read options to DM before DMSetFromOptions is called.

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