Merge branch 'master' into denera/lmvm-mat-and-pc

TAO: Fix 'extern' declarations

- Rename events following naming conventions in other packages
- Fix extern -> PETSC_EXTERN

derived LMVM types added and moved into the KSP package

Memory leaks in MAT_LMVM and TAO_BNK fixed

BNCG accelerator added into BNLS, works for TAO examples, segfaults on CUTEst probs

LMVM matrix can now deal with reduced systems that change in size based on # of active variables

Wrapping up for a pull request

- New active set estimation added based on Bertsekas' method
- Active set estimation split off into the utilities folder so that it can later be applied to BLMVM and B

Wrapping up for a pull request

- New active set estimation added based on Bertsekas' method
- Active set estimation split off into the utilities folder so that it can later be applied to BLMVM and BNCG
- Convergence of BNK methods exhaustively profiled on CUTEst problems

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Bounded NLS working on plate2

Box constraint projections added to BNLS, and it still works for unconstrained problems. Bounded problems are not yet tested.

just a few more PETSC_EXTERN changes

PETSC_EXTERN issue resolved for separately compiled libraries

PETSC_EXTERN and CHKERRQ fixes

Added view information for tracking total iterations across multiple TaoSolve() calls

BFGS statistics preserved across multiple TaoSolve() calls

Added simple test for recycling behavior

Wrapping up for a pull request

Begin refactorization of MatShell to make the code more straightforward and extensible

Introduce MatSetOperation() for changing operations on non-MATSHELLs
Introduce two modes for MATSHELL
1) MAT

Begin refactorization of MatShell to make the code more straightforward and extensible

Introduce MatSetOperation() for changing operations on non-MATSHELLs
Introduce two modes for MATSHELL
1) MATSHELL manages scalings and shifts automatically
2) Creator of MATSHELL can provide their own code for managing scaling and shifts
This is used by MatCreateADA() and MatCreateSubMatrixFree()

The extensibility is so that a MatShell can be easily used in as many places as possible as other matrices,
for example,

/* A = diag(u) G */
ierr = MatCopy(appctx->SEMop.grad,A,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatDiagonalScale(A,globalin,NULL);CHKERRQ(ierr);
/* A = A + diag(Gu) */
ierr = VecDuplicate(globalin,&Gglobalin);CHKERRQ(ierr);
ierr = MatMult(appctx->SEMop.grad,globalin,Gglobalin);CHKERRQ(ierr);
ierr = MatDiagonalSet(A,Gglobalin,ADD_VALUES);CHKERRQ(ierr);
ierr = VecDestroy(&Gglobalin);CHKERRQ(ierr);
/* A = K - A */
ierr = MatScale(A,-1.0);CHKERRQ(ierr);
ierr = MatAXPY(A,1.0,appctx->SEMop.keptstiff,SAME_NONZERO_PATTERN);

Commit-type: feature

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