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

Merge remote-tracking branch 'petsc/master' into matpartitioning-hierach

Merge remote-tracking branch 'petsc/master' into mat-increaseoverlap

Merge branch 'stefano_zampini/pcbddc-adaptive-selection'

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c

PCBDDC: better to use size_active_schur as a guard

PCBDDC: solve some errors in subschurs appearing when not restricting the work on active processes

PCBDDC: Replaced old non-memory scalable implementation of PCBDDCSubsetNumbering

New implementation is memory scalable and more efficient

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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PCBDDC: it does not have any sense to require adaptivity just for edges.

less stringent hermitian test in sub_schurs code

PCBDDC: improve logic around symmetric and positive definite

PCBDDC: reuse matrices with MatGetSubMatrices

PCBDDC: rearrange symmetry, positive-definitess stuffs

Added pc_bddc_symmetric command line options to shift to unsymmetric basis computation

PCBDDC: no need for eigensolver is S == St

PCBDDC: when n_subs == 1 and size_schur == size_active_schur reuse already inverted block

PCBDDC: fixes for compiler warnings

PCBDDC: fix for complexes

hermitian and positive definitess checks should be replaced by something which is more robust

PCBDDC: complete support for MUMPS Schur solver reusage

is_R and is_B should be created during SubSchursSetUp
Added preprocessor guards

PCBDDC: added support for transpose application of the BDDC when reusing MUMPS solver

PCBDDC: reuse Schur solver provided by MUMPS when possible

PCBDDC: optimize for reusage of Schur solver (if any)

R_to_B and (optionally) R_to_D scatters are different
reusage is not possible when change of basis has been requested

PCBDDC: reuse as much as possible the MUMPS Schur solver

optimizations still need to be applied

PCBDDC: remove is_I_layer from sub_schurs data structure

PCBDDC: fixes for preconditioner reuse

PCBDDC: optimized renumbering by subset

PCBDDC: fix multilevel issue with the computation of St