PCBDDC: fixes for preconditioner reuse

PCBDDC; another multilevel bugfix

it could happen that we have a subdomain completely disconnected from the others (with pcis->n_B = 0)
the adjacency list computed will be empty

PCBDDC: add argument to PCBDDCgraphInit to remove some communications during graph setup

PCBDDC: optimized eigenvalue problem

explicit inversions of sum(S_E) and sum(St_E) blocks have been removed and the eigenvalue problem has been recasted
remove unneded transpositions for the symmetr

PCBDDC: optimized eigenvalue problem

explicit inversions of sum(S_E) and sum(St_E) blocks have been removed and the eigenvalue problem has been recasted
remove unneded transpositions for the symmetric case

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PCBDDC: get rid of invert_stildas branch

Merge branch 'pr192/Fande-Kong/scalable-matincreaseoverlap/master' of https://bitbucket.org/petsc/petsc

Merged petsc/petsc into master

PCBDDC: reuse interior solver computed by MUMPS when computing the Schur complement

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

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/mat/impls/aij/mpi/mumps/mumps.c
s

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

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/mat/impls/aij/mpi/mumps/mumps.c
src/mat/impls/is/matis.h

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PCBDDC: add option to select faster application of deluxe scaling

QR factorization of constraints resulting in a unitary transformation is mandatory if a change of basis is requested with faster del

PCBDDC: add option to select faster application of deluxe scaling

QR factorization of constraints resulting in a unitary transformation is mandatory if a change of basis is requested with faster deluxe

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Merged master into semihozmen/ksp-fcg-eigen-comp-support

Merged petsc/petsc into master

Merge branch 'master' into pr192/Fande-Kong/scalable-matincreaseoverlap/master

Needed to merge master to update to new calling sequence PetscCommBuildTwoSided

fixed missing CHKERRQ() detected by clang's --analyze

Merged petsc/petsc into master

Merge branch 'barry/fix-directory-layout'

updated PETSc directory layout to match standard packaging strategies

include/petsc finclude,private,mpiuni
lib/petsc conf
bin/petsc*

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

PCBDDC: get rid of parallel application of deluxe scaling

code has been greatly simplified
introduced subcommunicators in PCBDDCSubSchursSetUp to improve performances in multilevel cases
adaptivity

PCBDDC: get rid of parallel application of deluxe scaling

code has been greatly simplified
introduced subcommunicators in PCBDDCSubSchursSetUp to improve performances in multilevel cases
adaptivity is supported only in combination with deluxe scaling

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PCBDDC: level details and coarsening ratio shoud be set before KSPSetFromOptions is called

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

PCBDDC: turn off vertices in the primal space for adaptive selection if requested

Added heuristic for eigenvalue threshold when the subset is shared by more than 2 subregions
Added constraints check

PCBDDC: more verbose output for primal indices

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