Merge branch 'barry/fixmultmallocs'

Merge branch 'stefano_zampini/pcbddc-improvecoarsesolver'

* stefano_zampini/pcbddc-improvecoarsesolver:
PCBDDC: Updated man pages
PCBDDC: change function name
PCBDDC: save flops when there is

Merge branch 'stefano_zampini/pcbddc-improvecoarsesolver'

* stefano_zampini/pcbddc-improvecoarsesolver:
PCBDDC: Updated man pages
PCBDDC: change function name
PCBDDC: save flops when there is only one primal dof on a single connected component
PCBDDC: fixed typo
PCBDDC: added workaround to deal with BAIJ local matrices
PCBDDC: fix broken compilation with cxx
PCBDDC: switch on exact dirichlet trick demanded to PCPreSolve
PCBDDC: avoid unneeded computations when zeroed rows are not present
PCBDDC: prefixes for internal solvers
PCIS: add field in pcis data for solver computation (defaults to true)
PCBDDC: improved support for multileveling when nullspace is present
PCBDDC: rearranging SetUpCoarseSolver
PCIS: matis pointer should be set after type checking
PCBDDC: remove enums for coarse problem type.
PCBDDC: further cleanup on old METIS-based code.
PCBDDC: removed explicit dependency from METIS.
PCBDDC: remove Enum on coarse communications since they are now the same
PCBDDC: PARALLEL_BDDC case now handled trough MatConvert_IS_AIJ
PCBDDC: Global numbering of coarse dofs moved to a separate routine
PCBDDC: move mpi calls outside block for primal dofs numbering
PCBDDC: remove integer arrays for primal indices from bddc private struct
PCBDDC: coarse_mat is no longer a member of bddc private struct.
PCBDDC: remove REPLICATED_BDDC and SEQUENTIAL_BDDC branches.
PCBDDC: protect code for mirrors by graph size.

Conflicts:
src/ksp/pc/impls/bddc/bddcgraph.c (PetscSubcommSetTypeGeneral API change)

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Merge branch 'stefano_zampini/pcbddc-improvelocalsolvers'

* stefano_zampini/pcbddc-improvelocalsolvers:
PCBDDC: Set defaults for BDDC customization
PCBDDC: Less tricky customization from options

Merge branch 'stefano_zampini/pcbddc-improvelocalsolvers'

* stefano_zampini/pcbddc-improvelocalsolvers:
PCBDDC: Set defaults for BDDC customization
PCBDDC: Less tricky customization from options
PCBDDC: Raise error instead of return to caller
PCBDDC: Move PCBDDCSetUpCoarseEnvironment outside PCBDDCSetUpCoarseLocal and rename it as PCBDDCSetUpCoarseSolver
PCBDDC: Use PetscBT instead of boolean array in graph struct
PCBDDC: use PetscBT instead of arrays of PetscBool
PCBDDC: begin rewriting of SetUpCoarseEnvironment
PCBDDC: move two remaining functions for private setup into bddcprivate.c
PCBDDC: change function name for solvers setup
PCBDDC: move PCBDDCSetLevels to bddcprivate.c
PCBDDC: is_R_local is now a member of bddc private struct
PCBDDC: change name of function for setup of local correction and coarse basis functions
PCBDDC: improved code for local corrections and coarse basis functions setup
PCBDDC: Move setup of data structures for substructure correction and coarse basis assembly into a separate routine
PCBDDC: move creation of parallel work vectors used in presolve/postsolve.
PCBDDC: Move creation of work vector on constraints
PCBDDC: move stack variables of PCBDDCCoarseSetUp to protected block
PCBDDC: Move work vector creation to a separate routine
PCBDDC: allow computation of number of vertices/constraints in GetPrimal functions without actually computing their local indices
PCBDDC: Move setup of local scatters into a routine
PCBDDC: use a boolean memory instead of scalar one to compute local scatters
PCBDDC: Setup of local matrices moved into a separate routine into bddcprivate.c
PCBDDC: better management of local matrices among repeated solves
PCBDDC: move setup of local solvers into a routine into bddcprivate.c
PCBDDC: create local solvers once. Reuse them during repeated linear solves

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replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN()
The only ones left are when the second array is set into the first array and one ugly

replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN()
The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed

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Merge branch 'stefano_zampini/pcbddc-mirrorsfix'

* stefano_zampini/pcbddc-mirrorsfix:
PCBDDC: protect code for mirrors by graph size.

PCBDDC: fixed typo

PCBDDC: improved support for multileveling when nullspace is present

Solved some deadlocks when assembling local nullspace corrections

PCBDDC: remove enums for coarse problem type.

Now the strategy for solving coarse problem is driven by the number of requested levels.
Added missing checks to public interface
Minor fixes in PCBDDCG

PCBDDC: remove enums for coarse problem type.

Now the strategy for solving coarse problem is driven by the number of requested levels.
Added missing checks to public interface
Minor fixes in PCBDDCGraph code to cope with tabs in dbg_viewer

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PCBDDC: further cleanup on old METIS-based code.

coarse ksp is now created only once.

Merge branch 'stefano_zampini/pcbddc-mirrorsfix' into stefano_zampini/pcbddc-improvecoarsesolver

PCBDDC: Use PetscBT instead of boolean array in graph struct

PCBDDC: protect code for mirrors by graph size.

These are invalid reads in multilevel

[Jed: tweak to follow formatting guidelines]

Merge remote-tracking branch 'origin/master' into stefano_zampini/pcbddc-improvelocalsolvers

Merge remote-tracking branch 'origin/master' into stefano_zampini/pcbddc-mirrorsfix

Merge remote-tracking branch 'origin/master' into stefano_zampini/pcbddc-constraintssetupimproved

Merge branch 'stefano_zampini/pcbddc-specialgraphnodes'

* stefano_zampini/pcbddc-specialgraphnodes:
PCBDDC: Store special marks for local dofs in a separate memory of PCBDDCGraph (not which_dof)

PCBDDC: protect code for mirrors by graph size.

These are invalid reads in multilevel

PCBDDC: Store special marks for local dofs in a separate memory of PCBDDCGraph (not which_dof)

Merged petsc/petsc into rmills/petsc master.

Merge branch 'stefano_zampini/pcbddc-for-complexes'

* stefano_zampini/pcbddc-for-complexes:
PCBDDC: Solved compilation errors and warnings for complex builds

Merge branch 'stefano_zampini/pcbddc-development'

Conflict with 'jed/matnullspaceremove-inplace', resolved using:

$ git merge -X theirs --no-commit stefano_zampini/pcbddc-development
$ git grep

Merge branch 'stefano_zampini/pcbddc-development'

Conflict with 'jed/matnullspaceremove-inplace', resolved using:

$ git merge -X theirs --no-commit stefano_zampini/pcbddc-development
$ git grep -l MatNullSpaceRemove src/ksp | xargs perl -pi -e 's@(MatNullSpaceRemove\([^,]+,[^,]+),NULL\)@$1)@'
$ git commit -a

* stefano_zampini/pcbddc-development:
PCBDDC: add wrappers for PetscStackCallBLAS
PCBDDC: Final fix for locally periodic problems
PCNNCreateCoarseMatrix: fix allocation error
PCIS: consider myself as a neighbor when classifying interface nodes
PCBDDC: Remove misuses of neighbours_set in FETI-DP code
PCBDDC: Coarse solution lives in the span of phi (not psi)
MATIS: Add IsSymmetric and IsHermitian implementations
PCBDDC: More robust method to compute local boundary nodes
PCBDDC: Add partial support for periodic problems replacing Sort with RemoveDups
PCBDDC: Add support for non-symmetric linear systems
PCBDDC: Stiffness scaling should be rebuilt in any case (just to be safe)
PCBDDC: Remove trailing blanks
PCBDDC: Consistency of CSR graph passed in postponed to PCSetUp
PCBDDC: Preliminary work to split PCBDDCCoarseSetUp in simpler pieces
PCBDDC: allow compilation without metis header
PCBDDC: Optimal allocation in PCBDDCGetPrinalVerticesLocalIdx
PCBDDC: add verbosity level to graph view
PCBDDC: change boolean debug flag to integer -pc_bddc_check_level
PCBDDC: Workaround for BAIJ local matrices: convert to AIJ for coarse matrix
PCIS: Use PETSC_COMM_SELF instead of MPI_COMM_SELF
PCBDDC: many changes
ISG2LMapApply: fix __FUNCT__ and invalid access before globals are set up

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PCBDDC: Solved compilation errors and warnings for complex builds

Example code changed by using LAPACK steqr method.

PCBDDC: Final fix for locally periodic problems

Added mirrors to graph structure

PCBDDC: Add partial support for periodic problems replacing Sort with RemoveDups

* Local-to-global maps which are not one-to-one if restricted to any
subdomain will still be a problem.
* Graph vie

PCBDDC: Add partial support for periodic problems replacing Sort with RemoveDups

* Local-to-global maps which are not one-to-one if restricted to any
subdomain will still be a problem.
* Graph view now prints also the global number of the queued indices.
* Optimal allocation for queue_in_global_numbering.

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PCBDDC: Remove trailing blanks