added bs argument to ISLocalToGlobalMappingCreate(), not yet used for bs > 1

fixes for BDDC
by the way not having BDDC always in the testing is going to lead to trouble

fix for BDDC example out of date source

the compute Jacobian functions for SNES and TS now do not take a MatStructure flag

KSPSetOperators() no longer has the MatStructure argument. The Mat objects now track that information themselves. Use KPS/PCSetReusePreconditioner() to prevent the recomputation of the preconditioner

KSPSetOperators() no longer has the MatStructure argument. The Mat objects now track that information themselves. Use KPS/PCSetReusePreconditioner() to prevent the recomputation of the preconditioner if the operator changed in the way that SAME_PRECONDITIONER did with KSPSetOperators()

SNES/TS still need to be cleaned up to better utilize the new interfaces

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PCBDDC: MPIAIJ setup of coarse matrix when coarse_size == 0 when performing the first setup of PCBDDC

PCBDDC: fix headers after batch change from <> to ""

fixed quote marks for includes to <>

Merge branch 'stefano_zampini/pcbddc-reusebddc'

* stefano_zampini/pcbddc-reusebddc:
PCBDDC: remove unneeded code to check nearnullspace
PCBDDC: remove trailing whitespaces from source
PCBDDC:

Merge branch 'stefano_zampini/pcbddc-reusebddc'

* stefano_zampini/pcbddc-reusebddc:
PCBDDC: remove unneeded code to check nearnullspace
PCBDDC: remove trailing whitespaces from source
PCBDDC: solved compilation error with complex build
PCBDDC: introduce a new variable in PCBDDC data stucture to store the actual number of current vertices (corners with constraints with basis changed)
PCBDDC: make BtoNmap a member of bddc data struct (created once after PCISSetUp)
PCBDDC: check of dirichlet and neumann solvers is not needed if pcbddc->NullSpace is not present
PCBDDC: improved reuse of coarse matrix
PCBDDC: better management of primal space. Now a coarse numbering is computed if and only if the primal space has been really changed
PCBDDC: allow different customization of dirichlet and neumann boundary indices among successive linear solves
PCBDDC: now PCBDDC reuses part of its private data if NearNullSpace customization is changed between different linear solves
PCBDDC: local work vectors should be created only if new constraints are created and the relevant sizes are different
PCBDDC/PCIS: make vec4_D a member of pcis, not pcbddc
PCBDDC: Prepare for different primal spaces customization among different linear solves
PCBDDC: demand object destruction to setup routines for BDDCGraph and constraints

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c (also update PetscMalloc[1-7])

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Merge branch 'jed/malloc-array'

* jed/malloc-array:
PCBDDC: fix PetscMalloc2 and PetscMalloc7 not auto-updated

PCBDDC: fix PetscMalloc2 and PetscMalloc7 not auto-updated

PCBDDC: error for subassembling is disabled

PCBDDC: nullspace functions are now consistents with the new coarse solver approach

PCBDDC: solved memory leaks when reusing the preconditioner

PCBDDC: Coarse solver on subcommunicators whenever possible

Now the bddc dispatches the coarse problem on empty processes (if any)
this allows to solve in parallel the local corrections and the (par

PCBDDC: Coarse solver on subcommunicators whenever possible

Now the bddc dispatches the coarse problem on empty processes (if any)
this allows to solve in parallel the local corrections and the (parallel on subcommicators) coarse problem

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PCBDDC: changed implementation of PCBDDCScatterCoarseDataBegin/End

these functions now scatter back and forth data from the private vectors of coarse KSP

nullspace code changed accordingly to preve

PCBDDC: changed implementation of PCBDDCScatterCoarseDataBegin/End

these functions now scatter back and forth data from the private vectors of coarse KSP

nullspace code changed accordingly to prevent from breaking builds
The code for nullspace has been temporarily disabled

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PCBDDC: major change in MatISSubassemble

now, MatISSubassemble handles the case of restricting the newly created/updated matrix to a subcommunicator

API change for MatISGetSubassemblingPattern: num

PCBDDC: major change in MatISSubassemble

now, MatISSubassemble handles the case of restricting the newly created/updated matrix to a subcommunicator

API change for MatISGetSubassemblingPattern: number of target subdomains instead of coarsening ratio

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PCBDDC: bug fix in MatISGetMPIXAIJ

PCBDDC: now each level can be customized indepently without interferences

in the previous version, coarse_X_option caused that coarse_X+1_option was set
Updated man page

PCBDDC: minor changes to bddcprivate

PCBDDC: add subassembling_init and use_coarse_estimates to private bddc data struct for future use

PCBDDC: coarse_subassembling uninitialized

PCBDDC: dbg viewer is the default viewer on the communicator

Merge branch 'barry/fix-mpiint-petscoptionsgetint'

Conflicts:
src/ksp/pc/impls/redistribute/redistribute.c
src/mat/impls/aij/mpi/mpiaij.c
src/mat/impls/dense/mpi/mpidense.c
src/mat/utils/matstas

Merge branch 'barry/fix-mpiint-petscoptionsgetint'

Conflicts:
src/ksp/pc/impls/redistribute/redistribute.c
src/mat/impls/aij/mpi/mpiaij.c
src/mat/impls/dense/mpi/mpidense.c
src/mat/utils/matstash.c
src/snes/examples/tutorials/ex28.c
src/sys/objects/pinit.c
src/vec/is/ao/impls/memscalable/aomemscalable.c

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Sys: drop explicit type arguments from PetscNew() and PetscNewLog()

git grep -l 'PetscNew\(Log\)\?(' -- $1 | xargs perl -pi -e '
s@PetscNew\([^,;()]+ *, *@PetscNew(@;
s@PetscNewLog\(([^,;()]+) *,[^,

Sys: drop explicit type arguments from PetscNew() and PetscNewLog()

git grep -l 'PetscNew\(Log\)\?(' -- $1 | xargs perl -pi -e '
s@PetscNew\([^,;()]+ *, *@PetscNew(@;
s@PetscNewLog\(([^,;()]+) *,[^,;()]+, *@PetscNewLog($1,@'

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Sys: add PetscMalloc1 macro, array allocation without redundant types

The type is inferred from the pointer return type. This patch is
automated via the following script:

git grep -l 'PetscMalloc(

Sys: add PetscMalloc1 macro, array allocation without redundant types

The type is inferred from the pointer return type. This patch is
automated via the following script:

git grep -l 'PetscMalloc(.*sizeof' src | xargs perl -pi -e 's@PetscMalloc\(([^,;]*[^,; ]) *\* *sizeof\([^,;()]+\),@PetscMalloc1($1,@'

This commit contains an additional bug-fix in csrperm.c, fixing pointer
arity. The code was introduced in 2006, but the allocation could not
have been correct at any time. This probably means that
MatDuplicate_SeqAIJPERM has never been tested.

a54129beb540034ba105796c682d589e7e1111f2
Richard Tran Mills <rmills@ornl.gov>

Added MATSEQCSRPERM support for MatDuplicate() and conversion to/from
MATSEQAIJ. Note that these changes are not quite debugged.

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