Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
s

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
src/snes/impls/composite/snescomposite.c
src/snes/impls/gs/snesgs.c
src/snes/impls/nasm/nasm.c
src/snes/impls/ngmres/snesngmres.c

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Merge branch 'master' into knepley/feature-dt-fem

* master: (211 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries

Merge branch 'master' into knepley/feature-dt-fem

* master: (211 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
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
...

Conflicts:
config/builder.py
src/dm/impls/plex/plexgeometry.c

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Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (273 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (273 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
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
...

Conflicts:
include/petscdmplex.h

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Merge branch 'master' into knepley/feature-dmda-section

* master: (287 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib e

Merge branch 'master' into knepley/feature-dmda-section

* master: (287 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
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 'master' of bitbucket.org:petsc/petsc

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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Merge branch 'stefano_zampini/pcbddc-constraintssetupimproved'

* stefano_zampini/pcbddc-constraintssetupimproved:
PCBDDC: further improvements to BLAS/LAPACK calls readibility
PCBDDC: Remove ali

Merge branch 'stefano_zampini/pcbddc-constraintssetupimproved'

* stefano_zampini/pcbddc-constraintssetupimproved:
PCBDDC: further improvements to BLAS/LAPACK calls readibility
PCBDDC: Remove aliased parameters for QR calls
PCBDDC: Remove aliased parameter from DDOT call
PCBDDC: Remove aliased parameters from GEMM calls.
PCBDDC: Remove aliased parameters from GESVD calls
PCBDDC: Remove aliased parameters from SYEV calls.
PCBDDC: protect queries to lapack GESVD/SYEV when there are no edges or faces (1D)
PCBDDC: Less tricky loop on constraints when changing the basis
PCBDDC: Constraints setup improved

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PCBDDC: change function name

PCBDDC: save flops when there is only one primal dof on a single connected component

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: prefixes for internal solvers

given a XXX prefixed KSP, options for the solvers can be set as
XXX_pc_bddc_dirichlet_
XXX_pc_bddc_neumann_
XXX_pc_bddc_coarse_

Multilevel case: options for th

PCBDDC: prefixes for internal solvers

given a XXX prefixed KSP, options for the solvers can be set as
XXX_pc_bddc_dirichlet_
XXX_pc_bddc_neumann_
XXX_pc_bddc_coarse_

Multilevel case: options for the N-th (N>1) coarse level can be set adding N_ to the previous prefixes

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PCBDDC: improved support for multileveling when nullspace is present

Solved some deadlocks when assembling local nullspace corrections

PCBDDC: rearranging SetUpCoarseSolver

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.

PCBDDC: removed explicit dependency from METIS.

Now a MATIS object can be partitioned using MatPartitioning interface
Added MatISSubassemble function to BDDC code. It will be moved to matis.c when c

PCBDDC: removed explicit dependency from METIS.

Now a MATIS object can be partitioned using MatPartitioning interface
Added MatISSubassemble function to BDDC code. It will be moved to matis.c when completed.

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PCBDDC: remove Enum on coarse communications since they are now the same

Partial cleanup of SetUpCoarseSolver. MULTILEVEL_BDDC will be wrapped into functions

PCBDDC: PARALLEL_BDDC case now handled trough MatConvert_IS_AIJ

MatConvert_IS_AIJ only supports MAT_INITIAL_MATRIX and MPIAIJ.
No reasons to make it public.

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.