Merge branch 'shri/update-SuiteSparse' into shri/external-package-KLU

Conflicts:
conf/test
config/examples/arch-linux-pkgs-dbg-ftn-interfaces.py
config/examples/arch-linux-pkgs-opt.py

Merge branch 'balay/tao-to-petsc'

Conflicts:
src/snes/impls/fas/fasfunc.c
src/snes/impls/fas/fasgalerkin.c

fixed quote marks for includes to <>

Merge branch 'master' into barry/xcode

Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

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
...

show more ...

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

Merge branch 'stefano_zampini/pcbddc-scalingbrokenbuild'

* stefano_zampini/pcbddc-scalingbrokenbuild:
PCBDDC: Hide deluxe functions.

PCBDDC: Hide deluxe functions.

Linking stage was broken on Tiger. Now fixed.

Merged petsc/petsc into rmills/petsc master.

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: Stiffness scaling should be rebuilt in any case (just to be safe)

PCBDDC: Remove trailing blanks

PCBDDC: many changes

- Source code split
- Added Reset procedures
- Support for different MatStructure flags