Merge branch 'master' into barry/saws

Conflicts:
src/ksp/pc/impls/gamg/gamg.c
src/sys/classes/viewer/impls/ams/ams.c
src/sys/objects/pinit.c

Merge branch 'master' into prbrune/fas-gscolorsecant

There was a build error in master when I last merged.

Merge branch 'knepley/fix-compiler-warnings'

* knepley/fix-compiler-warnings:
SNES: Fix missing include
Compiler: Fix warnings

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

* master: (397 commits)
PetscSynchronizedFGets: fix deadlock at EOF
Compiler: Fix warnings from MPI impls which do not initialize outputs

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

* master: (397 commits)
PetscSynchronizedFGets: fix deadlock at EOF
Compiler: Fix warnings from MPI impls which do not initialize outputs
Increase patchlevel to 3.4.3
SNES: Now work vectors come from the DM
SNES ex62: Remove code generation
SNES: Move setup involving snes->vec_sol from SNESSetUp() to SNESolve()
Compiler: Fix warnings from MPI impls which do not initialize outputs
DMPlex ex7: Added missing test output
SNES ex52: Removed old Jacobian stuff, and fixed call to DMPlexProjectFunction() - Fixed calls for new element handling
SNES ex12: Added a performance profiling mode
DMPlex ex8: Fixed leak
PetscSection: Must reset the section when changing the number of fields
DMPlex ex7: Fixed test output - Corrected orientations in interpolation
DMPlex ex1: Fixed test output - Uniform refinement for quads changed
DMPlex: Fix overagressive checks
PC: Removed support graph PC
configure: both downloadonWindows and worksonWindows refer to MS compilers. Also fix isWindows() -> isWindows(CC).
MatXAIJSetPreallocation: use array[] notation to help out Fortran
__float128: when blas/lapack is not found instruct using f2cblaslapack
Configure: Package.downloadonWindows is supposed to mean that Windows compilers work. not Cygwin - Also changed doc for Package.worksonWindows, which does refer to Cygwin
...

Conflicts:
src/dm/impls/da/dalocal.c

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Compiler: Fix warnings

Merge branch 'barry/dmvecmattypes' into shri/feature-dm-circuit

Conflicts:
src/dm/impls/makefile
src/dm/interface/dmregall.c

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

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Ste

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

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Stefano
fixed bug that has appeared recently of false positive errors when there are zero local equations on coarse grids in gamg-agg.
MatSchurComplement: Must initialize KSP package
bib: fix inbook citation
Bib: Updated some refs
SNES: fix copy/paste in man page
fortran: fix KSPCONVERGEDDEFAULT and SNESCONVERGEDSKIP in fortran includes
Mat SBAIJ: avoid invalid memory read in MatSOR_SBAIJ
Revert "MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values"
PCGAMG: fix corruption for multiple solves when MatSetNearNullSpace is used
PCGAMG: remove distracting comment
KSP ex49: restrict near-null space for elasticity example with sym BC
MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values was provided ordered by row within the block rows instead of by block as it was originally designed to be. Also added more discussion to the manual pages on the expected order of the values
Fix accidental creation of the matrices in SNESNCG used for linear analogue LS.
PCGAMG: add man page for PCGAMGType
fortran: fix snesconvergedskip_() kspconvergedskip_() kspconvergeddefault*_()
rm //
Sys: new_ir changed from PetscInt to PetscObjectState - so fix mallocs to use the new type
SNES: Fixed package init in SNESLineSearchCreate()
...

Conflicts:
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex5.c
src/dm/impls/plex/plex.c
src/dm/interface/dm.c

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Merge branch 'hzhang/snes-jacobiancoloropt' of bitbucket.org:petsc/petsc into hzhang/snes-jacobiancoloropt

Merge branch 'hzhang/snes-jacobiancoloropt' of bitbucket.org:petsc/petsc into hzhang/snes-jacobiancoloropt

Merge branch 'master' into barry/dmvecmattypes
possible some messed up manual merges!

Conflicts:
src/dm/impls/mesh/examples/tutorials/ex4f90.F
src/dm/impls/mesh/mesh.c
src/dm/impls/mesh/meshcreat

Merge branch 'master' into barry/dmvecmattypes
possible some messed up manual merges!

Conflicts:
src/dm/impls/mesh/examples/tutorials/ex4f90.F
src/dm/impls/mesh/mesh.c
src/dm/impls/mesh/meshcreate.c
src/dm/impls/mesh/section.c
src/snes/examples/tutorials/ex10.c
src/snes/examples/tutorials/ex12.c
src/snes/examples/tutorials/ex52.c
src/snes/examples/tutorials/ex62.c
src/snes/utils/mesh/dmmeshsnes.c

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Merge branch 'madams/sor-opt'

Reduce SSOR with nonzero initial guess from 2 work units to 1.5 by
caching application of lower-triangular part in the forward sweep, for
use in backward sweep.

* mada

Merge branch 'madams/sor-opt'

Reduce SSOR with nonzero initial guess from 2 work units to 1.5 by
caching application of lower-triangular part in the forward sweep, for
use in backward sweep.

* madams/sor-opt:
KSP ex54: explicitly call KSPSetUp so that it is distinct in the profile
MatSOR_SeqAIJ_Inode: optimize to cache lower-triangular part
MatSOR_SeqAIJ: optimize to cache the application of the lower-triangular part

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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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MatSOR_SeqAIJ_Inode: optimize to cache lower-triangular part

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 'barry/fixmultmallocs'

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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move Mat_CheckInode_FactorLU to symbolic factorization so it doesn't get called in EVERY numeric factorization

set matsolve function pointer for SeqAIJ in the numeric factorization, not in the check

move Mat_CheckInode_FactorLU to symbolic factorization so it doesn't get called in EVERY numeric factorization

set matsolve function pointer for SeqAIJ in the numeric factorization, not in the checkinode so matsolve cannot be called on matrix that has not been numerically factored

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removed mallocs from inner loop of Mat_CheckInode_FactorLU, also added a bunch of const to array variables in that file

Merged petsc/petsc into rmills/petsc master.

Merge branch 'knepley/fix-mat-chop' into master

* knepley/fix-mat-chop:
Mat: Changes to MatRestoreRow() broke MatChop()

Merge branch 'jed/fix-nightly-examples'

* jed/fix-nightly-examples:
SuperLU_DIST: upgrade to v3.3 @ 2013-04-10
parmetis: update to parmetis-4.0.2-p4.tar.gz fixes nightly build src/ksp/ksp/exampl

Merge branch 'jed/fix-nightly-examples'

* jed/fix-nightly-examples:
SuperLU_DIST: upgrade to v3.3 @ 2013-04-10
parmetis: update to parmetis-4.0.2-p4.tar.gz fixes nightly build src/ksp/ksp/examples/tests/ex31 in examples_next_arch-freebsd-cxx-pkgs-opt_wii.log
Mat test: compare using MatMultEqual (fuzzy) instead of MatEqual
DM test: move variable declaration due to unused warning
Fortran: define DMLabel for use --with-fortran-interfaces
tests: fix misuse of 64-bit indices
DM test: use "Interp" for variable name instead of imaginary "I"
TS: remove broken phasefield heat example from nightlies
AO ex3.cxx: include petsc header before mpi.h to deal with broken C++
TS ex9: s/static inline/PETSC_STATIC_INLINE/ for MSVC/C89
Mat ex125: initialize info.shifttype
TS ex2f: initialize variables before PetscOptionsGetBool
Mat inode: fix invalid access past end of array
IS test: fix typo in runex2 target
SF: do not use MPI_Type_free when MPI_Type_dup() was not available
SNES ex48: optimized SSE2 code cannot use __float128
SNES ex7: use PetscReal instead of double
MatGetFactor_seqaij_cusparse: set block size before preallocation

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