Merge branch 'jed/mat-baij-row-oriented'

API change: MatSeqBAIJSetPreallocationCSR and
MatMPIBAIJSetPreallocationCSR now expect values to match documented BAIJ
internal format (list of column-major

Merge branch 'jed/mat-baij-row-oriented'

API change: MatSeqBAIJSetPreallocationCSR and
MatMPIBAIJSetPreallocationCSR now expect values to match documented BAIJ
internal format (list of column-major bs*bs blocks).

* jed/mat-baij-row-oriented:
Mat BAIJ: fix typos (build errors)
Mat BAIJ: respect MAT_ROW_ORIENTED in Mat*BAIJSetPreallocationCSR

Conflicts:
src/docs/website/documentation/changes/dev.html

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Merge branch 'rlacroix/mpibaij-matgetcolumnnorms'

* rlacroix/mpibaij-matgetcolumnnorms:
Extend and enable the test for MatGetColumnNorms.
Add MatGetColumnNorms for MPIBAIJ matrices.
Add MatGet

Merge branch 'rlacroix/mpibaij-matgetcolumnnorms'

* rlacroix/mpibaij-matgetcolumnnorms:
Extend and enable the test for MatGetColumnNorms.
Add MatGetColumnNorms for MPIBAIJ matrices.
Add MatGetColumnNorms for MPIBAIJ matrices.
MatGetColumnNorms_MPIAIJ: Use PetscObjectComm to access the communicator.

Clean merge except for fixing trailing whitespace in test.

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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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implement MatFDColoringCreate_SeqXAIJ() s.t. it sets default brows and bcols.

add MatFDColoringSetUp(); rename MatFDColoringCreate_xxx -> MatFDColoringSetUp_xxx

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

Fix MatPermute for MPIBAIJ matrices.

MatPermute now behaves similarly for all matrix types it has been implemented
for. Previously you had to invert the row permutation for MPIBAIJ matrices to
get c

Fix MatPermute for MPIBAIJ matrices.

MatPermute now behaves similarly for all matrix types it has been implemented
for. Previously you had to invert the row permutation for MPIBAIJ matrices to
get correct results.

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Merge branch 'rlacroix/mpibaij_matgetcolumnnorms' of bitbucket:rlacroix/petsc into rlacroix/mpibaij-matgetcolumnnorms

New test and updated version of patch that now uses MatScalar.

* 'rlacroix/mpib

Merge branch 'rlacroix/mpibaij_matgetcolumnnorms' of bitbucket:rlacroix/petsc into rlacroix/mpibaij-matgetcolumnnorms

New test and updated version of patch that now uses MatScalar.

* 'rlacroix/mpibaij_matgetcolumnnorms' of bitbucket:rlacroix/petsc:
Extend and enable the test for MatGetColumnNorms.
Add MatGetColumnNorms for MPIBAIJ matrices.

Conflicts:
src/mat/impls/baij/mpi/mpibaij.c

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Mat BAIJ: fix typos (build errors)

Mat BAIJ: respect MAT_ROW_ORIENTED in Mat*BAIJSetPreallocationCSR

MatMPIBAIJSetPreallocationCSR() used to handle the input matrix entries
in a peculiar way, treating them as if each row of values wa

Mat BAIJ: respect MAT_ROW_ORIENTED in Mat*BAIJSetPreallocationCSR

MatMPIBAIJSetPreallocationCSR() used to handle the input matrix entries
in a peculiar way, treating them as if each row of values was provided
ordered by row within the block rows instead of by block as it was
originally intended to be. Now treat as array of contiguous blocks for
which the ordering within blocks is row-major or column-major according
to the MAT_ROW_ORIENTED option.

This also affects MatCreateMPIBAIJWithArrays() which now expects
contiguous blocks with column-major ordering within blocks, just like
the internal storage format. MatCreateSeqBAIJWithArrays is unaffected
since it uses the array as provided.

Reported-by: Matteo Parsani <parsani.matteo@gmail.com>
Reported-by: Lisandro Dalcin <dalcinl@gmail.com>
Helped-by: Barry Smith <bsmith@mcs.anl.gov>

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Revert "MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values"

This reverts commit 7ec8086be61cb5e804513b1f606792b24a91d2ca which
cha

Revert "MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values"

This reverts commit 7ec8086be61cb5e804513b1f606792b24a91d2ca which
changed the behavior of MatMPIBAIJSetPreallocationCSR() to use
consistent column alignment and left MAT_ROW_ORIENTED=PETSC_FALSE in
place in case of subsequent assemblies.

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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

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

Reported by Matteo Parsani <parsani.matteo@gmail.com> and Lisandro Dalcin <dalcinl@gmail.com>

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replace old impl of MatFDColoring routines with new ones.

add new impl of MatFDColoring routines for mpibaij - works for htype=wp

Merge branch 'madams/mat-residual'

* madams/mat-residual:
refactored residuals by adding a 'residual' method to Mat

Merge branch 'barry/fixmatmultseqaijflopcount'

* barry/fixmatmultseqaijflopcount:
removed Mat option for skipping checking of compressed row format since it is now free using the nonzerorowcnt pre

Merge branch 'barry/fixmatmultseqaijflopcount'

* barry/fixmatmultseqaijflopcount:
removed Mat option for skipping checking of compressed row format since it is now free using the nonzerorowcnt previously introduced
changed seqbaij to count nonzero rows in assembly and use those values to compute flops in MatMult
added seqij nonzerorowcnt used to determine flop count in MatMult_SeqAIJ()

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mv checking !mat->assembled from MatFDColoringCreate_xxx() to interface MatFDColoringCreate

Add MatGetColumnNorms for MPIBAIJ matrices.

Add MatGetColumnNorms for MPIBAIJ matrices.

refactored residuals by adding a 'residual' method to Mat

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

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

mv checking !mat->assembled from MatFDColoringCreate_xxx() to interface MatFDColoringCreate

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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