Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Merge branch 'master' of bitbucket.org:petsc/petsc into mark/gamg-crs-ksp2

manual merge of conflict

Three directory namespace changes for better --prefix install support

1) include/finclude becomes include/petsc-finclude
2) include/mpiuni becomes include/petsc-mpiuni
3) conf (both $PETSC_DIR/conf

Three directory namespace changes for better --prefix install support

1) include/finclude becomes include/petsc-finclude
2) include/mpiuni becomes include/petsc-mpiuni
3) conf (both $PETSC_DIR/conf and $PETSC_DIR/$PETSC_ARCH/conf become) lib/petsc-conf

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Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

Conflicts:
src/ts/examples/tutorials/advection-dif

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

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

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Merge branch 'master' into barry/xcode

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

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key

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

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
SNESQN: only monitor real part of dot product (fails with C++ complex)
Corrected the #include statement in the man pages for the PetscObjectComposedDataSet/Getwhatever routines.
DMPlex: Added doc for DMPlexGetHybridBounds()
winzip: detect if winzip is used to extract petsc.tar.gz and error out.
configure: remove self.archIndependent as its not being used. [it is used to create externalpackages/package/arch dir which is unused]
configure: fix packages using package-dir/PETSC_ARCH as out-of-source-build location Perhaps this should be changed to package-dir/build?
configure: remove dead code previously used to download BuildSystem
configure: check if compilerDefines [and compilerFixes] exist in framework before using them
configure: save/restore reconfigure.py when --with-clean is used
configure: add --with-clean option to delete buildfiles/externalpackages in PETSC_DIR/PETSC_ARCH and potential externalpackages in --with-external-package-dir/PETSC_ARCH
configure: With --with-externalpackages-dir=dir store/build packages in dir/PETSC_ARCH
Add MatSeqSBAIJSetPreallocationCSR()
configure: switch to using PETSC_DIR/PETSC_ARCH/externalpackages by updating package.py to use externalpackages.py as the externalPackagesDirProvider
configure: move dead code configureExternalPackagesDir() from petscdir.py to externalpackagesdir.py Also set PETSC_DIR/PETSC_ARCH/externalpackages as the externalpackagesdir
...

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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 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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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 'knepley/remove-sieve'

Conflicts:
src/dm/impls/mesh/examples/tests/output/ex10_0.out
src/dm/impls/mesh/examples/tests/output/ex10_1.out
src/dm/impls/mesh/examples/tests/output/ex11f9

Merge branch 'knepley/remove-sieve'

Conflicts:
src/dm/impls/mesh/examples/tests/output/ex10_0.out
src/dm/impls/mesh/examples/tests/output/ex10_1.out
src/dm/impls/mesh/examples/tests/output/ex11f90_0.out
src/dm/impls/mesh/examples/tests/output/ex11f90_1.out
src/dm/impls/mesh/examples/tests/output/ex3_0.out
src/dm/impls/mesh/examples/tests/output/ex3_1.out
src/dm/impls/mesh/examples/tests/output/ex3_2.out
src/dm/impls/mesh/examples/tests/output/ex3_3.out
src/dm/impls/mesh/examples/tests/output/ex8_0.out
src/dm/impls/mesh/examples/tests/output/ex9f90_0.out
src/dm/impls/mesh/examples/tests/output/ex9f90_1.out
src/dm/impls/mesh/mesh.c
src/dm/interface/dlregisdmdm.c
src/vec/vec/interface/vecregall.c

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DMMesh: Removed all trace and salted the earth, Carthago delenda est!

Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

DMMesh: I was forced to put back the old point interpolation for PyLith-stable

Hg-commit: 34c1b366b0f8fabca0e1f952a026363f6ea75443

Rename DMComplex -> DMPlex

Hg-commit: f768b4255f3d1c199623a7a4aeb9be630bec7076

2c253a6d31dc removed src/snes/utils/mesh/ - so update src/snes/utils/makefile

Hg-commit: cb95d3ee15a7e0cb55f26d4492a73d7a5d4deee7

DM: Adding basis for point location
- Added stub DMLocatePoints()

Hg-commit: 2c253a6d31dca4f89aa0bb3e3ff96f721d4ecdc2

merge VTU viewer

Hg-commit: f68babcf040286d4843b3544bb1e887ce1a50948

Automerge.

Hg-commit: 7aece89cbfcc2d8ec28613bbf68580206dd8ce11

added DMSNESSetFunction/JacobianLocal() and converted Matt's examples that use DMSetLocalFunction/Jacobian() to use it
left in #ifdef and print statements for debugging, will remove in next commit

H

added DMSNESSetFunction/JacobianLocal() and converted Matt's examples that use DMSetLocalFunction/Jacobian() to use it
left in #ifdef and print statements for debugging, will remove in next commit

Hg-commit: 300db2374b8c49ea2431500382b080f85a3cf887

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