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 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 'master' into prbrune/mat-matcolor

Conflicts:
src/snes/interface/snesj2.c

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 'barry/dmvecmattypes'

The MatType argument is removed from DMCreateMatrix(), you can use
DMSetMatType() to indicate the type you want used with a DM, defaults to
MATAIJ.

* barry/dmvecm

Merge branch 'barry/dmvecmattypes'

The MatType argument is removed from DMCreateMatrix(), you can use
DMSetMatType() to indicate the type you want used with a DM, defaults to
MATAIJ.

* barry/dmvecmattypes:
DMPlex ExodusII: fix dm->vectype pointer syntax
removed use of VecSetFromOptions() all over the placed, instead use MatGetVecs() or use dm->vectype to determine type added DMGetVecType() and DMGetMatTYpe()
removed MatType argument from DMCreateMatrix() and DMCreateColoring() since information is obtained from DM

Conflicts:
src/dm/impls/da/fdda.c
src/dm/impls/plex/plex.c

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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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removed use of VecSetFromOptions() all over the placed, instead use MatGetVecs() or use dm->vectype to determine type
added DMGetVecType() and DMGetMatTYpe()

DMDA: When creating vectors with a custom section, disable special view/load/ routines
- Need to replace them with the Plex versions I think

Merge branch 'master' into jed/ts-eimex

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

Conflicts:
src/ts/interface/tsregall.c

daimpl.h was never fixed? Well it is now

Hg-commit: a4f3f6d7e4f165ac5276405a089a596a28adc0b3

added PetscObjectComm() and used it to replace (((PetscObject)obj)->comm)

Hg-commit: 3da37c458124ad48ae939f4e9823e4430ee0b8be

Merge branch 'private-impl-headers'

petsc-private/petscimpl.h and vecimpl.h are no longer included by
petscsys.h and petscvec.h. Some inline functions become normal functions
as a consequence of the

Merge branch 'private-impl-headers'

petsc-private/petscimpl.h and vecimpl.h are no longer included by
petscsys.h and petscvec.h. Some inline functions become normal functions
as a consequence of these changes.

Hg-commit: 5c59734726c7c41f493a5f5b9303cfab5c66ae21

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Add VecGetLayout() and remove some needless dependencies on vecimpl.h

Hg-commit: 0d0721e64fa8861a4e7168e2a936ca714ebeebcb

petscvec.h no longer includes petsc-private/vecimpl.h

This makes dependence on Vec internals more explicit. Almost all
impacted dependencies fall in two categories:

* reference to vec->map: could b

petscvec.h no longer includes petsc-private/vecimpl.h

This makes dependence on Vec internals more explicit. Almost all
impacted dependencies fall in two categories:

* reference to vec->map: could be eliminated by adding VecGetLayout(),
which is probably a good idea anyway.

* dependence on VecScatter_MPI_General: this is low-level anyway, so I
don't think there is much to gain by abstraction.

Hg-commit: 612ef938483b9f0137f3e95bc1d14775547d74f1

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commit after merge

Hg-commit: 1fa981254c79c783277e37654668dfe698cddf41

Uncrustified src/dm/*. No re-uncrustification of un-uncrustified plex.c.

Hg-commit: 0eadce41498eb88aa85fb46f989ad9d09bfd9c3e

Relocate Vec creation with Section so it can be used by DMDA and DMComplex

Hg-commit: 29860ecac7a53df5f615e4e5d2dad88d9afd9d72

DM: Added MatGet/SetDM() and updated DMs to handle Vec and Mat for this

Hg-commit: d20ec0ce94bab2e32af8971314fa1b0124689ebf

Commit after merge

Hg-commit: 29c41d281e3ece3127c753661dccfd04e452b7f8

removed trailing blanks from source code
added rule rmtrailingblanks accessible via make ACTION=remtrailingblanks tree

Hg-commit: 6e3652165d48aa5f3e94dd66bf607adea6fac27a

backout all chmod stuff in bf971ba58125
[but keep diffs to src/mat/impls/aij/mpi/mpimatmatmult.c ]

Hg-commit: 4a812fc1f35496ce2717c7da9ef12ffabbd13258

removed a spurious call to MatSetBlockSize.

Hg-commit: bf971ba58125bd8cf7ceb2a9d0f5cdf27c27cc6a

DM CHANGE: Moved PetscSections describing layout and PetscSFs describing overlap int DM
- This allows unstructured layout on any DM, in particular DA
- Creation flows goes localSection --> pointSF --

DM CHANGE: Moved PetscSections describing layout and PetscSFs describing overlap int DM
- This allows unstructured layout on any DM, in particular DA
- Creation flows goes localSection --> pointSF --> globalSection --> dofSF
- DMGetGlobalVector() and DMGetLocalVector() use these layouts if they exist (DMComplex uses this now)
- Put in DA code for creating the Section and SF
- Cleaned up some memory problems

Hg-commit: 612ec4062f8f069f58c4aa2b66de5ea016ab8a63

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Added ex67 where a different layout is used with a DA

Hg-commit: 51435c26afcf8c9b770276864ab7aff7619e8770