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 'dalcinl/mat-getblocksize'

Allow calling MatGetBlockSize[s]() before matrix preallocation

Merge branch 'prbrune/mat-matcolor' into barry/saws

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

Merge branch 'jed/check-pointer-runtime' into barry/saws

Conflicts:
include/petscerror.h
src/sys/error/pstack.c

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 'jed/mat-setvalues-col-bs'

Support for assembling matrices with non-square blocks using
MatSetValuesBlocked.

* jed/mat-setvalues-col-bs:
Check column block size in MatSetBlockSizes

Merge branch 'jed/mat-setvalues-col-bs'

Support for assembling matrices with non-square blocks using
MatSetValuesBlocked.

* jed/mat-setvalues-col-bs:
Check column block size in MatSetBlockSizes
Mat: non-square block support for MatSetValuesBlocked

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Merge branch 'jed/mat-setvalues-col-bs' into maint

* jed/mat-setvalues-col-bs:
Check column block size in MatSetBlockSizes
Mat: non-square block support for MatSetValuesBlocked

Merge branch 'hzhang/snes-jacobiancoloropt'

Sys: add PetscFunctionBeginHot to switch to cheaper pointer checks

Some logging and debugging operations are expensive. In particular,
applications can see order of magnitude slowdowns when PetscCh

Sys: add PetscFunctionBeginHot to switch to cheaper pointer checks

Some logging and debugging operations are expensive. In particular,
applications can see order of magnitude slowdowns when PetscCheckPointer
configures a special signal handler (debug builds only). Additionally,
high-frequency events like MAT_SetValues are disabled by default because
it can be expensive to profile.

My marking "hot" regions, we can turn off the expensive operations by
default, but still have the ability to enable them at run-time. This
commit adds PetscFunctionBeginHot, with logic in PetscCheckPointer to
skip the check while inside a "hot" function.

Reported-by: Dave May <dave.mayhem23@gmail.com>

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Check column block size in MatSetBlockSizes

Previously, only the row block size was checked for consistency across
processes.

Merge branch 'madams/mat-residual' into hzhang/snes-jacobiancoloropt

Fix conflict between new MATOP_RESIDUAL and MATOP_FDCOLORING_SETUP.

* madams/mat-residual:
refactored residuals by adding a 'r

Merge branch 'madams/mat-residual' into hzhang/snes-jacobiancoloropt

Fix conflict between new MATOP_RESIDUAL and MATOP_FDCOLORING_SETUP.

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

Conflicts:
include/finclude/petscmat.h
include/petsc-private/matimpl.h
include/petscmat.h
src/mat/impls/aij/mpi/mpiaij.c
src/mat/impls/aij/seq/aij.c
src/mat/impls/baij/mpi/mpibaij.c
src/mat/impls/baij/seq/baij.c

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Mat: non-square block support for MatSetValuesBlocked

The old version always used row block size, which is incorrect for
non-square blocks.

Reported-by: Lawrence Mitchell <lawrence.mitchell@imperia

Mat: non-square block support for MatSetValuesBlocked

The old version always used row block size, which is incorrect for
non-square blocks.

Reported-by: Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk>

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Merge branch 'jed/doc-restore-zeros-pointer'

* jed/doc-restore-zeros-pointer:
DMPlex: fix my mistake using NULL in place of (int) 0
doc: restore functions in PETSc zero their arguments

Conflict

Merge branch 'jed/doc-restore-zeros-pointer'

* jed/doc-restore-zeros-pointer:
DMPlex: fix my mistake using NULL in place of (int) 0
doc: restore functions in PETSc zero their arguments

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

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Banished all mention of the old MatGetColoring() and use in examples

Merge branch 'prbrune/mat-matcolor' into prbrune/fas-gscolorsecant

Better logging of states of colorings; better error checking

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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add matentry2 for htype='wp'; cleanup

Added Mat_Coloring_Apply/Comm events and better -mat_coloring_view

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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Added MatColoring object to replace MatGetColor()

doc: restore functions in PETSc zero their arguments

This is done to prevent accidental misuse. In general, one can pass
NULL for the pointer argument to keep the pointer around for longer, but
use

doc: restore functions in PETSc zero their arguments

This is done to prevent accidental misuse. In general, one can pass
NULL for the pointer argument to keep the pointer around for longer, but
use of arrays after restoration is invalid.

Suggested-by: Wolfgang Bangerth <bangerth@math.tamu.edu>

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Merge branch 'madams/mat-residual'

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

refactored residuals by adding a 'residual' method to Mat