Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes

Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
superlu: libray is installed in PREFIX/lib64 - fix this to use PREFIX/lib
backport fixes cc105cc3 2b35c90a - required for 3bf428d - that was backported from master - 80c96bb
'echo -n' fails on opensolaris/osx - so avoid using it.
fix diffs in nightlybuilds due to options in ~/.petscrc
add Kelley03 to src/docs/tex/petsc.bib
build: determine moudles, mpi.h used during buildtime and print in 'info'
fix analyzer warnings
fix build failure on opensolaris - where -lm from flibs is removed due to -lm in cxxlibs. But then - only flib gets used for some configure tests [blaslapack, parms]
config: prefer __restrict over C99 restrict keyword
...

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PCMG should use the mat provided for each level, not the pmat, as the default
matrix to use for computing the residual before traversing to coarser level.

Reported-by: Matt Landreman <matt.landreman

PCMG should use the mat provided for each level, not the pmat, as the default
matrix to use for computing the residual before traversing to coarser level.

Reported-by: Matt Landreman <matt.landreman@gmail.com>

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Merge branch 'barry/remove-funct'

Merge branch 'barry/vecscattercreatetozero-fortran-null'

Add support for null argument from Fortran for VecScatterCreateToZero() VecScatterCreateToAll()

Also update a few uses of NULL_OBJECT to the appropriate PETSC_NULL_XXX

Time: .1 hours
Reported-by: T

Add support for null argument from Fortran for VecScatterCreateToZero() VecScatterCreateToAll()

Also update a few uses of NULL_OBJECT to the appropriate PETSC_NULL_XXX

Time: .1 hours
Reported-by: Tim Steinhoff <kandanovian@gmail.com>

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Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-t

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-to: Andreas Mang <andreas@ices.utexas.edu>

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Merge branch 'pefarrell/mat-galerkin'

Implement MatGalerkin, a specialised routine for Galerkin construction
of coarse grid problems.

This simplifies some code in mg.c, and also extends Galerkin construction
to certain cases of non-nest

Implement MatGalerkin, a specialised routine for Galerkin construction
of coarse grid problems.

This simplifies some code in mg.c, and also extends Galerkin construction
to certain cases of non-nested geometric multigrid where the interpolation
matrix is not of full rank.

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Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/featu

Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/feature-pcbddc-saddlepoint
that prevents me to smoothly merge stefano_zampini/feature-convert-matnest-matis into next.

This will also facilitate merging stefano_zampini/feature-pcbddc-saddlepoint into master

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

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Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in m

Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in master (the introduction of MatFactorGetError()) therefor need
to merge in master and use the new construct before merging to next

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Merge branch 'master' into psanan/pc-telescope-nearnullspace

fixed merge with master

Merge branch 'barry/extend-pcmg-galerkin'

Merge branch 'barry/pcmgsetsmoothupdown-if-no-change'

PCMGSetGalerkin() and -pc_mg_galerkin now take PC_MG_GALERKIN_BOTH,PC_MG_GALERKIN_PMAT,PC_MG_GALERKIN_MAT, PC_MG_GALERKIN_NONE as arguments instead of PetscBool

This allows computing either mat, or

PCMGSetGalerkin() and -pc_mg_galerkin now take PC_MG_GALERKIN_BOTH,PC_MG_GALERKIN_PMAT,PC_MG_GALERKIN_MAT, PC_MG_GALERKIN_NONE as arguments instead of PetscBool

This allows computing either mat, or pmat or both via the Galerkin process

Time: 16 hours
Reported-by: domenico lahaye <domenico_lahaye@yahoo.com>
Thanks-to: Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk>

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Added PCMGSetNumberSmooth() to complement PCMGSetNumberSmoothUp() and PCMGSetNumberSmoothDown()

Reported-by: Ed Bueler <elbueler@alaska.edu>

If PCMGSetNumberSmoothUp/Down or -pc_mg_number_smoothup/down is used and the number of smoothing steps is not changed
this does not trigger PCMGGetSmoothUp() and hence different KSP objects for the p

If PCMGSetNumberSmoothUp/Down or -pc_mg_number_smoothup/down is used and the number of smoothing steps is not changed
this does not trigger PCMGGetSmoothUp() and hence different KSP objects for the pre and post smoothers

Reported-by: Ed Bueler <elbueler@alaska.edu>

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Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcfetidp.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c
src/mat/impls/is/matis.h

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Merge branch 'barry/housekeeping-2'

removed a variety of #include <xxximpl.h> from source code that was not needed

Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary c

Merge branch 'master' into tisaac/ts-ex11-amr

* master: (141 commits)
chombo: fix dirname in tarball and update to use snapshot with gcc-6.1 compile fix
petsc4py: fix tarball url [for arbitary commitid] - and dirname in tarball
Plex: Moved ReconstructGradients_Internal() and ApplyLimiter_Internal() to Plex from SNES
CUDA: Added external declaration for cuBLAS handle.
docs: fix reference to KSP_Create in parent commit
Add information on PETSC_EXTERN and PETSC_INTERN to developers manual
Plex: Symbol is shared between DM and SNES, so must be EXTERN
Plex: Remove unused variables
Configure: Fix check for spaces in PETSC_DIR
Plex: Updated examples to new DMPlexCreateBoxMesh()
sick of failure due to incorrect master branch
SNES ex12: Fixed unstructured GMG test
SNES ex12: Added another unstructured GMG test
petsc4py: use the snapshot with the fix for dmplex change
Examples that require Fortran to compile but were listed in tests that did not require Fortran
Plex ex19: Added DMSetFromOptions()
Plex: Store a flag indicating whether the boundary should change during remeshing - Set using -dm_plex_remesh_bd - Changed Remesh_Internal() signature
Always coarsen boundaries.
Plex: Fixed option name
Plex: Protect unused variables
...

Conflicts:
src/dm/impls/plex/makefile
src/snes/utils/dmplexsnes.c

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Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/mat/impls/aij/seq/mkl_pardiso/mkl_pardiso.c

Merge branch 'master' into barral/feature-dmplex-adapt

Merge branch 'master' into knepley/fix-plex-mf-prec

* master:
fix typo with PETSCVIEWERASCIIPUSHSYNCHRONIZED and PETSCVIEWERASCIIPOPSYNCHRONIZED
KSP: fix ex51
updates for mstk.py git repositor

Merge branch 'master' into knepley/fix-plex-mf-prec

* master:
fix typo with PETSCVIEWERASCIIPUSHSYNCHRONIZED and PETSCVIEWERASCIIPOPSYNCHRONIZED
KSP: fix ex51
updates for mstk.py git repository and flags for external libraries needed with shared libaries
Fix outdated information in PCMG manual page regarding default Krylov method for smoother

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Merge branch 'maint'