MATIS: speed up matrix assembly by using MatSetValues with large blocks

Merge remote-tracking branch 'origin/jed/cholesky-sym'

Introduce a point block Jacobi preconditioner with variable sized blocks

Only SeqAIJ implemented so far, adding MPIAIJ is trivial

Thanks to Jed Brown for suggesting making the block sizes a propert

Introduce a point block Jacobi preconditioner with variable sized blocks

Only SeqAIJ implemented so far, adding MPIAIJ is trivial

Thanks to Jed Brown for suggesting making the block sizes a property of the matrix
Commit-type: feature
Reported-by: Ali Reza Khaz'ali <arkhazali@cc.iut.ac.ir>
Thanks-to: Jed Brown <jed@jedbrown.org>

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PCCholesky: add support for symmetric preconditioning

Merge branch 'master' into knepley/feature-pc-patch

* master: (281 commits)
compile fixes (workarround PGI bug?):
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix

Merge branch 'master' into knepley/feature-pc-patch

* master: (281 commits)
compile fixes (workarround PGI bug?):
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix Pardiso code to only compile pardiso_init64 when needed, otherwise can generate warnings/errors
jenkins: run 'cleantest' before 'allgtest-tap' - an attempt to fix errors of type:
cuda: protect cuda includes
fix cuda warnings.
fix complex compile error
Revert "Improved polymorphism of interfaces for MatSetValuesBlocked()"
Bib: Updated ref
Doc: More function documentation
petscvec: move PetscSFCreateFromZero from vscat to vec sources
Mat: obey options prefix of Mat in MatNullSpaceTest
Plex+SNES: Must pass user context through
vscat: move ftn-custom to correct location remove custom vecscatterdestroy_()
vscat: move interface routines to correct location
vscat: delete dead code
fix compile error
FE: Correct coordinates in IntegrateBd
Bib: Added refs
SNES ex17: 3D tests must require a 3D grid generator
Plex+TS: We cannot run the check with the same vector that is the TS solution
...

Conflicts:
include/petsc/private/dmpleximpl.h
src/docs/website/documentation/changes/dev.html
src/snes/examples/tutorials/ex13.c
src/snes/utils/dmplexsnes.c

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PetscOptionsDeprecated(): add option to print additional info

Reorganize logic to print warning, introducing a maximum length on the
warning message.

Move access of prefix until it is actually used

Commit-type: style-fix
Reported-by: clang static analyzer

Missing CHKERRQ(); Mostly in Tao code

Commit-type: testing-fix,style-fix
Reported-by: clang static analyzer

PCFactor: re-add deprecated -pc_factor_mat_solver_package command line option

Merge branch 'mark/gamg-doc2' [PR #1054]

* mark/gamg-doc2:
Clearified web docs for GAMG coarsening

clearified web docs for GAMG coarsening

Merge branch 'barry/clarify-dmplex-documentation' [PR #917]

* barry/clarify-dmplex-documentation:
Rename DM[GS]etDefault{Global}Section() to DM[GS]et{Global}Section().
Add DMPlexComputeGeometryFEM()

Merge branch 'maint'

Fix PCApplyTranspose_ASM() that accidently changed KSPSolveTranspose() to KSPSolve()

Commit-type: bug-fix
Reported-by: Marshall Galbraith

PCPatch: User patches and subspace exclusion are incompatible

PCPatch: Small fix

added comment for perf bug

Merge branch 'master' into knepley/feature-pc-patch

* master: (226 commits)
fix bib
type in bibtex entry
copy edits to bibtex items
Hypre matrix: small fix
Hypre matrix: fixed compiler war

Merge branch 'master' into knepley/feature-pc-patch

* master: (226 commits)
fix bib
type in bibtex entry
copy edits to bibtex items
Hypre matrix: small fix
Hypre matrix: fixed compiler warnings
Plex: Fixed missing PetscRealPart() in partition balance.
Added MatZeroEntries_HYPRE
Removed outdated mention of cusp and thrust from installations instructions; remove cusp from example configurations
Remove another location where fshift was used with -1 to indicate handling of error condition which was never handled
Generate an immediate error, if requested, if CG detects indefinite PC or Mat
Remove hack of using special fshift value of -1 to indicate error handling, was broken for MatSOR_SeqAIJ and did nothing constructive in the other cases
Options: Fix sys_tests-ex6 to not print options
PetscOptionsDestroy: Add missing free() call
Configure: Pragmatic now requires Cxx11
Error check that the communicator in the IS matches that in the matrix otherwise ISAllGather() produces incorrect results.
Options: Code reorganization and faster option lookup
fix compile warning
Doc: Fixed manpage for PCFieldSplitSetSchurPre()
mpiuni: build somempifort.o after mpiuni.mod
Remove use of common block from MPIUNI code
...

Conflicts:
include/petscdm.h
include/petscpc.h
include/petscpctypes.h
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexdistribute.c
src/ksp/pc/impls/makefile
src/ksp/pc/interface/pcregis.c

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Merge branch 'dalcinl/options'

Merge branch 'barry/rm-fshift-error-hack-sor/maint'

Remove another location where fshift was used with -1 to indicate handling of error condition
which was never handled

Commit-type: bug-fix
Reported-by: nightly tests

Remove hack of using special fshift value of -1 to indicate error handling, was broken for MatSOR_SeqAIJ
and did nothing constructive in the other cases

Commit-type: bug-fix,style-fix
Reported-by: V

Remove hack of using special fshift value of -1 to indicate error handling, was broken for MatSOR_SeqAIJ
and did nothing constructive in the other cases

Commit-type: bug-fix,style-fix
Reported-by: VEYS Stéphane <Stephane.VEYS@cea.fr>

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Options: Code reorganization and faster option lookup

* Speedup option lookup by using a auxiliary hash table.
* Move many routines around to make the implementation easier to follow.
Eventually,

Options: Code reorganization and faster option lookup

* Speedup option lookup by using a auxiliary hash table.
* Move many routines around to make the implementation easier to follow.
Eventually, we may split options.c in two, all of the query routines
PetscOptionsGetXXX() do not need (and should not have) access to the
PetscOptions data structure.
* Restore proper handling of monitors in set/clear option events.
* Add PetscOptionsHasHelp(), eventually we may add a "category" argument
to do special handling of let say `-help <package>`
* Change PetscOptionsReject() to handle option prefix, this makes the call
easier to use in XXXSetFromOptions() implementations.

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Doc: Fixed manpage for PCFieldSplitSetSchurPre()

MATIS/BDDC: handle a very strange case when MatISFixLocalEmpty gets called on a DMDA generated matrix with empty rows