Merge branch 'master' into knepley/fix-plex-project-tests

* master: (477 commits)
Added correct report number for PETSc Developers Guide
Update PETSc Developers Guide title and final pages to ne

Merge branch 'master' into knepley/fix-plex-project-tests

* master: (477 commits)
Added correct report number for PETSc Developers Guide
Update PETSc Developers Guide title and final pages to new ANL style
Hash: Quick documentation fix
PetscBinaryViewerRead -> PetscViewerBinaryRead
cast in GAMG_HASH so that it works for PetscInt32 near PETSC_INT_MAX without overflow to negative numbers
Add link for DrMemory which may serve as an alternative to valgrind on Windows
Finish Gail's copyedits for developers manual.
openmpi: fix namespace conflict [with static build on ppc64le]
two pages of Gail's edits to developers guide
Another chapter of Gail's copyedits for the developers guide
Gail's copyedits on two more chapters of the developers guide
Fix more %d to %D in GAMG code. Fix code style in GAMG code
DMPlexVTK: vertices is int! need to use %d instead of %D
TS ex18: update outputs (reported by nightly tests)
Use %D in error messages for GAMG hash; fix style issues with GAMG hash
config: Update petsc4py git commit
Fix bad plain extern declaration.
Add Gail's copyedits for the initial portion of the developers guide
Add missing common block to subroutine
fix mpiuni tests with xl compilers
...

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new PC type added around LMVM matrices

Plex+PCPatch: Converted to IS input and Toby's geometry
- This has broken all tests. Very depressing

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

* master: (562 commits)
fix clang-analyzer warning
Developers manual never use system randomizers in PETSc and example source code.
missing

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

* master: (562 commits)
fix clang-analyzer warning
Developers manual never use system randomizers in PETSc and example source code.
missing CHKERRQ()
DT: Reverting the tgamma change broke MPFR - I guess we need a nightly build with it in
Add a test for ex21
Fix error in ex21
Add missing fortran interface that handles null objects
DMComposite: add missing guards
MatPreallocate: fix overpreallocation of local rows
style fixes
MatView_MPI_DA: do not print twice the class prefix
MatSetOperation: stash the original MatView_XXX in the viewnative function pointer
DMCreateInterpolation_DA gracefully error instead of catching FPE signals
MatIncreaseOverlap: preserve communicator of index sets
MatMPIAIJ: fix indentation and missing CHKERRQ
ISBuildTwoSided: remove tabs and fix style
Fix documentation
PetscViewerDraw: fix unininitialized warning from valgrind
MatConvert_SeqAIJ_SeqBAIJ: remove error for non square matrices and add MAT_REUSE_MATRIX case
Mat: MAT_INPLACE_MATRIX can be used for transposition with rectangular matrices
...

Conflicts:
src/dm/dt/interface/dtfe.c
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexfem.c
src/snes/examples/tutorials/ex13.c
src/snes/examples/tutorials/ex62.c
src/snes/examples/tutorials/makefile
src/snes/examples/tutorials/output/ex62_18.out
src/snes/examples/tutorials/output/ex62_19.out
src/snes/examples/tutorials/output/ex62_20.out
src/snes/examples/tutorials/output/ex62_20_parmetis.out
src/snes/examples/tutorials/output/ex62_21.out
src/snes/examples/tutorials/output/ex62_22.out
src/snes/examples/tutorials/output/ex62_23.out
src/snes/examples/tutorials/output/ex62_24.out
src/snes/examples/tutorials/output/ex62_25.out
src/snes/examples/tutorials/output/ex62_26.out
src/snes/examples/tutorials/output/ex62_27.out
src/snes/examples/tutorials/output/ex62_28.out
src/snes/examples/tutorials/output/ex62_29.out
src/snes/examples/tutorials/output/ex62_2d_p3_1.out
src/snes/examples/tutorials/output/ex62_30.out
src/snes/examples/tutorials/output/ex62_31.out
src/snes/examples/tutorials/output/ex62_32.out
src/snes/examples/tutorials/output/ex62_33.out
src/snes/examples/tutorials/output/ex62_34.out
src/snes/examples/tutorials/output/ex62_35.out
src/snes/examples/tutorials/output/ex62_36.out
src/snes/examples/tutorials/output/ex62_pc_simple.out
src/snes/examples/tutorials/output/ex62_pc_simplec.out
src/snes/examples/tutorials/output/ex62_quad_q2p1_full.out
src/snes/examples/tutorials/output/ex62_quad_q2q1_full.out
src/snes/utils/dmplexsnes.c

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Merge branch 'knepley/feature-error-logging' of bitbucket.org:petsc/petsc into knepley/feature-error-logging

Merge branch 'master' into knepley/feature-error-logging

* master: (324 commits)
DT: Reverting the tgamma change broke MPFR - I guess we need a nightly build with it in
Revert "tgamma: icc on wi

Merge branch 'master' into knepley/feature-error-logging

* master: (324 commits)
DT: Reverting the tgamma change broke MPFR - I guess we need a nightly build with it in
Revert "tgamma: icc on windows requires mathimf.h for tgamma."
setup routine no longer calls PetscCalloc5 if the arrays have already been allocated in a previous setup call
clarify SNESGetFunction()
Move MOAB docs to submansec so as not to clutter DM mansec
doc: remove matlab from doc generation dependency - i.e remove 'alldoc3' and use 'html' to generate corresponding '*.m.html' files.
Remove matlab pounders related cruft that is not required. Document the matlab code better and include an appropriate message in the help text.
Fixed typo.
Remove the inclusion of matlab in testing.
Finalizing comments and the work for the test problems.
Finished the testing and generation of plots. Some simple bug fixes addressed.
Set -Wl,-rpath for Mac OS Matlab mkl directory; don't pass -nojvm to matlab since it causes crashes on Barry's machine and is not needed
Added list of known problems with the code.
Added a comment on ignoring the return from Tao.
Finish with initial implementation of matlab interface to test TAO pounders.
Working through the matlab interface for pounders testing.
Fix typo in manual Reported-by: Jaroslaw Piwonski (CAU) <jpi@informatik.uni-kiel.de>
Fixed mkl_sparse_sypr() calls that were using an unsupported value in the matrix descriptor.
test harness: simplify code that checks for sequential-only tests
Fix the doc for call-backs drdyf drdpf
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Merge branch 'maint'

Merge remote-tracking branch 'origin/jed/matsolverpackage-deprecate-stubs/maint' into maint

MatSolverType: add deprecated stubs for old name MatSolverPackage

Reported-by: Sébastien Gilles <sebastien.gilles@inria.fr>

Merge remote-tracking branch 'origin/psanan/pc-fieldsplit-detect-interface'

PCFieldSplit: Interface to set -pc_fieldsplit_detect_saddle_point programmatically

Adds a new boolean data field for this setting, and a setter and getter.

Removes a call to get the option outside

PCFieldSplit: Interface to set -pc_fieldsplit_detect_saddle_point programmatically

Adds a new boolean data field for this setting, and a setter and getter.

Removes a call to get the option outside of PCSetFromOptions_FieldSplit.

In PCSetFromOptions_Fieldsplit(), checks the flag and then immediately
calls PCFieldSplitSetDetectSaddlePoint(), which then set the split type
and SchurPre type, as before.

Wraps setting PC_FIELDSPLIT_SCHUR_PRE with the existing API.

Updates documentation, in particular removing a statement that negative diagonal
entries trigger a split (when only zero diagonal entries do).

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Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead code.
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
...

Conflicts:
src/snes/examples/tutorials/ex13.c

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PCPatch: Looks like Q1-Q0 Vanka for Stokes might work
- Now ComputeOperator() also gets the patch number (changes SetComputeOperator())
- Replaced ViewFromOptions() with flags to avoid string compari

PCPatch: Looks like Q1-Q0 Vanka for Stokes might work
- Now ComputeOperator() also gets the patch number (changes SetComputeOperator())
- Replaced ViewFromOptions() with flags to avoid string comparisons in tight loops
- Fixed loop bounds for closures
- Added -ignore_dim to ignore points of a given dimension on the patch boundary, rather than patch proper
- cellNodeMap is copied rather than being a borrowed reference
- Allow setting DiscretizationInfo from a combined DM
- CompleteCellPatch() now takes PC instead of DM
- GetPointsDofs() now takes PC instead of imll
- Also make point lists for patches, in addition to cell lists. We need this for Section indexing
- Put in SF support
- Create GlobalSection for each patch that can be passed to patch assembly routine
- Change mat prefix to pc_patch_sub_
- Added Plex operator construction
- Reformatting

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Merge branch 'karlrupp/feature-remove-cusp'

* karlrupp/feature-remove-cusp:
Removes VECCUSP vectors and AIJCUSP matrices, because they provide no added benefit over VECCUDA and AIJCUSPARSE.
Also rem

Merge branch 'karlrupp/feature-remove-cusp'

* karlrupp/feature-remove-cusp:
Removes VECCUSP vectors and AIJCUSP matrices, because they provide no added benefit over VECCUDA and AIJCUSPARSE.
Also removes the CUSP-based preconditioners for now.
SACUSP will be re-added later, after the new release is out.

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CUSP: Removed VECCUSP and AIJCUSP as well as preconditioners.

SA-AMG from CUSP will be re-added in a follow-up commit,
made to work with AIJCUSPARSE and VECCUDA.

Merge remote-tracking branch 'origin/knepley/fix-snes-ex69' into tisaac/feature-dmfield

* origin/knepley/fix-snes-ex69: (311 commits)
PetscFECreateDefault: fix custom Fortran interface to use MPI_

Merge remote-tracking branch 'origin/knepley/fix-snes-ex69' into tisaac/feature-dmfield

* origin/knepley/fix-snes-ex69: (311 commits)
PetscFECreateDefault: fix custom Fortran interface to use MPI_Comm
SNES ex69: Updated test output
SNES ex69: Removed all mantle stuff and change fields to constants - Also use dsymutil for executables
SNES ex69: Removed special partition
SNES ex69: Fixed null space creation - Null space locks its vectors
PetscFE: PetscFECreateDefault() now takes MPI_Comm instead of DM
cleanup very ugly PCGAMG manual page
minor clarifications for VecScatterCreate() manual page
gcov: PETSC_ARCH is required onlyfor -run_gcov - and not for -merge_gcov [where it doesn't exist]
make clearer in help statements what --with-external-packages-dir is for.
Website: Added news entry for PETSc User Meeting 2018 on main page.
CUDA: Further test output fixes for mat_tests-ex2
Turn off elemental test for parmetis running since this does not work on batch systems.
3.8 Changes: KSPCHEBYSHEV
CUDA: Fixed most test errors due to MatMultTranspose*
website: update urls
website: fix Jason's name to match pic. Also add Todd's pic
Dev manual: copyedit
DMPlexDistributeLabels: Propagate the output flag
cuda/cusp: update minimum supported versions of cuda to 7.5 and cusp to 0.5.0
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PCPatch: Initial checkin
Contributed-by: Patrick Farrell <patrick.farrell@maths.ox.ac.uk>
This PC uses mesh traversal to assemble particular ASM PCs, such as Vanka smoothers.

PC: Moved declarations to proper part of the header

Merge branch 'pr874/mapdes/pcmg-inject/master'

* pr874/mapdes/pcmg-inject/master:
This hooks everything up so that if the DM provides an injection we remember it in PCMG.
* Add DMHasCreateInjection

Merge branch 'pr874/mapdes/pcmg-inject/master'

* pr874/mapdes/pcmg-inject/master:
This hooks everything up so that if the DM provides an injection we remember it in PCMG.
* Add DMHasCreateInjection: Will be needed in PCMG.
* FAS: guard DMCreateInjection with DMHasCreateInjection
* PCMG: Use injection if the DM provides it

The mass-lumped scaling of the restriction is complete nonsense for most discretisations.
If the DM provides an injection, use it.
This injection is now used by DMRestrictHook_SNESVecSol for transferring the current state to the coarse grid.

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PCMG: Use injection if the DM provides it

The mass-lumped scaling of the restriction is complete nonsense for
most discretisations. If the DM provides an injection, use it. This
injection is now u

PCMG: Use injection if the DM provides it

The mass-lumped scaling of the restriction is complete nonsense for
most discretisations. If the DM provides an injection, use it. This
injection is now used by DMRestrictHook_SNESVecSol for transferring
the current state to the coarse grid.

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Merge branch 'barry/feature-mg-post-smooth'

MG: Remove PCMGSetNumberSmoothUp and PCMGSetNumberSmoothDown

These special case options (for configuring one particular aspect of
the up and down smoothers separately) are subsumed by the more gener

MG: Remove PCMGSetNumberSmoothUp and PCMGSetNumberSmoothDown

These special case options (for configuring one particular aspect of
the up and down smoothers separately) are subsumed by the more general
PCMGSetDistinctSmoothUp.

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Add support for selecting different down (pre) and up (post) smoother options with PCMG

Added function PCMGSetDistinctSmoothUp() and -pc_mg_distinct_smoothup
Commit-type: feature
Reported-by: Lawren

Add support for selecting different down (pre) and up (post) smoother options with PCMG

Added function PCMGSetDistinctSmoothUp() and -pc_mg_distinct_smoothup
Commit-type: feature
Reported-by: Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk>

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Merge branch 'barry/fix-matsolvertype'

change MatSolverType to be a const char* typedef to match other XXType

Commit-type: style-fix
Reported-by: Franck Houssen <franck.houssen@inria.fr>