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

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep us

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

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep usage on solaris [use egrep]
opensolaris: fix errors
Update timer reporting and minor reporting fix
Remove redundant if statement. Found by @jedbrown
Fixed problem with order of developer photos on website.
superlu_dist: use correct flag in example [PETSC_HAVE_SUPERLU -> PETSC_HAVE_SUPERLU_DIST]
Bib: PERMON ref
fix for osx
doc: more author fixes
doc: more author fixes
Italicized "orderings" in MPI process placement discussion.
Added Richard to the user manual author list.
Added Richard to the list of active developers on the website.
add string check for MS-MPI and IMPI timeout errors
opensolaris does not have multiple grep utils - but default one does not support -F. So use fgrep instead
Standardizing timeout checks
Report wall clock time of total tests
Use time instead of date %s
...

Conflicts:
include/petscpc.h
src/ksp/ksp/interface/itfunc.c

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DM: Finish up nullspace constructors
- This should move to DS I think

Deprecate DMSet/GetDefaultSection() for DMSet/GetSection()

Revert manual page change per Matt's preference

Commit-type: style-fix
Thanks-to: Matthew Knepley

fix unused variable warnings

Added DMSet/GetISColoringType() and cleaned up related manual pages slightly

Commit-type: feature, documentation

Development Tools: Vim, Emacs, Eclipse

Doc: Improve documentation for debugging options

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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Merge branch 'pr872/bourdin/dmplex-GlobalToNatural/master'

* pr872/bourdin/dmplex-GlobalToNatural/master:
Makes a subDM inherit the NaturalToGlobal SF from their parent upon creation.

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.

Merged in dalcinl/fix-glvis (pull request #899)

Minor fixes to GLVis viewer

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Karl Rupp <me@karlrupp.net>

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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DMGetCoordinatesLocalized(): Fix out-of-range access to section

In passing, let's make that piece of code slightly more readable.

Coordinate localization and periodicity should not be confused, thi

DMGetCoordinatesLocalized(): Fix out-of-range access to section

In passing, let's make that piece of code slightly more readable.

Coordinate localization and periodicity should not be confused, this
routine contains a hideous optimization assuming that non-periodic
meshes don do not have localized coordinates. This has to be fixed!

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DM: only create sfMigration if useNatural is true
Add reference counting on sfMigration so that it can be shared between subDMs

DM: pass naturaltoglobal SF to sub and superDM
fix bug with 64bit integers bugs in DMplex
fix bug in exodus view

wip: implement DMFieldEvaluate_DS()

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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Make DMHasCreateInjection overrideable by subclasses

Default to PETSC_FALSE. It's only provided by Plex, Pforest, and DA
in (if using DMDA_Q1 as interpolation type).

Merge branch 'denera/fix-tablevels-for-views' [PR #869]

* denera/fix-tablevels-for-views:
Instead of manual push-pop tab operations, views now inherit tablevels automatically.
This makes views consi

Merge branch 'denera/fix-tablevels-for-views' [PR #869]

* denera/fix-tablevels-for-views:
Instead of manual push-pop tab operations, views now inherit tablevels automatically.
This makes views consistent with default convergence monitors.

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Merge branch 'bourdin/dmplex-exodusiiView' of bitbucket:bourdin/petsc-dmplex-exodusiiview [PR #863]

* 'bourdin/dmplex-exodusiiView' of bitbucket:bourdin/petsc-dmplex-exodusiiview:
BuildSystem: bug

Merge branch 'bourdin/dmplex-exodusiiView' of bitbucket:bourdin/petsc-dmplex-exodusiiview [PR #863]

* 'bourdin/dmplex-exodusiiView' of bitbucket:bourdin/petsc-dmplex-exodusiiview:
BuildSystem: bug fixes in pnetcdf
dm: changed DMGetLabelIdIS to return an empty IS instead of NULL if the label is empty
BuildSystem: upgraded exodusII, removed fortran library
dmplex: bug fixes in exodus viewer, write side sets

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Merge branch 'barry/refactor-petscstrncat'

Change PetscStrncat() to PetscStrlcat() to match BSD API where l represents total length

Update many uses of PetscStrcpy() and PetscStrcat() to the safer PetscStrncpy() and PetscStrlcat()

Commit-ty

Change PetscStrncat() to PetscStrlcat() to match BSD API where l represents total length

Update many uses of PetscStrcpy() and PetscStrcat() to the safer PetscStrncpy() and PetscStrlcat()

Commit-type: style-fix, feature
Thanks-to: Jed Brown

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Add DMHasCreateInjection

Will be needed in PCMG.

DM: make subDM inherit the GlobaltoNatural flag and SF

Replaced leftover AddTab call with SetTab

Wrapping up for a pull request