Fix some 'may be used uninitialized warnings'

No need to get mtypes in PetscSFXxxEnd(). The cuda call is not cheap.

Merge branch 'stefanozampini/sfwin-reuse-win' into 'master'

Improve PETSCSFWINDOW

See merge request petsc/petsc!2336

PetscSFBcastAndOp_Window: delay completion of outstanding Get operations to the End routine

PETSCSFWINDOW: Improve the class

- fix bugs with sync type LOCK and ACTIVE
- add support for creating windows with different flavors
- add reusage of already created windows
- add support for MPI_in

PETSCSFWINDOW: Improve the class

- fix bugs with sync type LOCK and ACTIVE
- add support for creating windows with different flavors
- add reusage of already created windows
- add support for MPI_info customization of MPI_Wins
- use MPI_Get_accumulate in FetchAndOp if present
- PetscSFComposeInverse: use MPIU_REPLACE for 64bit installations and PETSCSFWINDOW

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Merge remote-tracking branch 'origin/jczhang/feature-sf-on-gpu'

Add GPU-aware VecScatter/PetscSF

See merge request petsc/petsc!1995

Added SF GPU support

Merge branch 'jczhang/fix-overlapped-sf' into maint [PR #1903]

* jczhang/fix-overlapped-sf:
SF: fix a bug when overlapped SF communications have NULL rootdata or leafdata on some ranks

Merge branch 'jczhang/sf-more-opts' [PR #1567]

* jczhang/sf-more-opts:
Add more optimizations in SF and use it as the default for VecScatter.

SF: Partially fix a bug when overlapped SF communications have same rootdata or leafdata on some ranks

Now we use two keys (rootdata, leafdata) to identify a pending communication. But that is still

SF: Partially fix a bug when overlapped SF communications have same rootdata or leafdata on some ranks

Now we use two keys (rootdata, leafdata) to identify a pending communication. But that is still not
enough for cases where communications have same rootdata and leafdata on some ranks. Currently We
error out on these cases. See ex2.c for various cases we can handle and we can not handle.

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Implement PetscSFBcast with PetscSFBcastAndOp

Deprecate PetscSFGetRanks with new PetscSFGetRootRanks

Since we have PetscSFGetLeafRanks, it is better to have a similar name.

Merge branch 'master' of bitbucket.org:petsc/petsc

Merge remote-tracking branch 'origin/jczhang/vecscat-in-sf' [PR #1396]

Add an MPI window implementation of PetscSFBcastAndOp

Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
config

Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
PetscFileRetrieve(): Suppress output to STDERR when downloading a file.
MatMatMult: Fixed unused variable pN.
DMDestroy: Guard call to dm->ops->destroy * Similar guards are in place in many other methods (IS,Vec,Mat) and permit the DM to be destroyed even if DMSetType() was never called.
...

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

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComp

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

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex type is missing from fortran
initialize variables so that static analyzer doesn't mistakenly think they are used uninitialized.
Move access of prefix until it is actually used
Remove DMDASplitComm2d(), used in one example that was not tested
Functions that do not return PetscErrorCode should not use PetscFunctionBegin/End paradgm
remove unneeded reassignment of same value
Missing CHKERRQ(); Mostly in Tao code
Remove clang static analyser warning about passing NULL variable to strncat()
missing newline in -ts_monitor_extreme
minor fixes for integer counters
Configure: Deal with '__func__' in C89 builds with newer Clang and GCC.
Jenkinsfile: Increased timeout for tests to 5 minutes.
3.9 changes: further clarify removal of -pc_factor_mat_solver_package
Options deprecations: add "PETSc" to inline warning
removing unused variable
MatShift support added to MATSUBMAT. Mimics MATSHELL functionality. Needed for matrix-free Hessians in TAO Newton-Line-Search methods.
Add -ts_monitor_extreme
Dev manual: add note on deprecating options database keys
...

Conflicts:
src/dm/impls/plex/examples/tests/ex4.c

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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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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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Merged in dalcinl/fix-sf (pull request #903)

PetscSF: Various fixes and cleanups

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Jed Brown <jed@59a2.org>

PetscSF: Various fixes and cleanups

* Add missing PetscSFGetType()
* PetscSFDestroy_XXX() now calls PetscSFReset_XXX(), otherwise changing
the SF type with PetscSFSetType() may leak memory.
* Fix

PetscSF: Various fixes and cleanups

* Add missing PetscSFGetType()
* PetscSFDestroy_XXX() now calls PetscSFReset_XXX(), otherwise changing
the SF type with PetscSFSetType() may leak memory.
* Fix init/computation of {min|max}leaf and use maxleaf where required
rather than recomputing the value in a loop
* Add logging event for PetscSFSetUp()
* Add tons of missing error checking
* Enable missing Fortran wrappers that can be generated automatically
* Support for command line options -{info|log}_exclude
* Various doc fixes
* Add tests for SFs with empty graphs

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Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

Obtain changed (v3.5) handling of MatMPIBAIJSetPreallocationCSR to match
documentation.

Merge branch 'jed/sf-shared-uni' [PR #736]

* jed/sf-shared-uni:
MPIUNI Fortran: fix predefined constants
MPIUNI: define MPI_OP_NULL so that example can compile
DMPlex tests: update output for

Merge branch 'jed/sf-shared-uni' [PR #736]

* jed/sf-shared-uni:
MPIUNI Fortran: fix predefined constants
MPIUNI: define MPI_OP_NULL so that example can compile
DMPlex tests: update output for SF type being set up before viewing
Remove !mpiuni from tests
SFBasic: circumvent send-to-self by marking self as a distinguished group
PetscSFView: dynamically sort by ranks for ASCII_INFO_DETAIL output
SF: add ability for implementations to identify a distinguished group of ranks
PetscSF: add distribution/transposition test
SFBasic: pack into non-contiguous (by rank) root/leaf buffers instead of contiguous buffer
SF: PetscSFGetRanks requires a setup SF, PetscSFView calls setup
MPIUNI: change datatype packing scheme; implement MPI_Type_get_contents
MPIUNI: fix use of MPIUni_Abort, which returns
Add PetscFindMPIInt for searching within sorted array of PetscMPIInt
SF: delay construction of rank mapping until SF type is set
PetscSFReset: call impl reset before corrupting interface data
SFSetGraph: remove support for nroots=PETSC_DETERMINE

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SF: add ability for implementations to identify a distinguished group of ranks

This will be used to optimize send-to-self (and work around broken MPI
lacking send-to-self) and to implement fast shar

SF: add ability for implementations to identify a distinguished group of ranks

This will be used to optimize send-to-self (and work around broken MPI
lacking send-to-self) and to implement fast shared memory exchange.

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SF: delay construction of rank mapping until SF type is set

To implement a shared memory optimization for PetscSF without ugly hacks
that scale poorly, we need to be aware of the shared ranks when
c

SF: delay construction of rank mapping until SF type is set

To implement a shared memory optimization for PetscSF without ugly hacks
that scale poorly, we need to be aware of the shared ranks when
constructing the rank mapping. With eager construction of rank mapping,
this means discarding that or doing fairly complicated and
memory-intense conversion. This commit delays that construction, but
has no further behavioral change.

ex1: explicitly call PetscSFSetUp so that PetscSFView shows the full communication graph.

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