Merge branch 'master' into shri/ts-is-for-differential-variables

Conflicts:
include/petsc-private/tsimpl.h
src/ts/impls/eimex/eimex.c
src/ts/interface/ts.c

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c

Merge branch 'jed/assembly-perf' into jed/mat-assembly-perf

Improve VecAssembly performance using BuildTwoSided

* jed/assembly-perf: (27 commits)
Vec: document when InsertMode cannot change betwe

Merge branch 'jed/assembly-perf' into jed/mat-assembly-perf

Improve VecAssembly performance using BuildTwoSided

* jed/assembly-perf: (27 commits)
Vec: document when InsertMode cannot change between reassemblies
VecAssembly BTS: allow reassembly with proper subsets of comm
BuildTwoSided: distinguish events BuildTwoSided vs BuildTwoSidedF
MPI: check for MPIX_Ibarrier (e.g., BG/Q)
VecAssembly BTS: enable by default, use -vec_assembly_bts 0 to disable
VecAssembly BTS: allow proper subsets with VEC_SUBSET_OFF_PROC_ENTRIES
VecAssembly BTS: VEC_SUBSET_OFF_PROC_ENTRIES elides global synchronization
VecAssembly BTS: elide sending empty scalar/block stashes
VecAssembly BTS: separate pending count for scalar and block stashes
VecAssembly BTS: use PetscCommBuildTwoSidedFReq and MPI_Waitsome
VecAssembly BTS: avoid copying data on receive by using pointer frames
Sys BuildTwoSidedFReq: generalization to return requests
VecAssembly: add more scalable implementation, -vec_assembly_bts
Vec_MPI: remove unused members conflated with VecStash
Sys: add PetscMergeMPIIntArray
Sys PetscMergeIntArrayPair: fix PetscFunctionBegin and comment
Sys BuildTwoSidedF_Ibarrier: less synchronous dynamic sparse data exchange
Sys BuildTwoSidedF: build two-sided network with functions in rendezvous
Sys BuildTwoSided test: extract datatype construction
Sys BuildTwoSided: update test for non-contiguous types and verbose output
...

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Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Merge branch 'barry/experiment'

simplify option object names

moved PetscOptionsObject from global variable to local variable in functions

Merge branch 'barry/remove-unneeded-paren-petscmalloc'

Conflicts:
src/mat/impls/baij/seq/baij.c

convert some PetscMalloc() to PetscMalloc1()
remove unneeded () in first argument to PetscMalloc/Calloc1()
fixes for MATLAB examples

Merge branch 'barry/always-include-complex'

remove PETSC_DESIRE_COMPLEX and instead include complex with petscmath.h UNLESS PETSC_SKIP_COMPLEX is set (for SSL includes currently)

Merge branch 'stefano_zampini/pcbddc-maint' into stefano_zampini/pcbddc_deluxe

fix compile warning

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]
gfortran: remove 132 char limit from f90 free-form
SNES: Set up matrix-free *after* copying the user Jacobian to snes->pc
DMPlex-Gmsh: Use trueNumCells when building the coordinate section
Sys: Got guard logic reversed
Sys: The #define guard for PetscMalloc*() must match the one for PetscFree*()
PetscFV: I hate fucking complex
removed ltog scatter from DMDA since functionality can be obtained with gtol scatter and less memory
fix test of DMLocalToGlobalBegin/End and add actual test cases
improve object memory logging for DA, ISLocalToGlobal and ISBLOCK
lower high water mark of constructing parallel scatter by allocating only as much room in svalues as needed
owner in VecScatter construction is the rank, therefor can use PetscMPIInt to hold it do not PetscInt
another reuse of allocated array in 2d/3d DMDA create
improved high water mark of DMDASetups by implementing and using PETSC_USE_POINTER for ISCreateBlock()
PetscFV: Another complex fix
DMPlex+TS: Fixing types
ISIdentity() was wrong for block IS! Indices are NOT scaled by bs
PetscFV: Straighten out complex types
TS ex11: Fix casts and remove unused variable
...

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Merge branch 'master' into barry/saws-options

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

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

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

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

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Merge remote-tracking branch 'origin/master' into feature-dmmoab

Merged petsc/petsc into master

Merge branch 'master' into knepley/feature-plex-hdf5-parallel-load

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this wa

Merge branch 'master' into knepley/feature-plex-hdf5-parallel-load

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this was really bad)
outdated example that doesn't match coding style removed and buggy
petscversion.h: workaround ifort -cpp lack of referential transparency
configure: ignore AR, MAKEFLAGS [if set in env]
incorrect first entry in array being zeroed in example
sizeof.c: remove dependence on petsc [and fix syntax error]
nightlybuilds: use consistant PETSC_ARCH, machine names
TS: Allow viewing of TS solutions
DMPlex: Fix comparison for complex
change MPIVersion streams to use MPI_Wtime() to be portable to Windows do not use scalar square root on real number; it upsets Microsoft
cannot use I in PETSc code because in complex it sometimes represents imaginary number cannot pass PetscScalar * to VecNorm()
in dashboard don't warn about SSL and BOI deprecated
TS ex11: Fixed output formatting
Doc+DMPlex: Added function documentation for some refinement functions
streams: translate code from 'bash' to 'sh' [fix freebsd]
barry is an idiot who doesn't have a clue as to what he is doing (and git's unfriendlyness doesn't help matters)
don't list examples under C that don't work with complex!
forgotten output file
removed valgrind warning about sending uninitialized data
nightly builds ignore unrecognized pragma and .c file as C++ code
...

Conflicts:
include/petsc-private/dmpleximpl.h

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Merge branch 'jed/sf-contig-op'

* jed/sf-contig-op:
SF: guard MPI_COMBINER_DUP
SF: add arithmetic op types for contiguous types

SF: add arithmetic op types for contiguous types

This allows operations like MPI_SUM on
MPI_Type_contiguous(3,MPI_DOUBLE). The total sizes are classified by
their largest divisor in (1,2,3,4,5,7).

SF: add arithmetic op types for contiguous types

This allows operations like MPI_SUM on
MPI_Type_contiguous(3,MPI_DOUBLE). The total sizes are classified by
their largest divisor in (1,2,3,4,5,7). The small size is specified at
compile-time, allowing the compiler to unroll.

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Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c

Merge branch 'master' into shri/feature-dm-circuit

Conflicts:
src/dm/impls/makefile