stub code for ADIOS viewer and vector viewing

Commit-type: feature

PetscViewerDraw: fix unininitialized warning from valgrind

Merge remote-tracking branch 'origin/tmunson/tao-pounders-matlab-interface'

Merge branch 'maint'

Silence GCC -Wparentheses warnings

Making matlab mex files compile (need main to be defined with matlab 2018a,
clang, and configured --with-mpi=0)

Create correct makefile for pounders testing.

Update tester of mathematica link to handle errors the modern way

Commit-type: testing-fix,style-fix

examples: add compile target 'ex%: ex%.o' etc - and remove the corresponding dups

Merge remote-tracking branch 'origin/barry/bugfix-petscformatconvert'

Merge branch 'maint'

fix variable names, fix comparison between signed and unsigned values

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

Merge branch 'haplav/feature-dmplex-distributed-hdf5-read' [PR #896]

* haplav/feature-dmplex-distributed-hdf5-read:
Implemented DMPlexLoad_HDF5_Xdmf_Internal which reads the XDMF-related HDF5 groups

Merge branch 'haplav/feature-dmplex-distributed-hdf5-read' [PR #896]

* haplav/feature-dmplex-distributed-hdf5-read:
Implemented DMPlexLoad_HDF5_Xdmf_Internal which reads the XDMF-related HDF5 groups for topology and geometry locally.
New formats PETSC_VIEWER_HDF5_{PETSC,XDMF} controlling both DMLoad and DMView:
PETSC_VIEWER_HDF5_PETSC, PETSC_VIEWER_HDF5_XDMF, PETSC_VIEWER_HDF5_VIZ, PETSC_VIEWER_DEFAULT.

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Add --with-matlab-socket=0 to turn off building PETSc-Matlab socket interface

This is because building Mex files may be difficult on MacOS systems while users still desire to
use the Matlab engine.

Add --with-matlab-socket=0 to turn off building PETSc-Matlab socket interface

This is because building Mex files may be difficult on MacOS systems while users still desire to
use the Matlab engine. So you can run with --with-matlab --with-matlab-engine --with-matlab-socket=0

Commit-type: portability-fix, feature

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New formats PETSC_VIEWER_HDF5_{PETSC,XDMF}.

DMPlexView_HDF5_Internal rewritten.

Insure PetscPrintf(), PetscVPrintfDefault(), PetscSynchronizedPrintf(), PetscSynchronizedFPrintf(), and PetscViewerASCIIPrintf() handle printed strings longer than the default buffer size of 8*1024 b

Insure PetscPrintf(), PetscVPrintfDefault(), PetscSynchronizedPrintf(), PetscSynchronizedFPrintf(), and PetscViewerASCIIPrintf() handle printed strings longer than the default buffer size of 8*1024 bytes properly

Commit-type: bug-fix, testing-fix, feature, example
Reported-by: Rongliang Chen <rongliang.chan@gmail.com>

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Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \(

Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \( -name "*.c" -or -name "*.h" -or -name "*.cxx" \) | xargs gsed -i 's/Notes\s*:\s*\(\w.*\)/Notes:\n \1/'

This adds a newline and 4 spaces whenever "Notes:" is followed by any "word" character, in any .c, .h, or .cxx file in src/ or include/

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Merge branch 'maint'

Merge remote-tracking branch 'origin/tisaac/feature-dmfield'

* origin/tisaac/feature-dmfield: (56 commits)
Plex: Updated test output for DMLabel change
DMLabel: make empty ISs strides
DMSwarm:

Merge remote-tracking branch 'origin/tisaac/feature-dmfield'

* origin/tisaac/feature-dmfield: (56 commits)
Plex: Updated test output for DMLabel change
DMLabel: make empty ISs strides
DMSwarm: silence static analyzer warning
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
DMField: default initialization of variable
PetscFE: fix integration for openCL
PetscFEGeomComplete(): correct normal vector in 2D.
DMField: c++/complex fixes
DMField: empty processor protections
DMField regression test fixes
DMLabel: try to keep stride IS as stride IS as much as possible
DMPlexRefine(): create depth before hybrid-bounded label
DMField: documentation of interface
DMField: implement shell
DMPlex: rename newly created label
...

Conflicts:
src/dm/dt/interface/dtfe.c
src/snes/examples/tutorials/ex69.c
src/snes/utils/dmplexsnes.c

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Fix some missing functionality for nested logging

Re: [petsc-dev] getting on with the nested timers
Re: nested timers transfers and reductions

Commit-type: feature, documentation, example
Reported-

Fix some missing functionality for nested logging

Re: [petsc-dev] getting on with the nested timers
Re: nested timers transfers and reductions

Commit-type: feature, documentation, example
Reported-by: "Klaij, Christiaan" <C.Klaij@marin.nl>

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Merge remote-tracking branch 'origin/knepley/fix-hdf5-attribute'

Consistent handling of command line options -info_exclude and -log_exclude

PETSCVIEWERDRAW: Add PetscViewerDraw{Get|Set}Title()

PETSCVIEWERDRAW: Add PetscViewerDrawGetDrawType()

PetscDrawGetTitle: Use const qualifier for the title argument

Merge branch 'stefano_zampini/fix-matis-dmda-l2g'