PETSCVIEWERGLVIS: add support for dumping at stdout

Merge branch 'barry/move-to-new-test-harness' into barry/all-new-test-harness-branches

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (251 commits)
yaml: add a backup download URL
Fix documentation of MatSetRandom function
Ignore -malloc-hbw option if m

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (251 commits)
yaml: add a backup download URL
Fix documentation of MatSetRandom function
Ignore -malloc-hbw option if malloc is already set
Plex: Fixed array initialization
pgi: compile fix
knl: update test to use memkind and remove option that worked arround a bug with intel 17
Check the return value for memkind_posix_memalign
Change the default behavour for -malloc_hbw
Bib: More refs
test: remove runex13f90 as its now converted to new test suite
fix win32 crash. This test was previously run with '-n 4' - so restoring it
Fix petscsfgetgraph_ to work for all Fortran compilers by directly using array of PetscSFNodes
bugfix for MatDuplicate_MPIAIJ_PtAP Reported-by: Samuel Lanthaler <s.lanthaler@gmail.com>
strip out dead sundials usage code; change sundials test to only run 5 timesteps to prevent different number of steps on different systems.
Remove extra lines of output file
Example uses C99 constructs so must mark with requires: c99
fix const missmatch for DMDAVecRestoreArrayRead()
remove conflict between function name in example and new PETSc TS function
builds: attempt to do maint/master/next test builds in separate clones
ex62: it turned out that CHACO partioning is not deterministic. Use a prescribed partition instead
...

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

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Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with

Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with updated 17.10 compilers
Fix for test dirs that are not tutorials/tests
fix use of double in PetscAbsReal() which produces compiler warnings with single precision build
elemental: remove info on conflict of -with-cxx-dialect=C++11 on osx - it works now.
Cleanup .bib files
Fix allfortranstubs rule to rm generated files from correct directory, not outdated location
ierr set but not checked
Remove initial refine so test runs faster and does not time out on some machines
Gail's copyedits for bibtex items
Docs: manual: add further description of 3 different current testing options
DM: check for ops->localtolocalbegin/end before calling
PetscSF: fix typo in tutorial ex1
Vec+HDF5: Fix output for complex - Need to check for empty group name
SNES: SNESDestroy() can be called with snes->dm == NULL
SNES: SNESDestroy() can be called with snes->dm == NULL
Vec+HDF5: Fix output for complex - Need to check for empty group name
Docs: Manual: Update tests section
gmakegentest: also exclude .#filenames created by emacs
DMPlex: Fix output of test ex1 after changes to Gmsh reader
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Merge remote-tracking branch 'origin/maint'

Merge branch 'stefano_zampini/feature-glvis-homesh' into maint

PetscViewerGLVis: added initial support for visualization of higher-order meshes

Added PetscViewerGLVisSetPrecision to reduce socket traffic

Merge remote-tracking branch 'origin/stefano_zampini/feature-glvis-supportdmcomposite'

PETSCVIEWERGLVIS: change some internal prototype to prepare for supporting DMComposite

Merge remote-tracking branch 'origin/stefano_zampini/smallfix-glvis'

PETSCVIEWERGLVIS: fix improper use of PetscFunctionBeginUser

Merge remote-tracking branch 'origin/stefano_zampini/feature-glvis-viewer-fixdmdependency2'

fixup earlier (broken) fix

clang analyzer fixes

PetscViewerGLVis: remove any dependency from the DM class in VecView_GLVis

PetscViewerGLVIS: revert commit 50daf06

Merge branch 'stefano_zampini/feature-glvis-viewer' of https://bitbucket.org/petsc/petsc into stefano_zampini/feature-glvis-viewer

PETSCSYS: protect PetscOpenSocket by ifdefs to avoid missing symbols when linking

fix opensolaris build issue:

Undefined first referenced
symbol in file
PetscOpenSocket /export/home/petsc/petsc.clone-3/arch-opensolaris-cmplx-pkgs-dbg

fix opensolaris build issue:

Undefined first referenced
symbol in file
PetscOpenSocket /export/home/petsc/petsc.clone-3/arch-opensolaris-cmplx-pkgs-dbg/lib/libpetsc.so

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PETSCVIEWERGLVIS: Jed's fix for fdopen

Yet another fix; this was missing in the message from the automatic mailer

Various fixes from nightly builds

Added initial implementation of GLVis viewer