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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dmplex: bug fixes in exodus viewer, write side sets

bug fix: exodus entities numbering was not save properly
enhancement: saving face sets
saving whole connectivity in one call inst

dmplex: bug fixes in exodus viewer, write side sets

bug fix: exodus entities numbering was not save properly
enhancement: saving face sets
saving whole connectivity in one call instead of cell by cell

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Additional alt files, fix PetscMalloc() that was not always large enough

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

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

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

Merge branch 'jed/tests-cxx-linker' into barry/more-to-new-test-harness

Merge branch 'knepley/feature-plex-exodus-update'

* knepley/feature-plex-exodus-update: (22 commits)
this test requires exodus to be built with pnetcdf
Plex ex26: Fix leak and bad merge
Plex+E

Merge branch 'knepley/feature-plex-exodus-update'

* knepley/feature-plex-exodus-update: (22 commits)
this test requires exodus to be built with pnetcdf
Plex ex26: Fix leak and bad merge
Plex+ExodusII: Make all ExodusII calls into PetscStackCall
test: use newer cmake version for exodus
pnetcdf: correctly use flibs
exodus: update pnetcdf dependency - and make netcdf optional on pnetcdf And update exodus tests to use --download-pnetcdf
c89: fix
dmplex/exodus: fix build errors with exodus disabled
Plex: Guard ExodusII use
Plex ex26: Test 18 now working
Plex+ExodusII: Fixed hex27 bug
Plex ex26: Check in meshes
Plex ex26: Update to check ExodusII input and output
Plex+ExodusII: Added ExodusII viewer functions
Plex: For NtoG, we need to zero the output entries
Plex: After creating GtoN map, set useNatural for parallel DM
Plex: DMPlexVecRestoreClosure() now sets the input array to NULL
Plex+Doc: Improve documentation of Closure functions
BuildSystem: Bump ExodusII version
BuildSystem: added pnetcdf required for parallel access to non netcdf4/hdf5 exodus files
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Plex+ExodusII: Make all ExodusII calls into PetscStackCall

dmplex/exodus: fix build errors with exodus disabled

Plex: Guard ExodusII use

Plex+ExodusII: Fixed hex27 bug

Plex+ExodusII: Added ExodusII viewer functions

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

* master: (60 commits)
petsc4py: update to use latest 3.8 snapshot
petsc4py: update to snapshot that syncs with 276c550
fix warni

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

* master: (60 commits)
petsc4py: update to use latest 3.8 snapshot
petsc4py: update to snapshot that syncs with 276c550
fix warning
Plex ex26: Protect ExodusII stuff
DM: DMCreateSubDM() field argument should be const
TS ex46: Newlines and some numerical jitter
TS ex45: Newlines and some numerical jitter
TS ex11: Fixed indentation and time step numbering
SNES ex12: Update for DM view changes
Plex tests: Update to new DM output
Plex ex23: Use Nc not dim for vector fields
Plex: Default section now ignores cells hanging off boundary meshes
Plex: Viewer now reports the cell Height
Increase patchlevel to 3.8.3
Plex: Fixed DMPlexInterpolate() bugs - Do not copy associated data if we are not interpolating - Do not interpolate if we already have full depth
fix valgrind errors with using PetscObjectGetName()/SetName() with the same object - resulting in a free() before copy.
ex4: fix compile warning and update makefile
Minor fixes
Improving report_tests
PetscDS: Must initialize the default adjacency
...

Conflicts:
include/petsc/private/dmimpl.h
include/petscdm.h
include/petscis.h
src/dm/impls/plex/plexcreate.c

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Plex+ExodusII: properly set CPU word size
- This determines the size of coordinate values

Merge remote-tracking branch 'origin/knepley/fix-plex-interpolation-consistency'

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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Plex: Update to new Interpolate interface

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 branch 'maint'

* maint:
Spell check: interger -> integer
petscsys.h : partial man page cleanup
configure exodusii: pass HDF5_DIR to Exodus cmake
Docs: DMPlex man page and source commen

Merge branch 'maint'

* maint:
Spell check: interger -> integer
petscsys.h : partial man page cleanup
configure exodusii: pass HDF5_DIR to Exodus cmake
Docs: DMPlex man page and source comments fixes
Docs: Manual: clarifications for DMPlex chapter

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Merged in psanan/petsc-docproject/psanan/dmplex-docs-update (pull request #773)

Psanan/dmplex docs update

Approved-by: Matthew Knepley <knepley@gmail.com>

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

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

Docs: DMPlex man page and source comments fixes

* remove sieve mentions from all DMPlex man pages and source comments
* DMPlexSymmetrize man page: typo fix
* DMPlexCreateExodusFromFile man page: fix

Docs: DMPlex man page and source comments fixes

* remove sieve mentions from all DMPlex man pages and source comments
* DMPlexSymmetrize man page: typo fix
* DMPlexCreateExodusFromFile man page: fix function name
* DMPlexCreateCubeBoundary man page typo fix

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Merge remote-tracking branch 'origin/blaise/exodus-update-git'

Removed one more call to a deprecated function

DM: replaced deprecated functions in dm/impl/plex/plexodusii.c