Merge branch 'pr520/psanan/psanan/vtk-viewer-leak-fix/master'

PetscViewerVTK: Move DM reference increment into the VTK viewer and out of the DM implementation, as suggested by Jed Brown

Merge branch 'maint'

Merge branch 'barry/housekeeping-2'

sys: int64_t shoud use PRId64 - and not '%ld'. Also add PetscInt64_FMT and PetscInt_FMT to better manage this

replace uses of PetscMalloc() with PetscNew() or PetscMalloc1() where appropriate

matlab: add nightlybuild with gcov

- convert test to use MPI - this way externalpacakge [MATLAB, MATLAB_ENGINE] tests are also run
- enable tests for MATLAB and MATLAB_ENGINE
- enable --with-matlabe

matlab: add nightlybuild with gcov

- convert test to use MPI - this way externalpacakge [MATLAB, MATLAB_ENGINE] tests are also run
- enable tests for MATLAB and MATLAB_ENGINE
- enable --with-matlabengine-lib option
- fix regression.py to use packages.PACKAGE - so that 'MATLAB_ENGINE' is used in TEST_RUNS - not 'MATLABENGINE'
- Fix MEX calls to use
- GCC - as version check is done in this compiler
- LDFLAGS - as -lgcov is listed here.

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Merge remote-tracking branch 'origin/balay/fix-PetscInt-scanf/maint'

sys: print scanf/PetscInt with --with-clanguage=C++ --with-64-bit-indices=1 --with-scalar-type=complex --with-mpi=0

Reported-by: Lisandro Dalcin <dalcinl@gmail.com>
Reported-by: bitbucket-pipelines

Merge branch 'tisaac/ts-ex11-amr'

We now have an example (ts/examples/tutorials/ex11.c) where we can
use either DMPlex or DMP4est to handle adaptivity when time stepping.
We have tried to minimize t

Merge branch 'tisaac/ts-ex11-amr'

We now have an example (ts/examples/tutorials/ex11.c) where we can
use either DMPlex or DMP4est to handle adaptivity when time stepping.
We have tried to minimize the amount of code that is specialized to the
different DMs, and in the future more work can be done to improve this
interface.

* tisaac/ts-ex11-amr: (62 commits)
DMP4est: type fix
Plex: Fixes for analyzer
DMP4est: update snes ex12 regressions
DMPlex: fix parent/child interpolation with numFields > 0
DMP4est: also compute anyChange for uniformly refined/coarsened meshes
TS ex11: fix command line for AMR without computed gradients
TS ex11: remove gradient reconstruction from adaptivity requirements
DMPlexTree: some compilers want this var initialized
Plex: Changed Get/RestoreFaceFields() and Get/RestoreFaceGeometry() to return the number of active faces - This fixes a long-standing bad access in FV, although the values were never actually used.
DMPlexTS: removed unused variables
DMPlex/DMP4est: small fixes for next warnings and errors
SNES ex36 and ex52: These do not work anymore
DMPforestGetTransferSF_Point(): try to match parents
PetscViewerHDF5: destroy old file data if setting new filename
DMPlex + FV: remove leaky references in projection functions
Plex: Fixed incredibly stupid bug in Jacobian computation
PetscViewer HDF5: added get name method
DMPlexTree: do not skip out of child matrix loops early
PetscFV: correct field offsets when limiting gradients
DMP4estTree: ignore negative values when getting/setting vector values for transfer
...

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PetscViewerHDF5: destroy old file data if setting new filename

I'm just mimicking the _Binary implementation, but I think I all I have to do is H5Fclose the file_id

PetscViewer HDF5: added get name method

Merge branch 'barry/housekeeping-1'

Merge remote-tracking branch 'origin/maint'

PetscViewerBinaryRead() only set the count value if MPI IO was used

Set the count value even without MPI IO. Note in the manual page the behavior of count.
Issue #131

Reported-by: Eike Moritz Wülfe

PetscViewerBinaryRead() only set the count value if MPI IO was used

Set the count value even without MPI IO. Note in the manual page the behavior of count.
Issue #131

Reported-by: Eike Moritz Wülfers

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add support for viewer draw:tikz:filename and added draw:tikz test

Reported-by: gcov

Add some missing Fortran wrappers for the PetscViewer functions.

* Added PetscViewerGetType and PetscViewerFileGetName
* Added HDF5WriteAttribute, HDF5ReadAttribute, HDF5HasAttribute
* Enabled HDF5B

Add some missing Fortran wrappers for the PetscViewer functions.

* Added PetscViewerGetType and PetscViewerFileGetName
* Added HDF5WriteAttribute, HDF5ReadAttribute, HDF5HasAttribute
* Enabled HDF5BaseDimension2 and HDF5SPOutput setters and getters

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Merge branch 'maint'

fix typo with PETSCVIEWERASCIIPUSHSYNCHRONIZED and PETSCVIEWERASCIIPOPSYNCHRONIZED

Reported-by: "Miorelli, Federico" <Federico.Miorelli@CGG.COM>

Merge branch 'maint'

Finally have clean runs using khash to avoid duplicating many options help messages

Removed unneeded memory usage, make copies even of name without pre
Organized the code into functions
Also use it

Finally have clean runs using khash to avoid duplicating many options help messages

Removed unneeded memory usage, make copies even of name without pre
Organized the code into functions
Also use it to remove duplicate help messages with PetscOptionsBegin()

Thanks-to: Jed Brown <jedbrown@mcs.anl.gov>

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remove dead code from original hash code

Changed to use khash() to prevent PetscOptionsGetViewer() from producing duplicate help messages

Eliminates direct search of previous hashes, prevents artificial limit on checked strings, and false

Changed to use khash() to prevent PetscOptionsGetViewer() from producing duplicate help messages

Eliminates direct search of previous hashes, prevents artificial limit on checked strings, and false positives

Thanks-to: Jed Brown <jed@jedbrown.org>

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PetscOptionsGetViewer() prints the same help message multiple times, fixed

by keeping a hash of the prefix + optionname string and checking against previous hashes
Also fixed a few typos in help mes

PetscOptionsGetViewer() prints the same help message multiple times, fixed

by keeping a hash of the prefix + optionname string and checking against previous hashes
Also fixed a few typos in help messages.

Time: 2 hours
Reported-by: Jose E. Roman <jroman@dsic.upv.es>

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Merge branch 'maint'