Merge branch 'jed/fix-viewer-matlab-info'

* jed/fix-viewer-matlab-info:
Viewer: fix Binary Matlab viewer info to use '#' instead of '%'

Merge branch 'schuang/vtk-vtr-writer'

* schuang/vtk-vtr-writer:
Viewer: fix Fortran enumeration after addition of VTR format
test code for vtk rectilinear grid (.vtr) viewer
add support for vt

Merge branch 'schuang/vtk-vtr-writer'

* schuang/vtk-vtr-writer:
Viewer: fix Fortran enumeration after addition of VTR format
test code for vtk rectilinear grid (.vtr) viewer
add support for vtk rectilinear grid (.vtr) viewer

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DMDA: fix bad cast of DM_DA to PetscObject

Merge branch 'barry/improve-memory-logging'

Conflicts:
src/ksp/pc/impls/redundant/redundant.c
src/mat/interface/matnull.c

Viewer: fix Binary Matlab viewer info to use '#' instead of '%'

The % character for comments in info files was removed in

7c43ebc8e6c "only use # for comments in PETSc options files"

but continu

Viewer: fix Binary Matlab viewer info to use '#' instead of '%'

The % character for comments in info files was removed in

7c43ebc8e6c "only use # for comments in PETSc options files"

but continued to be used for the PETSC_VIEWER_BINARY_MATLAB format
characters. This prevented loading these files from PETSc. This commit
switches to using '#' for those comment characters and updates
PetscReadBinaryMatlab to accept both '%$$ ' and '#$$ '.

Noticed-by: Richard Katz <richard.katz@earth.ox.ac.uk>

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Merge branch 'rmills/dm-localtolocal'

Introduces DMLocalToLocalxxx() (and deprecates DMDALocalToLocalxxx()) to
support local-to-local communication operations for any DM type, not just
DMDA. Adds D

Merge branch 'rmills/dm-localtolocal'

Introduces DMLocalToLocalxxx() (and deprecates DMDALocalToLocalxxx()) to
support local-to-local communication operations for any DM type, not just
DMDA. Adds DMShell routines to set up local-to-local operations.

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Changed remaining references to DMDALocalToLocalxxx() to references to DMLocalToLocalxxx().

DM: Added specialization for DMCreateSubDM() with a PetscSection
- Replace DMPlex implementation
- Is used by DMDA when a section is defined

DM: Fix DMDA clone
- Made it work for all dimensions (which makes DMCreateSubDM() work)
- Removed DMSetUp() which should be called by caller

DM: Added DMClone() which makes a shallow copy
- This is very useful for DM since it can have a lot of associated data and is used as a building block for different problems
- This replaces DMPlexClo

DM: Added DMClone() which makes a shallow copy
- This is very useful for DM since it can have a lot of associated data and is used as a building block for different problems
- This replaces DMPlexClone()

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DMDA: Fixed creation of point SF
- Put in BT to check for duplicate entries (this was the cause of a mysterious bug)
- Disabled faces until they are implemented

DMDA: When creating vectors with a custom section, disable special view/load/ routines
- Need to replace them with the Plex versions I think

Finished converting DMDALocalToLocalBegin()/End() to internal functions (DMLocalToLocalBegin()/End() should now be used) and deprecated this interface.

Fix for mixed declarations and code in DMCreateCoordinateDM_DA().

Pointed out by Satish.

add support for vtk rectilinear grid (.vtr) viewer

Fix for DMDACreatePatchIS in 3D.

DMDA: fix for getting coordinate DMDA for subdomains.

Get rid of code duplication between DMCreateCoordinateDM_DA and DMDAGetReducedDMDA() by having DMCreateCoordinateDM_DA
just call DMDAGetReducedD

DMDA: fix for getting coordinate DMDA for subdomains.

Get rid of code duplication between DMCreateCoordinateDM_DA and DMDAGetReducedDMDA() by having DMCreateCoordinateDM_DA
just call DMDAGetReducedDMDA(). The reason for this change is that DMDAGetReducedDMDA() automatically sets up the offset
while DMCreateCoordinateDM_DA did not.

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DMPlex: Must initialize argument to DMPlexVecGetClosure()

logging memory now credits to all ancestors

fixed bug where XXXViewFromOptions() used prefix of object rather than appropriate prefix of KSP or SNES

Merge branch 'prbrune/dmda-subdomains-per-process'

Fixed memory leak in DMCreateDomainDecomposition_DA() related to names.

Merge branch 'prbrune/dmda-subdomains-per-process'

Conflicts:
src/dm/impls/da/dadd.c

MatRestoreRowIJ/ColumnIJ: zero pointers to catch accidental misuse

Only zero in case where the operation is "done" so that user's
uninitialized arguments are not overwritten. I don't know if it's
b

MatRestoreRowIJ/ColumnIJ: zero pointers to catch accidental misuse

Only zero in case where the operation is "done" so that user's
uninitialized arguments are not overwritten. I don't know if it's
best, but this is consistent with done=FALSE meaning that the arguments
are not changed.

Explicitly pass NULL when intentionally using the number of rows after
restoring.

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LOCDIR: fix all outdated paths and normalize trailing slash

Update performed by:

git ls-files '*/makefile' | xargs perl -pi -MFile::Basename \
-e 's!(LOCDIR[[:space:]]+=) *(.+)$!$1." ".dirnam

LOCDIR: fix all outdated paths and normalize trailing slash

Update performed by:

git ls-files '*/makefile' | xargs perl -pi -MFile::Basename \
-e 's!(LOCDIR[[:space:]]+=) *(.+)$!$1." ".dirname($ARGV)."/"!e'

Fortran auto must be fixed using 'make allfortranstubs' and the result
can be checked by 'bin/maint/checkloc.py'.

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