Merge from doc-fixes branch

Fixes for doctext update

Merged in haplav/feature-hdf5-collective-options (pull request #1737)

add ability to turn on/off HDF5 collective transfer mode

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

Merged in haplav/feature-hdf5-collective-options (pull request #1737)

add ability to turn on/off HDF5 collective transfer mode

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

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PetscViewerView_HDF5: View collective property.

- Update tests sys_classes_viewer_tutorials-ex2%
- Added alt file for HDF5 < 1.10.3 for which this property is ignored.

HDF5: No need for H5Pset_fapl_mpio check anymore.

We already require HDF5 1.8.0+ and this was introduced in 1.4.0

Add PetscViewerHDF5{Get,Set}Collective and -viewer_hdf5_collective.

* Use H5_VERSION_GE to decide HDF5 version.
* If H5_VERSION_GE undefined, define it as 0.
* Discussed in https://bitbucket.org/pet

Add PetscViewerHDF5{Get,Set}Collective and -viewer_hdf5_collective.

* Use H5_VERSION_GE to decide HDF5 version.
* If H5_VERSION_GE undefined, define it as 0.
* Discussed in https://bitbucket.org/petsc/petsc/pull-requests/1737/add-ability-to-turn-on-off-hdf5-collective/diff#comment-105015892

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hdf5v.c: No need for HDF5 version check.

Leave it to the BuildSystem.

keep data transfer property list in PetscViewer_HDF5

PetscViewer_HDF5 moved to separate headerfile viewerhdf5impl.h

Update the use of Collective on in the manual pages to reflect the new style

Commit-type: style-fix, documentation
Thanks-to: Patrick Sanan <patrick.sanan@gmail.com>

Man pages: remove Concepts: fields

These fields were previously stripped from the man pages by logic removed in
21a59cba2737d49dc2f0bd12c08db0d2a3f3f209

Remove these fields from all man pages (but

Man pages: remove Concepts: fields

These fields were previously stripped from the man pages by logic removed in
21a59cba2737d49dc2f0bd12c08db0d2a3f3f209

Remove these fields from all man pages (but not from examples).

This is accomplished with GNU sed (gsed on OS X), with the following commands.
*Warning* that this type of command can corrupt a .git directory,
so be cautious in reusing or modifying these commands. They first look
for and delete matching lines with a following line consisting of only whitespace,
and then delete any remaining matching lines.

find src -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/ {N; /\n\s*$/d}' {} +
find src -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/d' {} +
find include -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/ {N; /\n\s*$/d}' {} +
find include -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/d' {} +

Hints on the sed command obtained from: https://unix.stackexchange.com/questions/100754/how-to-delete-a-specific-line-and-the-following-blank-line-using-gnu-sed

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PetscViewerView_HDF5 impl.

PetscViewerHDF5Open() now calls PetscViewerSetFromOptions().

Just like PetscViewerBinaryOpen().

Merge remote-tracking branch 'origin/maint'

Get rid of PetscViewerHDF5{Get,Set}AIJNames().

fix-issue-289

doc: no need to include petscsys.h because petscviewerhdf5.h does already

Move HDF5 array IO stuff from sys to vec.

- Fix issue 288.
- Moved PetscViewerHDF5Load,PetscViewerHDF5ReadSizes and their helpers from
src/sys/classes/viewer/impls/hdf5/hdf5v.c
into the new fi

Move HDF5 array IO stuff from sys to vec.

- Fix issue 288.
- Moved PetscViewerHDF5Load,PetscViewerHDF5ReadSizes and their helpers from
src/sys/classes/viewer/impls/hdf5/hdf5v.c
into the new file
src/vec/is/utils/hdf5io.c
- PetscViewerHDF5Load() header moved from viewerimpl.h to petscis.h
- PetscViewerHDF5ReadSizes() header moved from petscviewerhdf5.h to petscis.h

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PetscDataType of enum should map to hdf5 type of int

Commit-type: bug-fix

HDF5 viewer: revert MAT-file HDF5 group naming for now

PetscViewerHDF5OpenGroup: don't create group while viewer is read-only