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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HDF5: Transfer mode defaults to independent wherever applicable and for all HDF5 versions.

Use PetscViewer_HDF5.dxpl_id instead of making new property list everytime.

vsectionis.c edited online with Bitbucket

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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Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be unif

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be uniformly used or maintained.

Thus, remove all .keywords: fields, and a following blank line, if present.

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 -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find src/ -type f -exec gsed -i '/keywords:/d' {} +
find include/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find include/ -type f -exec gsed -i '/keywords:/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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PetscViewerHDF5Load: move to isimpl.h and make INTERN

This function does not have a man page and depends on H5Ipublic.h, which
should not be requried for users who don't intend to call HDF5.

PetscSFDistributeSection: Skip embedded sf if roots don't change

PetscSectionCreateGlobalSection: report error instead of segfaulting

PetscSF: added logging support for functions used by DMPlex

DMPLEX: add few missing events to help optimizing the code

Merged in dalcinl/fix-io-gmsh (pull request #1660)

Binary I/O And Gmsh DMPlex Reader

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

Binary I/O: Various fixes and enhancements

* Change PetscBinary[Synchronized]Read() to allow for reading
items up to EOF without erroring
* Fix PetscViewerBinaryRead() to properly return the numbe

Binary I/O: Various fixes and enhancements

* Change PetscBinary[Synchronized]Read() to allow for reading
items up to EOF without erroring
* Fix PetscViewerBinaryRead() to properly return the number of items read
* Fix PetscViewerRead() to prevent infinite loops at EOF
* Various fixes for PetscDataType PETSC_COMPLEX

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Minor code formatting

Merge remote-tracking branch 'origin/maint'

doc: fix PetscViewerHDF5ReadSizes manpage

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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Remove unneccesary references to petscvec.h and vecimpl.h from lower level routines such as IS

Commit-type: style-fix
Thanks-to: Matthew Knepley <knepley@gmail.com>

Merged in stefano_zampini/feature-matshell-zerorows (pull request #1547)

Add support for zeroing rows and columns of a MATSHELL

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

Merged in stefano_zampini/feature-matshell-zerorows (pull request #1547)

Add support for zeroing rows and columns of a MATSHELL

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

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MATIS: move PetscLayoutMapLocal_Private code to PetscLayout code

TODO: support nooffprocentries like MatZeroRowsMapLocal_Private() and get rid of it

Allow bs=1 in PetscLayoutSetISL2GMap