Merged in barry/rm-cmake-legacy (pull request #1714)

Remove legacy and cmake compile systems

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

attempt to improve quality of PetscViewerASCII{PushSynchronized,PopSynchronized,SynchronizedPrint} documentation

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*()

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*() with PetscArraymove()

Commit-type: style-fix, feature

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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>

Remove legacy and cmake compile systems

- Remove legacy and cmake compile systems from makefiles and config
- Clean out various dead code from makefile and lib/petsc/conf/rules
- Update lib/petsc/co

Remove legacy and cmake compile systems

- Remove legacy and cmake compile systems from makefiles and config
- Clean out various dead code from makefile and lib/petsc/conf/rules
- Update lib/petsc/conf/test to build all examples, not just those beginning with ex, update examples makefiles to remove now unneeded rules
- Deprecated make gnumake, replaced with make libs

Note: retained clean-legacy since it is used by clean in rules

Commit-type: style-fix, feature
Thanks-to: Jed Brown <jed@jedbrown.org> and Satish Balay <balay@mcs.anl.gov>

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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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Merged in haplav/feature-petscviewerview-hdf5 (pull request #1722)

add PetscViewerView_HDF5()

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

PetscViewerView_HDF5 impl.

PetscViewerHDF5Open() now calls PetscViewerSetFromOptions().

Just like PetscViewerBinaryOpen().

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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Add PetscBinaryBigEndian() for runtime detection of endianness

Fixed out-dated URLS using make checkbadURLS REPLACE=1

One manual fix of https://en.wikipedia.org/wiki/Buckingham_π_theorem since the automatic tool dropped the first _ for some reason
Manual fix of

Fixed out-dated URLS using make checkbadURLS REPLACE=1

One manual fix of https://en.wikipedia.org/wiki/Buckingham_π_theorem since the automatic tool dropped the first _ for some reason
Manual fix of //faq.html since the automatic tool incorrectly replaced /faq.html to //faq.html in some locations

These are largely updates of http to https but have a variety of other website location changes

Once this branch is in master individual developers can run make checkbadURLS and fix URLs related to their projects manually

Commit-type: bug-fix, documentation

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fix build errors with arch-linux-matlab-ilp64

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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Merged in barry/cleanup-petscstringviewer (pull request #1630)

Work on PetscViewerString. Fix use of PetscInt -> size_t, add new functionality, add usage by basic solver objects, add test case

Merge remote-tracking branch 'origin/maint'

Work on PetscViewerString. Fix use of PetscInt -> size_t, add new functionality, add usage by basic solver objects, add test case

Commit-type: style-fix, feature, documentation, example

Merged in haplav/remove-petscviewerhdf5setaijnames (pull request #1644)

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

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>