Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

1) PetscCalloc*() now uses system calloc()
2) Merged some Pets

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

1) PetscCalloc*() now uses system calloc()
2) Merged some PetscMalloc*()
3) Eliminated unneeded PetscCalloc*()
4) Removed some memory allocations and copies in MatFDColoringSetUp(), added local variables for better compiler optimization
5) Added MatSetValues_SeqAIJ_SortedFull(), added MatSetOption(MAT_SORTED_FULL)
6) Optimized DMCreateMatrix_DA_*AIJ for nonperiodic case to automatically have sorted columns (faster MatSetValues() times)
7) Eliminated call to PetscMemzero() in PetscFree()

Commit-type: style-fix, feature

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Merge branch 'barry/cleanup-oldfortran-rules' [PR #1808]

* barry/cleanup-oldfortran-rules:
Remove no longer needed buildmod rules for building Fortran libraries from various directories

Merged in dhsuh/petsc/dhsuh/tao-soft (pull request #1779)

TaoSoftThreshold implementation in util

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

Merge remote-tracking branch 'origin/barry/add-petscarrayxxx-ops' [PR #1771]

additional chkerrq

Remove no longer needed buildmod rules for building Fortran libraries from various directories

Commit-type: cleanup
Reported-by: Jose E. Roman <jroman@dsic.upv.es>

taosolver_fg.c edited online with Bitbucket

TaoSoftThresholding routine for Tao.
User can supply input and output vectors, and lower bound and upper bound, lb and ub, respectively.
Users have option to supply same vector for both input and out

TaoSoftThresholding routine for Tao.
User can supply input and output vectors, and lower bound and upper bound, lb and ub, respectively.
Users have option to supply same vector for both input and output.

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

Remove legacy and cmake compile systems

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

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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TAO man pages: fix some indentation errors for lists

Reported-by: Pierre Jolivet <pierre.jolivet@enseeiht.fr>

Merge branch 'denera/tao-steplength-typo-fix' [PR #1780]

* denera/tao-steplength-typo-fix:
Typo fixed in line search monitor.

test output updated for ls_monitor

line search step length monitor typo fixed

Merged in barry/update-collective-on (pull request #1744)

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

Merged in knepley/fix-subdm-fields (pull request #1702)

Knepley/fix subdm fields

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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documentation update

revert ex4 to original. change ordering of lookup table. add brgn l2 pure example to cs1

white space clean

TAOBRGN: Implemented L2pure regularization option for BRGN.

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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SNES+Plex: Update output for new check

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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