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

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

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>

Merge remote-tracking branch 'origin/psanan/docs-remove-manconcepts' [PR #1733]

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 jkruzik/petsc/jkruzik/feature-matptap-fallback (pull request #1695)

PtAP fallback

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

Merged in psanan/man-pages-remove-keywords (pull request #1717)

Man pages: Remove .keywords fields

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

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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rename fallback to Basic

fallback PtAP

Merged in barry/check-bad-urls (pull request #1685)

Barry/check bad urls

Approved-by: Patrick Sanan <patrick.sanan@gmail.com>
Approved-by: Junchao Zhang <junchao.zhang@gmail.com>

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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Merge branch 'master' of bitbucket.org:petsc/petsc

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

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>

Merge remote-tracking branch 'origin/maint'

Merged in jczhang/fix-matsetrandom-mpiaij (pull request #1647)

Fix a MatSetRandom() bug related to unassembled MATMPIAIJ matrices

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

Fix a MatSetRandom bug with unassembled MATMPIAIJ

When doing MatSetRandom on a preallocated but unassembled matrix X, we can not
simply calling MatSetRandom on X's B. Since B is not assembled, it ha

Fix a MatSetRandom bug with unassembled MATMPIAIJ

When doing MatSetRandom on a preallocated but unassembled matrix X, we can not
simply calling MatSetRandom on X's B. Since B is not assembled, it has a column
size as wide as X. Calling MatSetRandom(B,r) might generate nonzeros belonging
to X's A.

Reported-by: Jakub Kruzik <jakub.kruzik@vsb.cz>

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

fix-issue-289

Merged in hzhang/cleanup-mattranspose_seqaij (pull request #1635)

Hzhang/cleanup mattranspose seqaij

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

delete old MatTranspose_SeqAIJ, PetscLogEvent MAT_Transpose_SeqAIJ
rename MatTranspose_SeqAIJ_FAST -> MatTranspose_SeqAIJ
Requested by Barry

Merged in jczhang/fix-with-gcov (pull request #1618)

Enable gcov when --with-gcov regardless of having -g or not

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

fix -Wmaybe-uninitialized warnings triggered by gcov changes

arch-linux-pkgs-gcov:
/sandbox/petsc/petsc.next-2/src/mat/interface/matrix.c:4409:7: warning: ‘prev’ may be used uninitialized in thi

fix -Wmaybe-uninitialized warnings triggered by gcov changes

arch-linux-pkgs-gcov:
/sandbox/petsc/petsc.next-2/src/mat/interface/matrix.c:4409:7: warning: ‘prev’ may be used uninitialized in this function [-Wmaybe-uninitialized]
/sandbox/petsc/petsc.next-2/src/dm/impls/forest/p4est/pforest.c:2711:24: warning: ‘parentOrnt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
/sandbox/petsc/petsc.next-2/src/dm/impls/forest/p4est/pforest.c:2711:24: warning: ‘parentOrnt’ may be used uninitialized in this function [-Wmaybe-uninitialized]

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Merge remote-tracking branch 'origin/maint'