Multiple routines fixed with MATTRANSPOSEMAT.

Merged in haplav/feature-matload-dense-hdf5 (pull request #1795)

MatLoad_Dense_HDF5

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

docs update

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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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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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>

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>

Introduces a new Mat class that consists of a single constant value for all entries of the diagonal.

Very light-weight matrix class suports factorization, SSOR, MatMult(), MatShit(), MatScale()
Usef

Introduces a new Mat class that consists of a single constant value for all entries of the diagonal.

Very light-weight matrix class suports factorization, SSOR, MatMult(), MatShit(), MatScale()
Useful for IMEX methods when the user provides on a RHSJacobian

Commit-type: feature

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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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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'

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

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

shrink length of PetscLogEventRegister strings to acceptable size so it does not mess up the output table from -log_view

Commit-type: bug-fix

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'

Do not call MatStashScatterDestroy_BTS with MPIUNI

Update the MAT_SUBSET_OFF_PROC_ENTRIES logic

The old code is right. But the variable names are not expressive and are
different from what we have in vector assembly.

This commit makes them have the

Update the MAT_SUBSET_OFF_PROC_ENTRIES logic

The old code is right. But the variable names are not expressive and are
different from what we have in vector assembly.

This commit makes them have the same name and control flow and also adds
comments to cross reference vec and mat.

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