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

Added MatUpdateMPIAIJWithArrays()

Commit-type: optimization, feature, example
Reported-by: Hong Zhang <hongzhang@anl.gov>

Resolved issues brought up in PR

Commit-type: bug-fix, style-fix
Reported-by: Patrick Sanan <patrick.sanan@gmail.com>

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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Merge remote-tracking branch 'origin/maint'

Merged in rmills/fix-doc-paradigm-spelling/maint (pull request #1765)

Fixed misspelling of "paradigm" throughout manual pages.

Fixed misspelling of "paradigm" throughout manual pages.

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>

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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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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Merge remote-tracking branch 'origin/maint'

Merged in stefano_zampini/fix-matcopy-sbaij (pull request #1571)

Fix SBAIJ

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

Mat{MPI|MPISB|MPIB|Seq|SeqB|SeqSB}AIJSetPreallocation: optimize nonzeros

set number of columns of offdiag blocks to zero for sequential cases
no need to allocate more than the the number of columns

Mat{MPI|MPISB|MPIB|Seq|SeqB|SeqSB}AIJSetPreallocation: optimize nonzeros

set number of columns of offdiag blocks to zero for sequential cases
no need to allocate more than the the number of columns for sequential matrices

Update outputs for testsuite

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

Merge remote-tracking branch 'origin/jczhang/vecscat-in-sf' [PR #1396]

Fix more bugs when we lock vectors in VecScatter

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merged petsc/petsc into master

Merged petsc/petsc into master

Merge branch 'master' into knepley/feature-snes-patch