Merged in barry/optimize-aij-da (pull request #1762)

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

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

MatLoad_Dense_HDF5

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

PetscViewerHDF5Load added _Private suffix and made PETSC_EXTERN.

Needs to PETSC_EXTERN as it is now used in Mat.

Remove dead Matlab code, fix typo, fix caste needed for const free

Commit-type: portability-fix
Reported-by: Satish Balay <balay@mcs.anl.gov>

PetscViewerHDF5ReadSizes_Private & PetscViewerHDF5ReadSelectHyperslab_Private clearer & more general

Remove unneeded casts from vsectionis.c that broke PetscArrayzero(), add missing output file

Commit-type: bug-fix, testing-fix

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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HDF5: Transfer mode defaults to independent wherever applicable and for all HDF5 versions.

Use PetscViewer_HDF5.dxpl_id instead of making new property list everytime.

vsectionis.c edited online with Bitbucket

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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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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Merge remote-tracking branch 'origin/maint'

Fix a typo: errors should be PetscInt to match MPIU_INT

Add PetscSFSetFromOptions after PetscSFCreate

Change MPIU_SUM to MPI_SUM in the test

MPIU_SUM is supposed to be used for PetscScalars

PetscViewerHDF5Load: move to isimpl.h and make INTERN

This function does not have a man page and depends on H5Ipublic.h, which
should not be requried for users who don't intend to call HDF5.

Add a test for PetscSFCreateEmbeddedSF

Fix a bug in PetscSFCreateEmbeddedSF

When one leaf data item serves multiple leaves, the old code will give wrong results.

PetscSF: last obvious silly optimization

Silent GCC 9.0.1 warning

ex2f.F90:51:0:

51 | if (ii(i+iis) .ne. -11 + 3*i) then; SETERRA(PETSC_COMM_SELF,1,'Wrong result from ISGetIndices'); endif
|
Warning: iteration 1 invokes u

Silent GCC 9.0.1 warning

ex2f.F90:51:0:

51 | if (ii(i+iis) .ne. -11 + 3*i) then; SETERRA(PETSC_COMM_SELF,1,'Wrong result from ISGetIndices'); endif
|
Warning: iteration 1 invokes undefined behavior [-Waggressive-loop-optimizations]
ex2f.F90:50:0:

50 | do 10, i=1,10000
|
note: within this loop

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PetscSFDistributeSection: Skip embedded sf if roots don't change

PetscSFSetUp_Basic: fix coding standards