Added functionality to selectively filter PetscInfo() output based on calling class to
mimic some OS system logs. New functionality includes:
- Filter for a set of classes
- Filter out a set of class

Added functionality to selectively filter PetscInfo() output based on calling class to
mimic some OS system logs. New functionality includes:
- Filter for a set of classes
- Filter out a set of classes
- Filter for MPI/PETSC_COMM_SELF
- Filter for anything not on MPI/PETSC_COMM_SELF
- Writing PetscInfo() output to new file
- Appending output to existing PetscInfo() file
- Any combination of the above

Credit to Vaclav Hapla for raising the initial issue, helping design the eventual API, and
substantially assisting in debugging.

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Merge remote-tracking branch 'origin/hzhng/matproduct-api'

This branch reorganizes the API of mat-mat operations: A*B, At*B, A*Bt, PtAP, RARt, A*B*C
- See matproduct.c for detailed description of new API
- removed API function XXXSymbolic() and XXXNumeric()

This branch reorganizes the API of mat-mat operations: A*B, At*B, A*Bt, PtAP, RARt, A*B*C
- See matproduct.c for detailed description of new API
- removed API function XXXSymbolic() and XXXNumeric()
- removed subroutines MatMatMult_xxx, MatPtAP_xxx, ...
- modified MatxxxSymbolic_XXX() prototype (product is an input now)
- selection of algorithm is in MatProductSetFromOptions_xxx()

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Merge remote-tracking branch 'origin/maint'

Merge branch 'jacobf/init-vec_scatter_classid-in-vecinit' into 'maint'

Init VEC_SCATTER_CLASSID in VecInitializePackage

See merge request petsc/petsc!2463

Init VEC_SCATTER_CLASSID in VecInitializePackage

Merge branch 'stefanozampini/gpu-bddc' into 'master'

Improvements towards BDDC on GPUs

See merge request petsc/petsc!2067

MatFactor: added events for Schur complement numerical stages

Merge branch 'stefano_zampini/GPU-matdensecuda' [PR #1911]

* stefano_zampini/GPU-matdensecuda:
GPU: Initial implementation for SeqDense class on GPUs.

Added MATSEQDENSECUDA

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 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 barry/feature-matcreateconstantdiagonal (pull request #1678)

Introduces a new Mat class that consists of a single constant value for each enrty of the diagonal.

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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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

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

Commit-type: bug-fix

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

Merged in barry/improve-manual (pull request #1289)

Fixes for begining of users manual and a variety of webpages including manual pages

Fixes for begining of users manual and a variety of webpages including manual pages

Commit-type: bug-fix, documentation