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>

Merged in Fande-Kong/mpiptap-log_flops1 (pull request #1640)

MPIPtAP: Correct logflops for allatonce and allatonce_merged

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

MatSetValues_MPIAIJ/SeqAIJ: added logflops for additions

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

Fix a MatSetRandom() bug related to unassembled MATMPIAIJ matrices

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

Add support of MatSetRandom on assembled MPIAIJ matrices

This is to make concept of MatSetRandom() simpler and consistent with MatSetRandom on MPIDENSE.
We just need to change existing nonzeros to r

Add support of MatSetRandom on assembled MPIAIJ matrices

This is to make concept of MatSetRandom() simpler and consistent with MatSetRandom on MPIDENSE.
We just need to change existing nonzeros to random numbers as we do with MPIDENSE.

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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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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

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 'maint'

Merged in stefano_zampini/misc-fixes/maint (pull request #1550)

Stefano zampini/misc fixes/maint

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

MATSEQAIJ: fixes to MatZeroRows and MatShift for rectangular matrices

Diagonal entries must be set only when i < cmap->n

MatZeroRowsColumns_SeqAIJ: fixes for non-square matrices

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

Merged in Fande-Kong/fixed_PtAP (pull request #1452)

MPIPtAP: Enable large-scale simulations

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

Addressed Barry's comments: always use ctable

MPIPtAP: added a few tests using different MatMatMultSymbolic_SeqAIJ_SeqAIJ

MPIPtAP: Enable large-scale simulations

The old code uses a global size of columns when creating the local matrix

This uses a lot of memory when calling MatMatMultSymbolic_SeqAIJ_SeqAIJ

We here co

MPIPtAP: Enable large-scale simulations

The old code uses a global size of columns when creating the local matrix

This uses a lot of memory when calling MatMatMultSymbolic_SeqAIJ_SeqAIJ

We here compact out many extra columns, and construct a new local size.

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Merge branch 'master' into wence/feature-patch-all-at-once