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>

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>

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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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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housekeeping

remove trailing blanks
remove functions that are no longer part of PETSc

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>

MATMPIAIJ: Fix MatZeroRows and MatZeroRowsColumns

skip diagonal set if row index > number of global columns

x AND b must be present at the same time

raise error when layouts are not congruent (ins

MATMPIAIJ: Fix MatZeroRows and MatZeroRowsColumns

skip diagonal set if row index > number of global columns

x AND b must be present at the same time

raise error when layouts are not congruent (instead of segfaulting)

local nonew on diagonal block may be different across comm -> Always reduce

When asked to not keep the nonzero pattern with non-congruent layouts
it is better off allowing a small reallocation to happen instead of erroring

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Merge remote-tracking branch 'origin/maint'

Merged in stefano_zampini/feature-improve-matviewmpiaij-ascii-maint (pull request #1519)

MatView_MPIAIJ_ASCIIorSocket: speedup code

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

MatView_MPIAIJ_ASCIIorSocket: speedup code

This code in not performance critial, but it took 3 hours to dump a 2000x2000 MPIAIJ matrix with dense values
This is what we obtain by calling MatViewFrom

MatView_MPIAIJ_ASCIIorSocket: speedup code

This code in not performance critial, but it took 3 hours to dump a 2000x2000 MPIAIJ matrix with dense values
This is what we obtain by calling MatViewFromOptions on a MATSHELL in parallel

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

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