To refactor the comments to follow petsc style.

Merge remote-tracking branch 'petsc/master' into fixed-comment-space

Conflicts:
include/petsc/finclude/petscmat.h
src/mat/examples/tests/makefile

To refactor the comments to follow petsc style.

Merge remote-tracking branch 'petsc/master' into fixed-comment-space

Conflicts:
include/petsc/finclude/petscmat.h
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiov.c

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To add a space to all comments I have made before. Barry pointed out
that a comment without a space right after '/*' may cause bfort to crash

Merge remote-tracking branch 'petsc/master' into fixed-c

To add a space to all comments I have made before. Barry pointed out
that a comment without a space right after '/*' may cause bfort to crash

Merge remote-tracking branch 'petsc/master' into fixed-comment-space

Conflicts:
include/petsc/finclude/petscmat.h
include/petscmat.h
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiaij.h

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Merge branch 'pr329/master/Fande-Kong/matpartitioning-hierarch' into pr361/master/Fande-Kong/pcgasm-increaseoverlap: need hierarch to build GASM subdomains.

Conflicts:
src/mat/examples/tests/makefi

Merge branch 'pr329/master/Fande-Kong/matpartitioning-hierarch' into pr361/master/Fande-Kong/pcgasm-increaseoverlap: need hierarch to build GASM subdomains.

Conflicts:
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiaij.h

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Merge branch 'master' into pr352/dmay/pctelescope/master

Merge branch 'master' into pr358/buptphyphy/addmatcreatenormalhermitian/master

Merge branch 'tisaac/plex-feature-tree-fv'

Make the PetscFV gradient reconstruction method work for the
non-conforming meshes introduced by the Tree extension to DMPlex.

* tisaac/plex-feature-tree-

Merge branch 'tisaac/plex-feature-tree-fv'

Make the PetscFV gradient reconstruction method work for the
non-conforming meshes introduced by the Tree extension to DMPlex.

* tisaac/plex-feature-tree-fv: (52 commits)
Plex ex3: make test that works for single precision
PlexSNES: address compiler warning
DMPlex ex3: make test output PASS/FAIL rather than precision specific
Plex: fix type punning problem stuffing (PetscFECellGeom *) in a Vec
Plex: allow ex3 testFVgrad examples in complex
PetscFV: allow SVD pseudoinverse least squares gradient calculation for complex.
Plex ex3: put fv tensor examples in C_NoComplex tests
Plex ex3: update regression output for nonconforming examples
Plex ex3: make separate fe and fv tests
Plex ex3: use MPIU_MAX, not MPI_MAX
DMPlex: added DMPlexReconstructGradientsFVM()
Plex: fix typo in change to cohesive cell creation
Plex: add ex4 and ex5 to makefile so they can be used for regression tests
DMPlex: remove overzealous error condition from FV gradient reconstruction
DMPlex: correct pointSF size in new point shift approach
DMPlexMigrate(): use correct global indices when migrating tree
DMPlexMigrate(): Don't invalidate old DM by overwriting cones
Plex ex3: use DMPlexDistributeOverlap()
DMPlexPartitionLabelClosure: traverse the tree up and down
PetscPartitionerSimple: work in parallel
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Merge branch 'tisaac/dt-fix-geom-punning' into tisaac/plex-feature-tree-fv

Pull in a fix to FE geometry that affects the complex,64bit case

* tisaac/dt-fix-geom-punning: (240 commits)
Plex: fix t

Merge branch 'tisaac/dt-fix-geom-punning' into tisaac/plex-feature-tree-fv

Pull in a fix to FE geometry that affects the complex,64bit case

* tisaac/dt-fix-geom-punning: (240 commits)
Plex: fix type punning problem stuffing (PetscFECellGeom *) in a Vec
PGI compiler cannot handle [restrict] usage therefor disable restrict for PGI compiler Fix ex48.c to use PETSc standard way of marking restrict
PETSC_UNUSED must occur before the typename. With PGI compilers they error if it is after the type name
on solaris in TSAdaptChoose_Basic() negative root for zero could produce -infinity thus causing time step to be decreased even though the error estimate was zero
MatGetSchurComplement: revert test from LUMP back to DIAG and update output
there are no tests for opencl or viennacl so prevent warning message: make[2]: *** No rule to make target `testexamples_OPENCL', needed by `tree'. Stop. make[2]: *** No rule to make target `testexamples_VIENNACL', needed by `tree'. Stop.
incorrect initial conditions function that could produce floating point exception value (and does on windows) due to squareroot of non-negative number
forgot to fix rule for building ex194
move ex193.c to ex194 because someone else created a 193
remove outdate manual page comment
add missing VecRestoreArray()
add missing VecRestoreArray()
missing restore array in example
formating for print statements of test example with __float128 precision
fix example for __float128 precision by using PETSc math macros and casting PetscReal in print statements
remove Tao example custom monitor that produced different results for __float128 precision
all PETSc built in monitors require a valid PetscViewer, NULL is not acceptable
PETSc built in monitors always require viewers to be passed in, no longer support a NULL viewer
use tigher haptol for minres for quad precision because otherwise false positive of indefinite matrix appeared in example
check for PetscMPIInt overflow in ISAllGather()
...

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Merge branch 'master' into jed/process-options-handler

Merge branch 'tisaac/dmplex-stable-tet-refinement' into tisaac/plex-feature-tree-fv

This feature branch also changed the topology of nonconforming examples:
I am merging so that I can make the regre

Merge branch 'tisaac/dmplex-stable-tet-refinement' into tisaac/plex-feature-tree-fv

This feature branch also changed the topology of nonconforming examples:
I am merging so that I can make the regression output that should be
correct in master and next

* tisaac/dmplex-stable-tet-refinement: (594 commits)
plex: added tet shape regression test
plexrefine: remove replaced code
plex: update test output for new tet refinement order
plex: fix tet refinement for stable element shape
DMPlex: added test of shape quality to ex1
Better to use the proper error handling version of PetscViewerASCIIGetStdout() instead of PETSC_VIEWER_STDOUT_()
Generate a very useful error message if PetscLogView(), PetscLogEventGetPerfInfo() or PetscLogEventGetFlops() is called with a preceeding call to PetscLogBegin() and friends (also -log_summary which triggers a PetscLogBegin())
fix compile warnings
Plex: Fix bug with bcComps initialization
Turn off elemental shared libraries if --with-shared-libraries=0 is used
Bib: Added refs
Bib: Fixed a bunch of errors
add warning/error flag for '-mat_superlu_dist_parsymbfact' when MatInputMode=GLOBAL
makefile: fix format
tests: add back ex6f, runex6f targets - that got removed in 2f1d3d565a6a43067e6df75b043e6343b05fcd1d
accessing option that may never have been set
typo in DMNetworkSetNumVariables() reported by Sean Shahkarami
superlu_dist: update to using latest 4.1 version
fix compile warnings
Generate an error message when trying to overwrite default options of CN and BEULER
...

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Plex: fix typo in change to cohesive cell creation

DMPlex: correct pointSF size in new point shift approach

I wasn't update the number of roots, getting valgrind errors in parallel

Plex Tree: small fixes (bounds, frees) for Tree+FVM

Plex: fix DMPlexShiftTree_Internal()

I wasn't keeping track of the difference in size between the old section
and the new section

Plex: fixes in new DMPlexShiftPoint

Passes ex11 test in snes tutorials

Plex: make new DMPlexShiftPointSetUp_Internal work for ghosts and hybrids

Before: list changes by the start of the stratum and the number of
points to add to the end of the stratum

Now: list the pl

Plex: make new DMPlexShiftPointSetUp_Internal work for ghosts and hybrids

Before: list changes by the start of the stratum and the number of
points to add to the end of the stratum

Now: list the places where the points are inserted and how many points
are inserted. This seems obvious now.

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Plex: simplify DMPlexShiftPoint_Internal()

Only the depthShift[] argument is needed now, and it should work for
strata that are in different orders.

Plex: shift tree in DMPlexCreateGhosts()

- Ancestor faces don't create ghosts: only leaves are used for flux
calculations
- Shift the indices in the tree.
*NOTE* This should not work yet. I hav

Plex: shift tree in DMPlexCreateGhosts()

- Ancestor faces don't create ghosts: only leaves are used for flux
calculations
- Shift the indices in the tree.
*NOTE* This should not work yet. I haven't been conforming to Matt's
(cells, vertices, edges, faces) ordering of strata, I've been doing
(cells, edges, faces, vertices). DMPlexShiftPoint_Internal() assumes
Matt's ordering, I'd like to make it agnostic.

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Merging with Barry's refactor of PetscViewerGetSubComm

Merge branch 'barry/fix-petscviewer-attempt-2' into dmay/pcsemiredundant

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of git. I think it is not justified to ever have anything in next for more than a few weeks at most.
Either take it out of next if it is broken or put it in master if it is not broken. Hanging around in next but
not master for ever is not a good policy.

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Replaced PetscViewerASCIISynchronizedAllow() with PetscViewerASCIIPushSynchronized() PetscViewerASCIIPopSynchronized()

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

* master: (206 commits)
Bib: Added ref
fix the output file for the ts example ex20adj
Bugfix: setting post-step function in ztsf.c
f

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

* master: (206 commits)
Bib: Added ref
fix the output file for the ts example ex20adj
Bugfix: setting post-step function in ztsf.c
fix makefile format error with 'all-legacy'
doc: handle missing dev.html in a release tarball
doc: add in petscistypes.h to doc sourcefile list
Increase patchlevel to 3.6.1
update some example output files
Doc+Vec: Fixed VecSetValuesBlocked() Reported by: Shao-Ching Huang <huangsc@gmail.com>
clarify that PETSc's "thread safe" code only works with OpenMP
allow adjoint integration over split time intervals
DT: Goddman it. Why are people stepping on my commits
Bib: Added ref
fix the bug in the endpoint version of discrete adjoint theta and correct the affected example outputs
SNES: Added SNESQN types to Fortran Reported-by: Chris Bradley <c.bradley@auckland.ac.nz>
fix: buggy change in 33da457b864643cfcac2768e47197c286471a5a4
updated petscthreads.html with information on thread per object model
fix for ex56
removed the dead links to threads.html
send petsc repository messages to Karl no longer from his mcs address
...

Conflicts:
config/builder.py
src/dm/impls/plex/examples/tests/ex3.c
src/dm/impls/plex/examples/tests/makefile
src/dm/impls/plex/makefile

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Merge branch 'master' into knepley/feature-plex-point-location

* master: (202 commits)
Bib: Added ref
fix makefile format error with 'all-legacy'
Increase patchlevel to 3.6.1
update some exa

Merge branch 'master' into knepley/feature-plex-point-location

* master: (202 commits)
Bib: Added ref
fix makefile format error with 'all-legacy'
Increase patchlevel to 3.6.1
update some example output files
Doc+Vec: Fixed VecSetValuesBlocked() Reported by: Shao-Ching Huang <huangsc@gmail.com>
clarify that PETSc's "thread safe" code only works with OpenMP
allow adjoint integration over split time intervals
DT: Goddman it. Why are people stepping on my commits
Bib: Added ref
fix the bug in the endpoint version of discrete adjoint theta and correct the affected example outputs
SNES: Added SNESQN types to Fortran Reported-by: Chris Bradley <c.bradley@auckland.ac.nz>
fix: buggy change in 33da457b864643cfcac2768e47197c286471a5a4
updated petscthreads.html with information on thread per object model
fix for ex56
removed the dead links to threads.html
send petsc repository messages to Karl no longer from his mcs address
Plex: Fix for all the hidebound morons living with c89. Good luck doing computational science in the 80s!
DT: Fix tanh-sinh - Removed wrong var
SNES: Added SNESQN types to Fortran Reported-by: Chris Bradley <c.bradley@auckland.ac.nz>
Bib: More refs
...

Conflicts:
config/builder.py

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

Merge branch 'master' into mesgarnejad/feature-plex-globaltonatural

* master: (111 commits)
add filters for website tests that removes warnings about MPI type tag mismatches due to const
remove

Merge branch 'master' into mesgarnejad/feature-plex-globaltonatural

* master: (111 commits)
add filters for website tests that removes warnings about MPI type tag mismatches due to const
remove Peter from blame-email list.
don't warn about MPI const long * versus long long *
Configure: Added GMP an MPRF - These allow arbitrary precision arithmetic
SNES ex69: SolCx finally works - Fixed order of parameters - Made different versions of pointwise functions
SNES ex69: Fixed bug where SolKx and SolCx have different numbers of parameters
SNES ex69: Small bug fixes - Initialize coordinates for SolCx - Fixed declaration length
I believe this call on line 357: ierr = DMSetFromOptions(dau); should actually set `dak`. The DM `dau` is already set on line 349.
SNESSolve_KSPOnly() did not compute function at new solution unless monitoring is turned on but SNESSolve_FAS() internals assume that each subsnes solve it calls does compute the new function value so broke when -fas_levels_snes_monitor was not turned on but -fas_levels_snes_type kspmonitor was used
Have SNESVIGetInactiveSet return the *actual* current inactive set.
One now passes the nullspace in the matrix for a linear system as the first Amat argument to KSPSetOperators, SNESSetOperators, TSSetIJacobian() not the second pmat argument
Remove change documentation of Removed MatMFFDAddNullSpace() just use MatSetNullSpace() as it is now backported in maint (36.html)
MatMFFD doesn't need to have its own null space management cherry-picked from 39601f4 (barry/remove-matmffdaddnullspace/master)
Removed trailing '\\' in the authors line.
add note to PetscOptionsInsertFile() that it should not be used for PETSc wide options
Add Fortran stub for SNESSetUpdate()
improve manual page slightly for clarity
PCGASM.
Basic PCGASM description added to manual.
add DMDAVecGet/RestoreArrayReadF90()
...

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Merge branch 'knepley/plex-filter'

* knepley/plex-filter:
fix: nightlybuilds - move DMPlexFilter() to be after DMLabel definition
Plex: Added declaration of DMPlexFilter()
Plex ex16: Added tes

Merge branch 'knepley/plex-filter'

* knepley/plex-filter:
fix: nightlybuilds - move DMPlexFilter() to be after DMLabel definition
Plex: Added declaration of DMPlexFilter()
Plex ex16: Added test for DMPlexFilter()
Plex: Added DMPlexFilter() - This reuses DMPlexCreateSubmeshGeneric_Interpolated(), but extends it to handle subvolumes
Plex: Fixed error checking

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