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 barry/fix-petscviewer-attempt-2

Merge branch 'maint' of bitbucket.org:petsc/petsc into maint

Plex: Fix bug with bcComps initialization

Merge branch 'knepley/feature-patrick-control-problem'

* knepley/feature-patrick-control-problem:
TAO ex2: Add optimal control problem from Patrick
TAO ex1: Fix docs
Plex: Fix bug with bcComps

Merge branch 'knepley/feature-patrick-control-problem'

* knepley/feature-patrick-control-problem:
TAO ex2: Add optimal control problem from Patrick
TAO ex1: Fix docs
Plex: Fix bug with bcComps initialization

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

Plex: Fixed unused variables

Merge branch 'knepley/feature-plex-point-location' into knepley/feature-snes-deflation

* knepley/feature-plex-point-location:
Plex: Removed unused vars, Initialized vars
Plex: Fixed signature fo

Merge branch 'knepley/feature-plex-point-location' into knepley/feature-snes-deflation

* knepley/feature-plex-point-location:
Plex: Removed unused vars, Initialized vars
Plex: Fixed signature for PetscGridHashGetEnclosingBox()
Plex ex17: Tests point location - One test which locates cell centroids right now
Plex: Replaced brute force search with grid hashing for point location
Plex: Now every Plex has a PetscGridHash
PetscGridHash: Added a simple regular point location data structure
DMLabel: Added DMLabelConvertToSection() - This routine converts a label to a Section+IS
Doc+Plex: Fixed function name

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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 'mesgarnejad/feature-plex-globaltonatural'

* mesgarnejad/feature-plex-globaltonatural:
Plex ex15: This requires HDF5
Plex ex15: Fixed variable type
Plex: Fixed variable init
Ple

Merge branch 'mesgarnejad/feature-plex-globaltonatural'

* mesgarnejad/feature-plex-globaltonatural:
Plex ex15: This requires HDF5
Plex ex15: Fixed variable type
Plex: Fixed variable init
Plex ex15: Added test for reading and writing HDF5 in native format
Vec: Straighten out defines for VECOP
DM: Reminder to handle g2n in DMCreateSubDM()
Plex ex15: One test of g2n working
Plex: Fixed global to natural mapping creation
Plex: When creating g2n map, must use parallel DM
PetscSF: Corrected bug in PetscSFCreateInverseSF() for sparse leaves - Have to index over entire leaf space
PetscSection: PetscSectionCreateGlobalSection() now allows the user to keep local offsets - This is useful is all you want is to filter out the constrained points
Plex: Create the global to natural mapping during distribution if the flag is set
Plex: Added viewing in native format using the global to natural mapping
Plex: Added global to natural ordering support - The natural ordering is the one you have before distribution - Added DMPlexCreateGlobalToNaturalSF() - Added DMPlexGlobalToNaturalBegin/End() - Added DMPlexNaturaToGloballBegin/End()
SF: Added PetscSFCreateEmbeddedLeafSF() - This name sucks, but it subsets on leaves instead of roots
DM: Added an SF for the global to local mapping and a flag to enable its construction - Added DMGet/SetUseNatural() - Should hook this up to DMDA
SF: Added Fortran binding for SFView()
DM: Automatic Fortran binding should work for DMCreateSubDM()
SF: Added PetscSFCompose()
SF: Added PetscSFCreateFromZero()

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Plex: Fixed variable init

PetscSection: PetscSectionCreateGlobalSection() now allows the user to keep local offsets
- This is useful is all you want is to filter out the constrained points

Plex: Now every Plex has a PetscGridHash

Merge branch 'mat-increaseoverlap' of ssh://bitbucket.org/Fande-Kong/petsc into pr332/master/Fande-Kong/mat-increaseoverlap-scalable

Merge remote-tracking branch 'petsc/master' into pcgasm-increaseoverlap

Merge remote-tracking branch 'petsc/master' into matpartitioning-hierach

Merge remote-tracking branch 'petsc/master' into mat-increaseoverlap

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

* master: (239 commits)
Bib: Moved entry
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in c

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

* master: (239 commits)
Bib: Moved entry
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure
release: set v3.6 strings
doc: add PCGAMGSetReuseInterpolation() to changes file
fix: workarround static initialization issue (perhaps compiler bug) on opensolaris c/complex build
fix: ex40,ex41 errors in src/ts/examples/tutorials/ on bsd with c++/complex Perhaps this code nees a separate section when 'enorm == 0) - as pow(0,-0.33) = inf.
manual: fix format
more changes..
PCGASM/MatGetSubMatricesMPI() changes in dev.html.
changes: more updates
Add size checks for static arrays of assumed max size [-Warray-bounds]
Doc: Update to Changes
configure: default to useThreads= 0as the useThreads=1 code currently prints output in jumbled order [producing hard to read configure.log]
Delete PETSc viewer attribute if none are left on the linked list instead of putting an empty attribute
MatGetSubMatricesMPI_MPIAIJ(): guard for an empty B-matrix when delogging memory in MatSetSeqMats().
PCBDDC: fix typos in the specification of MPI operation
MPIU_SUM was used with MPIU_INT when it should only be used with MPIU_REAL or MPIU_SCALAR
fixed bad PetscPrintf() formatting in two examples
Plex: In pointwise callbacks, use embedding dimension
updates for generating Apple installations due to changes in locations of include files
...

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

* master: (219 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure

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

* master: (219 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure
release: set v3.6 strings
doc: add PCGAMGSetReuseInterpolation() to changes file
fix: workarround static initialization issue (perhaps compiler bug) on opensolaris c/complex build
fix: ex40,ex41 errors in src/ts/examples/tutorials/ on bsd with c++/complex Perhaps this code nees a separate section when 'enorm == 0) - as pow(0,-0.33) = inf.
manual: fix format
more changes..
PCGASM/MatGetSubMatricesMPI() changes in dev.html.
changes: more updates
Add size checks for static arrays of assumed max size [-Warray-bounds]
Doc: Update to Changes
configure: default to useThreads= 0as the useThreads=1 code currently prints output in jumbled order [producing hard to read configure.log]
Delete PETSc viewer attribute if none are left on the linked list instead of putting an empty attribute
MatGetSubMatricesMPI_MPIAIJ(): guard for an empty B-matrix when delogging memory in MatSetSeqMats().
PCBDDC: fix typos in the specification of MPI operation
MPIU_SUM was used with MPIU_INT when it should only be used with MPIU_REAL or MPIU_SCALAR
fixed bad PetscPrintf() formatting in two examples
Plex: In pointwise callbacks, use embedding dimension
updates for generating Apple installations due to changes in locations of include files
configure: do not fail when checking MPICH version [similar to 2cadc8fc42fbad3c229d43b955581b8d29e02ad6 ]
...

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Merge branch 'master' into knepley/fix-pc-composite-dm

* master:
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure
release: set v3.6 strings

Merge branch 'master' into knepley/fix-pc-composite-dm

* master:
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure
release: set v3.6 strings
doc: add PCGAMGSetReuseInterpolation() to changes file
fix: workarround static initialization issue (perhaps compiler bug) on opensolaris c/complex build
fix: ex40,ex41 errors in src/ts/examples/tutorials/ on bsd with c++/complex Perhaps this code nees a separate section when 'enorm == 0) - as pow(0,-0.33) = inf.
manual: fix format
more changes..
PCGASM/MatGetSubMatricesMPI() changes in dev.html.
changes: more updates
Add size checks for static arrays of assumed max size [-Warray-bounds]
Doc: Update to Changes
configure: default to useThreads= 0as the useThreads=1 code currently prints output in jumbled order [producing hard to read configure.log]
Delete PETSc viewer attribute if none are left on the linked list instead of putting an empty attribute
KSPComputeExplicitOperator: use KSP_PCApplyBAorAB

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Merge branch 'master' into knepley/plex-filter

* master:
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure
release: set v3.6 strings
doc:

Merge branch 'master' into knepley/plex-filter

* master:
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure
release: set v3.6 strings
doc: add PCGAMGSetReuseInterpolation() to changes file
fix: workarround static initialization issue (perhaps compiler bug) on opensolaris c/complex build
fix: ex40,ex41 errors in src/ts/examples/tutorials/ on bsd with c++/complex Perhaps this code nees a separate section when 'enorm == 0) - as pow(0,-0.33) = inf.
manual: fix format
more changes..
PCGASM/MatGetSubMatricesMPI() changes in dev.html.
changes: more updates
Add size checks for static arrays of assumed max size [-Warray-bounds]
Doc: Update to Changes
configure: default to useThreads= 0as the useThreads=1 code currently prints output in jumbled order [producing hard to read configure.log]
Delete PETSc viewer attribute if none are left on the linked list instead of putting an empty attribute
KSPComputeExplicitOperator: use KSP_PCApplyBAorAB

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