DM interfaces: New API's introduced
* Added the methods DMAppendOptionsPrefix() and DMGetOptionsPrefix()

DMSetOptionsPrefix:
* Manpage correction: DMDA --> DM

DMSetOptionsPrefix:
* Corrections to manpage. Function argument type changes (DMDA --> DM)

Merge branch 'maint'

update manual page for DMView

Reported-by: Dave May <dave.mayhem23@gmail.com>

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
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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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Profile DMCreateInterpolation (nontrivial cost for nonnested meshes)

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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Doc+DM: Make clear that VecSetDM() is not the same as DMCreateGlobalVector()

DM: Reminder to handle g2n in DMCreateSubDM()

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

Events for DMCoarsen and DMLocatePoints

Plex: Added global to natural ordering support
- The natural ordering is the one you have before distribution
- Added DMPlexCreateGlobalToNaturalSF()
- Added DMPlexGlobalToNaturalBegin/End()
- Added

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()

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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

DM: Automatic Fortran binding should work for DMCreateSubDM()

Merge branch 'knepley/fix-dm-default-section-null'

* knepley/fix-dm-default-section-null:
DM: Allow the default section to be set to NULL

changed second argument of PetscObjectViewFromOptions() to PetscObject and all routines that use this routine

Merge branch 'knepley/feature-plex-bc'

* knepley/feature-plex-bc:
TS: Take out unnecessary declaration
XDMF: Allow missing time dimension
MatSchur: Better check for missing D matrix
TAO ex1:

Merge branch 'knepley/feature-plex-bc'

* knepley/feature-plex-bc:
TS: Take out unnecessary declaration
XDMF: Allow missing time dimension
MatSchur: Better check for missing D matrix
TAO ex1: Updated to new Plex interface
Plex: Fixed bug for FV BCs in DMCreateSection_Plex()
Plex+TS: FIxed DMPlexTSCheckFromOptions()
Plex: Changed the signature of pointwise input functions - Now the spatial dimension and number of fields is passed in
Plex: Fixed bugs with DMPlexCreateSection() - F90 declaration - Do not constrain more than the dog
DM: Can view the global section using -global_section_view
Plex: Now DMPlexCreateSection() also takes the constrained components
Plex: Now BC take constrained field components as well - Changed DMPlexAdd/GetBoundary() - Can use -bc_<name>_comp <nums> to override
Plex: Now -dm_plex_separate_marker works correctly in DMPlexCreateSquareBoundary()
DMLabel: Added DMLabelInsertIS()
SNES: Added DMSNESCheckFromOptions() - Should simplify examples

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DM: Allow the default section to be set to NULL

Merge branch 'master' into tisaac/dmforest

directory layout changed again: merging to switching branches back and forth
doesn't cause reconfigure to have a hard time

* master: (357 commits)
remov

Merge branch 'master' into tisaac/dmforest

directory layout changed again: merging to switching branches back and forth
doesn't cause reconfigure to have a hard time

* master: (357 commits)
removed nonexistent ex46f from makefile test rule
Revert "fixed bad merge into master"
fixed bad merge into master
fix memory leak in mkl_pardiso fix some formatting in mkl_pardiso code
mv runex111 from TESTEXAMPLES_C to TESTEXAMPLES_DATAFILESPATH
Mat+Doc: More Fortran docs
Bib: Added TetGen cite
parmetis: make sure 'ldd libparmetis.so' points to the correct libmetis.so that its linked with.
small fix as reported by the nightly test
add a test for MatPtAP()
small cleanup; add tests
cleanup MatPtAPSymbolic_MPIAIJ_MPIAIJ()
Fix nonzerostate tracking in all MATMPI types.
update location of test matrices in faq.html file
unused variable still declared
Fix for MatLoad_MPIDense() from sparsely stored matrix also fix for MatLoad_MPIDense_DenseInFile() when matrix has not had its local sizes preset by user
Preserve the B nonzerostate during disassembly.
TSEvent: Fix arch-mswin nightly errors due to declaring variables in the middle of a function.
Fix error in parallel loading of dense format matrix
removed KSPSetNullSpace() since mat already carries that information and having two locations for it is confusing, unnecessary and prone to error added MatSetTransposeNullSpace() for providing the null space of the transpose of the matrix and added support in KSPSolve() to remove this null space from the right handside of the linear system thus making the system consistent.
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