Merged in dalcinl/fix-tsrollback (pull request #456)

TS: Refactor TSStep() and TSRollBack()

TS: Remove TSSetRetainStages()

TS: Add typedef TSForcingFunction

Merged in dalcinl/fix-ts-declarations (pull request #450)

TS: Fix function declarations and visibility

TS: Fix function declarations and visibility

* Most of these fixes where spotted by GCC -Wmissing-declarations

Merged in dalcinl/fix-tsadapt (pull request #441)

TSAdapt and related improvements

TSAdapt: Add TSAdaptBasic{Set|Get}Clip()

TS: Add TSEvaluateWLTE()

Merge branch 'tisaac/sf-fix-multi-sf-leaves' into tisaac/dmp4est-feature-injection

* tisaac/sf-fix-multi-sf-leaves: (174 commits)
PetscSF: fix PetscSFGetMultiSF() for sparse leaves
PetscSF: make

Merge branch 'tisaac/sf-fix-multi-sf-leaves' into tisaac/dmp4est-feature-injection

* tisaac/sf-fix-multi-sf-leaves: (174 commits)
PetscSF: fix PetscSFGetMultiSF() for sparse leaves
PetscSF: make regression test that fails
few more clang static analyzer fixes
many issues detected by clang static analyzer
Update hypre to its release version
Updates for xSDKTrilinos builds
Added --download-xsdktrilinos
Communicator passed to VecCreateSeq should be PETSC_COMM_SELF
PCMG man page: fix typo in options name
Bib: Added refs
DMLabel: Removed unused variable
Metis tries to use backtrace which requires -lexecinfo on some systems such as freebsd Remove -lexecinfo from freebsd configure files since it is only needed by metis
add alternative output that occurs on some systems due to use of random number generator in partitioner
Plex: When creating cohesive submeshes, fix memory leak
Plex ex11: Updated output for new distribution algorithm
Plex: When explicitly distributing the depth label, we must recreate empty strata
Plex: When partitioning, the cell numbering should include hybrid points
Plex: Allow cell and vertex numberings to include hybrid points
need to show diffs of ex22 if it fails
Support two different output for test example, since due to roundoff this example can produce slightly different convergence history
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Merge branch 'master' of https://bitbucket.org/petsc/petsc

Merge branch 'barry/monitor-fromoptions'

Merged in dalcinl/update-ts-alpha (pull request #437)

Refactor TSEvent and update TSALPHA

TSALPHA: Update implementation

* Support for event detection.
* Support for time adaptivity based on approximating the local truncation
error using backward difference formulas.
* Use an step-halv

TSALPHA: Update implementation

* Support for event detection.
* Support for time adaptivity based on approximating the local truncation
error using backward difference formulas.
* Use an step-halving approach in the initial step to compute a consistent
initial state as well as approximating the local truncation error.

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TSAdapt: Minor additional cleanups (mostly coding conventions)

TSEvent: Rename TSSetEventMonitor() -> TSSetEventHandler()

TSEvent: Various fixes and cleanups

* Rename most of TSEventMonitorXXX() to TSEvent[Handler]XXX
* Rename the private TSEvent structure as well as some slots within it

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Finished converting the XXXMonitorSetFromOptions() to use PetscViewerAndFormat object

Time: .5 hours

Merge branch 'hongzh/update-ts-trajectory'

updated TS and TSAdjoint MonitorSetFromOptions() to use PetscViewerAndFormat
to prevent excessive pushes to PetscViewer

Time: .5 hours

create tstrajectory_type visiaulzation

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax error with error message
SNES ex5: Correct Jacobian handling on patches
SNES ex5: Stupid complex fixes
DMP4est: fix transfer of labels to parents
petsc4py: update to latest snapshot. Fixes da example breakage in petsc4py test suite
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logging in interpolator creation
Plex: Correct use of tabs in ASCII viewer
DM: Shorten long event name
Plex ex12: Create boundary label automatically at all levels of mesh hierarchy
Plex ex12: Change PetscViewerSetFormat --> PetscViewerPushFormat - Fix order of SetMode and SetFilename
Plex ex12: Change all functions to static
Since DMDA with periodic boundary conditions does support P0 interpolation remove checks that error out under those conditions
ascem-io.py and amanzi.py need to handle self.hdf5.include being None correctly
fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests also fix check for location of python shared library on mac to check all cases each time
Switch back to Sherry's version since she accepted by pull request
PetscDraw: Update help messages for -draw_save* options
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Conflicts:
src/dm/impls/plex/plexfem.c

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Merged petsc/petsc into master

Merge branch 'mlange/fix-plex-multi-level-overlap'

* mlange/fix-plex-multi-level-overlap: (259 commits)
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelG

Merge branch 'mlange/fix-plex-multi-level-overlap'

* mlange/fix-plex-multi-level-overlap: (259 commits)
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelGather()
Plex ex12: Fixed variable initialization and some output
Plex ex11: Added error checking
Plex ex14: Now boundary label does not have cells
Plex ex1: Now boundary label does not have cells
Plex ex1: Fix for VTK format
added some debugging code, getting ready to branch
added some print statements, should be an -info...
smome cleaning up
restructured ex11 to allow for problem specific BCs
DMPlex: Update test ex12_5 with correct level-2 overlap
DMPlex: Use global processSF in DMPlexPartitionInvert
DMPlex: Add remote leaf contributions to roots in DMLabelPropagate
DMPlex: Add DMLabelGather to migrate label values from leafs to roots
DMPlex: Refactor DMLabelDistribute to separate point stratum distribution
DMPlex: Add propagation of remote point donations for multi-level overlap
DMPlex: Fix DMLabelDistribute for all-to-all migrations
Plex: make extern exactly match prototype: semantic match is not enough.
DMP4est: typo fix
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Merge branch 'tisaac/dmforest' into mlange/fix-plex-multi-level-overlap