Merge branch 'tisaac/dmforest' of bitbucket.org:petsc/petsc into tisaac/dmforest

Plex+TS: Added DMPlexTSComputeBoundaryFEM()
- Just calls DMPlexInsertBoundaryValues()

TS+Plex: added boundary routines for DMTSLocal, and PlexFEM/FVM implementations

SNES+Plex: added DMPlexSetSNESLocalFEM()

Plex: try to handle boundary conditions early

TS+Plex: Added IJacobian assembly functions

DM: Promote DMPlexLocalizeCoordinates --> DMLocalize coordinates
- There is one small problem here in that the iteration still needs Plex-like things. This will be rewritten to use a projection rathe

DM: Promote DMPlexLocalizeCoordinates --> DMLocalize coordinates
- There is one small problem here in that the iteration still needs Plex-like things. This will be rewritten to use a projection rather than Plex, but right now we need it for the magma presentation.

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Merge branch 'master' into barry/add-pcreset-hypre-for-master

Needed to move PCDestroy_HYPRE() added to master to PCReset_HYPRE() since that was introduced
as a bug fix for maint

Merge remote-tracking branch 'origin/tisaac/dm-label-promote'

* origin/tisaac/dm-label-promote:
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part of all

Merge remote-tracking branch 'origin/tisaac/dm-label-promote'

* origin/tisaac/dm-label-promote:
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part of all DMs
builder: update regression tests
builder: update some missing package requirements
DM: set coordinate vector name
ts tutorials ex11_sa: make it compile

Conflicts:
src/dm/impls/plex/plexcreate.c

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Plex: Fixed DMPlexProjectField()

Merge branch 'master' into hongzh/checkpointing

Manual merges for a couple of PetscOptions changes in master

Fix bad function rename and missed rename related to DMProject routines

DM: added DMComputeL2GradientDiff() for Plex and DA

Merge remote-tracking branch 'origin/knepley/feature-plex-add-time' into tisaac/dmforest

Both branches changeds DM projection behavior, so I wanted to sort it
out before merging

* origin/knepley/fe

Merge remote-tracking branch 'origin/knepley/feature-plex-add-time' into tisaac/dmforest

Both branches changeds DM projection behavior, so I wanted to sort it
out before merging

* origin/knepley/feature-plex-add-time: (59 commits)
SNES ex69: Updated to new function API, fixed test output
SNES ex75: Fixed for new function API
add fortran stub for TSMonitorLGSetTransform() and fix TSMonitorLG for multiple fields but no names provided for fields
add -binary_write_double so __float128 precision can save as double to binary files
TSClone() did not clone Fortran function pointers hence some TS methods would fail if functions provided in Fortan
petsc4py: update to snapshot with 'barry/petscoptions-object' changes
fix bad merge that introduced 2 copies of the MPI_Comm_free()
update example to use MAT_INPLACE_MATRIX, not REUSE
incorrect addition of float to PetscInt
update for new PetscOptions API
TS ex18: Fixed function API and test output
Function now takes PetscOptions as first argument, this was missed during the first round of updates
bugfix for MatSetOption_Elemental()
fix test example no change output that was missing a line
fixes for new PetscOptions.. API that are needed based on problems with nightly build
Plex ex3: Use new function API
SNES ex62: Use new function API
SNES ex12: Use new function API
Plex: Fixed unused options in examples
Plex+DMDA: Add time to signatures
...

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Merge branch 'master' into pr391/zianekhodja/lilia/tsirm/master

DM: move DMProjectFuncton() up from DMPlex

DM: DMBoundary is now in DM, not in DMPlex

All DMBoundary routines depend only on DMLabel, not on the DAG, so
there's nothing to prevent it being used in other DMs.

Merge branch 'knepley/feature-plex-add-time'

* knepley/feature-plex-add-time:
SNES ex69: Updated to new function API, fixed test output
SNES ex75: Fixed for new function API
TS ex18: Fixed fun

Merge branch 'knepley/feature-plex-add-time'

* knepley/feature-plex-add-time:
SNES ex69: Updated to new function API, fixed test output
SNES ex75: Fixed for new function API
TS ex18: Fixed function API and test output
Plex ex3: Use new function API
SNES ex62: Use new function API
SNES ex12: Use new function API
Plex: Fixed unused options in examples
Plex+DMDA: Add time to signatures
Plex+SNES+TS: Changed all of the callback function to take time as an argument

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DM: move Get/SetCoarseDM from DMPlex into DM

Merge branch 'tisaac/dm-label-promote' into tisaac/dmforest

* tisaac/dm-label-promote: (319 commits)
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part o

Merge branch 'tisaac/dm-label-promote' into tisaac/dmforest

* tisaac/dm-label-promote: (319 commits)
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part of all DMs
builder: update regression tests
builder: update some missing package requirements
DM: set coordinate vector name
ts tutorials ex11_sa: make it compile
mark variable as unused so compiler doesn't warn about unused value
configure: use 'git cat-file -e' to check for existance of a commit in localrepo. ['git rev-parse' does not give error for a hash thats not in repo]
petsc4py: revert to manually syncing petsc4py with petsc master changes
configure: revert gitcommit default value to Null. If a pacakge using giturl does not change this value - raise an error
fix: revert change in a44bcdf that breaks with pgf90
update test output for fixed to hypre interface that now actually pass the interp vectors to BoomerAMG
Error message should say use negative threshold value to prevent filtering out zeros
Calls to HYPRE_BoomerAMGSetInterpVectors() did not actually copy the vector data pointer from the PETSc vector to the hypre vector thus resulting in the hypre interp vectors being identically zero and hence not affecting the quality of the AMG hierarchy produced/
DMPlex: Silence overzealous compiler warnings
add row/col orientation to MatConvert_Elemental_Dense
fix formatting error in previous commit [broke nightlybuilds]
fix formating of TSTHETA manual page and add missing command line option
run hwloc with MPIEXEC and binding so it runs on the correct machine
fix: memory leaks [in valgrind test]
...

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DM: make DMLabel labels a part of all DMs

Most DMLabel routines do not depend on the internals of DMPlex, and I
want to reuse them in other DM types

DM: puth depthLabel in DM

I know that this is s

DM: make DMLabel labels a part of all DMs

Most DMLabel routines do not depend on the internals of DMPlex, and I
want to reuse them in other DM types

DM: puth depthLabel in DM

I know that this is something that's only used by plex, but I'm not sure
how else to do this.

DM: move MarkBoundaryFaces back to plex

DM: add reference counting to label linked list for cloning purposes

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Plex+SNES+TS: Changed all of the callback function to take time as an argument

Merge branch 'master' into barry-allow-vecset-nan-3.6

Merge branch 'master' into shri/add-tsevent-to-powergrid-examples

Merge branch 'master' into pr263/PierreBdR/ts-domain-error-in-stage/master