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
...

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

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Merged petsc/petsc into master

More work on complete DMSHELL example that wraps a DMDA1d. It crashes in valgrind with
==80209== Invalid read of size 8
==80209== at 0x100A9E2D5: DMCountNonCyclicReferences (dm.c:500)
==80209==

More work on complete DMSHELL example that wraps a DMDA1d. It crashes in valgrind with
==80209== Invalid read of size 8
==80209== at 0x100A9E2D5: DMCountNonCyclicReferences (dm.c:500)
==80209== by 0x100A8F70A: DMDestroy (dm.c:573)
==80209== by 0x101221BBE: KSPDestroy (itfunc.c:985)
==80209== by 0x1010BCBFC: PCDestroy_MG (mg.c:302)
==80209== by 0x1010E23F7: PCDestroy (precon.c:122)
==80209== by 0x101221C3A: KSPDestroy (itfunc.c:986)
==80209== by 0x100001C4C: main (in ./ex65)
==80209== Address 0x10398fd68 is 5,864 bytes inside a block of size 6,196 free'd
==80209== at 0x10001595D: free (vg_replace_malloc.c:480)
==80209== by 0x1000FE393: PetscFreeAlign (mal.c:72)
==80209== by 0x100100D1E: PetscTrFreeDefault (mtr.c:315)
==80209== by 0x100A91C5A: DMDestroy (dm.c:716)
==80209== by 0x1010E2478: PCDestroy (precon.c:123)
==80209== by 0x101221C3A: KSPDestroy (itfunc.c:986)
==80209== by 0x1010BCBFC: PCDestroy_MG (mg.c:302)
==80209== by 0x1010E23F7: PCDestroy (precon.c:122)
==80209== by 0x101221C3A: KSPDestroy (itfunc.c:986)
==80209== by 0x100001C4C: main (in ./ex65)

I am reporting to Toby who wrote that code because it is difficult for me to figure how to debug

Time: 3 hours

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Added DMShellSetRestriction() and ability of PCMG to use DMCreateRestriction()

Time: .2 hours
Reported-by: anton <popov@uni-mainz.de>

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 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/imp

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c

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Merge branch 'tisaac/dmforest' into mlange/fix-plex-multi-level-overlap

Conflicts:
src/dm/impls/plex/examples/tests/output/ex12_5.out
src/dm/label/dmlabel.c

Merge branch 'master' into barry/add-pcfieldsplit-logevent

DM: added DMClearLocalVectors()

DM: Added query functions for named vectors

DMPlex: propagate coordinate localization

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

DMComputeL2FieldDiff(): fixes, DMP4EST implementation

DM: added DMComputeL2FieldDiff() from DMPlex.

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

DM: create DMProjectField() from DMPlexProjectField()

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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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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DM: add DMComputeL2Diff()

Lifted from DMPlex

DM: typo fix

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.

DM: add DMGet/SetFineDM

This requires the introduction of some cycle-detection when destroying a
DM.

DM: refine NonCyclicReferenceCounting

Only recurse in the event of a doubly-linked list. This

DM: add DMGet/SetFineDM

This requires the introduction of some cycle-detection when destroying a
DM.

DM: refine NonCyclicReferenceCounting

Only recurse in the event of a doubly-linked list. This is to let the
swapping that is used to create a DMPlex hierarchy keep working
unaffected.

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