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

Read mesh boundary tags if provided

interface changed in petscdmplex.h for DMPlexAdapt

Add mesh adaptation for DMPlex

Adding a new file src/dm/impls/plex/plexadapt.c, which contains a new
function that calls the adaptation library (pragmatic):
PetscErrorCode DMPlexAdapt(DM, Vec, DM *)

Add mesh adaptation for DMPlex

Adding a new file src/dm/impls/plex/plexadapt.c, which contains a new
function that calls the adaptation library (pragmatic):
PetscErrorCode DMPlexAdapt(DM, Vec, DM *);
which is exposed in the interface in petscdmplex.h

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Plex+SNES: Added DMPlexSNESComputeJacobianActionFEM()
- And an internal version

Plex: Added DMPlexCreateFromCellListParallel()
- This directly creates a parallel mesh from pieces

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

Merge branch 'tisaac/dmp4est-feature-injection'

* tisaac/dmp4est-feature-injection: (27 commits)
DMP4est: linear solve regression tests
DMP4est: regression tests for exact interpolation/injectio

Merge branch 'tisaac/dmp4est-feature-injection'

* tisaac/dmp4est-feature-injection: (27 commits)
DMP4est: linear solve regression tests
DMP4est: regression tests for exact interpolation/injection
PetscDualSpace: create height subspaces at setup.
DMClone(): get agreement on cloning coordinates
DMP4est: bump number of procs in regression test
DMP4est: fix memory leaks
DMP4est: added diagnostic views
DMP4est: adding regression tests
SNES tutorials ex12: added RUN_EXACT, solve from exact solution
DMPlex: memory clean up in Injector/InterpolatorTree routines
DMP4est: use DMCoarsen_Forest
DMPlexComputerInterpolatorTree(): restore another work array
DMPlexAnchorsModifyMat(): restore work arrays
DMPlexComputeInjectorTree(): fix local / off-process bounds
DMPlexComputeInjectorTree(): more fixes
DMPlexComputeInjectorTree(): fix coarse/fine char mixup
DMPlexComputeInjectorTree() compiles
WIP: DMPlexComputeInjectorTree()
Plex tests ex3: added regression tests for injectors
DMPlex tests ex3: fix viewing, creating injectors
...

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dmplex: fix clang compiler warnings [incorrect usage of const]

DMPlex: added DMPlexComputeInjectorReferenceTree() to header for testing

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

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

dmplex: fix clang compiler warnings [incorrect usage of const]

Merge remote-tracking branch 'origin/knepley/fix-plex-hdf5-label' into tisaac/dmforest

* origin/knepley/fix-plex-hdf5-label: (50 commits)
Plex: Fixed HDF5 output for DMLabel - The ISAllGather() wa

Merge remote-tracking branch 'origin/knepley/fix-plex-hdf5-label' into tisaac/dmforest

* origin/knepley/fix-plex-hdf5-label: (50 commits)
Plex: Fixed HDF5 output for DMLabel - The ISAllGather() was being called with an IS that had COMM_SELF - Also, we needed to protect for empty index arrays
superlu_dist: install target should first make sure prefix/[include,lib] dirs exist - similar to superlu
dm: add DMRemoveLabel() fortran interface
nightlybuilds: allocate more time to run arch-linux-xsdk-dbg build...
Remove superfluous information messages
Cannot have rank 1 print before parallel print since it may end up before or after the print from process 0. There change to have rank 0 print the sequential matrix
Bib: Added ref
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelGather()
mpiuni: check for "long_long" before checking for "__int64" [as "typedef __int64" gives error with icc] Note: cannot use 'int64_t' as 'typedef unsigned int64_t foo' gives eror with icc
Add filter for solaris linker scope warning to master since that is used in nightly tests of next
Previous commit did not correctly handle downloading from --with-packages-dir
Use special error code of 10 for output list of needed downloaded package tarballs otherwise the outer configure.py script converts the error code to an error message we do not want.
Have ./configure return a nonzero exit code when --with-packages-dir detects missing packages so that calling scripts know this is occurred simplify some code
Completed support for --with-packages-dir=directory that allows --download-xxx features to be cleanly used behind firewalls etc also updated to docs to indicate this new feature
Adding supporting for --download-xxx to reported needed downloads when off line or behind a firewall and using local copies when available with the --with-packages-dir=directory option
Fix typos in linesearch impls:armijo, morethuente, owarmijo.
PetscDraw: Explicitly save draw in KSP/SNES/TS monitors
PetscViewerDraw: Propagate prefix from viewer to draw contexts
PetscDraw: Explicitly save draw in {Vec|Mat|DMDA}View() routines
...

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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

DMPlex: Add propagation of remote point donations for multi-level overlap

This is currently restricted to root-to-leaf propagation of remote
point connections between non-neighbouring partitions.

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

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

Plex: added DMPlexLabelClearCells()

WIP: DMPlexCreateInterpolatorTree()

WIP: DMPlexComputeInterpolatorTree()

Plex+TS: Condensing to one BC function

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

# By Toby Isaac (6) and Mark Adams (2)
# Via Mark Adams
* 'tisaac/dmforest' of bitbucket.org:petsc/petsc:
removed d

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

# By Toby Isaac (6) and Mark Adams (2)
# Via Mark Adams
* 'tisaac/dmforest' of bitbucket.org:petsc/petsc:
removed debugging print
DMP4est: regression test for ex11
Plex: correct memory management in DMProjectFunctionLocal_Plex()
Plex+FVM: correct counting of fluxes
trying to fix a BC bug
TS+Plex: provied face geometry for essential bcs
TS+Plex: added boundary routines for DMTSLocal, and PlexFEM/FVM implementations
SNES+Plex: added DMPlexSetSNESLocalFEM()

Conflicts:
include/petscdmplex.h
src/snes/examples/tutorials/ex62.c
src/ts/utils/dmlocalts.c
src/ts/utils/dmplexts.c

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