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

Plex+SNES: Must assembly Jac and JacP

SNES+Plex: Do not calculate BdResidual/BdJacobian for FV

Plex: Convert dmAux to plex in DMPlexComputeJacobian_Internal()

DM+SNES/TS: Fixed caching of Plex

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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Plex+FVM: correct counting of fluxes

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

SNES+Plex: added DMPlexSetSNESLocalFEM()

Plex+SNES: remote Dirichlet bcs from residual when printing

Even though we're handling Dirichlet BC's in DMLocalToGlobal, for
debugging purposes it's helpful to display local residuals without the
v

Plex+SNES: remote Dirichlet bcs from residual when printing

Even though we're handling Dirichlet BC's in DMLocalToGlobal, for
debugging purposes it's helpful to display local residuals without the
values that will be removed.

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Plex+SNES:always use ADD_ALL_VALUES when summing FEM element matrices

The problem is that a dof being constrained no long means just a bc dof:
it could also mean a hanging constraint. In that case t

Plex+SNES:always use ADD_ALL_VALUES when summing FEM element matrices

The problem is that a dof being constrained no long means just a bc dof:
it could also mean a hanging constraint. In that case that dof's
contribution can't be treated as just zero: it must be summed (via the
hanging constraint) into the residual. The stripping of dirichlet
constraints is handled by DMLocalToGlobal().

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Plex: try to handle boundary conditions early

SNES+Plex: Added dynamic Jacobian, dF/du_t, to assembly

added a todo note for something to fix eventually

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

DMP4est/DMPlex: Share DMSNES/DMTS information when converting

This includes "A", "dmAux" and "dmCh" for now.

DMComputeL2FieldDiff(): fixes, DMP4EST implementation

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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Merge branch 'master' into tisaac/dmforest

* master: (177 commits)
DT ex3: The test should check the number of digits requested
DT ex3: One test fails in single precision
Plex: Do not automati

Merge branch 'master' into tisaac/dmforest

* master: (177 commits)
DT ex3: The test should check the number of digits requested
DT ex3: One test fails in single precision
Plex: Do not automatically create a default section if no fields are defined
Plex: DMPlexCopyCoordinates() needs to create the coordinate section if it is missing
superlu: no longer requires xerbla slamch dlamch ?
superlu: update to v5.1
skip MatSolve() if matrix factorization fails
replacing SETERRQ with error output info and continue execution
SNES ex12: Added parallel tests - These test parallel, unstructured interpolation/restriction using FAS
Plex+SNES: Now in DMPlexComputeJacobian_Internal(), we also form the Jacobian preconditioner matrix
FE: Now we can form either the Jacobian or the Jacobian preconditioned matrix using a flag
DS: Now have point wise function slots for the Jacobian preconditioned matrix - This will allow us to form the "right" operator for preconditioning, like M in the (2,2) block for Stokes
Plex: When swapping Plexes, also swap point SF
Plex: Fix parallel error in Injector
Mat+Plex: Added MatPreallocator which can be called with MatSetValues() and preallocates another Mat - This could have been another "mode" of Mat, but I thought this was cleaner - Use MatPreallocator to preallocator Plex interpolators
DT ex3: Change tolerance and eliminate tests which need MPFR from regular runs
superlu: fix complex build
superlu: update to using 5.0 tarball with the fix for -Werror=format-security
superlu: update to use tarball with -Werror=format-security fix
DM: Clone the coordinate DM instead of reusing in Clone()
...

Conflicts:
config/builder.py
src/dm/impls/plex/plexcreate.c

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Merge branch 'knepley/feature-plex-jacp'

* knepley/feature-plex-jacp:
Plex: Do not automatically create a default section if no fields are defined
Plex: DMPlexCopyCoordinates() needs to create t

Merge branch 'knepley/feature-plex-jacp'

* knepley/feature-plex-jacp:
Plex: Do not automatically create a default section if no fields are defined
Plex: DMPlexCopyCoordinates() needs to create the coordinate section if it is missing
SNES ex12: Added parallel tests - These test parallel, unstructured interpolation/restriction using FAS
Plex+SNES: Now in DMPlexComputeJacobian_Internal(), we also form the Jacobian preconditioner matrix
FE: Now we can form either the Jacobian or the Jacobian preconditioned matrix using a flag
DS: Now have point wise function slots for the Jacobian preconditioned matrix - This will allow us to form the "right" operator for preconditioning, like M in the (2,2) block for Stokes
Plex: When swapping Plexes, also swap point SF
Plex: Fix parallel error in Injector
Mat+Plex: Added MatPreallocator which can be called with MatSetValues() and preallocates another Mat - This could have been another "mode" of Mat, but I thought this was cleaner - Use MatPreallocator to preallocator Plex interpolators

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Plex+SNES: Now in DMPlexComputeJacobian_Internal(), we also form the Jacobian preconditioner matrix

Merge branch 'master' into hongzh/checkpointing

Manual merges for a couple of PetscOptions changes in master

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