DMPlex: propagate coordinate localization

DMLocalizeCoordinates(): check if already localized

DM: Added some top-level DM content to DMConvert()

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

DM: DMClone() copies setupcalled state

DM: Should not clone a DM which is not setup

DMComputeL2FieldDiff(): fixes, DMP4EST implementation

DM: added DMComputeL2FieldDiff() from DMPlex.

Merge branch 'master' into tisaac/dmforest

* master: (136 commits)
Make error message specific to exactly what matrix is supported
Prevent fblaslapack or f2cblaslapack from being compiled with t

Merge branch 'master' into tisaac/dmforest

* master: (136 commits)
Make error message specific to exactly what matrix is supported
Prevent fblaslapack or f2cblaslapack from being compiled with the -no-prec-dev Intel compiler option since it can produce incorrect results
Fix for PCReset_HYPRE to make it reentrant.
replace default superlu_dist '-mat_superlu_dist_colperm METIS_AT_PLUS_A' with MMD_ATA to avoid different random numbers for nightly tests
fixes for merge from maint patch
Added PCReset_HYPRE() so it may be used with SNESVI solvers
remove Microsoft compiler message for paste macros used for handling Blas/Lapack macro name mangling for example
Increase the number of PetscViewerPushFormat() possible to 25 and use a macro PETSCVIEWERFORMATPUSHESMAX for the value
Configure: Remove redundant logging
Bib: Added ref
nightlybuids: fix permissions of script
MatRegisterDestroy() does not exist but it is listed in manual pages
externalpackages-git: save local changes if any - in git stash - before 'git checkout -f' Useful incase --with-package-commit=HEAD option was msissing [perhaps due to a typo]
nightlybuilds: add xsdk builds
Add architectures for testing xsdk package downloads (Trilinos, Hypre, SuperLU)
create another version of TurnForward() for adaptive time stepping specifically
Configure: Give proper default if HOME is missing from the environment
fix abbreviation
allow zeropivot for MatSOR_SeqAIJ_Inode, node size=1
add test case using adpative time stepping for checkpointing type 'NONE'
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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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DM: make DMDestroyLabelLinkList() for internal usage

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 'knepley/fix-dm-clone-coord-section'

* knepley/fix-dm-clone-coord-section:
DM: When cloning, need to propagate the coordinate DM section

DM: When cloning, need to propagate the coordinate DM section

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: Do not automatically create a default section if no fields are defined

Merge branch 'master' into knepley/feature-plex-jacp

* master:
DM: Clone the coordinate DM instead of reusing in Clone()
DM: Clone() should also copy the coordinate DM
Plex: Fixed complex inte

Merge branch 'master' into knepley/feature-plex-jacp

* master:
DM: Clone the coordinate DM instead of reusing in Clone()
DM: Clone() should also copy the coordinate DM
Plex: Fixed complex interpolation problem
Plex: Fixed bug with general interpolation - Was not setting coarse coordinates properly
Plex: Added diagnostic code to interpolation
Plex: Allow the user to override the regular refinement flag

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Merge branch 'knepley/fix-dm-clone-coordinates'

* knepley/fix-dm-clone-coordinates:
DM: Clone the coordinate DM instead of reusing in Clone()
DM: Clone() should also copy the coordinate DM

Merge branch 'master' into hongzh/checkpointing

Manual merges for a couple of PetscOptions changes in master

DM: Clone the coordinate DM instead of reusing in Clone()

DM: Clone() should also copy the coordinate DM