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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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

Plex: If user function fails, put back array

Plex: Update ex12_5 with correct level-2 overlap

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

Plex ex4, ex5, ex13, ex17: Fixed test partitions

Plex ex11: Fix Label usage

Plex ex12: Fixed variable initialization and some output

Merge remote-tracking branch 'origin/knepley/fix-plex-test-partitions' into tisaac/dmforest

* origin/knepley/fix-plex-test-partitions: (151 commits)
Plex ex5: Provide test partitions
Plex ex4: P

Merge remote-tracking branch 'origin/knepley/fix-plex-test-partitions' into tisaac/dmforest

* origin/knepley/fix-plex-test-partitions: (151 commits)
Plex ex5: Provide test partitions
Plex ex4: Provide test partitions
Configure: I really hate exceptions - We should rewrite this to eliminate all exceptions in favor of return codes
Configure: I hate exceptions
fix typo for 'runex19_superlu_dist_2'
Fix for freeing just what needs to be free when SuperLU_Dist factorizations reused
Updated to latest hypre pre-release with fixes for handling blas/lapack libraries
Switch back to petsc fork of SuperLU_Dist that turns of use of findMPI
PCFactorSetUpMatSolverPackage() should not crash but instead produce a useful error message if called before it is in the proper state.
Clarify that SNESGetLinearSolveIterations() does not include failed iterations.
User reported issues with downloading boost using the previous URL but not this one
Configure: Small change to log order
MatFDColoringSetUp_MPIXAIJ: fix broken initialization of colmap
Bib: Missing comma
add support for binary viewer for -ts_monitor that records time at each timestep
superlu_dist: set MPI_C_COMPILER etc options - so that superlu_dist cmake does not look for a different/incompatible mpi compiler. [and its CFLAGS].
remove reference to VecGetValuesBlocked() and VecGetValuesLocal() from manual page since they do not exist.
Stop configure if user builds with threadsafety and debugging on
Added configure option --with-viewfromoptions=0 which will speed up code with many small solves substantially
Only generate list of all PetscFunctionLists generated in debug mode since in some circumstances where many objects are created searching this list is very slow.
...

Conflicts:
src/ts/examples/tutorials/ex11.c

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Plex ex11: Added error checking

Plex ex5: Provide test partitions

Plex ex4: Provide test partitions

Plex ex14: Now boundary label does not have cells

Plex ex1: Now boundary label does not have cells

Plex ex1: Fix for VTK format

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: Update test ex12_5 with correct level-2 overlap

Level-2 overlap in a 2x2 square with 8 ranks should span the entire mesh
(9 vertices) for all but the two corner partitions, which only get
8

DMPlex: Update test ex12_5 with correct level-2 overlap

Level-2 overlap in a 2x2 square with 8 ranks should span the entire mesh
(9 vertices) for all but the two corner partitions, which only get
8 vertices.

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DMPlex: Use global processSF in DMPlexPartitionInvert

This ensures that even unconnected remote connections are migrated
during the inversion.

DMPlex: Add remote leaf contributions to roots in DMLabelPropagate

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.

Plex: make extern exactly match prototype: semantic match is not enough.

From the C++ standard (N3793:13.1/3 [over.load]):

Parameter declarations that differ only in a poitner * versus an
a

Plex: make extern exactly match prototype: semantic match is not enough.

From the C++ standard (N3793:13.1/3 [over.load]):

Parameter declarations that differ only in a poitner * versus an
array[] are equivalent. That is, the array declaration is adjusted
to become a pointer declaration (8.3.5).

Microsoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooft.

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Plex: fix typo in DMPlexComputeInterpolatorTree()

Plex: add and remove cells before inserting boundary values

Bound to be inefficient, but keeps cells from polluting refinements of
the label in refined meshes.

Plex: added DMPlexLabelClearCells()