Look for hwloc by default before downloading
Allows turning off whloc with the usual --with-hwloc=0
search for hwloc in some standard locations
hwloc.py should look first in '' instead of /usr/include so that
/usr/include doesn't get listed when it is not needed.
Sowing now first looks in --with-sowing-dir before other locations and building
hwloc.py needs to depend on MPI because OpenMPI installs hwloc
hwloc may depend on xml libs
upgraded to latest hwloc for download
turn off xml support for hwloc to reduce surface area of library
turn off external use of hwloc for OpenMPI to reduce possibility of PETSc and OpenMPI using different versions
Merge branch 'barry/reuse-hwloc' of bitbucket.org:petsc/petsc into barry/reuse-hwloc
bjacobi: fix incorrect read access of vecs.
This breakage caused runex43_bjacobi in src/ksp/ksp/examples/tutorials
to not converge (and take forever  to run in nightlybuilds)
hwloc: disable for pgf90 build (as -lnuma from PGI conflicts with system version)

/usr/lib/x86_64-linux-gnu/libhwloc.so: undefined reference to `set_mempolicy@libnuma_1.1'
fixed documentation for PetscOptionsXXX that refered to "default value" when they really mean current value
also fixed usage of PetscOptionsEnum() with regards to current value in several calls

Reported-by: Ed Bueler <elbueler@alaska.edu>
Revert "hwloc.py needs to depend on MPI because OpenMPI installs hwloc"

This reverts commit d8bf25455e53b5300e6dc4f62706aca8a3bdec97.

[but keep common chane with 2e08fceb9f9f13c54279c60d4bddc5f1cf115655 ]
cleanup of use of PetscOptionsInt and friends including use of flag final argument
SNES ex12: Fix refinement usage
SNES ex12: Fix SetFromOptions usage
Merge branch 'master' into knepley/fix-plex-examples-refinement

* master: (62 commits)
  Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would mean a ton of infrastructure I think
  Plex ex12: Fix output after label distribution fix
  Plex: Only call SetFromOptions() after Distribute, since we cannot avoid it
  TS ex11: Since DMPlexDistribute() calls SetFromOptions(), do not call it again, and cleaned up tests
  Plex+FV: If using FVM adjacency, do not create ghost cells for faces in the overlap, or set BC on them
  Plex: If using FVM adjacency, we must include the closure in the overlap
  Plex+Label: All processes with a valid label should participate in label distribution - Formerly it was just  proc 0
  Plex: Add check that parallel renumbering fully covers the cone points
  Plex: For one level adjacency, include the point itself since this makes sense when looking in parallel from the overlap
  Plex: Cannot Malloc2() the arrays passed to PetscSFSetGraph()
  Plex: Preallocation fixes for indegree > 1 - Again this should be rewritten
  SNES ex62: Changes to output for fixes with quads
  Plex+Label: Set default output flag to PETSC_TRUE
  Plex ex1: Fixed LaTeX output
  Plex ex12: Fixed overlap test
  Plex: Fixed incorrect usage of PetscSFGatherBegin/End() in preallocation - This should be rewritten using new style
  PetscSF: Incorrect check for computed degrees
  Builder: Fix bad search and replace
  Configure: Fix for Barry's change to organization - I do not know what happened here
  Builder: Fix for Barry's change
  ...

Conflicts:
	src/snes/examples/tutorials/ex12.c
Plex: Restore Fortran binding for DMPlexDistribute()
Plex ex12: Add test output
update use of PetscOptionsBool() to not rely on default setting automatically