fun3d: fix c89 warning
Merge branch 'jed/matmatmult-sort'

New version provides in the neighborhood of 20% speedup for MatMatMult
as used in PCGAMG.

* jed/matmatmult-sort:
  MatMatMultSymbolic_SeqAIJ_SeqAIJ: switch to "sort" version as default
  segbuffer: g++ does not like casting int*restrict* to void*, void** okay
  MatMatMult_SeqAIJ_SeqAIJ_Sort: new implementation using char flags and sorting
  segbuffer: add PetscSegBufferGetInts() to encourage use of PETSC_RESTRICT
  segbuffer: create wrapper structure
  segbuffer: add PetscSegBufferGetSize() and PetscSegBufferUnuse()
  segbuffer: fix bug in which seg->used was not reset
Merge branch 'jed/fix-optionsinsertfile-large'

* jed/fix-optionsinsertfile-large:
  PetscOptionsInsertFile: fix overflow for large file sizes [fix #39]
Merge branch 'jed/petscdlopen-extern'

* jed/petscdlopen-extern:
  PetscDL: use PETSC_EXTERN and remove obsolete header
Merge branch 'jed/exodusii-5.24'

* jed/exodusii-5.24:
  ExodusII: link Fortran if and only if using Fortran
  ExodusII: require HDF5 due to transitive dependency via --enable-netcdf-4
  ExodusII: update to 5.24
Merge branch 'jed/configure-check-once'

* jed/configure-check-once:
  config: test functions and headers only once
Merge branch 'dalcinl/ts-monitor'

* dalcinl/ts-monitor:
  TS: remove last-step '-1 TS' monitor lines from output
  TS: Remove last call to TSMonitor() with step=-1
Merge branch 'toby/pcml-nnz'

* toby/pcml-nnz:
  PCML: set N_nonzeros so thatfine-grid operator complexity is reported
Merge branch 'toby/fix-sor-baij'

Consolidates code and adds support for BAIJ SOR with nonzero initial
guess (required for use as a MG smoother).

* toby/fix-sor-baij:
  Mat: add MatSOR/BAIJ test to nightlies
  Mat: move new MatSOR macros to a common header blockmatmult.h
  MatSOR_SeqBAIJ: refactor, enable nonzero initial guess.
  MatSOR, test ex43: removed BlockMat from test
  MatSOR: added test ex43, currently fails
  MatSOR_SeqBAIJ: protect against zero vector length

Conflicts:
	src/ksp/ksp/examples/tests/makefile
Mat: fix test output after MPIAIJ preallocation change

The behavior change was introduced in 'karlrupp/fix-mpiaij-prealloc',
which was merged to 'master' in 714d7381235fa6b645d.
SNES ex12: Fix leak
Merge branch 'knepley/plex' into next

* knepley/plex:
  SNES ex12: Fix leak
Merge branch 'hzhang/update-nightlytestoutput'

Preallocation was simplified in 'karlrupp/fix-mpiaij-prealloc', but that
branch forgot to update test output.

* hzhang/update-nightlytestoutput:
  Mat: fix test output after MPIAIJ preallocation change
  update output file of nightly test
Merge branch 'balay/mpich-3.0.4'

Upgrade to v3.0.4-106-g3adb59c.  This nighly is used because it fixes
the FreeBSD bug identified in this branch.

* balay/mpich-3.0.4:
  mpich: revert workarround on freebsd as its fixed in the current tarball
  mpich: update to pre 3.0.5 snapshot. This fixes a malloc bug in mpiexec [this bug is visible on freebsd - but exists on other arches aswell] http://trac.mpich.org/projects/mpich/ticket/1820
  mpich: now 3.0.4 breaks on freebsd. [workarround by using 3.0.3 on it] https://trac.mpich.org/projects/mpich/ticket/1820
  mpich: 3.0.4 now works on opensloaris - so download_mpich_sol is not needed http://trac.mpich.org/projects/mpich/ticket/1772
  mpich: update to mpich-3.0.4.tar.gz
Merge branch 'knepley/pylith'

* knepley/pylith:
  DMPlex: Fixed DMPlexCreateSohesiveSubmesh() - We should take the fault face directly from the cohesive cell rather than using the face insertion routine
  DMPlex: Add argument to DMPlexCreateSubmesh() that allows user to choose stratum - Added Fortran binding - Updated test
  DMPlex: Added DMPlexCreateCohesiveSubmesh() - Needed to have submesh faces in the same order as cohesive cells
  DMPlex: Fix improper preallocation - The size for a closure is the sum
  Sieve: Missing VecDestroy() in conversion to DM
  DMPlex: Submesh extraction now works without coordinates
  ISieve: Fix conversion of orientations to DMPlex
ISieve: Coordinate conversion should add a field
DMPlex: Fix error in work space allocation
DMPlex: Interpolation of a submesh now starts at the faces
- Do not know a better way to do this right now
Merge branch 'master' into next

* master:
  Mat: fix test output after MPIAIJ preallocation change
  fun3d: fix c89 warning
DMPlex: Interpolation corner cases
- Do not interpolate a 1D mesh
- No need to copy coordinates of the same DM