Merge branch 'tisaac/feature-plex-tests-new'

This merge changes PetscSpace and PetscQuadrature to have a number of
components, so that vector-valued functionals can be defined for
non-Lagrange finit

Merge branch 'tisaac/feature-plex-tests-new'

This merge changes PetscSpace and PetscQuadrature to have a number of
components, so that vector-valued functionals can be defined for
non-Lagrange finite elements. Along the way, this branch also converts
the regression tests related to DMPlex that were in config/builder.py to
the new test harness, and makes lots of changes necessary for them to
be portable tests.

* tisaac/feature-plex-tests-new: (263 commits)
TS tutorials ex11: remove unused functions
DMPlex: missed viewer change in synchronized output
TS tutorials ex11: make work with complex scalars
TS ex18: Fix initializer
TS ex11: Fix M_PI
Plex ex1f90: FUCK FORTRAN
TS tutorials ex11: use a union when punning
silence compiler warnings
SNES tutorials ex56: set partitioner from options
Plex: once again, MPI_Barrier() can't be used to synch output
windows compile fixes balay@ps4 ~/petsc/src/ts/examples/tutorials $ make PETSC_DIR=$HOME/petsc ex11 /home/balay/petsc/bin/win32fe/win32fe cl -o ex11.o -c -MD -wd4996 -Z7 -I/home/balay/petsc/include -I/home/balay/petsc/arch-mswin-uni/include -I/home/balay/petsc/include/petsc/mpiuni `pwd`/ex11.c ex11.c C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(300): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(301): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(370): error C2229: struct '<unnamed-tag>' has an illegal zero-sized array C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(463): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(505): error C2229: struct '<unnamed-tag>' has an illegal zero-sized array C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(724): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(728): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1179): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1184): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1191): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1194): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1383): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1521): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1522): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1523): warning C4090: 'function': different 'const' qualifiers
PetscMath: check for math functions by function pointer resolvability
another windows fix for log2() C:\cygwin64\home\petsc\PETSC~1.CLO\include\petscmath.h(28): warning C4273: 'log2': inconsistent dll linkage C:\Program Files (x86)\Windows Kits\10\include\10.0.10240.0\ucrt\../ucrt/math.h(506): note: see previous definition of 'log2'
fix log2() compile error on windows /home/petsc/petsc.clone-4/include/petscmath.h:28:8: error: expected ‘)’ before ‘/’ token double log2(double); ^
SNES tutorials ex12: turn off complex for restart test
Add empty file to silence warnings
TS tutorials ex46: make output match floating point filter
TS tutorials ex18: remove unused flags
SNES tutorials ex69: use end of line anchor instead of word boundary
SNES tutorials ex69: portable word boundary regex
...

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Plex: Submeshes should set the embedding dimension

Plex: Point projection functions should be passed the effective height
- This makes projection over a boundary mesh work

DMPlex: missed viewer change in synchronized output

Plex ex1f90: FUCK FORTRAN

Merge remote-tracking branch 'origin/stefano_zampini/feature-plex-simplex-to-tensor'

silence compiler warnings

Plex: once again, MPI_Barrier() can't be used to synch output

windows compile fixes
balay@ps4 ~/petsc/src/ts/examples/tutorials
$ make PETSC_DIR=$HOME/petsc ex11
/home/balay/petsc/bin/win32fe/win32fe cl -o ex11.o -c -MD -wd4996 -Z7 -I/home/balay/petsc/include

windows compile fixes
balay@ps4 ~/petsc/src/ts/examples/tutorials
$ make PETSC_DIR=$HOME/petsc ex11
/home/balay/petsc/bin/win32fe/win32fe cl -o ex11.o -c -MD -wd4996 -Z7 -I/home/balay/petsc/include -I/home/balay/petsc/arch-mswin-uni/include
-I/home/balay/petsc/include/petsc/mpiuni `pwd`/ex11.c
ex11.c
C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(300): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)'
C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(301): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)'
C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(370): error C2229: struct '<unnamed-tag>' has an illegal zero-sized array
C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(463): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)'
C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(505): error C2229: struct '<unnamed-tag>' has an illegal zero-sized array
C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(724): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)'
C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(728): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)'
C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1179): warning C4090: 'function': different 'const' qualifiers
C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1184): warning C4090: 'function': different 'const' qualifiers
C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1191): warning C4090: 'function': different 'const' qualifiers
C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1194): warning C4090: 'function': different 'const' qualifiers
C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1383): warning C4090: 'function': different 'const' qualifiers
C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1521): warning C4090: 'function': different 'const' qualifiers
C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1522): warning C4090: 'function': different 'const' qualifiers
C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1523): warning C4090: 'function': different 'const' qualifiers

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Plex: Forgot guard when making periodic cut label

fix complile warning on arch-linux-IPL64
/sandbox/petsc/petsc.clone-2/src/dm/impls/plex/plexgmsh.c:334:11: warning: format ‘%d’ expects argument of type ‘int *’, but argument 3 has type ‘PetscInt *’

fix complile warning on arch-linux-IPL64
/sandbox/petsc/petsc.clone-2/src/dm/impls/plex/plexgmsh.c:334:11: warning: format ‘%d’ expects argument of type ‘int *’, but argument 3 has type ‘PetscInt *’ [-Wformat=]

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Plex+HDF5: Use label to decide which periodic cells need vertex replacement

Plex: Mark cells on one side of periodic cut
- Also use label object in routine

Plex+HDF5: Force coordinates onto same sheet when cutting periodic surfaces

Plex+HDF5: Fix vertex field output for periodic cuts

Plex: Fix periodic cut label
- Fix option spelling
- Add edges into cut label

Plex+HDF5: If periodic_cut label is defined, create extra vertices in periodic meshes for embedding in coordinate dimension

Plex: Now -dm_plex_periodic_cut creates a label with the cut necessary to embed a periodic domain
- Label is names "periodic_cut" and only has vertices right now

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-plex-torus

* knepley/feature-plex-tests-new: (40 commits)
SNES ex12: Allow more exotic periodicity
SNES ex69: Added to makefile

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-plex-torus

* knepley/feature-plex-tests-new: (40 commits)
SNES ex12: Allow more exotic periodicity
SNES ex69: Added to makefile
SNES ex69: Fix for parallelism
Plex+HDF5: Output mapping for torus
TS ex18: Shut off all these tests until we can figure out why you get NaNs on some builds
TS ex11: More fixes to the horrible Riemann code
Plex: Fix section creating for random partitioning
Plex-ex12: Fix LogStage scope for load balancing
TS ex11: Mark, this code is disgusting
TS ex18: Shut off all these tests until we can figure out why you get NaNs on some builds
TS ex11: Silence IDIOT FUCKING COMPILER that has no idea what it is talking about
Plex: I think I fixed random partitioning
Plex: Awful fix for partitioner options - I cannot see a better way to solve this right now
Plex: Bug fixes for shell partitioning
Plex ex12: Fix partitioning - Now give load balancing DM prefix "lb_" so I can change partitioners - Do not force test partition in load balancing
Plex: Now set partitioner type from options in GetPartitioner() instead of on creation - Also set it from options with DM, but this is probably useless because most DM are partitioned before SetFromOptions
Plex: Add DMPlexSetOptionsPrefix() - This gives the prefix to the partitioner
TS ex18: Indicate broken tests
TS ex11: Indicate broken test
SNES ex62: Added SIMPLE tests
...

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

* master: (174 commits)
Bib: Another ref
Increase patchlevel to 3.7.6
Explicitly listing the LTO library causes difficulties on MacOS so a

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

* master: (174 commits)
Bib: Another ref
Increase patchlevel to 3.7.6
Explicitly listing the LTO library causes difficulties on MacOS so avoid it
TSBDF: Update changes/dev.html
Added Fortran TaoType and TaoLineSearchType definitions
Add Fortran TaoType and TaoLineSearchType definitions
setblocksize for iscol_sub
TSBDF: Use standard TS API and options to control adaptivity
Bib: More refs and a correction
SNESTest: Bug-fix in SNESTest when threshold printing option is turned on.
fix warning and valgrind complains reported by the nightly tests
Section+Doc: Small doc fix
pflotran: switch to using the new upstream git repo
DMPlex: Error if attempt to partition a distributed graph with Chaco
fix complex build error
fix complex build
PetscError() did not properly copy over the specific error message when error type was PETSC_ERROR_INITIAL
TSAdapt: Refactor handling of the always_accept flag
Additional clarification for MatMeshToCellGraph() manual page
optimize MatCreateSubMatrix_MPIAIJ() by merging check of sameXXXDist() into one MPI_AllReduce
...

Conflicts:
config/BuildSystem/config/packages/med.py

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DMProject: If dmAux is a sub mesh, get correct mapped point corresponding to p

Plex tests ex8: missed quad precision protection

Complex scalar fixes

DMPlexMED: type guards

DMPlexHDF5: complex fixes