fix typo, missing e in baseptr

Commit-type: bug-fix
Reported-by: travis

Remove use of PetscDataType from DMGetWorkArray() and one absurd usage

Part of process of removing PetscDataType from PETSc since it duplicates MPI_Datatype
Commit-type: style-fix
Thanks-to: Jed Bro

Remove use of PetscDataType from DMGetWorkArray() and one absurd usage

Part of process of removing PetscDataType from PETSc since it duplicates MPI_Datatype
Commit-type: style-fix
Thanks-to: Jed Brown <jed@jedbrown.org>

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

* master: (56 commits)
test: Disable TS ex19 with single precision
PETSCVIEWERGLVIS: Support DMView_DA() out of VecView_GLVis()
test: Fi

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

* master: (56 commits)
test: Disable TS ex19 with single precision
PETSCVIEWERGLVIS: Support DMView_DA() out of VecView_GLVis()
test: Fix TS ex19 time drift issue with quad precision
testing
Minor edit to 3.8 changes log for AIJMKL/BAIJMKL.
Bib: Added ref
Plex: Change initializers for C89
small update as complained by nightly tests
doc: fix missing from 0e50f9e530a7b78427514d3e384f6941d4a9cc62
small fix for nightly tests
PetscDualSpaceApplyFVM(): Fix for change in dual space semantics
Plex: All tests now passing after DMPlexCreateBoxMesh() update
cleanup MatPtAP_MPIAIJ_MPIAIJ; rm MatPtAPXXX_MPIAIJ_MPIAIJ_ptap()
update MatView_MUMPS()
PFLOW: Bug-fix in parser.
PFLOW: Bug-fix in parser.
Plex: Small fix for box meshing
Plex: Unified box mesh creation to DMPlexCreateBoxMesh() - Makes simplices and tensor cells - Does not work for all combinations, but gives correct error
Plex: Added bounds and faces in each dim to DMPlexCreateBoxMesh()
Plex: Added domain bounds to HexBoxMesh()
...

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Merge branch 'karlrupp/fix-compiler-warnings-oct2017'

* karlrupp/fix-compiler-warnings-oct2017:
Fixes compiler warnings detected by SLEPc buildbot.

Fixed compiler warnings when using MPIUNI, optimized build.

Reported-by: Jose E. Roman <jroman@dsic.upv.es>

Merged in dalcinl/fix-dmplex (pull request #757)

DMPlex: Minor fixes

Approved-by: Matthew Knepley <knepley@gmail.com>

DMPlex: Fix GMSH reader

* Create marker label only in process rank 0.
* Fix misplaced counter increment in cell labeling loop.
* Honor shift command line option everywhere.

Merge branch 'master' into knepley/fix-fe-default

* master: (297 commits)
Bib: Added refs and fixed one
Doc: Fixed formatting problems for MatCreateAIJ() manual page.
Add to PCSOR manual page

Merge branch 'master' into knepley/fix-fe-default

* master: (297 commits)
Bib: Added refs and fixed one
Doc: Fixed formatting problems for MatCreateAIJ() manual page.
Add to PCSOR manual page information about convergence testing when using KSPRICHARDSON
SNES ex5: Restore old output since this breaks an example I have
Noted that some Cray XC systems will use 'aprun' instead of 'srun'. Thanks to Herr Doktor Hong Zhang for this suggestion.
Added example configure script for Cray XC40 with KNL processors (e.g., NERSC Cori).
Fix possible sprintf -Wformat-overflow
PetscMalloc2-7: fix -Wint-in-bool-context for GCC 7
SNES ex5: make boundary condition handling consistent for symmetry
SNES ex5: use L2 norm and *_monitor_short for output
SNES ex5: the L^2 norm scales with the l^2 norm over sqrt(N)
SNES ex5: refactor MMS capability to avoid extreme code duplication
Documentation fix: typo in PetscLogStageRegister manual page.
nodes -> vertices
rename DMNetworkGetComponentTypeOffset -> DMNetworkGetComponentKeyOffset
rename DMNetworkGetConnectedNodes() -> DMNetworkGetConnectedVertices()
Jacobians for adjoints for explicit methods and constant Jacobians never got initialized
fix complex build error
fix build failure with fortran interface
fix compile error with cdc753b64c658d532d7813e942002e67025667a6
...

Conflicts:
src/snes/examples/tutorials/ex13.c
src/snes/examples/tutorials/ex62.c
src/snes/examples/tutorials/ex69.c

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Merge remote-tracking branch 'origin/stefano_zampini/feature-gmsh-periodic'

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warni

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ may be used uninitialized in this function [-Wmaybe-uninitialized] ierr = DMInterpolationSetUp(interpolator, dm, pointsAllProcs);CHKERRQ(ierr);
migrate 'build requires: !mpiuni' to new format
migrate 'build requires: !complex' to new format
workarround 'division by zero' compiler warning on windows C:\cygwin64\home\petsc\PETSC~3.CLO\src\ts\examples\TUTORI~1\ex11.c(416): warning #39: division by zero if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = 0./0.; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */
dos2unix to prevent warnings on opensolaris "/export/home/petsc/petsc.clone/src/ksp/ksp/examples/tests/ex53.c", line 6: warning: invalid white space character in directive
fix output file - corresponding to code changes in efd4aadf157bf1ba2d80c2be092fcf4247860003
disable test on windows
update log from opensolaris so that the diff is clean on linux aswell
update grep in sync with change in efd4aadf157bf1ba2d80c2be092fcf4247860003
Fixed code that did not correctly set current color for block insertion
Update output files that did not get fixed after previous merges
Change MPIUni to not immediately abort on operations it cannot perform, instead return error code
Add filter for example that can produce 1 different iteration count
Example add system calloc, bad formating of %d in print, commented out code
Always use (void) for functions that take no arguments, never ()
always need to caste PetscReal variables to (double) in print statements
updates to manual page for clarity
update help menu for MatRARt() -- MatRARt_mpiaij_mpiaij is supported now, but not efficient.
fix nightlybuild error with c1cbb1def3f8ddca04c3998b9c06618fd1ffef35 on arch-linux-IPL64 src/ksp/pc/examples/tests ex5_1
...

Conflicts:
include/petscdm.h
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/dm/impls/plex/plexhdf5.c

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

* master: (61 commits)
Added ignore
Plex ex7: Fixed mesh name
Plex ex1/ex2: Fixed requirements
PCGAMG: fix spelling in option docs
Pet

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

* master: (61 commits)
Added ignore
Plex ex7: Fixed mesh name
Plex ex1/ex2: Fixed requirements
PCGAMG: fix spelling in option docs
PetscDS: Fix print
Plex ex19: Output fixes for proper destruction
TSMonitorDrawSolutionPhase: Add missing draw pause
fix warning with gcc-7.1
Docs+PetscFE: Evaluate() operates in reference space
Plex ex7: Added 600 cell test
Plex: Added 600-cell for S^3
Math: Add the golden ratio
Plex: Handle unused variable
Plex ex7: Meshing a sphere
Plex: Changed to DMPlexCreateSphereMesh() - Now can do quads or triangles
Share: Added large 3D mesh file - Its the only one I have gotten to work
Mat: Added example for MatIS
PetscSpace: Handle 0 point case for evaluation
PetscSpacePoint: Fix memory handling
PetscDS: Fix update fund for new API
...

Conflicts:
src/dm/impls/plex/plexcreate.c

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Merge branch 'master' into knepley/fix-fe-fortran

* master: (56 commits)
PCGAMG: fix spelling in option docs
PetscDS: Fix print
Plex ex19: Output fixes for proper destruction
TSMonitorDrawSo

Merge branch 'master' into knepley/fix-fe-fortran

* master: (56 commits)
PCGAMG: fix spelling in option docs
PetscDS: Fix print
Plex ex19: Output fixes for proper destruction
TSMonitorDrawSolutionPhase: Add missing draw pause
fix warning with gcc-7.1
Plex ex7: Added 600 cell test
Plex: Added 600-cell for S^3
Math: Add the golden ratio
Plex: Handle unused variable
Plex ex7: Meshing a sphere
Plex: Changed to DMPlexCreateSphereMesh() - Now can do quads or triangles
Share: Added large 3D mesh file - Its the only one I have gotten to work
PetscSpace: Handle 0 point case for evaluation
PetscSpacePoint: Fix memory handling
PetscDS: Fix update fund for new API
Plex: Fixing insertion of boundary values - If we have a dmAux that is a boundary, we need minHeight = 1, since faces can be mapped from submesh to mesh, but not cells (since they have incomplete cones) - However, in this case the effectiveHeight should be h, whereas when using a boundary as the mesh as well, the effectiveHeight should be h - minHeight - Obviously, we need more thinking here to make the iteration make sense in general
PetscFE: Derivatives for Point class are all zero
Small fixes
TS ex46: Fix sin and cos
TS ex18: Fix sin and cos
...

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Merge branch 'master' into knepley/feature-ex11-simplex

* master: (63 commits)
TSMonitorDrawSolutionPhase: Add missing draw pause
fix warning with gcc-7.1
Docs+PetscFE: Evaluate() operates in

Merge branch 'master' into knepley/feature-ex11-simplex

* master: (63 commits)
TSMonitorDrawSolutionPhase: Add missing draw pause
fix warning with gcc-7.1
Docs+PetscFE: Evaluate() operates in reference space
Plex ex7: Added 600 cell test
Plex: Added 600-cell for S^3
Math: Add the golden ratio
Plex ex7: Meshing a sphere
Plex: Changed to DMPlexCreateSphereMesh() - Now can do quads or triangles
Share: Added large 3D mesh file - Its the only one I have gotten to work
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Mat: Added example for MatIS
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
PetscSpace: Handle 0 point case for evaluation
PetscSpacePoint: Fix memory handling
update tests
...

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Merge branch 'knepley/feature-plex-sphere-mesh'

* knepley/feature-plex-sphere-mesh:
Plex ex7: Added 600 cell test
Plex: Added 600-cell for S^3
Math: Add the golden ratio
Plex ex7: Meshing a

Merge branch 'knepley/feature-plex-sphere-mesh'

* knepley/feature-plex-sphere-mesh:
Plex ex7: Added 600 cell test
Plex: Added 600-cell for S^3
Math: Add the golden ratio
Plex ex7: Meshing a sphere
Plex: Changed to DMPlexCreateSphereMesh() - Now can do quads or triangles
Share: Added large 3D mesh file - Its the only one I have gotten to work
Plex ex1: Added cow mesh - Not sure why TetGen is puking
CTetGen: Updated to newest commit
Plex ex7: Mesh a sphere
SNES ex63: Fixed help message
Plex: Added DMPlexCreateQuadSphereMesh() - Creates a spherical surface with 6 quads
Plex: Simple corrections
Plex ex1: Allow a mesh boundary to be loaded and meshed
Plex: Allow Gmsh loads that are zero-based and embedded meshes - I know this is non-standard, but its an easy format to manipulate

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Merge branch 'scott/test-datafiles-fix' of https://bitbucket.org/petsc/petsc into scott/test-datafiles-fix

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
ini

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
SNES ex12: Mix misnaming Nf --> Nc
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
typo
fill-in some references
Bib: Fixed ref
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
Plex tests: Updated to new point function API
SNES ex56: Moved tests to new format
DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tutorials/ex63.c

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Merge branch 'master' into stefano_zampini/feature-fetidp-ex69

Merge branch 'master' into knepley/feature-plex-boundary-values

* master: (487 commits)
Bib: More refs
Fixed errors in the manuals and ts_glee source code doc
fix bug to enable '-xxx_via [alg]

Merge branch 'master' into knepley/feature-plex-boundary-values

* master: (487 commits)
Bib: More refs
Fixed errors in the manuals and ts_glee source code doc
fix bug to enable '-xxx_via [alg]' to showup in '-help' Reported-by: Mark Adams <mfadams@lbl.gov>
Plex: Remove dead code
TS tutorials ex11: remove unused functions
TSAdapt: Set TSADAPTNONE as default adapt type
DMPlex: missed viewer change in synchronized output
Revert "Merge branch 'hzhang/ts-ex9busdmnetwork'"
TSAdapt: Update changes/dev.html
TSAdapt: Set default type for TSGLEE
TS tutorials ex11: make work with complex scalars
Bib: Added ref
TS ex18: Fix initializer
TS ex11: Fix M_PI
Plex ex1f90: FUCK FORTRAN
f2cblaslapack: remove duplicate xerbla.o and xerbla_array.o from lapack [they are already in blas]
TSAdapt: Refactor handling of default adapt type
TSAdapt: Update changes/dev.html
TSAdapt: Update manual
TSAdapt: Refactor interface and implementations
...

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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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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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Merge branch 'tisaac/feature-plex-deterministic-viewing' into tisaac/feature-plex-tests-new

* tisaac/feature-plex-deterministic-viewing:
DMLabel: sort strata after distributing
PetscError() did

Merge branch 'tisaac/feature-plex-deterministic-viewing' into tisaac/feature-plex-tests-new

* tisaac/feature-plex-deterministic-viewing:
DMLabel: sort strata after distributing
PetscError() did not properly copy over the specific error message when error type was PETSC_ERROR_INITIAL
Additional clarification for MatMeshToCellGraph() manual page
med: --with-hdf5, not --with-hdf5-dir
DMPlex_GMSH: revert to not inverting triangles
sys tests ex13f: fix type mismatch in composition test
PCBDDC: use a sparse rhs when the solver is MUMPS
Sys ex13: Added test for object composition in Fortran
Sys: Added Fortran binding for object composition
MatMUMPS: added support for sparse right-hand sides in sequential

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DMPlexCreateGmsh(): fix types when reading from binary

Merge branch 'tisaac/fix-dm-tests' into tisaac/feature-plex-tests-new

* tisaac/fix-dm-tests:
dmplex tests ex1: update output for ISLocalToGlobalMapping changes
DMNetwork: Use the default section

Merge branch 'tisaac/fix-dm-tests' into tisaac/feature-plex-tests-new

* tisaac/fix-dm-tests:
dmplex tests ex1: update output for ISLocalToGlobalMapping changes
DMNetwork: Use the default sections with plex when getting offset.
Add another extchem test case
Fix for extchem.c when envelop monitor is on, but graphical monitoring is off
TSAdapt ascii view should show dt_min and dt_max
Forgot to include example file
Change extchem.c to accept mole values for initial conditions instead of mole fractions
Update extchem.c example to 1) use pressure, 2) use options file, 3) read initial conditions from file
DMNetwork: API to return the underlying DMPlex.
deprecate MatGetSubMatXXX Requested-by: Jed Brown <jed@jedbrown.org>
Work around for Apple Xcode bug with rpath
DMPlex_GMSH: triangles are inverted
bib: fix URL for StarForest note
rm MatLUFactorNumeric_SeqBAIJ_11_NaturalOrdering() because it does not improve performance add MatSolve_SeqBAIJ_bs_NaturalOrdering(), bs=12,...,14 add test runex50_2
experiment PetscKernel_A_gets_A_minus_B_times_C_11
add timer to MatLUFactorNumeric_SeqBAIJ_11_NaturalOrdering()
test new A = A*B
implement MatSolve_SeqBAIJ_11_NaturalOrdering
Merge two line TSAdapt monitor to a single line, shorten line, reorder presented values
implement PetscKernel_A_gets_A_times_B_11()

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Merge branch 'tisaac/feature-fe-dual-apply' into tisaac/feature-plex-tests-new

There has unfortunately been a lot of interplay between our work to
change the petscspace/dualspace to accept vector co

Merge branch 'tisaac/feature-fe-dual-apply' into tisaac/feature-plex-tests-new

There has unfortunately been a lot of interplay between our work to
change the petscspace/dualspace to accept vector components, and the
work to transfer the tests in config/builder.py to the new test harness.
I'm merging them together to get them to play nice with each other, and
so that I only have one feature branch to handler when merging into
master/next.

* tisaac/feature-fe-dual-apply: (64 commits)
snes tutorials ex12: fix restart test arguments
nightly build fixes for arch-viennacl
fix run command to match the command in master/makefile. [the diff will be correct in master/next]
PetscFE: fix typo in for loop declaration
PetscPartitioner: use simple partitioning for regression tests
DT tests ex1: fix test arguments to match regression output
DT ex1: fix options
DMPlexCreateHexBoxMesh: no cells in z direction for 2D
PCBDDC: use %D for PetscInt printfs
Plex: helper function used in all cases now
Plex tests ex7: make partitions portable for testing
Plex: use MPIU_2INT instead of MPI_2INT
MatAIJ KLU: remove redefinition of SuiteSparse_long
DMPlexRefine_CTetgen() mimics DMPlexRefine_Tetgen()
DMPlexGenerate_Tetgen(): mimic ctetgen so it can be used equivalently
Plex: Cylinder fixes for complex
Plex ex1: Test for periodic cylinder
Plex: I think periodic cylinder is working
Plex ex1: Updated torus test
Plex: Torus can now be arbitrarily refined
...

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Fix compiler warnings