require PETSC_USE_COMPLEX for PetscScalar to be complex for PetscOptionsStringToScalar()

fix PetscOptionsStringToScalar() for missing complex

added PetscOptionsGetScalarArray() fixed a variety of examples with problems for complex scalar type

Merge branch 'barry/minor-draw-improvements' into jed/chem

introduce XXXViewFromOptions() and use consistently when possible

Merge branch 'stefano_zampini/pcbddc-applytranspose' into stefano_zampini/pcbddc-multilevel-improvement

Merge branch 'master' into knepley/feature-dmda-section

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fi

Merge branch 'master' into knepley/feature-dmda-section

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fix for TSGetRHSMats_Private() in the creation of the Arhs and Brhs matrices
protect logging of objects (which uses global variables) with PETSC_USE_LOG
error handler API had been previously changed but this example was not updated to new API.
DMPlex: Fixed bug in coordinate permutation
PetscSection: Doc fix for permutation
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bugfix of MatCreateSeqAIJFromTriple() contributed by Nicolas Marsic <nicolas.marsic@montefiore.ulg.ac.be>
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
completed removing server code that was not removed in previous commit
removed PETSc webserver and configure package files that supported it
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
fix outdated PetscOptionsList
SNESQN: only monitor real part of dot product (fails with C++ complex)
Fix for multiple definitions in mat/color/interface/ custom fortran bindings
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/da/dageometry.c
src/dm/impls/plex/examples/tests/ex4.c
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexinterpolate.c

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Merge branch 'barry/rm-strncmp'

Should not use strncmp() directly in PETSc code, use PetscStrncmp()

solaris system complained about strncmp() being unknown here

Merge branch 'barry/saws'

Merge branch 'master' into knepley/feature-fem-dgspace

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key

Merge branch 'master' into knepley/feature-fem-dgspace

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
SNESQN: only monitor real part of dot product (fails with C++ complex)
Corrected the #include statement in the man pages for the PetscObjectComposedDataSet/Getwhatever routines.
DMPlex: Added doc for DMPlexGetHybridBounds()
winzip: detect if winzip is used to extract petsc.tar.gz and error out.
configure: remove self.archIndependent as its not being used. [it is used to create externalpackages/package/arch dir which is unused]
configure: fix packages using package-dir/PETSC_ARCH as out-of-source-build location Perhaps this should be changed to package-dir/build?
configure: remove dead code previously used to download BuildSystem
configure: check if compilerDefines [and compilerFixes] exist in framework before using them
configure: save/restore reconfigure.py when --with-clean is used
configure: add --with-clean option to delete buildfiles/externalpackages in PETSC_DIR/PETSC_ARCH and potential externalpackages in --with-external-package-dir/PETSC_ARCH
configure: With --with-externalpackages-dir=dir store/build packages in dir/PETSC_ARCH
Add MatSeqSBAIJSetPreallocationCSR()
configure: switch to using PETSC_DIR/PETSC_ARCH/externalpackages by updating package.py to use externalpackages.py as the externalPackagesDirProvider
configure: move dead code configureExternalPackagesDir() from petscdir.py to externalpackagesdir.py Also set PETSC_DIR/PETSC_ARCH/externalpackages as the externalpackagesdir
...

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Merge branch 'master' into barry/saws

Conflicts:
src/ksp/pc/impls/gamg/gamg.c
src/sys/classes/viewer/impls/ams/ams.c
src/sys/objects/pinit.c

Merge branch 'master' into knepley/feature-dmda-section

* master: (397 commits)
PetscSynchronizedFGets: fix deadlock at EOF
Compiler: Fix warnings from MPI impls which do not initialize outputs

Merge branch 'master' into knepley/feature-dmda-section

* master: (397 commits)
PetscSynchronizedFGets: fix deadlock at EOF
Compiler: Fix warnings from MPI impls which do not initialize outputs
Increase patchlevel to 3.4.3
SNES: Now work vectors come from the DM
SNES ex62: Remove code generation
SNES: Move setup involving snes->vec_sol from SNESSetUp() to SNESolve()
Compiler: Fix warnings from MPI impls which do not initialize outputs
DMPlex ex7: Added missing test output
SNES ex52: Removed old Jacobian stuff, and fixed call to DMPlexProjectFunction() - Fixed calls for new element handling
SNES ex12: Added a performance profiling mode
DMPlex ex8: Fixed leak
PetscSection: Must reset the section when changing the number of fields
DMPlex ex7: Fixed test output - Corrected orientations in interpolation
DMPlex ex1: Fixed test output - Uniform refinement for quads changed
DMPlex: Fix overagressive checks
PC: Removed support graph PC
configure: both downloadonWindows and worksonWindows refer to MS compilers. Also fix isWindows() -> isWindows(CC).
MatXAIJSetPreallocation: use array[] notation to help out Fortran
__float128: when blas/lapack is not found instruct using f2cblaslapack
Configure: Package.downloadonWindows is supposed to mean that Windows compilers work. not Cygwin - Also changed doc for Package.worksonWindows, which does refer to Cygwin
...

Conflicts:
src/dm/impls/da/dalocal.c

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Merge branch 'knepley/fix-plex-examples' into knepley/feature-plex-refine-3d

* knepley/fix-plex-examples: (36 commits)
DMPlex ex7: Added missing test output
SNES ex52: Removed old Jacobian stuff

Merge branch 'knepley/fix-plex-examples' into knepley/feature-plex-refine-3d

* knepley/fix-plex-examples: (36 commits)
DMPlex ex7: Added missing test output
SNES ex52: Removed old Jacobian stuff, and fixed call to DMPlexProjectFunction() - Fixed calls for new element handling
SNES ex12: Added a performance profiling mode
DMPlex ex8: Fixed leak
PetscSection: Must reset the section when changing the number of fields
DMPlex ex7: Fixed test output - Corrected orientations in interpolation
DMPlex ex1: Fixed test output - Uniform refinement for quads changed
DMPlex: Fix overagressive checks
configure: both downloadonWindows and worksonWindows refer to MS compilers. Also fix isWindows() -> isWindows(CC).
MatXAIJSetPreallocation: use array[] notation to help out Fortran
__float128: when blas/lapack is not found instruct using f2cblaslapack
Configure: Package.downloadonWindows is supposed to mean that Windows compilers work. not Cygwin - Also changed doc for Package.worksonWindows, which does refer to Cygwin
SNES example: fix bad merge
config: only define DATAFILESPATH for non-null value
config: define lang-specific macros in petscconf.h, choose in petscsys.h
Mat: add MATOP_ values for missing functions
DMPlex: use VECSTANDARD for coordinates
PetscSF: Fixed PetscSFCreateEmbeddedSF() - We were using sf->nleaves for the leaf buffer, which is completely wrong. We have to use the largest thing in sf->mine[]
replaced ISCreateGeneral in CompositeDM with ISCreateStride. MatNest calls ISStrideGetInfo on these vectors, which was causing errors
DMPlex: Fix completely broken code in PetscSFCreateRemoteOffsets() - Non-broken example was in PetscSFDistributeSection()
...

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

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Merge branch 'master' into prbrune/mat-matcolor

Conflicts:
src/snes/interface/snesj2.c

Merge branch 'master' into prbrune/removeunwrappedmathfunctions

Merge branch 'jed/options-insert-bcast-bgq' into maint

Attempt to work around BG/Q MPI_Bcast bug. It is unknown whether it is
successful, but this uses fewer communications so it should not be
wors

Merge branch 'jed/options-insert-bcast-bgq' into maint

Attempt to work around BG/Q MPI_Bcast bug. It is unknown whether it is
successful, but this uses fewer communications so it should not be
worse.

* jed/options-insert-bcast-bgq:
PetscOptionsInsertFile: combine Bcasts for alias and values

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Merge branch 'jed/options-insert-bcast-bgq'

Attempt to work around BG/Q MPI_Bcast bug. It is unknown whether it is
successful, but this uses fewer communications so it should not be worse.

* jed/o

Merge branch 'jed/options-insert-bcast-bgq'

Attempt to work around BG/Q MPI_Bcast bug. It is unknown whether it is
successful, but this uses fewer communications so it should not be worse.

* jed/options-insert-bcast-bgq:
PetscOptionsInsertFile: combine Bcasts for alias and values

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Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

fix name for PetscOptionsFList() and get FList() and EList() working properly with SAWs legal values

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
s

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
src/snes/impls/composite/snescomposite.c
src/snes/impls/gs/snesgs.c
src/snes/impls/nasm/nasm.c
src/snes/impls/ngmres/snesngmres.c

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Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (71 commits)
Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
SNESMonitorCancel: enable fort

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (71 commits)
Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
SNESMonitorCancel: enable fortran interface
PetscSection: Added docs for Fortran binding for VecSetValuesSection()
Vec: Removed old F90 binding for PetscSection
bgq: fix deadlock on bgq due to inconsistant values returned by getpwuid(getuid()) on runs with 256nodes [or 4096 cores]. This fix removes the reliance on PetscGetHomeDirectory() returning 'same' value across nodes. [using the fact that PetscOptionsInsertFile() uses HOMEDIR from node-0 only]
DMPlex: change order of assignment to appease -Wmaybe-initialized (gcc-4.8.1)
DMPlex: Fix 64-bit int problem in VTK
Mat: Fix for PetscSparseDenseMaxDot() for complex
Vec: Correct VecUniqueEntries() for 64-bit indices
MatSeqAIJGetArrayF90: add man pages and fix typo in MatDense version
SF docs: add link to summary page and fix title
Doc: Fixed DM code in manual
metis/parmetis: update to metis-5.1.0/parmetis-4.0.3 Also update the test output as the partitioning appears to have changed.
DMPlex: remove unused variables
blaslapack: update f,f2c tarballs to 3.4.2 version
DMPlex ex5: Added test for 2 face cohesive submesh - Fixed old tests for cohesive cell orientation
DMPlex: Put in depth label optimization
DMPlex: Fix flipping of fault normal
DMPlex: We label cells with only vertices on the fault, but they have no cone replacement
DMPlex: Fix translation to cohesive edges in 3D - They are labeled by the vertices they connect
...

Conflicts:
include/petscdmplex.h

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Merge branch 'master' into knepley/feature-dt-fem

* master: (51 commits)
Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
SNESMonitorCancel: enable fortran inte

Merge branch 'master' into knepley/feature-dt-fem

* master: (51 commits)
Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
SNESMonitorCancel: enable fortran interface
PetscSection: Added docs for Fortran binding for VecSetValuesSection()
Vec: Removed old F90 binding for PetscSection
bgq: fix deadlock on bgq due to inconsistant values returned by getpwuid(getuid()) on runs with 256nodes [or 4096 cores]. This fix removes the reliance on PetscGetHomeDirectory() returning 'same' value across nodes. [using the fact that PetscOptionsInsertFile() uses HOMEDIR from node-0 only]
DMPlex: change order of assignment to appease -Wmaybe-initialized (gcc-4.8.1)
metis/parmetis: update to metis-5.1.0/parmetis-4.0.3 Also update the test output as the partitioning appears to have changed.
DMPlex: remove unused variables
blaslapack: update f,f2c tarballs to 3.4.2 version
DMPlex ex5: Added test for 2 face cohesive submesh - Fixed old tests for cohesive cell orientation
DMPlex: Put in depth label optimization
DMPlex: Fix flipping of fault normal
DMPlex: We label cells with only vertices on the fault, but they have no cone replacement
DMPlex: Fix translation to cohesive edges in 3D - They are labeled by the vertices they connect
DMPlex: Added flip argument to DMPlexLabelCohesiveComplete() to reverse submesh normal - Fixed ex5 test
DMPlex ex5: Fixed existing tests and added two cohesive cell test - Fixed tests for new cohesive cell orientation
DMPlex: Propagate orientation information to the submesh properly
DMPlex: Orientation of cohesive cell should come from face to which it is attached
DMPlex: Added subdm argument to DMPlexLabelCohesiveComplete() - Use the subdm for orientation information so we replace vertices all on the same side
DMPlex: Fix DMPlexOrient() for submeshes - Need to also reverse cone orientation of cells attached to fault faces when we flip them
...

Conflicts:
config/builder.py
include/petsc-private/dmpleximpl.h
include/petscdm.h
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexfem.c
src/dm/interface/dlregisdmdm.c
src/snes/examples/tutorials/ex52.c
src/snes/examples/tutorials/output/ex12_10.out
src/snes/examples/tutorials/output/ex12_11.out
src/snes/examples/tutorials/output/ex12_5.out
src/snes/examples/tutorials/output/ex12_6.out
src/snes/examples/tutorials/output/ex12_7.out
src/snes/examples/tutorials/output/ex12_8.out
src/snes/examples/tutorials/output/ex12_9.out

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PetscOptionsInsertFile: combine Bcasts for alias and values

This is an attempt to work around a BG/Q bug in which some sequences of
collectives deadlock. This packs the options aliases and values i

PetscOptionsInsertFile: combine Bcasts for alias and values

This is an attempt to work around a BG/Q bug in which some sequences of
collectives deadlock. This packs the options aliases and values into a
packed buffer that can be communicated with a single MPI_Bcast.

Suggested-by: Vitali Morozov <morozov@anl.gov>

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Merge branch 'maint'