DM: Added check for erroneous input when creating default SF

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

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bdd

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

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddcprivate.c

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removed blocked versions of ISLocalToGlobalMapping in Vec and Mat
the single ISLocalToGlobalMapping supports ISLocalToGlobalMappingApply and ISLocalToGlobalMappingApplyBlock
still some fixes need for

removed blocked versions of ISLocalToGlobalMapping in Vec and Mat
the single ISLocalToGlobalMapping supports ISLocalToGlobalMappingApply and ISLocalToGlobalMappingApplyBlock
still some fixes need for these extensive changes

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added bs argument to ISLocalToGlobalMappingCreate(), not yet used for bs > 1

Merge remote-tracking branch 'origin/master' into feature-dmmoab

Merged petsc/petsc into master

Merge branch 'master' into knepley/feature-plex-hdf5-parallel-load

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this wa

Merge branch 'master' into knepley/feature-plex-hdf5-parallel-load

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this was really bad)
outdated example that doesn't match coding style removed and buggy
petscversion.h: workaround ifort -cpp lack of referential transparency
configure: ignore AR, MAKEFLAGS [if set in env]
incorrect first entry in array being zeroed in example
sizeof.c: remove dependence on petsc [and fix syntax error]
nightlybuilds: use consistant PETSC_ARCH, machine names
TS: Allow viewing of TS solutions
DMPlex: Fix comparison for complex
change MPIVersion streams to use MPI_Wtime() to be portable to Windows do not use scalar square root on real number; it upsets Microsoft
cannot use I in PETSc code because in complex it sometimes represents imaginary number cannot pass PetscScalar * to VecNorm()
in dashboard don't warn about SSL and BOI deprecated
TS ex11: Fixed output formatting
Doc+DMPlex: Added function documentation for some refinement functions
streams: translate code from 'bash' to 'sh' [fix freebsd]
barry is an idiot who doesn't have a clue as to what he is doing (and git's unfriendlyness doesn't help matters)
don't list examples under C that don't work with complex!
forgotten output file
removed valgrind warning about sending uninitialized data
nightly builds ignore unrecognized pragma and .c file as C++ code
...

Conflicts:
include/petsc-private/dmpleximpl.h

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Merge branch 'master' of bitbucket.org:petsc/petsc
Fuck if git tells me to git pull then I pull, if you want me to do something else than have git tell what to do

Merge branch 'knepley/feature-plex-periodic'

* knepley/feature-plex-periodic:
TS: Allow viewing of TS solutions
DMPlex: Fix comparison for complex
Draw: Fixed bad check
SNES ex62: Enhance ex

Merge branch 'knepley/feature-plex-periodic'

* knepley/feature-plex-periodic:
TS: Allow viewing of TS solutions
DMPlex: Fix comparison for complex
Draw: Fixed bad check
SNES ex62: Enhance ex62 to use tensor-product cells
DMPlex: Now we are correctly creating the Mobius band - Coordinates for uniform refinement are still broken
DMPlex: If domain is periodic, uniform refinement of coordinates will respect this
DMPlex: Allow geometry routines to recognize periodic quads
DMPlex: Added DMPlexLocalizeCoordinates() - This pulls coordinates from vertices to the cell, which allows discontinuities - We use this for periodic problems
DM: Added preliminary support for periodic coordinates - Added DMGet/SetPeriodicity() which is for clipping coordinates to a periodic box
DMPlex: Needed a custom Fortran wrapper for DMPlexInterpolate() because now we require that the incoming mesh be NULL
DMPlex: Fix handling of Fortran NULLs
DMPlex: Updated test output - The DMView was changed
SNES ex12: Cleanup structure - Use PetscFECreateDefault()
PetscFE: Added a view for Basic
SNES ex12: Starting to cleanup test names
SNES ex62: Marked MF tests as broken

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Merge branch 'barry/add-names-for-all-ascii-viewers'

DM: Added preliminary support for periodic coordinates
- Added DMGet/SetPeriodicity() which is for clipping coordinates to a periodic box

Merge branch 'knepley/feature-plex-hdf5'

* knepley/feature-plex-hdf5: (63 commits)
DMPlex ex2: Added an example that checks a mesh
DMPlex: #ifdef support functions for HDF5
TS: Fix output sequ

Merge branch 'knepley/feature-plex-hdf5'

* knepley/feature-plex-hdf5: (63 commits)
DMPlex ex2: Added an example that checks a mesh
DMPlex: #ifdef support functions for HDF5
TS: Fix output sequence
DMPlex: Check for HDF5 attributes before writing them
DMPlex: Label with timestep number since we do not have times
Viewer+HDF5: Added PetscViewerHDF5HasAttribute()
TS: Set output sequence for timesteps
DMPlex: Handle output sequences - Added static to some functions
DM: Add idea of an output sequence - Added DMGet/SetOutputSequenceNumber() - Added doc for outputDM
REVERT TS: Timestep gets set into DMTS
DMPlex: Fix up HDF5 segregation
DMPlex: Replace MAXPATHLEN with PETSC_MAX_PATH_LEN
DMPlex: Fix HDF5 timestep handling
DMPlex: Set correct block size on HDF5 field vectors
TS: Timestep gets set into DMTS
DMTS: Added timestep
DMPlex: Fix output of fields - Corrected name - Fixed vector type
DMPlex: Return errors from HDF5 function
DMPlex+Viewer: Now output separate fields for viz - Added the PETSC_VIEWER_HDF5_VIZ format for creating viz fields - Added field type determination
Sys+HDF5: Added PetscDataType string and HDF5 support for it
...

Conflicts:
config/BuildSystem/config/packages/__init__.py
src/ts/interface/ts.c

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Merge branch 'knepley/feature-plex-hdf5' into knepley/feature-plex-bc

* knepley/feature-plex-hdf5: (61 commits)
TS: Fix output sequence
DMPlex: Check for HDF5 attributes before writing them
DM

Merge branch 'knepley/feature-plex-hdf5' into knepley/feature-plex-bc

* knepley/feature-plex-hdf5: (61 commits)
TS: Fix output sequence
DMPlex: Check for HDF5 attributes before writing them
DMPlex: Label with timestep number since we do not have times
Viewer+HDF5: Added PetscViewerHDF5HasAttribute()
TS: Set output sequence for timesteps
DMPlex: Handle output sequences - Added static to some functions
DM: Add idea of an output sequence - Added DMGet/SetOutputSequenceNumber() - Added doc for outputDM
REVERT TS: Timestep gets set into DMTS
DMPlex: Fix up HDF5 segregation
DMPlex: Replace MAXPATHLEN with PETSC_MAX_PATH_LEN
DMPlex: Fix HDF5 timestep handling
DMPlex: Set correct block size on HDF5 field vectors
TS: Timestep gets set into DMTS
DMTS: Added timestep
DMPlex: Fix output of fields - Corrected name - Fixed vector type
DMPlex: Return errors from HDF5 function
DMPlex+Viewer: Now output separate fields for viz - Added the PETSC_VIEWER_HDF5_VIZ format for creating viz fields - Added field type determination
Sys+HDF5: Added PetscDataType string and HDF5 support for it
IS: Fix compiler warning
IS: Forgot to protect HDF5
...

Conflicts:
config/BuildSystem/config/packages/__init__.py
src/ts/interface/ts.c

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DM: Add idea of an output sequence
- Added DMGet/SetOutputSequenceNumber()
- Added doc for outputDM

Insure that all ASCII viewers for PETSc objects call PetscObjectPrintClassNamePrefixType()

DM: DMLoad() now knows about HDF5 input

DM: Optimized DMGetOutputDM() to return the DM itself if there are no constraints

DM: Added the notion of an output DM
- This adds all the dofs constrained by BC to the global vector
- Used for visualization

Fixing merge conflicts in dmregall.

Merged petsc/petsc into master

Merge branch 'master' into shri/ts-events

Conflicts:
src/ts/interface/ts.c

Merge branch 'master' into shri/feature-dm-circuit

Conflicts:
src/dm/impls/makefile

Merge branch 'master' into prbrune/matcoloring-greedy

Merge branch 'master' into knepley/fix-fem-multifield

* master:
tests: move ex151 out of complex tests to avoid compile errors on windows
DM: Fixed pointer comparison
Microsoft C++ compiler ne

Merge branch 'master' into knepley/fix-fem-multifield

* master:
tests: move ex151 out of complex tests to avoid compile errors on windows
DM: Fixed pointer comparison
Microsoft C++ compiler needs extra care with complex numbers and casting
DMPlex: C++ has fucking namespaces, use them assholes
Field has 3 components therefor need to initialize three components, Microsoft C compiler demands it
DMPlex ex3: Added interpolation test - Only works for 2D simplices - Shows the restriction only gets constants right - Other small cleanup
DMPlex ex3: Change to interpolated meshes by default
DMPlex: Fix interpolation of multicomponent fields
DM: Fix reference counting in DMSetField()
DMPlex: Fix interpolation scaling
DMPlex: Fix allocation in DMPlexMatSetClosureRefined()
DMDA: Fixed signature of DMDACreateSection()
When configuring with MPIUni remove any MPI includes in the $PETSC_DIR/PETSC_ARCH/include directory that may have been put there by earlier ./configure runs.

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Merge branch 'knepley/feature-interpolation-testing'

* knepley/feature-interpolation-testing:
DM: Fixed pointer comparison
DMPlex ex3: Added interpolation test - Only works for 2D simplices - Sh

Merge branch 'knepley/feature-interpolation-testing'

* knepley/feature-interpolation-testing:
DM: Fixed pointer comparison
DMPlex ex3: Added interpolation test - Only works for 2D simplices - Shows the restriction only gets constants right - Other small cleanup
DMPlex ex3: Change to interpolated meshes by default
DMPlex: Fix interpolation of multicomponent fields
DM: Fix reference counting in DMSetField()
DMPlex: Fix interpolation scaling
DMPlex: Fix allocation in DMPlexMatSetClosureRefined()
DMDA: Fixed signature of DMDACreateSection()

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