PetscSection: add PetscSectionSym

This object's is essentially a Petsc-idiom way of letting the user
specify implementations of

PetscSectionGetPointSyms()
PetscSectionRestorePointSyms()
PetscSectio

PetscSection: add PetscSectionSym

This object's is essentially a Petsc-idiom way of letting the user
specify implementations of

PetscSectionGetPointSyms()
PetscSectionRestorePointSyms()
PetscSectionGetFieldPointSyms()
PetscSectionRestoreFieldPointSyms()

Like PetscDualSpaceGetSymmetries(), the symmetries are descibed by R *
P, where R is a flip (or rotation with complex scalars). I had thought
about a more managed approach, like PetscSectionGet/SetValues, which
entirely hid the existence of symmetries to begin with, but:

- then you have to differentiate between different PetscDataTypes (e.g.,
for indices, just perform the permutation, not the flips/rotations),
and
- what about inserting an element matrix? When inserting an element
matrix, it makes the most sense to apply flips/rotations to the
element matrix, and the permutations to the indices where the matrix
is to be inserted with MatSetValues().

so in the end I decided to just provide a simple interface to pass the
symmetries to the users and let them figure out how they want to use
them.

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Merge branch 'master' into mark/snes-ex56

* master: (93 commits)
Web: Added a tutorial
typo
rename X -> U
sowing: update to version that creates manpage URLs for 'enum' types/values
Increa

Merge branch 'master' into mark/snes-ex56

* master: (93 commits)
Web: Added a tutorial
typo
rename X -> U
sowing: update to version that creates manpage URLs for 'enum' types/values
Increase patchlevel to 3.7.3
move runex3_3 to NOTSINGLE [ partial backport 9ed0bd76d5c329eb91401ebabfbd851446214e20 ]
DMPlex: local coordinate vector should be a sequential vector
DM: Name coordinate vectors in subdomain and restrict hooks
tests: disable a couple of TS examples from single precision tests
reduce TS ex12_2 output
fix PetscFormatRealArray() to cast PetscReal in print statement to double so works for __float128 precision
Vec: enable Fortran interfaces for VecGetLocalVectorRead and VecRestoreLocalVectorRead
Bib: Added refs
PCShell: man page fixes
update handling of latex in example code to use https
fix typo in isltog comment
test: Avoid conversion of object <-> function pointer type [-Wpedantic]
fortran: enable interface for VecGetLocalVector(), VecRestoreLocalVector()
update citation for cmz2016
PCBDDC: silent compilation warnings from nightlybuilds
...

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

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Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

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

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcfetidp.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c
src/mat/impls/is/matis.h

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Merge branch 'stefano_zampini/fix-matis'

Conflicts:
src/mat/examples/tests/makefile

Move PCBDDCSubsetNumbering to ISRenumber

This function is needed by MatGetLocalSubMatrix_IS

MatIS: raise errors in MatSetValues if any of the indices is not mapped locally

Removed buggy ISG2LMapApply (just used by MATIS). Use ISGlobalToLocalMappingApply instead
Added MatSetValuesBlocked

Merge branch 'stefano_zampini/fix-matzerorowsaij-bug'

PetscLayout: added PetscLayoutCompare method

Merge branch 'tisaac/dm-label-use-is'

* tisaac/dm-label-use-is:
IS: fix ISLocate(): ex7 passes
IS: added test for ISLocate()
IS: added ISLocate implementations for block and stride
ISGeneral

Merge branch 'tisaac/dm-label-use-is'

* tisaac/dm-label-use-is:
IS: fix ISLocate(): ex7 passes
IS: added test for ISLocate()
IS: added ISLocate implementations for block and stride
ISGeneral: add locate implementation
DMLabel: use ISLocate()
IS: added ISLocate() interface and default implementation
change regression logs for increased number of index sets
DMLabel: added DMLabelSetStratumIS()
DMLabel: switch internal storage from array to IS

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IS: added ISLocate() interface and default implementation

Merge branch 'knepley/feature-plex-closure-reorder'

* knepley/feature-plex-closure-reorder:
IS+Plex: Changed interface to closure permutation to take an IS
IS+Plex: Changed interface to closure

Merge branch 'knepley/feature-plex-closure-reorder'

* knepley/feature-plex-closure-reorder:
IS+Plex: Changed interface to closure permutation to take an IS
IS+Plex: Changed interface to closure permutation to take an IS
Plex ex9: Can now test closure reordering - Also fixed some small bugs
Plex ex6: Example that shows how to set and retrieve values with the spectral element ordering
Plex: Allow closure permutation in PlexVecGet/SetClosure() - This supports spectral element ordering - This does not seem to introduce any performance degradation
Plex: Added DMPlexCreateSpectralClosurePermutation()
PetscSection: Added support for closure permutation - This supports entry in the spectral element ordering

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IS+Plex: Changed interface to closure permutation to take an IS

PetscSection: Added support for closure permutation
- This supports entry in the spectral element ordering

Merge branch 'master' into barry/add-pcfieldsplit-logevent

Merge branch 'master' into barry/add-pcreset-hypre-for-master

Needed to move PCDestroy_HYPRE() added to master to PCReset_HYPRE() since that was introduced
as a bug fix for maint

Merge branch 'master' into barry-allow-vecset-nan-3.6

Merge branch 'master' into pr263/PierreBdR/ts-domain-error-in-stage/master

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c

Merge branch 'master' into tisaac/dmforest

Get 3.6.2 patches

* master: (1360 commits)
remove nasty memory leak with CUDA code when using block Jacobi with multiple blocks per process
print abs

Merge branch 'master' into tisaac/dmforest

Get 3.6.2 patches

* master: (1360 commits)
remove nasty memory leak with CUDA code when using block Jacobi with multiple blocks per process
print abs in Fortran test example in order to have same result with real and complex builds
changed outdate mpirun and -np to mpiexec and -n
force sqrt to be taken in the precision of PetscReal in fortran examples
continuation line too soon for some compilers
stop configure if user selected C++ clanguage, single precision, complex combination since we do not support it
fixes for Fortran examples to compile cleanly in single precision that do not involve complex numbers
fixes to Fortran examples to compile cleanly in single precision complex
fix previous mistake
must cast 1. to PetscScalar before dividing by a PetscScalar (C++ complex class is terrible)
must cast 0.0 to PetscScalar before comparison with a PetscScalar
changed order of suggested locations of downloadable PETSc to Barry's preference
Increase patchlevel to 3.6.2
remove debug print statement from two commits before
remove debug print statements I accidently left in the last commit
PetscDraw: Fix dummy definition of PetscDrawCollective{Begin|End}()
remove cleanupMumps flag from MatDestroy_Mumps() it should always free the memory it allocated Bug detected while adding features to libMesh
improved viewing of fractional counts in xml nested log viewing fixed bug in output of doubles to xml nested log files
chombo: build only libs - not examples
fix typo. 'gcc-4.8 --with-cxx-dialect=C++11' gives a warning with this line - even though its in a #ifdef thats never enabled.
...

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To add a space to all comments I have made before. Barry pointed out
that a comment without a space right after '/*' may cause bfort to crash

Merge remote-tracking branch 'petsc/master' into fixed-c

To add a space to all comments I have made before. Barry pointed out
that a comment without a space right after '/*' may cause bfort to crash

Merge remote-tracking branch 'petsc/master' into fixed-comment-space

Conflicts:
include/petsc/finclude/petscmat.h
include/petscmat.h
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiaij.h

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Merge branch 'pr361/master/Fande-Kong/pcgasm-increaseoverlap'

Conflicts:
src/contrib/nightlysummary/runhtml.py
src/mat/examples/tests/makefile

Merge branch 'pr329/master/Fande-Kong/matpartitioning-hierarch' into pr361/master/Fande-Kong/pcgasm-increaseoverlap: need hierarch to build GASM subdomains.

Conflicts:
src/mat/examples/tests/makefi

Merge branch 'pr329/master/Fande-Kong/matpartitioning-hierarch' into pr361/master/Fande-Kong/pcgasm-increaseoverlap: need hierarch to build GASM subdomains.

Conflicts:
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiaij.h

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Merge branch 'master' into jed/process-options-handler

Merge branch 'tisaac/dmplex-stable-tet-refinement' into tisaac/plex-feature-tree-fv

This feature branch also changed the topology of nonconforming examples:
I am merging so that I can make the regre

Merge branch 'tisaac/dmplex-stable-tet-refinement' into tisaac/plex-feature-tree-fv

This feature branch also changed the topology of nonconforming examples:
I am merging so that I can make the regression output that should be
correct in master and next

* tisaac/dmplex-stable-tet-refinement: (594 commits)
plex: added tet shape regression test
plexrefine: remove replaced code
plex: update test output for new tet refinement order
plex: fix tet refinement for stable element shape
DMPlex: added test of shape quality to ex1
Better to use the proper error handling version of PetscViewerASCIIGetStdout() instead of PETSC_VIEWER_STDOUT_()
Generate a very useful error message if PetscLogView(), PetscLogEventGetPerfInfo() or PetscLogEventGetFlops() is called with a preceeding call to PetscLogBegin() and friends (also -log_summary which triggers a PetscLogBegin())
fix compile warnings
Plex: Fix bug with bcComps initialization
Turn off elemental shared libraries if --with-shared-libraries=0 is used
Bib: Added refs
Bib: Fixed a bunch of errors
add warning/error flag for '-mat_superlu_dist_parsymbfact' when MatInputMode=GLOBAL
makefile: fix format
tests: add back ex6f, runex6f targets - that got removed in 2f1d3d565a6a43067e6df75b043e6343b05fcd1d
accessing option that may never have been set
typo in DMNetworkSetNumVariables() reported by Sean Shahkarami
superlu_dist: update to using latest 4.1 version
fix compile warnings
Generate an error message when trying to overwrite default options of CN and BEULER
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Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of git. I think it is not justified to ever have anything in next for more than a few weeks at most.
Either take it out of next if it is broken or put it in master if it is not broken. Hanging around in next but
not master for ever is not a good policy.

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