Merge branch 'master' into psanan/pc-telescope-nearnullspace

fixed merge with master

Merge branch 'tisaac/dualspace-feature-symmetry'

In finite element assembly, to compute a residual or assemble a Jacobian
on an element, the dual space functionals of a reference finite element are

Merge branch 'tisaac/dualspace-feature-symmetry'

In finite element assembly, to compute a residual or assemble a Jacobian
on an element, the dual space functionals of a reference finite element are related
(i.e., pushed forward) to the functionals that make of the degrees of
freedom of the discretized system.

In doing so, we have to draw a correspondence between the boundary
points of the reference element (its edges and vertices) and the
boundary points of each cell in the mesh. Sometimes, this
correspondence is not perfect, because the orientations of the boundary
points of a cell may be different than the orientations of the boundary
points of the reference element. For example, an edge that runs
clockwise around the reference element may map onto an edge that runs
counter-clockwise around the real cell.

For some finite elements (such as the most common P1 Lagrange finite
elements) this doesn't matter. But for others---high-order elements,
H-div and H-curl conforming elements---a difference in orientation
affects the mapping between reference functionals and degrees of
freedom.

The simplest example is a high-order nodal Lagrange finite element in
2D: the degrees of freedom on an edge of the reference element are
numbered left-to-right, but if the orientation of the real edge is
reverse, then we must read/write degrees of freedom right-to-left.

Things get more complicated in 3D: a quadrilateral face between
hexahedra may have any of 8 different orientations (that make of the
dihedral symmetries), and each one corresponds to a different reordering
of the 2D grid of nodes supported on that quadrilateral.

Things also get more complicated for H-div elements. Functionals on the
interfaces between cells represent the flux from one cell to another,
and thus have direction. Reversing the orientation of an edge changes
the sign of the mapping between the reference functional and the degree
of freedom.

To assemble generic finite elements, we thus need to accommodate
transforms between reference functionals and degrees of freedom that
encompass (1) permutations, and (2) scalar multipliers.

This branch accomplishes this in two steps:

- We add PetscDualSpaceGetSymmetries() to the interface, to allow a dual
space to describe how symmetries of the mesh points affect
referent-to-real maps of functionals.

- We add PetscSectionSym, an object that encapsulates symmetries of the
degrees of freedom whose layout is described by a PetscSection.

When a section is created from a DM that has a finite element
discretization in its PetscDS, it will automatically construct the
appropriate PetscSectionSym when it creates a PetscSection to describe a
discretized function space.

If a PetsFE finite element discretization is not used, the user can
create a PetscSectionSym for their degrees of freedom for themselves.
We give an example of this for spectal elements in
src/dm/impls/plex/examples/tutoerials/ex6.c.

* tisaac/dualspace-feature-symmetry: (22 commits)
cast memzeros to void to avoid compiler complaints about const qualifiers
DMPlex: fix stray PetscScalar to PetscReal
DMPlex: fix stray PetscScalar to PetscReal
Plex tutorials ex6: use symmetries in SEM example
Plex tests ex3: added high order tests
Plex tests ex3: add matrix-free near null space test
DMPlex: fix PetscInt %D PetscPrintf character
DMPlexTree: use symmetries when computing constraint matrices
DMPlex: use symmetries in DMPlexGetIndicesPoint{Fields}_Internal() and DMPlexAnchorsModifyMat()
DMPlex: use PetscSectionGet/RestorePointSyms() in DMPlexVecGet/SetClosure()
DMPlex: added DMPlexGet/RestoreCompressedClosure()
DMPlex: added DMPlexGetPointDualSpaceFEM()
DMPlex: set PetscSectionSym in DMPlexCreateSectionInitial()
DMLabel: added PETSCSECTIONSYMLABEL
PetscSection: add PetscSectionSym
PetscDualSpace: added PetscDualSpaceGetSymmetries()
PetscDualSpace_Lagrange: setup recursively on dimension
PetscDualSpace_Lagrange: order functions now go after tuple used
PetscDualSpace_Lagrange: use lexicographic order for nodes
DMPlex: added DMPlexComputePointGeometry_Internal()
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DMLabel: added PETSCSECTIONSYMLABEL

Different symmetries are applied to different points (e.g. edges and
facets), so this is the most universal way I could come up with to

- break up the points in

DMLabel: added PETSCSECTIONSYMLABEL

Different symmetries are applied to different points (e.g. edges and
facets), so this is the most universal way I could come up with to

- break up the points in the section's chart into different symmetry
types, and
- specify what symmetries are acceptable (i.e., not assume automatically
that the range in [-coneSize,coneSize)

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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 '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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DMLabel: added DMLabelSetStratumIS()

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

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

Merge branch 'tisaac/sf-fix-multi-sf-leaves' into tisaac/dmp4est-feature-injection

* tisaac/sf-fix-multi-sf-leaves: (174 commits)
PetscSF: fix PetscSFGetMultiSF() for sparse leaves
PetscSF: make

Merge branch 'tisaac/sf-fix-multi-sf-leaves' into tisaac/dmp4est-feature-injection

* tisaac/sf-fix-multi-sf-leaves: (174 commits)
PetscSF: fix PetscSFGetMultiSF() for sparse leaves
PetscSF: make regression test that fails
few more clang static analyzer fixes
many issues detected by clang static analyzer
Update hypre to its release version
Updates for xSDKTrilinos builds
Added --download-xsdktrilinos
Communicator passed to VecCreateSeq should be PETSC_COMM_SELF
PCMG man page: fix typo in options name
Bib: Added refs
DMLabel: Removed unused variable
Metis tries to use backtrace which requires -lexecinfo on some systems such as freebsd Remove -lexecinfo from freebsd configure files since it is only needed by metis
add alternative output that occurs on some systems due to use of random number generator in partitioner
Plex: When creating cohesive submeshes, fix memory leak
Plex ex11: Updated output for new distribution algorithm
Plex: When explicitly distributing the depth label, we must recreate empty strata
Plex: When partitioning, the cell numbering should include hybrid points
Plex: Allow cell and vertex numberings to include hybrid points
need to show diffs of ex22 if it fails
Support two different output for test example, since due to roundoff this example can produce slightly different convergence history
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Merge branch 'master' into sanderarens/fix-plex-neumann-bc

* master: (28 commits)
few more clang static analyzer fixes
many issues detected by clang static analyzer
Update hypre to its release

Merge branch 'master' into sanderarens/fix-plex-neumann-bc

* master: (28 commits)
few more clang static analyzer fixes
many issues detected by clang static analyzer
Update hypre to its release version
Updates for xSDKTrilinos builds
Added --download-xsdktrilinos
DMLabel: Removed unused variable
Plex: When creating cohesive submeshes, fix memory leak
Plex ex11: Updated output for new distribution algorithm
Plex: When explicitly distributing the depth label, we must recreate empty strata
Plex: When partitioning, the cell numbering should include hybrid points
Plex: Allow cell and vertex numberings to include hybrid points
Plex ex1: Fixed output for empty strata
DMLabel: Added DMLabelHasStratum()
Minor changes and fix to bugs introduced in 82f73ecaa
Modified makefile to fix aijcusparse tests
Add missing code for the case PETSC_HAVE_VECCUDA
Fix bugs introduced in 82f73ecaa
Use VECCUDA with MATAIJCUSPARSE
CUDA: Fixed visibility and disabled Fortran bindings for VecScatters on GPU.
Replace kernels with thrust
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Merge branch 'knepley/fix-plex-examples'

* knepley/fix-plex-examples:
DMLabel: Removed unused variable
Plex: When creating cohesive submeshes, fix memory leak
Plex ex11: Updated output for new

Merge branch 'knepley/fix-plex-examples'

* knepley/fix-plex-examples:
DMLabel: Removed unused variable
Plex: When creating cohesive submeshes, fix memory leak
Plex ex11: Updated output for new distribution algorithm
Plex: When explicitly distributing the depth label, we must recreate empty strata
Plex: When partitioning, the cell numbering should include hybrid points
Plex: Allow cell and vertex numberings to include hybrid points
Plex ex1: Fixed output for empty strata
DMLabel: Added DMLabelHasStratum()

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Merge branch 'master' of https://bitbucket.org/petsc/petsc

DMLabel: Added DMLabelHasStratum()

Merge branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'knepley/fix-dmlabel-declaration'

* knepley/fix-dmlabel-declaration:
DMLabel: Moved declaration since dmlabel.h does not include dm.h

DMLabel: Moved declaration since dmlabel.h does not include dm.h

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

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax error with error message
SNES ex5: Correct Jacobian handling on patches
SNES ex5: Stupid complex fixes
DMP4est: fix transfer of labels to parents
petsc4py: update to latest snapshot. Fixes da example breakage in petsc4py test suite
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logging in interpolator creation
Plex: Correct use of tabs in ASCII viewer
DM: Shorten long event name
Plex ex12: Create boundary label automatically at all levels of mesh hierarchy
Plex ex12: Change PetscViewerSetFormat --> PetscViewerPushFormat - Fix order of SetMode and SetFilename
Plex ex12: Change all functions to static
Since DMDA with periodic boundary conditions does support P0 interpolation remove checks that error out under those conditions
ascem-io.py and amanzi.py need to handle self.hdf5.include being None correctly
fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests also fix check for location of python shared library on mac to check all cases each time
Switch back to Sherry's version since she accepted by pull request
PetscDraw: Update help messages for -draw_save* options
...

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

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Merged petsc/petsc into master

Merge remote-tracking branch 'origin/knepley/fix-plex-hdf5-label' into tisaac/dmforest

* origin/knepley/fix-plex-hdf5-label: (50 commits)
Plex: Fixed HDF5 output for DMLabel - The ISAllGather() wa

Merge remote-tracking branch 'origin/knepley/fix-plex-hdf5-label' into tisaac/dmforest

* origin/knepley/fix-plex-hdf5-label: (50 commits)
Plex: Fixed HDF5 output for DMLabel - The ISAllGather() was being called with an IS that had COMM_SELF - Also, we needed to protect for empty index arrays
superlu_dist: install target should first make sure prefix/[include,lib] dirs exist - similar to superlu
dm: add DMRemoveLabel() fortran interface
nightlybuilds: allocate more time to run arch-linux-xsdk-dbg build...
Remove superfluous information messages
Cannot have rank 1 print before parallel print since it may end up before or after the print from process 0. There change to have rank 0 print the sequential matrix
Bib: Added ref
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelGather()
mpiuni: check for "long_long" before checking for "__int64" [as "typedef __int64" gives error with icc] Note: cannot use 'int64_t' as 'typedef unsigned int64_t foo' gives eror with icc
Add filter for solaris linker scope warning to master since that is used in nightly tests of next
Previous commit did not correctly handle downloading from --with-packages-dir
Use special error code of 10 for output list of needed downloaded package tarballs otherwise the outer configure.py script converts the error code to an error message we do not want.
Have ./configure return a nonzero exit code when --with-packages-dir detects missing packages so that calling scripts know this is occurred simplify some code
Completed support for --with-packages-dir=directory that allows --download-xxx features to be cleanly used behind firewalls etc also updated to docs to indicate this new feature
Adding supporting for --download-xxx to reported needed downloads when off line or behind a firewall and using local copies when available with the --with-packages-dir=directory option
Fix typos in linesearch impls:armijo, morethuente, owarmijo.
PetscDraw: Explicitly save draw in KSP/SNES/TS monitors
PetscViewerDraw: Propagate prefix from viewer to draw contexts
PetscDraw: Explicitly save draw in {Vec|Mat|DMDA}View() routines
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Merge branch 'mlange/fix-plex-multi-level-overlap'

* mlange/fix-plex-multi-level-overlap: (259 commits)
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelG

Merge branch 'mlange/fix-plex-multi-level-overlap'

* mlange/fix-plex-multi-level-overlap: (259 commits)
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelGather()
Plex ex12: Fixed variable initialization and some output
Plex ex11: Added error checking
Plex ex14: Now boundary label does not have cells
Plex ex1: Now boundary label does not have cells
Plex ex1: Fix for VTK format
added some debugging code, getting ready to branch
added some print statements, should be an -info...
smome cleaning up
restructured ex11 to allow for problem specific BCs
DMPlex: Update test ex12_5 with correct level-2 overlap
DMPlex: Use global processSF in DMPlexPartitionInvert
DMPlex: Add remote leaf contributions to roots in DMLabelPropagate
DMPlex: Add DMLabelGather to migrate label values from leafs to roots
DMPlex: Refactor DMLabelDistribute to separate point stratum distribution
DMPlex: Add propagation of remote point donations for multi-level overlap
DMPlex: Fix DMLabelDistribute for all-to-all migrations
Plex: make extern exactly match prototype: semantic match is not enough.
DMP4est: typo fix
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Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

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

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c

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Merge branch 'tisaac/dmforest' into mlange/fix-plex-multi-level-overlap

Conflicts:
src/dm/impls/plex/examples/tests/output/ex12_5.out
src/dm/label/dmlabel.c

DMPlex: Add DMLabelGather to migrate label values from leafs to roots

This is effectively the inverse operation to DMLabelDistribute and it
reuses the underlying migration stratum value code.

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