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

This is needed to deal with some changes in MatNullSpace from commit 9d2471e

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_A

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_ATTRIBUTEALIGNED flag to makefile
PCSetUp_SVD() used incorrect matrix for matrix size in parallel, also need to skip LAPACK call if matrix size is zero
strumpack: update to latest version 1.0.4
Remove valgrind warning about MPI_Allreduce() with uninitialized data
sed for test output that has atol convergence with quad precision
updated ex1_nest tests
fixed incorrect key value
fix: bad merge a69d34a
test: move runex78 to TESTEXAMPLES_C_NOTSINGLE
build: fix warnings
sys: update test to produce same result - irrespective of debug/opt build - and presence of ~/.petscrc
sys: src/sys/examples/tests/ex30.c -> src/sys/examples/tests/ex32.c to avoid conflict in master
Sed output, since quad precision reduces below atol on these tests
remove automatically generated matrix names from test output files since can be different
Fixes for MatMPIXXXSetPreallocation(), they were not reentrant, since they kept the information used for matrix-vector products
GAMG: fix PCView_GAMG() format - and update output/ex56_0.out
superlu_dist: 64-bit-indices fix https://github.com/xiaoyeli/superlu_dist/issues/4
Add SNESSetDivergenceTolerance / -snes_divergence_tolerance.
fixed unit read in Plex
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Merge remote-tracking branch 'origin/mark/snes-ex56-b'

Merge branch 'knepley/feature-plex-bdfunc'

* knepley/feature-plex-bdfunc: (56 commits)
updated snes/ex56
updated snes/ex56
Plex: Goddamn it! Shadowing a variable name
PetscDS: Must be setup

Merge branch 'knepley/feature-plex-bdfunc'

* knepley/feature-plex-bdfunc: (56 commits)
updated snes/ex56
updated snes/ex56
Plex: Goddamn it! Shadowing a variable name
PetscDS: Must be setup in order to access field sizes and components
fix bad merge 44ac993612e1ca111ab14eba1c22039e0ba32a12 wrt src/snes/examples/tutorials/ex56.c [by attempting to redo the merge with kdiff3 - and then comparing the final result with the result in the above merge]
fixed snes/ex56 for PetscDSAddBoundary change
dmplexsnes: Remove more unused variables
Remove unused variables
SNES ex77: Must also set face quadrature
SNES ex12: No longer need boundary discretization orders
SNES ex62: Numerical flutter
SNES ex12: Numerical flutter
Plex: In projection, get Nc from DS instead of calculating it again
PetscFE: Added missing destroy
SNEX ex77: Update boundary args and FE creation
Plex: Update boundary integrals to new API
SNES ex12: Tests of bc from fields
SNES ex12: Added the ability to use finite element fields as boundary conditions
Plex: Need invJ for field projection
Plex: Fix bug with field projection - We must tabulate the FE on the dual basis quadrature points
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Merge branch 'knepley/feature-plex-interpolation-perf'

* knepley/feature-plex-interpolation-perf:
DM: Forgot in last commit
DM: Added timing of DMRefine()
Plex ex21: Test for interpolation per

Merge branch 'knepley/feature-plex-interpolation-perf'

* knepley/feature-plex-interpolation-perf:
DM: Forgot in last commit
DM: Added timing of DMRefine()
Plex ex21: Test for interpolation performance
Plex: Added event for SF interpolation

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fixed unit read in Plex

Plex: Goddamn it! Shadowing a variable name

Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/featu

Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/feature-pcbddc-saddlepoint
that prevents me to smoothly merge stefano_zampini/feature-convert-matnest-matis into next.

This will also facilitate merging stefano_zampini/feature-pcbddc-saddlepoint into master

Conflicts:
src/docs/website/documentation/changes/dev.html

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Merge branch 'knepley/fix-dm-ltog-bs'

* knepley/fix-dm-ltog-bs:
Plex: Fix L2G map for MatIS
DM: The L2G mapping is incorrect for bs > 1 - We should not give absolute indices, but block indices

Plex: Added event for SF interpolation

DM+DS: Allow different kinds of BC functions
- Added DMBoundaryConditionType
- Changed DMGetBoudnary() and DMAddBoundary() and the DS versions

Plex: Fix L2G map for MatIS

Merge branch 'tisaac/sys-fix-realloc' into tisaac/petscfe-matching-quadrature-order

* tisaac/sys-fix-realloc: (71 commits)
Sys: fix PetscTrReallocDefault() and PetscReallocAlign()
clearify when

Merge branch 'tisaac/sys-fix-realloc' into tisaac/petscfe-matching-quadrature-order

* tisaac/sys-fix-realloc: (71 commits)
Sys: fix PetscTrReallocDefault() and PetscReallocAlign()
clearify when MatMkl_CPardisoSetCntl() can be used in the manual pages
Fixed manual page for -snes_anderson_beta
Update zfftf.c
remove Hermitian information from output since it is only produced in complex case and thus produces different test output
fixes for 64 bit integers in test example, fix uninitialized variable in test example
tests: move runex49 to TESTEXAMPLES_C_NOTSINGLE
add a PCView_SVD to show parameters
-petscpartitioner_type simple was not being picked up by options thus generating test error
missing CHKERRQ(ierr) on PetscPrintf() statements in newly added test example
PetscViewerVTK: Move DM reference increment into the VTK viewer and out of the DM implementation, as suggested by Jed Brown
missing crosslinks between manual pages
Updated 3.7 release notes to clearly indicate how to update usage of KSP/SNES/TS/SetMonitor(xxx,XXXMonitorDefault,NULL,NULL);
Fix for commit b6480e041dd2293a65f96222772d68cdb4ed6306 that broke this example
Example of factorization of a singular matrix may actually work due to round off
removed unused variables
matshell: clean up and add some new MATOPs to Fortran.
Remove unneeded checks for use of the compressed row for diagonal block of matrices in GAMG
ptscotch: update to version 6.0.4
ptscotch: fix buggy pthread detection code on Mac/Linux
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Merge branch 'pr520/psanan/psanan/vtk-viewer-leak-fix/master' into maint

Merge branch 'pr520/psanan/psanan/vtk-viewer-leak-fix/master'

PetscViewerVTK: Move DM reference increment into the VTK viewer and out of the DM implementation, as suggested by Jed Brown

Merge branch 'knepley/fix-plex-spectral-order'

* knepley/fix-plex-spectral-order:
Plex ex6: Updated output for fix
The bottom orientation was incorrect. For order 3, the orientation was listed a

Merge branch 'knepley/fix-plex-spectral-order'

* knepley/fix-plex-spectral-order:
Plex ex6: Updated output for fix
The bottom orientation was incorrect. For order 3, the orientation was listed as: v1 v2 +---------------+ | | | 8 10 | top-to-bottom | | enumeration | | | 9 11 | | | +---------------+ v0 v3 However, it should have been bottom to top v1 v2 +---------------+ | | | 9 11 | bottom-to-top | | enumeration | | | 8 10 | | | +---------------+ v0 v3 This resulted in an incorrect permutation. From plex.c:DMPlexCreateSpectralClosurePermutation(), the perm had values: perm[5] = 9 perm[6] = 11 perm[9] = 8 perm[10] = 10 They should have been perm[5] = 8 perm[6] = 10 perm[9] = 9 perm[10] = 11 The fixed variable: o = ofb+n*(k-1)+(k-2)-i; was changed to o = ofb+n*(k-1)+i;, reversing the top-to-bottom to bottom-to-top. This continues to work for higher orders as well.

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Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in m

Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in master (the introduction of MatFactorGetError()) therefor need
to merge in master and use the new construct before merging to next

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The bottom orientation was incorrect. For order 3, the orientation was listed as:
v1 v2
+---------------+
| |
| 8 10 | top-to-bottom
|

The bottom orientation was incorrect. For order 3, the orientation was listed as:
v1 v2
+---------------+
| |
| 8 10 | top-to-bottom
| | enumeration
| |
| 9 11 |
| |
+---------------+
v0 v3
However, it should have been bottom to top
v1 v2
+---------------+
| |
| 9 11 | bottom-to-top
| | enumeration
| |
| 8 10 |
| |
+---------------+
v0 v3
This resulted in an incorrect permutation. From plex.c:DMPlexCreateSpectralClosurePermutation(), the perm had values:
perm[5] = 9
perm[6] = 11
perm[9] = 8
perm[10] = 10
They should have been
perm[5] = 8
perm[6] = 10
perm[9] = 9
perm[10] = 11
The fixed variable: o = ofb+n*(k-1)+(k-2)-i; was changed to o = ofb+n*(k-1)+i;, reversing the top-to-bottom to bottom-to-top. This continues to work for higher orders as well.

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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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DMPlex: fix stray PetscScalar to PetscReal

DMPlex: fix PetscInt %D PetscPrintf character

DMPlex: use symmetries in DMPlexGetIndicesPoint{Fields}_Internal() and DMPlexAnchorsModifyMat()

The permutations are passed now instead of the orientations. For
DMPlexGetIndicesPointFields_Internal

DMPlex: use symmetries in DMPlexGetIndicesPoint{Fields}_Internal() and DMPlexAnchorsModifyMat()

The permutations are passed now instead of the orientations. For
DMPlexGetIndicesPointFields_Internal(), we pass permutations for every
point (assuming PetscSectionGetFieldPointSyms() was called for multiple
points, such as for a closure set) of every field, so we have to pass an
additional parameter indicating the offset of the current point in the
set of points.

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