Merge branch 'knepley/feature-plex-reordering'

* knepley/feature-plex-reordering:
doc: update makefile with order.h -> ../../../include/petsc-private/matorderimpl.h rename
DMPlex: Fixed bug with

Merge branch 'knepley/feature-plex-reordering'

* knepley/feature-plex-reordering:
doc: update makefile with order.h -> ../../../include/petsc-private/matorderimpl.h rename
DMPlex: Fixed bug with DMPlexPermute - Fixed label permutation
DMPlex: Check whether default section exists to be reordered
DMPlex: Fixed compiler warning
DMPlex ex10: Fixed test output
DMPlex: Added missing declarations
DMPlex: Fixed misuse of PetscObjectSetName()
MatComputeBandwidth: use PetscInt instead of PetscMPIInt
Mat: Fixed declaration
Mat: Changed MatCalcBandwidth() to MatComputeBandwidth() - Added Fortran interface
DMPlex ex10: This tests reordering of meshes
DMPlex: Added DMPlexGetOrdering() and DMPlexPermute()
PetscSection: Added PetscSectionPermute()
DMLabel: Added DMLabelPermute()
DMPlex: Added DMPlexCreateDoublet()
DMPlex: Added DMPlexCopyLabels()
Mat: Added MatCalcBandwidth()
MatOrdering: Moved private header into petsc-private - Fix to pointer checks in sorder.c

Conflicts:
include/petscdmplex.h

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optimize ISLocalToGlobalMappingCreateIS() to reuse indices created in call to ISGetIndices()
for the case where they are immediately freed anyways no need to copy

Merge branch 'balay/remove-sdir'

__SDIR__ is gone. This is an ABI change (PetscError) so dependent
packages must be recompiled.

* balay/remove-sdir:
__SDIR__: remove remaining traces and documen

Merge branch 'balay/remove-sdir'

__SDIR__ is gone. This is an ABI change (PetscError) so dependent
packages must be recompiled.

* balay/remove-sdir:
__SDIR__: remove remaining traces and document in changes.html
__SDIR__: remove usage of __SDIR__ from PETSc sources.

This merge fixes one instance of __SDIR__ that was added after
'balay/remove-sdir' branched off.

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Merge branch 'jed/doc-restore-zeros-pointer'

* jed/doc-restore-zeros-pointer:
DMPlex: fix my mistake using NULL in place of (int) 0
doc: restore functions in PETSc zero their arguments

Conflict

Merge branch 'jed/doc-restore-zeros-pointer'

* jed/doc-restore-zeros-pointer:
DMPlex: fix my mistake using NULL in place of (int) 0
doc: restore functions in PETSc zero their arguments

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

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Banished all mention of the old MatGetColoring() and use in examples

__SDIR__: remove usage of __SDIR__ from PETSc sources.

PetscSection: Must reset the section when changing the number of fields

Added several additional MPI_Ops to PetscSFBasic.

Added MPI_LAND,MPI_BAND,MPI_LOR,MPI_BOR,MPI_LXOR,MPI_BXOR and MPI_PROD
implementations for FetchAndOp and Unpack instances. Changed ex1.c
so that t

Added several additional MPI_Ops to PetscSFBasic.

Added MPI_LAND,MPI_BAND,MPI_LOR,MPI_BOR,MPI_LXOR,MPI_BXOR and MPI_PROD
implementations for FetchAndOp and Unpack instances. Changed ex1.c
so that the user can specify the op by command line.

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Merge branch 'knepley/fix-plex-preallocation'

* knepley/fix-plex-preallocation:
PetscSF: Fixed PetscSFCreateEmbeddedSF() - We were using sf->nleaves for the leaf buffer, which is completely wrong.

Merge branch 'knepley/fix-plex-preallocation'

* knepley/fix-plex-preallocation:
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[]
DMPlex: Fix completely broken code in PetscSFCreateRemoteOffsets() - Non-broken example was in PetscSFDistributeSection()
DMPlex: Fix leaks in preallocation debugging
DMPlex: Put in guard for preallocation sections which are smaller than the SF

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Merge branch 'knepley/feature-closure-cache'

* knepley/feature-closure-cache:
DMPlex: Added declaration of DMPlexCreateClosureIndex()
SNES ex62: Use closure index
DMPlex: Use closure index if

Merge branch 'knepley/feature-closure-cache'

* knepley/feature-closure-cache:
DMPlex: Added declaration of DMPlexCreateClosureIndex()
SNES ex62: Use closure index
DMPlex: Use closure index if available for DMPlexVecGetClosure()
DMPlex: Added DMPlexCreateClosureIndex() - Uses a PetscSection+IS and stashes in the original Section
PetscSection: Added an index for optimization of closure queries - Added PetscSectionGet/SetClosureIndex() - The index is keyed to the DM which built it (use PetscObject) - Only use a single key for now since a lot of checking would be slow

Conflicts:
src/snes/examples/tutorials/ex62.c

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PetscSection: Added PetscSectionPermute()

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[]

Merge branch 'jed/remove-dynamic-loading-option'

Option --with-dynamic-loading has been removed. Similar functionality
is available via the run-time option -dynamic_library_preload.

* jed/remove-d

Merge branch 'jed/remove-dynamic-loading-option'

Option --with-dynamic-loading has been removed. Similar functionality
is available via the run-time option -dynamic_library_preload.

* jed/remove-dynamic-loading-option:
Sys: PetscContainerCreate must call PetscSysInitializePackage
Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

Conflicts:
src/dm/impls/mesh/mesh.c
src/dm/interface/dlregisdmdm.c
src/docs/website/documentation/changes/dev.html

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DMPlex: Fix completely broken code in PetscSFCreateRemoteOffsets()
- Non-broken example was in PetscSFDistributeSection()

doc: restore functions in PETSc zero their arguments

This is done to prevent accidental misuse. In general, one can pass
NULL for the pointer argument to keep the pointer around for longer, but
use

doc: restore functions in PETSc zero their arguments

This is done to prevent accidental misuse. In general, one can pass
NULL for the pointer argument to keep the pointer around for longer, but
use of arrays after restoration is invalid.

Suggested-by: Wolfgang Bangerth <bangerth@math.tamu.edu>

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Merge branch 'maint'

* maint:
Fix for accidentally duplicated refcount decrement in dm->x
PetscLayoutCreate doc: format code block and list

fixes to ex10.c Jacobian
fixes to PetscFGets()
revert attempt to inline ISLocalToGlobalApply()

PetscLayoutCreate doc: format code block and list

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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PetscSection: Added an index for optimization of closure queries
- Added PetscSectionGet/SetClosureIndex()
- The index is keyed to the DM which built it (use PetscObject)
- Only use a single key for

PetscSection: Added an index for optimization of closure queries
- Added PetscSectionGet/SetClosureIndex()
- The index is keyed to the DM which built it (use PetscObject)
- Only use a single key for now since a lot of checking would be slow

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Merge branch 'knepley/fix-plex-parallel'

* knepley/fix-plex-parallel:
DMPlex: Fixed creation of global sections - The size of neg[] must be all of nroots instead of pEnd-pStart
DMPlex: Fixed coh

Merge branch 'knepley/fix-plex-parallel'

* knepley/fix-plex-parallel:
DMPlex: Fixed creation of global sections - The size of neg[] must be all of nroots instead of pEnd-pStart
DMPlex: Fixed cohesive submesh SF - I misclassified points which were not owned in the original mesh, but are owned in the submesh
DMPlex: Fixed bug with cohesive submesh SF - Needed to put in owned subpoints since they do not come from leaves OR from the original mesh
DMPlex: Fix out of bounds access for empty mesh
DMPlex: Fixed creation of PetscSF in DMPlexCreateCohesiveSubmesh_Uninterpolated() - Could not assume that original owner of subvertex owned it in submesh because it might have no subcells - Needed to redetermine ownership of subpoints
Plex VTK: Handle missing submesh pieces in parallel
DMPlex: Initializeremote locations when calculating SF for submesh
DMPlex: FIxed hang in DMPlexCreateCohesiveSubmesh()
DMPlex: Added PetscSF creation to DMPlexCreateCohesiveSubmesh_Uninterpolated() - Added DMPlexFilterPoint_Internal() - Still need this for the interpolated variant
DMPlex: Remove dead code
DMPlex: Removed aggressive checks for cohesive cells - How should we handle extraction in parallel?
PetscSection: PetscSectionCreateSubmeshSection() now can take an empty IS
DMPlex: Allow submesh creation with empty mesh and empty label
DMPlex: Allow DMPlexOrient() of empty mesh

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

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Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

This option was mostly redundant because normal shared libraries satisfy
all the same needs. This commit adds the run-time option
-dynami

Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

This option was mostly redundant because normal shared libraries satisfy
all the same needs. This commit adds the run-time option
-dynamic_library_preload that can be used to load/initialize all the
packages in advance, as used to be done when --with-dynamic-loading.

The PetscDLLibraryRegister_petscxxx functions have been kept, but are
not called unless -dynamic_library_preload is used. The petsc-dev
discussion, "Why --with-dynamic-loading?" did not reach consensus about
whether this was ever useful, so it may also be removable.

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Merge branch 'jed/is-view-from-options'

Fix SEGV on -ao_view, which was being called from AOCreate.

* jed/is-view-from-options:
AO: fix erroneous processing of -ao_view and factor into AOViewFrom

Merge branch 'jed/is-view-from-options'

Fix SEGV on -ao_view, which was being called from AOCreate.

* jed/is-view-from-options:
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions

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AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions

AOCreate was calling -ao_view before ao->ops->view could be set, causing
SEGV. Move the dispatch to the convenience creati

AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions

AOCreate was calling -ao_view before ao->ops->view could be set, causing
SEGV. Move the dispatch to the convenience creation functions and
consolidate into AOViewFromOptions.

Reported-by: Shao-Ching Huang <huangsc@gmail.com>

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