Fix misuse of PETSC_COMM_WORLD in library code

There are still many left, I'm tired of fixing them

[szampini@localhost petsc]$ git grep PETSC_COMM_WORLD | grep -v tests | grep -v tutorials | grep '

Fix misuse of PETSC_COMM_WORLD in library code

There are still many left, I'm tired of fixing them

[szampini@localhost petsc]$ git grep PETSC_COMM_WORLD | grep -v tests | grep -v tutorials | grep '\.c' | awk '{print $1}' | uniq
src/benchmarks/streams/CUDAVersion.cu:
src/benchmarks/streams/SSEVersion.c:
src/contrib/fun3d/comp/flow.c:
src/contrib/fun3d/incomp/flow.c:
src/dm/impls/forest/p4est/petsc_p4est_package.c:
src/dm/impls/moab/dmmbfem.cxx:
src/dm/impls/moab/dmmbmg.cxx:
src/dm/impls/moab/dmmbutil.cxx:
src/dm/impls/moab/dmmbvec.cxx:
src/dm/impls/moab/dmmoab.cxx:
src/dm/impls/network/network.c:
src/dm/impls/stag/stag.c:
src/dm/impls/stag/stag1d.c:
src/dm/impls/stag/stag2d.c:
src/dm/impls/stag/stag3d.c:
src/dm/impls/stag/stagda.c:
src/dm/impls/stag/stagutils.c:$
src/dm/impls/swarm/data_ex.c:
src/dm/impls/swarm/swarm.c:
src/dm/impls/swarm/swarm_migrate.c:
src/ksp/ksp/impls/fcg/pipefcg/pipefcg.c:
src/ksp/ksp/impls/gcr/pipegcr/pipegcr.c:
src/ksp/ksp/impls/gmres/pipefgmres/pipefgmres.c:
src/ksp/ksp/impls/tsirm/tsirm.c:
src/ksp/ksp/interface/itcreate.c:
src/ksp/ksp/interface/iterativ.c:
src/ksp/ksp/interface/saws/kspsaws.c:
src/ksp/pc/impls/bddc/bddcfetidp.c:
src/ksp/pc/impls/fieldsplit/fieldsplit.c:
src/ksp/pc/impls/gamg/util.c:
src/ksp/pc/impls/gasm/gasm.c:
src/ksp/pc/impls/is/nn/nn.c:
src/ksp/pc/impls/patch/pcpatch.c:
src/ksp/pc/impls/tfs/gs.c:
src/ksp/pc/impls/tfs/tfs.c:
src/ksp/pc/impls/tfs/xxt.c:
src/ksp/pc/impls/tfs/xyt.c:
src/ksp/pc/interface/precon.c:
src/mat/impls/aij/mpi/mpiaij.c:#define
src/mat/interface/matrix.c:
src/mat/interface/matrix.c:.
src/mat/interface/matrix.c:
src/mat/interface/matrix.c:$
src/mat/utils/multequal.c:
src/snes/interface/saws/snessaws.c:
src/snes/interface/snes.c:
src/sys/classes/draw/interface/drawreg.c:
src/sys/classes/random/interface/random.c:
src/sys/classes/random/interface/randomc.c:
src/sys/classes/viewer/impls/ams/ams.c:
src/sys/classes/viewer/impls/ams/amsopen.c:
src/sys/classes/viewer/impls/ascii/vcreatea.c:
src/sys/classes/viewer/impls/mathematica/mathematica.c:
src/sys/dll/reg.c:
src/sys/dll/reg.c:static
src/sys/dll/reg.c:
src/sys/error/adebug.c:
src/sys/error/checkptr.c:
src/sys/error/errstop.c:
src/sys/error/pstack.c:
src/sys/error/signal.c:
src/sys/ftn-custom/zutils.c:
src/sys/info/verboseinfo.c:
src/sys/logging/plog.c:
src/sys/logging/utils/eventlog.c:
src/sys/logging/xmllogevent.c:
src/sys/memory/mal.c:
src/sys/memory/mtr.c:
src/sys/objects/aoptions.c:
src/sys/objects/aoptions.c:+
src/sys/objects/aoptions.c:
src/sys/objects/ftn-custom/zstart.c:
src/sys/objects/ftn-custom/zstartf.c:
src/sys/objects/inherit.c:
src/sys/objects/init.c:
src/sys/objects/options.c:+
src/sys/objects/options.c:
src/sys/objects/pinit.c:MPI_Comm
src/sys/objects/pinit.c:
src/sys/utils/mpitr.c:
src/sys/utils/mpits.c:+
src/sys/utils/pbarrier.c:
src/sys/utils/pdisplay.c:
src/sys/yaml/yamlimpls.c:
src/sys/yaml/yamlimpls.c:+
src/sys/yaml/yamlimpls.c:
src/tao/pde_constrained/impls/lcl/lcl.c:
src/ts/interface/ts.c:
src/vec/is/is/utils/iscoloring.c:
src/vec/vec/impls/seq/seqviennacl/vecviennacl.cxx:
src/vec/vec/interface/vector.c:.
src/vec/vec/interface/vector.c:

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Merge branch 'knepley/fix-plex-hybrid-assembly' into 'master'

Knepley/fix plex hybrid assembly

See merge request petsc/petsc!2793

Plex: More hybrid fixes
- Converted hybrid assembly to use PetscTabulation
- Protect for NULL discretizations, which happen with no dofs for a field
- Added PetscDiscType enum
- Changed PetscDSIsFE_I

Plex: More hybrid fixes
- Converted hybrid assembly to use PetscTabulation
- Protect for NULL discretizations, which happen with no dofs for a field
- Added PetscDiscType enum
- Changed PetscDSIsFE_Internal() to PetscDSGetDiscType_Internal()
- Must inject coordinates from hybrid cells into the ambient space

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Plex+FE: Updates for hybrid integration
- Added support for hybrid Jacobians
- Added PetscDSHasBdJacobian()
- Added boundary Jacobian preconditioner
- Needed a path to integrate the hybrid Jacobian p

Plex+FE: Updates for hybrid integration
- Added support for hybrid Jacobians
- Added PetscDSHasBdJacobian()
- Added boundary Jacobian preconditioner
- Needed a path to integrate the hybrid Jacobian preconditioner
- Fixed indexing in hybrid element mat update
- Be careful about the difference between intrinsic dimension and embedding dimension for hybrid integration
- Need to use rectangular transformation of gradient in case they are different
- Fix use of embedding dimension
- Make sure FEGeom struct has the dimensions set
- Pointwise function derivatives are in the embedding space
- Use PetscArrayzero()
- Change TransitiveClosure() for hybrid cells
- We get the closures of the endcaps, and then the hybrid faces, this allows degenerate cells that we need in PyLith

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Merge remote-tracking branch 'origin/dalcinl/fix-null'

TS/SNES/Tao: Fix 0 ->NULL for pointers

See merge request petsc/petsc!2783

SNES: Replace 0 -> NULL for pointers

Merge remote-tracking branch 'origin/maint'

Merge branch 'knepley/fix-plex-fem-small' into 'maint'

Knepley/fix plex fem small

See merge request petsc/petsc!2752

Plex: Prevent crash with no DS Jacobian functions set

Merge remote-tracking branch 'origin/psanan/docs-fixes-2020-03-25'

Doc fixes (prerequisites for Sphinx docs)

See merge request petsc/petsc!2633

docs: fix sowing list syntax/incomplete man page

Merge branch 'knepley/feature-project-different-spaces' into 'master'

Knepley/feature project different spaces

See merge request petsc/petsc!2153

FE+DS: Introduce PetscTabulation to hold tabulated function data
- This was created to prevent mismatches in sizes I was getting by just
passing around arrays
- FE+FV+DS now hold tabulations
- GetTab

FE+DS: Introduce PetscTabulation to hold tabulated function data
- This was created to prevent mismatches in sizes I was getting by just
passing around arrays
- FE+FV+DS now hold tabulations
- GetTabulation() --> CreateTabulation() and it creates an object rather
than using DMGetWorkArray(). I put in ComputeTabulation() to reuse
space, but there still may be performance regression.
- Default tabulations are now "cell tabulations"
- The replicas in the tabulation are used to index faces in a face
tabulation

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Plex: Now for projection allow 3 DMs: input, output, and auxiliary
- We get the input DM from the input Vec
- Now we can have more general relations between input/output/auxiliary meshes in projectio

Plex: Now for projection allow 3 DMs: input, output, and auxiliary
- We get the input DM from the input Vec
- Now we can have more general relations between input/output/auxiliary meshes in projection and integration
- Added DMEnclosureType
- Added DMGetEnclosureRelation() and DMGetEnclosurePoint()
- Removed DMPlexGetSubpoint() and DMPlexGetAuxiliaryPoint()
- In projection, convert output mesh points to input mesh points
- Coordinates must be reordered after depth label is constructed
- DMPlexLabelAddFaceCells() only adds cells adjacent to faces
- Put in extra debugging for missing point enclosures
- In boundary projection, calculate face data for geometry
- p4est: use known point maps instead of projection to interp from base to coarse

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Merge branch 'knepley/fix-plex-jacobian-assembly' into 'master'

Plex: Fixed DS retrieval in Jacobian assembly

See merge request petsc/petsc!2384

Plex: Fixed DS retrieval in Jacobian assembly

Merge branch 'master' into 'master'

Add --download-hpddm

See merge request petsc/petsc!1994

--download-hpddm for PCHPDDM and KSPHPDDM

Merge branch 'barry/2019-09-10/jed/gitlab-ci' into 'master'

Barry/2019 09 10/jed/gitlab ci

See merge request petsc/petsc!2042

Fix %D and (double) usage for PetscPrintf() and SETERRQ()

Commit-type: portability

Merge branch 'knepley/fix-plex-boundary-integral-mem' into 'master'

Plex: Fix leak in boundary integration

See merge request petsc/petsc!1997

Plex: Fix leak in boundary Jacobian integration

Plex: Fix leak in boundary integration

Merge branch 'jed/deprecate-dmgetdefaultsection' [PR #1969]

* jed/deprecate-dmgetdefaultsection:
DMGetDefaultSection et al: add PETSC_DEPRECATED_FUNCTION
These functions were deprecated in v3.9, but

Merge branch 'jed/deprecate-dmgetdefaultsection' [PR #1969]

* jed/deprecate-dmgetdefaultsection:
DMGetDefaultSection et al: add PETSC_DEPRECATED_FUNCTION
These functions were deprecated in v3.9, but no PETSC_DEPRECATED_FUNCTION was added at that time so many uses crept back into the source code. Here we mark it deprecated and fix all existing uses in PETSc.

DMGetLocalSection/DMSetLocalSection: add explicit names for DMGetSection/DMSetSection
These names are for symmetry with DMGetLocalVector() versus DMGetGlobalVector().

DMGetSection: replace all internal usage with DMGetLocalSection
Same for DMSetSection -> DMSetLocalSection. We retain the interface for DMGetSection/DMSetSection without deprecation warnings (for now).

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DMGetSection: replace all internal usage with DMGetLocalSection

Same for DMSetSection -> DMSetLocalSection. We retain the interface
for DMGetSection/DMSetSection without deprecation warnings (for n

DMGetSection: replace all internal usage with DMGetLocalSection

Same for DMSetSection -> DMSetLocalSection. We retain the interface
for DMGetSection/DMSetSection without deprecation warnings (for now).

Suggested-by: Barry Smith <bsmith@mcs.anl.gov>

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