Merge branch 'jczhang/sf-more-opts' [PR #1567]

* jczhang/sf-more-opts:
Add more optimizations in SF and use it as the default for VecScatter.

Code style change

SF: Partially fix a bug when overlapped SF communications have same rootdata or leafdata on some ranks

Now we use two keys (rootdata, leafdata) to identify a pending communication. But that is still

SF: Partially fix a bug when overlapped SF communications have same rootdata or leafdata on some ranks

Now we use two keys (rootdata, leafdata) to identify a pending communication. But that is still not
enough for cases where communications have same rootdata and leafdata on some ranks. Currently We
error out on these cases. See ex2.c for various cases we can handle and we can not handle.

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Ignore potential overlapping when rootdata=leafdata=NULL

This case happens with
ex62_fetidp_3d_tet – snes.tutorials
ex62_fetidp_3d_hex – snes.tutorials
ex59_bddc_fetidp_ml_eqlimit_2 – ksp.ksp.tutori

Ignore potential overlapping when rootdata=leafdata=NULL

This case happens with
ex62_fetidp_3d_tet – snes.tutorials
ex62_fetidp_3d_hex – snes.tutorials
ex59_bddc_fetidp_ml_eqlimit_2 – ksp.ksp.tutorials
ex59_bddc_fetidp_ml_eqlimit_1 – ksp.ksp.tutorials

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SF: Partially fix a bug when overlapped SF communications have same rootdata or leafdata on some ranks

Now we use two keys (rootdata, leafdata) to identify a pending communication. But that is still

SF: Partially fix a bug when overlapped SF communications have same rootdata or leafdata on some ranks

Now we use two keys (rootdata, leafdata) to identify a pending communication. But that is still not
enough for cases where communications have same rootdata and leafdata on some ranks. Currently We
error out on these cases. See src/vec/is/sf/examples/tutorials/ex2.c for various cases we can handle
and we can not handle.

show more ...

Fix a bunch of PetscValidPointer() -> PetscValidXXXPointer()

Replace PetscMemcpy with PetscArraycpy

Add a test for PetscSFFetchAndOp on patterned graphs

Add a test for VecScatterCreate{ToZero, ToAll}

Delete PetscSFCreateFromZero

PetscSFCreateFromZero is replaced with PetscSFCreate() + PetscSFSetGraphWithPattern(..,PETSC_PATTERN_GATHER)

Add PetscSFComposeInverse and revise PetscSFCompose

Add SF Neighbor test

Add PetscSF_Neighbor to use MPI3 neighborhood collectives

Set SF as the default vecscatter implementation

Optimize VecScatterSetUp_SF

Add patterned SF graphs and use x as roots and y as leaves in x to y vecscatter

Add op GetGraph in SF so that we can customize it

Add op CreateLocalSF in SF so that we can customize it

Also, we now create local SF on demand (i.e., lazily) since it is not always used.

Optimize the creation of embedded SFs for SFBasic

Simplify packing routines with macros and optimize packing by using index patterns

Implement PetscSFBcast with PetscSFBcastAndOp

Deprecate PetscSFGetRanks with new PetscSFGetRootRanks

Since we have PetscSFGetLeafRanks, it is better to have a similar name.

removing comments

adding GPU-GPU data movement to logging

Merged in barry/cleanup-petscconf-h (pull request #1834)

Remove testing and inserting into petscconf.h items that are not actually used by PETSc