Merge branch 'jczhang/fix-fortran-object-reinit' into 'main'

Fortran: re-init destroyed petsc objects so that they are different from null objects

See merge request petsc/petsc!3786

Fortran: re-init destroyed petsc objects so that they are different from null objects

Reported-by: Jose E. Roman <jroman@dsic.upv.es>

Fix compile warnings

Kokkos: do not redeclare functions if device is host

Merge remote-tracking branch 'origin/jczhang/add-DMDAVecGetKokkosOffsetView'

Add DMDAVecGetKokkosOffsetView and friends

See merge request petsc/petsc!3383

Merge branch 'knepley/feature-plex-ds-traversals' into 'main'

DS: Moved management of pointwise functions into PetscWeakForm object - Added...

See merge request petsc/petsc!3726

Plex+DS: Moved management of pointwise functions into PetscWeakForm object
- Added PetscChunkBuffer to manage contiguous buffer space
- WeakForm can index functions by Label/val, field
- WeakForm

Plex+DS: Moved management of pointwise functions into PetscWeakForm object
- Added PetscChunkBuffer to manage contiguous buffer space
- WeakForm can index functions by Label/val, field
- WeakForm allows multiple kernels per key

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Documentation fixes

Add template VecGetKokkosView

F90: Encapsulate the usage of MPI in petsc.mod and import only needed definitions into other petsc modules.

This requires an explicit use of petsc.mod [or mpi.mod or mpi_f18.mod] from user code

fixes for -i8, gfortran-10

fix makefile include directive

Merge branch 'balay/reorg-f90-for-xlf' into 'main'

generatefortranstubs: switch from 'use petscvecdef' to 'import tVec' etc.

See merge request petsc/petsc!3723

fix custom f90 stubs from 'use petscvec to 'import tVec'

test PetscSFCreateByMatchingIndices

add PetscSFCreateByMatchingIndices

Merge remote-tracking branch 'origin/release'

check: cleanup after hdf5 test

Reported-by: Lisandro Dalcin <dalcinl@gmail.com>

Add SF NVSHMEM support

Add non-null PetscDefault{Cuda,Hip}Stream

SF: rename SFCreateEmbeddedSF to SFCreateEmbeddedRootSF

SF: add an MPI_Op argument to SFBcast

Replace MPIU_REPLACE with MPI_REPLACE

Since we believe all MPI implementations support MPI_REPLACE

Merge branch 'barry/2021-02-02/petscsf-communication-specific' into 'main'

PetscSFView() never called viewer for the specific type (bug), hence many...

See merge request petsc/petsc!3606

PetscSFView() never called viewer for the specific type (bug), hence many output files were incorrect.

Added PetscSFView() support for basic MPI implementation and binary viewer saves communication

PetscSFView() never called viewer for the specific type (bug), hence many output files were incorrect.

Added PetscSFView() support for basic MPI implementation and binary viewer saves communication data to binary file.
This new viewer shows exactly how much data is sent from each rank to the other ranks
allowing fiting various performanace models to the data.

This uses MatView() to save the PetscSF data, but since Mat is above PetscSF in the software stack
the code will not work with multiple PETSc libraries. How should this be managed if one wishes to preserve the
traditionl PETSc algorithm stack?

Commit-type: bug-fix, feature
Funded-by: brain project
Project: brain project
spend 1h

Update sfbasic.c save the transpose of the matrix since that indicates the sends for each rank which is easier to understand

Enable PetscSFView_Basic_PatternAndSizes only with single library

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