Merge branch 'barry/2025-10-18/optimize-aij-ops' into 'main'

Refactor handling of diagonal marking in *AIJ and SELL matrices

See merge request petsc/petsc!8797

- Replace MatMissingDiagonal() and MatMarkDiagonals_SeqXXX() with MatGetDiagonalMarkers_SeqXXX()

- Mat_SeqXXX->diag is not automatically created during MatAssemblyEnd() saving memory and time

- Replace MatMissingDiagonal() and MatMarkDiagonals_SeqXXX() with MatGetDiagonalMarkers_SeqXXX()

- Mat_SeqXXX->diag is not automatically created during MatAssemblyEnd() saving memory and time

- Accessing Mat_SeqXXX->diag now requires the use of MatGetDiagonalMarkers_SeqXXX() except when the current values are known to be correct; for example during numerical factorizations and solves

- Mat_SeqXXX->diag is now never shared among matrices; hence the free_diag flag is gone. That was always a risky proposition since any of the owning matrices could chang the values thus making them incorrect for other owners.

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This MR optimize some MAT[SB]AIJ operations related to the diagonal

The longer term goal is to refactor some Mat_SeqXXX non-numeric code to make it easier to also implement it on GPUs. For example,

This MR optimize some MAT[SB]AIJ operations related to the diagonal

The longer term goal is to refactor some Mat_SeqXXX non-numeric code to make it easier to also implement it on GPUs. For example, MatGetDiagonal() and friends

This commit
- MatMarkDiagonal_SeqAIJ/ELL()
- now use change in mat->nonzerostate to determine if it needs to recheck the diagonal locations
- sets diagDense flag for a complete diagonal
- MatInvertDiagonal_SeqAIJ/ELL()
- now uses change in mat->state to determine if diagonal entries and inverses need to be recomputed
- name changed to MatInvertDiagonalForSOR_SeqAIJ/ELL() for code clarity
- Added MatInvertDiagonal_SeqAIJ_Inode() for use by MatSOR_SeqAIJ_Inode()
- now uses change in mat->state to determine if block diagonal entries and inverses need to be recomputed

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Merge branch 'jolivet/clang-format-21' into 'main'

clang-format-21

See merge request petsc/petsc!8202

Convert some SETERRQ() to PetscCheck()

Merge remote-tracking branch 'origin/release'

Merge branch 'jolivet/fix-factor-inode' into 'release'

MatFactor: fix MatLUFactorNumeric_SeqAIJ_Inode()

See merge request petsc/petsc!8581

MatFactor: fix MatLUFactorNumeric_SeqAIJ_Inode()

Reported-by: Matteo Colombo

Merge remote-tracking branch 'origin/release'

Merge branch 'jczhang/2025-04-18/fix-matmult-aij-openmp-inode' into 'release'

OpenMP: add OpenMP to MatMult_SeqAIJ with inode

See merge request petsc/petsc!8331

OpenMP: add OpenMP to MatMult_SeqAIJ with inode

So users won't get performance surprises.

close #1742

Mat: rename inode.size and change it to csr format to facilitate parallel computing

Merge remote-tracking branch 'origin/release'

Merge branch 'barry/2025-01-14/better-inode-error-message/release' into 'release'

Print the requested inode size when unsupported size generates an error

See merge request petsc/petsc!8080

Print the requested inode size when unsupported size generates an error

Merge remote-tracking branch 'origin/release'

Merge branch 'jrwrigh/cleanup_malloc' into 'release'

sys: Cleanup PetscMalloc and PetscCalloc

See merge request petsc/petsc!7892

Address potential Malloc/Calloc ternary operator bugs

- Bug either by the argument of the ternary operator being cast
inappropriately to `size_t` or by the values themselves not being cast
to `s

Address potential Malloc/Calloc ternary operator bugs

- Bug either by the argument of the ternary operator being cast
inappropriately to `size_t` or by the values themselves not being cast
to `size_t` when necessary.

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Merge branch 'barry/2024-09-02/rebased-fix-conversion-warnings' into 'main'

Compiler finds (and forbid) casts from higher precision integers to lower

See merge request petsc/petsc!7806

Add to CI compilers flags '-Wconversion', '-Wno-sign-conversion', '-Wno-float-conversion', '-Wno-implicit-float-conversion']

Also fix the code to repository to compile cleanly with these flags in th

Add to CI compilers flags '-Wconversion', '-Wno-sign-conversion', '-Wno-float-conversion', '-Wno-implicit-float-conversion']

Also fix the code to repository to compile cleanly with these flags in the CI

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Merge branch 'jolivet/add-matmatsolvetranspose_seqaij' into 'main'

MatMatSolveTranspose_SeqAIJ and minor housekeeping

See merge request petsc/petsc!7386

Add MatMatSolveTranspose_SeqAIJ

Merge branch 'jolivet/clang-format-18' into 'main'

clang-format version 18

See merge request petsc/petsc!6902

CI: update to clang-format-18

Merge remote-tracking branch 'origin/release'