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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Merge branch 'jacobf/2023-08-17/header-guard-check' into 'main'

Check header guards

See merge request petsc/petsc!6822

Convert all header guards to pragma once

Merge branch 'jolivet/feature-mateliminatezeros-sbaij' into 'main'

MatChop()/MatEliminateZeros() improvements and other minor fixes

See merge request petsc/petsc!6706

MatEliminateZeros(): add [S]BAIJ implementations

Merge branch 'jacobf/2022-09-21/2-bike-2-shed' into 'main'

Feature: Bicycle Storage Facility 2

See merge request petsc/petsc!5661

Transform all header-guards into ifndefs to make clang-format ignore them for preprocessor indentation

Merge branch 'barry/2022-08-21/clang-format-source' into 'main'

format repository with clang-format

See merge request petsc/petsc!5541

clang-format: convert PETSc sources to comply with clang-format

Merge remote-tracking branch 'origin/maint'

Merge branch 'jolivet/fix-hpddm-missing-interface' into 'maint'

Add KSPHPDDMMatSolve()

See merge request petsc/petsc!2730

Minor fixes and improvements

* Typos
* MatMatSolve() improvements
* MatDense[Get|Restore]ColumnF90()
* MatKAIJGetScaledIdentity()

Merge branch 'stefanozampini/update-suitesparse' into 'master'

Update SuiteSparse to use github releases + fixes to SBAIJ hermitian complex case

See merge request petsc/petsc!2305

MATSBAIJ: Fix Hermitian MatMult for Seq and MPI code paths

we can reuse the same MatMult operation with no impact for non-complex builds
Remove improper check for the hermitian complex case from Mat

MATSBAIJ: Fix Hermitian MatMult for Seq and MPI code paths

we can reuse the same MatMult operation with no impact for non-complex builds
Remove improper check for the hermitian complex case from MatGetFactor and move it where it actually belongs
Fix conversion routines from SBAIJ when the hermitian flag is set

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Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

Obtain changed (v3.5) handling of MatMPIBAIJSetPreallocationCSR to match
documentation.

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warni

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ may be used uninitialized in this function [-Wmaybe-uninitialized] ierr = DMInterpolationSetUp(interpolator, dm, pointsAllProcs);CHKERRQ(ierr);
migrate 'build requires: !mpiuni' to new format
migrate 'build requires: !complex' to new format
workarround 'division by zero' compiler warning on windows C:\cygwin64\home\petsc\PETSC~3.CLO\src\ts\examples\TUTORI~1\ex11.c(416): warning #39: division by zero if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = 0./0.; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */
dos2unix to prevent warnings on opensolaris "/export/home/petsc/petsc.clone/src/ksp/ksp/examples/tests/ex53.c", line 6: warning: invalid white space character in directive
fix output file - corresponding to code changes in efd4aadf157bf1ba2d80c2be092fcf4247860003
disable test on windows
update log from opensolaris so that the diff is clean on linux aswell
update grep in sync with change in efd4aadf157bf1ba2d80c2be092fcf4247860003
Fixed code that did not correctly set current color for block insertion
Update output files that did not get fixed after previous merges
Change MPIUni to not immediately abort on operations it cannot perform, instead return error code
Add filter for example that can produce 1 different iteration count
Example add system calloc, bad formating of %d in print, commented out code
Always use (void) for functions that take no arguments, never ()
always need to caste PetscReal variables to (double) in print statements
updates to manual page for clarity
update help menu for MatRARt() -- MatRARt_mpiaij_mpiaij is supported now, but not efficient.
fix nightlybuild error with c1cbb1def3f8ddca04c3998b9c06618fd1ffef35 on arch-linux-IPL64 src/ksp/pc/examples/tests ex5_1
...

Conflicts:
include/petscdm.h
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/dm/impls/plex/plexhdf5.c

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Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
ini

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
SNES ex12: Mix misnaming Nf --> Nc
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
typo
fill-in some references
Bib: Fixed ref
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
Plex tests: Updated to new point function API
SNES ex56: Moved tests to new format
DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tutorials/ex63.c

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Merge branch 'master' into knepley/feature-plex-torus

* master: (174 commits)
Bib: Another ref
Increase patchlevel to 3.7.6
Explicitly listing the LTO library causes difficulties on MacOS so a

Merge branch 'master' into knepley/feature-plex-torus

* master: (174 commits)
Bib: Another ref
Increase patchlevel to 3.7.6
Explicitly listing the LTO library causes difficulties on MacOS so avoid it
TSBDF: Update changes/dev.html
Added Fortran TaoType and TaoLineSearchType definitions
Add Fortran TaoType and TaoLineSearchType definitions
setblocksize for iscol_sub
TSBDF: Use standard TS API and options to control adaptivity
Bib: More refs and a correction
SNESTest: Bug-fix in SNESTest when threshold printing option is turned on.
fix warning and valgrind complains reported by the nightly tests
Section+Doc: Small doc fix
pflotran: switch to using the new upstream git repo
DMPlex: Error if attempt to partition a distributed graph with Chaco
fix complex build error
fix complex build
PetscError() did not properly copy over the specific error message when error type was PETSC_ERROR_INITIAL
TSAdapt: Refactor handling of the always_accept flag
Additional clarification for MatMeshToCellGraph() manual page
optimize MatCreateSubMatrix_MPIAIJ() by merging check of sameXXXDist() into one MPI_AllReduce
...

Conflicts:
config/BuildSystem/config/packages/med.py

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Merge branch 'master' into knepley/feature-plex-tests-new

* master: (108 commits)
Bib: Added ref
Bib: Updated reference
Bib: Updated reference
Work around problems with Apple Xcode 8.3 and h

Merge branch 'master' into knepley/feature-plex-tests-new

* master: (108 commits)
Bib: Added ref
Bib: Updated reference
Bib: Updated reference
Work around problems with Apple Xcode 8.3 and handling of rpath argument with gfortran
help menu update for MatCreateSubMatrices() Reported-by: Brad Aagaard <baagaard@usgs.gov>
fix flops for PCApply_PBJacobi_1 and PCApply_PBJacobi_7 Reported-by: Pierre Jolivet <pierre.jolivet@enseeiht.fr>
TSRK: Fix FSAL optimization to not skip update and check or stages.
Travis-CI: Workaround too long TMPDIR in macOS with Open MPI
test: Fix type mismatch in KSP test.
test: Fix warnings from gfortran -Wconversion (OS X, Homebrew build)
MPIUNI: Silence GCC -Wconversion warnings
Fortran: Add error checking for incorrect PETSC_NULL_XXX argument when expecting function
fix test output per changes in 517c9301b2e9239931bfd644803fd6bb859387ea
MUMPS: update to version 5.1.1 with opensolaris compile fixes
TSRK: Mention 5BS in the changelog.
TSRK: Mention the new 5BS scheme in the manual.
fix 'unused variable' warning
Remove unused code
added hbw_realloc
fixed undefined ptr
...

Conflicts:
config/BuildSystem/config/packages/med.py

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Merge remote-tracking branch 'origin/balay/fix-redundant-decls-warnings-master'

Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-torus

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stages

Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-torus

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stages
update to latest hypre tag on github
fix 'inf' vs 'Inf' diff wrt vec_vec_utils_tagger_tutorials-ex1_8,9,18,19
MatSetOption(mat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE) no longer applies to zero values set or added to the matrix diagonal, they are now not ignored and are included in the matrix nonzero structure. This is useful for Jacobians passed to TS.
replace use/mention of depreciated -log_summary in many places
add extchem.py which was written years ago but never put in the distribution (hence it is broken).
petsc4py: update to snapshot with MatGetSubMatrices -> MatCreateSubMatrices etc API changes
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
PetscCMPLX: assume type punning is safe
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
...

Conflicts:
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/examples/tests/ex12.c

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Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-tests-new

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stag

Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-tests-new

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stages
update to latest hypre tag on github
fix 'inf' vs 'Inf' diff wrt vec_vec_utils_tagger_tutorials-ex1_8,9,18,19
MatSetOption(mat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE) no longer applies to zero values set or added to the matrix diagonal, they are now not ignored and are included in the matrix nonzero structure. This is useful for Jacobians passed to TS.
replace use/mention of depreciated -log_summary in many places
add extchem.py which was written years ago but never put in the distribution (hence it is broken).
petsc4py: update to snapshot with MatGetSubMatrices -> MatCreateSubMatrices etc API changes
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
PetscCMPLX: assume type punning is safe
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
...

Conflicts:
src/dm/impls/plex/examples/tests/ex12.c

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Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes

Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
superlu: libray is installed in PREFIX/lib64 - fix this to use PREFIX/lib
backport fixes cc105cc3 2b35c90a - required for 3bf428d - that was backported from master - 80c96bb
'echo -n' fails on opensolaris/osx - so avoid using it.
fix diffs in nightlybuilds due to options in ~/.petscrc
add Kelley03 to src/docs/tex/petsc.bib
build: determine moudles, mpi.h used during buildtime and print in 'info'
fix analyzer warnings
fix build failure on opensolaris - where -lm from flibs is removed due to -lm in cxxlibs. But then - only flib gets used for some configure tests [blaslapack, parms]
config: prefer __restrict over C99 restrict keyword
...

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fix duplicate definitions warned by -Wredundant-decls

Also a bugfix? BLASdotu_ -> dotu

Reported-by: Till Martens <till.martens@dlr.de>