Merge branch 'jczhang/2024-06-26/revise-mpi-openmp-stream' into 'main'

Revise MPI and OpenMP stream benchmarks

See merge request petsc/petsc!7651

clangformat: apply to src/src/benchmarks

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

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

Merge branch 'master' into knepley/solkx

* master: (6933 commits)
Bib: Added reference
Includegraph: Updated for compatibility with new folder layout.
Add SNESLineSearchReason to fortran inclu

Merge branch 'master' into knepley/solkx

* master: (6933 commits)
Bib: Added reference
Includegraph: Updated for compatibility with new folder layout.
Add SNESLineSearchReason to fortran includes Also truncate names to fit 32 char fortran limit
fix compile warnings /usr/home/balay/petsc.clone-2/src/vec/vec/interface/vector.c:1944: warning: division by zero in '1.0e+0 / 0.' /usr/home/balay/petsc.clone-2/src/ksp/ksp/interface/itfunc.c:508: warning: 'vec_rhs' may be used uninitialized in this function
updated output for new trust region initial size
initial size of the trust region is set as a percent of the norm of the initial guess, it should not be related to the initial norm of the function (which is kind of nuts).
The default bounds for SNESVISetVariableBounds() in the manual page were reversed from correct values
Bib: Added refs
Bib: Update MPICH webpage
Plex: Forgot to close file
removed nonexistent ex46f from makefile test rule
Revert "fixed bad merge into master"
fixed bad merge into master
fix memory leak in mkl_pardiso fix some formatting in mkl_pardiso code
mv runex111 from TESTEXAMPLES_C to TESTEXAMPLES_DATAFILESPATH
Mat+Doc: More Fortran docs
Plex ex3: Run tests with the correct number of field components
Bib: Added TetGen cite
parmetis: make sure 'ldd libparmetis.so' points to the correct libmetis.so that its linked with.
small fix as reported by the nightly test
...

Conflicts:
config/builder.py

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Merge branch 'master' into shri/ts-is-for-differential-variables

Conflicts:
include/petsc-private/tsimpl.h
src/ts/impls/eimex/eimex.c
src/ts/interface/ts.c

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]
gfortran: remove 132 char limit from f90 free-form
SNES: Set up matrix-free *after* copying the user Jacobian to snes->pc
DMPlex-Gmsh: Use trueNumCells when building the coordinate section
Sys: Got guard logic reversed
Sys: The #define guard for PetscMalloc*() must match the one for PetscFree*()
PetscFV: I hate fucking complex
removed ltog scatter from DMDA since functionality can be obtained with gtol scatter and less memory
fix test of DMLocalToGlobalBegin/End and add actual test cases
improve object memory logging for DA, ISLocalToGlobal and ISBLOCK
lower high water mark of constructing parallel scatter by allocating only as much room in svalues as needed
owner in VecScatter construction is the rank, therefor can use PetscMPIInt to hold it do not PetscInt
another reuse of allocated array in 2d/3d DMDA create
improved high water mark of DMDASetups by implementing and using PETSC_USE_POINTER for ISCreateBlock()
PetscFV: Another complex fix
DMPlex+TS: Fixing types
ISIdentity() was wrong for block IS! Indices are NOT scaled by bs
PetscFV: Straighten out complex types
TS ex11: Fix casts and remove unused variable
...

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Merge branch 'master' into barry/saws-options

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bdd

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddcprivate.c

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Merge remote-tracking branch 'origin/master' into feature-dmmoab

Merged petsc/petsc into master

Merge branch 'master' into knepley/feature-plex-hdf5-parallel-load

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this wa

Merge branch 'master' into knepley/feature-plex-hdf5-parallel-load

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this was really bad)
outdated example that doesn't match coding style removed and buggy
petscversion.h: workaround ifort -cpp lack of referential transparency
configure: ignore AR, MAKEFLAGS [if set in env]
incorrect first entry in array being zeroed in example
sizeof.c: remove dependence on petsc [and fix syntax error]
nightlybuilds: use consistant PETSC_ARCH, machine names
TS: Allow viewing of TS solutions
DMPlex: Fix comparison for complex
change MPIVersion streams to use MPI_Wtime() to be portable to Windows do not use scalar square root on real number; it upsets Microsoft
cannot use I in PETSc code because in complex it sometimes represents imaginary number cannot pass PetscScalar * to VecNorm()
in dashboard don't warn about SSL and BOI deprecated
TS ex11: Fixed output formatting
Doc+DMPlex: Added function documentation for some refinement functions
streams: translate code from 'bash' to 'sh' [fix freebsd]
barry is an idiot who doesn't have a clue as to what he is doing (and git's unfriendlyness doesn't help matters)
don't list examples under C that don't work with complex!
forgotten output file
removed valgrind warning about sending uninitialized data
nightly builds ignore unrecognized pragma and .c file as C++ code
...

Conflicts:
include/petsc-private/dmpleximpl.h

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sizeof.c: remove dependence on petsc [and fix syntax error]

Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

minor cleanup of unneeded included files

Hg-commit: a1ec1768809a9512ac930c5b664efd3036507774

backout all chmod stuff in bf971ba58125
[but keep diffs to src/mat/impls/aij/mpi/mpimatmatmult.c ]

Hg-commit: 4a812fc1f35496ce2717c7da9ef12ffabbd13258

removed a spurious call to MatSetBlockSize.

Hg-commit: bf971ba58125bd8cf7ceb2a9d0f5cdf27c27cc6a

commit after merge

Hg-commit: d540875a63b3c979c82b6a7fa7f062571e906d10

Mass revert file modes that were made executable in f6e61ee9c329

Hg-commit: 116d90d0b66125cee0db3e7351047057e756baf5

Merge

Hg-commit: ee8d91ae0580d1d4fa92be38a18d40c838b9a257

changed MatMatMult to MatTranposeMatMult.

Hg-commit: f6e61ee9c329774cd5343eea1ee6b7432be17c3f

bk-changeset-1.3482
knepley@khan.(none)|ChangeSet|20050825210555|50813
ChangeSet
1.3482 05/08/25 16:05:55 knepley@khan.(none) +1 -0
Merge bk://petsc@petsc.bkbits.net/petsc-dev
into khan.(none)

bk-changeset-1.3482
knepley@khan.(none)|ChangeSet|20050825210555|50813
ChangeSet
1.3482 05/08/25 16:05:55 knepley@khan.(none) +1 -0
Merge bk://petsc@petsc.bkbits.net/petsc-dev
into khan.(none):/home/knepley/PETSc-dev/petsc-dev

src/mat/interface/matrix.c
1.191 05/08/25 16:05:54 knepley@khan.(none) +0 -0
Auto merged


Hg-commit: a35f89bbcfde354c6ecb2601f1bf553ccad7ac22

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bk-changeset-1.3473.1.50
balay@asterix.mcs.anl.gov|ChangeSet|20050825175605|50988
ChangeSet
1.3473.1.50 05/08/25 12:56:05 balay@asterix.mcs.anl.gov +1 -0
Merge asterix.mcs.anl.gov:/home/balay/pet

bk-changeset-1.3473.1.50
balay@asterix.mcs.anl.gov|ChangeSet|20050825175605|50988
ChangeSet
1.3473.1.50 05/08/25 12:56:05 balay@asterix.mcs.anl.gov +1 -0
Merge asterix.mcs.anl.gov:/home/balay/petsc-dist
into asterix.mcs.anl.gov:/home/balay/bk-rep/petsc-dev

include/petscversion.h
1.170 05/08/25 12:56:03 balay@asterix.mcs.anl.gov +0 -0
Auto merged


Hg-commit: b2b4914c962900cf49223e8ed90e464eeda1e4eb

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bk-changeset-1.3215.1.54
balay@asterix.mcs.anl.gov|ChangeSet|20050825175528|43098
ChangeSet
1.3215.1.54 05/08/25 12:55:28 balay@asterix.mcs.anl.gov +2 -0
%d doesn't work with size_t

src/benchm

bk-changeset-1.3215.1.54
balay@asterix.mcs.anl.gov|ChangeSet|20050825175528|43098
ChangeSet
1.3215.1.54 05/08/25 12:55:28 balay@asterix.mcs.anl.gov +2 -0
%d doesn't work with size_t

src/benchmarks/sizeof.c
1.4 05/08/25 12:55:26 balay@asterix.mcs.anl.gov +9 -8
%d doesn't work with size_t

include/petscversion.h
1.138.1.29 05/08/25 12:55:25 balay@asterix.mcs.anl.gov +2 -2
%d doesn't work with size_t


Hg-commit: f27d3995846f8235ac1c978b3c7c215b1d85af1a

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