Merge branch 'jczhang/2023-11-16/fix-aijkokkos-diag-bug' into 'main'

Fix some bugs in MATSEQAIJKOKKOS

Closes #1490

See merge request petsc/petsc!7032

Mat: let mpiaij and mpibaij share common fields to enable generic code

Merge branch 'jolivet/feature-matcreatesubmatrices-rectangular-sbaij' into 'main'

MatCreateSubMatrices: rectangular blocks with SBAIJ

See merge request petsc/petsc!6841

MatCreateSubMatrices: rectangular blocks with SBAIJ

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 'barry/2022-09-12/fix-mat-preallocation' into 'main'

try to build efficient hash table allocation directly into Mat

See merge request petsc/petsc!5621

Add support for Mat to allow skipping preallocation by having the first round of MatSetValues use hash

* MATPREALLOCATOR can be deprecated as well as possibly some other preallocation macros/routine

Add support for Mat to allow skipping preallocation by having the first round of MatSetValues use hash

* MATPREALLOCATOR can be deprecated as well as possibly some other preallocation macros/routines
* Optimizations such as direct support for MatSetValuesBlocked() for *BAIJ can be added in the future

Commit-type: feature
/spend 25h

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Merge branch 'jacobf/2022-11-08/remove-petsctable' into 'main'

Remove PetscTable

See merge request petsc/petsc!5819

- Replace PetscTable with PetscHMapI.
- Rename:
- PetscTableCreate() -> PetscHMapICreateWithSize()
- PetscTableFind() -> PetscHMapIGetWithDefault()
- PetscTableAdd() -> PetscHMapISetWithMode()

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

Feature: Bicycle Storage Facility 2

See merge request petsc/petsc!5661

source code format changes due to .clang-format changes

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 branch 'jolivet/feature-nest-tile' into 'main'

Tiles in MatNest

See merge request petsc/petsc!3630

Add MatConjugate_[MPI|Seq][S]BAIJ()

Merge branch 'dalcinl/binary-io' into 'master'

Binary IO Enhancements

See merge request petsc/petsc!2594

MATBAIJ: Add support for MPI-IO binary viewers

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

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

Merge branch 'pr746/irinasok/feature-baijmkl/master'

* pr746/irinasok/feature-baijmkl/master:
Implementation of BAIJMKL matrix type similar to AIJMKL.
Supports MKL calls for MatMult (add and transpo

Merge branch 'pr746/irinasok/feature-baijmkl/master'

* pr746/irinasok/feature-baijmkl/master:
Implementation of BAIJMKL matrix type similar to AIJMKL.
Supports MKL calls for MatMult (add and transposed).
In case if used MKL version does not support mkl_sparse_optimize() (MKL 11.2 and earlier) PETSc default kernels are used.
Test added on configuration step to check if used version of MKL supports column major layout with zero based indexing.
All released versions of MKL do not support such cross case and MatSeqBAIJMKL_create_mkl_handle() converts matrix arrays to one based indexing before passing them to mkl routines.

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Added new matrix classes to include files
Added define MKL_SUPPORTS_BAIJ_ZERO_BASED to suuport different versions
of MKL (older verions support only one based indexing for column major
blocks in baij

Added new matrix classes to include files
Added define MKL_SUPPORTS_BAIJ_ZERO_BASED to suuport different versions
of MKL (older verions support only one based indexing for column major
blocks in baij format)

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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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