Merge branch 'jolivet/housekeeping' into 'main'

Minor housekeeping

See merge request petsc/petsc!8811

checkbadSource: check style of config/*

Merge remote-tracking branch 'origin/release'

Merge branch 'jose/codespell-typos' into 'release'

A few more codespell fixes

See merge request petsc/petsc!5786

A few more codespell fixes

Merge remote-tracking branch 'origin/release'

Merge branch 'jose/codespell-fixes' into 'release'

A few codespell fixes

See merge request petsc/petsc!5259

A few codespell fixes

Merge branch 'balay/disable-python2' into 'main'

Balay/disable python2

See merge request petsc/petsc!5131

disable python2 support - now python3.4+ is required
- update CI tests to use python3
- continue to use python2 on MacOS CI [due to python3 issues on 10.15.7]

Merge branch 'balay/fix-mswin-C_DOUBLE_COMPLEX-check' into 'main'

MSWIN: set HAVE_MPI_C_DOUBLE_COMPLEX on successful compile, and always compile PetscSum_Local() etc MPI utilities

See merge request

Merge branch 'balay/fix-mswin-C_DOUBLE_COMPLEX-check' into 'main'

MSWIN: set HAVE_MPI_C_DOUBLE_COMPLEX on successful compile, and always compile PetscSum_Local() etc MPI utilities

See merge request petsc/petsc!3672

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configure: remove --known-mpi-long-double type options and have HAVE_MPI_C_DOUBLE_COMPLEX set on successful compile [no need for run]

running binaries via configure on windows is broken as its using

configure: remove --known-mpi-long-double type options and have HAVE_MPI_C_DOUBLE_COMPLEX set on successful compile [no need for run]

running binaries via configure on windows is broken as its using cygwin path for the binary [and the checkRun code is not needed anyway]

Reported-by: Milan Pelletier <milan.pelletier@protonmail.com>

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Merge branch 'barry/no-batch-script'

No more batch submission script; this is all due to a very smart idea of Lisandro Dalcin

*) removed or fixed all remaining --know-xx options that required a batch submission script
*) removed all de

No more batch submission script; this is all due to a very smart idea of Lisandro Dalcin

*) removed or fixed all remaining --know-xx options that required a batch submission script
*) removed all details of --known-size-- that are no longer needed
*) cleaned up BAIJMKL source code, made it work with the rest of PETSc and removed is
dependence on a batch submission script, added test case for BAIJMKL
*) update the installation guide on batsch submissions and OpenMP
*) print MKL version, print OpenMP usage with mkl_sparse options

Commit-type: bug-fix, portability-fix, style-fix, feature, documentation, example
Thanks-to: Lisandro Dalcin <dalcinl@gmail.com>

$ ./configure --with-batch
===============================================================================
Configuring PETSc to compile on your system
===============================================================================
=============================================================================== ***** WARNING: Cannot determine if MPI_INT64_T works on your system in batch-mode! Assuming it does work. Run with --known-mpi-int64_t=0 if you know it does not work (very unlikely). Run with --known-mpi-int64_t=1 to remove this warning message. warning message ***** =============================================================================== =============================================================================== ***** WARNING: Cannot determine if MPI_C_DOUBLE_COMPLEX works on your system in batch-mode! Assuming it does work. Run with --known-mpi-c-double-complex=0 if you know it does not work (very unlikely). Run with --known-mpi-c-double-complex=1 to remove this warning message. warning message ***** =============================================================================== =============================================================================== ***** WARNING: Cannot verify that MPI is a shared library - in batch-mode! If MPI is a static library but linked into multiple shared libraries that the application uses, sometimes compiles work - but one might get run-time errors. If you know that the MPI library is shared - run with --known-mpi-shared-libraries=1 option to remove this warning message ***** =============================================================================== =============================================================================== ***** WARNING: Cannot determine if BLAS/LAPACK uses 32 bit or 64 bit integers in batch-mode! Assuming 32 bit integers. Run with --known-64-bit-blas-indices if you know they are 64 bit. Run with --known-64-bit-blas-indices=0 to remove this warning message. warning message ***** ===============================================================================

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Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
config

Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
PetscFileRetrieve(): Suppress output to STDERR when downloading a file.
MatMatMult: Fixed unused variable pN.
DMDestroy: Guard call to dm->ops->destroy * Similar guards are in place in many other methods (IS,Vec,Mat) and permit the DM to be destroyed even if DMSetType() was never called.
...

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

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComp

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

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex type is missing from fortran
initialize variables so that static analyzer doesn't mistakenly think they are used uninitialized.
Move access of prefix until it is actually used
Remove DMDASplitComm2d(), used in one example that was not tested
Functions that do not return PetscErrorCode should not use PetscFunctionBegin/End paradgm
remove unneeded reassignment of same value
Missing CHKERRQ(); Mostly in Tao code
Remove clang static analyser warning about passing NULL variable to strncat()
missing newline in -ts_monitor_extreme
minor fixes for integer counters
Configure: Deal with '__func__' in C89 builds with newer Clang and GCC.
Jenkinsfile: Increased timeout for tests to 5 minutes.
3.9 changes: further clarify removal of -pc_factor_mat_solver_package
Options deprecations: add "PETSc" to inline warning
removing unused variable
MatShift support added to MATSUBMAT. Mimics MATSHELL functionality. Needed for matrix-free Hessians in TAO Newton-Line-Search methods.
Add -ts_monitor_extreme
Dev manual: add note on deprecating options database keys
...

Conflicts:
src/dm/impls/plex/examples/tests/ex4.c

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Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead code.
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
...

Conflicts:
src/snes/examples/tutorials/ex13.c

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Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep us

Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep usage on solaris [use egrep]
opensolaris: fix errors
Update timer reporting and minor reporting fix
Remove redundant if statement. Found by @jedbrown
Fixed problem with order of developer photos on website.
superlu_dist: use correct flag in example [PETSC_HAVE_SUPERLU -> PETSC_HAVE_SUPERLU_DIST]
Bib: PERMON ref
fix for osx
doc: more author fixes
doc: more author fixes
Italicized "orderings" in MPI process placement discussion.
Added Richard to the user manual author list.
Added Richard to the list of active developers on the website.
add string check for MS-MPI and IMPI timeout errors
opensolaris does not have multiple grep utils - but default one does not support -F. So use fgrep instead
Standardizing timeout checks
Report wall clock time of total tests
Use time instead of date %s
...

Conflicts:
include/petscpc.h
src/ksp/ksp/interface/itfunc.c

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Merge branch 'rmills/vectorize-aij-avx512-only'

Added configure option, "--with-avx512-kernels", to specify that kernels hand-coded with AXV-512 should be preferred.

Merge branch 'rmills/fix-remove-knl-compiler-workaround'

Removed -mP2OPT_hpo_vec_remainder=F Intel flag and "-fp_trap" from Allen-Cahn test.

The -mP2OPT_hpo_vec_remainder=F flag is not needed for current versions of the Intel Compiler.
The "-fp_trap" was

Removed -mP2OPT_hpo_vec_remainder=F Intel flag and "-fp_trap" from Allen-Cahn test.

The -mP2OPT_hpo_vec_remainder=F flag is not needed for current versions of the Intel Compiler.
The "-fp_trap" was removed because it results in detection of phantom floating-point exceptions when Short Vector Math Library (SVML) functions are used in AVX-512 executables.

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Merge branch 'barry/blaslapack-int-size'

update sample configuration options with required BLAS ones for batch systems

Commit-type: i.e. bug-fix, portability-fix, testing-fix,style-fix, feature, documentation, example
Funded-by:
Project:
T

update sample configuration options with required BLAS ones for batch systems

Commit-type: i.e. bug-fix, portability-fix, testing-fix,style-fix, feature, documentation, example
Funded-by:
Project:
Time: hours
Reported-by:
Thanks-to:
Development Tools: Vim, Emacs, Eclipse

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Typographical correction in example configure script.