Merge remote-tracking branch 'origin/release'

Merge branch 'barry/2021-12-26/cleanup-apple-valgrind-mkdtemp-workaround/release' into 'release'

Improve Apple valgrind work around for mkdtemp()

See merge request petsc/petsc!4674

Improve Apple valgrind work around for mkdtemp()

Commit-type: style-fix
\spend 5m
Reported-by: Jed Brown jed@jedbrown.org

Merge branch 'jacobf/2021-11-02/attribute-format-sys' into 'main'

Feature: PETSC_ATTRIBUTE_FORMAT - sys

See merge request petsc/petsc!4520

apply PETSC_ATTRIBUTE_FORMAT and related fixes to sys sources

Merge remote-tracking branch 'origin/balay/add-valgrind.h'

valgrind.h: add to petsc repo

See merge request petsc/petsc!4094

valgrind.h: add to petsc at include/private/valgrind

Merge branch 'barry/2020-11-13/fix-valgrind-macos-for-now' into 'master'

Turn off opencl support for MPICH if running on Apple MacOS with valgrind

See merge request petsc/petsc!3419

Provide support for using valgrind with PETSc on the Apple MacOS, all tests pass

Turn off opencl support for MPICH if running on Apple MacOS with valgrind,
because the check in hwloc() crashes un

Provide support for using valgrind with PETSc on the Apple MacOS, all tests pass

Turn off opencl support for MPICH if running on Apple MacOS with valgrind,
because the check in hwloc() crashes under valgrind
Turn off lazy dynamic loading of shared libraries with valgrind, because that crashes valgrind
Provide custom mkdtemp() with valgrind because Apple's system one is not supported by valgrind
Add Apple specific suppression files for valgrind
Update documentation for using valgrind with Apple
Warn user they must use --download-fblaslapack or --download-f2cblaslapack with valgrind

Commit-type: portability-fix
/spend 6h
Reported-by: Hapla Vaclav <vaclav.hapla@erdw.ethz.ch>
Thanks-to: Hong Zhang hongzhang@anl.gov

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Merge branch 'barry/2020-08-16/fix-source-formatting' into 'master'

Turn on checkbadSource test to generate an error when found; fix all source code that causes errors

See merge request petsc/petsc

Merge branch 'barry/2020-08-16/fix-source-formatting' into 'master'

Turn on checkbadSource test to generate an error when found; fix all source code that causes errors

See merge request petsc/petsc!3064

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Turn on checkbadSource test to generate an error when found; fix all source code that causes errors

Commit-type: portability-fix, testing-fix, style-fix, feature, maintainability
/spend 1.5h

Merged in Hong-Zhang/fdirc-edited-online-with-bitbucket-1558231127853 (pull request #1681)

Rename the variable max_retry_time

Rename the variable max_retry_time

fdir.c edited online with Bitbucket

Revert "PetscMkdtemp: remove duplicate copies"

This reverts commit 5896fb9e39e84ae2eb743f82d9026350ea94629a.

_mktemp_s takes a template as input, if it fails - we need to copy the template again

S

Revert "PetscMkdtemp: remove duplicate copies"

This reverts commit 5896fb9e39e84ae2eb743f82d9026350ea94629a.

_mktemp_s takes a template as input, if it fails - we need to copy the template again

Suggested-by: "Zhang, Hong" <hongzhang@anl.gov>

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PetscMkdtemp: remove duplicate copies

Suggested-by: "Smith, Barry F." <bsmith@mcs.anl.gov>

Merged in hongzh/improve-tstrajectory-folder (pull request #1673)

Generate unique folder names for TSTrajectory

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Emil Constantinescu <emcon

Merged in hongzh/improve-tstrajectory-folder (pull request #1673)

Generate unique folder names for TSTrajectory

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Emil Constantinescu <emconsta@mcs.anl.gov>
Approved-by: Stefano Zampini <stefano.zampini@gmail.com>

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fix PetscStrncpy() usage.

Suggested-by: "Smith, Barry F." <bsmith@mcs.anl.gov>

Add windows support for PetscMkdtemp

Funded-by:
Project: FASTMath adjoint
Time: 1.0 hours
Reported-by:
Thanks-to:

Generate unique folder names for TSTrajectory

- Added PetscMkdtemp()
- Removed -ts_trajectory_dirname in tests
- The changes are also applied to trajmemory.c

Funded-by:
Project: FASTMATH adjoint
Ti

Generate unique folder names for TSTrajectory

- Added PetscMkdtemp()
- Removed -ts_trajectory_dirname in tests
- The changes are also applied to trajmemory.c

Funded-by:
Project: FASTMATH adjoint
Time: 6.5 hours
Reported-by:
Thanks-to:

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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 remote-tracking branch 'origin/knepley/fix-snes-ex69' into tisaac/feature-dmfield

* origin/knepley/fix-snes-ex69: (311 commits)
PetscFECreateDefault: fix custom Fortran interface to use MPI_

Merge remote-tracking branch 'origin/knepley/fix-snes-ex69' into tisaac/feature-dmfield

* origin/knepley/fix-snes-ex69: (311 commits)
PetscFECreateDefault: fix custom Fortran interface to use MPI_Comm
SNES ex69: Updated test output
SNES ex69: Removed all mantle stuff and change fields to constants - Also use dsymutil for executables
SNES ex69: Removed special partition
SNES ex69: Fixed null space creation - Null space locks its vectors
PetscFE: PetscFECreateDefault() now takes MPI_Comm instead of DM
cleanup very ugly PCGAMG manual page
minor clarifications for VecScatterCreate() manual page
gcov: PETSC_ARCH is required onlyfor -run_gcov - and not for -merge_gcov [where it doesn't exist]
make clearer in help statements what --with-external-packages-dir is for.
Website: Added news entry for PETSc User Meeting 2018 on main page.
CUDA: Further test output fixes for mat_tests-ex2
Turn off elemental test for parmetis running since this does not work on batch systems.
3.8 Changes: KSPCHEBYSHEV
CUDA: Fixed most test errors due to MatMultTranspose*
website: update urls
website: fix Jason's name to match pic. Also add Todd's pic
Dev manual: copyedit
DMPlexDistributeLabels: Propagate the output flag
cuda/cusp: update minimum supported versions of cuda to 7.5 and cusp to 0.5.0
...

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Merge branch 'barry/refactor-petscstrncat'

Change PetscStrncat() to PetscStrlcat() to match BSD API where l represents total length

Update many uses of PetscStrcpy() and PetscStrcat() to the safer PetscStrncpy() and PetscStrlcat()

Commit-ty

Change PetscStrncat() to PetscStrlcat() to match BSD API where l represents total length

Update many uses of PetscStrcpy() and PetscStrcat() to the safer PetscStrncpy() and PetscStrlcat()

Commit-type: style-fix, feature
Thanks-to: Jed Brown

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add Burger's spectral test case

Improve PetscMkdir() if directory already exists

Commit-type: testing-fix, feature