Merge branch 'stefanozampini/h2opus-dmdakokkos' into 'main'

Add support for KOKKOS in H2OPUS

See merge request petsc/petsc!6408

Configure: add support to check if a package defines a macro

useful for example to test for some macros inside PETSc code without the need to include the relevant headers

Merge branch 'jolivet/configure-housekeeping' into 'main'

configure: remove unused variables/tests

See merge request petsc/petsc!5805

configure: remove unused variables/tests

Merge remote-tracking branch 'origin/release'

Merge branch 'jolivet/fix-warnings-buildsystem' into 'release'

configure: try to remove warnings from code generated by BuildSystem

See merge request petsc/petsc!5796

configure: remove warnings from generated-code

Merge branch 'barry/2022-06-19/improve-configure-logs' into 'main'

Remove some confusing and unneeded noise output in configure.log

See merge request petsc/petsc!5352

Remove some confusing and unneeded noise output in configure.log

add missing doc for many configure methods so that configure.log has clear explanation for more tests it runs

Commit-type: configure

Remove some confusing and unneeded noise output in configure.log

add missing doc for many configure methods so that configure.log has clear explanation for more tests it runs

Commit-type: configure, usability
/spend 2h

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Merge branch 'barry/2021-04-12/support-for-nvhpc' into 'main'

These are fixes needed for clean builds with NVIDIA's HPC software toolkit

See merge request petsc/petsc!3882

Various fixes for NVIDIA's nvhpc toolkit

The nvhpc systems separates the CUDA math libaries and includes from the regular CUDA material
thus cuda.py has to detect and manage this separation automati

Various fixes for NVIDIA's nvhpc toolkit

The nvhpc systems separates the CUDA math libaries and includes from the regular CUDA material
thus cuda.py has to detect and manage this separation automatically.

Note also the nvhpc includes the MPI compilers in another directory which should be used with MPI.

Do not use outer C++ compiler as Kokkos compiler as that may not match the compiler used by nvcc, instead use the C++ compiler that nvcc uses. This is tricky because this compiler has to have access to the MPI headers since it sees all of the PETSc headers.

/spend 14h

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Merge branch 'barry/2019-07-27/error-check-mpiexec' into 'master'

Large number of fixes, optimizations for configure, speeds up the configure

See merge request petsc/petsc!2046

Large number of fixes, optimizations for configure, speeds up the configure

1) turn off checking if MPI library is shared since that code has been broken for 3+ years

2) move pure Fortran configure

Large number of fixes, optimizations for configure, speeds up the configure

1) turn off checking if MPI library is shared since that code has been broken for 3+ years

2) move pure Fortran configure tests to compilersFortran.py

3) turned threads back on but only use them for performing timeout for *runtest() commands (since they slow everything down if used
everywhere)

4) changed parallel configure (which doesn't work anyways) to use --useParallel and not overload --useThreads

5) added runtime check of mpiexec that uses timeout (replaces previous test in MPI shared libraries)

6) removed unused tests in configure in the interest of speed

7) minor refactorization of configure for better support of parallel configure (which doesn't work)

8) added timing results in configure.log. These may be accessed with grep child configure.log | sort -k3 -g

9) add check that mpiexec given in configure test matches the MPI compilers and libraries used

Commit-type: optimization, bug-fix, portability-fix, feature
Reported-by: Carl Steefel <cisteefel@lbl.gov>

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Merged in barry/cleanup-petscconf-h (pull request #1834)

Remove testing and inserting into petscconf.h items that are not actually used by PETSc

Remove additional uneeded values from petscconf.h; reorganize handling of default debugger, make it lldb on darwin

Commit-type: style-fix
Thanks-to: Jed Brown <jed@jedbrown.org>

Remove testing and inserting into petscconf.h items that are not actually used by PETSc

1) PETSC_HAVE_LIBXXXX - which was rarely used
be careful with the package libpng and libjpeg since they hav

Remove testing and inserting into petscconf.h items that are not actually used by PETSc

1) PETSC_HAVE_LIBXXXX - which was rarely used
be careful with the package libpng and libjpeg since they have lib in the name of the package
2) various system include files that are never used or always exist: for example stdlib.h
3) various system functions that are never used or always exist
4) fixes for requires for MUMPS and SuperLU_DIST when dependent packages are installed or not installed (unrelated to the rest of this pull request)
5) packages that always exist such as PETSC_HAVE_BLASLAPACK, or are not used by PETSc such as PETSC_HAVE_NETCFD
6) remove a couple of uses of HAVE_LIB* in the code that were not needed by adjusting the configure code slightly
7) remove all the #if guards for each entry in petscconf.h since petscconf.h already has a guard and
the values are never defined else where the extra guards just make the file cluttered

For a build with about 10 external packages this reduced the size of petscconf.h from 1236 lines to 828/4 around 220 entries.

Commit-type: style-fix, cleanup

Reported-by: Jed Brown <jed@jedbrown.org

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Merged petsc/petsc into master

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merge branch 'master' into jpustay/feature-swarm-example

Merged petsc/petsc into master

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (393 commits)
Bib: Update reference
Mat: Doc fix
Bib: Updated ref
PetscDS: Doc fixes
PC+LU: Do not try to refactor an

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (393 commits)
Bib: Update reference
Mat: Doc fix
Bib: Updated ref
PetscDS: Doc fixes
PC+LU: Do not try to refactor an already factored matrix
Mat: Small fix for checking and docs
Mat: Added MatSetFactorType() - Needed it when making a shell matrix look factored
PetscDS: Added PetscDSUpdateBoundary() - Lets the user change the boundary condition
single precision produces different convergence history
p4est: has a dependency on zlib - so handle it correctly
Add -mat_mffd_complex to use the Lyness complex number trick to compute J_u * v instead of differencing.
Replace VecWAXPY by VecAXPY if needed
Revert "Replace VecWAXPY by VecAXPY if needed"
Replace VecWAXPY by VecAXPY if needed
MatHermitianTransposeGetMat and MatCreateVecs
ex19: Updated test filter to avoid false positives.
DM: Improved Global-To-Natural docs Suggested-by: Josh L <ysjosh.lo@gmail.com>
Do not build shared openblas when doing static build
Upgrade OpenBLAS to 0.3.3
test: add alt output file for changes in OSX-10.14 and Xcode-10.0 [perhaps related to ML]
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Conflicts:
src/vec/is/utils/vsectionis.c

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Merge branch 'jed/python3-futurize' [PR #1122]

Merge announces support for Python 3.4+ in changes/dev.html.

* jed/python3-futurize: (44 commits)
gmakegentest: avoid prefix matching in regex
dm

Merge branch 'jed/python3-futurize' [PR #1122]

Merge announces support for Python 3.4+ in changes/dev.html.

* jed/python3-futurize: (44 commits)
gmakegentest: avoid prefix matching in regex
dm tests ex23.c: fix test args: -one -two -three
gmakegentest: more fixes
gmakegentest: fix processing of arguments containing number followed by "-"
gmakegentest: always loop over nsize; Python-3 fixes
python3: add in a python-3.4 test
python: fix build on osx/opensolaris - where 'RANLIB=ranlib -c' i.e with a space..
python3: fix --download-ptscotch error
configure: glob() gets executed early - whereas we need to get file list later [after 'make all' or equivalent] so revert back to using shell to get file-list
python3: map() requires a list modifier for this usage.
python: replace ModuleNotFoundError a python3.6+ feature with ImportError
config: call setup to ensure that debugLevel is set
nightlies: switch linux-pkg-dbg-ftn-interfaces to python3
config: enable Python-3
config: urllib/urlparse updates for Python-3 compatibility
config fblaslapack: use isIBM instead of manual test
python: replace commands with subprocess
Fix LOCDIR paths
generateetags.py: switch from commands to subprocess; unicode fix
python: don't import commands when it isn't used
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config: use idiomatic loop instead of map

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

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