style-fixes

Merge branch 'psanan-release-patch-82973' into 'main'

Developer docs, style: remove rule about using "if (!rank)" and replace all "!rank" usage with "rank == 0"

See merge request petsc/petsc!4146

Style: replace "!rank" with "rank == 0"

In SF tutorial ex1 (src/vec/is/sf/tutorials/ex1.c), add parentheses around "rank == 0". This is relevant because ! binds more tightly than +, but == binds les

Style: replace "!rank" with "rank == 0"

In SF tutorial ex1 (src/vec/is/sf/tutorials/ex1.c), add parentheses around "rank == 0". This is relevant because ! binds more tightly than +, but == binds less
tightly, so the result of the computation would otherwise change.

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Merge branch 'barry/2021-05-16/fix-double-lines' into 'main'

Fix typos in source

See merge request petsc/petsc!3984

Remove all double blank lines from source

Commit-type: petsc-style
/2h

Merge branch 'barry/2020-10-08/fix-mpi-error-codes' into 'master'

Convert MPI error type to PETSc error with string message for all MPI calls

See merge request petsc/petsc!3326

Convert MPI error type to PETSc error with string message for all MPI calls

Now PETSc examples will ONLY return PETSc error codes and never MPI error codes directly so we can understand and post-pro

Convert MPI error type to PETSc error with string message for all MPI calls

Now PETSc examples will ONLY return PETSc error codes and never MPI error codes directly so we can understand and post-process their
errors better.

The test harness will now automatically retry tests that fail with MPI, this may help with Intel MPI that produces
seemingly random failures.

Commit-type: error-checking
/spend 30m

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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

Merge branch 'dalcinl/fix-null' into 'master'

KSP/PC: Fix 0 ->NULL for pointers

See merge request petsc/petsc!2794

KSP/PC: Fix 0 ->NULL for pointers

Merge branch 'barry/utilize-matdensegetarrayread' [PR #1598]

* barry/utilize-matdensegetarrayread:
Use MatDenseGetArrayRead() rather than MatDenseGetArray() when possible

Use MatDenseGetArrayRead() rather than MatDenseGetArray() when possible

Commit-type: style-fix, feature

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

Merged petsc/petsc into master

Merged petsc/petsc into master

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

Merge branch 'barry/improve-error-propagation-ksp-pc'

Improve the error propagation between and within KSPs and PCs

- Added KSPCheckSolve() to be called consistently by PCs to set failures if the inner solvers fail.
- Added use of KSPCheckNorm() and KS

Improve the error propagation between and within KSPs and PCs

- Added KSPCheckSolve() to be called consistently by PCs to set failures if the inner solvers fail.
- Added use of KSPCheckNorm() and KSPCheckDot() to all the Krylov methods to propagate errors from PCs to the KSPs.

Commit-type: feature

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Merge branch 'master' into knepley/feature-plex-functionals

* master: (984 commits)
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out

Merge branch 'master' into knepley/feature-plex-functionals

* master: (984 commits)
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out
fix gcov obj path
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Dev manual: remove duplicate entry
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.
...

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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-pc-patch

* master: (562 commits)
fix clang-analyzer warning
Developers manual never use system randomizers in PETSc and example source code.
missing

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

* master: (562 commits)
fix clang-analyzer warning
Developers manual never use system randomizers in PETSc and example source code.
missing CHKERRQ()
DT: Reverting the tgamma change broke MPFR - I guess we need a nightly build with it in
Add a test for ex21
Fix error in ex21
Add missing fortran interface that handles null objects
DMComposite: add missing guards
MatPreallocate: fix overpreallocation of local rows
style fixes
MatView_MPI_DA: do not print twice the class prefix
MatSetOperation: stash the original MatView_XXX in the viewnative function pointer
DMCreateInterpolation_DA gracefully error instead of catching FPE signals
MatIncreaseOverlap: preserve communicator of index sets
MatMPIAIJ: fix indentation and missing CHKERRQ
ISBuildTwoSided: remove tabs and fix style
Fix documentation
PetscViewerDraw: fix unininitialized warning from valgrind
MatConvert_SeqAIJ_SeqBAIJ: remove error for non square matrices and add MAT_REUSE_MATRIX case
Mat: MAT_INPLACE_MATRIX can be used for transposition with rectangular matrices
...

Conflicts:
src/dm/dt/interface/dtfe.c
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexfem.c
src/snes/examples/tutorials/ex13.c
src/snes/examples/tutorials/ex62.c
src/snes/examples/tutorials/makefile
src/snes/examples/tutorials/output/ex62_18.out
src/snes/examples/tutorials/output/ex62_19.out
src/snes/examples/tutorials/output/ex62_20.out
src/snes/examples/tutorials/output/ex62_20_parmetis.out
src/snes/examples/tutorials/output/ex62_21.out
src/snes/examples/tutorials/output/ex62_22.out
src/snes/examples/tutorials/output/ex62_23.out
src/snes/examples/tutorials/output/ex62_24.out
src/snes/examples/tutorials/output/ex62_25.out
src/snes/examples/tutorials/output/ex62_26.out
src/snes/examples/tutorials/output/ex62_27.out
src/snes/examples/tutorials/output/ex62_28.out
src/snes/examples/tutorials/output/ex62_29.out
src/snes/examples/tutorials/output/ex62_2d_p3_1.out
src/snes/examples/tutorials/output/ex62_30.out
src/snes/examples/tutorials/output/ex62_31.out
src/snes/examples/tutorials/output/ex62_32.out
src/snes/examples/tutorials/output/ex62_33.out
src/snes/examples/tutorials/output/ex62_34.out
src/snes/examples/tutorials/output/ex62_35.out
src/snes/examples/tutorials/output/ex62_36.out
src/snes/examples/tutorials/output/ex62_pc_simple.out
src/snes/examples/tutorials/output/ex62_pc_simplec.out
src/snes/examples/tutorials/output/ex62_quad_q2p1_full.out
src/snes/examples/tutorials/output/ex62_quad_q2q1_full.out
src/snes/utils/dmplexsnes.c

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Merge branch 'master' into knepley/feature-error-logging

* master: (221 commits)
dashboard: count and list example compile failures like:
fix fix-pr879-jczhang-optimize-vecscatter-multi-copy
a

Merge branch 'master' into knepley/feature-error-logging

* master: (221 commits)
dashboard: count and list example compile failures like:
fix fix-pr879-jczhang-optimize-vecscatter-multi-copy
add manual page cross links for SNESLineSearchSetPostCheck() and related routines
fix help manual of MatCreateSubmatrices() Reported-by: Tim Steinhoff <kandanovian@gmail.com>
Add manual pages for PetscRealPart() and PetscImaginaryPart()
fix compile error with missing MPI_C_DOBULE_COMPLEX
fix typo Reported-by: Febrian Setianto <febrian.setianto@gmail.com>
plex tutorial ex5: updated test requirements
DMPlexLoad_HDF5_Xdmf_Internal: fix for complex PetscScalar.
DMPlexLoad_HDF5_Xdmf_Internal: fix for 64-bit PetscInt.
DMPlexBuildFromCellList_Internal: use DMPlexInvertCell_Internal (with PetscInt* arg)
petscviewer.h: removed notice which is no longer relevant
DMPlexCreateFromFile: document option
check only if PETSC_USE_DEBUG
DMPlexBuildFromCellList_Internal optionally inverts cells.
ex5: new test 4 with -compare without repartitioning
ex5: new test 3 using -compare
ex5: HDF5 write+read moved to separate function
ex5: option -format processed in ProcessOptions()
ex5: added missing hdf5 requirement
...

Conflicts:
include/petsclog.h

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Merge branch 'psanan/manpages-notes-newlines' [PR #932]

* psanan/manpages-notes-newlines:
A large number of man pages are improperly formatted because of the lack of a newline after "Notes:", "Fortr

Merge branch 'psanan/manpages-notes-newlines' [PR #932]

* psanan/manpages-notes-newlines:
A large number of man pages are improperly formatted because of the lack of a newline after "Notes:", "Fortran Notes:", or "Developer Notes:".
This batch adds those newlines, with 4 spaces of indentation afterwards.
The uniform indentation arguably makes the man pages a little less readable in the source itself,
but overall this hopefully has a large positive impact on the readability of the HTML pages.

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