Merge branch 'jolivet/rm-explicit-empty-output_file' into 'main'

Remove 535 empty .out and consolidate the use of output/empty.out

See merge request petsc/petsc!8538

Remove explicitly listed empty files and switch to output/empty.out

Merge branch 'jolivet/rm-first-empty-line' into 'main'

Remove first and last empty lines

See merge request petsc/petsc!6892

Remove first and last empty lines

Merge branch 'balay/ci-migrate' into 'main'

CI: migrate some Ubuntu-18.04 jobs to 22.04

See merge request petsc/petsc!6119

CI: migrate to Ubuntu-22.04:

- arch-ci-linux-without-fc: use updated boost (from prior commit)
- arch-ci-linux-pkgs-dbg-ftn-interfaces: fix warning src/sys/tutorials/ex3.c, disable PETSC_HAVE_THREAD

CI: migrate to Ubuntu-22.04:

- arch-ci-linux-without-fc: use updated boost (from prior commit)
- arch-ci-linux-pkgs-dbg-ftn-interfaces: fix warning src/sys/tutorials/ex3.c, disable PETSC_HAVE_THREADSAFETY in src/ksp/ksp/tutorials/ex2.c, src/snes/tutorials/ex19.c, disable superlu_dist
- arch-ci-linux-pkgs-opt: use CXXFLAGS=-Wno-deprecated-declarations to suppress warnings from moab with gcc-12
- arch-ci-linux-xsdk-dbg: fix warnings with PetscFree() in src/dm/impls/swarm/swarm_migrate.c, src/dm/impls/swarm/tests/ex9.c, src/ts/utils/dmplexlandau/plexland.c
- arch-ci-linux-opt-misc
- arch-ci-linux-pkgs-64idx
- arch-ci-linux-64idx-i8: snes_tutorials-ex78_2 fail on es only? use mcpu
- arch-ci-linux-opt-cxx-quad
- arch-ci-linux-ILP64: Use -Wno-discarded-qualifiers to suppress warnings from mpich2
- arch-ci-linux-64idx-i8-uni: snes_tutorials-ex78_2 fail on es only? use mcpu

details: (arch-ci-linux-pkgs-dbg-ftn-interfaces: disable superlu_dist)

[balay@pj01 petsc]$ make check
> ** On entry to DGEMM parameter number 8 had an illegal value
Possible problem with ex19 running with superlu_dist, diffs above

[balay@pj01 tutorials]$ valgrind --tool=memcheck -q ./ex19 -da_grid_x 20 -da_grid_y 20 -pc_type lu -pc_factor_mat_solver_type superlu_dist
lid velocity = 0.0025, prandtl # = 1., grashof # = 1.
==1342260== Conditional jump or move depends on uninitialised value(s)
==1342260== at 0x6C918B2: __kmp_fork_call (runtime/src/kmp_runtime.cpp:2183)
==1342260== by 0x6C841BA: __kmpc_fork_call (runtime/src/kmp_csupport.cpp:300)
==1342260== by 0x61BAE8A: pdgstrf (SRC/dlook_ahead_update.c:124)
==1342260== by 0x618C523: pdgssvx (SRC/pdgssvx.c:1173)
==1342260== by 0x5047C39: MatLUFactorNumeric_SuperLU_DIST (superlu_dist.c:445)
==1342260== by 0x4CAB6B9: MatLUFactorNumeric (matrix.c:3224)
==1342260== by 0x58C0892: PCSetUp_LU (lu.c:120)
==1342260== by 0x56EFEC2: PCSetUp (precon.c:994)
==1342260== by 0x55B8181: KSPSetUp (itfunc.c:405)
==1342260== by 0x55BB878: KSPSolve_Private (itfunc.c:823)
==1342260== by 0x55BB3FC: KSPSolve (itfunc.c:1069)
==1342260== by 0x59AB119: SNESSolve_NEWTONLS (ls.c:210)

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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

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 'barry/2022-07-23/add-petscbeginuser' into 'main'

Add PetscFunctionBeginUser to all PETSc C/C++ examples

See merge request petsc/petsc!5470

Add PetscFunctionBeginUser to all PETSc C/C++ examples

Now the stack frames will contain the main program and the correct line numbers in them

git ls-files | egrep "(tutorials|tests)" | xargs sed -

Add PetscFunctionBeginUser to all PETSc C/C++ examples

Now the stack frames will contain the main program and the correct line numbers in them

git ls-files | egrep "(tutorials|tests)" | xargs sed -i "s?\(PetscCall(PetscInitialize(&argc\)?PetscFunctionBeginUser;\n \1?g"

Commit-type: error-checking, testing-fix
/spend 15m

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Merge remote-tracking branch 'origin/release'

Merge branch 'psanan/docs-remove-concepts' into 'release'

Docs: remove Concepts

See merge request petsc/petsc!5065

Docs: remove "Concepts:" and related comments in /*T .. T*/ blocks

Remove all \*T ... comment blocks with e.g.

cd src && find . -type f -exec sed -i '/^[! ] *\/\*T$/,/^[! ]*T\*\/$/d' {} \;

Clea

Docs: remove "Concepts:" and related comments in /*T .. T*/ blocks

Remove all \*T ... comment blocks with e.g.

cd src && find . -type f -exec sed -i '/^[! ] *\/\*T$/,/^[! ]*T\*\/$/d' {} \;

Clean up resulting double blank lines with e.g.

cd src && find . type f \( -name "*.c" -o -name "*.cxx" -o -name "*.F" -o -name "*.F90" \) -exec sh -c "cat -s {} > tmp && mv tmp {}" \;

Manually revert those changes from the vendored code (src/sys/yaml)

Manually restore a few comments from these blocks.

Manually remove "Concepts:" and "Processors:" comments from files
which have these outside of "\*T" blocks automatically deleted above.

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Merge branch 'jolivet/feature-less-checkfalse' into 'main'

Dividing by four the number of PetscCheckFalse()

See merge request petsc/petsc!5072

Remove some PetscCheckFalse()

Merge branch 'jacobf/2022-02-23/variadic-chkerr' into 'main'

Variadic CHKERRQ()

See merge request petsc/petsc!4889

The great renaming:

- CHKERRQ() -> PetscCall()
- CHKERRV() -> PetscCallVoid()
- CHKERRMPI() -> PetscCallMPI()
- CHKERRABORT() -> PetscCallAbort()
- CHKERRCONTINUE() -> PetscCallContinue()
- CHKERRXX

The great renaming:

- CHKERRQ() -> PetscCall()
- CHKERRV() -> PetscCallVoid()
- CHKERRMPI() -> PetscCallMPI()
- CHKERRABORT() -> PetscCallAbort()
- CHKERRCONTINUE() -> PetscCallContinue()
- CHKERRXX() -> PetscCallThrow()
- CHKERRCXX() -> PetscCallCXX()
- CHKERRCUDA() -> PetscCallCUDA()
- CHKERRCUBLAS() -> PetscCallCUBLAS()
- CHKERRCUSPARSE() -> PetscCallCUSPARSE()
- CHKERRCUSOLVER() -> PetscCallCUSOLVER()
- CHKERRCUFFT() -> PetscCallCUFFT()
- CHKERRCURAND() -> PetscCallCURAND()
- CHKERRHIP() -> PetscCallHIP()
- CHKERRHIPBLAS() -> PetscCallHIPBLAS()
- CHKERRHIPSOLVER() -> PetscCallHIPSOLVER()
- CHKERRQ_CEED() -> PetscCallCEED()
- CHKERR_FORTRAN_VOID_FUNCTION() -> PetscCallFortranVoidFunction()
- CHKERRMKL() -> PetscCallMKL()
- CHKERRMMG() -> PetscCallMMG()
- CHKERRMMG_NONSTANDARD() -> PetscCallMMG_NONSTANDARD()
- CHKERRCGNS() -> PetscCallCGNS()
- CHKERRPTSCOTCH() -> PetscCallPTSCOTCH()
- CHKERRSTR() -> PetscCallSTR()
- CHKERRTC() -> PetscCallTC()

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PetscInitialize() and PetscFinalize() wrapped:

- ierr = PetscInitialize();if (ierr) return ierr;
+ CHKERRQ(PetscInitialize());

- ierr = PetscFinalize();
- return ierr;
+ CHKERRQ(PetscFinalize());
+

PetscInitialize() and PetscFinalize() wrapped:

- ierr = PetscInitialize();if (ierr) return ierr;
+ CHKERRQ(PetscInitialize());

- ierr = PetscFinalize();
- return ierr;
+ CHKERRQ(PetscFinalize());
+ return 0;

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chkerr and friends wrapped

Merge branch 'jacobf/2022-01-05/c99' into 'main'

Feature: C99 and C++11

See merge request petsc/petsc!4700

rename PetscAssert() -> PetscCheck() and PetscAssertDebug() -> PetscAssert()

add PetscAssert() and PetscAssertFalse()

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