CI: add --download-amgx to linux-cuda-pkgs
And fix related issues

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 'adams/pcamgx' into 'main'

Add PC interface to AmgX

See merge request petsc/petsc!4323

Add PC interface to AmgX

https://developer.nvidia.com/amgx

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 branch 'adams/snesex13-fix' into 'main'

fixing snes/tests/ex13 mkl failure

See merge request petsc/petsc!5418

cleanup ex13 tests, switch GMRES to cg - in an attempt to fix this error

However there appears to be a non-deterministic bug in parallel MKL, in this older version

*** Error in `../ex13': free(): i

cleanup ex13 tests, switch GMRES to cg - in an attempt to fix this error

However there appears to be a non-deterministic bug in parallel MKL, in this older version

*** Error in `../ex13': free(): invalid next size (normal): 0x0000000000e210d0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x2b3c7c755329]
/homes/intel/18u2/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64_lin/libmkl_core.so(mkl_serv_free+0x2c4)[0x2b3c725d6504]
/homes/intel/18u2/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64_lin/libmkl_sequential.so(mkl_sparse_d_inspector_gen_mv_i4+0x4af)[0x2b3c767c166f]
/homes/intel/18u2/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64_lin/libmkl_sequential.so(mkl_sparse_d_optimize_csr_mv_i4+0xa5)[0x2b3c767c5515]
/homes/intel/18u2/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64_lin/libmkl_avx512_mic.so(mkl_sparse_optimize_i4_avx512_mic+0x220)[0x2b3ca3476bc0]
/home/petsc/builds/6i15ewNf/2/petsc/petsc/arch-ci-linux-knl/lib/libpetsc.so.3.017(+0x65e06a)[0x2b3c6f4f006a]
/home/petsc/builds/6i15ewNf/2/petsc/petsc/arch-ci-linux-knl/lib/libpetsc.so.3.017(MatMultTranspose_SeqAIJMKL_SpMV2+0x110)[0x2b3c6f4f14d0]
/home/petsc/builds/6i15ewNf/2/petsc/petsc/arch-ci-linux-knl/lib/libpetsc.so.3.017(MatMultTranspose_MPIAIJ+0x49)[0x2b3c6f3529e9]
/home/petsc/builds/6i15ewNf/2/petsc/petsc/arch-ci-linux-knl/lib/libpetsc.so.3.017(MatMultTranspose+0x15e)[0x2b3c6f8c828e]
/home/petsc/builds/6i15ewNf/2/petsc/petsc/arch-ci-linux-knl/lib/libpetsc.so.3.017(MatRestrict+0x7f)[0x2b3c6f8bcb4f]

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Merge branch 'barry/2022-06-11/improve-mat-setable-values' into 'main'

Refactor handling of settable properties of matrix via MatSetOptions

See merge request petsc/petsc!5338

Refactor handling of setable properties of matrices via MatSetOptions()

Introduce PetscBool3 with enum values true, false, and unknown

Use PetscBool3 to store matrices properties in a matrix and cl

Refactor handling of setable properties of matrices via MatSetOptions()

Introduce PetscBool3 with enum values true, false, and unknown

Use PetscBool3 to store matrices properties in a matrix and cleanup interface to check these values

Add full support for symmetric, Hermitian, structurally symmetric, and SPD.

Commit-type: feature
/spend 6h

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Merge branch 'adams/mataij-graph-filter' into 'main'

Move create and filter graph from PCGAMG to MATAIJ, add MIS-k

See merge request petsc/petsc!5331

added distance k MIS MatCoarsen type

Merge branch 'barry/2022-04-01/fix-petsc-options-begin-end/release' into 'main'

Remove bogus error returns from Begin/End() macros

See merge request petsc/petsc!5069

Cleanup of introduction of PetscCall()

* remove bogus error flags from XXXBegin()/End() macros such as PetscOptionsBegin()/End()

* rename for consistency certain XXXBegin()/End() macros such as Mat

Cleanup of introduction of PetscCall()

* remove bogus error flags from XXXBegin()/End() macros such as PetscOptionsBegin()/End()

* rename for consistency certain XXXBegin()/End() macros such as MatPreallocateInitialize()/Finalize()

* fix many lingering ierr = XXX that arose from multiline function calls

* sync slepc/hpddm - to use snapshots with the same changes

Commit-type: error-checking, style-fix
/spend 8h

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Merge branch 'adams/gamg-timers-benchmarks' into 'main'

Adams/gamg timers benchmarks

See merge request petsc/petsc!5032

fix format and update ex13

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 'jed/amg-symmetry' into 'main'

PCGAMG: skip symmetric non-SPD use of KSPCR for eigenvalues

See merge request petsc/petsc!4910

PCGAMG: update tests

* formatting of Chebyshev information
* use of GAMG SA eigenvalue estimates

Merge branch 'knepley/feature-plex-distribute-default' into 'main'

Plex: Change default to automatic distribution

See merge request petsc/petsc!4843

Plex: Change default to automatic distribution - Add DMPlexDistributeGet/SetDefault() to change this - Add DMPlexCopy_Internal() to keep state in Plex object consistent