Fix examples (without completion)

clean up makefiles for make check

Commit-type: error-checking, housekeeping
/spend 35m

Merge branch 'knepley/fix-plex-extrude-orientation' into 'main'

Knepley/fix plex extrude orientation

See merge request petsc/petsc!5430

Update test output

DMPlex: add support for writing CGNS files in parallel

Also --download-cgns. This supports most kinds of quadratic and
cubic elements, plus some quartic (not supported in Paraview-5.10.1).
Parallel

DMPlex: add support for writing CGNS files in parallel

Also --download-cgns. This supports most kinds of quadratic and
cubic elements, plus some quartic (not supported in Paraview-5.10.1).
Parallel IO uses collective contiguous writes.

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Add PETSc CI mode to allow better handling of errors and system dependent output when running in test harness

-petsc_ci - automatically set for all runs in test harness

-petsc_ci_portable_error_out

Add PETSc CI mode to allow better handling of errors and system dependent output when running in test harness

-petsc_ci - automatically set for all runs in test harness

-petsc_ci_portable_error_output - ensures all error messages (when possible are system and compiler information),
should be only used in tests that are explicitly testing the error handling

This allows proper comparisons of runs on different machines and when errors are intentionally triggered to test error handling

Commit-type: error-checking, testing-fix
/spend 5h

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Fix test output

Fixed examples

added distance k MIS MatCoarsen type

Change matrix factor database options that occur in KSP/PC to always use KSP/PC options prefix

Add MatSetOptionsPrefixFactor() and MatAppendOptionsPrefixFactor() to allow controlling the options pre

Change matrix factor database options that occur in KSP/PC to always use KSP/PC options prefix

Add MatSetOptionsPrefixFactor() and MatAppendOptionsPrefixFactor() to allow controlling the options prefix
used by factors created from this matrix

Change MatSetOptionsPrefix() to no longer affect the options prefix used by factors created from this matrix

As part of the above work the handling of the factor matrix options is now done in code in the factor matrix
not in the code that originates the factor matrix

Update examples output to the new approach where the factored matrix prefix is set from the KSP/PC

Much of this work was performed by Hong Zhang

Commit-type: usability
/spend 5h

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Merge branch 'stefanozampini/gdsw-mg' into 'main'

Implement AGDSW coarse spaces for PCMG

See merge request petsc/petsc!5256

GDSW: add tests

TAO: add support for Eisenstat and Walker trick for KSP