Crash when using MUMPs sequentially with -pc_factor_nonzeros_along_diagonal but using MUMPS ordering.

$ PETSC_OPTIONS="-pc_factor_mat_ordering_type external" python pythonprogram.py
[0]PETSC ERROR:

Crash when using MUMPs sequentially with -pc_factor_nonzeros_along_diagonal but using MUMPS ordering.

$ PETSC_OPTIONS="-pc_factor_mat_ordering_type external" python pythonprogram.py
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
[0]PETSC ERROR: --------------------- Stack Frames ------------------------------------
The line numbers in the error traceback are not always exact.
[0] #1 MatReorderForNonzeroDiagonal_SeqAIJ() at /Users/barrysmith/Src/petsc/src/mat/utils/zerodiag.c:77
[0] #2 MatReorderForNonzeroDiagonal() at /Users/barrysmith/Src/petsc/src/mat/utils/zerodiag.c:61
[0] #3 PCSetUp_LU() at /Users/barrysmith/Src/petsc/src/ksp/pc/impls/factor/lu/lu.c:84
[0] #4 PCSetUp() at /Users/barrysmith/Src/petsc/src/ksp/pc/interface/precon.c:1120
[0] #5 KSPSetUp() at /Users/barrysmith/Src/petsc/src/ksp/ksp/interface/itfunc.c:429

Bug was it still tried the nonzero diagonal reordering even when the ordering type was external so PETSc did not generate an ordering

Also fixed bug in PCSetUp_Cholesky() where it used GetBool on -pc_factor_nonzeros_along_diagonal when the argument may be followed by a numerical value

Reported-by: Jørgen Dokken

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One-liners from petsc/petsc!5344 and petsc/petsc!5557

Slightly reworked regular expression

git ls-files -z -- '*.c' '*.cxx' '*.cu' '*.h' '*.hpp' '*.cpp' | while IFS= read -r -d '' file; do
cat

One-liners from petsc/petsc!5344 and petsc/petsc!5557

Slightly reworked regular expression

git ls-files -z -- '*.c' '*.cxx' '*.cu' '*.h' '*.hpp' '*.cpp' | while IFS= read -r -d '' file; do
cat $file | tr '\n' '\r' | sed -E 's/\r([ ]*)(for|if|while|else) ([^\r]*)\{\r[ ]*Petsc([a-zA-Z]*)\(([^\r]*)\);\r[ ]*\}\r/\r\1\2 \3Petsc\4(\5);\r/g' | tr '\r' '\n' > ${file}.joe; mv ${file}.joe ${file}
done

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Merge branch 'jolivet/housekeeping' into 'main'

Housekeeping

See merge request petsc/petsc!8326

Remove unneeded variable and functions

PC: add PCMatApplyTranspose()