docs: fix conflict/false-positive with "ROOT" and "PETSC_DOC_OUT_ROOT_PLACEHOLDER"

Remove first and last empty lines

docs: misc fixes

docs, scripts: update from ftp.mcs.anl.gov to web.cels.anl.gov

and remove reference to a mirror from docs and configure script

Update the interface to STRUMPACK

STRUMPACK provides a sparse direct solver (but unlike fi SuperLU, it is based on the multifrontal method). STRUMPACK also provides preconditioners based on approxim

Update the interface to STRUMPACK

STRUMPACK provides a sparse direct solver (but unlike fi SuperLU, it is based on the multifrontal method). STRUMPACK also provides preconditioners based on approximate multifrontal LU factorization. In the precoditioners larger dense blocks in the sparse LU factors are compressed using rank-structured matrix approximations (or using lossy/lossless compression using the ZFP library).

See https://github.com/pghysels/STRUMPACK https://portal.nersc.gov/project/sparse/strumpack/

This commit adds different preconditioning options. Previously only the HSS (hierarchically Semi-Separable) format was supported. Now we also have BLR (Block Low Rank), HODLR (Hierarchically Off-Diagonal) with the option to replace low-rank with butterfly, Lossy and Lossless compression (through ZFP). The new methods work considerably better than the older HSS code. When using

-pc_type lu -pc_factor_mat_solver_type strumpack

the solver behaves as a direct solver. When using

-pc_type ilu -pc_factor_mat_solver_type strumpack

it will work as a preconditioner, using BLR compression. This should be a robust preconditioner for a wide range of problems. One can tune the compression tolerance, and the minimum block (separator) size for compression using:

-mat_strumpack_compression_rel_tol 1e-3 -mat_strumpack_compression_min_sep_size 500

You can also select the compression type explicitly

-pc_type ilu -pc_factor_mat_solver_type strumpack -mat_strumpack_compression LOSSY

For now we recommend BLR, as it seems to work best, and does not require additional external dependencies (it is also what MUMPS implements).

Also updates the test src/ksp/ksp/tutorials/ex52.c.

Also adds support for the solve with multiple RHS.

Also adds an option for the GEOMETRIC fill-reducing ordering which performs nested dissection on a regular nx x ny x nz grid with nc degrees of freedom per grid-point and a stencil (potentially a wider stencil). It is assumed that the matrix is in the natural (lexicographical?) ordering. This can make reordering much faster for regular grid problems.

Also adds installation scripts STRUMPACK dependencies SLATE, ZFP and ButterflyPACK. SLATE is a scalapack replacement with GPU capabilities. ZFP is used for floating point compression. ButterflyPACK is used for the HODLR and HODBF compression schemes.

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Merge branch 'jacobf/2023-08-17/header-guard-check' into 'main'

Check header guards

See merge request petsc/petsc!6822

Add slepcversion.h to ignored files

Enforce header guards in checkbadSource

Add header guard converter and checker

Misc

Linter now tries to detect functions that could be static, and makes it so.

Allow skipping mypy checks from makefile (to debug linter) since mypy barfs when importing ipdb

More robust hash combine for SourceLocation and SourceRange

Parallel pool consume results if queue put times out

Don't use up more than 16 cores on bigger machines for the work pool, as that is more than enough

Make verbosity an int so that --verbose doesn't output a ton of random debug garbage each time

Accept Calling [Ss]equence [Oo]f as heading

Fix mispelling bug in linter causing it to double-print errors

Add vermin and mypy version checks

Document linter and add type hints

Improve formatting and comments in rules.util file

Make clangformat check the clang-format version for match to PETSc requirements

Fix missing new lines at the end of PetscInfo() calls

Merge branch 'jacobf/2023-07-25/fix-nvcc-visibility' into 'main'

Pair -Xcompiler -fvisibility=hidden together as flags

See merge request petsc/petsc!6756

Profiling: Add PetscLogHandler interface

PetscStageLog tries to handle multiple ways of interpreting profiling
data:

* -log_view (default),
* -log_view ::ascii_xml and -log_view ::ascii_flamegraph

Profiling: Add PetscLogHandler interface

PetscStageLog tries to handle multiple ways of interpreting profiling
data:

* -log_view (default),
* -log_view ::ascii_xml and -log_view ::ascii_flamegraph (nested),
* -log_trace,
* -log_mpe,
* tau perfstubs (implicitly),
* nvidia

They can interact with petsc_logState in incompatible ways.

PetscLogHandler gives each handler its own interface so that
it can have its own data structures. They key operations
that a log handler can implement are:

- PetscLogHandlerEventBegin() / PetscLogHandlerEventEnd()
- PetscLogHandlerEventSync()
- PetscLogHandlerStagePush() / PetscLogHandlerStagePop()
- PetscLogHandlerObjectCreate() / PetscLogHandlerObjectDestroy()

The remaining operations are PetscObject standard functions,
with the except of `PetscLogHandlerSetState()` / `PetscLogHandlerGetState()`,
which control the `PetscLogState` that the handler can use to
get information about registered things and about the stage stack.

This change only introduces the type, it does not deploy it
to replace anything in the current profiling interface.
When it does, the user-defined log handling that was implemented
by setting callbacks in in PetscLogSet() will be replaced with
user-defined PetscLogHandler instances.

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