Merge branch 'jolivet/pacify-gcc' into 'main'

Fix (erroneous) -Wmaybe-uninitialized (#1847)

See merge request petsc/petsc!9036

Fix style of 6497c311e7b976d467be1503c1effce92a60525c

Merge branch 'barry/2024-09-02/rebased-fix-conversion-warnings' into 'main'

Compiler finds (and forbid) casts from higher precision integers to lower

See merge request petsc/petsc!7806

Fix MPIU_* routines to always return MPI error codes and thus be usable with PetscCallMPI()

Introduce MPIU_Count to be used when MPI_Count is not available

Merge branch 'stefanozampini/gamg' into 'main'

PCGAMG: some optimizations

See merge request petsc/petsc!7798

PetscLogEventNested: fix collectiveness specification of nested event

Merge branch 'jolivet/clang-format-18' into 'main'

clang-format version 18

See merge request petsc/petsc!6902

Remove carriage return in Petsc(Assert|Check)()

git grep -l -E "Petsc(Assert|Check)\(.*\\\n\"[,)]" | xargs sed -r -i'' 's#Petsc(Assert|Check)\((.*)\\n"([,)])#Petsc\1\(\2\"\3#g'

Suggested-by: Stefan

Remove carriage return in Petsc(Assert|Check)()

git grep -l -E "Petsc(Assert|Check)\(.*\\\n\"[,)]" | xargs sed -r -i'' 's#Petsc(Assert|Check)\((.*)\\n"([,)])#Petsc\1\(\2\"\3#g'

Suggested-by: Stefano Zampini

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Remove multiple parentheses and extra semicolon

git grep -l -E "\(\([a-zA-Z0-9_]+\)\(\*[a-zA-Z0-9_]+\)[, )]" | xargs sed -r -i'' 's#\(\(([a-zA-Z0-9_]+)\)\(\*([a-zA-Z0-9_]+)\)([, )])#\(\(\1\)\*\2\3#g

Remove multiple parentheses and extra semicolon

git grep -l -E "\(\([a-zA-Z0-9_]+\)\(\*[a-zA-Z0-9_]+\)[, )]" | xargs sed -r -i'' 's#\(\(([a-zA-Z0-9_]+)\)\(\*([a-zA-Z0-9_]+)\)([, )])#\(\(\1\)\*\2\3#g'
git grep -l -E "Petsc(.)*\(\(\*[a-zA-Z0-9_]*\)," | xargs sed -r -i'' 's#Petsc([a-zA-Z0-9_]*)\(\(\*([a-zA-Z0-9_]*)\), #Petsc\1(*\2, #g'
git grep -l -E "([\!\&\~\*\(]|\)\)|\([^,\*\(]+\**\))\(([a-zA-Z0-9_]+((\.|->)[a-zA-Z0-9_]+|\[[a-zA-Z0-9_ \%\+\*\-]+\])+)\)" | xargs sed -r -i'' 's#([\!\&\~\*\(]|\)\)|\([^,\*\(]+\**\))\(([a-zA-Z0-9_]+((\.|->)[a-zA-Z0-9_]+|\[[a-zA-Z0-9_ \%\+\*\-]+\])+)\)#\1\2#g'

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checkbadSource: rules for PetscFunctionBegin and derivatives

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 'tisaac/fix-nested-log-bug-2' into 'main'

Bugfixes for nested log handler

See merge request petsc/petsc!6859

Profiling: Try to unwind nested handler stack as much as possible

To avoid erroring in the log handler in the event that a log event doesn't end
for whatever reason

Profiling: Fix nested log handler performance data not being in tree order

Merge branch 'tisaac/feature-log-handler' into 'main'

Deglobalize logging into PetscLogHandler and PetscLogState

See merge request petsc/petsc!6709

Profiling: Add composed functions for default log handler functions

This makes them extensible to other implementations.
Where appropriate, the global log handler will now dispatch
these functions t

Profiling: Add composed functions for default log handler functions

This makes them extensible to other implementations.
Where appropriate, the global log handler will now dispatch
these functions to all running log handlers.

It is not always appropriate to dispatch to all running log handlers:
when a single return value is expected or when a filename
is given, it will continue to dispatch only to the default
log handler.

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Profiling: Rename PETSC_LOG_HANDLER_XXX -> PETSCLOGHANDLERXXX

Profiling: Switch logging over to the new PetscLogHandler infrastructure

- Move data structures only needed by the default logger now (Action,
Object) to logdefault.c

- Create petsclogdeprecated.

Profiling: Switch logging over to the new PetscLogHandler infrastructure

- Move data structures only needed by the default logger now (Action,
Object) to logdefault.c

- Create petsclogdeprecated.h and petsc/private/logimpldeprecated.h
for publicly visible symbols that are now deprecated. Yes,
lots of symbols in petsc/private/logimpl.h were not only visible
but had docstrings.

- The macros PetscLogEventBegin(), PetscLogEventEnd(),
PetscLogEventSync(), PetscLogObjectCreate(), and
PetscLogObjectDestroy() now looks through the log handlers
in PetscLogHandlers, sees if they have they appropriate
callbacks (Exposed in PetscLogHandlerHot), and calls them.
Up to 4 log handlers can run simultaneously.

- All queries about the registered things now go through
petsc_log_state.

- Output functions dispatch to the appropriate PetscLogHandler

- There is no need for xmllogevent.c, xmlviewer.c, eventlog.c,
classlog.c, and stagelog.c anymore. Some orphaned functions
(PetscLogSetThreshold(), PetscLogEventSetDof(),
PetscLogEventSetError(), PetscASend(), PetscARecv(), PetscAReduce())

- PetscFEOpenCLLogResidual() did some intrusive things related
to the old logging infrastruture: the private header
for the default log handler is now imported into feopencl.c
so that it can do equivalent things with the new infrastructure.

- PetscLogPauseCurrentEvent_Internal() is replaced with
PetscLogEventsPause()

Deprecated symbols include:

- All functions related to PetscStageLog and the resizable array structs
that it contained.

- The legacy EventBegin()/EventEnd() callbacks.

- PetscLogAllBegin(), which actually reported less information than
PetscLogDefaultBegin() because it was not kept up-to-date with
regards to GPU profiling.

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Profiling: Add nested PetscLogHandler implementation

This log handler has behavior like the behavior of
PetscLogNestedBegin().

Unlike the implementation of PetscLogHandler_Default, I did not try to

Profiling: Add nested PetscLogHandler implementation

This log handler has behavior like the behavior of
PetscLogNestedBegin().

Unlike the implementation of PetscLogHandler_Default, I did not try to
do a faithful translation of the existing nested logging behavior, for
two reasons.

- The existing implementation keeps sorted lists of nested paths ("Event
A;Event B;"), and for each of those paths keeps a sorted list of the
top-level events ("Event C", "Event D") that map that path to other
paths (path + event => other path). It's a complicated data structure,
and the benefit of the sorting (O(log n) lookup) is probably not worth
the more expensive insertion cost each time a new path + event combo
appears. Instead I implemented the path + event => other path
lookup as a hash map, which simplified the implementation
significantly.

- The existing implementation assigns an event to each path, modifying
the event registry in place. This messes things up if you want
to both -log_view and -log_view ::ascii_flamegraph output, the
original motivation for refactoring the profiling infrastructure.
In the new implementation, the nested handler has its own
PetscLogState that it modifies, and an inner copy of
PetscLogHandler_Default the acts on that nested state.

- The PetscLogGlobalNames data structure also simplifies the
construction of a linearized tree of events in the final
viewing stage, although the low-level xml construction
routines are copied almost verbatim from the previous
implementation.

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