Merge branch 'jolivet/checkbadSource' into 'main'

checkbadSource: enforce proper style in makefiles

See merge request petsc/petsc!8802

checkbadSource: enforce proper style in makefiles

Merge branch 'barry/2024-04-29/add-fortran-enums' into 'main'

Major updates to Fortran interface

See merge request petsc/petsc!7517

Fortran 90: fully embrace After 34 years!

- deprecate use of 'F90' in Fortran function names
- use Fortran pointers when appropriate
- the new Fortran API is not backward compatible with previous ve

Fortran 90: fully embrace After 34 years!

- deprecate use of 'F90' in Fortran function names
- use Fortran pointers when appropriate
- the new Fortran API is not backward compatible with previous versions!
- also clean up inconsistent PETSc code detected by new Fortran generation tools
- drop use of bfort
- automatically generate all the Fortran PETSc objects, enums etc from the include files
- generate most of the Fortran interface definitions and functions from the source code
- simplify the number and organization of Fortran modules

Co-authored-by: Jose E. Roman <jroman@dsic.upv.es>

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Merge branch 'barry/2023-12-22/rm-libbase' into 'main'

LIBBASE is no longer used in make so remove it

See merge request petsc/petsc!7139

LIBBASE is no longer used in make so remove it

Merge branch 'barry/2023-10-25/rename-rules-doc' into 'main'

Rename rules.doc and rules.utils because GitLab treats the former as a MS Word document.

See merge request petsc/petsc!6965

Rename rules.doc and rules.utils because GitLab treats the former as a MS Word document.

Thanks-to: Jed Brown

Merge branch 'barry/2023-10-18/rm-dirs-from-makefiles' into 'main'

Remove use of and the DIRS variables from the makefiles

See merge request petsc/petsc!6945

Remove DIRS variable and unneeded tabs from all makefiles since no longer needed

Commit-type: housekeeping

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

Profiling: Create PETSCLOGHANDLERNVTX (`-log_view` no longer required for Nsight ranges)

See merge request petsc/petsc!6884

Profiling: Create PETSCLOGHANDLERNVTX

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

Deglobalize logging into PetscLogHandler and PetscLogState

See merge request petsc/petsc!6709

Profiling: Add legacy callbacks implementation of PetscLogHandler

The existing logging infrastructures has four exposed callback pointers:

- PetscLogPLB / PetscLogPLE for PetscLogEventBegin() / Pet

Profiling: Add legacy callbacks implementation of PetscLogHandler

The existing logging infrastructures has four exposed callback pointers:

- PetscLogPLB / PetscLogPLE for PetscLogEventBegin() / PetscLogEventEnd()
These can also be set with PetscLogSet

- PetscLogPHC / PetscLogPHD for PetscLogObjectCreate() /
PetscLogObjectDestroy()

This log handler implementation provides a path for users who have been
setting their own callbacks with these functions to upgrade to the new
PetscLogHandler interface.

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Profiling: Add tau perfstubs implementation of PetscLogHandler

In the existing logging, perfstubs runs automatically with -log_view
if PETSc is configured --with-tau-perfstubs. This new PetscLogHan

Profiling: Add tau perfstubs implementation of PetscLogHandler

In the existing logging, perfstubs runs automatically with -log_view
if PETSc is configured --with-tau-perfstubs. This new PetscLogHandler
implementation will be used with a new -log_perfstubs command line
option that will only run this handler and not the default handler.

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Profiling: add MPE implementation of PetscLogHandler

This is meant to handle -log_mpe.

Profiling: Add trace implementation of PetscLogHandler

This is a minimal PetscLogHandler implementation for -log_trace.

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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Profiling: Implement the default PetscLogHandler

The existing default log handling that uses the PetscStageLog
is translated in the PetscLogHandler_Default implementation
of PetscLogHandler.

- Most

Profiling: Implement the default PetscLogHandler

The existing default log handling that uses the PetscStageLog
is translated in the PetscLogHandler_Default implementation
of PetscLogHandler.

- Most data that is global in the existing log handling
is moved into the struct, with the exception of the
raw counters.

- The registry data structures of PetscStageLog (eventLog,
classLog) are not reproduced because they are now in
the PetscLogState interface.

- PETSC_LOG_RESIZABLE_ARRAY is used to implement
resizable arrays instead of PetscStageInfo,
PetscEventPerfLog, and PetscClassPerfLog

- The tau perfstubs and MPE functionality is not
reproduced because they will become new
handlers on their own.

- The PetscLogGlobalNames provided by the
PetscLogRegistry interface make the logging
robust to differences in which events / stages are
registered on which process and in which order.

Otherwise the functions are relatively faithful translations
of the existing PetscStageLog functions into the new interface.
When reviewing this commit it might help to have a diff
between the PetscStageLog and PetscLogHandler_Default functions
to see what changes between them. I am working on a way to attach
that to the MR associated with this change.

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