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 'barry/2023-03-17/rm-unneeded-test-from-makefiles' into 'main'

simplify/cleanup makefile system

See merge request petsc/petsc!6201

non-test and tutorial makefiles only need rules.doc not the full rules

Commit-type: documentation

Only makefiles in the test and tutorial directories need lib/petsc/conf/test

Commit-type: housekeeping

Merge branch 'jolivet/follow-up-6107-6113' into 'main'

Remove unneeded (empty) makefile variables

See merge request petsc/petsc!6132

Remove empty preprocessor variables

Merge branch 'barry/2023-02-22/rm-locdir' into 'main'

Remove need for hardwired LOCDIR in all makefiles

See merge request petsc/petsc!6113

Remove unneeded declarations of LOCDIR from all the makefiles

Commit-type:documentation

Merge branch 'perfstubs' into 'main'

Add the perfstubs package to petsc.

See merge request petsc/petsc!5516

Add the perfstubs package to petsc.

Example usage:

Configure PETSc with: ./configure --download-mpich
--download-fblaslapack

Build PETSc
Setup TAU:

wget http://tau.uoregon.edu/tau.tgz
./configure

Add the perfstubs package to petsc.

Example usage:

Configure PETSc with: ./configure --download-mpich
--download-fblaslapack

Build PETSc
Setup TAU:

wget http://tau.uoregon.edu/tau.tgz
./configure -cc=mpicc -c++=mpicxx -mpi -bfd=download -unwind=download &&
make install
export PATH=<tau dir>/x86_64/bin:$PATH

Build and run PETSc example with TAU:

cd $PETSC_DIR/src/snes/tutorials
make ex56
mpirun -n 4 tau_exec ./ex56 <args>

This should produce 4 profile...* files with profile data that can be
viewed with paraprof/pprof:

Reading Profile files in profile.*

NODE 0;CONTEXT 0;THREAD 0:
---------------------------------------------------------------------------------------
%Time Exclusive Inclusive #Call #Subrs Inclusive Name
msec total msec usec/call
---------------------------------------------------------------------------------------
100.0 26 1,838 1 41322 1838424 .TAU
application
73.2 1 1,345 2 168 672950
SNESSolve
62.2 3 1,142 2 1282 571442
SNESJacobianEval
62.0 1,136 1,138 2 76 569494
DMPlexJacobianFE
60.1 0.046 1,105 1 32 1105001 Solve
1
15.2 87 279 5 11102 55943 Mesh
Setup
13.2 0.315 241 1 32 241765 Solve
0
7.8 80 144 38785 38785 4
MPI_Allreduce()
7.0 69 128 6 43386 21491
DualSpaceSetUp
6.2 1 114 4 54 28536
PCSetUp
6.0 12 110 2 892 55407
PCSetUp_GAMG+
3.9 70 70 1 0 70888
MPI_Init_thread()
3.7 68 68 41747 0 2 MPI
Collective Sync
3.6 8 66 4 3536 16548
SNESFunctionEval
2.6 45 48 171 171 281
MPI_Bcast()
1.9 34 34 7836 0 4
MPI_Barrier()
1.8 0.567 33 2 68 16912 GAMG
Coarsen

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Merge branch 'barry/2022-05-03/cleanup-makefiles' into 'main'

remove unneeded stuff from makefiles

See merge request petsc/petsc!5211

remove garbage from makefiles

Including
* unused FLAGS variables
* All: lib that did not work
* stray blank lines etc

Commit-type: housekeeping
/spend 1h

Merge branch 'barry/2022-04-15/add-manpages-hseti-etc' into 'main'

Automatically create manual pages for hash table objects created with PETSC_HASH_SET()

See merge request petsc/petsc!5129

Automatically create manual pages for hash table objects created with PETSC_HASH_SET()

Previous documention was not intuitive since it did not match the names in the source code usage

Identical cha

Automatically create manual pages for hash table objects created with PETSC_HASH_SET()

Previous documention was not intuitive since it did not match the names in the source code usage

Identical changes for documentation for PETSC_HASH_MAP objects must be made. I will do it once this MR is accepted so that the process will be quick and easy.

Commit-type: documentation, usability
/spend 2.5h

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Merge branch 'jed/makefile-dirs' into 'main'

makefile: add missing DIRS (squash gmakegen.py --verbose warnings)

See merge request petsc/petsc!4677

makefile: add missing DIRS (squash gmakegen.py --verbose warnings)

* enable dm partitioner tests
* yaml is a third-party library with different build procedure
* the cmap directory contains only hea

makefile: add missing DIRS (squash gmakegen.py --verbose warnings)

* enable dm partitioner tests
* yaml is a third-party library with different build procedure
* the cmap directory contains only headers
* fix Fortran callback for Riemann solver, which returns void

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Merge branch 'jed/rm-distutils' into 'main'

config: remove distutils from build

See merge request petsc/petsc!4253

config: remove distutils from build

distutils is deprecated and will be removed in Python-3.12:

https://www.python.org/dev/peps/pep-0632/

Most features carry over readily with sysconfig (part of

config: remove distutils from build

distutils is deprecated and will be removed in Python-3.12:

https://www.python.org/dev/peps/pep-0632/

Most features carry over readily with sysconfig (part of minimal python,
unlike distutils, which is often an optional package). One exception is
distutils.sysconfig.parse_makefile, which is more full-featured than
sysconfig._parse_makefile (a private method that exists in python 2.7
and all tested python 3 versions). Specifically, _parse_makefile()
cannot handled lines continued with trailing backslash (\) and thus we
must forbid continuations for DIRS and SOURCE* lines -- just use a line
as long as it needs to be. This system will hopefully be renovated anyway.

Commit-type: portability

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Merge branch 'dalcinl/vendor-libyaml' into 'master'

Vendor LibYAML

See merge request petsc/petsc!3652

YAML: Move YAML options implementation sources closer to related sources

Merge remote-tracking branch 'origin/maint'

Merge branch 'jolivet/fix-elemental-deadlock' into 'maint'

MATELEMENTAL deadlock when first Mat is on a subcommunicator

See merge request petsc/petsc!2862