Fix mismatched step index in adjoint

The step index is increased after TSStep(), so it should be decreased before TSAdjointStep() for consistency.

Funded-by:
Project: FASTMath adjoint
Time:
Reporte

Fix mismatched step index in adjoint

The step index is increased after TSStep(), so it should be decreased before TSAdjointStep() for consistency.

Funded-by:
Project: FASTMath adjoint
Time:
Reported-by: Satish Balay <balay@mcs.anl.gov>
Thanks-to:

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Merge remote-tracking branch 'origin/maint'

Single petscdir.mk

Example of an Advection-Diffusion model solved using grid created by DMPLEX. Aimed at easing the learning curves of the various functions of DMPLEX and DM.

Merge branch 'maint'

Typos

DM: Change examples to use DMAddBoundary() instead of PetscDSAddBoundary()
- Now you have to call DMCopyDS() after labels have been established on the coarse DM
- Also, p4est setup has to have happen

DM: Change examples to use DMAddBoundary() instead of PetscDSAddBoundary()
- Now you have to call DMCopyDS() after labels have been established on the coarse DM
- Also, p4est setup has to have happened before label completion

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ci: update alt files for osx

- src/snes/tutorials/output/ex12_44.out likely incorrectly updated in c4762a1b19cd2af06abeed90e8f9d34fb975dd94
- src/ts/tutorials/output/ex12_2_alt.out added for one of

ci: update alt files for osx

- src/snes/tutorials/output/ex12_44.out likely incorrectly updated in c4762a1b19cd2af06abeed90e8f9d34fb975dd94
- src/ts/tutorials/output/ex12_2_alt.out added for one of the 3 OSX boxes (jpro) - producing slightly different numbers

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PetscOptionsBegin: Title argument made obligatory

to avoid (null) headers in -help output.

Additionally
* PetscOptionsBegin() inarg validation
* fix a few examples which break this
* fix TaoMatGetS

PetscOptionsBegin: Title argument made obligatory

to avoid (null) headers in -help output.

Additionally
* PetscOptionsBegin() inarg validation
* fix a few examples which break this
* fix TaoMatGetSubMat() to use PetscObjectOptionsBegin() instead of PetscOptionsBegin()
* fix weird position of PetscOptionsEnd() in TAO examples

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DM+Plex: Example Fixes for cell type rewrite

refactored LMVM matrix names for Broyden-class methods

SNESQN harmonization with MATLMVM objects

Merge branch 'hongzh/fix-tstrajectory-examples' into 'master'

Adjust the TSTrajectory setup in adjoint examples

See merge request petsc/petsc!2609

Provide support for not setting PETSC_DIR when gnumake is being used; this will prevent some petsc-maint/petsc-users email threads

Commit-type: error-checking, testing-fix, feature, example
Thanks-t

Provide support for not setting PETSC_DIR when gnumake is being used; this will prevent some petsc-maint/petsc-users email threads

Commit-type: error-checking, testing-fix, feature, example
Thanks-to: Jed Brown <jed@jedbrown.org>
Thanks-to: Lisandro Dalcin <dalcinl@gmail.com>

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Promote examples/{tests,tutorials}/ to {tests,tutorials}/

This shortens paths and improves consistency between test target names
and paths to the source and output files. Most of the work was
compl

Promote examples/{tests,tutorials}/ to {tests,tutorials}/

This shortens paths and improves consistency between test target names
and paths to the source and output files. Most of the work was
completed by this script, followed by mild cleanup of nonconforming
cases.

for makefile in `git ls-files 'src/*makefile'`; do
if rg -q 'DIRS.*\bexamples\b' $makefile; then
base=$(dirname $makefile)
dirs=$(cd $base/examples && ls -d tests tutorials 2>/dev/null | xargs echo)
perl -pi -e "s#^(DIRS.*)\bexamples\b#\1${dirs}#" $makefile
git rm $base/examples/makefile
for t in $dirs; do
git mv $base/examples/$t $base/
perl -pi -e "s#^(LOCDIR[[:space:]]*=).*#\1 $base/$t/#" $base/$t
done
fi
done

git grep -l -E -z 'examples/(tutorials|tests)' | xargs -0 perl -pi -e 's#examples/(tutorials|tests)#\1#g'
git checkout @ \
src/docs/website/documentation/changes/ \
src/benchmarks/results/

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