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b9d6091d23-Dec-2021 Satish Balay <balay@mcs.anl.gov>

Merge remote-tracking branch 'origin/release'


/petsc/.gitlab-ci.yml
/petsc/config/examples/arch-ci-linux-hip-double.py
petsc.bib
/petsc/include/petsclandau.h
/petsc/src/mat/impls/aij/mpi/fdmpiaij.c
/petsc/src/mat/impls/cdiagonal/cdiagonal.c
/petsc/src/mat/impls/nest/matnest.c
/petsc/src/mat/impls/transpose/htransm.c
/petsc/src/mat/interface/matrix.c
/petsc/src/mat/tests/ex185.c
/petsc/src/mat/tests/ex253.c
/petsc/src/mat/tests/ex70.c
/petsc/src/mat/tests/output/ex253_1.out
/petsc/src/snes/tutorials/ex12.c
/petsc/src/snes/tutorials/output/ex12_tri_p1_adapt_analytic_mmg.out
/petsc/src/snes/tutorials/output/ex12_tri_p1_adapt_analytic_pragmatic.out
/petsc/src/snes/tutorials/output/ex12_tri_p1_adapt_uniform_mmg.out
/petsc/src/snes/tutorials/output/ex12_tri_p1_adapt_uniform_parmmg.out
/petsc/src/snes/utils/dmadapt.c
/petsc/src/ts/interface/sensitivity/tssen.c
/petsc/src/ts/utils/dmplexlandau/plexland.c
/petsc/src/ts/utils/dmplexlandau/tutorials/ex2.c
/petsc/src/ts/utils/dmplexlandau/tutorials/output/ex2_0.out
/petsc/src/vec/is/sf/impls/basic/hip/sfhip.hip.cpp
397d185221-Dec-2021 Junchao Zhang <jczhang@mcs.anl.gov>

Doc: update bib of the two recent petsc papers


/petsc/.gitlab-ci.yml
/petsc/config/BuildSystem/config/packages/MPICH.py
/petsc/config/BuildSystem/config/packages/cuda.py
/petsc/config/BuildSystem/config/packages/hip.py
/petsc/config/BuildSystem/config/packages/openblas.py
/petsc/config/examples/arch-ci-linux-hip-double.py
petsc.bib
/petsc/src/mat/interface/matrix.c
/petsc/src/sys/f90-mod/petscsysmod.F90
/petsc/src/sys/objects/device/impls/cupm/makefile
/petsc/src/ts/interface/sensitivity/tssen.c
/petsc/src/vec/is/section/interface/section.c
/petsc/src/vec/is/sf/impls/basic/hip/sfhip.hip.cpp
430074e115-Dec-2021 Joe Wallwork <j.wallwork16@imperial.ac.uk>

docs plex: mention ParMmg in manualpage header


classic/manualpages-sec/header_DMPLEX
/petsc/src/binding/petsc4py/src/PETSc/DMPlex.pyx
/petsc/src/binding/petsc4py/src/PETSc/petscdmplex.pxi
/petsc/src/dm/impls/plex/adaptors/mmg/mmgadapt.c
/petsc/src/dm/impls/plex/adaptors/parmmg/parmmgadapt.c
/petsc/src/dm/impls/plex/plexfem.c
/petsc/src/dm/impls/plex/tests/output/ex19_sensor_alt.out
/petsc/src/snes/tutorials/ex12.c
/petsc/src/snes/tutorials/output/ex12_tri_p1_adapt_analytic_mmg.out
/petsc/src/snes/tutorials/output/ex12_tri_p1_adapt_analytic_pragmatic.out
/petsc/src/snes/tutorials/output/ex12_tri_p1_adapt_init_mmg.out
/petsc/src/snes/tutorials/output/ex12_tri_p1_adapt_init_pragmatic.out
/petsc/src/snes/tutorials/output/ex12_tri_p1_adapt_seq_mmg.out
/petsc/src/snes/tutorials/output/ex12_tri_p1_adapt_seq_pragmatic.out
/petsc/src/snes/tutorials/output/ex12_tri_p1_adapt_uniform_mmg.out
/petsc/src/snes/tutorials/output/ex12_tri_p1_adapt_uniform_parmmg.out
/petsc/src/snes/tutorials/output/ex12_tri_p1_adapt_uniform_pragmatic.out
b465f1d717-Dec-2021 Satish Balay <balay@mcs.anl.gov>

Merge remote-tracking branch 'origin/release'


/petsc/config/BuildSystem/config/packages/MPI.py
/petsc/config/BuildSystem/config/packages/MPICH.py
/petsc/config/BuildSystem/config/packages/cuda.py
/petsc/config/BuildSystem/config/packages/hip.py
/petsc/config/BuildSystem/config/packages/kokkos.py
/petsc/config/BuildSystem/config/packages/openblas.py
/petsc/config/BuildSystem/script.py
tutorials/handson.rst
tutorials/physics/guide_to_stokes.rst
/petsc/share/petsc/valgrind/petsc-val.supp
/petsc/src/dm/impls/plex/plexmetric.c
/petsc/src/mat/impls/aij/mpi/kokkos/mpiaijkok.kokkos.cxx
/petsc/src/mat/impls/aij/seq/kokkos/aijkok.kokkos.cxx
/petsc/src/mat/impls/aij/seq/kokkos/aijkokkosimpl.hpp
/petsc/src/snes/tutorials/makefile
/petsc/src/sys/f90-mod/petscsysmod.F90
/petsc/src/sys/objects/device/impls/cupm/makefile
/petsc/src/ts/utils/dmplexlandau/plexland.c
/petsc/src/ts/utils/dmplexlandau/tutorials/ex1.c
/petsc/src/ts/utils/dmplexlandau/tutorials/ex2.c
/petsc/src/ts/utils/dmplexlandau/tutorials/output/ex1_0.out
/petsc/src/ts/utils/dmplexlandau/tutorials/output/ex2_0.out
/petsc/src/vec/is/section/interface/section.c
d3e1f4cc13-Dec-2021 Vaclav Hapla <vaclav.hapla@erdw.ethz.ch>

DMPlexFindVertices: change args to Vec+IS


docs/changes/dev.rst
/petsc/include/petscdmplex.h
/petsc/src/dm/impls/plex/plexgeometry.c
/petsc/src/dm/impls/plex/tests/ex18.c
c905e4ad15-Dec-2021 Satish Balay <balay@mcs.anl.gov>

Merge branch 'psanan/docs-handson-format-fix' into 'release'

Docs: hands-on tutorial page formatting

See merge request petsc/petsc!4632


tutorials/handson.rst
66c2f3ea14-Dec-2021 Satish Balay <balay@mcs.anl.gov>

Merge branch 'knepley/doc-stokes-tutorial' into 'release'

Doc: Small tutorial fixes

See merge request petsc/petsc!4643


tutorials/physics/guide_to_stokes.rst
/petsc/src/snes/tutorials/makefile
e97c8d6714-Dec-2021 Satish Balay <balay@mcs.anl.gov>

Merge remote-tracking branch 'origin/release'


/petsc/config/examples/arch-ci-linux-opt-misc.py
developers/testing.rst
faq/index.rst
/petsc/src/mat/impls/aij/seq/aij.c
/petsc/src/mat/impls/aij/seq/ftn-kernels/fmult.h
/petsc/src/sys/classes/viewer/tutorials/ex1f90.F90
/petsc/src/sys/f90-mod/petscsys.h90
/petsc/src/sys/f90-mod/petscsysmod.F90
/petsc/src/vec/vec/impls/seq/ftn-kernels/fmaxpy.F90
/petsc/src/vec/vec/tutorials/ex43f.F90
792affc014-Dec-2021 Satish Balay <balay@mcs.anl.gov>

Merge branch 'jwallwork23/fix-tag-preservation' into 'main'

Metric fixes 2: tag preservation

See merge request petsc/petsc!4627


docs/changes/dev.rst
docs/manual/dmplex.rst
/petsc/include/petscdmplex.h
/petsc/src/binding/petsc4py/demo/dmplex/anisotropic_adaptation.py
/petsc/src/binding/petsc4py/demo/dmplex/isotropic_adaptation.py
/petsc/src/binding/petsc4py/src/PETSc/DMPlex.pyx
/petsc/src/binding/petsc4py/src/PETSc/petscdmplex.pxi
/petsc/src/binding/petsc4py/test/test_dmplex.py
/petsc/src/dm/impls/plex/adaptors/mmg/mmgadapt.c
/petsc/src/dm/impls/plex/adaptors/parmmg/parmmgadapt.c
/petsc/src/dm/impls/plex/plexmetric.c
/petsc/src/dm/impls/plex/tests/ex60.c
/petsc/src/dm/impls/plex/tests/output/ex60_hessian_2d_mmg.out
/petsc/src/dm/impls/plex/tests/output/ex60_hessian_2d_pragmatic.out
/petsc/src/dm/impls/plex/tests/output/ex60_hessian_3d_mmg.out
/petsc/src/dm/impls/plex/tests/output/ex60_hessian_3d_parmmg.out
/petsc/src/dm/impls/plex/tests/output/ex60_hessian_3d_pragmatic.out
/petsc/src/dm/impls/plex/tests/output/ex60_iso_2d_mmg.out
/petsc/src/dm/impls/plex/tests/output/ex60_iso_2d_pragmatic.out
/petsc/src/dm/impls/plex/tests/output/ex60_iso_3d_mmg.out
/petsc/src/dm/impls/plex/tests/output/ex60_iso_3d_parmmg.out
/petsc/src/dm/impls/plex/tests/output/ex60_iso_3d_pragmatic.out
/petsc/src/dm/impls/plex/tests/output/ex60_uniform_2d_mmg.out
/petsc/src/dm/impls/plex/tests/output/ex60_uniform_2d_pragmatic.out
/petsc/src/dm/impls/plex/tests/output/ex60_uniform_3d_mmg.out
/petsc/src/dm/impls/plex/tests/output/ex60_uniform_3d_parmmg.out
/petsc/src/dm/impls/plex/tests/output/ex60_uniform_3d_pragmatic.out
/petsc/src/snes/tutorials/ex12.c
/petsc/src/snes/tutorials/output/ex12_tri_p1_adapt_0.out
/petsc/src/snes/tutorials/output/ex12_tri_p1_adapt_1.out
/petsc/src/snes/tutorials/output/ex12_tri_p1_adapt_analytic_0.out
/petsc/src/snes/utils/dmadapt.c
37ffe59013-Dec-2021 Satish Balay <balay@mcs.anl.gov>

Merge branch 'psanan/docs-testing-copyedit' into 'release'

Developers manual: fixes for testing chapter

See merge request petsc/petsc!4631


developers/testing.rst
4e2f990413-Dec-2021 Matthew G. Knepley <knepley@gmail.com>

Doc: Small tutorial fixes


tutorials/physics/guide_to_stokes.rst
/petsc/src/snes/tutorials/makefile
e983491913-Dec-2021 Patrick Sanan <patrick.sanan@gmail.com>

Change log guidelines: use full function names


/petsc/config/BuildSystem/config/package.py
docs/changes/dev.rst
/petsc/include/petscerror.h
/petsc/include/petscsys.h
/petsc/src/dm/impls/plex/plexcreate.c
/petsc/src/dm/impls/swarm/tests/ex7.c
/petsc/src/dm/impls/swarm/tests/output/ex7_0.out
/petsc/src/dm/impls/swarm/tests/output/ex7_1.out
/petsc/src/dm/impls/swarm/tests/output/ex7_2.out
/petsc/src/dm/impls/swarm/tutorials/ex1.c
/petsc/src/dm/impls/swarm/tutorials/output/ex1_0.out
/petsc/src/dm/impls/swarm/tutorials/output/ex1_bjacobi.out
7b6d55c210-Dec-2021 Satish Balay <balay@mcs.anl.gov>

Merge branch 'balay/fix-iso_c_binding' into 'release'

fortran: use,intrinsic :: iso_c_binding

See merge request petsc/petsc!4637


/petsc/config/examples/arch-olcf-spock.py
faq/index.rst
/petsc/src/sys/classes/viewer/tutorials/ex1f90.F90
/petsc/src/sys/f90-mod/petscsys.h90
/petsc/src/sys/f90-mod/petscsysmod.F90
/petsc/src/vec/vec/tutorials/ex43f.F90
eb20d01e09-Dec-2021 Satish Balay <balay@mcs.anl.gov>

fortran: use,intrinsic :: iso_c_binding

> Fatal Error: File 'iso_c_binding.mod' opened at (1) is not a GNU Fortran module file compilation terminated.


faq/index.rst
/petsc/src/sys/classes/viewer/tutorials/ex1f90.F90
/petsc/src/sys/f90-mod/petscsys.h90
/petsc/src/sys/f90-mod/petscsysmod.F90
/petsc/src/vec/vec/tutorials/ex43f.F90
adec9d8e10-Dec-2021 Satish Balay <balay@mcs.anl.gov>

Merge remote-tracking branch 'origin/release'


/petsc/config/examples/arch-olcf-spock.py
docs/manual/dmplex.rst
/petsc/include/petscaijdevice.h
/petsc/src/ksp/pc/impls/ksp/pcksp.c
/petsc/src/mat/impls/aij/mpi/kokkos/mpiaijkok.kokkos.cxx
/petsc/src/mat/impls/aij/mpi/mpicusparse/mpiaijcusparse.cu
/petsc/src/mat/tutorials/ex5cu.cu
/petsc/src/mat/tutorials/ex5k.kokkos.cxx
/petsc/src/mat/tutorials/output/ex5cu_0.out
/petsc/src/mat/tutorials/output/ex5cu_1.out
/petsc/src/mat/tutorials/output/ex5cu_2.out
/petsc/src/mat/tutorials/output/ex5k_0.out
182b02f625-Nov-2021 Patrick Sanan <patrick.sanan@gmail.com>

Docs: DMPlex manual: add missing math markup and update function name


docs/manual/dmplex.rst
1cb976dd09-Dec-2021 Patrick Sanan <patrick.sanan@gmail.com>

Docs: developer manual: testing examples as proper code blocks

Condense some individual "Example:" bullet points,
and fix an incorrect language specificiation for a code block.


developers/testing.rst
3f07679e08-Dec-2021 Joe Wallwork <j.wallwork16@imperial.ac.uk>

plex metric: compute determinant when modifying metric


docs/changes/dev.rst
docs/manual/dmplex.rst
/petsc/include/petscdmplex.h
/petsc/src/binding/petsc4py/demo/dmplex/isotropic_adaptation.py
/petsc/src/binding/petsc4py/src/PETSc/DMPlex.pyx
/petsc/src/binding/petsc4py/src/PETSc/petscdmplex.pxi
/petsc/src/binding/petsc4py/test/test_dmplex.py
/petsc/src/dm/impls/plex/plexmetric.c
9e39a8ac09-Dec-2021 Satish Balay <balay@mcs.anl.gov>

Merge branch 'psanan-release-patch-55755' into 'release'

Docs: DMPlex manual: add missing inline code formatting

See merge request petsc/petsc!4596


docs/manual/dmplex.rst
/petsc/src/ksp/pc/impls/ksp/pcksp.c
76524f8f09-Dec-2021 Satish Balay <balay@mcs.anl.gov>

Merge branch 'psanan-release-patch-48926' into 'release'

Docs: DMPlex manual: remove duplicated link text

See merge request petsc/petsc!4595


/petsc/config/BuildSystem/config/packages/hypre.py
docs/manual/dmplex.rst
/petsc/src/dm/impls/composite/makefile
/petsc/src/dm/impls/composite/tests/ex1.c
/petsc/src/dm/impls/composite/tests/makefile
/petsc/src/dm/impls/composite/tests/output/ex1_0.out
/petsc/src/dm/interface/dm.c
a8a8b9ed09-Dec-2021 Satish Balay <balay@mcs.anl.gov>

Merge branch 'stefanozampini/split-tao' into 'main'

TAO: unify options for bounded Newton-Krylov

See merge request petsc/petsc!4581


/petsc/config/BuildSystem/config/packages/hypre.py
docs/manual/tao.rst
/petsc/include/petsc/private/sectionimpl.h
/petsc/include/petsc/private/vecimpl.h
/petsc/include/petscis.h
/petsc/include/petscvec.h
/petsc/lib/petsc/bin/maint/petscClangLinter.py
/petsc/src/binding/petsc4py/src/PETSc/petsctao.pxi
/petsc/src/dm/impls/composite/makefile
/petsc/src/dm/impls/composite/tests/ex1.c
/petsc/src/dm/impls/composite/tests/makefile
/petsc/src/dm/impls/composite/tests/output/ex1_0.out
/petsc/src/dm/interface/dm.c
/petsc/src/ksp/pc/impls/bjacobi/bjacobi.c
/petsc/src/tao/bound/impls/bnk/bnk.c
/petsc/src/tao/bound/impls/bqnk/bqnk.c
/petsc/src/tao/bound/impls/bqnk/bqnkls.c
/petsc/src/tao/bound/impls/bqnk/bqnktl.c
/petsc/src/tao/bound/impls/bqnk/bqnktr.c
/petsc/src/tao/bound/impls/bqnls/bqnls.c
/petsc/src/tao/interface/taosolver.c
/petsc/src/tao/tutorials/ex4.c
/petsc/src/tao/tutorials/output/ex4_hessian_1.out
/petsc/src/tao/tutorials/output/ex4_hessian_2.out
/petsc/src/tao/unconstrained/tutorials/output/rosenbrock1_18_alt.out
/petsc/src/tao/unconstrained/tutorials/output/rosenbrock1_20_alt.out
/petsc/src/ts/impls/implicit/irk/irk.c
/petsc/src/ts/tutorials/output/ex2_tut_2_alt.out
/petsc/src/ts/tutorials/power_grid/stability_9bus/ex9busdmnetwork.c
/petsc/src/vec/is/ao/impls/basic/aobasic.c
/petsc/src/vec/is/ao/impls/mapping/aomapping.c
/petsc/src/vec/is/ao/impls/memscalable/aomemscalable.c
/petsc/src/vec/is/ao/interface/ao.c
/petsc/src/vec/is/ao/tests/ex1.c
/petsc/src/vec/is/ao/tests/ex2.c
/petsc/src/vec/is/ao/tests/ex3d/ex3.cxx
/petsc/src/vec/is/ao/tests/ex5.c
/petsc/src/vec/is/is/impls/block/block.c
/petsc/src/vec/is/is/impls/general/general.c
/petsc/src/vec/is/is/impls/stride/stride.c
/petsc/src/vec/is/is/interface/index.c
/petsc/src/vec/is/is/tests/ex10.c
/petsc/src/vec/is/is/tests/ex7.c
/petsc/src/vec/is/is/tests/ex9.c
/petsc/src/vec/is/is/tutorials/ex1.c
/petsc/src/vec/is/is/tutorials/ex2.c
/petsc/src/vec/is/is/tutorials/ex3.c
/petsc/src/vec/is/is/utils/iscoloring.c
/petsc/src/vec/is/is/utils/isdiff.c
/petsc/src/vec/is/section/interface/section.c
/petsc/src/vec/is/section/interface/sectionhdf5.c
/petsc/src/vec/is/sf/impls/basic/alltoall/sfalltoall.c
/petsc/src/vec/is/sf/impls/window/sfwindow.c
/petsc/src/vec/is/sf/interface/sf.c
/petsc/src/vec/is/sf/interface/vscat.c
/petsc/src/vec/is/sf/tests/ex14.c
/petsc/src/vec/is/sf/tests/ex2.c
/petsc/src/vec/is/sf/tests/ex6.c
/petsc/src/vec/is/sf/tutorials/ex1.c
/petsc/src/vec/is/sf/utils/sfutils.c
/petsc/src/vec/is/tests/ex2.c
/petsc/src/vec/is/utils/hdf5io.c
/petsc/src/vec/is/utils/isio.c
/petsc/src/vec/is/utils/isltog.c
/petsc/src/vec/is/utils/pmap.c
/petsc/src/vec/is/utils/psort.c
/petsc/src/vec/pf/impls/constant/const.c
/petsc/src/vec/pf/interface/pf.c
/petsc/src/vec/vec/impls/mpi/pbvec.c
/petsc/src/vec/vec/impls/mpi/pdvec.c
/petsc/src/vec/vec/impls/nest/vecnest.c
/petsc/src/vec/vec/impls/nest/vecnestimpl.h
/petsc/src/vec/vec/impls/seq/bvec2.c
/petsc/src/vec/vec/impls/seq/seqcuda/veccuda.c
/petsc/src/vec/vec/impls/seq/seqhip/vechip.hip.cpp
/petsc/src/vec/vec/impls/seq/seqviennacl/vecviennacl.cxx
/petsc/src/vec/vec/interface/rvector.c
/petsc/src/vec/vec/interface/vector.c
/petsc/src/vec/vec/tests/benchmark_veccreate.c
/petsc/src/vec/vec/tests/ex21.c
/petsc/src/vec/vec/tests/ex28.c
/petsc/src/vec/vec/tests/ex36.c
/petsc/src/vec/vec/tests/ex37.c
/petsc/src/vec/vec/tests/ex43.c
/petsc/src/vec/vec/tests/ex44.c
/petsc/src/vec/vec/tests/ex45.c
/petsc/src/vec/vec/tests/ex46.c
/petsc/src/vec/vec/tests/ex48.c
/petsc/src/vec/vec/tests/ex51.c
/petsc/src/vec/vec/tutorials/ex1.c
/petsc/src/vec/vec/tutorials/ex19.c
/petsc/src/vec/vec/tutorials/ex44.c
/petsc/src/vec/vec/tutorials/ex6.c
/petsc/src/vec/vec/tutorials/ex9.c
/petsc/src/vec/vec/utils/projection.c
/petsc/src/vec/vec/utils/tagger/impls/andor.c
/petsc/src/vec/vec/utils/tagger/impls/cdf.c
/petsc/src/vec/vec/utils/tagger/impls/simple.c
/petsc/src/vec/vec/utils/tagger/interface/tagger.c
/petsc/src/vec/vec/utils/tagger/tutorials/ex1.c
/petsc/src/vec/vec/utils/vecglvis.c
/petsc/src/vec/vec/utils/vecio.c
/petsc/src/vec/vec/utils/vecstash.c
/petsc/src/vec/vec/utils/vinv.c
/petsc/src/vec/vec/utils/vsection.c
3badecdb09-Dec-2021 Patrick Sanan <patrick.sanan@gmail.com>

Docs: hand-on tutorial page formatting

* Fix indentation
* Add link to configuration section
* convert :any: to :ref:


/petsc/config/BuildSystem/config/packages/hypre.py
tutorials/handson.rst
/petsc/src/dm/impls/composite/makefile
/petsc/src/dm/impls/composite/tests/ex1.c
/petsc/src/dm/impls/composite/tests/makefile
/petsc/src/dm/impls/composite/tests/output/ex1_0.out
/petsc/src/dm/interface/dm.c
4016b0de09-Dec-2021 Patrick Sanan <patrick.sanan@gmail.com>

Developer manual: testing: use proper link to TAP


developers/testing.rst
d225978b09-Dec-2021 Patrick Sanan <patrick.sanan@gmail.com>

Developer manual: testing: fix formatting conversion errors


developers/testing.rst
36bff7b209-Dec-2021 Patrick Sanan <patrick.sanan@gmail.com>

Developer manual: testing: edit introduction


developers/testing.rst
/petsc/include/petscerror.h
/petsc/src/dm/impls/plex/transform/interface/plextransform.c
/petsc/src/ts/impls/implicit/discgrad/tsdiscgrad.c

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