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Dealii 9.3 #13905

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wants to merge 138 commits into from
Closed

Dealii 9.3 #13905

wants to merge 138 commits into from

Commits on May 22, 2021

  1. update VERSION

    tamiko committed May 22, 2021
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  2. update AUTHORS

    tamiko committed May 22, 2021
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  3. update LICENSE

    tamiko committed May 22, 2021
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  5. remove bundled version

    tamiko committed May 22, 2021
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  7. remove dead code from source

    tamiko committed May 22, 2021
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  8. Merge pull request #12286 from tamiko/disable-taskflow

    [9.3.0] Remove Taskflow from 9.3 release branch
    tamiko committed May 22, 2021
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  9. update VERSION for release

    tamiko committed May 22, 2021
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Commits on May 24, 2021

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  2. Merge pull request #12297 from peterrum/authors_fix_formatting

    Fix formating of authors.md (release 9.3)
    masterleinad committed May 24, 2021
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  4. Fix typos

    masterleinad committed May 24, 2021
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Commits on May 25, 2021

  1. Update include/deal.II/grid/tria_accessor.h

    Co-authored-by: Bruno Turcksin <bruno.turcksin@gmail.com>
    masterleinad and Rombur committed May 25, 2021
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Commits on May 26, 2021

  1. Merge pull request #12305 from jppelteret/dealii-9.3-step-79-touchups_01

    [9.3] Take over #12292: Some minor changes to the step-79 documentation
    masterleinad committed May 26, 2021
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  3. Remove noexcept on TriaAccessor move constructor and assignment operator

    To avoid a compilation error with clang 6.0.0.
    simonsticko committed May 26, 2021
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  4. Fix warnings using clang 13.0

    Rombur committed May 26, 2021
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Commits on May 28, 2021

  1. Merge pull request #12318 from Rombur/clang_13_warnings_93

    [9.3] Take over #12299
    peterrum committed May 28, 2021
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Commits on May 29, 2021

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  3. Merge pull request #12345 from kronbichler/apply_12344

    [9.3] Take over #12344
    tamiko committed May 29, 2021
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  4. Remove noexcept on DoFAccessor move constructor and assignment operator

    To avoid a compilation error with clang 6.0.0
    simonsticko authored and masterleinad committed May 29, 2021
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Commits on May 30, 2021

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  2. Merge pull request #12355 from peterrum/point_values_93

    [9.3] Take over #12332: Rename VectorTools::evaluate_at_points() -> VectorTools::point_values()
    kronbichler committed May 30, 2021
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  3. Merge pull request #12354 from masterleinad/take_over_12335

    [9.3] Take over #12335: Remove noexcept on DoFAccessor move constructor and assignment operator
    kronbichler committed May 30, 2021
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Commits on May 31, 2021

  1. Avoid underlinkage with OpenMPI on Debian/Ubuntu

    Make sure that we do not run into underlinking on Debian/Ubuntu systems
    with lld / ld.gold and missing libopen-pal.so on the link line
    tamiko committed May 31, 2021
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  4. Merge pull request #12359 from tamiko/pr_12358

    [9.3] Take over #12358: Avoid underlinkage with OpenMPI on Debian/Ubuntu
    tamiko committed May 31, 2021
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  5. Merge pull request #12364 from peterrum/rpe_race_condition_

    [9.3] Take over #12363: RemotePointEvaluation: fix race condition if called multiple times
    tamiko committed May 31, 2021
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  6. Merge pull request #12362 from kronbichler/pr12361

    [9.3] Take over #12361: Remove changelog entry about taskflow
    tamiko committed May 31, 2021
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  9. Merge pull request #12369 from jppelteret/dealii-9.3-pr10932

    [9.3] Takeover #10932: Add changelog entry for step-74
    tjhei committed May 31, 2021
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  10. Merge pull request #12367 from marcfehling/fix-step-75-dealii-9.3

    [9.3] Take over #12366: Bugfix step-75: Call `get_fe()` only on locally owned cells.
    kronbichler committed May 31, 2021
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Commits on Jun 1, 2021

  1. update VERSION for release

    tamiko committed Jun 1, 2021
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Commits on Jun 22, 2021

  1. fix cmake underlinkage error

    The underlinkage MPI check under Ubuntu fails if MPI_CXX_LIBRARIES is
    empty, which happens if you configure with CXX=mpicxx (even though you
    should not).
    
    In this situation, just disable this hack. Errors look like this:
    
    CMake Error at cmake/modules/FindMPI.cmake:143 (LIST):
      LIST GET given empty list
    Call Stack (most recent call first):
      cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
      cmake/configure/configure_1_mpi.cmake:28 (FIND_PACKAGE)
    /a/CMakeFiles/CMakeTmp/evaluate_expression.tmp:1
    (FEATURE_MPI_FIND_EXTERNAL)
      cmake/macros/macro_evaluate_expression.cmake:30 (INCLUDE)
      cmake/macros/macro_configure_feature.cmake:237 (EVALUATE_EXPRESSION)
      cmake/configure/configure_1_mpi.cmake:81 (CONFIGURE_FEATURE)
      cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
      CMakeLists.txt:121 (VERBOSE_INCLUDE)
    
    CMake Error at cmake/modules/FindMPI.cmake:144 (GET_FILENAME_COMPONENT):
      GET_FILENAME_COMPONENT called with incorrect number of arguments
    Call Stack (most recent call first):
      cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
      cmake/configure/configure_1_mpi.cmake:28 (FIND_PACKAGE)
    /a/CMakeFiles/CMakeTmp/evaluate_expression.tmp:1
    (FEATURE_MPI_FIND_EXTERNAL)
      cmake/macros/macro_evaluate_expression.cmake:30 (INCLUDE)
      cmake/macros/macro_configure_feature.cmake:237 (EVALUATE_EXPRESSION)
      cmake/configure/configure_1_mpi.cmake:81 (CONFIGURE_FEATURE)
      cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
      CMakeLists.txt:121 (VERBOSE_INCLUDE)
    
    -- _mpi_libopen_pal_library not found! The call was:
    --     FIND_LIBRARY(_mpi_libopen_pal_library NAMES open-pal HINTS
    NO_DEFAULT_PATH NO_CMAKE_ENVIRONMENT_PATH NO_CMAKE_PATH
    NO_SYSTEM_ENVIRONMENT_PATH NO_CMAKE_SYSTEM_PATH NO_CMAKE_FIND_ROOT_PATH)
    tjhei authored and tamiko committed Jun 22, 2021
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Commits on Jun 27, 2021

  1. Merge pull request #12488 from tamiko/pr_12478

    [9.3.] fix cmake underlinkage error
    tamiko committed Jun 27, 2021
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  2. add missing inst

    fixes #12501 and #12490
    tjhei committed Jun 27, 2021
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  3. fix umfpack cmake 3.20 warning

    Fix the following warnings produced by CMake 3.20:
    
    CMake Warning (dev) at cmake/macros/macro_deal_ii_add_library.cmake:35
    (ADD_LIBRARY):
    Policy CMP0115 is not set: Source file extensions must be explicit.
    File:
    
        /home/heister/deal.ii-
    candi/tmp/unpack/deal.II-v9.3.0/bundled/umfpack/UMFPACK/Source/umf_dump.cc
       /home/heister/deal.ii-
    candi/tmp/unpack/deal.II-v9.3.0/bundled/umfpack/UMFPACK/Source/umf_init_front.cc
        /home/heister/deal.ii-
    candi/tmp/unpack/deal.II-v9.3.0/bundled/umfpack/UMFPACK/Source/umf_local_search.cc
        /home/heister/deal.ii-
    candi/tmp/unpack/deal.II-v9.3.0/bundled/umfpack/UMFPACK/Source/umfpack_report_numeric.cc
    tjhei committed Jun 27, 2021
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Commits on Jun 28, 2021

  1. Merge pull request #12510 from tjhei/pr_12506

    [9.3] take over #12506 - fix umfpack cmake 3.20 warning
    drwells committed Jun 28, 2021
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  2. Merge pull request #12509 from tjhei/pr_12505

    [9.3] take over #12505 add missing inst
    drwells committed Jun 28, 2021
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  4. Fix a segmentation fault at high optimization levels.

    I don't completely understand this but accessing these pointers causes
    segmentation faults. It's not due to type aliasing - converting both to 'const
    auto *' does not fix the problem.
    drwells committed Jun 28, 2021
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  6. Merge pull request #12518 from drwells/cherry-pick-12468

    [9.3] Take over #12468 - Fix a segmentation fault at high optimization levels.
    tamiko committed Jun 28, 2021
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  7. Merge pull request #12519 from drwells/cherry-pick-12398

    [9.3] Take over #12398 - Add grid reordering to read_exodusii function
    tamiko committed Jun 28, 2021
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  8. Merge pull request #12516 from drwells/cherry-pick-12511

    [9.3] take over #12511 - add one more missing file extension.
    tamiko committed Jun 28, 2021
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Commits on Jun 29, 2021

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  2. Tensor: refactor constructor and assignment operator guards

     * This commit guards some constructors and copy/move assignment
       operators that are necessary to work around a gcc 11 regression with
       DEAL_II_DELETED_MOVE_CONSTRUCTOR_BUG.
    
     * Add back explicitly guarded constructor working around a code
       generation issue with intel compilers
    tamiko committed Jun 29, 2021
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  3. add a news entry

    tamiko committed Jun 29, 2021
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  4. silence gcc 11 warning

    silence boost warning
    ../bundled/boost-1.70.0/include/boost/concept/usage.hpp:16:48: warning:
    'this' pointer is null [-Wnonnull]
       16 |     ~usage_requirements() { ((Model*)0)->~Model(); }
    tjhei authored and tamiko committed Jun 29, 2021
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  5. Merge pull request #12525 from tamiko/pr_12523

    [9.3] Take over #12523
    tamiko committed Jun 29, 2021
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  6. Merge pull request #12524 from tamiko/pr_12515

    [9.3] Take over #12515
    tamiko committed Jun 29, 2021
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Commits on Jun 30, 2021

  1. reorganize changelog entries for point release

     - create 9.3.0-vs-9.3.1.h file
     - remove individual entries
    tamiko committed Jun 30, 2021
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  2. Merge pull request #12527 from tamiko/update_changelog

    [9.3] reorganize changelog entries for point release
    drwells committed Jun 30, 2021
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  3. update VERSION

    tamiko committed Jun 30, 2021
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Commits on Oct 8, 2021

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  2. Merge pull request #12805 from masterleinad/9.3-fix-step-79

    9.3: cherry-picking #12533: step-79: Avoid using constructor which are incompatible to Intel 18.
    tamiko committed Oct 8, 2021
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Commits on Oct 9, 2021

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Commits on Oct 10, 2021

  1. Update include/deal.II/numerics/vector_tools_evaluate.h

    Co-authored-by: Peter Munch <peterrmuench@gmail.com>
    masterleinad and peterrum committed Oct 10, 2021
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  2. Merge pull request #12809 from masterleinad/pick_12548

    Avoid lambda function to compile with Intel 18/19.
    peterrum committed Oct 10, 2021
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Commits on Oct 25, 2021

  1. fix checkpointing for >4GB files

    We incorrectly compute MPI_Offset for MPI IO for checkpointing using
    SolutionTransfer using 32 bit indices, which means that files larger
    than 4GB end up being corrupted.
    This manifests in errors like
    
    n error occurred in line <749> of file
    <../source/distributed/tria_base.cc> in function
    void dealii::parallel::DistributedTriangulationBase<dim,
    spacedim>::load_attached_data(unsigned int, unsigned int, unsigned int,
    const string&, unsigned int, unsigned int) [with int dim = 3; int
    spacedim = 3; std::string = std::__cxx11::basic_string<char>]
    The violated condition was:
    (cell_rel.second == parallel::DistributedTriangulationBase<dim,
    spacedim>::CELL_PERSIST)
    
    part of #12752
    tjhei authored and tamiko committed Oct 25, 2021
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  2. adjust variable name

    tjhei authored and tamiko committed Oct 25, 2021
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  3. add broken test

    tjhei authored and tamiko committed Oct 25, 2021
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  4. actually fix the problem

    tjhei authored and tamiko committed Oct 25, 2021
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Commits on Oct 26, 2021

  1. Merge pull request #12881 from tamiko/pr_12830

    [9.3] Cherry pick #12830
    kronbichler committed Oct 26, 2021
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  2. Merge pull request #12882 from tamiko/pr_12634

    [9.3] Cherry pick #12634
    kronbichler committed Oct 26, 2021
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Commits on Nov 5, 2021

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  2. Revert "Fixed naming in IDA."

    This reverts commit 0b157b0.
    masterleinad committed Nov 5, 2021
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  3. Revert "Addressed comments by WB."

    This reverts commit ab509cd.
    masterleinad committed Nov 5, 2021
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  4. Revert "Minor updates to the SUNDIALS/IDA wrappers."

    This reverts commit 9e8dc71.
    masterleinad committed Nov 5, 2021
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  5. Revert "Fix Kinsol interface."

    This reverts commit 1032025.
    masterleinad committed Nov 5, 2021
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  6. Revert "Remove sudials/copy.h"

    This reverts commit 51b6f10.
    masterleinad committed Nov 5, 2021
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  7. Revert "Restructured and renamed functions."

    This reverts commit 64d87af.
    masterleinad committed Nov 5, 2021
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  8. Revert "Moved to new interface in sundials."

    This reverts commit b108fe7.
    masterleinad committed Nov 5, 2021
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  9. Revert "Make IDA work with new sundials."

    This reverts commit 67c15c8.
    masterleinad committed Nov 5, 2021
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  10. Revert "Remove copy from SUNDIALS::KINSOL"

    This reverts commit 422d57b.
    masterleinad committed Nov 5, 2021
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Commits on Nov 6, 2021

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  2. Merge pull request #12918 from tamiko/update_changelog_2

    [9.3] add changelog entry for point release
    drwells committed Nov 6, 2021
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Commits on Nov 7, 2021

  1. Merge pull request #12915 from masterleinad/9.3-revert-12216

    [9.3.2] Revert "Remove copy from SUNDIALS::KINSOL"
    tamiko committed Nov 7, 2021
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Commits on Nov 8, 2021

  1. update VERSION

    tamiko committed Nov 8, 2021
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Commits on Dec 25, 2021

  1. fix sundials compilation

    tjhei committed Dec 25, 2021
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Commits on Dec 26, 2021

  1. Merge pull request #13123 from tjhei/93-sundials-fix

    [9.3] sundials fix
    luca-heltai committed Dec 26, 2021
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Commits on Jan 6, 2022

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  2. Boost 1.77 compatibility: change order of includes

    Otherwise, including both header files in reverse order leads to a
    compilation failure:
    
    ```
    In file included from /usr/include/boost/geometry/index/detail/rtree/rstar/choose_next_node.hpp:25,
                     from /usr/include/boost/geometry/index/detail/rtree/rstar/rstar.hpp:15,
                     from /usr/include/boost/geometry/index/rtree.hpp:80,
                     from ../include/deal.II/numerics/rtree.h:29,
                     from ../include/deal.II/grid/grid_tools.h:49,
                     from ../include/deal.II/numerics/vector_tools_point_gradient.templates.h:22,
                     from ../source/numerics/vector_tools_point_gradient.cc:17:
    /usr/include/boost/geometry/index/detail/algorithms/intersection_content.hpp: In function ‘bool boost::geometry::index::detail::disjoint_box_box(const Box&, const Box&, const boost::geometry::default_strategy&)’:
    /usr/include/boost/geometry/index/detail/algorithms/intersection_content.hpp:35:32: error: ‘boost::geometry::strategy::disjoint’ has not been declared
       35 |     typedef typename strategy::disjoint::services::default_strategy<Box, Box>::type strategy_type;
          |                                ^~~~~~~~
    /usr/include/boost/geometry/index/detail/algorithms/intersection_content.hpp:35:68: error: expected unqualified-id before ‘<’ token
       35 |     typedef typename strategy::disjoint::services::default_strategy<Box, Box>::type strategy_type;
          |                                                                    ^
    /usr/include/boost/geometry/index/detail/algorithms/intersection_content.hpp:36:83: error: class template argument deduction failed:
       36 |     return geometry::detail::disjoint::disjoint_box_box(box1, box2, strategy_type());
    ```
    tamiko authored and drwells committed Jan 6, 2022
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  4. Boost: undo header adjustments

    This little trick does not solve the problem
    tamiko authored and drwells committed Jan 6, 2022
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  5. Fix compilation with boost 1.78.

    I bisected (fortunately Boost.Geometry a header-only library so adding the
    include directory sufficed) and
    boostorg/geometry@6eb9e23
    is where this problem starts for us. See also
    boostorg/geometry#792 - the easiest fix for all such
    issues is to just include the project header `boost/geometry/geometry.hpp`.
    
    In this particular case, if you look at the commit which causes grid_tools.cc
    fails to compile, its because we were relying on some implicit includes. In
    particular, we need the distance header to find the distance between points and
    boxes, but that was previously included in another file.
    drwells committed Jan 6, 2022
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  6. Merge pull request #13180 from drwells/boost-1.78-9.3

    [9.3] Boost 1.78
    tamiko committed Jan 6, 2022
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Commits on Jan 10, 2022

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  4. Merge pull request #13209 from marcfehling/fix-p4est-9.3

    [9.3] Fix setup script for p4est>=2.3.
    marcfehling committed Jan 10, 2022
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Commits on Jan 12, 2022

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  3. TBB OneAPI: Update includes

    tamiko committed Jan 12, 2022
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  9. Move a check out of an inner loop.

    bangerth authored and tamiko committed Jan 12, 2022
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  12. Break a loop early.

    The scratch objects can be in the list only once, so once we find it, we
    can stop the loop.
    bangerth authored and tamiko committed Jan 12, 2022
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  14. Name a function better.

    Previously, the TBB required it to be operator(), but the new system
    no longer requires this.
    bangerth authored and tamiko committed Jan 12, 2022
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  16. port workstream.h to oneAPI

    tamiko committed Jan 12, 2022
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  18. add a changelog entry

    tamiko committed Jan 12, 2022
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  19. CMake: remove oneAPI exclude

    tamiko committed Jan 12, 2022
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  20. disable threading in task_info.cc for oneAPI

    TBB with oneAPI API has deprecated and removed the
    <code>tbb::tasks</code> backend. With this it is no longer possible to
    compile the following code that builds a directed acyclic graph (DAG) of
    (thread parallel) tasks without a major porting effort. It turned out
    that such a dynamic handling of dependencies and structures is not as
    competitive as initially assumed. Consequently, this part of the matrix
    free infrastructure has seen less attention than the rest over the last
    years and is (presumably) rarely used.
    
    So in case of detected oneAPI backend we simply disable threading in the
    matrix free backend for now.
    tamiko committed Jan 12, 2022
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  21. make define guards more robust

    tamiko committed Jan 12, 2022
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  22. Merge pull request #13224 from tamiko/backport_oneapi_fixes

    [9.3] take over oneAPI fixes
    bangerth committed Jan 12, 2022
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Commits on Jan 13, 2022

  1. CMake: use portable "cmake -E remove" in quick_tests

    Closes: #13122
    
    PR: #13129
    tamiko authored and marcfehling committed Jan 13, 2022
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  5. Merge pull request #13233 from marcfehling/oneapi-9.3

    [9.3] Compatibility to oneAPI suite and oneTBB `apt` package.
    bangerth committed Jan 13, 2022
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  6. Merge pull request #13234 from marcfehling/cmake-windows

    [9.3] CMake: use portable "cmake -E remove" in quick_tests
    bangerth committed Jan 13, 2022
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Commits on Jan 24, 2022

  1. Fix flags bug point_values

    bergbauer committed Jan 24, 2022
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  2. Merge pull request #13284 from bergbauer/fix-flags-bug-point-values

    [9.3] Fix flags bug point_values
    tamiko committed Jan 24, 2022
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Commits on Jan 25, 2022

  1. update changelog entries

    tamiko committed Jan 25, 2022
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  2. Merge pull request #13292 from tamiko/update_changelog

    [9.3] update changelog entries for point release
    tamiko committed Jan 25, 2022
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Commits on Jan 26, 2022

  1. update VERSION

    tamiko committed Jan 26, 2022
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Commits on Feb 23, 2022

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Commits on Feb 25, 2022

  1. Merge pull request #13437 from rezarastak/fix_vertex_index

    Replace present_index by index() in DoFAccessor
    bangerth committed Feb 25, 2022
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Commits on May 25, 2022

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Commits on May 26, 2022

  1. Merge pull request #13819 from tamiko/deal_9.3_fix_doxygen

    [9.3] Take over doxygen fixes
    tamiko committed May 26, 2022
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