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Dealii 9.3 #13905
Dealii 9.3 #13905
Commits on May 22, 2021
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Merge pull request #12286 from tamiko/disable-taskflow
[9.3.0] Remove Taskflow from 9.3 release branch
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Commits on May 24, 2021
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Merge pull request #12297 from peterrum/authors_fix_formatting
Fix formating of authors.md (release 9.3)
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Commits on May 25, 2021
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Update include/deal.II/grid/tria_accessor.h
Co-authored-by: Bruno Turcksin <bruno.turcksin@gmail.com>
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Commits on May 26, 2021
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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
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Remove noexcept on TriaAccessor move constructor and assignment operator
To avoid a compilation error with clang 6.0.0.
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Commits on May 28, 2021
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Merge pull request #12318 from Rombur/clang_13_warnings_93
[9.3] Take over #12299
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Commits on May 29, 2021
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Merge pull request #12345 from kronbichler/apply_12344
[9.3] Take over #12344
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Remove noexcept on DoFAccessor move constructor and assignment operator
To avoid a compilation error with clang 6.0.0
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Commits on May 30, 2021
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Merge pull request #12355 from peterrum/point_values_93
[9.3] Take over #12332: Rename VectorTools::evaluate_at_points() -> VectorTools::point_values()
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Merge pull request #12354 from masterleinad/take_over_12335
[9.3] Take over #12335: Remove noexcept on DoFAccessor move constructor and assignment operator
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Commits on May 31, 2021
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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
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Merge pull request #12359 from tamiko/pr_12358
[9.3] Take over #12358: Avoid underlinkage with OpenMPI on Debian/Ubuntu
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Merge pull request #12364 from peterrum/rpe_race_condition_
[9.3] Take over #12363: RemotePointEvaluation: fix race condition if called multiple times
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Merge pull request #12362 from kronbichler/pr12361
[9.3] Take over #12361: Remove changelog entry about taskflow
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Merge pull request #12369 from jppelteret/dealii-9.3-pr10932
[9.3] Takeover #10932: Add changelog entry for step-74
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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.
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Commits on Jun 1, 2021
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Commits on Jun 22, 2021
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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)
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Commits on Jun 27, 2021
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Merge pull request #12488 from tamiko/pr_12478
[9.3.] fix cmake underlinkage error
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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
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Commits on Jun 28, 2021
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Merge pull request #12510 from tjhei/pr_12506
[9.3] take over #12506 - fix umfpack cmake 3.20 warning
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Merge pull request #12509 from tjhei/pr_12505
[9.3] take over #12505 add missing inst
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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.
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Merge pull request #12518 from drwells/cherry-pick-12468
[9.3] Take over #12468 - Fix a segmentation fault at high optimization levels.
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Merge pull request #12519 from drwells/cherry-pick-12398
[9.3] Take over #12398 - Add grid reordering to read_exodusii function
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Merge pull request #12516 from drwells/cherry-pick-12511
[9.3] take over #12511 - add one more missing file extension.
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Commits on Jun 29, 2021
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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
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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(); }
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Commits on Jun 30, 2021
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reorganize changelog entries for point release
- create 9.3.0-vs-9.3.1.h file - remove individual entries
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Merge pull request #12527 from tamiko/update_changelog
[9.3] reorganize changelog entries for point release
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Commits on Oct 8, 2021
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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.
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Commits on Oct 9, 2021
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Commits on Oct 10, 2021
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Update include/deal.II/numerics/vector_tools_evaluate.h
Co-authored-by: Peter Munch <peterrmuench@gmail.com>
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Merge pull request #12809 from masterleinad/pick_12548
Avoid lambda function to compile with Intel 18/19.
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Commits on Oct 25, 2021
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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
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Commits on Oct 26, 2021
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Merge pull request #12881 from tamiko/pr_12830
[9.3] Cherry pick #12830
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Merge pull request #12882 from tamiko/pr_12634
[9.3] Cherry pick #12634
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Commits on Nov 5, 2021
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Revert "Minor updates to the SUNDIALS/IDA wrappers."
This reverts commit 9e8dc71.
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Revert "Restructured and renamed functions."
This reverts commit 64d87af.
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Revert "Moved to new interface in sundials."
This reverts commit b108fe7.
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Revert "Make IDA work with new sundials."
This reverts commit 67c15c8.
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Revert "Remove copy from SUNDIALS::KINSOL"
This reverts commit 422d57b.
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Commits on Nov 6, 2021
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Merge pull request #12918 from tamiko/update_changelog_2
[9.3] add changelog entry for point release
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Commits on Nov 7, 2021
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Merge pull request #12915 from masterleinad/9.3-revert-12216
[9.3.2] Revert "Remove copy from SUNDIALS::KINSOL"
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Commits on Nov 8, 2021
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Commits on Dec 25, 2021
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Commits on Dec 26, 2021
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Merge pull request #13123 from tjhei/93-sundials-fix
[9.3] sundials fix
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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()); ```
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Boost: undo header adjustments
This little trick does not solve the problem
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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.
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Commits on Jan 10, 2022
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Merge pull request #13209 from marcfehling/fix-p4est-9.3
[9.3] Fix setup script for p4est>=2.3.
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The scratch objects can be in the list only once, so once we find it, we can stop the loop.
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Previously, the TBB required it to be operator(), but the new system no longer requires this.
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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.
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Merge pull request #13224 from tamiko/backport_oneapi_fixes
[9.3] take over oneAPI fixes
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Commits on Jan 13, 2022
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cmake: check_compiler_setup: move linker flags to correct CMAKE_REQUI…
…RED variable PR: #12568
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Merge pull request #13233 from marcfehling/oneapi-9.3
[9.3] Compatibility to oneAPI suite and oneTBB `apt` package.
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Merge pull request #13234 from marcfehling/cmake-windows
[9.3] CMake: use portable "cmake -E remove" in quick_tests
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Merge pull request #13284 from bergbauer/fix-flags-bug-point-values
[9.3] Fix flags bug point_values
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Commits on Jan 25, 2022
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Merge pull request #13292 from tamiko/update_changelog
[9.3] update changelog entries for point release
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Commits on Jan 26, 2022
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Commits on Feb 23, 2022
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Merge pull request #13437 from rezarastak/fix_vertex_index
Replace present_index by index() in DoFAccessor
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Commits on May 25, 2022
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Merge pull request #13819 from tamiko/deal_9.3_fix_doxygen
[9.3] Take over doxygen fixes
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