Merge branch 'main' into mleoni/make_read_meshtags_a_template_function

.github/workflows/oneapi.yml

@@ -56,7 +56,7 @@ jobs:
           conda list
 
       - name: Install Basix
-        run: pip install --no-build-isolation git+https://github.com/FEniCS/basix.git@${{ needs.fenicsx-refs.outputs.basix_ref }}
+        run: uv pip install --no-build-isolation git+https://github.com/FEniCS/basix.git@${{ needs.fenicsx-refs.outputs.basix_ref }}
 
       - name: Clone FFCx
         uses: actions/checkout@v4
@@ -82,8 +82,8 @@ jobs:
 
       - name: Install UFL and FFCx modules
         run: |
-          pip install --no-build-isolation git+https://github.com/FEniCS/ufl.git@${{ needs.fenicsx-refs.outputs.ufl_ref }}
-          pip install --no-build-isolation ffcx/
+          uv pip install --no-build-isolation git+https://github.com/FEniCS/ufl.git@${{ needs.fenicsx-refs.outputs.ufl_ref }}
+          uv pip install --no-build-isolation ffcx/
 
       - name: Build and run DOLFINx C++ unit tests (serial and MPI)
         run: |
@@ -102,7 +102,7 @@ jobs:
           ctest -R demo -R mpi_2
 
       - name: Build DOLFINx Python interface
-        run: pip -v install --check-build-dependencies --no-build-isolation --config-settings=cmake.build-type="Developer" python/
+        run: uv pip -v install --no-build-isolation --config-settings=cmake.build-type="Developer" python/
       - name: Run DOLFINx demos (Python, serial)
         run: python -m pytest -v -n=2 -m serial --durations=10 python/demo/test.py
       - name: Run DOLFINx demos (Python, MPI (np=2))

.github/workflows/windows.yml

@@ -104,7 +104,7 @@ jobs:
           (Get-Content __init__.py).Replace('# WINDOWSDLL', 'import os; os.add_dll_directory("D:/a/dolfinx/dolfinx-install/bin"); os.add_dll_directory("C:/Program Files (x86)/Intel/oneAPI/mpi/2021.12/opt/mpi/libfabric/bin")') | Set-Content __init__.py
           Get-Content __init__.py
 
-      - uses: mpi4py/[email protected].7
+      - uses: mpi4py/[email protected].8
         with:
           mpi: "intelmpi"
 

ChangeLog.rst

@@ -28,7 +28,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Remove ``Mesh::size``. Use ``Mesh::num_entities`` instead.
 - Improved mesh topology computation performance.
 - Remove excessive calls to MPI init. It may now be necessary in some
-  cases to explicitly intialise MPI.
+  cases to explicitly initialise MPI.
 - Improvements to sparsity pattern computation.
 - Addition of some interfaces using ``Eigen::Map/ref`` in addition to
   ``dolfin::Array(View)``.  ``dolfin::Array(View)``interfaces will be
@@ -146,7 +146,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Require polynomial degree or finite element for Expressions in the
   Python interface (fixes Issue #355,
   https://bitbucket.org/fenics-project/dolfin/issues/355)
-- Switch to Google Test framwork for C++ unit tests
+- Switch to Google Test framework for C++ unit tests
 - Fix bug when reading domain data from mesh file for a ghosted mesh
 - Add interface for manipulating mesh geometry using (higher-order) FE
   functions: free functions set_coordinates, get_coordinates,
@@ -223,7 +223,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
   #443)
 - Add quadrature rules for multimesh/cut-cell integration up to order
   6
-- Implement MPI reductions and XML ouput of Table class
+- Implement MPI reductions and XML output of Table class
 - list_timings() is now collective and returns MPI average across
   processes
 - Add dump_timings_to_xml()
@@ -324,7 +324,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
   module
 - Add function Form::set_some_coefficients()
 - Remove Boost.MPI dependency
-- Change GenericMatrix::compresss to return a new matrix (7be3a29)
+- Change GenericMatrix::compress to return a new matrix (7be3a29)
 - Add function GenericTensor::empty()
 - Deprecate resizing of linear algebra via the GenericFoo interfaces
   (fixes #213)
@@ -387,7 +387,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Fixes bug where child/parent hierarchy in Python were destroyed
 - Add utility script dolfin-get-demos
 - MeshFunctions in python now support iterable protocol
-- Add timed VTK output for Mesh and MeshFunction in addtion to
+- Add timed VTK output for Mesh and MeshFunction in addition to
   Functions
 - Expose ufc::dofmap::tabulate_entity_dofs to GenericDofMap interface
 - Expose ufc::dofmap::num_entity_dofs to GenericDofMap interface
@@ -477,7 +477,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Add sparray method in the Python interface of GenericMatrix,
   requires scipy.sparse
 - Make methods that return a view of contiguous c-arrays, via a NumPy
-  array, keep a reference from the object so it wont get out of scope
+  array, keep a reference from the object so it won't get out of scope
 - Add parameter: "use_petsc_signal_handler", which enables/disable
   PETSc system signals
 - Avoid unnecessary resize of result vector for A*b
@@ -684,7 +684,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Thread-safe fixed in Function class
 - Make GenericFunction::eval thread-safe (Data class removed)
 - Optimize and speedup topology computation (mesh.init())
-- Add function Mesh::clean() for cleaning out auxilliary topology data
+- Add function Mesh::clean() for cleaning out auxiliary topology data
 - Improve speed and accuracy of timers
 - Fix bug in 3D uniform mesh refinement
 - Add built-in meshes UnitTriangle and UnitTetrahedron
@@ -761,7 +761,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
   refinement
 - Add functionality for smoothing the boundary of a mesh
 - Speedup assembly over exterior facets by not using BoundaryMesh
-- Mesh refinement improvements, remove unecessary copying in Python
+- Mesh refinement improvements, remove unnecessary copying in Python
   interface
 - Clean PETSc and Epetra Krylov solvers
 - Add separate preconditioner classes for PETSc and Epetra solvers
@@ -935,7 +935,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
   check range
 - Add unit tests to the memorycheck
 - Add call to clean up libxml2 parser at exit
-- Remove unecessary arguments in DofMap member functions
+- Remove unnecessary arguments in DofMap member functions
 - Remove reference constructors from DofMap, FiniteElement and
   FunctionSpace
 - Use a shared_ptr to store the mesh in DofMap objects
@@ -1215,7 +1215,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Disable PETSc by default, use --enable-petsc to enable
 - Modify ODE solver interface for u0() and f()
 - Add class ConvectionMatrix
-- Readd classes LoadVector, MassMatrix, StiffnessMatrix
+- Read classes LoadVector, MassMatrix, StiffnessMatrix
 - Add matrix factory for simple creation of standard finite element
   matrices
 - Collect static solvers in LU and GMRES
@@ -1500,7 +1500,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Update PETSc wrappers NewVector, NewMatrix, and NewGMRES
 - Fix initialization of PETSc
 - Add mono-adaptive cG(q) and dG(q) solvers (experimental)
-- Implementation of new assebly: NewFEM, using output from FFC
+- Implementation of new assembly: NewFEM, using output from FFC
 - Add access to mesh for nodes, cells, faces and edges
 - Add Tecplot I/O interface; contributed by Garth N. Wells
 
@@ -1623,7 +1623,7 @@ solver <https://bitbucket.org/fenics-project/dolfin/>`_.
 - Optimize Lagrange polynomials
 - Optimize sparsity: use stl containers
 - Optimize choice of discrete residual for multi-adaptive solver
-- Don't save solution in benchmark proble
+- Don't save solution in benchmark problem
 - Improve computation of divergence factor for underdamped systems
 - Don't check residual on first slab for fixed time step
 - Decrease largest (default) time step to 0.1

README.md

@@ -12,6 +12,12 @@ DOLFINx is the computational environment of
 Solving Environment in C++ and Python. DOLFINx is a new version of
 DOLFIN and is actively developed.
 
+For questions about using DOLFINx, visit the [FEniCS
+Discourse](https://fenicsproject.discourse.group/) page or use the
+[FEniCS Slack channel](https://fenicsproject.slack.com/) (use
+[this](https://join.slack.com/t/fenicsproject/shared_invite/zt-1lraknsp1-6_3Js5kueDIyWgF192d3nA)
+link to sign up to the Slack channel).
+
 ## Documentation
 
 Documentation can be viewed at <https://docs.fenicsproject.org>.
@@ -191,19 +197,3 @@ Lesser General Public License for more details.
 You should have received a copy of the GNU Lesser General Public
 License along with DOLFINx. If not, see
 <https://www.gnu.org/licenses/>.
-
-## Contact
-
-For questions about using DOLFINx, visit the FEniCS Discourse page:
-
-<https://fenicsproject.discourse.group/>
-
-or use the FEniCS Slack channel:
-
-<https://fenicsproject.slack.com/>
-
-(use <https://join.slack.com/t/fenicsproject/shared_invite/zt-1lraknsp1-6_3Js5kueDIyWgF192d3nA> to sign up)
-
-For bug reports visit:
-
-<https://github.com/FEniCS/dolfinx>

cpp/CMakeLists.txt

@@ -382,7 +382,7 @@ if(NOT DOLFINX_UFCX_PYTHON)
   # Check in CONFIG mode, i.e. look for installed ufcxConfig.cmake
   find_package(ufcx 0.10 REQUIRED CONFIG)
 else()
-  # Check in MODULE mode (using FindUFCX.cmake) using Python intepreter.
+  # Check in MODULE mode (using FindUFCX.cmake) using Python interpreter.
   find_package(
     Python3
     COMPONENTS Interpreter

cpp/doc/Doxyfile

@@ -86,7 +86,7 @@ CREATE_SUBDIRS         = YES
 # level increment doubles the number of directories, resulting in 4096
 # directories at level 8 which is the default and also the maximum value. The
 # sub-directories are organized in 2 levels, the first level always has a fixed
-# numer of 16 directories.
+# number of 16 directories.
 # Minimum value: 0, maximum value: 8, default value: 8.
 # This tag requires that the tag CREATE_SUBDIRS is set to YES.
 
@@ -1007,7 +1007,7 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-# EXCLUDE                = 
+# EXCLUDE                =
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -2268,7 +2268,7 @@ PERLMOD_MAKEVAR_PREFIX =
 # C-preprocessor directives found in the sources and include files.
 # The default value is: YES.
 
-ENABLE_PREPROCESSING   = NO
+ENABLE_PREPROCESSING   = YES
 
 # If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
 # in the source code. If set to NO, only conditional compilation will be
@@ -2285,7 +2285,7 @@ MACRO_EXPANSION        = YES
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-EXPAND_ONLY_PREDEF     = YES
+EXPAND_ONLY_PREDEF     = NO
 
 # If the SEARCH_INCLUDES tag is set to YES, the include files in the
 # INCLUDE_PATH will be searched if a #include is found.

cpp/doc/source/jupytext_process.py

@@ -54,7 +54,7 @@ def process():
             with open(myst_file, "w") as fw:
                 fw.write(cpp_myst_text)
 
-            # There is a posibility to use jupyter-notebooks with C++/C kernels
+            # There is a possibility to use jupyter-notebooks with C++/C kernels
             # ipynb_file = (demo_doc_dir / fname.name).with_suffix(".ipynb")
             # jupytext.write(cpp_demo, ipynb_file, fmt="ipynb")
 

cpp/dolfinx/common/CMakeLists.txt

@@ -12,7 +12,6 @@ set(HEADERS_common
     ${CMAKE_CURRENT_SOURCE_DIR}/Table.h
     ${CMAKE_CURRENT_SOURCE_DIR}/Timer.h
     ${CMAKE_CURRENT_SOURCE_DIR}/TimeLogger.h
-    ${CMAKE_CURRENT_SOURCE_DIR}/TimeLogManager.h
     ${CMAKE_CURRENT_SOURCE_DIR}/timing.h
     ${CMAKE_CURRENT_SOURCE_DIR}/utils.h
     PARENT_SCOPE
@@ -26,6 +25,5 @@ target_sources(
           ${CMAKE_CURRENT_SOURCE_DIR}/MPI.cpp
           ${CMAKE_CURRENT_SOURCE_DIR}/Table.cpp
           ${CMAKE_CURRENT_SOURCE_DIR}/TimeLogger.cpp
-          ${CMAKE_CURRENT_SOURCE_DIR}/TimeLogManager.cpp
           ${CMAKE_CURRENT_SOURCE_DIR}/timing.cpp
 )

cpp/dolfinx/common/IndexMap.cpp

@@ -416,7 +416,7 @@ compute_submap_indices(const IndexMap& imap,
   // If required, preserve the order of the ghost indices
   if (order == IndexMapOrder::preserve)
   {
-    // Build (old postion, new position) list for ghosts and sort
+    // Build (old position, new position) list for ghosts and sort
     std::vector<std::pair<std::int32_t, std::int32_t>> pos;
     pos.reserve(submap_ghost.size());
     for (std::int32_t idx : submap_ghost)

cpp/dolfinx/common/MPI.h

@@ -1,4 +1,4 @@
-// Copyright (C) 2007-2023 Magnus Vikstrøm and Garth N. Wells
+// Copyright (C) 2007-2023 Magnus Vikstrøm, Garth N. Wells and Paul T. Kühner
 //
 // This file is part of DOLFINx (https://www.fenicsproject.org)
 //
@@ -271,39 +271,42 @@ struct dependent_false : std::false_type
 };
 
 /// MPI Type
+
+/// @brief Type trait for MPI type conversions.
 template <typename T>
-constexpr MPI_Datatype mpi_type()
-{
-  if constexpr (std::is_same_v<T, float>)
-    return MPI_FLOAT;
-  else if constexpr (std::is_same_v<T, double>)
-    return MPI_DOUBLE;
-  else if constexpr (std::is_same_v<T, std::complex<double>>)
-    return MPI_C_DOUBLE_COMPLEX;
-  else if constexpr (std::is_same_v<T, std::complex<float>>)
-    return MPI_C_FLOAT_COMPLEX;
-  else if constexpr (std::is_same_v<T, short int>)
-    return MPI_SHORT;
-  else if constexpr (std::is_same_v<T, int>)
-    return MPI_INT;
-  else if constexpr (std::is_same_v<T, unsigned int>)
-    return MPI_UNSIGNED;
-  else if constexpr (std::is_same_v<T, long int>)
-    return MPI_LONG;
-  else if constexpr (std::is_same_v<T, unsigned long>)
-    return MPI_UNSIGNED_LONG;
-  else if constexpr (std::is_same_v<T, long long>)
-    return MPI_LONG_LONG;
-  else if constexpr (std::is_same_v<T, unsigned long long>)
-    return MPI_UNSIGNED_LONG_LONG;
-  else if constexpr (std::is_same_v<T, bool>)
-    return MPI_C_BOOL;
-  else if constexpr (std::is_same_v<T, std::int8_t>)
-    return MPI_INT8_T;
-  else
-    // Issue compile time error
-    static_assert(!std::is_same_v<T, T>);
-}
+struct mpi_type_mapping;
+
+/// @brief Retrieves the MPI data type associated to the provided type.
+/// @tparam T cpp type to map
+template <typename T>
+MPI_Datatype mpi_t = mpi_type_mapping<T>::type;
+
+/// @brief Registers for cpp_t the corresponding mpi_t which can then be
+/// retrieved with mpi_t<cpp_t> from here on.
+#define MAP_TO_MPI_TYPE(cpp_t, mpi_t)                                          \
+  template <>                                                                  \
+  struct mpi_type_mapping<cpp_t>                                               \
+  {                                                                            \
+    static inline MPI_Datatype type = mpi_t;                                   \
+  };
+
+/// @defgroup MPI type mappings
+/// @{
+/// @cond
+MAP_TO_MPI_TYPE(float, MPI_FLOAT)
+MAP_TO_MPI_TYPE(double, MPI_DOUBLE)
+MAP_TO_MPI_TYPE(std::complex<float>, MPI_C_FLOAT_COMPLEX)
+MAP_TO_MPI_TYPE(std::complex<double>, MPI_C_DOUBLE_COMPLEX)
+MAP_TO_MPI_TYPE(std::int8_t, MPI_INT8_T)
+MAP_TO_MPI_TYPE(std::int16_t, MPI_INT16_T)
+MAP_TO_MPI_TYPE(std::int32_t, MPI_INT32_T)
+MAP_TO_MPI_TYPE(std::int64_t, MPI_INT64_T)
+MAP_TO_MPI_TYPE(std::uint8_t, MPI_UINT8_T)
+MAP_TO_MPI_TYPE(std::uint16_t, MPI_UINT16_T)
+MAP_TO_MPI_TYPE(std::uint32_t, MPI_UINT32_T)
+MAP_TO_MPI_TYPE(std::uint64_t, MPI_UINT64_T)
+/// @endcond
+/// @}
 
 //---------------------------------------------------------------------------
 template <typename U>
@@ -434,7 +437,7 @@ distribute_to_postoffice(MPI_Comm comm, const U& x,
 
   // Send/receive data (x)
   MPI_Datatype compound_type;
-  MPI_Type_contiguous(shape[1], dolfinx::MPI::mpi_type<T>(), &compound_type);
+  MPI_Type_contiguous(shape[1], dolfinx::MPI::mpi_t<T>, &compound_type);
   MPI_Type_commit(&compound_type);
   std::vector<T> recv_buffer_data(shape[1] * recv_disp.back());
   err = MPI_Neighbor_alltoallv(
@@ -616,7 +619,7 @@ distribute_from_postoffice(MPI_Comm comm, std::span<const std::int64_t> indices,
   dolfinx::MPI::check_error(comm, err);
 
   MPI_Datatype compound_type0;
-  MPI_Type_contiguous(shape[1], dolfinx::MPI::mpi_type<T>(), &compound_type0);
+  MPI_Type_contiguous(shape[1], dolfinx::MPI::mpi_t<T>, &compound_type0);
   MPI_Type_commit(&compound_type0);
 
   std::vector<T> recv_buffer_data(shape[1] * send_disp.back());
@@ -691,8 +694,8 @@ distribute_data(MPI_Comm comm0, std::span<const std::int64_t> indices,
   if (comm1 != MPI_COMM_NULL)
   {
     rank_offset = 0;
-    err = MPI_Exscan(&shape0_local, &rank_offset, 1, MPI_INT64_T, MPI_SUM,
-                     comm1);
+    err = MPI_Exscan(&shape0_local, &rank_offset, 1,
+                     dolfinx::MPI::mpi_t<std::int64_t>, MPI_SUM, comm1);
     dolfinx::MPI::check_error(comm1, err);
   }
   else