Switch to nanobind

.circleci/config.yml

@@ -51,7 +51,7 @@ regression-tests-cpp-mpi: &regression-tests-cpp-mpi
     ctest --verbose -R demo -R mpi_3
 
 build-python-interface: &build-python-interface
-  name: Build Python/pybind11 interface
+  name: Build Python/nanobind interface
   command: |
     export CMAKE_BUILD_PARALLEL_LEVEL=2
     cd python

.github/workflows/ccpp.yml

@@ -145,7 +145,8 @@ jobs:
 
       - name: Build Python interface
         run: |
-          python3 -m pip -v install --check-build-dependencies --no-build-isolation python/
+          python3 -m pip install -r python/build-requirements.txt # TO REMOVE
+          python3 -m pip -v install --check-build-dependencies --no-build-isolation --config-settings=cmake.build-type="Debug" python/
       - name: Build Python interface documentation
         run: |
           cd python/doc

.github/workflows/oneapi.yml

@@ -87,6 +87,7 @@ jobs:
       - name: Build DOLFINx Python interface
         run: |
           . /opt/intel/oneapi/setvars.sh
+          pip install -r python/build-requirements.txt # TO REMOVE
           pip -v install --check-build-dependencies --no-build-isolation python/
       - name: Set default DOLFINx JIT options
         run: |
@@ -99,14 +100,12 @@ jobs:
       - name: Run DOLFINx demos (Python, MPI (np=2))
         run: |
           . /opt/intel/oneapi/setvars.sh
-          pytest -v -m mpi --num-proc=2 python/demo/test.py
+          pytest -m mpi --num-proc=2 python/demo/test.py
       - name: Run DOLFINx Python unit tests (serial)
         run: |
           . /opt/intel/oneapi/setvars.sh
-          cd python/test
-          pytest -n=auto --durations=50 unit/
+          pytest -vs -n=auto --durations=50 python/test/unit/fem
       - name: Run DOLFINx Python unit tests (MPI, np=2)
         run: |
           . /opt/intel/oneapi/setvars.sh
-          cd python/test
-          mpiexec -n 2 pytest -vs unit/
+          mpiexec -n 2 pytest -vs python/test/unit/fem

.github/workflows/redhat.yml

@@ -64,6 +64,7 @@ jobs:
 
       - name: Build Python interface (editable install)
         run: |
+          python3 -m pip install -r python/build-requirements.txt # TO REMOVE
           python3 -m pip -v install --check-build-dependencies --no-build-isolation --config-settings=cmake.build-type=Debug --config-settings=build-dir="build" -e python/
 
       - name: Set default DOLFINx JIT options

cpp/dolfinx/fem/DofMap.h

@@ -111,7 +111,7 @@ class DofMap
   DofMap(DofMap&& dofmap) = default;
 
   // Destructor
-  virtual ~DofMap() = default;
+  ~DofMap() = default;
 
   // Copy assignment
   DofMap& operator=(const DofMap& dofmap) = delete;

cpp/dolfinx/fem/FiniteElement.h

@@ -47,7 +47,7 @@ class FiniteElement
   FiniteElement(FiniteElement&& element) = default;
 
   /// Destructor
-  virtual ~FiniteElement() = default;
+  ~FiniteElement() = default;
 
   /// Copy assignment
   FiniteElement& operator=(const FiniteElement& element) = delete;

cpp/dolfinx/geometry/utils.h

@@ -650,15 +650,16 @@ graph::AdjacencyList<std::int32_t> compute_colliding_cells(
 /// @param[in] mesh The mesh
 /// @param[in] points Points to check for collision (`shape=(num_points,
 /// 3)`). Storage is row-major.
-/// @return Quadratuplet (src_owner, dest_owner, dest_points,
-/// dest_cells), where src_owner is a list of ranks corresponding to the
-/// input points. dest_owner is a list of ranks corresponding to
-/// dest_points, the points that this process owns. dest_cells contains
-/// the corresponding cell for each entry in dest_points.
+/// @return Tuple `(src_owner, dest_owner, dest_points, dest_cells)`,
+/// where src_owner is a list of ranks corresponding to the input
+/// points. dest_owner is a list of ranks corresponding to dest_points,
+/// the points that this process owns. dest_cells contains the
+/// corresponding cell for each entry in dest_points.
 ///
-/// @note dest_owner is sorted
+/// @note `dest_owner` is sorted
 /// @note Returns -1 if no colliding process is found
-/// @note dest_points is flattened row-major, shape (dest_owner.size(), 3)
+/// @note dest_points is flattened row-major, shape `(dest_owner.size(),
+/// 3)`
 /// @note Only looks through cells owned by the process
 template <std::floating_point T>
 std::tuple<std::vector<std::int32_t>, std::vector<std::int32_t>, std::vector<T>,
@@ -700,8 +701,8 @@ determine_point_ownership(const mesh::Mesh<T>& mesh, std::span<const T> points)
       comm, in_ranks.size(), in_ranks.data(), MPI_UNWEIGHTED, out_ranks.size(),
       out_ranks.data(), MPI_UNWEIGHTED, MPI_INFO_NULL, false, &forward_comm);
 
-  // Compute map from global mpi rank to neighbor rank, "collisions" uses
-  // global rank
+  // Compute map from global mpi rank to neighbor rank, "collisions"
+  // uses global rank
   std::map<std::int32_t, std::int32_t> rank_to_neighbor;
   for (std::size_t i = 0; i < out_ranks.size(); i++)
     rank_to_neighbor[out_ranks[i]] = i;
@@ -755,8 +756,8 @@ determine_point_ownership(const mesh::Mesh<T>& mesh, std::span<const T> points)
       dolfinx::MPI::mpi_type<T>(), received_points.data(), recv_sizes.data(),
       recv_offsets.data(), dolfinx::MPI::mpi_type<T>(), forward_comm);
 
-  // Each process checks which local cell is closest and computes the squared
-  // distance to the cell
+  // Each process checks which local cell is closest and computes the
+  // squared distance to the cell
   const int rank = dolfinx::MPI::rank(comm);
   const std::vector<std::int32_t> closest_cells = compute_closest_entity(
       bb, midpoint_tree, mesh,
@@ -804,8 +805,8 @@ determine_point_ownership(const mesh::Mesh<T>& mesh, std::span<const T> points)
     for (std::int32_t j = recv_offsets[i]; j < recv_offsets[i + 1]; j++)
     {
       const std::int32_t pos = unpack_map[j];
-      // If point has not been found yet distance is negative
-      // If new received distance smaller than current distance choose owner
+      // If point has not been found yet distance is negative. If new
+      // received distance smaller than current distance choose owner.
       if (auto d = closest_distance[pos]; d < 0 or d > recv_distances[j])
       {
         point_owners[pos] = out_ranks[i];

cpp/dolfinx/la/MatrixCSR.h

@@ -20,7 +20,7 @@
 namespace dolfinx::la
 {
 /// @brief Modes for representing block structured matrices
-enum class BlockMode : int
+enum class BlockMode
 {
   compact = 0, /// Each entry in the sparsity pattern of the matrix refers to a
                /// block of data of size (bs[0], bs[1]).

cpp/dolfinx/la/petsc.cpp

@@ -131,8 +131,8 @@ std::vector<IS> la::petsc::create_index_sets(
   std::int64_t offset = 0;
   for (auto& map : maps)
   {
-    const int bs = map.second;
-    const std::int32_t size
+    int bs = map.second;
+    std::int32_t size
         = map.first.get().size_local() + map.first.get().num_ghosts();
     IS _is;
     ISCreateStride(PETSC_COMM_SELF, bs * size, offset, 1, &_is);

docker/Dockerfile.oneapi

@@ -13,7 +13,7 @@ ARG HDF5_PATCH=2
 ARG HDF5_FIX=
 ARG PETSC_VERSION=3.20.0
 ARG SLEPC_VERSION=3.20.0
-ARG PYBIND11_VERSION=2.11.1
+ARG NANOBIND_VERSION=1.8.0
 ARG KAHIP_VERSION=3.15
 
 WORKDIR /tmp
@@ -58,7 +58,7 @@ ENV CC=icx \
 
 # Install Python packages (via pip)
 RUN . /opt/intel/oneapi/setvars.sh && \
-    pip install --no-cache-dir cppimport matplotlib mpi4py pybind11==${PYBIND11_VERSION} pytest pytest-xdist scikit-build-core[pyproject]
+    pip install --no-cache-dir cppimport matplotlib mpi4py nanobind==${NANOBIND_VERSION} pytest pytest-xdist scikit-build-core[pyproject]
 
 # Install KaHIP
 RUN . /opt/intel/oneapi/setvars.sh && \

docker/Dockerfile.redhat

@@ -63,7 +63,7 @@ RUN curl -L -O https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_SERIES
 
 # First set of dependencies for building and running Python DOLFINx
 # Second set of dependencies for running DOLFINx tests
-RUN python3 -m pip install --no-cache-dir cffi numba mpi4py pybind11 scikit-build-core[pyproject] wheel && \
+RUN python3 -m pip install --no-cache-dir cffi numba mpi4py nanobind scikit-build-core[pyproject] wheel && \
     python3 -m pip install --no-cache-dir cppimport pytest pytest-xdist scipy matplotlib
 
 # Build PETSc

docker/Dockerfile.test-env

@@ -20,7 +20,7 @@ ARG HDF5_PATCH=2
 ARG HDF5_FIX=
 ARG KAHIP_VERSION=3.15
 ARG NUMPY_VERSION=1.23.2
-ARG PYBIND11_VERSION=2.11.1
+ARG NANOBIND_VERSION=1.8.0
 ARG PETSC_VERSION=3.20.0
 ARG SLEPC_VERSION=3.20.0
 
@@ -39,7 +39,7 @@ ARG GMSH_VERSION
 ARG HDF5_SERIES
 ARG HDF5_PATCH
 ARG HDF5_FIX
-ARG PYBIND11_VERSION
+ARG NANOBIND_VERSION
 ARG PETSC_VERSION
 ARG SLEPC_VERSION
 ARG ADIOS2_VERSION
@@ -153,8 +153,8 @@ RUN if [ "$MPI" = "mpich" ]; then \
 # - Second set of packages are recommended and/or required to build
 #   documentation or run tests.
 RUN pip3 install --no-cache-dir --upgrade setuptools pip && \
-    pip3 install --no-cache-dir cffi mpi4py numba numpy==${NUMPY_VERSION} scikit-build-core[pyproject] && \
-    pip3 install --no-cache-dir breathe clang-format cppimport cmakelang flake8 isort jupytext matplotlib mypy myst-parser pybind11==${PYBIND11_VERSION} pytest pytest-xdist scipy sphinx==5.0.2 sphinx_rtd_theme types-setuptools
+    pip3 install  -no-cache-dir cffi mpi4py numba numpy==${NUMPY_VERSION} scikit-build-core[pyproject] && \
+    pip3 install --no-cache-dir breathe clang-format cppimport cmakelang flake8 isort jupytext matplotlib mypy myst-parser nanobind==${NANOBIND_VERSION} pytest pytest-xdist scipy sphinx==5.0.2 sphinx_rtd_theme types-setuptools
 
 # Install KaHIP
 RUN wget -nc --quiet https://github.com/kahip/kahip/archive/v${KAHIP_VERSION}.tar.gz && \

python/CMakeLists.txt

@@ -1,43 +1,26 @@
 cmake_minimum_required(VERSION 3.18)
 
-project(fenics-dolfinx)
+project(dolfinx_nanobind)
 
-# Set C++ standard before finding pybind11
+# Set C++ standard
 set(CMAKE_CXX_STANDARD 20)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 
-find_package(
-  Python3
-  COMPONENTS Interpreter Development.Module
-  REQUIRED
-)
+# set(CMAKE_BUILD_TYPE Debug)
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE)
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+endif()
 
-# Help cmake find pybind11 installed as Python package
-execute_process(
-  COMMAND "${Python3_EXECUTABLE}" "-c"
-  "import pybind11; print(pybind11.get_cmake_dir())"
-  OUTPUT_VARIABLE PYBIND11_CMAKE_DIR
-  RESULT_VARIABLE PYBIND11_COMMAND_RESULT
-  ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE
-)
+find_package(Python COMPONENTS Interpreter Development REQUIRED)
 
-if(NOT PYBIND11_COMMAND_RESULT)
-  message(STATUS "Found pybind11 cmake directory at ${PYBIND11_CMAKE_DIR}")
-endif() 
-
-find_package(
-  pybind11
-  2.9.1
-  REQUIRED
-  CONFIG
-  HINTS
-  ${PYBIND11_CMAKE_DIR}
-  ${PYBIND11_DIR}
-  ${PYBIND11_ROOT}
-  $ENV{PYBIND11_DIR}
-  $ENV{PYBIND11_ROOT}
-)
+# Detect the installed nanobind package and import it into CMake
+execute_process(
+  COMMAND "${Python_EXECUTABLE}" -m nanobind --cmake_dir
+  OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE NB_DIR)
+list(APPEND CMAKE_PREFIX_PATH "${NB_DIR}")
+find_package(nanobind CONFIG REQUIRED)
 
 execute_process(
   COMMAND
@@ -46,16 +29,16 @@ execute_process(
   RESULT_VARIABLE BASIX_PY_COMMAND_RESULT
   ERROR_VARIABLE BASIX_ERROR_OUT OUTPUT_STRIP_TRAILING_WHITESPACE
 )
-
 find_package(Basix REQUIRED CONFIG HINTS ${BASIX_PY_DIR})
-
 find_package(DOLFINX REQUIRED CONFIG)
 
-# Create the binding library pybind11 handles its own calls to
+# Create the binding library nanobind handles its own calls to
 # target_link_libraries
-pybind11_add_module(
+nanobind_add_module(
   cpp
   MODULE
+
+  # NB_SHARED
   dolfinx/wrappers/dolfinx.cpp
   dolfinx/wrappers/assemble.cpp
   dolfinx/wrappers/common.cpp
@@ -71,26 +54,19 @@ pybind11_add_module(
 )
 
 # Add strict compiler flags
-include(CheckCXXCompilerFlag)
-check_cxx_compiler_flag("-Wall -Werror -pedantic" HAVE_PEDANTIC)
+# include(CheckCXXCompilerFlag)
+# check_cxx_compiler_flag("-Wall -Werror -pedantic" HAVE_PEDANTIC)
 
-if(HAVE_PEDANTIC)
-  target_compile_options(cpp PRIVATE -Wall;-Werror;-pedantic)
-endif()
-
-# In Debug mode override pybind11 symbols visibility Symbols must be visible to
-# backtrace_symbols() to produce nice logs
-if(CMAKE_BUILD_TYPE STREQUAL "Debug")
-  target_compile_options(cpp PRIVATE "-fvisibility=default")
-endif()
+# if(HAVE_PEDANTIC)
+#   # target_compile_options(cpp PRIVATE -Wall;-Werror;-pedantic)
+# endif()
 
-# Add DOLFINx libraries.
+# Add DOLFINx libraries
 target_link_libraries(cpp PRIVATE dolfinx)
 
 # Check for petsc4py
 execute_process(
-  COMMAND ${Python3_EXECUTABLE} -c
-  "import petsc4py; print(petsc4py.get_include())"
+  COMMAND ${Python_EXECUTABLE} -c "import petsc4py; print(petsc4py.get_include())"
   OUTPUT_VARIABLE PETSC4PY_INCLUDE_DIR
   RESULT_VARIABLE PETSC4PY_COMMAND_RESULT
   ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE
@@ -105,8 +81,7 @@ endif()
 
 # Check for mpi4py
 execute_process(
-  COMMAND "${Python3_EXECUTABLE}" "-c"
-  "import mpi4py; print(mpi4py.get_include())"
+  COMMAND "${Python_EXECUTABLE}" -c "import mpi4py; print(mpi4py.get_include())"
   OUTPUT_VARIABLE MPI4PY_INCLUDE_DIR
   RESULT_VARIABLE MPI4PY_COMMAND_RESULT
   ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE

python/build-requirements.txt

@@ -1,4 +1,4 @@
-pybind11>=2.9.1
+nanobind>=1.8.0
 scikit-build-core[pyproject]
 petsc4py
 mpi4py

python/demo/demo_axis/demo_axis.py

@@ -607,15 +607,15 @@ def create_eps_mu(pml, rho, eps_bkg, mu_bkg):
     print()
     print(f"The analytical absorption efficiency is {q_abs_analyt}")
     print(f"The numerical absorption efficiency is {q_abs_fenics}")
-    print(f"The error is {err_abs*100}%")
+    print(f"The error is {err_abs * 100}%")
     print()
     print(f"The analytical scattering efficiency is {q_sca_analyt}")
     print(f"The numerical scattering efficiency is {q_sca_fenics}")
-    print(f"The error is {err_sca*100}%")
+    print(f"The error is {err_sca * 100}%")
     print()
     print(f"The analytical extinction efficiency is {q_ext_analyt}")
     print(f"The numerical extinction efficiency is {q_ext_fenics}")
-    print(f"The error is {err_ext*100}%")
+    print(f"The error is {err_ext * 100}%")
 
 # Check whether the geometrical and optical parameters are correct
 # assert radius_sph / wl0 == 0.025 / 0.4

python/demo/demo_cahn-hilliard.py

@@ -307,7 +307,7 @@
 while (t < T):
     t += dt
     r = solver.solve(u)
-    print(f"Step {int(t/dt)}: num iterations: {r[0]}")
+    print(f"Step {int(t / dt)}: num iterations: {r[0]}")
     u0.x.array[:] = u.x.array
     file.write_function(c, t)
 

python/demo/demo_pml/demo_pml.py

@@ -548,15 +548,15 @@ def create_eps_mu(pml: ufl.tensors.ListTensor,
     print()
     print(f"The analytical absorption efficiency is {q_abs_analyt}")
     print(f"The numerical absorption efficiency is {q_abs_fenics}")
-    print(f"The error is {err_abs*100}%")
+    print(f"The error is {err_abs * 100}%")
     print()
     print(f"The analytical scattering efficiency is {q_sca_analyt}")
     print(f"The numerical scattering efficiency is {q_sca_fenics}")
-    print(f"The error is {err_sca*100}%")
+    print(f"The error is {err_sca * 100}%")
     print()
     print(f"The analytical extinction efficiency is {q_ext_analyt}")
     print(f"The numerical extinction efficiency is {q_ext_fenics}")
-    print(f"The error is {err_ext*100}%")
+    print(f"The error is {err_ext * 100}%")
 # -
 
 # Check if errors are smaller than 1%

python/demo/demo_scattering_boundary_conditions/demo_scattering_boundary_conditions.py

@@ -543,12 +543,12 @@ def curl_2d(f: fem.Function):
     print()
     print(f"The analytical absorption efficiency is {q_abs_analyt}")
     print(f"The numerical absorption efficiency is {q_abs_fenics}")
-    print(f"The error is {err_abs*100}%")
+    print(f"The error is {err_abs * 100}%")
     print()
     print(f"The analytical scattering efficiency is {q_sca_analyt}")
     print(f"The numerical scattering efficiency is {q_sca_fenics}")
-    print(f"The error is {err_sca*100}%")
+    print(f"The error is {err_sca * 100}%")
     print()
     print(f"The analytical extinction efficiency is {q_ext_analyt}")
     print(f"The numerical extinction efficiency is {q_ext_fenics}")
-    print(f"The error is {err_ext*100}%")
+    print(f"The error is {err_ext * 100}%")