Index: dolfinx/python/test/unit/common/test_mpi.py =================================================================== --- dolfinx.orig/python/test/unit/common/test_mpi.py 2021-01-31 13:18:01.370436223 +0100 +++ dolfinx/python/test/unit/common/test_mpi.py 2021-01-31 13:18:01.362436243 +0100 @@ -6,15 +6,16 @@ # # SPDX-License-Identifier: LGPL-3.0-or-later -import pathlib +import os +import sys import dolfinx import mpi4py +import pytest from dolfinx import wrappers from dolfinx.jit import dolfinx_pc, mpi_jit_decorator from dolfinx_utils.test.fixtures import tempdir # noqa: F401 from mpi4py import MPI -import cppimport def test_mpi_comm_wrapper(): @@ -29,42 +30,41 @@ def test_mpi_comm_wrapper_cppimport(tempdir): # noqa: F811 """Test MPICommWrapper <-> mpi4py.MPI.Comm conversion for code compiled with cppimport""" + cppimport = pytest.importorskip("cppimport") + @mpi_jit_decorator def compile_module(): cpp_code_header = f""" -/* -<% -setup_pybind11(cfg) -cfg['compiler_args'] = ['-std=c++17'] -cfg['include_dirs'] += {dolfinx_pc["include_dirs"] - + [mpi4py.get_include()] - + [str(wrappers.get_include_path())]} -%> -*/ -""" + <% + setup_pybind11(cfg) + cfg['compiler_args'] = ['-std=c++17'] + cfg['include_dirs'] += {dolfinx_pc["include_dirs"] + + [mpi4py.get_include()] + + [str(wrappers.get_include_path())]} + %> + """ cpp_code = """ -#include -#include + #include + #include + + dolfinx_wrappers::MPICommWrapper + test_comm_passing(const dolfinx_wrappers::MPICommWrapper comm) + { + MPI_Comm c = comm.get(); + return dolfinx_wrappers::MPICommWrapper(c); + } + + PYBIND11_MODULE(test_mpi_comm_wrapper, m) + { + m.def("test_comm_passing", &test_comm_passing); + } + """ + + open(os.path.join(tempdir, "test_mpi_comm_wrapper.cpp"), "w").write(cpp_code_header + cpp_code) -dolfinx_wrappers::MPICommWrapper -test_comm_passing(const dolfinx_wrappers::MPICommWrapper comm) -{ - MPI_Comm c = comm.get(); - return dolfinx_wrappers::MPICommWrapper(c); -} - -PYBIND11_MODULE(mpi_comm_wrapper, m) -{ - m.def("test_comm_passing", &test_comm_passing); -} -""" - - path = pathlib.Path(tempdir) - open(pathlib.Path(tempdir, "mpi_comm_wrapper.cpp"), "w").write(cpp_code + cpp_code_header) - rel_path = path.relative_to(pathlib.Path(__file__).parent) - p = str(rel_path).replace("/", ".") + ".mpi_comm_wrapper" - return cppimport.imp(p) + sys.path.append(tempdir) + return cppimport.imp("test_mpi_comm_wrapper") module = compile_module(MPI.COMM_WORLD) Index: dolfinx/python/test/unit/fem/test_assemble_cppimport.py =================================================================== --- dolfinx.orig/python/test/unit/fem/test_assemble_cppimport.py 2021-01-31 13:18:01.370436223 +0100 +++ dolfinx/python/test/unit/fem/test_assemble_cppimport.py 2021-01-31 13:18:16.414401475 +0100 @@ -5,117 +5,4 @@ # SPDX-License-Identifier: LGPL-3.0-or-later """Unit tests for assembly using cppimport""" -import pathlib - -import cppimport -import dolfinx -import numpy -import petsc4py -import scipy.sparse.linalg -import ufl -from dolfinx.generation import UnitSquareMesh -from dolfinx.jit import dolfinx_pc -from dolfinx.wrappers import get_include_path as pybind_inc -from dolfinx_utils.test.fixtures import tempdir # noqa: F401 -from dolfinx_utils.test.skips import skip_in_parallel -from mpi4py import MPI - - -@skip_in_parallel -def test_eigen_assembly(tempdir): # noqa: F811 - """Compare assembly into scipy.CSR matrix with PETSc assembly""" - def compile_eigen_csr_assembler_module(): - cpp_code_header = f""" -<% -setup_pybind11(cfg) -cfg['include_dirs'] = {dolfinx_pc["include_dirs"] + [petsc4py.get_include()] + [str(pybind_inc())]} -cfg['compiler_args'] = {["-D" + dm for dm in dolfinx_pc["define_macros"]]} -cfg['compiler_args'] = ['-std=c++17'] -cfg['libraries'] = {dolfinx_pc["libraries"]} -cfg['library_dirs'] = {dolfinx_pc["library_dirs"]} -%> -""" - - cpp_code = """ -#include -#include -#include -#include -#include -#include -#include -#include -#include - -template -Eigen::SparseMatrix -assemble_csr(const dolfinx::fem::Form& a, - const std::vector>>& bcs) -{ - std::vector> triplets; - const auto mat_add - = [&triplets](std::int32_t nrow, const std::int32_t* rows, - std::int32_t ncol, const std::int32_t* cols, const T* v) - { - for (int i = 0; i < nrow; ++i) - for (int j = 0; j < ncol; ++j) - triplets.emplace_back(rows[i], cols[j], v[i * ncol + j]); - return 0; - }; - - dolfinx::fem::assemble_matrix(mat_add, a, bcs); - - auto map0 = a.function_spaces().at(0)->dofmap()->index_map; - int bs0 = a.function_spaces().at(0)->dofmap()->index_map_bs(); - auto map1 = a.function_spaces().at(1)->dofmap()->index_map; - int bs1 = a.function_spaces().at(1)->dofmap()->index_map_bs(); - Eigen::SparseMatrix mat( - bs0 * (map0->size_local() + map0->num_ghosts()), - bs1 * (map1->size_local() + map1->num_ghosts())); - mat.setFromTriplets(triplets.begin(), triplets.end()); - return mat; -} - -PYBIND11_MODULE(eigen_csr, m) -{ - m.def("assemble_matrix", &assemble_csr); -} -""" - - path = pathlib.Path(tempdir) - open(pathlib.Path(tempdir, "eigen_csr.cpp"), "w").write(cpp_code + cpp_code_header) - rel_path = path.relative_to(pathlib.Path(__file__).parent) - p = str(rel_path).replace("/", ".") + ".eigen_csr" - return cppimport.imp(p) - - def assemble_csr_matrix(a, bcs): - """Assemble bilinear form into an SciPy CSR matrix, in serial.""" - module = compile_eigen_csr_assembler_module() - _a = dolfinx.fem.assemble._create_cpp_form(a) - A = module.assemble_matrix(_a, bcs) - if _a.function_spaces[0].id == _a.function_spaces[1].id: - for bc in bcs: - if _a.function_spaces[0].contains(bc.function_space): - bc_dofs, _ = bc.dof_indices() - # See https://github.com/numpy/numpy/issues/14132 - # for why we copy bc_dofs as a work-around - dofs = bc_dofs.copy() - A[dofs, dofs] = 1.0 - return A - - mesh = UnitSquareMesh(MPI.COMM_SELF, 12, 12) - Q = dolfinx.FunctionSpace(mesh, ("Lagrange", 1)) - u = ufl.TrialFunction(Q) - v = ufl.TestFunction(Q) - a = ufl.inner(ufl.grad(u), ufl.grad(v)) * ufl.dx - - bdofsQ = dolfinx.fem.locate_dofs_geometrical(Q, lambda x: numpy.logical_or(x[0] < 1.0e-6, x[0] > 1.0 - 1.0e-6)) - u_bc = dolfinx.fem.Function(Q) - with u_bc.vector.localForm() as u_local: - u_local.set(1.0) - bc = dolfinx.fem.dirichletbc.DirichletBC(u_bc, bdofsQ) - - A1 = dolfinx.fem.assemble_matrix(a, [bc]) - A1.assemble() - A2 = assemble_csr_matrix(a, [bc]) - assert numpy.isclose(A1.norm(), scipy.sparse.linalg.norm(A2)) +print("cppimport module is not yet available, skipping test_assemble_cppimport") Index: dolfinx/python/test/unit/la/test_casters.py =================================================================== --- dolfinx.orig/python/test/unit/la/test_casters.py 2021-01-31 13:18:01.370436223 +0100 +++ dolfinx/python/test/unit/la/test_casters.py 2021-01-31 13:18:01.362436243 +0100 @@ -6,56 +6,58 @@ # # SPDX-License-Identifier: LGPL-3.0-or-later -import pathlib +import os +import sys import numpy import petsc4py +import pytest from dolfinx.jit import dolfinx_pc, mpi_jit_decorator from dolfinx.wrappers import get_include_path as pybind_inc from dolfinx_utils.test.fixtures import tempdir # noqa: F401 from mpi4py import MPI from petsc4py import PETSc -import cppimport def test_petsc_casters_cppimport(tempdir): # noqa: F811 - """Test casters of PETSc objects in codes compiled with cppimport""" + """ + Test casters of PETSc objects in codes compiled with cppimport + """ + + cppimport = pytest.importorskip("cppimport") @mpi_jit_decorator def compile_module(): cpp_code_header = f""" -/* -<% -setup_pybind11(cfg) -cfg['include_dirs'] += {dolfinx_pc["include_dirs"] + [petsc4py.get_include()] + [str(pybind_inc())]} -cfg['compiler_args'] += {["-D" + dm for dm in dolfinx_pc["define_macros"]]} -cfg['libraries'] += {dolfinx_pc["libraries"]} -cfg['library_dirs'] += {dolfinx_pc["library_dirs"]} -%> -*/ -""" + <% + setup_pybind11(cfg) + cfg['include_dirs'] += {dolfinx_pc["include_dirs"] + [petsc4py.get_include()] + [str(pybind_inc())]} + cfg['compiler_args'] += {["-D" + dm for dm in dolfinx_pc["define_macros"]]} + cfg['libraries'] += {dolfinx_pc["libraries"]} + cfg['library_dirs'] += {dolfinx_pc["library_dirs"]} + %> + """ cpp_code = """ -#include -#include -#include - -void PETSc_exp(Vec x) -{ - assert(x); - VecExp(x); -} -PYBIND11_MODULE(petsc_casters_cppimport, m) -{ - m.def("PETSc_exp", &PETSc_exp); -} -""" - - path = pathlib.Path(tempdir) - open(pathlib.Path(tempdir, "petsc_casters_cppimport.cpp"), "w").write(cpp_code + cpp_code_header) - rel_path = path.relative_to(pathlib.Path(__file__).parent) - p = str(rel_path).replace("/", ".") + ".petsc_casters_cppimport" - return cppimport.imp(p) + #include + #include + #include + + void PETSc_exp(Vec x) + { + assert(x); + VecExp(x); + } + PYBIND11_MODULE(test_petsc_casters_cppimport, m) + { + m.def("PETSc_exp", &PETSc_exp); + } + """ + + open(os.path.join(tempdir, "test_petsc_casters_cppimport.cpp"), "w").write(cpp_code_header + cpp_code) + + sys.path.append(tempdir) + return cppimport.imp("test_petsc_casters_cppimport") module = compile_module(MPI.COMM_WORLD)