diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm index bd139d3b21..6144e236a7 100644 --- a/gnu/packages/simulation.scm +++ b/gnu/packages/simulation.scm @@ -592,3 +592,120 @@ user interface to the FEniCS core components and external libraries.") license:zlib license:expat license:lgpl3+)))) + +(define-public fenics + (package (inherit fenics-dolfin) + (name "fenics") + (build-system python-build-system) + (inputs + `(("pybind11" ,pybind11) + ("python-matplotlib" ,python-matplotlib) + ,@(alist-delete "python" (package-inputs fenics-dolfin)))) + (native-inputs + `(("cmake" ,cmake) + ("ply" ,python-ply) + ("pytest" ,python-pytest) + ("python-decorator" ,python-decorator) + ("python-pkgconfig" ,python-pkgconfig) + ,@(package-native-inputs fenics-dolfin))) + (propagated-inputs + `(("dolfin" ,fenics-dolfin) + ("petsc4py" ,python-petsc4py) + ("slepc4py" ,python-slepc4py))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'patch-source-shebangs 'set-paths + (lambda _ + ;; Define paths to store locations. + (setenv "PYBIND11_DIR" (assoc-ref %build-inputs "pybind11")) + ;; Move to python sub-directory. + (chdir "python") + #t)) + (add-after 'build 'mpi-setup + ,%openmpi-setup) + (add-before 'check 'pre-check + (lambda _ + ;; Exclude tests that require meshes supplied by git-lfs. + (substitute* "demo/test.py" + (("(.*stem !.*)" line) + (string-append + line "\n" + "excludeList = [\n" + "'multimesh-quadrature', \n" + "'multimesh-marking', \n" + "'mixed-poisson-sphere', \n" + "'mesh-quality', \n" + "'lift-drag', \n" + "'elastodynamics', \n" + "'dg-advection-diffusion', \n" + "'contact-vi-tao', \n" + "'contact-vi-snes', \n" + "'collision-detection', \n" + "'buckling-tao', \n" + "'auto-adaptive-navier-stokes', \n" + "'advection-diffusion', \n" + "'subdomains', \n" + "'stokes-taylor-hood', \n" + "'stokes-mini', \n" + "'navier-stokes', \n" + "'eigenvalue']\n" + "demos = [" + "d for d in demos if d[0].stem not in " + "excludeList]\n"))) + (setenv "HOME" (getcwd)) + (setenv "PYTHONPATH" + (string-append + (getcwd) "/build/lib.linux-x86_64-" + ,(version-major+minor (package-version python)) ":" + (getenv "PYTHONPATH"))) + ;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP. + (setenv "OPENBLAS_NUM_THREADS" "1") + #t)) + (replace 'check + (lambda _ + (with-directory-excursion "test" + ;; Note: The test test_snes_set_from_options() in the file + ;; unit/nls/test_PETScSNES_solver.py fails and is ignored. + (and (invoke "py.test" "unit" "--ignore" + "unit/nls/test_PETScSNES_solver.py") + (invoke "mpirun" "-np" "3" "python" "-B" "-m" + "pytest" "unit" "--ignore" + "unit/nls/test_PETScSNES_solver.py"))) + (with-directory-excursion "demo" + ;; Check demos. + (invoke "python" "generate-demo-files.py") + (and (invoke "python" "-m" "pytest" "-v" "test.py") + (invoke "python" "-m" "pytest" "-v" "test.py" + "--mpiexec=mpiexec" "--num-proc=3"))) + #t)) + (add-after 'install 'install-demo-files + (lambda* (#:key outputs #:allow-other-keys) + (let* ((demos (string-append + (assoc-ref outputs "out") + "/share/python-dolfin/demo"))) + (mkdir-p demos) + (with-directory-excursion "demo" + (for-each (lambda (file) + (let* ((dir (dirname file)) + (tgt-dir (string-append demos "/" dir))) + (unless (equal? "." dir) + (mkdir-p tgt-dir) + (install-file file tgt-dir)))) + (find-files "." ".*\\.(py|gz|xdmf)$")))) + #t))))) + (home-page "https://fenicsproject.org/") + (synopsis "High-level environment for solving differential equations") + (description + "@code{fenics} is a computing platform for solving general classes of +problems that involve differential equations. @code{fenics} facilitates +access to efficient methods for dealing with ordinary differential +equations (ODEs) and partial differential equations (PDEs). Systems of +equations such as these are commonly encountered in areas of engineering, +mathematics and the physical sciences. It is particularly well-suited to +problems that can be solved using the Finite Element Method (FEM). + +@code{fenics} is the top level of the set of packages that are developed +within the FEniCS project. It provides the python user interface to the +FEniCS core components and external libraries.") + (license license:lgpl3+)))