gnu: Add fenics.
* gnu/packages/simulation.scm (fenics): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
This commit is contained in:
Paul Garlick
Ludovic Courtès
parent
0ace6c0b84
commit
ae0f1dd1a4
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@ -592,3 +592,120 @@ user interface to the FEniCS core components and external libraries.")
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license:zlib
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license:zlib
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license:expat
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license:expat
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license:lgpl3+))))
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license:lgpl3+))))
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(define-public fenics
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(package (inherit fenics-dolfin)
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(name "fenics")
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(build-system python-build-system)
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(inputs
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`(("pybind11" ,pybind11)
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("python-matplotlib" ,python-matplotlib)
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,@(alist-delete "python" (package-inputs fenics-dolfin))))
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(native-inputs
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`(("cmake" ,cmake)
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("ply" ,python-ply)
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("pytest" ,python-pytest)
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("python-decorator" ,python-decorator)
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("python-pkgconfig" ,python-pkgconfig)
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,@(package-native-inputs fenics-dolfin)))
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(propagated-inputs
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`(("dolfin" ,fenics-dolfin)
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("petsc4py" ,python-petsc4py)
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("slepc4py" ,python-slepc4py)))
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-after 'patch-source-shebangs 'set-paths
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(lambda _
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;; Define paths to store locations.
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(setenv "PYBIND11_DIR" (assoc-ref %build-inputs "pybind11"))
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;; Move to python sub-directory.
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(chdir "python")
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#t))
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(add-after 'build 'mpi-setup
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,%openmpi-setup)
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(add-before 'check 'pre-check
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(lambda _
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;; Exclude tests that require meshes supplied by git-lfs.
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(substitute* "demo/test.py"
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(("(.*stem !.*)" line)
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(string-append
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line "\n"
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"excludeList = [\n"
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"'multimesh-quadrature', \n"
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"'multimesh-marking', \n"
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"'mixed-poisson-sphere', \n"
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"'mesh-quality', \n"
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"'lift-drag', \n"
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"'elastodynamics', \n"
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"'dg-advection-diffusion', \n"
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"'contact-vi-tao', \n"
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"'contact-vi-snes', \n"
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"'collision-detection', \n"
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"'buckling-tao', \n"
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"'auto-adaptive-navier-stokes', \n"
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"'advection-diffusion', \n"
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"'subdomains', \n"
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"'stokes-taylor-hood', \n"
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"'stokes-mini', \n"
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"'navier-stokes', \n"
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"'eigenvalue']\n"
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"demos = ["
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"d for d in demos if d[0].stem not in "
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"excludeList]\n")))
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(setenv "HOME" (getcwd))
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(setenv "PYTHONPATH"
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(string-append
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(getcwd) "/build/lib.linux-x86_64-"
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,(version-major+minor (package-version python)) ":"
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(getenv "PYTHONPATH")))
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;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
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(setenv "OPENBLAS_NUM_THREADS" "1")
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#t))
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(replace 'check
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(lambda _
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(with-directory-excursion "test"
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;; Note: The test test_snes_set_from_options() in the file
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;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
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(and (invoke "py.test" "unit" "--ignore"
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"unit/nls/test_PETScSNES_solver.py")
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(invoke "mpirun" "-np" "3" "python" "-B" "-m"
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"pytest" "unit" "--ignore"
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"unit/nls/test_PETScSNES_solver.py")))
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(with-directory-excursion "demo"
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;; Check demos.
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(invoke "python" "generate-demo-files.py")
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(and (invoke "python" "-m" "pytest" "-v" "test.py")
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(invoke "python" "-m" "pytest" "-v" "test.py"
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"--mpiexec=mpiexec" "--num-proc=3")))
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#t))
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(add-after 'install 'install-demo-files
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((demos (string-append
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(assoc-ref outputs "out")
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"/share/python-dolfin/demo")))
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(mkdir-p demos)
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(with-directory-excursion "demo"
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(for-each (lambda (file)
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(let* ((dir (dirname file))
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(tgt-dir (string-append demos "/" dir)))
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(unless (equal? "." dir)
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(mkdir-p tgt-dir)
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(install-file file tgt-dir))))
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(find-files "." ".*\\.(py|gz|xdmf)$"))))
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#t)))))
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(home-page "https://fenicsproject.org/")
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(synopsis "High-level environment for solving differential equations")
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(description
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"@code{fenics} is a computing platform for solving general classes of
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problems that involve differential equations. @code{fenics} facilitates
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access to efficient methods for dealing with ordinary differential
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equations (ODEs) and partial differential equations (PDEs). Systems of
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equations such as these are commonly encountered in areas of engineering,
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mathematics and the physical sciences. It is particularly well-suited to
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problems that can be solved using the Finite Element Method (FEM).
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@code{fenics} is the top level of the set of packages that are developed
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within the FEniCS project. It provides the python user interface to the
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FEniCS core components and external libraries.")
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(license license:lgpl3+)))
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