@@ -569,108 +569,111 @@ (define-public fenics-dolfin
"$ENV{CATCH_DIR}/include" back "\n")))))))
(build-system cmake-build-system)
(inputs
- `(("blas" ,openblas)
- ("boost" ,boost)
- ("eigen" ,eigen)
- ("hdf5" ,hdf5-parallel-openmpi)
- ("lapack" ,lapack)
- ("libxml2" ,libxml2)
- ("openmpi" ,openmpi)
- ("python" ,python-3)
- ("scotch" ,pt-scotch32)
- ("suitesparse" ,suitesparse)
- ("sundials" ,sundials-openmpi)
- ("zlib" ,zlib)))
+ (list openblas
+ boost
+ eigen
+ hdf5-parallel-openmpi
+ lapack
+ libxml2
+ openmpi
+ python-3
+ pt-scotch32
+ suitesparse
+ sundials-openmpi
+ zlib))
(native-inputs
- `(("catch" ,catch2-1)
- ("pkg-config" ,pkg-config)))
+ (list catch-framework pkg-config))
(propagated-inputs
- `(("ffc" ,python-fenics-ffc)
- ("petsc" ,petsc-openmpi)
- ("slepc" ,slepc-openmpi)))
+ (list python-fenics-ffc petsc-openmpi slepc-openmpi))
(arguments
- `(#:configure-flags
- `("-DDOLFIN_ENABLE_DOCS:BOOL=OFF"
- "-DDOLFIN_ENABLE_HDF5:BOOL=ON"
- "-DDOLFIN_ENABLE_MPI:BOOL=ON"
- "-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF"
- "-DDOLFIN_ENABLE_SCOTCH:BOOL=ON"
- "-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON"
- "-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF")
- #:phases
- (modify-phases %standard-phases
- (add-after 'patch-usr-bin-file 'mpi-setup
- ,%openmpi-setup)
- (add-after 'patch-source-shebangs 'set-paths
- (lambda _
- ;; Define paths to store locations.
- (setenv "BLAS_DIR" (assoc-ref %build-inputs "blas"))
- (setenv "CATCH_DIR" (assoc-ref %build-inputs "catch"))
- (setenv "LAPACK_DIR" (assoc-ref %build-inputs "lapack"))
- (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
- (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
- (setenv "SCOTCH_DIR" (assoc-ref %build-inputs "scotch"))
- (setenv "SUNDIALS_DIR" (assoc-ref %build-inputs "sundials"))
- (setenv "UMFPACK_DIR" (assoc-ref %build-inputs "suitesparse"))))
- (add-before 'check 'pre-check
- (lambda _
- ;; The Dolfin repository uses git-lfs, whereby web links are
- ;; substituted for large files. Guix does not currently support
- ;; git-lfs, so only the links are downloaded. The tests that
- ;; require the absent meshes cannot run and are skipped.
- ;;
- ;; One serial test fails and is skipped.
- ;; i) demo_multimesh-stokes_serial:
- ;; Warning: Found no facets matching domain for boundary
- ;; condition.
- ;;
- ;; One mpi test fails and is skipped.
- ;; i) demo_stokes-iterative_mpi:
- ;; The MPI_Comm_rank() function was called before MPI_INIT was
- ;; invoked
- (call-with-output-file "CTestCustom.cmake"
- (lambda (port)
- (display
- (string-append
- "set(CTEST_CUSTOM_TESTS_IGNORE "
- "demo_bcs_serial "
- "demo_bcs_mpi "
- "demo_eigenvalue_serial "
- "demo_eigenvalue_mpi "
- "demo_navier-stokes_serial "
- "demo_navier-stokes_mpi "
- "demo_stokes-taylor-hood_serial "
- "demo_stokes-taylor-hood_mpi "
- "demo_subdomains_serial "
- "demo_advection-diffusion_serial "
- "demo_advection-diffusion_mpi "
- "demo_auto-adaptive-navier-stokes_serial "
- "demo_contact-vi-snes_serial "
- "demo_contact-vi-snes_mpi "
- "demo_contact-vi-tao_serial "
- "demo_contact-vi-tao_mpi "
- "demo_curl-curl_serial "
- "demo_curl-curl_mpi "
- "demo_dg-advection-diffusion_serial "
- "demo_dg-advection-diffusion_mpi "
- "demo_elasticity_serial "
- "demo_elasticity_mpi "
- "demo_elastodynamics_serial "
- "demo_elastodynamics_mpi "
- "demo_lift-drag_serial "
- "demo_lift-drag_mpi "
- "demo_mesh-quality_serial "
- "demo_mesh-quality_mpi "
- "demo_multimesh-stokes_serial "
- ")\n") port)))))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "make" "unittests")
- (invoke "make" "demos")
- (invoke "ctest" "-R" "unittests")
- (invoke "ctest" "-R" "demo" "-R" "serial")
- (invoke "ctest" "-R" "demo" "-R" "mpi")))))))
+ (list #:configure-flags #~`("-DDOLFIN_ENABLE_DOCS:BOOL=OFF"
+ "-DDOLFIN_ENABLE_HDF5:BOOL=ON"
+ "-DDOLFIN_ENABLE_MPI:BOOL=ON"
+ "-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF"
+ "-DDOLFIN_ENABLE_SCOTCH:BOOL=ON"
+ "-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON"
+ "-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'patch-usr-bin-file 'mpi-setup
+ #$%openmpi-setup)
+ (add-after 'patch-source-shebangs 'set-paths
+ (lambda _
+ ;; Define paths to store locations.
+ (setenv "BLAS_DIR"
+ #$(this-package-input "openblas"))
+ (setenv "CATCH_DIR"
+ #$(this-package-input "catch"))
+ (setenv "LAPACK_DIR"
+ #$(this-package-input "lapack"))
+ (setenv "PETSC_DIR"
+ #$(this-package-input "petsc"))
+ (setenv "SLEPC_DIR"
+ #$(this-package-input "slepc"))
+ (setenv "SCOTCH_DIR"
+ #$(this-package-input "scotch"))
+ (setenv "SUNDIALS_DIR"
+ #$(this-package-input "sundials"))
+ (setenv "UMFPACK_DIR"
+ #$(this-package-input "suitesparse"))))
+ (add-before 'check 'pre-check
+ (lambda _
+ ;; The Dolfin repository uses git-lfs, whereby web links are
+ ;; substituted for large files. Guix does not currently support
+ ;; git-lfs, so only the links are downloaded. The tests that
+ ;; require the absent meshes cannot run and are skipped.
+ ;;
+ ;; One serial test fails and is skipped.
+ ;; i) demo_multimesh-stokes_serial:
+ ;; Warning: Found no facets matching domain for boundary
+ ;; condition.
+ ;;
+ ;; One mpi test fails and is skipped.
+ ;; i) demo_stokes-iterative_mpi:
+ ;; The MPI_Comm_rank() function was called before MPI_INIT was
+ ;; invoked
+ (call-with-output-file "CTestCustom.cmake"
+ (lambda (port)
+ (display (string-append
+ "set(CTEST_CUSTOM_TESTS_IGNORE "
+ "demo_bcs_serial "
+ "demo_bcs_mpi "
+ "demo_eigenvalue_serial "
+ "demo_eigenvalue_mpi "
+ "demo_navier-stokes_serial "
+ "demo_navier-stokes_mpi "
+ "demo_stokes-taylor-hood_serial "
+ "demo_stokes-taylor-hood_mpi "
+ "demo_subdomains_serial "
+ "demo_advection-diffusion_serial "
+ "demo_advection-diffusion_mpi "
+ "demo_auto-adaptive-navier-stokes_serial "
+ "demo_contact-vi-snes_serial "
+ "demo_contact-vi-snes_mpi "
+ "demo_contact-vi-tao_serial "
+ "demo_contact-vi-tao_mpi "
+ "demo_curl-curl_serial "
+ "demo_curl-curl_mpi "
+ "demo_dg-advection-diffusion_serial "
+ "demo_dg-advection-diffusion_mpi "
+ "demo_elasticity_serial "
+ "demo_elasticity_mpi "
+ "demo_elastodynamics_serial "
+ "demo_elastodynamics_mpi "
+ "demo_lift-drag_serial "
+ "demo_lift-drag_mpi "
+ "demo_mesh-quality_serial "
+ "demo_mesh-quality_mpi "
+ "demo_multimesh-stokes_serial "
+ ")\n") port)))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "make" "unittests")
+ (invoke "make" "demos")
+ (invoke "ctest" "-R" "unittests")
+ (invoke "ctest" "-R" "demo" "-R" "serial")
+ (invoke "ctest" "-R" "demo" "-R" "mpi")))))))
(home-page "https://bitbucket.org/fenics-project/dolfin/")
(synopsis "Problem solving environment for differential equations")
(description
@@ -708,112 +711,114 @@ (define-public fenics
(name "fenics")
(build-system python-build-system)
(inputs
- `(("pybind11" ,pybind11)
- ("python-matplotlib" ,python-matplotlib)
- ,@(alist-delete "python" (package-inputs fenics-dolfin))))
+ (modify-inputs (package-inputs fenics-dolfin)
+ (delete "python")
+ (prepend pybind11 python-matplotlib)))
(native-inputs
- `(("cmake" ,cmake-minimal)
- ("ply" ,python-ply)
- ("pytest" ,python-pytest)
- ("python-decorator" ,python-decorator)
- ,@(package-native-inputs fenics-dolfin)))
+ (modify-inputs (package-native-inputs fenics-dolfin)
+ (prepend cmake-minimal python-ply python-pytest python-decorator)))
(propagated-inputs
- `(("dolfin" ,fenics-dolfin)
- ("petsc4py" ,python-petsc4py)
- ("slepc4py" ,python-slepc4py)
+ (list fenics-dolfin
+ python-petsc4py
+ python-slepc4py
- ;; 'dolfin/jit/jit.py' parses 'dolfin.pc' at run time.
- ("python-pkgconfig" ,python-pkgconfig)))
+ ;; 'dolfin/jit/jit.py' parses 'dolfin.pc' at run time.
+ python-pkgconfig))
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'relax-requirements
- (lambda _
- (substitute* "python/setup.py"
- (("pybind11==") "pybind11>="))))
- (add-after 'unpack 'set-dolfin-pc-file-name
- (lambda* (#:key inputs #:allow-other-keys)
- ;; Instead of cluttering the user's 'PKG_CONFIG_PATH' environment
- ;; variable, hard-code the 'dolfin.pc' absolute file name.
- (let ((pc-file (search-input-file inputs
- "/lib/pkgconfig/dolfin.pc")))
- (substitute* "python/dolfin/jit/jit.py"
- (("pkgconfig\\.parse\\(\"dolfin\"\\)")
- (string-append "pkgconfig.parse(\"" pc-file "\")"))))))
- (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")))
- (add-after 'build 'mpi-setup
- ,%openmpi-setup)
- (add-before 'check 'pre-check
- (lambda _
- ;; Exclude three tests that generate
- ;; 'NotImplementedError' in matplotlib version 3.1.2.
- ;; See
- ;; <https://github.com/matplotlib/matplotlib/issues/15382>.
- ;; Also exclude tests that require meshes supplied by
- ;; git-lfs.
- (substitute* "demo/test.py"
- (("(.*stem !.*)" line)
- (string-append
- line "\n"
- "excludeList = [\n"
- "'built-in-meshes', \n"
- "'hyperelasticity', \n"
- "'elasticity', \n"
- "'multimesh-quadrature', \n"
- "'multimesh-marking', \n"
- "'mixed-poisson-sphere', \n"
- "'mesh-quality', \n"
- "'lift-drag', \n"
- "'elastodynamics', \n"
- "'dg-advection-diffusion', \n"
- "'curl-curl', \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))
- ;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
- (setenv "OPENBLAS_NUM_THREADS" "1")))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (with-directory-excursion "test"
- (invoke
- "pytest" "unit"
- ;; The test test_snes_set_from_options() in the file
- ;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
- "--ignore" "unit/nls/test_PETScSNES_solver.py"
- ;; Fails with a segfault.
- "--ignore" "unit/io/test_XDMF.py")))))
- (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)$")))))))))
+ (list #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "python/setup.py"
+ (("pybind11==")
+ "pybind11>="))))
+ (add-after 'unpack 'set-dolfin-pc-file-name
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; Instead of cluttering the user's 'PKG_CONFIG_PATH' environment
+ ;; variable, hard-code the 'dolfin.pc' absolute file name.
+ (let ((pc-file (search-input-file inputs
+ "/lib/pkgconfig/dolfin.pc")))
+ (substitute* "python/dolfin/jit/jit.py"
+ (("pkgconfig\\.parse\\(\"dolfin\"\\)")
+ (string-append "pkgconfig.parse(\"" pc-file
+ "\")"))))))
+ (add-after 'patch-source-shebangs 'set-paths
+ (lambda _
+ ;; Define paths to store locations.
+ (setenv "PYBIND11_DIR" #$(this-package-input "pybind11"))
+ ;; Move to python sub-directory.
+ (chdir "python")))
+ (add-after 'build 'mpi-setup
+ #$%openmpi-setup)
+ (add-before 'check 'pre-check
+ (lambda _
+ ;; Exclude three tests that generate
+ ;; 'NotImplementedError' in matplotlib version 3.1.2.
+ ;; See
+ ;; <https://github.com/matplotlib/matplotlib/issues/15382>.
+ ;; Also exclude tests that require meshes supplied by
+ ;; git-lfs.
+ (substitute* "demo/test.py"
+ (("(.*stem !.*)" line)
+ (string-append line
+ "\n"
+ "excludeList = [\n"
+ "'built-in-meshes', \n"
+ "'hyperelasticity', \n"
+ "'elasticity', \n"
+ "'multimesh-quadrature', \n"
+ "'multimesh-marking', \n"
+ "'mixed-poisson-sphere', \n"
+ "'mesh-quality', \n"
+ "'lift-drag', \n"
+ "'elastodynamics', \n"
+ "'dg-advection-diffusion', \n"
+ "'curl-curl', \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))
+ ;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
+ (setenv "OPENBLAS_NUM_THREADS" "1")))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (with-directory-excursion "test"
+ (invoke "pytest"
+ "unit"
+ ;; The test test_snes_set_from_options() in the file
+ ;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
+ "--ignore"
+ "unit/nls/test_PETScSNES_solver.py"
+ ;; Fails with a segfault.
+ "--ignore"
+ "unit/io/test_XDMF.py")))))
+ (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)$")))))))))
(home-page "https://fenicsproject.org/")
(synopsis "High-level environment for solving differential equations")
(description
From: Ludovic Courtès <ludovic.courtes@inria.fr> * gnu/packages/simulation.scm (fenics-dolfin)[inputs, native-inputs] [propagated-inputs]: Remove labels. Replace CATCH2-1, which was actually unused, by CATCH-FRAMEWORK. [arguments]: Rewrite using gexps. Adjust 'set-paths' phase accordingly. (fenics): Likewise. --- gnu/packages/simulation.scm | 407 ++++++++++++++++++------------------ 1 file changed, 206 insertions(+), 201 deletions(-)