gnu: Add fenics-dolfin.
* gnu/packages/simulation.scm (fenics-dolfin): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>master
Paul Garlick
Ludovic Courtès
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6b7f1f8afa
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0ace6c0b84
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@ -18,11 +18,13 @@
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(define-module (gnu packages simulation)
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#:use-module (gnu packages)
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#:use-module (gnu packages algebra)
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#:use-module (gnu packages base)
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#:use-module (gnu packages bash)
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#:use-module (gnu packages bison)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages check)
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#:use-module (gnu packages cmake)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages flex)
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#:use-module (gnu packages gettext)
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@ -36,6 +38,7 @@
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#:use-module (gnu packages mpi)
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#:use-module (gnu packages multiprecision)
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#:use-module (gnu packages ncurses)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages python)
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#:use-module (gnu packages readline)
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#:use-module (gnu packages tls)
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@ -44,6 +47,7 @@
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#:use-module (gnu packages xorg)
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#:use-module (guix download)
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#:use-module (guix build utils)
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#:use-module (guix build-system cmake)
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#:use-module (guix build-system gnu)
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#:use-module (guix build-system python)
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#:use-module ((guix licenses) #:prefix license:)
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@ -401,3 +405,190 @@ FFC is part of the FEniCS Project.")
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;; There are two files released with a public domain licence;
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;; ufc.h and ufc_geometry.h, in subdirectory 'ffc/backends/ufc'.
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(license (list license:public-domain license:lgpl3+))))
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(define-public fenics-dolfin
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(package
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(name "fenics-dolfin")
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(version "2018.1.0.post1")
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(source
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(origin
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(method url-fetch)
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(uri (string-append
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"https://bitbucket.org/fenics-project/dolfin/get/"
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version ".tar.gz"))
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(file-name (string-append name "-" version ".tar.gz"))
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(sha256
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(base32
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"12zkk8j3xsg6l8p0ggwsl03084vlcivw4h99b7z9kndg7k89b3ya"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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;; Make sure we don't use the bundled test framework.
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(delete-file-recursively "test/unit/cpp/catch")
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(substitute* "test/unit/cpp/main.cpp"
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;; Use standard search paths for 'catch' header file.
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(("#include.*")
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"#include <catch.hpp>\n"))
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(substitute* "test/unit/cpp/CMakeLists.txt"
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;; Add extra include directories required by the unit tests.
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(("(^target_link_libraries.*)" line)
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(string-append line "\n"
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"target_include_directories("
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"unittests PRIVATE "
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"${DOLFIN_SOURCE_DIR} "
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"${DOLFIN_SOURCE_DIR}/dolfin "
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"${DOLFIN_BINARY_DIR})\n"))
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(("(^set\\(CATCH_INCLUDE_DIR ).*(/catch\\))" _ front back)
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(string-append front
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"$ENV{CATCH_DIR}"
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"/include" back "\n")))
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(substitute* "demo/CMakeLists.txt"
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;; Add extra include directories required by the demo tests.
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(("(^#find_package.*)" line)
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(string-append line "\n"
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"include_directories("
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"${DOLFIN_SOURCE_DIR} "
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"${DOLFIN_SOURCE_DIR}/dolfin "
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"${DOLFIN_BINARY_DIR})\n")))
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#t))))
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(build-system cmake-build-system)
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(inputs
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`(("blas" ,openblas)
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("boost" ,boost)
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("eigen" ,eigen)
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("hdf5" ,hdf5-parallel-openmpi)
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("lapack" ,lapack)
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("libxml2" ,libxml2)
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("openmpi" ,openmpi)
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("python" ,python-3)
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("scotch" ,pt-scotch32)
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("suitesparse" ,suitesparse)
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("sundials" ,sundials-openmpi)
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("zlib" ,zlib)))
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(native-inputs
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`(("catch" ,catch-framework2)
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("pkg-config" ,pkg-config)))
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(propagated-inputs
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`(("ffc" ,python-fenics-ffc)
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("petsc" ,petsc-openmpi)
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("slepc" ,slepc-openmpi)))
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(arguments
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`(#:configure-flags
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`("-DDOLFIN_ENABLE_DOCS:BOOL=OFF"
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"-DDOLFIN_ENABLE_HDF5:BOOL=ON"
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"-DDOLFIN_ENABLE_MPI:BOOL=ON"
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"-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF"
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"-DDOLFIN_ENABLE_SCOTCH:BOOL=ON"
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"-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON"
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"-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF")
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#:phases
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(modify-phases %standard-phases
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(add-after 'patch-usr-bin-file 'mpi-setup
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,%openmpi-setup)
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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 "BLAS_DIR" (assoc-ref %build-inputs "blas"))
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(setenv "CATCH_DIR" (assoc-ref %build-inputs "catch"))
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(setenv "LAPACK_DIR" (assoc-ref %build-inputs "lapack"))
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(setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
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(setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
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(setenv "SCOTCH_DIR" (assoc-ref %build-inputs "scotch"))
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(setenv "SUNDIALS_DIR" (assoc-ref %build-inputs "sundials"))
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(setenv "UMFPACK_DIR" (assoc-ref %build-inputs "suitesparse"))
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#t))
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(add-before 'check 'pre-check
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(lambda _
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;; The Dolfin repository uses git-lfs, whereby web links are
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;; substituted for large files. Guix does not currently support
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;; git-lfs, so only the links are downloaded. The tests that
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;; require the absent meshes cannot run and are skipped.
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;;
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;; Two other serial tests fail and are skipped.
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;; i) demo_stokes-iterative_serial,
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;; The MPI_Comm_rank() function was called before MPI_INIT was
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;; invoked
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;; ii) demo_multimesh-stokes_serial:
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;; Warning: Found no facets matching domain for boundary
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;; condition.
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;;
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;; One mpi test fails and is skipped.
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;; i) demo_stokes-iterative_mpi:
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;; The MPI_Comm_rank() function was called before MPI_INIT was
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;; invoked
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(call-with-output-file "CTestCustom.cmake"
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(lambda (port)
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(display
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(string-append
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"set(CTEST_CUSTOM_TESTS_IGNORE "
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"demo_bcs_serial "
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"demo_bcs_mpi "
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"demo_eigenvalue_serial "
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"demo_eigenvalue_mpi "
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"demo_navier-stokes_serial "
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"demo_navier-stokes_mpi "
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"demo_stokes-taylor-hood_serial "
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"demo_stokes-taylor-hood_mpi "
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"demo_subdomains_serial "
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"demo_advection-diffusion_serial "
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"demo_advection-diffusion_mpi "
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"demo_auto-adaptive-navier-stokes_serial "
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"demo_contact-vi-snes_serial "
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"demo_contact-vi-snes_mpi "
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"demo_contact-vi-tao_serial "
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"demo_contact-vi-tao_mpi "
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"demo_curl-curl_serial "
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"demo_curl-curl_mpi "
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"demo_dg-advection-diffusion_serial "
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"demo_dg-advection-diffusion_mpi "
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"demo_elasticity_serial "
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"demo_elasticity_mpi "
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"demo_elastodynamics_serial "
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"demo_elastodynamics_mpi "
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"demo_lift-drag_serial "
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"demo_lift-drag_mpi "
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"demo_mesh-quality_serial "
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"demo_mesh-quality_mpi "
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"demo_multimesh-stokes_serial "
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"demo_stokes-iterative_serial "
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"demo_stokes-iterative_mpi "
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")\n") port)))
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#t))
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(replace 'check
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(lambda _
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(and (invoke "make" "unittests")
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(invoke "make" "demos")
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(invoke "ctest" "-R" "unittests")
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(invoke "ctest" "-R" "demo" "-R" "serial")
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(invoke "ctest" "-R" "demo" "-R" "mpi")))))))
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(home-page "https://bitbucket.org/fenics-project/dolfin/")
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(synopsis "Problem solving environment for differential equations")
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(description
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"DOLFIN is a computational framework for finding numerical
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solutions to problems described by differential equations. Numerical
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models in DOLFIN are constructed using general families of finite
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elements. Data structures are provided for discretizing the governing
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system on a computational mesh. A compact syntax, similar to
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mathematical notation, is made available for defining function spaces
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and expressing variational forms. Interfaces to specialized matrix
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solvers are provided for solving the resultant linear systems.
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@code{fenics-dolfin} is part of the FEniCS project. It is the C++
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user interface to the FEniCS core components and external libraries.")
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;; The source code for the DOLFIN C++ library is licensed under the
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;; GNU Lesser General Public License, version 3 or later, with the
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;; following exceptions:
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;;
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;; public-domain: dolfin/geometry/predicates.cpp
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;; dolfin/geometry/predicates.h
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;;
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;; zlib: dolfin/io/base64.cpp
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;; dolfin/io/base64.h
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;;
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;; expat: dolfin/io/pugiconfig.hpp
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;; dolfin/io/pugixml.cpp
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;; dolfin/io/pugixml.hpp
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(license (list license:public-domain
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license:zlib
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license:expat
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license:lgpl3+))))
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