mirror of
https://git.in.rschanz.org/ryan77627/guix.git
synced 2024-12-29 07:42:23 -05:00
c69959f054
This follows up commit 2f33a7321e which
introduced a new CMAKE-MINIMAL variant for use in package inputs.
* gnu/packages/databases.scm (python-pyarrow)[native-inputs]: Replace CMAKE
with CMAKE-MINIMAL.
* gnu/packages/emacs-xyz.scm (emacs-scel)[native-inputs]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[native-inputs]: Likewise.
* gnu/packages/games.scm (0ad, the-butterfly-effect)[native-inputs]: Likewise.
* gnu/packages/gnome.scm (deja-dup)[native-inputs]: Likewise.
* gnu/packages/ibus.scm (ibus-rime)[native-inputs]: Likewise.
* gnu/packages/rust.scm (rust-1.19)[native-inputs]: Likewise.
* gnu/packages/simulation.scm (fenics)[native-inputs]: Likewise.
* gnu/packages/squirrel.scm (squirrel)[native-inputs]: Likewise.
* gnu/packages/video.scm (handbrake)[native-inputs]: Likewise.
* gnu/packages/virtualization.scm (xen)[native-inputs]: Likewise.
* gnu/packages/vulkan.scm (shaderc)[native-inputs]: Likewise.
730 lines
31 KiB
Scheme
730 lines
31 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2017, 2018 Paul Garlick <pgarlick@tourbillion-technology.com>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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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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#:use-module (gnu packages gcc)
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#:use-module (gnu packages gl)
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#:use-module (gnu packages graphics)
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#:use-module (gnu packages gtk)
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#:use-module (gnu packages linux)
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#:use-module (gnu packages m4)
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#:use-module (gnu packages maths)
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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 python-xyz)
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#:use-module (gnu packages readline)
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#:use-module (gnu packages tls)
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#:use-module (gnu packages version-control)
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#:use-module (gnu packages xml)
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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-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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#:use-module (guix packages)
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#:use-module (guix utils)
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#:use-module (ice-9 ftw)
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#:use-module (ice-9 regex)
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#:use-module (srfi srfi-1))
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(define-public openfoam
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(package
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(name "openfoam")
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(version "4.1")
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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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"http://dl.openfoam.org/source/"
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(string-map (lambda (x) (if (eq? x #\.) #\- x)) version)))
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(file-name (string-append name "-" version ".tar.gz"))
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(sha256
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(base32 "0cgxh4h2hf50qbvvdg5miwc2nympb0nrv3md96vb3gbs9vk8vq9d"))
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(patches (search-patches "openfoam-4.1-cleanup.patch"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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;; Include <sys/sysmacros.h>, which is where glibc >= 2.28 provides
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;; 'major' and 'minor'.
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(substitute* "src/OSspecific/POSIX/fileStat.C"
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(("#include <unistd\\.h>")
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"#include <unistd.h>\n#include <sys/sysmacros.h>\n"))
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#t))))
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(build-system gnu-build-system)
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(inputs
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`(("boost" ,boost)
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("cgal" ,cgal)
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("flex" ,flex)
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("git" ,git)
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("gmp" ,gmp)
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("libxt" ,libxt)
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("metis" ,metis)
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("mpfr" ,mpfr)
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("ncurses" ,ncurses)
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("readline" ,readline)
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("scotch" ,pt-scotch32)
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("zlib" ,zlib)))
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(native-inputs
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`(("bison" ,bison)))
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(propagated-inputs
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`(("gzip" ,gzip)
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("gnuplot" ,gnuplot)
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("openmpi" ,openmpi)))
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(outputs '("debug" ;~60MB
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"out"))
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(arguments
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`( ;; Executable files and shared libraries are located in the 'platforms'
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;; subdirectory.
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#:strip-directories (list (string-append
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"lib/OpenFOAM-" ,version
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"/platforms/linux64GccDPInt32Opt/bin")
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(string-append
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"lib/OpenFOAM-" ,version
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"/platforms/linux64GccDPInt32Opt/lib"))
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#:tests? #f ; no tests to run
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#:modules ((ice-9 ftw)
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(ice-9 regex)
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(guix build gnu-build-system)
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(guix build utils))
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#:phases (modify-phases %standard-phases
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(add-after 'unpack 'rename-build-directory
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(lambda _
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(chdir "..")
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;; Use 'OpenFOAM-version' convention to match the file
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;; name expectations in the build phase.
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(let ((unpack-dir (string-append
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(getcwd) "/"
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(list-ref (scandir (getcwd) (lambda (name)
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(string-match "^OpenFOAM" name))) 0)))
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(build-dir (string-append
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(getcwd) "/OpenFOAM-" ,version)))
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(rename-file unpack-dir build-dir) ; rename build directory
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(chdir (basename build-dir))) ; move to build directory
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#t))
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(delete 'configure) ; no configure phase
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(replace 'build
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(lambda _
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(let ((libraries '("boost" "cgal" "gmp" "metis" "mpfr" "scotch")))
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;; set variables to define store paths
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(for-each (lambda (library)
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(setenv (string-append
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(string-upcase library) "_ROOT")
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(assoc-ref %build-inputs library))) libraries))
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;; set variables to define package versions
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(setenv "SCOTCHVERSION" ,(package-version scotch))
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(setenv "METISVERSION" ,(package-version metis))
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;; set variable to pass extra 'rpath' arguments to linker
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(setenv "LDFLAGS"
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(string-append
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"-Wl,"
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"-rpath=" %output "/lib/OpenFOAM-" ,version
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"/platforms/linux64GccDPInt32Opt/lib,"
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"-rpath=" %output "/lib/OpenFOAM-" ,version
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"/platforms/linux64GccDPInt32Opt/lib/dummy"))
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;; compile OpenFOAM libraries and applications
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(zero? (system (format #f
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"source ./etc/bashrc && ./Allwmake -j~a"
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(parallel-job-count))))))
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(add-after 'build 'update-configuration-files
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(lambda _
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;; record store paths and package versions in
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;; configuration files
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(substitute* "etc/config.sh/CGAL"
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(("$BOOST_ROOT") (getenv "BOOST_ROOT")))
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(substitute* "etc/config.sh/CGAL"
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(("$CGAL_ROOT") (getenv "CGAL_ROOT")))
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(substitute* "etc/config.sh/metis"
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(("$METIS_ROOT") (getenv "METIS_ROOT")))
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(substitute* "etc/config.sh/metis"
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(("$METISVERSION") (getenv "METISVERSION")))
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(substitute* "etc/config.sh/scotch"
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(("$SCOTCH_ROOT") (getenv "SCOTCH_ROOT")))
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(substitute* "etc/config.sh/scotch"
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(("$SCOTCHVERSION") (getenv "SCOTCHVERSION")))
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(substitute* "etc/config.sh/settings"
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(("$GMP_ROOT") (getenv "GMP_ROOT")))
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(substitute* "etc/config.sh/settings"
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(("$MPFR_ROOT") (getenv "MPFR_ROOT")))
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;; reset lockDir variable to refer to write-enabled
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;; directory
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(substitute* "wmake/wmake"
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((" lockDir=.*$")
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" lockDir=$HOME/.$WM_PROJECT/.wmake\n"))
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(substitute* "wmake/wmakeScheduler"
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(("lockDir=.*$")
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"lockDir=$HOME/.$WM_PROJECT/.wmake\n"))
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(substitute* "wmake/wmakeSchedulerUptime"
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(("lockDir=.*$")
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"lockDir=$HOME/.$WM_PROJECT/.wmake\n"))
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#t))
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(add-after 'build 'cleanup
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;; Avoid unncessary, voluminous object and dep files.
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(lambda _
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(delete-file-recursively
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"platforms/linux64GccDPInt32Opt/src")
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(delete-file-recursively
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"platforms/linux64GccDPInt32OptSYSTEMOPENMPI")
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(for-each delete-file (find-files "." "\\.o$"))
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#t))
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(replace 'install
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(lambda _
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;; use 'OpenFOAM-version' convention
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(let ((install-dir (string-append
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%output "/lib/OpenFOAM-" ,version)))
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(mkdir-p install-dir) ; create install directory
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;; move contents of build directory to install directory
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(copy-recursively "." install-dir))))
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(add-after 'install 'add-symbolic-link
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(lambda _
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;; add symbolic link for standard 'bin' directory
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(symlink
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(string-append "./lib/OpenFOAM-" ,version
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"/platforms/linux64GccDPInt32Opt/bin")
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(string-append %output "/bin"))
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#t)))))
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;; Note:
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;; Tutorial files are installed read-only in /gnu/store.
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;; To allow write permissions on files copied from the store a
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;; 'chmod' step is needed before running the applications. For
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;; example, from a user's login:
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;; $ source $GUIX_PROFILE/lib/OpenFOAM-4.1/etc/bashrc
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;; $ mkdir -p $FOAM_RUN
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;; $ cd $FOAM_RUN
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;; $ cp -r $FOAM_TUTORIALS/incompressible/simpleFoam/pitzDaily .
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;; $ cd pitzDaily
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;; $ chmod -R u+w .
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;; $ blockMesh
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(synopsis "Framework for numerical simulation of fluid flow")
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(description "OpenFOAM provides a set of solvers and methods for tackling
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problems in the field of Computational Fluid Dynamics (CFD). It is written in
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C++. Governing equations such as the Navier-Stokes equations can be solved in
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integral form. Physical processes such as phase change, droplet transport and
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chemical reaction can be modelled. Numerical methods are included to deal with
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sharp gradients, such as those encountered in flows with shock waves and flows
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with gas/liquid interfaces. Large problems may be split into smaller, connected
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problems for efficient solution on parallel systems.")
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(license license:gpl3+)
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(home-page "https://openfoam.org")))
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(define-public python-fenics-dijitso
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(package
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(name "python-fenics-dijitso")
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(version "2018.1.0")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "fenics-dijitso" version))
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(sha256
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(base32
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"1qax2f52qsjbd1h5lk5i5shp448qlakxabjjybrfc1w823p0yql9"))))
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(build-system python-build-system)
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(inputs
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`(("openmpi" ,openmpi)
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("python-numpy" ,python-numpy)))
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(native-inputs
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`(("python-pytest-cov" ,python-pytest-cov)))
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(propagated-inputs
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`(("python-mpi4py" ,python-mpi4py)))
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-after 'build 'mpi-setup
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,%openmpi-setup)
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(replace 'check
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(lambda _
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(setenv "HOME" "/tmp")
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(setenv "PYTHONPATH"
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(string-append (getcwd) ":" (getenv "PYTHONPATH")))
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(with-directory-excursion "test"
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;; Disable parallel tests to avoid race condition. See
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;; https://github.com/pytest-dev/pytest-cov/issues/237.
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(substitute* "runtests.sh"
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(("for p in 1 4 8 16; do")
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"for p in 1; do"))
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(invoke "./runtests.sh"))
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#t)))))
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(home-page "https://bitbucket.org/fenics-project/dijitso/")
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(synopsis "Distributed just-in-time building of shared libraries")
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(description
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"Dijitso provides a core component of the @code{FEniCS} framework,
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namely the just-in-time compilation of C++ code that is generated from
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Python modules. It is called from within a C++ library, using ctypes
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to import the dynamic shared library directly.
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As long as the compiled code can provide a simple factory function to
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a class implementing a predefined C++ interface, there is no limit to
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the complexity of that interface. Parallel support depends on the
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@code{mpi4py} interface.")
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(license license:lgpl3+)))
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(define-public python-fenics-ufl
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(package
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(name "python-fenics-ufl")
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(version "2018.1.0")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "fenics-ufl" version))
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(sha256
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(base32
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"1fq8yc86s1s3c8c0b1rc2vf265q0hrkzg57100fg1nghcz0p4vla"))))
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(build-system python-build-system)
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(inputs
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`(("python-numpy" ,python-numpy)))
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(native-inputs
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`(("python-pytest" ,python-pytest)))
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(arguments
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'(#:phases
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(modify-phases %standard-phases
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(replace 'check
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(lambda _
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(setenv "PYTHONPATH"
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(string-append (getcwd) ":" (getenv "PYTHONPATH")))
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(with-directory-excursion "test"
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(invoke "py.test"))
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#t)))))
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(home-page "https://bitbucket.org/fenics-project/ufl/")
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(synopsis "Unified language for form-compilers")
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(description "The Unified Form Language (UFL) is a domain specific
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language for declaration of finite element discretizations of
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variational forms. More precisely, it defines a flexible interface
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for choosing finite element spaces and defining expressions for weak
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forms in a notation close to mathematical notation.
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UFL is part of the FEniCS Project.")
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(license license:lgpl3+)))
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(define-public python-fenics-fiat
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(package
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(name "python-fenics-fiat")
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(version "2018.1.0")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "fenics-fiat" version))
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(sha256
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(base32
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"0fmjd93r6bwf6xs8csw86qzphrnr66xwv7f372w59gmq8mg6rljc"))))
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(build-system python-build-system)
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(native-inputs
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`(("python-pytest" ,python-pytest)))
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(propagated-inputs
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`(("python-numpy" ,python-numpy)
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("python-sympy" ,python-sympy)))
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(arguments
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'(#:phases
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(modify-phases %standard-phases
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(replace 'check
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(lambda _
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(setenv "PYTHONPATH"
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(string-append (getcwd) ":" (getenv "PYTHONPATH")))
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(with-directory-excursion "test"
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(invoke "py.test" "unit/"))
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#t)))))
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(home-page "https://bitbucket.org/fenics-project/fiat/")
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(synopsis "Tabulation of finite element function spaces")
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(description
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"The FInite element Automatic Tabulator (FIAT) supports
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generation of arbitrary order instances of the Lagrange elements on
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lines, triangles, and tetrahedra. It is also capable of generating
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arbitrary order instances of Jacobi-type quadrature rules on the same
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element shapes. Further, H(div) and H(curl) conforming finite element
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spaces such as the families of Raviart-Thomas, Brezzi-Douglas-Marini
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and Nedelec are supported on triangles and tetrahedra. Upcoming
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versions will also support Hermite and nonconforming elements.
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FIAT is part of the FEniCS Project.")
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(license license:lgpl3+)))
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(define-public python-fenics-ffc
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(package
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(name "python-fenics-ffc")
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(version "2018.1.0")
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(source
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|
(origin
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(method url-fetch)
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(uri (pypi-uri "fenics-ffc" version))
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(sha256
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(base32
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"1b2ia5vlkw298x7rf0k2p3ihlpwkwgc98p3s6sbpds3hqmfrzdz9"))))
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(build-system python-build-system)
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|
(native-inputs
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`(("python-pytest" ,python-pytest)))
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|
(propagated-inputs
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`(("python-fenics-dijitso" ,python-fenics-dijitso)
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|
("python-fenics-fiat" ,python-fenics-fiat)
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|
("python-fenics-ufl" ,python-fenics-ufl)))
|
|
(arguments
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'(#:phases
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|
(modify-phases %standard-phases
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|
(replace 'check
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|
(lambda _
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(setenv "HOME" (getcwd))
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(setenv "PYTHONPATH"
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(string-append (getcwd) ":" (getenv "PYTHONPATH")))
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(with-directory-excursion "test"
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;; FIXME: the tests in subdirectory
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;; 'unit/ufc/finite_element' require the ffc_factory
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;; extension module. This module, located in the 'libs'
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;; subdirectory, needs to be built and made accessible
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;; prior to running the tests.
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(invoke "py.test" "unit/" "--ignore=unit/ufc/")
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(with-directory-excursion "uflacs"
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(invoke "py.test" "unit/")))
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#t)))))
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(home-page "https://bitbucket.org/fenics-project/ffc/")
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(synopsis "Compiler for finite element variational forms")
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(description "The FEniCS Form Compiler (FFC) is a compiler for
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finite element variational forms. From a high-level description of
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the form, it generates efficient low-level C++ code that can be used
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to assemble the corresponding discrete operator (tensor). In
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particular, a bilinear form may be assembled into a matrix and a
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linear form may be assembled into a vector. FFC may be used either
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from the command line (by invoking the @code{ffc} command) or as a
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Python module (@code{import ffc}).
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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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(substitute* "dolfin/nls/PETScSNESSolver.cpp"
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;; Remove SNESTEST mapping. The SNESTEST symbol was removed
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;; from PETSc at version 3.10.3.
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((".*SNESTEST.*") "" ))
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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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(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-minimal)
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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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"'curl-curl', \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")
|
|
(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")
|
|
(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)
|
|
(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/")
|
|
(synopsis "High-level environment for solving differential equations")
|
|
(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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