1095 lines
42 KiB
Scheme
1095 lines
42 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2013, 2014 Andreas Enge <andreas@enge.fr>
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;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
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;;; Copyright © 2014 John Darrington <jmd@gnu.org>
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;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
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;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
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;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
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;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
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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 maths)
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#:use-module (ice-9 regex)
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#:use-module (gnu packages)
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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 download)
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#:use-module (guix 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 (gnu packages algebra)
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#:use-module (gnu packages bison)
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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 curl)
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#:use-module (gnu packages elf)
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#:use-module (gnu packages flex)
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#:use-module (gnu packages fltk)
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#:use-module (gnu packages fontutils)
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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 gd)
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#:use-module (gnu packages ghostscript)
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#:use-module (gnu packages glib)
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#:use-module (gnu packages gtk)
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#:use-module (gnu packages less)
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#:use-module (gnu packages lisp)
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#:use-module (gnu packages gnome)
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#:use-module (gnu packages xorg)
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#:use-module (gnu packages gl)
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#:use-module (gnu packages m4)
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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 pcre)
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#:use-module (gnu packages popt)
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#:use-module (gnu packages perl)
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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 tcsh)
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#:use-module (gnu packages tcl)
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#:use-module (gnu packages texinfo)
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#:use-module (gnu packages texlive)
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#:use-module (gnu packages xml))
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(define-public units
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(package
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(name "units")
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(version "2.11")
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(source (origin
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(method url-fetch)
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(uri (string-append "mirror://gnu/units/units-" version
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".tar.gz"))
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(sha256 (base32
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"1gjs3wc212aaiq4r76hx9nl1h3fa39n0ljwl9420d6ixl3rdmdjk"))))
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(build-system gnu-build-system)
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(synopsis "Conversion between thousands of scales")
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(description
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"GNU Units converts numeric quantities between units of measure. It
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can handle scale changes through adaptive usage of standard scale prefixes
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(micro-, kilo-, etc.). It can also handle nonlinear conversions such as
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Fahrenheit to Celsius. Its interpreter is powerful enough to be used
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effectively as a scientific calculator.")
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(license license:gpl3+)
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(home-page "http://www.gnu.org/software/units/")))
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(define-public dionysus
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(package
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(name "dionysus")
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(version "1.3.0")
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(source (origin
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(method url-fetch)
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(uri (string-append "mirror://gnu/dionysus/dionysus-" version
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".tar.gz"))
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(sha256
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(base32
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"1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs"))))
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(build-system gnu-build-system)
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(inputs `(("tcl" ,tcl))) ;for 'tclsh'
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(synopsis "Local search for universal constants and scientific values")
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(description
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"GNU Dionysus is a convenient system for quickly retrieving the values of
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mathematical constants used in science and engineering. Values can be
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searched using a simple command-line tool, choosing from three databases:
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universal constants, atomic numbers, and constants related to
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semiconductors.")
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(license license:gpl3+)
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(home-page "http://www.gnu.org/software/dionysus/")))
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(define-public gsl
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(package
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(name "gsl")
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(version "1.16")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "mirror://gnu/gsl/gsl-"
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version ".tar.gz"))
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(sha256
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(base32
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"0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k"))))
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(build-system gnu-build-system)
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(arguments
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`(#:parallel-tests? #f
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#:phases
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(alist-replace
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'configure
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(lambda* (#:key target system outputs #:allow-other-keys #:rest args)
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(let ((configure (assoc-ref %standard-phases 'configure)))
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;; disable numerically unstable test on i686, see thread at
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;; http://lists.gnu.org/archive/html/bug-gsl/2011-11/msg00019.html
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(if (string=? (or target system) "i686-linux")
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(substitute* "ode-initval2/Makefile.in"
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(("TESTS = \\$\\(check_PROGRAMS\\)") "TESTS =")))
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(apply configure args)))
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%standard-phases)))
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(home-page "http://www.gnu.org/software/gsl/")
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(synopsis "Numerical library for C and C++")
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(description
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"The GNU Scientific Library is a library for numerical analysis in C
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and C++. It includes a wide range of mathematical routines, with over 1000
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functions in total. Subject areas covered by the library include:
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differential equations, linear algebra, Fast Fourier Transforms and random
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numbers.")
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(license license:gpl3+)))
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(define-public glpk
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(package
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(name "glpk")
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(version "4.55")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "mirror://gnu/glpk/glpk-"
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version ".tar.gz"))
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(sha256
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(base32
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"1rqx5fzj1mhkifilip5mkxybpj2wkniq5qcn8h1w2vkr2rzhs29p"))))
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(build-system gnu-build-system)
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(inputs
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`(("gmp" ,gmp)))
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(arguments
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`(#:configure-flags '("--with-gmp")))
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(home-page "http://www.gnu.org/software/glpk/")
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(synopsis "GNU Linear Programming Kit, supporting the MathProg language")
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(description
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"GLPK is a C library for solving large-scale linear programming (LP),
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mixed integer programming (MIP), and other related problems. It supports the
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GNU MathProg modeling language, a subset of the AMPL language, and features a
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translator for the language. In addition to the C library, a stand-alone
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LP/MIP solver is included in the package.")
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(license license:gpl3+)))
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(define-public pspp
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(package
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(name "pspp")
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(version "0.8.4")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "mirror://gnu/pspp/pspp-"
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version ".tar.gz"))
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(sha256
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(base32
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"0b65q45x05ps95pph6glbg7ymdr638nfb0rk9x5x9qm5k073pk5z"))))
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(build-system gnu-build-system)
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(inputs
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`(("cairo" ,cairo)
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("fontconfig" ,fontconfig)
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("gettext" ,gnu-gettext)
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("gsl" ,gsl)
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("libxml2" ,libxml2)
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("pango" ,pango)
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("readline" ,readline)
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("gtk" ,gtk+-2)
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("gtksourceview" ,gtksourceview)
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("zlib" ,zlib)))
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(native-inputs
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`(("glib" ,glib "bin") ;for glib-genmarshal
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("perl" ,perl)
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("pkg-config" ,pkg-config)))
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(home-page "http://www.gnu.org/software/pspp/")
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(synopsis "Statistical analysis")
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(description
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"GNU PSPP is a statistical analysis program. It can perform
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descriptive statistics, T-tests, linear regression and non-parametric tests.
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It features both a graphical interface as well as command-line input. PSPP
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is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
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can be imported from spreadsheets, text files and database sources and it can
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be output in text, PostScript, PDF or HTML.")
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(license license:gpl3+)))
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(define-public arpack-ng
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(package
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(name "arpack-ng")
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(version "3.2.0")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "https://github.com/opencollab/arpack-ng/archive/"
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version ".tar.gz"))
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(sha256
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(base32
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"1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff"))))
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(build-system gnu-build-system)
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(home-page "https://github.com/opencollab/arpack-ng")
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(inputs
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`(("lapack" ,lapack)
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("fortran" ,gfortran-4.8)))
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(synopsis "Fortran subroutines for solving eigenvalue problems")
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(description
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"ARPACK-NG is a collection of Fortran77 subroutines designed to solve
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large scale eigenvalue problems.")
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(license (license:bsd-style "file://COPYING"
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"See COPYING in the distribution."))))
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(define-public lapack
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(package
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(name "lapack")
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(version "3.5.0")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "http://www.netlib.org/lapack/lapack-"
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version ".tgz"))
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(sha256
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(base32
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"0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s"))))
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(build-system cmake-build-system)
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(home-page "http://www.netlib.org/lapack/")
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(native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath
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(inputs `(("fortran" ,gfortran-4.8)
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("python" ,python-2)))
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(arguments
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`(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES")
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#:phases (alist-cons-before
|
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'check 'patch-python
|
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((python (assoc-ref inputs "python")))
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(substitute* "lapack_testing.py"
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(("/usr/bin/env python") python))))
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%standard-phases)))
|
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(synopsis "Library for numerical linear algebra")
|
|
(description
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"LAPACK is a Fortran 90 library for solving the most commonly occurring
|
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problems in numerical linear algebra.")
|
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(license (license:bsd-style "file://LICENSE"
|
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"See LICENSE in the distribution."))))
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(define-public gnuplot
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(package
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(name "gnuplot")
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(version "4.6.3")
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(source
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(origin
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|
(method url-fetch)
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(uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
|
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version "/gnuplot-" version ".tar.gz"))
|
|
(sha256
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|
(base32
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|
"1xd7gqdhlk7k1p9yyqf9vkk811nadc7m4si0q3nb6cpv4pxglpyz"))))
|
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(build-system gnu-build-system)
|
|
(inputs `(("readline" ,readline)
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("cairo" ,cairo)
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("pango" ,pango)
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("gd" ,gd)))
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(native-inputs `(("texlive" ,texlive)
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("pkg-config" ,pkg-config)))
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(home-page "http://www.gnuplot.info")
|
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(synopsis "Command-line driven graphing utility")
|
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(description "Gnuplot is a portable command-line driven graphing
|
|
utility. It was originally created to allow scientists and students to
|
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visualize mathematical functions and data interactively, but has grown to
|
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support many non-interactive uses such as web scripting. It is also used as a
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plotting engine by third-party applications like Octave.")
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;; X11 Style with the additional restriction that derived works may only be
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;; distributed as patches to the original.
|
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(license (license:fsf-free
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"http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
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(define-public hdf5
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(package
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(name "hdf5")
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(version "1.8.12")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-"
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version "/src/hdf5-"
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version ".tar.bz2"))
|
|
(sha256
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|
(base32 "0f9n0v3p3lwc7564791a39c6cn1d3dbrn7d1j3ikqsi27a8hy23d"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
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`(#:phases
|
|
(alist-cons-before
|
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'configure 'patch-configure
|
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(lambda _
|
|
(substitute* "configure"
|
|
(("/bin/mv") "mv")))
|
|
%standard-phases)))
|
|
(outputs '("out" "bin" "lib" "include"))
|
|
(home-page "http://www.hdfgroup.org")
|
|
(synopsis "Management suite for extremely large and complex data")
|
|
(description "HDF5 is a suite that makes possible the management of
|
|
extremely large and complex data collections.")
|
|
(license (license:x11-style
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"http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
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|
|
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;; For a fully featured Octave, users are strongly recommended also to install
|
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;; the following packages: texinfo, less, ghostscript, gnuplot.
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(define-public octave
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(package
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(name "octave")
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(version "3.8.0")
|
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(source
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|
(origin
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|
(method url-fetch)
|
|
(uri (string-append "mirror://gnu/octave/octave-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"0ks9pr154syw0vb3jn6xsnrkkrbvf9y7i7gaxa28rz6ngxbxvq9l"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("lapack" ,lapack)
|
|
("readline" ,readline)
|
|
("glpk" ,glpk)
|
|
("curl" ,curl)
|
|
("pcre" ,pcre)
|
|
("fltk" ,fltk)
|
|
("fontconfig" ,fontconfig)
|
|
("freetype" ,freetype)
|
|
("hdf5-lib" ,hdf5 "lib")
|
|
("hdf5-include" ,hdf5 "include")
|
|
("libxft" ,libxft)
|
|
("mesa" ,mesa)
|
|
("zlib" ,zlib)))
|
|
(native-inputs
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|
`(("gfortran" ,gfortran-4.8)
|
|
("pkg-config" ,pkg-config)
|
|
("perl" ,perl)
|
|
;; The following inputs are not actually used in the build process. However, the
|
|
;; ./configure gratuitously tests for their existence and assumes that programs not
|
|
;; present at build time are also not, and can never be, available at run time!
|
|
;; If these inputs are therefore not present, support for them will be built out.
|
|
;; However, Octave will still run without them, albeit without the features they
|
|
;; provide.
|
|
("less" ,less)
|
|
("texinfo" ,texinfo)
|
|
("ghostscript" ,ghostscript)
|
|
("gnuplot" ,gnuplot)))
|
|
(arguments
|
|
`(#:configure-flags (list (string-append "--with-shell="
|
|
(assoc-ref %build-inputs "bash")
|
|
"/bin/sh"))))
|
|
(home-page "http://www.gnu.org/software/octave/")
|
|
(synopsis "High-level language for numerical computation")
|
|
(description "GNU Octave is a high-level interpreted language that is specialized
|
|
for numerical computations. It can be used for both linear and non-linear
|
|
applications and it provides great support for visualizing results. Work may
|
|
be performed both at the interactive command-line as well as via script
|
|
files.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public gmsh
|
|
(package
|
|
(name "gmsh")
|
|
(version "2.8.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://www.geuz.org/gmsh/src/gmsh-"
|
|
version "-source.tgz"))
|
|
(sha256
|
|
(base32 "0jv2yvk28w86rx5mvjkb0w12ff2jxih7axnpvznpd295lg5jg7hr"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
;; Remove non-free METIS code
|
|
'(delete-file-recursively "contrib/Metis"))))
|
|
(build-system cmake-build-system)
|
|
(native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath
|
|
(propagated-inputs
|
|
`(("fltk" ,fltk)
|
|
("gfortran" ,gfortran-4.8)
|
|
("gmp" ,gmp)
|
|
("hdf5-lib" ,hdf5 "lib")
|
|
("hdf5-include" ,hdf5 "include")
|
|
("lapack" ,lapack)
|
|
("mesa" ,mesa)
|
|
("glu" ,glu)
|
|
("libx11" ,libx11)
|
|
("libxext" ,libxext)))
|
|
(arguments
|
|
`(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
|
|
"-DENABLE_BUILD_SHARED:BOOL=ON"
|
|
"-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
|
|
(home-page "http://www.geuz.org/gmsh/")
|
|
(synopsis "3D finite element grid generator")
|
|
(description "Gmsh is a 3D finite element grid generator with a built-in
|
|
CAD engine and post-processor. Its design goal is to provide a fast, light
|
|
and user-friendly meshing tool with parametric input and advanced
|
|
visualization capabilities. Gmsh is built around four modules: geometry,
|
|
mesh, solver and post-processing. The specification of any input to these
|
|
modules is done either interactively using the graphical user interface or in
|
|
ASCII text files using Gmsh's own scripting language.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public petsc
|
|
(package
|
|
(name "petsc")
|
|
(version "3.4.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
;; The *-lite-* tarball does not contain the *large* documentation
|
|
(uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
|
|
"petsc-lite-" version ".tar.gz"))
|
|
(sha256
|
|
(base32 "0v5dg6dhdjpi5ianvd4mm6hsvxzv1bsxwnh9f9myag0a0d9xk9iv"))
|
|
(patches
|
|
(list (search-patch "petsc-fix-threadcomm.patch")))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("python" ,python-2)
|
|
("perl" ,perl)))
|
|
(inputs
|
|
`(("gfortran" ,gfortran-4.8)
|
|
("lapack" ,lapack)
|
|
("superlu" ,superlu)
|
|
;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
|
|
;; leaving out opengl, as configuration seems to only be for mac
|
|
))
|
|
(arguments
|
|
`(#:test-target "test"
|
|
#:parallel-build? #f
|
|
#:configure-flags
|
|
`("--with-mpi=0"
|
|
"--with-openmp=1"
|
|
"--with-superlu=1"
|
|
,(string-append "--with-superlu-include="
|
|
(assoc-ref %build-inputs "superlu") "/include")
|
|
,(string-append "--with-superlu-lib="
|
|
(assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
|
|
#:phases
|
|
(alist-replace
|
|
'configure
|
|
;; PETSc's configure script is actually a python script, so we can't
|
|
;; run it with bash.
|
|
(lambda* (#:key outputs (configure-flags '())
|
|
#:allow-other-keys)
|
|
(let* ((prefix (assoc-ref outputs "out"))
|
|
(flags `(,(string-append "--prefix=" prefix)
|
|
,@configure-flags)))
|
|
(format #t "build directory: ~s~%" (getcwd))
|
|
(format #t "configure flags: ~s~%" flags)
|
|
(zero? (apply system* "./configure" flags))))
|
|
(alist-cons-after
|
|
'configure 'clean-local-references
|
|
;; Try to keep build directory names from leaking into compiled code
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(let ((out (assoc-ref outputs "out")))
|
|
(substitute* (find-files "." "^petsc(conf|machineinfo).h$")
|
|
(((getcwd)) out))))
|
|
(alist-cons-after
|
|
'install 'clean-install
|
|
;; Try to keep installed files from leaking build directory names.
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(let ((out (assoc-ref outputs "out"))
|
|
(fortran (assoc-ref inputs "gfortran")))
|
|
(substitute* (map (lambda (file)
|
|
(string-append out "/" file))
|
|
'("conf/petscvariables"
|
|
"conf/PETScConfig.cmake"))
|
|
(((getcwd)) out))
|
|
;; Make compiler references point to the store
|
|
(substitute* (string-append out "/conf/petscvariables")
|
|
(("= g(cc|\\+\\+|fortran)" _ suffix)
|
|
(string-append "= " fortran "/bin/g" suffix)))
|
|
;; PETSc installs some build logs, which aren't necessary.
|
|
(for-each (lambda (file)
|
|
(let ((f (string-append out "/" file)))
|
|
(when (file-exists? f)
|
|
(delete-file f))))
|
|
'("conf/configure.log"
|
|
"conf/make.log"
|
|
"conf/test.log"
|
|
"conf/error.log"
|
|
"conf/RDict.db"
|
|
;; Once installed, should uninstall with Guix
|
|
"conf/uninstall.py"))))
|
|
%standard-phases)))))
|
|
(home-page "http://www.mcs.anl.gov/petsc")
|
|
(synopsis "Library to solve PDEs")
|
|
(description "PETSc, pronounced PET-see (the S is silent), is a suite of
|
|
data structures and routines for the scalable (parallel) solution of
|
|
scientific applications modeled by partial differential equations.")
|
|
(license (license:bsd-style
|
|
"http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
|
|
|
|
(define-public petsc-complex
|
|
(package (inherit petsc)
|
|
(location (source-properties->location (current-source-location)))
|
|
(name "petsc-complex")
|
|
(arguments
|
|
(substitute-keyword-arguments (package-arguments petsc)
|
|
((#:configure-flags cf)
|
|
`(cons "--with-scalar-type=complex" ,cf))))
|
|
(synopsis "Library to solve PDEs (with complex scalars)")))
|
|
|
|
(define-public petsc-openmpi
|
|
(package (inherit petsc)
|
|
(name "petsc-openmpi")
|
|
(inputs
|
|
`(("openmpi" ,openmpi)
|
|
,@(package-inputs petsc)))
|
|
(arguments
|
|
(substitute-keyword-arguments (package-arguments petsc)
|
|
((#:configure-flags cf)
|
|
``("--with-mpiexec=mpirun"
|
|
,(string-append "--with-mpi-dir="
|
|
(assoc-ref %build-inputs "openmpi"))
|
|
,@(delete "--with-mpi=0" ,cf)))))
|
|
(synopsis "Library to solve PDEs (with MPI support)")))
|
|
|
|
(define-public petsc-complex-openmpi
|
|
(package (inherit petsc-complex)
|
|
(name "petsc-complex-openmpi")
|
|
(inputs
|
|
`(("openmpi" ,openmpi)
|
|
,@(package-inputs petsc-complex)))
|
|
(arguments
|
|
(substitute-keyword-arguments (package-arguments petsc-complex)
|
|
((#:configure-flags cf)
|
|
``("--with-mpiexec=mpirun"
|
|
,(string-append "--with-mpi-dir="
|
|
(assoc-ref %build-inputs "openmpi"))
|
|
,@(delete "--with-mpi=0" ,cf)))))
|
|
(synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
|
|
|
|
(define-public superlu
|
|
(package
|
|
(name "superlu")
|
|
(version "4.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
|
|
"superlu_" version ".tar.gz"))
|
|
(sha256
|
|
(base32 "10b785s9s4x0m9q7ihap09275pq4km3k2hk76jiwdfdr5qr2168n"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("tcsh" ,tcsh)))
|
|
(inputs
|
|
`(("lapack" ,lapack)
|
|
("gfortran" ,gfortran-4.8)))
|
|
(arguments
|
|
`(#:parallel-build? #f
|
|
#:tests? #f ;tests are run as part of `make all`
|
|
#:phases
|
|
(alist-replace
|
|
'configure
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(call-with-output-file "make.inc"
|
|
(lambda (port)
|
|
(format port "
|
|
PLAT =
|
|
SuperLUroot = ~a
|
|
SUPERLULIB = ~a/lib/libsuperlu.a
|
|
TMGLIB = libtmglib.a
|
|
BLASDEF = -DUSE_VENDOR_BLAS
|
|
BLASLIB = -L~a/lib -lblas
|
|
LIBS = $(SUPERLULIB) $(BLASLIB)
|
|
ARCH = ar
|
|
ARCHFLAGS = cr
|
|
RANLIB = ranlib
|
|
CC = gcc
|
|
PIC = -fPIC
|
|
CFLAGS = -O3 -DPRNTlevel=0 $(PIC)
|
|
NOOPTS = -O0 $(PIC)
|
|
FORTRAN = gfortran
|
|
FFLAGS = -O2 $(PIC)
|
|
LOADER = $(CC)
|
|
CDEFS = -DAdd_"
|
|
(getcwd)
|
|
(assoc-ref outputs "out")
|
|
(assoc-ref inputs "lapack")))))
|
|
(alist-cons-before
|
|
'build 'create-install-directories
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(for-each
|
|
(lambda (dir)
|
|
(mkdir-p (string-append (assoc-ref outputs "out")
|
|
"/" dir)))
|
|
'("lib" "include")))
|
|
(alist-replace
|
|
'install
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
;; Library is placed in lib during the build phase. Copy over
|
|
;; headers to include.
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
(incdir (string-append out "/include")))
|
|
(for-each (lambda (file)
|
|
(let ((base (basename file)))
|
|
(format #t "installing `~a' to `~a'~%"
|
|
base incdir)
|
|
(copy-file file
|
|
(string-append incdir "/" base))))
|
|
(find-files "SRC" ".*\\.h$"))))
|
|
%standard-phases)))))
|
|
(home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
|
|
(synopsis "Supernodal direct solver for sparse linear systems")
|
|
(description
|
|
"SuperLU is a general purpose library for the direct solution of large,
|
|
sparse, nonsymmetric systems of linear equations on high performance machines.
|
|
The library is written in C and is callable from either C or Fortran. The
|
|
library routines perform an LU decomposition with partial pivoting and
|
|
triangular system solves through forward and back substitution. The library
|
|
also provides threshold-based ILU factorization preconditioners.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public superlu-dist
|
|
(package
|
|
(name "superlu-dist")
|
|
(version "3.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
|
|
"superlu_dist_" version ".tar.gz"))
|
|
(sha256
|
|
(base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj"))
|
|
(patches (list (search-patch "superlu-dist-scotchmetis.patch")))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("tcsh" ,tcsh)))
|
|
(inputs
|
|
`(("gfortran" ,gfortran-4.8)))
|
|
(propagated-inputs
|
|
`(("openmpi" ,openmpi) ;headers include MPI heades
|
|
("lapack" ,lapack) ;required to link with output library
|
|
("pt-scotch" ,pt-scotch))) ;same
|
|
(arguments
|
|
`(#:parallel-build? #f ;race conditions using ar
|
|
#:phases
|
|
(alist-replace
|
|
'configure
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(call-with-output-file "make.inc"
|
|
(lambda (port)
|
|
(format port "
|
|
PLAT =
|
|
DSuperLUroot = ~a
|
|
DSUPERLULIB = ~a/lib/libsuperlu_dist.a
|
|
BLASDEF = -DUSE_VENDOR_BLAS
|
|
BLASLIB = -L~a/lib -lblas
|
|
PARMETISLIB = -L~a/lib \
|
|
-lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
|
|
-lscotch -lscotcherr -lscotcherrexit
|
|
METISLIB = -L~:*~a/lib \
|
|
-lscotchmetis -lscotch -lscotcherr -lscotcherrexit
|
|
LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
|
|
ARCH = ar
|
|
ARCHFLAGS = cr
|
|
RANLIB = ranlib
|
|
CC = mpicc
|
|
PIC = -fPIC
|
|
CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC)
|
|
NOOPTS = -O0 -g $(PIC)
|
|
FORTRAN = mpifort
|
|
FFLAGS = -O2 -g $(PIC)
|
|
LOADER = $(CC)
|
|
CDEFS = -DAdd_"
|
|
(getcwd)
|
|
(assoc-ref outputs "out")
|
|
(assoc-ref inputs "lapack")
|
|
(assoc-ref inputs "pt-scotch")))))
|
|
(alist-cons-after
|
|
'unpack 'remove-broken-symlinks
|
|
(lambda _
|
|
(for-each delete-file
|
|
(find-files "MAKE_INC" "\\.#make\\..*")))
|
|
(alist-cons-before
|
|
'build 'create-install-directories
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(for-each
|
|
(lambda (dir)
|
|
(mkdir-p (string-append (assoc-ref outputs "out")
|
|
"/" dir)))
|
|
'("lib" "include")))
|
|
(alist-replace
|
|
'check
|
|
(lambda _
|
|
(with-directory-excursion "EXAMPLE"
|
|
(and
|
|
(zero? (system* "mpirun" "-n" "2"
|
|
"./pddrive" "-r" "1" "-c" "2" "g20.rua"))
|
|
(zero? (system* "mpirun" "-n" "2"
|
|
"./pzdrive" "-r" "1" "-c" "2" "cg20.cua")))))
|
|
(alist-replace
|
|
'install
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
;; Library is placed in lib during the build phase. Copy over
|
|
;; headers to include.
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
(incdir (string-append out "/include")))
|
|
(for-each (lambda (file)
|
|
(let ((base (basename file)))
|
|
(format #t "installing `~a' to `~a'~%"
|
|
base incdir)
|
|
(copy-file file
|
|
(string-append incdir "/" base))))
|
|
(find-files "SRC" ".*\\.h$"))))
|
|
%standard-phases)))))))
|
|
(home-page (package-home-page superlu))
|
|
(synopsis "Parallel supernodal direct solver")
|
|
(description
|
|
"SuperLU_DIST is a parallel extension to the serial SuperLU library.
|
|
It is targeted for distributed memory parallel machines. SuperLU_DIST is
|
|
implemented in ANSI C, and MPI for communications.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public scotch
|
|
(package
|
|
(name "scotch")
|
|
(version "6.0.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://gforge.inria.fr/frs/download.php/31831/"
|
|
"scotch_" version ".tar.gz"))
|
|
(sha256
|
|
(base32 "0yfqf9lk7chb3h42777x42x4adx0v3n0b41q0cdqrdmscp4iczp5"))
|
|
(patches (list (search-patch "scotch-test-threading.patch")))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("zlib" ,zlib)
|
|
("flex" ,flex)
|
|
("bison" ,bison)))
|
|
(arguments
|
|
`(#:phases
|
|
(alist-cons-after
|
|
'unpack 'chdir-to-src
|
|
(lambda _ (chdir "src"))
|
|
(alist-replace
|
|
'configure
|
|
(lambda _
|
|
(call-with-output-file "Makefile.inc"
|
|
(lambda (port)
|
|
(format port "
|
|
EXE =
|
|
LIB = .a
|
|
OBJ = .o
|
|
MAKE = make
|
|
AR = ar
|
|
ARFLAGS = -ruv
|
|
CCS = gcc
|
|
CCP = mpicc
|
|
CCD = gcc
|
|
CPPFLAGS =~{ -D~a~}
|
|
CFLAGS = -O2 -g $(CPPFLAGS)
|
|
LDFLAGS = -lz -lm -lrt -lpthread
|
|
CP = cp
|
|
LEX = flex -Pscotchyy -olex.yy.c
|
|
LN = ln
|
|
MKDIR = mkdir
|
|
MV = mv
|
|
RANLIB = ranlib
|
|
YACC = bison -pscotchyy -y -b y
|
|
"
|
|
'("COMMON_FILE_COMPRESS_GZ"
|
|
"COMMON_PTHREAD"
|
|
"COMMON_RANDOM_FIXED_SEED"
|
|
;; TODO: Define once our MPI supports
|
|
;; MPI_THREAD_MULTIPLE
|
|
;; "SCOTCH_PTHREAD"
|
|
;; "SCOTCH_PTHREAD_NUMBER=2"
|
|
"restrict=__restrict")))))
|
|
(alist-replace
|
|
'install
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let ((out (assoc-ref outputs "out")))
|
|
(mkdir out)
|
|
(zero? (system* "make"
|
|
(string-append "prefix=" out)
|
|
"install"))))
|
|
%standard-phases)))))
|
|
(home-page "http://www.labri.fr/perso/pelegrin/scotch/")
|
|
(synopsis "Programs and libraries for graph algorithms")
|
|
(description "SCOTCH is a set of programs and libraries which implement
|
|
the static mapping and sparse matrix reordering algorithms developed within
|
|
the SCOTCH project. Its purpose is to apply graph theory, with a divide and
|
|
conquer approach, to scientific computing problems such as graph and mesh
|
|
partitioning, static mapping, and sparse matrix ordering, in application
|
|
domains ranging from structural mechanics to operating systems or
|
|
bio-chemistry.")
|
|
;; See LICENSE_en.txt
|
|
(license license:cecill-c)))
|
|
|
|
(define-public pt-scotch
|
|
(package (inherit scotch)
|
|
(name "pt-scotch")
|
|
(propagated-inputs
|
|
`(("openmpi" ,openmpi))) ;Headers include MPI headers
|
|
(arguments
|
|
(substitute-keyword-arguments (package-arguments scotch)
|
|
((#:phases scotch-phases)
|
|
`(alist-replace
|
|
'build
|
|
;; TODO: Would like to add parallelism here
|
|
(lambda _
|
|
(and
|
|
(zero? (system* "make" "ptscotch"))
|
|
;; Install the serial metis compatibility library
|
|
(zero? (system* "make" "-C" "libscotchmetis" "install"))))
|
|
(alist-replace
|
|
'check
|
|
(lambda _ (zero? (system* "make" "ptcheck")))
|
|
(alist-replace
|
|
'install
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let ((out (assoc-ref outputs "out")))
|
|
(mkdir out)
|
|
(zero? (system* "make"
|
|
(string-append "prefix=" out)
|
|
"install"))))
|
|
,scotch-phases))))))
|
|
(synopsis "Programs and libraries for graph algorithms (with MPI)")))
|
|
|
|
(define-public gsegrafix
|
|
(package
|
|
(name "gsegrafix")
|
|
(version "1.0.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://gnu/" name "/" name "-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:configure-flags '("LDFLAGS=-lm")))
|
|
(inputs
|
|
`(("libgnomecanvas" ,libgnomecanvas)
|
|
("libbonoboui" ,libbonoboui)
|
|
("libgnomeui" ,libgnomeui)
|
|
("libgnomeprintui" ,libgnomeprintui)
|
|
("popt" ,popt)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(home-page "http://www.gnu.org/software/gsegrafix/")
|
|
(synopsis "GNOME application to create scientific and engineering plots")
|
|
(description "GSEGrafix is an application which produces high-quality graphical
|
|
plots for science and engineering. Plots are specified via simple ASCII
|
|
parameter files and data files and are presented in an anti-aliased GNOME
|
|
canvas. The program supports rectangular two-dimensional plots, histograms,
|
|
polar-axis plots and three-dimensional plots. Plots can be printed or saved
|
|
to BMP, JPEG or PNG image formats.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public maxima
|
|
(package
|
|
(name "maxima")
|
|
(version "5.34.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
|
|
version "-source/" name "-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1dw9vfzldpj7lv303xbw0wpyn6ra6i2yzwlrjbcx7j0jm5n43ji0"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("gcl" ,gcl)
|
|
("gnuplot" ,gnuplot) ;for plots
|
|
("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
|
|
(native-inputs
|
|
`(("texinfo" ,texinfo)
|
|
("perl" ,perl)))
|
|
(arguments
|
|
`(#:configure-flags
|
|
(list "--enable-gcl"
|
|
(string-append "--with-posix-shell="
|
|
(assoc-ref %build-inputs "bash")
|
|
"/bin/sh")
|
|
(string-append "--with-wish="
|
|
(assoc-ref %build-inputs "tk")
|
|
"/bin/wish"
|
|
(let ((v ,(package-version tk)))
|
|
(string-take v (string-index-right v #\.)))))
|
|
;; By default Maxima attempts to write temporary files to
|
|
;; '/tmp/nix-build-maxima-5.34.1', which doesn't exist. Work around
|
|
;; that.
|
|
#:make-flags (list "TMPDIR=/tmp")
|
|
#:phases (alist-cons-before
|
|
'check 'pre-check
|
|
(lambda _
|
|
(chmod "src/maxima" #o555))
|
|
;; Make sure the doc and emacs files are found in the
|
|
;; standard location. Also configure maxima to find gnuplot
|
|
;; without having it on the PATH.
|
|
(alist-cons-after
|
|
'install 'post-install
|
|
(lambda* (#:key outputs inputs #:allow-other-keys)
|
|
(let* ((gnuplot (assoc-ref inputs "gnuplot"))
|
|
(out (assoc-ref outputs "out"))
|
|
(datadir (string-append out "/share/maxima/" ,version)))
|
|
(with-directory-excursion out
|
|
(mkdir-p "share/emacs")
|
|
(mkdir-p "share/doc")
|
|
(symlink
|
|
(string-append datadir "/emacs/")
|
|
(string-append out "/share/emacs/site-lisp"))
|
|
(symlink
|
|
(string-append datadir "/doc/")
|
|
(string-append out "/share/doc/maxima"))
|
|
(with-atomic-file-replacement
|
|
(string-append datadir "/share/maxima-init.lisp")
|
|
(lambda (in out)
|
|
(format out "~a ~s~a~%"
|
|
"(setf $gnuplot_command "
|
|
(string-append gnuplot "/bin/gnuplot") ")")
|
|
(dump-port in out))))))
|
|
%standard-phases))))
|
|
(home-page "http://maxima.sourceforge.net")
|
|
(synopsis "Numeric and symbolic expression manipulation")
|
|
(description "Maxima is a system for the manipulation of symbolic and
|
|
numerical expressions. It yields high precision numeric results by using
|
|
exact fractions, arbitrary precision integers, and variable precision floating
|
|
point numbers")
|
|
;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
|
|
;; Others simply say "GNU General Public License" without stating a
|
|
;; version (which implicitly means gpl1+).
|
|
;; At least one file (src/maxima.asd) says "version 2."
|
|
;; GPLv2 only is therefore the smallest subset.
|
|
(license license:gpl2)))
|
|
|
|
(define-public atlas
|
|
(package
|
|
(name "atlas")
|
|
(version "3.10.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://sourceforge/math-atlas/atlas"
|
|
version ".tar.bz2"))
|
|
(sha256
|
|
(base32
|
|
"0bqh4bdnjdyww4mcpg6kn0x7338mfqbdgysn97dzrwwb26di7ars"))))
|
|
(build-system gnu-build-system)
|
|
(home-page "http://math-atlas.sourceforge.net/")
|
|
(inputs `(("gfortran" ,gfortran-4.8)
|
|
("lapack-tar" ,(package-source lapack))))
|
|
(outputs '("out" "doc"))
|
|
;; For the moment we drop support for MIPS at it fails to compile. See
|
|
;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
|
|
(supported-systems (delete "mips64el-linux" %supported-systems))
|
|
(arguments
|
|
`(#:parallel-build? #f
|
|
#:parallel-tests? #f
|
|
|
|
;; ATLAS tunes itself for the machine it is built on, as explained at
|
|
;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
|
|
;; For this reason, we want users to build it locally instead of using
|
|
;; substitutes.
|
|
#:substitutable? #f
|
|
|
|
#:modules ((srfi srfi-26)
|
|
(srfi srfi-1)
|
|
(guix build gnu-build-system)
|
|
(guix build utils))
|
|
#:configure-flags
|
|
`(;; Generate position independent code suitable for dynamic libraries
|
|
;; and use WALL timer to get more accurate timing.
|
|
"-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
|
|
;; Set word width.
|
|
"-b"
|
|
,,(if (string-match "64" (%current-system))
|
|
"64"
|
|
"32")
|
|
;; Disable parallel build as it gives errors: atlas_pthread.h is
|
|
;; needed to compile C files before it is generated.
|
|
"-Ss" "pmake" "make -j 1"
|
|
;; Probe is failing for MIPS. We therefore define the system
|
|
;; architecture explicitly by setting (-A) MACHINETYPE = 49
|
|
;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
|
|
,,@(if (string-prefix? "mips" (%current-system))
|
|
(list "-A" "49" "-V" "1")
|
|
(list))
|
|
;; Generate shared libraries.
|
|
"--shared"
|
|
;; Build a full LAPACK library.
|
|
,(string-append "--with-netlib-lapack-tarfile="
|
|
(assoc-ref %build-inputs "lapack-tar")))
|
|
#:phases
|
|
(alist-cons-after
|
|
'install 'install-doc
|
|
(lambda* (#:key outputs inputs #:allow-other-keys)
|
|
(let ((doc (string-append (assoc-ref outputs "doc")
|
|
"/share/doc/atlas")))
|
|
(mkdir-p doc)
|
|
(fold (lambda (file previous)
|
|
(and previous (zero? (system* "cp" file doc))))
|
|
#t (find-files "../ATLAS/doc" ".*"))))
|
|
(alist-cons-after
|
|
'check 'check-pt
|
|
(lambda _ (zero? (system* "make" "ptcheck")))
|
|
;; Fix files required to run configure.
|
|
(alist-cons-before
|
|
'configure 'fix-/bin/sh
|
|
(lambda _
|
|
;; Use `sh', not `/bin/sh'.
|
|
(substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
|
|
(("/bin/sh")
|
|
"sh")))
|
|
;; Fix /bin/sh in generated make files.
|
|
(alist-cons-after
|
|
'configure 'fix-/bin/sh-in-generated-files
|
|
(lambda _
|
|
(substitute* (find-files "." "^[Mm]ake\\.inc.*")
|
|
(("/bin/sh")
|
|
"sh")))
|
|
;; ATLAS configure program does not accepts the default flags
|
|
;; passed by the 'gnu-build-system'.
|
|
(alist-replace
|
|
'configure
|
|
(lambda* (#:key native-inputs inputs outputs
|
|
(configure-flags '())
|
|
#:allow-other-keys #:rest args)
|
|
(let* ((prefix (assoc-ref outputs "out"))
|
|
(bash (or (and=> (assoc-ref
|
|
(or native-inputs inputs) "bash")
|
|
(cut string-append <> "/bin/bash"))
|
|
"/bin/sh"))
|
|
(flags `(,(string-append "--prefix=" prefix)
|
|
,@configure-flags))
|
|
(abs-srcdir (getcwd))
|
|
(srcdir (string-append "../" (basename abs-srcdir))))
|
|
(format #t "source directory: ~s (relative from build: ~s)~%"
|
|
abs-srcdir srcdir)
|
|
(mkdir "../build")
|
|
(chdir "../build")
|
|
(format #t "build directory: ~s~%" (getcwd))
|
|
(format #t "configure flags: ~s~%" flags)
|
|
(zero? (apply system* bash
|
|
(string-append srcdir "/configure")
|
|
flags))))
|
|
%standard-phases)))))))
|
|
(synopsis "Automatically Tuned Linear Algebra Software")
|
|
(description
|
|
"ATLAS is an automatically tuned linear algebra software library
|
|
providing C and Fortran77 interfaces to a portably efficient BLAS
|
|
implementation, as well as a few routines from LAPACK.
|
|
|
|
Optimization occurs at build time. For this reason, the library is built on
|
|
the machine where it is installed, without resorting to pre-built substitutes.
|
|
|
|
Before building the library, CPU throttling should be disabled. This can be
|
|
done in the BIOS, or, on GNU/Linux, with the following commands:
|
|
|
|
cpufreq-selector -g performance -c 0
|
|
...
|
|
cpufreq-selector -g performance -c N-1
|
|
|
|
where N is the number of cores of your CPU. Failure to do so will result in a
|
|
library with poor performance.")
|
|
(license license:bsd-3)))
|