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5321 lines
213 KiB
5321 lines
213 KiB
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2013, 2014, 2015, 2016, 2019, 2020 Andreas Enge <andreas@enge.fr>
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;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
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;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
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;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Eric Bavier <bavier@posteo.net>
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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, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
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;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
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;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
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;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
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;;; Copyright © 2016, 2018, 2020 Kei Kebreau <kkebreau@posteo.net>
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;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
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;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
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;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
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;;; Copyright © 2017, 2018, 2019, 2020 Paul Garlick <pgarlick@tourbillion-technology.com>
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;;; Copyright © 2017 ng0 <ng0@n0.is>
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;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
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;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
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;;; Copyright © 2017, 2019 Arun Isaac <arunisaac@systemreboot.net>
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;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
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;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
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;;; Copyright © 2018, 2019 Jan Nieuwenhuizen <janneke@gnu.org>
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;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
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;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
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;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
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;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
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;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
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;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
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;;; Copyright © 2018 Amin Bandali <mab@gnu.org>
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;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
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;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
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;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net>
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;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
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;;; Copyright © 2020 Felix Gruber <felgru@posteo.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 (ice-9 match)
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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)
|
|
#:use-module (guix download)
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|
#:use-module (guix git-download)
|
|
#:use-module (guix utils)
|
|
#:use-module ((guix build utils) #:select (alist-replace))
|
|
#:use-module (guix build-system cmake)
|
|
#:use-module (guix build-system gnu)
|
|
#:use-module (guix build-system python)
|
|
#:use-module (guix build-system ruby)
|
|
#:use-module (gnu packages algebra)
|
|
#:use-module (gnu packages audio)
|
|
#:use-module (gnu packages autotools)
|
|
#:use-module (gnu packages base)
|
|
#:use-module (gnu packages bison)
|
|
#:use-module (gnu packages boost)
|
|
#:use-module (gnu packages check)
|
|
#:use-module (gnu packages cmake)
|
|
#:use-module (gnu packages compression)
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|
#:use-module (gnu packages curl)
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|
#:use-module (gnu packages cyrus-sasl)
|
|
#:use-module (gnu packages dbm)
|
|
#:use-module (gnu packages documentation)
|
|
#:use-module (gnu packages elf)
|
|
#:use-module (gnu packages flex)
|
|
#:use-module (gnu packages fltk)
|
|
#:use-module (gnu packages fontutils)
|
|
#:use-module (gnu packages gettext)
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|
#:use-module (gnu packages gcc)
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|
#:use-module (gnu packages gd)
|
|
#:use-module (gnu packages ghostscript)
|
|
#:use-module (gnu packages graphviz)
|
|
#:use-module (gnu packages gtk)
|
|
#:use-module (gnu packages image)
|
|
#:use-module (gnu packages java)
|
|
#:use-module (gnu packages less)
|
|
#:use-module (gnu packages lisp)
|
|
#:use-module (gnu packages linux)
|
|
#:use-module (gnu packages logging)
|
|
#:use-module (gnu packages lua)
|
|
#:use-module (gnu packages gnome)
|
|
#:use-module (gnu packages guile)
|
|
#:use-module (gnu packages xorg)
|
|
#:use-module (gnu packages gl)
|
|
#:use-module (gnu packages imagemagick)
|
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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 netpbm)
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#:use-module (gnu packages onc-rpc)
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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 pulseaudio)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-web)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages qt)
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#:use-module (gnu packages readline)
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#:use-module (gnu packages ruby)
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#:use-module (gnu packages tbb)
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#:use-module (gnu packages scheme)
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#:use-module (gnu packages shells)
|
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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 tex)
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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 wxwidgets)
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#:use-module (gnu packages xml)
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#:use-module (srfi srfi-1))
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|
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(define-public aris
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(package
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(name "aris")
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(version "2.2")
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(source (origin
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(method url-fetch)
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(uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
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(sha256 (base32
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"1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
|
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(build-system gnu-build-system)
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(inputs `(("gtk+" ,gtk+)
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("libxml2" ,libxml2)))
|
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(native-inputs `(("pkg-config" ,pkg-config)))
|
|
(synopsis "Natural deduction first-order logic interface")
|
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(description "Aris is a program for performing logical proofs. It supports
|
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propositional and predicate logic, as well as Boolean algebra and
|
|
arithmetical logic. In addition to its predefined inference and equivalence
|
|
rules, Aris also supports references to older proofs. Its use of standard
|
|
logical symbols and its natural deduction interface make it easy to use for
|
|
beginners.")
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(license license:gpl3+)
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(home-page "https://www.gnu.org/software/aris/")))
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|
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(define-public c-graph
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(package
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(name "c-graph")
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(version "2.0.1")
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(source (origin
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(method url-fetch)
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(uri (string-append "mirror://gnu/c-graph/c-graph-" version
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|
".tar.gz"))
|
|
(sha256 (base32
|
|
"092412jzxy6wdvpk96pfj499hpmaww8xllavbvlqspfpr7ips9id"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("fortran" ,gfortran)))
|
|
(synopsis "Visualizing and demonstrating convolution")
|
|
(description
|
|
"GNU C-Graph is a tool for demonstrating the theory of convolution.
|
|
Thus, it can serve as an excellent aid to students of signal and systems
|
|
theory in visualizing the convolution process. Rather than forcing the
|
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student to write code, the program offers an intuitive interface with
|
|
interactive dialogs to guide them.")
|
|
(license license:gpl3+)
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(home-page "https://www.gnu.org/software/c-graph/")))
|
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|
|
(define-public coda
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|
(package
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(name "coda")
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(version "2.19")
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|
(source
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|
(origin
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|
(method url-fetch)
|
|
(uri (string-append "https://github.com/stcorp/coda/releases/download/"
|
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version "/coda-" version ".tar.gz"))
|
|
(sha256
|
|
(base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245"))
|
|
(patches (search-patches "coda-use-system-libs.patch"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
;; Make sure we don't use the bundled software.
|
|
'(begin
|
|
(for-each (lambda (d)
|
|
(delete-file-recursively (string-append "libcoda/" d)))
|
|
'("zlib" "pcre" "expat"))
|
|
#t))))
|
|
(native-inputs
|
|
`(("fortran" ,gfortran)
|
|
("python" ,python)
|
|
("python-numpy" ,python-numpy)))
|
|
(inputs
|
|
`(("zlib" ,zlib)
|
|
("pcre" ,pcre)
|
|
("expat" ,expat)
|
|
("hdf4" ,hdf4-alt)
|
|
("hdf5" ,hdf5)))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
'(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
|
|
"LIBS= -lz -lpcre -lexpat")))
|
|
(synopsis "A common interface to various earth observation data formats")
|
|
(description
|
|
"The Common Data Access toolbox (CODA) provides a set of interfaces for
|
|
reading remote sensing data from earth observation data files. It consists of
|
|
command line applications and interfaces to the C, Fortran, Python, and Java
|
|
programming languages.")
|
|
(home-page "https://stcorp.nl/coda")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public qhull
|
|
(package
|
|
(name "qhull")
|
|
(version "2015.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://www.qhull.org/download/qhull-"
|
|
(car (string-split version #\.))
|
|
"-src-7.2.0.tgz"))
|
|
(sha256
|
|
(base32
|
|
"0dm4b2xr3asy6w74khq2zg4gf26zsy3qf9sq7pf7lmrvbj911c3q"))))
|
|
(build-system cmake-build-system)
|
|
(synopsis "Calculate convex hulls and related structures")
|
|
(description
|
|
"@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
|
|
diagram, halfspace intersection about a point, furthest-site Delaunay
|
|
triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d,
|
|
3-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull
|
|
algorithm for computing the convex hull. It handles roundoff errors from
|
|
floating point arithmetic. It computes volumes, surface areas, and
|
|
approximations to the convex hull.
|
|
|
|
@code{Qhull} does not support triangulation of non-convex surfaces, mesh
|
|
generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
|
|
shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
|
|
triangulations.")
|
|
(home-page "http://qhull.org")
|
|
(license (license:non-copyleft "file://COPYING.txt"
|
|
"See COPYING in the distribution."))))
|
|
|
|
(define-public python-cvxopt
|
|
(package
|
|
(name "python-cvxopt")
|
|
(version "1.2.3")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/cvxopt/cvxopt.git")
|
|
(commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"1kiy2m62xgs2d5id6dnnwy4vap85cd70p7pgkb9nh23qf9xnak7b"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'find-libraries
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(setenv "CVXOPT_BLAS_LIB" "openblas")
|
|
(setenv "CVXOPT_BUILD_FFTW" "1")
|
|
(setenv "CVXOPT_BUILD_GLPK" "1")
|
|
(setenv "CVXOPT_BUILD_GSL" "1")
|
|
#t)))))
|
|
(inputs
|
|
`(("fftw" ,fftw)
|
|
("glpk" ,glpk)
|
|
("gsl" ,gsl)
|
|
("lapack" ,lapack)
|
|
("openblas" ,openblas)
|
|
("suitesparse" ,suitesparse)))
|
|
(home-page "https://www.cvxopt.org")
|
|
(synopsis "Python library for convex optimization")
|
|
(description
|
|
"CVXOPT is a package for convex optimization based on the Python
|
|
programming language. Its main purpose is to make the development of software
|
|
for convex optimization applications straightforward by building on Python’s
|
|
extensive standard library and on the strengths of Python as a high-level
|
|
programming language.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public python2-cvxopt
|
|
(package-with-python2 python-cvxopt))
|
|
|
|
(define-public units
|
|
(package
|
|
(name "units")
|
|
(version "2.19")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://gnu/units/units-" version
|
|
".tar.gz"))
|
|
(sha256 (base32
|
|
"0mk562g7dnidjgfgvkxxpvlba66fh1ykmfd9ylzvcln1vxmi6qj2"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("readline" ,readline)
|
|
("python" ,python-wrapper) ;for 'units_cur' script
|
|
("python-requests" ,python-requests)))
|
|
(arguments
|
|
`(#:phases (modify-phases %standard-phases
|
|
(add-after 'install 'wrap-units_cur
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
(bin (string-append out "/bin")))
|
|
(wrap-program (string-append bin "/units_cur")
|
|
`("PYTHONPATH" ":" prefix
|
|
,(search-path-as-string->list (getenv "PYTHONPATH"))))
|
|
#t))))))
|
|
(synopsis "Conversion between thousands of scales")
|
|
(description
|
|
"GNU Units converts numeric quantities between units of measure. It
|
|
can handle scale changes through adaptive usage of standard scale
|
|
prefixes (micro-, kilo-, etc.). It can also handle nonlinear
|
|
conversions such as Fahrenheit to Celsius. Its interpreter is powerful
|
|
enough to be used effectively as a scientific calculator.")
|
|
(license license:gpl3+)
|
|
(home-page "https://www.gnu.org/software/units/")))
|
|
|
|
(define-public double-conversion
|
|
(package
|
|
(name "double-conversion")
|
|
(version "3.1.5")
|
|
(home-page "https://github.com/google/double-conversion")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference (url home-page)
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"0csy4pjw1p8rp6g5qxi2h0ychhhp1fldv7gb761627fs2mclw9gv"))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
'(#:test-target "test"
|
|
#:configure-flags '("-DBUILD_SHARED_LIBS=ON"
|
|
"-DBUILD_TESTING=ON")))
|
|
(synopsis "Conversion routines for IEEE doubles")
|
|
(description
|
|
"The double-conversion library provides binary-decimal and decimal-binary
|
|
routines for IEEE doubles. The library consists of efficient conversion
|
|
routines that have been extracted from the V8 JavaScript engine.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public dionysus
|
|
(package
|
|
(name "dionysus")
|
|
(version "1.4.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://gnu/dionysus/dionysus-" version
|
|
".tar.xz"))
|
|
(sha256
|
|
(base32
|
|
"194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
|
|
(build-system gnu-build-system)
|
|
(inputs `(("tcl" ,tcl))) ;for 'tclsh'
|
|
(synopsis "Local search for universal constants and scientific values")
|
|
(description
|
|
"GNU Dionysus is a convenient system for quickly retrieving the values of
|
|
mathematical constants used in science and engineering. Values can be
|
|
searched using a simple command-line tool, choosing from three databases:
|
|
universal constants, atomic numbers, and constants related to
|
|
semiconductors.")
|
|
(license license:gpl3+)
|
|
(home-page "https://www.gnu.org/software/dionysus/")))
|
|
|
|
(define-public gsl
|
|
(package
|
|
(name "gsl")
|
|
(version "2.5")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://gnu/gsl/gsl-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
|
|
(patches (search-patches "gsl-test-i686.patch"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(;; Currently there are numerous tests that fail on "exotic"
|
|
;; architectures such as aarch64 and ppc64le.
|
|
,@(if (string-prefix? "aarch64-linux"
|
|
(or (%current-target-system) (%current-system)))
|
|
'(#:tests? #f)
|
|
'())))
|
|
(home-page "https://www.gnu.org/software/gsl/")
|
|
(synopsis "Numerical library for C and C++")
|
|
(description
|
|
"The GNU Scientific Library is a library for numerical analysis in C
|
|
and C++. It includes a wide range of mathematical routines, with over 1000
|
|
functions in total. Subject areas covered by the library include:
|
|
differential equations, linear algebra, Fast Fourier Transforms and random
|
|
numbers.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public glpk
|
|
(package
|
|
(name "glpk")
|
|
(version "4.65")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://gnu/glpk/glpk-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("gmp" ,gmp)))
|
|
(arguments
|
|
`(#:configure-flags '("--with-gmp")))
|
|
(home-page "https://www.gnu.org/software/glpk/")
|
|
(synopsis "GNU Linear Programming Kit, supporting the MathProg language")
|
|
(description
|
|
"GLPK is a C library for solving large-scale linear programming (LP),
|
|
mixed integer programming (MIP), and other related problems. It supports the
|
|
GNU MathProg modeling language, a subset of the AMPL language, and features a
|
|
translator for the language. In addition to the C library, a stand-alone
|
|
LP/MIP solver is included in the package.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public 4ti2
|
|
(package
|
|
(name "4ti2")
|
|
(version "1.6.9")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://github.com/4ti2/4ti2/releases/download/"
|
|
"Release_"
|
|
(string-map (lambda (c) (if (char=? c #\.) #\_ c))
|
|
version)
|
|
"/4ti2-" version ".tar.gz"))
|
|
(sha256
|
|
(base32 "0rj92x6p9m3la5gasjbj7sa569im527ffmka5y2sv1amgd3fflrh"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("which" ,(@ (gnu packages base) which)))) ; for the tests
|
|
(inputs
|
|
`(("glpk" ,glpk)
|
|
("gmp" ,gmp)))
|
|
(home-page "http://www.4ti2.de/")
|
|
(synopsis "Mathematical tool suite for problems on linear spaces")
|
|
(description
|
|
"4ti2 implements algorithms for solving algebraic, geometric and
|
|
combinatorial problems on linear spaces. Among others, it solves systems
|
|
of linear equations, computes extreme rays of polyhedral cones, solves
|
|
integer programming problems and computes Markov bases for statistics.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public cddlib
|
|
(package
|
|
(name "cddlib")
|
|
(version "0.94i")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
|
|
(string-delete #\. version) ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("gmp" ,gmp)))
|
|
(home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
|
|
(synopsis "Library for convex hulls and extreme rays of polyhedra")
|
|
(description
|
|
"The C-library cddlib implements the Double Description Method of
|
|
Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
|
|
rays of a general convex polyhedron given by a system of linear inequalities
|
|
in arbitrary dimension. It can also be used for the converse operation of
|
|
computing convex hulls.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public lrslib
|
|
(package
|
|
(name "lrslib")
|
|
(version "7.0a")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/"
|
|
"lrslib-0"
|
|
(string-delete #\. version) ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"034fa45r9hwx6ljmgpxk2872q34nklkalpdkc6s9hqw57rivi36k"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("gmp" ,gmp)))
|
|
(arguments
|
|
`(#:tests? #f ; no check phase
|
|
#:make-flags `("CC=gcc"
|
|
,(string-append "prefix=" (assoc-ref %outputs "out"))
|
|
"all-shared")
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'configure
|
|
(lambda _
|
|
(substitute* "makefile"
|
|
(("-L \\.") "-L . -Wl,-rpath='$$ORIGIN/../lib'"))
|
|
#t)))))
|
|
(home-page "http://cgm.cs.mcgill.ca/~avis/C/lrs.html")
|
|
(synopsis "Convex hulls of polyhedra with exact arithmetic")
|
|
(description
|
|
"The C code of lrslib implements the reverse search algorithm for
|
|
vertex enumeration and convex hull problems. Its input file format is
|
|
compatible with cddlib. All computations are done exactly in either
|
|
multiple precision or fixed integer arithmetic. Output is not stored
|
|
in memory, so even problems with very large output sizes can sometimes
|
|
be solved.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public vinci
|
|
(package
|
|
(name "vinci")
|
|
(version "1.0.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://www.math.u-bordeaux.fr/~aenge/software/"
|
|
"vinci/vinci-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1aq0qc1y27iw9grhgnyji3290wwfznsrk3sg6ynqpxwjdda53h4m"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("lrslib" ,lrslib)))
|
|
(arguments
|
|
`(#:tests? #f ; no check phase
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'configure
|
|
;; register the lrs location in the config file
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(let* ((lrs (assoc-ref inputs "lrslib"))
|
|
(lrsexec (string-append lrs "/bin/lrs")))
|
|
(substitute* "vinci.h"
|
|
(("#define LRS_EXEC \"lrs\"")
|
|
(string-append "#define LRS_EXEC \"" lrsexec "\""))))
|
|
#t))
|
|
(replace 'install
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
(bin (string-append out "/bin")))
|
|
(install-file "vinci" bin))
|
|
#t)))))
|
|
(home-page
|
|
"https://www.math.u-bordeaux.fr/~aenge/?category=software&page=vinci")
|
|
(synopsis "Volume computation for polytopes")
|
|
(description
|
|
"Vinci implements a number of volume computation algorithms for convex
|
|
polytopes in arbitrary dimension. The polytopes can be given by their
|
|
V-representation (as the convex hull of a finite number of vertices), by
|
|
their H-representation (as the bounded intersection of a finite number of
|
|
halfspaces) or by their double description with both representations.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public arpack-ng
|
|
(package
|
|
(name "arpack-ng")
|
|
(version "3.6.3")
|
|
(home-page "https://github.com/opencollab/arpack-ng")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference (url home-page) (commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("autoconf" ,autoconf)
|
|
("automake" ,automake)
|
|
("libtool" ,libtool)))
|
|
(inputs
|
|
`(("lapack" ,lapack)
|
|
("fortran" ,gfortran)))
|
|
(synopsis "Fortran subroutines for solving eigenvalue problems")
|
|
(description
|
|
"ARPACK-NG is a collection of Fortran77 subroutines designed to solve
|
|
large scale eigenvalue problems.")
|
|
(license (license:non-copyleft "file://COPYING"
|
|
"See COPYING in the distribution."))))
|
|
|
|
(define-public arpack-ng-3.3.0
|
|
(package
|
|
(inherit arpack-ng)
|
|
(version "3.3.0")
|
|
(name (package-name arpack-ng))
|
|
(home-page (package-home-page arpack-ng))
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append home-page "/archive/" version ".tar.gz"))
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
|
|
|
|
(define-public arpack-ng-openmpi
|
|
(package (inherit arpack-ng)
|
|
(name "arpack-ng-openmpi")
|
|
(inputs
|
|
`(("mpi" ,openmpi)
|
|
,@(package-inputs arpack-ng)))
|
|
(arguments
|
|
(substitute-keyword-arguments (package-arguments arpack-ng)
|
|
((#:configure-flags _ '())
|
|
''("--enable-mpi"))
|
|
((#:phases phases '%standard-phases)
|
|
`(modify-phases ,phases
|
|
(add-before 'check 'mpi-setup
|
|
,%openmpi-setup)))))
|
|
(synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
|
|
|
|
(define-public lapack
|
|
(package
|
|
(name "lapack")
|
|
(version "3.9.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://www.netlib.org/lapack/lapack-"
|
|
version ".tgz"))
|
|
(sha256
|
|
(base32
|
|
"1155qixp26c12yrxc76z9mlfw2h3xxymxxv5znpgzh5gaykpndgj"))))
|
|
(build-system cmake-build-system)
|
|
(home-page "http://www.netlib.org/lapack/")
|
|
(inputs `(("fortran" ,gfortran)
|
|
("python" ,python-wrapper)))
|
|
(arguments
|
|
`(#:configure-flags (list
|
|
"-DBUILD_SHARED_LIBS:BOOL=YES"
|
|
"-DLAPACKE=ON"
|
|
;; Build the 'LAPACKE_clatms' functions.
|
|
"-DLAPACKE_WITH_TMG=ON"
|
|
"-DBUILD_TESTING=ON")))
|
|
(synopsis "Library for numerical linear algebra")
|
|
(description
|
|
"LAPACK is a Fortran 90 library for solving the most commonly occurring
|
|
problems in numerical linear algebra.")
|
|
(license (license:non-copyleft "file://LICENSE"
|
|
"See LICENSE in the distribution."))))
|
|
|
|
(define-public scalapack
|
|
(package
|
|
(name "scalapack")
|
|
(version "2.0.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://www.netlib.org/scalapack/scalapack-"
|
|
version ".tgz"))
|
|
(sha256
|
|
(base32
|
|
"0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))
|
|
(patches (search-patches "scalapack-blacs-mpi-deprecations.patch"))))
|
|
(build-system cmake-build-system)
|
|
(inputs
|
|
`(("mpi" ,openmpi)
|
|
("fortran" ,gfortran)
|
|
("lapack" ,lapack))) ;for testing only
|
|
(arguments
|
|
`(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
|
|
#:phases (modify-phases %standard-phases
|
|
(add-before 'check 'mpi-setup
|
|
,%openmpi-setup))))
|
|
(home-page "http://www.netlib.org/scalapack/")
|
|
(synopsis "Library for scalable numerical linear algebra")
|
|
(description
|
|
"ScaLAPACK is a Fortran 90 library of high-performance linear algebra
|
|
routines on parallel distributed memory machines. ScaLAPACK solves dense and
|
|
banded linear systems, least squares problems, eigenvalue problems, and
|
|
singular value problems.")
|
|
(license (license:non-copyleft "file://LICENSE"
|
|
"See LICENSE in the distribution."))))
|
|
|
|
(define-public gnuplot
|
|
(package
|
|
(name "gnuplot")
|
|
(version "5.2.7")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
|
|
version "/gnuplot-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32 "1vglp4la40f5dpj0zdj63zprrkyjgzy068p35bz5dqxjyczm1zlp"))))
|
|
(build-system gnu-build-system)
|
|
(inputs `(("readline" ,readline)
|
|
("cairo" ,cairo)
|
|
("pango" ,pango)
|
|
("gd" ,gd)
|
|
("lua" ,lua)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)
|
|
("texlive" ,texlive-tiny)))
|
|
(arguments `(#:configure-flags (list (string-append
|
|
"--with-texdir=" %output
|
|
"/texmf-local/tex/latex/gnuplot"))))
|
|
(home-page "http://www.gnuplot.info")
|
|
(synopsis "Command-line driven graphing utility")
|
|
(description "Gnuplot is a portable command-line driven graphing
|
|
utility. It was originally created to allow scientists and students to
|
|
visualize mathematical functions and data interactively, but has grown to
|
|
support many non-interactive uses such as web scripting. It is also used as a
|
|
plotting engine by third-party applications like Octave.")
|
|
;; X11 Style with the additional restriction that derived works may only be
|
|
;; distributed as patches to the original.
|
|
(license (license:fsf-free
|
|
"http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
|
|
|
|
(define-public gctp
|
|
(package
|
|
(name "gctp")
|
|
(version "2.0.0")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/OkoSanto/GCTP.git")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
|
|
(native-inputs
|
|
`(("fortran" ,gfortran)))
|
|
(build-system gnu-build-system)
|
|
(synopsis "General Cartographic Transformation Package (GCTP)")
|
|
(description
|
|
"The General Cartographic Transformation Package (GCTP) is a system of
|
|
software routines designed to permit the transformation of coordinate pairs
|
|
from one map projection to another. The GCTP is the standard computer
|
|
software used by the National Mapping Division for map projection
|
|
computations.")
|
|
(home-page "https://github.com/OkoSanto/GCTP")
|
|
(license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
|
|
|
|
(define-public hdf4
|
|
(package
|
|
(name "hdf4")
|
|
(version "4.2.14")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
|
|
version "/src/hdf-" version ".tar.bz2"))
|
|
(sha256
|
|
(base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l"))
|
|
(patches (search-patches "hdf4-architectures.patch"
|
|
"hdf4-reproducibility.patch"
|
|
"hdf4-shared-fortran.patch"
|
|
"hdf4-tirpc.patch"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)
|
|
("bison" ,bison)
|
|
("flex" ,flex)))
|
|
(inputs
|
|
`(("zlib" ,zlib)
|
|
("libjpeg" ,libjpeg)
|
|
("libtirpc" ,libtirpc)))
|
|
(arguments
|
|
`(#:parallel-tests? #f
|
|
#:configure-flags (list "--enable-shared"
|
|
(string-append "CPPFLAGS=-I"
|
|
(assoc-ref %build-inputs "libtirpc")
|
|
"/include/tirpc"))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
;; This is inspired by two of Debian's patches.
|
|
(add-before 'configure 'add-more-aarch64-support
|
|
(lambda _
|
|
(substitute* '("mfhdf/ncgen/ncgen.l"
|
|
"mfhdf/ncgen/ncgenyy.c"
|
|
"mfhdf/libsrc/netcdf.h.in")
|
|
(("AIX5L64") "__aarch64__"))
|
|
#t))
|
|
(add-before 'configure 'patchbuild
|
|
(lambda _
|
|
(substitute*
|
|
'("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
|
|
(("/bin/rm") "rm")
|
|
(("/bin/mkdir") "mkdir"))
|
|
(substitute* (find-files "." "^Makefile\\.in$")
|
|
(("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
|
|
-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
|
|
(("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
|
|
-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
|
|
-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
|
|
#t))
|
|
(add-after 'configure 'patch-settings
|
|
(lambda _
|
|
;; libhdf4.settings contains the full path of the
|
|
;; compilers used, and its contents are included in
|
|
;; .so-files. We truncate the hashes to avoid
|
|
;; unnecessary store references to those compilers:
|
|
(substitute* "libhdf4.settings"
|
|
(("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
|
|
(string-append prefix (string-take hash 10) "...")))
|
|
#t))
|
|
)))
|
|
(home-page "https://www.hdfgroup.org/products/hdf4/")
|
|
(synopsis
|
|
"Library and multi-object file format for storing and managing data")
|
|
(description "HDF4 is a library and multi-object file format for storing
|
|
and managing data between machines. HDF4 is an older hierarchical data format,
|
|
incompatible with HDF5.")
|
|
(license
|
|
(license:non-copyleft
|
|
"https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
|
|
|
|
(define-public hdf4-alt
|
|
(package
|
|
(inherit hdf4)
|
|
(name "hdf4-alt")
|
|
(arguments
|
|
(substitute-keyword-arguments (package-arguments hdf4)
|
|
((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
|
|
(synopsis
|
|
"HDF4 without netCDF API, can be combined with the regular netCDF library")))
|
|
|
|
(define-public hdf5
|
|
(package
|
|
(name "hdf5")
|
|
(version "1.8.21")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
|
|
"hdf5-" (version-major+minor version)
|
|
"/hdf5-" version "/src/hdf5-"
|
|
version ".tar.bz2")
|
|
(string-append "https://support.hdfgroup.org/ftp/HDF5/"
|
|
"current"
|
|
(match (string-split version #\.)
|
|
((major minor _ ...)
|
|
(string-append major minor)))
|
|
"/src/hdf5-" version ".tar.bz2")))
|
|
(sha256
|
|
(base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5"))
|
|
(patches (search-patches "hdf5-config-date.patch"
|
|
"hdf5-1.8-mpi-deprecations.patch"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("zlib" ,zlib)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)
|
|
("perl" ,perl))) ;part of the test machinery needs Perl
|
|
(outputs '("out" ; core library
|
|
"fortran")) ; fortran interface
|
|
(arguments
|
|
`(;; Some of the users, notably Flann, need the C++ interface.
|
|
#:configure-flags '("--enable-cxx"
|
|
"--enable-fortran"
|
|
"--enable-fortran2003"
|
|
|
|
;; Build a thread-safe library. Unfortunately,
|
|
;; 'configure' invites you to either turn off C++,
|
|
;; Fortran, and the high-level interface (HL), or
|
|
;; to pass '--enable-unsupported'. Debian
|
|
;; packagers chose to pass '--enable-unsupported'
|
|
;; and we follow their lead here.
|
|
"--enable-threadsafe"
|
|
"--with-pthread"
|
|
"--enable-unsupported")
|
|
;; Use -fPIC to allow the R bindings to link with the static libraries
|
|
#:make-flags (list "CFLAGS=-fPIC"
|
|
"CXXFLAGS=-fPIC")
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-before 'configure 'patch-configure
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(substitute* "configure"
|
|
(("/bin/mv") "mv"))
|
|
(substitute* "fortran/src/Makefile.in"
|
|
(("libhdf5_fortran_la_LDFLAGS =")
|
|
(string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
|
|
(assoc-ref outputs "fortran") "/lib")))
|
|
(substitute* "hl/fortran/src/Makefile.in"
|
|
(("libhdf5hl_fortran_la_LDFLAGS =")
|
|
(string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
|
|
(assoc-ref outputs "fortran") "/lib")))
|
|
#t))
|
|
(add-after 'configure 'patch-settings
|
|
(lambda _
|
|
;; libhdf5.settings contains the full path of the
|
|
;; compilers used, and its contents are included in
|
|
;; libhdf5.so. We truncate the hashes to avoid
|
|
;; unnecessary store references to those compilers:
|
|
(substitute* "src/libhdf5.settings"
|
|
(("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
|
|
(string-append prefix (string-take hash 10) "..."))
|
|
;; Don't record the build-time kernel version to make the
|
|
;; settings file reproducible.
|
|
(("Uname information:.*")
|
|
"Uname information: Linux\n"))
|
|
#t))
|
|
(add-after 'install 'patch-references
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(let ((bin (string-append (assoc-ref outputs "out") "/bin"))
|
|
(zlib (assoc-ref inputs "zlib")))
|
|
(substitute* (find-files bin "h5p?cc")
|
|
(("-lz" lib)
|
|
(string-append "-L" zlib "/lib " lib)))
|
|
#t)))
|
|
(add-after 'install 'split
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
;; Move all fortran-related files
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
(bin (string-append out "/bin"))
|
|
(lib (string-append out "/lib"))
|
|
(inc (string-append out "/include"))
|
|
(ex (string-append out "/share/hdf5_examples/fortran"))
|
|
(fort (assoc-ref outputs "fortran"))
|
|
(fbin (string-append fort "/bin"))
|
|
(flib (string-append fort "/lib"))
|
|
(finc (string-append fort "/include"))
|
|
(fex (string-append fort "/share/hdf5_examples/fortran")))
|
|
(mkdir-p fbin)
|
|
(mkdir-p flib)
|
|
(mkdir-p finc)
|
|
(mkdir-p fex)
|
|
;; Note: When built with --enable-parallel, the 'h5fc' file
|
|
;; doesn't exist, hence this condition.
|
|
(when (file-exists? (string-append bin "/h5fc"))
|
|
(rename-file (string-append bin "/h5fc")
|
|
(string-append fbin "/h5fc")))
|
|
(for-each (lambda (file)
|
|
(rename-file file
|
|
(string-append flib "/" (basename file))))
|
|
(find-files lib ".*fortran.*"))
|
|
(for-each (lambda (file)
|
|
(rename-file file
|
|
(string-append finc "/" (basename file))))
|
|
(find-files inc ".*mod"))
|
|
(for-each (lambda (file)
|
|
(rename-file file
|
|
(string-append fex "/" (basename file))))
|
|
(find-files ex ".*"))
|
|
(delete-file-recursively ex))
|
|
#t)))))
|
|
(home-page "https://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
|
|
"https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
|
|
|
|
(define-public hdf5-1.10
|
|
(package (inherit hdf5)
|
|
(version "1.10.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
|
|
"hdf5-" (version-major+minor version)
|
|
"/hdf5-" version "/src/hdf5-"
|
|
version ".tar.bz2")
|
|
(string-append "https://support.hdfgroup.org/ftp/HDF5/"
|
|
"current"
|
|
(apply string-append
|
|
(take (string-split version #\.) 2))
|
|
"/src/hdf5-" version ".tar.bz2")))
|
|
(sha256
|
|
(base32 "1gf38x51128hn00744358w27xgzjk0ff4wra4yxh2lk804ck1mh9"))
|
|
(patches (search-patches "hdf5-config-date.patch"))))))
|
|
|
|
(define-public hdf-java
|
|
(package
|
|
(name "hdf-java")
|
|
(version "3.3.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"https://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
|
|
version "/src/CMake-hdfjava-" version ".tar.gz"))
|
|
(sha256
|
|
(base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
|
|
(modules '((guix build utils)))
|
|
(snippet ; Make sure we don't use the bundled sources and binaries.
|
|
`(begin
|
|
(for-each delete-file
|
|
(list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
|
|
"HDF4.tar.gz" "HDF5.tar.gz"))
|
|
(delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
|
|
#t))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("jdk" ,icedtea "jdk")
|
|
("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
|
|
;; For tests:
|
|
("hamcrest-core" ,java-hamcrest-core)
|
|
("junit" ,java-junit)
|
|
("slf4j-simple" ,java-slf4j-simple)))
|
|
(inputs
|
|
`(("hdf4" ,hdf4)
|
|
("hdf5" ,hdf5)
|
|
("zlib" ,zlib)
|
|
("libjpeg" ,libjpeg)
|
|
("slf4j-api" ,java-slf4j-api)))
|
|
(arguments
|
|
`(#:configure-flags
|
|
(list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
|
|
(string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
|
|
(assoc-ref %build-inputs "jdk") "/lib" )
|
|
(string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
|
|
(string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
|
|
|
|
#:make-flags
|
|
(list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
|
|
(string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
|
|
(string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
|
|
(string-append "JPEGLIB="
|
|
(assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
|
|
"LLEXT=so")
|
|
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-before 'configure 'chdir-to-source
|
|
(lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
|
|
(add-before 'configure 'patch-build
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(substitute* "configure"
|
|
(("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
|
|
(("/bin/cat") (which "cat")))
|
|
;; Set classpath for compilation
|
|
(substitute* '("hdf/hdf5lib/Makefile.in"
|
|
"hdf/hdf5lib/exceptions/Makefile.in"
|
|
"hdf/hdflib/Makefile.in")
|
|
(("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
|
|
(string-append (assoc-ref inputs "slf4j-api")
|
|
"/share/java/slf4j-api.jar")))
|
|
;; Replace outdated config.sub and config.guess:
|
|
(with-directory-excursion "config"
|
|
(for-each (lambda (file)
|
|
(install-file
|
|
(string-append (assoc-ref inputs "automake")
|
|
"/share/automake-"
|
|
,(version-major+minor (package-version automake))
|
|
"/" file) "."))
|
|
'("config.sub" "config.guess")))
|
|
|
|
;; Fix embedded version number
|
|
(let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
|
|
(substitute* "hdf/hdf5lib/H5.java"
|
|
(("1, 8, 19")
|
|
(string-join hdf5version ", "))))
|
|
|
|
(mkdir-p (string-append (assoc-ref outputs "out")))
|
|
;; Set classpath for tests
|
|
(let* ((build-dir (getcwd))
|
|
(lib (string-append build-dir "/lib"))
|
|
(jhdf (string-append lib "/jhdf.jar"))
|
|
(jhdf5 (string-append lib "/jhdf5.jar"))
|
|
(testjars
|
|
(map (lambda (i)
|
|
(string-append (assoc-ref inputs i)
|
|
"/share/java/" i ".jar"))
|
|
'("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
|
|
(class-path
|
|
(string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
|
|
|
|
(substitute* '("test/hdf5lib/Makefile.in"
|
|
"test/hdf5lib/junit.sh.in"
|
|
"examples/runExample.sh.in")
|
|
(("/usr/bin/test")
|
|
(string-append (assoc-ref inputs "coreutils")
|
|
"/bin/test"))
|
|
(("/usr/bin/uname")
|
|
(string-append (assoc-ref inputs "coreutils")
|
|
"/bin/uname"))
|
|
(("CLASSPATH=[^\n]*")
|
|
(string-append "CLASSPATH=" class-path)))
|
|
(setenv "CLASSPATH" class-path))
|
|
#t))
|
|
(add-before 'check 'build-examples
|
|
(lambda _
|
|
(apply invoke `("javac"
|
|
,@(find-files "examples" ".*\\.java"))))))
|
|
|
|
#:parallel-build? #f
|
|
|
|
#:parallel-tests? #f ))
|
|
(home-page "https://support.hdfgroup.org/products/java")
|
|
(synopsis "Java interface for the HDF4 and HDF5 libraries")
|
|
(description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
|
|
the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
|
|
implemented in C.")
|
|
|
|
;; BSD-style license:
|
|
(license (license:x11-style
|
|
"https://support.hdfgroup.org/ftp/HDF5/hdf-java\
|
|
/current/src/unpacked/COPYING"))))
|
|
|
|
(define-public hdf-eos2
|
|
(package
|
|
(name "hdf-eos2")
|
|
(version "19.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri "ftp://edhs1.gsfc.nasa.gov\
|
|
/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
|
|
(sha256
|
|
(base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
|
|
(patches (search-patches "hdf-eos2-remove-gctp.patch"
|
|
"hdf-eos2-build-shared.patch"
|
|
"hdf-eos2-fortrantests.patch"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(inputs
|
|
`(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
|
|
;; XXX: These inputs are really dependencies of hdf4.
|
|
("zlib" ,zlib)
|
|
("libjpeg" ,libjpeg)
|
|
("libtirpc" ,libtirpc)
|
|
|
|
("gctp" ,gctp)))
|
|
(arguments
|
|
`( #:configure-flags '("--enable-install-include" "--enable-shared"
|
|
"CC=h4cc -Df2cFortran" "LIBS=-lgctp")
|
|
#:parallel-tests? #f))
|
|
(home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
|
|
(synopsis "HDF4-based data format for NASA's Earth Observing System")
|
|
(description "HDF-EOS2 is a software library built on HDF4 which supports
|
|
the construction of data structures used in NASA's Earth Observing
|
|
System (Grid, Point and Swath).")
|
|
|
|
;; Source files carry a permissive license header.
|
|
(license (license:non-copyleft home-page))))
|
|
|
|
(define-public hdf-eos5
|
|
(package
|
|
(name "hdf-eos5")
|
|
(version "1.15")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "ftp://edhs1.gsfc.nasa.gov\
|
|
/edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
|
|
(sha256
|
|
(base32
|
|
"1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
|
|
(patches (search-patches "hdf-eos5-build-shared.patch"
|
|
"hdf-eos5-remove-gctp.patch"
|
|
"hdf-eos5-fix-szip.patch"
|
|
"hdf-eos5-fortrantests.patch"))))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("hdf5" ,hdf5)
|
|
("zlib" ,zlib)
|
|
("gctp" ,gctp)))
|
|
(arguments
|
|
`(#:configure-flags '("--enable-install-include" "--enable-shared"
|
|
"CC=h5cc -Df2cFortran" "LIBS=-lgctp")
|
|
#:parallel-tests? #f))
|
|
(synopsis "HDF5-based data format for NASA's Earth Observing System")
|
|
(description
|
|
"HDF-EOS5 is a software library built on HDF5 to support the construction
|
|
of data structures used in NASA's Earth Observing System (Grid, Point and
|
|
Swath).")
|
|
(home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
|
|
|
|
;; Source files carry a permissive license header.
|
|
(license (license:non-copyleft home-page))))
|
|
|
|
(define-public hdf5-parallel-openmpi
|
|
(package (inherit hdf5)
|
|
(name "hdf5-parallel-openmpi")
|
|
(inputs
|
|
`(("mpi" ,openmpi)
|
|
,@(package-inputs hdf5)))
|
|
(arguments
|
|
(substitute-keyword-arguments (package-arguments hdf5)
|
|
((#:configure-flags flags)
|
|
``("--enable-parallel"
|
|
,@(delete "--enable-cxx"
|
|
(delete "--enable-threadsafe" ,flags))))
|
|
((#:phases phases)
|
|
`(modify-phases ,phases
|
|
(add-after 'build 'mpi-setup
|
|
,%openmpi-setup)
|
|
(add-before 'check 'patch-tests
|
|
(lambda _
|
|
;; OpenMPI's mpirun will exit with non-zero status if it
|
|
;; detects an "abnormal termination", i.e. any process not
|
|
;; calling MPI_Finalize(). Since the test is explicitly
|
|
;; avoiding MPI_Finalize so as not to have at_exit and thus
|
|
;; H5C_flush_cache from being called, mpirun will always
|
|
;; complain, so turn this test off.
|
|
(substitute* "testpar/Makefile"
|
|
(("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
|
|
(string-append front back "\n")))
|
|
(substitute* "tools/h5diff/testph5diff.sh"
|
|
(("/bin/sh") (which "sh")))
|
|
#t))))))
|
|
(synopsis "Management suite for data with parallel IO support")))
|
|
|
|
(define-public h5check
|
|
(package
|
|
(name "h5check")
|
|
(version "2.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://www.hdfgroup.org/ftp/HDF5/tools/"
|
|
"h5check/src/h5check-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
|
|
(build-system gnu-build-system)
|
|
(inputs `(("hdf5" ,hdf5))) ;h5cc for tests
|
|
(home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
|
|
(synopsis "HDF5 format checker")
|
|
(description "@code{h5check} is a validation tool for verifying that an
|
|
HDF5 file is encoded according to the HDF File Format Specification.")
|
|
(license (license:x11-style "file://COPYING"))))
|
|
|
|
(define-public itpp
|
|
(package
|
|
(name "itpp")
|
|
(version "4.3.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://sourceforge/itpp/itpp/"
|
|
version "/itpp-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
|
|
(build-system cmake-build-system)
|
|
(arguments `(#:tests? #f)) ; Tests require googletest *sources*
|
|
(inputs `(("lapack" ,lapack)
|
|
("fftw" ,fftw)))
|
|
;; FIXME: Even though the fonts are available dvips complains:
|
|
;; "Font cmmi10 not found; characters will be left blank."
|
|
(native-inputs
|
|
`(("texlive" ,texlive-tiny)
|
|
("ghostscript" ,ghostscript)
|
|
("doxygen" ,doxygen)))
|
|
(home-page "http://itpp.sourceforge.net")
|
|
(synopsis "C++ library of maths, signal processing and communication classes")
|
|
(description "IT++ is a C++ library of mathematical, signal processing and
|
|
communication classes and functions. Its main use is in simulation of
|
|
communication systems and for performing research in the area of
|
|
communications. The kernel of the library consists of generic vector and
|
|
matrix classes, and a set of accompanying routines. Such a kernel makes IT++
|
|
similar to MATLAB, GNU Octave or SciPy.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public netcdf
|
|
(package
|
|
(name "netcdf")
|
|
(version "4.4.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
|
|
"netcdf-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
|
|
(patches (search-patches "netcdf-date-time.patch"
|
|
"netcdf-tst_h_par.patch"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("m4" ,m4)
|
|
("doxygen" ,doxygen)
|
|
("graphviz" ,graphviz)))
|
|
(inputs
|
|
`(("hdf4" ,hdf4-alt)
|
|
("hdf5" ,hdf5)
|
|
("zlib" ,zlib)
|
|
("libjpeg" ,libjpeg)))
|
|
(arguments
|
|
`(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
|
|
|
|
#:phases (modify-phases %standard-phases
|
|
(add-before 'configure 'fix-source-date
|
|
(lambda _
|
|
;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
|
|
;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
|
|
;; to '1st hour of the current day', and therefore makes the
|
|
;; package not reproducible.
|
|
(substitute* "./configure"
|
|
(("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
|
|
"date --date='@0'"))
|
|
#t))
|
|
(add-after 'configure 'patch-settings
|
|
(lambda _
|
|
;; libnetcdf.settings contains the full filename of the compilers
|
|
;; used to build the library. We truncate the hashes of those
|
|
;; filenames to avoid unnecessary references to the corresponding
|
|
;; store items.
|
|
(substitute* "libnetcdf.settings"
|
|
(("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
|
|
(string-append prefix (string-take hash 10) "...")))
|
|
#t)))
|
|
|
|
#:parallel-tests? #f)) ;various race conditions
|
|
(home-page "https://www.unidata.ucar.edu/software/netcdf/")
|
|
(synopsis "Library for scientific data")
|
|
(description "NetCDF is an interface for scientific data access and a
|
|
software library that provides an implementation of the interface. The netCDF
|
|
library defines a machine-independent format for representing scientific data.
|
|
Together, the interface, library, and format support the creation, access, and
|
|
sharing of scientific data.")
|
|
(license (license:x11-style "file://COPYRIGHT"))))
|
|
|
|
(define-public netcdf-parallel-openmpi
|
|
(package (inherit netcdf)
|
|
(name "netcdf-parallel-openmpi")
|
|
(inputs
|
|
`(("mpi" ,openmpi)
|
|
,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
|
|
(package-inputs netcdf))))
|
|
;; TODO: Replace pkg-config references in nc-config with absolute references
|
|
(arguments
|
|
(substitute-keyword-arguments (package-arguments netcdf)
|
|
((#:configure-flags flags)
|
|
`(cons* "CC=mpicc" "CXX=mpicxx"
|
|
"--enable-parallel-tests"
|
|
;; Shared libraries not supported with parallel IO.
|
|
"--disable-shared" "--with-pic"
|
|
,flags))))))
|
|
|
|
(define-public netcdf-fortran
|
|
(package
|
|
(name "netcdf-fortran")
|
|
(version "4.4.4")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:parallel-tests? #f))
|
|
(inputs
|
|
`(("netcdf" ,netcdf)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(synopsis "Fortran interface for the netCDF library")
|
|
(description (package-description netcdf))
|
|
(home-page (package-home-page netcdf))
|
|
(license (package-license netcdf))))
|
|
|
|
(define-public nlopt
|
|
(package
|
|
(name "nlopt")
|
|
(version "2.4.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(;; Shared libraries are not built by default. They are required to
|
|
;; build the Guile, Octave, and Python bindings.
|
|
#:configure-flags '("--enable-shared")
|
|
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-before 'configure 'set-libnlopt-file-name
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
;; Make sure the Scheme module refers to the library by its
|
|
;; absolute file name (we cannot do that from a snippet
|
|
;; because the expansion of @libdir@ contains
|
|
;; ${exec_prefix}.)
|
|
(let ((out (assoc-ref outputs "out")))
|
|
(substitute* "swig/nlopt.scm.in"
|
|
(("libnlopt")
|
|
(string-append out "/lib/libnlopt")))
|
|
#t))))))
|
|
(inputs `(("guile" ,guile-2.0)))
|
|
(native-inputs `(("pkg-config" ,pkg-config)))
|
|
(home-page "http://ab-initio.mit.edu/wiki/")
|
|
(synopsis "Library for nonlinear optimization")
|
|
(description "NLopt is a library for nonlinear optimization, providing a
|
|
common interface for a number of different free optimization routines available
|
|
online as well as original implementations of various other algorithms.")
|
|
(license license:lgpl2.1+)))
|
|
|
|
(define-public ipopt
|
|
(package
|
|
(name "ipopt")
|
|
(version "3.12.12")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"http://www.coin-or.org/download/source/Ipopt/Ipopt-"
|
|
version".tgz"))
|
|
(sha256
|
|
(base32
|
|
"07yn9rzdswjk8n246qq6ci9ssf2bcplkifcpsfz9j6cdxw9vgbkv"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
;; Make sure we don't use the bundled software.
|
|
'(begin
|
|
(delete-file-recursively "ThirdParty")
|
|
#t))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
'(#:phases (modify-phases %standard-phases
|
|
(add-after 'install 'add--L-flags-in-ipopt.pc
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
;; The '.pc' file lists '-llapack -lblas' in "Libs";
|
|
;; move it to "Libs.private" where it belongs, and add a
|
|
;; '-L' flag for LAPACK.
|
|
(let ((out (assoc-ref outputs "out"))
|
|
(lapack (assoc-ref inputs "lapack")))
|
|
(substitute* (string-append out "/lib/pkgconfig/"
|
|
"ipopt.pc")
|
|
(("Libs: (.*)-llapack -lblas(.*)$" _ before after)
|
|
(string-append "Libs: " before " " after "\n"
|
|
"Libs.private: " before
|
|
"-L" lapack "/lib -llapack -lblas "
|
|
after "\n")))
|
|
#t))))))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(inputs
|
|
;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
|
|
`(("lapack" ,lapack))) ;for both libblas and liblapack
|
|
(home-page "http://www.coin-or.org")
|
|
(synopsis "Large-scale nonlinear optimizer")
|
|
(description
|
|
"The Interior Point Optimizer (IPOPT) is a software package for
|
|
large-scale nonlinear optimization. It provides C++, C, and Fortran
|
|
interfaces.")
|
|
(license license:epl1.0)))
|
|
|
|
(define-public clp
|
|
(package
|
|
(name "clp")
|
|
(version "1.17.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://www.coin-or.org/download/source/"
|
|
"Clp/Clp-" version ".tgz"))
|
|
(sha256
|
|
(base32
|
|
"1wdg820g3iikf9344ijwsc8sy6c0m6im42bzzizm6rlmkvnmxhk9"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
;; Make sure we don't use the bundled software.
|
|
'(begin
|
|
(delete-file-recursively "ThirdParty")
|
|
#t))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)
|
|
("pkg-config" ,pkg-config)))
|
|
(inputs
|
|
`(("openblas" ,openblas)))
|
|
(home-page "https://www.coin-or.org")
|
|
(synopsis "Linear programming solver")
|
|
(description
|
|
"CLP is a high quality linear programming solver. Its main strengths are
|
|
its dual and primal Simplex algorithms. It also has a barrier algorithm for
|
|
linear and quadratic objectives. There are limited facilities for nonlinear
|
|
and quadratic objectives using the Simplex algorithm.")
|
|
(license license:epl1.0)))
|
|
|
|
(define-public ceres
|
|
(package
|
|
(name "ceres-solver")
|
|
(version "1.14.0")
|
|
(home-page "http://ceres-solver.org/")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append home-page "ceres-solver-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
;; TODO: Build HTML user documentation and install separately.
|
|
'(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
|
|
"-DBUILD_SHARED_LIBS=ON")
|
|
|
|
#:phases (modify-phases %standard-phases
|
|
(add-before 'configure 'set-library-directory
|
|
(lambda _
|
|
;; Install libraries to lib/, not lib64/.
|
|
(substitute* "internal/ceres/CMakeLists.txt"
|
|
(("set\\(LIB_SUFFIX \"64\"\\)")
|
|
"set(LIB_SUFFIX \"\")"))
|
|
#t)))))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(propagated-inputs
|
|
`(("glog" ,glog))) ;for #include <glog/glog.h>
|
|
(inputs
|
|
`(("eigen" ,eigen)
|
|
("blas" ,openblas)
|
|
("lapack" ,lapack)
|
|
("suitesparse" ,suitesparse)
|
|
("gflags" ,gflags)))
|
|
(synopsis "C++ library for solving large optimization problems")
|
|
(description
|
|
"Ceres Solver is a C++ library for modeling and solving large,
|
|
complicated optimization problems. It is a feature rich, mature and
|
|
performant library which has been used in production since 2010. Ceres Solver
|
|
can solve two kinds of problems:
|
|
@enumerate
|
|
@item non-linear least squares problems with bounds constraints;
|
|
@item general unconstrained optimization problems.
|
|
@end enumerate\n")
|
|
(license license:bsd-3)))
|
|
|
|
;; For a fully featured Octave, users are strongly recommended also to install
|
|
;; the following packages: less, ghostscript, gnuplot.
|
|
(define-public octave-cli
|
|
(package
|
|
(name "octave-cli")
|
|
(version "5.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://gnu/octave/octave-"
|
|
version ".tar.lz"))
|
|
(sha256
|
|
(base32
|
|
"1848dq6nxzal8gwjrcp6xhi5gq96w89nss9d9rz75q408gb3mbl6"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("alsa-lib" ,alsa-lib)
|
|
("arpack" ,arpack-ng)
|
|
("bdb" ,bdb)
|
|
("curl" ,curl)
|
|
("fftw" ,fftw)
|
|
("fftwf" ,fftwf)
|
|
("fltk" ,fltk)
|
|
("fontconfig" ,fontconfig)
|
|
("freetype" ,freetype)
|
|
("gl2ps" ,gl2ps)
|
|
("glpk" ,glpk)
|
|
("glu" ,glu)
|
|
("graphicsmagick" ,graphicsmagick)
|
|
("hdf5" ,hdf5)
|
|
("lapack" ,lapack)
|
|
("libsndfile" ,libsndfile)
|
|
("libxft" ,libxft)
|
|
("mesa" ,mesa)
|
|
("pcre" ,pcre)
|
|
("portaudio" ,portaudio)
|
|
("qhull" ,qhull)
|
|
("readline" ,readline)
|
|
("suitesparse" ,suitesparse)
|
|
("texinfo" ,texinfo)
|
|
("zlib" ,zlib)))
|
|
(native-inputs
|
|
`(("lzip" ,lzip)
|
|
("gfortran" ,gfortran)
|
|
("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)
|
|
("ghostscript" ,ghostscript)
|
|
("gnuplot" ,gnuplot)))
|
|
;; Octave code uses this variable to detect directories holding multiple CA
|
|
;; certificates to verify peers with. This is required for the networking
|
|
;; functions that require encryption to work properly.
|
|
(native-search-paths
|
|
(list (search-path-specification
|
|
(variable "CURLOPT_CAPATH")
|
|
(files '("etc/ssl/certs")))))
|
|
(arguments
|
|
`(#:configure-flags
|
|
(list (string-append "--with-shell="
|
|
(assoc-ref %build-inputs "bash")
|
|
"/bin/sh"))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'configure 'configure-makeinfo
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(substitute* "libinterp/corefcn/help.h"
|
|
(("\"makeinfo\"")
|
|
(string-append
|
|
"\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
|
|
#t)))))
|
|
(home-page "https://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 octave
|
|
(package (inherit octave-cli)
|
|
(name "octave")
|
|
(source (origin
|
|
(inherit (package-source octave-cli))))
|
|
(inputs
|
|
`(("qscintilla" ,qscintilla)
|
|
("qt" ,qtbase)
|
|
,@(package-inputs octave-cli)))
|
|
(native-inputs
|
|
`(("qttools" , qttools) ;for lrelease
|
|
("texlive" ,(texlive-union (list texlive-epsf))) ; for texi2dvi
|
|
,@(package-native-inputs octave-cli)))
|
|
(arguments
|
|
(substitute-keyword-arguments (package-arguments octave-cli)
|
|
((#:phases phases)
|
|
`(modify-phases ,phases
|
|
(add-before 'configure 'patch-qscintilla-library-name
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
;; The QScintilla library that the Octave configure script tries
|
|
;; to link with should be named libqscintilla-qt5.so, but the
|
|
;; QScintilla input provides the shared library as
|
|
;; libqscintilla2_qt5.so.
|
|
(substitute* "configure"
|
|
(("qscintilla2-qt5")
|
|
"qscintilla2_qt5"))
|
|
#t))))))))
|
|
|
|
(define-public qtoctave
|
|
(deprecated-package "qtoctave" octave))
|
|
|
|
(define-public opencascade-oce
|
|
(package
|
|
(name "opencascade-oce")
|
|
(version "0.17.2")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/tpaviot/oce.git")
|
|
(commit (string-append "OCE-" version))))
|
|
(file-name (git-file-name name version))
|
|
(patches (search-patches "opencascade-oce-glibc-2.26.patch"))
|
|
(sha256
|
|
(base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69"))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
'(#:configure-flags
|
|
(list "-DOCE_TESTING:BOOL=ON"
|
|
"-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
|
|
"-DOCE_DRAW:BOOL=ON"
|
|
(string-append "-DOCE_INSTALL_PREFIX:PATH="
|
|
(assoc-ref %outputs "out"))
|
|
"-UCMAKE_INSTALL_RPATH")))
|
|
(inputs
|
|
`(("freetype" ,freetype)
|
|
("glu" ,glu)
|
|
("libxmu" ,libxmu)
|
|
("mesa" ,mesa)
|
|
("tcl" ,tcl)
|
|
("tk" ,tk)))
|
|
(native-inputs
|
|
`(("python" ,python-wrapper)))
|
|
(home-page "https://github.com/tpaviot/oce")
|
|
(synopsis "Libraries for 3D modeling and numerical simulation")
|
|
(description
|
|
"Open CASCADE is a set of libraries for the development of applications
|
|
dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
|
|
C++ class libraries providing services for 3D surface and solid modeling, CAD
|
|
data exchange, and visualization. It is used for development of specialized
|
|
software dealing with 3D models in design (CAD), manufacturing (CAM),
|
|
numerical simulation (CAE), measurement equipment (CMM), and quality
|
|
control (CAQ) domains.
|
|
|
|
This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
|
|
patches, improvements, and experiments contributed by users over the official
|
|
Open CASCADE library.")
|
|
(license (list license:lgpl2.1; OCE libraries, with an exception for the
|
|
; use of header files; see
|
|
; OCCT_LGPL_EXCEPTION.txt
|
|
license:public-domain; files
|
|
; src/Standard/Standard_StdAllocator.hxx and
|
|
; src/NCollection/NCollection_StdAllocator.hxx
|
|
license:expat; file src/OpenGl/OpenGl_glext.h
|
|
license:bsd-3)))); test framework gtest
|
|
|
|
(define-public opencascade-occt
|
|
(package
|
|
(name "opencascade-occt")
|
|
(version "7.3.0p3")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://git.dev.opencascade.org/repos/occt.git")
|
|
(commit
|
|
(string-append "V"
|
|
(string-map (lambda (x) (if (eq? x #\.) #\_ x))
|
|
version)))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
'(begin
|
|
;; Remove files specific to non-free operating systems.
|
|
(delete-file-recursively "samples/ios")
|
|
(delete-file-recursively "samples/mfc")
|
|
(delete-file-recursively "samples/qt/FuncDemo")
|
|
(delete-file "genconf.bat")
|
|
(delete-file "gendoc.bat")
|
|
(delete-file "genproj.bat")
|
|
(delete-file "upgrade.bat")
|
|
;; Remove references to deleted files.
|
|
(substitute* "dox/FILES_HTML.txt"
|
|
((".*standard.*") "" )
|
|
((".*UIKitSample.*") ""))
|
|
#t))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
'(;; There is no test target for make. OCCT provides an
|
|
;; 'Automated Testing System', which may be accessed after
|
|
;; installation via the draw.sh script. draw.sh is located in
|
|
;; the bin directory. For details see:
|
|
;; https://www.opencascade.com/doc/occt-7.3.0/overview/html/\
|
|
;; occt_dev_guides__tests.html
|
|
#:tests? #f
|
|
;; Configure without freeimage: attempting to link against the
|
|
;; freeimage version 3.17 library leads to 'undefined
|
|
;; reference' errors.
|
|
#:configure-flags
|
|
(list "-DUSE_FREEIMAGE:BOOL=OFF"
|
|
"-DUSE_TBB:BOOL=ON"
|
|
"-DUSE_VTK:BOOL=OFF"
|
|
"-DBUILD_DOC_Overview:BOOL=OFF"
|
|
"-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON"
|
|
"-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON"
|
|
"-UCMAKE_INSTALL_LIBDIR")))
|
|
(inputs
|
|
`(("doxygen" ,doxygen)
|
|
;("freeimage" ,freeimage)
|
|
("freetype" ,freetype)
|
|
("glu" ,glu)
|
|
("libxext" ,libxext)
|
|
("libxi" ,libxi)
|
|
("libxmu" ,libxmu)
|
|
("mesa" ,mesa)
|
|
("tbb" ,tbb)
|
|
("tcl" ,tcl)
|
|
("tk" ,tk)))
|
|
;; TODO: build Overview documentation and add 'doc' output.
|
|
(home-page "https://www.opencascade.com")
|
|
(synopsis "Libraries for 3D modeling and numerical simulation")
|
|
(description
|
|
"Open CASCADE is a set of libraries for the development of applications
|
|
dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
|
|
C++ class libraries providing services for 3D surface and solid modeling, CAD
|
|
data exchange, and visualization. It is used for development of specialized
|
|
software dealing with 3D models in design (CAD), manufacturing (CAM),
|
|
numerical simulation (CAE), measurement equipment (CMM), and quality
|
|
control (CAQ) domains.
|
|
|
|
This is the certified version of the Open Cascade Technology (OCCT) library.")
|
|
(license (list ;; OCCT library:
|
|
license:lgpl2.1; with an exception for the use of header
|
|
; files, see OCCT_LGPL_EXCEPTION.txt.
|
|
;; Files src/OpenGl/glext.h, adm/cmake/cotire.cmake and
|
|
;; src/OpenGl/OpenGl_HaltonSampler.hxx:
|
|
license:expat
|
|
;; Files src/ExprIntrp/ExprIntrp.tab.* and
|
|
;; src/StepFile/step.tab.*:
|
|
license:gpl3+ ; with Bison 2.2 exception.
|
|
;; File src/NCollection/NCollection_UtfIterator.lxx:
|
|
(license:non-copyleft
|
|
"https://www.unicode.org/license.html")
|
|
;; File src/NCollection/NCollection_StdAllocator.hxx:
|
|
license:public-domain))))
|
|
|
|
(define-public gmsh
|
|
(package
|
|
(name "gmsh")
|
|
(version "2.16.0")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://gitlab.onelab.info/gmsh/gmsh.git")
|
|
(commit
|
|
(string-append "gmsh_"
|
|
(string-map (lambda (x) (if (eq? x #\.) #\_ x))
|
|
version)))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32 "08rq4jajwmlpivnm9yifz2jhaivnz065lnk0h2zv773nwl9wf162"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
;; Remove non-free METIS code
|
|
'(begin
|
|
(delete-file-recursively "contrib/Metis")
|
|
#t))))
|
|
(build-system cmake-build-system)
|
|
(propagated-inputs
|
|
`(("fltk" ,fltk)
|
|
("gfortran" ,gfortran)
|
|
("gmp" ,gmp)
|
|
("hdf5" ,hdf5)
|
|
("lapack" ,lapack)
|
|
("mesa" ,mesa)
|
|
("glu" ,glu)
|
|
("opencascade-oce" ,opencascade-oce)
|
|
("libx11" ,libx11)
|
|
("libxext" ,libxext)))
|
|
(inputs
|
|
`(("fontconfig" ,fontconfig)
|
|
("libxft" ,libxft)))
|
|
(arguments
|
|
`(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
|
|
"-DENABLE_BUILD_SHARED:BOOL=ON"
|
|
"-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
|
|
(home-page "http://gmsh.info/")
|
|
(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 maxflow
|
|
(package
|
|
(name "maxflow")
|
|
;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’,
|
|
;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’.
|
|
(version "3.0.5")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/gerddie/maxflow.git")
|
|
(commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
|
|
(build-system cmake-build-system)
|
|
(home-page "https://pub.ist.ac.at/~vnk/software.html")
|
|
(synopsis "Library implementing Maxflow algorithm")
|
|
(description "An implementation of the maxflow algorithm described in
|
|
@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
|
|
Energy Minimization in Computer Vision.\n
|
|
Yuri Boykov and Vladimir Kolmogorov.\n
|
|
In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
|
|
September 2004}")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public petsc
|
|
(package
|
|
(name "petsc")
|
|
(version "3.11.2")
|
|
(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 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx"))))
|
|
(outputs '("out" ; libraries and headers
|
|
"examples")) ; ~30MiB of examples
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("python" ,python-2)))
|
|
(inputs
|
|
`(("gfortran" ,gfortran)
|
|
("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 ; build is parallel by default
|
|
#:configure-flags
|
|
`("--with-mpi=0"
|
|
"--with-openmp=1"
|
|
"--with-superlu=1")
|
|
#:make-flags
|
|
;; Honor (parallel-job-count) for build. Do not use --with-make-np,
|
|
;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
|
|
(list (format #f "MAKE_NP=~a" (parallel-job-count)))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(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)
|
|
(apply invoke "./configure" flags))))
|
|
(add-after 'configure 'clean-local-references
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let ((out (assoc-ref outputs "out")))
|
|
(substitute* (find-files "." "^petsc(conf|machineinfo).h$")
|
|
;; Prevent build directory from leaking into compiled code
|
|
(((getcwd)) out)
|
|
;; Scrub timestamp for reproducibility
|
|
((".*Libraries compiled on.*") ""))
|
|
(substitute* (find-files "." "petscvariables")
|
|
;; Do not expose build machine characteristics, set to defaults.
|
|
(("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
|
|
(("NPMAX = [:digit:]+") "NPMAX = 2"))
|
|
#t)))
|
|
(add-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")))
|
|
(substitute* (map (lambda (file)
|
|
(string-append out "/lib/petsc/conf/" file))
|
|
'("petscvariables"))
|
|
(((getcwd)) out))
|
|
;; Make compiler references point to the store
|
|
(substitute* (string-append out "/lib/petsc/conf/petscvariables")
|
|
(("= (gcc|g\\+\\+|gfortran)" _ compiler)
|
|
(string-append "= " (which compiler))))
|
|
;; PETSc installs some build logs, which aren't necessary.
|
|
(for-each (lambda (file)
|
|
(let ((f (string-append out "/lib/petsc/conf/" file)))
|
|
(when (file-exists? f)
|
|
(delete-file f))))
|
|
'("configure.log" "make.log" "gmake.log"
|
|
"test.log" "error.log" "RDict.db"
|
|
"PETScBuildInternal.cmake"
|
|
;; Once installed, should uninstall with Guix
|
|
"uninstall.py"))
|
|
#t)))
|
|
(add-after 'install 'move-examples
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
(examples (assoc-ref outputs "examples"))
|
|
(exdir (string-append out "/share/petsc/examples"))
|
|
(exdir' (string-append examples "/share/petsc/examples")))
|
|
(copy-recursively exdir exdir')
|
|
(delete-file-recursively exdir)
|
|
#t))))))
|
|
(home-page "https://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:non-copyleft
|
|
"https://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
|
|
|
|
(define-public petsc-complex
|
|
(package (inherit petsc)
|
|
(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
|
|
`(("hdf5" ,hdf5-parallel-openmpi)
|
|
("hypre" ,hypre-openmpi)
|
|
("metis" ,metis)
|
|
("mumps" ,mumps-openmpi)
|
|
("openmpi" ,openmpi)
|
|
("scalapack" ,scalapack)
|
|
("scotch" ,pt-scotch32)
|
|
,@(package-inputs petsc)))
|
|
(arguments
|
|
(substitute-keyword-arguments (package-arguments petsc)
|
|
((#:configure-flags cf)
|
|
``("--with-hypre=1"
|
|
"--with-mpiexec=mpirun"
|
|
"--with-metis=1"
|
|
"--with-mumps=1"
|
|
"--with-scalapack=1"
|
|
"--with-ptscotch=1"
|
|
,(string-append "--with-mpi-dir="
|
|
(assoc-ref %build-inputs "openmpi"))
|
|
,(string-append "--with-hdf5-include="
|
|
(assoc-ref %build-inputs "hdf5") "/include")
|
|
,(string-append "--with-hdf5-lib="
|
|
(assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
|
|
,@(delete "--with-mpi=0" ,cf)))
|
|
((#:phases phases)
|
|
`(modify-phases ,phases
|
|
(add-before 'configure 'mpi-setup
|
|
,%openmpi-setup)))))
|
|
(synopsis "Library to solve PDEs (with MUMPS and 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)))
|
|
((#:phases phases)
|
|
`(modify-phases ,phases
|
|
(add-before 'configure 'mpi-setup
|
|
,%openmpi-setup)))))
|
|
(synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
|
|
|
|
(define-public python-petsc4py
|
|
(package
|
|
(name "python-petsc4py")
|
|
(version "3.11.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "petsc4py" version))
|
|
(sha256
|
|
(base32
|
|
"1rm1qj5wlkhxl39by9n78lh3gbmii31wsnb8j1rr5hvfr5xgbx2q"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-before 'build 'pre-build
|
|
(lambda _
|
|
;; Define path to PETSc installation.
|
|
(setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
|
|
#t))
|
|
(add-before 'check 'mpi-setup
|
|
,%openmpi-setup))))
|
|
(inputs
|
|
`(("petsc" ,petsc-openmpi)
|
|
("python-numpy" ,python-numpy)))
|
|
(home-page "https://bitbucket.org/petsc/petsc4py/")
|
|
(synopsis "Python bindings for PETSc")
|
|
(description "PETSc, the Portable, Extensible Toolkit for
|
|
Scientific Computation, is a suite of data structures and routines for
|
|
the scalable (parallel) solution of scientific applications modeled by
|
|
partial differential equations. It employs the MPI standard for all
|
|
message-passing communication. @code{petsc4py} provides Python
|
|
bindings to almost all functions of PETSc.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-kiwisolver
|
|
(package
|
|
(name "python-kiwisolver")
|
|
(version "1.0.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "kiwisolver" version))
|
|
(sha256
|
|
(base32
|
|
"0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
|
|
(build-system python-build-system)
|
|
(home-page "https://github.com/nucleic/kiwi")
|
|
(synopsis "Fast implementation of the Cassowary constraint solver")
|
|
(description
|
|
"Kiwi is an efficient C++ implementation of the Cassowary constraint
|
|
solving algorithm. Kiwi has been designed from the ground up to be
|
|
lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
|
|
Cassowary solver with typical use cases gaining a 40x improvement. Memory
|
|
savings are consistently > 5x.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python2-kiwisolver
|
|
(package-with-python2 python-kiwisolver))
|
|
|
|
(define-public slepc
|
|
(package
|
|
(name "slepc")
|
|
(version "3.11.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("python" ,python-2)
|
|
("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
|
|
(inputs
|
|
`(("arpack" ,arpack-ng)
|
|
("gfortran" ,gfortran)))
|
|
(propagated-inputs
|
|
`(("petsc" ,petsc)))
|
|
(arguments
|
|
`(#:parallel-build? #f ;build is parallel by default
|
|
#:configure-flags
|
|
`(,(string-append "--with-arpack-dir="
|
|
(assoc-ref %build-inputs "arpack") "/lib"))
|
|
#:make-flags ;honor (parallel-job-count)
|
|
`(,(format #f "MAKE_NP=~a" (parallel-job-count))
|
|
,(string-append "PETSCCONFIGDIR="
|
|
(assoc-ref %build-inputs "petsc:examples")
|
|
"/share/petsc/examples/config"))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'configure
|
|
;; configure is a python script, so we can't run it with bash.
|
|
(lambda* (#:key inputs 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)
|
|
(setenv "SLEPC_DIR" (getcwd))
|
|
(setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
|
|
(apply invoke "./configure" flags))))
|
|
(add-after 'install 'delete-doc
|
|
;; TODO: SLEPc installs HTML documentation alongside headers in
|
|
;; $out/include. We'd like to move them to share/doc, but delete
|
|
;; them for now, as they are incomplete and installing the complete
|
|
;; documentation is difficult.
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let* ((out (assoc-ref outputs "out")))
|
|
(for-each delete-file (find-files out "\\.html$"))
|
|
#t)))
|
|
(add-after 'install 'clean-install
|
|
;; Clean up unnecessary build logs from installation.
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let ((out (assoc-ref outputs "out")))
|
|
(for-each (lambda (file)
|
|
(let ((f (string-append out "/lib/slepc/conf/" file)))
|
|
(when (file-exists? f)
|
|
(delete-file f))))
|
|
'("configure.log" "make.log" "gmake.log"
|
|
"test.log" "error.log" "RDict.db"
|
|
"uninstall.py"))
|
|
#t))))))
|
|
(home-page "http://slepc.upv.es")
|
|
(synopsis "Scalable library for eigenproblems")
|
|
(description "SLEPc is a software library for the solution of large sparse
|
|
eigenproblems on parallel computers. It can be used for the solution of
|
|
linear eigenvalue problems formulated in either standard or generalized form,
|
|
as well as other related problems such as the singular value decomposition.
|
|
The emphasis of the software is on methods and techniques appropriate for
|
|
problems in which the associated matrices are sparse, for example, those
|
|
arising after the discretization of partial differential equations.")
|
|
(license license:bsd-2)))
|
|
|
|
(define-public slepc-complex
|
|
(package (inherit slepc)
|
|
(name "slepc-complex")
|
|
(propagated-inputs
|
|
`(("petsc" ,petsc-complex)
|
|
,@(alist-delete "petsc" (package-propagated-inputs slepc))))
|
|
(synopsis "Scalable library for eigenproblems (with complex scalars)")))
|
|
|
|
(define-public slepc-openmpi
|
|
(package (inherit slepc)
|
|
(name "slepc-openmpi")
|
|
(arguments
|
|
(substitute-keyword-arguments (package-arguments slepc)
|
|
((#:phases phases '%standard-phases)
|
|
`(modify-phases ,phases
|
|
(add-before 'check 'mpi-setup
|
|
,%openmpi-setup)))))
|
|
(inputs
|
|
`(("mpi" ,openmpi)
|
|
("arpack" ,arpack-ng-openmpi)
|
|
,@(alist-delete "arpack" (package-inputs slepc))))
|
|
(propagated-inputs
|
|
`(("petsc" ,petsc-openmpi)
|
|
,@(alist-delete "petsc" (package-propagated-inputs slepc))))
|
|
(synopsis "Scalable library for eigenproblems (with MPI support)")))
|
|
|
|
(define-public slepc-complex-openmpi
|
|
(package (inherit slepc-openmpi)
|
|
(name "slepc-complex-openmpi")
|
|
(propagated-inputs
|
|
`(("petsc" ,petsc-complex-openmpi)
|
|
,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
|
|
(synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
|
|
|
|
(define-public python-slepc4py
|
|
(package
|
|
(name "python-slepc4py")
|
|
(version "3.11.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "slepc4py" version))
|
|
(sha256
|
|
(base32
|
|
"1ksp08kxf4wg408b9nn39z3qfhy643j22d4rfbl30vzxk2rxh4lq"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-before 'build 'pre-build
|
|
(lambda _
|
|
;; Define path to PETSc installation.
|
|
(setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
|
|
;; Define path to SLEPc installation.
|
|
(setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
|
|
#t))
|
|
(add-before 'check 'mpi-setup
|
|
,%openmpi-setup))))
|
|
(inputs
|
|
`(("python-numpy" ,python-numpy)
|
|
("python-petsc4py" ,python-petsc4py)
|
|
("slepc" ,slepc-openmpi)))
|
|
(home-page "https://bitbucket.org/slepc/slepc4py/")
|
|
(synopsis "Python bindings for SLEPc")
|
|
(description "SLEPc, the Scalable Library for Eigenvalue Problem
|
|
Computations, is based on PETSc, the Portable, Extensible Toolkit for
|
|
Scientific Computation. It employs the MPI standard for all
|
|
message-passing communication. @code{slepc4py} provides Python
|
|
bindings to almost all functions of SLEPc.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public mumps
|
|
(package
|
|
(name "mumps")
|
|
(version "5.2.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r"))
|
|
(patches (search-patches "mumps-build-parallelism.patch"
|
|
"mumps-shared-libseq.patch"
|
|
"mumps-shared-mumps.patch"
|
|
"mumps-shared-pord.patch"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("fortran" ,gfortran)
|
|
;; These are required for linking against mumps, but we let the user
|
|
;; declare the dependency.
|
|
("blas" ,openblas)
|
|
("metis" ,metis)
|
|
("scotch" ,scotch)))
|
|
(arguments
|
|
`(#:modules ((ice-9 match)
|
|
(ice-9 popen)
|
|
(srfi srfi-1)
|
|
,@%gnu-build-system-modules)
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'configure
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(call-with-output-file "Makefile.inc"
|
|
(lambda (port)
|
|
(format port "
|
|
PLAT =
|
|
LIBEXT = .a
|
|
OUTC = -o
|
|
OUTF = -o
|
|
RM = rm -f~:[
|
|
CC = gcc
|
|
FC = gfortran
|
|
FL = gfortran
|
|
INCSEQ = -I$(topdir)/libseq
|
|
LIBSEQ = $(topdir)/libseq/libmpiseq.a
|
|
LIBSEQNEEDED = libseqneeded~;
|
|
CC = mpicc
|
|
FC = mpifort
|
|
FL = mpifort~]
|
|
AR = ar vr # rules require trailing space, ugh...
|
|
RANLIB = ranlib
|
|
BLASDIR = ~a
|
|
LIBBLAS = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[
|
|
SCALAPDIR = ~a
|
|
SCALAP = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~]
|
|
LIBOTHERS = -pthread
|
|
CDEFS = -DAdd_
|
|
PIC = -fPIC
|
|
OPTF = -O2 -DALLOW_NON_INIT $(PIC)
|
|
OPTL = -O2 $(PIC)
|
|
OPTC = -O2 $(PIC)
|
|
INCS = $(INCSEQ)
|
|
LIBS = $(SCALAP) $(LIBSEQ)
|
|
LPORDDIR = $(topdir)/PORD/lib
|
|
IPORD = -I$(topdir)/PORD/include
|
|
LPORD = $(LPORDDIR)/libpord.a
|
|
ORDERINGSF = -Dpord~@[
|
|
METISDIR = ~a
|
|
IMETIS = -I$(METISDIR)/include
|
|
LMETIS = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
|
|
ORDERINGSF += -Dmetis~]~@[~:{
|
|
SCOTCHDIR = ~a
|
|
ISCOTCH = -I$(SCOTCHDIR)/include
|
|
LSCOTCH = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
|
|
ORDERINGSF += ~a~}~]
|
|
ORDERINGSC = $(ORDERINGSF)
|
|
LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
|
|
IORDERINGSF = $(ISCOTCH)
|
|
IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
|
|
(assoc-ref inputs "mpi")
|
|
(assoc-ref inputs "blas")
|
|
(assoc-ref inputs "scalapack")
|
|
(assoc-ref inputs "metis")
|
|
(match (list (assoc-ref inputs "pt-scotch")
|
|
(assoc-ref inputs "scotch"))
|
|
((#f #f)
|
|
#f)
|
|
((#f scotch)
|
|
`((,scotch "" "-Dscotch")))
|
|
((ptscotch _)
|
|
`((,ptscotch
|
|
"-lptesmumps -lptscotch -lptscotcherr "
|
|
"-Dptscotch")))))))))
|
|
(replace 'build
|
|
;; By default only the d-precision library is built. Make with "all"
|
|
;; target so that all precision libraries and examples are built.
|
|
(lambda _
|
|
(invoke "make" "all"
|
|
(format #f "-j~a" (parallel-job-count)))))
|
|
(replace 'check
|
|
;; Run the simple test drivers, which read test input from stdin:
|
|
;; from the "real" input for the single- and double-precision
|
|
;; testers, and from the "cmplx" input for complex-precision
|
|
;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
|
|
;; package to prefix execution with "mpirun".
|
|
(lambda* (#:key (exec-prefix '()) #:allow-other-keys)
|
|
(with-directory-excursion "examples"
|
|
(every
|
|
(lambda (prec type)
|
|
(let ((tester (apply open-pipe*
|
|
`(,OPEN_WRITE
|
|
,@exec-prefix
|
|
,(string-append "./" prec
|
|
"simpletest"))))
|
|
(input (open-input-file
|
|
(string-append "input_simpletest_" type))))
|
|
(begin
|
|
(dump-port input tester)
|
|
(close-port input)
|
|
(zero? (close-pipe tester)))))
|
|
'("s" "d" "c" "z")
|
|
'("real" "real" "cmplx" "cmplx")))))
|
|
(replace 'install
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
(libdir (string-append out "/lib")))
|
|
(copy-recursively "lib" libdir)
|
|
(copy-recursively "include" (string-append out "/include"))
|
|
(when (file-exists? "libseq/libmpiseq.a")
|
|
(install-file "libseq/libmpiseq.a" libdir))
|
|
(when (file-exists? "libseq/libmpiseq.so")
|
|
(install-file "libseq/libmpiseq.so" libdir))
|
|
#t))))))
|
|
(home-page "http://mumps.enseeiht.fr")
|
|
(synopsis "Multifrontal sparse direct solver")
|
|
(description
|
|
"MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
|
|
sparse system of linear equations A x = b using Gaussian elimination.")
|
|
(license license:cecill-c)))
|
|
|
|
(define-public mumps-metis
|
|
(package (inherit mumps)
|
|
(name "mumps-metis")
|
|
(inputs
|
|
(alist-delete "scotch" (package-inputs mumps)))))
|
|
|
|
(define-public mumps-openmpi
|
|
(package (inherit mumps)
|
|
(name "mumps-openmpi")
|
|
(inputs
|
|
`(("mpi" ,openmpi)
|
|
("scalapack" ,scalapack)
|
|
("pt-scotch" ,pt-scotch)
|
|
,@(alist-delete "scotch" (package-inputs mumps))))
|
|
(arguments
|
|
(substitute-keyword-arguments (package-arguments mumps)
|
|
((#:phases phases)
|
|
`(modify-phases ,phases
|
|
(add-before 'check 'mpi-setup
|
|
,%openmpi-setup)
|
|
(replace 'check
|
|
(lambda _
|
|
((assoc-ref ,phases 'check)
|
|
#:exec-prefix '("mpirun" "-n" "2"))))))))
|
|
(synopsis "Multifrontal sparse direct solver (with MPI)")))
|
|
|
|
(define-public mumps-metis-openmpi
|
|
(package (inherit mumps-openmpi)
|
|
(name "mumps-metis-openmpi")
|
|
(inputs
|
|
(alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
|
|
|
|
(define-public ruby-asciimath
|
|
(package
|
|
(name "ruby-asciimath")
|
|
(version "1.0.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (rubygems-uri "asciimath" version))
|
|
(sha256
|
|
(base32
|
|
"1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
|
|
(build-system ruby-build-system)
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
;; Apply this patch
|
|
;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
|
|
(add-after 'unpack 'patch-remove-spurious-backslashes
|
|
(lambda _
|
|
(substitute* "spec/parser_spec.rb"
|
|
(("\\\\\"")
|
|
"\""))
|
|
#t)))))
|
|
(native-inputs
|
|
`(("bundler" ,bundler)
|
|
("ruby-rspec" ,ruby-rspec)))
|
|
(synopsis "AsciiMath parsing and conversion library")
|
|
(description
|
|
"A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
|
|
easy-to-write markup language for mathematics.")
|
|
(home-page "https://github.com/asciidoctor/asciimath")
|
|
(license license:expat)))
|
|
|
|
(define-public superlu
|
|
(package
|
|
(name "superlu")
|
|
(version "5.2.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://portal.nersc.gov/project/sparse/superlu/"
|
|
"superlu_" version ".tar.gz"))
|
|
(sha256
|
|
(base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
;; Replace the non-free implementation of MC64 with a stub adapted
|
|
;; from Debian
|
|
'(begin
|
|
(use-modules (ice-9 regex)
|
|
(ice-9 rdelim))
|
|
(call-with-output-file "SRC/mc64ad.c"
|
|
(lambda (port)
|
|
(display "
|
|
#include <stdio.h>
|
|
#include <stdlib.h>
|
|
void mc64id_(int *a) {
|
|
fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
|
|
abort ();
|
|
}
|
|
void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
|
|
int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
|
|
fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
|
|
abort ();
|
|
}\n" port)))
|
|
;; Remove the corresponding license verbiage. MC64 license follows
|
|
;; a "------" line separator.
|
|
(with-atomic-file-replacement "License.txt"
|
|
(let ((rx (make-regexp "-{8}")))
|
|
(lambda (in out)
|
|
(let loop ()
|
|
(let ((line (read-line in 'concat)))
|
|
(unless (regexp-exec rx line)
|
|
(display line out)
|
|
(loop))))
|
|
#t)))))))
|
|
(build-system cmake-build-system)
|
|
(native-inputs
|
|
`(("tcsh" ,tcsh)))
|
|
(inputs
|
|
`(("blas" ,openblas)
|
|
("gfortran" ,gfortran)))
|
|
(arguments
|
|
`(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
|
|
"-DTPL_BLAS_LIBRARIES=openblas"
|
|
"-DBUILD_SHARED_LIBS:BOOL=YES")))
|
|
(home-page "https://portal.nersc.gov/project/sparse/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 (list license:bsd-3
|
|
license:gpl2+ ;EXAMPLE/*fgmr.c
|
|
(license:fsf-free "file://SRC/colamd.h")))))
|
|
|
|
(define-public superlu-dist
|
|
(package
|
|
(name "superlu-dist")
|
|
(version "6.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://portal.nersc.gov/project/sparse/superlu/"
|
|
"superlu_dist_" version ".tar.gz"))
|
|
(sha256
|
|
(base32 "1ynmwqajc9sc3my2hssa5k9s58ggvizqv9rdss0j7w99pbh5mnvw"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
;; Replace the non-free implementation of MC64 with a stub
|
|
'(begin
|
|
(call-with-output-file "SRC/mc64ad_dist.c"
|
|
(lambda (port)
|
|
(display "
|
|
#include <stdio.h>
|
|
#include <stdlib.h>
|
|
void mc64id_dist(int *a) {
|
|
fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
|
|
abort ();
|
|
}
|
|
void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
|
|
int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
|
|
fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
|
|
abort ();
|
|
}\n" port)))
|
|
(substitute* "SRC/util.c" ;adjust default algorithm
|
|
(("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
|
|
;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
|
|
;; general (i.e. non-square) processor-grid support.
|
|
"RowPerm = NOROWPERM;"))
|
|
#t))
|
|
(patches (search-patches "superlu-dist-scotchmetis.patch"
|
|
"superlu-dist-awpm-grid.patch"))))
|
|
(build-system cmake-build-system)
|
|
(native-inputs
|
|
`(("tcsh" ,tcsh)))
|
|
(inputs
|
|
`(("gfortran" ,gfortran)
|
|
("blas" ,openblas)
|
|
("lapack" ,lapack)
|
|
("combblas" ,combinatorial-blas)))
|
|
(propagated-inputs
|
|
`(("mpi" ,openmpi) ;headers include MPI heades
|
|
("parmetis" ,pt-scotch32 "metis")
|
|
("pt-scotch" ,pt-scotch32)))
|
|
(arguments
|
|
`(#:parallel-tests? #f ;tests use MPI and OpenMP
|
|
#:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
|
|
"-DTPL_ENABLE_COMBBLASLIB=YES"
|
|
"-DTPL_BLAS_LIBRARIES=-lopenblas"
|
|
"-DTPL_LAPACK_LIBRARIES=-llapack"
|
|
(string-append "-DTPL_PARMETIS_LIBRARIES="
|
|
(string-join
|
|
'("ptscotchparmetis" "ptscotch" "ptscotcherr"
|
|
"scotchmetis" "scotch" "scotcherr")
|
|
";"))
|
|
(string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
|
|
(assoc-ref %build-inputs "parmetis")
|
|
"/include")
|
|
"-DTPL_ENABLE_COMBBLASLIB=ON"
|
|
(string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
|
|
(assoc-ref %build-inputs "combblas")
|
|
"/include/CombBLAS;"
|
|
(assoc-ref %build-inputs "combblas")
|
|
"/include/BipartiteMatchings")
|
|
"-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-before 'configure 'set-c++-standard
|
|
(lambda _
|
|
(substitute* "CMakeLists.txt"
|
|
;; AWPM headers require C++14
|
|
(("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
|
|
(add-before 'check 'mpi-setup
|
|
,%openmpi-setup)
|
|
(add-before 'check 'omp-setup
|
|
(lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
|
|
(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 "6.0.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "https://gforge.inria.fr/frs/download.php/"
|
|
"latestfile/298/scotch_" version ".tar.gz"))
|
|
(sha256
|
|
(base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8"))
|
|
(patches (search-patches "scotch-build-parallelism.patch"
|
|
"scotch-integer-declarations.patch"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("zlib" ,zlib)
|
|
("flex" ,flex)
|
|
("bison" ,bison)))
|
|
(outputs '("out" "metis"))
|
|
(arguments
|
|
`(#:make-flags (list (string-append "prefix=" %output))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after
|
|
'unpack 'chdir-to-src
|
|
(lambda _ (chdir "src") #t))
|
|
(replace
|
|
'configure
|
|
(lambda _
|
|
(call-with-output-file "Makefile.inc"
|
|
(lambda (port)
|
|
(format port "
|
|
EXE =
|
|
LIB = .a
|
|
OBJ = .o
|
|
MAKE = make
|
|
AR = ar
|
|
ARFLAGS = -ruv
|
|
CAT = cat
|
|
CCS = gcc
|
|
CCP = mpicc
|
|
CCD = gcc
|
|
CPPFLAGS =~{ -D~a~}
|
|
CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
|
|
LDFLAGS = -lz -lm -lrt -lpthread
|
|
CP = cp
|
|
LEX = flex -Pscotchyy -olex.yy.c
|
|
LN = ln
|
|