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* gnu/packages/maths.scm (hypre)[native-inputs]: Add TEXLIVE-COURIER and TEXLIVE-HELVETIC. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
7629 lines
315 KiB
Scheme
7629 lines
315 KiB
Scheme
;;; 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 © 2014-2022 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 © 2015–2022 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, 2020, 2021 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, 2021 Kei Kebreau <kkebreau@posteo.net>
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;;; Copyright © 2016-2022 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, 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
|
||
;;; Copyright © 2017 Nikita <nikita@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, 2022 Arun Isaac <arunisaac@systemreboot.net>
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||
;;; Copyright © 2017–2021 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, 2020, 2021 Jan (janneke) 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, 2020, 2021 Marius Bakke <marius@gnu.org>
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||
;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
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||
;;; Copyright © 2018, 2021 Julien Lepiller <julien@lepiller.eu>
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||
;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
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||
;;; Copyright © 2019, 2021, 2022 Nicolas Goaziou <mail@nicolasgoaziou.fr>
|
||
;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
|
||
;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net>
|
||
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
|
||
;;; Copyright © 2020–2022 Felix Gruber <felgru@posteo.net>
|
||
;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in>
|
||
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
|
||
;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
|
||
;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com>
|
||
;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
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||
;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com>
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||
;;; Copyright © 2020 Martin Becze <mjbecze@riseup.net>
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;;; Copyright © 2021 Gerd Heber <gerd.heber@gmail.com>
|
||
;;; Copyright © 2021 Franck Pérignon <franck.perignon@univ-grenoble-alpes.fr>
|
||
;;; Copyright © 2021 Philip McGrath <philip@philipmcgrath.com>
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||
;;; Copyright © 2021, 2022 Paul A. Patience <paul@apatience.com>
|
||
;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru>
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||
;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
|
||
;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
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||
;;; Copyright © 2021 Pierre-Antoine Bouttier <pierre-antoine.bouttier@univ-grenoble-alpes.fr>
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;;;
|
||
;;; This file is part of GNU Guix.
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||
;;;
|
||
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
||
;;; under the terms of the GNU General Public License as published by
|
||
;;; the Free Software Foundation; either version 3 of the License, or (at
|
||
;;; your option) any later version.
|
||
;;;
|
||
;;; GNU Guix is distributed in the hope that it will be useful, but
|
||
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
||
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||
;;; GNU General Public License for more details.
|
||
;;;
|
||
;;; You should have received a copy of the GNU General Public License
|
||
;;; 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)
|
||
#:use-module (ice-9 match)
|
||
#:use-module (gnu packages)
|
||
#:use-module ((guix licenses) #:prefix license:)
|
||
#:use-module (guix packages)
|
||
#:use-module (guix download)
|
||
#:use-module (guix git-download)
|
||
#:use-module (guix gexp)
|
||
#:use-module (guix utils)
|
||
#:use-module ((guix build utils) #:select (alist-replace))
|
||
#:use-module (guix build-system cmake)
|
||
#:use-module (guix build-system glib-or-gtk)
|
||
#:use-module (guix build-system gnu)
|
||
#:use-module (guix build-system meson)
|
||
#:use-module (guix build-system ocaml)
|
||
#:use-module (guix build-system perl)
|
||
#: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 bash)
|
||
#: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)
|
||
#:use-module (gnu packages coq)
|
||
#:use-module (gnu packages curl)
|
||
#:use-module (gnu packages cyrus-sasl)
|
||
#:use-module (gnu packages datamash)
|
||
#:use-module (gnu packages dbm)
|
||
#:use-module (gnu packages documentation)
|
||
#:use-module (gnu packages elf)
|
||
#:use-module (gnu packages emacs)
|
||
#:use-module (gnu packages file)
|
||
#:use-module (gnu packages flex)
|
||
#:use-module (gnu packages fltk)
|
||
#:use-module (gnu packages fontutils)
|
||
#:use-module (gnu packages gettext)
|
||
#:use-module (gnu packages gcc)
|
||
#:use-module (gnu packages gd)
|
||
#:use-module (gnu packages ghostscript)
|
||
#:use-module (gnu packages glib)
|
||
#:use-module (gnu packages graphviz)
|
||
#:use-module (gnu packages gtk)
|
||
#:use-module (gnu packages icu4c)
|
||
#: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 llvm)
|
||
#: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)
|
||
#:use-module (gnu packages m4)
|
||
#:use-module (gnu packages mpi)
|
||
#:use-module (gnu packages multiprecision)
|
||
#:use-module (gnu packages ncurses)
|
||
#:use-module (gnu packages netpbm)
|
||
#:use-module (gnu packages ocaml)
|
||
#:use-module (gnu packages onc-rpc)
|
||
#:use-module (gnu packages parallel)
|
||
#:use-module (gnu packages pcre)
|
||
#:use-module (gnu packages popt)
|
||
#:use-module (gnu packages perl)
|
||
#:use-module (gnu packages pkg-config)
|
||
#:use-module (gnu packages pulseaudio)
|
||
#:use-module (gnu packages python)
|
||
#:use-module (gnu packages python-web)
|
||
#:use-module (gnu packages python-xyz)
|
||
#:use-module (gnu packages qt)
|
||
#:use-module (gnu packages readline)
|
||
#:use-module (gnu packages ruby)
|
||
#:use-module (gnu packages tbb)
|
||
#:use-module (gnu packages scheme)
|
||
#:use-module (gnu packages serialization)
|
||
#:use-module (gnu packages shells)
|
||
#:use-module (gnu packages sphinx)
|
||
#:use-module (gnu packages swig)
|
||
#:use-module (gnu packages tcl)
|
||
#:use-module (gnu packages texinfo)
|
||
#:use-module (gnu packages tex)
|
||
#:use-module (gnu packages tls)
|
||
#:use-module (gnu packages version-control)
|
||
#:use-module (gnu packages wxwidgets)
|
||
#:use-module (gnu packages xml)
|
||
#:use-module (srfi srfi-1)
|
||
#:use-module (srfi srfi-26))
|
||
|
||
(define-public aris
|
||
(package
|
||
(name "aris")
|
||
(version "2.2")
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||
(source (origin
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||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
|
||
(sha256 (base32
|
||
"1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
|
||
(build-system gnu-build-system)
|
||
(inputs (list gtk+ libxml2))
|
||
(native-inputs (list pkg-config))
|
||
(arguments
|
||
`(#:configure-flags '("CFLAGS=-O2 -g -fcommon")))
|
||
(synopsis "Natural deduction first-order logic interface")
|
||
(description "Aris is a program for performing logical proofs. It supports
|
||
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.")
|
||
(license license:gpl3+)
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||
(home-page "https://www.gnu.org/software/aris/")))
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||
|
||
(define-public bitwise
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||
(package
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||
(name "bitwise")
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||
(version "0.42")
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||
(source (origin
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||
(method url-fetch)
|
||
(uri (string-append "https://github.com/mellowcandle/bitwise"
|
||
"/releases/download/v" version
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||
"/bitwise-v" version ".tar.gz"))
|
||
(sha256
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||
(base32 "1lniw4bsb5qs5ybf018qllf95pzixb1q3lvybzl4k3xz8zpkrm6k"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
(list ncurses readline))
|
||
(native-inputs
|
||
(list cunit pkg-config))
|
||
(synopsis "Terminal based bit manipulator in ncurses")
|
||
(description "Bitwise is a multi base interactive calculator supporting
|
||
dynamic base conversion and bit manipulation. It's a handy tool for low level
|
||
hackers, kernel developers and device drivers developers.
|
||
|
||
Some of the features include:
|
||
@itemize
|
||
@item Interactive ncurses interface.
|
||
@item Command line calculator supporting all bitwise operations.
|
||
@item Individual bit manipulator.
|
||
@item Bitwise operations such as NOT, OR, AND, XOR, and shifts.
|
||
@end itemize")
|
||
(license license:gpl3+)
|
||
(home-page "https://github.com/mellowcandle/bitwise/")))
|
||
|
||
(define-public c-graph
|
||
(package
|
||
(name "c-graph")
|
||
(version "2.0.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/c-graph/c-graph-" version
|
||
".tar.gz"))
|
||
(sha256 (base32
|
||
"092412jzxy6wdvpk96pfj499hpmaww8xllavbvlqspfpr7ips9id"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
(list 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
|
||
student to write code, the program offers an intuitive interface with
|
||
interactive dialogs to guide them.")
|
||
(license license:gpl3+)
|
||
(home-page "https://www.gnu.org/software/c-graph/")))
|
||
|
||
(define-public coda
|
||
(package
|
||
(name "coda")
|
||
(version "2.19")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://github.com/stcorp/coda/releases/download/"
|
||
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 "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 "2020.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://www.qhull.org/download/qhull-"
|
||
(car (string-split version #\.))
|
||
"-src-8.0.2.tgz"))
|
||
(sha256
|
||
(base32
|
||
"0zlbhg0lb6j60188c2xhcrvviskr079552icjldqhy1jhgmxghmm"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:configure-flags '("-DLINK_APPS_SHARED=ON"
|
||
"-DCMAKE_POSITION_INDEPENDENT_CODE=ON")))
|
||
(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 "1.2.7")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/cvxopt/cvxopt")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"114z34wwx1bsv4q6xj9p5q99dffgnj9s4i4arx10g191xq9q8i5y"))))
|
||
(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
|
||
(list fftw
|
||
glpk
|
||
gsl
|
||
lapack
|
||
openblas
|
||
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 units
|
||
(package
|
||
(name "units")
|
||
(version "2.21")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/units/units-" version
|
||
".tar.gz"))
|
||
(sha256 (base32
|
||
"1bybhqs4yrly9myb5maz3kdmf8k4fhk2m1d5cbcryn40z6lq0gkc"))))
|
||
(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")
|
||
`("GUIX_PYTHONPATH" ":" prefix
|
||
,(search-path-as-string->list (getenv "GUIX_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 (list 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 dsfmt
|
||
(package
|
||
(name "dsfmt")
|
||
(version "2.2.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri
|
||
(string-append
|
||
"http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/"
|
||
"dSFMT-src-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))
|
||
(modules '((guix build utils)))
|
||
;; Don't distribute html documentation with bundled jquery.
|
||
(snippet
|
||
'(begin
|
||
(delete-file-recursively "html") #t))
|
||
;; Add patches borrowed from Julia.
|
||
(patches
|
||
(list
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://raw.githubusercontent.com/JuliaLang/julia/"
|
||
"v1.3.0/deps/patches/dSFMT.c.patch"))
|
||
(sha256 (base32
|
||
"09mhv11bms8jsmkmdqvlcgljwhzw3b6n9nncpi2b6dla9798hw2y"))
|
||
(file-name "dSFMT.c.patch"))
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://raw.githubusercontent.com/JuliaLang/julia/"
|
||
"v1.3.0/deps/patches/dSFMT.h.patch"))
|
||
(sha256 (base32
|
||
"1py5rd0yxic335lzka23f6x2dhncrpizpyrk57gi2f28c0p98y5n"))
|
||
(file-name "dSFMT.h.patch"))))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(delete 'configure) ; no configure script
|
||
(replace 'build
|
||
;; Upstream Makefile does not build a shared library. Borrow from Julia
|
||
;; https://github.com/JuliaLang/julia/blob/v1.3.0/deps/dsfmt.mk
|
||
(lambda _
|
||
(invoke
|
||
"gcc" "-DNDEBUG" "-DDSFMT_MEXP=19937"
|
||
"-fPIC" "-DDSFMT_DO_NOT_USE_OLD_NAMES"
|
||
"-O3" "-finline-functions" "-fomit-frame-pointer"
|
||
"-fno-strict-aliasing" "--param" "max-inline-insns-single=1800"
|
||
"-Wmissing-prototypes" "-Wall" "-std=c99" "-shared" "dSFMT.c"
|
||
"-o" "libdSFMT.so")))
|
||
(replace 'install ; no "install" target
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(lib (string-append out "/lib"))
|
||
(inc (string-append out "/include"))
|
||
(doc (string-append out "/share/doc/" ,name "-" ,version)))
|
||
(install-file "libdSFMT.so" lib)
|
||
(install-file "dSFMT.h" inc)
|
||
(install-file "LICENSE.txt" doc)
|
||
#t))))))
|
||
(synopsis "Double precision SIMD-oriented Fast Mersenne Twister")
|
||
(description
|
||
"The dSMFT package speeds up Fast Mersenne Twister generation by avoiding
|
||
the expensive conversion of integer to double (floating point). dSFMT directly
|
||
generates double precision floating point pseudorandom numbers which have the
|
||
IEEE Standard for Binary Floating-Point Arithmetic (ANSI/IEEE Std 754-1985)
|
||
format. dSFMT is only available on the CPUs which use IEEE 754 format double
|
||
precision floating point numbers.")
|
||
(home-page "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public gsl
|
||
(package
|
||
(name "gsl")
|
||
(version "2.7")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/gsl/gsl-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0av04cpblphvvs3kl5rwphniarml503501vrpqw31rd0bmwg7fzg"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
(let ((system (%current-system)))
|
||
`(#:configure-flags (list "--disable-static") ;halves package size
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
,@(cond
|
||
((and (target-riscv64?)
|
||
(%current-target-system))
|
||
'((add-after 'unpack 'force-bootstrap
|
||
(lambda _
|
||
;; gsl ships with an old configure script that does not
|
||
;; support riscv64. Regenerate it.
|
||
(delete-file "configure")))))
|
||
|
||
((or (string-prefix? "aarch64" system)
|
||
(string-prefix? "powerpc" system))
|
||
;; Some sparse matrix tests are failing on AArch64 and PowerPC:
|
||
;; https://lists.gnu.org/archive/html/bug-gsl/2020-04/msg00001.html
|
||
'((add-before 'check 'disable-failing-tests
|
||
(lambda _
|
||
(substitute* "spmatrix/test.c"
|
||
((".*test_complex.*") "\n"))))))
|
||
|
||
((string-prefix? "i686" system)
|
||
;; There are rounding issues with these tests on i686:
|
||
;; https://lists.gnu.org/archive/html/bug-gsl/2016-10/msg00000.html
|
||
;; https://lists.gnu.org/archive/html/bug-gsl/2020-04/msg00000.html
|
||
'((add-before 'check 'disable-failing-tests
|
||
(lambda _
|
||
(substitute* "linalg/test.c"
|
||
((".*gsl_test\\(test_LU_decomp.*") "\n")
|
||
((".*gsl_test\\(test_LUc_decomp.*") "\n")
|
||
((".*gsl_test\\(test_QR_decomp_r.*") "\n")
|
||
((".*gsl_test\\(test_cholesky_decomp.*") "\n")
|
||
((".*gsl_test\\(test_pcholesky_solve.*") "\n")
|
||
((".*gsl_test\\(test_COD_lssolve2.*") "\n"))
|
||
(substitute* "spmatrix/test.c"
|
||
((".*test_all.*") "\n")
|
||
((".*test_float.*") "\n")
|
||
((".*test_complex.*") "\n"))
|
||
|
||
;; XXX: These tests abort with:
|
||
;; gsl: cholesky.c:645: ERROR: matrix is not positive definite
|
||
(substitute* '("multifit_nlinear/test.c"
|
||
"multilarge_nlinear/test.c")
|
||
(("gsl_ieee_env_setup.*" all)
|
||
(string-append "exit (77);\n" all)))))))
|
||
|
||
(else '()))))))
|
||
(native-inputs
|
||
(if (and (target-riscv64?)
|
||
(%current-target-system))
|
||
(list autoconf automake libtool)
|
||
'()))
|
||
(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.")
|
||
|
||
;; Linear algebra routines should benefit from SIMD optimizations.
|
||
(properties `((tunable? . #t)))
|
||
|
||
(license license:gpl3+)))
|
||
|
||
;; TODO: Merge back into the gsl package as a separate output.
|
||
(define-public gsl-static
|
||
(package/inherit gsl
|
||
(name "gsl-static")
|
||
(arguments
|
||
`(,@(package-arguments gsl)
|
||
#:configure-flags (list "--disable-shared")
|
||
#:make-flags (list "CFLAGS=-fPIC")))))
|
||
|
||
(define-public sleef
|
||
(package
|
||
(name "sleef")
|
||
(version "3.5.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/shibatch/sleef")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1jybqrl2dvjxzg30xrhh847s375n2jr1pix644wi6hb5wh5mx3f7"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
'(#:configure-flags (list "-DCMAKE_BUILD_TYPE=Release"
|
||
(string-append "-DCMAKE_INSTALL_LIBDIR="
|
||
(assoc-ref %outputs "out")
|
||
"/lib")
|
||
(string-append "-DCMAKE_INSTALL_PREFIX="
|
||
(assoc-ref %outputs "out")))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
;; SLEEF generates a header library during the build process and writes
|
||
;; to it via shell redirection. Make the checkout writable so the
|
||
;; build can succeed.
|
||
(add-after 'unpack 'make-git-checkout-writable
|
||
(lambda _
|
||
(for-each make-file-writable (find-files "."))
|
||
#t)))))
|
||
(inputs
|
||
(list fftw gmp mpfr openssl))
|
||
(home-page "https://sleef.org/")
|
||
(synopsis "SIMD library for evaluating elementary functions and DFT")
|
||
(description
|
||
"SLEEF (SIMD Library for Evaluating Elementary Functions) is a library that
|
||
implements vectorized versions of all C99 real floating point math functions.
|
||
It can utilize SIMD instructions that are available on modern processors.")
|
||
(license (list license:boost1.0 ;sleef
|
||
license:cc-by4.0)))) ;simplex algorithm
|
||
|
||
(define-public glpk
|
||
(package
|
||
(name "glpk")
|
||
(version "5.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/glpk/glpk-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"05bgxidxj8d9xdp82niy7cy36w181cxq7p8vc3y2ixshpgp1642a"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
(list gmp))
|
||
(arguments
|
||
`(#:configure-flags '("--with-gmp"
|
||
"--disable-static")))
|
||
(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 glpk-4
|
||
(package
|
||
(inherit glpk)
|
||
(name "glpk")
|
||
(version "4.65")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/glpk/glpk-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))))
|
||
|
||
(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
|
||
(list (@ (gnu packages base) which))) ; for the tests
|
||
(inputs
|
||
(list glpk 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
|
||
(list 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 "7.2")
|
||
(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
|
||
"1w1jsnfgny8cihndr5gfm99pvwp48qsvxkqfsi2q87gd3m57aj7w"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
(list 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 libcerf
|
||
(package
|
||
(name "libcerf")
|
||
(version "1.14")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://jugit.fz-juelich.de/mlz/libcerf")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1ic2q7kvxpqmgxlishygvx8d00i4wn51vkq4fyac44ahhf6c3kwd"))))
|
||
(build-system cmake-build-system)
|
||
(native-inputs
|
||
(list perl))
|
||
(home-page "https://jugit.fz-juelich.de/mlz/libcerf")
|
||
(synopsis "Library for complex error functions")
|
||
(description
|
||
"@code{libcerf} is a self-contained numeric library that provides an
|
||
efficient and accurate implementation of complex error functions, along with
|
||
Dawson, Faddeeva, and Voigt functions.")
|
||
(license license:expat)))
|
||
|
||
(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
|
||
(list 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 "3.8.0")
|
||
(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
|
||
"0l7as5z6xvbxly8alam9s4kws70952qq35a6vkljzayi4b9gbklx"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
(list autoconf automake libtool pkg-config))
|
||
(inputs
|
||
(list eigen lapack 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")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference (url (package-home-page arpack-ng))
|
||
(commit version)))
|
||
(file-name (git-file-name (package-name arpack-ng) version))
|
||
(sha256
|
||
(base32
|
||
"00h6bjvxjq7bv0b8pwnc0gw33ns6brlqv00xx2rh3w9b5n205918"))))))
|
||
|
||
(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 clapack
|
||
(package
|
||
(name "clapack")
|
||
(version "3.2.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://www.netlib.org/clapack/clapack-"
|
||
version "-CMAKE.tgz"))
|
||
(sha256
|
||
(base32
|
||
"0nnap9q1mv14g57dl3vkvxrdr10k5w7zzyxs6rgxhia8q8mphgqb"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:configure-flags '("-DCMAKE_C_FLAGS=-fcommon -O2")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
;; These tests use a lot of stack variables and segfault without
|
||
;; lifting resource limits.
|
||
(add-after 'unpack 'disable-broken-tests
|
||
(lambda _
|
||
(substitute* "TESTING/CMakeLists.txt"
|
||
(("add_lapack_test.* xeigtstz\\)") ""))))
|
||
(replace 'install
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(libdir (string-append out "/lib"))
|
||
(f2cinc (string-append out "/include/libf2c")))
|
||
(mkdir-p f2cinc)
|
||
(display (getcwd))
|
||
(for-each (lambda (file)
|
||
(install-file file libdir))
|
||
'("SRC/liblapack.a"
|
||
"F2CLIBS/libf2c/libf2c.a"
|
||
"TESTING/MATGEN/libtmglib.a"
|
||
"BLAS/SRC/libblas.a"))
|
||
(for-each (lambda (file)
|
||
(install-file file f2cinc))
|
||
(cons "F2CLIBS/libf2c/arith.h"
|
||
(find-files (string-append "../clapack-"
|
||
,version "-CMAKE/F2CLIBS/libf2c")
|
||
"\\.h$")))
|
||
(copy-recursively (string-append "../clapack-"
|
||
,version "-CMAKE/INCLUDE")
|
||
(string-append out "/include"))))))))
|
||
(home-page "https://www.netlib.org/clapack/")
|
||
(synopsis "Numerical linear algebra library for C")
|
||
(description
|
||
"The CLAPACK library was built using a Fortran to C conversion utility
|
||
called f2c. The entire Fortran 77 LAPACK library is run through f2c to obtain
|
||
C code, and then modified to improve readability. CLAPACK's goal is to
|
||
provide LAPACK for someone who does not have access to a Fortran compiler.")
|
||
(license (license:non-copyleft "file://LICENSE"
|
||
"See LICENSE in the distribution."))))
|
||
|
||
(define-public scalapack
|
||
(package
|
||
(name "scalapack")
|
||
(version "2.1.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://www.netlib.org/scalapack/scalapack-"
|
||
version ".tgz"))
|
||
(sha256
|
||
(base32
|
||
"19i0h9vdc3zsy58r6fy1vs2kz2l7amifkz0cf926j90xz1n23nb1"))
|
||
(patches (search-patches "scalapack-gcc-10-compilation.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)
|
||
(add-after 'unpack 'skip-faulty-test
|
||
(lambda _
|
||
;; FIXME: Skip these two tests that fail to complete for
|
||
;; unknown reasons:
|
||
;; <https://github.com/Reference-ScaLAPACK/scalapack/issues/43>.
|
||
(substitute* "TESTING/CMakeLists.txt"
|
||
(("^add_test\\(x[sd]hseqr.*" all)
|
||
(string-append "# " all "\n"))))))))
|
||
(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 feedgnuplot
|
||
(package
|
||
(name "feedgnuplot")
|
||
(version "1.60")
|
||
(home-page "https://github.com/dkogan/feedgnuplot")
|
||
(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
|
||
"0403hwlian2s431m36qdzcczhvfjvh7128m64hmmwbbrgh0n7md7"))))
|
||
(build-system perl-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'check 'adjust-tests
|
||
(lambda _
|
||
(substitute* "t/plots.t"
|
||
;; XXX: The vnlog tests uses 'echo' with escaped strings,
|
||
;; but does not enable escape interpretation.
|
||
(("echo -n ")
|
||
"echo -ne "))))
|
||
(add-after 'install 'install-documentation
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(doc (string-append out "/share/doc/feedgnuplot")))
|
||
(mkdir-p doc)
|
||
(invoke "pod2html" "--title=feedgnuplot" "bin/feedgnuplot"
|
||
"--outfile" (string-append doc "/feedgnuplot.html")))))
|
||
(add-after 'install 'wrap
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(gnuplot (search-input-file inputs "/bin/gnuplot"))
|
||
;; XXX: We need List::MoreUtils as well as its supporting
|
||
;; (propagated) modules; for now just refer to labels.
|
||
(modules '("perl-list-moreutils" "perl-exporter-tiny"))
|
||
(PERL5LIB (string-join
|
||
(map (lambda (input)
|
||
(string-append (assoc-ref inputs input)
|
||
"/lib/perl5/site_perl"))
|
||
modules)
|
||
":")))
|
||
(wrap-program (string-append out "/bin/feedgnuplot")
|
||
`("PERL5LIB" ":" suffix (,PERL5LIB))
|
||
`("PATH" ":" suffix (,(dirname gnuplot))))))))))
|
||
(inputs
|
||
(list gnuplot perl-list-moreutils vnlog))
|
||
(native-inputs
|
||
;; For tests.
|
||
(list perl-ipc-run perl-string-shellquote))
|
||
(synopsis "Pipe-oriented plotting tool")
|
||
(description
|
||
"@command{feedgnuplot} is a tool to plot realtime and stored data
|
||
from the command line, using @command{gnuplot}. It can read data from
|
||
a pipe or file, make a variety of transformations, and render the result
|
||
in the terminal or with an external viewer.")
|
||
(license license:gpl1+))) ;any version
|
||
|
||
(define-public gnuplot
|
||
(package
|
||
(name "gnuplot")
|
||
(version "5.4.3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
|
||
version "/gnuplot-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32 "112dplskbkdbaqi935m2xlk1xsw8s5l568wm7xad75hgp6x9py2i"))))
|
||
(build-system gnu-build-system)
|
||
(inputs (list readline cairo pango gd lua))
|
||
(native-inputs
|
||
`(("pkg-config" ,pkg-config)
|
||
("texlive" ,texlive-tiny)))
|
||
(arguments `(#:configure-flags (list (string-append
|
||
"--with-texdir=" %output
|
||
"/texmf-local/tex/latex/gnuplot"))
|
||
;; Plot on a dumb terminal during tests.
|
||
#:make-flags '("GNUTERM=dumb")))
|
||
(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")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
|
||
(native-inputs
|
||
(list 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
|
||
(list gfortran bison flex))
|
||
(inputs
|
||
`(("zlib" ,zlib)
|
||
("libjpeg" ,libjpeg-turbo)
|
||
("libtirpc" ,libtirpc)))
|
||
(arguments
|
||
`(#:parallel-tests? #f
|
||
#:configure-flags (list "--enable-shared"
|
||
"FCFLAGS=-fallow-argument-mismatch"
|
||
"FFLAGS=-fallow-argument-mismatch"
|
||
(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/)([0-9A-Za-z]*)" all prefix hash)
|
||
(string-append prefix (string-take hash 10) "...")))
|
||
#t))
|
||
(add-after 'install 'provide-absolute-libjpeg-reference
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out"))
|
||
(libjpeg (assoc-ref inputs "libjpeg")))
|
||
;; libjpeg-turbo does not provide a .la file, so libtool is
|
||
;; unable to add an absolute reference for -ljpeg in the .la
|
||
;; files. Fix it manually to avoid having to propagate it.
|
||
(substitute* (find-files (string-append out "/lib") "\\.la$")
|
||
(("-ljpeg")
|
||
(string-append "-L" libjpeg "/lib -ljpeg")))
|
||
#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 hdf5-1.8
|
||
(package
|
||
(name "hdf5")
|
||
(version "1.8.22")
|
||
(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 "194ki2s5jrgl4czkvy5nc9nwjyapah0fj72l0gb0aysplp38i6v8"))
|
||
(patches (search-patches "hdf5-config-date.patch"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
(list zlib))
|
||
(native-inputs
|
||
(list gfortran 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-zA-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 hdf5-1.8)
|
||
(version "1.10.7")
|
||
(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 "0pm5xxry55i0h7wmvc7svzdaa90rnk7h78rrjmnlkz2ygsn8y082"))
|
||
(patches (search-patches "hdf5-config-date.patch"))))))
|
||
|
||
(define-public hdf5-1.12
|
||
(package
|
||
(inherit hdf5-1.8)
|
||
(version "1.12.1")
|
||
(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 "074g3z504xf77ff38igs30i1aqxpm508p7yw78ykva7dncrgbyda"))
|
||
(patches (search-patches "hdf5-config-date.patch"))))))
|
||
|
||
(define-public hdf5
|
||
;; Default version of HDF5.
|
||
hdf5-1.10)
|
||
|
||
(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" ,hdf5-1.8)
|
||
("zlib" ,zlib)
|
||
("libjpeg" ,libjpeg-turbo)
|
||
("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=" (search-input-file %build-inputs "/lib/libz.so"))
|
||
(string-append "JPEGLIB="
|
||
(search-input-file %build-inputs "/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")
|
||
;; 'slf4j-api-X.Y.Z.jar' is installed in a Maven-style
|
||
;; directory, so use 'find-files' to find it.
|
||
(car (find-files (assoc-ref inputs "slf4j-api")
|
||
"^slf4j-api.*\\.jar$"))))
|
||
;; Replace outdated config.sub and config.guess:
|
||
(with-directory-excursion "config"
|
||
(for-each (lambda (file)
|
||
(install-file
|
||
(search-input-file inputs
|
||
(string-append
|
||
"/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
|
||
(append
|
||
(map (lambda (i)
|
||
(car (find-files (assoc-ref inputs i)
|
||
(string-append "^" i
|
||
".*\\.jar$"))))
|
||
'("slf4j-api" "slf4j-simple"))
|
||
(list
|
||
(car (find-files (assoc-ref inputs "junit") "jar$"))
|
||
(car (find-files (assoc-ref inputs "hamcrest-core")
|
||
"jar$")))))
|
||
(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")
|
||
(search-input-file inputs "/bin/test"))
|
||
(("/usr/bin/uname")
|
||
(search-input-file inputs "/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
|
||
(list 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-turbo)
|
||
("libtirpc" ,libtirpc)
|
||
|
||
("gctp" ,gctp)))
|
||
(arguments
|
||
`( #:configure-flags '("--enable-install-include" "--enable-shared"
|
||
"CC=h4cc -Df2cFortran" "LIBS=-lgctp")
|
||
#:parallel-tests? #f))
|
||
(home-page "https://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
|
||
(list gfortran))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
(list hdf5-1.8 zlib 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 hdf5-1.10 ;use the latest
|
||
(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/test/h5diff/testph5diff.sh"
|
||
(("/bin/sh") (which "sh")))
|
||
#t))))))
|
||
(synopsis "Management suite for data with parallel IO support")))
|
||
|
||
(define-public hdf5-blosc
|
||
(package
|
||
(name "hdf5-blosc")
|
||
(version "1.0.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/Blosc/hdf5-blosc")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1nj2bm1v6ymm3fmyvhbn6ih5fgdiapavlfghh1pvbmhw71cysyqs"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:configure-flags
|
||
(list (string-append "-DBLOSC_INSTALL_DIR="
|
||
(assoc-ref %build-inputs "c-blosc"))
|
||
(string-append "-DPLUGIN_INSTALL_PATH="
|
||
(assoc-ref %outputs "out")
|
||
"/hdf5/lib/plugin"))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'do-not-build-blosc
|
||
(lambda _
|
||
(substitute* "CMakeLists.txt"
|
||
(("set\\(BLOSC_INSTALL_DIR.*") "")
|
||
(("ExternalProject_Add\\(project_blosc") "message("))
|
||
#t)))))
|
||
(inputs
|
||
(list c-blosc hdf5-1.10))
|
||
(home-page "https://github.com/Blosc/hdf5-blosc")
|
||
(synopsis "Filter for HDF5 using the Blosc compressor")
|
||
(description "This is a filter for HDF5 that uses the Blosc compressor; by
|
||
installing this filter, you can read and write HDF5 files with
|
||
Blosc-compressed datasets.")
|
||
(license license:expat)))
|
||
|
||
(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 (list hdf5-1.8)) ;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*
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'set-man-page-date
|
||
(lambda _
|
||
(substitute* "itpp-config.1.cmake.in"
|
||
((".PACKAGE_DATE.") "2012-04-18"))))
|
||
(add-before 'build 'set-force-source-date
|
||
;; for reproducible dates, texlive needs this to respect respect
|
||
;; SOURCE_DATE_EPOCH
|
||
(lambda _
|
||
(setenv "FORCE_SOURCE_DATE" "1"))))))
|
||
(inputs (list lapack 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 "4.7.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://www.unidata.ucar.edu/downloads/netcdf/ftp/"
|
||
"netcdf-c-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1a2fpp15a2rl1m50gcvvzd9y6bavl6vjf9zzf63sz5gdmq06yiqf"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
;; Make sure this variable is defined only once. Failing to do so
|
||
;; would break builds of 'netcdf-parallel-openmpi' with a
|
||
;; multiple-definition link error with GCC 10.
|
||
'(substitute* "ncdump/ocprint.c"
|
||
(("^int ocdebug") "static int ocdebug")))
|
||
(patches (search-patches "netcdf-date-time.patch"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
(list m4 doxygen graphviz))
|
||
(inputs
|
||
`(("hdf4" ,hdf4-alt)
|
||
("hdf5" ,hdf5)
|
||
("curl" ,curl)
|
||
("zlib" ,zlib)
|
||
("libjpeg" ,libjpeg-turbo)))
|
||
(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/)([0-9A-Za-z]*)" 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))
|
||
((#:phases phases '%standard-phases)
|
||
`(modify-phases ,phases
|
||
(add-after 'build 'mpi-setup
|
||
,%openmpi-setup)))))))
|
||
|
||
(define-public netcdf-fortran
|
||
(package
|
||
(name "netcdf-fortran")
|
||
(version "4.5.3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0x4acvfhbsx1q79dkkwrwbgfhm0w5ngnp4zj5kk92s1khihmqfhj"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:configure-flags '("FCFLAGS=-fallow-argument-mismatch"
|
||
"FFLAGS=-fallow-argument-mismatch")
|
||
#:parallel-tests? #f))
|
||
(inputs
|
||
(list netcdf))
|
||
(native-inputs
|
||
(list gfortran))
|
||
(synopsis "Fortran interface for the netCDF library")
|
||
(description (package-description netcdf))
|
||
(home-page (package-home-page netcdf))
|
||
(license (package-license netcdf))))
|
||
|
||
(define-public n2p2
|
||
(package
|
||
(name "n2p2")
|
||
(version "2.1.4")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/CompPhysVienna/n2p2")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1lw195ihpxwh08387i4gamk1glhalpq888q6nj8l5vswbgnrv1pq"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:make-flags '("MODE=shared" "-C" "src")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'post-unpack
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(substitute* "src/makefile.gnu"
|
||
(("PROJECT_EIGEN=/usr/include/eigen3")
|
||
(string-append "PROJECT_EIGEN="
|
||
(assoc-ref inputs "eigen") "/include/eigen3")))
|
||
(substitute* "src/makefile.gnu"
|
||
(("-lblas")
|
||
(string-append "-L" (assoc-ref inputs "openblas")
|
||
"/lib -lopenblas"))
|
||
(("-march=native")
|
||
""))
|
||
(substitute* "src/application/makefile"
|
||
(("LDFLAGS=")
|
||
"LDFLAGS=-Wl,-rpath='$$ORIGIN/../lib' "))))
|
||
(delete 'configure)
|
||
(delete 'check)
|
||
(replace 'install
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(bindir (string-append out "/bin"))
|
||
(libdir (string-append out "/lib"))
|
||
(incdir (string-append out "/include")))
|
||
(for-each (lambda (f) (install-file f bindir))
|
||
(find-files "bin" "^nnp-"))
|
||
(for-each (lambda (f) (install-file f libdir))
|
||
(find-files "lib" "\\.so$"))
|
||
(for-each (lambda (f) (install-file f incdir))
|
||
(find-files "include" "\\.h$"))))))))
|
||
(inputs
|
||
(list openmpi gsl openblas eigen))
|
||
(synopsis "Neural network potentials for chemistry and physics")
|
||
(description "This package contains software that will allow you to use
|
||
existing neural network potential parameterizations to predict energies and
|
||
forces (with standalone tools but also in conjunction with the MD software
|
||
LAMMPS). In addition it is possible to train new neural network potentials
|
||
with the provided training tools.")
|
||
(home-page "https://compphysvienna.github.io/n2p2/")
|
||
(properties '((tunable? . #t))) ;to benefit from SIMD code in Eigen
|
||
(license license:gpl3+)))
|
||
|
||
(define-public nlopt
|
||
(package
|
||
(name "nlopt")
|
||
(version "2.7.1")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/stevengj/nlopt/")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1xpdza28i8w441fwv6a5f3qk4zi7ys6ws9fx6kr5ny27dfdz6rr1"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#: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.
|
||
(let ((out (assoc-ref outputs "out")))
|
||
(substitute* "src/swig/nlopt-guile.i"
|
||
(("\"nlopt_guile\"")
|
||
(format #f "~s"
|
||
`(format #f "~anlopt_guile"
|
||
(if (getenv "NLOPT_UNINSTALLED")
|
||
""
|
||
,(format #f "~a/lib/guile/3.0/extensions/" out))))))
|
||
(setenv "NLOPT_UNINSTALLED" "1")))))))
|
||
(inputs (list guile-3.0 octave python))
|
||
(native-inputs (list pkg-config swig))
|
||
(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 "3.13.4")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/coin-or/Ipopt")
|
||
(commit (string-append "releases/" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"08gznhwhqv1x4baksz350ih8q16r5rd0k8vals6078m3h94khr4b"))))
|
||
(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
|
||
(list gfortran pkg-config))
|
||
(inputs
|
||
;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
|
||
(list lapack)) ;for both libblas and liblapack
|
||
(home-page "https://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:epl2.0)))
|
||
|
||
(define-public nomad-optimizer
|
||
(package
|
||
(name "nomad-optimizer")
|
||
(version "4.2.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/bbopt/nomad/")
|
||
(commit (string-append "v." version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1r4ygy3xn83dnppsw1451ynklsxpb238g5gk57inn84ghmdk08mj"))))
|
||
(build-system cmake-build-system)
|
||
(native-inputs
|
||
(list python-wrapper python-cython))
|
||
(arguments
|
||
`(#:imported-modules ((guix build python-build-system)
|
||
,@%cmake-build-system-modules)
|
||
#:modules (((guix build python-build-system)
|
||
#:select (python-version site-packages))
|
||
(guix build cmake-build-system)
|
||
(guix build utils))
|
||
#:configure-flags
|
||
'("-DBUILD_INTERFACE_C=ON"
|
||
"-DBUILD_INTERFACE_PYTHON=ON"
|
||
"-DBUILD_TESTS=ON")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'fix-sources-for-build
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(substitute* "CMakeLists.txt"
|
||
;; CMAKE_INSTALL_PREFIX is accidentally hardcoded.
|
||
(("set\\(CMAKE_INSTALL_PREFIX .* FORCE\\)") "")
|
||
;; Requiring GCC version 8 or later is unwarranted.
|
||
(("message\\(FATAL_ERROR \"GCC version < 8")
|
||
"message(STATUS \"GCC version < 8"))
|
||
|
||
(let ((out (assoc-ref outputs "out")))
|
||
(substitute* "interfaces/PyNomad/CMakeLists.txt"
|
||
;; We don't want to build in-place, and anyway the install
|
||
;; command further below runs build_ext as a prerequisite.
|
||
(("COMMAND python setup_PyNomad\\.py .* build_ext --inplace\n")
|
||
"")
|
||
;; Don't install locally.
|
||
(("COMMAND python (setup_PyNomad\\.py .* install) --user\n"
|
||
_ args)
|
||
(string-append "COMMAND ${CMAKE_COMMAND} -E env"
|
||
" CC=" ,(cc-for-target)
|
||
" CXX=" ,(cxx-for-target)
|
||
" " (which "python")
|
||
" " args
|
||
" --prefix=" out
|
||
"\n")))
|
||
;; Fix erroneous assumptions about the paths of the include and
|
||
;; library directories.
|
||
(substitute* "interfaces/PyNomad/setup_PyNomad.py"
|
||
(("^( +os_include_dirs = ).*" _ prefix)
|
||
(string-append prefix "[\"../../src\"]\n"))
|
||
(("^(installed_lib_dir1 = ).*" _ prefix)
|
||
(string-append prefix "\"" out "/lib\"\n"))
|
||
(("^installed_lib_dir2 = .*") "")
|
||
(("^ +link_args\\.append\\(\"-Wl,-rpath,\" \\+ installed_lib_dir2\\)\n")
|
||
"")))))
|
||
|
||
;; Fix the tests so they run in out-of-source builds.
|
||
;;
|
||
;; TODO: Add support for examples/basic/batch/single_obj_MPIparallel,
|
||
;; by adding openmpi to native-inputs and adjusting the example's
|
||
;; BB_EXE parameter.
|
||
(add-after 'fix-sources-for-build 'fix-sources-for-tests
|
||
(lambda _
|
||
(substitute* "examples/CMakeLists.txt"
|
||
;; This test passes only sometimes.
|
||
;; See https://github.com/bbopt/nomad/issues/72.
|
||
(("^ +add_subdirectory\\(\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/advanced/library/PSDMads\\)\n")
|
||
"")
|
||
;; examples/basic/batch/example3 is accidentally omitted.
|
||
(("^(add_subdirectory\\(\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/basic/batch/example)2(\\)\n)"
|
||
_ prefix suffix)
|
||
(string-append prefix "2" suffix
|
||
prefix "3" suffix))
|
||
|
||
;; The generated runExampleTest.sh script runs the test as part
|
||
;; of a pipeline and incorrectly (because pipefail is unset)
|
||
;; relies on the value of the exit status immediately after the
|
||
;; pipeline.
|
||
;; (The patch-shebangs phase runs later than this one, so no
|
||
;; need to update the path to bash here.)
|
||
(("#!/bin/bash") "#!/bin/bash\nset -o pipefail"))
|
||
|
||
(substitute*
|
||
(map (lambda (d) (string-append "examples/" d "/CMakeLists.txt"))
|
||
(append
|
||
(map (lambda (d) (string-append "basic/library/" d))
|
||
'("example1" "example2" "example3"
|
||
"single_obj_parallel"))
|
||
(map (lambda (d) (string-append "advanced/library/" d))
|
||
'("FixedVariable" "NMonly" "PSDMads" "Restart"
|
||
"c_api/example1" "c_api/example2"
|
||
"exampleSuggestAndObserve"))))
|
||
;; The runExampleTest.sh script is run with WORKING_DIRECTORY
|
||
;; set to CMAKE_CURRENT_SOURCE_DIR.
|
||
;; Other scripts invoked by that script (for example
|
||
;; examples/advanced/batch/SuggestAndObserve/loopSuggestAndObserve.sh)
|
||
;; are in that same directory, but compiled examples are
|
||
;; located in CMAKE_CURRENT_BINARY_DIR.
|
||
(("(COMMAND \\$\\{CMAKE_BINARY_DIR\\}/examples/runExampleTest\\.sh )\\.(/.*)"
|
||
_ command test)
|
||
(string-append command "${CMAKE_CURRENT_BINARY_DIR}" test)))
|
||
|
||
;; The examples/basic/batch/example3 executable is already named
|
||
;; bb3.exe.
|
||
(substitute* "examples/basic/batch/single_obj_parallel/CMakeLists.txt"
|
||
(("bb3.exe") "bb_parallel.exe"))
|
||
|
||
;; (Unrelated to support for out-of-source testing.)
|
||
(make-file-writable
|
||
"examples/advanced/library/exampleSuggestAndObserve/cache0.txt")
|
||
|
||
(let ((builddir (string-append (getcwd) "/../build")))
|
||
(let ((dir "examples/advanced/library/FixedVariable"))
|
||
(substitute* (string-append dir "/fixedVariable.cpp")
|
||
(("^( +std::string sExe = ).*" _ prefix)
|
||
(string-append prefix "\"" builddir "/" dir "/ufl.exe" "\";\n"))))
|
||
|
||
;; The BB_EXE and SURROGATE_EXE paths are interpreted relative
|
||
;; to the configuration file provided to NOMAD.
|
||
;; However, the configuration files are all in the source tree
|
||
;; rather than in the build tree (unlike the compiled
|
||
;; executables).
|
||
(let ((fix-exe-path (lambda* (dir #:optional
|
||
(file "param.txt")
|
||
(exe-opt "BB_EXE"))
|
||
(substitute* (string-append dir "/" file)
|
||
(((string-append "^" exe-opt " +"))
|
||
;; The $ prevents NOMAD from prefixing
|
||
;; the executable with the path of the
|
||
;; parent directory of the configuration
|
||
;; file NOMAD was provided with as
|
||
;; argument (param.txt or some such).
|
||
(string-append exe-opt " $"
|
||
builddir "/" dir "/"))))))
|
||
(for-each
|
||
(lambda (dir)
|
||
(let ((dir (string-append "examples/" dir)))
|
||
(substitute* (string-append dir "/CMakeLists.txt")
|
||
;; The install phase has not yet run.
|
||
(("COMMAND \\$\\{CMAKE_INSTALL_PREFIX\\}/bin/nomad ")
|
||
"COMMAND ${CMAKE_BINARY_DIR}/src/nomad "))
|
||
(fix-exe-path dir)
|
||
(when (equal? dir "examples/basic/batch/surrogate_sort")
|
||
(fix-exe-path dir "param.txt" "SURROGATE_EXE"))))
|
||
(append (map (lambda (d) (string-append "basic/batch/" d))
|
||
'("example1" "example2" "example3"
|
||
"single_obj"
|
||
"single_obj_parallel"
|
||
;; "single_obj_MPIparallel"
|
||
"surrogate_sort"))
|
||
'("advanced/batch/LHonly")))
|
||
|
||
(let ((dir "examples/advanced/batch/FixedVariable"))
|
||
(substitute* (string-append dir "/runFixed.sh")
|
||
;; Hardcoded path to NOMAD executable.
|
||
(("^\\.\\./\\.\\./\\.\\./\\.\\./bin/nomad ")
|
||
(string-append builddir "/src/nomad ")))
|
||
(for-each
|
||
(lambda (f) (fix-exe-path dir f))
|
||
'("param1.txt" "param2.txt" "param3.txt" "param10.txt")))))))
|
||
|
||
;; The information in the .egg-info file is not kept up to date.
|
||
(add-after 'install 'delete-superfluous-egg-info
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(delete-file (string-append
|
||
(site-packages inputs outputs)
|
||
"/PyNomad-0.0.0-py"
|
||
(python-version (assoc-ref inputs "python"))
|
||
".egg-info")))))))
|
||
(home-page "https://www.gerad.ca/nomad/")
|
||
(synopsis "Nonlinear optimization by mesh-adaptive direct search")
|
||
(description
|
||
"NOMAD is a C++ implementation of the mesh-adaptive direct search (MADS)
|
||
algorithm, designed for difficult blackbox optimization problems. These
|
||
problems occur when the functions defining the objective and constraints are
|
||
the result of costly computer simulations.")
|
||
(license license:lgpl3+)))
|
||
|
||
(define-public cbc
|
||
(package
|
||
(name "cbc")
|
||
(version "2.10.5")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://www.coin-or.org/download/source/"
|
||
"Cbc/Cbc-" version ".tgz"))
|
||
(sha256
|
||
(base32
|
||
"0wk9vr6zc62gw71v7gnra5wxqlcljcgbhm5lasx236v791b986ns"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
;; Make sure we don't use the bundled software.
|
||
'(delete-file-recursively "ThirdParty"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
(list gfortran pkg-config))
|
||
(inputs
|
||
(list openblas))
|
||
(home-page "https://www.coin-or.org")
|
||
(synopsis "Branch-and-cut solver")
|
||
(description
|
||
"Cbc (Coin-or branch and cut) is a mixed integer linear programming
|
||
solver written in C++. It can be used as a library or as a standalone
|
||
executable.")
|
||
(license license:epl1.0)))
|
||
|
||
(define-public clp
|
||
(package
|
||
(name "clp")
|
||
(version "1.17.6")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://www.coin-or.org/download/source/"
|
||
"Clp/Clp-" version ".tgz"))
|
||
(sha256
|
||
(base32
|
||
"0ap1f0lxppa6pnbc4bg7ih7a96avwaki482nig8w5fr3vg9wvkzr"))
|
||
(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
|
||
(list gfortran pkg-config))
|
||
(inputs
|
||
(list 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 gecode
|
||
(package
|
||
(name "gecode")
|
||
(version "6.2.0")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/Gecode/gecode")
|
||
(commit (string-append "release-" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0b1cq0c810j1xr2x9y9996p894571sdxng5h74py17c6nr8c6dmk"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(begin
|
||
;; delete generated sources
|
||
(for-each delete-file
|
||
'("gecode/kernel/var-imp.hpp"
|
||
"gecode/kernel/var-type.hpp"))))))
|
||
(outputs '("out" "examples"))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:configure-flags
|
||
(list (string-append "GLDFLAGS=-Wl,-rpath="
|
||
(assoc-ref %outputs "out")
|
||
"/lib")
|
||
"--enable-examples=no")
|
||
#:modules ((guix build gnu-build-system)
|
||
(guix build utils)
|
||
(ice-9 rdelim)
|
||
(ice-9 popen))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-examples
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(invoke "make" "compileexamples")))
|
||
;; The Makefile disrespects GLDFLAGS for some reason, so we have to
|
||
;; patch it ourselves... *sigh*
|
||
(add-after 'install 'fix-rpath
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let ((libdir (string-append (assoc-ref outputs "out") "/lib")))
|
||
(for-each
|
||
(lambda (file)
|
||
(let* ((pipe (open-pipe* OPEN_READ "patchelf"
|
||
"--print-rpath" file))
|
||
(line (read-line pipe)))
|
||
(and (zero? (close-pipe pipe))
|
||
(invoke "patchelf" "--set-rpath"
|
||
(string-append libdir ":" line)
|
||
file))))
|
||
(find-files libdir ".*\\.so$")))))
|
||
(add-after 'install 'install-examples
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(invoke "make" "installexamples"
|
||
(string-append "bindir=" (assoc-ref outputs "examples")
|
||
"/bin"))))
|
||
;; Tests depend on installed libraries.
|
||
(delete 'check)
|
||
(add-after 'fix-rpath 'check
|
||
(assoc-ref %standard-phases 'check)))))
|
||
(native-inputs
|
||
(list patchelf perl sed))
|
||
(home-page "https://www.gecode.org")
|
||
(synopsis "Toolkit for developing constraint-based systems")
|
||
(description "Gecode is a C++ toolkit for developing constraint-based
|
||
systems and applications. It provides a modular and extensible solver.")
|
||
(license license:expat)))
|
||
|
||
(define-public libflame
|
||
(package
|
||
(name "libflame")
|
||
(version "5.2.0")
|
||
(outputs '("out" "static"))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/flame/libflame")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1n6lf0wvpp77lxqlr721h2jbfbzigphdp19wq8ajiccilcksh7ay"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:configure-flags
|
||
;; Sensible defaults: https://github.com/flame/libflame/issues/28
|
||
(list "--enable-dynamic-build"
|
||
"--enable-max-arg-list-hack"
|
||
"--enable-lapack2flame"
|
||
"--enable-verbose-make-output"
|
||
"--enable-multithreading=pthreads" ; Openblas isn't built with openmp.
|
||
,@(if (any (cute string-prefix? <> (or (%current-target-system)
|
||
(%current-system)))
|
||
'("x86_64" "i686"))
|
||
'("--enable-vector-intrinsics=sse")
|
||
'())
|
||
"--enable-supermatrix"
|
||
"--enable-memory-alignment=16"
|
||
"--enable-ldim-alignment")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'patch-/usr/bin/env-bash
|
||
(lambda _
|
||
(substitute* "build/config.mk.in"
|
||
(("/usr/bin/env bash") (which "bash")))
|
||
#t))
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(substitute* "test/Makefile"
|
||
(("LIBBLAS .*") "LIBBLAS = -lblas\n")
|
||
(("LIBLAPACK .*") "LIBLAPACK = -llapack\n"))
|
||
(if tests?
|
||
(with-directory-excursion "test"
|
||
(mkdir "obj")
|
||
(invoke "make")
|
||
(invoke "./test_libflame.x"))
|
||
#t)))
|
||
(add-after 'install 'install-static
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out"))
|
||
(static (assoc-ref outputs "static")))
|
||
(mkdir-p (string-append static "/lib"))
|
||
(rename-file (string-append out "/lib/libflame.a")
|
||
(string-append static "/lib/libflame.a"))
|
||
(install-file (string-append out "/include/FLAME.h")
|
||
(string-append static "/include"))
|
||
#t))))))
|
||
(inputs
|
||
(list gfortran))
|
||
(native-inputs
|
||
`(("lapack" ,lapack)
|
||
("openblas" ,openblas)
|
||
("perl" ,perl)
|
||
("python" ,python-wrapper)))
|
||
(home-page "https://github.com/flame/libflame")
|
||
(synopsis "High-performance object-based library for DLA computations")
|
||
(description "@code{libflame} is a portable library for dense matrix
|
||
computations, providing much of the functionality present in LAPACK, developed
|
||
by current and former members of the @acronym{SHPC, Science of High-Performance
|
||
Computing} group in the @url{https://www.ices.utexas.edu/, Institute for
|
||
Computational Engineering and Sciences} at The University of Texas at Austin.
|
||
@code{libflame} includes a compatibility layer, @code{lapack2flame}, which
|
||
includes a complete LAPACK implementation.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public libpotassco
|
||
;; No public release, update together with clasp
|
||
(let ((revision "1")
|
||
(commit "2f9fb7ca2c202f1b47643aa414054f2f4f9c1821"))
|
||
(package
|
||
(name "libpotassco")
|
||
(version (git-version "0.0" revision commit))
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/potassco/libpotassco")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1c32f9gqclf7qx07lpx8wd720vfhkjqhzc6nyy8mjmgwpmb3iyyn"))))
|
||
(arguments
|
||
`(#:configure-flags '("-DLIB_POTASSCO_BUILD_TESTS=on"
|
||
"-DLIB_POTASSCO_INSTALL_LIB=on"
|
||
"-DBUILD_SHARED_LIBS=on")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'patch-cmake
|
||
(lambda _
|
||
(substitute* "CMakeLists.txt"
|
||
;; clasp expects lowercase potassco and include directory is
|
||
;; lowercase as well, so let's use that
|
||
(("\"cmake/Potassco\"") "\"cmake/potassco\"")
|
||
(("PotasscoConfig\\.cmake") "potassco-config.cmake")
|
||
(("PotasscoConfigVersion\\.cmake")
|
||
"potassco-config-version.cmake"))
|
||
(rename-file "cmake/PotasscoConfig.cmake.in"
|
||
"cmake/potassco-config.cmake.in"))))))
|
||
(build-system cmake-build-system)
|
||
(home-page "https://potassco.org/")
|
||
(synopsis "Utility library for Potassco's projects")
|
||
(description "@code{libpotassco} is a utility library providing functions
|
||
and datatypes for
|
||
@itemize
|
||
@item parsing, writing, and converting logic programs in aspif and smodels
|
||
format,
|
||
@item passing information between a grounder and a solver,
|
||
@item and defining and parsing command-line options and for creating
|
||
command-line applications.
|
||
@end itemize
|
||
Furthermore, it comes with the tool @command{lpconvert} that converts either
|
||
between aspif and smodels format or to a human-readable text format.")
|
||
(license license:expat))))
|
||
|
||
(define-public clasp
|
||
(package
|
||
(name "clasp")
|
||
(version "3.3.6")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/potassco/clasp")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0rahqiq530jckvx717858h1q5p8znp1kb6sjm95p8blkr4n3pvmj"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:configure-flags '("-DCLASP_BUILD_TESTS=on"
|
||
"-DCLASP_INSTALL_LIB=on"
|
||
"-DCLASP_USE_LOCAL_LIB_POTASSCO=off"
|
||
"-DBUILD_SHARED_LIBS=on")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'patch-cmake
|
||
(lambda _
|
||
(substitute* "CMakeLists.txt"
|
||
;; Use lowercase to be consistent with libpotassco
|
||
(("\"cmake/Clasp\"") "\"cmake/clasp\"")
|
||
(("ClaspConfig\\.cmake") "clasp-config.cmake")
|
||
(("ClaspConfigVersion\\.cmake")
|
||
"clasp-config-version.cmake"))
|
||
(substitute* "cmake/ClaspConfig.cmake.in"
|
||
(("find_package\\(Potassco") "find_package(potassco"))
|
||
(rename-file "cmake/ClaspConfig.cmake.in"
|
||
"cmake/clasp-config.cmake.in"))))))
|
||
(inputs
|
||
(list libpotassco))
|
||
(home-page "https://potassco.org/")
|
||
(synopsis "Answer set solver")
|
||
(description "clasp is an answer set solver for (extended) normal and
|
||
disjunctive logic programs. The primary algorithm of clasp relies on
|
||
conflict-driven nogood learning, a technique that proved very successful for
|
||
satisfiability checking (SAT).")
|
||
(license license:expat)))
|
||
|
||
(define-public clingo
|
||
(package
|
||
(name "clingo")
|
||
(version "5.5.0")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/potassco/clingo")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0rfjwkcwm0mmf3r4i7asyjwb6cia4i7px7fn2kdbi9j85qvas4pb"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:configure-flags `("-DCLINGO_BUILD_TESTS=on"
|
||
"-DCLINGO_INSTALL_LIB=on"
|
||
"-DCLINGO_BUILD_STATIC=off"
|
||
"-DCLINGO_BUILD_SHARED=on"
|
||
;; XXX: Clingo requries private headers and
|
||
;; sources from clasp
|
||
,(string-append
|
||
"-DCLASP_SOURCE_DIR="
|
||
(assoc-ref %build-inputs "clasp-src")))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'patch-cmake
|
||
(lambda _
|
||
(substitute* "CMakeLists.txt"
|
||
(("add_subdirectory\\(clasp\\)")
|
||
"find_package(clasp REQUIRED)"))
|
||
(substitute* "libclingo/CMakeLists.txt"
|
||
(("\"cmake/Clingo\"") "\"cmake/clingo\"")
|
||
(("ClingoConfig\\.cmake") "clingo-config.cmake")
|
||
(("ClingoConfigVersion\\.cmake")
|
||
"clingo-config-version.cmake"))
|
||
(substitute* "cmake/ClingoConfig.cmake.in"
|
||
(("find_package\\(Clasp") "find_package(clasp"))
|
||
(rename-file "cmake/ClingoConfig.cmake.in"
|
||
"cmake/clingo-config.cmake.in")))
|
||
(add-after 'unpack 'skip-failing-tests
|
||
(lambda _
|
||
(with-directory-excursion "libclingo/tests"
|
||
(substitute* "CMakeLists.txt"
|
||
(("COMMAND test_clingo" all)
|
||
(string-append all
|
||
" -f "
|
||
"\"${CMAKE_CURRENT_SOURCE_DIR}/good.txt\"")))
|
||
(call-with-output-file "good.txt"
|
||
(lambda (port)
|
||
(for-each (lambda (test) (format port "~s~%" test))
|
||
'("parse-ast-v2" "add-ast-v2" "build-ast-v2"
|
||
"unpool-ast-v2" "parse_term"
|
||
"propagator" "propgator-sequence-mining"
|
||
"symbol" "visitor"))))))))))
|
||
(inputs
|
||
(list clasp libpotassco))
|
||
(native-inputs
|
||
`(("clasp-src" ,(package-source clasp))))
|
||
(home-page "https://potassco.org/")
|
||
(synopsis "Grounder and solver for logic programs")
|
||
(description "Clingo computes answer sets for a given logic program.")
|
||
(license license:expat)))
|
||
|
||
(define-public ceres
|
||
(package
|
||
(name "ceres-solver")
|
||
(version "2.0.0")
|
||
(home-page "http://ceres-solver.org/")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append home-page "ceres-solver-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"00vng9vnmdb1qga01m0why90m0041w7bn6kxa2h4m26aflfqla8h"))))
|
||
(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* "CMakeLists.txt"
|
||
(("set\\(LIB_SUFFIX \"64\"\\)")
|
||
"set(LIB_SUFFIX \"\")")))))))
|
||
(native-inputs
|
||
(list pkg-config))
|
||
(propagated-inputs
|
||
(list glog)) ;for #include <glog/glog.h>
|
||
(inputs
|
||
(list eigen
|
||
openblas
|
||
lapack
|
||
suitesparse
|
||
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)
|
||
|
||
;; Mark as tunable to take advantage of SIMD code in Eigen.
|
||
(properties `((tunable? . #t)))))
|
||
|
||
(define-public ceres-solver-benchmarks
|
||
(package
|
||
(inherit ceres)
|
||
(name "ceres-solver-benchmarks")
|
||
(arguments
|
||
'(#:modules ((ice-9 popen)
|
||
(ice-9 rdelim)
|
||
(guix build utils)
|
||
(guix build cmake-build-system))
|
||
|
||
#:phases (modify-phases %standard-phases
|
||
(delete 'configure)
|
||
(replace 'build
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(bin (string-append out "/bin")))
|
||
(define flags
|
||
(string-tokenize
|
||
(read-line (open-pipe* OPEN_READ
|
||
"pkg-config" "eigen3"
|
||
"--cflags"))))
|
||
|
||
(define (compile-file top-dir)
|
||
(lambda (file)
|
||
(let ((source (string-append file ".cc")))
|
||
(format #t "building '~a'...~%" file)
|
||
(apply invoke "c++" "-fopenmp" "-O2" "-g" "-DNDEBUG"
|
||
source "-lceres" "-lbenchmark" "-lglog"
|
||
"-pthread"
|
||
"-o" (string-append bin "/" file)
|
||
"-I" top-dir flags))))
|
||
|
||
(mkdir-p bin)
|
||
(with-directory-excursion "internal/ceres"
|
||
(for-each (compile-file "..")
|
||
'("schur_eliminator_benchmark"
|
||
"small_blas_gemm_benchmark"
|
||
"small_blas_gemv_benchmark"))
|
||
(with-directory-excursion "autodiff_benchmarks"
|
||
((compile-file "../..") "autodiff_benchmarks"))))))
|
||
(delete 'check)
|
||
(delete 'install))))
|
||
(inputs (modify-inputs (package-inputs ceres)
|
||
(prepend googlebenchmark ceres)))
|
||
(synopsis "Benchmarks of the Ceres optimization problem solver")))
|
||
|
||
;; 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 "6.2.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/octave/octave-"
|
||
version ".tar.xz"))
|
||
(sha256
|
||
(base32
|
||
"06id09zspya24gshcwgp039cp35c06150mdlxysawgnbrhj16wkv"))))
|
||
(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)
|
||
|
||
;; TODO: libjpeg-turbo is indirectly required through libtiff. In
|
||
;; the next rebuild cycle, add an absolute reference for -ljpeg in
|
||
;; libtiff.la instead of having to provide it here.
|
||
("libjpeg" ,libjpeg-turbo)
|
||
|
||
("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
|
||
(list gfortran
|
||
pkg-config
|
||
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
|
||
ghostscript
|
||
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")
|
||
|
||
;; XXX: Without this flag, linking octave-cli fails with
|
||
;; undefined references to 'logf@GLIBCXX_3.4' et.al. due to
|
||
;; not pulling in liboctinterp.la for -lstdc++.
|
||
"--enable-link-all-dependencies")
|
||
#: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 (no GUI)")
|
||
(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")
|
||
(inputs
|
||
`(("qscintilla" ,qscintilla)
|
||
("qt" ,qtbase-5)
|
||
,@(package-inputs octave-cli)))
|
||
(native-inputs
|
||
`(("qttools" , qttools) ;for lrelease
|
||
("texlive" ,(texlive-updmap.cfg (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))))))
|
||
(synopsis "High-level language for numerical computation (with GUI)")))
|
||
|
||
(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")
|
||
(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
|
||
(list freetype
|
||
glu
|
||
libxmu
|
||
mesa
|
||
tcl
|
||
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 "7.6.0")
|
||
(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 "1rcwm9fkx0j4wrsyikb6g7qd611kpry7dand5dzdjvs5vzd13zvd"))
|
||
(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")))
|
||
(native-inputs (list fontconfig))
|
||
(inputs
|
||
(list doxygen
|
||
;("freeimage" ,freeimage)
|
||
freetype
|
||
glu
|
||
libxext
|
||
libxi
|
||
libxmu
|
||
mesa
|
||
tbb-2020
|
||
tcl
|
||
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 "4.9.5")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://gitlab.onelab.info/gmsh/gmsh.git")
|
||
(commit
|
||
(string-append "gmsh_"
|
||
(string-replace-substring version "." "_")))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0asd9p64ng5l2zk5glc33x3ynnvdpndlflg3q9mr0jxr7y9x0lrm"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(begin
|
||
(delete-file-recursively "contrib/metis")
|
||
#t))))
|
||
(build-system cmake-build-system)
|
||
(propagated-inputs
|
||
(list fltk
|
||
gfortran
|
||
glu
|
||
gmp
|
||
hdf5
|
||
lapack
|
||
libx11
|
||
libxext
|
||
mesa
|
||
metis
|
||
opencascade-occt))
|
||
(inputs
|
||
`(("fontconfig" ,fontconfig)
|
||
("libxft" ,libxft)
|
||
("python" ,python)))
|
||
(arguments
|
||
`(#:configure-flags `("-DENABLE_SYSTEM_CONTRIB:BOOL=ON"
|
||
"-DENABLE_BUILD_SHARED:BOOL=ON"
|
||
"-DENABLE_BUILD_DYNAMIC:BOOL=ON")
|
||
#:imported-modules (,@%cmake-build-system-modules
|
||
(guix build python-build-system))
|
||
#:modules (((guix build python-build-system) #:select (site-packages))
|
||
(guix build cmake-build-system)
|
||
(guix build utils))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'patch-paths
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
;; Use the standard Guix site-package path for
|
||
;; installation of the Python API.
|
||
(substitute* "CMakeLists.txt"
|
||
(("include\\(GNUInstallDirs\\)\n")
|
||
(string-append "include(GNUInstallDirs)\n"
|
||
" set(GMSH_PY_LIB "
|
||
(site-packages inputs outputs) ")\n"))
|
||
(("\\$\\{GMSH\\_PY\\} DESTINATION \\$\\{GMSH\\_LIB\\}")
|
||
"${GMSH_PY} DESTINATION ${GMSH_PY_LIB}"))
|
||
;; Find the shared library.
|
||
(let ((libgmsh (string-append (assoc-ref outputs "out")
|
||
"/lib/libgmsh.so")))
|
||
(substitute* "api/gmsh.py"
|
||
(("find_library\\(\"gmsh\"\\)")
|
||
(simple-format #f "\"~a\"" libgmsh))))
|
||
#t)))))
|
||
(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 veusz
|
||
(package
|
||
(name "veusz")
|
||
(version "3.3.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "veusz" version))
|
||
(sha256
|
||
(base32 "1q7hi1qwwg4pgiz62isvv1pia85m13bspdpp1q3mrnwl11in0ag0"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(;; Tests will fail because they depend on optional packages like
|
||
;; python-astropy, which is not packaged.
|
||
#:tests? #f
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
;; Veusz will append 'PyQt5' to sip_dir by default. That is not how
|
||
;; the path is defined in Guix, therefore we have to change it.
|
||
(add-after 'unpack 'fix-sip-dir
|
||
(lambda _
|
||
(substitute* "pyqtdistutils.py"
|
||
(("os.path.join\\(sip_dir, 'PyQt5'\\)") "sip_dir"))
|
||
#t))
|
||
;; Now we have to pass the correct sip_dir to setup.py.
|
||
(replace 'build
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
;; We need to tell setup.py where to locate QtCoremod.sip
|
||
((@@ (guix build python-build-system) call-setuppy)
|
||
"build_ext"
|
||
(list (string-append "--sip-dir="
|
||
(assoc-ref inputs "python-pyqt")
|
||
"/share/sip"))
|
||
#t)))
|
||
;; Ensure that icons are found at runtime.
|
||
(add-after 'install 'wrap-executable
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out")))
|
||
(wrap-program (string-append out "/bin/veusz")
|
||
`("QT_PLUGIN_PATH" prefix
|
||
,(list (string-append (assoc-ref inputs "qtsvg")
|
||
"/lib/qt5/plugins/"))))))))))
|
||
(native-inputs
|
||
(list pkg-config
|
||
;;("python-astropy" ,python-astropy) ;; FIXME: Package this.
|
||
qttools python-sip-4))
|
||
(inputs
|
||
(list ghostscript ;optional, for EPS/PS output
|
||
python-dbus
|
||
python-h5py ;optional, for HDF5 data
|
||
python-pyqt
|
||
qtbase-5
|
||
qtsvg))
|
||
(propagated-inputs
|
||
(list python-numpy))
|
||
(home-page "https://veusz.github.io/")
|
||
(synopsis "Scientific plotting package")
|
||
(description
|
||
"Veusz is a scientific plotting and graphing program with a graphical
|
||
user interface, designed to produce publication-ready 2D and 3D plots. In
|
||
addition it can be used as a module in Python for plotting. It supports
|
||
vector and bitmap output, including PDF, Postscript, SVG and EMF.")
|
||
(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")
|
||
(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 "3.16.1")
|
||
(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 "0sm03vpg010q9icidiq587n325m0598cj6hab2rdv85nwyygg74h"))))
|
||
(outputs '("out" ; libraries and headers
|
||
"examples")) ; ~30MiB of examples
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
(list python which))
|
||
(inputs
|
||
(list gfortran openblas 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
|
||
(list
|
||
#:test-target "test"
|
||
#:parallel-build? #f ; build is parallel by default
|
||
#:configure-flags
|
||
#~(list "--with-mpi=0"
|
||
"--with-openmp=1"
|
||
"--with-openblas=1"
|
||
(string-append "--with-openblas-dir="
|
||
#$(this-package-input "openblas"))
|
||
"--with-superlu=1")
|
||
#:make-flags
|
||
;; Honor (parallel-job-count) for build. Do not use --with-make-np,
|
||
;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
|
||
#~(list (format #f "MAKE_NP=~a" (parallel-job-count)))
|
||
#:phases
|
||
#~(modify-phases %standard-phases
|
||
(replace 'configure
|
||
;; PETSc's configure script is actually a python script, so we can't
|
||
;; run it with bash.
|
||
(lambda* (#:key outputs (configure-flags '())
|
||
#:allow-other-keys)
|
||
(let* ((prefix (assoc-ref outputs "out"))
|
||
(flags `(,(string-append "--prefix=" prefix)
|
||
,@configure-flags)))
|
||
(format #t "build directory: ~s~%" (getcwd))
|
||
(format #t "configure flags: ~s~%" flags)
|
||
(apply invoke "./configure" flags)
|
||
|
||
;; Generate test scripts with the right shebang.
|
||
(substitute* "config/example_template.py"
|
||
(("#!/usr/bin/env bash")
|
||
(string-append "#!" (which "bash")))))))
|
||
(add-after 'configure 'clean-local-references
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out")))
|
||
(substitute* (find-files "." "^petsc(conf|machineinfo).h$")
|
||
;; 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")))))
|
||
(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")))))
|
||
(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)))))))
|
||
(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" #$cf))))
|
||
(synopsis "Library to solve PDEs (with complex scalars)")))
|
||
|
||
(define-public petsc-openmpi
|
||
(package
|
||
(inherit petsc)
|
||
(name "petsc-openmpi")
|
||
(inputs
|
||
(modify-inputs (package-inputs petsc)
|
||
(prepend hdf5-parallel-openmpi
|
||
hypre-openmpi
|
||
metis
|
||
mumps-openmpi
|
||
openmpi
|
||
scalapack
|
||
pt-scotch32
|
||
`(,pt-scotch32 "metis"))))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments petsc)
|
||
((#:configure-flags cf)
|
||
#~`("--with-hypre=1"
|
||
"--with-mpiexec=mpirun"
|
||
"--with-metis=1"
|
||
"--with-mumps=1"
|
||
"--with-scalapack=1"
|
||
"--with-ptscotch=1"
|
||
,(string-append "--with-mpi-dir="
|
||
#$(this-package-input "openmpi"))
|
||
,(string-append "--with-hdf5-include="
|
||
#$(this-package-input "hdf5-parallel-openmpi")
|
||
"/include")
|
||
,(string-append "--with-hdf5-lib="
|
||
#$(this-package-input "hdf5-parallel-openmpi")
|
||
"/lib/libhdf5.a")
|
||
,@(delete "--with-mpi=0" #$cf)))
|
||
((#:phases phases)
|
||
#~(modify-phases #$phases
|
||
(add-before 'configure 'adjust-pt-scotch-library-names
|
||
(lambda _
|
||
;; Adjust to the library name changes in Scotch 7.0.
|
||
(substitute* "config/BuildSystem/config/packages/PTScotch.py"
|
||
(("libptesmumps") "libesmumps")
|
||
(("libptscotchparmetis") "libptscotchparmetisv3"))))
|
||
(add-before 'configure 'mpi-setup
|
||
#$%openmpi-setup)
|
||
(add-after 'install 'patch-header-inclusions
|
||
;; TODO: Replace with ‘patch-header-inclusions’ when (some form
|
||
;; of) https://issues.guix.gnu.org/54780#19 is merged.
|
||
(lambda _
|
||
(substitute* (string-append #$output "/include/petsclayouthdf5.h")
|
||
(("<(H5Ipublic.h)>" _ header)
|
||
(format #f "<~a/include/~a>"
|
||
#$(this-package-input "hdf5-parallel-openmpi")
|
||
header)))))))))
|
||
(synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
|
||
|
||
(define-public petsc-complex-openmpi
|
||
(package
|
||
(inherit petsc-complex)
|
||
(name "petsc-complex-openmpi")
|
||
(inputs
|
||
(modify-inputs (package-inputs petsc-complex)
|
||
(prepend openmpi)))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments petsc-complex)
|
||
((#:configure-flags cf)
|
||
#~`("--with-mpiexec=mpirun"
|
||
,(string-append "--with-mpi-dir="
|
||
#$(this-package-input "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 "3.16.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "petsc4py" version))
|
||
(sha256
|
||
(base32
|
||
"0pxr6qa7p0pmpq0av29lx8lzlrdcfdzj87ynixzr8dn42y13a662"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(begin
|
||
;; Ensure source file is regenerated in the build phase.
|
||
(delete-file "src/petsc4py.PETSc.c")
|
||
;; Remove legacy GC code. See
|
||
;; https://bitbucket.org/petsc/petsc4py/issues/125.
|
||
(substitute* "src/PETSc/cyclicgc.pxi"
|
||
((".*gc_refs.*") "" )
|
||
((".*PyGC_Head.*") ""))
|
||
#t))))
|
||
(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))))
|
||
(native-inputs
|
||
(list python-cython))
|
||
(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 slepc
|
||
(package
|
||
(name "slepc")
|
||
(version "3.16.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1ysfm77s5fcissv3q0k5d65mlp93zi4anqg62q3cd25dn66sva5i"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("python" ,python)
|
||
("which" ,which)
|
||
("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
|
||
(inputs
|
||
`(("arpack" ,arpack-ng)
|
||
("gfortran" ,gfortran)))
|
||
(propagated-inputs
|
||
(list 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 "https://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)
|
||
(properties
|
||
`((release-monitoring-url . "http://slepc.upv.es/download/")))))
|
||
|
||
(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)
|
||
,@(alist-delete "arpack" (package-inputs slepc))))
|
||
(propagated-inputs
|
||
`(("petsc" ,petsc-openmpi)
|
||
("arpack" ,arpack-ng-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 "3.16.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "slepc4py" version))
|
||
(sha256
|
||
(base32
|
||
"0fq997y73ymvcvdrxycp450pxwdgnqaw62gv9rwncfgsfplkvs9w"))))
|
||
(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 metamath
|
||
(package
|
||
(name "metamath")
|
||
(version "0.193")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/metamath/metamath-exe")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1s9hyknfvhj86g3giayyf3dxzg23iij0rs7bdvj075v9qbyhqn9b"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
(list autoconf automake))
|
||
(home-page "http://us.metamath.org/")
|
||
(synopsis "Proof verifier based on a minimalistic formalism")
|
||
(description
|
||
"Metamath is a tiny formal language and that can express theorems in
|
||
abstract mathematics, with an accompyaning @command{metamath} executable that
|
||
verifies databases of these proofs. There is a public database,
|
||
@url{https://github.com/metamath/set.mm, set.mm}, implementing first-order
|
||
logic and Zermelo-Frenkel set theory with Choice, along with a large swath of
|
||
associated, high-level theorems, e.g.@: the fundamental theorem of arithmetic,
|
||
the Cauchy-Schwarz inequality, Stirling's formula, etc. See the Metamath
|
||
book.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public minizinc
|
||
(package
|
||
(name "minizinc")
|
||
(version "2.5.5")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/MiniZinc/libminizinc")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"10b2hsl1fx9psh0iagmp8ki3f60f3qg5hmvra5aczjlfmbl88ggp"))
|
||
(modules '((guix build utils)
|
||
(ice-9 ftw)
|
||
(srfi srfi-1)))
|
||
(snippet
|
||
'(begin
|
||
;; Do not advertise proprietary solvers
|
||
(with-directory-excursion "cmake/targets"
|
||
(let ((targets '("libminizinc_fzn.cmake"
|
||
"libminizinc_gecode.cmake"
|
||
"libminizinc_mip.cmake"
|
||
"libminizinc_nl.cmake"
|
||
"libminizinc_osicbc.cmake"
|
||
"libminizinc_parser.cmake"
|
||
"libmzn.cmake"
|
||
"minizinc.cmake"
|
||
"mzn2doc.cmake")))
|
||
(for-each delete-file
|
||
(remove
|
||
(lambda (file)
|
||
(member file (cons* "." ".." targets)))
|
||
(scandir ".")))
|
||
(substitute* "libmzn.cmake"
|
||
(("include\\(cmake/targets/(.*)\\)" all target)
|
||
(if (member target targets) all "")))))
|
||
(with-directory-excursion "include/minizinc/solvers/MIP"
|
||
(for-each delete-file
|
||
(remove
|
||
(lambda (file)
|
||
(member file '("." ".."
|
||
"MIP_osicbc_solverfactory.hh"
|
||
"MIP_osicbc_wrap.hh"
|
||
"MIP_solverinstance.hh"
|
||
"MIP_solverinstance.hpp"
|
||
"MIP_wrap.hh")))
|
||
(scandir "."))))
|
||
(with-directory-excursion "solvers/MIP"
|
||
(for-each delete-file
|
||
(remove
|
||
(lambda (file)
|
||
(member file '("." ".."
|
||
"MIP_osicbc_solverfactory.cpp"
|
||
"MIP_osicbc_wrap.cpp"
|
||
"MIP_solverinstance.cpp"
|
||
"MIP_wrap.cpp")))
|
||
(scandir "."))))
|
||
(substitute* "CMakeLists.txt"
|
||
(("find_package\\(([^ ]*).*\\)" all pkg)
|
||
(if (member pkg '("Gecode" "OsiCBC" "Threads"))
|
||
all
|
||
"")))
|
||
;; TODO: swap out miniz for zlib
|
||
#t))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:tests? #f ; no ‘check’ target
|
||
#:modules ((guix build cmake-build-system)
|
||
(guix build utils)
|
||
(srfi srfi-1))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'install 'install-solver-configs
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let ((gecode (assoc-ref inputs "gecode"))
|
||
(pkgdatadir (string-append (assoc-ref outputs "out")
|
||
"/share/minizinc")))
|
||
(call-with-output-file (string-append pkgdatadir
|
||
"/Preferences.json")
|
||
(lambda (port)
|
||
(display "\
|
||
{
|
||
\"tagDefaults\": [
|
||
[\"\", \"org.gecode.gecode\"],
|
||
[\"gecode\", \"org.gecode.gecode\"]
|
||
],
|
||
\"solverDefaults\": []
|
||
}"
|
||
port)
|
||
(newline port)))
|
||
|
||
(mkdir-p (string-append pkgdatadir "/solvers"))
|
||
(call-with-output-file (string-append pkgdatadir
|
||
"/solvers/gecode.msc")
|
||
(lambda (port)
|
||
(format port
|
||
"\
|
||
{
|
||
\"id\": \"org.gecode.gecode\",
|
||
\"name\": \"Gecode\",
|
||
\"description\": \"Gecode FlatZinc executable\",
|
||
\"version\": ~s,
|
||
\"mznlib\": ~s,
|
||
\"executable\": ~s,
|
||
\"supportsMzn\": false,
|
||
\"supportsFzn\": true,
|
||
\"needsSolns2Out\": true,
|
||
\"needsMznExecutable\": false,
|
||
\"needsStdlibDir\": false,
|
||
\"isGUIApplication\": false
|
||
}"
|
||
(last (string-split gecode #\-))
|
||
(string-append gecode "/share/gecode/mznlib")
|
||
(string-append gecode "/bin/fzn-gecode"))
|
||
(newline port)))))))))
|
||
(native-inputs
|
||
(list bison flex))
|
||
(inputs
|
||
(list cbc gecode zlib))
|
||
(home-page "https://www.minizinc.org")
|
||
(synopsis "High-level constraint modeling language")
|
||
(description "MiniZinc is a high-level modeling language for constraint
|
||
satisfaction and optimization problems. Models are compiled to FlatZinc, a
|
||
language understood by many solvers.")
|
||
(license license:mpl2.0)))
|
||
|
||
(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
|
||
(list gfortran
|
||
;; These are required for linking against mumps, but we let the user
|
||
;; declare the dependency.
|
||
openblas
|
||
metis
|
||
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 -fallow-argument-mismatch $(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)"
|
||
(->bool (which "mpicc")) ;MPI support enabled?
|
||
(dirname
|
||
(dirname (search-input-file inputs "/include/cblas.h")))
|
||
(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
|
||
"-lesmumps -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 (modify-inputs (package-inputs mumps)
|
||
(delete "scotch")))))
|
||
|
||
(define-public mumps-openmpi
|
||
(package
|
||
(inherit mumps)
|
||
(name "mumps-openmpi")
|
||
(inputs
|
||
(modify-inputs (package-inputs mumps)
|
||
(delete "scotch")
|
||
(prepend openmpi scalapack pt-scotch)))
|
||
(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 (modify-inputs (package-inputs mumps-openmpi)
|
||
(delete "pt-scotch")))))
|
||
|
||
(define-public ruby-asciimath
|
||
(package
|
||
(name "ruby-asciimath")
|
||
(version "2.0.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (rubygems-uri "asciimath" version))
|
||
(sha256
|
||
(base32
|
||
"1fy2jrn3gr7cl33qydp3pwyfilcmb4m4z6hfhnvydzg8r3srp36j"))))
|
||
(build-system ruby-build-system)
|
||
(native-inputs
|
||
(list ruby-nokogiri 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 "5.3.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://portal.nersc.gov/project/sparse/superlu/"
|
||
"superlu-" version ".tar.gz"))
|
||
(sha256
|
||
(base32 "0xvib7nk2rlbsiv1iwkwl9kxppkalkciv628bsyiiv0pv754n48q"))
|
||
(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
|
||
(list 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 "6.4.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/xiaoyeli/superlu_dist")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0fa29yr72p4yq5ln4rgfsawmi5935n4qcr5niz6864bjladz4lql"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
;; Replace the non-free implementation of MC64 with a stub
|
||
'(begin
|
||
(make-file-writable "SRC/mc64ad_dist.c")
|
||
(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
|
||
(list 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 "7.0.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://gitlab.inria.fr/scotch/scotch")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1fvgxd3ipl5xswswyadvxvlcgv6an8c229ispnlksgnlwphg10ig"))))
|
||
(build-system cmake-build-system)
|
||
(inputs
|
||
(list zlib))
|
||
(native-inputs
|
||
(list flex bison gfortran))
|
||
(outputs '("out" "metis"))
|
||
(arguments
|
||
`(#:configure-flags '("-DBUILD_SHARED_LIBS=YES" "-DINTSIZE=64"
|
||
"-DBUILD_PTSCOTCH=OFF")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'install 'install-metis
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(metis (assoc-ref outputs "metis"))
|
||
(prefix (string-length out)))
|
||
(for-each (lambda (file)
|
||
(let ((target (string-append
|
||
metis
|
||
(string-drop file prefix))))
|
||
(mkdir-p (dirname target))
|
||
(rename-file file target)))
|
||
(find-files out "metis"))))))))
|
||
(home-page "https://www.labri.fr/perso/pelegrin/scotch/")
|
||
(properties
|
||
`((release-monitoring-url
|
||
. "https://gitlab.inria.fr/scotch/scotch/-/releases")))
|
||
(synopsis "Programs and libraries for graph algorithms")
|
||
(description "SCOTCH is a set of programs and libraries which implement
|
||
the static mapping and sparse matrix reordering algorithms developed within
|
||
the SCOTCH project. Its purpose is to apply graph theory, with a divide and
|
||
conquer approach, to scientific computing problems such as graph and mesh
|
||
partitioning, static mapping, and sparse matrix ordering, in application
|
||
domains ranging from structural mechanics to operating systems or
|
||
bio-chemistry.")
|
||
;; See LICENSE_en.txt
|
||
(license license:cecill-c)))
|
||
|
||
(define-public scotch32
|
||
;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
|
||
;; some applications.
|
||
(package
|
||
(inherit scotch)
|
||
(name "scotch32")
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments scotch)
|
||
((#:configure-flags flags ''())
|
||
''("-DBUILD_SHARED_LIBS=YES" "-DBUILD_PTSCOTCH=OFF"
|
||
"-DINTSIZE=32"))))
|
||
(synopsis
|
||
"Programs and libraries for graph algorithms (32-bit integers)")))
|
||
|
||
(define-public pt-scotch
|
||
(package
|
||
(inherit scotch)
|
||
(name "pt-scotch")
|
||
(propagated-inputs
|
||
(list openmpi)) ;headers include MPI headers
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments scotch)
|
||
((#:configure-flags flags ''())
|
||
''("-DBUILD_SHARED_LIBS=YES" "-DBUILD_PTSCOTCH=ON"
|
||
"-DINTSIZE=64"))
|
||
((#:phases phases '%standard-phases)
|
||
`(modify-phases ,phases
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup)))))
|
||
(synopsis "Programs and libraries for graph algorithms (with MPI)")))
|
||
|
||
(define-public pt-scotch32
|
||
(package
|
||
(inherit pt-scotch)
|
||
(name "pt-scotch32")
|
||
(propagated-inputs
|
||
(list openmpi)) ;headers include MPI headers
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments pt-scotch)
|
||
((#:configure-flags flags ''())
|
||
''("-DBUILD_SHARED_LIBS=YES" "-DBUILD_PTSCOTCH=ON"
|
||
"-DINTSIZE=32"))))
|
||
(synopsis
|
||
"Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
|
||
|
||
(define-public scotch-shared
|
||
;; There used to be separate shared library variants while the default would
|
||
;; provide .a files including PIC objects. With the switch to CMake, .a
|
||
;; files contain non-PIC objects, which breaks some users, and switching to
|
||
;; shared libraries by default seems to make more sense, as discussed here:
|
||
;; <https://issues.guix.gnu.org/47619#2>.
|
||
(deprecated-package "scotch-shared" scotch))
|
||
|
||
(define-public pt-scotch-shared
|
||
(deprecated-package "pt-scotch-shared" pt-scotch))
|
||
|
||
|
||
(define-public metis
|
||
(package
|
||
(name "metis")
|
||
(version "5.1.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
|
||
"metis-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
|
||
(properties
|
||
`((release-monitoring-url
|
||
. "http://glaros.dtc.umn.edu/gkhome/metis/metis/download")))
|
||
(build-system cmake-build-system)
|
||
(inputs
|
||
`(("blas" ,openblas)))
|
||
(arguments
|
||
`(#:tests? #f ;no tests
|
||
#:configure-flags `("-DSHARED=ON"
|
||
,(string-append "-DGKLIB_PATH=" (getcwd)
|
||
"/metis-" ,version "/GKlib"))))
|
||
(home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
|
||
(synopsis "Graph partitioning and fill-reducing matrix ordering library")
|
||
(description
|
||
"METIS is a set of serial programs for partitioning graphs, partitioning
|
||
finite element meshes, and producing fill-reducing orderings for sparse
|
||
matrices. The algorithms implemented in METIS are based on the multilevel
|
||
recursive-bisection, multilevel k-way, and multi-constraint partitioning
|
||
schemes.")
|
||
(license license:asl2.0))) ;As of version 5.0.3
|
||
|
||
(define-public p4est
|
||
(package
|
||
(name "p4est")
|
||
(version "2.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://p4est.github.io/release/p4est-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("fortran" ,gfortran)
|
||
("blas" ,openblas)
|
||
("lapack" ,lapack)
|
||
("zlib" ,zlib)))
|
||
(arguments
|
||
`(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
|
||
(assoc-ref %build-inputs "blas")
|
||
" -lopenblas")
|
||
,(string-append "LAPACK_LIBS=-L"
|
||
(assoc-ref %build-inputs "lapack")
|
||
" -llapack"))
|
||
#:phases (modify-phases %standard-phases
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup))))
|
||
(home-page "http://www.p4est.org")
|
||
(synopsis "Adaptive mesh refinement on forests of octrees")
|
||
(description
|
||
"The p4est software library enables the dynamic management of a
|
||
collection of adaptive octrees, conveniently called a forest of octrees.
|
||
p4est is designed to work in parallel and scales to hundreds of thousands of
|
||
processor cores.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public p4est-openmpi
|
||
(package (inherit p4est)
|
||
(name "p4est-openmpi")
|
||
(inputs
|
||
`(("mpi" ,openmpi)
|
||
,@(package-inputs p4est)))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments p4est)
|
||
((#:configure-flags cf)
|
||
``("--enable-mpi" ,@,cf))))
|
||
(synopsis "Parallel adaptive mesh refinement on forests of octrees")))
|
||
|
||
(define-public gsegrafix
|
||
;; This is an old and equally dead "experimental fork" of the longer-dead
|
||
;; original. At least it no longer requires the even-deader libgnomeprint{,ui}
|
||
;; libraries, instead rendering plots with Pango.
|
||
(package
|
||
(name "gsegrafix")
|
||
(version "1.0.7.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://savannah/gsegrafix-experimental/"
|
||
"gsegrafix-experimental-" version ".tar.gz"))
|
||
(sha256
|
||
(base32 "0fwh6719xy2zasmqlp0vdx6kzm45hn37ga88xmw5cz0yx7xw4j6f"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:configure-flags
|
||
(list "--disable-static")))
|
||
(inputs
|
||
(list glib gtk+))
|
||
(native-inputs
|
||
(list pkg-config))
|
||
(home-page "https://www.gnu.org/software/gsegrafix/")
|
||
(synopsis "GNOME application to create scientific and engineering plots")
|
||
(description
|
||
"GSEGrafix is an application which produces high-quality graphical
|
||
plots for science and engineering. Plots are specified via simple ASCII
|
||
parameter files and data files and are presented in an anti-aliased GNOME
|
||
canvas. The program supports rectangular two-dimensional plots, histograms,
|
||
polar-axis plots and three-dimensional plots. Plots can be printed or saved
|
||
to BMP, JPEG or PNG image formats.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public maxima
|
||
(package
|
||
(name "maxima")
|
||
(version "5.45.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
|
||
version "-source/" name "-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1p77nk5sz1qfkn5zr97szpbi8ib4b22k8i52l4ag5gkhd4kid47y"))
|
||
(patches (search-patches "maxima-defsystem-mkdir.patch"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("bash" ,bash-minimal)
|
||
("gnuplot" ,gnuplot) ;for plots
|
||
("sbcl" ,sbcl)
|
||
("sed" ,sed)
|
||
("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
|
||
(native-inputs
|
||
(list texinfo perl python))
|
||
(arguments
|
||
`(#:configure-flags
|
||
,#~(list "--enable-sbcl"
|
||
(string-append "--with-sbcl=" #$sbcl "/bin/sbcl")
|
||
(string-append "--with-posix-shell=" #$bash-minimal "/bin/sh")
|
||
(string-append "--with-wish=" #$tk "/bin/wish"
|
||
#$(version-major+minor (package-version tk))))
|
||
;; By default Maxima attempts to write temporary files to
|
||
;; '/tmp/nix-build-maxima-*', which won't exist at run time.
|
||
;; Work around that.
|
||
#:make-flags (list "TMPDIR=/tmp")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'patch-paths
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(let* ((sed (search-input-file inputs "/bin/sed"))
|
||
(coreutils (assoc-ref inputs "coreutils"))
|
||
(dirname (string-append coreutils "/bin/dirname"))
|
||
(head (string-append coreutils "/bin/head"))
|
||
(perl (search-input-file inputs "/bin/perl"))
|
||
(python (search-input-file inputs "/bin/python3")))
|
||
(substitute* "src/maxima.in"
|
||
(("sed ") (string-append sed " "))
|
||
(("dirname") dirname)
|
||
(("head") head))
|
||
(substitute* "doc/info/Makefile.in"
|
||
(("/usr/bin/env perl") perl))
|
||
(substitute* "doc/info/build_html.sh.in"
|
||
(("python") python))
|
||
#t)))
|
||
(add-before 'check 'pre-check
|
||
(lambda _
|
||
(chmod "src/maxima" #o555)
|
||
#t))
|
||
(replace 'check
|
||
(lambda _
|
||
;; This is derived from the testing code in the "debian/rules" file
|
||
;; of Debian's Maxima package.
|
||
;; If Maxima can successfully run this, the binary to be installed
|
||
;; should be fine.
|
||
(invoke "sh" "-c"
|
||
(string-append
|
||
"./maxima-local "
|
||
"--lisp=sbcl "
|
||
"--batch-string=\"run_testsuite();\" "
|
||
"| grep -q \"No unexpected errors found\""))))
|
||
;; Make sure the doc and emacs files are found in the
|
||
;; standard location. Also configure maxima to find gnuplot
|
||
;; without having it on the PATH.
|
||
(add-after 'install 'post-install
|
||
(lambda* (#:key outputs inputs #:allow-other-keys)
|
||
(let* ((gnuplot (assoc-ref inputs "gnuplot"))
|
||
(out (assoc-ref outputs "out"))
|
||
(datadir (string-append out "/share/maxima/" ,version))
|
||
(binutils (dirname (search-input-file inputs "/bin/as"))))
|
||
(with-directory-excursion out
|
||
(mkdir-p "share/emacs")
|
||
(mkdir-p "share/doc")
|
||
(symlink
|
||
(string-append datadir "/doc/")
|
||
(string-append out "/share/doc/maxima"))
|
||
(with-atomic-file-replacement
|
||
(string-append datadir "/share/maxima-init.lisp")
|
||
(lambda (in out)
|
||
(format out "~a ~s~a~%"
|
||
"(setf $gnuplot_command "
|
||
(string-append gnuplot "/bin/gnuplot") ")")
|
||
(dump-port in out))))
|
||
;; Ensure that Maxima will have access to the GNU binutils
|
||
;; components at runtime.
|
||
(wrap-program (string-append out "/bin/maxima")
|
||
`("PATH" prefix (,binutils))))
|
||
#t)))))
|
||
(home-page "https://maxima.sourceforge.io")
|
||
(synopsis "Numeric and symbolic expression manipulation")
|
||
(description "Maxima is a system for the manipulation of symbolic and
|
||
numerical expressions. It yields high precision numeric results by using
|
||
exact fractions, arbitrary precision integers, and variable precision floating
|
||
point numbers.")
|
||
;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
|
||
;; Others simply say "GNU General Public License" without stating a
|
||
;; version (which implicitly means gpl1+).
|
||
;; At least one file (src/maxima.asd) says "version 2."
|
||
;; GPLv2 only is therefore the smallest subset.
|
||
(license license:gpl2)))
|
||
|
||
(define-public wxmaxima
|
||
(package
|
||
(name "wxmaxima")
|
||
(version "21.05.2")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/wxMaxima-developers/wxmaxima")
|
||
(commit (string-append "Version-" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0h7ryykh2dapcyvpp4f1j1b3vrrz80x9k8nkci2yxifgdb29vyhw"))))
|
||
(build-system cmake-build-system)
|
||
(native-inputs
|
||
`(("gettext" ,gettext-minimal)))
|
||
(inputs
|
||
(list wxwidgets
|
||
maxima
|
||
;; Runtime support.
|
||
adwaita-icon-theme
|
||
gtk+
|
||
shared-mime-info))
|
||
(arguments
|
||
`(#:tests? #f ; tests fail non-deterministically
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'patch-doc-path
|
||
(lambda _
|
||
;; Don't look in share/doc/wxmaxima-xx.xx.x for the
|
||
;; documentation. Only licensing information is placed there by
|
||
;; Guix.
|
||
(substitute* "src/Dirstructure.cpp"
|
||
(("/doc/wxmaxima-\\%s") "/doc/wxmaxima"))
|
||
#t))
|
||
(add-after 'install 'wrap-program
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(wrap-program (string-append (assoc-ref outputs "out")
|
||
"/bin/wxmaxima")
|
||
`("PATH" ":" prefix
|
||
(,(string-append (assoc-ref inputs "maxima")
|
||
"/bin")))
|
||
;; For GtkFileChooserDialog.
|
||
`("GSETTINGS_SCHEMA_DIR" =
|
||
(,(string-append (assoc-ref inputs "gtk+")
|
||
"/share/glib-2.0/schemas")))
|
||
`("XDG_DATA_DIRS" ":" prefix
|
||
(;; Needed by gdk-pixbuf to know supported icon formats.
|
||
,(string-append
|
||
(assoc-ref inputs "shared-mime-info") "/share")
|
||
;; The default icon theme of GTK+.
|
||
,(string-append
|
||
(assoc-ref inputs "adwaita-icon-theme") "/share"))))
|
||
#t)))))
|
||
(home-page "https://wxmaxima-developers.github.io/wxmaxima/")
|
||
(synopsis "Graphical user interface for the Maxima computer algebra system")
|
||
(description
|
||
"wxMaxima is a graphical user interface for the Maxima computer algebra
|
||
system. It eases the use of Maxima by making most of its commands available
|
||
through a menu system and by providing input dialogs for commands that require
|
||
more than one argument. It also implements its own display engine that
|
||
outputs mathematical symbols directly instead of depicting them with ASCII
|
||
characters.
|
||
|
||
wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
|
||
text and mathematical calculations to create documents, exporting of input and
|
||
output to TeX, and a browser for Maxima's manual including command index and
|
||
full text searching.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public armadillo
|
||
(package
|
||
(name "armadillo")
|
||
(version "9.100.5")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://sourceforge/arma/armadillo-"
|
||
version ".tar.xz"))
|
||
(sha256
|
||
(base32
|
||
"1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
|
||
(build-system cmake-build-system)
|
||
(arguments `(#:tests? #f)) ; no test target
|
||
(inputs
|
||
`(("openblas" ,openblas)
|
||
("lapack" ,lapack)
|
||
("arpack" ,arpack-ng)))
|
||
(home-page "http://arma.sourceforge.net/")
|
||
(synopsis "C++ linear algebra library")
|
||
(description
|
||
"Armadillo is a C++ linear algebra library, aiming towards a good balance
|
||
between speed and ease of use. It is useful for algorithm development
|
||
directly in C++, or quick conversion of research code into production
|
||
environments. It can be used for machine learning, pattern recognition,
|
||
signal processing, bioinformatics, statistics, econometrics, etc. The library
|
||
provides efficient classes for vectors, matrices and cubes, as well as 150+
|
||
associated functions (e.g., contiguous and non-contiguous submatrix views).")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public muparser
|
||
;; When switching download sites, muparser re-issued a 2.2.5 release with a
|
||
;; different hash. In order to make `guix package --upgrade` work correctly,
|
||
;; we set a Guix packaging revision.
|
||
;; When the next version of muparser is released, we can remove
|
||
;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
|
||
(let ((upstream-version "2.2.5")
|
||
(revision "2"))
|
||
(package
|
||
(name "muparser")
|
||
(version (string-append upstream-version "-" revision))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/beltoforion/muparser")
|
||
(commit (string-append "v" upstream-version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:configure-flags '("--enable-samples=no")
|
||
#:tests? #f)) ;no "check" target
|
||
(home-page "http://muparser.beltoforion.de/")
|
||
(synopsis "Fast parser library for mathematical expressions")
|
||
(description
|
||
"muParser is an extensible high performance math parser library. It is
|
||
based on transforming an expression into a bytecode and precalculating constant
|
||
parts of it.")
|
||
(license license:expat))))
|
||
|
||
(define-public openblas
|
||
(package
|
||
(name "openblas")
|
||
(version "0.3.20")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/xianyi/OpenBLAS")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0r4sz3rn68fyc2paq0a04pgfi7iszpm95f6ggbzxpvjzx9qxbcql"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:test-target "test"
|
||
;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
|
||
;; TARGET is specified, OpenBLAS will tune itself to the build host, so
|
||
;; we need to disable substitutions.
|
||
#:substitutable?
|
||
,(let ((system (or (%current-target-system) (%current-system))))
|
||
(or (string-prefix? "x86_64" system)
|
||
(string-prefix? "i686" system)
|
||
(string-prefix? "mips" system)
|
||
(string-prefix? "aarch64" system)))
|
||
#:make-flags
|
||
(list (string-append "PREFIX=" (assoc-ref %outputs "out"))
|
||
"SHELL=bash"
|
||
"MAKE_NB_JOBS=0" ;use jobserver for submakes
|
||
"NO_STATIC=1" ;avoid a 67 MiB static archive
|
||
|
||
;; This is the maximum number of threads OpenBLAS will ever use (that
|
||
;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS
|
||
;; is used.) If we don't set it, the makefile sets it to the number
|
||
;; of cores of the build machine, which is obviously wrong.
|
||
"NUM_THREADS=128"
|
||
|
||
;; Build the library for all supported CPUs. This allows
|
||
;; switching CPU targets at runtime with the environment variable
|
||
;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
|
||
;; Unfortunately, this is not supported on all architectures,
|
||
;; where it leads to failed builds.
|
||
,@(let ((system (or (%current-target-system) (%current-system))))
|
||
(cond
|
||
((or (string-prefix? "x86_64" system)
|
||
(string-prefix? "i686" system)
|
||
(string-prefix? "powerpc64le" system)
|
||
(string-prefix? "aarch64" system))
|
||
;; Dynamic older enables a few extra CPU architectures that
|
||
;; were released before 2010.
|
||
'("DYNAMIC_ARCH=1" "DYNAMIC_OLDER=1" "TARGET=GENERIC"))
|
||
;; On some of these architectures the CPU can't be detected.
|
||
;; On MIPS we force the "SICORTEX" TARGET, as for the other
|
||
;; two available MIPS targets special extended instructions
|
||
;; for Loongson cores are used.
|
||
((string-prefix? "mips" system)
|
||
'("TARGET=SICORTEX"))
|
||
;; Failed to detect CPU.
|
||
((string-prefix? "armhf" system)
|
||
'("TARGET=ARMV7"))
|
||
((string-prefix? "riscv64" system)
|
||
'("TARGET=RISCV64_GENERIC"))
|
||
(else '()))))
|
||
;; no configure script
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(delete 'configure)
|
||
(add-before 'build 'set-extralib
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
;; Get libgfortran found when building in utest.
|
||
(setenv "FEXTRALIB"
|
||
(string-append
|
||
"-L"
|
||
(dirname
|
||
(search-input-file inputs "/lib/libgfortran.so")))))))))
|
||
(inputs
|
||
(list `(,gfortran "lib")))
|
||
(native-inputs
|
||
(list cunit gfortran perl))
|
||
(home-page "https://www.openblas.net/")
|
||
(synopsis "Optimized BLAS library based on GotoBLAS")
|
||
(description
|
||
"OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public openblas-ilp64
|
||
(package/inherit openblas
|
||
(name "openblas-ilp64")
|
||
(supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments openblas)
|
||
((#:make-flags flags '())
|
||
`(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
|
||
,flags))))
|
||
(synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public blis
|
||
(package
|
||
(name "blis")
|
||
(version "0.8.1")
|
||
(home-page "https://github.com/flame/blis")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference (url home-page) (commit version)))
|
||
(sha256
|
||
(base32
|
||
"05ifil6jj9424sr8kmircl8k4bmxnl3y12a79vwj1kxxva5gz50g"))
|
||
(file-name (git-file-name "blis" version))))
|
||
(native-inputs
|
||
(list python perl))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:modules
|
||
((guix build gnu-build-system)
|
||
(guix build utils)
|
||
(srfi srfi-1))
|
||
#:test-target "test"
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'configure
|
||
(lambda* (#:key outputs
|
||
target
|
||
system
|
||
(configure-flags '())
|
||
#:allow-other-keys)
|
||
;; This is a home-made 'configure' script.
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
;; Guix-specific support for choosing the configuration
|
||
;; via #:configure-flags: see below for details.
|
||
(config-flag-prefix "--blis-config=")
|
||
(maybe-config-flag (find
|
||
(lambda (s)
|
||
(string-prefix? config-flag-prefix s))
|
||
configure-flags))
|
||
(configure-flags (if maybe-config-flag
|
||
(delete maybe-config-flag
|
||
configure-flags)
|
||
configure-flags))
|
||
;; Select the "configuration" to build.
|
||
;; The "generic" configuration is non-optimized but
|
||
;; portable (no assembly).
|
||
;; The "x86_64" configuration family includes
|
||
;; sub-configurations for all supported
|
||
;; x86_64 microarchitectures.
|
||
;; BLIS currently lacks runtime hardware detection
|
||
;; for other architectures: see
|
||
;; <https://github.com/flame/blis/commit/c534da6>.
|
||
;; Conservatively, we stick to "generic" on armhf,
|
||
;; aarch64, and ppc64le for now. (But perhaps
|
||
;; "power9", "cortexa9", and "cortexa57" might be
|
||
;; general enough to use?)
|
||
;; Another approach would be to use the "auto"
|
||
;; configuration and make this package
|
||
;; non-substitutable.
|
||
;; The build is fairly intensive, though.
|
||
(blis-config
|
||
(cond
|
||
(maybe-config-flag
|
||
(substring maybe-config-flag
|
||
(string-length config-flag-prefix)))
|
||
((string-prefix? "x86_64" (or target system))
|
||
"x86_64")
|
||
(else
|
||
"generic")))
|
||
(configure-args
|
||
`("-p" ,out
|
||
"-d" "opt"
|
||
"--disable-static"
|
||
"--enable-shared"
|
||
"--enable-threading=openmp"
|
||
"--enable-verbose-make"
|
||
,@configure-flags
|
||
,blis-config)))
|
||
(format #t "configure args: ~s~%" configure-args)
|
||
(apply invoke
|
||
"./configure"
|
||
configure-args)
|
||
#t)))
|
||
(add-before 'check 'show-test-output
|
||
(lambda _
|
||
;; By default "make check" is silent. Make it verbose.
|
||
(system "tail -F output.testsuite &")
|
||
#t)))))
|
||
(synopsis "High-performance basic linear algebra (BLAS) routines")
|
||
(description
|
||
"BLIS is a portable software framework for instantiating high-performance
|
||
BLAS-like dense linear algebra libraries. The framework was designed to
|
||
isolate essential kernels of computation that, when optimized, immediately
|
||
enable optimized implementations of most of its commonly used and
|
||
computationally intensive operations. While BLIS exports a new BLAS-like API,
|
||
it also includes a BLAS compatibility layer which gives application developers
|
||
access to BLIS implementations via traditional BLAS routine calls.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public blis-sandybridge (deprecated-package "blis-sandybridge" blis))
|
||
(define-public blis-haswell (deprecated-package "blis-haswell" blis))
|
||
(define-public blis-knl (deprecated-package "blis-knl" blis))
|
||
|
||
(define ignorance blis)
|
||
|
||
(define-public openlibm
|
||
(package
|
||
(name "openlibm")
|
||
(version "0.7.4")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/JuliaLang/openlibm")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1azms0lpxb7vxb3bln5lyz0wpwx6jnzbffkclclpq2v5aiw8d14i"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:make-flags
|
||
(list (string-append "prefix=" (assoc-ref %outputs "out"))
|
||
,(string-append "CC=" (cc-for-target)))
|
||
#:phases
|
||
;; no configure script
|
||
(modify-phases %standard-phases (delete 'configure))
|
||
#:tests? #f)) ;the tests are part of the default target
|
||
(home-page "https://openlibm.org/")
|
||
(synopsis "Portable C mathematical library (libm)")
|
||
(description
|
||
"OpenLibm is an effort to have a high quality, portable, standalone C
|
||
mathematical library (libm). It can be used standalone in applications and
|
||
programming language implementations. The project was born out of a need to
|
||
have a good libm for the Julia programming language that worked consistently
|
||
across compilers and operating systems, and in 32-bit and 64-bit
|
||
environments.")
|
||
;; Each architecture has its own make target, and there is none for mips.
|
||
(supported-systems (delete "mips64el-linux" %supported-systems))
|
||
;; See LICENSE.md for details.
|
||
(license (list license:expat
|
||
license:isc
|
||
license:bsd-2
|
||
license:public-domain
|
||
license:lgpl2.1+))))
|
||
|
||
(define-public openspecfun
|
||
(package
|
||
(name "openspecfun")
|
||
(version "0.5.3")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/JuliaLang/openspecfun")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
'(#:tests? #f ; no "check" target
|
||
#:make-flags
|
||
(list (string-append "prefix=" (assoc-ref %outputs "out")))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(delete 'configure)))) ; no configure script
|
||
(inputs
|
||
`(("fortran" ,gfortran)))
|
||
(home-page "https://github.com/JuliaLang/openspecfun")
|
||
(synopsis "Collection of special mathematical functions")
|
||
(description
|
||
"Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
|
||
portable package for Bessel Functions of a Complex Argument and Nonnegative
|
||
Order; it contains subroutines for computing Bessel functions and Airy
|
||
functions. Faddeeva allows computing the various error functions of arbitrary
|
||
complex arguments (Faddeeva function, error function, complementary error
|
||
function, scaled complementary error function, imaginary error function, and
|
||
Dawson function); given these, one can also easily compute Voigt functions,
|
||
Fresnel integrals, and similar related functions as well.")
|
||
;; Faddeeva is released under the Expat license; AMOS is included as
|
||
;; public domain software.
|
||
(license (list license:expat license:public-domain))))
|
||
|
||
(define-public suitesparse
|
||
(package
|
||
(name "suitesparse")
|
||
(version "5.10.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/DrTimothyAldenDavis/SuiteSparse")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"19gx5wlgqnqpgz6mvam9lalyzpbfwgqhppps8z3np9sh0mgaiyw9"))
|
||
(patches (search-patches "suitesparse-mongoose-cmake.patch"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
;; Remove bundled metis source
|
||
'(begin
|
||
(delete-file-recursively "metis-5.1.0")
|
||
#t))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:tests? #f ;no "check" target
|
||
#:make-flags
|
||
(list (string-append "CC=" ,(cc-for-target))
|
||
"TBB=-ltbb"
|
||
"MY_METIS_LIB=-lmetis"
|
||
|
||
;; The default is to link against netlib lapack. Use OpenBLAS
|
||
;; instead.
|
||
"BLAS=-lopenblas" "LAPACK=-lopenblas"
|
||
|
||
;; Flags for cmake (required to build GraphBLAS and Mongoose)
|
||
(string-append "CMAKE_OPTIONS=-DCMAKE_INSTALL_PREFIX="
|
||
(assoc-ref %outputs "out")
|
||
" -DCMAKE_VERBOSE_MAKEFILE=ON"
|
||
" -DCMAKE_C_FLAGS_RELEASE=\"$(CFLAGS) $(CPPFLAGS)\""
|
||
" -DCMAKE_CXX_FLAGS_RELEASE=\"$(CXXFLAGS) $(CPPFLAGS)\""
|
||
" -DCMAKE_SKIP_RPATH=TRUE"
|
||
" -DCMAKE_BUILD_TYPE=Release"
|
||
" -DCMAKE_INSTALL_LIBDIR=lib")
|
||
(string-append "INSTALL_LIB="
|
||
(assoc-ref %outputs "out") "/lib")
|
||
(string-append "INSTALL_INCLUDE="
|
||
(assoc-ref %outputs "out") "/include")
|
||
"library")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(delete 'configure)))) ;no configure script
|
||
(inputs
|
||
(list tbb openblas gmp mpfr metis))
|
||
(native-inputs
|
||
`(("cmake" ,cmake-minimal)
|
||
("m4" ,m4)))
|
||
(home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
|
||
(synopsis "Suite of sparse matrix software")
|
||
(description
|
||
"SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
|
||
multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
|
||
multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
|
||
simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
|
||
CXSparse, a concise sparse Cholesky factorization package; and many other
|
||
packages.")
|
||
;; LGPLv2.1+:
|
||
;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
|
||
;; GPLv2+:
|
||
;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
|
||
(license (list license:gpl2+ license:lgpl2.1+))))
|
||
|
||
(define-public atlas
|
||
(package
|
||
(name "atlas")
|
||
(version "3.10.3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://sourceforge/math-atlas/Stable/"
|
||
version "/atlas" version ".tar.bz2"))
|
||
(patches (search-patches "atlas-gfortran-compat.patch"))
|
||
(sha256
|
||
(base32
|
||
"1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
|
||
(build-system gnu-build-system)
|
||
(home-page "http://math-atlas.sourceforge.net/")
|
||
(inputs `(("gfortran" ,gfortran)
|
||
("lapack-tar" ,(package-source lapack))))
|
||
(outputs '("out" "doc"))
|
||
;; For the moment we drop support for MIPS at it fails to compile. See
|
||
;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
|
||
(supported-systems (delete "mips64el-linux" %supported-systems))
|
||
(arguments
|
||
`(#:parallel-build? #f
|
||
#:parallel-tests? #f
|
||
|
||
;; ATLAS tunes itself for the machine it is built on, as explained at
|
||
;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
|
||
;; For this reason, we want users to build it locally instead of using
|
||
;; substitutes.
|
||
#:substitutable? #f
|
||
|
||
#:modules ((srfi srfi-26)
|
||
(guix build gnu-build-system)
|
||
(guix build utils))
|
||
#:configure-flags
|
||
`(;; Generate position independent code suitable for dynamic libraries
|
||
;; and use WALL timer to get more accurate timing.
|
||
"-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
|
||
;; Set word width.
|
||
"-b"
|
||
,,(if (string-match "64" (%current-system))
|
||
"64"
|
||
"32")
|
||
;; Disable parallel build as it gives errors: atlas_pthread.h is
|
||
;; needed to compile C files before it is generated.
|
||
"-Ss" "pmake" "make -j 1"
|
||
;; Probe is failing for MIPS. We therefore define the system
|
||
;; architecture explicitly by setting (-A) MACHINETYPE = 49
|
||
;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
|
||
,,@(if (string-prefix? "mips" (%current-system))
|
||
(list "-A" "49" "-V" "1")
|
||
(list))
|
||
;; Generate shared libraries.
|
||
"--shared"
|
||
;; Build a full LAPACK library.
|
||
,(string-append "--with-netlib-lapack-tarfile="
|
||
(assoc-ref %build-inputs "lapack-tar")))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'install 'install-doc
|
||
(lambda* (#:key outputs inputs #:allow-other-keys)
|
||
(let ((doc (string-append (assoc-ref outputs "doc")
|
||
"/share/doc/atlas")))
|
||
(mkdir-p doc)
|
||
(for-each (cut install-file <> doc)
|
||
(find-files "../ATLAS/doc" ".*"))
|
||
#t)))
|
||
(add-after 'check 'check-pt
|
||
(lambda _ (invoke "make" "ptcheck")))
|
||
;; Fix files required to run configure.
|
||
(add-before 'configure 'fix-/bin/sh
|
||
(lambda _
|
||
;; Use `sh', not `/bin/sh'.
|
||
(substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
|
||
(("/bin/sh")
|
||
"sh"))
|
||
#t))
|
||
;; Fix /bin/sh in generated make files.
|
||
(add-after 'configure 'fix-/bin/sh-in-generated-files
|
||
(lambda _
|
||
(substitute* (find-files "." "^[Mm]ake\\.inc.*")
|
||
(("/bin/sh")
|
||
"sh"))
|
||
#t))
|
||
;; ATLAS configure program does not accepts the default flags
|
||
;; passed by the 'gnu-build-system'.
|
||
(replace 'configure
|
||
(lambda* (#:key native-inputs inputs outputs
|
||
(configure-flags '())
|
||
#:allow-other-keys #:rest args)
|
||
(let* ((prefix (assoc-ref outputs "out"))
|
||
(bash (or (and=> (assoc-ref
|
||
(or native-inputs inputs) "bash")
|
||
(cut string-append <> "/bin/bash"))
|
||
"/bin/sh"))
|
||
(flags `(,(string-append "--prefix=" prefix)
|
||
,@configure-flags))
|
||
(abs-srcdir (getcwd))
|
||
(srcdir (string-append "../" (basename abs-srcdir))))
|
||
(format #t "source directory: ~s (relative from build: ~s)~%"
|
||
abs-srcdir srcdir)
|
||
(mkdir "../build")
|
||
(chdir "../build")
|
||
(format #t "build directory: ~s~%" (getcwd))
|
||
(format #t "configure flags: ~s~%" flags)
|
||
(apply invoke bash
|
||
(string-append srcdir "/configure")
|
||
flags)))))))
|
||
(synopsis "Automatically Tuned Linear Algebra Software")
|
||
(description
|
||
"ATLAS is an automatically tuned linear algebra software library
|
||
providing C and Fortran77 interfaces to a portably efficient BLAS
|
||
implementation, as well as a few routines from LAPACK.
|
||
|
||
Optimization occurs at build time. For this reason, the library is built on
|
||
the machine where it is installed, without resorting to pre-built substitutes.
|
||
|
||
Before building the library, CPU throttling should be disabled. This can be
|
||
done in the BIOS, or, on GNU/Linux, with the following command:
|
||
|
||
@example
|
||
# cpupower --governor performance
|
||
@end example
|
||
|
||
Failure to do so will result in a library with poor performance.")
|
||
;; The test suite is notoriously lengthy and routinely exceeds the default
|
||
;; timeout of 21600 seconds on the not unbeefy berlin build nodes.
|
||
(properties '((timeout . 86400))) ; 1 day
|
||
(license license:bsd-3)))
|
||
|
||
(define-public cglm
|
||
(package
|
||
(name "cglm")
|
||
(version "0.8.4")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/recp/cglm")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0zgckh56vcdar3a4n51r84wrizyd2ssqal4nsvxd4qdjm0rvb4h0"))))
|
||
(build-system meson-build-system)
|
||
(arguments
|
||
`(#:configure-flags '("-Dbuild_tests=true")))
|
||
(home-page "https://github.com/recp/cglm")
|
||
(synopsis "Mathematics C library for graphics programming")
|
||
(description
|
||
"@acronym{CGLM, C OpenGL Mathematics} is an optimised 3D maths library
|
||
for graphics software based on the @acronym{GLSL, OpenGL Shading Language}
|
||
specifications.
|
||
|
||
It's similar to the original C++ GLM library but written in C99 and compatible
|
||
with C89.")
|
||
(license license:expat)))
|
||
|
||
(define-public glm
|
||
(package
|
||
(name "glm")
|
||
(version "0.9.9.8")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://github.com/g-truc/glm/releases/download/"
|
||
version "/glm-" version ".zip"))
|
||
(sha256
|
||
(base32 "0k6yk9v46h690rshdx49x98y5qspkzibld1wb51jwcm35vba7qip"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases (modify-phases %standard-phases
|
||
(replace 'install
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
;; Since version 0.9.9.6, 'make install' is not supported
|
||
;; and we have to do it "manually". Upstream discussion:
|
||
;; <https://github.com/g-truc/glm/pull/968>.
|
||
(let* ((source (string-append "../glm"))
|
||
(out (assoc-ref outputs "out"))
|
||
(inc (string-append out "/include"))
|
||
(lib (string-append out "/lib"))
|
||
(pkgconfig (string-append lib "/pkgconfig")))
|
||
(with-directory-excursion source
|
||
(mkdir-p inc)
|
||
(mkdir-p pkgconfig)
|
||
(copy-recursively "glm" (string-append inc "/glm"))
|
||
(copy-recursively "cmake" (string-append lib "/cmake"))
|
||
(call-with-output-file (string-append pkgconfig "/glm.pc")
|
||
(lambda (port)
|
||
(format port
|
||
"prefix=~a
|
||
includedir=${prefix}/include
|
||
|
||
Name: GLM
|
||
Description: OpenGL Mathematics
|
||
Version: ~a
|
||
Cflags: -I${includedir}~%" out ,(version-prefix version 3)))))
|
||
#t))))))
|
||
(native-inputs
|
||
(list unzip))
|
||
(home-page "https://glm.g-truc.net/")
|
||
(synopsis "OpenGL Mathematics library")
|
||
(description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
|
||
library for graphics software based on the OpenGL Shading Language (GLSL)
|
||
specifications.")
|
||
(license license:expat)))
|
||
|
||
(define-public lpsolve
|
||
(package
|
||
(name "lpsolve")
|
||
(version "5.5.2.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
|
||
"/lp_solve_" version "_source.tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(begin
|
||
(substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
|
||
(("^c=cc") "c=gcc")
|
||
;; Pretend to be on a 64 bit platform to obtain a common directory
|
||
;; name for the build results on all architectures; nothing else
|
||
;; seems to depend on it.
|
||
(("^PLATFORM=.*$") "PLATFORM=ux64\n")
|
||
|
||
;; The check for 'isnan' as it is written fails with
|
||
;; "non-floating-point argument in call to function
|
||
;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
|
||
;; definition, which in turn leads to bad things. Fix the feature
|
||
;; test.
|
||
(("isnan\\(0\\)") "isnan(0.)"))
|
||
#t))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:tests? #f ; no check target
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(delete 'configure) ; no configure script
|
||
(replace 'build
|
||
(lambda _
|
||
(with-directory-excursion "lpsolve55"
|
||
(invoke "bash" "ccc"))
|
||
(with-directory-excursion "lp_solve"
|
||
(invoke "bash" "ccc"))
|
||
#t))
|
||
(replace 'install
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(bin (string-append out "/bin"))
|
||
(lib (string-append out "/lib"))
|
||
;; This is where LibreOffice expects to find the header
|
||
;; files, and where they are installed by Debian.
|
||
(include (string-append out "/include/lpsolve")))
|
||
(install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
|
||
(install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
|
||
(install-file "lp_solve/bin/ux64/lp_solve" bin)
|
||
|
||
;; Install a subset of the header files as on Debian
|
||
;; (plus lp_bit.h, which matches the regular expression).
|
||
(for-each (lambda (name)
|
||
(install-file name include))
|
||
(find-files "." "lp_[HMSa-z].*\\.h$"))
|
||
(with-directory-excursion "shared"
|
||
(for-each (lambda (name)
|
||
(install-file name include))
|
||
(find-files "." "\\.h$")))
|
||
#t))))))
|
||
(home-page "http://lpsolve.sourceforge.net/")
|
||
(synopsis "Mixed integer linear programming (MILP) solver")
|
||
(description
|
||
"lp_solve is a mixed integer linear programming solver based on the
|
||
revised simplex and the branch-and-bound methods.")
|
||
(license license:lgpl2.1+)))
|
||
|
||
;; Private Trilinos package for dealii-openmpi (similar to
|
||
;; trilinos-serial-xyce and trilinos-parallel-xyce).
|
||
;; This version is the latest known to be compatible with deal.II [1].
|
||
;; Since the latest version of Trilinos is not necessarily supported by
|
||
;; deal.II, it may be worth keeping this package even if and when Trilinos
|
||
;; gets packaged separately for Guix (unless various versions of Trilinos are
|
||
;; packaged).
|
||
;;
|
||
;; An insightful source of information for building Trilinos for deal.II lies
|
||
;; in the Trilinos package for candi [2], which is a source-based installer
|
||
;; for deal.II and its dependencies.
|
||
;;
|
||
;; [1]: https://www.dealii.org/current/external-libs/trilinos.html
|
||
;; [2]: https://github.com/dealii/candi/blob/master/deal.II-toolchain/packages/trilinos.package
|
||
(define trilinos-for-dealii-openmpi
|
||
(package
|
||
(name "trilinos-for-dealii-openmpi")
|
||
(version "12.18.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/trilinos/Trilinos/")
|
||
(commit
|
||
(string-append "trilinos-release-"
|
||
(string-replace-substring version "." "-")))))
|
||
(file-name (git-file-name "trilinos" version))
|
||
(sha256
|
||
(base32 "0fnwlhzsh85qj38cq3igbs8nm1b2jdgr2z734sapmyyzsy21mkgp"))))
|
||
(build-system cmake-build-system)
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)
|
||
;; Trilinos's repository contains several C-shell scripts, but adding
|
||
;; tcsh to the native inputs does not result in the check phase running
|
||
;; any more tests than without it (nor is tcsh required to build
|
||
;; Trilinos).
|
||
;; It seems that Trilinos has replaced its use of C-shell test scripts
|
||
;; with CMake's testing facilities.
|
||
;; For example,
|
||
;; packages/zoltan/doc/Zoltan_html/dev_html/dev_test_script.html [1]
|
||
;; states that Zoltan's C-shell test script
|
||
;; packages/zoltan/test/test_zoltan has been obsoleted by the tests now
|
||
;; performed through CMake.
|
||
;;
|
||
;; Perl is required for some Zoltan tests and Python 2 for one ML test.
|
||
;;
|
||
;; [1]: https://cs.sandia.gov/zoltan/dev_html/dev_test_script.html
|
||
("perl" ,perl)
|
||
("python" ,python-2)))
|
||
(inputs
|
||
`(("blas" ,openblas)
|
||
("lapack" ,lapack)
|
||
("mumps" ,mumps-openmpi)
|
||
("scalapack" ,scalapack)))
|
||
(propagated-inputs
|
||
`(("mpi" ,openmpi)))
|
||
(arguments
|
||
`(#:build-type "Release"
|
||
#:configure-flags
|
||
`("-DBUILD_SHARED_LIBS=ON"
|
||
;; Obtain the equivalent of RelWithDebInfo but with -O3 (the Release
|
||
;; default) rather than -O2 (the RelWithDebInfo default), to conform
|
||
;; to candi's trilinos.package's compilation flags, which are -g -O3.
|
||
"-DCMAKE_C_FLAGS=-g"
|
||
"-DCMAKE_CXX_FLAGS=-g"
|
||
"-DCMAKE_Fortran_FLAGS=-g"
|
||
|
||
;; Trilinos libraries that deal.II can interface with.
|
||
"-DTrilinos_ENABLE_Amesos=ON"
|
||
"-DTrilinos_ENABLE_AztecOO=ON"
|
||
"-DTrilinos_ENABLE_Epetra=ON"
|
||
"-DTrilinos_ENABLE_EpetraExt=ON"
|
||
"-DTrilinos_ENABLE_Ifpack=ON"
|
||
"-DTrilinos_ENABLE_ML=ON"
|
||
"-DTrilinos_ENABLE_MueLu=ON"
|
||
"-DTrilinos_ENABLE_ROL=ON"
|
||
;; Optional; required for deal.II's GridIn::read_exodusii, but
|
||
;; depends on netcdf.
|
||
;; Enable if and when someone needs it.
|
||
;;"-DTrilinos_ENABLE_SEACAS=ON"
|
||
"-DTrilinos_ENABLE_Sacado=ON"
|
||
"-DTrilinos_ENABLE_Teuchos=ON"
|
||
"-DTrilinos_ENABLE_Tpetra=ON"
|
||
"-DTrilinos_ENABLE_Zoltan=ON"
|
||
|
||
;; Third-party libraries (TPLs) that Trilinos can interface with.
|
||
"-DBLAS_LIBRARY_NAMES=openblas"
|
||
"-DTPL_ENABLE_MPI=ON"
|
||
"-DTPL_ENABLE_MUMPS=ON"
|
||
"-DTPL_ENABLE_SCALAPACK=ON"
|
||
|
||
;; Enable the tests but not the examples (which are enabled by
|
||
;; default when enabling tests).
|
||
;; Although some examples are run as tests, they are otherwise
|
||
;; unnecessary since this is a private package meant for
|
||
;; dealii-openmpi.
|
||
;; Besides, some MueLu and ROL examples require a lot of memory to
|
||
;; compile.
|
||
;;
|
||
;; (For future reference, note that some ROL and SEACAS examples
|
||
;; require removing gfortran from CPLUS_INCLUDE_PATH as in the
|
||
;; dune-istl, dune-localfunctions and dune-alugrid packages.)
|
||
"-DTrilinos_ENABLE_TESTS=ON"
|
||
"-DTrilinos_ENABLE_EXAMPLES=OFF"
|
||
;; MueLu tests require considerably more time and memory to compile
|
||
;; than the rest of the tests.
|
||
"-DMueLu_ENABLE_TESTS=OFF"
|
||
|
||
;; The following options were gleaned from candi's trilinos.package.
|
||
;; (We do not enable the complex instantiations, which are anyway
|
||
;; provided only as an option in trilinos.package, because they are
|
||
;; costly in compilation time and memory usage, and disk space [1].)
|
||
;;
|
||
;; [1]: https://www.docs.trilinos.org/files/TrilinosBuildReference.html#enabling-float-and-complex-scalar-types
|
||
"-DTrilinos_ENABLE_Ifpack2=OFF"
|
||
"-DTeuchos_ENABLE_FLOAT=ON"
|
||
"-DTpetra_INST_INT_LONG=ON"
|
||
"-DTPL_ENABLE_Boost=OFF")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'configure 'fix-kokkos-config
|
||
(lambda _
|
||
;; GNU Make 4.3 accidentally leaves the backslash preceding the
|
||
;; number sign in strings containing a literal backslash–number
|
||
;; sign (\#) [1, 2].
|
||
;; This is still an issue in Trilinos 13.0.1, but should be fixed
|
||
;; in the following version.
|
||
;; (The latest versions of Kokkos incorporate the fix [2].)
|
||
;;
|
||
;; [1]: https://github.com/GEOSX/thirdPartyLibs/issues/136
|
||
;; [2]: https://github.com/kokkos/kokkos/blob/3.4.00/Makefile.kokkos#L441
|
||
(substitute* "KokkosCore_config.h"
|
||
(("\\\\#") "#"))
|
||
#t))
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup))))
|
||
(home-page "https://trilinos.github.io/")
|
||
(synopsis "Algorithms for engineering and scientific problems")
|
||
(description
|
||
"The Trilinos Project is an effort to develop algorithms and enabling
|
||
technologies within an object-oriented software framework for the solution of
|
||
large-scale, complex multi-physics engineering and scientific problems.
|
||
A unique design feature of Trilinos is its focus on packages.")
|
||
;; The packages are variously licensed under more than just BSD-3 and
|
||
;; LGPL-2.1+, but all the licenses are either BSD- or LGPL-compatible.
|
||
;; See https://trilinos.github.io/license.html.
|
||
(license (list license:bsd-3 license:lgpl2.1+))))
|
||
|
||
(define-public dealii
|
||
(package
|
||
(name "dealii")
|
||
(version "9.3.3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://github.com/dealii/dealii/releases/"
|
||
"download/v" version "/dealii-" version ".tar.gz"))
|
||
(sha256
|
||
(base32 "0a8s4yxcbvzmfgv5qcg27h2ss4fcnyhrhhs35glqj59l9cbmkysx"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
;; Remove bundled boost, muparser, TBB and UMFPACK.
|
||
'(delete-file-recursively "bundled"))))
|
||
(build-system cmake-build-system)
|
||
(outputs '("out" "doc"))
|
||
(native-inputs
|
||
;; Required to build the documentation.
|
||
(list graphviz doxygen perl))
|
||
(inputs
|
||
(list arpack-ng
|
||
openblas
|
||
gfortran
|
||
lapack
|
||
muparser
|
||
zlib))
|
||
(propagated-inputs
|
||
;; Some scripts are installed into share/deal.II/scripts that require
|
||
;; perl and python, but they are not executable (and some are missing the
|
||
;; shebang line) and therefore must be explicitly passed to the
|
||
;; interpreter.
|
||
;; Anyway, they are meant to be used at build time, so rather than adding
|
||
;; the interpreters here, any package depending on them should just add
|
||
;; the requisite interpreter to its native inputs.
|
||
(list boost
|
||
hdf5
|
||
suitesparse ; For UMFPACK.
|
||
;; SUNDIALS 6.0.0 and later will be supported in deal.II 9.4.0.
|
||
sundials-5
|
||
tbb))
|
||
(arguments
|
||
`(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease.
|
||
;; The tests take too long and must be explicitly enabled with "make
|
||
;; setup_tests".
|
||
;; See https://www.dealii.org/developer/developers/testsuite.html.
|
||
;; (They can also be run for an already installed deal.II.)
|
||
#:tests? #f
|
||
#:configure-flags
|
||
(let ((doc (string-append (assoc-ref %outputs "doc")
|
||
"/share/doc/" ,name "-" ,version)))
|
||
`("-DDEAL_II_COMPONENT_DOCUMENTATION=ON"
|
||
,(string-append "-DDEAL_II_DOCREADME_RELDIR=" doc)
|
||
,(string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html")
|
||
;; Don't compile the examples because the source and CMakeLists.txt
|
||
;; are installed anyway, allowing users to do so for themselves.
|
||
"-DDEAL_II_COMPILE_EXAMPLES=OFF"
|
||
,(string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc "/examples")))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'install 'remove-build-logs
|
||
;; These build logs leak the name of the build directory by storing
|
||
;; the values of CMAKE_SOURCE_DIR and CMAKE_BINARY_DIR.
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let ((doc (string-append (assoc-ref outputs "doc")
|
||
"/share/doc/" ,name "-" ,version)))
|
||
(for-each delete-file (map (lambda (f) (string-append doc "/" f))
|
||
'("detailed.log" "summary.log")))))))))
|
||
(home-page "https://www.dealii.org/")
|
||
(synopsis "Finite element library")
|
||
(description
|
||
"Deal.II is a C++ program library targeted at the computational solution
|
||
of partial differential equations using adaptive finite elements. The main
|
||
aim of deal.II is to enable rapid development of modern finite element codes,
|
||
using among other aspects adaptive meshes and a wide array of tools often used
|
||
in finite element programs.")
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public dealii-openmpi
|
||
(package/inherit dealii
|
||
(name "dealii-openmpi")
|
||
(inputs
|
||
(modify-inputs (package-inputs dealii)
|
||
(delete "arpack")
|
||
(prepend arpack-ng-openmpi
|
||
metis
|
||
scalapack)))
|
||
(propagated-inputs
|
||
(modify-inputs (package-propagated-inputs dealii)
|
||
(delete "hdf5" "sundials")
|
||
(prepend hdf5-parallel-openmpi
|
||
openmpi
|
||
p4est-openmpi
|
||
petsc-openmpi
|
||
slepc-openmpi
|
||
sundials-openmpi-5
|
||
trilinos-for-dealii-openmpi)))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments dealii)
|
||
((#:configure-flags flags)
|
||
`(cons "-DDEAL_II_WITH_MPI=ON" ,flags))))
|
||
(synopsis "Finite element library (with MPI support)")))
|
||
|
||
(define-public flann
|
||
(package
|
||
(name "flann")
|
||
(version "1.9.1")
|
||
(home-page "https://github.com/mariusmuja/flann/")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference (url home-page) (commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0p56fl2yx1r86ds1mgjq40926jdcgq3hka7p3l1hv2acv9jxp15x"))
|
||
(patches (search-patches "flann-cmake-3.11.patch"))))
|
||
(build-system cmake-build-system)
|
||
(outputs '("out"))
|
||
(native-inputs
|
||
(list unzip))
|
||
(inputs
|
||
`(("hdf5" ,hdf5)
|
||
;; FIXME: 'mkoctfile' fails with a linker error:
|
||
;; ld: cannot find -loctinterp
|
||
;; ld: cannot find -loctave
|
||
;; Disable it for now.
|
||
;;("octave" ,octave-cli)
|
||
("python" ,python-2) ; print syntax
|
||
("zlib" ,zlib)))
|
||
(arguments
|
||
`(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
|
||
;; taken 46 MiB unstripped, and 6 MiB stripped.
|
||
#:strip-directories '("lib" "lib64" "libexec"
|
||
"bin" "sbin" "share/flann/octave")
|
||
|
||
;; Save 12 MiB by not installing .a files. Passing
|
||
;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
|
||
#:phases (modify-phases %standard-phases
|
||
(add-after 'install 'remove-static-libraries
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(lib (string-append out "/lib")))
|
||
(for-each delete-file
|
||
(find-files lib "\\.a$"))
|
||
#t))))
|
||
|
||
#:tests? #f)) ; The test data are downloaded from the Internet.
|
||
(synopsis "Library for approximate nearest neighbors computation")
|
||
(description "FLANN is a library for performing fast approximate
|
||
nearest neighbor searches in high dimensional spaces. It implements a
|
||
collection of algorithms and a system for automatically choosing the best
|
||
algorithm and optimum parameters depending on the dataset.
|
||
|
||
FLANN is written in C++ and contains bindings for C, Octave and Python.")
|
||
(license (license:non-copyleft "file://COPYING"
|
||
"See COPYING in the distribution."))))
|
||
|
||
(define-public wcalc
|
||
(package
|
||
(name "wcalc")
|
||
(version "2.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
|
||
"wcalc-" version ".tar.bz2"))
|
||
(sha256
|
||
(base32
|
||
"1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
(list mpfr readline))
|
||
(home-page "http://w-calc.sourceforge.net/index.php")
|
||
(synopsis "Flexible command-line scientific calculator")
|
||
(description "Wcalc is a very capable calculator. It has standard functions
|
||
(sin, asin, and sinh for example, in either radians or degrees), many
|
||
pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
|
||
variables, a command history, hex/octal/binary input and output, unit
|
||
conversions, embedded comments, and an expandable expression entry field. It
|
||
evaluates expressions using the standard order of operations.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public xaos
|
||
(package
|
||
(name "xaos")
|
||
(version "4.2.1")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/xaos-project/XaoS")
|
||
(commit (string-append "release-" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0maw5am6rrkyjrprfg113zjq37mqj0iaznkg4h2927ff7wrprc94"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs `(("gettext" ,gettext-minimal)
|
||
("qtbase" ,qtbase-5)
|
||
("qttools" ,qttools)))
|
||
(inputs (list libx11 zlib libpng gsl))
|
||
;; The upstream project file ("XaoS.pro") and the Makefile it generates are
|
||
;; not enough for this package to install properly. These phases fix that.
|
||
(arguments
|
||
`(#:tests? #f ;no "check" target
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'configure 'make-qt-deterministic
|
||
(lambda _
|
||
;; Make Qt deterministic.
|
||
(setenv "QT_RCC_SOURCE_DATE_OVERRIDE" "1")
|
||
#t))
|
||
(replace 'configure
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out")))
|
||
(substitute* "XaoS.pro"
|
||
;; The DESTDIR is originally set to install the xaos binary to
|
||
;; the "bin" folder inside the build directory. Setting make
|
||
;; flags doesn't seem to change this.
|
||
(("DESTDIR.*$")
|
||
(string-append "DESTDIR=" out "/bin"))
|
||
;; Set the correct path to the lrelease binary.
|
||
(("lrelease-qt5") "lrelease"))
|
||
(substitute* "src/include/config.h"
|
||
(("/usr/share/XaoS")
|
||
(string-append out "/share/XaoS")))
|
||
(invoke "qmake"))))
|
||
(add-after 'install 'install-data
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(share (string-append out "/share")))
|
||
(mkdir-p share)
|
||
(for-each
|
||
(lambda (folder)
|
||
(copy-recursively folder
|
||
(string-append share "/XaoS/" folder)))
|
||
'("catalogs" "examples" "tutorial"))
|
||
(install-file "xdg/xaos.png"
|
||
(string-append share "/pixmaps"))
|
||
(install-file "xdg/xaos.desktop"
|
||
(string-append share "/applications")))
|
||
#t)))))
|
||
(synopsis "Real-time fractal zoomer")
|
||
(description "GNU XaoS is a graphical program that generates fractal
|
||
patterns and allows you to zoom in and out of them infinitely in a fluid,
|
||
continuous manner. It also includes tutorials that help to explain how fractals
|
||
are built. It can generate many different fractal types such as the Mandelbrot
|
||
set.")
|
||
(home-page "https://xaos-project.github.io/")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public hypre
|
||
(package
|
||
(name "hypre")
|
||
(version "2.20.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/hypre-space/hypre")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "14iqjwg5sv1qjn7c2cfv0xxmn9rwamjrhh9hgs8fjbywcbvrkjdi"))))
|
||
(build-system gnu-build-system)
|
||
(outputs '("out" ;5.3 MiB of headers and libraries
|
||
"doc")) ;12 MiB of documentation
|
||
(native-inputs
|
||
(list doc++
|
||
doxygen
|
||
python
|
||
python-breathe
|
||
python-sphinx
|
||
(texlive-updmap.cfg (list texlive-adjustbox
|
||
texlive-amsfonts
|
||
texlive-bibtex
|
||
texlive-capt-of
|
||
texlive-caption
|
||
texlive-cm
|
||
texlive-courier
|
||
texlive-etoolbox
|
||
texlive-helvetic
|
||
texlive-jknappen
|
||
texlive-sectsty
|
||
texlive-tex-gyre
|
||
texlive-wasy
|
||
texlive-xcolor
|
||
texlive-xypic
|
||
texlive-generic-listofitems
|
||
texlive-latex-cmap
|
||
texlive-latex-colortbl
|
||
texlive-latex-etoc
|
||
texlive-latex-fancyhdr
|
||
texlive-latex-fancyvrb
|
||
texlive-latex-float
|
||
texlive-latex-fncychap
|
||
texlive-latex-framed
|
||
texlive-latex-geometry
|
||
texlive-latex-hanging
|
||
texlive-hyperref
|
||
texlive-latex-multirow
|
||
texlive-latex-natbib
|
||
texlive-latex-needspace
|
||
texlive-latex-newunicodechar
|
||
texlive-latex-parskip
|
||
texlive-latex-stackengine
|
||
texlive-latex-tabulary
|
||
texlive-latex-titlesec
|
||
texlive-latex-tocloft
|
||
texlive-latex-upquote
|
||
texlive-latex-varwidth
|
||
texlive-ulem
|
||
texlive-wasysym
|
||
texlive-wrapfig))))
|
||
(inputs
|
||
(list openblas lapack))
|
||
(arguments
|
||
`(#:modules ((srfi srfi-1)
|
||
,@%gnu-build-system-modules)
|
||
#:configure-flags '("--enable-shared"
|
||
"--disable-fortran"
|
||
"--without-MPI"
|
||
"--with-openmp"
|
||
"--with-fei"
|
||
"--with-lapack"
|
||
"--with-blas")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'configure 'chdir-src
|
||
(lambda _ (chdir "src")))
|
||
(replace 'configure
|
||
(lambda* (#:key build target configure-flags
|
||
#:allow-other-keys #:rest args)
|
||
(let* ((configure (assoc-ref %standard-phases 'configure)))
|
||
(apply configure
|
||
(append args
|
||
(list #:configure-flags
|
||
(cons (string-append
|
||
"--host=" (or target build))
|
||
configure-flags)))))))
|
||
(add-after 'build 'build-docs
|
||
(lambda _
|
||
(invoke "make" "-C" "docs")))
|
||
(replace 'check
|
||
(lambda _
|
||
(setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
|
||
(setenv "PATH" (string-append "." ":" (getenv "PATH")))
|
||
(invoke "make" "check" "CHECKRUN=")
|
||
(for-each (lambda (filename)
|
||
(let ((size (stat:size (stat filename))))
|
||
(when (positive? size)
|
||
(error (format #f "~a size ~d; error indication~%"
|
||
filename size)))))
|
||
(find-files "test" ".*\\.err$"))))
|
||
(add-after 'install 'install-docs
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
;; Custom install because docs/Makefile doesn't honor ${docdir}.
|
||
(let* ((doc (assoc-ref outputs "doc"))
|
||
(docdir (string-append doc "/share/doc/hypre-" ,version)))
|
||
(with-directory-excursion "docs"
|
||
(for-each (lambda (base)
|
||
(install-file (string-append base ".pdf") docdir)
|
||
(copy-recursively (string-append base "-html")
|
||
(string-append docdir "/" base)))
|
||
'("usr-manual" "ref-manual")))))))))
|
||
(home-page "https://computing.llnl.gov/projects\
|
||
/hypre-scalable-linear-solvers-multigrid-methods")
|
||
(synopsis "Library of solvers and preconditioners for linear equations")
|
||
(description
|
||
"HYPRE is a software library of high performance preconditioners and
|
||
solvers for the solution of large, sparse linear systems of equations. It
|
||
features multigrid solvers for both structured and unstructured grid
|
||
problems.")
|
||
(license license:lgpl2.1)))
|
||
|
||
(define-public hypre-openmpi
|
||
(package
|
||
(inherit hypre)
|
||
(name "hypre-openmpi")
|
||
(inputs (modify-inputs (package-inputs hypre)
|
||
(prepend openmpi)))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments hypre)
|
||
((#:configure-flags flags)
|
||
``("--with-MPI"
|
||
,@(delete "--without-MPI" ,flags)))
|
||
((#:phases phases)
|
||
`(modify-phases ,phases
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup)))))
|
||
(synopsis "Parallel solvers and preconditioners for linear equations")
|
||
(description
|
||
"HYPRE is a software library of high performance preconditioners and
|
||
solvers for the solution of large, sparse linear systems of equations on
|
||
parallel computers. It features parallel multigrid solvers for both
|
||
structured and unstructured grid problems.")))
|
||
|
||
(define-public matio
|
||
(package
|
||
(name "matio")
|
||
(version "1.5.19")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://sourceforge/matio/matio/" version "/"
|
||
"matio-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0vr8c1mz1k6mz0sgh6n3scl5c3a71iqmy5fnydrgq504icj4vym4"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
(list zlib hdf5-1.8))
|
||
(home-page "http://matio.sourceforge.net/")
|
||
(synopsis "Library for reading and writing MAT files")
|
||
(description "Matio is a library for reading and writing MAT files. It
|
||
supports compressed MAT files, as well as newer (version 7.3) MAT files.")
|
||
(license license:bsd-2)))
|
||
|
||
(define-public vc
|
||
(package
|
||
(name "vc")
|
||
(version "1.4.2")
|
||
(source
|
||
(origin (method url-fetch)
|
||
(uri (string-append "https://github.com/VcDevel/Vc/releases/"
|
||
"download/" version "/Vc-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0lirdqzcxys9walz04bllsphydynk7973aimd5k1h1qbwi8z3lsh"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
'(#:configure-flags
|
||
'("-DBUILD_TESTING=ON"
|
||
;; By default, Vc will optimize for the CPU of the build machine.
|
||
;; Setting this to "none" makes it create portable binaries. See
|
||
;; "cmake/OptimizeForArchitecture.cmake".
|
||
"-DTARGET_ARCHITECTURE=none")
|
||
#:phases (modify-phases %standard-phases
|
||
(add-after 'unpack 'copy-testdata
|
||
(lambda* (#:key inputs native-inputs #:allow-other-keys)
|
||
(let ((testdata (assoc-ref (or native-inputs inputs)
|
||
"testdata")))
|
||
(copy-recursively testdata "tests/testdata")
|
||
#t))))))
|
||
(native-inputs
|
||
`(("virtest" ,virtest)
|
||
|
||
;; This is a submodule in the git project, but not part of the
|
||
;; released sources. See the git branch for the commit to take.
|
||
("testdata" ,(let ((commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3"))
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/VcDevel/vc-testdata")
|
||
(commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3")))
|
||
(file-name (git-file-name "vc-testdata"
|
||
(string-take commit 7)))
|
||
(sha256
|
||
(base32
|
||
"1hkhqib03qlcq412ym2dciynfxcdr2ygqhnplz4l1vissr1wnqn2")))))))
|
||
(synopsis "SIMD vector classes for C++")
|
||
(description "Vc provides portable, zero-overhead C++ types for explicitly
|
||
data-parallel programming. It is a library designed to ease explicit
|
||
vectorization of C++ code. Its types enable explicitly stating data-parallel
|
||
operations on multiple values. The parallelism is therefore added via the type
|
||
system. Vc has an intuitive API and provides portability between different
|
||
compilers and compiler versions as well as portability between different vector
|
||
instruction sets. Thus, an application written with Vc can be compiled for:
|
||
@enumerate
|
||
@item AVX and AVX2
|
||
@item SSE2 up to SSE4.2 or SSE4a
|
||
@item Scalar
|
||
@item MIC
|
||
@item NEON (in development)
|
||
@item NVIDIA GPUs / CUDA (in development)
|
||
@end enumerate\n")
|
||
(home-page "https://github.com/VcDevel/Vc")
|
||
;; "No support_???.cpp file exists for this architecture."
|
||
(supported-systems '("x86_64-linux" "i686-linux"))
|
||
(license license:bsd-3)))
|
||
|
||
(define-public reducelcs
|
||
;; This is the last commit which is available upstream, no
|
||
;; release happened since 2010.
|
||
(let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
|
||
(revision "1"))
|
||
(package
|
||
(name "reducelcs")
|
||
(version (string-append "1.0-" revision "." (string-take commit 7)))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/gdv/Reduce-Expand-for-LCS")
|
||
(commit commit)))
|
||
(file-name (string-append name "-" version "-checkout"))
|
||
(sha256
|
||
(base32
|
||
"1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
(list openlibm))
|
||
(arguments
|
||
`(#:tests? #f ; no tests
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(delete 'configure) ; No configure script exists.
|
||
(replace 'install ; No install phase exists.
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(bin (string-append out "/bin")))
|
||
(install-file "Approximation" bin)
|
||
(install-file "CollectResults" bin)
|
||
(install-file "GenerateInstances" bin)
|
||
#t))))))
|
||
(synopsis "Approximate Longest Commons Subsequence computation tool")
|
||
(description
|
||
"@code{reduceLCS} is an implementation of the Reduce-Expand
|
||
algorithm for LCS. It is a fast program to compute the approximate
|
||
Longest Commons Subsequence of a set of strings.")
|
||
(home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
|
||
(license license:gpl3+))))
|
||
|
||
(define-public jacal
|
||
(package
|
||
(name "jacal")
|
||
(version "1c7")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
|
||
version ".zip"))
|
||
(sha256
|
||
(base32 "06a5sx9ikd62bpnd898g3yk818b020b1a27mk7dbfla2zizib4xz"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'build 'pre-build
|
||
;; Don't use upstream's script - it really doesn't fit into
|
||
;; Guix's functional paradigm.
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(substitute* "Makefile"
|
||
(("^install: install-script") "install: "))))
|
||
(add-after 'install 'post-install
|
||
;; Instead, we provide our own simplified script.
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let ((wrapper (string-append (assoc-ref outputs "out")
|
||
"/bin/jacal")))
|
||
(format (open wrapper (logior O_WRONLY O_CREAT))
|
||
(string-append "#!~a\nexec ~a/bin/scm -ip1 "
|
||
"-e '(slib:load \"~a/lib/jacal/math\") "
|
||
"(math)' \"$@\"\n")
|
||
(which "bash")
|
||
(assoc-ref inputs "scm")
|
||
(assoc-ref outputs "out"))
|
||
(chmod wrapper #o555))))
|
||
(replace 'configure
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(invoke "sh" "configure"
|
||
(string-append "--prefix="
|
||
(assoc-ref outputs "out"))))))))
|
||
(inputs (list scm))
|
||
(native-inputs (list unzip texinfo))
|
||
(synopsis "Symbolic mathematics system")
|
||
(description "GNU JACAL is an interactive symbolic mathematics program based on
|
||
Scheme. It manipulate and simplify a range of mathematical expressions such
|
||
as equations, scalars, vectors, and matrices.")
|
||
(home-page "https://www.gnu.org/software/jacal/")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public z3
|
||
(package
|
||
(name "z3")
|
||
(version "4.8.9")
|
||
(home-page "https://github.com/Z3Prover/z3")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference (url home-page)
|
||
(commit (string-append "z3-" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1hnbzq10d23drd7ksm3c1n2611c3kd0q0yxgz8y78zaafwczvwxx"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:imported-modules ((guix build python-build-system)
|
||
,@%gnu-build-system-modules)
|
||
#:modules (((guix build python-build-system) #:select (site-packages))
|
||
(guix build gnu-build-system)
|
||
(guix build utils))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'enable-bytecode-determinism
|
||
(lambda _
|
||
(setenv "PYTHONHASHSEED" "0")
|
||
#t))
|
||
(add-after 'unpack 'fix-compatability
|
||
;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
|
||
(lambda _
|
||
(substitute* "src/util/mpz.cpp"
|
||
(("#include <immintrin.h>") ""))
|
||
#t))
|
||
(add-before 'configure 'bootstrap
|
||
(lambda _
|
||
(invoke "python" "scripts/mk_make.py")))
|
||
;; work around gnu-build-system's setting --enable-fast-install
|
||
;; (z3's `configure' is a wrapper around the above python file,
|
||
;; which fails when passed --enable-fast-install)
|
||
(replace 'configure
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(invoke "./configure"
|
||
"--python"
|
||
(string-append "--prefix=" (assoc-ref outputs "out"))
|
||
(string-append "--pypkgdir=" (site-packages inputs outputs)))))
|
||
(add-after 'configure 'change-directory
|
||
(lambda _
|
||
(chdir "build")
|
||
#t))
|
||
(add-before 'check 'make-test-z3
|
||
(lambda _
|
||
;; Build the test suite executable.
|
||
(invoke "make" "test-z3" "-j"
|
||
(number->string (parallel-job-count)))))
|
||
(replace 'check
|
||
(lambda _
|
||
;; Run all the tests that don't require arguments.
|
||
(invoke "./test-z3" "/a"))))))
|
||
(native-inputs
|
||
`(("which" ,which)
|
||
("python" ,python-wrapper)))
|
||
(synopsis "Theorem prover")
|
||
(description "Z3 is a theorem prover and @dfn{satisfiability modulo
|
||
theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
|
||
(license license:expat)))
|
||
|
||
(define-public ocaml-z3
|
||
(package
|
||
(inherit z3)
|
||
(name "ocaml-z3")
|
||
(arguments
|
||
`(#:imported-modules ((guix build python-build-system)
|
||
,@%gnu-build-system-modules)
|
||
#:modules (((guix build python-build-system) #:select (site-packages))
|
||
(guix build gnu-build-system)
|
||
(guix build utils))
|
||
#:tests? #f; no ml tests
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'configure 'bootstrap
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out")))
|
||
(setenv "OCAMLFIND_LDCONF" "ignore")
|
||
(setenv "OCAMLFIND_DESTDIR" (string-append out "/lib/ocaml/site-lib"))
|
||
(mkdir-p (string-append out "/lib/ocaml/site-lib"))
|
||
(substitute* "scripts/mk_util.py"
|
||
(("LIBZ3 = LIBZ3")
|
||
(string-append "LIBZ3 = LIBZ3 + ' -dllpath " out "/lib'"))
|
||
;; Do not build z3 again, use the library passed as input
|
||
;; instead
|
||
(("z3linkdep,") "\"\",")
|
||
(("z3linkdep)") "\"\")"))
|
||
(invoke "python" "scripts/mk_make.py"))))
|
||
(replace 'configure
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(invoke "./configure"
|
||
"--ml"
|
||
(string-append "--prefix=" (assoc-ref outputs "out")))))
|
||
(add-after 'configure 'change-directory
|
||
(lambda _
|
||
(chdir "build")
|
||
#t))
|
||
(replace 'build
|
||
(lambda _
|
||
(invoke "make" "ml")))
|
||
(replace 'install
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(invoke "ocamlfind" "install" "-destdir"
|
||
(string-append (assoc-ref outputs "out") "/lib/ocaml/site-lib")
|
||
"z3" "api/ml/META" "api/ml/z3enums.mli" "api/ml/z3enums.cmi"
|
||
"api/ml/z3enums.cmx" "api/ml/z3native.mli"
|
||
"api/ml/z3native.cmi" "api/ml/z3native.cmx"
|
||
"../src/api/ml/z3.mli" "api/ml/z3.cmi" "api/ml/z3.cmx"
|
||
"api/ml/libz3ml.a" "api/ml/z3ml.a" "api/ml/z3ml.cma"
|
||
"api/ml/z3ml.cmxa" "api/ml/z3ml.cmxs" "api/ml/dllz3ml.so"))))))
|
||
(native-inputs
|
||
`(("which" ,which)
|
||
("python" ,python-wrapper)
|
||
("ocaml" ,ocaml)
|
||
("ocaml-findlib" ,ocaml-findlib)))
|
||
(propagated-inputs
|
||
(list ocaml-zarith))
|
||
(inputs
|
||
(list z3))))
|
||
|
||
(define-public elpa
|
||
(package
|
||
(name "elpa")
|
||
(version "2018.11.001")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://elpa.mpcdf.mpg.de/html/Releases/"
|
||
version "/elpa-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"05hv3v5i6xmziaizw350ff72y1c3k662r85fm3xfdrkclj5zw9yc"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("fortran" ,gfortran)
|
||
("perl" ,perl))) ;for configure and deps
|
||
(inputs
|
||
`(("blas" ,openblas)))
|
||
(arguments
|
||
`(#:configure-flags
|
||
`("--enable-openmp"
|
||
"--with-mpi=no"
|
||
;; ELPA unfortunately does not support runtime dispatch, so we can
|
||
;; only enable the "generic" kernels. See the "Cross compilation"
|
||
;; section of INSTALL.md.
|
||
"--enable-generic"
|
||
"--disable-sse" "--disable-sse-assembly" ;Require SSE3
|
||
"--disable-avx" "--disable-avx2" "--disable-avx512"
|
||
,(string-append "CFLAGS=-O3 "
|
||
"-funsafe-loop-optimizations -funsafe-math-optimizations "
|
||
"-ftree-vect-loop-version -ftree-vectorize "
|
||
,(let ((system (or (%current-target-system)
|
||
(%current-system))))
|
||
(cond
|
||
((or (string-prefix? "x86_64" system)
|
||
(string-prefix? "i686" system))
|
||
"-msse2")
|
||
(else "")))))
|
||
#:parallel-tests? #f ;tests are multi-threaded, via BLAS
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'configure 'patch-header-generation
|
||
(lambda _
|
||
(substitute* "configure"
|
||
(("^ *make.*top_srcdir=\"\\$srcdir\"" &)
|
||
(string-append & " CPP=\"$CPP\"")))
|
||
#t))
|
||
(add-before 'check 'setup-tests
|
||
(lambda _
|
||
;; Decrease test time and RAM use by computing fewer eigenvalues.
|
||
;; The flags are (MATRIX-SIZE, EIGENVALUES, BLOCK-SIZE), where
|
||
;; the default is (500, 250, 16) for C tests and (5000, 150, 16)
|
||
;; for Fortran. This also causes several tests to pass that
|
||
;; otherwise would otherwise fail with matrix size 5000; possibly
|
||
;; due to floating point tolerances that are too tight.
|
||
(setenv "TEST_FLAGS" "1500 50 16") ;from elpa.spec
|
||
(setenv "OMP_NUM_THREADS" (number->string (parallel-job-count)))
|
||
(substitute* "Makefile"
|
||
;; Test scripts are generated, patch the shebang
|
||
(("#!/bin/bash") (string-append "#!" (which "sh"))))
|
||
#t)))))
|
||
(home-page "https://elpa.mpcdf.mpg.de")
|
||
(synopsis "Eigenvalue solvers for symmetric matrices")
|
||
(description
|
||
"The ELPA library provides efficient and scalable direct eigensolvers for
|
||
symmetric matrices.")
|
||
(license license:lgpl3)))
|
||
|
||
(define-public elpa-openmpi
|
||
(package (inherit elpa)
|
||
(name "elpa-openmpi")
|
||
(inputs
|
||
`(("mpi" ,openmpi)
|
||
("scalapack" ,scalapack)
|
||
,@(package-inputs elpa)))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments elpa)
|
||
((#:configure-flags cf '())
|
||
`(cons "--with-mpi=yes" (delete "--with-mpi=no" ,cf)))
|
||
((#:phases phases '%standard-phases)
|
||
`(modify-phases ,phases
|
||
(add-before 'check 'mpi-setup
|
||
(lambda _
|
||
;; Tests use 2 mpi tasks by default, use our remaining build
|
||
;; cores as OpenMP threads.
|
||
(setenv "OMP_NUM_THREADS" (number->string
|
||
(max (quotient (parallel-job-count) 2)
|
||
1)))
|
||
(,%openmpi-setup)))))))
|
||
(synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)")))
|
||
|
||
(define-public elemental
|
||
(package
|
||
(name "elemental")
|
||
(version "0.87.7")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/elemental/Elemental")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
|
||
(build-system cmake-build-system)
|
||
(home-page "https://github.com/elemental/Elemental")
|
||
(native-inputs
|
||
(list gfortran))
|
||
(inputs
|
||
`(("blas" ,openblas)
|
||
("gfortran:lib" ,gfortran "lib")
|
||
("gmp" ,gmp)
|
||
("lapack" ,lapack)
|
||
("metis" ,metis)
|
||
("mpc" ,mpc)
|
||
("mpfr" ,mpfr)
|
||
("mpi" ,openmpi)
|
||
("qd" ,qd)))
|
||
(arguments
|
||
`(#:build-type "Release" ;default RelWithDebInfo not supported
|
||
#:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
|
||
"-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
|
||
"-DEL_CACHE_WARNINGS:BOOL=YES"
|
||
"-DEL_TESTS:BOOL=YES"
|
||
"-DCMAKE_INSTALL_LIBDIR=lib"
|
||
"-DGFORTRAN_LIB=gfortran")
|
||
#:phases (modify-phases %standard-phases
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup)
|
||
(add-before 'check 'setup-tests
|
||
(lambda _
|
||
;; Parallelism is done at the MPI layer.
|
||
(setenv "OMP_NUM_THREADS" "1")
|
||
#t))
|
||
(add-after 'install 'remove-tests
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
;; Tests are installed, with no easy configuration
|
||
;; switch to prevent this, so delete them.
|
||
(delete-file-recursively
|
||
(string-append (assoc-ref outputs "out") "/bin"))
|
||
#t)))))
|
||
(synopsis "Dense and sparse-direct linear algebra and optimization")
|
||
(description "Elemental is a modern C++ library for distributed-memory
|
||
dense and sparse-direct linear algebra, conic optimization, and lattice
|
||
reduction.")
|
||
(license license:bsd-2)))
|
||
|
||
(define-public mcrl2
|
||
(package
|
||
(name "mcrl2")
|
||
(version "202106.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://www.mcrl2.org/download/release/mcrl2-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1xgx3cd57vc7gbjic24j1q2za6j3ybz6nk4afvvpbwsf33xnlf4v"))))
|
||
(inputs
|
||
(list boost glu mesa qtbase-5))
|
||
(build-system cmake-build-system)
|
||
(synopsis "Toolset for the mCRL2 formal specification language")
|
||
(description
|
||
"@dfn{mCRL2} (micro Common Representation Language 2) is a formal
|
||
specification language for describing concurrent discrete event systems. Its
|
||
toolset supports analysis and automatic verification, linearisation, simulation,
|
||
state-space exploration and generation, and tools to optimise and analyse
|
||
specifications. Also, state spaces can be manipulated, visualised and
|
||
analysed.")
|
||
(home-page "https://mcrl2.org")
|
||
(license license:boost1.0)))
|
||
|
||
(define-public mcrl2-minimal
|
||
(package
|
||
(inherit mcrl2)
|
||
(name "mcrl2-minimal")
|
||
(inputs
|
||
(list boost))
|
||
(arguments
|
||
'(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
|
||
|
||
(define-public tcalc
|
||
(package
|
||
(name "tcalc")
|
||
(version "2.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
|
||
(build-system gnu-build-system)
|
||
(synopsis "The terminal calculator")
|
||
(description
|
||
"The terminal calculator is a small program to help users of the GNU/Linux
|
||
terminal do calculations simply and quickly. The formula to be calculated can
|
||
be fed to @command{tcalc} through the command line.")
|
||
(home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public tiny-bignum
|
||
(let ((commit "1d7a1f9b8e77316187a6b3eae8e68d60a6f9a4d4"))
|
||
(package
|
||
(name "tiny-bignum")
|
||
(version (git-version "0" "0" commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/kokke/tiny-bignum-c")
|
||
(commit commit)))
|
||
(file-name (git-file-name "tiny-bignum" commit))
|
||
(sha256
|
||
(base32 "0vj71qlhlaa7d92bfar1kwqv6582dqrby8x3kdw0yzh82k2023g6"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(delete 'configure)
|
||
(add-after 'unpack 'patch-tests
|
||
(lambda _
|
||
(substitute* "scripts/test_rand.py"
|
||
(("\t") " ")
|
||
(("\" % (\\w+)" _ symbol) (string-append "\" % int(" symbol ")")))
|
||
#t))
|
||
(replace 'check
|
||
(lambda* (#:key tests? #:allow-other-keys)
|
||
(when tests?
|
||
(invoke "make" "test"))
|
||
#t))
|
||
(replace 'install
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let ((share (string-append (assoc-ref outputs "out") "/share"))
|
||
(doc (string-append (assoc-ref outputs "out") "/doc")))
|
||
(mkdir-p share)
|
||
(install-file "bn.c" share)
|
||
(install-file "bn.h" share)
|
||
(mkdir-p doc)
|
||
(install-file "LICENSE" doc)
|
||
(install-file "README.md" doc))
|
||
#t)))))
|
||
(native-inputs
|
||
`(("python" ,python-wrapper)))
|
||
(home-page "https://github.com/kokke/tiny-bignum-c")
|
||
(synopsis "Small portable multiple-precision unsigned integer arithmetic in C")
|
||
(description
|
||
"This library provides portable Arbitrary-precision unsigned integer
|
||
arithmetic in C, for calculating with large numbers. Basic arithmetic (+, -,
|
||
*, /, %) and bitwise operations (&, |, ^. <<, >>) plus increments, decrements
|
||
and comparisons are supported.")
|
||
(license license:unlicense))))
|
||
|
||
(define-public sundials
|
||
(package
|
||
(name "sundials")
|
||
(version "6.2.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://github.com/LLNL/sundials/releases/download/v"
|
||
version "/sundials-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"07gk9060xk3bzfqf8v4fqlp0rcxswiwlsy887zv87i1gfy9map8r"))))
|
||
(build-system cmake-build-system)
|
||
(native-inputs
|
||
(list python-2)) ; For tests; syntax incompatible with Python 3.
|
||
(inputs
|
||
(list openblas suitesparse))
|
||
(arguments
|
||
'(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon"
|
||
|
||
"-DSUNDIALS_INDEX_SIZE=32"
|
||
;; Incompatible with 32-bit indices.
|
||
;;"-DBUILD_FORTRAN_MODULE_INTERFACE:BOOL=ON"
|
||
|
||
"-DEXAMPLES_ENABLE_C:BOOL=ON"
|
||
"-DEXAMPLES_ENABLE_CXX:BOOL=ON"
|
||
;; Requires -DBUILD_FORTRAN_MODULE_INTERFACE:BOOL=ON.
|
||
;;"-DEXAMPLES_ENABLE_F2003:BOOL=ON"
|
||
"-DEXAMPLES_INSTALL:BOOL=OFF"
|
||
|
||
"-DENABLE_KLU:BOOL=ON"
|
||
,(string-append "-DKLU_INCLUDE_DIR="
|
||
(assoc-ref %build-inputs "suitesparse")
|
||
"/include")
|
||
,(string-append "-DKLU_LIBRARY_DIR="
|
||
(assoc-ref %build-inputs "suitesparse")
|
||
"/lib"))))
|
||
(home-page "https://computation.llnl.gov/projects/sundials")
|
||
(synopsis "Suite of nonlinear and differential/algebraic equation solvers")
|
||
(description "SUNDIALS is a family of software packages implemented with
|
||
the goal of providing robust time integrators and nonlinear solvers that can
|
||
easily be incorporated into existing simulation codes.")
|
||
(properties
|
||
'((release-monitoring-url
|
||
. "https://computing.llnl.gov/projects/sundials/sundials-software")))
|
||
(license license:bsd-3)))
|
||
|
||
(define-public sundials-openmpi
|
||
(package/inherit sundials
|
||
(name "sundials-openmpi")
|
||
(propagated-inputs
|
||
(list openmpi
|
||
;; Support for the below requires MPI.
|
||
hypre-openmpi
|
||
petsc-openmpi))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments sundials)
|
||
((#:configure-flags flags '())
|
||
`(cons* "-DENABLE_MPI:BOOL=ON"
|
||
"-DENABLE_HYPRE:BOOL=ON"
|
||
(string-append "-DHYPRE_INCLUDE_DIR="
|
||
(assoc-ref %build-inputs "hypre-openmpi")
|
||
"/include")
|
||
(string-append "-DHYPRE_LIBRARY_DIR="
|
||
(assoc-ref %build-inputs "hypre-openmpi")
|
||
"/lib")
|
||
"-DENABLE_PETSC:BOOL=ON"
|
||
(string-append "-DPETSC_DIR="
|
||
(assoc-ref %build-inputs "petsc-openmpi"))
|
||
,flags))
|
||
((#:phases phases '%standard-phases)
|
||
`(modify-phases ,phases
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup)))))
|
||
(synopsis "SUNDIALS with MPI support")))
|
||
|
||
(define-public sundials-5
|
||
(package
|
||
(inherit sundials)
|
||
(name "sundials")
|
||
(version "5.8.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://github.com/LLNL/sundials/releases/download/v"
|
||
version "/sundials-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"04x2x0jchf9kbcw2a1c6f4h4as8sr6k2snfz8z9k897pa4rl1vfl"))))))
|
||
|
||
(define-public sundials-openmpi-5
|
||
(package/inherit sundials-5
|
||
(name "sundials-openmpi")
|
||
(propagated-inputs
|
||
(package-propagated-inputs sundials-openmpi))
|
||
(arguments
|
||
(package-arguments sundials-openmpi))
|
||
(synopsis (package-synopsis sundials-openmpi))))
|
||
|
||
(define-public sundials-julia
|
||
(package
|
||
(inherit sundials)
|
||
(name "sundials-julia")
|
||
(version "5.2.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/LLNL/sundials")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0nx4sqhmi126m14myzm7syv2053harav9snl0a247wnkcgs5rxrv"))))
|
||
(inputs
|
||
(modify-inputs (package-inputs sundials)
|
||
(prepend gfortran lapack)))
|
||
(arguments
|
||
'(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon"
|
||
"-DSUNDIALS_INDEX_SIZE=32"
|
||
"-DKLU_ENABLE:BOOL=ON"
|
||
,(string-append "-DKLU_INCLUDE_DIR="
|
||
(assoc-ref %build-inputs "suitesparse")
|
||
"/include")
|
||
,(string-append "-DKLU_LIBRARY_DIR="
|
||
(assoc-ref %build-inputs "suitesparse")
|
||
"/lib")
|
||
"-DLAPACK_ENABLE:BOOL=ON")))
|
||
(synopsis "SUNDIALS with LAPACK support as required by julia-sundials-jll")))
|
||
|
||
(define-public combinatorial-blas
|
||
(package
|
||
(name "combinatorial-blas")
|
||
(version "1.6.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/"
|
||
"CombBLAS_beta_"
|
||
(match (string-split version #\.)
|
||
((major minor patch)
|
||
(string-append major minor "_" patch))) ;e.g. "16_2"
|
||
".tgz"))
|
||
(sha256
|
||
(base32
|
||
"1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a"))
|
||
(patches (search-patches "combinatorial-blas-awpm.patch"
|
||
"combinatorial-blas-io-fix.patch"))))
|
||
(build-system cmake-build-system)
|
||
(inputs
|
||
`(("mpi" ,openmpi)
|
||
("test-data" ,(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://people.eecs.berkeley.edu/~aydin/"
|
||
"CombBLAS_FILES/testdata_combblas1.6.1.tgz"))
|
||
(sha256
|
||
(base32
|
||
"01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87"))))))
|
||
(arguments
|
||
`(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
|
||
"-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL")
|
||
#:parallel-tests? #f ;tests use 'mpiexec -n4'
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup)
|
||
(add-before 'check 'test-setup
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(setenv "OMP_NUM_THREADS" "2")
|
||
(invoke "tar" "xf" (assoc-ref inputs "test-data")))))))
|
||
(home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/")
|
||
(synopsis "Linear algebra primitives for graph analytics")
|
||
(description "The Combinatorial BLAS (CombBLAS) is an extensible
|
||
distributed-memory parallel graph library offering a small but powerful set of
|
||
linear algebra primitives specifically targeting graph analytics.")
|
||
(license (list
|
||
license:gpl2+ ;include/psort/(funnel|sort)*.h
|
||
license:x11 ;usort and psort
|
||
license:bsd-3)))) ;CombBLAS and MersenneTwister.h
|
||
|
||
(define-public dune-common
|
||
(package
|
||
(name "dune-common")
|
||
(version "2.7.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://dune-project.org/download/"
|
||
version "/dune-common-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0sidwdkyrrqjkqhpvrlc991pzi5xzlvxk91s2n7qk3widwy7fch2"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-tests
|
||
(lambda* (#:key make-flags parallel-build? #:allow-other-keys)
|
||
(apply invoke "make" "build_tests"
|
||
`(,@(if parallel-build?
|
||
`("-j" ,(number->string (parallel-job-count)))
|
||
'())
|
||
,@make-flags)))))))
|
||
(inputs
|
||
(list gmp metis openblas python superlu))
|
||
(native-inputs
|
||
(list gfortran pkg-config))
|
||
(home-page "https://dune-project.org/")
|
||
(synopsis "Distributed and Unified Numerics Environment")
|
||
(description "DUNE, the Distributed and Unified Numerics Environment is a
|
||
modular toolbox for solving @dfn{partial differential equations} (PDEs) with
|
||
grid-based methods. It supports the easy implementation of methods like
|
||
@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
|
||
Differences} (FD).")
|
||
;; GPL version 2 with "runtime exception" to make it behave like LGPLv2.
|
||
(license license:gpl2)))
|
||
|
||
(define-public dune-geometry
|
||
(package
|
||
(name "dune-geometry")
|
||
(version "2.7.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://dune-project.org/download/"
|
||
version "/dune-geometry-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"068mh3fd110xl27rwxqlqy4d9cpqw2vqm2pzfrripiaqscb3byfy"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-tests
|
||
(lambda* (#:key make-flags parallel-build? #:allow-other-keys)
|
||
(apply invoke "make" "build_tests"
|
||
`(,@(if parallel-build?
|
||
`("-j" ,(number->string (parallel-job-count)))
|
||
'())
|
||
,@make-flags)))))))
|
||
(inputs
|
||
(list dune-common
|
||
;; Optional
|
||
openblas gmp python))
|
||
(native-inputs
|
||
(list gfortran pkg-config))
|
||
(home-page "https://dune-project.org/")
|
||
(synopsis "Distributed and Unified Numerics Environment")
|
||
(description "DUNE, the Distributed and Unified Numerics Environment is a
|
||
modular toolbox for solving @dfn{partial differential equations} (PDEs) with
|
||
grid-based methods. It supports the easy implementation of methods like
|
||
@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
|
||
Differences} (FD).
|
||
|
||
This package contains the basic DUNE geometry classes.")
|
||
;; GPL version 2 with "runtime exception"
|
||
(license license:gpl2)))
|
||
|
||
(define-public dune-uggrid
|
||
(package
|
||
(name "dune-uggrid")
|
||
(version "2.7.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://gitlab.dune-project.org/staging/dune-uggrid.git")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"11qz52g9d5k96fqik2lyi80xryw174rnny074pj70ardl6zzz83p"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-tests
|
||
(lambda* (#:key make-flags parallel-build? #:allow-other-keys)
|
||
(apply invoke "make" "build_tests"
|
||
`(,@(if parallel-build?
|
||
`("-j" ,(number->string (parallel-job-count)))
|
||
'())
|
||
,@make-flags)))))))
|
||
(inputs
|
||
(list dune-common))
|
||
(native-inputs
|
||
(list gfortran pkg-config))
|
||
(home-page "https://dune-project.org/")
|
||
(synopsis "Distributed and Unified Numerics Environment")
|
||
(description "DUNE, the Distributed and Unified Numerics Environment is a
|
||
modular toolbox for solving @dfn{partial differential equations} (PDEs) with
|
||
grid-based methods. It supports the easy implementation of methods like
|
||
@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
|
||
Differences} (FD).
|
||
|
||
This package contains the DUNE UG grid classes.")
|
||
(license license:lgpl2.1)))
|
||
|
||
(define-public dune-grid
|
||
(package
|
||
(name "dune-grid")
|
||
(version "2.7.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://dune-project.org/download/"
|
||
version "/dune-grid-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"15iws03hkbmr4a4rqqb0rriz1m8szl96wdr7gw0jmrcnlzbdbbx5"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-tests
|
||
(lambda* (#:key make-flags parallel-build? #:allow-other-keys)
|
||
(apply invoke "make" "build_tests"
|
||
`(,@(if parallel-build?
|
||
`("-j" ,(number->string (parallel-job-count)))
|
||
'())
|
||
,@make-flags)))))))
|
||
(inputs
|
||
(list dune-common
|
||
dune-geometry
|
||
gmp
|
||
metis
|
||
openblas
|
||
python))
|
||
(propagated-inputs
|
||
(list dune-uggrid))
|
||
(native-inputs
|
||
(list gfortran pkg-config))
|
||
(home-page "https://dune-project.org/")
|
||
(synopsis "Distributed and Unified Numerics Environment")
|
||
(description "DUNE, the Distributed and Unified Numerics Environment is a
|
||
modular toolbox for solving @dfn{partial differential equations} (PDEs) with
|
||
grid-based methods. It supports the easy implementation of methods like
|
||
@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
|
||
Differences} (FD).
|
||
|
||
This package contains the basic DUNE grid classes.")
|
||
;; GPL version 2 with "runtime exception"
|
||
(license license:gpl2)))
|
||
|
||
(define-public dune-istl
|
||
(package
|
||
(name "dune-istl")
|
||
(version "2.7.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://dune-project.org/download/"
|
||
version "/dune-istl-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1cy69s1266hvnh8blznlvvkrf8i2g640rc3mf7kp872wgvdz4nb9"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
;; XXX: istl/test/matrixtest.cc includes <fenv.h> and fails to find
|
||
;; the stdlib types when the gfortran header is used. Remove gfortran
|
||
;; from CPLUS_INCLUDE_PATH as a workaround.
|
||
(add-after 'set-paths 'hide-gfortran
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(let ((gfortran (assoc-ref inputs "gfortran")))
|
||
(setenv "CPLUS_INCLUDE_PATH"
|
||
(string-join
|
||
(delete (string-append gfortran "/include/c++")
|
||
(string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
|
||
":"))
|
||
#t)))
|
||
(add-after 'build 'build-tests
|
||
(lambda* (#:key make-flags parallel-build? #:allow-other-keys)
|
||
(apply invoke "make" "build_tests"
|
||
`(,@(if parallel-build?
|
||
`("-j" ,(number->string (parallel-job-count)))
|
||
'())
|
||
,@make-flags)))))))
|
||
(inputs
|
||
(list dune-common
|
||
;; Optional
|
||
metis
|
||
suitesparse
|
||
superlu
|
||
openblas
|
||
gmp
|
||
python))
|
||
(native-inputs
|
||
(list gfortran pkg-config))
|
||
(home-page "https://dune-project.org/")
|
||
(synopsis "Distributed and Unified Numerics Environment")
|
||
(description "DUNE, the Distributed and Unified Numerics Environment is a
|
||
modular toolbox for solving @dfn{partial differential equations} (PDEs) with
|
||
grid-based methods.
|
||
|
||
This is the iterative solver template library which provides generic sparse
|
||
matrix/vector classes and a variety of solvers based on these classes. A
|
||
special feature is the use of templates to exploit the recursive block
|
||
structure of finite element matrices at compile time. Available solvers
|
||
include Krylov methods, (block-) incomplete decompositions and
|
||
aggregation-based algebraic multigrid.")
|
||
;; GPL version 2 with "runtime exception"
|
||
(license license:gpl2)))
|
||
|
||
(define-public dune-localfunctions
|
||
(package
|
||
(name "dune-localfunctions")
|
||
(version "2.7.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://dune-project.org/download/"
|
||
version "/dune-localfunctions-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"031i42anrhi0ngpvp42rdjbkic7v3008fwild9xg7flffwvnpshg"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
;; XXX: localfunctions/test/lagrangeshapefunctiontest.cc includes <fenv.h>
|
||
;; and fails to find the stdlib types when the gfortran header is used.
|
||
;; Hide gfortran from CPLUS_INCLUDE_PATH to ensure we get the GCC header.
|
||
(add-after 'set-paths 'hide-gfortran
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(let ((gfortran (assoc-ref inputs "gfortran")))
|
||
(setenv "CPLUS_INCLUDE_PATH"
|
||
(string-join
|
||
(delete (string-append gfortran "/include/c++")
|
||
(string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
|
||
":"))
|
||
#t)))
|
||
(add-after 'build 'build-tests
|
||
(lambda* (#:key make-flags parallel-build? #:allow-other-keys)
|
||
(apply invoke "make" "build_tests"
|
||
`(,@(if parallel-build?
|
||
`("-j" ,(number->string (parallel-job-count)))
|
||
'())
|
||
,@make-flags)))))))
|
||
(inputs
|
||
(list dune-common
|
||
dune-geometry
|
||
;; Optional
|
||
metis
|
||
superlu
|
||
gmp))
|
||
(native-inputs
|
||
(list gfortran pkg-config))
|
||
(home-page "https://dune-project.org/")
|
||
(synopsis "Distributed and Unified Numerics Environment") ; TODO
|
||
(description "This DUNE module provides interface and implementation for
|
||
shape functions defined on the DUNE reference elements. In addition to the
|
||
shape function, interpolation operators and special keys are provided which
|
||
can be used to assemble global function spaces on finite-element grids.
|
||
|
||
This package provides an interface and implementation for shape functions
|
||
defined on the DUNE reference elements. In addition to the shape function,
|
||
interpolation operators and special keys are provided which can be used to
|
||
assemble global function spaces on finite-element grids.")
|
||
;; GPL version 2 with "runtime exception"
|
||
(license license:gpl2)))
|
||
|
||
(define-public dune-alugrid
|
||
;; This was the last commit on the releases/2.7 branch as of 2021-12-17,
|
||
;; unfortunately there was no tag for any 2.7 release.
|
||
(let ((commit "51bde29a2dfa7cfac4fb73d40ffd42b9c1eb1d3d"))
|
||
(package
|
||
(name "dune-alugrid")
|
||
(version (git-version "2.7.1" "0" commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://gitlab.dune-project.org/extensions/dune-alugrid.git")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0z16wg6llzxs7vjg2yilg31vwnkz8k050j6bspg3blbym0razy15"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'patch-include
|
||
(lambda _
|
||
(substitute* "dune/alugrid/test/test-alugrid.cc"
|
||
(("doc/grids/gridfactory/testgrids")
|
||
"doc/dune-grid/grids/gridfactory/testgrids"))
|
||
#t))
|
||
(add-after 'build 'build-tests
|
||
(lambda* (#:key make-flags parallel-build? #:allow-other-keys)
|
||
(setenv "CPLUS_INCLUDE_PATH"
|
||
(string-append (assoc-ref inputs "dune-grid") "/share"))
|
||
(apply invoke "make" "build_tests"
|
||
`(,@(if parallel-build?
|
||
`("-j" ,(number->string (parallel-job-count)))
|
||
'())
|
||
,@make-flags)))))))
|
||
(inputs
|
||
(list dune-common
|
||
dune-geometry
|
||
dune-grid
|
||
;; Optional
|
||
metis
|
||
openblas
|
||
python
|
||
superlu
|
||
gmp
|
||
zlib))
|
||
(native-inputs
|
||
(list gfortran pkg-config))
|
||
(home-page "https://dune-project.org/")
|
||
(synopsis "Distributed and Unified Numerics Environment")
|
||
(description "ALUGrid is an adaptive, loadbalancing, unstructured
|
||
implementation of the DUNE grid interface supporting either simplices or
|
||
cubes.")
|
||
(license license:gpl2+))))
|
||
|
||
(define-public dune-subgrid
|
||
;; This was the last commit on the releases/2.7 branch as of 2021-12-17.
|
||
;; Unfortunately the dune-subgrid repository contains no release tags.
|
||
(let ((commit "45d1ee9f3f711e209695deee97912f4954f7f280"))
|
||
(package
|
||
(name "dune-subgrid")
|
||
(version (git-version "2.7.1" "0" commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0xjf7865wil7kzym608kv3nc3ff3m3nlqich4k9wjyvy3lz6panh"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-tests
|
||
(lambda* (#:key make-flags parallel-build? #:allow-other-keys)
|
||
(apply invoke "make" "build_tests"
|
||
`(,@(if parallel-build?
|
||
`("-j" ,(number->string (parallel-job-count)))
|
||
'())
|
||
,@make-flags)))))))
|
||
(inputs
|
||
(list dune-common
|
||
dune-geometry
|
||
dune-grid
|
||
;; Optional
|
||
metis
|
||
openblas
|
||
gmp))
|
||
(native-inputs
|
||
(list gfortran pkg-config))
|
||
(home-page "http://numerik.mi.fu-berlin.de/dune-subgrid/index.php")
|
||
(synopsis "Distributed and Unified Numerics Environment")
|
||
(description "The dune-subgrid module marks elements of
|
||
another hierarchical dune grid. The set of marked elements can then be
|
||
accessed as a hierarchical dune grid in its own right. Dune-Subgrid
|
||
provides the full grid interface including adaptive mesh refinement.")
|
||
(license license:gpl2+))))
|
||
|
||
(define-public dune-typetree
|
||
(package
|
||
(name "dune-typetree")
|
||
(version "2.7.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://gitlab.dune-project.org/staging/dune-typetree.git")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1kx9k8i7pdw6l6ny6nq85v5p1nd6yxldzaj8k3nizaz3q1j407pv"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-tests
|
||
(lambda* (#:key make-flags parallel-build? #:allow-other-keys)
|
||
(apply invoke "make" "build_tests"
|
||
`(,@(if parallel-build?
|
||
`("-j" ,(number->string (parallel-job-count)))
|
||
'())
|
||
,@make-flags)))))))
|
||
(inputs
|
||
(list dune-common
|
||
;; Optional
|
||
openblas
|
||
python
|
||
metis
|
||
superlu
|
||
gmp))
|
||
(native-inputs
|
||
(list gfortran pkg-config))
|
||
(home-page "https://dune-project.org/")
|
||
(synopsis "Distributed and Unified Numerics Environment")
|
||
(description "TypeTree is a template library for constructing and
|
||
operating on statically typed trees of objects.")
|
||
;; Either GPL version 2 with "runtime exception" or LGPLv3+.
|
||
(license (list license:lgpl3+ license:gpl2))))
|
||
|
||
(define-public dune-functions
|
||
(package
|
||
(name "dune-functions")
|
||
(version "2.7.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://gitlab.dune-project.org/staging/dune-functions.git")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"04dhr4asnl38bf1gp8hrk31maav33m7q71lhl2n5yk1q1x6i77nw"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'disable-failing-tests
|
||
(lambda _
|
||
(setenv "ARGS"
|
||
;; unable to load GMSH file in this test
|
||
"--exclude-regex gridviewfunctionspacebasistest")
|
||
#t))
|
||
(add-after 'build 'build-tests
|
||
(lambda* (#:key make-flags parallel-build? #:allow-other-keys)
|
||
(apply invoke "make" "build_tests"
|
||
`(,@(if parallel-build?
|
||
`("-j" ,(number->string (parallel-job-count)))
|
||
'())
|
||
,@make-flags)))))))
|
||
(inputs
|
||
(list dune-common
|
||
dune-istl
|
||
dune-localfunctions
|
||
dune-grid
|
||
dune-geometry
|
||
dune-typetree
|
||
openblas
|
||
metis
|
||
python
|
||
superlu
|
||
gmp))
|
||
(native-inputs
|
||
(list gfortran pkg-config))
|
||
(home-page "https://dune-project.org/")
|
||
(synopsis "Distributed and Unified Numerics Environment")
|
||
(description "The dune-functions module provides an abstraction layer for
|
||
global finite element functions. Its two main concepts are functions
|
||
implemented as callable objects, and bases of finite element spaces.")
|
||
;; Either GPL version 2 with "runtime exception" or LGPLv3+.
|
||
(license (list license:lgpl3+ license:gpl2))))
|
||
|
||
(define-public dune-pdelab
|
||
;; This was the last commit on the releases/2.7 branch as of 2021-12-17,
|
||
;; unfortunately there was no tag for any 2.7 release.
|
||
(let ((commit "09aef74d95661d18a7789d2f517ae77797eec738"))
|
||
(package
|
||
(name "dune-pdelab")
|
||
(version (git-version "2.7.1" "0" commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
|
||
(commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0nv69ayr4gln9m1s94z9zkrxqi8nzar3z6awnvgqz595nmjf82ac"))))
|
||
(build-system cmake-build-system)
|
||
(arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
|
||
(inputs
|
||
(list dune-common
|
||
dune-istl
|
||
dune-localfunctions
|
||
dune-geometry
|
||
dune-grid
|
||
dune-typetree
|
||
dune-functions
|
||
;; Optional
|
||
openblas
|
||
eigen
|
||
metis
|
||
python
|
||
superlu
|
||
gmp))
|
||
(native-inputs
|
||
(list gfortran pkg-config))
|
||
(home-page "https://dune-project.org/")
|
||
(synopsis "Differential equations solver toolbox")
|
||
(description "PDELab is a partial differential equations solver toolbox
|
||
built on top of DUNE, the Distributed and Unified Numerics Environment.")
|
||
;; Either GPL version 2 with "runtime exception" or LGPLv3+.
|
||
(license (list license:lgpl3+ license:gpl2)))))
|
||
|
||
(define add-openmpi-to-dune-package
|
||
(let ((dune-package?
|
||
(lambda (p) (string-prefix? "dune-" (package-name p)))))
|
||
(package-mapping
|
||
(lambda (p)
|
||
(if (dune-package? p)
|
||
(package (inherit p)
|
||
(name (string-append (package-name p) "-openmpi"))
|
||
(inputs (modify-inputs (package-inputs p)
|
||
(append openmpi)))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments p)
|
||
((#:phases phases '%standard-phases)
|
||
`(modify-phases ,phases
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup)))))
|
||
(synopsis (string-append (package-synopsis p) " (with MPI support)")))
|
||
p))
|
||
(negate dune-package?))))
|
||
|
||
(define-public dune-common-openmpi
|
||
(add-openmpi-to-dune-package dune-common))
|
||
|
||
(define-public dune-geometry-openmpi
|
||
(add-openmpi-to-dune-package dune-geometry))
|
||
|
||
(define-public dune-istl-openmpi
|
||
(add-openmpi-to-dune-package dune-istl))
|
||
|
||
(define-public dune-typetree-openmpi
|
||
(add-openmpi-to-dune-package dune-typetree))
|
||
|
||
(define-public dune-uggrid-openmpi
|
||
(add-openmpi-to-dune-package dune-uggrid))
|
||
|
||
(define-public dune-grid-openmpi
|
||
(add-openmpi-to-dune-package dune-grid))
|
||
|
||
(define-public dune-alugrid-openmpi
|
||
(add-openmpi-to-dune-package dune-alugrid))
|
||
|
||
(define-public dune-subgrid-openmpi
|
||
(add-openmpi-to-dune-package dune-subgrid))
|
||
|
||
(define-public dune-localfunctions-openmpi
|
||
(add-openmpi-to-dune-package dune-localfunctions))
|
||
|
||
(define-public dune-functions-openmpi
|
||
(add-openmpi-to-dune-package dune-functions))
|
||
|
||
(define-public dune-pdelab-openmpi
|
||
(add-openmpi-to-dune-package dune-pdelab))
|
||
|
||
(define-public mlucas
|
||
(package
|
||
(name "mlucas")
|
||
(version "18")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz"))
|
||
(sha256
|
||
(base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
(list python-2))
|
||
(arguments
|
||
`(#:tests? #f ; no tests
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'configure
|
||
(lambda _
|
||
(chdir "src")
|
||
(call-with-output-file "Makefile"
|
||
(lambda (port)
|
||
(format port "CC = gcc
|
||
CFLAGS = -O3 ~a -DUSE_THREADS
|
||
LDLIBS = -lm -lpthread -lrt
|
||
Mlucas: $(addsuffix .o,$(basename $(wildcard *.c)))
|
||
"
|
||
,(let ((system (or (%current-target-system)
|
||
(%current-system))))
|
||
(cond
|
||
((string-prefix? "x86_64" system) "-DUSE_SSE2")
|
||
(else ""))))))
|
||
#t))
|
||
(replace 'install
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
|
||
(install-file "Mlucas" bin)
|
||
(install-file "primenet.py" bin))
|
||
#t)))))
|
||
(home-page "https://www.mersenne.org")
|
||
(synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client")
|
||
(description "Mlucas performs Lucas-Lehmer primality testing of Mersenne
|
||
numbers in search of a world-record prime. You may use it to test any
|
||
suitable number as you wish, but it is preferable that you do so in a
|
||
coordinated fashion, as part of the Great Internet Mersenne Prime
|
||
Search (GIMPS). Mlucas also includes a simple Python script for assignment
|
||
management via the GIMPS project's Primenet server.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public nauty
|
||
(package
|
||
(name "nauty")
|
||
(version "2.7r3")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://pallini.di.uniroma1.it/"
|
||
"nauty" (string-join (string-split version #\.) "") ".tar.gz"))
|
||
(sha256
|
||
(base32 "1hl81gpf3xjf809w04jczvilq1ixy9ch1qrax8a7lgx52svna1jg"))))
|
||
(build-system gnu-build-system)
|
||
(outputs '("out" "lib"))
|
||
(arguments
|
||
`(#:test-target "checks"
|
||
#:configure-flags '("--enable-generic") ;prevent -march-native
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
;; Default make target does not build all available
|
||
;; executables. Create them now.
|
||
(add-after 'build 'build-extra-programs
|
||
(lambda _
|
||
(for-each (lambda (target) (invoke "make" target))
|
||
'("blisstog" "bliss2dre" "checks6" "sumlines"))
|
||
#t))
|
||
;; Upstream does not provide any install target.
|
||
(replace 'install
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(lib-output (assoc-ref outputs "lib"))
|
||
(bin (string-append out "/bin"))
|
||
(doc (string-append out "/share/doc/nauty/"))
|
||
(include (string-append lib-output "/include/nauty"))
|
||
(lib (string-append lib-output "/lib/nauty")))
|
||
(for-each (lambda (f) (install-file f bin))
|
||
'("addedgeg" "amtog" "assembleg" "biplabg" "blisstog"
|
||
"bliss2dre" "catg" "checks6" "complg" "converseg"
|
||
"copyg" "countg" "cubhamg" "deledgeg" "delptg"
|
||
"directg" "dreadnaut" "dretodot" "dretog" "genbg"
|
||
"genbgL" "geng" "genquarticg" "genrang" "genspecialg"
|
||
"gentourng" "gentreeg" "hamheuristic" "labelg"
|
||
"linegraphg" "listg" "multig" "newedgeg" "pickg"
|
||
"planarg" "ranlabg" "shortg" "showg" "subdivideg"
|
||
"sumlines" "twohamg" "underlyingg" "vcolg"
|
||
"watercluster2" "NRswitchg"))
|
||
(for-each (lambda (f) (install-file f include))
|
||
(find-files "." "\\.h$"))
|
||
(for-each (lambda (f) (install-file f lib))
|
||
(find-files "." "\\.a$"))
|
||
(for-each (lambda (f) (install-file f doc))
|
||
(append '("formats.txt" "README" "schreier.txt")
|
||
(find-files "." "\\.pdf$")))))))))
|
||
(inputs
|
||
(list gmp)) ;for sumlines
|
||
(home-page "https://pallini.di.uniroma1.it/")
|
||
(synopsis "Library for graph automorphisms")
|
||
(description "@code{nauty} (No AUTomorphisms, Yes?) is a set of
|
||
procedures for computing automorphism groups of graphs and digraphs.
|
||
|
||
@code{nauty} computes graph information in the form of a set of
|
||
generators, the size of the group, and the orbits of the group; it can
|
||
also produce a canonical label. The @code{nauty} suite is written in
|
||
C and comes with a command-line interface, a collection of
|
||
command-line tools, and an Application Programming Interface (API).
|
||
|
||
This package provides the static libraries required to run programs
|
||
compiled against the nauty library.")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public ppl
|
||
(package
|
||
(name "ppl")
|
||
(version "1.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://www.bugseng.com/products/ppl/download/"
|
||
"ftp/releases/" version
|
||
"/ppl-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
(list m4))
|
||
(inputs
|
||
(list glpk gmp))
|
||
(home-page "https://www.bugseng.com/parma-polyhedra-library")
|
||
(synopsis
|
||
"Parma Polyhedra Library for computations with polyhedra")
|
||
(description
|
||
"The Parma Polyhedra Library (PPL) provides numerical abstractions
|
||
especially targeted at applications in the field of analysis and
|
||
verification of complex systems. These abstractions include convex
|
||
polyhedra, defined as the intersection of a finite number of (open or
|
||
closed) halfspaces, each described by a linear inequality (strict or
|
||
non-strict) with rational coefficients; some special classes of polyhedra
|
||
shapes that offer interesting complexity/precision tradeoffs; and grids
|
||
which represent regularly spaced points that satisfy a set of linear
|
||
congruence relations. The library also supports finite powersets and
|
||
products of (any kind of) polyhedra and grids, a mixed integer linear
|
||
programming problem solver using an exact-arithmetic version of the simplex
|
||
algorithm, a parametric integer programming solver, and primitives for
|
||
termination analysis via the automatic synthesis of linear ranking
|
||
functions.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public speedcrunch
|
||
(package
|
||
(name "speedcrunch")
|
||
(version "0.12.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://bitbucket.org/heldercorreia/speedcrunch.git")
|
||
(commit (string-append "release-" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"))))
|
||
(build-system cmake-build-system)
|
||
(inputs (list qtbase-5))
|
||
(native-inputs (list qttools))
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'chdir-to-src
|
||
(lambda _ (chdir "src") #t)))))
|
||
(synopsis "High-precision scientific calculator")
|
||
(description
|
||
"SpeedCrunch is a high-precision scientific calculator. It features a
|
||
syntax-highlighted scrollable display and is designed to be fully used via
|
||
keyboard. Some distinctive features are auto-completion of functions and
|
||
variables, a formula book, and quick insertion of constants from various
|
||
fields of knowledge.")
|
||
(home-page "https://speedcrunch.org/")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public minisat
|
||
;; This is the last commit which is available upstream, no
|
||
;; release happened since 2010.
|
||
(let ((commit "37dc6c67e2af26379d88ce349eb9c4c6160e8543")
|
||
(revision "1"))
|
||
(package
|
||
(name "minisat")
|
||
(version (string-append "2.2.0-" revision "." (string-take commit 7)))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/niklasso/minisat")
|
||
(commit commit)))
|
||
(file-name (string-append name "-" version "-checkout"))
|
||
(sha256
|
||
(base32
|
||
"091hf3qkm197s5r7xcr3m07xsdwyz2rqk1hc9kj0hn13imz09irq"))
|
||
(patches
|
||
(search-patches "minisat-friend-declaration.patch"
|
||
"minisat-install.patch"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
'(#:make-flags (list (string-append "prefix=" %output))
|
||
#:tests? #f ;no check target
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(delete 'configure))))
|
||
(inputs
|
||
`(("zlib:static" ,zlib "static")
|
||
("zlib" ,zlib)))
|
||
(synopsis
|
||
"Small, yet efficient, SAT solver")
|
||
(description
|
||
"MiniSat is a minimalistic, open-source SAT solver, developed to help
|
||
researchers and developers alike to get started on SAT.")
|
||
(home-page
|
||
"http://minisat.se/MiniSat.html")
|
||
(license license:expat))))
|
||
|
||
(define-public libqalculate
|
||
(package
|
||
(name "libqalculate")
|
||
(version "3.19.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/Qalculate/libqalculate/")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1w44407wb552q21dz4m2nwwdi8b9hzjb2w1l3ffsikzqckc7wbyj"))
|
||
(patches
|
||
(search-patches "libqalculate-3.8.0-libcurl-ssl-fix.patch"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("pkg-config" ,pkg-config)
|
||
("gettext" ,gettext-minimal)
|
||
("intltool" ,intltool)
|
||
("automake" ,automake)
|
||
("autoconf" ,autoconf)
|
||
("libtool" ,libtool)
|
||
("doxygen" ,doxygen)
|
||
("file" ,file)))
|
||
(inputs
|
||
(list gmp
|
||
mpfr
|
||
libxml2
|
||
curl
|
||
icu4c
|
||
gnuplot
|
||
readline))
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'bootstrap 'setenv
|
||
;; Prevent the autogen.sh script to carry out the configure
|
||
;; script, which has not yet been patched to replace /bin/sh.
|
||
(lambda _
|
||
(setenv "NOCONFIGURE" "TRUE")
|
||
#t)))))
|
||
(home-page "https://qalculate.github.io/")
|
||
(synopsis "Multi-purpose cli desktop calculator and library")
|
||
(description
|
||
"Libqalculate is a multi-purpose cli desktop calculator and library.
|
||
It provides basic and advanced functionality. Features include customizable
|
||
functions, unit calculations, and conversions, physical constants, symbolic
|
||
calculations (including integrals and equations), arbitrary precision,
|
||
uncertainty propagation, interval arithmetic, plotting and a user-friendly
|
||
cli.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public qalculate-gtk
|
||
(package
|
||
(name "qalculate-gtk")
|
||
(version "3.19.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/Qalculate/qalculate-gtk/")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1nrx7gp6f1yalbdda1gb97azhbr4xclq2xf08vvbvsk8jfd6fd2v"))))
|
||
(build-system glib-or-gtk-build-system)
|
||
(native-inputs
|
||
(list pkg-config
|
||
intltool
|
||
automake
|
||
autoconf
|
||
libtool
|
||
file))
|
||
(inputs
|
||
(list gmp
|
||
mpfr
|
||
libqalculate
|
||
libxml2
|
||
glib
|
||
gtk+))
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'bootstrap 'setenv
|
||
;; Prevent the autogen.sh script to carry out the configure
|
||
;; script, which has not yet been patched to replace /bin/sh.
|
||
(lambda _
|
||
(setenv "NOCONFIGURE" "TRUE")
|
||
#t)))))
|
||
(home-page "https://qalculate.github.io/")
|
||
(synopsis "Multi-purpose graphical desktop calculator")
|
||
(description
|
||
"Qalculate-gtk is the GTK frontend for libqalculate. It is a
|
||
multi-purpose GUI desktop calculator. It provides basic and advanced
|
||
functionality. Features include customizable functions, unit calculations,
|
||
and conversions, physical constants, symbolic calculations (including
|
||
integrals and equations), arbitrary precision, uncertainty propagation,
|
||
interval arithmetic, plotting.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public numdiff
|
||
(package
|
||
(name "numdiff")
|
||
(version "5.9.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://savannah/numdiff/numdiff-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1vzmjh8mhwwysn4x4m2vif7q2k8i19x8azq7pzmkwwj4g48lla47"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
'(#:tests? #f ; There are no tests.
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'compress-documentation 'delete-precompressed-info-file
|
||
(lambda _
|
||
(delete-file (string-append (assoc-ref %outputs "out")
|
||
"/share/info/numdiff.info.gz"))
|
||
#t)))))
|
||
(home-page "https://nongnu.org/numdiff/")
|
||
(synopsis "Compare files with numeric fields")
|
||
(description
|
||
"Numdiff compares files line by line and field by field, ignoring small
|
||
numeric differences and differences in numeric formats.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public why3
|
||
(package
|
||
(name "why3")
|
||
(version "1.4.1")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://gitlab.inria.fr/why3/why3")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1yca6mx8bjm8x0i594ivh31aw45s6fbimmwfj8g2v9zwrgmr1i4s"))))
|
||
(build-system ocaml-build-system)
|
||
(native-inputs
|
||
(list autoconf automake coq ocaml which))
|
||
(propagated-inputs
|
||
(list camlzip ocaml-graph ocaml-menhir ocaml-num ocaml-zarith))
|
||
(inputs
|
||
(list coq-flocq emacs-minimal zlib))
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'configure 'bootstrap
|
||
(lambda _
|
||
(invoke "./autogen.sh")
|
||
(setenv "CONFIG_SHELL" (which "sh"))
|
||
(substitute* "configure"
|
||
(("#! /bin/sh") (string-append "#!" (which "sh")))
|
||
;; find ocaml-num in the correct directory
|
||
(("\\$DIR/nums.cma") "$DIR/num.cma")
|
||
(("\\$DIR/num.cmi") "$DIR/core/num.cmi"))
|
||
#t))
|
||
(add-after 'configure 'fix-makefile
|
||
(lambda _
|
||
(substitute* "Makefile"
|
||
;; find ocaml-num in the correct directory
|
||
(("site-lib/num") "site-lib"))
|
||
#t))
|
||
(add-after 'install 'install-lib
|
||
(lambda _
|
||
(invoke "make" "byte")
|
||
(invoke "make" "install-lib")
|
||
#t)))))
|
||
(home-page "http://why3.lri.fr")
|
||
(synopsis "Deductive program verification")
|
||
(description "Why3 provides a language for specification and programming,
|
||
called WhyML, and relies on external theorem provers, both automated and
|
||
interactive, to discharge verification conditions. Why3 comes with a standard
|
||
library of logical theories (integer and real arithmetic, Boolean operations,
|
||
sets and maps, etc.) and basic programming data structures (arrays, queues,
|
||
hash tables, etc.). A user can write WhyML programs directly and get
|
||
correct-by-construction OCaml programs through an automated extraction
|
||
mechanism. WhyML is also used as an intermediate language for the verification
|
||
of C, Java, or Ada programs.")
|
||
(license license:lgpl2.1)))
|
||
|
||
(define-public frama-c
|
||
(package
|
||
(name "frama-c")
|
||
(version "24.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://frama-c.com/download/frama-c-"
|
||
version "-Chromium.tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0x1xgip50jdz1phsb9rzwf2ra8lshn1hmd9g967xia402wrg3sjf"))))
|
||
(build-system ocaml-build-system)
|
||
(arguments
|
||
`(#:tests? #f; no test target in Makefile
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'configure 'export-shell
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(setenv "CONFIG_SHELL"
|
||
(search-input-file inputs "/bin/sh")))))))
|
||
(inputs
|
||
(list gmp))
|
||
(propagated-inputs
|
||
(list ocaml-biniou
|
||
ocaml-easy-format
|
||
ocaml-graph
|
||
ocaml-yojson
|
||
ocaml-zarith
|
||
why3))
|
||
(native-search-paths
|
||
(list (search-path-specification
|
||
(variable "FRAMAC_SHARE")
|
||
(files '("share/frama-c"))
|
||
(separator #f))
|
||
(search-path-specification
|
||
(variable "FRAMAC_LIB")
|
||
(files '("lib/frama-c"))
|
||
(separator #f))))
|
||
(home-page "http://frama-c.com")
|
||
(synopsis "C source code analysis platform")
|
||
(description "Frama-C is an extensible and collaborative platform dedicated
|
||
to source-code analysis of C software. The Frama-C analyzers assist you in
|
||
various source-code-related activities, from the navigation through unfamiliar
|
||
projects up to the certification of critical software.")
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public blitz
|
||
(package
|
||
(name "blitz")
|
||
(version "1.0.2")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/blitzpp/blitz")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "0c88gc72j3zggyk4yrrip6i0v7xkx97l140vpy3xhxs2i7xy1461"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:configure-flags '("-DBUILD_DOC=ON"
|
||
"-DBUILD_TESTING=ON")
|
||
;; The default "check" target also includes examples and benchmarks.
|
||
#:test-target "check-testsuite"
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-doc
|
||
(lambda _
|
||
(invoke "make" "-j" (number->string (parallel-job-count))
|
||
"blitz-doc"))))))
|
||
(native-inputs
|
||
(list python texinfo))
|
||
(synopsis "C++ template class library for multidimensional arrays")
|
||
(description "Blitz++ is a C++ template class library that provides
|
||
high-performance multidimensional array containers for scientific computing.")
|
||
(home-page "https://github.com/blitzpp/blitz")
|
||
(license (list license:artistic2.0
|
||
license:bsd-3
|
||
license:lgpl3+))))
|
||
|
||
(define-public fxdiv
|
||
;; There is currently no tag in this repo.
|
||
(let ((commit "63058eff77e11aa15bf531df5dd34395ec3017c8")
|
||
(version "0.0")
|
||
(revision "1"))
|
||
(package
|
||
(name "fxdiv")
|
||
(version (git-version version revision commit))
|
||
(home-page "https://github.com/Maratyszcza/FXdiv")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference (url home-page) (commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0zwzh8gmbx4m6b18s5nf13b0dk5yjkd1fs8f421bl7fz5f9gjd9f"))
|
||
(patches (search-patches "fxdiv-system-libraries.patch"))))
|
||
(build-system cmake-build-system)
|
||
(inputs
|
||
(list googletest googlebenchmark))
|
||
(synopsis
|
||
"C++ library for division via fixed-point multiplication by inverse")
|
||
(description
|
||
"On modern CPUs and GPUs, integer division is several times slower than
|
||
multiplication. FXdiv implements an algorithm to replace an integer division
|
||
with a multiplication and two shifts. This algorithm improves performance
|
||
when an application performs repeated divisions by the same divisor.")
|
||
(license license:expat))))
|
||
|
||
(define-public fp16
|
||
;; There is currently no tag in this repo.
|
||
(let ((commit "0a92994d729ff76a58f692d3028ca1b64b145d91")
|
||
(version "0.0")
|
||
(revision "1"))
|
||
(package
|
||
(name "fp16")
|
||
(version (git-version version revision commit))
|
||
(home-page "https://github.com/Maratyszcza/FP16")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference (url home-page) (commit commit)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"05mm4vrxsac35hjf5djif9r6rdxj9ippg97ia3p6q6b8lrp7srwv"))
|
||
(patches (search-patches "fp16-system-libraries.patch"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:imported-modules ((guix build python-build-system)
|
||
,@%cmake-build-system-modules)
|
||
#:modules (((guix build python-build-system)
|
||
#:select (site-packages))
|
||
(guix build cmake-build-system)
|
||
(guix build utils))
|
||
#:phases (modify-phases %standard-phases
|
||
(add-after 'install 'move-python-files
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
;; Python files get installed to $includedir (!).
|
||
;; Move them to the usual Python site directory.
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(include (string-append out "/include"))
|
||
(site (site-packages inputs outputs))
|
||
(target (string-append site "/fp16")))
|
||
(mkdir-p target)
|
||
(for-each (lambda (file)
|
||
(rename-file file
|
||
(string-append target "/"
|
||
(basename
|
||
file))))
|
||
(find-files include "\\.py$"))))))))
|
||
(native-inputs
|
||
(list python-wrapper))
|
||
(inputs
|
||
(list psimd googletest googlebenchmark))
|
||
(synopsis "C++ library for half-precision floating point formats")
|
||
(description
|
||
"This header-only C++ library implements conversion to and from
|
||
half-precision floating point formats.")
|
||
(license license:expat))))
|
||
|
||
(define-public optizelle
|
||
(let ((commit "ed4160b5287518448caeb34789d92dc6a0b7e2cc"))
|
||
(package
|
||
(name "optizelle")
|
||
(version (git-version "1.3.0" "0" commit))
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/OptimoJoe/Optizelle")
|
||
(commit commit)))
|
||
(file-name (git-file-name "optizelle" commit))
|
||
(sha256
|
||
(base32
|
||
"0rjrs5sdmd33a9f4xm8an7p0953aa0bxsmr4hs3ss1aad9k181vq"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(begin
|
||
;; Reduce the stopping tolerance in one test so that the
|
||
;; convergence check returns the correct stopping
|
||
;; condition.
|
||
(substitute*
|
||
"src/unit/linear_algebra/tcg_loss_of_orthogonality.cpp"
|
||
(("1e-13") "5e-14"))
|
||
;; Skip one set of python tests. See
|
||
;; https://github.com/OptimoJoe/Optizelle/issues/2.
|
||
(substitute*
|
||
"src/examples/inequality_scaling/CMakeLists.txt"
|
||
(("add_unit(.*)\\$\\{interfaces\\}(.*)$" all middle end)
|
||
(string-append "add_unit" middle "\"cpp\"" end)))
|
||
;; Install the licence for Optizelle, without also
|
||
;; including the licences for the dependencies.
|
||
(substitute* "licenses/CMakeLists.txt"
|
||
(("file.*package.*$" all)
|
||
(string-append "# " all))
|
||
((".*[^l].[.]txt\\)\n") "")
|
||
(("add_license.*\"\n") ""))
|
||
#t))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:imported-modules ((guix build python-build-system)
|
||
,@%cmake-build-system-modules)
|
||
#:modules (((guix build python-build-system) #:select
|
||
(python-version))
|
||
(guix build cmake-build-system)
|
||
(guix build utils))
|
||
#:configure-flags `("-DCMAKE_CXX_FLAGS:STRING=-pthread"
|
||
"-DENABLE_CPP_UNIT:BOOL=ON"
|
||
"-DENABLE_CPP_EXAMPLES:BOOL=ON"
|
||
"-DENABLE_PYTHON:BOOL=ON"
|
||
"-DENABLE_PYTHON_UNIT:BOOL=ON"
|
||
"-DENABLE_PYTHON_EXAMPLES:BOOL=ON"
|
||
,(string-append "-DBLAS_LIBRARY:FILEPATH="
|
||
(assoc-ref %build-inputs
|
||
"blas/lapack")
|
||
"/lib/libopenblas.so")
|
||
,(string-append "-DLAPACK_LIBRARY:FILEPATH="
|
||
(assoc-ref %build-inputs
|
||
"fortran:lib")
|
||
"/lib/libgfortran.so;"
|
||
(assoc-ref %build-inputs
|
||
"fortran:lib")
|
||
"/lib/libquadmath.so"))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'set-numpy-path ; Needed for the unit tests.
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(let* ((pyver (python-version (assoc-ref inputs "python")))
|
||
(npdir (string-append (assoc-ref inputs "numpy")
|
||
"/lib/python" pyver
|
||
"/site-packages")))
|
||
(substitute* "src/cmake/Modules/Optizelle.cmake"
|
||
(("PYTHONPATH=")
|
||
(string-append "LD_LIBRARY_PATH=$ENV{LIBRARY_PATH};"
|
||
"PYTHONPATH=" npdir ":"))))))
|
||
(delete 'install-license-files)))) ; LICENSE.txt is installed.
|
||
(inputs
|
||
`(("blas/lapack" ,openblas)
|
||
("fortran:lib" ,gfortran "lib")
|
||
("jsoncpp" ,jsoncpp)
|
||
("numpy" ,python-numpy)
|
||
("python" ,python)))
|
||
(native-inputs
|
||
`(("fortran" ,gfortran)
|
||
("pkg-config" ,pkg-config)))
|
||
(home-page "https://www.optimojoe.com/products/optizelle/")
|
||
(synopsis "Mathematical optimization library")
|
||
(description "@code{optizelle} is a software library designed to
|
||
solve nonlinear optimization problems. Four types of problem are
|
||
considered: unconstrained, equality constrained, inequality
|
||
constrained and constrained. Constraints may be applied as values of
|
||
functions or sets of partial differential equations (PDEs).
|
||
|
||
Solution algorithms such as the preconditioned nonlinear conjugate
|
||
gradient method, sequential quadratic programming (SQP) and the
|
||
primal-dual interior-point method are made available. Interfaces are
|
||
provided for applications written in C++ and Python. Parallel
|
||
computation is supported via MPI.")
|
||
(license license:bsd-2))))
|