5047 lines
203 KiB
Scheme
5047 lines
203 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
||
;;; Copyright © 2013, 2014, 2015, 2016, 2019 Andreas Enge <andreas@enge.fr>
|
||
;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
|
||
;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
|
||
;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Eric Bavier <bavier@member.fsf.org>
|
||
;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
|
||
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
|
||
;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
|
||
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
|
||
;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
|
||
;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
|
||
;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
|
||
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
|
||
;;; Copyright © 2016, 2018 Kei Kebreau <kkebreau@posteo.net>
|
||
;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
|
||
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
|
||
;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
|
||
;;; Copyright © 2017, 2018 Paul Garlick <pgarlick@tourbillion-technology.com>
|
||
;;; Copyright © 2017 ng0 <ng0@n0.is>
|
||
;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
|
||
;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
|
||
;;; Copyright © 2017, 2019 Arun Isaac <arunisaac@systemreboot.net>
|
||
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
|
||
;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
|
||
;;; Copyright © 2018 Jan Nieuwenhuizen <janneke@gnu.org>
|
||
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
|
||
;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
|
||
;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
|
||
;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
|
||
;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
|
||
;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
|
||
;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
|
||
;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
|
||
;;;
|
||
;;; This file is part of GNU Guix.
|
||
;;;
|
||
;;; 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/>.
|
||
|
||
(define-module (gnu packages maths)
|
||
#: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 utils)
|
||
#:use-module ((guix build utils) #:select (alist-replace))
|
||
#:use-module (guix build-system cmake)
|
||
#:use-module (guix build-system gnu)
|
||
#:use-module (guix build-system python)
|
||
#:use-module (guix build-system r)
|
||
#:use-module (guix build-system ruby)
|
||
#:use-module (gnu packages algebra)
|
||
#:use-module (gnu packages audio)
|
||
#:use-module (gnu packages autotools)
|
||
#:use-module (gnu packages base)
|
||
#:use-module (gnu packages bison)
|
||
#:use-module (gnu packages boost)
|
||
#:use-module (gnu packages check)
|
||
#:use-module (gnu packages cmake)
|
||
#:use-module (gnu packages compression)
|
||
#:use-module (gnu packages curl)
|
||
#:use-module (gnu packages cyrus-sasl)
|
||
#:use-module (gnu packages documentation)
|
||
#:use-module (gnu packages elf)
|
||
#:use-module (gnu packages flex)
|
||
#:use-module (gnu packages fltk)
|
||
#:use-module (gnu packages fontutils)
|
||
#:use-module (gnu packages gettext)
|
||
#:use-module (gnu packages gcc)
|
||
#:use-module (gnu packages gd)
|
||
#:use-module (gnu packages ghostscript)
|
||
#:use-module (gnu packages graphviz)
|
||
#:use-module (gnu packages gtk)
|
||
#:use-module (gnu packages image)
|
||
#:use-module (gnu packages java)
|
||
#:use-module (gnu packages less)
|
||
#:use-module (gnu packages lisp)
|
||
#:use-module (gnu packages linux)
|
||
#:use-module (gnu packages logging)
|
||
#:use-module (gnu packages lua)
|
||
#:use-module (gnu packages gnome)
|
||
#:use-module (gnu packages guile)
|
||
#:use-module (gnu packages xorg)
|
||
#:use-module (gnu packages gl)
|
||
#:use-module (gnu packages imagemagick)
|
||
#:use-module (gnu packages m4)
|
||
#:use-module (gnu packages mpi)
|
||
#:use-module (gnu packages multiprecision)
|
||
#:use-module (gnu packages netpbm)
|
||
#: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 shells)
|
||
#: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))
|
||
|
||
(define-public aris
|
||
(package
|
||
(name "aris")
|
||
(version "2.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
|
||
(sha256 (base32
|
||
"1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
|
||
(build-system gnu-build-system)
|
||
(inputs `(("gtk+" ,gtk+)
|
||
("libxml2" ,libxml2)))
|
||
(native-inputs `(("pkg-config" ,pkg-config)))
|
||
(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+)
|
||
(home-page "https://www.gnu.org/software/aris/")))
|
||
|
||
(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
|
||
`(("fortran" ,gfortran)))
|
||
(synopsis "Visualizing and demonstrating convolution")
|
||
(description
|
||
"GNU C-Graph is a tool for demonstrating the theory of convolution.
|
||
Thus, it can serve as an excellent aid to students of signal and systems
|
||
theory in visualizing the convolution process. Rather than forcing the
|
||
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 "A common interface to various earth observation data formats")
|
||
(description
|
||
"The Common Data Access toolbox (CODA) provides a set of interfaces for
|
||
reading remote sensing data from earth observation data files. It consists of
|
||
command line applications and interfaces to the C, Fortran, Python, and Java
|
||
programming languages.")
|
||
(home-page "https://stcorp.nl/coda")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public qhull
|
||
(package
|
||
(name "qhull")
|
||
(version "2015.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://www.qhull.org/download/qhull-"
|
||
(car (string-split version #\.))
|
||
"-src-7.2.0.tgz"))
|
||
(sha256
|
||
(base32
|
||
"0dm4b2xr3asy6w74khq2zg4gf26zsy3qf9sq7pf7lmrvbj911c3q"))))
|
||
(build-system cmake-build-system)
|
||
(synopsis "Calculate convex hulls and related structures")
|
||
(description
|
||
"@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
|
||
diagram, halfspace intersection about a point, furthest-site Delaunay
|
||
triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d,
|
||
3-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull
|
||
algorithm for computing the convex hull. It handles roundoff errors from
|
||
floating point arithmetic. It computes volumes, surface areas, and
|
||
approximations to the convex hull.
|
||
|
||
@code{Qhull} does not support triangulation of non-convex surfaces, mesh
|
||
generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
|
||
shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
|
||
triangulations.")
|
||
(home-page "http://qhull.org")
|
||
(license (license:non-copyleft "file://COPYING.txt"
|
||
"See COPYING in the distribution."))))
|
||
|
||
(define-public python-cvxopt
|
||
(package
|
||
(name "python-cvxopt")
|
||
(version "1.2.1")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/cvxopt/cvxopt.git")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"05mnjil9palaa48xafdfh4f5pr4z7aqjr995rwl08qfyxs8y0crf"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'find-libraries
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(setenv "CVXOPT_BLAS_LIB" "openblas")
|
||
(setenv "CVXOPT_BUILD_FFTW" "1")
|
||
(setenv "CVXOPT_BUILD_GLPK" "1")
|
||
(setenv "CVXOPT_BUILD_GSL" "1")
|
||
#t)))))
|
||
(inputs
|
||
`(("fftw" ,fftw)
|
||
("glpk" ,glpk)
|
||
("gsl" ,gsl)
|
||
("lapack" ,lapack)
|
||
("openblas" ,openblas)
|
||
("suitesparse" ,suitesparse)))
|
||
(home-page "https://www.cvxopt.org")
|
||
(synopsis "Python library for convex optimization")
|
||
(description
|
||
"CVXOPT is a package for convex optimization based on the Python
|
||
programming language. Its main purpose is to make the development of software
|
||
for convex optimization applications straightforward by building on Python’s
|
||
extensive standard library and on the strengths of Python as a high-level
|
||
programming language.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public python2-cvxopt
|
||
(package-with-python2 python-cvxopt))
|
||
|
||
(define-public units
|
||
(package
|
||
(name "units")
|
||
(version "2.19")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/units/units-" version
|
||
".tar.gz"))
|
||
(sha256 (base32
|
||
"0mk562g7dnidjgfgvkxxpvlba66fh1ykmfd9ylzvcln1vxmi6qj2"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("readline" ,readline)
|
||
("python" ,python-wrapper) ;for 'units_cur' script
|
||
("python-requests" ,python-requests)))
|
||
(arguments
|
||
`(#:phases (modify-phases %standard-phases
|
||
(add-after 'install 'wrap-units_cur
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(bin (string-append out "/bin")))
|
||
(wrap-program (string-append bin "/units_cur")
|
||
`("PYTHONPATH" ":" prefix
|
||
,(search-path-as-string->list (getenv "PYTHONPATH"))))
|
||
#t))))))
|
||
(synopsis "Conversion between thousands of scales")
|
||
(description
|
||
"GNU Units converts numeric quantities between units of measure. It
|
||
can handle scale changes through adaptive usage of standard scale
|
||
prefixes (micro-, kilo-, etc.). It can also handle nonlinear
|
||
conversions such as Fahrenheit to Celsius. Its interpreter is powerful
|
||
enough to be used effectively as a scientific calculator.")
|
||
(license license:gpl3+)
|
||
(home-page "https://www.gnu.org/software/units/")))
|
||
|
||
(define-public double-conversion
|
||
(package
|
||
(name "double-conversion")
|
||
(version "3.1.4")
|
||
(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
|
||
"13xwcqk2c0q8c1siw566clxcpvp0xrxvb72mra42wa3nvq9wlsv6"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
'(#:test-target "test"
|
||
#:configure-flags '("-DBUILD_SHARED_LIBS=ON"
|
||
"-DBUILD_TESTING=ON")))
|
||
(synopsis "Conversion routines for IEEE doubles")
|
||
(description
|
||
"The double-conversion library provides binary-decimal and decimal-binary
|
||
routines for IEEE doubles. The library consists of efficient conversion
|
||
routines that have been extracted from the V8 JavaScript engine.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public dionysus
|
||
(package
|
||
(name "dionysus")
|
||
(version "1.4.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/dionysus/dionysus-" version
|
||
".tar.xz"))
|
||
(sha256
|
||
(base32
|
||
"194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
|
||
(build-system gnu-build-system)
|
||
(inputs `(("tcl" ,tcl))) ;for 'tclsh'
|
||
(synopsis "Local search for universal constants and scientific values")
|
||
(description
|
||
"GNU Dionysus is a convenient system for quickly retrieving the values of
|
||
mathematical constants used in science and engineering. Values can be
|
||
searched using a simple command-line tool, choosing from three databases:
|
||
universal constants, atomic numbers, and constants related to
|
||
semiconductors.")
|
||
(license license:gpl3+)
|
||
(home-page "https://www.gnu.org/software/dionysus/")))
|
||
|
||
(define-public gsl
|
||
(package
|
||
(name "gsl")
|
||
(version "2.5")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/gsl/gsl-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
|
||
(patches (search-patches "gsl-test-i686.patch"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(;; Currently there are numerous tests that fail on "exotic"
|
||
;; architectures such as aarch64 and ppc64le.
|
||
,@(if (string-prefix? "aarch64-linux"
|
||
(or (%current-target-system) (%current-system)))
|
||
'(#:tests? #f)
|
||
'())))
|
||
(home-page "https://www.gnu.org/software/gsl/")
|
||
(synopsis "Numerical library for C and C++")
|
||
(description
|
||
"The GNU Scientific Library is a library for numerical analysis in C
|
||
and C++. It includes a wide range of mathematical routines, with over 1000
|
||
functions in total. Subject areas covered by the library include:
|
||
differential equations, linear algebra, Fast Fourier Transforms and random
|
||
numbers.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public glpk
|
||
(package
|
||
(name "glpk")
|
||
(version "4.65")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/glpk/glpk-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("gmp" ,gmp)))
|
||
(arguments
|
||
`(#:configure-flags '("--with-gmp")))
|
||
(home-page "https://www.gnu.org/software/glpk/")
|
||
(synopsis "GNU Linear Programming Kit, supporting the MathProg language")
|
||
(description
|
||
"GLPK is a C library for solving large-scale linear programming (LP),
|
||
mixed integer programming (MIP), and other related problems. It supports the
|
||
GNU MathProg modeling language, a subset of the AMPL language, and features a
|
||
translator for the language. In addition to the C library, a stand-alone
|
||
LP/MIP solver is included in the package.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public 4ti2
|
||
(package
|
||
(name "4ti2")
|
||
(version "1.6.9")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://github.com/4ti2/4ti2/releases/download/"
|
||
"Release_"
|
||
(string-map (lambda (c) (if (char=? c #\.) #\_ c))
|
||
version)
|
||
"/4ti2-" version ".tar.gz"))
|
||
(sha256
|
||
(base32 "0rj92x6p9m3la5gasjbj7sa569im527ffmka5y2sv1amgd3fflrh"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("which" ,(@ (gnu packages base) which)))) ; for the tests
|
||
(inputs
|
||
`(("glpk" ,glpk)
|
||
("gmp" ,gmp)))
|
||
(home-page "http://www.4ti2.de/")
|
||
(synopsis "Mathematical tool suite for problems on linear spaces")
|
||
(description
|
||
"4ti2 implements algorithms for solving algebraic, geometric and
|
||
combinatorial problems on linear spaces. Among others, it solves systems
|
||
of linear equations, computes extreme rays of polyhedral cones, solves
|
||
integer programming problems and computes Markov bases for statistics.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public cddlib
|
||
(package
|
||
(name "cddlib")
|
||
(version "0.94i")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
|
||
(string-delete #\. version) ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("gmp" ,gmp)))
|
||
(home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
|
||
(synopsis "Library for convex hulls and extreme rays of polyhedra")
|
||
(description
|
||
"The C-library cddlib implements the Double Description Method of
|
||
Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
|
||
rays of a general convex polyhedron given by a system of linear inequalities
|
||
in arbitrary dimension. It can also be used for the converse operation of
|
||
computing convex hulls.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public arpack-ng
|
||
(package
|
||
(name "arpack-ng")
|
||
(version "3.6.3")
|
||
(home-page "https://github.com/opencollab/arpack-ng")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference (url home-page) (commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("autoconf" ,autoconf)
|
||
("automake" ,automake)
|
||
("libtool" ,libtool)))
|
||
(inputs
|
||
`(("lapack" ,lapack)
|
||
("fortran" ,gfortran)))
|
||
(synopsis "Fortran subroutines for solving eigenvalue problems")
|
||
(description
|
||
"ARPACK-NG is a collection of Fortran77 subroutines designed to solve
|
||
large scale eigenvalue problems.")
|
||
(license (license:non-copyleft "file://COPYING"
|
||
"See COPYING in the distribution."))))
|
||
|
||
(define-public arpack-ng-3.3.0
|
||
(package
|
||
(inherit arpack-ng)
|
||
(version "3.3.0")
|
||
(name (package-name arpack-ng))
|
||
(home-page (package-home-page arpack-ng))
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append home-page "/archive/" version ".tar.gz"))
|
||
(file-name (string-append name "-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
|
||
|
||
(define-public arpack-ng-openmpi
|
||
(package (inherit arpack-ng)
|
||
(name "arpack-ng-openmpi")
|
||
(inputs
|
||
`(("mpi" ,openmpi)
|
||
,@(package-inputs arpack-ng)))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments arpack-ng)
|
||
((#:configure-flags _ '())
|
||
''("--enable-mpi"))
|
||
((#:phases phases '%standard-phases)
|
||
`(modify-phases ,phases
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup)))))
|
||
(synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
|
||
|
||
(define-public lapack
|
||
(package
|
||
(name "lapack")
|
||
(version "3.7.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://www.netlib.org/lapack/lapack-"
|
||
version ".tgz"))
|
||
(sha256
|
||
(base32
|
||
"1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
|
||
(build-system cmake-build-system)
|
||
(home-page "http://www.netlib.org/lapack/")
|
||
(inputs `(("fortran" ,gfortran)
|
||
("python" ,python-2)))
|
||
(arguments
|
||
`(#:configure-flags (list
|
||
"-DBUILD_SHARED_LIBS:BOOL=YES"
|
||
"-DLAPACKE=ON"
|
||
|
||
;; Build the 'LAPACKE_clatms' functions.
|
||
"-DLAPACKE_WITH_TMG=ON")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'check 'patch-python
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(let ((python (assoc-ref inputs "python")))
|
||
(substitute* "lapack_testing.py"
|
||
(("/usr/bin/env python") python)))
|
||
#t)))))
|
||
(synopsis "Library for numerical linear algebra")
|
||
(description
|
||
"LAPACK is a Fortran 90 library for solving the most commonly occurring
|
||
problems in numerical linear algebra.")
|
||
(license (license:non-copyleft "file://LICENSE"
|
||
"See LICENSE in the distribution."))))
|
||
|
||
(define-public scalapack
|
||
(package
|
||
(name "scalapack")
|
||
(version "2.0.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://www.netlib.org/scalapack/scalapack-"
|
||
version ".tgz"))
|
||
(sha256
|
||
(base32
|
||
"0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))
|
||
(patches (search-patches "scalapack-blacs-mpi-deprecations.patch"))))
|
||
(build-system cmake-build-system)
|
||
(inputs
|
||
`(("mpi" ,openmpi)
|
||
("fortran" ,gfortran)
|
||
("lapack" ,lapack))) ;for testing only
|
||
(arguments
|
||
`(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
|
||
#:phases (modify-phases %standard-phases
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup))))
|
||
(home-page "http://www.netlib.org/scalapack/")
|
||
(synopsis "Library for scalable numerical linear algebra")
|
||
(description
|
||
"ScaLAPACK is a Fortran 90 library of high-performance linear algebra
|
||
routines on parallel distributed memory machines. ScaLAPACK solves dense and
|
||
banded linear systems, least squares problems, eigenvalue problems, and
|
||
singular value problems.")
|
||
(license (license:non-copyleft "file://LICENSE"
|
||
"See LICENSE in the distribution."))))
|
||
|
||
(define-public gnuplot
|
||
(package
|
||
(name "gnuplot")
|
||
(version "5.2.7")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
|
||
version "/gnuplot-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32 "1vglp4la40f5dpj0zdj63zprrkyjgzy068p35bz5dqxjyczm1zlp"))))
|
||
(build-system gnu-build-system)
|
||
(inputs `(("readline" ,readline)
|
||
("cairo" ,cairo)
|
||
("pango" ,pango)
|
||
("gd" ,gd)
|
||
("lua" ,lua)))
|
||
(native-inputs
|
||
`(("pkg-config" ,pkg-config)
|
||
("texlive" ,texlive-tiny)))
|
||
(arguments `(#:configure-flags (list (string-append
|
||
"--with-texdir=" %output
|
||
"/texmf-local/tex/latex/gnuplot"))))
|
||
(home-page "http://www.gnuplot.info")
|
||
(synopsis "Command-line driven graphing utility")
|
||
(description "Gnuplot is a portable command-line driven graphing
|
||
utility. It was originally created to allow scientists and students to
|
||
visualize mathematical functions and data interactively, but has grown to
|
||
support many non-interactive uses such as web scripting. It is also used as a
|
||
plotting engine by third-party applications like Octave.")
|
||
;; X11 Style with the additional restriction that derived works may only be
|
||
;; distributed as patches to the original.
|
||
(license (license:fsf-free
|
||
"http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
|
||
|
||
(define-public gctp
|
||
(package
|
||
(name "gctp")
|
||
(version "2.0.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/OkoSanto/GCTP.git")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
|
||
(native-inputs
|
||
`(("fortran" ,gfortran)))
|
||
(build-system gnu-build-system)
|
||
(synopsis "General Cartographic Transformation Package (GCTP)")
|
||
(description
|
||
"The General Cartographic Transformation Package (GCTP) is a system of
|
||
software routines designed to permit the transformation of coordinate pairs
|
||
from one map projection to another. The GCTP is the standard computer
|
||
software used by the National Mapping Division for map projection
|
||
computations.")
|
||
(home-page "https://github.com/OkoSanto/GCTP")
|
||
(license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
|
||
|
||
(define-public hdf4
|
||
(package
|
||
(name "hdf4")
|
||
(version "4.2.13")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
|
||
version "/src/hdf-" version ".tar.bz2"))
|
||
(sha256
|
||
(base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
|
||
(patches (search-patches "hdf4-architectures.patch"
|
||
"hdf4-reproducibility.patch"
|
||
"hdf4-shared-fortran.patch"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)
|
||
("bison" ,bison)
|
||
("flex" ,flex)))
|
||
(inputs
|
||
`(("zlib" ,zlib)
|
||
("libjpeg" ,libjpeg)))
|
||
(arguments
|
||
`(#:parallel-tests? #f
|
||
#:configure-flags '("--enable-shared")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
;; This is inspired by two of Debian's patches.
|
||
(add-before 'configure 'add-more-aarch64-support
|
||
(lambda _
|
||
(substitute* '("mfhdf/ncgen/ncgen.l"
|
||
"mfhdf/ncgen/ncgenyy.c"
|
||
"mfhdf/libsrc/netcdf.h.in")
|
||
(("AIX5L64") "__aarch64__"))
|
||
#t))
|
||
(add-before 'configure 'patchbuild
|
||
(lambda _
|
||
(substitute*
|
||
'("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
|
||
(("/bin/rm") "rm")
|
||
(("/bin/mkdir") "mkdir"))
|
||
(substitute* (find-files "." "^Makefile\\.in$")
|
||
(("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
|
||
-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
|
||
(("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
|
||
-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
|
||
-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
|
||
#t))
|
||
(add-after 'configure 'patch-settings
|
||
(lambda _
|
||
;; libhdf4.settings contains the full path of the
|
||
;; compilers used, and its contents are included in
|
||
;; .so-files. We truncate the hashes to avoid
|
||
;; unnecessary store references to those compilers:
|
||
(substitute* "libhdf4.settings"
|
||
(("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
|
||
(string-append prefix (string-take hash 10) "...")))
|
||
#t))
|
||
)))
|
||
(home-page "https://www.hdfgroup.org/products/hdf4/")
|
||
(synopsis
|
||
"Library and multi-object file format for storing and managing data")
|
||
(description "HDF4 is a library and multi-object file format for storing
|
||
and managing data between machines. HDF4 is an older hierarchical data format,
|
||
incompatible with HDF5.")
|
||
(license
|
||
(license:non-copyleft
|
||
"https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
|
||
|
||
(define-public hdf4-alt
|
||
(package
|
||
(inherit hdf4)
|
||
(name "hdf4-alt")
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments hdf4)
|
||
((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
|
||
(synopsis
|
||
"HDF4 without netCDF API, can be combined with the regular netCDF library")))
|
||
|
||
(define-public hdf5
|
||
(package
|
||
(name "hdf5")
|
||
(version "1.8.21")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
|
||
"hdf5-" (version-major+minor version)
|
||
"/hdf5-" version "/src/hdf5-"
|
||
version ".tar.bz2")
|
||
(string-append "https://support.hdfgroup.org/ftp/HDF5/"
|
||
"current"
|
||
(match (string-split version #\.)
|
||
((major minor _ ...)
|
||
(string-append major minor)))
|
||
"/src/hdf5-" version ".tar.bz2")))
|
||
(sha256
|
||
(base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5"))
|
||
(patches (search-patches "hdf5-config-date.patch"
|
||
"hdf5-1.8-mpi-deprecations.patch"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("zlib" ,zlib)))
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)
|
||
("perl" ,perl))) ;part of the test machinery needs Perl
|
||
(outputs '("out" ; core library
|
||
"fortran")) ; fortran interface
|
||
(arguments
|
||
`(;; Some of the users, notably Flann, need the C++ interface.
|
||
#:configure-flags '("--enable-cxx"
|
||
"--enable-fortran"
|
||
"--enable-fortran2003"
|
||
|
||
;; Build a thread-safe library. Unfortunately,
|
||
;; 'configure' invites you to either turn off C++,
|
||
;; Fortran, and the high-level interface (HL), or
|
||
;; to pass '--enable-unsupported'. Debian
|
||
;; packagers chose to pass '--enable-unsupported'
|
||
;; and we follow their lead here.
|
||
"--enable-threadsafe"
|
||
"--with-pthread"
|
||
"--enable-unsupported")
|
||
;; Use -fPIC to allow the R bindings to link with the static libraries
|
||
#:make-flags (list "CFLAGS=-fPIC"
|
||
"CXXFLAGS=-fPIC")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'configure 'patch-configure
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(substitute* "configure"
|
||
(("/bin/mv") "mv"))
|
||
(substitute* "fortran/src/Makefile.in"
|
||
(("libhdf5_fortran_la_LDFLAGS =")
|
||
(string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
|
||
(assoc-ref outputs "fortran") "/lib")))
|
||
(substitute* "hl/fortran/src/Makefile.in"
|
||
(("libhdf5hl_fortran_la_LDFLAGS =")
|
||
(string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
|
||
(assoc-ref outputs "fortran") "/lib")))
|
||
#t))
|
||
(add-after 'configure 'patch-settings
|
||
(lambda _
|
||
;; libhdf5.settings contains the full path of the
|
||
;; compilers used, and its contents are included in
|
||
;; libhdf5.so. We truncate the hashes to avoid
|
||
;; unnecessary store references to those compilers:
|
||
(substitute* "src/libhdf5.settings"
|
||
(("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
|
||
(string-append prefix (string-take hash 10) "..."))
|
||
;; Don't record the build-time kernel version to make the
|
||
;; settings file reproducible.
|
||
(("Uname information:.*")
|
||
"Uname information: Linux\n"))
|
||
#t))
|
||
(add-after 'install 'patch-references
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let ((bin (string-append (assoc-ref outputs "out") "/bin"))
|
||
(zlib (assoc-ref inputs "zlib")))
|
||
(substitute* (find-files bin "h5p?cc")
|
||
(("-lz" lib)
|
||
(string-append "-L" zlib "/lib " lib)))
|
||
#t)))
|
||
(add-after 'install 'split
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
;; Move all fortran-related files
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(bin (string-append out "/bin"))
|
||
(lib (string-append out "/lib"))
|
||
(inc (string-append out "/include"))
|
||
(ex (string-append out "/share/hdf5_examples/fortran"))
|
||
(fort (assoc-ref outputs "fortran"))
|
||
(fbin (string-append fort "/bin"))
|
||
(flib (string-append fort "/lib"))
|
||
(finc (string-append fort "/include"))
|
||
(fex (string-append fort "/share/hdf5_examples/fortran")))
|
||
(mkdir-p fbin)
|
||
(mkdir-p flib)
|
||
(mkdir-p finc)
|
||
(mkdir-p fex)
|
||
;; Note: When built with --enable-parallel, the 'h5fc' file
|
||
;; doesn't exist, hence this condition.
|
||
(when (file-exists? (string-append bin "/h5fc"))
|
||
(rename-file (string-append bin "/h5fc")
|
||
(string-append fbin "/h5fc")))
|
||
(for-each (lambda (file)
|
||
(rename-file file
|
||
(string-append flib "/" (basename file))))
|
||
(find-files lib ".*fortran.*"))
|
||
(for-each (lambda (file)
|
||
(rename-file file
|
||
(string-append finc "/" (basename file))))
|
||
(find-files inc ".*mod"))
|
||
(for-each (lambda (file)
|
||
(rename-file file
|
||
(string-append fex "/" (basename file))))
|
||
(find-files ex ".*"))
|
||
(delete-file-recursively ex))
|
||
#t)))))
|
||
(home-page "http://www.hdfgroup.org")
|
||
(synopsis "Management suite for extremely large and complex data")
|
||
(description "HDF5 is a suite that makes possible the management of
|
||
extremely large and complex data collections.")
|
||
(license (license:x11-style
|
||
"http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
|
||
|
||
(define-public hdf5-1.10
|
||
(package (inherit hdf5)
|
||
(version "1.10.4")
|
||
(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 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
|
||
(patches (search-patches "hdf5-config-date.patch"
|
||
"hdf5-mpi-deprecations.patch"))))))
|
||
|
||
(define-public hdf-java
|
||
(package
|
||
(name "hdf-java")
|
||
(version "3.3.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
|
||
version "/src/CMake-hdfjava-" version ".tar.gz"))
|
||
(sha256
|
||
(base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
|
||
(modules '((guix build utils)))
|
||
(snippet ; Make sure we don't use the bundled sources and binaries.
|
||
`(begin
|
||
(for-each delete-file
|
||
(list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
|
||
"HDF4.tar.gz" "HDF5.tar.gz"))
|
||
(delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
|
||
#t))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("jdk" ,icedtea "jdk")
|
||
("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
|
||
;; For tests:
|
||
("hamcrest-core" ,java-hamcrest-core)
|
||
("junit" ,java-junit)
|
||
("slf4j-simple" ,java-slf4j-simple)))
|
||
(inputs
|
||
`(("hdf4" ,hdf4)
|
||
("hdf5" ,hdf5)
|
||
("zlib" ,zlib)
|
||
("libjpeg" ,libjpeg)
|
||
("slf4j-api" ,java-slf4j-api)))
|
||
(arguments
|
||
`(#:configure-flags
|
||
(list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
|
||
(string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
|
||
(assoc-ref %build-inputs "jdk") "/lib" )
|
||
(string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
|
||
(string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
|
||
|
||
#:make-flags
|
||
(list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
|
||
(string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
|
||
(string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
|
||
(string-append "JPEGLIB="
|
||
(assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
|
||
"LLEXT=so")
|
||
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'configure 'chdir-to-source
|
||
(lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
|
||
(add-before 'configure 'patch-build
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(substitute* "configure"
|
||
(("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
|
||
(("/bin/cat") (which "cat")))
|
||
;; Set classpath for compilation
|
||
(substitute* '("hdf/hdf5lib/Makefile.in"
|
||
"hdf/hdf5lib/exceptions/Makefile.in"
|
||
"hdf/hdflib/Makefile.in")
|
||
(("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
|
||
(string-append (assoc-ref inputs "slf4j-api")
|
||
"/share/java/slf4j-api.jar")))
|
||
;; Replace outdated config.sub and config.guess:
|
||
(with-directory-excursion "config"
|
||
(for-each (lambda (file)
|
||
(install-file
|
||
(string-append (assoc-ref inputs "automake")
|
||
"/share/automake-"
|
||
,(version-major+minor (package-version automake))
|
||
"/" file) "."))
|
||
'("config.sub" "config.guess")))
|
||
|
||
;; Fix embedded version number
|
||
(let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
|
||
(substitute* "hdf/hdf5lib/H5.java"
|
||
(("1, 8, 19")
|
||
(string-join hdf5version ", "))))
|
||
|
||
(mkdir-p (string-append (assoc-ref outputs "out")))
|
||
;; Set classpath for tests
|
||
(let* ((build-dir (getcwd))
|
||
(lib (string-append build-dir "/lib"))
|
||
(jhdf (string-append lib "/jhdf.jar"))
|
||
(jhdf5 (string-append lib "/jhdf5.jar"))
|
||
(testjars
|
||
(map (lambda (i)
|
||
(string-append (assoc-ref inputs i)
|
||
"/share/java/" i ".jar"))
|
||
'("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
|
||
(class-path
|
||
(string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
|
||
|
||
(substitute* '("test/hdf5lib/Makefile.in"
|
||
"test/hdf5lib/junit.sh.in"
|
||
"examples/runExample.sh.in")
|
||
(("/usr/bin/test")
|
||
(string-append (assoc-ref inputs "coreutils")
|
||
"/bin/test"))
|
||
(("/usr/bin/uname")
|
||
(string-append (assoc-ref inputs "coreutils")
|
||
"/bin/uname"))
|
||
(("CLASSPATH=[^\n]*")
|
||
(string-append "CLASSPATH=" class-path)))
|
||
(setenv "CLASSPATH" class-path))
|
||
#t))
|
||
(add-before 'check 'build-examples
|
||
(lambda _
|
||
(apply invoke `("javac"
|
||
,@(find-files "examples" ".*\\.java"))))))
|
||
|
||
#:parallel-build? #f
|
||
|
||
#:parallel-tests? #f ))
|
||
(home-page "https://support.hdfgroup.org/products/java")
|
||
(synopsis "Java interface for the HDF4 and HDF5 libraries")
|
||
(description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
|
||
the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
|
||
implemented in C.")
|
||
|
||
;; BSD-style license:
|
||
(license (license:x11-style
|
||
"https://support.hdfgroup.org/ftp/HDF5/hdf-java\
|
||
/current/src/unpacked/COPYING"))))
|
||
|
||
(define-public hdf-eos2
|
||
(package
|
||
(name "hdf-eos2")
|
||
(version "19.1.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri "ftp://edhs1.gsfc.nasa.gov\
|
||
/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
|
||
(sha256
|
||
(base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
|
||
(patches (search-patches "hdf-eos2-remove-gctp.patch"
|
||
"hdf-eos2-build-shared.patch"
|
||
"hdf-eos2-fortrantests.patch"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)))
|
||
(inputs
|
||
`(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
|
||
("zlib" ,zlib)
|
||
("libjpeg" ,libjpeg)
|
||
("gctp" ,gctp)))
|
||
(arguments
|
||
`( #:configure-flags '("--enable-install-include" "--enable-shared"
|
||
"CC=h4cc -Df2cFortran" "LIBS=-lgctp")
|
||
#:parallel-tests? #f))
|
||
(home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
|
||
(synopsis "HDF4-based data format for NASA's Earth Observing System")
|
||
(description "HDF-EOS2 is a software library built on HDF4 which supports
|
||
the construction of data structures used in NASA's Earth Observing
|
||
System (Grid, Point and Swath).")
|
||
|
||
;; Source files carry a permissive license header.
|
||
(license (license:non-copyleft home-page))))
|
||
|
||
(define-public hdf-eos5
|
||
(package
|
||
(name "hdf-eos5")
|
||
(version "1.15")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "ftp://edhs1.gsfc.nasa.gov\
|
||
/edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
|
||
(sha256
|
||
(base32
|
||
"1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
|
||
(patches (search-patches "hdf-eos5-build-shared.patch"
|
||
"hdf-eos5-remove-gctp.patch"
|
||
"hdf-eos5-fix-szip.patch"
|
||
"hdf-eos5-fortrantests.patch"))))
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("hdf5" ,hdf5)
|
||
("zlib" ,zlib)
|
||
("gctp" ,gctp)))
|
||
(arguments
|
||
`(#:configure-flags '("--enable-install-include" "--enable-shared"
|
||
"CC=h5cc -Df2cFortran" "LIBS=-lgctp")
|
||
#:parallel-tests? #f))
|
||
(synopsis "HDF5-based data format for NASA's Earth Observing System")
|
||
(description
|
||
"HDF-EOS5 is a software library built on HDF5 to support the construction
|
||
of data structures used in NASA's Earth Observing System (Grid, Point and
|
||
Swath).")
|
||
(home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
|
||
|
||
;; Source files carry a permissive license header.
|
||
(license (license:non-copyleft home-page))))
|
||
|
||
(define-public hdf5-parallel-openmpi
|
||
(package (inherit hdf5)
|
||
(name "hdf5-parallel-openmpi")
|
||
(inputs
|
||
`(("mpi" ,openmpi)
|
||
,@(package-inputs hdf5)))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments hdf5)
|
||
((#:configure-flags flags)
|
||
``("--enable-parallel"
|
||
,@(delete "--enable-cxx"
|
||
(delete "--enable-threadsafe" ,flags))))
|
||
((#:phases phases)
|
||
`(modify-phases ,phases
|
||
(add-after 'build 'mpi-setup
|
||
,%openmpi-setup)
|
||
(add-before 'check 'patch-tests
|
||
(lambda _
|
||
;; OpenMPI's mpirun will exit with non-zero status if it
|
||
;; detects an "abnormal termination", i.e. any process not
|
||
;; calling MPI_Finalize(). Since the test is explicitly
|
||
;; avoiding MPI_Finalize so as not to have at_exit and thus
|
||
;; H5C_flush_cache from being called, mpirun will always
|
||
;; complain, so turn this test off.
|
||
(substitute* "testpar/Makefile"
|
||
(("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
|
||
(string-append front back "\n")))
|
||
(substitute* "tools/h5diff/testph5diff.sh"
|
||
(("/bin/sh") (which "sh")))
|
||
#t))))))
|
||
(synopsis "Management suite for data with parallel IO support")))
|
||
|
||
(define-public h5check
|
||
(package
|
||
(name "h5check")
|
||
(version "2.0.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
|
||
"h5check/src/h5check-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
|
||
(build-system gnu-build-system)
|
||
(inputs `(("hdf5" ,hdf5))) ;h5cc for tests
|
||
(home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
|
||
(synopsis "HDF5 format checker")
|
||
(description "@code{h5check} is a validation tool for verifying that an
|
||
HDF5 file is encoded according to the HDF File Format Specification.")
|
||
(license (license:x11-style "file://COPYING"))))
|
||
|
||
(define-public itpp
|
||
(package
|
||
(name "itpp")
|
||
(version "4.3.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://sourceforge/itpp/itpp/"
|
||
version "/itpp-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
|
||
(build-system cmake-build-system)
|
||
(arguments `(#:tests? #f)) ; Tests require googletest *sources*
|
||
(inputs `(("lapack" ,lapack)
|
||
("fftw" ,fftw)))
|
||
;; FIXME: Even though the fonts are available dvips complains:
|
||
;; "Font cmmi10 not found; characters will be left blank."
|
||
(native-inputs
|
||
`(("texlive" ,texlive-tiny)
|
||
("ghostscript" ,ghostscript)
|
||
("doxygen" ,doxygen)))
|
||
(home-page "http://itpp.sourceforge.net")
|
||
(synopsis "C++ library of maths, signal processing and communication classes")
|
||
(description "IT++ is a C++ library of mathematical, signal processing and
|
||
communication classes and functions. Its main use is in simulation of
|
||
communication systems and for performing research in the area of
|
||
communications. The kernel of the library consists of generic vector and
|
||
matrix classes, and a set of accompanying routines. Such a kernel makes IT++
|
||
similar to MATLAB, GNU Octave or SciPy.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public netcdf
|
||
(package
|
||
(name "netcdf")
|
||
(version "4.4.1.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
|
||
"netcdf-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
|
||
(patches (search-patches "netcdf-date-time.patch"
|
||
"netcdf-tst_h_par.patch"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("m4" ,m4)
|
||
("doxygen" ,doxygen)
|
||
("graphviz" ,graphviz)))
|
||
(inputs
|
||
`(("hdf4" ,hdf4-alt)
|
||
("hdf5" ,hdf5)
|
||
("zlib" ,zlib)
|
||
("libjpeg" ,libjpeg)))
|
||
(arguments
|
||
`(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
|
||
|
||
#:phases (modify-phases %standard-phases
|
||
(add-before 'configure 'fix-source-date
|
||
(lambda _
|
||
;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
|
||
;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
|
||
;; to '1st hour of the current day', and therefore makes the
|
||
;; package not reproducible.
|
||
(substitute* "./configure"
|
||
(("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
|
||
"date --date='@0'"))
|
||
#t))
|
||
(add-after 'configure 'patch-settings
|
||
(lambda _
|
||
;; libnetcdf.settings contains the full filename of the compilers
|
||
;; used to build the library. We truncate the hashes of those
|
||
;; filenames to avoid unnecessary references to the corresponding
|
||
;; store items.
|
||
(substitute* "libnetcdf.settings"
|
||
(("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
|
||
(string-append prefix (string-take hash 10) "...")))
|
||
#t)))
|
||
|
||
#:parallel-tests? #f)) ;various race conditions
|
||
(home-page "http://www.unidata.ucar.edu/software/netcdf/")
|
||
(synopsis "Library for scientific data")
|
||
(description "NetCDF is an interface for scientific data access and a
|
||
software library that provides an implementation of the interface. The netCDF
|
||
library defines a machine-independent format for representing scientific data.
|
||
Together, the interface, library, and format support the creation, access, and
|
||
sharing of scientific data.")
|
||
(license (license:x11-style "file://COPYRIGHT"))))
|
||
|
||
(define-public netcdf-parallel-openmpi
|
||
(package (inherit netcdf)
|
||
(name "netcdf-parallel-openmpi")
|
||
(inputs
|
||
`(("mpi" ,openmpi)
|
||
,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
|
||
(package-inputs netcdf))))
|
||
;; TODO: Replace pkg-config references in nc-config with absolute references
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments netcdf)
|
||
((#:configure-flags flags)
|
||
`(cons* "CC=mpicc" "CXX=mpicxx"
|
||
"--enable-parallel-tests"
|
||
;; Shared libraries not supported with parallel IO.
|
||
"--disable-shared" "--with-pic"
|
||
,flags))))))
|
||
|
||
(define-public netcdf-fortran
|
||
(package
|
||
(name "netcdf-fortran")
|
||
(version "4.4.4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:parallel-tests? #f))
|
||
(inputs
|
||
`(("netcdf" ,netcdf)))
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)))
|
||
(synopsis "Fortran interface for the netCDF library")
|
||
(description (package-description netcdf))
|
||
(home-page (package-home-page netcdf))
|
||
(license (package-license netcdf))))
|
||
|
||
(define-public nlopt
|
||
(package
|
||
(name "nlopt")
|
||
(version "2.4.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(;; Shared libraries are not built by default. They are required to
|
||
;; build the Guile, Octave, and Python bindings.
|
||
#:configure-flags '("--enable-shared")
|
||
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'configure 'set-libnlopt-file-name
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
;; Make sure the Scheme module refers to the library by its
|
||
;; absolute file name (we cannot do that from a snippet
|
||
;; because the expansion of @libdir@ contains
|
||
;; ${exec_prefix}.)
|
||
(let ((out (assoc-ref outputs "out")))
|
||
(substitute* "swig/nlopt.scm.in"
|
||
(("libnlopt")
|
||
(string-append out "/lib/libnlopt")))
|
||
#t))))))
|
||
(inputs `(("guile" ,guile-2.0)))
|
||
(native-inputs `(("pkg-config" ,pkg-config)))
|
||
(home-page "http://ab-initio.mit.edu/wiki/")
|
||
(synopsis "Library for nonlinear optimization")
|
||
(description "NLopt is a library for nonlinear optimization, providing a
|
||
common interface for a number of different free optimization routines available
|
||
online as well as original implementations of various other algorithms.")
|
||
(license license:lgpl2.1+)))
|
||
|
||
(define-public ipopt
|
||
(package
|
||
(name "ipopt")
|
||
(version "3.12.12")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"http://www.coin-or.org/download/source/Ipopt/Ipopt-"
|
||
version".tgz"))
|
||
(sha256
|
||
(base32
|
||
"07yn9rzdswjk8n246qq6ci9ssf2bcplkifcpsfz9j6cdxw9vgbkv"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
;; Make sure we don't use the bundled software.
|
||
'(begin
|
||
(delete-file-recursively "ThirdParty")
|
||
#t))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
'(#:phases (modify-phases %standard-phases
|
||
(add-after 'install 'add--L-flags-in-ipopt.pc
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
;; The '.pc' file lists '-llapack -lblas' in "Libs";
|
||
;; move it to "Libs.private" where it belongs, and add a
|
||
;; '-L' flag for LAPACK.
|
||
(let ((out (assoc-ref outputs "out"))
|
||
(lapack (assoc-ref inputs "lapack")))
|
||
(substitute* (string-append out "/lib/pkgconfig/"
|
||
"ipopt.pc")
|
||
(("Libs: (.*)-llapack -lblas(.*)$" _ before after)
|
||
(string-append "Libs: " before " " after "\n"
|
||
"Libs.private: " before
|
||
"-L" lapack "/lib -llapack -lblas "
|
||
after "\n")))
|
||
#t))))))
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)))
|
||
(inputs
|
||
;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
|
||
`(("lapack" ,lapack))) ;for both libblas and liblapack
|
||
(home-page "http://www.coin-or.org")
|
||
(synopsis "Large-scale nonlinear optimizer")
|
||
(description
|
||
"The Interior Point Optimizer (IPOPT) is a software package for
|
||
large-scale nonlinear optimization. It provides C++, C, and Fortran
|
||
interfaces.")
|
||
(license license:epl1.0)))
|
||
|
||
(define-public clp
|
||
(package
|
||
(name "clp")
|
||
(version "1.17.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://www.coin-or.org/download/source/"
|
||
"Clp/Clp-" version ".tgz"))
|
||
(sha256
|
||
(base32
|
||
"1wdg820g3iikf9344ijwsc8sy6c0m6im42bzzizm6rlmkvnmxhk9"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
;; Make sure we don't use the bundled software.
|
||
'(begin
|
||
(delete-file-recursively "ThirdParty")
|
||
#t))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)
|
||
("pkg-config" ,pkg-config)))
|
||
(inputs
|
||
`(("openblas" ,openblas)))
|
||
(home-page "https://www.coin-or.org")
|
||
(synopsis "Linear programming solver")
|
||
(description
|
||
"CLP is a high quality linear programming solver. Its main strengths are
|
||
its dual and primal Simplex algorithms. It also has a barrier algorithm for
|
||
linear and quadratic objectives. There are limited facilities for nonlinear
|
||
and quadratic objectives using the Simplex algorithm.")
|
||
(license license:epl1.0)))
|
||
|
||
(define-public ceres
|
||
(package
|
||
(name "ceres-solver")
|
||
(version "1.14.0")
|
||
(home-page "http://ceres-solver.org/")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append home-page "ceres-solver-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
;; TODO: Build HTML user documentation and install separately.
|
||
'(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
|
||
"-DBUILD_SHARED_LIBS=ON")
|
||
|
||
#:phases (modify-phases %standard-phases
|
||
(add-before 'configure 'set-library-directory
|
||
(lambda _
|
||
;; Install libraries to lib/, not lib64/.
|
||
(substitute* "internal/ceres/CMakeLists.txt"
|
||
(("set\\(LIB_SUFFIX \"64\"\\)")
|
||
"set(LIB_SUFFIX \"\")"))
|
||
#t)))))
|
||
(native-inputs
|
||
`(("pkg-config" ,pkg-config)))
|
||
(propagated-inputs
|
||
`(("glog" ,glog))) ;for #include <glog/glog.h>
|
||
(inputs
|
||
`(("eigen" ,eigen)
|
||
("blas" ,openblas)
|
||
("lapack" ,lapack)
|
||
("suitesparse" ,suitesparse)
|
||
("gflags" ,gflags)))
|
||
(synopsis "C++ library for solving large optimization problems")
|
||
(description
|
||
"Ceres Solver is a C++ library for modeling and solving large,
|
||
complicated optimization problems. It is a feature rich, mature and
|
||
performant library which has been used in production since 2010. Ceres Solver
|
||
can solve two kinds of problems:
|
||
@enumerate
|
||
@item non-linear least squares problems with bounds constraints;
|
||
@item general unconstrained optimization problems.
|
||
@end enumerate\n")
|
||
(license license:bsd-3)))
|
||
|
||
;; For a fully featured Octave, users are strongly recommended also to install
|
||
;; the following packages: less, ghostscript, gnuplot.
|
||
(define-public octave-cli
|
||
(package
|
||
(name "octave-cli")
|
||
(version "5.1.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/octave/octave-"
|
||
version ".tar.lz"))
|
||
(sha256
|
||
(base32
|
||
"11wwxpy2q1bhxs2v41bqn05i2sb0905cj1xil6mg8l4k2kka4cq6"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("lapack" ,lapack)
|
||
("qhull" ,qhull)
|
||
("readline" ,readline)
|
||
("gl2ps" ,gl2ps)
|
||
("glpk" ,glpk)
|
||
("fftw" ,fftw)
|
||
("fftwf" ,fftwf)
|
||
("arpack" ,arpack-ng)
|
||
("pcre" ,pcre)
|
||
("fltk" ,fltk)
|
||
("fontconfig" ,fontconfig)
|
||
("freetype" ,freetype)
|
||
("hdf5" ,hdf5)
|
||
("libxft" ,libxft)
|
||
("mesa" ,mesa)
|
||
("glu" ,glu)
|
||
("zlib" ,zlib)
|
||
("curl" ,curl)
|
||
("texinfo" ,texinfo)
|
||
("graphicsmagick" ,graphicsmagick)
|
||
("suitesparse" ,suitesparse)
|
||
("libsndfile" ,libsndfile)
|
||
("portaudio" ,portaudio)
|
||
("alsa-lib" ,alsa-lib)))
|
||
(native-inputs
|
||
`(("lzip" ,lzip)
|
||
("gfortran" ,gfortran)
|
||
("pkg-config" ,pkg-config)
|
||
("perl" ,perl)
|
||
;; The following inputs are not actually used in the build process.
|
||
;; However, the ./configure gratuitously tests for their existence and
|
||
;; assumes that programs not present at build time are also not, and
|
||
;; can never be, available at run time! If these inputs are therefore
|
||
;; not present, support for them will be built out. However, Octave
|
||
;; will still run without them, albeit without the features they
|
||
;; provide.
|
||
("less" ,less)
|
||
("ghostscript" ,ghostscript)
|
||
("gnuplot" ,gnuplot)))
|
||
;; Octave code uses this variable to detect directories holding multiple CA
|
||
;; certificates to verify peers with. This is required for the networking
|
||
;; functions that require encryption to work properly.
|
||
(native-search-paths
|
||
(list (search-path-specification
|
||
(variable "CURLOPT_CAPATH")
|
||
(files '("etc/ssl/certs")))))
|
||
(arguments
|
||
`(#:configure-flags
|
||
(list (string-append "--with-shell="
|
||
(assoc-ref %build-inputs "bash")
|
||
"/bin/sh"))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'configure 'configure-makeinfo
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(substitute* "libinterp/corefcn/help.h"
|
||
(("\"makeinfo\"")
|
||
(string-append
|
||
"\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
|
||
#t)))))
|
||
(home-page "https://www.gnu.org/software/octave/")
|
||
(synopsis "High-level language for numerical computation")
|
||
(description "GNU Octave is a high-level interpreted language that is
|
||
specialized for numerical computations. It can be used for both linear and
|
||
non-linear applications and it provides great support for visualizing results.
|
||
Work may be performed both at the interactive command-line as well as via
|
||
script files.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public octave
|
||
(package (inherit octave-cli)
|
||
(name "octave")
|
||
(source (origin
|
||
(inherit (package-source octave-cli))))
|
||
(inputs
|
||
`(("qscintilla" ,qscintilla)
|
||
("qt" ,qtbase)
|
||
,@(package-inputs octave-cli)))
|
||
(native-inputs
|
||
`(("qttools" , qttools) ;for lrelease
|
||
("texlive" ,texlive) ;for texi2dvi
|
||
,@(package-native-inputs octave-cli)))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments octave-cli)
|
||
((#:phases phases)
|
||
`(modify-phases ,phases
|
||
(add-before 'configure 'patch-qscintilla-library-name
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
;; The QScintilla library that the Octave configure script tries
|
||
;; to link with should be named libqscintilla-qt5.so, but the
|
||
;; QScintilla input provides the shared library as
|
||
;; libqscintilla2_qt5.so.
|
||
(substitute* "configure"
|
||
(("qscintilla2-qt5")
|
||
"qscintilla2_qt5"))
|
||
#t))))))))
|
||
|
||
(define-public qtoctave
|
||
(deprecated-package "qtoctave" octave))
|
||
|
||
(define-public opencascade-oce
|
||
(package
|
||
(name "opencascade-oce")
|
||
(version "0.17.2")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/tpaviot/oce.git")
|
||
(commit (string-append "OCE-" version))))
|
||
(file-name (git-file-name name version))
|
||
(patches (search-patches "opencascade-oce-glibc-2.26.patch"))
|
||
(sha256
|
||
(base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
'(#:configure-flags
|
||
(list "-DOCE_TESTING:BOOL=ON"
|
||
"-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
|
||
"-DOCE_DRAW:BOOL=ON"
|
||
(string-append "-DOCE_INSTALL_PREFIX:PATH="
|
||
(assoc-ref %outputs "out"))
|
||
"-UCMAKE_INSTALL_RPATH")))
|
||
(inputs
|
||
`(("freetype" ,freetype)
|
||
("glu" ,glu)
|
||
("libxmu" ,libxmu)
|
||
("mesa" ,mesa)
|
||
("tcl" ,tcl)
|
||
("tk" ,tk)))
|
||
(native-inputs
|
||
`(("python" ,python-wrapper)))
|
||
(home-page "https://github.com/tpaviot/oce")
|
||
(synopsis "Libraries for 3D modeling and numerical simulation")
|
||
(description
|
||
"Open CASCADE is a set of libraries for the development of applications
|
||
dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
|
||
C++ class libraries providing services for 3D surface and solid modeling, CAD
|
||
data exchange, and visualization. It is used for development of specialized
|
||
software dealing with 3D models in design (CAD), manufacturing (CAM),
|
||
numerical simulation (CAE), measurement equipment (CMM), and quality
|
||
control (CAQ) domains.
|
||
|
||
This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
|
||
patches, improvements, and experiments contributed by users over the official
|
||
Open CASCADE library.")
|
||
(license (list license:lgpl2.1; OCE libraries, with an exception for the
|
||
; use of header files; see
|
||
; OCCT_LGPL_EXCEPTION.txt
|
||
license:public-domain; files
|
||
; src/Standard/Standard_StdAllocator.hxx and
|
||
; src/NCollection/NCollection_StdAllocator.hxx
|
||
license:expat; file src/OpenGl/OpenGl_glext.h
|
||
license:bsd-3)))); test framework gtest
|
||
|
||
(define-public gmsh
|
||
(package
|
||
(name "gmsh")
|
||
(version "2.16.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://gmsh.info/src/gmsh-"
|
||
version "-source.tgz"))
|
||
(sha256
|
||
(base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
;; Remove non-free METIS code
|
||
'(begin
|
||
(delete-file-recursively "contrib/Metis")
|
||
#t))))
|
||
(build-system cmake-build-system)
|
||
(propagated-inputs
|
||
`(("fltk" ,fltk)
|
||
("gfortran" ,gfortran)
|
||
("gmp" ,gmp)
|
||
("hdf5" ,hdf5)
|
||
("lapack" ,lapack)
|
||
("mesa" ,mesa)
|
||
("glu" ,glu)
|
||
("opencascade-oce" ,opencascade-oce)
|
||
("libx11" ,libx11)
|
||
("libxext" ,libxext)))
|
||
(inputs
|
||
`(("fontconfig" ,fontconfig)
|
||
("libxft" ,libxft)))
|
||
(arguments
|
||
`(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
|
||
"-DENABLE_BUILD_SHARED:BOOL=ON"
|
||
"-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
|
||
(home-page "http://www.geuz.org/gmsh/")
|
||
(synopsis "3D finite element grid generator")
|
||
(description "Gmsh is a 3D finite element grid generator with a built-in
|
||
CAD engine and post-processor. Its design goal is to provide a fast, light
|
||
and user-friendly meshing tool with parametric input and advanced
|
||
visualization capabilities. Gmsh is built around four modules: geometry,
|
||
mesh, solver and post-processing. The specification of any input to these
|
||
modules is done either interactively using the graphical user interface or in
|
||
ASCII text files using Gmsh's own scripting language.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public maxflow
|
||
(package
|
||
(name "maxflow")
|
||
(version "3.04")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/gerddie/maxflow.git")
|
||
(commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
|
||
(file-name (string-append name "-" version "-checkout"))
|
||
(sha256
|
||
(base32
|
||
"0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
|
||
(build-system cmake-build-system)
|
||
(home-page "http://pub.ist.ac.at/~vnk/software.html")
|
||
(synopsis "Library implementing Maxflow algorithm")
|
||
(description "An implementation of the maxflow algorithm described in
|
||
@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
|
||
Energy Minimization in Computer Vision.\n
|
||
Yuri Boykov and Vladimir Kolmogorov.\n
|
||
In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
|
||
September 2004}")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public petsc
|
||
(package
|
||
(name "petsc")
|
||
(version "3.11.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
;; The *-lite-* tarball does not contain the *large* documentation
|
||
(uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
|
||
"petsc-lite-" version ".tar.gz"))
|
||
(sha256
|
||
(base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx"))))
|
||
(outputs '("out" ; libraries and headers
|
||
"examples")) ; ~30MiB of examples
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("python" ,python-2)))
|
||
(inputs
|
||
`(("gfortran" ,gfortran)
|
||
("lapack" ,lapack)
|
||
("superlu" ,superlu)
|
||
;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
|
||
;; leaving out opengl, as configuration seems to only be for mac
|
||
))
|
||
(arguments
|
||
`(#:test-target "test"
|
||
#:parallel-build? #f ; build is parallel by default
|
||
#:configure-flags
|
||
`("--with-mpi=0"
|
||
"--with-openmp=1"
|
||
"--with-superlu=1")
|
||
#:make-flags
|
||
;; Honor (parallel-job-count) for build. Do not use --with-make-np,
|
||
;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
|
||
(list (format #f "MAKE_NP=~a" (parallel-job-count)))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'configure
|
||
;; PETSc's configure script is actually a python script, so we can't
|
||
;; run it with bash.
|
||
(lambda* (#:key outputs (configure-flags '())
|
||
#:allow-other-keys)
|
||
(let* ((prefix (assoc-ref outputs "out"))
|
||
(flags `(,(string-append "--prefix=" prefix)
|
||
,@configure-flags)))
|
||
(format #t "build directory: ~s~%" (getcwd))
|
||
(format #t "configure flags: ~s~%" flags)
|
||
(apply invoke "./configure" flags))))
|
||
(add-after 'configure 'clean-local-references
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out")))
|
||
(substitute* (find-files "." "^petsc(conf|machineinfo).h$")
|
||
;; Prevent build directory from leaking into compiled code
|
||
(((getcwd)) out)
|
||
;; Scrub timestamp for reproducibility
|
||
((".*Libraries compiled on.*") ""))
|
||
(substitute* (find-files "." "petscvariables")
|
||
;; Do not expose build machine characteristics, set to defaults.
|
||
(("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
|
||
(("NPMAX = [:digit:]+") "NPMAX = 2"))
|
||
#t)))
|
||
(add-after 'install 'clean-install
|
||
;; Try to keep installed files from leaking build directory names.
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out")))
|
||
(substitute* (map (lambda (file)
|
||
(string-append out "/lib/petsc/conf/" file))
|
||
'("petscvariables"))
|
||
(((getcwd)) out))
|
||
;; Make compiler references point to the store
|
||
(substitute* (string-append out "/lib/petsc/conf/petscvariables")
|
||
(("= (gcc|g\\+\\+|gfortran)" _ compiler)
|
||
(string-append "= " (which compiler))))
|
||
;; PETSc installs some build logs, which aren't necessary.
|
||
(for-each (lambda (file)
|
||
(let ((f (string-append out "/lib/petsc/conf/" file)))
|
||
(when (file-exists? f)
|
||
(delete-file f))))
|
||
'("configure.log" "make.log" "gmake.log"
|
||
"test.log" "error.log" "RDict.db"
|
||
"PETScBuildInternal.cmake"
|
||
;; Once installed, should uninstall with Guix
|
||
"uninstall.py"))
|
||
#t)))
|
||
(add-after 'install 'move-examples
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(examples (assoc-ref outputs "examples"))
|
||
(exdir (string-append out "/share/petsc/examples"))
|
||
(exdir' (string-append examples "/share/petsc/examples")))
|
||
(copy-recursively exdir exdir')
|
||
(delete-file-recursively exdir)
|
||
#t))))))
|
||
(home-page "http://www.mcs.anl.gov/petsc")
|
||
(synopsis "Library to solve PDEs")
|
||
(description "PETSc, pronounced PET-see (the S is silent), is a suite of
|
||
data structures and routines for the scalable (parallel) solution of
|
||
scientific applications modeled by partial differential equations.")
|
||
(license (license:non-copyleft
|
||
"http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
|
||
|
||
(define-public petsc-complex
|
||
(package (inherit petsc)
|
||
(name "petsc-complex")
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments petsc)
|
||
((#:configure-flags cf)
|
||
`(cons "--with-scalar-type=complex" ,cf))))
|
||
(synopsis "Library to solve PDEs (with complex scalars)")))
|
||
|
||
(define-public petsc-openmpi
|
||
(package (inherit petsc)
|
||
(name "petsc-openmpi")
|
||
(inputs
|
||
`(("hdf5" ,hdf5-parallel-openmpi)
|
||
("hypre" ,hypre-openmpi)
|
||
("metis" ,metis)
|
||
("mumps" ,mumps-openmpi)
|
||
("openmpi" ,openmpi)
|
||
("scalapack" ,scalapack)
|
||
("scotch" ,pt-scotch32)
|
||
,@(package-inputs petsc)))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments petsc)
|
||
((#:configure-flags cf)
|
||
``("--with-hypre=1"
|
||
"--with-mpiexec=mpirun"
|
||
"--with-metis=1"
|
||
"--with-mumps=1"
|
||
"--with-scalapack=1"
|
||
"--with-ptscotch=1"
|
||
,(string-append "--with-mpi-dir="
|
||
(assoc-ref %build-inputs "openmpi"))
|
||
,(string-append "--with-hdf5-include="
|
||
(assoc-ref %build-inputs "hdf5") "/include")
|
||
,(string-append "--with-hdf5-lib="
|
||
(assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
|
||
,@(delete "--with-mpi=0" ,cf)))
|
||
((#:phases phases)
|
||
`(modify-phases ,phases
|
||
(add-before 'configure 'mpi-setup
|
||
,%openmpi-setup)))))
|
||
(synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
|
||
|
||
(define-public petsc-complex-openmpi
|
||
(package (inherit petsc-complex)
|
||
(name "petsc-complex-openmpi")
|
||
(inputs
|
||
`(("openmpi" ,openmpi)
|
||
,@(package-inputs petsc-complex)))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments petsc-complex)
|
||
((#:configure-flags cf)
|
||
``("--with-mpiexec=mpirun"
|
||
,(string-append "--with-mpi-dir="
|
||
(assoc-ref %build-inputs "openmpi"))
|
||
,@(delete "--with-mpi=0" ,cf)))
|
||
((#:phases phases)
|
||
`(modify-phases ,phases
|
||
(add-before 'configure 'mpi-setup
|
||
,%openmpi-setup)))))
|
||
(synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
|
||
|
||
(define-public python-petsc4py
|
||
(package
|
||
(name "python-petsc4py")
|
||
(version "3.10.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "petsc4py" version))
|
||
(sha256
|
||
(base32
|
||
"094hcnran0r2z1wlvmjswsz3ski1m9kqrl5l0ax8jjhnk55x0flh"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'build 'pre-build
|
||
(lambda _
|
||
;; Define path to PETSc installation.
|
||
(setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
|
||
#t))
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup))))
|
||
(inputs
|
||
`(("petsc" ,petsc-openmpi)
|
||
("python-numpy" ,python-numpy)))
|
||
(home-page "https://bitbucket.org/petsc/petsc4py/")
|
||
(synopsis "Python bindings for PETSc")
|
||
(description "PETSc, the Portable, Extensible Toolkit for
|
||
Scientific Computation, is a suite of data structures and routines for
|
||
the scalable (parallel) solution of scientific applications modeled by
|
||
partial differential equations. It employs the MPI standard for all
|
||
message-passing communication. @code{petsc4py} provides Python
|
||
bindings to almost all functions of PETSc.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python-kiwisolver
|
||
(package
|
||
(name "python-kiwisolver")
|
||
(version "1.0.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "kiwisolver" version))
|
||
(sha256
|
||
(base32
|
||
"0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
|
||
(build-system python-build-system)
|
||
(home-page "https://github.com/nucleic/kiwi")
|
||
(synopsis "Fast implementation of the Cassowary constraint solver")
|
||
(description
|
||
"Kiwi is an efficient C++ implementation of the Cassowary constraint
|
||
solving algorithm. Kiwi has been designed from the ground up to be
|
||
lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
|
||
Cassowary solver with typical use cases gaining a 40x improvement. Memory
|
||
savings are consistently > 5x.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public python2-kiwisolver
|
||
(package-with-python2 python-kiwisolver))
|
||
|
||
(define-public slepc
|
||
(package
|
||
(name "slepc")
|
||
(version "3.11.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("python" ,python-2)
|
||
("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
|
||
(inputs
|
||
`(("arpack" ,arpack-ng)
|
||
("gfortran" ,gfortran)))
|
||
(propagated-inputs
|
||
`(("petsc" ,petsc)))
|
||
(arguments
|
||
`(#:parallel-build? #f ;build is parallel by default
|
||
#:configure-flags
|
||
`(,(string-append "--with-arpack-dir="
|
||
(assoc-ref %build-inputs "arpack") "/lib"))
|
||
#:make-flags ;honor (parallel-job-count)
|
||
`(,(format #f "MAKE_NP=~a" (parallel-job-count))
|
||
,(string-append "PETSCCONFIGDIR="
|
||
(assoc-ref %build-inputs "petsc:examples")
|
||
"/share/petsc/examples/config"))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'configure
|
||
;; configure is a python script, so we can't run it with bash.
|
||
(lambda* (#:key inputs outputs (configure-flags '())
|
||
#:allow-other-keys)
|
||
(let* ((prefix (assoc-ref outputs "out"))
|
||
(flags `(,(string-append "--prefix=" prefix)
|
||
,@configure-flags)))
|
||
(format #t "build directory: ~s~%" (getcwd))
|
||
(format #t "configure flags: ~s~%" flags)
|
||
(setenv "SLEPC_DIR" (getcwd))
|
||
(setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
|
||
(apply invoke "./configure" flags))))
|
||
(add-after 'install 'delete-doc
|
||
;; TODO: SLEPc installs HTML documentation alongside headers in
|
||
;; $out/include. We'd like to move them to share/doc, but delete
|
||
;; them for now, as they are incomplete and installing the complete
|
||
;; documentation is difficult.
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out")))
|
||
(for-each delete-file (find-files out "\\.html$"))
|
||
#t)))
|
||
(add-after 'install 'clean-install
|
||
;; Clean up unnecessary build logs from installation.
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out")))
|
||
(for-each (lambda (file)
|
||
(let ((f (string-append out "/lib/slepc/conf/" file)))
|
||
(when (file-exists? f)
|
||
(delete-file f))))
|
||
'("configure.log" "make.log" "gmake.log"
|
||
"test.log" "error.log" "RDict.db"
|
||
"uninstall.py"))
|
||
#t))))))
|
||
(home-page "http://slepc.upv.es")
|
||
(synopsis "Scalable library for eigenproblems")
|
||
(description "SLEPc is a software library for the solution of large sparse
|
||
eigenproblems on parallel computers. It can be used for the solution of
|
||
linear eigenvalue problems formulated in either standard or generalized form,
|
||
as well as other related problems such as the singular value decomposition.
|
||
The emphasis of the software is on methods and techniques appropriate for
|
||
problems in which the associated matrices are sparse, for example, those
|
||
arising after the discretization of partial differential equations.")
|
||
(license license:bsd-2)))
|
||
|
||
(define-public slepc-complex
|
||
(package (inherit slepc)
|
||
(name "slepc-complex")
|
||
(propagated-inputs
|
||
`(("petsc" ,petsc-complex)
|
||
,@(alist-delete "petsc" (package-propagated-inputs slepc))))
|
||
(synopsis "Scalable library for eigenproblems (with complex scalars)")))
|
||
|
||
(define-public slepc-openmpi
|
||
(package (inherit slepc)
|
||
(name "slepc-openmpi")
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments slepc)
|
||
((#:phases phases '%standard-phases)
|
||
`(modify-phases ,phases
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup)))))
|
||
(inputs
|
||
`(("mpi" ,openmpi)
|
||
("arpack" ,arpack-ng-openmpi)
|
||
,@(alist-delete "arpack" (package-inputs slepc))))
|
||
(propagated-inputs
|
||
`(("petsc" ,petsc-openmpi)
|
||
,@(alist-delete "petsc" (package-propagated-inputs slepc))))
|
||
(synopsis "Scalable library for eigenproblems (with MPI support)")))
|
||
|
||
(define-public slepc-complex-openmpi
|
||
(package (inherit slepc-openmpi)
|
||
(name "slepc-complex-openmpi")
|
||
(propagated-inputs
|
||
`(("petsc" ,petsc-complex-openmpi)
|
||
,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
|
||
(synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
|
||
|
||
(define-public python-slepc4py
|
||
(package
|
||
(name "python-slepc4py")
|
||
(version "3.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (pypi-uri "slepc4py" version))
|
||
(sha256
|
||
(base32
|
||
"0x049dyc8frgh79fvvavf4vlbqp4mgm61nsaivzdav4316vvlv1j"))))
|
||
(build-system python-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'build 'pre-build
|
||
(lambda _
|
||
;; Define path to PETSc installation.
|
||
(setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
|
||
;; Define path to SLEPc installation.
|
||
(setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
|
||
#t))
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup))))
|
||
(inputs
|
||
`(("python-numpy" ,python-numpy)
|
||
("python-petsc4py" ,python-petsc4py)
|
||
("slepc" ,slepc-openmpi)))
|
||
(home-page "https://bitbucket.org/slepc/slepc4py/")
|
||
(synopsis "Python bindings for SLEPc")
|
||
(description "SLEPc, the Scalable Library for Eigenvalue Problem
|
||
Computations, is based on PETSc, the Portable, Extensible Toolkit for
|
||
Scientific Computation. It employs the MPI standard for all
|
||
message-passing communication. @code{slepc4py} provides Python
|
||
bindings to almost all functions of SLEPc.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public mumps
|
||
(package
|
||
(name "mumps")
|
||
(version "5.1.2")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1s9asin08zqzmh08257sdghhivvy9vjif7c53fhaxaax2kd5qd7b"))
|
||
(patches (search-patches "mumps-build-parallelism.patch"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("fortran" ,gfortran)
|
||
;; These are required for linking against mumps, but we let the user
|
||
;; declare the dependency.
|
||
("blas" ,openblas)
|
||
("metis" ,metis)
|
||
("scotch" ,scotch)))
|
||
(arguments
|
||
`(#:modules ((ice-9 match)
|
||
(ice-9 popen)
|
||
(srfi srfi-1)
|
||
,@%gnu-build-system-modules)
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'configure
|
||
(lambda* (#:key inputs #:allow-other-keys)
|
||
(call-with-output-file "Makefile.inc"
|
||
(lambda (port)
|
||
(format port "
|
||
PLAT =
|
||
LIBEXT = .a
|
||
OUTC = -o
|
||
OUTF = -o
|
||
RM = rm -f~:[
|
||
CC = gcc
|
||
FC = gfortran
|
||
FL = gfortran
|
||
INCSEQ = -I$(topdir)/libseq
|
||
LIBSEQ = -L$(topdir)/libseq -lmpiseq
|
||
LIBSEQNEEDED = libseqneeded~;
|
||
CC = mpicc
|
||
FC = mpifort
|
||
FL = mpifort~]
|
||
AR = ar vr # rules require trailing space, ugh...
|
||
RANLIB = ranlib
|
||
LIBBLAS = -L~a -lopenblas~@[
|
||
SCALAP = -L~a -lscalapack~]
|
||
LIBOTHERS = -pthread
|
||
CDEFS = -DAdd_
|
||
PIC = -fPIC
|
||
OPTF = -O2 -DALLOW_NON_INIT $(PIC)
|
||
OPTL = -O2 $(PIC)
|
||
OPTC = -O2 $(PIC)
|
||
INCS = $(INCSEQ)
|
||
LIBS = $(SCALAP) $(LIBSEQ)
|
||
LPORDDIR = $(topdir)/PORD/lib
|
||
IPORD = -I$(topdir)/PORD/include
|
||
LPORD = -L$(LPORDDIR) -lpord
|
||
ORDERINGSF = -Dpord~@[
|
||
METISDIR = ~a
|
||
IMETIS = -I$(METISDIR)/include
|
||
LMETIS = -L$(METISDIR)/lib -lmetis
|
||
ORDERINGSF += -Dmetis~]~@[~:{
|
||
SCOTCHDIR = ~a
|
||
ISCOTCH = -I$(SCOTCHDIR)/include
|
||
LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
|
||
ORDERINGSF += ~a~}~]
|
||
ORDERINGSC = $(ORDERINGSF)
|
||
LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
|
||
IORDERINGSF = $(ISCOTCH)
|
||
IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
|
||
(assoc-ref inputs "mpi")
|
||
(assoc-ref inputs "blas")
|
||
(assoc-ref inputs "scalapack")
|
||
(assoc-ref inputs "metis")
|
||
(match (list (assoc-ref inputs "pt-scotch")
|
||
(assoc-ref inputs "scotch"))
|
||
((#f #f)
|
||
#f)
|
||
((#f scotch)
|
||
`((,scotch "" "-Dscotch")))
|
||
((ptscotch _)
|
||
`((,ptscotch
|
||
"-lptesmumps -lptscotch -lptscotcherr "
|
||
"-Dptscotch")))))))))
|
||
(replace 'build
|
||
;; By default only the d-precision library is built. Make with "all"
|
||
;; target so that all precision libraries and examples are built.
|
||
(lambda _
|
||
(invoke "make" "all"
|
||
(format #f "-j~a" (parallel-job-count)))))
|
||
(replace 'check
|
||
;; Run the simple test drivers, which read test input from stdin:
|
||
;; from the "real" input for the single- and double-precision
|
||
;; testers, and from the "cmplx" input for complex-precision
|
||
;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
|
||
;; package to prefix execution with "mpirun".
|
||
(lambda* (#:key (exec-prefix '()) #:allow-other-keys)
|
||
(with-directory-excursion "examples"
|
||
(every
|
||
(lambda (prec type)
|
||
(let ((tester (apply open-pipe*
|
||
`(,OPEN_WRITE
|
||
,@exec-prefix
|
||
,(string-append "./" prec
|
||
"simpletest"))))
|
||
(input (open-input-file
|
||
(string-append "input_simpletest_" type))))
|
||
(begin
|
||
(dump-port input tester)
|
||
(close-port input)
|
||
(zero? (close-pipe tester)))))
|
||
'("s" "d" "c" "z")
|
||
'("real" "real" "cmplx" "cmplx")))))
|
||
(replace 'install
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(libdir (string-append out "/lib")))
|
||
(copy-recursively "lib" libdir)
|
||
(copy-recursively "include" (string-append out "/include"))
|
||
(when (file-exists? "libseq/libmpiseq.a")
|
||
(install-file "libseq/libmpiseq.a" libdir))
|
||
#t))))))
|
||
(home-page "http://mumps.enseeiht.fr")
|
||
(synopsis "Multifrontal sparse direct solver")
|
||
(description
|
||
"MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
|
||
sparse system of linear equations A x = b using Gaussian elimination.")
|
||
(license license:cecill-c)))
|
||
|
||
(define-public mumps-metis
|
||
(package (inherit mumps)
|
||
(name "mumps-metis")
|
||
(inputs
|
||
(alist-delete "scotch" (package-inputs mumps)))))
|
||
|
||
(define-public mumps-openmpi
|
||
(package (inherit mumps)
|
||
(name "mumps-openmpi")
|
||
(inputs
|
||
`(("mpi" ,openmpi)
|
||
("scalapack" ,scalapack)
|
||
("pt-scotch" ,pt-scotch)
|
||
,@(alist-delete "scotch" (package-inputs mumps))))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments mumps)
|
||
((#:phases phases)
|
||
`(modify-phases ,phases
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup)
|
||
(replace 'check
|
||
(lambda _
|
||
((assoc-ref ,phases 'check)
|
||
#:exec-prefix '("mpirun" "-n" "2"))))))))
|
||
(synopsis "Multifrontal sparse direct solver (with MPI)")))
|
||
|
||
(define-public mumps-metis-openmpi
|
||
(package (inherit mumps-openmpi)
|
||
(name "mumps-metis-openmpi")
|
||
(inputs
|
||
(alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
|
||
|
||
(define-public r-quadprog
|
||
(package
|
||
(name "r-quadprog")
|
||
(version "1.5-7")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "quadprog" version))
|
||
(sha256
|
||
(base32
|
||
"0vg7i9p241bwvfdspjbydjrsvgipl6nsb8bjigp0hbbgvxbixx0s"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)))
|
||
(home-page "https://cran.r-project.org/web/packages/quadprog")
|
||
(synopsis "Functions to solve quadratic programming problems")
|
||
(description
|
||
"This package contains routines and documentation for solving quadratic
|
||
programming problems.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-pracma
|
||
(package
|
||
(name "r-pracma")
|
||
(version "2.2.5")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "pracma" version))
|
||
(sha256
|
||
(base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g"))))
|
||
(build-system r-build-system)
|
||
(home-page "https://cran.r-project.org/web/packages/pracma/")
|
||
(synopsis "Practical numerical math functions")
|
||
(description "This package provides functions for numerical analysis and
|
||
linear algebra, numerical optimization, differential equations, plus some
|
||
special functions. It uses Matlab function names where appropriate to simplify
|
||
porting.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public ruby-asciimath
|
||
(package
|
||
(name "ruby-asciimath")
|
||
(version "1.0.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (rubygems-uri "asciimath" version))
|
||
(sha256
|
||
(base32
|
||
"1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
|
||
(build-system ruby-build-system)
|
||
(arguments
|
||
'(#:phases
|
||
(modify-phases %standard-phases
|
||
;; Apply this patch
|
||
;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
|
||
(add-after 'unpack 'patch-remove-spurious-backslashes
|
||
(lambda _
|
||
(substitute* "spec/parser_spec.rb"
|
||
(("\\\\\"")
|
||
"\""))
|
||
#t)))))
|
||
(native-inputs
|
||
`(("bundler" ,bundler)
|
||
("ruby-rspec" ,ruby-rspec)))
|
||
(synopsis "AsciiMath parsing and conversion library")
|
||
(description
|
||
"A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
|
||
easy-to-write markup language for mathematics.")
|
||
(home-page "https://github.com/asciidoctor/asciimath")
|
||
(license license:expat)))
|
||
|
||
(define-public superlu
|
||
(package
|
||
(name "superlu")
|
||
(version "5.2.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
|
||
"superlu_" version ".tar.gz"))
|
||
(sha256
|
||
(base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
;; Replace the non-free implementation of MC64 with a stub adapted
|
||
;; from Debian
|
||
'(begin
|
||
(use-modules (ice-9 regex)
|
||
(ice-9 rdelim))
|
||
(call-with-output-file "SRC/mc64ad.c"
|
||
(lambda (port)
|
||
(display "
|
||
#include <stdio.h>
|
||
#include <stdlib.h>
|
||
void mc64id_(int *a) {
|
||
fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
|
||
abort ();
|
||
}
|
||
void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
|
||
int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
|
||
fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
|
||
abort ();
|
||
}\n" port)))
|
||
;; Remove the corresponding license verbiage. MC64 license follows
|
||
;; a "------" line separator.
|
||
(with-atomic-file-replacement "License.txt"
|
||
(let ((rx (make-regexp "-{8}")))
|
||
(lambda (in out)
|
||
(let loop ()
|
||
(let ((line (read-line in 'concat)))
|
||
(unless (regexp-exec rx line)
|
||
(display line out)
|
||
(loop))))
|
||
#t)))))))
|
||
(build-system cmake-build-system)
|
||
(native-inputs
|
||
`(("tcsh" ,tcsh)))
|
||
(inputs
|
||
`(("blas" ,openblas)
|
||
("gfortran" ,gfortran)))
|
||
(arguments
|
||
`(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
|
||
"-DTPL_BLAS_LIBRARIES=openblas"
|
||
"-DBUILD_SHARED_LIBS:BOOL=YES")))
|
||
(home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
|
||
(synopsis "Supernodal direct solver for sparse linear systems")
|
||
(description
|
||
"SuperLU is a general purpose library for the direct solution of large,
|
||
sparse, nonsymmetric systems of linear equations on high performance machines.
|
||
The library is written in C and is callable from either C or Fortran. The
|
||
library routines perform an LU decomposition with partial pivoting and
|
||
triangular system solves through forward and back substitution. The library
|
||
also provides threshold-based ILU factorization preconditioners.")
|
||
(license (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 "6.1.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
|
||
"superlu_dist_" version ".tar.gz"))
|
||
(sha256
|
||
(base32 "0pqgcgh1yxhfzs99fas3mggajzd5wca3nbyp878rziy74gfk03dl"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
;; Replace the non-free implementation of MC64 with a stub
|
||
'(begin
|
||
(call-with-output-file "SRC/mc64ad_dist.c"
|
||
(lambda (port)
|
||
(display "
|
||
#include <stdio.h>
|
||
#include <stdlib.h>
|
||
void mc64id_dist(int *a) {
|
||
fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
|
||
abort ();
|
||
}
|
||
void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
|
||
int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
|
||
fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
|
||
abort ();
|
||
}\n" port)))
|
||
(substitute* "SRC/util.c" ;adjust default algorithm
|
||
(("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
|
||
;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
|
||
;; general (i.e. non-square) processor-grid support.
|
||
"RowPerm = NOROWPERM;"))
|
||
#t))
|
||
(patches (search-patches "superlu-dist-scotchmetis.patch"
|
||
"superlu-dist-awpm-grid.patch"
|
||
"superlu-dist-fix-mpi-deprecations.patch"))))
|
||
(build-system cmake-build-system)
|
||
(native-inputs
|
||
`(("tcsh" ,tcsh)))
|
||
(inputs
|
||
`(("gfortran" ,gfortran)
|
||
("blas" ,openblas)
|
||
("lapack" ,lapack)
|
||
("combblas" ,combinatorial-blas)))
|
||
(propagated-inputs
|
||
`(("mpi" ,openmpi) ;headers include MPI heades
|
||
("parmetis" ,pt-scotch32 "metis")
|
||
("pt-scotch" ,pt-scotch32)))
|
||
(arguments
|
||
`(#:parallel-tests? #f ;tests use MPI and OpenMP
|
||
#:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
|
||
"-DTPL_ENABLE_COMBBLASLIB=YES"
|
||
"-DTPL_BLAS_LIBRARIES=-lopenblas"
|
||
"-DTPL_LAPACK_LIBRARIES=-llapack"
|
||
(string-append "-DTPL_PARMETIS_LIBRARIES="
|
||
(string-join
|
||
'("ptscotchparmetis" "ptscotch" "ptscotcherr"
|
||
"scotchmetis" "scotch" "scotcherr")
|
||
";"))
|
||
(string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
|
||
(assoc-ref %build-inputs "parmetis")
|
||
"/include")
|
||
"-DTPL_ENABLE_COMBBLASLIB=ON"
|
||
(string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
|
||
(assoc-ref %build-inputs "combblas")
|
||
"/include/CombBLAS;"
|
||
(assoc-ref %build-inputs "combblas")
|
||
"/include/BipartiteMatchings")
|
||
"-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'configure 'set-c++-standard
|
||
(lambda _
|
||
(substitute* "CMakeLists.txt"
|
||
;; AWPM headers require C++14
|
||
(("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup)
|
||
(add-before 'check 'omp-setup
|
||
(lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
|
||
(home-page (package-home-page superlu))
|
||
(synopsis "Parallel supernodal direct solver")
|
||
(description
|
||
"SuperLU_DIST is a parallel extension to the serial SuperLU library.
|
||
It is targeted for distributed memory parallel machines. SuperLU_DIST is
|
||
implemented in ANSI C, and MPI for communications.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public scotch
|
||
(package
|
||
(name "scotch")
|
||
(version "6.0.6")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://gforge.inria.fr/frs/download.php/"
|
||
"latestfile/298/scotch_" version ".tar.gz"))
|
||
(sha256
|
||
(base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8"))
|
||
(patches (search-patches "scotch-build-parallelism.patch"
|
||
"scotch-integer-declarations.patch"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("zlib" ,zlib)
|
||
("flex" ,flex)
|
||
("bison" ,bison)))
|
||
(outputs '("out" "metis"))
|
||
(arguments
|
||
`(#:make-flags (list (string-append "prefix=" %output))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after
|
||
'unpack 'chdir-to-src
|
||
(lambda _ (chdir "src") #t))
|
||
(replace
|
||
'configure
|
||
(lambda _
|
||
(call-with-output-file "Makefile.inc"
|
||
(lambda (port)
|
||
(format port "
|
||
EXE =
|
||
LIB = .a
|
||
OBJ = .o
|
||
MAKE = make
|
||
AR = ar
|
||
ARFLAGS = -ruv
|
||
CAT = cat
|
||
CCS = gcc
|
||
CCP = mpicc
|
||
CCD = gcc
|
||
CPPFLAGS =~{ -D~a~}
|
||
CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
|
||
LDFLAGS = -lz -lm -lrt -lpthread
|
||
CP = cp
|
||
LEX = flex -Pscotchyy -olex.yy.c
|
||
LN = ln
|
||
MKDIR = mkdir
|
||
MV = mv
|
||
RANLIB = ranlib
|
||
YACC = bison -pscotchyy -y -b y
|
||
"
|
||
'("COMMON_FILE_COMPRESS_GZ"
|
||
"COMMON_PTHREAD"
|
||
"COMMON_RANDOM_FIXED_SEED"
|
||
"INTSIZE64" ;use 'int64_t'
|
||
;; Prevents symbolc clashes with libesmumps
|
||
"SCOTCH_RENAME"
|
||
;; XXX: Causes invalid frees in superlu-dist tests
|
||
;; "SCOTCH_PTHREAD"
|
||
;; "SCOTCH_PTHREAD_NUMBER=2"
|
||
"restrict=__restrict"))))
|
||
#t))
|
||
(add-after 'build 'build-esmumps
|
||
(lambda _
|
||
(invoke "make"
|
||
(format #f "-j~a" (parallel-job-count))
|
||
"esmumps")))
|
||
(add-before 'install 'make-install-dirs
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(mkdir (assoc-ref outputs "out"))))
|
||
(add-after 'install 'install-metis
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "metis")))
|
||
(mkdir out)
|
||
;; metis files are not installed with 'make install'
|
||
(for-each (lambda (f)
|
||
(install-file f (string-append out "/include")))
|
||
(find-files "../include/" ".*metis\\.h"))
|
||
(for-each (lambda (f)
|
||
(install-file f (string-append out "/lib")))
|
||
(find-files "../lib/" ".*metis\\..*"))
|
||
#t))))))
|
||
(home-page "http://www.labri.fr/perso/pelegrin/scotch/")
|
||
(synopsis "Programs and libraries for graph algorithms")
|
||
(description "SCOTCH is a set of programs and libraries which implement
|
||
the static mapping and sparse matrix reordering algorithms developed within
|
||
the SCOTCH project. Its purpose is to apply graph theory, with a divide and
|
||
conquer approach, to scientific computing problems such as graph and mesh
|
||
partitioning, static mapping, and sparse matrix ordering, in application
|
||
domains ranging from structural mechanics to operating systems or
|
||
bio-chemistry.")
|
||
;; See LICENSE_en.txt
|
||
(license license:cecill-c)))
|
||
|
||
(define-public 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)
|
||
((#:phases scotch-phases)
|
||
`(modify-phases ,scotch-phases
|
||
(replace
|
||
'configure
|
||
(lambda _
|
||
(call-with-output-file "Makefile.inc"
|
||
(lambda (port)
|
||
(format port "
|
||
EXE =
|
||
LIB = .a
|
||
OBJ = .o
|
||
MAKE = make
|
||
AR = ar
|
||
ARFLAGS = -ruv
|
||
CAT = cat
|
||
CCS = gcc
|
||
CCP = mpicc
|
||
CCD = gcc
|
||
CPPFLAGS =~{ -D~a~}
|
||
CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
|
||
LDFLAGS = -lz -lm -lrt -lpthread
|
||
CP = cp
|
||
LEX = flex -Pscotchyy -olex.yy.c
|
||
LN = ln
|
||
MKDIR = mkdir
|
||
MV = mv
|
||
RANLIB = ranlib
|
||
YACC = bison -pscotchyy -y -b y
|
||
"
|
||
'("COMMON_FILE_COMPRESS_GZ"
|
||
"COMMON_PTHREAD"
|
||
"COMMON_RANDOM_FIXED_SEED"
|
||
"INTSIZE32" ;use 32-bit integers. See INSTALL.txt
|
||
;; Prevents symbolc clashes with libesmumps
|
||
"SCOTCH_RENAME"
|
||
;; XXX: Causes invalid frees in superlu-dist tests
|
||
;; "SCOTCH_PTHREAD"
|
||
;; "SCOTCH_PTHREAD_NUMBER=2"
|
||
"restrict=__restrict"))))))))))
|
||
(synopsis
|
||
"Programs and libraries for graph algorithms (32-bit integers)")))
|
||
|
||
(define-public pt-scotch
|
||
(package (inherit scotch)
|
||
(name "pt-scotch")
|
||
(propagated-inputs
|
||
`(("openmpi" ,openmpi))) ;Headers include MPI headers
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments scotch)
|
||
((#:phases scotch-phases)
|
||
`(modify-phases ,scotch-phases
|
||
(replace
|
||
'build
|
||
(lambda _
|
||
(invoke "make" (format #f "-j~a" (parallel-job-count))
|
||
"ptscotch" "ptesmumps")
|
||
|
||
;; Install the serial metis compatibility library
|
||
(invoke "make" "-C" "libscotchmetis" "install")))
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup)
|
||
(replace 'check
|
||
(lambda _
|
||
(invoke "make" "ptcheck")))))))
|
||
(synopsis "Programs and libraries for graph algorithms (with MPI)")))
|
||
|
||
(define-public pt-scotch32
|
||
(package (inherit scotch32)
|
||
(name "pt-scotch32")
|
||
(propagated-inputs
|
||
`(("openmpi" ,openmpi))) ;headers include MPI headers
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments scotch32)
|
||
((#:phases scotch32-phases)
|
||
`(modify-phases ,scotch32-phases
|
||
(replace 'build
|
||
(lambda _
|
||
(invoke "make" (format #f "-j~a" (parallel-job-count))
|
||
"ptscotch" "ptesmumps")
|
||
;; Install the serial metis compatibility library
|
||
(invoke "make" "-C" "libscotchmetis" "install")))
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup)
|
||
(replace 'check
|
||
(lambda _
|
||
(invoke "make" "ptcheck")))))))
|
||
(synopsis
|
||
"Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
|
||
|
||
(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"))))
|
||
(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
|
||
(package
|
||
(name "gsegrafix")
|
||
(version "1.0.6")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/" name "/" name "-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:configure-flags '("LDFLAGS=-lm")))
|
||
(inputs
|
||
`(("libgnomecanvas" ,libgnomecanvas)
|
||
("libbonoboui" ,libbonoboui)
|
||
("libgnomeui" ,libgnomeui)
|
||
("libgnomeprintui" ,libgnomeprintui)
|
||
("popt" ,popt)))
|
||
(native-inputs
|
||
`(("pkg-config" ,pkg-config)))
|
||
(home-page "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 "5.43.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
|
||
version "-source/" name "-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0xyahp4c6509haxh4n1swiqm3421gplkdisa0zypclh3252sbzfw"))
|
||
(patches (search-patches "maxima-defsystem-mkdir.patch"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("gcl" ,gcl)
|
||
("gnuplot" ,gnuplot) ;for plots
|
||
("sed" ,sed)
|
||
("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
|
||
(native-inputs
|
||
`(("texinfo" ,texinfo)
|
||
("perl" ,perl)
|
||
("python" ,python)))
|
||
(arguments
|
||
`(#:configure-flags
|
||
(list "--enable-gcl"
|
||
(string-append "--with-posix-shell="
|
||
(assoc-ref %build-inputs "bash")
|
||
"/bin/sh")
|
||
(string-append "--with-wish="
|
||
(assoc-ref %build-inputs "tk")
|
||
"/bin/wish"
|
||
(let ((v ,(package-version tk)))
|
||
(string-take v (string-index-right v #\.)))))
|
||
;; By default Maxima attempts to write temporary files to
|
||
;; '/tmp/nix-build-maxima-*', 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 (string-append (assoc-ref inputs "sed") "/bin/sed"))
|
||
(coreutils (assoc-ref inputs "coreutils"))
|
||
(dirname (string-append coreutils "/bin/dirname"))
|
||
(head (string-append coreutils "/bin/head"))
|
||
(perl (string-append (assoc-ref inputs "perl") "/bin/perl"))
|
||
(python (string-append (assoc-ref inputs "python")
|
||
"/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=gcl "
|
||
"--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 (string-append (assoc-ref inputs "binutils")
|
||
"/bin")))
|
||
(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 "http://maxima.sourceforge.net")
|
||
(synopsis "Numeric and symbolic expression manipulation")
|
||
(description "Maxima is a system for the manipulation of symbolic and
|
||
numerical expressions. It yields high precision numeric results by using
|
||
exact fractions, arbitrary precision integers, and variable precision floating
|
||
point numbers.")
|
||
;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
|
||
;; Others simply say "GNU General Public License" without stating a
|
||
;; version (which implicitly means gpl1+).
|
||
;; At least one file (src/maxima.asd) says "version 2."
|
||
;; GPLv2 only is therefore the smallest subset.
|
||
(license license:gpl2)))
|
||
|
||
(define-public wxmaxima
|
||
(package
|
||
(name "wxmaxima")
|
||
(version "19.05.7")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/wxMaxima-developers/wxmaxima.git")
|
||
(commit (string-append "Version-" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0zaz71fh156b9inrxf86scnix247al5pl9v18cxhjxcm0lanqxdp"))))
|
||
(build-system cmake-build-system)
|
||
(native-inputs
|
||
`(("gettext" ,gettext-minimal)))
|
||
(inputs
|
||
`(("wxwidgets" ,wxwidgets)
|
||
("maxima" ,maxima)
|
||
;; Runtime support.
|
||
("adwaita-icon-theme" ,adwaita-icon-theme)
|
||
("gtk+" ,gtk+)
|
||
("shared-mime-info" ,shared-mime-info)))
|
||
(arguments
|
||
`(#:tests? #f ; no check target
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(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://andrejv.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 (eg. 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.git")
|
||
(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 "0.3.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
|
||
version "%20version.tar.gz"))
|
||
(file-name (string-append name "-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"062kg4ny1ywz7k5grpb4pbf0hba0w6manbajwkmv4f477a31sxpl"))))
|
||
(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
|
||
;; 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 non-x86 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))
|
||
'("DYNAMIC_ARCH=1"))
|
||
;; 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"))
|
||
;; On aarch64 force the generic 'armv8-a' target
|
||
((string-prefix? "aarch64" system)
|
||
'("TARGET=ARMV8"))
|
||
(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" (assoc-ref inputs "fortran-lib")
|
||
"/lib"))
|
||
#t)))))
|
||
(inputs
|
||
`(("fortran-lib" ,gfortran "lib")))
|
||
(native-inputs
|
||
`(("cunit" ,cunit)
|
||
("fortran" ,gfortran)
|
||
("perl" ,perl)))
|
||
(home-page "http://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* (make-blis implementation #:optional substitutable?)
|
||
"Return a BLIS package with the given IMPLEMENTATION (see config/ in the
|
||
source tree for a list of implementations.)
|
||
|
||
SUBSTITUTABLE? determines whether the package is made available as a
|
||
substitute.
|
||
|
||
Currently the specialization must be selected at configure-time, but work is
|
||
underway to allow BLIS to select the right optimized kernels at run time:
|
||
<https://github.com/flame/blis/issues/129>."
|
||
(package
|
||
(name (if (string=? implementation "reference")
|
||
"blis"
|
||
(string-append "blis-" implementation)))
|
||
(version "0.2.2")
|
||
(home-page "https://github.com/flame/blis")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference (url home-page) (commit version)))
|
||
(sha256
|
||
(base32
|
||
"1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
|
||
(file-name (git-file-name "blis" version))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:test-target "test"
|
||
|
||
#:substitutable? ,substitutable?
|
||
|
||
#:phases (modify-phases %standard-phases
|
||
(replace 'configure
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
;; This is a home-made 'configure' script.
|
||
(let ((out (assoc-ref outputs "out")))
|
||
(invoke "./configure" "-p" out
|
||
"-d" "opt"
|
||
"--disable-static"
|
||
"--enable-shared"
|
||
"--enable-threading=openmp"
|
||
|
||
,implementation))))
|
||
(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
|
||
;; This is the "reference" implementation, which is the non-optimized but
|
||
;; portable variant (no assembly).
|
||
(make-blis "reference" #t))
|
||
|
||
(define ignorance blis)
|
||
|
||
(define-syntax-rule (blis/x86_64 processor)
|
||
"Expand to a package specialized for PROCESSOR."
|
||
(package
|
||
(inherit (make-blis processor))
|
||
(supported-systems '("x86_64-linux"))))
|
||
|
||
(define-public blis-sandybridge
|
||
;; BLIS specialized for Sandy Bridge processors (launched 2011):
|
||
;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
|
||
(blis/x86_64 "sandybridge"))
|
||
|
||
(define-public blis-haswell
|
||
;; BLIS specialized for Haswell processors (launched 2013):
|
||
;; <http://ark.intel.com/products/codename/42174/Haswell>.
|
||
(blis/x86_64 "haswell"))
|
||
|
||
(define-public blis-knl
|
||
;; BLIS specialized for Knights Landing processor (launched 2016):
|
||
;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
|
||
(blis/x86_64 "knl"))
|
||
|
||
|
||
(define-public openlibm
|
||
(package
|
||
(name "openlibm")
|
||
(version "0.6.0")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/JuliaLang/openlibm.git")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "08wfchmmr5200fvmn1kwq9byc1fhsq46hn0y5k8scdl74771c7gh"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:make-flags
|
||
(list (string-append "prefix=" (assoc-ref %outputs "out")))
|
||
#:phases
|
||
;; no configure script
|
||
(modify-phases %standard-phases (delete 'configure))
|
||
#:tests? #f)) ;the tests are part of the default target
|
||
(home-page "http://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.git")
|
||
(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 "4.5.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
|
||
(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 "CC=gcc"
|
||
"BLAS=-lblas"
|
||
"TBB=-ltbb"
|
||
"MY_METIS_LIB=-lmetis"
|
||
(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
|
||
`(("tbb" ,tbb)
|
||
("lapack" ,lapack)
|
||
("metis" ,metis)))
|
||
(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"))
|
||
(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.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public glm
|
||
(package
|
||
(name "glm")
|
||
(version "0.9.9.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://github.com/g-truc/glm/releases/download/"
|
||
version "/glm-" version ".zip"))
|
||
(sha256
|
||
(base32
|
||
"1vmg7hb4xvsa77zpbwiw6lqc7pyaj56dihx6xriny5b9rrh4iqsg"))))
|
||
(build-system cmake-build-system)
|
||
(native-inputs
|
||
`(("unzip" ,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+)))
|
||
|
||
(define-public dealii
|
||
(package
|
||
(name "dealii")
|
||
(version "9.0.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://github.com/dealii/dealii/releases/"
|
||
"download/v" version "/dealii-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0r7f8rhl3xr94imd372plizdcbqk0a70w73lwc3vw912dxk0sbyz"))
|
||
(patches (search-patches "dealii-mpi-deprecations.patch"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
|
||
'(begin
|
||
(delete-file-recursively "bundled")
|
||
#t))))
|
||
(build-system cmake-build-system)
|
||
(inputs
|
||
`(("tbb" ,tbb)
|
||
("zlib" ,zlib)
|
||
("boost" ,boost)
|
||
("p4est" ,p4est)
|
||
("blas" ,openblas)
|
||
("lapack" ,lapack)
|
||
("arpack" ,arpack-ng)
|
||
("muparser" ,muparser)
|
||
("gfortran" ,gfortran)
|
||
("suitesparse" ,suitesparse))) ;for UMFPACK
|
||
(arguments
|
||
`(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
|
||
#:configure-flags
|
||
;; Work around a bug in libsuitesparseconfig linking
|
||
;; see https://github.com/dealii/dealii/issues/4745
|
||
'("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
|
||
(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
|
||
`(("mpi" ,openmpi)
|
||
;;Supported only with MPI:
|
||
("hdf5" ,hdf5-parallel-openmpi) ;TODO: have petsc-openmpi propagate?
|
||
("p4est" ,p4est-openmpi)
|
||
("petsc" ,petsc-openmpi)
|
||
("slepc" ,slepc-openmpi)
|
||
("metis" ,metis) ;for MUMPS
|
||
("scalapack" ,scalapack) ;for MUMPS
|
||
("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
|
||
("arpack" ,arpack-ng-openmpi)
|
||
,@(fold alist-delete (package-inputs dealii)
|
||
'("p4est" "arpack"))))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments dealii)
|
||
((#:configure-flags cf)
|
||
`(cons "-DDEAL_II_WITH_MPI:BOOL=ON"
|
||
,cf))
|
||
((#:phases phases '%standard-phases)
|
||
`(modify-phases ,phases
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup)))))
|
||
(synopsis "Finite element library (with MPI support)")))
|
||
|
||
(define-public flann
|
||
(package
|
||
(name "flann")
|
||
(version "1.8.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri
|
||
(string-append
|
||
"http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
|
||
version "-src.zip"))
|
||
(sha256
|
||
(base32
|
||
"022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
|
||
(patches (search-patches "flann-cmake-3.11.patch"))))
|
||
(build-system cmake-build-system)
|
||
(outputs '("out"
|
||
"octave")) ;46 MiB .mex file that pulls Octave
|
||
(native-inputs
|
||
`(("unzip" ,unzip)))
|
||
(inputs
|
||
`(("hdf5" ,hdf5)
|
||
("octave" ,octave-cli)
|
||
("python" ,python-2) ; print syntax
|
||
;; ("python2-numpy" ,python2-numpy) ; only required for the tests
|
||
("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-before 'configure 'set-octave-directory
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
;; Install the .mex file in the "octave" output.
|
||
(let ((out (assoc-ref outputs "octave")))
|
||
(substitute* "src/matlab/CMakeLists.txt"
|
||
(("share/flann/octave")
|
||
(string-append out "/share/flann/octave")))
|
||
#t)))
|
||
(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.
|
||
(home-page "http://www.cs.ubc.ca/research/flann/")
|
||
(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
|
||
`(("mpfr" ,mpfr)
|
||
("readline" ,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 "3.6")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://sourceforge/xaos/XaoS/" version
|
||
"/xaos-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs `(("gettext" ,gettext-minimal)))
|
||
(inputs `(("libx11" ,libx11)
|
||
("zlib" ,zlib)
|
||
("libpng" ,libpng)
|
||
("gsl" ,gsl)))
|
||
(arguments
|
||
`(#:tests? #f ;no "check" target
|
||
#:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
|
||
(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://www.gnu.org/software/xaos/")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public hypre
|
||
(package
|
||
(name "hypre")
|
||
(version "2.15.1")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/LLNL/hypre.git")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32 "1lvh4ybqkriyqfg2zmic6mrg1981qv1i9vry1fdgsabn81hb71g4"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(begin
|
||
;; Remove use of __DATE__ and __TIME__ for reproducibility;
|
||
;; substitute the release date.
|
||
(substitute* "src/utilities/HYPRE_utilities.h"
|
||
(("Date Compiled: .*$")
|
||
"Date Compiled: Oct 19 2018 15:23:00 +0000\"\n"))
|
||
#t))))
|
||
(build-system gnu-build-system)
|
||
(outputs '("out" ; 6.1 MiB of headers and libraries
|
||
"doc")) ; 4.8 MiB of documentation
|
||
(native-inputs
|
||
`(("doc++" ,doc++)
|
||
("netpbm" ,netpbm)
|
||
("perl" ,perl) ; needed to run 'ppmquant' during tests
|
||
("texlive" ,(texlive-union (list texlive-generic-xypic
|
||
texlive-fonts-xypic
|
||
texlive-latex-hyperref
|
||
texlive-bibtex)))
|
||
("ghostscript" ,ghostscript)))
|
||
(inputs
|
||
`(("blas" ,openblas)
|
||
("lapack" ,lapack)))
|
||
(arguments
|
||
`(#:modules ((srfi srfi-1)
|
||
,@%gnu-build-system-modules)
|
||
#:configure-flags '("--enable-shared"
|
||
"--disable-fortran"
|
||
"--without-MPI"
|
||
"--with-openmp"
|
||
"--with-fei"
|
||
"--with-lapack"
|
||
"--with-blas")
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'build 'set-HOME
|
||
(lambda _
|
||
;; FIXME: texlive-union does not find the built
|
||
;; metafonts, so it tries to generate them in HOME.
|
||
(setenv "HOME" "/tmp")
|
||
#t))
|
||
(add-before 'configure 'chdir-src
|
||
(lambda _ (chdir "src")))
|
||
(replace 'configure
|
||
(lambda* (#:key build target configure-flags
|
||
#:allow-other-keys #:rest args)
|
||
(let* ((configure (assoc-ref %standard-phases 'configure)))
|
||
(apply configure
|
||
(append args
|
||
(list #:configure-flags
|
||
(cons (string-append
|
||
"--host=" (or target build))
|
||
configure-flags)))))))
|
||
(add-after 'build 'build-docs
|
||
(lambda _
|
||
(invoke "make" "-Cdocs" "pdf" "html")))
|
||
(replace 'check
|
||
(lambda _
|
||
(setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
|
||
(setenv "PATH" (string-append "." ":" (getenv "PATH")))
|
||
(invoke "make" "check" "CHECKRUN=")
|
||
(for-each (lambda (filename)
|
||
(let ((size (stat:size (stat filename))))
|
||
(when (positive? size)
|
||
(error (format #f "~a size ~d; error indication~%"
|
||
filename size)))))
|
||
(find-files "test" ".*\\.err$"))
|
||
#t))
|
||
(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 base docdir)) ; html docs
|
||
'("HYPRE_usr_manual"
|
||
"HYPRE_ref_manual")))
|
||
#t))))))
|
||
(home-page "http://www.llnl.gov/casc/hypre/")
|
||
(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
|
||
`(("mpi" ,openmpi)
|
||
,@(package-inputs hypre)))
|
||
(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 "1.5.6")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://sourceforge/matio/matio/" version "/"
|
||
"matio-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("zlib" ,zlib)
|
||
("hdf5" ,hdf5)))
|
||
(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 "1.3.3")
|
||
(source
|
||
(origin (method url-fetch)
|
||
(uri (string-append "https://github.com/VcDevel/Vc/releases/"
|
||
"download/" version "/Vc-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1zmlpn32jzb38smp3j834llmbix3whsrbw0h397qxysbw792kih8"))))
|
||
(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")))
|
||
(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
|
||
`(("openlibm" ,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 "1c4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
|
||
version ".zip"))
|
||
(sha256 (base32
|
||
"055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
|
||
(patches (search-patches "jacal-fix-texinfo.patch"))))
|
||
(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 "./configure"
|
||
(string-append "--prefix="
|
||
(assoc-ref outputs "out"))))))))
|
||
(inputs `(("scm" ,scm)))
|
||
(native-inputs `(("unzip" ,unzip)
|
||
("texinfo" ,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 "4.8.4")
|
||
(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
|
||
"014igqm5vwswz0yhz0cdxsj3a6dh7i79hvhgc3jmmmz3z0xm1gyn"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(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"
|
||
(string-append "--prefix=" (assoc-ref outputs "out")))))
|
||
(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 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 "http://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.git")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
|
||
(build-system cmake-build-system)
|
||
(home-page "http://libelemental.org")
|
||
(native-inputs
|
||
`(("gfortran" ,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 "201707.1.15162")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://www.mcrl2.org/download/devel/mcrl2-"
|
||
version
|
||
".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1ziww2fchsklm25hl9p2mngssxfh9w07nc114cncqaxfibqp2p8f"))))
|
||
(native-inputs
|
||
`(("subversion" ,subversion)))
|
||
(inputs
|
||
`(("boost" ,boost)
|
||
("glu" ,glu)
|
||
("mesa" ,mesa)
|
||
("qtbase" ,qtbase)))
|
||
(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 r-subplex
|
||
(package
|
||
(name "r-subplex")
|
||
(version "1.5-4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "subplex" version))
|
||
(sha256
|
||
(base32
|
||
"10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)))
|
||
(home-page "https://cran.r-project.org/web/packages/subplex")
|
||
(synopsis "Unconstrained optimization using the subplex algorithm")
|
||
(description "This package implements the Subplex optimization algorithm.
|
||
It solves unconstrained optimization problems using a simplex method on
|
||
subspaces. The method is well suited for optimizing objective functions that
|
||
are noisy or are discontinuous at the solution.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public r-desolve
|
||
(package
|
||
(name "r-desolve")
|
||
(version "1.21")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (cran-uri "deSolve" version))
|
||
(sha256
|
||
(base32
|
||
"0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"))))
|
||
(properties `((upstream-name . "deSolve")))
|
||
(build-system r-build-system)
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)))
|
||
(home-page "https://desolve.r-forge.r-project.org/")
|
||
(synopsis "Solvers for initial value problems of differential equations")
|
||
(description "This package provides functions that solve initial
|
||
value problems of a system of first-order ordinary differential equations (ODE),
|
||
of partial differential equations (PDE), of differential algebraic equations
|
||
(DAE), and of delay differential equations. The functions provide an interface
|
||
to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
|
||
to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
|
||
the Runge-Kutta family with fixed or variable time steps. The package contains
|
||
routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
|
||
differential equations (PDE) that have been converted to ODEs by numerical
|
||
differencing.")
|
||
(license license:gpl2+)))
|
||
|
||
(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 sundials
|
||
(package
|
||
(name "sundials")
|
||
(version "3.1.1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
|
||
"sundials-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
|
||
(build-system cmake-build-system)
|
||
(native-inputs
|
||
`(("python" ,python-2))) ;for tests; syntax incompatible with python 3
|
||
(inputs
|
||
`(("fortran" ,gfortran) ;for fcmix
|
||
("blas" ,openblas)
|
||
("suitesparse" ,suitesparse))) ;TODO: Add hypre
|
||
(arguments
|
||
`(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
|
||
"-DEXAMPLES_ENABLE_CXX:BOOL=ON"
|
||
"-DEXAMPLES_ENABLE_F77:BOOL=ON"
|
||
"-DEXAMPLES_ENABLE_F90:BOOL=ON"
|
||
"-DEXAMPLES_INSTALL:BOOL=OFF"
|
||
|
||
"-DFCMIX_ENABLE:BOOL=ON"
|
||
|
||
"-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"))))
|
||
(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.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public sundials-openmpi
|
||
(package (inherit sundials)
|
||
(name "sundials-openmpi")
|
||
(inputs
|
||
`(("mpi" ,openmpi)
|
||
("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
|
||
,@(package-inputs sundials)))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments sundials)
|
||
((#:configure-flags flags '())
|
||
`(cons* "-DMPI_ENABLE:BOOL=ON"
|
||
"-DPETSC_ENABLE:BOOL=ON"
|
||
(string-append "-DPETSC_INCLUDE_DIR="
|
||
(assoc-ref %build-inputs "petsc")
|
||
"/include")
|
||
(string-append "-DPETSC_LIBRARY_DIR="
|
||
(assoc-ref %build-inputs "petsc")
|
||
"/lib")
|
||
,flags))
|
||
((#:phases phases '%standard-phases)
|
||
`(modify-phases ,phases
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup)))))
|
||
(synopsis "SUNDIALS with OpenMPI support")))
|
||
|
||
(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 "2.6.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://dune-project.org/download/"
|
||
version "/dune-common-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"019wcr1qf7jwyxx1y5y290wdlglylskvbb2m01ljkzcza2xnlmhw"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-tests
|
||
(lambda* (#:key make-flags #:allow-other-keys)
|
||
(apply invoke "make" "build_tests" make-flags)))
|
||
;; These tests fail because they require a fully functional MPI
|
||
;; environment.
|
||
(add-after 'unpack 'disable-failing-tests
|
||
(lambda _
|
||
(setenv "ARGS"
|
||
(string-append "--exclude-regex '("
|
||
(string-join
|
||
(list
|
||
"remoteindicestest"
|
||
"remoteindicestest-mpi-2"
|
||
"syncertest"
|
||
"syncertest-mpi-2"
|
||
"variablesizecommunicatortest"
|
||
"variablesizecommunicatortest-mpi-2"
|
||
"arithmetictestsuitetest"
|
||
"assertandreturntest"
|
||
"assertandreturntest_ndebug"
|
||
"concept"
|
||
"debugaligntest"
|
||
"mpicollectivecommunication"
|
||
"mpicollectivecommunication-mpi-2"
|
||
"mpiguardtest"
|
||
"mpiguardtest-mpi-2"
|
||
"mpihelpertest"
|
||
"mpihelpertest-mpi-2"
|
||
"mpihelpertest2"
|
||
"mpihelpertest2-mpi-2")
|
||
"|")
|
||
")'"))
|
||
#t)))))
|
||
(inputs
|
||
`(("gmp" ,gmp)
|
||
("metis" ,metis)
|
||
("openmpi" ,openmpi)
|
||
("openblas" ,openblas)
|
||
("python" ,python)
|
||
("superlu" ,superlu)))
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)
|
||
("pkg-config" ,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 "2.6.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://dune-project.org/download/"
|
||
version "/dune-geometry-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0hlaaxjyv9j05blasvb67sy02hd0w4g9znf68gdh3l731dd1aqbn"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-tests
|
||
(lambda* (#:key make-flags #:allow-other-keys)
|
||
(apply invoke "make" "build_tests" make-flags))))))
|
||
(inputs
|
||
`(("dune-common" ,dune-common)
|
||
("openmpi" ,openmpi)
|
||
;; Optional
|
||
("openblas" ,openblas)
|
||
("gmp" ,gmp)
|
||
("python" ,python)))
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)
|
||
("pkg-config" ,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-grid
|
||
(package
|
||
(name "dune-grid")
|
||
(version "2.6.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://dune-project.org/download/"
|
||
version "/dune-grid-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1jp4vscm9yb9xg0lh7apzccfkhvgbnk652yahigmh3cvzpl4acd0"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-tests
|
||
(lambda* (#:key make-flags #:allow-other-keys)
|
||
(apply invoke "make" "build_tests" make-flags)))
|
||
;; These tests fail because they require a fully functional MPI
|
||
;; environment.
|
||
(add-after 'unpack 'disable-failing-tests
|
||
(lambda _
|
||
(setenv "ARGS"
|
||
(string-append "--exclude-regex '("
|
||
(string-join
|
||
(list
|
||
"scsgmappertest"
|
||
"conformvolumevtktest"
|
||
"gnuplottest"
|
||
"nonconformboundaryvtktest"
|
||
"subsamplingvtktest"
|
||
"vtktest"
|
||
"vtktest-mpi-2"
|
||
"vtksequencetest"
|
||
"gmshtest-onedgrid"
|
||
"test-dgf-yasp"
|
||
"test-dgf-yasp-offset"
|
||
"test-dgf-oned"
|
||
"test-geogrid-yaspgrid"
|
||
"test-gridinfo"
|
||
"test-identitygrid"
|
||
"testiteratorranges"
|
||
"test-hierarchicsearch"
|
||
"test-parallel-ug-mpi-2"
|
||
"test-yaspgrid-backuprestore-equidistant"
|
||
"test-yaspgrid-backuprestore-equidistant-mpi-2"
|
||
"test-yaspgrid-backuprestore-equidistantoffset"
|
||
"test-yaspgrid-backuprestore-equidistantoffset-mpi-2"
|
||
"test-yaspgrid-backuprestore-tensor"
|
||
"test-yaspgrid-backuprestore-tensor-mpi-2"
|
||
"test-yaspgrid-tensorgridfactory"
|
||
"test-yaspgrid-tensorgridfactory-mpi-2"
|
||
"test-yaspgrid-yaspfactory-1d"
|
||
"test-yaspgrid-yaspfactory-1d-mpi-2"
|
||
"test-yaspgrid-yaspfactory-2d"
|
||
"test-yaspgrid-yaspfactory-2d-mpi-2"
|
||
"test-yaspgrid-yaspfactory-3d"
|
||
"test-yaspgrid-yaspfactory-3d-mpi-2"
|
||
"globalindexsettest"
|
||
"persistentcontainertest"
|
||
"structuredgridfactorytest"
|
||
"tensorgridfactorytest"
|
||
"vertexordertest")
|
||
"|")
|
||
")'"))
|
||
#t)))))
|
||
(inputs
|
||
`(("dune-common" ,dune-common)
|
||
("dune-geometry" ,dune-geometry)
|
||
("gmp" ,gmp)
|
||
("metis" ,metis)
|
||
("openblas" ,openblas)
|
||
("openmpi" ,openmpi)
|
||
("python" ,python)))
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)
|
||
("pkg-config" ,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 "2.6.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://dune-project.org/download/"
|
||
version "/dune-istl-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0l2gyrvys5w6wsmk0ckbb7295s80b7yk7qrl7x66akv2jv1nzq2w"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-tests
|
||
(lambda* (#:key make-flags #:allow-other-keys)
|
||
(apply invoke "make" "build_tests" make-flags)))
|
||
;; These tests fail because they require a fully functional MPI
|
||
;; environment.
|
||
(add-after 'unpack 'disable-failing-tests
|
||
(lambda _
|
||
(setenv "ARGS"
|
||
(string-append "--exclude-regex '("
|
||
(string-join
|
||
(list
|
||
"galerkintest"
|
||
"hierarchytest"
|
||
"pamgtest"
|
||
"pamg_comm_repart_test"
|
||
"matrixredisttest"
|
||
"vectorcommtest"
|
||
"matrixmarkettest")
|
||
"|")
|
||
")'"))
|
||
#t)))))
|
||
(inputs
|
||
`(("dune-common" ,dune-common)
|
||
("openmpi" ,openmpi)
|
||
;; Optional
|
||
("metis" ,metis)
|
||
("superlu" ,superlu)
|
||
("openblas" ,openblas)
|
||
("gmp" ,gmp)
|
||
("python" ,python)))
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)
|
||
("pkg-config" ,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 "2.6.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://dune-project.org/download/"
|
||
version "/dune-localfunctions-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"19c6zjinwwpy8jh4v4prhphyd438rapd4x80fj93apmwgw04nrhl"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-tests
|
||
(lambda* (#:key make-flags #:allow-other-keys)
|
||
(apply invoke "make" "build_tests" make-flags))))))
|
||
(inputs
|
||
`(("dune-common" ,dune-common)
|
||
("dune-geometry" ,dune-geometry)
|
||
("openmpi" ,openmpi)
|
||
;; Optional
|
||
("metis" ,metis)
|
||
("superlu" ,superlu)
|
||
("gmp" ,gmp)))
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)
|
||
("pkg-config" ,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
|
||
(package
|
||
(name "dune-alugrid")
|
||
(version "2.6.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://dune-project.org/download/"
|
||
version "/dune-alugrid-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:tests? #f ; 7 of 8 tests fail because they need a full MPI
|
||
; environment
|
||
#: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 inputs make-flags #:allow-other-keys)
|
||
(setenv "CPLUS_INCLUDE_PATH"
|
||
(string-append (assoc-ref inputs "dune-grid") "/share:"
|
||
(getenv "CPLUS_INCLUDE_PATH")))
|
||
(apply invoke "make" "build_tests" make-flags))))))
|
||
(inputs
|
||
`(("dune-common" ,dune-common)
|
||
("dune-geometry" ,dune-geometry)
|
||
("dune-grid" ,dune-grid)
|
||
("openmpi" ,openmpi)
|
||
;; Optional
|
||
("metis" ,metis)
|
||
("openblas" ,openblas)
|
||
("python" ,python)
|
||
("superlu" ,superlu)
|
||
("gmp" ,gmp)
|
||
("zlib" ,zlib)))
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)
|
||
("pkg-config" ,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-typetree
|
||
(package
|
||
(name "dune-typetree")
|
||
(version "2.6.0")
|
||
(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
|
||
"0mnv6w2f22lz3j4bdpdjq55vjm8xxfx9v4vvhg9bd36xpsbjpjp9"))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-tests
|
||
(lambda* (#:key make-flags #:allow-other-keys)
|
||
(apply invoke "make" "build_tests" make-flags))))))
|
||
(inputs
|
||
`(("dune-common" ,dune-common)
|
||
("openmpi" ,openmpi)
|
||
;; Optional
|
||
("openblas" ,openblas)
|
||
("python" ,python)
|
||
("metis" ,metis)
|
||
("superlu" ,superlu)
|
||
("gmp" ,gmp)))
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)
|
||
("pkg-config" ,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 "2.6.0")
|
||
(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
|
||
"1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200"))))
|
||
(build-system cmake-build-system)
|
||
(arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid
|
||
(inputs
|
||
`(("dune-common" ,dune-common)
|
||
("dune-istl" ,dune-istl)
|
||
("dune-localfunctions" ,dune-localfunctions)
|
||
("dune-grid" ,dune-grid)
|
||
("dune-geometry" ,dune-geometry)
|
||
("dune-typetree" ,dune-typetree)
|
||
("openmpi" ,openmpi)
|
||
("openblas" ,openblas)
|
||
("metis" ,metis)
|
||
("python" ,python)
|
||
("superlu" ,superlu)
|
||
("gmp" ,gmp)))
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)
|
||
("pkg-config" ,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
|
||
(package
|
||
(name "dune-pdelab")
|
||
(version "2.6.0-rc1")
|
||
(source
|
||
(origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"07g0s9448z65vjrq88g5rv3340iifil85k170n8kbqchsvi4ny5v"))))
|
||
(build-system cmake-build-system)
|
||
(arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
|
||
(inputs
|
||
`(("dune-common" ,dune-common)
|
||
("dune-istl" ,dune-istl)
|
||
("dune-localfunctions" ,dune-localfunctions)
|
||
("dune-geometry" ,dune-geometry)
|
||
("dune-grid" ,dune-grid)
|
||
("dune-typetree" ,dune-typetree)
|
||
("dune-functions" ,dune-functions)
|
||
("openmpi" ,openmpi)
|
||
;; Optional
|
||
("openblas" ,openblas)
|
||
("eigen" ,eigen)
|
||
("metis" ,metis)
|
||
("python" ,python)
|
||
("superlu" ,superlu)
|
||
("gmp" ,gmp)))
|
||
(native-inputs
|
||
`(("gfortran" ,gfortran)
|
||
("pkg-config" ,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-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
|
||
`(("python2" ,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 "2.6r11")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://pallini.di.uniroma1.it/"
|
||
"nauty" (string-join (string-split version #\.) "")
|
||
".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"05z6mk7c31j70md83396cdjmvzzip1hqb88pfszzc6k4gy8h3m2y"))))
|
||
(build-system gnu-build-system)
|
||
(outputs '("out" "lib"))
|
||
(arguments
|
||
`(#:test-target "checks"
|
||
#: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))
|
||
'("dreadnaut" "NRswitchg" "addedgeg" "amtog" "biplabg"
|
||
"blisstog" "bliss2dre" "catg" "checks6" "complg"
|
||
"converseg" "copyg" "countg" "cubhamg" "deledgeg"
|
||
"delptg" "directg" "dretodot" "dretog" "genbg"
|
||
"genbgL" "geng" "genquarticg" "genrang" "genspecialg"
|
||
"gentourng" "gentreeg" "hamheuristic" "labelg"
|
||
"linegraphg" "listg" "multig" "newedgeg" "pickg"
|
||
"planarg" "ranlabg" "shortg" "showg" "subdivideg"
|
||
"sumlines" "twohamg" "vcolg" "watercluster2"))
|
||
(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
|
||
`(("gmp" ,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
|
||
`(("m4", m4)))
|
||
(inputs
|
||
`(("glpk" ,glpk)
|
||
("gmp", 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+)))
|