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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015, 2016, 2019, 2020 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, 2020 Eric Bavier <bavier@posteo.net>
;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 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, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2018, 2020 Kei Kebreau <kkebreau@posteo.net>
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
;;; Copyright © 2017, 2018, 2019, 2020 Paul Garlick <pgarlick@tourbillion-technology.com>
;;; Copyright © 2017 Nikita <nikita@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, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
;;; Copyright © 2018, 2019 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, 2020 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>
;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;; Copyright © 2020 Felix Gruber <felgru@posteo.net>
;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com>
;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
;;;
;;; 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 glib-or-gtk)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
#:use-module (guix build-system ruby)
#:use-module (gnu packages algebra)
#:use-module (gnu packages audio)
#:use-module (gnu packages autotools)
#:use-module (gnu packages base)
#:use-module (gnu packages bison)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages cmake)
#:use-module (gnu packages compression)
#:use-module (gnu packages curl)
#:use-module (gnu packages cyrus-sasl)
#:use-module (gnu packages dbm)
#:use-module (gnu packages documentation)
#:use-module (gnu packages elf)
#:use-module (gnu packages file)
#:use-module (gnu packages flex)
#:use-module (gnu packages fltk)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gettext)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gd)
#:use-module (gnu packages ghostscript)
#:use-module (gnu packages glib)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages gtk)
#:use-module (gnu packages icu4c)
#:use-module (gnu packages image)
#:use-module (gnu packages java)
#:use-module (gnu packages less)
#:use-module (gnu packages lisp)
#:use-module (gnu packages linux)
#:use-module (gnu packages 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 onc-rpc)
#: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 "2019.1")
(source (origin
(method url-fetch)
(uri (string-append "http://www.qhull.org/download/qhull-"
(car (string-split version #\.))
"-src-7.3.2.tgz"))
(sha256
(base32
"1ys3vh3qq0v9lh452xb932vp63advds1pxk42lk7cc1niiar0y9b"))))
(build-system cmake-build-system)
(synopsis "Calculate convex hulls and related structures")
(description
"@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
diagram, halfspace intersection about a point, furthest-site Delaunay
triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d,
3-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull
algorithm for computing the convex hull. It handles roundoff errors from
floating point arithmetic. It computes volumes, surface areas, and
approximations to the convex hull.
@code{Qhull} does not support triangulation of non-convex surfaces, mesh
generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
triangulations.")
(home-page "http://qhull.org")
(license (license:non-copyleft "file://COPYING.txt"
"See COPYING in the distribution."))))
(define-public python-cvxopt
(package
(name "python-cvxopt")
(version "1.2.3")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/cvxopt/cvxopt")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1kiy2m62xgs2d5id6dnnwy4vap85cd70p7pgkb9nh23qf9xnak7b"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'find-libraries
(lambda* (#:key inputs #:allow-other-keys)
(setenv "CVXOPT_BLAS_LIB" "openblas")
(setenv "CVXOPT_BUILD_FFTW" "1")
(setenv "CVXOPT_BUILD_GLPK" "1")
(setenv "CVXOPT_BUILD_GSL" "1")
#t)))))
(inputs
`(("fftw" ,fftw)
("glpk" ,glpk)
("gsl" ,gsl)
("lapack" ,lapack)
("openblas" ,openblas)
("suitesparse" ,suitesparse)))
(home-page "https://www.cvxopt.org")
(synopsis "Python library for convex optimization")
(description
"CVXOPT is a package for convex optimization based on the Python
programming language. Its main purpose is to make the development of software
for convex optimization applications straightforward by building on Python’s
extensive standard library and on the strengths of Python as a high-level
programming language.")
(license license:gpl3+)))
(define-public python2-cvxopt
(package-with-python2 python-cvxopt))
(define-public units
(package
(name "units")
(version "2.19")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/units/units-" version
".tar.gz"))
(sha256 (base32
"0mk562g7dnidjgfgvkxxpvlba66fh1ykmfd9ylzvcln1vxmi6qj2"))))
(build-system gnu-build-system)
(inputs
`(("readline" ,readline)
("python" ,python-wrapper) ;for 'units_cur' script
("python-requests" ,python-requests)))
(arguments
`(#:phases (modify-phases %standard-phases
(add-after 'install 'wrap-units_cur
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(wrap-program (string-append bin "/units_cur")
`("PYTHONPATH" ":" prefix
,(search-path-as-string->list (getenv "PYTHONPATH"))))
#t))))))
(synopsis "Conversion between thousands of scales")
(description
"GNU Units converts numeric quantities between units of measure. It
can handle scale changes through adaptive usage of standard scale
prefixes (micro-, kilo-, etc.). It can also handle nonlinear
conversions such as Fahrenheit to Celsius. Its interpreter is powerful
enough to be used effectively as a scientific calculator.")
(license license:gpl3+)
(home-page "https://www.gnu.org/software/units/")))
(define-public double-conversion
(package
(name "double-conversion")
(version "3.1.5")
(home-page "https://github.com/google/double-conversion")
(source (origin
(method git-fetch)
(uri (git-reference (url home-page)
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0csy4pjw1p8rp6g5qxi2h0ychhhp1fldv7gb761627fs2mclw9gv"))))
(build-system cmake-build-system)
(arguments
'(#:test-target "test"
#:configure-flags '("-DBUILD_SHARED_LIBS=ON"
"-DBUILD_TESTING=ON")))
(synopsis "Conversion routines for IEEE doubles")
(description
"The double-conversion library provides binary-decimal and decimal-binary
routines for IEEE doubles. The library consists of efficient conversion
routines that have been extracted from the V8 JavaScript engine.")
(license license:bsd-3)))
(define-public dionysus
(package
(name "dionysus")
(version "1.4.0")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/dionysus/dionysus-" version
".tar.xz"))
(sha256
(base32
"194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
(build-system gnu-build-system)
(inputs `(("tcl" ,tcl))) ;for 'tclsh'
(synopsis "Local search for universal constants and scientific values")
(description
"GNU Dionysus is a convenient system for quickly retrieving the values of
mathematical constants used in science and engineering. Values can be
searched using a simple command-line tool, choosing from three databases:
universal constants, atomic numbers, and constants related to
semiconductors.")
(license license:gpl3+)
(home-page "https://www.gnu.org/software/dionysus/")))
(define-public dsfmt
(package
(name "dsfmt")
(version "2.2.3")
(source
(origin
(method url-fetch)
(uri
(string-append
"http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/"
"dSFMT-src-" version ".tar.gz"))
(sha256
(base32
"03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))
(modules '((guix build utils)))
;; Don't distribute html documentation with bundled jquery.
(snippet
'(begin
(delete-file-recursively "html") #t))
;; Add patches borrowed from Julia.
(patches
(list
(origin
(method url-fetch)
(uri (string-append
"https://raw.githubusercontent.com/JuliaLang/julia/"
"v1.3.0/deps/patches/dSFMT.c.patch"))
(sha256 (base32
"09mhv11bms8jsmkmdqvlcgljwhzw3b6n9nncpi2b6dla9798hw2y"))
(file-name "dSFMT.c.patch"))
(origin
(method url-fetch)
(uri (string-append
"https://raw.githubusercontent.com/JuliaLang/julia/"
"v1.3.0/deps/patches/dSFMT.h.patch"))
(sha256 (base32
"1py5rd0yxic335lzka23f6x2dhncrpizpyrk57gi2f28c0p98y5n"))
(file-name "dSFMT.h.patch"))))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(delete 'configure) ; no configure script
(replace 'build
;; Upstream Makefile does not build a shared library. Borrow from Julia
;; https://github.com/JuliaLang/julia/blob/v1.3.0/deps/dsfmt.mk
(lambda _
(invoke
"gcc" "-DNDEBUG" "-DDSFMT_MEXP=19937"
"-fPIC" "-DDSFMT_DO_NOT_USE_OLD_NAMES"
"-O3" "-finline-functions" "-fomit-frame-pointer"
"-fno-strict-aliasing" "--param" "max-inline-insns-single=1800"
"-Wmissing-prototypes" "-Wall" "-std=c99" "-shared" "dSFMT.c"
"-o" "libdSFMT.so")))
(replace 'install ; no "install" target
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(lib (string-append out "/lib"))
(inc (string-append out "/include"))
(doc (string-append out "/share/doc/" ,name "-" ,version)))
(install-file "libdSFMT.so" lib)
(install-file "dSFMT.h" inc)
(install-file "LICENSE.txt" doc)
#t))))))
(synopsis "Double precision SIMD-oriented Fast Mersenne Twister")
(description
"The dSMFT package speeds up Fast Mersenne Twister generation by avoiding
the expensive conversion of integer to double (floating point). dSFMT directly
generates double precision floating point pseudorandom numbers which have the
IEEE Standard for Binary Floating-Point Arithmetic (ANSI/IEEE Std 754-1985)
format. dSFMT is only available on the CPUs which use IEEE 754 format double
precision floating point numbers.")
(home-page "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/")
(license license:bsd-3)))
(define-public gsl
(package
(name "gsl")
(version "2.6")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/gsl/gsl-"
version ".tar.gz"))
(sha256
(base32
"1a460zj9xmbgvcymkdhqh313c4l29mn9cffbi5vf33x3qygk70mp"))))
(build-system gnu-build-system)
(arguments
(let ((system (%current-system)))
(cond
((or (string-prefix? "aarch64" system)
(string-prefix? "powerpc" system))
;; Some sparse matrix tests are failing on AArch64 and PowerPC:
;; https://lists.gnu.org/archive/html/bug-gsl/2020-04/msg00001.html
'(#:phases (modify-phases %standard-phases
(add-before 'check 'disable-failing-tests
(lambda _
(substitute* "spmatrix/test.c"
((".*test_complex.*") "\n"))
#t)))))
((string-prefix? "i686" system)
;; There are rounding issues with these tests on i686:
;; https://lists.gnu.org/archive/html/bug-gsl/2016-10/msg00000.html
;; https://lists.gnu.org/archive/html/bug-gsl/2020-04/msg00000.html
'(#:phases (modify-phases %standard-phases
(add-before 'check 'disable-failing-tests
(lambda _
(substitute* "linalg/test.c"
((".*gsl_test\\(test_LU_decomp.*") "\n")
((".*gsl_test\\(test_LUc_decomp.*") "\n")
((".*gsl_test\\(test_cholesky_decomp.*") "\n")
((".*gsl_test\\(test_COD_lssolve2.*") "\n"))
(substitute* "spmatrix/test.c"
((".*test_all.*") "\n")
((".*test_float.*") "\n")
((".*test_complex.*") "\n"))
#t)))))
(else '()))))
(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 sleef
(package
(name "sleef")
(version "3.4.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/shibatch/sleef")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "1gvf7cfvszmgjrsqivwmyy1jnp3hy80dmszxx827lhjz8yqq5019"))))
(build-system cmake-build-system)
(arguments
'(#:configure-flags (list "-DCMAKE_BUILD_TYPE=Release"
(string-append "-DCMAKE_INSTALL_LIBDIR="
(assoc-ref %outputs "out")
"/lib")
(string-append "-DCMAKE_INSTALL_PREFIX="
(assoc-ref %outputs "out")))
#:phases
(modify-phases %standard-phases
;; SLEEF generates a header library during the build process and writes
;; to it via shell redirection. Make the checkout writable so the
;; build can succeed.
(add-after 'unpack 'make-git-checkout-writable
(lambda _
(for-each make-file-writable (find-files "."))
#t)))))
(inputs
`(("fftw" ,fftw)
("gmp" ,gmp)
("mpfr" ,mpfr)
("openssl" ,openssl)))
(home-page "https://sleef.org/")
(synopsis "SIMD library for evaluating elementary functions and DFT")
(description
"SLEEF (SIMD Library for Evaluating Elementary Functions) is a library that
implements vectorized versions of all C99 real floating point math functions.
It can utilize SIMD instructions that are available on modern processors.")
(license (list license:boost1.0 ;sleef
license:cc-by4.0)))) ;simplex algorithm
(define-public glpk
(package
(name "glpk")
(version "4.65")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://gnu/glpk/glpk-"
version ".tar.gz"))
(sha256
(base32
"040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
(build-system gnu-build-system)
(inputs
`(("gmp" ,gmp)))
(arguments
`(#:configure-flags '("--with-gmp")))
(home-page "https://www.gnu.org/software/glpk/")
(synopsis "GNU Linear Programming Kit, supporting the MathProg language")
(description
"GLPK is a C library for solving large-scale linear programming (LP),
mixed integer programming (MIP), and other related problems. It supports the
GNU MathProg modeling language, a subset of the AMPL language, and features a
translator for the language. In addition to the C library, a stand-alone
LP/MIP solver is included in the package.")
(license license:gpl3+)))
(define-public 4ti2
(package
(name "4ti2")
(version "1.6.9")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/4ti2/4ti2/releases/download/"
"Release_"
(string-map (lambda (c) (if (char=? c #\.) #\_ c))
version)
"/4ti2-" version ".tar.gz"))
(sha256
(base32 "0rj92x6p9m3la5gasjbj7sa569im527ffmka5y2sv1amgd3fflrh"))))
(build-system gnu-build-system)
(native-inputs
`(("which" ,(@ (gnu packages base) which)))) ; for the tests
(inputs
`(("glpk" ,glpk)
("gmp" ,gmp)))
(home-page "http://www.4ti2.de/")
(synopsis "Mathematical tool suite for problems on linear spaces")
(description
"4ti2 implements algorithms for solving algebraic, geometric and
combinatorial problems on linear spaces. Among others, it solves systems
of linear equations, computes extreme rays of polyhedral cones, solves
integer programming problems and computes Markov bases for statistics.")
(license license:gpl2+)))
(define-public cddlib
(package
(name "cddlib")
(version "0.94i")
(source
(origin
(method url-fetch)
(uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
(string-delete #\. version) ".tar.gz"))
(sha256
(base32
"00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
(build-system gnu-build-system)
(inputs
`(("gmp" ,gmp)))
(home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
(synopsis "Library for convex hulls and extreme rays of polyhedra")
(description
"The C-library cddlib implements the Double Description Method of
Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
rays of a general convex polyhedron given by a system of linear inequalities
in arbitrary dimension. It can also be used for the converse operation of
computing convex hulls.")
(license license:gpl2+)))
(define-public lrslib
(package
(name "lrslib")
(version "7.0a")
(source
(origin
(method url-fetch)
(uri (string-append "http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/"
"lrslib-0"
(string-delete #\. version) ".tar.gz"))
(sha256
(base32
"034fa45r9hwx6ljmgpxk2872q34nklkalpdkc6s9hqw57rivi36k"))))
(build-system gnu-build-system)
(inputs
`(("gmp" ,gmp)))
(arguments
`(#:tests? #f ; no check phase
#:make-flags `("CC=gcc"
,(string-append "prefix=" (assoc-ref %outputs "out"))
"all-shared")
#:phases
(modify-phases %standard-phases
(replace 'configure
(lambda _
(substitute* "makefile"
(("-L \\.") "-L . -Wl,-rpath='$$ORIGIN/../lib'"))
#t)))))
(home-page "http://cgm.cs.mcgill.ca/~avis/C/lrs.html")
(synopsis "Convex hulls of polyhedra with exact arithmetic")
(description
"The C code of lrslib implements the reverse search algorithm for
vertex enumeration and convex hull problems. Its input file format is
compatible with cddlib. All computations are done exactly in either
multiple precision or fixed integer arithmetic. Output is not stored
in memory, so even problems with very large output sizes can sometimes
be solved.")
(license license:gpl2+)))
(define-public vinci
(package
(name "vinci")
(version "1.0.5")
(source
(origin
(method url-fetch)
(uri (string-append "https://www.math.u-bordeaux.fr/~aenge/software/"
"vinci/vinci-" version ".tar.gz"))
(sha256
(base32
"1aq0qc1y27iw9grhgnyji3290wwfznsrk3sg6ynqpxwjdda53h4m"))))
(build-system gnu-build-system)
(inputs
`(("lrslib" ,lrslib)))
(arguments
`(#:tests? #f ; no check phase
#:phases
(modify-phases %standard-phases
(replace 'configure
;; register the lrs location in the config file
(lambda* (#:key inputs #:allow-other-keys)
(let* ((lrs (assoc-ref inputs "lrslib"))
(lrsexec (string-append lrs "/bin/lrs")))
(substitute* "vinci.h"
(("#define LRS_EXEC \"lrs\"")
(string-append "#define LRS_EXEC \"" lrsexec "\""))))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(install-file "vinci" bin))
#t)))))
(home-page
"https://www.math.u-bordeaux.fr/~aenge/?category=software&page=vinci")
(synopsis "Volume computation for polytopes")
(description
"Vinci implements a number of volume computation algorithms for convex
polytopes in arbitrary dimension. The polytopes can be given by their
V-representation (as the convex hull of a finite number of vertices), by
their H-representation (as the bounded intersection of a finite number of
halfspaces) or by their double description with both representations.")
(license license:gpl2+)))
(define-public arpack-ng
(package
(name "arpack-ng")
(version "3.6.3")
(home-page "https://github.com/opencollab/arpack-ng")
(source (origin
(method git-fetch)
(uri (git-reference (url home-page) (commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
(build-system gnu-build-system)
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("libtool" ,libtool)))
(inputs
`(("lapack" ,lapack)
("fortran" ,gfortran)))
(synopsis "Fortran subroutines for solving eigenvalue problems")
(description
"ARPACK-NG is a collection of Fortran77 subroutines designed to solve
large scale eigenvalue problems.")
(license (license:non-copyleft "file://COPYING"
"See COPYING in the distribution."))))
(define-public arpack-ng-3.3.0
(package
(inherit arpack-ng)
(version "3.3.0")
(name (package-name arpack-ng))
(home-page (package-home-page arpack-ng))
(source
(origin
(method url-fetch)
(uri (string-append home-page "/archive/" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
(define-public arpack-ng-openmpi
(package (inherit arpack-ng)
(name "arpack-ng-openmpi")
(inputs
`(("mpi" ,openmpi)
,@(package-inputs arpack-ng)))
(arguments
(substitute-keyword-arguments (package-arguments arpack-ng)
((#:configure-flags _ '())
''("--enable-mpi"))
((#:phases phases '%standard-phases)
`(modify-phases ,phases
(add-before 'check 'mpi-setup
,%openmpi-setup)))))
(synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
(define-public lapack
(package
(name "lapack")
(version "3.9.0")
(source
(origin
(method url-fetch)
(uri (string-append "http://www.netlib.org/lapack/lapack-"
version ".tgz"))
(sha256
(base32
"1155qixp26c12yrxc76z9mlfw2h3xxymxxv5znpgzh5gaykpndgj"))))
(build-system cmake-build-system)
(home-page "http://www.netlib.org/lapack/")
(inputs `(("fortran" ,gfortran)
("python" ,python-wrapper)))
(arguments
`(#:configure-flags (list
"-DBUILD_SHARED_LIBS:BOOL=YES"
"-DLAPACKE=ON"
;; Build the 'LAPACKE_clatms' functions.
"-DLAPACKE_WITH_TMG=ON"
"-DBUILD_TESTING=ON")))
(synopsis "Library for numerical linear algebra")
(description
"LAPACK is a Fortran 90 library for solving the most commonly occurring
problems in numerical linear algebra.")
(license (license:non-copyleft "file://LICENSE"
"See LICENSE in the distribution."))))
(define-public scalapack
(package
(name "scalapack")
(version "2.0.2")
(source
(origin
(method url-fetch)
(uri (string-append "http://www.netlib.org/scalapack/scalapack-"
version ".tgz"))
(sha256
(base32
"0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))
(patches (search-patches "scalapack-blacs-mpi-deprecations.patch"))))
(build-system cmake-build-system)
(inputs
`(("mpi" ,openmpi)
("fortran" ,gfortran)
("lapack" ,lapack))) ;for testing only
(arguments
`(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
#:phases (modify-phases %standard-phases
(add-before 'check 'mpi-setup
,%openmpi-setup))))
(home-page "http://www.netlib.org/scalapack/")
(synopsis "Library for scalable numerical linear algebra")
(description
"ScaLAPACK is a Fortran 90 library of high-performance linear algebra
routines on parallel distributed memory machines. ScaLAPACK solves dense and
banded linear systems, least squares problems, eigenvalue problems, and
singular value problems.")
(license (license:non-copyleft "file://LICENSE"
"See LICENSE in the distribution."))))
(define-public gnuplot
(package
(name "gnuplot")
(version "5.2.7")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
version "/gnuplot-"
version ".tar.gz"))
(sha256
(base32 "1vglp4la40f5dpj0zdj63zprrkyjgzy068p35bz5dqxjyczm1zlp"))))
(build-system gnu-build-system)
(inputs `(("readline" ,readline)
("cairo" ,cairo)
("pango" ,pango)
("gd" ,gd)
("lua" ,lua)))
(native-inputs
`(("pkg-config" ,pkg-config)
("texlive" ,texlive-tiny)))
(arguments `(#:configure-flags (list (string-append
"--with-texdir=" %output
"/texmf-local/tex/latex/gnuplot"))))
(home-page "http://www.gnuplot.info")
(synopsis "Command-line driven graphing utility")
(description "Gnuplot is a portable command-line driven graphing
utility. It was originally created to allow scientists and students to
visualize mathematical functions and data interactively, but has grown to
support many non-interactive uses such as web scripting. It is also used as a
plotting engine by third-party applications like Octave.")
;; X11 Style with the additional restriction that derived works may only be
;; distributed as patches to the original.
(license (license:fsf-free
"http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
(define-public gctp
(package
(name "gctp")
(version "2.0.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/OkoSanto/GCTP")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
(native-inputs
`(("fortran" ,gfortran)))
(build-system gnu-build-system)
(synopsis "General Cartographic Transformation Package (GCTP)")
(description
"The General Cartographic Transformation Package (GCTP) is a system of
software routines designed to permit the transformation of coordinate pairs
from one map projection to another. The GCTP is the standard computer
software used by the National Mapping Division for map projection
computations.")
(home-page "https://github.com/OkoSanto/GCTP")
(license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
(define-public hdf4
(package
(name "hdf4")
(version "4.2.14")
(source
(origin
(method url-fetch)
(uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
version "/src/hdf-" version ".tar.bz2"))
(sha256
(base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l"))
(patches (search-patches "hdf4-architectures.patch"
"hdf4-reproducibility.patch"
"hdf4-shared-fortran.patch"
"hdf4-tirpc.patch"))))
(build-system gnu-build-system)
(native-inputs
`(("gfortran" ,gfortran)
("bison" ,bison)
("flex" ,flex)))
(inputs
`(("zlib" ,zlib)
("libjpeg" ,libjpeg-turbo)
("libtirpc" ,libtirpc)))
(arguments
`(#:parallel-tests? #f
#:configure-flags (list "--enable-shared"
(string-append "CPPFLAGS=-I"
(assoc-ref %build-inputs "libtirpc")
"/include/tirpc"))
#:phases
(modify-phases %standard-phases
;; This is inspired by two of Debian's patches.
(add-before 'configure 'add-more-aarch64-support
(lambda _
(substitute* '("mfhdf/ncgen/ncgen.l"
"mfhdf/ncgen/ncgenyy.c"
"mfhdf/libsrc/netcdf.h.in")
(("AIX5L64") "__aarch64__"))
#t))
(add-before 'configure 'patchbuild
(lambda _
(substitute*
'("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
(("/bin/rm") "rm")
(("/bin/mkdir") "mkdir"))
(substitute* (find-files "." "^Makefile\\.in$")
(("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
(("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
#t))
(add-after 'configure 'patch-settings
(lambda _
;; libhdf4.settings contains the full path of the
;; compilers used, and its contents are included in
;; .so-files. We truncate the hashes to avoid
;; unnecessary store references to those compilers:
(substitute* "libhdf4.settings"
(("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
(string-append prefix (string-take hash 10) "...")))
#t))
(add-after 'install 'provide-absolute-libjpeg-reference
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(libjpeg (assoc-ref inputs "libjpeg")))
;; libjpeg-turbo does not provide a .la file, so libtool is
;; unable to add an absolute reference for -ljpeg in the .la
;; files. Fix it manually to avoid having to propagate it.
(substitute* (find-files (string-append out "/lib") "\\.la$")
(("-ljpeg")
(string-append "-L" libjpeg "/lib -ljpeg")))
#t))))))
(home-page "https://www.hdfgroup.org/products/hdf4/")
(synopsis
"Library and multi-object file format for storing and managing data")
(description "HDF4 is a library and multi-object file format for storing
and managing data between machines. HDF4 is an older hierarchical data format,
incompatible with HDF5.")
(license
(license:non-copyleft
"https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
(define-public hdf4-alt
(package
(inherit hdf4)
(name "hdf4-alt")
(arguments
(substitute-keyword-arguments (package-arguments hdf4)
((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
(synopsis
"HDF4 without netCDF API, can be combined with the regular netCDF library")))
(define-public hdf5
(package
(name "hdf5")
(version "1.8.21")
(source
(origin
(method url-fetch)
(uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
"hdf5-" (version-major+minor version)
"/hdf5-" version "/src/hdf5-"
version ".tar.bz2")
(string-append "https://support.hdfgroup.org/ftp/HDF5/"
"current"
(match (string-split version #\.)
((major minor _ ...)
(string-append major minor)))
"/src/hdf5-" version ".tar.bz2")))
(sha256
(base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5"))
(patches (search-patches "hdf5-config-date.patch"
"hdf5-1.8-mpi-deprecations.patch"))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)))
(native-inputs
`(("gfortran" ,gfortran)
("perl" ,perl))) ;part of the test machinery needs Perl
(outputs '("out" ; core library
"fortran")) ; fortran interface
(arguments
`(;; Some of the users, notably Flann, need the C++ interface.
#:configure-flags '("--enable-cxx"
"--enable-fortran"
"--enable-fortran2003"
;; Build a thread-safe library. Unfortunately,
;; 'configure' invites you to either turn off C++,
;; Fortran, and the high-level interface (HL), or
;; to pass '--enable-unsupported'. Debian
;; packagers chose to pass '--enable-unsupported'
;; and we follow their lead here.
"--enable-threadsafe"
"--with-pthread"
"--enable-unsupported")
;; Use -fPIC to allow the R bindings to link with the static libraries
#:make-flags (list "CFLAGS=-fPIC"
"CXXFLAGS=-fPIC")
#:phases
(modify-phases %standard-phases
(add-before 'configure 'patch-configure
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "configure"
(("/bin/mv") "mv"))
(substitute* "fortran/src/Makefile.in"
(("libhdf5_fortran_la_LDFLAGS =")
(string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
(assoc-ref outputs "fortran") "/lib")))
(substitute* "hl/fortran/src/Makefile.in"
(("libhdf5hl_fortran_la_LDFLAGS =")
(string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
(assoc-ref outputs "fortran") "/lib")))
#t))
(add-after 'configure 'patch-settings
(lambda _
;; libhdf5.settings contains the full path of the
;; compilers used, and its contents are included in
;; libhdf5.so. We truncate the hashes to avoid
;; unnecessary store references to those compilers:
(substitute* "src/libhdf5.settings"
(("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
(string-append prefix (string-take hash 10) "..."))
;; Don't record the build-time kernel version to make the
;; settings file reproducible.
(("Uname information:.*")
"Uname information: Linux\n"))
#t))
(add-after 'install 'patch-references
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin"))
(zlib (assoc-ref inputs "zlib")))
(substitute* (find-files bin "h5p?cc")
(("-lz" lib)
(string-append "-L" zlib "/lib " lib)))
#t)))
(add-after 'install 'split
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Move all fortran-related files
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(lib (string-append out "/lib"))
(inc (string-append out "/include"))
(ex (string-append out "/share/hdf5_examples/fortran"))
(fort (assoc-ref outputs "fortran"))
(fbin (string-append fort "/bin"))
(flib (string-append fort "/lib"))
(finc (string-append fort "/include"))
(fex (string-append fort "/share/hdf5_examples/fortran")))
(mkdir-p fbin)
(mkdir-p flib)
(mkdir-p finc)
(mkdir-p fex)
;; Note: When built with --enable-parallel, the 'h5fc' file
;; doesn't exist, hence this condition.
(when (file-exists? (string-append bin "/h5fc"))
(rename-file (string-append bin "/h5fc")
(string-append fbin "/h5fc")))
(for-each (lambda (file)
(rename-file file
(string-append flib "/" (basename file))))
(find-files lib ".*fortran.*"))
(for-each (lambda (file)
(rename-file file
(string-append finc "/" (basename file))))
(find-files inc ".*mod"))
(for-each (lambda (file)
(rename-file file
(string-append fex "/" (basename file))))
(find-files ex ".*"))
(delete-file-recursively ex))
#t)))))
(home-page "https://www.hdfgroup.org")
(synopsis "Management suite for extremely large and complex data")
(description "HDF5 is a suite that makes possible the management of
extremely large and complex data collections.")
(license (license:x11-style
"https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
(define-public hdf5-1.10
(package (inherit hdf5)
(version "1.10.6")
(source
(origin
(method url-fetch)
(uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
"hdf5-" (version-major+minor version)
"/hdf5-" version "/src/hdf5-"
version ".tar.bz2")
(string-append "https://support.hdfgroup.org/ftp/HDF5/"
"current"
(apply string-append
(take (string-split version #\.) 2))
"/src/hdf5-" version ".tar.bz2")))
(sha256
(base32 "1gf38x51128hn00744358w27xgzjk0ff4wra4yxh2lk804ck1mh9"))
(patches (search-patches "hdf5-config-date.patch"))))))
(define-public hdf-java
(package
(name "hdf-java")
(version "3.3.2")
(source
(origin
(method url-fetch)
(uri (string-append
"https://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
version "/src/CMake-hdfjava-" version ".tar.gz"))
(sha256
(base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
(modules '((guix build utils)))
(snippet ; Make sure we don't use the bundled sources and binaries.
`(begin
(for-each delete-file
(list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
"HDF4.tar.gz" "HDF5.tar.gz"))
(delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
#t))))
(build-system gnu-build-system)
(native-inputs
`(("jdk" ,icedtea "jdk")
("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
;; For tests:
("hamcrest-core" ,java-hamcrest-core)
("junit" ,java-junit)
("slf4j-simple" ,java-slf4j-simple)))
(inputs
`(("hdf4" ,hdf4)
("hdf5" ,hdf5)
("zlib" ,zlib)
("libjpeg" ,libjpeg-turbo)
("slf4j-api" ,java-slf4j-api)))
(arguments
`(#:configure-flags
(list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
(string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
(assoc-ref %build-inputs "jdk") "/lib" )
(string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
(string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
#:make-flags
(list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
(string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
(string-append "ZLIB=" (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
(append
(map (lambda (i)
(string-append (assoc-ref inputs i)
"/share/java/" i ".jar"))
'("slf4j-api" "slf4j-simple"))
(list
(car (find-files (assoc-ref inputs "junit") "jar$"))
(car (find-files (assoc-ref inputs "hamcrest-core")
"jar$")))))
(class-path
(string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
(substitute* '("test/hdf5lib/Makefile.in"
"test/hdf5lib/junit.sh.in"
"examples/runExample.sh.in")
(("/usr/bin/test")
(string-append (assoc-ref inputs "coreutils")
"/bin/test"))
(("/usr/bin/uname")
(string-append (assoc-ref inputs "coreutils")
"/bin/uname"))
(("CLASSPATH=[^\n]*")
(string-append "CLASSPATH=" class-path)))
(setenv "CLASSPATH" class-path))
#t))
(add-before 'check 'build-examples
(lambda _
(apply invoke `("javac"
,@(find-files "examples" ".*\\.java"))))))
#:parallel-build? #f
#:parallel-tests? #f ))
(home-page "https://support.hdfgroup.org/products/java")
(synopsis "Java interface for the HDF4 and HDF5 libraries")
(description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
implemented in C.")
;; BSD-style license:
(license (license:x11-style
"https://support.hdfgroup.org/ftp/HDF5/hdf-java\
/current/src/unpacked/COPYING"))))
(define-public hdf-eos2
(package
(name "hdf-eos2")
(version "19.1.0")
(source
(origin
(method url-fetch)
(uri "ftp://edhs1.gsfc.nasa.gov\
/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
(sha256
(base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
(patches (search-patches "hdf-eos2-remove-gctp.patch"
"hdf-eos2-build-shared.patch"
"hdf-eos2-fortrantests.patch"))))
(build-system gnu-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(inputs
`(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
;; XXX: These inputs are really dependencies of hdf4.
("zlib" ,zlib)
("libjpeg" ,libjpeg-turbo)
("libtirpc" ,libtirpc)
("gctp" ,gctp)))
(arguments
`( #:configure-flags '("--enable-install-include" "--enable-shared"
"CC=h4cc -Df2cFortran" "LIBS=-lgctp")
#:parallel-tests? #f))
(home-page "https://hdfeos.org/software/library.php#HDF-EOS2")
(synopsis "HDF4-based data format for NASA's Earth Observing System")
(description "HDF-EOS2 is a software library built on HDF4 which supports
the construction of data structures used in NASA's Earth Observing
System (Grid, Point and Swath).")
;; Source files carry a permissive license header.
(license (license:non-copyleft home-page))))
(define-public hdf-eos5
(package
(name "hdf-eos5")
(version "1.15")
(source (origin
(method url-fetch)
(uri (string-append "ftp://edhs1.gsfc.nasa.gov\
/edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
(sha256
(base32
"1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
(patches (search-patches "hdf-eos5-build-shared.patch"
"hdf-eos5-remove-gctp.patch"
"hdf-eos5-fix-szip.patch"
"hdf-eos5-fortrantests.patch"))))
(native-inputs
`(("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 hdf5-blosc
(package
(name "hdf5-blosc")
(version "1.0.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Blosc/hdf5-blosc")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1nj2bm1v6ymm3fmyvhbn6ih5fgdiapavlfghh1pvbmhw71cysyqs"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags
(list (string-append "-DBLOSC_INSTALL_DIR="
(assoc-ref %build-inputs "c-blosc"))
(string-append "-DPLUGIN_INSTALL_PATH="
(assoc-ref %outputs "out")
"/hdf5/lib/plugin"))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'do-not-build-blosc
(lambda _
(substitute* "CMakeLists.txt"
(("set\\(BLOSC_INSTALL_DIR.*") "")
(("ExternalProject_Add\\(project_blosc") "message("))
#t)))))
(inputs
`(("c-blosc" ,c-blosc)
("hdf5" ,hdf5-1.10)))
(home-page "https://github.com/Blosc/hdf5-blosc")
(synopsis "Filter for HDF5 using the Blosc compressor")
(description "This is a filter for HDF5 that uses the Blosc compressor; by
installing this filter, you can read and write HDF5 files with
Blosc-compressed datasets.")
(license license:expat)))
(define-public h5check
(package
(name "h5check")
(version "2.0.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://www.hdfgroup.org/ftp/HDF5/tools/"
"h5check/src/h5check-" version ".tar.gz"))
(sha256
(base32
"1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
(build-system gnu-build-system)
(inputs `(("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-turbo)))
(arguments
`(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
#:phases (modify-phases %standard-phases
(add-before 'configure 'fix-source-date
(lambda _
;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
;; to '1st hour of the current day', and therefore makes the
;; package not reproducible.
(substitute* "./configure"
(("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
"date --date='@0'"))
#t))
(add-after 'configure 'patch-settings
(lambda _
;; libnetcdf.settings contains the full filename of the compilers
;; used to build the library. We truncate the hashes of those
;; filenames to avoid unnecessary references to the corresponding
;; store items.
(substitute* "libnetcdf.settings"
(("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
(string-append prefix (string-take hash 10) "...")))
#t)))
#:parallel-tests? #f)) ;various race conditions
(home-page "https://www.unidata.ucar.edu/software/netcdf/")
(synopsis "Library for scientific data")
(description "NetCDF is an interface for scientific data access and a
software library that provides an implementation of the interface. The netCDF
library defines a machine-independent format for representing scientific data.
Together, the interface, library, and format support the creation, access, and
sharing of scientific data.")
(license (license:x11-style "file://COPYRIGHT"))))
(define-public netcdf-parallel-openmpi
(package (inherit netcdf)
(name "netcdf-parallel-openmpi")
(inputs
`(("mpi" ,openmpi)
,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
(package-inputs netcdf))))
;; TODO: Replace pkg-config references in nc-config with absolute references
(arguments
(substitute-keyword-arguments (package-arguments netcdf)
((#:configure-flags flags)
`(cons* "CC=mpicc" "CXX=mpicxx"
"--enable-parallel-tests"
;; Shared libraries not supported with parallel IO.
"--disable-shared" "--with-pic"
,flags))))))
(define-public netcdf-fortran
(package
(name "netcdf-fortran")
(version "4.4.4")
(source (origin
(method url-fetch)
(uri (string-append
"ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
version ".tar.gz"))
(sha256
(base32
"0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-tests? #f))
(inputs
`(("netcdf" ,netcdf)))
(native-inputs
`(("gfortran" ,gfortran)))
(synopsis "Fortran interface for the netCDF library")
(description (package-description netcdf))
(home-page (package-home-page netcdf))
(license (package-license netcdf))))
(define-public nlopt
(package
(name "nlopt")
(version "2.4.2")
(source (origin
(method url-fetch)
(uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
version ".tar.gz"))
(sha256
(base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
(build-system gnu-build-system)
(arguments
`(;; Shared libraries are not built by default. They are required to
;; build the Guile, Octave, and Python bindings.
#:configure-flags '("--enable-shared")
#:phases
(modify-phases %standard-phases
(add-before 'configure 'set-libnlopt-file-name
(lambda* (#:key outputs #:allow-other-keys)
;; Make sure the Scheme module refers to the library by its
;; absolute file name (we cannot do that from a snippet
;; because the expansion of @libdir@ contains
;; ${exec_prefix}.)
(let ((out (assoc-ref outputs "out")))
(substitute* "swig/nlopt.scm.in"
(("libnlopt")
(string-append out "/lib/libnlopt")))
#t))))))
(inputs `(("guile" ,guile-2.0)))
(native-inputs `(("pkg-config" ,pkg-config)))
(home-page "http://ab-initio.mit.edu/wiki/")
(synopsis "Library for nonlinear optimization")
(description "NLopt is a library for nonlinear optimization, providing a
common interface for a number of different free optimization routines available
online as well as original implementations of various other algorithms.")
(license license:lgpl2.1+)))
(define-public ipopt
(package
(name "ipopt")
(version "3.12.12")
(source (origin
(method url-fetch)
(uri (string-append
"https://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 "https://www.coin-or.org")
(synopsis "Large-scale nonlinear optimizer")
(description
"The Interior Point Optimizer (IPOPT) is a software package for
large-scale nonlinear optimization. It provides C++, C, and Fortran
interfaces.")
(license license:epl1.0)))
(define-public clp
(package
(name "clp")
(version "1.17.6")
(source (origin
(method url-fetch)
(uri (string-append "https://www.coin-or.org/download/source/"
"Clp/Clp-" version ".tgz"))
(sha256
(base32
"0ap1f0lxppa6pnbc4bg7ih7a96avwaki482nig8w5fr3vg9wvkzr"))
(modules '((guix build utils)))
(snippet
;; Make sure we don't use the bundled software.
'(begin
(delete-file-recursively "ThirdParty")
#t))))
(build-system gnu-build-system)
(native-inputs
`(("gfortran" ,gfortran)
("pkg-config" ,pkg-config)))
(inputs
`(("openblas" ,openblas)))
(home-page "https://www.coin-or.org")
(synopsis "Linear programming solver")
(description
"CLP is a high quality linear programming solver. Its main strengths are
its dual and primal Simplex algorithms. It also has a barrier algorithm for
linear and quadratic objectives. There are limited facilities for nonlinear
and quadratic objectives using the Simplex algorithm.")
(license license:epl1.0)))
(define-public ceres
(package
(name "ceres-solver")
(version "1.14.0")
(home-page "http://ceres-solver.org/")
(source (origin
(method url-fetch)
(uri (string-append home-page "ceres-solver-"
version ".tar.gz"))
(sha256
(base32
"13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
(build-system cmake-build-system)
(arguments
;; TODO: Build HTML user documentation and install separately.
'(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
"-DBUILD_SHARED_LIBS=ON")
#:phases (modify-phases %standard-phases
(add-before 'configure 'set-library-directory
(lambda _
;; Install libraries to lib/, not lib64/.
(substitute* "internal/ceres/CMakeLists.txt"
(("set\\(LIB_SUFFIX \"64\"\\)")
"set(LIB_SUFFIX \"\")"))
#t)))))
(native-inputs
`(("pkg-config" ,pkg-config)))
(propagated-inputs
`(("glog" ,glog))) ;for #include <glog/glog.h>
(inputs
`(("eigen" ,eigen)
("blas" ,openblas)
("lapack" ,lapack)
("suitesparse" ,suitesparse)
("gflags" ,gflags)))
(synopsis "C++ library for solving large optimization problems")
(description
"Ceres Solver is a C++ library for modeling and solving large,
complicated optimization problems. It is a feature rich, mature and
performant library which has been used in production since 2010. Ceres Solver
can solve two kinds of problems:
@enumerate
@item non-linear least squares problems with bounds constraints;
@item general unconstrained optimization problems.
@end enumerate\n")
(license license:bsd-3)))
;; For a fully featured Octave, users are strongly recommended also to install
;; the following packages: less, ghostscript, gnuplot.
(define-public octave-cli
(package
(name "octave-cli")
(version "5.2.0")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://gnu/octave/octave-"
version ".tar.lz"))
(sha256
(base32
"1848dq6nxzal8gwjrcp6xhi5gq96w89nss9d9rz75q408gb3mbl6"))))
(build-system gnu-build-system)
(inputs
`(("alsa-lib" ,alsa-lib)
("arpack" ,arpack-ng)
("bdb" ,bdb)
("curl" ,curl)
("fftw" ,fftw)
("fftwf" ,fftwf)
("fltk" ,fltk)
("fontconfig" ,fontconfig)
("freetype" ,freetype)
("gl2ps" ,gl2ps)
("glpk" ,glpk)
("glu" ,glu)
("graphicsmagick" ,graphicsmagick)
;; TODO: libjpeg-turbo is indirectly required through libtiff. In
;; the next rebuild cycle, add an absolute reference for -ljpeg in
;; libtiff.la instead of having to provide it here.
("libjpeg" ,libjpeg-turbo)
("hdf5" ,hdf5)
("lapack" ,lapack)
("libsndfile" ,libsndfile)
("libxft" ,libxft)
("mesa" ,mesa)
("pcre" ,pcre)
("portaudio" ,portaudio)
("qhull" ,qhull)
("readline" ,readline)
("suitesparse" ,suitesparse)
("texinfo" ,texinfo)
("zlib" ,zlib)))
(native-inputs
`(("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")
;; XXX: Without this flag, linking octave-cli fails with
;; undefined references to 'logf@GLIBCXX_3.4' et.al. due to
;; not pulling in liboctinterp.la for -lstdc++.
"--enable-link-all-dependencies")
#:phases
(modify-phases %standard-phases
(add-after 'configure 'configure-makeinfo
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "libinterp/corefcn/help.h"
(("\"makeinfo\"")
(string-append
"\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
#t)))))
(home-page "https://www.gnu.org/software/octave/")
(synopsis "High-level language for numerical computation")
(description "GNU Octave is a high-level interpreted language that is
specialized for numerical computations. It can be used for both linear and
non-linear applications and it provides great support for visualizing results.
Work may be performed both at the interactive command-line as well as via
script files.")
(license license:gpl3+)))
(define-public octave
(package (inherit octave-cli)
(name "octave")
(source (origin
(inherit (package-source octave-cli))))
(inputs
`(("qscintilla" ,qscintilla)
("qt" ,qtbase)
,@(package-inputs octave-cli)))
(native-inputs
`(("qttools" , qttools) ;for lrelease
("texlive" ,(texlive-union (list texlive-epsf))) ; for texi2dvi
,@(package-native-inputs octave-cli)))
(arguments
(substitute-keyword-arguments (package-arguments octave-cli)
((#:phases phases)
`(modify-phases ,phases
(add-before 'configure 'patch-qscintilla-library-name
(lambda* (#:key inputs #:allow-other-keys)
;; The QScintilla library that the Octave configure script tries
;; to link with should be named libqscintilla-qt5.so, but the
;; QScintilla input provides the shared library as
;; libqscintilla2_qt5.so.
(substitute* "configure"
(("qscintilla2-qt5")
"qscintilla2_qt5"))
#t))))))))
(define-public opencascade-oce
(package
(name "opencascade-oce")
(version "0.17.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/tpaviot/oce")
(commit (string-append "OCE-" version))))
(file-name (git-file-name name version))
(patches (search-patches "opencascade-oce-glibc-2.26.patch"))
(sha256
(base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69"))))
(build-system cmake-build-system)
(arguments
'(#:configure-flags
(list "-DOCE_TESTING:BOOL=ON"
"-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
"-DOCE_DRAW:BOOL=ON"
(string-append "-DOCE_INSTALL_PREFIX:PATH="
(assoc-ref %outputs "out"))
"-UCMAKE_INSTALL_RPATH")))
(inputs
`(("freetype" ,freetype)
("glu" ,glu)
("libxmu" ,libxmu)
("mesa" ,mesa)
("tcl" ,tcl)
("tk" ,tk)))
(native-inputs
`(("python" ,python-wrapper)))
(home-page "https://github.com/tpaviot/oce")
(synopsis "Libraries for 3D modeling and numerical simulation")
(description
"Open CASCADE is a set of libraries for the development of applications
dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
C++ class libraries providing services for 3D surface and solid modeling, CAD
data exchange, and visualization. It is used for development of specialized
software dealing with 3D models in design (CAD), manufacturing (CAM),
numerical simulation (CAE), measurement equipment (CMM), and quality
control (CAQ) domains.
This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
patches, improvements, and experiments contributed by users over the official
Open CASCADE library.")
(license (list license:lgpl2.1; OCE libraries, with an exception for the
; use of header files; see
; OCCT_LGPL_EXCEPTION.txt
license:public-domain; files
; src/Standard/Standard_StdAllocator.hxx and
; src/NCollection/NCollection_StdAllocator.hxx
license:expat; file src/OpenGl/OpenGl_glext.h
license:bsd-3)))); test framework gtest
(define-public opencascade-occt
(package
(name "opencascade-occt")
(version "7.3.0p3")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://git.dev.opencascade.org/repos/occt.git")
(commit
(string-append "V"
(string-map (lambda (x) (if (eq? x #\.) #\_ x))
version)))))
(file-name (git-file-name name version))
(sha256
(base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4"))
(modules '((guix build utils)))
(snippet
'(begin
;; Remove files specific to non-free operating systems.
(delete-file-recursively "samples/ios")
(delete-file-recursively "samples/mfc")
(delete-file-recursively "samples/qt/FuncDemo")
(delete-file "genconf.bat")
(delete-file "gendoc.bat")
(delete-file "genproj.bat")
(delete-file "upgrade.bat")
;; Remove references to deleted files.
(substitute* "dox/FILES_HTML.txt"
((".*standard.*") "" )
((".*UIKitSample.*") ""))
#t))))
(build-system cmake-build-system)
(arguments
'(;; There is no test target for make. OCCT provides an
;; 'Automated Testing System', which may be accessed after
;; installation via the draw.sh script. draw.sh is located in
;; the bin directory. For details see:
;; https://www.opencascade.com/doc/occt-7.3.0/overview/html/\
;; occt_dev_guides__tests.html
#:tests? #f
;; Configure without freeimage: attempting to link against the
;; freeimage version 3.17 library leads to 'undefined
;; reference' errors.
#:configure-flags
(list "-DUSE_FREEIMAGE:BOOL=OFF"
"-DUSE_TBB:BOOL=ON"
"-DUSE_VTK:BOOL=OFF"
"-DBUILD_DOC_Overview:BOOL=OFF"
"-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON"
"-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON"
"-UCMAKE_INSTALL_LIBDIR")))
(inputs
`(("doxygen" ,doxygen)
;("freeimage" ,freeimage)
("freetype" ,freetype)
("glu" ,glu)
("libxext" ,libxext)
("libxi" ,libxi)
("libxmu" ,libxmu)
("mesa" ,mesa)
("tbb" ,tbb)
("tcl" ,tcl)
("tk" ,tk)))
;; TODO: build Overview documentation and add 'doc' output.
(home-page "https://www.opencascade.com")
(synopsis "Libraries for 3D modeling and numerical simulation")
(description
"Open CASCADE is a set of libraries for the development of applications
dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
C++ class libraries providing services for 3D surface and solid modeling, CAD
data exchange, and visualization. It is used for development of specialized
software dealing with 3D models in design (CAD), manufacturing (CAM),
numerical simulation (CAE), measurement equipment (CMM), and quality
control (CAQ) domains.
This is the certified version of the Open Cascade Technology (OCCT) library.")
(license (list ;; OCCT library:
license:lgpl2.1; with an exception for the use of header
; files, see OCCT_LGPL_EXCEPTION.txt.
;; Files src/OpenGl/glext.h, adm/cmake/cotire.cmake and
;; src/OpenGl/OpenGl_HaltonSampler.hxx:
license:expat
;; Files src/ExprIntrp/ExprIntrp.tab.* and
;; src/StepFile/step.tab.*:
license:gpl3+ ; with Bison 2.2 exception.
;; File src/NCollection/NCollection_UtfIterator.lxx:
(license:non-copyleft
"https://www.unicode.org/license.html")
;; File src/NCollection/NCollection_StdAllocator.hxx:
license:public-domain))))
(define-public gmsh
(package
(name "gmsh")
(version "2.16.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://gitlab.onelab.info/gmsh/gmsh.git")
(commit
(string-append "gmsh_"
(string-map (lambda (x) (if (eq? x #\.) #\_ x))
version)))))
(file-name (git-file-name name version))
(sha256
(base32 "08rq4jajwmlpivnm9yifz2jhaivnz065lnk0h2zv773nwl9wf162"))
(modules '((guix build utils)))
(snippet
;; Remove non-free METIS code
'(begin
(delete-file-recursively "contrib/Metis")
#t))))
(build-system cmake-build-system)
(propagated-inputs
`(("fltk" ,fltk)
("gfortran" ,gfortran)
("gmp" ,gmp)
("hdf5" ,hdf5)
("lapack" ,lapack)
("mesa" ,mesa)
("glu" ,glu)
("opencascade-oce" ,opencascade-oce)
("libx11" ,libx11)
("libxext" ,libxext)))
(inputs
`(("fontconfig" ,fontconfig)
("libxft" ,libxft)))
(arguments
`(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
"-DENABLE_BUILD_SHARED:BOOL=ON"
"-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
(home-page "http://gmsh.info/")
(synopsis "3D finite element grid generator")
(description "Gmsh is a 3D finite element grid generator with a built-in
CAD engine and post-processor. Its design goal is to provide a fast, light
and user-friendly meshing tool with parametric input and advanced
visualization capabilities. Gmsh is built around four modules: geometry,
mesh, solver and post-processing. The specification of any input to these
modules is done either interactively using the graphical user interface or in
ASCII text files using Gmsh's own scripting language.")
(license license:gpl2+)))
(define-public maxflow
(package
(name "maxflow")
;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’,
;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’.
(version "3.0.5")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gerddie/maxflow")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
(build-system cmake-build-system)
(home-page "https://pub.ist.ac.at/~vnk/software.html")
(synopsis "Library implementing Maxflow algorithm")
(description "An implementation of the maxflow algorithm described in
@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
Energy Minimization in Computer Vision.\n
Yuri Boykov and Vladimir Kolmogorov.\n
In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
September 2004}")
(license license:gpl3+)))
(define-public petsc
(package
(name "petsc")
(version "3.11.2")
(source
(origin
(method url-fetch)
;; The *-lite-* tarball does not contain the *large* documentation
(uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
"petsc-lite-" version ".tar.gz"))
(sha256
(base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx"))))
(outputs '("out" ; libraries and headers
"examples")) ; ~30MiB of examples
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)))
(inputs
`(("gfortran" ,gfortran)
("lapack" ,lapack)
("superlu" ,superlu)
;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
;; leaving out opengl, as configuration seems to only be for mac
))
(arguments
`(#:test-target "test"
#:parallel-build? #f ; build is parallel by default
#:configure-flags
`("--with-mpi=0"
"--with-openmp=1"
"--with-superlu=1")
#:make-flags
;; Honor (parallel-job-count) for build. Do not use --with-make-np,
;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
(list (format #f "MAKE_NP=~a" (parallel-job-count)))
#:phases
(modify-phases %standard-phases
(replace 'configure
;; PETSc's configure script is actually a python script, so we can't
;; run it with bash.
(lambda* (#:key outputs (configure-flags '())
#:allow-other-keys)
(let* ((prefix (assoc-ref outputs "out"))
(flags `(,(string-append "--prefix=" prefix)
,@configure-flags)))
(format #t "build directory: ~s~%" (getcwd))
(format #t "configure flags: ~s~%" flags)
(apply invoke "./configure" flags))))
(add-after 'configure 'clean-local-references
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(substitute* (find-files "." "^petsc(conf|machineinfo).h$")
;; Prevent build directory from leaking into compiled code
(((getcwd)) out)
;; Scrub timestamp for reproducibility
((".*Libraries compiled on.*") ""))
(substitute* (find-files "." "petscvariables")
;; Do not expose build machine characteristics, set to defaults.
(("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
(("NPMAX = [:digit:]+") "NPMAX = 2"))
#t)))
(add-after 'install 'clean-install
;; Try to keep installed files from leaking build directory names.
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(substitute* (map (lambda (file)
(string-append out "/lib/petsc/conf/" file))
'("petscvariables"))
(((getcwd)) out))
;; Make compiler references point to the store
(substitute* (string-append out "/lib/petsc/conf/petscvariables")
(("= (gcc|g\\+\\+|gfortran)" _ compiler)
(string-append "= " (which compiler))))
;; PETSc installs some build logs, which aren't necessary.
(for-each (lambda (file)
(let ((f (string-append out "/lib/petsc/conf/" file)))
(when (file-exists? f)
(delete-file f))))
'("configure.log" "make.log" "gmake.log"
"test.log" "error.log" "RDict.db"
"PETScBuildInternal.cmake"
;; Once installed, should uninstall with Guix
"uninstall.py"))
#t)))
(add-after 'install 'move-examples
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(examples (assoc-ref outputs "examples"))
(exdir (string-append out "/share/petsc/examples"))
(exdir' (string-append examples "/share/petsc/examples")))
(copy-recursively exdir exdir')
(delete-file-recursively exdir)
#t))))))
(home-page "https://www.mcs.anl.gov/petsc")
(synopsis "Library to solve PDEs")
(description "PETSc, pronounced PET-see (the S is silent), is a suite of
data structures and routines for the scalable (parallel) solution of
scientific applications modeled by partial differential equations.")
(license (license:non-copyleft
"https://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
(define-public petsc-complex
(package (inherit petsc)
(name "petsc-complex")
(arguments
(substitute-keyword-arguments (package-arguments petsc)
((#:configure-flags cf)
`(cons "--with-scalar-type=complex" ,cf))))
(synopsis "Library to solve PDEs (with complex scalars)")))
(define-public petsc-openmpi
(package (inherit petsc)
(name "petsc-openmpi")
(inputs
`(("hdf5" ,hdf5-parallel-openmpi)
("hypre" ,hypre-openmpi)
("metis" ,metis)
("mumps" ,mumps-openmpi)
("openmpi" ,openmpi)
("scalapack" ,scalapack)
("scotch" ,pt-scotch32)
,@(package-inputs petsc)))
(arguments
(substitute-keyword-arguments (package-arguments petsc)
((#:configure-flags cf)
``("--with-hypre=1"
"--with-mpiexec=mpirun"
"--with-metis=1"
"--with-mumps=1"
"--with-scalapack=1"
"--with-ptscotch=1"
,(string-append "--with-mpi-dir="
(assoc-ref %build-inputs "openmpi"))
,(string-append "--with-hdf5-include="
(assoc-ref %build-inputs "hdf5") "/include")
,(string-append "--with-hdf5-lib="
(assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
,@(delete "--with-mpi=0" ,cf)))
((#:phases phases)
`(modify-phases ,phases
(add-before 'configure 'mpi-setup
,%openmpi-setup)))))
(synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
(define-public petsc-complex-openmpi
(package (inherit petsc-complex)
(name "petsc-complex-openmpi")
(inputs
`(("openmpi" ,openmpi)
,@(package-inputs petsc-complex)))
(arguments
(substitute-keyword-arguments (package-arguments petsc-complex)
((#:configure-flags cf)
``("--with-mpiexec=mpirun"
,(string-append "--with-mpi-dir="
(assoc-ref %build-inputs "openmpi"))
,@(delete "--with-mpi=0" ,cf)))
((#:phases phases)
`(modify-phases ,phases
(add-before 'configure 'mpi-setup
,%openmpi-setup)))))
(synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
(define-public python-petsc4py
(package
(name "python-petsc4py")
(version "3.11.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "petsc4py" version))
(sha256
(base32
"1rm1qj5wlkhxl39by9n78lh3gbmii31wsnb8j1rr5hvfr5xgbx2q"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-before 'build 'pre-build
(lambda _
;; Define path to PETSc installation.
(setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
#t))
(add-before 'check 'mpi-setup
,%openmpi-setup))))
(inputs
`(("petsc" ,petsc-openmpi)
("python-numpy" ,python-numpy)))
(home-page "https://bitbucket.org/petsc/petsc4py/")
(synopsis "Python bindings for PETSc")
(description "PETSc, the Portable, Extensible Toolkit for
Scientific Computation, is a suite of data structures and routines for
the scalable (parallel) solution of scientific applications modeled by
partial differential equations. It employs the MPI standard for all
message-passing communication. @code{petsc4py} provides Python
bindings to almost all functions of PETSc.")
(license license:bsd-3)))
(define-public python-kiwisolver
(package
(name "python-kiwisolver")
(version "1.0.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "kiwisolver" version))
(sha256
(base32
"0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
(build-system python-build-system)
(home-page "https://github.com/nucleic/kiwi")
(synopsis "Fast implementation of the Cassowary constraint solver")
(description
"Kiwi is an efficient C++ implementation of the Cassowary constraint
solving algorithm. Kiwi has been designed from the ground up to be
lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
Cassowary solver with typical use cases gaining a 40x improvement. Memory
savings are consistently > 5x.")
(license license:bsd-3)))
(define-public python2-kiwisolver
(package-with-python2 python-kiwisolver))
(define-public slepc
(package
(name "slepc")
(version "3.11.1")
(source
(origin
(method url-fetch)
(uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
version ".tar.gz"))
(sha256
(base32
"1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8"))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)
("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
(inputs
`(("arpack" ,arpack-ng)
("gfortran" ,gfortran)))
(propagated-inputs
`(("petsc" ,petsc)))
(arguments
`(#:parallel-build? #f ;build is parallel by default
#:configure-flags
`(,(string-append "--with-arpack-dir="
(assoc-ref %build-inputs "arpack") "/lib"))
#:make-flags ;honor (parallel-job-count)
`(,(format #f "MAKE_NP=~a" (parallel-job-count))
,(string-append "PETSCCONFIGDIR="
(assoc-ref %build-inputs "petsc:examples")
"/share/petsc/examples/config"))
#:phases
(modify-phases %standard-phases
(replace 'configure
;; configure is a python script, so we can't run it with bash.
(lambda* (#:key inputs outputs (configure-flags '())
#:allow-other-keys)
(let* ((prefix (assoc-ref outputs "out"))
(flags `(,(string-append "--prefix=" prefix)
,@configure-flags)))
(format #t "build directory: ~s~%" (getcwd))
(format #t "configure flags: ~s~%" flags)
(setenv "SLEPC_DIR" (getcwd))
(setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
(apply invoke "./configure" flags))))
(add-after 'install 'delete-doc
;; TODO: SLEPc installs HTML documentation alongside headers in
;; $out/include. We'd like to move them to share/doc, but delete
;; them for now, as they are incomplete and installing the complete
;; documentation is difficult.
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")))
(for-each delete-file (find-files out "\\.html$"))
#t)))
(add-after 'install 'clean-install
;; Clean up unnecessary build logs from installation.
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(for-each (lambda (file)
(let ((f (string-append out "/lib/slepc/conf/" file)))
(when (file-exists? f)
(delete-file f))))
'("configure.log" "make.log" "gmake.log"
"test.log" "error.log" "RDict.db"
"uninstall.py"))
#t))))))
(home-page "http://slepc.upv.es")
(synopsis "Scalable library for eigenproblems")
(description "SLEPc is a software library for the solution of large sparse
eigenproblems on parallel computers. It can be used for the solution of
linear eigenvalue problems formulated in either standard or generalized form,
as well as other related problems such as the singular value decomposition.
The emphasis of the software is on methods and techniques appropriate for
problems in which the associated matrices are sparse, for example, those
arising after the discretization of partial differential equations.")
(license license:bsd-2)))
(define-public slepc-complex
(package (inherit slepc)
(name "slepc-complex")
(propagated-inputs
`(("petsc" ,petsc-complex)
,@(alist-delete "petsc" (package-propagated-inputs slepc))))
(synopsis "Scalable library for eigenproblems (with complex scalars)")))
(define-public slepc-openmpi
(package (inherit slepc)
(name "slepc-openmpi")
(arguments
(substitute-keyword-arguments (package-arguments slepc)
((#:phases phases '%standard-phases)
`(modify-phases ,phases
(add-before 'check 'mpi-setup
,%openmpi-setup)))))
(inputs
`(("mpi" ,openmpi)
("arpack" ,arpack-ng-openmpi)
,@(alist-delete "arpack" (package-inputs slepc))))
(propagated-inputs
`(("petsc" ,petsc-openmpi)
,@(alist-delete "petsc" (package-propagated-inputs slepc))))
(synopsis "Scalable library for eigenproblems (with MPI support)")))
(define-public slepc-complex-openmpi
(package (inherit slepc-openmpi)
(name "slepc-complex-openmpi")
(propagated-inputs
`(("petsc" ,petsc-complex-openmpi)
,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
(synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
(define-public python-slepc4py
(package
(name "python-slepc4py")
(version "3.11.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "slepc4py" version))
(sha256
(base32
"1ksp08kxf4wg408b9nn39z3qfhy643j22d4rfbl30vzxk2rxh4lq"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-before 'build 'pre-build
(lambda _
;; Define path to PETSc installation.
(setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
;; Define path to SLEPc installation.
(setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
#t))
(add-before 'check 'mpi-setup
,%openmpi-setup))))
(inputs
`(("python-numpy" ,python-numpy)
("python-petsc4py" ,python-petsc4py)
("slepc" ,slepc-openmpi)))
(home-page "https://bitbucket.org/slepc/slepc4py/")
(synopsis "Python bindings for SLEPc")
(description "SLEPc, the Scalable Library for Eigenvalue Problem
Computations, is based on PETSc, the Portable, Extensible Toolkit for
Scientific Computation. It employs the MPI standard for all
message-passing communication. @code{slepc4py} provides Python
bindings to almost all functions of SLEPc.")
(license license:bsd-3)))
(define-public metamath
(package
(name "metamath")
(version "0.183")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/metamath/metamath-exe")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1jjf4fy6j53i40dh0yv0f9sngnw4gs24cig99vsg3q0303pwrhg7"))))
(build-system gnu-build-system)
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)))
(home-page "http://us.metamath.org/")
(synopsis "Proof verifier based on a minimalistic formalism")
(description
"Metamath is a tiny formal language and that can express theorems in
abstract mathematics, with an accompyaning @command{metamath} executable that
verifies databases of these proofs. There is a public database,
@url{https://github.com/metamath/set.mm, set.mm}, implementing first-order
logic and Zermelo-Frenkel set theory with Choice, along with a large swath of
associated, high-level theorems, e.g.@: the fundamental theorem of arithmetic,
the Cauchy-Schwarz inequality, Stirling's formula, etc. See the Metamath
book.")
(license license:gpl2+)))
(define-public mumps
(package
(name "mumps")
(version "5.2.1")
(source
(origin
(method url-fetch)
(uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
version ".tar.gz"))
(sha256
(base32
"0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r"))
(patches (search-patches "mumps-build-parallelism.patch"
"mumps-shared-libseq.patch"
"mumps-shared-mumps.patch"
"mumps-shared-pord.patch"))))
(build-system gnu-build-system)
(inputs
`(("fortran" ,gfortran)
;; These are required for linking against mumps, but we let the user
;; declare the dependency.
("blas" ,openblas)
("metis" ,metis)
("scotch" ,scotch)))
(arguments
`(#:modules ((ice-9 match)
(ice-9 popen)
(srfi srfi-1)
,@%gnu-build-system-modules)
#:phases
(modify-phases %standard-phases
(replace 'configure
(lambda* (#:key inputs #:allow-other-keys)
(call-with-output-file "Makefile.inc"
(lambda (port)
(format port "
PLAT =
LIBEXT = .a
OUTC = -o
OUTF = -o
RM = rm -f~:[
CC = gcc
FC = gfortran
FL = gfortran
INCSEQ = -I$(topdir)/libseq
LIBSEQ = $(topdir)/libseq/libmpiseq.a
LIBSEQNEEDED = libseqneeded~;
CC = mpicc
FC = mpifort
FL = mpifort~]
AR = ar vr # rules require trailing space, ugh...
RANLIB = ranlib
BLASDIR = ~a
LIBBLAS = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[
SCALAPDIR = ~a
SCALAP = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~]
LIBOTHERS = -pthread
CDEFS = -DAdd_
PIC = -fPIC
OPTF = -O2 -DALLOW_NON_INIT $(PIC)
OPTL = -O2 $(PIC)
OPTC = -O2 $(PIC)
INCS = $(INCSEQ)
LIBS = $(SCALAP) $(LIBSEQ)
LPORDDIR = $(topdir)/PORD/lib
IPORD = -I$(topdir)/PORD/include
LPORD = $(LPORDDIR)/libpord.a
ORDERINGSF = -Dpord~@[
METISDIR = ~a
IMETIS = -I$(METISDIR)/include
LMETIS = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
ORDERINGSF += -Dmetis~]~@[~:{
SCOTCHDIR = ~a
ISCOTCH = -I$(SCOTCHDIR)/include
LSCOTCH = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
ORDERINGSF += ~a~}~]
ORDERINGSC = $(ORDERINGSF)
LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
IORDERINGSF = $(ISCOTCH)
IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
(assoc-ref inputs "mpi")
(assoc-ref inputs "blas")
(assoc-ref inputs "scalapack")
(assoc-ref inputs "metis")
(match (list (assoc-ref inputs "pt-scotch")
(assoc-ref inputs "scotch"))
((#f #f)
#f)
((#f scotch)
`((,scotch "" "-Dscotch")))
((ptscotch _)
`((,ptscotch
"-lptesmumps -lptscotch -lptscotcherr "
"-Dptscotch")))))))))
(replace 'build
;; By default only the d-precision library is built. Make with "all"
;; target so that all precision libraries and examples are built.
(lambda _
(invoke "make" "all"
(format #f "-j~a" (parallel-job-count)))))
(replace 'check
;; Run the simple test drivers, which read test input from stdin:
;; from the "real" input for the single- and double-precision
;; testers, and from the "cmplx" input for complex-precision
;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
;; package to prefix execution with "mpirun".
(lambda* (#:key (exec-prefix '()) #:allow-other-keys)
(with-directory-excursion "examples"
(every
(lambda (prec type)
(let ((tester (apply open-pipe*
`(,OPEN_WRITE
,@exec-prefix
,(string-append "./" prec
"simpletest"))))
(input (open-input-file
(string-append "input_simpletest_" type))))
(begin
(dump-port input tester)
(close-port input)
(zero? (close-pipe tester)))))
'("s" "d" "c" "z")
'("real" "real" "cmplx" "cmplx")))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(libdir (string-append out "/lib")))
(copy-recursively "lib" libdir)
(copy-recursively "include" (string-append out "/include"))
(when (file-exists? "libseq/libmpiseq.a")
(install-file "libseq/libmpiseq.a" libdir))
(when (file-exists? "libseq/libmpiseq.so")
(install-file "libseq/libmpiseq.so" libdir))
#t))))))
(home-page "http://mumps.enseeiht.fr")
(synopsis "Multifrontal sparse direct solver")
(description
"MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
sparse system of linear equations A x = b using Gaussian elimination.")
(license license:cecill-c)))
(define-public mumps-metis
(package (inherit mumps)
(name "mumps-metis")
(inputs
(alist-delete "scotch" (package-inputs mumps)))))
(define-public mumps-openmpi
(package (inherit mumps)
(name "mumps-openmpi")
(inputs
`(("mpi" ,openmpi)
("scalapack" ,scalapack)
("pt-scotch" ,pt-scotch)
,@(alist-delete "scotch" (package-inputs mumps))))
(arguments
(substitute-keyword-arguments (package-arguments mumps)
((#:phases phases)
`(modify-phases ,phases
(add-before 'check 'mpi-setup
,%openmpi-setup)
(replace 'check
(lambda _
((assoc-ref ,phases 'check)
#:exec-prefix '("mpirun" "-n" "2"))))))))
(synopsis "Multifrontal sparse direct solver (with MPI)")))
(define-public mumps-metis-openmpi
(package (inherit mumps-openmpi)
(name "mumps-metis-openmpi")
(inputs
(alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
(define-public ruby-asciimath
(package
(name "ruby-asciimath")
(version "2.0.1")
(source
(origin
(method url-fetch)
(uri (rubygems-uri "asciimath" version))
(sha256
(base32
"1aapydwwkydbwgz07n7ma3a5jy9n3v0shy6q6j8mi4wr3crhx45a"))))
(build-system ruby-build-system)
(native-inputs
`(("ruby-nokogiri" ,ruby-nokogiri)
("ruby-rspec" ,ruby-rspec)))
(synopsis "AsciiMath parsing and conversion library")
(description
"A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
easy-to-write markup language for mathematics.")
(home-page "https://github.com/asciidoctor/asciimath")
(license license:expat)))
(define-public superlu
(package
(name "superlu")
(version "5.2.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://portal.nersc.gov/project/sparse/superlu/"
"superlu_" version ".tar.gz"))
(sha256
(base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
(modules '((guix build utils)))
(snippet
;; Replace the non-free implementation of MC64 with a stub adapted
;; from Debian
'(begin
(use-modules (ice-9 regex)
(ice-9 rdelim))
(call-with-output-file "SRC/mc64ad.c"
(lambda (port)
(display "
#include <stdio.h>
#include <stdlib.h>
void mc64id_(int *a) {
fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
abort ();
}
void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
abort ();
}\n" port)))
;; Remove the corresponding license verbiage. MC64 license follows
;; a "------" line separator.
(with-atomic-file-replacement "License.txt"
(let ((rx (make-regexp "-{8}")))
(lambda (in out)
(let loop ()
(let ((line (read-line in 'concat)))
(unless (regexp-exec rx line)
(display line out)
(loop))))
#t)))))))
(build-system cmake-build-system)
(native-inputs
`(("tcsh" ,tcsh)))
(inputs
`(("blas" ,openblas)
("gfortran" ,gfortran)))
(arguments
`(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
"-DTPL_BLAS_LIBRARIES=openblas"
"-DBUILD_SHARED_LIBS:BOOL=YES")))
(home-page "https://portal.nersc.gov/project/sparse/superlu/")
(synopsis "Supernodal direct solver for sparse linear systems")
(description
"SuperLU is a general purpose library for the direct solution of large,
sparse, nonsymmetric systems of linear equations on high performance machines.
The library is written in C and is callable from either C or Fortran. The
library routines perform an LU decomposition with partial pivoting and
triangular system solves through forward and back substitution. The library
also provides threshold-based ILU factorization preconditioners.")
(license (list license:bsd-3
license:gpl2+ ;EXAMPLE/*fgmr.c
(license:fsf-free "file://SRC/colamd.h")))))
(define-public superlu-dist
(package
(name "superlu-dist")
(version "6.2.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://portal.nersc.gov/project/sparse/superlu/"
"superlu_dist_" version ".tar.gz"))
(sha256
(base32 "1ynmwqajc9sc3my2hssa5k9s58ggvizqv9rdss0j7w99pbh5mnvw"))
(modules '((guix build utils)))
(snippet
;; Replace the non-free implementation of MC64 with a stub
'(begin
(call-with-output-file "SRC/mc64ad_dist.c"
(lambda (port)
(display "
#include <stdio.h>
#include <stdlib.h>
void mc64id_dist(int *a) {
fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
abort ();
}
void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
abort ();
}\n" port)))
(substitute* "SRC/util.c" ;adjust default algorithm
(("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
;; general (i.e. non-square) processor-grid support.
"RowPerm = NOROWPERM;"))
#t))
(patches (search-patches "superlu-dist-scotchmetis.patch"
"superlu-dist-awpm-grid.patch"))))
(build-system cmake-build-system)
(native-inputs
`(("tcsh" ,tcsh)))
(inputs
`(("gfortran" ,gfortran)
("blas" ,openblas)
("lapack" ,lapack)
("combblas" ,combinatorial-blas)))
(propagated-inputs
`(("mpi" ,openmpi) ;headers include MPI heades
("parmetis" ,pt-scotch32 "metis")
("pt-scotch" ,pt-scotch32)))
(arguments
`(#:parallel-tests? #f ;tests use MPI and OpenMP
#:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
"-DTPL_ENABLE_COMBBLASLIB=YES"
"-DTPL_BLAS_LIBRARIES=-lopenblas"
"-DTPL_LAPACK_LIBRARIES=-llapack"
(string-append "-DTPL_PARMETIS_LIBRARIES="
(string-join
'("ptscotchparmetis" "ptscotch" "ptscotcherr"
"scotchmetis" "scotch" "scotcherr")
";"))
(string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
(assoc-ref %build-inputs "parmetis")
"/include")
"-DTPL_ENABLE_COMBBLASLIB=ON"
(string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
(assoc-ref %build-inputs "combblas")
"/include/CombBLAS;"
(assoc-ref %build-inputs "combblas")
"/include/BipartiteMatchings")
"-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
#:phases
(modify-phases %standard-phases
(add-before 'configure 'set-c++-standard
(lambda _
(substitute* "CMakeLists.txt"
;; AWPM headers require C++14
(("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
(add-before 'check