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gnu: mumps: Build and install shared libraries.
[jackhill/guix/guix.git] / gnu / packages / maths.scm
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8f8b2451 1;;; GNU Guix --- Functional package management for GNU
26433471 2;;; Copyright © 2013, 2014, 2015, 2016, 2019 Andreas Enge <andreas@enge.fr>
da95c817 3;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
a53d6719 4;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
6d433d6e 5;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Eric Bavier <bavier@member.fsf.org>
df354a77 6;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
182d6311 7;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
0aad198e 8;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
32158110 9;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
df129041 10;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
0ef54303 11;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
45147b0c 12;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
ec8c7e47 13;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
ab5f3f21 14;;; Copyright © 2016, 2018 Kei Kebreau <kkebreau@posteo.net>
59a07504 15;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
d7cff656 16;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
2fd26d05 17;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
37dc2920 18;;; Copyright © 2017, 2018, 2019 Paul Garlick <pgarlick@tourbillion-technology.com>
47956fa0 19;;; Copyright © 2017 ng0 <ng0@n0.is>
ba1be533 20;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
d109b1e8 21;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
b18b9d20 22;;; Copyright © 2017, 2019 Arun Isaac <arunisaac@systemreboot.net>
98a5cd51 23;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
dc7d6d4e 24;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
3bc74090 25;;; Copyright © 2018, 2019 Jan Nieuwenhuizen <janneke@gnu.org>
41835f94 26;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
910deec6 27;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
07254d8b 28;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
560acf25 29;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
daa6036f 30;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
564cf93f 31;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
fa574a6d 32;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
6f8c4195 33;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
4cb5d251 34;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
8f8b2451
AE		 35;;;
36;;; This file is part of GNU Guix.
37;;;
38;;; GNU Guix is free software; you can redistribute it and/or modify it
39;;; under the terms of the GNU General Public License as published by
40;;; the Free Software Foundation; either version 3 of the License, or (at
41;;; your option) any later version.
42;;;
43;;; GNU Guix is distributed in the hope that it will be useful, but
44;;; WITHOUT ANY WARRANTY; without even the implied warranty of
45;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
46;;; GNU General Public License for more details.
47;;;
48;;; You should have received a copy of the GNU General Public License
49;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
50
51(define-module (gnu packages maths)
ec322be2 52 #:use-module (ice-9 regex)
a6b9ebc2 53 #:use-module (ice-9 match)
8f8b2451 54 #:use-module (gnu packages)
b5b73a82 55 #:use-module ((guix licenses) #:prefix license:)
8f8b2451
AE		 56 #:use-module (guix packages)
57 #:use-module (guix download)
54052a54 58 #:use-module (guix git-download)
0e2672ae 59 #:use-module (guix utils)
fa574a6d 60 #:use-module ((guix build utils) #:select (alist-replace))
da95c817 61 #:use-module (guix build-system cmake)
c9dfa3c7 62 #:use-module (guix build-system gnu)
560acf25 63 #:use-module (guix build-system python)
ec8c7e47 64 #:use-module (guix build-system r)
63e07468 65 #:use-module (guix build-system ruby)
3de01d3f 66 #:use-module (gnu packages algebra)
ab5f3f21 67 #:use-module (gnu packages audio)
5143517c 68 #:use-module (gnu packages autotools)
fa574a6d 69 #:use-module (gnu packages base)
3de01d3f 70 #:use-module (gnu packages bison)
a17d4564 71 #:use-module (gnu packages boost)
e73b49fb 72 #:use-module (gnu packages check)
3de01d3f 73 #:use-module (gnu packages cmake)
c9dfa3c7 74 #:use-module (gnu packages compression)
668c06ac 75 #:use-module (gnu packages curl)
b7b27a8f 76 #:use-module (gnu packages cyrus-sasl)
528bb464 77 #:use-module (gnu packages documentation)
57e544e8 78 #:use-module (gnu packages elf)
3de01d3f 79 #:use-module (gnu packages flex)
668c06ac 80 #:use-module (gnu packages fltk)
f3929800 81 #:use-module (gnu packages fontutils)
1dba6407 82 #:use-module (gnu packages gettext)
da95c817 83 #:use-module (gnu packages gcc)
73fed4f8 84 #:use-module (gnu packages gd)
668c06ac 85 #:use-module (gnu packages ghostscript)
889187a4 86 #:use-module (gnu packages graphviz)
f3929800 87 #:use-module (gnu packages gtk)
45147b0c 88 #:use-module (gnu packages image)
2fd26d05 89 #:use-module (gnu packages java)
668c06ac 90 #:use-module (gnu packages less)
8731e527 91 #:use-module (gnu packages lisp)
ab5f3f21 92 #:use-module (gnu packages linux)
bc3a2e35 93 #:use-module (gnu packages logging)
6e64766a 94 #:use-module (gnu packages lua)
5698b8b8 95 #:use-module (gnu packages gnome)
1b39a196 96 #:use-module (gnu packages guile)
668c06ac
JD		 97 #:use-module (gnu packages xorg)
98 #:use-module (gnu packages gl)
9f913401 99 #:use-module (gnu packages imagemagick)
8731e527 100 #:use-module (gnu packages m4)
d8c7eeb9 101 #:use-module (gnu packages mpi)
b92eee75 102 #:use-module (gnu packages multiprecision)
528bb464 103 #:use-module (gnu packages netpbm)
bd3d71cb 104 #:use-module (gnu packages onc-rpc)
668c06ac 105 #:use-module (gnu packages pcre)
5698b8b8 106 #:use-module (gnu packages popt)
c9dfa3c7
AE		 107 #:use-module (gnu packages perl)
108 #:use-module (gnu packages pkg-config)
ab5f3f21 109 #:use-module (gnu packages pulseaudio)
da95c817 110 #:use-module (gnu packages python)
589e3f4e 111 #:use-module (gnu packages python-web)
44d10b1f 112 #:use-module (gnu packages python-xyz)
5b05dce7 113 #:use-module (gnu packages qt)
c9dfa3c7 114 #:use-module (gnu packages readline)
63e07468 115 #:use-module (gnu packages ruby)
2742f87e 116 #:use-module (gnu packages tbb)
479c4273 117 #:use-module (gnu packages scheme)
b7194849 118 #:use-module (gnu packages shells)
df354a77 119 #:use-module (gnu packages tcl)
668c06ac 120 #:use-module (gnu packages texinfo)
8f9ac901 121 #:use-module (gnu packages tex)
b7b27a8f 122 #:use-module (gnu packages tls)
5b05dce7 123 #:use-module (gnu packages version-control)
9aafbc0c 124 #:use-module (gnu packages wxwidgets)
c12efc72 125 #:use-module (gnu packages xml)
a17d4564 126 #:use-module (srfi srfi-1))
8f8b2451 127
193abc82
JD		 128(define-public aris
129 (package
1f45f18a
JD		 130 (name "aris")
131 (version "2.2")
132 (source (origin
133 (method url-fetch)
134 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
135 (sha256 (base32
136 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
137 (build-system gnu-build-system)
138 (inputs `(("gtk+" ,gtk+)
139 ("libxml2" ,libxml2)))
140 (native-inputs `(("pkg-config" ,pkg-config)))
141 (synopsis "Natural deduction first-order logic interface")
142 (description "Aris is a program for performing logical proofs. It supports
143propositional and predicate logic, as well as Boolean algebra and
144arithmetical logic. In addition to its predefined inference and equivalence
145rules, Aris also supports references to older proofs. Its use of standard
146logical symbols and its natural deduction interface make it easy to use for
147beginners.")
148 (license license:gpl3+)
6fd52309 149 (home-page "https://www.gnu.org/software/aris/")))
193abc82 150
9c45c519
JD		 151(define-public c-graph
152 (package
153 (name "c-graph")
0ef54303 154 (version "2.0.1")
9c45c519
JD		 155 (source (origin
156 (method url-fetch)
157 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
158 ".tar.gz"))
159 (sha256 (base32
0ef54303 160 "092412jzxy6wdvpk96pfj499hpmaww8xllavbvlqspfpr7ips9id"))))
9c45c519
JD		 161 (build-system gnu-build-system)
162 (inputs
0ef54303 163 `(("fortran" ,gfortran)))
a3947cb1 164 (synopsis "Visualizing and demonstrating convolution")
9c45c519 165 (description
0ef54303 166 "GNU C-Graph is a tool for demonstrating the theory of convolution.
a3947cb1
LC		 167Thus, it can serve as an excellent aid to students of signal and systems
168theory in visualizing the convolution process. Rather than forcing the
169student to write code, the program offers an intuitive interface with
170interactive dialogs to guide them.")
9c45c519 171 (license license:gpl3+)
6fd52309 172 (home-page "https://www.gnu.org/software/c-graph/")))
9c45c519 173
d91025e3
TD		 174(define-public coda
175 (package
176 (name "coda")
9285f8bb 177 (version "2.19")
d91025e3
TD		 178 (source
179 (origin
180 (method url-fetch)
181 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
182 version "/coda-" version ".tar.gz"))
183 (sha256
9285f8bb 184 (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245"))
4b12fe5c
TD		 185 (patches (search-patches "coda-use-system-libs.patch"))
186 (modules '((guix build utils)))
187 (snippet
188 ;; Make sure we don't use the bundled software.
6cbee49d
MW		 189 '(begin
190 (for-each (lambda (d)
191 (delete-file-recursively (string-append "libcoda/" d)))
192 '("zlib" "pcre" "expat"))
193 #t))))
d91025e3
TD		 194 (native-inputs
195 `(("fortran" ,gfortran)
196 ("python" ,python)
197 ("python-numpy" ,python-numpy)))
198 (inputs
199 `(("zlib" ,zlib)
4b12fe5c
TD		 200 ("pcre" ,pcre)
201 ("expat" ,expat)
d91025e3
TD		 202 ("hdf4" ,hdf4-alt)
203 ("hdf5" ,hdf5)))
204 (build-system gnu-build-system)
205 (arguments
4b12fe5c
TD		 206 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
207 "LIBS= -lz -lpcre -lexpat")))
d91025e3
TD		 208 (synopsis "A common interface to various earth observation data formats")
209 (description
210 "The Common Data Access toolbox (CODA) provides a set of interfaces for
211reading remote sensing data from earth observation data files. It consists of
212command line applications and interfaces to the C, Fortran, Python, and Java
213programming languages.")
214 (home-page "https://stcorp.nl/coda")
215 (license license:gpl2+)))
216
d65f0661
KK		 217(define-public qhull
218 (package
219 (name "qhull")
220 (version "2015.2")
221 (source (origin
222 (method url-fetch)
223 (uri (string-append "http://www.qhull.org/download/qhull-"
224 (car (string-split version #\.))
225 "-src-7.2.0.tgz"))
226 (sha256
227 (base32
228 "0dm4b2xr3asy6w74khq2zg4gf26zsy3qf9sq7pf7lmrvbj911c3q"))))
229 (build-system cmake-build-system)
230 (synopsis "Calculate convex hulls and related structures")
231 (description
232 "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
233diagram, halfspace intersection about a point, furthest-site Delaunay
234triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d,
2353-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull
236algorithm for computing the convex hull. It handles roundoff errors from
237floating point arithmetic. It computes volumes, surface areas, and
238approximations to the convex hull.
239
240@code{Qhull} does not support triangulation of non-convex surfaces, mesh
241generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
242shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
243triangulations.")
244 (home-page "http://qhull.org")
245 (license (license:non-copyleft "file://COPYING.txt"
246 "See COPYING in the distribution."))))
247
a8fa86c4
RW		 248(define-public python-cvxopt
249 (package
250 (name "python-cvxopt")
a7c7015a 251 (version "1.2.3")
a8fa86c4
RW		 252 (source (origin
253 (method git-fetch)
254 (uri (git-reference
255 (url "https://github.com/cvxopt/cvxopt.git")
256 (commit version)))
257 (file-name (git-file-name name version))
258 (sha256
259 (base32
a7c7015a 260 "1kiy2m62xgs2d5id6dnnwy4vap85cd70p7pgkb9nh23qf9xnak7b"))))
a8fa86c4
RW		 261 (build-system python-build-system)
262 (arguments
263 `(#:phases
264 (modify-phases %standard-phases
265 (add-after 'unpack 'find-libraries
266 (lambda* (#:key inputs #:allow-other-keys)
267 (setenv "CVXOPT_BLAS_LIB" "openblas")
268 (setenv "CVXOPT_BUILD_FFTW" "1")
269 (setenv "CVXOPT_BUILD_GLPK" "1")
270 (setenv "CVXOPT_BUILD_GSL" "1")
271 #t)))))
272 (inputs
273 `(("fftw" ,fftw)
274 ("glpk" ,glpk)
275 ("gsl" ,gsl)
276 ("lapack" ,lapack)
277 ("openblas" ,openblas)
278 ("suitesparse" ,suitesparse)))
279 (home-page "https://www.cvxopt.org")
280 (synopsis "Python library for convex optimization")
281 (description
282 "CVXOPT is a package for convex optimization based on the Python
283programming language. Its main purpose is to make the development of software
284for convex optimization applications straightforward by building on Python’s
285extensive standard library and on the strengths of Python as a high-level
286programming language.")
287 (license license:gpl3+)))
288
289(define-public python2-cvxopt
290 (package-with-python2 python-cvxopt))
291
8f8b2451
AE		 292(define-public units
293 (package
294 (name "units")
494a8cd0 295 (version "2.19")
8f8b2451
AE		 296 (source (origin
297 (method url-fetch)
298 (uri (string-append "mirror://gnu/units/units-" version
299 ".tar.gz"))
300 (sha256 (base32
494a8cd0 301 "0mk562g7dnidjgfgvkxxpvlba66fh1ykmfd9ylzvcln1vxmi6qj2"))))
8f8b2451 302 (build-system gnu-build-system)
0498d248 303 (inputs
a2549713
EB		 304 `(("readline" ,readline)
305 ("python" ,python-wrapper) ;for 'units_cur' script
0498d248
EB		 306 ("python-requests" ,python-requests)))
307 (arguments
308 `(#:phases (modify-phases %standard-phases
309 (add-after 'install 'wrap-units_cur
310 (lambda* (#:key outputs #:allow-other-keys)
311 (let* ((out (assoc-ref outputs "out"))
312 (bin (string-append out "/bin")))
313 (wrap-program (string-append bin "/units_cur")
314 `("PYTHONPATH" ":" prefix
315 ,(search-path-as-string->list (getenv "PYTHONPATH"))))
316 #t))))))
8f8b2451
AE		 317 (synopsis "Conversion between thousands of scales")
318 (description
574e86f9 319 "GNU Units converts numeric quantities between units of measure. It
7c125ce0
AK		 320can handle scale changes through adaptive usage of standard scale
321prefixes (micro-, kilo-, etc.). It can also handle nonlinear
322conversions such as Fahrenheit to Celsius. Its interpreter is powerful
323enough to be used effectively as a scientific calculator.")
8f8b2451 324 (license license:gpl3+)
6fd52309 325 (home-page "https://www.gnu.org/software/units/")))
c9dfa3c7 326
61a529b4
RW		 327(define-public double-conversion
328 (package
329 (name "double-conversion")
1c7d7f3f 330 (version "3.1.5")
b343850e 331 (home-page "https://github.com/google/double-conversion")
61a529b4 332 (source (origin
2bdc73fb 333 (method git-fetch)
a4de1a65
MB		 334 (uri (git-reference (url home-page)
335 (commit (string-append "v" version))))
2bdc73fb 336 (file-name (git-file-name name version))
61a529b4
RW		 337 (sha256
338 (base32
1c7d7f3f 339 "0csy4pjw1p8rp6g5qxi2h0ychhhp1fldv7gb761627fs2mclw9gv"))))
61a529b4
RW		 340 (build-system cmake-build-system)
341 (arguments
342 '(#:test-target "test"
343 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
344 "-DBUILD_TESTING=ON")))
61a529b4
RW		 345 (synopsis "Conversion routines for IEEE doubles")
346 (description
347 "The double-conversion library provides binary-decimal and decimal-binary
348routines for IEEE doubles. The library consists of efficient conversion
349routines that have been extracted from the V8 JavaScript engine.")
350 (license license:bsd-3)))
351
182d6311
ML		 352(define-public dionysus
353 (package
354 (name "dionysus")
bd041e7f 355 (version "1.4.0")
182d6311
ML		 356 (source (origin
357 (method url-fetch)
358 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
bd041e7f 359 ".tar.xz"))
182d6311
ML		 360 (sha256
361 (base32
bd041e7f 362 "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
182d6311
ML		 363 (build-system gnu-build-system)
364 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
365 (synopsis "Local search for universal constants and scientific values")
366 (description
367 "GNU Dionysus is a convenient system for quickly retrieving the values of
368mathematical constants used in science and engineering. Values can be
369searched using a simple command-line tool, choosing from three databases:
370universal constants, atomic numbers, and constants related to
371semiconductors.")
372 (license license:gpl3+)
6fd52309 373 (home-page "https://www.gnu.org/software/dionysus/")))
182d6311 374
88bd1804
AE		 375(define-public gsl
376 (package
377 (name "gsl")
f3a34b9d 378 (version "2.5")
ab2cc5cd
LC		 379 (source (origin
380 (method url-fetch)
381 (uri (string-append "mirror://gnu/gsl/gsl-"
382 version ".tar.gz"))
383 (sha256
384 (base32
f3a34b9d 385 "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
ab2cc5cd 386 (patches (search-patches "gsl-test-i686.patch"))))
88bd1804 387 (build-system gnu-build-system)
71e0f288 388 (arguments
f885fc05 389 `(;; Currently there are numerous tests that fail on "exotic"
6f766069
EF		 390 ;; architectures such as aarch64 and ppc64le.
391 ,@(if (string-prefix? "aarch64-linux"
392 (or (%current-target-system) (%current-system)))
393 '(#:tests? #f)
394 '())))
395 (home-page "https://www.gnu.org/software/gsl/")
88bd1804
AE		 396 (synopsis "Numerical library for C and C++")
397 (description
a22dc0c4
LC		 398 "The GNU Scientific Library is a library for numerical analysis in C
399and C++. It includes a wide range of mathematical routines, with over 1000
400functions in total. Subject areas covered by the library include:
401differential equations, linear algebra, Fast Fourier Transforms and random
402numbers.")
88bd1804
AE		 403 (license license:gpl3+)))
404
b92eee75
AE		 405(define-public glpk
406 (package
407 (name "glpk")
445929e0 408 (version "4.65")
b92eee75
AE		 409 (source
410 (origin
411 (method url-fetch)
412 (uri (string-append "mirror://gnu/glpk/glpk-"
413 version ".tar.gz"))
414 (sha256
415 (base32
445929e0 416 "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
b92eee75
AE		 417 (build-system gnu-build-system)
418 (inputs
419 `(("gmp" ,gmp)))
420 (arguments
421 `(#:configure-flags '("--with-gmp")))
82110ef6 422 (home-page "https://www.gnu.org/software/glpk/")
79c311b8 423 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
b92eee75
AE		 424 (description
425 "GLPK is a C library for solving large-scale linear programming (LP),
426mixed integer programming (MIP), and other related problems. It supports the
427GNU MathProg modeling language, a subset of the AMPL language, and features a
428translator for the language. In addition to the C library, a stand-alone
429LP/MIP solver is included in the package.")
430 (license license:gpl3+)))
431
b146763a
AE		 432(define-public 4ti2
433 (package
434 (name "4ti2")
eea4a091 435 (version "1.6.9")
b146763a
AE		 436 (source
437 (origin
eea4a091
TGR		 438 (method url-fetch)
439 (uri (string-append "https://github.com/4ti2/4ti2/releases/download/"
440 "Release_"
441 (string-map (lambda (c) (if (char=? c #\.) #\_ c))
442 version)
443 "/4ti2-" version ".tar.gz"))
444 (sha256
445 (base32 "0rj92x6p9m3la5gasjbj7sa569im527ffmka5y2sv1amgd3fflrh"))))
b146763a
AE		 446 (build-system gnu-build-system)
447 (native-inputs
448 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
449 (inputs
450 `(("glpk" ,glpk)
451 ("gmp" ,gmp)))
452 (home-page "http://www.4ti2.de/")
453 (synopsis "Mathematical tool suite for problems on linear spaces")
454 (description
455 "4ti2 implements algorithms for solving algebraic, geometric and
456combinatorial problems on linear spaces. Among others, it solves systems
457of linear equations, computes extreme rays of polyhedral cones, solves
458integer programming problems and computes Markov bases for statistics.")
459 (license license:gpl2+)))
460
53696f10
AE		 461(define-public cddlib
462 (package
463 (name "cddlib")
7fe491fb 464 (version "0.94i")
53696f10
AE		 465 (source
466 (origin
467 (method url-fetch)
182dde82 468 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
53696f10
AE		 469 (string-delete #\. version) ".tar.gz"))
470 (sha256
471 (base32
7fe491fb 472 "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
53696f10
AE		 473 (build-system gnu-build-system)
474 (inputs
475 `(("gmp" ,gmp)))
476 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
477 (synopsis "Library for convex hulls and extreme rays of polyhedra")
478 (description
479 "The C-library cddlib implements the Double Description Method of
480Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
481rays of a general convex polyhedron given by a system of linear inequalities
482in arbitrary dimension. It can also be used for the converse operation of
483computing convex hulls.")
484 (license license:gpl2+)))
485
865a69dd
RW		 486(define-public arpack-ng
487 (package
488 (name "arpack-ng")
f03c4ec6 489 (version "3.6.3")
c0edb5b5 490 (home-page "https://github.com/opencollab/arpack-ng")
622ef2b9
MB		 491 (source (origin
492 (method git-fetch)
493 (uri (git-reference (url home-page) (commit version)))
494 (file-name (git-file-name name version))
495 (sha256
496 (base32
f03c4ec6 497 "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
865a69dd 498 (build-system gnu-build-system)
c0edb5b5
LC		 499 (native-inputs
500 `(("autoconf" ,autoconf)
501 ("automake" ,automake)
502 ("libtool" ,libtool)))
865a69dd
RW		 503 (inputs
504 `(("lapack" ,lapack)
19afbea1 505 ("fortran" ,gfortran)))
865a69dd
RW		 506 (synopsis "Fortran subroutines for solving eigenvalue problems")
507 (description
508 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
509large scale eigenvalue problems.")
166191b3 510 (license (license:non-copyleft "file://COPYING"
865a69dd
RW		 511 "See COPYING in the distribution."))))
512
c0edb5b5
LC		 513(define-public arpack-ng-3.3.0
514 (package
515 (inherit arpack-ng)
516 (version "3.3.0")
517 (name (package-name arpack-ng))
518 (home-page (package-home-page arpack-ng))
519 (source
520 (origin
521 (method url-fetch)
522 (uri (string-append home-page "/archive/" version ".tar.gz"))
523 (file-name (string-append name "-" version ".tar.gz"))
524 (sha256
525 (base32
526 "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
527
8c94c886
EB		 528(define-public arpack-ng-openmpi
529 (package (inherit arpack-ng)
530 (name "arpack-ng-openmpi")
531 (inputs
532 `(("mpi" ,openmpi)
533 ,@(package-inputs arpack-ng)))
4f387541
LC		 534 (arguments
535 (substitute-keyword-arguments (package-arguments arpack-ng)
536 ((#:configure-flags _ '())
aa82260b
PG		 537 ''("--enable-mpi"))
538 ((#:phases phases '%standard-phases)
539 `(modify-phases ,phases
bbe46a4a
EB		 540 (add-before 'check 'mpi-setup
541 ,%openmpi-setup)))))
8c94c886
EB		 542 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
543
da95c817
NK		 544(define-public lapack
545 (package
546 (name "lapack")
ef39a177 547 (version "3.7.1")
da95c817
NK		 548 (source
549 (origin
550 (method url-fetch)
551 (uri (string-append "http://www.netlib.org/lapack/lapack-"
552 version ".tgz"))
553 (sha256
554 (base32
7c0d4c3a 555 "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
da95c817
NK		 556 (build-system cmake-build-system)
557 (home-page "http://www.netlib.org/lapack/")
19afbea1 558 (inputs `(("fortran" ,gfortran)
da95c817
NK		 559 ("python" ,python-2)))
560 (arguments
3ab869b6 561 `(#:configure-flags (list
3ab869b6
LC		 562 "-DBUILD_SHARED_LIBS:BOOL=YES"
563 "-DLAPACKE=ON"
564
565 ;; Build the 'LAPACKE_clatms' functions.
566 "-DLAPACKE_WITH_TMG=ON")
dc1d3cde
KK		 567 #:phases
568 (modify-phases %standard-phases
569 (add-before 'check 'patch-python
570 (lambda* (#:key inputs #:allow-other-keys)
571 (let ((python (assoc-ref inputs "python")))
572 (substitute* "lapack_testing.py"
573 (("/usr/bin/env python") python)))
574 #t)))))
da95c817
NK		 575 (synopsis "Library for numerical linear algebra")
576 (description
577 "LAPACK is a Fortran 90 library for solving the most commonly occurring
578problems in numerical linear algebra.")
166191b3 579 (license (license:non-copyleft "file://LICENSE"
da95c817 580 "See LICENSE in the distribution."))))
73fed4f8 581
e1ff597a
EB		 582(define-public scalapack
583 (package
584 (name "scalapack")
585 (version "2.0.2")
586 (source
587 (origin
588 (method url-fetch)
589 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
590 version ".tgz"))
591 (sha256
592 (base32
f73750e6
EB		 593 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))
594 (patches (search-patches "scalapack-blacs-mpi-deprecations.patch"))))
e1ff597a
EB		 595 (build-system cmake-build-system)
596 (inputs
597 `(("mpi" ,openmpi)
598 ("fortran" ,gfortran)
599 ("lapack" ,lapack))) ;for testing only
600 (arguments
6df2a50a
LC		 601 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
602 #:phases (modify-phases %standard-phases
bbe46a4a
EB		 603 (add-before 'check 'mpi-setup
604 ,%openmpi-setup))))
e1ff597a
EB		 605 (home-page "http://www.netlib.org/scalapack/")
606 (synopsis "Library for scalable numerical linear algebra")
607 (description
608 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
609routines on parallel distributed memory machines. ScaLAPACK solves dense and
610banded linear systems, least squares problems, eigenvalue problems, and
611singular value problems.")
adb223b8
LC		 612 (license (license:non-copyleft "file://LICENSE"
613 "See LICENSE in the distribution."))))
e1ff597a 614
73fed4f8 615(define-public gnuplot
5f800540
KK		 616 (package
617 (name "gnuplot")
cb1d8aee 618 (version "5.2.7")
5f800540
KK		 619 (source (origin
620 (method url-fetch)
621 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
622 version "/gnuplot-"
623 version ".tar.gz"))
624 (sha256
cb1d8aee 625 (base32 "1vglp4la40f5dpj0zdj63zprrkyjgzy068p35bz5dqxjyczm1zlp"))))
5f800540
KK		 626 (build-system gnu-build-system)
627 (inputs `(("readline" ,readline)
628 ("cairo" ,cairo)
629 ("pango" ,pango)
6e64766a
DM		 630 ("gd" ,gd)
631 ("lua" ,lua)))
612a387f
RW		 632 (native-inputs
633 `(("pkg-config" ,pkg-config)
634 ("texlive" ,texlive-tiny)))
07254d8b
AM		 635 (arguments `(#:configure-flags (list (string-append
636 "--with-texdir=" %output
637 "/texmf-local/tex/latex/gnuplot"))))
5f800540
KK		 638 (home-page "http://www.gnuplot.info")
639 (synopsis "Command-line driven graphing utility")
640 (description "Gnuplot is a portable command-line driven graphing
35b9e423 641utility. It was originally created to allow scientists and students to
73fed4f8 642visualize mathematical functions and data interactively, but has grown to
35b9e423 643support many non-interactive uses such as web scripting. It is also used as a
73fed4f8 644plotting engine by third-party applications like Octave.")
5f800540
KK		 645 ;; X11 Style with the additional restriction that derived works may only be
646 ;; distributed as patches to the original.
647 (license (license:fsf-free
648 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
668c06ac 649
32f70e1f
TD		 650(define-public gctp
651 (package
652 (name "gctp")
653 (version "2.0.0")
654 (source
655 (origin
5db874d1
TGR		 656 (method git-fetch)
657 (uri (git-reference
658 (url "https://github.com/OkoSanto/GCTP.git")
659 (commit (string-append "v" version))))
660 (file-name (git-file-name name version))
32f70e1f 661 (sha256
5db874d1 662 (base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
32f70e1f
TD		 663 (native-inputs
664 `(("fortran" ,gfortran)))
665 (build-system gnu-build-system)
666 (synopsis "General Cartographic Transformation Package (GCTP)")
667 (description
668 "The General Cartographic Transformation Package (GCTP) is a system of
669software routines designed to permit the transformation of coordinate pairs
670from one map projection to another. The GCTP is the standard computer
671software used by the National Mapping Division for map projection
672computations.")
673 (home-page "https://github.com/OkoSanto/GCTP")
0f7cd95b 674 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
32f70e1f 675
becbbefc
TD		 676(define-public hdf4
677 (package
678 (name "hdf4")
c959d99f 679 (version "4.2.14")
becbbefc
TD		 680 (source
681 (origin
682 (method url-fetch)
683 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
684 version "/src/hdf-" version ".tar.bz2"))
685 (sha256
c959d99f 686 (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l"))
15ca49b2
AE		 687 (patches (search-patches "hdf4-architectures.patch"
688 "hdf4-reproducibility.patch"
bd3d71cb
MB		 689 "hdf4-shared-fortran.patch"
690 "hdf4-tirpc.patch"))))
becbbefc
TD		 691 (build-system gnu-build-system)
692 (native-inputs
693 `(("gfortran" ,gfortran)
694 ("bison" ,bison)
695 ("flex" ,flex)))
696 (inputs
697 `(("zlib" ,zlib)
bd3d71cb
MB		 698 ("libjpeg" ,libjpeg)
699 ("libtirpc" ,libtirpc)))
becbbefc
TD		 700 (arguments
701 `(#:parallel-tests? #f
bd3d71cb
MB		 702 #:configure-flags (list "--enable-shared"
703 (string-append "CPPFLAGS=-I"
704 (assoc-ref %build-inputs "libtirpc")
705 "/include/tirpc"))
becbbefc
TD		 706 #:phases
707 (modify-phases %standard-phases
953a12fa
EF		 708 ;; This is inspired by two of Debian's patches.
709 (add-before 'configure 'add-more-aarch64-support
710 (lambda _
711 (substitute* '("mfhdf/ncgen/ncgen.l"
712 "mfhdf/ncgen/ncgenyy.c"
713 "mfhdf/libsrc/netcdf.h.in")
714 (("AIX5L64") "__aarch64__"))
715 #t))
becbbefc
TD		 716 (add-before 'configure 'patchbuild
717 (lambda _
718 (substitute*
719 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
720 (("/bin/rm") "rm")
721 (("/bin/mkdir") "mkdir"))
722 (substitute* (find-files "." "^Makefile\\.in$")
723 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
724-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
725 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
726-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
953a12fa 727-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
e464b455
TD		 728 #t))
729 (add-after 'configure 'patch-settings
730 (lambda _
731 ;; libhdf4.settings contains the full path of the
732 ;; compilers used, and its contents are included in
733 ;; .so-files. We truncate the hashes to avoid
734 ;; unnecessary store references to those compilers:
735 (substitute* "libhdf4.settings"
736 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
737 (string-append prefix (string-take hash 10) "...")))
738 #t))
739 )))
becbbefc
TD		 740 (home-page "https://www.hdfgroup.org/products/hdf4/")
741 (synopsis
742 "Library and multi-object file format for storing and managing data")
743 (description "HDF4 is a library and multi-object file format for storing
744and managing data between machines. HDF4 is an older hierarchical data format,
745incompatible with HDF5.")
746 (license
747 (license:non-copyleft
748 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
749
750(define-public hdf4-alt
751 (package
752 (inherit hdf4)
753 (name "hdf4-alt")
754 (arguments
755 (substitute-keyword-arguments (package-arguments hdf4)
756 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
757 (synopsis
758 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
759
7ee3f1a2
JD		 760(define-public hdf5
761 (package
762 (name "hdf5")
7b84610e 763 (version "1.8.21")
7ee3f1a2
JD		 764 (source
765 (origin
766 (method url-fetch)
2da63064
TD		 767 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
768 "hdf5-" (version-major+minor version)
769 "/hdf5-" version "/src/hdf5-"
dcd9d163
LF		 770 version ".tar.bz2")
771 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
772 "current"
7b84610e
EB		 773 (match (string-split version #\.)
774 ((major minor _ ...)
775 (string-append major minor)))
dcd9d163 776 "/src/hdf5-" version ".tar.bz2")))
7ee3f1a2 777 (sha256
7b84610e 778 (base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5"))
7fedc3fd
EB		 779 (patches (search-patches "hdf5-config-date.patch"
780 "hdf5-1.8-mpi-deprecations.patch"))))
7ee3f1a2 781 (build-system gnu-build-system)
12ed1216
AE		 782 (inputs
783 `(("zlib" ,zlib)))
e3a1a1de 784 (native-inputs
3ea420f3
LC		 785 `(("gfortran" ,gfortran)
786 ("perl" ,perl))) ;part of the test machinery needs Perl
e3a1a1de
TD		 787 (outputs '("out" ; core library
788 "fortran")) ; fortran interface
7ee3f1a2 789 (arguments
62126576 790 `(;; Some of the users, notably Flann, need the C++ interface.
e3a1a1de
TD		 791 #:configure-flags '("--enable-cxx"
792 "--enable-fortran"
549d1571
LC		 793 "--enable-fortran2003"
794
795 ;; Build a thread-safe library. Unfortunately,
796 ;; 'configure' invites you to either turn off C++,
797 ;; Fortran, and the high-level interface (HL), or
798 ;; to pass '--enable-unsupported'. Debian
799 ;; packagers chose to pass '--enable-unsupported'
800 ;; and we follow their lead here.
801 "--enable-threadsafe"
802 "--with-pthread"
803 "--enable-unsupported")
4dba441c
RW		 804 ;; Use -fPIC to allow the R bindings to link with the static libraries
805 #:make-flags (list "CFLAGS=-fPIC"
806 "CXXFLAGS=-fPIC")
62126576 807 #:phases
f622e212
EB		 808 (modify-phases %standard-phases
809 (add-before 'configure 'patch-configure
e3a1a1de 810 (lambda* (#:key outputs #:allow-other-keys)
f622e212 811 (substitute* "configure"
b8d9c93b 812 (("/bin/mv") "mv"))
e3a1a1de
TD		 813 (substitute* "fortran/src/Makefile.in"
814 (("libhdf5_fortran_la_LDFLAGS =")
815 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
816 (assoc-ref outputs "fortran") "/lib")))
817 (substitute* "hl/fortran/src/Makefile.in"
818 (("libhdf5hl_fortran_la_LDFLAGS =")
819 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
820 (assoc-ref outputs "fortran") "/lib")))
b8d9c93b 821 #t))
fd0378a1
TD		 822 (add-after 'configure 'patch-settings
823 (lambda _
824 ;; libhdf5.settings contains the full path of the
825 ;; compilers used, and its contents are included in
826 ;; libhdf5.so. We truncate the hashes to avoid
827 ;; unnecessary store references to those compilers:
828 (substitute* "src/libhdf5.settings"
829 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
d8f46d52
RW		 830 (string-append prefix (string-take hash 10) "..."))
831 ;; Don't record the build-time kernel version to make the
832 ;; settings file reproducible.
833 (("Uname information:.*")
834 "Uname information: Linux\n"))
b8d9c93b 835 #t))
f622e212
EB		 836 (add-after 'install 'patch-references
837 (lambda* (#:key inputs outputs #:allow-other-keys)
838 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
839 (zlib (assoc-ref inputs "zlib")))
840 (substitute* (find-files bin "h5p?cc")
841 (("-lz" lib)
842 (string-append "-L" zlib "/lib " lib)))
e3a1a1de
TD		 843 #t)))
844 (add-after 'install 'split
845 (lambda* (#:key inputs outputs #:allow-other-keys)
846 ;; Move all fortran-related files
847 (let* ((out (assoc-ref outputs "out"))
848 (bin (string-append out "/bin"))
849 (lib (string-append out "/lib"))
850 (inc (string-append out "/include"))
851 (ex (string-append out "/share/hdf5_examples/fortran"))
852 (fort (assoc-ref outputs "fortran"))
853 (fbin (string-append fort "/bin"))
854 (flib (string-append fort "/lib"))
855 (finc (string-append fort "/include"))
856 (fex (string-append fort "/share/hdf5_examples/fortran")))
857 (mkdir-p fbin)
858 (mkdir-p flib)
859 (mkdir-p finc)
860 (mkdir-p fex)
b0d1e60f
PG		 861 ;; Note: When built with --enable-parallel, the 'h5fc' file
862 ;; doesn't exist, hence this condition.
863 (when (file-exists? (string-append bin "/h5fc"))
864 (rename-file (string-append bin "/h5fc")
865 (string-append fbin "/h5fc")))
e3a1a1de
TD		 866 (for-each (lambda (file)
867 (rename-file file
868 (string-append flib "/" (basename file))))
869 (find-files lib ".*fortran.*"))
870 (for-each (lambda (file)
871 (rename-file file
872 (string-append finc "/" (basename file))))
873 (find-files inc ".*mod"))
874 (for-each (lambda (file)
875 (rename-file file
876 (string-append fex "/" (basename file))))
877 (find-files ex ".*"))
878 (delete-file-recursively ex))
879 #t)))))
7ee3f1a2 880 (home-page "http://www.hdfgroup.org")
516e93f8 881 (synopsis "Management suite for extremely large and complex data")
7ee3f1a2
JD		 882 (description "HDF5 is a suite that makes possible the management of
883extremely large and complex data collections.")
d4bf49b1
EB		 884 (license (license:x11-style
885 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
7ee3f1a2 886
bb47aca5
RW		 887(define-public hdf5-1.10
888 (package (inherit hdf5)
889 (version "1.10.4")
890 (source
891 (origin
892 (method url-fetch)
893 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
894 "hdf5-" (version-major+minor version)
895 "/hdf5-" version "/src/hdf5-"
896 version ".tar.bz2")
897 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
898 "current"
899 (apply string-append
900 (take (string-split version #\.) 2))
901 "/src/hdf5-" version ".tar.bz2")))
902 (sha256
903 (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
7fedc3fd
EB		 904 (patches (search-patches "hdf5-config-date.patch"
905 "hdf5-mpi-deprecations.patch"))))))
bb47aca5 906
2fd26d05
TD		 907(define-public hdf-java
908 (package
2a509880
RW		 909 (name "hdf-java")
910 (version "3.3.2")
911 (source
912 (origin
913 (method url-fetch)
914 (uri (string-append
915 "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
916 version "/src/CMake-hdfjava-" version ".tar.gz"))
917 (sha256
918 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
919 (modules '((guix build utils)))
920 (snippet ; Make sure we don't use the bundled sources and binaries.
921 `(begin
922 (for-each delete-file
923 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
924 "HDF4.tar.gz" "HDF5.tar.gz"))
925 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
926 #t))))
927 (build-system gnu-build-system)
928 (native-inputs
929 `(("jdk" ,icedtea "jdk")
930 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
931 ;; For tests:
932 ("hamcrest-core" ,java-hamcrest-core)
933 ("junit" ,java-junit)
934 ("slf4j-simple" ,java-slf4j-simple)))
935 (inputs
936 `(("hdf4" ,hdf4)
937 ("hdf5" ,hdf5)
938 ("zlib" ,zlib)
939 ("libjpeg" ,libjpeg)
940 ("slf4j-api" ,java-slf4j-api)))
941 (arguments
942 `(#:configure-flags
943 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
944 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
945 (assoc-ref %build-inputs "jdk") "/lib" )
946 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
947 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
2fd26d05 948
2a509880
RW		 949 #:make-flags
950 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
951 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
952 (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
953 (string-append "JPEGLIB="
954 (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
955 "LLEXT=so")
2fd26d05 956
2a509880
RW		 957 #:phases
958 (modify-phases %standard-phases
959 (add-before 'configure 'chdir-to-source
960 (lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
961 (add-before 'configure 'patch-build
962 (lambda* (#:key inputs outputs #:allow-other-keys)
963 (substitute* "configure"
964 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
965 (("/bin/cat") (which "cat")))
966 ;; Set classpath for compilation
967 (substitute* '("hdf/hdf5lib/Makefile.in"
968 "hdf/hdf5lib/exceptions/Makefile.in"
969 "hdf/hdflib/Makefile.in")
970 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
971 (string-append (assoc-ref inputs "slf4j-api")
972 "/share/java/slf4j-api.jar")))
973 ;; Replace outdated config.sub and config.guess:
974 (with-directory-excursion "config"
975 (for-each (lambda (file)
976 (install-file
977 (string-append (assoc-ref inputs "automake")
978 "/share/automake-"
979 ,(version-major+minor (package-version automake))
980 "/" file) "."))
981 '("config.sub" "config.guess")))
64dc8b0b 982
2a509880
RW		 983 ;; Fix embedded version number
984 (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
985 (substitute* "hdf/hdf5lib/H5.java"
986 (("1, 8, 19")
987 (string-join hdf5version ", "))))
64dc8b0b 988
2a509880
RW		 989 (mkdir-p (string-append (assoc-ref outputs "out")))
990 ;; Set classpath for tests
991 (let* ((build-dir (getcwd))
992 (lib (string-append build-dir "/lib"))
993 (jhdf (string-append lib "/jhdf.jar"))
994 (jhdf5 (string-append lib "/jhdf5.jar"))
995 (testjars
996 (map (lambda (i)
997 (string-append (assoc-ref inputs i)
998 "/share/java/" i ".jar"))
999 '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
1000 (class-path
1001 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
2fd26d05 1002
2a509880
RW		 1003 (substitute* '("test/hdf5lib/Makefile.in"
1004 "test/hdf5lib/junit.sh.in"
1005 "examples/runExample.sh.in")
1006 (("/usr/bin/test")
1007 (string-append (assoc-ref inputs "coreutils")
1008 "/bin/test"))
1009 (("/usr/bin/uname")
1010 (string-append (assoc-ref inputs "coreutils")
1011 "/bin/uname"))
1012 (("CLASSPATH=[^\n]*")
1013 (string-append "CLASSPATH=" class-path)))
1014 (setenv "CLASSPATH" class-path))
1015 #t))
1016 (add-before 'check 'build-examples
1017 (lambda _
1018 (apply invoke `("javac"
1019 ,@(find-files "examples" ".*\\.java"))))))
2fd26d05 1020
2a509880 1021 #:parallel-build? #f
2fd26d05 1022
2a509880
RW		 1023 #:parallel-tests? #f ))
1024 (home-page "https://support.hdfgroup.org/products/java")
1025 (synopsis "Java interface for the HDF4 and HDF5 libraries")
1026 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
2fd26d05
TD		 1027the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
1028implemented in C.")
1029
2a509880
RW		 1030 ;; BSD-style license:
1031 (license (license:x11-style
1032 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
2fd26d05
TD		 1033/current/src/unpacked/COPYING"))))
1034
d3c4f3bb
TD		 1035(define-public hdf-eos2
1036 (package
1037 (name "hdf-eos2")
1038 (version "19.1.0")
1039 (source
1040 (origin
1041 (method url-fetch)
1042 (uri "ftp://edhs1.gsfc.nasa.gov\
1043/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
1044 (sha256
1045 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
1046 (patches (search-patches "hdf-eos2-remove-gctp.patch"
1047 "hdf-eos2-build-shared.patch"
1048 "hdf-eos2-fortrantests.patch"))))
1049 (build-system gnu-build-system)
1050 (native-inputs
1051 `(("gfortran" ,gfortran)))
1052 (inputs
1053 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
25bdbb61 1054 ;; XXX: These inputs are really dependencies of hdf4.
d3c4f3bb
TD		 1055 ("zlib" ,zlib)
1056 ("libjpeg" ,libjpeg)
25bdbb61
MB		 1057 ("libtirpc" ,libtirpc)
1058
d3c4f3bb
TD		 1059 ("gctp" ,gctp)))
1060 (arguments
1061 `( #:configure-flags '("--enable-install-include" "--enable-shared"
1062 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
1063 #:parallel-tests? #f))
1064 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
1065 (synopsis "HDF4-based data format for NASA's Earth Observing System")
1066 (description "HDF-EOS2 is a software library built on HDF4 which supports
1067the construction of data structures used in NASA's Earth Observing
1068System (Grid, Point and Swath).")
1069
1070 ;; Source files carry a permissive license header.
1071 (license (license:non-copyleft home-page))))
1072
0f43f835
TD		 1073(define-public hdf-eos5
1074 (package
1075 (name "hdf-eos5")
1076 (version "1.15")
1077 (source (origin
1078 (method url-fetch)
1079 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1080/edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1081 (sha256
1082 (base32
1083 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1084 (patches (search-patches "hdf-eos5-build-shared.patch"
1085 "hdf-eos5-remove-gctp.patch"
1086 "hdf-eos5-fix-szip.patch"
1087 "hdf-eos5-fortrantests.patch"))))
1088 (native-inputs
1089 `(("gfortran" ,gfortran)))
1090 (build-system gnu-build-system)
1091 (inputs
1092 `(("hdf5" ,hdf5)
1093 ("zlib" ,zlib)
1094 ("gctp" ,gctp)))
1095 (arguments
1096 `(#:configure-flags '("--enable-install-include" "--enable-shared"
1097 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1098 #:parallel-tests? #f))
1099 (synopsis "HDF5-based data format for NASA's Earth Observing System")
1100 (description
1101 "HDF-EOS5 is a software library built on HDF5 to support the construction
1102of data structures used in NASA's Earth Observing System (Grid, Point and
1103Swath).")
1104 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1105
1106 ;; Source files carry a permissive license header.
1107 (license (license:non-copyleft home-page))))
1108
c8378eea
EB		 1109(define-public hdf5-parallel-openmpi
1110 (package (inherit hdf5)
1111 (name "hdf5-parallel-openmpi")
1112 (inputs
1113 `(("mpi" ,openmpi)
1114 ,@(package-inputs hdf5)))
1115 (arguments
45201bf2
PG		 1116 (substitute-keyword-arguments (package-arguments hdf5)
1117 ((#:configure-flags flags)
549d1571
LC		 1118 ``("--enable-parallel"
1119 ,@(delete "--enable-cxx"
1120 (delete "--enable-threadsafe" ,flags))))
c8378eea
EB		 1121 ((#:phases phases)
1122 `(modify-phases ,phases
45201bf2
PG		 1123 (add-after 'build 'mpi-setup
1124 ,%openmpi-setup)
c8378eea
EB		 1125 (add-before 'check 'patch-tests
1126 (lambda _
1127 ;; OpenMPI's mpirun will exit with non-zero status if it
1128 ;; detects an "abnormal termination", i.e. any process not
784c3da1 1129 ;; calling MPI_Finalize(). Since the test is explicitly
c8378eea
EB		 1130 ;; avoiding MPI_Finalize so as not to have at_exit and thus
1131 ;; H5C_flush_cache from being called, mpirun will always
1132 ;; complain, so turn this test off.
1133 (substitute* "testpar/Makefile"
1134 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1135 (string-append front back "\n")))
1136 (substitute* "tools/h5diff/testph5diff.sh"
1137 (("/bin/sh") (which "sh")))
1138 #t))))))
1139 (synopsis "Management suite for data with parallel IO support")))
1140
00775104
EB		 1141(define-public h5check
1142 (package
1143 (name "h5check")
1144 (version "2.0.1")
1145 (source
1146 (origin
1147 (method url-fetch)
1148 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
1149 "h5check/src/h5check-" version ".tar.gz"))
1150 (sha256
1151 (base32
1152 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1153 (build-system gnu-build-system)
1154 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
1155 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1156 (synopsis "HDF5 format checker")
1157 (description "@code{h5check} is a validation tool for verifying that an
1158HDF5 file is encoded according to the HDF File Format Specification.")
1159 (license (license:x11-style "file://COPYING"))))
1160
a53d6719
JD		 1161(define-public itpp
1162 (package
1163 (name "itpp")
1164 (version "4.3.1")
1165 (source (origin
1166 (method url-fetch)
1167 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1168 version "/itpp-"
1169 version ".tar.gz"))
1170 (sha256
1171 (base32
1172 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1173 (build-system cmake-build-system)
1174 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1175 (inputs `(("lapack" ,lapack)
1176 ("fftw" ,fftw)))
3a4d5df2
RW		 1177 ;; FIXME: Even though the fonts are available dvips complains:
1178 ;; "Font cmmi10 not found; characters will be left blank."
1179 (native-inputs
1180 `(("texlive" ,texlive-tiny)
1181 ("ghostscript" ,ghostscript)
1182 ("doxygen" ,doxygen)))
a53d6719
JD		 1183 (home-page "http://itpp.sourceforge.net")
1184 (synopsis "C++ library of maths, signal processing and communication classes")
1185 (description "IT++ is a C++ library of mathematical, signal processing and
1186communication classes and functions. Its main use is in simulation of
1187communication systems and for performing research in the area of
1188communications. The kernel of the library consists of generic vector and
1189matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1190similar to MATLAB, GNU Octave or SciPy.")
1191 (license license:gpl3+)))
1192
889187a4
EB		 1193(define-public netcdf
1194 (package
1195 (name "netcdf")
a4b0bfb1 1196 (version "4.4.1.1")
889187a4
EB		 1197 (source
1198 (origin
1199 (method url-fetch)
1200 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1201 "netcdf-" version ".tar.gz"))
1202 (sha256
1203 (base32
a4b0bfb1
EB		 1204 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1205 (patches (search-patches "netcdf-date-time.patch"
1206 "netcdf-tst_h_par.patch"))))
889187a4
EB		 1207 (build-system gnu-build-system)
1208 (native-inputs
1209 `(("m4" ,m4)
1210 ("doxygen" ,doxygen)
1211 ("graphviz" ,graphviz)))
1212 (inputs
db825570
TD		 1213 `(("hdf4" ,hdf4-alt)
1214 ("hdf5" ,hdf5)
1215 ("zlib" ,zlib)
1216 ("libjpeg" ,libjpeg)))
889187a4 1217 (arguments
db825570 1218 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
43d01672
TD		 1219
1220 #:phases (modify-phases %standard-phases
1221 (add-before 'configure 'fix-source-date
1222 (lambda _
1223 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1224 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1225 ;; to '1st hour of the current day', and therefore makes the
1226 ;; package not reproducible.
1227 (substitute* "./configure"
1228 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1229 "date --date='@0'"))
1230 #t))
1231 (add-after 'configure 'patch-settings
1232 (lambda _
1233 ;; libnetcdf.settings contains the full filename of the compilers
1234 ;; used to build the library. We truncate the hashes of those
1235 ;; filenames to avoid unnecessary references to the corresponding
1236 ;; store items.
1237 (substitute* "libnetcdf.settings"
1238 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1239 (string-append prefix (string-take hash 10) "...")))
1240 #t)))
1241
889187a4
EB		 1242 #:parallel-tests? #f)) ;various race conditions
1243 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
1244 (synopsis "Library for scientific data")
1245 (description "NetCDF is an interface for scientific data access and a
1246software library that provides an implementation of the interface. The netCDF
1247library defines a machine-independent format for representing scientific data.
1248Together, the interface, library, and format support the creation, access, and
1249sharing of scientific data.")
1250 (license (license:x11-style "file://COPYRIGHT"))))
1251
1252(define-public netcdf-parallel-openmpi
1253 (package (inherit netcdf)
1254 (name "netcdf-parallel-openmpi")
1255 (inputs
1256 `(("mpi" ,openmpi)
1257 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1258 (package-inputs netcdf))))
1259 ;; TODO: Replace pkg-config references in nc-config with absolute references
1260 (arguments
1261 (substitute-keyword-arguments (package-arguments netcdf)
1262 ((#:configure-flags flags)
1263 `(cons* "CC=mpicc" "CXX=mpicxx"
1264 "--enable-parallel-tests"
1265 ;; Shared libraries not supported with parallel IO.
1266 "--disable-shared" "--with-pic"
1267 ,flags))))))
1268
300200b6
TD		 1269(define-public netcdf-fortran
1270 (package
1271 (name "netcdf-fortran")
1272 (version "4.4.4")
1273 (source (origin
1274 (method url-fetch)
1275 (uri (string-append
1276 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1277 version ".tar.gz"))
1278 (sha256
1279 (base32
1280 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1281 (build-system gnu-build-system)
1282 (arguments
1283 `(#:parallel-tests? #f))
1284 (inputs
1285 `(("netcdf" ,netcdf)))
1286 (native-inputs
1287 `(("gfortran" ,gfortran)))
1288 (synopsis "Fortran interface for the netCDF library")
1289 (description (package-description netcdf))
1290 (home-page (package-home-page netcdf))
1291 (license (package-license netcdf))))
1292
1b39a196
RJ		 1293(define-public nlopt
1294 (package
1295 (name "nlopt")
1296 (version "2.4.2")
1297 (source (origin
1298 (method url-fetch)
1299 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1300 version ".tar.gz"))
1301 (sha256
1302 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1303 (build-system gnu-build-system)
1304 (arguments
1305 `(;; Shared libraries are not built by default. They are required to
1306 ;; build the Guile, Octave, and Python bindings.
1307 #:configure-flags '("--enable-shared")
1308
1309 #:phases
1310 (modify-phases %standard-phases
1311 (add-before 'configure 'set-libnlopt-file-name
1312 (lambda* (#:key outputs #:allow-other-keys)
1313 ;; Make sure the Scheme module refers to the library by its
1314 ;; absolute file name (we cannot do that from a snippet
1315 ;; because the expansion of @libdir@ contains
1316 ;; ${exec_prefix}.)
1317 (let ((out (assoc-ref outputs "out")))
1318 (substitute* "swig/nlopt.scm.in"
1319 (("libnlopt")
1320 (string-append out "/lib/libnlopt")))
1321 #t))))))
1322 (inputs `(("guile" ,guile-2.0)))
1323 (native-inputs `(("pkg-config" ,pkg-config)))
1324 (home-page "http://ab-initio.mit.edu/wiki/")
1325 (synopsis "Library for nonlinear optimization")
1326 (description "NLopt is a library for nonlinear optimization, providing a
1327common interface for a number of different free optimization routines available
1328online as well as original implementations of various other algorithms.")
1329 (license license:lgpl2.1+)))
1330
005c787d
LC		 1331(define-public ipopt
1332 (package
1333 (name "ipopt")
98a5cd51 1334 (version "3.12.12")
005c787d
LC		 1335 (source (origin
1336 (method url-fetch)
1337 (uri (string-append
1338 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1339 version".tgz"))
1340 (sha256
1341 (base32
98a5cd51 1342 "07yn9rzdswjk8n246qq6ci9ssf2bcplkifcpsfz9j6cdxw9vgbkv"))
005c787d
LC		 1343 (modules '((guix build utils)))
1344 (snippet
1345 ;; Make sure we don't use the bundled software.
6cbee49d
MW		 1346 '(begin
1347 (delete-file-recursively "ThirdParty")
1348 #t))))
005c787d 1349 (build-system gnu-build-system)
ad1c4537
LC		 1350 (arguments
1351 '(#:phases (modify-phases %standard-phases
1352 (add-after 'install 'add--L-flags-in-ipopt.pc
1353 (lambda* (#:key inputs outputs #:allow-other-keys)
1354 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1355 ;; move it to "Libs.private" where it belongs, and add a
1356 ;; '-L' flag for LAPACK.
1357 (let ((out (assoc-ref outputs "out"))
1358 (lapack (assoc-ref inputs "lapack")))
1359 (substitute* (string-append out "/lib/pkgconfig/"
1360 "ipopt.pc")
1361 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1362 (string-append "Libs: " before " " after "\n"
1363 "Libs.private: " before
1364 "-L" lapack "/lib -llapack -lblas "
1365 after "\n")))
1366 #t))))))
005c787d
LC		 1367 (native-inputs
1368 `(("gfortran" ,gfortran)))
1369 (inputs
1370 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
ad1c4537 1371 `(("lapack" ,lapack))) ;for both libblas and liblapack
005c787d
LC		 1372 (home-page "http://www.coin-or.org")
1373 (synopsis "Large-scale nonlinear optimizer")
1374 (description
1375 "The Interior Point Optimizer (IPOPT) is a software package for
1376large-scale nonlinear optimization. It provides C++, C, and Fortran
1377interfaces.")
1378 (license license:epl1.0)))
1379
ecfbc51f
RW		 1380(define-public clp
1381 (package
1382 (name "clp")
1383 (version "1.17.1")
1384 (source (origin
1385 (method url-fetch)
1386 (uri (string-append "https://www.coin-or.org/download/source/"
1387 "Clp/Clp-" version ".tgz"))
1388 (sha256
1389 (base32
1390 "1wdg820g3iikf9344ijwsc8sy6c0m6im42bzzizm6rlmkvnmxhk9"))
1391 (modules '((guix build utils)))
1392 (snippet
1393 ;; Make sure we don't use the bundled software.
1394 '(begin
1395 (delete-file-recursively "ThirdParty")
1396 #t))))
1397 (build-system gnu-build-system)
1398 (native-inputs
1399 `(("gfortran" ,gfortran)
1400 ("pkg-config" ,pkg-config)))
1401 (inputs
1402 `(("openblas" ,openblas)))
1403 (home-page "https://www.coin-or.org")
1404 (synopsis "Linear programming solver")
1405 (description
1406 "CLP is a high quality linear programming solver. Its main strengths are
1407its dual and primal Simplex algorithms. It also has a barrier algorithm for
1408linear and quadratic objectives. There are limited facilities for nonlinear
1409and quadratic objectives using the Simplex algorithm.")
1410 (license license:epl1.0)))
1411
f9940ef1
LC		 1412(define-public ceres
1413 (package
1414 (name "ceres-solver")
e0bee0de 1415 (version "1.14.0")
f9940ef1
LC		 1416 (home-page "http://ceres-solver.org/")
1417 (source (origin
1418 (method url-fetch)
1419 (uri (string-append home-page "ceres-solver-"
1420 version ".tar.gz"))
1421 (sha256
1422 (base32
e0bee0de 1423 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
f9940ef1
LC		 1424 (build-system cmake-build-system)
1425 (arguments
1426 ;; TODO: Build HTML user documentation and install separately.
bc3a2e35 1427 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
f9940ef1
LC		 1428 "-DBUILD_SHARED_LIBS=ON")
1429
1430 #:phases (modify-phases %standard-phases
1431 (add-before 'configure 'set-library-directory
1432 (lambda _
1433 ;; Install libraries to lib/, not lib64/.
1434 (substitute* "internal/ceres/CMakeLists.txt"
1435 (("set\\(LIB_SUFFIX \"64\"\\)")
1436 "set(LIB_SUFFIX \"\")"))
1437 #t)))))
1438 (native-inputs
1439 `(("pkg-config" ,pkg-config)))
468e0b18
LC		 1440 (propagated-inputs
1441 `(("glog" ,glog))) ;for #include <glog/glog.h>
f9940ef1
LC		 1442 (inputs
1443 `(("eigen" ,eigen)
1444 ("blas" ,openblas)
1445 ("lapack" ,lapack)
1446 ("suitesparse" ,suitesparse)
1447 ("gflags" ,gflags)))
1448 (synopsis "C++ library for solving large optimization problems")
1449 (description
1450 "Ceres Solver is a C++ library for modeling and solving large,
1451complicated optimization problems. It is a feature rich, mature and
1452performant library which has been used in production since 2010. Ceres Solver
1453can solve two kinds of problems:
1454@enumerate
1455@item non-linear least squares problems with bounds constraints;
1456@item general unconstrained optimization problems.
1457@end enumerate\n")
1458 (license license:bsd-3)))
1459
b66741ed 1460;; For a fully featured Octave, users are strongly recommended also to install
5ca4fe96 1461;; the following packages: less, ghostscript, gnuplot.
5537603f 1462(define-public octave-cli
668c06ac 1463 (package
5537603f 1464 (name "octave-cli")
5b8f8928 1465 (version "5.1.0")
668c06ac
JD		 1466 (source
1467 (origin
1468 (method url-fetch)
1469 (uri (string-append "mirror://gnu/octave/octave-"
f5a077b1 1470 version ".tar.lz"))
668c06ac
JD		 1471 (sha256
1472 (base32
5b8f8928 1473 "11wwxpy2q1bhxs2v41bqn05i2sb0905cj1xil6mg8l4k2kka4cq6"))))
668c06ac
JD		 1474 (build-system gnu-build-system)
1475 (inputs
697df13f
EF		 1476 `(("alsa-lib" ,alsa-lib)
1477 ("arpack" ,arpack-ng)
1478 ("curl" ,curl)
1ec78e9d
EB		 1479 ("fftw" ,fftw)
1480 ("fftwf" ,fftwf)
668c06ac
JD		 1481 ("fltk" ,fltk)
1482 ("fontconfig" ,fontconfig)
1483 ("freetype" ,freetype)
697df13f
EF		 1484 ("gl2ps" ,gl2ps)
1485 ("glpk" ,glpk)
1ec78e9d 1486 ("glu" ,glu)
ab5f3f21 1487 ("graphicsmagick" ,graphicsmagick)
697df13f
EF		 1488 ("hdf5" ,hdf5)
1489 ("lapack" ,lapack)
ab5f3f21 1490 ("libsndfile" ,libsndfile)
697df13f
EF		 1491 ("libxft" ,libxft)
1492 ("mesa" ,mesa)
1493 ("pcre" ,pcre)
ab5f3f21 1494 ("portaudio" ,portaudio)
697df13f
EF		 1495 ("qhull" ,qhull)
1496 ("readline" ,readline)
1497 ("suitesparse" ,suitesparse)
1498 ("texinfo" ,texinfo)
1499 ("zlib" ,zlib)))
668c06ac 1500 (native-inputs
f5a077b1
EF		 1501 `(("lzip" ,lzip)
1502 ("gfortran" ,gfortran)
668c06ac
JD		 1503 ("pkg-config" ,pkg-config)
1504 ("perl" ,perl)
1ec78e9d
EB		 1505 ;; The following inputs are not actually used in the build process.
1506 ;; However, the ./configure gratuitously tests for their existence and
1507 ;; assumes that programs not present at build time are also not, and
1508 ;; can never be, available at run time! If these inputs are therefore
1509 ;; not present, support for them will be built out. However, Octave
1510 ;; will still run without them, albeit without the features they
668c06ac
JD		 1511 ;; provide.
1512 ("less" ,less)
668c06ac
JD		 1513 ("ghostscript" ,ghostscript)
1514 ("gnuplot" ,gnuplot)))
116af86f
KK		 1515 ;; Octave code uses this variable to detect directories holding multiple CA
1516 ;; certificates to verify peers with. This is required for the networking
1517 ;; functions that require encryption to work properly.
1518 (native-search-paths
1519 (list (search-path-specification
1520 (variable "CURLOPT_CAPATH")
1521 (files '("etc/ssl/certs")))))
668c06ac 1522 (arguments
b7b27a8f
KY		 1523 `(#:configure-flags
1524 (list (string-append "--with-shell="
1525 (assoc-ref %build-inputs "bash")
5ca4fe96
AI		 1526 "/bin/sh"))
1527 #:phases
1528 (modify-phases %standard-phases
1529 (add-after 'configure 'configure-makeinfo
1530 (lambda* (#:key inputs #:allow-other-keys)
b18b9d20
AI		 1531 (substitute* "libinterp/corefcn/help.h"
1532 (("\"makeinfo\"")
1533 (string-append
1534 "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
5ca4fe96 1535 #t)))))
f5a077b1 1536 (home-page "https://www.gnu.org/software/octave/")
668c06ac 1537 (synopsis "High-level language for numerical computation")
1ec78e9d
EB		 1538 (description "GNU Octave is a high-level interpreted language that is
1539specialized for numerical computations. It can be used for both linear and
1540non-linear applications and it provides great support for visualizing results.
1541Work may be performed both at the interactive command-line as well as via
1542script files.")
668c06ac 1543 (license license:gpl3+)))
3de01d3f 1544
e0ae7e73 1545(define-public octave
5537603f 1546 (package (inherit octave-cli)
e0ae7e73 1547 (name "octave")
7a3772b3 1548 (source (origin
5537603f 1549 (inherit (package-source octave-cli))))
36ce25f0
KK		 1550 (inputs
1551 `(("qscintilla" ,qscintilla)
1552 ("qt" ,qtbase)
5537603f 1553 ,@(package-inputs octave-cli)))
36ce25f0
KK		 1554 (native-inputs
1555 `(("qttools" , qttools) ;for lrelease
70bb5d88 1556 ("texlive" ,(texlive-union (list texlive-epsf))) ; for texi2dvi
5537603f 1557 ,@(package-native-inputs octave-cli)))
36ce25f0 1558 (arguments
5537603f 1559 (substitute-keyword-arguments (package-arguments octave-cli)
36ce25f0
KK		 1560 ((#:phases phases)
1561 `(modify-phases ,phases
1562 (add-before 'configure 'patch-qscintilla-library-name
1563 (lambda* (#:key inputs #:allow-other-keys)
1564 ;; The QScintilla library that the Octave configure script tries
1565 ;; to link with should be named libqscintilla-qt5.so, but the
1566 ;; QScintilla input provides the shared library as
1567 ;; libqscintilla2_qt5.so.
1568 (substitute* "configure"
1569 (("qscintilla2-qt5")
1570 "qscintilla2_qt5"))
1571 #t))))))))
1572
e0ae7e73
KK		 1573(define-public qtoctave
1574 (deprecated-package "qtoctave" octave))
1575
5d4bd4cc
PG		 1576(define-public opencascade-oce
1577 (package
1578 (name "opencascade-oce")
1579 (version "0.17.2")
1580 (source
1581 (origin
830971bf
TGR		 1582 (method git-fetch)
1583 (uri (git-reference
1584 (url "https://github.com/tpaviot/oce.git")
1585 (commit (string-append "OCE-" version))))
1586 (file-name (git-file-name name version))
a4f393b7 1587 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
5d4bd4cc 1588 (sha256
830971bf 1589 (base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69"))))
5d4bd4cc
PG		 1590 (build-system cmake-build-system)
1591 (arguments
1592 '(#:configure-flags
1593 (list "-DOCE_TESTING:BOOL=ON"
1594 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1595 "-DOCE_DRAW:BOOL=ON"
1596 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1597 (assoc-ref %outputs "out"))
1598 "-UCMAKE_INSTALL_RPATH")))
1599 (inputs
1600 `(("freetype" ,freetype)
1601 ("glu" ,glu)
1602 ("libxmu" ,libxmu)
1603 ("mesa" ,mesa)
1604 ("tcl" ,tcl)
1605 ("tk" ,tk)))
1606 (native-inputs
1607 `(("python" ,python-wrapper)))
1608 (home-page "https://github.com/tpaviot/oce")
1609 (synopsis "Libraries for 3D modeling and numerical simulation")
1610 (description
1611 "Open CASCADE is a set of libraries for the development of applications
1612dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1613C++ class libraries providing services for 3D surface and solid modeling, CAD
1614data exchange, and visualization. It is used for development of specialized
1615software dealing with 3D models in design (CAD), manufacturing (CAM),
1616numerical simulation (CAE), measurement equipment (CMM), and quality
1617control (CAQ) domains.
1618
1619This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1620patches, improvements, and experiments contributed by users over the official
1621Open CASCADE library.")
1622 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1623 ; use of header files; see
1624 ; OCCT_LGPL_EXCEPTION.txt
1625 license:public-domain; files
1626 ; src/Standard/Standard_StdAllocator.hxx and
1627 ; src/NCollection/NCollection_StdAllocator.hxx
1628 license:expat; file src/OpenGl/OpenGl_glext.h
1629 license:bsd-3)))); test framework gtest
1630
37dc2920
PG		 1631(define-public opencascade-occt
1632 (package
1633 (name "opencascade-occt")
1634 (version "7.3.0p3")
1635 (source
1636 (origin
1637 (method git-fetch)
1638 (uri (git-reference
1639 (url "https://git.dev.opencascade.org/repos/occt.git")
1640 (commit
1641 (string-append "V"
1642 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
1643 version)))))
1644 (file-name (git-file-name name version))
1645 (sha256
1646 (base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4"))
1647 (modules '((guix build utils)))
1648 (snippet
1649 '(begin
1650 ;; Remove files specific to non-free operating systems.
1651 (delete-file-recursively "samples/ios")
1652 (delete-file-recursively "samples/mfc")
1653 (delete-file-recursively "samples/qt/FuncDemo")
1654 (delete-file "genconf.bat")
1655 (delete-file "gendoc.bat")
1656 (delete-file "genproj.bat")
1657 (delete-file "upgrade.bat")
1658 ;; Remove references to deleted files.
1659 (substitute* "dox/FILES_HTML.txt"
1660 ((".*standard.*") "" )
1661 ((".*UIKitSample.*") ""))
1662 #t))))
1663 (build-system cmake-build-system)
1664 (arguments
1665 '(;; There is no test target for make. OCCT provides an
1666 ;; 'Automated Testing System', which may be accessed after
1667 ;; installation via the draw.sh script. draw.sh is located in
1668 ;; the bin directory. For details see:
1669 ;; https://www.opencascade.com/doc/occt-7.3.0/overview/html/\
1670 ;; occt_dev_guides__tests.html
1671 #:tests? #f
1672 ;; Configure without freeimage: attempting to link against the
1673 ;; freeimage version 3.17 library leads to 'undefined
1674 ;; reference' errors.
1675 #:configure-flags
1676 (list "-DUSE_FREEIMAGE:BOOL=OFF"
1677 "-DUSE_TBB:BOOL=ON"
1678 "-DUSE_VTK:BOOL=OFF"
1679 "-DBUILD_DOC_Overview:BOOL=OFF"
1680 "-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON"
1681 "-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON"
1682 "-UCMAKE_INSTALL_LIBDIR")))
1683 (inputs
1684 `(("doxygen" ,doxygen)
1685 ;("freeimage" ,freeimage)
1686 ("freetype" ,freetype)
1687 ("glu" ,glu)
1688 ("libxext" ,libxext)
1689 ("libxi" ,libxi)
1690 ("libxmu" ,libxmu)
1691 ("mesa" ,mesa)
1692 ("tbb" ,tbb)
1693 ("tcl" ,tcl)
1694 ("tk" ,tk)))
1695 ;; TODO: build Overview documentation and add 'doc' output.
1696 (home-page "https://www.opencascade.com")
1697 (synopsis "Libraries for 3D modeling and numerical simulation")
1698 (description
1699 "Open CASCADE is a set of libraries for the development of applications
1700dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1701C++ class libraries providing services for 3D surface and solid modeling, CAD
1702data exchange, and visualization. It is used for development of specialized
1703software dealing with 3D models in design (CAD), manufacturing (CAM),
1704numerical simulation (CAE), measurement equipment (CMM), and quality
1705control (CAQ) domains.
1706
1707This is the certified version of the Open Cascade Technology (OCCT) library.")
1708 (license (list ;; OCCT library:
1709 license:lgpl2.1; with an exception for the use of header
1710 ; files, see OCCT_LGPL_EXCEPTION.txt.
1711 ;; Files src/OpenGl/glext.h, adm/cmake/cotire.cmake and
1712 ;; src/OpenGl/OpenGl_HaltonSampler.hxx:
1713 license:expat
1714 ;; Files src/ExprIntrp/ExprIntrp.tab.* and
1715 ;; src/StepFile/step.tab.*:
1716 license:gpl3+ ; with Bison 2.2 exception.
1717 ;; File src/NCollection/NCollection_UtfIterator.lxx:
1718 (license:non-copyleft
1719 "https://www.unicode.org/license.html")
1720 ;; File src/NCollection/NCollection_StdAllocator.hxx:
1721 license:public-domain))))
1722
3de01d3f
EB		 1723(define-public gmsh
1724 (package
1725 (name "gmsh")
8a4d14fa 1726 (version "2.16.0")
3de01d3f
EB		 1727 (source
1728 (origin
abed5df7
PG		 1729 (method git-fetch)
1730 (uri (git-reference
1731 (url "https://gitlab.onelab.info/gmsh/gmsh.git")
1732 (commit
1733 (string-append "gmsh_"
1734 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
1735 version)))))
1736 (file-name (git-file-name name version))
3de01d3f 1737 (sha256
abed5df7 1738 (base32 "08rq4jajwmlpivnm9yifz2jhaivnz065lnk0h2zv773nwl9wf162"))
3de01d3f
EB		 1739 (modules '((guix build utils)))
1740 (snippet
1741 ;; Remove non-free METIS code
6cbee49d
MW		 1742 '(begin
1743 (delete-file-recursively "contrib/Metis")
1744 #t))))
3de01d3f 1745 (build-system cmake-build-system)
3de01d3f
EB		 1746 (propagated-inputs
1747 `(("fltk" ,fltk)
19afbea1 1748 ("gfortran" ,gfortran)
3de01d3f 1749 ("gmp" ,gmp)
40029cbe 1750 ("hdf5" ,hdf5)
3de01d3f
EB		 1751 ("lapack" ,lapack)
1752 ("mesa" ,mesa)
85f41902 1753 ("glu" ,glu)
45548139 1754 ("opencascade-oce" ,opencascade-oce)
3de01d3f
EB		 1755 ("libx11" ,libx11)
1756 ("libxext" ,libxext)))
66395a61
EF		 1757 (inputs
1758 `(("fontconfig" ,fontconfig)
1759 ("libxft" ,libxft)))
3de01d3f
EB		 1760 (arguments
1761 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1762 "-DENABLE_BUILD_SHARED:BOOL=ON"
45548139 1763 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
0746c33e 1764 (home-page "http://gmsh.info/")
3de01d3f 1765 (synopsis "3D finite element grid generator")
edf684ef
EB		 1766 (description "Gmsh is a 3D finite element grid generator with a built-in
1767CAD engine and post-processor. Its design goal is to provide a fast, light
1768and user-friendly meshing tool with parametric input and advanced
1769visualization capabilities. Gmsh is built around four modules: geometry,
1770mesh, solver and post-processing. The specification of any input to these
1771modules is done either interactively using the graphical user interface or in
1772ASCII text files using Gmsh's own scripting language.")
3de01d3f 1773 (license license:gpl2+)))
b9100e2f 1774
6d5f63b6
JD		 1775(define-public maxflow
1776 (package
1777 (name "maxflow")
0af12a13
TGR		 1778 ;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’,
1779 ;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’.
1780 (version "3.0.5")
6d5f63b6
JD		 1781 (source (origin
1782 (method git-fetch)
1783 (uri (git-reference
1784 (url "https://github.com/gerddie/maxflow.git")
0af12a13 1785 (commit version)))
2dc0a6cf 1786 (file-name (git-file-name name version))
6d5f63b6
JD		 1787 (sha256
1788 (base32
1789 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1790 (build-system cmake-build-system)
0be9038c 1791 (home-page "https://pub.ist.ac.at/~vnk/software.html")
6d5f63b6
JD		 1792 (synopsis "Library implementing Maxflow algorithm")
1793 (description "An implementation of the maxflow algorithm described in
1794@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1795Energy Minimization in Computer Vision.\n
1796Yuri Boykov and Vladimir Kolmogorov.\n
1797In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1798September 2004}")
1799 (license license:gpl3+)))
1800
b9100e2f
EB		 1801(define-public petsc
1802 (package
1803 (name "petsc")
4f7a4a06 1804 (version "3.11.2")
b9100e2f
EB		 1805 (source
1806 (origin
1807 (method url-fetch)
1808 ;; The *-lite-* tarball does not contain the *large* documentation
1809 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1810 "petsc-lite-" version ".tar.gz"))
1811 (sha256
4f7a4a06 1812 (base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx"))))
b2c52fc9
TGR		 1813 (outputs '("out" ; libraries and headers
1814 "examples")) ; ~30MiB of examples
b9100e2f
EB		 1815 (build-system gnu-build-system)
1816 (native-inputs
6fec298d 1817 `(("python" ,python-2)))
b9100e2f 1818 (inputs
19afbea1 1819 `(("gfortran" ,gfortran)
b9100e2f 1820 ("lapack" ,lapack)
f258212d 1821 ("superlu" ,superlu)
b9100e2f
EB		 1822 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1823 ;; leaving out opengl, as configuration seems to only be for mac
1824 ))
1825 (arguments
1826 `(#:test-target "test"
b2c52fc9 1827 #:parallel-build? #f ; build is parallel by default
b9100e2f
EB		 1828 #:configure-flags
1829 `("--with-mpi=0"
f258212d 1830 "--with-openmp=1"
c15be128 1831 "--with-superlu=1")
9731c412
EB		 1832 #:make-flags
1833 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1834 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1835 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
b9100e2f 1836 #:phases
64dcc289
EB		 1837 (modify-phases %standard-phases
1838 (replace 'configure
1839 ;; PETSc's configure script is actually a python script, so we can't
1840 ;; run it with bash.
1841 (lambda* (#:key outputs (configure-flags '())
1842 #:allow-other-keys)
1843 (let* ((prefix (assoc-ref outputs "out"))
1844 (flags `(,(string-append "--prefix=" prefix)
1845 ,@configure-flags)))
1846 (format #t "build directory: ~s~%" (getcwd))
1847 (format #t "configure flags: ~s~%" flags)
49fdd357 1848 (apply invoke "./configure" flags))))
64dcc289 1849 (add-after 'configure 'clean-local-references
9731c412 1850 (lambda* (#:key outputs #:allow-other-keys)
64dcc289
EB		 1851 (let ((out (assoc-ref outputs "out")))
1852 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
b730b437
EB		 1853 ;; Prevent build directory from leaking into compiled code
1854 (((getcwd)) out)
1855 ;; Scrub timestamp for reproducibility
fafd623e 1856 ((".*Libraries compiled on.*") ""))
9731c412
EB		 1857 (substitute* (find-files "." "petscvariables")
1858 ;; Do not expose build machine characteristics, set to defaults.
1859 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1860 (("NPMAX = [:digit:]+") "NPMAX = 2"))
fafd623e 1861 #t)))
64dcc289 1862 (add-after 'install 'clean-install
10b11968
EB		 1863 ;; Try to keep installed files from leaking build directory names.
1864 (lambda* (#:key inputs outputs #:allow-other-keys)
64dcc289 1865 (let ((out (assoc-ref outputs "out")))
10b11968 1866 (substitute* (map (lambda (file)
9a899cce 1867 (string-append out "/lib/petsc/conf/" file))
fafd623e 1868 '("petscvariables"))
10b11968
EB		 1869 (((getcwd)) out))
1870 ;; Make compiler references point to the store
9a899cce 1871 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
dfdf5716
EB		 1872 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1873 (string-append "= " (which compiler))))
10b11968
EB		 1874 ;; PETSc installs some build logs, which aren't necessary.
1875 (for-each (lambda (file)
9a899cce 1876 (let ((f (string-append out "/lib/petsc/conf/" file)))
10b11968
EB		 1877 (when (file-exists? f)
1878 (delete-file f))))
9a899cce
EB		 1879 '("configure.log" "make.log" "gmake.log"
1880 "test.log" "error.log" "RDict.db"
fafd623e 1881 "PETScBuildInternal.cmake"
10b11968 1882 ;; Once installed, should uninstall with Guix
fafd623e 1883 "uninstall.py"))
a3a99e27
EB		 1884 #t)))
1885 (add-after 'install 'move-examples
1886 (lambda* (#:key outputs #:allow-other-keys)
1887 (let* ((out (assoc-ref outputs "out"))
1888 (examples (assoc-ref outputs "examples"))
1889 (exdir (string-append out "/share/petsc/examples"))
1890 (exdir' (string-append examples "/share/petsc/examples")))
1891 (copy-recursively exdir exdir')
1892 (delete-file-recursively exdir)
fafd623e 1893 #t))))))
b9100e2f 1894 (home-page "http://www.mcs.anl.gov/petsc")
16ecf3ff 1895 (synopsis "Library to solve PDEs")
b9100e2f
EB		 1896 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1897data structures and routines for the scalable (parallel) solution of
1898scientific applications modeled by partial differential equations.")
166191b3 1899 (license (license:non-copyleft
b9100e2f
EB		 1900 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1901
1902(define-public petsc-complex
1903 (package (inherit petsc)
1904 (name "petsc-complex")
1905 (arguments
1906 (substitute-keyword-arguments (package-arguments petsc)
1907 ((#:configure-flags cf)
1908 `(cons "--with-scalar-type=complex" ,cf))))
16ecf3ff 1909 (synopsis "Library to solve PDEs (with complex scalars)")))
183e44ae 1910
d8c7eeb9
EB		 1911(define-public petsc-openmpi
1912 (package (inherit petsc)
1913 (name "petsc-openmpi")
1914 (inputs
9e2aa70b 1915 `(("hdf5" ,hdf5-parallel-openmpi)
af523673 1916 ("hypre" ,hypre-openmpi)
9e2aa70b
PG		 1917 ("metis" ,metis)
1918 ("mumps" ,mumps-openmpi)
1919 ("openmpi" ,openmpi)
1920 ("scalapack" ,scalapack)
72f95783 1921 ("scotch" ,pt-scotch32)
d8c7eeb9
EB		 1922 ,@(package-inputs petsc)))
1923 (arguments
1924 (substitute-keyword-arguments (package-arguments petsc)
1925 ((#:configure-flags cf)
af523673
PG		 1926 ``("--with-hypre=1"
1927 "--with-mpiexec=mpirun"
9e2aa70b
PG		 1928 "--with-metis=1"
1929 "--with-mumps=1"
1930 "--with-scalapack=1"
1931 "--with-ptscotch=1"
d8c7eeb9
EB		 1932 ,(string-append "--with-mpi-dir="
1933 (assoc-ref %build-inputs "openmpi"))
71ca16b5
PG		 1934 ,(string-append "--with-hdf5-include="
1935 (assoc-ref %build-inputs "hdf5") "/include")
1936 ,(string-append "--with-hdf5-lib="
1937 (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
1938 ,@(delete "--with-mpi=0" ,cf)))
1939 ((#:phases phases)
1940 `(modify-phases ,phases
9e2aa70b 1941 (add-before 'configure 'mpi-setup
bbe46a4a 1942 ,%openmpi-setup)))))
9e2aa70b 1943 (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
d8c7eeb9
EB		 1944
1945(define-public petsc-complex-openmpi
1946 (package (inherit petsc-complex)
1947 (name "petsc-complex-openmpi")
1948 (inputs
1949 `(("openmpi" ,openmpi)
1950 ,@(package-inputs petsc-complex)))
1951 (arguments
1952 (substitute-keyword-arguments (package-arguments petsc-complex)
1953 ((#:configure-flags cf)
1954 ``("--with-mpiexec=mpirun"
1955 ,(string-append "--with-mpi-dir="
1956 (assoc-ref %build-inputs "openmpi"))
e586c6fa
EB		 1957 ,@(delete "--with-mpi=0" ,cf)))
1958 ((#:phases phases)
1959 `(modify-phases ,phases
1960 (add-before 'configure 'mpi-setup
1961 ,%openmpi-setup)))))
16ecf3ff 1962 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
d8c7eeb9 1963
90ff2874
PG		 1964(define-public python-petsc4py
1965 (package
1966 (name "python-petsc4py")
758439cf 1967 (version "3.10.1")
90ff2874
PG		 1968 (source
1969 (origin
1970 (method url-fetch)
1971 (uri (pypi-uri "petsc4py" version))
1972 (sha256
1973 (base32
758439cf 1974 "094hcnran0r2z1wlvmjswsz3ski1m9kqrl5l0ax8jjhnk55x0flh"))))
90ff2874
PG		 1975 (build-system python-build-system)
1976 (arguments
1977 `(#:phases
1978 (modify-phases %standard-phases
1979 (add-before 'build 'pre-build
1980 (lambda _
1981 ;; Define path to PETSc installation.
1982 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
1983 #t))
1984 (add-before 'check 'mpi-setup
1985 ,%openmpi-setup))))
1986 (inputs
1987 `(("petsc" ,petsc-openmpi)
1988 ("python-numpy" ,python-numpy)))
1989 (home-page "https://bitbucket.org/petsc/petsc4py/")
1990 (synopsis "Python bindings for PETSc")
1991 (description "PETSc, the Portable, Extensible Toolkit for
1992Scientific Computation, is a suite of data structures and routines for
1993the scalable (parallel) solution of scientific applications modeled by
1994partial differential equations. It employs the MPI standard for all
1995message-passing communication. @code{petsc4py} provides Python
1996bindings to almost all functions of PETSc.")
1997 (license license:bsd-3)))
1998
560acf25
MB		 1999(define-public python-kiwisolver
2000 (package
2001 (name "python-kiwisolver")
2002 (version "1.0.1")
2003 (source (origin
2004 (method url-fetch)
2005 (uri (pypi-uri "kiwisolver" version))
2006 (sha256
2007 (base32
2008 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
2009 (build-system python-build-system)
2010 (home-page "https://github.com/nucleic/kiwi")
2011 (synopsis "Fast implementation of the Cassowary constraint solver")
2012 (description
2013 "Kiwi is an efficient C++ implementation of the Cassowary constraint
2014solving algorithm. Kiwi has been designed from the ground up to be
2015lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
2016Cassowary solver with typical use cases gaining a 40x improvement. Memory
2017savings are consistently > 5x.")
2018 (license license:bsd-3)))
2019
2020(define-public python2-kiwisolver
2021 (package-with-python2 python-kiwisolver))
2022
a7f01414
EB		 2023(define-public slepc
2024 (package
2025 (name "slepc")
a13e0f3d 2026 (version "3.11.1")
a7f01414
EB		 2027 (source
2028 (origin
2029 (method url-fetch)
baeaf882
EB		 2030 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
2031 version ".tar.gz"))
a7f01414
EB		 2032 (sha256
2033 (base32
a13e0f3d 2034 "1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8"))))
a7f01414
EB		 2035 (build-system gnu-build-system)
2036 (native-inputs
a13e0f3d
EB		 2037 `(("python" ,python-2)
2038 ("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
a7f01414
EB		 2039 (inputs
2040 `(("arpack" ,arpack-ng)
2041 ("gfortran" ,gfortran)))
2042 (propagated-inputs
2043 `(("petsc" ,petsc)))
2044 (arguments
2045 `(#:parallel-build? #f ;build is parallel by default
2046 #:configure-flags
2047 `(,(string-append "--with-arpack-dir="
9cf52454 2048 (assoc-ref %build-inputs "arpack") "/lib"))
9731c412 2049 #:make-flags ;honor (parallel-job-count)
a13e0f3d
EB		 2050 `(,(format #f "MAKE_NP=~a" (parallel-job-count))
2051 ,(string-append "PETSCCONFIGDIR="
2052 (assoc-ref %build-inputs "petsc:examples")
2053 "/share/petsc/examples/config"))
a7f01414
EB		 2054 #:phases
2055 (modify-phases %standard-phases
8787c555 2056 (replace 'configure
a7f01414
EB		 2057 ;; configure is a python script, so we can't run it with bash.
2058 (lambda* (#:key inputs outputs (configure-flags '())
2059 #:allow-other-keys)
2060 (let* ((prefix (assoc-ref outputs "out"))
2061 (flags `(,(string-append "--prefix=" prefix)
2062 ,@configure-flags)))
2063 (format #t "build directory: ~s~%" (getcwd))
2064 (format #t "configure flags: ~s~%" flags)
2065 (setenv "SLEPC_DIR" (getcwd))
9cf52454 2066 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
c6840089 2067 (apply invoke "./configure" flags))))
8787c555 2068 (add-after 'install 'delete-doc
a7f01414
EB		 2069 ;; TODO: SLEPc installs HTML documentation alongside headers in
2070 ;; $out/include. We'd like to move them to share/doc, but delete
2071 ;; them for now, as they are incomplete and installing the complete
2072 ;; documentation is difficult.
2073 (lambda* (#:key outputs #:allow-other-keys)
2074 (let* ((out (assoc-ref outputs "out")))
0f6dc120
TGR		 2075 (for-each delete-file (find-files out "\\.html$"))
2076 #t)))
8787c555 2077 (add-after 'install 'clean-install
a7f01414
EB		 2078 ;; Clean up unnecessary build logs from installation.
2079 (lambda* (#:key outputs #:allow-other-keys)
2080 (let ((out (assoc-ref outputs "out")))
2081 (for-each (lambda (file)
2082 (let ((f (string-append out "/lib/slepc/conf/" file)))
2083 (when (file-exists? f)
2084 (delete-file f))))
2085 '("configure.log" "make.log" "gmake.log"
2086 "test.log" "error.log" "RDict.db"
0f6dc120
TGR		 2087 "uninstall.py"))
2088 #t))))))
a7f01414
EB		 2089 (home-page "http://slepc.upv.es")
2090 (synopsis "Scalable library for eigenproblems")
2091 (description "SLEPc is a software library for the solution of large sparse
2092eigenproblems on parallel computers. It can be used for the solution of
2093linear eigenvalue problems formulated in either standard or generalized form,
2094as well as other related problems such as the singular value decomposition.
2095The emphasis of the software is on methods and techniques appropriate for
2096problems in which the associated matrices are sparse, for example, those
2097arising after the discretization of partial differential equations.")
3c524f21 2098 (license license:bsd-2)))
a7f01414
EB		 2099
2100(define-public slepc-complex
2101 (package (inherit slepc)
2102 (name "slepc-complex")
2103 (propagated-inputs
2104 `(("petsc" ,petsc-complex)
2105 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
2106 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
2107
2108(define-public slepc-openmpi
2109 (package (inherit slepc)
2110 (name "slepc-openmpi")
6df2a50a
LC		 2111 (arguments
2112 (substitute-keyword-arguments (package-arguments slepc)
2113 ((#:phases phases '%standard-phases)
2114 `(modify-phases ,phases
bbe46a4a
EB		 2115 (add-before 'check 'mpi-setup
2116 ,%openmpi-setup)))))
a7f01414
EB		 2117 (inputs
2118 `(("mpi" ,openmpi)
2119 ("arpack" ,arpack-ng-openmpi)
2120 ,@(alist-delete "arpack" (package-inputs slepc))))
2121 (propagated-inputs
2122 `(("petsc" ,petsc-openmpi)
2123 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
2124 (synopsis "Scalable library for eigenproblems (with MPI support)")))
2125
2126(define-public slepc-complex-openmpi
2127 (package (inherit slepc-openmpi)
2128 (name "slepc-complex-openmpi")
2129 (propagated-inputs
2130 `(("petsc" ,petsc-complex-openmpi)
2131 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
2132 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
2133
6b5687d0
PG		 2134(define-public python-slepc4py
2135 (package
2136 (name "python-slepc4py")
57d30004 2137 (version "3.10.0")
6b5687d0
PG		 2138 (source
2139 (origin
2140 (method url-fetch)
2141 (uri (pypi-uri "slepc4py" version))
2142 (sha256
2143 (base32
57d30004 2144 "0x049dyc8frgh79fvvavf4vlbqp4mgm61nsaivzdav4316vvlv1j"))))
6b5687d0
PG		 2145 (build-system python-build-system)
2146 (arguments
2147 `(#:phases
2148 (modify-phases %standard-phases
2149 (add-before 'build 'pre-build
2150 (lambda _
2151 ;; Define path to PETSc installation.
2152 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
2153 ;; Define path to SLEPc installation.
2154 (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
2155 #t))
2156 (add-before 'check 'mpi-setup
2157 ,%openmpi-setup))))
2158 (inputs
2159 `(("python-numpy" ,python-numpy)
2160 ("python-petsc4py" ,python-petsc4py)
2161 ("slepc" ,slepc-openmpi)))
2162 (home-page "https://bitbucket.org/slepc/slepc4py/")
2163 (synopsis "Python bindings for SLEPc")
2164 (description "SLEPc, the Scalable Library for Eigenvalue Problem
2165Computations, is based on PETSc, the Portable, Extensible Toolkit for
2166Scientific Computation. It employs the MPI standard for all
2167message-passing communication. @code{slepc4py} provides Python
2168bindings to almost all functions of SLEPc.")
2169 (license license:bsd-3)))
2170
cec86422
EB		 2171(define-public mumps
2172 (package
2173 (name "mumps")
5dbc79eb 2174 (version "5.2.1")
cec86422
EB		 2175 (source
2176 (origin
2177 (method url-fetch)
2178 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
2179 version ".tar.gz"))
2180 (sha256
2181 (base32
5dbc79eb 2182 "0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r"))
06e12395
MB		 2183 (patches (search-patches "mumps-build-parallelism.patch"
2184 "mumps-shared-libseq.patch"
2185 "mumps-shared-mumps.patch"
2186 "mumps-shared-pord.patch"))))
cec86422
EB		 2187 (build-system gnu-build-system)
2188 (inputs
2189 `(("fortran" ,gfortran)
2190 ;; These are required for linking against mumps, but we let the user
2191 ;; declare the dependency.
2192 ("blas" ,openblas)
2193 ("metis" ,metis)
2194 ("scotch" ,scotch)))
2195 (arguments
2196 `(#:modules ((ice-9 match)
2197 (ice-9 popen)
2198 (srfi srfi-1)
2199 ,@%gnu-build-system-modules)
2200 #:phases
2201 (modify-phases %standard-phases
fba78d18 2202 (replace 'configure
cec86422
EB		 2203 (lambda* (#:key inputs #:allow-other-keys)
2204 (call-with-output-file "Makefile.inc"
2205 (lambda (port)
2206 (format port "
2207PLAT =
2208LIBEXT = .a
2209OUTC = -o
2210OUTF = -o
2211RM = rm -f~:[
2212CC = gcc
2213FC = gfortran
2214FL = gfortran
2215INCSEQ = -I$(topdir)/libseq
06e12395 2216LIBSEQ = $(topdir)/libseq/libmpiseq.a
cec86422
EB		 2217LIBSEQNEEDED = libseqneeded~;
2218CC = mpicc
2219FC = mpifort
2220FL = mpifort~]
2221AR = ar vr # rules require trailing space, ugh...
2222RANLIB = ranlib
06e12395
MB		 2223BLASDIR = ~a
2224LIBBLAS = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[
2225SCALAPDIR = ~a
2226SCALAP = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~]
cec86422
EB		 2227LIBOTHERS = -pthread
2228CDEFS = -DAdd_
2229PIC = -fPIC
2230OPTF = -O2 -DALLOW_NON_INIT $(PIC)
2231OPTL = -O2 $(PIC)
2232OPTC = -O2 $(PIC)
2233INCS = $(INCSEQ)
2234LIBS = $(SCALAP) $(LIBSEQ)
2235LPORDDIR = $(topdir)/PORD/lib
2236IPORD = -I$(topdir)/PORD/include
06e12395 2237LPORD = $(LPORDDIR)/libpord.a
cec86422
EB		 2238ORDERINGSF = -Dpord~@[
2239METISDIR = ~a
2240IMETIS = -I$(METISDIR)/include
06e12395 2241LMETIS = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
cec86422
EB		 2242ORDERINGSF += -Dmetis~]~@[~:{
2243SCOTCHDIR = ~a
2244ISCOTCH = -I$(SCOTCHDIR)/include
06e12395 2245LSCOTCH = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
cec86422
EB		 2246ORDERINGSF += ~a~}~]
2247ORDERINGSC = $(ORDERINGSF)
06e12395 2248LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
cec86422
EB		 2249IORDERINGSF = $(ISCOTCH)
2250IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
2251 (assoc-ref inputs "mpi")
2252 (assoc-ref inputs "blas")
2253 (assoc-ref inputs "scalapack")
2254 (assoc-ref inputs "metis")
2255 (match (list (assoc-ref inputs "pt-scotch")
2256 (assoc-ref inputs "scotch"))
2257 ((#f #f)
2258 #f)
2259 ((#f scotch)
2260 `((,scotch "" "-Dscotch")))
2261 ((ptscotch _)
2262 `((,ptscotch
2263 "-lptesmumps -lptscotch -lptscotcherr "
2264 "-Dptscotch")))))))))
fba78d18 2265 (replace 'build
cec86422
EB		 2266 ;; By default only the d-precision library is built. Make with "all"
2267 ;; target so that all precision libraries and examples are built.
2268 (lambda _
b414cf52
TGR		 2269 (invoke "make" "all"
2270 (format #f "-j~a" (parallel-job-count)))))
fba78d18 2271 (replace 'check
cec86422
EB		 2272 ;; Run the simple test drivers, which read test input from stdin:
2273 ;; from the "real" input for the single- and double-precision
2274 ;; testers, and from the "cmplx" input for complex-precision
2275 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
2276 ;; package to prefix execution with "mpirun".
2277 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
2278 (with-directory-excursion "examples"
2279 (every
2280 (lambda (prec type)
2281 (let ((tester (apply open-pipe*
2282 `(,OPEN_WRITE
2283 ,@exec-prefix
2284 ,(string-append "./" prec
2285 "simpletest"))))
2286 (input (open-input-file
2287 (string-append "input_simpletest_" type))))
2288 (begin
2289 (dump-port input tester)
2290 (close-port input)
2291 (zero? (close-pipe tester)))))
2292 '("s" "d" "c" "z")
2293 '("real" "real" "cmplx" "cmplx")))))
fba78d18
EB		 2294 (replace 'install
2295 (lambda* (#:key outputs #:allow-other-keys)
2296 (let* ((out (assoc-ref outputs "out"))
2297 (libdir (string-append out "/lib")))
2298 (copy-recursively "lib" libdir)
2299 (copy-recursively "include" (string-append out "/include"))
2300 (when (file-exists? "libseq/libmpiseq.a")
2301 (install-file "libseq/libmpiseq.a" libdir))
06e12395
MB		 2302 (when (file-exists? "libseq/libmpiseq.so")
2303 (install-file "libseq/libmpiseq.so" libdir))
fba78d18 2304 #t))))))
cec86422
EB		 2305 (home-page "http://mumps.enseeiht.fr")
2306 (synopsis "Multifrontal sparse direct solver")
2307 (description
2308 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
57e69c1d 2309sparse system of linear equations A x = b using Gaussian elimination.")
cec86422
EB		 2310 (license license:cecill-c)))
2311
2312(define-public mumps-metis
2313 (package (inherit mumps)
2314 (name "mumps-metis")
2315 (inputs
2316 (alist-delete "scotch" (package-inputs mumps)))))
2317
2318(define-public mumps-openmpi
2319 (package (inherit mumps)
2320 (name "mumps-openmpi")
2321 (inputs
2322 `(("mpi" ,openmpi)
2323 ("scalapack" ,scalapack)
2324 ("pt-scotch" ,pt-scotch)
2325 ,@(alist-delete "scotch" (package-inputs mumps))))
2326 (arguments
2327 (substitute-keyword-arguments (package-arguments mumps)
2328 ((#:phases phases)
2329 `(modify-phases ,phases
bbe46a4a
EB		 2330 (add-before 'check 'mpi-setup
2331 ,%openmpi-setup)
6df2a50a
LC		 2332 (replace 'check
2333 (lambda _
2334 ((assoc-ref ,phases 'check)
2335 #:exec-prefix '("mpirun" "-n" "2"))))))))
cec86422
EB		 2336 (synopsis "Multifrontal sparse direct solver (with MPI)")))
2337
2338(define-public mumps-metis-openmpi
2339 (package (inherit mumps-openmpi)
2340 (name "mumps-metis-openmpi")
2341 (inputs
2342 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
2343
2d047896
RW		 2344(define-public r-quadprog
2345 (package
2346 (name "r-quadprog")
ae9ed139 2347 (version "1.5-7")
2d047896
RW		 2348 (source
2349 (origin
2350 (method url-fetch)
2351 (uri (cran-uri "quadprog" version))
2352 (sha256
2353 (base32
ae9ed139 2354 "0vg7i9p241bwvfdspjbydjrsvgipl6nsb8bjigp0hbbgvxbixx0s"))))
2d047896
RW		 2355 (build-system r-build-system)
2356 (native-inputs
2357 `(("gfortran" ,gfortran)))
e9960d8c 2358 (home-page "https://cran.r-project.org/web/packages/quadprog")
2d047896
RW		 2359 (synopsis "Functions to solve quadratic programming problems")
2360 (description
2361 "This package contains routines and documentation for solving quadratic
2362programming problems.")
2363 (license license:gpl3+)))
2364
ec8c7e47
RJ		 2365(define-public r-pracma
2366 (package
2367 (name "r-pracma")
9f2a87d1 2368 (version "2.2.5")
ec8c7e47
RJ		 2369 (source (origin
2370 (method url-fetch)
2371 (uri (cran-uri "pracma" version))
2372 (sha256
9f2a87d1 2373 (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g"))))
ec8c7e47 2374 (build-system r-build-system)
39528a5e 2375 (home-page "https://cran.r-project.org/web/packages/pracma/")
ec8c7e47
RJ		 2376 (synopsis "Practical numerical math functions")
2377 (description "This package provides functions for numerical analysis and
2378linear algebra, numerical optimization, differential equations, plus some
2379special functions. It uses Matlab function names where appropriate to simplify
2380porting.")
2381 (license license:gpl3+)))
2382
63e07468
BW		 2383(define-public ruby-asciimath
2384 (package
2385 (name "ruby-asciimath")
2386 (version "1.0.4")
2387 (source
2388 (origin
2389 (method url-fetch)
2390 (uri (rubygems-uri "asciimath" version))
2391 (sha256
2392 (base32
2393 "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
2394 (build-system ruby-build-system)
2395 (arguments
2396 '(#:phases
2397 (modify-phases %standard-phases
2398 ;; Apply this patch
2399 ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
2400 (add-after 'unpack 'patch-remove-spurious-backslashes
2401 (lambda _
2402 (substitute* "spec/parser_spec.rb"
2403 (("\\\\\"")
9923d5a4
TGR		 2404 "\""))
2405 #t)))))
63e07468
BW		 2406 (native-inputs
2407 `(("bundler" ,bundler)
2408 ("ruby-rspec" ,ruby-rspec)))
2409 (synopsis "AsciiMath parsing and conversion library")
2410 (description
2411 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
2412easy-to-write markup language for mathematics.")
2413 (home-page "https://github.com/asciidoctor/asciimath")
2414 (license license:expat)))
2415
183e44ae
EB		 2416(define-public superlu
2417 (package
2418 (name "superlu")
995a09e0 2419 (version "5.2.1")
183e44ae
EB		 2420 (source
2421 (origin
2422 (method url-fetch)
2423 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2424 "superlu_" version ".tar.gz"))
2425 (sha256
995a09e0
EB		 2426 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
2427 (modules '((guix build utils)))
2428 (snippet
2429 ;; Replace the non-free implementation of MC64 with a stub adapted
2430 ;; from Debian
2431 '(begin
2432 (use-modules (ice-9 regex)
2433 (ice-9 rdelim))
2434 (call-with-output-file "SRC/mc64ad.c"
2435 (lambda (port)
2436 (display "
2437#include <stdio.h>
2438#include <stdlib.h>
2439void mc64id_(int *a) {
2440 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2441 abort ();
2442}
2443void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2444 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2445 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2446 abort ();
2447}\n" port)))
2448 ;; Remove the corresponding license verbiage. MC64 license follows
2449 ;; a "------" line separator.
2450 (with-atomic-file-replacement "License.txt"
2451 (let ((rx (make-regexp "-{8}")))
2452 (lambda (in out)
2453 (let loop ()
2454 (let ((line (read-line in 'concat)))
2455 (unless (regexp-exec rx line)
2456 (display line out)
6cbee49d
MW		 2457 (loop))))
2458 #t)))))))
995a09e0 2459 (build-system cmake-build-system)
183e44ae
EB		 2460 (native-inputs
2461 `(("tcsh" ,tcsh)))
2462 (inputs
995a09e0 2463 `(("blas" ,openblas)
19afbea1 2464 ("gfortran" ,gfortran)))
183e44ae 2465 (arguments
995a09e0
EB		 2466 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2467 "-DTPL_BLAS_LIBRARIES=openblas"
677bc34d 2468 "-DBUILD_SHARED_LIBS:BOOL=YES")))
183e44ae
EB		 2469 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
2470 (synopsis "Supernodal direct solver for sparse linear systems")
2471 (description
2472 "SuperLU is a general purpose library for the direct solution of large,
2473sparse, nonsymmetric systems of linear equations on high performance machines.
2474The library is written in C and is callable from either C or Fortran. The
2475library routines perform an LU decomposition with partial pivoting and
2476triangular system solves through forward and back substitution. The library
2477also provides threshold-based ILU factorization preconditioners.")
995a09e0
EB		 2478 (license (list license:bsd-3
2479 license:gpl2+ ;EXAMPLE/*fgmr.c
2480 (license:fsf-free "file://SRC/colamd.h")))))
f8ed036a 2481
a54aefea
EB		 2482(define-public superlu-dist
2483 (package
2484 (name "superlu-dist")
6161141e 2485 (version "6.1.0")
a54aefea
EB		 2486 (source
2487 (origin
2488 (method url-fetch)
2489 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2490 "superlu_dist_" version ".tar.gz"))
2491 (sha256
6161141e 2492 (base32 "0pqgcgh1yxhfzs99fas3mggajzd5wca3nbyp878rziy74gfk03dl"))
0921eff2 2493 (modules '((guix build utils)))
29080870
EB		 2494 (snippet
2495 ;; Replace the non-free implementation of MC64 with a stub
2496 '(begin
0921eff2 2497 (call-with-output-file "SRC/mc64ad_dist.c"
29080870
EB		 2498 (lambda (port)
2499 (display "
2500#include <stdio.h>
2501#include <stdlib.h>
0921eff2 2502void mc64id_dist(int *a) {
29080870
EB		 2503 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2504 abort ();
2505}
0921eff2 2506void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
29080870
EB		 2507 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2508 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2509 abort ();
2510}\n" port)))
29080870 2511 (substitute* "SRC/util.c" ;adjust default algorithm
6161141e
EB		 2512 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
2513 ;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
2514 ;; general (i.e. non-square) processor-grid support.
2515 "RowPerm = NOROWPERM;"))
6cbee49d 2516 #t))
6161141e 2517 (patches (search-patches "superlu-dist-scotchmetis.patch"
2bdf26f1
EB		 2518 "superlu-dist-awpm-grid.patch"
2519 "superlu-dist-fix-mpi-deprecations.patch"))))
6161141e 2520 (build-system cmake-build-system)
a54aefea
EB		 2521 (native-inputs
2522 `(("tcsh" ,tcsh)))
2523 (inputs
6161141e
EB		 2524 `(("gfortran" ,gfortran)
2525 ("blas" ,openblas)
2526 ("lapack" ,lapack)
2527 ("combblas" ,combinatorial-blas)))
a54aefea 2528 (propagated-inputs
6161141e
EB		 2529 `(("mpi" ,openmpi) ;headers include MPI heades
2530 ("parmetis" ,pt-scotch32 "metis")
2531 ("pt-scotch" ,pt-scotch32)))
a54aefea 2532 (arguments
6161141e
EB		 2533 `(#:parallel-tests? #f ;tests use MPI and OpenMP
2534 #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
2535 "-DTPL_ENABLE_COMBBLASLIB=YES"
2536 "-DTPL_BLAS_LIBRARIES=-lopenblas"
2537 "-DTPL_LAPACK_LIBRARIES=-llapack"
2538 (string-append "-DTPL_PARMETIS_LIBRARIES="
2539 (string-join
2540 '("ptscotchparmetis" "ptscotch" "ptscotcherr"
2541 "scotchmetis" "scotch" "scotcherr")
2542 ";"))
2543 (string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
2544 (assoc-ref %build-inputs "parmetis")
2545 "/include")
2546 "-DTPL_ENABLE_COMBBLASLIB=ON"
2547 (string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
2548 (assoc-ref %build-inputs "combblas")
2549 "/include/CombBLAS;"
2550 (assoc-ref %build-inputs "combblas")
2551 "/include/BipartiteMatchings")
2552 "-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
a54aefea 2553 #:phases
dc1d3cde 2554 (modify-phases %standard-phases
6161141e 2555 (add-before 'configure 'set-c++-standard
dc1d3cde 2556 (lambda _
6161141e
EB		 2557 (substitute* "CMakeLists.txt"
2558 ;; AWPM headers require C++14
2559 (("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
bbe46a4a
EB		 2560 (add-before 'check 'mpi-setup
2561 ,%openmpi-setup)
6161141e
EB		 2562 (add-before 'check 'omp-setup
2563 (lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
a54aefea
EB		 2564 (home-page (package-home-page superlu))
2565 (synopsis "Parallel supernodal direct solver")
2566 (description
2567 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2568It is targeted for distributed memory parallel machines. SuperLU_DIST is
2569implemented in ANSI C, and MPI for communications.")
2570 (license license:bsd-3)))
2571
f8ed036a
EB		 2572(define-public scotch
2573 (package
2574 (name "scotch")
fd373343 2575 (version "6.0.6")
f8ed036a
EB		 2576 (source
2577 (origin
2578 (method url-fetch)
1dc31097
TGR		 2579 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
2580 "latestfile/298/scotch_" version ".tar.gz"))
f8ed036a 2581 (sha256
fd373343
EB		 2582 (base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8"))
2583 (patches (search-patches "scotch-build-parallelism.patch"
2584 "scotch-integer-declarations.patch"))))
f8ed036a
EB		 2585 (build-system gnu-build-system)
2586 (inputs
2587 `(("zlib" ,zlib)
5e54f4ad 2588 ("flex" ,flex)
f8ed036a 2589 ("bison" ,bison)))
fd373343 2590 (outputs '("out" "metis"))
f8ed036a 2591 (arguments
fd373343
EB		 2592 `(#:make-flags (list (string-append "prefix=" %output))
2593 #:phases
d6602ee9
EB		 2594 (modify-phases %standard-phases
2595 (add-after
2596 'unpack 'chdir-to-src
d67a7e9e 2597 (lambda _ (chdir "src") #t))
d6602ee9
EB		 2598 (replace
2599 'configure
2600 (lambda _
2601 (call-with-output-file "Makefile.inc"
2602 (lambda (port)
2603 (format port "
f8ed036a
EB		 2604EXE =
2605LIB = .a
2606OBJ = .o
2607MAKE = make
2608AR = ar
2609ARFLAGS = -ruv
cf0ec6c4 2610CAT = cat
f8ed036a
EB		 2611CCS = gcc
2612CCP = mpicc
2613CCD = gcc
2614CPPFLAGS =~{ -D~a~}
6c798540 2615CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
f8ed036a
EB		 2616LDFLAGS = -lz -lm -lrt -lpthread
2617CP = cp
2618LEX = flex -Pscotchyy -olex.yy.c
2619LN = ln
2620MKDIR = mkdir
2621MV = mv
2622RANLIB = ranlib
2623YACC = bison -pscotchyy -y -b y
2624"
d6602ee9
EB		 2625 '("COMMON_FILE_COMPRESS_GZ"
2626 "COMMON_PTHREAD"
2627 "COMMON_RANDOM_FIXED_SEED"
fd373343 2628 "INTSIZE64" ;use 'int64_t'
cf0ec6c4
EB		 2629 ;; Prevents symbolc clashes with libesmumps
2630 "SCOTCH_RENAME"
d6602ee9
EB		 2631 ;; XXX: Causes invalid frees in superlu-dist tests
2632 ;; "SCOTCH_PTHREAD"
2633 ;; "SCOTCH_PTHREAD_NUMBER=2"
d67a7e9e
TGR		 2634 "restrict=__restrict"))))
2635 #t))
bbe46a4a 2636 (add-after 'build 'build-esmumps
cf0ec6c4 2637 (lambda _
d67a7e9e
TGR		 2638 (invoke "make"
2639 (format #f "-j~a" (parallel-job-count))
2640 "esmumps")))
fd373343
EB		 2641 (add-before 'install 'make-install-dirs
2642 (lambda* (#:key outputs #:allow-other-keys)
2643 (mkdir (assoc-ref outputs "out"))))
2644 (add-after 'install 'install-metis
2645 (lambda* (#:key outputs #:allow-other-keys)
2646 (let ((out (assoc-ref outputs "metis")))
2647 (mkdir out)
2648 ;; metis files are not installed with 'make install'
2649 (for-each (lambda (f)
2650 (install-file f (string-append out "/include")))
2651 (find-files "../include/" ".*metis\\.h"))
2652 (for-each (lambda (f)
2653 (install-file f (string-append out "/lib")))
2654 (find-files "../lib/" ".*metis\\..*"))
2655 #t))))))
f8ed036a
EB		 2656 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
2657 (synopsis "Programs and libraries for graph algorithms")
2658 (description "SCOTCH is a set of programs and libraries which implement
2659the static mapping and sparse matrix reordering algorithms developed within
2660the SCOTCH project. Its purpose is to apply graph theory, with a divide and
2661conquer approach, to scientific computing problems such as graph and mesh
2662partitioning, static mapping, and sparse matrix ordering, in application
2663domains ranging from structural mechanics to operating systems or
2664bio-chemistry.")
2665 ;; See LICENSE_en.txt
2666 (license license:cecill-c)))
6acb4adb 2667
1c39f3b8
PG		 2668(define-public scotch32
2669 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2670 ;; some applications.
2671 (package (inherit scotch)
2672 (name "scotch32")
2673 (arguments
2674 (substitute-keyword-arguments (package-arguments scotch)
2675 ((#:phases scotch-phases)
2676 `(modify-phases ,scotch-phases
2677 (replace
2678 'configure
2679 (lambda _
2680 (call-with-output-file "Makefile.inc"
2681 (lambda (port)
2682 (format port "
2683EXE =
2684LIB = .a
2685OBJ = .o
2686MAKE = make
2687AR = ar
2688ARFLAGS = -ruv
2689CAT = cat
2690CCS = gcc
2691CCP = mpicc
2692CCD = gcc
2693CPPFLAGS =~{ -D~a~}
2694CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2695LDFLAGS = -lz -lm -lrt -lpthread
2696CP = cp
2697LEX = flex -Pscotchyy -olex.yy.c
2698LN = ln
2699MKDIR = mkdir
2700MV = mv
2701RANLIB = ranlib
2702YACC = bison -pscotchyy -y -b y
2703"
2704 '("COMMON_FILE_COMPRESS_GZ"
2705 "COMMON_PTHREAD"
2706 "COMMON_RANDOM_FIXED_SEED"
2707 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
2708 ;; Prevents symbolc clashes with libesmumps
2709 "SCOTCH_RENAME"
2710 ;; XXX: Causes invalid frees in superlu-dist tests
2711 ;; "SCOTCH_PTHREAD"
2712 ;; "SCOTCH_PTHREAD_NUMBER=2"
2713 "restrict=__restrict"))))))))))
2714 (synopsis
2715 "Programs and libraries for graph algorithms (32-bit integers)")))
2716
6acb4adb
EB		 2717(define-public pt-scotch
2718 (package (inherit scotch)
2719 (name "pt-scotch")
2720 (propagated-inputs
2721 `(("openmpi" ,openmpi))) ;Headers include MPI headers
2722 (arguments
2723 (substitute-keyword-arguments (package-arguments scotch)
2724 ((#:phases scotch-phases)
d6602ee9
EB		 2725 `(modify-phases ,scotch-phases
2726 (replace
2727 'build
d6602ee9 2728 (lambda _
c491f7f8
LC		 2729 (invoke "make" (format #f "-j~a" (parallel-job-count))
2730 "ptscotch" "ptesmumps")
2731
2732 ;; Install the serial metis compatibility library
2733 (invoke "make" "-C" "libscotchmetis" "install")))
2734 (add-before 'check 'mpi-setup
2735 ,%openmpi-setup)
2736 (replace 'check
2737 (lambda _
2738 (invoke "make" "ptcheck")))))))
6acb4adb 2739 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
5698b8b8 2740
1c25a52c
PG		 2741(define-public pt-scotch32
2742 (package (inherit scotch32)
2743 (name "pt-scotch32")
2744 (propagated-inputs
2745 `(("openmpi" ,openmpi))) ;headers include MPI headers
2746 (arguments
c4d4a779
PG		 2747 (substitute-keyword-arguments (package-arguments scotch32)
2748 ((#:phases scotch32-phases)
2749 `(modify-phases ,scotch32-phases
1c25a52c
PG		 2750 (replace 'build
2751 (lambda _
c491f7f8
LC		 2752 (invoke "make" (format #f "-j~a" (parallel-job-count))
2753 "ptscotch" "ptesmumps")
2754 ;; Install the serial metis compatibility library
2755 (invoke "make" "-C" "libscotchmetis" "install")))
2756 (add-before 'check 'mpi-setup
2757 ,%openmpi-setup)
1c25a52c
PG		 2758 (replace 'check
2759 (lambda _
c491f7f8 2760 (invoke "make" "ptcheck")))))))
1c25a52c
PG		 2761 (synopsis
2762 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2763
aa75ad00
EB		 2764(define-public metis
2765 (package
2766 (name "metis")
2767 (version "5.1.0")
2768 (source
2769 (origin
2770 (method url-fetch)
2771 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2772 "metis-" version ".tar.gz"))
2773 (sha256
2774 (base32
2775 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2776 (build-system cmake-build-system)
2777 (inputs
2778 `(("blas" ,openblas)))
2779 (arguments
2780 `(#:tests? #f ;no tests
2781 #:configure-flags `("-DSHARED=ON"
2782 ,(string-append "-DGKLIB_PATH=" (getcwd)
2783 "/metis-" ,version "/GKlib"))))
2784 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2785 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2786 (description
2787 "METIS is a set of serial programs for partitioning graphs, partitioning
2788finite element meshes, and producing fill-reducing orderings for sparse
2789matrices. The algorithms implemented in METIS are based on the multilevel
2790recursive-bisection, multilevel k-way, and multi-constraint partitioning
2791schemes.")
2792 (license license:asl2.0))) ;As of version 5.0.3
2793
700ff222
EB		 2794(define-public p4est
2795 (package
2796 (name "p4est")
4150da63 2797 (version "2.0")
700ff222
EB		 2798 (source
2799 (origin
2800 (method url-fetch)
2801 (uri (string-append "http://p4est.github.io/release/p4est-"
2802 version ".tar.gz"))
2803 (sha256
2804 (base32
4150da63 2805 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
700ff222
EB		 2806 (build-system gnu-build-system)
2807 (inputs
2808 `(("fortran" ,gfortran)
2809 ("blas" ,openblas)
2810 ("lapack" ,lapack)
2811 ("zlib" ,zlib)))
2812 (arguments
2813 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2814 (assoc-ref %build-inputs "blas")
2815 " -lopenblas")
2816 ,(string-append "LAPACK_LIBS=-L"
2817 (assoc-ref %build-inputs "lapack")
6df2a50a
LC		 2818 " -llapack"))
2819 #:phases (modify-phases %standard-phases
bbe46a4a
EB		 2820 (add-before 'check 'mpi-setup
2821 ,%openmpi-setup))))
700ff222
EB		 2822 (home-page "http://www.p4est.org")
2823 (synopsis "Adaptive mesh refinement on forests of octrees")
2824 (description
2825 "The p4est software library enables the dynamic management of a
2826collection of adaptive octrees, conveniently called a forest of octrees.
2827p4est is designed to work in parallel and scales to hundreds of thousands of
2828processor cores.")
2829 (license license:gpl2+)))
2830
2831(define-public p4est-openmpi
2832 (package (inherit p4est)
2833 (name "p4est-openmpi")
2834 (inputs
2835 `(("mpi" ,openmpi)
2836 ,@(package-inputs p4est)))
2837 (arguments
2838 (substitute-keyword-arguments (package-arguments p4est)
2839 ((#:configure-flags cf)
2840 ``("--enable-mpi" ,@,cf))))
2841 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2842
5698b8b8
JD		 2843(define-public gsegrafix
2844 (package
2845 (name "gsegrafix")
2846 (version "1.0.6")
2847 (source
2848 (origin
2849 (method url-fetch)
2850 (uri (string-append "mirror://gnu/" name "/" name "-"
2851 version ".tar.gz"))
2852 (sha256
2853 (base32
2854 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2855 (build-system gnu-build-system)
2856 (arguments
2857 `(#:configure-flags '("LDFLAGS=-lm")))
2858 (inputs
2859 `(("libgnomecanvas" ,libgnomecanvas)
2860 ("libbonoboui" ,libbonoboui)
2861 ("libgnomeui" ,libgnomeui)
2862 ("libgnomeprintui" ,libgnomeprintui)
2863 ("popt" ,popt)))
2864 (native-inputs
2865 `(("pkg-config" ,pkg-config)))
6fd52309 2866 (home-page "https://www.gnu.org/software/gsegrafix/")
5698b8b8
JD		 2867 (synopsis "GNOME application to create scientific and engineering plots")
2868 (description "GSEGrafix is an application which produces high-quality graphical
2869plots for science and engineering. Plots are specified via simple ASCII
2870parameter files and data files and are presented in an anti-aliased GNOME
2871canvas. The program supports rectangular two-dimensional plots, histograms,
2872polar-axis plots and three-dimensional plots. Plots can be printed or saved
2873to BMP, JPEG or PNG image formats.")
2874 (license license:gpl3+)))
8731e527
JD		 2875
2876(define-public maxima
2877 (package
2878 (name "maxima")
ccc963d5 2879 (version "5.43.0")
8731e527
JD		 2880 (source
2881 (origin
2882 (method url-fetch)
2883 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2884 version "-source/" name "-" version ".tar.gz"))
2885 (sha256
2886 (base32
ccc963d5 2887 "0xyahp4c6509haxh4n1swiqm3421gplkdisa0zypclh3252sbzfw"))
fc1adab1 2888 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
8731e527 2889 (build-system gnu-build-system)
df354a77 2890 (inputs
6b2eafaa 2891 `(("gcl" ,gcl)
df354a77 2892 ("gnuplot" ,gnuplot) ;for plots
fc9c47bd 2893 ("sed" ,sed)
f36afe4d 2894 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
df354a77
FB		 2895 (native-inputs
2896 `(("texinfo" ,texinfo)
ccbc5758
KK		 2897 ("perl" ,perl)
2898 ("python" ,python)))
8731e527 2899 (arguments
df354a77
FB		 2900 `(#:configure-flags
2901 (list "--enable-gcl"
2902 (string-append "--with-posix-shell="
2903 (assoc-ref %build-inputs "bash")
2904 "/bin/sh")
2905 (string-append "--with-wish="
2906 (assoc-ref %build-inputs "tk")
2907 "/bin/wish"
2908 (let ((v ,(package-version tk)))
2909 (string-take v (string-index-right v #\.)))))
df354a77 2910 ;; By default Maxima attempts to write temporary files to
77af7b24
MW		 2911 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2912 ;; Work around that.
df354a77 2913 #:make-flags (list "TMPDIR=/tmp")
0093b126
KK		 2914 #:phases
2915 (modify-phases %standard-phases
fc9c47bd
KK		 2916 (add-after 'unpack 'patch-paths
2917 (lambda* (#:key inputs #:allow-other-keys)
2918 (let* ((sed (string-append (assoc-ref inputs "sed") "/bin/sed"))
2919 (coreutils (assoc-ref inputs "coreutils"))
2920 (dirname (string-append coreutils "/bin/dirname"))
ccc963d5
KK		 2921 (head (string-append coreutils "/bin/head"))
2922 (perl (string-append (assoc-ref inputs "perl") "/bin/perl"))
2923 (python (string-append (assoc-ref inputs "python")
2924 "/bin/python3")))
fc9c47bd
KK		 2925 (substitute* "src/maxima.in"
2926 (("sed ") (string-append sed " "))
2927 (("dirname") dirname)
2928 (("head") head))
ccc963d5
KK		 2929 (substitute* "doc/info/Makefile.in"
2930 (("/usr/bin/env perl") perl))
2931 (substitute* "doc/info/build_html.sh.in"
2932 (("python") python))
fc9c47bd 2933 #t)))
0093b126
KK		 2934 (add-before 'check 'pre-check
2935 (lambda _
2936 (chmod "src/maxima" #o555)
2937 #t))
1472d19a
KK		 2938 (replace 'check
2939 (lambda _
2940 ;; This is derived from the testing code in the "debian/rules" file
2941 ;; of Debian's Maxima package.
2942 ;; If Maxima can successfully run this, the binary to be installed
2943 ;; should be fine.
df129041
MW		 2944 (invoke "sh" "-c"
2945 (string-append
2946 "./maxima-local "
2947 "--lisp=gcl "
2948 "--batch-string=\"run_testsuite();\" "
2949 "| grep -q \"No unexpected errors found\""))))
0093b126
KK		 2950 ;; Make sure the doc and emacs files are found in the
2951 ;; standard location. Also configure maxima to find gnuplot
2952 ;; without having it on the PATH.
2953 (add-after 'install 'post-install
2954 (lambda* (#:key outputs inputs #:allow-other-keys)
2955 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2956 (out (assoc-ref outputs "out"))
2957 (datadir (string-append out "/share/maxima/" ,version))
2958 (binutils (string-append (assoc-ref inputs "binutils")
2959 "/bin")))
2960 (with-directory-excursion out
2961 (mkdir-p "share/emacs")
2962 (mkdir-p "share/doc")
0093b126
KK		 2963 (symlink
2964 (string-append datadir "/doc/")
2965 (string-append out "/share/doc/maxima"))
2966 (with-atomic-file-replacement
2967 (string-append datadir "/share/maxima-init.lisp")
2968 (lambda (in out)
2969 (format out "~a ~s~a~%"
2970 "(setf $gnuplot_command "
2971 (string-append gnuplot "/bin/gnuplot") ")")
2972 (dump-port in out))))
2973 ;; Ensure that Maxima will have access to the GNU binutils
2974 ;; components at runtime.
2975 (wrap-program (string-append out "/bin/maxima")
2976 `("PATH" prefix (,binutils))))
2977 #t)))))
8731e527
JD		 2978 (home-page "http://maxima.sourceforge.net")
2979 (synopsis "Numeric and symbolic expression manipulation")
2980 (description "Maxima is a system for the manipulation of symbolic and
2981numerical expressions. It yields high precision numeric results by using
2982exact fractions, arbitrary precision integers, and variable precision floating
e881752c 2983point numbers.")
8731e527
JD		 2984 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2985 ;; Others simply say "GNU General Public License" without stating a
2986 ;; version (which implicitly means gpl1+).
2987 ;; At least one file (src/maxima.asd) says "version 2."
2988 ;; GPLv2 only is therefore the smallest subset.
f36afe4d 2989 (license license:gpl2)))
ec322be2 2990
9aafbc0c
MW		 2991(define-public wxmaxima
2992 (package
2993 (name "wxmaxima")
ca2ead31 2994 (version "19.09.0")
9aafbc0c
MW		 2995 (source
2996 (origin
c93b77ad
KK		 2997 (method git-fetch)
2998 (uri (git-reference
2999 (url "https://github.com/wxMaxima-developers/wxmaxima.git")
3000 (commit (string-append "Version-" version))))
3001 (file-name (git-file-name name version))
9aafbc0c 3002 (sha256
ca2ead31 3003 (base32 "195j6j8z0jd6xg3a63ywbrbsc6dany795m3fb95nbx1vq0bqqvvn"))))
0181df53 3004 (build-system cmake-build-system)
5143517c 3005 (native-inputs
0181df53 3006 `(("gettext" ,gettext-minimal)))
9aafbc0c
MW		 3007 (inputs
3008 `(("wxwidgets" ,wxwidgets)
de477809
SB		 3009 ("maxima" ,maxima)
3010 ;; Runtime support.
3011 ("adwaita-icon-theme" ,adwaita-icon-theme)
3012 ("gtk+" ,gtk+)
3013 ("shared-mime-info" ,shared-mime-info)))
9aafbc0c 3014 (arguments
0181df53
KK		 3015 `(#:tests? #f ; no check target
3016 #:phases
ac2ddcc6 3017 (modify-phases %standard-phases
ac2ddcc6
KK		 3018 (add-after 'install 'wrap-program
3019 (lambda* (#:key inputs outputs #:allow-other-keys)
3020 (wrap-program (string-append (assoc-ref outputs "out")
3021 "/bin/wxmaxima")
3022 `("PATH" ":" prefix
3023 (,(string-append (assoc-ref inputs "maxima")
3024 "/bin")))
3025 ;; For GtkFileChooserDialog.
3026 `("GSETTINGS_SCHEMA_DIR" =
3027 (,(string-append (assoc-ref inputs "gtk+")
3028 "/share/glib-2.0/schemas")))
3029 `("XDG_DATA_DIRS" ":" prefix
3030 (;; Needed by gdk-pixbuf to know supported icon formats.
3031 ,(string-append
3032 (assoc-ref inputs "shared-mime-info") "/share")
3033 ;; The default icon theme of GTK+.
3034 ,(string-append
3035 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
3036 #t)))))
9aafbc0c
MW		 3037 (home-page "https://andrejv.github.io/wxmaxima/")
3038 (synopsis "Graphical user interface for the Maxima computer algebra system")
3039 (description
3040 "wxMaxima is a graphical user interface for the Maxima computer algebra
3041system. It eases the use of Maxima by making most of its commands available
3042through a menu system and by providing input dialogs for commands that require
3043more than one argument. It also implements its own display engine that
3044outputs mathematical symbols directly instead of depicting them with ASCII
3045characters.
3046
3047wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
3048text and mathematical calculations to create documents, exporting of input and
3049output to TeX, and a browser for Maxima's manual including command index and
3050full text searching.")
3051 (license license:gpl2+)))
3052
b15e47f9
RW		 3053(define-public armadillo
3054 (package
3055 (name "armadillo")
f133e244 3056 (version "9.100.5")
b15e47f9
RW		 3057 (source (origin
3058 (method url-fetch)
3059 (uri (string-append "mirror://sourceforge/arma/armadillo-"
7397cd9e 3060 version ".tar.xz"))
b15e47f9
RW		 3061 (sha256
3062 (base32
f133e244 3063 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
b15e47f9 3064 (build-system cmake-build-system)
e405c0bc 3065 (arguments `(#:tests? #f)) ; no test target
b15e47f9
RW		 3066 (inputs
3067 `(("openblas" ,openblas)
3068 ("lapack" ,lapack)
3069 ("arpack" ,arpack-ng)))
3070 (home-page "http://arma.sourceforge.net/")
3071 (synopsis "C++ linear algebra library")
3072 (description
3073 "Armadillo is a C++ linear algebra library, aiming towards a good balance
3074between speed and ease of use. It is useful for algorithm development
3075directly in C++, or quick conversion of research code into production
3076environments. It can be used for machine learning, pattern recognition,
3077signal processing, bioinformatics, statistics, econometrics, etc. The library
3078provides efficient classes for vectors, matrices and cubes, as well as 150+
3079associated functions (eg. contiguous and non-contiguous submatrix views).")
fe418cc5 3080 (license license:asl2.0)))
b15e47f9 3081
279663ef 3082(define-public muparser
d7cff656
LF		 3083 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
3084 ;; different hash. In order to make `guix package --upgrade` work correctly,
3085 ;; we set a Guix packaging revision.
3086 ;; When the next version of muparser is released, we can remove
3087 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
3088 (let ((upstream-version "2.2.5")
3089 (revision "2"))
3090 (package
3091 (name "muparser")
3092 (version (string-append upstream-version "-" revision))
3093 (source
3094 (origin
67f1db38
TGR		 3095 (method git-fetch)
3096 (uri (git-reference
3097 (url "https://github.com/beltoforion/muparser.git")
3098 (commit (string-append "v" upstream-version))))
3099 (file-name (git-file-name name version))
d7cff656 3100 (sha256
67f1db38 3101 (base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24"))))
d7cff656
LF		 3102 (build-system gnu-build-system)
3103 (arguments
3104 `(#:configure-flags '("--enable-samples=no")
3105 #:tests? #f)) ;no "check" target
3106 (home-page "http://muparser.beltoforion.de/")
3107 (synopsis "Fast parser library for mathematical expressions")
3108 (description
3109 "muParser is an extensible high performance math parser library. It is
3110based on transforming an expression into a bytecode and precalculating constant
3111parts of it.")
3112 (license license:expat))))
279663ef 3113
e73b49fb
RW		 3114(define-public openblas
3115 (package
ba05be22
LC		 3116 ;; TODO: Incorporate 'openblas/fixed-num-threads' changes on the next
3117 ;; rebuild cycle.
3118 (replacement openblas/fixed-num-threads)
3119
e73b49fb 3120 (name "openblas")
e7741236 3121 (version "0.3.6")
e73b49fb
RW		 3122 (source
3123 (origin
3124 (method url-fetch)
a617fd55
MB		 3125 (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
3126 version "%20version.tar.gz"))
e73b49fb
RW		 3127 (file-name (string-append name "-" version ".tar.gz"))
3128 (sha256
3129 (base32
e7741236 3130 "1r2g9zzwq5dm8vjd19pxwggfvfzy56cvkmpmp5d014qr3svgmsap"))))
e73b49fb
RW		 3131 (build-system gnu-build-system)
3132 (arguments
5789566a 3133 `(#:test-target "test"
bd0b4379
RW		 3134 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
3135 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
3136 ;; we need to disable substitutions.
71923a91
AE		 3137 #:substitutable?
3138 ,(let ((system (or (%current-target-system) (%current-system))))
3139 (or (string-prefix? "x86_64" system)
bd0b4379 3140 (string-prefix? "i686" system)
83a34647
EF		 3141 (string-prefix? "mips" system)
3142 (string-prefix? "aarch64" system)))
e73b49fb
RW		 3143 #:make-flags
3144 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
3145 "SHELL=bash"
5855756c 3146 "MAKE_NB_JOBS=0" ;use jobserver for submakes
af5b817e
RW		 3147 ;; Build the library for all supported CPUs. This allows
3148 ;; switching CPU targets at runtime with the environment variable
3149 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
71923a91
AE		 3150 ;; Unfortunately, this is not supported on non-x86 architectures,
3151 ;; where it leads to failed builds.
3152 ,@(let ((system (or (%current-target-system) (%current-system))))
8a637e79
RW		 3153 (cond
3154 ((or (string-prefix? "x86_64" system)
71923a91 3155 (string-prefix? "i686" system))
8a637e79
RW		 3156 '("DYNAMIC_ARCH=1"))
3157 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
3158 ;; two available MIPS targets special extended instructions
3159 ;; for Loongson cores are used.
3160 ((string-prefix? "mips" system)
3161 '("TARGET=SICORTEX"))
83a34647
EF		 3162 ;; On aarch64 force the generic 'armv8-a' target
3163 ((string-prefix? "aarch64" system)
3164 '("TARGET=ARMV8"))
8a637e79 3165 (else '()))))
e73b49fb 3166 ;; no configure script
493937ae
DL		 3167 #:phases
3168 (modify-phases %standard-phases
3169 (delete 'configure)
3170 (add-before 'build 'set-extralib
3171 (lambda* (#:key inputs #:allow-other-keys)
3172 ;; Get libgfortran found when building in utest.
3173 (setenv "FEXTRALIB"
3174 (string-append "-L" (assoc-ref inputs "fortran-lib")
3175 "/lib"))
3176 #t)))))
e73b49fb 3177 (inputs
493937ae 3178 `(("fortran-lib" ,gfortran "lib")))
e73b49fb
RW		 3179 (native-inputs
3180 `(("cunit" ,cunit)
493937ae 3181 ("fortran" ,gfortran)
e73b49fb
RW		 3182 ("perl" ,perl)))
3183 (home-page "http://www.openblas.net/")
3184 (synopsis "Optimized BLAS library based on GotoBLAS")
3185 (description
3186 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
3187 (license license:bsd-3)))
3188
daa6036f 3189(define-public openblas-ilp64
ba05be22 3190 (package/inherit openblas
daa6036f
EB		 3191 (name "openblas-ilp64")
3192 (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
3193 (arguments
3194 (substitute-keyword-arguments (package-arguments openblas)
3195 ((#:make-flags flags '())
3196 `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
3197 ,flags))))
3198 (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
3199 (license license:bsd-3)))
3200
ba05be22
LC		 3201(define openblas/fixed-num-threads
3202 ;; TODO: Move that to 'openblas' proper on the next rebuild cycle.
3203 (package
3204 (inherit openblas)
3205 (version (match (string-split (package-version openblas) #\.)
3206 ((numbers ... (= string-length len))
3207 (string-join (append numbers
3208 (list (make-string len #\a)))
3209 "."))))
3210 (arguments
3211 (substitute-keyword-arguments (package-arguments openblas)
3212 ((#:make-flags flags ''())
3213 ;; This is the maximum number of threads OpenBLAS will ever use (that
3214 ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS
3215 ;; is used.) If we don't set it, the makefile sets it to the number
3216 ;; of cores of the build machine, which is obviously wrong.
3217 `(cons "NUM_THREADS=128" ,flags))))))
3218
5a7deb11
LC		 3219(define* (make-blis implementation #:optional substitutable?)
3220 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
3221source tree for a list of implementations.)
3222
3223SUBSTITUTABLE? determines whether the package is made available as a
3224substitute.
3225
3226Currently the specialization must be selected at configure-time, but work is
3227underway to allow BLIS to select the right optimized kernels at run time:
3228<https://github.com/flame/blis/issues/129>."
3229 (package
3230 (name (if (string=? implementation "reference")
3231 "blis"
3232 (string-append "blis-" implementation)))
3233 (version "0.2.2")
3234 (home-page "https://github.com/flame/blis")
3235 (source (origin
3236 (method git-fetch)
3237 (uri (git-reference (url home-page) (commit version)))
3238 (sha256
3239 (base32
3240 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
3241 (file-name (git-file-name "blis" version))))
3242 (build-system gnu-build-system)
3243 (arguments
3244 `(#:test-target "test"
3245
3246 #:substitutable? ,substitutable?
3247
3248 #:phases (modify-phases %standard-phases
3249 (replace 'configure
3250 (lambda* (#:key outputs #:allow-other-keys)
3251 ;; This is a home-made 'configure' script.
3252 (let ((out (assoc-ref outputs "out")))
1ec17821
RW		 3253 (invoke "./configure" "-p" out
3254 "-d" "opt"
3255 "--disable-static"
3256 "--enable-shared"
3257 "--enable-threading=openmp"
5a7deb11 3258
1ec17821 3259 ,implementation))))
5a7deb11
LC		 3260 (add-before 'check 'show-test-output
3261 (lambda _
3262 ;; By default "make check" is silent. Make it verbose.
3263 (system "tail -F output.testsuite &")
3264 #t)))))
3265 (synopsis "High-performance basic linear algebra (BLAS) routines")
3266 (description
3267 "BLIS is a portable software framework for instantiating high-performance
3268BLAS-like dense linear algebra libraries. The framework was designed to
3269isolate essential kernels of computation that, when optimized, immediately
3270enable optimized implementations of most of its commonly used and
3271computationally intensive operations. While BLIS exports a new BLAS-like API,
3272it also includes a BLAS compatibility layer which gives application developers
3273access to BLIS implementations via traditional BLAS routine calls.")
3274 (license license:bsd-3)))
3275
3276(define-public blis
3277 ;; This is the "reference" implementation, which is the non-optimized but
3278 ;; portable variant (no assembly).
3279 (make-blis "reference" #t))
3280
3281(define ignorance blis)
3282
3283(define-syntax-rule (blis/x86_64 processor)
3284 "Expand to a package specialized for PROCESSOR."
3285 (package
3286 (inherit (make-blis processor))
3287 (supported-systems '("x86_64-linux"))))
3288
3289(define-public blis-sandybridge
3290 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
3291 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
3292 (blis/x86_64 "sandybridge"))
3293
3294(define-public blis-haswell
3295 ;; BLIS specialized for Haswell processors (launched 2013):
3296 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
3297 (blis/x86_64 "haswell"))
3298
3299(define-public blis-knl
3300 ;; BLIS specialized for Knights Landing processor (launched 2016):
3301 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
3302 (blis/x86_64 "knl"))
3303
3304
e1605e36
RW		 3305(define-public openlibm
3306 (package
3307 (name "openlibm")
48d7ac17 3308 (version "0.6.0")
e1605e36
RW		 3309 (source
3310 (origin
ca72dd2c
TGR		 3311 (method git-fetch)
3312 (uri (git-reference
3313 (url "https://github.com/JuliaLang/openlibm.git")
3314 (commit (string-append "v" version))))
3315 (file-name (git-file-name name version))
e1605e36 3316 (sha256
ca72dd2c 3317 (base32 "08wfchmmr5200fvmn1kwq9byc1fhsq46hn0y5k8scdl74771c7gh"))))
e1605e36
RW		 3318 (build-system gnu-build-system)
3319 (arguments
3320 `(#:make-flags
3321 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3322 #:phases
3323 ;; no configure script
dc1d3cde 3324 (modify-phases %standard-phases (delete 'configure))
e1605e36
RW		 3325 #:tests? #f)) ;the tests are part of the default target
3326 (home-page "http://openlibm.org/")
3327 (synopsis "Portable C mathematical library (libm)")
3328 (description
3329 "OpenLibm is an effort to have a high quality, portable, standalone C
3330mathematical library (libm). It can be used standalone in applications and
3331programming language implementations. The project was born out of a need to
e881752c 3332have a good libm for the Julia programming language that worked consistently
e1605e36
RW		 3333across compilers and operating systems, and in 32-bit and 64-bit
3334environments.")
538c0e3b
EF		 3335 ;; Each architecture has its own make target, and there is none for mips.
3336 (supported-systems (delete "mips64el-linux" %supported-systems))
e1605e36
RW		 3337 ;; See LICENSE.md for details.
3338 (license (list license:expat
3339 license:isc
3340 license:bsd-2
3341 license:public-domain
3342 license:lgpl2.1+))))
3343
e62be58f
RW		 3344(define-public openspecfun
3345 (package
3346 (name "openspecfun")
59cd0ba4 3347 (version "0.5.3")
e62be58f
RW		 3348 (source
3349 (origin
90cea671
TGR		 3350 (method git-fetch)
3351 (uri (git-reference
3352 (url "https://github.com/JuliaLang/openspecfun.git")
3353 (commit (string-append "v" version))))
3354 (file-name (git-file-name name version))
e62be58f 3355 (sha256
90cea671 3356 (base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh"))))
e62be58f
RW		 3357 (build-system gnu-build-system)
3358 (arguments
59cd0ba4 3359 '(#:tests? #f ; no "check" target
e62be58f
RW		 3360 #:make-flags
3361 (list (string-append "prefix=" (assoc-ref %outputs "out")))
59cd0ba4
TGR		 3362 #:phases
3363 (modify-phases %standard-phases
3364 (delete 'configure)))) ; no configure script
e62be58f 3365 (inputs
19afbea1 3366 `(("fortran" ,gfortran)))
e62be58f
RW		 3367 (home-page "https://github.com/JuliaLang/openspecfun")
3368 (synopsis "Collection of special mathematical functions")
3369 (description
3370 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
3371portable package for Bessel Functions of a Complex Argument and Nonnegative
3372Order; it contains subroutines for computing Bessel functions and Airy
3373functions. Faddeeva allows computing the various error functions of arbitrary
3374complex arguments (Faddeeva function, error function, complementary error
3375function, scaled complementary error function, imaginary error function, and
3376Dawson function); given these, one can also easily compute Voigt functions,
3377Fresnel integrals, and similar related functions as well.")
3378 ;; Faddeeva is released under the Expat license; AMOS is included as
3379 ;; public domain software.
3380 (license (list license:expat license:public-domain))))
3381
2742f87e
RW		 3382(define-public suitesparse
3383 (package
3384 (name "suitesparse")
bd5b5ac0 3385 (version "4.5.5")
2742f87e
RW		 3386 (source
3387 (origin
3388 (method url-fetch)
3389 (uri (string-append
3390 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
3391 version ".tar.gz"))
3392 (sha256
3393 (base32
bd5b5ac0
EB		 3394 "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
3395 (modules '((guix build utils)))
3396 (snippet
3397 ;; Remove bundled metis source
6cbee49d
MW		 3398 '(begin
3399 (delete-file-recursively "metis-5.1.0")
3400 #t))))
2742f87e
RW		 3401 (build-system gnu-build-system)
3402 (arguments
bd5b5ac0 3403 '(#:tests? #f ;no "check" target
2742f87e
RW		 3404 #:make-flags
3405 (list "CC=gcc"
3406 "BLAS=-lblas"
3407 "TBB=-ltbb"
bd5b5ac0 3408 "MY_METIS_LIB=-lmetis"
2742f87e
RW		 3409 (string-append "INSTALL_LIB="
3410 (assoc-ref %outputs "out") "/lib")
3411 (string-append "INSTALL_INCLUDE="
bd5b5ac0
EB		 3412 (assoc-ref %outputs "out") "/include")
3413 "library")
2742f87e 3414 #:phases
2509522c 3415 (modify-phases %standard-phases
bd5b5ac0 3416 (delete 'configure)))) ;no configure script
2742f87e
RW		 3417 (inputs
3418 `(("tbb" ,tbb)
bd5b5ac0
EB		 3419 ("lapack" ,lapack)
3420 ("metis" ,metis)))
2742f87e
RW		 3421 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
3422 (synopsis "Suite of sparse matrix software")
3423 (description
3424 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
3425multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
3426multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
3427simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
3428CXSparse, a concise sparse Cholesky factorization package; and many other
3429packages.")
3430 ;; LGPLv2.1+:
3431 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
3432 ;; GPLv2+:
3433 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
3434 (license (list license:gpl2+ license:lgpl2.1+))))
3435
ec322be2
FB		 3436(define-public atlas
3437 (package
3438 (name "atlas")
3c98ac02 3439 (version "3.10.3")
ec322be2
FB		 3440 (source (origin
3441 (method url-fetch)
de67e922
LF		 3442 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
3443 version "/atlas" version ".tar.bz2"))
ec322be2
FB		 3444 (sha256
3445 (base32
3c98ac02 3446 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
ec322be2
FB		 3447 (build-system gnu-build-system)
3448 (home-page "http://math-atlas.sourceforge.net/")
19afbea1 3449 (inputs `(("gfortran" ,gfortran)
ec322be2
FB		 3450 ("lapack-tar" ,(package-source lapack))))
3451 (outputs '("out" "doc"))
01480b9e
FB		 3452 ;; For the moment we drop support for MIPS at it fails to compile. See
3453 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
3454 (supported-systems (delete "mips64el-linux" %supported-systems))
ec322be2
FB		 3455 (arguments
3456 `(#:parallel-build? #f
3457 #:parallel-tests? #f
f15615b1
LC		 3458
3459 ;; ATLAS tunes itself for the machine it is built on, as explained at
3460 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
3461 ;; For this reason, we want users to build it locally instead of using
3462 ;; substitutes.
3463 #:substitutable? #f
3464
ec322be2 3465 #:modules ((srfi srfi-26)
ec322be2
FB		 3466 (guix build gnu-build-system)
3467 (guix build utils))
40029cbe 3468 #:configure-flags
ec322be2
FB		 3469 `(;; Generate position independent code suitable for dynamic libraries
3470 ;; and use WALL timer to get more accurate timing.
3471 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
3472 ;; Set word width.
3473 "-b"
3474 ,,(if (string-match "64" (%current-system))
3475 "64"
3476 "32")
3477 ;; Disable parallel build as it gives errors: atlas_pthread.h is
3478 ;; needed to compile C files before it is generated.
3479 "-Ss" "pmake" "make -j 1"
af89a667
FB		 3480 ;; Probe is failing for MIPS. We therefore define the system
3481 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3482 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3483 ,,@(if (string-prefix? "mips" (%current-system))
3484 (list "-A" "49" "-V" "1")
3485 (list))
ec322be2
FB		 3486 ;; Generate shared libraries.
3487 "--shared"
3488 ;; Build a full LAPACK library.
3489 ,(string-append "--with-netlib-lapack-tarfile="
3490 (assoc-ref %build-inputs "lapack-tar")))
3491 #:phases
e5b4b96b
EF		 3492 (modify-phases %standard-phases
3493 (add-after 'install 'install-doc
3494 (lambda* (#:key outputs inputs #:allow-other-keys)
3495 (let ((doc (string-append (assoc-ref outputs "doc")
3496 "/share/doc/atlas")))
3497 (mkdir-p doc)
cb6f44d4
RW		 3498 (for-each (cut install-file <> doc)
3499 (find-files "../ATLAS/doc" ".*"))
3500 #t)))
e5b4b96b 3501 (add-after 'check 'check-pt
cb6f44d4 3502 (lambda _ (invoke "make" "ptcheck")))
e5b4b96b
EF		 3503 ;; Fix files required to run configure.
3504 (add-before 'configure 'fix-/bin/sh
ec322be2
FB		 3505 (lambda _
3506 ;; Use `sh', not `/bin/sh'.
3507 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3508 (("/bin/sh")
5b786db8
EF		 3509 "sh"))
3510 #t))
e5b4b96b
EF		 3511 ;; Fix /bin/sh in generated make files.
3512 (add-after 'configure 'fix-/bin/sh-in-generated-files
3513 (lambda _
3514 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3515 (("/bin/sh")
5b786db8
EF		 3516 "sh"))
3517 #t))
e5b4b96b
EF		 3518 ;; ATLAS configure program does not accepts the default flags
3519 ;; passed by the 'gnu-build-system'.
3520 (replace 'configure
3521 (lambda* (#:key native-inputs inputs outputs
3522 (configure-flags '())
3523 #:allow-other-keys #:rest args)
3524 (let* ((prefix (assoc-ref outputs "out"))
3525 (bash (or (and=> (assoc-ref
3526 (or native-inputs inputs) "bash")
3527 (cut string-append <> "/bin/bash"))
3528 "/bin/sh"))
3529 (flags `(,(string-append "--prefix=" prefix)
3530 ,@configure-flags))
3531 (abs-srcdir (getcwd))
3532 (srcdir (string-append "../" (basename abs-srcdir))))
3533 (format #t "source directory: ~s (relative from build: ~s)~%"
3534 abs-srcdir srcdir)
3535 (mkdir "../build")
3536 (chdir "../build")
3537 (format #t "build directory: ~s~%" (getcwd))
3538 (format #t "configure flags: ~s~%" flags)
cb6f44d4
RW		 3539 (apply invoke bash
3540 (string-append srcdir "/configure")
3541 flags)))))))
ec322be2
FB		 3542 (synopsis "Automatically Tuned Linear Algebra Software")
3543 (description
3544 "ATLAS is an automatically tuned linear algebra software library
3545providing C and Fortran77 interfaces to a portably efficient BLAS
3546implementation, as well as a few routines from LAPACK.
3547
f15615b1
LC		 3548Optimization occurs at build time. For this reason, the library is built on
3549the machine where it is installed, without resorting to pre-built substitutes.
ec322be2 3550
f15615b1 3551Before building the library, CPU throttling should be disabled. This can be
d97c429a 3552done in the BIOS, or, on GNU/Linux, with the following command:
ec322be2 3553
8e9ba611 3554@example
d97c429a 3555# cpupower --governor performance
8e9ba611 3556@end example
ec322be2 3557
d97c429a 3558Failure to do so will result in a library with poor performance.")
ec322be2 3559 (license license:bsd-3)))
c12efc72
AE		 3560
3561(define-public glm
3562 (package
3563 (name "glm")
3f55b7be 3564 (version "0.9.9.6")
c12efc72
AE		 3565 (source
3566 (origin
3567 (method url-fetch)
5ea4b594
MB		 3568 (uri (string-append "https://github.com/g-truc/glm/releases/download/"
3569 version "/glm-" version ".zip"))
c12efc72 3570 (sha256
3f55b7be
TGR		 3571 (base32 "1l0pi1qi37mk6s0yrkrw07lspv4gcqnr9ryg3521hrl77ff37dwx"))
3572 (patches (search-patches "glm-restore-install-target.patch"))))
c12efc72
AE		 3573 (build-system cmake-build-system)
3574 (native-inputs
3575 `(("unzip" ,unzip)))
46bda5eb 3576 (home-page "https://glm.g-truc.net/")
c12efc72
AE		 3577 (synopsis "OpenGL Mathematics library")
3578 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3579library for graphics software based on the OpenGL Shading Language (GLSL)
3580specifications.")
3581 (license license:expat)))
7f18257b
AE		 3582
3583(define-public lpsolve
3584 (package
3585 (name "lpsolve")
a89e0cf5 3586 (version "5.5.2.5")
7f18257b
AE		 3587 (source
3588 (origin
3589 (method url-fetch)
3590 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3591 "/lp_solve_" version "_source.tar.gz"))
3592 (sha256
3593 (base32
a89e0cf5 3594 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
7f18257b
AE		 3595 (modules '((guix build utils)))
3596 (snippet
6cbee49d
MW		 3597 '(begin
3598 (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3599 (("^c=cc") "c=gcc")
3600 ;; Pretend to be on a 64 bit platform to obtain a common directory
3601 ;; name for the build results on all architectures; nothing else
3602 ;; seems to depend on it.
3603 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3604
3605 ;; The check for 'isnan' as it is written fails with
3606 ;; "non-floating-point argument in call to function
3607 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3608 ;; definition, which in turn leads to bad things. Fix the feature
3609 ;; test.
3610 (("isnan\\(0\\)") "isnan(0.)"))
3611 #t))))
7f18257b
AE		 3612 (build-system gnu-build-system)
3613 (arguments
6c96b545 3614 `(#:tests? #f ; no check target
7f18257b
AE		 3615 #:phases
3616 (modify-phases %standard-phases
6c96b545 3617 (delete 'configure) ; no configure script
7f18257b
AE		 3618 (replace 'build
3619 (lambda _
6c96b545
TGR		 3620 (with-directory-excursion "lpsolve55"
3621 (invoke "bash" "ccc"))
3622 (with-directory-excursion "lp_solve"
3623 (invoke "bash" "ccc"))
3624 #t))
7f18257b
AE		 3625 (replace 'install
3626 (lambda* (#:key outputs #:allow-other-keys)
3627 (let* ((out (assoc-ref outputs "out"))
3628 (bin (string-append out "/bin"))
3629 (lib (string-append out "/lib"))
3630 ;; This is where LibreOffice expects to find the header
3631 ;; files, and where they are installed by Debian.
3632 (include (string-append out "/include/lpsolve")))
6c96b545
TGR		 3633 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3634 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
96c46210
LC		 3635 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3636
7f18257b
AE		 3637 ;; Install a subset of the header files as on Debian
3638 ;; (plus lp_bit.h, which matches the regular expression).
96c46210
LC		 3639 (for-each (lambda (name)
3640 (install-file name include))
3641 (find-files "." "lp_[HMSa-z].*\\.h$"))
7f18257b 3642 (with-directory-excursion "shared"
96c46210
LC		 3643 (for-each (lambda (name)
3644 (install-file name include))
3645 (find-files "." "\\.h$")))
7f18257b
AE		 3646 #t))))))
3647 (home-page "http://lpsolve.sourceforge.net/")
3648 (synopsis "Mixed integer linear programming (MILP) solver")
3649 (description
3650 "lp_solve is a mixed integer linear programming solver based on the
3651revised simplex and the branch-and-bound methods.")
3652 (license license:lgpl2.1+)))
a17d4564
EB		 3653
3654(define-public dealii
3655 (package
3656 (name "dealii")
ba567cae 3657 (version "9.1.1")
a17d4564
EB		 3658 (source
3659 (origin
3660 (method url-fetch)
3661 (uri (string-append "https://github.com/dealii/dealii/releases/"
3662 "download/v" version "/dealii-" version ".tar.gz"))
3663 (sha256
3664 (base32
ba567cae 3665 "0xhjv0gzswpjbc43xbrpwfc5848g508l01855nszx3g5gwzlhnzw"))
a17d4564
EB		 3666 (modules '((guix build utils)))
3667 (snippet
3668 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
6cbee49d
MW		 3669 '(begin
3670 (delete-file-recursively "bundled")
3671 #t))))
a17d4564
EB		 3672 (build-system cmake-build-system)
3673 (inputs
3674 `(("tbb" ,tbb)
3675 ("zlib" ,zlib)
3676 ("boost" ,boost)
3677 ("p4est" ,p4est)
3678 ("blas" ,openblas)
3679 ("lapack" ,lapack)
3680 ("arpack" ,arpack-ng)
3681 ("muparser" ,muparser)
3682 ("gfortran" ,gfortran)
3683 ("suitesparse" ,suitesparse))) ;for UMFPACK
3684 (arguments
3685 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
d84b09e9
EB		 3686 #:configure-flags
3687 ;; Work around a bug in libsuitesparseconfig linking
3688 ;; see https://github.com/dealii/dealii/issues/4745
3689 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
a17d4564
EB		 3690 (home-page "https://www.dealii.org")
3691 (synopsis "Finite element library")
3692 (description
3693 "Deal.II is a C++ program library targeted at the computational solution
3694of partial differential equations using adaptive finite elements. The main
3695aim of deal.II is to enable rapid development of modern finite element codes,
3696using among other aspects adaptive meshes and a wide array of tools often used
3697in finite element programs.")
3698 (license license:lgpl2.1+)))
3699
3700(define-public dealii-openmpi
3701 (package (inherit dealii)
3702 (name "dealii-openmpi")
3703 (inputs
3704 `(("mpi" ,openmpi)
3705 ;;Supported only with MPI:
4d44bcad 3706 ("hdf5" ,hdf5-parallel-openmpi) ;TODO: have petsc-openmpi propagate?
a17d4564
EB		 3707 ("p4est" ,p4est-openmpi)
3708 ("petsc" ,petsc-openmpi)
3709 ("slepc" ,slepc-openmpi)
3710 ("metis" ,metis) ;for MUMPS
3711 ("scalapack" ,scalapack) ;for MUMPS
3712 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3713 ("arpack" ,arpack-ng-openmpi)
3714 ,@(fold alist-delete (package-inputs dealii)
3715 '("p4est" "arpack"))))
3716 (arguments
3717 (substitute-keyword-arguments (package-arguments dealii)
3718 ((#:configure-flags cf)
40b114c0
EB		 3719 `(cons "-DDEAL_II_WITH_MPI:BOOL=ON"
3720 ,cf))
7e309e8a
EB		 3721 ((#:phases phases '%standard-phases)
3722 `(modify-phases ,phases
3723 (add-before 'check 'mpi-setup
3724 ,%openmpi-setup)))))
a17d4564 3725 (synopsis "Finite element library (with MPI support)")))
194c7f95
AE		 3726
3727(define-public flann
3728 (package
3729 (name "flann")
3730 (version "1.8.4")
3731 (source
3732 (origin
3733 (method url-fetch)
3734 (uri
3735 (string-append
3736 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3737 version "-src.zip"))
3738 (sha256
3739 (base32
b5edc479
LC		 3740 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
3741 (patches (search-patches "flann-cmake-3.11.patch"))))
194c7f95 3742 (build-system cmake-build-system)
6b6aca9b
LC		 3743 (outputs '("out"
3744 "octave")) ;46 MiB .mex file that pulls Octave
194c7f95
AE		 3745 (native-inputs
3746 `(("unzip" ,unzip)))
3747 (inputs
3748 `(("hdf5" ,hdf5)
5537603f 3749 ("octave" ,octave-cli)
194c7f95
AE		 3750 ("python" ,python-2) ; print syntax
3751 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3752 ("zlib" ,zlib)))
3753 (arguments
39b30337
LC		 3754 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3755 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3756 #:strip-directories '("lib" "lib64" "libexec"
3757 "bin" "sbin" "share/flann/octave")
3758
9684e30b
LC		 3759 ;; Save 12 MiB by not installing .a files. Passing
3760 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3761 #:phases (modify-phases %standard-phases
6b6aca9b
LC		 3762 (add-before 'configure 'set-octave-directory
3763 (lambda* (#:key outputs #:allow-other-keys)
3764 ;; Install the .mex file in the "octave" output.
3765 (let ((out (assoc-ref outputs "octave")))
3766 (substitute* "src/matlab/CMakeLists.txt"
3767 (("share/flann/octave")
3768 (string-append out "/share/flann/octave")))
3769 #t)))
9684e30b
LC		 3770 (add-after 'install 'remove-static-libraries
3771 (lambda* (#:key outputs #:allow-other-keys)
3772 (let* ((out (assoc-ref outputs "out"))
3773 (lib (string-append out "/lib")))
3774 (for-each delete-file
3775 (find-files lib "\\.a$"))
3776 #t))))
3777
39b30337 3778 #:tests? #f)) ; The test data are downloaded from the Internet.
194c7f95
AE		 3779 (home-page "http://www.cs.ubc.ca/research/flann/")
3780 (synopsis "Library for approximate nearest neighbors computation")
3781 (description "FLANN is a library for performing fast approximate
3782nearest neighbor searches in high dimensional spaces. It implements a
3783collection of algorithms and a system for automatically choosing the best
3784algorithm and optimum parameters depending on the dataset.
3785
3786FLANN is written in C++ and contains bindings for C, Octave and Python.")
3787 (license (license:non-copyleft "file://COPYING"
3788 "See COPYING in the distribution."))))
d8c97beb
EF		 3789
3790(define-public wcalc
3791 (package
3792 (name "wcalc")
3793 (version "2.5")
3794 (source
3795 (origin
3796 (method url-fetch)
de67e922
LF		 3797 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3798 "wcalc-" version ".tar.bz2"))
d8c97beb
EF		 3799 (sha256
3800 (base32
3801 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3802 (build-system gnu-build-system)
3803 (inputs
3804 `(("mpfr" ,mpfr)
3805 ("readline" ,readline)))
3806 (home-page "http://w-calc.sourceforge.net/index.php")
3807 (synopsis "Flexible command-line scientific calculator")
3808 (description "Wcalc is a very capable calculator. It has standard functions
3809(sin, asin, and sinh for example, in either radians or degrees), many
3810pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3811variables, a command history, hex/octal/binary input and output, unit
3812conversions, embedded comments, and an expandable expression entry field. It
3813evaluates expressions using the standard order of operations.")
3814 (license license:gpl2+)))
45147b0c
FH		 3815
3816(define-public xaos
3817 (package
3818 (name "xaos")
3819 (version "3.6")
3820 (source (origin
3821 (method url-fetch)
de67e922
LF		 3822 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3823 "/xaos-" version ".tar.gz"))
45147b0c
FH		 3824 (sha256
3825 (base32
3826 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3827 (build-system gnu-build-system)
b94a6ca0 3828 (native-inputs `(("gettext" ,gettext-minimal)))
45147b0c
FH		 3829 (inputs `(("libx11" ,libx11)
3830 ("zlib" ,zlib)
3831 ("libpng" ,libpng)
3832 ("gsl" ,gsl)))
3833 (arguments
3834 `(#:tests? #f ;no "check" target
3835 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3836 (synopsis "Real-time fractal zoomer")
3837 (description "GNU XaoS is a graphical program that generates fractal
3838patterns and allows you to zoom in and out of them infinitely in a fluid,
3839continuous manner. It also includes tutorials that help to explain how fractals
3840are built. It can generate many different fractal types such as the Mandelbrot
3841set.")
6fd52309 3842 (home-page "https://www.gnu.org/software/xaos/")
45147b0c 3843 (license license:gpl2+)))
528bb464
EB		 3844
3845(define-public hypre
3846 (package
3847 (name "hypre")
be099727 3848 (version "2.15.1")
fabcbf32
TGR		 3849 (source
3850 (origin
3851 (method git-fetch)
3852 (uri (git-reference
3853 (url "https://github.com/LLNL/hypre.git")
3854 (commit (string-append "v" version))))
3855 (file-name (git-file-name name version))
3856 (sha256
be099727 3857 (base32 "1lvh4ybqkriyqfg2zmic6mrg1981qv1i9vry1fdgsabn81hb71g4"))
fabcbf32
TGR		 3858 (modules '((guix build utils)))
3859 (snippet
3860 '(begin
3861 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
be099727 3862 ;; substitute the release date.
fabcbf32
TGR		 3863 (substitute* "src/utilities/HYPRE_utilities.h"
3864 (("Date Compiled: .*$")
be099727 3865 "Date Compiled: Oct 19 2018 15:23:00 +0000\"\n"))
fabcbf32 3866 #t))))
528bb464 3867 (build-system gnu-build-system)
be099727
TGR		 3868 (outputs '("out" ; 6.1 MiB of headers and libraries
3869 "doc")) ; 4.8 MiB of documentation
528bb464
EB		 3870 (native-inputs
3871 `(("doc++" ,doc++)
3872 ("netpbm" ,netpbm)
be099727 3873 ("perl" ,perl) ; needed to run 'ppmquant' during tests
8b35c8cd
RW		 3874 ("texlive" ,(texlive-union (list texlive-xypic
3875 texlive-cm
9b405aea 3876 texlive-latex-hyperref
9b405aea 3877 texlive-bibtex)))
528bb464
EB		 3878 ("ghostscript" ,ghostscript)))
3879 (inputs
3880 `(("blas" ,openblas)
3881 ("lapack" ,lapack)))
3882 (arguments
3883 `(#:modules ((srfi srfi-1)
3884 ,@%gnu-build-system-modules)
3885 #:configure-flags '("--enable-shared"
3886 "--disable-fortran"
3887 "--without-MPI"
3888 "--with-openmp"
3889 "--with-fei"
3890 "--with-lapack"
3891 "--with-blas")
3892 #:phases
3893 (modify-phases %standard-phases
9b405aea
PN		 3894 (add-before 'build 'set-HOME
3895 (lambda _
3896 ;; FIXME: texlive-union does not find the built
3897 ;; metafonts, so it tries to generate them in HOME.
3898 (setenv "HOME" "/tmp")
3899 #t))
528bb464
EB		 3900 (add-before 'configure 'chdir-src
3901 (lambda _ (chdir "src")))
3902 (replace 'configure
3903 (lambda* (#:key build target configure-flags
3904 #:allow-other-keys #:rest args)
3905 (let* ((configure (assoc-ref %standard-phases 'configure)))
3906 (apply configure
3907 (append args
3908 (list #:configure-flags
3909 (cons (string-append
3910 "--host=" (or target build))
3911 configure-flags)))))))
3912 (add-after 'build 'build-docs
3913 (lambda _
9b405aea 3914 (invoke "make" "-Cdocs" "pdf" "html")))
528bb464
EB		 3915 (replace 'check
3916 (lambda _
3917 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3918 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
6b1c7ac8
RW		 3919 (invoke "make" "check" "CHECKRUN=")
3920 (for-each (lambda (filename)
3921 (let ((size (stat:size (stat filename))))
3922 (when (positive? size)
3923 (error (format #f "~a size ~d; error indication~%"
3924 filename size)))))
3925 (find-files "test" ".*\\.err$"))
3926 #t))
528bb464
EB		 3927 (add-after 'install 'install-docs
3928 (lambda* (#:key outputs #:allow-other-keys)
3929 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3930 (let* ((doc (assoc-ref outputs "doc"))
3931 (docdir (string-append doc "/share/doc/hypre-" ,version)))
528bb464
EB		 3932 (with-directory-excursion "docs"
3933 (for-each (lambda (base)
3934 (install-file (string-append base ".pdf") docdir)
be099727 3935 (copy-recursively base docdir)) ; html docs
528bb464
EB		 3936 '("HYPRE_usr_manual"
3937 "HYPRE_ref_manual")))
3938 #t))))))
3939 (home-page "http://www.llnl.gov/casc/hypre/")
3940 (synopsis "Library of solvers and preconditioners for linear equations")
3941 (description
3942 "HYPRE is a software library of high performance preconditioners and
3943solvers for the solution of large, sparse linear systems of equations. It
3944features multigrid solvers for both structured and unstructured grid
3945problems.")
3946 (license license:lgpl2.1)))
3947
3948(define-public hypre-openmpi
3949 (package (inherit hypre)
3950 (name "hypre-openmpi")
3951 (inputs
3952 `(("mpi" ,openmpi)
3953 ,@(package-inputs hypre)))
3954 (arguments
3955 (substitute-keyword-arguments (package-arguments hypre)
3956 ((#:configure-flags flags)
3957 ``("--with-MPI"
6df2a50a
LC		 3958 ,@(delete "--without-MPI" ,flags)))
3959 ((#:phases phases)
3960 `(modify-phases ,phases
bbe46a4a
EB		 3961 (add-before 'check 'mpi-setup
3962 ,%openmpi-setup)))))
528bb464
EB		 3963 (synopsis "Parallel solvers and preconditioners for linear equations")
3964 (description
3965 "HYPRE is a software library of high performance preconditioners and
3966solvers for the solution of large, sparse linear systems of equations on
3967parallel computers. It features parallel multigrid solvers for both
3968structured and unstructured grid problems.")))
6c90e183
EB		 3969
3970(define-public matio
3971 (package
3972 (name "matio")
3973 (version "1.5.6")
3974 (source
3975 (origin
3976 (method url-fetch)
de67e922 3977 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
6c90e183
EB		 3978 "matio-" version ".tar.gz"))
3979 (sha256
3980 (base32
3981 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3982 (build-system gnu-build-system)
3983 (inputs
3984 `(("zlib" ,zlib)
3985 ("hdf5" ,hdf5)))
3986 (home-page "http://matio.sourceforge.net/")
3987 (synopsis "Library for reading and writing MAT files")
3988 (description "Matio is a library for reading and writing MAT files. It
3989supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3990 (license license:bsd-2)))
d721c83a 3991
517318ad
LF		 3992(define-public vc
3993 (package
3994 (name "vc")
853b0292 3995 (version "1.3.3")
517318ad
LF		 3996 (source
3997 (origin (method url-fetch)
3998 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3999 "download/" version "/Vc-" version ".tar.gz"))
4000 (sha256
4001 (base32
853b0292 4002 "1zmlpn32jzb38smp3j834llmbix3whsrbw0h397qxysbw792kih8"))))
517318ad
LF		 4003 (build-system cmake-build-system)
4004 (arguments
4005 '(#:configure-flags
33d82486
MB		 4006 '("-DBUILD_TESTING=ON"
4007 ;; By default, Vc will optimize for the CPU of the build machine.
4008 ;; Setting this to "none" makes it create portable binaries. See
4009 ;; "cmake/OptimizeForArchitecture.cmake".
4010 "-DTARGET_ARCHITECTURE=none")))
517318ad
LF		 4011 (synopsis "SIMD vector classes for C++")
4012 (description "Vc provides portable, zero-overhead C++ types for explicitly
4013data-parallel programming. It is a library designed to ease explicit
4014vectorization of C++ code. Its types enable explicitly stating data-parallel
4015operations on multiple values. The parallelism is therefore added via the type
4016system. Vc has an intuitive API and provides portability between different
4017compilers and compiler versions as well as portability between different vector
4018instruction sets. Thus, an application written with Vc can be compiled for:
4019@enumerate
4020@item AVX and AVX2
d1e4ad1b 4021@item SSE2 up to SSE4.2 or SSE4a
517318ad
LF		 4022@item Scalar
4023@item MIC
4024@item NEON (in development)
4025@item NVIDIA GPUs / CUDA (in development)
4026@end enumerate\n")
4027 (home-page "https://github.com/VcDevel/Vc")
a8ead6f9
EF		 4028 ;; "No support_???.cpp file exists for this architecture."
4029 (supported-systems '("x86_64-linux" "i686-linux"))
517318ad 4030 (license license:bsd-3)))
54052a54 4031
4032(define-public reducelcs
4033 ;; This is the last commit which is available upstream, no
4034 ;; release happened since 2010.
4035 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
4036 (revision "1"))
4037 (package
4038 (name "reducelcs")
4039 (version (string-append "1.0-" revision "." (string-take commit 7)))
4040 (source
4041 (origin
4042 (method git-fetch)
4043 (uri (git-reference
4044 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
4045 (commit commit)))
4046 (file-name (string-append name "-" version "-checkout"))
4047 (sha256
4048 (base32
4049 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
4050 (build-system gnu-build-system)
4051 (inputs
4052 `(("openlibm" ,openlibm)))
4053 (arguments
4054 `(#:tests? #f ; no tests
4055 #:phases
4056 (modify-phases %standard-phases
4057 (delete 'configure) ; No configure script exists.
4058 (replace 'install ; No install phase exists.
4059 (lambda* (#:key outputs #:allow-other-keys)
4060 (let* ((out (assoc-ref outputs "out"))
4061 (bin (string-append out "/bin")))
4062 (install-file "Approximation" bin)
4063 (install-file "CollectResults" bin)
4064 (install-file "GenerateInstances" bin)
4065 #t))))))
4066 (synopsis "Approximate Longest Commons Subsequence computation tool")
4067 (description
4068 "@code{reduceLCS} is an implementation of the Reduce-Expand
4069algorithm for LCS. It is a fast program to compute the approximate
4070Longest Commons Subsequence of a set of strings.")
4071 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
c000b6b1 4072 (license license:gpl3+))))
479c4273
JD		 4073
4074(define-public jacal
4075 (package
4076 (name "jacal")
4077 (version "1c4")
4078 (source (origin
4079 (method url-fetch)
4080 (uri (string-append
4081 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
4082 version ".zip"))
4083 (sha256 (base32
4084 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
4085 (patches (search-patches "jacal-fix-texinfo.patch"))))
4086 (build-system gnu-build-system)
4087 (arguments
4088 `(#:phases
4089 (modify-phases %standard-phases
4090 (add-before 'build 'pre-build
4091 ;; Don't use upstream's script - it really doesn't fit into
4092 ;; Guix's functional paradigm.
4093 (lambda* (#:key inputs outputs #:allow-other-keys)
4094 (substitute* "Makefile"
4095 (("^install: install-script") "install: "))))
4096 (add-after 'install 'post-install
4097 ;; Instead, we provide our own simplified script.
4098 (lambda* (#:key inputs outputs #:allow-other-keys)
4099 (let ((wrapper (string-append (assoc-ref outputs "out")
4100 "/bin/jacal")))
4101 (format (open wrapper (logior O_WRONLY O_CREAT))
4102 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
4103 "-e '(slib:load \"~a/lib/jacal/math\") "
4104 "(math)' \"$@\"\n")
4105 (which "bash")
4106 (assoc-ref inputs "scm")
4107 (assoc-ref outputs "out"))
4108 (chmod wrapper #o555))))
4109 (replace 'configure
9cd82b1c
RW		 4110 (lambda* (#:key outputs #:allow-other-keys)
4111 (invoke "./configure"
4112 (string-append "--prefix="
4113 (assoc-ref outputs "out"))))))))
479c4273
JD		 4114 (inputs `(("scm" ,scm)))
4115 (native-inputs `(("unzip" ,unzip)
4116 ("texinfo" ,texinfo)))
4117 (synopsis "Symbolic mathematics system")
4118 (description "GNU JACAL is an interactive symbolic mathematics program based on
4119Scheme. It manipulate and simplify a range of mathematical expressions such
4120as equations, scalars, vectors, and matrices.")
6fd52309 4121 (home-page "https://www.gnu.org/software/jacal/")
479c4273
JD		 4122 (license license:gpl3+)))
4123
313844d9
TF		 4124(define-public z3
4125 (package
4126 (name "z3")
d49375c7 4127 (version "4.8.6")
fb525bfd 4128 (home-page "https://github.com/Z3Prover/z3")
313844d9 4129 (source (origin
fb525bfd
MB		 4130 (method git-fetch)
4131 (uri (git-reference (url home-page)
4132 (commit (string-append "z3-" version))))
2d7b99b3 4133 (file-name (git-file-name name version))
313844d9
TF		 4134 (sha256
4135 (base32
d49375c7 4136 "1sywcqj5y8yp28m4cdvzsgw74kd6zr1s3y1x17ky8pr9prvpvl6x"))))
fa574a6d 4137 (build-system gnu-build-system)
313844d9 4138 (arguments
fa574a6d 4139 `(#:phases
313844d9 4140 (modify-phases %standard-phases
ad6c6a5b
EF		 4141 (add-after 'unpack 'fix-compatability
4142 ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
4143 (lambda _
4144 (substitute* "src/util/mpz.cpp"
4145 (("#include <immintrin.h>") ""))
4146 #t))
cf684d87
TF		 4147 (add-before 'configure 'bootstrap
4148 (lambda _
32d5360f 4149 (invoke "python" "scripts/mk_make.py")))
fa574a6d
AB		 4150 ;; work around gnu-build-system's setting --enable-fast-install
4151 ;; (z3's `configure' is a wrapper around the above python file,
4152 ;; which fails when passed --enable-fast-install)
4153 (replace 'configure
4154 (lambda* (#:key inputs outputs #:allow-other-keys)
4155 (invoke "./configure"
4156 (string-append "--prefix=" (assoc-ref outputs "out")))))
4157 (add-after 'configure 'change-directory
4158 (lambda _
4159 (chdir "build")
4160 #t))
cf684d87 4161 (add-before 'check 'make-test-z3
313844d9 4162 (lambda _
cf684d87 4163 ;; Build the test suite executable.
32d5360f
RW		 4164 (invoke "make" "test-z3" "-j"
4165 (number->string (parallel-job-count)))))
cf684d87
TF		 4166 (replace 'check
4167 (lambda _
4168 ;; Run all the tests that don't require arguments.
32d5360f 4169 (invoke "./test-z3" "/a"))))))
313844d9 4170 (native-inputs
fa574a6d
AB		 4171 `(("which" ,which)
4172 ("python" ,python-wrapper)))
313844d9
TF		 4173 (synopsis "Theorem prover")
4174 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
cf684d87 4175theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
313844d9 4176 (license license:expat)))
3d5d87a3 4177
6d433d6e
EB		 4178(define-public elpa
4179 (package
4180 (name "elpa")
4181 (version "2018.11.001")
4182 (source (origin
4183 (method url-fetch)
4184 (uri (string-append "http://elpa.mpcdf.mpg.de/html/Releases/"
4185 version "/elpa-" version ".tar.gz"))
4186 (sha256
4187 (base32
4188 "05hv3v5i6xmziaizw350ff72y1c3k662r85fm3xfdrkclj5zw9yc"))))
4189 (build-system gnu-build-system)
4190 (native-inputs
4191 `(("fortran" ,gfortran)
4192 ("perl" ,perl))) ;for configure and deps
4193 (inputs
4194 `(("blas" ,openblas)))
4195 (arguments
4196 `(#:configure-flags
4197 `("--enable-openmp"
4198 "--with-mpi=no"
4199 ;; ELPA unfortunately does not support runtime dispatch, so we can
4200 ;; only enable the "generic" kernels. See the "Cross compilation"
4201 ;; section of INSTALL.md.
4202 "--enable-generic"
4203 "--disable-sse" "--disable-sse-assembly" ;Require SSE3
4204 "--disable-avx" "--disable-avx2" "--disable-avx512"
4205 ,(string-append "CFLAGS=-O3 "
4206 "-funsafe-loop-optimizations -funsafe-math-optimizations "
4207 "-ftree-vect-loop-version -ftree-vectorize "
4208 ,(let ((system (or (%current-target-system)
4209 (%current-system))))
4210 (cond
4211 ((or (string-prefix? "x86_64" system)
4212 (string-prefix? "i686" system))
4213 "-msse2")
4214 (else "")))))
4215 #:parallel-tests? #f ;tests are multi-threaded, via BLAS
4216 #:phases
4217 (modify-phases %standard-phases
4218 (add-before 'configure 'patch-header-generation
4219 (lambda _
4220 (substitute* "configure"
4221 (("^ *make.*top_srcdir=\"\\$srcdir\"" &)
4222 (string-append & " CPP=\"$CPP\"")))
4223 #t))
4224 (add-before 'check 'setup-tests
4225 (lambda _
4226 ;; Decrease test time and RAM use by computing fewer eigenvalues.
4227 ;; The flags are (MATRIX-SIZE, EIGENVALUES, BLOCK-SIZE), where
4228 ;; the default is (500, 250, 16) for C tests and (5000, 150, 16)
4229 ;; for Fortran. This also causes several tests to pass that
4230 ;; otherwise would otherwise fail with matrix size 5000; possibly
4231 ;; due to floating point tolerances that are too tight.
4232 (setenv "TEST_FLAGS" "1500 50 16") ;from elpa.spec
4233 (setenv "OMP_NUM_THREADS" (number->string (parallel-job-count)))
4234 (substitute* "Makefile"
4235 ;; Test scripts are generated, patch the shebang
4236 (("#!/bin/bash") (string-append "#!" (which "sh"))))
4237 #t)))))
4238 (home-page "http://elpa.mpcdf.mpg.de")
4239 (synopsis "Eigenvalue solvers for symmetric matrices")
4240 (description
4241 "The ELPA library provides efficient and scalable direct eigensolvers for
4242symmetric matrices.")
4243 (license license:lgpl3)))
4244
4245(define-public elpa-openmpi
4246 (package (inherit elpa)
4247 (name "elpa-openmpi")
4248 (inputs
4249 `(("mpi" ,openmpi)
4250 ("scalapack" ,scalapack)
4251 ,@(package-inputs elpa)))
4252 (arguments
4253 (substitute-keyword-arguments (package-arguments elpa)
4254 ((#:configure-flags cf '())
4255 `(cons "--with-mpi=yes" (delete "--with-mpi=no" ,cf)))
4256 ((#:phases phases '%standard-phases)
4257 `(modify-phases ,phases
4258 (add-before 'check 'mpi-setup
4259 (lambda _
4260 ;; Tests use 2 mpi tasks by default, use our remaining build
4261 ;; cores as OpenMP threads.
4262 (setenv "OMP_NUM_THREADS" (number->string
4263 (max (quotient (parallel-job-count) 2)
4264 1)))
4265 (,%openmpi-setup)))))))
4266 (synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)")))
4267
e01397b4
EB		 4268(define-public elemental
4269 (package
4270 (name "elemental")
4271 (version "0.87.7")
4272 (source (origin
5c0b6d1b
EF		 4273 (method git-fetch)
4274 (uri (git-reference
4275 (url "https://github.com/elemental/Elemental.git")
4276 (commit (string-append "v" version))))
4277 (file-name (git-file-name name version))
e01397b4
EB		 4278 (sha256
4279 (base32
5c0b6d1b 4280 "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
e01397b4
EB		 4281 (build-system cmake-build-system)
4282 (home-page "http://libelemental.org")
4283 (native-inputs
4284 `(("gfortran" ,gfortran)))
4285 (inputs
4286 `(("blas" ,openblas)
4287 ("gfortran:lib" ,gfortran "lib")
4288 ("gmp" ,gmp)
4289 ("lapack" ,lapack)
4290 ("metis" ,metis)
4291 ("mpc" ,mpc)
4292 ("mpfr" ,mpfr)
4293 ("mpi" ,openmpi)
4294 ("qd" ,qd)))
4295 (arguments
4296 `(#:build-type "Release" ;default RelWithDebInfo not supported
4297 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
4298 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
4299 "-DEL_CACHE_WARNINGS:BOOL=YES"
4300 "-DEL_TESTS:BOOL=YES"
4301 "-DCMAKE_INSTALL_LIBDIR=lib"
4302 "-DGFORTRAN_LIB=gfortran")
4303 #:phases (modify-phases %standard-phases
3b42e2be
EF		 4304 (add-before 'check 'mpi-setup
4305 ,%openmpi-setup)
e01397b4
EB		 4306 (add-before 'check 'setup-tests
4307 (lambda _
4308 ;; Parallelism is done at the MPI layer.
4309 (setenv "OMP_NUM_THREADS" "1")
4310 #t))
4311 (add-after 'install 'remove-tests
4312 (lambda* (#:key outputs #:allow-other-keys)
4313 ;; Tests are installed, with no easy configuration
4314 ;; switch to prevent this, so delete them.
4315 (delete-file-recursively
3b42e2be 4316 (string-append (assoc-ref outputs "out") "/bin"))
e01397b4
EB		 4317 #t)))))
4318 (synopsis "Dense and sparse-direct linear algebra and optimization")
4319 (description "Elemental is a modern C++ library for distributed-memory
4320dense and sparse-direct linear algebra, conic optimization, and lattice
4321reduction.")
4322 (license license:bsd-2)))
5b05dce7
JN		 4323
4324(define-public mcrl2
4325 (package
4326 (name "mcrl2")
3bc74090 4327 (version "201908.0")
5b05dce7
JN		 4328 (source (origin
4329 (method url-fetch)
185152e3
JN		 4330 (uri (string-append
4331 "https://www.mcrl2.org/download/release/mcrl2-"
4332 version ".tar.gz"))
5b05dce7
JN		 4333 (sha256
4334 (base32
3bc74090 4335 "1i4xgl2d5fgiz1mwi50cyfkrrcpm8nxfayfjgmhq7chs58wlhfsz"))))
5b05dce7
JN		 4336 (inputs
4337 `(("boost" ,boost)
4338 ("glu" ,glu)
4339 ("mesa" ,mesa)
077d66ed 4340 ("qtbase" ,qtbase)))
5b05dce7 4341 (build-system cmake-build-system)
ed0c5d3c 4342 (synopsis "Toolset for the mCRL2 formal specification language")
5b05dce7 4343 (description
ed0c5d3c
TGR		 4344 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
4345specification language for describing concurrent discrete event systems. Its
4346toolset supports analysis and automatic verification, linearisation, simulation,
4347state-space exploration and generation, and tools to optimise and analyse
5b05dce7
JN		 4348specifications. Also, state spaces can be manipulated, visualised and
4349analysed.")
b3882709 4350 (home-page "https://mcrl2.org")
5b05dce7 4351 (license license:boost1.0)))
41835f94 4352
e03b9126
JN		 4353(define-public mcrl2-minimal
4354 (package
4355 (inherit mcrl2)
4356 (name "mcrl2-minimal")
4357 (inputs
4358 `(("boost" ,boost)))
4359 (arguments
4360 '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
4361
41835f94
LF		 4362(define-public r-subplex
4363 (package
4364 (name "r-subplex")
2bcf5fd3 4365 (version "1.5-4")
41835f94
LF		 4366 (source
4367 (origin
4368 (method url-fetch)
4369 (uri (cran-uri "subplex" version))
4370 (sha256
4371 (base32
2bcf5fd3 4372 "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
41835f94
LF		 4373 (build-system r-build-system)
4374 (native-inputs
4375 `(("gfortran" ,gfortran)))
4376 (home-page "https://cran.r-project.org/web/packages/subplex")
4377 (synopsis "Unconstrained optimization using the subplex algorithm")
4378 (description "This package implements the Subplex optimization algorithm.
4379It solves unconstrained optimization problems using a simplex method on
4380subspaces. The method is well suited for optimizing objective functions that
4381are noisy or are discontinuous at the solution.")
4382 (license license:gpl3+)))
799ad71b
LF		 4383
4384(define-public r-desolve
4385 (package
4386 (name "r-desolve")
d36430d2 4387 (version "1.24")
799ad71b
LF		 4388 (source
4389 (origin
4390 (method url-fetch)
4391 (uri (cran-uri "deSolve" version))
4392 (sha256
4393 (base32
d36430d2 4394 "0hkvspq0fp8j64l9zayab2l2nazazhwfgfym0jllh0xv5a12r99s"))))
799ad71b
LF		 4395 (properties `((upstream-name . "deSolve")))
4396 (build-system r-build-system)
4397 (native-inputs
4398 `(("gfortran" ,gfortran)))
4399 (home-page "https://desolve.r-forge.r-project.org/")
4400 (synopsis "Solvers for initial value problems of differential equations")
4401 (description "This package provides functions that solve initial
4402value problems of a system of first-order ordinary differential equations (ODE),
4403of partial differential equations (PDE), of differential algebraic equations
4404(DAE), and of delay differential equations. The functions provide an interface
4405to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
4406to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
4407the Runge-Kutta family with fixed or variable time steps. The package contains
4408routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
4409differential equations (PDE) that have been converted to ODEs by numerical
4410differencing.")
4411 (license license:gpl2+)))
910deec6
NV		 4412
4413(define-public tcalc
4414 (package
4415 (name "tcalc")
4416 (version "2.0")
4417 (source
4418 (origin
4419 (method url-fetch)
4420 (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
4421 version ".tar.gz"))
4422 (sha256
4423 (base32
4424 "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
4425 (build-system gnu-build-system)
4426 (synopsis "The terminal calculator")
4427 (description
4428 "The terminal calculator is a small program to help users of the GNU/Linux
4429terminal do calculations simply and quickly. The formula to be calculated can
4430be fed to @command{tcalc} through the command line.")
4431 (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
4432 (license license:gpl3+)))
b26e4f26
EB		 4433
4434(define-public sundials
4435 (package
4436 (name "sundials")
4437 (version "3.1.1")
4438 (source
4439 (origin
4440 (method url-fetch)
4441 (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
4442 "sundials-" version ".tar.gz"))
4443 (sha256
4444 (base32
4445 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
4446 (build-system cmake-build-system)
4447 (native-inputs
4448 `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
4449 (inputs
4450 `(("fortran" ,gfortran) ;for fcmix
4451 ("blas" ,openblas)
4452 ("suitesparse" ,suitesparse))) ;TODO: Add hypre
4453 (arguments
4454 `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
4455 "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
4456 "-DEXAMPLES_ENABLE_F77:BOOL=ON"
4457 "-DEXAMPLES_ENABLE_F90:BOOL=ON"
4458 "-DEXAMPLES_INSTALL:BOOL=OFF"
4459
4460 "-DFCMIX_ENABLE:BOOL=ON"
4461
4462 "-DKLU_ENABLE:BOOL=ON"
4463 ,(string-append "-DKLU_INCLUDE_DIR="
4464 (assoc-ref %build-inputs "suitesparse")
4465 "/include")
4466 ,(string-append "-DKLU_LIBRARY_DIR="
4467 (assoc-ref %build-inputs "suitesparse")
4468 "/lib"))))
4469 (home-page "https://computation.llnl.gov/projects/sundials")
4470 (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
4471 (description "SUNDIALS is a family of software packages implemented with
4472the goal of providing robust time integrators and nonlinear solvers that can
4473easily be incorporated into existing simulation codes.")
4474 (license license:bsd-3)))
4475
4476(define-public sundials-openmpi
4477 (package (inherit sundials)
4478 (name "sundials-openmpi")
4479 (inputs
4480 `(("mpi" ,openmpi)
4481 ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
4482 ,@(package-inputs sundials)))
4483 (arguments
4484 (substitute-keyword-arguments (package-arguments sundials)
4485 ((#:configure-flags flags '())
4486 `(cons* "-DMPI_ENABLE:BOOL=ON"
4487 "-DPETSC_ENABLE:BOOL=ON"
4488 (string-append "-DPETSC_INCLUDE_DIR="
4489 (assoc-ref %build-inputs "petsc")
4490 "/include")
4491 (string-append "-DPETSC_LIBRARY_DIR="
4492 (assoc-ref %build-inputs "petsc")
4493 "/lib")
4494 ,flags))
4495 ((#:phases phases '%standard-phases)
4496 `(modify-phases ,phases
bbe46a4a
EB		 4497 (add-before 'check 'mpi-setup
4498 ,%openmpi-setup)))))
b26e4f26 4499 (synopsis "SUNDIALS with OpenMPI support")))
a6b9ebc2
EB		 4500
4501(define-public combinatorial-blas
4502 (package
4503 (name "combinatorial-blas")
4504 (version "1.6.2")
4505 (source
4506 (origin
4507 (method url-fetch)
4508 (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/"
4509 "CombBLAS_beta_"
4510 (match (string-split version #\.)
4511 ((major minor patch)
4512 (string-append major minor "_" patch))) ;e.g. "16_2"
4513 ".tgz"))
4514 (sha256
4515 (base32
4516 "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a"))
4517 (patches (search-patches "combinatorial-blas-awpm.patch"
4518 "combinatorial-blas-io-fix.patch"))))
4519 (build-system cmake-build-system)
4520 (inputs
4521 `(("mpi" ,openmpi)
4522 ("test-data" ,(origin
4523 (method url-fetch)
4524 (uri (string-append "https://people.eecs.berkeley.edu/~aydin/"
4525 "CombBLAS_FILES/testdata_combblas1.6.1.tgz"))
4526 (sha256
4527 (base32
4528 "01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87"))))))
4529 (arguments
4530 `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
4531 "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL")
4532 #:parallel-tests? #f ;tests use 'mpiexec -n4'
4533 #:phases
4534 (modify-phases %standard-phases
4535 (add-before 'check 'mpi-setup
4536 ,%openmpi-setup)
4537 (add-before 'check 'test-setup
4538 (lambda* (#:key inputs #:allow-other-keys)
4539 (setenv "OMP_NUM_THREADS" "2")
4540 (invoke "tar" "xf" (assoc-ref inputs "test-data")))))))
4541 (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/")
4542 (synopsis "Linear algebra primitives for graph analytics")
4543 (description "The Combinatorial BLAS (CombBLAS) is an extensible
4544distributed-memory parallel graph library offering a small but powerful set of
4545linear algebra primitives specifically targeting graph analytics.")
4546 (license (list
4547 license:gpl2+ ;include/psort/(funnel|sort)*.h
4548 license:x11 ;usort and psort
4549 license:bsd-3)))) ;CombBLAS and MersenneTwister.h
3847d1f2
RW		 4550
4551(define-public dune-common
4552 (package
4553 (name "dune-common")
4554 (version "2.6.0")
4555 (source
4556 (origin
4557 (method url-fetch)
4558 (uri (string-append "https://dune-project.org/download/"
4559 version "/dune-common-" version ".tar.gz"))
4560 (sha256
4561 (base32
4562 "019wcr1qf7jwyxx1y5y290wdlglylskvbb2m01ljkzcza2xnlmhw"))))
4563 (build-system cmake-build-system)
4564 (arguments
4565 `(#:phases
4566 (modify-phases %standard-phases
4567 (add-after 'build 'build-tests
4568 (lambda* (#:key make-flags #:allow-other-keys)
4569 (apply invoke "make" "build_tests" make-flags)))
4570 ;; These tests fail because they require a fully functional MPI
4571 ;; environment.
4572 (add-after 'unpack 'disable-failing-tests
4573 (lambda _
4574 (setenv "ARGS"
4575 (string-append "--exclude-regex '("
4576 (string-join
4577 (list
4578 "remoteindicestest"
4579 "remoteindicestest-mpi-2"
4580 "syncertest"
4581 "syncertest-mpi-2"
4582 "variablesizecommunicatortest"
4583 "variablesizecommunicatortest-mpi-2"
4584 "arithmetictestsuitetest"
4585 "assertandreturntest"
4586 "assertandreturntest_ndebug"
4587 "concept"
4588 "debugaligntest"
4589 "mpicollectivecommunication"
4590 "mpicollectivecommunication-mpi-2"
4591 "mpiguardtest"
4592 "mpiguardtest-mpi-2"
4593 "mpihelpertest"
4594 "mpihelpertest-mpi-2"
4595 "mpihelpertest2"
4596 "mpihelpertest2-mpi-2")
4597 "|")
4598 ")'"))
4599 #t)))))
4600 (inputs
4601 `(("gmp" ,gmp)
4602 ("metis" ,metis)
4603 ("openmpi" ,openmpi)
4604 ("openblas" ,openblas)
4605 ("python" ,python)
4606 ("superlu" ,superlu)))
4607 (native-inputs
4608 `(("gfortran" ,gfortran)
4609 ("pkg-config" ,pkg-config)))
4610 (home-page "https://dune-project.org/")
4611 (synopsis "Distributed and Unified Numerics Environment")
4612 (description "DUNE, the Distributed and Unified Numerics Environment is a
4613modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4614grid-based methods. It supports the easy implementation of methods like
4615@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4616Differences} (FD).")
4617 ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2.
4618 (license license:gpl2)))
242dbd8e
RW		 4619
4620(define-public dune-geometry
4621 (package
4622 (name "dune-geometry")
4623 (version "2.6.0")
4624 (source
4625 (origin
4626 (method url-fetch)
4627 (uri (string-append "https://dune-project.org/download/"
4628 version "/dune-geometry-" version ".tar.gz"))
4629 (sha256
4630 (base32
4631 "0hlaaxjyv9j05blasvb67sy02hd0w4g9znf68gdh3l731dd1aqbn"))))
4632 (build-system cmake-build-system)
4633 (arguments
4634 `(#:phases
4635 (modify-phases %standard-phases
4636 (add-after 'build 'build-tests
4637 (lambda* (#:key make-flags #:allow-other-keys)
4638 (apply invoke "make" "build_tests" make-flags))))))
4639 (inputs
4640 `(("dune-common" ,dune-common)
4641 ("openmpi" ,openmpi)
4642 ;; Optional
4643 ("openblas" ,openblas)
4644 ("gmp" ,gmp)
4645 ("python" ,python)))
4646 (native-inputs
4647 `(("gfortran" ,gfortran)
4648 ("pkg-config" ,pkg-config)))
4649 (home-page "https://dune-project.org/")
4650 (synopsis "Distributed and Unified Numerics Environment")
4651 (description "DUNE, the Distributed and Unified Numerics Environment is a
4652modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4653grid-based methods. It supports the easy implementation of methods like
4654@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4655Differences} (FD).
4656
4657This package contains the basic DUNE geometry classes.")
4658 ;; GPL version 2 with "runtime exception"
4659 (license license:gpl2)))
ef6e69fd
RW		 4660
4661(define-public dune-grid
4662 (package
4663 (name "dune-grid")
4664 (version "2.6.0")
4665 (source
4666 (origin
4667 (method url-fetch)
4668 (uri (string-append "https://dune-project.org/download/"
4669 version "/dune-grid-" version ".tar.gz"))
4670 (sha256
4671 (base32
4672 "1jp4vscm9yb9xg0lh7apzccfkhvgbnk652yahigmh3cvzpl4acd0"))))
4673 (build-system cmake-build-system)
4674 (arguments
4675 `(#:phases
4676 (modify-phases %standard-phases
4677 (add-after 'build 'build-tests
4678 (lambda* (#:key make-flags #:allow-other-keys)
4679 (apply invoke "make" "build_tests" make-flags)))
4680 ;; These tests fail because they require a fully functional MPI
4681 ;; environment.
4682 (add-after 'unpack 'disable-failing-tests
4683 (lambda _
4684 (setenv "ARGS"
4685 (string-append "--exclude-regex '("
4686 (string-join
4687 (list
4688 "scsgmappertest"
4689 "conformvolumevtktest"
4690 "gnuplottest"
4691 "nonconformboundaryvtktest"
4692 "subsamplingvtktest"
4693 "vtktest"
4694 "vtktest-mpi-2"
4695 "vtksequencetest"
4696 "gmshtest-onedgrid"
4697 "test-dgf-yasp"
4698 "test-dgf-yasp-offset"
4699 "test-dgf-oned"
4700 "test-geogrid-yaspgrid"
4701 "test-gridinfo"
4702 "test-identitygrid"
4703 "testiteratorranges"
4704 "test-hierarchicsearch"
4705 "test-parallel-ug-mpi-2"
4706 "test-yaspgrid-backuprestore-equidistant"
4707 "test-yaspgrid-backuprestore-equidistant-mpi-2"
4708 "test-yaspgrid-backuprestore-equidistantoffset"
4709 "test-yaspgrid-backuprestore-equidistantoffset-mpi-2"
4710 "test-yaspgrid-backuprestore-tensor"
4711 "test-yaspgrid-backuprestore-tensor-mpi-2"
4712 "test-yaspgrid-tensorgridfactory"
4713 "test-yaspgrid-tensorgridfactory-mpi-2"
4714 "test-yaspgrid-yaspfactory-1d"
4715 "test-yaspgrid-yaspfactory-1d-mpi-2"
4716 "test-yaspgrid-yaspfactory-2d"
4717 "test-yaspgrid-yaspfactory-2d-mpi-2"
4718 "test-yaspgrid-yaspfactory-3d"
4719 "test-yaspgrid-yaspfactory-3d-mpi-2"
4720 "globalindexsettest"
4721 "persistentcontainertest"
4722 "structuredgridfactorytest"
4723 "tensorgridfactorytest"
4724 "vertexordertest")
4725 "|")
4726 ")'"))
4727 #t)))))
4728 (inputs
4729 `(("dune-common" ,dune-common)
4730 ("dune-geometry" ,dune-geometry)
4731 ("gmp" ,gmp)
4732 ("metis" ,metis)
4733 ("openblas" ,openblas)
4734 ("openmpi" ,openmpi)
4735 ("python" ,python)))
4736 (native-inputs
4737 `(("gfortran" ,gfortran)
4738 ("pkg-config" ,pkg-config)))
4739 (home-page "https://dune-project.org/")
4740 (synopsis "Distributed and Unified Numerics Environment")
4741 (description "DUNE, the Distributed and Unified Numerics Environment is a
4742modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4743grid-based methods. It supports the easy implementation of methods like
4744@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4745Differences} (FD).
4746
4747This package contains the basic DUNE grid classes.")
4748 ;; GPL version 2 with "runtime exception"
4749 (license license:gpl2)))
ea51d357
RW		 4750
4751(define-public dune-istl
4752 (package
4753 (name "dune-istl")
4754 (version "2.6.0")
4755 (source
4756 (origin
4757 (method url-fetch)
4758 (uri (string-append "https://dune-project.org/download/"
4759 version "/dune-istl-" version ".tar.gz"))
4760 (sha256
4761 (base32
4762 "0l2gyrvys5w6wsmk0ckbb7295s80b7yk7qrl7x66akv2jv1nzq2w"))))
4763 (build-system cmake-build-system)
4764 (arguments
4765 `(#:phases
4766 (modify-phases %standard-phases
4767 (add-after 'build 'build-tests
4768 (lambda* (#:key make-flags #:allow-other-keys)
4769 (apply invoke "make" "build_tests" make-flags)))
4770 ;; These tests fail because they require a fully functional MPI
4771 ;; environment.
4772 (add-after 'unpack 'disable-failing-tests
4773 (lambda _
4774 (setenv "ARGS"
4775 (string-append "--exclude-regex '("
4776 (string-join
4777 (list
4778 "galerkintest"
4779 "hierarchytest"
4780 "pamgtest"
4781 "pamg_comm_repart_test"
4782 "matrixredisttest"
4783 "vectorcommtest"
4784 "matrixmarkettest")
4785 "|")
4786 ")'"))
4787 #t)))))
4788 (inputs
4789 `(("dune-common" ,dune-common)
4790 ("openmpi" ,openmpi)
4791 ;; Optional
4792 ("metis" ,metis)
4793 ("superlu" ,superlu)
4794 ("openblas" ,openblas)
4795 ("gmp" ,gmp)
4796 ("python" ,python)))
4797 (native-inputs
4798 `(("gfortran" ,gfortran)
4799 ("pkg-config" ,pkg-config)))
4800 (home-page "https://dune-project.org/")
4801 (synopsis "Distributed and Unified Numerics Environment")
4802 (description "DUNE, the Distributed and Unified Numerics Environment is a
4803modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4804grid-based methods.
4805
4806This is the iterative solver template library which provides generic sparse
4807matrix/vector classes and a variety of solvers based on these classes. A
4808special feature is the use of templates to exploit the recursive block
4809structure of finite element matrices at compile time. Available solvers
4810include Krylov methods, (block-) incomplete decompositions and
4811aggregation-based algebraic multigrid.")
4812 ;; GPL version 2 with "runtime exception"
4813 (license license:gpl2)))
5a70aa7d
RW		 4814
4815(define-public dune-localfunctions
4816 (package
4817 (name "dune-localfunctions")
4818 (version "2.6.0")
4819 (source
4820 (origin
4821 (method url-fetch)
4822 (uri (string-append "https://dune-project.org/download/"
4823 version "/dune-localfunctions-" version ".tar.gz"))
4824 (sha256
4825 (base32
4826 "19c6zjinwwpy8jh4v4prhphyd438rapd4x80fj93apmwgw04nrhl"))))
4827 (build-system cmake-build-system)
4828 (arguments
4829 `(#:phases
4830 (modify-phases %standard-phases
4831 (add-after 'build 'build-tests
4832 (lambda* (#:key make-flags #:allow-other-keys)
4833 (apply invoke "make" "build_tests" make-flags))))))
4834 (inputs
4835 `(("dune-common" ,dune-common)
4836 ("dune-geometry" ,dune-geometry)
4837 ("openmpi" ,openmpi)
4838 ;; Optional
4839 ("metis" ,metis)
4840 ("superlu" ,superlu)
4841 ("gmp" ,gmp)))
4842 (native-inputs
4843 `(("gfortran" ,gfortran)
4844 ("pkg-config" ,pkg-config)))
4845 (home-page "https://dune-project.org/")
4846 (synopsis "Distributed and Unified Numerics Environment") ; TODO
4847 (description "This DUNE module provides interface and implementation for
4848shape functions defined on the DUNE reference elements. In addition to the
4849shape function, interpolation operators and special keys are provided which
4850can be used to assemble global function spaces on finite-element grids.
4851
4852This package provides an interface and implementation for shape functions
4853defined on the DUNE reference elements. In addition to the shape function,
4854interpolation operators and special keys are provided which can be used to
4855assemble global function spaces on finite-element grids.")
4856 ;; GPL version 2 with "runtime exception"
4857 (license license:gpl2)))
ab03d899
RW		 4858
4859(define-public dune-alugrid
4860 (package
4861 (name "dune-alugrid")
4862 (version "2.6.0")
4863 (source
4864 (origin
4865 (method url-fetch)
4866 (uri (string-append "https://dune-project.org/download/"
4867 version "/dune-alugrid-" version ".tar.gz"))
4868 (sha256
4869 (base32
4870 "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj"))))
4871 (build-system cmake-build-system)
4872 (arguments
4873 `(#:tests? #f ; 7 of 8 tests fail because they need a full MPI
4874 ; environment
4875 #:phases
4876 (modify-phases %standard-phases
4877 (add-after 'unpack 'patch-include
4878 (lambda _
4879 (substitute* "dune/alugrid/test/test-alugrid.cc"
4880 (("doc/grids/gridfactory/testgrids")
4881 "doc/dune-grid/grids/gridfactory/testgrids"))
4882 #t))
4883 (add-after 'build 'build-tests
4884 (lambda* (#:key inputs make-flags #:allow-other-keys)
4885 (setenv "CPLUS_INCLUDE_PATH"
97149c57 4886 (string-append (assoc-ref inputs "dune-grid") "/share"))
ab03d899
RW		 4887 (apply invoke "make" "build_tests" make-flags))))))
4888 (inputs
4889 `(("dune-common" ,dune-common)
4890 ("dune-geometry" ,dune-geometry)
4891 ("dune-grid" ,dune-grid)
4892 ("openmpi" ,openmpi)
4893 ;; Optional
4894 ("metis" ,metis)
4895 ("openblas" ,openblas)
4896 ("python" ,python)
4897 ("superlu" ,superlu)
4898 ("gmp" ,gmp)
4899 ("zlib" ,zlib)))
4900 (native-inputs
4901 `(("gfortran" ,gfortran)
4902 ("pkg-config" ,pkg-config)))
4903 (home-page "https://dune-project.org/")
4904 (synopsis "Distributed and Unified Numerics Environment")
4905 (description "ALUGrid is an adaptive, loadbalancing, unstructured
4906implementation of the DUNE grid interface supporting either simplices or
4907cubes.")
4908 (license license:gpl2+)))
0e50630f
RW		 4909
4910(define-public dune-typetree
4911 (package
4912 (name "dune-typetree")
4913 (version "2.6.0")
4914 (source
4915 (origin
4916 (method git-fetch)
4917 (uri (git-reference
4918 (url "https://gitlab.dune-project.org/staging/dune-typetree.git")
4919 (commit (string-append "v" version))))
4920 (file-name (git-file-name name version))
4921 (sha256
4922 (base32
4923 "0mnv6w2f22lz3j4bdpdjq55vjm8xxfx9v4vvhg9bd36xpsbjpjp9"))))
4924 (build-system cmake-build-system)
4925 (arguments
4926 `(#:phases
4927 (modify-phases %standard-phases
4928 (add-after 'build 'build-tests
4929 (lambda* (#:key make-flags #:allow-other-keys)
4930 (apply invoke "make" "build_tests" make-flags))))))
4931 (inputs
4932 `(("dune-common" ,dune-common)
4933 ("openmpi" ,openmpi)
4934 ;; Optional
4935 ("openblas" ,openblas)
4936 ("python" ,python)
4937 ("metis" ,metis)
4938 ("superlu" ,superlu)
4939 ("gmp" ,gmp)))
4940 (native-inputs
4941 `(("gfortran" ,gfortran)
4942 ("pkg-config" ,pkg-config)))
4943 (home-page "https://dune-project.org/")
4944 (synopsis "Distributed and Unified Numerics Environment")
4945 (description "TypeTree is a template library for constructing and
4946operating on statically typed trees of objects.")
4947 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4948 (license (list license:lgpl3+ license:gpl2))))
85b9371c
RW		 4949
4950(define-public dune-functions
4951 (package
4952 (name "dune-functions")
4953 (version "2.6.0")
4954 (source
4955 (origin
4956 (method git-fetch)
4957 (uri (git-reference
4958 (url "https://gitlab.dune-project.org/staging/dune-functions.git")
4959 (commit (string-append "v" version))))
4960 (file-name (git-file-name name version))
4961 (sha256
4962 (base32
4963 "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200"))))
4964 (build-system cmake-build-system)
4965 (arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid
4966 (inputs
4967 `(("dune-common" ,dune-common)
4968 ("dune-istl" ,dune-istl)
4969 ("dune-localfunctions" ,dune-localfunctions)
4970 ("dune-grid" ,dune-grid)
4971 ("dune-geometry" ,dune-geometry)
4972 ("dune-typetree" ,dune-typetree)
4973 ("openmpi" ,openmpi)
4974 ("openblas" ,openblas)
4975 ("metis" ,metis)
4976 ("python" ,python)
4977 ("superlu" ,superlu)
4978 ("gmp" ,gmp)))
4979 (native-inputs
4980 `(("gfortran" ,gfortran)
4981 ("pkg-config" ,pkg-config)))
4982 (home-page "https://dune-project.org/")
4983 (synopsis "Distributed and Unified Numerics Environment")
4984 (description "The dune-functions module provides an abstraction layer for
4985global finite element functions. Its two main concepts are functions
4986implemented as callable objects, and bases of finite element spaces.")
4987 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4988 (license (list license:lgpl3+ license:gpl2))))
4714b00e
RW		 4989
4990(define-public dune-pdelab
4991 (package
4992 (name "dune-pdelab")
4993 (version "2.6.0-rc1")
4994 (source
4995 (origin
4996 (method git-fetch)
4997 (uri (git-reference
4998 (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
4999 (commit (string-append "v" version))))
5000 (file-name (git-file-name name version))
5001 (sha256
5002 (base32
5003 "07g0s9448z65vjrq88g5rv3340iifil85k170n8kbqchsvi4ny5v"))))
5004 (build-system cmake-build-system)
5005 (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
5006 (inputs
5007 `(("dune-common" ,dune-common)
5008 ("dune-istl" ,dune-istl)
5009 ("dune-localfunctions" ,dune-localfunctions)
5010 ("dune-geometry" ,dune-geometry)
5011 ("dune-grid" ,dune-grid)
5012 ("dune-typetree" ,dune-typetree)
5013 ("dune-functions" ,dune-functions)
5014 ("openmpi" ,openmpi)
5015 ;; Optional
5016 ("openblas" ,openblas)
5017 ("eigen" ,eigen)
5018 ("metis" ,metis)
5019 ("python" ,python)
5020 ("superlu" ,superlu)
5021 ("gmp" ,gmp)))
5022 (native-inputs
5023 `(("gfortran" ,gfortran)
5024 ("pkg-config" ,pkg-config)))
5025 (home-page "https://dune-project.org/")
5026 (synopsis "Differential equations solver toolbox")
5027 (description "PDELab is a partial differential equations solver toolbox
5028built on top of DUNE, the Distributed and Unified Numerics Environment.")
5029 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
5030 (license (list license:lgpl3+ license:gpl2))))
413f6126
AI		 5031
5032(define-public mlucas
5033 (package
5034 (name "mlucas")
5035 (version "18")
5036 (source
5037 (origin
5038 (method url-fetch)
5039 (uri (string-append
5040 "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz"))
5041 (sha256
a36efdbc 5042 (base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447"))))
413f6126
AI		 5043 (build-system gnu-build-system)
5044 (inputs
5045 `(("python2" ,python-2)))
5046 (arguments
a36efdbc 5047 `(#:tests? #f ; no tests
413f6126
AI		 5048 #:phases
5049 (modify-phases %standard-phases
5050 (replace 'configure
5051 (lambda _
5052 (chdir "src")
5053 (call-with-output-file "Makefile"
5054 (lambda (port)
5055 (format port "CC = gcc
5056CFLAGS = -O3 ~a -DUSE_THREADS
5057LDLIBS = -lm -lpthread -lrt
5058Mlucas: $(addsuffix .o,$(basename $(wildcard *.c)))
5059"
5060 ,(let ((system (or (%current-target-system)
5061 (%current-system))))
5062 (cond
5063 ((string-prefix? "x86_64" system) "-DUSE_SSE2")
5064 (else ""))))))
5065 #t))
5066 (replace 'install
5067 (lambda* (#:key outputs #:allow-other-keys)
5068 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
5069 (install-file "Mlucas" bin)
5070 (install-file "primenet.py" bin))
5071 #t)))))
5072 (home-page "https://www.mersenne.org")
5073 (synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client")
5074 (description "Mlucas performs Lucas-Lehmer primality testing of Mersenne
5075numbers in search of a world-record prime. You may use it to test any
5076suitable number as you wish, but it is preferable that you do so in a
5077coordinated fashion, as part of the Great Internet Mersenne Prime
5078Search (GIMPS). Mlucas also includes a simple Python script for assignment
5079management via the GIMPS project's Primenet server.")
5080 (license license:gpl2+)))
6f8c4195
NG		 5081
5082(define-public nauty
5083 (package
5084 (name "nauty")
5085 (version "2.6r11")
5086 (source (origin
5087 (method url-fetch)
5088 (uri (string-append
5089 "https://pallini.di.uniroma1.it/"
5090 "nauty" (string-join (string-split version #\.) "")
5091 ".tar.gz"))
5092 (sha256
5093 (base32
5094 "05z6mk7c31j70md83396cdjmvzzip1hqb88pfszzc6k4gy8h3m2y"))))
5095 (build-system gnu-build-system)
5096 (outputs '("out" "lib"))
5097 (arguments
5098 `(#:test-target "checks"
5099 #:phases
5100 (modify-phases %standard-phases
5101 ;; Default make target does not build all available
5102 ;; executables. Create them now.
5103 (add-after 'build 'build-extra-programs
5104 (lambda _
5105 (for-each (lambda (target) (invoke "make" target))
5106 '("blisstog" "bliss2dre" "checks6" "sumlines"))
5107 #t))
5108 ;; Upstream does not provide any install target.
5109 (replace 'install
5110 (lambda* (#:key outputs #:allow-other-keys)
5111 (let* ((out (assoc-ref outputs "out"))
5112 (lib-output (assoc-ref outputs "lib"))
5113 (bin (string-append out "/bin"))
5114 (doc (string-append out "/share/doc/nauty/"))
5115 (include (string-append lib-output "/include/nauty"))
5116 (lib (string-append lib-output "/lib/nauty")))
5117 (for-each (lambda (f) (install-file f bin))
5118 '("dreadnaut" "NRswitchg" "addedgeg" "amtog" "biplabg"
5119 "blisstog" "bliss2dre" "catg" "checks6" "complg"
5120 "converseg" "copyg" "countg" "cubhamg" "deledgeg"
5121 "delptg" "directg" "dretodot" "dretog" "genbg"
5122 "genbgL" "geng" "genquarticg" "genrang" "genspecialg"
5123 "gentourng" "gentreeg" "hamheuristic" "labelg"
5124 "linegraphg" "listg" "multig" "newedgeg" "pickg"
5125 "planarg" "ranlabg" "shortg" "showg" "subdivideg"
5126 "sumlines" "twohamg" "vcolg" "watercluster2"))
5127 (for-each (lambda (f) (install-file f include))
5128 (find-files "." "\\.h$"))
5129 (for-each (lambda (f) (install-file f lib))
5130 (find-files "." "\\.a$"))
5131 (for-each (lambda (f) (install-file f doc))
5132 (append '("formats.txt" "README" "schreier.txt")
5133 (find-files "." "\\.pdf$")))))))))
5134 (inputs
5135 `(("gmp" ,gmp))) ;for sumlines
5136 (home-page "https://pallini.di.uniroma1.it/")
5137 (synopsis "Library for graph automorphisms")
5138 (description "@code{nauty} (No AUTomorphisms, Yes?) is a set of
5139procedures for computing automorphism groups of graphs and digraphs.
5140
5141@code{nauty} computes graph information in the form of a set of
5142generators, the size of the group, and the orbits of the group; it can
5143also produce a canonical label. The @code{nauty} suite is written in
5144C and comes with a command-line interface, a collection of
5145command-line tools, and an Application Programming Interface (API).
5146
5147This package provides the static libraries required to run programs
5148compiled against the nauty library.")
5149 (license license:asl2.0)))
26433471
AE		 5150
5151(define-public ppl
5152 (package
5153 (name "ppl")
5154 (version "1.2")
5155 (source
5156 (origin
5157 (method url-fetch)
5158 (uri (string-append "https://www.bugseng.com/products/ppl/download/"
5159 "ftp/releases/" version
5160 "/ppl-" version ".tar.gz"))
5161 (sha256
5162 (base32
5163 "1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb"))))
5164 (build-system gnu-build-system)
5165 (native-inputs
5166 `(("m4", m4)))
5167 (inputs
5168 `(("glpk" ,glpk)
5169 ("gmp", gmp)))
5170 (home-page "https://www.bugseng.com/parma-polyhedra-library")
5171 (synopsis
5172 "Parma Polyhedra Library for computations with polyhedra")
5173 (description
5174 "The Parma Polyhedra Library (PPL) provides numerical abstractions
5175especially targeted at applications in the field of analysis and
5176verification of complex systems. These abstractions include convex
5177polyhedra, defined as the intersection of a finite number of (open or
5178closed) halfspaces, each described by a linear inequality (strict or
5179non-strict) with rational coefficients; some special classes of polyhedra
5180shapes that offer interesting complexity/precision tradeoffs; and grids
5181which represent regularly spaced points that satisfy a set of linear
5182congruence relations. The library also supports finite powersets and
5183products of (any kind of) polyhedra and grids, a mixed integer linear
5184programming problem solver using an exact-arithmetic version of the simplex
5185algorithm, a parametric integer programming solver, and primitives for
5186termination analysis via the automatic synthesis of linear ranking
5187functions.")
5188 (license license:gpl3+)))
4cb5d251
SS		 5189
5190(define-public speedcrunch
5191 (package
5192 (name "speedcrunch")
5193 (version "0.12.0")
5194 (source
5195 (origin
5196 (method git-fetch)
5197 (uri (git-reference
5198 (url "https://bitbucket.org/heldercorreia/speedcrunch.git")
5199 (commit (string-append "release-" version))))
5200 (file-name (git-file-name name version))
5201 (sha256
5202 (base32
5203 "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"))))
5204 (build-system cmake-build-system)
5205 (inputs `(("qtbase" ,qtbase)))
5206 (native-inputs `(("qttools" ,qttools)))
5207 (arguments
5208 `(#:phases
5209 (modify-phases %standard-phases
5210 (add-after 'unpack 'chdir-to-src
5211 (lambda _ (chdir "src") #t)))))
5212 (synopsis "High-precision scientific calculator")
5213 (description
5214 "SpeedCrunch is a high-precision scientific calculator. It features a
5215syntax-highlighted scrollable display and is designed to be fully used via
5216keyboard. Some distinctive features are auto-completion of functions and
5217variables, a formula book, and quick insertion of constants from various
5218fields of knowledge.")
5219 (home-page "http://speedcrunch.org/")
5220 (license license:gpl2+)))
5221
jackhill's copy of GNU Guix: https://guix.gnu.org/