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gnu: coq: Update to 8.10.2.
[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>
3b7828cc 35;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net>
8f8b2451
AE		 36;;;
37;;; This file is part of GNU Guix.
38;;;
39;;; GNU Guix is free software; you can redistribute it and/or modify it
40;;; under the terms of the GNU General Public License as published by
41;;; the Free Software Foundation; either version 3 of the License, or (at
42;;; your option) any later version.
43;;;
44;;; GNU Guix is distributed in the hope that it will be useful, but
45;;; WITHOUT ANY WARRANTY; without even the implied warranty of
46;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
47;;; GNU General Public License for more details.
48;;;
49;;; You should have received a copy of the GNU General Public License
50;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
51
52(define-module (gnu packages maths)
ec322be2 53 #:use-module (ice-9 regex)
a6b9ebc2 54 #:use-module (ice-9 match)
8f8b2451 55 #:use-module (gnu packages)
b5b73a82 56 #:use-module ((guix licenses) #:prefix license:)
8f8b2451
AE		 57 #:use-module (guix packages)
58 #:use-module (guix download)
54052a54 59 #:use-module (guix git-download)
0e2672ae 60 #:use-module (guix utils)
fa574a6d 61 #:use-module ((guix build utils) #:select (alist-replace))
da95c817 62 #:use-module (guix build-system cmake)
c9dfa3c7 63 #:use-module (guix build-system gnu)
560acf25 64 #:use-module (guix build-system python)
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
0ffc2d53
AE		 486(define-public lrslib
487 (package
488 (name "lrslib")
489 (version "7.0a")
490 (source
491 (origin
492 (method url-fetch)
493 (uri (string-append "http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/"
494 "lrslib-0"
495 (string-delete #\. version) ".tar.gz"))
496 (sha256
497 (base32
498 "034fa45r9hwx6ljmgpxk2872q34nklkalpdkc6s9hqw57rivi36k"))))
499 (build-system gnu-build-system)
500 (inputs
501 `(("gmp" ,gmp)))
502 (arguments
503 `(#:tests? #f ; no check phase
504 #:make-flags `("CC=gcc"
505 ,(string-append "prefix=" (assoc-ref %outputs "out"))
506 "all-shared")
507 #:phases
508 (modify-phases %standard-phases
509 (replace 'configure
510 (lambda _
511 (substitute* "makefile"
512 (("-L \\.") "-L . -Wl,-rpath='$$ORIGIN/../lib'"))
513 #t)))))
514 (home-page "http://cgm.cs.mcgill.ca/~avis/C/lrs.html")
515 (synopsis "Convex hulls of polyhedra with exact arithmetic")
516 (description
517 "The C code of lrslib implements the reverse search algorithm for
518vertex enumeration and convex hull problems. Its input file format is
519compatible with cddlib. All computations are done exactly in either
520multiple precision or fixed integer arithmetic. Output is not stored
521in memory, so even problems with very large output sizes can sometimes
522be solved.")
523 (license license:gpl2+)))
524
865a69dd
RW		 525(define-public arpack-ng
526 (package
527 (name "arpack-ng")
f03c4ec6 528 (version "3.6.3")
c0edb5b5 529 (home-page "https://github.com/opencollab/arpack-ng")
622ef2b9
MB		 530 (source (origin
531 (method git-fetch)
532 (uri (git-reference (url home-page) (commit version)))
533 (file-name (git-file-name name version))
534 (sha256
535 (base32
f03c4ec6 536 "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
865a69dd 537 (build-system gnu-build-system)
c0edb5b5
LC		 538 (native-inputs
539 `(("autoconf" ,autoconf)
540 ("automake" ,automake)
541 ("libtool" ,libtool)))
865a69dd
RW		 542 (inputs
543 `(("lapack" ,lapack)
19afbea1 544 ("fortran" ,gfortran)))
865a69dd
RW		 545 (synopsis "Fortran subroutines for solving eigenvalue problems")
546 (description
547 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
548large scale eigenvalue problems.")
166191b3 549 (license (license:non-copyleft "file://COPYING"
865a69dd
RW		 550 "See COPYING in the distribution."))))
551
c0edb5b5
LC		 552(define-public arpack-ng-3.3.0
553 (package
554 (inherit arpack-ng)
555 (version "3.3.0")
556 (name (package-name arpack-ng))
557 (home-page (package-home-page arpack-ng))
558 (source
559 (origin
560 (method url-fetch)
561 (uri (string-append home-page "/archive/" version ".tar.gz"))
562 (file-name (string-append name "-" version ".tar.gz"))
563 (sha256
564 (base32
565 "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
566
8c94c886
EB		 567(define-public arpack-ng-openmpi
568 (package (inherit arpack-ng)
569 (name "arpack-ng-openmpi")
570 (inputs
571 `(("mpi" ,openmpi)
572 ,@(package-inputs arpack-ng)))
4f387541
LC		 573 (arguments
574 (substitute-keyword-arguments (package-arguments arpack-ng)
575 ((#:configure-flags _ '())
aa82260b
PG		 576 ''("--enable-mpi"))
577 ((#:phases phases '%standard-phases)
578 `(modify-phases ,phases
bbe46a4a
EB		 579 (add-before 'check 'mpi-setup
580 ,%openmpi-setup)))))
8c94c886
EB		 581 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
582
da95c817
NK		 583(define-public lapack
584 (package
585 (name "lapack")
ef39a177 586 (version "3.7.1")
da95c817
NK		 587 (source
588 (origin
589 (method url-fetch)
590 (uri (string-append "http://www.netlib.org/lapack/lapack-"
591 version ".tgz"))
592 (sha256
593 (base32
7c0d4c3a 594 "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
da95c817
NK		 595 (build-system cmake-build-system)
596 (home-page "http://www.netlib.org/lapack/")
19afbea1 597 (inputs `(("fortran" ,gfortran)
da95c817
NK		 598 ("python" ,python-2)))
599 (arguments
3ab869b6 600 `(#:configure-flags (list
3ab869b6
LC		 601 "-DBUILD_SHARED_LIBS:BOOL=YES"
602 "-DLAPACKE=ON"
603
604 ;; Build the 'LAPACKE_clatms' functions.
605 "-DLAPACKE_WITH_TMG=ON")
dc1d3cde
KK		 606 #:phases
607 (modify-phases %standard-phases
608 (add-before 'check 'patch-python
609 (lambda* (#:key inputs #:allow-other-keys)
610 (let ((python (assoc-ref inputs "python")))
611 (substitute* "lapack_testing.py"
612 (("/usr/bin/env python") python)))
613 #t)))))
da95c817
NK		 614 (synopsis "Library for numerical linear algebra")
615 (description
616 "LAPACK is a Fortran 90 library for solving the most commonly occurring
617problems in numerical linear algebra.")
166191b3 618 (license (license:non-copyleft "file://LICENSE"
da95c817 619 "See LICENSE in the distribution."))))
73fed4f8 620
e1ff597a
EB		 621(define-public scalapack
622 (package
623 (name "scalapack")
624 (version "2.0.2")
625 (source
626 (origin
627 (method url-fetch)
628 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
629 version ".tgz"))
630 (sha256
631 (base32
f73750e6
EB		 632 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))
633 (patches (search-patches "scalapack-blacs-mpi-deprecations.patch"))))
e1ff597a
EB		 634 (build-system cmake-build-system)
635 (inputs
636 `(("mpi" ,openmpi)
637 ("fortran" ,gfortran)
638 ("lapack" ,lapack))) ;for testing only
639 (arguments
6df2a50a
LC		 640 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
641 #:phases (modify-phases %standard-phases
bbe46a4a
EB		 642 (add-before 'check 'mpi-setup
643 ,%openmpi-setup))))
e1ff597a
EB		 644 (home-page "http://www.netlib.org/scalapack/")
645 (synopsis "Library for scalable numerical linear algebra")
646 (description
647 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
648routines on parallel distributed memory machines. ScaLAPACK solves dense and
649banded linear systems, least squares problems, eigenvalue problems, and
650singular value problems.")
adb223b8
LC		 651 (license (license:non-copyleft "file://LICENSE"
652 "See LICENSE in the distribution."))))
e1ff597a 653
73fed4f8 654(define-public gnuplot
5f800540
KK		 655 (package
656 (name "gnuplot")
cb1d8aee 657 (version "5.2.7")
5f800540
KK		 658 (source (origin
659 (method url-fetch)
660 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
661 version "/gnuplot-"
662 version ".tar.gz"))
663 (sha256
cb1d8aee 664 (base32 "1vglp4la40f5dpj0zdj63zprrkyjgzy068p35bz5dqxjyczm1zlp"))))
5f800540
KK		 665 (build-system gnu-build-system)
666 (inputs `(("readline" ,readline)
667 ("cairo" ,cairo)
668 ("pango" ,pango)
6e64766a
DM		 669 ("gd" ,gd)
670 ("lua" ,lua)))
612a387f
RW		 671 (native-inputs
672 `(("pkg-config" ,pkg-config)
673 ("texlive" ,texlive-tiny)))
07254d8b
AM		 674 (arguments `(#:configure-flags (list (string-append
675 "--with-texdir=" %output
676 "/texmf-local/tex/latex/gnuplot"))))
5f800540
KK		 677 (home-page "http://www.gnuplot.info")
678 (synopsis "Command-line driven graphing utility")
679 (description "Gnuplot is a portable command-line driven graphing
35b9e423 680utility. It was originally created to allow scientists and students to
73fed4f8 681visualize mathematical functions and data interactively, but has grown to
35b9e423 682support many non-interactive uses such as web scripting. It is also used as a
73fed4f8 683plotting engine by third-party applications like Octave.")
5f800540
KK		 684 ;; X11 Style with the additional restriction that derived works may only be
685 ;; distributed as patches to the original.
686 (license (license:fsf-free
687 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
668c06ac 688
32f70e1f
TD		 689(define-public gctp
690 (package
691 (name "gctp")
692 (version "2.0.0")
693 (source
694 (origin
5db874d1
TGR		 695 (method git-fetch)
696 (uri (git-reference
697 (url "https://github.com/OkoSanto/GCTP.git")
698 (commit (string-append "v" version))))
699 (file-name (git-file-name name version))
32f70e1f 700 (sha256
5db874d1 701 (base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
32f70e1f
TD		 702 (native-inputs
703 `(("fortran" ,gfortran)))
704 (build-system gnu-build-system)
705 (synopsis "General Cartographic Transformation Package (GCTP)")
706 (description
707 "The General Cartographic Transformation Package (GCTP) is a system of
708software routines designed to permit the transformation of coordinate pairs
709from one map projection to another. The GCTP is the standard computer
710software used by the National Mapping Division for map projection
711computations.")
712 (home-page "https://github.com/OkoSanto/GCTP")
0f7cd95b 713 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
32f70e1f 714
becbbefc
TD		 715(define-public hdf4
716 (package
717 (name "hdf4")
c959d99f 718 (version "4.2.14")
becbbefc
TD		 719 (source
720 (origin
721 (method url-fetch)
722 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
723 version "/src/hdf-" version ".tar.bz2"))
724 (sha256
c959d99f 725 (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l"))
15ca49b2
AE		 726 (patches (search-patches "hdf4-architectures.patch"
727 "hdf4-reproducibility.patch"
bd3d71cb
MB		 728 "hdf4-shared-fortran.patch"
729 "hdf4-tirpc.patch"))))
becbbefc
TD		 730 (build-system gnu-build-system)
731 (native-inputs
732 `(("gfortran" ,gfortran)
733 ("bison" ,bison)
734 ("flex" ,flex)))
735 (inputs
736 `(("zlib" ,zlib)
bd3d71cb
MB		 737 ("libjpeg" ,libjpeg)
738 ("libtirpc" ,libtirpc)))
becbbefc
TD		 739 (arguments
740 `(#:parallel-tests? #f
bd3d71cb
MB		 741 #:configure-flags (list "--enable-shared"
742 (string-append "CPPFLAGS=-I"
743 (assoc-ref %build-inputs "libtirpc")
744 "/include/tirpc"))
becbbefc
TD		 745 #:phases
746 (modify-phases %standard-phases
953a12fa
EF		 747 ;; This is inspired by two of Debian's patches.
748 (add-before 'configure 'add-more-aarch64-support
749 (lambda _
750 (substitute* '("mfhdf/ncgen/ncgen.l"
751 "mfhdf/ncgen/ncgenyy.c"
752 "mfhdf/libsrc/netcdf.h.in")
753 (("AIX5L64") "__aarch64__"))
754 #t))
becbbefc
TD		 755 (add-before 'configure 'patchbuild
756 (lambda _
757 (substitute*
758 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
759 (("/bin/rm") "rm")
760 (("/bin/mkdir") "mkdir"))
761 (substitute* (find-files "." "^Makefile\\.in$")
762 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
763-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
764 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
765-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
953a12fa 766-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
e464b455
TD		 767 #t))
768 (add-after 'configure 'patch-settings
769 (lambda _
770 ;; libhdf4.settings contains the full path of the
771 ;; compilers used, and its contents are included in
772 ;; .so-files. We truncate the hashes to avoid
773 ;; unnecessary store references to those compilers:
774 (substitute* "libhdf4.settings"
775 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
776 (string-append prefix (string-take hash 10) "...")))
777 #t))
778 )))
becbbefc
TD		 779 (home-page "https://www.hdfgroup.org/products/hdf4/")
780 (synopsis
781 "Library and multi-object file format for storing and managing data")
782 (description "HDF4 is a library and multi-object file format for storing
783and managing data between machines. HDF4 is an older hierarchical data format,
784incompatible with HDF5.")
785 (license
786 (license:non-copyleft
787 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
788
789(define-public hdf4-alt
790 (package
791 (inherit hdf4)
792 (name "hdf4-alt")
793 (arguments
794 (substitute-keyword-arguments (package-arguments hdf4)
795 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
796 (synopsis
797 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
798
7ee3f1a2
JD		 799(define-public hdf5
800 (package
801 (name "hdf5")
7b84610e 802 (version "1.8.21")
7ee3f1a2
JD		 803 (source
804 (origin
805 (method url-fetch)
2da63064
TD		 806 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
807 "hdf5-" (version-major+minor version)
808 "/hdf5-" version "/src/hdf5-"
dcd9d163
LF		 809 version ".tar.bz2")
810 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
811 "current"
7b84610e
EB		 812 (match (string-split version #\.)
813 ((major minor _ ...)
814 (string-append major minor)))
dcd9d163 815 "/src/hdf5-" version ".tar.bz2")))
7ee3f1a2 816 (sha256
7b84610e 817 (base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5"))
7fedc3fd
EB		 818 (patches (search-patches "hdf5-config-date.patch"
819 "hdf5-1.8-mpi-deprecations.patch"))))
7ee3f1a2 820 (build-system gnu-build-system)
12ed1216
AE		 821 (inputs
822 `(("zlib" ,zlib)))
e3a1a1de 823 (native-inputs
3ea420f3
LC		 824 `(("gfortran" ,gfortran)
825 ("perl" ,perl))) ;part of the test machinery needs Perl
e3a1a1de
TD		 826 (outputs '("out" ; core library
827 "fortran")) ; fortran interface
7ee3f1a2 828 (arguments
62126576 829 `(;; Some of the users, notably Flann, need the C++ interface.
e3a1a1de
TD		 830 #:configure-flags '("--enable-cxx"
831 "--enable-fortran"
549d1571
LC		 832 "--enable-fortran2003"
833
834 ;; Build a thread-safe library. Unfortunately,
835 ;; 'configure' invites you to either turn off C++,
836 ;; Fortran, and the high-level interface (HL), or
837 ;; to pass '--enable-unsupported'. Debian
838 ;; packagers chose to pass '--enable-unsupported'
839 ;; and we follow their lead here.
840 "--enable-threadsafe"
841 "--with-pthread"
842 "--enable-unsupported")
4dba441c
RW		 843 ;; Use -fPIC to allow the R bindings to link with the static libraries
844 #:make-flags (list "CFLAGS=-fPIC"
845 "CXXFLAGS=-fPIC")
62126576 846 #:phases
f622e212
EB		 847 (modify-phases %standard-phases
848 (add-before 'configure 'patch-configure
e3a1a1de 849 (lambda* (#:key outputs #:allow-other-keys)
f622e212 850 (substitute* "configure"
b8d9c93b 851 (("/bin/mv") "mv"))
e3a1a1de
TD		 852 (substitute* "fortran/src/Makefile.in"
853 (("libhdf5_fortran_la_LDFLAGS =")
854 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
855 (assoc-ref outputs "fortran") "/lib")))
856 (substitute* "hl/fortran/src/Makefile.in"
857 (("libhdf5hl_fortran_la_LDFLAGS =")
858 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
859 (assoc-ref outputs "fortran") "/lib")))
b8d9c93b 860 #t))
fd0378a1
TD		 861 (add-after 'configure 'patch-settings
862 (lambda _
863 ;; libhdf5.settings contains the full path of the
864 ;; compilers used, and its contents are included in
865 ;; libhdf5.so. We truncate the hashes to avoid
866 ;; unnecessary store references to those compilers:
867 (substitute* "src/libhdf5.settings"
868 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
d8f46d52
RW		 869 (string-append prefix (string-take hash 10) "..."))
870 ;; Don't record the build-time kernel version to make the
871 ;; settings file reproducible.
872 (("Uname information:.*")
873 "Uname information: Linux\n"))
b8d9c93b 874 #t))
f622e212
EB		 875 (add-after 'install 'patch-references
876 (lambda* (#:key inputs outputs #:allow-other-keys)
877 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
878 (zlib (assoc-ref inputs "zlib")))
879 (substitute* (find-files bin "h5p?cc")
880 (("-lz" lib)
881 (string-append "-L" zlib "/lib " lib)))
e3a1a1de
TD		 882 #t)))
883 (add-after 'install 'split
884 (lambda* (#:key inputs outputs #:allow-other-keys)
885 ;; Move all fortran-related files
886 (let* ((out (assoc-ref outputs "out"))
887 (bin (string-append out "/bin"))
888 (lib (string-append out "/lib"))
889 (inc (string-append out "/include"))
890 (ex (string-append out "/share/hdf5_examples/fortran"))
891 (fort (assoc-ref outputs "fortran"))
892 (fbin (string-append fort "/bin"))
893 (flib (string-append fort "/lib"))
894 (finc (string-append fort "/include"))
895 (fex (string-append fort "/share/hdf5_examples/fortran")))
896 (mkdir-p fbin)
897 (mkdir-p flib)
898 (mkdir-p finc)
899 (mkdir-p fex)
b0d1e60f
PG		 900 ;; Note: When built with --enable-parallel, the 'h5fc' file
901 ;; doesn't exist, hence this condition.
902 (when (file-exists? (string-append bin "/h5fc"))
903 (rename-file (string-append bin "/h5fc")
904 (string-append fbin "/h5fc")))
e3a1a1de
TD		 905 (for-each (lambda (file)
906 (rename-file file
907 (string-append flib "/" (basename file))))
908 (find-files lib ".*fortran.*"))
909 (for-each (lambda (file)
910 (rename-file file
911 (string-append finc "/" (basename file))))
912 (find-files inc ".*mod"))
913 (for-each (lambda (file)
914 (rename-file file
915 (string-append fex "/" (basename file))))
916 (find-files ex ".*"))
917 (delete-file-recursively ex))
918 #t)))))
7ee3f1a2 919 (home-page "http://www.hdfgroup.org")
516e93f8 920 (synopsis "Management suite for extremely large and complex data")
7ee3f1a2
JD		 921 (description "HDF5 is a suite that makes possible the management of
922extremely large and complex data collections.")
d4bf49b1
EB		 923 (license (license:x11-style
924 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
7ee3f1a2 925
bb47aca5
RW		 926(define-public hdf5-1.10
927 (package (inherit hdf5)
94fea21b 928 (version "1.10.5")
bb47aca5
RW		 929 (source
930 (origin
931 (method url-fetch)
932 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
933 "hdf5-" (version-major+minor version)
934 "/hdf5-" version "/src/hdf5-"
935 version ".tar.bz2")
936 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
937 "current"
938 (apply string-append
939 (take (string-split version #\.) 2))
940 "/src/hdf5-" version ".tar.bz2")))
941 (sha256
94fea21b
LC		 942 (base32 "0i3g6v521vigzbx8wpd32ibsiiw92r65ca3qdbn0d8fj8f4fmmk8"))
943 (patches (search-patches "hdf5-config-date.patch"))))))
bb47aca5 944
2fd26d05
TD		 945(define-public hdf-java
946 (package
2a509880
RW		 947 (name "hdf-java")
948 (version "3.3.2")
949 (source
950 (origin
951 (method url-fetch)
952 (uri (string-append
953 "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
954 version "/src/CMake-hdfjava-" version ".tar.gz"))
955 (sha256
956 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
957 (modules '((guix build utils)))
958 (snippet ; Make sure we don't use the bundled sources and binaries.
959 `(begin
960 (for-each delete-file
961 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
962 "HDF4.tar.gz" "HDF5.tar.gz"))
963 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
964 #t))))
965 (build-system gnu-build-system)
966 (native-inputs
967 `(("jdk" ,icedtea "jdk")
968 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
969 ;; For tests:
970 ("hamcrest-core" ,java-hamcrest-core)
971 ("junit" ,java-junit)
972 ("slf4j-simple" ,java-slf4j-simple)))
973 (inputs
974 `(("hdf4" ,hdf4)
975 ("hdf5" ,hdf5)
976 ("zlib" ,zlib)
977 ("libjpeg" ,libjpeg)
978 ("slf4j-api" ,java-slf4j-api)))
979 (arguments
980 `(#:configure-flags
981 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
982 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
983 (assoc-ref %build-inputs "jdk") "/lib" )
984 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
985 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
2fd26d05 986
2a509880
RW		 987 #:make-flags
988 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
989 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
990 (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
991 (string-append "JPEGLIB="
992 (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
993 "LLEXT=so")
2fd26d05 994
2a509880
RW		 995 #:phases
996 (modify-phases %standard-phases
997 (add-before 'configure 'chdir-to-source
998 (lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
999 (add-before 'configure 'patch-build
1000 (lambda* (#:key inputs outputs #:allow-other-keys)
1001 (substitute* "configure"
1002 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
1003 (("/bin/cat") (which "cat")))
1004 ;; Set classpath for compilation
1005 (substitute* '("hdf/hdf5lib/Makefile.in"
1006 "hdf/hdf5lib/exceptions/Makefile.in"
1007 "hdf/hdflib/Makefile.in")
1008 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
1009 (string-append (assoc-ref inputs "slf4j-api")
1010 "/share/java/slf4j-api.jar")))
1011 ;; Replace outdated config.sub and config.guess:
1012 (with-directory-excursion "config"
1013 (for-each (lambda (file)
1014 (install-file
1015 (string-append (assoc-ref inputs "automake")
1016 "/share/automake-"
1017 ,(version-major+minor (package-version automake))
1018 "/" file) "."))
1019 '("config.sub" "config.guess")))
64dc8b0b 1020
2a509880
RW		 1021 ;; Fix embedded version number
1022 (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
1023 (substitute* "hdf/hdf5lib/H5.java"
1024 (("1, 8, 19")
1025 (string-join hdf5version ", "))))
64dc8b0b 1026
2a509880
RW		 1027 (mkdir-p (string-append (assoc-ref outputs "out")))
1028 ;; Set classpath for tests
1029 (let* ((build-dir (getcwd))
1030 (lib (string-append build-dir "/lib"))
1031 (jhdf (string-append lib "/jhdf.jar"))
1032 (jhdf5 (string-append lib "/jhdf5.jar"))
1033 (testjars
1034 (map (lambda (i)
1035 (string-append (assoc-ref inputs i)
1036 "/share/java/" i ".jar"))
1037 '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
1038 (class-path
1039 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
2fd26d05 1040
2a509880
RW		 1041 (substitute* '("test/hdf5lib/Makefile.in"
1042 "test/hdf5lib/junit.sh.in"
1043 "examples/runExample.sh.in")
1044 (("/usr/bin/test")
1045 (string-append (assoc-ref inputs "coreutils")
1046 "/bin/test"))
1047 (("/usr/bin/uname")
1048 (string-append (assoc-ref inputs "coreutils")
1049 "/bin/uname"))
1050 (("CLASSPATH=[^\n]*")
1051 (string-append "CLASSPATH=" class-path)))
1052 (setenv "CLASSPATH" class-path))
1053 #t))
1054 (add-before 'check 'build-examples
1055 (lambda _
1056 (apply invoke `("javac"
1057 ,@(find-files "examples" ".*\\.java"))))))
2fd26d05 1058
2a509880 1059 #:parallel-build? #f
2fd26d05 1060
2a509880
RW		 1061 #:parallel-tests? #f ))
1062 (home-page "https://support.hdfgroup.org/products/java")
1063 (synopsis "Java interface for the HDF4 and HDF5 libraries")
1064 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
2fd26d05
TD		 1065the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
1066implemented in C.")
1067
2a509880
RW		 1068 ;; BSD-style license:
1069 (license (license:x11-style
1070 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
2fd26d05
TD		 1071/current/src/unpacked/COPYING"))))
1072
d3c4f3bb
TD		 1073(define-public hdf-eos2
1074 (package
1075 (name "hdf-eos2")
1076 (version "19.1.0")
1077 (source
1078 (origin
1079 (method url-fetch)
1080 (uri "ftp://edhs1.gsfc.nasa.gov\
1081/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
1082 (sha256
1083 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
1084 (patches (search-patches "hdf-eos2-remove-gctp.patch"
1085 "hdf-eos2-build-shared.patch"
1086 "hdf-eos2-fortrantests.patch"))))
1087 (build-system gnu-build-system)
1088 (native-inputs
1089 `(("gfortran" ,gfortran)))
1090 (inputs
1091 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
25bdbb61 1092 ;; XXX: These inputs are really dependencies of hdf4.
d3c4f3bb
TD		 1093 ("zlib" ,zlib)
1094 ("libjpeg" ,libjpeg)
25bdbb61
MB		 1095 ("libtirpc" ,libtirpc)
1096
d3c4f3bb
TD		 1097 ("gctp" ,gctp)))
1098 (arguments
1099 `( #:configure-flags '("--enable-install-include" "--enable-shared"
1100 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
1101 #:parallel-tests? #f))
1102 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
1103 (synopsis "HDF4-based data format for NASA's Earth Observing System")
1104 (description "HDF-EOS2 is a software library built on HDF4 which supports
1105the construction of data structures used in NASA's Earth Observing
1106System (Grid, Point and Swath).")
1107
1108 ;; Source files carry a permissive license header.
1109 (license (license:non-copyleft home-page))))
1110
0f43f835
TD		 1111(define-public hdf-eos5
1112 (package
1113 (name "hdf-eos5")
1114 (version "1.15")
1115 (source (origin
1116 (method url-fetch)
1117 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1118/edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1119 (sha256
1120 (base32
1121 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1122 (patches (search-patches "hdf-eos5-build-shared.patch"
1123 "hdf-eos5-remove-gctp.patch"
1124 "hdf-eos5-fix-szip.patch"
1125 "hdf-eos5-fortrantests.patch"))))
1126 (native-inputs
1127 `(("gfortran" ,gfortran)))
1128 (build-system gnu-build-system)
1129 (inputs
1130 `(("hdf5" ,hdf5)
1131 ("zlib" ,zlib)
1132 ("gctp" ,gctp)))
1133 (arguments
1134 `(#:configure-flags '("--enable-install-include" "--enable-shared"
1135 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1136 #:parallel-tests? #f))
1137 (synopsis "HDF5-based data format for NASA's Earth Observing System")
1138 (description
1139 "HDF-EOS5 is a software library built on HDF5 to support the construction
1140of data structures used in NASA's Earth Observing System (Grid, Point and
1141Swath).")
1142 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1143
1144 ;; Source files carry a permissive license header.
1145 (license (license:non-copyleft home-page))))
1146
c8378eea
EB		 1147(define-public hdf5-parallel-openmpi
1148 (package (inherit hdf5)
1149 (name "hdf5-parallel-openmpi")
1150 (inputs
1151 `(("mpi" ,openmpi)
1152 ,@(package-inputs hdf5)))
1153 (arguments
45201bf2
PG		 1154 (substitute-keyword-arguments (package-arguments hdf5)
1155 ((#:configure-flags flags)
549d1571
LC		 1156 ``("--enable-parallel"
1157 ,@(delete "--enable-cxx"
1158 (delete "--enable-threadsafe" ,flags))))
c8378eea
EB		 1159 ((#:phases phases)
1160 `(modify-phases ,phases
45201bf2
PG		 1161 (add-after 'build 'mpi-setup
1162 ,%openmpi-setup)
c8378eea
EB		 1163 (add-before 'check 'patch-tests
1164 (lambda _
1165 ;; OpenMPI's mpirun will exit with non-zero status if it
1166 ;; detects an "abnormal termination", i.e. any process not
784c3da1 1167 ;; calling MPI_Finalize(). Since the test is explicitly
c8378eea
EB		 1168 ;; avoiding MPI_Finalize so as not to have at_exit and thus
1169 ;; H5C_flush_cache from being called, mpirun will always
1170 ;; complain, so turn this test off.
1171 (substitute* "testpar/Makefile"
1172 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1173 (string-append front back "\n")))
1174 (substitute* "tools/h5diff/testph5diff.sh"
1175 (("/bin/sh") (which "sh")))
1176 #t))))))
1177 (synopsis "Management suite for data with parallel IO support")))
1178
00775104
EB		 1179(define-public h5check
1180 (package
1181 (name "h5check")
1182 (version "2.0.1")
1183 (source
1184 (origin
1185 (method url-fetch)
1186 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
1187 "h5check/src/h5check-" version ".tar.gz"))
1188 (sha256
1189 (base32
1190 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1191 (build-system gnu-build-system)
1192 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
1193 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1194 (synopsis "HDF5 format checker")
1195 (description "@code{h5check} is a validation tool for verifying that an
1196HDF5 file is encoded according to the HDF File Format Specification.")
1197 (license (license:x11-style "file://COPYING"))))
1198
a53d6719
JD		 1199(define-public itpp
1200 (package
1201 (name "itpp")
1202 (version "4.3.1")
1203 (source (origin
1204 (method url-fetch)
1205 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1206 version "/itpp-"
1207 version ".tar.gz"))
1208 (sha256
1209 (base32
1210 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1211 (build-system cmake-build-system)
1212 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1213 (inputs `(("lapack" ,lapack)
1214 ("fftw" ,fftw)))
3a4d5df2
RW		 1215 ;; FIXME: Even though the fonts are available dvips complains:
1216 ;; "Font cmmi10 not found; characters will be left blank."
1217 (native-inputs
1218 `(("texlive" ,texlive-tiny)
1219 ("ghostscript" ,ghostscript)
1220 ("doxygen" ,doxygen)))
a53d6719
JD		 1221 (home-page "http://itpp.sourceforge.net")
1222 (synopsis "C++ library of maths, signal processing and communication classes")
1223 (description "IT++ is a C++ library of mathematical, signal processing and
1224communication classes and functions. Its main use is in simulation of
1225communication systems and for performing research in the area of
1226communications. The kernel of the library consists of generic vector and
1227matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1228similar to MATLAB, GNU Octave or SciPy.")
1229 (license license:gpl3+)))
1230
889187a4
EB		 1231(define-public netcdf
1232 (package
1233 (name "netcdf")
a4b0bfb1 1234 (version "4.4.1.1")
889187a4
EB		 1235 (source
1236 (origin
1237 (method url-fetch)
1238 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1239 "netcdf-" version ".tar.gz"))
1240 (sha256
1241 (base32
a4b0bfb1
EB		 1242 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1243 (patches (search-patches "netcdf-date-time.patch"
1244 "netcdf-tst_h_par.patch"))))
889187a4
EB		 1245 (build-system gnu-build-system)
1246 (native-inputs
1247 `(("m4" ,m4)
1248 ("doxygen" ,doxygen)
1249 ("graphviz" ,graphviz)))
1250 (inputs
db825570
TD		 1251 `(("hdf4" ,hdf4-alt)
1252 ("hdf5" ,hdf5)
1253 ("zlib" ,zlib)
1254 ("libjpeg" ,libjpeg)))
889187a4 1255 (arguments
db825570 1256 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
43d01672
TD		 1257
1258 #:phases (modify-phases %standard-phases
1259 (add-before 'configure 'fix-source-date
1260 (lambda _
1261 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1262 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1263 ;; to '1st hour of the current day', and therefore makes the
1264 ;; package not reproducible.
1265 (substitute* "./configure"
1266 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1267 "date --date='@0'"))
1268 #t))
1269 (add-after 'configure 'patch-settings
1270 (lambda _
1271 ;; libnetcdf.settings contains the full filename of the compilers
1272 ;; used to build the library. We truncate the hashes of those
1273 ;; filenames to avoid unnecessary references to the corresponding
1274 ;; store items.
1275 (substitute* "libnetcdf.settings"
1276 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1277 (string-append prefix (string-take hash 10) "...")))
1278 #t)))
1279
889187a4
EB		 1280 #:parallel-tests? #f)) ;various race conditions
1281 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
1282 (synopsis "Library for scientific data")
1283 (description "NetCDF is an interface for scientific data access and a
1284software library that provides an implementation of the interface. The netCDF
1285library defines a machine-independent format for representing scientific data.
1286Together, the interface, library, and format support the creation, access, and
1287sharing of scientific data.")
1288 (license (license:x11-style "file://COPYRIGHT"))))
1289
1290(define-public netcdf-parallel-openmpi
1291 (package (inherit netcdf)
1292 (name "netcdf-parallel-openmpi")
1293 (inputs
1294 `(("mpi" ,openmpi)
1295 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1296 (package-inputs netcdf))))
1297 ;; TODO: Replace pkg-config references in nc-config with absolute references
1298 (arguments
1299 (substitute-keyword-arguments (package-arguments netcdf)
1300 ((#:configure-flags flags)
1301 `(cons* "CC=mpicc" "CXX=mpicxx"
1302 "--enable-parallel-tests"
1303 ;; Shared libraries not supported with parallel IO.
1304 "--disable-shared" "--with-pic"
1305 ,flags))))))
1306
300200b6
TD		 1307(define-public netcdf-fortran
1308 (package
1309 (name "netcdf-fortran")
1310 (version "4.4.4")
1311 (source (origin
1312 (method url-fetch)
1313 (uri (string-append
1314 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1315 version ".tar.gz"))
1316 (sha256
1317 (base32
1318 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1319 (build-system gnu-build-system)
1320 (arguments
1321 `(#:parallel-tests? #f))
1322 (inputs
1323 `(("netcdf" ,netcdf)))
1324 (native-inputs
1325 `(("gfortran" ,gfortran)))
1326 (synopsis "Fortran interface for the netCDF library")
1327 (description (package-description netcdf))
1328 (home-page (package-home-page netcdf))
1329 (license (package-license netcdf))))
1330
1b39a196
RJ		 1331(define-public nlopt
1332 (package
1333 (name "nlopt")
1334 (version "2.4.2")
1335 (source (origin
1336 (method url-fetch)
1337 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1338 version ".tar.gz"))
1339 (sha256
1340 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1341 (build-system gnu-build-system)
1342 (arguments
1343 `(;; Shared libraries are not built by default. They are required to
1344 ;; build the Guile, Octave, and Python bindings.
1345 #:configure-flags '("--enable-shared")
1346
1347 #:phases
1348 (modify-phases %standard-phases
1349 (add-before 'configure 'set-libnlopt-file-name
1350 (lambda* (#:key outputs #:allow-other-keys)
1351 ;; Make sure the Scheme module refers to the library by its
1352 ;; absolute file name (we cannot do that from a snippet
1353 ;; because the expansion of @libdir@ contains
1354 ;; ${exec_prefix}.)
1355 (let ((out (assoc-ref outputs "out")))
1356 (substitute* "swig/nlopt.scm.in"
1357 (("libnlopt")
1358 (string-append out "/lib/libnlopt")))
1359 #t))))))
1360 (inputs `(("guile" ,guile-2.0)))
1361 (native-inputs `(("pkg-config" ,pkg-config)))
1362 (home-page "http://ab-initio.mit.edu/wiki/")
1363 (synopsis "Library for nonlinear optimization")
1364 (description "NLopt is a library for nonlinear optimization, providing a
1365common interface for a number of different free optimization routines available
1366online as well as original implementations of various other algorithms.")
1367 (license license:lgpl2.1+)))
1368
005c787d
LC		 1369(define-public ipopt
1370 (package
1371 (name "ipopt")
98a5cd51 1372 (version "3.12.12")
005c787d
LC		 1373 (source (origin
1374 (method url-fetch)
1375 (uri (string-append
1376 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1377 version".tgz"))
1378 (sha256
1379 (base32
98a5cd51 1380 "07yn9rzdswjk8n246qq6ci9ssf2bcplkifcpsfz9j6cdxw9vgbkv"))
005c787d
LC		 1381 (modules '((guix build utils)))
1382 (snippet
1383 ;; Make sure we don't use the bundled software.
6cbee49d
MW		 1384 '(begin
1385 (delete-file-recursively "ThirdParty")
1386 #t))))
005c787d 1387 (build-system gnu-build-system)
ad1c4537
LC		 1388 (arguments
1389 '(#:phases (modify-phases %standard-phases
1390 (add-after 'install 'add--L-flags-in-ipopt.pc
1391 (lambda* (#:key inputs outputs #:allow-other-keys)
1392 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1393 ;; move it to "Libs.private" where it belongs, and add a
1394 ;; '-L' flag for LAPACK.
1395 (let ((out (assoc-ref outputs "out"))
1396 (lapack (assoc-ref inputs "lapack")))
1397 (substitute* (string-append out "/lib/pkgconfig/"
1398 "ipopt.pc")
1399 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1400 (string-append "Libs: " before " " after "\n"
1401 "Libs.private: " before
1402 "-L" lapack "/lib -llapack -lblas "
1403 after "\n")))
1404 #t))))))
005c787d
LC		 1405 (native-inputs
1406 `(("gfortran" ,gfortran)))
1407 (inputs
1408 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
ad1c4537 1409 `(("lapack" ,lapack))) ;for both libblas and liblapack
005c787d
LC		 1410 (home-page "http://www.coin-or.org")
1411 (synopsis "Large-scale nonlinear optimizer")
1412 (description
1413 "The Interior Point Optimizer (IPOPT) is a software package for
1414large-scale nonlinear optimization. It provides C++, C, and Fortran
1415interfaces.")
1416 (license license:epl1.0)))
1417
ecfbc51f
RW		 1418(define-public clp
1419 (package
1420 (name "clp")
1421 (version "1.17.1")
1422 (source (origin
1423 (method url-fetch)
1424 (uri (string-append "https://www.coin-or.org/download/source/"
1425 "Clp/Clp-" version ".tgz"))
1426 (sha256
1427 (base32
1428 "1wdg820g3iikf9344ijwsc8sy6c0m6im42bzzizm6rlmkvnmxhk9"))
1429 (modules '((guix build utils)))
1430 (snippet
1431 ;; Make sure we don't use the bundled software.
1432 '(begin
1433 (delete-file-recursively "ThirdParty")
1434 #t))))
1435 (build-system gnu-build-system)
1436 (native-inputs
1437 `(("gfortran" ,gfortran)
1438 ("pkg-config" ,pkg-config)))
1439 (inputs
1440 `(("openblas" ,openblas)))
1441 (home-page "https://www.coin-or.org")
1442 (synopsis "Linear programming solver")
1443 (description
1444 "CLP is a high quality linear programming solver. Its main strengths are
1445its dual and primal Simplex algorithms. It also has a barrier algorithm for
1446linear and quadratic objectives. There are limited facilities for nonlinear
1447and quadratic objectives using the Simplex algorithm.")
1448 (license license:epl1.0)))
1449
f9940ef1
LC		 1450(define-public ceres
1451 (package
1452 (name "ceres-solver")
e0bee0de 1453 (version "1.14.0")
f9940ef1
LC		 1454 (home-page "http://ceres-solver.org/")
1455 (source (origin
1456 (method url-fetch)
1457 (uri (string-append home-page "ceres-solver-"
1458 version ".tar.gz"))
1459 (sha256
1460 (base32
e0bee0de 1461 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
f9940ef1
LC		 1462 (build-system cmake-build-system)
1463 (arguments
1464 ;; TODO: Build HTML user documentation and install separately.
bc3a2e35 1465 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
f9940ef1
LC		 1466 "-DBUILD_SHARED_LIBS=ON")
1467
1468 #:phases (modify-phases %standard-phases
1469 (add-before 'configure 'set-library-directory
1470 (lambda _
1471 ;; Install libraries to lib/, not lib64/.
1472 (substitute* "internal/ceres/CMakeLists.txt"
1473 (("set\\(LIB_SUFFIX \"64\"\\)")
1474 "set(LIB_SUFFIX \"\")"))
1475 #t)))))
1476 (native-inputs
1477 `(("pkg-config" ,pkg-config)))
468e0b18
LC		 1478 (propagated-inputs
1479 `(("glog" ,glog))) ;for #include <glog/glog.h>
f9940ef1
LC		 1480 (inputs
1481 `(("eigen" ,eigen)
1482 ("blas" ,openblas)
1483 ("lapack" ,lapack)
1484 ("suitesparse" ,suitesparse)
1485 ("gflags" ,gflags)))
1486 (synopsis "C++ library for solving large optimization problems")
1487 (description
1488 "Ceres Solver is a C++ library for modeling and solving large,
1489complicated optimization problems. It is a feature rich, mature and
1490performant library which has been used in production since 2010. Ceres Solver
1491can solve two kinds of problems:
1492@enumerate
1493@item non-linear least squares problems with bounds constraints;
1494@item general unconstrained optimization problems.
1495@end enumerate\n")
1496 (license license:bsd-3)))
1497
b66741ed 1498;; For a fully featured Octave, users are strongly recommended also to install
5ca4fe96 1499;; the following packages: less, ghostscript, gnuplot.
5537603f 1500(define-public octave-cli
668c06ac 1501 (package
5537603f 1502 (name "octave-cli")
5b8f8928 1503 (version "5.1.0")
668c06ac
JD		 1504 (source
1505 (origin
1506 (method url-fetch)
1507 (uri (string-append "mirror://gnu/octave/octave-"
f5a077b1 1508 version ".tar.lz"))
668c06ac
JD		 1509 (sha256
1510 (base32
5b8f8928 1511 "11wwxpy2q1bhxs2v41bqn05i2sb0905cj1xil6mg8l4k2kka4cq6"))))
668c06ac
JD		 1512 (build-system gnu-build-system)
1513 (inputs
697df13f
EF		 1514 `(("alsa-lib" ,alsa-lib)
1515 ("arpack" ,arpack-ng)
1516 ("curl" ,curl)
1ec78e9d
EB		 1517 ("fftw" ,fftw)
1518 ("fftwf" ,fftwf)
668c06ac
JD		 1519 ("fltk" ,fltk)
1520 ("fontconfig" ,fontconfig)
1521 ("freetype" ,freetype)
697df13f
EF		 1522 ("gl2ps" ,gl2ps)
1523 ("glpk" ,glpk)
1ec78e9d 1524 ("glu" ,glu)
ab5f3f21 1525 ("graphicsmagick" ,graphicsmagick)
697df13f
EF		 1526 ("hdf5" ,hdf5)
1527 ("lapack" ,lapack)
ab5f3f21 1528 ("libsndfile" ,libsndfile)
697df13f
EF		 1529 ("libxft" ,libxft)
1530 ("mesa" ,mesa)
1531 ("pcre" ,pcre)
ab5f3f21 1532 ("portaudio" ,portaudio)
697df13f
EF		 1533 ("qhull" ,qhull)
1534 ("readline" ,readline)
1535 ("suitesparse" ,suitesparse)
1536 ("texinfo" ,texinfo)
1537 ("zlib" ,zlib)))
668c06ac 1538 (native-inputs
f5a077b1
EF		 1539 `(("lzip" ,lzip)
1540 ("gfortran" ,gfortran)
668c06ac
JD		 1541 ("pkg-config" ,pkg-config)
1542 ("perl" ,perl)
1ec78e9d
EB		 1543 ;; The following inputs are not actually used in the build process.
1544 ;; However, the ./configure gratuitously tests for their existence and
1545 ;; assumes that programs not present at build time are also not, and
1546 ;; can never be, available at run time! If these inputs are therefore
1547 ;; not present, support for them will be built out. However, Octave
1548 ;; will still run without them, albeit without the features they
668c06ac
JD		 1549 ;; provide.
1550 ("less" ,less)
668c06ac
JD		 1551 ("ghostscript" ,ghostscript)
1552 ("gnuplot" ,gnuplot)))
116af86f
KK		 1553 ;; Octave code uses this variable to detect directories holding multiple CA
1554 ;; certificates to verify peers with. This is required for the networking
1555 ;; functions that require encryption to work properly.
1556 (native-search-paths
1557 (list (search-path-specification
1558 (variable "CURLOPT_CAPATH")
1559 (files '("etc/ssl/certs")))))
668c06ac 1560 (arguments
b7b27a8f
KY		 1561 `(#:configure-flags
1562 (list (string-append "--with-shell="
1563 (assoc-ref %build-inputs "bash")
5ca4fe96
AI		 1564 "/bin/sh"))
1565 #:phases
1566 (modify-phases %standard-phases
1567 (add-after 'configure 'configure-makeinfo
1568 (lambda* (#:key inputs #:allow-other-keys)
b18b9d20
AI		 1569 (substitute* "libinterp/corefcn/help.h"
1570 (("\"makeinfo\"")
1571 (string-append
1572 "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
5ca4fe96 1573 #t)))))
f5a077b1 1574 (home-page "https://www.gnu.org/software/octave/")
668c06ac 1575 (synopsis "High-level language for numerical computation")
1ec78e9d
EB		 1576 (description "GNU Octave is a high-level interpreted language that is
1577specialized for numerical computations. It can be used for both linear and
1578non-linear applications and it provides great support for visualizing results.
1579Work may be performed both at the interactive command-line as well as via
1580script files.")
668c06ac 1581 (license license:gpl3+)))
3de01d3f 1582
e0ae7e73 1583(define-public octave
5537603f 1584 (package (inherit octave-cli)
e0ae7e73 1585 (name "octave")
7a3772b3 1586 (source (origin
5537603f 1587 (inherit (package-source octave-cli))))
36ce25f0
KK		 1588 (inputs
1589 `(("qscintilla" ,qscintilla)
1590 ("qt" ,qtbase)
5537603f 1591 ,@(package-inputs octave-cli)))
36ce25f0
KK		 1592 (native-inputs
1593 `(("qttools" , qttools) ;for lrelease
70bb5d88 1594 ("texlive" ,(texlive-union (list texlive-epsf))) ; for texi2dvi
5537603f 1595 ,@(package-native-inputs octave-cli)))
36ce25f0 1596 (arguments
5537603f 1597 (substitute-keyword-arguments (package-arguments octave-cli)
36ce25f0
KK		 1598 ((#:phases phases)
1599 `(modify-phases ,phases
1600 (add-before 'configure 'patch-qscintilla-library-name
1601 (lambda* (#:key inputs #:allow-other-keys)
1602 ;; The QScintilla library that the Octave configure script tries
1603 ;; to link with should be named libqscintilla-qt5.so, but the
1604 ;; QScintilla input provides the shared library as
1605 ;; libqscintilla2_qt5.so.
1606 (substitute* "configure"
1607 (("qscintilla2-qt5")
1608 "qscintilla2_qt5"))
1609 #t))))))))
1610
e0ae7e73
KK		 1611(define-public qtoctave
1612 (deprecated-package "qtoctave" octave))
1613
5d4bd4cc
PG		 1614(define-public opencascade-oce
1615 (package
1616 (name "opencascade-oce")
1617 (version "0.17.2")
1618 (source
1619 (origin
830971bf
TGR		 1620 (method git-fetch)
1621 (uri (git-reference
1622 (url "https://github.com/tpaviot/oce.git")
1623 (commit (string-append "OCE-" version))))
1624 (file-name (git-file-name name version))
a4f393b7 1625 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
5d4bd4cc 1626 (sha256
830971bf 1627 (base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69"))))
5d4bd4cc
PG		 1628 (build-system cmake-build-system)
1629 (arguments
1630 '(#:configure-flags
1631 (list "-DOCE_TESTING:BOOL=ON"
1632 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1633 "-DOCE_DRAW:BOOL=ON"
1634 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1635 (assoc-ref %outputs "out"))
1636 "-UCMAKE_INSTALL_RPATH")))
1637 (inputs
1638 `(("freetype" ,freetype)
1639 ("glu" ,glu)
1640 ("libxmu" ,libxmu)
1641 ("mesa" ,mesa)
1642 ("tcl" ,tcl)
1643 ("tk" ,tk)))
1644 (native-inputs
1645 `(("python" ,python-wrapper)))
1646 (home-page "https://github.com/tpaviot/oce")
1647 (synopsis "Libraries for 3D modeling and numerical simulation")
1648 (description
1649 "Open CASCADE is a set of libraries for the development of applications
1650dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1651C++ class libraries providing services for 3D surface and solid modeling, CAD
1652data exchange, and visualization. It is used for development of specialized
1653software dealing with 3D models in design (CAD), manufacturing (CAM),
1654numerical simulation (CAE), measurement equipment (CMM), and quality
1655control (CAQ) domains.
1656
1657This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1658patches, improvements, and experiments contributed by users over the official
1659Open CASCADE library.")
1660 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1661 ; use of header files; see
1662 ; OCCT_LGPL_EXCEPTION.txt
1663 license:public-domain; files
1664 ; src/Standard/Standard_StdAllocator.hxx and
1665 ; src/NCollection/NCollection_StdAllocator.hxx
1666 license:expat; file src/OpenGl/OpenGl_glext.h
1667 license:bsd-3)))); test framework gtest
1668
37dc2920
PG		 1669(define-public opencascade-occt
1670 (package
1671 (name "opencascade-occt")
1672 (version "7.3.0p3")
1673 (source
1674 (origin
1675 (method git-fetch)
1676 (uri (git-reference
1677 (url "https://git.dev.opencascade.org/repos/occt.git")
1678 (commit
1679 (string-append "V"
1680 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
1681 version)))))
1682 (file-name (git-file-name name version))
1683 (sha256
1684 (base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4"))
1685 (modules '((guix build utils)))
1686 (snippet
1687 '(begin
1688 ;; Remove files specific to non-free operating systems.
1689 (delete-file-recursively "samples/ios")
1690 (delete-file-recursively "samples/mfc")
1691 (delete-file-recursively "samples/qt/FuncDemo")
1692 (delete-file "genconf.bat")
1693 (delete-file "gendoc.bat")
1694 (delete-file "genproj.bat")
1695 (delete-file "upgrade.bat")
1696 ;; Remove references to deleted files.
1697 (substitute* "dox/FILES_HTML.txt"
1698 ((".*standard.*") "" )
1699 ((".*UIKitSample.*") ""))
1700 #t))))
1701 (build-system cmake-build-system)
1702 (arguments
1703 '(;; There is no test target for make. OCCT provides an
1704 ;; 'Automated Testing System', which may be accessed after
1705 ;; installation via the draw.sh script. draw.sh is located in
1706 ;; the bin directory. For details see:
1707 ;; https://www.opencascade.com/doc/occt-7.3.0/overview/html/\
1708 ;; occt_dev_guides__tests.html
1709 #:tests? #f
1710 ;; Configure without freeimage: attempting to link against the
1711 ;; freeimage version 3.17 library leads to 'undefined
1712 ;; reference' errors.
1713 #:configure-flags
1714 (list "-DUSE_FREEIMAGE:BOOL=OFF"
1715 "-DUSE_TBB:BOOL=ON"
1716 "-DUSE_VTK:BOOL=OFF"
1717 "-DBUILD_DOC_Overview:BOOL=OFF"
1718 "-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON"
1719 "-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON"
1720 "-UCMAKE_INSTALL_LIBDIR")))
1721 (inputs
1722 `(("doxygen" ,doxygen)
1723 ;("freeimage" ,freeimage)
1724 ("freetype" ,freetype)
1725 ("glu" ,glu)
1726 ("libxext" ,libxext)
1727 ("libxi" ,libxi)
1728 ("libxmu" ,libxmu)
1729 ("mesa" ,mesa)
1730 ("tbb" ,tbb)
1731 ("tcl" ,tcl)
1732 ("tk" ,tk)))
1733 ;; TODO: build Overview documentation and add 'doc' output.
1734 (home-page "https://www.opencascade.com")
1735 (synopsis "Libraries for 3D modeling and numerical simulation")
1736 (description
1737 "Open CASCADE is a set of libraries for the development of applications
1738dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1739C++ class libraries providing services for 3D surface and solid modeling, CAD
1740data exchange, and visualization. It is used for development of specialized
1741software dealing with 3D models in design (CAD), manufacturing (CAM),
1742numerical simulation (CAE), measurement equipment (CMM), and quality
1743control (CAQ) domains.
1744
1745This is the certified version of the Open Cascade Technology (OCCT) library.")
1746 (license (list ;; OCCT library:
1747 license:lgpl2.1; with an exception for the use of header
1748 ; files, see OCCT_LGPL_EXCEPTION.txt.
1749 ;; Files src/OpenGl/glext.h, adm/cmake/cotire.cmake and
1750 ;; src/OpenGl/OpenGl_HaltonSampler.hxx:
1751 license:expat
1752 ;; Files src/ExprIntrp/ExprIntrp.tab.* and
1753 ;; src/StepFile/step.tab.*:
1754 license:gpl3+ ; with Bison 2.2 exception.
1755 ;; File src/NCollection/NCollection_UtfIterator.lxx:
1756 (license:non-copyleft
1757 "https://www.unicode.org/license.html")
1758 ;; File src/NCollection/NCollection_StdAllocator.hxx:
1759 license:public-domain))))
1760
3de01d3f
EB		 1761(define-public gmsh
1762 (package
1763 (name "gmsh")
8a4d14fa 1764 (version "2.16.0")
3de01d3f
EB		 1765 (source
1766 (origin
abed5df7
PG		 1767 (method git-fetch)
1768 (uri (git-reference
1769 (url "https://gitlab.onelab.info/gmsh/gmsh.git")
1770 (commit
1771 (string-append "gmsh_"
1772 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
1773 version)))))
1774 (file-name (git-file-name name version))
3de01d3f 1775 (sha256
abed5df7 1776 (base32 "08rq4jajwmlpivnm9yifz2jhaivnz065lnk0h2zv773nwl9wf162"))
3de01d3f
EB		 1777 (modules '((guix build utils)))
1778 (snippet
1779 ;; Remove non-free METIS code
6cbee49d
MW		 1780 '(begin
1781 (delete-file-recursively "contrib/Metis")
1782 #t))))
3de01d3f 1783 (build-system cmake-build-system)
3de01d3f
EB		 1784 (propagated-inputs
1785 `(("fltk" ,fltk)
19afbea1 1786 ("gfortran" ,gfortran)
3de01d3f 1787 ("gmp" ,gmp)
40029cbe 1788 ("hdf5" ,hdf5)
3de01d3f
EB		 1789 ("lapack" ,lapack)
1790 ("mesa" ,mesa)
85f41902 1791 ("glu" ,glu)
45548139 1792 ("opencascade-oce" ,opencascade-oce)
3de01d3f
EB		 1793 ("libx11" ,libx11)
1794 ("libxext" ,libxext)))
66395a61
EF		 1795 (inputs
1796 `(("fontconfig" ,fontconfig)
1797 ("libxft" ,libxft)))
3de01d3f
EB		 1798 (arguments
1799 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1800 "-DENABLE_BUILD_SHARED:BOOL=ON"
45548139 1801 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
0746c33e 1802 (home-page "http://gmsh.info/")
3de01d3f 1803 (synopsis "3D finite element grid generator")
edf684ef
EB		 1804 (description "Gmsh is a 3D finite element grid generator with a built-in
1805CAD engine and post-processor. Its design goal is to provide a fast, light
1806and user-friendly meshing tool with parametric input and advanced
1807visualization capabilities. Gmsh is built around four modules: geometry,
1808mesh, solver and post-processing. The specification of any input to these
1809modules is done either interactively using the graphical user interface or in
1810ASCII text files using Gmsh's own scripting language.")
3de01d3f 1811 (license license:gpl2+)))
b9100e2f 1812
6d5f63b6
JD		 1813(define-public maxflow
1814 (package
1815 (name "maxflow")
0af12a13
TGR		 1816 ;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’,
1817 ;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’.
1818 (version "3.0.5")
6d5f63b6
JD		 1819 (source (origin
1820 (method git-fetch)
1821 (uri (git-reference
1822 (url "https://github.com/gerddie/maxflow.git")
0af12a13 1823 (commit version)))
2dc0a6cf 1824 (file-name (git-file-name name version))
6d5f63b6
JD		 1825 (sha256
1826 (base32
1827 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1828 (build-system cmake-build-system)
0be9038c 1829 (home-page "https://pub.ist.ac.at/~vnk/software.html")
6d5f63b6
JD		 1830 (synopsis "Library implementing Maxflow algorithm")
1831 (description "An implementation of the maxflow algorithm described in
1832@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1833Energy Minimization in Computer Vision.\n
1834Yuri Boykov and Vladimir Kolmogorov.\n
1835In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1836September 2004}")
1837 (license license:gpl3+)))
1838
b9100e2f
EB		 1839(define-public petsc
1840 (package
1841 (name "petsc")
4f7a4a06 1842 (version "3.11.2")
b9100e2f
EB		 1843 (source
1844 (origin
1845 (method url-fetch)
1846 ;; The *-lite-* tarball does not contain the *large* documentation
1847 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1848 "petsc-lite-" version ".tar.gz"))
1849 (sha256
4f7a4a06 1850 (base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx"))))
b2c52fc9
TGR		 1851 (outputs '("out" ; libraries and headers
1852 "examples")) ; ~30MiB of examples
b9100e2f
EB		 1853 (build-system gnu-build-system)
1854 (native-inputs
6fec298d 1855 `(("python" ,python-2)))
b9100e2f 1856 (inputs
19afbea1 1857 `(("gfortran" ,gfortran)
b9100e2f 1858 ("lapack" ,lapack)
f258212d 1859 ("superlu" ,superlu)
b9100e2f
EB		 1860 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1861 ;; leaving out opengl, as configuration seems to only be for mac
1862 ))
1863 (arguments
1864 `(#:test-target "test"
b2c52fc9 1865 #:parallel-build? #f ; build is parallel by default
b9100e2f
EB		 1866 #:configure-flags
1867 `("--with-mpi=0"
f258212d 1868 "--with-openmp=1"
c15be128 1869 "--with-superlu=1")
9731c412
EB		 1870 #:make-flags
1871 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1872 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1873 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
b9100e2f 1874 #:phases
64dcc289
EB		 1875 (modify-phases %standard-phases
1876 (replace 'configure
1877 ;; PETSc's configure script is actually a python script, so we can't
1878 ;; run it with bash.
1879 (lambda* (#:key outputs (configure-flags '())
1880 #:allow-other-keys)
1881 (let* ((prefix (assoc-ref outputs "out"))
1882 (flags `(,(string-append "--prefix=" prefix)
1883 ,@configure-flags)))
1884 (format #t "build directory: ~s~%" (getcwd))
1885 (format #t "configure flags: ~s~%" flags)
49fdd357 1886 (apply invoke "./configure" flags))))
64dcc289 1887 (add-after 'configure 'clean-local-references
9731c412 1888 (lambda* (#:key outputs #:allow-other-keys)
64dcc289
EB		 1889 (let ((out (assoc-ref outputs "out")))
1890 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
b730b437
EB		 1891 ;; Prevent build directory from leaking into compiled code
1892 (((getcwd)) out)
1893 ;; Scrub timestamp for reproducibility
fafd623e 1894 ((".*Libraries compiled on.*") ""))
9731c412
EB		 1895 (substitute* (find-files "." "petscvariables")
1896 ;; Do not expose build machine characteristics, set to defaults.
1897 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1898 (("NPMAX = [:digit:]+") "NPMAX = 2"))
fafd623e 1899 #t)))
64dcc289 1900 (add-after 'install 'clean-install
10b11968
EB		 1901 ;; Try to keep installed files from leaking build directory names.
1902 (lambda* (#:key inputs outputs #:allow-other-keys)
64dcc289 1903 (let ((out (assoc-ref outputs "out")))
10b11968 1904 (substitute* (map (lambda (file)
9a899cce 1905 (string-append out "/lib/petsc/conf/" file))
fafd623e 1906 '("petscvariables"))
10b11968
EB		 1907 (((getcwd)) out))
1908 ;; Make compiler references point to the store
9a899cce 1909 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
dfdf5716
EB		 1910 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1911 (string-append "= " (which compiler))))
10b11968
EB		 1912 ;; PETSc installs some build logs, which aren't necessary.
1913 (for-each (lambda (file)
9a899cce 1914 (let ((f (string-append out "/lib/petsc/conf/" file)))
10b11968
EB		 1915 (when (file-exists? f)
1916 (delete-file f))))
9a899cce
EB		 1917 '("configure.log" "make.log" "gmake.log"
1918 "test.log" "error.log" "RDict.db"
fafd623e 1919 "PETScBuildInternal.cmake"
10b11968 1920 ;; Once installed, should uninstall with Guix
fafd623e 1921 "uninstall.py"))
a3a99e27
EB		 1922 #t)))
1923 (add-after 'install 'move-examples
1924 (lambda* (#:key outputs #:allow-other-keys)
1925 (let* ((out (assoc-ref outputs "out"))
1926 (examples (assoc-ref outputs "examples"))
1927 (exdir (string-append out "/share/petsc/examples"))
1928 (exdir' (string-append examples "/share/petsc/examples")))
1929 (copy-recursively exdir exdir')
1930 (delete-file-recursively exdir)
fafd623e 1931 #t))))))
b9100e2f 1932 (home-page "http://www.mcs.anl.gov/petsc")
16ecf3ff 1933 (synopsis "Library to solve PDEs")
b9100e2f
EB		 1934 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1935data structures and routines for the scalable (parallel) solution of
1936scientific applications modeled by partial differential equations.")
166191b3 1937 (license (license:non-copyleft
b9100e2f
EB		 1938 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1939
1940(define-public petsc-complex
1941 (package (inherit petsc)
1942 (name "petsc-complex")
1943 (arguments
1944 (substitute-keyword-arguments (package-arguments petsc)
1945 ((#:configure-flags cf)
1946 `(cons "--with-scalar-type=complex" ,cf))))
16ecf3ff 1947 (synopsis "Library to solve PDEs (with complex scalars)")))
183e44ae 1948
d8c7eeb9
EB		 1949(define-public petsc-openmpi
1950 (package (inherit petsc)
1951 (name "petsc-openmpi")
1952 (inputs
9e2aa70b 1953 `(("hdf5" ,hdf5-parallel-openmpi)
af523673 1954 ("hypre" ,hypre-openmpi)
9e2aa70b
PG		 1955 ("metis" ,metis)
1956 ("mumps" ,mumps-openmpi)
1957 ("openmpi" ,openmpi)
1958 ("scalapack" ,scalapack)
72f95783 1959 ("scotch" ,pt-scotch32)
d8c7eeb9
EB		 1960 ,@(package-inputs petsc)))
1961 (arguments
1962 (substitute-keyword-arguments (package-arguments petsc)
1963 ((#:configure-flags cf)
af523673
PG		 1964 ``("--with-hypre=1"
1965 "--with-mpiexec=mpirun"
9e2aa70b
PG		 1966 "--with-metis=1"
1967 "--with-mumps=1"
1968 "--with-scalapack=1"
1969 "--with-ptscotch=1"
d8c7eeb9
EB		 1970 ,(string-append "--with-mpi-dir="
1971 (assoc-ref %build-inputs "openmpi"))
71ca16b5
PG		 1972 ,(string-append "--with-hdf5-include="
1973 (assoc-ref %build-inputs "hdf5") "/include")
1974 ,(string-append "--with-hdf5-lib="
1975 (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
1976 ,@(delete "--with-mpi=0" ,cf)))
1977 ((#:phases phases)
1978 `(modify-phases ,phases
9e2aa70b 1979 (add-before 'configure 'mpi-setup
bbe46a4a 1980 ,%openmpi-setup)))))
9e2aa70b 1981 (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
d8c7eeb9
EB		 1982
1983(define-public petsc-complex-openmpi
1984 (package (inherit petsc-complex)
1985 (name "petsc-complex-openmpi")
1986 (inputs
1987 `(("openmpi" ,openmpi)
1988 ,@(package-inputs petsc-complex)))
1989 (arguments
1990 (substitute-keyword-arguments (package-arguments petsc-complex)
1991 ((#:configure-flags cf)
1992 ``("--with-mpiexec=mpirun"
1993 ,(string-append "--with-mpi-dir="
1994 (assoc-ref %build-inputs "openmpi"))
e586c6fa
EB		 1995 ,@(delete "--with-mpi=0" ,cf)))
1996 ((#:phases phases)
1997 `(modify-phases ,phases
1998 (add-before 'configure 'mpi-setup
1999 ,%openmpi-setup)))))
16ecf3ff 2000 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
d8c7eeb9 2001
90ff2874
PG		 2002(define-public python-petsc4py
2003 (package
2004 (name "python-petsc4py")
758439cf 2005 (version "3.10.1")
90ff2874
PG		 2006 (source
2007 (origin
2008 (method url-fetch)
2009 (uri (pypi-uri "petsc4py" version))
2010 (sha256
2011 (base32
758439cf 2012 "094hcnran0r2z1wlvmjswsz3ski1m9kqrl5l0ax8jjhnk55x0flh"))))
90ff2874
PG		 2013 (build-system python-build-system)
2014 (arguments
2015 `(#:phases
2016 (modify-phases %standard-phases
2017 (add-before 'build 'pre-build
2018 (lambda _
2019 ;; Define path to PETSc installation.
2020 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
2021 #t))
2022 (add-before 'check 'mpi-setup
2023 ,%openmpi-setup))))
2024 (inputs
2025 `(("petsc" ,petsc-openmpi)
2026 ("python-numpy" ,python-numpy)))
2027 (home-page "https://bitbucket.org/petsc/petsc4py/")
2028 (synopsis "Python bindings for PETSc")
2029 (description "PETSc, the Portable, Extensible Toolkit for
2030Scientific Computation, is a suite of data structures and routines for
2031the scalable (parallel) solution of scientific applications modeled by
2032partial differential equations. It employs the MPI standard for all
2033message-passing communication. @code{petsc4py} provides Python
2034bindings to almost all functions of PETSc.")
2035 (license license:bsd-3)))
2036
560acf25
MB		 2037(define-public python-kiwisolver
2038 (package
2039 (name "python-kiwisolver")
2040 (version "1.0.1")
2041 (source (origin
2042 (method url-fetch)
2043 (uri (pypi-uri "kiwisolver" version))
2044 (sha256
2045 (base32
2046 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
2047 (build-system python-build-system)
2048 (home-page "https://github.com/nucleic/kiwi")
2049 (synopsis "Fast implementation of the Cassowary constraint solver")
2050 (description
2051 "Kiwi is an efficient C++ implementation of the Cassowary constraint
2052solving algorithm. Kiwi has been designed from the ground up to be
2053lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
2054Cassowary solver with typical use cases gaining a 40x improvement. Memory
2055savings are consistently > 5x.")
2056 (license license:bsd-3)))
2057
2058(define-public python2-kiwisolver
2059 (package-with-python2 python-kiwisolver))
2060
a7f01414
EB		 2061(define-public slepc
2062 (package
2063 (name "slepc")
a13e0f3d 2064 (version "3.11.1")
a7f01414
EB		 2065 (source
2066 (origin
2067 (method url-fetch)
baeaf882
EB		 2068 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
2069 version ".tar.gz"))
a7f01414
EB		 2070 (sha256
2071 (base32
a13e0f3d 2072 "1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8"))))
a7f01414
EB		 2073 (build-system gnu-build-system)
2074 (native-inputs
a13e0f3d
EB		 2075 `(("python" ,python-2)
2076 ("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
a7f01414
EB		 2077 (inputs
2078 `(("arpack" ,arpack-ng)
2079 ("gfortran" ,gfortran)))
2080 (propagated-inputs
2081 `(("petsc" ,petsc)))
2082 (arguments
2083 `(#:parallel-build? #f ;build is parallel by default
2084 #:configure-flags
2085 `(,(string-append "--with-arpack-dir="
9cf52454 2086 (assoc-ref %build-inputs "arpack") "/lib"))
9731c412 2087 #:make-flags ;honor (parallel-job-count)
a13e0f3d
EB		 2088 `(,(format #f "MAKE_NP=~a" (parallel-job-count))
2089 ,(string-append "PETSCCONFIGDIR="
2090 (assoc-ref %build-inputs "petsc:examples")
2091 "/share/petsc/examples/config"))
a7f01414
EB		 2092 #:phases
2093 (modify-phases %standard-phases
8787c555 2094 (replace 'configure
a7f01414
EB		 2095 ;; configure is a python script, so we can't run it with bash.
2096 (lambda* (#:key inputs outputs (configure-flags '())
2097 #:allow-other-keys)
2098 (let* ((prefix (assoc-ref outputs "out"))
2099 (flags `(,(string-append "--prefix=" prefix)
2100 ,@configure-flags)))
2101 (format #t "build directory: ~s~%" (getcwd))
2102 (format #t "configure flags: ~s~%" flags)
2103 (setenv "SLEPC_DIR" (getcwd))
9cf52454 2104 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
c6840089 2105 (apply invoke "./configure" flags))))
8787c555 2106 (add-after 'install 'delete-doc
a7f01414
EB		 2107 ;; TODO: SLEPc installs HTML documentation alongside headers in
2108 ;; $out/include. We'd like to move them to share/doc, but delete
2109 ;; them for now, as they are incomplete and installing the complete
2110 ;; documentation is difficult.
2111 (lambda* (#:key outputs #:allow-other-keys)
2112 (let* ((out (assoc-ref outputs "out")))
0f6dc120
TGR		 2113 (for-each delete-file (find-files out "\\.html$"))
2114 #t)))
8787c555 2115 (add-after 'install 'clean-install
a7f01414
EB		 2116 ;; Clean up unnecessary build logs from installation.
2117 (lambda* (#:key outputs #:allow-other-keys)
2118 (let ((out (assoc-ref outputs "out")))
2119 (for-each (lambda (file)
2120 (let ((f (string-append out "/lib/slepc/conf/" file)))
2121 (when (file-exists? f)
2122 (delete-file f))))
2123 '("configure.log" "make.log" "gmake.log"
2124 "test.log" "error.log" "RDict.db"
0f6dc120
TGR		 2125 "uninstall.py"))
2126 #t))))))
a7f01414
EB		 2127 (home-page "http://slepc.upv.es")
2128 (synopsis "Scalable library for eigenproblems")
2129 (description "SLEPc is a software library for the solution of large sparse
2130eigenproblems on parallel computers. It can be used for the solution of
2131linear eigenvalue problems formulated in either standard or generalized form,
2132as well as other related problems such as the singular value decomposition.
2133The emphasis of the software is on methods and techniques appropriate for
2134problems in which the associated matrices are sparse, for example, those
2135arising after the discretization of partial differential equations.")
3c524f21 2136 (license license:bsd-2)))
a7f01414
EB		 2137
2138(define-public slepc-complex
2139 (package (inherit slepc)
2140 (name "slepc-complex")
2141 (propagated-inputs
2142 `(("petsc" ,petsc-complex)
2143 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
2144 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
2145
2146(define-public slepc-openmpi
2147 (package (inherit slepc)
2148 (name "slepc-openmpi")
6df2a50a
LC		 2149 (arguments
2150 (substitute-keyword-arguments (package-arguments slepc)
2151 ((#:phases phases '%standard-phases)
2152 `(modify-phases ,phases
bbe46a4a
EB		 2153 (add-before 'check 'mpi-setup
2154 ,%openmpi-setup)))))
a7f01414
EB		 2155 (inputs
2156 `(("mpi" ,openmpi)
2157 ("arpack" ,arpack-ng-openmpi)
2158 ,@(alist-delete "arpack" (package-inputs slepc))))
2159 (propagated-inputs
2160 `(("petsc" ,petsc-openmpi)
2161 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
2162 (synopsis "Scalable library for eigenproblems (with MPI support)")))
2163
2164(define-public slepc-complex-openmpi
2165 (package (inherit slepc-openmpi)
2166 (name "slepc-complex-openmpi")
2167 (propagated-inputs
2168 `(("petsc" ,petsc-complex-openmpi)
2169 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
2170 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
2171
6b5687d0
PG		 2172(define-public python-slepc4py
2173 (package
2174 (name "python-slepc4py")
57d30004 2175 (version "3.10.0")
6b5687d0
PG		 2176 (source
2177 (origin
2178 (method url-fetch)
2179 (uri (pypi-uri "slepc4py" version))
2180 (sha256
2181 (base32
57d30004 2182 "0x049dyc8frgh79fvvavf4vlbqp4mgm61nsaivzdav4316vvlv1j"))))
6b5687d0
PG		 2183 (build-system python-build-system)
2184 (arguments
2185 `(#:phases
2186 (modify-phases %standard-phases
2187 (add-before 'build 'pre-build
2188 (lambda _
2189 ;; Define path to PETSc installation.
2190 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
2191 ;; Define path to SLEPc installation.
2192 (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
2193 #t))
2194 (add-before 'check 'mpi-setup
2195 ,%openmpi-setup))))
2196 (inputs
2197 `(("python-numpy" ,python-numpy)
2198 ("python-petsc4py" ,python-petsc4py)
2199 ("slepc" ,slepc-openmpi)))
2200 (home-page "https://bitbucket.org/slepc/slepc4py/")
2201 (synopsis "Python bindings for SLEPc")
2202 (description "SLEPc, the Scalable Library for Eigenvalue Problem
2203Computations, is based on PETSc, the Portable, Extensible Toolkit for
2204Scientific Computation. It employs the MPI standard for all
2205message-passing communication. @code{slepc4py} provides Python
2206bindings to almost all functions of SLEPc.")
2207 (license license:bsd-3)))
2208
cec86422
EB		 2209(define-public mumps
2210 (package
2211 (name "mumps")
5dbc79eb 2212 (version "5.2.1")
cec86422
EB		 2213 (source
2214 (origin
2215 (method url-fetch)
2216 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
2217 version ".tar.gz"))
2218 (sha256
2219 (base32
5dbc79eb 2220 "0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r"))
06e12395
MB		 2221 (patches (search-patches "mumps-build-parallelism.patch"
2222 "mumps-shared-libseq.patch"
2223 "mumps-shared-mumps.patch"
2224 "mumps-shared-pord.patch"))))
cec86422
EB		 2225 (build-system gnu-build-system)
2226 (inputs
2227 `(("fortran" ,gfortran)
2228 ;; These are required for linking against mumps, but we let the user
2229 ;; declare the dependency.
2230 ("blas" ,openblas)
2231 ("metis" ,metis)
2232 ("scotch" ,scotch)))
2233 (arguments
2234 `(#:modules ((ice-9 match)
2235 (ice-9 popen)
2236 (srfi srfi-1)
2237 ,@%gnu-build-system-modules)
2238 #:phases
2239 (modify-phases %standard-phases
fba78d18 2240 (replace 'configure
cec86422
EB		 2241 (lambda* (#:key inputs #:allow-other-keys)
2242 (call-with-output-file "Makefile.inc"
2243 (lambda (port)
2244 (format port "
2245PLAT =
2246LIBEXT = .a
2247OUTC = -o
2248OUTF = -o
2249RM = rm -f~:[
2250CC = gcc
2251FC = gfortran
2252FL = gfortran
2253INCSEQ = -I$(topdir)/libseq
06e12395 2254LIBSEQ = $(topdir)/libseq/libmpiseq.a
cec86422
EB		 2255LIBSEQNEEDED = libseqneeded~;
2256CC = mpicc
2257FC = mpifort
2258FL = mpifort~]
2259AR = ar vr # rules require trailing space, ugh...
2260RANLIB = ranlib
06e12395
MB		 2261BLASDIR = ~a
2262LIBBLAS = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[
2263SCALAPDIR = ~a
2264SCALAP = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~]
cec86422
EB		 2265LIBOTHERS = -pthread
2266CDEFS = -DAdd_
2267PIC = -fPIC
2268OPTF = -O2 -DALLOW_NON_INIT $(PIC)
2269OPTL = -O2 $(PIC)
2270OPTC = -O2 $(PIC)
2271INCS = $(INCSEQ)
2272LIBS = $(SCALAP) $(LIBSEQ)
2273LPORDDIR = $(topdir)/PORD/lib
2274IPORD = -I$(topdir)/PORD/include
06e12395 2275LPORD = $(LPORDDIR)/libpord.a
cec86422
EB		 2276ORDERINGSF = -Dpord~@[
2277METISDIR = ~a
2278IMETIS = -I$(METISDIR)/include
06e12395 2279LMETIS = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
cec86422
EB		 2280ORDERINGSF += -Dmetis~]~@[~:{
2281SCOTCHDIR = ~a
2282ISCOTCH = -I$(SCOTCHDIR)/include
06e12395 2283LSCOTCH = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
cec86422
EB		 2284ORDERINGSF += ~a~}~]
2285ORDERINGSC = $(ORDERINGSF)
06e12395 2286LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
cec86422
EB		 2287IORDERINGSF = $(ISCOTCH)
2288IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
2289 (assoc-ref inputs "mpi")
2290 (assoc-ref inputs "blas")
2291 (assoc-ref inputs "scalapack")
2292 (assoc-ref inputs "metis")
2293 (match (list (assoc-ref inputs "pt-scotch")
2294 (assoc-ref inputs "scotch"))
2295 ((#f #f)
2296 #f)
2297 ((#f scotch)
2298 `((,scotch "" "-Dscotch")))
2299 ((ptscotch _)
2300 `((,ptscotch
2301 "-lptesmumps -lptscotch -lptscotcherr "
2302 "-Dptscotch")))))))))
fba78d18 2303 (replace 'build
cec86422
EB		 2304 ;; By default only the d-precision library is built. Make with "all"
2305 ;; target so that all precision libraries and examples are built.
2306 (lambda _
b414cf52
TGR		 2307 (invoke "make" "all"
2308 (format #f "-j~a" (parallel-job-count)))))
fba78d18 2309 (replace 'check
cec86422
EB		 2310 ;; Run the simple test drivers, which read test input from stdin:
2311 ;; from the "real" input for the single- and double-precision
2312 ;; testers, and from the "cmplx" input for complex-precision
2313 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
2314 ;; package to prefix execution with "mpirun".
2315 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
2316 (with-directory-excursion "examples"
2317 (every
2318 (lambda (prec type)
2319 (let ((tester (apply open-pipe*
2320 `(,OPEN_WRITE
2321 ,@exec-prefix
2322 ,(string-append "./" prec
2323 "simpletest"))))
2324 (input (open-input-file
2325 (string-append "input_simpletest_" type))))
2326 (begin
2327 (dump-port input tester)
2328 (close-port input)
2329 (zero? (close-pipe tester)))))
2330 '("s" "d" "c" "z")
2331 '("real" "real" "cmplx" "cmplx")))))
fba78d18
EB		 2332 (replace 'install
2333 (lambda* (#:key outputs #:allow-other-keys)
2334 (let* ((out (assoc-ref outputs "out"))
2335 (libdir (string-append out "/lib")))
2336 (copy-recursively "lib" libdir)
2337 (copy-recursively "include" (string-append out "/include"))
2338 (when (file-exists? "libseq/libmpiseq.a")
2339 (install-file "libseq/libmpiseq.a" libdir))
06e12395
MB		 2340 (when (file-exists? "libseq/libmpiseq.so")
2341 (install-file "libseq/libmpiseq.so" libdir))
fba78d18 2342 #t))))))
cec86422
EB		 2343 (home-page "http://mumps.enseeiht.fr")
2344 (synopsis "Multifrontal sparse direct solver")
2345 (description
2346 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
57e69c1d 2347sparse system of linear equations A x = b using Gaussian elimination.")
cec86422
EB		 2348 (license license:cecill-c)))
2349
2350(define-public mumps-metis
2351 (package (inherit mumps)
2352 (name "mumps-metis")
2353 (inputs
2354 (alist-delete "scotch" (package-inputs mumps)))))
2355
2356(define-public mumps-openmpi
2357 (package (inherit mumps)
2358 (name "mumps-openmpi")
2359 (inputs
2360 `(("mpi" ,openmpi)
2361 ("scalapack" ,scalapack)
2362 ("pt-scotch" ,pt-scotch)
2363 ,@(alist-delete "scotch" (package-inputs mumps))))
2364 (arguments
2365 (substitute-keyword-arguments (package-arguments mumps)
2366 ((#:phases phases)
2367 `(modify-phases ,phases
bbe46a4a
EB		 2368 (add-before 'check 'mpi-setup
2369 ,%openmpi-setup)
6df2a50a
LC		 2370 (replace 'check
2371 (lambda _
2372 ((assoc-ref ,phases 'check)
2373 #:exec-prefix '("mpirun" "-n" "2"))))))))
cec86422
EB		 2374 (synopsis "Multifrontal sparse direct solver (with MPI)")))
2375
2376(define-public mumps-metis-openmpi
2377 (package (inherit mumps-openmpi)
2378 (name "mumps-metis-openmpi")
2379 (inputs
2380 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
2381
63e07468
BW		 2382(define-public ruby-asciimath
2383 (package
2384 (name "ruby-asciimath")
2385 (version "1.0.4")
2386 (source
2387 (origin
2388 (method url-fetch)
2389 (uri (rubygems-uri "asciimath" version))
2390 (sha256
2391 (base32
2392 "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
2393 (build-system ruby-build-system)
2394 (arguments
2395 '(#:phases
2396 (modify-phases %standard-phases
2397 ;; Apply this patch
2398 ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
2399 (add-after 'unpack 'patch-remove-spurious-backslashes
2400 (lambda _
2401 (substitute* "spec/parser_spec.rb"
2402 (("\\\\\"")
9923d5a4
TGR		 2403 "\""))
2404 #t)))))
63e07468
BW		 2405 (native-inputs
2406 `(("bundler" ,bundler)
2407 ("ruby-rspec" ,ruby-rspec)))
2408 (synopsis "AsciiMath parsing and conversion library")
2409 (description
2410 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
2411easy-to-write markup language for mathematics.")
2412 (home-page "https://github.com/asciidoctor/asciimath")
2413 (license license:expat)))
2414
183e44ae
EB		 2415(define-public superlu
2416 (package
2417 (name "superlu")
995a09e0 2418 (version "5.2.1")
183e44ae
EB		 2419 (source
2420 (origin
2421 (method url-fetch)
2422 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2423 "superlu_" version ".tar.gz"))
2424 (sha256
995a09e0
EB		 2425 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
2426 (modules '((guix build utils)))
2427 (snippet
2428 ;; Replace the non-free implementation of MC64 with a stub adapted
2429 ;; from Debian
2430 '(begin
2431 (use-modules (ice-9 regex)
2432 (ice-9 rdelim))
2433 (call-with-output-file "SRC/mc64ad.c"
2434 (lambda (port)
2435 (display "
2436#include <stdio.h>
2437#include <stdlib.h>
2438void mc64id_(int *a) {
2439 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2440 abort ();
2441}
2442void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2443 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2444 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2445 abort ();
2446}\n" port)))
2447 ;; Remove the corresponding license verbiage. MC64 license follows
2448 ;; a "------" line separator.
2449 (with-atomic-file-replacement "License.txt"
2450 (let ((rx (make-regexp "-{8}")))
2451 (lambda (in out)
2452 (let loop ()
2453 (let ((line (read-line in 'concat)))
2454 (unless (regexp-exec rx line)
2455 (display line out)
6cbee49d
MW		 2456 (loop))))
2457 #t)))))))
995a09e0 2458 (build-system cmake-build-system)
183e44ae
EB		 2459 (native-inputs
2460 `(("tcsh" ,tcsh)))
2461 (inputs
995a09e0 2462 `(("blas" ,openblas)
19afbea1 2463 ("gfortran" ,gfortran)))
183e44ae 2464 (arguments
995a09e0
EB		 2465 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2466 "-DTPL_BLAS_LIBRARIES=openblas"
677bc34d 2467 "-DBUILD_SHARED_LIBS:BOOL=YES")))
183e44ae
EB		 2468 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
2469 (synopsis "Supernodal direct solver for sparse linear systems")
2470 (description
2471 "SuperLU is a general purpose library for the direct solution of large,
2472sparse, nonsymmetric systems of linear equations on high performance machines.
2473The library is written in C and is callable from either C or Fortran. The
2474library routines perform an LU decomposition with partial pivoting and
2475triangular system solves through forward and back substitution. The library
2476also provides threshold-based ILU factorization preconditioners.")
995a09e0
EB		 2477 (license (list license:bsd-3
2478 license:gpl2+ ;EXAMPLE/*fgmr.c
2479 (license:fsf-free "file://SRC/colamd.h")))))
f8ed036a 2480
a54aefea
EB		 2481(define-public superlu-dist
2482 (package
2483 (name "superlu-dist")
6161141e 2484 (version "6.1.0")
a54aefea
EB		 2485 (source
2486 (origin
2487 (method url-fetch)
2488 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2489 "superlu_dist_" version ".tar.gz"))
2490 (sha256
6161141e 2491 (base32 "0pqgcgh1yxhfzs99fas3mggajzd5wca3nbyp878rziy74gfk03dl"))
0921eff2 2492 (modules '((guix build utils)))
29080870
EB		 2493 (snippet
2494 ;; Replace the non-free implementation of MC64 with a stub
2495 '(begin
0921eff2 2496 (call-with-output-file "SRC/mc64ad_dist.c"
29080870
EB		 2497 (lambda (port)
2498 (display "
2499#include <stdio.h>
2500#include <stdlib.h>
0921eff2 2501void mc64id_dist(int *a) {
29080870
EB		 2502 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2503 abort ();
2504}
0921eff2 2505void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
29080870
EB		 2506 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2507 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2508 abort ();
2509}\n" port)))
29080870 2510 (substitute* "SRC/util.c" ;adjust default algorithm
6161141e
EB		 2511 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
2512 ;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
2513 ;; general (i.e. non-square) processor-grid support.
2514 "RowPerm = NOROWPERM;"))
6cbee49d 2515 #t))
6161141e 2516 (patches (search-patches "superlu-dist-scotchmetis.patch"
2bdf26f1
EB		 2517 "superlu-dist-awpm-grid.patch"
2518 "superlu-dist-fix-mpi-deprecations.patch"))))
6161141e 2519 (build-system cmake-build-system)
a54aefea
EB		 2520 (native-inputs
2521 `(("tcsh" ,tcsh)))
2522 (inputs
6161141e
EB		 2523 `(("gfortran" ,gfortran)
2524 ("blas" ,openblas)
2525 ("lapack" ,lapack)
2526 ("combblas" ,combinatorial-blas)))
a54aefea 2527 (propagated-inputs
6161141e
EB		 2528 `(("mpi" ,openmpi) ;headers include MPI heades
2529 ("parmetis" ,pt-scotch32 "metis")
2530 ("pt-scotch" ,pt-scotch32)))
a54aefea 2531 (arguments
6161141e
EB		 2532 `(#:parallel-tests? #f ;tests use MPI and OpenMP
2533 #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
2534 "-DTPL_ENABLE_COMBBLASLIB=YES"
2535 "-DTPL_BLAS_LIBRARIES=-lopenblas"
2536 "-DTPL_LAPACK_LIBRARIES=-llapack"
2537 (string-append "-DTPL_PARMETIS_LIBRARIES="
2538 (string-join
2539 '("ptscotchparmetis" "ptscotch" "ptscotcherr"
2540 "scotchmetis" "scotch" "scotcherr")
2541 ";"))
2542 (string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
2543 (assoc-ref %build-inputs "parmetis")
2544 "/include")
2545 "-DTPL_ENABLE_COMBBLASLIB=ON"
2546 (string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
2547 (assoc-ref %build-inputs "combblas")
2548 "/include/CombBLAS;"
2549 (assoc-ref %build-inputs "combblas")
2550 "/include/BipartiteMatchings")
2551 "-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
a54aefea 2552 #:phases
dc1d3cde 2553 (modify-phases %standard-phases
6161141e 2554 (add-before 'configure 'set-c++-standard
dc1d3cde 2555 (lambda _
6161141e
EB		 2556 (substitute* "CMakeLists.txt"
2557 ;; AWPM headers require C++14
2558 (("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
bbe46a4a
EB		 2559 (add-before 'check 'mpi-setup
2560 ,%openmpi-setup)
6161141e
EB		 2561 (add-before 'check 'omp-setup
2562 (lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
a54aefea
EB		 2563 (home-page (package-home-page superlu))
2564 (synopsis "Parallel supernodal direct solver")
2565 (description
2566 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2567It is targeted for distributed memory parallel machines. SuperLU_DIST is
2568implemented in ANSI C, and MPI for communications.")
2569 (license license:bsd-3)))
2570
f8ed036a
EB		 2571(define-public scotch
2572 (package
2573 (name "scotch")
fd373343 2574 (version "6.0.6")
f8ed036a
EB		 2575 (source
2576 (origin
2577 (method url-fetch)
1dc31097
TGR		 2578 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
2579 "latestfile/298/scotch_" version ".tar.gz"))
f8ed036a 2580 (sha256
fd373343
EB		 2581 (base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8"))
2582 (patches (search-patches "scotch-build-parallelism.patch"
2583 "scotch-integer-declarations.patch"))))
f8ed036a
EB		 2584 (build-system gnu-build-system)
2585 (inputs
2586 `(("zlib" ,zlib)
5e54f4ad 2587 ("flex" ,flex)
f8ed036a 2588 ("bison" ,bison)))
fd373343 2589 (outputs '("out" "metis"))
f8ed036a 2590 (arguments
fd373343
EB		 2591 `(#:make-flags (list (string-append "prefix=" %output))
2592 #:phases
d6602ee9
EB		 2593 (modify-phases %standard-phases
2594 (add-after
2595 'unpack 'chdir-to-src
d67a7e9e 2596 (lambda _ (chdir "src") #t))
d6602ee9
EB		 2597 (replace
2598 'configure
2599 (lambda _
2600 (call-with-output-file "Makefile.inc"
2601 (lambda (port)
2602 (format port "
f8ed036a
EB		 2603EXE =
2604LIB = .a
2605OBJ = .o
2606MAKE = make
2607AR = ar
2608ARFLAGS = -ruv
cf0ec6c4 2609CAT = cat
f8ed036a
EB		 2610CCS = gcc
2611CCP = mpicc
2612CCD = gcc
2613CPPFLAGS =~{ -D~a~}
6c798540 2614CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
f8ed036a
EB		 2615LDFLAGS = -lz -lm -lrt -lpthread
2616CP = cp
2617LEX = flex -Pscotchyy -olex.yy.c
2618LN = ln
2619MKDIR = mkdir
2620MV = mv
2621RANLIB = ranlib
2622YACC = bison -pscotchyy -y -b y
2623"
d6602ee9
EB		 2624 '("COMMON_FILE_COMPRESS_GZ"
2625 "COMMON_PTHREAD"
2626 "COMMON_RANDOM_FIXED_SEED"
fd373343 2627 "INTSIZE64" ;use 'int64_t'
cf0ec6c4
EB		 2628 ;; Prevents symbolc clashes with libesmumps
2629 "SCOTCH_RENAME"
d6602ee9
EB		 2630 ;; XXX: Causes invalid frees in superlu-dist tests
2631 ;; "SCOTCH_PTHREAD"
2632 ;; "SCOTCH_PTHREAD_NUMBER=2"
d67a7e9e
TGR		 2633 "restrict=__restrict"))))
2634 #t))
bbe46a4a 2635 (add-after 'build 'build-esmumps
cf0ec6c4 2636 (lambda _
d67a7e9e
TGR		 2637 (invoke "make"
2638 (format #f "-j~a" (parallel-job-count))
2639 "esmumps")))
fd373343
EB		 2640 (add-before 'install 'make-install-dirs
2641 (lambda* (#:key outputs #:allow-other-keys)
2642 (mkdir (assoc-ref outputs "out"))))
2643 (add-after 'install 'install-metis
2644 (lambda* (#:key outputs #:allow-other-keys)
2645 (let ((out (assoc-ref outputs "metis")))
2646 (mkdir out)
2647 ;; metis files are not installed with 'make install'
2648 (for-each (lambda (f)
2649 (install-file f (string-append out "/include")))
2650 (find-files "../include/" ".*metis\\.h"))
2651 (for-each (lambda (f)
2652 (install-file f (string-append out "/lib")))
2653 (find-files "../lib/" ".*metis\\..*"))
2654 #t))))))
f8ed036a
EB		 2655 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
2656 (synopsis "Programs and libraries for graph algorithms")
2657 (description "SCOTCH is a set of programs and libraries which implement
2658the static mapping and sparse matrix reordering algorithms developed within
2659the SCOTCH project. Its purpose is to apply graph theory, with a divide and
2660conquer approach, to scientific computing problems such as graph and mesh
2661partitioning, static mapping, and sparse matrix ordering, in application
2662domains ranging from structural mechanics to operating systems or
2663bio-chemistry.")
2664 ;; See LICENSE_en.txt
2665 (license license:cecill-c)))
6acb4adb 2666
1c39f3b8
PG		 2667(define-public scotch32
2668 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2669 ;; some applications.
2670 (package (inherit scotch)
2671 (name "scotch32")
2672 (arguments
2673 (substitute-keyword-arguments (package-arguments scotch)
2674 ((#:phases scotch-phases)
2675 `(modify-phases ,scotch-phases
2676 (replace
2677 'configure
2678 (lambda _
2679 (call-with-output-file "Makefile.inc"
2680 (lambda (port)
2681 (format port "
2682EXE =
2683LIB = .a
2684OBJ = .o
2685MAKE = make
2686AR = ar
2687ARFLAGS = -ruv
2688CAT = cat
2689CCS = gcc
2690CCP = mpicc
2691CCD = gcc
2692CPPFLAGS =~{ -D~a~}
2693CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2694LDFLAGS = -lz -lm -lrt -lpthread
2695CP = cp
2696LEX = flex -Pscotchyy -olex.yy.c
2697LN = ln
2698MKDIR = mkdir
2699MV = mv
2700RANLIB = ranlib
2701YACC = bison -pscotchyy -y -b y
2702"
2703 '("COMMON_FILE_COMPRESS_GZ"
2704 "COMMON_PTHREAD"
2705 "COMMON_RANDOM_FIXED_SEED"
2706 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
2707 ;; Prevents symbolc clashes with libesmumps
2708 "SCOTCH_RENAME"
2709 ;; XXX: Causes invalid frees in superlu-dist tests
2710 ;; "SCOTCH_PTHREAD"
2711 ;; "SCOTCH_PTHREAD_NUMBER=2"
2712 "restrict=__restrict"))))))))))
2713 (synopsis
2714 "Programs and libraries for graph algorithms (32-bit integers)")))
2715
6acb4adb
EB		 2716(define-public pt-scotch
2717 (package (inherit scotch)
2718 (name "pt-scotch")
2719 (propagated-inputs
2720 `(("openmpi" ,openmpi))) ;Headers include MPI headers
2721 (arguments
2722 (substitute-keyword-arguments (package-arguments scotch)
2723 ((#:phases scotch-phases)
d6602ee9
EB		 2724 `(modify-phases ,scotch-phases
2725 (replace
2726 'build
d6602ee9 2727 (lambda _
c491f7f8
LC		 2728 (invoke "make" (format #f "-j~a" (parallel-job-count))
2729 "ptscotch" "ptesmumps")
2730
2731 ;; Install the serial metis compatibility library
2732 (invoke "make" "-C" "libscotchmetis" "install")))
2733 (add-before 'check 'mpi-setup
2734 ,%openmpi-setup)
2735 (replace 'check
2736 (lambda _
2737 (invoke "make" "ptcheck")))))))
6acb4adb 2738 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
5698b8b8 2739
1c25a52c
PG		 2740(define-public pt-scotch32
2741 (package (inherit scotch32)
2742 (name "pt-scotch32")
2743 (propagated-inputs
2744 `(("openmpi" ,openmpi))) ;headers include MPI headers
2745 (arguments
c4d4a779
PG		 2746 (substitute-keyword-arguments (package-arguments scotch32)
2747 ((#:phases scotch32-phases)
2748 `(modify-phases ,scotch32-phases
1c25a52c
PG		 2749 (replace 'build
2750 (lambda _
c491f7f8
LC		 2751 (invoke "make" (format #f "-j~a" (parallel-job-count))
2752 "ptscotch" "ptesmumps")
2753 ;; Install the serial metis compatibility library
2754 (invoke "make" "-C" "libscotchmetis" "install")))
2755 (add-before 'check 'mpi-setup
2756 ,%openmpi-setup)
1c25a52c
PG		 2757 (replace 'check
2758 (lambda _
c491f7f8 2759 (invoke "make" "ptcheck")))))))
1c25a52c
PG		 2760 (synopsis
2761 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2762
aa75ad00
EB		 2763(define-public metis
2764 (package
2765 (name "metis")
2766 (version "5.1.0")
2767 (source
2768 (origin
2769 (method url-fetch)
2770 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2771 "metis-" version ".tar.gz"))
2772 (sha256
2773 (base32
2774 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2775 (build-system cmake-build-system)
2776 (inputs
2777 `(("blas" ,openblas)))
2778 (arguments
2779 `(#:tests? #f ;no tests
2780 #:configure-flags `("-DSHARED=ON"
2781 ,(string-append "-DGKLIB_PATH=" (getcwd)
2782 "/metis-" ,version "/GKlib"))))
2783 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2784 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2785 (description
2786 "METIS is a set of serial programs for partitioning graphs, partitioning
2787finite element meshes, and producing fill-reducing orderings for sparse
2788matrices. The algorithms implemented in METIS are based on the multilevel
2789recursive-bisection, multilevel k-way, and multi-constraint partitioning
2790schemes.")
2791 (license license:asl2.0))) ;As of version 5.0.3
2792
700ff222
EB		 2793(define-public p4est
2794 (package
2795 (name "p4est")
4150da63 2796 (version "2.0")
700ff222
EB		 2797 (source
2798 (origin
2799 (method url-fetch)
2800 (uri (string-append "http://p4est.github.io/release/p4est-"
2801 version ".tar.gz"))
2802 (sha256
2803 (base32
4150da63 2804 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
700ff222
EB		 2805 (build-system gnu-build-system)
2806 (inputs
2807 `(("fortran" ,gfortran)
2808 ("blas" ,openblas)
2809 ("lapack" ,lapack)
2810 ("zlib" ,zlib)))
2811 (arguments
2812 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2813 (assoc-ref %build-inputs "blas")
2814 " -lopenblas")
2815 ,(string-append "LAPACK_LIBS=-L"
2816 (assoc-ref %build-inputs "lapack")
6df2a50a
LC		 2817 " -llapack"))
2818 #:phases (modify-phases %standard-phases
bbe46a4a
EB		 2819 (add-before 'check 'mpi-setup
2820 ,%openmpi-setup))))
700ff222
EB		 2821 (home-page "http://www.p4est.org")
2822 (synopsis "Adaptive mesh refinement on forests of octrees")
2823 (description
2824 "The p4est software library enables the dynamic management of a
2825collection of adaptive octrees, conveniently called a forest of octrees.
2826p4est is designed to work in parallel and scales to hundreds of thousands of
2827processor cores.")
2828 (license license:gpl2+)))
2829
2830(define-public p4est-openmpi
2831 (package (inherit p4est)
2832 (name "p4est-openmpi")
2833 (inputs
2834 `(("mpi" ,openmpi)
2835 ,@(package-inputs p4est)))
2836 (arguments
2837 (substitute-keyword-arguments (package-arguments p4est)
2838 ((#:configure-flags cf)
2839 ``("--enable-mpi" ,@,cf))))
2840 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2841
5698b8b8
JD		 2842(define-public gsegrafix
2843 (package
2844 (name "gsegrafix")
2845 (version "1.0.6")
2846 (source
2847 (origin
2848 (method url-fetch)
2849 (uri (string-append "mirror://gnu/" name "/" name "-"
2850 version ".tar.gz"))
2851 (sha256
2852 (base32
2853 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2854 (build-system gnu-build-system)
2855 (arguments
2856 `(#:configure-flags '("LDFLAGS=-lm")))
2857 (inputs
2858 `(("libgnomecanvas" ,libgnomecanvas)
2859 ("libbonoboui" ,libbonoboui)
2860 ("libgnomeui" ,libgnomeui)
2861 ("libgnomeprintui" ,libgnomeprintui)
2862 ("popt" ,popt)))
2863 (native-inputs
2864 `(("pkg-config" ,pkg-config)))
6fd52309 2865 (home-page "https://www.gnu.org/software/gsegrafix/")
5698b8b8
JD		 2866 (synopsis "GNOME application to create scientific and engineering plots")
2867 (description "GSEGrafix is an application which produces high-quality graphical
2868plots for science and engineering. Plots are specified via simple ASCII
2869parameter files and data files and are presented in an anti-aliased GNOME
2870canvas. The program supports rectangular two-dimensional plots, histograms,
2871polar-axis plots and three-dimensional plots. Plots can be printed or saved
2872to BMP, JPEG or PNG image formats.")
2873 (license license:gpl3+)))
8731e527
JD		 2874
2875(define-public maxima
2876 (package
2877 (name "maxima")
ccc963d5 2878 (version "5.43.0")
8731e527
JD		 2879 (source
2880 (origin
2881 (method url-fetch)
2882 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2883 version "-source/" name "-" version ".tar.gz"))
2884 (sha256
2885 (base32
ccc963d5 2886 "0xyahp4c6509haxh4n1swiqm3421gplkdisa0zypclh3252sbzfw"))
fc1adab1 2887 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
8731e527 2888 (build-system gnu-build-system)
df354a77 2889 (inputs
6b2eafaa 2890 `(("gcl" ,gcl)
df354a77 2891 ("gnuplot" ,gnuplot) ;for plots
fc9c47bd 2892 ("sed" ,sed)
f36afe4d 2893 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
df354a77
FB		 2894 (native-inputs
2895 `(("texinfo" ,texinfo)
ccbc5758
KK		 2896 ("perl" ,perl)
2897 ("python" ,python)))
8731e527 2898 (arguments
df354a77
FB		 2899 `(#:configure-flags
2900 (list "--enable-gcl"
2901 (string-append "--with-posix-shell="
2902 (assoc-ref %build-inputs "bash")
2903 "/bin/sh")
2904 (string-append "--with-wish="
2905 (assoc-ref %build-inputs "tk")
2906 "/bin/wish"
2907 (let ((v ,(package-version tk)))
2908 (string-take v (string-index-right v #\.)))))
df354a77 2909 ;; By default Maxima attempts to write temporary files to
77af7b24
MW		 2910 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2911 ;; Work around that.
df354a77 2912 #:make-flags (list "TMPDIR=/tmp")
0093b126
KK		 2913 #:phases
2914 (modify-phases %standard-phases
fc9c47bd
KK		 2915 (add-after 'unpack 'patch-paths
2916 (lambda* (#:key inputs #:allow-other-keys)
2917 (let* ((sed (string-append (assoc-ref inputs "sed") "/bin/sed"))
2918 (coreutils (assoc-ref inputs "coreutils"))
2919 (dirname (string-append coreutils "/bin/dirname"))
ccc963d5
KK		 2920 (head (string-append coreutils "/bin/head"))
2921 (perl (string-append (assoc-ref inputs "perl") "/bin/perl"))
2922 (python (string-append (assoc-ref inputs "python")
2923 "/bin/python3")))
fc9c47bd
KK		 2924 (substitute* "src/maxima.in"
2925 (("sed ") (string-append sed " "))
2926 (("dirname") dirname)
2927 (("head") head))
ccc963d5
KK		 2928 (substitute* "doc/info/Makefile.in"
2929 (("/usr/bin/env perl") perl))
2930 (substitute* "doc/info/build_html.sh.in"
2931 (("python") python))
fc9c47bd 2932 #t)))
0093b126
KK		 2933 (add-before 'check 'pre-check
2934 (lambda _
2935 (chmod "src/maxima" #o555)
2936 #t))
1472d19a
KK		 2937 (replace 'check
2938 (lambda _
2939 ;; This is derived from the testing code in the "debian/rules" file
2940 ;; of Debian's Maxima package.
2941 ;; If Maxima can successfully run this, the binary to be installed
2942 ;; should be fine.
df129041
MW		 2943 (invoke "sh" "-c"
2944 (string-append
2945 "./maxima-local "
2946 "--lisp=gcl "
2947 "--batch-string=\"run_testsuite();\" "
2948 "| grep -q \"No unexpected errors found\""))))
0093b126
KK		 2949 ;; Make sure the doc and emacs files are found in the
2950 ;; standard location. Also configure maxima to find gnuplot
2951 ;; without having it on the PATH.
2952 (add-after 'install 'post-install
2953 (lambda* (#:key outputs inputs #:allow-other-keys)
2954 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2955 (out (assoc-ref outputs "out"))
2956 (datadir (string-append out "/share/maxima/" ,version))
2957 (binutils (string-append (assoc-ref inputs "binutils")
2958 "/bin")))
2959 (with-directory-excursion out
2960 (mkdir-p "share/emacs")
2961 (mkdir-p "share/doc")
0093b126
KK		 2962 (symlink
2963 (string-append datadir "/doc/")
2964 (string-append out "/share/doc/maxima"))
2965 (with-atomic-file-replacement
2966 (string-append datadir "/share/maxima-init.lisp")
2967 (lambda (in out)
2968 (format out "~a ~s~a~%"
2969 "(setf $gnuplot_command "
2970 (string-append gnuplot "/bin/gnuplot") ")")
2971 (dump-port in out))))
2972 ;; Ensure that Maxima will have access to the GNU binutils
2973 ;; components at runtime.
2974 (wrap-program (string-append out "/bin/maxima")
2975 `("PATH" prefix (,binutils))))
2976 #t)))))
8731e527
JD		 2977 (home-page "http://maxima.sourceforge.net")
2978 (synopsis "Numeric and symbolic expression manipulation")
2979 (description "Maxima is a system for the manipulation of symbolic and
2980numerical expressions. It yields high precision numeric results by using
2981exact fractions, arbitrary precision integers, and variable precision floating
e881752c 2982point numbers.")
8731e527
JD		 2983 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2984 ;; Others simply say "GNU General Public License" without stating a
2985 ;; version (which implicitly means gpl1+).
2986 ;; At least one file (src/maxima.asd) says "version 2."
2987 ;; GPLv2 only is therefore the smallest subset.
f36afe4d 2988 (license license:gpl2)))
ec322be2 2989
9aafbc0c
MW		 2990(define-public wxmaxima
2991 (package
2992 (name "wxmaxima")
1e8609f2 2993 (version "19.11.1")
9aafbc0c
MW		 2994 (source
2995 (origin
c93b77ad
KK		 2996 (method git-fetch)
2997 (uri (git-reference
2998 (url "https://github.com/wxMaxima-developers/wxmaxima.git")
2999 (commit (string-append "Version-" version))))
3000 (file-name (git-file-name name version))
9aafbc0c 3001 (sha256
1e8609f2 3002 (base32 "16xizaddb27432n1083y89ir5zdqvllsgbwrzzk4jc2rw1ldxfsv"))))
0181df53 3003 (build-system cmake-build-system)
5143517c 3004 (native-inputs
0181df53 3005 `(("gettext" ,gettext-minimal)))
9aafbc0c
MW		 3006 (inputs
3007 `(("wxwidgets" ,wxwidgets)
de477809
SB		 3008 ("maxima" ,maxima)
3009 ;; Runtime support.
3010 ("adwaita-icon-theme" ,adwaita-icon-theme)
3011 ("gtk+" ,gtk+)
3012 ("shared-mime-info" ,shared-mime-info)))
9aafbc0c 3013 (arguments
0181df53
KK		 3014 `(#:tests? #f ; no check target
3015 #:phases
ac2ddcc6 3016 (modify-phases %standard-phases
ac2ddcc6
KK		 3017 (add-after 'install 'wrap-program
3018 (lambda* (#:key inputs outputs #:allow-other-keys)
3019 (wrap-program (string-append (assoc-ref outputs "out")
3020 "/bin/wxmaxima")
3021 `("PATH" ":" prefix
3022 (,(string-append (assoc-ref inputs "maxima")
3023 "/bin")))
3024 ;; For GtkFileChooserDialog.
3025 `("GSETTINGS_SCHEMA_DIR" =
3026 (,(string-append (assoc-ref inputs "gtk+")
3027 "/share/glib-2.0/schemas")))
3028 `("XDG_DATA_DIRS" ":" prefix
3029 (;; Needed by gdk-pixbuf to know supported icon formats.
3030 ,(string-append
3031 (assoc-ref inputs "shared-mime-info") "/share")
3032 ;; The default icon theme of GTK+.
3033 ,(string-append
3034 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
3035 #t)))))
9aafbc0c
MW		 3036 (home-page "https://andrejv.github.io/wxmaxima/")
3037 (synopsis "Graphical user interface for the Maxima computer algebra system")
3038 (description
3039 "wxMaxima is a graphical user interface for the Maxima computer algebra
3040system. It eases the use of Maxima by making most of its commands available
3041through a menu system and by providing input dialogs for commands that require
3042more than one argument. It also implements its own display engine that
3043outputs mathematical symbols directly instead of depicting them with ASCII
3044characters.
3045
3046wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
3047text and mathematical calculations to create documents, exporting of input and
3048output to TeX, and a browser for Maxima's manual including command index and
3049full text searching.")
3050 (license license:gpl2+)))
3051
b15e47f9
RW		 3052(define-public armadillo
3053 (package
3054 (name "armadillo")
f133e244 3055 (version "9.100.5")
b15e47f9
RW		 3056 (source (origin
3057 (method url-fetch)
3058 (uri (string-append "mirror://sourceforge/arma/armadillo-"
7397cd9e 3059 version ".tar.xz"))
b15e47f9
RW		 3060 (sha256
3061 (base32
f133e244 3062 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
b15e47f9 3063 (build-system cmake-build-system)
e405c0bc 3064 (arguments `(#:tests? #f)) ; no test target
b15e47f9
RW		 3065 (inputs
3066 `(("openblas" ,openblas)
3067 ("lapack" ,lapack)
3068 ("arpack" ,arpack-ng)))
3069 (home-page "http://arma.sourceforge.net/")
3070 (synopsis "C++ linear algebra library")
3071 (description
3072 "Armadillo is a C++ linear algebra library, aiming towards a good balance
3073between speed and ease of use. It is useful for algorithm development
3074directly in C++, or quick conversion of research code into production
3075environments. It can be used for machine learning, pattern recognition,
3076signal processing, bioinformatics, statistics, econometrics, etc. The library
3077provides efficient classes for vectors, matrices and cubes, as well as 150+
3078associated functions (eg. contiguous and non-contiguous submatrix views).")
fe418cc5 3079 (license license:asl2.0)))
b15e47f9 3080
279663ef 3081(define-public muparser
d7cff656
LF		 3082 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
3083 ;; different hash. In order to make `guix package --upgrade` work correctly,
3084 ;; we set a Guix packaging revision.
3085 ;; When the next version of muparser is released, we can remove
3086 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
3087 (let ((upstream-version "2.2.5")
3088 (revision "2"))
3089 (package
3090 (name "muparser")
3091 (version (string-append upstream-version "-" revision))
3092 (source
3093 (origin
67f1db38
TGR		 3094 (method git-fetch)
3095 (uri (git-reference
3096 (url "https://github.com/beltoforion/muparser.git")
3097 (commit (string-append "v" upstream-version))))
3098 (file-name (git-file-name name version))
d7cff656 3099 (sha256
67f1db38 3100 (base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24"))))
d7cff656
LF		 3101 (build-system gnu-build-system)
3102 (arguments
3103 `(#:configure-flags '("--enable-samples=no")
3104 #:tests? #f)) ;no "check" target
3105 (home-page "http://muparser.beltoforion.de/")
3106 (synopsis "Fast parser library for mathematical expressions")
3107 (description
3108 "muParser is an extensible high performance math parser library. It is
3109based on transforming an expression into a bytecode and precalculating constant
3110parts of it.")
3111 (license license:expat))))
279663ef 3112
e73b49fb
RW		 3113(define-public openblas
3114 (package
3115 (name "openblas")
2ea09530 3116 (version "0.3.7")
e73b49fb
RW		 3117 (source
3118 (origin
3119 (method url-fetch)
a617fd55
MB		 3120 (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
3121 version "%20version.tar.gz"))
e73b49fb
RW		 3122 (file-name (string-append name "-" version ".tar.gz"))
3123 (sha256
3124 (base32
2ea09530 3125 "0jbdjsi0qsxahdcm42agnn1y7xpmg0hrhwjsxg0zbhs9wwy3p568"))))
e73b49fb
RW		 3126 (build-system gnu-build-system)
3127 (arguments
5789566a 3128 `(#:test-target "test"
bd0b4379
RW		 3129 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
3130 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
3131 ;; we need to disable substitutions.
71923a91
AE		 3132 #:substitutable?
3133 ,(let ((system (or (%current-target-system) (%current-system))))
3134 (or (string-prefix? "x86_64" system)
bd0b4379 3135 (string-prefix? "i686" system)
83a34647
EF		 3136 (string-prefix? "mips" system)
3137 (string-prefix? "aarch64" system)))
e73b49fb
RW		 3138 #:make-flags
3139 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
3140 "SHELL=bash"
5855756c 3141 "MAKE_NB_JOBS=0" ;use jobserver for submakes
a4384dc9
MB		 3142
3143 ;; This is the maximum number of threads OpenBLAS will ever use (that
3144 ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS
3145 ;; is used.) If we don't set it, the makefile sets it to the number
3146 ;; of cores of the build machine, which is obviously wrong.
3147 "NUM_THREADS=128"
3148
af5b817e
RW		 3149 ;; Build the library for all supported CPUs. This allows
3150 ;; switching CPU targets at runtime with the environment variable
3151 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
71923a91
AE		 3152 ;; Unfortunately, this is not supported on non-x86 architectures,
3153 ;; where it leads to failed builds.
3154 ,@(let ((system (or (%current-target-system) (%current-system))))
8a637e79
RW		 3155 (cond
3156 ((or (string-prefix? "x86_64" system)
71923a91 3157 (string-prefix? "i686" system))
8a637e79
RW		 3158 '("DYNAMIC_ARCH=1"))
3159 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
3160 ;; two available MIPS targets special extended instructions
3161 ;; for Loongson cores are used.
3162 ((string-prefix? "mips" system)
3163 '("TARGET=SICORTEX"))
83a34647
EF		 3164 ;; On aarch64 force the generic 'armv8-a' target
3165 ((string-prefix? "aarch64" system)
3166 '("TARGET=ARMV8"))
8a637e79 3167 (else '()))))
e73b49fb 3168 ;; no configure script
493937ae
DL		 3169 #:phases
3170 (modify-phases %standard-phases
3171 (delete 'configure)
3172 (add-before 'build 'set-extralib
3173 (lambda* (#:key inputs #:allow-other-keys)
3174 ;; Get libgfortran found when building in utest.
3175 (setenv "FEXTRALIB"
3176 (string-append "-L" (assoc-ref inputs "fortran-lib")
3177 "/lib"))
3178 #t)))))
e73b49fb 3179 (inputs
493937ae 3180 `(("fortran-lib" ,gfortran "lib")))
e73b49fb
RW		 3181 (native-inputs
3182 `(("cunit" ,cunit)
493937ae 3183 ("fortran" ,gfortran)
e73b49fb
RW		 3184 ("perl" ,perl)))
3185 (home-page "http://www.openblas.net/")
3186 (synopsis "Optimized BLAS library based on GotoBLAS")
3187 (description
3188 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
3189 (license license:bsd-3)))
3190
daa6036f 3191(define-public openblas-ilp64
ba05be22 3192 (package/inherit openblas
daa6036f
EB		 3193 (name "openblas-ilp64")
3194 (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
3195 (arguments
3196 (substitute-keyword-arguments (package-arguments openblas)
3197 ((#:make-flags flags '())
3198 `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
3199 ,flags))))
3200 (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
3201 (license license:bsd-3)))
3202
5a7deb11
LC		 3203(define* (make-blis implementation #:optional substitutable?)
3204 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
3205source tree for a list of implementations.)
3206
3207SUBSTITUTABLE? determines whether the package is made available as a
3208substitute.
3209
3210Currently the specialization must be selected at configure-time, but work is
3211underway to allow BLIS to select the right optimized kernels at run time:
3212<https://github.com/flame/blis/issues/129>."
3213 (package
3214 (name (if (string=? implementation "reference")
3215 "blis"
3216 (string-append "blis-" implementation)))
3217 (version "0.2.2")
3218 (home-page "https://github.com/flame/blis")
3219 (source (origin
3220 (method git-fetch)
3221 (uri (git-reference (url home-page) (commit version)))
3222 (sha256
3223 (base32
3224 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
3225 (file-name (git-file-name "blis" version))))
3226 (build-system gnu-build-system)
3227 (arguments
3228 `(#:test-target "test"
3229
3230 #:substitutable? ,substitutable?
3231
3232 #:phases (modify-phases %standard-phases
3233 (replace 'configure
3234 (lambda* (#:key outputs #:allow-other-keys)
3235 ;; This is a home-made 'configure' script.
3236 (let ((out (assoc-ref outputs "out")))
1ec17821
RW		 3237 (invoke "./configure" "-p" out
3238 "-d" "opt"
3239 "--disable-static"
3240 "--enable-shared"
3241 "--enable-threading=openmp"
5a7deb11 3242
1ec17821 3243 ,implementation))))
5a7deb11
LC		 3244 (add-before 'check 'show-test-output
3245 (lambda _
3246 ;; By default "make check" is silent. Make it verbose.
3247 (system "tail -F output.testsuite &")
3248 #t)))))
3249 (synopsis "High-performance basic linear algebra (BLAS) routines")
3250 (description
3251 "BLIS is a portable software framework for instantiating high-performance
3252BLAS-like dense linear algebra libraries. The framework was designed to
3253isolate essential kernels of computation that, when optimized, immediately
3254enable optimized implementations of most of its commonly used and
3255computationally intensive operations. While BLIS exports a new BLAS-like API,
3256it also includes a BLAS compatibility layer which gives application developers
3257access to BLIS implementations via traditional BLAS routine calls.")
3258 (license license:bsd-3)))
3259
3260(define-public blis
3261 ;; This is the "reference" implementation, which is the non-optimized but
3262 ;; portable variant (no assembly).
3263 (make-blis "reference" #t))
3264
3265(define ignorance blis)
3266
3267(define-syntax-rule (blis/x86_64 processor)
3268 "Expand to a package specialized for PROCESSOR."
3269 (package
3270 (inherit (make-blis processor))
3271 (supported-systems '("x86_64-linux"))))
3272
3273(define-public blis-sandybridge
3274 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
3275 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
3276 (blis/x86_64 "sandybridge"))
3277
3278(define-public blis-haswell
3279 ;; BLIS specialized for Haswell processors (launched 2013):
3280 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
3281 (blis/x86_64 "haswell"))
3282
3283(define-public blis-knl
3284 ;; BLIS specialized for Knights Landing processor (launched 2016):
3285 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
3286 (blis/x86_64 "knl"))
3287
3288
e1605e36
RW		 3289(define-public openlibm
3290 (package
3291 (name "openlibm")
48d7ac17 3292 (version "0.6.0")
e1605e36
RW		 3293 (source
3294 (origin
ca72dd2c
TGR		 3295 (method git-fetch)
3296 (uri (git-reference
3297 (url "https://github.com/JuliaLang/openlibm.git")
3298 (commit (string-append "v" version))))
3299 (file-name (git-file-name name version))
e1605e36 3300 (sha256
ca72dd2c 3301 (base32 "08wfchmmr5200fvmn1kwq9byc1fhsq46hn0y5k8scdl74771c7gh"))))
e1605e36
RW		 3302 (build-system gnu-build-system)
3303 (arguments
3304 `(#:make-flags
3305 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3306 #:phases
3307 ;; no configure script
dc1d3cde 3308 (modify-phases %standard-phases (delete 'configure))
e1605e36
RW		 3309 #:tests? #f)) ;the tests are part of the default target
3310 (home-page "http://openlibm.org/")
3311 (synopsis "Portable C mathematical library (libm)")
3312 (description
3313 "OpenLibm is an effort to have a high quality, portable, standalone C
3314mathematical library (libm). It can be used standalone in applications and
3315programming language implementations. The project was born out of a need to
e881752c 3316have a good libm for the Julia programming language that worked consistently
e1605e36
RW		 3317across compilers and operating systems, and in 32-bit and 64-bit
3318environments.")
538c0e3b
EF		 3319 ;; Each architecture has its own make target, and there is none for mips.
3320 (supported-systems (delete "mips64el-linux" %supported-systems))
e1605e36
RW		 3321 ;; See LICENSE.md for details.
3322 (license (list license:expat
3323 license:isc
3324 license:bsd-2
3325 license:public-domain
3326 license:lgpl2.1+))))
3327
e62be58f
RW		 3328(define-public openspecfun
3329 (package
3330 (name "openspecfun")
59cd0ba4 3331 (version "0.5.3")
e62be58f
RW		 3332 (source
3333 (origin
90cea671
TGR		 3334 (method git-fetch)
3335 (uri (git-reference
3336 (url "https://github.com/JuliaLang/openspecfun.git")
3337 (commit (string-append "v" version))))
3338 (file-name (git-file-name name version))
e62be58f 3339 (sha256
90cea671 3340 (base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh"))))
e62be58f
RW		 3341 (build-system gnu-build-system)
3342 (arguments
59cd0ba4 3343 '(#:tests? #f ; no "check" target
e62be58f
RW		 3344 #:make-flags
3345 (list (string-append "prefix=" (assoc-ref %outputs "out")))
59cd0ba4
TGR		 3346 #:phases
3347 (modify-phases %standard-phases
3348 (delete 'configure)))) ; no configure script
e62be58f 3349 (inputs
19afbea1 3350 `(("fortran" ,gfortran)))
e62be58f
RW		 3351 (home-page "https://github.com/JuliaLang/openspecfun")
3352 (synopsis "Collection of special mathematical functions")
3353 (description
3354 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
3355portable package for Bessel Functions of a Complex Argument and Nonnegative
3356Order; it contains subroutines for computing Bessel functions and Airy
3357functions. Faddeeva allows computing the various error functions of arbitrary
3358complex arguments (Faddeeva function, error function, complementary error
3359function, scaled complementary error function, imaginary error function, and
3360Dawson function); given these, one can also easily compute Voigt functions,
3361Fresnel integrals, and similar related functions as well.")
3362 ;; Faddeeva is released under the Expat license; AMOS is included as
3363 ;; public domain software.
3364 (license (list license:expat license:public-domain))))
3365
2742f87e
RW		 3366(define-public suitesparse
3367 (package
3368 (name "suitesparse")
bd5b5ac0 3369 (version "4.5.5")
2742f87e
RW		 3370 (source
3371 (origin
3372 (method url-fetch)
3373 (uri (string-append
3374 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
3375 version ".tar.gz"))
3376 (sha256
3377 (base32
bd5b5ac0
EB		 3378 "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
3379 (modules '((guix build utils)))
3380 (snippet
3381 ;; Remove bundled metis source
6cbee49d
MW		 3382 '(begin
3383 (delete-file-recursively "metis-5.1.0")
3384 #t))))
2742f87e
RW		 3385 (build-system gnu-build-system)
3386 (arguments
bd5b5ac0 3387 '(#:tests? #f ;no "check" target
2742f87e
RW		 3388 #:make-flags
3389 (list "CC=gcc"
3390 "BLAS=-lblas"
3391 "TBB=-ltbb"
bd5b5ac0 3392 "MY_METIS_LIB=-lmetis"
2742f87e
RW		 3393 (string-append "INSTALL_LIB="
3394 (assoc-ref %outputs "out") "/lib")
3395 (string-append "INSTALL_INCLUDE="
bd5b5ac0
EB		 3396 (assoc-ref %outputs "out") "/include")
3397 "library")
2742f87e 3398 #:phases
2509522c 3399 (modify-phases %standard-phases
bd5b5ac0 3400 (delete 'configure)))) ;no configure script
2742f87e
RW		 3401 (inputs
3402 `(("tbb" ,tbb)
bd5b5ac0
EB		 3403 ("lapack" ,lapack)
3404 ("metis" ,metis)))
2742f87e
RW		 3405 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
3406 (synopsis "Suite of sparse matrix software")
3407 (description
3408 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
3409multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
3410multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
3411simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
3412CXSparse, a concise sparse Cholesky factorization package; and many other
3413packages.")
3414 ;; LGPLv2.1+:
3415 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
3416 ;; GPLv2+:
3417 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
3418 (license (list license:gpl2+ license:lgpl2.1+))))
3419
ec322be2
FB		 3420(define-public atlas
3421 (package
3422 (name "atlas")
3c98ac02 3423 (version "3.10.3")
ec322be2
FB		 3424 (source (origin
3425 (method url-fetch)
de67e922
LF		 3426 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
3427 version "/atlas" version ".tar.bz2"))
ec322be2
FB		 3428 (sha256
3429 (base32
3c98ac02 3430 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
ec322be2
FB		 3431 (build-system gnu-build-system)
3432 (home-page "http://math-atlas.sourceforge.net/")
19afbea1 3433 (inputs `(("gfortran" ,gfortran)
ec322be2
FB		 3434 ("lapack-tar" ,(package-source lapack))))
3435 (outputs '("out" "doc"))
01480b9e
FB		 3436 ;; For the moment we drop support for MIPS at it fails to compile. See
3437 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
3438 (supported-systems (delete "mips64el-linux" %supported-systems))
ec322be2
FB		 3439 (arguments
3440 `(#:parallel-build? #f
3441 #:parallel-tests? #f
f15615b1
LC		 3442
3443 ;; ATLAS tunes itself for the machine it is built on, as explained at
3444 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
3445 ;; For this reason, we want users to build it locally instead of using
3446 ;; substitutes.
3447 #:substitutable? #f
3448
ec322be2 3449 #:modules ((srfi srfi-26)
ec322be2
FB		 3450 (guix build gnu-build-system)
3451 (guix build utils))
40029cbe 3452 #:configure-flags
ec322be2
FB		 3453 `(;; Generate position independent code suitable for dynamic libraries
3454 ;; and use WALL timer to get more accurate timing.
3455 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
3456 ;; Set word width.
3457 "-b"
3458 ,,(if (string-match "64" (%current-system))
3459 "64"
3460 "32")
3461 ;; Disable parallel build as it gives errors: atlas_pthread.h is
3462 ;; needed to compile C files before it is generated.
3463 "-Ss" "pmake" "make -j 1"
af89a667
FB		 3464 ;; Probe is failing for MIPS. We therefore define the system
3465 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3466 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3467 ,,@(if (string-prefix? "mips" (%current-system))
3468 (list "-A" "49" "-V" "1")
3469 (list))
ec322be2
FB		 3470 ;; Generate shared libraries.
3471 "--shared"
3472 ;; Build a full LAPACK library.
3473 ,(string-append "--with-netlib-lapack-tarfile="
3474 (assoc-ref %build-inputs "lapack-tar")))
3475 #:phases
e5b4b96b
EF		 3476 (modify-phases %standard-phases
3477 (add-after 'install 'install-doc
3478 (lambda* (#:key outputs inputs #:allow-other-keys)
3479 (let ((doc (string-append (assoc-ref outputs "doc")
3480 "/share/doc/atlas")))
3481 (mkdir-p doc)
cb6f44d4
RW		 3482 (for-each (cut install-file <> doc)
3483 (find-files "../ATLAS/doc" ".*"))
3484 #t)))
e5b4b96b 3485 (add-after 'check 'check-pt
cb6f44d4 3486 (lambda _ (invoke "make" "ptcheck")))
e5b4b96b
EF		 3487 ;; Fix files required to run configure.
3488 (add-before 'configure 'fix-/bin/sh
ec322be2
FB		 3489 (lambda _
3490 ;; Use `sh', not `/bin/sh'.
3491 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3492 (("/bin/sh")
5b786db8
EF		 3493 "sh"))
3494 #t))
e5b4b96b
EF		 3495 ;; Fix /bin/sh in generated make files.
3496 (add-after 'configure 'fix-/bin/sh-in-generated-files
3497 (lambda _
3498 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3499 (("/bin/sh")
5b786db8
EF		 3500 "sh"))
3501 #t))
e5b4b96b
EF		 3502 ;; ATLAS configure program does not accepts the default flags
3503 ;; passed by the 'gnu-build-system'.
3504 (replace 'configure
3505 (lambda* (#:key native-inputs inputs outputs
3506 (configure-flags '())
3507 #:allow-other-keys #:rest args)
3508 (let* ((prefix (assoc-ref outputs "out"))
3509 (bash (or (and=> (assoc-ref
3510 (or native-inputs inputs) "bash")
3511 (cut string-append <> "/bin/bash"))
3512 "/bin/sh"))
3513 (flags `(,(string-append "--prefix=" prefix)
3514 ,@configure-flags))
3515 (abs-srcdir (getcwd))
3516 (srcdir (string-append "../" (basename abs-srcdir))))
3517 (format #t "source directory: ~s (relative from build: ~s)~%"
3518 abs-srcdir srcdir)
3519 (mkdir "../build")
3520 (chdir "../build")
3521 (format #t "build directory: ~s~%" (getcwd))
3522 (format #t "configure flags: ~s~%" flags)
cb6f44d4
RW		 3523 (apply invoke bash
3524 (string-append srcdir "/configure")
3525 flags)))))))
ec322be2
FB		 3526 (synopsis "Automatically Tuned Linear Algebra Software")
3527 (description
3528 "ATLAS is an automatically tuned linear algebra software library
3529providing C and Fortran77 interfaces to a portably efficient BLAS
3530implementation, as well as a few routines from LAPACK.
3531
f15615b1
LC		 3532Optimization occurs at build time. For this reason, the library is built on
3533the machine where it is installed, without resorting to pre-built substitutes.
ec322be2 3534
f15615b1 3535Before building the library, CPU throttling should be disabled. This can be
d97c429a 3536done in the BIOS, or, on GNU/Linux, with the following command:
ec322be2 3537
8e9ba611 3538@example
d97c429a 3539# cpupower --governor performance
8e9ba611 3540@end example
ec322be2 3541
d97c429a 3542Failure to do so will result in a library with poor performance.")
ec322be2 3543 (license license:bsd-3)))
c12efc72
AE		 3544
3545(define-public glm
3546 (package
3547 (name "glm")
3f55b7be 3548 (version "0.9.9.6")
c12efc72
AE		 3549 (source
3550 (origin
3551 (method url-fetch)
5ea4b594
MB		 3552 (uri (string-append "https://github.com/g-truc/glm/releases/download/"
3553 version "/glm-" version ".zip"))
c12efc72 3554 (sha256
3f55b7be
TGR		 3555 (base32 "1l0pi1qi37mk6s0yrkrw07lspv4gcqnr9ryg3521hrl77ff37dwx"))
3556 (patches (search-patches "glm-restore-install-target.patch"))))
c12efc72
AE		 3557 (build-system cmake-build-system)
3558 (native-inputs
3559 `(("unzip" ,unzip)))
46bda5eb 3560 (home-page "https://glm.g-truc.net/")
c12efc72
AE		 3561 (synopsis "OpenGL Mathematics library")
3562 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3563library for graphics software based on the OpenGL Shading Language (GLSL)
3564specifications.")
3565 (license license:expat)))
7f18257b
AE		 3566
3567(define-public lpsolve
3568 (package
3569 (name "lpsolve")
a89e0cf5 3570 (version "5.5.2.5")
7f18257b
AE		 3571 (source
3572 (origin
3573 (method url-fetch)
3574 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3575 "/lp_solve_" version "_source.tar.gz"))
3576 (sha256
3577 (base32
a89e0cf5 3578 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
7f18257b
AE		 3579 (modules '((guix build utils)))
3580 (snippet
6cbee49d
MW		 3581 '(begin
3582 (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3583 (("^c=cc") "c=gcc")
3584 ;; Pretend to be on a 64 bit platform to obtain a common directory
3585 ;; name for the build results on all architectures; nothing else
3586 ;; seems to depend on it.
3587 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3588
3589 ;; The check for 'isnan' as it is written fails with
3590 ;; "non-floating-point argument in call to function
3591 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3592 ;; definition, which in turn leads to bad things. Fix the feature
3593 ;; test.
3594 (("isnan\\(0\\)") "isnan(0.)"))
3595 #t))))
7f18257b
AE		 3596 (build-system gnu-build-system)
3597 (arguments
6c96b545 3598 `(#:tests? #f ; no check target
7f18257b
AE		 3599 #:phases
3600 (modify-phases %standard-phases
6c96b545 3601 (delete 'configure) ; no configure script
7f18257b
AE		 3602 (replace 'build
3603 (lambda _
6c96b545
TGR		 3604 (with-directory-excursion "lpsolve55"
3605 (invoke "bash" "ccc"))
3606 (with-directory-excursion "lp_solve"
3607 (invoke "bash" "ccc"))
3608 #t))
7f18257b
AE		 3609 (replace 'install
3610 (lambda* (#:key outputs #:allow-other-keys)
3611 (let* ((out (assoc-ref outputs "out"))
3612 (bin (string-append out "/bin"))
3613 (lib (string-append out "/lib"))
3614 ;; This is where LibreOffice expects to find the header
3615 ;; files, and where they are installed by Debian.
3616 (include (string-append out "/include/lpsolve")))
6c96b545
TGR		 3617 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3618 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
96c46210
LC		 3619 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3620
7f18257b
AE		 3621 ;; Install a subset of the header files as on Debian
3622 ;; (plus lp_bit.h, which matches the regular expression).
96c46210
LC		 3623 (for-each (lambda (name)
3624 (install-file name include))
3625 (find-files "." "lp_[HMSa-z].*\\.h$"))
7f18257b 3626 (with-directory-excursion "shared"
96c46210
LC		 3627 (for-each (lambda (name)
3628 (install-file name include))
3629 (find-files "." "\\.h$")))
7f18257b
AE		 3630 #t))))))
3631 (home-page "http://lpsolve.sourceforge.net/")
3632 (synopsis "Mixed integer linear programming (MILP) solver")
3633 (description
3634 "lp_solve is a mixed integer linear programming solver based on the
3635revised simplex and the branch-and-bound methods.")
3636 (license license:lgpl2.1+)))
a17d4564
EB		 3637
3638(define-public dealii
3639 (package
3640 (name "dealii")
ba567cae 3641 (version "9.1.1")
a17d4564
EB		 3642 (source
3643 (origin
3644 (method url-fetch)
3645 (uri (string-append "https://github.com/dealii/dealii/releases/"
3646 "download/v" version "/dealii-" version ".tar.gz"))
3647 (sha256
3648 (base32
ba567cae 3649 "0xhjv0gzswpjbc43xbrpwfc5848g508l01855nszx3g5gwzlhnzw"))
a17d4564
EB		 3650 (modules '((guix build utils)))
3651 (snippet
3652 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
6cbee49d
MW		 3653 '(begin
3654 (delete-file-recursively "bundled")
3655 #t))))
a17d4564
EB		 3656 (build-system cmake-build-system)
3657 (inputs
3658 `(("tbb" ,tbb)
3659 ("zlib" ,zlib)
3660 ("boost" ,boost)
3661 ("p4est" ,p4est)
3662 ("blas" ,openblas)
3663 ("lapack" ,lapack)
3664 ("arpack" ,arpack-ng)
3665 ("muparser" ,muparser)
3666 ("gfortran" ,gfortran)
3667 ("suitesparse" ,suitesparse))) ;for UMFPACK
3668 (arguments
3669 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
d84b09e9
EB		 3670 #:configure-flags
3671 ;; Work around a bug in libsuitesparseconfig linking
3672 ;; see https://github.com/dealii/dealii/issues/4745
3673 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
a17d4564
EB		 3674 (home-page "https://www.dealii.org")
3675 (synopsis "Finite element library")
3676 (description
3677 "Deal.II is a C++ program library targeted at the computational solution
3678of partial differential equations using adaptive finite elements. The main
3679aim of deal.II is to enable rapid development of modern finite element codes,
3680using among other aspects adaptive meshes and a wide array of tools often used
3681in finite element programs.")
3682 (license license:lgpl2.1+)))
3683
3684(define-public dealii-openmpi
3685 (package (inherit dealii)
3686 (name "dealii-openmpi")
3687 (inputs
3688 `(("mpi" ,openmpi)
3689 ;;Supported only with MPI:
4d44bcad 3690 ("hdf5" ,hdf5-parallel-openmpi) ;TODO: have petsc-openmpi propagate?
a17d4564
EB		 3691 ("p4est" ,p4est-openmpi)
3692 ("petsc" ,petsc-openmpi)
3693 ("slepc" ,slepc-openmpi)
3694 ("metis" ,metis) ;for MUMPS
3695 ("scalapack" ,scalapack) ;for MUMPS
3696 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3697 ("arpack" ,arpack-ng-openmpi)
3698 ,@(fold alist-delete (package-inputs dealii)
3699 '("p4est" "arpack"))))
3700 (arguments
3701 (substitute-keyword-arguments (package-arguments dealii)
3702 ((#:configure-flags cf)
40b114c0
EB		 3703 `(cons "-DDEAL_II_WITH_MPI:BOOL=ON"
3704 ,cf))
7e309e8a
EB		 3705 ((#:phases phases '%standard-phases)
3706 `(modify-phases ,phases
3707 (add-before 'check 'mpi-setup
3708 ,%openmpi-setup)))))
a17d4564 3709 (synopsis "Finite element library (with MPI support)")))
194c7f95
AE		 3710
3711(define-public flann
3712 (package
3713 (name "flann")
3714 (version "1.8.4")
3715 (source
3716 (origin
3717 (method url-fetch)
3718 (uri
3719 (string-append
3720 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3721 version "-src.zip"))
3722 (sha256
3723 (base32
b5edc479
LC		 3724 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
3725 (patches (search-patches "flann-cmake-3.11.patch"))))
194c7f95 3726 (build-system cmake-build-system)
6b6aca9b
LC		 3727 (outputs '("out"
3728 "octave")) ;46 MiB .mex file that pulls Octave
194c7f95
AE		 3729 (native-inputs
3730 `(("unzip" ,unzip)))
3731 (inputs
3732 `(("hdf5" ,hdf5)
5537603f 3733 ("octave" ,octave-cli)
194c7f95
AE		 3734 ("python" ,python-2) ; print syntax
3735 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3736 ("zlib" ,zlib)))
3737 (arguments
39b30337
LC		 3738 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3739 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3740 #:strip-directories '("lib" "lib64" "libexec"
3741 "bin" "sbin" "share/flann/octave")
3742
9684e30b
LC		 3743 ;; Save 12 MiB by not installing .a files. Passing
3744 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3745 #:phases (modify-phases %standard-phases
6b6aca9b
LC		 3746 (add-before 'configure 'set-octave-directory
3747 (lambda* (#:key outputs #:allow-other-keys)
3748 ;; Install the .mex file in the "octave" output.
3749 (let ((out (assoc-ref outputs "octave")))
3750 (substitute* "src/matlab/CMakeLists.txt"
3751 (("share/flann/octave")
3752 (string-append out "/share/flann/octave")))
3753 #t)))
9684e30b
LC		 3754 (add-after 'install 'remove-static-libraries
3755 (lambda* (#:key outputs #:allow-other-keys)
3756 (let* ((out (assoc-ref outputs "out"))
3757 (lib (string-append out "/lib")))
3758 (for-each delete-file
3759 (find-files lib "\\.a$"))
3760 #t))))
3761
39b30337 3762 #:tests? #f)) ; The test data are downloaded from the Internet.
194c7f95
AE		 3763 (home-page "http://www.cs.ubc.ca/research/flann/")
3764 (synopsis "Library for approximate nearest neighbors computation")
3765 (description "FLANN is a library for performing fast approximate
3766nearest neighbor searches in high dimensional spaces. It implements a
3767collection of algorithms and a system for automatically choosing the best
3768algorithm and optimum parameters depending on the dataset.
3769
3770FLANN is written in C++ and contains bindings for C, Octave and Python.")
3771 (license (license:non-copyleft "file://COPYING"
3772 "See COPYING in the distribution."))))
d8c97beb
EF		 3773
3774(define-public wcalc
3775 (package
3776 (name "wcalc")
3777 (version "2.5")
3778 (source
3779 (origin
3780 (method url-fetch)
de67e922
LF		 3781 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3782 "wcalc-" version ".tar.bz2"))
d8c97beb
EF		 3783 (sha256
3784 (base32
3785 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3786 (build-system gnu-build-system)
3787 (inputs
3788 `(("mpfr" ,mpfr)
3789 ("readline" ,readline)))
3790 (home-page "http://w-calc.sourceforge.net/index.php")
3791 (synopsis "Flexible command-line scientific calculator")
3792 (description "Wcalc is a very capable calculator. It has standard functions
3793(sin, asin, and sinh for example, in either radians or degrees), many
3794pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3795variables, a command history, hex/octal/binary input and output, unit
3796conversions, embedded comments, and an expandable expression entry field. It
3797evaluates expressions using the standard order of operations.")
3798 (license license:gpl2+)))
45147b0c
FH		 3799
3800(define-public xaos
3801 (package
3802 (name "xaos")
3803 (version "3.6")
3804 (source (origin
3805 (method url-fetch)
de67e922
LF		 3806 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3807 "/xaos-" version ".tar.gz"))
45147b0c
FH		 3808 (sha256
3809 (base32
3810 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3811 (build-system gnu-build-system)
b94a6ca0 3812 (native-inputs `(("gettext" ,gettext-minimal)))
45147b0c
FH		 3813 (inputs `(("libx11" ,libx11)
3814 ("zlib" ,zlib)
3815 ("libpng" ,libpng)
3816 ("gsl" ,gsl)))
3817 (arguments
3818 `(#:tests? #f ;no "check" target
3819 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3820 (synopsis "Real-time fractal zoomer")
3821 (description "GNU XaoS is a graphical program that generates fractal
3822patterns and allows you to zoom in and out of them infinitely in a fluid,
3823continuous manner. It also includes tutorials that help to explain how fractals
3824are built. It can generate many different fractal types such as the Mandelbrot
3825set.")
6fd52309 3826 (home-page "https://www.gnu.org/software/xaos/")
45147b0c 3827 (license license:gpl2+)))
528bb464
EB		 3828
3829(define-public hypre
3830 (package
3831 (name "hypre")
be099727 3832 (version "2.15.1")
fabcbf32
TGR		 3833 (source
3834 (origin
3835 (method git-fetch)
3836 (uri (git-reference
3837 (url "https://github.com/LLNL/hypre.git")
3838 (commit (string-append "v" version))))
3839 (file-name (git-file-name name version))
3840 (sha256
be099727 3841 (base32 "1lvh4ybqkriyqfg2zmic6mrg1981qv1i9vry1fdgsabn81hb71g4"))
fabcbf32
TGR		 3842 (modules '((guix build utils)))
3843 (snippet
3844 '(begin
3845 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
be099727 3846 ;; substitute the release date.
fabcbf32
TGR		 3847 (substitute* "src/utilities/HYPRE_utilities.h"
3848 (("Date Compiled: .*$")
be099727 3849 "Date Compiled: Oct 19 2018 15:23:00 +0000\"\n"))
fabcbf32 3850 #t))))
528bb464 3851 (build-system gnu-build-system)
be099727
TGR		 3852 (outputs '("out" ; 6.1 MiB of headers and libraries
3853 "doc")) ; 4.8 MiB of documentation
528bb464
EB		 3854 (native-inputs
3855 `(("doc++" ,doc++)
3856 ("netpbm" ,netpbm)
be099727 3857 ("perl" ,perl) ; needed to run 'ppmquant' during tests
8b35c8cd
RW		 3858 ("texlive" ,(texlive-union (list texlive-xypic
3859 texlive-cm
9b405aea 3860 texlive-latex-hyperref
9b405aea 3861 texlive-bibtex)))
528bb464
EB		 3862 ("ghostscript" ,ghostscript)))
3863 (inputs
3864 `(("blas" ,openblas)
3865 ("lapack" ,lapack)))
3866 (arguments
3867 `(#:modules ((srfi srfi-1)
3868 ,@%gnu-build-system-modules)
3869 #:configure-flags '("--enable-shared"
3870 "--disable-fortran"
3871 "--without-MPI"
3872 "--with-openmp"
3873 "--with-fei"
3874 "--with-lapack"
3875 "--with-blas")
3876 #:phases
3877 (modify-phases %standard-phases
9b405aea
PN		 3878 (add-before 'build 'set-HOME
3879 (lambda _
3880 ;; FIXME: texlive-union does not find the built
3881 ;; metafonts, so it tries to generate them in HOME.
3882 (setenv "HOME" "/tmp")
3883 #t))
528bb464
EB		 3884 (add-before 'configure 'chdir-src
3885 (lambda _ (chdir "src")))
3886 (replace 'configure
3887 (lambda* (#:key build target configure-flags
3888 #:allow-other-keys #:rest args)
3889 (let* ((configure (assoc-ref %standard-phases 'configure)))
3890 (apply configure
3891 (append args
3892 (list #:configure-flags
3893 (cons (string-append
3894 "--host=" (or target build))
3895 configure-flags)))))))
3896 (add-after 'build 'build-docs
3897 (lambda _
9b405aea 3898 (invoke "make" "-Cdocs" "pdf" "html")))
528bb464
EB		 3899 (replace 'check
3900 (lambda _
3901 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3902 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
6b1c7ac8
RW		 3903 (invoke "make" "check" "CHECKRUN=")
3904 (for-each (lambda (filename)
3905 (let ((size (stat:size (stat filename))))
3906 (when (positive? size)
3907 (error (format #f "~a size ~d; error indication~%"
3908 filename size)))))
3909 (find-files "test" ".*\\.err$"))
3910 #t))
528bb464
EB		 3911 (add-after 'install 'install-docs
3912 (lambda* (#:key outputs #:allow-other-keys)
3913 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3914 (let* ((doc (assoc-ref outputs "doc"))
3915 (docdir (string-append doc "/share/doc/hypre-" ,version)))
528bb464
EB		 3916 (with-directory-excursion "docs"
3917 (for-each (lambda (base)
3918 (install-file (string-append base ".pdf") docdir)
be099727 3919 (copy-recursively base docdir)) ; html docs
528bb464
EB		 3920 '("HYPRE_usr_manual"
3921 "HYPRE_ref_manual")))
3922 #t))))))
3923 (home-page "http://www.llnl.gov/casc/hypre/")
3924 (synopsis "Library of solvers and preconditioners for linear equations")
3925 (description
3926 "HYPRE is a software library of high performance preconditioners and
3927solvers for the solution of large, sparse linear systems of equations. It
3928features multigrid solvers for both structured and unstructured grid
3929problems.")
3930 (license license:lgpl2.1)))
3931
3932(define-public hypre-openmpi
3933 (package (inherit hypre)
3934 (name "hypre-openmpi")
3935 (inputs
3936 `(("mpi" ,openmpi)
3937 ,@(package-inputs hypre)))
3938 (arguments
3939 (substitute-keyword-arguments (package-arguments hypre)
3940 ((#:configure-flags flags)
3941 ``("--with-MPI"
6df2a50a
LC		 3942 ,@(delete "--without-MPI" ,flags)))
3943 ((#:phases phases)
3944 `(modify-phases ,phases
bbe46a4a
EB		 3945 (add-before 'check 'mpi-setup
3946 ,%openmpi-setup)))))
528bb464
EB		 3947 (synopsis "Parallel solvers and preconditioners for linear equations")
3948 (description
3949 "HYPRE is a software library of high performance preconditioners and
3950solvers for the solution of large, sparse linear systems of equations on
3951parallel computers. It features parallel multigrid solvers for both
3952structured and unstructured grid problems.")))
6c90e183
EB		 3953
3954(define-public matio
3955 (package
3956 (name "matio")
3957 (version "1.5.6")
3958 (source
3959 (origin
3960 (method url-fetch)
de67e922 3961 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
6c90e183
EB		 3962 "matio-" version ".tar.gz"))
3963 (sha256
3964 (base32
3965 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3966 (build-system gnu-build-system)
3967 (inputs
3968 `(("zlib" ,zlib)
3969 ("hdf5" ,hdf5)))
3970 (home-page "http://matio.sourceforge.net/")
3971 (synopsis "Library for reading and writing MAT files")
3972 (description "Matio is a library for reading and writing MAT files. It
3973supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3974 (license license:bsd-2)))
d721c83a 3975
517318ad
LF		 3976(define-public vc
3977 (package
3978 (name "vc")
9d731fb6 3979 (version "1.4.1")
517318ad
LF		 3980 (source
3981 (origin (method url-fetch)
3982 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3983 "download/" version "/Vc-" version ".tar.gz"))
3984 (sha256
3985 (base32
9d731fb6 3986 "17qili8bf8r78cng65yf4qmgna8kiqjqbgcqbric6v9j6nkhkrk8"))))
517318ad
LF		 3987 (build-system cmake-build-system)
3988 (arguments
3989 '(#:configure-flags
33d82486
MB		 3990 '("-DBUILD_TESTING=ON"
3991 ;; By default, Vc will optimize for the CPU of the build machine.
3992 ;; Setting this to "none" makes it create portable binaries. See
3993 ;; "cmake/OptimizeForArchitecture.cmake".
9d731fb6
MB		 3994 "-DTARGET_ARCHITECTURE=none")
3995 #:phases (modify-phases %standard-phases
3996 (add-after 'unpack 'copy-testdata
3997 (lambda* (#:key inputs native-inputs #:allow-other-keys)
3998 (let ((testdata (assoc-ref (or native-inputs inputs)
3999 "testdata")))
4000 (copy-recursively testdata "tests/testdata")
4001 #t))))))
4002 (native-inputs
4003 `(("virtest" ,virtest)
4004
4005 ;; This is a submodule in the git project, but not part of the
4006 ;; released sources. See the git branch for the commit to take.
4007 ("testdata" ,(let ((commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3"))
4008 (origin
4009 (method git-fetch)
4010 (uri (git-reference
4011 (url "https://github.com/VcDevel/vc-testdata")
4012 (commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3")))
4013 (file-name (git-file-name "vc-testdata"
4014 (string-take commit 7)))
4015 (sha256
4016 (base32
4017 "1hkhqib03qlcq412ym2dciynfxcdr2ygqhnplz4l1vissr1wnqn2")))))))
517318ad
LF		 4018 (synopsis "SIMD vector classes for C++")
4019 (description "Vc provides portable, zero-overhead C++ types for explicitly
4020data-parallel programming. It is a library designed to ease explicit
4021vectorization of C++ code. Its types enable explicitly stating data-parallel
4022operations on multiple values. The parallelism is therefore added via the type
4023system. Vc has an intuitive API and provides portability between different
4024compilers and compiler versions as well as portability between different vector
4025instruction sets. Thus, an application written with Vc can be compiled for:
4026@enumerate
4027@item AVX and AVX2
d1e4ad1b 4028@item SSE2 up to SSE4.2 or SSE4a
517318ad
LF		 4029@item Scalar
4030@item MIC
4031@item NEON (in development)
4032@item NVIDIA GPUs / CUDA (in development)
4033@end enumerate\n")
4034 (home-page "https://github.com/VcDevel/Vc")
a8ead6f9
EF		 4035 ;; "No support_???.cpp file exists for this architecture."
4036 (supported-systems '("x86_64-linux" "i686-linux"))
517318ad 4037 (license license:bsd-3)))
54052a54 4038
4039(define-public reducelcs
4040 ;; This is the last commit which is available upstream, no
4041 ;; release happened since 2010.
4042 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
4043 (revision "1"))
4044 (package
4045 (name "reducelcs")
4046 (version (string-append "1.0-" revision "." (string-take commit 7)))
4047 (source
4048 (origin
4049 (method git-fetch)
4050 (uri (git-reference
4051 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
4052 (commit commit)))
4053 (file-name (string-append name "-" version "-checkout"))
4054 (sha256
4055 (base32
4056 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
4057 (build-system gnu-build-system)
4058 (inputs
4059 `(("openlibm" ,openlibm)))
4060 (arguments
4061 `(#:tests? #f ; no tests
4062 #:phases
4063 (modify-phases %standard-phases
4064 (delete 'configure) ; No configure script exists.
4065 (replace 'install ; No install phase exists.
4066 (lambda* (#:key outputs #:allow-other-keys)
4067 (let* ((out (assoc-ref outputs "out"))
4068 (bin (string-append out "/bin")))
4069 (install-file "Approximation" bin)
4070 (install-file "CollectResults" bin)
4071 (install-file "GenerateInstances" bin)
4072 #t))))))
4073 (synopsis "Approximate Longest Commons Subsequence computation tool")
4074 (description
4075 "@code{reduceLCS} is an implementation of the Reduce-Expand
4076algorithm for LCS. It is a fast program to compute the approximate
4077Longest Commons Subsequence of a set of strings.")
4078 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
c000b6b1 4079 (license license:gpl3+))))
479c4273
JD		 4080
4081(define-public jacal
4082 (package
4083 (name "jacal")
4084 (version "1c4")
4085 (source (origin
4086 (method url-fetch)
4087 (uri (string-append
4088 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
4089 version ".zip"))
4090 (sha256 (base32
4091 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
4092 (patches (search-patches "jacal-fix-texinfo.patch"))))
4093 (build-system gnu-build-system)
4094 (arguments
4095 `(#:phases
4096 (modify-phases %standard-phases
4097 (add-before 'build 'pre-build
4098 ;; Don't use upstream's script - it really doesn't fit into
4099 ;; Guix's functional paradigm.
4100 (lambda* (#:key inputs outputs #:allow-other-keys)
4101 (substitute* "Makefile"
4102 (("^install: install-script") "install: "))))
4103 (add-after 'install 'post-install
4104 ;; Instead, we provide our own simplified script.
4105 (lambda* (#:key inputs outputs #:allow-other-keys)
4106 (let ((wrapper (string-append (assoc-ref outputs "out")
4107 "/bin/jacal")))
4108 (format (open wrapper (logior O_WRONLY O_CREAT))
4109 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
4110 "-e '(slib:load \"~a/lib/jacal/math\") "
4111 "(math)' \"$@\"\n")
4112 (which "bash")
4113 (assoc-ref inputs "scm")
4114 (assoc-ref outputs "out"))
4115 (chmod wrapper #o555))))
4116 (replace 'configure
9cd82b1c
RW		 4117 (lambda* (#:key outputs #:allow-other-keys)
4118 (invoke "./configure"
4119 (string-append "--prefix="
4120 (assoc-ref outputs "out"))))))))
479c4273
JD		 4121 (inputs `(("scm" ,scm)))
4122 (native-inputs `(("unzip" ,unzip)
4123 ("texinfo" ,texinfo)))
4124 (synopsis "Symbolic mathematics system")
4125 (description "GNU JACAL is an interactive symbolic mathematics program based on
4126Scheme. It manipulate and simplify a range of mathematical expressions such
4127as equations, scalars, vectors, and matrices.")
6fd52309 4128 (home-page "https://www.gnu.org/software/jacal/")
479c4273
JD		 4129 (license license:gpl3+)))
4130
313844d9
TF		 4131(define-public z3
4132 (package
4133 (name "z3")
dbef037f 4134 (version "4.8.7")
fb525bfd 4135 (home-page "https://github.com/Z3Prover/z3")
313844d9 4136 (source (origin
fb525bfd
MB		 4137 (method git-fetch)
4138 (uri (git-reference (url home-page)
4139 (commit (string-append "z3-" version))))
2d7b99b3 4140 (file-name (git-file-name name version))
313844d9
TF		 4141 (sha256
4142 (base32
dbef037f 4143 "0hprcdwhhyjigmhhk6514m71bnmvqci9r8gglrqilgx424r6ff7q"))))
fa574a6d 4144 (build-system gnu-build-system)
313844d9 4145 (arguments
fa574a6d 4146 `(#:phases
313844d9 4147 (modify-phases %standard-phases
ad6c6a5b
EF		 4148 (add-after 'unpack 'fix-compatability
4149 ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
4150 (lambda _
4151 (substitute* "src/util/mpz.cpp"
4152 (("#include <immintrin.h>") ""))
4153 #t))
cf684d87
TF		 4154 (add-before 'configure 'bootstrap
4155 (lambda _
32d5360f 4156 (invoke "python" "scripts/mk_make.py")))
fa574a6d
AB		 4157 ;; work around gnu-build-system's setting --enable-fast-install
4158 ;; (z3's `configure' is a wrapper around the above python file,
4159 ;; which fails when passed --enable-fast-install)
4160 (replace 'configure
4161 (lambda* (#:key inputs outputs #:allow-other-keys)
4162 (invoke "./configure"
4163 (string-append "--prefix=" (assoc-ref outputs "out")))))
4164 (add-after 'configure 'change-directory
4165 (lambda _
4166 (chdir "build")
4167 #t))
cf684d87 4168 (add-before 'check 'make-test-z3
313844d9 4169 (lambda _
cf684d87 4170 ;; Build the test suite executable.
32d5360f
RW		 4171 (invoke "make" "test-z3" "-j"
4172 (number->string (parallel-job-count)))))
cf684d87
TF		 4173 (replace 'check
4174 (lambda _
4175 ;; Run all the tests that don't require arguments.
32d5360f 4176 (invoke "./test-z3" "/a"))))))
313844d9 4177 (native-inputs
fa574a6d
AB		 4178 `(("which" ,which)
4179 ("python" ,python-wrapper)))
313844d9
TF		 4180 (synopsis "Theorem prover")
4181 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
cf684d87 4182theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
313844d9 4183 (license license:expat)))
3d5d87a3 4184
6d433d6e
EB		 4185(define-public elpa
4186 (package
4187 (name "elpa")
4188 (version "2018.11.001")
4189 (source (origin
4190 (method url-fetch)
4191 (uri (string-append "http://elpa.mpcdf.mpg.de/html/Releases/"
4192 version "/elpa-" version ".tar.gz"))
4193 (sha256
4194 (base32
4195 "05hv3v5i6xmziaizw350ff72y1c3k662r85fm3xfdrkclj5zw9yc"))))
4196 (build-system gnu-build-system)
4197 (native-inputs
4198 `(("fortran" ,gfortran)
4199 ("perl" ,perl))) ;for configure and deps
4200 (inputs
4201 `(("blas" ,openblas)))
4202 (arguments
4203 `(#:configure-flags
4204 `("--enable-openmp"
4205 "--with-mpi=no"
4206 ;; ELPA unfortunately does not support runtime dispatch, so we can
4207 ;; only enable the "generic" kernels. See the "Cross compilation"
4208 ;; section of INSTALL.md.
4209 "--enable-generic"
4210 "--disable-sse" "--disable-sse-assembly" ;Require SSE3
4211 "--disable-avx" "--disable-avx2" "--disable-avx512"
4212 ,(string-append "CFLAGS=-O3 "
4213 "-funsafe-loop-optimizations -funsafe-math-optimizations "
4214 "-ftree-vect-loop-version -ftree-vectorize "
4215 ,(let ((system (or (%current-target-system)
4216 (%current-system))))
4217 (cond
4218 ((or (string-prefix? "x86_64" system)
4219 (string-prefix? "i686" system))
4220 "-msse2")
4221 (else "")))))
4222 #:parallel-tests? #f ;tests are multi-threaded, via BLAS
4223 #:phases
4224 (modify-phases %standard-phases
4225 (add-before 'configure 'patch-header-generation
4226 (lambda _
4227 (substitute* "configure"
4228 (("^ *make.*top_srcdir=\"\\$srcdir\"" &)
4229 (string-append & " CPP=\"$CPP\"")))
4230 #t))
4231 (add-before 'check 'setup-tests
4232 (lambda _
4233 ;; Decrease test time and RAM use by computing fewer eigenvalues.
4234 ;; The flags are (MATRIX-SIZE, EIGENVALUES, BLOCK-SIZE), where
4235 ;; the default is (500, 250, 16) for C tests and (5000, 150, 16)
4236 ;; for Fortran. This also causes several tests to pass that
4237 ;; otherwise would otherwise fail with matrix size 5000; possibly
4238 ;; due to floating point tolerances that are too tight.
4239 (setenv "TEST_FLAGS" "1500 50 16") ;from elpa.spec
4240 (setenv "OMP_NUM_THREADS" (number->string (parallel-job-count)))
4241 (substitute* "Makefile"
4242 ;; Test scripts are generated, patch the shebang
4243 (("#!/bin/bash") (string-append "#!" (which "sh"))))
4244 #t)))))
4245 (home-page "http://elpa.mpcdf.mpg.de")
4246 (synopsis "Eigenvalue solvers for symmetric matrices")
4247 (description
4248 "The ELPA library provides efficient and scalable direct eigensolvers for
4249symmetric matrices.")
4250 (license license:lgpl3)))
4251
4252(define-public elpa-openmpi
4253 (package (inherit elpa)
4254 (name "elpa-openmpi")
4255 (inputs
4256 `(("mpi" ,openmpi)
4257 ("scalapack" ,scalapack)
4258 ,@(package-inputs elpa)))
4259 (arguments
4260 (substitute-keyword-arguments (package-arguments elpa)
4261 ((#:configure-flags cf '())
4262 `(cons "--with-mpi=yes" (delete "--with-mpi=no" ,cf)))
4263 ((#:phases phases '%standard-phases)
4264 `(modify-phases ,phases
4265 (add-before 'check 'mpi-setup
4266 (lambda _
4267 ;; Tests use 2 mpi tasks by default, use our remaining build
4268 ;; cores as OpenMP threads.
4269 (setenv "OMP_NUM_THREADS" (number->string
4270 (max (quotient (parallel-job-count) 2)
4271 1)))
4272 (,%openmpi-setup)))))))
4273 (synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)")))
4274
e01397b4
EB		 4275(define-public elemental
4276 (package
4277 (name "elemental")
4278 (version "0.87.7")
4279 (source (origin
5c0b6d1b
EF		 4280 (method git-fetch)
4281 (uri (git-reference
4282 (url "https://github.com/elemental/Elemental.git")
4283 (commit (string-append "v" version))))
4284 (file-name (git-file-name name version))
e01397b4
EB		 4285 (sha256
4286 (base32
5c0b6d1b 4287 "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
e01397b4
EB		 4288 (build-system cmake-build-system)
4289 (home-page "http://libelemental.org")
4290 (native-inputs
4291 `(("gfortran" ,gfortran)))
4292 (inputs
4293 `(("blas" ,openblas)
4294 ("gfortran:lib" ,gfortran "lib")
4295 ("gmp" ,gmp)
4296 ("lapack" ,lapack)
4297 ("metis" ,metis)
4298 ("mpc" ,mpc)
4299 ("mpfr" ,mpfr)
4300 ("mpi" ,openmpi)
4301 ("qd" ,qd)))
4302 (arguments
4303 `(#:build-type "Release" ;default RelWithDebInfo not supported
4304 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
4305 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
4306 "-DEL_CACHE_WARNINGS:BOOL=YES"
4307 "-DEL_TESTS:BOOL=YES"
4308 "-DCMAKE_INSTALL_LIBDIR=lib"
4309 "-DGFORTRAN_LIB=gfortran")
4310 #:phases (modify-phases %standard-phases
3b42e2be
EF		 4311 (add-before 'check 'mpi-setup
4312 ,%openmpi-setup)
e01397b4
EB		 4313 (add-before 'check 'setup-tests
4314 (lambda _
4315 ;; Parallelism is done at the MPI layer.
4316 (setenv "OMP_NUM_THREADS" "1")
4317 #t))
4318 (add-after 'install 'remove-tests
4319 (lambda* (#:key outputs #:allow-other-keys)
4320 ;; Tests are installed, with no easy configuration
4321 ;; switch to prevent this, so delete them.
4322 (delete-file-recursively
3b42e2be 4323 (string-append (assoc-ref outputs "out") "/bin"))
e01397b4
EB		 4324 #t)))))
4325 (synopsis "Dense and sparse-direct linear algebra and optimization")
4326 (description "Elemental is a modern C++ library for distributed-memory
4327dense and sparse-direct linear algebra, conic optimization, and lattice
4328reduction.")
4329 (license license:bsd-2)))
5b05dce7
JN		 4330
4331(define-public mcrl2
4332 (package
4333 (name "mcrl2")
3bc74090 4334 (version "201908.0")
5b05dce7
JN		 4335 (source (origin
4336 (method url-fetch)
185152e3
JN		 4337 (uri (string-append
4338 "https://www.mcrl2.org/download/release/mcrl2-"
4339 version ".tar.gz"))
5b05dce7
JN		 4340 (sha256
4341 (base32
3bc74090 4342 "1i4xgl2d5fgiz1mwi50cyfkrrcpm8nxfayfjgmhq7chs58wlhfsz"))))
5b05dce7
JN		 4343 (inputs
4344 `(("boost" ,boost)
4345 ("glu" ,glu)
4346 ("mesa" ,mesa)
077d66ed 4347 ("qtbase" ,qtbase)))
5b05dce7 4348 (build-system cmake-build-system)
ed0c5d3c 4349 (synopsis "Toolset for the mCRL2 formal specification language")
5b05dce7 4350 (description
ed0c5d3c
TGR		 4351 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
4352specification language for describing concurrent discrete event systems. Its
4353toolset supports analysis and automatic verification, linearisation, simulation,
4354state-space exploration and generation, and tools to optimise and analyse
5b05dce7
JN		 4355specifications. Also, state spaces can be manipulated, visualised and
4356analysed.")
b3882709 4357 (home-page "https://mcrl2.org")
5b05dce7 4358 (license license:boost1.0)))
41835f94 4359
e03b9126
JN		 4360(define-public mcrl2-minimal
4361 (package
4362 (inherit mcrl2)
4363 (name "mcrl2-minimal")
4364 (inputs
4365 `(("boost" ,boost)))
4366 (arguments
4367 '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
4368
910deec6
NV		 4369(define-public tcalc
4370 (package
4371 (name "tcalc")
4372 (version "2.0")
4373 (source
4374 (origin
4375 (method url-fetch)
4376 (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
4377 version ".tar.gz"))
4378 (sha256
4379 (base32
4380 "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
4381 (build-system gnu-build-system)
4382 (synopsis "The terminal calculator")
4383 (description
4384 "The terminal calculator is a small program to help users of the GNU/Linux
4385terminal do calculations simply and quickly. The formula to be calculated can
4386be fed to @command{tcalc} through the command line.")
4387 (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
4388 (license license:gpl3+)))
b26e4f26
EB		 4389
4390(define-public sundials
4391 (package
4392 (name "sundials")
4393 (version "3.1.1")
4394 (source
4395 (origin
4396 (method url-fetch)
4397 (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
4398 "sundials-" version ".tar.gz"))
4399 (sha256
4400 (base32
4401 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
4402 (build-system cmake-build-system)
4403 (native-inputs
4404 `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
4405 (inputs
4406 `(("fortran" ,gfortran) ;for fcmix
4407 ("blas" ,openblas)
4408 ("suitesparse" ,suitesparse))) ;TODO: Add hypre
4409 (arguments
4410 `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
4411 "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
4412 "-DEXAMPLES_ENABLE_F77:BOOL=ON"
4413 "-DEXAMPLES_ENABLE_F90:BOOL=ON"
4414 "-DEXAMPLES_INSTALL:BOOL=OFF"
4415
4416 "-DFCMIX_ENABLE:BOOL=ON"
4417
4418 "-DKLU_ENABLE:BOOL=ON"
4419 ,(string-append "-DKLU_INCLUDE_DIR="
4420 (assoc-ref %build-inputs "suitesparse")
4421 "/include")
4422 ,(string-append "-DKLU_LIBRARY_DIR="
4423 (assoc-ref %build-inputs "suitesparse")
4424 "/lib"))))
4425 (home-page "https://computation.llnl.gov/projects/sundials")
4426 (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
4427 (description "SUNDIALS is a family of software packages implemented with
4428the goal of providing robust time integrators and nonlinear solvers that can
4429easily be incorporated into existing simulation codes.")
4430 (license license:bsd-3)))
4431
4432(define-public sundials-openmpi
4433 (package (inherit sundials)
4434 (name "sundials-openmpi")
4435 (inputs
4436 `(("mpi" ,openmpi)
4437 ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
4438 ,@(package-inputs sundials)))
4439 (arguments
4440 (substitute-keyword-arguments (package-arguments sundials)
4441 ((#:configure-flags flags '())
4442 `(cons* "-DMPI_ENABLE:BOOL=ON"
4443 "-DPETSC_ENABLE:BOOL=ON"
4444 (string-append "-DPETSC_INCLUDE_DIR="
4445 (assoc-ref %build-inputs "petsc")
4446 "/include")
4447 (string-append "-DPETSC_LIBRARY_DIR="
4448 (assoc-ref %build-inputs "petsc")
4449 "/lib")
4450 ,flags))
4451 ((#:phases phases '%standard-phases)
4452 `(modify-phases ,phases
bbe46a4a
EB		 4453 (add-before 'check 'mpi-setup
4454 ,%openmpi-setup)))))
b26e4f26 4455 (synopsis "SUNDIALS with OpenMPI support")))
a6b9ebc2
EB		 4456
4457(define-public combinatorial-blas
4458 (package
4459 (name "combinatorial-blas")
4460 (version "1.6.2")
4461 (source
4462 (origin
4463 (method url-fetch)
4464 (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/"
4465 "CombBLAS_beta_"
4466 (match (string-split version #\.)
4467 ((major minor patch)
4468 (string-append major minor "_" patch))) ;e.g. "16_2"
4469 ".tgz"))
4470 (sha256
4471 (base32
4472 "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a"))
4473 (patches (search-patches "combinatorial-blas-awpm.patch"
4474 "combinatorial-blas-io-fix.patch"))))
4475 (build-system cmake-build-system)
4476 (inputs
4477 `(("mpi" ,openmpi)
4478 ("test-data" ,(origin
4479 (method url-fetch)
4480 (uri (string-append "https://people.eecs.berkeley.edu/~aydin/"
4481 "CombBLAS_FILES/testdata_combblas1.6.1.tgz"))
4482 (sha256
4483 (base32
4484 "01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87"))))))
4485 (arguments
4486 `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
4487 "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL")
4488 #:parallel-tests? #f ;tests use 'mpiexec -n4'
4489 #:phases
4490 (modify-phases %standard-phases
4491 (add-before 'check 'mpi-setup
4492 ,%openmpi-setup)
4493 (add-before 'check 'test-setup
4494 (lambda* (#:key inputs #:allow-other-keys)
4495 (setenv "OMP_NUM_THREADS" "2")
4496 (invoke "tar" "xf" (assoc-ref inputs "test-data")))))))
4497 (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/")
4498 (synopsis "Linear algebra primitives for graph analytics")
4499 (description "The Combinatorial BLAS (CombBLAS) is an extensible
4500distributed-memory parallel graph library offering a small but powerful set of
4501linear algebra primitives specifically targeting graph analytics.")
4502 (license (list
4503 license:gpl2+ ;include/psort/(funnel|sort)*.h
4504 license:x11 ;usort and psort
4505 license:bsd-3)))) ;CombBLAS and MersenneTwister.h
3847d1f2
RW		 4506
4507(define-public dune-common
4508 (package
4509 (name "dune-common")
4510 (version "2.6.0")
4511 (source
4512 (origin
4513 (method url-fetch)
4514 (uri (string-append "https://dune-project.org/download/"
4515 version "/dune-common-" version ".tar.gz"))
4516 (sha256
4517 (base32
4518 "019wcr1qf7jwyxx1y5y290wdlglylskvbb2m01ljkzcza2xnlmhw"))))
4519 (build-system cmake-build-system)
4520 (arguments
4521 `(#:phases
4522 (modify-phases %standard-phases
4523 (add-after 'build 'build-tests
4524 (lambda* (#:key make-flags #:allow-other-keys)
4525 (apply invoke "make" "build_tests" make-flags)))
4526 ;; These tests fail because they require a fully functional MPI
4527 ;; environment.
4528 (add-after 'unpack 'disable-failing-tests
4529 (lambda _
4530 (setenv "ARGS"
4531 (string-append "--exclude-regex '("
4532 (string-join
4533 (list
4534 "remoteindicestest"
4535 "remoteindicestest-mpi-2"
4536 "syncertest"
4537 "syncertest-mpi-2"
4538 "variablesizecommunicatortest"
4539 "variablesizecommunicatortest-mpi-2"
4540 "arithmetictestsuitetest"
4541 "assertandreturntest"
4542 "assertandreturntest_ndebug"
4543 "concept"
4544 "debugaligntest"
4545 "mpicollectivecommunication"
4546 "mpicollectivecommunication-mpi-2"
4547 "mpiguardtest"
4548 "mpiguardtest-mpi-2"
4549 "mpihelpertest"
4550 "mpihelpertest-mpi-2"
4551 "mpihelpertest2"
4552 "mpihelpertest2-mpi-2")
4553 "|")
4554 ")'"))
4555 #t)))))
4556 (inputs
4557 `(("gmp" ,gmp)
4558 ("metis" ,metis)
4559 ("openmpi" ,openmpi)
4560 ("openblas" ,openblas)
4561 ("python" ,python)
4562 ("superlu" ,superlu)))
4563 (native-inputs
4564 `(("gfortran" ,gfortran)
4565 ("pkg-config" ,pkg-config)))
4566 (home-page "https://dune-project.org/")
4567 (synopsis "Distributed and Unified Numerics Environment")
4568 (description "DUNE, the Distributed and Unified Numerics Environment is a
4569modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4570grid-based methods. It supports the easy implementation of methods like
4571@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4572Differences} (FD).")
4573 ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2.
4574 (license license:gpl2)))
242dbd8e
RW		 4575
4576(define-public dune-geometry
4577 (package
4578 (name "dune-geometry")
4579 (version "2.6.0")
4580 (source
4581 (origin
4582 (method url-fetch)
4583 (uri (string-append "https://dune-project.org/download/"
4584 version "/dune-geometry-" version ".tar.gz"))
4585 (sha256
4586 (base32
4587 "0hlaaxjyv9j05blasvb67sy02hd0w4g9znf68gdh3l731dd1aqbn"))))
4588 (build-system cmake-build-system)
4589 (arguments
4590 `(#:phases
4591 (modify-phases %standard-phases
4592 (add-after 'build 'build-tests
4593 (lambda* (#:key make-flags #:allow-other-keys)
4594 (apply invoke "make" "build_tests" make-flags))))))
4595 (inputs
4596 `(("dune-common" ,dune-common)
4597 ("openmpi" ,openmpi)
4598 ;; Optional
4599 ("openblas" ,openblas)
4600 ("gmp" ,gmp)
4601 ("python" ,python)))
4602 (native-inputs
4603 `(("gfortran" ,gfortran)
4604 ("pkg-config" ,pkg-config)))
4605 (home-page "https://dune-project.org/")
4606 (synopsis "Distributed and Unified Numerics Environment")
4607 (description "DUNE, the Distributed and Unified Numerics Environment is a
4608modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4609grid-based methods. It supports the easy implementation of methods like
4610@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4611Differences} (FD).
4612
4613This package contains the basic DUNE geometry classes.")
4614 ;; GPL version 2 with "runtime exception"
4615 (license license:gpl2)))
ef6e69fd
RW		 4616
4617(define-public dune-grid
4618 (package
4619 (name "dune-grid")
4620 (version "2.6.0")
4621 (source
4622 (origin
4623 (method url-fetch)
4624 (uri (string-append "https://dune-project.org/download/"
4625 version "/dune-grid-" version ".tar.gz"))
4626 (sha256
4627 (base32
4628 "1jp4vscm9yb9xg0lh7apzccfkhvgbnk652yahigmh3cvzpl4acd0"))))
4629 (build-system cmake-build-system)
4630 (arguments
4631 `(#:phases
4632 (modify-phases %standard-phases
4633 (add-after 'build 'build-tests
4634 (lambda* (#:key make-flags #:allow-other-keys)
4635 (apply invoke "make" "build_tests" make-flags)))
4636 ;; These tests fail because they require a fully functional MPI
4637 ;; environment.
4638 (add-after 'unpack 'disable-failing-tests
4639 (lambda _
4640 (setenv "ARGS"
4641 (string-append "--exclude-regex '("
4642 (string-join
4643 (list
4644 "scsgmappertest"
4645 "conformvolumevtktest"
4646 "gnuplottest"
4647 "nonconformboundaryvtktest"
4648 "subsamplingvtktest"
4649 "vtktest"
4650 "vtktest-mpi-2"
4651 "vtksequencetest"
4652 "gmshtest-onedgrid"
4653 "test-dgf-yasp"
4654 "test-dgf-yasp-offset"
4655 "test-dgf-oned"
4656 "test-geogrid-yaspgrid"
4657 "test-gridinfo"
4658 "test-identitygrid"
4659 "testiteratorranges"
4660 "test-hierarchicsearch"
4661 "test-parallel-ug-mpi-2"
4662 "test-yaspgrid-backuprestore-equidistant"
4663 "test-yaspgrid-backuprestore-equidistant-mpi-2"
4664 "test-yaspgrid-backuprestore-equidistantoffset"
4665 "test-yaspgrid-backuprestore-equidistantoffset-mpi-2"
4666 "test-yaspgrid-backuprestore-tensor"
4667 "test-yaspgrid-backuprestore-tensor-mpi-2"
4668 "test-yaspgrid-tensorgridfactory"
4669 "test-yaspgrid-tensorgridfactory-mpi-2"
4670 "test-yaspgrid-yaspfactory-1d"
4671 "test-yaspgrid-yaspfactory-1d-mpi-2"
4672 "test-yaspgrid-yaspfactory-2d"
4673 "test-yaspgrid-yaspfactory-2d-mpi-2"
4674 "test-yaspgrid-yaspfactory-3d"
4675 "test-yaspgrid-yaspfactory-3d-mpi-2"
4676 "globalindexsettest"
4677 "persistentcontainertest"
4678 "structuredgridfactorytest"
4679 "tensorgridfactorytest"
4680 "vertexordertest")
4681 "|")
4682 ")'"))
4683 #t)))))
4684 (inputs
4685 `(("dune-common" ,dune-common)
4686 ("dune-geometry" ,dune-geometry)
4687 ("gmp" ,gmp)
4688 ("metis" ,metis)
4689 ("openblas" ,openblas)
4690 ("openmpi" ,openmpi)
4691 ("python" ,python)))
4692 (native-inputs
4693 `(("gfortran" ,gfortran)
4694 ("pkg-config" ,pkg-config)))
4695 (home-page "https://dune-project.org/")
4696 (synopsis "Distributed and Unified Numerics Environment")
4697 (description "DUNE, the Distributed and Unified Numerics Environment is a
4698modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4699grid-based methods. It supports the easy implementation of methods like
4700@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4701Differences} (FD).
4702
4703This package contains the basic DUNE grid classes.")
4704 ;; GPL version 2 with "runtime exception"
4705 (license license:gpl2)))
ea51d357
RW		 4706
4707(define-public dune-istl
4708 (package
4709 (name "dune-istl")
4710 (version "2.6.0")
4711 (source
4712 (origin
4713 (method url-fetch)
4714 (uri (string-append "https://dune-project.org/download/"
4715 version "/dune-istl-" version ".tar.gz"))
4716 (sha256
4717 (base32
4718 "0l2gyrvys5w6wsmk0ckbb7295s80b7yk7qrl7x66akv2jv1nzq2w"))))
4719 (build-system cmake-build-system)
4720 (arguments
4721 `(#:phases
4722 (modify-phases %standard-phases
4723 (add-after 'build 'build-tests
4724 (lambda* (#:key make-flags #:allow-other-keys)
4725 (apply invoke "make" "build_tests" make-flags)))
4726 ;; These tests fail because they require a fully functional MPI
4727 ;; environment.
4728 (add-after 'unpack 'disable-failing-tests
4729 (lambda _
4730 (setenv "ARGS"
4731 (string-append "--exclude-regex '("
4732 (string-join
4733 (list
4734 "galerkintest"
4735 "hierarchytest"
4736 "pamgtest"
4737 "pamg_comm_repart_test"
4738 "matrixredisttest"
4739 "vectorcommtest"
4740 "matrixmarkettest")
4741 "|")
4742 ")'"))
4743 #t)))))
4744 (inputs
4745 `(("dune-common" ,dune-common)
4746 ("openmpi" ,openmpi)
4747 ;; Optional
4748 ("metis" ,metis)
4749 ("superlu" ,superlu)
4750 ("openblas" ,openblas)
4751 ("gmp" ,gmp)
4752 ("python" ,python)))
4753 (native-inputs
4754 `(("gfortran" ,gfortran)
4755 ("pkg-config" ,pkg-config)))
4756 (home-page "https://dune-project.org/")
4757 (synopsis "Distributed and Unified Numerics Environment")
4758 (description "DUNE, the Distributed and Unified Numerics Environment is a
4759modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4760grid-based methods.
4761
4762This is the iterative solver template library which provides generic sparse
4763matrix/vector classes and a variety of solvers based on these classes. A
4764special feature is the use of templates to exploit the recursive block
4765structure of finite element matrices at compile time. Available solvers
4766include Krylov methods, (block-) incomplete decompositions and
4767aggregation-based algebraic multigrid.")
4768 ;; GPL version 2 with "runtime exception"
4769 (license license:gpl2)))
5a70aa7d
RW		 4770
4771(define-public dune-localfunctions
4772 (package
4773 (name "dune-localfunctions")
4774 (version "2.6.0")
4775 (source
4776 (origin
4777 (method url-fetch)
4778 (uri (string-append "https://dune-project.org/download/"
4779 version "/dune-localfunctions-" version ".tar.gz"))
4780 (sha256
4781 (base32
4782 "19c6zjinwwpy8jh4v4prhphyd438rapd4x80fj93apmwgw04nrhl"))))
4783 (build-system cmake-build-system)
4784 (arguments
4785 `(#:phases
4786 (modify-phases %standard-phases
4787 (add-after 'build 'build-tests
4788 (lambda* (#:key make-flags #:allow-other-keys)
4789 (apply invoke "make" "build_tests" make-flags))))))
4790 (inputs
4791 `(("dune-common" ,dune-common)
4792 ("dune-geometry" ,dune-geometry)
4793 ("openmpi" ,openmpi)
4794 ;; Optional
4795 ("metis" ,metis)
4796 ("superlu" ,superlu)
4797 ("gmp" ,gmp)))
4798 (native-inputs
4799 `(("gfortran" ,gfortran)
4800 ("pkg-config" ,pkg-config)))
4801 (home-page "https://dune-project.org/")
4802 (synopsis "Distributed and Unified Numerics Environment") ; TODO
4803 (description "This DUNE module provides interface and implementation for
4804shape functions defined on the DUNE reference elements. In addition to the
4805shape function, interpolation operators and special keys are provided which
4806can be used to assemble global function spaces on finite-element grids.
4807
4808This package provides an interface and implementation for shape functions
4809defined on the DUNE reference elements. In addition to the shape function,
4810interpolation operators and special keys are provided which can be used to
4811assemble global function spaces on finite-element grids.")
4812 ;; GPL version 2 with "runtime exception"
4813 (license license:gpl2)))
ab03d899
RW		 4814
4815(define-public dune-alugrid
4816 (package
4817 (name "dune-alugrid")
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-alugrid-" version ".tar.gz"))
4824 (sha256
4825 (base32
4826 "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj"))))
4827 (build-system cmake-build-system)
4828 (arguments
4829 `(#:tests? #f ; 7 of 8 tests fail because they need a full MPI
4830 ; environment
4831 #:phases
4832 (modify-phases %standard-phases
4833 (add-after 'unpack 'patch-include
4834 (lambda _
4835 (substitute* "dune/alugrid/test/test-alugrid.cc"
4836 (("doc/grids/gridfactory/testgrids")
4837 "doc/dune-grid/grids/gridfactory/testgrids"))
4838 #t))
4839 (add-after 'build 'build-tests
4840 (lambda* (#:key inputs make-flags #:allow-other-keys)
4841 (setenv "CPLUS_INCLUDE_PATH"
97149c57 4842 (string-append (assoc-ref inputs "dune-grid") "/share"))
ab03d899
RW		 4843 (apply invoke "make" "build_tests" make-flags))))))
4844 (inputs
4845 `(("dune-common" ,dune-common)
4846 ("dune-geometry" ,dune-geometry)
4847 ("dune-grid" ,dune-grid)
4848 ("openmpi" ,openmpi)
4849 ;; Optional
4850 ("metis" ,metis)
4851 ("openblas" ,openblas)
4852 ("python" ,python)
4853 ("superlu" ,superlu)
4854 ("gmp" ,gmp)
4855 ("zlib" ,zlib)))
4856 (native-inputs
4857 `(("gfortran" ,gfortran)
4858 ("pkg-config" ,pkg-config)))
4859 (home-page "https://dune-project.org/")
4860 (synopsis "Distributed and Unified Numerics Environment")
4861 (description "ALUGrid is an adaptive, loadbalancing, unstructured
4862implementation of the DUNE grid interface supporting either simplices or
4863cubes.")
4864 (license license:gpl2+)))
0e50630f
RW		 4865
4866(define-public dune-typetree
4867 (package
4868 (name "dune-typetree")
4869 (version "2.6.0")
4870 (source
4871 (origin
4872 (method git-fetch)
4873 (uri (git-reference
4874 (url "https://gitlab.dune-project.org/staging/dune-typetree.git")
4875 (commit (string-append "v" version))))
4876 (file-name (git-file-name name version))
4877 (sha256
4878 (base32
4879 "0mnv6w2f22lz3j4bdpdjq55vjm8xxfx9v4vvhg9bd36xpsbjpjp9"))))
4880 (build-system cmake-build-system)
4881 (arguments
4882 `(#:phases
4883 (modify-phases %standard-phases
4884 (add-after 'build 'build-tests
4885 (lambda* (#:key make-flags #:allow-other-keys)
4886 (apply invoke "make" "build_tests" make-flags))))))
4887 (inputs
4888 `(("dune-common" ,dune-common)
4889 ("openmpi" ,openmpi)
4890 ;; Optional
4891 ("openblas" ,openblas)
4892 ("python" ,python)
4893 ("metis" ,metis)
4894 ("superlu" ,superlu)
4895 ("gmp" ,gmp)))
4896 (native-inputs
4897 `(("gfortran" ,gfortran)
4898 ("pkg-config" ,pkg-config)))
4899 (home-page "https://dune-project.org/")
4900 (synopsis "Distributed and Unified Numerics Environment")
4901 (description "TypeTree is a template library for constructing and
4902operating on statically typed trees of objects.")
4903 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4904 (license (list license:lgpl3+ license:gpl2))))
85b9371c
RW		 4905
4906(define-public dune-functions
4907 (package
4908 (name "dune-functions")
4909 (version "2.6.0")
4910 (source
4911 (origin
4912 (method git-fetch)
4913 (uri (git-reference
4914 (url "https://gitlab.dune-project.org/staging/dune-functions.git")
4915 (commit (string-append "v" version))))
4916 (file-name (git-file-name name version))
4917 (sha256
4918 (base32
4919 "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200"))))
4920 (build-system cmake-build-system)
4921 (arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid
4922 (inputs
4923 `(("dune-common" ,dune-common)
4924 ("dune-istl" ,dune-istl)
4925 ("dune-localfunctions" ,dune-localfunctions)
4926 ("dune-grid" ,dune-grid)
4927 ("dune-geometry" ,dune-geometry)
4928 ("dune-typetree" ,dune-typetree)
4929 ("openmpi" ,openmpi)
4930 ("openblas" ,openblas)
4931 ("metis" ,metis)
4932 ("python" ,python)
4933 ("superlu" ,superlu)
4934 ("gmp" ,gmp)))
4935 (native-inputs
4936 `(("gfortran" ,gfortran)
4937 ("pkg-config" ,pkg-config)))
4938 (home-page "https://dune-project.org/")
4939 (synopsis "Distributed and Unified Numerics Environment")
4940 (description "The dune-functions module provides an abstraction layer for
4941global finite element functions. Its two main concepts are functions
4942implemented as callable objects, and bases of finite element spaces.")
4943 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4944 (license (list license:lgpl3+ license:gpl2))))
4714b00e
RW		 4945
4946(define-public dune-pdelab
4947 (package
4948 (name "dune-pdelab")
4949 (version "2.6.0-rc1")
4950 (source
4951 (origin
4952 (method git-fetch)
4953 (uri (git-reference
4954 (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
4955 (commit (string-append "v" version))))
4956 (file-name (git-file-name name version))
4957 (sha256
4958 (base32
4959 "07g0s9448z65vjrq88g5rv3340iifil85k170n8kbqchsvi4ny5v"))))
4960 (build-system cmake-build-system)
4961 (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
4962 (inputs
4963 `(("dune-common" ,dune-common)
4964 ("dune-istl" ,dune-istl)
4965 ("dune-localfunctions" ,dune-localfunctions)
4966 ("dune-geometry" ,dune-geometry)
4967 ("dune-grid" ,dune-grid)
4968 ("dune-typetree" ,dune-typetree)
4969 ("dune-functions" ,dune-functions)
4970 ("openmpi" ,openmpi)
4971 ;; Optional
4972 ("openblas" ,openblas)
4973 ("eigen" ,eigen)
4974 ("metis" ,metis)
4975 ("python" ,python)
4976 ("superlu" ,superlu)
4977 ("gmp" ,gmp)))
4978 (native-inputs
4979 `(("gfortran" ,gfortran)
4980 ("pkg-config" ,pkg-config)))
4981 (home-page "https://dune-project.org/")
4982 (synopsis "Differential equations solver toolbox")
4983 (description "PDELab is a partial differential equations solver toolbox
4984built on top of DUNE, the Distributed and Unified Numerics Environment.")
4985 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4986 (license (list license:lgpl3+ license:gpl2))))
413f6126
AI		 4987
4988(define-public mlucas
4989 (package
4990 (name "mlucas")
4991 (version "18")
4992 (source
4993 (origin
4994 (method url-fetch)
4995 (uri (string-append
4996 "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz"))
4997 (sha256
a36efdbc 4998 (base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447"))))
413f6126
AI		 4999 (build-system gnu-build-system)
5000 (inputs
5001 `(("python2" ,python-2)))
5002 (arguments
a36efdbc 5003 `(#:tests? #f ; no tests
413f6126
AI		 5004 #:phases
5005 (modify-phases %standard-phases
5006 (replace 'configure
5007 (lambda _
5008 (chdir "src")
5009 (call-with-output-file "Makefile"
5010 (lambda (port)
5011 (format port "CC = gcc
5012CFLAGS = -O3 ~a -DUSE_THREADS
5013LDLIBS = -lm -lpthread -lrt
5014Mlucas: $(addsuffix .o,$(basename $(wildcard *.c)))
5015"
5016 ,(let ((system (or (%current-target-system)
5017 (%current-system))))
5018 (cond
5019 ((string-prefix? "x86_64" system) "-DUSE_SSE2")
5020 (else ""))))))
5021 #t))
5022 (replace 'install
5023 (lambda* (#:key outputs #:allow-other-keys)
5024 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
5025 (install-file "Mlucas" bin)
5026 (install-file "primenet.py" bin))
5027 #t)))))
5028 (home-page "https://www.mersenne.org")
5029 (synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client")
5030 (description "Mlucas performs Lucas-Lehmer primality testing of Mersenne
5031numbers in search of a world-record prime. You may use it to test any
5032suitable number as you wish, but it is preferable that you do so in a
5033coordinated fashion, as part of the Great Internet Mersenne Prime
5034Search (GIMPS). Mlucas also includes a simple Python script for assignment
5035management via the GIMPS project's Primenet server.")
5036 (license license:gpl2+)))
6f8c4195
NG		 5037
5038(define-public nauty
5039 (package
5040 (name "nauty")
1ff64c50 5041 (version "2.6r12")
6f8c4195
NG		 5042 (source (origin
5043 (method url-fetch)
5044 (uri (string-append
5045 "https://pallini.di.uniroma1.it/"
5046 "nauty" (string-join (string-split version #\.) "")
5047 ".tar.gz"))
5048 (sha256
5049 (base32
1ff64c50 5050 "1p4mxf8q5wm47nxyskxbqwa5p1vvkycv1zgswvnk9nsn6vff0al6"))))
6f8c4195
NG		 5051 (build-system gnu-build-system)
5052 (outputs '("out" "lib"))
5053 (arguments
5054 `(#:test-target "checks"
5055 #:phases
5056 (modify-phases %standard-phases
5057 ;; Default make target does not build all available
5058 ;; executables. Create them now.
5059 (add-after 'build 'build-extra-programs
5060 (lambda _
5061 (for-each (lambda (target) (invoke "make" target))
5062 '("blisstog" "bliss2dre" "checks6" "sumlines"))
5063 #t))
5064 ;; Upstream does not provide any install target.
5065 (replace 'install
5066 (lambda* (#:key outputs #:allow-other-keys)
5067 (let* ((out (assoc-ref outputs "out"))
5068 (lib-output (assoc-ref outputs "lib"))
5069 (bin (string-append out "/bin"))
5070 (doc (string-append out "/share/doc/nauty/"))
5071 (include (string-append lib-output "/include/nauty"))
5072 (lib (string-append lib-output "/lib/nauty")))
5073 (for-each (lambda (f) (install-file f bin))
5074 '("dreadnaut" "NRswitchg" "addedgeg" "amtog" "biplabg"
5075 "blisstog" "bliss2dre" "catg" "checks6" "complg"
5076 "converseg" "copyg" "countg" "cubhamg" "deledgeg"
5077 "delptg" "directg" "dretodot" "dretog" "genbg"
5078 "genbgL" "geng" "genquarticg" "genrang" "genspecialg"
5079 "gentourng" "gentreeg" "hamheuristic" "labelg"
5080 "linegraphg" "listg" "multig" "newedgeg" "pickg"
5081 "planarg" "ranlabg" "shortg" "showg" "subdivideg"
5082 "sumlines" "twohamg" "vcolg" "watercluster2"))
5083 (for-each (lambda (f) (install-file f include))
5084 (find-files "." "\\.h$"))
5085 (for-each (lambda (f) (install-file f lib))
5086 (find-files "." "\\.a$"))
5087 (for-each (lambda (f) (install-file f doc))
5088 (append '("formats.txt" "README" "schreier.txt")
5089 (find-files "." "\\.pdf$")))))))))
5090 (inputs
5091 `(("gmp" ,gmp))) ;for sumlines
5092 (home-page "https://pallini.di.uniroma1.it/")
5093 (synopsis "Library for graph automorphisms")
5094 (description "@code{nauty} (No AUTomorphisms, Yes?) is a set of
5095procedures for computing automorphism groups of graphs and digraphs.
5096
5097@code{nauty} computes graph information in the form of a set of
5098generators, the size of the group, and the orbits of the group; it can
5099also produce a canonical label. The @code{nauty} suite is written in
5100C and comes with a command-line interface, a collection of
5101command-line tools, and an Application Programming Interface (API).
5102
5103This package provides the static libraries required to run programs
5104compiled against the nauty library.")
5105 (license license:asl2.0)))
26433471
AE		 5106
5107(define-public ppl
5108 (package
5109 (name "ppl")
5110 (version "1.2")
5111 (source
5112 (origin
5113 (method url-fetch)
5114 (uri (string-append "https://www.bugseng.com/products/ppl/download/"
5115 "ftp/releases/" version
5116 "/ppl-" version ".tar.gz"))
5117 (sha256
5118 (base32
5119 "1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb"))))
5120 (build-system gnu-build-system)
5121 (native-inputs
5122 `(("m4", m4)))
5123 (inputs
5124 `(("glpk" ,glpk)
5125 ("gmp", gmp)))
5126 (home-page "https://www.bugseng.com/parma-polyhedra-library")
5127 (synopsis
5128 "Parma Polyhedra Library for computations with polyhedra")
5129 (description
5130 "The Parma Polyhedra Library (PPL) provides numerical abstractions
5131especially targeted at applications in the field of analysis and
5132verification of complex systems. These abstractions include convex
5133polyhedra, defined as the intersection of a finite number of (open or
5134closed) halfspaces, each described by a linear inequality (strict or
5135non-strict) with rational coefficients; some special classes of polyhedra
5136shapes that offer interesting complexity/precision tradeoffs; and grids
5137which represent regularly spaced points that satisfy a set of linear
5138congruence relations. The library also supports finite powersets and
5139products of (any kind of) polyhedra and grids, a mixed integer linear
5140programming problem solver using an exact-arithmetic version of the simplex
5141algorithm, a parametric integer programming solver, and primitives for
5142termination analysis via the automatic synthesis of linear ranking
5143functions.")
5144 (license license:gpl3+)))
4cb5d251
SS		 5145
5146(define-public speedcrunch
5147 (package
5148 (name "speedcrunch")
5149 (version "0.12.0")
5150 (source
5151 (origin
5152 (method git-fetch)
5153 (uri (git-reference
5154 (url "https://bitbucket.org/heldercorreia/speedcrunch.git")
5155 (commit (string-append "release-" version))))
5156 (file-name (git-file-name name version))
5157 (sha256
5158 (base32
5159 "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"))))
5160 (build-system cmake-build-system)
5161 (inputs `(("qtbase" ,qtbase)))
5162 (native-inputs `(("qttools" ,qttools)))
5163 (arguments
5164 `(#:phases
5165 (modify-phases %standard-phases
5166 (add-after 'unpack 'chdir-to-src
5167 (lambda _ (chdir "src") #t)))))
5168 (synopsis "High-precision scientific calculator")
5169 (description
5170 "SpeedCrunch is a high-precision scientific calculator. It features a
5171syntax-highlighted scrollable display and is designed to be fully used via
5172keyboard. Some distinctive features are auto-completion of functions and
5173variables, a formula book, and quick insertion of constants from various
5174fields of knowledge.")
5175 (home-page "http://speedcrunch.org/")
5176 (license license:gpl2+)))
5177
3b7828cc
RS		 5178(define-public minisat
5179 ;; This is the last commit which is available upstream, no
5180 ;; release happened since 2010.
5181 (let ((commit "37dc6c67e2af26379d88ce349eb9c4c6160e8543")
5182 (revision "1"))
5183 (package
5184 (name "minisat")
5185 (version (string-append "2.2.0-" revision "." (string-take commit 7)))
5186 (source
5187 (origin
5188 (method git-fetch)
5189 (uri (git-reference
5190 (url "https://github.com/niklasso/minisat.git")
5191 (commit commit)))
5192 (file-name (string-append name "-" version "-checkout"))
5193 (sha256
5194 (base32
5195 "091hf3qkm197s5r7xcr3m07xsdwyz2rqk1hc9kj0hn13imz09irq"))
5196 (patches
5197 (search-patches "minisat-friend-declaration.patch"
5198 "minisat-install.patch"))))
5199 (build-system gnu-build-system)
5200 (arguments
5201 '(#:make-flags (list (string-append "prefix=" %output))
5202 #:tests? #f ;no check target
5203 #:phases
5204 (modify-phases %standard-phases
5205 (delete 'configure))))
5206 (inputs
5207 `(("zlib:static" ,zlib "static")
5208 ("zlib" ,zlib)))
5209 (synopsis
5210 "Small, yet efficient, SAT solver")
5211 (description
5212 "MiniSat is a minimalistic, open-source SAT solver, developed to help
5213researchers and developers alike to get started on SAT.")
5214 (home-page
5215 "http://minisat.se/MiniSat.html")
5216 (license license:expat))))
jackhill's copy of GNU Guix: https://guix.gnu.org/