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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>
f1cc312e 18;;; Copyright © 2017, 2018, 2019, 2020 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>
a3143063 32;;; Copyright © 2018 Amin Bandali <mab@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")
e6de152d 586 (version "3.9.0")
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
e6de152d 594 "1155qixp26c12yrxc76z9mlfw2h3xxymxxv5znpgzh5gaykpndgj"))))
da95c817
NK		 595 (build-system cmake-build-system)
596 (home-page "http://www.netlib.org/lapack/")
19afbea1 597 (inputs `(("fortran" ,gfortran)
e6de152d 598 ("python" ,python-wrapper)))
da95c817 599 (arguments
3ab869b6 600 `(#:configure-flags (list
3ab869b6
LC		 601 "-DBUILD_SHARED_LIBS:BOOL=YES"
602 "-DLAPACKE=ON"
3ab869b6 603 ;; Build the 'LAPACKE_clatms' functions.
e6de152d
KH		 604 "-DLAPACKE_WITH_TMG=ON"
605 "-DBUILD_TESTING=ON")))
da95c817
NK		 606 (synopsis "Library for numerical linear algebra")
607 (description
608 "LAPACK is a Fortran 90 library for solving the most commonly occurring
609problems in numerical linear algebra.")
166191b3 610 (license (license:non-copyleft "file://LICENSE"
da95c817 611 "See LICENSE in the distribution."))))
73fed4f8 612
e1ff597a
EB		 613(define-public scalapack
614 (package
615 (name "scalapack")
616 (version "2.0.2")
617 (source
618 (origin
619 (method url-fetch)
620 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
621 version ".tgz"))
622 (sha256
623 (base32
f73750e6
EB		 624 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))
625 (patches (search-patches "scalapack-blacs-mpi-deprecations.patch"))))
e1ff597a
EB		 626 (build-system cmake-build-system)
627 (inputs
628 `(("mpi" ,openmpi)
629 ("fortran" ,gfortran)
630 ("lapack" ,lapack))) ;for testing only
631 (arguments
6df2a50a
LC		 632 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
633 #:phases (modify-phases %standard-phases
bbe46a4a
EB		 634 (add-before 'check 'mpi-setup
635 ,%openmpi-setup))))
e1ff597a
EB		 636 (home-page "http://www.netlib.org/scalapack/")
637 (synopsis "Library for scalable numerical linear algebra")
638 (description
639 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
640routines on parallel distributed memory machines. ScaLAPACK solves dense and
641banded linear systems, least squares problems, eigenvalue problems, and
642singular value problems.")
adb223b8
LC		 643 (license (license:non-copyleft "file://LICENSE"
644 "See LICENSE in the distribution."))))
e1ff597a 645
73fed4f8 646(define-public gnuplot
5f800540
KK		 647 (package
648 (name "gnuplot")
cb1d8aee 649 (version "5.2.7")
5f800540
KK		 650 (source (origin
651 (method url-fetch)
652 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
653 version "/gnuplot-"
654 version ".tar.gz"))
655 (sha256
cb1d8aee 656 (base32 "1vglp4la40f5dpj0zdj63zprrkyjgzy068p35bz5dqxjyczm1zlp"))))
5f800540
KK		 657 (build-system gnu-build-system)
658 (inputs `(("readline" ,readline)
659 ("cairo" ,cairo)
660 ("pango" ,pango)
6e64766a
DM		 661 ("gd" ,gd)
662 ("lua" ,lua)))
612a387f
RW		 663 (native-inputs
664 `(("pkg-config" ,pkg-config)
665 ("texlive" ,texlive-tiny)))
07254d8b
AM		 666 (arguments `(#:configure-flags (list (string-append
667 "--with-texdir=" %output
668 "/texmf-local/tex/latex/gnuplot"))))
5f800540
KK		 669 (home-page "http://www.gnuplot.info")
670 (synopsis "Command-line driven graphing utility")
671 (description "Gnuplot is a portable command-line driven graphing
35b9e423 672utility. It was originally created to allow scientists and students to
73fed4f8 673visualize mathematical functions and data interactively, but has grown to
35b9e423 674support many non-interactive uses such as web scripting. It is also used as a
73fed4f8 675plotting engine by third-party applications like Octave.")
5f800540
KK		 676 ;; X11 Style with the additional restriction that derived works may only be
677 ;; distributed as patches to the original.
678 (license (license:fsf-free
679 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
668c06ac 680
32f70e1f
TD		 681(define-public gctp
682 (package
683 (name "gctp")
684 (version "2.0.0")
685 (source
686 (origin
5db874d1
TGR		 687 (method git-fetch)
688 (uri (git-reference
689 (url "https://github.com/OkoSanto/GCTP.git")
690 (commit (string-append "v" version))))
691 (file-name (git-file-name name version))
32f70e1f 692 (sha256
5db874d1 693 (base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
32f70e1f
TD		 694 (native-inputs
695 `(("fortran" ,gfortran)))
696 (build-system gnu-build-system)
697 (synopsis "General Cartographic Transformation Package (GCTP)")
698 (description
699 "The General Cartographic Transformation Package (GCTP) is a system of
700software routines designed to permit the transformation of coordinate pairs
701from one map projection to another. The GCTP is the standard computer
702software used by the National Mapping Division for map projection
703computations.")
704 (home-page "https://github.com/OkoSanto/GCTP")
0f7cd95b 705 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
32f70e1f 706
becbbefc
TD		 707(define-public hdf4
708 (package
709 (name "hdf4")
c959d99f 710 (version "4.2.14")
becbbefc
TD		 711 (source
712 (origin
713 (method url-fetch)
714 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
715 version "/src/hdf-" version ".tar.bz2"))
716 (sha256
c959d99f 717 (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l"))
15ca49b2
AE		 718 (patches (search-patches "hdf4-architectures.patch"
719 "hdf4-reproducibility.patch"
bd3d71cb
MB		 720 "hdf4-shared-fortran.patch"
721 "hdf4-tirpc.patch"))))
becbbefc
TD		 722 (build-system gnu-build-system)
723 (native-inputs
724 `(("gfortran" ,gfortran)
725 ("bison" ,bison)
726 ("flex" ,flex)))
727 (inputs
728 `(("zlib" ,zlib)
bd3d71cb
MB		 729 ("libjpeg" ,libjpeg)
730 ("libtirpc" ,libtirpc)))
becbbefc
TD		 731 (arguments
732 `(#:parallel-tests? #f
bd3d71cb
MB		 733 #:configure-flags (list "--enable-shared"
734 (string-append "CPPFLAGS=-I"
735 (assoc-ref %build-inputs "libtirpc")
736 "/include/tirpc"))
becbbefc
TD		 737 #:phases
738 (modify-phases %standard-phases
953a12fa
EF		 739 ;; This is inspired by two of Debian's patches.
740 (add-before 'configure 'add-more-aarch64-support
741 (lambda _
742 (substitute* '("mfhdf/ncgen/ncgen.l"
743 "mfhdf/ncgen/ncgenyy.c"
744 "mfhdf/libsrc/netcdf.h.in")
745 (("AIX5L64") "__aarch64__"))
746 #t))
becbbefc
TD		 747 (add-before 'configure 'patchbuild
748 (lambda _
749 (substitute*
750 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
751 (("/bin/rm") "rm")
752 (("/bin/mkdir") "mkdir"))
753 (substitute* (find-files "." "^Makefile\\.in$")
754 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
755-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
756 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
757-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
953a12fa 758-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
e464b455
TD		 759 #t))
760 (add-after 'configure 'patch-settings
761 (lambda _
762 ;; libhdf4.settings contains the full path of the
763 ;; compilers used, and its contents are included in
764 ;; .so-files. We truncate the hashes to avoid
765 ;; unnecessary store references to those compilers:
766 (substitute* "libhdf4.settings"
767 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
768 (string-append prefix (string-take hash 10) "...")))
769 #t))
770 )))
becbbefc
TD		 771 (home-page "https://www.hdfgroup.org/products/hdf4/")
772 (synopsis
773 "Library and multi-object file format for storing and managing data")
774 (description "HDF4 is a library and multi-object file format for storing
775and managing data between machines. HDF4 is an older hierarchical data format,
776incompatible with HDF5.")
777 (license
778 (license:non-copyleft
779 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
780
781(define-public hdf4-alt
782 (package
783 (inherit hdf4)
784 (name "hdf4-alt")
785 (arguments
786 (substitute-keyword-arguments (package-arguments hdf4)
787 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
788 (synopsis
789 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
790
7ee3f1a2
JD		 791(define-public hdf5
792 (package
793 (name "hdf5")
7b84610e 794 (version "1.8.21")
7ee3f1a2
JD		 795 (source
796 (origin
797 (method url-fetch)
2da63064
TD		 798 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
799 "hdf5-" (version-major+minor version)
800 "/hdf5-" version "/src/hdf5-"
dcd9d163
LF		 801 version ".tar.bz2")
802 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
803 "current"
7b84610e
EB		 804 (match (string-split version #\.)
805 ((major minor _ ...)
806 (string-append major minor)))
dcd9d163 807 "/src/hdf5-" version ".tar.bz2")))
7ee3f1a2 808 (sha256
7b84610e 809 (base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5"))
7fedc3fd
EB		 810 (patches (search-patches "hdf5-config-date.patch"
811 "hdf5-1.8-mpi-deprecations.patch"))))
7ee3f1a2 812 (build-system gnu-build-system)
12ed1216
AE		 813 (inputs
814 `(("zlib" ,zlib)))
e3a1a1de 815 (native-inputs
3ea420f3
LC		 816 `(("gfortran" ,gfortran)
817 ("perl" ,perl))) ;part of the test machinery needs Perl
e3a1a1de
TD		 818 (outputs '("out" ; core library
819 "fortran")) ; fortran interface
7ee3f1a2 820 (arguments
62126576 821 `(;; Some of the users, notably Flann, need the C++ interface.
e3a1a1de
TD		 822 #:configure-flags '("--enable-cxx"
823 "--enable-fortran"
549d1571
LC		 824 "--enable-fortran2003"
825
826 ;; Build a thread-safe library. Unfortunately,
827 ;; 'configure' invites you to either turn off C++,
828 ;; Fortran, and the high-level interface (HL), or
829 ;; to pass '--enable-unsupported'. Debian
830 ;; packagers chose to pass '--enable-unsupported'
831 ;; and we follow their lead here.
832 "--enable-threadsafe"
833 "--with-pthread"
834 "--enable-unsupported")
4dba441c
RW		 835 ;; Use -fPIC to allow the R bindings to link with the static libraries
836 #:make-flags (list "CFLAGS=-fPIC"
837 "CXXFLAGS=-fPIC")
62126576 838 #:phases
f622e212
EB		 839 (modify-phases %standard-phases
840 (add-before 'configure 'patch-configure
e3a1a1de 841 (lambda* (#:key outputs #:allow-other-keys)
f622e212 842 (substitute* "configure"
b8d9c93b 843 (("/bin/mv") "mv"))
e3a1a1de
TD		 844 (substitute* "fortran/src/Makefile.in"
845 (("libhdf5_fortran_la_LDFLAGS =")
846 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
847 (assoc-ref outputs "fortran") "/lib")))
848 (substitute* "hl/fortran/src/Makefile.in"
849 (("libhdf5hl_fortran_la_LDFLAGS =")
850 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
851 (assoc-ref outputs "fortran") "/lib")))
b8d9c93b 852 #t))
fd0378a1
TD		 853 (add-after 'configure 'patch-settings
854 (lambda _
855 ;; libhdf5.settings contains the full path of the
856 ;; compilers used, and its contents are included in
857 ;; libhdf5.so. We truncate the hashes to avoid
858 ;; unnecessary store references to those compilers:
859 (substitute* "src/libhdf5.settings"
860 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
d8f46d52
RW		 861 (string-append prefix (string-take hash 10) "..."))
862 ;; Don't record the build-time kernel version to make the
863 ;; settings file reproducible.
864 (("Uname information:.*")
865 "Uname information: Linux\n"))
b8d9c93b 866 #t))
f622e212
EB		 867 (add-after 'install 'patch-references
868 (lambda* (#:key inputs outputs #:allow-other-keys)
869 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
870 (zlib (assoc-ref inputs "zlib")))
871 (substitute* (find-files bin "h5p?cc")
872 (("-lz" lib)
873 (string-append "-L" zlib "/lib " lib)))
e3a1a1de
TD		 874 #t)))
875 (add-after 'install 'split
876 (lambda* (#:key inputs outputs #:allow-other-keys)
877 ;; Move all fortran-related files
878 (let* ((out (assoc-ref outputs "out"))
879 (bin (string-append out "/bin"))
880 (lib (string-append out "/lib"))
881 (inc (string-append out "/include"))
882 (ex (string-append out "/share/hdf5_examples/fortran"))
883 (fort (assoc-ref outputs "fortran"))
884 (fbin (string-append fort "/bin"))
885 (flib (string-append fort "/lib"))
886 (finc (string-append fort "/include"))
887 (fex (string-append fort "/share/hdf5_examples/fortran")))
888 (mkdir-p fbin)
889 (mkdir-p flib)
890 (mkdir-p finc)
891 (mkdir-p fex)
b0d1e60f
PG		 892 ;; Note: When built with --enable-parallel, the 'h5fc' file
893 ;; doesn't exist, hence this condition.
894 (when (file-exists? (string-append bin "/h5fc"))
895 (rename-file (string-append bin "/h5fc")
896 (string-append fbin "/h5fc")))
e3a1a1de
TD		 897 (for-each (lambda (file)
898 (rename-file file
899 (string-append flib "/" (basename file))))
900 (find-files lib ".*fortran.*"))
901 (for-each (lambda (file)
902 (rename-file file
903 (string-append finc "/" (basename file))))
904 (find-files inc ".*mod"))
905 (for-each (lambda (file)
906 (rename-file file
907 (string-append fex "/" (basename file))))
908 (find-files ex ".*"))
909 (delete-file-recursively ex))
910 #t)))))
7ee3f1a2 911 (home-page "http://www.hdfgroup.org")
516e93f8 912 (synopsis "Management suite for extremely large and complex data")
7ee3f1a2
JD		 913 (description "HDF5 is a suite that makes possible the management of
914extremely large and complex data collections.")
d4bf49b1
EB		 915 (license (license:x11-style
916 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
7ee3f1a2 917
bb47aca5
RW		 918(define-public hdf5-1.10
919 (package (inherit hdf5)
cb169aae 920 (version "1.10.6")
bb47aca5
RW		 921 (source
922 (origin
923 (method url-fetch)
924 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
925 "hdf5-" (version-major+minor version)
926 "/hdf5-" version "/src/hdf5-"
927 version ".tar.bz2")
928 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
929 "current"
930 (apply string-append
931 (take (string-split version #\.) 2))
932 "/src/hdf5-" version ".tar.bz2")))
933 (sha256
cb169aae 934 (base32 "1gf38x51128hn00744358w27xgzjk0ff4wra4yxh2lk804ck1mh9"))
94fea21b 935 (patches (search-patches "hdf5-config-date.patch"))))))
bb47aca5 936
2fd26d05
TD		 937(define-public hdf-java
938 (package
2a509880
RW		 939 (name "hdf-java")
940 (version "3.3.2")
941 (source
942 (origin
943 (method url-fetch)
944 (uri (string-append
945 "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
946 version "/src/CMake-hdfjava-" version ".tar.gz"))
947 (sha256
948 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
949 (modules '((guix build utils)))
950 (snippet ; Make sure we don't use the bundled sources and binaries.
951 `(begin
952 (for-each delete-file
953 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
954 "HDF4.tar.gz" "HDF5.tar.gz"))
955 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
956 #t))))
957 (build-system gnu-build-system)
958 (native-inputs
959 `(("jdk" ,icedtea "jdk")
960 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
961 ;; For tests:
962 ("hamcrest-core" ,java-hamcrest-core)
963 ("junit" ,java-junit)
964 ("slf4j-simple" ,java-slf4j-simple)))
965 (inputs
966 `(("hdf4" ,hdf4)
967 ("hdf5" ,hdf5)
968 ("zlib" ,zlib)
969 ("libjpeg" ,libjpeg)
970 ("slf4j-api" ,java-slf4j-api)))
971 (arguments
972 `(#:configure-flags
973 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
974 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
975 (assoc-ref %build-inputs "jdk") "/lib" )
976 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
977 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
2fd26d05 978
2a509880
RW		 979 #:make-flags
980 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
981 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
982 (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
983 (string-append "JPEGLIB="
984 (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
985 "LLEXT=so")
2fd26d05 986
2a509880
RW		 987 #:phases
988 (modify-phases %standard-phases
989 (add-before 'configure 'chdir-to-source
990 (lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
991 (add-before 'configure 'patch-build
992 (lambda* (#:key inputs outputs #:allow-other-keys)
993 (substitute* "configure"
994 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
995 (("/bin/cat") (which "cat")))
996 ;; Set classpath for compilation
997 (substitute* '("hdf/hdf5lib/Makefile.in"
998 "hdf/hdf5lib/exceptions/Makefile.in"
999 "hdf/hdflib/Makefile.in")
1000 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
1001 (string-append (assoc-ref inputs "slf4j-api")
1002 "/share/java/slf4j-api.jar")))
1003 ;; Replace outdated config.sub and config.guess:
1004 (with-directory-excursion "config"
1005 (for-each (lambda (file)
1006 (install-file
1007 (string-append (assoc-ref inputs "automake")
1008 "/share/automake-"
1009 ,(version-major+minor (package-version automake))
1010 "/" file) "."))
1011 '("config.sub" "config.guess")))
64dc8b0b 1012
2a509880
RW		 1013 ;; Fix embedded version number
1014 (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
1015 (substitute* "hdf/hdf5lib/H5.java"
1016 (("1, 8, 19")
1017 (string-join hdf5version ", "))))
64dc8b0b 1018
2a509880
RW		 1019 (mkdir-p (string-append (assoc-ref outputs "out")))
1020 ;; Set classpath for tests
1021 (let* ((build-dir (getcwd))
1022 (lib (string-append build-dir "/lib"))
1023 (jhdf (string-append lib "/jhdf.jar"))
1024 (jhdf5 (string-append lib "/jhdf5.jar"))
1025 (testjars
1026 (map (lambda (i)
1027 (string-append (assoc-ref inputs i)
1028 "/share/java/" i ".jar"))
1029 '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
1030 (class-path
1031 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
2fd26d05 1032
2a509880
RW		 1033 (substitute* '("test/hdf5lib/Makefile.in"
1034 "test/hdf5lib/junit.sh.in"
1035 "examples/runExample.sh.in")
1036 (("/usr/bin/test")
1037 (string-append (assoc-ref inputs "coreutils")
1038 "/bin/test"))
1039 (("/usr/bin/uname")
1040 (string-append (assoc-ref inputs "coreutils")
1041 "/bin/uname"))
1042 (("CLASSPATH=[^\n]*")
1043 (string-append "CLASSPATH=" class-path)))
1044 (setenv "CLASSPATH" class-path))
1045 #t))
1046 (add-before 'check 'build-examples
1047 (lambda _
1048 (apply invoke `("javac"
1049 ,@(find-files "examples" ".*\\.java"))))))
2fd26d05 1050
2a509880 1051 #:parallel-build? #f
2fd26d05 1052
2a509880
RW		 1053 #:parallel-tests? #f ))
1054 (home-page "https://support.hdfgroup.org/products/java")
1055 (synopsis "Java interface for the HDF4 and HDF5 libraries")
1056 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
2fd26d05
TD		 1057the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
1058implemented in C.")
1059
2a509880
RW		 1060 ;; BSD-style license:
1061 (license (license:x11-style
1062 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
2fd26d05
TD		 1063/current/src/unpacked/COPYING"))))
1064
d3c4f3bb
TD		 1065(define-public hdf-eos2
1066 (package
1067 (name "hdf-eos2")
1068 (version "19.1.0")
1069 (source
1070 (origin
1071 (method url-fetch)
1072 (uri "ftp://edhs1.gsfc.nasa.gov\
1073/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
1074 (sha256
1075 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
1076 (patches (search-patches "hdf-eos2-remove-gctp.patch"
1077 "hdf-eos2-build-shared.patch"
1078 "hdf-eos2-fortrantests.patch"))))
1079 (build-system gnu-build-system)
1080 (native-inputs
1081 `(("gfortran" ,gfortran)))
1082 (inputs
1083 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
25bdbb61 1084 ;; XXX: These inputs are really dependencies of hdf4.
d3c4f3bb
TD		 1085 ("zlib" ,zlib)
1086 ("libjpeg" ,libjpeg)
25bdbb61
MB		 1087 ("libtirpc" ,libtirpc)
1088
d3c4f3bb
TD		 1089 ("gctp" ,gctp)))
1090 (arguments
1091 `( #:configure-flags '("--enable-install-include" "--enable-shared"
1092 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
1093 #:parallel-tests? #f))
1094 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
1095 (synopsis "HDF4-based data format for NASA's Earth Observing System")
1096 (description "HDF-EOS2 is a software library built on HDF4 which supports
1097the construction of data structures used in NASA's Earth Observing
1098System (Grid, Point and Swath).")
1099
1100 ;; Source files carry a permissive license header.
1101 (license (license:non-copyleft home-page))))
1102
0f43f835
TD		 1103(define-public hdf-eos5
1104 (package
1105 (name "hdf-eos5")
1106 (version "1.15")
1107 (source (origin
1108 (method url-fetch)
1109 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1110/edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1111 (sha256
1112 (base32
1113 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1114 (patches (search-patches "hdf-eos5-build-shared.patch"
1115 "hdf-eos5-remove-gctp.patch"
1116 "hdf-eos5-fix-szip.patch"
1117 "hdf-eos5-fortrantests.patch"))))
1118 (native-inputs
1119 `(("gfortran" ,gfortran)))
1120 (build-system gnu-build-system)
1121 (inputs
1122 `(("hdf5" ,hdf5)
1123 ("zlib" ,zlib)
1124 ("gctp" ,gctp)))
1125 (arguments
1126 `(#:configure-flags '("--enable-install-include" "--enable-shared"
1127 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1128 #:parallel-tests? #f))
1129 (synopsis "HDF5-based data format for NASA's Earth Observing System")
1130 (description
1131 "HDF-EOS5 is a software library built on HDF5 to support the construction
1132of data structures used in NASA's Earth Observing System (Grid, Point and
1133Swath).")
1134 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1135
1136 ;; Source files carry a permissive license header.
1137 (license (license:non-copyleft home-page))))
1138
c8378eea
EB		 1139(define-public hdf5-parallel-openmpi
1140 (package (inherit hdf5)
1141 (name "hdf5-parallel-openmpi")
1142 (inputs
1143 `(("mpi" ,openmpi)
1144 ,@(package-inputs hdf5)))
1145 (arguments
45201bf2
PG		 1146 (substitute-keyword-arguments (package-arguments hdf5)
1147 ((#:configure-flags flags)
549d1571
LC		 1148 ``("--enable-parallel"
1149 ,@(delete "--enable-cxx"
1150 (delete "--enable-threadsafe" ,flags))))
c8378eea
EB		 1151 ((#:phases phases)
1152 `(modify-phases ,phases
45201bf2
PG		 1153 (add-after 'build 'mpi-setup
1154 ,%openmpi-setup)
c8378eea
EB		 1155 (add-before 'check 'patch-tests
1156 (lambda _
1157 ;; OpenMPI's mpirun will exit with non-zero status if it
1158 ;; detects an "abnormal termination", i.e. any process not
784c3da1 1159 ;; calling MPI_Finalize(). Since the test is explicitly
c8378eea
EB		 1160 ;; avoiding MPI_Finalize so as not to have at_exit and thus
1161 ;; H5C_flush_cache from being called, mpirun will always
1162 ;; complain, so turn this test off.
1163 (substitute* "testpar/Makefile"
1164 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1165 (string-append front back "\n")))
1166 (substitute* "tools/h5diff/testph5diff.sh"
1167 (("/bin/sh") (which "sh")))
1168 #t))))))
1169 (synopsis "Management suite for data with parallel IO support")))
1170
00775104
EB		 1171(define-public h5check
1172 (package
1173 (name "h5check")
1174 (version "2.0.1")
1175 (source
1176 (origin
1177 (method url-fetch)
1178 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
1179 "h5check/src/h5check-" version ".tar.gz"))
1180 (sha256
1181 (base32
1182 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1183 (build-system gnu-build-system)
1184 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
1185 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1186 (synopsis "HDF5 format checker")
1187 (description "@code{h5check} is a validation tool for verifying that an
1188HDF5 file is encoded according to the HDF File Format Specification.")
1189 (license (license:x11-style "file://COPYING"))))
1190
a53d6719
JD		 1191(define-public itpp
1192 (package
1193 (name "itpp")
1194 (version "4.3.1")
1195 (source (origin
1196 (method url-fetch)
1197 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1198 version "/itpp-"
1199 version ".tar.gz"))
1200 (sha256
1201 (base32
1202 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1203 (build-system cmake-build-system)
1204 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1205 (inputs `(("lapack" ,lapack)
1206 ("fftw" ,fftw)))
3a4d5df2
RW		 1207 ;; FIXME: Even though the fonts are available dvips complains:
1208 ;; "Font cmmi10 not found; characters will be left blank."
1209 (native-inputs
1210 `(("texlive" ,texlive-tiny)
1211 ("ghostscript" ,ghostscript)
1212 ("doxygen" ,doxygen)))
a53d6719
JD		 1213 (home-page "http://itpp.sourceforge.net")
1214 (synopsis "C++ library of maths, signal processing and communication classes")
1215 (description "IT++ is a C++ library of mathematical, signal processing and
1216communication classes and functions. Its main use is in simulation of
1217communication systems and for performing research in the area of
1218communications. The kernel of the library consists of generic vector and
1219matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1220similar to MATLAB, GNU Octave or SciPy.")
1221 (license license:gpl3+)))
1222
889187a4
EB		 1223(define-public netcdf
1224 (package
1225 (name "netcdf")
a4b0bfb1 1226 (version "4.4.1.1")
889187a4
EB		 1227 (source
1228 (origin
1229 (method url-fetch)
1230 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1231 "netcdf-" version ".tar.gz"))
1232 (sha256
1233 (base32
a4b0bfb1
EB		 1234 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1235 (patches (search-patches "netcdf-date-time.patch"
1236 "netcdf-tst_h_par.patch"))))
889187a4
EB		 1237 (build-system gnu-build-system)
1238 (native-inputs
1239 `(("m4" ,m4)
1240 ("doxygen" ,doxygen)
1241 ("graphviz" ,graphviz)))
1242 (inputs
db825570
TD		 1243 `(("hdf4" ,hdf4-alt)
1244 ("hdf5" ,hdf5)
1245 ("zlib" ,zlib)
1246 ("libjpeg" ,libjpeg)))
889187a4 1247 (arguments
db825570 1248 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
43d01672
TD		 1249
1250 #:phases (modify-phases %standard-phases
1251 (add-before 'configure 'fix-source-date
1252 (lambda _
1253 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1254 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1255 ;; to '1st hour of the current day', and therefore makes the
1256 ;; package not reproducible.
1257 (substitute* "./configure"
1258 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1259 "date --date='@0'"))
1260 #t))
1261 (add-after 'configure 'patch-settings
1262 (lambda _
1263 ;; libnetcdf.settings contains the full filename of the compilers
1264 ;; used to build the library. We truncate the hashes of those
1265 ;; filenames to avoid unnecessary references to the corresponding
1266 ;; store items.
1267 (substitute* "libnetcdf.settings"
1268 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1269 (string-append prefix (string-take hash 10) "...")))
1270 #t)))
1271
889187a4
EB		 1272 #:parallel-tests? #f)) ;various race conditions
1273 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
1274 (synopsis "Library for scientific data")
1275 (description "NetCDF is an interface for scientific data access and a
1276software library that provides an implementation of the interface. The netCDF
1277library defines a machine-independent format for representing scientific data.
1278Together, the interface, library, and format support the creation, access, and
1279sharing of scientific data.")
1280 (license (license:x11-style "file://COPYRIGHT"))))
1281
1282(define-public netcdf-parallel-openmpi
1283 (package (inherit netcdf)
1284 (name "netcdf-parallel-openmpi")
1285 (inputs
1286 `(("mpi" ,openmpi)
1287 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1288 (package-inputs netcdf))))
1289 ;; TODO: Replace pkg-config references in nc-config with absolute references
1290 (arguments
1291 (substitute-keyword-arguments (package-arguments netcdf)
1292 ((#:configure-flags flags)
1293 `(cons* "CC=mpicc" "CXX=mpicxx"
1294 "--enable-parallel-tests"
1295 ;; Shared libraries not supported with parallel IO.
1296 "--disable-shared" "--with-pic"
1297 ,flags))))))
1298
300200b6
TD		 1299(define-public netcdf-fortran
1300 (package
1301 (name "netcdf-fortran")
1302 (version "4.4.4")
1303 (source (origin
1304 (method url-fetch)
1305 (uri (string-append
1306 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1307 version ".tar.gz"))
1308 (sha256
1309 (base32
1310 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1311 (build-system gnu-build-system)
1312 (arguments
1313 `(#:parallel-tests? #f))
1314 (inputs
1315 `(("netcdf" ,netcdf)))
1316 (native-inputs
1317 `(("gfortran" ,gfortran)))
1318 (synopsis "Fortran interface for the netCDF library")
1319 (description (package-description netcdf))
1320 (home-page (package-home-page netcdf))
1321 (license (package-license netcdf))))
1322
1b39a196
RJ		 1323(define-public nlopt
1324 (package
1325 (name "nlopt")
1326 (version "2.4.2")
1327 (source (origin
1328 (method url-fetch)
1329 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1330 version ".tar.gz"))
1331 (sha256
1332 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1333 (build-system gnu-build-system)
1334 (arguments
1335 `(;; Shared libraries are not built by default. They are required to
1336 ;; build the Guile, Octave, and Python bindings.
1337 #:configure-flags '("--enable-shared")
1338
1339 #:phases
1340 (modify-phases %standard-phases
1341 (add-before 'configure 'set-libnlopt-file-name
1342 (lambda* (#:key outputs #:allow-other-keys)
1343 ;; Make sure the Scheme module refers to the library by its
1344 ;; absolute file name (we cannot do that from a snippet
1345 ;; because the expansion of @libdir@ contains
1346 ;; ${exec_prefix}.)
1347 (let ((out (assoc-ref outputs "out")))
1348 (substitute* "swig/nlopt.scm.in"
1349 (("libnlopt")
1350 (string-append out "/lib/libnlopt")))
1351 #t))))))
1352 (inputs `(("guile" ,guile-2.0)))
1353 (native-inputs `(("pkg-config" ,pkg-config)))
1354 (home-page "http://ab-initio.mit.edu/wiki/")
1355 (synopsis "Library for nonlinear optimization")
1356 (description "NLopt is a library for nonlinear optimization, providing a
1357common interface for a number of different free optimization routines available
1358online as well as original implementations of various other algorithms.")
1359 (license license:lgpl2.1+)))
1360
005c787d
LC		 1361(define-public ipopt
1362 (package
1363 (name "ipopt")
98a5cd51 1364 (version "3.12.12")
005c787d
LC		 1365 (source (origin
1366 (method url-fetch)
1367 (uri (string-append
1368 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1369 version".tgz"))
1370 (sha256
1371 (base32
98a5cd51 1372 "07yn9rzdswjk8n246qq6ci9ssf2bcplkifcpsfz9j6cdxw9vgbkv"))
005c787d
LC		 1373 (modules '((guix build utils)))
1374 (snippet
1375 ;; Make sure we don't use the bundled software.
6cbee49d
MW		 1376 '(begin
1377 (delete-file-recursively "ThirdParty")
1378 #t))))
005c787d 1379 (build-system gnu-build-system)
ad1c4537
LC		 1380 (arguments
1381 '(#:phases (modify-phases %standard-phases
1382 (add-after 'install 'add--L-flags-in-ipopt.pc
1383 (lambda* (#:key inputs outputs #:allow-other-keys)
1384 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1385 ;; move it to "Libs.private" where it belongs, and add a
1386 ;; '-L' flag for LAPACK.
1387 (let ((out (assoc-ref outputs "out"))
1388 (lapack (assoc-ref inputs "lapack")))
1389 (substitute* (string-append out "/lib/pkgconfig/"
1390 "ipopt.pc")
1391 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1392 (string-append "Libs: " before " " after "\n"
1393 "Libs.private: " before
1394 "-L" lapack "/lib -llapack -lblas "
1395 after "\n")))
1396 #t))))))
005c787d
LC		 1397 (native-inputs
1398 `(("gfortran" ,gfortran)))
1399 (inputs
1400 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
ad1c4537 1401 `(("lapack" ,lapack))) ;for both libblas and liblapack
005c787d
LC		 1402 (home-page "http://www.coin-or.org")
1403 (synopsis "Large-scale nonlinear optimizer")
1404 (description
1405 "The Interior Point Optimizer (IPOPT) is a software package for
1406large-scale nonlinear optimization. It provides C++, C, and Fortran
1407interfaces.")
1408 (license license:epl1.0)))
1409
ecfbc51f
RW		 1410(define-public clp
1411 (package
1412 (name "clp")
1413 (version "1.17.1")
1414 (source (origin
1415 (method url-fetch)
1416 (uri (string-append "https://www.coin-or.org/download/source/"
1417 "Clp/Clp-" version ".tgz"))
1418 (sha256
1419 (base32
1420 "1wdg820g3iikf9344ijwsc8sy6c0m6im42bzzizm6rlmkvnmxhk9"))
1421 (modules '((guix build utils)))
1422 (snippet
1423 ;; Make sure we don't use the bundled software.
1424 '(begin
1425 (delete-file-recursively "ThirdParty")
1426 #t))))
1427 (build-system gnu-build-system)
1428 (native-inputs
1429 `(("gfortran" ,gfortran)
1430 ("pkg-config" ,pkg-config)))
1431 (inputs
1432 `(("openblas" ,openblas)))
1433 (home-page "https://www.coin-or.org")
1434 (synopsis "Linear programming solver")
1435 (description
1436 "CLP is a high quality linear programming solver. Its main strengths are
1437its dual and primal Simplex algorithms. It also has a barrier algorithm for
1438linear and quadratic objectives. There are limited facilities for nonlinear
1439and quadratic objectives using the Simplex algorithm.")
1440 (license license:epl1.0)))
1441
f9940ef1
LC		 1442(define-public ceres
1443 (package
1444 (name "ceres-solver")
e0bee0de 1445 (version "1.14.0")
f9940ef1
LC		 1446 (home-page "http://ceres-solver.org/")
1447 (source (origin
1448 (method url-fetch)
1449 (uri (string-append home-page "ceres-solver-"
1450 version ".tar.gz"))
1451 (sha256
1452 (base32
e0bee0de 1453 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
f9940ef1
LC		 1454 (build-system cmake-build-system)
1455 (arguments
1456 ;; TODO: Build HTML user documentation and install separately.
bc3a2e35 1457 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
f9940ef1
LC		 1458 "-DBUILD_SHARED_LIBS=ON")
1459
1460 #:phases (modify-phases %standard-phases
1461 (add-before 'configure 'set-library-directory
1462 (lambda _
1463 ;; Install libraries to lib/, not lib64/.
1464 (substitute* "internal/ceres/CMakeLists.txt"
1465 (("set\\(LIB_SUFFIX \"64\"\\)")
1466 "set(LIB_SUFFIX \"\")"))
1467 #t)))))
1468 (native-inputs
1469 `(("pkg-config" ,pkg-config)))
468e0b18
LC		 1470 (propagated-inputs
1471 `(("glog" ,glog))) ;for #include <glog/glog.h>
f9940ef1
LC		 1472 (inputs
1473 `(("eigen" ,eigen)
1474 ("blas" ,openblas)
1475 ("lapack" ,lapack)
1476 ("suitesparse" ,suitesparse)
1477 ("gflags" ,gflags)))
1478 (synopsis "C++ library for solving large optimization problems")
1479 (description
1480 "Ceres Solver is a C++ library for modeling and solving large,
1481complicated optimization problems. It is a feature rich, mature and
1482performant library which has been used in production since 2010. Ceres Solver
1483can solve two kinds of problems:
1484@enumerate
1485@item non-linear least squares problems with bounds constraints;
1486@item general unconstrained optimization problems.
1487@end enumerate\n")
1488 (license license:bsd-3)))
1489
b66741ed 1490;; For a fully featured Octave, users are strongly recommended also to install
5ca4fe96 1491;; the following packages: less, ghostscript, gnuplot.
5537603f 1492(define-public octave-cli
668c06ac 1493 (package
5537603f 1494 (name "octave-cli")
5b8f8928 1495 (version "5.1.0")
668c06ac
JD		 1496 (source
1497 (origin
1498 (method url-fetch)
1499 (uri (string-append "mirror://gnu/octave/octave-"
f5a077b1 1500 version ".tar.lz"))
668c06ac
JD		 1501 (sha256
1502 (base32
5b8f8928 1503 "11wwxpy2q1bhxs2v41bqn05i2sb0905cj1xil6mg8l4k2kka4cq6"))))
668c06ac
JD		 1504 (build-system gnu-build-system)
1505 (inputs
697df13f
EF		 1506 `(("alsa-lib" ,alsa-lib)
1507 ("arpack" ,arpack-ng)
1508 ("curl" ,curl)
1ec78e9d
EB		 1509 ("fftw" ,fftw)
1510 ("fftwf" ,fftwf)
668c06ac
JD		 1511 ("fltk" ,fltk)
1512 ("fontconfig" ,fontconfig)
1513 ("freetype" ,freetype)
697df13f
EF		 1514 ("gl2ps" ,gl2ps)
1515 ("glpk" ,glpk)
1ec78e9d 1516 ("glu" ,glu)
ab5f3f21 1517 ("graphicsmagick" ,graphicsmagick)
697df13f
EF		 1518 ("hdf5" ,hdf5)
1519 ("lapack" ,lapack)
ab5f3f21 1520 ("libsndfile" ,libsndfile)
697df13f
EF		 1521 ("libxft" ,libxft)
1522 ("mesa" ,mesa)
1523 ("pcre" ,pcre)
ab5f3f21 1524 ("portaudio" ,portaudio)
697df13f
EF		 1525 ("qhull" ,qhull)
1526 ("readline" ,readline)
1527 ("suitesparse" ,suitesparse)
1528 ("texinfo" ,texinfo)
1529 ("zlib" ,zlib)))
668c06ac 1530 (native-inputs
f5a077b1
EF		 1531 `(("lzip" ,lzip)
1532 ("gfortran" ,gfortran)
668c06ac
JD		 1533 ("pkg-config" ,pkg-config)
1534 ("perl" ,perl)
1ec78e9d
EB		 1535 ;; The following inputs are not actually used in the build process.
1536 ;; However, the ./configure gratuitously tests for their existence and
1537 ;; assumes that programs not present at build time are also not, and
1538 ;; can never be, available at run time! If these inputs are therefore
1539 ;; not present, support for them will be built out. However, Octave
1540 ;; will still run without them, albeit without the features they
668c06ac
JD		 1541 ;; provide.
1542 ("less" ,less)
668c06ac
JD		 1543 ("ghostscript" ,ghostscript)
1544 ("gnuplot" ,gnuplot)))
116af86f
KK		 1545 ;; Octave code uses this variable to detect directories holding multiple CA
1546 ;; certificates to verify peers with. This is required for the networking
1547 ;; functions that require encryption to work properly.
1548 (native-search-paths
1549 (list (search-path-specification
1550 (variable "CURLOPT_CAPATH")
1551 (files '("etc/ssl/certs")))))
668c06ac 1552 (arguments
b7b27a8f
KY		 1553 `(#:configure-flags
1554 (list (string-append "--with-shell="
1555 (assoc-ref %build-inputs "bash")
5ca4fe96
AI		 1556 "/bin/sh"))
1557 #:phases
1558 (modify-phases %standard-phases
1559 (add-after 'configure 'configure-makeinfo
1560 (lambda* (#:key inputs #:allow-other-keys)
b18b9d20
AI		 1561 (substitute* "libinterp/corefcn/help.h"
1562 (("\"makeinfo\"")
1563 (string-append
1564 "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
5ca4fe96 1565 #t)))))
f5a077b1 1566 (home-page "https://www.gnu.org/software/octave/")
668c06ac 1567 (synopsis "High-level language for numerical computation")
1ec78e9d
EB		 1568 (description "GNU Octave is a high-level interpreted language that is
1569specialized for numerical computations. It can be used for both linear and
1570non-linear applications and it provides great support for visualizing results.
1571Work may be performed both at the interactive command-line as well as via
1572script files.")
668c06ac 1573 (license license:gpl3+)))
3de01d3f 1574
e0ae7e73 1575(define-public octave
5537603f 1576 (package (inherit octave-cli)
e0ae7e73 1577 (name "octave")
7a3772b3 1578 (source (origin
5537603f 1579 (inherit (package-source octave-cli))))
36ce25f0
KK		 1580 (inputs
1581 `(("qscintilla" ,qscintilla)
1582 ("qt" ,qtbase)
5537603f 1583 ,@(package-inputs octave-cli)))
36ce25f0
KK		 1584 (native-inputs
1585 `(("qttools" , qttools) ;for lrelease
70bb5d88 1586 ("texlive" ,(texlive-union (list texlive-epsf))) ; for texi2dvi
5537603f 1587 ,@(package-native-inputs octave-cli)))
36ce25f0 1588 (arguments
5537603f 1589 (substitute-keyword-arguments (package-arguments octave-cli)
36ce25f0
KK		 1590 ((#:phases phases)
1591 `(modify-phases ,phases
1592 (add-before 'configure 'patch-qscintilla-library-name
1593 (lambda* (#:key inputs #:allow-other-keys)
1594 ;; The QScintilla library that the Octave configure script tries
1595 ;; to link with should be named libqscintilla-qt5.so, but the
1596 ;; QScintilla input provides the shared library as
1597 ;; libqscintilla2_qt5.so.
1598 (substitute* "configure"
1599 (("qscintilla2-qt5")
1600 "qscintilla2_qt5"))
1601 #t))))))))
1602
e0ae7e73
KK		 1603(define-public qtoctave
1604 (deprecated-package "qtoctave" octave))
1605
5d4bd4cc
PG		 1606(define-public opencascade-oce
1607 (package
1608 (name "opencascade-oce")
1609 (version "0.17.2")
1610 (source
1611 (origin
830971bf
TGR		 1612 (method git-fetch)
1613 (uri (git-reference
1614 (url "https://github.com/tpaviot/oce.git")
1615 (commit (string-append "OCE-" version))))
1616 (file-name (git-file-name name version))
a4f393b7 1617 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
5d4bd4cc 1618 (sha256
830971bf 1619 (base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69"))))
5d4bd4cc
PG		 1620 (build-system cmake-build-system)
1621 (arguments
1622 '(#:configure-flags
1623 (list "-DOCE_TESTING:BOOL=ON"
1624 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1625 "-DOCE_DRAW:BOOL=ON"
1626 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1627 (assoc-ref %outputs "out"))
1628 "-UCMAKE_INSTALL_RPATH")))
1629 (inputs
1630 `(("freetype" ,freetype)
1631 ("glu" ,glu)
1632 ("libxmu" ,libxmu)
1633 ("mesa" ,mesa)
1634 ("tcl" ,tcl)
1635 ("tk" ,tk)))
1636 (native-inputs
1637 `(("python" ,python-wrapper)))
1638 (home-page "https://github.com/tpaviot/oce")
1639 (synopsis "Libraries for 3D modeling and numerical simulation")
1640 (description
1641 "Open CASCADE is a set of libraries for the development of applications
1642dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1643C++ class libraries providing services for 3D surface and solid modeling, CAD
1644data exchange, and visualization. It is used for development of specialized
1645software dealing with 3D models in design (CAD), manufacturing (CAM),
1646numerical simulation (CAE), measurement equipment (CMM), and quality
1647control (CAQ) domains.
1648
1649This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1650patches, improvements, and experiments contributed by users over the official
1651Open CASCADE library.")
1652 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1653 ; use of header files; see
1654 ; OCCT_LGPL_EXCEPTION.txt
1655 license:public-domain; files
1656 ; src/Standard/Standard_StdAllocator.hxx and
1657 ; src/NCollection/NCollection_StdAllocator.hxx
1658 license:expat; file src/OpenGl/OpenGl_glext.h
1659 license:bsd-3)))); test framework gtest
1660
37dc2920
PG		 1661(define-public opencascade-occt
1662 (package
1663 (name "opencascade-occt")
1664 (version "7.3.0p3")
1665 (source
1666 (origin
1667 (method git-fetch)
1668 (uri (git-reference
1669 (url "https://git.dev.opencascade.org/repos/occt.git")
1670 (commit
1671 (string-append "V"
1672 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
1673 version)))))
1674 (file-name (git-file-name name version))
1675 (sha256
1676 (base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4"))
1677 (modules '((guix build utils)))
1678 (snippet
1679 '(begin
1680 ;; Remove files specific to non-free operating systems.
1681 (delete-file-recursively "samples/ios")
1682 (delete-file-recursively "samples/mfc")
1683 (delete-file-recursively "samples/qt/FuncDemo")
1684 (delete-file "genconf.bat")
1685 (delete-file "gendoc.bat")
1686 (delete-file "genproj.bat")
1687 (delete-file "upgrade.bat")
1688 ;; Remove references to deleted files.
1689 (substitute* "dox/FILES_HTML.txt"
1690 ((".*standard.*") "" )
1691 ((".*UIKitSample.*") ""))
1692 #t))))
1693 (build-system cmake-build-system)
1694 (arguments
1695 '(;; There is no test target for make. OCCT provides an
1696 ;; 'Automated Testing System', which may be accessed after
1697 ;; installation via the draw.sh script. draw.sh is located in
1698 ;; the bin directory. For details see:
1699 ;; https://www.opencascade.com/doc/occt-7.3.0/overview/html/\
1700 ;; occt_dev_guides__tests.html
1701 #:tests? #f
1702 ;; Configure without freeimage: attempting to link against the
1703 ;; freeimage version 3.17 library leads to 'undefined
1704 ;; reference' errors.
1705 #:configure-flags
1706 (list "-DUSE_FREEIMAGE:BOOL=OFF"
1707 "-DUSE_TBB:BOOL=ON"
1708 "-DUSE_VTK:BOOL=OFF"
1709 "-DBUILD_DOC_Overview:BOOL=OFF"
1710 "-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON"
1711 "-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON"
1712 "-UCMAKE_INSTALL_LIBDIR")))
1713 (inputs
1714 `(("doxygen" ,doxygen)
1715 ;("freeimage" ,freeimage)
1716 ("freetype" ,freetype)
1717 ("glu" ,glu)
1718 ("libxext" ,libxext)
1719 ("libxi" ,libxi)
1720 ("libxmu" ,libxmu)
1721 ("mesa" ,mesa)
1722 ("tbb" ,tbb)
1723 ("tcl" ,tcl)
1724 ("tk" ,tk)))
1725 ;; TODO: build Overview documentation and add 'doc' output.
1726 (home-page "https://www.opencascade.com")
1727 (synopsis "Libraries for 3D modeling and numerical simulation")
1728 (description
1729 "Open CASCADE is a set of libraries for the development of applications
1730dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1731C++ class libraries providing services for 3D surface and solid modeling, CAD
1732data exchange, and visualization. It is used for development of specialized
1733software dealing with 3D models in design (CAD), manufacturing (CAM),
1734numerical simulation (CAE), measurement equipment (CMM), and quality
1735control (CAQ) domains.
1736
1737This is the certified version of the Open Cascade Technology (OCCT) library.")
1738 (license (list ;; OCCT library:
1739 license:lgpl2.1; with an exception for the use of header
1740 ; files, see OCCT_LGPL_EXCEPTION.txt.
1741 ;; Files src/OpenGl/glext.h, adm/cmake/cotire.cmake and
1742 ;; src/OpenGl/OpenGl_HaltonSampler.hxx:
1743 license:expat
1744 ;; Files src/ExprIntrp/ExprIntrp.tab.* and
1745 ;; src/StepFile/step.tab.*:
1746 license:gpl3+ ; with Bison 2.2 exception.
1747 ;; File src/NCollection/NCollection_UtfIterator.lxx:
1748 (license:non-copyleft
1749 "https://www.unicode.org/license.html")
1750 ;; File src/NCollection/NCollection_StdAllocator.hxx:
1751 license:public-domain))))
1752
3de01d3f
EB		 1753(define-public gmsh
1754 (package
1755 (name "gmsh")
8a4d14fa 1756 (version "2.16.0")
3de01d3f
EB		 1757 (source
1758 (origin
abed5df7
PG		 1759 (method git-fetch)
1760 (uri (git-reference
1761 (url "https://gitlab.onelab.info/gmsh/gmsh.git")
1762 (commit
1763 (string-append "gmsh_"
1764 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
1765 version)))))
1766 (file-name (git-file-name name version))
3de01d3f 1767 (sha256
abed5df7 1768 (base32 "08rq4jajwmlpivnm9yifz2jhaivnz065lnk0h2zv773nwl9wf162"))
3de01d3f
EB		 1769 (modules '((guix build utils)))
1770 (snippet
1771 ;; Remove non-free METIS code
6cbee49d
MW		 1772 '(begin
1773 (delete-file-recursively "contrib/Metis")
1774 #t))))
3de01d3f 1775 (build-system cmake-build-system)
3de01d3f
EB		 1776 (propagated-inputs
1777 `(("fltk" ,fltk)
19afbea1 1778 ("gfortran" ,gfortran)
3de01d3f 1779 ("gmp" ,gmp)
40029cbe 1780 ("hdf5" ,hdf5)
3de01d3f
EB		 1781 ("lapack" ,lapack)
1782 ("mesa" ,mesa)
85f41902 1783 ("glu" ,glu)
45548139 1784 ("opencascade-oce" ,opencascade-oce)
3de01d3f
EB		 1785 ("libx11" ,libx11)
1786 ("libxext" ,libxext)))
66395a61
EF		 1787 (inputs
1788 `(("fontconfig" ,fontconfig)
1789 ("libxft" ,libxft)))
3de01d3f
EB		 1790 (arguments
1791 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1792 "-DENABLE_BUILD_SHARED:BOOL=ON"
45548139 1793 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
0746c33e 1794 (home-page "http://gmsh.info/")
3de01d3f 1795 (synopsis "3D finite element grid generator")
edf684ef
EB		 1796 (description "Gmsh is a 3D finite element grid generator with a built-in
1797CAD engine and post-processor. Its design goal is to provide a fast, light
1798and user-friendly meshing tool with parametric input and advanced
1799visualization capabilities. Gmsh is built around four modules: geometry,
1800mesh, solver and post-processing. The specification of any input to these
1801modules is done either interactively using the graphical user interface or in
1802ASCII text files using Gmsh's own scripting language.")
3de01d3f 1803 (license license:gpl2+)))
b9100e2f 1804
6d5f63b6
JD		 1805(define-public maxflow
1806 (package
1807 (name "maxflow")
0af12a13
TGR		 1808 ;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’,
1809 ;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’.
1810 (version "3.0.5")
6d5f63b6
JD		 1811 (source (origin
1812 (method git-fetch)
1813 (uri (git-reference
1814 (url "https://github.com/gerddie/maxflow.git")
0af12a13 1815 (commit version)))
2dc0a6cf 1816 (file-name (git-file-name name version))
6d5f63b6
JD		 1817 (sha256
1818 (base32
1819 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1820 (build-system cmake-build-system)
0be9038c 1821 (home-page "https://pub.ist.ac.at/~vnk/software.html")
6d5f63b6
JD		 1822 (synopsis "Library implementing Maxflow algorithm")
1823 (description "An implementation of the maxflow algorithm described in
1824@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1825Energy Minimization in Computer Vision.\n
1826Yuri Boykov and Vladimir Kolmogorov.\n
1827In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1828September 2004}")
1829 (license license:gpl3+)))
1830
b9100e2f
EB		 1831(define-public petsc
1832 (package
1833 (name "petsc")
4f7a4a06 1834 (version "3.11.2")
b9100e2f
EB		 1835 (source
1836 (origin
1837 (method url-fetch)
1838 ;; The *-lite-* tarball does not contain the *large* documentation
1839 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1840 "petsc-lite-" version ".tar.gz"))
1841 (sha256
4f7a4a06 1842 (base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx"))))
b2c52fc9
TGR		 1843 (outputs '("out" ; libraries and headers
1844 "examples")) ; ~30MiB of examples
b9100e2f
EB		 1845 (build-system gnu-build-system)
1846 (native-inputs
6fec298d 1847 `(("python" ,python-2)))
b9100e2f 1848 (inputs
19afbea1 1849 `(("gfortran" ,gfortran)
b9100e2f 1850 ("lapack" ,lapack)
f258212d 1851 ("superlu" ,superlu)
b9100e2f
EB		 1852 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1853 ;; leaving out opengl, as configuration seems to only be for mac
1854 ))
1855 (arguments
1856 `(#:test-target "test"
b2c52fc9 1857 #:parallel-build? #f ; build is parallel by default
b9100e2f
EB		 1858 #:configure-flags
1859 `("--with-mpi=0"
f258212d 1860 "--with-openmp=1"
c15be128 1861 "--with-superlu=1")
9731c412
EB		 1862 #:make-flags
1863 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1864 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1865 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
b9100e2f 1866 #:phases
64dcc289
EB		 1867 (modify-phases %standard-phases
1868 (replace 'configure
1869 ;; PETSc's configure script is actually a python script, so we can't
1870 ;; run it with bash.
1871 (lambda* (#:key outputs (configure-flags '())
1872 #:allow-other-keys)
1873 (let* ((prefix (assoc-ref outputs "out"))
1874 (flags `(,(string-append "--prefix=" prefix)
1875 ,@configure-flags)))
1876 (format #t "build directory: ~s~%" (getcwd))
1877 (format #t "configure flags: ~s~%" flags)
49fdd357 1878 (apply invoke "./configure" flags))))
64dcc289 1879 (add-after 'configure 'clean-local-references
9731c412 1880 (lambda* (#:key outputs #:allow-other-keys)
64dcc289
EB		 1881 (let ((out (assoc-ref outputs "out")))
1882 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
b730b437
EB		 1883 ;; Prevent build directory from leaking into compiled code
1884 (((getcwd)) out)
1885 ;; Scrub timestamp for reproducibility
fafd623e 1886 ((".*Libraries compiled on.*") ""))
9731c412
EB		 1887 (substitute* (find-files "." "petscvariables")
1888 ;; Do not expose build machine characteristics, set to defaults.
1889 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1890 (("NPMAX = [:digit:]+") "NPMAX = 2"))
fafd623e 1891 #t)))
64dcc289 1892 (add-after 'install 'clean-install
10b11968
EB		 1893 ;; Try to keep installed files from leaking build directory names.
1894 (lambda* (#:key inputs outputs #:allow-other-keys)
64dcc289 1895 (let ((out (assoc-ref outputs "out")))
10b11968 1896 (substitute* (map (lambda (file)
9a899cce 1897 (string-append out "/lib/petsc/conf/" file))
fafd623e 1898 '("petscvariables"))
10b11968
EB		 1899 (((getcwd)) out))
1900 ;; Make compiler references point to the store
9a899cce 1901 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
dfdf5716
EB		 1902 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1903 (string-append "= " (which compiler))))
10b11968
EB		 1904 ;; PETSc installs some build logs, which aren't necessary.
1905 (for-each (lambda (file)
9a899cce 1906 (let ((f (string-append out "/lib/petsc/conf/" file)))
10b11968
EB		 1907 (when (file-exists? f)
1908 (delete-file f))))
9a899cce
EB		 1909 '("configure.log" "make.log" "gmake.log"
1910 "test.log" "error.log" "RDict.db"
fafd623e 1911 "PETScBuildInternal.cmake"
10b11968 1912 ;; Once installed, should uninstall with Guix
fafd623e 1913 "uninstall.py"))
a3a99e27
EB		 1914 #t)))
1915 (add-after 'install 'move-examples
1916 (lambda* (#:key outputs #:allow-other-keys)
1917 (let* ((out (assoc-ref outputs "out"))
1918 (examples (assoc-ref outputs "examples"))
1919 (exdir (string-append out "/share/petsc/examples"))
1920 (exdir' (string-append examples "/share/petsc/examples")))
1921 (copy-recursively exdir exdir')
1922 (delete-file-recursively exdir)
fafd623e 1923 #t))))))
b9100e2f 1924 (home-page "http://www.mcs.anl.gov/petsc")
16ecf3ff 1925 (synopsis "Library to solve PDEs")
b9100e2f
EB		 1926 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1927data structures and routines for the scalable (parallel) solution of
1928scientific applications modeled by partial differential equations.")
166191b3 1929 (license (license:non-copyleft
b9100e2f
EB		 1930 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1931
1932(define-public petsc-complex
1933 (package (inherit petsc)
1934 (name "petsc-complex")
1935 (arguments
1936 (substitute-keyword-arguments (package-arguments petsc)
1937 ((#:configure-flags cf)
1938 `(cons "--with-scalar-type=complex" ,cf))))
16ecf3ff 1939 (synopsis "Library to solve PDEs (with complex scalars)")))
183e44ae 1940
d8c7eeb9
EB		 1941(define-public petsc-openmpi
1942 (package (inherit petsc)
1943 (name "petsc-openmpi")
1944 (inputs
9e2aa70b 1945 `(("hdf5" ,hdf5-parallel-openmpi)
af523673 1946 ("hypre" ,hypre-openmpi)
9e2aa70b
PG		 1947 ("metis" ,metis)
1948 ("mumps" ,mumps-openmpi)
1949 ("openmpi" ,openmpi)
1950 ("scalapack" ,scalapack)
72f95783 1951 ("scotch" ,pt-scotch32)
d8c7eeb9
EB		 1952 ,@(package-inputs petsc)))
1953 (arguments
1954 (substitute-keyword-arguments (package-arguments petsc)
1955 ((#:configure-flags cf)
af523673
PG		 1956 ``("--with-hypre=1"
1957 "--with-mpiexec=mpirun"
9e2aa70b
PG		 1958 "--with-metis=1"
1959 "--with-mumps=1"
1960 "--with-scalapack=1"
1961 "--with-ptscotch=1"
d8c7eeb9
EB		 1962 ,(string-append "--with-mpi-dir="
1963 (assoc-ref %build-inputs "openmpi"))
71ca16b5
PG		 1964 ,(string-append "--with-hdf5-include="
1965 (assoc-ref %build-inputs "hdf5") "/include")
1966 ,(string-append "--with-hdf5-lib="
1967 (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
1968 ,@(delete "--with-mpi=0" ,cf)))
1969 ((#:phases phases)
1970 `(modify-phases ,phases
9e2aa70b 1971 (add-before 'configure 'mpi-setup
bbe46a4a 1972 ,%openmpi-setup)))))
9e2aa70b 1973 (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
d8c7eeb9
EB		 1974
1975(define-public petsc-complex-openmpi
1976 (package (inherit petsc-complex)
1977 (name "petsc-complex-openmpi")
1978 (inputs
1979 `(("openmpi" ,openmpi)
1980 ,@(package-inputs petsc-complex)))
1981 (arguments
1982 (substitute-keyword-arguments (package-arguments petsc-complex)
1983 ((#:configure-flags cf)
1984 ``("--with-mpiexec=mpirun"
1985 ,(string-append "--with-mpi-dir="
1986 (assoc-ref %build-inputs "openmpi"))
e586c6fa
EB		 1987 ,@(delete "--with-mpi=0" ,cf)))
1988 ((#:phases phases)
1989 `(modify-phases ,phases
1990 (add-before 'configure 'mpi-setup
1991 ,%openmpi-setup)))))
16ecf3ff 1992 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
d8c7eeb9 1993
90ff2874
PG		 1994(define-public python-petsc4py
1995 (package
1996 (name "python-petsc4py")
f1cc312e 1997 (version "3.11.0")
90ff2874
PG		 1998 (source
1999 (origin
2000 (method url-fetch)
2001 (uri (pypi-uri "petsc4py" version))
2002 (sha256
2003 (base32
f1cc312e 2004 "1rm1qj5wlkhxl39by9n78lh3gbmii31wsnb8j1rr5hvfr5xgbx2q"))))
90ff2874
PG		 2005 (build-system python-build-system)
2006 (arguments
2007 `(#:phases
2008 (modify-phases %standard-phases
2009 (add-before 'build 'pre-build
2010 (lambda _
2011 ;; Define path to PETSc installation.
2012 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
2013 #t))
2014 (add-before 'check 'mpi-setup
2015 ,%openmpi-setup))))
2016 (inputs
2017 `(("petsc" ,petsc-openmpi)
2018 ("python-numpy" ,python-numpy)))
2019 (home-page "https://bitbucket.org/petsc/petsc4py/")
2020 (synopsis "Python bindings for PETSc")
2021 (description "PETSc, the Portable, Extensible Toolkit for
2022Scientific Computation, is a suite of data structures and routines for
2023the scalable (parallel) solution of scientific applications modeled by
2024partial differential equations. It employs the MPI standard for all
2025message-passing communication. @code{petsc4py} provides Python
2026bindings to almost all functions of PETSc.")
2027 (license license:bsd-3)))
2028
560acf25
MB		 2029(define-public python-kiwisolver
2030 (package
2031 (name "python-kiwisolver")
2032 (version "1.0.1")
2033 (source (origin
2034 (method url-fetch)
2035 (uri (pypi-uri "kiwisolver" version))
2036 (sha256
2037 (base32
2038 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
2039 (build-system python-build-system)
2040 (home-page "https://github.com/nucleic/kiwi")
2041 (synopsis "Fast implementation of the Cassowary constraint solver")
2042 (description
2043 "Kiwi is an efficient C++ implementation of the Cassowary constraint
2044solving algorithm. Kiwi has been designed from the ground up to be
2045lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
2046Cassowary solver with typical use cases gaining a 40x improvement. Memory
2047savings are consistently > 5x.")
2048 (license license:bsd-3)))
2049
2050(define-public python2-kiwisolver
2051 (package-with-python2 python-kiwisolver))
2052
a7f01414
EB		 2053(define-public slepc
2054 (package
2055 (name "slepc")
a13e0f3d 2056 (version "3.11.1")
a7f01414
EB		 2057 (source
2058 (origin
2059 (method url-fetch)
baeaf882
EB		 2060 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
2061 version ".tar.gz"))
a7f01414
EB		 2062 (sha256
2063 (base32
a13e0f3d 2064 "1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8"))))
a7f01414
EB		 2065 (build-system gnu-build-system)
2066 (native-inputs
a13e0f3d
EB		 2067 `(("python" ,python-2)
2068 ("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
a7f01414
EB		 2069 (inputs
2070 `(("arpack" ,arpack-ng)
2071 ("gfortran" ,gfortran)))
2072 (propagated-inputs
2073 `(("petsc" ,petsc)))
2074 (arguments
2075 `(#:parallel-build? #f ;build is parallel by default
2076 #:configure-flags
2077 `(,(string-append "--with-arpack-dir="
9cf52454 2078 (assoc-ref %build-inputs "arpack") "/lib"))
9731c412 2079 #:make-flags ;honor (parallel-job-count)
a13e0f3d
EB		 2080 `(,(format #f "MAKE_NP=~a" (parallel-job-count))
2081 ,(string-append "PETSCCONFIGDIR="
2082 (assoc-ref %build-inputs "petsc:examples")
2083 "/share/petsc/examples/config"))
a7f01414
EB		 2084 #:phases
2085 (modify-phases %standard-phases
8787c555 2086 (replace 'configure
a7f01414
EB		 2087 ;; configure is a python script, so we can't run it with bash.
2088 (lambda* (#:key inputs outputs (configure-flags '())
2089 #:allow-other-keys)
2090 (let* ((prefix (assoc-ref outputs "out"))
2091 (flags `(,(string-append "--prefix=" prefix)
2092 ,@configure-flags)))
2093 (format #t "build directory: ~s~%" (getcwd))
2094 (format #t "configure flags: ~s~%" flags)
2095 (setenv "SLEPC_DIR" (getcwd))
9cf52454 2096 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
c6840089 2097 (apply invoke "./configure" flags))))
8787c555 2098 (add-after 'install 'delete-doc
a7f01414
EB		 2099 ;; TODO: SLEPc installs HTML documentation alongside headers in
2100 ;; $out/include. We'd like to move them to share/doc, but delete
2101 ;; them for now, as they are incomplete and installing the complete
2102 ;; documentation is difficult.
2103 (lambda* (#:key outputs #:allow-other-keys)
2104 (let* ((out (assoc-ref outputs "out")))
0f6dc120
TGR		 2105 (for-each delete-file (find-files out "\\.html$"))
2106 #t)))
8787c555 2107 (add-after 'install 'clean-install
a7f01414
EB		 2108 ;; Clean up unnecessary build logs from installation.
2109 (lambda* (#:key outputs #:allow-other-keys)
2110 (let ((out (assoc-ref outputs "out")))
2111 (for-each (lambda (file)
2112 (let ((f (string-append out "/lib/slepc/conf/" file)))
2113 (when (file-exists? f)
2114 (delete-file f))))
2115 '("configure.log" "make.log" "gmake.log"
2116 "test.log" "error.log" "RDict.db"
0f6dc120
TGR		 2117 "uninstall.py"))
2118 #t))))))
a7f01414
EB		 2119 (home-page "http://slepc.upv.es")
2120 (synopsis "Scalable library for eigenproblems")
2121 (description "SLEPc is a software library for the solution of large sparse
2122eigenproblems on parallel computers. It can be used for the solution of
2123linear eigenvalue problems formulated in either standard or generalized form,
2124as well as other related problems such as the singular value decomposition.
2125The emphasis of the software is on methods and techniques appropriate for
2126problems in which the associated matrices are sparse, for example, those
2127arising after the discretization of partial differential equations.")
3c524f21 2128 (license license:bsd-2)))
a7f01414
EB		 2129
2130(define-public slepc-complex
2131 (package (inherit slepc)
2132 (name "slepc-complex")
2133 (propagated-inputs
2134 `(("petsc" ,petsc-complex)
2135 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
2136 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
2137
2138(define-public slepc-openmpi
2139 (package (inherit slepc)
2140 (name "slepc-openmpi")
6df2a50a
LC		 2141 (arguments
2142 (substitute-keyword-arguments (package-arguments slepc)
2143 ((#:phases phases '%standard-phases)
2144 `(modify-phases ,phases
bbe46a4a
EB		 2145 (add-before 'check 'mpi-setup
2146 ,%openmpi-setup)))))
a7f01414
EB		 2147 (inputs
2148 `(("mpi" ,openmpi)
2149 ("arpack" ,arpack-ng-openmpi)
2150 ,@(alist-delete "arpack" (package-inputs slepc))))
2151 (propagated-inputs
2152 `(("petsc" ,petsc-openmpi)
2153 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
2154 (synopsis "Scalable library for eigenproblems (with MPI support)")))
2155
2156(define-public slepc-complex-openmpi
2157 (package (inherit slepc-openmpi)
2158 (name "slepc-complex-openmpi")
2159 (propagated-inputs
2160 `(("petsc" ,petsc-complex-openmpi)
2161 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
2162 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
2163
6b5687d0
PG		 2164(define-public python-slepc4py
2165 (package
2166 (name "python-slepc4py")
09bad3cd 2167 (version "3.11.0")
6b5687d0
PG		 2168 (source
2169 (origin
2170 (method url-fetch)
2171 (uri (pypi-uri "slepc4py" version))
2172 (sha256
2173 (base32
09bad3cd 2174 "1ksp08kxf4wg408b9nn39z3qfhy643j22d4rfbl30vzxk2rxh4lq"))))
6b5687d0
PG		 2175 (build-system python-build-system)
2176 (arguments
2177 `(#:phases
2178 (modify-phases %standard-phases
2179 (add-before 'build 'pre-build
2180 (lambda _
2181 ;; Define path to PETSc installation.
2182 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
2183 ;; Define path to SLEPc installation.
2184 (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
2185 #t))
2186 (add-before 'check 'mpi-setup
2187 ,%openmpi-setup))))
2188 (inputs
2189 `(("python-numpy" ,python-numpy)
2190 ("python-petsc4py" ,python-petsc4py)
2191 ("slepc" ,slepc-openmpi)))
2192 (home-page "https://bitbucket.org/slepc/slepc4py/")
2193 (synopsis "Python bindings for SLEPc")
2194 (description "SLEPc, the Scalable Library for Eigenvalue Problem
2195Computations, is based on PETSc, the Portable, Extensible Toolkit for
2196Scientific Computation. It employs the MPI standard for all
2197message-passing communication. @code{slepc4py} provides Python
2198bindings to almost all functions of SLEPc.")
2199 (license license:bsd-3)))
2200
cec86422
EB		 2201(define-public mumps
2202 (package
2203 (name "mumps")
5dbc79eb 2204 (version "5.2.1")
cec86422
EB		 2205 (source
2206 (origin
2207 (method url-fetch)
2208 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
2209 version ".tar.gz"))
2210 (sha256
2211 (base32
5dbc79eb 2212 "0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r"))
06e12395
MB		 2213 (patches (search-patches "mumps-build-parallelism.patch"
2214 "mumps-shared-libseq.patch"
2215 "mumps-shared-mumps.patch"
2216 "mumps-shared-pord.patch"))))
cec86422
EB		 2217 (build-system gnu-build-system)
2218 (inputs
2219 `(("fortran" ,gfortran)
2220 ;; These are required for linking against mumps, but we let the user
2221 ;; declare the dependency.
2222 ("blas" ,openblas)
2223 ("metis" ,metis)
2224 ("scotch" ,scotch)))
2225 (arguments
2226 `(#:modules ((ice-9 match)
2227 (ice-9 popen)
2228 (srfi srfi-1)
2229 ,@%gnu-build-system-modules)
2230 #:phases
2231 (modify-phases %standard-phases
fba78d18 2232 (replace 'configure
cec86422
EB		 2233 (lambda* (#:key inputs #:allow-other-keys)
2234 (call-with-output-file "Makefile.inc"
2235 (lambda (port)
2236 (format port "
2237PLAT =
2238LIBEXT = .a
2239OUTC = -o
2240OUTF = -o
2241RM = rm -f~:[
2242CC = gcc
2243FC = gfortran
2244FL = gfortran
2245INCSEQ = -I$(topdir)/libseq
06e12395 2246LIBSEQ = $(topdir)/libseq/libmpiseq.a
cec86422
EB		 2247LIBSEQNEEDED = libseqneeded~;
2248CC = mpicc
2249FC = mpifort
2250FL = mpifort~]
2251AR = ar vr # rules require trailing space, ugh...
2252RANLIB = ranlib
06e12395
MB		 2253BLASDIR = ~a
2254LIBBLAS = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[
2255SCALAPDIR = ~a
2256SCALAP = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~]
cec86422
EB		 2257LIBOTHERS = -pthread
2258CDEFS = -DAdd_
2259PIC = -fPIC
2260OPTF = -O2 -DALLOW_NON_INIT $(PIC)
2261OPTL = -O2 $(PIC)
2262OPTC = -O2 $(PIC)
2263INCS = $(INCSEQ)
2264LIBS = $(SCALAP) $(LIBSEQ)
2265LPORDDIR = $(topdir)/PORD/lib
2266IPORD = -I$(topdir)/PORD/include
06e12395 2267LPORD = $(LPORDDIR)/libpord.a
cec86422
EB		 2268ORDERINGSF = -Dpord~@[
2269METISDIR = ~a
2270IMETIS = -I$(METISDIR)/include
06e12395 2271LMETIS = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
cec86422
EB		 2272ORDERINGSF += -Dmetis~]~@[~:{
2273SCOTCHDIR = ~a
2274ISCOTCH = -I$(SCOTCHDIR)/include
06e12395 2275LSCOTCH = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
cec86422
EB		 2276ORDERINGSF += ~a~}~]
2277ORDERINGSC = $(ORDERINGSF)
06e12395 2278LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
cec86422
EB		 2279IORDERINGSF = $(ISCOTCH)
2280IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
2281 (assoc-ref inputs "mpi")
2282 (assoc-ref inputs "blas")
2283 (assoc-ref inputs "scalapack")
2284 (assoc-ref inputs "metis")
2285 (match (list (assoc-ref inputs "pt-scotch")
2286 (assoc-ref inputs "scotch"))
2287 ((#f #f)
2288 #f)
2289 ((#f scotch)
2290 `((,scotch "" "-Dscotch")))
2291 ((ptscotch _)
2292 `((,ptscotch
2293 "-lptesmumps -lptscotch -lptscotcherr "
2294 "-Dptscotch")))))))))
fba78d18 2295 (replace 'build
cec86422
EB		 2296 ;; By default only the d-precision library is built. Make with "all"
2297 ;; target so that all precision libraries and examples are built.
2298 (lambda _
b414cf52
TGR		 2299 (invoke "make" "all"
2300 (format #f "-j~a" (parallel-job-count)))))
fba78d18 2301 (replace 'check
cec86422
EB		 2302 ;; Run the simple test drivers, which read test input from stdin:
2303 ;; from the "real" input for the single- and double-precision
2304 ;; testers, and from the "cmplx" input for complex-precision
2305 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
2306 ;; package to prefix execution with "mpirun".
2307 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
2308 (with-directory-excursion "examples"
2309 (every
2310 (lambda (prec type)
2311 (let ((tester (apply open-pipe*
2312 `(,OPEN_WRITE
2313 ,@exec-prefix
2314 ,(string-append "./" prec
2315 "simpletest"))))
2316 (input (open-input-file
2317 (string-append "input_simpletest_" type))))
2318 (begin
2319 (dump-port input tester)
2320 (close-port input)
2321 (zero? (close-pipe tester)))))
2322 '("s" "d" "c" "z")
2323 '("real" "real" "cmplx" "cmplx")))))
fba78d18
EB		 2324 (replace 'install
2325 (lambda* (#:key outputs #:allow-other-keys)
2326 (let* ((out (assoc-ref outputs "out"))
2327 (libdir (string-append out "/lib")))
2328 (copy-recursively "lib" libdir)
2329 (copy-recursively "include" (string-append out "/include"))
2330 (when (file-exists? "libseq/libmpiseq.a")
2331 (install-file "libseq/libmpiseq.a" libdir))
06e12395
MB		 2332 (when (file-exists? "libseq/libmpiseq.so")
2333 (install-file "libseq/libmpiseq.so" libdir))
fba78d18 2334 #t))))))
cec86422
EB		 2335 (home-page "http://mumps.enseeiht.fr")
2336 (synopsis "Multifrontal sparse direct solver")
2337 (description
2338 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
57e69c1d 2339sparse system of linear equations A x = b using Gaussian elimination.")
cec86422
EB		 2340 (license license:cecill-c)))
2341
2342(define-public mumps-metis
2343 (package (inherit mumps)
2344 (name "mumps-metis")
2345 (inputs
2346 (alist-delete "scotch" (package-inputs mumps)))))
2347
2348(define-public mumps-openmpi
2349 (package (inherit mumps)
2350 (name "mumps-openmpi")
2351 (inputs
2352 `(("mpi" ,openmpi)
2353 ("scalapack" ,scalapack)
2354 ("pt-scotch" ,pt-scotch)
2355 ,@(alist-delete "scotch" (package-inputs mumps))))
2356 (arguments
2357 (substitute-keyword-arguments (package-arguments mumps)
2358 ((#:phases phases)
2359 `(modify-phases ,phases
bbe46a4a
EB		 2360 (add-before 'check 'mpi-setup
2361 ,%openmpi-setup)
6df2a50a
LC		 2362 (replace 'check
2363 (lambda _
2364 ((assoc-ref ,phases 'check)
2365 #:exec-prefix '("mpirun" "-n" "2"))))))))
cec86422
EB		 2366 (synopsis "Multifrontal sparse direct solver (with MPI)")))
2367
2368(define-public mumps-metis-openmpi
2369 (package (inherit mumps-openmpi)
2370 (name "mumps-metis-openmpi")
2371 (inputs
2372 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
2373
63e07468
BW		 2374(define-public ruby-asciimath
2375 (package
2376 (name "ruby-asciimath")
2377 (version "1.0.4")
2378 (source
2379 (origin
2380 (method url-fetch)
2381 (uri (rubygems-uri "asciimath" version))
2382 (sha256
2383 (base32
2384 "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
2385 (build-system ruby-build-system)
2386 (arguments
2387 '(#:phases
2388 (modify-phases %standard-phases
2389 ;; Apply this patch
2390 ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
2391 (add-after 'unpack 'patch-remove-spurious-backslashes
2392 (lambda _
2393 (substitute* "spec/parser_spec.rb"
2394 (("\\\\\"")
9923d5a4
TGR		 2395 "\""))
2396 #t)))))
63e07468
BW		 2397 (native-inputs
2398 `(("bundler" ,bundler)
2399 ("ruby-rspec" ,ruby-rspec)))
2400 (synopsis "AsciiMath parsing and conversion library")
2401 (description
2402 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
2403easy-to-write markup language for mathematics.")
2404 (home-page "https://github.com/asciidoctor/asciimath")
2405 (license license:expat)))
2406
183e44ae
EB		 2407(define-public superlu
2408 (package
2409 (name "superlu")
995a09e0 2410 (version "5.2.1")
183e44ae
EB		 2411 (source
2412 (origin
2413 (method url-fetch)
2414 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2415 "superlu_" version ".tar.gz"))
2416 (sha256
995a09e0
EB		 2417 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
2418 (modules '((guix build utils)))
2419 (snippet
2420 ;; Replace the non-free implementation of MC64 with a stub adapted
2421 ;; from Debian
2422 '(begin
2423 (use-modules (ice-9 regex)
2424 (ice-9 rdelim))
2425 (call-with-output-file "SRC/mc64ad.c"
2426 (lambda (port)
2427 (display "
2428#include <stdio.h>
2429#include <stdlib.h>
2430void mc64id_(int *a) {
2431 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2432 abort ();
2433}
2434void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2435 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2436 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2437 abort ();
2438}\n" port)))
2439 ;; Remove the corresponding license verbiage. MC64 license follows
2440 ;; a "------" line separator.
2441 (with-atomic-file-replacement "License.txt"
2442 (let ((rx (make-regexp "-{8}")))
2443 (lambda (in out)
2444 (let loop ()
2445 (let ((line (read-line in 'concat)))
2446 (unless (regexp-exec rx line)
2447 (display line out)
6cbee49d
MW		 2448 (loop))))
2449 #t)))))))
995a09e0 2450 (build-system cmake-build-system)
183e44ae
EB		 2451 (native-inputs
2452 `(("tcsh" ,tcsh)))
2453 (inputs
995a09e0 2454 `(("blas" ,openblas)
19afbea1 2455 ("gfortran" ,gfortran)))
183e44ae 2456 (arguments
995a09e0
EB		 2457 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2458 "-DTPL_BLAS_LIBRARIES=openblas"
677bc34d 2459 "-DBUILD_SHARED_LIBS:BOOL=YES")))
183e44ae
EB		 2460 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
2461 (synopsis "Supernodal direct solver for sparse linear systems")
2462 (description
2463 "SuperLU is a general purpose library for the direct solution of large,
2464sparse, nonsymmetric systems of linear equations on high performance machines.
2465The library is written in C and is callable from either C or Fortran. The
2466library routines perform an LU decomposition with partial pivoting and
2467triangular system solves through forward and back substitution. The library
2468also provides threshold-based ILU factorization preconditioners.")
995a09e0
EB		 2469 (license (list license:bsd-3
2470 license:gpl2+ ;EXAMPLE/*fgmr.c
2471 (license:fsf-free "file://SRC/colamd.h")))))
f8ed036a 2472
a54aefea
EB		 2473(define-public superlu-dist
2474 (package
2475 (name "superlu-dist")
6161141e 2476 (version "6.1.0")
a54aefea
EB		 2477 (source
2478 (origin
2479 (method url-fetch)
2480 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2481 "superlu_dist_" version ".tar.gz"))
2482 (sha256
6161141e 2483 (base32 "0pqgcgh1yxhfzs99fas3mggajzd5wca3nbyp878rziy74gfk03dl"))
0921eff2 2484 (modules '((guix build utils)))
29080870
EB		 2485 (snippet
2486 ;; Replace the non-free implementation of MC64 with a stub
2487 '(begin
0921eff2 2488 (call-with-output-file "SRC/mc64ad_dist.c"
29080870
EB		 2489 (lambda (port)
2490 (display "
2491#include <stdio.h>
2492#include <stdlib.h>
0921eff2 2493void mc64id_dist(int *a) {
29080870
EB		 2494 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2495 abort ();
2496}
0921eff2 2497void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
29080870
EB		 2498 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2499 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2500 abort ();
2501}\n" port)))
29080870 2502 (substitute* "SRC/util.c" ;adjust default algorithm
6161141e
EB		 2503 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
2504 ;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
2505 ;; general (i.e. non-square) processor-grid support.
2506 "RowPerm = NOROWPERM;"))
6cbee49d 2507 #t))
6161141e 2508 (patches (search-patches "superlu-dist-scotchmetis.patch"
2bdf26f1
EB		 2509 "superlu-dist-awpm-grid.patch"
2510 "superlu-dist-fix-mpi-deprecations.patch"))))
6161141e 2511 (build-system cmake-build-system)
a54aefea
EB		 2512 (native-inputs
2513 `(("tcsh" ,tcsh)))
2514 (inputs
6161141e
EB		 2515 `(("gfortran" ,gfortran)
2516 ("blas" ,openblas)
2517 ("lapack" ,lapack)
2518 ("combblas" ,combinatorial-blas)))
a54aefea 2519 (propagated-inputs
6161141e
EB		 2520 `(("mpi" ,openmpi) ;headers include MPI heades
2521 ("parmetis" ,pt-scotch32 "metis")
2522 ("pt-scotch" ,pt-scotch32)))
a54aefea 2523 (arguments
6161141e
EB		 2524 `(#:parallel-tests? #f ;tests use MPI and OpenMP
2525 #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
2526 "-DTPL_ENABLE_COMBBLASLIB=YES"
2527 "-DTPL_BLAS_LIBRARIES=-lopenblas"
2528 "-DTPL_LAPACK_LIBRARIES=-llapack"
2529 (string-append "-DTPL_PARMETIS_LIBRARIES="
2530 (string-join
2531 '("ptscotchparmetis" "ptscotch" "ptscotcherr"
2532 "scotchmetis" "scotch" "scotcherr")
2533 ";"))
2534 (string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
2535 (assoc-ref %build-inputs "parmetis")
2536 "/include")
2537 "-DTPL_ENABLE_COMBBLASLIB=ON"
2538 (string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
2539 (assoc-ref %build-inputs "combblas")
2540 "/include/CombBLAS;"
2541 (assoc-ref %build-inputs "combblas")
2542 "/include/BipartiteMatchings")
2543 "-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
a54aefea 2544 #:phases
dc1d3cde 2545 (modify-phases %standard-phases
6161141e 2546 (add-before 'configure 'set-c++-standard
dc1d3cde 2547 (lambda _
6161141e
EB		 2548 (substitute* "CMakeLists.txt"
2549 ;; AWPM headers require C++14
2550 (("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
bbe46a4a
EB		 2551 (add-before 'check 'mpi-setup
2552 ,%openmpi-setup)
6161141e
EB		 2553 (add-before 'check 'omp-setup
2554 (lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
a54aefea
EB		 2555 (home-page (package-home-page superlu))
2556 (synopsis "Parallel supernodal direct solver")
2557 (description
2558 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2559It is targeted for distributed memory parallel machines. SuperLU_DIST is
2560implemented in ANSI C, and MPI for communications.")
2561 (license license:bsd-3)))
2562
f8ed036a
EB		 2563(define-public scotch
2564 (package
2565 (name "scotch")
fd373343 2566 (version "6.0.6")
f8ed036a
EB		 2567 (source
2568 (origin
2569 (method url-fetch)
1dc31097
TGR		 2570 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
2571 "latestfile/298/scotch_" version ".tar.gz"))
f8ed036a 2572 (sha256
fd373343
EB		 2573 (base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8"))
2574 (patches (search-patches "scotch-build-parallelism.patch"
2575 "scotch-integer-declarations.patch"))))
f8ed036a
EB		 2576 (build-system gnu-build-system)
2577 (inputs
2578 `(("zlib" ,zlib)
5e54f4ad 2579 ("flex" ,flex)
f8ed036a 2580 ("bison" ,bison)))
fd373343 2581 (outputs '("out" "metis"))
f8ed036a 2582 (arguments
fd373343
EB		 2583 `(#:make-flags (list (string-append "prefix=" %output))
2584 #:phases
d6602ee9
EB		 2585 (modify-phases %standard-phases
2586 (add-after
2587 'unpack 'chdir-to-src
d67a7e9e 2588 (lambda _ (chdir "src") #t))
d6602ee9
EB		 2589 (replace
2590 'configure
2591 (lambda _
2592 (call-with-output-file "Makefile.inc"
2593 (lambda (port)
2594 (format port "
f8ed036a
EB		 2595EXE =
2596LIB = .a
2597OBJ = .o
2598MAKE = make
2599AR = ar
2600ARFLAGS = -ruv
cf0ec6c4 2601CAT = cat
f8ed036a
EB		 2602CCS = gcc
2603CCP = mpicc
2604CCD = gcc
2605CPPFLAGS =~{ -D~a~}
6c798540 2606CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
f8ed036a
EB		 2607LDFLAGS = -lz -lm -lrt -lpthread
2608CP = cp
2609LEX = flex -Pscotchyy -olex.yy.c
2610LN = ln
2611MKDIR = mkdir
2612MV = mv
2613RANLIB = ranlib
2614YACC = bison -pscotchyy -y -b y
2615"
d6602ee9
EB		 2616 '("COMMON_FILE_COMPRESS_GZ"
2617 "COMMON_PTHREAD"
2618 "COMMON_RANDOM_FIXED_SEED"
fd373343 2619 "INTSIZE64" ;use 'int64_t'
cf0ec6c4
EB		 2620 ;; Prevents symbolc clashes with libesmumps
2621 "SCOTCH_RENAME"
d6602ee9
EB		 2622 ;; XXX: Causes invalid frees in superlu-dist tests
2623 ;; "SCOTCH_PTHREAD"
2624 ;; "SCOTCH_PTHREAD_NUMBER=2"
d67a7e9e
TGR		 2625 "restrict=__restrict"))))
2626 #t))
bbe46a4a 2627 (add-after 'build 'build-esmumps
cf0ec6c4 2628 (lambda _
d67a7e9e
TGR		 2629 (invoke "make"
2630 (format #f "-j~a" (parallel-job-count))
2631 "esmumps")))
fd373343
EB		 2632 (add-before 'install 'make-install-dirs
2633 (lambda* (#:key outputs #:allow-other-keys)
2634 (mkdir (assoc-ref outputs "out"))))
2635 (add-after 'install 'install-metis
2636 (lambda* (#:key outputs #:allow-other-keys)
2637 (let ((out (assoc-ref outputs "metis")))
2638 (mkdir out)
2639 ;; metis files are not installed with 'make install'
2640 (for-each (lambda (f)
2641 (install-file f (string-append out "/include")))
2642 (find-files "../include/" ".*metis\\.h"))
2643 (for-each (lambda (f)
2644 (install-file f (string-append out "/lib")))
2645 (find-files "../lib/" ".*metis\\..*"))
2646 #t))))))
f8ed036a
EB		 2647 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
2648 (synopsis "Programs and libraries for graph algorithms")
2649 (description "SCOTCH is a set of programs and libraries which implement
2650the static mapping and sparse matrix reordering algorithms developed within
2651the SCOTCH project. Its purpose is to apply graph theory, with a divide and
2652conquer approach, to scientific computing problems such as graph and mesh
2653partitioning, static mapping, and sparse matrix ordering, in application
2654domains ranging from structural mechanics to operating systems or
2655bio-chemistry.")
2656 ;; See LICENSE_en.txt
2657 (license license:cecill-c)))
6acb4adb 2658
1c39f3b8
PG		 2659(define-public scotch32
2660 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2661 ;; some applications.
2662 (package (inherit scotch)
2663 (name "scotch32")
2664 (arguments
2665 (substitute-keyword-arguments (package-arguments scotch)
2666 ((#:phases scotch-phases)
2667 `(modify-phases ,scotch-phases
2668 (replace
2669 'configure
2670 (lambda _
2671 (call-with-output-file "Makefile.inc"
2672 (lambda (port)
2673 (format port "
2674EXE =
2675LIB = .a
2676OBJ = .o
2677MAKE = make
2678AR = ar
2679ARFLAGS = -ruv
2680CAT = cat
2681CCS = gcc
2682CCP = mpicc
2683CCD = gcc
2684CPPFLAGS =~{ -D~a~}
2685CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2686LDFLAGS = -lz -lm -lrt -lpthread
2687CP = cp
2688LEX = flex -Pscotchyy -olex.yy.c
2689LN = ln
2690MKDIR = mkdir
2691MV = mv
2692RANLIB = ranlib
2693YACC = bison -pscotchyy -y -b y
2694"
2695 '("COMMON_FILE_COMPRESS_GZ"
2696 "COMMON_PTHREAD"
2697 "COMMON_RANDOM_FIXED_SEED"
2698 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
2699 ;; Prevents symbolc clashes with libesmumps
2700 "SCOTCH_RENAME"
2701 ;; XXX: Causes invalid frees in superlu-dist tests
2702 ;; "SCOTCH_PTHREAD"
2703 ;; "SCOTCH_PTHREAD_NUMBER=2"
2704 "restrict=__restrict"))))))))))
2705 (synopsis
2706 "Programs and libraries for graph algorithms (32-bit integers)")))
2707
6acb4adb
EB		 2708(define-public pt-scotch
2709 (package (inherit scotch)
2710 (name "pt-scotch")
2711 (propagated-inputs
2712 `(("openmpi" ,openmpi))) ;Headers include MPI headers
2713 (arguments
2714 (substitute-keyword-arguments (package-arguments scotch)
2715 ((#:phases scotch-phases)
d6602ee9
EB		 2716 `(modify-phases ,scotch-phases
2717 (replace
2718 'build
d6602ee9 2719 (lambda _
c491f7f8
LC		 2720 (invoke "make" (format #f "-j~a" (parallel-job-count))
2721 "ptscotch" "ptesmumps")
2722
2723 ;; Install the serial metis compatibility library
2724 (invoke "make" "-C" "libscotchmetis" "install")))
2725 (add-before 'check 'mpi-setup
2726 ,%openmpi-setup)
2727 (replace 'check
2728 (lambda _
2729 (invoke "make" "ptcheck")))))))
6acb4adb 2730 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
5698b8b8 2731
1c25a52c
PG		 2732(define-public pt-scotch32
2733 (package (inherit scotch32)
2734 (name "pt-scotch32")
2735 (propagated-inputs
2736 `(("openmpi" ,openmpi))) ;headers include MPI headers
2737 (arguments
c4d4a779
PG		 2738 (substitute-keyword-arguments (package-arguments scotch32)
2739 ((#:phases scotch32-phases)
2740 `(modify-phases ,scotch32-phases
1c25a52c
PG		 2741 (replace 'build
2742 (lambda _
c491f7f8
LC		 2743 (invoke "make" (format #f "-j~a" (parallel-job-count))
2744 "ptscotch" "ptesmumps")
2745 ;; Install the serial metis compatibility library
2746 (invoke "make" "-C" "libscotchmetis" "install")))
2747 (add-before 'check 'mpi-setup
2748 ,%openmpi-setup)
1c25a52c
PG		 2749 (replace 'check
2750 (lambda _
c491f7f8 2751 (invoke "make" "ptcheck")))))))
1c25a52c
PG		 2752 (synopsis
2753 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2754
aa75ad00
EB		 2755(define-public metis
2756 (package
2757 (name "metis")
2758 (version "5.1.0")
2759 (source
2760 (origin
2761 (method url-fetch)
2762 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2763 "metis-" version ".tar.gz"))
2764 (sha256
2765 (base32
2766 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2767 (build-system cmake-build-system)
2768 (inputs
2769 `(("blas" ,openblas)))
2770 (arguments
2771 `(#:tests? #f ;no tests
2772 #:configure-flags `("-DSHARED=ON"
2773 ,(string-append "-DGKLIB_PATH=" (getcwd)
2774 "/metis-" ,version "/GKlib"))))
2775 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2776 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2777 (description
2778 "METIS is a set of serial programs for partitioning graphs, partitioning
2779finite element meshes, and producing fill-reducing orderings for sparse
2780matrices. The algorithms implemented in METIS are based on the multilevel
2781recursive-bisection, multilevel k-way, and multi-constraint partitioning
2782schemes.")
2783 (license license:asl2.0))) ;As of version 5.0.3
2784
700ff222
EB		 2785(define-public p4est
2786 (package
2787 (name "p4est")
4150da63 2788 (version "2.0")
700ff222
EB		 2789 (source
2790 (origin
2791 (method url-fetch)
2792 (uri (string-append "http://p4est.github.io/release/p4est-"
2793 version ".tar.gz"))
2794 (sha256
2795 (base32
4150da63 2796 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
700ff222
EB		 2797 (build-system gnu-build-system)
2798 (inputs
2799 `(("fortran" ,gfortran)
2800 ("blas" ,openblas)
2801 ("lapack" ,lapack)
2802 ("zlib" ,zlib)))
2803 (arguments
2804 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2805 (assoc-ref %build-inputs "blas")
2806 " -lopenblas")
2807 ,(string-append "LAPACK_LIBS=-L"
2808 (assoc-ref %build-inputs "lapack")
6df2a50a
LC		 2809 " -llapack"))
2810 #:phases (modify-phases %standard-phases
bbe46a4a
EB		 2811 (add-before 'check 'mpi-setup
2812 ,%openmpi-setup))))
700ff222
EB		 2813 (home-page "http://www.p4est.org")
2814 (synopsis "Adaptive mesh refinement on forests of octrees")
2815 (description
2816 "The p4est software library enables the dynamic management of a
2817collection of adaptive octrees, conveniently called a forest of octrees.
2818p4est is designed to work in parallel and scales to hundreds of thousands of
2819processor cores.")
2820 (license license:gpl2+)))
2821
2822(define-public p4est-openmpi
2823 (package (inherit p4est)
2824 (name "p4est-openmpi")
2825 (inputs
2826 `(("mpi" ,openmpi)
2827 ,@(package-inputs p4est)))
2828 (arguments
2829 (substitute-keyword-arguments (package-arguments p4est)
2830 ((#:configure-flags cf)
2831 ``("--enable-mpi" ,@,cf))))
2832 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2833
5698b8b8
JD		 2834(define-public gsegrafix
2835 (package
2836 (name "gsegrafix")
2837 (version "1.0.6")
2838 (source
2839 (origin
2840 (method url-fetch)
2841 (uri (string-append "mirror://gnu/" name "/" name "-"
2842 version ".tar.gz"))
2843 (sha256
2844 (base32
2845 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2846 (build-system gnu-build-system)
2847 (arguments
2848 `(#:configure-flags '("LDFLAGS=-lm")))
2849 (inputs
2850 `(("libgnomecanvas" ,libgnomecanvas)
2851 ("libbonoboui" ,libbonoboui)
2852 ("libgnomeui" ,libgnomeui)
2853 ("libgnomeprintui" ,libgnomeprintui)
2854 ("popt" ,popt)))
2855 (native-inputs
2856 `(("pkg-config" ,pkg-config)))
6fd52309 2857 (home-page "https://www.gnu.org/software/gsegrafix/")
5698b8b8
JD		 2858 (synopsis "GNOME application to create scientific and engineering plots")
2859 (description "GSEGrafix is an application which produces high-quality graphical
2860plots for science and engineering. Plots are specified via simple ASCII
2861parameter files and data files and are presented in an anti-aliased GNOME
2862canvas. The program supports rectangular two-dimensional plots, histograms,
2863polar-axis plots and three-dimensional plots. Plots can be printed or saved
2864to BMP, JPEG or PNG image formats.")
2865 (license license:gpl3+)))
8731e527
JD		 2866
2867(define-public maxima
2868 (package
2869 (name "maxima")
ccc963d5 2870 (version "5.43.0")
8731e527
JD		 2871 (source
2872 (origin
2873 (method url-fetch)
2874 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2875 version "-source/" name "-" version ".tar.gz"))
2876 (sha256
2877 (base32
ccc963d5 2878 "0xyahp4c6509haxh4n1swiqm3421gplkdisa0zypclh3252sbzfw"))
fc1adab1 2879 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
8731e527 2880 (build-system gnu-build-system)
df354a77 2881 (inputs
6b2eafaa 2882 `(("gcl" ,gcl)
df354a77 2883 ("gnuplot" ,gnuplot) ;for plots
fc9c47bd 2884 ("sed" ,sed)
f36afe4d 2885 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
df354a77
FB		 2886 (native-inputs
2887 `(("texinfo" ,texinfo)
ccbc5758
KK		 2888 ("perl" ,perl)
2889 ("python" ,python)))
8731e527 2890 (arguments
df354a77
FB		 2891 `(#:configure-flags
2892 (list "--enable-gcl"
2893 (string-append "--with-posix-shell="
2894 (assoc-ref %build-inputs "bash")
2895 "/bin/sh")
2896 (string-append "--with-wish="
2897 (assoc-ref %build-inputs "tk")
2898 "/bin/wish"
2899 (let ((v ,(package-version tk)))
2900 (string-take v (string-index-right v #\.)))))
df354a77 2901 ;; By default Maxima attempts to write temporary files to
77af7b24
MW		 2902 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2903 ;; Work around that.
df354a77 2904 #:make-flags (list "TMPDIR=/tmp")
0093b126
KK		 2905 #:phases
2906 (modify-phases %standard-phases
fc9c47bd
KK		 2907 (add-after 'unpack 'patch-paths
2908 (lambda* (#:key inputs #:allow-other-keys)
2909 (let* ((sed (string-append (assoc-ref inputs "sed") "/bin/sed"))
2910 (coreutils (assoc-ref inputs "coreutils"))
2911 (dirname (string-append coreutils "/bin/dirname"))
ccc963d5
KK		 2912 (head (string-append coreutils "/bin/head"))
2913 (perl (string-append (assoc-ref inputs "perl") "/bin/perl"))
2914 (python (string-append (assoc-ref inputs "python")
2915 "/bin/python3")))
fc9c47bd
KK		 2916 (substitute* "src/maxima.in"
2917 (("sed ") (string-append sed " "))
2918 (("dirname") dirname)
2919 (("head") head))
ccc963d5
KK		 2920 (substitute* "doc/info/Makefile.in"
2921 (("/usr/bin/env perl") perl))
2922 (substitute* "doc/info/build_html.sh.in"
2923 (("python") python))
fc9c47bd 2924 #t)))
0093b126
KK		 2925 (add-before 'check 'pre-check
2926 (lambda _
2927 (chmod "src/maxima" #o555)
2928 #t))
1472d19a
KK		 2929 (replace 'check
2930 (lambda _
2931 ;; This is derived from the testing code in the "debian/rules" file
2932 ;; of Debian's Maxima package.
2933 ;; If Maxima can successfully run this, the binary to be installed
2934 ;; should be fine.
df129041
MW		 2935 (invoke "sh" "-c"
2936 (string-append
2937 "./maxima-local "
2938 "--lisp=gcl "
2939 "--batch-string=\"run_testsuite();\" "
2940 "| grep -q \"No unexpected errors found\""))))
0093b126
KK		 2941 ;; Make sure the doc and emacs files are found in the
2942 ;; standard location. Also configure maxima to find gnuplot
2943 ;; without having it on the PATH.
2944 (add-after 'install 'post-install
2945 (lambda* (#:key outputs inputs #:allow-other-keys)
2946 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2947 (out (assoc-ref outputs "out"))
2948 (datadir (string-append out "/share/maxima/" ,version))
2949 (binutils (string-append (assoc-ref inputs "binutils")
2950 "/bin")))
2951 (with-directory-excursion out
2952 (mkdir-p "share/emacs")
2953 (mkdir-p "share/doc")
0093b126
KK		 2954 (symlink
2955 (string-append datadir "/doc/")
2956 (string-append out "/share/doc/maxima"))
2957 (with-atomic-file-replacement
2958 (string-append datadir "/share/maxima-init.lisp")
2959 (lambda (in out)
2960 (format out "~a ~s~a~%"
2961 "(setf $gnuplot_command "
2962 (string-append gnuplot "/bin/gnuplot") ")")
2963 (dump-port in out))))
2964 ;; Ensure that Maxima will have access to the GNU binutils
2965 ;; components at runtime.
2966 (wrap-program (string-append out "/bin/maxima")
2967 `("PATH" prefix (,binutils))))
2968 #t)))))
8731e527
JD		 2969 (home-page "http://maxima.sourceforge.net")
2970 (synopsis "Numeric and symbolic expression manipulation")
2971 (description "Maxima is a system for the manipulation of symbolic and
2972numerical expressions. It yields high precision numeric results by using
2973exact fractions, arbitrary precision integers, and variable precision floating
e881752c 2974point numbers.")
8731e527
JD		 2975 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2976 ;; Others simply say "GNU General Public License" without stating a
2977 ;; version (which implicitly means gpl1+).
2978 ;; At least one file (src/maxima.asd) says "version 2."
2979 ;; GPLv2 only is therefore the smallest subset.
f36afe4d 2980 (license license:gpl2)))
ec322be2 2981
9aafbc0c
MW		 2982(define-public wxmaxima
2983 (package
2984 (name "wxmaxima")
1e8609f2 2985 (version "19.11.1")
9aafbc0c
MW		 2986 (source
2987 (origin
c93b77ad
KK		 2988 (method git-fetch)
2989 (uri (git-reference
2990 (url "https://github.com/wxMaxima-developers/wxmaxima.git")
2991 (commit (string-append "Version-" version))))
2992 (file-name (git-file-name name version))
9aafbc0c 2993 (sha256
1e8609f2 2994 (base32 "16xizaddb27432n1083y89ir5zdqvllsgbwrzzk4jc2rw1ldxfsv"))))
0181df53 2995 (build-system cmake-build-system)
5143517c 2996 (native-inputs
0181df53 2997 `(("gettext" ,gettext-minimal)))
9aafbc0c
MW		 2998 (inputs
2999 `(("wxwidgets" ,wxwidgets)
de477809
SB		 3000 ("maxima" ,maxima)
3001 ;; Runtime support.
3002 ("adwaita-icon-theme" ,adwaita-icon-theme)
3003 ("gtk+" ,gtk+)
3004 ("shared-mime-info" ,shared-mime-info)))
9aafbc0c 3005 (arguments
0181df53
KK		 3006 `(#:tests? #f ; no check target
3007 #:phases
ac2ddcc6 3008 (modify-phases %standard-phases
ac2ddcc6
KK		 3009 (add-after 'install 'wrap-program
3010 (lambda* (#:key inputs outputs #:allow-other-keys)
3011 (wrap-program (string-append (assoc-ref outputs "out")
3012 "/bin/wxmaxima")
3013 `("PATH" ":" prefix
3014 (,(string-append (assoc-ref inputs "maxima")
3015 "/bin")))
3016 ;; For GtkFileChooserDialog.
3017 `("GSETTINGS_SCHEMA_DIR" =
3018 (,(string-append (assoc-ref inputs "gtk+")
3019 "/share/glib-2.0/schemas")))
3020 `("XDG_DATA_DIRS" ":" prefix
3021 (;; Needed by gdk-pixbuf to know supported icon formats.
3022 ,(string-append
3023 (assoc-ref inputs "shared-mime-info") "/share")
3024 ;; The default icon theme of GTK+.
3025 ,(string-append
3026 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
3027 #t)))))
9aafbc0c
MW		 3028 (home-page "https://andrejv.github.io/wxmaxima/")
3029 (synopsis "Graphical user interface for the Maxima computer algebra system")
3030 (description
3031 "wxMaxima is a graphical user interface for the Maxima computer algebra
3032system. It eases the use of Maxima by making most of its commands available
3033through a menu system and by providing input dialogs for commands that require
3034more than one argument. It also implements its own display engine that
3035outputs mathematical symbols directly instead of depicting them with ASCII
3036characters.
3037
3038wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
3039text and mathematical calculations to create documents, exporting of input and
3040output to TeX, and a browser for Maxima's manual including command index and
3041full text searching.")
3042 (license license:gpl2+)))
3043
b15e47f9
RW		 3044(define-public armadillo
3045 (package
3046 (name "armadillo")
f133e244 3047 (version "9.100.5")
b15e47f9
RW		 3048 (source (origin
3049 (method url-fetch)
3050 (uri (string-append "mirror://sourceforge/arma/armadillo-"
7397cd9e 3051 version ".tar.xz"))
b15e47f9
RW		 3052 (sha256
3053 (base32
f133e244 3054 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
b15e47f9 3055 (build-system cmake-build-system)
e405c0bc 3056 (arguments `(#:tests? #f)) ; no test target
b15e47f9
RW		 3057 (inputs
3058 `(("openblas" ,openblas)
3059 ("lapack" ,lapack)
3060 ("arpack" ,arpack-ng)))
3061 (home-page "http://arma.sourceforge.net/")
3062 (synopsis "C++ linear algebra library")
3063 (description
3064 "Armadillo is a C++ linear algebra library, aiming towards a good balance
3065between speed and ease of use. It is useful for algorithm development
3066directly in C++, or quick conversion of research code into production
3067environments. It can be used for machine learning, pattern recognition,
3068signal processing, bioinformatics, statistics, econometrics, etc. The library
3069provides efficient classes for vectors, matrices and cubes, as well as 150+
3070associated functions (eg. contiguous and non-contiguous submatrix views).")
fe418cc5 3071 (license license:asl2.0)))
b15e47f9 3072
279663ef 3073(define-public muparser
d7cff656
LF		 3074 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
3075 ;; different hash. In order to make `guix package --upgrade` work correctly,
3076 ;; we set a Guix packaging revision.
3077 ;; When the next version of muparser is released, we can remove
3078 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
3079 (let ((upstream-version "2.2.5")
3080 (revision "2"))
3081 (package
3082 (name "muparser")
3083 (version (string-append upstream-version "-" revision))
3084 (source
3085 (origin
67f1db38
TGR		 3086 (method git-fetch)
3087 (uri (git-reference
3088 (url "https://github.com/beltoforion/muparser.git")
3089 (commit (string-append "v" upstream-version))))
3090 (file-name (git-file-name name version))
d7cff656 3091 (sha256
67f1db38 3092 (base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24"))))
d7cff656
LF		 3093 (build-system gnu-build-system)
3094 (arguments
3095 `(#:configure-flags '("--enable-samples=no")
3096 #:tests? #f)) ;no "check" target
3097 (home-page "http://muparser.beltoforion.de/")
3098 (synopsis "Fast parser library for mathematical expressions")
3099 (description
3100 "muParser is an extensible high performance math parser library. It is
3101based on transforming an expression into a bytecode and precalculating constant
3102parts of it.")
3103 (license license:expat))))
279663ef 3104
e73b49fb
RW		 3105(define-public openblas
3106 (package
3107 (name "openblas")
2ea09530 3108 (version "0.3.7")
e73b49fb
RW		 3109 (source
3110 (origin
3111 (method url-fetch)
a617fd55
MB		 3112 (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
3113 version "%20version.tar.gz"))
e73b49fb
RW		 3114 (file-name (string-append name "-" version ".tar.gz"))
3115 (sha256
3116 (base32
2ea09530 3117 "0jbdjsi0qsxahdcm42agnn1y7xpmg0hrhwjsxg0zbhs9wwy3p568"))))
e73b49fb
RW		 3118 (build-system gnu-build-system)
3119 (arguments
5789566a 3120 `(#:test-target "test"
bd0b4379
RW		 3121 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
3122 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
3123 ;; we need to disable substitutions.
71923a91
AE		 3124 #:substitutable?
3125 ,(let ((system (or (%current-target-system) (%current-system))))
3126 (or (string-prefix? "x86_64" system)
bd0b4379 3127 (string-prefix? "i686" system)
83a34647
EF		 3128 (string-prefix? "mips" system)
3129 (string-prefix? "aarch64" system)))
e73b49fb
RW		 3130 #:make-flags
3131 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
3132 "SHELL=bash"
5855756c 3133 "MAKE_NB_JOBS=0" ;use jobserver for submakes
a4384dc9
MB		 3134
3135 ;; This is the maximum number of threads OpenBLAS will ever use (that
3136 ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS
3137 ;; is used.) If we don't set it, the makefile sets it to the number
3138 ;; of cores of the build machine, which is obviously wrong.
3139 "NUM_THREADS=128"
3140
af5b817e
RW		 3141 ;; Build the library for all supported CPUs. This allows
3142 ;; switching CPU targets at runtime with the environment variable
3143 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
71923a91
AE		 3144 ;; Unfortunately, this is not supported on non-x86 architectures,
3145 ;; where it leads to failed builds.
3146 ,@(let ((system (or (%current-target-system) (%current-system))))
8a637e79
RW		 3147 (cond
3148 ((or (string-prefix? "x86_64" system)
71923a91 3149 (string-prefix? "i686" system))
8a637e79
RW		 3150 '("DYNAMIC_ARCH=1"))
3151 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
3152 ;; two available MIPS targets special extended instructions
3153 ;; for Loongson cores are used.
3154 ((string-prefix? "mips" system)
3155 '("TARGET=SICORTEX"))
83a34647
EF		 3156 ;; On aarch64 force the generic 'armv8-a' target
3157 ((string-prefix? "aarch64" system)
3158 '("TARGET=ARMV8"))
8a637e79 3159 (else '()))))
e73b49fb 3160 ;; no configure script
493937ae
DL		 3161 #:phases
3162 (modify-phases %standard-phases
3163 (delete 'configure)
3164 (add-before 'build 'set-extralib
3165 (lambda* (#:key inputs #:allow-other-keys)
3166 ;; Get libgfortran found when building in utest.
3167 (setenv "FEXTRALIB"
3168 (string-append "-L" (assoc-ref inputs "fortran-lib")
3169 "/lib"))
3170 #t)))))
e73b49fb 3171 (inputs
493937ae 3172 `(("fortran-lib" ,gfortran "lib")))
e73b49fb
RW		 3173 (native-inputs
3174 `(("cunit" ,cunit)
493937ae 3175 ("fortran" ,gfortran)
e73b49fb
RW		 3176 ("perl" ,perl)))
3177 (home-page "http://www.openblas.net/")
3178 (synopsis "Optimized BLAS library based on GotoBLAS")
3179 (description
3180 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
3181 (license license:bsd-3)))
3182
daa6036f 3183(define-public openblas-ilp64
ba05be22 3184 (package/inherit openblas
daa6036f
EB		 3185 (name "openblas-ilp64")
3186 (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
3187 (arguments
3188 (substitute-keyword-arguments (package-arguments openblas)
3189 ((#:make-flags flags '())
3190 `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
3191 ,flags))))
3192 (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
3193 (license license:bsd-3)))
3194
5a7deb11
LC		 3195(define* (make-blis implementation #:optional substitutable?)
3196 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
3197source tree for a list of implementations.)
3198
3199SUBSTITUTABLE? determines whether the package is made available as a
3200substitute.
3201
3202Currently the specialization must be selected at configure-time, but work is
3203underway to allow BLIS to select the right optimized kernels at run time:
3204<https://github.com/flame/blis/issues/129>."
3205 (package
3206 (name (if (string=? implementation "reference")
3207 "blis"
3208 (string-append "blis-" implementation)))
3209 (version "0.2.2")
3210 (home-page "https://github.com/flame/blis")
3211 (source (origin
3212 (method git-fetch)
3213 (uri (git-reference (url home-page) (commit version)))
3214 (sha256
3215 (base32
3216 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
3217 (file-name (git-file-name "blis" version))))
3218 (build-system gnu-build-system)
3219 (arguments
3220 `(#:test-target "test"
3221
3222 #:substitutable? ,substitutable?
3223
3224 #:phases (modify-phases %standard-phases
3225 (replace 'configure
3226 (lambda* (#:key outputs #:allow-other-keys)
3227 ;; This is a home-made 'configure' script.
3228 (let ((out (assoc-ref outputs "out")))
1ec17821
RW		 3229 (invoke "./configure" "-p" out
3230 "-d" "opt"
3231 "--disable-static"
3232 "--enable-shared"
3233 "--enable-threading=openmp"
5a7deb11 3234
1ec17821 3235 ,implementation))))
5a7deb11
LC		 3236 (add-before 'check 'show-test-output
3237 (lambda _
3238 ;; By default "make check" is silent. Make it verbose.
3239 (system "tail -F output.testsuite &")
3240 #t)))))
3241 (synopsis "High-performance basic linear algebra (BLAS) routines")
3242 (description
3243 "BLIS is a portable software framework for instantiating high-performance
3244BLAS-like dense linear algebra libraries. The framework was designed to
3245isolate essential kernels of computation that, when optimized, immediately
3246enable optimized implementations of most of its commonly used and
3247computationally intensive operations. While BLIS exports a new BLAS-like API,
3248it also includes a BLAS compatibility layer which gives application developers
3249access to BLIS implementations via traditional BLAS routine calls.")
3250 (license license:bsd-3)))
3251
3252(define-public blis
3253 ;; This is the "reference" implementation, which is the non-optimized but
3254 ;; portable variant (no assembly).
3255 (make-blis "reference" #t))
3256
3257(define ignorance blis)
3258
3259(define-syntax-rule (blis/x86_64 processor)
3260 "Expand to a package specialized for PROCESSOR."
3261 (package
3262 (inherit (make-blis processor))
3263 (supported-systems '("x86_64-linux"))))
3264
3265(define-public blis-sandybridge
3266 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
3267 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
3268 (blis/x86_64 "sandybridge"))
3269
3270(define-public blis-haswell
3271 ;; BLIS specialized for Haswell processors (launched 2013):
3272 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
3273 (blis/x86_64 "haswell"))
3274
3275(define-public blis-knl
3276 ;; BLIS specialized for Knights Landing processor (launched 2016):
3277 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
3278 (blis/x86_64 "knl"))
3279
3280
e1605e36
RW		 3281(define-public openlibm
3282 (package
3283 (name "openlibm")
48d7ac17 3284 (version "0.6.0")
e1605e36
RW		 3285 (source
3286 (origin
ca72dd2c
TGR		 3287 (method git-fetch)
3288 (uri (git-reference
3289 (url "https://github.com/JuliaLang/openlibm.git")
3290 (commit (string-append "v" version))))
3291 (file-name (git-file-name name version))
e1605e36 3292 (sha256
ca72dd2c 3293 (base32 "08wfchmmr5200fvmn1kwq9byc1fhsq46hn0y5k8scdl74771c7gh"))))
e1605e36
RW		 3294 (build-system gnu-build-system)
3295 (arguments
3296 `(#:make-flags
3297 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3298 #:phases
3299 ;; no configure script
dc1d3cde 3300 (modify-phases %standard-phases (delete 'configure))
e1605e36
RW		 3301 #:tests? #f)) ;the tests are part of the default target
3302 (home-page "http://openlibm.org/")
3303 (synopsis "Portable C mathematical library (libm)")
3304 (description
3305 "OpenLibm is an effort to have a high quality, portable, standalone C
3306mathematical library (libm). It can be used standalone in applications and
3307programming language implementations. The project was born out of a need to
e881752c 3308have a good libm for the Julia programming language that worked consistently
e1605e36
RW		 3309across compilers and operating systems, and in 32-bit and 64-bit
3310environments.")
538c0e3b
EF		 3311 ;; Each architecture has its own make target, and there is none for mips.
3312 (supported-systems (delete "mips64el-linux" %supported-systems))
e1605e36
RW		 3313 ;; See LICENSE.md for details.
3314 (license (list license:expat
3315 license:isc
3316 license:bsd-2
3317 license:public-domain
3318 license:lgpl2.1+))))
3319
e62be58f
RW		 3320(define-public openspecfun
3321 (package
3322 (name "openspecfun")
59cd0ba4 3323 (version "0.5.3")
e62be58f
RW		 3324 (source
3325 (origin
90cea671
TGR		 3326 (method git-fetch)
3327 (uri (git-reference
3328 (url "https://github.com/JuliaLang/openspecfun.git")
3329 (commit (string-append "v" version))))
3330 (file-name (git-file-name name version))
e62be58f 3331 (sha256
90cea671 3332 (base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh"))))
e62be58f
RW		 3333 (build-system gnu-build-system)
3334 (arguments
59cd0ba4 3335 '(#:tests? #f ; no "check" target
e62be58f
RW		 3336 #:make-flags
3337 (list (string-append "prefix=" (assoc-ref %outputs "out")))
59cd0ba4
TGR		 3338 #:phases
3339 (modify-phases %standard-phases
3340 (delete 'configure)))) ; no configure script
e62be58f 3341 (inputs
19afbea1 3342 `(("fortran" ,gfortran)))
e62be58f
RW		 3343 (home-page "https://github.com/JuliaLang/openspecfun")
3344 (synopsis "Collection of special mathematical functions")
3345 (description
3346 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
3347portable package for Bessel Functions of a Complex Argument and Nonnegative
3348Order; it contains subroutines for computing Bessel functions and Airy
3349functions. Faddeeva allows computing the various error functions of arbitrary
3350complex arguments (Faddeeva function, error function, complementary error
3351function, scaled complementary error function, imaginary error function, and
3352Dawson function); given these, one can also easily compute Voigt functions,
3353Fresnel integrals, and similar related functions as well.")
3354 ;; Faddeeva is released under the Expat license; AMOS is included as
3355 ;; public domain software.
3356 (license (list license:expat license:public-domain))))
3357
2742f87e
RW		 3358(define-public suitesparse
3359 (package
3360 (name "suitesparse")
bd5b5ac0 3361 (version "4.5.5")
2742f87e
RW		 3362 (source
3363 (origin
3364 (method url-fetch)
3365 (uri (string-append
3366 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
3367 version ".tar.gz"))
3368 (sha256
3369 (base32
bd5b5ac0
EB		 3370 "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
3371 (modules '((guix build utils)))
3372 (snippet
3373 ;; Remove bundled metis source
6cbee49d
MW		 3374 '(begin
3375 (delete-file-recursively "metis-5.1.0")
3376 #t))))
2742f87e
RW		 3377 (build-system gnu-build-system)
3378 (arguments
bd5b5ac0 3379 '(#:tests? #f ;no "check" target
2742f87e
RW		 3380 #:make-flags
3381 (list "CC=gcc"
3382 "BLAS=-lblas"
3383 "TBB=-ltbb"
bd5b5ac0 3384 "MY_METIS_LIB=-lmetis"
2742f87e
RW		 3385 (string-append "INSTALL_LIB="
3386 (assoc-ref %outputs "out") "/lib")
3387 (string-append "INSTALL_INCLUDE="
bd5b5ac0
EB		 3388 (assoc-ref %outputs "out") "/include")
3389 "library")
2742f87e 3390 #:phases
2509522c 3391 (modify-phases %standard-phases
bd5b5ac0 3392 (delete 'configure)))) ;no configure script
2742f87e
RW		 3393 (inputs
3394 `(("tbb" ,tbb)
bd5b5ac0
EB		 3395 ("lapack" ,lapack)
3396 ("metis" ,metis)))
2742f87e
RW		 3397 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
3398 (synopsis "Suite of sparse matrix software")
3399 (description
3400 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
3401multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
3402multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
3403simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
3404CXSparse, a concise sparse Cholesky factorization package; and many other
3405packages.")
3406 ;; LGPLv2.1+:
3407 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
3408 ;; GPLv2+:
3409 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
3410 (license (list license:gpl2+ license:lgpl2.1+))))
3411
ec322be2
FB		 3412(define-public atlas
3413 (package
3414 (name "atlas")
3c98ac02 3415 (version "3.10.3")
ec322be2
FB		 3416 (source (origin
3417 (method url-fetch)
de67e922
LF		 3418 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
3419 version "/atlas" version ".tar.bz2"))
ec322be2
FB		 3420 (sha256
3421 (base32
3c98ac02 3422 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
ec322be2
FB		 3423 (build-system gnu-build-system)
3424 (home-page "http://math-atlas.sourceforge.net/")
19afbea1 3425 (inputs `(("gfortran" ,gfortran)
ec322be2
FB		 3426 ("lapack-tar" ,(package-source lapack))))
3427 (outputs '("out" "doc"))
01480b9e
FB		 3428 ;; For the moment we drop support for MIPS at it fails to compile. See
3429 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
3430 (supported-systems (delete "mips64el-linux" %supported-systems))
ec322be2
FB		 3431 (arguments
3432 `(#:parallel-build? #f
3433 #:parallel-tests? #f
f15615b1
LC		 3434
3435 ;; ATLAS tunes itself for the machine it is built on, as explained at
3436 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
3437 ;; For this reason, we want users to build it locally instead of using
3438 ;; substitutes.
3439 #:substitutable? #f
3440
ec322be2 3441 #:modules ((srfi srfi-26)
ec322be2
FB		 3442 (guix build gnu-build-system)
3443 (guix build utils))
40029cbe 3444 #:configure-flags
ec322be2
FB		 3445 `(;; Generate position independent code suitable for dynamic libraries
3446 ;; and use WALL timer to get more accurate timing.
3447 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
3448 ;; Set word width.
3449 "-b"
3450 ,,(if (string-match "64" (%current-system))
3451 "64"
3452 "32")
3453 ;; Disable parallel build as it gives errors: atlas_pthread.h is
3454 ;; needed to compile C files before it is generated.
3455 "-Ss" "pmake" "make -j 1"
af89a667
FB		 3456 ;; Probe is failing for MIPS. We therefore define the system
3457 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3458 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3459 ,,@(if (string-prefix? "mips" (%current-system))
3460 (list "-A" "49" "-V" "1")
3461 (list))
ec322be2
FB		 3462 ;; Generate shared libraries.
3463 "--shared"
3464 ;; Build a full LAPACK library.
3465 ,(string-append "--with-netlib-lapack-tarfile="
3466 (assoc-ref %build-inputs "lapack-tar")))
3467 #:phases
e5b4b96b
EF		 3468 (modify-phases %standard-phases
3469 (add-after 'install 'install-doc
3470 (lambda* (#:key outputs inputs #:allow-other-keys)
3471 (let ((doc (string-append (assoc-ref outputs "doc")
3472 "/share/doc/atlas")))
3473 (mkdir-p doc)
cb6f44d4
RW		 3474 (for-each (cut install-file <> doc)
3475 (find-files "../ATLAS/doc" ".*"))
3476 #t)))
e5b4b96b 3477 (add-after 'check 'check-pt
cb6f44d4 3478 (lambda _ (invoke "make" "ptcheck")))
e5b4b96b
EF		 3479 ;; Fix files required to run configure.
3480 (add-before 'configure 'fix-/bin/sh
ec322be2
FB		 3481 (lambda _
3482 ;; Use `sh', not `/bin/sh'.
3483 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3484 (("/bin/sh")
5b786db8
EF		 3485 "sh"))
3486 #t))
e5b4b96b
EF		 3487 ;; Fix /bin/sh in generated make files.
3488 (add-after 'configure 'fix-/bin/sh-in-generated-files
3489 (lambda _
3490 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3491 (("/bin/sh")
5b786db8
EF		 3492 "sh"))
3493 #t))
e5b4b96b
EF		 3494 ;; ATLAS configure program does not accepts the default flags
3495 ;; passed by the 'gnu-build-system'.
3496 (replace 'configure
3497 (lambda* (#:key native-inputs inputs outputs
3498 (configure-flags '())
3499 #:allow-other-keys #:rest args)
3500 (let* ((prefix (assoc-ref outputs "out"))
3501 (bash (or (and=> (assoc-ref
3502 (or native-inputs inputs) "bash")
3503 (cut string-append <> "/bin/bash"))
3504 "/bin/sh"))
3505 (flags `(,(string-append "--prefix=" prefix)
3506 ,@configure-flags))
3507 (abs-srcdir (getcwd))
3508 (srcdir (string-append "../" (basename abs-srcdir))))
3509 (format #t "source directory: ~s (relative from build: ~s)~%"
3510 abs-srcdir srcdir)
3511 (mkdir "../build")
3512 (chdir "../build")
3513 (format #t "build directory: ~s~%" (getcwd))
3514 (format #t "configure flags: ~s~%" flags)
cb6f44d4
RW		 3515 (apply invoke bash
3516 (string-append srcdir "/configure")
3517 flags)))))))
ec322be2
FB		 3518 (synopsis "Automatically Tuned Linear Algebra Software")
3519 (description
3520 "ATLAS is an automatically tuned linear algebra software library
3521providing C and Fortran77 interfaces to a portably efficient BLAS
3522implementation, as well as a few routines from LAPACK.
3523
f15615b1
LC		 3524Optimization occurs at build time. For this reason, the library is built on
3525the machine where it is installed, without resorting to pre-built substitutes.
ec322be2 3526
f15615b1 3527Before building the library, CPU throttling should be disabled. This can be
d97c429a 3528done in the BIOS, or, on GNU/Linux, with the following command:
ec322be2 3529
8e9ba611 3530@example
d97c429a 3531# cpupower --governor performance
8e9ba611 3532@end example
ec322be2 3533
d97c429a 3534Failure to do so will result in a library with poor performance.")
ec322be2 3535 (license license:bsd-3)))
c12efc72
AE		 3536
3537(define-public glm
3538 (package
3539 (name "glm")
3f55b7be 3540 (version "0.9.9.6")
c12efc72
AE		 3541 (source
3542 (origin
3543 (method url-fetch)
5ea4b594
MB		 3544 (uri (string-append "https://github.com/g-truc/glm/releases/download/"
3545 version "/glm-" version ".zip"))
c12efc72 3546 (sha256
3f55b7be
TGR		 3547 (base32 "1l0pi1qi37mk6s0yrkrw07lspv4gcqnr9ryg3521hrl77ff37dwx"))
3548 (patches (search-patches "glm-restore-install-target.patch"))))
c12efc72
AE		 3549 (build-system cmake-build-system)
3550 (native-inputs
3551 `(("unzip" ,unzip)))
46bda5eb 3552 (home-page "https://glm.g-truc.net/")
c12efc72
AE		 3553 (synopsis "OpenGL Mathematics library")
3554 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3555library for graphics software based on the OpenGL Shading Language (GLSL)
3556specifications.")
3557 (license license:expat)))
7f18257b
AE		 3558
3559(define-public lpsolve
3560 (package
3561 (name "lpsolve")
a89e0cf5 3562 (version "5.5.2.5")
7f18257b
AE		 3563 (source
3564 (origin
3565 (method url-fetch)
3566 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3567 "/lp_solve_" version "_source.tar.gz"))
3568 (sha256
3569 (base32
a89e0cf5 3570 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
7f18257b
AE		 3571 (modules '((guix build utils)))
3572 (snippet
6cbee49d
MW		 3573 '(begin
3574 (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3575 (("^c=cc") "c=gcc")
3576 ;; Pretend to be on a 64 bit platform to obtain a common directory
3577 ;; name for the build results on all architectures; nothing else
3578 ;; seems to depend on it.
3579 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3580
3581 ;; The check for 'isnan' as it is written fails with
3582 ;; "non-floating-point argument in call to function
3583 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3584 ;; definition, which in turn leads to bad things. Fix the feature
3585 ;; test.
3586 (("isnan\\(0\\)") "isnan(0.)"))
3587 #t))))
7f18257b
AE		 3588 (build-system gnu-build-system)
3589 (arguments
6c96b545 3590 `(#:tests? #f ; no check target
7f18257b
AE		 3591 #:phases
3592 (modify-phases %standard-phases
6c96b545 3593 (delete 'configure) ; no configure script
7f18257b
AE		 3594 (replace 'build
3595 (lambda _
6c96b545
TGR		 3596 (with-directory-excursion "lpsolve55"
3597 (invoke "bash" "ccc"))
3598 (with-directory-excursion "lp_solve"
3599 (invoke "bash" "ccc"))
3600 #t))
7f18257b
AE		 3601 (replace 'install
3602 (lambda* (#:key outputs #:allow-other-keys)
3603 (let* ((out (assoc-ref outputs "out"))
3604 (bin (string-append out "/bin"))
3605 (lib (string-append out "/lib"))
3606 ;; This is where LibreOffice expects to find the header
3607 ;; files, and where they are installed by Debian.
3608 (include (string-append out "/include/lpsolve")))
6c96b545
TGR		 3609 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3610 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
96c46210
LC		 3611 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3612
7f18257b
AE		 3613 ;; Install a subset of the header files as on Debian
3614 ;; (plus lp_bit.h, which matches the regular expression).
96c46210
LC		 3615 (for-each (lambda (name)
3616 (install-file name include))
3617 (find-files "." "lp_[HMSa-z].*\\.h$"))
7f18257b 3618 (with-directory-excursion "shared"
96c46210
LC		 3619 (for-each (lambda (name)
3620 (install-file name include))
3621 (find-files "." "\\.h$")))
7f18257b
AE		 3622 #t))))))
3623 (home-page "http://lpsolve.sourceforge.net/")
3624 (synopsis "Mixed integer linear programming (MILP) solver")
3625 (description
3626 "lp_solve is a mixed integer linear programming solver based on the
3627revised simplex and the branch-and-bound methods.")
3628 (license license:lgpl2.1+)))
a17d4564
EB		 3629
3630(define-public dealii
3631 (package
3632 (name "dealii")
ba567cae 3633 (version "9.1.1")
a17d4564
EB		 3634 (source
3635 (origin
3636 (method url-fetch)
3637 (uri (string-append "https://github.com/dealii/dealii/releases/"
3638 "download/v" version "/dealii-" version ".tar.gz"))
3639 (sha256
3640 (base32
ba567cae 3641 "0xhjv0gzswpjbc43xbrpwfc5848g508l01855nszx3g5gwzlhnzw"))
a17d4564
EB		 3642 (modules '((guix build utils)))
3643 (snippet
3644 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
6cbee49d
MW		 3645 '(begin
3646 (delete-file-recursively "bundled")
3647 #t))))
a17d4564
EB		 3648 (build-system cmake-build-system)
3649 (inputs
3650 `(("tbb" ,tbb)
3651 ("zlib" ,zlib)
3652 ("boost" ,boost)
3653 ("p4est" ,p4est)
3654 ("blas" ,openblas)
3655 ("lapack" ,lapack)
3656 ("arpack" ,arpack-ng)
3657 ("muparser" ,muparser)
3658 ("gfortran" ,gfortran)
3659 ("suitesparse" ,suitesparse))) ;for UMFPACK
3660 (arguments
3661 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
d84b09e9
EB		 3662 #:configure-flags
3663 ;; Work around a bug in libsuitesparseconfig linking
3664 ;; see https://github.com/dealii/dealii/issues/4745
3665 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
a17d4564
EB		 3666 (home-page "https://www.dealii.org")
3667 (synopsis "Finite element library")
3668 (description
3669 "Deal.II is a C++ program library targeted at the computational solution
3670of partial differential equations using adaptive finite elements. The main
3671aim of deal.II is to enable rapid development of modern finite element codes,
3672using among other aspects adaptive meshes and a wide array of tools often used
3673in finite element programs.")
3674 (license license:lgpl2.1+)))
3675
3676(define-public dealii-openmpi
3677 (package (inherit dealii)
3678 (name "dealii-openmpi")
3679 (inputs
3680 `(("mpi" ,openmpi)
3681 ;;Supported only with MPI:
4d44bcad 3682 ("hdf5" ,hdf5-parallel-openmpi) ;TODO: have petsc-openmpi propagate?
a17d4564
EB		 3683 ("p4est" ,p4est-openmpi)
3684 ("petsc" ,petsc-openmpi)
3685 ("slepc" ,slepc-openmpi)
3686 ("metis" ,metis) ;for MUMPS
3687 ("scalapack" ,scalapack) ;for MUMPS
3688 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3689 ("arpack" ,arpack-ng-openmpi)
3690 ,@(fold alist-delete (package-inputs dealii)
3691 '("p4est" "arpack"))))
3692 (arguments
3693 (substitute-keyword-arguments (package-arguments dealii)
3694 ((#:configure-flags cf)
40b114c0
EB		 3695 `(cons "-DDEAL_II_WITH_MPI:BOOL=ON"
3696 ,cf))
7e309e8a
EB		 3697 ((#:phases phases '%standard-phases)
3698 `(modify-phases ,phases
3699 (add-before 'check 'mpi-setup
3700 ,%openmpi-setup)))))
a17d4564 3701 (synopsis "Finite element library (with MPI support)")))
194c7f95
AE		 3702
3703(define-public flann
3704 (package
3705 (name "flann")
3706 (version "1.8.4")
3707 (source
3708 (origin
3709 (method url-fetch)
3710 (uri
3711 (string-append
3712 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3713 version "-src.zip"))
3714 (sha256
3715 (base32
b5edc479
LC		 3716 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
3717 (patches (search-patches "flann-cmake-3.11.patch"))))
194c7f95 3718 (build-system cmake-build-system)
6b6aca9b
LC		 3719 (outputs '("out"
3720 "octave")) ;46 MiB .mex file that pulls Octave
194c7f95
AE		 3721 (native-inputs
3722 `(("unzip" ,unzip)))
3723 (inputs
3724 `(("hdf5" ,hdf5)
5537603f 3725 ("octave" ,octave-cli)
194c7f95
AE		 3726 ("python" ,python-2) ; print syntax
3727 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3728 ("zlib" ,zlib)))
3729 (arguments
39b30337
LC		 3730 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3731 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3732 #:strip-directories '("lib" "lib64" "libexec"
3733 "bin" "sbin" "share/flann/octave")
3734
9684e30b
LC		 3735 ;; Save 12 MiB by not installing .a files. Passing
3736 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3737 #:phases (modify-phases %standard-phases
6b6aca9b
LC		 3738 (add-before 'configure 'set-octave-directory
3739 (lambda* (#:key outputs #:allow-other-keys)
3740 ;; Install the .mex file in the "octave" output.
3741 (let ((out (assoc-ref outputs "octave")))
3742 (substitute* "src/matlab/CMakeLists.txt"
3743 (("share/flann/octave")
3744 (string-append out "/share/flann/octave")))
3745 #t)))
9684e30b
LC		 3746 (add-after 'install 'remove-static-libraries
3747 (lambda* (#:key outputs #:allow-other-keys)
3748 (let* ((out (assoc-ref outputs "out"))
3749 (lib (string-append out "/lib")))
3750 (for-each delete-file
3751 (find-files lib "\\.a$"))
3752 #t))))
3753
39b30337 3754 #:tests? #f)) ; The test data are downloaded from the Internet.
194c7f95
AE		 3755 (home-page "http://www.cs.ubc.ca/research/flann/")
3756 (synopsis "Library for approximate nearest neighbors computation")
3757 (description "FLANN is a library for performing fast approximate
3758nearest neighbor searches in high dimensional spaces. It implements a
3759collection of algorithms and a system for automatically choosing the best
3760algorithm and optimum parameters depending on the dataset.
3761
3762FLANN is written in C++ and contains bindings for C, Octave and Python.")
3763 (license (license:non-copyleft "file://COPYING"
3764 "See COPYING in the distribution."))))
d8c97beb
EF		 3765
3766(define-public wcalc
3767 (package
3768 (name "wcalc")
3769 (version "2.5")
3770 (source
3771 (origin
3772 (method url-fetch)
de67e922
LF		 3773 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3774 "wcalc-" version ".tar.bz2"))
d8c97beb
EF		 3775 (sha256
3776 (base32
3777 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3778 (build-system gnu-build-system)
3779 (inputs
3780 `(("mpfr" ,mpfr)
3781 ("readline" ,readline)))
3782 (home-page "http://w-calc.sourceforge.net/index.php")
3783 (synopsis "Flexible command-line scientific calculator")
3784 (description "Wcalc is a very capable calculator. It has standard functions
3785(sin, asin, and sinh for example, in either radians or degrees), many
3786pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3787variables, a command history, hex/octal/binary input and output, unit
3788conversions, embedded comments, and an expandable expression entry field. It
3789evaluates expressions using the standard order of operations.")
3790 (license license:gpl2+)))
45147b0c
FH		 3791
3792(define-public xaos
3793 (package
3794 (name "xaos")
3795 (version "3.6")
3796 (source (origin
3797 (method url-fetch)
de67e922
LF		 3798 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3799 "/xaos-" version ".tar.gz"))
45147b0c
FH		 3800 (sha256
3801 (base32
3802 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3803 (build-system gnu-build-system)
b94a6ca0 3804 (native-inputs `(("gettext" ,gettext-minimal)))
45147b0c
FH		 3805 (inputs `(("libx11" ,libx11)
3806 ("zlib" ,zlib)
3807 ("libpng" ,libpng)
3808 ("gsl" ,gsl)))
3809 (arguments
3810 `(#:tests? #f ;no "check" target
3811 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3812 (synopsis "Real-time fractal zoomer")
3813 (description "GNU XaoS is a graphical program that generates fractal
3814patterns and allows you to zoom in and out of them infinitely in a fluid,
3815continuous manner. It also includes tutorials that help to explain how fractals
3816are built. It can generate many different fractal types such as the Mandelbrot
3817set.")
6fd52309 3818 (home-page "https://www.gnu.org/software/xaos/")
45147b0c 3819 (license license:gpl2+)))
528bb464
EB		 3820
3821(define-public hypre
3822 (package
3823 (name "hypre")
be099727 3824 (version "2.15.1")
fabcbf32
TGR		 3825 (source
3826 (origin
3827 (method git-fetch)
3828 (uri (git-reference
3829 (url "https://github.com/LLNL/hypre.git")
3830 (commit (string-append "v" version))))
3831 (file-name (git-file-name name version))
3832 (sha256
be099727 3833 (base32 "1lvh4ybqkriyqfg2zmic6mrg1981qv1i9vry1fdgsabn81hb71g4"))
fabcbf32
TGR		 3834 (modules '((guix build utils)))
3835 (snippet
3836 '(begin
3837 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
be099727 3838 ;; substitute the release date.
fabcbf32
TGR		 3839 (substitute* "src/utilities/HYPRE_utilities.h"
3840 (("Date Compiled: .*$")
be099727 3841 "Date Compiled: Oct 19 2018 15:23:00 +0000\"\n"))
fabcbf32 3842 #t))))
528bb464 3843 (build-system gnu-build-system)
be099727
TGR		 3844 (outputs '("out" ; 6.1 MiB of headers and libraries
3845 "doc")) ; 4.8 MiB of documentation
528bb464
EB		 3846 (native-inputs
3847 `(("doc++" ,doc++)
3848 ("netpbm" ,netpbm)
be099727 3849 ("perl" ,perl) ; needed to run 'ppmquant' during tests
8b35c8cd
RW		 3850 ("texlive" ,(texlive-union (list texlive-xypic
3851 texlive-cm
9b405aea 3852 texlive-latex-hyperref
9b405aea 3853 texlive-bibtex)))
528bb464
EB		 3854 ("ghostscript" ,ghostscript)))
3855 (inputs
3856 `(("blas" ,openblas)
3857 ("lapack" ,lapack)))
3858 (arguments
3859 `(#:modules ((srfi srfi-1)
3860 ,@%gnu-build-system-modules)
3861 #:configure-flags '("--enable-shared"
3862 "--disable-fortran"
3863 "--without-MPI"
3864 "--with-openmp"
3865 "--with-fei"
3866 "--with-lapack"
3867 "--with-blas")
3868 #:phases
3869 (modify-phases %standard-phases
9b405aea
PN		 3870 (add-before 'build 'set-HOME
3871 (lambda _
3872 ;; FIXME: texlive-union does not find the built
3873 ;; metafonts, so it tries to generate them in HOME.
3874 (setenv "HOME" "/tmp")
3875 #t))
528bb464
EB		 3876 (add-before 'configure 'chdir-src
3877 (lambda _ (chdir "src")))
3878 (replace 'configure
3879 (lambda* (#:key build target configure-flags
3880 #:allow-other-keys #:rest args)
3881 (let* ((configure (assoc-ref %standard-phases 'configure)))
3882 (apply configure
3883 (append args
3884 (list #:configure-flags
3885 (cons (string-append
3886 "--host=" (or target build))
3887 configure-flags)))))))
3888 (add-after 'build 'build-docs
3889 (lambda _
9b405aea 3890 (invoke "make" "-Cdocs" "pdf" "html")))
528bb464
EB		 3891 (replace 'check
3892 (lambda _
3893 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3894 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
6b1c7ac8
RW		 3895 (invoke "make" "check" "CHECKRUN=")
3896 (for-each (lambda (filename)
3897 (let ((size (stat:size (stat filename))))
3898 (when (positive? size)
3899 (error (format #f "~a size ~d; error indication~%"
3900 filename size)))))
3901 (find-files "test" ".*\\.err$"))
3902 #t))
528bb464
EB		 3903 (add-after 'install 'install-docs
3904 (lambda* (#:key outputs #:allow-other-keys)
3905 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3906 (let* ((doc (assoc-ref outputs "doc"))
3907 (docdir (string-append doc "/share/doc/hypre-" ,version)))
528bb464
EB		 3908 (with-directory-excursion "docs"
3909 (for-each (lambda (base)
3910 (install-file (string-append base ".pdf") docdir)
be099727 3911 (copy-recursively base docdir)) ; html docs
528bb464
EB		 3912 '("HYPRE_usr_manual"
3913 "HYPRE_ref_manual")))
3914 #t))))))
3915 (home-page "http://www.llnl.gov/casc/hypre/")
3916 (synopsis "Library of solvers and preconditioners for linear equations")
3917 (description
3918 "HYPRE is a software library of high performance preconditioners and
3919solvers for the solution of large, sparse linear systems of equations. It
3920features multigrid solvers for both structured and unstructured grid
3921problems.")
3922 (license license:lgpl2.1)))
3923
3924(define-public hypre-openmpi
3925 (package (inherit hypre)
3926 (name "hypre-openmpi")
3927 (inputs
3928 `(("mpi" ,openmpi)
3929 ,@(package-inputs hypre)))
3930 (arguments
3931 (substitute-keyword-arguments (package-arguments hypre)
3932 ((#:configure-flags flags)
3933 ``("--with-MPI"
6df2a50a
LC		 3934 ,@(delete "--without-MPI" ,flags)))
3935 ((#:phases phases)
3936 `(modify-phases ,phases
bbe46a4a
EB		 3937 (add-before 'check 'mpi-setup
3938 ,%openmpi-setup)))))
528bb464
EB		 3939 (synopsis "Parallel solvers and preconditioners for linear equations")
3940 (description
3941 "HYPRE is a software library of high performance preconditioners and
3942solvers for the solution of large, sparse linear systems of equations on
3943parallel computers. It features parallel multigrid solvers for both
3944structured and unstructured grid problems.")))
6c90e183
EB		 3945
3946(define-public matio
3947 (package
3948 (name "matio")
3949 (version "1.5.6")
3950 (source
3951 (origin
3952 (method url-fetch)
de67e922 3953 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
6c90e183
EB		 3954 "matio-" version ".tar.gz"))
3955 (sha256
3956 (base32
3957 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3958 (build-system gnu-build-system)
3959 (inputs
3960 `(("zlib" ,zlib)
3961 ("hdf5" ,hdf5)))
3962 (home-page "http://matio.sourceforge.net/")
3963 (synopsis "Library for reading and writing MAT files")
3964 (description "Matio is a library for reading and writing MAT files. It
3965supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3966 (license license:bsd-2)))
d721c83a 3967
517318ad
LF		 3968(define-public vc
3969 (package
3970 (name "vc")
9d731fb6 3971 (version "1.4.1")
517318ad
LF		 3972 (source
3973 (origin (method url-fetch)
3974 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3975 "download/" version "/Vc-" version ".tar.gz"))
3976 (sha256
3977 (base32
9d731fb6 3978 "17qili8bf8r78cng65yf4qmgna8kiqjqbgcqbric6v9j6nkhkrk8"))))
517318ad
LF		 3979 (build-system cmake-build-system)
3980 (arguments
3981 '(#:configure-flags
33d82486
MB		 3982 '("-DBUILD_TESTING=ON"
3983 ;; By default, Vc will optimize for the CPU of the build machine.
3984 ;; Setting this to "none" makes it create portable binaries. See
3985 ;; "cmake/OptimizeForArchitecture.cmake".
9d731fb6
MB		 3986 "-DTARGET_ARCHITECTURE=none")
3987 #:phases (modify-phases %standard-phases
3988 (add-after 'unpack 'copy-testdata
3989 (lambda* (#:key inputs native-inputs #:allow-other-keys)
3990 (let ((testdata (assoc-ref (or native-inputs inputs)
3991 "testdata")))
3992 (copy-recursively testdata "tests/testdata")
3993 #t))))))
3994 (native-inputs
3995 `(("virtest" ,virtest)
3996
3997 ;; This is a submodule in the git project, but not part of the
3998 ;; released sources. See the git branch for the commit to take.
3999 ("testdata" ,(let ((commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3"))
4000 (origin
4001 (method git-fetch)
4002 (uri (git-reference
4003 (url "https://github.com/VcDevel/vc-testdata")
4004 (commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3")))
4005 (file-name (git-file-name "vc-testdata"
4006 (string-take commit 7)))
4007 (sha256
4008 (base32
4009 "1hkhqib03qlcq412ym2dciynfxcdr2ygqhnplz4l1vissr1wnqn2")))))))
517318ad
LF		 4010 (synopsis "SIMD vector classes for C++")
4011 (description "Vc provides portable, zero-overhead C++ types for explicitly
4012data-parallel programming. It is a library designed to ease explicit
4013vectorization of C++ code. Its types enable explicitly stating data-parallel
4014operations on multiple values. The parallelism is therefore added via the type
4015system. Vc has an intuitive API and provides portability between different
4016compilers and compiler versions as well as portability between different vector
4017instruction sets. Thus, an application written with Vc can be compiled for:
4018@enumerate
4019@item AVX and AVX2
d1e4ad1b 4020@item SSE2 up to SSE4.2 or SSE4a
517318ad
LF		 4021@item Scalar
4022@item MIC
4023@item NEON (in development)
4024@item NVIDIA GPUs / CUDA (in development)
4025@end enumerate\n")
4026 (home-page "https://github.com/VcDevel/Vc")
a8ead6f9
EF		 4027 ;; "No support_???.cpp file exists for this architecture."
4028 (supported-systems '("x86_64-linux" "i686-linux"))
517318ad 4029 (license license:bsd-3)))
54052a54 4030
4031(define-public reducelcs
4032 ;; This is the last commit which is available upstream, no
4033 ;; release happened since 2010.
4034 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
4035 (revision "1"))
4036 (package
4037 (name "reducelcs")
4038 (version (string-append "1.0-" revision "." (string-take commit 7)))
4039 (source
4040 (origin
4041 (method git-fetch)
4042 (uri (git-reference
4043 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
4044 (commit commit)))
4045 (file-name (string-append name "-" version "-checkout"))
4046 (sha256
4047 (base32
4048 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
4049 (build-system gnu-build-system)
4050 (inputs
4051 `(("openlibm" ,openlibm)))
4052 (arguments
4053 `(#:tests? #f ; no tests
4054 #:phases
4055 (modify-phases %standard-phases
4056 (delete 'configure) ; No configure script exists.
4057 (replace 'install ; No install phase exists.
4058 (lambda* (#:key outputs #:allow-other-keys)
4059 (let* ((out (assoc-ref outputs "out"))
4060 (bin (string-append out "/bin")))
4061 (install-file "Approximation" bin)
4062 (install-file "CollectResults" bin)
4063 (install-file "GenerateInstances" bin)
4064 #t))))))
4065 (synopsis "Approximate Longest Commons Subsequence computation tool")
4066 (description
4067 "@code{reduceLCS} is an implementation of the Reduce-Expand
4068algorithm for LCS. It is a fast program to compute the approximate
4069Longest Commons Subsequence of a set of strings.")
4070 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
c000b6b1 4071 (license license:gpl3+))))
479c4273
JD		 4072
4073(define-public jacal
4074 (package
4075 (name "jacal")
4076 (version "1c4")
4077 (source (origin
4078 (method url-fetch)
4079 (uri (string-append
4080 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
4081 version ".zip"))
4082 (sha256 (base32
4083 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
4084 (patches (search-patches "jacal-fix-texinfo.patch"))))
4085 (build-system gnu-build-system)
4086 (arguments
4087 `(#:phases
4088 (modify-phases %standard-phases
4089 (add-before 'build 'pre-build
4090 ;; Don't use upstream's script - it really doesn't fit into
4091 ;; Guix's functional paradigm.
4092 (lambda* (#:key inputs outputs #:allow-other-keys)
4093 (substitute* "Makefile"
4094 (("^install: install-script") "install: "))))
4095 (add-after 'install 'post-install
4096 ;; Instead, we provide our own simplified script.
4097 (lambda* (#:key inputs outputs #:allow-other-keys)
4098 (let ((wrapper (string-append (assoc-ref outputs "out")
4099 "/bin/jacal")))
4100 (format (open wrapper (logior O_WRONLY O_CREAT))
4101 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
4102 "-e '(slib:load \"~a/lib/jacal/math\") "
4103 "(math)' \"$@\"\n")
4104 (which "bash")
4105 (assoc-ref inputs "scm")
4106 (assoc-ref outputs "out"))
4107 (chmod wrapper #o555))))
4108 (replace 'configure
9cd82b1c
RW		 4109 (lambda* (#:key outputs #:allow-other-keys)
4110 (invoke "./configure"
4111 (string-append "--prefix="
4112 (assoc-ref outputs "out"))))))))
479c4273
JD		 4113 (inputs `(("scm" ,scm)))
4114 (native-inputs `(("unzip" ,unzip)
4115 ("texinfo" ,texinfo)))
4116 (synopsis "Symbolic mathematics system")
4117 (description "GNU JACAL is an interactive symbolic mathematics program based on
4118Scheme. It manipulate and simplify a range of mathematical expressions such
4119as equations, scalars, vectors, and matrices.")
6fd52309 4120 (home-page "https://www.gnu.org/software/jacal/")
479c4273
JD		 4121 (license license:gpl3+)))
4122
313844d9
TF		 4123(define-public z3
4124 (package
4125 (name "z3")
dbef037f 4126 (version "4.8.7")
fb525bfd 4127 (home-page "https://github.com/Z3Prover/z3")
313844d9 4128 (source (origin
fb525bfd
MB		 4129 (method git-fetch)
4130 (uri (git-reference (url home-page)
4131 (commit (string-append "z3-" version))))
2d7b99b3 4132 (file-name (git-file-name name version))
313844d9
TF		 4133 (sha256
4134 (base32
dbef037f 4135 "0hprcdwhhyjigmhhk6514m71bnmvqci9r8gglrqilgx424r6ff7q"))))
fa574a6d 4136 (build-system gnu-build-system)
313844d9 4137 (arguments
fa574a6d 4138 `(#:phases
313844d9 4139 (modify-phases %standard-phases
ad6c6a5b
EF		 4140 (add-after 'unpack 'fix-compatability
4141 ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
4142 (lambda _
4143 (substitute* "src/util/mpz.cpp"
4144 (("#include <immintrin.h>") ""))
4145 #t))
cf684d87
TF		 4146 (add-before 'configure 'bootstrap
4147 (lambda _
32d5360f 4148 (invoke "python" "scripts/mk_make.py")))
fa574a6d
AB		 4149 ;; work around gnu-build-system's setting --enable-fast-install
4150 ;; (z3's `configure' is a wrapper around the above python file,
4151 ;; which fails when passed --enable-fast-install)
4152 (replace 'configure
4153 (lambda* (#:key inputs outputs #:allow-other-keys)
4154 (invoke "./configure"
4155 (string-append "--prefix=" (assoc-ref outputs "out")))))
4156 (add-after 'configure 'change-directory
4157 (lambda _
4158 (chdir "build")
4159 #t))
cf684d87 4160 (add-before 'check 'make-test-z3
313844d9 4161 (lambda _
cf684d87 4162 ;; Build the test suite executable.
32d5360f
RW		 4163 (invoke "make" "test-z3" "-j"
4164 (number->string (parallel-job-count)))))
cf684d87
TF		 4165 (replace 'check
4166 (lambda _
4167 ;; Run all the tests that don't require arguments.
32d5360f 4168 (invoke "./test-z3" "/a"))))))
313844d9 4169 (native-inputs
fa574a6d
AB		 4170 `(("which" ,which)
4171 ("python" ,python-wrapper)))
313844d9
TF		 4172 (synopsis "Theorem prover")
4173 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
cf684d87 4174theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
313844d9 4175 (license license:expat)))
3d5d87a3 4176
6d433d6e
EB		 4177(define-public elpa
4178 (package
4179 (name "elpa")
4180 (version "2018.11.001")
4181 (source (origin
4182 (method url-fetch)
4183 (uri (string-append "http://elpa.mpcdf.mpg.de/html/Releases/"
4184 version "/elpa-" version ".tar.gz"))
4185 (sha256
4186 (base32
4187 "05hv3v5i6xmziaizw350ff72y1c3k662r85fm3xfdrkclj5zw9yc"))))
4188 (build-system gnu-build-system)
4189 (native-inputs
4190 `(("fortran" ,gfortran)
4191 ("perl" ,perl))) ;for configure and deps
4192 (inputs
4193 `(("blas" ,openblas)))
4194 (arguments
4195 `(#:configure-flags
4196 `("--enable-openmp"
4197 "--with-mpi=no"
4198 ;; ELPA unfortunately does not support runtime dispatch, so we can
4199 ;; only enable the "generic" kernels. See the "Cross compilation"
4200 ;; section of INSTALL.md.
4201 "--enable-generic"
4202 "--disable-sse" "--disable-sse-assembly" ;Require SSE3
4203 "--disable-avx" "--disable-avx2" "--disable-avx512"
4204 ,(string-append "CFLAGS=-O3 "
4205 "-funsafe-loop-optimizations -funsafe-math-optimizations "
4206 "-ftree-vect-loop-version -ftree-vectorize "
4207 ,(let ((system (or (%current-target-system)
4208 (%current-system))))
4209 (cond
4210 ((or (string-prefix? "x86_64" system)
4211 (string-prefix? "i686" system))
4212 "-msse2")
4213 (else "")))))
4214 #:parallel-tests? #f ;tests are multi-threaded, via BLAS
4215 #:phases
4216 (modify-phases %standard-phases
4217 (add-before 'configure 'patch-header-generation
4218 (lambda _
4219 (substitute* "configure"
4220 (("^ *make.*top_srcdir=\"\\$srcdir\"" &)
4221 (string-append & " CPP=\"$CPP\"")))
4222 #t))
4223 (add-before 'check 'setup-tests
4224 (lambda _
4225 ;; Decrease test time and RAM use by computing fewer eigenvalues.
4226 ;; The flags are (MATRIX-SIZE, EIGENVALUES, BLOCK-SIZE), where
4227 ;; the default is (500, 250, 16) for C tests and (5000, 150, 16)
4228 ;; for Fortran. This also causes several tests to pass that
4229 ;; otherwise would otherwise fail with matrix size 5000; possibly
4230 ;; due to floating point tolerances that are too tight.
4231 (setenv "TEST_FLAGS" "1500 50 16") ;from elpa.spec
4232 (setenv "OMP_NUM_THREADS" (number->string (parallel-job-count)))
4233 (substitute* "Makefile"
4234 ;; Test scripts are generated, patch the shebang
4235 (("#!/bin/bash") (string-append "#!" (which "sh"))))
4236 #t)))))
4237 (home-page "http://elpa.mpcdf.mpg.de")
4238 (synopsis "Eigenvalue solvers for symmetric matrices")
4239 (description
4240 "The ELPA library provides efficient and scalable direct eigensolvers for
4241symmetric matrices.")
4242 (license license:lgpl3)))
4243
4244(define-public elpa-openmpi
4245 (package (inherit elpa)
4246 (name "elpa-openmpi")
4247 (inputs
4248 `(("mpi" ,openmpi)
4249 ("scalapack" ,scalapack)
4250 ,@(package-inputs elpa)))
4251 (arguments
4252 (substitute-keyword-arguments (package-arguments elpa)
4253 ((#:configure-flags cf '())
4254 `(cons "--with-mpi=yes" (delete "--with-mpi=no" ,cf)))
4255 ((#:phases phases '%standard-phases)
4256 `(modify-phases ,phases
4257 (add-before 'check 'mpi-setup
4258 (lambda _
4259 ;; Tests use 2 mpi tasks by default, use our remaining build
4260 ;; cores as OpenMP threads.
4261 (setenv "OMP_NUM_THREADS" (number->string
4262 (max (quotient (parallel-job-count) 2)
4263 1)))
4264 (,%openmpi-setup)))))))
4265 (synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)")))
4266
e01397b4
EB		 4267(define-public elemental
4268 (package
4269 (name "elemental")
4270 (version "0.87.7")
4271 (source (origin
5c0b6d1b
EF		 4272 (method git-fetch)
4273 (uri (git-reference
4274 (url "https://github.com/elemental/Elemental.git")
4275 (commit (string-append "v" version))))
4276 (file-name (git-file-name name version))
e01397b4
EB		 4277 (sha256
4278 (base32
5c0b6d1b 4279 "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
e01397b4
EB		 4280 (build-system cmake-build-system)
4281 (home-page "http://libelemental.org")
4282 (native-inputs
4283 `(("gfortran" ,gfortran)))
4284 (inputs
4285 `(("blas" ,openblas)
4286 ("gfortran:lib" ,gfortran "lib")
4287 ("gmp" ,gmp)
4288 ("lapack" ,lapack)
4289 ("metis" ,metis)
4290 ("mpc" ,mpc)
4291 ("mpfr" ,mpfr)
4292 ("mpi" ,openmpi)
4293 ("qd" ,qd)))
4294 (arguments
4295 `(#:build-type "Release" ;default RelWithDebInfo not supported
4296 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
4297 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
4298 "-DEL_CACHE_WARNINGS:BOOL=YES"
4299 "-DEL_TESTS:BOOL=YES"
4300 "-DCMAKE_INSTALL_LIBDIR=lib"
4301 "-DGFORTRAN_LIB=gfortran")
4302 #:phases (modify-phases %standard-phases
3b42e2be
EF		 4303 (add-before 'check 'mpi-setup
4304 ,%openmpi-setup)
e01397b4
EB		 4305 (add-before 'check 'setup-tests
4306 (lambda _
4307 ;; Parallelism is done at the MPI layer.
4308 (setenv "OMP_NUM_THREADS" "1")
4309 #t))
4310 (add-after 'install 'remove-tests
4311 (lambda* (#:key outputs #:allow-other-keys)
4312 ;; Tests are installed, with no easy configuration
4313 ;; switch to prevent this, so delete them.
4314 (delete-file-recursively
3b42e2be 4315 (string-append (assoc-ref outputs "out") "/bin"))
e01397b4
EB		 4316 #t)))))
4317 (synopsis "Dense and sparse-direct linear algebra and optimization")
4318 (description "Elemental is a modern C++ library for distributed-memory
4319dense and sparse-direct linear algebra, conic optimization, and lattice
4320reduction.")
4321 (license license:bsd-2)))
5b05dce7
JN		 4322
4323(define-public mcrl2
4324 (package
4325 (name "mcrl2")
3bc74090 4326 (version "201908.0")
5b05dce7
JN		 4327 (source (origin
4328 (method url-fetch)
185152e3
JN		 4329 (uri (string-append
4330 "https://www.mcrl2.org/download/release/mcrl2-"
4331 version ".tar.gz"))
5b05dce7
JN		 4332 (sha256
4333 (base32
3bc74090 4334 "1i4xgl2d5fgiz1mwi50cyfkrrcpm8nxfayfjgmhq7chs58wlhfsz"))))
5b05dce7
JN		 4335 (inputs
4336 `(("boost" ,boost)
4337 ("glu" ,glu)
4338 ("mesa" ,mesa)
077d66ed 4339 ("qtbase" ,qtbase)))
5b05dce7 4340 (build-system cmake-build-system)
ed0c5d3c 4341 (synopsis "Toolset for the mCRL2 formal specification language")
5b05dce7 4342 (description
ed0c5d3c
TGR		 4343 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
4344specification language for describing concurrent discrete event systems. Its
4345toolset supports analysis and automatic verification, linearisation, simulation,
4346state-space exploration and generation, and tools to optimise and analyse
5b05dce7
JN		 4347specifications. Also, state spaces can be manipulated, visualised and
4348analysed.")
b3882709 4349 (home-page "https://mcrl2.org")
5b05dce7 4350 (license license:boost1.0)))
41835f94 4351
e03b9126
JN		 4352(define-public mcrl2-minimal
4353 (package
4354 (inherit mcrl2)
4355 (name "mcrl2-minimal")
4356 (inputs
4357 `(("boost" ,boost)))
4358 (arguments
4359 '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
4360
910deec6
NV		 4361(define-public tcalc
4362 (package
4363 (name "tcalc")
4364 (version "2.0")
4365 (source
4366 (origin
4367 (method url-fetch)
4368 (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
4369 version ".tar.gz"))
4370 (sha256
4371 (base32
4372 "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
4373 (build-system gnu-build-system)
4374 (synopsis "The terminal calculator")
4375 (description
4376 "The terminal calculator is a small program to help users of the GNU/Linux
4377terminal do calculations simply and quickly. The formula to be calculated can
4378be fed to @command{tcalc} through the command line.")
4379 (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
4380 (license license:gpl3+)))
b26e4f26
EB		 4381
4382(define-public sundials
4383 (package
4384 (name "sundials")
4385 (version "3.1.1")
4386 (source
4387 (origin
4388 (method url-fetch)
4389 (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
4390 "sundials-" version ".tar.gz"))
4391 (sha256
4392 (base32
4393 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
4394 (build-system cmake-build-system)
4395 (native-inputs
4396 `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
4397 (inputs
4398 `(("fortran" ,gfortran) ;for fcmix
4399 ("blas" ,openblas)
4400 ("suitesparse" ,suitesparse))) ;TODO: Add hypre
4401 (arguments
4402 `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
4403 "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
4404 "-DEXAMPLES_ENABLE_F77:BOOL=ON"
4405 "-DEXAMPLES_ENABLE_F90:BOOL=ON"
4406 "-DEXAMPLES_INSTALL:BOOL=OFF"
4407
4408 "-DFCMIX_ENABLE:BOOL=ON"
4409
4410 "-DKLU_ENABLE:BOOL=ON"
4411 ,(string-append "-DKLU_INCLUDE_DIR="
4412 (assoc-ref %build-inputs "suitesparse")
4413 "/include")
4414 ,(string-append "-DKLU_LIBRARY_DIR="
4415 (assoc-ref %build-inputs "suitesparse")
4416 "/lib"))))
4417 (home-page "https://computation.llnl.gov/projects/sundials")
4418 (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
4419 (description "SUNDIALS is a family of software packages implemented with
4420the goal of providing robust time integrators and nonlinear solvers that can
4421easily be incorporated into existing simulation codes.")
4422 (license license:bsd-3)))
4423
4424(define-public sundials-openmpi
4425 (package (inherit sundials)
4426 (name "sundials-openmpi")
4427 (inputs
4428 `(("mpi" ,openmpi)
4429 ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
4430 ,@(package-inputs sundials)))
4431 (arguments
4432 (substitute-keyword-arguments (package-arguments sundials)
4433 ((#:configure-flags flags '())
4434 `(cons* "-DMPI_ENABLE:BOOL=ON"
4435 "-DPETSC_ENABLE:BOOL=ON"
4436 (string-append "-DPETSC_INCLUDE_DIR="
4437 (assoc-ref %build-inputs "petsc")
4438 "/include")
4439 (string-append "-DPETSC_LIBRARY_DIR="
4440 (assoc-ref %build-inputs "petsc")
4441 "/lib")
4442 ,flags))
4443 ((#:phases phases '%standard-phases)
4444 `(modify-phases ,phases
bbe46a4a
EB		 4445 (add-before 'check 'mpi-setup
4446 ,%openmpi-setup)))))
b26e4f26 4447 (synopsis "SUNDIALS with OpenMPI support")))
a6b9ebc2
EB		 4448
4449(define-public combinatorial-blas
4450 (package
4451 (name "combinatorial-blas")
4452 (version "1.6.2")
4453 (source
4454 (origin
4455 (method url-fetch)
4456 (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/"
4457 "CombBLAS_beta_"
4458 (match (string-split version #\.)
4459 ((major minor patch)
4460 (string-append major minor "_" patch))) ;e.g. "16_2"
4461 ".tgz"))
4462 (sha256
4463 (base32
4464 "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a"))
4465 (patches (search-patches "combinatorial-blas-awpm.patch"
4466 "combinatorial-blas-io-fix.patch"))))
4467 (build-system cmake-build-system)
4468 (inputs
4469 `(("mpi" ,openmpi)
4470 ("test-data" ,(origin
4471 (method url-fetch)
4472 (uri (string-append "https://people.eecs.berkeley.edu/~aydin/"
4473 "CombBLAS_FILES/testdata_combblas1.6.1.tgz"))
4474 (sha256
4475 (base32
4476 "01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87"))))))
4477 (arguments
4478 `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
4479 "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL")
4480 #:parallel-tests? #f ;tests use 'mpiexec -n4'
4481 #:phases
4482 (modify-phases %standard-phases
4483 (add-before 'check 'mpi-setup
4484 ,%openmpi-setup)
4485 (add-before 'check 'test-setup
4486 (lambda* (#:key inputs #:allow-other-keys)
4487 (setenv "OMP_NUM_THREADS" "2")
4488 (invoke "tar" "xf" (assoc-ref inputs "test-data")))))))
4489 (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/")
4490 (synopsis "Linear algebra primitives for graph analytics")
4491 (description "The Combinatorial BLAS (CombBLAS) is an extensible
4492distributed-memory parallel graph library offering a small but powerful set of
4493linear algebra primitives specifically targeting graph analytics.")
4494 (license (list
4495 license:gpl2+ ;include/psort/(funnel|sort)*.h
4496 license:x11 ;usort and psort
4497 license:bsd-3)))) ;CombBLAS and MersenneTwister.h
3847d1f2
RW		 4498
4499(define-public dune-common
4500 (package
4501 (name "dune-common")
4502 (version "2.6.0")
4503 (source
4504 (origin
4505 (method url-fetch)
4506 (uri (string-append "https://dune-project.org/download/"
4507 version "/dune-common-" version ".tar.gz"))
4508 (sha256
4509 (base32
4510 "019wcr1qf7jwyxx1y5y290wdlglylskvbb2m01ljkzcza2xnlmhw"))))
4511 (build-system cmake-build-system)
4512 (arguments
4513 `(#:phases
4514 (modify-phases %standard-phases
4515 (add-after 'build 'build-tests
4516 (lambda* (#:key make-flags #:allow-other-keys)
4517 (apply invoke "make" "build_tests" make-flags)))
4518 ;; These tests fail because they require a fully functional MPI
4519 ;; environment.
4520 (add-after 'unpack 'disable-failing-tests
4521 (lambda _
4522 (setenv "ARGS"
4523 (string-append "--exclude-regex '("
4524 (string-join
4525 (list
4526 "remoteindicestest"
4527 "remoteindicestest-mpi-2"
4528 "syncertest"
4529 "syncertest-mpi-2"
4530 "variablesizecommunicatortest"
4531 "variablesizecommunicatortest-mpi-2"
4532 "arithmetictestsuitetest"
4533 "assertandreturntest"
4534 "assertandreturntest_ndebug"
4535 "concept"
4536 "debugaligntest"
4537 "mpicollectivecommunication"
4538 "mpicollectivecommunication-mpi-2"
4539 "mpiguardtest"
4540 "mpiguardtest-mpi-2"
4541 "mpihelpertest"
4542 "mpihelpertest-mpi-2"
4543 "mpihelpertest2"
4544 "mpihelpertest2-mpi-2")
4545 "|")
4546 ")'"))
4547 #t)))))
4548 (inputs
4549 `(("gmp" ,gmp)
4550 ("metis" ,metis)
4551 ("openmpi" ,openmpi)
4552 ("openblas" ,openblas)
4553 ("python" ,python)
4554 ("superlu" ,superlu)))
4555 (native-inputs
4556 `(("gfortran" ,gfortran)
4557 ("pkg-config" ,pkg-config)))
4558 (home-page "https://dune-project.org/")
4559 (synopsis "Distributed and Unified Numerics Environment")
4560 (description "DUNE, the Distributed and Unified Numerics Environment is a
4561modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4562grid-based methods. It supports the easy implementation of methods like
4563@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4564Differences} (FD).")
4565 ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2.
4566 (license license:gpl2)))
242dbd8e
RW		 4567
4568(define-public dune-geometry
4569 (package
4570 (name "dune-geometry")
4571 (version "2.6.0")
4572 (source
4573 (origin
4574 (method url-fetch)
4575 (uri (string-append "https://dune-project.org/download/"
4576 version "/dune-geometry-" version ".tar.gz"))
4577 (sha256
4578 (base32
4579 "0hlaaxjyv9j05blasvb67sy02hd0w4g9znf68gdh3l731dd1aqbn"))))
4580 (build-system cmake-build-system)
4581 (arguments
4582 `(#:phases
4583 (modify-phases %standard-phases
4584 (add-after 'build 'build-tests
4585 (lambda* (#:key make-flags #:allow-other-keys)
4586 (apply invoke "make" "build_tests" make-flags))))))
4587 (inputs
4588 `(("dune-common" ,dune-common)
4589 ("openmpi" ,openmpi)
4590 ;; Optional
4591 ("openblas" ,openblas)
4592 ("gmp" ,gmp)
4593 ("python" ,python)))
4594 (native-inputs
4595 `(("gfortran" ,gfortran)
4596 ("pkg-config" ,pkg-config)))
4597 (home-page "https://dune-project.org/")
4598 (synopsis "Distributed and Unified Numerics Environment")
4599 (description "DUNE, the Distributed and Unified Numerics Environment is a
4600modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4601grid-based methods. It supports the easy implementation of methods like
4602@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4603Differences} (FD).
4604
4605This package contains the basic DUNE geometry classes.")
4606 ;; GPL version 2 with "runtime exception"
4607 (license license:gpl2)))
ef6e69fd
RW		 4608
4609(define-public dune-grid
4610 (package
4611 (name "dune-grid")
4612 (version "2.6.0")
4613 (source
4614 (origin
4615 (method url-fetch)
4616 (uri (string-append "https://dune-project.org/download/"
4617 version "/dune-grid-" version ".tar.gz"))
4618 (sha256
4619 (base32
4620 "1jp4vscm9yb9xg0lh7apzccfkhvgbnk652yahigmh3cvzpl4acd0"))))
4621 (build-system cmake-build-system)
4622 (arguments
4623 `(#:phases
4624 (modify-phases %standard-phases
4625 (add-after 'build 'build-tests
4626 (lambda* (#:key make-flags #:allow-other-keys)
4627 (apply invoke "make" "build_tests" make-flags)))
4628 ;; These tests fail because they require a fully functional MPI
4629 ;; environment.
4630 (add-after 'unpack 'disable-failing-tests
4631 (lambda _
4632 (setenv "ARGS"
4633 (string-append "--exclude-regex '("
4634 (string-join
4635 (list
4636 "scsgmappertest"
4637 "conformvolumevtktest"
4638 "gnuplottest"
4639 "nonconformboundaryvtktest"
4640 "subsamplingvtktest"
4641 "vtktest"
4642 "vtktest-mpi-2"
4643 "vtksequencetest"
4644 "gmshtest-onedgrid"
4645 "test-dgf-yasp"
4646 "test-dgf-yasp-offset"
4647 "test-dgf-oned"
4648 "test-geogrid-yaspgrid"
4649 "test-gridinfo"
4650 "test-identitygrid"
4651 "testiteratorranges"
4652 "test-hierarchicsearch"
4653 "test-parallel-ug-mpi-2"
4654 "test-yaspgrid-backuprestore-equidistant"
4655 "test-yaspgrid-backuprestore-equidistant-mpi-2"
4656 "test-yaspgrid-backuprestore-equidistantoffset"
4657 "test-yaspgrid-backuprestore-equidistantoffset-mpi-2"
4658 "test-yaspgrid-backuprestore-tensor"
4659 "test-yaspgrid-backuprestore-tensor-mpi-2"
4660 "test-yaspgrid-tensorgridfactory"
4661 "test-yaspgrid-tensorgridfactory-mpi-2"
4662 "test-yaspgrid-yaspfactory-1d"
4663 "test-yaspgrid-yaspfactory-1d-mpi-2"
4664 "test-yaspgrid-yaspfactory-2d"
4665 "test-yaspgrid-yaspfactory-2d-mpi-2"
4666 "test-yaspgrid-yaspfactory-3d"
4667 "test-yaspgrid-yaspfactory-3d-mpi-2"
4668 "globalindexsettest"
4669 "persistentcontainertest"
4670 "structuredgridfactorytest"
4671 "tensorgridfactorytest"
4672 "vertexordertest")
4673 "|")
4674 ")'"))
4675 #t)))))
4676 (inputs
4677 `(("dune-common" ,dune-common)
4678 ("dune-geometry" ,dune-geometry)
4679 ("gmp" ,gmp)
4680 ("metis" ,metis)
4681 ("openblas" ,openblas)
4682 ("openmpi" ,openmpi)
4683 ("python" ,python)))
4684 (native-inputs
4685 `(("gfortran" ,gfortran)
4686 ("pkg-config" ,pkg-config)))
4687 (home-page "https://dune-project.org/")
4688 (synopsis "Distributed and Unified Numerics Environment")
4689 (description "DUNE, the Distributed and Unified Numerics Environment is a
4690modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4691grid-based methods. It supports the easy implementation of methods like
4692@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4693Differences} (FD).
4694
4695This package contains the basic DUNE grid classes.")
4696 ;; GPL version 2 with "runtime exception"
4697 (license license:gpl2)))
ea51d357
RW		 4698
4699(define-public dune-istl
4700 (package
4701 (name "dune-istl")
4702 (version "2.6.0")
4703 (source
4704 (origin
4705 (method url-fetch)
4706 (uri (string-append "https://dune-project.org/download/"
4707 version "/dune-istl-" version ".tar.gz"))
4708 (sha256
4709 (base32
4710 "0l2gyrvys5w6wsmk0ckbb7295s80b7yk7qrl7x66akv2jv1nzq2w"))))
4711 (build-system cmake-build-system)
4712 (arguments
4713 `(#:phases
4714 (modify-phases %standard-phases
4715 (add-after 'build 'build-tests
4716 (lambda* (#:key make-flags #:allow-other-keys)
4717 (apply invoke "make" "build_tests" make-flags)))
4718 ;; These tests fail because they require a fully functional MPI
4719 ;; environment.
4720 (add-after 'unpack 'disable-failing-tests
4721 (lambda _
4722 (setenv "ARGS"
4723 (string-append "--exclude-regex '("
4724 (string-join
4725 (list
4726 "galerkintest"
4727 "hierarchytest"
4728 "pamgtest"
4729 "pamg_comm_repart_test"
4730 "matrixredisttest"
4731 "vectorcommtest"
4732 "matrixmarkettest")
4733 "|")
4734 ")'"))
4735 #t)))))
4736 (inputs
4737 `(("dune-common" ,dune-common)
4738 ("openmpi" ,openmpi)
4739 ;; Optional
4740 ("metis" ,metis)
4741 ("superlu" ,superlu)
4742 ("openblas" ,openblas)
4743 ("gmp" ,gmp)
4744 ("python" ,python)))
4745 (native-inputs
4746 `(("gfortran" ,gfortran)
4747 ("pkg-config" ,pkg-config)))
4748 (home-page "https://dune-project.org/")
4749 (synopsis "Distributed and Unified Numerics Environment")
4750 (description "DUNE, the Distributed and Unified Numerics Environment is a
4751modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4752grid-based methods.
4753
4754This is the iterative solver template library which provides generic sparse
4755matrix/vector classes and a variety of solvers based on these classes. A
4756special feature is the use of templates to exploit the recursive block
4757structure of finite element matrices at compile time. Available solvers
4758include Krylov methods, (block-) incomplete decompositions and
4759aggregation-based algebraic multigrid.")
4760 ;; GPL version 2 with "runtime exception"
4761 (license license:gpl2)))
5a70aa7d
RW		 4762
4763(define-public dune-localfunctions
4764 (package
4765 (name "dune-localfunctions")
4766 (version "2.6.0")
4767 (source
4768 (origin
4769 (method url-fetch)
4770 (uri (string-append "https://dune-project.org/download/"
4771 version "/dune-localfunctions-" version ".tar.gz"))
4772 (sha256
4773 (base32
4774 "19c6zjinwwpy8jh4v4prhphyd438rapd4x80fj93apmwgw04nrhl"))))
4775 (build-system cmake-build-system)
4776 (arguments
4777 `(#:phases
4778 (modify-phases %standard-phases
4779 (add-after 'build 'build-tests
4780 (lambda* (#:key make-flags #:allow-other-keys)
4781 (apply invoke "make" "build_tests" make-flags))))))
4782 (inputs
4783 `(("dune-common" ,dune-common)
4784 ("dune-geometry" ,dune-geometry)
4785 ("openmpi" ,openmpi)
4786 ;; Optional
4787 ("metis" ,metis)
4788 ("superlu" ,superlu)
4789 ("gmp" ,gmp)))
4790 (native-inputs
4791 `(("gfortran" ,gfortran)
4792 ("pkg-config" ,pkg-config)))
4793 (home-page "https://dune-project.org/")
4794 (synopsis "Distributed and Unified Numerics Environment") ; TODO
4795 (description "This DUNE module provides interface and implementation for
4796shape functions defined on the DUNE reference elements. In addition to the
4797shape function, interpolation operators and special keys are provided which
4798can be used to assemble global function spaces on finite-element grids.
4799
4800This package provides an interface and implementation for shape functions
4801defined on the DUNE reference elements. In addition to the shape function,
4802interpolation operators and special keys are provided which can be used to
4803assemble global function spaces on finite-element grids.")
4804 ;; GPL version 2 with "runtime exception"
4805 (license license:gpl2)))
ab03d899
RW		 4806
4807(define-public dune-alugrid
4808 (package
4809 (name "dune-alugrid")
4810 (version "2.6.0")
4811 (source
4812 (origin
4813 (method url-fetch)
4814 (uri (string-append "https://dune-project.org/download/"
4815 version "/dune-alugrid-" version ".tar.gz"))
4816 (sha256
4817 (base32
4818 "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj"))))
4819 (build-system cmake-build-system)
4820 (arguments
4821 `(#:tests? #f ; 7 of 8 tests fail because they need a full MPI
4822 ; environment
4823 #:phases
4824 (modify-phases %standard-phases
4825 (add-after 'unpack 'patch-include
4826 (lambda _
4827 (substitute* "dune/alugrid/test/test-alugrid.cc"
4828 (("doc/grids/gridfactory/testgrids")
4829 "doc/dune-grid/grids/gridfactory/testgrids"))
4830 #t))
4831 (add-after 'build 'build-tests
4832 (lambda* (#:key inputs make-flags #:allow-other-keys)
4833 (setenv "CPLUS_INCLUDE_PATH"
97149c57 4834 (string-append (assoc-ref inputs "dune-grid") "/share"))
ab03d899
RW		 4835 (apply invoke "make" "build_tests" make-flags))))))
4836 (inputs
4837 `(("dune-common" ,dune-common)
4838 ("dune-geometry" ,dune-geometry)
4839 ("dune-grid" ,dune-grid)
4840 ("openmpi" ,openmpi)
4841 ;; Optional
4842 ("metis" ,metis)
4843 ("openblas" ,openblas)
4844 ("python" ,python)
4845 ("superlu" ,superlu)
4846 ("gmp" ,gmp)
4847 ("zlib" ,zlib)))
4848 (native-inputs
4849 `(("gfortran" ,gfortran)
4850 ("pkg-config" ,pkg-config)))
4851 (home-page "https://dune-project.org/")
4852 (synopsis "Distributed and Unified Numerics Environment")
4853 (description "ALUGrid is an adaptive, loadbalancing, unstructured
4854implementation of the DUNE grid interface supporting either simplices or
4855cubes.")
4856 (license license:gpl2+)))
0e50630f
RW		 4857
4858(define-public dune-typetree
4859 (package
4860 (name "dune-typetree")
4861 (version "2.6.0")
4862 (source
4863 (origin
4864 (method git-fetch)
4865 (uri (git-reference
4866 (url "https://gitlab.dune-project.org/staging/dune-typetree.git")
4867 (commit (string-append "v" version))))
4868 (file-name (git-file-name name version))
4869 (sha256
4870 (base32
4871 "0mnv6w2f22lz3j4bdpdjq55vjm8xxfx9v4vvhg9bd36xpsbjpjp9"))))
4872 (build-system cmake-build-system)
4873 (arguments
4874 `(#:phases
4875 (modify-phases %standard-phases
4876 (add-after 'build 'build-tests
4877 (lambda* (#:key make-flags #:allow-other-keys)
4878 (apply invoke "make" "build_tests" make-flags))))))
4879 (inputs
4880 `(("dune-common" ,dune-common)
4881 ("openmpi" ,openmpi)
4882 ;; Optional
4883 ("openblas" ,openblas)
4884 ("python" ,python)
4885 ("metis" ,metis)
4886 ("superlu" ,superlu)
4887 ("gmp" ,gmp)))
4888 (native-inputs
4889 `(("gfortran" ,gfortran)
4890 ("pkg-config" ,pkg-config)))
4891 (home-page "https://dune-project.org/")
4892 (synopsis "Distributed and Unified Numerics Environment")
4893 (description "TypeTree is a template library for constructing and
4894operating on statically typed trees of objects.")
4895 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4896 (license (list license:lgpl3+ license:gpl2))))
85b9371c
RW		 4897
4898(define-public dune-functions
4899 (package
4900 (name "dune-functions")
4901 (version "2.6.0")
4902 (source
4903 (origin
4904 (method git-fetch)
4905 (uri (git-reference
4906 (url "https://gitlab.dune-project.org/staging/dune-functions.git")
4907 (commit (string-append "v" version))))
4908 (file-name (git-file-name name version))
4909 (sha256
4910 (base32
4911 "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200"))))
4912 (build-system cmake-build-system)
4913 (arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid
4914 (inputs
4915 `(("dune-common" ,dune-common)
4916 ("dune-istl" ,dune-istl)
4917 ("dune-localfunctions" ,dune-localfunctions)
4918 ("dune-grid" ,dune-grid)
4919 ("dune-geometry" ,dune-geometry)
4920 ("dune-typetree" ,dune-typetree)
4921 ("openmpi" ,openmpi)
4922 ("openblas" ,openblas)
4923 ("metis" ,metis)
4924 ("python" ,python)
4925 ("superlu" ,superlu)
4926 ("gmp" ,gmp)))
4927 (native-inputs
4928 `(("gfortran" ,gfortran)
4929 ("pkg-config" ,pkg-config)))
4930 (home-page "https://dune-project.org/")
4931 (synopsis "Distributed and Unified Numerics Environment")
4932 (description "The dune-functions module provides an abstraction layer for
4933global finite element functions. Its two main concepts are functions
4934implemented as callable objects, and bases of finite element spaces.")
4935 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4936 (license (list license:lgpl3+ license:gpl2))))
4714b00e
RW		 4937
4938(define-public dune-pdelab
4939 (package
4940 (name "dune-pdelab")
4941 (version "2.6.0-rc1")
4942 (source
4943 (origin
4944 (method git-fetch)
4945 (uri (git-reference
4946 (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
4947 (commit (string-append "v" version))))
4948 (file-name (git-file-name name version))
4949 (sha256
4950 (base32
4951 "07g0s9448z65vjrq88g5rv3340iifil85k170n8kbqchsvi4ny5v"))))
4952 (build-system cmake-build-system)
4953 (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
4954 (inputs
4955 `(("dune-common" ,dune-common)
4956 ("dune-istl" ,dune-istl)
4957 ("dune-localfunctions" ,dune-localfunctions)
4958 ("dune-geometry" ,dune-geometry)
4959 ("dune-grid" ,dune-grid)
4960 ("dune-typetree" ,dune-typetree)
4961 ("dune-functions" ,dune-functions)
4962 ("openmpi" ,openmpi)
4963 ;; Optional
4964 ("openblas" ,openblas)
4965 ("eigen" ,eigen)
4966 ("metis" ,metis)
4967 ("python" ,python)
4968 ("superlu" ,superlu)
4969 ("gmp" ,gmp)))
4970 (native-inputs
4971 `(("gfortran" ,gfortran)
4972 ("pkg-config" ,pkg-config)))
4973 (home-page "https://dune-project.org/")
4974 (synopsis "Differential equations solver toolbox")
4975 (description "PDELab is a partial differential equations solver toolbox
4976built on top of DUNE, the Distributed and Unified Numerics Environment.")
4977 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4978 (license (list license:lgpl3+ license:gpl2))))
413f6126
AI		 4979
4980(define-public mlucas
4981 (package
4982 (name "mlucas")
4983 (version "18")
4984 (source
4985 (origin
4986 (method url-fetch)
4987 (uri (string-append
4988 "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz"))
4989 (sha256
a36efdbc 4990 (base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447"))))
413f6126
AI		 4991 (build-system gnu-build-system)
4992 (inputs
4993 `(("python2" ,python-2)))
4994 (arguments
a36efdbc 4995 `(#:tests? #f ; no tests
413f6126
AI		 4996 #:phases
4997 (modify-phases %standard-phases
4998 (replace 'configure
4999 (lambda _
5000 (chdir "src")
5001 (call-with-output-file "Makefile"
5002 (lambda (port)
5003 (format port "CC = gcc
5004CFLAGS = -O3 ~a -DUSE_THREADS
5005LDLIBS = -lm -lpthread -lrt
5006Mlucas: $(addsuffix .o,$(basename $(wildcard *.c)))
5007"
5008 ,(let ((system (or (%current-target-system)
5009 (%current-system))))
5010 (cond
5011 ((string-prefix? "x86_64" system) "-DUSE_SSE2")
5012 (else ""))))))
5013 #t))
5014 (replace 'install
5015 (lambda* (#:key outputs #:allow-other-keys)
5016 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
5017 (install-file "Mlucas" bin)
5018 (install-file "primenet.py" bin))
5019 #t)))))
5020 (home-page "https://www.mersenne.org")
5021 (synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client")
5022 (description "Mlucas performs Lucas-Lehmer primality testing of Mersenne
5023numbers in search of a world-record prime. You may use it to test any
5024suitable number as you wish, but it is preferable that you do so in a
5025coordinated fashion, as part of the Great Internet Mersenne Prime
5026Search (GIMPS). Mlucas also includes a simple Python script for assignment
5027management via the GIMPS project's Primenet server.")
5028 (license license:gpl2+)))
6f8c4195
NG		 5029
5030(define-public nauty
5031 (package
5032 (name "nauty")
1ff64c50 5033 (version "2.6r12")
6f8c4195
NG		 5034 (source (origin
5035 (method url-fetch)
5036 (uri (string-append
5037 "https://pallini.di.uniroma1.it/"
5038 "nauty" (string-join (string-split version #\.) "")
5039 ".tar.gz"))
5040 (sha256
5041 (base32
1ff64c50 5042 "1p4mxf8q5wm47nxyskxbqwa5p1vvkycv1zgswvnk9nsn6vff0al6"))))
6f8c4195
NG		 5043 (build-system gnu-build-system)
5044 (outputs '("out" "lib"))
5045 (arguments
5046 `(#:test-target "checks"
5047 #:phases
5048 (modify-phases %standard-phases
5049 ;; Default make target does not build all available
5050 ;; executables. Create them now.
5051 (add-after 'build 'build-extra-programs
5052 (lambda _
5053 (for-each (lambda (target) (invoke "make" target))
5054 '("blisstog" "bliss2dre" "checks6" "sumlines"))
5055 #t))
5056 ;; Upstream does not provide any install target.
5057 (replace 'install
5058 (lambda* (#:key outputs #:allow-other-keys)
5059 (let* ((out (assoc-ref outputs "out"))
5060 (lib-output (assoc-ref outputs "lib"))
5061 (bin (string-append out "/bin"))
5062 (doc (string-append out "/share/doc/nauty/"))
5063 (include (string-append lib-output "/include/nauty"))
5064 (lib (string-append lib-output "/lib/nauty")))
5065 (for-each (lambda (f) (install-file f bin))
5066 '("dreadnaut" "NRswitchg" "addedgeg" "amtog" "biplabg"
5067 "blisstog" "bliss2dre" "catg" "checks6" "complg"
5068 "converseg" "copyg" "countg" "cubhamg" "deledgeg"
5069 "delptg" "directg" "dretodot" "dretog" "genbg"
5070 "genbgL" "geng" "genquarticg" "genrang" "genspecialg"
5071 "gentourng" "gentreeg" "hamheuristic" "labelg"
5072 "linegraphg" "listg" "multig" "newedgeg" "pickg"
5073 "planarg" "ranlabg" "shortg" "showg" "subdivideg"
5074 "sumlines" "twohamg" "vcolg" "watercluster2"))
5075 (for-each (lambda (f) (install-file f include))
5076 (find-files "." "\\.h$"))
5077 (for-each (lambda (f) (install-file f lib))
5078 (find-files "." "\\.a$"))
5079 (for-each (lambda (f) (install-file f doc))
5080 (append '("formats.txt" "README" "schreier.txt")
5081 (find-files "." "\\.pdf$")))))))))
5082 (inputs
5083 `(("gmp" ,gmp))) ;for sumlines
5084 (home-page "https://pallini.di.uniroma1.it/")
5085 (synopsis "Library for graph automorphisms")
5086 (description "@code{nauty} (No AUTomorphisms, Yes?) is a set of
5087procedures for computing automorphism groups of graphs and digraphs.
5088
5089@code{nauty} computes graph information in the form of a set of
5090generators, the size of the group, and the orbits of the group; it can
5091also produce a canonical label. The @code{nauty} suite is written in
5092C and comes with a command-line interface, a collection of
5093command-line tools, and an Application Programming Interface (API).
5094
5095This package provides the static libraries required to run programs
5096compiled against the nauty library.")
5097 (license license:asl2.0)))
26433471
AE		 5098
5099(define-public ppl
5100 (package
5101 (name "ppl")
5102 (version "1.2")
5103 (source
5104 (origin
5105 (method url-fetch)
5106 (uri (string-append "https://www.bugseng.com/products/ppl/download/"
5107 "ftp/releases/" version
5108 "/ppl-" version ".tar.gz"))
5109 (sha256
5110 (base32
5111 "1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb"))))
5112 (build-system gnu-build-system)
5113 (native-inputs
5114 `(("m4", m4)))
5115 (inputs
5116 `(("glpk" ,glpk)
5117 ("gmp", gmp)))
5118 (home-page "https://www.bugseng.com/parma-polyhedra-library")
5119 (synopsis
5120 "Parma Polyhedra Library for computations with polyhedra")
5121 (description
5122 "The Parma Polyhedra Library (PPL) provides numerical abstractions
5123especially targeted at applications in the field of analysis and
5124verification of complex systems. These abstractions include convex
5125polyhedra, defined as the intersection of a finite number of (open or
5126closed) halfspaces, each described by a linear inequality (strict or
5127non-strict) with rational coefficients; some special classes of polyhedra
5128shapes that offer interesting complexity/precision tradeoffs; and grids
5129which represent regularly spaced points that satisfy a set of linear
5130congruence relations. The library also supports finite powersets and
5131products of (any kind of) polyhedra and grids, a mixed integer linear
5132programming problem solver using an exact-arithmetic version of the simplex
5133algorithm, a parametric integer programming solver, and primitives for
5134termination analysis via the automatic synthesis of linear ranking
5135functions.")
5136 (license license:gpl3+)))
4cb5d251
SS		 5137
5138(define-public speedcrunch
5139 (package
5140 (name "speedcrunch")
5141 (version "0.12.0")
5142 (source
5143 (origin
5144 (method git-fetch)
5145 (uri (git-reference
5146 (url "https://bitbucket.org/heldercorreia/speedcrunch.git")
5147 (commit (string-append "release-" version))))
5148 (file-name (git-file-name name version))
5149 (sha256
5150 (base32
5151 "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"))))
5152 (build-system cmake-build-system)
5153 (inputs `(("qtbase" ,qtbase)))
5154 (native-inputs `(("qttools" ,qttools)))
5155 (arguments
5156 `(#:phases
5157 (modify-phases %standard-phases
5158 (add-after 'unpack 'chdir-to-src
5159 (lambda _ (chdir "src") #t)))))
5160 (synopsis "High-precision scientific calculator")
5161 (description
5162 "SpeedCrunch is a high-precision scientific calculator. It features a
5163syntax-highlighted scrollable display and is designed to be fully used via
5164keyboard. Some distinctive features are auto-completion of functions and
5165variables, a formula book, and quick insertion of constants from various
5166fields of knowledge.")
5167 (home-page "http://speedcrunch.org/")
5168 (license license:gpl2+)))
5169
3b7828cc
RS		 5170(define-public minisat
5171 ;; This is the last commit which is available upstream, no
5172 ;; release happened since 2010.
5173 (let ((commit "37dc6c67e2af26379d88ce349eb9c4c6160e8543")
5174 (revision "1"))
5175 (package
5176 (name "minisat")
5177 (version (string-append "2.2.0-" revision "." (string-take commit 7)))
5178 (source
5179 (origin
5180 (method git-fetch)
5181 (uri (git-reference
5182 (url "https://github.com/niklasso/minisat.git")
5183 (commit commit)))
5184 (file-name (string-append name "-" version "-checkout"))
5185 (sha256
5186 (base32
5187 "091hf3qkm197s5r7xcr3m07xsdwyz2rqk1hc9kj0hn13imz09irq"))
5188 (patches
5189 (search-patches "minisat-friend-declaration.patch"
5190 "minisat-install.patch"))))
5191 (build-system gnu-build-system)
5192 (arguments
5193 '(#:make-flags (list (string-append "prefix=" %output))
5194 #:tests? #f ;no check target
5195 #:phases
5196 (modify-phases %standard-phases
5197 (delete 'configure))))
5198 (inputs
5199 `(("zlib:static" ,zlib "static")
5200 ("zlib" ,zlib)))
5201 (synopsis
5202 "Small, yet efficient, SAT solver")
5203 (description
5204 "MiniSat is a minimalistic, open-source SAT solver, developed to help
5205researchers and developers alike to get started on SAT.")
5206 (home-page
5207 "http://minisat.se/MiniSat.html")
5208 (license license:expat))))
jackhill's copy of GNU Guix: https://guix.gnu.org/