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8f8b2451 1;;; GNU Guix --- Functional package management for GNU
26433471 2;;; Copyright © 2013, 2014, 2015, 2016, 2019 Andreas Enge <andreas@enge.fr>
da95c817 3;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
a53d6719 4;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
6d433d6e 5;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Eric Bavier <bavier@member.fsf.org>
df354a77 6;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
182d6311 7;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
0aad198e 8;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
32158110 9;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
df129041 10;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
0ef54303 11;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
45147b0c 12;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
ec8c7e47 13;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
ab5f3f21 14;;; Copyright © 2016, 2018 Kei Kebreau <kkebreau@posteo.net>
59a07504 15;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
d7cff656 16;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
2fd26d05 17;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
37dc2920 18;;; Copyright © 2017, 2018, 2019 Paul Garlick <pgarlick@tourbillion-technology.com>
47956fa0 19;;; Copyright © 2017 ng0 <ng0@n0.is>
ba1be533 20;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
d109b1e8 21;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
b18b9d20 22;;; Copyright © 2017, 2019 Arun Isaac <arunisaac@systemreboot.net>
98a5cd51 23;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
dc7d6d4e 24;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
3bc74090 25;;; Copyright © 2018, 2019 Jan Nieuwenhuizen <janneke@gnu.org>
41835f94 26;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
910deec6 27;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
07254d8b 28;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
560acf25 29;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
daa6036f 30;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
564cf93f 31;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
fa574a6d 32;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
6f8c4195 33;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
4cb5d251 34;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
3b7828cc 35;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net>
8f8b2451
AE		 36;;;
37;;; This file is part of GNU Guix.
38;;;
39;;; GNU Guix is free software; you can redistribute it and/or modify it
40;;; under the terms of the GNU General Public License as published by
41;;; the Free Software Foundation; either version 3 of the License, or (at
42;;; your option) any later version.
43;;;
44;;; GNU Guix is distributed in the hope that it will be useful, but
45;;; WITHOUT ANY WARRANTY; without even the implied warranty of
46;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
47;;; GNU General Public License for more details.
48;;;
49;;; You should have received a copy of the GNU General Public License
50;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
51
52(define-module (gnu packages maths)
ec322be2 53 #:use-module (ice-9 regex)
a6b9ebc2 54 #:use-module (ice-9 match)
8f8b2451 55 #:use-module (gnu packages)
b5b73a82 56 #:use-module ((guix licenses) #:prefix license:)
8f8b2451
AE		 57 #:use-module (guix packages)
58 #:use-module (guix download)
54052a54 59 #:use-module (guix git-download)
0e2672ae 60 #:use-module (guix utils)
fa574a6d 61 #:use-module ((guix build utils) #:select (alist-replace))
da95c817 62 #:use-module (guix build-system cmake)
c9dfa3c7 63 #:use-module (guix build-system gnu)
560acf25 64 #:use-module (guix build-system python)
ec8c7e47 65 #:use-module (guix build-system r)
63e07468 66 #:use-module (guix build-system ruby)
3de01d3f 67 #:use-module (gnu packages algebra)
ab5f3f21 68 #:use-module (gnu packages audio)
5143517c 69 #:use-module (gnu packages autotools)
fa574a6d 70 #:use-module (gnu packages base)
3de01d3f 71 #:use-module (gnu packages bison)
a17d4564 72 #:use-module (gnu packages boost)
e73b49fb 73 #:use-module (gnu packages check)
3de01d3f 74 #:use-module (gnu packages cmake)
c9dfa3c7 75 #:use-module (gnu packages compression)
668c06ac 76 #:use-module (gnu packages curl)
b7b27a8f 77 #:use-module (gnu packages cyrus-sasl)
528bb464 78 #:use-module (gnu packages documentation)
57e544e8 79 #:use-module (gnu packages elf)
3de01d3f 80 #:use-module (gnu packages flex)
668c06ac 81 #:use-module (gnu packages fltk)
f3929800 82 #:use-module (gnu packages fontutils)
1dba6407 83 #:use-module (gnu packages gettext)
da95c817 84 #:use-module (gnu packages gcc)
73fed4f8 85 #:use-module (gnu packages gd)
668c06ac 86 #:use-module (gnu packages ghostscript)
889187a4 87 #:use-module (gnu packages graphviz)
f3929800 88 #:use-module (gnu packages gtk)
45147b0c 89 #:use-module (gnu packages image)
2fd26d05 90 #:use-module (gnu packages java)
668c06ac 91 #:use-module (gnu packages less)
8731e527 92 #:use-module (gnu packages lisp)
ab5f3f21 93 #:use-module (gnu packages linux)
bc3a2e35 94 #:use-module (gnu packages logging)
6e64766a 95 #:use-module (gnu packages lua)
5698b8b8 96 #:use-module (gnu packages gnome)
1b39a196 97 #:use-module (gnu packages guile)
668c06ac
JD		 98 #:use-module (gnu packages xorg)
99 #:use-module (gnu packages gl)
9f913401 100 #:use-module (gnu packages imagemagick)
8731e527 101 #:use-module (gnu packages m4)
d8c7eeb9 102 #:use-module (gnu packages mpi)
b92eee75 103 #:use-module (gnu packages multiprecision)
528bb464 104 #:use-module (gnu packages netpbm)
bd3d71cb 105 #:use-module (gnu packages onc-rpc)
668c06ac 106 #:use-module (gnu packages pcre)
5698b8b8 107 #:use-module (gnu packages popt)
c9dfa3c7
AE		 108 #:use-module (gnu packages perl)
109 #:use-module (gnu packages pkg-config)
ab5f3f21 110 #:use-module (gnu packages pulseaudio)
da95c817 111 #:use-module (gnu packages python)
589e3f4e 112 #:use-module (gnu packages python-web)
44d10b1f 113 #:use-module (gnu packages python-xyz)
5b05dce7 114 #:use-module (gnu packages qt)
c9dfa3c7 115 #:use-module (gnu packages readline)
63e07468 116 #:use-module (gnu packages ruby)
2742f87e 117 #:use-module (gnu packages tbb)
479c4273 118 #:use-module (gnu packages scheme)
b7194849 119 #:use-module (gnu packages shells)
df354a77 120 #:use-module (gnu packages tcl)
668c06ac 121 #:use-module (gnu packages texinfo)
8f9ac901 122 #:use-module (gnu packages tex)
b7b27a8f 123 #:use-module (gnu packages tls)
5b05dce7 124 #:use-module (gnu packages version-control)
9aafbc0c 125 #:use-module (gnu packages wxwidgets)
c12efc72 126 #:use-module (gnu packages xml)
a17d4564 127 #:use-module (srfi srfi-1))
8f8b2451 128
193abc82
JD		 129(define-public aris
130 (package
1f45f18a
JD		 131 (name "aris")
132 (version "2.2")
133 (source (origin
134 (method url-fetch)
135 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
136 (sha256 (base32
137 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
138 (build-system gnu-build-system)
139 (inputs `(("gtk+" ,gtk+)
140 ("libxml2" ,libxml2)))
141 (native-inputs `(("pkg-config" ,pkg-config)))
142 (synopsis "Natural deduction first-order logic interface")
143 (description "Aris is a program for performing logical proofs. It supports
144propositional and predicate logic, as well as Boolean algebra and
145arithmetical logic. In addition to its predefined inference and equivalence
146rules, Aris also supports references to older proofs. Its use of standard
147logical symbols and its natural deduction interface make it easy to use for
148beginners.")
149 (license license:gpl3+)
6fd52309 150 (home-page "https://www.gnu.org/software/aris/")))
193abc82 151
9c45c519
JD		 152(define-public c-graph
153 (package
154 (name "c-graph")
0ef54303 155 (version "2.0.1")
9c45c519
JD		 156 (source (origin
157 (method url-fetch)
158 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
159 ".tar.gz"))
160 (sha256 (base32
0ef54303 161 "092412jzxy6wdvpk96pfj499hpmaww8xllavbvlqspfpr7ips9id"))))
9c45c519
JD		 162 (build-system gnu-build-system)
163 (inputs
0ef54303 164 `(("fortran" ,gfortran)))
a3947cb1 165 (synopsis "Visualizing and demonstrating convolution")
9c45c519 166 (description
0ef54303 167 "GNU C-Graph is a tool for demonstrating the theory of convolution.
a3947cb1
LC		 168Thus, it can serve as an excellent aid to students of signal and systems
169theory in visualizing the convolution process. Rather than forcing the
170student to write code, the program offers an intuitive interface with
171interactive dialogs to guide them.")
9c45c519 172 (license license:gpl3+)
6fd52309 173 (home-page "https://www.gnu.org/software/c-graph/")))
9c45c519 174
d91025e3
TD		 175(define-public coda
176 (package
177 (name "coda")
9285f8bb 178 (version "2.19")
d91025e3
TD		 179 (source
180 (origin
181 (method url-fetch)
182 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
183 version "/coda-" version ".tar.gz"))
184 (sha256
9285f8bb 185 (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245"))
4b12fe5c
TD		 186 (patches (search-patches "coda-use-system-libs.patch"))
187 (modules '((guix build utils)))
188 (snippet
189 ;; Make sure we don't use the bundled software.
6cbee49d
MW		 190 '(begin
191 (for-each (lambda (d)
192 (delete-file-recursively (string-append "libcoda/" d)))
193 '("zlib" "pcre" "expat"))
194 #t))))
d91025e3
TD		 195 (native-inputs
196 `(("fortran" ,gfortran)
197 ("python" ,python)
198 ("python-numpy" ,python-numpy)))
199 (inputs
200 `(("zlib" ,zlib)
4b12fe5c
TD		 201 ("pcre" ,pcre)
202 ("expat" ,expat)
d91025e3
TD		 203 ("hdf4" ,hdf4-alt)
204 ("hdf5" ,hdf5)))
205 (build-system gnu-build-system)
206 (arguments
4b12fe5c
TD		 207 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
208 "LIBS= -lz -lpcre -lexpat")))
d91025e3
TD		 209 (synopsis "A common interface to various earth observation data formats")
210 (description
211 "The Common Data Access toolbox (CODA) provides a set of interfaces for
212reading remote sensing data from earth observation data files. It consists of
213command line applications and interfaces to the C, Fortran, Python, and Java
214programming languages.")
215 (home-page "https://stcorp.nl/coda")
216 (license license:gpl2+)))
217
d65f0661
KK		 218(define-public qhull
219 (package
220 (name "qhull")
221 (version "2015.2")
222 (source (origin
223 (method url-fetch)
224 (uri (string-append "http://www.qhull.org/download/qhull-"
225 (car (string-split version #\.))
226 "-src-7.2.0.tgz"))
227 (sha256
228 (base32
229 "0dm4b2xr3asy6w74khq2zg4gf26zsy3qf9sq7pf7lmrvbj911c3q"))))
230 (build-system cmake-build-system)
231 (synopsis "Calculate convex hulls and related structures")
232 (description
233 "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
234diagram, halfspace intersection about a point, furthest-site Delaunay
235triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d,
2363-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull
237algorithm for computing the convex hull. It handles roundoff errors from
238floating point arithmetic. It computes volumes, surface areas, and
239approximations to the convex hull.
240
241@code{Qhull} does not support triangulation of non-convex surfaces, mesh
242generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
243shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
244triangulations.")
245 (home-page "http://qhull.org")
246 (license (license:non-copyleft "file://COPYING.txt"
247 "See COPYING in the distribution."))))
248
a8fa86c4
RW		 249(define-public python-cvxopt
250 (package
251 (name "python-cvxopt")
a7c7015a 252 (version "1.2.3")
a8fa86c4
RW		 253 (source (origin
254 (method git-fetch)
255 (uri (git-reference
256 (url "https://github.com/cvxopt/cvxopt.git")
257 (commit version)))
258 (file-name (git-file-name name version))
259 (sha256
260 (base32
a7c7015a 261 "1kiy2m62xgs2d5id6dnnwy4vap85cd70p7pgkb9nh23qf9xnak7b"))))
a8fa86c4
RW		 262 (build-system python-build-system)
263 (arguments
264 `(#:phases
265 (modify-phases %standard-phases
266 (add-after 'unpack 'find-libraries
267 (lambda* (#:key inputs #:allow-other-keys)
268 (setenv "CVXOPT_BLAS_LIB" "openblas")
269 (setenv "CVXOPT_BUILD_FFTW" "1")
270 (setenv "CVXOPT_BUILD_GLPK" "1")
271 (setenv "CVXOPT_BUILD_GSL" "1")
272 #t)))))
273 (inputs
274 `(("fftw" ,fftw)
275 ("glpk" ,glpk)
276 ("gsl" ,gsl)
277 ("lapack" ,lapack)
278 ("openblas" ,openblas)
279 ("suitesparse" ,suitesparse)))
280 (home-page "https://www.cvxopt.org")
281 (synopsis "Python library for convex optimization")
282 (description
283 "CVXOPT is a package for convex optimization based on the Python
284programming language. Its main purpose is to make the development of software
285for convex optimization applications straightforward by building on Python’s
286extensive standard library and on the strengths of Python as a high-level
287programming language.")
288 (license license:gpl3+)))
289
290(define-public python2-cvxopt
291 (package-with-python2 python-cvxopt))
292
8f8b2451
AE		 293(define-public units
294 (package
295 (name "units")
494a8cd0 296 (version "2.19")
8f8b2451
AE		 297 (source (origin
298 (method url-fetch)
299 (uri (string-append "mirror://gnu/units/units-" version
300 ".tar.gz"))
301 (sha256 (base32
494a8cd0 302 "0mk562g7dnidjgfgvkxxpvlba66fh1ykmfd9ylzvcln1vxmi6qj2"))))
8f8b2451 303 (build-system gnu-build-system)
0498d248 304 (inputs
a2549713
EB		 305 `(("readline" ,readline)
306 ("python" ,python-wrapper) ;for 'units_cur' script
0498d248
EB		 307 ("python-requests" ,python-requests)))
308 (arguments
309 `(#:phases (modify-phases %standard-phases
310 (add-after 'install 'wrap-units_cur
311 (lambda* (#:key outputs #:allow-other-keys)
312 (let* ((out (assoc-ref outputs "out"))
313 (bin (string-append out "/bin")))
314 (wrap-program (string-append bin "/units_cur")
315 `("PYTHONPATH" ":" prefix
316 ,(search-path-as-string->list (getenv "PYTHONPATH"))))
317 #t))))))
8f8b2451
AE		 318 (synopsis "Conversion between thousands of scales")
319 (description
574e86f9 320 "GNU Units converts numeric quantities between units of measure. It
7c125ce0
AK		 321can handle scale changes through adaptive usage of standard scale
322prefixes (micro-, kilo-, etc.). It can also handle nonlinear
323conversions such as Fahrenheit to Celsius. Its interpreter is powerful
324enough to be used effectively as a scientific calculator.")
8f8b2451 325 (license license:gpl3+)
6fd52309 326 (home-page "https://www.gnu.org/software/units/")))
c9dfa3c7 327
61a529b4
RW		 328(define-public double-conversion
329 (package
330 (name "double-conversion")
1c7d7f3f 331 (version "3.1.5")
b343850e 332 (home-page "https://github.com/google/double-conversion")
61a529b4 333 (source (origin
2bdc73fb 334 (method git-fetch)
a4de1a65
MB		 335 (uri (git-reference (url home-page)
336 (commit (string-append "v" version))))
2bdc73fb 337 (file-name (git-file-name name version))
61a529b4
RW		 338 (sha256
339 (base32
1c7d7f3f 340 "0csy4pjw1p8rp6g5qxi2h0ychhhp1fldv7gb761627fs2mclw9gv"))))
61a529b4
RW		 341 (build-system cmake-build-system)
342 (arguments
343 '(#:test-target "test"
344 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
345 "-DBUILD_TESTING=ON")))
61a529b4
RW		 346 (synopsis "Conversion routines for IEEE doubles")
347 (description
348 "The double-conversion library provides binary-decimal and decimal-binary
349routines for IEEE doubles. The library consists of efficient conversion
350routines that have been extracted from the V8 JavaScript engine.")
351 (license license:bsd-3)))
352
182d6311
ML		 353(define-public dionysus
354 (package
355 (name "dionysus")
bd041e7f 356 (version "1.4.0")
182d6311
ML		 357 (source (origin
358 (method url-fetch)
359 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
bd041e7f 360 ".tar.xz"))
182d6311
ML		 361 (sha256
362 (base32
bd041e7f 363 "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
182d6311
ML		 364 (build-system gnu-build-system)
365 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
366 (synopsis "Local search for universal constants and scientific values")
367 (description
368 "GNU Dionysus is a convenient system for quickly retrieving the values of
369mathematical constants used in science and engineering. Values can be
370searched using a simple command-line tool, choosing from three databases:
371universal constants, atomic numbers, and constants related to
372semiconductors.")
373 (license license:gpl3+)
6fd52309 374 (home-page "https://www.gnu.org/software/dionysus/")))
182d6311 375
88bd1804
AE		 376(define-public gsl
377 (package
378 (name "gsl")
f3a34b9d 379 (version "2.5")
ab2cc5cd
LC		 380 (source (origin
381 (method url-fetch)
382 (uri (string-append "mirror://gnu/gsl/gsl-"
383 version ".tar.gz"))
384 (sha256
385 (base32
f3a34b9d 386 "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
ab2cc5cd 387 (patches (search-patches "gsl-test-i686.patch"))))
88bd1804 388 (build-system gnu-build-system)
71e0f288 389 (arguments
f885fc05 390 `(;; Currently there are numerous tests that fail on "exotic"
6f766069
EF		 391 ;; architectures such as aarch64 and ppc64le.
392 ,@(if (string-prefix? "aarch64-linux"
393 (or (%current-target-system) (%current-system)))
394 '(#:tests? #f)
395 '())))
396 (home-page "https://www.gnu.org/software/gsl/")
88bd1804
AE		 397 (synopsis "Numerical library for C and C++")
398 (description
a22dc0c4
LC		 399 "The GNU Scientific Library is a library for numerical analysis in C
400and C++. It includes a wide range of mathematical routines, with over 1000
401functions in total. Subject areas covered by the library include:
402differential equations, linear algebra, Fast Fourier Transforms and random
403numbers.")
88bd1804
AE		 404 (license license:gpl3+)))
405
b92eee75
AE		 406(define-public glpk
407 (package
408 (name "glpk")
445929e0 409 (version "4.65")
b92eee75
AE		 410 (source
411 (origin
412 (method url-fetch)
413 (uri (string-append "mirror://gnu/glpk/glpk-"
414 version ".tar.gz"))
415 (sha256
416 (base32
445929e0 417 "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
b92eee75
AE		 418 (build-system gnu-build-system)
419 (inputs
420 `(("gmp" ,gmp)))
421 (arguments
422 `(#:configure-flags '("--with-gmp")))
82110ef6 423 (home-page "https://www.gnu.org/software/glpk/")
79c311b8 424 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
b92eee75
AE		 425 (description
426 "GLPK is a C library for solving large-scale linear programming (LP),
427mixed integer programming (MIP), and other related problems. It supports the
428GNU MathProg modeling language, a subset of the AMPL language, and features a
429translator for the language. In addition to the C library, a stand-alone
430LP/MIP solver is included in the package.")
431 (license license:gpl3+)))
432
b146763a
AE		 433(define-public 4ti2
434 (package
435 (name "4ti2")
eea4a091 436 (version "1.6.9")
b146763a
AE		 437 (source
438 (origin
eea4a091
TGR		 439 (method url-fetch)
440 (uri (string-append "https://github.com/4ti2/4ti2/releases/download/"
441 "Release_"
442 (string-map (lambda (c) (if (char=? c #\.) #\_ c))
443 version)
444 "/4ti2-" version ".tar.gz"))
445 (sha256
446 (base32 "0rj92x6p9m3la5gasjbj7sa569im527ffmka5y2sv1amgd3fflrh"))))
b146763a
AE		 447 (build-system gnu-build-system)
448 (native-inputs
449 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
450 (inputs
451 `(("glpk" ,glpk)
452 ("gmp" ,gmp)))
453 (home-page "http://www.4ti2.de/")
454 (synopsis "Mathematical tool suite for problems on linear spaces")
455 (description
456 "4ti2 implements algorithms for solving algebraic, geometric and
457combinatorial problems on linear spaces. Among others, it solves systems
458of linear equations, computes extreme rays of polyhedral cones, solves
459integer programming problems and computes Markov bases for statistics.")
460 (license license:gpl2+)))
461
53696f10
AE		 462(define-public cddlib
463 (package
464 (name "cddlib")
7fe491fb 465 (version "0.94i")
53696f10
AE		 466 (source
467 (origin
468 (method url-fetch)
182dde82 469 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
53696f10
AE		 470 (string-delete #\. version) ".tar.gz"))
471 (sha256
472 (base32
7fe491fb 473 "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
53696f10
AE		 474 (build-system gnu-build-system)
475 (inputs
476 `(("gmp" ,gmp)))
477 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
478 (synopsis "Library for convex hulls and extreme rays of polyhedra")
479 (description
480 "The C-library cddlib implements the Double Description Method of
481Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
482rays of a general convex polyhedron given by a system of linear inequalities
483in arbitrary dimension. It can also be used for the converse operation of
484computing convex hulls.")
485 (license license:gpl2+)))
486
865a69dd
RW		 487(define-public arpack-ng
488 (package
489 (name "arpack-ng")
f03c4ec6 490 (version "3.6.3")
c0edb5b5 491 (home-page "https://github.com/opencollab/arpack-ng")
622ef2b9
MB		 492 (source (origin
493 (method git-fetch)
494 (uri (git-reference (url home-page) (commit version)))
495 (file-name (git-file-name name version))
496 (sha256
497 (base32
f03c4ec6 498 "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
865a69dd 499 (build-system gnu-build-system)
c0edb5b5
LC		 500 (native-inputs
501 `(("autoconf" ,autoconf)
502 ("automake" ,automake)
503 ("libtool" ,libtool)))
865a69dd
RW		 504 (inputs
505 `(("lapack" ,lapack)
19afbea1 506 ("fortran" ,gfortran)))
865a69dd
RW		 507 (synopsis "Fortran subroutines for solving eigenvalue problems")
508 (description
509 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
510large scale eigenvalue problems.")
166191b3 511 (license (license:non-copyleft "file://COPYING"
865a69dd
RW		 512 "See COPYING in the distribution."))))
513
c0edb5b5
LC		 514(define-public arpack-ng-3.3.0
515 (package
516 (inherit arpack-ng)
517 (version "3.3.0")
518 (name (package-name arpack-ng))
519 (home-page (package-home-page arpack-ng))
520 (source
521 (origin
522 (method url-fetch)
523 (uri (string-append home-page "/archive/" version ".tar.gz"))
524 (file-name (string-append name "-" version ".tar.gz"))
525 (sha256
526 (base32
527 "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
528
8c94c886
EB		 529(define-public arpack-ng-openmpi
530 (package (inherit arpack-ng)
531 (name "arpack-ng-openmpi")
532 (inputs
533 `(("mpi" ,openmpi)
534 ,@(package-inputs arpack-ng)))
4f387541
LC		 535 (arguments
536 (substitute-keyword-arguments (package-arguments arpack-ng)
537 ((#:configure-flags _ '())
aa82260b
PG		 538 ''("--enable-mpi"))
539 ((#:phases phases '%standard-phases)
540 `(modify-phases ,phases
bbe46a4a
EB		 541 (add-before 'check 'mpi-setup
542 ,%openmpi-setup)))))
8c94c886
EB		 543 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
544
da95c817
NK		 545(define-public lapack
546 (package
547 (name "lapack")
ef39a177 548 (version "3.7.1")
da95c817
NK		 549 (source
550 (origin
551 (method url-fetch)
552 (uri (string-append "http://www.netlib.org/lapack/lapack-"
553 version ".tgz"))
554 (sha256
555 (base32
7c0d4c3a 556 "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
da95c817
NK		 557 (build-system cmake-build-system)
558 (home-page "http://www.netlib.org/lapack/")
19afbea1 559 (inputs `(("fortran" ,gfortran)
da95c817
NK		 560 ("python" ,python-2)))
561 (arguments
3ab869b6 562 `(#:configure-flags (list
3ab869b6
LC		 563 "-DBUILD_SHARED_LIBS:BOOL=YES"
564 "-DLAPACKE=ON"
565
566 ;; Build the 'LAPACKE_clatms' functions.
567 "-DLAPACKE_WITH_TMG=ON")
dc1d3cde
KK		 568 #:phases
569 (modify-phases %standard-phases
570 (add-before 'check 'patch-python
571 (lambda* (#:key inputs #:allow-other-keys)
572 (let ((python (assoc-ref inputs "python")))
573 (substitute* "lapack_testing.py"
574 (("/usr/bin/env python") python)))
575 #t)))))
da95c817
NK		 576 (synopsis "Library for numerical linear algebra")
577 (description
578 "LAPACK is a Fortran 90 library for solving the most commonly occurring
579problems in numerical linear algebra.")
166191b3 580 (license (license:non-copyleft "file://LICENSE"
da95c817 581 "See LICENSE in the distribution."))))
73fed4f8 582
e1ff597a
EB		 583(define-public scalapack
584 (package
585 (name "scalapack")
586 (version "2.0.2")
587 (source
588 (origin
589 (method url-fetch)
590 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
591 version ".tgz"))
592 (sha256
593 (base32
f73750e6
EB		 594 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))
595 (patches (search-patches "scalapack-blacs-mpi-deprecations.patch"))))
e1ff597a
EB		 596 (build-system cmake-build-system)
597 (inputs
598 `(("mpi" ,openmpi)
599 ("fortran" ,gfortran)
600 ("lapack" ,lapack))) ;for testing only
601 (arguments
6df2a50a
LC		 602 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
603 #:phases (modify-phases %standard-phases
bbe46a4a
EB		 604 (add-before 'check 'mpi-setup
605 ,%openmpi-setup))))
e1ff597a
EB		 606 (home-page "http://www.netlib.org/scalapack/")
607 (synopsis "Library for scalable numerical linear algebra")
608 (description
609 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
610routines on parallel distributed memory machines. ScaLAPACK solves dense and
611banded linear systems, least squares problems, eigenvalue problems, and
612singular value problems.")
adb223b8
LC		 613 (license (license:non-copyleft "file://LICENSE"
614 "See LICENSE in the distribution."))))
e1ff597a 615
73fed4f8 616(define-public gnuplot
5f800540
KK		 617 (package
618 (name "gnuplot")
cb1d8aee 619 (version "5.2.7")
5f800540
KK		 620 (source (origin
621 (method url-fetch)
622 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
623 version "/gnuplot-"
624 version ".tar.gz"))
625 (sha256
cb1d8aee 626 (base32 "1vglp4la40f5dpj0zdj63zprrkyjgzy068p35bz5dqxjyczm1zlp"))))
5f800540
KK		 627 (build-system gnu-build-system)
628 (inputs `(("readline" ,readline)
629 ("cairo" ,cairo)
630 ("pango" ,pango)
6e64766a
DM		 631 ("gd" ,gd)
632 ("lua" ,lua)))
612a387f
RW		 633 (native-inputs
634 `(("pkg-config" ,pkg-config)
635 ("texlive" ,texlive-tiny)))
07254d8b
AM		 636 (arguments `(#:configure-flags (list (string-append
637 "--with-texdir=" %output
638 "/texmf-local/tex/latex/gnuplot"))))
5f800540
KK		 639 (home-page "http://www.gnuplot.info")
640 (synopsis "Command-line driven graphing utility")
641 (description "Gnuplot is a portable command-line driven graphing
35b9e423 642utility. It was originally created to allow scientists and students to
73fed4f8 643visualize mathematical functions and data interactively, but has grown to
35b9e423 644support many non-interactive uses such as web scripting. It is also used as a
73fed4f8 645plotting engine by third-party applications like Octave.")
5f800540
KK		 646 ;; X11 Style with the additional restriction that derived works may only be
647 ;; distributed as patches to the original.
648 (license (license:fsf-free
649 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
668c06ac 650
32f70e1f
TD		 651(define-public gctp
652 (package
653 (name "gctp")
654 (version "2.0.0")
655 (source
656 (origin
5db874d1
TGR		 657 (method git-fetch)
658 (uri (git-reference
659 (url "https://github.com/OkoSanto/GCTP.git")
660 (commit (string-append "v" version))))
661 (file-name (git-file-name name version))
32f70e1f 662 (sha256
5db874d1 663 (base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
32f70e1f
TD		 664 (native-inputs
665 `(("fortran" ,gfortran)))
666 (build-system gnu-build-system)
667 (synopsis "General Cartographic Transformation Package (GCTP)")
668 (description
669 "The General Cartographic Transformation Package (GCTP) is a system of
670software routines designed to permit the transformation of coordinate pairs
671from one map projection to another. The GCTP is the standard computer
672software used by the National Mapping Division for map projection
673computations.")
674 (home-page "https://github.com/OkoSanto/GCTP")
0f7cd95b 675 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
32f70e1f 676
becbbefc
TD		 677(define-public hdf4
678 (package
679 (name "hdf4")
c959d99f 680 (version "4.2.14")
becbbefc
TD		 681 (source
682 (origin
683 (method url-fetch)
684 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
685 version "/src/hdf-" version ".tar.bz2"))
686 (sha256
c959d99f 687 (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l"))
15ca49b2
AE		 688 (patches (search-patches "hdf4-architectures.patch"
689 "hdf4-reproducibility.patch"
bd3d71cb
MB		 690 "hdf4-shared-fortran.patch"
691 "hdf4-tirpc.patch"))))
becbbefc
TD		 692 (build-system gnu-build-system)
693 (native-inputs
694 `(("gfortran" ,gfortran)
695 ("bison" ,bison)
696 ("flex" ,flex)))
697 (inputs
698 `(("zlib" ,zlib)
bd3d71cb
MB		 699 ("libjpeg" ,libjpeg)
700 ("libtirpc" ,libtirpc)))
becbbefc
TD		 701 (arguments
702 `(#:parallel-tests? #f
bd3d71cb
MB		 703 #:configure-flags (list "--enable-shared"
704 (string-append "CPPFLAGS=-I"
705 (assoc-ref %build-inputs "libtirpc")
706 "/include/tirpc"))
becbbefc
TD		 707 #:phases
708 (modify-phases %standard-phases
953a12fa
EF		 709 ;; This is inspired by two of Debian's patches.
710 (add-before 'configure 'add-more-aarch64-support
711 (lambda _
712 (substitute* '("mfhdf/ncgen/ncgen.l"
713 "mfhdf/ncgen/ncgenyy.c"
714 "mfhdf/libsrc/netcdf.h.in")
715 (("AIX5L64") "__aarch64__"))
716 #t))
becbbefc
TD		 717 (add-before 'configure 'patchbuild
718 (lambda _
719 (substitute*
720 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
721 (("/bin/rm") "rm")
722 (("/bin/mkdir") "mkdir"))
723 (substitute* (find-files "." "^Makefile\\.in$")
724 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
725-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
726 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
727-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
953a12fa 728-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
e464b455
TD		 729 #t))
730 (add-after 'configure 'patch-settings
731 (lambda _
732 ;; libhdf4.settings contains the full path of the
733 ;; compilers used, and its contents are included in
734 ;; .so-files. We truncate the hashes to avoid
735 ;; unnecessary store references to those compilers:
736 (substitute* "libhdf4.settings"
737 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
738 (string-append prefix (string-take hash 10) "...")))
739 #t))
740 )))
becbbefc
TD		 741 (home-page "https://www.hdfgroup.org/products/hdf4/")
742 (synopsis
743 "Library and multi-object file format for storing and managing data")
744 (description "HDF4 is a library and multi-object file format for storing
745and managing data between machines. HDF4 is an older hierarchical data format,
746incompatible with HDF5.")
747 (license
748 (license:non-copyleft
749 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
750
751(define-public hdf4-alt
752 (package
753 (inherit hdf4)
754 (name "hdf4-alt")
755 (arguments
756 (substitute-keyword-arguments (package-arguments hdf4)
757 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
758 (synopsis
759 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
760
7ee3f1a2
JD		 761(define-public hdf5
762 (package
763 (name "hdf5")
7b84610e 764 (version "1.8.21")
7ee3f1a2
JD		 765 (source
766 (origin
767 (method url-fetch)
2da63064
TD		 768 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
769 "hdf5-" (version-major+minor version)
770 "/hdf5-" version "/src/hdf5-"
dcd9d163
LF		 771 version ".tar.bz2")
772 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
773 "current"
7b84610e
EB		 774 (match (string-split version #\.)
775 ((major minor _ ...)
776 (string-append major minor)))
dcd9d163 777 "/src/hdf5-" version ".tar.bz2")))
7ee3f1a2 778 (sha256
7b84610e 779 (base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5"))
7fedc3fd
EB		 780 (patches (search-patches "hdf5-config-date.patch"
781 "hdf5-1.8-mpi-deprecations.patch"))))
7ee3f1a2 782 (build-system gnu-build-system)
12ed1216
AE		 783 (inputs
784 `(("zlib" ,zlib)))
e3a1a1de 785 (native-inputs
3ea420f3
LC		 786 `(("gfortran" ,gfortran)
787 ("perl" ,perl))) ;part of the test machinery needs Perl
e3a1a1de
TD		 788 (outputs '("out" ; core library
789 "fortran")) ; fortran interface
7ee3f1a2 790 (arguments
62126576 791 `(;; Some of the users, notably Flann, need the C++ interface.
e3a1a1de
TD		 792 #:configure-flags '("--enable-cxx"
793 "--enable-fortran"
549d1571
LC		 794 "--enable-fortran2003"
795
796 ;; Build a thread-safe library. Unfortunately,
797 ;; 'configure' invites you to either turn off C++,
798 ;; Fortran, and the high-level interface (HL), or
799 ;; to pass '--enable-unsupported'. Debian
800 ;; packagers chose to pass '--enable-unsupported'
801 ;; and we follow their lead here.
802 "--enable-threadsafe"
803 "--with-pthread"
804 "--enable-unsupported")
4dba441c
RW		 805 ;; Use -fPIC to allow the R bindings to link with the static libraries
806 #:make-flags (list "CFLAGS=-fPIC"
807 "CXXFLAGS=-fPIC")
62126576 808 #:phases
f622e212
EB		 809 (modify-phases %standard-phases
810 (add-before 'configure 'patch-configure
e3a1a1de 811 (lambda* (#:key outputs #:allow-other-keys)
f622e212 812 (substitute* "configure"
b8d9c93b 813 (("/bin/mv") "mv"))
e3a1a1de
TD		 814 (substitute* "fortran/src/Makefile.in"
815 (("libhdf5_fortran_la_LDFLAGS =")
816 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
817 (assoc-ref outputs "fortran") "/lib")))
818 (substitute* "hl/fortran/src/Makefile.in"
819 (("libhdf5hl_fortran_la_LDFLAGS =")
820 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
821 (assoc-ref outputs "fortran") "/lib")))
b8d9c93b 822 #t))
fd0378a1
TD		 823 (add-after 'configure 'patch-settings
824 (lambda _
825 ;; libhdf5.settings contains the full path of the
826 ;; compilers used, and its contents are included in
827 ;; libhdf5.so. We truncate the hashes to avoid
828 ;; unnecessary store references to those compilers:
829 (substitute* "src/libhdf5.settings"
830 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
d8f46d52
RW		 831 (string-append prefix (string-take hash 10) "..."))
832 ;; Don't record the build-time kernel version to make the
833 ;; settings file reproducible.
834 (("Uname information:.*")
835 "Uname information: Linux\n"))
b8d9c93b 836 #t))
f622e212
EB		 837 (add-after 'install 'patch-references
838 (lambda* (#:key inputs outputs #:allow-other-keys)
839 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
840 (zlib (assoc-ref inputs "zlib")))
841 (substitute* (find-files bin "h5p?cc")
842 (("-lz" lib)
843 (string-append "-L" zlib "/lib " lib)))
e3a1a1de
TD		 844 #t)))
845 (add-after 'install 'split
846 (lambda* (#:key inputs outputs #:allow-other-keys)
847 ;; Move all fortran-related files
848 (let* ((out (assoc-ref outputs "out"))
849 (bin (string-append out "/bin"))
850 (lib (string-append out "/lib"))
851 (inc (string-append out "/include"))
852 (ex (string-append out "/share/hdf5_examples/fortran"))
853 (fort (assoc-ref outputs "fortran"))
854 (fbin (string-append fort "/bin"))
855 (flib (string-append fort "/lib"))
856 (finc (string-append fort "/include"))
857 (fex (string-append fort "/share/hdf5_examples/fortran")))
858 (mkdir-p fbin)
859 (mkdir-p flib)
860 (mkdir-p finc)
861 (mkdir-p fex)
b0d1e60f
PG		 862 ;; Note: When built with --enable-parallel, the 'h5fc' file
863 ;; doesn't exist, hence this condition.
864 (when (file-exists? (string-append bin "/h5fc"))
865 (rename-file (string-append bin "/h5fc")
866 (string-append fbin "/h5fc")))
e3a1a1de
TD		 867 (for-each (lambda (file)
868 (rename-file file
869 (string-append flib "/" (basename file))))
870 (find-files lib ".*fortran.*"))
871 (for-each (lambda (file)
872 (rename-file file
873 (string-append finc "/" (basename file))))
874 (find-files inc ".*mod"))
875 (for-each (lambda (file)
876 (rename-file file
877 (string-append fex "/" (basename file))))
878 (find-files ex ".*"))
879 (delete-file-recursively ex))
880 #t)))))
7ee3f1a2 881 (home-page "http://www.hdfgroup.org")
516e93f8 882 (synopsis "Management suite for extremely large and complex data")
7ee3f1a2
JD		 883 (description "HDF5 is a suite that makes possible the management of
884extremely large and complex data collections.")
d4bf49b1
EB		 885 (license (license:x11-style
886 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
7ee3f1a2 887
bb47aca5
RW		 888(define-public hdf5-1.10
889 (package (inherit hdf5)
890 (version "1.10.4")
891 (source
892 (origin
893 (method url-fetch)
894 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
895 "hdf5-" (version-major+minor version)
896 "/hdf5-" version "/src/hdf5-"
897 version ".tar.bz2")
898 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
899 "current"
900 (apply string-append
901 (take (string-split version #\.) 2))
902 "/src/hdf5-" version ".tar.bz2")))
903 (sha256
904 (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
7fedc3fd
EB		 905 (patches (search-patches "hdf5-config-date.patch"
906 "hdf5-mpi-deprecations.patch"))))))
bb47aca5 907
2fd26d05
TD		 908(define-public hdf-java
909 (package
2a509880
RW		 910 (name "hdf-java")
911 (version "3.3.2")
912 (source
913 (origin
914 (method url-fetch)
915 (uri (string-append
916 "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
917 version "/src/CMake-hdfjava-" version ".tar.gz"))
918 (sha256
919 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
920 (modules '((guix build utils)))
921 (snippet ; Make sure we don't use the bundled sources and binaries.
922 `(begin
923 (for-each delete-file
924 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
925 "HDF4.tar.gz" "HDF5.tar.gz"))
926 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
927 #t))))
928 (build-system gnu-build-system)
929 (native-inputs
930 `(("jdk" ,icedtea "jdk")
931 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
932 ;; For tests:
933 ("hamcrest-core" ,java-hamcrest-core)
934 ("junit" ,java-junit)
935 ("slf4j-simple" ,java-slf4j-simple)))
936 (inputs
937 `(("hdf4" ,hdf4)
938 ("hdf5" ,hdf5)
939 ("zlib" ,zlib)
940 ("libjpeg" ,libjpeg)
941 ("slf4j-api" ,java-slf4j-api)))
942 (arguments
943 `(#:configure-flags
944 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
945 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
946 (assoc-ref %build-inputs "jdk") "/lib" )
947 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
948 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
2fd26d05 949
2a509880
RW		 950 #:make-flags
951 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
952 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
953 (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
954 (string-append "JPEGLIB="
955 (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
956 "LLEXT=so")
2fd26d05 957
2a509880
RW		 958 #:phases
959 (modify-phases %standard-phases
960 (add-before 'configure 'chdir-to-source
961 (lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
962 (add-before 'configure 'patch-build
963 (lambda* (#:key inputs outputs #:allow-other-keys)
964 (substitute* "configure"
965 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
966 (("/bin/cat") (which "cat")))
967 ;; Set classpath for compilation
968 (substitute* '("hdf/hdf5lib/Makefile.in"
969 "hdf/hdf5lib/exceptions/Makefile.in"
970 "hdf/hdflib/Makefile.in")
971 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
972 (string-append (assoc-ref inputs "slf4j-api")
973 "/share/java/slf4j-api.jar")))
974 ;; Replace outdated config.sub and config.guess:
975 (with-directory-excursion "config"
976 (for-each (lambda (file)
977 (install-file
978 (string-append (assoc-ref inputs "automake")
979 "/share/automake-"
980 ,(version-major+minor (package-version automake))
981 "/" file) "."))
982 '("config.sub" "config.guess")))
64dc8b0b 983
2a509880
RW		 984 ;; Fix embedded version number
985 (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
986 (substitute* "hdf/hdf5lib/H5.java"
987 (("1, 8, 19")
988 (string-join hdf5version ", "))))
64dc8b0b 989
2a509880
RW		 990 (mkdir-p (string-append (assoc-ref outputs "out")))
991 ;; Set classpath for tests
992 (let* ((build-dir (getcwd))
993 (lib (string-append build-dir "/lib"))
994 (jhdf (string-append lib "/jhdf.jar"))
995 (jhdf5 (string-append lib "/jhdf5.jar"))
996 (testjars
997 (map (lambda (i)
998 (string-append (assoc-ref inputs i)
999 "/share/java/" i ".jar"))
1000 '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
1001 (class-path
1002 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
2fd26d05 1003
2a509880
RW		 1004 (substitute* '("test/hdf5lib/Makefile.in"
1005 "test/hdf5lib/junit.sh.in"
1006 "examples/runExample.sh.in")
1007 (("/usr/bin/test")
1008 (string-append (assoc-ref inputs "coreutils")
1009 "/bin/test"))
1010 (("/usr/bin/uname")
1011 (string-append (assoc-ref inputs "coreutils")
1012 "/bin/uname"))
1013 (("CLASSPATH=[^\n]*")
1014 (string-append "CLASSPATH=" class-path)))
1015 (setenv "CLASSPATH" class-path))
1016 #t))
1017 (add-before 'check 'build-examples
1018 (lambda _
1019 (apply invoke `("javac"
1020 ,@(find-files "examples" ".*\\.java"))))))
2fd26d05 1021
2a509880 1022 #:parallel-build? #f
2fd26d05 1023
2a509880
RW		 1024 #:parallel-tests? #f ))
1025 (home-page "https://support.hdfgroup.org/products/java")
1026 (synopsis "Java interface for the HDF4 and HDF5 libraries")
1027 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
2fd26d05
TD		 1028the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
1029implemented in C.")
1030
2a509880
RW		 1031 ;; BSD-style license:
1032 (license (license:x11-style
1033 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
2fd26d05
TD		 1034/current/src/unpacked/COPYING"))))
1035
d3c4f3bb
TD		 1036(define-public hdf-eos2
1037 (package
1038 (name "hdf-eos2")
1039 (version "19.1.0")
1040 (source
1041 (origin
1042 (method url-fetch)
1043 (uri "ftp://edhs1.gsfc.nasa.gov\
1044/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
1045 (sha256
1046 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
1047 (patches (search-patches "hdf-eos2-remove-gctp.patch"
1048 "hdf-eos2-build-shared.patch"
1049 "hdf-eos2-fortrantests.patch"))))
1050 (build-system gnu-build-system)
1051 (native-inputs
1052 `(("gfortran" ,gfortran)))
1053 (inputs
1054 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
25bdbb61 1055 ;; XXX: These inputs are really dependencies of hdf4.
d3c4f3bb
TD		 1056 ("zlib" ,zlib)
1057 ("libjpeg" ,libjpeg)
25bdbb61
MB		 1058 ("libtirpc" ,libtirpc)
1059
d3c4f3bb
TD		 1060 ("gctp" ,gctp)))
1061 (arguments
1062 `( #:configure-flags '("--enable-install-include" "--enable-shared"
1063 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
1064 #:parallel-tests? #f))
1065 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
1066 (synopsis "HDF4-based data format for NASA's Earth Observing System")
1067 (description "HDF-EOS2 is a software library built on HDF4 which supports
1068the construction of data structures used in NASA's Earth Observing
1069System (Grid, Point and Swath).")
1070
1071 ;; Source files carry a permissive license header.
1072 (license (license:non-copyleft home-page))))
1073
0f43f835
TD		 1074(define-public hdf-eos5
1075 (package
1076 (name "hdf-eos5")
1077 (version "1.15")
1078 (source (origin
1079 (method url-fetch)
1080 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1081/edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1082 (sha256
1083 (base32
1084 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1085 (patches (search-patches "hdf-eos5-build-shared.patch"
1086 "hdf-eos5-remove-gctp.patch"
1087 "hdf-eos5-fix-szip.patch"
1088 "hdf-eos5-fortrantests.patch"))))
1089 (native-inputs
1090 `(("gfortran" ,gfortran)))
1091 (build-system gnu-build-system)
1092 (inputs
1093 `(("hdf5" ,hdf5)
1094 ("zlib" ,zlib)
1095 ("gctp" ,gctp)))
1096 (arguments
1097 `(#:configure-flags '("--enable-install-include" "--enable-shared"
1098 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1099 #:parallel-tests? #f))
1100 (synopsis "HDF5-based data format for NASA's Earth Observing System")
1101 (description
1102 "HDF-EOS5 is a software library built on HDF5 to support the construction
1103of data structures used in NASA's Earth Observing System (Grid, Point and
1104Swath).")
1105 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1106
1107 ;; Source files carry a permissive license header.
1108 (license (license:non-copyleft home-page))))
1109
c8378eea
EB		 1110(define-public hdf5-parallel-openmpi
1111 (package (inherit hdf5)
1112 (name "hdf5-parallel-openmpi")
1113 (inputs
1114 `(("mpi" ,openmpi)
1115 ,@(package-inputs hdf5)))
1116 (arguments
45201bf2
PG		 1117 (substitute-keyword-arguments (package-arguments hdf5)
1118 ((#:configure-flags flags)
549d1571
LC		 1119 ``("--enable-parallel"
1120 ,@(delete "--enable-cxx"
1121 (delete "--enable-threadsafe" ,flags))))
c8378eea
EB		 1122 ((#:phases phases)
1123 `(modify-phases ,phases
45201bf2
PG		 1124 (add-after 'build 'mpi-setup
1125 ,%openmpi-setup)
c8378eea
EB		 1126 (add-before 'check 'patch-tests
1127 (lambda _
1128 ;; OpenMPI's mpirun will exit with non-zero status if it
1129 ;; detects an "abnormal termination", i.e. any process not
784c3da1 1130 ;; calling MPI_Finalize(). Since the test is explicitly
c8378eea
EB		 1131 ;; avoiding MPI_Finalize so as not to have at_exit and thus
1132 ;; H5C_flush_cache from being called, mpirun will always
1133 ;; complain, so turn this test off.
1134 (substitute* "testpar/Makefile"
1135 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1136 (string-append front back "\n")))
1137 (substitute* "tools/h5diff/testph5diff.sh"
1138 (("/bin/sh") (which "sh")))
1139 #t))))))
1140 (synopsis "Management suite for data with parallel IO support")))
1141
00775104
EB		 1142(define-public h5check
1143 (package
1144 (name "h5check")
1145 (version "2.0.1")
1146 (source
1147 (origin
1148 (method url-fetch)
1149 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
1150 "h5check/src/h5check-" version ".tar.gz"))
1151 (sha256
1152 (base32
1153 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1154 (build-system gnu-build-system)
1155 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
1156 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1157 (synopsis "HDF5 format checker")
1158 (description "@code{h5check} is a validation tool for verifying that an
1159HDF5 file is encoded according to the HDF File Format Specification.")
1160 (license (license:x11-style "file://COPYING"))))
1161
a53d6719
JD		 1162(define-public itpp
1163 (package
1164 (name "itpp")
1165 (version "4.3.1")
1166 (source (origin
1167 (method url-fetch)
1168 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1169 version "/itpp-"
1170 version ".tar.gz"))
1171 (sha256
1172 (base32
1173 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1174 (build-system cmake-build-system)
1175 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1176 (inputs `(("lapack" ,lapack)
1177 ("fftw" ,fftw)))
3a4d5df2
RW		 1178 ;; FIXME: Even though the fonts are available dvips complains:
1179 ;; "Font cmmi10 not found; characters will be left blank."
1180 (native-inputs
1181 `(("texlive" ,texlive-tiny)
1182 ("ghostscript" ,ghostscript)
1183 ("doxygen" ,doxygen)))
a53d6719
JD		 1184 (home-page "http://itpp.sourceforge.net")
1185 (synopsis "C++ library of maths, signal processing and communication classes")
1186 (description "IT++ is a C++ library of mathematical, signal processing and
1187communication classes and functions. Its main use is in simulation of
1188communication systems and for performing research in the area of
1189communications. The kernel of the library consists of generic vector and
1190matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1191similar to MATLAB, GNU Octave or SciPy.")
1192 (license license:gpl3+)))
1193
889187a4
EB		 1194(define-public netcdf
1195 (package
1196 (name "netcdf")
a4b0bfb1 1197 (version "4.4.1.1")
889187a4
EB		 1198 (source
1199 (origin
1200 (method url-fetch)
1201 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1202 "netcdf-" version ".tar.gz"))
1203 (sha256
1204 (base32
a4b0bfb1
EB		 1205 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1206 (patches (search-patches "netcdf-date-time.patch"
1207 "netcdf-tst_h_par.patch"))))
889187a4
EB		 1208 (build-system gnu-build-system)
1209 (native-inputs
1210 `(("m4" ,m4)
1211 ("doxygen" ,doxygen)
1212 ("graphviz" ,graphviz)))
1213 (inputs
db825570
TD		 1214 `(("hdf4" ,hdf4-alt)
1215 ("hdf5" ,hdf5)
1216 ("zlib" ,zlib)
1217 ("libjpeg" ,libjpeg)))
889187a4 1218 (arguments
db825570 1219 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
43d01672
TD		 1220
1221 #:phases (modify-phases %standard-phases
1222 (add-before 'configure 'fix-source-date
1223 (lambda _
1224 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1225 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1226 ;; to '1st hour of the current day', and therefore makes the
1227 ;; package not reproducible.
1228 (substitute* "./configure"
1229 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1230 "date --date='@0'"))
1231 #t))
1232 (add-after 'configure 'patch-settings
1233 (lambda _
1234 ;; libnetcdf.settings contains the full filename of the compilers
1235 ;; used to build the library. We truncate the hashes of those
1236 ;; filenames to avoid unnecessary references to the corresponding
1237 ;; store items.
1238 (substitute* "libnetcdf.settings"
1239 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1240 (string-append prefix (string-take hash 10) "...")))
1241 #t)))
1242
889187a4
EB		 1243 #:parallel-tests? #f)) ;various race conditions
1244 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
1245 (synopsis "Library for scientific data")
1246 (description "NetCDF is an interface for scientific data access and a
1247software library that provides an implementation of the interface. The netCDF
1248library defines a machine-independent format for representing scientific data.
1249Together, the interface, library, and format support the creation, access, and
1250sharing of scientific data.")
1251 (license (license:x11-style "file://COPYRIGHT"))))
1252
1253(define-public netcdf-parallel-openmpi
1254 (package (inherit netcdf)
1255 (name "netcdf-parallel-openmpi")
1256 (inputs
1257 `(("mpi" ,openmpi)
1258 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1259 (package-inputs netcdf))))
1260 ;; TODO: Replace pkg-config references in nc-config with absolute references
1261 (arguments
1262 (substitute-keyword-arguments (package-arguments netcdf)
1263 ((#:configure-flags flags)
1264 `(cons* "CC=mpicc" "CXX=mpicxx"
1265 "--enable-parallel-tests"
1266 ;; Shared libraries not supported with parallel IO.
1267 "--disable-shared" "--with-pic"
1268 ,flags))))))
1269
300200b6
TD		 1270(define-public netcdf-fortran
1271 (package
1272 (name "netcdf-fortran")
1273 (version "4.4.4")
1274 (source (origin
1275 (method url-fetch)
1276 (uri (string-append
1277 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1278 version ".tar.gz"))
1279 (sha256
1280 (base32
1281 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1282 (build-system gnu-build-system)
1283 (arguments
1284 `(#:parallel-tests? #f))
1285 (inputs
1286 `(("netcdf" ,netcdf)))
1287 (native-inputs
1288 `(("gfortran" ,gfortran)))
1289 (synopsis "Fortran interface for the netCDF library")
1290 (description (package-description netcdf))
1291 (home-page (package-home-page netcdf))
1292 (license (package-license netcdf))))
1293
1b39a196
RJ		 1294(define-public nlopt
1295 (package
1296 (name "nlopt")
1297 (version "2.4.2")
1298 (source (origin
1299 (method url-fetch)
1300 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1301 version ".tar.gz"))
1302 (sha256
1303 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1304 (build-system gnu-build-system)
1305 (arguments
1306 `(;; Shared libraries are not built by default. They are required to
1307 ;; build the Guile, Octave, and Python bindings.
1308 #:configure-flags '("--enable-shared")
1309
1310 #:phases
1311 (modify-phases %standard-phases
1312 (add-before 'configure 'set-libnlopt-file-name
1313 (lambda* (#:key outputs #:allow-other-keys)
1314 ;; Make sure the Scheme module refers to the library by its
1315 ;; absolute file name (we cannot do that from a snippet
1316 ;; because the expansion of @libdir@ contains
1317 ;; ${exec_prefix}.)
1318 (let ((out (assoc-ref outputs "out")))
1319 (substitute* "swig/nlopt.scm.in"
1320 (("libnlopt")
1321 (string-append out "/lib/libnlopt")))
1322 #t))))))
1323 (inputs `(("guile" ,guile-2.0)))
1324 (native-inputs `(("pkg-config" ,pkg-config)))
1325 (home-page "http://ab-initio.mit.edu/wiki/")
1326 (synopsis "Library for nonlinear optimization")
1327 (description "NLopt is a library for nonlinear optimization, providing a
1328common interface for a number of different free optimization routines available
1329online as well as original implementations of various other algorithms.")
1330 (license license:lgpl2.1+)))
1331
005c787d
LC		 1332(define-public ipopt
1333 (package
1334 (name "ipopt")
98a5cd51 1335 (version "3.12.12")
005c787d
LC		 1336 (source (origin
1337 (method url-fetch)
1338 (uri (string-append
1339 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1340 version".tgz"))
1341 (sha256
1342 (base32
98a5cd51 1343 "07yn9rzdswjk8n246qq6ci9ssf2bcplkifcpsfz9j6cdxw9vgbkv"))
005c787d
LC		 1344 (modules '((guix build utils)))
1345 (snippet
1346 ;; Make sure we don't use the bundled software.
6cbee49d
MW		 1347 '(begin
1348 (delete-file-recursively "ThirdParty")
1349 #t))))
005c787d 1350 (build-system gnu-build-system)
ad1c4537
LC		 1351 (arguments
1352 '(#:phases (modify-phases %standard-phases
1353 (add-after 'install 'add--L-flags-in-ipopt.pc
1354 (lambda* (#:key inputs outputs #:allow-other-keys)
1355 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1356 ;; move it to "Libs.private" where it belongs, and add a
1357 ;; '-L' flag for LAPACK.
1358 (let ((out (assoc-ref outputs "out"))
1359 (lapack (assoc-ref inputs "lapack")))
1360 (substitute* (string-append out "/lib/pkgconfig/"
1361 "ipopt.pc")
1362 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1363 (string-append "Libs: " before " " after "\n"
1364 "Libs.private: " before
1365 "-L" lapack "/lib -llapack -lblas "
1366 after "\n")))
1367 #t))))))
005c787d
LC		 1368 (native-inputs
1369 `(("gfortran" ,gfortran)))
1370 (inputs
1371 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
ad1c4537 1372 `(("lapack" ,lapack))) ;for both libblas and liblapack
005c787d
LC		 1373 (home-page "http://www.coin-or.org")
1374 (synopsis "Large-scale nonlinear optimizer")
1375 (description
1376 "The Interior Point Optimizer (IPOPT) is a software package for
1377large-scale nonlinear optimization. It provides C++, C, and Fortran
1378interfaces.")
1379 (license license:epl1.0)))
1380
ecfbc51f
RW		 1381(define-public clp
1382 (package
1383 (name "clp")
1384 (version "1.17.1")
1385 (source (origin
1386 (method url-fetch)
1387 (uri (string-append "https://www.coin-or.org/download/source/"
1388 "Clp/Clp-" version ".tgz"))
1389 (sha256
1390 (base32
1391 "1wdg820g3iikf9344ijwsc8sy6c0m6im42bzzizm6rlmkvnmxhk9"))
1392 (modules '((guix build utils)))
1393 (snippet
1394 ;; Make sure we don't use the bundled software.
1395 '(begin
1396 (delete-file-recursively "ThirdParty")
1397 #t))))
1398 (build-system gnu-build-system)
1399 (native-inputs
1400 `(("gfortran" ,gfortran)
1401 ("pkg-config" ,pkg-config)))
1402 (inputs
1403 `(("openblas" ,openblas)))
1404 (home-page "https://www.coin-or.org")
1405 (synopsis "Linear programming solver")
1406 (description
1407 "CLP is a high quality linear programming solver. Its main strengths are
1408its dual and primal Simplex algorithms. It also has a barrier algorithm for
1409linear and quadratic objectives. There are limited facilities for nonlinear
1410and quadratic objectives using the Simplex algorithm.")
1411 (license license:epl1.0)))
1412
f9940ef1
LC		 1413(define-public ceres
1414 (package
1415 (name "ceres-solver")
e0bee0de 1416 (version "1.14.0")
f9940ef1
LC		 1417 (home-page "http://ceres-solver.org/")
1418 (source (origin
1419 (method url-fetch)
1420 (uri (string-append home-page "ceres-solver-"
1421 version ".tar.gz"))
1422 (sha256
1423 (base32
e0bee0de 1424 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
f9940ef1
LC		 1425 (build-system cmake-build-system)
1426 (arguments
1427 ;; TODO: Build HTML user documentation and install separately.
bc3a2e35 1428 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
f9940ef1
LC		 1429 "-DBUILD_SHARED_LIBS=ON")
1430
1431 #:phases (modify-phases %standard-phases
1432 (add-before 'configure 'set-library-directory
1433 (lambda _
1434 ;; Install libraries to lib/, not lib64/.
1435 (substitute* "internal/ceres/CMakeLists.txt"
1436 (("set\\(LIB_SUFFIX \"64\"\\)")
1437 "set(LIB_SUFFIX \"\")"))
1438 #t)))))
1439 (native-inputs
1440 `(("pkg-config" ,pkg-config)))
468e0b18
LC		 1441 (propagated-inputs
1442 `(("glog" ,glog))) ;for #include <glog/glog.h>
f9940ef1
LC		 1443 (inputs
1444 `(("eigen" ,eigen)
1445 ("blas" ,openblas)
1446 ("lapack" ,lapack)
1447 ("suitesparse" ,suitesparse)
1448 ("gflags" ,gflags)))
1449 (synopsis "C++ library for solving large optimization problems")
1450 (description
1451 "Ceres Solver is a C++ library for modeling and solving large,
1452complicated optimization problems. It is a feature rich, mature and
1453performant library which has been used in production since 2010. Ceres Solver
1454can solve two kinds of problems:
1455@enumerate
1456@item non-linear least squares problems with bounds constraints;
1457@item general unconstrained optimization problems.
1458@end enumerate\n")
1459 (license license:bsd-3)))
1460
b66741ed 1461;; For a fully featured Octave, users are strongly recommended also to install
5ca4fe96 1462;; the following packages: less, ghostscript, gnuplot.
5537603f 1463(define-public octave-cli
668c06ac 1464 (package
5537603f 1465 (name "octave-cli")
5b8f8928 1466 (version "5.1.0")
668c06ac
JD		 1467 (source
1468 (origin
1469 (method url-fetch)
1470 (uri (string-append "mirror://gnu/octave/octave-"
f5a077b1 1471 version ".tar.lz"))
668c06ac
JD		 1472 (sha256
1473 (base32
5b8f8928 1474 "11wwxpy2q1bhxs2v41bqn05i2sb0905cj1xil6mg8l4k2kka4cq6"))))
668c06ac
JD		 1475 (build-system gnu-build-system)
1476 (inputs
697df13f
EF		 1477 `(("alsa-lib" ,alsa-lib)
1478 ("arpack" ,arpack-ng)
1479 ("curl" ,curl)
1ec78e9d
EB		 1480 ("fftw" ,fftw)
1481 ("fftwf" ,fftwf)
668c06ac
JD		 1482 ("fltk" ,fltk)
1483 ("fontconfig" ,fontconfig)
1484 ("freetype" ,freetype)
697df13f
EF		 1485 ("gl2ps" ,gl2ps)
1486 ("glpk" ,glpk)
1ec78e9d 1487 ("glu" ,glu)
ab5f3f21 1488 ("graphicsmagick" ,graphicsmagick)
697df13f
EF		 1489 ("hdf5" ,hdf5)
1490 ("lapack" ,lapack)
ab5f3f21 1491 ("libsndfile" ,libsndfile)
697df13f
EF		 1492 ("libxft" ,libxft)
1493 ("mesa" ,mesa)
1494 ("pcre" ,pcre)
ab5f3f21 1495 ("portaudio" ,portaudio)
697df13f
EF		 1496 ("qhull" ,qhull)
1497 ("readline" ,readline)
1498 ("suitesparse" ,suitesparse)
1499 ("texinfo" ,texinfo)
1500 ("zlib" ,zlib)))
668c06ac 1501 (native-inputs
f5a077b1
EF		 1502 `(("lzip" ,lzip)
1503 ("gfortran" ,gfortran)
668c06ac
JD		 1504 ("pkg-config" ,pkg-config)
1505 ("perl" ,perl)
1ec78e9d
EB		 1506 ;; The following inputs are not actually used in the build process.
1507 ;; However, the ./configure gratuitously tests for their existence and
1508 ;; assumes that programs not present at build time are also not, and
1509 ;; can never be, available at run time! If these inputs are therefore
1510 ;; not present, support for them will be built out. However, Octave
1511 ;; will still run without them, albeit without the features they
668c06ac
JD		 1512 ;; provide.
1513 ("less" ,less)
668c06ac
JD		 1514 ("ghostscript" ,ghostscript)
1515 ("gnuplot" ,gnuplot)))
116af86f
KK		 1516 ;; Octave code uses this variable to detect directories holding multiple CA
1517 ;; certificates to verify peers with. This is required for the networking
1518 ;; functions that require encryption to work properly.
1519 (native-search-paths
1520 (list (search-path-specification
1521 (variable "CURLOPT_CAPATH")
1522 (files '("etc/ssl/certs")))))
668c06ac 1523 (arguments
b7b27a8f
KY		 1524 `(#:configure-flags
1525 (list (string-append "--with-shell="
1526 (assoc-ref %build-inputs "bash")
5ca4fe96
AI		 1527 "/bin/sh"))
1528 #:phases
1529 (modify-phases %standard-phases
1530 (add-after 'configure 'configure-makeinfo
1531 (lambda* (#:key inputs #:allow-other-keys)
b18b9d20
AI		 1532 (substitute* "libinterp/corefcn/help.h"
1533 (("\"makeinfo\"")
1534 (string-append
1535 "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
5ca4fe96 1536 #t)))))
f5a077b1 1537 (home-page "https://www.gnu.org/software/octave/")
668c06ac 1538 (synopsis "High-level language for numerical computation")
1ec78e9d
EB		 1539 (description "GNU Octave is a high-level interpreted language that is
1540specialized for numerical computations. It can be used for both linear and
1541non-linear applications and it provides great support for visualizing results.
1542Work may be performed both at the interactive command-line as well as via
1543script files.")
668c06ac 1544 (license license:gpl3+)))
3de01d3f 1545
e0ae7e73 1546(define-public octave
5537603f 1547 (package (inherit octave-cli)
e0ae7e73 1548 (name "octave")
7a3772b3 1549 (source (origin
5537603f 1550 (inherit (package-source octave-cli))))
36ce25f0
KK		 1551 (inputs
1552 `(("qscintilla" ,qscintilla)
1553 ("qt" ,qtbase)
5537603f 1554 ,@(package-inputs octave-cli)))
36ce25f0
KK		 1555 (native-inputs
1556 `(("qttools" , qttools) ;for lrelease
70bb5d88 1557 ("texlive" ,(texlive-union (list texlive-epsf))) ; for texi2dvi
5537603f 1558 ,@(package-native-inputs octave-cli)))
36ce25f0 1559 (arguments
5537603f 1560 (substitute-keyword-arguments (package-arguments octave-cli)
36ce25f0
KK		 1561 ((#:phases phases)
1562 `(modify-phases ,phases
1563 (add-before 'configure 'patch-qscintilla-library-name
1564 (lambda* (#:key inputs #:allow-other-keys)
1565 ;; The QScintilla library that the Octave configure script tries
1566 ;; to link with should be named libqscintilla-qt5.so, but the
1567 ;; QScintilla input provides the shared library as
1568 ;; libqscintilla2_qt5.so.
1569 (substitute* "configure"
1570 (("qscintilla2-qt5")
1571 "qscintilla2_qt5"))
1572 #t))))))))
1573
e0ae7e73
KK		 1574(define-public qtoctave
1575 (deprecated-package "qtoctave" octave))
1576
5d4bd4cc
PG		 1577(define-public opencascade-oce
1578 (package
1579 (name "opencascade-oce")
1580 (version "0.17.2")
1581 (source
1582 (origin
830971bf
TGR		 1583 (method git-fetch)
1584 (uri (git-reference
1585 (url "https://github.com/tpaviot/oce.git")
1586 (commit (string-append "OCE-" version))))
1587 (file-name (git-file-name name version))
a4f393b7 1588 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
5d4bd4cc 1589 (sha256
830971bf 1590 (base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69"))))
5d4bd4cc
PG		 1591 (build-system cmake-build-system)
1592 (arguments
1593 '(#:configure-flags
1594 (list "-DOCE_TESTING:BOOL=ON"
1595 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1596 "-DOCE_DRAW:BOOL=ON"
1597 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1598 (assoc-ref %outputs "out"))
1599 "-UCMAKE_INSTALL_RPATH")))
1600 (inputs
1601 `(("freetype" ,freetype)
1602 ("glu" ,glu)
1603 ("libxmu" ,libxmu)
1604 ("mesa" ,mesa)
1605 ("tcl" ,tcl)
1606 ("tk" ,tk)))
1607 (native-inputs
1608 `(("python" ,python-wrapper)))
1609 (home-page "https://github.com/tpaviot/oce")
1610 (synopsis "Libraries for 3D modeling and numerical simulation")
1611 (description
1612 "Open CASCADE is a set of libraries for the development of applications
1613dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1614C++ class libraries providing services for 3D surface and solid modeling, CAD
1615data exchange, and visualization. It is used for development of specialized
1616software dealing with 3D models in design (CAD), manufacturing (CAM),
1617numerical simulation (CAE), measurement equipment (CMM), and quality
1618control (CAQ) domains.
1619
1620This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1621patches, improvements, and experiments contributed by users over the official
1622Open CASCADE library.")
1623 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1624 ; use of header files; see
1625 ; OCCT_LGPL_EXCEPTION.txt
1626 license:public-domain; files
1627 ; src/Standard/Standard_StdAllocator.hxx and
1628 ; src/NCollection/NCollection_StdAllocator.hxx
1629 license:expat; file src/OpenGl/OpenGl_glext.h
1630 license:bsd-3)))); test framework gtest
1631
37dc2920
PG		 1632(define-public opencascade-occt
1633 (package
1634 (name "opencascade-occt")
1635 (version "7.3.0p3")
1636 (source
1637 (origin
1638 (method git-fetch)
1639 (uri (git-reference
1640 (url "https://git.dev.opencascade.org/repos/occt.git")
1641 (commit
1642 (string-append "V"
1643 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
1644 version)))))
1645 (file-name (git-file-name name version))
1646 (sha256
1647 (base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4"))
1648 (modules '((guix build utils)))
1649 (snippet
1650 '(begin
1651 ;; Remove files specific to non-free operating systems.
1652 (delete-file-recursively "samples/ios")
1653 (delete-file-recursively "samples/mfc")
1654 (delete-file-recursively "samples/qt/FuncDemo")
1655 (delete-file "genconf.bat")
1656 (delete-file "gendoc.bat")
1657 (delete-file "genproj.bat")
1658 (delete-file "upgrade.bat")
1659 ;; Remove references to deleted files.
1660 (substitute* "dox/FILES_HTML.txt"
1661 ((".*standard.*") "" )
1662 ((".*UIKitSample.*") ""))
1663 #t))))
1664 (build-system cmake-build-system)
1665 (arguments
1666 '(;; There is no test target for make. OCCT provides an
1667 ;; 'Automated Testing System', which may be accessed after
1668 ;; installation via the draw.sh script. draw.sh is located in
1669 ;; the bin directory. For details see:
1670 ;; https://www.opencascade.com/doc/occt-7.3.0/overview/html/\
1671 ;; occt_dev_guides__tests.html
1672 #:tests? #f
1673 ;; Configure without freeimage: attempting to link against the
1674 ;; freeimage version 3.17 library leads to 'undefined
1675 ;; reference' errors.
1676 #:configure-flags
1677 (list "-DUSE_FREEIMAGE:BOOL=OFF"
1678 "-DUSE_TBB:BOOL=ON"
1679 "-DUSE_VTK:BOOL=OFF"
1680 "-DBUILD_DOC_Overview:BOOL=OFF"
1681 "-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON"
1682 "-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON"
1683 "-UCMAKE_INSTALL_LIBDIR")))
1684 (inputs
1685 `(("doxygen" ,doxygen)
1686 ;("freeimage" ,freeimage)
1687 ("freetype" ,freetype)
1688 ("glu" ,glu)
1689 ("libxext" ,libxext)
1690 ("libxi" ,libxi)
1691 ("libxmu" ,libxmu)
1692 ("mesa" ,mesa)
1693 ("tbb" ,tbb)
1694 ("tcl" ,tcl)
1695 ("tk" ,tk)))
1696 ;; TODO: build Overview documentation and add 'doc' output.
1697 (home-page "https://www.opencascade.com")
1698 (synopsis "Libraries for 3D modeling and numerical simulation")
1699 (description
1700 "Open CASCADE is a set of libraries for the development of applications
1701dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1702C++ class libraries providing services for 3D surface and solid modeling, CAD
1703data exchange, and visualization. It is used for development of specialized
1704software dealing with 3D models in design (CAD), manufacturing (CAM),
1705numerical simulation (CAE), measurement equipment (CMM), and quality
1706control (CAQ) domains.
1707
1708This is the certified version of the Open Cascade Technology (OCCT) library.")
1709 (license (list ;; OCCT library:
1710 license:lgpl2.1; with an exception for the use of header
1711 ; files, see OCCT_LGPL_EXCEPTION.txt.
1712 ;; Files src/OpenGl/glext.h, adm/cmake/cotire.cmake and
1713 ;; src/OpenGl/OpenGl_HaltonSampler.hxx:
1714 license:expat
1715 ;; Files src/ExprIntrp/ExprIntrp.tab.* and
1716 ;; src/StepFile/step.tab.*:
1717 license:gpl3+ ; with Bison 2.2 exception.
1718 ;; File src/NCollection/NCollection_UtfIterator.lxx:
1719 (license:non-copyleft
1720 "https://www.unicode.org/license.html")
1721 ;; File src/NCollection/NCollection_StdAllocator.hxx:
1722 license:public-domain))))
1723
3de01d3f
EB		 1724(define-public gmsh
1725 (package
1726 (name "gmsh")
8a4d14fa 1727 (version "2.16.0")
3de01d3f
EB		 1728 (source
1729 (origin
abed5df7
PG		 1730 (method git-fetch)
1731 (uri (git-reference
1732 (url "https://gitlab.onelab.info/gmsh/gmsh.git")
1733 (commit
1734 (string-append "gmsh_"
1735 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
1736 version)))))
1737 (file-name (git-file-name name version))
3de01d3f 1738 (sha256
abed5df7 1739 (base32 "08rq4jajwmlpivnm9yifz2jhaivnz065lnk0h2zv773nwl9wf162"))
3de01d3f
EB		 1740 (modules '((guix build utils)))
1741 (snippet
1742 ;; Remove non-free METIS code
6cbee49d
MW		 1743 '(begin
1744 (delete-file-recursively "contrib/Metis")
1745 #t))))
3de01d3f 1746 (build-system cmake-build-system)
3de01d3f
EB		 1747 (propagated-inputs
1748 `(("fltk" ,fltk)
19afbea1 1749 ("gfortran" ,gfortran)
3de01d3f 1750 ("gmp" ,gmp)
40029cbe 1751 ("hdf5" ,hdf5)
3de01d3f
EB		 1752 ("lapack" ,lapack)
1753 ("mesa" ,mesa)
85f41902 1754 ("glu" ,glu)
45548139 1755 ("opencascade-oce" ,opencascade-oce)
3de01d3f
EB		 1756 ("libx11" ,libx11)
1757 ("libxext" ,libxext)))
66395a61
EF		 1758 (inputs
1759 `(("fontconfig" ,fontconfig)
1760 ("libxft" ,libxft)))
3de01d3f
EB		 1761 (arguments
1762 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1763 "-DENABLE_BUILD_SHARED:BOOL=ON"
45548139 1764 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
0746c33e 1765 (home-page "http://gmsh.info/")
3de01d3f 1766 (synopsis "3D finite element grid generator")
edf684ef
EB		 1767 (description "Gmsh is a 3D finite element grid generator with a built-in
1768CAD engine and post-processor. Its design goal is to provide a fast, light
1769and user-friendly meshing tool with parametric input and advanced
1770visualization capabilities. Gmsh is built around four modules: geometry,
1771mesh, solver and post-processing. The specification of any input to these
1772modules is done either interactively using the graphical user interface or in
1773ASCII text files using Gmsh's own scripting language.")
3de01d3f 1774 (license license:gpl2+)))
b9100e2f 1775
6d5f63b6
JD		 1776(define-public maxflow
1777 (package
1778 (name "maxflow")
0af12a13
TGR		 1779 ;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’,
1780 ;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’.
1781 (version "3.0.5")
6d5f63b6
JD		 1782 (source (origin
1783 (method git-fetch)
1784 (uri (git-reference
1785 (url "https://github.com/gerddie/maxflow.git")
0af12a13 1786 (commit version)))
2dc0a6cf 1787 (file-name (git-file-name name version))
6d5f63b6
JD		 1788 (sha256
1789 (base32
1790 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1791 (build-system cmake-build-system)
0be9038c 1792 (home-page "https://pub.ist.ac.at/~vnk/software.html")
6d5f63b6
JD		 1793 (synopsis "Library implementing Maxflow algorithm")
1794 (description "An implementation of the maxflow algorithm described in
1795@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1796Energy Minimization in Computer Vision.\n
1797Yuri Boykov and Vladimir Kolmogorov.\n
1798In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1799September 2004}")
1800 (license license:gpl3+)))
1801
b9100e2f
EB		 1802(define-public petsc
1803 (package
1804 (name "petsc")
4f7a4a06 1805 (version "3.11.2")
b9100e2f
EB		 1806 (source
1807 (origin
1808 (method url-fetch)
1809 ;; The *-lite-* tarball does not contain the *large* documentation
1810 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1811 "petsc-lite-" version ".tar.gz"))
1812 (sha256
4f7a4a06 1813 (base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx"))))
b2c52fc9
TGR		 1814 (outputs '("out" ; libraries and headers
1815 "examples")) ; ~30MiB of examples
b9100e2f
EB		 1816 (build-system gnu-build-system)
1817 (native-inputs
6fec298d 1818 `(("python" ,python-2)))
b9100e2f 1819 (inputs
19afbea1 1820 `(("gfortran" ,gfortran)
b9100e2f 1821 ("lapack" ,lapack)
f258212d 1822 ("superlu" ,superlu)
b9100e2f
EB		 1823 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1824 ;; leaving out opengl, as configuration seems to only be for mac
1825 ))
1826 (arguments
1827 `(#:test-target "test"
b2c52fc9 1828 #:parallel-build? #f ; build is parallel by default
b9100e2f
EB		 1829 #:configure-flags
1830 `("--with-mpi=0"
f258212d 1831 "--with-openmp=1"
c15be128 1832 "--with-superlu=1")
9731c412
EB		 1833 #:make-flags
1834 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1835 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1836 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
b9100e2f 1837 #:phases
64dcc289
EB		 1838 (modify-phases %standard-phases
1839 (replace 'configure
1840 ;; PETSc's configure script is actually a python script, so we can't
1841 ;; run it with bash.
1842 (lambda* (#:key outputs (configure-flags '())
1843 #:allow-other-keys)
1844 (let* ((prefix (assoc-ref outputs "out"))
1845 (flags `(,(string-append "--prefix=" prefix)
1846 ,@configure-flags)))
1847 (format #t "build directory: ~s~%" (getcwd))
1848 (format #t "configure flags: ~s~%" flags)
49fdd357 1849 (apply invoke "./configure" flags))))
64dcc289 1850 (add-after 'configure 'clean-local-references
9731c412 1851 (lambda* (#:key outputs #:allow-other-keys)
64dcc289
EB		 1852 (let ((out (assoc-ref outputs "out")))
1853 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
b730b437
EB		 1854 ;; Prevent build directory from leaking into compiled code
1855 (((getcwd)) out)
1856 ;; Scrub timestamp for reproducibility
fafd623e 1857 ((".*Libraries compiled on.*") ""))
9731c412
EB		 1858 (substitute* (find-files "." "petscvariables")
1859 ;; Do not expose build machine characteristics, set to defaults.
1860 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1861 (("NPMAX = [:digit:]+") "NPMAX = 2"))
fafd623e 1862 #t)))
64dcc289 1863 (add-after 'install 'clean-install
10b11968
EB		 1864 ;; Try to keep installed files from leaking build directory names.
1865 (lambda* (#:key inputs outputs #:allow-other-keys)
64dcc289 1866 (let ((out (assoc-ref outputs "out")))
10b11968 1867 (substitute* (map (lambda (file)
9a899cce 1868 (string-append out "/lib/petsc/conf/" file))
fafd623e 1869 '("petscvariables"))
10b11968
EB		 1870 (((getcwd)) out))
1871 ;; Make compiler references point to the store
9a899cce 1872 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
dfdf5716
EB		 1873 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1874 (string-append "= " (which compiler))))
10b11968
EB		 1875 ;; PETSc installs some build logs, which aren't necessary.
1876 (for-each (lambda (file)
9a899cce 1877 (let ((f (string-append out "/lib/petsc/conf/" file)))
10b11968
EB		 1878 (when (file-exists? f)
1879 (delete-file f))))
9a899cce
EB		 1880 '("configure.log" "make.log" "gmake.log"
1881 "test.log" "error.log" "RDict.db"
fafd623e 1882 "PETScBuildInternal.cmake"
10b11968 1883 ;; Once installed, should uninstall with Guix
fafd623e 1884 "uninstall.py"))
a3a99e27
EB		 1885 #t)))
1886 (add-after 'install 'move-examples
1887 (lambda* (#:key outputs #:allow-other-keys)
1888 (let* ((out (assoc-ref outputs "out"))
1889 (examples (assoc-ref outputs "examples"))
1890 (exdir (string-append out "/share/petsc/examples"))
1891 (exdir' (string-append examples "/share/petsc/examples")))
1892 (copy-recursively exdir exdir')
1893 (delete-file-recursively exdir)
fafd623e 1894 #t))))))
b9100e2f 1895 (home-page "http://www.mcs.anl.gov/petsc")
16ecf3ff 1896 (synopsis "Library to solve PDEs")
b9100e2f
EB		 1897 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1898data structures and routines for the scalable (parallel) solution of
1899scientific applications modeled by partial differential equations.")
166191b3 1900 (license (license:non-copyleft
b9100e2f
EB		 1901 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1902
1903(define-public petsc-complex
1904 (package (inherit petsc)
1905 (name "petsc-complex")
1906 (arguments
1907 (substitute-keyword-arguments (package-arguments petsc)
1908 ((#:configure-flags cf)
1909 `(cons "--with-scalar-type=complex" ,cf))))
16ecf3ff 1910 (synopsis "Library to solve PDEs (with complex scalars)")))
183e44ae 1911
d8c7eeb9
EB		 1912(define-public petsc-openmpi
1913 (package (inherit petsc)
1914 (name "petsc-openmpi")
1915 (inputs
9e2aa70b 1916 `(("hdf5" ,hdf5-parallel-openmpi)
af523673 1917 ("hypre" ,hypre-openmpi)
9e2aa70b
PG		 1918 ("metis" ,metis)
1919 ("mumps" ,mumps-openmpi)
1920 ("openmpi" ,openmpi)
1921 ("scalapack" ,scalapack)
72f95783 1922 ("scotch" ,pt-scotch32)
d8c7eeb9
EB		 1923 ,@(package-inputs petsc)))
1924 (arguments
1925 (substitute-keyword-arguments (package-arguments petsc)
1926 ((#:configure-flags cf)
af523673
PG		 1927 ``("--with-hypre=1"
1928 "--with-mpiexec=mpirun"
9e2aa70b
PG		 1929 "--with-metis=1"
1930 "--with-mumps=1"
1931 "--with-scalapack=1"
1932 "--with-ptscotch=1"
d8c7eeb9
EB		 1933 ,(string-append "--with-mpi-dir="
1934 (assoc-ref %build-inputs "openmpi"))
71ca16b5
PG		 1935 ,(string-append "--with-hdf5-include="
1936 (assoc-ref %build-inputs "hdf5") "/include")
1937 ,(string-append "--with-hdf5-lib="
1938 (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
1939 ,@(delete "--with-mpi=0" ,cf)))
1940 ((#:phases phases)
1941 `(modify-phases ,phases
9e2aa70b 1942 (add-before 'configure 'mpi-setup
bbe46a4a 1943 ,%openmpi-setup)))))
9e2aa70b 1944 (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
d8c7eeb9
EB		 1945
1946(define-public petsc-complex-openmpi
1947 (package (inherit petsc-complex)
1948 (name "petsc-complex-openmpi")
1949 (inputs
1950 `(("openmpi" ,openmpi)
1951 ,@(package-inputs petsc-complex)))
1952 (arguments
1953 (substitute-keyword-arguments (package-arguments petsc-complex)
1954 ((#:configure-flags cf)
1955 ``("--with-mpiexec=mpirun"
1956 ,(string-append "--with-mpi-dir="
1957 (assoc-ref %build-inputs "openmpi"))
e586c6fa
EB		 1958 ,@(delete "--with-mpi=0" ,cf)))
1959 ((#:phases phases)
1960 `(modify-phases ,phases
1961 (add-before 'configure 'mpi-setup
1962 ,%openmpi-setup)))))
16ecf3ff 1963 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
d8c7eeb9 1964
90ff2874
PG		 1965(define-public python-petsc4py
1966 (package
1967 (name "python-petsc4py")
758439cf 1968 (version "3.10.1")
90ff2874
PG		 1969 (source
1970 (origin
1971 (method url-fetch)
1972 (uri (pypi-uri "petsc4py" version))
1973 (sha256
1974 (base32
758439cf 1975 "094hcnran0r2z1wlvmjswsz3ski1m9kqrl5l0ax8jjhnk55x0flh"))))
90ff2874
PG		 1976 (build-system python-build-system)
1977 (arguments
1978 `(#:phases
1979 (modify-phases %standard-phases
1980 (add-before 'build 'pre-build
1981 (lambda _
1982 ;; Define path to PETSc installation.
1983 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
1984 #t))
1985 (add-before 'check 'mpi-setup
1986 ,%openmpi-setup))))
1987 (inputs
1988 `(("petsc" ,petsc-openmpi)
1989 ("python-numpy" ,python-numpy)))
1990 (home-page "https://bitbucket.org/petsc/petsc4py/")
1991 (synopsis "Python bindings for PETSc")
1992 (description "PETSc, the Portable, Extensible Toolkit for
1993Scientific Computation, is a suite of data structures and routines for
1994the scalable (parallel) solution of scientific applications modeled by
1995partial differential equations. It employs the MPI standard for all
1996message-passing communication. @code{petsc4py} provides Python
1997bindings to almost all functions of PETSc.")
1998 (license license:bsd-3)))
1999
560acf25
MB		 2000(define-public python-kiwisolver
2001 (package
2002 (name "python-kiwisolver")
2003 (version "1.0.1")
2004 (source (origin
2005 (method url-fetch)
2006 (uri (pypi-uri "kiwisolver" version))
2007 (sha256
2008 (base32
2009 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
2010 (build-system python-build-system)
2011 (home-page "https://github.com/nucleic/kiwi")
2012 (synopsis "Fast implementation of the Cassowary constraint solver")
2013 (description
2014 "Kiwi is an efficient C++ implementation of the Cassowary constraint
2015solving algorithm. Kiwi has been designed from the ground up to be
2016lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
2017Cassowary solver with typical use cases gaining a 40x improvement. Memory
2018savings are consistently > 5x.")
2019 (license license:bsd-3)))
2020
2021(define-public python2-kiwisolver
2022 (package-with-python2 python-kiwisolver))
2023
a7f01414
EB		 2024(define-public slepc
2025 (package
2026 (name "slepc")
a13e0f3d 2027 (version "3.11.1")
a7f01414
EB		 2028 (source
2029 (origin
2030 (method url-fetch)
baeaf882
EB		 2031 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
2032 version ".tar.gz"))
a7f01414
EB		 2033 (sha256
2034 (base32
a13e0f3d 2035 "1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8"))))
a7f01414
EB		 2036 (build-system gnu-build-system)
2037 (native-inputs
a13e0f3d
EB		 2038 `(("python" ,python-2)
2039 ("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
a7f01414
EB		 2040 (inputs
2041 `(("arpack" ,arpack-ng)
2042 ("gfortran" ,gfortran)))
2043 (propagated-inputs
2044 `(("petsc" ,petsc)))
2045 (arguments
2046 `(#:parallel-build? #f ;build is parallel by default
2047 #:configure-flags
2048 `(,(string-append "--with-arpack-dir="
9cf52454 2049 (assoc-ref %build-inputs "arpack") "/lib"))
9731c412 2050 #:make-flags ;honor (parallel-job-count)
a13e0f3d
EB		 2051 `(,(format #f "MAKE_NP=~a" (parallel-job-count))
2052 ,(string-append "PETSCCONFIGDIR="
2053 (assoc-ref %build-inputs "petsc:examples")
2054 "/share/petsc/examples/config"))
a7f01414
EB		 2055 #:phases
2056 (modify-phases %standard-phases
8787c555 2057 (replace 'configure
a7f01414
EB		 2058 ;; configure is a python script, so we can't run it with bash.
2059 (lambda* (#:key inputs outputs (configure-flags '())
2060 #:allow-other-keys)
2061 (let* ((prefix (assoc-ref outputs "out"))
2062 (flags `(,(string-append "--prefix=" prefix)
2063 ,@configure-flags)))
2064 (format #t "build directory: ~s~%" (getcwd))
2065 (format #t "configure flags: ~s~%" flags)
2066 (setenv "SLEPC_DIR" (getcwd))
9cf52454 2067 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
c6840089 2068 (apply invoke "./configure" flags))))
8787c555 2069 (add-after 'install 'delete-doc
a7f01414
EB		 2070 ;; TODO: SLEPc installs HTML documentation alongside headers in
2071 ;; $out/include. We'd like to move them to share/doc, but delete
2072 ;; them for now, as they are incomplete and installing the complete
2073 ;; documentation is difficult.
2074 (lambda* (#:key outputs #:allow-other-keys)
2075 (let* ((out (assoc-ref outputs "out")))
0f6dc120
TGR		 2076 (for-each delete-file (find-files out "\\.html$"))
2077 #t)))
8787c555 2078 (add-after 'install 'clean-install
a7f01414
EB		 2079 ;; Clean up unnecessary build logs from installation.
2080 (lambda* (#:key outputs #:allow-other-keys)
2081 (let ((out (assoc-ref outputs "out")))
2082 (for-each (lambda (file)
2083 (let ((f (string-append out "/lib/slepc/conf/" file)))
2084 (when (file-exists? f)
2085 (delete-file f))))
2086 '("configure.log" "make.log" "gmake.log"
2087 "test.log" "error.log" "RDict.db"
0f6dc120
TGR		 2088 "uninstall.py"))
2089 #t))))))
a7f01414
EB		 2090 (home-page "http://slepc.upv.es")
2091 (synopsis "Scalable library for eigenproblems")
2092 (description "SLEPc is a software library for the solution of large sparse
2093eigenproblems on parallel computers. It can be used for the solution of
2094linear eigenvalue problems formulated in either standard or generalized form,
2095as well as other related problems such as the singular value decomposition.
2096The emphasis of the software is on methods and techniques appropriate for
2097problems in which the associated matrices are sparse, for example, those
2098arising after the discretization of partial differential equations.")
3c524f21 2099 (license license:bsd-2)))
a7f01414
EB		 2100
2101(define-public slepc-complex
2102 (package (inherit slepc)
2103 (name "slepc-complex")
2104 (propagated-inputs
2105 `(("petsc" ,petsc-complex)
2106 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
2107 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
2108
2109(define-public slepc-openmpi
2110 (package (inherit slepc)
2111 (name "slepc-openmpi")
6df2a50a
LC		 2112 (arguments
2113 (substitute-keyword-arguments (package-arguments slepc)
2114 ((#:phases phases '%standard-phases)
2115 `(modify-phases ,phases
bbe46a4a
EB		 2116 (add-before 'check 'mpi-setup
2117 ,%openmpi-setup)))))
a7f01414
EB		 2118 (inputs
2119 `(("mpi" ,openmpi)
2120 ("arpack" ,arpack-ng-openmpi)
2121 ,@(alist-delete "arpack" (package-inputs slepc))))
2122 (propagated-inputs
2123 `(("petsc" ,petsc-openmpi)
2124 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
2125 (synopsis "Scalable library for eigenproblems (with MPI support)")))
2126
2127(define-public slepc-complex-openmpi
2128 (package (inherit slepc-openmpi)
2129 (name "slepc-complex-openmpi")
2130 (propagated-inputs
2131 `(("petsc" ,petsc-complex-openmpi)
2132 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
2133 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
2134
6b5687d0
PG		 2135(define-public python-slepc4py
2136 (package
2137 (name "python-slepc4py")
57d30004 2138 (version "3.10.0")
6b5687d0
PG		 2139 (source
2140 (origin
2141 (method url-fetch)
2142 (uri (pypi-uri "slepc4py" version))
2143 (sha256
2144 (base32
57d30004 2145 "0x049dyc8frgh79fvvavf4vlbqp4mgm61nsaivzdav4316vvlv1j"))))
6b5687d0
PG		 2146 (build-system python-build-system)
2147 (arguments
2148 `(#:phases
2149 (modify-phases %standard-phases
2150 (add-before 'build 'pre-build
2151 (lambda _
2152 ;; Define path to PETSc installation.
2153 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
2154 ;; Define path to SLEPc installation.
2155 (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
2156 #t))
2157 (add-before 'check 'mpi-setup
2158 ,%openmpi-setup))))
2159 (inputs
2160 `(("python-numpy" ,python-numpy)
2161 ("python-petsc4py" ,python-petsc4py)
2162 ("slepc" ,slepc-openmpi)))
2163 (home-page "https://bitbucket.org/slepc/slepc4py/")
2164 (synopsis "Python bindings for SLEPc")
2165 (description "SLEPc, the Scalable Library for Eigenvalue Problem
2166Computations, is based on PETSc, the Portable, Extensible Toolkit for
2167Scientific Computation. It employs the MPI standard for all
2168message-passing communication. @code{slepc4py} provides Python
2169bindings to almost all functions of SLEPc.")
2170 (license license:bsd-3)))
2171
cec86422
EB		 2172(define-public mumps
2173 (package
2174 (name "mumps")
5dbc79eb 2175 (version "5.2.1")
cec86422
EB		 2176 (source
2177 (origin
2178 (method url-fetch)
2179 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
2180 version ".tar.gz"))
2181 (sha256
2182 (base32
5dbc79eb 2183 "0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r"))
06e12395
MB		 2184 (patches (search-patches "mumps-build-parallelism.patch"
2185 "mumps-shared-libseq.patch"
2186 "mumps-shared-mumps.patch"
2187 "mumps-shared-pord.patch"))))
cec86422
EB		 2188 (build-system gnu-build-system)
2189 (inputs
2190 `(("fortran" ,gfortran)
2191 ;; These are required for linking against mumps, but we let the user
2192 ;; declare the dependency.
2193 ("blas" ,openblas)
2194 ("metis" ,metis)
2195 ("scotch" ,scotch)))
2196 (arguments
2197 `(#:modules ((ice-9 match)
2198 (ice-9 popen)
2199 (srfi srfi-1)
2200 ,@%gnu-build-system-modules)
2201 #:phases
2202 (modify-phases %standard-phases
fba78d18 2203 (replace 'configure
cec86422
EB		 2204 (lambda* (#:key inputs #:allow-other-keys)
2205 (call-with-output-file "Makefile.inc"
2206 (lambda (port)
2207 (format port "
2208PLAT =
2209LIBEXT = .a
2210OUTC = -o
2211OUTF = -o
2212RM = rm -f~:[
2213CC = gcc
2214FC = gfortran
2215FL = gfortran
2216INCSEQ = -I$(topdir)/libseq
06e12395 2217LIBSEQ = $(topdir)/libseq/libmpiseq.a
cec86422
EB		 2218LIBSEQNEEDED = libseqneeded~;
2219CC = mpicc
2220FC = mpifort
2221FL = mpifort~]
2222AR = ar vr # rules require trailing space, ugh...
2223RANLIB = ranlib
06e12395
MB		 2224BLASDIR = ~a
2225LIBBLAS = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[
2226SCALAPDIR = ~a
2227SCALAP = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~]
cec86422
EB		 2228LIBOTHERS = -pthread
2229CDEFS = -DAdd_
2230PIC = -fPIC
2231OPTF = -O2 -DALLOW_NON_INIT $(PIC)
2232OPTL = -O2 $(PIC)
2233OPTC = -O2 $(PIC)
2234INCS = $(INCSEQ)
2235LIBS = $(SCALAP) $(LIBSEQ)
2236LPORDDIR = $(topdir)/PORD/lib
2237IPORD = -I$(topdir)/PORD/include
06e12395 2238LPORD = $(LPORDDIR)/libpord.a
cec86422
EB		 2239ORDERINGSF = -Dpord~@[
2240METISDIR = ~a
2241IMETIS = -I$(METISDIR)/include
06e12395 2242LMETIS = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
cec86422
EB		 2243ORDERINGSF += -Dmetis~]~@[~:{
2244SCOTCHDIR = ~a
2245ISCOTCH = -I$(SCOTCHDIR)/include
06e12395 2246LSCOTCH = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
cec86422
EB		 2247ORDERINGSF += ~a~}~]
2248ORDERINGSC = $(ORDERINGSF)
06e12395 2249LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
cec86422
EB		 2250IORDERINGSF = $(ISCOTCH)
2251IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
2252 (assoc-ref inputs "mpi")
2253 (assoc-ref inputs "blas")
2254 (assoc-ref inputs "scalapack")
2255 (assoc-ref inputs "metis")
2256 (match (list (assoc-ref inputs "pt-scotch")
2257 (assoc-ref inputs "scotch"))
2258 ((#f #f)
2259 #f)
2260 ((#f scotch)
2261 `((,scotch "" "-Dscotch")))
2262 ((ptscotch _)
2263 `((,ptscotch
2264 "-lptesmumps -lptscotch -lptscotcherr "
2265 "-Dptscotch")))))))))
fba78d18 2266 (replace 'build
cec86422
EB		 2267 ;; By default only the d-precision library is built. Make with "all"
2268 ;; target so that all precision libraries and examples are built.
2269 (lambda _
b414cf52
TGR		 2270 (invoke "make" "all"
2271 (format #f "-j~a" (parallel-job-count)))))
fba78d18 2272 (replace 'check
cec86422
EB		 2273 ;; Run the simple test drivers, which read test input from stdin:
2274 ;; from the "real" input for the single- and double-precision
2275 ;; testers, and from the "cmplx" input for complex-precision
2276 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
2277 ;; package to prefix execution with "mpirun".
2278 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
2279 (with-directory-excursion "examples"
2280 (every
2281 (lambda (prec type)
2282 (let ((tester (apply open-pipe*
2283 `(,OPEN_WRITE
2284 ,@exec-prefix
2285 ,(string-append "./" prec
2286 "simpletest"))))
2287 (input (open-input-file
2288 (string-append "input_simpletest_" type))))
2289 (begin
2290 (dump-port input tester)
2291 (close-port input)
2292 (zero? (close-pipe tester)))))
2293 '("s" "d" "c" "z")
2294 '("real" "real" "cmplx" "cmplx")))))
fba78d18
EB		 2295 (replace 'install
2296 (lambda* (#:key outputs #:allow-other-keys)
2297 (let* ((out (assoc-ref outputs "out"))
2298 (libdir (string-append out "/lib")))
2299 (copy-recursively "lib" libdir)
2300 (copy-recursively "include" (string-append out "/include"))
2301 (when (file-exists? "libseq/libmpiseq.a")
2302 (install-file "libseq/libmpiseq.a" libdir))
06e12395
MB		 2303 (when (file-exists? "libseq/libmpiseq.so")
2304 (install-file "libseq/libmpiseq.so" libdir))
fba78d18 2305 #t))))))
cec86422
EB		 2306 (home-page "http://mumps.enseeiht.fr")
2307 (synopsis "Multifrontal sparse direct solver")
2308 (description
2309 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
57e69c1d 2310sparse system of linear equations A x = b using Gaussian elimination.")
cec86422
EB		 2311 (license license:cecill-c)))
2312
2313(define-public mumps-metis
2314 (package (inherit mumps)
2315 (name "mumps-metis")
2316 (inputs
2317 (alist-delete "scotch" (package-inputs mumps)))))
2318
2319(define-public mumps-openmpi
2320 (package (inherit mumps)
2321 (name "mumps-openmpi")
2322 (inputs
2323 `(("mpi" ,openmpi)
2324 ("scalapack" ,scalapack)
2325 ("pt-scotch" ,pt-scotch)
2326 ,@(alist-delete "scotch" (package-inputs mumps))))
2327 (arguments
2328 (substitute-keyword-arguments (package-arguments mumps)
2329 ((#:phases phases)
2330 `(modify-phases ,phases
bbe46a4a
EB		 2331 (add-before 'check 'mpi-setup
2332 ,%openmpi-setup)
6df2a50a
LC		 2333 (replace 'check
2334 (lambda _
2335 ((assoc-ref ,phases 'check)
2336 #:exec-prefix '("mpirun" "-n" "2"))))))))
cec86422
EB		 2337 (synopsis "Multifrontal sparse direct solver (with MPI)")))
2338
2339(define-public mumps-metis-openmpi
2340 (package (inherit mumps-openmpi)
2341 (name "mumps-metis-openmpi")
2342 (inputs
2343 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
2344
63e07468
BW		 2345(define-public ruby-asciimath
2346 (package
2347 (name "ruby-asciimath")
2348 (version "1.0.4")
2349 (source
2350 (origin
2351 (method url-fetch)
2352 (uri (rubygems-uri "asciimath" version))
2353 (sha256
2354 (base32
2355 "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
2356 (build-system ruby-build-system)
2357 (arguments
2358 '(#:phases
2359 (modify-phases %standard-phases
2360 ;; Apply this patch
2361 ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
2362 (add-after 'unpack 'patch-remove-spurious-backslashes
2363 (lambda _
2364 (substitute* "spec/parser_spec.rb"
2365 (("\\\\\"")
9923d5a4
TGR		 2366 "\""))
2367 #t)))))
63e07468
BW		 2368 (native-inputs
2369 `(("bundler" ,bundler)
2370 ("ruby-rspec" ,ruby-rspec)))
2371 (synopsis "AsciiMath parsing and conversion library")
2372 (description
2373 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
2374easy-to-write markup language for mathematics.")
2375 (home-page "https://github.com/asciidoctor/asciimath")
2376 (license license:expat)))
2377
183e44ae
EB		 2378(define-public superlu
2379 (package
2380 (name "superlu")
995a09e0 2381 (version "5.2.1")
183e44ae
EB		 2382 (source
2383 (origin
2384 (method url-fetch)
2385 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2386 "superlu_" version ".tar.gz"))
2387 (sha256
995a09e0
EB		 2388 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
2389 (modules '((guix build utils)))
2390 (snippet
2391 ;; Replace the non-free implementation of MC64 with a stub adapted
2392 ;; from Debian
2393 '(begin
2394 (use-modules (ice-9 regex)
2395 (ice-9 rdelim))
2396 (call-with-output-file "SRC/mc64ad.c"
2397 (lambda (port)
2398 (display "
2399#include <stdio.h>
2400#include <stdlib.h>
2401void mc64id_(int *a) {
2402 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2403 abort ();
2404}
2405void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2406 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2407 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2408 abort ();
2409}\n" port)))
2410 ;; Remove the corresponding license verbiage. MC64 license follows
2411 ;; a "------" line separator.
2412 (with-atomic-file-replacement "License.txt"
2413 (let ((rx (make-regexp "-{8}")))
2414 (lambda (in out)
2415 (let loop ()
2416 (let ((line (read-line in 'concat)))
2417 (unless (regexp-exec rx line)
2418 (display line out)
6cbee49d
MW		 2419 (loop))))
2420 #t)))))))
995a09e0 2421 (build-system cmake-build-system)
183e44ae
EB		 2422 (native-inputs
2423 `(("tcsh" ,tcsh)))
2424 (inputs
995a09e0 2425 `(("blas" ,openblas)
19afbea1 2426 ("gfortran" ,gfortran)))
183e44ae 2427 (arguments
995a09e0
EB		 2428 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2429 "-DTPL_BLAS_LIBRARIES=openblas"
677bc34d 2430 "-DBUILD_SHARED_LIBS:BOOL=YES")))
183e44ae
EB		 2431 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
2432 (synopsis "Supernodal direct solver for sparse linear systems")
2433 (description
2434 "SuperLU is a general purpose library for the direct solution of large,
2435sparse, nonsymmetric systems of linear equations on high performance machines.
2436The library is written in C and is callable from either C or Fortran. The
2437library routines perform an LU decomposition with partial pivoting and
2438triangular system solves through forward and back substitution. The library
2439also provides threshold-based ILU factorization preconditioners.")
995a09e0
EB		 2440 (license (list license:bsd-3
2441 license:gpl2+ ;EXAMPLE/*fgmr.c
2442 (license:fsf-free "file://SRC/colamd.h")))))
f8ed036a 2443
a54aefea
EB		 2444(define-public superlu-dist
2445 (package
2446 (name "superlu-dist")
6161141e 2447 (version "6.1.0")
a54aefea
EB		 2448 (source
2449 (origin
2450 (method url-fetch)
2451 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2452 "superlu_dist_" version ".tar.gz"))
2453 (sha256
6161141e 2454 (base32 "0pqgcgh1yxhfzs99fas3mggajzd5wca3nbyp878rziy74gfk03dl"))
0921eff2 2455 (modules '((guix build utils)))
29080870
EB		 2456 (snippet
2457 ;; Replace the non-free implementation of MC64 with a stub
2458 '(begin
0921eff2 2459 (call-with-output-file "SRC/mc64ad_dist.c"
29080870
EB		 2460 (lambda (port)
2461 (display "
2462#include <stdio.h>
2463#include <stdlib.h>
0921eff2 2464void mc64id_dist(int *a) {
29080870
EB		 2465 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2466 abort ();
2467}
0921eff2 2468void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
29080870
EB		 2469 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2470 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2471 abort ();
2472}\n" port)))
29080870 2473 (substitute* "SRC/util.c" ;adjust default algorithm
6161141e
EB		 2474 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
2475 ;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
2476 ;; general (i.e. non-square) processor-grid support.
2477 "RowPerm = NOROWPERM;"))
6cbee49d 2478 #t))
6161141e 2479 (patches (search-patches "superlu-dist-scotchmetis.patch"
2bdf26f1
EB		 2480 "superlu-dist-awpm-grid.patch"
2481 "superlu-dist-fix-mpi-deprecations.patch"))))
6161141e 2482 (build-system cmake-build-system)
a54aefea
EB		 2483 (native-inputs
2484 `(("tcsh" ,tcsh)))
2485 (inputs
6161141e
EB		 2486 `(("gfortran" ,gfortran)
2487 ("blas" ,openblas)
2488 ("lapack" ,lapack)
2489 ("combblas" ,combinatorial-blas)))
a54aefea 2490 (propagated-inputs
6161141e
EB		 2491 `(("mpi" ,openmpi) ;headers include MPI heades
2492 ("parmetis" ,pt-scotch32 "metis")
2493 ("pt-scotch" ,pt-scotch32)))
a54aefea 2494 (arguments
6161141e
EB		 2495 `(#:parallel-tests? #f ;tests use MPI and OpenMP
2496 #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
2497 "-DTPL_ENABLE_COMBBLASLIB=YES"
2498 "-DTPL_BLAS_LIBRARIES=-lopenblas"
2499 "-DTPL_LAPACK_LIBRARIES=-llapack"
2500 (string-append "-DTPL_PARMETIS_LIBRARIES="
2501 (string-join
2502 '("ptscotchparmetis" "ptscotch" "ptscotcherr"
2503 "scotchmetis" "scotch" "scotcherr")
2504 ";"))
2505 (string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
2506 (assoc-ref %build-inputs "parmetis")
2507 "/include")
2508 "-DTPL_ENABLE_COMBBLASLIB=ON"
2509 (string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
2510 (assoc-ref %build-inputs "combblas")
2511 "/include/CombBLAS;"
2512 (assoc-ref %build-inputs "combblas")
2513 "/include/BipartiteMatchings")
2514 "-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
a54aefea 2515 #:phases
dc1d3cde 2516 (modify-phases %standard-phases
6161141e 2517 (add-before 'configure 'set-c++-standard
dc1d3cde 2518 (lambda _
6161141e
EB		 2519 (substitute* "CMakeLists.txt"
2520 ;; AWPM headers require C++14
2521 (("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
bbe46a4a
EB		 2522 (add-before 'check 'mpi-setup
2523 ,%openmpi-setup)
6161141e
EB		 2524 (add-before 'check 'omp-setup
2525 (lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
a54aefea
EB		 2526 (home-page (package-home-page superlu))
2527 (synopsis "Parallel supernodal direct solver")
2528 (description
2529 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2530It is targeted for distributed memory parallel machines. SuperLU_DIST is
2531implemented in ANSI C, and MPI for communications.")
2532 (license license:bsd-3)))
2533
f8ed036a
EB		 2534(define-public scotch
2535 (package
2536 (name "scotch")
fd373343 2537 (version "6.0.6")
f8ed036a
EB		 2538 (source
2539 (origin
2540 (method url-fetch)
1dc31097
TGR		 2541 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
2542 "latestfile/298/scotch_" version ".tar.gz"))
f8ed036a 2543 (sha256
fd373343
EB		 2544 (base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8"))
2545 (patches (search-patches "scotch-build-parallelism.patch"
2546 "scotch-integer-declarations.patch"))))
f8ed036a
EB		 2547 (build-system gnu-build-system)
2548 (inputs
2549 `(("zlib" ,zlib)
5e54f4ad 2550 ("flex" ,flex)
f8ed036a 2551 ("bison" ,bison)))
fd373343 2552 (outputs '("out" "metis"))
f8ed036a 2553 (arguments
fd373343
EB		 2554 `(#:make-flags (list (string-append "prefix=" %output))
2555 #:phases
d6602ee9
EB		 2556 (modify-phases %standard-phases
2557 (add-after
2558 'unpack 'chdir-to-src
d67a7e9e 2559 (lambda _ (chdir "src") #t))
d6602ee9
EB		 2560 (replace
2561 'configure
2562 (lambda _
2563 (call-with-output-file "Makefile.inc"
2564 (lambda (port)
2565 (format port "
f8ed036a
EB		 2566EXE =
2567LIB = .a
2568OBJ = .o
2569MAKE = make
2570AR = ar
2571ARFLAGS = -ruv
cf0ec6c4 2572CAT = cat
f8ed036a
EB		 2573CCS = gcc
2574CCP = mpicc
2575CCD = gcc
2576CPPFLAGS =~{ -D~a~}
6c798540 2577CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
f8ed036a
EB		 2578LDFLAGS = -lz -lm -lrt -lpthread
2579CP = cp
2580LEX = flex -Pscotchyy -olex.yy.c
2581LN = ln
2582MKDIR = mkdir
2583MV = mv
2584RANLIB = ranlib
2585YACC = bison -pscotchyy -y -b y
2586"
d6602ee9
EB		 2587 '("COMMON_FILE_COMPRESS_GZ"
2588 "COMMON_PTHREAD"
2589 "COMMON_RANDOM_FIXED_SEED"
fd373343 2590 "INTSIZE64" ;use 'int64_t'
cf0ec6c4
EB		 2591 ;; Prevents symbolc clashes with libesmumps
2592 "SCOTCH_RENAME"
d6602ee9
EB		 2593 ;; XXX: Causes invalid frees in superlu-dist tests
2594 ;; "SCOTCH_PTHREAD"
2595 ;; "SCOTCH_PTHREAD_NUMBER=2"
d67a7e9e
TGR		 2596 "restrict=__restrict"))))
2597 #t))
bbe46a4a 2598 (add-after 'build 'build-esmumps
cf0ec6c4 2599 (lambda _
d67a7e9e
TGR		 2600 (invoke "make"
2601 (format #f "-j~a" (parallel-job-count))
2602 "esmumps")))
fd373343
EB		 2603 (add-before 'install 'make-install-dirs
2604 (lambda* (#:key outputs #:allow-other-keys)
2605 (mkdir (assoc-ref outputs "out"))))
2606 (add-after 'install 'install-metis
2607 (lambda* (#:key outputs #:allow-other-keys)
2608 (let ((out (assoc-ref outputs "metis")))
2609 (mkdir out)
2610 ;; metis files are not installed with 'make install'
2611 (for-each (lambda (f)
2612 (install-file f (string-append out "/include")))
2613 (find-files "../include/" ".*metis\\.h"))
2614 (for-each (lambda (f)
2615 (install-file f (string-append out "/lib")))
2616 (find-files "../lib/" ".*metis\\..*"))
2617 #t))))))
f8ed036a
EB		 2618 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
2619 (synopsis "Programs and libraries for graph algorithms")
2620 (description "SCOTCH is a set of programs and libraries which implement
2621the static mapping and sparse matrix reordering algorithms developed within
2622the SCOTCH project. Its purpose is to apply graph theory, with a divide and
2623conquer approach, to scientific computing problems such as graph and mesh
2624partitioning, static mapping, and sparse matrix ordering, in application
2625domains ranging from structural mechanics to operating systems or
2626bio-chemistry.")
2627 ;; See LICENSE_en.txt
2628 (license license:cecill-c)))
6acb4adb 2629
1c39f3b8
PG		 2630(define-public scotch32
2631 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2632 ;; some applications.
2633 (package (inherit scotch)
2634 (name "scotch32")
2635 (arguments
2636 (substitute-keyword-arguments (package-arguments scotch)
2637 ((#:phases scotch-phases)
2638 `(modify-phases ,scotch-phases
2639 (replace
2640 'configure
2641 (lambda _
2642 (call-with-output-file "Makefile.inc"
2643 (lambda (port)
2644 (format port "
2645EXE =
2646LIB = .a
2647OBJ = .o
2648MAKE = make
2649AR = ar
2650ARFLAGS = -ruv
2651CAT = cat
2652CCS = gcc
2653CCP = mpicc
2654CCD = gcc
2655CPPFLAGS =~{ -D~a~}
2656CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2657LDFLAGS = -lz -lm -lrt -lpthread
2658CP = cp
2659LEX = flex -Pscotchyy -olex.yy.c
2660LN = ln
2661MKDIR = mkdir
2662MV = mv
2663RANLIB = ranlib
2664YACC = bison -pscotchyy -y -b y
2665"
2666 '("COMMON_FILE_COMPRESS_GZ"
2667 "COMMON_PTHREAD"
2668 "COMMON_RANDOM_FIXED_SEED"
2669 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
2670 ;; Prevents symbolc clashes with libesmumps
2671 "SCOTCH_RENAME"
2672 ;; XXX: Causes invalid frees in superlu-dist tests
2673 ;; "SCOTCH_PTHREAD"
2674 ;; "SCOTCH_PTHREAD_NUMBER=2"
2675 "restrict=__restrict"))))))))))
2676 (synopsis
2677 "Programs and libraries for graph algorithms (32-bit integers)")))
2678
6acb4adb
EB		 2679(define-public pt-scotch
2680 (package (inherit scotch)
2681 (name "pt-scotch")
2682 (propagated-inputs
2683 `(("openmpi" ,openmpi))) ;Headers include MPI headers
2684 (arguments
2685 (substitute-keyword-arguments (package-arguments scotch)
2686 ((#:phases scotch-phases)
d6602ee9
EB		 2687 `(modify-phases ,scotch-phases
2688 (replace
2689 'build
d6602ee9 2690 (lambda _
c491f7f8
LC		 2691 (invoke "make" (format #f "-j~a" (parallel-job-count))
2692 "ptscotch" "ptesmumps")
2693
2694 ;; Install the serial metis compatibility library
2695 (invoke "make" "-C" "libscotchmetis" "install")))
2696 (add-before 'check 'mpi-setup
2697 ,%openmpi-setup)
2698 (replace 'check
2699 (lambda _
2700 (invoke "make" "ptcheck")))))))
6acb4adb 2701 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
5698b8b8 2702
1c25a52c
PG		 2703(define-public pt-scotch32
2704 (package (inherit scotch32)
2705 (name "pt-scotch32")
2706 (propagated-inputs
2707 `(("openmpi" ,openmpi))) ;headers include MPI headers
2708 (arguments
c4d4a779
PG		 2709 (substitute-keyword-arguments (package-arguments scotch32)
2710 ((#:phases scotch32-phases)
2711 `(modify-phases ,scotch32-phases
1c25a52c
PG		 2712 (replace 'build
2713 (lambda _
c491f7f8
LC		 2714 (invoke "make" (format #f "-j~a" (parallel-job-count))
2715 "ptscotch" "ptesmumps")
2716 ;; Install the serial metis compatibility library
2717 (invoke "make" "-C" "libscotchmetis" "install")))
2718 (add-before 'check 'mpi-setup
2719 ,%openmpi-setup)
1c25a52c
PG		 2720 (replace 'check
2721 (lambda _
c491f7f8 2722 (invoke "make" "ptcheck")))))))
1c25a52c
PG		 2723 (synopsis
2724 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2725
aa75ad00
EB		 2726(define-public metis
2727 (package
2728 (name "metis")
2729 (version "5.1.0")
2730 (source
2731 (origin
2732 (method url-fetch)
2733 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2734 "metis-" version ".tar.gz"))
2735 (sha256
2736 (base32
2737 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2738 (build-system cmake-build-system)
2739 (inputs
2740 `(("blas" ,openblas)))
2741 (arguments
2742 `(#:tests? #f ;no tests
2743 #:configure-flags `("-DSHARED=ON"
2744 ,(string-append "-DGKLIB_PATH=" (getcwd)
2745 "/metis-" ,version "/GKlib"))))
2746 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2747 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2748 (description
2749 "METIS is a set of serial programs for partitioning graphs, partitioning
2750finite element meshes, and producing fill-reducing orderings for sparse
2751matrices. The algorithms implemented in METIS are based on the multilevel
2752recursive-bisection, multilevel k-way, and multi-constraint partitioning
2753schemes.")
2754 (license license:asl2.0))) ;As of version 5.0.3
2755
700ff222
EB		 2756(define-public p4est
2757 (package
2758 (name "p4est")
4150da63 2759 (version "2.0")
700ff222
EB		 2760 (source
2761 (origin
2762 (method url-fetch)
2763 (uri (string-append "http://p4est.github.io/release/p4est-"
2764 version ".tar.gz"))
2765 (sha256
2766 (base32
4150da63 2767 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
700ff222
EB		 2768 (build-system gnu-build-system)
2769 (inputs
2770 `(("fortran" ,gfortran)
2771 ("blas" ,openblas)
2772 ("lapack" ,lapack)
2773 ("zlib" ,zlib)))
2774 (arguments
2775 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2776 (assoc-ref %build-inputs "blas")
2777 " -lopenblas")
2778 ,(string-append "LAPACK_LIBS=-L"
2779 (assoc-ref %build-inputs "lapack")
6df2a50a
LC		 2780 " -llapack"))
2781 #:phases (modify-phases %standard-phases
bbe46a4a
EB		 2782 (add-before 'check 'mpi-setup
2783 ,%openmpi-setup))))
700ff222
EB		 2784 (home-page "http://www.p4est.org")
2785 (synopsis "Adaptive mesh refinement on forests of octrees")
2786 (description
2787 "The p4est software library enables the dynamic management of a
2788collection of adaptive octrees, conveniently called a forest of octrees.
2789p4est is designed to work in parallel and scales to hundreds of thousands of
2790processor cores.")
2791 (license license:gpl2+)))
2792
2793(define-public p4est-openmpi
2794 (package (inherit p4est)
2795 (name "p4est-openmpi")
2796 (inputs
2797 `(("mpi" ,openmpi)
2798 ,@(package-inputs p4est)))
2799 (arguments
2800 (substitute-keyword-arguments (package-arguments p4est)
2801 ((#:configure-flags cf)
2802 ``("--enable-mpi" ,@,cf))))
2803 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2804
5698b8b8
JD		 2805(define-public gsegrafix
2806 (package
2807 (name "gsegrafix")
2808 (version "1.0.6")
2809 (source
2810 (origin
2811 (method url-fetch)
2812 (uri (string-append "mirror://gnu/" name "/" name "-"
2813 version ".tar.gz"))
2814 (sha256
2815 (base32
2816 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2817 (build-system gnu-build-system)
2818 (arguments
2819 `(#:configure-flags '("LDFLAGS=-lm")))
2820 (inputs
2821 `(("libgnomecanvas" ,libgnomecanvas)
2822 ("libbonoboui" ,libbonoboui)
2823 ("libgnomeui" ,libgnomeui)
2824 ("libgnomeprintui" ,libgnomeprintui)
2825 ("popt" ,popt)))
2826 (native-inputs
2827 `(("pkg-config" ,pkg-config)))
6fd52309 2828 (home-page "https://www.gnu.org/software/gsegrafix/")
5698b8b8
JD		 2829 (synopsis "GNOME application to create scientific and engineering plots")
2830 (description "GSEGrafix is an application which produces high-quality graphical
2831plots for science and engineering. Plots are specified via simple ASCII
2832parameter files and data files and are presented in an anti-aliased GNOME
2833canvas. The program supports rectangular two-dimensional plots, histograms,
2834polar-axis plots and three-dimensional plots. Plots can be printed or saved
2835to BMP, JPEG or PNG image formats.")
2836 (license license:gpl3+)))
8731e527
JD		 2837
2838(define-public maxima
2839 (package
2840 (name "maxima")
ccc963d5 2841 (version "5.43.0")
8731e527
JD		 2842 (source
2843 (origin
2844 (method url-fetch)
2845 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2846 version "-source/" name "-" version ".tar.gz"))
2847 (sha256
2848 (base32
ccc963d5 2849 "0xyahp4c6509haxh4n1swiqm3421gplkdisa0zypclh3252sbzfw"))
fc1adab1 2850 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
8731e527 2851 (build-system gnu-build-system)
df354a77 2852 (inputs
6b2eafaa 2853 `(("gcl" ,gcl)
df354a77 2854 ("gnuplot" ,gnuplot) ;for plots
fc9c47bd 2855 ("sed" ,sed)
f36afe4d 2856 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
df354a77
FB		 2857 (native-inputs
2858 `(("texinfo" ,texinfo)
ccbc5758
KK		 2859 ("perl" ,perl)
2860 ("python" ,python)))
8731e527 2861 (arguments
df354a77
FB		 2862 `(#:configure-flags
2863 (list "--enable-gcl"
2864 (string-append "--with-posix-shell="
2865 (assoc-ref %build-inputs "bash")
2866 "/bin/sh")
2867 (string-append "--with-wish="
2868 (assoc-ref %build-inputs "tk")
2869 "/bin/wish"
2870 (let ((v ,(package-version tk)))
2871 (string-take v (string-index-right v #\.)))))
df354a77 2872 ;; By default Maxima attempts to write temporary files to
77af7b24
MW		 2873 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2874 ;; Work around that.
df354a77 2875 #:make-flags (list "TMPDIR=/tmp")
0093b126
KK		 2876 #:phases
2877 (modify-phases %standard-phases
fc9c47bd
KK		 2878 (add-after 'unpack 'patch-paths
2879 (lambda* (#:key inputs #:allow-other-keys)
2880 (let* ((sed (string-append (assoc-ref inputs "sed") "/bin/sed"))
2881 (coreutils (assoc-ref inputs "coreutils"))
2882 (dirname (string-append coreutils "/bin/dirname"))
ccc963d5
KK		 2883 (head (string-append coreutils "/bin/head"))
2884 (perl (string-append (assoc-ref inputs "perl") "/bin/perl"))
2885 (python (string-append (assoc-ref inputs "python")
2886 "/bin/python3")))
fc9c47bd
KK		 2887 (substitute* "src/maxima.in"
2888 (("sed ") (string-append sed " "))
2889 (("dirname") dirname)
2890 (("head") head))
ccc963d5
KK		 2891 (substitute* "doc/info/Makefile.in"
2892 (("/usr/bin/env perl") perl))
2893 (substitute* "doc/info/build_html.sh.in"
2894 (("python") python))
fc9c47bd 2895 #t)))
0093b126
KK		 2896 (add-before 'check 'pre-check
2897 (lambda _
2898 (chmod "src/maxima" #o555)
2899 #t))
1472d19a
KK		 2900 (replace 'check
2901 (lambda _
2902 ;; This is derived from the testing code in the "debian/rules" file
2903 ;; of Debian's Maxima package.
2904 ;; If Maxima can successfully run this, the binary to be installed
2905 ;; should be fine.
df129041
MW		 2906 (invoke "sh" "-c"
2907 (string-append
2908 "./maxima-local "
2909 "--lisp=gcl "
2910 "--batch-string=\"run_testsuite();\" "
2911 "| grep -q \"No unexpected errors found\""))))
0093b126
KK		 2912 ;; Make sure the doc and emacs files are found in the
2913 ;; standard location. Also configure maxima to find gnuplot
2914 ;; without having it on the PATH.
2915 (add-after 'install 'post-install
2916 (lambda* (#:key outputs inputs #:allow-other-keys)
2917 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2918 (out (assoc-ref outputs "out"))
2919 (datadir (string-append out "/share/maxima/" ,version))
2920 (binutils (string-append (assoc-ref inputs "binutils")
2921 "/bin")))
2922 (with-directory-excursion out
2923 (mkdir-p "share/emacs")
2924 (mkdir-p "share/doc")
0093b126
KK		 2925 (symlink
2926 (string-append datadir "/doc/")
2927 (string-append out "/share/doc/maxima"))
2928 (with-atomic-file-replacement
2929 (string-append datadir "/share/maxima-init.lisp")
2930 (lambda (in out)
2931 (format out "~a ~s~a~%"
2932 "(setf $gnuplot_command "
2933 (string-append gnuplot "/bin/gnuplot") ")")
2934 (dump-port in out))))
2935 ;; Ensure that Maxima will have access to the GNU binutils
2936 ;; components at runtime.
2937 (wrap-program (string-append out "/bin/maxima")
2938 `("PATH" prefix (,binutils))))
2939 #t)))))
8731e527
JD		 2940 (home-page "http://maxima.sourceforge.net")
2941 (synopsis "Numeric and symbolic expression manipulation")
2942 (description "Maxima is a system for the manipulation of symbolic and
2943numerical expressions. It yields high precision numeric results by using
2944exact fractions, arbitrary precision integers, and variable precision floating
e881752c 2945point numbers.")
8731e527
JD		 2946 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2947 ;; Others simply say "GNU General Public License" without stating a
2948 ;; version (which implicitly means gpl1+).
2949 ;; At least one file (src/maxima.asd) says "version 2."
2950 ;; GPLv2 only is therefore the smallest subset.
f36afe4d 2951 (license license:gpl2)))
ec322be2 2952
9aafbc0c
MW		 2953(define-public wxmaxima
2954 (package
2955 (name "wxmaxima")
1e8609f2 2956 (version "19.11.1")
9aafbc0c
MW		 2957 (source
2958 (origin
c93b77ad
KK		 2959 (method git-fetch)
2960 (uri (git-reference
2961 (url "https://github.com/wxMaxima-developers/wxmaxima.git")
2962 (commit (string-append "Version-" version))))
2963 (file-name (git-file-name name version))
9aafbc0c 2964 (sha256
1e8609f2 2965 (base32 "16xizaddb27432n1083y89ir5zdqvllsgbwrzzk4jc2rw1ldxfsv"))))
0181df53 2966 (build-system cmake-build-system)
5143517c 2967 (native-inputs
0181df53 2968 `(("gettext" ,gettext-minimal)))
9aafbc0c
MW		 2969 (inputs
2970 `(("wxwidgets" ,wxwidgets)
de477809
SB		 2971 ("maxima" ,maxima)
2972 ;; Runtime support.
2973 ("adwaita-icon-theme" ,adwaita-icon-theme)
2974 ("gtk+" ,gtk+)
2975 ("shared-mime-info" ,shared-mime-info)))
9aafbc0c 2976 (arguments
0181df53
KK		 2977 `(#:tests? #f ; no check target
2978 #:phases
ac2ddcc6 2979 (modify-phases %standard-phases
ac2ddcc6
KK		 2980 (add-after 'install 'wrap-program
2981 (lambda* (#:key inputs outputs #:allow-other-keys)
2982 (wrap-program (string-append (assoc-ref outputs "out")
2983 "/bin/wxmaxima")
2984 `("PATH" ":" prefix
2985 (,(string-append (assoc-ref inputs "maxima")
2986 "/bin")))
2987 ;; For GtkFileChooserDialog.
2988 `("GSETTINGS_SCHEMA_DIR" =
2989 (,(string-append (assoc-ref inputs "gtk+")
2990 "/share/glib-2.0/schemas")))
2991 `("XDG_DATA_DIRS" ":" prefix
2992 (;; Needed by gdk-pixbuf to know supported icon formats.
2993 ,(string-append
2994 (assoc-ref inputs "shared-mime-info") "/share")
2995 ;; The default icon theme of GTK+.
2996 ,(string-append
2997 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
2998 #t)))))
9aafbc0c
MW		 2999 (home-page "https://andrejv.github.io/wxmaxima/")
3000 (synopsis "Graphical user interface for the Maxima computer algebra system")
3001 (description
3002 "wxMaxima is a graphical user interface for the Maxima computer algebra
3003system. It eases the use of Maxima by making most of its commands available
3004through a menu system and by providing input dialogs for commands that require
3005more than one argument. It also implements its own display engine that
3006outputs mathematical symbols directly instead of depicting them with ASCII
3007characters.
3008
3009wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
3010text and mathematical calculations to create documents, exporting of input and
3011output to TeX, and a browser for Maxima's manual including command index and
3012full text searching.")
3013 (license license:gpl2+)))
3014
b15e47f9
RW		 3015(define-public armadillo
3016 (package
3017 (name "armadillo")
f133e244 3018 (version "9.100.5")
b15e47f9
RW		 3019 (source (origin
3020 (method url-fetch)
3021 (uri (string-append "mirror://sourceforge/arma/armadillo-"
7397cd9e 3022 version ".tar.xz"))
b15e47f9
RW		 3023 (sha256
3024 (base32
f133e244 3025 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
b15e47f9 3026 (build-system cmake-build-system)
e405c0bc 3027 (arguments `(#:tests? #f)) ; no test target
b15e47f9
RW		 3028 (inputs
3029 `(("openblas" ,openblas)
3030 ("lapack" ,lapack)
3031 ("arpack" ,arpack-ng)))
3032 (home-page "http://arma.sourceforge.net/")
3033 (synopsis "C++ linear algebra library")
3034 (description
3035 "Armadillo is a C++ linear algebra library, aiming towards a good balance
3036between speed and ease of use. It is useful for algorithm development
3037directly in C++, or quick conversion of research code into production
3038environments. It can be used for machine learning, pattern recognition,
3039signal processing, bioinformatics, statistics, econometrics, etc. The library
3040provides efficient classes for vectors, matrices and cubes, as well as 150+
3041associated functions (eg. contiguous and non-contiguous submatrix views).")
fe418cc5 3042 (license license:asl2.0)))
b15e47f9 3043
279663ef 3044(define-public muparser
d7cff656
LF		 3045 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
3046 ;; different hash. In order to make `guix package --upgrade` work correctly,
3047 ;; we set a Guix packaging revision.
3048 ;; When the next version of muparser is released, we can remove
3049 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
3050 (let ((upstream-version "2.2.5")
3051 (revision "2"))
3052 (package
3053 (name "muparser")
3054 (version (string-append upstream-version "-" revision))
3055 (source
3056 (origin
67f1db38
TGR		 3057 (method git-fetch)
3058 (uri (git-reference
3059 (url "https://github.com/beltoforion/muparser.git")
3060 (commit (string-append "v" upstream-version))))
3061 (file-name (git-file-name name version))
d7cff656 3062 (sha256
67f1db38 3063 (base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24"))))
d7cff656
LF		 3064 (build-system gnu-build-system)
3065 (arguments
3066 `(#:configure-flags '("--enable-samples=no")
3067 #:tests? #f)) ;no "check" target
3068 (home-page "http://muparser.beltoforion.de/")
3069 (synopsis "Fast parser library for mathematical expressions")
3070 (description
3071 "muParser is an extensible high performance math parser library. It is
3072based on transforming an expression into a bytecode and precalculating constant
3073parts of it.")
3074 (license license:expat))))
279663ef 3075
e73b49fb
RW		 3076(define-public openblas
3077 (package
ba05be22
LC		 3078 ;; TODO: Incorporate 'openblas/fixed-num-threads' changes on the next
3079 ;; rebuild cycle.
3080 (replacement openblas/fixed-num-threads)
3081
e73b49fb 3082 (name "openblas")
e7741236 3083 (version "0.3.6")
e73b49fb
RW		 3084 (source
3085 (origin
3086 (method url-fetch)
a617fd55
MB		 3087 (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
3088 version "%20version.tar.gz"))
e73b49fb
RW		 3089 (file-name (string-append name "-" version ".tar.gz"))
3090 (sha256
3091 (base32
e7741236 3092 "1r2g9zzwq5dm8vjd19pxwggfvfzy56cvkmpmp5d014qr3svgmsap"))))
e73b49fb
RW		 3093 (build-system gnu-build-system)
3094 (arguments
5789566a 3095 `(#:test-target "test"
bd0b4379
RW		 3096 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
3097 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
3098 ;; we need to disable substitutions.
71923a91
AE		 3099 #:substitutable?
3100 ,(let ((system (or (%current-target-system) (%current-system))))
3101 (or (string-prefix? "x86_64" system)
bd0b4379 3102 (string-prefix? "i686" system)
83a34647
EF		 3103 (string-prefix? "mips" system)
3104 (string-prefix? "aarch64" system)))
e73b49fb
RW		 3105 #:make-flags
3106 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
3107 "SHELL=bash"
5855756c 3108 "MAKE_NB_JOBS=0" ;use jobserver for submakes
af5b817e
RW		 3109 ;; Build the library for all supported CPUs. This allows
3110 ;; switching CPU targets at runtime with the environment variable
3111 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
71923a91
AE		 3112 ;; Unfortunately, this is not supported on non-x86 architectures,
3113 ;; where it leads to failed builds.
3114 ,@(let ((system (or (%current-target-system) (%current-system))))
8a637e79
RW		 3115 (cond
3116 ((or (string-prefix? "x86_64" system)
71923a91 3117 (string-prefix? "i686" system))
8a637e79
RW		 3118 '("DYNAMIC_ARCH=1"))
3119 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
3120 ;; two available MIPS targets special extended instructions
3121 ;; for Loongson cores are used.
3122 ((string-prefix? "mips" system)
3123 '("TARGET=SICORTEX"))
83a34647
EF		 3124 ;; On aarch64 force the generic 'armv8-a' target
3125 ((string-prefix? "aarch64" system)
3126 '("TARGET=ARMV8"))
8a637e79 3127 (else '()))))
e73b49fb 3128 ;; no configure script
493937ae
DL		 3129 #:phases
3130 (modify-phases %standard-phases
3131 (delete 'configure)
3132 (add-before 'build 'set-extralib
3133 (lambda* (#:key inputs #:allow-other-keys)
3134 ;; Get libgfortran found when building in utest.
3135 (setenv "FEXTRALIB"
3136 (string-append "-L" (assoc-ref inputs "fortran-lib")
3137 "/lib"))
3138 #t)))))
e73b49fb 3139 (inputs
493937ae 3140 `(("fortran-lib" ,gfortran "lib")))
e73b49fb
RW		 3141 (native-inputs
3142 `(("cunit" ,cunit)
493937ae 3143 ("fortran" ,gfortran)
e73b49fb
RW		 3144 ("perl" ,perl)))
3145 (home-page "http://www.openblas.net/")
3146 (synopsis "Optimized BLAS library based on GotoBLAS")
3147 (description
3148 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
3149 (license license:bsd-3)))
3150
daa6036f 3151(define-public openblas-ilp64
ba05be22 3152 (package/inherit openblas
daa6036f
EB		 3153 (name "openblas-ilp64")
3154 (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
3155 (arguments
3156 (substitute-keyword-arguments (package-arguments openblas)
3157 ((#:make-flags flags '())
3158 `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
3159 ,flags))))
3160 (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
3161 (license license:bsd-3)))
3162
ba05be22
LC		 3163(define openblas/fixed-num-threads
3164 ;; TODO: Move that to 'openblas' proper on the next rebuild cycle.
3165 (package
3166 (inherit openblas)
3167 (version (match (string-split (package-version openblas) #\.)
3168 ((numbers ... (= string-length len))
3169 (string-join (append numbers
3170 (list (make-string len #\a)))
3171 "."))))
3172 (arguments
3173 (substitute-keyword-arguments (package-arguments openblas)
3174 ((#:make-flags flags ''())
3175 ;; This is the maximum number of threads OpenBLAS will ever use (that
3176 ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS
3177 ;; is used.) If we don't set it, the makefile sets it to the number
3178 ;; of cores of the build machine, which is obviously wrong.
3179 `(cons "NUM_THREADS=128" ,flags))))))
3180
5a7deb11
LC		 3181(define* (make-blis implementation #:optional substitutable?)
3182 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
3183source tree for a list of implementations.)
3184
3185SUBSTITUTABLE? determines whether the package is made available as a
3186substitute.
3187
3188Currently the specialization must be selected at configure-time, but work is
3189underway to allow BLIS to select the right optimized kernels at run time:
3190<https://github.com/flame/blis/issues/129>."
3191 (package
3192 (name (if (string=? implementation "reference")
3193 "blis"
3194 (string-append "blis-" implementation)))
3195 (version "0.2.2")
3196 (home-page "https://github.com/flame/blis")
3197 (source (origin
3198 (method git-fetch)
3199 (uri (git-reference (url home-page) (commit version)))
3200 (sha256
3201 (base32
3202 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
3203 (file-name (git-file-name "blis" version))))
3204 (build-system gnu-build-system)
3205 (arguments
3206 `(#:test-target "test"
3207
3208 #:substitutable? ,substitutable?
3209
3210 #:phases (modify-phases %standard-phases
3211 (replace 'configure
3212 (lambda* (#:key outputs #:allow-other-keys)
3213 ;; This is a home-made 'configure' script.
3214 (let ((out (assoc-ref outputs "out")))
1ec17821
RW		 3215 (invoke "./configure" "-p" out
3216 "-d" "opt"
3217 "--disable-static"
3218 "--enable-shared"
3219 "--enable-threading=openmp"
5a7deb11 3220
1ec17821 3221 ,implementation))))
5a7deb11
LC		 3222 (add-before 'check 'show-test-output
3223 (lambda _
3224 ;; By default "make check" is silent. Make it verbose.
3225 (system "tail -F output.testsuite &")
3226 #t)))))
3227 (synopsis "High-performance basic linear algebra (BLAS) routines")
3228 (description
3229 "BLIS is a portable software framework for instantiating high-performance
3230BLAS-like dense linear algebra libraries. The framework was designed to
3231isolate essential kernels of computation that, when optimized, immediately
3232enable optimized implementations of most of its commonly used and
3233computationally intensive operations. While BLIS exports a new BLAS-like API,
3234it also includes a BLAS compatibility layer which gives application developers
3235access to BLIS implementations via traditional BLAS routine calls.")
3236 (license license:bsd-3)))
3237
3238(define-public blis
3239 ;; This is the "reference" implementation, which is the non-optimized but
3240 ;; portable variant (no assembly).
3241 (make-blis "reference" #t))
3242
3243(define ignorance blis)
3244
3245(define-syntax-rule (blis/x86_64 processor)
3246 "Expand to a package specialized for PROCESSOR."
3247 (package
3248 (inherit (make-blis processor))
3249 (supported-systems '("x86_64-linux"))))
3250
3251(define-public blis-sandybridge
3252 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
3253 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
3254 (blis/x86_64 "sandybridge"))
3255
3256(define-public blis-haswell
3257 ;; BLIS specialized for Haswell processors (launched 2013):
3258 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
3259 (blis/x86_64 "haswell"))
3260
3261(define-public blis-knl
3262 ;; BLIS specialized for Knights Landing processor (launched 2016):
3263 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
3264 (blis/x86_64 "knl"))
3265
3266
e1605e36
RW		 3267(define-public openlibm
3268 (package
3269 (name "openlibm")
48d7ac17 3270 (version "0.6.0")
e1605e36
RW		 3271 (source
3272 (origin
ca72dd2c
TGR		 3273 (method git-fetch)
3274 (uri (git-reference
3275 (url "https://github.com/JuliaLang/openlibm.git")
3276 (commit (string-append "v" version))))
3277 (file-name (git-file-name name version))
e1605e36 3278 (sha256
ca72dd2c 3279 (base32 "08wfchmmr5200fvmn1kwq9byc1fhsq46hn0y5k8scdl74771c7gh"))))
e1605e36
RW		 3280 (build-system gnu-build-system)
3281 (arguments
3282 `(#:make-flags
3283 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3284 #:phases
3285 ;; no configure script
dc1d3cde 3286 (modify-phases %standard-phases (delete 'configure))
e1605e36
RW		 3287 #:tests? #f)) ;the tests are part of the default target
3288 (home-page "http://openlibm.org/")
3289 (synopsis "Portable C mathematical library (libm)")
3290 (description
3291 "OpenLibm is an effort to have a high quality, portable, standalone C
3292mathematical library (libm). It can be used standalone in applications and
3293programming language implementations. The project was born out of a need to
e881752c 3294have a good libm for the Julia programming language that worked consistently
e1605e36
RW		 3295across compilers and operating systems, and in 32-bit and 64-bit
3296environments.")
538c0e3b
EF		 3297 ;; Each architecture has its own make target, and there is none for mips.
3298 (supported-systems (delete "mips64el-linux" %supported-systems))
e1605e36
RW		 3299 ;; See LICENSE.md for details.
3300 (license (list license:expat
3301 license:isc
3302 license:bsd-2
3303 license:public-domain
3304 license:lgpl2.1+))))
3305
e62be58f
RW		 3306(define-public openspecfun
3307 (package
3308 (name "openspecfun")
59cd0ba4 3309 (version "0.5.3")
e62be58f
RW		 3310 (source
3311 (origin
90cea671
TGR		 3312 (method git-fetch)
3313 (uri (git-reference
3314 (url "https://github.com/JuliaLang/openspecfun.git")
3315 (commit (string-append "v" version))))
3316 (file-name (git-file-name name version))
e62be58f 3317 (sha256
90cea671 3318 (base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh"))))
e62be58f
RW		 3319 (build-system gnu-build-system)
3320 (arguments
59cd0ba4 3321 '(#:tests? #f ; no "check" target
e62be58f
RW		 3322 #:make-flags
3323 (list (string-append "prefix=" (assoc-ref %outputs "out")))
59cd0ba4
TGR		 3324 #:phases
3325 (modify-phases %standard-phases
3326 (delete 'configure)))) ; no configure script
e62be58f 3327 (inputs
19afbea1 3328 `(("fortran" ,gfortran)))
e62be58f
RW		 3329 (home-page "https://github.com/JuliaLang/openspecfun")
3330 (synopsis "Collection of special mathematical functions")
3331 (description
3332 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
3333portable package for Bessel Functions of a Complex Argument and Nonnegative
3334Order; it contains subroutines for computing Bessel functions and Airy
3335functions. Faddeeva allows computing the various error functions of arbitrary
3336complex arguments (Faddeeva function, error function, complementary error
3337function, scaled complementary error function, imaginary error function, and
3338Dawson function); given these, one can also easily compute Voigt functions,
3339Fresnel integrals, and similar related functions as well.")
3340 ;; Faddeeva is released under the Expat license; AMOS is included as
3341 ;; public domain software.
3342 (license (list license:expat license:public-domain))))
3343
2742f87e
RW		 3344(define-public suitesparse
3345 (package
3346 (name "suitesparse")
bd5b5ac0 3347 (version "4.5.5")
2742f87e
RW		 3348 (source
3349 (origin
3350 (method url-fetch)
3351 (uri (string-append
3352 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
3353 version ".tar.gz"))
3354 (sha256
3355 (base32
bd5b5ac0
EB		 3356 "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
3357 (modules '((guix build utils)))
3358 (snippet
3359 ;; Remove bundled metis source
6cbee49d
MW		 3360 '(begin
3361 (delete-file-recursively "metis-5.1.0")
3362 #t))))
2742f87e
RW		 3363 (build-system gnu-build-system)
3364 (arguments
bd5b5ac0 3365 '(#:tests? #f ;no "check" target
2742f87e
RW		 3366 #:make-flags
3367 (list "CC=gcc"
3368 "BLAS=-lblas"
3369 "TBB=-ltbb"
bd5b5ac0 3370 "MY_METIS_LIB=-lmetis"
2742f87e
RW		 3371 (string-append "INSTALL_LIB="
3372 (assoc-ref %outputs "out") "/lib")
3373 (string-append "INSTALL_INCLUDE="
bd5b5ac0
EB		 3374 (assoc-ref %outputs "out") "/include")
3375 "library")
2742f87e 3376 #:phases
2509522c 3377 (modify-phases %standard-phases
bd5b5ac0 3378 (delete 'configure)))) ;no configure script
2742f87e
RW		 3379 (inputs
3380 `(("tbb" ,tbb)
bd5b5ac0
EB		 3381 ("lapack" ,lapack)
3382 ("metis" ,metis)))
2742f87e
RW		 3383 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
3384 (synopsis "Suite of sparse matrix software")
3385 (description
3386 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
3387multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
3388multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
3389simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
3390CXSparse, a concise sparse Cholesky factorization package; and many other
3391packages.")
3392 ;; LGPLv2.1+:
3393 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
3394 ;; GPLv2+:
3395 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
3396 (license (list license:gpl2+ license:lgpl2.1+))))
3397
ec322be2
FB		 3398(define-public atlas
3399 (package
3400 (name "atlas")
3c98ac02 3401 (version "3.10.3")
ec322be2
FB		 3402 (source (origin
3403 (method url-fetch)
de67e922
LF		 3404 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
3405 version "/atlas" version ".tar.bz2"))
ec322be2
FB		 3406 (sha256
3407 (base32
3c98ac02 3408 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
ec322be2
FB		 3409 (build-system gnu-build-system)
3410 (home-page "http://math-atlas.sourceforge.net/")
19afbea1 3411 (inputs `(("gfortran" ,gfortran)
ec322be2
FB		 3412 ("lapack-tar" ,(package-source lapack))))
3413 (outputs '("out" "doc"))
01480b9e
FB		 3414 ;; For the moment we drop support for MIPS at it fails to compile. See
3415 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
3416 (supported-systems (delete "mips64el-linux" %supported-systems))
ec322be2
FB		 3417 (arguments
3418 `(#:parallel-build? #f
3419 #:parallel-tests? #f
f15615b1
LC		 3420
3421 ;; ATLAS tunes itself for the machine it is built on, as explained at
3422 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
3423 ;; For this reason, we want users to build it locally instead of using
3424 ;; substitutes.
3425 #:substitutable? #f
3426
ec322be2 3427 #:modules ((srfi srfi-26)
ec322be2
FB		 3428 (guix build gnu-build-system)
3429 (guix build utils))
40029cbe 3430 #:configure-flags
ec322be2
FB		 3431 `(;; Generate position independent code suitable for dynamic libraries
3432 ;; and use WALL timer to get more accurate timing.
3433 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
3434 ;; Set word width.
3435 "-b"
3436 ,,(if (string-match "64" (%current-system))
3437 "64"
3438 "32")
3439 ;; Disable parallel build as it gives errors: atlas_pthread.h is
3440 ;; needed to compile C files before it is generated.
3441 "-Ss" "pmake" "make -j 1"
af89a667
FB		 3442 ;; Probe is failing for MIPS. We therefore define the system
3443 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3444 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3445 ,,@(if (string-prefix? "mips" (%current-system))
3446 (list "-A" "49" "-V" "1")
3447 (list))
ec322be2
FB		 3448 ;; Generate shared libraries.
3449 "--shared"
3450 ;; Build a full LAPACK library.
3451 ,(string-append "--with-netlib-lapack-tarfile="
3452 (assoc-ref %build-inputs "lapack-tar")))
3453 #:phases
e5b4b96b
EF		 3454 (modify-phases %standard-phases
3455 (add-after 'install 'install-doc
3456 (lambda* (#:key outputs inputs #:allow-other-keys)
3457 (let ((doc (string-append (assoc-ref outputs "doc")
3458 "/share/doc/atlas")))
3459 (mkdir-p doc)
cb6f44d4
RW		 3460 (for-each (cut install-file <> doc)
3461 (find-files "../ATLAS/doc" ".*"))
3462 #t)))
e5b4b96b 3463 (add-after 'check 'check-pt
cb6f44d4 3464 (lambda _ (invoke "make" "ptcheck")))
e5b4b96b
EF		 3465 ;; Fix files required to run configure.
3466 (add-before 'configure 'fix-/bin/sh
ec322be2
FB		 3467 (lambda _
3468 ;; Use `sh', not `/bin/sh'.
3469 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3470 (("/bin/sh")
5b786db8
EF		 3471 "sh"))
3472 #t))
e5b4b96b
EF		 3473 ;; Fix /bin/sh in generated make files.
3474 (add-after 'configure 'fix-/bin/sh-in-generated-files
3475 (lambda _
3476 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3477 (("/bin/sh")
5b786db8
EF		 3478 "sh"))
3479 #t))
e5b4b96b
EF		 3480 ;; ATLAS configure program does not accepts the default flags
3481 ;; passed by the 'gnu-build-system'.
3482 (replace 'configure
3483 (lambda* (#:key native-inputs inputs outputs
3484 (configure-flags '())
3485 #:allow-other-keys #:rest args)
3486 (let* ((prefix (assoc-ref outputs "out"))
3487 (bash (or (and=> (assoc-ref
3488 (or native-inputs inputs) "bash")
3489 (cut string-append <> "/bin/bash"))
3490 "/bin/sh"))
3491 (flags `(,(string-append "--prefix=" prefix)
3492 ,@configure-flags))
3493 (abs-srcdir (getcwd))
3494 (srcdir (string-append "../" (basename abs-srcdir))))
3495 (format #t "source directory: ~s (relative from build: ~s)~%"
3496 abs-srcdir srcdir)
3497 (mkdir "../build")
3498 (chdir "../build")
3499 (format #t "build directory: ~s~%" (getcwd))
3500 (format #t "configure flags: ~s~%" flags)
cb6f44d4
RW		 3501 (apply invoke bash
3502 (string-append srcdir "/configure")
3503 flags)))))))
ec322be2
FB		 3504 (synopsis "Automatically Tuned Linear Algebra Software")
3505 (description
3506 "ATLAS is an automatically tuned linear algebra software library
3507providing C and Fortran77 interfaces to a portably efficient BLAS
3508implementation, as well as a few routines from LAPACK.
3509
f15615b1
LC		 3510Optimization occurs at build time. For this reason, the library is built on
3511the machine where it is installed, without resorting to pre-built substitutes.
ec322be2 3512
f15615b1 3513Before building the library, CPU throttling should be disabled. This can be
d97c429a 3514done in the BIOS, or, on GNU/Linux, with the following command:
ec322be2 3515
8e9ba611 3516@example
d97c429a 3517# cpupower --governor performance
8e9ba611 3518@end example
ec322be2 3519
d97c429a 3520Failure to do so will result in a library with poor performance.")
ec322be2 3521 (license license:bsd-3)))
c12efc72
AE		 3522
3523(define-public glm
3524 (package
3525 (name "glm")
3f55b7be 3526 (version "0.9.9.6")
c12efc72
AE		 3527 (source
3528 (origin
3529 (method url-fetch)
5ea4b594
MB		 3530 (uri (string-append "https://github.com/g-truc/glm/releases/download/"
3531 version "/glm-" version ".zip"))
c12efc72 3532 (sha256
3f55b7be
TGR		 3533 (base32 "1l0pi1qi37mk6s0yrkrw07lspv4gcqnr9ryg3521hrl77ff37dwx"))
3534 (patches (search-patches "glm-restore-install-target.patch"))))
c12efc72
AE		 3535 (build-system cmake-build-system)
3536 (native-inputs
3537 `(("unzip" ,unzip)))
46bda5eb 3538 (home-page "https://glm.g-truc.net/")
c12efc72
AE		 3539 (synopsis "OpenGL Mathematics library")
3540 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3541library for graphics software based on the OpenGL Shading Language (GLSL)
3542specifications.")
3543 (license license:expat)))
7f18257b
AE		 3544
3545(define-public lpsolve
3546 (package
3547 (name "lpsolve")
a89e0cf5 3548 (version "5.5.2.5")
7f18257b
AE		 3549 (source
3550 (origin
3551 (method url-fetch)
3552 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3553 "/lp_solve_" version "_source.tar.gz"))
3554 (sha256
3555 (base32
a89e0cf5 3556 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
7f18257b
AE		 3557 (modules '((guix build utils)))
3558 (snippet
6cbee49d
MW		 3559 '(begin
3560 (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3561 (("^c=cc") "c=gcc")
3562 ;; Pretend to be on a 64 bit platform to obtain a common directory
3563 ;; name for the build results on all architectures; nothing else
3564 ;; seems to depend on it.
3565 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3566
3567 ;; The check for 'isnan' as it is written fails with
3568 ;; "non-floating-point argument in call to function
3569 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3570 ;; definition, which in turn leads to bad things. Fix the feature
3571 ;; test.
3572 (("isnan\\(0\\)") "isnan(0.)"))
3573 #t))))
7f18257b
AE		 3574 (build-system gnu-build-system)
3575 (arguments
6c96b545 3576 `(#:tests? #f ; no check target
7f18257b
AE		 3577 #:phases
3578 (modify-phases %standard-phases
6c96b545 3579 (delete 'configure) ; no configure script
7f18257b
AE		 3580 (replace 'build
3581 (lambda _
6c96b545
TGR		 3582 (with-directory-excursion "lpsolve55"
3583 (invoke "bash" "ccc"))
3584 (with-directory-excursion "lp_solve"
3585 (invoke "bash" "ccc"))
3586 #t))
7f18257b
AE		 3587 (replace 'install
3588 (lambda* (#:key outputs #:allow-other-keys)
3589 (let* ((out (assoc-ref outputs "out"))
3590 (bin (string-append out "/bin"))
3591 (lib (string-append out "/lib"))
3592 ;; This is where LibreOffice expects to find the header
3593 ;; files, and where they are installed by Debian.
3594 (include (string-append out "/include/lpsolve")))
6c96b545
TGR		 3595 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3596 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
96c46210
LC		 3597 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3598
7f18257b
AE		 3599 ;; Install a subset of the header files as on Debian
3600 ;; (plus lp_bit.h, which matches the regular expression).
96c46210
LC		 3601 (for-each (lambda (name)
3602 (install-file name include))
3603 (find-files "." "lp_[HMSa-z].*\\.h$"))
7f18257b 3604 (with-directory-excursion "shared"
96c46210
LC		 3605 (for-each (lambda (name)
3606 (install-file name include))
3607 (find-files "." "\\.h$")))
7f18257b
AE		 3608 #t))))))
3609 (home-page "http://lpsolve.sourceforge.net/")
3610 (synopsis "Mixed integer linear programming (MILP) solver")
3611 (description
3612 "lp_solve is a mixed integer linear programming solver based on the
3613revised simplex and the branch-and-bound methods.")
3614 (license license:lgpl2.1+)))
a17d4564
EB		 3615
3616(define-public dealii
3617 (package
3618 (name "dealii")
ba567cae 3619 (version "9.1.1")
a17d4564
EB		 3620 (source
3621 (origin
3622 (method url-fetch)
3623 (uri (string-append "https://github.com/dealii/dealii/releases/"
3624 "download/v" version "/dealii-" version ".tar.gz"))
3625 (sha256
3626 (base32
ba567cae 3627 "0xhjv0gzswpjbc43xbrpwfc5848g508l01855nszx3g5gwzlhnzw"))
a17d4564
EB		 3628 (modules '((guix build utils)))
3629 (snippet
3630 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
6cbee49d
MW		 3631 '(begin
3632 (delete-file-recursively "bundled")
3633 #t))))
a17d4564
EB		 3634 (build-system cmake-build-system)
3635 (inputs
3636 `(("tbb" ,tbb)
3637 ("zlib" ,zlib)
3638 ("boost" ,boost)
3639 ("p4est" ,p4est)
3640 ("blas" ,openblas)
3641 ("lapack" ,lapack)
3642 ("arpack" ,arpack-ng)
3643 ("muparser" ,muparser)
3644 ("gfortran" ,gfortran)
3645 ("suitesparse" ,suitesparse))) ;for UMFPACK
3646 (arguments
3647 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
d84b09e9
EB		 3648 #:configure-flags
3649 ;; Work around a bug in libsuitesparseconfig linking
3650 ;; see https://github.com/dealii/dealii/issues/4745
3651 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
a17d4564
EB		 3652 (home-page "https://www.dealii.org")
3653 (synopsis "Finite element library")
3654 (description
3655 "Deal.II is a C++ program library targeted at the computational solution
3656of partial differential equations using adaptive finite elements. The main
3657aim of deal.II is to enable rapid development of modern finite element codes,
3658using among other aspects adaptive meshes and a wide array of tools often used
3659in finite element programs.")
3660 (license license:lgpl2.1+)))
3661
3662(define-public dealii-openmpi
3663 (package (inherit dealii)
3664 (name "dealii-openmpi")
3665 (inputs
3666 `(("mpi" ,openmpi)
3667 ;;Supported only with MPI:
4d44bcad 3668 ("hdf5" ,hdf5-parallel-openmpi) ;TODO: have petsc-openmpi propagate?
a17d4564
EB		 3669 ("p4est" ,p4est-openmpi)
3670 ("petsc" ,petsc-openmpi)
3671 ("slepc" ,slepc-openmpi)
3672 ("metis" ,metis) ;for MUMPS
3673 ("scalapack" ,scalapack) ;for MUMPS
3674 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3675 ("arpack" ,arpack-ng-openmpi)
3676 ,@(fold alist-delete (package-inputs dealii)
3677 '("p4est" "arpack"))))
3678 (arguments
3679 (substitute-keyword-arguments (package-arguments dealii)
3680 ((#:configure-flags cf)
40b114c0
EB		 3681 `(cons "-DDEAL_II_WITH_MPI:BOOL=ON"
3682 ,cf))
7e309e8a
EB		 3683 ((#:phases phases '%standard-phases)
3684 `(modify-phases ,phases
3685 (add-before 'check 'mpi-setup
3686 ,%openmpi-setup)))))
a17d4564 3687 (synopsis "Finite element library (with MPI support)")))
194c7f95
AE		 3688
3689(define-public flann
3690 (package
3691 (name "flann")
3692 (version "1.8.4")
3693 (source
3694 (origin
3695 (method url-fetch)
3696 (uri
3697 (string-append
3698 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3699 version "-src.zip"))
3700 (sha256
3701 (base32
b5edc479
LC		 3702 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
3703 (patches (search-patches "flann-cmake-3.11.patch"))))
194c7f95 3704 (build-system cmake-build-system)
6b6aca9b
LC		 3705 (outputs '("out"
3706 "octave")) ;46 MiB .mex file that pulls Octave
194c7f95
AE		 3707 (native-inputs
3708 `(("unzip" ,unzip)))
3709 (inputs
3710 `(("hdf5" ,hdf5)
5537603f 3711 ("octave" ,octave-cli)
194c7f95
AE		 3712 ("python" ,python-2) ; print syntax
3713 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3714 ("zlib" ,zlib)))
3715 (arguments
39b30337
LC		 3716 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3717 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3718 #:strip-directories '("lib" "lib64" "libexec"
3719 "bin" "sbin" "share/flann/octave")
3720
9684e30b
LC		 3721 ;; Save 12 MiB by not installing .a files. Passing
3722 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3723 #:phases (modify-phases %standard-phases
6b6aca9b
LC		 3724 (add-before 'configure 'set-octave-directory
3725 (lambda* (#:key outputs #:allow-other-keys)
3726 ;; Install the .mex file in the "octave" output.
3727 (let ((out (assoc-ref outputs "octave")))
3728 (substitute* "src/matlab/CMakeLists.txt"
3729 (("share/flann/octave")
3730 (string-append out "/share/flann/octave")))
3731 #t)))
9684e30b
LC		 3732 (add-after 'install 'remove-static-libraries
3733 (lambda* (#:key outputs #:allow-other-keys)
3734 (let* ((out (assoc-ref outputs "out"))
3735 (lib (string-append out "/lib")))
3736 (for-each delete-file
3737 (find-files lib "\\.a$"))
3738 #t))))
3739
39b30337 3740 #:tests? #f)) ; The test data are downloaded from the Internet.
194c7f95
AE		 3741 (home-page "http://www.cs.ubc.ca/research/flann/")
3742 (synopsis "Library for approximate nearest neighbors computation")
3743 (description "FLANN is a library for performing fast approximate
3744nearest neighbor searches in high dimensional spaces. It implements a
3745collection of algorithms and a system for automatically choosing the best
3746algorithm and optimum parameters depending on the dataset.
3747
3748FLANN is written in C++ and contains bindings for C, Octave and Python.")
3749 (license (license:non-copyleft "file://COPYING"
3750 "See COPYING in the distribution."))))
d8c97beb
EF		 3751
3752(define-public wcalc
3753 (package
3754 (name "wcalc")
3755 (version "2.5")
3756 (source
3757 (origin
3758 (method url-fetch)
de67e922
LF		 3759 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3760 "wcalc-" version ".tar.bz2"))
d8c97beb
EF		 3761 (sha256
3762 (base32
3763 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3764 (build-system gnu-build-system)
3765 (inputs
3766 `(("mpfr" ,mpfr)
3767 ("readline" ,readline)))
3768 (home-page "http://w-calc.sourceforge.net/index.php")
3769 (synopsis "Flexible command-line scientific calculator")
3770 (description "Wcalc is a very capable calculator. It has standard functions
3771(sin, asin, and sinh for example, in either radians or degrees), many
3772pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3773variables, a command history, hex/octal/binary input and output, unit
3774conversions, embedded comments, and an expandable expression entry field. It
3775evaluates expressions using the standard order of operations.")
3776 (license license:gpl2+)))
45147b0c
FH		 3777
3778(define-public xaos
3779 (package
3780 (name "xaos")
3781 (version "3.6")
3782 (source (origin
3783 (method url-fetch)
de67e922
LF		 3784 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3785 "/xaos-" version ".tar.gz"))
45147b0c
FH		 3786 (sha256
3787 (base32
3788 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3789 (build-system gnu-build-system)
b94a6ca0 3790 (native-inputs `(("gettext" ,gettext-minimal)))
45147b0c
FH		 3791 (inputs `(("libx11" ,libx11)
3792 ("zlib" ,zlib)
3793 ("libpng" ,libpng)
3794 ("gsl" ,gsl)))
3795 (arguments
3796 `(#:tests? #f ;no "check" target
3797 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3798 (synopsis "Real-time fractal zoomer")
3799 (description "GNU XaoS is a graphical program that generates fractal
3800patterns and allows you to zoom in and out of them infinitely in a fluid,
3801continuous manner. It also includes tutorials that help to explain how fractals
3802are built. It can generate many different fractal types such as the Mandelbrot
3803set.")
6fd52309 3804 (home-page "https://www.gnu.org/software/xaos/")
45147b0c 3805 (license license:gpl2+)))
528bb464
EB		 3806
3807(define-public hypre
3808 (package
3809 (name "hypre")
be099727 3810 (version "2.15.1")
fabcbf32
TGR		 3811 (source
3812 (origin
3813 (method git-fetch)
3814 (uri (git-reference
3815 (url "https://github.com/LLNL/hypre.git")
3816 (commit (string-append "v" version))))
3817 (file-name (git-file-name name version))
3818 (sha256
be099727 3819 (base32 "1lvh4ybqkriyqfg2zmic6mrg1981qv1i9vry1fdgsabn81hb71g4"))
fabcbf32
TGR		 3820 (modules '((guix build utils)))
3821 (snippet
3822 '(begin
3823 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
be099727 3824 ;; substitute the release date.
fabcbf32
TGR		 3825 (substitute* "src/utilities/HYPRE_utilities.h"
3826 (("Date Compiled: .*$")
be099727 3827 "Date Compiled: Oct 19 2018 15:23:00 +0000\"\n"))
fabcbf32 3828 #t))))
528bb464 3829 (build-system gnu-build-system)
be099727
TGR		 3830 (outputs '("out" ; 6.1 MiB of headers and libraries
3831 "doc")) ; 4.8 MiB of documentation
528bb464
EB		 3832 (native-inputs
3833 `(("doc++" ,doc++)
3834 ("netpbm" ,netpbm)
be099727 3835 ("perl" ,perl) ; needed to run 'ppmquant' during tests
8b35c8cd
RW		 3836 ("texlive" ,(texlive-union (list texlive-xypic
3837 texlive-cm
9b405aea 3838 texlive-latex-hyperref
9b405aea 3839 texlive-bibtex)))
528bb464
EB		 3840 ("ghostscript" ,ghostscript)))
3841 (inputs
3842 `(("blas" ,openblas)
3843 ("lapack" ,lapack)))
3844 (arguments
3845 `(#:modules ((srfi srfi-1)
3846 ,@%gnu-build-system-modules)
3847 #:configure-flags '("--enable-shared"
3848 "--disable-fortran"
3849 "--without-MPI"
3850 "--with-openmp"
3851 "--with-fei"
3852 "--with-lapack"
3853 "--with-blas")
3854 #:phases
3855 (modify-phases %standard-phases
9b405aea
PN		 3856 (add-before 'build 'set-HOME
3857 (lambda _
3858 ;; FIXME: texlive-union does not find the built
3859 ;; metafonts, so it tries to generate them in HOME.
3860 (setenv "HOME" "/tmp")
3861 #t))
528bb464
EB		 3862 (add-before 'configure 'chdir-src
3863 (lambda _ (chdir "src")))
3864 (replace 'configure
3865 (lambda* (#:key build target configure-flags
3866 #:allow-other-keys #:rest args)
3867 (let* ((configure (assoc-ref %standard-phases 'configure)))
3868 (apply configure
3869 (append args
3870 (list #:configure-flags
3871 (cons (string-append
3872 "--host=" (or target build))
3873 configure-flags)))))))
3874 (add-after 'build 'build-docs
3875 (lambda _
9b405aea 3876 (invoke "make" "-Cdocs" "pdf" "html")))
528bb464
EB		 3877 (replace 'check
3878 (lambda _
3879 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3880 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
6b1c7ac8
RW		 3881 (invoke "make" "check" "CHECKRUN=")
3882 (for-each (lambda (filename)
3883 (let ((size (stat:size (stat filename))))
3884 (when (positive? size)
3885 (error (format #f "~a size ~d; error indication~%"
3886 filename size)))))
3887 (find-files "test" ".*\\.err$"))
3888 #t))
528bb464
EB		 3889 (add-after 'install 'install-docs
3890 (lambda* (#:key outputs #:allow-other-keys)
3891 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3892 (let* ((doc (assoc-ref outputs "doc"))
3893 (docdir (string-append doc "/share/doc/hypre-" ,version)))
528bb464
EB		 3894 (with-directory-excursion "docs"
3895 (for-each (lambda (base)
3896 (install-file (string-append base ".pdf") docdir)
be099727 3897 (copy-recursively base docdir)) ; html docs
528bb464
EB		 3898 '("HYPRE_usr_manual"
3899 "HYPRE_ref_manual")))
3900 #t))))))
3901 (home-page "http://www.llnl.gov/casc/hypre/")
3902 (synopsis "Library of solvers and preconditioners for linear equations")
3903 (description
3904 "HYPRE is a software library of high performance preconditioners and
3905solvers for the solution of large, sparse linear systems of equations. It
3906features multigrid solvers for both structured and unstructured grid
3907problems.")
3908 (license license:lgpl2.1)))
3909
3910(define-public hypre-openmpi
3911 (package (inherit hypre)
3912 (name "hypre-openmpi")
3913 (inputs
3914 `(("mpi" ,openmpi)
3915 ,@(package-inputs hypre)))
3916 (arguments
3917 (substitute-keyword-arguments (package-arguments hypre)
3918 ((#:configure-flags flags)
3919 ``("--with-MPI"
6df2a50a
LC		 3920 ,@(delete "--without-MPI" ,flags)))
3921 ((#:phases phases)
3922 `(modify-phases ,phases
bbe46a4a
EB		 3923 (add-before 'check 'mpi-setup
3924 ,%openmpi-setup)))))
528bb464
EB		 3925 (synopsis "Parallel solvers and preconditioners for linear equations")
3926 (description
3927 "HYPRE is a software library of high performance preconditioners and
3928solvers for the solution of large, sparse linear systems of equations on
3929parallel computers. It features parallel multigrid solvers for both
3930structured and unstructured grid problems.")))
6c90e183
EB		 3931
3932(define-public matio
3933 (package
3934 (name "matio")
3935 (version "1.5.6")
3936 (source
3937 (origin
3938 (method url-fetch)
de67e922 3939 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
6c90e183
EB		 3940 "matio-" version ".tar.gz"))
3941 (sha256
3942 (base32
3943 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3944 (build-system gnu-build-system)
3945 (inputs
3946 `(("zlib" ,zlib)
3947 ("hdf5" ,hdf5)))
3948 (home-page "http://matio.sourceforge.net/")
3949 (synopsis "Library for reading and writing MAT files")
3950 (description "Matio is a library for reading and writing MAT files. It
3951supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3952 (license license:bsd-2)))
d721c83a 3953
517318ad
LF		 3954(define-public vc
3955 (package
3956 (name "vc")
9d731fb6 3957 (version "1.4.1")
517318ad
LF		 3958 (source
3959 (origin (method url-fetch)
3960 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3961 "download/" version "/Vc-" version ".tar.gz"))
3962 (sha256
3963 (base32
9d731fb6 3964 "17qili8bf8r78cng65yf4qmgna8kiqjqbgcqbric6v9j6nkhkrk8"))))
517318ad
LF		 3965 (build-system cmake-build-system)
3966 (arguments
3967 '(#:configure-flags
33d82486
MB		 3968 '("-DBUILD_TESTING=ON"
3969 ;; By default, Vc will optimize for the CPU of the build machine.
3970 ;; Setting this to "none" makes it create portable binaries. See
3971 ;; "cmake/OptimizeForArchitecture.cmake".
9d731fb6
MB		 3972 "-DTARGET_ARCHITECTURE=none")
3973 #:phases (modify-phases %standard-phases
3974 (add-after 'unpack 'copy-testdata
3975 (lambda* (#:key inputs native-inputs #:allow-other-keys)
3976 (let ((testdata (assoc-ref (or native-inputs inputs)
3977 "testdata")))
3978 (copy-recursively testdata "tests/testdata")
3979 #t))))))
3980 (native-inputs
3981 `(("virtest" ,virtest)
3982
3983 ;; This is a submodule in the git project, but not part of the
3984 ;; released sources. See the git branch for the commit to take.
3985 ("testdata" ,(let ((commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3"))
3986 (origin
3987 (method git-fetch)
3988 (uri (git-reference
3989 (url "https://github.com/VcDevel/vc-testdata")
3990 (commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3")))
3991 (file-name (git-file-name "vc-testdata"
3992 (string-take commit 7)))
3993 (sha256
3994 (base32
3995 "1hkhqib03qlcq412ym2dciynfxcdr2ygqhnplz4l1vissr1wnqn2")))))))
517318ad
LF		 3996 (synopsis "SIMD vector classes for C++")
3997 (description "Vc provides portable, zero-overhead C++ types for explicitly
3998data-parallel programming. It is a library designed to ease explicit
3999vectorization of C++ code. Its types enable explicitly stating data-parallel
4000operations on multiple values. The parallelism is therefore added via the type
4001system. Vc has an intuitive API and provides portability between different
4002compilers and compiler versions as well as portability between different vector
4003instruction sets. Thus, an application written with Vc can be compiled for:
4004@enumerate
4005@item AVX and AVX2
d1e4ad1b 4006@item SSE2 up to SSE4.2 or SSE4a
517318ad
LF		 4007@item Scalar
4008@item MIC
4009@item NEON (in development)
4010@item NVIDIA GPUs / CUDA (in development)
4011@end enumerate\n")
4012 (home-page "https://github.com/VcDevel/Vc")
a8ead6f9
EF		 4013 ;; "No support_???.cpp file exists for this architecture."
4014 (supported-systems '("x86_64-linux" "i686-linux"))
517318ad 4015 (license license:bsd-3)))
54052a54 4016
4017(define-public reducelcs
4018 ;; This is the last commit which is available upstream, no
4019 ;; release happened since 2010.
4020 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
4021 (revision "1"))
4022 (package
4023 (name "reducelcs")
4024 (version (string-append "1.0-" revision "." (string-take commit 7)))
4025 (source
4026 (origin
4027 (method git-fetch)
4028 (uri (git-reference
4029 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
4030 (commit commit)))
4031 (file-name (string-append name "-" version "-checkout"))
4032 (sha256
4033 (base32
4034 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
4035 (build-system gnu-build-system)
4036 (inputs
4037 `(("openlibm" ,openlibm)))
4038 (arguments
4039 `(#:tests? #f ; no tests
4040 #:phases
4041 (modify-phases %standard-phases
4042 (delete 'configure) ; No configure script exists.
4043 (replace 'install ; No install phase exists.
4044 (lambda* (#:key outputs #:allow-other-keys)
4045 (let* ((out (assoc-ref outputs "out"))
4046 (bin (string-append out "/bin")))
4047 (install-file "Approximation" bin)
4048 (install-file "CollectResults" bin)
4049 (install-file "GenerateInstances" bin)
4050 #t))))))
4051 (synopsis "Approximate Longest Commons Subsequence computation tool")
4052 (description
4053 "@code{reduceLCS} is an implementation of the Reduce-Expand
4054algorithm for LCS. It is a fast program to compute the approximate
4055Longest Commons Subsequence of a set of strings.")
4056 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
c000b6b1 4057 (license license:gpl3+))))
479c4273
JD		 4058
4059(define-public jacal
4060 (package
4061 (name "jacal")
4062 (version "1c4")
4063 (source (origin
4064 (method url-fetch)
4065 (uri (string-append
4066 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
4067 version ".zip"))
4068 (sha256 (base32
4069 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
4070 (patches (search-patches "jacal-fix-texinfo.patch"))))
4071 (build-system gnu-build-system)
4072 (arguments
4073 `(#:phases
4074 (modify-phases %standard-phases
4075 (add-before 'build 'pre-build
4076 ;; Don't use upstream's script - it really doesn't fit into
4077 ;; Guix's functional paradigm.
4078 (lambda* (#:key inputs outputs #:allow-other-keys)
4079 (substitute* "Makefile"
4080 (("^install: install-script") "install: "))))
4081 (add-after 'install 'post-install
4082 ;; Instead, we provide our own simplified script.
4083 (lambda* (#:key inputs outputs #:allow-other-keys)
4084 (let ((wrapper (string-append (assoc-ref outputs "out")
4085 "/bin/jacal")))
4086 (format (open wrapper (logior O_WRONLY O_CREAT))
4087 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
4088 "-e '(slib:load \"~a/lib/jacal/math\") "
4089 "(math)' \"$@\"\n")
4090 (which "bash")
4091 (assoc-ref inputs "scm")
4092 (assoc-ref outputs "out"))
4093 (chmod wrapper #o555))))
4094 (replace 'configure
9cd82b1c
RW		 4095 (lambda* (#:key outputs #:allow-other-keys)
4096 (invoke "./configure"
4097 (string-append "--prefix="
4098 (assoc-ref outputs "out"))))))))
479c4273
JD		 4099 (inputs `(("scm" ,scm)))
4100 (native-inputs `(("unzip" ,unzip)
4101 ("texinfo" ,texinfo)))
4102 (synopsis "Symbolic mathematics system")
4103 (description "GNU JACAL is an interactive symbolic mathematics program based on
4104Scheme. It manipulate and simplify a range of mathematical expressions such
4105as equations, scalars, vectors, and matrices.")
6fd52309 4106 (home-page "https://www.gnu.org/software/jacal/")
479c4273
JD		 4107 (license license:gpl3+)))
4108
313844d9
TF		 4109(define-public z3
4110 (package
4111 (name "z3")
d49375c7 4112 (version "4.8.6")
fb525bfd 4113 (home-page "https://github.com/Z3Prover/z3")
313844d9 4114 (source (origin
fb525bfd
MB		 4115 (method git-fetch)
4116 (uri (git-reference (url home-page)
4117 (commit (string-append "z3-" version))))
2d7b99b3 4118 (file-name (git-file-name name version))
313844d9
TF		 4119 (sha256
4120 (base32
d49375c7 4121 "1sywcqj5y8yp28m4cdvzsgw74kd6zr1s3y1x17ky8pr9prvpvl6x"))))
fa574a6d 4122 (build-system gnu-build-system)
313844d9 4123 (arguments
fa574a6d 4124 `(#:phases
313844d9 4125 (modify-phases %standard-phases
ad6c6a5b
EF		 4126 (add-after 'unpack 'fix-compatability
4127 ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
4128 (lambda _
4129 (substitute* "src/util/mpz.cpp"
4130 (("#include <immintrin.h>") ""))
4131 #t))
cf684d87
TF		 4132 (add-before 'configure 'bootstrap
4133 (lambda _
32d5360f 4134 (invoke "python" "scripts/mk_make.py")))
fa574a6d
AB		 4135 ;; work around gnu-build-system's setting --enable-fast-install
4136 ;; (z3's `configure' is a wrapper around the above python file,
4137 ;; which fails when passed --enable-fast-install)
4138 (replace 'configure
4139 (lambda* (#:key inputs outputs #:allow-other-keys)
4140 (invoke "./configure"
4141 (string-append "--prefix=" (assoc-ref outputs "out")))))
4142 (add-after 'configure 'change-directory
4143 (lambda _
4144 (chdir "build")
4145 #t))
cf684d87 4146 (add-before 'check 'make-test-z3
313844d9 4147 (lambda _
cf684d87 4148 ;; Build the test suite executable.
32d5360f
RW		 4149 (invoke "make" "test-z3" "-j"
4150 (number->string (parallel-job-count)))))
cf684d87
TF		 4151 (replace 'check
4152 (lambda _
4153 ;; Run all the tests that don't require arguments.
32d5360f 4154 (invoke "./test-z3" "/a"))))))
313844d9 4155 (native-inputs
fa574a6d
AB		 4156 `(("which" ,which)
4157 ("python" ,python-wrapper)))
313844d9
TF		 4158 (synopsis "Theorem prover")
4159 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
cf684d87 4160theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
313844d9 4161 (license license:expat)))
3d5d87a3 4162
6d433d6e
EB		 4163(define-public elpa
4164 (package
4165 (name "elpa")
4166 (version "2018.11.001")
4167 (source (origin
4168 (method url-fetch)
4169 (uri (string-append "http://elpa.mpcdf.mpg.de/html/Releases/"
4170 version "/elpa-" version ".tar.gz"))
4171 (sha256
4172 (base32
4173 "05hv3v5i6xmziaizw350ff72y1c3k662r85fm3xfdrkclj5zw9yc"))))
4174 (build-system gnu-build-system)
4175 (native-inputs
4176 `(("fortran" ,gfortran)
4177 ("perl" ,perl))) ;for configure and deps
4178 (inputs
4179 `(("blas" ,openblas)))
4180 (arguments
4181 `(#:configure-flags
4182 `("--enable-openmp"
4183 "--with-mpi=no"
4184 ;; ELPA unfortunately does not support runtime dispatch, so we can
4185 ;; only enable the "generic" kernels. See the "Cross compilation"
4186 ;; section of INSTALL.md.
4187 "--enable-generic"
4188 "--disable-sse" "--disable-sse-assembly" ;Require SSE3
4189 "--disable-avx" "--disable-avx2" "--disable-avx512"
4190 ,(string-append "CFLAGS=-O3 "
4191 "-funsafe-loop-optimizations -funsafe-math-optimizations "
4192 "-ftree-vect-loop-version -ftree-vectorize "
4193 ,(let ((system (or (%current-target-system)
4194 (%current-system))))
4195 (cond
4196 ((or (string-prefix? "x86_64" system)
4197 (string-prefix? "i686" system))
4198 "-msse2")
4199 (else "")))))
4200 #:parallel-tests? #f ;tests are multi-threaded, via BLAS
4201 #:phases
4202 (modify-phases %standard-phases
4203 (add-before 'configure 'patch-header-generation
4204 (lambda _
4205 (substitute* "configure"
4206 (("^ *make.*top_srcdir=\"\\$srcdir\"" &)
4207 (string-append & " CPP=\"$CPP\"")))
4208 #t))
4209 (add-before 'check 'setup-tests
4210 (lambda _
4211 ;; Decrease test time and RAM use by computing fewer eigenvalues.
4212 ;; The flags are (MATRIX-SIZE, EIGENVALUES, BLOCK-SIZE), where
4213 ;; the default is (500, 250, 16) for C tests and (5000, 150, 16)
4214 ;; for Fortran. This also causes several tests to pass that
4215 ;; otherwise would otherwise fail with matrix size 5000; possibly
4216 ;; due to floating point tolerances that are too tight.
4217 (setenv "TEST_FLAGS" "1500 50 16") ;from elpa.spec
4218 (setenv "OMP_NUM_THREADS" (number->string (parallel-job-count)))
4219 (substitute* "Makefile"
4220 ;; Test scripts are generated, patch the shebang
4221 (("#!/bin/bash") (string-append "#!" (which "sh"))))
4222 #t)))))
4223 (home-page "http://elpa.mpcdf.mpg.de")
4224 (synopsis "Eigenvalue solvers for symmetric matrices")
4225 (description
4226 "The ELPA library provides efficient and scalable direct eigensolvers for
4227symmetric matrices.")
4228 (license license:lgpl3)))
4229
4230(define-public elpa-openmpi
4231 (package (inherit elpa)
4232 (name "elpa-openmpi")
4233 (inputs
4234 `(("mpi" ,openmpi)
4235 ("scalapack" ,scalapack)
4236 ,@(package-inputs elpa)))
4237 (arguments
4238 (substitute-keyword-arguments (package-arguments elpa)
4239 ((#:configure-flags cf '())
4240 `(cons "--with-mpi=yes" (delete "--with-mpi=no" ,cf)))
4241 ((#:phases phases '%standard-phases)
4242 `(modify-phases ,phases
4243 (add-before 'check 'mpi-setup
4244 (lambda _
4245 ;; Tests use 2 mpi tasks by default, use our remaining build
4246 ;; cores as OpenMP threads.
4247 (setenv "OMP_NUM_THREADS" (number->string
4248 (max (quotient (parallel-job-count) 2)
4249 1)))
4250 (,%openmpi-setup)))))))
4251 (synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)")))
4252
e01397b4
EB		 4253(define-public elemental
4254 (package
4255 (name "elemental")
4256 (version "0.87.7")
4257 (source (origin
5c0b6d1b
EF		 4258 (method git-fetch)
4259 (uri (git-reference
4260 (url "https://github.com/elemental/Elemental.git")
4261 (commit (string-append "v" version))))
4262 (file-name (git-file-name name version))
e01397b4
EB		 4263 (sha256
4264 (base32
5c0b6d1b 4265 "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
e01397b4
EB		 4266 (build-system cmake-build-system)
4267 (home-page "http://libelemental.org")
4268 (native-inputs
4269 `(("gfortran" ,gfortran)))
4270 (inputs
4271 `(("blas" ,openblas)
4272 ("gfortran:lib" ,gfortran "lib")
4273 ("gmp" ,gmp)
4274 ("lapack" ,lapack)
4275 ("metis" ,metis)
4276 ("mpc" ,mpc)
4277 ("mpfr" ,mpfr)
4278 ("mpi" ,openmpi)
4279 ("qd" ,qd)))
4280 (arguments
4281 `(#:build-type "Release" ;default RelWithDebInfo not supported
4282 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
4283 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
4284 "-DEL_CACHE_WARNINGS:BOOL=YES"
4285 "-DEL_TESTS:BOOL=YES"
4286 "-DCMAKE_INSTALL_LIBDIR=lib"
4287 "-DGFORTRAN_LIB=gfortran")
4288 #:phases (modify-phases %standard-phases
3b42e2be
EF		 4289 (add-before 'check 'mpi-setup
4290 ,%openmpi-setup)
e01397b4
EB		 4291 (add-before 'check 'setup-tests
4292 (lambda _
4293 ;; Parallelism is done at the MPI layer.
4294 (setenv "OMP_NUM_THREADS" "1")
4295 #t))
4296 (add-after 'install 'remove-tests
4297 (lambda* (#:key outputs #:allow-other-keys)
4298 ;; Tests are installed, with no easy configuration
4299 ;; switch to prevent this, so delete them.
4300 (delete-file-recursively
3b42e2be 4301 (string-append (assoc-ref outputs "out") "/bin"))
e01397b4
EB		 4302 #t)))))
4303 (synopsis "Dense and sparse-direct linear algebra and optimization")
4304 (description "Elemental is a modern C++ library for distributed-memory
4305dense and sparse-direct linear algebra, conic optimization, and lattice
4306reduction.")
4307 (license license:bsd-2)))
5b05dce7
JN		 4308
4309(define-public mcrl2
4310 (package
4311 (name "mcrl2")
3bc74090 4312 (version "201908.0")
5b05dce7
JN		 4313 (source (origin
4314 (method url-fetch)
185152e3
JN		 4315 (uri (string-append
4316 "https://www.mcrl2.org/download/release/mcrl2-"
4317 version ".tar.gz"))
5b05dce7
JN		 4318 (sha256
4319 (base32
3bc74090 4320 "1i4xgl2d5fgiz1mwi50cyfkrrcpm8nxfayfjgmhq7chs58wlhfsz"))))
5b05dce7
JN		 4321 (inputs
4322 `(("boost" ,boost)
4323 ("glu" ,glu)
4324 ("mesa" ,mesa)
077d66ed 4325 ("qtbase" ,qtbase)))
5b05dce7 4326 (build-system cmake-build-system)
ed0c5d3c 4327 (synopsis "Toolset for the mCRL2 formal specification language")
5b05dce7 4328 (description
ed0c5d3c
TGR		 4329 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
4330specification language for describing concurrent discrete event systems. Its
4331toolset supports analysis and automatic verification, linearisation, simulation,
4332state-space exploration and generation, and tools to optimise and analyse
5b05dce7
JN		 4333specifications. Also, state spaces can be manipulated, visualised and
4334analysed.")
b3882709 4335 (home-page "https://mcrl2.org")
5b05dce7 4336 (license license:boost1.0)))
41835f94 4337
e03b9126
JN		 4338(define-public mcrl2-minimal
4339 (package
4340 (inherit mcrl2)
4341 (name "mcrl2-minimal")
4342 (inputs
4343 `(("boost" ,boost)))
4344 (arguments
4345 '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
4346
41835f94
LF		 4347(define-public r-subplex
4348 (package
4349 (name "r-subplex")
2bcf5fd3 4350 (version "1.5-4")
41835f94
LF		 4351 (source
4352 (origin
4353 (method url-fetch)
4354 (uri (cran-uri "subplex" version))
4355 (sha256
4356 (base32
2bcf5fd3 4357 "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
41835f94
LF		 4358 (build-system r-build-system)
4359 (native-inputs
4360 `(("gfortran" ,gfortran)))
4361 (home-page "https://cran.r-project.org/web/packages/subplex")
4362 (synopsis "Unconstrained optimization using the subplex algorithm")
4363 (description "This package implements the Subplex optimization algorithm.
4364It solves unconstrained optimization problems using a simplex method on
4365subspaces. The method is well suited for optimizing objective functions that
4366are noisy or are discontinuous at the solution.")
4367 (license license:gpl3+)))
799ad71b 4368
910deec6
NV		 4369(define-public tcalc
4370 (package
4371 (name "tcalc")
4372 (version "2.0")
4373 (source
4374 (origin
4375 (method url-fetch)
4376 (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
4377 version ".tar.gz"))
4378 (sha256
4379 (base32
4380 "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
4381 (build-system gnu-build-system)
4382 (synopsis "The terminal calculator")
4383 (description
4384 "The terminal calculator is a small program to help users of the GNU/Linux
4385terminal do calculations simply and quickly. The formula to be calculated can
4386be fed to @command{tcalc} through the command line.")
4387 (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
4388 (license license:gpl3+)))
b26e4f26
EB		 4389
4390(define-public sundials
4391 (package
4392 (name "sundials")
4393 (version "3.1.1")
4394 (source
4395 (origin
4396 (method url-fetch)
4397 (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
4398 "sundials-" version ".tar.gz"))
4399 (sha256
4400 (base32
4401 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
4402 (build-system cmake-build-system)
4403 (native-inputs
4404 `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
4405 (inputs
4406 `(("fortran" ,gfortran) ;for fcmix
4407 ("blas" ,openblas)
4408 ("suitesparse" ,suitesparse))) ;TODO: Add hypre
4409 (arguments
4410 `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
4411 "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
4412 "-DEXAMPLES_ENABLE_F77:BOOL=ON"
4413 "-DEXAMPLES_ENABLE_F90:BOOL=ON"
4414 "-DEXAMPLES_INSTALL:BOOL=OFF"
4415
4416 "-DFCMIX_ENABLE:BOOL=ON"
4417
4418 "-DKLU_ENABLE:BOOL=ON"
4419 ,(string-append "-DKLU_INCLUDE_DIR="
4420 (assoc-ref %build-inputs "suitesparse")
4421 "/include")
4422 ,(string-append "-DKLU_LIBRARY_DIR="
4423 (assoc-ref %build-inputs "suitesparse")
4424 "/lib"))))
4425 (home-page "https://computation.llnl.gov/projects/sundials")
4426 (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
4427 (description "SUNDIALS is a family of software packages implemented with
4428the goal of providing robust time integrators and nonlinear solvers that can
4429easily be incorporated into existing simulation codes.")
4430 (license license:bsd-3)))
4431
4432(define-public sundials-openmpi
4433 (package (inherit sundials)
4434 (name "sundials-openmpi")
4435 (inputs
4436 `(("mpi" ,openmpi)
4437 ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
4438 ,@(package-inputs sundials)))
4439 (arguments
4440 (substitute-keyword-arguments (package-arguments sundials)
4441 ((#:configure-flags flags '())
4442 `(cons* "-DMPI_ENABLE:BOOL=ON"
4443 "-DPETSC_ENABLE:BOOL=ON"
4444 (string-append "-DPETSC_INCLUDE_DIR="
4445 (assoc-ref %build-inputs "petsc")
4446 "/include")
4447 (string-append "-DPETSC_LIBRARY_DIR="
4448 (assoc-ref %build-inputs "petsc")
4449 "/lib")
4450 ,flags))
4451 ((#:phases phases '%standard-phases)
4452 `(modify-phases ,phases
bbe46a4a
EB		 4453 (add-before 'check 'mpi-setup
4454 ,%openmpi-setup)))))
b26e4f26 4455 (synopsis "SUNDIALS with OpenMPI support")))
a6b9ebc2
EB		 4456
4457(define-public combinatorial-blas
4458 (package
4459 (name "combinatorial-blas")
4460 (version "1.6.2")
4461 (source
4462 (origin
4463 (method url-fetch)
4464 (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/"
4465 "CombBLAS_beta_"
4466 (match (string-split version #\.)
4467 ((major minor patch)
4468 (string-append major minor "_" patch))) ;e.g. "16_2"
4469 ".tgz"))
4470 (sha256
4471 (base32
4472 "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a"))
4473 (patches (search-patches "combinatorial-blas-awpm.patch"
4474 "combinatorial-blas-io-fix.patch"))))
4475 (build-system cmake-build-system)
4476 (inputs
4477 `(("mpi" ,openmpi)
4478 ("test-data" ,(origin
4479 (method url-fetch)
4480 (uri (string-append "https://people.eecs.berkeley.edu/~aydin/"
4481 "CombBLAS_FILES/testdata_combblas1.6.1.tgz"))
4482 (sha256
4483 (base32
4484 "01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87"))))))
4485 (arguments
4486 `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
4487 "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL")
4488 #:parallel-tests? #f ;tests use 'mpiexec -n4'
4489 #:phases
4490 (modify-phases %standard-phases
4491 (add-before 'check 'mpi-setup
4492 ,%openmpi-setup)
4493 (add-before 'check 'test-setup
4494 (lambda* (#:key inputs #:allow-other-keys)
4495 (setenv "OMP_NUM_THREADS" "2")
4496 (invoke "tar" "xf" (assoc-ref inputs "test-data")))))))
4497 (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/")
4498 (synopsis "Linear algebra primitives for graph analytics")
4499 (description "The Combinatorial BLAS (CombBLAS) is an extensible
4500distributed-memory parallel graph library offering a small but powerful set of
4501linear algebra primitives specifically targeting graph analytics.")
4502 (license (list
4503 license:gpl2+ ;include/psort/(funnel|sort)*.h
4504 license:x11 ;usort and psort
4505 license:bsd-3)))) ;CombBLAS and MersenneTwister.h
3847d1f2
RW		 4506
4507(define-public dune-common
4508 (package
4509 (name "dune-common")
4510 (version "2.6.0")
4511 (source
4512 (origin
4513 (method url-fetch)
4514 (uri (string-append "https://dune-project.org/download/"
4515 version "/dune-common-" version ".tar.gz"))
4516 (sha256
4517 (base32
4518 "019wcr1qf7jwyxx1y5y290wdlglylskvbb2m01ljkzcza2xnlmhw"))))
4519 (build-system cmake-build-system)
4520 (arguments
4521 `(#:phases
4522 (modify-phases %standard-phases
4523 (add-after 'build 'build-tests
4524 (lambda* (#:key make-flags #:allow-other-keys)
4525 (apply invoke "make" "build_tests" make-flags)))
4526 ;; These tests fail because they require a fully functional MPI
4527 ;; environment.
4528 (add-after 'unpack 'disable-failing-tests
4529 (lambda _
4530 (setenv "ARGS"
4531 (string-append "--exclude-regex '("
4532 (string-join
4533 (list
4534 "remoteindicestest"
4535 "remoteindicestest-mpi-2"
4536 "syncertest"
4537 "syncertest-mpi-2"
4538 "variablesizecommunicatortest"
4539 "variablesizecommunicatortest-mpi-2"
4540 "arithmetictestsuitetest"
4541 "assertandreturntest"
4542 "assertandreturntest_ndebug"
4543 "concept"
4544 "debugaligntest"
4545 "mpicollectivecommunication"
4546 "mpicollectivecommunication-mpi-2"
4547 "mpiguardtest"
4548 "mpiguardtest-mpi-2"
4549 "mpihelpertest"
4550 "mpihelpertest-mpi-2"
4551 "mpihelpertest2"
4552 "mpihelpertest2-mpi-2")
4553 "|")
4554 ")'"))
4555 #t)))))
4556 (inputs
4557 `(("gmp" ,gmp)
4558 ("metis" ,metis)
4559 ("openmpi" ,openmpi)
4560 ("openblas" ,openblas)
4561 ("python" ,python)
4562 ("superlu" ,superlu)))
4563 (native-inputs
4564 `(("gfortran" ,gfortran)
4565 ("pkg-config" ,pkg-config)))
4566 (home-page "https://dune-project.org/")
4567 (synopsis "Distributed and Unified Numerics Environment")
4568 (description "DUNE, the Distributed and Unified Numerics Environment is a
4569modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4570grid-based methods. It supports the easy implementation of methods like
4571@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4572Differences} (FD).")
4573 ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2.
4574 (license license:gpl2)))
242dbd8e
RW		 4575
4576(define-public dune-geometry
4577 (package
4578 (name "dune-geometry")
4579 (version "2.6.0")
4580 (source
4581 (origin
4582 (method url-fetch)
4583 (uri (string-append "https://dune-project.org/download/"
4584 version "/dune-geometry-" version ".tar.gz"))
4585 (sha256
4586 (base32
4587 "0hlaaxjyv9j05blasvb67sy02hd0w4g9znf68gdh3l731dd1aqbn"))))
4588 (build-system cmake-build-system)
4589 (arguments
4590 `(#:phases
4591 (modify-phases %standard-phases
4592 (add-after 'build 'build-tests
4593 (lambda* (#:key make-flags #:allow-other-keys)
4594 (apply invoke "make" "build_tests" make-flags))))))
4595 (inputs
4596 `(("dune-common" ,dune-common)
4597 ("openmpi" ,openmpi)
4598 ;; Optional
4599 ("openblas" ,openblas)
4600 ("gmp" ,gmp)
4601 ("python" ,python)))
4602 (native-inputs
4603 `(("gfortran" ,gfortran)
4604 ("pkg-config" ,pkg-config)))
4605 (home-page "https://dune-project.org/")
4606 (synopsis "Distributed and Unified Numerics Environment")
4607 (description "DUNE, the Distributed and Unified Numerics Environment is a
4608modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4609grid-based methods. It supports the easy implementation of methods like
4610@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4611Differences} (FD).
4612
4613This package contains the basic DUNE geometry classes.")
4614 ;; GPL version 2 with "runtime exception"
4615 (license license:gpl2)))
ef6e69fd
RW		 4616
4617(define-public dune-grid
4618 (package
4619 (name "dune-grid")
4620 (version "2.6.0")
4621 (source
4622 (origin
4623 (method url-fetch)
4624 (uri (string-append "https://dune-project.org/download/"
4625 version "/dune-grid-" version ".tar.gz"))
4626 (sha256
4627 (base32
4628 "1jp4vscm9yb9xg0lh7apzccfkhvgbnk652yahigmh3cvzpl4acd0"))))
4629 (build-system cmake-build-system)
4630 (arguments
4631 `(#:phases
4632 (modify-phases %standard-phases
4633 (add-after 'build 'build-tests
4634 (lambda* (#:key make-flags #:allow-other-keys)
4635 (apply invoke "make" "build_tests" make-flags)))
4636 ;; These tests fail because they require a fully functional MPI
4637 ;; environment.
4638 (add-after 'unpack 'disable-failing-tests
4639 (lambda _
4640 (setenv "ARGS"
4641 (string-append "--exclude-regex '("
4642 (string-join
4643 (list
4644 "scsgmappertest"
4645 "conformvolumevtktest"
4646 "gnuplottest"
4647 "nonconformboundaryvtktest"
4648 "subsamplingvtktest"
4649 "vtktest"
4650 "vtktest-mpi-2"
4651 "vtksequencetest"
4652 "gmshtest-onedgrid"
4653 "test-dgf-yasp"
4654 "test-dgf-yasp-offset"
4655 "test-dgf-oned"
4656 "test-geogrid-yaspgrid"
4657 "test-gridinfo"
4658 "test-identitygrid"
4659 "testiteratorranges"
4660 "test-hierarchicsearch"
4661 "test-parallel-ug-mpi-2"
4662 "test-yaspgrid-backuprestore-equidistant"
4663 "test-yaspgrid-backuprestore-equidistant-mpi-2"
4664 "test-yaspgrid-backuprestore-equidistantoffset"
4665 "test-yaspgrid-backuprestore-equidistantoffset-mpi-2"
4666 "test-yaspgrid-backuprestore-tensor"
4667 "test-yaspgrid-backuprestore-tensor-mpi-2"
4668 "test-yaspgrid-tensorgridfactory"
4669 "test-yaspgrid-tensorgridfactory-mpi-2"
4670 "test-yaspgrid-yaspfactory-1d"
4671 "test-yaspgrid-yaspfactory-1d-mpi-2"
4672 "test-yaspgrid-yaspfactory-2d"
4673 "test-yaspgrid-yaspfactory-2d-mpi-2"
4674 "test-yaspgrid-yaspfactory-3d"
4675 "test-yaspgrid-yaspfactory-3d-mpi-2"
4676 "globalindexsettest"
4677 "persistentcontainertest"
4678 "structuredgridfactorytest"
4679 "tensorgridfactorytest"
4680 "vertexordertest")
4681 "|")
4682 ")'"))
4683 #t)))))
4684 (inputs
4685 `(("dune-common" ,dune-common)
4686 ("dune-geometry" ,dune-geometry)
4687 ("gmp" ,gmp)
4688 ("metis" ,metis)
4689 ("openblas" ,openblas)
4690 ("openmpi" ,openmpi)
4691 ("python" ,python)))
4692 (native-inputs
4693 `(("gfortran" ,gfortran)
4694 ("pkg-config" ,pkg-config)))
4695 (home-page "https://dune-project.org/")
4696 (synopsis "Distributed and Unified Numerics Environment")
4697 (description "DUNE, the Distributed and Unified Numerics Environment is a
4698modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4699grid-based methods. It supports the easy implementation of methods like
4700@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4701Differences} (FD).
4702
4703This package contains the basic DUNE grid classes.")
4704 ;; GPL version 2 with "runtime exception"
4705 (license license:gpl2)))
ea51d357
RW		 4706
4707(define-public dune-istl
4708 (package
4709 (name "dune-istl")
4710 (version "2.6.0")
4711 (source
4712 (origin
4713 (method url-fetch)
4714 (uri (string-append "https://dune-project.org/download/"
4715 version "/dune-istl-" version ".tar.gz"))
4716 (sha256
4717 (base32
4718 "0l2gyrvys5w6wsmk0ckbb7295s80b7yk7qrl7x66akv2jv1nzq2w"))))
4719 (build-system cmake-build-system)
4720 (arguments
4721 `(#:phases
4722 (modify-phases %standard-phases
4723 (add-after 'build 'build-tests
4724 (lambda* (#:key make-flags #:allow-other-keys)
4725 (apply invoke "make" "build_tests" make-flags)))
4726 ;; These tests fail because they require a fully functional MPI
4727 ;; environment.
4728 (add-after 'unpack 'disable-failing-tests
4729 (lambda _
4730 (setenv "ARGS"
4731 (string-append "--exclude-regex '("
4732 (string-join
4733 (list
4734 "galerkintest"
4735 "hierarchytest"
4736 "pamgtest"
4737 "pamg_comm_repart_test"
4738 "matrixredisttest"
4739 "vectorcommtest"
4740 "matrixmarkettest")
4741 "|")
4742 ")'"))
4743 #t)))))
4744 (inputs
4745 `(("dune-common" ,dune-common)
4746 ("openmpi" ,openmpi)
4747 ;; Optional
4748 ("metis" ,metis)
4749 ("superlu" ,superlu)
4750 ("openblas" ,openblas)
4751 ("gmp" ,gmp)
4752 ("python" ,python)))
4753 (native-inputs
4754 `(("gfortran" ,gfortran)
4755 ("pkg-config" ,pkg-config)))
4756 (home-page "https://dune-project.org/")
4757 (synopsis "Distributed and Unified Numerics Environment")
4758 (description "DUNE, the Distributed and Unified Numerics Environment is a
4759modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4760grid-based methods.
4761
4762This is the iterative solver template library which provides generic sparse
4763matrix/vector classes and a variety of solvers based on these classes. A
4764special feature is the use of templates to exploit the recursive block
4765structure of finite element matrices at compile time. Available solvers
4766include Krylov methods, (block-) incomplete decompositions and
4767aggregation-based algebraic multigrid.")
4768 ;; GPL version 2 with "runtime exception"
4769 (license license:gpl2)))
5a70aa7d
RW		 4770
4771(define-public dune-localfunctions
4772 (package
4773 (name "dune-localfunctions")
4774 (version "2.6.0")
4775 (source
4776 (origin
4777 (method url-fetch)
4778 (uri (string-append "https://dune-project.org/download/"
4779 version "/dune-localfunctions-" version ".tar.gz"))
4780 (sha256
4781 (base32
4782 "19c6zjinwwpy8jh4v4prhphyd438rapd4x80fj93apmwgw04nrhl"))))
4783 (build-system cmake-build-system)
4784 (arguments
4785 `(#:phases
4786 (modify-phases %standard-phases
4787 (add-after 'build 'build-tests
4788 (lambda* (#:key make-flags #:allow-other-keys)
4789 (apply invoke "make" "build_tests" make-flags))))))
4790 (inputs
4791 `(("dune-common" ,dune-common)
4792 ("dune-geometry" ,dune-geometry)
4793 ("openmpi" ,openmpi)
4794 ;; Optional
4795 ("metis" ,metis)
4796 ("superlu" ,superlu)
4797 ("gmp" ,gmp)))
4798 (native-inputs
4799 `(("gfortran" ,gfortran)
4800 ("pkg-config" ,pkg-config)))
4801 (home-page "https://dune-project.org/")
4802 (synopsis "Distributed and Unified Numerics Environment") ; TODO
4803 (description "This DUNE module provides interface and implementation for
4804shape functions defined on the DUNE reference elements. In addition to the
4805shape function, interpolation operators and special keys are provided which
4806can be used to assemble global function spaces on finite-element grids.
4807
4808This package provides an interface and implementation for shape functions
4809defined on the DUNE reference elements. In addition to the shape function,
4810interpolation operators and special keys are provided which can be used to
4811assemble global function spaces on finite-element grids.")
4812 ;; GPL version 2 with "runtime exception"
4813 (license license:gpl2)))
ab03d899
RW		 4814
4815(define-public dune-alugrid
4816 (package
4817 (name "dune-alugrid")
4818 (version "2.6.0")
4819 (source
4820 (origin
4821 (method url-fetch)
4822 (uri (string-append "https://dune-project.org/download/"
4823 version "/dune-alugrid-" version ".tar.gz"))
4824 (sha256
4825 (base32
4826 "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj"))))
4827 (build-system cmake-build-system)
4828 (arguments
4829 `(#:tests? #f ; 7 of 8 tests fail because they need a full MPI
4830 ; environment
4831 #:phases
4832 (modify-phases %standard-phases
4833 (add-after 'unpack 'patch-include
4834 (lambda _
4835 (substitute* "dune/alugrid/test/test-alugrid.cc"
4836 (("doc/grids/gridfactory/testgrids")
4837 "doc/dune-grid/grids/gridfactory/testgrids"))
4838 #t))
4839 (add-after 'build 'build-tests
4840 (lambda* (#:key inputs make-flags #:allow-other-keys)
4841 (setenv "CPLUS_INCLUDE_PATH"
97149c57 4842 (string-append (assoc-ref inputs "dune-grid") "/share"))
ab03d899
RW		 4843 (apply invoke "make" "build_tests" make-flags))))))
4844 (inputs
4845 `(("dune-common" ,dune-common)
4846 ("dune-geometry" ,dune-geometry)
4847 ("dune-grid" ,dune-grid)
4848 ("openmpi" ,openmpi)
4849 ;; Optional
4850 ("metis" ,metis)
4851 ("openblas" ,openblas)
4852 ("python" ,python)
4853 ("superlu" ,superlu)
4854 ("gmp" ,gmp)
4855 ("zlib" ,zlib)))
4856 (native-inputs
4857 `(("gfortran" ,gfortran)
4858 ("pkg-config" ,pkg-config)))
4859 (home-page "https://dune-project.org/")
4860 (synopsis "Distributed and Unified Numerics Environment")
4861 (description "ALUGrid is an adaptive, loadbalancing, unstructured
4862implementation of the DUNE grid interface supporting either simplices or
4863cubes.")
4864 (license license:gpl2+)))
0e50630f
RW		 4865
4866(define-public dune-typetree
4867 (package
4868 (name "dune-typetree")
4869 (version "2.6.0")
4870 (source
4871 (origin
4872 (method git-fetch)
4873 (uri (git-reference
4874 (url "https://gitlab.dune-project.org/staging/dune-typetree.git")
4875 (commit (string-append "v" version))))
4876 (file-name (git-file-name name version))
4877 (sha256
4878 (base32
4879 "0mnv6w2f22lz3j4bdpdjq55vjm8xxfx9v4vvhg9bd36xpsbjpjp9"))))
4880 (build-system cmake-build-system)
4881 (arguments
4882 `(#:phases
4883 (modify-phases %standard-phases
4884 (add-after 'build 'build-tests
4885 (lambda* (#:key make-flags #:allow-other-keys)
4886 (apply invoke "make" "build_tests" make-flags))))))
4887 (inputs
4888 `(("dune-common" ,dune-common)
4889 ("openmpi" ,openmpi)
4890 ;; Optional
4891 ("openblas" ,openblas)
4892 ("python" ,python)
4893 ("metis" ,metis)
4894 ("superlu" ,superlu)
4895 ("gmp" ,gmp)))
4896 (native-inputs
4897 `(("gfortran" ,gfortran)
4898 ("pkg-config" ,pkg-config)))
4899 (home-page "https://dune-project.org/")
4900 (synopsis "Distributed and Unified Numerics Environment")
4901 (description "TypeTree is a template library for constructing and
4902operating on statically typed trees of objects.")
4903 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4904 (license (list license:lgpl3+ license:gpl2))))
85b9371c
RW		 4905
4906(define-public dune-functions
4907 (package
4908 (name "dune-functions")
4909 (version "2.6.0")
4910 (source
4911 (origin
4912 (method git-fetch)
4913 (uri (git-reference
4914 (url "https://gitlab.dune-project.org/staging/dune-functions.git")
4915 (commit (string-append "v" version))))
4916 (file-name (git-file-name name version))
4917 (sha256
4918 (base32
4919 "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200"))))
4920 (build-system cmake-build-system)
4921 (arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid
4922 (inputs
4923 `(("dune-common" ,dune-common)
4924 ("dune-istl" ,dune-istl)
4925 ("dune-localfunctions" ,dune-localfunctions)
4926 ("dune-grid" ,dune-grid)
4927 ("dune-geometry" ,dune-geometry)
4928 ("dune-typetree" ,dune-typetree)
4929 ("openmpi" ,openmpi)
4930 ("openblas" ,openblas)
4931 ("metis" ,metis)
4932 ("python" ,python)
4933 ("superlu" ,superlu)
4934 ("gmp" ,gmp)))
4935 (native-inputs
4936 `(("gfortran" ,gfortran)
4937 ("pkg-config" ,pkg-config)))
4938 (home-page "https://dune-project.org/")
4939 (synopsis "Distributed and Unified Numerics Environment")
4940 (description "The dune-functions module provides an abstraction layer for
4941global finite element functions. Its two main concepts are functions
4942implemented as callable objects, and bases of finite element spaces.")
4943 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4944 (license (list license:lgpl3+ license:gpl2))))
4714b00e
RW		 4945
4946(define-public dune-pdelab
4947 (package
4948 (name "dune-pdelab")
4949 (version "2.6.0-rc1")
4950 (source
4951 (origin
4952 (method git-fetch)
4953 (uri (git-reference
4954 (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
4955 (commit (string-append "v" version))))
4956 (file-name (git-file-name name version))
4957 (sha256
4958 (base32
4959 "07g0s9448z65vjrq88g5rv3340iifil85k170n8kbqchsvi4ny5v"))))
4960 (build-system cmake-build-system)
4961 (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
4962 (inputs
4963 `(("dune-common" ,dune-common)
4964 ("dune-istl" ,dune-istl)
4965 ("dune-localfunctions" ,dune-localfunctions)
4966 ("dune-geometry" ,dune-geometry)
4967 ("dune-grid" ,dune-grid)
4968 ("dune-typetree" ,dune-typetree)
4969 ("dune-functions" ,dune-functions)
4970 ("openmpi" ,openmpi)
4971 ;; Optional
4972 ("openblas" ,openblas)
4973 ("eigen" ,eigen)
4974 ("metis" ,metis)
4975 ("python" ,python)
4976 ("superlu" ,superlu)
4977 ("gmp" ,gmp)))
4978 (native-inputs
4979 `(("gfortran" ,gfortran)
4980 ("pkg-config" ,pkg-config)))
4981 (home-page "https://dune-project.org/")
4982 (synopsis "Differential equations solver toolbox")
4983 (description "PDELab is a partial differential equations solver toolbox
4984built on top of DUNE, the Distributed and Unified Numerics Environment.")
4985 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4986 (license (list license:lgpl3+ license:gpl2))))
413f6126
AI		 4987
4988(define-public mlucas
4989 (package
4990 (name "mlucas")
4991 (version "18")
4992 (source
4993 (origin
4994 (method url-fetch)
4995 (uri (string-append
4996 "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz"))
4997 (sha256
a36efdbc 4998 (base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447"))))
413f6126
AI		 4999 (build-system gnu-build-system)
5000 (inputs
5001 `(("python2" ,python-2)))
5002 (arguments
a36efdbc 5003 `(#:tests? #f ; no tests
413f6126
AI		 5004 #:phases
5005 (modify-phases %standard-phases
5006 (replace 'configure
5007 (lambda _
5008 (chdir "src")
5009 (call-with-output-file "Makefile"
5010 (lambda (port)
5011 (format port "CC = gcc
5012CFLAGS = -O3 ~a -DUSE_THREADS
5013LDLIBS = -lm -lpthread -lrt
5014Mlucas: $(addsuffix .o,$(basename $(wildcard *.c)))
5015"
5016 ,(let ((system (or (%current-target-system)
5017 (%current-system))))
5018 (cond
5019 ((string-prefix? "x86_64" system) "-DUSE_SSE2")
5020 (else ""))))))
5021 #t))
5022 (replace 'install
5023 (lambda* (#:key outputs #:allow-other-keys)
5024 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
5025 (install-file "Mlucas" bin)
5026 (install-file "primenet.py" bin))
5027 #t)))))
5028 (home-page "https://www.mersenne.org")
5029 (synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client")
5030 (description "Mlucas performs Lucas-Lehmer primality testing of Mersenne
5031numbers in search of a world-record prime. You may use it to test any
5032suitable number as you wish, but it is preferable that you do so in a
5033coordinated fashion, as part of the Great Internet Mersenne Prime
5034Search (GIMPS). Mlucas also includes a simple Python script for assignment
5035management via the GIMPS project's Primenet server.")
5036 (license license:gpl2+)))
6f8c4195
NG		 5037
5038(define-public nauty
5039 (package
5040 (name "nauty")
5041 (version "2.6r11")
5042 (source (origin
5043 (method url-fetch)
5044 (uri (string-append
5045 "https://pallini.di.uniroma1.it/"
5046 "nauty" (string-join (string-split version #\.) "")
5047 ".tar.gz"))
5048 (sha256
5049 (base32
5050 "05z6mk7c31j70md83396cdjmvzzip1hqb88pfszzc6k4gy8h3m2y"))))
5051 (build-system gnu-build-system)
5052 (outputs '("out" "lib"))
5053 (arguments
5054 `(#:test-target "checks"
5055 #:phases
5056 (modify-phases %standard-phases
5057 ;; Default make target does not build all available
5058 ;; executables. Create them now.
5059 (add-after 'build 'build-extra-programs
5060 (lambda _
5061 (for-each (lambda (target) (invoke "make" target))
5062 '("blisstog" "bliss2dre" "checks6" "sumlines"))
5063 #t))
5064 ;; Upstream does not provide any install target.
5065 (replace 'install
5066 (lambda* (#:key outputs #:allow-other-keys)
5067 (let* ((out (assoc-ref outputs "out"))
5068 (lib-output (assoc-ref outputs "lib"))
5069 (bin (string-append out "/bin"))
5070 (doc (string-append out "/share/doc/nauty/"))
5071 (include (string-append lib-output "/include/nauty"))
5072 (lib (string-append lib-output "/lib/nauty")))
5073 (for-each (lambda (f) (install-file f bin))
5074 '("dreadnaut" "NRswitchg" "addedgeg" "amtog" "biplabg"
5075 "blisstog" "bliss2dre" "catg" "checks6" "complg"
5076 "converseg" "copyg" "countg" "cubhamg" "deledgeg"
5077 "delptg" "directg" "dretodot" "dretog" "genbg"
5078 "genbgL" "geng" "genquarticg" "genrang" "genspecialg"
5079 "gentourng" "gentreeg" "hamheuristic" "labelg"
5080 "linegraphg" "listg" "multig" "newedgeg" "pickg"
5081 "planarg" "ranlabg" "shortg" "showg" "subdivideg"
5082 "sumlines" "twohamg" "vcolg" "watercluster2"))
5083 (for-each (lambda (f) (install-file f include))
5084 (find-files "." "\\.h$"))
5085 (for-each (lambda (f) (install-file f lib))
5086 (find-files "." "\\.a$"))
5087 (for-each (lambda (f) (install-file f doc))
5088 (append '("formats.txt" "README" "schreier.txt")
5089 (find-files "." "\\.pdf$")))))))))
5090 (inputs
5091 `(("gmp" ,gmp))) ;for sumlines
5092 (home-page "https://pallini.di.uniroma1.it/")
5093 (synopsis "Library for graph automorphisms")
5094 (description "@code{nauty} (No AUTomorphisms, Yes?) is a set of
5095procedures for computing automorphism groups of graphs and digraphs.
5096
5097@code{nauty} computes graph information in the form of a set of
5098generators, the size of the group, and the orbits of the group; it can
5099also produce a canonical label. The @code{nauty} suite is written in
5100C and comes with a command-line interface, a collection of
5101command-line tools, and an Application Programming Interface (API).
5102
5103This package provides the static libraries required to run programs
5104compiled against the nauty library.")
5105 (license license:asl2.0)))
26433471
AE		 5106
5107(define-public ppl
5108 (package
5109 (name "ppl")
5110 (version "1.2")
5111 (source
5112 (origin
5113 (method url-fetch)
5114 (uri (string-append "https://www.bugseng.com/products/ppl/download/"
5115 "ftp/releases/" version
5116 "/ppl-" version ".tar.gz"))
5117 (sha256
5118 (base32
5119 "1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb"))))
5120 (build-system gnu-build-system)
5121 (native-inputs
5122 `(("m4", m4)))
5123 (inputs
5124 `(("glpk" ,glpk)
5125 ("gmp", gmp)))
5126 (home-page "https://www.bugseng.com/parma-polyhedra-library")
5127 (synopsis
5128 "Parma Polyhedra Library for computations with polyhedra")
5129 (description
5130 "The Parma Polyhedra Library (PPL) provides numerical abstractions
5131especially targeted at applications in the field of analysis and
5132verification of complex systems. These abstractions include convex
5133polyhedra, defined as the intersection of a finite number of (open or
5134closed) halfspaces, each described by a linear inequality (strict or
5135non-strict) with rational coefficients; some special classes of polyhedra
5136shapes that offer interesting complexity/precision tradeoffs; and grids
5137which represent regularly spaced points that satisfy a set of linear
5138congruence relations. The library also supports finite powersets and
5139products of (any kind of) polyhedra and grids, a mixed integer linear
5140programming problem solver using an exact-arithmetic version of the simplex
5141algorithm, a parametric integer programming solver, and primitives for
5142termination analysis via the automatic synthesis of linear ranking
5143functions.")
5144 (license license:gpl3+)))
4cb5d251
SS		 5145
5146(define-public speedcrunch
5147 (package
5148 (name "speedcrunch")
5149 (version "0.12.0")
5150 (source
5151 (origin
5152 (method git-fetch)
5153 (uri (git-reference
5154 (url "https://bitbucket.org/heldercorreia/speedcrunch.git")
5155 (commit (string-append "release-" version))))
5156 (file-name (git-file-name name version))
5157 (sha256
5158 (base32
5159 "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"))))
5160 (build-system cmake-build-system)
5161 (inputs `(("qtbase" ,qtbase)))
5162 (native-inputs `(("qttools" ,qttools)))
5163 (arguments
5164 `(#:phases
5165 (modify-phases %standard-phases
5166 (add-after 'unpack 'chdir-to-src
5167 (lambda _ (chdir "src") #t)))))
5168 (synopsis "High-precision scientific calculator")
5169 (description
5170 "SpeedCrunch is a high-precision scientific calculator. It features a
5171syntax-highlighted scrollable display and is designed to be fully used via
5172keyboard. Some distinctive features are auto-completion of functions and
5173variables, a formula book, and quick insertion of constants from various
5174fields of knowledge.")
5175 (home-page "http://speedcrunch.org/")
5176 (license license:gpl2+)))
5177
3b7828cc
RS		 5178(define-public minisat
5179 ;; This is the last commit which is available upstream, no
5180 ;; release happened since 2010.
5181 (let ((commit "37dc6c67e2af26379d88ce349eb9c4c6160e8543")
5182 (revision "1"))
5183 (package
5184 (name "minisat")
5185 (version (string-append "2.2.0-" revision "." (string-take commit 7)))
5186 (source
5187 (origin
5188 (method git-fetch)
5189 (uri (git-reference
5190 (url "https://github.com/niklasso/minisat.git")
5191 (commit commit)))
5192 (file-name (string-append name "-" version "-checkout"))
5193 (sha256
5194 (base32
5195 "091hf3qkm197s5r7xcr3m07xsdwyz2rqk1hc9kj0hn13imz09irq"))
5196 (patches
5197 (search-patches "minisat-friend-declaration.patch"
5198 "minisat-install.patch"))))
5199 (build-system gnu-build-system)
5200 (arguments
5201 '(#:make-flags (list (string-append "prefix=" %output))
5202 #:tests? #f ;no check target
5203 #:phases
5204 (modify-phases %standard-phases
5205 (delete 'configure))))
5206 (inputs
5207 `(("zlib:static" ,zlib "static")
5208 ("zlib" ,zlib)))
5209 (synopsis
5210 "Small, yet efficient, SAT solver")
5211 (description
5212 "MiniSat is a minimalistic, open-source SAT solver, developed to help
5213researchers and developers alike to get started on SAT.")
5214 (home-page
5215 "http://minisat.se/MiniSat.html")
5216 (license license:expat))))
jackhill's copy of GNU Guix: https://guix.gnu.org/