Commit | Line | Data |
---|---|---|
8f8b2451 | 1 | ;;; GNU Guix --- Functional package management for GNU |
b457f3cc | 2 | ;;; Copyright © 2013, 2014, 2015, 2016, 2019, 2020 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> |
8effdd19 | 5 | ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Eric Bavier <bavier@posteo.net> |
df354a77 | 6 | ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch> |
182d6311 | 7 | ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org> |
0b2c8838 | 8 | ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 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> |
a2da6074 | 11 | ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il> |
45147b0c | 12 | ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de> |
ec8c7e47 | 13 | ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> |
a029cb5e | 14 | ;;; Copyright © 2016, 2018, 2020, 2021 Kei Kebreau <kkebreau@posteo.net> |
de2e3641 | 15 | ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès <ludo@gnu.org> |
d7cff656 | 16 | ;;; Copyright © 2016 Leo Famulari <leo@famulari.name> |
2fd26d05 | 17 | ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be> |
b9fd7f9d | 18 | ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <pgarlick@tourbillion-technology.com> |
3c986a7d | 19 | ;;; Copyright © 2017 Nikita <nikita@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> |
25631d6f | 23 | ;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr> |
dc7d6d4e | 24 | ;;; Copyright © 2017 Dave Love <me@fx@gnu.org> |
9bd65f05 | 25 | ;;; Copyright © 2018, 2019, 2020, 2021 Jan (janneke) 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> |
f72a1253 | 29 | ;;; Copyright © 2018, 2020, 2021 Marius Bakke <marius@gnu.org> |
daa6036f | 30 | ;;; Copyright © 2018 Eric Brown <brown@fastmail.com> |
c9b3627d | 31 | ;;; Copyright © 2018, 2021 Julien Lepiller <julien@lepiller.eu> |
c2cf286c | 32 | ;;; Copyright © 2018 Amin Bandali <bandali@gnu.org> |
bebfe067 | 33 | ;;; Copyright © 2019, 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr> |
4cb5d251 | 34 | ;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com> |
3b7828cc | 35 | ;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net> |
f6b4d395 | 36 | ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> |
bab809ce | 37 | ;;; Copyright © 2020, 2021 Felix Gruber <felgru@posteo.net> |
70c98efa | 38 | ;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in> |
525e83ec | 39 | ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com> |
b60e2d48 | 40 | ;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz> |
d277c00e | 41 | ;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com> |
adc96e1d | 42 | ;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net> |
229e04c6 | 43 | ;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com> |
62671027 | 44 | ;;; Copyright © 2020 Martin Becze <mjbecze@riseup.net> |
f601cdc6 | 45 | ;;; Copyright © 2021 Gerd Heber <gerd.heber@gmail.com> |
5fd046cb | 46 | ;;; Copyright © 2021 Franck Pérignon <franck.perignon@univ-grenoble-alpes.fr> |
969adb23 | 47 | ;;; Copyright © 2021 Philip McGrath <philip@philipmcgrath.com> |
d2e531fa | 48 | ;;; Copyright © 2021 Paul A. Patience <paul@apatience.com> |
68ce40ca | 49 | ;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru> |
4709b74b | 50 | ;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me> |
e1b711b1 | 51 | ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net> |
8f8b2451 AE |
52 | ;;; |
53 | ;;; This file is part of GNU Guix. | |
54 | ;;; | |
55 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
56 | ;;; under the terms of the GNU General Public License as published by | |
57 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
58 | ;;; your option) any later version. | |
59 | ;;; | |
60 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
61 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
62 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
63 | ;;; GNU General Public License for more details. | |
64 | ;;; | |
65 | ;;; You should have received a copy of the GNU General Public License | |
66 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
67 | ||
68 | (define-module (gnu packages maths) | |
ec322be2 | 69 | #:use-module (ice-9 regex) |
a6b9ebc2 | 70 | #:use-module (ice-9 match) |
8f8b2451 | 71 | #:use-module (gnu packages) |
b5b73a82 | 72 | #:use-module ((guix licenses) #:prefix license:) |
8f8b2451 AE |
73 | #:use-module (guix packages) |
74 | #:use-module (guix download) | |
54052a54 | 75 | #:use-module (guix git-download) |
e1b711b1 | 76 | #:use-module (guix gexp) |
0e2672ae | 77 | #:use-module (guix utils) |
fa574a6d | 78 | #:use-module ((guix build utils) #:select (alist-replace)) |
da95c817 | 79 | #:use-module (guix build-system cmake) |
72c71d24 | 80 | #:use-module (guix build-system glib-or-gtk) |
c9dfa3c7 | 81 | #:use-module (guix build-system gnu) |
c9b3627d | 82 | #:use-module (guix build-system ocaml) |
560acf25 | 83 | #:use-module (guix build-system python) |
63e07468 | 84 | #:use-module (guix build-system ruby) |
3de01d3f | 85 | #:use-module (gnu packages algebra) |
ab5f3f21 | 86 | #:use-module (gnu packages audio) |
5143517c | 87 | #:use-module (gnu packages autotools) |
fa574a6d | 88 | #:use-module (gnu packages base) |
e1b711b1 | 89 | #:use-module (gnu packages bash) |
3de01d3f | 90 | #:use-module (gnu packages bison) |
a17d4564 | 91 | #:use-module (gnu packages boost) |
e73b49fb | 92 | #:use-module (gnu packages check) |
3de01d3f | 93 | #:use-module (gnu packages cmake) |
c9dfa3c7 | 94 | #:use-module (gnu packages compression) |
c9b3627d | 95 | #:use-module (gnu packages coq) |
668c06ac | 96 | #:use-module (gnu packages curl) |
b7b27a8f | 97 | #:use-module (gnu packages cyrus-sasl) |
8a0dd289 | 98 | #:use-module (gnu packages dbm) |
528bb464 | 99 | #:use-module (gnu packages documentation) |
57e544e8 | 100 | #:use-module (gnu packages elf) |
c9b3627d | 101 | #:use-module (gnu packages emacs) |
70c98efa | 102 | #:use-module (gnu packages file) |
3de01d3f | 103 | #:use-module (gnu packages flex) |
668c06ac | 104 | #:use-module (gnu packages fltk) |
f3929800 | 105 | #:use-module (gnu packages fontutils) |
1dba6407 | 106 | #:use-module (gnu packages gettext) |
da95c817 | 107 | #:use-module (gnu packages gcc) |
73fed4f8 | 108 | #:use-module (gnu packages gd) |
668c06ac | 109 | #:use-module (gnu packages ghostscript) |
70c98efa | 110 | #:use-module (gnu packages glib) |
889187a4 | 111 | #:use-module (gnu packages graphviz) |
f3929800 | 112 | #:use-module (gnu packages gtk) |
70c98efa | 113 | #:use-module (gnu packages icu4c) |
45147b0c | 114 | #:use-module (gnu packages image) |
2fd26d05 | 115 | #:use-module (gnu packages java) |
668c06ac | 116 | #:use-module (gnu packages less) |
8731e527 | 117 | #:use-module (gnu packages lisp) |
ab5f3f21 | 118 | #:use-module (gnu packages linux) |
f5f64205 | 119 | #:use-module (gnu packages llvm) |
bc3a2e35 | 120 | #:use-module (gnu packages logging) |
6e64766a | 121 | #:use-module (gnu packages lua) |
5698b8b8 | 122 | #:use-module (gnu packages gnome) |
1b39a196 | 123 | #:use-module (gnu packages guile) |
668c06ac JD |
124 | #:use-module (gnu packages xorg) |
125 | #:use-module (gnu packages gl) | |
9f913401 | 126 | #:use-module (gnu packages imagemagick) |
8731e527 | 127 | #:use-module (gnu packages m4) |
d8c7eeb9 | 128 | #:use-module (gnu packages mpi) |
b92eee75 | 129 | #:use-module (gnu packages multiprecision) |
d3ede451 | 130 | #:use-module (gnu packages ncurses) |
528bb464 | 131 | #:use-module (gnu packages netpbm) |
c9b3627d | 132 | #:use-module (gnu packages ocaml) |
bd3d71cb | 133 | #:use-module (gnu packages onc-rpc) |
a9bc8a25 | 134 | #:use-module (gnu packages parallel) |
668c06ac | 135 | #:use-module (gnu packages pcre) |
5698b8b8 | 136 | #:use-module (gnu packages popt) |
c9dfa3c7 AE |
137 | #:use-module (gnu packages perl) |
138 | #:use-module (gnu packages pkg-config) | |
ab5f3f21 | 139 | #:use-module (gnu packages pulseaudio) |
da95c817 | 140 | #:use-module (gnu packages python) |
589e3f4e | 141 | #:use-module (gnu packages python-web) |
44d10b1f | 142 | #:use-module (gnu packages python-xyz) |
5b05dce7 | 143 | #:use-module (gnu packages qt) |
c9dfa3c7 | 144 | #:use-module (gnu packages readline) |
63e07468 | 145 | #:use-module (gnu packages ruby) |
2742f87e | 146 | #:use-module (gnu packages tbb) |
479c4273 | 147 | #:use-module (gnu packages scheme) |
64d4bc08 | 148 | #:use-module (gnu packages serialization) |
b7194849 | 149 | #:use-module (gnu packages shells) |
f72a1253 | 150 | #:use-module (gnu packages sphinx) |
df354a77 | 151 | #:use-module (gnu packages tcl) |
668c06ac | 152 | #:use-module (gnu packages texinfo) |
8f9ac901 | 153 | #:use-module (gnu packages tex) |
b7b27a8f | 154 | #:use-module (gnu packages tls) |
5b05dce7 | 155 | #:use-module (gnu packages version-control) |
9aafbc0c | 156 | #:use-module (gnu packages wxwidgets) |
c12efc72 | 157 | #:use-module (gnu packages xml) |
9bb7534a EF |
158 | #:use-module (srfi srfi-1) |
159 | #:use-module (srfi srfi-26)) | |
8f8b2451 | 160 | |
193abc82 JD |
161 | (define-public aris |
162 | (package | |
1f45f18a JD |
163 | (name "aris") |
164 | (version "2.2") | |
165 | (source (origin | |
166 | (method url-fetch) | |
167 | (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz")) | |
168 | (sha256 (base32 | |
169 | "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q")))) | |
170 | (build-system gnu-build-system) | |
171 | (inputs `(("gtk+" ,gtk+) | |
172 | ("libxml2" ,libxml2))) | |
173 | (native-inputs `(("pkg-config" ,pkg-config))) | |
bad54e63 GLV |
174 | (arguments |
175 | `(#:configure-flags '("CFLAGS=-fcommon"))) | |
1f45f18a JD |
176 | (synopsis "Natural deduction first-order logic interface") |
177 | (description "Aris is a program for performing logical proofs. It supports | |
178 | propositional and predicate logic, as well as Boolean algebra and | |
179 | arithmetical logic. In addition to its predefined inference and equivalence | |
180 | rules, Aris also supports references to older proofs. Its use of standard | |
181 | logical symbols and its natural deduction interface make it easy to use for | |
182 | beginners.") | |
183 | (license license:gpl3+) | |
6fd52309 | 184 | (home-page "https://www.gnu.org/software/aris/"))) |
193abc82 | 185 | |
d3ede451 GT |
186 | (define-public bitwise |
187 | (package | |
188 | (name "bitwise") | |
189 | (version "0.42") | |
190 | (source (origin | |
191 | (method url-fetch) | |
192 | (uri (string-append "https://github.com/mellowcandle/bitwise" | |
193 | "/releases/download/v" version | |
194 | "/bitwise-v" version ".tar.gz")) | |
195 | (sha256 | |
196 | (base32 "1lniw4bsb5qs5ybf018qllf95pzixb1q3lvybzl4k3xz8zpkrm6k")))) | |
197 | (build-system gnu-build-system) | |
198 | (inputs | |
199 | `(("ncurses" ,ncurses) | |
200 | ("readline" ,readline))) | |
201 | (native-inputs | |
202 | `(("cunit" ,cunit) | |
203 | ("pkg-config" ,pkg-config))) | |
204 | (synopsis "Terminal based bit manipulator in ncurses") | |
205 | (description "Bitwise is a multi base interactive calculator supporting | |
206 | dynamic base conversion and bit manipulation. It's a handy tool for low level | |
207 | hackers, kernel developers and device drivers developers. | |
208 | ||
209 | Some of the features include: | |
210 | @itemize | |
211 | @item Interactive ncurses interface. | |
212 | @item Command line calculator supporting all bitwise operations. | |
213 | @item Individual bit manipulator. | |
214 | @item Bitwise operations such as NOT, OR, AND, XOR, and shifts. | |
215 | @end itemize") | |
216 | (license license:gpl3+) | |
217 | (home-page "https://github.com/mellowcandle/bitwise/"))) | |
218 | ||
9c45c519 JD |
219 | (define-public c-graph |
220 | (package | |
221 | (name "c-graph") | |
0ef54303 | 222 | (version "2.0.1") |
9c45c519 JD |
223 | (source (origin |
224 | (method url-fetch) | |
225 | (uri (string-append "mirror://gnu/c-graph/c-graph-" version | |
226 | ".tar.gz")) | |
227 | (sha256 (base32 | |
0ef54303 | 228 | "092412jzxy6wdvpk96pfj499hpmaww8xllavbvlqspfpr7ips9id")))) |
9c45c519 JD |
229 | (build-system gnu-build-system) |
230 | (inputs | |
0ef54303 | 231 | `(("fortran" ,gfortran))) |
a3947cb1 | 232 | (synopsis "Visualizing and demonstrating convolution") |
9c45c519 | 233 | (description |
0ef54303 | 234 | "GNU C-Graph is a tool for demonstrating the theory of convolution. |
a3947cb1 LC |
235 | Thus, it can serve as an excellent aid to students of signal and systems |
236 | theory in visualizing the convolution process. Rather than forcing the | |
237 | student to write code, the program offers an intuitive interface with | |
238 | interactive dialogs to guide them.") | |
9c45c519 | 239 | (license license:gpl3+) |
6fd52309 | 240 | (home-page "https://www.gnu.org/software/c-graph/"))) |
9c45c519 | 241 | |
d91025e3 TD |
242 | (define-public coda |
243 | (package | |
244 | (name "coda") | |
9285f8bb | 245 | (version "2.19") |
d91025e3 TD |
246 | (source |
247 | (origin | |
248 | (method url-fetch) | |
249 | (uri (string-append "https://github.com/stcorp/coda/releases/download/" | |
250 | version "/coda-" version ".tar.gz")) | |
251 | (sha256 | |
9285f8bb | 252 | (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245")) |
4b12fe5c TD |
253 | (patches (search-patches "coda-use-system-libs.patch")) |
254 | (modules '((guix build utils))) | |
255 | (snippet | |
256 | ;; Make sure we don't use the bundled software. | |
6cbee49d MW |
257 | '(begin |
258 | (for-each (lambda (d) | |
259 | (delete-file-recursively (string-append "libcoda/" d))) | |
260 | '("zlib" "pcre" "expat")) | |
261 | #t)))) | |
d91025e3 TD |
262 | (native-inputs |
263 | `(("fortran" ,gfortran) | |
264 | ("python" ,python) | |
265 | ("python-numpy" ,python-numpy))) | |
266 | (inputs | |
267 | `(("zlib" ,zlib) | |
4b12fe5c TD |
268 | ("pcre" ,pcre) |
269 | ("expat" ,expat) | |
d91025e3 TD |
270 | ("hdf4" ,hdf4-alt) |
271 | ("hdf5" ,hdf5))) | |
272 | (build-system gnu-build-system) | |
273 | (arguments | |
4b12fe5c TD |
274 | '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python" |
275 | "LIBS= -lz -lpcre -lexpat"))) | |
d91025e3 TD |
276 | (synopsis "A common interface to various earth observation data formats") |
277 | (description | |
278 | "The Common Data Access toolbox (CODA) provides a set of interfaces for | |
279 | reading remote sensing data from earth observation data files. It consists of | |
280 | command line applications and interfaces to the C, Fortran, Python, and Java | |
281 | programming languages.") | |
282 | (home-page "https://stcorp.nl/coda") | |
283 | (license license:gpl2+))) | |
284 | ||
d65f0661 KK |
285 | (define-public qhull |
286 | (package | |
287 | (name "qhull") | |
c6f1e13a | 288 | (version "2020.2") |
d65f0661 KK |
289 | (source (origin |
290 | (method url-fetch) | |
291 | (uri (string-append "http://www.qhull.org/download/qhull-" | |
292 | (car (string-split version #\.)) | |
c6f1e13a | 293 | "-src-8.0.2.tgz")) |
d65f0661 KK |
294 | (sha256 |
295 | (base32 | |
c6f1e13a | 296 | "0zlbhg0lb6j60188c2xhcrvviskr079552icjldqhy1jhgmxghmm")))) |
d65f0661 | 297 | (build-system cmake-build-system) |
c942e17c | 298 | (arguments |
0ffac75e EF |
299 | `(#:configure-flags '("-DLINK_APPS_SHARED=ON" |
300 | "-DCMAKE_POSITION_INDEPENDENT_CODE=ON"))) | |
d65f0661 KK |
301 | (synopsis "Calculate convex hulls and related structures") |
302 | (description | |
303 | "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi | |
304 | diagram, halfspace intersection about a point, furthest-site Delaunay | |
305 | triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, | |
306 | 3-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull | |
307 | algorithm for computing the convex hull. It handles roundoff errors from | |
308 | floating point arithmetic. It computes volumes, surface areas, and | |
309 | approximations to the convex hull. | |
310 | ||
311 | @code{Qhull} does not support triangulation of non-convex surfaces, mesh | |
312 | generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha | |
313 | shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay | |
314 | triangulations.") | |
315 | (home-page "http://qhull.org") | |
316 | (license (license:non-copyleft "file://COPYING.txt" | |
317 | "See COPYING in the distribution.")))) | |
318 | ||
a8fa86c4 RW |
319 | (define-public python-cvxopt |
320 | (package | |
321 | (name "python-cvxopt") | |
a7c7015a | 322 | (version "1.2.3") |
a8fa86c4 RW |
323 | (source (origin |
324 | (method git-fetch) | |
325 | (uri (git-reference | |
b0e7b699 | 326 | (url "https://github.com/cvxopt/cvxopt") |
a8fa86c4 RW |
327 | (commit version))) |
328 | (file-name (git-file-name name version)) | |
329 | (sha256 | |
330 | (base32 | |
a7c7015a | 331 | "1kiy2m62xgs2d5id6dnnwy4vap85cd70p7pgkb9nh23qf9xnak7b")))) |
a8fa86c4 RW |
332 | (build-system python-build-system) |
333 | (arguments | |
334 | `(#:phases | |
335 | (modify-phases %standard-phases | |
336 | (add-after 'unpack 'find-libraries | |
337 | (lambda* (#:key inputs #:allow-other-keys) | |
338 | (setenv "CVXOPT_BLAS_LIB" "openblas") | |
339 | (setenv "CVXOPT_BUILD_FFTW" "1") | |
340 | (setenv "CVXOPT_BUILD_GLPK" "1") | |
341 | (setenv "CVXOPT_BUILD_GSL" "1") | |
342 | #t))))) | |
343 | (inputs | |
344 | `(("fftw" ,fftw) | |
345 | ("glpk" ,glpk) | |
346 | ("gsl" ,gsl) | |
347 | ("lapack" ,lapack) | |
348 | ("openblas" ,openblas) | |
349 | ("suitesparse" ,suitesparse))) | |
350 | (home-page "https://www.cvxopt.org") | |
351 | (synopsis "Python library for convex optimization") | |
352 | (description | |
353 | "CVXOPT is a package for convex optimization based on the Python | |
354 | programming language. Its main purpose is to make the development of software | |
355 | for convex optimization applications straightforward by building on Python’s | |
356 | extensive standard library and on the strengths of Python as a high-level | |
357 | programming language.") | |
358 | (license license:gpl3+))) | |
359 | ||
360 | (define-public python2-cvxopt | |
361 | (package-with-python2 python-cvxopt)) | |
362 | ||
8f8b2451 AE |
363 | (define-public units |
364 | (package | |
365 | (name "units") | |
1b16727c | 366 | (version "2.21") |
8f8b2451 AE |
367 | (source (origin |
368 | (method url-fetch) | |
369 | (uri (string-append "mirror://gnu/units/units-" version | |
370 | ".tar.gz")) | |
371 | (sha256 (base32 | |
1b16727c | 372 | "1bybhqs4yrly9myb5maz3kdmf8k4fhk2m1d5cbcryn40z6lq0gkc")))) |
8f8b2451 | 373 | (build-system gnu-build-system) |
0498d248 | 374 | (inputs |
a2549713 EB |
375 | `(("readline" ,readline) |
376 | ("python" ,python-wrapper) ;for 'units_cur' script | |
0498d248 EB |
377 | ("python-requests" ,python-requests))) |
378 | (arguments | |
379 | `(#:phases (modify-phases %standard-phases | |
380 | (add-after 'install 'wrap-units_cur | |
381 | (lambda* (#:key outputs #:allow-other-keys) | |
382 | (let* ((out (assoc-ref outputs "out")) | |
383 | (bin (string-append out "/bin"))) | |
384 | (wrap-program (string-append bin "/units_cur") | |
d42245d4 MC |
385 | `("GUIX_PYTHONPATH" ":" prefix |
386 | ,(search-path-as-string->list (getenv "GUIX_PYTHONPATH")))) | |
0498d248 | 387 | #t)))))) |
8f8b2451 AE |
388 | (synopsis "Conversion between thousands of scales") |
389 | (description | |
574e86f9 | 390 | "GNU Units converts numeric quantities between units of measure. It |
7c125ce0 AK |
391 | can handle scale changes through adaptive usage of standard scale |
392 | prefixes (micro-, kilo-, etc.). It can also handle nonlinear | |
393 | conversions such as Fahrenheit to Celsius. Its interpreter is powerful | |
394 | enough to be used effectively as a scientific calculator.") | |
8f8b2451 | 395 | (license license:gpl3+) |
6fd52309 | 396 | (home-page "https://www.gnu.org/software/units/"))) |
c9dfa3c7 | 397 | |
61a529b4 RW |
398 | (define-public double-conversion |
399 | (package | |
400 | (name "double-conversion") | |
1c7d7f3f | 401 | (version "3.1.5") |
b343850e | 402 | (home-page "https://github.com/google/double-conversion") |
61a529b4 | 403 | (source (origin |
2bdc73fb | 404 | (method git-fetch) |
a4de1a65 MB |
405 | (uri (git-reference (url home-page) |
406 | (commit (string-append "v" version)))) | |
2bdc73fb | 407 | (file-name (git-file-name name version)) |
61a529b4 RW |
408 | (sha256 |
409 | (base32 | |
1c7d7f3f | 410 | "0csy4pjw1p8rp6g5qxi2h0ychhhp1fldv7gb761627fs2mclw9gv")))) |
61a529b4 RW |
411 | (build-system cmake-build-system) |
412 | (arguments | |
413 | '(#:test-target "test" | |
414 | #:configure-flags '("-DBUILD_SHARED_LIBS=ON" | |
415 | "-DBUILD_TESTING=ON"))) | |
61a529b4 RW |
416 | (synopsis "Conversion routines for IEEE doubles") |
417 | (description | |
418 | "The double-conversion library provides binary-decimal and decimal-binary | |
419 | routines for IEEE doubles. The library consists of efficient conversion | |
420 | routines that have been extracted from the V8 JavaScript engine.") | |
421 | (license license:bsd-3))) | |
422 | ||
182d6311 ML |
423 | (define-public dionysus |
424 | (package | |
425 | (name "dionysus") | |
bd041e7f | 426 | (version "1.4.0") |
182d6311 ML |
427 | (source (origin |
428 | (method url-fetch) | |
429 | (uri (string-append "mirror://gnu/dionysus/dionysus-" version | |
bd041e7f | 430 | ".tar.xz")) |
182d6311 ML |
431 | (sha256 |
432 | (base32 | |
bd041e7f | 433 | "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk")))) |
182d6311 ML |
434 | (build-system gnu-build-system) |
435 | (inputs `(("tcl" ,tcl))) ;for 'tclsh' | |
436 | (synopsis "Local search for universal constants and scientific values") | |
437 | (description | |
438 | "GNU Dionysus is a convenient system for quickly retrieving the values of | |
439 | mathematical constants used in science and engineering. Values can be | |
440 | searched using a simple command-line tool, choosing from three databases: | |
441 | universal constants, atomic numbers, and constants related to | |
442 | semiconductors.") | |
443 | (license license:gpl3+) | |
6fd52309 | 444 | (home-page "https://www.gnu.org/software/dionysus/"))) |
182d6311 | 445 | |
b60e2d48 NB |
446 | (define-public dsfmt |
447 | (package | |
448 | (name "dsfmt") | |
449 | (version "2.2.3") | |
450 | (source | |
451 | (origin | |
452 | (method url-fetch) | |
453 | (uri | |
454 | (string-append | |
455 | "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/" | |
456 | "dSFMT-src-" version ".tar.gz")) | |
457 | (sha256 | |
458 | (base32 | |
459 | "03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42")) | |
460 | (modules '((guix build utils))) | |
461 | ;; Don't distribute html documentation with bundled jquery. | |
462 | (snippet | |
463 | '(begin | |
464 | (delete-file-recursively "html") #t)) | |
465 | ;; Add patches borrowed from Julia. | |
466 | (patches | |
467 | (list | |
468 | (origin | |
469 | (method url-fetch) | |
470 | (uri (string-append | |
471 | "https://raw.githubusercontent.com/JuliaLang/julia/" | |
472 | "v1.3.0/deps/patches/dSFMT.c.patch")) | |
473 | (sha256 (base32 | |
474 | "09mhv11bms8jsmkmdqvlcgljwhzw3b6n9nncpi2b6dla9798hw2y")) | |
475 | (file-name "dSFMT.c.patch")) | |
476 | (origin | |
477 | (method url-fetch) | |
478 | (uri (string-append | |
479 | "https://raw.githubusercontent.com/JuliaLang/julia/" | |
480 | "v1.3.0/deps/patches/dSFMT.h.patch")) | |
481 | (sha256 (base32 | |
482 | "1py5rd0yxic335lzka23f6x2dhncrpizpyrk57gi2f28c0p98y5n")) | |
483 | (file-name "dSFMT.h.patch")))))) | |
484 | (build-system gnu-build-system) | |
485 | (arguments | |
486 | `(#:phases | |
487 | (modify-phases %standard-phases | |
488 | (delete 'configure) ; no configure script | |
489 | (replace 'build | |
490 | ;; Upstream Makefile does not build a shared library. Borrow from Julia | |
491 | ;; https://github.com/JuliaLang/julia/blob/v1.3.0/deps/dsfmt.mk | |
492 | (lambda _ | |
493 | (invoke | |
494 | "gcc" "-DNDEBUG" "-DDSFMT_MEXP=19937" | |
495 | "-fPIC" "-DDSFMT_DO_NOT_USE_OLD_NAMES" | |
496 | "-O3" "-finline-functions" "-fomit-frame-pointer" | |
497 | "-fno-strict-aliasing" "--param" "max-inline-insns-single=1800" | |
498 | "-Wmissing-prototypes" "-Wall" "-std=c99" "-shared" "dSFMT.c" | |
499 | "-o" "libdSFMT.so"))) | |
500 | (replace 'install ; no "install" target | |
501 | (lambda* (#:key outputs #:allow-other-keys) | |
502 | (let* ((out (assoc-ref outputs "out")) | |
503 | (lib (string-append out "/lib")) | |
504 | (inc (string-append out "/include")) | |
505 | (doc (string-append out "/share/doc/" ,name "-" ,version))) | |
506 | (install-file "libdSFMT.so" lib) | |
507 | (install-file "dSFMT.h" inc) | |
508 | (install-file "LICENSE.txt" doc) | |
509 | #t)))))) | |
510 | (synopsis "Double precision SIMD-oriented Fast Mersenne Twister") | |
511 | (description | |
512 | "The dSMFT package speeds up Fast Mersenne Twister generation by avoiding | |
513 | the expensive conversion of integer to double (floating point). dSFMT directly | |
514 | generates double precision floating point pseudorandom numbers which have the | |
515 | IEEE Standard for Binary Floating-Point Arithmetic (ANSI/IEEE Std 754-1985) | |
516 | format. dSFMT is only available on the CPUs which use IEEE 754 format double | |
517 | precision floating point numbers.") | |
518 | (home-page "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/") | |
519 | (license license:bsd-3))) | |
520 | ||
88bd1804 AE |
521 | (define-public gsl |
522 | (package | |
523 | (name "gsl") | |
b51bb5bc | 524 | (version "2.7") |
ab2cc5cd LC |
525 | (source (origin |
526 | (method url-fetch) | |
527 | (uri (string-append "mirror://gnu/gsl/gsl-" | |
528 | version ".tar.gz")) | |
529 | (sha256 | |
530 | (base32 | |
b51bb5bc | 531 | "0av04cpblphvvs3kl5rwphniarml503501vrpqw31rd0bmwg7fzg")))) |
88bd1804 | 532 | (build-system gnu-build-system) |
71e0f288 | 533 | (arguments |
c745b6f6 | 534 | (let ((system (%current-system))) |
03cb1140 LC |
535 | `(#:configure-flags (list "--disable-static") ;halves package size |
536 | #:phases | |
4f6fbe75 LC |
537 | (modify-phases %standard-phases |
538 | ,@(cond | |
539 | ((or (string-prefix? "aarch64" system) | |
540 | (string-prefix? "powerpc" system)) | |
541 | ;; Some sparse matrix tests are failing on AArch64 and PowerPC: | |
542 | ;; https://lists.gnu.org/archive/html/bug-gsl/2020-04/msg00001.html | |
543 | '((add-before 'check 'disable-failing-tests | |
544 | (lambda _ | |
545 | (substitute* "spmatrix/test.c" | |
b51bb5bc | 546 | ((".*test_complex.*") "\n")))))) |
4f6fbe75 LC |
547 | |
548 | ((string-prefix? "i686" system) | |
549 | ;; There are rounding issues with these tests on i686: | |
550 | ;; https://lists.gnu.org/archive/html/bug-gsl/2016-10/msg00000.html | |
551 | ;; https://lists.gnu.org/archive/html/bug-gsl/2020-04/msg00000.html | |
552 | '((add-before 'check 'disable-failing-tests | |
553 | (lambda _ | |
554 | (substitute* "linalg/test.c" | |
555 | ((".*gsl_test\\(test_LU_decomp.*") "\n") | |
556 | ((".*gsl_test\\(test_LUc_decomp.*") "\n") | |
921595fa | 557 | ((".*gsl_test\\(test_QR_decomp_r.*") "\n") |
4f6fbe75 | 558 | ((".*gsl_test\\(test_cholesky_decomp.*") "\n") |
921595fa | 559 | ((".*gsl_test\\(test_pcholesky_solve.*") "\n") |
4f6fbe75 LC |
560 | ((".*gsl_test\\(test_COD_lssolve2.*") "\n")) |
561 | (substitute* "spmatrix/test.c" | |
562 | ((".*test_all.*") "\n") | |
563 | ((".*test_float.*") "\n") | |
921595fa LC |
564 | ((".*test_complex.*") "\n")) |
565 | ||
566 | ;; XXX: These tests abort with: | |
567 | ;; gsl: cholesky.c:645: ERROR: matrix is not positive definite | |
568 | (substitute* '("multifit_nlinear/test.c" | |
569 | "multilarge_nlinear/test.c") | |
570 | (("gsl_ieee_env_setup.*" all) | |
571 | (string-append "exit (77);\n" all))))))) | |
4f6fbe75 LC |
572 | |
573 | (else '())))))) | |
6f766069 | 574 | (home-page "https://www.gnu.org/software/gsl/") |
88bd1804 AE |
575 | (synopsis "Numerical library for C and C++") |
576 | (description | |
a22dc0c4 LC |
577 | "The GNU Scientific Library is a library for numerical analysis in C |
578 | and C++. It includes a wide range of mathematical routines, with over 1000 | |
579 | functions in total. Subject areas covered by the library include: | |
580 | differential equations, linear algebra, Fast Fourier Transforms and random | |
581 | numbers.") | |
88bd1804 AE |
582 | (license license:gpl3+))) |
583 | ||
c1f38577 VM |
584 | (define-public sleef |
585 | (package | |
586 | (name "sleef") | |
5f40ad9a | 587 | (version "3.5.1") |
c1f38577 VM |
588 | (source |
589 | (origin | |
590 | (method git-fetch) | |
591 | (uri (git-reference | |
592 | (url "https://github.com/shibatch/sleef") | |
593 | (commit version))) | |
594 | (file-name (git-file-name name version)) | |
595 | (sha256 | |
5f40ad9a | 596 | (base32 "1jybqrl2dvjxzg30xrhh847s375n2jr1pix644wi6hb5wh5mx3f7")))) |
c1f38577 VM |
597 | (build-system cmake-build-system) |
598 | (arguments | |
599 | '(#:configure-flags (list "-DCMAKE_BUILD_TYPE=Release" | |
600 | (string-append "-DCMAKE_INSTALL_LIBDIR=" | |
601 | (assoc-ref %outputs "out") | |
602 | "/lib") | |
603 | (string-append "-DCMAKE_INSTALL_PREFIX=" | |
604 | (assoc-ref %outputs "out"))) | |
605 | #:phases | |
606 | (modify-phases %standard-phases | |
607 | ;; SLEEF generates a header library during the build process and writes | |
608 | ;; to it via shell redirection. Make the checkout writable so the | |
609 | ;; build can succeed. | |
610 | (add-after 'unpack 'make-git-checkout-writable | |
611 | (lambda _ | |
612 | (for-each make-file-writable (find-files ".")) | |
613 | #t))))) | |
614 | (inputs | |
615 | `(("fftw" ,fftw) | |
616 | ("gmp" ,gmp) | |
617 | ("mpfr" ,mpfr) | |
618 | ("openssl" ,openssl))) | |
619 | (home-page "https://sleef.org/") | |
620 | (synopsis "SIMD library for evaluating elementary functions and DFT") | |
621 | (description | |
622 | "SLEEF (SIMD Library for Evaluating Elementary Functions) is a library that | |
623 | implements vectorized versions of all C99 real floating point math functions. | |
624 | It can utilize SIMD instructions that are available on modern processors.") | |
625 | (license (list license:boost1.0 ;sleef | |
626 | license:cc-by4.0)))) ;simplex algorithm | |
627 | ||
b92eee75 AE |
628 | (define-public glpk |
629 | (package | |
630 | (name "glpk") | |
885fe927 | 631 | (version "5.0") |
b92eee75 AE |
632 | (source |
633 | (origin | |
634 | (method url-fetch) | |
635 | (uri (string-append "mirror://gnu/glpk/glpk-" | |
636 | version ".tar.gz")) | |
637 | (sha256 | |
638 | (base32 | |
885fe927 | 639 | "05bgxidxj8d9xdp82niy7cy36w181cxq7p8vc3y2ixshpgp1642a")))) |
b92eee75 AE |
640 | (build-system gnu-build-system) |
641 | (inputs | |
642 | `(("gmp" ,gmp))) | |
643 | (arguments | |
9a6cf550 EF |
644 | `(#:configure-flags '("--with-gmp" |
645 | "--disable-static"))) | |
82110ef6 | 646 | (home-page "https://www.gnu.org/software/glpk/") |
79c311b8 | 647 | (synopsis "GNU Linear Programming Kit, supporting the MathProg language") |
b92eee75 AE |
648 | (description |
649 | "GLPK is a C library for solving large-scale linear programming (LP), | |
650 | mixed integer programming (MIP), and other related problems. It supports the | |
651 | GNU MathProg modeling language, a subset of the AMPL language, and features a | |
652 | translator for the language. In addition to the C library, a stand-alone | |
653 | LP/MIP solver is included in the package.") | |
654 | (license license:gpl3+))) | |
655 | ||
885fe927 EF |
656 | (define-public glpk-4 |
657 | (package | |
658 | (inherit glpk) | |
659 | (name "glpk") | |
660 | (version "4.65") | |
661 | (source | |
662 | (origin | |
663 | (method url-fetch) | |
664 | (uri (string-append "mirror://gnu/glpk/glpk-" | |
665 | version ".tar.gz")) | |
666 | (sha256 | |
667 | (base32 | |
668 | "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2")))))) | |
669 | ||
b146763a AE |
670 | (define-public 4ti2 |
671 | (package | |
672 | (name "4ti2") | |
eea4a091 | 673 | (version "1.6.9") |
b146763a AE |
674 | (source |
675 | (origin | |
eea4a091 TGR |
676 | (method url-fetch) |
677 | (uri (string-append "https://github.com/4ti2/4ti2/releases/download/" | |
678 | "Release_" | |
679 | (string-map (lambda (c) (if (char=? c #\.) #\_ c)) | |
680 | version) | |
681 | "/4ti2-" version ".tar.gz")) | |
682 | (sha256 | |
683 | (base32 "0rj92x6p9m3la5gasjbj7sa569im527ffmka5y2sv1amgd3fflrh")))) | |
b146763a AE |
684 | (build-system gnu-build-system) |
685 | (native-inputs | |
686 | `(("which" ,(@ (gnu packages base) which)))) ; for the tests | |
687 | (inputs | |
688 | `(("glpk" ,glpk) | |
689 | ("gmp" ,gmp))) | |
690 | (home-page "http://www.4ti2.de/") | |
691 | (synopsis "Mathematical tool suite for problems on linear spaces") | |
692 | (description | |
693 | "4ti2 implements algorithms for solving algebraic, geometric and | |
694 | combinatorial problems on linear spaces. Among others, it solves systems | |
695 | of linear equations, computes extreme rays of polyhedral cones, solves | |
696 | integer programming problems and computes Markov bases for statistics.") | |
697 | (license license:gpl2+))) | |
698 | ||
53696f10 AE |
699 | (define-public cddlib |
700 | (package | |
701 | (name "cddlib") | |
7fe491fb | 702 | (version "0.94i") |
53696f10 AE |
703 | (source |
704 | (origin | |
705 | (method url-fetch) | |
182dde82 | 706 | (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-" |
53696f10 AE |
707 | (string-delete #\. version) ".tar.gz")) |
708 | (sha256 | |
709 | (base32 | |
7fe491fb | 710 | "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq")))) |
53696f10 AE |
711 | (build-system gnu-build-system) |
712 | (inputs | |
713 | `(("gmp" ,gmp))) | |
714 | (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html") | |
715 | (synopsis "Library for convex hulls and extreme rays of polyhedra") | |
716 | (description | |
717 | "The C-library cddlib implements the Double Description Method of | |
718 | Motzkin et al. for generating all vertices (i.e. extreme points) and extreme | |
719 | rays of a general convex polyhedron given by a system of linear inequalities | |
720 | in arbitrary dimension. It can also be used for the converse operation of | |
721 | computing convex hulls.") | |
722 | (license license:gpl2+))) | |
723 | ||
0ffc2d53 AE |
724 | (define-public lrslib |
725 | (package | |
726 | (name "lrslib") | |
f37e2388 | 727 | (version "7.1") |
0ffc2d53 AE |
728 | (source |
729 | (origin | |
730 | (method url-fetch) | |
731 | (uri (string-append "http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/" | |
732 | "lrslib-0" | |
733 | (string-delete #\. version) ".tar.gz")) | |
734 | (sha256 | |
735 | (base32 | |
f37e2388 | 736 | "05kq3hzam31dlmkccv3v358r478kpvx76mw37ka12c6ypwv5dsnk")))) |
0ffc2d53 AE |
737 | (build-system gnu-build-system) |
738 | (inputs | |
739 | `(("gmp" ,gmp))) | |
740 | (arguments | |
741 | `(#:tests? #f ; no check phase | |
742 | #:make-flags `("CC=gcc" | |
743 | ,(string-append "prefix=" (assoc-ref %outputs "out")) | |
744 | "all-shared") | |
745 | #:phases | |
746 | (modify-phases %standard-phases | |
747 | (replace 'configure | |
748 | (lambda _ | |
749 | (substitute* "makefile" | |
750 | (("-L \\.") "-L . -Wl,-rpath='$$ORIGIN/../lib'")) | |
751 | #t))))) | |
752 | (home-page "http://cgm.cs.mcgill.ca/~avis/C/lrs.html") | |
753 | (synopsis "Convex hulls of polyhedra with exact arithmetic") | |
754 | (description | |
755 | "The C code of lrslib implements the reverse search algorithm for | |
756 | vertex enumeration and convex hull problems. Its input file format is | |
757 | compatible with cddlib. All computations are done exactly in either | |
758 | multiple precision or fixed integer arithmetic. Output is not stored | |
759 | in memory, so even problems with very large output sizes can sometimes | |
760 | be solved.") | |
761 | (license license:gpl2+))) | |
762 | ||
adc96e1d VM |
763 | (define-public libcerf |
764 | (package | |
765 | (name "libcerf") | |
766 | (version "1.14") | |
767 | (source | |
768 | (origin | |
769 | (method git-fetch) | |
770 | (uri (git-reference | |
771 | (url "https://jugit.fz-juelich.de/mlz/libcerf") | |
772 | (commit (string-append "v" version)))) | |
773 | (file-name (git-file-name name version)) | |
774 | (sha256 | |
775 | (base32 "1ic2q7kvxpqmgxlishygvx8d00i4wn51vkq4fyac44ahhf6c3kwd")))) | |
776 | (build-system cmake-build-system) | |
777 | (native-inputs | |
778 | `(("perl" ,perl))) | |
779 | (home-page "https://jugit.fz-juelich.de/mlz/libcerf") | |
780 | (synopsis "Library for complex error functions") | |
781 | (description | |
782 | "@code{libcerf} is a self-contained numeric library that provides an | |
783 | efficient and accurate implementation of complex error functions, along with | |
784 | Dawson, Faddeeva, and Voigt functions.") | |
785 | (license license:expat))) | |
786 | ||
b457f3cc AE |
787 | (define-public vinci |
788 | (package | |
789 | (name "vinci") | |
790 | (version "1.0.5") | |
791 | (source | |
792 | (origin | |
793 | (method url-fetch) | |
794 | (uri (string-append "https://www.math.u-bordeaux.fr/~aenge/software/" | |
795 | "vinci/vinci-" version ".tar.gz")) | |
796 | (sha256 | |
797 | (base32 | |
798 | "1aq0qc1y27iw9grhgnyji3290wwfznsrk3sg6ynqpxwjdda53h4m")))) | |
799 | (build-system gnu-build-system) | |
800 | (inputs | |
801 | `(("lrslib" ,lrslib))) | |
802 | (arguments | |
803 | `(#:tests? #f ; no check phase | |
804 | #:phases | |
805 | (modify-phases %standard-phases | |
806 | (replace 'configure | |
807 | ;; register the lrs location in the config file | |
808 | (lambda* (#:key inputs #:allow-other-keys) | |
809 | (let* ((lrs (assoc-ref inputs "lrslib")) | |
810 | (lrsexec (string-append lrs "/bin/lrs"))) | |
811 | (substitute* "vinci.h" | |
812 | (("#define LRS_EXEC \"lrs\"") | |
813 | (string-append "#define LRS_EXEC \"" lrsexec "\"")))) | |
814 | #t)) | |
815 | (replace 'install | |
816 | (lambda* (#:key outputs #:allow-other-keys) | |
817 | (let* ((out (assoc-ref outputs "out")) | |
818 | (bin (string-append out "/bin"))) | |
819 | (install-file "vinci" bin)) | |
820 | #t))))) | |
821 | (home-page | |
822 | "https://www.math.u-bordeaux.fr/~aenge/?category=software&page=vinci") | |
823 | (synopsis "Volume computation for polytopes") | |
824 | (description | |
825 | "Vinci implements a number of volume computation algorithms for convex | |
826 | polytopes in arbitrary dimension. The polytopes can be given by their | |
827 | V-representation (as the convex hull of a finite number of vertices), by | |
828 | their H-representation (as the bounded intersection of a finite number of | |
829 | halfspaces) or by their double description with both representations.") | |
830 | (license license:gpl2+))) | |
831 | ||
865a69dd RW |
832 | (define-public arpack-ng |
833 | (package | |
834 | (name "arpack-ng") | |
6b496f7b | 835 | (version "3.8.0") |
c0edb5b5 | 836 | (home-page "https://github.com/opencollab/arpack-ng") |
622ef2b9 MB |
837 | (source (origin |
838 | (method git-fetch) | |
839 | (uri (git-reference (url home-page) (commit version))) | |
840 | (file-name (git-file-name name version)) | |
841 | (sha256 | |
842 | (base32 | |
6b496f7b | 843 | "0l7as5z6xvbxly8alam9s4kws70952qq35a6vkljzayi4b9gbklx")))) |
865a69dd | 844 | (build-system gnu-build-system) |
c0edb5b5 LC |
845 | (native-inputs |
846 | `(("autoconf" ,autoconf) | |
847 | ("automake" ,automake) | |
6b496f7b MB |
848 | ("libtool" ,libtool) |
849 | ("pkg-config" ,pkg-config))) | |
865a69dd | 850 | (inputs |
6b496f7b MB |
851 | `(("eigen" ,eigen) |
852 | ("lapack" ,lapack) | |
19afbea1 | 853 | ("fortran" ,gfortran))) |
865a69dd RW |
854 | (synopsis "Fortran subroutines for solving eigenvalue problems") |
855 | (description | |
856 | "ARPACK-NG is a collection of Fortran77 subroutines designed to solve | |
857 | large scale eigenvalue problems.") | |
166191b3 | 858 | (license (license:non-copyleft "file://COPYING" |
865a69dd RW |
859 | "See COPYING in the distribution.")))) |
860 | ||
c0edb5b5 LC |
861 | (define-public arpack-ng-3.3.0 |
862 | (package | |
863 | (inherit arpack-ng) | |
864 | (version "3.3.0") | |
c0edb5b5 LC |
865 | (source |
866 | (origin | |
d6915cb8 MB |
867 | (method git-fetch) |
868 | (uri (git-reference (url (package-home-page arpack-ng)) | |
869 | (commit version))) | |
870 | (file-name (git-file-name (package-name arpack-ng) version)) | |
c0edb5b5 LC |
871 | (sha256 |
872 | (base32 | |
d6915cb8 | 873 | "00h6bjvxjq7bv0b8pwnc0gw33ns6brlqv00xx2rh3w9b5n205918")))))) |
c0edb5b5 | 874 | |
8c94c886 EB |
875 | (define-public arpack-ng-openmpi |
876 | (package (inherit arpack-ng) | |
877 | (name "arpack-ng-openmpi") | |
878 | (inputs | |
879 | `(("mpi" ,openmpi) | |
880 | ,@(package-inputs arpack-ng))) | |
4f387541 LC |
881 | (arguments |
882 | (substitute-keyword-arguments (package-arguments arpack-ng) | |
883 | ((#:configure-flags _ '()) | |
aa82260b PG |
884 | ''("--enable-mpi")) |
885 | ((#:phases phases '%standard-phases) | |
886 | `(modify-phases ,phases | |
bbe46a4a EB |
887 | (add-before 'check 'mpi-setup |
888 | ,%openmpi-setup))))) | |
8c94c886 EB |
889 | (synopsis "Fortran subroutines for solving eigenvalue problems with MPI"))) |
890 | ||
da95c817 NK |
891 | (define-public lapack |
892 | (package | |
893 | (name "lapack") | |
e6de152d | 894 | (version "3.9.0") |
da95c817 NK |
895 | (source |
896 | (origin | |
897 | (method url-fetch) | |
898 | (uri (string-append "http://www.netlib.org/lapack/lapack-" | |
899 | version ".tgz")) | |
900 | (sha256 | |
901 | (base32 | |
e6de152d | 902 | "1155qixp26c12yrxc76z9mlfw2h3xxymxxv5znpgzh5gaykpndgj")))) |
da95c817 NK |
903 | (build-system cmake-build-system) |
904 | (home-page "http://www.netlib.org/lapack/") | |
19afbea1 | 905 | (inputs `(("fortran" ,gfortran) |
e6de152d | 906 | ("python" ,python-wrapper))) |
da95c817 | 907 | (arguments |
3ab869b6 | 908 | `(#:configure-flags (list |
3ab869b6 LC |
909 | "-DBUILD_SHARED_LIBS:BOOL=YES" |
910 | "-DLAPACKE=ON" | |
3ab869b6 | 911 | ;; Build the 'LAPACKE_clatms' functions. |
e6de152d KH |
912 | "-DLAPACKE_WITH_TMG=ON" |
913 | "-DBUILD_TESTING=ON"))) | |
da95c817 NK |
914 | (synopsis "Library for numerical linear algebra") |
915 | (description | |
916 | "LAPACK is a Fortran 90 library for solving the most commonly occurring | |
917 | problems in numerical linear algebra.") | |
166191b3 | 918 | (license (license:non-copyleft "file://LICENSE" |
da95c817 | 919 | "See LICENSE in the distribution.")))) |
73fed4f8 | 920 | |
69867369 RW |
921 | (define-public clapack |
922 | (package | |
923 | (name "clapack") | |
924 | (version "3.2.1") | |
925 | (source | |
926 | (origin | |
927 | (method url-fetch) | |
928 | (uri (string-append "http://www.netlib.org/clapack/clapack-" | |
929 | version "-CMAKE.tgz")) | |
930 | (sha256 | |
931 | (base32 | |
932 | "0nnap9q1mv14g57dl3vkvxrdr10k5w7zzyxs6rgxhia8q8mphgqb")))) | |
933 | (build-system cmake-build-system) | |
934 | (arguments | |
935 | `(#:phases | |
936 | (modify-phases %standard-phases | |
937 | ;; These tests use a lot of stack variables and segfault without | |
938 | ;; lifting resource limits. | |
939 | (add-after 'unpack 'disable-broken-tests | |
940 | (lambda _ | |
941 | (substitute* "TESTING/CMakeLists.txt" | |
942 | (("add_lapack_test.* xeigtstz\\)") "")) | |
943 | #t)) | |
944 | (replace 'install | |
945 | (lambda* (#:key outputs #:allow-other-keys) | |
946 | (let* ((out (assoc-ref outputs "out")) | |
947 | (libdir (string-append out "/lib")) | |
948 | (f2cinc (string-append out "/include/libf2c"))) | |
949 | (mkdir-p f2cinc) | |
950 | (display (getcwd)) | |
951 | (for-each (lambda (file) | |
952 | (install-file file libdir)) | |
953 | '("SRC/liblapack.a" | |
954 | "F2CLIBS/libf2c/libf2c.a" | |
955 | "TESTING/MATGEN/libtmglib.a" | |
956 | "BLAS/SRC/libblas.a")) | |
957 | (for-each (lambda (file) | |
958 | (install-file file f2cinc)) | |
959 | (cons "F2CLIBS/libf2c/arith.h" | |
960 | (find-files (string-append "../clapack-" | |
961 | ,version "-CMAKE/F2CLIBS/libf2c") | |
962 | "\\.h$"))) | |
963 | (copy-recursively (string-append "../clapack-" | |
964 | ,version "-CMAKE/INCLUDE") | |
965 | (string-append out "/include")) | |
966 | #t)))))) | |
967 | (home-page "https://www.netlib.org/clapack/") | |
968 | (synopsis "Numerical linear algebra library for C") | |
969 | (description | |
970 | "The CLAPACK library was built using a Fortran to C conversion utility | |
971 | called f2c. The entire Fortran 77 LAPACK library is run through f2c to obtain | |
972 | C code, and then modified to improve readability. CLAPACK's goal is to | |
973 | provide LAPACK for someone who does not have access to a Fortran compiler.") | |
974 | (license (license:non-copyleft "file://LICENSE" | |
975 | "See LICENSE in the distribution.")))) | |
976 | ||
e1ff597a EB |
977 | (define-public scalapack |
978 | (package | |
979 | (name "scalapack") | |
980 | (version "2.0.2") | |
981 | (source | |
982 | (origin | |
983 | (method url-fetch) | |
984 | (uri (string-append "http://www.netlib.org/scalapack/scalapack-" | |
985 | version ".tgz")) | |
986 | (sha256 | |
987 | (base32 | |
f73750e6 EB |
988 | "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c")) |
989 | (patches (search-patches "scalapack-blacs-mpi-deprecations.patch")))) | |
e1ff597a EB |
990 | (build-system cmake-build-system) |
991 | (inputs | |
992 | `(("mpi" ,openmpi) | |
993 | ("fortran" ,gfortran) | |
994 | ("lapack" ,lapack))) ;for testing only | |
995 | (arguments | |
6df2a50a LC |
996 | `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES") |
997 | #:phases (modify-phases %standard-phases | |
bbe46a4a EB |
998 | (add-before 'check 'mpi-setup |
999 | ,%openmpi-setup)))) | |
e1ff597a EB |
1000 | (home-page "http://www.netlib.org/scalapack/") |
1001 | (synopsis "Library for scalable numerical linear algebra") | |
1002 | (description | |
1003 | "ScaLAPACK is a Fortran 90 library of high-performance linear algebra | |
1004 | routines on parallel distributed memory machines. ScaLAPACK solves dense and | |
1005 | banded linear systems, least squares problems, eigenvalue problems, and | |
1006 | singular value problems.") | |
adb223b8 LC |
1007 | (license (license:non-copyleft "file://LICENSE" |
1008 | "See LICENSE in the distribution.")))) | |
e1ff597a | 1009 | |
73fed4f8 | 1010 | (define-public gnuplot |
5f800540 KK |
1011 | (package |
1012 | (name "gnuplot") | |
25631d6f | 1013 | (version "5.4.2") |
5f800540 KK |
1014 | (source (origin |
1015 | (method url-fetch) | |
1016 | (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" | |
1017 | version "/gnuplot-" | |
1018 | version ".tar.gz")) | |
1019 | (sha256 | |
25631d6f | 1020 | (base32 "1fp7rbhjmz2w63r72kicf8lfszzimz2csfx868fracw167hpaz75")))) |
5f800540 KK |
1021 | (build-system gnu-build-system) |
1022 | (inputs `(("readline" ,readline) | |
1023 | ("cairo" ,cairo) | |
1024 | ("pango" ,pango) | |
6e64766a DM |
1025 | ("gd" ,gd) |
1026 | ("lua" ,lua))) | |
612a387f RW |
1027 | (native-inputs |
1028 | `(("pkg-config" ,pkg-config) | |
1029 | ("texlive" ,texlive-tiny))) | |
07254d8b AM |
1030 | (arguments `(#:configure-flags (list (string-append |
1031 | "--with-texdir=" %output | |
9aa0a98e KK |
1032 | "/texmf-local/tex/latex/gnuplot")) |
1033 | ;; Plot on a dumb terminal during tests. | |
1034 | #:make-flags '("GNUTERM=dumb"))) | |
5f800540 KK |
1035 | (home-page "http://www.gnuplot.info") |
1036 | (synopsis "Command-line driven graphing utility") | |
1037 | (description "Gnuplot is a portable command-line driven graphing | |
35b9e423 | 1038 | utility. It was originally created to allow scientists and students to |
73fed4f8 | 1039 | visualize mathematical functions and data interactively, but has grown to |
35b9e423 | 1040 | support many non-interactive uses such as web scripting. It is also used as a |
73fed4f8 | 1041 | plotting engine by third-party applications like Octave.") |
5f800540 KK |
1042 | ;; X11 Style with the additional restriction that derived works may only be |
1043 | ;; distributed as patches to the original. | |
1044 | (license (license:fsf-free | |
1045 | "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright")))) | |
668c06ac | 1046 | |
32f70e1f TD |
1047 | (define-public gctp |
1048 | (package | |
1049 | (name "gctp") | |
1050 | (version "2.0.0") | |
1051 | (source | |
1052 | (origin | |
5db874d1 TGR |
1053 | (method git-fetch) |
1054 | (uri (git-reference | |
b0e7b699 | 1055 | (url "https://github.com/OkoSanto/GCTP") |
5db874d1 TGR |
1056 | (commit (string-append "v" version)))) |
1057 | (file-name (git-file-name name version)) | |
32f70e1f | 1058 | (sha256 |
5db874d1 | 1059 | (base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd")))) |
32f70e1f TD |
1060 | (native-inputs |
1061 | `(("fortran" ,gfortran))) | |
1062 | (build-system gnu-build-system) | |
1063 | (synopsis "General Cartographic Transformation Package (GCTP)") | |
1064 | (description | |
1065 | "The General Cartographic Transformation Package (GCTP) is a system of | |
1066 | software routines designed to permit the transformation of coordinate pairs | |
1067 | from one map projection to another. The GCTP is the standard computer | |
1068 | software used by the National Mapping Division for map projection | |
1069 | computations.") | |
1070 | (home-page "https://github.com/OkoSanto/GCTP") | |
0f7cd95b | 1071 | (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html |
32f70e1f | 1072 | |
becbbefc TD |
1073 | (define-public hdf4 |
1074 | (package | |
1075 | (name "hdf4") | |
c959d99f | 1076 | (version "4.2.14") |
becbbefc TD |
1077 | (source |
1078 | (origin | |
1079 | (method url-fetch) | |
1080 | (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF" | |
1081 | version "/src/hdf-" version ".tar.bz2")) | |
1082 | (sha256 | |
c959d99f | 1083 | (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l")) |
15ca49b2 AE |
1084 | (patches (search-patches "hdf4-architectures.patch" |
1085 | "hdf4-reproducibility.patch" | |
bd3d71cb MB |
1086 | "hdf4-shared-fortran.patch" |
1087 | "hdf4-tirpc.patch")))) | |
becbbefc TD |
1088 | (build-system gnu-build-system) |
1089 | (native-inputs | |
1090 | `(("gfortran" ,gfortran) | |
1091 | ("bison" ,bison) | |
1092 | ("flex" ,flex))) | |
1093 | (inputs | |
1094 | `(("zlib" ,zlib) | |
4bd428a7 | 1095 | ("libjpeg" ,libjpeg-turbo) |
bd3d71cb | 1096 | ("libtirpc" ,libtirpc))) |
becbbefc TD |
1097 | (arguments |
1098 | `(#:parallel-tests? #f | |
bd3d71cb | 1099 | #:configure-flags (list "--enable-shared" |
979611d4 GLV |
1100 | "FCFLAGS=-fallow-argument-mismatch" |
1101 | "FFLAGS=-fallow-argument-mismatch" | |
bd3d71cb MB |
1102 | (string-append "CPPFLAGS=-I" |
1103 | (assoc-ref %build-inputs "libtirpc") | |
1104 | "/include/tirpc")) | |
becbbefc TD |
1105 | #:phases |
1106 | (modify-phases %standard-phases | |
953a12fa EF |
1107 | ;; This is inspired by two of Debian's patches. |
1108 | (add-before 'configure 'add-more-aarch64-support | |
1109 | (lambda _ | |
1110 | (substitute* '("mfhdf/ncgen/ncgen.l" | |
1111 | "mfhdf/ncgen/ncgenyy.c" | |
1112 | "mfhdf/libsrc/netcdf.h.in") | |
1113 | (("AIX5L64") "__aarch64__")) | |
1114 | #t)) | |
becbbefc TD |
1115 | (add-before 'configure 'patchbuild |
1116 | (lambda _ | |
1117 | (substitute* | |
1118 | '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in") | |
1119 | (("/bin/rm") "rm") | |
1120 | (("/bin/mkdir") "mkdir")) | |
1121 | (substitute* (find-files "." "^Makefile\\.in$") | |
1122 | (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \ | |
1123 | -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "") | |
1124 | (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \ | |
1125 | -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \ | |
953a12fa | 1126 | -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")) |
e464b455 TD |
1127 | #t)) |
1128 | (add-after 'configure 'patch-settings | |
1129 | (lambda _ | |
1130 | ;; libhdf4.settings contains the full path of the | |
1131 | ;; compilers used, and its contents are included in | |
1132 | ;; .so-files. We truncate the hashes to avoid | |
1133 | ;; unnecessary store references to those compilers: | |
1134 | (substitute* "libhdf4.settings" | |
979611d4 | 1135 | (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash) |
e464b455 TD |
1136 | (string-append prefix (string-take hash 10) "..."))) |
1137 | #t)) | |
fadd962f MB |
1138 | (add-after 'install 'provide-absolute-libjpeg-reference |
1139 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1140 | (let ((out (assoc-ref outputs "out")) | |
1141 | (libjpeg (assoc-ref inputs "libjpeg"))) | |
1142 | ;; libjpeg-turbo does not provide a .la file, so libtool is | |
1143 | ;; unable to add an absolute reference for -ljpeg in the .la | |
1144 | ;; files. Fix it manually to avoid having to propagate it. | |
1145 | (substitute* (find-files (string-append out "/lib") "\\.la$") | |
1146 | (("-ljpeg") | |
1147 | (string-append "-L" libjpeg "/lib -ljpeg"))) | |
1148 | #t)))))) | |
becbbefc TD |
1149 | (home-page "https://www.hdfgroup.org/products/hdf4/") |
1150 | (synopsis | |
1151 | "Library and multi-object file format for storing and managing data") | |
1152 | (description "HDF4 is a library and multi-object file format for storing | |
1153 | and managing data between machines. HDF4 is an older hierarchical data format, | |
1154 | incompatible with HDF5.") | |
1155 | (license | |
1156 | (license:non-copyleft | |
1157 | "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING")))) | |
1158 | ||
1159 | (define-public hdf4-alt | |
1160 | (package | |
1161 | (inherit hdf4) | |
1162 | (name "hdf4-alt") | |
1163 | (arguments | |
1164 | (substitute-keyword-arguments (package-arguments hdf4) | |
1165 | ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags)))) | |
1166 | (synopsis | |
1167 | "HDF4 without netCDF API, can be combined with the regular netCDF library"))) | |
1168 | ||
3b8eea1c | 1169 | (define-public hdf5-1.8 |
7ee3f1a2 JD |
1170 | (package |
1171 | (name "hdf5") | |
8effdd19 | 1172 | (version "1.8.22") |
7ee3f1a2 JD |
1173 | (source |
1174 | (origin | |
1175 | (method url-fetch) | |
2da63064 TD |
1176 | (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/" |
1177 | "hdf5-" (version-major+minor version) | |
1178 | "/hdf5-" version "/src/hdf5-" | |
dcd9d163 LF |
1179 | version ".tar.bz2") |
1180 | (string-append "https://support.hdfgroup.org/ftp/HDF5/" | |
1181 | "current" | |
7b84610e EB |
1182 | (match (string-split version #\.) |
1183 | ((major minor _ ...) | |
1184 | (string-append major minor))) | |
dcd9d163 | 1185 | "/src/hdf5-" version ".tar.bz2"))) |
7ee3f1a2 | 1186 | (sha256 |
8effdd19 EB |
1187 | (base32 "194ki2s5jrgl4czkvy5nc9nwjyapah0fj72l0gb0aysplp38i6v8")) |
1188 | (patches (search-patches "hdf5-config-date.patch")))) | |
7ee3f1a2 | 1189 | (build-system gnu-build-system) |
12ed1216 AE |
1190 | (inputs |
1191 | `(("zlib" ,zlib))) | |
e3a1a1de | 1192 | (native-inputs |
3ea420f3 LC |
1193 | `(("gfortran" ,gfortran) |
1194 | ("perl" ,perl))) ;part of the test machinery needs Perl | |
e3a1a1de TD |
1195 | (outputs '("out" ; core library |
1196 | "fortran")) ; fortran interface | |
7ee3f1a2 | 1197 | (arguments |
62126576 | 1198 | `(;; Some of the users, notably Flann, need the C++ interface. |
e3a1a1de TD |
1199 | #:configure-flags '("--enable-cxx" |
1200 | "--enable-fortran" | |
549d1571 LC |
1201 | "--enable-fortran2003" |
1202 | ||
1203 | ;; Build a thread-safe library. Unfortunately, | |
1204 | ;; 'configure' invites you to either turn off C++, | |
1205 | ;; Fortran, and the high-level interface (HL), or | |
1206 | ;; to pass '--enable-unsupported'. Debian | |
1207 | ;; packagers chose to pass '--enable-unsupported' | |
1208 | ;; and we follow their lead here. | |
1209 | "--enable-threadsafe" | |
1210 | "--with-pthread" | |
1211 | "--enable-unsupported") | |
4dba441c RW |
1212 | ;; Use -fPIC to allow the R bindings to link with the static libraries |
1213 | #:make-flags (list "CFLAGS=-fPIC" | |
1214 | "CXXFLAGS=-fPIC") | |
62126576 | 1215 | #:phases |
f622e212 EB |
1216 | (modify-phases %standard-phases |
1217 | (add-before 'configure 'patch-configure | |
e3a1a1de | 1218 | (lambda* (#:key outputs #:allow-other-keys) |
f622e212 | 1219 | (substitute* "configure" |
b8d9c93b | 1220 | (("/bin/mv") "mv")) |
e3a1a1de TD |
1221 | (substitute* "fortran/src/Makefile.in" |
1222 | (("libhdf5_fortran_la_LDFLAGS =") | |
1223 | (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath=" | |
1224 | (assoc-ref outputs "fortran") "/lib"))) | |
1225 | (substitute* "hl/fortran/src/Makefile.in" | |
1226 | (("libhdf5hl_fortran_la_LDFLAGS =") | |
1227 | (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath=" | |
1228 | (assoc-ref outputs "fortran") "/lib"))) | |
b8d9c93b | 1229 | #t)) |
fd0378a1 TD |
1230 | (add-after 'configure 'patch-settings |
1231 | (lambda _ | |
1232 | ;; libhdf5.settings contains the full path of the | |
1233 | ;; compilers used, and its contents are included in | |
1234 | ;; libhdf5.so. We truncate the hashes to avoid | |
1235 | ;; unnecessary store references to those compilers: | |
1236 | (substitute* "src/libhdf5.settings" | |
b52f635e | 1237 | (("(/gnu/store/)([a-zA-Z0-9]*)" all prefix hash) |
d8f46d52 RW |
1238 | (string-append prefix (string-take hash 10) "...")) |
1239 | ;; Don't record the build-time kernel version to make the | |
1240 | ;; settings file reproducible. | |
1241 | (("Uname information:.*") | |
1242 | "Uname information: Linux\n")) | |
b8d9c93b | 1243 | #t)) |
f622e212 EB |
1244 | (add-after 'install 'patch-references |
1245 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1246 | (let ((bin (string-append (assoc-ref outputs "out") "/bin")) | |
1247 | (zlib (assoc-ref inputs "zlib"))) | |
1248 | (substitute* (find-files bin "h5p?cc") | |
1249 | (("-lz" lib) | |
1250 | (string-append "-L" zlib "/lib " lib))) | |
e3a1a1de TD |
1251 | #t))) |
1252 | (add-after 'install 'split | |
1253 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1254 | ;; Move all fortran-related files | |
1255 | (let* ((out (assoc-ref outputs "out")) | |
1256 | (bin (string-append out "/bin")) | |
1257 | (lib (string-append out "/lib")) | |
1258 | (inc (string-append out "/include")) | |
1259 | (ex (string-append out "/share/hdf5_examples/fortran")) | |
1260 | (fort (assoc-ref outputs "fortran")) | |
1261 | (fbin (string-append fort "/bin")) | |
1262 | (flib (string-append fort "/lib")) | |
1263 | (finc (string-append fort "/include")) | |
1264 | (fex (string-append fort "/share/hdf5_examples/fortran"))) | |
1265 | (mkdir-p fbin) | |
1266 | (mkdir-p flib) | |
1267 | (mkdir-p finc) | |
1268 | (mkdir-p fex) | |
b0d1e60f PG |
1269 | ;; Note: When built with --enable-parallel, the 'h5fc' file |
1270 | ;; doesn't exist, hence this condition. | |
1271 | (when (file-exists? (string-append bin "/h5fc")) | |
1272 | (rename-file (string-append bin "/h5fc") | |
1273 | (string-append fbin "/h5fc"))) | |
e3a1a1de TD |
1274 | (for-each (lambda (file) |
1275 | (rename-file file | |
1276 | (string-append flib "/" (basename file)))) | |
1277 | (find-files lib ".*fortran.*")) | |
1278 | (for-each (lambda (file) | |
1279 | (rename-file file | |
1280 | (string-append finc "/" (basename file)))) | |
1281 | (find-files inc ".*mod")) | |
1282 | (for-each (lambda (file) | |
1283 | (rename-file file | |
1284 | (string-append fex "/" (basename file)))) | |
1285 | (find-files ex ".*")) | |
1286 | (delete-file-recursively ex)) | |
1287 | #t))))) | |
0a44f9c4 | 1288 | (home-page "https://www.hdfgroup.org") |
516e93f8 | 1289 | (synopsis "Management suite for extremely large and complex data") |
7ee3f1a2 JD |
1290 | (description "HDF5 is a suite that makes possible the management of |
1291 | extremely large and complex data collections.") | |
d4bf49b1 | 1292 | (license (license:x11-style |
0a44f9c4 | 1293 | "https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) |
7ee3f1a2 | 1294 | |
bb47aca5 | 1295 | (define-public hdf5-1.10 |
dbcf2b61 MB |
1296 | (package |
1297 | (inherit hdf5-1.8) | |
34d150dc | 1298 | (version "1.10.7") |
bb47aca5 RW |
1299 | (source |
1300 | (origin | |
4788e554 LC |
1301 | (method url-fetch) |
1302 | (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/" | |
1303 | "hdf5-" (version-major+minor version) | |
1304 | "/hdf5-" version "/src/hdf5-" | |
1305 | version ".tar.bz2") | |
1306 | (string-append "https://support.hdfgroup.org/ftp/HDF5/" | |
1307 | "current" | |
1308 | (apply string-append | |
1309 | (take (string-split version #\.) 2)) | |
1310 | "/src/hdf5-" version ".tar.bz2"))) | |
1311 | (sha256 | |
34d150dc | 1312 | (base32 "0pm5xxry55i0h7wmvc7svzdaa90rnk7h78rrjmnlkz2ygsn8y082")) |
4788e554 | 1313 | (patches (search-patches "hdf5-config-date.patch")))))) |
bb47aca5 | 1314 | |
f601cdc6 | 1315 | (define-public hdf5-1.12 |
dbcf2b61 MB |
1316 | (package |
1317 | (inherit hdf5-1.8) | |
7c783975 | 1318 | (version "1.12.1") |
f601cdc6 GH |
1319 | (source |
1320 | (origin | |
1321 | (method url-fetch) | |
1322 | (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/" | |
1323 | "hdf5-" (version-major+minor version) | |
1324 | "/hdf5-" version "/src/hdf5-" | |
1325 | version ".tar.bz2") | |
1326 | (string-append "https://support.hdfgroup.org/ftp/HDF5/" | |
1327 | "current" | |
1328 | (apply string-append | |
1329 | (take (string-split version #\.) 2)) | |
1330 | "/src/hdf5-" version ".tar.bz2"))) | |
1331 | (sha256 | |
7c783975 | 1332 | (base32 "074g3z504xf77ff38igs30i1aqxpm508p7yw78ykva7dncrgbyda")) |
f601cdc6 GH |
1333 | (patches (search-patches "hdf5-config-date.patch")))))) |
1334 | ||
3b8eea1c LC |
1335 | (define-public hdf5 |
1336 | ;; Default version of HDF5. | |
c5372cd4 | 1337 | hdf5-1.10) |
3b8eea1c | 1338 | |
2fd26d05 TD |
1339 | (define-public hdf-java |
1340 | (package | |
2a509880 RW |
1341 | (name "hdf-java") |
1342 | (version "3.3.2") | |
1343 | (source | |
1344 | (origin | |
1345 | (method url-fetch) | |
1346 | (uri (string-append | |
0a44f9c4 | 1347 | "https://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-" |
2a509880 RW |
1348 | version "/src/CMake-hdfjava-" version ".tar.gz")) |
1349 | (sha256 | |
1350 | (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr")) | |
1351 | (modules '((guix build utils))) | |
1352 | (snippet ; Make sure we don't use the bundled sources and binaries. | |
1353 | `(begin | |
1354 | (for-each delete-file | |
1355 | (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz" | |
1356 | "HDF4.tar.gz" "HDF5.tar.gz")) | |
1357 | (delete-file-recursively ,(string-append "hdfjava-" version "/lib")) | |
1358 | #t)))) | |
1359 | (build-system gnu-build-system) | |
1360 | (native-inputs | |
1361 | `(("jdk" ,icedtea "jdk") | |
1362 | ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'. | |
1363 | ;; For tests: | |
1364 | ("hamcrest-core" ,java-hamcrest-core) | |
1365 | ("junit" ,java-junit) | |
1366 | ("slf4j-simple" ,java-slf4j-simple))) | |
1367 | (inputs | |
1368 | `(("hdf4" ,hdf4) | |
c5372cd4 | 1369 | ("hdf5" ,hdf5-1.8) |
2a509880 | 1370 | ("zlib" ,zlib) |
4bd428a7 | 1371 | ("libjpeg" ,libjpeg-turbo) |
2a509880 RW |
1372 | ("slf4j-api" ,java-slf4j-api))) |
1373 | (arguments | |
1374 | `(#:configure-flags | |
1375 | (list (string-append "--target=" ,(or (%current-target-system) (%current-system))) | |
1376 | (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include," | |
1377 | (assoc-ref %build-inputs "jdk") "/lib" ) | |
1378 | (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib") | |
1379 | (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib")) | |
2fd26d05 | 1380 | |
2a509880 RW |
1381 | #:make-flags |
1382 | (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib") | |
1383 | (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib") | |
2dffe476 | 1384 | (string-append "ZLIB=" (search-input-file %build-inputs "/lib/libz.so")) |
2a509880 | 1385 | (string-append "JPEGLIB=" |
2dffe476 | 1386 | (search-input-file %build-inputs "/lib/libjpeg.so")) |
2a509880 | 1387 | "LLEXT=so") |
2fd26d05 | 1388 | |
2a509880 RW |
1389 | #:phases |
1390 | (modify-phases %standard-phases | |
1391 | (add-before 'configure 'chdir-to-source | |
1392 | (lambda _ (chdir ,(string-append "hdfjava-" version)) #t)) | |
1393 | (add-before 'configure 'patch-build | |
1394 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1395 | (substitute* "configure" | |
1396 | (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles | |
1397 | (("/bin/cat") (which "cat"))) | |
1398 | ;; Set classpath for compilation | |
1399 | (substitute* '("hdf/hdf5lib/Makefile.in" | |
1400 | "hdf/hdf5lib/exceptions/Makefile.in" | |
1401 | "hdf/hdflib/Makefile.in") | |
1402 | (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar") | |
22e753b9 LC |
1403 | ;; 'slf4j-api-X.Y.Z.jar' is installed in a Maven-style |
1404 | ;; directory, so use 'find-files' to find it. | |
1405 | (car (find-files (assoc-ref inputs "slf4j-api") | |
1406 | "^slf4j-api.*\\.jar$")))) | |
2a509880 RW |
1407 | ;; Replace outdated config.sub and config.guess: |
1408 | (with-directory-excursion "config" | |
1409 | (for-each (lambda (file) | |
1410 | (install-file | |
ae112039 LC |
1411 | (search-input-file inputs |
1412 | (string-append | |
1413 | "/share/automake-" | |
1414 | ,(version-major+minor (package-version automake)) | |
1415 | "/" file)) | |
1416 | ".")) | |
2a509880 | 1417 | '("config.sub" "config.guess"))) |
64dc8b0b | 1418 | |
2a509880 RW |
1419 | ;; Fix embedded version number |
1420 | (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.)))) | |
1421 | (substitute* "hdf/hdf5lib/H5.java" | |
1422 | (("1, 8, 19") | |
1423 | (string-join hdf5version ", ")))) | |
64dc8b0b | 1424 | |
2a509880 RW |
1425 | (mkdir-p (string-append (assoc-ref outputs "out"))) |
1426 | ;; Set classpath for tests | |
1427 | (let* ((build-dir (getcwd)) | |
1428 | (lib (string-append build-dir "/lib")) | |
1429 | (jhdf (string-append lib "/jhdf.jar")) | |
1430 | (jhdf5 (string-append lib "/jhdf5.jar")) | |
1431 | (testjars | |
fff4fcc4 JL |
1432 | (append |
1433 | (map (lambda (i) | |
22e753b9 LC |
1434 | (car (find-files (assoc-ref inputs i) |
1435 | (string-append "^" i | |
1436 | ".*\\.jar$")))) | |
fff4fcc4 JL |
1437 | '("slf4j-api" "slf4j-simple")) |
1438 | (list | |
1439 | (car (find-files (assoc-ref inputs "junit") "jar$")) | |
1440 | (car (find-files (assoc-ref inputs "hamcrest-core") | |
1441 | "jar$"))))) | |
2a509880 RW |
1442 | (class-path |
1443 | (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":"))) | |
2fd26d05 | 1444 | |
2a509880 RW |
1445 | (substitute* '("test/hdf5lib/Makefile.in" |
1446 | "test/hdf5lib/junit.sh.in" | |
1447 | "examples/runExample.sh.in") | |
1448 | (("/usr/bin/test") | |
bc64d955 | 1449 | (search-input-file inputs "/bin/test")) |
2a509880 | 1450 | (("/usr/bin/uname") |
bc64d955 | 1451 | (search-input-file inputs "/bin/uname")) |
2a509880 RW |
1452 | (("CLASSPATH=[^\n]*") |
1453 | (string-append "CLASSPATH=" class-path))) | |
1454 | (setenv "CLASSPATH" class-path)) | |
1455 | #t)) | |
1456 | (add-before 'check 'build-examples | |
1457 | (lambda _ | |
1458 | (apply invoke `("javac" | |
1459 | ,@(find-files "examples" ".*\\.java")))))) | |
2fd26d05 | 1460 | |
2a509880 | 1461 | #:parallel-build? #f |
2fd26d05 | 1462 | |
2a509880 RW |
1463 | #:parallel-tests? #f )) |
1464 | (home-page "https://support.hdfgroup.org/products/java") | |
1465 | (synopsis "Java interface for the HDF4 and HDF5 libraries") | |
1466 | (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use | |
2fd26d05 TD |
1467 | the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are |
1468 | implemented in C.") | |
1469 | ||
2a509880 RW |
1470 | ;; BSD-style license: |
1471 | (license (license:x11-style | |
1472 | "https://support.hdfgroup.org/ftp/HDF5/hdf-java\ | |
2fd26d05 TD |
1473 | /current/src/unpacked/COPYING")))) |
1474 | ||
d3c4f3bb TD |
1475 | (define-public hdf-eos2 |
1476 | (package | |
1477 | (name "hdf-eos2") | |
1478 | (version "19.1.0") | |
1479 | (source | |
1480 | (origin | |
1481 | (method url-fetch) | |
1482 | (uri "ftp://edhs1.gsfc.nasa.gov\ | |
1483 | /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z") | |
1484 | (sha256 | |
1485 | (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz")) | |
1486 | (patches (search-patches "hdf-eos2-remove-gctp.patch" | |
1487 | "hdf-eos2-build-shared.patch" | |
1488 | "hdf-eos2-fortrantests.patch")))) | |
1489 | (build-system gnu-build-system) | |
1490 | (native-inputs | |
1491 | `(("gfortran" ,gfortran))) | |
1492 | (inputs | |
1493 | `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API | |
25bdbb61 | 1494 | ;; XXX: These inputs are really dependencies of hdf4. |
d3c4f3bb | 1495 | ("zlib" ,zlib) |
4bd428a7 | 1496 | ("libjpeg" ,libjpeg-turbo) |
25bdbb61 MB |
1497 | ("libtirpc" ,libtirpc) |
1498 | ||
d3c4f3bb TD |
1499 | ("gctp" ,gctp))) |
1500 | (arguments | |
1501 | `( #:configure-flags '("--enable-install-include" "--enable-shared" | |
1502 | "CC=h4cc -Df2cFortran" "LIBS=-lgctp") | |
1503 | #:parallel-tests? #f)) | |
2aaa09f1 | 1504 | (home-page "https://hdfeos.org/software/library.php#HDF-EOS2") |
d3c4f3bb TD |
1505 | (synopsis "HDF4-based data format for NASA's Earth Observing System") |
1506 | (description "HDF-EOS2 is a software library built on HDF4 which supports | |
1507 | the construction of data structures used in NASA's Earth Observing | |
1508 | System (Grid, Point and Swath).") | |
1509 | ||
1510 | ;; Source files carry a permissive license header. | |
1511 | (license (license:non-copyleft home-page)))) | |
1512 | ||
0f43f835 TD |
1513 | (define-public hdf-eos5 |
1514 | (package | |
1515 | (name "hdf-eos5") | |
1516 | (version "1.15") | |
1517 | (source (origin | |
1518 | (method url-fetch) | |
1519 | (uri (string-append "ftp://edhs1.gsfc.nasa.gov\ | |
1520 | /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z")) | |
1521 | (sha256 | |
1522 | (base32 | |
1523 | "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i")) | |
1524 | (patches (search-patches "hdf-eos5-build-shared.patch" | |
1525 | "hdf-eos5-remove-gctp.patch" | |
1526 | "hdf-eos5-fix-szip.patch" | |
1527 | "hdf-eos5-fortrantests.patch")))) | |
1528 | (native-inputs | |
1529 | `(("gfortran" ,gfortran))) | |
1530 | (build-system gnu-build-system) | |
1531 | (inputs | |
c5372cd4 | 1532 | `(("hdf5" ,hdf5-1.8) |
0f43f835 TD |
1533 | ("zlib" ,zlib) |
1534 | ("gctp" ,gctp))) | |
1535 | (arguments | |
1536 | `(#:configure-flags '("--enable-install-include" "--enable-shared" | |
1537 | "CC=h5cc -Df2cFortran" "LIBS=-lgctp") | |
1538 | #:parallel-tests? #f)) | |
1539 | (synopsis "HDF5-based data format for NASA's Earth Observing System") | |
1540 | (description | |
1541 | "HDF-EOS5 is a software library built on HDF5 to support the construction | |
1542 | of data structures used in NASA's Earth Observing System (Grid, Point and | |
1543 | Swath).") | |
1544 | (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5") | |
1545 | ||
1546 | ;; Source files carry a permissive license header. | |
1547 | (license (license:non-copyleft home-page)))) | |
1548 | ||
c8378eea | 1549 | (define-public hdf5-parallel-openmpi |
59309635 | 1550 | (package/inherit hdf5-1.10 ;use the latest |
c8378eea EB |
1551 | (name "hdf5-parallel-openmpi") |
1552 | (inputs | |
1553 | `(("mpi" ,openmpi) | |
1554 | ,@(package-inputs hdf5))) | |
1555 | (arguments | |
45201bf2 PG |
1556 | (substitute-keyword-arguments (package-arguments hdf5) |
1557 | ((#:configure-flags flags) | |
549d1571 LC |
1558 | ``("--enable-parallel" |
1559 | ,@(delete "--enable-cxx" | |
1560 | (delete "--enable-threadsafe" ,flags)))) | |
c8378eea EB |
1561 | ((#:phases phases) |
1562 | `(modify-phases ,phases | |
45201bf2 PG |
1563 | (add-after 'build 'mpi-setup |
1564 | ,%openmpi-setup) | |
c8378eea EB |
1565 | (add-before 'check 'patch-tests |
1566 | (lambda _ | |
1567 | ;; OpenMPI's mpirun will exit with non-zero status if it | |
1568 | ;; detects an "abnormal termination", i.e. any process not | |
784c3da1 | 1569 | ;; calling MPI_Finalize(). Since the test is explicitly |
c8378eea EB |
1570 | ;; avoiding MPI_Finalize so as not to have at_exit and thus |
1571 | ;; H5C_flush_cache from being called, mpirun will always | |
1572 | ;; complain, so turn this test off. | |
1573 | (substitute* "testpar/Makefile" | |
1574 | (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back) | |
1575 | (string-append front back "\n"))) | |
59309635 | 1576 | (substitute* "tools/test/h5diff/testph5diff.sh" |
c8378eea EB |
1577 | (("/bin/sh") (which "sh"))) |
1578 | #t)))))) | |
1579 | (synopsis "Management suite for data with parallel IO support"))) | |
1580 | ||
0b2c8838 RW |
1581 | (define-public hdf5-blosc |
1582 | (package | |
1583 | (name "hdf5-blosc") | |
1584 | (version "1.0.0") | |
1585 | (source | |
1586 | (origin | |
1587 | (method git-fetch) | |
1588 | (uri (git-reference | |
b0e7b699 | 1589 | (url "https://github.com/Blosc/hdf5-blosc") |
0b2c8838 RW |
1590 | (commit (string-append "v" version)))) |
1591 | (file-name (git-file-name name version)) | |
1592 | (sha256 | |
1593 | (base32 "1nj2bm1v6ymm3fmyvhbn6ih5fgdiapavlfghh1pvbmhw71cysyqs")))) | |
1594 | (build-system cmake-build-system) | |
1595 | (arguments | |
1596 | `(#:configure-flags | |
1597 | (list (string-append "-DBLOSC_INSTALL_DIR=" | |
1598 | (assoc-ref %build-inputs "c-blosc")) | |
1599 | (string-append "-DPLUGIN_INSTALL_PATH=" | |
1600 | (assoc-ref %outputs "out") | |
1601 | "/hdf5/lib/plugin")) | |
1602 | #:phases | |
1603 | (modify-phases %standard-phases | |
1604 | (add-after 'unpack 'do-not-build-blosc | |
1605 | (lambda _ | |
1606 | (substitute* "CMakeLists.txt" | |
1607 | (("set\\(BLOSC_INSTALL_DIR.*") "") | |
1608 | (("ExternalProject_Add\\(project_blosc") "message(")) | |
1609 | #t))))) | |
1610 | (inputs | |
1611 | `(("c-blosc" ,c-blosc) | |
1612 | ("hdf5" ,hdf5-1.10))) | |
1613 | (home-page "https://github.com/Blosc/hdf5-blosc") | |
1614 | (synopsis "Filter for HDF5 using the Blosc compressor") | |
1615 | (description "This is a filter for HDF5 that uses the Blosc compressor; by | |
1616 | installing this filter, you can read and write HDF5 files with | |
1617 | Blosc-compressed datasets.") | |
1618 | (license license:expat))) | |
c8378eea | 1619 | |
00775104 EB |
1620 | (define-public h5check |
1621 | (package | |
1622 | (name "h5check") | |
1623 | (version "2.0.1") | |
1624 | (source | |
1625 | (origin | |
1626 | (method url-fetch) | |
0a44f9c4 | 1627 | (uri (string-append "https://www.hdfgroup.org/ftp/HDF5/tools/" |
00775104 EB |
1628 | "h5check/src/h5check-" version ".tar.gz")) |
1629 | (sha256 | |
1630 | (base32 | |
1631 | "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj")))) | |
1632 | (build-system gnu-build-system) | |
c5372cd4 | 1633 | (inputs `(("hdf5" ,hdf5-1.8))) ;h5cc for tests |
00775104 EB |
1634 | (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html") |
1635 | (synopsis "HDF5 format checker") | |
1636 | (description "@code{h5check} is a validation tool for verifying that an | |
1637 | HDF5 file is encoded according to the HDF File Format Specification.") | |
1638 | (license (license:x11-style "file://COPYING")))) | |
1639 | ||
a53d6719 JD |
1640 | (define-public itpp |
1641 | (package | |
1642 | (name "itpp") | |
1643 | (version "4.3.1") | |
1644 | (source (origin | |
1645 | (method url-fetch) | |
1646 | (uri (string-append "mirror://sourceforge/itpp/itpp/" | |
1647 | version "/itpp-" | |
1648 | version ".tar.gz")) | |
1649 | (sha256 | |
1650 | (base32 | |
1651 | "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm")))) | |
1652 | (build-system cmake-build-system) | |
1653 | (arguments `(#:tests? #f)) ; Tests require googletest *sources* | |
1654 | (inputs `(("lapack" ,lapack) | |
1655 | ("fftw" ,fftw))) | |
3a4d5df2 RW |
1656 | ;; FIXME: Even though the fonts are available dvips complains: |
1657 | ;; "Font cmmi10 not found; characters will be left blank." | |
1658 | (native-inputs | |
1659 | `(("texlive" ,texlive-tiny) | |
1660 | ("ghostscript" ,ghostscript) | |
1661 | ("doxygen" ,doxygen))) | |
a53d6719 JD |
1662 | (home-page "http://itpp.sourceforge.net") |
1663 | (synopsis "C++ library of maths, signal processing and communication classes") | |
1664 | (description "IT++ is a C++ library of mathematical, signal processing and | |
1665 | communication classes and functions. Its main use is in simulation of | |
1666 | communication systems and for performing research in the area of | |
1667 | communications. The kernel of the library consists of generic vector and | |
1668 | matrix classes, and a set of accompanying routines. Such a kernel makes IT++ | |
1669 | similar to MATLAB, GNU Octave or SciPy.") | |
1670 | (license license:gpl3+))) | |
1671 | ||
889187a4 EB |
1672 | (define-public netcdf |
1673 | (package | |
1674 | (name "netcdf") | |
a9291a28 | 1675 | (version "4.7.4") |
889187a4 EB |
1676 | (source |
1677 | (origin | |
1678 | (method url-fetch) | |
a9291a28 CB |
1679 | (uri (string-append |
1680 | "https://www.unidata.ucar.edu/downloads/netcdf/ftp/" | |
1681 | "netcdf-c-" version ".tar.gz")) | |
889187a4 EB |
1682 | (sha256 |
1683 | (base32 | |
a9291a28 | 1684 | "1a2fpp15a2rl1m50gcvvzd9y6bavl6vjf9zzf63sz5gdmq06yiqf")) |
7be2b831 LC |
1685 | (modules '((guix build utils))) |
1686 | (snippet | |
1687 | ;; Make sure this variable is defined only once. Failing to do so | |
1688 | ;; would break builds of 'netcdf-parallel-openmpi' with a | |
1689 | ;; multiple-definition link error with GCC 10. | |
1690 | '(substitute* "ncdump/ocprint.c" | |
1691 | (("^int ocdebug") "static int ocdebug"))) | |
a9291a28 | 1692 | (patches (search-patches "netcdf-date-time.patch")))) |
889187a4 EB |
1693 | (build-system gnu-build-system) |
1694 | (native-inputs | |
1695 | `(("m4" ,m4) | |
1696 | ("doxygen" ,doxygen) | |
1697 | ("graphviz" ,graphviz))) | |
1698 | (inputs | |
db825570 TD |
1699 | `(("hdf4" ,hdf4-alt) |
1700 | ("hdf5" ,hdf5) | |
a9291a28 | 1701 | ("curl" ,curl) |
db825570 | 1702 | ("zlib" ,zlib) |
4bd428a7 | 1703 | ("libjpeg" ,libjpeg-turbo))) |
889187a4 | 1704 | (arguments |
db825570 | 1705 | `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4") |
43d01672 TD |
1706 | |
1707 | #:phases (modify-phases %standard-phases | |
1708 | (add-before 'configure 'fix-source-date | |
1709 | (lambda _ | |
1710 | ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build | |
1711 | ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate | |
1712 | ;; to '1st hour of the current day', and therefore makes the | |
1713 | ;; package not reproducible. | |
1714 | (substitute* "./configure" | |
1715 | (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"") | |
1716 | "date --date='@0'")) | |
1717 | #t)) | |
1718 | (add-after 'configure 'patch-settings | |
1719 | (lambda _ | |
1720 | ;; libnetcdf.settings contains the full filename of the compilers | |
1721 | ;; used to build the library. We truncate the hashes of those | |
1722 | ;; filenames to avoid unnecessary references to the corresponding | |
1723 | ;; store items. | |
1724 | (substitute* "libnetcdf.settings" | |
361d4627 | 1725 | (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash) |
43d01672 TD |
1726 | (string-append prefix (string-take hash 10) "..."))) |
1727 | #t))) | |
1728 | ||
889187a4 | 1729 | #:parallel-tests? #f)) ;various race conditions |
821aa687 | 1730 | (home-page "https://www.unidata.ucar.edu/software/netcdf/") |
889187a4 EB |
1731 | (synopsis "Library for scientific data") |
1732 | (description "NetCDF is an interface for scientific data access and a | |
1733 | software library that provides an implementation of the interface. The netCDF | |
1734 | library defines a machine-independent format for representing scientific data. | |
1735 | Together, the interface, library, and format support the creation, access, and | |
1736 | sharing of scientific data.") | |
1737 | (license (license:x11-style "file://COPYRIGHT")))) | |
1738 | ||
1739 | (define-public netcdf-parallel-openmpi | |
1740 | (package (inherit netcdf) | |
1741 | (name "netcdf-parallel-openmpi") | |
1742 | (inputs | |
1743 | `(("mpi" ,openmpi) | |
1744 | ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi) | |
1745 | (package-inputs netcdf)))) | |
1746 | ;; TODO: Replace pkg-config references in nc-config with absolute references | |
1747 | (arguments | |
1748 | (substitute-keyword-arguments (package-arguments netcdf) | |
1749 | ((#:configure-flags flags) | |
1750 | `(cons* "CC=mpicc" "CXX=mpicxx" | |
1751 | "--enable-parallel-tests" | |
1752 | ;; Shared libraries not supported with parallel IO. | |
1753 | "--disable-shared" "--with-pic" | |
51c55ced LC |
1754 | ,flags)) |
1755 | ((#:phases phases '%standard-phases) | |
1756 | `(modify-phases ,phases | |
1757 | (add-after 'build 'mpi-setup | |
1758 | ,%openmpi-setup))))))) | |
889187a4 | 1759 | |
300200b6 TD |
1760 | (define-public netcdf-fortran |
1761 | (package | |
1762 | (name "netcdf-fortran") | |
d50ad6a7 | 1763 | (version "4.5.3") |
300200b6 TD |
1764 | (source (origin |
1765 | (method url-fetch) | |
1766 | (uri (string-append | |
1767 | "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-" | |
1768 | version ".tar.gz")) | |
1769 | (sha256 | |
1770 | (base32 | |
d50ad6a7 | 1771 | "0x4acvfhbsx1q79dkkwrwbgfhm0w5ngnp4zj5kk92s1khihmqfhj")))) |
300200b6 TD |
1772 | (build-system gnu-build-system) |
1773 | (arguments | |
d130eaf1 GLV |
1774 | `(#:configure-flags '("FCFLAGS=-fallow-argument-mismatch" |
1775 | "FFLAGS=-fallow-argument-mismatch") | |
1776 | #:parallel-tests? #f)) | |
300200b6 TD |
1777 | (inputs |
1778 | `(("netcdf" ,netcdf))) | |
1779 | (native-inputs | |
1780 | `(("gfortran" ,gfortran))) | |
1781 | (synopsis "Fortran interface for the netCDF library") | |
1782 | (description (package-description netcdf)) | |
1783 | (home-page (package-home-page netcdf)) | |
1784 | (license (package-license netcdf)))) | |
1785 | ||
1b39a196 RJ |
1786 | (define-public nlopt |
1787 | (package | |
1788 | (name "nlopt") | |
1789 | (version "2.4.2") | |
1790 | (source (origin | |
1791 | (method url-fetch) | |
1792 | (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-" | |
1793 | version ".tar.gz")) | |
1794 | (sha256 | |
1795 | (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0")))) | |
1796 | (build-system gnu-build-system) | |
1797 | (arguments | |
1798 | `(;; Shared libraries are not built by default. They are required to | |
1799 | ;; build the Guile, Octave, and Python bindings. | |
1800 | #:configure-flags '("--enable-shared") | |
1801 | ||
1802 | #:phases | |
1803 | (modify-phases %standard-phases | |
1804 | (add-before 'configure 'set-libnlopt-file-name | |
1805 | (lambda* (#:key outputs #:allow-other-keys) | |
1806 | ;; Make sure the Scheme module refers to the library by its | |
1807 | ;; absolute file name (we cannot do that from a snippet | |
1808 | ;; because the expansion of @libdir@ contains | |
1809 | ;; ${exec_prefix}.) | |
1810 | (let ((out (assoc-ref outputs "out"))) | |
1811 | (substitute* "swig/nlopt.scm.in" | |
1812 | (("libnlopt") | |
1813 | (string-append out "/lib/libnlopt"))) | |
1814 | #t)))))) | |
1815 | (inputs `(("guile" ,guile-2.0))) | |
1816 | (native-inputs `(("pkg-config" ,pkg-config))) | |
1817 | (home-page "http://ab-initio.mit.edu/wiki/") | |
1818 | (synopsis "Library for nonlinear optimization") | |
1819 | (description "NLopt is a library for nonlinear optimization, providing a | |
1820 | common interface for a number of different free optimization routines available | |
1821 | online as well as original implementations of various other algorithms.") | |
1822 | (license license:lgpl2.1+))) | |
1823 | ||
005c787d LC |
1824 | (define-public ipopt |
1825 | (package | |
1826 | (name "ipopt") | |
30713c2c | 1827 | (version "3.13.4") |
005c787d | 1828 | (source (origin |
30713c2c EB |
1829 | (method git-fetch) |
1830 | (uri (git-reference | |
1831 | (url "https://github.com/coin-or/Ipopt") | |
1832 | (commit (string-append "releases/" version)))) | |
1833 | (file-name (git-file-name name version)) | |
005c787d LC |
1834 | (sha256 |
1835 | (base32 | |
30713c2c | 1836 | "08gznhwhqv1x4baksz350ih8q16r5rd0k8vals6078m3h94khr4b")))) |
005c787d | 1837 | (build-system gnu-build-system) |
ad1c4537 LC |
1838 | (arguments |
1839 | '(#:phases (modify-phases %standard-phases | |
1840 | (add-after 'install 'add--L-flags-in-ipopt.pc | |
1841 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1842 | ;; The '.pc' file lists '-llapack -lblas' in "Libs"; | |
1843 | ;; move it to "Libs.private" where it belongs, and add a | |
1844 | ;; '-L' flag for LAPACK. | |
1845 | (let ((out (assoc-ref outputs "out")) | |
1846 | (lapack (assoc-ref inputs "lapack"))) | |
1847 | (substitute* (string-append out "/lib/pkgconfig/" | |
1848 | "ipopt.pc") | |
1849 | (("Libs: (.*)-llapack -lblas(.*)$" _ before after) | |
1850 | (string-append "Libs: " before " " after "\n" | |
1851 | "Libs.private: " before | |
1852 | "-L" lapack "/lib -llapack -lblas " | |
1853 | after "\n"))) | |
1854 | #t)))))) | |
005c787d | 1855 | (native-inputs |
30713c2c EB |
1856 | `(("gfortran" ,gfortran) |
1857 | ("pkg-config" ,pkg-config))) | |
005c787d LC |
1858 | (inputs |
1859 | ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL. | |
ad1c4537 | 1860 | `(("lapack" ,lapack))) ;for both libblas and liblapack |
d5fd9c72 | 1861 | (home-page "https://www.coin-or.org") |
005c787d LC |
1862 | (synopsis "Large-scale nonlinear optimizer") |
1863 | (description | |
1864 | "The Interior Point Optimizer (IPOPT) is a software package for | |
1865 | large-scale nonlinear optimization. It provides C++, C, and Fortran | |
1866 | interfaces.") | |
30713c2c | 1867 | (license license:epl2.0))) |
005c787d | 1868 | |
6bd1d4a1 PP |
1869 | (define-public nomad-optimizer |
1870 | (package | |
1871 | (name "nomad-optimizer") | |
1872 | (version "4.1.0") | |
1873 | (source | |
1874 | (origin | |
1875 | (method git-fetch) | |
1876 | (uri (git-reference | |
1877 | (url "https://github.com/bbopt/nomad/") | |
1878 | (commit (string-append "v" version)))) | |
1879 | (file-name (git-file-name name version)) | |
1880 | (sha256 | |
1881 | (base32 | |
1882 | "0w386d8r5ldbvnv0c0g7vz95pfpvwdxis26vaalk2amsa5akl775")))) | |
1883 | (build-system cmake-build-system) | |
1884 | (native-inputs | |
1885 | `(("python" ,python-wrapper) | |
1886 | ("python-cython" ,python-cython))) | |
1887 | (arguments | |
1888 | `(#:imported-modules ((guix build python-build-system) | |
1889 | ,@%cmake-build-system-modules) | |
1890 | #:modules (((guix build python-build-system) | |
1891 | #:select (python-version site-packages)) | |
1892 | (guix build cmake-build-system) | |
1893 | (guix build utils)) | |
1894 | #:configure-flags | |
1895 | '("-DBUILD_INTERFACES=ON" | |
1896 | "-DBUILD_TESTS=ON") | |
1897 | #:phases | |
1898 | (modify-phases %standard-phases | |
1899 | (add-after 'unpack 'fix-sources-for-build | |
1900 | (lambda* (#:key outputs #:allow-other-keys) | |
1901 | (substitute* "CMakeLists.txt" | |
1902 | ;; CMAKE_INSTALL_PREFIX is accidentally hardcoded. | |
1903 | (("set\\(CMAKE_INSTALL_PREFIX .* FORCE\\)") "") | |
1904 | ;; Requiring GCC version 8 or later is unwarranted. | |
1905 | (("message\\(FATAL_ERROR \"GCC version < 8") | |
1906 | "message(STATUS \"GCC version < 8")) | |
1907 | ||
1908 | (let ((out (assoc-ref outputs "out"))) | |
1909 | (substitute* "interfaces/PyNomad/CMakeLists.txt" | |
1910 | ;; We don't want to build in-place, and anyway the install | |
1911 | ;; command further below runs build_ext as a prerequisite. | |
1912 | (("COMMAND python setup_PyNomad\\.py .* build_ext --inplace\n") | |
1913 | "") | |
1914 | ;; Don't install locally. | |
1915 | (("COMMAND python (setup_PyNomad\\.py .* install) --user\n" | |
1916 | _ args) | |
1917 | (string-append "COMMAND ${CMAKE_COMMAND} -E env" | |
1918 | " CC=" ,(cc-for-target) | |
1919 | " CXX=" ,(cxx-for-target) | |
1920 | " " (which "python") | |
1921 | " " args | |
1922 | " --prefix=" out | |
1923 | "\n"))) | |
1924 | ;; Fix erroneous assumptions about the paths of the include and | |
1925 | ;; library directories. | |
1926 | (substitute* "interfaces/PyNomad/setup_PyNomad.py" | |
1927 | (("^( +os_include_dirs = ).*" _ prefix) | |
1928 | (string-append prefix "[\"../../src\"]\n")) | |
1929 | (("^(installed_lib_dir = ).*" _ prefix) | |
1930 | (string-append prefix "\"" out "/lib\"\n")))) | |
1931 | #t)) | |
1932 | ||
1933 | ;; Fix the tests so they run in out-of-source builds. | |
1934 | (add-after 'fix-sources-for-build 'fix-sources-for-tests | |
1935 | (lambda _ | |
1936 | (substitute* | |
1937 | (map (lambda (d) (string-append "examples/" d "/CMakeLists.txt")) | |
1938 | (append | |
1939 | (map (lambda (d) (string-append "basic/library/" d)) | |
1940 | '("example1" "example2" "example3" | |
1941 | "single_obj_parallel")) | |
1942 | (map (lambda (d) (string-append "advanced/library/" d)) | |
1943 | '("FixedVariable" "NMonly" "PSDMads" "Restart" | |
1944 | "c_api/example1" "c_api/example2" | |
1945 | "exampleSuggestAndObserve")))) | |
1946 | ;; The built examples are assumed to be in the source tree | |
1947 | ;; (which isn't the case here). | |
1948 | (("(COMMAND \\$\\{CMAKE_BINARY_DIR\\}/examples/runExampleTest\\.sh )\\.(/.*)" | |
1949 | _ command test) | |
1950 | (string-append command "${CMAKE_CURRENT_BINARY_DIR}" test))) | |
1951 | ;; (Unrelated to support for out-of-source testing.) | |
1952 | (make-file-writable | |
1953 | "examples/advanced/library/exampleSuggestAndObserve/cache0.txt") | |
1954 | ||
1955 | (let* ((builddir (string-append (getcwd) "/../build")) | |
1956 | ;; The BB_EXE and SURROGATE_EXE paths are interpreted | |
1957 | ;; relative to the configuration file provided to NOMAD. | |
1958 | ;; However, the configuration files are all in the source | |
1959 | ;; tree rather than in the build tree (unlike the compiled | |
1960 | ;; executables). | |
1961 | (fix-exe-path (lambda* (dir #:optional | |
1962 | (file "param.txt") | |
1963 | (exe-opt "BB_EXE")) | |
1964 | (substitute* (string-append dir "/" file) | |
1965 | (((string-append "^" exe-opt " +")) | |
1966 | ;; The $ prevents NOMAD from prefixing | |
1967 | ;; the executable with the path of the | |
1968 | ;; parent directory of the configuration | |
1969 | ;; file NOMAD was provided with as | |
1970 | ;; argument (param.txt or some such). | |
1971 | (string-append exe-opt " $" | |
1972 | builddir "/" dir "/")))))) | |
1973 | (for-each | |
1974 | (lambda (dir) | |
1975 | (let ((dir (string-append "examples/" dir))) | |
1976 | (substitute* (string-append dir "/CMakeLists.txt") | |
1977 | ;; The install phase has not yet run. | |
1978 | (("COMMAND \\$\\{CMAKE_INSTALL_PREFIX\\}/bin/nomad ") | |
1979 | "COMMAND ${CMAKE_BINARY_DIR}/src/nomad ")) | |
1980 | (fix-exe-path dir) | |
1981 | (when (equal? dir "examples/basic/batch/surrogate_sort") | |
1982 | (fix-exe-path dir "param.txt" "SURROGATE_EXE")))) | |
1983 | (append (map (lambda (d) (string-append "basic/batch/" d)) | |
1984 | '("example1" "example2" | |
1985 | "single_obj" "single_obj_parallel" | |
1986 | "surrogate_sort")) | |
1987 | '("advanced/batch/LHonly"))) | |
1988 | ||
1989 | (let ((dir "examples/advanced/batch/FixedVariable")) | |
1990 | (substitute* (string-append dir "/runFixed.sh") | |
1991 | ;; Hardcoded path to NOMAD executable. | |
1992 | (("^\\.\\./\\.\\./\\.\\./\\.\\./bin/nomad ") | |
1993 | (string-append builddir "/src/nomad "))) | |
1994 | (for-each | |
1995 | (lambda (f) (fix-exe-path dir f)) | |
1996 | '("param1.txt" "param2.txt" "param3.txt" "param10.txt")))) | |
1997 | #t)) | |
1998 | ||
1999 | ;; The information in the .egg-info file is not kept up to date. | |
2000 | (add-after 'install 'delete-superfluous-egg-info | |
2001 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
2002 | (delete-file (string-append | |
2003 | (site-packages inputs outputs) | |
2004 | "PyNomad-0.0.0-py" | |
2005 | (python-version (assoc-ref inputs "python")) | |
2006 | ".egg-info")) | |
2007 | #t))))) | |
2008 | (home-page "https://www.gerad.ca/nomad/") | |
2009 | (synopsis "Nonlinear optimization by mesh-adaptive direct search") | |
2010 | (description | |
2011 | "NOMAD is a C++ implementation of the mesh-adaptive direct search (MADS) | |
2012 | algorithm, designed for difficult blackbox optimization problems. These | |
2013 | problems occur when the functions defining the objective and constraints are | |
2014 | the result of costly computer simulations.") | |
2015 | (license license:lgpl3+))) | |
2016 | ||
f5871b19 EB |
2017 | (define-public cbc |
2018 | (package | |
2019 | (name "cbc") | |
2020 | (version "2.10.5") | |
2021 | (source (origin | |
2022 | (method url-fetch) | |
2023 | (uri (string-append "https://www.coin-or.org/download/source/" | |
2024 | "Cbc/Cbc-" version ".tgz")) | |
2025 | (sha256 | |
2026 | (base32 | |
2027 | "0wk9vr6zc62gw71v7gnra5wxqlcljcgbhm5lasx236v791b986ns")) | |
2028 | (modules '((guix build utils))) | |
2029 | (snippet | |
2030 | ;; Make sure we don't use the bundled software. | |
2031 | '(delete-file-recursively "ThirdParty")))) | |
2032 | (build-system gnu-build-system) | |
2033 | (native-inputs | |
2034 | `(("gfortran" ,gfortran) | |
2035 | ("pkg-config" ,pkg-config))) | |
2036 | (inputs | |
2037 | `(("openblas" ,openblas))) | |
2038 | (home-page "https://www.coin-or.org") | |
2039 | (synopsis "Branch-and-cut solver") | |
2040 | (description | |
2041 | "Cbc (Coin-or branch and cut) is a mixed integer linear programming | |
2042 | solver written in C++. It can be used as a library or as a standalone | |
2043 | executable.") | |
005c787d LC |
2044 | (license license:epl1.0))) |
2045 | ||
ecfbc51f RW |
2046 | (define-public clp |
2047 | (package | |
2048 | (name "clp") | |
bb9f9e1d | 2049 | (version "1.17.6") |
ecfbc51f RW |
2050 | (source (origin |
2051 | (method url-fetch) | |
2052 | (uri (string-append "https://www.coin-or.org/download/source/" | |
2053 | "Clp/Clp-" version ".tgz")) | |
2054 | (sha256 | |
2055 | (base32 | |
bb9f9e1d | 2056 | "0ap1f0lxppa6pnbc4bg7ih7a96avwaki482nig8w5fr3vg9wvkzr")) |
ecfbc51f RW |
2057 | (modules '((guix build utils))) |
2058 | (snippet | |
2059 | ;; Make sure we don't use the bundled software. | |
2060 | '(begin | |
2061 | (delete-file-recursively "ThirdParty") | |
2062 | #t)))) | |
2063 | (build-system gnu-build-system) | |
2064 | (native-inputs | |
2065 | `(("gfortran" ,gfortran) | |
2066 | ("pkg-config" ,pkg-config))) | |
2067 | (inputs | |
2068 | `(("openblas" ,openblas))) | |
2069 | (home-page "https://www.coin-or.org") | |
2070 | (synopsis "Linear programming solver") | |
2071 | (description | |
2072 | "CLP is a high quality linear programming solver. Its main strengths are | |
2073 | its dual and primal Simplex algorithms. It also has a barrier algorithm for | |
2074 | linear and quadratic objectives. There are limited facilities for nonlinear | |
2075 | and quadratic objectives using the Simplex algorithm.") | |
2076 | (license license:epl1.0))) | |
2077 | ||
93cef6e7 LMP |
2078 | (define-public gecode |
2079 | (package | |
2080 | (name "gecode") | |
2081 | (version "6.2.0") | |
2082 | (source (origin | |
2083 | (method git-fetch) | |
2084 | (uri (git-reference | |
2085 | (url "https://github.com/Gecode/gecode") | |
2086 | (commit (string-append "release-" version)))) | |
2087 | (file-name (git-file-name name version)) | |
2088 | (sha256 | |
2089 | (base32 | |
2090 | "0b1cq0c810j1xr2x9y9996p894571sdxng5h74py17c6nr8c6dmk")) | |
2091 | (modules '((guix build utils))) | |
2092 | (snippet | |
2093 | '(begin | |
2094 | ;; delete generated sources | |
2095 | (for-each delete-file | |
2096 | '("gecode/kernel/var-imp.hpp" | |
2097 | "gecode/kernel/var-type.hpp")))))) | |
2098 | (outputs '("out" "examples")) | |
2099 | (build-system gnu-build-system) | |
2100 | (arguments | |
2101 | `(#:configure-flags | |
2102 | (list (string-append "GLDFLAGS=-Wl,-rpath=" | |
2103 | (assoc-ref %outputs "out") | |
2104 | "/lib") | |
2105 | "--enable-examples=no") | |
2106 | #:modules ((guix build gnu-build-system) | |
2107 | (guix build utils) | |
2108 | (ice-9 rdelim) | |
2109 | (ice-9 popen)) | |
2110 | #:phases | |
2111 | (modify-phases %standard-phases | |
2112 | (add-after 'build 'build-examples | |
2113 | (lambda* (#:key outputs #:allow-other-keys) | |
2114 | (invoke "make" "compileexamples"))) | |
2115 | ;; The Makefile disrespects GLDFLAGS for some reason, so we have to | |
2116 | ;; patch it ourselves... *sigh* | |
2117 | (add-after 'install 'fix-rpath | |
2118 | (lambda* (#:key outputs #:allow-other-keys) | |
2119 | (let ((libdir (string-append (assoc-ref outputs "out") "/lib"))) | |
2120 | (for-each | |
2121 | (lambda (file) | |
2122 | (let* ((pipe (open-pipe* OPEN_READ "patchelf" | |
2123 | "--print-rpath" file)) | |
2124 | (line (read-line pipe))) | |
2125 | (and (zero? (close-pipe pipe)) | |
2126 | (invoke "patchelf" "--set-rpath" | |
2127 | (string-append libdir ":" line) | |
2128 | file)))) | |
2129 | (find-files libdir ".*\\.so$"))))) | |
2130 | (add-after 'install 'install-examples | |
2131 | (lambda* (#:key outputs #:allow-other-keys) | |
2132 | (invoke "make" "installexamples" | |
2133 | (string-append "bindir=" (assoc-ref outputs "examples") | |
2134 | "/bin")))) | |
2135 | ;; Tests depend on installed libraries. | |
2136 | (delete 'check) | |
2137 | (add-after 'fix-rpath 'check | |
2138 | (assoc-ref %standard-phases 'check))))) | |
2139 | (native-inputs | |
2140 | `(("patchelf" ,patchelf) | |
2141 | ("perl" ,perl) | |
2142 | ("sed" ,sed))) | |
2143 | (home-page "https://www.gecode.org") | |
2144 | (synopsis "Toolkit for developing constraint-based systems") | |
2145 | (description "Gecode is a C++ toolkit for developing constraint-based | |
2146 | systems and applications. It provides a modular and extensible solver.") | |
2147 | (license license:expat))) | |
2148 | ||
9bb7534a EF |
2149 | (define-public libflame |
2150 | (package | |
2151 | (name "libflame") | |
2152 | (version "5.2.0") | |
2153 | (outputs '("out" "static")) | |
2154 | (source | |
2155 | (origin | |
2156 | (method git-fetch) | |
2157 | (uri (git-reference | |
2158 | (url "https://github.com/flame/libflame") | |
2159 | (commit version))) | |
2160 | (file-name (git-file-name name version)) | |
2161 | (sha256 | |
2162 | (base32 | |
2163 | "1n6lf0wvpp77lxqlr721h2jbfbzigphdp19wq8ajiccilcksh7ay")))) | |
2164 | (build-system gnu-build-system) | |
2165 | (arguments | |
2166 | `(#:configure-flags | |
2167 | ;; Sensible defaults: https://github.com/flame/libflame/issues/28 | |
2168 | (list "--enable-dynamic-build" | |
2169 | "--enable-max-arg-list-hack" | |
2170 | "--enable-lapack2flame" | |
2171 | "--enable-verbose-make-output" | |
2172 | "--enable-multithreading=pthreads" ; Openblas isn't built with openmp. | |
2173 | ,@(if (any (cute string-prefix? <> (or (%current-target-system) | |
2174 | (%current-system))) | |
2175 | '("x86_64" "i686")) | |
2176 | '("--enable-vector-intrinsics=sse") | |
2177 | '()) | |
2178 | "--enable-supermatrix" | |
2179 | "--enable-memory-alignment=16" | |
2180 | "--enable-ldim-alignment") | |
2181 | #:phases | |
2182 | (modify-phases %standard-phases | |
2183 | (add-after 'unpack 'patch-/usr/bin/env-bash | |
2184 | (lambda _ | |
2185 | (substitute* "build/config.mk.in" | |
2186 | (("/usr/bin/env bash") (which "bash"))) | |
2187 | #t)) | |
2188 | (replace 'check | |
2189 | (lambda* (#:key tests? #:allow-other-keys) | |
2190 | (substitute* "test/Makefile" | |
2191 | (("LIBBLAS .*") "LIBBLAS = -lblas\n") | |
2192 | (("LIBLAPACK .*") "LIBLAPACK = -llapack\n")) | |
2193 | (if tests? | |
2194 | (with-directory-excursion "test" | |
2195 | (mkdir "obj") | |
2196 | (invoke "make") | |
2197 | (invoke "./test_libflame.x")) | |
2198 | #t))) | |
2199 | (add-after 'install 'install-static | |
2200 | (lambda* (#:key outputs #:allow-other-keys) | |
2201 | (let ((out (assoc-ref outputs "out")) | |
2202 | (static (assoc-ref outputs "static"))) | |
2203 | (mkdir-p (string-append static "/lib")) | |
2204 | (rename-file (string-append out "/lib/libflame.a") | |
2205 | (string-append static "/lib/libflame.a")) | |
2206 | (install-file (string-append out "/include/FLAME.h") | |
2207 | (string-append static "/include")) | |
2208 | #t)))))) | |
2209 | (inputs | |
2210 | `(("gfortran" ,gfortran))) | |
2211 | (native-inputs | |
2212 | `(("lapack" ,lapack) | |
2213 | ("openblas" ,openblas) | |
2214 | ("perl" ,perl) | |
2215 | ("python" ,python-wrapper))) | |
2216 | (home-page "https://github.com/flame/libflame") | |
2217 | (synopsis "High-performance object-based library for DLA computations") | |
2218 | (description "@code{libflame} is a portable library for dense matrix | |
2219 | computations, providing much of the functionality present in LAPACK, developed | |
2220 | by current and former members of the @acronym{SHPC, Science of High-Performance | |
2221 | Computing} group in the @url{https://www.ices.utexas.edu/, Institute for | |
2222 | Computational Engineering and Sciences} at The University of Texas at Austin. | |
2223 | @code{libflame} includes a compatibility layer, @code{lapack2flame}, which | |
2224 | includes a complete LAPACK implementation.") | |
2225 | (license license:bsd-3))) | |
2226 | ||
92d3f267 LMP |
2227 | (define-public libpotassco |
2228 | ;; No public release, update together with clasp | |
2229 | (let ((revision "1") | |
2230 | (commit "2f9fb7ca2c202f1b47643aa414054f2f4f9c1821")) | |
2231 | (package | |
2232 | (name "libpotassco") | |
2233 | (version (git-version "0.0" revision commit)) | |
2234 | (source (origin | |
2235 | (method git-fetch) | |
2236 | (uri (git-reference | |
2237 | (url "https://github.com/potassco/libpotassco") | |
2238 | (commit commit))) | |
2239 | (file-name (git-file-name name version)) | |
2240 | (sha256 | |
2241 | (base32 | |
2242 | "1c32f9gqclf7qx07lpx8wd720vfhkjqhzc6nyy8mjmgwpmb3iyyn")))) | |
2243 | (arguments | |
2244 | `(#:configure-flags '("-DLIB_POTASSCO_BUILD_TESTS=on" | |
2245 | "-DLIB_POTASSCO_INSTALL_LIB=on" | |
2246 | "-DBUILD_SHARED_LIBS=on") | |
2247 | #:phases | |
2248 | (modify-phases %standard-phases | |
2249 | (add-after 'unpack 'patch-cmake | |
2250 | (lambda _ | |
2251 | (substitute* "CMakeLists.txt" | |
2252 | ;; clasp expects lowercase potassco and include directory is | |
2253 | ;; lowercase as well, so let's use that | |
2254 | (("\"cmake/Potassco\"") "\"cmake/potassco\"") | |
2255 | (("PotasscoConfig\\.cmake") "potassco-config.cmake") | |
2256 | (("PotasscoConfigVersion\\.cmake") | |
2257 | "potassco-config-version.cmake")) | |
2258 | (rename-file "cmake/PotasscoConfig.cmake.in" | |
2259 | "cmake/potassco-config.cmake.in")))))) | |
2260 | (build-system cmake-build-system) | |
2261 | (home-page "https://potassco.org/") | |
2262 | (synopsis "Utility library for Potassco's projects") | |
2263 | (description "@code{libpotassco} is a utility library providing functions | |
2264 | and datatypes for | |
2265 | @itemize | |
2266 | @item parsing, writing, and converting logic programs in aspif and smodels | |
2267 | format, | |
2268 | @item passing information between a grounder and a solver, | |
2269 | @item and defining and parsing command-line options and for creating | |
2270 | command-line applications. | |
2271 | @end itemize | |
2272 | Furthermore, it comes with the tool @command{lpconvert} that converts either | |
2273 | between aspif and smodels format or to a human-readable text format.") | |
2274 | (license license:expat)))) | |
2275 | ||
2dfc574b LMP |
2276 | (define-public clasp |
2277 | (package | |
2278 | (name "clasp") | |
2279 | (version "3.3.6") | |
2280 | (source (origin | |
2281 | (method git-fetch) | |
2282 | (uri (git-reference | |
2283 | (url "https://github.com/potassco/clasp") | |
2284 | (commit (string-append "v" version)))) | |
2285 | (file-name (git-file-name name version)) | |
2286 | (sha256 | |
2287 | (base32 | |
2288 | "0rahqiq530jckvx717858h1q5p8znp1kb6sjm95p8blkr4n3pvmj")))) | |
2289 | (build-system cmake-build-system) | |
2290 | (arguments | |
2291 | `(#:configure-flags '("-DCLASP_BUILD_TESTS=on" | |
2292 | "-DCLASP_INSTALL_LIB=on" | |
2293 | "-DCLASP_USE_LOCAL_LIB_POTASSCO=off" | |
2294 | "-DBUILD_SHARED_LIBS=on") | |
2295 | #:phases | |
2296 | (modify-phases %standard-phases | |
2297 | (add-after 'unpack 'patch-cmake | |
2298 | (lambda _ | |
2299 | (substitute* "CMakeLists.txt" | |
2300 | ;; Use lowercase to be consistent with libpotassco | |
2301 | (("\"cmake/Clasp\"") "\"cmake/clasp\"") | |
2302 | (("ClaspConfig\\.cmake") "clasp-config.cmake") | |
2303 | (("ClaspConfigVersion\\.cmake") | |
2304 | "clasp-config-version.cmake")) | |
2305 | (substitute* "cmake/ClaspConfig.cmake.in" | |
2306 | (("find_package\\(Potassco") "find_package(potassco")) | |
2307 | (rename-file "cmake/ClaspConfig.cmake.in" | |
2308 | "cmake/clasp-config.cmake.in")))))) | |
2309 | (inputs | |
2310 | `(("libpotassco" ,libpotassco))) | |
2311 | (home-page "https://potassco.org/") | |
2312 | (synopsis "Answer set solver") | |
2313 | (description "clasp is an answer set solver for (extended) normal and | |
2314 | disjunctive logic programs. The primary algorithm of clasp relies on | |
2315 | conflict-driven nogood learning, a technique that proved very successful for | |
2316 | satisfiability checking (SAT).") | |
2317 | (license license:expat))) | |
2318 | ||
505d53a4 LMP |
2319 | (define-public clingo |
2320 | (package | |
2321 | (name "clingo") | |
2322 | (version "5.5.0") | |
2323 | (source (origin | |
2324 | (method git-fetch) | |
2325 | (uri (git-reference | |
2326 | (url "https://github.com/potassco/clingo") | |
2327 | (commit (string-append "v" version)))) | |
2328 | (file-name (git-file-name name version)) | |
2329 | (sha256 | |
2330 | (base32 | |
2331 | "0rfjwkcwm0mmf3r4i7asyjwb6cia4i7px7fn2kdbi9j85qvas4pb")))) | |
2332 | (build-system cmake-build-system) | |
2333 | (arguments | |
2334 | `(#:configure-flags `("-DCLINGO_BUILD_TESTS=on" | |
2335 | "-DCLINGO_INSTALL_LIB=on" | |
2336 | "-DCLINGO_BUILD_STATIC=off" | |
2337 | "-DCLINGO_BUILD_SHARED=on" | |
2338 | ;; XXX: Clingo requries private headers and | |
2339 | ;; sources from clasp | |
2340 | ,(string-append | |
2341 | "-DCLASP_SOURCE_DIR=" | |
2342 | (assoc-ref %build-inputs "clasp-src"))) | |
2343 | #:phases | |
2344 | (modify-phases %standard-phases | |
2345 | (add-after 'unpack 'patch-cmake | |
2346 | (lambda _ | |
2347 | (substitute* "CMakeLists.txt" | |
2348 | (("add_subdirectory\\(clasp\\)") | |
2349 | "find_package(clasp REQUIRED)")) | |
2350 | (substitute* "libclingo/CMakeLists.txt" | |
2351 | (("\"cmake/Clingo\"") "\"cmake/clingo\"") | |
2352 | (("ClingoConfig\\.cmake") "clingo-config.cmake") | |
2353 | (("ClingoConfigVersion\\.cmake") | |
2354 | "clingo-config-version.cmake")) | |
2355 | (substitute* "cmake/ClingoConfig.cmake.in" | |
2356 | (("find_package\\(Clasp") "find_package(clasp")) | |
2357 | (rename-file "cmake/ClingoConfig.cmake.in" | |
2358 | "cmake/clingo-config.cmake.in"))) | |
2359 | (add-after 'unpack 'skip-failing-tests | |
2360 | (lambda _ | |
2361 | (with-directory-excursion "libclingo/tests" | |
2362 | (substitute* "CMakeLists.txt" | |
2363 | (("COMMAND test_clingo" all) | |
2364 | (string-append all | |
2365 | " -f " | |
2366 | "\"${CMAKE_CURRENT_SOURCE_DIR}/good.txt\""))) | |
2367 | (call-with-output-file "good.txt" | |
2368 | (lambda (port) | |
2369 | (for-each (lambda (test) (format port "~s~%" test)) | |
2370 | '("parse-ast-v2" "add-ast-v2" "build-ast-v2" | |
2371 | "unpool-ast-v2" "parse_term" | |
2372 | "propagator" "propgator-sequence-mining" | |
2373 | "symbol" "visitor")))))))))) | |
2374 | (inputs | |
2375 | `(("clasp" ,clasp) | |
2376 | ("libpotassco" ,libpotassco))) | |
2377 | (native-inputs | |
2378 | `(("clasp-src" ,(package-source clasp)))) | |
2379 | (home-page "https://potassco.org/") | |
2380 | (synopsis "Grounder and solver for logic programs") | |
2381 | (description "Clingo computes answer sets for a given logic program.") | |
2382 | (license license:expat))) | |
2383 | ||
f9940ef1 LC |
2384 | (define-public ceres |
2385 | (package | |
2386 | (name "ceres-solver") | |
e0bee0de | 2387 | (version "1.14.0") |
f9940ef1 LC |
2388 | (home-page "http://ceres-solver.org/") |
2389 | (source (origin | |
2390 | (method url-fetch) | |
2391 | (uri (string-append home-page "ceres-solver-" | |
2392 | version ".tar.gz")) | |
2393 | (sha256 | |
2394 | (base32 | |
e0bee0de | 2395 | "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27")))) |
f9940ef1 LC |
2396 | (build-system cmake-build-system) |
2397 | (arguments | |
2398 | ;; TODO: Build HTML user documentation and install separately. | |
bc3a2e35 | 2399 | '(#:configure-flags '("-DBUILD_EXAMPLES=OFF" |
f9940ef1 LC |
2400 | "-DBUILD_SHARED_LIBS=ON") |
2401 | ||
2402 | #:phases (modify-phases %standard-phases | |
2403 | (add-before 'configure 'set-library-directory | |
2404 | (lambda _ | |
2405 | ;; Install libraries to lib/, not lib64/. | |
2406 | (substitute* "internal/ceres/CMakeLists.txt" | |
2407 | (("set\\(LIB_SUFFIX \"64\"\\)") | |
2408 | "set(LIB_SUFFIX \"\")")) | |
2409 | #t))))) | |
2410 | (native-inputs | |
2411 | `(("pkg-config" ,pkg-config))) | |
468e0b18 LC |
2412 | (propagated-inputs |
2413 | `(("glog" ,glog))) ;for #include <glog/glog.h> | |
f9940ef1 LC |
2414 | (inputs |
2415 | `(("eigen" ,eigen) | |
2416 | ("blas" ,openblas) | |
2417 | ("lapack" ,lapack) | |
2418 | ("suitesparse" ,suitesparse) | |
2419 | ("gflags" ,gflags))) | |
2420 | (synopsis "C++ library for solving large optimization problems") | |
2421 | (description | |
2422 | "Ceres Solver is a C++ library for modeling and solving large, | |
2423 | complicated optimization problems. It is a feature rich, mature and | |
2424 | performant library which has been used in production since 2010. Ceres Solver | |
2425 | can solve two kinds of problems: | |
2426 | @enumerate | |
2427 | @item non-linear least squares problems with bounds constraints; | |
2428 | @item general unconstrained optimization problems. | |
2429 | @end enumerate\n") | |
2430 | (license license:bsd-3))) | |
2431 | ||
b66741ed | 2432 | ;; For a fully featured Octave, users are strongly recommended also to install |
5ca4fe96 | 2433 | ;; the following packages: less, ghostscript, gnuplot. |
5537603f | 2434 | (define-public octave-cli |
668c06ac | 2435 | (package |
5537603f | 2436 | (name "octave-cli") |
0f8a646e | 2437 | (version "6.2.0") |
668c06ac JD |
2438 | (source |
2439 | (origin | |
2440 | (method url-fetch) | |
2441 | (uri (string-append "mirror://gnu/octave/octave-" | |
0f8a646e | 2442 | version ".tar.xz")) |
668c06ac JD |
2443 | (sha256 |
2444 | (base32 | |
0f8a646e | 2445 | "06id09zspya24gshcwgp039cp35c06150mdlxysawgnbrhj16wkv")))) |
668c06ac JD |
2446 | (build-system gnu-build-system) |
2447 | (inputs | |
697df13f EF |
2448 | `(("alsa-lib" ,alsa-lib) |
2449 | ("arpack" ,arpack-ng) | |
8a0dd289 | 2450 | ("bdb" ,bdb) |
697df13f | 2451 | ("curl" ,curl) |
1ec78e9d EB |
2452 | ("fftw" ,fftw) |
2453 | ("fftwf" ,fftwf) | |
668c06ac JD |
2454 | ("fltk" ,fltk) |
2455 | ("fontconfig" ,fontconfig) | |
2456 | ("freetype" ,freetype) | |
697df13f EF |
2457 | ("gl2ps" ,gl2ps) |
2458 | ("glpk" ,glpk) | |
1ec78e9d | 2459 | ("glu" ,glu) |
ab5f3f21 | 2460 | ("graphicsmagick" ,graphicsmagick) |
a533c5a1 MB |
2461 | |
2462 | ;; TODO: libjpeg-turbo is indirectly required through libtiff. In | |
2463 | ;; the next rebuild cycle, add an absolute reference for -ljpeg in | |
2464 | ;; libtiff.la instead of having to provide it here. | |
2465 | ("libjpeg" ,libjpeg-turbo) | |
2466 | ||
697df13f EF |
2467 | ("hdf5" ,hdf5) |
2468 | ("lapack" ,lapack) | |
ab5f3f21 | 2469 | ("libsndfile" ,libsndfile) |
697df13f EF |
2470 | ("libxft" ,libxft) |
2471 | ("mesa" ,mesa) | |
2472 | ("pcre" ,pcre) | |
ab5f3f21 | 2473 | ("portaudio" ,portaudio) |
697df13f EF |
2474 | ("qhull" ,qhull) |
2475 | ("readline" ,readline) | |
2476 | ("suitesparse" ,suitesparse) | |
2477 | ("texinfo" ,texinfo) | |
2478 | ("zlib" ,zlib))) | |
668c06ac | 2479 | (native-inputs |
0f8a646e | 2480 | `(("gfortran" ,gfortran) |
668c06ac JD |
2481 | ("pkg-config" ,pkg-config) |
2482 | ("perl" ,perl) | |
1ec78e9d EB |
2483 | ;; The following inputs are not actually used in the build process. |
2484 | ;; However, the ./configure gratuitously tests for their existence and | |
2485 | ;; assumes that programs not present at build time are also not, and | |
2486 | ;; can never be, available at run time! If these inputs are therefore | |
2487 | ;; not present, support for them will be built out. However, Octave | |
2488 | ;; will still run without them, albeit without the features they | |
668c06ac JD |
2489 | ;; provide. |
2490 | ("less" ,less) | |
668c06ac JD |
2491 | ("ghostscript" ,ghostscript) |
2492 | ("gnuplot" ,gnuplot))) | |
116af86f KK |
2493 | ;; Octave code uses this variable to detect directories holding multiple CA |
2494 | ;; certificates to verify peers with. This is required for the networking | |
2495 | ;; functions that require encryption to work properly. | |
2496 | (native-search-paths | |
2497 | (list (search-path-specification | |
2498 | (variable "CURLOPT_CAPATH") | |
2499 | (files '("etc/ssl/certs"))))) | |
668c06ac | 2500 | (arguments |
b7b27a8f KY |
2501 | `(#:configure-flags |
2502 | (list (string-append "--with-shell=" | |
2503 | (assoc-ref %build-inputs "bash") | |
a533c5a1 MB |
2504 | "/bin/sh") |
2505 | ||
2506 | ;; XXX: Without this flag, linking octave-cli fails with | |
2507 | ;; undefined references to 'logf@GLIBCXX_3.4' et.al. due to | |
2508 | ;; not pulling in liboctinterp.la for -lstdc++. | |
2509 | "--enable-link-all-dependencies") | |
5ca4fe96 AI |
2510 | #:phases |
2511 | (modify-phases %standard-phases | |
2512 | (add-after 'configure 'configure-makeinfo | |
2513 | (lambda* (#:key inputs #:allow-other-keys) | |
b18b9d20 AI |
2514 | (substitute* "libinterp/corefcn/help.h" |
2515 | (("\"makeinfo\"") | |
2516 | (string-append | |
2517 | "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\""))) | |
5ca4fe96 | 2518 | #t))))) |
f5a077b1 | 2519 | (home-page "https://www.gnu.org/software/octave/") |
36252dff | 2520 | (synopsis "High-level language for numerical computation (no GUI)") |
1ec78e9d EB |
2521 | (description "GNU Octave is a high-level interpreted language that is |
2522 | specialized for numerical computations. It can be used for both linear and | |
2523 | non-linear applications and it provides great support for visualizing results. | |
2524 | Work may be performed both at the interactive command-line as well as via | |
2525 | script files.") | |
668c06ac | 2526 | (license license:gpl3+))) |
3de01d3f | 2527 | |
e0ae7e73 | 2528 | (define-public octave |
5537603f | 2529 | (package (inherit octave-cli) |
e0ae7e73 | 2530 | (name "octave") |
36ce25f0 KK |
2531 | (inputs |
2532 | `(("qscintilla" ,qscintilla) | |
ea0a5107 | 2533 | ("qt" ,qtbase-5) |
5537603f | 2534 | ,@(package-inputs octave-cli))) |
36ce25f0 KK |
2535 | (native-inputs |
2536 | `(("qttools" , qttools) ;for lrelease | |
82f5f6b1 | 2537 | ("texlive" ,(texlive-updmap.cfg (list texlive-epsf))) ; for texi2dvi |
5537603f | 2538 | ,@(package-native-inputs octave-cli))) |
36ce25f0 | 2539 | (arguments |
5537603f | 2540 | (substitute-keyword-arguments (package-arguments octave-cli) |
36ce25f0 KK |
2541 | ((#:phases phases) |
2542 | `(modify-phases ,phases | |
2543 | (add-before 'configure 'patch-qscintilla-library-name | |
2544 | (lambda* (#:key inputs #:allow-other-keys) | |
2545 | ;; The QScintilla library that the Octave configure script tries | |
2546 | ;; to link with should be named libqscintilla-qt5.so, but the | |
2547 | ;; QScintilla input provides the shared library as | |
2548 | ;; libqscintilla2_qt5.so. | |
2549 | (substitute* "configure" | |
2550 | (("qscintilla2-qt5") | |
2551 | "qscintilla2_qt5")) | |
36252dff KH |
2552 | #t)))))) |
2553 | (synopsis "High-level language for numerical computation (with GUI)"))) | |
36ce25f0 | 2554 | |
5d4bd4cc PG |
2555 | (define-public opencascade-oce |
2556 | (package | |
2557 | (name "opencascade-oce") | |
2558 | (version "0.17.2") | |
2559 | (source | |
2560 | (origin | |
830971bf TGR |
2561 | (method git-fetch) |
2562 | (uri (git-reference | |
b0e7b699 | 2563 | (url "https://github.com/tpaviot/oce") |
830971bf TGR |
2564 | (commit (string-append "OCE-" version)))) |
2565 | (file-name (git-file-name name version)) | |
a4f393b7 | 2566 | (patches (search-patches "opencascade-oce-glibc-2.26.patch")) |
5d4bd4cc | 2567 | (sha256 |
830971bf | 2568 | (base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69")))) |
5d4bd4cc PG |
2569 | (build-system cmake-build-system) |
2570 | (arguments | |
2571 | '(#:configure-flags | |
2572 | (list "-DOCE_TESTING:BOOL=ON" | |
2573 | "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON" | |
2574 | "-DOCE_DRAW:BOOL=ON" | |
2575 | (string-append "-DOCE_INSTALL_PREFIX:PATH=" | |
2576 | (assoc-ref %outputs "out")) | |
2577 | "-UCMAKE_INSTALL_RPATH"))) | |
2578 | (inputs | |
2579 | `(("freetype" ,freetype) | |
2580 | ("glu" ,glu) | |
2581 | ("libxmu" ,libxmu) | |
2582 | ("mesa" ,mesa) | |
2583 | ("tcl" ,tcl) | |
2584 | ("tk" ,tk))) | |
2585 | (native-inputs | |
2586 | `(("python" ,python-wrapper))) | |
2587 | (home-page "https://github.com/tpaviot/oce") | |
2588 | (synopsis "Libraries for 3D modeling and numerical simulation") | |
2589 | (description | |
2590 | "Open CASCADE is a set of libraries for the development of applications | |
2591 | dealing with 3D CAD data or requiring industrial 3D capabilities. It includes | |
2592 | C++ class libraries providing services for 3D surface and solid modeling, CAD | |
2593 | data exchange, and visualization. It is used for development of specialized | |
2594 | software dealing with 3D models in design (CAD), manufacturing (CAM), | |
2595 | numerical simulation (CAE), measurement equipment (CMM), and quality | |
2596 | control (CAQ) domains. | |
2597 | ||
2598 | This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers | |
2599 | patches, improvements, and experiments contributed by users over the official | |
2600 | Open CASCADE library.") | |
2601 | (license (list license:lgpl2.1; OCE libraries, with an exception for the | |
2602 | ; use of header files; see | |
2603 | ; OCCT_LGPL_EXCEPTION.txt | |
2604 | license:public-domain; files | |
2605 | ; src/Standard/Standard_StdAllocator.hxx and | |
2606 | ; src/NCollection/NCollection_StdAllocator.hxx | |
2607 | license:expat; file src/OpenGl/OpenGl_glext.h | |
2608 | license:bsd-3)))); test framework gtest | |
2609 | ||
37dc2920 PG |
2610 | (define-public opencascade-occt |
2611 | (package | |
2612 | (name "opencascade-occt") | |
2613 | (version "7.3.0p3") | |
2614 | (source | |
2615 | (origin | |
2616 | (method git-fetch) | |
2617 | (uri (git-reference | |
2618 | (url "https://git.dev.opencascade.org/repos/occt.git") | |
2619 | (commit | |
2620 | (string-append "V" | |
2621 | (string-map (lambda (x) (if (eq? x #\.) #\_ x)) | |
2622 | version))))) | |
2623 | (file-name (git-file-name name version)) | |
2624 | (sha256 | |
2625 | (base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4")) | |
2626 | (modules '((guix build utils))) | |
2627 | (snippet | |
2628 | '(begin | |
2629 | ;; Remove files specific to non-free operating systems. | |
2630 | (delete-file-recursively "samples/ios") | |
2631 | (delete-file-recursively "samples/mfc") | |
2632 | (delete-file-recursively "samples/qt/FuncDemo") | |
2633 | (delete-file "genconf.bat") | |
2634 | (delete-file "gendoc.bat") | |
2635 | (delete-file "genproj.bat") | |
2636 | (delete-file "upgrade.bat") | |
2637 | ;; Remove references to deleted files. | |
2638 | (substitute* "dox/FILES_HTML.txt" | |
2639 | ((".*standard.*") "" ) | |
2640 | ((".*UIKitSample.*") "")) | |
2641 | #t)))) | |
2642 | (build-system cmake-build-system) | |
2643 | (arguments | |
2644 | '(;; There is no test target for make. OCCT provides an | |
2645 | ;; 'Automated Testing System', which may be accessed after | |
2646 | ;; installation via the draw.sh script. draw.sh is located in | |
2647 | ;; the bin directory. For details see: | |
2648 | ;; https://www.opencascade.com/doc/occt-7.3.0/overview/html/\ | |
2649 | ;; occt_dev_guides__tests.html | |
2650 | #:tests? #f | |
2651 | ;; Configure without freeimage: attempting to link against the | |
2652 | ;; freeimage version 3.17 library leads to 'undefined | |
2653 | ;; reference' errors. | |
2654 | #:configure-flags | |
2655 | (list "-DUSE_FREEIMAGE:BOOL=OFF" | |
2656 | "-DUSE_TBB:BOOL=ON" | |
2657 | "-DUSE_VTK:BOOL=OFF" | |
2658 | "-DBUILD_DOC_Overview:BOOL=OFF" | |
2659 | "-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON" | |
2660 | "-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON" | |
2661 | "-UCMAKE_INSTALL_LIBDIR"))) | |
2662 | (inputs | |
2663 | `(("doxygen" ,doxygen) | |
2664 | ;("freeimage" ,freeimage) | |
2665 | ("freetype" ,freetype) | |
2666 | ("glu" ,glu) | |
2667 | ("libxext" ,libxext) | |
2668 | ("libxi" ,libxi) | |
2669 | ("libxmu" ,libxmu) | |
2670 | ("mesa" ,mesa) | |
2671 | ("tbb" ,tbb) | |
2672 | ("tcl" ,tcl) | |
2673 | ("tk" ,tk))) | |
2674 | ;; TODO: build Overview documentation and add 'doc' output. | |
2675 | (home-page "https://www.opencascade.com") | |
2676 | (synopsis "Libraries for 3D modeling and numerical simulation") | |
2677 | (description | |
2678 | "Open CASCADE is a set of libraries for the development of applications | |
2679 | dealing with 3D CAD data or requiring industrial 3D capabilities. It includes | |
2680 | C++ class libraries providing services for 3D surface and solid modeling, CAD | |
2681 | data exchange, and visualization. It is used for development of specialized | |
2682 | software dealing with 3D models in design (CAD), manufacturing (CAM), | |
2683 | numerical simulation (CAE), measurement equipment (CMM), and quality | |
2684 | control (CAQ) domains. | |
2685 | ||
2686 | This is the certified version of the Open Cascade Technology (OCCT) library.") | |
2687 | (license (list ;; OCCT library: | |
2688 | license:lgpl2.1; with an exception for the use of header | |
2689 | ; files, see OCCT_LGPL_EXCEPTION.txt. | |
2690 | ;; Files src/OpenGl/glext.h, adm/cmake/cotire.cmake and | |
2691 | ;; src/OpenGl/OpenGl_HaltonSampler.hxx: | |
2692 | license:expat | |
2693 | ;; Files src/ExprIntrp/ExprIntrp.tab.* and | |
2694 | ;; src/StepFile/step.tab.*: | |
2695 | license:gpl3+ ; with Bison 2.2 exception. | |
2696 | ;; File src/NCollection/NCollection_UtfIterator.lxx: | |
2697 | (license:non-copyleft | |
2698 | "https://www.unicode.org/license.html") | |
2699 | ;; File src/NCollection/NCollection_StdAllocator.hxx: | |
2700 | license:public-domain)))) | |
2701 | ||
3de01d3f EB |
2702 | (define-public gmsh |
2703 | (package | |
2704 | (name "gmsh") | |
cb78595f | 2705 | (version "4.8.4") |
3de01d3f EB |
2706 | (source |
2707 | (origin | |
abed5df7 PG |
2708 | (method git-fetch) |
2709 | (uri (git-reference | |
2710 | (url "https://gitlab.onelab.info/gmsh/gmsh.git") | |
2711 | (commit | |
2712 | (string-append "gmsh_" | |
c5cfa23b | 2713 | (string-replace-substring version "." "_"))))) |
abed5df7 | 2714 | (file-name (git-file-name name version)) |
3de01d3f | 2715 | (sha256 |
cb78595f | 2716 | (base32 "07mi6ja3b9libgcdp2b4dwnkap1b9ha2wi2zdn9mhmwvp3g1pxhp")) |
3de01d3f EB |
2717 | (modules '((guix build utils))) |
2718 | (snippet | |
6cbee49d | 2719 | '(begin |
229e04c6 | 2720 | (delete-file-recursively "contrib/metis") |
6cbee49d | 2721 | #t)))) |
3de01d3f | 2722 | (build-system cmake-build-system) |
3de01d3f EB |
2723 | (propagated-inputs |
2724 | `(("fltk" ,fltk) | |
19afbea1 | 2725 | ("gfortran" ,gfortran) |
7a27129c | 2726 | ("glu" ,glu) |
3de01d3f | 2727 | ("gmp" ,gmp) |
40029cbe | 2728 | ("hdf5" ,hdf5) |
3de01d3f | 2729 | ("lapack" ,lapack) |
7a27129c EF |
2730 | ("libx11" ,libx11) |
2731 | ("libxext" ,libxext) | |
3de01d3f | 2732 | ("mesa" ,mesa) |
229e04c6 | 2733 | ("metis" ,metis) |
7a27129c | 2734 | ("opencascade-occt" ,opencascade-occt))) |
66395a61 EF |
2735 | (inputs |
2736 | `(("fontconfig" ,fontconfig) | |
b9fd7f9d PG |
2737 | ("libxft" ,libxft) |
2738 | ("python" ,python))) | |
3de01d3f | 2739 | (arguments |
229e04c6 | 2740 | `(#:configure-flags `("-DENABLE_SYSTEM_CONTRIB:BOOL=ON" |
3de01d3f | 2741 | "-DENABLE_BUILD_SHARED:BOOL=ON" |
b9fd7f9d PG |
2742 | "-DENABLE_BUILD_DYNAMIC:BOOL=ON") |
2743 | #:imported-modules (,@%cmake-build-system-modules | |
2744 | (guix build python-build-system)) | |
2745 | #:modules (((guix build python-build-system) #:select (site-packages)) | |
2746 | (guix build cmake-build-system) | |
2747 | (guix build utils)) | |
2748 | #:phases | |
2749 | (modify-phases %standard-phases | |
2750 | (add-after 'unpack 'patch-paths | |
2751 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
2752 | ;; Use the standard Guix site-package path for | |
2753 | ;; installation of the Python API. | |
2754 | (substitute* "CMakeLists.txt" | |
2755 | (("include\\(GNUInstallDirs\\)\n") | |
2756 | (string-append "include(GNUInstallDirs)\n" | |
2757 | " set(GMSH_PY_LIB " | |
2758 | (site-packages inputs outputs) ")\n")) | |
2759 | (("\\$\\{GMSH\\_PY\\} DESTINATION \\$\\{GMSH\\_LIB\\}") | |
2760 | "${GMSH_PY} DESTINATION ${GMSH_PY_LIB}")) | |
2761 | ;; Find the shared library. | |
2762 | (let ((libgmsh (string-append (assoc-ref outputs "out") | |
2763 | "/lib/libgmsh.so"))) | |
2764 | (substitute* "api/gmsh.py" | |
2765 | (("find_library\\(\"gmsh\"\\)") | |
2766 | (simple-format #f "\"~a\"" libgmsh)))) | |
2767 | #t))))) | |
0746c33e | 2768 | (home-page "http://gmsh.info/") |
3de01d3f | 2769 | (synopsis "3D finite element grid generator") |
edf684ef EB |
2770 | (description "Gmsh is a 3D finite element grid generator with a built-in |
2771 | CAD engine and post-processor. Its design goal is to provide a fast, light | |
2772 | and user-friendly meshing tool with parametric input and advanced | |
2773 | visualization capabilities. Gmsh is built around four modules: geometry, | |
2774 | mesh, solver and post-processing. The specification of any input to these | |
2775 | modules is done either interactively using the graphical user interface or in | |
2776 | ASCII text files using Gmsh's own scripting language.") | |
3de01d3f | 2777 | (license license:gpl2+))) |
b9100e2f | 2778 | |
7294cbec VM |
2779 | (define-public veusz |
2780 | (package | |
2781 | (name "veusz") | |
0313617f | 2782 | (version "3.3.1") |
7294cbec VM |
2783 | (source |
2784 | (origin | |
2785 | (method url-fetch) | |
2786 | (uri (pypi-uri "veusz" version)) | |
2787 | (sha256 | |
0313617f | 2788 | (base32 "1q7hi1qwwg4pgiz62isvv1pia85m13bspdpp1q3mrnwl11in0ag0")))) |
7294cbec VM |
2789 | (build-system python-build-system) |
2790 | (arguments | |
2791 | `(;; Tests will fail because they depend on optional packages like | |
2792 | ;; python-astropy, which is not packaged. | |
2793 | #:tests? #f | |
2794 | #:phases | |
2795 | (modify-phases %standard-phases | |
2796 | ;; Veusz will append 'PyQt5' to sip_dir by default. That is not how | |
2797 | ;; the path is defined in Guix, therefore we have to change it. | |
2798 | (add-after 'unpack 'fix-sip-dir | |
2799 | (lambda _ | |
2800 | (substitute* "pyqtdistutils.py" | |
2801 | (("os.path.join\\(sip_dir, 'PyQt5'\\)") "sip_dir")) | |
2802 | #t)) | |
2803 | ;; Now we have to pass the correct sip_dir to setup.py. | |
2804 | (replace 'build | |
2805 | (lambda* (#:key inputs #:allow-other-keys) | |
2806 | ;; We need to tell setup.py where to locate QtCoremod.sip | |
2807 | ((@@ (guix build python-build-system) call-setuppy) | |
2808 | "build_ext" | |
2809 | (list (string-append "--sip-dir=" | |
2810 | (assoc-ref inputs "python-pyqt") | |
2811 | "/share/sip")) | |
2812 | #t))) | |
2813 | ;; Ensure that icons are found at runtime. | |
2814 | (add-after 'install 'wrap-executable | |
2815 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
2816 | (let ((out (assoc-ref outputs "out"))) | |
2817 | (wrap-program (string-append out "/bin/veusz") | |
2818 | `("QT_PLUGIN_PATH" prefix | |
2819 | ,(list (string-append (assoc-ref inputs "qtsvg") | |
2820 | "/lib/qt5/plugins/")))))))))) | |
2821 | (native-inputs | |
2822 | `(("pkg-config" ,pkg-config) | |
2823 | ;;("python-astropy" ,python-astropy) ;; FIXME: Package this. | |
c990604c BT |
2824 | ("qttools" ,qttools) |
2825 | ("python-sip" ,python-sip-4))) | |
7294cbec VM |
2826 | (inputs |
2827 | `(("ghostscript" ,ghostscript) ;optional, for EPS/PS output | |
2828 | ("python-dbus" ,python-dbus) | |
2829 | ("python-h5py" ,python-h5py) ;optional, for HDF5 data | |
2830 | ("python-pyqt" ,python-pyqt) | |
ea0a5107 | 2831 | ("qtbase" ,qtbase-5) |
7294cbec VM |
2832 | ("qtsvg" ,qtsvg))) |
2833 | (propagated-inputs | |
2834 | `(("python-numpy" ,python-numpy))) | |
2835 | (home-page "https://veusz.github.io/") | |
2836 | (synopsis "Scientific plotting package") | |
2837 | (description | |
2838 | "Veusz is a scientific plotting and graphing program with a graphical | |
2839 | user interface, designed to produce publication-ready 2D and 3D plots. In | |
2840 | addition it can be used as a module in Python for plotting. It supports | |
2841 | vector and bitmap output, including PDF, Postscript, SVG and EMF.") | |
2842 | (license license:gpl2+))) | |
2843 | ||
6d5f63b6 JD |
2844 | (define-public maxflow |
2845 | (package | |
2846 | (name "maxflow") | |
0af12a13 TGR |
2847 | ;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’, |
2848 | ;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’. | |
2849 | (version "3.0.5") | |
6d5f63b6 JD |
2850 | (source (origin |
2851 | (method git-fetch) | |
2852 | (uri (git-reference | |
b0e7b699 | 2853 | (url "https://github.com/gerddie/maxflow") |
0af12a13 | 2854 | (commit version))) |
2dc0a6cf | 2855 | (file-name (git-file-name name version)) |
6d5f63b6 JD |
2856 | (sha256 |
2857 | (base32 | |
2858 | "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb")))) | |
2859 | (build-system cmake-build-system) | |
0be9038c | 2860 | (home-page "https://pub.ist.ac.at/~vnk/software.html") |
6d5f63b6 JD |
2861 | (synopsis "Library implementing Maxflow algorithm") |
2862 | (description "An implementation of the maxflow algorithm described in | |
2863 | @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for | |
2864 | Energy Minimization in Computer Vision.\n | |
2865 | Yuri Boykov and Vladimir Kolmogorov.\n | |
2866 | In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n | |
2867 | September 2004}") | |
2868 | (license license:gpl3+))) | |
2869 | ||
b9100e2f EB |
2870 | (define-public petsc |
2871 | (package | |
2872 | (name "petsc") | |
4f7a4a06 | 2873 | (version "3.11.2") |
b9100e2f EB |
2874 | (source |
2875 | (origin | |
2876 | (method url-fetch) | |
2877 | ;; The *-lite-* tarball does not contain the *large* documentation | |
2878 | (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" | |
2879 | "petsc-lite-" version ".tar.gz")) | |
2880 | (sha256 | |
4f7a4a06 | 2881 | (base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx")))) |
b2c52fc9 TGR |
2882 | (outputs '("out" ; libraries and headers |
2883 | "examples")) ; ~30MiB of examples | |
b9100e2f EB |
2884 | (build-system gnu-build-system) |
2885 | (native-inputs | |
6fec298d | 2886 | `(("python" ,python-2))) |
b9100e2f | 2887 | (inputs |
19afbea1 | 2888 | `(("gfortran" ,gfortran) |
c7a5c3e0 | 2889 | ("openblas" ,openblas) |
f258212d | 2890 | ("superlu" ,superlu) |
b9100e2f EB |
2891 | ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi |
2892 | ;; leaving out opengl, as configuration seems to only be for mac | |
2893 | )) | |
2894 | (arguments | |
2895 | `(#:test-target "test" | |
b2c52fc9 | 2896 | #:parallel-build? #f ; build is parallel by default |
b9100e2f EB |
2897 | #:configure-flags |
2898 | `("--with-mpi=0" | |
f258212d | 2899 | "--with-openmp=1" |
c7a5c3e0 | 2900 | "--with-openblas=1" |
c15be128 | 2901 | "--with-superlu=1") |
9731c412 EB |
2902 | #:make-flags |
2903 | ;; Honor (parallel-job-count) for build. Do not use --with-make-np, | |
2904 | ;; whose value is dumped to $out/lib/petsc/conf/petscvariables. | |
2905 | (list (format #f "MAKE_NP=~a" (parallel-job-count))) | |
b9100e2f | 2906 | #:phases |
64dcc289 EB |
2907 | (modify-phases %standard-phases |
2908 | (replace 'configure | |
2909 | ;; PETSc's configure script is actually a python script, so we can't | |
2910 | ;; run it with bash. | |
2911 | (lambda* (#:key outputs (configure-flags '()) | |
2912 | #:allow-other-keys) | |
2913 | (let* ((prefix (assoc-ref outputs "out")) | |
2914 | (flags `(,(string-append "--prefix=" prefix) | |
2915 | ,@configure-flags))) | |
2916 | (format #t "build directory: ~s~%" (getcwd)) | |
2917 | (format #t "configure flags: ~s~%" flags) | |
49fdd357 | 2918 | (apply invoke "./configure" flags)))) |
64dcc289 | 2919 | (add-after 'configure 'clean-local-references |
9731c412 | 2920 | (lambda* (#:key outputs #:allow-other-keys) |
64dcc289 EB |
2921 | (let ((out (assoc-ref outputs "out"))) |
2922 | (substitute* (find-files "." "^petsc(conf|machineinfo).h$") | |
b730b437 EB |
2923 | ;; Prevent build directory from leaking into compiled code |
2924 | (((getcwd)) out) | |
2925 | ;; Scrub timestamp for reproducibility | |
fafd623e | 2926 | ((".*Libraries compiled on.*") "")) |
9731c412 EB |
2927 | (substitute* (find-files "." "petscvariables") |
2928 | ;; Do not expose build machine characteristics, set to defaults. | |
2929 | (("MAKE_NP = [:digit:]+") "MAKE_NP = 2") | |
2930 | (("NPMAX = [:digit:]+") "NPMAX = 2")) | |
fafd623e | 2931 | #t))) |
64dcc289 | 2932 | (add-after 'install 'clean-install |
10b11968 EB |
2933 | ;; Try to keep installed files from leaking build directory names. |
2934 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
64dcc289 | 2935 | (let ((out (assoc-ref outputs "out"))) |
10b11968 | 2936 | (substitute* (map (lambda (file) |
9a899cce | 2937 | (string-append out "/lib/petsc/conf/" file)) |
fafd623e | 2938 | '("petscvariables")) |
10b11968 EB |
2939 | (((getcwd)) out)) |
2940 | ;; Make compiler references point to the store | |
9a899cce | 2941 | (substitute* (string-append out "/lib/petsc/conf/petscvariables") |
dfdf5716 EB |
2942 | (("= (gcc|g\\+\\+|gfortran)" _ compiler) |
2943 | (string-append "= " (which compiler)))) | |
10b11968 EB |
2944 | ;; PETSc installs some build logs, which aren't necessary. |
2945 | (for-each (lambda (file) | |
9a899cce | 2946 | (let ((f (string-append out "/lib/petsc/conf/" file))) |
10b11968 EB |
2947 | (when (file-exists? f) |
2948 | (delete-file f)))) | |
9a899cce EB |
2949 | '("configure.log" "make.log" "gmake.log" |
2950 | "test.log" "error.log" "RDict.db" | |
fafd623e | 2951 | "PETScBuildInternal.cmake" |
10b11968 | 2952 | ;; Once installed, should uninstall with Guix |
fafd623e | 2953 | "uninstall.py")) |
a3a99e27 EB |
2954 | #t))) |
2955 | (add-after 'install 'move-examples | |
2956 | (lambda* (#:key outputs #:allow-other-keys) | |
2957 | (let* ((out (assoc-ref outputs "out")) | |
2958 | (examples (assoc-ref outputs "examples")) | |
2959 | (exdir (string-append out "/share/petsc/examples")) | |
2960 | (exdir' (string-append examples "/share/petsc/examples"))) | |
2961 | (copy-recursively exdir exdir') | |
2962 | (delete-file-recursively exdir) | |
fafd623e | 2963 | #t)))))) |
2299d83e | 2964 | (home-page "https://www.mcs.anl.gov/petsc") |
16ecf3ff | 2965 | (synopsis "Library to solve PDEs") |
b9100e2f EB |
2966 | (description "PETSc, pronounced PET-see (the S is silent), is a suite of |
2967 | data structures and routines for the scalable (parallel) solution of | |
2968 | scientific applications modeled by partial differential equations.") | |
166191b3 | 2969 | (license (license:non-copyleft |
2299d83e | 2970 | "https://www.mcs.anl.gov/petsc/documentation/copyright.html")))) |
b9100e2f EB |
2971 | |
2972 | (define-public petsc-complex | |
2973 | (package (inherit petsc) | |
2974 | (name "petsc-complex") | |
2975 | (arguments | |
2976 | (substitute-keyword-arguments (package-arguments petsc) | |
2977 | ((#:configure-flags cf) | |
2978 | `(cons "--with-scalar-type=complex" ,cf)))) | |
16ecf3ff | 2979 | (synopsis "Library to solve PDEs (with complex scalars)"))) |
183e44ae | 2980 | |
d8c7eeb9 EB |
2981 | (define-public petsc-openmpi |
2982 | (package (inherit petsc) | |
2983 | (name "petsc-openmpi") | |
2984 | (inputs | |
9e2aa70b | 2985 | `(("hdf5" ,hdf5-parallel-openmpi) |
af523673 | 2986 | ("hypre" ,hypre-openmpi) |
9e2aa70b PG |
2987 | ("metis" ,metis) |
2988 | ("mumps" ,mumps-openmpi) | |
2989 | ("openmpi" ,openmpi) | |
2990 | ("scalapack" ,scalapack) | |
72f95783 | 2991 | ("scotch" ,pt-scotch32) |
d8c7eeb9 EB |
2992 | ,@(package-inputs petsc))) |
2993 | (arguments | |
2994 | (substitute-keyword-arguments (package-arguments petsc) | |
2995 | ((#:configure-flags cf) | |
af523673 PG |
2996 | ``("--with-hypre=1" |
2997 | "--with-mpiexec=mpirun" | |
9e2aa70b PG |
2998 | "--with-metis=1" |
2999 | "--with-mumps=1" | |
3000 | "--with-scalapack=1" | |
3001 | "--with-ptscotch=1" | |
d8c7eeb9 EB |
3002 | ,(string-append "--with-mpi-dir=" |
3003 | (assoc-ref %build-inputs "openmpi")) | |
71ca16b5 PG |
3004 | ,(string-append "--with-hdf5-include=" |
3005 | (assoc-ref %build-inputs "hdf5") "/include") | |
3006 | ,(string-append "--with-hdf5-lib=" | |
3007 | (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a") | |
3008 | ,@(delete "--with-mpi=0" ,cf))) | |
3009 | ((#:phases phases) | |
3010 | `(modify-phases ,phases | |
9e2aa70b | 3011 | (add-before 'configure 'mpi-setup |
bbe46a4a | 3012 | ,%openmpi-setup))))) |
9e2aa70b | 3013 | (synopsis "Library to solve PDEs (with MUMPS and MPI support)"))) |
d8c7eeb9 EB |
3014 | |
3015 | (define-public petsc-complex-openmpi | |
3016 | (package (inherit petsc-complex) | |
3017 | (name "petsc-complex-openmpi") | |
3018 | (inputs | |
3019 | `(("openmpi" ,openmpi) | |
3020 | ,@(package-inputs petsc-complex))) | |
3021 | (arguments | |
3022 | (substitute-keyword-arguments (package-arguments petsc-complex) | |
3023 | ((#:configure-flags cf) | |
3024 | ``("--with-mpiexec=mpirun" | |
3025 | ,(string-append "--with-mpi-dir=" | |
3026 | (assoc-ref %build-inputs "openmpi")) | |
e586c6fa EB |
3027 | ,@(delete "--with-mpi=0" ,cf))) |
3028 | ((#:phases phases) | |
3029 | `(modify-phases ,phases | |
3030 | (add-before 'configure 'mpi-setup | |
3031 | ,%openmpi-setup))))) | |
16ecf3ff | 3032 | (synopsis "Library to solve PDEs (with complex scalars and MPI support)"))) |
d8c7eeb9 | 3033 | |
90ff2874 PG |
3034 | (define-public python-petsc4py |
3035 | (package | |
3036 | (name "python-petsc4py") | |
f1cc312e | 3037 | (version "3.11.0") |
90ff2874 PG |
3038 | (source |
3039 | (origin | |
3040 | (method url-fetch) | |
3041 | (uri (pypi-uri "petsc4py" version)) | |
3042 | (sha256 | |
3043 | (base32 | |
c6843f17 PG |
3044 | "1rm1qj5wlkhxl39by9n78lh3gbmii31wsnb8j1rr5hvfr5xgbx2q")) |
3045 | (modules '((guix build utils))) | |
3046 | (snippet | |
3047 | '(begin | |
3048 | ;; Ensure source file is regenerated in the build phase. | |
3049 | (delete-file "src/petsc4py.PETSc.c") | |
3050 | ;; Remove legacy GC code. See | |
3051 | ;; https://bitbucket.org/petsc/petsc4py/issues/125. | |
3052 | (substitute* "src/PETSc/cyclicgc.pxi" | |
3053 | ((".*gc_refs.*") "" ) | |
3054 | ((".*PyGC_Head.*") "")) | |
3055 | #t)))) | |
90ff2874 PG |
3056 | (build-system python-build-system) |
3057 | (arguments | |
3058 | `(#:phases | |
3059 | (modify-phases %standard-phases | |
3060 | (add-before 'build 'pre-build | |
3061 | (lambda _ | |
3062 | ;; Define path to PETSc installation. | |
3063 | (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) | |
3064 | #t)) | |
3065 | (add-before 'check 'mpi-setup | |
3066 | ,%openmpi-setup)))) | |
c6843f17 PG |
3067 | (native-inputs |
3068 | `(("python-cython" ,python-cython))) | |
90ff2874 PG |
3069 | (inputs |
3070 | `(("petsc" ,petsc-openmpi) | |
3071 | ("python-numpy" ,python-numpy))) | |
3072 | (home-page "https://bitbucket.org/petsc/petsc4py/") | |
3073 | (synopsis "Python bindings for PETSc") | |
3074 | (description "PETSc, the Portable, Extensible Toolkit for | |
3075 | Scientific Computation, is a suite of data structures and routines for | |
3076 | the scalable (parallel) solution of scientific applications modeled by | |
3077 | partial differential equations. It employs the MPI standard for all | |
3078 | message-passing communication. @code{petsc4py} provides Python | |
3079 | bindings to almost all functions of PETSc.") | |
3080 | (license license:bsd-3))) | |
3081 | ||
560acf25 MB |
3082 | (define-public python-kiwisolver |
3083 | (package | |
3084 | (name "python-kiwisolver") | |
3085 | (version "1.0.1") | |
3086 | (source (origin | |
3087 | (method url-fetch) | |
3088 | (uri (pypi-uri "kiwisolver" version)) | |
3089 | (sha256 | |
3090 | (base32 | |
3091 | "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf")))) | |
3092 | (build-system python-build-system) | |
3093 | (home-page "https://github.com/nucleic/kiwi") | |
3094 | (synopsis "Fast implementation of the Cassowary constraint solver") | |
3095 | (description | |
3096 | "Kiwi is an efficient C++ implementation of the Cassowary constraint | |
3097 | solving algorithm. Kiwi has been designed from the ground up to be | |
3098 | lightweight and fast. Kiwi ranges from 10x to 500x faster than the original | |
3099 | Cassowary solver with typical use cases gaining a 40x improvement. Memory | |
3100 | savings are consistently > 5x.") | |
3101 | (license license:bsd-3))) | |
3102 | ||
3103 | (define-public python2-kiwisolver | |
3104 | (package-with-python2 python-kiwisolver)) | |
3105 | ||
a7f01414 EB |
3106 | (define-public slepc |
3107 | (package | |
3108 | (name "slepc") | |
a13e0f3d | 3109 | (version "3.11.1") |
a7f01414 EB |
3110 | (source |
3111 | (origin | |
3112 | (method url-fetch) | |
baeaf882 EB |
3113 | (uri (string-append "http://slepc.upv.es/download/distrib/slepc-" |
3114 | version ".tar.gz")) | |
a7f01414 EB |
3115 | (sha256 |
3116 | (base32 | |
a13e0f3d | 3117 | "1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8")))) |
a7f01414 EB |
3118 | (build-system gnu-build-system) |
3119 | (native-inputs | |
a13e0f3d EB |
3120 | `(("python" ,python-2) |
3121 | ("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script | |
a7f01414 EB |
3122 | (inputs |
3123 | `(("arpack" ,arpack-ng) | |
3124 | ("gfortran" ,gfortran))) | |
3125 | (propagated-inputs | |
3126 | `(("petsc" ,petsc))) | |
3127 | (arguments | |
3128 | `(#:parallel-build? #f ;build is parallel by default | |
3129 | #:configure-flags | |
3130 | `(,(string-append "--with-arpack-dir=" | |
9cf52454 | 3131 | (assoc-ref %build-inputs "arpack") "/lib")) |
9731c412 | 3132 | #:make-flags ;honor (parallel-job-count) |
a13e0f3d EB |
3133 | `(,(format #f "MAKE_NP=~a" (parallel-job-count)) |
3134 | ,(string-append "PETSCCONFIGDIR=" | |
3135 | (assoc-ref %build-inputs "petsc:examples") | |
3136 | "/share/petsc/examples/config")) | |
a7f01414 EB |
3137 | #:phases |
3138 | (modify-phases %standard-phases | |
8787c555 | 3139 | (replace 'configure |
a7f01414 EB |
3140 | ;; configure is a python script, so we can't run it with bash. |
3141 | (lambda* (#:key inputs outputs (configure-flags '()) | |
3142 | #:allow-other-keys) | |
3143 | (let* ((prefix (assoc-ref outputs "out")) | |
3144 | (flags `(,(string-append "--prefix=" prefix) | |
3145 | ,@configure-flags))) | |
3146 | (format #t "build directory: ~s~%" (getcwd)) | |
3147 | (format #t "configure flags: ~s~%" flags) | |
3148 | (setenv "SLEPC_DIR" (getcwd)) | |
9cf52454 | 3149 | (setenv "PETSC_DIR" (assoc-ref inputs "petsc")) |
c6840089 | 3150 | (apply invoke "./configure" flags)))) |
8787c555 | 3151 | (add-after 'install 'delete-doc |
a7f01414 EB |
3152 | ;; TODO: SLEPc installs HTML documentation alongside headers in |
3153 | ;; $out/include. We'd like to move them to share/doc, but delete | |
3154 | ;; them for now, as they are incomplete and installing the complete | |
3155 | ;; documentation is difficult. | |
3156 | (lambda* (#:key outputs #:allow-other-keys) | |
3157 | (let* ((out (assoc-ref outputs "out"))) | |
0f6dc120 TGR |
3158 | (for-each delete-file (find-files out "\\.html$")) |
3159 | #t))) | |
8787c555 | 3160 | (add-after 'install 'clean-install |
a7f01414 EB |
3161 | ;; Clean up unnecessary build logs from installation. |
3162 | (lambda* (#:key outputs #:allow-other-keys) | |
3163 | (let ((out (assoc-ref outputs "out"))) | |
3164 | (for-each (lambda (file) | |
3165 | (let ((f (string-append out "/lib/slepc/conf/" file))) | |
3166 | (when (file-exists? f) | |
3167 | (delete-file f)))) | |
3168 | '("configure.log" "make.log" "gmake.log" | |
3169 | "test.log" "error.log" "RDict.db" | |
0f6dc120 TGR |
3170 | "uninstall.py")) |
3171 | #t)))))) | |
1ca4b76b | 3172 | (home-page "https://slepc.upv.es") |
a7f01414 EB |
3173 | (synopsis "Scalable library for eigenproblems") |
3174 | (description "SLEPc is a software library for the solution of large sparse | |
3175 | eigenproblems on parallel computers. It can be used for the solution of | |
3176 | linear eigenvalue problems formulated in either standard or generalized form, | |
3177 | as well as other related problems such as the singular value decomposition. | |
3178 | The emphasis of the software is on methods and techniques appropriate for | |
3179 | problems in which the associated matrices are sparse, for example, those | |
3180 | arising after the discretization of partial differential equations.") | |
3c524f21 | 3181 | (license license:bsd-2))) |
a7f01414 EB |
3182 | |
3183 | (define-public slepc-complex | |
3184 | (package (inherit slepc) | |
3185 | (name "slepc-complex") | |
3186 | (propagated-inputs | |
3187 | `(("petsc" ,petsc-complex) | |
3188 | ,@(alist-delete "petsc" (package-propagated-inputs slepc)))) | |
3189 | (synopsis "Scalable library for eigenproblems (with complex scalars)"))) | |
3190 | ||
3191 | (define-public slepc-openmpi | |
3192 | (package (inherit slepc) | |
3193 | (name "slepc-openmpi") | |
6df2a50a LC |
3194 | (arguments |
3195 | (substitute-keyword-arguments (package-arguments slepc) | |
3196 | ((#:phases phases '%standard-phases) | |
3197 | `(modify-phases ,phases | |
bbe46a4a EB |
3198 | (add-before 'check 'mpi-setup |
3199 | ,%openmpi-setup))))) | |
a7f01414 EB |
3200 | (inputs |
3201 | `(("mpi" ,openmpi) | |
3202 | ("arpack" ,arpack-ng-openmpi) | |
3203 | ,@(alist-delete "arpack" (package-inputs slepc)))) | |
3204 | (propagated-inputs | |
3205 | `(("petsc" ,petsc-openmpi) | |
3206 | ,@(alist-delete "petsc" (package-propagated-inputs slepc)))) | |
3207 | (synopsis "Scalable library for eigenproblems (with MPI support)"))) | |
3208 | ||
3209 | (define-public slepc-complex-openmpi | |
3210 | (package (inherit slepc-openmpi) | |
3211 | (name "slepc-complex-openmpi") | |
3212 | (propagated-inputs | |
3213 | `(("petsc" ,petsc-complex-openmpi) | |
3214 | ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi)))) | |
3215 | (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)"))) | |
3216 | ||
6b5687d0 PG |
3217 | (define-public python-slepc4py |
3218 | (package | |
3219 | (name "python-slepc4py") | |
09bad3cd | 3220 | (version "3.11.0") |
6b5687d0 PG |
3221 | (source |
3222 | (origin | |
3223 | (method url-fetch) | |
3224 | (uri (pypi-uri "slepc4py" version)) | |
3225 | (sha256 | |
3226 | (base32 | |
09bad3cd | 3227 | "1ksp08kxf4wg408b9nn39z3qfhy643j22d4rfbl30vzxk2rxh4lq")))) |
6b5687d0 PG |
3228 | (build-system python-build-system) |
3229 | (arguments | |
3230 | `(#:phases | |
3231 | (modify-phases %standard-phases | |
3232 | (add-before 'build 'pre-build | |
3233 | (lambda _ | |
3234 | ;; Define path to PETSc installation. | |
3235 | (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) | |
3236 | ;; Define path to SLEPc installation. | |
3237 | (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc")) | |
3238 | #t)) | |
3239 | (add-before 'check 'mpi-setup | |
3240 | ,%openmpi-setup)))) | |
3241 | (inputs | |
3242 | `(("python-numpy" ,python-numpy) | |
3243 | ("python-petsc4py" ,python-petsc4py) | |
3244 | ("slepc" ,slepc-openmpi))) | |
3245 | (home-page "https://bitbucket.org/slepc/slepc4py/") | |
3246 | (synopsis "Python bindings for SLEPc") | |
3247 | (description "SLEPc, the Scalable Library for Eigenvalue Problem | |
3248 | Computations, is based on PETSc, the Portable, Extensible Toolkit for | |
3249 | Scientific Computation. It employs the MPI standard for all | |
3250 | message-passing communication. @code{slepc4py} provides Python | |
3251 | bindings to almost all functions of SLEPc.") | |
3252 | (license license:bsd-3))) | |
3253 | ||
d277c00e | 3254 | (define-public metamath |
6667576b W |
3255 | (package |
3256 | (name "metamath") | |
23682250 | 3257 | (version "0.193") |
6667576b W |
3258 | (source |
3259 | (origin | |
3260 | (method git-fetch) | |
3261 | (uri (git-reference | |
b0e7b699 | 3262 | (url "https://github.com/metamath/metamath-exe") |
6667576b W |
3263 | (commit (string-append "v" version)))) |
3264 | (file-name (git-file-name name version)) | |
3265 | (sha256 | |
23682250 | 3266 | (base32 "1s9hyknfvhj86g3giayyf3dxzg23iij0rs7bdvj075v9qbyhqn9b")))) |
6667576b W |
3267 | (build-system gnu-build-system) |
3268 | (native-inputs | |
3269 | `(("autoconf" ,autoconf) | |
3270 | ("automake" ,automake))) | |
3271 | (home-page "http://us.metamath.org/") | |
3272 | (synopsis "Proof verifier based on a minimalistic formalism") | |
3273 | (description | |
3274 | "Metamath is a tiny formal language and that can express theorems in | |
d277c00e W |
3275 | abstract mathematics, with an accompyaning @command{metamath} executable that |
3276 | verifies databases of these proofs. There is a public database, | |
3277 | @url{https://github.com/metamath/set.mm, set.mm}, implementing first-order | |
3278 | logic and Zermelo-Frenkel set theory with Choice, along with a large swath of | |
3279 | associated, high-level theorems, e.g.@: the fundamental theorem of arithmetic, | |
3280 | the Cauchy-Schwarz inequality, Stirling's formula, etc. See the Metamath | |
3281 | book.") | |
6667576b | 3282 | (license license:gpl2+))) |
d277c00e | 3283 | |
95c88e38 LMP |
3284 | (define-public minizinc |
3285 | (package | |
3286 | (name "minizinc") | |
3287 | (version "2.5.5") | |
3288 | (source (origin | |
3289 | (method git-fetch) | |
3290 | (uri (git-reference | |
3291 | (url "https://github.com/MiniZinc/libminizinc") | |
3292 | (commit version))) | |
3293 | (file-name (git-file-name name version)) | |
3294 | (sha256 | |
3295 | (base32 | |
3296 | "10b2hsl1fx9psh0iagmp8ki3f60f3qg5hmvra5aczjlfmbl88ggp")) | |
3297 | (modules '((guix build utils) | |
3298 | (ice-9 ftw) | |
3299 | (srfi srfi-1))) | |
3300 | (snippet | |
3301 | '(begin | |
3302 | ;; Do not advertise proprietary solvers | |
3303 | (with-directory-excursion "cmake/targets" | |
3304 | (let ((targets '("libminizinc_fzn.cmake" | |
3305 | "libminizinc_gecode.cmake" | |
3306 | "libminizinc_mip.cmake" | |
3307 | "libminizinc_nl.cmake" | |
3308 | "libminizinc_osicbc.cmake" | |
3309 | "libminizinc_parser.cmake" | |
3310 | "libmzn.cmake" | |
3311 | "minizinc.cmake" | |
3312 | "mzn2doc.cmake"))) | |
3313 | (for-each delete-file | |
3314 | (remove | |
3315 | (lambda (file) | |
3316 | (member file (cons* "." ".." targets))) | |
3317 | (scandir "."))) | |
3318 | (substitute* "libmzn.cmake" | |
3319 | (("include\\(cmake/targets/(.*)\\)" all target) | |
3320 | (if (member target targets) all ""))))) | |
3321 | (with-directory-excursion "include/minizinc/solvers/MIP" | |
3322 | (for-each delete-file | |
3323 | (remove | |
3324 | (lambda (file) | |
3325 | (member file '("." ".." | |
3326 | "MIP_osicbc_solverfactory.hh" | |
3327 | "MIP_osicbc_wrap.hh" | |
3328 | "MIP_solverinstance.hh" | |
3329 | "MIP_solverinstance.hpp" | |
3330 | "MIP_wrap.hh"))) | |
3331 | (scandir ".")))) | |
3332 | (with-directory-excursion "solvers/MIP" | |
3333 | (for-each delete-file | |
3334 | (remove | |
3335 | (lambda (file) | |
3336 | (member file '("." ".." | |
3337 | "MIP_osicbc_solverfactory.cpp" | |
3338 | "MIP_osicbc_wrap.cpp" | |
3339 | "MIP_solverinstance.cpp" | |
3340 | "MIP_wrap.cpp"))) | |
3341 | (scandir ".")))) | |
3342 | (substitute* "CMakeLists.txt" | |
3343 | (("find_package\\(([^ ]*).*\\)" all pkg) | |
3344 | (if (member pkg '("Gecode" "OsiCBC" "Threads")) | |
3345 | all | |
3346 | ""))) | |
3347 | ;; TODO: swap out miniz for zlib | |
3348 | #t)))) | |
3349 | (build-system cmake-build-system) | |
3350 | (arguments | |
3351 | `(#:tests? #f ; no ‘check’ target | |
3352 | #:modules ((guix build cmake-build-system) | |
3353 | (guix build utils) | |
3354 | (srfi srfi-1)) | |
3355 | #:phases | |
3356 | (modify-phases %standard-phases | |
3357 | (add-after 'install 'install-solver-configs | |
3358 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
3359 | (let ((gecode (assoc-ref inputs "gecode")) | |
3360 | (pkgdatadir (string-append (assoc-ref outputs "out") | |
3361 | "/share/minizinc"))) | |
3362 | (call-with-output-file (string-append pkgdatadir | |
3363 | "/Preferences.json") | |
3364 | (lambda (port) | |
3365 | (display "\ | |
3366 | { | |
3367 | \"tagDefaults\": [ | |
3368 | [\"\", \"org.gecode.gecode\"], | |
3369 | [\"gecode\", \"org.gecode.gecode\"] | |
3370 | ], | |
3371 | \"solverDefaults\": [] | |
3372 | }" | |
3373 | port) | |
3374 | (newline port))) | |
3375 | ||
3376 | (mkdir-p (string-append pkgdatadir "/solvers")) | |
3377 | (call-with-output-file (string-append pkgdatadir | |
3378 | "/solvers/gecode.msc") | |
3379 | (lambda (port) | |
3380 | (format port | |
3381 | "\ | |
3382 | { | |
3383 | \"id\": \"org.gecode.gecode\", | |
3384 | \"name\": \"Gecode\", | |
3385 | \"description\": \"Gecode FlatZinc executable\", | |
3386 | \"version\": ~s, | |
3387 | \"mznlib\": ~s, | |
3388 | \"executable\": ~s, | |
3389 | \"supportsMzn\": false, | |
3390 | \"supportsFzn\": true, | |
3391 | \"needsSolns2Out\": true, | |
3392 | \"needsMznExecutable\": false, | |
3393 | \"needsStdlibDir\": false, | |
3394 | \"isGUIApplication\": false | |
3395 | }" | |
3396 | (last (string-split gecode #\-)) | |
3397 | (string-append gecode "/share/gecode/mznlib") | |
3398 | (string-append gecode "/bin/fzn-gecode")) | |
3399 | (newline port))))))))) | |
3400 | (native-inputs | |
3401 | `(("bison" ,bison) | |
3402 | ("flex" ,flex))) | |
3403 | (inputs | |
3404 | `(("cbc" ,cbc) | |
3405 | ("gecode" ,gecode) | |
3406 | ("zlib" ,zlib))) | |
3407 | (home-page "https://www.minizinc.org") | |
3408 | (synopsis "High-level constraint modeling language") | |
3409 | (description "MiniZinc is a high-level modeling language for constraint | |
3410 | satisfaction and optimization problems. Models are compiled to FlatZinc, a | |
3411 | language understood by many solvers.") | |
3412 | (license license:mpl2.0))) | |
3413 | ||
cec86422 EB |
3414 | (define-public mumps |
3415 | (package | |
3416 | (name "mumps") | |
5dbc79eb | 3417 | (version "5.2.1") |
cec86422 EB |
3418 | (source |
3419 | (origin | |
3420 | (method url-fetch) | |
3421 | (uri (string-append "http://mumps.enseeiht.fr/MUMPS_" | |
3422 | version ".tar.gz")) | |
3423 | (sha256 | |
3424 | (base32 | |
5dbc79eb | 3425 | "0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r")) |
06e12395 MB |
3426 | (patches (search-patches "mumps-build-parallelism.patch" |
3427 | "mumps-shared-libseq.patch" | |
3428 | "mumps-shared-mumps.patch" | |
3429 | "mumps-shared-pord.patch")))) | |
cec86422 EB |
3430 | (build-system gnu-build-system) |
3431 | (inputs | |
3432 | `(("fortran" ,gfortran) | |
3433 | ;; These are required for linking against mumps, but we let the user | |
3434 | ;; declare the dependency. | |
3435 | ("blas" ,openblas) | |
3436 | ("metis" ,metis) | |
3437 | ("scotch" ,scotch))) | |
3438 | (arguments | |
3439 | `(#:modules ((ice-9 match) | |
3440 | (ice-9 popen) | |
3441 | (srfi srfi-1) | |
3442 | ,@%gnu-build-system-modules) | |
3443 | #:phases | |
3444 | (modify-phases %standard-phases | |
fba78d18 | 3445 | (replace 'configure |
cec86422 EB |
3446 | (lambda* (#:key inputs #:allow-other-keys) |
3447 | (call-with-output-file "Makefile.inc" | |
3448 | (lambda (port) | |
3449 | (format port " | |
3450 | PLAT = | |
3451 | LIBEXT = .a | |
3452 | OUTC = -o | |
3453 | OUTF = -o | |
3454 | RM = rm -f~:[ | |
3455 | CC = gcc | |
3456 | FC = gfortran | |
3457 | FL = gfortran | |
3458 | INCSEQ = -I$(topdir)/libseq | |
06e12395 | 3459 | LIBSEQ = $(topdir)/libseq/libmpiseq.a |
cec86422 EB |
3460 | LIBSEQNEEDED = libseqneeded~; |
3461 | CC = mpicc | |
3462 | FC = mpifort | |
3463 | FL = mpifort~] | |
3464 | AR = ar vr # rules require trailing space, ugh... | |
3465 | RANLIB = ranlib | |
06e12395 MB |
3466 | BLASDIR = ~a |
3467 | LIBBLAS = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[ | |
3468 | SCALAPDIR = ~a | |
3469 | SCALAP = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~] | |
cec86422 EB |
3470 | LIBOTHERS = -pthread |
3471 | CDEFS = -DAdd_ | |
3472 | PIC = -fPIC | |
3473 | OPTF = -O2 -DALLOW_NON_INIT $(PIC) | |
3474 | OPTL = -O2 $(PIC) | |
3475 | OPTC = -O2 $(PIC) | |
3476 | INCS = $(INCSEQ) | |
3477 | LIBS = $(SCALAP) $(LIBSEQ) | |
3478 | LPORDDIR = $(topdir)/PORD/lib | |
3479 | IPORD = -I$(topdir)/PORD/include | |
06e12395 | 3480 | LPORD = $(LPORDDIR)/libpord.a |
cec86422 EB |
3481 | ORDERINGSF = -Dpord~@[ |
3482 | METISDIR = ~a | |
3483 | IMETIS = -I$(METISDIR)/include | |
06e12395 | 3484 | LMETIS = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis |
cec86422 EB |
3485 | ORDERINGSF += -Dmetis~]~@[~:{ |
3486 | SCOTCHDIR = ~a | |
3487 | ISCOTCH = -I$(SCOTCHDIR)/include | |
06e12395 | 3488 | LSCOTCH = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr |
cec86422 EB |
3489 | ORDERINGSF += ~a~}~] |
3490 | ORDERINGSC = $(ORDERINGSF) | |
06e12395 | 3491 | LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ) |
cec86422 EB |
3492 | IORDERINGSF = $(ISCOTCH) |
3493 | IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)" | |
3494 | (assoc-ref inputs "mpi") | |
3495 | (assoc-ref inputs "blas") | |
3496 | (assoc-ref inputs "scalapack") | |
3497 | (assoc-ref inputs "metis") | |
3498 | (match (list (assoc-ref inputs "pt-scotch") | |
3499 | (assoc-ref inputs "scotch")) | |
3500 | ((#f #f) | |
3501 | #f) | |
3502 | ((#f scotch) | |
3503 | `((,scotch "" "-Dscotch"))) | |
3504 | ((ptscotch _) | |
3505 | `((,ptscotch | |
3506 | "-lptesmumps -lptscotch -lptscotcherr " | |
3507 | "-Dptscotch"))))))))) | |
fba78d18 | 3508 | (replace 'build |
cec86422 EB |
3509 | ;; By default only the d-precision library is built. Make with "all" |
3510 | ;; target so that all precision libraries and examples are built. | |
3511 | (lambda _ | |
b414cf52 TGR |
3512 | (invoke "make" "all" |
3513 | (format #f "-j~a" (parallel-job-count))))) | |
fba78d18 | 3514 | (replace 'check |
cec86422 EB |
3515 | ;; Run the simple test drivers, which read test input from stdin: |
3516 | ;; from the "real" input for the single- and double-precision | |
3517 | ;; testers, and from the "cmplx" input for complex-precision | |
3518 | ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi | |
3519 | ;; package to prefix execution with "mpirun". | |
3520 | (lambda* (#:key (exec-prefix '()) #:allow-other-keys) | |
3521 | (with-directory-excursion "examples" | |
3522 | (every | |
3523 | (lambda (prec type) | |
3524 | (let ((tester (apply open-pipe* | |
3525 | `(,OPEN_WRITE | |
3526 | ,@exec-prefix | |
3527 | ,(string-append "./" prec | |
3528 | "simpletest")))) | |
3529 | (input (open-input-file | |
3530 | (string-append "input_simpletest_" type)))) | |
3531 | (begin | |
3532 | (dump-port input tester) | |
3533 | (close-port input) | |
3534 | (zero? (close-pipe tester))))) | |
3535 | '("s" "d" "c" "z") | |
3536 | '("real" "real" "cmplx" "cmplx"))))) | |
fba78d18 EB |
3537 | (replace 'install |
3538 | (lambda* (#:key outputs #:allow-other-keys) | |
3539 | (let* ((out (assoc-ref outputs "out")) | |
3540 | (libdir (string-append out "/lib"))) | |
3541 | (copy-recursively "lib" libdir) | |
3542 | (copy-recursively "include" (string-append out "/include")) | |
3543 | (when (file-exists? "libseq/libmpiseq.a") | |
3544 | (install-file "libseq/libmpiseq.a" libdir)) | |
06e12395 MB |
3545 | (when (file-exists? "libseq/libmpiseq.so") |
3546 | (install-file "libseq/libmpiseq.so" libdir)) | |
fba78d18 | 3547 | #t)))))) |
cec86422 EB |
3548 | (home-page "http://mumps.enseeiht.fr") |
3549 | (synopsis "Multifrontal sparse direct solver") | |
3550 | (description | |
3551 | "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a | |
57e69c1d | 3552 | sparse system of linear equations A x = b using Gaussian elimination.") |
cec86422 EB |
3553 | (license license:cecill-c))) |
3554 | ||
3555 | (define-public mumps-metis | |
3556 | (package (inherit mumps) | |
3557 | (name "mumps-metis") | |
3558 | (inputs | |
3559 | (alist-delete "scotch" (package-inputs mumps))))) | |
3560 | ||
3561 | (define-public mumps-openmpi | |
3562 | (package (inherit mumps) | |
3563 | (name "mumps-openmpi") | |
3564 | (inputs | |
3565 | `(("mpi" ,openmpi) | |
3566 | ("scalapack" ,scalapack) | |
3567 | ("pt-scotch" ,pt-scotch) | |
3568 | ,@(alist-delete "scotch" (package-inputs mumps)))) | |
3569 | (arguments | |
3570 | (substitute-keyword-arguments (package-arguments mumps) | |
3571 | ((#:phases phases) | |
3572 | `(modify-phases ,phases | |
bbe46a4a EB |
3573 | (add-before 'check 'mpi-setup |
3574 | ,%openmpi-setup) | |
6df2a50a LC |
3575 | (replace 'check |
3576 | (lambda _ | |
3577 | ((assoc-ref ,phases 'check) | |
3578 | #:exec-prefix '("mpirun" "-n" "2")))))))) | |
cec86422 EB |
3579 | (synopsis "Multifrontal sparse direct solver (with MPI)"))) |
3580 | ||
3581 | (define-public mumps-metis-openmpi | |
3582 | (package (inherit mumps-openmpi) | |
3583 | (name "mumps-metis-openmpi") | |
3584 | (inputs | |
3585 | (alist-delete "pt-scotch" (package-inputs mumps-openmpi))))) | |
3586 | ||
63e07468 BW |
3587 | (define-public ruby-asciimath |
3588 | (package | |
3589 | (name "ruby-asciimath") | |
b17a48d0 | 3590 | (version "2.0.1") |
63e07468 BW |
3591 | (source |
3592 | (origin | |
3593 | (method url-fetch) | |
3594 | (uri (rubygems-uri "asciimath" version)) | |
3595 | (sha256 | |
3596 | (base32 | |
b17a48d0 | 3597 | "1aapydwwkydbwgz07n7ma3a5jy9n3v0shy6q6j8mi4wr3crhx45a")))) |
63e07468 | 3598 | (build-system ruby-build-system) |
63e07468 | 3599 | (native-inputs |
b17a48d0 | 3600 | `(("ruby-nokogiri" ,ruby-nokogiri) |
63e07468 BW |
3601 | ("ruby-rspec" ,ruby-rspec))) |
3602 | (synopsis "AsciiMath parsing and conversion library") | |
3603 | (description | |
3604 | "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an | |
3605 | easy-to-write markup language for mathematics.") | |
3606 | (home-page "https://github.com/asciidoctor/asciimath") | |
3607 | (license license:expat))) | |
3608 | ||
183e44ae EB |
3609 | (define-public superlu |
3610 | (package | |
3611 | (name "superlu") | |
7ea957e2 | 3612 | (version "5.2.2") |
183e44ae EB |
3613 | (source |
3614 | (origin | |
3615 | (method url-fetch) | |
48fe5c36 | 3616 | (uri (string-append "https://portal.nersc.gov/project/sparse/superlu/" |
183e44ae EB |
3617 | "superlu_" version ".tar.gz")) |
3618 | (sha256 | |
7ea957e2 | 3619 | (base32 "13520vk6fqspyl22cq4ak2jh3rlmhja4czq56j75fdx65fkk80s7")) |
995a09e0 EB |
3620 | (modules '((guix build utils))) |
3621 | (snippet | |
3622 | ;; Replace the non-free implementation of MC64 with a stub adapted | |
3623 | ;; from Debian | |
3624 | '(begin | |
3625 | (use-modules (ice-9 regex) | |
3626 | (ice-9 rdelim)) | |
3627 | (call-with-output-file "SRC/mc64ad.c" | |
3628 | (lambda (port) | |
3629 | (display " | |
3630 | #include <stdio.h> | |
3631 | #include <stdlib.h> | |
3632 | void mc64id_(int *a) { | |
3633 | fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\"); | |
3634 | abort (); | |
3635 | } | |
3636 | void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g, | |
3637 | int *h, int *i, int *j, int *k, double *l, int *m, int *n) { | |
3638 | fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\"); | |
3639 | abort (); | |
3640 | }\n" port))) | |
3641 | ;; Remove the corresponding license verbiage. MC64 license follows | |
3642 | ;; a "------" line separator. | |
3643 | (with-atomic-file-replacement "License.txt" | |
3644 | (let ((rx (make-regexp "-{8}"))) | |
3645 | (lambda (in out) | |
3646 | (let loop () | |
3647 | (let ((line (read-line in 'concat))) | |
3648 | (unless (regexp-exec rx line) | |
3649 | (display line out) | |
6cbee49d MW |
3650 | (loop)))) |
3651 | #t))))))) | |
995a09e0 | 3652 | (build-system cmake-build-system) |
183e44ae EB |
3653 | (native-inputs |
3654 | `(("tcsh" ,tcsh))) | |
3655 | (inputs | |
995a09e0 | 3656 | `(("blas" ,openblas) |
19afbea1 | 3657 | ("gfortran" ,gfortran))) |
183e44ae | 3658 | (arguments |
995a09e0 EB |
3659 | `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas |
3660 | "-DTPL_BLAS_LIBRARIES=openblas" | |
677bc34d | 3661 | "-DBUILD_SHARED_LIBS:BOOL=YES"))) |
48fe5c36 | 3662 | (home-page "https://portal.nersc.gov/project/sparse/superlu/") |
183e44ae EB |
3663 | (synopsis "Supernodal direct solver for sparse linear systems") |
3664 | (description | |
3665 | "SuperLU is a general purpose library for the direct solution of large, | |
3666 | sparse, nonsymmetric systems of linear equations on high performance machines. | |
3667 | The library is written in C and is callable from either C or Fortran. The | |
3668 | library routines perform an LU decomposition with partial pivoting and | |
3669 | triangular system solves through forward and back substitution. The library | |
3670 | also provides threshold-based ILU factorization preconditioners.") | |
995a09e0 EB |
3671 | (license (list license:bsd-3 |
3672 | license:gpl2+ ;EXAMPLE/*fgmr.c | |
3673 | (license:fsf-free "file://SRC/colamd.h"))))) | |
f8ed036a | 3674 | |
a54aefea EB |
3675 | (define-public superlu-dist |
3676 | (package | |
3677 | (name "superlu-dist") | |
705af540 | 3678 | (version "6.4.0") |
a54aefea EB |
3679 | (source |
3680 | (origin | |
705af540 EB |
3681 | (method git-fetch) |
3682 | (uri (git-reference | |
3683 | (url "https://github.com/xiaoyeli/superlu_dist") | |
3684 | (commit (string-append "v" version)))) | |
3685 | (file-name (git-file-name name version)) | |
a54aefea | 3686 | (sha256 |
705af540 | 3687 | (base32 "0fa29yr72p4yq5ln4rgfsawmi5935n4qcr5niz6864bjladz4lql")) |
0921eff2 | 3688 | (modules '((guix build utils))) |
29080870 EB |
3689 | (snippet |
3690 | ;; Replace the non-free implementation of MC64 with a stub | |
3691 | '(begin | |
705af540 | 3692 | (make-file-writable "SRC/mc64ad_dist.c") |
0921eff2 | 3693 | (call-with-output-file "SRC/mc64ad_dist.c" |
29080870 EB |
3694 | (lambda (port) |
3695 | (display " | |
3696 | #include <stdio.h> | |
3697 | #include <stdlib.h> | |
0921eff2 | 3698 | void mc64id_dist(int *a) { |
29080870 EB |
3699 | fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\"); |
3700 | abort (); | |
3701 | } | |
0921eff2 | 3702 | void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g, |
29080870 EB |
3703 | int *h, int *i, int *j, int *k, double *l, int *m, int *n) { |
3704 | fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\"); | |
3705 | abort (); | |
3706 | }\n" port))) | |
29080870 | 3707 | (substitute* "SRC/util.c" ;adjust default algorithm |
6161141e EB |
3708 | (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;") |
3709 | ;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has | |
3710 | ;; general (i.e. non-square) processor-grid support. | |
3711 | "RowPerm = NOROWPERM;")) | |
6cbee49d | 3712 | #t)) |
6161141e | 3713 | (patches (search-patches "superlu-dist-scotchmetis.patch" |
aa2e83cc | 3714 | "superlu-dist-awpm-grid.patch")))) |
6161141e | 3715 | (build-system cmake-build-system) |
a54aefea EB |
3716 | (native-inputs |
3717 | `(("tcsh" ,tcsh))) | |
3718 | (inputs | |
6161141e EB |
3719 | `(("gfortran" ,gfortran) |
3720 | ("blas" ,openblas) | |
3721 | ("lapack" ,lapack) | |
3722 | ("combblas" ,combinatorial-blas))) | |
a54aefea | 3723 | (propagated-inputs |
6161141e EB |
3724 | `(("mpi" ,openmpi) ;headers include MPI heades |
3725 | ("parmetis" ,pt-scotch32 "metis") | |
3726 | ("pt-scotch" ,pt-scotch32))) | |
a54aefea | 3727 | (arguments |
6161141e EB |
3728 | `(#:parallel-tests? #f ;tests use MPI and OpenMP |
3729 | #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES" | |
3730 | "-DTPL_ENABLE_COMBBLASLIB=YES" | |
3731 | "-DTPL_BLAS_LIBRARIES=-lopenblas" | |
3732 | "-DTPL_LAPACK_LIBRARIES=-llapack" | |
3733 | (string-append "-DTPL_PARMETIS_LIBRARIES=" | |
3734 | (string-join | |
3735 | '("ptscotchparmetis" "ptscotch" "ptscotcherr" | |
3736 | "scotchmetis" "scotch" "scotcherr") | |
3737 | ";")) | |
3738 | (string-append "-DTPL_PARMETIS_INCLUDE_DIRS=" | |
3739 | (assoc-ref %build-inputs "parmetis") | |
3740 | "/include") | |
3741 | "-DTPL_ENABLE_COMBBLASLIB=ON" | |
3742 | (string-append "-DTPL_COMBBLAS_INCLUDE_DIRS=" | |
3743 | (assoc-ref %build-inputs "combblas") | |
3744 | "/include/CombBLAS;" | |
3745 | (assoc-ref %build-inputs "combblas") | |
3746 | "/include/BipartiteMatchings") | |
3747 | "-DTPL_COMBBLAS_LIBRARIES=CombBLAS") | |
a54aefea | 3748 | #:phases |
dc1d3cde | 3749 | (modify-phases %standard-phases |
6161141e | 3750 | (add-before 'configure 'set-c++-standard |
dc1d3cde | 3751 | (lambda _ |
6161141e EB |
3752 | (substitute* "CMakeLists.txt" |
3753 | ;; AWPM headers require C++14 | |
3754 | (("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14")))) | |
bbe46a4a EB |
3755 | (add-before 'check 'mpi-setup |
3756 | ,%openmpi-setup) | |
6161141e EB |
3757 | (add-before 'check 'omp-setup |
3758 | (lambda _ (setenv "OMP_NUM_THREADS" "1") #t))))) | |
a54aefea EB |
3759 | (home-page (package-home-page superlu)) |
3760 | (synopsis "Parallel supernodal direct solver") | |
3761 | (description | |
3762 | "SuperLU_DIST is a parallel extension to the serial SuperLU library. | |
3763 | It is targeted for distributed memory parallel machines. SuperLU_DIST is | |
3764 | implemented in ANSI C, and MPI for communications.") | |
3765 | (license license:bsd-3))) | |
3766 | ||
f8ed036a EB |
3767 | (define-public scotch |
3768 | (package | |
3769 | (name "scotch") | |
94bae222 | 3770 | (version "6.1.1") |
f8ed036a EB |
3771 | (source |
3772 | (origin | |
3773 | (method url-fetch) | |
1dc31097 TGR |
3774 | (uri (string-append "https://gforge.inria.fr/frs/download.php/" |
3775 | "latestfile/298/scotch_" version ".tar.gz")) | |
f8ed036a | 3776 | (sha256 |
94bae222 | 3777 | (base32 "04dkz24a2g20wq703fnyi4440ac4mwycy9gwrrllljj7zxcjy19r")) |
fd373343 EB |
3778 | (patches (search-patches "scotch-build-parallelism.patch" |
3779 | "scotch-integer-declarations.patch")))) | |
f8ed036a EB |
3780 | (build-system gnu-build-system) |
3781 | (inputs | |
525e83ec VL |
3782 | `(("zlib" ,zlib))) |
3783 | (native-inputs | |
3784 | `(("flex" ,flex) | |
94bae222 LC |
3785 | ("bison" ,bison) |
3786 | ("gfortran" ,gfortran))) | |
fd373343 | 3787 | (outputs '("out" "metis")) |
f8ed036a | 3788 | (arguments |
fd373343 EB |
3789 | `(#:make-flags (list (string-append "prefix=" %output)) |
3790 | #:phases | |
d6602ee9 EB |
3791 | (modify-phases %standard-phases |
3792 | (add-after | |
3793 | 'unpack 'chdir-to-src | |
d67a7e9e | 3794 | (lambda _ (chdir "src") #t)) |
d6602ee9 EB |
3795 | (replace |
3796 | 'configure | |
3797 | (lambda _ | |
3798 | (call-with-output-file "Makefile.inc" | |
3799 | (lambda (port) | |
3800 | (format port " | |
f8ed036a EB |
3801 | EXE = |
3802 | LIB = .a | |
3803 | OBJ = .o | |
3804 | MAKE = make | |
3805 | AR = ar | |
3806 | ARFLAGS = -ruv | |
cf0ec6c4 | 3807 | CAT = cat |
f8ed036a EB |
3808 | CCS = gcc |
3809 | CCP = mpicc | |
3810 | CCD = gcc | |
94bae222 | 3811 | FC = gfortran |
f8ed036a | 3812 | CPPFLAGS =~{ -D~a~} |
6c798540 | 3813 | CFLAGS = -O2 -g -fPIC $(CPPFLAGS) |
f8ed036a EB |
3814 | LDFLAGS = -lz -lm -lrt -lpthread |
3815 | CP = cp | |
3816 | LEX = flex -Pscotchyy -olex.yy.c | |
3817 | LN = ln | |
3818 | MKDIR = mkdir | |
3819 | MV = mv | |
3820 | RANLIB = ranlib | |
3821 | YACC = bison -pscotchyy -y -b y | |
3822 | " | |
d6602ee9 EB |
3823 | '("COMMON_FILE_COMPRESS_GZ" |
3824 | "COMMON_PTHREAD" | |
3825 | "COMMON_RANDOM_FIXED_SEED" | |
fd373343 | 3826 | "INTSIZE64" ;use 'int64_t' |
013cf932 | 3827 | ;; Prevents symbol clashes with libesmumps |
cf0ec6c4 | 3828 | "SCOTCH_RENAME" |
d6602ee9 EB |
3829 | ;; XXX: Causes invalid frees in superlu-dist tests |
3830 | ;; "SCOTCH_PTHREAD" | |
3831 | ;; "SCOTCH_PTHREAD_NUMBER=2" | |
d67a7e9e TGR |
3832 | "restrict=__restrict")))) |
3833 | #t)) | |
bbe46a4a | 3834 | (add-after 'build 'build-esmumps |
cf0ec6c4 | 3835 | (lambda _ |
d67a7e9e TGR |
3836 | (invoke "make" |
3837 | (format #f "-j~a" (parallel-job-count)) | |
3838 | "esmumps"))) | |
fd373343 EB |
3839 | (add-before 'install 'make-install-dirs |
3840 | (lambda* (#:key outputs #:allow-other-keys) | |
3841 | (mkdir (assoc-ref outputs "out")))) | |
3842 | (add-after 'install 'install-metis | |
3843 | (lambda* (#:key outputs #:allow-other-keys) | |
3844 | (let ((out (assoc-ref outputs "metis"))) | |
3845 | (mkdir out) | |
3846 | ;; metis files are not installed with 'make install' | |
3847 | (for-each (lambda (f) | |
3848 | (install-file f (string-append out "/include"))) | |
3849 | (find-files "../include/" ".*metis\\.h")) | |
3850 | (for-each (lambda (f) | |
3851 | (install-file f (string-append out "/lib"))) | |
3852 | (find-files "../lib/" ".*metis\\..*")) | |
3853 | #t)))))) | |
d5730000 | 3854 | (home-page "https://www.labri.fr/perso/pelegrin/scotch/") |
a09d69f6 LC |
3855 | (properties |
3856 | `((release-monitoring-url . "https://gforge.inria.fr/frs/?group_id=248"))) | |
f8ed036a EB |
3857 | (synopsis "Programs and libraries for graph algorithms") |
3858 | (description "SCOTCH is a set of programs and libraries which implement | |
3859 | the static mapping and sparse matrix reordering algorithms developed within | |
3860 | the SCOTCH project. Its purpose is to apply graph theory, with a divide and | |
3861 | conquer approach, to scientific computing problems such as graph and mesh | |
3862 | partitioning, static mapping, and sparse matrix ordering, in application | |
3863 | domains ranging from structural mechanics to operating systems or | |
3864 | bio-chemistry.") | |
3865 | ;; See LICENSE_en.txt | |
3866 | (license license:cecill-c))) | |
6acb4adb | 3867 | |
1c39f3b8 PG |
3868 | (define-public scotch32 |
3869 | ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by | |
3870 | ;; some applications. | |
3871 | (package (inherit scotch) | |
3872 | (name "scotch32") | |
3873 | (arguments | |
3874 | (substitute-keyword-arguments (package-arguments scotch) | |
3875 | ((#:phases scotch-phases) | |
3876 | `(modify-phases ,scotch-phases | |
3877 | (replace | |
3878 | 'configure | |
3879 | (lambda _ | |
3880 | (call-with-output-file "Makefile.inc" | |
3881 | (lambda (port) | |
3882 | (format port " | |
3883 | EXE = | |
3884 | LIB = .a | |
3885 | OBJ = .o | |
3886 | MAKE = make | |
3887 | AR = ar | |
3888 | ARFLAGS = -ruv | |
3889 | CAT = cat | |
3890 | CCS = gcc | |
3891 | CCP = mpicc | |
3892 | CCD = gcc | |
94bae222 | 3893 | FC = gfortran |
1c39f3b8 PG |
3894 | CPPFLAGS =~{ -D~a~} |
3895 | CFLAGS = -O2 -g -fPIC $(CPPFLAGS) | |
3896 | LDFLAGS = -lz -lm -lrt -lpthread | |
3897 | CP = cp | |
3898 | LEX = flex -Pscotchyy -olex.yy.c | |
3899 | LN = ln | |
3900 | MKDIR = mkdir | |
3901 | MV = mv | |
3902 | RANLIB = ranlib | |
3903 | YACC = bison -pscotchyy -y -b y | |
3904 | " | |
3905 | '("COMMON_FILE_COMPRESS_GZ" | |
3906 | "COMMON_PTHREAD" | |
3907 | "COMMON_RANDOM_FIXED_SEED" | |
3908 | "INTSIZE32" ;use 32-bit integers. See INSTALL.txt | |
3909 | ;; Prevents symbolc clashes with libesmumps | |
3910 | "SCOTCH_RENAME" | |
3911 | ;; XXX: Causes invalid frees in superlu-dist tests | |
3912 | ;; "SCOTCH_PTHREAD" | |
3913 | ;; "SCOTCH_PTHREAD_NUMBER=2" | |
3914 | "restrict=__restrict")))))))))) | |
3915 | (synopsis | |
3916 | "Programs and libraries for graph algorithms (32-bit integers)"))) | |
3917 | ||
5fd046cb FP |
3918 | (define-public scotch-shared |
3919 | (package (inherit scotch) | |
3920 | (name "scotch-shared") | |
3921 | (native-inputs | |
3922 | `(("gcc" ,gcc) | |
3923 | ("flex" ,flex) | |
3924 | ("bison" ,bison))) | |
3925 | (arguments | |
3926 | (substitute-keyword-arguments (package-arguments scotch) | |
3927 | ((#:phases scotch-shared-phases) | |
3928 | `(modify-phases ,scotch-shared-phases | |
3929 | (replace | |
3930 | 'configure | |
3931 | (lambda _ | |
3932 | ;; Otherwise, the RUNPATH will lack the final path component. | |
3933 | (setenv "RPATHFLAGS" (string-append "-Wl,-rpath=" | |
3934 | (assoc-ref %outputs "out") "/lib")) | |
3935 | (call-with-output-file "Makefile.inc" | |
3936 | (lambda (port) | |
3937 | (format port " | |
3938 | EXE = | |
3939 | LIB = .so | |
3940 | OBJ = .o | |
3941 | MAKE = make | |
3942 | AR = gcc | |
3943 | ARFLAGS = -shared -o | |
3944 | CAT = cat | |
3945 | CCS = gcc | |
3946 | CCP = mpicc | |
3947 | CCD = gcc | |
94bae222 | 3948 | FC = gfortran |
5fd046cb FP |
3949 | CPPFLAGS =~{ -D~a~} |
3950 | CFLAGS = -O2 -g -fPIC $(CPPFLAGS) $(RPATHFLAGS) | |
3951 | CLIBFLAGS = -shared -fPIC | |
3952 | LDFLAGS = -lz -lm -lrt -lpthread -Xlinker --no-as-needed | |
3953 | CP = cp | |
3954 | LEX = flex -Pscotchyy -olex.yy.c | |
3955 | LN = ln | |
3956 | MKDIR = mkdir | |
3957 | MV = mv | |
3958 | RANLIB = echo | |
3959 | YACC = bison -pscotchyy -y -b y | |
3960 | " | |
3961 | '("COMMON_FILE_COMPRESS_GZ" | |
3962 | "COMMON_PTHREAD" | |
3963 | "COMMON_RANDOM_FIXED_SEED" | |
3964 | "INTSIZE64" ;use 'int64_t' | |
3965 | ;; Prevents symbolc clashes with libesmumps | |
3966 | "SCOTCH_RENAME" | |
3967 | ;; XXX: Causes invalid frees in superlu-dist tests | |
3968 | ;; "SCOTCH_PTHREAD" | |
3969 | ;; "SCOTCH_PTHREAD_NUMBER=2" | |
3970 | "restrict=__restrict" | |
3971 | ))))#t)) | |
3972 | (delete 'check))))) | |
3973 | (synopsis | |
3974 | "Programs and libraries for graph algorithms (shared libraries version)"))) | |
3975 | ||
6acb4adb EB |
3976 | (define-public pt-scotch |
3977 | (package (inherit scotch) | |
3978 | (name "pt-scotch") | |
3979 | (propagated-inputs | |
3980 | `(("openmpi" ,openmpi))) ;Headers include MPI headers | |
3981 | (arguments | |
3982 | (substitute-keyword-arguments (package-arguments scotch) | |
3983 | ((#:phases scotch-phases) | |
d6602ee9 EB |
3984 | `(modify-phases ,scotch-phases |
3985 | (replace | |
3986 | 'build | |
d6602ee9 | 3987 | (lambda _ |
c491f7f8 LC |
3988 | (invoke "make" (format #f "-j~a" (parallel-job-count)) |
3989 | "ptscotch" "ptesmumps") | |
3990 | ||
3991 | ;; Install the serial metis compatibility library | |
3992 | (invoke "make" "-C" "libscotchmetis" "install"))) | |
3993 | (add-before 'check 'mpi-setup | |
3994 | ,%openmpi-setup) | |
3995 | (replace 'check | |
3996 | (lambda _ | |
3997 | (invoke "make" "ptcheck"))))))) | |
6acb4adb | 3998 | (synopsis "Programs and libraries for graph algorithms (with MPI)"))) |
5698b8b8 | 3999 | |
1c25a52c PG |
4000 | (define-public pt-scotch32 |
4001 | (package (inherit scotch32) | |
4002 | (name "pt-scotch32") | |
4003 | (propagated-inputs | |
4004 | `(("openmpi" ,openmpi))) ;headers include MPI headers | |
4005 | (arguments | |
c4d4a779 PG |
4006 | (substitute-keyword-arguments (package-arguments scotch32) |
4007 | ((#:phases scotch32-phases) | |
4008 | `(modify-phases ,scotch32-phases | |
1c25a52c PG |
4009 | (replace 'build |
4010 | (lambda _ | |
c491f7f8 LC |
4011 | (invoke "make" (format #f "-j~a" (parallel-job-count)) |
4012 | "ptscotch" "ptesmumps") | |
4013 | ;; Install the serial metis compatibility library | |
4014 | (invoke "make" "-C" "libscotchmetis" "install"))) | |
4015 | (add-before 'check 'mpi-setup | |
4016 | ,%openmpi-setup) | |
1c25a52c PG |
4017 | (replace 'check |
4018 | (lambda _ | |
c491f7f8 | 4019 | (invoke "make" "ptcheck"))))))) |
1c25a52c PG |
4020 | (synopsis |
4021 | "Programs and libraries for graph algorithms (with MPI and 32-bit integers)"))) | |
4022 | ||
5fd046cb FP |
4023 | (define-public pt-scotch-shared |
4024 | (package (inherit scotch-shared) | |
4025 | (name "pt-scotch-shared") | |
4026 | (propagated-inputs | |
4027 | `(("openmpi" ,openmpi))) ;Headers include MPI headers | |
4028 | (arguments | |
4029 | (substitute-keyword-arguments (package-arguments scotch-shared) | |
4030 | ((#:phases scotch-shared-phases) | |
4031 | `(modify-phases ,scotch-shared-phases | |
4032 | (replace | |
4033 | 'build | |
4034 | (lambda _ | |
4035 | (invoke "make" (format #f "-j~a" (parallel-job-count)) | |
4036 | "ptscotch" "ptesmumps") | |
4037 | ||
4038 | ;; Install the serial metis compatibility library | |
4039 | (invoke "make" "-C" "libscotchmetis" "install"))) | |
4040 | (add-before 'check 'mpi-setup | |
4041 | ,%openmpi-setup))))) | |
4042 | (synopsis "Graph algorithms (shared libraries version, with MPI)"))) | |
4043 | ||
4044 | ||
aa75ad00 EB |
4045 | (define-public metis |
4046 | (package | |
4047 | (name "metis") | |
4048 | (version "5.1.0") | |
4049 | (source | |
4050 | (origin | |
4051 | (method url-fetch) | |
4052 | (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/" | |
4053 | "metis-" version ".tar.gz")) | |
4054 | (sha256 | |
4055 | (base32 | |
4056 | "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn")))) | |
de2e3641 LC |
4057 | (properties |
4058 | `((release-monitoring-url | |
4059 | . "http://glaros.dtc.umn.edu/gkhome/metis/metis/download"))) | |
aa75ad00 EB |
4060 | (build-system cmake-build-system) |
4061 | (inputs | |
4062 | `(("blas" ,openblas))) | |
4063 | (arguments | |
4064 | `(#:tests? #f ;no tests | |
4065 | #:configure-flags `("-DSHARED=ON" | |
4066 | ,(string-append "-DGKLIB_PATH=" (getcwd) | |
4067 | "/metis-" ,version "/GKlib")))) | |
4068 | (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview") | |
4069 | (synopsis "Graph partitioning and fill-reducing matrix ordering library") | |
4070 | (description | |
4071 | "METIS is a set of serial programs for partitioning graphs, partitioning | |
4072 | finite element meshes, and producing fill-reducing orderings for sparse | |
4073 | matrices. The algorithms implemented in METIS are based on the multilevel | |
4074 | recursive-bisection, multilevel k-way, and multi-constraint partitioning | |
4075 | schemes.") | |
4076 | (license license:asl2.0))) ;As of version 5.0.3 | |
4077 | ||
700ff222 EB |
4078 | (define-public p4est |
4079 | (package | |
4080 | (name "p4est") | |
4150da63 | 4081 | (version "2.0") |
700ff222 EB |
4082 | (source |
4083 | (origin | |
4084 | (method url-fetch) | |
4085 | (uri (string-append "http://p4est.github.io/release/p4est-" | |
4086 | version ".tar.gz")) | |
4087 | (sha256 | |
4088 | (base32 | |
4150da63 | 4089 | "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5")))) |
700ff222 EB |
4090 | (build-system gnu-build-system) |
4091 | (inputs | |
4092 | `(("fortran" ,gfortran) | |
4093 | ("blas" ,openblas) | |
4094 | ("lapack" ,lapack) | |
4095 | ("zlib" ,zlib))) | |
4096 | (arguments | |
4097 | `(#:configure-flags `(,(string-append "BLAS_LIBS=-L" | |
4098 | (assoc-ref %build-inputs "blas") | |
4099 | " -lopenblas") | |
4100 | ,(string-append "LAPACK_LIBS=-L" | |
4101 | (assoc-ref %build-inputs "lapack") | |
6df2a50a LC |
4102 | " -llapack")) |
4103 | #:phases (modify-phases %standard-phases | |
bbe46a4a EB |
4104 | (add-before 'check 'mpi-setup |
4105 | ,%openmpi-setup)))) | |
700ff222 EB |
4106 | (home-page "http://www.p4est.org") |
4107 | (synopsis "Adaptive mesh refinement on forests of octrees") | |
4108 | (description | |
4109 | "The p4est software library enables the dynamic management of a | |
4110 | collection of adaptive octrees, conveniently called a forest of octrees. | |
4111 | p4est is designed to work in parallel and scales to hundreds of thousands of | |
4112 | processor cores.") | |
4113 | (license license:gpl2+))) | |
4114 | ||
4115 | (define-public p4est-openmpi | |
4116 | (package (inherit p4est) | |
4117 | (name "p4est-openmpi") | |
4118 | (inputs | |
4119 | `(("mpi" ,openmpi) | |
4120 | ,@(package-inputs p4est))) | |
4121 | (arguments | |
4122 | (substitute-keyword-arguments (package-arguments p4est) | |
4123 | ((#:configure-flags cf) | |
4124 | ``("--enable-mpi" ,@,cf)))) | |
4125 | (synopsis "Parallel adaptive mesh refinement on forests of octrees"))) | |
4126 | ||
5698b8b8 | 4127 | (define-public gsegrafix |
781a2bef TGR |
4128 | ;; This is an old and equally dead "experimental fork" of the longer-dead |
4129 | ;; original. At least it no longer requires the even-deader libgnomeprint{,ui} | |
4130 | ;; libraries, instead rendering plots with Pango. | |
5698b8b8 JD |
4131 | (package |
4132 | (name "gsegrafix") | |
781a2bef | 4133 | (version "1.0.7.2") |
5698b8b8 JD |
4134 | (source |
4135 | (origin | |
781a2bef TGR |
4136 | (method url-fetch) |
4137 | (uri (string-append "mirror://savannah/gsegrafix-experimental/" | |
4138 | "gsegrafix-experimental-" version ".tar.gz")) | |
4139 | (sha256 | |
4140 | (base32 "0fwh6719xy2zasmqlp0vdx6kzm45hn37ga88xmw5cz0yx7xw4j6f")))) | |
5698b8b8 JD |
4141 | (build-system gnu-build-system) |
4142 | (arguments | |
781a2bef TGR |
4143 | `(#:configure-flags |
4144 | (list "--disable-static"))) | |
5698b8b8 | 4145 | (inputs |
781a2bef TGR |
4146 | `(("glib" ,glib) |
4147 | ("gtk+" ,gtk+))) | |
5698b8b8 JD |
4148 | (native-inputs |
4149 | `(("pkg-config" ,pkg-config))) | |
6fd52309 | 4150 | (home-page "https://www.gnu.org/software/gsegrafix/") |
5698b8b8 | 4151 | (synopsis "GNOME application to create scientific and engineering plots") |
781a2bef TGR |
4152 | (description |
4153 | "GSEGrafix is an application which produces high-quality graphical | |
5698b8b8 JD |
4154 | plots for science and engineering. Plots are specified via simple ASCII |
4155 | parameter files and data files and are presented in an anti-aliased GNOME | |
4156 | canvas. The program supports rectangular two-dimensional plots, histograms, | |
4157 | polar-axis plots and three-dimensional plots. Plots can be printed or saved | |
4158 | to BMP, JPEG or PNG image formats.") | |
4159 | (license license:gpl3+))) | |
8731e527 JD |
4160 | |
4161 | (define-public maxima | |
4162 | (package | |
4163 | (name "maxima") | |
6dafd60b | 4164 | (version "5.45.1") |
8731e527 JD |
4165 | (source |
4166 | (origin | |
4167 | (method url-fetch) | |
4168 | (uri (string-append "mirror://sourceforge/maxima/Maxima-source/" | |
4169 | version "-source/" name "-" version ".tar.gz")) | |
4170 | (sha256 | |
4171 | (base32 | |
6dafd60b | 4172 | "1p77nk5sz1qfkn5zr97szpbi8ib4b22k8i52l4ag5gkhd4kid47y")) |
fc1adab1 | 4173 | (patches (search-patches "maxima-defsystem-mkdir.patch")))) |
8731e527 | 4174 | (build-system gnu-build-system) |
df354a77 | 4175 | (inputs |
e1b711b1 | 4176 | `(("bash" ,bash-minimal) |
df354a77 | 4177 | ("gnuplot" ,gnuplot) ;for plots |
e1b711b1 | 4178 | ("sbcl" ,sbcl) |
fc9c47bd | 4179 | ("sed" ,sed) |
f36afe4d | 4180 | ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima' |
df354a77 FB |
4181 | (native-inputs |
4182 | `(("texinfo" ,texinfo) | |
ccbc5758 KK |
4183 | ("perl" ,perl) |
4184 | ("python" ,python))) | |
8731e527 | 4185 | (arguments |
df354a77 | 4186 | `(#:configure-flags |
e1b711b1 GLV |
4187 | ,#~(list "--enable-sbcl" |
4188 | (string-append "--with-sbcl=" #$sbcl "/bin/sbcl") | |
4189 | (string-append "--with-posix-shell=" #$bash-minimal "/bin/sh") | |
4190 | (string-append "--with-wish=" #$tk "/bin/wish" | |
4191 | #$(version-major+minor (package-version tk)))) | |
df354a77 | 4192 | ;; By default Maxima attempts to write temporary files to |
77af7b24 MW |
4193 | ;; '/tmp/nix-build-maxima-*', which won't exist at run time. |
4194 | ;; Work around that. | |
df354a77 | 4195 | #:make-flags (list "TMPDIR=/tmp") |
0093b126 KK |
4196 | #:phases |
4197 | (modify-phases %standard-phases | |
fc9c47bd KK |
4198 | (add-after 'unpack 'patch-paths |
4199 | (lambda* (#:key inputs #:allow-other-keys) | |
bc64d955 | 4200 | (let* ((sed (search-input-file inputs "/bin/sed")) |
fc9c47bd KK |
4201 | (coreutils (assoc-ref inputs "coreutils")) |
4202 | (dirname (string-append coreutils "/bin/dirname")) | |
ccc963d5 | 4203 | (head (string-append coreutils "/bin/head")) |
bc64d955 LC |
4204 | (perl (search-input-file inputs "/bin/perl")) |
4205 | (python (search-input-file inputs "/bin/python3"))) | |
fc9c47bd KK |
4206 | (substitute* "src/maxima.in" |
4207 | (("sed ") (string-append sed " ")) | |
4208 | (("dirname") dirname) | |
4209 | (("head") head)) | |
ccc963d5 KK |
4210 | (substitute* "doc/info/Makefile.in" |
4211 | (("/usr/bin/env perl") perl)) | |
4212 | (substitute* "doc/info/build_html.sh.in" | |
4213 | (("python") python)) | |
fc9c47bd | 4214 | #t))) |
0093b126 KK |
4215 | (add-before 'check 'pre-check |
4216 | (lambda _ | |
4217 | (chmod "src/maxima" #o555) | |
4218 | #t)) | |
1472d19a KK |
4219 | (replace 'check |
4220 | (lambda _ | |
4221 | ;; This is derived from the testing code in the "debian/rules" file | |
4222 | ;; of Debian's Maxima package. | |
4223 | ;; If Maxima can successfully run this, the binary to be installed | |
4224 | ;; should be fine. | |
df129041 MW |
4225 | (invoke "sh" "-c" |
4226 | (string-append | |
4227 | "./maxima-local " | |
e1b711b1 | 4228 | "--lisp=sbcl " |
df129041 MW |
4229 | "--batch-string=\"run_testsuite();\" " |
4230 | "| grep -q \"No unexpected errors found\"")))) | |
0093b126 KK |
4231 | ;; Make sure the doc and emacs files are found in the |
4232 | ;; standard location. Also configure maxima to find gnuplot | |
4233 | ;; without having it on the PATH. | |
4234 | (add-after 'install 'post-install | |
4235 | (lambda* (#:key outputs inputs #:allow-other-keys) | |
4236 | (let* ((gnuplot (assoc-ref inputs "gnuplot")) | |
4237 | (out (assoc-ref outputs "out")) | |
4238 | (datadir (string-append out "/share/maxima/" ,version)) | |
bc64d955 | 4239 | (binutils (dirname (search-input-file inputs "/bin/as")))) |
0093b126 KK |
4240 | (with-directory-excursion out |
4241 | (mkdir-p "share/emacs") | |
4242 | (mkdir-p "share/doc") | |
0093b126 KK |
4243 | (symlink |
4244 | (string-append datadir "/doc/") | |
4245 | (string-append out "/share/doc/maxima")) | |
4246 | (with-atomic-file-replacement | |
4247 | (string-append datadir "/share/maxima-init.lisp") | |
4248 | (lambda (in out) | |
4249 | (format out "~a ~s~a~%" | |
4250 | "(setf $gnuplot_command " | |
4251 | (string-append gnuplot "/bin/gnuplot") ")") | |
4252 | (dump-port in out)))) | |
4253 | ;; Ensure that Maxima will have access to the GNU binutils | |
4254 | ;; components at runtime. | |
4255 | (wrap-program (string-append out "/bin/maxima") | |
4256 | `("PATH" prefix (,binutils)))) | |
4257 | #t))))) | |
6dafd60b | 4258 | (home-page "https://maxima.sourceforge.io") |
8731e527 JD |
4259 | (synopsis "Numeric and symbolic expression manipulation") |
4260 | (description "Maxima is a system for the manipulation of symbolic and | |
4261 | numerical expressions. It yields high precision numeric results by using | |
4262 | exact fractions, arbitrary precision integers, and variable precision floating | |
e881752c | 4263 | point numbers.") |
8731e527 JD |
4264 | ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+. |
4265 | ;; Others simply say "GNU General Public License" without stating a | |
4266 | ;; version (which implicitly means gpl1+). | |
4267 | ;; At least one file (src/maxima.asd) says "version 2." | |
4268 | ;; GPLv2 only is therefore the smallest subset. | |
f36afe4d | 4269 | (license license:gpl2))) |
ec322be2 | 4270 | |
9aafbc0c MW |
4271 | (define-public wxmaxima |
4272 | (package | |
4273 | (name "wxmaxima") | |
e84a710b | 4274 | (version "21.05.2") |
9aafbc0c MW |
4275 | (source |
4276 | (origin | |
c93b77ad KK |
4277 | (method git-fetch) |
4278 | (uri (git-reference | |
b0e7b699 | 4279 | (url "https://github.com/wxMaxima-developers/wxmaxima") |
c93b77ad KK |
4280 | (commit (string-append "Version-" version)))) |
4281 | (file-name (git-file-name name version)) | |
9aafbc0c | 4282 | (sha256 |
e84a710b | 4283 | (base32 "0h7ryykh2dapcyvpp4f1j1b3vrrz80x9k8nkci2yxifgdb29vyhw")))) |
0181df53 | 4284 | (build-system cmake-build-system) |
5143517c | 4285 | (native-inputs |
f5f64205 | 4286 | `(("gettext" ,gettext-minimal))) |
9aafbc0c | 4287 | (inputs |
311e8d72 | 4288 | `(("wxwidgets" ,wxwidgets) |
de477809 SB |
4289 | ("maxima" ,maxima) |
4290 | ;; Runtime support. | |
4291 | ("adwaita-icon-theme" ,adwaita-icon-theme) | |
4292 | ("gtk+" ,gtk+) | |
4293 | ("shared-mime-info" ,shared-mime-info))) | |
9aafbc0c | 4294 | (arguments |
f5f64205 | 4295 | `(#:tests? #f ; tests fail non-deterministically |
0181df53 | 4296 | #:phases |
ac2ddcc6 | 4297 | (modify-phases %standard-phases |
e79fe4f6 KK |
4298 | (add-after 'unpack 'patch-doc-path |
4299 | (lambda _ | |
4300 | ;; Don't look in share/doc/wxmaxima-xx.xx.x for the | |
4301 | ;; documentation. Only licensing information is placed there by | |
4302 | ;; Guix. | |
4303 | (substitute* "src/Dirstructure.cpp" | |
4304 | (("/doc/wxmaxima-\\%s") "/doc/wxmaxima")) | |
4305 | #t)) | |
ac2ddcc6 KK |
4306 | (add-after 'install 'wrap-program |
4307 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
4308 | (wrap-program (string-append (assoc-ref outputs "out") | |
4309 | "/bin/wxmaxima") | |
4310 | `("PATH" ":" prefix | |
4311 | (,(string-append (assoc-ref inputs "maxima") | |
4312 | "/bin"))) | |
4313 | ;; For GtkFileChooserDialog. | |
4314 | `("GSETTINGS_SCHEMA_DIR" = | |
4315 | (,(string-append (assoc-ref inputs "gtk+") | |
4316 | "/share/glib-2.0/schemas"))) | |
4317 | `("XDG_DATA_DIRS" ":" prefix | |
4318 | (;; Needed by gdk-pixbuf to know supported icon formats. | |
4319 | ,(string-append | |
4320 | (assoc-ref inputs "shared-mime-info") "/share") | |
4321 | ;; The default icon theme of GTK+. | |
4322 | ,(string-append | |
4323 | (assoc-ref inputs "adwaita-icon-theme") "/share")))) | |
4324 | #t))))) | |
48446f0f | 4325 | (home-page "https://wxmaxima-developers.github.io/wxmaxima/") |
9aafbc0c MW |
4326 | (synopsis "Graphical user interface for the Maxima computer algebra system") |
4327 | (description | |
4328 | "wxMaxima is a graphical user interface for the Maxima computer algebra | |
4329 | system. It eases the use of Maxima by making most of its commands available | |
4330 | through a menu system and by providing input dialogs for commands that require | |
4331 | more than one argument. It also implements its own display engine that | |
4332 | outputs mathematical symbols directly instead of depicting them with ASCII | |
4333 | characters. | |
4334 | ||
4335 | wxMaxima also features 2D and 3D inline plots, simple animations, mixing of | |
4336 | text and mathematical calculations to create documents, exporting of input and | |
4337 | output to TeX, and a browser for Maxima's manual including command index and | |
4338 | full text searching.") | |
4339 | (license license:gpl2+))) | |
4340 | ||
b15e47f9 RW |
4341 | (define-public armadillo |
4342 | (package | |
4343 | (name "armadillo") | |
f133e244 | 4344 | (version "9.100.5") |
b15e47f9 RW |
4345 | (source (origin |
4346 | (method url-fetch) | |
4347 | (uri (string-append "mirror://sourceforge/arma/armadillo-" | |
7397cd9e | 4348 | version ".tar.xz")) |
b15e47f9 RW |
4349 | (sha256 |
4350 | (base32 | |
f133e244 | 4351 | "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby")))) |
b15e47f9 | 4352 | (build-system cmake-build-system) |
e405c0bc | 4353 | (arguments `(#:tests? #f)) ; no test target |
b15e47f9 RW |
4354 | (inputs |
4355 | `(("openblas" ,openblas) | |
4356 | ("lapack" ,lapack) | |
4357 | ("arpack" ,arpack-ng))) | |
4358 | (home-page "http://arma.sourceforge.net/") | |
4359 | (synopsis "C++ linear algebra library") | |
4360 | (description | |
4361 | "Armadillo is a C++ linear algebra library, aiming towards a good balance | |
4362 | between speed and ease of use. It is useful for algorithm development | |
4363 | directly in C++, or quick conversion of research code into production | |
4364 | environments. It can be used for machine learning, pattern recognition, | |
4365 | signal processing, bioinformatics, statistics, econometrics, etc. The library | |
4366 | provides efficient classes for vectors, matrices and cubes, as well as 150+ | |
255fb17b | 4367 | associated functions (e.g., contiguous and non-contiguous submatrix views).") |
fe418cc5 | 4368 | (license license:asl2.0))) |
b15e47f9 | 4369 | |
279663ef | 4370 | (define-public muparser |
d7cff656 LF |
4371 | ;; When switching download sites, muparser re-issued a 2.2.5 release with a |
4372 | ;; different hash. In order to make `guix package --upgrade` work correctly, | |
4373 | ;; we set a Guix packaging revision. | |
4374 | ;; When the next version of muparser is released, we can remove | |
4375 | ;; UPSTREAM-VERSION and REVISION and use the plain VERSION. | |
4376 | (let ((upstream-version "2.2.5") | |
4377 | (revision "2")) | |
4378 | (package | |
4379 | (name "muparser") | |
4380 | (version (string-append upstream-version "-" revision)) | |
4381 | (source | |
4382 | (origin | |
67f1db38 TGR |
4383 | (method git-fetch) |
4384 | (uri (git-reference | |
b0e7b699 | 4385 | (url "https://github.com/beltoforion/muparser") |
67f1db38 TGR |
4386 | (commit (string-append "v" upstream-version)))) |
4387 | (file-name (git-file-name name version)) | |
d7cff656 | 4388 | (sha256 |
67f1db38 | 4389 | (base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24")))) |
d7cff656 LF |
4390 | (build-system gnu-build-system) |
4391 | (arguments | |
4392 | `(#:configure-flags '("--enable-samples=no") | |
4393 | #:tests? #f)) ;no "check" target | |
4394 | (home-page "http://muparser.beltoforion.de/") | |
4395 | (synopsis "Fast parser library for mathematical expressions") | |
4396 | (description | |
4397 | "muParser is an extensible high performance math parser library. It is | |
4398 | based on transforming an expression into a bytecode and precalculating constant | |
4399 | parts of it.") | |
4400 | (license license:expat)))) | |
279663ef | 4401 | |
e73b49fb RW |
4402 | (define-public openblas |
4403 | (package | |
4404 | (name "openblas") | |
bbd28642 | 4405 | (version "0.3.13") |
e73b49fb RW |
4406 | (source |
4407 | (origin | |
e364758d GH |
4408 | (method git-fetch) |
4409 | (uri (git-reference | |
4410 | (url "https://github.com/xianyi/OpenBLAS") | |
4411 | (commit (string-append "v" version)))) | |
4412 | (file-name (git-file-name name version)) | |
e73b49fb RW |
4413 | (sha256 |
4414 | (base32 | |
bbd28642 | 4415 | "14jxh0v3jfbw4mfjx4mcz4dd51lyq7pqvh9k8dg94539ypzjr2lj")))) |
e73b49fb RW |
4416 | (build-system gnu-build-system) |
4417 | (arguments | |
5789566a | 4418 | `(#:test-target "test" |
bd0b4379 RW |
4419 | ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no |
4420 | ;; TARGET is specified, OpenBLAS will tune itself to the build host, so | |
4421 | ;; we need to disable substitutions. | |
71923a91 AE |
4422 | #:substitutable? |
4423 | ,(let ((system (or (%current-target-system) (%current-system)))) | |
4424 | (or (string-prefix? "x86_64" system) | |
bd0b4379 | 4425 | (string-prefix? "i686" system) |
83a34647 EF |
4426 | (string-prefix? "mips" system) |
4427 | (string-prefix? "aarch64" system))) | |
e73b49fb RW |
4428 | #:make-flags |
4429 | (list (string-append "PREFIX=" (assoc-ref %outputs "out")) | |
4430 | "SHELL=bash" | |
5855756c | 4431 | "MAKE_NB_JOBS=0" ;use jobserver for submakes |
a4384dc9 MB |
4432 | |
4433 | ;; This is the maximum number of threads OpenBLAS will ever use (that | |
4434 | ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS | |
4435 | ;; is used.) If we don't set it, the makefile sets it to the number | |
4436 | ;; of cores of the build machine, which is obviously wrong. | |
4437 | "NUM_THREADS=128" | |
4438 | ||
af5b817e RW |
4439 | ;; Build the library for all supported CPUs. This allows |
4440 | ;; switching CPU targets at runtime with the environment variable | |
4441 | ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type. | |
4b4d4d7b | 4442 | ;; Unfortunately, this is not supported on all architectures, |
71923a91 AE |
4443 | ;; where it leads to failed builds. |
4444 | ,@(let ((system (or (%current-target-system) (%current-system)))) | |
8a637e79 RW |
4445 | (cond |
4446 | ((or (string-prefix? "x86_64" system) | |
71923a91 | 4447 | (string-prefix? "i686" system)) |
8a637e79 | 4448 | '("DYNAMIC_ARCH=1")) |
4b4d4d7b | 4449 | ;; On some of these architectures the CPU can't be detected. |
b8894e80 EF |
4450 | ((or (string-prefix? "powerpc64le" system) |
4451 | (string-prefix? "aarch64" system)) | |
4b4d4d7b EF |
4452 | '("DYNAMIC_ARCH=1" |
4453 | "TARGET=GENERIC")) | |
8a637e79 RW |
4454 | ;; On MIPS we force the "SICORTEX" TARGET, as for the other |
4455 | ;; two available MIPS targets special extended instructions | |
4456 | ;; for Loongson cores are used. | |
4457 | ((string-prefix? "mips" system) | |
4458 | '("TARGET=SICORTEX")) | |
67ce43c0 EF |
4459 | ;; Failed to detect CPU. |
4460 | ((string-prefix? "armhf" system) | |
4461 | '("TARGET=ARMV7")) | |
8a637e79 | 4462 | (else '())))) |
e73b49fb | 4463 | ;; no configure script |
493937ae DL |
4464 | #:phases |
4465 | (modify-phases %standard-phases | |
4466 | (delete 'configure) | |
4467 | (add-before 'build 'set-extralib | |
4468 | (lambda* (#:key inputs #:allow-other-keys) | |
4469 | ;; Get libgfortran found when building in utest. | |
4470 | (setenv "FEXTRALIB" | |
4471 | (string-append "-L" (assoc-ref inputs "fortran-lib") | |
4472 | "/lib")) | |
4473 | #t))))) | |
e73b49fb | 4474 | (inputs |
493937ae | 4475 | `(("fortran-lib" ,gfortran "lib"))) |
e73b49fb RW |
4476 | (native-inputs |
4477 | `(("cunit" ,cunit) | |
493937ae | 4478 | ("fortran" ,gfortran) |
e73b49fb | 4479 | ("perl" ,perl))) |
59695981 | 4480 | (home-page "https://www.openblas.net/") |
e73b49fb RW |
4481 | (synopsis "Optimized BLAS library based on GotoBLAS") |
4482 | (description | |
4483 | "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.") | |
4484 | (license license:bsd-3))) | |
4485 | ||
daa6036f | 4486 | (define-public openblas-ilp64 |
ba05be22 | 4487 | (package/inherit openblas |
daa6036f EB |
4488 | (name "openblas-ilp64") |
4489 | (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux")) | |
4490 | (arguments | |
4491 | (substitute-keyword-arguments (package-arguments openblas) | |
4492 | ((#:make-flags flags '()) | |
4493 | `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64") | |
4494 | ,flags)))) | |
4495 | (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)") | |
4496 | (license license:bsd-3))) | |
4497 | ||
969adb23 | 4498 | (define-public blis |
5a7deb11 | 4499 | (package |
969adb23 PM |
4500 | (name "blis") |
4501 | (version "0.8.1") | |
5a7deb11 LC |
4502 | (home-page "https://github.com/flame/blis") |
4503 | (source (origin | |
4504 | (method git-fetch) | |
4505 | (uri (git-reference (url home-page) (commit version))) | |
4506 | (sha256 | |
4507 | (base32 | |
969adb23 | 4508 | "05ifil6jj9424sr8kmircl8k4bmxnl3y12a79vwj1kxxva5gz50g")) |
5a7deb11 | 4509 | (file-name (git-file-name "blis" version)))) |
969adb23 PM |
4510 | (native-inputs |
4511 | `(("python" ,python) | |
4512 | ("perl" ,perl))) | |
5a7deb11 LC |
4513 | (build-system gnu-build-system) |
4514 | (arguments | |
969adb23 PM |
4515 | `(#:modules |
4516 | ((guix build gnu-build-system) | |
4517 | (guix build utils) | |
4518 | (srfi srfi-1)) | |
4519 | #:test-target "test" | |
4520 | #:phases | |
4521 | (modify-phases %standard-phases | |
4522 | (replace 'configure | |
4523 | (lambda* (#:key outputs | |
4524 | target | |
4525 | system | |
4526 | (configure-flags '()) | |
4527 | #:allow-other-keys) | |
4528 | ;; This is a home-made 'configure' script. | |
4529 | (let* ((out (assoc-ref outputs "out")) | |
4530 | ;; Guix-specific support for choosing the configuration | |
4531 | ;; via #:configure-flags: see below for details. | |
4532 | (config-flag-prefix "--blis-config=") | |
4533 | (maybe-config-flag (find | |
4534 | (lambda (s) | |
4535 | (string-prefix? config-flag-prefix s)) | |
4536 | configure-flags)) | |
4537 | (configure-flags (if maybe-config-flag | |
4538 | (delete maybe-config-flag | |
4539 | configure-flags) | |
4540 | configure-flags)) | |
4541 | ;; Select the "configuration" to build. | |
4542 | ;; The "generic" configuration is non-optimized but | |
4543 | ;; portable (no assembly). | |
4544 | ;; The "x86_64" configuration family includes | |
4545 | ;; sub-configurations for all supported | |
4546 | ;; x86_64 microarchitectures. | |
4547 | ;; BLIS currently lacks runtime hardware detection | |
4548 | ;; for other architectures: see | |
4549 | ;; <https://github.com/flame/blis/commit/c534da6>. | |
4550 | ;; Conservatively, we stick to "generic" on armhf, | |
4551 | ;; aarch64, and ppc64le for now. (But perhaps | |
4552 | ;; "power9", "cortexa9", and "cortexa57" might be | |
4553 | ;; general enough to use?) | |
4554 | ;; Another approach would be to use the "auto" | |
4555 | ;; configuration and make this package | |
4556 | ;; non-substitutable. | |
4557 | ;; The build is fairly intensive, though. | |
4558 | (blis-config | |
4559 | (cond | |
4560 | (maybe-config-flag | |
4561 | (substring maybe-config-flag | |
4562 | (string-length config-flag-prefix))) | |
4563 | ((string-prefix? "x86_64" (or target system)) | |
4564 | "x86_64") | |
4565 | (else | |
4566 | "generic"))) | |
4567 | (configure-args | |
4568 | `("-p" ,out | |
4569 | "-d" "opt" | |
4570 | "--disable-static" | |
4571 | "--enable-shared" | |
4572 | "--enable-threading=openmp" | |
4573 | "--enable-verbose-make" | |
4574 | ,@configure-flags | |
4575 | ,blis-config))) | |
4576 | (format #t "configure args: ~s~%" configure-args) | |
4577 | (apply invoke | |
4578 | "./configure" | |
4579 | configure-args) | |
4580 | #t))) | |
4581 | (add-before 'check 'show-test-output | |
4582 | (lambda _ | |
4583 | ;; By default "make check" is silent. Make it verbose. | |
4584 | (system "tail -F output.testsuite &") | |
4585 | #t))))) | |
5a7deb11 LC |
4586 | (synopsis "High-performance basic linear algebra (BLAS) routines") |
4587 | (description | |
4588 | "BLIS is a portable software framework for instantiating high-performance | |
4589 | BLAS-like dense linear algebra libraries. The framework was designed to | |
4590 | isolate essential kernels of computation that, when optimized, immediately | |
4591 | enable optimized implementations of most of its commonly used and | |
4592 | computationally intensive operations. While BLIS exports a new BLAS-like API, | |
4593 | it also includes a BLAS compatibility layer which gives application developers | |
4594 | access to BLIS implementations via traditional BLAS routine calls.") | |
4595 | (license license:bsd-3))) | |
4596 | ||
f67663d6 LC |
4597 | (define-public blis-sandybridge (deprecated-package "blis-sandybridge" blis)) |
4598 | (define-public blis-haswell (deprecated-package "blis-haswell" blis)) | |
4599 | (define-public blis-knl (deprecated-package "blis-knl" blis)) | |
5a7deb11 LC |
4600 | |
4601 | (define ignorance blis) | |
4602 | ||
e1605e36 RW |
4603 | (define-public openlibm |
4604 | (package | |
4605 | (name "openlibm") | |
4709b74b | 4606 | (version "0.7.4") |
e1605e36 RW |
4607 | (source |
4608 | (origin | |
ca72dd2c TGR |
4609 | (method git-fetch) |
4610 | (uri (git-reference | |
b0e7b699 | 4611 | (url "https://github.com/JuliaLang/openlibm") |
ca72dd2c TGR |
4612 | (commit (string-append "v" version)))) |
4613 | (file-name (git-file-name name version)) | |
e1605e36 | 4614 | (sha256 |
4709b74b | 4615 | (base32 "1azms0lpxb7vxb3bln5lyz0wpwx6jnzbffkclclpq2v5aiw8d14i")))) |
e1605e36 RW |
4616 | (build-system gnu-build-system) |
4617 | (arguments | |
4618 | `(#:make-flags | |
1978d716 JBV |
4619 | (list (string-append "prefix=" (assoc-ref %outputs "out")) |
4620 | ,(string-append "CC=" (cc-for-target))) | |
e1605e36 RW |
4621 | #:phases |
4622 | ;; no configure script | |
dc1d3cde | 4623 | (modify-phases %standard-phases (delete 'configure)) |
e1605e36 | 4624 | #:tests? #f)) ;the tests are part of the default target |
d3be5220 | 4625 | (home-page "https://openlibm.org/") |
e1605e36 RW |
4626 | (synopsis "Portable C mathematical library (libm)") |
4627 | (description | |
4628 | "OpenLibm is an effort to have a high quality, portable, standalone C | |
4629 | mathematical library (libm). It can be used standalone in applications and | |
4630 | programming language implementations. The project was born out of a need to | |
e881752c | 4631 | have a good libm for the Julia programming language that worked consistently |
e1605e36 RW |
4632 | across compilers and operating systems, and in 32-bit and 64-bit |
4633 | environments.") | |
538c0e3b EF |
4634 | ;; Each architecture has its own make target, and there is none for mips. |
4635 | (supported-systems (delete "mips64el-linux" %supported-systems)) | |
e1605e36 RW |
4636 | ;; See LICENSE.md for details. |
4637 | (license (list license:expat | |
4638 | license:isc | |
4639 | license:bsd-2 | |
4640 | license:public-domain | |
4641 | license:lgpl2.1+)))) | |
4642 | ||
e62be58f RW |
4643 | (define-public openspecfun |
4644 | (package | |
4645 | (name "openspecfun") | |
59cd0ba4 | 4646 | (version "0.5.3") |
e62be58f RW |
4647 | (source |
4648 | (origin | |
90cea671 TGR |
4649 | (method git-fetch) |
4650 | (uri (git-reference | |
b0e7b699 | 4651 | (url "https://github.com/JuliaLang/openspecfun") |
90cea671 TGR |
4652 | (commit (string-append "v" version)))) |
4653 | (file-name (git-file-name name version)) | |
e62be58f | 4654 | (sha256 |
90cea671 | 4655 | (base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh")))) |
e62be58f RW |
4656 | (build-system gnu-build-system) |
4657 | (arguments | |
59cd0ba4 | 4658 | '(#:tests? #f ; no "check" target |
e62be58f RW |
4659 | #:make-flags |
4660 | (list (string-append "prefix=" (assoc-ref %outputs "out"))) | |
59cd0ba4 TGR |
4661 | #:phases |
4662 | (modify-phases %standard-phases | |
4663 | (delete 'configure)))) ; no configure script | |
e62be58f | 4664 | (inputs |
19afbea1 | 4665 | `(("fortran" ,gfortran))) |
e62be58f RW |
4666 | (home-page "https://github.com/JuliaLang/openspecfun") |
4667 | (synopsis "Collection of special mathematical functions") | |
4668 | (description | |
4669 | "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a | |
4670 | portable package for Bessel Functions of a Complex Argument and Nonnegative | |
4671 | Order; it contains subroutines for computing Bessel functions and Airy | |
4672 | functions. Faddeeva allows computing the various error functions of arbitrary | |
4673 | complex arguments (Faddeeva function, error function, complementary error | |
4674 | function, scaled complementary error function, imaginary error function, and | |
4675 | Dawson function); given these, one can also easily compute Voigt functions, | |
4676 | Fresnel integrals, and similar related functions as well.") | |
4677 | ;; Faddeeva is released under the Expat license; AMOS is included as | |
4678 | ;; public domain software. | |
4679 | (license (list license:expat license:public-domain)))) | |
4680 | ||
2742f87e RW |
4681 | (define-public suitesparse |
4682 | (package | |
4683 | (name "suitesparse") | |
9931d277 | 4684 | (version "5.10.1") |
2742f87e RW |
4685 | (source |
4686 | (origin | |
aac148a8 FG |
4687 | (method git-fetch) |
4688 | (uri (git-reference | |
b0e7b699 | 4689 | (url "https://github.com/DrTimothyAldenDavis/SuiteSparse") |
aac148a8 FG |
4690 | (commit (string-append "v" version)))) |
4691 | (file-name (git-file-name name version)) | |
2742f87e RW |
4692 | (sha256 |
4693 | (base32 | |
9931d277 | 4694 | "19gx5wlgqnqpgz6mvam9lalyzpbfwgqhppps8z3np9sh0mgaiyw9")) |
aac148a8 | 4695 | (patches (search-patches "suitesparse-mongoose-cmake.patch")) |
bd5b5ac0 EB |
4696 | (modules '((guix build utils))) |
4697 | (snippet | |
4698 | ;; Remove bundled metis source | |
6cbee49d MW |
4699 | '(begin |
4700 | (delete-file-recursively "metis-5.1.0") | |
4701 | #t)))) | |
2742f87e RW |
4702 | (build-system gnu-build-system) |
4703 | (arguments | |
bab809ce | 4704 | `(#:tests? #f ;no "check" target |
2742f87e | 4705 | #:make-flags |
bab809ce | 4706 | (list (string-append "CC=" ,(cc-for-target)) |
2742f87e | 4707 | "TBB=-ltbb" |
bd5b5ac0 | 4708 | "MY_METIS_LIB=-lmetis" |
285f9d5e LC |
4709 | |
4710 | ;; The default is to link against netlib lapack. Use OpenBLAS | |
4711 | ;; instead. | |
4712 | "BLAS=-lopenblas" "LAPACK=-lopenblas" | |
4713 | ||
aac148a8 FG |
4714 | ;; Flags for cmake (required to build GraphBLAS and Mongoose) |
4715 | (string-append "CMAKE_OPTIONS=-DCMAKE_INSTALL_PREFIX=" | |
4716 | (assoc-ref %outputs "out") | |
4717 | " -DCMAKE_VERBOSE_MAKEFILE=ON" | |
4718 | " -DCMAKE_C_FLAGS_RELEASE=\"$(CFLAGS) $(CPPFLAGS)\"" | |
4719 | " -DCMAKE_CXX_FLAGS_RELEASE=\"$(CXXFLAGS) $(CPPFLAGS)\"" | |
4720 | " -DCMAKE_SKIP_RPATH=TRUE" | |
a2da6074 EF |
4721 | " -DCMAKE_BUILD_TYPE=Release" |
4722 | " -DCMAKE_INSTALL_LIBDIR=lib") | |
2742f87e RW |
4723 | (string-append "INSTALL_LIB=" |
4724 | (assoc-ref %outputs "out") "/lib") | |
4725 | (string-append "INSTALL_INCLUDE=" | |
bd5b5ac0 EB |
4726 | (assoc-ref %outputs "out") "/include") |
4727 | "library") | |
2742f87e | 4728 | #:phases |
2509522c | 4729 | (modify-phases %standard-phases |
bd5b5ac0 | 4730 | (delete 'configure)))) ;no configure script |
2742f87e RW |
4731 | (inputs |
4732 | `(("tbb" ,tbb) | |
285f9d5e | 4733 | ("openblas" ,openblas) |
786a04c9 GH |
4734 | ("gmp" ,gmp) |
4735 | ("mpfr" ,mpfr) | |
bd5b5ac0 | 4736 | ("metis" ,metis))) |
aac148a8 | 4737 | (native-inputs |
b471337d | 4738 | `(("cmake" ,cmake-minimal) |
aac148a8 | 4739 | ("m4" ,m4))) |
2742f87e RW |
4740 | (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html") |
4741 | (synopsis "Suite of sparse matrix software") | |
4742 | (description | |
4743 | "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK, | |
4744 | multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR, | |
4745 | multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit | |
4746 | simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and | |
4747 | CXSparse, a concise sparse Cholesky factorization package; and many other | |
4748 | packages.") | |
4749 | ;; LGPLv2.1+: | |
4750 | ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL | |
4751 | ;; GPLv2+: | |
4752 | ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK | |
4753 | (license (list license:gpl2+ license:lgpl2.1+)))) | |
4754 | ||
ec322be2 FB |
4755 | (define-public atlas |
4756 | (package | |
4757 | (name "atlas") | |
3c98ac02 | 4758 | (version "3.10.3") |
ec322be2 FB |
4759 | (source (origin |
4760 | (method url-fetch) | |
de67e922 LF |
4761 | (uri (string-append "mirror://sourceforge/math-atlas/Stable/" |
4762 | version "/atlas" version ".tar.bz2")) | |
f20de616 | 4763 | (patches (search-patches "atlas-gfortran-compat.patch")) |
ec322be2 FB |
4764 | (sha256 |
4765 | (base32 | |
3c98ac02 | 4766 | "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216")))) |
ec322be2 FB |
4767 | (build-system gnu-build-system) |
4768 | (home-page "http://math-atlas.sourceforge.net/") | |
19afbea1 | 4769 | (inputs `(("gfortran" ,gfortran) |
ec322be2 FB |
4770 | ("lapack-tar" ,(package-source lapack)))) |
4771 | (outputs '("out" "doc")) | |
01480b9e FB |
4772 | ;; For the moment we drop support for MIPS at it fails to compile. See |
4773 | ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html | |
4774 | (supported-systems (delete "mips64el-linux" %supported-systems)) | |
ec322be2 FB |
4775 | (arguments |
4776 | `(#:parallel-build? #f | |
4777 | #:parallel-tests? #f | |
f15615b1 LC |
4778 | |
4779 | ;; ATLAS tunes itself for the machine it is built on, as explained at | |
4780 | ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>. | |
4781 | ;; For this reason, we want users to build it locally instead of using | |
4782 | ;; substitutes. | |
4783 | #:substitutable? #f | |
4784 | ||
ec322be2 | 4785 | #:modules ((srfi srfi-26) |
ec322be2 FB |
4786 | (guix build gnu-build-system) |
4787 | (guix build utils)) | |
40029cbe | 4788 | #:configure-flags |
ec322be2 FB |
4789 | `(;; Generate position independent code suitable for dynamic libraries |
4790 | ;; and use WALL timer to get more accurate timing. | |
4791 | "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL" | |
4792 | ;; Set word width. | |
4793 | "-b" | |
4794 | ,,(if (string-match "64" (%current-system)) | |
4795 | "64" | |
4796 | "32") | |
4797 | ;; Disable parallel build as it gives errors: atlas_pthread.h is | |
4798 | ;; needed to compile C files before it is generated. | |
4799 | "-Ss" "pmake" "make -j 1" | |
af89a667 FB |
4800 | ;; Probe is failing for MIPS. We therefore define the system |
4801 | ;; architecture explicitly by setting (-A) MACHINETYPE = 49 | |
4802 | ;; 'MIPSR1xK' and (-V) ISA = 1 'none'. | |
4803 | ,,@(if (string-prefix? "mips" (%current-system)) | |
4804 | (list "-A" "49" "-V" "1") | |
4805 | (list)) | |
ec322be2 FB |
4806 | ;; Generate shared libraries. |
4807 | "--shared" | |
4808 | ;; Build a full LAPACK library. | |
4809 | ,(string-append "--with-netlib-lapack-tarfile=" | |
4810 | (assoc-ref %build-inputs "lapack-tar"))) | |
4811 | #:phases | |
e5b4b96b EF |
4812 | (modify-phases %standard-phases |
4813 | (add-after 'install 'install-doc | |
4814 | (lambda* (#:key outputs inputs #:allow-other-keys) | |
4815 | (let ((doc (string-append (assoc-ref outputs "doc") | |
4816 | "/share/doc/atlas"))) | |
4817 | (mkdir-p doc) | |
cb6f44d4 RW |
4818 | (for-each (cut install-file <> doc) |
4819 | (find-files "../ATLAS/doc" ".*")) | |
4820 | #t))) | |
e5b4b96b | 4821 | (add-after 'check 'check-pt |
cb6f44d4 | 4822 | (lambda _ (invoke "make" "ptcheck"))) |
e5b4b96b EF |
4823 | ;; Fix files required to run configure. |
4824 | (add-before 'configure 'fix-/bin/sh | |
ec322be2 FB |
4825 | (lambda _ |
4826 | ;; Use `sh', not `/bin/sh'. | |
4827 | (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c") | |
4828 | (("/bin/sh") | |
5b786db8 EF |
4829 | "sh")) |
4830 | #t)) | |
e5b4b96b EF |
4831 | ;; Fix /bin/sh in generated make files. |
4832 | (add-after 'configure 'fix-/bin/sh-in-generated-files | |
4833 | (lambda _ | |
4834 | (substitute* (find-files "." "^[Mm]ake\\.inc.*") | |
4835 | (("/bin/sh") | |
5b786db8 EF |
4836 | "sh")) |
4837 | #t)) | |
e5b4b96b EF |
4838 | ;; ATLAS configure program does not accepts the default flags |
4839 | ;; passed by the 'gnu-build-system'. | |
4840 | (replace 'configure | |
4841 | (lambda* (#:key native-inputs inputs outputs | |
4842 | (configure-flags '()) | |
4843 | #:allow-other-keys #:rest args) | |
4844 | (let* ((prefix (assoc-ref outputs "out")) | |
4845 | (bash (or (and=> (assoc-ref | |
4846 | (or native-inputs inputs) "bash") | |
4847 | (cut string-append <> "/bin/bash")) | |
4848 | "/bin/sh")) | |
4849 | (flags `(,(string-append "--prefix=" prefix) | |
4850 | ,@configure-flags)) | |
4851 | (abs-srcdir (getcwd)) | |
4852 | (srcdir (string-append "../" (basename abs-srcdir)))) | |
4853 | (format #t "source directory: ~s (relative from build: ~s)~%" | |
4854 | abs-srcdir srcdir) | |
4855 | (mkdir "../build") | |
4856 | (chdir "../build") | |
4857 | (format #t "build directory: ~s~%" (getcwd)) | |
4858 | (format #t "configure flags: ~s~%" flags) | |
cb6f44d4 RW |
4859 | (apply invoke bash |
4860 | (string-append srcdir "/configure") | |
4861 | flags))))))) | |
ec322be2 FB |
4862 | (synopsis "Automatically Tuned Linear Algebra Software") |
4863 | (description | |
4864 | "ATLAS is an automatically tuned linear algebra software library | |
4865 | providing C and Fortran77 interfaces to a portably efficient BLAS | |
4866 | implementation, as well as a few routines from LAPACK. | |
4867 | ||
f15615b1 LC |
4868 | Optimization occurs at build time. For this reason, the library is built on |
4869 | the machine where it is installed, without resorting to pre-built substitutes. | |
ec322be2 | 4870 | |
f15615b1 | 4871 | Before building the library, CPU throttling should be disabled. This can be |
d97c429a | 4872 | done in the BIOS, or, on GNU/Linux, with the following command: |
ec322be2 | 4873 | |
8e9ba611 | 4874 | @example |
d97c429a | 4875 | # cpupower --governor performance |
8e9ba611 | 4876 | @end example |
ec322be2 | 4877 | |
d97c429a | 4878 | Failure to do so will result in a library with poor performance.") |
b9aab8e8 TGR |
4879 | ;; The test suite is notoriously lengthy and routinely exceeds the default |
4880 | ;; timeout of 21600 seconds on the not unbeefy berlin build nodes. | |
4881 | (properties '((timeout . 86400))) ; 1 day | |
ec322be2 | 4882 | (license license:bsd-3))) |
c12efc72 | 4883 | |
72e2e8fa TGR |
4884 | (define-public cglm |
4885 | (package | |
4886 | (name "cglm") | |
4887 | (version "0.8.2") | |
4888 | (source | |
4889 | (origin | |
4890 | (method git-fetch) | |
4891 | (uri (git-reference | |
4892 | (url "https://github.com/recp/cglm") | |
4893 | (commit (string-append "v" version)))) | |
4894 | (file-name (git-file-name name version)) | |
4895 | (sha256 | |
4896 | (base32 "1lcfl9ph4bnl3hckpx4hzwh8r4llnw94ik75igc5qy38wk468gmk")))) | |
4897 | (build-system cmake-build-system) | |
4898 | (arguments | |
4899 | `(#:configure-flags | |
4900 | (list "-DCGLM_USE_TEST=ON"))) | |
4901 | (home-page "https://github.com/recp/cglm") | |
4902 | (synopsis "Mathematics C library for graphics programming") | |
4903 | (description | |
4904 | "@acronym{CGLM, C OpenGL Mathematics} is an optimised 3D maths library | |
4905 | for graphics software based on the @acronym{GLSL, OpenGL Shading Language} | |
4906 | specifications. | |
4907 | ||
4908 | It's similar to the original C++ GLM library but written in C99 and compatible | |
4909 | with C89.") | |
4910 | (license license:expat))) | |
4911 | ||
c12efc72 AE |
4912 | (define-public glm |
4913 | (package | |
4914 | (name "glm") | |
1a75fc84 | 4915 | (version "0.9.9.8") |
c12efc72 AE |
4916 | (source |
4917 | (origin | |
4918 | (method url-fetch) | |
5ea4b594 MB |
4919 | (uri (string-append "https://github.com/g-truc/glm/releases/download/" |
4920 | version "/glm-" version ".zip")) | |
c12efc72 | 4921 | (sha256 |
1a75fc84 | 4922 | (base32 "0k6yk9v46h690rshdx49x98y5qspkzibld1wb51jwcm35vba7qip")))) |
c12efc72 | 4923 | (build-system cmake-build-system) |
1a75fc84 MB |
4924 | (arguments |
4925 | `(#:phases (modify-phases %standard-phases | |
4926 | (replace 'install | |
4927 | (lambda* (#:key outputs #:allow-other-keys) | |
4928 | ;; Since version 0.9.9.6, 'make install' is not supported | |
4929 | ;; and we have to do it "manually". Upstream discussion: | |
4930 | ;; <https://github.com/g-truc/glm/pull/968>. | |
4931 | (let* ((source (string-append "../glm")) | |
4932 | (out (assoc-ref outputs "out")) | |
4933 | (inc (string-append out "/include")) | |
4934 | (lib (string-append out "/lib")) | |
4935 | (pkgconfig (string-append lib "/pkgconfig"))) | |
4936 | (with-directory-excursion source | |
4937 | (mkdir-p inc) | |
4938 | (mkdir-p pkgconfig) | |
4939 | (copy-recursively "glm" (string-append inc "/glm")) | |
4940 | (copy-recursively "cmake" (string-append lib "/cmake")) | |
4941 | (call-with-output-file (string-append pkgconfig "/glm.pc") | |
4942 | (lambda (port) | |
4943 | (format port | |
4944 | "prefix=~a | |
4945 | includedir=${prefix}/include | |
4946 | ||
4947 | Name: GLM | |
4948 | Description: OpenGL Mathematics | |
4949 | Version: ~a | |
4950 | Cflags: -I${includedir}~%" out ,(version-prefix version 3))))) | |
4951 | #t)))))) | |
c12efc72 AE |
4952 | (native-inputs |
4953 | `(("unzip" ,unzip))) | |
46bda5eb | 4954 | (home-page "https://glm.g-truc.net/") |
c12efc72 AE |
4955 | (synopsis "OpenGL Mathematics library") |
4956 | (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics | |
4957 | library for graphics software based on the OpenGL Shading Language (GLSL) | |
4958 | specifications.") | |
4959 | (license license:expat))) | |
7f18257b AE |
4960 | |
4961 | (define-public lpsolve | |
4962 | (package | |
4963 | (name "lpsolve") | |
a89e0cf5 | 4964 | (version "5.5.2.5") |
7f18257b AE |
4965 | (source |
4966 | (origin | |
4967 | (method url-fetch) | |
4968 | (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version | |
4969 | "/lp_solve_" version "_source.tar.gz")) | |
4970 | (sha256 | |
4971 | (base32 | |
a89e0cf5 | 4972 | "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0")) |
7f18257b AE |
4973 | (modules '((guix build utils))) |
4974 | (snippet | |
6cbee49d MW |
4975 | '(begin |
4976 | (substitute* (list "lp_solve/ccc" "lpsolve55/ccc") | |
4977 | (("^c=cc") "c=gcc") | |
4978 | ;; Pretend to be on a 64 bit platform to obtain a common directory | |
4979 | ;; name for the build results on all architectures; nothing else | |
4980 | ;; seems to depend on it. | |
4981 | (("^PLATFORM=.*$") "PLATFORM=ux64\n") | |
4982 | ||
4983 | ;; The check for 'isnan' as it is written fails with | |
4984 | ;; "non-floating-point argument in call to function | |
4985 | ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro | |
4986 | ;; definition, which in turn leads to bad things. Fix the feature | |
4987 | ;; test. | |
4988 | (("isnan\\(0\\)") "isnan(0.)")) | |
4989 | #t)))) | |
7f18257b AE |
4990 | (build-system gnu-build-system) |
4991 | (arguments | |
6c96b545 | 4992 | `(#:tests? #f ; no check target |
7f18257b AE |
4993 | #:phases |
4994 | (modify-phases %standard-phases | |
6c96b545 | 4995 | (delete 'configure) ; no configure script |
7f18257b AE |
4996 | (replace 'build |
4997 | (lambda _ | |
6c96b545 TGR |
4998 | (with-directory-excursion "lpsolve55" |
4999 | (invoke "bash" "ccc")) | |
5000 | (with-directory-excursion "lp_solve" | |
5001 | (invoke "bash" "ccc")) | |
5002 | #t)) | |
7f18257b AE |
5003 | (replace 'install |
5004 | (lambda* (#:key outputs #:allow-other-keys) | |
5005 | (let* ((out (assoc-ref outputs "out")) | |
5006 | (bin (string-append out "/bin")) | |
5007 | (lib (string-append out "/lib")) | |
5008 | ;; This is where LibreOffice expects to find the header | |
5009 | ;; files, and where they are installed by Debian. | |
5010 | (include (string-append out "/include/lpsolve"))) | |
6c96b545 TGR |
5011 | (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib) |
5012 | (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib) | |
96c46210 LC |
5013 | (install-file "lp_solve/bin/ux64/lp_solve" bin) |
5014 | ||
7f18257b AE |
5015 | ;; Install a subset of the header files as on Debian |
5016 | ;; (plus lp_bit.h, which matches the regular expression). | |
96c46210 LC |
5017 | (for-each (lambda (name) |
5018 | (install-file name include)) | |
5019 | (find-files "." "lp_[HMSa-z].*\\.h$")) | |
7f18257b | 5020 | (with-directory-excursion "shared" |
96c46210 LC |
5021 | (for-each (lambda (name) |
5022 | (install-file name include)) | |
5023 | (find-files "." "\\.h$"))) | |
7f18257b AE |
5024 | #t)))))) |
5025 | (home-page "http://lpsolve.sourceforge.net/") | |
5026 | (synopsis "Mixed integer linear programming (MILP) solver") | |
5027 | (description | |
5028 | "lp_solve is a mixed integer linear programming solver based on the | |
5029 | revised simplex and the branch-and-bound methods.") | |
5030 | (license license:lgpl2.1+))) | |
a17d4564 | 5031 | |
06c11434 PP |
5032 | ;; Private Trilinos package for dealii-openmpi (similar to |
5033 | ;; trilinos-serial-xyce and trilinos-parallel-xyce). | |
5034 | ;; This version is the latest known to be compatible with deal.II [1]. | |
5035 | ;; Since the latest version of Trilinos is not necessarily supported by | |
5036 | ;; deal.II, it may be worth keeping this package even if and when Trilinos | |
5037 | ;; gets packaged separately for Guix (unless various versions of Trilinos are | |
5038 | ;; packaged). | |
5039 | ;; | |
5040 | ;; An insightful source of information for building Trilinos for deal.II lies | |
5041 | ;; in the Trilinos package for candi [2], which is a source-based installer | |
5042 | ;; for deal.II and its dependencies. | |
5043 | ;; | |
5044 | ;; [1]: https://www.dealii.org/current/external-libs/trilinos.html | |
5045 | ;; [2]: https://github.com/dealii/candi/blob/master/deal.II-toolchain/packages/trilinos.package | |
5046 | (define trilinos-for-dealii-openmpi | |
5047 | (package | |
5048 | (name "trilinos-for-dealii-openmpi") | |
5049 | (version "12.18.1") | |
5050 | (source | |
5051 | (origin | |
5052 | (method git-fetch) | |
5053 | (uri (git-reference | |
5054 | (url "https://github.com/trilinos/Trilinos/") | |
5055 | (commit | |
5056 | (string-append "trilinos-release-" | |
5057 | (string-replace-substring version "." "-"))))) | |
5058 | (file-name (git-file-name "trilinos" version)) | |
5059 | (sha256 | |
5060 | (base32 "0fnwlhzsh85qj38cq3igbs8nm1b2jdgr2z734sapmyyzsy21mkgp")))) | |
5061 | (build-system cmake-build-system) | |
5062 | (native-inputs | |
5063 | `(("gfortran" ,gfortran) | |
5064 | ;; Trilinos's repository contains several C-shell scripts, but adding | |
5065 | ;; tcsh to the native inputs does not result in the check phase running | |
5066 | ;; any more tests than without it (nor is tcsh required to build | |
5067 | ;; Trilinos). | |
5068 | ;; It seems that Trilinos has replaced its use of C-shell test scripts | |
5069 | ;; with CMake's testing facilities. | |
5070 | ;; For example, | |
5071 | ;; packages/zoltan/doc/Zoltan_html/dev_html/dev_test_script.html [1] | |
5072 | ;; states that Zoltan's C-shell test script | |
5073 | ;; packages/zoltan/test/test_zoltan has been obsoleted by the tests now | |
5074 | ;; performed through CMake. | |
5075 | ;; | |
5076 | ;; Perl is required for some Zoltan tests and Python 2 for one ML test. | |
5077 | ;; | |
5078 | ;; [1]: https://cs.sandia.gov/zoltan/dev_html/dev_test_script.html | |
5079 | ("perl" ,perl) | |
5080 | ("python" ,python-2))) | |
5081 | (inputs | |
5082 | `(("blas" ,openblas) | |
5083 | ("lapack" ,lapack) | |
5084 | ("mumps" ,mumps-openmpi) | |
5085 | ("scalapack" ,scalapack))) | |
5086 | (propagated-inputs | |
5087 | `(("mpi" ,openmpi))) | |
5088 | (arguments | |
5089 | `(#:build-type "Release" | |
5090 | #:configure-flags | |
5091 | `("-DBUILD_SHARED_LIBS=ON" | |
5092 | ;; Obtain the equivalent of RelWithDebInfo but with -O3 (the Release | |
5093 | ;; default) rather than -O2 (the RelWithDebInfo default), to conform | |
5094 | ;; to candi's trilinos.package's compilation flags, which are -g -O3. | |
5095 | "-DCMAKE_C_FLAGS=-g" | |
5096 | "-DCMAKE_CXX_FLAGS=-g" | |
5097 | "-DCMAKE_Fortran_FLAGS=-g" | |
5098 | ||
5099 | ;; Trilinos libraries that deal.II can interface with. | |
5100 | "-DTrilinos_ENABLE_Amesos=ON" | |
5101 | "-DTrilinos_ENABLE_AztecOO=ON" | |
5102 | "-DTrilinos_ENABLE_Epetra=ON" | |
5103 | "-DTrilinos_ENABLE_EpetraExt=ON" | |
5104 | "-DTrilinos_ENABLE_Ifpack=ON" | |
5105 | "-DTrilinos_ENABLE_ML=ON" | |
5106 | "-DTrilinos_ENABLE_MueLu=ON" | |
5107 | "-DTrilinos_ENABLE_ROL=ON" | |
5108 | ;; Optional; required for deal.II's GridIn::read_exodusii, but | |
5109 | ;; depends on netcdf. | |
5110 | ;; Enable if and when someone needs it. | |
5111 | ;;"-DTrilinos_ENABLE_SEACAS=ON" | |
5112 | "-DTrilinos_ENABLE_Sacado=ON" | |
5113 | "-DTrilinos_ENABLE_Teuchos=ON" | |
5114 | "-DTrilinos_ENABLE_Tpetra=ON" | |
5115 | "-DTrilinos_ENABLE_Zoltan=ON" | |
5116 | ||
5117 | ;; Third-party libraries (TPLs) that Trilinos can interface with. | |
5118 | "-DBLAS_LIBRARY_NAMES=openblas" | |
5119 | "-DTPL_ENABLE_MPI=ON" | |
5120 | "-DTPL_ENABLE_MUMPS=ON" | |
5121 | "-DTPL_ENABLE_SCALAPACK=ON" | |
5122 | ||
5123 | ;; Enable the tests but not the examples (which are enabled by | |
5124 | ;; default when enabling tests). | |
5125 | ;; Although some examples are run as tests, they are otherwise | |
5126 | ;; unnecessary since this is a private package meant for | |
5127 | ;; dealii-openmpi. | |
5128 | ;; Besides, some MueLu and ROL examples require a lot of memory to | |
5129 | ;; compile. | |
5130 | ;; | |
5131 | ;; (For future reference, note that some ROL and SEACAS examples | |
5132 | ;; require removing gfortran from CPLUS_INCLUDE_PATH as in the | |
5133 | ;; dune-istl, dune-localfunctions and dune-alugrid packages.) | |
5134 | "-DTrilinos_ENABLE_TESTS=ON" | |
5135 | "-DTrilinos_ENABLE_EXAMPLES=OFF" | |
5136 | ;; MueLu tests require considerably more time and memory to compile | |
5137 | ;; than the rest of the tests. | |
5138 | "-DMueLu_ENABLE_TESTS=OFF" | |
5139 | ||
5140 | ;; The following options were gleaned from candi's trilinos.package. | |
5141 | ;; (We do not enable the complex instantiations, which are anyway | |
5142 | ;; provided only as an option in trilinos.package, because they are | |
5143 | ;; costly in compilation time and memory usage, and disk space [1].) | |
5144 | ;; | |
5145 | ;; [1]: https://www.docs.trilinos.org/files/TrilinosBuildReference.html#enabling-float-and-complex-scalar-types | |
5146 | "-DTrilinos_ENABLE_Ifpack2=OFF" | |
5147 | "-DTeuchos_ENABLE_FLOAT=ON" | |
5148 | "-DTpetra_INST_INT_LONG=ON" | |
5149 | "-DTPL_ENABLE_Boost=OFF") | |
5150 | #:phases | |
5151 | (modify-phases %standard-phases | |
5152 | (add-after 'configure 'fix-kokkos-config | |
5153 | (lambda _ | |
5154 | ;; GNU Make 4.3 accidentally leaves the backslash preceding the | |
5155 | ;; number sign in strings containing a literal backslash–number | |
5156 | ;; sign (\#) [1, 2]. | |
5157 | ;; This is still an issue in Trilinos 13.0.1, but should be fixed | |
5158 | ;; in the following version. | |
5159 | ;; (The latest versions of Kokkos incorporate the fix [2].) | |
5160 | ;; | |
5161 | ;; [1]: https://github.com/GEOSX/thirdPartyLibs/issues/136 | |
5162 | ;; [2]: https://github.com/kokkos/kokkos/blob/3.4.00/Makefile.kokkos#L441 | |
5163 | (substitute* "KokkosCore_config.h" | |
5164 | (("\\\\#") "#")) | |
5165 | #t)) | |
5166 | (add-before 'check 'mpi-setup | |
5167 | ,%openmpi-setup)))) | |
5168 | (home-page "https://trilinos.github.io/") | |
5169 | (synopsis "Algorithms for engineering and scientific problems") | |
5170 | (description | |
5171 | "The Trilinos Project is an effort to develop algorithms and enabling | |
5172 | technologies within an object-oriented software framework for the solution of | |
5173 | large-scale, complex multi-physics engineering and scientific problems. | |
5174 | A unique design feature of Trilinos is its focus on packages.") | |
5175 | ;; The packages are variously licensed under more than just BSD-3 and | |
5176 | ;; LGPL-2.1+, but all the licenses are either BSD- or LGPL-compatible. | |
5177 | ;; See https://trilinos.github.io/license.html. | |
5178 | (license (list license:bsd-3 license:lgpl2.1+)))) | |
5179 | ||
a17d4564 EB |
5180 | (define-public dealii |
5181 | (package | |
5182 | (name "dealii") | |
4a136a3b | 5183 | (version "9.3.1") |
a17d4564 EB |
5184 | (source |
5185 | (origin | |
5186 | (method url-fetch) | |
5187 | (uri (string-append "https://github.com/dealii/dealii/releases/" | |
5188 | "download/v" version "/dealii-" version ".tar.gz")) | |
5189 | (sha256 | |
4a136a3b | 5190 | (base32 "1f0sqvlxvl0myqcn0q6xrn1vnp5pgx143lai4a4jkh1dmdv4cbx6")) |
a17d4564 EB |
5191 | (modules '((guix build utils))) |
5192 | (snippet | |
6cbee49d | 5193 | '(begin |
4a136a3b | 5194 | ;; Remove bundled boost, muparser, TBB and UMFPACK. |
6cbee49d MW |
5195 | (delete-file-recursively "bundled") |
5196 | #t)))) | |
a17d4564 | 5197 | (build-system cmake-build-system) |
4a136a3b PP |
5198 | (outputs '("out" "doc")) |
5199 | (native-inputs | |
5200 | ;; Required to build the documentation. | |
5201 | `(("dot" ,graphviz) | |
5202 | ("doxygen" ,doxygen) | |
5203 | ("perl" ,perl))) | |
a17d4564 | 5204 | (inputs |
4a136a3b | 5205 | `(("arpack" ,arpack-ng) |
a17d4564 | 5206 | ("blas" ,openblas) |
4a136a3b | 5207 | ("gfortran" ,gfortran) |
a17d4564 | 5208 | ("lapack" ,lapack) |
a17d4564 | 5209 | ("muparser" ,muparser) |
4a136a3b PP |
5210 | ("zlib" ,zlib))) |
5211 | (propagated-inputs | |
5212 | ;; Some scripts are installed into share/deal.II/scripts that require | |
5213 | ;; perl and python, but they are not executable (and some are missing the | |
5214 | ;; shebang line) and therefore must be explicitly passed to the | |
5215 | ;; interpreter. | |
5216 | ;; Anyway, they are meant to be used at build time, so rather than adding | |
5217 | ;; the interpreters here, any package depending on them should just add | |
5218 | ;; the requisite interpreter to its native inputs. | |
5219 | `(("boost" ,boost) | |
5220 | ("hdf5" ,hdf5) | |
5221 | ("suitesparse" ,suitesparse) ; For UMFPACK. | |
5222 | ("tbb" ,tbb))) | |
a17d4564 | 5223 | (arguments |
4a136a3b PP |
5224 | `(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease. |
5225 | ;; The tests take too long and must be explicitly enabled with "make | |
5226 | ;; setup_tests". | |
5227 | ;; See https://www.dealii.org/developer/developers/testsuite.html. | |
5228 | ;; (They can also be run for an already installed deal.II.) | |
5229 | #:tests? #f | |
d84b09e9 | 5230 | #:configure-flags |
4a136a3b PP |
5231 | (let ((doc (string-append (assoc-ref %outputs "doc") |
5232 | "/share/doc/" ,name "-" ,version))) | |
5233 | `("-DDEAL_II_COMPONENT_DOCUMENTATION=ON" | |
5234 | ,(string-append "-DDEAL_II_DOCREADME_RELDIR=" doc) | |
5235 | ,(string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html") | |
5236 | ;; Don't compile the examples because the source and CMakeLists.txt | |
5237 | ;; are installed anyway, allowing users to do so for themselves. | |
5238 | "-DDEAL_II_COMPILE_EXAMPLES=OFF" | |
5239 | ,(string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc "/examples"))) | |
5240 | #:phases | |
5241 | (modify-phases %standard-phases | |
5242 | (add-after 'install 'remove-build-logs | |
5243 | ;; These build logs leak the name of the build directory by storing | |
5244 | ;; the values of CMAKE_SOURCE_DIR and CMAKE_BINARY_DIR. | |
5245 | (lambda* (#:key outputs #:allow-other-keys) | |
5246 | (let ((doc (string-append (assoc-ref outputs "doc") | |
5247 | "/share/doc/" ,name "-" ,version))) | |
5248 | (for-each delete-file (map (lambda (f) (string-append doc "/" f)) | |
5249 | '("detailed.log" "summary.log")))) | |
5250 | #t))))) | |
5251 | (home-page "https://www.dealii.org/") | |
a17d4564 EB |
5252 | (synopsis "Finite element library") |
5253 | (description | |
5254 | "Deal.II is a C++ program library targeted at the computational solution | |
5255 | of partial differential equations using adaptive finite elements. The main | |
5256 | aim of deal.II is to enable rapid development of modern finite element codes, | |
5257 | using among other aspects adaptive meshes and a wide array of tools often used | |
5258 | in finite element programs.") | |
5259 | (license license:lgpl2.1+))) | |
5260 | ||
5261 | (define-public dealii-openmpi | |
4a136a3b | 5262 | (package/inherit dealii |
a17d4564 EB |
5263 | (name "dealii-openmpi") |
5264 | (inputs | |
4a136a3b PP |
5265 | `(("arpack" ,arpack-ng-openmpi) |
5266 | ("metis" ,metis) | |
5267 | ("scalapack" ,scalapack) | |
5268 | ,@(alist-delete "arpack" (package-inputs dealii)))) | |
5269 | (propagated-inputs | |
5270 | `(("hdf5" ,hdf5-parallel-openmpi) | |
5271 | ("mpi" ,openmpi) | |
a17d4564 EB |
5272 | ("p4est" ,p4est-openmpi) |
5273 | ("petsc" ,petsc-openmpi) | |
5274 | ("slepc" ,slepc-openmpi) | |
06c11434 | 5275 | ("trilinos" ,trilinos-for-dealii-openmpi) |
4a136a3b | 5276 | ,@(alist-delete "hdf5" (package-propagated-inputs dealii)))) |
a17d4564 EB |
5277 | (arguments |
5278 | (substitute-keyword-arguments (package-arguments dealii) | |
4a136a3b PP |
5279 | ((#:configure-flags flags) |
5280 | `(cons "-DDEAL_II_WITH_MPI=ON" ,flags)))) | |
a17d4564 | 5281 | (synopsis "Finite element library (with MPI support)"))) |
194c7f95 AE |
5282 | |
5283 | (define-public flann | |
5284 | (package | |
5285 | (name "flann") | |
ba40ce5b LC |
5286 | (version "1.9.1") |
5287 | (home-page "https://github.com/mariusmuja/flann/") | |
194c7f95 AE |
5288 | (source |
5289 | (origin | |
ba40ce5b LC |
5290 | (method git-fetch) |
5291 | (uri (git-reference (url home-page) (commit version))) | |
5292 | (file-name (git-file-name name version)) | |
194c7f95 AE |
5293 | (sha256 |
5294 | (base32 | |
ba40ce5b | 5295 | "0p56fl2yx1r86ds1mgjq40926jdcgq3hka7p3l1hv2acv9jxp15x")) |
b5edc479 | 5296 | (patches (search-patches "flann-cmake-3.11.patch")))) |
194c7f95 | 5297 | (build-system cmake-build-system) |
f8bb53ca | 5298 | (outputs '("out")) |
194c7f95 AE |
5299 | (native-inputs |
5300 | `(("unzip" ,unzip))) | |
5301 | (inputs | |
5302 | `(("hdf5" ,hdf5) | |
f8bb53ca LC |
5303 | ;; FIXME: 'mkoctfile' fails with a linker error: |
5304 | ;; ld: cannot find -loctinterp | |
5305 | ;; ld: cannot find -loctave | |
5306 | ;; Disable it for now. | |
5307 | ;;("octave" ,octave-cli) | |
194c7f95 AE |
5308 | ("python" ,python-2) ; print syntax |
5309 | ;; ("python2-numpy" ,python2-numpy) ; only required for the tests | |
5310 | ("zlib" ,zlib))) | |
5311 | (arguments | |
39b30337 LC |
5312 | `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file |
5313 | ;; taken 46 MiB unstripped, and 6 MiB stripped. | |
5314 | #:strip-directories '("lib" "lib64" "libexec" | |
5315 | "bin" "sbin" "share/flann/octave") | |
5316 | ||
9684e30b LC |
5317 | ;; Save 12 MiB by not installing .a files. Passing |
5318 | ;; '-DBUILD_STATIC_LIBS=OFF' has no effect. | |
5319 | #:phases (modify-phases %standard-phases | |
5320 | (add-after 'install 'remove-static-libraries | |
5321 | (lambda* (#:key outputs #:allow-other-keys) | |
5322 | (let* ((out (assoc-ref outputs "out")) | |
5323 | (lib (string-append out "/lib"))) | |
5324 | (for-each delete-file | |
5325 | (find-files lib "\\.a$")) | |
5326 | #t)))) | |
5327 | ||
39b30337 | 5328 | #:tests? #f)) ; The test data are downloaded from the Internet. |
194c7f95 AE |
5329 | (synopsis "Library for approximate nearest neighbors computation") |
5330 | (description "FLANN is a library for performing fast approximate | |
5331 | nearest neighbor searches in high dimensional spaces. It implements a | |
5332 | collection of algorithms and a system for automatically choosing the best | |
5333 | algorithm and optimum parameters depending on the dataset. | |
5334 | ||
5335 | FLANN is written in C++ and contains bindings for C, Octave and Python.") | |
5336 | (license (license:non-copyleft "file://COPYING" | |
5337 | "See COPYING in the distribution.")))) | |
d8c97beb EF |
5338 | |
5339 | (define-public wcalc | |
5340 | (package | |
5341 | (name "wcalc") | |
5342 | (version "2.5") | |
5343 | (source | |
5344 | (origin | |
5345 | (method url-fetch) | |
de67e922 LF |
5346 | (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/" |
5347 | "wcalc-" version ".tar.bz2")) | |
d8c97beb EF |
5348 | (sha256 |
5349 | (base32 | |
5350 | "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f")))) | |
5351 | (build-system gnu-build-system) | |
5352 | (inputs | |
5353 | `(("mpfr" ,mpfr) | |
5354 | ("readline" ,readline))) | |
5355 | (home-page "http://w-calc.sourceforge.net/index.php") | |
5356 | (synopsis "Flexible command-line scientific calculator") | |
5357 | (description "Wcalc is a very capable calculator. It has standard functions | |
5358 | (sin, asin, and sinh for example, in either radians or degrees), many | |
5359 | pre-defined constants (pi, e, c, etc.), support for using variables, \"active\" | |
5360 | variables, a command history, hex/octal/binary input and output, unit | |
5361 | conversions, embedded comments, and an expandable expression entry field. It | |
5362 | evaluates expressions using the standard order of operations.") | |
5363 | (license license:gpl2+))) | |
45147b0c FH |
5364 | |
5365 | (define-public xaos | |
5366 | (package | |
5367 | (name "xaos") | |
685e4733 | 5368 | (version "4.2.1") |
45147b0c | 5369 | (source (origin |
49de3274 KK |
5370 | (method git-fetch) |
5371 | (uri (git-reference | |
5372 | (url "https://github.com/xaos-project/XaoS") | |
5373 | (commit (string-append "release-" version)))) | |
352e09a5 | 5374 | (file-name (git-file-name name version)) |
45147b0c FH |
5375 | (sha256 |
5376 | (base32 | |
685e4733 | 5377 | "0maw5am6rrkyjrprfg113zjq37mqj0iaznkg4h2927ff7wrprc94")))) |
45147b0c | 5378 | (build-system gnu-build-system) |
49de3274 | 5379 | (native-inputs `(("gettext" ,gettext-minimal) |
ea0a5107 | 5380 | ("qtbase" ,qtbase-5) |
49de3274 | 5381 | ("qttools" ,qttools))) |
45147b0c FH |
5382 | (inputs `(("libx11" ,libx11) |
5383 | ("zlib" ,zlib) | |
5384 | ("libpng" ,libpng) | |
5385 | ("gsl" ,gsl))) | |
49de3274 KK |
5386 | ;; The upstream project file ("XaoS.pro") and the Makefile it generates are |
5387 | ;; not enough for this package to install properly. These phases fix that. | |
45147b0c FH |
5388 | (arguments |
5389 | `(#:tests? #f ;no "check" target | |
49de3274 KK |
5390 | #:phases |
5391 | (modify-phases %standard-phases | |
5392 | (add-before 'configure 'make-qt-deterministic | |
5393 | (lambda _ | |
5394 | ;; Make Qt deterministic. | |
5395 | (setenv "QT_RCC_SOURCE_DATE_OVERRIDE" "1") | |
5396 | #t)) | |
5397 | (replace 'configure | |
5398 | (lambda* (#:key outputs #:allow-other-keys) | |
5399 | (let ((out (assoc-ref outputs "out"))) | |
49de3274 | 5400 | (substitute* "XaoS.pro" |
685e4733 KK |
5401 | ;; The DESTDIR is originally set to install the xaos binary to |
5402 | ;; the "bin" folder inside the build directory. Setting make | |
5403 | ;; flags doesn't seem to change this. | |
49de3274 | 5404 | (("DESTDIR.*$") |
685e4733 KK |
5405 | (string-append "DESTDIR=" out "/bin")) |
5406 | ;; Set the correct path to the lrelease binary. | |
5407 | (("lrelease-qt5") "lrelease")) | |
49de3274 KK |
5408 | (substitute* "src/include/config.h" |
5409 | (("/usr/share/XaoS") | |
5410 | (string-append out "/share/XaoS"))) | |
5411 | (invoke "qmake")))) | |
5412 | (add-after 'install 'install-data | |
5413 | (lambda* (#:key outputs #:allow-other-keys) | |
5414 | (let* ((out (assoc-ref outputs "out")) | |
5415 | (share (string-append out "/share"))) | |
5416 | (mkdir-p share) | |
5417 | (for-each | |
5418 | (lambda (folder) | |
5419 | (copy-recursively folder | |
5420 | (string-append share "/XaoS/" folder))) | |
5421 | '("catalogs" "examples" "tutorial")) | |
5422 | (install-file "xdg/xaos.png" | |
5423 | (string-append share "/pixmaps")) | |
5424 | (install-file "xdg/xaos.desktop" | |
5425 | (string-append share "/applications"))) | |
5426 | #t))))) | |
45147b0c FH |
5427 | (synopsis "Real-time fractal zoomer") |
5428 | (description "GNU XaoS is a graphical program that generates fractal | |
5429 | patterns and allows you to zoom in and out of them infinitely in a fluid, | |
5430 | continuous manner. It also includes tutorials that help to explain how fractals | |
5431 | are built. It can generate many different fractal types such as the Mandelbrot | |
5432 | set.") | |
49de3274 | 5433 | (home-page "https://xaos-project.github.io/") |
45147b0c | 5434 | (license license:gpl2+))) |
528bb464 EB |
5435 | |
5436 | (define-public hypre | |
5437 | (package | |
5438 | (name "hypre") | |
f72a1253 | 5439 | (version "2.20.0") |
fabcbf32 TGR |
5440 | (source |
5441 | (origin | |
5442 | (method git-fetch) | |
5443 | (uri (git-reference | |
9b4f9039 | 5444 | (url "https://github.com/hypre-space/hypre") |
fabcbf32 TGR |
5445 | (commit (string-append "v" version)))) |
5446 | (file-name (git-file-name name version)) | |
5447 | (sha256 | |
f72a1253 | 5448 | (base32 "14iqjwg5sv1qjn7c2cfv0xxmn9rwamjrhh9hgs8fjbywcbvrkjdi")))) |
528bb464 | 5449 | (build-system gnu-build-system) |
f72a1253 MB |
5450 | (outputs '("out" ;5.3 MiB of headers and libraries |
5451 | "doc")) ;12 MiB of documentation | |
528bb464 EB |
5452 | (native-inputs |
5453 | `(("doc++" ,doc++) | |
f72a1253 MB |
5454 | ("doxygen" ,doxygen) |
5455 | ("python" ,python) | |
5456 | ("python-breathe" ,python-breathe) | |
5457 | ("python-sphinx" ,python-sphinx) | |
5458 | ("texlive" ,(texlive-updmap.cfg (list texlive-adjustbox | |
5459 | texlive-amsfonts | |
5460 | texlive-bibtex | |
5461 | texlive-caption | |
5462 | texlive-cm | |
5463 | texlive-etoolbox | |
5464 | texlive-jknappen | |
5465 | texlive-sectsty | |
5466 | texlive-tex-gyre | |
5467 | texlive-wasy | |
5468 | texlive-xcolor | |
5469 | texlive-xypic | |
5470 | texlive-generic-listofitems | |
5471 | texlive-generic-ulem | |
5472 | texlive-latex-capt-of | |
5473 | texlive-latex-cmap | |
5474 | texlive-latex-colortbl | |
5475 | texlive-latex-etoc | |
5476 | texlive-latex-fancyhdr | |
5477 | texlive-latex-fancyvrb | |
5478 | texlive-latex-float | |
5479 | texlive-latex-fncychap | |
5480 | texlive-latex-framed | |
5481 | texlive-latex-geometry | |
5482 | texlive-latex-hanging | |
b949f34f | 5483 | texlive-hyperref |
f72a1253 MB |
5484 | texlive-latex-multirow |
5485 | texlive-latex-natbib | |
5486 | texlive-latex-needspace | |
5487 | texlive-latex-newunicodechar | |
5488 | texlive-latex-parskip | |
5489 | texlive-latex-stackengine | |
5490 | texlive-latex-tabulary | |
5491 | texlive-latex-titlesec | |
5492 | texlive-latex-tocloft | |
5493 | texlive-latex-upquote | |
5494 | texlive-latex-varwidth | |
b949f34f | 5495 | texlive-wasysym |
f72a1253 | 5496 | texlive-latex-wrapfig))))) |
528bb464 EB |
5497 | (inputs |
5498 | `(("blas" ,openblas) | |
5499 | ("lapack" ,lapack))) | |
5500 | (arguments | |
5501 | `(#:modules ((srfi srfi-1) | |
5502 | ,@%gnu-build-system-modules) | |
5503 | #:configure-flags '("--enable-shared" | |
5504 | "--disable-fortran" | |
5505 | "--without-MPI" | |
5506 | "--with-openmp" | |
5507 | "--with-fei" | |
5508 | "--with-lapack" | |
5509 | "--with-blas") | |
5510 | #:phases | |
5511 | (modify-phases %standard-phases | |
5512 | (add-before 'configure 'chdir-src | |
5513 | (lambda _ (chdir "src"))) | |
5514 | (replace 'configure | |
5515 | (lambda* (#:key build target configure-flags | |
5516 | #:allow-other-keys #:rest args) | |
5517 | (let* ((configure (assoc-ref %standard-phases 'configure))) | |
5518 | (apply configure | |
5519 | (append args | |
5520 | (list #:configure-flags | |
5521 | (cons (string-append | |
5522 | "--host=" (or target build)) | |
5523 | configure-flags))))))) | |
5524 | (add-after 'build 'build-docs | |
5525 | (lambda _ | |
f72a1253 | 5526 | (invoke "make" "-C" "docs"))) |
528bb464 EB |
5527 | (replace 'check |
5528 | (lambda _ | |
5529 | (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib")) | |
5530 | (setenv "PATH" (string-append "." ":" (getenv "PATH"))) | |
6b1c7ac8 RW |
5531 | (invoke "make" "check" "CHECKRUN=") |
5532 | (for-each (lambda (filename) | |
5533 | (let ((size (stat:size (stat filename)))) | |
5534 | (when (positive? size) | |
5535 | (error (format #f "~a size ~d; error indication~%" | |
5536 | filename size))))) | |
f72a1253 | 5537 | (find-files "test" ".*\\.err$")))) |
528bb464 EB |
5538 | (add-after 'install 'install-docs |
5539 | (lambda* (#:key outputs #:allow-other-keys) | |
5540 | ;; Custom install because docs/Makefile doesn't honor ${docdir}. | |
5541 | (let* ((doc (assoc-ref outputs "doc")) | |
5542 | (docdir (string-append doc "/share/doc/hypre-" ,version))) | |
528bb464 EB |
5543 | (with-directory-excursion "docs" |
5544 | (for-each (lambda (base) | |
5545 | (install-file (string-append base ".pdf") docdir) | |
f72a1253 MB |
5546 | (copy-recursively (string-append base "-html") |
5547 | (string-append docdir "/" base))) | |
5548 | '("usr-manual" "ref-manual"))))))))) | |
9b4f9039 MB |
5549 | (home-page "https://computing.llnl.gov/projects\ |
5550 | /hypre-scalable-linear-solvers-multigrid-methods") | |
528bb464 EB |
5551 | (synopsis "Library of solvers and preconditioners for linear equations") |
5552 | (description | |
5553 | "HYPRE is a software library of high performance preconditioners and | |
5554 | solvers for the solution of large, sparse linear systems of equations. It | |
5555 | features multigrid solvers for both structured and unstructured grid | |
5556 | problems.") | |
5557 | (license license:lgpl2.1))) | |
5558 | ||
5559 | (define-public hypre-openmpi | |
5560 | (package (inherit hypre) | |
5561 | (name "hypre-openmpi") | |
5562 | (inputs | |
5563 | `(("mpi" ,openmpi) | |
5564 | ,@(package-inputs hypre))) | |
5565 | (arguments | |
5566 | (substitute-keyword-arguments (package-arguments hypre) | |
5567 | ((#:configure-flags flags) | |
5568 | ``("--with-MPI" | |
6df2a50a LC |
5569 | ,@(delete "--without-MPI" ,flags))) |
5570 | ((#:phases phases) | |
5571 | `(modify-phases ,phases | |
bbe46a4a EB |
5572 | (add-before 'check 'mpi-setup |
5573 | ,%openmpi-setup))))) | |
528bb464 EB |
5574 | (synopsis "Parallel solvers and preconditioners for linear equations") |
5575 | (description | |
5576 | "HYPRE is a software library of high performance preconditioners and | |
5577 | solvers for the solution of large, sparse linear systems of equations on | |
5578 | parallel computers. It features parallel multigrid solvers for both | |
5579 | structured and unstructured grid problems."))) | |
6c90e183 EB |
5580 | |
5581 | (define-public matio | |
5582 | (package | |
5583 | (name "matio") | |
75166b29 | 5584 | (version "1.5.19") |
6c90e183 EB |
5585 | (source |
5586 | (origin | |
5587 | (method url-fetch) | |
de67e922 | 5588 | (uri (string-append "mirror://sourceforge/matio/matio/" version "/" |
6c90e183 EB |
5589 | "matio-" version ".tar.gz")) |
5590 | (sha256 | |
5591 | (base32 | |
75166b29 | 5592 | "0vr8c1mz1k6mz0sgh6n3scl5c3a71iqmy5fnydrgq504icj4vym4")))) |
6c90e183 EB |
5593 | (build-system gnu-build-system) |
5594 | (inputs | |
5595 | `(("zlib" ,zlib) | |
c5372cd4 | 5596 | ("hdf5" ,hdf5-1.8))) |
6c90e183 EB |
5597 | (home-page "http://matio.sourceforge.net/") |
5598 | (synopsis "Library for reading and writing MAT files") | |
5599 | (description "Matio is a library for reading and writing MAT files. It | |
5600 | supports compressed MAT files, as well as newer (version 7.3) MAT files.") | |
5601 | (license license:bsd-2))) | |
d721c83a | 5602 | |
517318ad LF |
5603 | (define-public vc |
5604 | (package | |
5605 | (name "vc") | |
0eea6168 | 5606 | (version "1.4.2") |
517318ad LF |
5607 | (source |
5608 | (origin (method url-fetch) | |
5609 | (uri (string-append "https://github.com/VcDevel/Vc/releases/" | |
5610 | "download/" version "/Vc-" version ".tar.gz")) | |
5611 | (sha256 | |
5612 | (base32 | |
0eea6168 | 5613 | "0lirdqzcxys9walz04bllsphydynk7973aimd5k1h1qbwi8z3lsh")))) |
517318ad LF |
5614 | (build-system cmake-build-system) |
5615 | (arguments | |
5616 | '(#:configure-flags | |
33d82486 MB |
5617 | '("-DBUILD_TESTING=ON" |
5618 | ;; By default, Vc will optimize for the CPU of the build machine. | |
5619 | ;; Setting this to "none" makes it create portable binaries. See | |
5620 | ;; "cmake/OptimizeForArchitecture.cmake". | |
9d731fb6 MB |
5621 | "-DTARGET_ARCHITECTURE=none") |
5622 | #:phases (modify-phases %standard-phases | |
5623 | (add-after 'unpack 'copy-testdata | |
5624 | (lambda* (#:key inputs native-inputs #:allow-other-keys) | |
5625 | (let ((testdata (assoc-ref (or native-inputs inputs) | |
5626 | "testdata"))) | |
5627 | (copy-recursively testdata "tests/testdata") | |
5628 | #t)))))) | |
5629 | (native-inputs | |
5630 | `(("virtest" ,virtest) | |
5631 | ||
5632 | ;; This is a submodule in the git project, but not part of the | |
5633 | ;; released sources. See the git branch for the commit to take. | |
5634 | ("testdata" ,(let ((commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3")) | |
5635 | (origin | |
5636 | (method git-fetch) | |
5637 | (uri (git-reference | |
5638 | (url "https://github.com/VcDevel/vc-testdata") | |
5639 | (commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3"))) | |
5640 | (file-name (git-file-name "vc-testdata" | |
5641 | (string-take commit 7))) | |
5642 | (sha256 | |
5643 | (base32 | |
5644 | "1hkhqib03qlcq412ym2dciynfxcdr2ygqhnplz4l1vissr1wnqn2"))))))) | |
517318ad LF |
5645 | (synopsis "SIMD vector classes for C++") |
5646 | (description "Vc provides portable, zero-overhead C++ types for explicitly | |
5647 | data-parallel programming. It is a library designed to ease explicit | |
5648 | vectorization of C++ code. Its types enable explicitly stating data-parallel | |
5649 | operations on multiple values. The parallelism is therefore added via the type | |
5650 | system. Vc has an intuitive API and provides portability between different | |
5651 | compilers and compiler versions as well as portability between different vector | |
5652 | instruction sets. Thus, an application written with Vc can be compiled for: | |
5653 | @enumerate | |
5654 | @item AVX and AVX2 | |
d1e4ad1b | 5655 | @item SSE2 up to SSE4.2 or SSE4a |
517318ad LF |
5656 | @item Scalar |
5657 | @item MIC | |
5658 | @item NEON (in development) | |
5659 | @item NVIDIA GPUs / CUDA (in development) | |
5660 | @end enumerate\n") | |
5661 | (home-page "https://github.com/VcDevel/Vc") | |
a8ead6f9 EF |
5662 | ;; "No support_???.cpp file exists for this architecture." |
5663 | (supported-systems '("x86_64-linux" "i686-linux")) | |
517318ad | 5664 | (license license:bsd-3))) |
54052a54 | 5665 | |
5666 | (define-public reducelcs | |
5667 | ;; This is the last commit which is available upstream, no | |
5668 | ;; release happened since 2010. | |
5669 | (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0") | |
5670 | (revision "1")) | |
5671 | (package | |
5672 | (name "reducelcs") | |
5673 | (version (string-append "1.0-" revision "." (string-take commit 7))) | |
5674 | (source | |
5675 | (origin | |
5676 | (method git-fetch) | |
5677 | (uri (git-reference | |
5678 | (url "https://github.com/gdv/Reduce-Expand-for-LCS") | |
5679 | (commit commit))) | |
5680 | (file-name (string-append name "-" version "-checkout")) | |
5681 | (sha256 | |
5682 | (base32 | |
5683 | "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm")))) | |
5684 | (build-system gnu-build-system) | |
5685 | (inputs | |
5686 | `(("openlibm" ,openlibm))) | |
5687 | (arguments | |
5688 | `(#:tests? #f ; no tests | |
5689 | #:phases | |
5690 | (modify-phases %standard-phases | |
5691 | (delete 'configure) ; No configure script exists. | |
5692 | (replace 'install ; No install phase exists. | |
5693 | (lambda* (#:key outputs #:allow-other-keys) | |
5694 | (let* ((out (assoc-ref outputs "out")) | |
5695 | (bin (string-append out "/bin"))) | |
5696 | (install-file "Approximation" bin) | |
5697 | (install-file "CollectResults" bin) | |
5698 | (install-file "GenerateInstances" bin) | |
5699 | #t)))))) | |
5700 | (synopsis "Approximate Longest Commons Subsequence computation tool") | |
5701 | (description | |
5702 | "@code{reduceLCS} is an implementation of the Reduce-Expand | |
5703 | algorithm for LCS. It is a fast program to compute the approximate | |
5704 | Longest Commons Subsequence of a set of strings.") | |
5705 | (home-page "https://github.com/gdv/Reduce-Expand-for-LCS") | |
c000b6b1 | 5706 | (license license:gpl3+)))) |
479c4273 JD |
5707 | |
5708 | (define-public jacal | |
5709 | (package | |
5710 | (name "jacal") | |
5711 | (version "1c4") | |
5712 | (source (origin | |
5713 | (method url-fetch) | |
5714 | (uri (string-append | |
5715 | "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-" | |
5716 | version ".zip")) | |
5717 | (sha256 (base32 | |
5718 | "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q")) | |
5719 | (patches (search-patches "jacal-fix-texinfo.patch")))) | |
5720 | (build-system gnu-build-system) | |
5721 | (arguments | |
5722 | `(#:phases | |
5723 | (modify-phases %standard-phases | |
5724 | (add-before 'build 'pre-build | |
5725 | ;; Don't use upstream's script - it really doesn't fit into | |
5726 | ;; Guix's functional paradigm. | |
5727 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
5728 | (substitute* "Makefile" | |
5729 | (("^install: install-script") "install: ")))) | |
5730 | (add-after 'install 'post-install | |
5731 | ;; Instead, we provide our own simplified script. | |
5732 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
5733 | (let ((wrapper (string-append (assoc-ref outputs "out") | |
5734 | "/bin/jacal"))) | |
5735 | (format (open wrapper (logior O_WRONLY O_CREAT)) | |
5736 | (string-append "#!~a\nexec ~a/bin/scm -ip1 " | |
5737 | "-e '(slib:load \"~a/lib/jacal/math\") " | |
5738 | "(math)' \"$@\"\n") | |
5739 | (which "bash") | |
5740 | (assoc-ref inputs "scm") | |
5741 | (assoc-ref outputs "out")) | |
5742 | (chmod wrapper #o555)))) | |
5743 | (replace 'configure | |
9cd82b1c RW |
5744 | (lambda* (#:key outputs #:allow-other-keys) |
5745 | (invoke "./configure" | |
5746 | (string-append "--prefix=" | |
5747 | (assoc-ref outputs "out")))))))) | |
479c4273 JD |
5748 | (inputs `(("scm" ,scm))) |
5749 | (native-inputs `(("unzip" ,unzip) | |
5750 | ("texinfo" ,texinfo))) | |
5751 | (synopsis "Symbolic mathematics system") | |
5752 | (description "GNU JACAL is an interactive symbolic mathematics program based on | |
5753 | Scheme. It manipulate and simplify a range of mathematical expressions such | |
5754 | as equations, scalars, vectors, and matrices.") | |
6fd52309 | 5755 | (home-page "https://www.gnu.org/software/jacal/") |
479c4273 JD |
5756 | (license license:gpl3+))) |
5757 | ||
313844d9 TF |
5758 | (define-public z3 |
5759 | (package | |
5760 | (name "z3") | |
62671027 | 5761 | (version "4.8.9") |
fb525bfd | 5762 | (home-page "https://github.com/Z3Prover/z3") |
313844d9 | 5763 | (source (origin |
fb525bfd MB |
5764 | (method git-fetch) |
5765 | (uri (git-reference (url home-page) | |
5766 | (commit (string-append "z3-" version)))) | |
2d7b99b3 | 5767 | (file-name (git-file-name name version)) |
313844d9 TF |
5768 | (sha256 |
5769 | (base32 | |
62671027 | 5770 | "1hnbzq10d23drd7ksm3c1n2611c3kd0q0yxgz8y78zaafwczvwxx")))) |
fa574a6d | 5771 | (build-system gnu-build-system) |
313844d9 | 5772 | (arguments |
f6b4d395 JK |
5773 | `(#:imported-modules ((guix build python-build-system) |
5774 | ,@%gnu-build-system-modules) | |
5775 | #:modules (((guix build python-build-system) #:select (site-packages)) | |
5776 | (guix build gnu-build-system) | |
5777 | (guix build utils)) | |
5778 | #:phases | |
313844d9 | 5779 | (modify-phases %standard-phases |
8b87d095 JK |
5780 | (add-after 'unpack 'enable-bytecode-determinism |
5781 | (lambda _ | |
5782 | (setenv "PYTHONHASHSEED" "0") | |
5783 | #t)) | |
ad6c6a5b EF |
5784 | (add-after 'unpack 'fix-compatability |
5785 | ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only. | |
5786 | (lambda _ | |
5787 | (substitute* "src/util/mpz.cpp" | |
5788 | (("#include <immintrin.h>") "")) | |
5789 | #t)) | |
cf684d87 TF |
5790 | (add-before 'configure 'bootstrap |
5791 | (lambda _ | |
32d5360f | 5792 | (invoke "python" "scripts/mk_make.py"))) |
fa574a6d AB |
5793 | ;; work around gnu-build-system's setting --enable-fast-install |
5794 | ;; (z3's `configure' is a wrapper around the above python file, | |
5795 | ;; which fails when passed --enable-fast-install) | |
5796 | (replace 'configure | |
5797 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
5798 | (invoke "./configure" | |
f6b4d395 JK |
5799 | "--python" |
5800 | (string-append "--prefix=" (assoc-ref outputs "out")) | |
5801 | (string-append "--pypkgdir=" (site-packages inputs outputs))))) | |
fa574a6d AB |
5802 | (add-after 'configure 'change-directory |
5803 | (lambda _ | |
5804 | (chdir "build") | |
5805 | #t)) | |
cf684d87 | 5806 | (add-before 'check 'make-test-z3 |
313844d9 | 5807 | (lambda _ |
cf684d87 | 5808 | ;; Build the test suite executable. |
32d5360f RW |
5809 | (invoke "make" "test-z3" "-j" |
5810 | (number->string (parallel-job-count))))) | |
cf684d87 TF |
5811 | (replace 'check |
5812 | (lambda _ | |
5813 | ;; Run all the tests that don't require arguments. | |
32d5360f | 5814 | (invoke "./test-z3" "/a")))))) |
313844d9 | 5815 | (native-inputs |
fa574a6d AB |
5816 | `(("which" ,which) |
5817 | ("python" ,python-wrapper))) | |
313844d9 TF |
5818 | (synopsis "Theorem prover") |
5819 | (description "Z3 is a theorem prover and @dfn{satisfiability modulo | |
cf684d87 | 5820 | theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.") |
313844d9 | 5821 | (license license:expat))) |
3d5d87a3 | 5822 | |
a8c69e22 JL |
5823 | (define-public ocaml-z3 |
5824 | (package | |
5825 | (inherit z3) | |
5826 | (name "ocaml-z3") | |
5827 | (arguments | |
5828 | `(#:imported-modules ((guix build python-build-system) | |
5829 | ,@%gnu-build-system-modules) | |
5830 | #:modules (((guix build python-build-system) #:select (site-packages)) | |
5831 | (guix build gnu-build-system) | |
5832 | (guix build utils)) | |
5833 | #:tests? #f; no ml tests | |
5834 | #:phases | |
5835 | (modify-phases %standard-phases | |
5836 | (add-before 'configure 'bootstrap | |
5837 | (lambda* (#:key outputs #:allow-other-keys) | |
5838 | (let ((out (assoc-ref outputs "out"))) | |
5839 | (setenv "OCAMLFIND_LDCONF" "ignore") | |
5840 | (setenv "OCAMLFIND_DESTDIR" (string-append out "/lib/ocaml/site-lib")) | |
5841 | (mkdir-p (string-append out "/lib/ocaml/site-lib")) | |
5842 | (substitute* "scripts/mk_util.py" | |
5843 | (("LIBZ3 = LIBZ3") | |
5844 | (string-append "LIBZ3 = LIBZ3 + ' -dllpath " out "/lib'")) | |
5845 | ;; Do not build z3 again, use the library passed as input | |
5846 | ;; instead | |
5847 | (("z3linkdep,") "\"\",") | |
5848 | (("z3linkdep)") "\"\")")) | |
5849 | (invoke "python" "scripts/mk_make.py")))) | |
5850 | (replace 'configure | |
5851 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
5852 | (invoke "./configure" | |
5853 | "--ml" | |
5854 | (string-append "--prefix=" (assoc-ref outputs "out"))))) | |
5855 | (add-after 'configure 'change-directory | |
5856 | (lambda _ | |
5857 | (chdir "build") | |
5858 | #t)) | |
5859 | (replace 'build | |
5860 | (lambda _ | |
5861 | (invoke "make" "ml"))) | |
5862 | (replace 'install | |
5863 | (lambda* (#:key outputs #:allow-other-keys) | |
5864 | (invoke "ocamlfind" "install" "-destdir" | |
5865 | (string-append (assoc-ref outputs "out") "/lib/ocaml/site-lib") | |
5866 | "z3" "api/ml/META" "api/ml/z3enums.mli" "api/ml/z3enums.cmi" | |
5867 | "api/ml/z3enums.cmx" "api/ml/z3native.mli" | |
5868 | "api/ml/z3native.cmi" "api/ml/z3native.cmx" | |
5869 | "../src/api/ml/z3.mli" "api/ml/z3.cmi" "api/ml/z3.cmx" | |
5870 | "api/ml/libz3ml.a" "api/ml/z3ml.a" "api/ml/z3ml.cma" | |
5871 | "api/ml/z3ml.cmxa" "api/ml/z3ml.cmxs" "api/ml/dllz3ml.so")))))) | |
5872 | (native-inputs | |
5873 | `(("which" ,which) | |
5874 | ("python" ,python-wrapper) | |
5875 | ("ocaml" ,ocaml) | |
5876 | ("ocaml-findlib" ,ocaml-findlib))) | |
5877 | (propagated-inputs | |
5878 | `(("ocaml-zarith" ,ocaml-zarith))) | |
5879 | (inputs | |
5880 | `(("z3" ,z3))))) | |
5881 | ||
6d433d6e EB |
5882 | (define-public elpa |
5883 | (package | |
5884 | (name "elpa") | |
5885 | (version "2018.11.001") | |
5886 | (source (origin | |
5887 | (method url-fetch) | |
5888 | (uri (string-append "http://elpa.mpcdf.mpg.de/html/Releases/" | |
5889 | version "/elpa-" version ".tar.gz")) | |
5890 | (sha256 | |
5891 | (base32 | |
5892 | "05hv3v5i6xmziaizw350ff72y1c3k662r85fm3xfdrkclj5zw9yc")))) | |
5893 | (build-system gnu-build-system) | |
5894 | (native-inputs | |
5895 | `(("fortran" ,gfortran) | |
5896 | ("perl" ,perl))) ;for configure and deps | |
5897 | (inputs | |
5898 | `(("blas" ,openblas))) | |
5899 | (arguments | |
5900 | `(#:configure-flags | |
5901 | `("--enable-openmp" | |
5902 | "--with-mpi=no" | |
5903 | ;; ELPA unfortunately does not support runtime dispatch, so we can | |
5904 | ;; only enable the "generic" kernels. See the "Cross compilation" | |
5905 | ;; section of INSTALL.md. | |
5906 | "--enable-generic" | |
5907 | "--disable-sse" "--disable-sse-assembly" ;Require SSE3 | |
5908 | "--disable-avx" "--disable-avx2" "--disable-avx512" | |
5909 | ,(string-append "CFLAGS=-O3 " | |
5910 | "-funsafe-loop-optimizations -funsafe-math-optimizations " | |
5911 | "-ftree-vect-loop-version -ftree-vectorize " | |
5912 | ,(let ((system (or (%current-target-system) | |
5913 | (%current-system)))) | |
5914 | (cond | |
5915 | ((or (string-prefix? "x86_64" system) | |
5916 | (string-prefix? "i686" system)) | |
5917 | "-msse2") | |
5918 | (else ""))))) | |
5919 | #:parallel-tests? #f ;tests are multi-threaded, via BLAS | |
5920 | #:phases | |
5921 | (modify-phases %standard-phases | |
5922 | (add-before 'configure 'patch-header-generation | |
5923 | (lambda _ | |
5924 | (substitute* "configure" | |
5925 | (("^ *make.*top_srcdir=\"\\$srcdir\"" &) | |
5926 | (string-append & " CPP=\"$CPP\""))) | |
5927 | #t)) | |
5928 | (add-before 'check 'setup-tests | |
5929 | (lambda _ | |
5930 | ;; Decrease test time and RAM use by computing fewer eigenvalues. | |
5931 | ;; The flags are (MATRIX-SIZE, EIGENVALUES, BLOCK-SIZE), where | |
5932 | ;; the default is (500, 250, 16) for C tests and (5000, 150, 16) | |
5933 | ;; for Fortran. This also causes several tests to pass that | |
5934 | ;; otherwise would otherwise fail with matrix size 5000; possibly | |
5935 | ;; due to floating point tolerances that are too tight. | |
5936 | (setenv "TEST_FLAGS" "1500 50 16") ;from elpa.spec | |
5937 | (setenv "OMP_NUM_THREADS" (number->string (parallel-job-count))) | |
5938 | (substitute* "Makefile" | |
5939 | ;; Test scripts are generated, patch the shebang | |
5940 | (("#!/bin/bash") (string-append "#!" (which "sh")))) | |
5941 | #t))))) | |
bebfe067 | 5942 | (home-page "https://elpa.mpcdf.mpg.de") |
6d433d6e EB |
5943 | (synopsis "Eigenvalue solvers for symmetric matrices") |
5944 | (description | |
5945 | "The ELPA library provides efficient and scalable direct eigensolvers for | |
5946 | symmetric matrices.") | |
5947 | (license license:lgpl3))) | |
5948 | ||
5949 | (define-public elpa-openmpi | |
5950 | (package (inherit elpa) | |
5951 | (name "elpa-openmpi") | |
5952 | (inputs | |
5953 | `(("mpi" ,openmpi) | |
5954 | ("scalapack" ,scalapack) | |
5955 | ,@(package-inputs elpa))) | |
5956 | (arguments | |
5957 | (substitute-keyword-arguments (package-arguments elpa) | |
5958 | ((#:configure-flags cf '()) | |
5959 | `(cons "--with-mpi=yes" (delete "--with-mpi=no" ,cf))) | |
5960 | ((#:phases phases '%standard-phases) | |
5961 | `(modify-phases ,phases | |
5962 | (add-before 'check 'mpi-setup | |
5963 | (lambda _ | |
5964 | ;; Tests use 2 mpi tasks by default, use our remaining build | |
5965 | ;; cores as OpenMP threads. | |
5966 | (setenv "OMP_NUM_THREADS" (number->string | |
5967 | (max (quotient (parallel-job-count) 2) | |
5968 | 1))) | |
5969 | (,%openmpi-setup))))))) | |
5970 | (synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)"))) | |
5971 | ||
e01397b4 EB |
5972 | (define-public elemental |
5973 | (package | |
5974 | (name "elemental") | |
5975 | (version "0.87.7") | |
5976 | (source (origin | |
5c0b6d1b EF |
5977 | (method git-fetch) |
5978 | (uri (git-reference | |
b0e7b699 | 5979 | (url "https://github.com/elemental/Elemental") |
5c0b6d1b EF |
5980 | (commit (string-append "v" version)))) |
5981 | (file-name (git-file-name name version)) | |
e01397b4 EB |
5982 | (sha256 |
5983 | (base32 | |
5c0b6d1b | 5984 | "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc")))) |
e01397b4 | 5985 | (build-system cmake-build-system) |
1e05e837 | 5986 | (home-page "https://github.com/elemental/Elemental") |
e01397b4 EB |
5987 | (native-inputs |
5988 | `(("gfortran" ,gfortran))) | |
5989 | (inputs | |
5990 | `(("blas" ,openblas) | |
5991 | ("gfortran:lib" ,gfortran "lib") | |
5992 | ("gmp" ,gmp) | |
5993 | ("lapack" ,lapack) | |
5994 | ("metis" ,metis) | |
5995 | ("mpc" ,mpc) | |
5996 | ("mpfr" ,mpfr) | |
5997 | ("mpi" ,openmpi) | |
5998 | ("qd" ,qd))) | |
5999 | (arguments | |
6000 | `(#:build-type "Release" ;default RelWithDebInfo not supported | |
6001 | #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES" | |
6002 | "-DEL_AVOID_COMPLEX_MPI:BOOL=NO" | |
6003 | "-DEL_CACHE_WARNINGS:BOOL=YES" | |
6004 | "-DEL_TESTS:BOOL=YES" | |
6005 | "-DCMAKE_INSTALL_LIBDIR=lib" | |
6006 | "-DGFORTRAN_LIB=gfortran") | |
6007 | #:phases (modify-phases %standard-phases | |
3b42e2be EF |
6008 | (add-before 'check 'mpi-setup |
6009 | ,%openmpi-setup) | |
e01397b4 EB |
6010 | (add-before 'check 'setup-tests |
6011 | (lambda _ | |
6012 | ;; Parallelism is done at the MPI layer. | |
6013 | (setenv "OMP_NUM_THREADS" "1") | |
6014 | #t)) | |
6015 | (add-after 'install 'remove-tests | |
6016 | (lambda* (#:key outputs #:allow-other-keys) | |
6017 | ;; Tests are installed, with no easy configuration | |
6018 | ;; switch to prevent this, so delete them. | |
6019 | (delete-file-recursively | |
3b42e2be | 6020 | (string-append (assoc-ref outputs "out") "/bin")) |
e01397b4 EB |
6021 | #t))))) |
6022 | (synopsis "Dense and sparse-direct linear algebra and optimization") | |
6023 | (description "Elemental is a modern C++ library for distributed-memory | |
6024 | dense and sparse-direct linear algebra, conic optimization, and lattice | |
6025 | reduction.") | |
6026 | (license license:bsd-2))) | |
5b05dce7 JN |
6027 | |
6028 | (define-public mcrl2 | |
6029 | (package | |
6030 | (name "mcrl2") | |
9bd65f05 | 6031 | (version "202106.0") |
5b05dce7 JN |
6032 | (source (origin |
6033 | (method url-fetch) | |
185152e3 JN |
6034 | (uri (string-append |
6035 | "https://www.mcrl2.org/download/release/mcrl2-" | |
6036 | version ".tar.gz")) | |
5b05dce7 JN |
6037 | (sha256 |
6038 | (base32 | |
16e3f8d9 | 6039 | "1xgx3cd57vc7gbjic24j1q2za6j3ybz6nk4afvvpbwsf33xnlf4v")))) |
5b05dce7 JN |
6040 | (inputs |
6041 | `(("boost" ,boost) | |
6042 | ("glu" ,glu) | |
6043 | ("mesa" ,mesa) | |
ea0a5107 | 6044 | ("qtbase" ,qtbase-5))) |
5b05dce7 | 6045 | (build-system cmake-build-system) |
ed0c5d3c | 6046 | (synopsis "Toolset for the mCRL2 formal specification language") |
5b05dce7 | 6047 | (description |
ed0c5d3c TGR |
6048 | "@dfn{mCRL2} (micro Common Representation Language 2) is a formal |
6049 | specification language for describing concurrent discrete event systems. Its | |
6050 | toolset supports analysis and automatic verification, linearisation, simulation, | |
6051 | state-space exploration and generation, and tools to optimise and analyse | |
5b05dce7 JN |
6052 | specifications. Also, state spaces can be manipulated, visualised and |
6053 | analysed.") | |
b3882709 | 6054 | (home-page "https://mcrl2.org") |
5b05dce7 | 6055 | (license license:boost1.0))) |
41835f94 | 6056 | |
e03b9126 JN |
6057 | (define-public mcrl2-minimal |
6058 | (package | |
6059 | (inherit mcrl2) | |
6060 | (name "mcrl2-minimal") | |
6061 | (inputs | |
6062 | `(("boost" ,boost))) | |
6063 | (arguments | |
6064 | '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF"))))) | |
6065 | ||
910deec6 NV |
6066 | (define-public tcalc |
6067 | (package | |
6068 | (name "tcalc") | |
6069 | (version "2.0") | |
6070 | (source | |
6071 | (origin | |
6072 | (method url-fetch) | |
6073 | (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-" | |
6074 | version ".tar.gz")) | |
6075 | (sha256 | |
6076 | (base32 | |
6077 | "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m")))) | |
6078 | (build-system gnu-build-system) | |
6079 | (synopsis "The terminal calculator") | |
6080 | (description | |
6081 | "The terminal calculator is a small program to help users of the GNU/Linux | |
6082 | terminal do calculations simply and quickly. The formula to be calculated can | |
6083 | be fed to @command{tcalc} through the command line.") | |
6084 | (home-page "https://sites.google.com/site/mohammedisam2000/tcalc") | |
6085 | (license license:gpl3+))) | |
b26e4f26 | 6086 | |
b5c51ae0 RP |
6087 | (define-public tiny-bignum |
6088 | (let ((commit "1d7a1f9b8e77316187a6b3eae8e68d60a6f9a4d4")) | |
6089 | (package | |
6090 | (name "tiny-bignum") | |
6091 | (version (git-version "0" "0" commit)) | |
6092 | (source | |
6093 | (origin | |
6094 | (method git-fetch) | |
6095 | (uri (git-reference | |
6096 | (url "https://github.com/kokke/tiny-bignum-c") | |
6097 | (commit commit))) | |
6098 | (file-name (git-file-name "tiny-bignum" commit)) | |
6099 | (sha256 | |
6100 | (base32 "0vj71qlhlaa7d92bfar1kwqv6582dqrby8x3kdw0yzh82k2023g6")))) | |
6101 | (build-system gnu-build-system) | |
6102 | (arguments | |
6103 | `(#:phases | |
6104 | (modify-phases %standard-phases | |
6105 | (delete 'configure) | |
6106 | (add-after 'unpack 'patch-tests | |
6107 | (lambda _ | |
6108 | (substitute* "scripts/test_rand.py" | |
6109 | (("\t") " ") | |
6110 | (("\" % (\\w+)" _ symbol) (string-append "\" % int(" symbol ")"))) | |
6111 | #t)) | |
6112 | (replace 'check | |
6113 | (lambda* (#:key tests? #:allow-other-keys) | |
6114 | (when tests? | |
6115 | (invoke "make" "test")) | |
6116 | #t)) | |
6117 | (replace 'install | |
6118 | (lambda* (#:key outputs #:allow-other-keys) | |
6119 | (let ((share (string-append (assoc-ref outputs "out") "/share")) | |
6120 | (doc (string-append (assoc-ref outputs "out") "/doc"))) | |
6121 | (mkdir-p share) | |
6122 | (install-file "bn.c" share) | |
6123 | (install-file "bn.h" share) | |
6124 | (mkdir-p doc) | |
6125 | (install-file "LICENSE" doc) | |
6126 | (install-file "README.md" doc)) | |
6127 | #t))))) | |
6128 | (native-inputs | |
6129 | `(("python" ,python-wrapper))) | |
6130 | (home-page "https://github.com/kokke/tiny-bignum-c") | |
6131 | (synopsis "Small portable multiple-precision unsigned integer arithmetic in C") | |
6132 | (description | |
6133 | "This library provides portable Arbitrary-precision unsigned integer | |
6134 | arithmetic in C, for calculating with large numbers. Basic arithmetic (+, -, | |
6135 | *, /, %) and bitwise operations (&, |, ^. <<, >>) plus increments, decrements | |
6136 | and comparisons are supported.") | |
6137 | (license license:unlicense)))) | |
6138 | ||
b26e4f26 EB |
6139 | (define-public sundials |
6140 | (package | |
6141 | (name "sundials") | |
6142 | (version "3.1.1") | |
6143 | (source | |
6144 | (origin | |
6145 | (method url-fetch) | |
6146 | (uri (string-append "https://computation.llnl.gov/projects/sundials/download/" | |
6147 | "sundials-" version ".tar.gz")) | |
6148 | (sha256 | |
6149 | (base32 | |
6150 | "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2")))) | |
6151 | (build-system cmake-build-system) | |
6152 | (native-inputs | |
6153 | `(("python" ,python-2))) ;for tests; syntax incompatible with python 3 | |
6154 | (inputs | |
6155 | `(("fortran" ,gfortran) ;for fcmix | |
6156 | ("blas" ,openblas) | |
6157 | ("suitesparse" ,suitesparse))) ;TODO: Add hypre | |
6158 | (arguments | |
6159 | `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON" | |
6160 | "-DEXAMPLES_ENABLE_CXX:BOOL=ON" | |
6161 | "-DEXAMPLES_ENABLE_F77:BOOL=ON" | |
6162 | "-DEXAMPLES_ENABLE_F90:BOOL=ON" | |
6163 | "-DEXAMPLES_INSTALL:BOOL=OFF" | |
6164 | ||
6165 | "-DFCMIX_ENABLE:BOOL=ON" | |
6166 | ||
6167 | "-DKLU_ENABLE:BOOL=ON" | |
6168 | ,(string-append "-DKLU_INCLUDE_DIR=" | |
6169 | (assoc-ref %build-inputs "suitesparse") | |
6170 | "/include") | |
6171 | ,(string-append "-DKLU_LIBRARY_DIR=" | |
6172 | (assoc-ref %build-inputs "suitesparse") | |
6173 | "/lib")))) | |
6174 | (home-page "https://computation.llnl.gov/projects/sundials") | |
6175 | (synopsis "Suite of nonlinear and differential/algebraic equation solvers") | |
6176 | (description "SUNDIALS is a family of software packages implemented with | |
6177 | the goal of providing robust time integrators and nonlinear solvers that can | |
6178 | easily be incorporated into existing simulation codes.") | |
6179 | (license license:bsd-3))) | |
6180 | ||
6181 | (define-public sundials-openmpi | |
6182 | (package (inherit sundials) | |
6183 | (name "sundials-openmpi") | |
6184 | (inputs | |
6185 | `(("mpi" ,openmpi) | |
6186 | ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI | |
6187 | ,@(package-inputs sundials))) | |
6188 | (arguments | |
6189 | (substitute-keyword-arguments (package-arguments sundials) | |
6190 | ((#:configure-flags flags '()) | |
6191 | `(cons* "-DMPI_ENABLE:BOOL=ON" | |
6192 | "-DPETSC_ENABLE:BOOL=ON" | |
6193 | (string-append "-DPETSC_INCLUDE_DIR=" | |
6194 | (assoc-ref %build-inputs "petsc") | |
6195 | "/include") | |
6196 | (string-append "-DPETSC_LIBRARY_DIR=" | |
6197 | (assoc-ref %build-inputs "petsc") | |
6198 | "/lib") | |
6199 | ,flags)) | |
6200 | ((#:phases phases '%standard-phases) | |
6201 | `(modify-phases ,phases | |
bbe46a4a EB |
6202 | (add-before 'check 'mpi-setup |
6203 | ,%openmpi-setup))))) | |
b26e4f26 | 6204 | (synopsis "SUNDIALS with OpenMPI support"))) |
a6b9ebc2 EB |
6205 | |
6206 | (define-public combinatorial-blas | |
6207 | (package | |
6208 | (name "combinatorial-blas") | |
6209 | (version "1.6.2") | |
6210 | (source | |
6211 | (origin | |
6212 | (method url-fetch) | |
6213 | (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/" | |
6214 | "CombBLAS_beta_" | |
6215 | (match (string-split version #\.) | |
6216 | ((major minor patch) | |
6217 | (string-append major minor "_" patch))) ;e.g. "16_2" | |
6218 | ".tgz")) | |
6219 | (sha256 | |
6220 | (base32 | |
6221 | "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a")) | |
6222 | (patches (search-patches "combinatorial-blas-awpm.patch" | |
6223 | "combinatorial-blas-io-fix.patch")))) | |
6224 | (build-system cmake-build-system) | |
6225 | (inputs | |
6226 | `(("mpi" ,openmpi) | |
6227 | ("test-data" ,(origin | |
6228 | (method url-fetch) | |
6229 | (uri (string-append "https://people.eecs.berkeley.edu/~aydin/" | |
6230 | "CombBLAS_FILES/testdata_combblas1.6.1.tgz")) | |
6231 | (sha256 | |
6232 | (base32 | |
6233 | "01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87")))))) | |
6234 | (arguments | |
6235 | `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES" | |
6236 | "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL") | |
6237 | #:parallel-tests? #f ;tests use 'mpiexec -n4' | |
6238 | #:phases | |
6239 | (modify-phases %standard-phases | |
6240 | (add-before 'check 'mpi-setup | |
6241 | ,%openmpi-setup) | |
6242 | (add-before 'check 'test-setup | |
6243 | (lambda* (#:key inputs #:allow-other-keys) | |
6244 | (setenv "OMP_NUM_THREADS" "2") | |
6245 | (invoke "tar" "xf" (assoc-ref inputs "test-data"))))))) | |
6246 | (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/") | |
6247 | (synopsis "Linear algebra primitives for graph analytics") | |
6248 | (description "The Combinatorial BLAS (CombBLAS) is an extensible | |
6249 | distributed-memory parallel graph library offering a small but powerful set of | |
6250 | linear algebra primitives specifically targeting graph analytics.") | |
6251 | (license (list | |
6252 | license:gpl2+ ;include/psort/(funnel|sort)*.h | |
6253 | license:x11 ;usort and psort | |
6254 | license:bsd-3)))) ;CombBLAS and MersenneTwister.h | |
3847d1f2 RW |
6255 | |
6256 | (define-public dune-common | |
6257 | (package | |
6258 | (name "dune-common") | |
6ca2d7da | 6259 | (version "2.7.0") |
3847d1f2 RW |
6260 | (source |
6261 | (origin | |
6262 | (method url-fetch) | |
6263 | (uri (string-append "https://dune-project.org/download/" | |
6264 | version "/dune-common-" version ".tar.gz")) | |
6265 | (sha256 | |
6266 | (base32 | |
6ca2d7da | 6267 | "140q1zh44cr5yrjwg4b5ga803rkqv55vk30l2cqm29aklj1wb0rw")))) |
3847d1f2 RW |
6268 | (build-system cmake-build-system) |
6269 | (arguments | |
6270 | `(#:phases | |
6271 | (modify-phases %standard-phases | |
6272 | (add-after 'build 'build-tests | |
6273 | (lambda* (#:key make-flags #:allow-other-keys) | |
393dc1cc | 6274 | (apply invoke "make" "build_tests" make-flags)))))) |
3847d1f2 RW |
6275 | (inputs |
6276 | `(("gmp" ,gmp) | |
6277 | ("metis" ,metis) | |
3847d1f2 RW |
6278 | ("openblas" ,openblas) |
6279 | ("python" ,python) | |
6280 | ("superlu" ,superlu))) | |
6281 | (native-inputs | |
6282 | `(("gfortran" ,gfortran) | |
6283 | ("pkg-config" ,pkg-config))) | |
6284 | (home-page "https://dune-project.org/") | |
6285 | (synopsis "Distributed and Unified Numerics Environment") | |
6286 | (description "DUNE, the Distributed and Unified Numerics Environment is a | |
6287 | modular toolbox for solving @dfn{partial differential equations} (PDEs) with | |
6288 | grid-based methods. It supports the easy implementation of methods like | |
6289 | @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite | |
6290 | Differences} (FD).") | |
6291 | ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2. | |
6292 | (license license:gpl2))) | |
242dbd8e RW |
6293 | |
6294 | (define-public dune-geometry | |
6295 | (package | |
6296 | (name "dune-geometry") | |
6ca2d7da | 6297 | (version "2.7.0") |
242dbd8e RW |
6298 | (source |
6299 | (origin | |
6300 | (method url-fetch) | |
6301 | (uri (string-append "https://dune-project.org/download/" | |
6302 | version "/dune-geometry-" version ".tar.gz")) | |
6303 | (sha256 | |
6304 | (base32 | |
6ca2d7da | 6305 | "1cicvlwbyyw76npicnblxckyvhbfn3ip8isydiv3hlrlz8zcg5nr")))) |
242dbd8e RW |
6306 | (build-system cmake-build-system) |
6307 | (arguments | |
6308 | `(#:phases | |
6309 | (modify-phases %standard-phases | |
6310 | (add-after 'build 'build-tests | |
6311 | (lambda* (#:key make-flags #:allow-other-keys) | |
6312 | (apply invoke "make" "build_tests" make-flags)))))) | |
6313 | (inputs | |
6314 | `(("dune-common" ,dune-common) | |
242dbd8e RW |
6315 | ;; Optional |
6316 | ("openblas" ,openblas) | |
6317 | ("gmp" ,gmp) | |
6318 | ("python" ,python))) | |
6319 | (native-inputs | |
6320 | `(("gfortran" ,gfortran) | |
6321 | ("pkg-config" ,pkg-config))) | |
6322 | (home-page "https://dune-project.org/") | |
6323 | (synopsis "Distributed and Unified Numerics Environment") | |
6324 | (description "DUNE, the Distributed and Unified Numerics Environment is a | |
6325 | modular toolbox for solving @dfn{partial differential equations} (PDEs) with | |
6326 | grid-based methods. It supports the easy implementation of methods like | |
6327 | @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite | |
6328 | Differences} (FD). | |
6329 | ||
6330 | This package contains the basic DUNE geometry classes.") | |
6331 | ;; GPL version 2 with "runtime exception" | |
6332 | (license license:gpl2))) | |
ef6e69fd | 6333 | |
07ebb75d FG |
6334 | (define-public dune-uggrid |
6335 | (package | |
6336 | (name "dune-uggrid") | |
6ca2d7da | 6337 | (version "2.7.0") |
07ebb75d FG |
6338 | (source |
6339 | (origin | |
6ca2d7da FG |
6340 | (method git-fetch) |
6341 | (uri (git-reference | |
6342 | (url "https://gitlab.dune-project.org/staging/dune-uggrid.git") | |
6343 | (commit (string-append "v" version)))) | |
6344 | (file-name (git-file-name name version)) | |
07ebb75d FG |
6345 | (sha256 |
6346 | (base32 | |
6ca2d7da | 6347 | "192miqgmfj6jwk969gydzpbv9ki7jg5nky3ydnrwa2nq29b5xkh0")))) |
07ebb75d FG |
6348 | (build-system cmake-build-system) |
6349 | (arguments | |
6350 | `(#:phases | |
6351 | (modify-phases %standard-phases | |
6352 | (add-after 'build 'build-tests | |
6353 | (lambda* (#:key make-flags #:allow-other-keys) | |
6354 | (apply invoke "make" "build_tests" make-flags)))))) | |
6355 | (inputs | |
393dc1cc | 6356 | `(("dune-common" ,dune-common))) |
07ebb75d FG |
6357 | (native-inputs |
6358 | `(("gfortran" ,gfortran) | |
6359 | ("pkg-config" ,pkg-config))) | |
6360 | (home-page "https://dune-project.org/") | |
6361 | (synopsis "Distributed and Unified Numerics Environment") | |
6362 | (description "DUNE, the Distributed and Unified Numerics Environment is a | |
6363 | modular toolbox for solving @dfn{partial differential equations} (PDEs) with | |
6364 | grid-based methods. It supports the easy implementation of methods like | |
6365 | @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite | |
6366 | Differences} (FD). | |
6367 | ||
6368 | This package contains the DUNE UG grid classes.") | |
6369 | (license license:lgpl2.1))) | |
6370 | ||
ef6e69fd RW |
6371 | (define-public dune-grid |
6372 | (package | |
6373 | (name "dune-grid") | |
6ca2d7da | 6374 | (version "2.7.0") |
ef6e69fd RW |
6375 | (source |
6376 | (origin | |
6377 | (method url-fetch) | |
6378 | (uri (string-append "https://dune-project.org/download/" | |
6379 | version "/dune-grid-" version ".tar.gz")) | |
6380 | (sha256 | |
6381 | (base32 | |
6ca2d7da | 6382 | "17fjz30qazjgl11sryyxnw9klai4yz1ji4bs68013xcxc5hdv27s")))) |
ef6e69fd RW |
6383 | (build-system cmake-build-system) |
6384 | (arguments | |
6385 | `(#:phases | |
6386 | (modify-phases %standard-phases | |
6387 | (add-after 'build 'build-tests | |
6388 | (lambda* (#:key make-flags #:allow-other-keys) | |
393dc1cc | 6389 | (apply invoke "make" "build_tests" make-flags)))))) |
ef6e69fd RW |
6390 | (inputs |
6391 | `(("dune-common" ,dune-common) | |
6392 | ("dune-geometry" ,dune-geometry) | |
6393 | ("gmp" ,gmp) | |
6394 | ("metis" ,metis) | |
6395 | ("openblas" ,openblas) | |
ef6e69fd | 6396 | ("python" ,python))) |
07ebb75d FG |
6397 | (propagated-inputs |
6398 | `(("dune-uggrid" ,dune-uggrid))) | |
ef6e69fd RW |
6399 | (native-inputs |
6400 | `(("gfortran" ,gfortran) | |
6401 | ("pkg-config" ,pkg-config))) | |
6402 | (home-page "https://dune-project.org/") | |
6403 | (synopsis "Distributed and Unified Numerics Environment") | |
6404 | (description "DUNE, the Distributed and Unified Numerics Environment is a | |
6405 | modular toolbox for solving @dfn{partial differential equations} (PDEs) with | |
6406 | grid-based methods. It supports the easy implementation of methods like | |
6407 | @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite | |
6408 | Differences} (FD). | |
6409 | ||
6410 | This package contains the basic DUNE grid classes.") | |
6411 | ;; GPL version 2 with "runtime exception" | |
6412 | (license license:gpl2))) | |
ea51d357 RW |
6413 | |
6414 | (define-public dune-istl | |
6415 | (package | |
6416 | (name "dune-istl") | |
6ca2d7da | 6417 | (version "2.7.0") |
ea51d357 RW |
6418 | (source |
6419 | (origin | |
6420 | (method url-fetch) | |
6421 | (uri (string-append "https://dune-project.org/download/" | |
6422 | version "/dune-istl-" version ".tar.gz")) | |
6423 | (sha256 | |
6424 | (base32 | |
6ca2d7da FG |
6425 | "0gl3wgz5rs6sb4m83440ny45sbx7z7lnbi3gx6r9nm3rvy5j33f9")) |
6426 | (patches (search-patches "dune-istl-2.7-fix-non-mpi-tests.patch")))) | |
ea51d357 RW |
6427 | (build-system cmake-build-system) |
6428 | (arguments | |
6429 | `(#:phases | |
6430 | (modify-phases %standard-phases | |
f7cbf403 MB |
6431 | ;; XXX: istl/test/matrixtest.cc includes <fenv.h> and fails to find |
6432 | ;; the stdlib types when the gfortran header is used. Remove gfortran | |
6433 | ;; from CPLUS_INCLUDE_PATH as a workaround. | |
6434 | (add-after 'set-paths 'hide-gfortran | |
6435 | (lambda* (#:key inputs #:allow-other-keys) | |
6436 | (let ((gfortran (assoc-ref inputs "gfortran"))) | |
6437 | (setenv "CPLUS_INCLUDE_PATH" | |
6438 | (string-join | |
6439 | (delete (string-append gfortran "/include/c++") | |
6440 | (string-split (getenv "CPLUS_INCLUDE_PATH") #\:)) | |
6441 | ":")) | |
6442 | #t))) | |
ea51d357 RW |
6443 | (add-after 'build 'build-tests |
6444 | (lambda* (#:key make-flags #:allow-other-keys) | |
393dc1cc | 6445 | (apply invoke "make" "build_tests" make-flags)))))) |
ea51d357 RW |
6446 | (inputs |
6447 | `(("dune-common" ,dune-common) | |
ea51d357 RW |
6448 | ;; Optional |
6449 | ("metis" ,metis) | |
0a703c04 | 6450 | ("suitesparse" ,suitesparse) |
ea51d357 RW |
6451 | ("superlu" ,superlu) |
6452 | ("openblas" ,openblas) | |
6453 | ("gmp" ,gmp) | |
6454 | ("python" ,python))) | |
6455 | (native-inputs | |
6456 | `(("gfortran" ,gfortran) | |
6457 | ("pkg-config" ,pkg-config))) | |
6458 | (home-page "https://dune-project.org/") | |
6459 | (synopsis "Distributed and Unified Numerics Environment") | |
6460 | (description "DUNE, the Distributed and Unified Numerics Environment is a | |
6461 | modular toolbox for solving @dfn{partial differential equations} (PDEs) with | |
6462 | grid-based methods. | |
6463 | ||
6464 | This is the iterative solver template library which provides generic sparse | |
6465 | matrix/vector classes and a variety of solvers based on these classes. A | |
6466 | special feature is the use of templates to exploit the recursive block | |
6467 | structure of finite element matrices at compile time. Available solvers | |
6468 | include Krylov methods, (block-) incomplete decompositions and | |
6469 | aggregation-based algebraic multigrid.") | |
6470 | ;; GPL version 2 with "runtime exception" | |
6471 | (license license:gpl2))) | |
5a70aa7d RW |
6472 | |
6473 | (define-public dune-localfunctions | |
6474 | (package | |
6475 | (name "dune-localfunctions") | |
6ca2d7da | 6476 | (version "2.7.0") |
5a70aa7d RW |
6477 | (source |
6478 | (origin | |
6479 | (method url-fetch) | |
6480 | (uri (string-append "https://dune-project.org/download/" | |
6481 | version "/dune-localfunctions-" version ".tar.gz")) | |
6482 | (sha256 | |
6483 | (base32 | |
6ca2d7da | 6484 | "1yih59h6vngii696bx1c2vil02lriij4kz0nc583mjn9kiaqxfqd")))) |
5a70aa7d RW |
6485 | (build-system cmake-build-system) |
6486 | (arguments | |
6487 | `(#:phases | |
6488 | (modify-phases %standard-phases | |
109bf6a0 MB |
6489 | ;; XXX: localfunctions/test/lagrangeshapefunctiontest.cc includes <fenv.h> |
6490 | ;; and fails to find the stdlib types when the gfortran header is used. | |
6491 | ;; Hide gfortran from CPLUS_INCLUDE_PATH to ensure we get the GCC header. | |
6492 | (add-after 'set-paths 'hide-gfortran | |
6493 | (lambda* (#:key inputs #:allow-other-keys) | |
6494 | (let ((gfortran (assoc-ref inputs "gfortran"))) | |
6495 | (setenv "CPLUS_INCLUDE_PATH" | |
6496 | (string-join | |
6497 | (delete (string-append gfortran "/include/c++") | |
6498 | (string-split (getenv "CPLUS_INCLUDE_PATH") #\:)) | |
6499 | ":")) | |
6500 | #t))) | |
5a70aa7d RW |
6501 | (add-after 'build 'build-tests |
6502 | (lambda* (#:key make-flags #:allow-other-keys) | |
6503 | (apply invoke "make" "build_tests" make-flags)))))) | |
6504 | (inputs | |
6505 | `(("dune-common" ,dune-common) | |
6506 | ("dune-geometry" ,dune-geometry) | |
5a70aa7d RW |
6507 | ;; Optional |
6508 | ("metis" ,metis) | |
6509 | ("superlu" ,superlu) | |
6510 | ("gmp" ,gmp))) | |
6511 | (native-inputs | |
6512 | `(("gfortran" ,gfortran) | |
6513 | ("pkg-config" ,pkg-config))) | |
6514 | (home-page "https://dune-project.org/") | |
6515 | (synopsis "Distributed and Unified Numerics Environment") ; TODO | |
6516 | (description "This DUNE module provides interface and implementation for | |
6517 | shape functions defined on the DUNE reference elements. In addition to the | |
6518 | shape function, interpolation operators and special keys are provided which | |
6519 | can be used to assemble global function spaces on finite-element grids. | |
6520 | ||
6521 | This package provides an interface and implementation for shape functions | |
6522 | defined on the DUNE reference elements. In addition to the shape function, | |
6523 | interpolation operators and special keys are provided which can be used to | |
6524 | assemble global function spaces on finite-element grids.") | |
6525 | ;; GPL version 2 with "runtime exception" | |
6526 | (license license:gpl2))) | |
ab03d899 RW |
6527 | |
6528 | (define-public dune-alugrid | |
6529 | (package | |
6530 | (name "dune-alugrid") | |
6ca2d7da | 6531 | (version "2.7.0-git-81d35682") |
ab03d899 RW |
6532 | (source |
6533 | (origin | |
6ca2d7da FG |
6534 | (method git-fetch) |
6535 | (uri (git-reference | |
6536 | (url "https://gitlab.dune-project.org/extensions/dune-alugrid.git") | |
6537 | (commit "81d356827c84454b971937db02c02b90bbcd7fe5"))) | |
6538 | (file-name (git-file-name name version)) | |
ab03d899 RW |
6539 | (sha256 |
6540 | (base32 | |
6ca2d7da | 6541 | "0z54lwfp53prcrs94k8gwh047l9z642jll3l56xlyfr69z0b2zz1")))) |
ab03d899 RW |
6542 | (build-system cmake-build-system) |
6543 | (arguments | |
a669f6e2 | 6544 | `(#:phases |
ab03d899 RW |
6545 | (modify-phases %standard-phases |
6546 | (add-after 'unpack 'patch-include | |
6547 | (lambda _ | |
6548 | (substitute* "dune/alugrid/test/test-alugrid.cc" | |
6549 | (("doc/grids/gridfactory/testgrids") | |
6550 | "doc/dune-grid/grids/gridfactory/testgrids")) | |
6551 | #t)) | |
6552 | (add-after 'build 'build-tests | |
6553 | (lambda* (#:key inputs make-flags #:allow-other-keys) | |
6554 | (setenv "CPLUS_INCLUDE_PATH" | |
97149c57 | 6555 | (string-append (assoc-ref inputs "dune-grid") "/share")) |
393dc1cc | 6556 | (apply invoke "make" "build_tests" make-flags)))))) |
ab03d899 RW |
6557 | (inputs |
6558 | `(("dune-common" ,dune-common) | |
6559 | ("dune-geometry" ,dune-geometry) | |
6560 | ("dune-grid" ,dune-grid) | |
ab03d899 RW |
6561 | ;; Optional |
6562 | ("metis" ,metis) | |
6563 | ("openblas" ,openblas) | |
6564 | ("python" ,python) | |
6565 | ("superlu" ,superlu) | |
6566 | ("gmp" ,gmp) | |
6567 | ("zlib" ,zlib))) | |
6568 | (native-inputs | |
6569 | `(("gfortran" ,gfortran) | |
6570 | ("pkg-config" ,pkg-config))) | |
6571 | (home-page "https://dune-project.org/") | |
6572 | (synopsis "Distributed and Unified Numerics Environment") | |
6573 | (description "ALUGrid is an adaptive, loadbalancing, unstructured | |
6574 | implementation of the DUNE grid interface supporting either simplices or | |
6575 | cubes.") | |
6576 | (license license:gpl2+))) | |
0e50630f | 6577 | |
f1f9466e FG |
6578 | (define-public dune-subgrid |
6579 | (package | |
6580 | (name "dune-subgrid") | |
6ca2d7da | 6581 | (version "2.7.0-git-2103a363") |
f1f9466e FG |
6582 | (source |
6583 | (origin | |
6584 | (method git-fetch) | |
6585 | (uri (git-reference | |
6586 | (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid") | |
6ca2d7da | 6587 | (commit "2103a363f32e8d7b60e66eee7ddecf969f6cf762"))) |
f1f9466e FG |
6588 | (file-name (git-file-name name version)) |
6589 | (sha256 | |
6590 | (base32 | |
6ca2d7da | 6591 | "1wsjlypd3835c3arqjkw836cxx5q67zy447wa65q634lf6f6v9ia")))) |
f1f9466e FG |
6592 | (build-system cmake-build-system) |
6593 | (arguments | |
6594 | `(#:phases | |
6595 | (modify-phases %standard-phases | |
6596 | (add-after 'build 'build-tests | |
6597 | (lambda* (#:key make-flags #:allow-other-keys) | |
393dc1cc | 6598 | (apply invoke "make" "build_tests" make-flags)))))) |
f1f9466e FG |
6599 | (inputs |
6600 | `(("dune-common" ,dune-common) | |
6601 | ("dune-geometry" ,dune-geometry) | |
6602 | ("dune-grid" ,dune-grid) | |
f1f9466e FG |
6603 | ;; Optional |
6604 | ("metis" ,metis) | |
6605 | ("openblas" ,openblas) | |
6606 | ("gmp" ,gmp))) | |
6607 | (native-inputs | |
6608 | `(("gfortran" ,gfortran) | |
6609 | ("pkg-config" ,pkg-config))) | |
6610 | (home-page "http://numerik.mi.fu-berlin.de/dune-subgrid/index.php") | |
6611 | (synopsis "Distributed and Unified Numerics Environment") | |
48b0d9c0 | 6612 | (description "The dune-subgrid module marks elements of |
f1f9466e FG |
6613 | another hierarchical dune grid. The set of marked elements can then be |
6614 | accessed as a hierarchical dune grid in its own right. Dune-Subgrid | |
6615 | provides the full grid interface including adaptive mesh refinement.") | |
6616 | (license license:gpl2+))) | |
6617 | ||
0e50630f RW |
6618 | (define-public dune-typetree |
6619 | (package | |
6620 | (name "dune-typetree") | |
6ca2d7da | 6621 | (version "2.7.0") |
0e50630f RW |
6622 | (source |
6623 | (origin | |
6624 | (method git-fetch) | |
6625 | (uri (git-reference | |
6626 | (url "https://gitlab.dune-project.org/staging/dune-typetree.git") | |
6627 | (commit (string-append "v" version)))) | |
6628 | (file-name (git-file-name name version)) | |
6629 | (sha256 | |
6630 | (base32 | |
6ca2d7da | 6631 | "1rhv25yg0q1hw50c8wlfqhgwrjl4mh62zq9v14ilwgzbfgxmpiy7")))) |
0e50630f RW |
6632 | (build-system cmake-build-system) |
6633 | (arguments | |
6634 | `(#:phases | |
6635 | (modify-phases %standard-phases | |
6636 | (add-after 'build 'build-tests | |
6637 | (lambda* (#:key make-flags #:allow-other-keys) | |
6638 | (apply invoke "make" "build_tests" make-flags)))))) | |
6639 | (inputs | |
6640 | `(("dune-common" ,dune-common) | |
0e50630f RW |
6641 | ;; Optional |
6642 | ("openblas" ,openblas) | |
6643 | ("python" ,python) | |
6644 | ("metis" ,metis) | |
6645 | ("superlu" ,superlu) | |
6646 | ("gmp" ,gmp))) | |
6647 | (native-inputs | |
6648 | `(("gfortran" ,gfortran) | |
6649 | ("pkg-config" ,pkg-config))) | |
6650 | (home-page "https://dune-project.org/") | |
6651 | (synopsis "Distributed and Unified Numerics Environment") | |
6652 | (description "TypeTree is a template library for constructing and | |
6653 | operating on statically typed trees of objects.") | |
6654 | ;; Either GPL version 2 with "runtime exception" or LGPLv3+. | |
6655 | (license (list license:lgpl3+ license:gpl2)))) | |
85b9371c RW |
6656 | |
6657 | (define-public dune-functions | |
6658 | (package | |
6659 | (name "dune-functions") | |
6ca2d7da | 6660 | (version "2.7.0") |
85b9371c RW |
6661 | (source |
6662 | (origin | |
6663 | (method git-fetch) | |
6664 | (uri (git-reference | |
6665 | (url "https://gitlab.dune-project.org/staging/dune-functions.git") | |
6666 | (commit (string-append "v" version)))) | |
6667 | (file-name (git-file-name name version)) | |
6668 | (sha256 | |
6669 | (base32 | |
6ca2d7da | 6670 | "1na4gcih0kin37ksj2xj07ds04v7zx53pjdhm1hzy55jjfqdjk8h")))) |
85b9371c | 6671 | (build-system cmake-build-system) |
07ebb75d FG |
6672 | (arguments |
6673 | `(#:phases | |
6674 | (modify-phases %standard-phases | |
6675 | (add-after 'unpack 'disable-failing-tests | |
6676 | (lambda _ | |
6677 | (setenv "ARGS" | |
6678 | ;; unable to load GMSH file in this test | |
6679 | "--exclude-regex gridviewfunctionspacebasistest") | |
6680 | #t)) | |
6681 | (add-after 'build 'build-tests | |
6682 | (lambda* (#:key make-flags #:allow-other-keys) | |
393dc1cc | 6683 | (apply invoke "make" "build_tests" make-flags)))))) |
85b9371c RW |
6684 | (inputs |
6685 | `(("dune-common" ,dune-common) | |
6686 | ("dune-istl" ,dune-istl) | |
6687 | ("dune-localfunctions" ,dune-localfunctions) | |
6688 | ("dune-grid" ,dune-grid) | |
6689 | ("dune-geometry" ,dune-geometry) | |
6690 | ("dune-typetree" ,dune-typetree) | |
85b9371c RW |
6691 | ("openblas" ,openblas) |
6692 | ("metis" ,metis) | |
6693 | ("python" ,python) | |
6694 | ("superlu" ,superlu) | |
6695 | ("gmp" ,gmp))) | |
6696 | (native-inputs | |
6697 | `(("gfortran" ,gfortran) | |
6698 | ("pkg-config" ,pkg-config))) | |
6699 | (home-page "https://dune-project.org/") | |
6700 | (synopsis "Distributed and Unified Numerics Environment") | |
6701 | (description "The dune-functions module provides an abstraction layer for | |
6702 | global finite element functions. Its two main concepts are functions | |
6703 | implemented as callable objects, and bases of finite element spaces.") | |
6704 | ;; Either GPL version 2 with "runtime exception" or LGPLv3+. | |
6705 | (license (list license:lgpl3+ license:gpl2)))) | |
4714b00e RW |
6706 | |
6707 | (define-public dune-pdelab | |
6708 | (package | |
6709 | (name "dune-pdelab") | |
6ca2d7da | 6710 | (version "2.7.0-git-476fe437") |
4714b00e RW |
6711 | (source |
6712 | (origin | |
6713 | (method git-fetch) | |
6714 | (uri (git-reference | |
6715 | (url "https://gitlab.dune-project.org/pdelab/dune-pdelab") | |
6ca2d7da | 6716 | (commit "476fe43763fa6f459c5e4658e2a2b4b5582db834"))) |
4714b00e RW |
6717 | (file-name (git-file-name name version)) |
6718 | (sha256 | |
6719 | (base32 | |
6ca2d7da | 6720 | "0cs36piqzn6rq0j2ih3ab3q3q9yg199wk72k5qi86pkzh7i7fdn1")))) |
4714b00e RW |
6721 | (build-system cmake-build-system) |
6722 | (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled | |
6723 | (inputs | |
6724 | `(("dune-common" ,dune-common) | |
6725 | ("dune-istl" ,dune-istl) | |
6726 | ("dune-localfunctions" ,dune-localfunctions) | |
6727 | ("dune-geometry" ,dune-geometry) | |
6728 | ("dune-grid" ,dune-grid) | |
6729 | ("dune-typetree" ,dune-typetree) | |
6730 | ("dune-functions" ,dune-functions) | |
4714b00e RW |
6731 | ;; Optional |
6732 | ("openblas" ,openblas) | |
6733 | ("eigen" ,eigen) | |
6734 | ("metis" ,metis) | |
6735 | ("python" ,python) | |
6736 | ("superlu" ,superlu) | |
6737 | ("gmp" ,gmp))) | |
6738 | (native-inputs | |
6739 | `(("gfortran" ,gfortran) | |
6740 | ("pkg-config" ,pkg-config))) | |
6741 | (home-page "https://dune-project.org/") | |
6742 | (synopsis "Differential equations solver toolbox") | |
6743 | (description "PDELab is a partial differential equations solver toolbox | |
6744 | built on top of DUNE, the Distributed and Unified Numerics Environment.") | |
6745 | ;; Either GPL version 2 with "runtime exception" or LGPLv3+. | |
6746 | (license (list license:lgpl3+ license:gpl2)))) | |
413f6126 | 6747 | |
6ceb7716 FG |
6748 | (define add-openmpi-to-dune-package |
6749 | (let ((dune-package? | |
6750 | (lambda (p) (string-prefix? "dune-" (package-name p))))) | |
6751 | (package-mapping | |
6752 | (lambda (p) | |
6753 | (if (dune-package? p) | |
6754 | (package (inherit p) | |
6755 | (name (string-append (package-name p) "-openmpi")) | |
6756 | (inputs `(,@(package-inputs p) | |
6757 | ("openmpi" ,openmpi))) | |
6758 | (arguments | |
6759 | (substitute-keyword-arguments (package-arguments p) | |
6760 | ((#:phases phases '%standard-phases) | |
6761 | `(modify-phases ,phases | |
6762 | (add-before 'check 'mpi-setup | |
6763 | ,%openmpi-setup))))) | |
6764 | (synopsis (string-append (package-synopsis p) " (with MPI support)"))) | |
6765 | p)) | |
6766 | (negate dune-package?)))) | |
6767 | ||
6768 | (define-public dune-common-openmpi | |
6769 | (add-openmpi-to-dune-package dune-common)) | |
6770 | ||
6771 | (define-public dune-geometry-openmpi | |
6772 | (add-openmpi-to-dune-package dune-geometry)) | |
6773 | ||
6774 | (define-public dune-istl-openmpi | |
6775 | (add-openmpi-to-dune-package dune-istl)) | |
6776 | ||
6777 | (define-public dune-typetree-openmpi | |
6778 | (add-openmpi-to-dune-package dune-typetree)) | |
6779 | ||
6780 | (define-public dune-uggrid-openmpi | |
6781 | (add-openmpi-to-dune-package dune-uggrid)) | |
6782 | ||
6783 | (define-public dune-grid-openmpi | |
6784 | (add-openmpi-to-dune-package dune-grid)) | |
6785 | ||
6786 | (define-public dune-alugrid-openmpi | |
6787 | (add-openmpi-to-dune-package dune-alugrid)) | |
6788 | ||
6789 | (define-public dune-subgrid-openmpi | |
6790 | (add-openmpi-to-dune-package dune-subgrid)) | |
6791 | ||
6792 | (define-public dune-localfunctions-openmpi | |
6793 | (add-openmpi-to-dune-package dune-localfunctions)) | |
6794 | ||
6795 | (define-public dune-functions-openmpi | |
6796 | (add-openmpi-to-dune-package dune-functions)) | |
6797 | ||
6798 | (define-public dune-pdelab-openmpi | |
6799 | (add-openmpi-to-dune-package dune-pdelab)) | |
6800 | ||
413f6126 AI |
6801 | (define-public mlucas |
6802 | (package | |
6803 | (name "mlucas") | |
6804 | (version "18") | |
6805 | (source | |
6806 | (origin | |
6807 | (method url-fetch) | |
6808 | (uri (string-append | |
6809 | "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz")) | |
6810 | (sha256 | |
a36efdbc | 6811 | (base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447")))) |
413f6126 AI |
6812 | (build-system gnu-build-system) |
6813 | (inputs | |
6814 | `(("python2" ,python-2))) | |
6815 | (arguments | |
a36efdbc | 6816 | `(#:tests? #f ; no tests |
413f6126 AI |
6817 | #:phases |
6818 | (modify-phases %standard-phases | |
6819 | (replace 'configure | |
6820 | (lambda _ | |
6821 | (chdir "src") | |
6822 | (call-with-output-file "Makefile" | |
6823 | (lambda (port) | |
6824 | (format port "CC = gcc | |
6825 | CFLAGS = -O3 ~a -DUSE_THREADS | |
6826 | LDLIBS = -lm -lpthread -lrt | |
6827 | Mlucas: $(addsuffix .o,$(basename $(wildcard *.c))) | |
6828 | " | |
6829 | ,(let ((system (or (%current-target-system) | |
6830 | (%current-system)))) | |
6831 | (cond | |
6832 | ((string-prefix? "x86_64" system) "-DUSE_SSE2") | |
6833 | (else "")))))) | |
6834 | #t)) | |
6835 | (replace 'install | |
6836 | (lambda* (#:key outputs #:allow-other-keys) | |
6837 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) | |
6838 | (install-file "Mlucas" bin) | |
6839 | (install-file "primenet.py" bin)) | |
6840 | #t))))) | |
6841 | (home-page "https://www.mersenne.org") | |
6842 | (synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client") | |
6843 | (description "Mlucas performs Lucas-Lehmer primality testing of Mersenne | |
6844 | numbers in search of a world-record prime. You may use it to test any | |
6845 | suitable number as you wish, but it is preferable that you do so in a | |
6846 | coordinated fashion, as part of the Great Internet Mersenne Prime | |
6847 | Search (GIMPS). Mlucas also includes a simple Python script for assignment | |
6848 | management via the GIMPS project's Primenet server.") | |
6849 | (license license:gpl2+))) | |
6f8c4195 NG |
6850 | |
6851 | (define-public nauty | |
6852 | (package | |
6853 | (name "nauty") | |
e02984ac | 6854 | (version "2.7r3") |
4b01930f NG |
6855 | (source |
6856 | (origin | |
6857 | (method url-fetch) | |
6858 | (uri (string-append | |
6859 | "https://pallini.di.uniroma1.it/" | |
6860 | "nauty" (string-join (string-split version #\.) "") ".tar.gz")) | |
6861 | (sha256 | |
e02984ac | 6862 | (base32 "1hl81gpf3xjf809w04jczvilq1ixy9ch1qrax8a7lgx52svna1jg")))) |
6f8c4195 NG |
6863 | (build-system gnu-build-system) |
6864 | (outputs '("out" "lib")) | |
6865 | (arguments | |
6866 | `(#:test-target "checks" | |
4b01930f | 6867 | #:configure-flags '("--enable-generic") ;prevent -march-native |
6f8c4195 NG |
6868 | #:phases |
6869 | (modify-phases %standard-phases | |
6870 | ;; Default make target does not build all available | |
6871 | ;; executables. Create them now. | |
6872 | (add-after 'build 'build-extra-programs | |
6873 | (lambda _ | |
6874 | (for-each (lambda (target) (invoke "make" target)) | |
6875 | '("blisstog" "bliss2dre" "checks6" "sumlines")) | |
6876 | #t)) | |
6877 | ;; Upstream does not provide any install target. | |
6878 | (replace 'install | |
6879 | (lambda* (#:key outputs #:allow-other-keys) | |
6880 | (let* ((out (assoc-ref outputs "out")) | |
6881 | (lib-output (assoc-ref outputs "lib")) | |
6882 | (bin (string-append out "/bin")) | |
6883 | (doc (string-append out "/share/doc/nauty/")) | |
6884 | (include (string-append lib-output "/include/nauty")) | |
6885 | (lib (string-append lib-output "/lib/nauty"))) | |
6886 | (for-each (lambda (f) (install-file f bin)) | |
4b01930f NG |
6887 | '("addedgeg" "amtog" "assembleg" "biplabg" "blisstog" |
6888 | "bliss2dre" "catg" "checks6" "complg" "converseg" | |
6889 | "copyg" "countg" "cubhamg" "deledgeg" "delptg" | |
6890 | "directg" "dreadnaut" "dretodot" "dretog" "genbg" | |
6f8c4195 NG |
6891 | "genbgL" "geng" "genquarticg" "genrang" "genspecialg" |
6892 | "gentourng" "gentreeg" "hamheuristic" "labelg" | |
6893 | "linegraphg" "listg" "multig" "newedgeg" "pickg" | |
6894 | "planarg" "ranlabg" "shortg" "showg" "subdivideg" | |
4b01930f NG |
6895 | "sumlines" "twohamg" "underlyingg" "vcolg" |
6896 | "watercluster2" "NRswitchg")) | |
6f8c4195 NG |
6897 | (for-each (lambda (f) (install-file f include)) |
6898 | (find-files "." "\\.h$")) | |
6899 | (for-each (lambda (f) (install-file f lib)) | |
6900 | (find-files "." "\\.a$")) | |
6901 | (for-each (lambda (f) (install-file f doc)) | |
6902 | (append '("formats.txt" "README" "schreier.txt") | |
6903 | (find-files "." "\\.pdf$"))))))))) | |
6904 | (inputs | |
6905 | `(("gmp" ,gmp))) ;for sumlines | |
6906 | (home-page "https://pallini.di.uniroma1.it/") | |
6907 | (synopsis "Library for graph automorphisms") | |
6908 | (description "@code{nauty} (No AUTomorphisms, Yes?) is a set of | |
6909 | procedures for computing automorphism groups of graphs and digraphs. | |
6910 | ||
6911 | @code{nauty} computes graph information in the form of a set of | |
6912 | generators, the size of the group, and the orbits of the group; it can | |
6913 | also produce a canonical label. The @code{nauty} suite is written in | |
6914 | C and comes with a command-line interface, a collection of | |
6915 | command-line tools, and an Application Programming Interface (API). | |
6916 | ||
6917 | This package provides the static libraries required to run programs | |
6918 | compiled against the nauty library.") | |
6919 | (license license:asl2.0))) | |
26433471 AE |
6920 | |
6921 | (define-public ppl | |
6922 | (package | |
6923 | (name "ppl") | |
6924 | (version "1.2") | |
6925 | (source | |
6926 | (origin | |
6927 | (method url-fetch) | |
6928 | (uri (string-append "https://www.bugseng.com/products/ppl/download/" | |
6929 | "ftp/releases/" version | |
6930 | "/ppl-" version ".tar.gz")) | |
6931 | (sha256 | |
6932 | (base32 | |
6933 | "1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb")))) | |
6934 | (build-system gnu-build-system) | |
6935 | (native-inputs | |
1628d57b | 6936 | `(("m4" ,m4))) |
26433471 AE |
6937 | (inputs |
6938 | `(("glpk" ,glpk) | |
1628d57b | 6939 | ("gmp" ,gmp))) |
26433471 AE |
6940 | (home-page "https://www.bugseng.com/parma-polyhedra-library") |
6941 | (synopsis | |
6942 | "Parma Polyhedra Library for computations with polyhedra") | |
6943 | (description | |
6944 | "The Parma Polyhedra Library (PPL) provides numerical abstractions | |
6945 | especially targeted at applications in the field of analysis and | |
6946 | verification of complex systems. These abstractions include convex | |
6947 | polyhedra, defined as the intersection of a finite number of (open or | |
6948 | closed) halfspaces, each described by a linear inequality (strict or | |
6949 | non-strict) with rational coefficients; some special classes of polyhedra | |
6950 | shapes that offer interesting complexity/precision tradeoffs; and grids | |
6951 | which represent regularly spaced points that satisfy a set of linear | |
6952 | congruence relations. The library also supports finite powersets and | |
6953 | products of (any kind of) polyhedra and grids, a mixed integer linear | |
6954 | programming problem solver using an exact-arithmetic version of the simplex | |
6955 | algorithm, a parametric integer programming solver, and primitives for | |
6956 | termination analysis via the automatic synthesis of linear ranking | |
6957 | functions.") | |
6958 | (license license:gpl3+))) | |
4cb5d251 SS |
6959 | |
6960 | (define-public speedcrunch | |
6961 | (package | |
6962 | (name "speedcrunch") | |
6963 | (version "0.12.0") | |
6964 | (source | |
6965 | (origin | |
6966 | (method git-fetch) | |
6967 | (uri (git-reference | |
6968 | (url "https://bitbucket.org/heldercorreia/speedcrunch.git") | |
6969 | (commit (string-append "release-" version)))) | |
6970 | (file-name (git-file-name name version)) | |
6971 | (sha256 | |
6972 | (base32 | |
6973 | "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk")))) | |
6974 | (build-system cmake-build-system) | |
ea0a5107 | 6975 | (inputs `(("qtbase" ,qtbase-5))) |
4cb5d251 SS |
6976 | (native-inputs `(("qttools" ,qttools))) |
6977 | (arguments | |
6978 | `(#:phases | |
6979 | (modify-phases %standard-phases | |
6980 | (add-after 'unpack 'chdir-to-src | |
6981 | (lambda _ (chdir "src") #t))))) | |
6982 | (synopsis "High-precision scientific calculator") | |
6983 | (description | |
6984 | "SpeedCrunch is a high-precision scientific calculator. It features a | |
6985 | syntax-highlighted scrollable display and is designed to be fully used via | |
6986 | keyboard. Some distinctive features are auto-completion of functions and | |
6987 | variables, a formula book, and quick insertion of constants from various | |
6988 | fields of knowledge.") | |
80fafdba | 6989 | (home-page "https://speedcrunch.org/") |
4cb5d251 SS |
6990 | (license license:gpl2+))) |
6991 | ||
3b7828cc RS |
6992 | (define-public minisat |
6993 | ;; This is the last commit which is available upstream, no | |
6994 | ;; release happened since 2010. | |
6995 | (let ((commit "37dc6c67e2af26379d88ce349eb9c4c6160e8543") | |
6996 | (revision "1")) | |
6997 | (package | |
6998 | (name "minisat") | |
6999 | (version (string-append "2.2.0-" revision "." (string-take commit 7))) | |
7000 | (source | |
7001 | (origin | |
7002 | (method git-fetch) | |
7003 | (uri (git-reference | |
b0e7b699 | 7004 | (url "https://github.com/niklasso/minisat") |
3b7828cc RS |
7005 | (commit commit))) |
7006 | (file-name (string-append name "-" version "-checkout")) | |
7007 | (sha256 | |
7008 | (base32 | |
7009 | "091hf3qkm197s5r7xcr3m07xsdwyz2rqk1hc9kj0hn13imz09irq")) | |
7010 | (patches | |
7011 | (search-patches "minisat-friend-declaration.patch" | |
7012 | "minisat-install.patch")))) | |
7013 | (build-system gnu-build-system) | |
7014 | (arguments | |
7015 | '(#:make-flags (list (string-append "prefix=" %output)) | |
7016 | #:tests? #f ;no check target | |
7017 | #:phases | |
7018 | (modify-phases %standard-phases | |
7019 | (delete 'configure)))) | |
7020 | (inputs | |
7021 | `(("zlib:static" ,zlib "static") | |
7022 | ("zlib" ,zlib))) | |
7023 | (synopsis | |
7024 | "Small, yet efficient, SAT solver") | |
7025 | (description | |
7026 | "MiniSat is a minimalistic, open-source SAT solver, developed to help | |
7027 | researchers and developers alike to get started on SAT.") | |
7028 | (home-page | |
7029 | "http://minisat.se/MiniSat.html") | |
7030 | (license license:expat)))) | |
70c98efa VK |
7031 | |
7032 | (define-public libqalculate | |
7033 | (package | |
7034 | (name "libqalculate") | |
ea1778eb | 7035 | (version "3.19.0") |
70c98efa VK |
7036 | (source |
7037 | (origin | |
7038 | (method git-fetch) | |
7039 | (uri (git-reference | |
7040 | (url "https://github.com/Qalculate/libqalculate/") | |
7041 | (commit (string-append "v" version)))) | |
7042 | (file-name (git-file-name name version)) | |
7043 | (sha256 | |
ea1778eb | 7044 | (base32 "1w44407wb552q21dz4m2nwwdi8b9hzjb2w1l3ffsikzqckc7wbyj")) |
9b3c231e VK |
7045 | (patches |
7046 | (search-patches "libqalculate-3.8.0-libcurl-ssl-fix.patch")))) | |
70c98efa VK |
7047 | (build-system gnu-build-system) |
7048 | (native-inputs | |
7049 | `(("pkg-config" ,pkg-config) | |
7050 | ("gettext" ,gettext-minimal) | |
7051 | ("intltool" ,intltool) | |
7052 | ("automake" ,automake) | |
7053 | ("autoconf" ,autoconf) | |
7054 | ("libtool" ,libtool) | |
7055 | ("doxygen" ,doxygen) | |
7056 | ("file" ,file))) | |
7057 | (inputs | |
7058 | `(("gmp" ,gmp) | |
7059 | ("mpfr" ,mpfr) | |
7060 | ("libxml2" ,libxml2) | |
7061 | ("curl" ,curl) | |
7062 | ("icu4c" ,icu4c) | |
7063 | ("gnuplot" ,gnuplot) | |
7064 | ("readline" ,readline) | |
7065 | ("libiconv" ,libiconv))) | |
7066 | (arguments | |
7067 | `(#:phases | |
7068 | (modify-phases %standard-phases | |
7069 | (add-before 'bootstrap 'setenv | |
7070 | ;; Prevent the autogen.sh script to carry out the configure | |
7071 | ;; script, which has not yet been patched to replace /bin/sh. | |
7072 | (lambda _ | |
7073 | (setenv "NOCONFIGURE" "TRUE") | |
7074 | #t))))) | |
7075 | (home-page "https://qalculate.github.io/") | |
7076 | (synopsis "Multi-purpose cli desktop calculator and library") | |
7077 | (description | |
7078 | "Libqalculate is a multi-purpose cli desktop calculator and library. | |
7079 | It provides basic and advanced functionality. Features include customizable | |
7080 | functions, unit calculations, and conversions, physical constants, symbolic | |
7081 | calculations (including integrals and equations), arbitrary precision, | |
67e2e171 | 7082 | uncertainty propagation, interval arithmetic, plotting and a user-friendly |
70c98efa VK |
7083 | cli.") |
7084 | (license license:gpl2+))) | |
72c71d24 VK |
7085 | |
7086 | (define-public qalculate-gtk | |
7087 | (package | |
7088 | (name "qalculate-gtk") | |
b7363347 | 7089 | (version "3.19.0") |
72c71d24 VK |
7090 | (source |
7091 | (origin | |
7092 | (method git-fetch) | |
7093 | (uri (git-reference | |
7094 | (url "https://github.com/Qalculate/qalculate-gtk/") | |
7095 | (commit (string-append "v" version)))) | |
7096 | (file-name (git-file-name name version)) | |
7097 | (sha256 | |
b7363347 | 7098 | (base32 "1nrx7gp6f1yalbdda1gb97azhbr4xclq2xf08vvbvsk8jfd6fd2v")))) |
72c71d24 VK |
7099 | (build-system glib-or-gtk-build-system) |
7100 | (native-inputs | |
7101 | `(("pkg-config" ,pkg-config) | |
7102 | ("intltool" ,intltool) | |
7103 | ("automake" ,automake) | |
7104 | ("autoconf" ,autoconf) | |
7105 | ("libtool" ,libtool) | |
7106 | ("file" ,file))) | |
7107 | (inputs | |
7108 | `(("gmp" ,gmp) | |
7109 | ("mpfr" ,mpfr) | |
7110 | ("libqalculate" ,libqalculate) | |
7111 | ("libxml2" ,libxml2) | |
7112 | ("glib" ,glib) | |
7113 | ("gtk+" ,gtk+))) | |
7114 | (arguments | |
7115 | `(#:phases | |
7116 | (modify-phases %standard-phases | |
7117 | (add-before 'bootstrap 'setenv | |
7118 | ;; Prevent the autogen.sh script to carry out the configure | |
7119 | ;; script, which has not yet been patched to replace /bin/sh. | |
7120 | (lambda _ | |
7121 | (setenv "NOCONFIGURE" "TRUE") | |
72c71d24 VK |
7122 | #t))))) |
7123 | (home-page "https://qalculate.github.io/") | |
7124 | (synopsis "Multi-purpose graphical desktop calculator") | |
7125 | (description | |
7126 | "Qalculate-gtk is the GTK frontend for libqalculate. It is a | |
7127 | multi-purpose GUI desktop calculator. It provides basic and advanced | |
7128 | functionality. Features include customizable functions, unit calculations, | |
7129 | and conversions, physical constants, symbolic calculations (including | |
1480d212 | 7130 | integrals and equations), arbitrary precision, uncertainty propagation, |
72c71d24 VK |
7131 | interval arithmetic, plotting.") |
7132 | (license license:gpl2+))) | |
d2e531fa PP |
7133 | |
7134 | (define-public numdiff | |
7135 | (package | |
7136 | (name "numdiff") | |
7137 | (version "5.9.0") | |
7138 | (source | |
7139 | (origin | |
7140 | (method url-fetch) | |
7141 | (uri (string-append "mirror://savannah/numdiff/numdiff-" | |
7142 | version ".tar.gz")) | |
7143 | (sha256 | |
7144 | (base32 | |
7145 | "1vzmjh8mhwwysn4x4m2vif7q2k8i19x8azq7pzmkwwj4g48lla47")))) | |
7146 | (build-system gnu-build-system) | |
7147 | (arguments | |
7148 | '(#:tests? #f ; There are no tests. | |
7149 | #:phases | |
7150 | (modify-phases %standard-phases | |
7151 | (add-before 'compress-documentation 'delete-precompressed-info-file | |
7152 | (lambda _ | |
7153 | (delete-file (string-append (assoc-ref %outputs "out") | |
7154 | "/share/info/numdiff.info.gz")) | |
7155 | #t))))) | |
7156 | (home-page "https://nongnu.org/numdiff/") | |
7157 | (synopsis "Compare files with numeric fields") | |
7158 | (description | |
7159 | "Numdiff compares files line by line and field by field, ignoring small | |
7160 | numeric differences and differences in numeric formats.") | |
7161 | (license license:gpl3+))) | |
c9b3627d JL |
7162 | |
7163 | (define-public why3 | |
7164 | (package | |
7165 | (name "why3") | |
26dd2321 | 7166 | (version "1.4.0") |
c9b3627d | 7167 | (source (origin |
26dd2321 JL |
7168 | (method git-fetch) |
7169 | (uri (git-reference | |
7170 | (url "https://gitlab.inria.fr/why3/why3") | |
7171 | (commit version))) | |
7172 | (file-name (git-file-name name version)) | |
c9b3627d JL |
7173 | (sha256 |
7174 | (base32 | |
26dd2321 | 7175 | "0pfsiddnk26f384wbazfpgzh1n1ibf3xq101q74mxvczi7z0a791")))) |
c9b3627d JL |
7176 | (build-system ocaml-build-system) |
7177 | (native-inputs | |
26dd2321 JL |
7178 | `(("autoconf" ,autoconf) |
7179 | ("automake" ,automake) | |
7180 | ("coq" ,coq) | |
c9b3627d JL |
7181 | ("ocaml" ,ocaml) |
7182 | ("which" ,which))) | |
7183 | (propagated-inputs | |
7184 | `(("camlzip" ,camlzip) | |
7185 | ("ocaml-graph" ,ocaml-graph) | |
7186 | ("ocaml-menhir" ,ocaml-menhir) | |
7187 | ("ocaml-num" ,ocaml-num) | |
7188 | ("ocaml-zarith" ,ocaml-zarith))) | |
7189 | (inputs | |
7190 | `(("coq-flocq" ,coq-flocq) | |
7191 | ("emacs-minimal" ,emacs-minimal) | |
7192 | ("zlib" ,zlib))) | |
7193 | (arguments | |
7194 | `(#:phases | |
7195 | (modify-phases %standard-phases | |
26dd2321 | 7196 | (add-before 'configure 'bootstrap |
c9b3627d | 7197 | (lambda _ |
26dd2321 | 7198 | (invoke "./autogen.sh") |
c9b3627d JL |
7199 | (setenv "CONFIG_SHELL" (which "sh")) |
7200 | (substitute* "configure" | |
26dd2321 | 7201 | (("#! /bin/sh") (string-append "#!" (which "sh"))) |
c9b3627d | 7202 | ;; find ocaml-num in the correct directory |
6e6769dd JL |
7203 | (("\\$DIR/nums.cma") "$DIR/num.cma") |
7204 | (("\\$DIR/num.cmi") "$DIR/core/num.cmi")) | |
c9b3627d JL |
7205 | #t)) |
7206 | (add-after 'configure 'fix-makefile | |
7207 | (lambda _ | |
7208 | (substitute* "Makefile" | |
7209 | ;; find ocaml-num in the correct directory | |
7210 | (("site-lib/num") "site-lib")) | |
7211 | #t)) | |
7212 | (add-after 'install 'install-lib | |
7213 | (lambda _ | |
7214 | (invoke "make" "byte") | |
7215 | (invoke "make" "install-lib") | |
7216 | #t))))) | |
7217 | (home-page "http://why3.lri.fr") | |
7218 | (synopsis "Deductive program verification") | |
7219 | (description "Why3 provides a language for specification and programming, | |
7220 | called WhyML, and relies on external theorem provers, both automated and | |
7221 | interactive, to discharge verification conditions. Why3 comes with a standard | |
7222 | library of logical theories (integer and real arithmetic, Boolean operations, | |
7223 | sets and maps, etc.) and basic programming data structures (arrays, queues, | |
7224 | hash tables, etc.). A user can write WhyML programs directly and get | |
7225 | correct-by-construction OCaml programs through an automated extraction | |
7226 | mechanism. WhyML is also used as an intermediate language for the verification | |
7227 | of C, Java, or Ada programs.") | |
7228 | (license license:lgpl2.1))) | |
b94bc3ea JL |
7229 | |
7230 | (define-public frama-c | |
7231 | (package | |
7232 | (name "frama-c") | |
6516e88f | 7233 | (version "23.1") |
b94bc3ea JL |
7234 | (source (origin |
7235 | (method url-fetch) | |
7236 | (uri (string-append "http://frama-c.com/download/frama-c-" | |
6516e88f | 7237 | version "-Vanadium.tar.gz")) |
b94bc3ea JL |
7238 | (sha256 |
7239 | (base32 | |
6516e88f | 7240 | "1rgkq9sg436smw005ag0j6y3xryhjn18a07m5wjfrfp0s1438nnj")))) |
b94bc3ea JL |
7241 | (build-system ocaml-build-system) |
7242 | (arguments | |
7243 | `(#:tests? #f; no test target in Makefile | |
7244 | #:phases | |
7245 | (modify-phases %standard-phases | |
7246 | (add-before 'configure 'export-shell | |
7247 | (lambda* (#:key inputs #:allow-other-keys) | |
bc64d955 LC |
7248 | (setenv "CONFIG_SHELL" |
7249 | (search-input-file inputs "/bin/sh"))))))) | |
b94bc3ea JL |
7250 | (inputs |
7251 | `(("gmp" ,gmp))) | |
7252 | (propagated-inputs | |
7253 | `(("ocaml-biniou" ,ocaml-biniou) | |
7254 | ("ocaml-easy-format" ,ocaml-easy-format) | |
7255 | ("ocaml-graph" ,ocaml-graph) | |
7256 | ("ocaml-yojson" ,ocaml-yojson) | |
7257 | ("ocaml-zarith" ,ocaml-zarith) | |
7258 | ("why3" ,why3))) | |
7259 | (native-search-paths | |
7260 | (list (search-path-specification | |
7261 | (variable "FRAMAC_SHARE") | |
7262 | (files '("share/frama-c")) | |
7263 | (separator #f)) | |
7264 | (search-path-specification | |
7265 | (variable "FRAMAC_LIB") | |
7266 | (files '("lib/frama-c")) | |
7267 | (separator #f)))) | |
7268 | (home-page "http://frama-c.com") | |
7269 | (synopsis "C source code analysis platform") | |
7270 | (description "Frama-C is an extensible and collaborative platform dedicated | |
7271 | to source-code analysis of C software. The Frama-C analyzers assist you in | |
7272 | various source-code-related activities, from the navigation through unfamiliar | |
7273 | projects up to the certification of critical software.") | |
7274 | (license license:lgpl2.1+))) | |
68ce40ca IG |
7275 | |
7276 | (define-public blitz | |
7277 | (package | |
7278 | (name "blitz") | |
7279 | (version "1.0.2") | |
7280 | (source | |
7281 | (origin | |
7282 | (method git-fetch) | |
7283 | (uri (git-reference | |
7284 | (url "https://github.com/blitzpp/blitz") | |
7285 | (commit version))) | |
7286 | (file-name (git-file-name name version)) | |
7287 | (sha256 | |
7288 | (base32 "0c88gc72j3zggyk4yrrip6i0v7xkx97l140vpy3xhxs2i7xy1461")))) | |
7289 | (build-system cmake-build-system) | |
7290 | (arguments | |
7291 | `(#:configure-flags '("-DBUILD_DOC=ON" | |
7292 | "-DBUILD_TESTING=ON") | |
7293 | ;; The default "check" target also includes examples and benchmarks. | |
7294 | #:test-target "check-testsuite" | |
7295 | #:phases | |
7296 | (modify-phases %standard-phases | |
7297 | (add-after 'build 'build-doc | |
7298 | (lambda _ | |
7299 | (invoke "make" "-j" (number->string (parallel-job-count)) | |
7300 | "blitz-doc")))))) | |
7301 | (native-inputs | |
7302 | `(("python" ,python) | |
7303 | ("texinfo" ,texinfo))) | |
7304 | (synopsis "C++ template class library for multidimensional arrays") | |
7305 | (description "Blitz++ is a C++ template class library that provides | |
7306 | high-performance multidimensional array containers for scientific computing.") | |
7307 | (home-page "https://github.com/blitzpp/blitz") | |
7308 | (license (list license:artistic2.0 | |
7309 | license:bsd-3 | |
7310 | license:lgpl3+)))) | |
a9bc8a25 LC |
7311 | |
7312 | (define-public fxdiv | |
7313 | ;; There is currently no tag in this repo. | |
7314 | (let ((commit "63058eff77e11aa15bf531df5dd34395ec3017c8") | |
7315 | (version "0.0") | |
7316 | (revision "1")) | |
7317 | (package | |
7318 | (name "fxdiv") | |
7319 | (version (git-version version revision commit)) | |
7320 | (home-page "https://github.com/Maratyszcza/FXdiv") | |
7321 | (source (origin | |
7322 | (method git-fetch) | |
7323 | (uri (git-reference (url home-page) (commit commit))) | |
7324 | (file-name (git-file-name name version)) | |
7325 | (sha256 | |
7326 | (base32 | |
7327 | "0zwzh8gmbx4m6b18s5nf13b0dk5yjkd1fs8f421bl7fz5f9gjd9f")) | |
7328 | (patches (search-patches "fxdiv-system-libraries.patch")))) | |
7329 | (build-system cmake-build-system) | |
7330 | (inputs | |
7331 | `(("googletest" ,googletest) | |
7332 | ("googlebenchmark" ,googlebenchmark))) | |
7333 | (synopsis | |
7334 | "C++ library for division via fixed-point multiplication by inverse") | |
7335 | (description | |
7336 | "On modern CPUs and GPUs, integer division is several times slower than | |
7337 | multiplication. FXdiv implements an algorithm to replace an integer division | |
7338 | with a multiplication and two shifts. This algorithm improves performance | |
7339 | when an application performs repeated divisions by the same divisor.") | |
7340 | (license license:expat)))) | |
1daa6627 LC |
7341 | |
7342 | (define-public fp16 | |
7343 | ;; There is currently no tag in this repo. | |
7344 | (let ((commit "0a92994d729ff76a58f692d3028ca1b64b145d91") | |
7345 | (version "0.0") | |
7346 | (revision "1")) | |
7347 | (package | |
7348 | (name "fp16") | |
7349 | (version (git-version version revision commit)) | |
7350 | (home-page "https://github.com/Maratyszcza/FP16") | |
7351 | (source (origin | |
7352 | (method git-fetch) | |
7353 | (uri (git-reference (url home-page) (commit commit))) | |
7354 | (file-name (git-file-name name version)) | |
7355 | (sha256 | |
7356 | (base32 | |
7357 | "05mm4vrxsac35hjf5djif9r6rdxj9ippg97ia3p6q6b8lrp7srwv")) | |
7358 | (patches (search-patches "fp16-system-libraries.patch")))) | |
7359 | (build-system cmake-build-system) | |
3cdb16cb LC |
7360 | (arguments |
7361 | `(#:imported-modules ((guix build python-build-system) | |
7362 | ,@%cmake-build-system-modules) | |
7363 | #:modules (((guix build python-build-system) | |
7364 | #:select (site-packages)) | |
7365 | (guix build cmake-build-system) | |
7366 | (guix build utils)) | |
7367 | #:phases (modify-phases %standard-phases | |
7368 | (add-after 'install 'move-python-files | |
7369 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
7370 | ;; Python files get installed to $includedir (!). | |
7371 | ;; Move them to the usual Python site directory. | |
7372 | (let* ((out (assoc-ref outputs "out")) | |
7373 | (include (string-append out "/include")) | |
7374 | (site (site-packages inputs outputs)) | |
7375 | (target (string-append site "/fp16"))) | |
7376 | (mkdir-p target) | |
7377 | (for-each (lambda (file) | |
7378 | (rename-file file | |
7379 | (string-append target "/" | |
7380 | (basename | |
7381 | file)))) | |
7382 | (find-files include "\\.py$")))))))) | |
1daa6627 LC |
7383 | (native-inputs |
7384 | `(("python-wrapper" ,python-wrapper))) | |
7385 | (inputs | |
7386 | `(("psimd" ,psimd) | |
7387 | ("googletest" ,googletest) | |
7388 | ("googlebenchmark" ,googlebenchmark))) | |
7389 | (synopsis "C++ library for half-precision floating point formats") | |
7390 | (description | |
7391 | "This header-only C++ library implements conversion to and from | |
7392 | half-precision floating point formats.") | |
7393 | (license license:expat)))) | |
64d4bc08 PG |
7394 | |
7395 | (define-public optizelle | |
7396 | (let ((commit "ed4160b5287518448caeb34789d92dc6a0b7e2cc")) | |
7397 | (package | |
7398 | (name "optizelle") | |
7399 | (version (git-version "1.3.0" "0" commit)) | |
7400 | (source | |
7401 | (origin | |
7402 | (method git-fetch) | |
7403 | (uri (git-reference | |
7404 | (url "https://github.com/OptimoJoe/Optizelle") | |
7405 | (commit commit))) | |
7406 | (file-name (git-file-name "optizelle" commit)) | |
7407 | (sha256 | |
7408 | (base32 | |
7409 | "0rjrs5sdmd33a9f4xm8an7p0953aa0bxsmr4hs3ss1aad9k181vq")) | |
7410 | (modules '((guix build utils))) | |
7411 | (snippet | |
7412 | '(begin | |
7413 | ;; Reduce the stopping tolerance in one test so that the | |
7414 | ;; convergence check returns the correct stopping | |
7415 | ;; condition. | |
7416 | (substitute* | |
7417 | "src/unit/linear_algebra/tcg_loss_of_orthogonality.cpp" | |
7418 | (("1e-13") "5e-14")) | |
7419 | ;; Skip one set of python tests. See | |
7420 | ;; https://github.com/OptimoJoe/Optizelle/issues/2. | |
7421 | (substitute* | |
7422 | "src/examples/inequality_scaling/CMakeLists.txt" | |
7423 | (("add_unit(.*)\\$\\{interfaces\\}(.*)$" all middle end) | |
7424 | (string-append "add_unit" middle "\"cpp\"" end))) | |
7425 | ;; Install the licence for Optizelle, without also | |
7426 | ;; including the licences for the dependencies. | |
7427 | (substitute* "licenses/CMakeLists.txt" | |
7428 | (("file.*package.*$" all) | |
7429 | (string-append "# " all)) | |
7430 | ((".*[^l].[.]txt\\)\n") "") | |
7431 | (("add_license.*\"\n") "")) | |
7432 | #t)))) | |
7433 | (build-system cmake-build-system) | |
7434 | (arguments | |
7435 | `(#:imported-modules ((guix build python-build-system) | |
7436 | ,@%cmake-build-system-modules) | |
7437 | #:modules (((guix build python-build-system) #:select | |
7438 | (python-version)) | |
7439 | (guix build cmake-build-system) | |
7440 | (guix build utils)) | |
7441 | #:configure-flags `("-DCMAKE_CXX_FLAGS:STRING=-pthread" | |
7442 | "-DENABLE_CPP_UNIT:BOOL=ON" | |
7443 | "-DENABLE_CPP_EXAMPLES:BOOL=ON" | |
7444 | "-DENABLE_PYTHON:BOOL=ON" | |
7445 | "-DENABLE_PYTHON_UNIT:BOOL=ON" | |
7446 | "-DENABLE_PYTHON_EXAMPLES:BOOL=ON" | |
7447 | ,(string-append "-DBLAS_LIBRARY:FILEPATH=" | |
7448 | (assoc-ref %build-inputs | |
7449 | "blas/lapack") | |
7450 | "/lib/libopenblas.so") | |
7451 | ,(string-append "-DLAPACK_LIBRARY:FILEPATH=" | |
7452 | (assoc-ref %build-inputs | |
7453 | "fortran:lib") | |
7454 | "/lib/libgfortran.so;" | |
7455 | (assoc-ref %build-inputs | |
7456 | "fortran:lib") | |
7457 | "/lib/libquadmath.so")) | |
7458 | #:phases | |
7459 | (modify-phases %standard-phases | |
7460 | (add-after 'unpack 'set-numpy-path ; Needed for the unit tests. | |
7461 | (lambda* (#:key inputs #:allow-other-keys) | |
7462 | (let* ((pyver (python-version (assoc-ref inputs "python"))) | |
7463 | (npdir (string-append (assoc-ref inputs "numpy") | |
7464 | "/lib/python" pyver | |
7465 | "/site-packages"))) | |
7466 | (substitute* "src/cmake/Modules/Optizelle.cmake" | |
7467 | (("PYTHONPATH=") | |
7468 | (string-append "LD_LIBRARY_PATH=$ENV{LIBRARY_PATH};" | |
7469 | "PYTHONPATH=" npdir ":")))))) | |
7470 | (delete 'install-license-files)))) ; LICENSE.txt is installed. | |
7471 | (inputs | |
7472 | `(("blas/lapack" ,openblas) | |
7473 | ("fortran:lib" ,gfortran "lib") | |
7474 | ("jsoncpp" ,jsoncpp) | |
7475 | ("numpy" ,python-numpy) | |
7476 | ("python" ,python))) | |
7477 | (native-inputs | |
7478 | `(("fortran" ,gfortran) | |
7479 | ("pkg-config" ,pkg-config))) | |
7480 | (home-page "https://www.optimojoe.com/products/optizelle/") | |
7481 | (synopsis "Mathematical optimization library") | |
7482 | (description "@code{optizelle} is a software library designed to | |
7483 | solve nonlinear optimization problems. Four types of problem are | |
7484 | considered: unconstrained, equality constrained, inequality | |
7485 | constrained and constrained. Constraints may be applied as values of | |
7486 | functions or sets of partial differential equations (PDEs). | |
7487 | ||
7488 | Solution algorithms such as the preconditioned nonlinear conjugate | |
7489 | gradient method, sequential quadratic programming (SQP) and the | |
7490 | primal-dual interior-point method are made available. Interfaces are | |
7491 | provided for applications written in C++ and Python. Parallel | |
7492 | computation is supported via MPI.") | |
7493 | (license license:bsd-2)))) |