Commit | Line | Data |
---|---|---|
8f8b2451 | 1 | ;;; GNU Guix --- Functional package management for GNU |
26433471 | 2 | ;;; Copyright © 2013, 2014, 2015, 2016, 2019 Andreas Enge <andreas@enge.fr> |
da95c817 | 3 | ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org> |
a53d6719 | 4 | ;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org> |
aa2e83cc | 5 | ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Eric Bavier <bavier@posteo.net> |
df354a77 | 6 | ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch> |
182d6311 | 7 | ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org> |
0aad198e | 8 | ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net> |
32158110 | 9 | ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com> |
df129041 | 10 | ;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org> |
0ef54303 | 11 | ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il> |
45147b0c | 12 | ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de> |
ec8c7e47 | 13 | ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> |
ab5f3f21 | 14 | ;;; Copyright © 2016, 2018 Kei Kebreau <kkebreau@posteo.net> |
59a07504 | 15 | ;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org> |
d7cff656 | 16 | ;;; Copyright © 2016 Leo Famulari <leo@famulari.name> |
2fd26d05 | 17 | ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be> |
f1cc312e | 18 | ;;; Copyright © 2017, 2018, 2019, 2020 Paul Garlick <pgarlick@tourbillion-technology.com> |
47956fa0 | 19 | ;;; Copyright © 2017 ng0 <ng0@n0.is> |
ba1be533 | 20 | ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com> |
d109b1e8 | 21 | ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org> |
b18b9d20 | 22 | ;;; Copyright © 2017, 2019 Arun Isaac <arunisaac@systemreboot.net> |
98a5cd51 | 23 | ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> |
dc7d6d4e | 24 | ;;; Copyright © 2017 Dave Love <me@fx@gnu.org> |
3bc74090 | 25 | ;;; Copyright © 2018, 2019 Jan Nieuwenhuizen <janneke@gnu.org> |
41835f94 | 26 | ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> |
910deec6 | 27 | ;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com> |
07254d8b | 28 | ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com> |
560acf25 | 29 | ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> |
daa6036f | 30 | ;;; Copyright © 2018 Eric Brown <brown@fastmail.com> |
564cf93f | 31 | ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu> |
a3143063 | 32 | ;;; Copyright © 2018 Amin Bandali <mab@gnu.org> |
6f8c4195 | 33 | ;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr> |
4cb5d251 | 34 | ;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com> |
3b7828cc | 35 | ;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net> |
8f8b2451 AE |
36 | ;;; |
37 | ;;; This file is part of GNU Guix. | |
38 | ;;; | |
39 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
40 | ;;; under the terms of the GNU General Public License as published by | |
41 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
42 | ;;; your option) any later version. | |
43 | ;;; | |
44 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
45 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
46 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
47 | ;;; GNU General Public License for more details. | |
48 | ;;; | |
49 | ;;; You should have received a copy of the GNU General Public License | |
50 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
51 | ||
52 | (define-module (gnu packages maths) | |
ec322be2 | 53 | #:use-module (ice-9 regex) |
a6b9ebc2 | 54 | #:use-module (ice-9 match) |
8f8b2451 | 55 | #:use-module (gnu packages) |
b5b73a82 | 56 | #:use-module ((guix licenses) #:prefix license:) |
8f8b2451 AE |
57 | #:use-module (guix packages) |
58 | #:use-module (guix download) | |
54052a54 | 59 | #:use-module (guix git-download) |
0e2672ae | 60 | #:use-module (guix utils) |
fa574a6d | 61 | #:use-module ((guix build utils) #:select (alist-replace)) |
da95c817 | 62 | #:use-module (guix build-system cmake) |
c9dfa3c7 | 63 | #:use-module (guix build-system gnu) |
560acf25 | 64 | #:use-module (guix build-system python) |
63e07468 | 65 | #:use-module (guix build-system ruby) |
3de01d3f | 66 | #:use-module (gnu packages algebra) |
ab5f3f21 | 67 | #:use-module (gnu packages audio) |
5143517c | 68 | #:use-module (gnu packages autotools) |
fa574a6d | 69 | #:use-module (gnu packages base) |
3de01d3f | 70 | #:use-module (gnu packages bison) |
a17d4564 | 71 | #:use-module (gnu packages boost) |
e73b49fb | 72 | #:use-module (gnu packages check) |
3de01d3f | 73 | #:use-module (gnu packages cmake) |
c9dfa3c7 | 74 | #:use-module (gnu packages compression) |
668c06ac | 75 | #:use-module (gnu packages curl) |
b7b27a8f | 76 | #:use-module (gnu packages cyrus-sasl) |
8a0dd289 | 77 | #:use-module (gnu packages dbm) |
528bb464 | 78 | #:use-module (gnu packages documentation) |
57e544e8 | 79 | #:use-module (gnu packages elf) |
3de01d3f | 80 | #:use-module (gnu packages flex) |
668c06ac | 81 | #:use-module (gnu packages fltk) |
f3929800 | 82 | #:use-module (gnu packages fontutils) |
1dba6407 | 83 | #:use-module (gnu packages gettext) |
da95c817 | 84 | #:use-module (gnu packages gcc) |
73fed4f8 | 85 | #:use-module (gnu packages gd) |
668c06ac | 86 | #:use-module (gnu packages ghostscript) |
889187a4 | 87 | #:use-module (gnu packages graphviz) |
f3929800 | 88 | #:use-module (gnu packages gtk) |
45147b0c | 89 | #:use-module (gnu packages image) |
2fd26d05 | 90 | #:use-module (gnu packages java) |
668c06ac | 91 | #:use-module (gnu packages less) |
8731e527 | 92 | #:use-module (gnu packages lisp) |
ab5f3f21 | 93 | #:use-module (gnu packages linux) |
bc3a2e35 | 94 | #:use-module (gnu packages logging) |
6e64766a | 95 | #:use-module (gnu packages lua) |
5698b8b8 | 96 | #:use-module (gnu packages gnome) |
1b39a196 | 97 | #:use-module (gnu packages guile) |
668c06ac JD |
98 | #:use-module (gnu packages xorg) |
99 | #:use-module (gnu packages gl) | |
9f913401 | 100 | #:use-module (gnu packages imagemagick) |
8731e527 | 101 | #:use-module (gnu packages m4) |
d8c7eeb9 | 102 | #:use-module (gnu packages mpi) |
b92eee75 | 103 | #:use-module (gnu packages multiprecision) |
528bb464 | 104 | #:use-module (gnu packages netpbm) |
bd3d71cb | 105 | #:use-module (gnu packages onc-rpc) |
668c06ac | 106 | #:use-module (gnu packages pcre) |
5698b8b8 | 107 | #:use-module (gnu packages popt) |
c9dfa3c7 AE |
108 | #:use-module (gnu packages perl) |
109 | #:use-module (gnu packages pkg-config) | |
ab5f3f21 | 110 | #:use-module (gnu packages pulseaudio) |
da95c817 | 111 | #:use-module (gnu packages python) |
589e3f4e | 112 | #:use-module (gnu packages python-web) |
44d10b1f | 113 | #:use-module (gnu packages python-xyz) |
5b05dce7 | 114 | #:use-module (gnu packages qt) |
c9dfa3c7 | 115 | #:use-module (gnu packages readline) |
63e07468 | 116 | #:use-module (gnu packages ruby) |
2742f87e | 117 | #:use-module (gnu packages tbb) |
479c4273 | 118 | #:use-module (gnu packages scheme) |
b7194849 | 119 | #:use-module (gnu packages shells) |
df354a77 | 120 | #:use-module (gnu packages tcl) |
668c06ac | 121 | #:use-module (gnu packages texinfo) |
8f9ac901 | 122 | #:use-module (gnu packages tex) |
b7b27a8f | 123 | #:use-module (gnu packages tls) |
5b05dce7 | 124 | #:use-module (gnu packages version-control) |
9aafbc0c | 125 | #:use-module (gnu packages wxwidgets) |
c12efc72 | 126 | #:use-module (gnu packages xml) |
a17d4564 | 127 | #:use-module (srfi srfi-1)) |
8f8b2451 | 128 | |
193abc82 JD |
129 | (define-public aris |
130 | (package | |
1f45f18a JD |
131 | (name "aris") |
132 | (version "2.2") | |
133 | (source (origin | |
134 | (method url-fetch) | |
135 | (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz")) | |
136 | (sha256 (base32 | |
137 | "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q")))) | |
138 | (build-system gnu-build-system) | |
139 | (inputs `(("gtk+" ,gtk+) | |
140 | ("libxml2" ,libxml2))) | |
141 | (native-inputs `(("pkg-config" ,pkg-config))) | |
142 | (synopsis "Natural deduction first-order logic interface") | |
143 | (description "Aris is a program for performing logical proofs. It supports | |
144 | propositional and predicate logic, as well as Boolean algebra and | |
145 | arithmetical logic. In addition to its predefined inference and equivalence | |
146 | rules, Aris also supports references to older proofs. Its use of standard | |
147 | logical symbols and its natural deduction interface make it easy to use for | |
148 | beginners.") | |
149 | (license license:gpl3+) | |
6fd52309 | 150 | (home-page "https://www.gnu.org/software/aris/"))) |
193abc82 | 151 | |
9c45c519 JD |
152 | (define-public c-graph |
153 | (package | |
154 | (name "c-graph") | |
0ef54303 | 155 | (version "2.0.1") |
9c45c519 JD |
156 | (source (origin |
157 | (method url-fetch) | |
158 | (uri (string-append "mirror://gnu/c-graph/c-graph-" version | |
159 | ".tar.gz")) | |
160 | (sha256 (base32 | |
0ef54303 | 161 | "092412jzxy6wdvpk96pfj499hpmaww8xllavbvlqspfpr7ips9id")))) |
9c45c519 JD |
162 | (build-system gnu-build-system) |
163 | (inputs | |
0ef54303 | 164 | `(("fortran" ,gfortran))) |
a3947cb1 | 165 | (synopsis "Visualizing and demonstrating convolution") |
9c45c519 | 166 | (description |
0ef54303 | 167 | "GNU C-Graph is a tool for demonstrating the theory of convolution. |
a3947cb1 LC |
168 | Thus, it can serve as an excellent aid to students of signal and systems |
169 | theory in visualizing the convolution process. Rather than forcing the | |
170 | student to write code, the program offers an intuitive interface with | |
171 | interactive dialogs to guide them.") | |
9c45c519 | 172 | (license license:gpl3+) |
6fd52309 | 173 | (home-page "https://www.gnu.org/software/c-graph/"))) |
9c45c519 | 174 | |
d91025e3 TD |
175 | (define-public coda |
176 | (package | |
177 | (name "coda") | |
9285f8bb | 178 | (version "2.19") |
d91025e3 TD |
179 | (source |
180 | (origin | |
181 | (method url-fetch) | |
182 | (uri (string-append "https://github.com/stcorp/coda/releases/download/" | |
183 | version "/coda-" version ".tar.gz")) | |
184 | (sha256 | |
9285f8bb | 185 | (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245")) |
4b12fe5c TD |
186 | (patches (search-patches "coda-use-system-libs.patch")) |
187 | (modules '((guix build utils))) | |
188 | (snippet | |
189 | ;; Make sure we don't use the bundled software. | |
6cbee49d MW |
190 | '(begin |
191 | (for-each (lambda (d) | |
192 | (delete-file-recursively (string-append "libcoda/" d))) | |
193 | '("zlib" "pcre" "expat")) | |
194 | #t)))) | |
d91025e3 TD |
195 | (native-inputs |
196 | `(("fortran" ,gfortran) | |
197 | ("python" ,python) | |
198 | ("python-numpy" ,python-numpy))) | |
199 | (inputs | |
200 | `(("zlib" ,zlib) | |
4b12fe5c TD |
201 | ("pcre" ,pcre) |
202 | ("expat" ,expat) | |
d91025e3 TD |
203 | ("hdf4" ,hdf4-alt) |
204 | ("hdf5" ,hdf5))) | |
205 | (build-system gnu-build-system) | |
206 | (arguments | |
4b12fe5c TD |
207 | '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python" |
208 | "LIBS= -lz -lpcre -lexpat"))) | |
d91025e3 TD |
209 | (synopsis "A common interface to various earth observation data formats") |
210 | (description | |
211 | "The Common Data Access toolbox (CODA) provides a set of interfaces for | |
212 | reading remote sensing data from earth observation data files. It consists of | |
213 | command line applications and interfaces to the C, Fortran, Python, and Java | |
214 | programming languages.") | |
215 | (home-page "https://stcorp.nl/coda") | |
216 | (license license:gpl2+))) | |
217 | ||
d65f0661 KK |
218 | (define-public qhull |
219 | (package | |
220 | (name "qhull") | |
221 | (version "2015.2") | |
222 | (source (origin | |
223 | (method url-fetch) | |
224 | (uri (string-append "http://www.qhull.org/download/qhull-" | |
225 | (car (string-split version #\.)) | |
226 | "-src-7.2.0.tgz")) | |
227 | (sha256 | |
228 | (base32 | |
229 | "0dm4b2xr3asy6w74khq2zg4gf26zsy3qf9sq7pf7lmrvbj911c3q")))) | |
230 | (build-system cmake-build-system) | |
231 | (synopsis "Calculate convex hulls and related structures") | |
232 | (description | |
233 | "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi | |
234 | diagram, halfspace intersection about a point, furthest-site Delaunay | |
235 | triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, | |
236 | 3-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull | |
237 | algorithm for computing the convex hull. It handles roundoff errors from | |
238 | floating point arithmetic. It computes volumes, surface areas, and | |
239 | approximations to the convex hull. | |
240 | ||
241 | @code{Qhull} does not support triangulation of non-convex surfaces, mesh | |
242 | generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha | |
243 | shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay | |
244 | triangulations.") | |
245 | (home-page "http://qhull.org") | |
246 | (license (license:non-copyleft "file://COPYING.txt" | |
247 | "See COPYING in the distribution.")))) | |
248 | ||
a8fa86c4 RW |
249 | (define-public python-cvxopt |
250 | (package | |
251 | (name "python-cvxopt") | |
a7c7015a | 252 | (version "1.2.3") |
a8fa86c4 RW |
253 | (source (origin |
254 | (method git-fetch) | |
255 | (uri (git-reference | |
256 | (url "https://github.com/cvxopt/cvxopt.git") | |
257 | (commit version))) | |
258 | (file-name (git-file-name name version)) | |
259 | (sha256 | |
260 | (base32 | |
a7c7015a | 261 | "1kiy2m62xgs2d5id6dnnwy4vap85cd70p7pgkb9nh23qf9xnak7b")))) |
a8fa86c4 RW |
262 | (build-system python-build-system) |
263 | (arguments | |
264 | `(#:phases | |
265 | (modify-phases %standard-phases | |
266 | (add-after 'unpack 'find-libraries | |
267 | (lambda* (#:key inputs #:allow-other-keys) | |
268 | (setenv "CVXOPT_BLAS_LIB" "openblas") | |
269 | (setenv "CVXOPT_BUILD_FFTW" "1") | |
270 | (setenv "CVXOPT_BUILD_GLPK" "1") | |
271 | (setenv "CVXOPT_BUILD_GSL" "1") | |
272 | #t))))) | |
273 | (inputs | |
274 | `(("fftw" ,fftw) | |
275 | ("glpk" ,glpk) | |
276 | ("gsl" ,gsl) | |
277 | ("lapack" ,lapack) | |
278 | ("openblas" ,openblas) | |
279 | ("suitesparse" ,suitesparse))) | |
280 | (home-page "https://www.cvxopt.org") | |
281 | (synopsis "Python library for convex optimization") | |
282 | (description | |
283 | "CVXOPT is a package for convex optimization based on the Python | |
284 | programming language. Its main purpose is to make the development of software | |
285 | for convex optimization applications straightforward by building on Python’s | |
286 | extensive standard library and on the strengths of Python as a high-level | |
287 | programming language.") | |
288 | (license license:gpl3+))) | |
289 | ||
290 | (define-public python2-cvxopt | |
291 | (package-with-python2 python-cvxopt)) | |
292 | ||
8f8b2451 AE |
293 | (define-public units |
294 | (package | |
295 | (name "units") | |
494a8cd0 | 296 | (version "2.19") |
8f8b2451 AE |
297 | (source (origin |
298 | (method url-fetch) | |
299 | (uri (string-append "mirror://gnu/units/units-" version | |
300 | ".tar.gz")) | |
301 | (sha256 (base32 | |
494a8cd0 | 302 | "0mk562g7dnidjgfgvkxxpvlba66fh1ykmfd9ylzvcln1vxmi6qj2")))) |
8f8b2451 | 303 | (build-system gnu-build-system) |
0498d248 | 304 | (inputs |
a2549713 EB |
305 | `(("readline" ,readline) |
306 | ("python" ,python-wrapper) ;for 'units_cur' script | |
0498d248 EB |
307 | ("python-requests" ,python-requests))) |
308 | (arguments | |
309 | `(#:phases (modify-phases %standard-phases | |
310 | (add-after 'install 'wrap-units_cur | |
311 | (lambda* (#:key outputs #:allow-other-keys) | |
312 | (let* ((out (assoc-ref outputs "out")) | |
313 | (bin (string-append out "/bin"))) | |
314 | (wrap-program (string-append bin "/units_cur") | |
315 | `("PYTHONPATH" ":" prefix | |
316 | ,(search-path-as-string->list (getenv "PYTHONPATH")))) | |
317 | #t)))))) | |
8f8b2451 AE |
318 | (synopsis "Conversion between thousands of scales") |
319 | (description | |
574e86f9 | 320 | "GNU Units converts numeric quantities between units of measure. It |
7c125ce0 AK |
321 | can handle scale changes through adaptive usage of standard scale |
322 | prefixes (micro-, kilo-, etc.). It can also handle nonlinear | |
323 | conversions such as Fahrenheit to Celsius. Its interpreter is powerful | |
324 | enough to be used effectively as a scientific calculator.") | |
8f8b2451 | 325 | (license license:gpl3+) |
6fd52309 | 326 | (home-page "https://www.gnu.org/software/units/"))) |
c9dfa3c7 | 327 | |
61a529b4 RW |
328 | (define-public double-conversion |
329 | (package | |
330 | (name "double-conversion") | |
1c7d7f3f | 331 | (version "3.1.5") |
b343850e | 332 | (home-page "https://github.com/google/double-conversion") |
61a529b4 | 333 | (source (origin |
2bdc73fb | 334 | (method git-fetch) |
a4de1a65 MB |
335 | (uri (git-reference (url home-page) |
336 | (commit (string-append "v" version)))) | |
2bdc73fb | 337 | (file-name (git-file-name name version)) |
61a529b4 RW |
338 | (sha256 |
339 | (base32 | |
1c7d7f3f | 340 | "0csy4pjw1p8rp6g5qxi2h0ychhhp1fldv7gb761627fs2mclw9gv")))) |
61a529b4 RW |
341 | (build-system cmake-build-system) |
342 | (arguments | |
343 | '(#:test-target "test" | |
344 | #:configure-flags '("-DBUILD_SHARED_LIBS=ON" | |
345 | "-DBUILD_TESTING=ON"))) | |
61a529b4 RW |
346 | (synopsis "Conversion routines for IEEE doubles") |
347 | (description | |
348 | "The double-conversion library provides binary-decimal and decimal-binary | |
349 | routines for IEEE doubles. The library consists of efficient conversion | |
350 | routines that have been extracted from the V8 JavaScript engine.") | |
351 | (license license:bsd-3))) | |
352 | ||
182d6311 ML |
353 | (define-public dionysus |
354 | (package | |
355 | (name "dionysus") | |
bd041e7f | 356 | (version "1.4.0") |
182d6311 ML |
357 | (source (origin |
358 | (method url-fetch) | |
359 | (uri (string-append "mirror://gnu/dionysus/dionysus-" version | |
bd041e7f | 360 | ".tar.xz")) |
182d6311 ML |
361 | (sha256 |
362 | (base32 | |
bd041e7f | 363 | "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk")))) |
182d6311 ML |
364 | (build-system gnu-build-system) |
365 | (inputs `(("tcl" ,tcl))) ;for 'tclsh' | |
366 | (synopsis "Local search for universal constants and scientific values") | |
367 | (description | |
368 | "GNU Dionysus is a convenient system for quickly retrieving the values of | |
369 | mathematical constants used in science and engineering. Values can be | |
370 | searched using a simple command-line tool, choosing from three databases: | |
371 | universal constants, atomic numbers, and constants related to | |
372 | semiconductors.") | |
373 | (license license:gpl3+) | |
6fd52309 | 374 | (home-page "https://www.gnu.org/software/dionysus/"))) |
182d6311 | 375 | |
88bd1804 AE |
376 | (define-public gsl |
377 | (package | |
378 | (name "gsl") | |
f3a34b9d | 379 | (version "2.5") |
ab2cc5cd LC |
380 | (source (origin |
381 | (method url-fetch) | |
382 | (uri (string-append "mirror://gnu/gsl/gsl-" | |
383 | version ".tar.gz")) | |
384 | (sha256 | |
385 | (base32 | |
f3a34b9d | 386 | "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04")) |
ab2cc5cd | 387 | (patches (search-patches "gsl-test-i686.patch")))) |
88bd1804 | 388 | (build-system gnu-build-system) |
71e0f288 | 389 | (arguments |
f885fc05 | 390 | `(;; Currently there are numerous tests that fail on "exotic" |
6f766069 EF |
391 | ;; architectures such as aarch64 and ppc64le. |
392 | ,@(if (string-prefix? "aarch64-linux" | |
393 | (or (%current-target-system) (%current-system))) | |
394 | '(#:tests? #f) | |
395 | '()))) | |
396 | (home-page "https://www.gnu.org/software/gsl/") | |
88bd1804 AE |
397 | (synopsis "Numerical library for C and C++") |
398 | (description | |
a22dc0c4 LC |
399 | "The GNU Scientific Library is a library for numerical analysis in C |
400 | and C++. It includes a wide range of mathematical routines, with over 1000 | |
401 | functions in total. Subject areas covered by the library include: | |
402 | differential equations, linear algebra, Fast Fourier Transforms and random | |
403 | numbers.") | |
88bd1804 AE |
404 | (license license:gpl3+))) |
405 | ||
b92eee75 AE |
406 | (define-public glpk |
407 | (package | |
408 | (name "glpk") | |
445929e0 | 409 | (version "4.65") |
b92eee75 AE |
410 | (source |
411 | (origin | |
412 | (method url-fetch) | |
413 | (uri (string-append "mirror://gnu/glpk/glpk-" | |
414 | version ".tar.gz")) | |
415 | (sha256 | |
416 | (base32 | |
445929e0 | 417 | "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2")))) |
b92eee75 AE |
418 | (build-system gnu-build-system) |
419 | (inputs | |
420 | `(("gmp" ,gmp))) | |
421 | (arguments | |
422 | `(#:configure-flags '("--with-gmp"))) | |
82110ef6 | 423 | (home-page "https://www.gnu.org/software/glpk/") |
79c311b8 | 424 | (synopsis "GNU Linear Programming Kit, supporting the MathProg language") |
b92eee75 AE |
425 | (description |
426 | "GLPK is a C library for solving large-scale linear programming (LP), | |
427 | mixed integer programming (MIP), and other related problems. It supports the | |
428 | GNU MathProg modeling language, a subset of the AMPL language, and features a | |
429 | translator for the language. In addition to the C library, a stand-alone | |
430 | LP/MIP solver is included in the package.") | |
431 | (license license:gpl3+))) | |
432 | ||
b146763a AE |
433 | (define-public 4ti2 |
434 | (package | |
435 | (name "4ti2") | |
eea4a091 | 436 | (version "1.6.9") |
b146763a AE |
437 | (source |
438 | (origin | |
eea4a091 TGR |
439 | (method url-fetch) |
440 | (uri (string-append "https://github.com/4ti2/4ti2/releases/download/" | |
441 | "Release_" | |
442 | (string-map (lambda (c) (if (char=? c #\.) #\_ c)) | |
443 | version) | |
444 | "/4ti2-" version ".tar.gz")) | |
445 | (sha256 | |
446 | (base32 "0rj92x6p9m3la5gasjbj7sa569im527ffmka5y2sv1amgd3fflrh")))) | |
b146763a AE |
447 | (build-system gnu-build-system) |
448 | (native-inputs | |
449 | `(("which" ,(@ (gnu packages base) which)))) ; for the tests | |
450 | (inputs | |
451 | `(("glpk" ,glpk) | |
452 | ("gmp" ,gmp))) | |
453 | (home-page "http://www.4ti2.de/") | |
454 | (synopsis "Mathematical tool suite for problems on linear spaces") | |
455 | (description | |
456 | "4ti2 implements algorithms for solving algebraic, geometric and | |
457 | combinatorial problems on linear spaces. Among others, it solves systems | |
458 | of linear equations, computes extreme rays of polyhedral cones, solves | |
459 | integer programming problems and computes Markov bases for statistics.") | |
460 | (license license:gpl2+))) | |
461 | ||
53696f10 AE |
462 | (define-public cddlib |
463 | (package | |
464 | (name "cddlib") | |
7fe491fb | 465 | (version "0.94i") |
53696f10 AE |
466 | (source |
467 | (origin | |
468 | (method url-fetch) | |
182dde82 | 469 | (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-" |
53696f10 AE |
470 | (string-delete #\. version) ".tar.gz")) |
471 | (sha256 | |
472 | (base32 | |
7fe491fb | 473 | "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq")))) |
53696f10 AE |
474 | (build-system gnu-build-system) |
475 | (inputs | |
476 | `(("gmp" ,gmp))) | |
477 | (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html") | |
478 | (synopsis "Library for convex hulls and extreme rays of polyhedra") | |
479 | (description | |
480 | "The C-library cddlib implements the Double Description Method of | |
481 | Motzkin et al. for generating all vertices (i.e. extreme points) and extreme | |
482 | rays of a general convex polyhedron given by a system of linear inequalities | |
483 | in arbitrary dimension. It can also be used for the converse operation of | |
484 | computing convex hulls.") | |
485 | (license license:gpl2+))) | |
486 | ||
0ffc2d53 AE |
487 | (define-public lrslib |
488 | (package | |
489 | (name "lrslib") | |
490 | (version "7.0a") | |
491 | (source | |
492 | (origin | |
493 | (method url-fetch) | |
494 | (uri (string-append "http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/" | |
495 | "lrslib-0" | |
496 | (string-delete #\. version) ".tar.gz")) | |
497 | (sha256 | |
498 | (base32 | |
499 | "034fa45r9hwx6ljmgpxk2872q34nklkalpdkc6s9hqw57rivi36k")))) | |
500 | (build-system gnu-build-system) | |
501 | (inputs | |
502 | `(("gmp" ,gmp))) | |
503 | (arguments | |
504 | `(#:tests? #f ; no check phase | |
505 | #:make-flags `("CC=gcc" | |
506 | ,(string-append "prefix=" (assoc-ref %outputs "out")) | |
507 | "all-shared") | |
508 | #:phases | |
509 | (modify-phases %standard-phases | |
510 | (replace 'configure | |
511 | (lambda _ | |
512 | (substitute* "makefile" | |
513 | (("-L \\.") "-L . -Wl,-rpath='$$ORIGIN/../lib'")) | |
514 | #t))))) | |
515 | (home-page "http://cgm.cs.mcgill.ca/~avis/C/lrs.html") | |
516 | (synopsis "Convex hulls of polyhedra with exact arithmetic") | |
517 | (description | |
518 | "The C code of lrslib implements the reverse search algorithm for | |
519 | vertex enumeration and convex hull problems. Its input file format is | |
520 | compatible with cddlib. All computations are done exactly in either | |
521 | multiple precision or fixed integer arithmetic. Output is not stored | |
522 | in memory, so even problems with very large output sizes can sometimes | |
523 | be solved.") | |
524 | (license license:gpl2+))) | |
525 | ||
865a69dd RW |
526 | (define-public arpack-ng |
527 | (package | |
528 | (name "arpack-ng") | |
f03c4ec6 | 529 | (version "3.6.3") |
c0edb5b5 | 530 | (home-page "https://github.com/opencollab/arpack-ng") |
622ef2b9 MB |
531 | (source (origin |
532 | (method git-fetch) | |
533 | (uri (git-reference (url home-page) (commit version))) | |
534 | (file-name (git-file-name name version)) | |
535 | (sha256 | |
536 | (base32 | |
f03c4ec6 | 537 | "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y")))) |
865a69dd | 538 | (build-system gnu-build-system) |
c0edb5b5 LC |
539 | (native-inputs |
540 | `(("autoconf" ,autoconf) | |
541 | ("automake" ,automake) | |
542 | ("libtool" ,libtool))) | |
865a69dd RW |
543 | (inputs |
544 | `(("lapack" ,lapack) | |
19afbea1 | 545 | ("fortran" ,gfortran))) |
865a69dd RW |
546 | (synopsis "Fortran subroutines for solving eigenvalue problems") |
547 | (description | |
548 | "ARPACK-NG is a collection of Fortran77 subroutines designed to solve | |
549 | large scale eigenvalue problems.") | |
166191b3 | 550 | (license (license:non-copyleft "file://COPYING" |
865a69dd RW |
551 | "See COPYING in the distribution.")))) |
552 | ||
c0edb5b5 LC |
553 | (define-public arpack-ng-3.3.0 |
554 | (package | |
555 | (inherit arpack-ng) | |
556 | (version "3.3.0") | |
557 | (name (package-name arpack-ng)) | |
558 | (home-page (package-home-page arpack-ng)) | |
559 | (source | |
560 | (origin | |
561 | (method url-fetch) | |
562 | (uri (string-append home-page "/archive/" version ".tar.gz")) | |
563 | (file-name (string-append name "-" version ".tar.gz")) | |
564 | (sha256 | |
565 | (base32 | |
566 | "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd")))))) | |
567 | ||
8c94c886 EB |
568 | (define-public arpack-ng-openmpi |
569 | (package (inherit arpack-ng) | |
570 | (name "arpack-ng-openmpi") | |
571 | (inputs | |
572 | `(("mpi" ,openmpi) | |
573 | ,@(package-inputs arpack-ng))) | |
4f387541 LC |
574 | (arguments |
575 | (substitute-keyword-arguments (package-arguments arpack-ng) | |
576 | ((#:configure-flags _ '()) | |
aa82260b PG |
577 | ''("--enable-mpi")) |
578 | ((#:phases phases '%standard-phases) | |
579 | `(modify-phases ,phases | |
bbe46a4a EB |
580 | (add-before 'check 'mpi-setup |
581 | ,%openmpi-setup))))) | |
8c94c886 EB |
582 | (synopsis "Fortran subroutines for solving eigenvalue problems with MPI"))) |
583 | ||
da95c817 NK |
584 | (define-public lapack |
585 | (package | |
586 | (name "lapack") | |
e6de152d | 587 | (version "3.9.0") |
da95c817 NK |
588 | (source |
589 | (origin | |
590 | (method url-fetch) | |
591 | (uri (string-append "http://www.netlib.org/lapack/lapack-" | |
592 | version ".tgz")) | |
593 | (sha256 | |
594 | (base32 | |
e6de152d | 595 | "1155qixp26c12yrxc76z9mlfw2h3xxymxxv5znpgzh5gaykpndgj")))) |
da95c817 NK |
596 | (build-system cmake-build-system) |
597 | (home-page "http://www.netlib.org/lapack/") | |
19afbea1 | 598 | (inputs `(("fortran" ,gfortran) |
e6de152d | 599 | ("python" ,python-wrapper))) |
da95c817 | 600 | (arguments |
3ab869b6 | 601 | `(#:configure-flags (list |
3ab869b6 LC |
602 | "-DBUILD_SHARED_LIBS:BOOL=YES" |
603 | "-DLAPACKE=ON" | |
3ab869b6 | 604 | ;; Build the 'LAPACKE_clatms' functions. |
e6de152d KH |
605 | "-DLAPACKE_WITH_TMG=ON" |
606 | "-DBUILD_TESTING=ON"))) | |
da95c817 NK |
607 | (synopsis "Library for numerical linear algebra") |
608 | (description | |
609 | "LAPACK is a Fortran 90 library for solving the most commonly occurring | |
610 | problems in numerical linear algebra.") | |
166191b3 | 611 | (license (license:non-copyleft "file://LICENSE" |
da95c817 | 612 | "See LICENSE in the distribution.")))) |
73fed4f8 | 613 | |
e1ff597a EB |
614 | (define-public scalapack |
615 | (package | |
616 | (name "scalapack") | |
617 | (version "2.0.2") | |
618 | (source | |
619 | (origin | |
620 | (method url-fetch) | |
621 | (uri (string-append "http://www.netlib.org/scalapack/scalapack-" | |
622 | version ".tgz")) | |
623 | (sha256 | |
624 | (base32 | |
f73750e6 EB |
625 | "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c")) |
626 | (patches (search-patches "scalapack-blacs-mpi-deprecations.patch")))) | |
e1ff597a EB |
627 | (build-system cmake-build-system) |
628 | (inputs | |
629 | `(("mpi" ,openmpi) | |
630 | ("fortran" ,gfortran) | |
631 | ("lapack" ,lapack))) ;for testing only | |
632 | (arguments | |
6df2a50a LC |
633 | `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES") |
634 | #:phases (modify-phases %standard-phases | |
bbe46a4a EB |
635 | (add-before 'check 'mpi-setup |
636 | ,%openmpi-setup)))) | |
e1ff597a EB |
637 | (home-page "http://www.netlib.org/scalapack/") |
638 | (synopsis "Library for scalable numerical linear algebra") | |
639 | (description | |
640 | "ScaLAPACK is a Fortran 90 library of high-performance linear algebra | |
641 | routines on parallel distributed memory machines. ScaLAPACK solves dense and | |
642 | banded linear systems, least squares problems, eigenvalue problems, and | |
643 | singular value problems.") | |
adb223b8 LC |
644 | (license (license:non-copyleft "file://LICENSE" |
645 | "See LICENSE in the distribution.")))) | |
e1ff597a | 646 | |
73fed4f8 | 647 | (define-public gnuplot |
5f800540 KK |
648 | (package |
649 | (name "gnuplot") | |
cb1d8aee | 650 | (version "5.2.7") |
5f800540 KK |
651 | (source (origin |
652 | (method url-fetch) | |
653 | (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" | |
654 | version "/gnuplot-" | |
655 | version ".tar.gz")) | |
656 | (sha256 | |
cb1d8aee | 657 | (base32 "1vglp4la40f5dpj0zdj63zprrkyjgzy068p35bz5dqxjyczm1zlp")))) |
5f800540 KK |
658 | (build-system gnu-build-system) |
659 | (inputs `(("readline" ,readline) | |
660 | ("cairo" ,cairo) | |
661 | ("pango" ,pango) | |
6e64766a DM |
662 | ("gd" ,gd) |
663 | ("lua" ,lua))) | |
612a387f RW |
664 | (native-inputs |
665 | `(("pkg-config" ,pkg-config) | |
666 | ("texlive" ,texlive-tiny))) | |
07254d8b AM |
667 | (arguments `(#:configure-flags (list (string-append |
668 | "--with-texdir=" %output | |
669 | "/texmf-local/tex/latex/gnuplot")))) | |
5f800540 KK |
670 | (home-page "http://www.gnuplot.info") |
671 | (synopsis "Command-line driven graphing utility") | |
672 | (description "Gnuplot is a portable command-line driven graphing | |
35b9e423 | 673 | utility. It was originally created to allow scientists and students to |
73fed4f8 | 674 | visualize mathematical functions and data interactively, but has grown to |
35b9e423 | 675 | support many non-interactive uses such as web scripting. It is also used as a |
73fed4f8 | 676 | plotting engine by third-party applications like Octave.") |
5f800540 KK |
677 | ;; X11 Style with the additional restriction that derived works may only be |
678 | ;; distributed as patches to the original. | |
679 | (license (license:fsf-free | |
680 | "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright")))) | |
668c06ac | 681 | |
32f70e1f TD |
682 | (define-public gctp |
683 | (package | |
684 | (name "gctp") | |
685 | (version "2.0.0") | |
686 | (source | |
687 | (origin | |
5db874d1 TGR |
688 | (method git-fetch) |
689 | (uri (git-reference | |
690 | (url "https://github.com/OkoSanto/GCTP.git") | |
691 | (commit (string-append "v" version)))) | |
692 | (file-name (git-file-name name version)) | |
32f70e1f | 693 | (sha256 |
5db874d1 | 694 | (base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd")))) |
32f70e1f TD |
695 | (native-inputs |
696 | `(("fortran" ,gfortran))) | |
697 | (build-system gnu-build-system) | |
698 | (synopsis "General Cartographic Transformation Package (GCTP)") | |
699 | (description | |
700 | "The General Cartographic Transformation Package (GCTP) is a system of | |
701 | software routines designed to permit the transformation of coordinate pairs | |
702 | from one map projection to another. The GCTP is the standard computer | |
703 | software used by the National Mapping Division for map projection | |
704 | computations.") | |
705 | (home-page "https://github.com/OkoSanto/GCTP") | |
0f7cd95b | 706 | (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html |
32f70e1f | 707 | |
becbbefc TD |
708 | (define-public hdf4 |
709 | (package | |
710 | (name "hdf4") | |
c959d99f | 711 | (version "4.2.14") |
becbbefc TD |
712 | (source |
713 | (origin | |
714 | (method url-fetch) | |
715 | (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF" | |
716 | version "/src/hdf-" version ".tar.bz2")) | |
717 | (sha256 | |
c959d99f | 718 | (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l")) |
15ca49b2 AE |
719 | (patches (search-patches "hdf4-architectures.patch" |
720 | "hdf4-reproducibility.patch" | |
bd3d71cb MB |
721 | "hdf4-shared-fortran.patch" |
722 | "hdf4-tirpc.patch")))) | |
becbbefc TD |
723 | (build-system gnu-build-system) |
724 | (native-inputs | |
725 | `(("gfortran" ,gfortran) | |
726 | ("bison" ,bison) | |
727 | ("flex" ,flex))) | |
728 | (inputs | |
729 | `(("zlib" ,zlib) | |
bd3d71cb MB |
730 | ("libjpeg" ,libjpeg) |
731 | ("libtirpc" ,libtirpc))) | |
becbbefc TD |
732 | (arguments |
733 | `(#:parallel-tests? #f | |
bd3d71cb MB |
734 | #:configure-flags (list "--enable-shared" |
735 | (string-append "CPPFLAGS=-I" | |
736 | (assoc-ref %build-inputs "libtirpc") | |
737 | "/include/tirpc")) | |
becbbefc TD |
738 | #:phases |
739 | (modify-phases %standard-phases | |
953a12fa EF |
740 | ;; This is inspired by two of Debian's patches. |
741 | (add-before 'configure 'add-more-aarch64-support | |
742 | (lambda _ | |
743 | (substitute* '("mfhdf/ncgen/ncgen.l" | |
744 | "mfhdf/ncgen/ncgenyy.c" | |
745 | "mfhdf/libsrc/netcdf.h.in") | |
746 | (("AIX5L64") "__aarch64__")) | |
747 | #t)) | |
becbbefc TD |
748 | (add-before 'configure 'patchbuild |
749 | (lambda _ | |
750 | (substitute* | |
751 | '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in") | |
752 | (("/bin/rm") "rm") | |
753 | (("/bin/mkdir") "mkdir")) | |
754 | (substitute* (find-files "." "^Makefile\\.in$") | |
755 | (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \ | |
756 | -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "") | |
757 | (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \ | |
758 | -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \ | |
953a12fa | 759 | -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")) |
e464b455 TD |
760 | #t)) |
761 | (add-after 'configure 'patch-settings | |
762 | (lambda _ | |
763 | ;; libhdf4.settings contains the full path of the | |
764 | ;; compilers used, and its contents are included in | |
765 | ;; .so-files. We truncate the hashes to avoid | |
766 | ;; unnecessary store references to those compilers: | |
767 | (substitute* "libhdf4.settings" | |
768 | (("(/gnu/store/)([a-Z0-9]*)" all prefix hash) | |
769 | (string-append prefix (string-take hash 10) "..."))) | |
770 | #t)) | |
771 | ))) | |
becbbefc TD |
772 | (home-page "https://www.hdfgroup.org/products/hdf4/") |
773 | (synopsis | |
774 | "Library and multi-object file format for storing and managing data") | |
775 | (description "HDF4 is a library and multi-object file format for storing | |
776 | and managing data between machines. HDF4 is an older hierarchical data format, | |
777 | incompatible with HDF5.") | |
778 | (license | |
779 | (license:non-copyleft | |
780 | "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING")))) | |
781 | ||
782 | (define-public hdf4-alt | |
783 | (package | |
784 | (inherit hdf4) | |
785 | (name "hdf4-alt") | |
786 | (arguments | |
787 | (substitute-keyword-arguments (package-arguments hdf4) | |
788 | ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags)))) | |
789 | (synopsis | |
790 | "HDF4 without netCDF API, can be combined with the regular netCDF library"))) | |
791 | ||
7ee3f1a2 JD |
792 | (define-public hdf5 |
793 | (package | |
794 | (name "hdf5") | |
7b84610e | 795 | (version "1.8.21") |
7ee3f1a2 JD |
796 | (source |
797 | (origin | |
798 | (method url-fetch) | |
2da63064 TD |
799 | (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/" |
800 | "hdf5-" (version-major+minor version) | |
801 | "/hdf5-" version "/src/hdf5-" | |
dcd9d163 LF |
802 | version ".tar.bz2") |
803 | (string-append "https://support.hdfgroup.org/ftp/HDF5/" | |
804 | "current" | |
7b84610e EB |
805 | (match (string-split version #\.) |
806 | ((major minor _ ...) | |
807 | (string-append major minor))) | |
dcd9d163 | 808 | "/src/hdf5-" version ".tar.bz2"))) |
7ee3f1a2 | 809 | (sha256 |
7b84610e | 810 | (base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5")) |
7fedc3fd EB |
811 | (patches (search-patches "hdf5-config-date.patch" |
812 | "hdf5-1.8-mpi-deprecations.patch")))) | |
7ee3f1a2 | 813 | (build-system gnu-build-system) |
12ed1216 AE |
814 | (inputs |
815 | `(("zlib" ,zlib))) | |
e3a1a1de | 816 | (native-inputs |
3ea420f3 LC |
817 | `(("gfortran" ,gfortran) |
818 | ("perl" ,perl))) ;part of the test machinery needs Perl | |
e3a1a1de TD |
819 | (outputs '("out" ; core library |
820 | "fortran")) ; fortran interface | |
7ee3f1a2 | 821 | (arguments |
62126576 | 822 | `(;; Some of the users, notably Flann, need the C++ interface. |
e3a1a1de TD |
823 | #:configure-flags '("--enable-cxx" |
824 | "--enable-fortran" | |
549d1571 LC |
825 | "--enable-fortran2003" |
826 | ||
827 | ;; Build a thread-safe library. Unfortunately, | |
828 | ;; 'configure' invites you to either turn off C++, | |
829 | ;; Fortran, and the high-level interface (HL), or | |
830 | ;; to pass '--enable-unsupported'. Debian | |
831 | ;; packagers chose to pass '--enable-unsupported' | |
832 | ;; and we follow their lead here. | |
833 | "--enable-threadsafe" | |
834 | "--with-pthread" | |
835 | "--enable-unsupported") | |
4dba441c RW |
836 | ;; Use -fPIC to allow the R bindings to link with the static libraries |
837 | #:make-flags (list "CFLAGS=-fPIC" | |
838 | "CXXFLAGS=-fPIC") | |
62126576 | 839 | #:phases |
f622e212 EB |
840 | (modify-phases %standard-phases |
841 | (add-before 'configure 'patch-configure | |
e3a1a1de | 842 | (lambda* (#:key outputs #:allow-other-keys) |
f622e212 | 843 | (substitute* "configure" |
b8d9c93b | 844 | (("/bin/mv") "mv")) |
e3a1a1de TD |
845 | (substitute* "fortran/src/Makefile.in" |
846 | (("libhdf5_fortran_la_LDFLAGS =") | |
847 | (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath=" | |
848 | (assoc-ref outputs "fortran") "/lib"))) | |
849 | (substitute* "hl/fortran/src/Makefile.in" | |
850 | (("libhdf5hl_fortran_la_LDFLAGS =") | |
851 | (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath=" | |
852 | (assoc-ref outputs "fortran") "/lib"))) | |
b8d9c93b | 853 | #t)) |
fd0378a1 TD |
854 | (add-after 'configure 'patch-settings |
855 | (lambda _ | |
856 | ;; libhdf5.settings contains the full path of the | |
857 | ;; compilers used, and its contents are included in | |
858 | ;; libhdf5.so. We truncate the hashes to avoid | |
859 | ;; unnecessary store references to those compilers: | |
860 | (substitute* "src/libhdf5.settings" | |
861 | (("(/gnu/store/)([a-Z0-9]*)" all prefix hash) | |
d8f46d52 RW |
862 | (string-append prefix (string-take hash 10) "...")) |
863 | ;; Don't record the build-time kernel version to make the | |
864 | ;; settings file reproducible. | |
865 | (("Uname information:.*") | |
866 | "Uname information: Linux\n")) | |
b8d9c93b | 867 | #t)) |
f622e212 EB |
868 | (add-after 'install 'patch-references |
869 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
870 | (let ((bin (string-append (assoc-ref outputs "out") "/bin")) | |
871 | (zlib (assoc-ref inputs "zlib"))) | |
872 | (substitute* (find-files bin "h5p?cc") | |
873 | (("-lz" lib) | |
874 | (string-append "-L" zlib "/lib " lib))) | |
e3a1a1de TD |
875 | #t))) |
876 | (add-after 'install 'split | |
877 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
878 | ;; Move all fortran-related files | |
879 | (let* ((out (assoc-ref outputs "out")) | |
880 | (bin (string-append out "/bin")) | |
881 | (lib (string-append out "/lib")) | |
882 | (inc (string-append out "/include")) | |
883 | (ex (string-append out "/share/hdf5_examples/fortran")) | |
884 | (fort (assoc-ref outputs "fortran")) | |
885 | (fbin (string-append fort "/bin")) | |
886 | (flib (string-append fort "/lib")) | |
887 | (finc (string-append fort "/include")) | |
888 | (fex (string-append fort "/share/hdf5_examples/fortran"))) | |
889 | (mkdir-p fbin) | |
890 | (mkdir-p flib) | |
891 | (mkdir-p finc) | |
892 | (mkdir-p fex) | |
b0d1e60f PG |
893 | ;; Note: When built with --enable-parallel, the 'h5fc' file |
894 | ;; doesn't exist, hence this condition. | |
895 | (when (file-exists? (string-append bin "/h5fc")) | |
896 | (rename-file (string-append bin "/h5fc") | |
897 | (string-append fbin "/h5fc"))) | |
e3a1a1de TD |
898 | (for-each (lambda (file) |
899 | (rename-file file | |
900 | (string-append flib "/" (basename file)))) | |
901 | (find-files lib ".*fortran.*")) | |
902 | (for-each (lambda (file) | |
903 | (rename-file file | |
904 | (string-append finc "/" (basename file)))) | |
905 | (find-files inc ".*mod")) | |
906 | (for-each (lambda (file) | |
907 | (rename-file file | |
908 | (string-append fex "/" (basename file)))) | |
909 | (find-files ex ".*")) | |
910 | (delete-file-recursively ex)) | |
911 | #t))))) | |
0a44f9c4 | 912 | (home-page "https://www.hdfgroup.org") |
516e93f8 | 913 | (synopsis "Management suite for extremely large and complex data") |
7ee3f1a2 JD |
914 | (description "HDF5 is a suite that makes possible the management of |
915 | extremely large and complex data collections.") | |
d4bf49b1 | 916 | (license (license:x11-style |
0a44f9c4 | 917 | "https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) |
7ee3f1a2 | 918 | |
bb47aca5 RW |
919 | (define-public hdf5-1.10 |
920 | (package (inherit hdf5) | |
cb169aae | 921 | (version "1.10.6") |
bb47aca5 RW |
922 | (source |
923 | (origin | |
924 | (method url-fetch) | |
925 | (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/" | |
926 | "hdf5-" (version-major+minor version) | |
927 | "/hdf5-" version "/src/hdf5-" | |
928 | version ".tar.bz2") | |
929 | (string-append "https://support.hdfgroup.org/ftp/HDF5/" | |
930 | "current" | |
931 | (apply string-append | |
932 | (take (string-split version #\.) 2)) | |
933 | "/src/hdf5-" version ".tar.bz2"))) | |
934 | (sha256 | |
cb169aae | 935 | (base32 "1gf38x51128hn00744358w27xgzjk0ff4wra4yxh2lk804ck1mh9")) |
94fea21b | 936 | (patches (search-patches "hdf5-config-date.patch")))))) |
bb47aca5 | 937 | |
2fd26d05 TD |
938 | (define-public hdf-java |
939 | (package | |
2a509880 RW |
940 | (name "hdf-java") |
941 | (version "3.3.2") | |
942 | (source | |
943 | (origin | |
944 | (method url-fetch) | |
945 | (uri (string-append | |
0a44f9c4 | 946 | "https://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-" |
2a509880 RW |
947 | version "/src/CMake-hdfjava-" version ".tar.gz")) |
948 | (sha256 | |
949 | (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr")) | |
950 | (modules '((guix build utils))) | |
951 | (snippet ; Make sure we don't use the bundled sources and binaries. | |
952 | `(begin | |
953 | (for-each delete-file | |
954 | (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz" | |
955 | "HDF4.tar.gz" "HDF5.tar.gz")) | |
956 | (delete-file-recursively ,(string-append "hdfjava-" version "/lib")) | |
957 | #t)))) | |
958 | (build-system gnu-build-system) | |
959 | (native-inputs | |
960 | `(("jdk" ,icedtea "jdk") | |
961 | ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'. | |
962 | ;; For tests: | |
963 | ("hamcrest-core" ,java-hamcrest-core) | |
964 | ("junit" ,java-junit) | |
965 | ("slf4j-simple" ,java-slf4j-simple))) | |
966 | (inputs | |
967 | `(("hdf4" ,hdf4) | |
968 | ("hdf5" ,hdf5) | |
969 | ("zlib" ,zlib) | |
970 | ("libjpeg" ,libjpeg) | |
971 | ("slf4j-api" ,java-slf4j-api))) | |
972 | (arguments | |
973 | `(#:configure-flags | |
974 | (list (string-append "--target=" ,(or (%current-target-system) (%current-system))) | |
975 | (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include," | |
976 | (assoc-ref %build-inputs "jdk") "/lib" ) | |
977 | (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib") | |
978 | (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib")) | |
2fd26d05 | 979 | |
2a509880 RW |
980 | #:make-flags |
981 | (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib") | |
982 | (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib") | |
983 | (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so") | |
984 | (string-append "JPEGLIB=" | |
985 | (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so") | |
986 | "LLEXT=so") | |
2fd26d05 | 987 | |
2a509880 RW |
988 | #:phases |
989 | (modify-phases %standard-phases | |
990 | (add-before 'configure 'chdir-to-source | |
991 | (lambda _ (chdir ,(string-append "hdfjava-" version)) #t)) | |
992 | (add-before 'configure 'patch-build | |
993 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
994 | (substitute* "configure" | |
995 | (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles | |
996 | (("/bin/cat") (which "cat"))) | |
997 | ;; Set classpath for compilation | |
998 | (substitute* '("hdf/hdf5lib/Makefile.in" | |
999 | "hdf/hdf5lib/exceptions/Makefile.in" | |
1000 | "hdf/hdflib/Makefile.in") | |
1001 | (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar") | |
1002 | (string-append (assoc-ref inputs "slf4j-api") | |
1003 | "/share/java/slf4j-api.jar"))) | |
1004 | ;; Replace outdated config.sub and config.guess: | |
1005 | (with-directory-excursion "config" | |
1006 | (for-each (lambda (file) | |
1007 | (install-file | |
1008 | (string-append (assoc-ref inputs "automake") | |
1009 | "/share/automake-" | |
1010 | ,(version-major+minor (package-version automake)) | |
1011 | "/" file) ".")) | |
1012 | '("config.sub" "config.guess"))) | |
64dc8b0b | 1013 | |
2a509880 RW |
1014 | ;; Fix embedded version number |
1015 | (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.)))) | |
1016 | (substitute* "hdf/hdf5lib/H5.java" | |
1017 | (("1, 8, 19") | |
1018 | (string-join hdf5version ", ")))) | |
64dc8b0b | 1019 | |
2a509880 RW |
1020 | (mkdir-p (string-append (assoc-ref outputs "out"))) |
1021 | ;; Set classpath for tests | |
1022 | (let* ((build-dir (getcwd)) | |
1023 | (lib (string-append build-dir "/lib")) | |
1024 | (jhdf (string-append lib "/jhdf.jar")) | |
1025 | (jhdf5 (string-append lib "/jhdf5.jar")) | |
1026 | (testjars | |
1027 | (map (lambda (i) | |
1028 | (string-append (assoc-ref inputs i) | |
1029 | "/share/java/" i ".jar")) | |
1030 | '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple"))) | |
1031 | (class-path | |
1032 | (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":"))) | |
2fd26d05 | 1033 | |
2a509880 RW |
1034 | (substitute* '("test/hdf5lib/Makefile.in" |
1035 | "test/hdf5lib/junit.sh.in" | |
1036 | "examples/runExample.sh.in") | |
1037 | (("/usr/bin/test") | |
1038 | (string-append (assoc-ref inputs "coreutils") | |
1039 | "/bin/test")) | |
1040 | (("/usr/bin/uname") | |
1041 | (string-append (assoc-ref inputs "coreutils") | |
1042 | "/bin/uname")) | |
1043 | (("CLASSPATH=[^\n]*") | |
1044 | (string-append "CLASSPATH=" class-path))) | |
1045 | (setenv "CLASSPATH" class-path)) | |
1046 | #t)) | |
1047 | (add-before 'check 'build-examples | |
1048 | (lambda _ | |
1049 | (apply invoke `("javac" | |
1050 | ,@(find-files "examples" ".*\\.java")))))) | |
2fd26d05 | 1051 | |
2a509880 | 1052 | #:parallel-build? #f |
2fd26d05 | 1053 | |
2a509880 RW |
1054 | #:parallel-tests? #f )) |
1055 | (home-page "https://support.hdfgroup.org/products/java") | |
1056 | (synopsis "Java interface for the HDF4 and HDF5 libraries") | |
1057 | (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use | |
2fd26d05 TD |
1058 | the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are |
1059 | implemented in C.") | |
1060 | ||
2a509880 RW |
1061 | ;; BSD-style license: |
1062 | (license (license:x11-style | |
1063 | "https://support.hdfgroup.org/ftp/HDF5/hdf-java\ | |
2fd26d05 TD |
1064 | /current/src/unpacked/COPYING")))) |
1065 | ||
d3c4f3bb TD |
1066 | (define-public hdf-eos2 |
1067 | (package | |
1068 | (name "hdf-eos2") | |
1069 | (version "19.1.0") | |
1070 | (source | |
1071 | (origin | |
1072 | (method url-fetch) | |
1073 | (uri "ftp://edhs1.gsfc.nasa.gov\ | |
1074 | /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z") | |
1075 | (sha256 | |
1076 | (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz")) | |
1077 | (patches (search-patches "hdf-eos2-remove-gctp.patch" | |
1078 | "hdf-eos2-build-shared.patch" | |
1079 | "hdf-eos2-fortrantests.patch")))) | |
1080 | (build-system gnu-build-system) | |
1081 | (native-inputs | |
1082 | `(("gfortran" ,gfortran))) | |
1083 | (inputs | |
1084 | `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API | |
25bdbb61 | 1085 | ;; XXX: These inputs are really dependencies of hdf4. |
d3c4f3bb TD |
1086 | ("zlib" ,zlib) |
1087 | ("libjpeg" ,libjpeg) | |
25bdbb61 MB |
1088 | ("libtirpc" ,libtirpc) |
1089 | ||
d3c4f3bb TD |
1090 | ("gctp" ,gctp))) |
1091 | (arguments | |
1092 | `( #:configure-flags '("--enable-install-include" "--enable-shared" | |
1093 | "CC=h4cc -Df2cFortran" "LIBS=-lgctp") | |
1094 | #:parallel-tests? #f)) | |
1095 | (home-page "http://hdfeos.org/software/library.php#HDF-EOS2") | |
1096 | (synopsis "HDF4-based data format for NASA's Earth Observing System") | |
1097 | (description "HDF-EOS2 is a software library built on HDF4 which supports | |
1098 | the construction of data structures used in NASA's Earth Observing | |
1099 | System (Grid, Point and Swath).") | |
1100 | ||
1101 | ;; Source files carry a permissive license header. | |
1102 | (license (license:non-copyleft home-page)))) | |
1103 | ||
0f43f835 TD |
1104 | (define-public hdf-eos5 |
1105 | (package | |
1106 | (name "hdf-eos5") | |
1107 | (version "1.15") | |
1108 | (source (origin | |
1109 | (method url-fetch) | |
1110 | (uri (string-append "ftp://edhs1.gsfc.nasa.gov\ | |
1111 | /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z")) | |
1112 | (sha256 | |
1113 | (base32 | |
1114 | "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i")) | |
1115 | (patches (search-patches "hdf-eos5-build-shared.patch" | |
1116 | "hdf-eos5-remove-gctp.patch" | |
1117 | "hdf-eos5-fix-szip.patch" | |
1118 | "hdf-eos5-fortrantests.patch")))) | |
1119 | (native-inputs | |
1120 | `(("gfortran" ,gfortran))) | |
1121 | (build-system gnu-build-system) | |
1122 | (inputs | |
1123 | `(("hdf5" ,hdf5) | |
1124 | ("zlib" ,zlib) | |
1125 | ("gctp" ,gctp))) | |
1126 | (arguments | |
1127 | `(#:configure-flags '("--enable-install-include" "--enable-shared" | |
1128 | "CC=h5cc -Df2cFortran" "LIBS=-lgctp") | |
1129 | #:parallel-tests? #f)) | |
1130 | (synopsis "HDF5-based data format for NASA's Earth Observing System") | |
1131 | (description | |
1132 | "HDF-EOS5 is a software library built on HDF5 to support the construction | |
1133 | of data structures used in NASA's Earth Observing System (Grid, Point and | |
1134 | Swath).") | |
1135 | (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5") | |
1136 | ||
1137 | ;; Source files carry a permissive license header. | |
1138 | (license (license:non-copyleft home-page)))) | |
1139 | ||
c8378eea EB |
1140 | (define-public hdf5-parallel-openmpi |
1141 | (package (inherit hdf5) | |
1142 | (name "hdf5-parallel-openmpi") | |
1143 | (inputs | |
1144 | `(("mpi" ,openmpi) | |
1145 | ,@(package-inputs hdf5))) | |
1146 | (arguments | |
45201bf2 PG |
1147 | (substitute-keyword-arguments (package-arguments hdf5) |
1148 | ((#:configure-flags flags) | |
549d1571 LC |
1149 | ``("--enable-parallel" |
1150 | ,@(delete "--enable-cxx" | |
1151 | (delete "--enable-threadsafe" ,flags)))) | |
c8378eea EB |
1152 | ((#:phases phases) |
1153 | `(modify-phases ,phases | |
45201bf2 PG |
1154 | (add-after 'build 'mpi-setup |
1155 | ,%openmpi-setup) | |
c8378eea EB |
1156 | (add-before 'check 'patch-tests |
1157 | (lambda _ | |
1158 | ;; OpenMPI's mpirun will exit with non-zero status if it | |
1159 | ;; detects an "abnormal termination", i.e. any process not | |
784c3da1 | 1160 | ;; calling MPI_Finalize(). Since the test is explicitly |
c8378eea EB |
1161 | ;; avoiding MPI_Finalize so as not to have at_exit and thus |
1162 | ;; H5C_flush_cache from being called, mpirun will always | |
1163 | ;; complain, so turn this test off. | |
1164 | (substitute* "testpar/Makefile" | |
1165 | (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back) | |
1166 | (string-append front back "\n"))) | |
1167 | (substitute* "tools/h5diff/testph5diff.sh" | |
1168 | (("/bin/sh") (which "sh"))) | |
1169 | #t)))))) | |
1170 | (synopsis "Management suite for data with parallel IO support"))) | |
1171 | ||
00775104 EB |
1172 | (define-public h5check |
1173 | (package | |
1174 | (name "h5check") | |
1175 | (version "2.0.1") | |
1176 | (source | |
1177 | (origin | |
1178 | (method url-fetch) | |
0a44f9c4 | 1179 | (uri (string-append "https://www.hdfgroup.org/ftp/HDF5/tools/" |
00775104 EB |
1180 | "h5check/src/h5check-" version ".tar.gz")) |
1181 | (sha256 | |
1182 | (base32 | |
1183 | "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj")))) | |
1184 | (build-system gnu-build-system) | |
1185 | (inputs `(("hdf5" ,hdf5))) ;h5cc for tests | |
1186 | (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html") | |
1187 | (synopsis "HDF5 format checker") | |
1188 | (description "@code{h5check} is a validation tool for verifying that an | |
1189 | HDF5 file is encoded according to the HDF File Format Specification.") | |
1190 | (license (license:x11-style "file://COPYING")))) | |
1191 | ||
a53d6719 JD |
1192 | (define-public itpp |
1193 | (package | |
1194 | (name "itpp") | |
1195 | (version "4.3.1") | |
1196 | (source (origin | |
1197 | (method url-fetch) | |
1198 | (uri (string-append "mirror://sourceforge/itpp/itpp/" | |
1199 | version "/itpp-" | |
1200 | version ".tar.gz")) | |
1201 | (sha256 | |
1202 | (base32 | |
1203 | "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm")))) | |
1204 | (build-system cmake-build-system) | |
1205 | (arguments `(#:tests? #f)) ; Tests require googletest *sources* | |
1206 | (inputs `(("lapack" ,lapack) | |
1207 | ("fftw" ,fftw))) | |
3a4d5df2 RW |
1208 | ;; FIXME: Even though the fonts are available dvips complains: |
1209 | ;; "Font cmmi10 not found; characters will be left blank." | |
1210 | (native-inputs | |
1211 | `(("texlive" ,texlive-tiny) | |
1212 | ("ghostscript" ,ghostscript) | |
1213 | ("doxygen" ,doxygen))) | |
a53d6719 JD |
1214 | (home-page "http://itpp.sourceforge.net") |
1215 | (synopsis "C++ library of maths, signal processing and communication classes") | |
1216 | (description "IT++ is a C++ library of mathematical, signal processing and | |
1217 | communication classes and functions. Its main use is in simulation of | |
1218 | communication systems and for performing research in the area of | |
1219 | communications. The kernel of the library consists of generic vector and | |
1220 | matrix classes, and a set of accompanying routines. Such a kernel makes IT++ | |
1221 | similar to MATLAB, GNU Octave or SciPy.") | |
1222 | (license license:gpl3+))) | |
1223 | ||
889187a4 EB |
1224 | (define-public netcdf |
1225 | (package | |
1226 | (name "netcdf") | |
a4b0bfb1 | 1227 | (version "4.4.1.1") |
889187a4 EB |
1228 | (source |
1229 | (origin | |
1230 | (method url-fetch) | |
1231 | (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/" | |
1232 | "netcdf-" version ".tar.gz")) | |
1233 | (sha256 | |
1234 | (base32 | |
a4b0bfb1 EB |
1235 | "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d")) |
1236 | (patches (search-patches "netcdf-date-time.patch" | |
1237 | "netcdf-tst_h_par.patch")))) | |
889187a4 EB |
1238 | (build-system gnu-build-system) |
1239 | (native-inputs | |
1240 | `(("m4" ,m4) | |
1241 | ("doxygen" ,doxygen) | |
1242 | ("graphviz" ,graphviz))) | |
1243 | (inputs | |
db825570 TD |
1244 | `(("hdf4" ,hdf4-alt) |
1245 | ("hdf5" ,hdf5) | |
1246 | ("zlib" ,zlib) | |
1247 | ("libjpeg" ,libjpeg))) | |
889187a4 | 1248 | (arguments |
db825570 | 1249 | `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4") |
43d01672 TD |
1250 | |
1251 | #:phases (modify-phases %standard-phases | |
1252 | (add-before 'configure 'fix-source-date | |
1253 | (lambda _ | |
1254 | ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build | |
1255 | ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate | |
1256 | ;; to '1st hour of the current day', and therefore makes the | |
1257 | ;; package not reproducible. | |
1258 | (substitute* "./configure" | |
1259 | (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"") | |
1260 | "date --date='@0'")) | |
1261 | #t)) | |
1262 | (add-after 'configure 'patch-settings | |
1263 | (lambda _ | |
1264 | ;; libnetcdf.settings contains the full filename of the compilers | |
1265 | ;; used to build the library. We truncate the hashes of those | |
1266 | ;; filenames to avoid unnecessary references to the corresponding | |
1267 | ;; store items. | |
1268 | (substitute* "libnetcdf.settings" | |
1269 | (("(/gnu/store/)([a-Z0-9]*)" all prefix hash) | |
1270 | (string-append prefix (string-take hash 10) "..."))) | |
1271 | #t))) | |
1272 | ||
889187a4 | 1273 | #:parallel-tests? #f)) ;various race conditions |
821aa687 | 1274 | (home-page "https://www.unidata.ucar.edu/software/netcdf/") |
889187a4 EB |
1275 | (synopsis "Library for scientific data") |
1276 | (description "NetCDF is an interface for scientific data access and a | |
1277 | software library that provides an implementation of the interface. The netCDF | |
1278 | library defines a machine-independent format for representing scientific data. | |
1279 | Together, the interface, library, and format support the creation, access, and | |
1280 | sharing of scientific data.") | |
1281 | (license (license:x11-style "file://COPYRIGHT")))) | |
1282 | ||
1283 | (define-public netcdf-parallel-openmpi | |
1284 | (package (inherit netcdf) | |
1285 | (name "netcdf-parallel-openmpi") | |
1286 | (inputs | |
1287 | `(("mpi" ,openmpi) | |
1288 | ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi) | |
1289 | (package-inputs netcdf)))) | |
1290 | ;; TODO: Replace pkg-config references in nc-config with absolute references | |
1291 | (arguments | |
1292 | (substitute-keyword-arguments (package-arguments netcdf) | |
1293 | ((#:configure-flags flags) | |
1294 | `(cons* "CC=mpicc" "CXX=mpicxx" | |
1295 | "--enable-parallel-tests" | |
1296 | ;; Shared libraries not supported with parallel IO. | |
1297 | "--disable-shared" "--with-pic" | |
1298 | ,flags)))))) | |
1299 | ||
300200b6 TD |
1300 | (define-public netcdf-fortran |
1301 | (package | |
1302 | (name "netcdf-fortran") | |
1303 | (version "4.4.4") | |
1304 | (source (origin | |
1305 | (method url-fetch) | |
1306 | (uri (string-append | |
1307 | "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-" | |
1308 | version ".tar.gz")) | |
1309 | (sha256 | |
1310 | (base32 | |
1311 | "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj")))) | |
1312 | (build-system gnu-build-system) | |
1313 | (arguments | |
1314 | `(#:parallel-tests? #f)) | |
1315 | (inputs | |
1316 | `(("netcdf" ,netcdf))) | |
1317 | (native-inputs | |
1318 | `(("gfortran" ,gfortran))) | |
1319 | (synopsis "Fortran interface for the netCDF library") | |
1320 | (description (package-description netcdf)) | |
1321 | (home-page (package-home-page netcdf)) | |
1322 | (license (package-license netcdf)))) | |
1323 | ||
1b39a196 RJ |
1324 | (define-public nlopt |
1325 | (package | |
1326 | (name "nlopt") | |
1327 | (version "2.4.2") | |
1328 | (source (origin | |
1329 | (method url-fetch) | |
1330 | (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-" | |
1331 | version ".tar.gz")) | |
1332 | (sha256 | |
1333 | (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0")))) | |
1334 | (build-system gnu-build-system) | |
1335 | (arguments | |
1336 | `(;; Shared libraries are not built by default. They are required to | |
1337 | ;; build the Guile, Octave, and Python bindings. | |
1338 | #:configure-flags '("--enable-shared") | |
1339 | ||
1340 | #:phases | |
1341 | (modify-phases %standard-phases | |
1342 | (add-before 'configure 'set-libnlopt-file-name | |
1343 | (lambda* (#:key outputs #:allow-other-keys) | |
1344 | ;; Make sure the Scheme module refers to the library by its | |
1345 | ;; absolute file name (we cannot do that from a snippet | |
1346 | ;; because the expansion of @libdir@ contains | |
1347 | ;; ${exec_prefix}.) | |
1348 | (let ((out (assoc-ref outputs "out"))) | |
1349 | (substitute* "swig/nlopt.scm.in" | |
1350 | (("libnlopt") | |
1351 | (string-append out "/lib/libnlopt"))) | |
1352 | #t)))))) | |
1353 | (inputs `(("guile" ,guile-2.0))) | |
1354 | (native-inputs `(("pkg-config" ,pkg-config))) | |
1355 | (home-page "http://ab-initio.mit.edu/wiki/") | |
1356 | (synopsis "Library for nonlinear optimization") | |
1357 | (description "NLopt is a library for nonlinear optimization, providing a | |
1358 | common interface for a number of different free optimization routines available | |
1359 | online as well as original implementations of various other algorithms.") | |
1360 | (license license:lgpl2.1+))) | |
1361 | ||
005c787d LC |
1362 | (define-public ipopt |
1363 | (package | |
1364 | (name "ipopt") | |
98a5cd51 | 1365 | (version "3.12.12") |
005c787d LC |
1366 | (source (origin |
1367 | (method url-fetch) | |
1368 | (uri (string-append | |
1369 | "http://www.coin-or.org/download/source/Ipopt/Ipopt-" | |
1370 | version".tgz")) | |
1371 | (sha256 | |
1372 | (base32 | |
98a5cd51 | 1373 | "07yn9rzdswjk8n246qq6ci9ssf2bcplkifcpsfz9j6cdxw9vgbkv")) |
005c787d LC |
1374 | (modules '((guix build utils))) |
1375 | (snippet | |
1376 | ;; Make sure we don't use the bundled software. | |
6cbee49d MW |
1377 | '(begin |
1378 | (delete-file-recursively "ThirdParty") | |
1379 | #t)))) | |
005c787d | 1380 | (build-system gnu-build-system) |
ad1c4537 LC |
1381 | (arguments |
1382 | '(#:phases (modify-phases %standard-phases | |
1383 | (add-after 'install 'add--L-flags-in-ipopt.pc | |
1384 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1385 | ;; The '.pc' file lists '-llapack -lblas' in "Libs"; | |
1386 | ;; move it to "Libs.private" where it belongs, and add a | |
1387 | ;; '-L' flag for LAPACK. | |
1388 | (let ((out (assoc-ref outputs "out")) | |
1389 | (lapack (assoc-ref inputs "lapack"))) | |
1390 | (substitute* (string-append out "/lib/pkgconfig/" | |
1391 | "ipopt.pc") | |
1392 | (("Libs: (.*)-llapack -lblas(.*)$" _ before after) | |
1393 | (string-append "Libs: " before " " after "\n" | |
1394 | "Libs.private: " before | |
1395 | "-L" lapack "/lib -llapack -lblas " | |
1396 | after "\n"))) | |
1397 | #t)))))) | |
005c787d LC |
1398 | (native-inputs |
1399 | `(("gfortran" ,gfortran))) | |
1400 | (inputs | |
1401 | ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL. | |
ad1c4537 | 1402 | `(("lapack" ,lapack))) ;for both libblas and liblapack |
005c787d LC |
1403 | (home-page "http://www.coin-or.org") |
1404 | (synopsis "Large-scale nonlinear optimizer") | |
1405 | (description | |
1406 | "The Interior Point Optimizer (IPOPT) is a software package for | |
1407 | large-scale nonlinear optimization. It provides C++, C, and Fortran | |
1408 | interfaces.") | |
1409 | (license license:epl1.0))) | |
1410 | ||
ecfbc51f RW |
1411 | (define-public clp |
1412 | (package | |
1413 | (name "clp") | |
1414 | (version "1.17.1") | |
1415 | (source (origin | |
1416 | (method url-fetch) | |
1417 | (uri (string-append "https://www.coin-or.org/download/source/" | |
1418 | "Clp/Clp-" version ".tgz")) | |
1419 | (sha256 | |
1420 | (base32 | |
1421 | "1wdg820g3iikf9344ijwsc8sy6c0m6im42bzzizm6rlmkvnmxhk9")) | |
1422 | (modules '((guix build utils))) | |
1423 | (snippet | |
1424 | ;; Make sure we don't use the bundled software. | |
1425 | '(begin | |
1426 | (delete-file-recursively "ThirdParty") | |
1427 | #t)))) | |
1428 | (build-system gnu-build-system) | |
1429 | (native-inputs | |
1430 | `(("gfortran" ,gfortran) | |
1431 | ("pkg-config" ,pkg-config))) | |
1432 | (inputs | |
1433 | `(("openblas" ,openblas))) | |
1434 | (home-page "https://www.coin-or.org") | |
1435 | (synopsis "Linear programming solver") | |
1436 | (description | |
1437 | "CLP is a high quality linear programming solver. Its main strengths are | |
1438 | its dual and primal Simplex algorithms. It also has a barrier algorithm for | |
1439 | linear and quadratic objectives. There are limited facilities for nonlinear | |
1440 | and quadratic objectives using the Simplex algorithm.") | |
1441 | (license license:epl1.0))) | |
1442 | ||
f9940ef1 LC |
1443 | (define-public ceres |
1444 | (package | |
1445 | (name "ceres-solver") | |
e0bee0de | 1446 | (version "1.14.0") |
f9940ef1 LC |
1447 | (home-page "http://ceres-solver.org/") |
1448 | (source (origin | |
1449 | (method url-fetch) | |
1450 | (uri (string-append home-page "ceres-solver-" | |
1451 | version ".tar.gz")) | |
1452 | (sha256 | |
1453 | (base32 | |
e0bee0de | 1454 | "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27")))) |
f9940ef1 LC |
1455 | (build-system cmake-build-system) |
1456 | (arguments | |
1457 | ;; TODO: Build HTML user documentation and install separately. | |
bc3a2e35 | 1458 | '(#:configure-flags '("-DBUILD_EXAMPLES=OFF" |
f9940ef1 LC |
1459 | "-DBUILD_SHARED_LIBS=ON") |
1460 | ||
1461 | #:phases (modify-phases %standard-phases | |
1462 | (add-before 'configure 'set-library-directory | |
1463 | (lambda _ | |
1464 | ;; Install libraries to lib/, not lib64/. | |
1465 | (substitute* "internal/ceres/CMakeLists.txt" | |
1466 | (("set\\(LIB_SUFFIX \"64\"\\)") | |
1467 | "set(LIB_SUFFIX \"\")")) | |
1468 | #t))))) | |
1469 | (native-inputs | |
1470 | `(("pkg-config" ,pkg-config))) | |
468e0b18 LC |
1471 | (propagated-inputs |
1472 | `(("glog" ,glog))) ;for #include <glog/glog.h> | |
f9940ef1 LC |
1473 | (inputs |
1474 | `(("eigen" ,eigen) | |
1475 | ("blas" ,openblas) | |
1476 | ("lapack" ,lapack) | |
1477 | ("suitesparse" ,suitesparse) | |
1478 | ("gflags" ,gflags))) | |
1479 | (synopsis "C++ library for solving large optimization problems") | |
1480 | (description | |
1481 | "Ceres Solver is a C++ library for modeling and solving large, | |
1482 | complicated optimization problems. It is a feature rich, mature and | |
1483 | performant library which has been used in production since 2010. Ceres Solver | |
1484 | can solve two kinds of problems: | |
1485 | @enumerate | |
1486 | @item non-linear least squares problems with bounds constraints; | |
1487 | @item general unconstrained optimization problems. | |
1488 | @end enumerate\n") | |
1489 | (license license:bsd-3))) | |
1490 | ||
b66741ed | 1491 | ;; For a fully featured Octave, users are strongly recommended also to install |
5ca4fe96 | 1492 | ;; the following packages: less, ghostscript, gnuplot. |
5537603f | 1493 | (define-public octave-cli |
668c06ac | 1494 | (package |
5537603f | 1495 | (name "octave-cli") |
8a0dd289 | 1496 | (version "5.2.0") |
668c06ac JD |
1497 | (source |
1498 | (origin | |
1499 | (method url-fetch) | |
1500 | (uri (string-append "mirror://gnu/octave/octave-" | |
f5a077b1 | 1501 | version ".tar.lz")) |
668c06ac JD |
1502 | (sha256 |
1503 | (base32 | |
8a0dd289 | 1504 | "1848dq6nxzal8gwjrcp6xhi5gq96w89nss9d9rz75q408gb3mbl6")))) |
668c06ac JD |
1505 | (build-system gnu-build-system) |
1506 | (inputs | |
697df13f EF |
1507 | `(("alsa-lib" ,alsa-lib) |
1508 | ("arpack" ,arpack-ng) | |
8a0dd289 | 1509 | ("bdb" ,bdb) |
697df13f | 1510 | ("curl" ,curl) |
1ec78e9d EB |
1511 | ("fftw" ,fftw) |
1512 | ("fftwf" ,fftwf) | |
668c06ac JD |
1513 | ("fltk" ,fltk) |
1514 | ("fontconfig" ,fontconfig) | |
1515 | ("freetype" ,freetype) | |
697df13f EF |
1516 | ("gl2ps" ,gl2ps) |
1517 | ("glpk" ,glpk) | |
1ec78e9d | 1518 | ("glu" ,glu) |
ab5f3f21 | 1519 | ("graphicsmagick" ,graphicsmagick) |
697df13f EF |
1520 | ("hdf5" ,hdf5) |
1521 | ("lapack" ,lapack) | |
ab5f3f21 | 1522 | ("libsndfile" ,libsndfile) |
697df13f EF |
1523 | ("libxft" ,libxft) |
1524 | ("mesa" ,mesa) | |
1525 | ("pcre" ,pcre) | |
ab5f3f21 | 1526 | ("portaudio" ,portaudio) |
697df13f EF |
1527 | ("qhull" ,qhull) |
1528 | ("readline" ,readline) | |
1529 | ("suitesparse" ,suitesparse) | |
1530 | ("texinfo" ,texinfo) | |
1531 | ("zlib" ,zlib))) | |
668c06ac | 1532 | (native-inputs |
f5a077b1 EF |
1533 | `(("lzip" ,lzip) |
1534 | ("gfortran" ,gfortran) | |
668c06ac JD |
1535 | ("pkg-config" ,pkg-config) |
1536 | ("perl" ,perl) | |
1ec78e9d EB |
1537 | ;; The following inputs are not actually used in the build process. |
1538 | ;; However, the ./configure gratuitously tests for their existence and | |
1539 | ;; assumes that programs not present at build time are also not, and | |
1540 | ;; can never be, available at run time! If these inputs are therefore | |
1541 | ;; not present, support for them will be built out. However, Octave | |
1542 | ;; will still run without them, albeit without the features they | |
668c06ac JD |
1543 | ;; provide. |
1544 | ("less" ,less) | |
668c06ac JD |
1545 | ("ghostscript" ,ghostscript) |
1546 | ("gnuplot" ,gnuplot))) | |
116af86f KK |
1547 | ;; Octave code uses this variable to detect directories holding multiple CA |
1548 | ;; certificates to verify peers with. This is required for the networking | |
1549 | ;; functions that require encryption to work properly. | |
1550 | (native-search-paths | |
1551 | (list (search-path-specification | |
1552 | (variable "CURLOPT_CAPATH") | |
1553 | (files '("etc/ssl/certs"))))) | |
668c06ac | 1554 | (arguments |
b7b27a8f KY |
1555 | `(#:configure-flags |
1556 | (list (string-append "--with-shell=" | |
1557 | (assoc-ref %build-inputs "bash") | |
5ca4fe96 AI |
1558 | "/bin/sh")) |
1559 | #:phases | |
1560 | (modify-phases %standard-phases | |
1561 | (add-after 'configure 'configure-makeinfo | |
1562 | (lambda* (#:key inputs #:allow-other-keys) | |
b18b9d20 AI |
1563 | (substitute* "libinterp/corefcn/help.h" |
1564 | (("\"makeinfo\"") | |
1565 | (string-append | |
1566 | "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\""))) | |
5ca4fe96 | 1567 | #t))))) |
f5a077b1 | 1568 | (home-page "https://www.gnu.org/software/octave/") |
668c06ac | 1569 | (synopsis "High-level language for numerical computation") |
1ec78e9d EB |
1570 | (description "GNU Octave is a high-level interpreted language that is |
1571 | specialized for numerical computations. It can be used for both linear and | |
1572 | non-linear applications and it provides great support for visualizing results. | |
1573 | Work may be performed both at the interactive command-line as well as via | |
1574 | script files.") | |
668c06ac | 1575 | (license license:gpl3+))) |
3de01d3f | 1576 | |
e0ae7e73 | 1577 | (define-public octave |
5537603f | 1578 | (package (inherit octave-cli) |
e0ae7e73 | 1579 | (name "octave") |
7a3772b3 | 1580 | (source (origin |
5537603f | 1581 | (inherit (package-source octave-cli)))) |
36ce25f0 KK |
1582 | (inputs |
1583 | `(("qscintilla" ,qscintilla) | |
1584 | ("qt" ,qtbase) | |
5537603f | 1585 | ,@(package-inputs octave-cli))) |
36ce25f0 KK |
1586 | (native-inputs |
1587 | `(("qttools" , qttools) ;for lrelease | |
70bb5d88 | 1588 | ("texlive" ,(texlive-union (list texlive-epsf))) ; for texi2dvi |
5537603f | 1589 | ,@(package-native-inputs octave-cli))) |
36ce25f0 | 1590 | (arguments |
5537603f | 1591 | (substitute-keyword-arguments (package-arguments octave-cli) |
36ce25f0 KK |
1592 | ((#:phases phases) |
1593 | `(modify-phases ,phases | |
1594 | (add-before 'configure 'patch-qscintilla-library-name | |
1595 | (lambda* (#:key inputs #:allow-other-keys) | |
1596 | ;; The QScintilla library that the Octave configure script tries | |
1597 | ;; to link with should be named libqscintilla-qt5.so, but the | |
1598 | ;; QScintilla input provides the shared library as | |
1599 | ;; libqscintilla2_qt5.so. | |
1600 | (substitute* "configure" | |
1601 | (("qscintilla2-qt5") | |
1602 | "qscintilla2_qt5")) | |
1603 | #t)))))))) | |
1604 | ||
e0ae7e73 KK |
1605 | (define-public qtoctave |
1606 | (deprecated-package "qtoctave" octave)) | |
1607 | ||
5d4bd4cc PG |
1608 | (define-public opencascade-oce |
1609 | (package | |
1610 | (name "opencascade-oce") | |
1611 | (version "0.17.2") | |
1612 | (source | |
1613 | (origin | |
830971bf TGR |
1614 | (method git-fetch) |
1615 | (uri (git-reference | |
1616 | (url "https://github.com/tpaviot/oce.git") | |
1617 | (commit (string-append "OCE-" version)))) | |
1618 | (file-name (git-file-name name version)) | |
a4f393b7 | 1619 | (patches (search-patches "opencascade-oce-glibc-2.26.patch")) |
5d4bd4cc | 1620 | (sha256 |
830971bf | 1621 | (base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69")))) |
5d4bd4cc PG |
1622 | (build-system cmake-build-system) |
1623 | (arguments | |
1624 | '(#:configure-flags | |
1625 | (list "-DOCE_TESTING:BOOL=ON" | |
1626 | "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON" | |
1627 | "-DOCE_DRAW:BOOL=ON" | |
1628 | (string-append "-DOCE_INSTALL_PREFIX:PATH=" | |
1629 | (assoc-ref %outputs "out")) | |
1630 | "-UCMAKE_INSTALL_RPATH"))) | |
1631 | (inputs | |
1632 | `(("freetype" ,freetype) | |
1633 | ("glu" ,glu) | |
1634 | ("libxmu" ,libxmu) | |
1635 | ("mesa" ,mesa) | |
1636 | ("tcl" ,tcl) | |
1637 | ("tk" ,tk))) | |
1638 | (native-inputs | |
1639 | `(("python" ,python-wrapper))) | |
1640 | (home-page "https://github.com/tpaviot/oce") | |
1641 | (synopsis "Libraries for 3D modeling and numerical simulation") | |
1642 | (description | |
1643 | "Open CASCADE is a set of libraries for the development of applications | |
1644 | dealing with 3D CAD data or requiring industrial 3D capabilities. It includes | |
1645 | C++ class libraries providing services for 3D surface and solid modeling, CAD | |
1646 | data exchange, and visualization. It is used for development of specialized | |
1647 | software dealing with 3D models in design (CAD), manufacturing (CAM), | |
1648 | numerical simulation (CAE), measurement equipment (CMM), and quality | |
1649 | control (CAQ) domains. | |
1650 | ||
1651 | This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers | |
1652 | patches, improvements, and experiments contributed by users over the official | |
1653 | Open CASCADE library.") | |
1654 | (license (list license:lgpl2.1; OCE libraries, with an exception for the | |
1655 | ; use of header files; see | |
1656 | ; OCCT_LGPL_EXCEPTION.txt | |
1657 | license:public-domain; files | |
1658 | ; src/Standard/Standard_StdAllocator.hxx and | |
1659 | ; src/NCollection/NCollection_StdAllocator.hxx | |
1660 | license:expat; file src/OpenGl/OpenGl_glext.h | |
1661 | license:bsd-3)))); test framework gtest | |
1662 | ||
37dc2920 PG |
1663 | (define-public opencascade-occt |
1664 | (package | |
1665 | (name "opencascade-occt") | |
1666 | (version "7.3.0p3") | |
1667 | (source | |
1668 | (origin | |
1669 | (method git-fetch) | |
1670 | (uri (git-reference | |
1671 | (url "https://git.dev.opencascade.org/repos/occt.git") | |
1672 | (commit | |
1673 | (string-append "V" | |
1674 | (string-map (lambda (x) (if (eq? x #\.) #\_ x)) | |
1675 | version))))) | |
1676 | (file-name (git-file-name name version)) | |
1677 | (sha256 | |
1678 | (base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4")) | |
1679 | (modules '((guix build utils))) | |
1680 | (snippet | |
1681 | '(begin | |
1682 | ;; Remove files specific to non-free operating systems. | |
1683 | (delete-file-recursively "samples/ios") | |
1684 | (delete-file-recursively "samples/mfc") | |
1685 | (delete-file-recursively "samples/qt/FuncDemo") | |
1686 | (delete-file "genconf.bat") | |
1687 | (delete-file "gendoc.bat") | |
1688 | (delete-file "genproj.bat") | |
1689 | (delete-file "upgrade.bat") | |
1690 | ;; Remove references to deleted files. | |
1691 | (substitute* "dox/FILES_HTML.txt" | |
1692 | ((".*standard.*") "" ) | |
1693 | ((".*UIKitSample.*") "")) | |
1694 | #t)))) | |
1695 | (build-system cmake-build-system) | |
1696 | (arguments | |
1697 | '(;; There is no test target for make. OCCT provides an | |
1698 | ;; 'Automated Testing System', which may be accessed after | |
1699 | ;; installation via the draw.sh script. draw.sh is located in | |
1700 | ;; the bin directory. For details see: | |
1701 | ;; https://www.opencascade.com/doc/occt-7.3.0/overview/html/\ | |
1702 | ;; occt_dev_guides__tests.html | |
1703 | #:tests? #f | |
1704 | ;; Configure without freeimage: attempting to link against the | |
1705 | ;; freeimage version 3.17 library leads to 'undefined | |
1706 | ;; reference' errors. | |
1707 | #:configure-flags | |
1708 | (list "-DUSE_FREEIMAGE:BOOL=OFF" | |
1709 | "-DUSE_TBB:BOOL=ON" | |
1710 | "-DUSE_VTK:BOOL=OFF" | |
1711 | "-DBUILD_DOC_Overview:BOOL=OFF" | |
1712 | "-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON" | |
1713 | "-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON" | |
1714 | "-UCMAKE_INSTALL_LIBDIR"))) | |
1715 | (inputs | |
1716 | `(("doxygen" ,doxygen) | |
1717 | ;("freeimage" ,freeimage) | |
1718 | ("freetype" ,freetype) | |
1719 | ("glu" ,glu) | |
1720 | ("libxext" ,libxext) | |
1721 | ("libxi" ,libxi) | |
1722 | ("libxmu" ,libxmu) | |
1723 | ("mesa" ,mesa) | |
1724 | ("tbb" ,tbb) | |
1725 | ("tcl" ,tcl) | |
1726 | ("tk" ,tk))) | |
1727 | ;; TODO: build Overview documentation and add 'doc' output. | |
1728 | (home-page "https://www.opencascade.com") | |
1729 | (synopsis "Libraries for 3D modeling and numerical simulation") | |
1730 | (description | |
1731 | "Open CASCADE is a set of libraries for the development of applications | |
1732 | dealing with 3D CAD data or requiring industrial 3D capabilities. It includes | |
1733 | C++ class libraries providing services for 3D surface and solid modeling, CAD | |
1734 | data exchange, and visualization. It is used for development of specialized | |
1735 | software dealing with 3D models in design (CAD), manufacturing (CAM), | |
1736 | numerical simulation (CAE), measurement equipment (CMM), and quality | |
1737 | control (CAQ) domains. | |
1738 | ||
1739 | This is the certified version of the Open Cascade Technology (OCCT) library.") | |
1740 | (license (list ;; OCCT library: | |
1741 | license:lgpl2.1; with an exception for the use of header | |
1742 | ; files, see OCCT_LGPL_EXCEPTION.txt. | |
1743 | ;; Files src/OpenGl/glext.h, adm/cmake/cotire.cmake and | |
1744 | ;; src/OpenGl/OpenGl_HaltonSampler.hxx: | |
1745 | license:expat | |
1746 | ;; Files src/ExprIntrp/ExprIntrp.tab.* and | |
1747 | ;; src/StepFile/step.tab.*: | |
1748 | license:gpl3+ ; with Bison 2.2 exception. | |
1749 | ;; File src/NCollection/NCollection_UtfIterator.lxx: | |
1750 | (license:non-copyleft | |
1751 | "https://www.unicode.org/license.html") | |
1752 | ;; File src/NCollection/NCollection_StdAllocator.hxx: | |
1753 | license:public-domain)))) | |
1754 | ||
3de01d3f EB |
1755 | (define-public gmsh |
1756 | (package | |
1757 | (name "gmsh") | |
8a4d14fa | 1758 | (version "2.16.0") |
3de01d3f EB |
1759 | (source |
1760 | (origin | |
abed5df7 PG |
1761 | (method git-fetch) |
1762 | (uri (git-reference | |
1763 | (url "https://gitlab.onelab.info/gmsh/gmsh.git") | |
1764 | (commit | |
1765 | (string-append "gmsh_" | |
1766 | (string-map (lambda (x) (if (eq? x #\.) #\_ x)) | |
1767 | version))))) | |
1768 | (file-name (git-file-name name version)) | |
3de01d3f | 1769 | (sha256 |
abed5df7 | 1770 | (base32 "08rq4jajwmlpivnm9yifz2jhaivnz065lnk0h2zv773nwl9wf162")) |
3de01d3f EB |
1771 | (modules '((guix build utils))) |
1772 | (snippet | |
1773 | ;; Remove non-free METIS code | |
6cbee49d MW |
1774 | '(begin |
1775 | (delete-file-recursively "contrib/Metis") | |
1776 | #t)))) | |
3de01d3f | 1777 | (build-system cmake-build-system) |
3de01d3f EB |
1778 | (propagated-inputs |
1779 | `(("fltk" ,fltk) | |
19afbea1 | 1780 | ("gfortran" ,gfortran) |
3de01d3f | 1781 | ("gmp" ,gmp) |
40029cbe | 1782 | ("hdf5" ,hdf5) |
3de01d3f EB |
1783 | ("lapack" ,lapack) |
1784 | ("mesa" ,mesa) | |
85f41902 | 1785 | ("glu" ,glu) |
45548139 | 1786 | ("opencascade-oce" ,opencascade-oce) |
3de01d3f EB |
1787 | ("libx11" ,libx11) |
1788 | ("libxext" ,libxext))) | |
66395a61 EF |
1789 | (inputs |
1790 | `(("fontconfig" ,fontconfig) | |
1791 | ("libxft" ,libxft))) | |
3de01d3f EB |
1792 | (arguments |
1793 | `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF" | |
1794 | "-DENABLE_BUILD_SHARED:BOOL=ON" | |
45548139 | 1795 | "-DENABLE_BUILD_DYNAMIC:BOOL=ON"))) |
0746c33e | 1796 | (home-page "http://gmsh.info/") |
3de01d3f | 1797 | (synopsis "3D finite element grid generator") |
edf684ef EB |
1798 | (description "Gmsh is a 3D finite element grid generator with a built-in |
1799 | CAD engine and post-processor. Its design goal is to provide a fast, light | |
1800 | and user-friendly meshing tool with parametric input and advanced | |
1801 | visualization capabilities. Gmsh is built around four modules: geometry, | |
1802 | mesh, solver and post-processing. The specification of any input to these | |
1803 | modules is done either interactively using the graphical user interface or in | |
1804 | ASCII text files using Gmsh's own scripting language.") | |
3de01d3f | 1805 | (license license:gpl2+))) |
b9100e2f | 1806 | |
6d5f63b6 JD |
1807 | (define-public maxflow |
1808 | (package | |
1809 | (name "maxflow") | |
0af12a13 TGR |
1810 | ;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’, |
1811 | ;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’. | |
1812 | (version "3.0.5") | |
6d5f63b6 JD |
1813 | (source (origin |
1814 | (method git-fetch) | |
1815 | (uri (git-reference | |
1816 | (url "https://github.com/gerddie/maxflow.git") | |
0af12a13 | 1817 | (commit version))) |
2dc0a6cf | 1818 | (file-name (git-file-name name version)) |
6d5f63b6 JD |
1819 | (sha256 |
1820 | (base32 | |
1821 | "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb")))) | |
1822 | (build-system cmake-build-system) | |
0be9038c | 1823 | (home-page "https://pub.ist.ac.at/~vnk/software.html") |
6d5f63b6 JD |
1824 | (synopsis "Library implementing Maxflow algorithm") |
1825 | (description "An implementation of the maxflow algorithm described in | |
1826 | @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for | |
1827 | Energy Minimization in Computer Vision.\n | |
1828 | Yuri Boykov and Vladimir Kolmogorov.\n | |
1829 | In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n | |
1830 | September 2004}") | |
1831 | (license license:gpl3+))) | |
1832 | ||
b9100e2f EB |
1833 | (define-public petsc |
1834 | (package | |
1835 | (name "petsc") | |
4f7a4a06 | 1836 | (version "3.11.2") |
b9100e2f EB |
1837 | (source |
1838 | (origin | |
1839 | (method url-fetch) | |
1840 | ;; The *-lite-* tarball does not contain the *large* documentation | |
1841 | (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" | |
1842 | "petsc-lite-" version ".tar.gz")) | |
1843 | (sha256 | |
4f7a4a06 | 1844 | (base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx")))) |
b2c52fc9 TGR |
1845 | (outputs '("out" ; libraries and headers |
1846 | "examples")) ; ~30MiB of examples | |
b9100e2f EB |
1847 | (build-system gnu-build-system) |
1848 | (native-inputs | |
6fec298d | 1849 | `(("python" ,python-2))) |
b9100e2f | 1850 | (inputs |
19afbea1 | 1851 | `(("gfortran" ,gfortran) |
b9100e2f | 1852 | ("lapack" ,lapack) |
f258212d | 1853 | ("superlu" ,superlu) |
b9100e2f EB |
1854 | ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi |
1855 | ;; leaving out opengl, as configuration seems to only be for mac | |
1856 | )) | |
1857 | (arguments | |
1858 | `(#:test-target "test" | |
b2c52fc9 | 1859 | #:parallel-build? #f ; build is parallel by default |
b9100e2f EB |
1860 | #:configure-flags |
1861 | `("--with-mpi=0" | |
f258212d | 1862 | "--with-openmp=1" |
c15be128 | 1863 | "--with-superlu=1") |
9731c412 EB |
1864 | #:make-flags |
1865 | ;; Honor (parallel-job-count) for build. Do not use --with-make-np, | |
1866 | ;; whose value is dumped to $out/lib/petsc/conf/petscvariables. | |
1867 | (list (format #f "MAKE_NP=~a" (parallel-job-count))) | |
b9100e2f | 1868 | #:phases |
64dcc289 EB |
1869 | (modify-phases %standard-phases |
1870 | (replace 'configure | |
1871 | ;; PETSc's configure script is actually a python script, so we can't | |
1872 | ;; run it with bash. | |
1873 | (lambda* (#:key outputs (configure-flags '()) | |
1874 | #:allow-other-keys) | |
1875 | (let* ((prefix (assoc-ref outputs "out")) | |
1876 | (flags `(,(string-append "--prefix=" prefix) | |
1877 | ,@configure-flags))) | |
1878 | (format #t "build directory: ~s~%" (getcwd)) | |
1879 | (format #t "configure flags: ~s~%" flags) | |
49fdd357 | 1880 | (apply invoke "./configure" flags)))) |
64dcc289 | 1881 | (add-after 'configure 'clean-local-references |
9731c412 | 1882 | (lambda* (#:key outputs #:allow-other-keys) |
64dcc289 EB |
1883 | (let ((out (assoc-ref outputs "out"))) |
1884 | (substitute* (find-files "." "^petsc(conf|machineinfo).h$") | |
b730b437 EB |
1885 | ;; Prevent build directory from leaking into compiled code |
1886 | (((getcwd)) out) | |
1887 | ;; Scrub timestamp for reproducibility | |
fafd623e | 1888 | ((".*Libraries compiled on.*") "")) |
9731c412 EB |
1889 | (substitute* (find-files "." "petscvariables") |
1890 | ;; Do not expose build machine characteristics, set to defaults. | |
1891 | (("MAKE_NP = [:digit:]+") "MAKE_NP = 2") | |
1892 | (("NPMAX = [:digit:]+") "NPMAX = 2")) | |
fafd623e | 1893 | #t))) |
64dcc289 | 1894 | (add-after 'install 'clean-install |
10b11968 EB |
1895 | ;; Try to keep installed files from leaking build directory names. |
1896 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
64dcc289 | 1897 | (let ((out (assoc-ref outputs "out"))) |
10b11968 | 1898 | (substitute* (map (lambda (file) |
9a899cce | 1899 | (string-append out "/lib/petsc/conf/" file)) |
fafd623e | 1900 | '("petscvariables")) |
10b11968 EB |
1901 | (((getcwd)) out)) |
1902 | ;; Make compiler references point to the store | |
9a899cce | 1903 | (substitute* (string-append out "/lib/petsc/conf/petscvariables") |
dfdf5716 EB |
1904 | (("= (gcc|g\\+\\+|gfortran)" _ compiler) |
1905 | (string-append "= " (which compiler)))) | |
10b11968 EB |
1906 | ;; PETSc installs some build logs, which aren't necessary. |
1907 | (for-each (lambda (file) | |
9a899cce | 1908 | (let ((f (string-append out "/lib/petsc/conf/" file))) |
10b11968 EB |
1909 | (when (file-exists? f) |
1910 | (delete-file f)))) | |
9a899cce EB |
1911 | '("configure.log" "make.log" "gmake.log" |
1912 | "test.log" "error.log" "RDict.db" | |
fafd623e | 1913 | "PETScBuildInternal.cmake" |
10b11968 | 1914 | ;; Once installed, should uninstall with Guix |
fafd623e | 1915 | "uninstall.py")) |
a3a99e27 EB |
1916 | #t))) |
1917 | (add-after 'install 'move-examples | |
1918 | (lambda* (#:key outputs #:allow-other-keys) | |
1919 | (let* ((out (assoc-ref outputs "out")) | |
1920 | (examples (assoc-ref outputs "examples")) | |
1921 | (exdir (string-append out "/share/petsc/examples")) | |
1922 | (exdir' (string-append examples "/share/petsc/examples"))) | |
1923 | (copy-recursively exdir exdir') | |
1924 | (delete-file-recursively exdir) | |
fafd623e | 1925 | #t)))))) |
2299d83e | 1926 | (home-page "https://www.mcs.anl.gov/petsc") |
16ecf3ff | 1927 | (synopsis "Library to solve PDEs") |
b9100e2f EB |
1928 | (description "PETSc, pronounced PET-see (the S is silent), is a suite of |
1929 | data structures and routines for the scalable (parallel) solution of | |
1930 | scientific applications modeled by partial differential equations.") | |
166191b3 | 1931 | (license (license:non-copyleft |
2299d83e | 1932 | "https://www.mcs.anl.gov/petsc/documentation/copyright.html")))) |
b9100e2f EB |
1933 | |
1934 | (define-public petsc-complex | |
1935 | (package (inherit petsc) | |
1936 | (name "petsc-complex") | |
1937 | (arguments | |
1938 | (substitute-keyword-arguments (package-arguments petsc) | |
1939 | ((#:configure-flags cf) | |
1940 | `(cons "--with-scalar-type=complex" ,cf)))) | |
16ecf3ff | 1941 | (synopsis "Library to solve PDEs (with complex scalars)"))) |
183e44ae | 1942 | |
d8c7eeb9 EB |
1943 | (define-public petsc-openmpi |
1944 | (package (inherit petsc) | |
1945 | (name "petsc-openmpi") | |
1946 | (inputs | |
9e2aa70b | 1947 | `(("hdf5" ,hdf5-parallel-openmpi) |
af523673 | 1948 | ("hypre" ,hypre-openmpi) |
9e2aa70b PG |
1949 | ("metis" ,metis) |
1950 | ("mumps" ,mumps-openmpi) | |
1951 | ("openmpi" ,openmpi) | |
1952 | ("scalapack" ,scalapack) | |
72f95783 | 1953 | ("scotch" ,pt-scotch32) |
d8c7eeb9 EB |
1954 | ,@(package-inputs petsc))) |
1955 | (arguments | |
1956 | (substitute-keyword-arguments (package-arguments petsc) | |
1957 | ((#:configure-flags cf) | |
af523673 PG |
1958 | ``("--with-hypre=1" |
1959 | "--with-mpiexec=mpirun" | |
9e2aa70b PG |
1960 | "--with-metis=1" |
1961 | "--with-mumps=1" | |
1962 | "--with-scalapack=1" | |
1963 | "--with-ptscotch=1" | |
d8c7eeb9 EB |
1964 | ,(string-append "--with-mpi-dir=" |
1965 | (assoc-ref %build-inputs "openmpi")) | |
71ca16b5 PG |
1966 | ,(string-append "--with-hdf5-include=" |
1967 | (assoc-ref %build-inputs "hdf5") "/include") | |
1968 | ,(string-append "--with-hdf5-lib=" | |
1969 | (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a") | |
1970 | ,@(delete "--with-mpi=0" ,cf))) | |
1971 | ((#:phases phases) | |
1972 | `(modify-phases ,phases | |
9e2aa70b | 1973 | (add-before 'configure 'mpi-setup |
bbe46a4a | 1974 | ,%openmpi-setup))))) |
9e2aa70b | 1975 | (synopsis "Library to solve PDEs (with MUMPS and MPI support)"))) |
d8c7eeb9 EB |
1976 | |
1977 | (define-public petsc-complex-openmpi | |
1978 | (package (inherit petsc-complex) | |
1979 | (name "petsc-complex-openmpi") | |
1980 | (inputs | |
1981 | `(("openmpi" ,openmpi) | |
1982 | ,@(package-inputs petsc-complex))) | |
1983 | (arguments | |
1984 | (substitute-keyword-arguments (package-arguments petsc-complex) | |
1985 | ((#:configure-flags cf) | |
1986 | ``("--with-mpiexec=mpirun" | |
1987 | ,(string-append "--with-mpi-dir=" | |
1988 | (assoc-ref %build-inputs "openmpi")) | |
e586c6fa EB |
1989 | ,@(delete "--with-mpi=0" ,cf))) |
1990 | ((#:phases phases) | |
1991 | `(modify-phases ,phases | |
1992 | (add-before 'configure 'mpi-setup | |
1993 | ,%openmpi-setup))))) | |
16ecf3ff | 1994 | (synopsis "Library to solve PDEs (with complex scalars and MPI support)"))) |
d8c7eeb9 | 1995 | |
90ff2874 PG |
1996 | (define-public python-petsc4py |
1997 | (package | |
1998 | (name "python-petsc4py") | |
f1cc312e | 1999 | (version "3.11.0") |
90ff2874 PG |
2000 | (source |
2001 | (origin | |
2002 | (method url-fetch) | |
2003 | (uri (pypi-uri "petsc4py" version)) | |
2004 | (sha256 | |
2005 | (base32 | |
f1cc312e | 2006 | "1rm1qj5wlkhxl39by9n78lh3gbmii31wsnb8j1rr5hvfr5xgbx2q")))) |
90ff2874 PG |
2007 | (build-system python-build-system) |
2008 | (arguments | |
2009 | `(#:phases | |
2010 | (modify-phases %standard-phases | |
2011 | (add-before 'build 'pre-build | |
2012 | (lambda _ | |
2013 | ;; Define path to PETSc installation. | |
2014 | (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) | |
2015 | #t)) | |
2016 | (add-before 'check 'mpi-setup | |
2017 | ,%openmpi-setup)))) | |
2018 | (inputs | |
2019 | `(("petsc" ,petsc-openmpi) | |
2020 | ("python-numpy" ,python-numpy))) | |
2021 | (home-page "https://bitbucket.org/petsc/petsc4py/") | |
2022 | (synopsis "Python bindings for PETSc") | |
2023 | (description "PETSc, the Portable, Extensible Toolkit for | |
2024 | Scientific Computation, is a suite of data structures and routines for | |
2025 | the scalable (parallel) solution of scientific applications modeled by | |
2026 | partial differential equations. It employs the MPI standard for all | |
2027 | message-passing communication. @code{petsc4py} provides Python | |
2028 | bindings to almost all functions of PETSc.") | |
2029 | (license license:bsd-3))) | |
2030 | ||
560acf25 MB |
2031 | (define-public python-kiwisolver |
2032 | (package | |
2033 | (name "python-kiwisolver") | |
2034 | (version "1.0.1") | |
2035 | (source (origin | |
2036 | (method url-fetch) | |
2037 | (uri (pypi-uri "kiwisolver" version)) | |
2038 | (sha256 | |
2039 | (base32 | |
2040 | "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf")))) | |
2041 | (build-system python-build-system) | |
2042 | (home-page "https://github.com/nucleic/kiwi") | |
2043 | (synopsis "Fast implementation of the Cassowary constraint solver") | |
2044 | (description | |
2045 | "Kiwi is an efficient C++ implementation of the Cassowary constraint | |
2046 | solving algorithm. Kiwi has been designed from the ground up to be | |
2047 | lightweight and fast. Kiwi ranges from 10x to 500x faster than the original | |
2048 | Cassowary solver with typical use cases gaining a 40x improvement. Memory | |
2049 | savings are consistently > 5x.") | |
2050 | (license license:bsd-3))) | |
2051 | ||
2052 | (define-public python2-kiwisolver | |
2053 | (package-with-python2 python-kiwisolver)) | |
2054 | ||
a7f01414 EB |
2055 | (define-public slepc |
2056 | (package | |
2057 | (name "slepc") | |
a13e0f3d | 2058 | (version "3.11.1") |
a7f01414 EB |
2059 | (source |
2060 | (origin | |
2061 | (method url-fetch) | |
baeaf882 EB |
2062 | (uri (string-append "http://slepc.upv.es/download/distrib/slepc-" |
2063 | version ".tar.gz")) | |
a7f01414 EB |
2064 | (sha256 |
2065 | (base32 | |
a13e0f3d | 2066 | "1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8")))) |
a7f01414 EB |
2067 | (build-system gnu-build-system) |
2068 | (native-inputs | |
a13e0f3d EB |
2069 | `(("python" ,python-2) |
2070 | ("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script | |
a7f01414 EB |
2071 | (inputs |
2072 | `(("arpack" ,arpack-ng) | |
2073 | ("gfortran" ,gfortran))) | |
2074 | (propagated-inputs | |
2075 | `(("petsc" ,petsc))) | |
2076 | (arguments | |
2077 | `(#:parallel-build? #f ;build is parallel by default | |
2078 | #:configure-flags | |
2079 | `(,(string-append "--with-arpack-dir=" | |
9cf52454 | 2080 | (assoc-ref %build-inputs "arpack") "/lib")) |
9731c412 | 2081 | #:make-flags ;honor (parallel-job-count) |
a13e0f3d EB |
2082 | `(,(format #f "MAKE_NP=~a" (parallel-job-count)) |
2083 | ,(string-append "PETSCCONFIGDIR=" | |
2084 | (assoc-ref %build-inputs "petsc:examples") | |
2085 | "/share/petsc/examples/config")) | |
a7f01414 EB |
2086 | #:phases |
2087 | (modify-phases %standard-phases | |
8787c555 | 2088 | (replace 'configure |
a7f01414 EB |
2089 | ;; configure is a python script, so we can't run it with bash. |
2090 | (lambda* (#:key inputs outputs (configure-flags '()) | |
2091 | #:allow-other-keys) | |
2092 | (let* ((prefix (assoc-ref outputs "out")) | |
2093 | (flags `(,(string-append "--prefix=" prefix) | |
2094 | ,@configure-flags))) | |
2095 | (format #t "build directory: ~s~%" (getcwd)) | |
2096 | (format #t "configure flags: ~s~%" flags) | |
2097 | (setenv "SLEPC_DIR" (getcwd)) | |
9cf52454 | 2098 | (setenv "PETSC_DIR" (assoc-ref inputs "petsc")) |
c6840089 | 2099 | (apply invoke "./configure" flags)))) |
8787c555 | 2100 | (add-after 'install 'delete-doc |
a7f01414 EB |
2101 | ;; TODO: SLEPc installs HTML documentation alongside headers in |
2102 | ;; $out/include. We'd like to move them to share/doc, but delete | |
2103 | ;; them for now, as they are incomplete and installing the complete | |
2104 | ;; documentation is difficult. | |
2105 | (lambda* (#:key outputs #:allow-other-keys) | |
2106 | (let* ((out (assoc-ref outputs "out"))) | |
0f6dc120 TGR |
2107 | (for-each delete-file (find-files out "\\.html$")) |
2108 | #t))) | |
8787c555 | 2109 | (add-after 'install 'clean-install |
a7f01414 EB |
2110 | ;; Clean up unnecessary build logs from installation. |
2111 | (lambda* (#:key outputs #:allow-other-keys) | |
2112 | (let ((out (assoc-ref outputs "out"))) | |
2113 | (for-each (lambda (file) | |
2114 | (let ((f (string-append out "/lib/slepc/conf/" file))) | |
2115 | (when (file-exists? f) | |
2116 | (delete-file f)))) | |
2117 | '("configure.log" "make.log" "gmake.log" | |
2118 | "test.log" "error.log" "RDict.db" | |
0f6dc120 TGR |
2119 | "uninstall.py")) |
2120 | #t)))))) | |
a7f01414 EB |
2121 | (home-page "http://slepc.upv.es") |
2122 | (synopsis "Scalable library for eigenproblems") | |
2123 | (description "SLEPc is a software library for the solution of large sparse | |
2124 | eigenproblems on parallel computers. It can be used for the solution of | |
2125 | linear eigenvalue problems formulated in either standard or generalized form, | |
2126 | as well as other related problems such as the singular value decomposition. | |
2127 | The emphasis of the software is on methods and techniques appropriate for | |
2128 | problems in which the associated matrices are sparse, for example, those | |
2129 | arising after the discretization of partial differential equations.") | |
3c524f21 | 2130 | (license license:bsd-2))) |
a7f01414 EB |
2131 | |
2132 | (define-public slepc-complex | |
2133 | (package (inherit slepc) | |
2134 | (name "slepc-complex") | |
2135 | (propagated-inputs | |
2136 | `(("petsc" ,petsc-complex) | |
2137 | ,@(alist-delete "petsc" (package-propagated-inputs slepc)))) | |
2138 | (synopsis "Scalable library for eigenproblems (with complex scalars)"))) | |
2139 | ||
2140 | (define-public slepc-openmpi | |
2141 | (package (inherit slepc) | |
2142 | (name "slepc-openmpi") | |
6df2a50a LC |
2143 | (arguments |
2144 | (substitute-keyword-arguments (package-arguments slepc) | |
2145 | ((#:phases phases '%standard-phases) | |
2146 | `(modify-phases ,phases | |
bbe46a4a EB |
2147 | (add-before 'check 'mpi-setup |
2148 | ,%openmpi-setup))))) | |
a7f01414 EB |
2149 | (inputs |
2150 | `(("mpi" ,openmpi) | |
2151 | ("arpack" ,arpack-ng-openmpi) | |
2152 | ,@(alist-delete "arpack" (package-inputs slepc)))) | |
2153 | (propagated-inputs | |
2154 | `(("petsc" ,petsc-openmpi) | |
2155 | ,@(alist-delete "petsc" (package-propagated-inputs slepc)))) | |
2156 | (synopsis "Scalable library for eigenproblems (with MPI support)"))) | |
2157 | ||
2158 | (define-public slepc-complex-openmpi | |
2159 | (package (inherit slepc-openmpi) | |
2160 | (name "slepc-complex-openmpi") | |
2161 | (propagated-inputs | |
2162 | `(("petsc" ,petsc-complex-openmpi) | |
2163 | ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi)))) | |
2164 | (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)"))) | |
2165 | ||
6b5687d0 PG |
2166 | (define-public python-slepc4py |
2167 | (package | |
2168 | (name "python-slepc4py") | |
09bad3cd | 2169 | (version "3.11.0") |
6b5687d0 PG |
2170 | (source |
2171 | (origin | |
2172 | (method url-fetch) | |
2173 | (uri (pypi-uri "slepc4py" version)) | |
2174 | (sha256 | |
2175 | (base32 | |
09bad3cd | 2176 | "1ksp08kxf4wg408b9nn39z3qfhy643j22d4rfbl30vzxk2rxh4lq")))) |
6b5687d0 PG |
2177 | (build-system python-build-system) |
2178 | (arguments | |
2179 | `(#:phases | |
2180 | (modify-phases %standard-phases | |
2181 | (add-before 'build 'pre-build | |
2182 | (lambda _ | |
2183 | ;; Define path to PETSc installation. | |
2184 | (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) | |
2185 | ;; Define path to SLEPc installation. | |
2186 | (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc")) | |
2187 | #t)) | |
2188 | (add-before 'check 'mpi-setup | |
2189 | ,%openmpi-setup)))) | |
2190 | (inputs | |
2191 | `(("python-numpy" ,python-numpy) | |
2192 | ("python-petsc4py" ,python-petsc4py) | |
2193 | ("slepc" ,slepc-openmpi))) | |
2194 | (home-page "https://bitbucket.org/slepc/slepc4py/") | |
2195 | (synopsis "Python bindings for SLEPc") | |
2196 | (description "SLEPc, the Scalable Library for Eigenvalue Problem | |
2197 | Computations, is based on PETSc, the Portable, Extensible Toolkit for | |
2198 | Scientific Computation. It employs the MPI standard for all | |
2199 | message-passing communication. @code{slepc4py} provides Python | |
2200 | bindings to almost all functions of SLEPc.") | |
2201 | (license license:bsd-3))) | |
2202 | ||
cec86422 EB |
2203 | (define-public mumps |
2204 | (package | |
2205 | (name "mumps") | |
5dbc79eb | 2206 | (version "5.2.1") |
cec86422 EB |
2207 | (source |
2208 | (origin | |
2209 | (method url-fetch) | |
2210 | (uri (string-append "http://mumps.enseeiht.fr/MUMPS_" | |
2211 | version ".tar.gz")) | |
2212 | (sha256 | |
2213 | (base32 | |
5dbc79eb | 2214 | "0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r")) |
06e12395 MB |
2215 | (patches (search-patches "mumps-build-parallelism.patch" |
2216 | "mumps-shared-libseq.patch" | |
2217 | "mumps-shared-mumps.patch" | |
2218 | "mumps-shared-pord.patch")))) | |
cec86422 EB |
2219 | (build-system gnu-build-system) |
2220 | (inputs | |
2221 | `(("fortran" ,gfortran) | |
2222 | ;; These are required for linking against mumps, but we let the user | |
2223 | ;; declare the dependency. | |
2224 | ("blas" ,openblas) | |
2225 | ("metis" ,metis) | |
2226 | ("scotch" ,scotch))) | |
2227 | (arguments | |
2228 | `(#:modules ((ice-9 match) | |
2229 | (ice-9 popen) | |
2230 | (srfi srfi-1) | |
2231 | ,@%gnu-build-system-modules) | |
2232 | #:phases | |
2233 | (modify-phases %standard-phases | |
fba78d18 | 2234 | (replace 'configure |
cec86422 EB |
2235 | (lambda* (#:key inputs #:allow-other-keys) |
2236 | (call-with-output-file "Makefile.inc" | |
2237 | (lambda (port) | |
2238 | (format port " | |
2239 | PLAT = | |
2240 | LIBEXT = .a | |
2241 | OUTC = -o | |
2242 | OUTF = -o | |
2243 | RM = rm -f~:[ | |
2244 | CC = gcc | |
2245 | FC = gfortran | |
2246 | FL = gfortran | |
2247 | INCSEQ = -I$(topdir)/libseq | |
06e12395 | 2248 | LIBSEQ = $(topdir)/libseq/libmpiseq.a |
cec86422 EB |
2249 | LIBSEQNEEDED = libseqneeded~; |
2250 | CC = mpicc | |
2251 | FC = mpifort | |
2252 | FL = mpifort~] | |
2253 | AR = ar vr # rules require trailing space, ugh... | |
2254 | RANLIB = ranlib | |
06e12395 MB |
2255 | BLASDIR = ~a |
2256 | LIBBLAS = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[ | |
2257 | SCALAPDIR = ~a | |
2258 | SCALAP = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~] | |
cec86422 EB |
2259 | LIBOTHERS = -pthread |
2260 | CDEFS = -DAdd_ | |
2261 | PIC = -fPIC | |
2262 | OPTF = -O2 -DALLOW_NON_INIT $(PIC) | |
2263 | OPTL = -O2 $(PIC) | |
2264 | OPTC = -O2 $(PIC) | |
2265 | INCS = $(INCSEQ) | |
2266 | LIBS = $(SCALAP) $(LIBSEQ) | |
2267 | LPORDDIR = $(topdir)/PORD/lib | |
2268 | IPORD = -I$(topdir)/PORD/include | |
06e12395 | 2269 | LPORD = $(LPORDDIR)/libpord.a |
cec86422 EB |
2270 | ORDERINGSF = -Dpord~@[ |
2271 | METISDIR = ~a | |
2272 | IMETIS = -I$(METISDIR)/include | |
06e12395 | 2273 | LMETIS = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis |
cec86422 EB |
2274 | ORDERINGSF += -Dmetis~]~@[~:{ |
2275 | SCOTCHDIR = ~a | |
2276 | ISCOTCH = -I$(SCOTCHDIR)/include | |
06e12395 | 2277 | LSCOTCH = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr |
cec86422 EB |
2278 | ORDERINGSF += ~a~}~] |
2279 | ORDERINGSC = $(ORDERINGSF) | |
06e12395 | 2280 | LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ) |
cec86422 EB |
2281 | IORDERINGSF = $(ISCOTCH) |
2282 | IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)" | |
2283 | (assoc-ref inputs "mpi") | |
2284 | (assoc-ref inputs "blas") | |
2285 | (assoc-ref inputs "scalapack") | |
2286 | (assoc-ref inputs "metis") | |
2287 | (match (list (assoc-ref inputs "pt-scotch") | |
2288 | (assoc-ref inputs "scotch")) | |
2289 | ((#f #f) | |
2290 | #f) | |
2291 | ((#f scotch) | |
2292 | `((,scotch "" "-Dscotch"))) | |
2293 | ((ptscotch _) | |
2294 | `((,ptscotch | |
2295 | "-lptesmumps -lptscotch -lptscotcherr " | |
2296 | "-Dptscotch"))))))))) | |
fba78d18 | 2297 | (replace 'build |
cec86422 EB |
2298 | ;; By default only the d-precision library is built. Make with "all" |
2299 | ;; target so that all precision libraries and examples are built. | |
2300 | (lambda _ | |
b414cf52 TGR |
2301 | (invoke "make" "all" |
2302 | (format #f "-j~a" (parallel-job-count))))) | |
fba78d18 | 2303 | (replace 'check |
cec86422 EB |
2304 | ;; Run the simple test drivers, which read test input from stdin: |
2305 | ;; from the "real" input for the single- and double-precision | |
2306 | ;; testers, and from the "cmplx" input for complex-precision | |
2307 | ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi | |
2308 | ;; package to prefix execution with "mpirun". | |
2309 | (lambda* (#:key (exec-prefix '()) #:allow-other-keys) | |
2310 | (with-directory-excursion "examples" | |
2311 | (every | |
2312 | (lambda (prec type) | |
2313 | (let ((tester (apply open-pipe* | |
2314 | `(,OPEN_WRITE | |
2315 | ,@exec-prefix | |
2316 | ,(string-append "./" prec | |
2317 | "simpletest")))) | |
2318 | (input (open-input-file | |
2319 | (string-append "input_simpletest_" type)))) | |
2320 | (begin | |
2321 | (dump-port input tester) | |
2322 | (close-port input) | |
2323 | (zero? (close-pipe tester))))) | |
2324 | '("s" "d" "c" "z") | |
2325 | '("real" "real" "cmplx" "cmplx"))))) | |
fba78d18 EB |
2326 | (replace 'install |
2327 | (lambda* (#:key outputs #:allow-other-keys) | |
2328 | (let* ((out (assoc-ref outputs "out")) | |
2329 | (libdir (string-append out "/lib"))) | |
2330 | (copy-recursively "lib" libdir) | |
2331 | (copy-recursively "include" (string-append out "/include")) | |
2332 | (when (file-exists? "libseq/libmpiseq.a") | |
2333 | (install-file "libseq/libmpiseq.a" libdir)) | |
06e12395 MB |
2334 | (when (file-exists? "libseq/libmpiseq.so") |
2335 | (install-file "libseq/libmpiseq.so" libdir)) | |
fba78d18 | 2336 | #t)))))) |
cec86422 EB |
2337 | (home-page "http://mumps.enseeiht.fr") |
2338 | (synopsis "Multifrontal sparse direct solver") | |
2339 | (description | |
2340 | "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a | |
57e69c1d | 2341 | sparse system of linear equations A x = b using Gaussian elimination.") |
cec86422 EB |
2342 | (license license:cecill-c))) |
2343 | ||
2344 | (define-public mumps-metis | |
2345 | (package (inherit mumps) | |
2346 | (name "mumps-metis") | |
2347 | (inputs | |
2348 | (alist-delete "scotch" (package-inputs mumps))))) | |
2349 | ||
2350 | (define-public mumps-openmpi | |
2351 | (package (inherit mumps) | |
2352 | (name "mumps-openmpi") | |
2353 | (inputs | |
2354 | `(("mpi" ,openmpi) | |
2355 | ("scalapack" ,scalapack) | |
2356 | ("pt-scotch" ,pt-scotch) | |
2357 | ,@(alist-delete "scotch" (package-inputs mumps)))) | |
2358 | (arguments | |
2359 | (substitute-keyword-arguments (package-arguments mumps) | |
2360 | ((#:phases phases) | |
2361 | `(modify-phases ,phases | |
bbe46a4a EB |
2362 | (add-before 'check 'mpi-setup |
2363 | ,%openmpi-setup) | |
6df2a50a LC |
2364 | (replace 'check |
2365 | (lambda _ | |
2366 | ((assoc-ref ,phases 'check) | |
2367 | #:exec-prefix '("mpirun" "-n" "2")))))))) | |
cec86422 EB |
2368 | (synopsis "Multifrontal sparse direct solver (with MPI)"))) |
2369 | ||
2370 | (define-public mumps-metis-openmpi | |
2371 | (package (inherit mumps-openmpi) | |
2372 | (name "mumps-metis-openmpi") | |
2373 | (inputs | |
2374 | (alist-delete "pt-scotch" (package-inputs mumps-openmpi))))) | |
2375 | ||
63e07468 BW |
2376 | (define-public ruby-asciimath |
2377 | (package | |
2378 | (name "ruby-asciimath") | |
2379 | (version "1.0.4") | |
2380 | (source | |
2381 | (origin | |
2382 | (method url-fetch) | |
2383 | (uri (rubygems-uri "asciimath" version)) | |
2384 | (sha256 | |
2385 | (base32 | |
2386 | "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc")))) | |
2387 | (build-system ruby-build-system) | |
2388 | (arguments | |
2389 | '(#:phases | |
2390 | (modify-phases %standard-phases | |
2391 | ;; Apply this patch | |
2392 | ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948 | |
2393 | (add-after 'unpack 'patch-remove-spurious-backslashes | |
2394 | (lambda _ | |
2395 | (substitute* "spec/parser_spec.rb" | |
2396 | (("\\\\\"") | |
9923d5a4 TGR |
2397 | "\"")) |
2398 | #t))))) | |
63e07468 BW |
2399 | (native-inputs |
2400 | `(("bundler" ,bundler) | |
2401 | ("ruby-rspec" ,ruby-rspec))) | |
2402 | (synopsis "AsciiMath parsing and conversion library") | |
2403 | (description | |
2404 | "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an | |
2405 | easy-to-write markup language for mathematics.") | |
2406 | (home-page "https://github.com/asciidoctor/asciimath") | |
2407 | (license license:expat))) | |
2408 | ||
183e44ae EB |
2409 | (define-public superlu |
2410 | (package | |
2411 | (name "superlu") | |
995a09e0 | 2412 | (version "5.2.1") |
183e44ae EB |
2413 | (source |
2414 | (origin | |
2415 | (method url-fetch) | |
48fe5c36 | 2416 | (uri (string-append "https://portal.nersc.gov/project/sparse/superlu/" |
183e44ae EB |
2417 | "superlu_" version ".tar.gz")) |
2418 | (sha256 | |
995a09e0 EB |
2419 | (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8")) |
2420 | (modules '((guix build utils))) | |
2421 | (snippet | |
2422 | ;; Replace the non-free implementation of MC64 with a stub adapted | |
2423 | ;; from Debian | |
2424 | '(begin | |
2425 | (use-modules (ice-9 regex) | |
2426 | (ice-9 rdelim)) | |
2427 | (call-with-output-file "SRC/mc64ad.c" | |
2428 | (lambda (port) | |
2429 | (display " | |
2430 | #include <stdio.h> | |
2431 | #include <stdlib.h> | |
2432 | void mc64id_(int *a) { | |
2433 | fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\"); | |
2434 | abort (); | |
2435 | } | |
2436 | void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g, | |
2437 | int *h, int *i, int *j, int *k, double *l, int *m, int *n) { | |
2438 | fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\"); | |
2439 | abort (); | |
2440 | }\n" port))) | |
2441 | ;; Remove the corresponding license verbiage. MC64 license follows | |
2442 | ;; a "------" line separator. | |
2443 | (with-atomic-file-replacement "License.txt" | |
2444 | (let ((rx (make-regexp "-{8}"))) | |
2445 | (lambda (in out) | |
2446 | (let loop () | |
2447 | (let ((line (read-line in 'concat))) | |
2448 | (unless (regexp-exec rx line) | |
2449 | (display line out) | |
6cbee49d MW |
2450 | (loop)))) |
2451 | #t))))))) | |
995a09e0 | 2452 | (build-system cmake-build-system) |
183e44ae EB |
2453 | (native-inputs |
2454 | `(("tcsh" ,tcsh))) | |
2455 | (inputs | |
995a09e0 | 2456 | `(("blas" ,openblas) |
19afbea1 | 2457 | ("gfortran" ,gfortran))) |
183e44ae | 2458 | (arguments |
995a09e0 EB |
2459 | `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas |
2460 | "-DTPL_BLAS_LIBRARIES=openblas" | |
677bc34d | 2461 | "-DBUILD_SHARED_LIBS:BOOL=YES"))) |
48fe5c36 | 2462 | (home-page "https://portal.nersc.gov/project/sparse/superlu/") |
183e44ae EB |
2463 | (synopsis "Supernodal direct solver for sparse linear systems") |
2464 | (description | |
2465 | "SuperLU is a general purpose library for the direct solution of large, | |
2466 | sparse, nonsymmetric systems of linear equations on high performance machines. | |
2467 | The library is written in C and is callable from either C or Fortran. The | |
2468 | library routines perform an LU decomposition with partial pivoting and | |
2469 | triangular system solves through forward and back substitution. The library | |
2470 | also provides threshold-based ILU factorization preconditioners.") | |
995a09e0 EB |
2471 | (license (list license:bsd-3 |
2472 | license:gpl2+ ;EXAMPLE/*fgmr.c | |
2473 | (license:fsf-free "file://SRC/colamd.h"))))) | |
f8ed036a | 2474 | |
a54aefea EB |
2475 | (define-public superlu-dist |
2476 | (package | |
2477 | (name "superlu-dist") | |
aa2e83cc | 2478 | (version "6.2.0") |
a54aefea EB |
2479 | (source |
2480 | (origin | |
2481 | (method url-fetch) | |
aa2e83cc | 2482 | (uri (string-append "https://portal.nersc.gov/project/sparse/superlu/" |
a54aefea EB |
2483 | "superlu_dist_" version ".tar.gz")) |
2484 | (sha256 | |
aa2e83cc | 2485 | (base32 "1ynmwqajc9sc3my2hssa5k9s58ggvizqv9rdss0j7w99pbh5mnvw")) |
0921eff2 | 2486 | (modules '((guix build utils))) |
29080870 EB |
2487 | (snippet |
2488 | ;; Replace the non-free implementation of MC64 with a stub | |
2489 | '(begin | |
0921eff2 | 2490 | (call-with-output-file "SRC/mc64ad_dist.c" |
29080870 EB |
2491 | (lambda (port) |
2492 | (display " | |
2493 | #include <stdio.h> | |
2494 | #include <stdlib.h> | |
0921eff2 | 2495 | void mc64id_dist(int *a) { |
29080870 EB |
2496 | fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\"); |
2497 | abort (); | |
2498 | } | |
0921eff2 | 2499 | void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g, |
29080870 EB |
2500 | int *h, int *i, int *j, int *k, double *l, int *m, int *n) { |
2501 | fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\"); | |
2502 | abort (); | |
2503 | }\n" port))) | |
29080870 | 2504 | (substitute* "SRC/util.c" ;adjust default algorithm |
6161141e EB |
2505 | (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;") |
2506 | ;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has | |
2507 | ;; general (i.e. non-square) processor-grid support. | |
2508 | "RowPerm = NOROWPERM;")) | |
6cbee49d | 2509 | #t)) |
6161141e | 2510 | (patches (search-patches "superlu-dist-scotchmetis.patch" |
aa2e83cc | 2511 | "superlu-dist-awpm-grid.patch")))) |
6161141e | 2512 | (build-system cmake-build-system) |
a54aefea EB |
2513 | (native-inputs |
2514 | `(("tcsh" ,tcsh))) | |
2515 | (inputs | |
6161141e EB |
2516 | `(("gfortran" ,gfortran) |
2517 | ("blas" ,openblas) | |
2518 | ("lapack" ,lapack) | |
2519 | ("combblas" ,combinatorial-blas))) | |
a54aefea | 2520 | (propagated-inputs |
6161141e EB |
2521 | `(("mpi" ,openmpi) ;headers include MPI heades |
2522 | ("parmetis" ,pt-scotch32 "metis") | |
2523 | ("pt-scotch" ,pt-scotch32))) | |
a54aefea | 2524 | (arguments |
6161141e EB |
2525 | `(#:parallel-tests? #f ;tests use MPI and OpenMP |
2526 | #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES" | |
2527 | "-DTPL_ENABLE_COMBBLASLIB=YES" | |
2528 | "-DTPL_BLAS_LIBRARIES=-lopenblas" | |
2529 | "-DTPL_LAPACK_LIBRARIES=-llapack" | |
2530 | (string-append "-DTPL_PARMETIS_LIBRARIES=" | |
2531 | (string-join | |
2532 | '("ptscotchparmetis" "ptscotch" "ptscotcherr" | |
2533 | "scotchmetis" "scotch" "scotcherr") | |
2534 | ";")) | |
2535 | (string-append "-DTPL_PARMETIS_INCLUDE_DIRS=" | |
2536 | (assoc-ref %build-inputs "parmetis") | |
2537 | "/include") | |
2538 | "-DTPL_ENABLE_COMBBLASLIB=ON" | |
2539 | (string-append "-DTPL_COMBBLAS_INCLUDE_DIRS=" | |
2540 | (assoc-ref %build-inputs "combblas") | |
2541 | "/include/CombBLAS;" | |
2542 | (assoc-ref %build-inputs "combblas") | |
2543 | "/include/BipartiteMatchings") | |
2544 | "-DTPL_COMBBLAS_LIBRARIES=CombBLAS") | |
a54aefea | 2545 | #:phases |
dc1d3cde | 2546 | (modify-phases %standard-phases |
6161141e | 2547 | (add-before 'configure 'set-c++-standard |
dc1d3cde | 2548 | (lambda _ |
6161141e EB |
2549 | (substitute* "CMakeLists.txt" |
2550 | ;; AWPM headers require C++14 | |
2551 | (("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14")))) | |
bbe46a4a EB |
2552 | (add-before 'check 'mpi-setup |
2553 | ,%openmpi-setup) | |
6161141e EB |
2554 | (add-before 'check 'omp-setup |
2555 | (lambda _ (setenv "OMP_NUM_THREADS" "1") #t))))) | |
a54aefea EB |
2556 | (home-page (package-home-page superlu)) |
2557 | (synopsis "Parallel supernodal direct solver") | |
2558 | (description | |
2559 | "SuperLU_DIST is a parallel extension to the serial SuperLU library. | |
2560 | It is targeted for distributed memory parallel machines. SuperLU_DIST is | |
2561 | implemented in ANSI C, and MPI for communications.") | |
2562 | (license license:bsd-3))) | |
2563 | ||
f8ed036a EB |
2564 | (define-public scotch |
2565 | (package | |
2566 | (name "scotch") | |
fd373343 | 2567 | (version "6.0.6") |
f8ed036a EB |
2568 | (source |
2569 | (origin | |
2570 | (method url-fetch) | |
1dc31097 TGR |
2571 | (uri (string-append "https://gforge.inria.fr/frs/download.php/" |
2572 | "latestfile/298/scotch_" version ".tar.gz")) | |
f8ed036a | 2573 | (sha256 |
fd373343 EB |
2574 | (base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8")) |
2575 | (patches (search-patches "scotch-build-parallelism.patch" | |
2576 | "scotch-integer-declarations.patch")))) | |
f8ed036a EB |
2577 | (build-system gnu-build-system) |
2578 | (inputs | |
2579 | `(("zlib" ,zlib) | |
5e54f4ad | 2580 | ("flex" ,flex) |
f8ed036a | 2581 | ("bison" ,bison))) |
fd373343 | 2582 | (outputs '("out" "metis")) |
f8ed036a | 2583 | (arguments |
fd373343 EB |
2584 | `(#:make-flags (list (string-append "prefix=" %output)) |
2585 | #:phases | |
d6602ee9 EB |
2586 | (modify-phases %standard-phases |
2587 | (add-after | |
2588 | 'unpack 'chdir-to-src | |
d67a7e9e | 2589 | (lambda _ (chdir "src") #t)) |
d6602ee9 EB |
2590 | (replace |
2591 | 'configure | |
2592 | (lambda _ | |
2593 | (call-with-output-file "Makefile.inc" | |
2594 | (lambda (port) | |
2595 | (format port " | |
f8ed036a EB |
2596 | EXE = |
2597 | LIB = .a | |
2598 | OBJ = .o | |
2599 | MAKE = make | |
2600 | AR = ar | |
2601 | ARFLAGS = -ruv | |
cf0ec6c4 | 2602 | CAT = cat |
f8ed036a EB |
2603 | CCS = gcc |
2604 | CCP = mpicc | |
2605 | CCD = gcc | |
2606 | CPPFLAGS =~{ -D~a~} | |
6c798540 | 2607 | CFLAGS = -O2 -g -fPIC $(CPPFLAGS) |
f8ed036a EB |
2608 | LDFLAGS = -lz -lm -lrt -lpthread |
2609 | CP = cp | |
2610 | LEX = flex -Pscotchyy -olex.yy.c | |
2611 | LN = ln | |
2612 | MKDIR = mkdir | |
2613 | MV = mv | |
2614 | RANLIB = ranlib | |
2615 | YACC = bison -pscotchyy -y -b y | |
2616 | " | |
d6602ee9 EB |
2617 | '("COMMON_FILE_COMPRESS_GZ" |
2618 | "COMMON_PTHREAD" | |
2619 | "COMMON_RANDOM_FIXED_SEED" | |
fd373343 | 2620 | "INTSIZE64" ;use 'int64_t' |
cf0ec6c4 EB |
2621 | ;; Prevents symbolc clashes with libesmumps |
2622 | "SCOTCH_RENAME" | |
d6602ee9 EB |
2623 | ;; XXX: Causes invalid frees in superlu-dist tests |
2624 | ;; "SCOTCH_PTHREAD" | |
2625 | ;; "SCOTCH_PTHREAD_NUMBER=2" | |
d67a7e9e TGR |
2626 | "restrict=__restrict")))) |
2627 | #t)) | |
bbe46a4a | 2628 | (add-after 'build 'build-esmumps |
cf0ec6c4 | 2629 | (lambda _ |
d67a7e9e TGR |
2630 | (invoke "make" |
2631 | (format #f "-j~a" (parallel-job-count)) | |
2632 | "esmumps"))) | |
fd373343 EB |
2633 | (add-before 'install 'make-install-dirs |
2634 | (lambda* (#:key outputs #:allow-other-keys) | |
2635 | (mkdir (assoc-ref outputs "out")))) | |
2636 | (add-after 'install 'install-metis | |
2637 | (lambda* (#:key outputs #:allow-other-keys) | |
2638 | (let ((out (assoc-ref outputs "metis"))) | |
2639 | (mkdir out) | |
2640 | ;; metis files are not installed with 'make install' | |
2641 | (for-each (lambda (f) | |
2642 | (install-file f (string-append out "/include"))) | |
2643 | (find-files "../include/" ".*metis\\.h")) | |
2644 | (for-each (lambda (f) | |
2645 | (install-file f (string-append out "/lib"))) | |
2646 | (find-files "../lib/" ".*metis\\..*")) | |
2647 | #t)))))) | |
d5730000 | 2648 | (home-page "https://www.labri.fr/perso/pelegrin/scotch/") |
f8ed036a EB |
2649 | (synopsis "Programs and libraries for graph algorithms") |
2650 | (description "SCOTCH is a set of programs and libraries which implement | |
2651 | the static mapping and sparse matrix reordering algorithms developed within | |
2652 | the SCOTCH project. Its purpose is to apply graph theory, with a divide and | |
2653 | conquer approach, to scientific computing problems such as graph and mesh | |
2654 | partitioning, static mapping, and sparse matrix ordering, in application | |
2655 | domains ranging from structural mechanics to operating systems or | |
2656 | bio-chemistry.") | |
2657 | ;; See LICENSE_en.txt | |
2658 | (license license:cecill-c))) | |
6acb4adb | 2659 | |
1c39f3b8 PG |
2660 | (define-public scotch32 |
2661 | ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by | |
2662 | ;; some applications. | |
2663 | (package (inherit scotch) | |
2664 | (name "scotch32") | |
2665 | (arguments | |
2666 | (substitute-keyword-arguments (package-arguments scotch) | |
2667 | ((#:phases scotch-phases) | |
2668 | `(modify-phases ,scotch-phases | |
2669 | (replace | |
2670 | 'configure | |
2671 | (lambda _ | |
2672 | (call-with-output-file "Makefile.inc" | |
2673 | (lambda (port) | |
2674 | (format port " | |
2675 | EXE = | |
2676 | LIB = .a | |
2677 | OBJ = .o | |
2678 | MAKE = make | |
2679 | AR = ar | |
2680 | ARFLAGS = -ruv | |
2681 | CAT = cat | |
2682 | CCS = gcc | |
2683 | CCP = mpicc | |
2684 | CCD = gcc | |
2685 | CPPFLAGS =~{ -D~a~} | |
2686 | CFLAGS = -O2 -g -fPIC $(CPPFLAGS) | |
2687 | LDFLAGS = -lz -lm -lrt -lpthread | |
2688 | CP = cp | |
2689 | LEX = flex -Pscotchyy -olex.yy.c | |
2690 | LN = ln | |
2691 | MKDIR = mkdir | |
2692 | MV = mv | |
2693 | RANLIB = ranlib | |
2694 | YACC = bison -pscotchyy -y -b y | |
2695 | " | |
2696 | '("COMMON_FILE_COMPRESS_GZ" | |
2697 | "COMMON_PTHREAD" | |
2698 | "COMMON_RANDOM_FIXED_SEED" | |
2699 | "INTSIZE32" ;use 32-bit integers. See INSTALL.txt | |
2700 | ;; Prevents symbolc clashes with libesmumps | |
2701 | "SCOTCH_RENAME" | |
2702 | ;; XXX: Causes invalid frees in superlu-dist tests | |
2703 | ;; "SCOTCH_PTHREAD" | |
2704 | ;; "SCOTCH_PTHREAD_NUMBER=2" | |
2705 | "restrict=__restrict")))))))))) | |
2706 | (synopsis | |
2707 | "Programs and libraries for graph algorithms (32-bit integers)"))) | |
2708 | ||
6acb4adb EB |
2709 | (define-public pt-scotch |
2710 | (package (inherit scotch) | |
2711 | (name "pt-scotch") | |
2712 | (propagated-inputs | |
2713 | `(("openmpi" ,openmpi))) ;Headers include MPI headers | |
2714 | (arguments | |
2715 | (substitute-keyword-arguments (package-arguments scotch) | |
2716 | ((#:phases scotch-phases) | |
d6602ee9 EB |
2717 | `(modify-phases ,scotch-phases |
2718 | (replace | |
2719 | 'build | |
d6602ee9 | 2720 | (lambda _ |
c491f7f8 LC |
2721 | (invoke "make" (format #f "-j~a" (parallel-job-count)) |
2722 | "ptscotch" "ptesmumps") | |
2723 | ||
2724 | ;; Install the serial metis compatibility library | |
2725 | (invoke "make" "-C" "libscotchmetis" "install"))) | |
2726 | (add-before 'check 'mpi-setup | |
2727 | ,%openmpi-setup) | |
2728 | (replace 'check | |
2729 | (lambda _ | |
2730 | (invoke "make" "ptcheck"))))))) | |
6acb4adb | 2731 | (synopsis "Programs and libraries for graph algorithms (with MPI)"))) |
5698b8b8 | 2732 | |
1c25a52c PG |
2733 | (define-public pt-scotch32 |
2734 | (package (inherit scotch32) | |
2735 | (name "pt-scotch32") | |
2736 | (propagated-inputs | |
2737 | `(("openmpi" ,openmpi))) ;headers include MPI headers | |
2738 | (arguments | |
c4d4a779 PG |
2739 | (substitute-keyword-arguments (package-arguments scotch32) |
2740 | ((#:phases scotch32-phases) | |
2741 | `(modify-phases ,scotch32-phases | |
1c25a52c PG |
2742 | (replace 'build |
2743 | (lambda _ | |
c491f7f8 LC |
2744 | (invoke "make" (format #f "-j~a" (parallel-job-count)) |
2745 | "ptscotch" "ptesmumps") | |
2746 | ;; Install the serial metis compatibility library | |
2747 | (invoke "make" "-C" "libscotchmetis" "install"))) | |
2748 | (add-before 'check 'mpi-setup | |
2749 | ,%openmpi-setup) | |
1c25a52c PG |
2750 | (replace 'check |
2751 | (lambda _ | |
c491f7f8 | 2752 | (invoke "make" "ptcheck"))))))) |
1c25a52c PG |
2753 | (synopsis |
2754 | "Programs and libraries for graph algorithms (with MPI and 32-bit integers)"))) | |
2755 | ||
aa75ad00 EB |
2756 | (define-public metis |
2757 | (package | |
2758 | (name "metis") | |
2759 | (version "5.1.0") | |
2760 | (source | |
2761 | (origin | |
2762 | (method url-fetch) | |
2763 | (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/" | |
2764 | "metis-" version ".tar.gz")) | |
2765 | (sha256 | |
2766 | (base32 | |
2767 | "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn")))) | |
2768 | (build-system cmake-build-system) | |
2769 | (inputs | |
2770 | `(("blas" ,openblas))) | |
2771 | (arguments | |
2772 | `(#:tests? #f ;no tests | |
2773 | #:configure-flags `("-DSHARED=ON" | |
2774 | ,(string-append "-DGKLIB_PATH=" (getcwd) | |
2775 | "/metis-" ,version "/GKlib")))) | |
2776 | (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview") | |
2777 | (synopsis "Graph partitioning and fill-reducing matrix ordering library") | |
2778 | (description | |
2779 | "METIS is a set of serial programs for partitioning graphs, partitioning | |
2780 | finite element meshes, and producing fill-reducing orderings for sparse | |
2781 | matrices. The algorithms implemented in METIS are based on the multilevel | |
2782 | recursive-bisection, multilevel k-way, and multi-constraint partitioning | |
2783 | schemes.") | |
2784 | (license license:asl2.0))) ;As of version 5.0.3 | |
2785 | ||
700ff222 EB |
2786 | (define-public p4est |
2787 | (package | |
2788 | (name "p4est") | |
4150da63 | 2789 | (version "2.0") |
700ff222 EB |
2790 | (source |
2791 | (origin | |
2792 | (method url-fetch) | |
2793 | (uri (string-append "http://p4est.github.io/release/p4est-" | |
2794 | version ".tar.gz")) | |
2795 | (sha256 | |
2796 | (base32 | |
4150da63 | 2797 | "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5")))) |
700ff222 EB |
2798 | (build-system gnu-build-system) |
2799 | (inputs | |
2800 | `(("fortran" ,gfortran) | |
2801 | ("blas" ,openblas) | |
2802 | ("lapack" ,lapack) | |
2803 | ("zlib" ,zlib))) | |
2804 | (arguments | |
2805 | `(#:configure-flags `(,(string-append "BLAS_LIBS=-L" | |
2806 | (assoc-ref %build-inputs "blas") | |
2807 | " -lopenblas") | |
2808 | ,(string-append "LAPACK_LIBS=-L" | |
2809 | (assoc-ref %build-inputs "lapack") | |
6df2a50a LC |
2810 | " -llapack")) |
2811 | #:phases (modify-phases %standard-phases | |
bbe46a4a EB |
2812 | (add-before 'check 'mpi-setup |
2813 | ,%openmpi-setup)))) | |
700ff222 EB |
2814 | (home-page "http://www.p4est.org") |
2815 | (synopsis "Adaptive mesh refinement on forests of octrees") | |
2816 | (description | |
2817 | "The p4est software library enables the dynamic management of a | |
2818 | collection of adaptive octrees, conveniently called a forest of octrees. | |
2819 | p4est is designed to work in parallel and scales to hundreds of thousands of | |
2820 | processor cores.") | |
2821 | (license license:gpl2+))) | |
2822 | ||
2823 | (define-public p4est-openmpi | |
2824 | (package (inherit p4est) | |
2825 | (name "p4est-openmpi") | |
2826 | (inputs | |
2827 | `(("mpi" ,openmpi) | |
2828 | ,@(package-inputs p4est))) | |
2829 | (arguments | |
2830 | (substitute-keyword-arguments (package-arguments p4est) | |
2831 | ((#:configure-flags cf) | |
2832 | ``("--enable-mpi" ,@,cf)))) | |
2833 | (synopsis "Parallel adaptive mesh refinement on forests of octrees"))) | |
2834 | ||
5698b8b8 JD |
2835 | (define-public gsegrafix |
2836 | (package | |
2837 | (name "gsegrafix") | |
2838 | (version "1.0.6") | |
2839 | (source | |
2840 | (origin | |
2841 | (method url-fetch) | |
2842 | (uri (string-append "mirror://gnu/" name "/" name "-" | |
2843 | version ".tar.gz")) | |
2844 | (sha256 | |
2845 | (base32 | |
2846 | "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda")))) | |
2847 | (build-system gnu-build-system) | |
2848 | (arguments | |
2849 | `(#:configure-flags '("LDFLAGS=-lm"))) | |
2850 | (inputs | |
2851 | `(("libgnomecanvas" ,libgnomecanvas) | |
2852 | ("libbonoboui" ,libbonoboui) | |
2853 | ("libgnomeui" ,libgnomeui) | |
2854 | ("libgnomeprintui" ,libgnomeprintui) | |
2855 | ("popt" ,popt))) | |
2856 | (native-inputs | |
2857 | `(("pkg-config" ,pkg-config))) | |
6fd52309 | 2858 | (home-page "https://www.gnu.org/software/gsegrafix/") |
5698b8b8 JD |
2859 | (synopsis "GNOME application to create scientific and engineering plots") |
2860 | (description "GSEGrafix is an application which produces high-quality graphical | |
2861 | plots for science and engineering. Plots are specified via simple ASCII | |
2862 | parameter files and data files and are presented in an anti-aliased GNOME | |
2863 | canvas. The program supports rectangular two-dimensional plots, histograms, | |
2864 | polar-axis plots and three-dimensional plots. Plots can be printed or saved | |
2865 | to BMP, JPEG or PNG image formats.") | |
2866 | (license license:gpl3+))) | |
8731e527 JD |
2867 | |
2868 | (define-public maxima | |
2869 | (package | |
2870 | (name "maxima") | |
ccc963d5 | 2871 | (version "5.43.0") |
8731e527 JD |
2872 | (source |
2873 | (origin | |
2874 | (method url-fetch) | |
2875 | (uri (string-append "mirror://sourceforge/maxima/Maxima-source/" | |
2876 | version "-source/" name "-" version ".tar.gz")) | |
2877 | (sha256 | |
2878 | (base32 | |
ccc963d5 | 2879 | "0xyahp4c6509haxh4n1swiqm3421gplkdisa0zypclh3252sbzfw")) |
fc1adab1 | 2880 | (patches (search-patches "maxima-defsystem-mkdir.patch")))) |
8731e527 | 2881 | (build-system gnu-build-system) |
df354a77 | 2882 | (inputs |
6b2eafaa | 2883 | `(("gcl" ,gcl) |
df354a77 | 2884 | ("gnuplot" ,gnuplot) ;for plots |
fc9c47bd | 2885 | ("sed" ,sed) |
f36afe4d | 2886 | ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima' |
df354a77 FB |
2887 | (native-inputs |
2888 | `(("texinfo" ,texinfo) | |
ccbc5758 KK |
2889 | ("perl" ,perl) |
2890 | ("python" ,python))) | |
8731e527 | 2891 | (arguments |
df354a77 FB |
2892 | `(#:configure-flags |
2893 | (list "--enable-gcl" | |
2894 | (string-append "--with-posix-shell=" | |
2895 | (assoc-ref %build-inputs "bash") | |
2896 | "/bin/sh") | |
2897 | (string-append "--with-wish=" | |
2898 | (assoc-ref %build-inputs "tk") | |
2899 | "/bin/wish" | |
2900 | (let ((v ,(package-version tk))) | |
2901 | (string-take v (string-index-right v #\.))))) | |
df354a77 | 2902 | ;; By default Maxima attempts to write temporary files to |
77af7b24 MW |
2903 | ;; '/tmp/nix-build-maxima-*', which won't exist at run time. |
2904 | ;; Work around that. | |
df354a77 | 2905 | #:make-flags (list "TMPDIR=/tmp") |
0093b126 KK |
2906 | #:phases |
2907 | (modify-phases %standard-phases | |
fc9c47bd KK |
2908 | (add-after 'unpack 'patch-paths |
2909 | (lambda* (#:key inputs #:allow-other-keys) | |
2910 | (let* ((sed (string-append (assoc-ref inputs "sed") "/bin/sed")) | |
2911 | (coreutils (assoc-ref inputs "coreutils")) | |
2912 | (dirname (string-append coreutils "/bin/dirname")) | |
ccc963d5 KK |
2913 | (head (string-append coreutils "/bin/head")) |
2914 | (perl (string-append (assoc-ref inputs "perl") "/bin/perl")) | |
2915 | (python (string-append (assoc-ref inputs "python") | |
2916 | "/bin/python3"))) | |
fc9c47bd KK |
2917 | (substitute* "src/maxima.in" |
2918 | (("sed ") (string-append sed " ")) | |
2919 | (("dirname") dirname) | |
2920 | (("head") head)) | |
ccc963d5 KK |
2921 | (substitute* "doc/info/Makefile.in" |
2922 | (("/usr/bin/env perl") perl)) | |
2923 | (substitute* "doc/info/build_html.sh.in" | |
2924 | (("python") python)) | |
fc9c47bd | 2925 | #t))) |
0093b126 KK |
2926 | (add-before 'check 'pre-check |
2927 | (lambda _ | |
2928 | (chmod "src/maxima" #o555) | |
2929 | #t)) | |
1472d19a KK |
2930 | (replace 'check |
2931 | (lambda _ | |
2932 | ;; This is derived from the testing code in the "debian/rules" file | |
2933 | ;; of Debian's Maxima package. | |
2934 | ;; If Maxima can successfully run this, the binary to be installed | |
2935 | ;; should be fine. | |
df129041 MW |
2936 | (invoke "sh" "-c" |
2937 | (string-append | |
2938 | "./maxima-local " | |
2939 | "--lisp=gcl " | |
2940 | "--batch-string=\"run_testsuite();\" " | |
2941 | "| grep -q \"No unexpected errors found\"")))) | |
0093b126 KK |
2942 | ;; Make sure the doc and emacs files are found in the |
2943 | ;; standard location. Also configure maxima to find gnuplot | |
2944 | ;; without having it on the PATH. | |
2945 | (add-after 'install 'post-install | |
2946 | (lambda* (#:key outputs inputs #:allow-other-keys) | |
2947 | (let* ((gnuplot (assoc-ref inputs "gnuplot")) | |
2948 | (out (assoc-ref outputs "out")) | |
2949 | (datadir (string-append out "/share/maxima/" ,version)) | |
2950 | (binutils (string-append (assoc-ref inputs "binutils") | |
2951 | "/bin"))) | |
2952 | (with-directory-excursion out | |
2953 | (mkdir-p "share/emacs") | |
2954 | (mkdir-p "share/doc") | |
0093b126 KK |
2955 | (symlink |
2956 | (string-append datadir "/doc/") | |
2957 | (string-append out "/share/doc/maxima")) | |
2958 | (with-atomic-file-replacement | |
2959 | (string-append datadir "/share/maxima-init.lisp") | |
2960 | (lambda (in out) | |
2961 | (format out "~a ~s~a~%" | |
2962 | "(setf $gnuplot_command " | |
2963 | (string-append gnuplot "/bin/gnuplot") ")") | |
2964 | (dump-port in out)))) | |
2965 | ;; Ensure that Maxima will have access to the GNU binutils | |
2966 | ;; components at runtime. | |
2967 | (wrap-program (string-append out "/bin/maxima") | |
2968 | `("PATH" prefix (,binutils)))) | |
2969 | #t))))) | |
8731e527 JD |
2970 | (home-page "http://maxima.sourceforge.net") |
2971 | (synopsis "Numeric and symbolic expression manipulation") | |
2972 | (description "Maxima is a system for the manipulation of symbolic and | |
2973 | numerical expressions. It yields high precision numeric results by using | |
2974 | exact fractions, arbitrary precision integers, and variable precision floating | |
e881752c | 2975 | point numbers.") |
8731e527 JD |
2976 | ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+. |
2977 | ;; Others simply say "GNU General Public License" without stating a | |
2978 | ;; version (which implicitly means gpl1+). | |
2979 | ;; At least one file (src/maxima.asd) says "version 2." | |
2980 | ;; GPLv2 only is therefore the smallest subset. | |
f36afe4d | 2981 | (license license:gpl2))) |
ec322be2 | 2982 | |
9aafbc0c MW |
2983 | (define-public wxmaxima |
2984 | (package | |
2985 | (name "wxmaxima") | |
48446f0f | 2986 | (version "20.01.3") |
9aafbc0c MW |
2987 | (source |
2988 | (origin | |
c93b77ad KK |
2989 | (method git-fetch) |
2990 | (uri (git-reference | |
2991 | (url "https://github.com/wxMaxima-developers/wxmaxima.git") | |
2992 | (commit (string-append "Version-" version)))) | |
2993 | (file-name (git-file-name name version)) | |
9aafbc0c | 2994 | (sha256 |
48446f0f | 2995 | (base32 "18fj2m1qwlbavivpixph112wq9hxy3hh7c8q07djc3bhrzf2a7v7")))) |
0181df53 | 2996 | (build-system cmake-build-system) |
5143517c | 2997 | (native-inputs |
0181df53 | 2998 | `(("gettext" ,gettext-minimal))) |
9aafbc0c MW |
2999 | (inputs |
3000 | `(("wxwidgets" ,wxwidgets) | |
de477809 SB |
3001 | ("maxima" ,maxima) |
3002 | ;; Runtime support. | |
3003 | ("adwaita-icon-theme" ,adwaita-icon-theme) | |
3004 | ("gtk+" ,gtk+) | |
3005 | ("shared-mime-info" ,shared-mime-info))) | |
9aafbc0c | 3006 | (arguments |
0181df53 KK |
3007 | `(#:tests? #f ; no check target |
3008 | #:phases | |
ac2ddcc6 | 3009 | (modify-phases %standard-phases |
ac2ddcc6 KK |
3010 | (add-after 'install 'wrap-program |
3011 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
3012 | (wrap-program (string-append (assoc-ref outputs "out") | |
3013 | "/bin/wxmaxima") | |
3014 | `("PATH" ":" prefix | |
3015 | (,(string-append (assoc-ref inputs "maxima") | |
3016 | "/bin"))) | |
3017 | ;; For GtkFileChooserDialog. | |
3018 | `("GSETTINGS_SCHEMA_DIR" = | |
3019 | (,(string-append (assoc-ref inputs "gtk+") | |
3020 | "/share/glib-2.0/schemas"))) | |
3021 | `("XDG_DATA_DIRS" ":" prefix | |
3022 | (;; Needed by gdk-pixbuf to know supported icon formats. | |
3023 | ,(string-append | |
3024 | (assoc-ref inputs "shared-mime-info") "/share") | |
3025 | ;; The default icon theme of GTK+. | |
3026 | ,(string-append | |
3027 | (assoc-ref inputs "adwaita-icon-theme") "/share")))) | |
3028 | #t))))) | |
48446f0f | 3029 | (home-page "https://wxmaxima-developers.github.io/wxmaxima/") |
9aafbc0c MW |
3030 | (synopsis "Graphical user interface for the Maxima computer algebra system") |
3031 | (description | |
3032 | "wxMaxima is a graphical user interface for the Maxima computer algebra | |
3033 | system. It eases the use of Maxima by making most of its commands available | |
3034 | through a menu system and by providing input dialogs for commands that require | |
3035 | more than one argument. It also implements its own display engine that | |
3036 | outputs mathematical symbols directly instead of depicting them with ASCII | |
3037 | characters. | |
3038 | ||
3039 | wxMaxima also features 2D and 3D inline plots, simple animations, mixing of | |
3040 | text and mathematical calculations to create documents, exporting of input and | |
3041 | output to TeX, and a browser for Maxima's manual including command index and | |
3042 | full text searching.") | |
3043 | (license license:gpl2+))) | |
3044 | ||
b15e47f9 RW |
3045 | (define-public armadillo |
3046 | (package | |
3047 | (name "armadillo") | |
f133e244 | 3048 | (version "9.100.5") |
b15e47f9 RW |
3049 | (source (origin |
3050 | (method url-fetch) | |
3051 | (uri (string-append "mirror://sourceforge/arma/armadillo-" | |
7397cd9e | 3052 | version ".tar.xz")) |
b15e47f9 RW |
3053 | (sha256 |
3054 | (base32 | |
f133e244 | 3055 | "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby")))) |
b15e47f9 | 3056 | (build-system cmake-build-system) |
e405c0bc | 3057 | (arguments `(#:tests? #f)) ; no test target |
b15e47f9 RW |
3058 | (inputs |
3059 | `(("openblas" ,openblas) | |
3060 | ("lapack" ,lapack) | |
3061 | ("arpack" ,arpack-ng))) | |
3062 | (home-page "http://arma.sourceforge.net/") | |
3063 | (synopsis "C++ linear algebra library") | |
3064 | (description | |
3065 | "Armadillo is a C++ linear algebra library, aiming towards a good balance | |
3066 | between speed and ease of use. It is useful for algorithm development | |
3067 | directly in C++, or quick conversion of research code into production | |
3068 | environments. It can be used for machine learning, pattern recognition, | |
3069 | signal processing, bioinformatics, statistics, econometrics, etc. The library | |
3070 | provides efficient classes for vectors, matrices and cubes, as well as 150+ | |
3071 | associated functions (eg. contiguous and non-contiguous submatrix views).") | |
fe418cc5 | 3072 | (license license:asl2.0))) |
b15e47f9 | 3073 | |
279663ef | 3074 | (define-public muparser |
d7cff656 LF |
3075 | ;; When switching download sites, muparser re-issued a 2.2.5 release with a |
3076 | ;; different hash. In order to make `guix package --upgrade` work correctly, | |
3077 | ;; we set a Guix packaging revision. | |
3078 | ;; When the next version of muparser is released, we can remove | |
3079 | ;; UPSTREAM-VERSION and REVISION and use the plain VERSION. | |
3080 | (let ((upstream-version "2.2.5") | |
3081 | (revision "2")) | |
3082 | (package | |
3083 | (name "muparser") | |
3084 | (version (string-append upstream-version "-" revision)) | |
3085 | (source | |
3086 | (origin | |
67f1db38 TGR |
3087 | (method git-fetch) |
3088 | (uri (git-reference | |
3089 | (url "https://github.com/beltoforion/muparser.git") | |
3090 | (commit (string-append "v" upstream-version)))) | |
3091 | (file-name (git-file-name name version)) | |
d7cff656 | 3092 | (sha256 |
67f1db38 | 3093 | (base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24")))) |
d7cff656 LF |
3094 | (build-system gnu-build-system) |
3095 | (arguments | |
3096 | `(#:configure-flags '("--enable-samples=no") | |
3097 | #:tests? #f)) ;no "check" target | |
3098 | (home-page "http://muparser.beltoforion.de/") | |
3099 | (synopsis "Fast parser library for mathematical expressions") | |
3100 | (description | |
3101 | "muParser is an extensible high performance math parser library. It is | |
3102 | based on transforming an expression into a bytecode and precalculating constant | |
3103 | parts of it.") | |
3104 | (license license:expat)))) | |
279663ef | 3105 | |
e73b49fb RW |
3106 | (define-public openblas |
3107 | (package | |
3108 | (name "openblas") | |
2ea09530 | 3109 | (version "0.3.7") |
e73b49fb RW |
3110 | (source |
3111 | (origin | |
3112 | (method url-fetch) | |
a617fd55 MB |
3113 | (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20" |
3114 | version "%20version.tar.gz")) | |
e73b49fb RW |
3115 | (file-name (string-append name "-" version ".tar.gz")) |
3116 | (sha256 | |
3117 | (base32 | |
2ea09530 | 3118 | "0jbdjsi0qsxahdcm42agnn1y7xpmg0hrhwjsxg0zbhs9wwy3p568")))) |
e73b49fb RW |
3119 | (build-system gnu-build-system) |
3120 | (arguments | |
5789566a | 3121 | `(#:test-target "test" |
bd0b4379 RW |
3122 | ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no |
3123 | ;; TARGET is specified, OpenBLAS will tune itself to the build host, so | |
3124 | ;; we need to disable substitutions. | |
71923a91 AE |
3125 | #:substitutable? |
3126 | ,(let ((system (or (%current-target-system) (%current-system)))) | |
3127 | (or (string-prefix? "x86_64" system) | |
bd0b4379 | 3128 | (string-prefix? "i686" system) |
83a34647 EF |
3129 | (string-prefix? "mips" system) |
3130 | (string-prefix? "aarch64" system))) | |
e73b49fb RW |
3131 | #:make-flags |
3132 | (list (string-append "PREFIX=" (assoc-ref %outputs "out")) | |
3133 | "SHELL=bash" | |
5855756c | 3134 | "MAKE_NB_JOBS=0" ;use jobserver for submakes |
a4384dc9 MB |
3135 | |
3136 | ;; This is the maximum number of threads OpenBLAS will ever use (that | |
3137 | ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS | |
3138 | ;; is used.) If we don't set it, the makefile sets it to the number | |
3139 | ;; of cores of the build machine, which is obviously wrong. | |
3140 | "NUM_THREADS=128" | |
3141 | ||
af5b817e RW |
3142 | ;; Build the library for all supported CPUs. This allows |
3143 | ;; switching CPU targets at runtime with the environment variable | |
3144 | ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type. | |
71923a91 AE |
3145 | ;; Unfortunately, this is not supported on non-x86 architectures, |
3146 | ;; where it leads to failed builds. | |
3147 | ,@(let ((system (or (%current-target-system) (%current-system)))) | |
8a637e79 RW |
3148 | (cond |
3149 | ((or (string-prefix? "x86_64" system) | |
71923a91 | 3150 | (string-prefix? "i686" system)) |
8a637e79 RW |
3151 | '("DYNAMIC_ARCH=1")) |
3152 | ;; On MIPS we force the "SICORTEX" TARGET, as for the other | |
3153 | ;; two available MIPS targets special extended instructions | |
3154 | ;; for Loongson cores are used. | |
3155 | ((string-prefix? "mips" system) | |
3156 | '("TARGET=SICORTEX")) | |
83a34647 EF |
3157 | ;; On aarch64 force the generic 'armv8-a' target |
3158 | ((string-prefix? "aarch64" system) | |
3159 | '("TARGET=ARMV8")) | |
8a637e79 | 3160 | (else '())))) |
e73b49fb | 3161 | ;; no configure script |
493937ae DL |
3162 | #:phases |
3163 | (modify-phases %standard-phases | |
3164 | (delete 'configure) | |
3165 | (add-before 'build 'set-extralib | |
3166 | (lambda* (#:key inputs #:allow-other-keys) | |
3167 | ;; Get libgfortran found when building in utest. | |
3168 | (setenv "FEXTRALIB" | |
3169 | (string-append "-L" (assoc-ref inputs "fortran-lib") | |
3170 | "/lib")) | |
3171 | #t))))) | |
e73b49fb | 3172 | (inputs |
493937ae | 3173 | `(("fortran-lib" ,gfortran "lib"))) |
e73b49fb RW |
3174 | (native-inputs |
3175 | `(("cunit" ,cunit) | |
493937ae | 3176 | ("fortran" ,gfortran) |
e73b49fb RW |
3177 | ("perl" ,perl))) |
3178 | (home-page "http://www.openblas.net/") | |
3179 | (synopsis "Optimized BLAS library based on GotoBLAS") | |
3180 | (description | |
3181 | "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.") | |
3182 | (license license:bsd-3))) | |
3183 | ||
daa6036f | 3184 | (define-public openblas-ilp64 |
ba05be22 | 3185 | (package/inherit openblas |
daa6036f EB |
3186 | (name "openblas-ilp64") |
3187 | (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux")) | |
3188 | (arguments | |
3189 | (substitute-keyword-arguments (package-arguments openblas) | |
3190 | ((#:make-flags flags '()) | |
3191 | `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64") | |
3192 | ,flags)))) | |
3193 | (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)") | |
3194 | (license license:bsd-3))) | |
3195 | ||
5a7deb11 LC |
3196 | (define* (make-blis implementation #:optional substitutable?) |
3197 | "Return a BLIS package with the given IMPLEMENTATION (see config/ in the | |
3198 | source tree for a list of implementations.) | |
3199 | ||
3200 | SUBSTITUTABLE? determines whether the package is made available as a | |
3201 | substitute. | |
3202 | ||
3203 | Currently the specialization must be selected at configure-time, but work is | |
3204 | underway to allow BLIS to select the right optimized kernels at run time: | |
3205 | <https://github.com/flame/blis/issues/129>." | |
3206 | (package | |
3207 | (name (if (string=? implementation "reference") | |
3208 | "blis" | |
3209 | (string-append "blis-" implementation))) | |
3210 | (version "0.2.2") | |
3211 | (home-page "https://github.com/flame/blis") | |
3212 | (source (origin | |
3213 | (method git-fetch) | |
3214 | (uri (git-reference (url home-page) (commit version))) | |
3215 | (sha256 | |
3216 | (base32 | |
3217 | "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh")) | |
3218 | (file-name (git-file-name "blis" version)))) | |
3219 | (build-system gnu-build-system) | |
3220 | (arguments | |
3221 | `(#:test-target "test" | |
3222 | ||
3223 | #:substitutable? ,substitutable? | |
3224 | ||
3225 | #:phases (modify-phases %standard-phases | |
3226 | (replace 'configure | |
3227 | (lambda* (#:key outputs #:allow-other-keys) | |
3228 | ;; This is a home-made 'configure' script. | |
3229 | (let ((out (assoc-ref outputs "out"))) | |
1ec17821 RW |
3230 | (invoke "./configure" "-p" out |
3231 | "-d" "opt" | |
3232 | "--disable-static" | |
3233 | "--enable-shared" | |
3234 | "--enable-threading=openmp" | |
5a7deb11 | 3235 | |
1ec17821 | 3236 | ,implementation)))) |
5a7deb11 LC |
3237 | (add-before 'check 'show-test-output |
3238 | (lambda _ | |
3239 | ;; By default "make check" is silent. Make it verbose. | |
3240 | (system "tail -F output.testsuite &") | |
3241 | #t))))) | |
3242 | (synopsis "High-performance basic linear algebra (BLAS) routines") | |
3243 | (description | |
3244 | "BLIS is a portable software framework for instantiating high-performance | |
3245 | BLAS-like dense linear algebra libraries. The framework was designed to | |
3246 | isolate essential kernels of computation that, when optimized, immediately | |
3247 | enable optimized implementations of most of its commonly used and | |
3248 | computationally intensive operations. While BLIS exports a new BLAS-like API, | |
3249 | it also includes a BLAS compatibility layer which gives application developers | |
3250 | access to BLIS implementations via traditional BLAS routine calls.") | |
3251 | (license license:bsd-3))) | |
3252 | ||
3253 | (define-public blis | |
3254 | ;; This is the "reference" implementation, which is the non-optimized but | |
3255 | ;; portable variant (no assembly). | |
3256 | (make-blis "reference" #t)) | |
3257 | ||
3258 | (define ignorance blis) | |
3259 | ||
3260 | (define-syntax-rule (blis/x86_64 processor) | |
3261 | "Expand to a package specialized for PROCESSOR." | |
3262 | (package | |
3263 | (inherit (make-blis processor)) | |
3264 | (supported-systems '("x86_64-linux")))) | |
3265 | ||
3266 | (define-public blis-sandybridge | |
3267 | ;; BLIS specialized for Sandy Bridge processors (launched 2011): | |
3268 | ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>. | |
3269 | (blis/x86_64 "sandybridge")) | |
3270 | ||
3271 | (define-public blis-haswell | |
3272 | ;; BLIS specialized for Haswell processors (launched 2013): | |
3273 | ;; <http://ark.intel.com/products/codename/42174/Haswell>. | |
3274 | (blis/x86_64 "haswell")) | |
3275 | ||
3276 | (define-public blis-knl | |
3277 | ;; BLIS specialized for Knights Landing processor (launched 2016): | |
3278 | ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>. | |
3279 | (blis/x86_64 "knl")) | |
3280 | ||
3281 | ||
e1605e36 RW |
3282 | (define-public openlibm |
3283 | (package | |
3284 | (name "openlibm") | |
48d7ac17 | 3285 | (version "0.6.0") |
e1605e36 RW |
3286 | (source |
3287 | (origin | |
ca72dd2c TGR |
3288 | (method git-fetch) |
3289 | (uri (git-reference | |
3290 | (url "https://github.com/JuliaLang/openlibm.git") | |
3291 | (commit (string-append "v" version)))) | |
3292 | (file-name (git-file-name name version)) | |
e1605e36 | 3293 | (sha256 |
ca72dd2c | 3294 | (base32 "08wfchmmr5200fvmn1kwq9byc1fhsq46hn0y5k8scdl74771c7gh")))) |
e1605e36 RW |
3295 | (build-system gnu-build-system) |
3296 | (arguments | |
3297 | `(#:make-flags | |
3298 | (list (string-append "prefix=" (assoc-ref %outputs "out"))) | |
3299 | #:phases | |
3300 | ;; no configure script | |
dc1d3cde | 3301 | (modify-phases %standard-phases (delete 'configure)) |
e1605e36 RW |
3302 | #:tests? #f)) ;the tests are part of the default target |
3303 | (home-page "http://openlibm.org/") | |
3304 | (synopsis "Portable C mathematical library (libm)") | |
3305 | (description | |
3306 | "OpenLibm is an effort to have a high quality, portable, standalone C | |
3307 | mathematical library (libm). It can be used standalone in applications and | |
3308 | programming language implementations. The project was born out of a need to | |
e881752c | 3309 | have a good libm for the Julia programming language that worked consistently |
e1605e36 RW |
3310 | across compilers and operating systems, and in 32-bit and 64-bit |
3311 | environments.") | |
538c0e3b EF |
3312 | ;; Each architecture has its own make target, and there is none for mips. |
3313 | (supported-systems (delete "mips64el-linux" %supported-systems)) | |
e1605e36 RW |
3314 | ;; See LICENSE.md for details. |
3315 | (license (list license:expat | |
3316 | license:isc | |
3317 | license:bsd-2 | |
3318 | license:public-domain | |
3319 | license:lgpl2.1+)))) | |
3320 | ||
e62be58f RW |
3321 | (define-public openspecfun |
3322 | (package | |
3323 | (name "openspecfun") | |
59cd0ba4 | 3324 | (version "0.5.3") |
e62be58f RW |
3325 | (source |
3326 | (origin | |
90cea671 TGR |
3327 | (method git-fetch) |
3328 | (uri (git-reference | |
3329 | (url "https://github.com/JuliaLang/openspecfun.git") | |
3330 | (commit (string-append "v" version)))) | |
3331 | (file-name (git-file-name name version)) | |
e62be58f | 3332 | (sha256 |
90cea671 | 3333 | (base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh")))) |
e62be58f RW |
3334 | (build-system gnu-build-system) |
3335 | (arguments | |
59cd0ba4 | 3336 | '(#:tests? #f ; no "check" target |
e62be58f RW |
3337 | #:make-flags |
3338 | (list (string-append "prefix=" (assoc-ref %outputs "out"))) | |
59cd0ba4 TGR |
3339 | #:phases |
3340 | (modify-phases %standard-phases | |
3341 | (delete 'configure)))) ; no configure script | |
e62be58f | 3342 | (inputs |
19afbea1 | 3343 | `(("fortran" ,gfortran))) |
e62be58f RW |
3344 | (home-page "https://github.com/JuliaLang/openspecfun") |
3345 | (synopsis "Collection of special mathematical functions") | |
3346 | (description | |
3347 | "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a | |
3348 | portable package for Bessel Functions of a Complex Argument and Nonnegative | |
3349 | Order; it contains subroutines for computing Bessel functions and Airy | |
3350 | functions. Faddeeva allows computing the various error functions of arbitrary | |
3351 | complex arguments (Faddeeva function, error function, complementary error | |
3352 | function, scaled complementary error function, imaginary error function, and | |
3353 | Dawson function); given these, one can also easily compute Voigt functions, | |
3354 | Fresnel integrals, and similar related functions as well.") | |
3355 | ;; Faddeeva is released under the Expat license; AMOS is included as | |
3356 | ;; public domain software. | |
3357 | (license (list license:expat license:public-domain)))) | |
3358 | ||
2742f87e RW |
3359 | (define-public suitesparse |
3360 | (package | |
3361 | (name "suitesparse") | |
bd5b5ac0 | 3362 | (version "4.5.5") |
2742f87e RW |
3363 | (source |
3364 | (origin | |
3365 | (method url-fetch) | |
3366 | (uri (string-append | |
3367 | "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-" | |
3368 | version ".tar.gz")) | |
3369 | (sha256 | |
3370 | (base32 | |
bd5b5ac0 EB |
3371 | "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr")) |
3372 | (modules '((guix build utils))) | |
3373 | (snippet | |
3374 | ;; Remove bundled metis source | |
6cbee49d MW |
3375 | '(begin |
3376 | (delete-file-recursively "metis-5.1.0") | |
3377 | #t)))) | |
2742f87e RW |
3378 | (build-system gnu-build-system) |
3379 | (arguments | |
bd5b5ac0 | 3380 | '(#:tests? #f ;no "check" target |
2742f87e RW |
3381 | #:make-flags |
3382 | (list "CC=gcc" | |
3383 | "BLAS=-lblas" | |
3384 | "TBB=-ltbb" | |
bd5b5ac0 | 3385 | "MY_METIS_LIB=-lmetis" |
2742f87e RW |
3386 | (string-append "INSTALL_LIB=" |
3387 | (assoc-ref %outputs "out") "/lib") | |
3388 | (string-append "INSTALL_INCLUDE=" | |
bd5b5ac0 EB |
3389 | (assoc-ref %outputs "out") "/include") |
3390 | "library") | |
2742f87e | 3391 | #:phases |
2509522c | 3392 | (modify-phases %standard-phases |
bd5b5ac0 | 3393 | (delete 'configure)))) ;no configure script |
2742f87e RW |
3394 | (inputs |
3395 | `(("tbb" ,tbb) | |
bd5b5ac0 EB |
3396 | ("lapack" ,lapack) |
3397 | ("metis" ,metis))) | |
2742f87e RW |
3398 | (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html") |
3399 | (synopsis "Suite of sparse matrix software") | |
3400 | (description | |
3401 | "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK, | |
3402 | multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR, | |
3403 | multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit | |
3404 | simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and | |
3405 | CXSparse, a concise sparse Cholesky factorization package; and many other | |
3406 | packages.") | |
3407 | ;; LGPLv2.1+: | |
3408 | ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL | |
3409 | ;; GPLv2+: | |
3410 | ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK | |
3411 | (license (list license:gpl2+ license:lgpl2.1+)))) | |
3412 | ||
ec322be2 FB |
3413 | (define-public atlas |
3414 | (package | |
3415 | (name "atlas") | |
3c98ac02 | 3416 | (version "3.10.3") |
ec322be2 FB |
3417 | (source (origin |
3418 | (method url-fetch) | |
de67e922 LF |
3419 | (uri (string-append "mirror://sourceforge/math-atlas/Stable/" |
3420 | version "/atlas" version ".tar.bz2")) | |
ec322be2 FB |
3421 | (sha256 |
3422 | (base32 | |
3c98ac02 | 3423 | "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216")))) |
ec322be2 FB |
3424 | (build-system gnu-build-system) |
3425 | (home-page "http://math-atlas.sourceforge.net/") | |
19afbea1 | 3426 | (inputs `(("gfortran" ,gfortran) |
ec322be2 FB |
3427 | ("lapack-tar" ,(package-source lapack)))) |
3428 | (outputs '("out" "doc")) | |
01480b9e FB |
3429 | ;; For the moment we drop support for MIPS at it fails to compile. See |
3430 | ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html | |
3431 | (supported-systems (delete "mips64el-linux" %supported-systems)) | |
ec322be2 FB |
3432 | (arguments |
3433 | `(#:parallel-build? #f | |
3434 | #:parallel-tests? #f | |
f15615b1 LC |
3435 | |
3436 | ;; ATLAS tunes itself for the machine it is built on, as explained at | |
3437 | ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>. | |
3438 | ;; For this reason, we want users to build it locally instead of using | |
3439 | ;; substitutes. | |
3440 | #:substitutable? #f | |
3441 | ||
ec322be2 | 3442 | #:modules ((srfi srfi-26) |
ec322be2 FB |
3443 | (guix build gnu-build-system) |
3444 | (guix build utils)) | |
40029cbe | 3445 | #:configure-flags |
ec322be2 FB |
3446 | `(;; Generate position independent code suitable for dynamic libraries |
3447 | ;; and use WALL timer to get more accurate timing. | |
3448 | "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL" | |
3449 | ;; Set word width. | |
3450 | "-b" | |
3451 | ,,(if (string-match "64" (%current-system)) | |
3452 | "64" | |
3453 | "32") | |
3454 | ;; Disable parallel build as it gives errors: atlas_pthread.h is | |
3455 | ;; needed to compile C files before it is generated. | |
3456 | "-Ss" "pmake" "make -j 1" | |
af89a667 FB |
3457 | ;; Probe is failing for MIPS. We therefore define the system |
3458 | ;; architecture explicitly by setting (-A) MACHINETYPE = 49 | |
3459 | ;; 'MIPSR1xK' and (-V) ISA = 1 'none'. | |
3460 | ,,@(if (string-prefix? "mips" (%current-system)) | |
3461 | (list "-A" "49" "-V" "1") | |
3462 | (list)) | |
ec322be2 FB |
3463 | ;; Generate shared libraries. |
3464 | "--shared" | |
3465 | ;; Build a full LAPACK library. | |
3466 | ,(string-append "--with-netlib-lapack-tarfile=" | |
3467 | (assoc-ref %build-inputs "lapack-tar"))) | |
3468 | #:phases | |
e5b4b96b EF |
3469 | (modify-phases %standard-phases |
3470 | (add-after 'install 'install-doc | |
3471 | (lambda* (#:key outputs inputs #:allow-other-keys) | |
3472 | (let ((doc (string-append (assoc-ref outputs "doc") | |
3473 | "/share/doc/atlas"))) | |
3474 | (mkdir-p doc) | |
cb6f44d4 RW |
3475 | (for-each (cut install-file <> doc) |
3476 | (find-files "../ATLAS/doc" ".*")) | |
3477 | #t))) | |
e5b4b96b | 3478 | (add-after 'check 'check-pt |
cb6f44d4 | 3479 | (lambda _ (invoke "make" "ptcheck"))) |
e5b4b96b EF |
3480 | ;; Fix files required to run configure. |
3481 | (add-before 'configure 'fix-/bin/sh | |
ec322be2 FB |
3482 | (lambda _ |
3483 | ;; Use `sh', not `/bin/sh'. | |
3484 | (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c") | |
3485 | (("/bin/sh") | |
5b786db8 EF |
3486 | "sh")) |
3487 | #t)) | |
e5b4b96b EF |
3488 | ;; Fix /bin/sh in generated make files. |
3489 | (add-after 'configure 'fix-/bin/sh-in-generated-files | |
3490 | (lambda _ | |
3491 | (substitute* (find-files "." "^[Mm]ake\\.inc.*") | |
3492 | (("/bin/sh") | |
5b786db8 EF |
3493 | "sh")) |
3494 | #t)) | |
e5b4b96b EF |
3495 | ;; ATLAS configure program does not accepts the default flags |
3496 | ;; passed by the 'gnu-build-system'. | |
3497 | (replace 'configure | |
3498 | (lambda* (#:key native-inputs inputs outputs | |
3499 | (configure-flags '()) | |
3500 | #:allow-other-keys #:rest args) | |
3501 | (let* ((prefix (assoc-ref outputs "out")) | |
3502 | (bash (or (and=> (assoc-ref | |
3503 | (or native-inputs inputs) "bash") | |
3504 | (cut string-append <> "/bin/bash")) | |
3505 | "/bin/sh")) | |
3506 | (flags `(,(string-append "--prefix=" prefix) | |
3507 | ,@configure-flags)) | |
3508 | (abs-srcdir (getcwd)) | |
3509 | (srcdir (string-append "../" (basename abs-srcdir)))) | |
3510 | (format #t "source directory: ~s (relative from build: ~s)~%" | |
3511 | abs-srcdir srcdir) | |
3512 | (mkdir "../build") | |
3513 | (chdir "../build") | |
3514 | (format #t "build directory: ~s~%" (getcwd)) | |
3515 | (format #t "configure flags: ~s~%" flags) | |
cb6f44d4 RW |
3516 | (apply invoke bash |
3517 | (string-append srcdir "/configure") | |
3518 | flags))))))) | |
ec322be2 FB |
3519 | (synopsis "Automatically Tuned Linear Algebra Software") |
3520 | (description | |
3521 | "ATLAS is an automatically tuned linear algebra software library | |
3522 | providing C and Fortran77 interfaces to a portably efficient BLAS | |
3523 | implementation, as well as a few routines from LAPACK. | |
3524 | ||
f15615b1 LC |
3525 | Optimization occurs at build time. For this reason, the library is built on |
3526 | the machine where it is installed, without resorting to pre-built substitutes. | |
ec322be2 | 3527 | |
f15615b1 | 3528 | Before building the library, CPU throttling should be disabled. This can be |
d97c429a | 3529 | done in the BIOS, or, on GNU/Linux, with the following command: |
ec322be2 | 3530 | |
8e9ba611 | 3531 | @example |
d97c429a | 3532 | # cpupower --governor performance |
8e9ba611 | 3533 | @end example |
ec322be2 | 3534 | |
d97c429a | 3535 | Failure to do so will result in a library with poor performance.") |
ec322be2 | 3536 | (license license:bsd-3))) |
c12efc72 AE |
3537 | |
3538 | (define-public glm | |
3539 | (package | |
3540 | (name "glm") | |
3f55b7be | 3541 | (version "0.9.9.6") |
c12efc72 AE |
3542 | (source |
3543 | (origin | |
3544 | (method url-fetch) | |
5ea4b594 MB |
3545 | (uri (string-append "https://github.com/g-truc/glm/releases/download/" |
3546 | version "/glm-" version ".zip")) | |
c12efc72 | 3547 | (sha256 |
3f55b7be TGR |
3548 | (base32 "1l0pi1qi37mk6s0yrkrw07lspv4gcqnr9ryg3521hrl77ff37dwx")) |
3549 | (patches (search-patches "glm-restore-install-target.patch")))) | |
c12efc72 AE |
3550 | (build-system cmake-build-system) |
3551 | (native-inputs | |
3552 | `(("unzip" ,unzip))) | |
46bda5eb | 3553 | (home-page "https://glm.g-truc.net/") |
c12efc72 AE |
3554 | (synopsis "OpenGL Mathematics library") |
3555 | (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics | |
3556 | library for graphics software based on the OpenGL Shading Language (GLSL) | |
3557 | specifications.") | |
3558 | (license license:expat))) | |
7f18257b AE |
3559 | |
3560 | (define-public lpsolve | |
3561 | (package | |
3562 | (name "lpsolve") | |
a89e0cf5 | 3563 | (version "5.5.2.5") |
7f18257b AE |
3564 | (source |
3565 | (origin | |
3566 | (method url-fetch) | |
3567 | (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version | |
3568 | "/lp_solve_" version "_source.tar.gz")) | |
3569 | (sha256 | |
3570 | (base32 | |
a89e0cf5 | 3571 | "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0")) |
7f18257b AE |
3572 | (modules '((guix build utils))) |
3573 | (snippet | |
6cbee49d MW |
3574 | '(begin |
3575 | (substitute* (list "lp_solve/ccc" "lpsolve55/ccc") | |
3576 | (("^c=cc") "c=gcc") | |
3577 | ;; Pretend to be on a 64 bit platform to obtain a common directory | |
3578 | ;; name for the build results on all architectures; nothing else | |
3579 | ;; seems to depend on it. | |
3580 | (("^PLATFORM=.*$") "PLATFORM=ux64\n") | |
3581 | ||
3582 | ;; The check for 'isnan' as it is written fails with | |
3583 | ;; "non-floating-point argument in call to function | |
3584 | ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro | |
3585 | ;; definition, which in turn leads to bad things. Fix the feature | |
3586 | ;; test. | |
3587 | (("isnan\\(0\\)") "isnan(0.)")) | |
3588 | #t)))) | |
7f18257b AE |
3589 | (build-system gnu-build-system) |
3590 | (arguments | |
6c96b545 | 3591 | `(#:tests? #f ; no check target |
7f18257b AE |
3592 | #:phases |
3593 | (modify-phases %standard-phases | |
6c96b545 | 3594 | (delete 'configure) ; no configure script |
7f18257b AE |
3595 | (replace 'build |
3596 | (lambda _ | |
6c96b545 TGR |
3597 | (with-directory-excursion "lpsolve55" |
3598 | (invoke "bash" "ccc")) | |
3599 | (with-directory-excursion "lp_solve" | |
3600 | (invoke "bash" "ccc")) | |
3601 | #t)) | |
7f18257b AE |
3602 | (replace 'install |
3603 | (lambda* (#:key outputs #:allow-other-keys) | |
3604 | (let* ((out (assoc-ref outputs "out")) | |
3605 | (bin (string-append out "/bin")) | |
3606 | (lib (string-append out "/lib")) | |
3607 | ;; This is where LibreOffice expects to find the header | |
3608 | ;; files, and where they are installed by Debian. | |
3609 | (include (string-append out "/include/lpsolve"))) | |
6c96b545 TGR |
3610 | (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib) |
3611 | (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib) | |
96c46210 LC |
3612 | (install-file "lp_solve/bin/ux64/lp_solve" bin) |
3613 | ||
7f18257b AE |
3614 | ;; Install a subset of the header files as on Debian |
3615 | ;; (plus lp_bit.h, which matches the regular expression). | |
96c46210 LC |
3616 | (for-each (lambda (name) |
3617 | (install-file name include)) | |
3618 | (find-files "." "lp_[HMSa-z].*\\.h$")) | |
7f18257b | 3619 | (with-directory-excursion "shared" |
96c46210 LC |
3620 | (for-each (lambda (name) |
3621 | (install-file name include)) | |
3622 | (find-files "." "\\.h$"))) | |
7f18257b AE |
3623 | #t)))))) |
3624 | (home-page "http://lpsolve.sourceforge.net/") | |
3625 | (synopsis "Mixed integer linear programming (MILP) solver") | |
3626 | (description | |
3627 | "lp_solve is a mixed integer linear programming solver based on the | |
3628 | revised simplex and the branch-and-bound methods.") | |
3629 | (license license:lgpl2.1+))) | |
a17d4564 EB |
3630 | |
3631 | (define-public dealii | |
3632 | (package | |
3633 | (name "dealii") | |
ba567cae | 3634 | (version "9.1.1") |
a17d4564 EB |
3635 | (source |
3636 | (origin | |
3637 | (method url-fetch) | |
3638 | (uri (string-append "https://github.com/dealii/dealii/releases/" | |
3639 | "download/v" version "/dealii-" version ".tar.gz")) | |
3640 | (sha256 | |
3641 | (base32 | |
ba567cae | 3642 | "0xhjv0gzswpjbc43xbrpwfc5848g508l01855nszx3g5gwzlhnzw")) |
a17d4564 EB |
3643 | (modules '((guix build utils))) |
3644 | (snippet | |
3645 | ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost | |
6cbee49d MW |
3646 | '(begin |
3647 | (delete-file-recursively "bundled") | |
3648 | #t)))) | |
a17d4564 EB |
3649 | (build-system cmake-build-system) |
3650 | (inputs | |
3651 | `(("tbb" ,tbb) | |
3652 | ("zlib" ,zlib) | |
3653 | ("boost" ,boost) | |
3654 | ("p4est" ,p4est) | |
3655 | ("blas" ,openblas) | |
3656 | ("lapack" ,lapack) | |
3657 | ("arpack" ,arpack-ng) | |
3658 | ("muparser" ,muparser) | |
3659 | ("gfortran" ,gfortran) | |
3660 | ("suitesparse" ,suitesparse))) ;for UMFPACK | |
3661 | (arguments | |
3662 | `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease | |
d84b09e9 EB |
3663 | #:configure-flags |
3664 | ;; Work around a bug in libsuitesparseconfig linking | |
3665 | ;; see https://github.com/dealii/dealii/issues/4745 | |
3666 | '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON"))) | |
a17d4564 EB |
3667 | (home-page "https://www.dealii.org") |
3668 | (synopsis "Finite element library") | |
3669 | (description | |
3670 | "Deal.II is a C++ program library targeted at the computational solution | |
3671 | of partial differential equations using adaptive finite elements. The main | |
3672 | aim of deal.II is to enable rapid development of modern finite element codes, | |
3673 | using among other aspects adaptive meshes and a wide array of tools often used | |
3674 | in finite element programs.") | |
3675 | (license license:lgpl2.1+))) | |
3676 | ||
3677 | (define-public dealii-openmpi | |
3678 | (package (inherit dealii) | |
3679 | (name "dealii-openmpi") | |
3680 | (inputs | |
3681 | `(("mpi" ,openmpi) | |
3682 | ;;Supported only with MPI: | |
4d44bcad | 3683 | ("hdf5" ,hdf5-parallel-openmpi) ;TODO: have petsc-openmpi propagate? |
a17d4564 EB |
3684 | ("p4est" ,p4est-openmpi) |
3685 | ("petsc" ,petsc-openmpi) | |
3686 | ("slepc" ,slepc-openmpi) | |
3687 | ("metis" ,metis) ;for MUMPS | |
3688 | ("scalapack" ,scalapack) ;for MUMPS | |
3689 | ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings | |
3690 | ("arpack" ,arpack-ng-openmpi) | |
3691 | ,@(fold alist-delete (package-inputs dealii) | |
3692 | '("p4est" "arpack")))) | |
3693 | (arguments | |
3694 | (substitute-keyword-arguments (package-arguments dealii) | |
3695 | ((#:configure-flags cf) | |
40b114c0 EB |
3696 | `(cons "-DDEAL_II_WITH_MPI:BOOL=ON" |
3697 | ,cf)) | |
7e309e8a EB |
3698 | ((#:phases phases '%standard-phases) |
3699 | `(modify-phases ,phases | |
3700 | (add-before 'check 'mpi-setup | |
3701 | ,%openmpi-setup))))) | |
a17d4564 | 3702 | (synopsis "Finite element library (with MPI support)"))) |
194c7f95 AE |
3703 | |
3704 | (define-public flann | |
3705 | (package | |
3706 | (name "flann") | |
3707 | (version "1.8.4") | |
3708 | (source | |
3709 | (origin | |
3710 | (method url-fetch) | |
3711 | (uri | |
3712 | (string-append | |
3713 | "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-" | |
3714 | version "-src.zip")) | |
3715 | (sha256 | |
3716 | (base32 | |
b5edc479 LC |
3717 | "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz")) |
3718 | (patches (search-patches "flann-cmake-3.11.patch")))) | |
194c7f95 | 3719 | (build-system cmake-build-system) |
6b6aca9b LC |
3720 | (outputs '("out" |
3721 | "octave")) ;46 MiB .mex file that pulls Octave | |
194c7f95 AE |
3722 | (native-inputs |
3723 | `(("unzip" ,unzip))) | |
3724 | (inputs | |
3725 | `(("hdf5" ,hdf5) | |
5537603f | 3726 | ("octave" ,octave-cli) |
194c7f95 AE |
3727 | ("python" ,python-2) ; print syntax |
3728 | ;; ("python2-numpy" ,python2-numpy) ; only required for the tests | |
3729 | ("zlib" ,zlib))) | |
3730 | (arguments | |
39b30337 LC |
3731 | `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file |
3732 | ;; taken 46 MiB unstripped, and 6 MiB stripped. | |
3733 | #:strip-directories '("lib" "lib64" "libexec" | |
3734 | "bin" "sbin" "share/flann/octave") | |
3735 | ||
9684e30b LC |
3736 | ;; Save 12 MiB by not installing .a files. Passing |
3737 | ;; '-DBUILD_STATIC_LIBS=OFF' has no effect. | |
3738 | #:phases (modify-phases %standard-phases | |
6b6aca9b LC |
3739 | (add-before 'configure 'set-octave-directory |
3740 | (lambda* (#:key outputs #:allow-other-keys) | |
3741 | ;; Install the .mex file in the "octave" output. | |
3742 | (let ((out (assoc-ref outputs "octave"))) | |
3743 | (substitute* "src/matlab/CMakeLists.txt" | |
3744 | (("share/flann/octave") | |
3745 | (string-append out "/share/flann/octave"))) | |
3746 | #t))) | |
9684e30b LC |
3747 | (add-after 'install 'remove-static-libraries |
3748 | (lambda* (#:key outputs #:allow-other-keys) | |
3749 | (let* ((out (assoc-ref outputs "out")) | |
3750 | (lib (string-append out "/lib"))) | |
3751 | (for-each delete-file | |
3752 | (find-files lib "\\.a$")) | |
3753 | #t)))) | |
3754 | ||
39b30337 | 3755 | #:tests? #f)) ; The test data are downloaded from the Internet. |
194c7f95 AE |
3756 | (home-page "http://www.cs.ubc.ca/research/flann/") |
3757 | (synopsis "Library for approximate nearest neighbors computation") | |
3758 | (description "FLANN is a library for performing fast approximate | |
3759 | nearest neighbor searches in high dimensional spaces. It implements a | |
3760 | collection of algorithms and a system for automatically choosing the best | |
3761 | algorithm and optimum parameters depending on the dataset. | |
3762 | ||
3763 | FLANN is written in C++ and contains bindings for C, Octave and Python.") | |
3764 | (license (license:non-copyleft "file://COPYING" | |
3765 | "See COPYING in the distribution.")))) | |
d8c97beb EF |
3766 | |
3767 | (define-public wcalc | |
3768 | (package | |
3769 | (name "wcalc") | |
3770 | (version "2.5") | |
3771 | (source | |
3772 | (origin | |
3773 | (method url-fetch) | |
de67e922 LF |
3774 | (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/" |
3775 | "wcalc-" version ".tar.bz2")) | |
d8c97beb EF |
3776 | (sha256 |
3777 | (base32 | |
3778 | "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f")))) | |
3779 | (build-system gnu-build-system) | |
3780 | (inputs | |
3781 | `(("mpfr" ,mpfr) | |
3782 | ("readline" ,readline))) | |
3783 | (home-page "http://w-calc.sourceforge.net/index.php") | |
3784 | (synopsis "Flexible command-line scientific calculator") | |
3785 | (description "Wcalc is a very capable calculator. It has standard functions | |
3786 | (sin, asin, and sinh for example, in either radians or degrees), many | |
3787 | pre-defined constants (pi, e, c, etc.), support for using variables, \"active\" | |
3788 | variables, a command history, hex/octal/binary input and output, unit | |
3789 | conversions, embedded comments, and an expandable expression entry field. It | |
3790 | evaluates expressions using the standard order of operations.") | |
3791 | (license license:gpl2+))) | |
45147b0c FH |
3792 | |
3793 | (define-public xaos | |
3794 | (package | |
3795 | (name "xaos") | |
3796 | (version "3.6") | |
3797 | (source (origin | |
3798 | (method url-fetch) | |
de67e922 LF |
3799 | (uri (string-append "mirror://sourceforge/xaos/XaoS/" version |
3800 | "/xaos-" version ".tar.gz")) | |
45147b0c FH |
3801 | (sha256 |
3802 | (base32 | |
3803 | "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq")))) | |
3804 | (build-system gnu-build-system) | |
b94a6ca0 | 3805 | (native-inputs `(("gettext" ,gettext-minimal))) |
45147b0c FH |
3806 | (inputs `(("libx11" ,libx11) |
3807 | ("zlib" ,zlib) | |
3808 | ("libpng" ,libpng) | |
3809 | ("gsl" ,gsl))) | |
3810 | (arguments | |
3811 | `(#:tests? #f ;no "check" target | |
3812 | #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale"))) | |
3813 | (synopsis "Real-time fractal zoomer") | |
3814 | (description "GNU XaoS is a graphical program that generates fractal | |
3815 | patterns and allows you to zoom in and out of them infinitely in a fluid, | |
3816 | continuous manner. It also includes tutorials that help to explain how fractals | |
3817 | are built. It can generate many different fractal types such as the Mandelbrot | |
3818 | set.") | |
6fd52309 | 3819 | (home-page "https://www.gnu.org/software/xaos/") |
45147b0c | 3820 | (license license:gpl2+))) |
528bb464 EB |
3821 | |
3822 | (define-public hypre | |
3823 | (package | |
3824 | (name "hypre") | |
be099727 | 3825 | (version "2.15.1") |
fabcbf32 TGR |
3826 | (source |
3827 | (origin | |
3828 | (method git-fetch) | |
3829 | (uri (git-reference | |
3830 | (url "https://github.com/LLNL/hypre.git") | |
3831 | (commit (string-append "v" version)))) | |
3832 | (file-name (git-file-name name version)) | |
3833 | (sha256 | |
be099727 | 3834 | (base32 "1lvh4ybqkriyqfg2zmic6mrg1981qv1i9vry1fdgsabn81hb71g4")) |
fabcbf32 TGR |
3835 | (modules '((guix build utils))) |
3836 | (snippet | |
3837 | '(begin | |
3838 | ;; Remove use of __DATE__ and __TIME__ for reproducibility; | |
be099727 | 3839 | ;; substitute the release date. |
fabcbf32 TGR |
3840 | (substitute* "src/utilities/HYPRE_utilities.h" |
3841 | (("Date Compiled: .*$") | |
be099727 | 3842 | "Date Compiled: Oct 19 2018 15:23:00 +0000\"\n")) |
fabcbf32 | 3843 | #t)))) |
528bb464 | 3844 | (build-system gnu-build-system) |
be099727 TGR |
3845 | (outputs '("out" ; 6.1 MiB of headers and libraries |
3846 | "doc")) ; 4.8 MiB of documentation | |
528bb464 EB |
3847 | (native-inputs |
3848 | `(("doc++" ,doc++) | |
3849 | ("netpbm" ,netpbm) | |
be099727 | 3850 | ("perl" ,perl) ; needed to run 'ppmquant' during tests |
8b35c8cd RW |
3851 | ("texlive" ,(texlive-union (list texlive-xypic |
3852 | texlive-cm | |
9b405aea | 3853 | texlive-latex-hyperref |
9b405aea | 3854 | texlive-bibtex))) |
528bb464 EB |
3855 | ("ghostscript" ,ghostscript))) |
3856 | (inputs | |
3857 | `(("blas" ,openblas) | |
3858 | ("lapack" ,lapack))) | |
3859 | (arguments | |
3860 | `(#:modules ((srfi srfi-1) | |
3861 | ,@%gnu-build-system-modules) | |
3862 | #:configure-flags '("--enable-shared" | |
3863 | "--disable-fortran" | |
3864 | "--without-MPI" | |
3865 | "--with-openmp" | |
3866 | "--with-fei" | |
3867 | "--with-lapack" | |
3868 | "--with-blas") | |
3869 | #:phases | |
3870 | (modify-phases %standard-phases | |
9b405aea PN |
3871 | (add-before 'build 'set-HOME |
3872 | (lambda _ | |
3873 | ;; FIXME: texlive-union does not find the built | |
3874 | ;; metafonts, so it tries to generate them in HOME. | |
3875 | (setenv "HOME" "/tmp") | |
3876 | #t)) | |
528bb464 EB |
3877 | (add-before 'configure 'chdir-src |
3878 | (lambda _ (chdir "src"))) | |
3879 | (replace 'configure | |
3880 | (lambda* (#:key build target configure-flags | |
3881 | #:allow-other-keys #:rest args) | |
3882 | (let* ((configure (assoc-ref %standard-phases 'configure))) | |
3883 | (apply configure | |
3884 | (append args | |
3885 | (list #:configure-flags | |
3886 | (cons (string-append | |
3887 | "--host=" (or target build)) | |
3888 | configure-flags))))))) | |
3889 | (add-after 'build 'build-docs | |
3890 | (lambda _ | |
9b405aea | 3891 | (invoke "make" "-Cdocs" "pdf" "html"))) |
528bb464 EB |
3892 | (replace 'check |
3893 | (lambda _ | |
3894 | (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib")) | |
3895 | (setenv "PATH" (string-append "." ":" (getenv "PATH"))) | |
6b1c7ac8 RW |
3896 | (invoke "make" "check" "CHECKRUN=") |
3897 | (for-each (lambda (filename) | |
3898 | (let ((size (stat:size (stat filename)))) | |
3899 | (when (positive? size) | |
3900 | (error (format #f "~a size ~d; error indication~%" | |
3901 | filename size))))) | |
3902 | (find-files "test" ".*\\.err$")) | |
3903 | #t)) | |
528bb464 EB |
3904 | (add-after 'install 'install-docs |
3905 | (lambda* (#:key outputs #:allow-other-keys) | |
3906 | ;; Custom install because docs/Makefile doesn't honor ${docdir}. | |
3907 | (let* ((doc (assoc-ref outputs "doc")) | |
3908 | (docdir (string-append doc "/share/doc/hypre-" ,version))) | |
528bb464 EB |
3909 | (with-directory-excursion "docs" |
3910 | (for-each (lambda (base) | |
3911 | (install-file (string-append base ".pdf") docdir) | |
be099727 | 3912 | (copy-recursively base docdir)) ; html docs |
528bb464 EB |
3913 | '("HYPRE_usr_manual" |
3914 | "HYPRE_ref_manual"))) | |
3915 | #t)))))) | |
3916 | (home-page "http://www.llnl.gov/casc/hypre/") | |
3917 | (synopsis "Library of solvers and preconditioners for linear equations") | |
3918 | (description | |
3919 | "HYPRE is a software library of high performance preconditioners and | |
3920 | solvers for the solution of large, sparse linear systems of equations. It | |
3921 | features multigrid solvers for both structured and unstructured grid | |
3922 | problems.") | |
3923 | (license license:lgpl2.1))) | |
3924 | ||
3925 | (define-public hypre-openmpi | |
3926 | (package (inherit hypre) | |
3927 | (name "hypre-openmpi") | |
3928 | (inputs | |
3929 | `(("mpi" ,openmpi) | |
3930 | ,@(package-inputs hypre))) | |
3931 | (arguments | |
3932 | (substitute-keyword-arguments (package-arguments hypre) | |
3933 | ((#:configure-flags flags) | |
3934 | ``("--with-MPI" | |
6df2a50a LC |
3935 | ,@(delete "--without-MPI" ,flags))) |
3936 | ((#:phases phases) | |
3937 | `(modify-phases ,phases | |
bbe46a4a EB |
3938 | (add-before 'check 'mpi-setup |
3939 | ,%openmpi-setup))))) | |
528bb464 EB |
3940 | (synopsis "Parallel solvers and preconditioners for linear equations") |
3941 | (description | |
3942 | "HYPRE is a software library of high performance preconditioners and | |
3943 | solvers for the solution of large, sparse linear systems of equations on | |
3944 | parallel computers. It features parallel multigrid solvers for both | |
3945 | structured and unstructured grid problems."))) | |
6c90e183 EB |
3946 | |
3947 | (define-public matio | |
3948 | (package | |
3949 | (name "matio") | |
3950 | (version "1.5.6") | |
3951 | (source | |
3952 | (origin | |
3953 | (method url-fetch) | |
de67e922 | 3954 | (uri (string-append "mirror://sourceforge/matio/matio/" version "/" |
6c90e183 EB |
3955 | "matio-" version ".tar.gz")) |
3956 | (sha256 | |
3957 | (base32 | |
3958 | "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir")))) | |
3959 | (build-system gnu-build-system) | |
3960 | (inputs | |
3961 | `(("zlib" ,zlib) | |
3962 | ("hdf5" ,hdf5))) | |
3963 | (home-page "http://matio.sourceforge.net/") | |
3964 | (synopsis "Library for reading and writing MAT files") | |
3965 | (description "Matio is a library for reading and writing MAT files. It | |
3966 | supports compressed MAT files, as well as newer (version 7.3) MAT files.") | |
3967 | (license license:bsd-2))) | |
d721c83a | 3968 | |
517318ad LF |
3969 | (define-public vc |
3970 | (package | |
3971 | (name "vc") | |
9d731fb6 | 3972 | (version "1.4.1") |
517318ad LF |
3973 | (source |
3974 | (origin (method url-fetch) | |
3975 | (uri (string-append "https://github.com/VcDevel/Vc/releases/" | |
3976 | "download/" version "/Vc-" version ".tar.gz")) | |
3977 | (sha256 | |
3978 | (base32 | |
9d731fb6 | 3979 | "17qili8bf8r78cng65yf4qmgna8kiqjqbgcqbric6v9j6nkhkrk8")))) |
517318ad LF |
3980 | (build-system cmake-build-system) |
3981 | (arguments | |
3982 | '(#:configure-flags | |
33d82486 MB |
3983 | '("-DBUILD_TESTING=ON" |
3984 | ;; By default, Vc will optimize for the CPU of the build machine. | |
3985 | ;; Setting this to "none" makes it create portable binaries. See | |
3986 | ;; "cmake/OptimizeForArchitecture.cmake". | |
9d731fb6 MB |
3987 | "-DTARGET_ARCHITECTURE=none") |
3988 | #:phases (modify-phases %standard-phases | |
3989 | (add-after 'unpack 'copy-testdata | |
3990 | (lambda* (#:key inputs native-inputs #:allow-other-keys) | |
3991 | (let ((testdata (assoc-ref (or native-inputs inputs) | |
3992 | "testdata"))) | |
3993 | (copy-recursively testdata "tests/testdata") | |
3994 | #t)))))) | |
3995 | (native-inputs | |
3996 | `(("virtest" ,virtest) | |
3997 | ||
3998 | ;; This is a submodule in the git project, but not part of the | |
3999 | ;; released sources. See the git branch for the commit to take. | |
4000 | ("testdata" ,(let ((commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3")) | |
4001 | (origin | |
4002 | (method git-fetch) | |
4003 | (uri (git-reference | |
4004 | (url "https://github.com/VcDevel/vc-testdata") | |
4005 | (commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3"))) | |
4006 | (file-name (git-file-name "vc-testdata" | |
4007 | (string-take commit 7))) | |
4008 | (sha256 | |
4009 | (base32 | |
4010 | "1hkhqib03qlcq412ym2dciynfxcdr2ygqhnplz4l1vissr1wnqn2"))))))) | |
517318ad LF |
4011 | (synopsis "SIMD vector classes for C++") |
4012 | (description "Vc provides portable, zero-overhead C++ types for explicitly | |
4013 | data-parallel programming. It is a library designed to ease explicit | |
4014 | vectorization of C++ code. Its types enable explicitly stating data-parallel | |
4015 | operations on multiple values. The parallelism is therefore added via the type | |
4016 | system. Vc has an intuitive API and provides portability between different | |
4017 | compilers and compiler versions as well as portability between different vector | |
4018 | instruction sets. Thus, an application written with Vc can be compiled for: | |
4019 | @enumerate | |
4020 | @item AVX and AVX2 | |
d1e4ad1b | 4021 | @item SSE2 up to SSE4.2 or SSE4a |
517318ad LF |
4022 | @item Scalar |
4023 | @item MIC | |
4024 | @item NEON (in development) | |
4025 | @item NVIDIA GPUs / CUDA (in development) | |
4026 | @end enumerate\n") | |
4027 | (home-page "https://github.com/VcDevel/Vc") | |
a8ead6f9 EF |
4028 | ;; "No support_???.cpp file exists for this architecture." |
4029 | (supported-systems '("x86_64-linux" "i686-linux")) | |
517318ad | 4030 | (license license:bsd-3))) |
54052a54 | 4031 | |
4032 | (define-public reducelcs | |
4033 | ;; This is the last commit which is available upstream, no | |
4034 | ;; release happened since 2010. | |
4035 | (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0") | |
4036 | (revision "1")) | |
4037 | (package | |
4038 | (name "reducelcs") | |
4039 | (version (string-append "1.0-" revision "." (string-take commit 7))) | |
4040 | (source | |
4041 | (origin | |
4042 | (method git-fetch) | |
4043 | (uri (git-reference | |
4044 | (url "https://github.com/gdv/Reduce-Expand-for-LCS") | |
4045 | (commit commit))) | |
4046 | (file-name (string-append name "-" version "-checkout")) | |
4047 | (sha256 | |
4048 | (base32 | |
4049 | "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm")))) | |
4050 | (build-system gnu-build-system) | |
4051 | (inputs | |
4052 | `(("openlibm" ,openlibm))) | |
4053 | (arguments | |
4054 | `(#:tests? #f ; no tests | |
4055 | #:phases | |
4056 | (modify-phases %standard-phases | |
4057 | (delete 'configure) ; No configure script exists. | |
4058 | (replace 'install ; No install phase exists. | |
4059 | (lambda* (#:key outputs #:allow-other-keys) | |
4060 | (let* ((out (assoc-ref outputs "out")) | |
4061 | (bin (string-append out "/bin"))) | |
4062 | (install-file "Approximation" bin) | |
4063 | (install-file "CollectResults" bin) | |
4064 | (install-file "GenerateInstances" bin) | |
4065 | #t)))))) | |
4066 | (synopsis "Approximate Longest Commons Subsequence computation tool") | |
4067 | (description | |
4068 | "@code{reduceLCS} is an implementation of the Reduce-Expand | |
4069 | algorithm for LCS. It is a fast program to compute the approximate | |
4070 | Longest Commons Subsequence of a set of strings.") | |
4071 | (home-page "https://github.com/gdv/Reduce-Expand-for-LCS") | |
c000b6b1 | 4072 | (license license:gpl3+)))) |
479c4273 JD |
4073 | |
4074 | (define-public jacal | |
4075 | (package | |
4076 | (name "jacal") | |
4077 | (version "1c4") | |
4078 | (source (origin | |
4079 | (method url-fetch) | |
4080 | (uri (string-append | |
4081 | "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-" | |
4082 | version ".zip")) | |
4083 | (sha256 (base32 | |
4084 | "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q")) | |
4085 | (patches (search-patches "jacal-fix-texinfo.patch")))) | |
4086 | (build-system gnu-build-system) | |
4087 | (arguments | |
4088 | `(#:phases | |
4089 | (modify-phases %standard-phases | |
4090 | (add-before 'build 'pre-build | |
4091 | ;; Don't use upstream's script - it really doesn't fit into | |
4092 | ;; Guix's functional paradigm. | |
4093 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
4094 | (substitute* "Makefile" | |
4095 | (("^install: install-script") "install: ")))) | |
4096 | (add-after 'install 'post-install | |
4097 | ;; Instead, we provide our own simplified script. | |
4098 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
4099 | (let ((wrapper (string-append (assoc-ref outputs "out") | |
4100 | "/bin/jacal"))) | |
4101 | (format (open wrapper (logior O_WRONLY O_CREAT)) | |
4102 | (string-append "#!~a\nexec ~a/bin/scm -ip1 " | |
4103 | "-e '(slib:load \"~a/lib/jacal/math\") " | |
4104 | "(math)' \"$@\"\n") | |
4105 | (which "bash") | |
4106 | (assoc-ref inputs "scm") | |
4107 | (assoc-ref outputs "out")) | |
4108 | (chmod wrapper #o555)))) | |
4109 | (replace 'configure | |
9cd82b1c RW |
4110 | (lambda* (#:key outputs #:allow-other-keys) |
4111 | (invoke "./configure" | |
4112 | (string-append "--prefix=" | |
4113 | (assoc-ref outputs "out")))))))) | |
479c4273 JD |
4114 | (inputs `(("scm" ,scm))) |
4115 | (native-inputs `(("unzip" ,unzip) | |
4116 | ("texinfo" ,texinfo))) | |
4117 | (synopsis "Symbolic mathematics system") | |
4118 | (description "GNU JACAL is an interactive symbolic mathematics program based on | |
4119 | Scheme. It manipulate and simplify a range of mathematical expressions such | |
4120 | as equations, scalars, vectors, and matrices.") | |
6fd52309 | 4121 | (home-page "https://www.gnu.org/software/jacal/") |
479c4273 JD |
4122 | (license license:gpl3+))) |
4123 | ||
313844d9 TF |
4124 | (define-public z3 |
4125 | (package | |
4126 | (name "z3") | |
dbef037f | 4127 | (version "4.8.7") |
fb525bfd | 4128 | (home-page "https://github.com/Z3Prover/z3") |
313844d9 | 4129 | (source (origin |
fb525bfd MB |
4130 | (method git-fetch) |
4131 | (uri (git-reference (url home-page) | |
4132 | (commit (string-append "z3-" version)))) | |
2d7b99b3 | 4133 | (file-name (git-file-name name version)) |
313844d9 TF |
4134 | (sha256 |
4135 | (base32 | |
dbef037f | 4136 | "0hprcdwhhyjigmhhk6514m71bnmvqci9r8gglrqilgx424r6ff7q")))) |
fa574a6d | 4137 | (build-system gnu-build-system) |
313844d9 | 4138 | (arguments |
fa574a6d | 4139 | `(#:phases |
313844d9 | 4140 | (modify-phases %standard-phases |
ad6c6a5b EF |
4141 | (add-after 'unpack 'fix-compatability |
4142 | ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only. | |
4143 | (lambda _ | |
4144 | (substitute* "src/util/mpz.cpp" | |
4145 | (("#include <immintrin.h>") "")) | |
4146 | #t)) | |
cf684d87 TF |
4147 | (add-before 'configure 'bootstrap |
4148 | (lambda _ | |
32d5360f | 4149 | (invoke "python" "scripts/mk_make.py"))) |
fa574a6d AB |
4150 | ;; work around gnu-build-system's setting --enable-fast-install |
4151 | ;; (z3's `configure' is a wrapper around the above python file, | |
4152 | ;; which fails when passed --enable-fast-install) | |
4153 | (replace 'configure | |
4154 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
4155 | (invoke "./configure" | |
4156 | (string-append "--prefix=" (assoc-ref outputs "out"))))) | |
4157 | (add-after 'configure 'change-directory | |
4158 | (lambda _ | |
4159 | (chdir "build") | |
4160 | #t)) | |
cf684d87 | 4161 | (add-before 'check 'make-test-z3 |
313844d9 | 4162 | (lambda _ |
cf684d87 | 4163 | ;; Build the test suite executable. |
32d5360f RW |
4164 | (invoke "make" "test-z3" "-j" |
4165 | (number->string (parallel-job-count))))) | |
cf684d87 TF |
4166 | (replace 'check |
4167 | (lambda _ | |
4168 | ;; Run all the tests that don't require arguments. | |
32d5360f | 4169 | (invoke "./test-z3" "/a")))))) |
313844d9 | 4170 | (native-inputs |
fa574a6d AB |
4171 | `(("which" ,which) |
4172 | ("python" ,python-wrapper))) | |
313844d9 TF |
4173 | (synopsis "Theorem prover") |
4174 | (description "Z3 is a theorem prover and @dfn{satisfiability modulo | |
cf684d87 | 4175 | theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.") |
313844d9 | 4176 | (license license:expat))) |
3d5d87a3 | 4177 | |
6d433d6e EB |
4178 | (define-public elpa |
4179 | (package | |
4180 | (name "elpa") | |
4181 | (version "2018.11.001") | |
4182 | (source (origin | |
4183 | (method url-fetch) | |
4184 | (uri (string-append "http://elpa.mpcdf.mpg.de/html/Releases/" | |
4185 | version "/elpa-" version ".tar.gz")) | |
4186 | (sha256 | |
4187 | (base32 | |
4188 | "05hv3v5i6xmziaizw350ff72y1c3k662r85fm3xfdrkclj5zw9yc")))) | |
4189 | (build-system gnu-build-system) | |
4190 | (native-inputs | |
4191 | `(("fortran" ,gfortran) | |
4192 | ("perl" ,perl))) ;for configure and deps | |
4193 | (inputs | |
4194 | `(("blas" ,openblas))) | |
4195 | (arguments | |
4196 | `(#:configure-flags | |
4197 | `("--enable-openmp" | |
4198 | "--with-mpi=no" | |
4199 | ;; ELPA unfortunately does not support runtime dispatch, so we can | |
4200 | ;; only enable the "generic" kernels. See the "Cross compilation" | |
4201 | ;; section of INSTALL.md. | |
4202 | "--enable-generic" | |
4203 | "--disable-sse" "--disable-sse-assembly" ;Require SSE3 | |
4204 | "--disable-avx" "--disable-avx2" "--disable-avx512" | |
4205 | ,(string-append "CFLAGS=-O3 " | |
4206 | "-funsafe-loop-optimizations -funsafe-math-optimizations " | |
4207 | "-ftree-vect-loop-version -ftree-vectorize " | |
4208 | ,(let ((system (or (%current-target-system) | |
4209 | (%current-system)))) | |
4210 | (cond | |
4211 | ((or (string-prefix? "x86_64" system) | |
4212 | (string-prefix? "i686" system)) | |
4213 | "-msse2") | |
4214 | (else ""))))) | |
4215 | #:parallel-tests? #f ;tests are multi-threaded, via BLAS | |
4216 | #:phases | |
4217 | (modify-phases %standard-phases | |
4218 | (add-before 'configure 'patch-header-generation | |
4219 | (lambda _ | |
4220 | (substitute* "configure" | |
4221 | (("^ *make.*top_srcdir=\"\\$srcdir\"" &) | |
4222 | (string-append & " CPP=\"$CPP\""))) | |
4223 | #t)) | |
4224 | (add-before 'check 'setup-tests | |
4225 | (lambda _ | |
4226 | ;; Decrease test time and RAM use by computing fewer eigenvalues. | |
4227 | ;; The flags are (MATRIX-SIZE, EIGENVALUES, BLOCK-SIZE), where | |
4228 | ;; the default is (500, 250, 16) for C tests and (5000, 150, 16) | |
4229 | ;; for Fortran. This also causes several tests to pass that | |
4230 | ;; otherwise would otherwise fail with matrix size 5000; possibly | |
4231 | ;; due to floating point tolerances that are too tight. | |
4232 | (setenv "TEST_FLAGS" "1500 50 16") ;from elpa.spec | |
4233 | (setenv "OMP_NUM_THREADS" (number->string (parallel-job-count))) | |
4234 | (substitute* "Makefile" | |
4235 | ;; Test scripts are generated, patch the shebang | |
4236 | (("#!/bin/bash") (string-append "#!" (which "sh")))) | |
4237 | #t))))) | |
4238 | (home-page "http://elpa.mpcdf.mpg.de") | |
4239 | (synopsis "Eigenvalue solvers for symmetric matrices") | |
4240 | (description | |
4241 | "The ELPA library provides efficient and scalable direct eigensolvers for | |
4242 | symmetric matrices.") | |
4243 | (license license:lgpl3))) | |
4244 | ||
4245 | (define-public elpa-openmpi | |
4246 | (package (inherit elpa) | |
4247 | (name "elpa-openmpi") | |
4248 | (inputs | |
4249 | `(("mpi" ,openmpi) | |
4250 | ("scalapack" ,scalapack) | |
4251 | ,@(package-inputs elpa))) | |
4252 | (arguments | |
4253 | (substitute-keyword-arguments (package-arguments elpa) | |
4254 | ((#:configure-flags cf '()) | |
4255 | `(cons "--with-mpi=yes" (delete "--with-mpi=no" ,cf))) | |
4256 | ((#:phases phases '%standard-phases) | |
4257 | `(modify-phases ,phases | |
4258 | (add-before 'check 'mpi-setup | |
4259 | (lambda _ | |
4260 | ;; Tests use 2 mpi tasks by default, use our remaining build | |
4261 | ;; cores as OpenMP threads. | |
4262 | (setenv "OMP_NUM_THREADS" (number->string | |
4263 | (max (quotient (parallel-job-count) 2) | |
4264 | 1))) | |
4265 | (,%openmpi-setup))))))) | |
4266 | (synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)"))) | |
4267 | ||
e01397b4 EB |
4268 | (define-public elemental |
4269 | (package | |
4270 | (name "elemental") | |
4271 | (version "0.87.7") | |
4272 | (source (origin | |
5c0b6d1b EF |
4273 | (method git-fetch) |
4274 | (uri (git-reference | |
4275 | (url "https://github.com/elemental/Elemental.git") | |
4276 | (commit (string-append "v" version)))) | |
4277 | (file-name (git-file-name name version)) | |
e01397b4 EB |
4278 | (sha256 |
4279 | (base32 | |
5c0b6d1b | 4280 | "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc")))) |
e01397b4 | 4281 | (build-system cmake-build-system) |
1e05e837 | 4282 | (home-page "https://github.com/elemental/Elemental") |
e01397b4 EB |
4283 | (native-inputs |
4284 | `(("gfortran" ,gfortran))) | |
4285 | (inputs | |
4286 | `(("blas" ,openblas) | |
4287 | ("gfortran:lib" ,gfortran "lib") | |
4288 | ("gmp" ,gmp) | |
4289 | ("lapack" ,lapack) | |
4290 | ("metis" ,metis) | |
4291 | ("mpc" ,mpc) | |
4292 | ("mpfr" ,mpfr) | |
4293 | ("mpi" ,openmpi) | |
4294 | ("qd" ,qd))) | |
4295 | (arguments | |
4296 | `(#:build-type "Release" ;default RelWithDebInfo not supported | |
4297 | #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES" | |
4298 | "-DEL_AVOID_COMPLEX_MPI:BOOL=NO" | |
4299 | "-DEL_CACHE_WARNINGS:BOOL=YES" | |
4300 | "-DEL_TESTS:BOOL=YES" | |
4301 | "-DCMAKE_INSTALL_LIBDIR=lib" | |
4302 | "-DGFORTRAN_LIB=gfortran") | |
4303 | #:phases (modify-phases %standard-phases | |
3b42e2be EF |
4304 | (add-before 'check 'mpi-setup |
4305 | ,%openmpi-setup) | |
e01397b4 EB |
4306 | (add-before 'check 'setup-tests |
4307 | (lambda _ | |
4308 | ;; Parallelism is done at the MPI layer. | |
4309 | (setenv "OMP_NUM_THREADS" "1") | |
4310 | #t)) | |
4311 | (add-after 'install 'remove-tests | |
4312 | (lambda* (#:key outputs #:allow-other-keys) | |
4313 | ;; Tests are installed, with no easy configuration | |
4314 | ;; switch to prevent this, so delete them. | |
4315 | (delete-file-recursively | |
3b42e2be | 4316 | (string-append (assoc-ref outputs "out") "/bin")) |
e01397b4 EB |
4317 | #t))))) |
4318 | (synopsis "Dense and sparse-direct linear algebra and optimization") | |
4319 | (description "Elemental is a modern C++ library for distributed-memory | |
4320 | dense and sparse-direct linear algebra, conic optimization, and lattice | |
4321 | reduction.") | |
4322 | (license license:bsd-2))) | |
5b05dce7 JN |
4323 | |
4324 | (define-public mcrl2 | |
4325 | (package | |
4326 | (name "mcrl2") | |
3bc74090 | 4327 | (version "201908.0") |
5b05dce7 JN |
4328 | (source (origin |
4329 | (method url-fetch) | |
185152e3 JN |
4330 | (uri (string-append |
4331 | "https://www.mcrl2.org/download/release/mcrl2-" | |
4332 | version ".tar.gz")) | |
5b05dce7 JN |
4333 | (sha256 |
4334 | (base32 | |
3bc74090 | 4335 | "1i4xgl2d5fgiz1mwi50cyfkrrcpm8nxfayfjgmhq7chs58wlhfsz")))) |
5b05dce7 JN |
4336 | (inputs |
4337 | `(("boost" ,boost) | |
4338 | ("glu" ,glu) | |
4339 | ("mesa" ,mesa) | |
077d66ed | 4340 | ("qtbase" ,qtbase))) |
5b05dce7 | 4341 | (build-system cmake-build-system) |
ed0c5d3c | 4342 | (synopsis "Toolset for the mCRL2 formal specification language") |
5b05dce7 | 4343 | (description |
ed0c5d3c TGR |
4344 | "@dfn{mCRL2} (micro Common Representation Language 2) is a formal |
4345 | specification language for describing concurrent discrete event systems. Its | |
4346 | toolset supports analysis and automatic verification, linearisation, simulation, | |
4347 | state-space exploration and generation, and tools to optimise and analyse | |
5b05dce7 JN |
4348 | specifications. Also, state spaces can be manipulated, visualised and |
4349 | analysed.") | |
b3882709 | 4350 | (home-page "https://mcrl2.org") |
5b05dce7 | 4351 | (license license:boost1.0))) |
41835f94 | 4352 | |
e03b9126 JN |
4353 | (define-public mcrl2-minimal |
4354 | (package | |
4355 | (inherit mcrl2) | |
4356 | (name "mcrl2-minimal") | |
4357 | (inputs | |
4358 | `(("boost" ,boost))) | |
4359 | (arguments | |
4360 | '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF"))))) | |
4361 | ||
910deec6 NV |
4362 | (define-public tcalc |
4363 | (package | |
4364 | (name "tcalc") | |
4365 | (version "2.0") | |
4366 | (source | |
4367 | (origin | |
4368 | (method url-fetch) | |
4369 | (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-" | |
4370 | version ".tar.gz")) | |
4371 | (sha256 | |
4372 | (base32 | |
4373 | "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m")))) | |
4374 | (build-system gnu-build-system) | |
4375 | (synopsis "The terminal calculator") | |
4376 | (description | |
4377 | "The terminal calculator is a small program to help users of the GNU/Linux | |
4378 | terminal do calculations simply and quickly. The formula to be calculated can | |
4379 | be fed to @command{tcalc} through the command line.") | |
4380 | (home-page "https://sites.google.com/site/mohammedisam2000/tcalc") | |
4381 | (license license:gpl3+))) | |
b26e4f26 EB |
4382 | |
4383 | (define-public sundials | |
4384 | (package | |
4385 | (name "sundials") | |
4386 | (version "3.1.1") | |
4387 | (source | |
4388 | (origin | |
4389 | (method url-fetch) | |
4390 | (uri (string-append "https://computation.llnl.gov/projects/sundials/download/" | |
4391 | "sundials-" version ".tar.gz")) | |
4392 | (sha256 | |
4393 | (base32 | |
4394 | "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2")))) | |
4395 | (build-system cmake-build-system) | |
4396 | (native-inputs | |
4397 | `(("python" ,python-2))) ;for tests; syntax incompatible with python 3 | |
4398 | (inputs | |
4399 | `(("fortran" ,gfortran) ;for fcmix | |
4400 | ("blas" ,openblas) | |
4401 | ("suitesparse" ,suitesparse))) ;TODO: Add hypre | |
4402 | (arguments | |
4403 | `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON" | |
4404 | "-DEXAMPLES_ENABLE_CXX:BOOL=ON" | |
4405 | "-DEXAMPLES_ENABLE_F77:BOOL=ON" | |
4406 | "-DEXAMPLES_ENABLE_F90:BOOL=ON" | |
4407 | "-DEXAMPLES_INSTALL:BOOL=OFF" | |
4408 | ||
4409 | "-DFCMIX_ENABLE:BOOL=ON" | |
4410 | ||
4411 | "-DKLU_ENABLE:BOOL=ON" | |
4412 | ,(string-append "-DKLU_INCLUDE_DIR=" | |
4413 | (assoc-ref %build-inputs "suitesparse") | |
4414 | "/include") | |
4415 | ,(string-append "-DKLU_LIBRARY_DIR=" | |
4416 | (assoc-ref %build-inputs "suitesparse") | |
4417 | "/lib")))) | |
4418 | (home-page "https://computation.llnl.gov/projects/sundials") | |
4419 | (synopsis "Suite of nonlinear and differential/algebraic equation solvers") | |
4420 | (description "SUNDIALS is a family of software packages implemented with | |
4421 | the goal of providing robust time integrators and nonlinear solvers that can | |
4422 | easily be incorporated into existing simulation codes.") | |
4423 | (license license:bsd-3))) | |
4424 | ||
4425 | (define-public sundials-openmpi | |
4426 | (package (inherit sundials) | |
4427 | (name "sundials-openmpi") | |
4428 | (inputs | |
4429 | `(("mpi" ,openmpi) | |
4430 | ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI | |
4431 | ,@(package-inputs sundials))) | |
4432 | (arguments | |
4433 | (substitute-keyword-arguments (package-arguments sundials) | |
4434 | ((#:configure-flags flags '()) | |
4435 | `(cons* "-DMPI_ENABLE:BOOL=ON" | |
4436 | "-DPETSC_ENABLE:BOOL=ON" | |
4437 | (string-append "-DPETSC_INCLUDE_DIR=" | |
4438 | (assoc-ref %build-inputs "petsc") | |
4439 | "/include") | |
4440 | (string-append "-DPETSC_LIBRARY_DIR=" | |
4441 | (assoc-ref %build-inputs "petsc") | |
4442 | "/lib") | |
4443 | ,flags)) | |
4444 | ((#:phases phases '%standard-phases) | |
4445 | `(modify-phases ,phases | |
bbe46a4a EB |
4446 | (add-before 'check 'mpi-setup |
4447 | ,%openmpi-setup))))) | |
b26e4f26 | 4448 | (synopsis "SUNDIALS with OpenMPI support"))) |
a6b9ebc2 EB |
4449 | |
4450 | (define-public combinatorial-blas | |
4451 | (package | |
4452 | (name "combinatorial-blas") | |
4453 | (version "1.6.2") | |
4454 | (source | |
4455 | (origin | |
4456 | (method url-fetch) | |
4457 | (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/" | |
4458 | "CombBLAS_beta_" | |
4459 | (match (string-split version #\.) | |
4460 | ((major minor patch) | |
4461 | (string-append major minor "_" patch))) ;e.g. "16_2" | |
4462 | ".tgz")) | |
4463 | (sha256 | |
4464 | (base32 | |
4465 | "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a")) | |
4466 | (patches (search-patches "combinatorial-blas-awpm.patch" | |
4467 | "combinatorial-blas-io-fix.patch")))) | |
4468 | (build-system cmake-build-system) | |
4469 | (inputs | |
4470 | `(("mpi" ,openmpi) | |
4471 | ("test-data" ,(origin | |
4472 | (method url-fetch) | |
4473 | (uri (string-append "https://people.eecs.berkeley.edu/~aydin/" | |
4474 | "CombBLAS_FILES/testdata_combblas1.6.1.tgz")) | |
4475 | (sha256 | |
4476 | (base32 | |
4477 | "01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87")))))) | |
4478 | (arguments | |
4479 | `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES" | |
4480 | "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL") | |
4481 | #:parallel-tests? #f ;tests use 'mpiexec -n4' | |
4482 | #:phases | |
4483 | (modify-phases %standard-phases | |
4484 | (add-before 'check 'mpi-setup | |
4485 | ,%openmpi-setup) | |
4486 | (add-before 'check 'test-setup | |
4487 | (lambda* (#:key inputs #:allow-other-keys) | |
4488 | (setenv "OMP_NUM_THREADS" "2") | |
4489 | (invoke "tar" "xf" (assoc-ref inputs "test-data"))))))) | |
4490 | (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/") | |
4491 | (synopsis "Linear algebra primitives for graph analytics") | |
4492 | (description "The Combinatorial BLAS (CombBLAS) is an extensible | |
4493 | distributed-memory parallel graph library offering a small but powerful set of | |
4494 | linear algebra primitives specifically targeting graph analytics.") | |
4495 | (license (list | |
4496 | license:gpl2+ ;include/psort/(funnel|sort)*.h | |
4497 | license:x11 ;usort and psort | |
4498 | license:bsd-3)))) ;CombBLAS and MersenneTwister.h | |
3847d1f2 RW |
4499 | |
4500 | (define-public dune-common | |
4501 | (package | |
4502 | (name "dune-common") | |
4503 | (version "2.6.0") | |
4504 | (source | |
4505 | (origin | |
4506 | (method url-fetch) | |
4507 | (uri (string-append "https://dune-project.org/download/" | |
4508 | version "/dune-common-" version ".tar.gz")) | |
4509 | (sha256 | |
4510 | (base32 | |
4511 | "019wcr1qf7jwyxx1y5y290wdlglylskvbb2m01ljkzcza2xnlmhw")))) | |
4512 | (build-system cmake-build-system) | |
4513 | (arguments | |
4514 | `(#:phases | |
4515 | (modify-phases %standard-phases | |
4516 | (add-after 'build 'build-tests | |
4517 | (lambda* (#:key make-flags #:allow-other-keys) | |
4518 | (apply invoke "make" "build_tests" make-flags))) | |
4519 | ;; These tests fail because they require a fully functional MPI | |
4520 | ;; environment. | |
4521 | (add-after 'unpack 'disable-failing-tests | |
4522 | (lambda _ | |
4523 | (setenv "ARGS" | |
4524 | (string-append "--exclude-regex '(" | |
4525 | (string-join | |
4526 | (list | |
4527 | "remoteindicestest" | |
4528 | "remoteindicestest-mpi-2" | |
4529 | "syncertest" | |
4530 | "syncertest-mpi-2" | |
4531 | "variablesizecommunicatortest" | |
4532 | "variablesizecommunicatortest-mpi-2" | |
4533 | "arithmetictestsuitetest" | |
4534 | "assertandreturntest" | |
4535 | "assertandreturntest_ndebug" | |
4536 | "concept" | |
4537 | "debugaligntest" | |
4538 | "mpicollectivecommunication" | |
4539 | "mpicollectivecommunication-mpi-2" | |
4540 | "mpiguardtest" | |
4541 | "mpiguardtest-mpi-2" | |
4542 | "mpihelpertest" | |
4543 | "mpihelpertest-mpi-2" | |
4544 | "mpihelpertest2" | |
4545 | "mpihelpertest2-mpi-2") | |
4546 | "|") | |
4547 | ")'")) | |
4548 | #t))))) | |
4549 | (inputs | |
4550 | `(("gmp" ,gmp) | |
4551 | ("metis" ,metis) | |
4552 | ("openmpi" ,openmpi) | |
4553 | ("openblas" ,openblas) | |
4554 | ("python" ,python) | |
4555 | ("superlu" ,superlu))) | |
4556 | (native-inputs | |
4557 | `(("gfortran" ,gfortran) | |
4558 | ("pkg-config" ,pkg-config))) | |
4559 | (home-page "https://dune-project.org/") | |
4560 | (synopsis "Distributed and Unified Numerics Environment") | |
4561 | (description "DUNE, the Distributed and Unified Numerics Environment is a | |
4562 | modular toolbox for solving @dfn{partial differential equations} (PDEs) with | |
4563 | grid-based methods. It supports the easy implementation of methods like | |
4564 | @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite | |
4565 | Differences} (FD).") | |
4566 | ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2. | |
4567 | (license license:gpl2))) | |
242dbd8e RW |
4568 | |
4569 | (define-public dune-geometry | |
4570 | (package | |
4571 | (name "dune-geometry") | |
4572 | (version "2.6.0") | |
4573 | (source | |
4574 | (origin | |
4575 | (method url-fetch) | |
4576 | (uri (string-append "https://dune-project.org/download/" | |
4577 | version "/dune-geometry-" version ".tar.gz")) | |
4578 | (sha256 | |
4579 | (base32 | |
4580 | "0hlaaxjyv9j05blasvb67sy02hd0w4g9znf68gdh3l731dd1aqbn")))) | |
4581 | (build-system cmake-build-system) | |
4582 | (arguments | |
4583 | `(#:phases | |
4584 | (modify-phases %standard-phases | |
4585 | (add-after 'build 'build-tests | |
4586 | (lambda* (#:key make-flags #:allow-other-keys) | |
4587 | (apply invoke "make" "build_tests" make-flags)))))) | |
4588 | (inputs | |
4589 | `(("dune-common" ,dune-common) | |
4590 | ("openmpi" ,openmpi) | |
4591 | ;; Optional | |
4592 | ("openblas" ,openblas) | |
4593 | ("gmp" ,gmp) | |
4594 | ("python" ,python))) | |
4595 | (native-inputs | |
4596 | `(("gfortran" ,gfortran) | |
4597 | ("pkg-config" ,pkg-config))) | |
4598 | (home-page "https://dune-project.org/") | |
4599 | (synopsis "Distributed and Unified Numerics Environment") | |
4600 | (description "DUNE, the Distributed and Unified Numerics Environment is a | |
4601 | modular toolbox for solving @dfn{partial differential equations} (PDEs) with | |
4602 | grid-based methods. It supports the easy implementation of methods like | |
4603 | @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite | |
4604 | Differences} (FD). | |
4605 | ||
4606 | This package contains the basic DUNE geometry classes.") | |
4607 | ;; GPL version 2 with "runtime exception" | |
4608 | (license license:gpl2))) | |
ef6e69fd RW |
4609 | |
4610 | (define-public dune-grid | |
4611 | (package | |
4612 | (name "dune-grid") | |
4613 | (version "2.6.0") | |
4614 | (source | |
4615 | (origin | |
4616 | (method url-fetch) | |
4617 | (uri (string-append "https://dune-project.org/download/" | |
4618 | version "/dune-grid-" version ".tar.gz")) | |
4619 | (sha256 | |
4620 | (base32 | |
4621 | "1jp4vscm9yb9xg0lh7apzccfkhvgbnk652yahigmh3cvzpl4acd0")))) | |
4622 | (build-system cmake-build-system) | |
4623 | (arguments | |
4624 | `(#:phases | |
4625 | (modify-phases %standard-phases | |
4626 | (add-after 'build 'build-tests | |
4627 | (lambda* (#:key make-flags #:allow-other-keys) | |
4628 | (apply invoke "make" "build_tests" make-flags))) | |
4629 | ;; These tests fail because they require a fully functional MPI | |
4630 | ;; environment. | |
4631 | (add-after 'unpack 'disable-failing-tests | |
4632 | (lambda _ | |
4633 | (setenv "ARGS" | |
4634 | (string-append "--exclude-regex '(" | |
4635 | (string-join | |
4636 | (list | |
4637 | "scsgmappertest" | |
4638 | "conformvolumevtktest" | |
4639 | "gnuplottest" | |
4640 | "nonconformboundaryvtktest" | |
4641 | "subsamplingvtktest" | |
4642 | "vtktest" | |
4643 | "vtktest-mpi-2" | |
4644 | "vtksequencetest" | |
4645 | "gmshtest-onedgrid" | |
4646 | "test-dgf-yasp" | |
4647 | "test-dgf-yasp-offset" | |
4648 | "test-dgf-oned" | |
4649 | "test-geogrid-yaspgrid" | |
4650 | "test-gridinfo" | |
4651 | "test-identitygrid" | |
4652 | "testiteratorranges" | |
4653 | "test-hierarchicsearch" | |
4654 | "test-parallel-ug-mpi-2" | |
4655 | "test-yaspgrid-backuprestore-equidistant" | |
4656 | "test-yaspgrid-backuprestore-equidistant-mpi-2" | |
4657 | "test-yaspgrid-backuprestore-equidistantoffset" | |
4658 | "test-yaspgrid-backuprestore-equidistantoffset-mpi-2" | |
4659 | "test-yaspgrid-backuprestore-tensor" | |
4660 | "test-yaspgrid-backuprestore-tensor-mpi-2" | |
4661 | "test-yaspgrid-tensorgridfactory" | |
4662 | "test-yaspgrid-tensorgridfactory-mpi-2" | |
4663 | "test-yaspgrid-yaspfactory-1d" | |
4664 | "test-yaspgrid-yaspfactory-1d-mpi-2" | |
4665 | "test-yaspgrid-yaspfactory-2d" | |
4666 | "test-yaspgrid-yaspfactory-2d-mpi-2" | |
4667 | "test-yaspgrid-yaspfactory-3d" | |
4668 | "test-yaspgrid-yaspfactory-3d-mpi-2" | |
4669 | "globalindexsettest" | |
4670 | "persistentcontainertest" | |
4671 | "structuredgridfactorytest" | |
4672 | "tensorgridfactorytest" | |
4673 | "vertexordertest") | |
4674 | "|") | |
4675 | ")'")) | |
4676 | #t))))) | |
4677 | (inputs | |
4678 | `(("dune-common" ,dune-common) | |
4679 | ("dune-geometry" ,dune-geometry) | |
4680 | ("gmp" ,gmp) | |
4681 | ("metis" ,metis) | |
4682 | ("openblas" ,openblas) | |
4683 | ("openmpi" ,openmpi) | |
4684 | ("python" ,python))) | |
4685 | (native-inputs | |
4686 | `(("gfortran" ,gfortran) | |
4687 | ("pkg-config" ,pkg-config))) | |
4688 | (home-page "https://dune-project.org/") | |
4689 | (synopsis "Distributed and Unified Numerics Environment") | |
4690 | (description "DUNE, the Distributed and Unified Numerics Environment is a | |
4691 | modular toolbox for solving @dfn{partial differential equations} (PDEs) with | |
4692 | grid-based methods. It supports the easy implementation of methods like | |
4693 | @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite | |
4694 | Differences} (FD). | |
4695 | ||
4696 | This package contains the basic DUNE grid classes.") | |
4697 | ;; GPL version 2 with "runtime exception" | |
4698 | (license license:gpl2))) | |
ea51d357 RW |
4699 | |
4700 | (define-public dune-istl | |
4701 | (package | |
4702 | (name "dune-istl") | |
4703 | (version "2.6.0") | |
4704 | (source | |
4705 | (origin | |
4706 | (method url-fetch) | |
4707 | (uri (string-append "https://dune-project.org/download/" | |
4708 | version "/dune-istl-" version ".tar.gz")) | |
4709 | (sha256 | |
4710 | (base32 | |
4711 | "0l2gyrvys5w6wsmk0ckbb7295s80b7yk7qrl7x66akv2jv1nzq2w")))) | |
4712 | (build-system cmake-build-system) | |
4713 | (arguments | |
4714 | `(#:phases | |
4715 | (modify-phases %standard-phases | |
4716 | (add-after 'build 'build-tests | |
4717 | (lambda* (#:key make-flags #:allow-other-keys) | |
4718 | (apply invoke "make" "build_tests" make-flags))) | |
4719 | ;; These tests fail because they require a fully functional MPI | |
4720 | ;; environment. | |
4721 | (add-after 'unpack 'disable-failing-tests | |
4722 | (lambda _ | |
4723 | (setenv "ARGS" | |
4724 | (string-append "--exclude-regex '(" | |
4725 | (string-join | |
4726 | (list | |
4727 | "galerkintest" | |
4728 | "hierarchytest" | |
4729 | "pamgtest" | |
4730 | "pamg_comm_repart_test" | |
4731 | "matrixredisttest" | |
4732 | "vectorcommtest" | |
4733 | "matrixmarkettest") | |
4734 | "|") | |
4735 | ")'")) | |
4736 | #t))))) | |
4737 | (inputs | |
4738 | `(("dune-common" ,dune-common) | |
4739 | ("openmpi" ,openmpi) | |
4740 | ;; Optional | |
4741 | ("metis" ,metis) | |
4742 | ("superlu" ,superlu) | |
4743 | ("openblas" ,openblas) | |
4744 | ("gmp" ,gmp) | |
4745 | ("python" ,python))) | |
4746 | (native-inputs | |
4747 | `(("gfortran" ,gfortran) | |
4748 | ("pkg-config" ,pkg-config))) | |
4749 | (home-page "https://dune-project.org/") | |
4750 | (synopsis "Distributed and Unified Numerics Environment") | |
4751 | (description "DUNE, the Distributed and Unified Numerics Environment is a | |
4752 | modular toolbox for solving @dfn{partial differential equations} (PDEs) with | |
4753 | grid-based methods. | |
4754 | ||
4755 | This is the iterative solver template library which provides generic sparse | |
4756 | matrix/vector classes and a variety of solvers based on these classes. A | |
4757 | special feature is the use of templates to exploit the recursive block | |
4758 | structure of finite element matrices at compile time. Available solvers | |
4759 | include Krylov methods, (block-) incomplete decompositions and | |
4760 | aggregation-based algebraic multigrid.") | |
4761 | ;; GPL version 2 with "runtime exception" | |
4762 | (license license:gpl2))) | |
5a70aa7d RW |
4763 | |
4764 | (define-public dune-localfunctions | |
4765 | (package | |
4766 | (name "dune-localfunctions") | |
4767 | (version "2.6.0") | |
4768 | (source | |
4769 | (origin | |
4770 | (method url-fetch) | |
4771 | (uri (string-append "https://dune-project.org/download/" | |
4772 | version "/dune-localfunctions-" version ".tar.gz")) | |
4773 | (sha256 | |
4774 | (base32 | |
4775 | "19c6zjinwwpy8jh4v4prhphyd438rapd4x80fj93apmwgw04nrhl")))) | |
4776 | (build-system cmake-build-system) | |
4777 | (arguments | |
4778 | `(#:phases | |
4779 | (modify-phases %standard-phases | |
4780 | (add-after 'build 'build-tests | |
4781 | (lambda* (#:key make-flags #:allow-other-keys) | |
4782 | (apply invoke "make" "build_tests" make-flags)))))) | |
4783 | (inputs | |
4784 | `(("dune-common" ,dune-common) | |
4785 | ("dune-geometry" ,dune-geometry) | |
4786 | ("openmpi" ,openmpi) | |
4787 | ;; Optional | |
4788 | ("metis" ,metis) | |
4789 | ("superlu" ,superlu) | |
4790 | ("gmp" ,gmp))) | |
4791 | (native-inputs | |
4792 | `(("gfortran" ,gfortran) | |
4793 | ("pkg-config" ,pkg-config))) | |
4794 | (home-page "https://dune-project.org/") | |
4795 | (synopsis "Distributed and Unified Numerics Environment") ; TODO | |
4796 | (description "This DUNE module provides interface and implementation for | |
4797 | shape functions defined on the DUNE reference elements. In addition to the | |
4798 | shape function, interpolation operators and special keys are provided which | |
4799 | can be used to assemble global function spaces on finite-element grids. | |
4800 | ||
4801 | This package provides an interface and implementation for shape functions | |
4802 | defined on the DUNE reference elements. In addition to the shape function, | |
4803 | interpolation operators and special keys are provided which can be used to | |
4804 | assemble global function spaces on finite-element grids.") | |
4805 | ;; GPL version 2 with "runtime exception" | |
4806 | (license license:gpl2))) | |
ab03d899 RW |
4807 | |
4808 | (define-public dune-alugrid | |
4809 | (package | |
4810 | (name "dune-alugrid") | |
4811 | (version "2.6.0") | |
4812 | (source | |
4813 | (origin | |
4814 | (method url-fetch) | |
4815 | (uri (string-append "https://dune-project.org/download/" | |
4816 | version "/dune-alugrid-" version ".tar.gz")) | |
4817 | (sha256 | |
4818 | (base32 | |
4819 | "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj")))) | |
4820 | (build-system cmake-build-system) | |
4821 | (arguments | |
4822 | `(#:tests? #f ; 7 of 8 tests fail because they need a full MPI | |
4823 | ; environment | |
4824 | #:phases | |
4825 | (modify-phases %standard-phases | |
4826 | (add-after 'unpack 'patch-include | |
4827 | (lambda _ | |
4828 | (substitute* "dune/alugrid/test/test-alugrid.cc" | |
4829 | (("doc/grids/gridfactory/testgrids") | |
4830 | "doc/dune-grid/grids/gridfactory/testgrids")) | |
4831 | #t)) | |
4832 | (add-after 'build 'build-tests | |
4833 | (lambda* (#:key inputs make-flags #:allow-other-keys) | |
4834 | (setenv "CPLUS_INCLUDE_PATH" | |
97149c57 | 4835 | (string-append (assoc-ref inputs "dune-grid") "/share")) |
ab03d899 RW |
4836 | (apply invoke "make" "build_tests" make-flags)))))) |
4837 | (inputs | |
4838 | `(("dune-common" ,dune-common) | |
4839 | ("dune-geometry" ,dune-geometry) | |
4840 | ("dune-grid" ,dune-grid) | |
4841 | ("openmpi" ,openmpi) | |
4842 | ;; Optional | |
4843 | ("metis" ,metis) | |
4844 | ("openblas" ,openblas) | |
4845 | ("python" ,python) | |
4846 | ("superlu" ,superlu) | |
4847 | ("gmp" ,gmp) | |
4848 | ("zlib" ,zlib))) | |
4849 | (native-inputs | |
4850 | `(("gfortran" ,gfortran) | |
4851 | ("pkg-config" ,pkg-config))) | |
4852 | (home-page "https://dune-project.org/") | |
4853 | (synopsis "Distributed and Unified Numerics Environment") | |
4854 | (description "ALUGrid is an adaptive, loadbalancing, unstructured | |
4855 | implementation of the DUNE grid interface supporting either simplices or | |
4856 | cubes.") | |
4857 | (license license:gpl2+))) | |
0e50630f RW |
4858 | |
4859 | (define-public dune-typetree | |
4860 | (package | |
4861 | (name "dune-typetree") | |
4862 | (version "2.6.0") | |
4863 | (source | |
4864 | (origin | |
4865 | (method git-fetch) | |
4866 | (uri (git-reference | |
4867 | (url "https://gitlab.dune-project.org/staging/dune-typetree.git") | |
4868 | (commit (string-append "v" version)))) | |
4869 | (file-name (git-file-name name version)) | |
4870 | (sha256 | |
4871 | (base32 | |
4872 | "0mnv6w2f22lz3j4bdpdjq55vjm8xxfx9v4vvhg9bd36xpsbjpjp9")))) | |
4873 | (build-system cmake-build-system) | |
4874 | (arguments | |
4875 | `(#:phases | |
4876 | (modify-phases %standard-phases | |
4877 | (add-after 'build 'build-tests | |
4878 | (lambda* (#:key make-flags #:allow-other-keys) | |
4879 | (apply invoke "make" "build_tests" make-flags)))))) | |
4880 | (inputs | |
4881 | `(("dune-common" ,dune-common) | |
4882 | ("openmpi" ,openmpi) | |
4883 | ;; Optional | |
4884 | ("openblas" ,openblas) | |
4885 | ("python" ,python) | |
4886 | ("metis" ,metis) | |
4887 | ("superlu" ,superlu) | |
4888 | ("gmp" ,gmp))) | |
4889 | (native-inputs | |
4890 | `(("gfortran" ,gfortran) | |
4891 | ("pkg-config" ,pkg-config))) | |
4892 | (home-page "https://dune-project.org/") | |
4893 | (synopsis "Distributed and Unified Numerics Environment") | |
4894 | (description "TypeTree is a template library for constructing and | |
4895 | operating on statically typed trees of objects.") | |
4896 | ;; Either GPL version 2 with "runtime exception" or LGPLv3+. | |
4897 | (license (list license:lgpl3+ license:gpl2)))) | |
85b9371c RW |
4898 | |
4899 | (define-public dune-functions | |
4900 | (package | |
4901 | (name "dune-functions") | |
4902 | (version "2.6.0") | |
4903 | (source | |
4904 | (origin | |
4905 | (method git-fetch) | |
4906 | (uri (git-reference | |
4907 | (url "https://gitlab.dune-project.org/staging/dune-functions.git") | |
4908 | (commit (string-append "v" version)))) | |
4909 | (file-name (git-file-name name version)) | |
4910 | (sha256 | |
4911 | (base32 | |
4912 | "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200")))) | |
4913 | (build-system cmake-build-system) | |
4914 | (arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid | |
4915 | (inputs | |
4916 | `(("dune-common" ,dune-common) | |
4917 | ("dune-istl" ,dune-istl) | |
4918 | ("dune-localfunctions" ,dune-localfunctions) | |
4919 | ("dune-grid" ,dune-grid) | |
4920 | ("dune-geometry" ,dune-geometry) | |
4921 | ("dune-typetree" ,dune-typetree) | |
4922 | ("openmpi" ,openmpi) | |
4923 | ("openblas" ,openblas) | |
4924 | ("metis" ,metis) | |
4925 | ("python" ,python) | |
4926 | ("superlu" ,superlu) | |
4927 | ("gmp" ,gmp))) | |
4928 | (native-inputs | |
4929 | `(("gfortran" ,gfortran) | |
4930 | ("pkg-config" ,pkg-config))) | |
4931 | (home-page "https://dune-project.org/") | |
4932 | (synopsis "Distributed and Unified Numerics Environment") | |
4933 | (description "The dune-functions module provides an abstraction layer for | |
4934 | global finite element functions. Its two main concepts are functions | |
4935 | implemented as callable objects, and bases of finite element spaces.") | |
4936 | ;; Either GPL version 2 with "runtime exception" or LGPLv3+. | |
4937 | (license (list license:lgpl3+ license:gpl2)))) | |
4714b00e RW |
4938 | |
4939 | (define-public dune-pdelab | |
4940 | (package | |
4941 | (name "dune-pdelab") | |
4942 | (version "2.6.0-rc1") | |
4943 | (source | |
4944 | (origin | |
4945 | (method git-fetch) | |
4946 | (uri (git-reference | |
4947 | (url "https://gitlab.dune-project.org/pdelab/dune-pdelab") | |
4948 | (commit (string-append "v" version)))) | |
4949 | (file-name (git-file-name name version)) | |
4950 | (sha256 | |
4951 | (base32 | |
4952 | "07g0s9448z65vjrq88g5rv3340iifil85k170n8kbqchsvi4ny5v")))) | |
4953 | (build-system cmake-build-system) | |
4954 | (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled | |
4955 | (inputs | |
4956 | `(("dune-common" ,dune-common) | |
4957 | ("dune-istl" ,dune-istl) | |
4958 | ("dune-localfunctions" ,dune-localfunctions) | |
4959 | ("dune-geometry" ,dune-geometry) | |
4960 | ("dune-grid" ,dune-grid) | |
4961 | ("dune-typetree" ,dune-typetree) | |
4962 | ("dune-functions" ,dune-functions) | |
4963 | ("openmpi" ,openmpi) | |
4964 | ;; Optional | |
4965 | ("openblas" ,openblas) | |
4966 | ("eigen" ,eigen) | |
4967 | ("metis" ,metis) | |
4968 | ("python" ,python) | |
4969 | ("superlu" ,superlu) | |
4970 | ("gmp" ,gmp))) | |
4971 | (native-inputs | |
4972 | `(("gfortran" ,gfortran) | |
4973 | ("pkg-config" ,pkg-config))) | |
4974 | (home-page "https://dune-project.org/") | |
4975 | (synopsis "Differential equations solver toolbox") | |
4976 | (description "PDELab is a partial differential equations solver toolbox | |
4977 | built on top of DUNE, the Distributed and Unified Numerics Environment.") | |
4978 | ;; Either GPL version 2 with "runtime exception" or LGPLv3+. | |
4979 | (license (list license:lgpl3+ license:gpl2)))) | |
413f6126 AI |
4980 | |
4981 | (define-public mlucas | |
4982 | (package | |
4983 | (name "mlucas") | |
4984 | (version "18") | |
4985 | (source | |
4986 | (origin | |
4987 | (method url-fetch) | |
4988 | (uri (string-append | |
4989 | "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz")) | |
4990 | (sha256 | |
a36efdbc | 4991 | (base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447")))) |
413f6126 AI |
4992 | (build-system gnu-build-system) |
4993 | (inputs | |
4994 | `(("python2" ,python-2))) | |
4995 | (arguments | |
a36efdbc | 4996 | `(#:tests? #f ; no tests |
413f6126 AI |
4997 | #:phases |
4998 | (modify-phases %standard-phases | |
4999 | (replace 'configure | |
5000 | (lambda _ | |
5001 | (chdir "src") | |
5002 | (call-with-output-file "Makefile" | |
5003 | (lambda (port) | |
5004 | (format port "CC = gcc | |
5005 | CFLAGS = -O3 ~a -DUSE_THREADS | |
5006 | LDLIBS = -lm -lpthread -lrt | |
5007 | Mlucas: $(addsuffix .o,$(basename $(wildcard *.c))) | |
5008 | " | |
5009 | ,(let ((system (or (%current-target-system) | |
5010 | (%current-system)))) | |
5011 | (cond | |
5012 | ((string-prefix? "x86_64" system) "-DUSE_SSE2") | |
5013 | (else "")))))) | |
5014 | #t)) | |
5015 | (replace 'install | |
5016 | (lambda* (#:key outputs #:allow-other-keys) | |
5017 | (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) | |
5018 | (install-file "Mlucas" bin) | |
5019 | (install-file "primenet.py" bin)) | |
5020 | #t))))) | |
5021 | (home-page "https://www.mersenne.org") | |
5022 | (synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client") | |
5023 | (description "Mlucas performs Lucas-Lehmer primality testing of Mersenne | |
5024 | numbers in search of a world-record prime. You may use it to test any | |
5025 | suitable number as you wish, but it is preferable that you do so in a | |
5026 | coordinated fashion, as part of the Great Internet Mersenne Prime | |
5027 | Search (GIMPS). Mlucas also includes a simple Python script for assignment | |
5028 | management via the GIMPS project's Primenet server.") | |
5029 | (license license:gpl2+))) | |
6f8c4195 NG |
5030 | |
5031 | (define-public nauty | |
5032 | (package | |
5033 | (name "nauty") | |
1ff64c50 | 5034 | (version "2.6r12") |
6f8c4195 NG |
5035 | (source (origin |
5036 | (method url-fetch) | |
5037 | (uri (string-append | |
5038 | "https://pallini.di.uniroma1.it/" | |
5039 | "nauty" (string-join (string-split version #\.) "") | |
5040 | ".tar.gz")) | |
5041 | (sha256 | |
5042 | (base32 | |
1ff64c50 | 5043 | "1p4mxf8q5wm47nxyskxbqwa5p1vvkycv1zgswvnk9nsn6vff0al6")))) |
6f8c4195 NG |
5044 | (build-system gnu-build-system) |
5045 | (outputs '("out" "lib")) | |
5046 | (arguments | |
5047 | `(#:test-target "checks" | |
5048 | #:phases | |
5049 | (modify-phases %standard-phases | |
5050 | ;; Default make target does not build all available | |
5051 | ;; executables. Create them now. | |
5052 | (add-after 'build 'build-extra-programs | |
5053 | (lambda _ | |
5054 | (for-each (lambda (target) (invoke "make" target)) | |
5055 | '("blisstog" "bliss2dre" "checks6" "sumlines")) | |
5056 | #t)) | |
5057 | ;; Upstream does not provide any install target. | |
5058 | (replace 'install | |
5059 | (lambda* (#:key outputs #:allow-other-keys) | |
5060 | (let* ((out (assoc-ref outputs "out")) | |
5061 | (lib-output (assoc-ref outputs "lib")) | |
5062 | (bin (string-append out "/bin")) | |
5063 | (doc (string-append out "/share/doc/nauty/")) | |
5064 | (include (string-append lib-output "/include/nauty")) | |
5065 | (lib (string-append lib-output "/lib/nauty"))) | |
5066 | (for-each (lambda (f) (install-file f bin)) | |
5067 | '("dreadnaut" "NRswitchg" "addedgeg" "amtog" "biplabg" | |
5068 | "blisstog" "bliss2dre" "catg" "checks6" "complg" | |
5069 | "converseg" "copyg" "countg" "cubhamg" "deledgeg" | |
5070 | "delptg" "directg" "dretodot" "dretog" "genbg" | |
5071 | "genbgL" "geng" "genquarticg" "genrang" "genspecialg" | |
5072 | "gentourng" "gentreeg" "hamheuristic" "labelg" | |
5073 | "linegraphg" "listg" "multig" "newedgeg" "pickg" | |
5074 | "planarg" "ranlabg" "shortg" "showg" "subdivideg" | |
5075 | "sumlines" "twohamg" "vcolg" "watercluster2")) | |
5076 | (for-each (lambda (f) (install-file f include)) | |
5077 | (find-files "." "\\.h$")) | |
5078 | (for-each (lambda (f) (install-file f lib)) | |
5079 | (find-files "." "\\.a$")) | |
5080 | (for-each (lambda (f) (install-file f doc)) | |
5081 | (append '("formats.txt" "README" "schreier.txt") | |
5082 | (find-files "." "\\.pdf$"))))))))) | |
5083 | (inputs | |
5084 | `(("gmp" ,gmp))) ;for sumlines | |
5085 | (home-page "https://pallini.di.uniroma1.it/") | |
5086 | (synopsis "Library for graph automorphisms") | |
5087 | (description "@code{nauty} (No AUTomorphisms, Yes?) is a set of | |
5088 | procedures for computing automorphism groups of graphs and digraphs. | |
5089 | ||
5090 | @code{nauty} computes graph information in the form of a set of | |
5091 | generators, the size of the group, and the orbits of the group; it can | |
5092 | also produce a canonical label. The @code{nauty} suite is written in | |
5093 | C and comes with a command-line interface, a collection of | |
5094 | command-line tools, and an Application Programming Interface (API). | |
5095 | ||
5096 | This package provides the static libraries required to run programs | |
5097 | compiled against the nauty library.") | |
5098 | (license license:asl2.0))) | |
26433471 AE |
5099 | |
5100 | (define-public ppl | |
5101 | (package | |
5102 | (name "ppl") | |
5103 | (version "1.2") | |
5104 | (source | |
5105 | (origin | |
5106 | (method url-fetch) | |
5107 | (uri (string-append "https://www.bugseng.com/products/ppl/download/" | |
5108 | "ftp/releases/" version | |
5109 | "/ppl-" version ".tar.gz")) | |
5110 | (sha256 | |
5111 | (base32 | |
5112 | "1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb")))) | |
5113 | (build-system gnu-build-system) | |
5114 | (native-inputs | |
5115 | `(("m4", m4))) | |
5116 | (inputs | |
5117 | `(("glpk" ,glpk) | |
5118 | ("gmp", gmp))) | |
5119 | (home-page "https://www.bugseng.com/parma-polyhedra-library") | |
5120 | (synopsis | |
5121 | "Parma Polyhedra Library for computations with polyhedra") | |
5122 | (description | |
5123 | "The Parma Polyhedra Library (PPL) provides numerical abstractions | |
5124 | especially targeted at applications in the field of analysis and | |
5125 | verification of complex systems. These abstractions include convex | |
5126 | polyhedra, defined as the intersection of a finite number of (open or | |
5127 | closed) halfspaces, each described by a linear inequality (strict or | |
5128 | non-strict) with rational coefficients; some special classes of polyhedra | |
5129 | shapes that offer interesting complexity/precision tradeoffs; and grids | |
5130 | which represent regularly spaced points that satisfy a set of linear | |
5131 | congruence relations. The library also supports finite powersets and | |
5132 | products of (any kind of) polyhedra and grids, a mixed integer linear | |
5133 | programming problem solver using an exact-arithmetic version of the simplex | |
5134 | algorithm, a parametric integer programming solver, and primitives for | |
5135 | termination analysis via the automatic synthesis of linear ranking | |
5136 | functions.") | |
5137 | (license license:gpl3+))) | |
4cb5d251 SS |
5138 | |
5139 | (define-public speedcrunch | |
5140 | (package | |
5141 | (name "speedcrunch") | |
5142 | (version "0.12.0") | |
5143 | (source | |
5144 | (origin | |
5145 | (method git-fetch) | |
5146 | (uri (git-reference | |
5147 | (url "https://bitbucket.org/heldercorreia/speedcrunch.git") | |
5148 | (commit (string-append "release-" version)))) | |
5149 | (file-name (git-file-name name version)) | |
5150 | (sha256 | |
5151 | (base32 | |
5152 | "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk")))) | |
5153 | (build-system cmake-build-system) | |
5154 | (inputs `(("qtbase" ,qtbase))) | |
5155 | (native-inputs `(("qttools" ,qttools))) | |
5156 | (arguments | |
5157 | `(#:phases | |
5158 | (modify-phases %standard-phases | |
5159 | (add-after 'unpack 'chdir-to-src | |
5160 | (lambda _ (chdir "src") #t))))) | |
5161 | (synopsis "High-precision scientific calculator") | |
5162 | (description | |
5163 | "SpeedCrunch is a high-precision scientific calculator. It features a | |
5164 | syntax-highlighted scrollable display and is designed to be fully used via | |
5165 | keyboard. Some distinctive features are auto-completion of functions and | |
5166 | variables, a formula book, and quick insertion of constants from various | |
5167 | fields of knowledge.") | |
5168 | (home-page "http://speedcrunch.org/") | |
5169 | (license license:gpl2+))) | |
5170 | ||
3b7828cc RS |
5171 | (define-public minisat |
5172 | ;; This is the last commit which is available upstream, no | |
5173 | ;; release happened since 2010. | |
5174 | (let ((commit "37dc6c67e2af26379d88ce349eb9c4c6160e8543") | |
5175 | (revision "1")) | |
5176 | (package | |
5177 | (name "minisat") | |
5178 | (version (string-append "2.2.0-" revision "." (string-take commit 7))) | |
5179 | (source | |
5180 | (origin | |
5181 | (method git-fetch) | |
5182 | (uri (git-reference | |
5183 | (url "https://github.com/niklasso/minisat.git") | |
5184 | (commit commit))) | |
5185 | (file-name (string-append name "-" version "-checkout")) | |
5186 | (sha256 | |
5187 | (base32 | |
5188 | "091hf3qkm197s5r7xcr3m07xsdwyz2rqk1hc9kj0hn13imz09irq")) | |
5189 | (patches | |
5190 | (search-patches "minisat-friend-declaration.patch" | |
5191 | "minisat-install.patch")))) | |
5192 | (build-system gnu-build-system) | |
5193 | (arguments | |
5194 | '(#:make-flags (list (string-append "prefix=" %output)) | |
5195 | #:tests? #f ;no check target | |
5196 | #:phases | |
5197 | (modify-phases %standard-phases | |
5198 | (delete 'configure)))) | |
5199 | (inputs | |
5200 | `(("zlib:static" ,zlib "static") | |
5201 | ("zlib" ,zlib))) | |
5202 | (synopsis | |
5203 | "Small, yet efficient, SAT solver") | |
5204 | (description | |
5205 | "MiniSat is a minimalistic, open-source SAT solver, developed to help | |
5206 | researchers and developers alike to get started on SAT.") | |
5207 | (home-page | |
5208 | "http://minisat.se/MiniSat.html") | |
5209 | (license license:expat)))) |