Commit | Line | Data |
---|---|---|
8f8b2451 | 1 | ;;; GNU Guix --- Functional package management for GNU |
b146763a | 2 | ;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr> |
da95c817 | 3 | ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org> |
9c45c519 | 4 | ;;; Copyright © 2014, 2016 John Darrington <jmd@gnu.org> |
dfdf5716 | 5 | ;;; Copyright © 2014, 2015, 2016 Eric Bavier <bavier@member.fsf.org> |
df354a77 | 6 | ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch> |
182d6311 | 7 | ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org> |
458b47e3 | 8 | ;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net> |
32158110 | 9 | ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com> |
9aafbc0c | 10 | ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org> |
723a6910 | 11 | ;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il> |
45147b0c | 12 | ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de> |
ec8c7e47 | 13 | ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> |
b7b27a8f | 14 | ;;; Copyright © 2016 Kei Kebreau <kei@openmailbox.org> |
5d4bd4cc | 15 | ;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org> |
d7cff656 | 16 | ;;; Copyright © 2016 Leo Famulari <leo@famulari.name> |
0f43f835 | 17 | ;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be> |
5d4bd4cc | 18 | ;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com> |
54052a54 | 19 | ;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net> |
8f8b2451 AE |
20 | ;;; |
21 | ;;; This file is part of GNU Guix. | |
22 | ;;; | |
23 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
24 | ;;; under the terms of the GNU General Public License as published by | |
25 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
26 | ;;; your option) any later version. | |
27 | ;;; | |
28 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
29 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
30 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
31 | ;;; GNU General Public License for more details. | |
32 | ;;; | |
33 | ;;; You should have received a copy of the GNU General Public License | |
34 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
35 | ||
36 | (define-module (gnu packages maths) | |
ec322be2 | 37 | #:use-module (ice-9 regex) |
8f8b2451 | 38 | #:use-module (gnu packages) |
b5b73a82 | 39 | #:use-module ((guix licenses) #:prefix license:) |
8f8b2451 AE |
40 | #:use-module (guix packages) |
41 | #:use-module (guix download) | |
54052a54 | 42 | #:use-module (guix git-download) |
0e2672ae | 43 | #:use-module (guix utils) |
cec86422 | 44 | #:use-module (guix build utils) |
da95c817 | 45 | #:use-module (guix build-system cmake) |
c9dfa3c7 | 46 | #:use-module (guix build-system gnu) |
ec8c7e47 | 47 | #:use-module (guix build-system r) |
3de01d3f EB |
48 | #:use-module (gnu packages algebra) |
49 | #:use-module (gnu packages bison) | |
a17d4564 | 50 | #:use-module (gnu packages boost) |
e73b49fb | 51 | #:use-module (gnu packages check) |
3de01d3f | 52 | #:use-module (gnu packages cmake) |
c9dfa3c7 | 53 | #:use-module (gnu packages compression) |
668c06ac | 54 | #:use-module (gnu packages curl) |
b7b27a8f | 55 | #:use-module (gnu packages cyrus-sasl) |
528bb464 | 56 | #:use-module (gnu packages documentation) |
57e544e8 | 57 | #:use-module (gnu packages elf) |
3de01d3f | 58 | #:use-module (gnu packages flex) |
668c06ac | 59 | #:use-module (gnu packages fltk) |
f3929800 | 60 | #:use-module (gnu packages fontutils) |
1dba6407 | 61 | #:use-module (gnu packages gettext) |
da95c817 | 62 | #:use-module (gnu packages gcc) |
73fed4f8 | 63 | #:use-module (gnu packages gd) |
668c06ac | 64 | #:use-module (gnu packages ghostscript) |
889187a4 | 65 | #:use-module (gnu packages graphviz) |
f3929800 | 66 | #:use-module (gnu packages gtk) |
45147b0c | 67 | #:use-module (gnu packages image) |
668c06ac | 68 | #:use-module (gnu packages less) |
8731e527 | 69 | #:use-module (gnu packages lisp) |
bc3a2e35 | 70 | #:use-module (gnu packages logging) |
5698b8b8 | 71 | #:use-module (gnu packages gnome) |
1b39a196 | 72 | #:use-module (gnu packages guile) |
668c06ac JD |
73 | #:use-module (gnu packages xorg) |
74 | #:use-module (gnu packages gl) | |
8731e527 | 75 | #:use-module (gnu packages m4) |
d8c7eeb9 | 76 | #:use-module (gnu packages mpi) |
b92eee75 | 77 | #:use-module (gnu packages multiprecision) |
528bb464 | 78 | #:use-module (gnu packages netpbm) |
668c06ac | 79 | #:use-module (gnu packages pcre) |
5698b8b8 | 80 | #:use-module (gnu packages popt) |
c9dfa3c7 AE |
81 | #:use-module (gnu packages perl) |
82 | #:use-module (gnu packages pkg-config) | |
da95c817 | 83 | #:use-module (gnu packages python) |
c9dfa3c7 | 84 | #:use-module (gnu packages readline) |
2742f87e | 85 | #:use-module (gnu packages tbb) |
479c4273 | 86 | #:use-module (gnu packages scheme) |
b7194849 | 87 | #:use-module (gnu packages shells) |
df354a77 | 88 | #:use-module (gnu packages tcl) |
668c06ac | 89 | #:use-module (gnu packages texinfo) |
8f9ac901 | 90 | #:use-module (gnu packages tex) |
b7b27a8f | 91 | #:use-module (gnu packages tls) |
9aafbc0c | 92 | #:use-module (gnu packages wxwidgets) |
c12efc72 | 93 | #:use-module (gnu packages xml) |
a17d4564 EB |
94 | #:use-module (gnu packages zip) |
95 | #:use-module (srfi srfi-1)) | |
8f8b2451 | 96 | |
193abc82 JD |
97 | (define-public aris |
98 | (package | |
1f45f18a JD |
99 | (name "aris") |
100 | (version "2.2") | |
101 | (source (origin | |
102 | (method url-fetch) | |
103 | (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz")) | |
104 | (sha256 (base32 | |
105 | "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q")))) | |
106 | (build-system gnu-build-system) | |
107 | (inputs `(("gtk+" ,gtk+) | |
108 | ("libxml2" ,libxml2))) | |
109 | (native-inputs `(("pkg-config" ,pkg-config))) | |
110 | (synopsis "Natural deduction first-order logic interface") | |
111 | (description "Aris is a program for performing logical proofs. It supports | |
112 | propositional and predicate logic, as well as Boolean algebra and | |
113 | arithmetical logic. In addition to its predefined inference and equivalence | |
114 | rules, Aris also supports references to older proofs. Its use of standard | |
115 | logical symbols and its natural deduction interface make it easy to use for | |
116 | beginners.") | |
117 | (license license:gpl3+) | |
118 | (home-page "http://www.gnu.org/software/aris/"))) | |
193abc82 | 119 | |
9c45c519 JD |
120 | (define-public c-graph |
121 | (package | |
122 | (name "c-graph") | |
123 | (version "2.0") | |
124 | (source (origin | |
125 | (method url-fetch) | |
126 | (uri (string-append "mirror://gnu/c-graph/c-graph-" version | |
127 | ".tar.gz")) | |
128 | (sha256 (base32 | |
129 | "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01")))) | |
130 | (build-system gnu-build-system) | |
131 | (inputs | |
132 | `(("fortran" ,gfortran))) | |
a3947cb1 | 133 | (synopsis "Visualizing and demonstrating convolution") |
9c45c519 | 134 | (description |
a3947cb1 LC |
135 | "GNU C-Graph is a tool for demonstrating the theory of convolution. |
136 | Thus, it can serve as an excellent aid to students of signal and systems | |
137 | theory in visualizing the convolution process. Rather than forcing the | |
138 | student to write code, the program offers an intuitive interface with | |
139 | interactive dialogs to guide them.") | |
9c45c519 JD |
140 | (license license:gpl3+) |
141 | (home-page "http://www.gnu.org/software/c-graph/"))) | |
142 | ||
d91025e3 TD |
143 | (define-public coda |
144 | (package | |
145 | (name "coda") | |
cbfbcb21 | 146 | (version "2.18") |
d91025e3 TD |
147 | (source |
148 | (origin | |
149 | (method url-fetch) | |
150 | (uri (string-append "https://github.com/stcorp/coda/releases/download/" | |
151 | version "/coda-" version ".tar.gz")) | |
152 | (sha256 | |
cbfbcb21 | 153 | (base32 "11asla1ap8vd73farqjlpb179sfiy0biydcwxjfcakrp9sf8v9bs")) |
4b12fe5c TD |
154 | (patches (search-patches "coda-use-system-libs.patch")) |
155 | (modules '((guix build utils))) | |
156 | (snippet | |
157 | ;; Make sure we don't use the bundled software. | |
158 | '(for-each (lambda (d) | |
159 | (delete-file-recursively (string-append "libcoda/" d))) | |
160 | '("zlib" "pcre" "expat"))))) | |
d91025e3 TD |
161 | (native-inputs |
162 | `(("fortran" ,gfortran) | |
163 | ("python" ,python) | |
164 | ("python-numpy" ,python-numpy))) | |
165 | (inputs | |
166 | `(("zlib" ,zlib) | |
4b12fe5c TD |
167 | ("pcre" ,pcre) |
168 | ("expat" ,expat) | |
d91025e3 TD |
169 | ("hdf4" ,hdf4-alt) |
170 | ("hdf5" ,hdf5))) | |
171 | (build-system gnu-build-system) | |
172 | (arguments | |
4b12fe5c TD |
173 | '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python" |
174 | "LIBS= -lz -lpcre -lexpat"))) | |
d91025e3 TD |
175 | (synopsis "A common interface to various earth observation data formats") |
176 | (description | |
177 | "The Common Data Access toolbox (CODA) provides a set of interfaces for | |
178 | reading remote sensing data from earth observation data files. It consists of | |
179 | command line applications and interfaces to the C, Fortran, Python, and Java | |
180 | programming languages.") | |
181 | (home-page "https://stcorp.nl/coda") | |
182 | (license license:gpl2+))) | |
183 | ||
8f8b2451 AE |
184 | (define-public units |
185 | (package | |
186 | (name "units") | |
5e745292 | 187 | (version "2.13") |
8f8b2451 AE |
188 | (source (origin |
189 | (method url-fetch) | |
190 | (uri (string-append "mirror://gnu/units/units-" version | |
191 | ".tar.gz")) | |
192 | (sha256 (base32 | |
5e745292 | 193 | "1awhjw9zjlfb8s5g3yyx63f7ddfcr1sanlbxpqifmrgq24ql198b")))) |
8f8b2451 AE |
194 | (build-system gnu-build-system) |
195 | (synopsis "Conversion between thousands of scales") | |
196 | (description | |
574e86f9 | 197 | "GNU Units converts numeric quantities between units of measure. It |
7c125ce0 AK |
198 | can handle scale changes through adaptive usage of standard scale |
199 | prefixes (micro-, kilo-, etc.). It can also handle nonlinear | |
200 | conversions such as Fahrenheit to Celsius. Its interpreter is powerful | |
201 | enough to be used effectively as a scientific calculator.") | |
8f8b2451 AE |
202 | (license license:gpl3+) |
203 | (home-page "http://www.gnu.org/software/units/"))) | |
c9dfa3c7 | 204 | |
61a529b4 RW |
205 | (define-public double-conversion |
206 | (package | |
207 | (name "double-conversion") | |
208 | (version "1.1.5") | |
209 | (source (origin | |
210 | (method url-fetch) | |
211 | (uri (string-append | |
212 | "https://github.com/floitsch/double-conversion/archive/v" | |
213 | version ".tar.gz")) | |
214 | (file-name (string-append name "-" version ".tar.gz")) | |
215 | (sha256 | |
216 | (base32 | |
217 | "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83")))) | |
218 | (build-system cmake-build-system) | |
219 | (arguments | |
220 | '(#:test-target "test" | |
221 | #:configure-flags '("-DBUILD_SHARED_LIBS=ON" | |
222 | "-DBUILD_TESTING=ON"))) | |
223 | (home-page "https://github.com/floitsch/double-conversion") | |
224 | (synopsis "Conversion routines for IEEE doubles") | |
225 | (description | |
226 | "The double-conversion library provides binary-decimal and decimal-binary | |
227 | routines for IEEE doubles. The library consists of efficient conversion | |
228 | routines that have been extracted from the V8 JavaScript engine.") | |
229 | (license license:bsd-3))) | |
230 | ||
182d6311 ML |
231 | (define-public dionysus |
232 | (package | |
233 | (name "dionysus") | |
234 | (version "1.3.0") | |
235 | (source (origin | |
236 | (method url-fetch) | |
237 | (uri (string-append "mirror://gnu/dionysus/dionysus-" version | |
238 | ".tar.gz")) | |
239 | (sha256 | |
240 | (base32 | |
241 | "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs")))) | |
242 | (build-system gnu-build-system) | |
243 | (inputs `(("tcl" ,tcl))) ;for 'tclsh' | |
244 | (synopsis "Local search for universal constants and scientific values") | |
245 | (description | |
246 | "GNU Dionysus is a convenient system for quickly retrieving the values of | |
247 | mathematical constants used in science and engineering. Values can be | |
248 | searched using a simple command-line tool, choosing from three databases: | |
249 | universal constants, atomic numbers, and constants related to | |
250 | semiconductors.") | |
251 | (license license:gpl3+) | |
252 | (home-page "http://www.gnu.org/software/dionysus/"))) | |
253 | ||
88bd1804 AE |
254 | (define-public gsl |
255 | (package | |
256 | (name "gsl") | |
bea3cf4b | 257 | (version "2.3") |
ab2cc5cd LC |
258 | (source (origin |
259 | (method url-fetch) | |
260 | (uri (string-append "mirror://gnu/gsl/gsl-" | |
261 | version ".tar.gz")) | |
262 | (sha256 | |
263 | (base32 | |
bea3cf4b | 264 | "1yxdzqjwmi2aid650fa9zyr8llw069x7lm489wx9nnfdi6vh09an")) |
ab2cc5cd | 265 | (patches (search-patches "gsl-test-i686.patch")))) |
88bd1804 | 266 | (build-system gnu-build-system) |
71e0f288 | 267 | (arguments |
5adbe65f | 268 | `(#:parallel-tests? #f)) |
88bd1804 AE |
269 | (home-page "http://www.gnu.org/software/gsl/") |
270 | (synopsis "Numerical library for C and C++") | |
271 | (description | |
a22dc0c4 LC |
272 | "The GNU Scientific Library is a library for numerical analysis in C |
273 | and C++. It includes a wide range of mathematical routines, with over 1000 | |
274 | functions in total. Subject areas covered by the library include: | |
275 | differential equations, linear algebra, Fast Fourier Transforms and random | |
276 | numbers.") | |
88bd1804 AE |
277 | (license license:gpl3+))) |
278 | ||
b92eee75 AE |
279 | (define-public glpk |
280 | (package | |
281 | (name "glpk") | |
82110ef6 | 282 | (version "4.61") |
b92eee75 AE |
283 | (source |
284 | (origin | |
285 | (method url-fetch) | |
286 | (uri (string-append "mirror://gnu/glpk/glpk-" | |
287 | version ".tar.gz")) | |
288 | (sha256 | |
289 | (base32 | |
82110ef6 | 290 | "1adbvwiaqrv9pql9ry3lhn2vfsxnff2vh4fs477d90kpfx0xwrlq")))) |
b92eee75 AE |
291 | (build-system gnu-build-system) |
292 | (inputs | |
293 | `(("gmp" ,gmp))) | |
294 | (arguments | |
295 | `(#:configure-flags '("--with-gmp"))) | |
82110ef6 | 296 | (home-page "https://www.gnu.org/software/glpk/") |
79c311b8 | 297 | (synopsis "GNU Linear Programming Kit, supporting the MathProg language") |
b92eee75 AE |
298 | (description |
299 | "GLPK is a C library for solving large-scale linear programming (LP), | |
300 | mixed integer programming (MIP), and other related problems. It supports the | |
301 | GNU MathProg modeling language, a subset of the AMPL language, and features a | |
302 | translator for the language. In addition to the C library, a stand-alone | |
303 | LP/MIP solver is included in the package.") | |
304 | (license license:gpl3+))) | |
305 | ||
b146763a AE |
306 | (define-public 4ti2 |
307 | (package | |
308 | (name "4ti2") | |
309 | (version "1.6.7") | |
310 | (source | |
311 | (origin | |
312 | (method url-fetch) | |
313 | (uri (string-append "http://www.4ti2.de/version_" version | |
314 | "/4ti2-" version ".tar.gz")) | |
315 | (sha256 | |
316 | (base32 | |
317 | "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl")))) | |
318 | (build-system gnu-build-system) | |
319 | (native-inputs | |
320 | `(("which" ,(@ (gnu packages base) which)))) ; for the tests | |
321 | (inputs | |
322 | `(("glpk" ,glpk) | |
323 | ("gmp" ,gmp))) | |
324 | (home-page "http://www.4ti2.de/") | |
325 | (synopsis "Mathematical tool suite for problems on linear spaces") | |
326 | (description | |
327 | "4ti2 implements algorithms for solving algebraic, geometric and | |
328 | combinatorial problems on linear spaces. Among others, it solves systems | |
329 | of linear equations, computes extreme rays of polyhedral cones, solves | |
330 | integer programming problems and computes Markov bases for statistics.") | |
331 | (license license:gpl2+))) | |
332 | ||
53696f10 AE |
333 | (define-public cddlib |
334 | (package | |
335 | (name "cddlib") | |
336 | (version "0.94h") | |
337 | (source | |
338 | (origin | |
339 | (method url-fetch) | |
182dde82 | 340 | (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-" |
53696f10 AE |
341 | (string-delete #\. version) ".tar.gz")) |
342 | (sha256 | |
343 | (base32 | |
344 | "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy")))) | |
345 | (build-system gnu-build-system) | |
346 | (inputs | |
347 | `(("gmp" ,gmp))) | |
348 | (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html") | |
349 | (synopsis "Library for convex hulls and extreme rays of polyhedra") | |
350 | (description | |
351 | "The C-library cddlib implements the Double Description Method of | |
352 | Motzkin et al. for generating all vertices (i.e. extreme points) and extreme | |
353 | rays of a general convex polyhedron given by a system of linear inequalities | |
354 | in arbitrary dimension. It can also be used for the converse operation of | |
355 | computing convex hulls.") | |
356 | (license license:gpl2+))) | |
357 | ||
865a69dd RW |
358 | (define-public arpack-ng |
359 | (package | |
360 | (name "arpack-ng") | |
361 | (version "3.2.0") | |
362 | (source | |
363 | (origin | |
364 | (method url-fetch) | |
365 | (uri (string-append "https://github.com/opencollab/arpack-ng/archive/" | |
366 | version ".tar.gz")) | |
f586c877 | 367 | (file-name (string-append name "-" version ".tar.gz")) |
865a69dd RW |
368 | (sha256 |
369 | (base32 | |
370 | "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff")))) | |
371 | (build-system gnu-build-system) | |
372 | (home-page "https://github.com/opencollab/arpack-ng") | |
373 | (inputs | |
374 | `(("lapack" ,lapack) | |
19afbea1 | 375 | ("fortran" ,gfortran))) |
865a69dd RW |
376 | (synopsis "Fortran subroutines for solving eigenvalue problems") |
377 | (description | |
378 | "ARPACK-NG is a collection of Fortran77 subroutines designed to solve | |
379 | large scale eigenvalue problems.") | |
166191b3 | 380 | (license (license:non-copyleft "file://COPYING" |
865a69dd RW |
381 | "See COPYING in the distribution.")))) |
382 | ||
8c94c886 EB |
383 | (define-public arpack-ng-openmpi |
384 | (package (inherit arpack-ng) | |
385 | (name "arpack-ng-openmpi") | |
386 | (inputs | |
387 | `(("mpi" ,openmpi) | |
388 | ,@(package-inputs arpack-ng))) | |
389 | (arguments `(#:configure-flags '("--enable-mpi"))) | |
390 | (synopsis "Fortran subroutines for solving eigenvalue problems with MPI"))) | |
391 | ||
da95c817 NK |
392 | (define-public lapack |
393 | (package | |
394 | (name "lapack") | |
566146ab | 395 | (version "3.5.0") |
da95c817 NK |
396 | (source |
397 | (origin | |
398 | (method url-fetch) | |
399 | (uri (string-append "http://www.netlib.org/lapack/lapack-" | |
400 | version ".tgz")) | |
401 | (sha256 | |
402 | (base32 | |
566146ab | 403 | "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s")))) |
da95c817 NK |
404 | (build-system cmake-build-system) |
405 | (home-page "http://www.netlib.org/lapack/") | |
19afbea1 | 406 | (inputs `(("fortran" ,gfortran) |
da95c817 NK |
407 | ("python" ,python-2))) |
408 | (arguments | |
7b569b01 RW |
409 | `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES" |
410 | "-DLAPACKE=ON") | |
da95c817 | 411 | #:phases (alist-cons-before |
6a995754 LC |
412 | 'check 'patch-python |
413 | (lambda* (#:key inputs #:allow-other-keys) | |
414 | (let ((python (assoc-ref inputs "python"))) | |
415 | (substitute* "lapack_testing.py" | |
416 | (("/usr/bin/env python") python)))) | |
06ed5982 | 417 | %standard-phases))) |
da95c817 NK |
418 | (synopsis "Library for numerical linear algebra") |
419 | (description | |
420 | "LAPACK is a Fortran 90 library for solving the most commonly occurring | |
421 | problems in numerical linear algebra.") | |
166191b3 | 422 | (license (license:non-copyleft "file://LICENSE" |
da95c817 | 423 | "See LICENSE in the distribution.")))) |
73fed4f8 | 424 | |
e1ff597a EB |
425 | (define-public scalapack |
426 | (package | |
427 | (name "scalapack") | |
428 | (version "2.0.2") | |
429 | (source | |
430 | (origin | |
431 | (method url-fetch) | |
432 | (uri (string-append "http://www.netlib.org/scalapack/scalapack-" | |
433 | version ".tgz")) | |
434 | (sha256 | |
435 | (base32 | |
436 | "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c")))) | |
437 | (build-system cmake-build-system) | |
438 | (inputs | |
439 | `(("mpi" ,openmpi) | |
440 | ("fortran" ,gfortran) | |
441 | ("lapack" ,lapack))) ;for testing only | |
442 | (arguments | |
443 | `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES"))) | |
444 | (home-page "http://www.netlib.org/scalapack/") | |
445 | (synopsis "Library for scalable numerical linear algebra") | |
446 | (description | |
447 | "ScaLAPACK is a Fortran 90 library of high-performance linear algebra | |
448 | routines on parallel distributed memory machines. ScaLAPACK solves dense and | |
449 | banded linear systems, least squares problems, eigenvalue problems, and | |
450 | singular value problems.") | |
451 | (license (license:bsd-style "file://LICENSE" | |
452 | "See LICENSE in the distribution.")))) | |
453 | ||
73fed4f8 | 454 | (define-public gnuplot |
5f800540 KK |
455 | (package |
456 | (name "gnuplot") | |
457 | (version "5.0.5") | |
458 | (source (origin | |
459 | (method url-fetch) | |
460 | (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" | |
461 | version "/gnuplot-" | |
462 | version ".tar.gz")) | |
463 | (sha256 | |
464 | (base32 | |
465 | "0lr065qdlgss8lmy31l7hkmnk9fp4lvqq9qgb1f1209f36zy1wr5")))) | |
466 | (build-system gnu-build-system) | |
467 | (inputs `(("readline" ,readline) | |
468 | ("cairo" ,cairo) | |
469 | ("pango" ,pango) | |
470 | ("gd" ,gd))) | |
471 | (native-inputs `(("pkg-config" ,pkg-config) | |
472 | ("texlive" ,texlive-minimal))) | |
473 | (home-page "http://www.gnuplot.info") | |
474 | (synopsis "Command-line driven graphing utility") | |
475 | (description "Gnuplot is a portable command-line driven graphing | |
35b9e423 | 476 | utility. It was originally created to allow scientists and students to |
73fed4f8 | 477 | visualize mathematical functions and data interactively, but has grown to |
35b9e423 | 478 | support many non-interactive uses such as web scripting. It is also used as a |
73fed4f8 | 479 | plotting engine by third-party applications like Octave.") |
5f800540 KK |
480 | ;; X11 Style with the additional restriction that derived works may only be |
481 | ;; distributed as patches to the original. | |
482 | (license (license:fsf-free | |
483 | "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright")))) | |
668c06ac | 484 | |
32f70e1f TD |
485 | (define-public gctp |
486 | (package | |
487 | (name "gctp") | |
488 | (version "2.0.0") | |
489 | (source | |
490 | (origin | |
491 | (method url-fetch) | |
492 | (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v" | |
493 | version ".tar.gz")) | |
494 | (file-name (string-append name "-" version ".tar.gz")) | |
495 | (sha256 | |
496 | (base32 | |
497 | "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4")))) | |
498 | (native-inputs | |
499 | `(("fortran" ,gfortran))) | |
500 | (build-system gnu-build-system) | |
501 | (synopsis "General Cartographic Transformation Package (GCTP)") | |
502 | (description | |
503 | "The General Cartographic Transformation Package (GCTP) is a system of | |
504 | software routines designed to permit the transformation of coordinate pairs | |
505 | from one map projection to another. The GCTP is the standard computer | |
506 | software used by the National Mapping Division for map projection | |
507 | computations.") | |
508 | (home-page "https://github.com/OkoSanto/GCTP") | |
0f7cd95b | 509 | (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html |
32f70e1f | 510 | |
becbbefc TD |
511 | (define-public hdf4 |
512 | (package | |
513 | (name "hdf4") | |
7bbf2e39 | 514 | (version "4.2.12") |
becbbefc TD |
515 | (source |
516 | (origin | |
517 | (method url-fetch) | |
518 | (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF" | |
519 | version "/src/hdf-" version ".tar.bz2")) | |
520 | (sha256 | |
7bbf2e39 | 521 | (base32 "020jh563sjyxsgml8l809d2i1d4ms9shivwj3gbm7n0ilxbll8id")) |
15ca49b2 AE |
522 | (patches (search-patches "hdf4-architectures.patch" |
523 | "hdf4-reproducibility.patch" | |
becbbefc TD |
524 | "hdf4-shared-fortran.patch")))) |
525 | ||
526 | (build-system gnu-build-system) | |
527 | (native-inputs | |
528 | `(("gfortran" ,gfortran) | |
529 | ("bison" ,bison) | |
530 | ("flex" ,flex))) | |
531 | (inputs | |
532 | `(("zlib" ,zlib) | |
533 | ("libjpeg" ,libjpeg))) | |
534 | (arguments | |
535 | `(#:parallel-tests? #f | |
536 | #:configure-flags '("--enable-shared") | |
537 | #:phases | |
538 | (modify-phases %standard-phases | |
539 | (add-before 'configure 'patchbuild | |
540 | (lambda _ | |
541 | (substitute* | |
542 | '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in") | |
543 | (("/bin/rm") "rm") | |
544 | (("/bin/mkdir") "mkdir")) | |
545 | (substitute* (find-files "." "^Makefile\\.in$") | |
546 | (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \ | |
547 | -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "") | |
548 | (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \ | |
549 | -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \ | |
550 | -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))))))) | |
551 | (home-page "https://www.hdfgroup.org/products/hdf4/") | |
552 | (synopsis | |
553 | "Library and multi-object file format for storing and managing data") | |
554 | (description "HDF4 is a library and multi-object file format for storing | |
555 | and managing data between machines. HDF4 is an older hierarchical data format, | |
556 | incompatible with HDF5.") | |
557 | (license | |
558 | (license:non-copyleft | |
559 | "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING")))) | |
560 | ||
561 | (define-public hdf4-alt | |
562 | (package | |
563 | (inherit hdf4) | |
564 | (name "hdf4-alt") | |
565 | (arguments | |
566 | (substitute-keyword-arguments (package-arguments hdf4) | |
567 | ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags)))) | |
568 | (synopsis | |
569 | "HDF4 without netCDF API, can be combined with the regular netCDF library"))) | |
570 | ||
7ee3f1a2 JD |
571 | (define-public hdf5 |
572 | (package | |
573 | (name "hdf5") | |
dcd9d163 | 574 | (version "1.8.18") |
7ee3f1a2 JD |
575 | (source |
576 | (origin | |
577 | (method url-fetch) | |
dcd9d163 LF |
578 | (uri (list (string-append "http://www.hdfgroup.org/ftp/HDF5/releases/" |
579 | "hdf5-" version "/src/hdf5-" | |
580 | version ".tar.bz2") | |
581 | (string-append "https://support.hdfgroup.org/ftp/HDF5/" | |
582 | "current" | |
583 | (apply string-append | |
584 | (take (string-split version #\.) 2)) | |
585 | "/src/hdf5-" version ".tar.bz2"))) | |
7ee3f1a2 | 586 | (sha256 |
dcd9d163 | 587 | (base32 "13542vrnl1p35n8vbq0wzk40vddmm33q5nh04j98c7r1yjnxxih1")) |
b8d9c93b | 588 | (patches (list (search-patch "hdf5-config-date.patch"))))) |
7ee3f1a2 | 589 | (build-system gnu-build-system) |
12ed1216 AE |
590 | (inputs |
591 | `(("zlib" ,zlib))) | |
7ee3f1a2 | 592 | (arguments |
62126576 LC |
593 | `(;; Some of the users, notably Flann, need the C++ interface. |
594 | #:configure-flags '("--enable-cxx") | |
595 | ||
596 | #:phases | |
f622e212 EB |
597 | (modify-phases %standard-phases |
598 | (add-before 'configure 'patch-configure | |
599 | (lambda _ | |
600 | (substitute* "configure" | |
b8d9c93b EB |
601 | (("/bin/mv") "mv")) |
602 | #t)) | |
f622e212 EB |
603 | (add-after 'install 'patch-references |
604 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
605 | (let ((bin (string-append (assoc-ref outputs "out") "/bin")) | |
606 | (zlib (assoc-ref inputs "zlib"))) | |
607 | (substitute* (find-files bin "h5p?cc") | |
608 | (("-lz" lib) | |
609 | (string-append "-L" zlib "/lib " lib))) | |
610 | #t)))))) | |
7ee3f1a2 | 611 | (home-page "http://www.hdfgroup.org") |
516e93f8 | 612 | (synopsis "Management suite for extremely large and complex data") |
7ee3f1a2 JD |
613 | (description "HDF5 is a suite that makes possible the management of |
614 | extremely large and complex data collections.") | |
d4bf49b1 EB |
615 | (license (license:x11-style |
616 | "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) | |
7ee3f1a2 | 617 | |
d3c4f3bb TD |
618 | (define-public hdf-eos2 |
619 | (package | |
620 | (name "hdf-eos2") | |
621 | (version "19.1.0") | |
622 | (source | |
623 | (origin | |
624 | (method url-fetch) | |
625 | (uri "ftp://edhs1.gsfc.nasa.gov\ | |
626 | /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z") | |
627 | (sha256 | |
628 | (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz")) | |
629 | (patches (search-patches "hdf-eos2-remove-gctp.patch" | |
630 | "hdf-eos2-build-shared.patch" | |
631 | "hdf-eos2-fortrantests.patch")))) | |
632 | (build-system gnu-build-system) | |
633 | (native-inputs | |
634 | `(("gfortran" ,gfortran))) | |
635 | (inputs | |
636 | `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API | |
637 | ("zlib" ,zlib) | |
638 | ("libjpeg" ,libjpeg) | |
639 | ("gctp" ,gctp))) | |
640 | (arguments | |
641 | `( #:configure-flags '("--enable-install-include" "--enable-shared" | |
642 | "CC=h4cc -Df2cFortran" "LIBS=-lgctp") | |
643 | #:parallel-tests? #f)) | |
644 | (home-page "http://hdfeos.org/software/library.php#HDF-EOS2") | |
645 | (synopsis "HDF4-based data format for NASA's Earth Observing System") | |
646 | (description "HDF-EOS2 is a software library built on HDF4 which supports | |
647 | the construction of data structures used in NASA's Earth Observing | |
648 | System (Grid, Point and Swath).") | |
649 | ||
650 | ;; Source files carry a permissive license header. | |
651 | (license (license:non-copyleft home-page)))) | |
652 | ||
0f43f835 TD |
653 | (define-public hdf-eos5 |
654 | (package | |
655 | (name "hdf-eos5") | |
656 | (version "1.15") | |
657 | (source (origin | |
658 | (method url-fetch) | |
659 | (uri (string-append "ftp://edhs1.gsfc.nasa.gov\ | |
660 | /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z")) | |
661 | (sha256 | |
662 | (base32 | |
663 | "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i")) | |
664 | (patches (search-patches "hdf-eos5-build-shared.patch" | |
665 | "hdf-eos5-remove-gctp.patch" | |
666 | "hdf-eos5-fix-szip.patch" | |
667 | "hdf-eos5-fortrantests.patch")))) | |
668 | (native-inputs | |
669 | `(("gfortran" ,gfortran))) | |
670 | (build-system gnu-build-system) | |
671 | (inputs | |
672 | `(("hdf5" ,hdf5) | |
673 | ("zlib" ,zlib) | |
674 | ("gctp" ,gctp))) | |
675 | (arguments | |
676 | `(#:configure-flags '("--enable-install-include" "--enable-shared" | |
677 | "CC=h5cc -Df2cFortran" "LIBS=-lgctp") | |
678 | #:parallel-tests? #f)) | |
679 | (synopsis "HDF5-based data format for NASA's Earth Observing System") | |
680 | (description | |
681 | "HDF-EOS5 is a software library built on HDF5 to support the construction | |
682 | of data structures used in NASA's Earth Observing System (Grid, Point and | |
683 | Swath).") | |
684 | (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5") | |
685 | ||
686 | ;; Source files carry a permissive license header. | |
687 | (license (license:non-copyleft home-page)))) | |
688 | ||
c8378eea EB |
689 | (define-public hdf5-parallel-openmpi |
690 | (package (inherit hdf5) | |
691 | (name "hdf5-parallel-openmpi") | |
692 | (inputs | |
693 | `(("mpi" ,openmpi) | |
694 | ,@(package-inputs hdf5))) | |
695 | (arguments | |
696 | (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel") | |
697 | ,@(package-arguments hdf5)) | |
698 | ((#:phases phases) | |
699 | `(modify-phases ,phases | |
700 | (add-before 'check 'patch-tests | |
701 | (lambda _ | |
702 | ;; OpenMPI's mpirun will exit with non-zero status if it | |
703 | ;; detects an "abnormal termination", i.e. any process not | |
704 | ;; calling MPI_Finalize(). Since the test is explicitely | |
705 | ;; avoiding MPI_Finalize so as not to have at_exit and thus | |
706 | ;; H5C_flush_cache from being called, mpirun will always | |
707 | ;; complain, so turn this test off. | |
708 | (substitute* "testpar/Makefile" | |
709 | (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back) | |
710 | (string-append front back "\n"))) | |
711 | (substitute* "tools/h5diff/testph5diff.sh" | |
712 | (("/bin/sh") (which "sh"))) | |
713 | #t)))))) | |
714 | (synopsis "Management suite for data with parallel IO support"))) | |
715 | ||
00775104 EB |
716 | (define-public h5check |
717 | (package | |
718 | (name "h5check") | |
719 | (version "2.0.1") | |
720 | (source | |
721 | (origin | |
722 | (method url-fetch) | |
723 | (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/" | |
724 | "h5check/src/h5check-" version ".tar.gz")) | |
725 | (sha256 | |
726 | (base32 | |
727 | "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj")))) | |
728 | (build-system gnu-build-system) | |
729 | (inputs `(("hdf5" ,hdf5))) ;h5cc for tests | |
730 | (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html") | |
731 | (synopsis "HDF5 format checker") | |
732 | (description "@code{h5check} is a validation tool for verifying that an | |
733 | HDF5 file is encoded according to the HDF File Format Specification.") | |
734 | (license (license:x11-style "file://COPYING")))) | |
735 | ||
889187a4 EB |
736 | (define-public netcdf |
737 | (package | |
738 | (name "netcdf") | |
a4b0bfb1 | 739 | (version "4.4.1.1") |
889187a4 EB |
740 | (source |
741 | (origin | |
742 | (method url-fetch) | |
743 | (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/" | |
744 | "netcdf-" version ".tar.gz")) | |
745 | (sha256 | |
746 | (base32 | |
a4b0bfb1 EB |
747 | "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d")) |
748 | (patches (search-patches "netcdf-date-time.patch" | |
749 | "netcdf-tst_h_par.patch")))) | |
889187a4 EB |
750 | (build-system gnu-build-system) |
751 | (native-inputs | |
752 | `(("m4" ,m4) | |
753 | ("doxygen" ,doxygen) | |
754 | ("graphviz" ,graphviz))) | |
755 | (inputs | |
db825570 TD |
756 | `(("hdf4" ,hdf4-alt) |
757 | ("hdf5" ,hdf5) | |
758 | ("zlib" ,zlib) | |
759 | ("libjpeg" ,libjpeg))) | |
889187a4 | 760 | (arguments |
db825570 | 761 | `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4") |
889187a4 EB |
762 | #:parallel-tests? #f)) ;various race conditions |
763 | (home-page "http://www.unidata.ucar.edu/software/netcdf/") | |
764 | (synopsis "Library for scientific data") | |
765 | (description "NetCDF is an interface for scientific data access and a | |
766 | software library that provides an implementation of the interface. The netCDF | |
767 | library defines a machine-independent format for representing scientific data. | |
768 | Together, the interface, library, and format support the creation, access, and | |
769 | sharing of scientific data.") | |
770 | (license (license:x11-style "file://COPYRIGHT")))) | |
771 | ||
772 | (define-public netcdf-parallel-openmpi | |
773 | (package (inherit netcdf) | |
774 | (name "netcdf-parallel-openmpi") | |
775 | (inputs | |
776 | `(("mpi" ,openmpi) | |
777 | ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi) | |
778 | (package-inputs netcdf)))) | |
779 | ;; TODO: Replace pkg-config references in nc-config with absolute references | |
780 | (arguments | |
781 | (substitute-keyword-arguments (package-arguments netcdf) | |
782 | ((#:configure-flags flags) | |
783 | `(cons* "CC=mpicc" "CXX=mpicxx" | |
784 | "--enable-parallel-tests" | |
785 | ;; Shared libraries not supported with parallel IO. | |
786 | "--disable-shared" "--with-pic" | |
787 | ,flags)))))) | |
788 | ||
1b39a196 RJ |
789 | (define-public nlopt |
790 | (package | |
791 | (name "nlopt") | |
792 | (version "2.4.2") | |
793 | (source (origin | |
794 | (method url-fetch) | |
795 | (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-" | |
796 | version ".tar.gz")) | |
797 | (sha256 | |
798 | (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0")))) | |
799 | (build-system gnu-build-system) | |
800 | (arguments | |
801 | `(;; Shared libraries are not built by default. They are required to | |
802 | ;; build the Guile, Octave, and Python bindings. | |
803 | #:configure-flags '("--enable-shared") | |
804 | ||
805 | #:phases | |
806 | (modify-phases %standard-phases | |
807 | (add-before 'configure 'set-libnlopt-file-name | |
808 | (lambda* (#:key outputs #:allow-other-keys) | |
809 | ;; Make sure the Scheme module refers to the library by its | |
810 | ;; absolute file name (we cannot do that from a snippet | |
811 | ;; because the expansion of @libdir@ contains | |
812 | ;; ${exec_prefix}.) | |
813 | (let ((out (assoc-ref outputs "out"))) | |
814 | (substitute* "swig/nlopt.scm.in" | |
815 | (("libnlopt") | |
816 | (string-append out "/lib/libnlopt"))) | |
817 | #t)))))) | |
818 | (inputs `(("guile" ,guile-2.0))) | |
819 | (native-inputs `(("pkg-config" ,pkg-config))) | |
820 | (home-page "http://ab-initio.mit.edu/wiki/") | |
821 | (synopsis "Library for nonlinear optimization") | |
822 | (description "NLopt is a library for nonlinear optimization, providing a | |
823 | common interface for a number of different free optimization routines available | |
824 | online as well as original implementations of various other algorithms.") | |
825 | (license license:lgpl2.1+))) | |
826 | ||
005c787d LC |
827 | (define-public ipopt |
828 | (package | |
829 | (name "ipopt") | |
830 | (version "3.12.5") | |
831 | (source (origin | |
832 | (method url-fetch) | |
833 | (uri (string-append | |
834 | "http://www.coin-or.org/download/source/Ipopt/Ipopt-" | |
835 | version".tgz")) | |
836 | (sha256 | |
837 | (base32 | |
838 | "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk")) | |
839 | (modules '((guix build utils))) | |
840 | (snippet | |
841 | ;; Make sure we don't use the bundled software. | |
842 | '(delete-file-recursively "ThirdParty")))) | |
843 | (build-system gnu-build-system) | |
ad1c4537 LC |
844 | (arguments |
845 | '(#:phases (modify-phases %standard-phases | |
846 | (add-after 'install 'add--L-flags-in-ipopt.pc | |
847 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
848 | ;; The '.pc' file lists '-llapack -lblas' in "Libs"; | |
849 | ;; move it to "Libs.private" where it belongs, and add a | |
850 | ;; '-L' flag for LAPACK. | |
851 | (let ((out (assoc-ref outputs "out")) | |
852 | (lapack (assoc-ref inputs "lapack"))) | |
853 | (substitute* (string-append out "/lib/pkgconfig/" | |
854 | "ipopt.pc") | |
855 | (("Libs: (.*)-llapack -lblas(.*)$" _ before after) | |
856 | (string-append "Libs: " before " " after "\n" | |
857 | "Libs.private: " before | |
858 | "-L" lapack "/lib -llapack -lblas " | |
859 | after "\n"))) | |
860 | #t)))))) | |
005c787d LC |
861 | (native-inputs |
862 | `(("gfortran" ,gfortran))) | |
863 | (inputs | |
864 | ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL. | |
ad1c4537 | 865 | `(("lapack" ,lapack))) ;for both libblas and liblapack |
005c787d LC |
866 | (home-page "http://www.coin-or.org") |
867 | (synopsis "Large-scale nonlinear optimizer") | |
868 | (description | |
869 | "The Interior Point Optimizer (IPOPT) is a software package for | |
870 | large-scale nonlinear optimization. It provides C++, C, and Fortran | |
871 | interfaces.") | |
872 | (license license:epl1.0))) | |
873 | ||
f9940ef1 LC |
874 | (define-public ceres |
875 | (package | |
876 | (name "ceres-solver") | |
877 | (version "1.11.0") | |
878 | (home-page "http://ceres-solver.org/") | |
879 | (source (origin | |
880 | (method url-fetch) | |
881 | (uri (string-append home-page "ceres-solver-" | |
882 | version ".tar.gz")) | |
883 | (sha256 | |
884 | (base32 | |
885 | "0i7qkbf8g6pd8arxzldppga26ckv93y8zldsfz6wbd4n6b1nqrjd")))) | |
886 | (build-system cmake-build-system) | |
887 | (arguments | |
888 | ;; TODO: Build HTML user documentation and install separately. | |
bc3a2e35 | 889 | '(#:configure-flags '("-DBUILD_EXAMPLES=OFF" |
f9940ef1 LC |
890 | "-DBUILD_SHARED_LIBS=ON") |
891 | ||
892 | #:phases (modify-phases %standard-phases | |
893 | (add-before 'configure 'set-library-directory | |
894 | (lambda _ | |
895 | ;; Install libraries to lib/, not lib64/. | |
896 | (substitute* "internal/ceres/CMakeLists.txt" | |
897 | (("set\\(LIB_SUFFIX \"64\"\\)") | |
898 | "set(LIB_SUFFIX \"\")")) | |
899 | #t))))) | |
900 | (native-inputs | |
901 | `(("pkg-config" ,pkg-config))) | |
468e0b18 LC |
902 | (propagated-inputs |
903 | `(("glog" ,glog))) ;for #include <glog/glog.h> | |
f9940ef1 LC |
904 | (inputs |
905 | `(("eigen" ,eigen) | |
906 | ("blas" ,openblas) | |
907 | ("lapack" ,lapack) | |
908 | ("suitesparse" ,suitesparse) | |
909 | ("gflags" ,gflags))) | |
910 | (synopsis "C++ library for solving large optimization problems") | |
911 | (description | |
912 | "Ceres Solver is a C++ library for modeling and solving large, | |
913 | complicated optimization problems. It is a feature rich, mature and | |
914 | performant library which has been used in production since 2010. Ceres Solver | |
915 | can solve two kinds of problems: | |
916 | @enumerate | |
917 | @item non-linear least squares problems with bounds constraints; | |
918 | @item general unconstrained optimization problems. | |
919 | @end enumerate\n") | |
920 | (license license:bsd-3))) | |
921 | ||
668c06ac JD |
922 | ;; For a fully featured Octave, users are strongly recommended also to install |
923 | ;; the following packages: texinfo, less, ghostscript, gnuplot. | |
924 | (define-public octave | |
925 | (package | |
926 | (name "octave") | |
e9d60eba | 927 | (version "4.2.1") |
668c06ac JD |
928 | (source |
929 | (origin | |
930 | (method url-fetch) | |
931 | (uri (string-append "mirror://gnu/octave/octave-" | |
f5a077b1 | 932 | version ".tar.lz")) |
668c06ac JD |
933 | (sha256 |
934 | (base32 | |
e9d60eba | 935 | "09zhhch79jw3ynw39vizx0i2cbd2bjz3sp38pjdzraqrbivpwp92")))) |
668c06ac JD |
936 | (build-system gnu-build-system) |
937 | (inputs | |
938 | `(("lapack" ,lapack) | |
939 | ("readline" ,readline) | |
940 | ("glpk" ,glpk) | |
1ec78e9d EB |
941 | ("fftw" ,fftw) |
942 | ("fftwf" ,fftwf) | |
943 | ("arpack" ,arpack-ng) | |
668c06ac JD |
944 | ("pcre" ,pcre) |
945 | ("fltk" ,fltk) | |
946 | ("fontconfig" ,fontconfig) | |
947 | ("freetype" ,freetype) | |
40029cbe | 948 | ("hdf5" ,hdf5) |
668c06ac JD |
949 | ("libxft" ,libxft) |
950 | ("mesa" ,mesa) | |
1ec78e9d | 951 | ("glu" ,glu) |
668c06ac JD |
952 | ("zlib" ,zlib))) |
953 | (native-inputs | |
f5a077b1 EF |
954 | `(("lzip" ,lzip) |
955 | ("gfortran" ,gfortran) | |
668c06ac JD |
956 | ("pkg-config" ,pkg-config) |
957 | ("perl" ,perl) | |
1ec78e9d EB |
958 | ;; The following inputs are not actually used in the build process. |
959 | ;; However, the ./configure gratuitously tests for their existence and | |
960 | ;; assumes that programs not present at build time are also not, and | |
961 | ;; can never be, available at run time! If these inputs are therefore | |
962 | ;; not present, support for them will be built out. However, Octave | |
963 | ;; will still run without them, albeit without the features they | |
668c06ac JD |
964 | ;; provide. |
965 | ("less" ,less) | |
966 | ("texinfo" ,texinfo) | |
967 | ("ghostscript" ,ghostscript) | |
968 | ("gnuplot" ,gnuplot))) | |
969 | (arguments | |
b7b27a8f KY |
970 | `(#:configure-flags |
971 | (list (string-append "--with-shell=" | |
972 | (assoc-ref %build-inputs "bash") | |
973 | "/bin/sh")))) | |
f5a077b1 | 974 | (home-page "https://www.gnu.org/software/octave/") |
668c06ac | 975 | (synopsis "High-level language for numerical computation") |
1ec78e9d EB |
976 | (description "GNU Octave is a high-level interpreted language that is |
977 | specialized for numerical computations. It can be used for both linear and | |
978 | non-linear applications and it provides great support for visualizing results. | |
979 | Work may be performed both at the interactive command-line as well as via | |
980 | script files.") | |
668c06ac | 981 | (license license:gpl3+))) |
3de01d3f | 982 | |
5d4bd4cc PG |
983 | (define-public opencascade-oce |
984 | (package | |
985 | (name "opencascade-oce") | |
986 | (version "0.17.2") | |
987 | (source | |
988 | (origin | |
989 | (method url-fetch) | |
990 | (uri (string-append | |
991 | "https://github.com/tpaviot/oce/archive/OCE-" | |
992 | version | |
993 | ".tar.gz")) | |
994 | (sha256 | |
995 | (base32 | |
996 | "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd")))) | |
997 | (build-system cmake-build-system) | |
998 | (arguments | |
999 | '(#:configure-flags | |
1000 | (list "-DOCE_TESTING:BOOL=ON" | |
1001 | "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON" | |
1002 | "-DOCE_DRAW:BOOL=ON" | |
1003 | (string-append "-DOCE_INSTALL_PREFIX:PATH=" | |
1004 | (assoc-ref %outputs "out")) | |
1005 | "-UCMAKE_INSTALL_RPATH"))) | |
1006 | (inputs | |
1007 | `(("freetype" ,freetype) | |
1008 | ("glu" ,glu) | |
1009 | ("libxmu" ,libxmu) | |
1010 | ("mesa" ,mesa) | |
1011 | ("tcl" ,tcl) | |
1012 | ("tk" ,tk))) | |
1013 | (native-inputs | |
1014 | `(("python" ,python-wrapper))) | |
1015 | (home-page "https://github.com/tpaviot/oce") | |
1016 | (synopsis "Libraries for 3D modeling and numerical simulation") | |
1017 | (description | |
1018 | "Open CASCADE is a set of libraries for the development of applications | |
1019 | dealing with 3D CAD data or requiring industrial 3D capabilities. It includes | |
1020 | C++ class libraries providing services for 3D surface and solid modeling, CAD | |
1021 | data exchange, and visualization. It is used for development of specialized | |
1022 | software dealing with 3D models in design (CAD), manufacturing (CAM), | |
1023 | numerical simulation (CAE), measurement equipment (CMM), and quality | |
1024 | control (CAQ) domains. | |
1025 | ||
1026 | This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers | |
1027 | patches, improvements, and experiments contributed by users over the official | |
1028 | Open CASCADE library.") | |
1029 | (license (list license:lgpl2.1; OCE libraries, with an exception for the | |
1030 | ; use of header files; see | |
1031 | ; OCCT_LGPL_EXCEPTION.txt | |
1032 | license:public-domain; files | |
1033 | ; src/Standard/Standard_StdAllocator.hxx and | |
1034 | ; src/NCollection/NCollection_StdAllocator.hxx | |
1035 | license:expat; file src/OpenGl/OpenGl_glext.h | |
1036 | license:bsd-3)))); test framework gtest | |
1037 | ||
3de01d3f EB |
1038 | (define-public gmsh |
1039 | (package | |
1040 | (name "gmsh") | |
8a4d14fa | 1041 | (version "2.16.0") |
3de01d3f EB |
1042 | (source |
1043 | (origin | |
1044 | (method url-fetch) | |
1c79e086 | 1045 | (uri (string-append "http://gmsh.info/src/gmsh-" |
3de01d3f EB |
1046 | version "-source.tgz")) |
1047 | (sha256 | |
8a4d14fa | 1048 | (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8")) |
3de01d3f EB |
1049 | (modules '((guix build utils))) |
1050 | (snippet | |
1051 | ;; Remove non-free METIS code | |
1052 | '(delete-file-recursively "contrib/Metis")))) | |
1053 | (build-system cmake-build-system) | |
3de01d3f EB |
1054 | (propagated-inputs |
1055 | `(("fltk" ,fltk) | |
19afbea1 | 1056 | ("gfortran" ,gfortran) |
3de01d3f | 1057 | ("gmp" ,gmp) |
40029cbe | 1058 | ("hdf5" ,hdf5) |
3de01d3f EB |
1059 | ("lapack" ,lapack) |
1060 | ("mesa" ,mesa) | |
85f41902 | 1061 | ("glu" ,glu) |
45548139 | 1062 | ("opencascade-oce" ,opencascade-oce) |
3de01d3f EB |
1063 | ("libx11" ,libx11) |
1064 | ("libxext" ,libxext))) | |
66395a61 EF |
1065 | (inputs |
1066 | `(("fontconfig" ,fontconfig) | |
1067 | ("libxft" ,libxft))) | |
3de01d3f EB |
1068 | (arguments |
1069 | `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF" | |
1070 | "-DENABLE_BUILD_SHARED:BOOL=ON" | |
45548139 | 1071 | "-DENABLE_BUILD_DYNAMIC:BOOL=ON"))) |
3de01d3f EB |
1072 | (home-page "http://www.geuz.org/gmsh/") |
1073 | (synopsis "3D finite element grid generator") | |
edf684ef EB |
1074 | (description "Gmsh is a 3D finite element grid generator with a built-in |
1075 | CAD engine and post-processor. Its design goal is to provide a fast, light | |
1076 | and user-friendly meshing tool with parametric input and advanced | |
1077 | visualization capabilities. Gmsh is built around four modules: geometry, | |
1078 | mesh, solver and post-processing. The specification of any input to these | |
1079 | modules is done either interactively using the graphical user interface or in | |
1080 | ASCII text files using Gmsh's own scripting language.") | |
3de01d3f | 1081 | (license license:gpl2+))) |
b9100e2f EB |
1082 | |
1083 | (define-public petsc | |
1084 | (package | |
1085 | (name "petsc") | |
fafd623e | 1086 | (version "3.7.2") |
b9100e2f EB |
1087 | (source |
1088 | (origin | |
1089 | (method url-fetch) | |
1090 | ;; The *-lite-* tarball does not contain the *large* documentation | |
1091 | (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" | |
1092 | "petsc-lite-" version ".tar.gz")) | |
1093 | (sha256 | |
fafd623e | 1094 | (base32 "0jfrq6rd4zagw1iimz05m2w91k0jvz3qbik1lk8pqcxw3rvdqk5d")))) |
b9100e2f EB |
1095 | (build-system gnu-build-system) |
1096 | (native-inputs | |
1097 | `(("python" ,python-2) | |
1098 | ("perl" ,perl))) | |
1099 | (inputs | |
19afbea1 | 1100 | `(("gfortran" ,gfortran) |
b9100e2f | 1101 | ("lapack" ,lapack) |
f258212d | 1102 | ("superlu" ,superlu) |
b9100e2f EB |
1103 | ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi |
1104 | ;; leaving out opengl, as configuration seems to only be for mac | |
1105 | )) | |
1106 | (arguments | |
1107 | `(#:test-target "test" | |
9a899cce | 1108 | #:parallel-build? #f ;build is parallel by default |
b9100e2f EB |
1109 | #:configure-flags |
1110 | `("--with-mpi=0" | |
f258212d EB |
1111 | "--with-openmp=1" |
1112 | "--with-superlu=1" | |
1113 | ,(string-append "--with-superlu-include=" | |
1114 | (assoc-ref %build-inputs "superlu") "/include") | |
1115 | ,(string-append "--with-superlu-lib=" | |
1116 | (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a")) | |
b9100e2f | 1117 | #:phases |
64dcc289 EB |
1118 | (modify-phases %standard-phases |
1119 | (replace 'configure | |
1120 | ;; PETSc's configure script is actually a python script, so we can't | |
1121 | ;; run it with bash. | |
1122 | (lambda* (#:key outputs (configure-flags '()) | |
1123 | #:allow-other-keys) | |
1124 | (let* ((prefix (assoc-ref outputs "out")) | |
1125 | (flags `(,(string-append "--prefix=" prefix) | |
1126 | ,@configure-flags))) | |
1127 | (format #t "build directory: ~s~%" (getcwd)) | |
1128 | (format #t "configure flags: ~s~%" flags) | |
1129 | (zero? (apply system* "./configure" flags))))) | |
1130 | (add-after 'configure 'clean-local-references | |
64dcc289 EB |
1131 | (lambda* (#:key inputs outputs #:allow-other-keys) |
1132 | (let ((out (assoc-ref outputs "out"))) | |
1133 | (substitute* (find-files "." "^petsc(conf|machineinfo).h$") | |
b730b437 EB |
1134 | ;; Prevent build directory from leaking into compiled code |
1135 | (((getcwd)) out) | |
1136 | ;; Scrub timestamp for reproducibility | |
fafd623e EB |
1137 | ((".*Libraries compiled on.*") "")) |
1138 | #t))) | |
64dcc289 | 1139 | (add-after 'install 'clean-install |
10b11968 EB |
1140 | ;; Try to keep installed files from leaking build directory names. |
1141 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
64dcc289 | 1142 | (let ((out (assoc-ref outputs "out"))) |
10b11968 | 1143 | (substitute* (map (lambda (file) |
9a899cce | 1144 | (string-append out "/lib/petsc/conf/" file)) |
fafd623e | 1145 | '("petscvariables")) |
10b11968 EB |
1146 | (((getcwd)) out)) |
1147 | ;; Make compiler references point to the store | |
9a899cce | 1148 | (substitute* (string-append out "/lib/petsc/conf/petscvariables") |
dfdf5716 EB |
1149 | (("= (gcc|g\\+\\+|gfortran)" _ compiler) |
1150 | (string-append "= " (which compiler)))) | |
10b11968 EB |
1151 | ;; PETSc installs some build logs, which aren't necessary. |
1152 | (for-each (lambda (file) | |
9a899cce | 1153 | (let ((f (string-append out "/lib/petsc/conf/" file))) |
10b11968 EB |
1154 | (when (file-exists? f) |
1155 | (delete-file f)))) | |
9a899cce EB |
1156 | '("configure.log" "make.log" "gmake.log" |
1157 | "test.log" "error.log" "RDict.db" | |
fafd623e | 1158 | "PETScBuildInternal.cmake" |
10b11968 | 1159 | ;; Once installed, should uninstall with Guix |
fafd623e EB |
1160 | "uninstall.py")) |
1161 | #t)))))) | |
b9100e2f | 1162 | (home-page "http://www.mcs.anl.gov/petsc") |
16ecf3ff | 1163 | (synopsis "Library to solve PDEs") |
b9100e2f EB |
1164 | (description "PETSc, pronounced PET-see (the S is silent), is a suite of |
1165 | data structures and routines for the scalable (parallel) solution of | |
1166 | scientific applications modeled by partial differential equations.") | |
166191b3 | 1167 | (license (license:non-copyleft |
b9100e2f EB |
1168 | "http://www.mcs.anl.gov/petsc/documentation/copyright.html")))) |
1169 | ||
1170 | (define-public petsc-complex | |
1171 | (package (inherit petsc) | |
1172 | (name "petsc-complex") | |
1173 | (arguments | |
1174 | (substitute-keyword-arguments (package-arguments petsc) | |
1175 | ((#:configure-flags cf) | |
1176 | `(cons "--with-scalar-type=complex" ,cf)))) | |
16ecf3ff | 1177 | (synopsis "Library to solve PDEs (with complex scalars)"))) |
183e44ae | 1178 | |
d8c7eeb9 EB |
1179 | (define-public petsc-openmpi |
1180 | (package (inherit petsc) | |
1181 | (name "petsc-openmpi") | |
1182 | (inputs | |
1183 | `(("openmpi" ,openmpi) | |
1184 | ,@(package-inputs petsc))) | |
1185 | (arguments | |
1186 | (substitute-keyword-arguments (package-arguments petsc) | |
1187 | ((#:configure-flags cf) | |
1188 | ``("--with-mpiexec=mpirun" | |
1189 | ,(string-append "--with-mpi-dir=" | |
1190 | (assoc-ref %build-inputs "openmpi")) | |
1191 | ,@(delete "--with-mpi=0" ,cf))))) | |
16ecf3ff | 1192 | (synopsis "Library to solve PDEs (with MPI support)"))) |
d8c7eeb9 EB |
1193 | |
1194 | (define-public petsc-complex-openmpi | |
1195 | (package (inherit petsc-complex) | |
1196 | (name "petsc-complex-openmpi") | |
1197 | (inputs | |
1198 | `(("openmpi" ,openmpi) | |
1199 | ,@(package-inputs petsc-complex))) | |
1200 | (arguments | |
1201 | (substitute-keyword-arguments (package-arguments petsc-complex) | |
1202 | ((#:configure-flags cf) | |
1203 | ``("--with-mpiexec=mpirun" | |
1204 | ,(string-append "--with-mpi-dir=" | |
1205 | (assoc-ref %build-inputs "openmpi")) | |
1206 | ,@(delete "--with-mpi=0" ,cf))))) | |
16ecf3ff | 1207 | (synopsis "Library to solve PDEs (with complex scalars and MPI support)"))) |
d8c7eeb9 | 1208 | |
a7f01414 EB |
1209 | (define-public slepc |
1210 | (package | |
1211 | (name "slepc") | |
8787c555 | 1212 | (version "3.7.1") |
a7f01414 EB |
1213 | (source |
1214 | (origin | |
1215 | (method url-fetch) | |
1216 | (uri (string-append "http://slepc.upv.es/download/download.php?" | |
1217 | "filename=slepc-" version ".tar.gz")) | |
d588422e | 1218 | (file-name (string-append name "-" version ".tar.gz")) |
a7f01414 EB |
1219 | (sha256 |
1220 | (base32 | |
8787c555 | 1221 | "1hijlmrvxvfqslnx8yydzw5xqbsn1yy02g32w0hln1z3cgr1c0k7")))) |
a7f01414 EB |
1222 | (build-system gnu-build-system) |
1223 | (native-inputs | |
1224 | `(("python" ,python-2))) | |
1225 | (inputs | |
1226 | `(("arpack" ,arpack-ng) | |
1227 | ("gfortran" ,gfortran))) | |
1228 | (propagated-inputs | |
1229 | `(("petsc" ,petsc))) | |
1230 | (arguments | |
1231 | `(#:parallel-build? #f ;build is parallel by default | |
1232 | #:configure-flags | |
1233 | `(,(string-append "--with-arpack-dir=" | |
9cf52454 | 1234 | (assoc-ref %build-inputs "arpack") "/lib")) |
a7f01414 EB |
1235 | #:phases |
1236 | (modify-phases %standard-phases | |
8787c555 | 1237 | (replace 'configure |
a7f01414 EB |
1238 | ;; configure is a python script, so we can't run it with bash. |
1239 | (lambda* (#:key inputs outputs (configure-flags '()) | |
1240 | #:allow-other-keys) | |
1241 | (let* ((prefix (assoc-ref outputs "out")) | |
1242 | (flags `(,(string-append "--prefix=" prefix) | |
1243 | ,@configure-flags))) | |
1244 | (format #t "build directory: ~s~%" (getcwd)) | |
1245 | (format #t "configure flags: ~s~%" flags) | |
1246 | (setenv "SLEPC_DIR" (getcwd)) | |
9cf52454 | 1247 | (setenv "PETSC_DIR" (assoc-ref inputs "petsc")) |
a7f01414 | 1248 | (zero? (apply system* "./configure" flags))))) |
8787c555 | 1249 | (add-after 'install 'delete-doc |
a7f01414 EB |
1250 | ;; TODO: SLEPc installs HTML documentation alongside headers in |
1251 | ;; $out/include. We'd like to move them to share/doc, but delete | |
1252 | ;; them for now, as they are incomplete and installing the complete | |
1253 | ;; documentation is difficult. | |
1254 | (lambda* (#:key outputs #:allow-other-keys) | |
1255 | (let* ((out (assoc-ref outputs "out"))) | |
1256 | (for-each delete-file (find-files out "\\.html$"))))) | |
8787c555 | 1257 | (add-after 'install 'clean-install |
a7f01414 EB |
1258 | ;; Clean up unnecessary build logs from installation. |
1259 | (lambda* (#:key outputs #:allow-other-keys) | |
1260 | (let ((out (assoc-ref outputs "out"))) | |
1261 | (for-each (lambda (file) | |
1262 | (let ((f (string-append out "/lib/slepc/conf/" file))) | |
1263 | (when (file-exists? f) | |
1264 | (delete-file f)))) | |
1265 | '("configure.log" "make.log" "gmake.log" | |
1266 | "test.log" "error.log" "RDict.db" | |
1267 | "uninstall.py")))))))) | |
1268 | (home-page "http://slepc.upv.es") | |
1269 | (synopsis "Scalable library for eigenproblems") | |
1270 | (description "SLEPc is a software library for the solution of large sparse | |
1271 | eigenproblems on parallel computers. It can be used for the solution of | |
1272 | linear eigenvalue problems formulated in either standard or generalized form, | |
1273 | as well as other related problems such as the singular value decomposition. | |
1274 | The emphasis of the software is on methods and techniques appropriate for | |
1275 | problems in which the associated matrices are sparse, for example, those | |
1276 | arising after the discretization of partial differential equations.") | |
1277 | (license license:lgpl3))) | |
1278 | ||
1279 | (define-public slepc-complex | |
1280 | (package (inherit slepc) | |
1281 | (name "slepc-complex") | |
1282 | (propagated-inputs | |
1283 | `(("petsc" ,petsc-complex) | |
1284 | ,@(alist-delete "petsc" (package-propagated-inputs slepc)))) | |
1285 | (synopsis "Scalable library for eigenproblems (with complex scalars)"))) | |
1286 | ||
1287 | (define-public slepc-openmpi | |
1288 | (package (inherit slepc) | |
1289 | (name "slepc-openmpi") | |
1290 | (inputs | |
1291 | `(("mpi" ,openmpi) | |
1292 | ("arpack" ,arpack-ng-openmpi) | |
1293 | ,@(alist-delete "arpack" (package-inputs slepc)))) | |
1294 | (propagated-inputs | |
1295 | `(("petsc" ,petsc-openmpi) | |
1296 | ,@(alist-delete "petsc" (package-propagated-inputs slepc)))) | |
1297 | (synopsis "Scalable library for eigenproblems (with MPI support)"))) | |
1298 | ||
1299 | (define-public slepc-complex-openmpi | |
1300 | (package (inherit slepc-openmpi) | |
1301 | (name "slepc-complex-openmpi") | |
1302 | (propagated-inputs | |
1303 | `(("petsc" ,petsc-complex-openmpi) | |
1304 | ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi)))) | |
1305 | (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)"))) | |
1306 | ||
cec86422 EB |
1307 | (define-public mumps |
1308 | (package | |
1309 | (name "mumps") | |
fba78d18 | 1310 | (version "5.0.2") |
cec86422 EB |
1311 | (source |
1312 | (origin | |
1313 | (method url-fetch) | |
1314 | (uri (string-append "http://mumps.enseeiht.fr/MUMPS_" | |
1315 | version ".tar.gz")) | |
1316 | (sha256 | |
1317 | (base32 | |
fba78d18 | 1318 | "0igyc1pfzxdhpbad3v3lb86ixkdbqa1a8gbs15b04r2294h2nabp")) |
fc1adab1 | 1319 | (patches (search-patches "mumps-build-parallelism.patch")))) |
cec86422 EB |
1320 | (build-system gnu-build-system) |
1321 | (inputs | |
1322 | `(("fortran" ,gfortran) | |
1323 | ;; These are required for linking against mumps, but we let the user | |
1324 | ;; declare the dependency. | |
1325 | ("blas" ,openblas) | |
1326 | ("metis" ,metis) | |
1327 | ("scotch" ,scotch))) | |
1328 | (arguments | |
1329 | `(#:modules ((ice-9 match) | |
1330 | (ice-9 popen) | |
1331 | (srfi srfi-1) | |
1332 | ,@%gnu-build-system-modules) | |
1333 | #:phases | |
1334 | (modify-phases %standard-phases | |
fba78d18 | 1335 | (replace 'configure |
cec86422 EB |
1336 | (lambda* (#:key inputs #:allow-other-keys) |
1337 | (call-with-output-file "Makefile.inc" | |
1338 | (lambda (port) | |
1339 | (format port " | |
1340 | PLAT = | |
1341 | LIBEXT = .a | |
1342 | OUTC = -o | |
1343 | OUTF = -o | |
1344 | RM = rm -f~:[ | |
1345 | CC = gcc | |
1346 | FC = gfortran | |
1347 | FL = gfortran | |
1348 | INCSEQ = -I$(topdir)/libseq | |
1349 | LIBSEQ = -L$(topdir)/libseq -lmpiseq | |
1350 | LIBSEQNEEDED = libseqneeded~; | |
1351 | CC = mpicc | |
1352 | FC = mpifort | |
1353 | FL = mpifort~] | |
1354 | AR = ar vr # rules require trailing space, ugh... | |
1355 | RANLIB = ranlib | |
1356 | LIBBLAS = -L~a -lopenblas~@[ | |
1357 | SCALAP = -L~a -lscalapack~] | |
1358 | LIBOTHERS = -pthread | |
1359 | CDEFS = -DAdd_ | |
1360 | PIC = -fPIC | |
1361 | OPTF = -O2 -DALLOW_NON_INIT $(PIC) | |
1362 | OPTL = -O2 $(PIC) | |
1363 | OPTC = -O2 $(PIC) | |
1364 | INCS = $(INCSEQ) | |
1365 | LIBS = $(SCALAP) $(LIBSEQ) | |
1366 | LPORDDIR = $(topdir)/PORD/lib | |
1367 | IPORD = -I$(topdir)/PORD/include | |
1368 | LPORD = -L$(LPORDDIR) -lpord | |
1369 | ORDERINGSF = -Dpord~@[ | |
1370 | METISDIR = ~a | |
1371 | IMETIS = -I$(METISDIR)/include | |
1372 | LMETIS = -L$(METISDIR)/lib -lmetis | |
1373 | ORDERINGSF += -Dmetis~]~@[~:{ | |
1374 | SCOTCHDIR = ~a | |
1375 | ISCOTCH = -I$(SCOTCHDIR)/include | |
1376 | LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr | |
1377 | ORDERINGSF += ~a~}~] | |
1378 | ORDERINGSC = $(ORDERINGSF) | |
1379 | LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) | |
1380 | IORDERINGSF = $(ISCOTCH) | |
1381 | IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)" | |
1382 | (assoc-ref inputs "mpi") | |
1383 | (assoc-ref inputs "blas") | |
1384 | (assoc-ref inputs "scalapack") | |
1385 | (assoc-ref inputs "metis") | |
1386 | (match (list (assoc-ref inputs "pt-scotch") | |
1387 | (assoc-ref inputs "scotch")) | |
1388 | ((#f #f) | |
1389 | #f) | |
1390 | ((#f scotch) | |
1391 | `((,scotch "" "-Dscotch"))) | |
1392 | ((ptscotch _) | |
1393 | `((,ptscotch | |
1394 | "-lptesmumps -lptscotch -lptscotcherr " | |
1395 | "-Dptscotch"))))))))) | |
fba78d18 | 1396 | (replace 'build |
cec86422 EB |
1397 | ;; By default only the d-precision library is built. Make with "all" |
1398 | ;; target so that all precision libraries and examples are built. | |
1399 | (lambda _ | |
1400 | (zero? (system* "make" "all" | |
1401 | (format #f "-j~a" (parallel-job-count)))))) | |
fba78d18 | 1402 | (replace 'check |
cec86422 EB |
1403 | ;; Run the simple test drivers, which read test input from stdin: |
1404 | ;; from the "real" input for the single- and double-precision | |
1405 | ;; testers, and from the "cmplx" input for complex-precision | |
1406 | ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi | |
1407 | ;; package to prefix execution with "mpirun". | |
1408 | (lambda* (#:key (exec-prefix '()) #:allow-other-keys) | |
1409 | (with-directory-excursion "examples" | |
1410 | (every | |
1411 | (lambda (prec type) | |
1412 | (let ((tester (apply open-pipe* | |
1413 | `(,OPEN_WRITE | |
1414 | ,@exec-prefix | |
1415 | ,(string-append "./" prec | |
1416 | "simpletest")))) | |
1417 | (input (open-input-file | |
1418 | (string-append "input_simpletest_" type)))) | |
1419 | (begin | |
1420 | (dump-port input tester) | |
1421 | (close-port input) | |
1422 | (zero? (close-pipe tester))))) | |
1423 | '("s" "d" "c" "z") | |
1424 | '("real" "real" "cmplx" "cmplx"))))) | |
fba78d18 EB |
1425 | (replace 'install |
1426 | (lambda* (#:key outputs #:allow-other-keys) | |
1427 | (let* ((out (assoc-ref outputs "out")) | |
1428 | (libdir (string-append out "/lib"))) | |
1429 | (copy-recursively "lib" libdir) | |
1430 | (copy-recursively "include" (string-append out "/include")) | |
1431 | (when (file-exists? "libseq/libmpiseq.a") | |
1432 | (install-file "libseq/libmpiseq.a" libdir)) | |
1433 | #t)))))) | |
cec86422 EB |
1434 | (home-page "http://mumps.enseeiht.fr") |
1435 | (synopsis "Multifrontal sparse direct solver") | |
1436 | (description | |
1437 | "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a | |
1438 | sparse system of linear equations A x = b using Guassian elimination.") | |
1439 | (license license:cecill-c))) | |
1440 | ||
1441 | (define-public mumps-metis | |
1442 | (package (inherit mumps) | |
1443 | (name "mumps-metis") | |
1444 | (inputs | |
1445 | (alist-delete "scotch" (package-inputs mumps))))) | |
1446 | ||
1447 | (define-public mumps-openmpi | |
1448 | (package (inherit mumps) | |
1449 | (name "mumps-openmpi") | |
1450 | (inputs | |
1451 | `(("mpi" ,openmpi) | |
1452 | ("scalapack" ,scalapack) | |
1453 | ("pt-scotch" ,pt-scotch) | |
1454 | ,@(alist-delete "scotch" (package-inputs mumps)))) | |
1455 | (arguments | |
1456 | (substitute-keyword-arguments (package-arguments mumps) | |
1457 | ((#:phases phases) | |
1458 | `(modify-phases ,phases | |
1459 | (replace | |
1460 | 'check | |
1461 | (lambda _ | |
1462 | ((assoc-ref ,phases 'check) | |
1463 | #:exec-prefix '("mpirun" "-n" "2")))))))) | |
1464 | (synopsis "Multifrontal sparse direct solver (with MPI)"))) | |
1465 | ||
1466 | (define-public mumps-metis-openmpi | |
1467 | (package (inherit mumps-openmpi) | |
1468 | (name "mumps-metis-openmpi") | |
1469 | (inputs | |
1470 | (alist-delete "pt-scotch" (package-inputs mumps-openmpi))))) | |
1471 | ||
2d047896 RW |
1472 | (define-public r-quadprog |
1473 | (package | |
1474 | (name "r-quadprog") | |
1475 | (version "1.5-5") | |
1476 | (source | |
1477 | (origin | |
1478 | (method url-fetch) | |
1479 | (uri (cran-uri "quadprog" version)) | |
1480 | (sha256 | |
1481 | (base32 | |
1482 | "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr")))) | |
1483 | (build-system r-build-system) | |
1484 | (native-inputs | |
1485 | `(("gfortran" ,gfortran))) | |
1486 | (home-page "http://cran.r-project.org/web/packages/quadprog") | |
1487 | (synopsis "Functions to solve quadratic programming problems") | |
1488 | (description | |
1489 | "This package contains routines and documentation for solving quadratic | |
1490 | programming problems.") | |
1491 | (license license:gpl3+))) | |
1492 | ||
ec8c7e47 RJ |
1493 | (define-public r-pracma |
1494 | (package | |
1495 | (name "r-pracma") | |
ccd9b151 | 1496 | (version "1.9.5") |
ec8c7e47 RJ |
1497 | (source (origin |
1498 | (method url-fetch) | |
1499 | (uri (cran-uri "pracma" version)) | |
1500 | (sha256 | |
ccd9b151 | 1501 | (base32 "19nr2jlkbcdgvw3gx5hry12av565lmvqd5q4h7zlch3q13avwwl2")))) |
ec8c7e47 | 1502 | (build-system r-build-system) |
ccd9b151 RW |
1503 | (propagated-inputs |
1504 | `(("r-quadprog" ,r-quadprog))) | |
ec8c7e47 RJ |
1505 | (home-page "http://cran.r-project.org/web/packages/pracma") |
1506 | (synopsis "Practical numerical math functions") | |
1507 | (description "This package provides functions for numerical analysis and | |
1508 | linear algebra, numerical optimization, differential equations, plus some | |
1509 | special functions. It uses Matlab function names where appropriate to simplify | |
1510 | porting.") | |
1511 | (license license:gpl3+))) | |
1512 | ||
183e44ae EB |
1513 | (define-public superlu |
1514 | (package | |
1515 | (name "superlu") | |
995a09e0 | 1516 | (version "5.2.1") |
183e44ae EB |
1517 | (source |
1518 | (origin | |
1519 | (method url-fetch) | |
1520 | (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" | |
1521 | "superlu_" version ".tar.gz")) | |
1522 | (sha256 | |
995a09e0 EB |
1523 | (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8")) |
1524 | (modules '((guix build utils))) | |
1525 | (snippet | |
1526 | ;; Replace the non-free implementation of MC64 with a stub adapted | |
1527 | ;; from Debian | |
1528 | '(begin | |
1529 | (use-modules (ice-9 regex) | |
1530 | (ice-9 rdelim)) | |
1531 | (call-with-output-file "SRC/mc64ad.c" | |
1532 | (lambda (port) | |
1533 | (display " | |
1534 | #include <stdio.h> | |
1535 | #include <stdlib.h> | |
1536 | void mc64id_(int *a) { | |
1537 | fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\"); | |
1538 | abort (); | |
1539 | } | |
1540 | void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g, | |
1541 | int *h, int *i, int *j, int *k, double *l, int *m, int *n) { | |
1542 | fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\"); | |
1543 | abort (); | |
1544 | }\n" port))) | |
1545 | ;; Remove the corresponding license verbiage. MC64 license follows | |
1546 | ;; a "------" line separator. | |
1547 | (with-atomic-file-replacement "License.txt" | |
1548 | (let ((rx (make-regexp "-{8}"))) | |
1549 | (lambda (in out) | |
1550 | (let loop () | |
1551 | (let ((line (read-line in 'concat))) | |
1552 | (unless (regexp-exec rx line) | |
1553 | (display line out) | |
1554 | (loop))))))))))) | |
1555 | (build-system cmake-build-system) | |
183e44ae EB |
1556 | (native-inputs |
1557 | `(("tcsh" ,tcsh))) | |
1558 | (inputs | |
995a09e0 | 1559 | `(("blas" ,openblas) |
19afbea1 | 1560 | ("gfortran" ,gfortran))) |
183e44ae | 1561 | (arguments |
995a09e0 EB |
1562 | `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas |
1563 | "-DTPL_BLAS_LIBRARIES=openblas" | |
1564 | "-DBUILD_SHARED_LIBS:BOOL=YES" | |
1565 | "-DCMAKE_INSTALL_LIBDIR=lib"))) | |
183e44ae EB |
1566 | (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/") |
1567 | (synopsis "Supernodal direct solver for sparse linear systems") | |
1568 | (description | |
1569 | "SuperLU is a general purpose library for the direct solution of large, | |
1570 | sparse, nonsymmetric systems of linear equations on high performance machines. | |
1571 | The library is written in C and is callable from either C or Fortran. The | |
1572 | library routines perform an LU decomposition with partial pivoting and | |
1573 | triangular system solves through forward and back substitution. The library | |
1574 | also provides threshold-based ILU factorization preconditioners.") | |
995a09e0 EB |
1575 | (license (list license:bsd-3 |
1576 | license:gpl2+ ;EXAMPLE/*fgmr.c | |
1577 | (license:fsf-free "file://SRC/colamd.h"))))) | |
f8ed036a | 1578 | |
a54aefea EB |
1579 | (define-public superlu-dist |
1580 | (package | |
1581 | (name "superlu-dist") | |
1582 | (version "3.3") | |
1583 | (source | |
1584 | (origin | |
1585 | (method url-fetch) | |
1586 | (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" | |
1587 | "superlu_dist_" version ".tar.gz")) | |
1588 | (sha256 | |
1589 | (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj")) | |
29080870 EB |
1590 | (modules '((guix build utils))) |
1591 | (snippet | |
1592 | ;; Replace the non-free implementation of MC64 with a stub | |
1593 | '(begin | |
1594 | (use-modules (ice-9 regex) | |
1595 | (ice-9 rdelim)) | |
1596 | (call-with-output-file "SRC/mc64ad.c" | |
1597 | (lambda (port) | |
1598 | (display " | |
1599 | #include <stdio.h> | |
1600 | #include <stdlib.h> | |
1601 | void mc64id_(int *a) { | |
1602 | fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\"); | |
1603 | abort (); | |
1604 | } | |
1605 | void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g, | |
1606 | int *h, int *i, int *j, int *k, double *l, int *m, int *n) { | |
1607 | fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\"); | |
1608 | abort (); | |
1609 | }\n" port))) | |
1610 | (delete-file "SRC/mc64ad.f.bak") | |
1611 | (substitute* "SRC/util.c" ;adjust default algorithm | |
1612 | (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag") | |
1613 | "RowPerm = NOROWPERM")))) | |
fc1adab1 | 1614 | (patches (search-patches "superlu-dist-scotchmetis.patch")))) |
a54aefea EB |
1615 | (build-system gnu-build-system) |
1616 | (native-inputs | |
1617 | `(("tcsh" ,tcsh))) | |
1618 | (inputs | |
19afbea1 | 1619 | `(("gfortran" ,gfortran))) |
a54aefea EB |
1620 | (propagated-inputs |
1621 | `(("openmpi" ,openmpi) ;headers include MPI heades | |
1622 | ("lapack" ,lapack) ;required to link with output library | |
1623 | ("pt-scotch" ,pt-scotch))) ;same | |
1624 | (arguments | |
1625 | `(#:parallel-build? #f ;race conditions using ar | |
1626 | #:phases | |
1627 | (alist-replace | |
1628 | 'configure | |
1629 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1630 | (call-with-output-file "make.inc" | |
1631 | (lambda (port) | |
1632 | (format port " | |
1633 | PLAT = | |
1634 | DSuperLUroot = ~a | |
1635 | DSUPERLULIB = ~a/lib/libsuperlu_dist.a | |
1636 | BLASDEF = -DUSE_VENDOR_BLAS | |
1637 | BLASLIB = -L~a/lib -lblas | |
1638 | PARMETISLIB = -L~a/lib \ | |
1639 | -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \ | |
1640 | -lscotch -lscotcherr -lscotcherrexit | |
1641 | METISLIB = -L~:*~a/lib \ | |
1642 | -lscotchmetis -lscotch -lscotcherr -lscotcherrexit | |
1643 | LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB) | |
1644 | ARCH = ar | |
1645 | ARCHFLAGS = cr | |
1646 | RANLIB = ranlib | |
1647 | CC = mpicc | |
1648 | PIC = -fPIC | |
1649 | CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC) | |
1650 | NOOPTS = -O0 -g $(PIC) | |
1651 | FORTRAN = mpifort | |
1652 | FFLAGS = -O2 -g $(PIC) | |
1653 | LOADER = $(CC) | |
1654 | CDEFS = -DAdd_" | |
1655 | (getcwd) | |
1656 | (assoc-ref outputs "out") | |
1657 | (assoc-ref inputs "lapack") | |
1658 | (assoc-ref inputs "pt-scotch"))))) | |
1659 | (alist-cons-after | |
1660 | 'unpack 'remove-broken-symlinks | |
1661 | (lambda _ | |
1662 | (for-each delete-file | |
1663 | (find-files "MAKE_INC" "\\.#make\\..*"))) | |
1664 | (alist-cons-before | |
1665 | 'build 'create-install-directories | |
1666 | (lambda* (#:key outputs #:allow-other-keys) | |
1667 | (for-each | |
1668 | (lambda (dir) | |
1669 | (mkdir-p (string-append (assoc-ref outputs "out") | |
1670 | "/" dir))) | |
1671 | '("lib" "include"))) | |
1672 | (alist-replace | |
1673 | 'check | |
1674 | (lambda _ | |
1675 | (with-directory-excursion "EXAMPLE" | |
1676 | (and | |
1677 | (zero? (system* "mpirun" "-n" "2" | |
1678 | "./pddrive" "-r" "1" "-c" "2" "g20.rua")) | |
1679 | (zero? (system* "mpirun" "-n" "2" | |
1680 | "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))))) | |
1681 | (alist-replace | |
1682 | 'install | |
1683 | (lambda* (#:key outputs #:allow-other-keys) | |
1684 | ;; Library is placed in lib during the build phase. Copy over | |
1685 | ;; headers to include. | |
1686 | (let* ((out (assoc-ref outputs "out")) | |
1687 | (incdir (string-append out "/include"))) | |
1688 | (for-each (lambda (file) | |
1689 | (let ((base (basename file))) | |
1690 | (format #t "installing `~a' to `~a'~%" | |
1691 | base incdir) | |
1692 | (copy-file file | |
1693 | (string-append incdir "/" base)))) | |
1694 | (find-files "SRC" ".*\\.h$")))) | |
1695 | %standard-phases))))))) | |
1696 | (home-page (package-home-page superlu)) | |
1697 | (synopsis "Parallel supernodal direct solver") | |
1698 | (description | |
1699 | "SuperLU_DIST is a parallel extension to the serial SuperLU library. | |
1700 | It is targeted for distributed memory parallel machines. SuperLU_DIST is | |
1701 | implemented in ANSI C, and MPI for communications.") | |
1702 | (license license:bsd-3))) | |
1703 | ||
f8ed036a EB |
1704 | (define-public scotch |
1705 | (package | |
1706 | (name "scotch") | |
6c798540 | 1707 | (version "6.0.4") |
f8ed036a EB |
1708 | (source |
1709 | (origin | |
1710 | (method url-fetch) | |
6c798540 | 1711 | (uri (string-append "https://gforge.inria.fr/frs/download.php/34618/" |
f8ed036a EB |
1712 | "scotch_" version ".tar.gz")) |
1713 | (sha256 | |
6c798540 | 1714 | (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm")) |
fc1adab1 AK |
1715 | (patches (search-patches "scotch-test-threading.patch" |
1716 | "pt-scotch-build-parallelism.patch")))) | |
f8ed036a EB |
1717 | (build-system gnu-build-system) |
1718 | (inputs | |
1719 | `(("zlib" ,zlib) | |
1720 | ("flex" ,flex) | |
1721 | ("bison" ,bison))) | |
1722 | (arguments | |
1723 | `(#:phases | |
d6602ee9 EB |
1724 | (modify-phases %standard-phases |
1725 | (add-after | |
1726 | 'unpack 'chdir-to-src | |
1727 | (lambda _ (chdir "src"))) | |
1728 | (replace | |
1729 | 'configure | |
1730 | (lambda _ | |
1731 | (call-with-output-file "Makefile.inc" | |
1732 | (lambda (port) | |
1733 | (format port " | |
f8ed036a EB |
1734 | EXE = |
1735 | LIB = .a | |
1736 | OBJ = .o | |
1737 | MAKE = make | |
1738 | AR = ar | |
1739 | ARFLAGS = -ruv | |
cf0ec6c4 | 1740 | CAT = cat |
f8ed036a EB |
1741 | CCS = gcc |
1742 | CCP = mpicc | |
1743 | CCD = gcc | |
1744 | CPPFLAGS =~{ -D~a~} | |
6c798540 | 1745 | CFLAGS = -O2 -g -fPIC $(CPPFLAGS) |
f8ed036a EB |
1746 | LDFLAGS = -lz -lm -lrt -lpthread |
1747 | CP = cp | |
1748 | LEX = flex -Pscotchyy -olex.yy.c | |
1749 | LN = ln | |
1750 | MKDIR = mkdir | |
1751 | MV = mv | |
1752 | RANLIB = ranlib | |
1753 | YACC = bison -pscotchyy -y -b y | |
1754 | " | |
d6602ee9 EB |
1755 | '("COMMON_FILE_COMPRESS_GZ" |
1756 | "COMMON_PTHREAD" | |
1757 | "COMMON_RANDOM_FIXED_SEED" | |
cf0ec6c4 EB |
1758 | ;; Prevents symbolc clashes with libesmumps |
1759 | "SCOTCH_RENAME" | |
d6602ee9 EB |
1760 | ;; XXX: Causes invalid frees in superlu-dist tests |
1761 | ;; "SCOTCH_PTHREAD" | |
1762 | ;; "SCOTCH_PTHREAD_NUMBER=2" | |
1763 | "restrict=__restrict")))))) | |
cf0ec6c4 EB |
1764 | (add-after |
1765 | 'build 'build-esmumps | |
1766 | (lambda _ | |
1767 | (zero? (system* "make" | |
1768 | (format #f "-j~a" (parallel-job-count)) | |
1769 | "esmumps")))) | |
d6602ee9 | 1770 | (replace |
f8ed036a EB |
1771 | 'install |
1772 | (lambda* (#:key outputs #:allow-other-keys) | |
1773 | (let ((out (assoc-ref outputs "out"))) | |
1774 | (mkdir out) | |
1775 | (zero? (system* "make" | |
1776 | (string-append "prefix=" out) | |
cf0ec6c4 EB |
1777 | "install")) |
1778 | ;; esmumps files are not installed with the above | |
1779 | (for-each (lambda (f) | |
1780 | (copy-file f (string-append out "/include/" f))) | |
1781 | (find-files "../include" ".*esmumps.h$")) | |
1782 | (for-each (lambda (f) | |
1783 | (copy-file f (string-append out "/lib/" f))) | |
1784 | (find-files "../lib" "^lib.*esmumps.*")))))))) | |
f8ed036a EB |
1785 | (home-page "http://www.labri.fr/perso/pelegrin/scotch/") |
1786 | (synopsis "Programs and libraries for graph algorithms") | |
1787 | (description "SCOTCH is a set of programs and libraries which implement | |
1788 | the static mapping and sparse matrix reordering algorithms developed within | |
1789 | the SCOTCH project. Its purpose is to apply graph theory, with a divide and | |
1790 | conquer approach, to scientific computing problems such as graph and mesh | |
1791 | partitioning, static mapping, and sparse matrix ordering, in application | |
1792 | domains ranging from structural mechanics to operating systems or | |
1793 | bio-chemistry.") | |
1794 | ;; See LICENSE_en.txt | |
1795 | (license license:cecill-c))) | |
6acb4adb EB |
1796 | |
1797 | (define-public pt-scotch | |
1798 | (package (inherit scotch) | |
1799 | (name "pt-scotch") | |
1800 | (propagated-inputs | |
1801 | `(("openmpi" ,openmpi))) ;Headers include MPI headers | |
1802 | (arguments | |
1803 | (substitute-keyword-arguments (package-arguments scotch) | |
1804 | ((#:phases scotch-phases) | |
d6602ee9 EB |
1805 | `(modify-phases ,scotch-phases |
1806 | (replace | |
1807 | 'build | |
d6602ee9 EB |
1808 | (lambda _ |
1809 | (and | |
cf0ec6c4 EB |
1810 | (zero? (system* "make" |
1811 | (format #f "-j~a" (parallel-job-count)) | |
1812 | "ptscotch" "ptesmumps")) | |
d6602ee9 EB |
1813 | ;; Install the serial metis compatibility library |
1814 | (zero? (system* "make" "-C" "libscotchmetis" "install"))))) | |
1815 | (replace | |
1816 | 'check | |
1817 | (lambda _ (zero? (system* "make" "ptcheck")))))))) | |
6acb4adb | 1818 | (synopsis "Programs and libraries for graph algorithms (with MPI)"))) |
5698b8b8 | 1819 | |
aa75ad00 EB |
1820 | (define-public metis |
1821 | (package | |
1822 | (name "metis") | |
1823 | (version "5.1.0") | |
1824 | (source | |
1825 | (origin | |
1826 | (method url-fetch) | |
1827 | (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/" | |
1828 | "metis-" version ".tar.gz")) | |
1829 | (sha256 | |
1830 | (base32 | |
1831 | "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn")))) | |
1832 | (build-system cmake-build-system) | |
1833 | (inputs | |
1834 | `(("blas" ,openblas))) | |
1835 | (arguments | |
1836 | `(#:tests? #f ;no tests | |
1837 | #:configure-flags `("-DSHARED=ON" | |
1838 | ,(string-append "-DGKLIB_PATH=" (getcwd) | |
1839 | "/metis-" ,version "/GKlib")))) | |
1840 | (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview") | |
1841 | (synopsis "Graph partitioning and fill-reducing matrix ordering library") | |
1842 | (description | |
1843 | "METIS is a set of serial programs for partitioning graphs, partitioning | |
1844 | finite element meshes, and producing fill-reducing orderings for sparse | |
1845 | matrices. The algorithms implemented in METIS are based on the multilevel | |
1846 | recursive-bisection, multilevel k-way, and multi-constraint partitioning | |
1847 | schemes.") | |
1848 | (license license:asl2.0))) ;As of version 5.0.3 | |
1849 | ||
700ff222 EB |
1850 | (define-public p4est |
1851 | (package | |
1852 | (name "p4est") | |
1853 | (version "1.1") | |
1854 | (source | |
1855 | (origin | |
1856 | (method url-fetch) | |
1857 | (uri (string-append "http://p4est.github.io/release/p4est-" | |
1858 | version ".tar.gz")) | |
1859 | (sha256 | |
1860 | (base32 | |
1861 | "0faina2h5qsx3m2izbzaj9bbakma1krbbjmq43wrp1hcbyijflqb")))) | |
1862 | (build-system gnu-build-system) | |
1863 | (inputs | |
1864 | `(("fortran" ,gfortran) | |
1865 | ("blas" ,openblas) | |
1866 | ("lapack" ,lapack) | |
1867 | ("zlib" ,zlib))) | |
1868 | (arguments | |
1869 | `(#:configure-flags `(,(string-append "BLAS_LIBS=-L" | |
1870 | (assoc-ref %build-inputs "blas") | |
1871 | " -lopenblas") | |
1872 | ,(string-append "LAPACK_LIBS=-L" | |
1873 | (assoc-ref %build-inputs "lapack") | |
1874 | " -llapack")))) | |
1875 | (home-page "http://www.p4est.org") | |
1876 | (synopsis "Adaptive mesh refinement on forests of octrees") | |
1877 | (description | |
1878 | "The p4est software library enables the dynamic management of a | |
1879 | collection of adaptive octrees, conveniently called a forest of octrees. | |
1880 | p4est is designed to work in parallel and scales to hundreds of thousands of | |
1881 | processor cores.") | |
1882 | (license license:gpl2+))) | |
1883 | ||
1884 | (define-public p4est-openmpi | |
1885 | (package (inherit p4est) | |
1886 | (name "p4est-openmpi") | |
1887 | (inputs | |
1888 | `(("mpi" ,openmpi) | |
1889 | ,@(package-inputs p4est))) | |
1890 | (arguments | |
1891 | (substitute-keyword-arguments (package-arguments p4est) | |
1892 | ((#:configure-flags cf) | |
1893 | ``("--enable-mpi" ,@,cf)))) | |
1894 | (synopsis "Parallel adaptive mesh refinement on forests of octrees"))) | |
1895 | ||
5698b8b8 JD |
1896 | (define-public gsegrafix |
1897 | (package | |
1898 | (name "gsegrafix") | |
1899 | (version "1.0.6") | |
1900 | (source | |
1901 | (origin | |
1902 | (method url-fetch) | |
1903 | (uri (string-append "mirror://gnu/" name "/" name "-" | |
1904 | version ".tar.gz")) | |
1905 | (sha256 | |
1906 | (base32 | |
1907 | "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda")))) | |
1908 | (build-system gnu-build-system) | |
1909 | (arguments | |
1910 | `(#:configure-flags '("LDFLAGS=-lm"))) | |
1911 | (inputs | |
1912 | `(("libgnomecanvas" ,libgnomecanvas) | |
1913 | ("libbonoboui" ,libbonoboui) | |
1914 | ("libgnomeui" ,libgnomeui) | |
1915 | ("libgnomeprintui" ,libgnomeprintui) | |
1916 | ("popt" ,popt))) | |
1917 | (native-inputs | |
1918 | `(("pkg-config" ,pkg-config))) | |
1919 | (home-page "http://www.gnu.org/software/gsegrafix/") | |
1920 | (synopsis "GNOME application to create scientific and engineering plots") | |
1921 | (description "GSEGrafix is an application which produces high-quality graphical | |
1922 | plots for science and engineering. Plots are specified via simple ASCII | |
1923 | parameter files and data files and are presented in an anti-aliased GNOME | |
1924 | canvas. The program supports rectangular two-dimensional plots, histograms, | |
1925 | polar-axis plots and three-dimensional plots. Plots can be printed or saved | |
1926 | to BMP, JPEG or PNG image formats.") | |
1927 | (license license:gpl3+))) | |
8731e527 JD |
1928 | |
1929 | (define-public maxima | |
1930 | (package | |
1931 | (name "maxima") | |
4a652c78 | 1932 | (version "5.39.0") |
8731e527 JD |
1933 | (source |
1934 | (origin | |
1935 | (method url-fetch) | |
1936 | (uri (string-append "mirror://sourceforge/maxima/Maxima-source/" | |
1937 | version "-source/" name "-" version ".tar.gz")) | |
1938 | (sha256 | |
1939 | (base32 | |
4a652c78 | 1940 | "1cvignn5y6qzrby6qb885yc8zdcdqdr1d50vcvc3gapw2f0gk3zm")) |
fc1adab1 | 1941 | (patches (search-patches "maxima-defsystem-mkdir.patch")))) |
8731e527 | 1942 | (build-system gnu-build-system) |
df354a77 FB |
1943 | (inputs |
1944 | `(("gcl" ,gcl) | |
1945 | ("gnuplot" ,gnuplot) ;for plots | |
f36afe4d | 1946 | ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima' |
df354a77 FB |
1947 | (native-inputs |
1948 | `(("texinfo" ,texinfo) | |
ccbc5758 KK |
1949 | ("perl" ,perl) |
1950 | ("python" ,python))) | |
8731e527 | 1951 | (arguments |
df354a77 FB |
1952 | `(#:configure-flags |
1953 | (list "--enable-gcl" | |
1954 | (string-append "--with-posix-shell=" | |
1955 | (assoc-ref %build-inputs "bash") | |
1956 | "/bin/sh") | |
1957 | (string-append "--with-wish=" | |
1958 | (assoc-ref %build-inputs "tk") | |
1959 | "/bin/wish" | |
1960 | (let ((v ,(package-version tk))) | |
1961 | (string-take v (string-index-right v #\.))))) | |
df354a77 | 1962 | ;; By default Maxima attempts to write temporary files to |
77af7b24 MW |
1963 | ;; '/tmp/nix-build-maxima-*', which won't exist at run time. |
1964 | ;; Work around that. | |
df354a77 | 1965 | #:make-flags (list "TMPDIR=/tmp") |
df354a77 | 1966 | #:phases (alist-cons-before |
8731e527 | 1967 | 'check 'pre-check |
df354a77 | 1968 | (lambda _ |
8731e527 | 1969 | (chmod "src/maxima" #o555)) |
f36afe4d FB |
1970 | ;; Make sure the doc and emacs files are found in the |
1971 | ;; standard location. Also configure maxima to find gnuplot | |
1972 | ;; without having it on the PATH. | |
1973 | (alist-cons-after | |
1974 | 'install 'post-install | |
1975 | (lambda* (#:key outputs inputs #:allow-other-keys) | |
1976 | (let* ((gnuplot (assoc-ref inputs "gnuplot")) | |
1977 | (out (assoc-ref outputs "out")) | |
1978 | (datadir (string-append out "/share/maxima/" ,version))) | |
1979 | (with-directory-excursion out | |
1980 | (mkdir-p "share/emacs") | |
1981 | (mkdir-p "share/doc") | |
1982 | (symlink | |
1983 | (string-append datadir "/emacs/") | |
1984 | (string-append out "/share/emacs/site-lisp")) | |
1985 | (symlink | |
1986 | (string-append datadir "/doc/") | |
1987 | (string-append out "/share/doc/maxima")) | |
1988 | (with-atomic-file-replacement | |
1989 | (string-append datadir "/share/maxima-init.lisp") | |
1990 | (lambda (in out) | |
1991 | (format out "~a ~s~a~%" | |
1992 | "(setf $gnuplot_command " | |
1993 | (string-append gnuplot "/bin/gnuplot") ")") | |
1994 | (dump-port in out)))))) | |
1995 | %standard-phases)))) | |
8731e527 JD |
1996 | (home-page "http://maxima.sourceforge.net") |
1997 | (synopsis "Numeric and symbolic expression manipulation") | |
1998 | (description "Maxima is a system for the manipulation of symbolic and | |
1999 | numerical expressions. It yields high precision numeric results by using | |
2000 | exact fractions, arbitrary precision integers, and variable precision floating | |
e881752c | 2001 | point numbers.") |
8731e527 JD |
2002 | ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+. |
2003 | ;; Others simply say "GNU General Public License" without stating a | |
2004 | ;; version (which implicitly means gpl1+). | |
2005 | ;; At least one file (src/maxima.asd) says "version 2." | |
2006 | ;; GPLv2 only is therefore the smallest subset. | |
f36afe4d | 2007 | (license license:gpl2))) |
ec322be2 | 2008 | |
9aafbc0c MW |
2009 | (define-public wxmaxima |
2010 | (package | |
2011 | (name "wxmaxima") | |
a995251d FB |
2012 | ;; Versions 16.12.0 to 16.12.2 have a bug which causes output lines to |
2013 | ;; overlap. See <https://debbugs.gnu.org/25793> | |
2014 | (version "16.04.2") | |
9aafbc0c MW |
2015 | (source |
2016 | (origin | |
2017 | (method url-fetch) | |
2018 | (uri (string-append "mirror://sourceforge/wxmaxima/wxMaxima/" | |
2019 | version "/" name "-" version ".tar.gz")) | |
2020 | (sha256 | |
2021 | (base32 | |
a995251d | 2022 | "1fpqzk1921isiqrpgpf433ldq41924qs9sy99fl1zn5661b2l73n")))) |
9aafbc0c MW |
2023 | (build-system gnu-build-system) |
2024 | (inputs | |
2025 | `(("wxwidgets" ,wxwidgets) | |
de477809 SB |
2026 | ("maxima" ,maxima) |
2027 | ;; Runtime support. | |
2028 | ("adwaita-icon-theme" ,adwaita-icon-theme) | |
2029 | ("gtk+" ,gtk+) | |
2030 | ("shared-mime-info" ,shared-mime-info))) | |
9aafbc0c MW |
2031 | (arguments |
2032 | `(#:phases (modify-phases %standard-phases | |
2033 | (add-after | |
2034 | 'install 'wrap-program | |
2035 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
2036 | (wrap-program (string-append (assoc-ref outputs "out") | |
2037 | "/bin/wxmaxima") | |
2038 | `("PATH" ":" prefix | |
2039 | (,(string-append (assoc-ref inputs "maxima") | |
de477809 SB |
2040 | "/bin"))) |
2041 | ;; For GtkFileChooserDialog. | |
2042 | `("GSETTINGS_SCHEMA_DIR" = | |
2043 | (,(string-append (assoc-ref inputs "gtk+") | |
2044 | "/share/glib-2.0/schemas"))) | |
2045 | `("XDG_DATA_DIRS" ":" prefix | |
2046 | (;; Needed by gdk-pixbuf to know supported icon formats. | |
2047 | ,(string-append | |
2048 | (assoc-ref inputs "shared-mime-info") "/share") | |
2049 | ;; The default icon theme of GTK+. | |
2050 | ,(string-append | |
2051 | (assoc-ref inputs "adwaita-icon-theme") "/share")))) | |
9aafbc0c MW |
2052 | #t))))) |
2053 | (home-page "https://andrejv.github.io/wxmaxima/") | |
2054 | (synopsis "Graphical user interface for the Maxima computer algebra system") | |
2055 | (description | |
2056 | "wxMaxima is a graphical user interface for the Maxima computer algebra | |
2057 | system. It eases the use of Maxima by making most of its commands available | |
2058 | through a menu system and by providing input dialogs for commands that require | |
2059 | more than one argument. It also implements its own display engine that | |
2060 | outputs mathematical symbols directly instead of depicting them with ASCII | |
2061 | characters. | |
2062 | ||
2063 | wxMaxima also features 2D and 3D inline plots, simple animations, mixing of | |
2064 | text and mathematical calculations to create documents, exporting of input and | |
2065 | output to TeX, and a browser for Maxima's manual including command index and | |
2066 | full text searching.") | |
2067 | (license license:gpl2+))) | |
2068 | ||
b15e47f9 RW |
2069 | (define-public armadillo |
2070 | (package | |
2071 | (name "armadillo") | |
b1c1f4d0 | 2072 | (version "7.600.2") |
b15e47f9 RW |
2073 | (source (origin |
2074 | (method url-fetch) | |
2075 | (uri (string-append "mirror://sourceforge/arma/armadillo-" | |
7397cd9e | 2076 | version ".tar.xz")) |
b15e47f9 RW |
2077 | (sha256 |
2078 | (base32 | |
b1c1f4d0 | 2079 | "0bac9y46m61zxinj51l82w06v01ra9vw7a9j6rrwdjhznkkdb437")))) |
b15e47f9 RW |
2080 | (build-system cmake-build-system) |
2081 | (arguments `(#:tests? #f)) ;no test target | |
2082 | (inputs | |
2083 | `(("openblas" ,openblas) | |
2084 | ("lapack" ,lapack) | |
2085 | ("arpack" ,arpack-ng))) | |
2086 | (home-page "http://arma.sourceforge.net/") | |
2087 | (synopsis "C++ linear algebra library") | |
2088 | (description | |
2089 | "Armadillo is a C++ linear algebra library, aiming towards a good balance | |
2090 | between speed and ease of use. It is useful for algorithm development | |
2091 | directly in C++, or quick conversion of research code into production | |
2092 | environments. It can be used for machine learning, pattern recognition, | |
2093 | signal processing, bioinformatics, statistics, econometrics, etc. The library | |
2094 | provides efficient classes for vectors, matrices and cubes, as well as 150+ | |
2095 | associated functions (eg. contiguous and non-contiguous submatrix views).") | |
2096 | (license license:mpl2.0))) | |
2097 | ||
e22d4ca4 RW |
2098 | (define-public armadillo-for-rcpparmadillo |
2099 | (package (inherit armadillo) | |
a8e45b32 | 2100 | (version "7.600.1") |
e22d4ca4 RW |
2101 | (source (origin |
2102 | (method url-fetch) | |
2103 | (uri (string-append "mirror://sourceforge/arma/armadillo-" | |
5e675072 | 2104 | version ".tar.xz")) |
e22d4ca4 RW |
2105 | (sha256 |
2106 | (base32 | |
a8e45b32 | 2107 | "1dxgfd2r9lbh24nszvqm2lag439s0srxaf1l86f6ww6waqm5r8zk")))))) |
e22d4ca4 | 2108 | |
279663ef | 2109 | (define-public muparser |
d7cff656 LF |
2110 | ;; When switching download sites, muparser re-issued a 2.2.5 release with a |
2111 | ;; different hash. In order to make `guix package --upgrade` work correctly, | |
2112 | ;; we set a Guix packaging revision. | |
2113 | ;; When the next version of muparser is released, we can remove | |
2114 | ;; UPSTREAM-VERSION and REVISION and use the plain VERSION. | |
2115 | (let ((upstream-version "2.2.5") | |
2116 | (revision "2")) | |
2117 | (package | |
2118 | (name "muparser") | |
2119 | (version (string-append upstream-version "-" revision)) | |
2120 | (source | |
2121 | (origin | |
2122 | (method url-fetch) | |
2123 | (uri (string-append "https://github.com/beltoforion/muparser/archive/v" | |
2124 | upstream-version ".tar.gz")) | |
2125 | (file-name (string-append name "-" version ".tar.gz")) | |
2126 | (sha256 | |
2127 | (base32 | |
2128 | "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6")))) | |
2129 | (build-system gnu-build-system) | |
2130 | (arguments | |
2131 | `(#:configure-flags '("--enable-samples=no") | |
2132 | #:tests? #f)) ;no "check" target | |
2133 | (home-page "http://muparser.beltoforion.de/") | |
2134 | (synopsis "Fast parser library for mathematical expressions") | |
2135 | (description | |
2136 | "muParser is an extensible high performance math parser library. It is | |
2137 | based on transforming an expression into a bytecode and precalculating constant | |
2138 | parts of it.") | |
2139 | (license license:expat)))) | |
279663ef | 2140 | |
e73b49fb RW |
2141 | (define-public openblas |
2142 | (package | |
2143 | (name "openblas") | |
883d0a7d | 2144 | (version "0.2.19") |
e73b49fb RW |
2145 | (source |
2146 | (origin | |
2147 | (method url-fetch) | |
2148 | (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v" | |
2149 | version)) | |
2150 | (file-name (string-append name "-" version ".tar.gz")) | |
2151 | (sha256 | |
2152 | (base32 | |
883d0a7d | 2153 | "071zqnmnxhh0c9phzyn3f198yxa0hjxda7016azdbq2056sm70w7")))) |
e73b49fb RW |
2154 | (build-system gnu-build-system) |
2155 | (arguments | |
5b5ea159 | 2156 | `(#:tests? #f ;no "check" target |
bd0b4379 RW |
2157 | ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no |
2158 | ;; TARGET is specified, OpenBLAS will tune itself to the build host, so | |
2159 | ;; we need to disable substitutions. | |
71923a91 AE |
2160 | #:substitutable? |
2161 | ,(let ((system (or (%current-target-system) (%current-system)))) | |
2162 | (or (string-prefix? "x86_64" system) | |
bd0b4379 RW |
2163 | (string-prefix? "i686" system) |
2164 | (string-prefix? "mips" system))) | |
e73b49fb RW |
2165 | #:make-flags |
2166 | (list (string-append "PREFIX=" (assoc-ref %outputs "out")) | |
2167 | "SHELL=bash" | |
af5b817e RW |
2168 | "NO_LAPACK=1" |
2169 | ;; Build the library for all supported CPUs. This allows | |
2170 | ;; switching CPU targets at runtime with the environment variable | |
2171 | ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type. | |
71923a91 AE |
2172 | ;; Unfortunately, this is not supported on non-x86 architectures, |
2173 | ;; where it leads to failed builds. | |
2174 | ,@(let ((system (or (%current-target-system) (%current-system)))) | |
8a637e79 RW |
2175 | (cond |
2176 | ((or (string-prefix? "x86_64" system) | |
71923a91 | 2177 | (string-prefix? "i686" system)) |
8a637e79 RW |
2178 | '("DYNAMIC_ARCH=1")) |
2179 | ;; On MIPS we force the "SICORTEX" TARGET, as for the other | |
2180 | ;; two available MIPS targets special extended instructions | |
2181 | ;; for Loongson cores are used. | |
2182 | ((string-prefix? "mips" system) | |
2183 | '("TARGET=SICORTEX")) | |
2184 | (else '())))) | |
e73b49fb RW |
2185 | ;; no configure script |
2186 | #:phases (alist-delete 'configure %standard-phases))) | |
2187 | (inputs | |
19afbea1 | 2188 | `(("fortran" ,gfortran))) |
e73b49fb RW |
2189 | (native-inputs |
2190 | `(("cunit" ,cunit) | |
2191 | ("perl" ,perl))) | |
2192 | (home-page "http://www.openblas.net/") | |
2193 | (synopsis "Optimized BLAS library based on GotoBLAS") | |
2194 | (description | |
2195 | "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.") | |
2196 | (license license:bsd-3))) | |
2197 | ||
e1605e36 RW |
2198 | (define-public openlibm |
2199 | (package | |
2200 | (name "openlibm") | |
26f6e565 | 2201 | (version "0.5.1") |
e1605e36 RW |
2202 | (source |
2203 | (origin | |
2204 | (method url-fetch) | |
2205 | (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v" | |
2206 | version ".tar.gz")) | |
2207 | (file-name (string-append name "-" version ".tar.gz")) | |
2208 | (sha256 | |
2209 | (base32 | |
26f6e565 | 2210 | "11czx2z7nh6dfpz45s3xl7v38hw36jxzxfvny454bk3if14pfakq")))) |
e1605e36 RW |
2211 | (build-system gnu-build-system) |
2212 | (arguments | |
2213 | `(#:make-flags | |
2214 | (list (string-append "prefix=" (assoc-ref %outputs "out"))) | |
2215 | #:phases | |
2216 | ;; no configure script | |
2217 | (alist-delete 'configure %standard-phases) | |
2218 | #:tests? #f)) ;the tests are part of the default target | |
2219 | (home-page "http://openlibm.org/") | |
2220 | (synopsis "Portable C mathematical library (libm)") | |
2221 | (description | |
2222 | "OpenLibm is an effort to have a high quality, portable, standalone C | |
2223 | mathematical library (libm). It can be used standalone in applications and | |
2224 | programming language implementations. The project was born out of a need to | |
e881752c | 2225 | have a good libm for the Julia programming language that worked consistently |
e1605e36 RW |
2226 | across compilers and operating systems, and in 32-bit and 64-bit |
2227 | environments.") | |
538c0e3b EF |
2228 | ;; Each architecture has its own make target, and there is none for mips. |
2229 | (supported-systems (delete "mips64el-linux" %supported-systems)) | |
e1605e36 RW |
2230 | ;; See LICENSE.md for details. |
2231 | (license (list license:expat | |
2232 | license:isc | |
2233 | license:bsd-2 | |
2234 | license:public-domain | |
2235 | license:lgpl2.1+)))) | |
2236 | ||
e62be58f RW |
2237 | (define-public openspecfun |
2238 | (package | |
2239 | (name "openspecfun") | |
49f54a74 | 2240 | (version "0.5.2") |
e62be58f RW |
2241 | (source |
2242 | (origin | |
2243 | (method url-fetch) | |
2244 | (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v" | |
2245 | version ".tar.gz")) | |
2246 | (file-name (string-append name "-" version ".tar.gz")) | |
2247 | (sha256 | |
2248 | (base32 | |
49f54a74 | 2249 | "1y5b2h6f2k72536kym3vzy3li3bhpd23x463g7hdmjdi3cncavz1")))) |
e62be58f RW |
2250 | (build-system gnu-build-system) |
2251 | (arguments | |
2252 | '(#:tests? #f ;no "check" target | |
2253 | #:make-flags | |
2254 | (list (string-append "prefix=" (assoc-ref %outputs "out"))) | |
2255 | ;; no configure script | |
2256 | #:phases (alist-delete 'configure %standard-phases))) | |
2257 | (inputs | |
19afbea1 | 2258 | `(("fortran" ,gfortran))) |
e62be58f RW |
2259 | (home-page "https://github.com/JuliaLang/openspecfun") |
2260 | (synopsis "Collection of special mathematical functions") | |
2261 | (description | |
2262 | "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a | |
2263 | portable package for Bessel Functions of a Complex Argument and Nonnegative | |
2264 | Order; it contains subroutines for computing Bessel functions and Airy | |
2265 | functions. Faddeeva allows computing the various error functions of arbitrary | |
2266 | complex arguments (Faddeeva function, error function, complementary error | |
2267 | function, scaled complementary error function, imaginary error function, and | |
2268 | Dawson function); given these, one can also easily compute Voigt functions, | |
2269 | Fresnel integrals, and similar related functions as well.") | |
2270 | ;; Faddeeva is released under the Expat license; AMOS is included as | |
2271 | ;; public domain software. | |
2272 | (license (list license:expat license:public-domain)))) | |
2273 | ||
2742f87e RW |
2274 | (define-public suitesparse |
2275 | (package | |
2276 | (name "suitesparse") | |
2277 | (version "4.4.3") | |
2278 | (source | |
2279 | (origin | |
2280 | (method url-fetch) | |
2281 | (uri (string-append | |
2282 | "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-" | |
2283 | version ".tar.gz")) | |
2284 | (sha256 | |
2285 | (base32 | |
2286 | "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5")))) | |
2287 | (build-system gnu-build-system) | |
2288 | (arguments | |
2289 | '(#:parallel-build? #f ;cholmod build fails otherwise | |
2290 | #:tests? #f ;no "check" target | |
2291 | #:make-flags | |
2292 | (list "CC=gcc" | |
2293 | "BLAS=-lblas" | |
2294 | "TBB=-ltbb" | |
2295 | "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used | |
2296 | (string-append "INSTALL_LIB=" | |
2297 | (assoc-ref %outputs "out") "/lib") | |
2298 | (string-append "INSTALL_INCLUDE=" | |
2299 | (assoc-ref %outputs "out") "/include")) | |
2300 | #:phases | |
2301 | (alist-cons-before | |
2302 | 'install 'prepare-out | |
2303 | ;; README.txt states that the target directories must exist prior to | |
2304 | ;; running "make install". | |
2305 | (lambda _ | |
2306 | (mkdir-p (string-append (assoc-ref %outputs "out") "/lib")) | |
2307 | (mkdir-p (string-append (assoc-ref %outputs "out") "/include"))) | |
2308 | ;; no configure script | |
2309 | (alist-delete 'configure %standard-phases)))) | |
2310 | (inputs | |
2311 | `(("tbb" ,tbb) | |
2312 | ("lapack" ,lapack))) | |
2313 | (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html") | |
2314 | (synopsis "Suite of sparse matrix software") | |
2315 | (description | |
2316 | "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK, | |
2317 | multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR, | |
2318 | multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit | |
2319 | simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and | |
2320 | CXSparse, a concise sparse Cholesky factorization package; and many other | |
2321 | packages.") | |
2322 | ;; LGPLv2.1+: | |
2323 | ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL | |
2324 | ;; GPLv2+: | |
2325 | ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK | |
2326 | (license (list license:gpl2+ license:lgpl2.1+)))) | |
2327 | ||
ec322be2 FB |
2328 | (define-public atlas |
2329 | (package | |
2330 | (name "atlas") | |
3c98ac02 | 2331 | (version "3.10.3") |
ec322be2 FB |
2332 | (source (origin |
2333 | (method url-fetch) | |
de67e922 LF |
2334 | (uri (string-append "mirror://sourceforge/math-atlas/Stable/" |
2335 | version "/atlas" version ".tar.bz2")) | |
ec322be2 FB |
2336 | (sha256 |
2337 | (base32 | |
3c98ac02 | 2338 | "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216")))) |
ec322be2 FB |
2339 | (build-system gnu-build-system) |
2340 | (home-page "http://math-atlas.sourceforge.net/") | |
19afbea1 | 2341 | (inputs `(("gfortran" ,gfortran) |
ec322be2 FB |
2342 | ("lapack-tar" ,(package-source lapack)))) |
2343 | (outputs '("out" "doc")) | |
01480b9e FB |
2344 | ;; For the moment we drop support for MIPS at it fails to compile. See |
2345 | ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html | |
2346 | (supported-systems (delete "mips64el-linux" %supported-systems)) | |
ec322be2 FB |
2347 | (arguments |
2348 | `(#:parallel-build? #f | |
2349 | #:parallel-tests? #f | |
f15615b1 LC |
2350 | |
2351 | ;; ATLAS tunes itself for the machine it is built on, as explained at | |
2352 | ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>. | |
2353 | ;; For this reason, we want users to build it locally instead of using | |
2354 | ;; substitutes. | |
2355 | #:substitutable? #f | |
2356 | ||
ec322be2 FB |
2357 | #:modules ((srfi srfi-26) |
2358 | (srfi srfi-1) | |
2359 | (guix build gnu-build-system) | |
2360 | (guix build utils)) | |
40029cbe | 2361 | #:configure-flags |
ec322be2 FB |
2362 | `(;; Generate position independent code suitable for dynamic libraries |
2363 | ;; and use WALL timer to get more accurate timing. | |
2364 | "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL" | |
2365 | ;; Set word width. | |
2366 | "-b" | |
2367 | ,,(if (string-match "64" (%current-system)) | |
2368 | "64" | |
2369 | "32") | |
2370 | ;; Disable parallel build as it gives errors: atlas_pthread.h is | |
2371 | ;; needed to compile C files before it is generated. | |
2372 | "-Ss" "pmake" "make -j 1" | |
af89a667 FB |
2373 | ;; Probe is failing for MIPS. We therefore define the system |
2374 | ;; architecture explicitly by setting (-A) MACHINETYPE = 49 | |
2375 | ;; 'MIPSR1xK' and (-V) ISA = 1 'none'. | |
2376 | ,,@(if (string-prefix? "mips" (%current-system)) | |
2377 | (list "-A" "49" "-V" "1") | |
2378 | (list)) | |
ec322be2 FB |
2379 | ;; Generate shared libraries. |
2380 | "--shared" | |
2381 | ;; Build a full LAPACK library. | |
2382 | ,(string-append "--with-netlib-lapack-tarfile=" | |
2383 | (assoc-ref %build-inputs "lapack-tar"))) | |
2384 | #:phases | |
e5b4b96b EF |
2385 | (modify-phases %standard-phases |
2386 | (add-after 'install 'install-doc | |
2387 | (lambda* (#:key outputs inputs #:allow-other-keys) | |
2388 | (let ((doc (string-append (assoc-ref outputs "doc") | |
2389 | "/share/doc/atlas"))) | |
2390 | (mkdir-p doc) | |
2391 | (fold (lambda (file previous) | |
2392 | (and previous (zero? (system* "cp" file doc)))) | |
2393 | #t (find-files "../ATLAS/doc" ".*"))))) | |
2394 | (add-after 'check 'check-pt | |
2395 | (lambda _ (zero? (system* "make" "ptcheck")))) | |
2396 | ;; Fix files required to run configure. | |
2397 | (add-before 'configure 'fix-/bin/sh | |
ec322be2 FB |
2398 | (lambda _ |
2399 | ;; Use `sh', not `/bin/sh'. | |
2400 | (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c") | |
2401 | (("/bin/sh") | |
e5b4b96b EF |
2402 | "sh")))) |
2403 | ;; Fix /bin/sh in generated make files. | |
2404 | (add-after 'configure 'fix-/bin/sh-in-generated-files | |
2405 | (lambda _ | |
2406 | (substitute* (find-files "." "^[Mm]ake\\.inc.*") | |
2407 | (("/bin/sh") | |
2408 | "sh")))) | |
2409 | ;; ATLAS configure program does not accepts the default flags | |
2410 | ;; passed by the 'gnu-build-system'. | |
2411 | (replace 'configure | |
2412 | (lambda* (#:key native-inputs inputs outputs | |
2413 | (configure-flags '()) | |
2414 | #:allow-other-keys #:rest args) | |
2415 | (let* ((prefix (assoc-ref outputs "out")) | |
2416 | (bash (or (and=> (assoc-ref | |
2417 | (or native-inputs inputs) "bash") | |
2418 | (cut string-append <> "/bin/bash")) | |
2419 | "/bin/sh")) | |
2420 | (flags `(,(string-append "--prefix=" prefix) | |
2421 | ,@configure-flags)) | |
2422 | (abs-srcdir (getcwd)) | |
2423 | (srcdir (string-append "../" (basename abs-srcdir)))) | |
2424 | (format #t "source directory: ~s (relative from build: ~s)~%" | |
2425 | abs-srcdir srcdir) | |
2426 | (mkdir "../build") | |
2427 | (chdir "../build") | |
2428 | (format #t "build directory: ~s~%" (getcwd)) | |
2429 | (format #t "configure flags: ~s~%" flags) | |
2430 | (zero? (apply system* bash | |
2431 | (string-append srcdir "/configure") | |
2432 | flags)))))))) | |
ec322be2 FB |
2433 | (synopsis "Automatically Tuned Linear Algebra Software") |
2434 | (description | |
2435 | "ATLAS is an automatically tuned linear algebra software library | |
2436 | providing C and Fortran77 interfaces to a portably efficient BLAS | |
2437 | implementation, as well as a few routines from LAPACK. | |
2438 | ||
f15615b1 LC |
2439 | Optimization occurs at build time. For this reason, the library is built on |
2440 | the machine where it is installed, without resorting to pre-built substitutes. | |
ec322be2 | 2441 | |
f15615b1 | 2442 | Before building the library, CPU throttling should be disabled. This can be |
d97c429a | 2443 | done in the BIOS, or, on GNU/Linux, with the following command: |
ec322be2 | 2444 | |
8e9ba611 | 2445 | @example |
d97c429a | 2446 | # cpupower --governor performance |
8e9ba611 | 2447 | @end example |
ec322be2 | 2448 | |
d97c429a | 2449 | Failure to do so will result in a library with poor performance.") |
ec322be2 | 2450 | (license license:bsd-3))) |
c12efc72 AE |
2451 | |
2452 | (define-public glm | |
2453 | (package | |
2454 | (name "glm") | |
2455 | (version "0.9.6.3") | |
2456 | (source | |
2457 | (origin | |
2458 | (method url-fetch) | |
de67e922 LF |
2459 | (uri (string-append "mirror://sourceforge/ogl-math/glm-" version |
2460 | "/glm-" version ".zip")) | |
c12efc72 AE |
2461 | (sha256 |
2462 | (base32 | |
2463 | "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l")))) | |
2464 | (build-system cmake-build-system) | |
2465 | (native-inputs | |
2466 | `(("unzip" ,unzip))) | |
2467 | (home-page "http://glm.g-truc.net") | |
2468 | (synopsis "OpenGL Mathematics library") | |
2469 | (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics | |
2470 | library for graphics software based on the OpenGL Shading Language (GLSL) | |
2471 | specifications.") | |
2472 | (license license:expat))) | |
7f18257b AE |
2473 | |
2474 | (define-public lpsolve | |
2475 | (package | |
2476 | (name "lpsolve") | |
2477 | (version "5.5.2.0") | |
2478 | (source | |
2479 | (origin | |
2480 | (method url-fetch) | |
2481 | (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version | |
2482 | "/lp_solve_" version "_source.tar.gz")) | |
2483 | (sha256 | |
2484 | (base32 | |
2485 | "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq")) | |
2486 | (modules '((guix build utils))) | |
2487 | (snippet | |
2488 | '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc") | |
2489 | (("^c=cc") "c=gcc") | |
2490 | ;; Pretend to be on a 64 bit platform to obtain a common directory | |
2491 | ;; name for the build results on all architectures; nothing else | |
2492 | ;; seems to depend on it. | |
5dbfbef7 LC |
2493 | (("^PLATFORM=.*$") "PLATFORM=ux64\n") |
2494 | ||
2495 | ;; The check for 'isnan' as it is written fails with | |
2496 | ;; "non-floating-point argument in call to function | |
2497 | ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro | |
2498 | ;; definition, which in turn leads to bad things. Fix the feature | |
2499 | ;; test. | |
2500 | (("isnan\\(0\\)") "isnan(0.)"))))) | |
7f18257b AE |
2501 | (build-system gnu-build-system) |
2502 | (arguments | |
2503 | `(#:tests? #f ; no check target | |
2504 | #:phases | |
2505 | (modify-phases %standard-phases | |
2506 | (delete 'configure) | |
2507 | (replace 'build | |
2508 | (lambda _ | |
6689d094 LC |
2509 | (and (with-directory-excursion "lpsolve55" |
2510 | (zero? (system* "bash" "ccc"))) | |
2511 | (with-directory-excursion "lp_solve" | |
2512 | (zero? (system* "bash" "ccc")))))) | |
7f18257b AE |
2513 | (replace 'install |
2514 | (lambda* (#:key outputs #:allow-other-keys) | |
2515 | (let* ((out (assoc-ref outputs "out")) | |
2516 | (bin (string-append out "/bin")) | |
2517 | (lib (string-append out "/lib")) | |
2518 | ;; This is where LibreOffice expects to find the header | |
2519 | ;; files, and where they are installed by Debian. | |
2520 | (include (string-append out "/include/lpsolve"))) | |
2521 | (mkdir-p lib) | |
2522 | (copy-file "lpsolve55/bin/ux64/liblpsolve55.a" | |
2523 | (string-append lib "/liblpsolve55.a")) | |
2524 | (copy-file "lpsolve55/bin/ux64/liblpsolve55.so" | |
2525 | (string-append lib "/liblpsolve55.so")) | |
96c46210 LC |
2526 | (install-file "lp_solve/bin/ux64/lp_solve" bin) |
2527 | ||
7f18257b AE |
2528 | ;; Install a subset of the header files as on Debian |
2529 | ;; (plus lp_bit.h, which matches the regular expression). | |
96c46210 LC |
2530 | (for-each (lambda (name) |
2531 | (install-file name include)) | |
2532 | (find-files "." "lp_[HMSa-z].*\\.h$")) | |
7f18257b | 2533 | (with-directory-excursion "shared" |
96c46210 LC |
2534 | (for-each (lambda (name) |
2535 | (install-file name include)) | |
2536 | (find-files "." "\\.h$"))) | |
7f18257b AE |
2537 | #t)))))) |
2538 | (home-page "http://lpsolve.sourceforge.net/") | |
2539 | (synopsis "Mixed integer linear programming (MILP) solver") | |
2540 | (description | |
2541 | "lp_solve is a mixed integer linear programming solver based on the | |
2542 | revised simplex and the branch-and-bound methods.") | |
2543 | (license license:lgpl2.1+))) | |
a17d4564 EB |
2544 | |
2545 | (define-public dealii | |
2546 | (package | |
2547 | (name "dealii") | |
101e8472 | 2548 | (version "8.4.1") |
a17d4564 EB |
2549 | (source |
2550 | (origin | |
2551 | (method url-fetch) | |
2552 | (uri (string-append "https://github.com/dealii/dealii/releases/" | |
2553 | "download/v" version "/dealii-" version ".tar.gz")) | |
2554 | (sha256 | |
2555 | (base32 | |
101e8472 | 2556 | "1bdksvvyp1rj37df1ndh8j3x9nzpc3sazw8nd0hzvnlw0qnyk800")) |
a17d4564 EB |
2557 | (modules '((guix build utils))) |
2558 | (snippet | |
2559 | ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost | |
2560 | '(delete-file-recursively "bundled")))) | |
2561 | (build-system cmake-build-system) | |
2562 | (inputs | |
2563 | `(("tbb" ,tbb) | |
2564 | ("zlib" ,zlib) | |
2565 | ("boost" ,boost) | |
2566 | ("p4est" ,p4est) | |
2567 | ("blas" ,openblas) | |
2568 | ("lapack" ,lapack) | |
2569 | ("arpack" ,arpack-ng) | |
2570 | ("muparser" ,muparser) | |
2571 | ("gfortran" ,gfortran) | |
2572 | ("suitesparse" ,suitesparse))) ;for UMFPACK | |
2573 | (arguments | |
2574 | `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease | |
2575 | #:configure-flags '("-DCOMPAT_FILES=OFF") ;Follow new directory structure | |
2576 | #:phases (modify-phases %standard-phases | |
2577 | (add-after | |
2578 | 'install 'hint-example-prefix | |
2579 | ;; Set Cmake hints in examples so that they can find this | |
2580 | ;; deal.II when configuring. | |
2581 | (lambda* (#:key outputs #:allow-other-keys) | |
2582 | (let* ((out (assoc-ref %outputs "out")) | |
2583 | (exmpl (string-append out "/share/doc" | |
2584 | "/dealii/examples"))) | |
2585 | (substitute* (find-files exmpl "CMakeLists.txt") | |
2586 | (("([[:space:]]*HINTS.*)\n" _ line) | |
2587 | (string-append line " $ENV{HOME}/.guix-profile " | |
2588 | out "\n"))) | |
2589 | #t)))))) | |
2590 | (home-page "https://www.dealii.org") | |
2591 | (synopsis "Finite element library") | |
2592 | (description | |
2593 | "Deal.II is a C++ program library targeted at the computational solution | |
2594 | of partial differential equations using adaptive finite elements. The main | |
2595 | aim of deal.II is to enable rapid development of modern finite element codes, | |
2596 | using among other aspects adaptive meshes and a wide array of tools often used | |
2597 | in finite element programs.") | |
2598 | (license license:lgpl2.1+))) | |
2599 | ||
2600 | (define-public dealii-openmpi | |
2601 | (package (inherit dealii) | |
2602 | (name "dealii-openmpi") | |
2603 | (inputs | |
2604 | `(("mpi" ,openmpi) | |
2605 | ;;Supported only with MPI: | |
2606 | ("p4est" ,p4est-openmpi) | |
2607 | ("petsc" ,petsc-openmpi) | |
2608 | ("slepc" ,slepc-openmpi) | |
2609 | ("metis" ,metis) ;for MUMPS | |
2610 | ("scalapack" ,scalapack) ;for MUMPS | |
2611 | ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings | |
2612 | ("arpack" ,arpack-ng-openmpi) | |
2613 | ,@(fold alist-delete (package-inputs dealii) | |
2614 | '("p4est" "arpack")))) | |
2615 | (arguments | |
2616 | (substitute-keyword-arguments (package-arguments dealii) | |
2617 | ((#:configure-flags cf) | |
2618 | ``("-DMPI_C_COMPILER=mpicc" | |
2619 | "-DMPI_CXX_COMPILER=mpicxx" | |
2620 | "-DMPI_Fortran_COMPILER=mpifort" | |
2621 | ,@,cf)))) | |
2622 | (synopsis "Finite element library (with MPI support)"))) | |
194c7f95 AE |
2623 | |
2624 | (define-public flann | |
2625 | (package | |
2626 | (name "flann") | |
2627 | (version "1.8.4") | |
2628 | (source | |
2629 | (origin | |
2630 | (method url-fetch) | |
2631 | (uri | |
2632 | (string-append | |
2633 | "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-" | |
2634 | version "-src.zip")) | |
2635 | (sha256 | |
2636 | (base32 | |
2637 | "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz")))) | |
2638 | (build-system cmake-build-system) | |
2639 | (native-inputs | |
2640 | `(("unzip" ,unzip))) | |
2641 | (inputs | |
2642 | `(("hdf5" ,hdf5) | |
2643 | ("octave" ,octave) | |
2644 | ("python" ,python-2) ; print syntax | |
2645 | ;; ("python2-numpy" ,python2-numpy) ; only required for the tests | |
2646 | ("zlib" ,zlib))) | |
2647 | (arguments | |
39b30337 LC |
2648 | `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file |
2649 | ;; taken 46 MiB unstripped, and 6 MiB stripped. | |
2650 | #:strip-directories '("lib" "lib64" "libexec" | |
2651 | "bin" "sbin" "share/flann/octave") | |
2652 | ||
9684e30b LC |
2653 | ;; Save 12 MiB by not installing .a files. Passing |
2654 | ;; '-DBUILD_STATIC_LIBS=OFF' has no effect. | |
2655 | #:phases (modify-phases %standard-phases | |
2656 | (add-after 'install 'remove-static-libraries | |
2657 | (lambda* (#:key outputs #:allow-other-keys) | |
2658 | (let* ((out (assoc-ref outputs "out")) | |
2659 | (lib (string-append out "/lib"))) | |
2660 | (for-each delete-file | |
2661 | (find-files lib "\\.a$")) | |
2662 | #t)))) | |
2663 | ||
39b30337 | 2664 | #:tests? #f)) ; The test data are downloaded from the Internet. |
194c7f95 AE |
2665 | (home-page "http://www.cs.ubc.ca/research/flann/") |
2666 | (synopsis "Library for approximate nearest neighbors computation") | |
2667 | (description "FLANN is a library for performing fast approximate | |
2668 | nearest neighbor searches in high dimensional spaces. It implements a | |
2669 | collection of algorithms and a system for automatically choosing the best | |
2670 | algorithm and optimum parameters depending on the dataset. | |
2671 | ||
2672 | FLANN is written in C++ and contains bindings for C, Octave and Python.") | |
2673 | (license (license:non-copyleft "file://COPYING" | |
2674 | "See COPYING in the distribution.")))) | |
d8c97beb EF |
2675 | |
2676 | (define-public wcalc | |
2677 | (package | |
2678 | (name "wcalc") | |
2679 | (version "2.5") | |
2680 | (source | |
2681 | (origin | |
2682 | (method url-fetch) | |
de67e922 LF |
2683 | (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/" |
2684 | "wcalc-" version ".tar.bz2")) | |
d8c97beb EF |
2685 | (sha256 |
2686 | (base32 | |
2687 | "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f")))) | |
2688 | (build-system gnu-build-system) | |
2689 | (inputs | |
2690 | `(("mpfr" ,mpfr) | |
2691 | ("readline" ,readline))) | |
2692 | (home-page "http://w-calc.sourceforge.net/index.php") | |
2693 | (synopsis "Flexible command-line scientific calculator") | |
2694 | (description "Wcalc is a very capable calculator. It has standard functions | |
2695 | (sin, asin, and sinh for example, in either radians or degrees), many | |
2696 | pre-defined constants (pi, e, c, etc.), support for using variables, \"active\" | |
2697 | variables, a command history, hex/octal/binary input and output, unit | |
2698 | conversions, embedded comments, and an expandable expression entry field. It | |
2699 | evaluates expressions using the standard order of operations.") | |
2700 | (license license:gpl2+))) | |
45147b0c FH |
2701 | |
2702 | (define-public xaos | |
2703 | (package | |
2704 | (name "xaos") | |
2705 | (version "3.6") | |
2706 | (source (origin | |
2707 | (method url-fetch) | |
de67e922 LF |
2708 | (uri (string-append "mirror://sourceforge/xaos/XaoS/" version |
2709 | "/xaos-" version ".tar.gz")) | |
45147b0c FH |
2710 | (sha256 |
2711 | (base32 | |
2712 | "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq")))) | |
2713 | (build-system gnu-build-system) | |
b94a6ca0 | 2714 | (native-inputs `(("gettext" ,gettext-minimal))) |
45147b0c FH |
2715 | (inputs `(("libx11" ,libx11) |
2716 | ("zlib" ,zlib) | |
2717 | ("libpng" ,libpng) | |
2718 | ("gsl" ,gsl))) | |
2719 | (arguments | |
2720 | `(#:tests? #f ;no "check" target | |
2721 | #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale"))) | |
2722 | (synopsis "Real-time fractal zoomer") | |
2723 | (description "GNU XaoS is a graphical program that generates fractal | |
2724 | patterns and allows you to zoom in and out of them infinitely in a fluid, | |
2725 | continuous manner. It also includes tutorials that help to explain how fractals | |
2726 | are built. It can generate many different fractal types such as the Mandelbrot | |
2727 | set.") | |
2728 | (home-page "http://www.gnu.org/software/xaos/") | |
2729 | (license license:gpl2+))) | |
528bb464 EB |
2730 | |
2731 | (define-public hypre | |
2732 | (package | |
2733 | (name "hypre") | |
2734 | (version "2.11.0") | |
2735 | (source (origin | |
2736 | (method url-fetch) | |
2737 | (uri (string-append "https://github.com/LLNL/hypre/archive/" | |
2738 | "v" version ".tar.gz")) | |
2739 | (file-name (string-append name "-" version ".tar.gz")) | |
2740 | (sha256 | |
2741 | (base32 | |
2742 | "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m")) | |
2743 | (modules '((guix build utils))) | |
2744 | (snippet | |
2745 | '(begin | |
2746 | ;; Remove use of __DATE__ and __TIME__ for reproducibility; | |
2747 | ;; substitute the tarball creation time. | |
2748 | (substitute* "src/utilities/HYPRE_utilities.h" | |
2749 | (("Date Compiled: .*$") | |
2750 | "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n")) | |
2751 | #t)))) | |
2752 | (build-system gnu-build-system) | |
2753 | (outputs '("out" ;6.1 MiB of headers and libraries | |
2754 | "doc")) ;4.8 MiB of documentation | |
2755 | (native-inputs | |
2756 | `(("doc++" ,doc++) | |
2757 | ("netpbm" ,netpbm) | |
2758 | ("texlive" ,texlive) ;full package required for fonts | |
2759 | ("ghostscript" ,ghostscript))) | |
2760 | (inputs | |
2761 | `(("blas" ,openblas) | |
2762 | ("lapack" ,lapack))) | |
2763 | (arguments | |
2764 | `(#:modules ((srfi srfi-1) | |
2765 | ,@%gnu-build-system-modules) | |
2766 | #:configure-flags '("--enable-shared" | |
2767 | "--disable-fortran" | |
2768 | "--without-MPI" | |
2769 | "--with-openmp" | |
2770 | "--with-fei" | |
2771 | "--with-lapack" | |
2772 | "--with-blas") | |
2773 | #:phases | |
2774 | (modify-phases %standard-phases | |
2775 | (add-before 'configure 'chdir-src | |
2776 | (lambda _ (chdir "src"))) | |
2777 | (replace 'configure | |
2778 | (lambda* (#:key build target configure-flags | |
2779 | #:allow-other-keys #:rest args) | |
2780 | (let* ((configure (assoc-ref %standard-phases 'configure))) | |
2781 | (apply configure | |
2782 | (append args | |
2783 | (list #:configure-flags | |
2784 | (cons (string-append | |
2785 | "--host=" (or target build)) | |
2786 | configure-flags))))))) | |
2787 | (add-after 'build 'build-docs | |
2788 | (lambda _ | |
2789 | (zero? (system* "make" "-Cdocs" "pdf" "html")))) | |
2790 | (replace 'check | |
2791 | (lambda _ | |
2792 | (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib")) | |
2793 | (setenv "PATH" (string-append "." ":" (getenv "PATH"))) | |
2794 | (and (system* "make" "check" "CHECKRUN=") | |
2795 | (fold (lambda (filename result) | |
2796 | (and result | |
2797 | (let ((size (stat:size (stat filename)))) | |
2798 | (when (not (zero? size)) | |
2799 | (format #t "~a size ~d; error indication~%" | |
2800 | filename size)) | |
2801 | (zero? size)))) | |
2802 | #t | |
2803 | (find-files "test" ".*\\.err$"))))) | |
2804 | (add-after 'install 'install-docs | |
2805 | (lambda* (#:key outputs #:allow-other-keys) | |
2806 | ;; Custom install because docs/Makefile doesn't honor ${docdir}. | |
2807 | (let* ((doc (assoc-ref outputs "doc")) | |
2808 | (docdir (string-append doc "/share/doc/hypre-" ,version))) | |
528bb464 EB |
2809 | (with-directory-excursion "docs" |
2810 | (for-each (lambda (base) | |
2811 | (install-file (string-append base ".pdf") docdir) | |
2812 | (copy-recursively base docdir)) ;html docs | |
2813 | '("HYPRE_usr_manual" | |
2814 | "HYPRE_ref_manual"))) | |
2815 | #t)))))) | |
2816 | (home-page "http://www.llnl.gov/casc/hypre/") | |
2817 | (synopsis "Library of solvers and preconditioners for linear equations") | |
2818 | (description | |
2819 | "HYPRE is a software library of high performance preconditioners and | |
2820 | solvers for the solution of large, sparse linear systems of equations. It | |
2821 | features multigrid solvers for both structured and unstructured grid | |
2822 | problems.") | |
2823 | (license license:lgpl2.1))) | |
2824 | ||
2825 | (define-public hypre-openmpi | |
2826 | (package (inherit hypre) | |
2827 | (name "hypre-openmpi") | |
2828 | (inputs | |
2829 | `(("mpi" ,openmpi) | |
2830 | ,@(package-inputs hypre))) | |
2831 | (arguments | |
2832 | (substitute-keyword-arguments (package-arguments hypre) | |
2833 | ((#:configure-flags flags) | |
2834 | ``("--with-MPI" | |
2835 | ,@(delete "--without-MPI" ,flags))))) | |
2836 | (synopsis "Parallel solvers and preconditioners for linear equations") | |
2837 | (description | |
2838 | "HYPRE is a software library of high performance preconditioners and | |
2839 | solvers for the solution of large, sparse linear systems of equations on | |
2840 | parallel computers. It features parallel multigrid solvers for both | |
2841 | structured and unstructured grid problems."))) | |
6c90e183 EB |
2842 | |
2843 | (define-public matio | |
2844 | (package | |
2845 | (name "matio") | |
2846 | (version "1.5.6") | |
2847 | (source | |
2848 | (origin | |
2849 | (method url-fetch) | |
de67e922 | 2850 | (uri (string-append "mirror://sourceforge/matio/matio/" version "/" |
6c90e183 EB |
2851 | "matio-" version ".tar.gz")) |
2852 | (sha256 | |
2853 | (base32 | |
2854 | "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir")))) | |
2855 | (build-system gnu-build-system) | |
2856 | (inputs | |
2857 | `(("zlib" ,zlib) | |
2858 | ("hdf5" ,hdf5))) | |
2859 | (home-page "http://matio.sourceforge.net/") | |
2860 | (synopsis "Library for reading and writing MAT files") | |
2861 | (description "Matio is a library for reading and writing MAT files. It | |
2862 | supports compressed MAT files, as well as newer (version 7.3) MAT files.") | |
2863 | (license license:bsd-2))) | |
d721c83a EB |
2864 | |
2865 | (define-public libhilbert | |
2866 | (package | |
2867 | (name "libhilbert") | |
2868 | (version "0.2-1") | |
2869 | (source | |
2870 | (origin | |
2871 | (method url-fetch) | |
2872 | (uri (string-append "http://web.cs.dal.ca/~chamilto/hilbert/" | |
2873 | "libhilbert-" version ".tar.gz")) | |
2874 | (sha256 | |
2875 | (base32 | |
2876 | "0v48x8405dj95gjn2saja4bzhw86d6zl6d3dg8h7dzac2qr97s34")))) | |
2877 | (build-system gnu-build-system) | |
2878 | (home-page "http://web.cs.dal.ca/~chamilto/hilbert") | |
2879 | (synopsis "Hilbert indices for multidimensional data") | |
2880 | (description "The libhilbert library can efficiently calculate Hilbert | |
2881 | curves and order-preserving representations of Hilbert curve indices that use | |
2882 | the same amount of space as the original point representation. This is useful | |
2883 | when using the Gilbert curve as a space filling curve through a | |
2884 | high-dimensional space where not all demensions have the same cardinality.") | |
2885 | (license license:lgpl2.1+))) | |
517318ad LF |
2886 | |
2887 | (define-public vc | |
2888 | (package | |
2889 | (name "vc") | |
2890 | (version "1.2.0") | |
2891 | (source | |
2892 | (origin (method url-fetch) | |
2893 | (uri (string-append "https://github.com/VcDevel/Vc/releases/" | |
2894 | "download/" version "/Vc-" version ".tar.gz")) | |
2895 | (sha256 | |
2896 | (base32 | |
2897 | "1rh6dhqar3y07n4xqyml0sa0v48qv3ch9dc3yc2in855hlh4vnqi")))) | |
2898 | (build-system cmake-build-system) | |
2899 | (arguments | |
2900 | '(#:configure-flags | |
2901 | '("-DBUILD_TESTING=ON"))) | |
2902 | (synopsis "SIMD vector classes for C++") | |
2903 | (description "Vc provides portable, zero-overhead C++ types for explicitly | |
2904 | data-parallel programming. It is a library designed to ease explicit | |
2905 | vectorization of C++ code. Its types enable explicitly stating data-parallel | |
2906 | operations on multiple values. The parallelism is therefore added via the type | |
2907 | system. Vc has an intuitive API and provides portability between different | |
2908 | compilers and compiler versions as well as portability between different vector | |
2909 | instruction sets. Thus, an application written with Vc can be compiled for: | |
2910 | @enumerate | |
2911 | @item AVX and AVX2 | |
2912 | @item SSE2 upto SSE4.2 or SSE4a | |
2913 | @item Scalar | |
2914 | @item MIC | |
2915 | @item NEON (in development) | |
2916 | @item NVIDIA GPUs / CUDA (in development) | |
2917 | @end enumerate\n") | |
2918 | (home-page "https://github.com/VcDevel/Vc") | |
2919 | (license license:bsd-3))) | |
54052a54 | 2920 | |
2921 | (define-public reducelcs | |
2922 | ;; This is the last commit which is available upstream, no | |
2923 | ;; release happened since 2010. | |
2924 | (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0") | |
2925 | (revision "1")) | |
2926 | (package | |
2927 | (name "reducelcs") | |
2928 | (version (string-append "1.0-" revision "." (string-take commit 7))) | |
2929 | (source | |
2930 | (origin | |
2931 | (method git-fetch) | |
2932 | (uri (git-reference | |
2933 | (url "https://github.com/gdv/Reduce-Expand-for-LCS") | |
2934 | (commit commit))) | |
2935 | (file-name (string-append name "-" version "-checkout")) | |
2936 | (sha256 | |
2937 | (base32 | |
2938 | "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm")))) | |
2939 | (build-system gnu-build-system) | |
2940 | (inputs | |
2941 | `(("openlibm" ,openlibm))) | |
2942 | (arguments | |
2943 | `(#:tests? #f ; no tests | |
2944 | #:phases | |
2945 | (modify-phases %standard-phases | |
2946 | (delete 'configure) ; No configure script exists. | |
2947 | (replace 'install ; No install phase exists. | |
2948 | (lambda* (#:key outputs #:allow-other-keys) | |
2949 | (let* ((out (assoc-ref outputs "out")) | |
2950 | (bin (string-append out "/bin"))) | |
2951 | (install-file "Approximation" bin) | |
2952 | (install-file "CollectResults" bin) | |
2953 | (install-file "GenerateInstances" bin) | |
2954 | #t)))))) | |
2955 | (synopsis "Approximate Longest Commons Subsequence computation tool") | |
2956 | (description | |
2957 | "@code{reduceLCS} is an implementation of the Reduce-Expand | |
2958 | algorithm for LCS. It is a fast program to compute the approximate | |
2959 | Longest Commons Subsequence of a set of strings.") | |
2960 | (home-page "https://github.com/gdv/Reduce-Expand-for-LCS") | |
c000b6b1 | 2961 | (license license:gpl3+)))) |
479c4273 JD |
2962 | |
2963 | (define-public jacal | |
2964 | (package | |
2965 | (name "jacal") | |
2966 | (version "1c4") | |
2967 | (source (origin | |
2968 | (method url-fetch) | |
2969 | (uri (string-append | |
2970 | "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-" | |
2971 | version ".zip")) | |
2972 | (sha256 (base32 | |
2973 | "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q")) | |
2974 | (patches (search-patches "jacal-fix-texinfo.patch")))) | |
2975 | (build-system gnu-build-system) | |
2976 | (arguments | |
2977 | `(#:phases | |
2978 | (modify-phases %standard-phases | |
2979 | (add-before 'build 'pre-build | |
2980 | ;; Don't use upstream's script - it really doesn't fit into | |
2981 | ;; Guix's functional paradigm. | |
2982 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
2983 | (substitute* "Makefile" | |
2984 | (("^install: install-script") "install: ")))) | |
2985 | (add-after 'install 'post-install | |
2986 | ;; Instead, we provide our own simplified script. | |
2987 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
2988 | (let ((wrapper (string-append (assoc-ref outputs "out") | |
2989 | "/bin/jacal"))) | |
2990 | (format (open wrapper (logior O_WRONLY O_CREAT)) | |
2991 | (string-append "#!~a\nexec ~a/bin/scm -ip1 " | |
2992 | "-e '(slib:load \"~a/lib/jacal/math\") " | |
2993 | "(math)' \"$@\"\n") | |
2994 | (which "bash") | |
2995 | (assoc-ref inputs "scm") | |
2996 | (assoc-ref outputs "out")) | |
2997 | (chmod wrapper #o555)))) | |
2998 | (replace 'configure | |
2999 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
3000 | (zero? (system* "./configure" | |
3001 | (string-append "--prefix=" | |
3002 | (assoc-ref outputs "out"))))))))) | |
3003 | (inputs `(("scm" ,scm))) | |
3004 | (native-inputs `(("unzip" ,unzip) | |
3005 | ("texinfo" ,texinfo))) | |
3006 | (synopsis "Symbolic mathematics system") | |
3007 | (description "GNU JACAL is an interactive symbolic mathematics program based on | |
3008 | Scheme. It manipulate and simplify a range of mathematical expressions such | |
3009 | as equations, scalars, vectors, and matrices.") | |
3010 | (home-page "http://www.gnu.org/software/jacal") | |
3011 | (license license:gpl3+))) | |
3012 |