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> |
8f8b2451 AE |
14 | ;;; |
15 | ;;; This file is part of GNU Guix. | |
16 | ;;; | |
17 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
18 | ;;; under the terms of the GNU General Public License as published by | |
19 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
20 | ;;; your option) any later version. | |
21 | ;;; | |
22 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
23 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
24 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
25 | ;;; GNU General Public License for more details. | |
26 | ;;; | |
27 | ;;; You should have received a copy of the GNU General Public License | |
28 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
29 | ||
30 | (define-module (gnu packages maths) | |
ec322be2 | 31 | #:use-module (ice-9 regex) |
8f8b2451 | 32 | #:use-module (gnu packages) |
b5b73a82 | 33 | #:use-module ((guix licenses) #:prefix license:) |
8f8b2451 AE |
34 | #:use-module (guix packages) |
35 | #:use-module (guix download) | |
279663ef | 36 | #:use-module (guix svn-download) |
0e2672ae | 37 | #:use-module (guix utils) |
cec86422 | 38 | #:use-module (guix build utils) |
da95c817 | 39 | #:use-module (guix build-system cmake) |
c9dfa3c7 | 40 | #:use-module (guix build-system gnu) |
ec8c7e47 | 41 | #:use-module (guix build-system r) |
3de01d3f EB |
42 | #:use-module (gnu packages algebra) |
43 | #:use-module (gnu packages bison) | |
a17d4564 | 44 | #:use-module (gnu packages boost) |
e73b49fb | 45 | #:use-module (gnu packages check) |
3de01d3f | 46 | #:use-module (gnu packages cmake) |
c9dfa3c7 | 47 | #:use-module (gnu packages compression) |
668c06ac | 48 | #:use-module (gnu packages curl) |
528bb464 | 49 | #:use-module (gnu packages documentation) |
57e544e8 | 50 | #:use-module (gnu packages elf) |
3de01d3f | 51 | #:use-module (gnu packages flex) |
668c06ac | 52 | #:use-module (gnu packages fltk) |
f3929800 | 53 | #:use-module (gnu packages fontutils) |
1dba6407 | 54 | #:use-module (gnu packages gettext) |
da95c817 | 55 | #:use-module (gnu packages gcc) |
73fed4f8 | 56 | #:use-module (gnu packages gd) |
668c06ac | 57 | #:use-module (gnu packages ghostscript) |
f3929800 | 58 | #:use-module (gnu packages gtk) |
45147b0c | 59 | #:use-module (gnu packages image) |
668c06ac | 60 | #:use-module (gnu packages less) |
8731e527 | 61 | #:use-module (gnu packages lisp) |
5698b8b8 | 62 | #:use-module (gnu packages gnome) |
1b39a196 | 63 | #:use-module (gnu packages guile) |
668c06ac JD |
64 | #:use-module (gnu packages xorg) |
65 | #:use-module (gnu packages gl) | |
8731e527 | 66 | #:use-module (gnu packages m4) |
d8c7eeb9 | 67 | #:use-module (gnu packages mpi) |
b92eee75 | 68 | #:use-module (gnu packages multiprecision) |
528bb464 | 69 | #:use-module (gnu packages netpbm) |
668c06ac | 70 | #:use-module (gnu packages pcre) |
5698b8b8 | 71 | #:use-module (gnu packages popt) |
c9dfa3c7 AE |
72 | #:use-module (gnu packages perl) |
73 | #:use-module (gnu packages pkg-config) | |
da95c817 | 74 | #:use-module (gnu packages python) |
c9dfa3c7 | 75 | #:use-module (gnu packages readline) |
2742f87e | 76 | #:use-module (gnu packages tbb) |
183e44ae | 77 | #:use-module (gnu packages tcsh) |
df354a77 | 78 | #:use-module (gnu packages tcl) |
668c06ac | 79 | #:use-module (gnu packages texinfo) |
73fed4f8 | 80 | #:use-module (gnu packages texlive) |
9aafbc0c | 81 | #:use-module (gnu packages wxwidgets) |
c12efc72 | 82 | #:use-module (gnu packages xml) |
a17d4564 EB |
83 | #:use-module (gnu packages zip) |
84 | #:use-module (srfi srfi-1)) | |
8f8b2451 | 85 | |
9c45c519 JD |
86 | (define-public c-graph |
87 | (package | |
88 | (name "c-graph") | |
89 | (version "2.0") | |
90 | (source (origin | |
91 | (method url-fetch) | |
92 | (uri (string-append "mirror://gnu/c-graph/c-graph-" version | |
93 | ".tar.gz")) | |
94 | (sha256 (base32 | |
95 | "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01")))) | |
96 | (build-system gnu-build-system) | |
97 | (inputs | |
98 | `(("fortran" ,gfortran))) | |
99 | (synopsis "Visualize and analyze convolution operations") | |
100 | (description | |
101 | "GNU C-Graph demonstrates the theory of convolution underlying | |
102 | engineering systems and signal analysis.") | |
103 | (license license:gpl3+) | |
104 | (home-page "http://www.gnu.org/software/c-graph/"))) | |
105 | ||
8f8b2451 AE |
106 | (define-public units |
107 | (package | |
108 | (name "units") | |
cbe95057 | 109 | (version "2.12") |
8f8b2451 AE |
110 | (source (origin |
111 | (method url-fetch) | |
112 | (uri (string-append "mirror://gnu/units/units-" version | |
113 | ".tar.gz")) | |
114 | (sha256 (base32 | |
cbe95057 | 115 | "1jxvjknz2jhq773jrwx9gc1df3gfy73yqmkjkygqxzpi318yls3q")))) |
8f8b2451 AE |
116 | (build-system gnu-build-system) |
117 | (synopsis "Conversion between thousands of scales") | |
118 | (description | |
574e86f9 | 119 | "GNU Units converts numeric quantities between units of measure. It |
7c125ce0 AK |
120 | can handle scale changes through adaptive usage of standard scale |
121 | prefixes (micro-, kilo-, etc.). It can also handle nonlinear | |
122 | conversions such as Fahrenheit to Celsius. Its interpreter is powerful | |
123 | enough to be used effectively as a scientific calculator.") | |
8f8b2451 AE |
124 | (license license:gpl3+) |
125 | (home-page "http://www.gnu.org/software/units/"))) | |
c9dfa3c7 | 126 | |
61a529b4 RW |
127 | (define-public double-conversion |
128 | (package | |
129 | (name "double-conversion") | |
130 | (version "1.1.5") | |
131 | (source (origin | |
132 | (method url-fetch) | |
133 | (uri (string-append | |
134 | "https://github.com/floitsch/double-conversion/archive/v" | |
135 | version ".tar.gz")) | |
136 | (file-name (string-append name "-" version ".tar.gz")) | |
137 | (sha256 | |
138 | (base32 | |
139 | "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83")))) | |
140 | (build-system cmake-build-system) | |
141 | (arguments | |
142 | '(#:test-target "test" | |
143 | #:configure-flags '("-DBUILD_SHARED_LIBS=ON" | |
144 | "-DBUILD_TESTING=ON"))) | |
145 | (home-page "https://github.com/floitsch/double-conversion") | |
146 | (synopsis "Conversion routines for IEEE doubles") | |
147 | (description | |
148 | "The double-conversion library provides binary-decimal and decimal-binary | |
149 | routines for IEEE doubles. The library consists of efficient conversion | |
150 | routines that have been extracted from the V8 JavaScript engine.") | |
151 | (license license:bsd-3))) | |
152 | ||
182d6311 ML |
153 | (define-public dionysus |
154 | (package | |
155 | (name "dionysus") | |
156 | (version "1.3.0") | |
157 | (source (origin | |
158 | (method url-fetch) | |
159 | (uri (string-append "mirror://gnu/dionysus/dionysus-" version | |
160 | ".tar.gz")) | |
161 | (sha256 | |
162 | (base32 | |
163 | "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs")))) | |
164 | (build-system gnu-build-system) | |
165 | (inputs `(("tcl" ,tcl))) ;for 'tclsh' | |
166 | (synopsis "Local search for universal constants and scientific values") | |
167 | (description | |
168 | "GNU Dionysus is a convenient system for quickly retrieving the values of | |
169 | mathematical constants used in science and engineering. Values can be | |
170 | searched using a simple command-line tool, choosing from three databases: | |
171 | universal constants, atomic numbers, and constants related to | |
172 | semiconductors.") | |
173 | (license license:gpl3+) | |
174 | (home-page "http://www.gnu.org/software/dionysus/"))) | |
175 | ||
88bd1804 AE |
176 | (define-public gsl |
177 | (package | |
178 | (name "gsl") | |
0534dd93 | 179 | (version "2.1") |
88bd1804 AE |
180 | (source |
181 | (origin | |
182 | (method url-fetch) | |
183 | (uri (string-append "mirror://gnu/gsl/gsl-" | |
184 | version ".tar.gz")) | |
185 | (sha256 | |
186 | (base32 | |
0534dd93 | 187 | "0rhcia9jhr3p1f1wybwyllwqfs9bggz99i3mi5lpyqcpff1hdbar")))) |
88bd1804 | 188 | (build-system gnu-build-system) |
71e0f288 | 189 | (arguments |
5adbe65f | 190 | `(#:parallel-tests? #f)) |
88bd1804 AE |
191 | (home-page "http://www.gnu.org/software/gsl/") |
192 | (synopsis "Numerical library for C and C++") | |
193 | (description | |
a22dc0c4 LC |
194 | "The GNU Scientific Library is a library for numerical analysis in C |
195 | and C++. It includes a wide range of mathematical routines, with over 1000 | |
196 | functions in total. Subject areas covered by the library include: | |
197 | differential equations, linear algebra, Fast Fourier Transforms and random | |
198 | numbers.") | |
88bd1804 AE |
199 | (license license:gpl3+))) |
200 | ||
b92eee75 AE |
201 | (define-public glpk |
202 | (package | |
203 | (name "glpk") | |
f0443377 | 204 | (version "4.60") |
b92eee75 AE |
205 | (source |
206 | (origin | |
207 | (method url-fetch) | |
208 | (uri (string-append "mirror://gnu/glpk/glpk-" | |
209 | version ".tar.gz")) | |
210 | (sha256 | |
211 | (base32 | |
f0443377 | 212 | "15z2ymzqhxwss6wgdj5f7vkyqlqdsjgrvm0x871kmlx0n0664mhk")))) |
b92eee75 AE |
213 | (build-system gnu-build-system) |
214 | (inputs | |
215 | `(("gmp" ,gmp))) | |
216 | (arguments | |
217 | `(#:configure-flags '("--with-gmp"))) | |
218 | (home-page "http://www.gnu.org/software/glpk/") | |
79c311b8 | 219 | (synopsis "GNU Linear Programming Kit, supporting the MathProg language") |
b92eee75 AE |
220 | (description |
221 | "GLPK is a C library for solving large-scale linear programming (LP), | |
222 | mixed integer programming (MIP), and other related problems. It supports the | |
223 | GNU MathProg modeling language, a subset of the AMPL language, and features a | |
224 | translator for the language. In addition to the C library, a stand-alone | |
225 | LP/MIP solver is included in the package.") | |
226 | (license license:gpl3+))) | |
227 | ||
b146763a AE |
228 | (define-public 4ti2 |
229 | (package | |
230 | (name "4ti2") | |
231 | (version "1.6.7") | |
232 | (source | |
233 | (origin | |
234 | (method url-fetch) | |
235 | (uri (string-append "http://www.4ti2.de/version_" version | |
236 | "/4ti2-" version ".tar.gz")) | |
237 | (sha256 | |
238 | (base32 | |
239 | "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl")))) | |
240 | (build-system gnu-build-system) | |
241 | (native-inputs | |
242 | `(("which" ,(@ (gnu packages base) which)))) ; for the tests | |
243 | (inputs | |
244 | `(("glpk" ,glpk) | |
245 | ("gmp" ,gmp))) | |
246 | (home-page "http://www.4ti2.de/") | |
247 | (synopsis "Mathematical tool suite for problems on linear spaces") | |
248 | (description | |
249 | "4ti2 implements algorithms for solving algebraic, geometric and | |
250 | combinatorial problems on linear spaces. Among others, it solves systems | |
251 | of linear equations, computes extreme rays of polyhedral cones, solves | |
252 | integer programming problems and computes Markov bases for statistics.") | |
253 | (license license:gpl2+))) | |
254 | ||
53696f10 AE |
255 | (define-public cddlib |
256 | (package | |
257 | (name "cddlib") | |
258 | (version "0.94h") | |
259 | (source | |
260 | (origin | |
261 | (method url-fetch) | |
262 | (uri (string-append "ftp://ftp.ifor.math.ethz.ch/pub/fukuda/cdd/cddlib-" | |
263 | (string-delete #\. version) ".tar.gz")) | |
264 | (sha256 | |
265 | (base32 | |
266 | "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy")))) | |
267 | (build-system gnu-build-system) | |
268 | (inputs | |
269 | `(("gmp" ,gmp))) | |
270 | (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html") | |
271 | (synopsis "Library for convex hulls and extreme rays of polyhedra") | |
272 | (description | |
273 | "The C-library cddlib implements the Double Description Method of | |
274 | Motzkin et al. for generating all vertices (i.e. extreme points) and extreme | |
275 | rays of a general convex polyhedron given by a system of linear inequalities | |
276 | in arbitrary dimension. It can also be used for the converse operation of | |
277 | computing convex hulls.") | |
278 | (license license:gpl2+))) | |
279 | ||
865a69dd RW |
280 | (define-public arpack-ng |
281 | (package | |
282 | (name "arpack-ng") | |
283 | (version "3.2.0") | |
284 | (source | |
285 | (origin | |
286 | (method url-fetch) | |
287 | (uri (string-append "https://github.com/opencollab/arpack-ng/archive/" | |
288 | version ".tar.gz")) | |
f586c877 | 289 | (file-name (string-append name "-" version ".tar.gz")) |
865a69dd RW |
290 | (sha256 |
291 | (base32 | |
292 | "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff")))) | |
293 | (build-system gnu-build-system) | |
294 | (home-page "https://github.com/opencollab/arpack-ng") | |
295 | (inputs | |
296 | `(("lapack" ,lapack) | |
19afbea1 | 297 | ("fortran" ,gfortran))) |
865a69dd RW |
298 | (synopsis "Fortran subroutines for solving eigenvalue problems") |
299 | (description | |
300 | "ARPACK-NG is a collection of Fortran77 subroutines designed to solve | |
301 | large scale eigenvalue problems.") | |
166191b3 | 302 | (license (license:non-copyleft "file://COPYING" |
865a69dd RW |
303 | "See COPYING in the distribution.")))) |
304 | ||
8c94c886 EB |
305 | (define-public arpack-ng-openmpi |
306 | (package (inherit arpack-ng) | |
307 | (name "arpack-ng-openmpi") | |
308 | (inputs | |
309 | `(("mpi" ,openmpi) | |
310 | ,@(package-inputs arpack-ng))) | |
311 | (arguments `(#:configure-flags '("--enable-mpi"))) | |
312 | (synopsis "Fortran subroutines for solving eigenvalue problems with MPI"))) | |
313 | ||
da95c817 NK |
314 | (define-public lapack |
315 | (package | |
316 | (name "lapack") | |
566146ab | 317 | (version "3.5.0") |
da95c817 NK |
318 | (source |
319 | (origin | |
320 | (method url-fetch) | |
321 | (uri (string-append "http://www.netlib.org/lapack/lapack-" | |
322 | version ".tgz")) | |
323 | (sha256 | |
324 | (base32 | |
566146ab | 325 | "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s")))) |
da95c817 NK |
326 | (build-system cmake-build-system) |
327 | (home-page "http://www.netlib.org/lapack/") | |
19afbea1 | 328 | (inputs `(("fortran" ,gfortran) |
da95c817 NK |
329 | ("python" ,python-2))) |
330 | (arguments | |
06ed5982 | 331 | `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES") |
da95c817 | 332 | #:phases (alist-cons-before |
6a995754 LC |
333 | 'check 'patch-python |
334 | (lambda* (#:key inputs #:allow-other-keys) | |
335 | (let ((python (assoc-ref inputs "python"))) | |
336 | (substitute* "lapack_testing.py" | |
337 | (("/usr/bin/env python") python)))) | |
06ed5982 | 338 | %standard-phases))) |
da95c817 NK |
339 | (synopsis "Library for numerical linear algebra") |
340 | (description | |
341 | "LAPACK is a Fortran 90 library for solving the most commonly occurring | |
342 | problems in numerical linear algebra.") | |
166191b3 | 343 | (license (license:non-copyleft "file://LICENSE" |
da95c817 | 344 | "See LICENSE in the distribution.")))) |
73fed4f8 | 345 | |
e1ff597a EB |
346 | (define-public scalapack |
347 | (package | |
348 | (name "scalapack") | |
349 | (version "2.0.2") | |
350 | (source | |
351 | (origin | |
352 | (method url-fetch) | |
353 | (uri (string-append "http://www.netlib.org/scalapack/scalapack-" | |
354 | version ".tgz")) | |
355 | (sha256 | |
356 | (base32 | |
357 | "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c")))) | |
358 | (build-system cmake-build-system) | |
359 | (inputs | |
360 | `(("mpi" ,openmpi) | |
361 | ("fortran" ,gfortran) | |
362 | ("lapack" ,lapack))) ;for testing only | |
363 | (arguments | |
364 | `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES"))) | |
365 | (home-page "http://www.netlib.org/scalapack/") | |
366 | (synopsis "Library for scalable numerical linear algebra") | |
367 | (description | |
368 | "ScaLAPACK is a Fortran 90 library of high-performance linear algebra | |
369 | routines on parallel distributed memory machines. ScaLAPACK solves dense and | |
370 | banded linear systems, least squares problems, eigenvalue problems, and | |
371 | singular value problems.") | |
372 | (license (license:bsd-style "file://LICENSE" | |
373 | "See LICENSE in the distribution.")))) | |
374 | ||
73fed4f8 JD |
375 | (define-public gnuplot |
376 | (package | |
377 | (name "gnuplot") | |
ec4130b7 | 378 | (version "5.0.2") |
73fed4f8 JD |
379 | (source |
380 | (origin | |
381 | (method url-fetch) | |
382 | (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" | |
97003b5c | 383 | version "/gnuplot-" version ".tar.gz")) |
73fed4f8 JD |
384 | (sha256 |
385 | (base32 | |
ec4130b7 | 386 | "146qn414z96c7cc42a1kb9a4kpjc2q2hfdwk44kjjvgmfp9k2ass")))) |
73fed4f8 JD |
387 | (build-system gnu-build-system) |
388 | (inputs `(("readline" ,readline) | |
389 | ("cairo" ,cairo) | |
390 | ("pango" ,pango) | |
391 | ("gd" ,gd))) | |
97003b5c | 392 | (native-inputs `(("pkg-config" ,pkg-config) |
289adba7 | 393 | ("texlive" ,texlive-minimal))) |
73fed4f8 JD |
394 | (home-page "http://www.gnuplot.info") |
395 | (synopsis "Command-line driven graphing utility") | |
396 | (description "Gnuplot is a portable command-line driven graphing | |
35b9e423 | 397 | utility. It was originally created to allow scientists and students to |
73fed4f8 | 398 | visualize mathematical functions and data interactively, but has grown to |
35b9e423 | 399 | support many non-interactive uses such as web scripting. It is also used as a |
73fed4f8 JD |
400 | plotting engine by third-party applications like Octave.") |
401 | ;; X11 Style with the additional restriction that derived works may only be | |
402 | ;; distributed as patches to the original. | |
403 | (license (license:fsf-free | |
a124bbd2 | 404 | "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright")))) |
668c06ac | 405 | |
7ee3f1a2 JD |
406 | (define-public hdf5 |
407 | (package | |
408 | (name "hdf5") | |
04b7a7cd | 409 | (version "1.8.17") |
7ee3f1a2 JD |
410 | (source |
411 | (origin | |
412 | (method url-fetch) | |
93c3de92 AE |
413 | (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" |
414 | version "/src/hdf5-" | |
7ee3f1a2 JD |
415 | version ".tar.bz2")) |
416 | (sha256 | |
b8d9c93b EB |
417 | (base32 "0sj8x0gfs5fb28gipnynb9wpkz113h8wq9sva9mxx66kv27xsdgw")) |
418 | (patches (list (search-patch "hdf5-config-date.patch"))))) | |
7ee3f1a2 | 419 | (build-system gnu-build-system) |
12ed1216 AE |
420 | (inputs |
421 | `(("zlib" ,zlib))) | |
7ee3f1a2 JD |
422 | (arguments |
423 | `(#:phases | |
f622e212 EB |
424 | (modify-phases %standard-phases |
425 | (add-before 'configure 'patch-configure | |
426 | (lambda _ | |
427 | (substitute* "configure" | |
b8d9c93b EB |
428 | (("/bin/mv") "mv")) |
429 | #t)) | |
f622e212 EB |
430 | (add-after 'install 'patch-references |
431 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
432 | (let ((bin (string-append (assoc-ref outputs "out") "/bin")) | |
433 | (zlib (assoc-ref inputs "zlib"))) | |
434 | (substitute* (find-files bin "h5p?cc") | |
435 | (("-lz" lib) | |
436 | (string-append "-L" zlib "/lib " lib))) | |
437 | #t)))))) | |
7ee3f1a2 | 438 | (home-page "http://www.hdfgroup.org") |
516e93f8 | 439 | (synopsis "Management suite for extremely large and complex data") |
7ee3f1a2 JD |
440 | (description "HDF5 is a suite that makes possible the management of |
441 | extremely large and complex data collections.") | |
d4bf49b1 EB |
442 | (license (license:x11-style |
443 | "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) | |
7ee3f1a2 | 444 | |
1b39a196 RJ |
445 | (define-public nlopt |
446 | (package | |
447 | (name "nlopt") | |
448 | (version "2.4.2") | |
449 | (source (origin | |
450 | (method url-fetch) | |
451 | (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-" | |
452 | version ".tar.gz")) | |
453 | (sha256 | |
454 | (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0")))) | |
455 | (build-system gnu-build-system) | |
456 | (arguments | |
457 | `(;; Shared libraries are not built by default. They are required to | |
458 | ;; build the Guile, Octave, and Python bindings. | |
459 | #:configure-flags '("--enable-shared") | |
460 | ||
461 | #:phases | |
462 | (modify-phases %standard-phases | |
463 | (add-before 'configure 'set-libnlopt-file-name | |
464 | (lambda* (#:key outputs #:allow-other-keys) | |
465 | ;; Make sure the Scheme module refers to the library by its | |
466 | ;; absolute file name (we cannot do that from a snippet | |
467 | ;; because the expansion of @libdir@ contains | |
468 | ;; ${exec_prefix}.) | |
469 | (let ((out (assoc-ref outputs "out"))) | |
470 | (substitute* "swig/nlopt.scm.in" | |
471 | (("libnlopt") | |
472 | (string-append out "/lib/libnlopt"))) | |
473 | #t)))))) | |
474 | (inputs `(("guile" ,guile-2.0))) | |
475 | (native-inputs `(("pkg-config" ,pkg-config))) | |
476 | (home-page "http://ab-initio.mit.edu/wiki/") | |
477 | (synopsis "Library for nonlinear optimization") | |
478 | (description "NLopt is a library for nonlinear optimization, providing a | |
479 | common interface for a number of different free optimization routines available | |
480 | online as well as original implementations of various other algorithms.") | |
481 | (license license:lgpl2.1+))) | |
482 | ||
7ee3f1a2 | 483 | |
668c06ac JD |
484 | ;; For a fully featured Octave, users are strongly recommended also to install |
485 | ;; the following packages: texinfo, less, ghostscript, gnuplot. | |
486 | (define-public octave | |
487 | (package | |
488 | (name "octave") | |
19659acc | 489 | (version "4.0.0") |
668c06ac JD |
490 | (source |
491 | (origin | |
492 | (method url-fetch) | |
493 | (uri (string-append "mirror://gnu/octave/octave-" | |
a124bbd2 | 494 | version ".tar.gz")) |
668c06ac JD |
495 | (sha256 |
496 | (base32 | |
a124bbd2 | 497 | "101jr9yck798586jz4vkjcgk36zksmxf1pxrzvipgn2xgyay0zjc")))) |
668c06ac JD |
498 | (build-system gnu-build-system) |
499 | (inputs | |
500 | `(("lapack" ,lapack) | |
501 | ("readline" ,readline) | |
502 | ("glpk" ,glpk) | |
1ec78e9d EB |
503 | ("fftw" ,fftw) |
504 | ("fftwf" ,fftwf) | |
505 | ("arpack" ,arpack-ng) | |
668c06ac JD |
506 | ("curl" ,curl) |
507 | ("pcre" ,pcre) | |
508 | ("fltk" ,fltk) | |
509 | ("fontconfig" ,fontconfig) | |
510 | ("freetype" ,freetype) | |
40029cbe | 511 | ("hdf5" ,hdf5) |
668c06ac JD |
512 | ("libxft" ,libxft) |
513 | ("mesa" ,mesa) | |
1ec78e9d | 514 | ("glu" ,glu) |
668c06ac JD |
515 | ("zlib" ,zlib))) |
516 | (native-inputs | |
19afbea1 | 517 | `(("gfortran" ,gfortran) |
668c06ac JD |
518 | ("pkg-config" ,pkg-config) |
519 | ("perl" ,perl) | |
1ec78e9d EB |
520 | ;; The following inputs are not actually used in the build process. |
521 | ;; However, the ./configure gratuitously tests for their existence and | |
522 | ;; assumes that programs not present at build time are also not, and | |
523 | ;; can never be, available at run time! If these inputs are therefore | |
524 | ;; not present, support for them will be built out. However, Octave | |
525 | ;; will still run without them, albeit without the features they | |
668c06ac JD |
526 | ;; provide. |
527 | ("less" ,less) | |
528 | ("texinfo" ,texinfo) | |
529 | ("ghostscript" ,ghostscript) | |
530 | ("gnuplot" ,gnuplot))) | |
531 | (arguments | |
532 | `(#:configure-flags (list (string-append "--with-shell=" | |
533 | (assoc-ref %build-inputs "bash") | |
534 | "/bin/sh")))) | |
535 | (home-page "http://www.gnu.org/software/octave/") | |
536 | (synopsis "High-level language for numerical computation") | |
1ec78e9d EB |
537 | (description "GNU Octave is a high-level interpreted language that is |
538 | specialized for numerical computations. It can be used for both linear and | |
539 | non-linear applications and it provides great support for visualizing results. | |
540 | Work may be performed both at the interactive command-line as well as via | |
541 | script files.") | |
668c06ac | 542 | (license license:gpl3+))) |
3de01d3f EB |
543 | |
544 | (define-public gmsh | |
545 | (package | |
546 | (name "gmsh") | |
c7b08410 | 547 | (version "2.11.0") |
3de01d3f EB |
548 | (source |
549 | (origin | |
550 | (method url-fetch) | |
551 | (uri (string-append "http://www.geuz.org/gmsh/src/gmsh-" | |
552 | version "-source.tgz")) | |
553 | (sha256 | |
c7b08410 | 554 | (base32 "1ilplibvjgf7a905grpnclrvkmqy9fgrpl7xyp3w4yl1qc682v9b")) |
3de01d3f EB |
555 | (modules '((guix build utils))) |
556 | (snippet | |
557 | ;; Remove non-free METIS code | |
558 | '(delete-file-recursively "contrib/Metis")))) | |
559 | (build-system cmake-build-system) | |
3de01d3f EB |
560 | (propagated-inputs |
561 | `(("fltk" ,fltk) | |
19afbea1 | 562 | ("gfortran" ,gfortran) |
3de01d3f | 563 | ("gmp" ,gmp) |
40029cbe | 564 | ("hdf5" ,hdf5) |
3de01d3f EB |
565 | ("lapack" ,lapack) |
566 | ("mesa" ,mesa) | |
85f41902 | 567 | ("glu" ,glu) |
3de01d3f EB |
568 | ("libx11" ,libx11) |
569 | ("libxext" ,libxext))) | |
570 | (arguments | |
571 | `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF" | |
572 | "-DENABLE_BUILD_SHARED:BOOL=ON" | |
c7b08410 EB |
573 | "-DENABLE_BUILD_DYNAMIC:BOOL=ON") |
574 | #:phases (modify-phases %standard-phases | |
575 | (replace | |
576 | 'check | |
577 | (lambda _ | |
578 | (zero? (system* "make" "test" | |
579 | ;; Disable this test. See | |
580 | ;; https://geuz.org/trac/gmsh/ticket/271 | |
581 | "ARGS=-E component8_in_a_box"))))))) | |
3de01d3f EB |
582 | (home-page "http://www.geuz.org/gmsh/") |
583 | (synopsis "3D finite element grid generator") | |
edf684ef EB |
584 | (description "Gmsh is a 3D finite element grid generator with a built-in |
585 | CAD engine and post-processor. Its design goal is to provide a fast, light | |
586 | and user-friendly meshing tool with parametric input and advanced | |
587 | visualization capabilities. Gmsh is built around four modules: geometry, | |
588 | mesh, solver and post-processing. The specification of any input to these | |
589 | modules is done either interactively using the graphical user interface or in | |
590 | ASCII text files using Gmsh's own scripting language.") | |
3de01d3f | 591 | (license license:gpl2+))) |
b9100e2f EB |
592 | |
593 | (define-public petsc | |
594 | (package | |
595 | (name "petsc") | |
32187d99 | 596 | (version "3.6.2") |
b9100e2f EB |
597 | (source |
598 | (origin | |
599 | (method url-fetch) | |
600 | ;; The *-lite-* tarball does not contain the *large* documentation | |
601 | (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" | |
602 | "petsc-lite-" version ".tar.gz")) | |
603 | (sha256 | |
32187d99 | 604 | (base32 "13h0m5f9xsdpps4lsp59iz2m7zkapwavq2zfkfvs3ab6sndla0l9")))) |
b9100e2f EB |
605 | (build-system gnu-build-system) |
606 | (native-inputs | |
607 | `(("python" ,python-2) | |
608 | ("perl" ,perl))) | |
609 | (inputs | |
19afbea1 | 610 | `(("gfortran" ,gfortran) |
b9100e2f | 611 | ("lapack" ,lapack) |
f258212d | 612 | ("superlu" ,superlu) |
b9100e2f EB |
613 | ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi |
614 | ;; leaving out opengl, as configuration seems to only be for mac | |
615 | )) | |
616 | (arguments | |
617 | `(#:test-target "test" | |
9a899cce | 618 | #:parallel-build? #f ;build is parallel by default |
b9100e2f EB |
619 | #:configure-flags |
620 | `("--with-mpi=0" | |
f258212d EB |
621 | "--with-openmp=1" |
622 | "--with-superlu=1" | |
623 | ,(string-append "--with-superlu-include=" | |
624 | (assoc-ref %build-inputs "superlu") "/include") | |
625 | ,(string-append "--with-superlu-lib=" | |
626 | (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a")) | |
b9100e2f EB |
627 | #:phases |
628 | (alist-replace | |
629 | 'configure | |
630 | ;; PETSc's configure script is actually a python script, so we can't | |
631 | ;; run it with bash. | |
632 | (lambda* (#:key outputs (configure-flags '()) | |
633 | #:allow-other-keys) | |
634 | (let* ((prefix (assoc-ref outputs "out")) | |
635 | (flags `(,(string-append "--prefix=" prefix) | |
636 | ,@configure-flags))) | |
637 | (format #t "build directory: ~s~%" (getcwd)) | |
638 | (format #t "configure flags: ~s~%" flags) | |
639 | (zero? (apply system* "./configure" flags)))) | |
640 | (alist-cons-after | |
10b11968 EB |
641 | 'configure 'clean-local-references |
642 | ;; Try to keep build directory names from leaking into compiled code | |
b9100e2f | 643 | (lambda* (#:key inputs outputs #:allow-other-keys) |
10b11968 EB |
644 | (let ((out (assoc-ref outputs "out"))) |
645 | (substitute* (find-files "." "^petsc(conf|machineinfo).h$") | |
646 | (((getcwd)) out)))) | |
647 | (alist-cons-after | |
648 | 'install 'clean-install | |
649 | ;; Try to keep installed files from leaking build directory names. | |
650 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
dfdf5716 | 651 | (let ((out (assoc-ref outputs "out"))) |
10b11968 | 652 | (substitute* (map (lambda (file) |
9a899cce EB |
653 | (string-append out "/lib/petsc/conf/" file)) |
654 | '("petscvariables" "PETScConfig.cmake")) | |
10b11968 EB |
655 | (((getcwd)) out)) |
656 | ;; Make compiler references point to the store | |
9a899cce | 657 | (substitute* (string-append out "/lib/petsc/conf/petscvariables") |
dfdf5716 EB |
658 | (("= (gcc|g\\+\\+|gfortran)" _ compiler) |
659 | (string-append "= " (which compiler)))) | |
10b11968 EB |
660 | ;; PETSc installs some build logs, which aren't necessary. |
661 | (for-each (lambda (file) | |
9a899cce | 662 | (let ((f (string-append out "/lib/petsc/conf/" file))) |
10b11968 EB |
663 | (when (file-exists? f) |
664 | (delete-file f)))) | |
9a899cce EB |
665 | '("configure.log" "make.log" "gmake.log" |
666 | "test.log" "error.log" "RDict.db" | |
10b11968 | 667 | ;; Once installed, should uninstall with Guix |
9a899cce | 668 | "uninstall.py")))) |
10b11968 | 669 | %standard-phases))))) |
b9100e2f | 670 | (home-page "http://www.mcs.anl.gov/petsc") |
16ecf3ff | 671 | (synopsis "Library to solve PDEs") |
b9100e2f EB |
672 | (description "PETSc, pronounced PET-see (the S is silent), is a suite of |
673 | data structures and routines for the scalable (parallel) solution of | |
674 | scientific applications modeled by partial differential equations.") | |
166191b3 | 675 | (license (license:non-copyleft |
b9100e2f EB |
676 | "http://www.mcs.anl.gov/petsc/documentation/copyright.html")))) |
677 | ||
678 | (define-public petsc-complex | |
679 | (package (inherit petsc) | |
680 | (name "petsc-complex") | |
681 | (arguments | |
682 | (substitute-keyword-arguments (package-arguments petsc) | |
683 | ((#:configure-flags cf) | |
684 | `(cons "--with-scalar-type=complex" ,cf)))) | |
16ecf3ff | 685 | (synopsis "Library to solve PDEs (with complex scalars)"))) |
183e44ae | 686 | |
d8c7eeb9 EB |
687 | (define-public petsc-openmpi |
688 | (package (inherit petsc) | |
689 | (name "petsc-openmpi") | |
690 | (inputs | |
691 | `(("openmpi" ,openmpi) | |
692 | ,@(package-inputs petsc))) | |
693 | (arguments | |
694 | (substitute-keyword-arguments (package-arguments petsc) | |
695 | ((#:configure-flags cf) | |
696 | ``("--with-mpiexec=mpirun" | |
697 | ,(string-append "--with-mpi-dir=" | |
698 | (assoc-ref %build-inputs "openmpi")) | |
699 | ,@(delete "--with-mpi=0" ,cf))))) | |
16ecf3ff | 700 | (synopsis "Library to solve PDEs (with MPI support)"))) |
d8c7eeb9 EB |
701 | |
702 | (define-public petsc-complex-openmpi | |
703 | (package (inherit petsc-complex) | |
704 | (name "petsc-complex-openmpi") | |
705 | (inputs | |
706 | `(("openmpi" ,openmpi) | |
707 | ,@(package-inputs petsc-complex))) | |
708 | (arguments | |
709 | (substitute-keyword-arguments (package-arguments petsc-complex) | |
710 | ((#:configure-flags cf) | |
711 | ``("--with-mpiexec=mpirun" | |
712 | ,(string-append "--with-mpi-dir=" | |
713 | (assoc-ref %build-inputs "openmpi")) | |
714 | ,@(delete "--with-mpi=0" ,cf))))) | |
16ecf3ff | 715 | (synopsis "Library to solve PDEs (with complex scalars and MPI support)"))) |
d8c7eeb9 | 716 | |
a7f01414 EB |
717 | (define-public slepc |
718 | (package | |
719 | (name "slepc") | |
9cf52454 | 720 | (version "3.6.2") |
a7f01414 EB |
721 | (source |
722 | (origin | |
723 | (method url-fetch) | |
724 | (uri (string-append "http://slepc.upv.es/download/download.php?" | |
725 | "filename=slepc-" version ".tar.gz")) | |
d588422e | 726 | (file-name (string-append name "-" version ".tar.gz")) |
a7f01414 EB |
727 | (sha256 |
728 | (base32 | |
9cf52454 | 729 | "1pv5iqz2kc8sj49zsabyz4arnfpana8mjrhq31vzgk16xldk3d1a")))) |
a7f01414 EB |
730 | (build-system gnu-build-system) |
731 | (native-inputs | |
732 | `(("python" ,python-2))) | |
733 | (inputs | |
734 | `(("arpack" ,arpack-ng) | |
735 | ("gfortran" ,gfortran))) | |
736 | (propagated-inputs | |
737 | `(("petsc" ,petsc))) | |
738 | (arguments | |
739 | `(#:parallel-build? #f ;build is parallel by default | |
740 | #:configure-flags | |
741 | `(,(string-append "--with-arpack-dir=" | |
9cf52454 | 742 | (assoc-ref %build-inputs "arpack") "/lib")) |
a7f01414 EB |
743 | #:phases |
744 | (modify-phases %standard-phases | |
745 | (replace | |
746 | 'configure | |
747 | ;; configure is a python script, so we can't run it with bash. | |
748 | (lambda* (#:key inputs outputs (configure-flags '()) | |
749 | #:allow-other-keys) | |
750 | (let* ((prefix (assoc-ref outputs "out")) | |
751 | (flags `(,(string-append "--prefix=" prefix) | |
752 | ,@configure-flags))) | |
753 | (format #t "build directory: ~s~%" (getcwd)) | |
754 | (format #t "configure flags: ~s~%" flags) | |
755 | (setenv "SLEPC_DIR" (getcwd)) | |
9cf52454 | 756 | (setenv "PETSC_DIR" (assoc-ref inputs "petsc")) |
a7f01414 EB |
757 | (zero? (apply system* "./configure" flags))))) |
758 | (add-after | |
759 | 'install 'delete-doc | |
760 | ;; TODO: SLEPc installs HTML documentation alongside headers in | |
761 | ;; $out/include. We'd like to move them to share/doc, but delete | |
762 | ;; them for now, as they are incomplete and installing the complete | |
763 | ;; documentation is difficult. | |
764 | (lambda* (#:key outputs #:allow-other-keys) | |
765 | (let* ((out (assoc-ref outputs "out"))) | |
766 | (for-each delete-file (find-files out "\\.html$"))))) | |
767 | (add-after | |
768 | 'install 'clean-install | |
769 | ;; Clean up unnecessary build logs from installation. | |
770 | (lambda* (#:key outputs #:allow-other-keys) | |
771 | (let ((out (assoc-ref outputs "out"))) | |
772 | (for-each (lambda (file) | |
773 | (let ((f (string-append out "/lib/slepc/conf/" file))) | |
774 | (when (file-exists? f) | |
775 | (delete-file f)))) | |
776 | '("configure.log" "make.log" "gmake.log" | |
777 | "test.log" "error.log" "RDict.db" | |
778 | "uninstall.py")))))))) | |
779 | (home-page "http://slepc.upv.es") | |
780 | (synopsis "Scalable library for eigenproblems") | |
781 | (description "SLEPc is a software library for the solution of large sparse | |
782 | eigenproblems on parallel computers. It can be used for the solution of | |
783 | linear eigenvalue problems formulated in either standard or generalized form, | |
784 | as well as other related problems such as the singular value decomposition. | |
785 | The emphasis of the software is on methods and techniques appropriate for | |
786 | problems in which the associated matrices are sparse, for example, those | |
787 | arising after the discretization of partial differential equations.") | |
788 | (license license:lgpl3))) | |
789 | ||
790 | (define-public slepc-complex | |
791 | (package (inherit slepc) | |
792 | (name "slepc-complex") | |
793 | (propagated-inputs | |
794 | `(("petsc" ,petsc-complex) | |
795 | ,@(alist-delete "petsc" (package-propagated-inputs slepc)))) | |
796 | (synopsis "Scalable library for eigenproblems (with complex scalars)"))) | |
797 | ||
798 | (define-public slepc-openmpi | |
799 | (package (inherit slepc) | |
800 | (name "slepc-openmpi") | |
801 | (inputs | |
802 | `(("mpi" ,openmpi) | |
803 | ("arpack" ,arpack-ng-openmpi) | |
804 | ,@(alist-delete "arpack" (package-inputs slepc)))) | |
805 | (propagated-inputs | |
806 | `(("petsc" ,petsc-openmpi) | |
807 | ,@(alist-delete "petsc" (package-propagated-inputs slepc)))) | |
808 | (synopsis "Scalable library for eigenproblems (with MPI support)"))) | |
809 | ||
810 | (define-public slepc-complex-openmpi | |
811 | (package (inherit slepc-openmpi) | |
812 | (name "slepc-complex-openmpi") | |
813 | (propagated-inputs | |
814 | `(("petsc" ,petsc-complex-openmpi) | |
815 | ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi)))) | |
816 | (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)"))) | |
817 | ||
cec86422 EB |
818 | (define-public mumps |
819 | (package | |
820 | (name "mumps") | |
c69fa438 | 821 | (version "5.0.1") |
cec86422 EB |
822 | (source |
823 | (origin | |
824 | (method url-fetch) | |
825 | (uri (string-append "http://mumps.enseeiht.fr/MUMPS_" | |
826 | version ".tar.gz")) | |
827 | (sha256 | |
828 | (base32 | |
c69fa438 | 829 | "1820jfp3mbl7n85765v5mp6p0gzqpgr4d2lrnhwj4gl7cwp5ndah")) |
fc1adab1 | 830 | (patches (search-patches "mumps-build-parallelism.patch")))) |
cec86422 EB |
831 | (build-system gnu-build-system) |
832 | (inputs | |
833 | `(("fortran" ,gfortran) | |
834 | ;; These are required for linking against mumps, but we let the user | |
835 | ;; declare the dependency. | |
836 | ("blas" ,openblas) | |
837 | ("metis" ,metis) | |
838 | ("scotch" ,scotch))) | |
839 | (arguments | |
840 | `(#:modules ((ice-9 match) | |
841 | (ice-9 popen) | |
842 | (srfi srfi-1) | |
843 | ,@%gnu-build-system-modules) | |
844 | #:phases | |
845 | (modify-phases %standard-phases | |
846 | (replace | |
847 | 'configure | |
848 | (lambda* (#:key inputs #:allow-other-keys) | |
849 | (call-with-output-file "Makefile.inc" | |
850 | (lambda (port) | |
851 | (format port " | |
852 | PLAT = | |
853 | LIBEXT = .a | |
854 | OUTC = -o | |
855 | OUTF = -o | |
856 | RM = rm -f~:[ | |
857 | CC = gcc | |
858 | FC = gfortran | |
859 | FL = gfortran | |
860 | INCSEQ = -I$(topdir)/libseq | |
861 | LIBSEQ = -L$(topdir)/libseq -lmpiseq | |
862 | LIBSEQNEEDED = libseqneeded~; | |
863 | CC = mpicc | |
864 | FC = mpifort | |
865 | FL = mpifort~] | |
866 | AR = ar vr # rules require trailing space, ugh... | |
867 | RANLIB = ranlib | |
868 | LIBBLAS = -L~a -lopenblas~@[ | |
869 | SCALAP = -L~a -lscalapack~] | |
870 | LIBOTHERS = -pthread | |
871 | CDEFS = -DAdd_ | |
872 | PIC = -fPIC | |
873 | OPTF = -O2 -DALLOW_NON_INIT $(PIC) | |
874 | OPTL = -O2 $(PIC) | |
875 | OPTC = -O2 $(PIC) | |
876 | INCS = $(INCSEQ) | |
877 | LIBS = $(SCALAP) $(LIBSEQ) | |
878 | LPORDDIR = $(topdir)/PORD/lib | |
879 | IPORD = -I$(topdir)/PORD/include | |
880 | LPORD = -L$(LPORDDIR) -lpord | |
881 | ORDERINGSF = -Dpord~@[ | |
882 | METISDIR = ~a | |
883 | IMETIS = -I$(METISDIR)/include | |
884 | LMETIS = -L$(METISDIR)/lib -lmetis | |
885 | ORDERINGSF += -Dmetis~]~@[~:{ | |
886 | SCOTCHDIR = ~a | |
887 | ISCOTCH = -I$(SCOTCHDIR)/include | |
888 | LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr | |
889 | ORDERINGSF += ~a~}~] | |
890 | ORDERINGSC = $(ORDERINGSF) | |
891 | LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) | |
892 | IORDERINGSF = $(ISCOTCH) | |
893 | IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)" | |
894 | (assoc-ref inputs "mpi") | |
895 | (assoc-ref inputs "blas") | |
896 | (assoc-ref inputs "scalapack") | |
897 | (assoc-ref inputs "metis") | |
898 | (match (list (assoc-ref inputs "pt-scotch") | |
899 | (assoc-ref inputs "scotch")) | |
900 | ((#f #f) | |
901 | #f) | |
902 | ((#f scotch) | |
903 | `((,scotch "" "-Dscotch"))) | |
904 | ((ptscotch _) | |
905 | `((,ptscotch | |
906 | "-lptesmumps -lptscotch -lptscotcherr " | |
907 | "-Dptscotch"))))))))) | |
908 | (replace | |
909 | 'build | |
910 | ;; By default only the d-precision library is built. Make with "all" | |
911 | ;; target so that all precision libraries and examples are built. | |
912 | (lambda _ | |
913 | (zero? (system* "make" "all" | |
914 | (format #f "-j~a" (parallel-job-count)))))) | |
915 | (replace | |
916 | 'check | |
917 | ;; Run the simple test drivers, which read test input from stdin: | |
918 | ;; from the "real" input for the single- and double-precision | |
919 | ;; testers, and from the "cmplx" input for complex-precision | |
920 | ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi | |
921 | ;; package to prefix execution with "mpirun". | |
922 | (lambda* (#:key (exec-prefix '()) #:allow-other-keys) | |
923 | (with-directory-excursion "examples" | |
924 | (every | |
925 | (lambda (prec type) | |
926 | (let ((tester (apply open-pipe* | |
927 | `(,OPEN_WRITE | |
928 | ,@exec-prefix | |
929 | ,(string-append "./" prec | |
930 | "simpletest")))) | |
931 | (input (open-input-file | |
932 | (string-append "input_simpletest_" type)))) | |
933 | (begin | |
934 | (dump-port input tester) | |
935 | (close-port input) | |
936 | (zero? (close-pipe tester))))) | |
937 | '("s" "d" "c" "z") | |
938 | '("real" "real" "cmplx" "cmplx"))))) | |
939 | (replace | |
940 | 'install | |
941 | (lambda* (#:key outputs #:allow-other-keys) | |
942 | (let ((out (assoc-ref outputs "out"))) | |
943 | (copy-recursively "lib" (string-append out "/lib")) | |
944 | (copy-recursively "include" (string-append out "/include")) | |
945 | (when (file-exists? "libseq/libmpiseq.a") | |
946 | (copy-file "libseq/libmpiseq.a" | |
947 | (string-append out "/lib/libmpiseq.a"))))))))) | |
948 | (home-page "http://mumps.enseeiht.fr") | |
949 | (synopsis "Multifrontal sparse direct solver") | |
950 | (description | |
951 | "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a | |
952 | sparse system of linear equations A x = b using Guassian elimination.") | |
953 | (license license:cecill-c))) | |
954 | ||
955 | (define-public mumps-metis | |
956 | (package (inherit mumps) | |
957 | (name "mumps-metis") | |
958 | (inputs | |
959 | (alist-delete "scotch" (package-inputs mumps))))) | |
960 | ||
961 | (define-public mumps-openmpi | |
962 | (package (inherit mumps) | |
963 | (name "mumps-openmpi") | |
964 | (inputs | |
965 | `(("mpi" ,openmpi) | |
966 | ("scalapack" ,scalapack) | |
967 | ("pt-scotch" ,pt-scotch) | |
968 | ,@(alist-delete "scotch" (package-inputs mumps)))) | |
969 | (arguments | |
970 | (substitute-keyword-arguments (package-arguments mumps) | |
971 | ((#:phases phases) | |
972 | `(modify-phases ,phases | |
973 | (replace | |
974 | 'check | |
975 | (lambda _ | |
976 | ((assoc-ref ,phases 'check) | |
977 | #:exec-prefix '("mpirun" "-n" "2")))))))) | |
978 | (synopsis "Multifrontal sparse direct solver (with MPI)"))) | |
979 | ||
980 | (define-public mumps-metis-openmpi | |
981 | (package (inherit mumps-openmpi) | |
982 | (name "mumps-metis-openmpi") | |
983 | (inputs | |
984 | (alist-delete "pt-scotch" (package-inputs mumps-openmpi))))) | |
985 | ||
ec8c7e47 RJ |
986 | (define-public r-pracma |
987 | (package | |
988 | (name "r-pracma") | |
989 | (version "1.8.8") | |
990 | (source (origin | |
991 | (method url-fetch) | |
992 | (uri (cran-uri "pracma" version)) | |
993 | (sha256 | |
994 | (base32 "0ans9l5rrb7a38gyi4qx4258sd5r5668vyrk02yzjpg9k3h8l165")))) | |
995 | (build-system r-build-system) | |
996 | (home-page "http://cran.r-project.org/web/packages/pracma") | |
997 | (synopsis "Practical numerical math functions") | |
998 | (description "This package provides functions for numerical analysis and | |
999 | linear algebra, numerical optimization, differential equations, plus some | |
1000 | special functions. It uses Matlab function names where appropriate to simplify | |
1001 | porting.") | |
1002 | (license license:gpl3+))) | |
1003 | ||
183e44ae EB |
1004 | (define-public superlu |
1005 | (package | |
1006 | (name "superlu") | |
1007 | (version "4.3") | |
1008 | (source | |
1009 | (origin | |
1010 | (method url-fetch) | |
1011 | (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" | |
1012 | "superlu_" version ".tar.gz")) | |
1013 | (sha256 | |
1014 | (base32 "10b785s9s4x0m9q7ihap09275pq4km3k2hk76jiwdfdr5qr2168n")))) | |
1015 | (build-system gnu-build-system) | |
1016 | (native-inputs | |
1017 | `(("tcsh" ,tcsh))) | |
1018 | (inputs | |
1019 | `(("lapack" ,lapack) | |
19afbea1 | 1020 | ("gfortran" ,gfortran))) |
183e44ae EB |
1021 | (arguments |
1022 | `(#:parallel-build? #f | |
1023 | #:tests? #f ;tests are run as part of `make all` | |
1024 | #:phases | |
1025 | (alist-replace | |
1026 | 'configure | |
1027 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1028 | (call-with-output-file "make.inc" | |
1029 | (lambda (port) | |
1030 | (format port " | |
1031 | PLAT = | |
1032 | SuperLUroot = ~a | |
1033 | SUPERLULIB = ~a/lib/libsuperlu.a | |
1034 | TMGLIB = libtmglib.a | |
1035 | BLASDEF = -DUSE_VENDOR_BLAS | |
1036 | BLASLIB = -L~a/lib -lblas | |
1037 | LIBS = $(SUPERLULIB) $(BLASLIB) | |
1038 | ARCH = ar | |
1039 | ARCHFLAGS = cr | |
1040 | RANLIB = ranlib | |
1041 | CC = gcc | |
1042 | PIC = -fPIC | |
1043 | CFLAGS = -O3 -DPRNTlevel=0 $(PIC) | |
1044 | NOOPTS = -O0 $(PIC) | |
1045 | FORTRAN = gfortran | |
1046 | FFLAGS = -O2 $(PIC) | |
1047 | LOADER = $(CC) | |
1048 | CDEFS = -DAdd_" | |
1049 | (getcwd) | |
1050 | (assoc-ref outputs "out") | |
1051 | (assoc-ref inputs "lapack"))))) | |
1052 | (alist-cons-before | |
1053 | 'build 'create-install-directories | |
1054 | (lambda* (#:key outputs #:allow-other-keys) | |
1055 | (for-each | |
1056 | (lambda (dir) | |
1057 | (mkdir-p (string-append (assoc-ref outputs "out") | |
1058 | "/" dir))) | |
1059 | '("lib" "include"))) | |
1060 | (alist-replace | |
1061 | 'install | |
1062 | (lambda* (#:key outputs #:allow-other-keys) | |
1063 | ;; Library is placed in lib during the build phase. Copy over | |
1064 | ;; headers to include. | |
1065 | (let* ((out (assoc-ref outputs "out")) | |
1066 | (incdir (string-append out "/include"))) | |
1067 | (for-each (lambda (file) | |
1068 | (let ((base (basename file))) | |
1069 | (format #t "installing `~a' to `~a'~%" | |
1070 | base incdir) | |
1071 | (copy-file file | |
1072 | (string-append incdir "/" base)))) | |
1073 | (find-files "SRC" ".*\\.h$")))) | |
1074 | %standard-phases))))) | |
1075 | (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/") | |
1076 | (synopsis "Supernodal direct solver for sparse linear systems") | |
1077 | (description | |
1078 | "SuperLU is a general purpose library for the direct solution of large, | |
1079 | sparse, nonsymmetric systems of linear equations on high performance machines. | |
1080 | The library is written in C and is callable from either C or Fortran. The | |
1081 | library routines perform an LU decomposition with partial pivoting and | |
1082 | triangular system solves through forward and back substitution. The library | |
1083 | also provides threshold-based ILU factorization preconditioners.") | |
1084 | (license license:bsd-3))) | |
f8ed036a | 1085 | |
a54aefea EB |
1086 | (define-public superlu-dist |
1087 | (package | |
1088 | (name "superlu-dist") | |
1089 | (version "3.3") | |
1090 | (source | |
1091 | (origin | |
1092 | (method url-fetch) | |
1093 | (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" | |
1094 | "superlu_dist_" version ".tar.gz")) | |
1095 | (sha256 | |
1096 | (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj")) | |
fc1adab1 | 1097 | (patches (search-patches "superlu-dist-scotchmetis.patch")))) |
a54aefea EB |
1098 | (build-system gnu-build-system) |
1099 | (native-inputs | |
1100 | `(("tcsh" ,tcsh))) | |
1101 | (inputs | |
19afbea1 | 1102 | `(("gfortran" ,gfortran))) |
a54aefea EB |
1103 | (propagated-inputs |
1104 | `(("openmpi" ,openmpi) ;headers include MPI heades | |
1105 | ("lapack" ,lapack) ;required to link with output library | |
1106 | ("pt-scotch" ,pt-scotch))) ;same | |
1107 | (arguments | |
1108 | `(#:parallel-build? #f ;race conditions using ar | |
1109 | #:phases | |
1110 | (alist-replace | |
1111 | 'configure | |
1112 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1113 | (call-with-output-file "make.inc" | |
1114 | (lambda (port) | |
1115 | (format port " | |
1116 | PLAT = | |
1117 | DSuperLUroot = ~a | |
1118 | DSUPERLULIB = ~a/lib/libsuperlu_dist.a | |
1119 | BLASDEF = -DUSE_VENDOR_BLAS | |
1120 | BLASLIB = -L~a/lib -lblas | |
1121 | PARMETISLIB = -L~a/lib \ | |
1122 | -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \ | |
1123 | -lscotch -lscotcherr -lscotcherrexit | |
1124 | METISLIB = -L~:*~a/lib \ | |
1125 | -lscotchmetis -lscotch -lscotcherr -lscotcherrexit | |
1126 | LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB) | |
1127 | ARCH = ar | |
1128 | ARCHFLAGS = cr | |
1129 | RANLIB = ranlib | |
1130 | CC = mpicc | |
1131 | PIC = -fPIC | |
1132 | CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC) | |
1133 | NOOPTS = -O0 -g $(PIC) | |
1134 | FORTRAN = mpifort | |
1135 | FFLAGS = -O2 -g $(PIC) | |
1136 | LOADER = $(CC) | |
1137 | CDEFS = -DAdd_" | |
1138 | (getcwd) | |
1139 | (assoc-ref outputs "out") | |
1140 | (assoc-ref inputs "lapack") | |
1141 | (assoc-ref inputs "pt-scotch"))))) | |
1142 | (alist-cons-after | |
1143 | 'unpack 'remove-broken-symlinks | |
1144 | (lambda _ | |
1145 | (for-each delete-file | |
1146 | (find-files "MAKE_INC" "\\.#make\\..*"))) | |
1147 | (alist-cons-before | |
1148 | 'build 'create-install-directories | |
1149 | (lambda* (#:key outputs #:allow-other-keys) | |
1150 | (for-each | |
1151 | (lambda (dir) | |
1152 | (mkdir-p (string-append (assoc-ref outputs "out") | |
1153 | "/" dir))) | |
1154 | '("lib" "include"))) | |
1155 | (alist-replace | |
1156 | 'check | |
1157 | (lambda _ | |
1158 | (with-directory-excursion "EXAMPLE" | |
1159 | (and | |
1160 | (zero? (system* "mpirun" "-n" "2" | |
1161 | "./pddrive" "-r" "1" "-c" "2" "g20.rua")) | |
1162 | (zero? (system* "mpirun" "-n" "2" | |
1163 | "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))))) | |
1164 | (alist-replace | |
1165 | 'install | |
1166 | (lambda* (#:key outputs #:allow-other-keys) | |
1167 | ;; Library is placed in lib during the build phase. Copy over | |
1168 | ;; headers to include. | |
1169 | (let* ((out (assoc-ref outputs "out")) | |
1170 | (incdir (string-append out "/include"))) | |
1171 | (for-each (lambda (file) | |
1172 | (let ((base (basename file))) | |
1173 | (format #t "installing `~a' to `~a'~%" | |
1174 | base incdir) | |
1175 | (copy-file file | |
1176 | (string-append incdir "/" base)))) | |
1177 | (find-files "SRC" ".*\\.h$")))) | |
1178 | %standard-phases))))))) | |
1179 | (home-page (package-home-page superlu)) | |
1180 | (synopsis "Parallel supernodal direct solver") | |
1181 | (description | |
1182 | "SuperLU_DIST is a parallel extension to the serial SuperLU library. | |
1183 | It is targeted for distributed memory parallel machines. SuperLU_DIST is | |
1184 | implemented in ANSI C, and MPI for communications.") | |
1185 | (license license:bsd-3))) | |
1186 | ||
f8ed036a EB |
1187 | (define-public scotch |
1188 | (package | |
1189 | (name "scotch") | |
6c798540 | 1190 | (version "6.0.4") |
f8ed036a EB |
1191 | (source |
1192 | (origin | |
1193 | (method url-fetch) | |
6c798540 | 1194 | (uri (string-append "https://gforge.inria.fr/frs/download.php/34618/" |
f8ed036a EB |
1195 | "scotch_" version ".tar.gz")) |
1196 | (sha256 | |
6c798540 | 1197 | (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm")) |
fc1adab1 AK |
1198 | (patches (search-patches "scotch-test-threading.patch" |
1199 | "pt-scotch-build-parallelism.patch")))) | |
f8ed036a EB |
1200 | (build-system gnu-build-system) |
1201 | (inputs | |
1202 | `(("zlib" ,zlib) | |
1203 | ("flex" ,flex) | |
1204 | ("bison" ,bison))) | |
1205 | (arguments | |
1206 | `(#:phases | |
d6602ee9 EB |
1207 | (modify-phases %standard-phases |
1208 | (add-after | |
1209 | 'unpack 'chdir-to-src | |
1210 | (lambda _ (chdir "src"))) | |
1211 | (replace | |
1212 | 'configure | |
1213 | (lambda _ | |
1214 | (call-with-output-file "Makefile.inc" | |
1215 | (lambda (port) | |
1216 | (format port " | |
f8ed036a EB |
1217 | EXE = |
1218 | LIB = .a | |
1219 | OBJ = .o | |
1220 | MAKE = make | |
1221 | AR = ar | |
1222 | ARFLAGS = -ruv | |
cf0ec6c4 | 1223 | CAT = cat |
f8ed036a EB |
1224 | CCS = gcc |
1225 | CCP = mpicc | |
1226 | CCD = gcc | |
1227 | CPPFLAGS =~{ -D~a~} | |
6c798540 | 1228 | CFLAGS = -O2 -g -fPIC $(CPPFLAGS) |
f8ed036a EB |
1229 | LDFLAGS = -lz -lm -lrt -lpthread |
1230 | CP = cp | |
1231 | LEX = flex -Pscotchyy -olex.yy.c | |
1232 | LN = ln | |
1233 | MKDIR = mkdir | |
1234 | MV = mv | |
1235 | RANLIB = ranlib | |
1236 | YACC = bison -pscotchyy -y -b y | |
1237 | " | |
d6602ee9 EB |
1238 | '("COMMON_FILE_COMPRESS_GZ" |
1239 | "COMMON_PTHREAD" | |
1240 | "COMMON_RANDOM_FIXED_SEED" | |
cf0ec6c4 EB |
1241 | ;; Prevents symbolc clashes with libesmumps |
1242 | "SCOTCH_RENAME" | |
d6602ee9 EB |
1243 | ;; XXX: Causes invalid frees in superlu-dist tests |
1244 | ;; "SCOTCH_PTHREAD" | |
1245 | ;; "SCOTCH_PTHREAD_NUMBER=2" | |
1246 | "restrict=__restrict")))))) | |
cf0ec6c4 EB |
1247 | (add-after |
1248 | 'build 'build-esmumps | |
1249 | (lambda _ | |
1250 | (zero? (system* "make" | |
1251 | (format #f "-j~a" (parallel-job-count)) | |
1252 | "esmumps")))) | |
d6602ee9 | 1253 | (replace |
f8ed036a EB |
1254 | 'install |
1255 | (lambda* (#:key outputs #:allow-other-keys) | |
1256 | (let ((out (assoc-ref outputs "out"))) | |
1257 | (mkdir out) | |
1258 | (zero? (system* "make" | |
1259 | (string-append "prefix=" out) | |
cf0ec6c4 EB |
1260 | "install")) |
1261 | ;; esmumps files are not installed with the above | |
1262 | (for-each (lambda (f) | |
1263 | (copy-file f (string-append out "/include/" f))) | |
1264 | (find-files "../include" ".*esmumps.h$")) | |
1265 | (for-each (lambda (f) | |
1266 | (copy-file f (string-append out "/lib/" f))) | |
1267 | (find-files "../lib" "^lib.*esmumps.*")))))))) | |
f8ed036a EB |
1268 | (home-page "http://www.labri.fr/perso/pelegrin/scotch/") |
1269 | (synopsis "Programs and libraries for graph algorithms") | |
1270 | (description "SCOTCH is a set of programs and libraries which implement | |
1271 | the static mapping and sparse matrix reordering algorithms developed within | |
1272 | the SCOTCH project. Its purpose is to apply graph theory, with a divide and | |
1273 | conquer approach, to scientific computing problems such as graph and mesh | |
1274 | partitioning, static mapping, and sparse matrix ordering, in application | |
1275 | domains ranging from structural mechanics to operating systems or | |
1276 | bio-chemistry.") | |
1277 | ;; See LICENSE_en.txt | |
1278 | (license license:cecill-c))) | |
6acb4adb EB |
1279 | |
1280 | (define-public pt-scotch | |
1281 | (package (inherit scotch) | |
1282 | (name "pt-scotch") | |
1283 | (propagated-inputs | |
1284 | `(("openmpi" ,openmpi))) ;Headers include MPI headers | |
1285 | (arguments | |
1286 | (substitute-keyword-arguments (package-arguments scotch) | |
1287 | ((#:phases scotch-phases) | |
d6602ee9 EB |
1288 | `(modify-phases ,scotch-phases |
1289 | (replace | |
1290 | 'build | |
d6602ee9 EB |
1291 | (lambda _ |
1292 | (and | |
cf0ec6c4 EB |
1293 | (zero? (system* "make" |
1294 | (format #f "-j~a" (parallel-job-count)) | |
1295 | "ptscotch" "ptesmumps")) | |
d6602ee9 EB |
1296 | ;; Install the serial metis compatibility library |
1297 | (zero? (system* "make" "-C" "libscotchmetis" "install"))))) | |
1298 | (replace | |
1299 | 'check | |
1300 | (lambda _ (zero? (system* "make" "ptcheck")))))))) | |
6acb4adb | 1301 | (synopsis "Programs and libraries for graph algorithms (with MPI)"))) |
5698b8b8 | 1302 | |
aa75ad00 EB |
1303 | (define-public metis |
1304 | (package | |
1305 | (name "metis") | |
1306 | (version "5.1.0") | |
1307 | (source | |
1308 | (origin | |
1309 | (method url-fetch) | |
1310 | (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/" | |
1311 | "metis-" version ".tar.gz")) | |
1312 | (sha256 | |
1313 | (base32 | |
1314 | "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn")))) | |
1315 | (build-system cmake-build-system) | |
1316 | (inputs | |
1317 | `(("blas" ,openblas))) | |
1318 | (arguments | |
1319 | `(#:tests? #f ;no tests | |
1320 | #:configure-flags `("-DSHARED=ON" | |
1321 | ,(string-append "-DGKLIB_PATH=" (getcwd) | |
1322 | "/metis-" ,version "/GKlib")))) | |
1323 | (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview") | |
1324 | (synopsis "Graph partitioning and fill-reducing matrix ordering library") | |
1325 | (description | |
1326 | "METIS is a set of serial programs for partitioning graphs, partitioning | |
1327 | finite element meshes, and producing fill-reducing orderings for sparse | |
1328 | matrices. The algorithms implemented in METIS are based on the multilevel | |
1329 | recursive-bisection, multilevel k-way, and multi-constraint partitioning | |
1330 | schemes.") | |
1331 | (license license:asl2.0))) ;As of version 5.0.3 | |
1332 | ||
700ff222 EB |
1333 | (define-public p4est |
1334 | (package | |
1335 | (name "p4est") | |
1336 | (version "1.1") | |
1337 | (source | |
1338 | (origin | |
1339 | (method url-fetch) | |
1340 | (uri (string-append "http://p4est.github.io/release/p4est-" | |
1341 | version ".tar.gz")) | |
1342 | (sha256 | |
1343 | (base32 | |
1344 | "0faina2h5qsx3m2izbzaj9bbakma1krbbjmq43wrp1hcbyijflqb")))) | |
1345 | (build-system gnu-build-system) | |
1346 | (inputs | |
1347 | `(("fortran" ,gfortran) | |
1348 | ("blas" ,openblas) | |
1349 | ("lapack" ,lapack) | |
1350 | ("zlib" ,zlib))) | |
1351 | (arguments | |
1352 | `(#:configure-flags `(,(string-append "BLAS_LIBS=-L" | |
1353 | (assoc-ref %build-inputs "blas") | |
1354 | " -lopenblas") | |
1355 | ,(string-append "LAPACK_LIBS=-L" | |
1356 | (assoc-ref %build-inputs "lapack") | |
1357 | " -llapack")))) | |
1358 | (home-page "http://www.p4est.org") | |
1359 | (synopsis "Adaptive mesh refinement on forests of octrees") | |
1360 | (description | |
1361 | "The p4est software library enables the dynamic management of a | |
1362 | collection of adaptive octrees, conveniently called a forest of octrees. | |
1363 | p4est is designed to work in parallel and scales to hundreds of thousands of | |
1364 | processor cores.") | |
1365 | (license license:gpl2+))) | |
1366 | ||
1367 | (define-public p4est-openmpi | |
1368 | (package (inherit p4est) | |
1369 | (name "p4est-openmpi") | |
1370 | (inputs | |
1371 | `(("mpi" ,openmpi) | |
1372 | ,@(package-inputs p4est))) | |
1373 | (arguments | |
1374 | (substitute-keyword-arguments (package-arguments p4est) | |
1375 | ((#:configure-flags cf) | |
1376 | ``("--enable-mpi" ,@,cf)))) | |
1377 | (synopsis "Parallel adaptive mesh refinement on forests of octrees"))) | |
1378 | ||
5698b8b8 JD |
1379 | (define-public gsegrafix |
1380 | (package | |
1381 | (name "gsegrafix") | |
1382 | (version "1.0.6") | |
1383 | (source | |
1384 | (origin | |
1385 | (method url-fetch) | |
1386 | (uri (string-append "mirror://gnu/" name "/" name "-" | |
1387 | version ".tar.gz")) | |
1388 | (sha256 | |
1389 | (base32 | |
1390 | "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda")))) | |
1391 | (build-system gnu-build-system) | |
1392 | (arguments | |
1393 | `(#:configure-flags '("LDFLAGS=-lm"))) | |
1394 | (inputs | |
1395 | `(("libgnomecanvas" ,libgnomecanvas) | |
1396 | ("libbonoboui" ,libbonoboui) | |
1397 | ("libgnomeui" ,libgnomeui) | |
1398 | ("libgnomeprintui" ,libgnomeprintui) | |
1399 | ("popt" ,popt))) | |
1400 | (native-inputs | |
1401 | `(("pkg-config" ,pkg-config))) | |
1402 | (home-page "http://www.gnu.org/software/gsegrafix/") | |
1403 | (synopsis "GNOME application to create scientific and engineering plots") | |
1404 | (description "GSEGrafix is an application which produces high-quality graphical | |
1405 | plots for science and engineering. Plots are specified via simple ASCII | |
1406 | parameter files and data files and are presented in an anti-aliased GNOME | |
1407 | canvas. The program supports rectangular two-dimensional plots, histograms, | |
1408 | polar-axis plots and three-dimensional plots. Plots can be printed or saved | |
1409 | to BMP, JPEG or PNG image formats.") | |
1410 | (license license:gpl3+))) | |
8731e527 JD |
1411 | |
1412 | (define-public maxima | |
1413 | (package | |
1414 | (name "maxima") | |
77af7b24 | 1415 | (version "5.36.1") |
8731e527 JD |
1416 | (source |
1417 | (origin | |
1418 | (method url-fetch) | |
1419 | (uri (string-append "mirror://sourceforge/maxima/Maxima-source/" | |
1420 | version "-source/" name "-" version ".tar.gz")) | |
1421 | (sha256 | |
1422 | (base32 | |
77af7b24 | 1423 | "0x1rk659sn3cq0n5c90848ilzr1gb1wf0072fl6jhkdq00qgh2s0")) |
fc1adab1 | 1424 | (patches (search-patches "maxima-defsystem-mkdir.patch")))) |
8731e527 | 1425 | (build-system gnu-build-system) |
df354a77 FB |
1426 | (inputs |
1427 | `(("gcl" ,gcl) | |
1428 | ("gnuplot" ,gnuplot) ;for plots | |
f36afe4d | 1429 | ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima' |
df354a77 FB |
1430 | (native-inputs |
1431 | `(("texinfo" ,texinfo) | |
1432 | ("perl" ,perl))) | |
8731e527 | 1433 | (arguments |
df354a77 FB |
1434 | `(#:configure-flags |
1435 | (list "--enable-gcl" | |
1436 | (string-append "--with-posix-shell=" | |
1437 | (assoc-ref %build-inputs "bash") | |
1438 | "/bin/sh") | |
1439 | (string-append "--with-wish=" | |
1440 | (assoc-ref %build-inputs "tk") | |
1441 | "/bin/wish" | |
1442 | (let ((v ,(package-version tk))) | |
1443 | (string-take v (string-index-right v #\.))))) | |
df354a77 | 1444 | ;; By default Maxima attempts to write temporary files to |
77af7b24 MW |
1445 | ;; '/tmp/nix-build-maxima-*', which won't exist at run time. |
1446 | ;; Work around that. | |
df354a77 | 1447 | #:make-flags (list "TMPDIR=/tmp") |
df354a77 | 1448 | #:phases (alist-cons-before |
8731e527 | 1449 | 'check 'pre-check |
df354a77 | 1450 | (lambda _ |
8731e527 | 1451 | (chmod "src/maxima" #o555)) |
f36afe4d FB |
1452 | ;; Make sure the doc and emacs files are found in the |
1453 | ;; standard location. Also configure maxima to find gnuplot | |
1454 | ;; without having it on the PATH. | |
1455 | (alist-cons-after | |
1456 | 'install 'post-install | |
1457 | (lambda* (#:key outputs inputs #:allow-other-keys) | |
1458 | (let* ((gnuplot (assoc-ref inputs "gnuplot")) | |
1459 | (out (assoc-ref outputs "out")) | |
1460 | (datadir (string-append out "/share/maxima/" ,version))) | |
1461 | (with-directory-excursion out | |
1462 | (mkdir-p "share/emacs") | |
1463 | (mkdir-p "share/doc") | |
1464 | (symlink | |
1465 | (string-append datadir "/emacs/") | |
1466 | (string-append out "/share/emacs/site-lisp")) | |
1467 | (symlink | |
1468 | (string-append datadir "/doc/") | |
1469 | (string-append out "/share/doc/maxima")) | |
1470 | (with-atomic-file-replacement | |
1471 | (string-append datadir "/share/maxima-init.lisp") | |
1472 | (lambda (in out) | |
1473 | (format out "~a ~s~a~%" | |
1474 | "(setf $gnuplot_command " | |
1475 | (string-append gnuplot "/bin/gnuplot") ")") | |
1476 | (dump-port in out)))))) | |
1477 | %standard-phases)))) | |
8731e527 JD |
1478 | (home-page "http://maxima.sourceforge.net") |
1479 | (synopsis "Numeric and symbolic expression manipulation") | |
1480 | (description "Maxima is a system for the manipulation of symbolic and | |
1481 | numerical expressions. It yields high precision numeric results by using | |
1482 | exact fractions, arbitrary precision integers, and variable precision floating | |
e881752c | 1483 | point numbers.") |
8731e527 JD |
1484 | ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+. |
1485 | ;; Others simply say "GNU General Public License" without stating a | |
1486 | ;; version (which implicitly means gpl1+). | |
1487 | ;; At least one file (src/maxima.asd) says "version 2." | |
1488 | ;; GPLv2 only is therefore the smallest subset. | |
f36afe4d | 1489 | (license license:gpl2))) |
ec322be2 | 1490 | |
9aafbc0c MW |
1491 | (define-public wxmaxima |
1492 | (package | |
1493 | (name "wxmaxima") | |
1494 | (version "15.04.0") | |
1495 | (source | |
1496 | (origin | |
1497 | (method url-fetch) | |
1498 | (uri (string-append "mirror://sourceforge/wxmaxima/wxMaxima/" | |
1499 | version "/" name "-" version ".tar.gz")) | |
1500 | (sha256 | |
1501 | (base32 | |
1502 | "1fm47ah4aw5qdjqhkz67w5fwhy8yfffa5z896crp0d3hk2bh4180")))) | |
1503 | (build-system gnu-build-system) | |
1504 | (inputs | |
1505 | `(("wxwidgets" ,wxwidgets) | |
1506 | ("maxima" ,maxima))) | |
1507 | (arguments | |
1508 | `(#:phases (modify-phases %standard-phases | |
1509 | (add-after | |
1510 | 'install 'wrap-program | |
1511 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1512 | (wrap-program (string-append (assoc-ref outputs "out") | |
1513 | "/bin/wxmaxima") | |
1514 | `("PATH" ":" prefix | |
1515 | (,(string-append (assoc-ref inputs "maxima") | |
1516 | "/bin")))) | |
1517 | #t))))) | |
1518 | (home-page "https://andrejv.github.io/wxmaxima/") | |
1519 | (synopsis "Graphical user interface for the Maxima computer algebra system") | |
1520 | (description | |
1521 | "wxMaxima is a graphical user interface for the Maxima computer algebra | |
1522 | system. It eases the use of Maxima by making most of its commands available | |
1523 | through a menu system and by providing input dialogs for commands that require | |
1524 | more than one argument. It also implements its own display engine that | |
1525 | outputs mathematical symbols directly instead of depicting them with ASCII | |
1526 | characters. | |
1527 | ||
1528 | wxMaxima also features 2D and 3D inline plots, simple animations, mixing of | |
1529 | text and mathematical calculations to create documents, exporting of input and | |
1530 | output to TeX, and a browser for Maxima's manual including command index and | |
1531 | full text searching.") | |
1532 | (license license:gpl2+))) | |
1533 | ||
b15e47f9 RW |
1534 | (define-public armadillo |
1535 | (package | |
1536 | (name "armadillo") | |
458b47e3 | 1537 | (version "6.700.4") |
b15e47f9 RW |
1538 | (source (origin |
1539 | (method url-fetch) | |
1540 | (uri (string-append "mirror://sourceforge/arma/armadillo-" | |
1541 | version ".tar.gz")) | |
1542 | (sha256 | |
1543 | (base32 | |
458b47e3 | 1544 | "0dsdjcps5l2nhg0455rrc708inffarzj7n435vj4sm9lxwf21wg9")))) |
b15e47f9 RW |
1545 | (build-system cmake-build-system) |
1546 | (arguments `(#:tests? #f)) ;no test target | |
1547 | (inputs | |
1548 | `(("openblas" ,openblas) | |
1549 | ("lapack" ,lapack) | |
1550 | ("arpack" ,arpack-ng))) | |
1551 | (home-page "http://arma.sourceforge.net/") | |
1552 | (synopsis "C++ linear algebra library") | |
1553 | (description | |
1554 | "Armadillo is a C++ linear algebra library, aiming towards a good balance | |
1555 | between speed and ease of use. It is useful for algorithm development | |
1556 | directly in C++, or quick conversion of research code into production | |
1557 | environments. It can be used for machine learning, pattern recognition, | |
1558 | signal processing, bioinformatics, statistics, econometrics, etc. The library | |
1559 | provides efficient classes for vectors, matrices and cubes, as well as 150+ | |
1560 | associated functions (eg. contiguous and non-contiguous submatrix views).") | |
1561 | (license license:mpl2.0))) | |
1562 | ||
e22d4ca4 RW |
1563 | (define-public armadillo-for-rcpparmadillo |
1564 | (package (inherit armadillo) | |
c5ad883b | 1565 | (version "6.700.3") |
e22d4ca4 RW |
1566 | (source (origin |
1567 | (method url-fetch) | |
1568 | (uri (string-append "mirror://sourceforge/arma/armadillo-" | |
1569 | version ".tar.gz")) | |
1570 | (sha256 | |
1571 | (base32 | |
c5ad883b | 1572 | "1vnhifa7d0aij3kv5bxf6m91d99h3y2fyj48jrx7jcvwyb1q5wwq")))))) |
e22d4ca4 | 1573 | |
279663ef RW |
1574 | (define-public muparser |
1575 | (package | |
1576 | (name "muparser") | |
1577 | (version "2.2.5") | |
1578 | (source | |
1579 | (origin | |
1580 | (method svn-fetch) | |
1581 | (uri (svn-reference | |
1582 | (url "http://muparser.googlecode.com/svn/trunk/") | |
1583 | (revision 34))) | |
1584 | (sha256 | |
1585 | (base32 | |
1586 | "1d6bdbhx9zj3srwj3m7c9hvr18gnx1fx43h6d25my7q85gicpcwn")))) | |
1587 | (build-system gnu-build-system) | |
1588 | (arguments | |
1589 | `(#:configure-flags '("--enable-samples=no") | |
1590 | #:tests? #f)) ;no "check" target | |
1591 | (home-page "http://muparser.beltoforion.de/") | |
1592 | (synopsis "Fast parser library for mathematical expressions") | |
1593 | (description | |
1594 | "muParser is an extensible high performance math parser library. It is | |
1595 | based on transforming an expression into a bytecode and precalculating | |
1596 | constant parts of it.") | |
1597 | (license license:expat))) | |
1598 | ||
e73b49fb RW |
1599 | (define-public openblas |
1600 | (package | |
1601 | (name "openblas") | |
69851c59 | 1602 | (version "0.2.15") |
e73b49fb RW |
1603 | (source |
1604 | (origin | |
1605 | (method url-fetch) | |
1606 | (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v" | |
1607 | version)) | |
1608 | (file-name (string-append name "-" version ".tar.gz")) | |
1609 | (sha256 | |
1610 | (base32 | |
69851c59 | 1611 | "1k5f6vjlk54qlplk5m7xkbaw6g2y7dl50lwwdv6xsbcsgsbxfcpy")))) |
e73b49fb RW |
1612 | (build-system gnu-build-system) |
1613 | (arguments | |
5b5ea159 | 1614 | `(#:tests? #f ;no "check" target |
bd0b4379 RW |
1615 | ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no |
1616 | ;; TARGET is specified, OpenBLAS will tune itself to the build host, so | |
1617 | ;; we need to disable substitutions. | |
71923a91 AE |
1618 | #:substitutable? |
1619 | ,(let ((system (or (%current-target-system) (%current-system)))) | |
1620 | (or (string-prefix? "x86_64" system) | |
bd0b4379 RW |
1621 | (string-prefix? "i686" system) |
1622 | (string-prefix? "mips" system))) | |
e73b49fb RW |
1623 | #:make-flags |
1624 | (list (string-append "PREFIX=" (assoc-ref %outputs "out")) | |
1625 | "SHELL=bash" | |
af5b817e RW |
1626 | "NO_LAPACK=1" |
1627 | ;; Build the library for all supported CPUs. This allows | |
1628 | ;; switching CPU targets at runtime with the environment variable | |
1629 | ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type. | |
71923a91 AE |
1630 | ;; Unfortunately, this is not supported on non-x86 architectures, |
1631 | ;; where it leads to failed builds. | |
1632 | ,@(let ((system (or (%current-target-system) (%current-system)))) | |
8a637e79 RW |
1633 | (cond |
1634 | ((or (string-prefix? "x86_64" system) | |
71923a91 | 1635 | (string-prefix? "i686" system)) |
8a637e79 RW |
1636 | '("DYNAMIC_ARCH=1")) |
1637 | ;; On MIPS we force the "SICORTEX" TARGET, as for the other | |
1638 | ;; two available MIPS targets special extended instructions | |
1639 | ;; for Loongson cores are used. | |
1640 | ((string-prefix? "mips" system) | |
1641 | '("TARGET=SICORTEX")) | |
1642 | (else '())))) | |
e73b49fb RW |
1643 | ;; no configure script |
1644 | #:phases (alist-delete 'configure %standard-phases))) | |
1645 | (inputs | |
19afbea1 | 1646 | `(("fortran" ,gfortran))) |
e73b49fb RW |
1647 | (native-inputs |
1648 | `(("cunit" ,cunit) | |
1649 | ("perl" ,perl))) | |
1650 | (home-page "http://www.openblas.net/") | |
1651 | (synopsis "Optimized BLAS library based on GotoBLAS") | |
1652 | (description | |
1653 | "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.") | |
1654 | (license license:bsd-3))) | |
1655 | ||
e1605e36 RW |
1656 | (define-public openlibm |
1657 | (package | |
1658 | (name "openlibm") | |
1659 | (version "0.4.1") | |
1660 | (source | |
1661 | (origin | |
1662 | (method url-fetch) | |
1663 | (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v" | |
1664 | version ".tar.gz")) | |
1665 | (file-name (string-append name "-" version ".tar.gz")) | |
1666 | (sha256 | |
1667 | (base32 | |
1668 | "0cwqqqlblj3kzp9aq1wnpfs1fl0qd1wp1xzm5shb09w06i4rh9nn")))) | |
1669 | (build-system gnu-build-system) | |
1670 | (arguments | |
1671 | `(#:make-flags | |
1672 | (list (string-append "prefix=" (assoc-ref %outputs "out"))) | |
1673 | #:phases | |
1674 | ;; no configure script | |
1675 | (alist-delete 'configure %standard-phases) | |
1676 | #:tests? #f)) ;the tests are part of the default target | |
1677 | (home-page "http://openlibm.org/") | |
1678 | (synopsis "Portable C mathematical library (libm)") | |
1679 | (description | |
1680 | "OpenLibm is an effort to have a high quality, portable, standalone C | |
1681 | mathematical library (libm). It can be used standalone in applications and | |
1682 | programming language implementations. The project was born out of a need to | |
e881752c | 1683 | have a good libm for the Julia programming language that worked consistently |
e1605e36 RW |
1684 | across compilers and operating systems, and in 32-bit and 64-bit |
1685 | environments.") | |
1686 | ;; See LICENSE.md for details. | |
1687 | (license (list license:expat | |
1688 | license:isc | |
1689 | license:bsd-2 | |
1690 | license:public-domain | |
1691 | license:lgpl2.1+)))) | |
1692 | ||
e62be58f RW |
1693 | (define-public openspecfun |
1694 | (package | |
1695 | (name "openspecfun") | |
1696 | (version "0.4") | |
1697 | (source | |
1698 | (origin | |
1699 | (method url-fetch) | |
1700 | (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v" | |
1701 | version ".tar.gz")) | |
1702 | (file-name (string-append name "-" version ".tar.gz")) | |
1703 | (sha256 | |
1704 | (base32 | |
1705 | "0nsa3jjmlhcqkw5ba5ypbn3n0c8b6lc22zzlxnmxkxi9shhdx65z")))) | |
1706 | (build-system gnu-build-system) | |
1707 | (arguments | |
1708 | '(#:tests? #f ;no "check" target | |
1709 | #:make-flags | |
1710 | (list (string-append "prefix=" (assoc-ref %outputs "out"))) | |
1711 | ;; no configure script | |
1712 | #:phases (alist-delete 'configure %standard-phases))) | |
1713 | (inputs | |
19afbea1 | 1714 | `(("fortran" ,gfortran))) |
e62be58f RW |
1715 | (home-page "https://github.com/JuliaLang/openspecfun") |
1716 | (synopsis "Collection of special mathematical functions") | |
1717 | (description | |
1718 | "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a | |
1719 | portable package for Bessel Functions of a Complex Argument and Nonnegative | |
1720 | Order; it contains subroutines for computing Bessel functions and Airy | |
1721 | functions. Faddeeva allows computing the various error functions of arbitrary | |
1722 | complex arguments (Faddeeva function, error function, complementary error | |
1723 | function, scaled complementary error function, imaginary error function, and | |
1724 | Dawson function); given these, one can also easily compute Voigt functions, | |
1725 | Fresnel integrals, and similar related functions as well.") | |
1726 | ;; Faddeeva is released under the Expat license; AMOS is included as | |
1727 | ;; public domain software. | |
1728 | (license (list license:expat license:public-domain)))) | |
1729 | ||
2742f87e RW |
1730 | (define-public suitesparse |
1731 | (package | |
1732 | (name "suitesparse") | |
1733 | (version "4.4.3") | |
1734 | (source | |
1735 | (origin | |
1736 | (method url-fetch) | |
1737 | (uri (string-append | |
1738 | "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-" | |
1739 | version ".tar.gz")) | |
1740 | (sha256 | |
1741 | (base32 | |
1742 | "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5")))) | |
1743 | (build-system gnu-build-system) | |
1744 | (arguments | |
1745 | '(#:parallel-build? #f ;cholmod build fails otherwise | |
1746 | #:tests? #f ;no "check" target | |
1747 | #:make-flags | |
1748 | (list "CC=gcc" | |
1749 | "BLAS=-lblas" | |
1750 | "TBB=-ltbb" | |
1751 | "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used | |
1752 | (string-append "INSTALL_LIB=" | |
1753 | (assoc-ref %outputs "out") "/lib") | |
1754 | (string-append "INSTALL_INCLUDE=" | |
1755 | (assoc-ref %outputs "out") "/include")) | |
1756 | #:phases | |
1757 | (alist-cons-before | |
1758 | 'install 'prepare-out | |
1759 | ;; README.txt states that the target directories must exist prior to | |
1760 | ;; running "make install". | |
1761 | (lambda _ | |
1762 | (mkdir-p (string-append (assoc-ref %outputs "out") "/lib")) | |
1763 | (mkdir-p (string-append (assoc-ref %outputs "out") "/include"))) | |
1764 | ;; no configure script | |
1765 | (alist-delete 'configure %standard-phases)))) | |
1766 | (inputs | |
1767 | `(("tbb" ,tbb) | |
1768 | ("lapack" ,lapack))) | |
1769 | (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html") | |
1770 | (synopsis "Suite of sparse matrix software") | |
1771 | (description | |
1772 | "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK, | |
1773 | multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR, | |
1774 | multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit | |
1775 | simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and | |
1776 | CXSparse, a concise sparse Cholesky factorization package; and many other | |
1777 | packages.") | |
1778 | ;; LGPLv2.1+: | |
1779 | ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL | |
1780 | ;; GPLv2+: | |
1781 | ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK | |
1782 | (license (list license:gpl2+ license:lgpl2.1+)))) | |
1783 | ||
ec322be2 FB |
1784 | (define-public atlas |
1785 | (package | |
1786 | (name "atlas") | |
1787 | (version "3.10.2") | |
1788 | (source (origin | |
1789 | (method url-fetch) | |
1790 | (uri (string-append "mirror://sourceforge/math-atlas/atlas" | |
1791 | version ".tar.bz2")) | |
1792 | (sha256 | |
1793 | (base32 | |
1794 | "0bqh4bdnjdyww4mcpg6kn0x7338mfqbdgysn97dzrwwb26di7ars")))) | |
1795 | (build-system gnu-build-system) | |
1796 | (home-page "http://math-atlas.sourceforge.net/") | |
19afbea1 | 1797 | (inputs `(("gfortran" ,gfortran) |
ec322be2 FB |
1798 | ("lapack-tar" ,(package-source lapack)))) |
1799 | (outputs '("out" "doc")) | |
01480b9e FB |
1800 | ;; For the moment we drop support for MIPS at it fails to compile. See |
1801 | ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html | |
1802 | (supported-systems (delete "mips64el-linux" %supported-systems)) | |
ec322be2 FB |
1803 | (arguments |
1804 | `(#:parallel-build? #f | |
1805 | #:parallel-tests? #f | |
f15615b1 LC |
1806 | |
1807 | ;; ATLAS tunes itself for the machine it is built on, as explained at | |
1808 | ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>. | |
1809 | ;; For this reason, we want users to build it locally instead of using | |
1810 | ;; substitutes. | |
1811 | #:substitutable? #f | |
1812 | ||
ec322be2 FB |
1813 | #:modules ((srfi srfi-26) |
1814 | (srfi srfi-1) | |
1815 | (guix build gnu-build-system) | |
1816 | (guix build utils)) | |
40029cbe | 1817 | #:configure-flags |
ec322be2 FB |
1818 | `(;; Generate position independent code suitable for dynamic libraries |
1819 | ;; and use WALL timer to get more accurate timing. | |
1820 | "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL" | |
1821 | ;; Set word width. | |
1822 | "-b" | |
1823 | ,,(if (string-match "64" (%current-system)) | |
1824 | "64" | |
1825 | "32") | |
1826 | ;; Disable parallel build as it gives errors: atlas_pthread.h is | |
1827 | ;; needed to compile C files before it is generated. | |
1828 | "-Ss" "pmake" "make -j 1" | |
af89a667 FB |
1829 | ;; Probe is failing for MIPS. We therefore define the system |
1830 | ;; architecture explicitly by setting (-A) MACHINETYPE = 49 | |
1831 | ;; 'MIPSR1xK' and (-V) ISA = 1 'none'. | |
1832 | ,,@(if (string-prefix? "mips" (%current-system)) | |
1833 | (list "-A" "49" "-V" "1") | |
1834 | (list)) | |
ec322be2 FB |
1835 | ;; Generate shared libraries. |
1836 | "--shared" | |
1837 | ;; Build a full LAPACK library. | |
1838 | ,(string-append "--with-netlib-lapack-tarfile=" | |
1839 | (assoc-ref %build-inputs "lapack-tar"))) | |
1840 | #:phases | |
1841 | (alist-cons-after | |
1842 | 'install 'install-doc | |
1843 | (lambda* (#:key outputs inputs #:allow-other-keys) | |
40029cbe | 1844 | (let ((doc (string-append (assoc-ref outputs "doc") |
ec322be2 FB |
1845 | "/share/doc/atlas"))) |
1846 | (mkdir-p doc) | |
40029cbe | 1847 | (fold (lambda (file previous) |
ec322be2 FB |
1848 | (and previous (zero? (system* "cp" file doc)))) |
1849 | #t (find-files "../ATLAS/doc" ".*")))) | |
1850 | (alist-cons-after | |
1851 | 'check 'check-pt | |
1852 | (lambda _ (zero? (system* "make" "ptcheck"))) | |
1853 | ;; Fix files required to run configure. | |
1854 | (alist-cons-before | |
1855 | 'configure 'fix-/bin/sh | |
1856 | (lambda _ | |
1857 | ;; Use `sh', not `/bin/sh'. | |
1858 | (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c") | |
1859 | (("/bin/sh") | |
1860 | "sh"))) | |
1861 | ;; Fix /bin/sh in generated make files. | |
1862 | (alist-cons-after | |
1863 | 'configure 'fix-/bin/sh-in-generated-files | |
1864 | (lambda _ | |
1865 | (substitute* (find-files "." "^[Mm]ake\\.inc.*") | |
1866 | (("/bin/sh") | |
1867 | "sh"))) | |
1868 | ;; ATLAS configure program does not accepts the default flags | |
1869 | ;; passed by the 'gnu-build-system'. | |
1870 | (alist-replace | |
1871 | 'configure | |
1872 | (lambda* (#:key native-inputs inputs outputs | |
1873 | (configure-flags '()) | |
1874 | #:allow-other-keys #:rest args) | |
1875 | (let* ((prefix (assoc-ref outputs "out")) | |
1876 | (bash (or (and=> (assoc-ref | |
1877 | (or native-inputs inputs) "bash") | |
1878 | (cut string-append <> "/bin/bash")) | |
1879 | "/bin/sh")) | |
1880 | (flags `(,(string-append "--prefix=" prefix) | |
1881 | ,@configure-flags)) | |
1882 | (abs-srcdir (getcwd)) | |
1883 | (srcdir (string-append "../" (basename abs-srcdir)))) | |
1884 | (format #t "source directory: ~s (relative from build: ~s)~%" | |
1885 | abs-srcdir srcdir) | |
1886 | (mkdir "../build") | |
1887 | (chdir "../build") | |
1888 | (format #t "build directory: ~s~%" (getcwd)) | |
1889 | (format #t "configure flags: ~s~%" flags) | |
1890 | (zero? (apply system* bash | |
1891 | (string-append srcdir "/configure") | |
1892 | flags)))) | |
1893 | %standard-phases))))))) | |
1894 | (synopsis "Automatically Tuned Linear Algebra Software") | |
1895 | (description | |
1896 | "ATLAS is an automatically tuned linear algebra software library | |
1897 | providing C and Fortran77 interfaces to a portably efficient BLAS | |
1898 | implementation, as well as a few routines from LAPACK. | |
1899 | ||
f15615b1 LC |
1900 | Optimization occurs at build time. For this reason, the library is built on |
1901 | the machine where it is installed, without resorting to pre-built substitutes. | |
ec322be2 | 1902 | |
f15615b1 LC |
1903 | Before building the library, CPU throttling should be disabled. This can be |
1904 | done in the BIOS, or, on GNU/Linux, with the following commands: | |
ec322be2 FB |
1905 | |
1906 | cpufreq-selector -g performance -c 0 | |
1907 | ... | |
1908 | cpufreq-selector -g performance -c N-1 | |
1909 | ||
1910 | where N is the number of cores of your CPU. Failure to do so will result in a | |
1911 | library with poor performance.") | |
1912 | (license license:bsd-3))) | |
c12efc72 AE |
1913 | |
1914 | (define-public glm | |
1915 | (package | |
1916 | (name "glm") | |
1917 | (version "0.9.6.3") | |
1918 | (source | |
1919 | (origin | |
1920 | (method url-fetch) | |
1921 | (uri (string-append "mirror://sourceforge/ogl-math/glm-" | |
1922 | version ".zip")) | |
1923 | (sha256 | |
1924 | (base32 | |
1925 | "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l")))) | |
1926 | (build-system cmake-build-system) | |
1927 | (native-inputs | |
1928 | `(("unzip" ,unzip))) | |
1929 | (home-page "http://glm.g-truc.net") | |
1930 | (synopsis "OpenGL Mathematics library") | |
1931 | (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics | |
1932 | library for graphics software based on the OpenGL Shading Language (GLSL) | |
1933 | specifications.") | |
1934 | (license license:expat))) | |
7f18257b AE |
1935 | |
1936 | (define-public lpsolve | |
1937 | (package | |
1938 | (name "lpsolve") | |
1939 | (version "5.5.2.0") | |
1940 | (source | |
1941 | (origin | |
1942 | (method url-fetch) | |
1943 | (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version | |
1944 | "/lp_solve_" version "_source.tar.gz")) | |
1945 | (sha256 | |
1946 | (base32 | |
1947 | "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq")) | |
1948 | (modules '((guix build utils))) | |
1949 | (snippet | |
1950 | '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc") | |
1951 | (("^c=cc") "c=gcc") | |
1952 | ;; Pretend to be on a 64 bit platform to obtain a common directory | |
1953 | ;; name for the build results on all architectures; nothing else | |
1954 | ;; seems to depend on it. | |
1955 | (("^PLATFORM=.*$") "PLATFORM=ux64\n"))))) | |
1956 | (build-system gnu-build-system) | |
1957 | (arguments | |
1958 | `(#:tests? #f ; no check target | |
1959 | #:phases | |
1960 | (modify-phases %standard-phases | |
1961 | (delete 'configure) | |
1962 | (replace 'build | |
1963 | (lambda _ | |
1964 | (with-directory-excursion "lpsolve55" | |
1965 | (system* "bash" "ccc")) | |
1966 | (with-directory-excursion "lp_solve" | |
1967 | (system* "bash" "ccc")) | |
1968 | #t)) | |
1969 | (replace 'install | |
1970 | (lambda* (#:key outputs #:allow-other-keys) | |
1971 | (let* ((out (assoc-ref outputs "out")) | |
1972 | (bin (string-append out "/bin")) | |
1973 | (lib (string-append out "/lib")) | |
1974 | ;; This is where LibreOffice expects to find the header | |
1975 | ;; files, and where they are installed by Debian. | |
1976 | (include (string-append out "/include/lpsolve"))) | |
1977 | (mkdir-p lib) | |
1978 | (copy-file "lpsolve55/bin/ux64/liblpsolve55.a" | |
1979 | (string-append lib "/liblpsolve55.a")) | |
1980 | (copy-file "lpsolve55/bin/ux64/liblpsolve55.so" | |
1981 | (string-append lib "/liblpsolve55.so")) | |
96c46210 LC |
1982 | (install-file "lp_solve/bin/ux64/lp_solve" bin) |
1983 | ||
7f18257b AE |
1984 | ;; Install a subset of the header files as on Debian |
1985 | ;; (plus lp_bit.h, which matches the regular expression). | |
96c46210 LC |
1986 | (for-each (lambda (name) |
1987 | (install-file name include)) | |
1988 | (find-files "." "lp_[HMSa-z].*\\.h$")) | |
7f18257b | 1989 | (with-directory-excursion "shared" |
96c46210 LC |
1990 | (for-each (lambda (name) |
1991 | (install-file name include)) | |
1992 | (find-files "." "\\.h$"))) | |
7f18257b AE |
1993 | #t)))))) |
1994 | (home-page "http://lpsolve.sourceforge.net/") | |
1995 | (synopsis "Mixed integer linear programming (MILP) solver") | |
1996 | (description | |
1997 | "lp_solve is a mixed integer linear programming solver based on the | |
1998 | revised simplex and the branch-and-bound methods.") | |
1999 | (license license:lgpl2.1+))) | |
a17d4564 EB |
2000 | |
2001 | (define-public dealii | |
2002 | (package | |
2003 | (name "dealii") | |
2004 | (version "8.2.1") | |
2005 | (source | |
2006 | (origin | |
2007 | (method url-fetch) | |
2008 | (uri (string-append "https://github.com/dealii/dealii/releases/" | |
2009 | "download/v" version "/dealii-" version ".tar.gz")) | |
2010 | (sha256 | |
2011 | (base32 | |
2012 | "185jych0gdnpkjwxni7pd0dda149492zwq2457xdjg76bzj78mnp")) | |
fc1adab1 | 2013 | (patches (search-patches "dealii-p4est-interface.patch")) |
a17d4564 EB |
2014 | (modules '((guix build utils))) |
2015 | (snippet | |
2016 | ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost | |
2017 | '(delete-file-recursively "bundled")))) | |
2018 | (build-system cmake-build-system) | |
2019 | (inputs | |
2020 | `(("tbb" ,tbb) | |
2021 | ("zlib" ,zlib) | |
2022 | ("boost" ,boost) | |
2023 | ("p4est" ,p4est) | |
2024 | ("blas" ,openblas) | |
2025 | ("lapack" ,lapack) | |
2026 | ("arpack" ,arpack-ng) | |
2027 | ("muparser" ,muparser) | |
2028 | ("gfortran" ,gfortran) | |
2029 | ("suitesparse" ,suitesparse))) ;for UMFPACK | |
2030 | (arguments | |
2031 | `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease | |
2032 | #:configure-flags '("-DCOMPAT_FILES=OFF") ;Follow new directory structure | |
2033 | #:phases (modify-phases %standard-phases | |
2034 | (add-after | |
2035 | 'install 'hint-example-prefix | |
2036 | ;; Set Cmake hints in examples so that they can find this | |
2037 | ;; deal.II when configuring. | |
2038 | (lambda* (#:key outputs #:allow-other-keys) | |
2039 | (let* ((out (assoc-ref %outputs "out")) | |
2040 | (exmpl (string-append out "/share/doc" | |
2041 | "/dealii/examples"))) | |
2042 | (substitute* (find-files exmpl "CMakeLists.txt") | |
2043 | (("([[:space:]]*HINTS.*)\n" _ line) | |
2044 | (string-append line " $ENV{HOME}/.guix-profile " | |
2045 | out "\n"))) | |
2046 | #t)))))) | |
2047 | (home-page "https://www.dealii.org") | |
2048 | (synopsis "Finite element library") | |
2049 | (description | |
2050 | "Deal.II is a C++ program library targeted at the computational solution | |
2051 | of partial differential equations using adaptive finite elements. The main | |
2052 | aim of deal.II is to enable rapid development of modern finite element codes, | |
2053 | using among other aspects adaptive meshes and a wide array of tools often used | |
2054 | in finite element programs.") | |
2055 | (license license:lgpl2.1+))) | |
2056 | ||
2057 | (define-public dealii-openmpi | |
2058 | (package (inherit dealii) | |
2059 | (name "dealii-openmpi") | |
2060 | (inputs | |
2061 | `(("mpi" ,openmpi) | |
2062 | ;;Supported only with MPI: | |
2063 | ("p4est" ,p4est-openmpi) | |
2064 | ("petsc" ,petsc-openmpi) | |
2065 | ("slepc" ,slepc-openmpi) | |
2066 | ("metis" ,metis) ;for MUMPS | |
2067 | ("scalapack" ,scalapack) ;for MUMPS | |
2068 | ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings | |
2069 | ("arpack" ,arpack-ng-openmpi) | |
2070 | ,@(fold alist-delete (package-inputs dealii) | |
2071 | '("p4est" "arpack")))) | |
2072 | (arguments | |
2073 | (substitute-keyword-arguments (package-arguments dealii) | |
2074 | ((#:configure-flags cf) | |
2075 | ``("-DMPI_C_COMPILER=mpicc" | |
2076 | "-DMPI_CXX_COMPILER=mpicxx" | |
2077 | "-DMPI_Fortran_COMPILER=mpifort" | |
2078 | ,@,cf)))) | |
2079 | (synopsis "Finite element library (with MPI support)"))) | |
194c7f95 AE |
2080 | |
2081 | (define-public flann | |
2082 | (package | |
2083 | (name "flann") | |
2084 | (version "1.8.4") | |
2085 | (source | |
2086 | (origin | |
2087 | (method url-fetch) | |
2088 | (uri | |
2089 | (string-append | |
2090 | "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-" | |
2091 | version "-src.zip")) | |
2092 | (sha256 | |
2093 | (base32 | |
2094 | "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz")))) | |
2095 | (build-system cmake-build-system) | |
2096 | (native-inputs | |
2097 | `(("unzip" ,unzip))) | |
2098 | (inputs | |
2099 | `(("hdf5" ,hdf5) | |
2100 | ("octave" ,octave) | |
2101 | ("python" ,python-2) ; print syntax | |
2102 | ;; ("python2-numpy" ,python2-numpy) ; only required for the tests | |
2103 | ("zlib" ,zlib))) | |
2104 | (arguments | |
2105 | `(#:tests? #f)) ; The test data are downloaded from the Internet. | |
2106 | (home-page "http://www.cs.ubc.ca/research/flann/") | |
2107 | (synopsis "Library for approximate nearest neighbors computation") | |
2108 | (description "FLANN is a library for performing fast approximate | |
2109 | nearest neighbor searches in high dimensional spaces. It implements a | |
2110 | collection of algorithms and a system for automatically choosing the best | |
2111 | algorithm and optimum parameters depending on the dataset. | |
2112 | ||
2113 | FLANN is written in C++ and contains bindings for C, Octave and Python.") | |
2114 | (license (license:non-copyleft "file://COPYING" | |
2115 | "See COPYING in the distribution.")))) | |
d8c97beb EF |
2116 | |
2117 | (define-public wcalc | |
2118 | (package | |
2119 | (name "wcalc") | |
2120 | (version "2.5") | |
2121 | (source | |
2122 | (origin | |
2123 | (method url-fetch) | |
2124 | (uri | |
2125 | (string-append | |
2126 | "mirror://sourceforge/w-calc/wcalc-" version ".tar.bz2")) | |
2127 | (sha256 | |
2128 | (base32 | |
2129 | "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f")))) | |
2130 | (build-system gnu-build-system) | |
2131 | (inputs | |
2132 | `(("mpfr" ,mpfr) | |
2133 | ("readline" ,readline))) | |
2134 | (home-page "http://w-calc.sourceforge.net/index.php") | |
2135 | (synopsis "Flexible command-line scientific calculator") | |
2136 | (description "Wcalc is a very capable calculator. It has standard functions | |
2137 | (sin, asin, and sinh for example, in either radians or degrees), many | |
2138 | pre-defined constants (pi, e, c, etc.), support for using variables, \"active\" | |
2139 | variables, a command history, hex/octal/binary input and output, unit | |
2140 | conversions, embedded comments, and an expandable expression entry field. It | |
2141 | evaluates expressions using the standard order of operations.") | |
2142 | (license license:gpl2+))) | |
45147b0c FH |
2143 | |
2144 | (define-public xaos | |
2145 | (package | |
2146 | (name "xaos") | |
2147 | (version "3.6") | |
2148 | (source (origin | |
2149 | (method url-fetch) | |
2150 | (uri (string-append "mirror://sourceforge/xaos/xaos-" | |
2151 | version ".tar.gz")) | |
2152 | (sha256 | |
2153 | (base32 | |
2154 | "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq")))) | |
2155 | (build-system gnu-build-system) | |
2156 | (native-inputs `(("gettext" ,gnu-gettext))) | |
2157 | (inputs `(("libx11" ,libx11) | |
2158 | ("zlib" ,zlib) | |
2159 | ("libpng" ,libpng) | |
2160 | ("gsl" ,gsl))) | |
2161 | (arguments | |
2162 | `(#:tests? #f ;no "check" target | |
2163 | #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale"))) | |
2164 | (synopsis "Real-time fractal zoomer") | |
2165 | (description "GNU XaoS is a graphical program that generates fractal | |
2166 | patterns and allows you to zoom in and out of them infinitely in a fluid, | |
2167 | continuous manner. It also includes tutorials that help to explain how fractals | |
2168 | are built. It can generate many different fractal types such as the Mandelbrot | |
2169 | set.") | |
2170 | (home-page "http://www.gnu.org/software/xaos/") | |
2171 | (license license:gpl2+))) | |
528bb464 EB |
2172 | |
2173 | (define-public hypre | |
2174 | (package | |
2175 | (name "hypre") | |
2176 | (version "2.11.0") | |
2177 | (source (origin | |
2178 | (method url-fetch) | |
2179 | (uri (string-append "https://github.com/LLNL/hypre/archive/" | |
2180 | "v" version ".tar.gz")) | |
2181 | (file-name (string-append name "-" version ".tar.gz")) | |
2182 | (sha256 | |
2183 | (base32 | |
2184 | "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m")) | |
2185 | (modules '((guix build utils))) | |
2186 | (snippet | |
2187 | '(begin | |
2188 | ;; Remove use of __DATE__ and __TIME__ for reproducibility; | |
2189 | ;; substitute the tarball creation time. | |
2190 | (substitute* "src/utilities/HYPRE_utilities.h" | |
2191 | (("Date Compiled: .*$") | |
2192 | "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n")) | |
2193 | #t)))) | |
2194 | (build-system gnu-build-system) | |
2195 | (outputs '("out" ;6.1 MiB of headers and libraries | |
2196 | "doc")) ;4.8 MiB of documentation | |
2197 | (native-inputs | |
2198 | `(("doc++" ,doc++) | |
2199 | ("netpbm" ,netpbm) | |
2200 | ("texlive" ,texlive) ;full package required for fonts | |
2201 | ("ghostscript" ,ghostscript))) | |
2202 | (inputs | |
2203 | `(("blas" ,openblas) | |
2204 | ("lapack" ,lapack))) | |
2205 | (arguments | |
2206 | `(#:modules ((srfi srfi-1) | |
2207 | ,@%gnu-build-system-modules) | |
2208 | #:configure-flags '("--enable-shared" | |
2209 | "--disable-fortran" | |
2210 | "--without-MPI" | |
2211 | "--with-openmp" | |
2212 | "--with-fei" | |
2213 | "--with-lapack" | |
2214 | "--with-blas") | |
2215 | #:phases | |
2216 | (modify-phases %standard-phases | |
2217 | (add-before 'configure 'chdir-src | |
2218 | (lambda _ (chdir "src"))) | |
2219 | (replace 'configure | |
2220 | (lambda* (#:key build target configure-flags | |
2221 | #:allow-other-keys #:rest args) | |
2222 | (let* ((configure (assoc-ref %standard-phases 'configure))) | |
2223 | (apply configure | |
2224 | (append args | |
2225 | (list #:configure-flags | |
2226 | (cons (string-append | |
2227 | "--host=" (or target build)) | |
2228 | configure-flags))))))) | |
2229 | (add-after 'build 'build-docs | |
2230 | (lambda _ | |
2231 | (zero? (system* "make" "-Cdocs" "pdf" "html")))) | |
2232 | (replace 'check | |
2233 | (lambda _ | |
2234 | (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib")) | |
2235 | (setenv "PATH" (string-append "." ":" (getenv "PATH"))) | |
2236 | (and (system* "make" "check" "CHECKRUN=") | |
2237 | (fold (lambda (filename result) | |
2238 | (and result | |
2239 | (let ((size (stat:size (stat filename)))) | |
2240 | (when (not (zero? size)) | |
2241 | (format #t "~a size ~d; error indication~%" | |
2242 | filename size)) | |
2243 | (zero? size)))) | |
2244 | #t | |
2245 | (find-files "test" ".*\\.err$"))))) | |
2246 | (add-after 'install 'install-docs | |
2247 | (lambda* (#:key outputs #:allow-other-keys) | |
2248 | ;; Custom install because docs/Makefile doesn't honor ${docdir}. | |
2249 | (let* ((doc (assoc-ref outputs "doc")) | |
2250 | (docdir (string-append doc "/share/doc/hypre-" ,version))) | |
2251 | (mkdir-p docdir) | |
2252 | (with-directory-excursion "docs" | |
2253 | (for-each (lambda (base) | |
2254 | (install-file (string-append base ".pdf") docdir) | |
2255 | (copy-recursively base docdir)) ;html docs | |
2256 | '("HYPRE_usr_manual" | |
2257 | "HYPRE_ref_manual"))) | |
2258 | #t)))))) | |
2259 | (home-page "http://www.llnl.gov/casc/hypre/") | |
2260 | (synopsis "Library of solvers and preconditioners for linear equations") | |
2261 | (description | |
2262 | "HYPRE is a software library of high performance preconditioners and | |
2263 | solvers for the solution of large, sparse linear systems of equations. It | |
2264 | features multigrid solvers for both structured and unstructured grid | |
2265 | problems.") | |
2266 | (license license:lgpl2.1))) | |
2267 | ||
2268 | (define-public hypre-openmpi | |
2269 | (package (inherit hypre) | |
2270 | (name "hypre-openmpi") | |
2271 | (inputs | |
2272 | `(("mpi" ,openmpi) | |
2273 | ,@(package-inputs hypre))) | |
2274 | (arguments | |
2275 | (substitute-keyword-arguments (package-arguments hypre) | |
2276 | ((#:configure-flags flags) | |
2277 | ``("--with-MPI" | |
2278 | ,@(delete "--without-MPI" ,flags))))) | |
2279 | (synopsis "Parallel solvers and preconditioners for linear equations") | |
2280 | (description | |
2281 | "HYPRE is a software library of high performance preconditioners and | |
2282 | solvers for the solution of large, sparse linear systems of equations on | |
2283 | parallel computers. It features parallel multigrid solvers for both | |
2284 | structured and unstructured grid problems."))) |