Commit | Line | Data |
---|---|---|
8f8b2451 | 1 | ;;; GNU Guix --- Functional package management for GNU |
b146763a | 2 | ;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr> |
da95c817 | 3 | ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org> |
9c45c519 | 4 | ;;; Copyright © 2014, 2016 John Darrington <jmd@gnu.org> |
dfdf5716 | 5 | ;;; Copyright © 2014, 2015, 2016 Eric Bavier <bavier@member.fsf.org> |
df354a77 | 6 | ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch> |
182d6311 | 7 | ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org> |
458b47e3 | 8 | ;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net> |
32158110 | 9 | ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com> |
9aafbc0c | 10 | ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org> |
723a6910 | 11 | ;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il> |
45147b0c | 12 | ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de> |
ec8c7e47 | 13 | ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> |
b7b27a8f | 14 | ;;; Copyright © 2016 Kei Kebreau <kei@openmailbox.org> |
39b30337 | 15 | ;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org> |
d7cff656 | 16 | ;;; Copyright © 2016 Leo Famulari <leo@famulari.name> |
8f8b2451 AE |
17 | ;;; |
18 | ;;; This file is part of GNU Guix. | |
19 | ;;; | |
20 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
21 | ;;; under the terms of the GNU General Public License as published by | |
22 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
23 | ;;; your option) any later version. | |
24 | ;;; | |
25 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
26 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
27 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
28 | ;;; GNU General Public License for more details. | |
29 | ;;; | |
30 | ;;; You should have received a copy of the GNU General Public License | |
31 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
32 | ||
33 | (define-module (gnu packages maths) | |
ec322be2 | 34 | #:use-module (ice-9 regex) |
8f8b2451 | 35 | #:use-module (gnu packages) |
b5b73a82 | 36 | #:use-module ((guix licenses) #:prefix license:) |
8f8b2451 AE |
37 | #:use-module (guix packages) |
38 | #:use-module (guix download) | |
0e2672ae | 39 | #:use-module (guix utils) |
cec86422 | 40 | #:use-module (guix build utils) |
da95c817 | 41 | #:use-module (guix build-system cmake) |
c9dfa3c7 | 42 | #:use-module (guix build-system gnu) |
ec8c7e47 | 43 | #:use-module (guix build-system r) |
3de01d3f EB |
44 | #:use-module (gnu packages algebra) |
45 | #:use-module (gnu packages bison) | |
a17d4564 | 46 | #:use-module (gnu packages boost) |
e73b49fb | 47 | #:use-module (gnu packages check) |
3de01d3f | 48 | #:use-module (gnu packages cmake) |
c9dfa3c7 | 49 | #:use-module (gnu packages compression) |
668c06ac | 50 | #:use-module (gnu packages curl) |
b7b27a8f | 51 | #:use-module (gnu packages cyrus-sasl) |
528bb464 | 52 | #:use-module (gnu packages documentation) |
57e544e8 | 53 | #:use-module (gnu packages elf) |
3de01d3f | 54 | #:use-module (gnu packages flex) |
668c06ac | 55 | #:use-module (gnu packages fltk) |
f3929800 | 56 | #:use-module (gnu packages fontutils) |
1dba6407 | 57 | #:use-module (gnu packages gettext) |
da95c817 | 58 | #:use-module (gnu packages gcc) |
73fed4f8 | 59 | #:use-module (gnu packages gd) |
668c06ac | 60 | #:use-module (gnu packages ghostscript) |
889187a4 | 61 | #:use-module (gnu packages graphviz) |
f3929800 | 62 | #:use-module (gnu packages gtk) |
45147b0c | 63 | #:use-module (gnu packages image) |
668c06ac | 64 | #:use-module (gnu packages less) |
8731e527 | 65 | #:use-module (gnu packages lisp) |
bc3a2e35 | 66 | #:use-module (gnu packages logging) |
5698b8b8 | 67 | #:use-module (gnu packages gnome) |
1b39a196 | 68 | #:use-module (gnu packages guile) |
668c06ac JD |
69 | #:use-module (gnu packages xorg) |
70 | #:use-module (gnu packages gl) | |
8731e527 | 71 | #:use-module (gnu packages m4) |
d8c7eeb9 | 72 | #:use-module (gnu packages mpi) |
b92eee75 | 73 | #:use-module (gnu packages multiprecision) |
528bb464 | 74 | #:use-module (gnu packages netpbm) |
668c06ac | 75 | #:use-module (gnu packages pcre) |
5698b8b8 | 76 | #:use-module (gnu packages popt) |
c9dfa3c7 AE |
77 | #:use-module (gnu packages perl) |
78 | #:use-module (gnu packages pkg-config) | |
da95c817 | 79 | #:use-module (gnu packages python) |
c9dfa3c7 | 80 | #:use-module (gnu packages readline) |
2742f87e | 81 | #:use-module (gnu packages tbb) |
b7194849 | 82 | #:use-module (gnu packages shells) |
df354a77 | 83 | #:use-module (gnu packages tcl) |
668c06ac | 84 | #:use-module (gnu packages texinfo) |
8f9ac901 | 85 | #:use-module (gnu packages tex) |
b7b27a8f | 86 | #:use-module (gnu packages tls) |
9aafbc0c | 87 | #:use-module (gnu packages wxwidgets) |
c12efc72 | 88 | #:use-module (gnu packages xml) |
a17d4564 EB |
89 | #:use-module (gnu packages zip) |
90 | #:use-module (srfi srfi-1)) | |
8f8b2451 | 91 | |
9c45c519 JD |
92 | (define-public c-graph |
93 | (package | |
94 | (name "c-graph") | |
95 | (version "2.0") | |
96 | (source (origin | |
97 | (method url-fetch) | |
98 | (uri (string-append "mirror://gnu/c-graph/c-graph-" version | |
99 | ".tar.gz")) | |
100 | (sha256 (base32 | |
101 | "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01")))) | |
102 | (build-system gnu-build-system) | |
103 | (inputs | |
104 | `(("fortran" ,gfortran))) | |
a3947cb1 | 105 | (synopsis "Visualizing and demonstrating convolution") |
9c45c519 | 106 | (description |
a3947cb1 LC |
107 | "GNU C-Graph is a tool for demonstrating the theory of convolution. |
108 | Thus, it can serve as an excellent aid to students of signal and systems | |
109 | theory in visualizing the convolution process. Rather than forcing the | |
110 | student to write code, the program offers an intuitive interface with | |
111 | interactive dialogs to guide them.") | |
9c45c519 JD |
112 | (license license:gpl3+) |
113 | (home-page "http://www.gnu.org/software/c-graph/"))) | |
114 | ||
8f8b2451 AE |
115 | (define-public units |
116 | (package | |
117 | (name "units") | |
5e745292 | 118 | (version "2.13") |
8f8b2451 AE |
119 | (source (origin |
120 | (method url-fetch) | |
121 | (uri (string-append "mirror://gnu/units/units-" version | |
122 | ".tar.gz")) | |
123 | (sha256 (base32 | |
5e745292 | 124 | "1awhjw9zjlfb8s5g3yyx63f7ddfcr1sanlbxpqifmrgq24ql198b")))) |
8f8b2451 AE |
125 | (build-system gnu-build-system) |
126 | (synopsis "Conversion between thousands of scales") | |
127 | (description | |
574e86f9 | 128 | "GNU Units converts numeric quantities between units of measure. It |
7c125ce0 AK |
129 | can handle scale changes through adaptive usage of standard scale |
130 | prefixes (micro-, kilo-, etc.). It can also handle nonlinear | |
131 | conversions such as Fahrenheit to Celsius. Its interpreter is powerful | |
132 | enough to be used effectively as a scientific calculator.") | |
8f8b2451 AE |
133 | (license license:gpl3+) |
134 | (home-page "http://www.gnu.org/software/units/"))) | |
c9dfa3c7 | 135 | |
61a529b4 RW |
136 | (define-public double-conversion |
137 | (package | |
138 | (name "double-conversion") | |
139 | (version "1.1.5") | |
140 | (source (origin | |
141 | (method url-fetch) | |
142 | (uri (string-append | |
143 | "https://github.com/floitsch/double-conversion/archive/v" | |
144 | version ".tar.gz")) | |
145 | (file-name (string-append name "-" version ".tar.gz")) | |
146 | (sha256 | |
147 | (base32 | |
148 | "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83")))) | |
149 | (build-system cmake-build-system) | |
150 | (arguments | |
151 | '(#:test-target "test" | |
152 | #:configure-flags '("-DBUILD_SHARED_LIBS=ON" | |
153 | "-DBUILD_TESTING=ON"))) | |
154 | (home-page "https://github.com/floitsch/double-conversion") | |
155 | (synopsis "Conversion routines for IEEE doubles") | |
156 | (description | |
157 | "The double-conversion library provides binary-decimal and decimal-binary | |
158 | routines for IEEE doubles. The library consists of efficient conversion | |
159 | routines that have been extracted from the V8 JavaScript engine.") | |
160 | (license license:bsd-3))) | |
161 | ||
182d6311 ML |
162 | (define-public dionysus |
163 | (package | |
164 | (name "dionysus") | |
165 | (version "1.3.0") | |
166 | (source (origin | |
167 | (method url-fetch) | |
168 | (uri (string-append "mirror://gnu/dionysus/dionysus-" version | |
169 | ".tar.gz")) | |
170 | (sha256 | |
171 | (base32 | |
172 | "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs")))) | |
173 | (build-system gnu-build-system) | |
174 | (inputs `(("tcl" ,tcl))) ;for 'tclsh' | |
175 | (synopsis "Local search for universal constants and scientific values") | |
176 | (description | |
177 | "GNU Dionysus is a convenient system for quickly retrieving the values of | |
178 | mathematical constants used in science and engineering. Values can be | |
179 | searched using a simple command-line tool, choosing from three databases: | |
180 | universal constants, atomic numbers, and constants related to | |
181 | semiconductors.") | |
182 | (license license:gpl3+) | |
183 | (home-page "http://www.gnu.org/software/dionysus/"))) | |
184 | ||
88bd1804 AE |
185 | (define-public gsl |
186 | (package | |
187 | (name "gsl") | |
0534dd93 | 188 | (version "2.1") |
88bd1804 AE |
189 | (source |
190 | (origin | |
191 | (method url-fetch) | |
192 | (uri (string-append "mirror://gnu/gsl/gsl-" | |
193 | version ".tar.gz")) | |
194 | (sha256 | |
195 | (base32 | |
0534dd93 | 196 | "0rhcia9jhr3p1f1wybwyllwqfs9bggz99i3mi5lpyqcpff1hdbar")))) |
88bd1804 | 197 | (build-system gnu-build-system) |
71e0f288 | 198 | (arguments |
5adbe65f | 199 | `(#:parallel-tests? #f)) |
88bd1804 AE |
200 | (home-page "http://www.gnu.org/software/gsl/") |
201 | (synopsis "Numerical library for C and C++") | |
202 | (description | |
a22dc0c4 LC |
203 | "The GNU Scientific Library is a library for numerical analysis in C |
204 | and C++. It includes a wide range of mathematical routines, with over 1000 | |
205 | functions in total. Subject areas covered by the library include: | |
206 | differential equations, linear algebra, Fast Fourier Transforms and random | |
207 | numbers.") | |
88bd1804 AE |
208 | (license license:gpl3+))) |
209 | ||
b92eee75 AE |
210 | (define-public glpk |
211 | (package | |
212 | (name "glpk") | |
f0443377 | 213 | (version "4.60") |
b92eee75 AE |
214 | (source |
215 | (origin | |
216 | (method url-fetch) | |
217 | (uri (string-append "mirror://gnu/glpk/glpk-" | |
218 | version ".tar.gz")) | |
219 | (sha256 | |
220 | (base32 | |
f0443377 | 221 | "15z2ymzqhxwss6wgdj5f7vkyqlqdsjgrvm0x871kmlx0n0664mhk")))) |
b92eee75 AE |
222 | (build-system gnu-build-system) |
223 | (inputs | |
224 | `(("gmp" ,gmp))) | |
225 | (arguments | |
226 | `(#:configure-flags '("--with-gmp"))) | |
227 | (home-page "http://www.gnu.org/software/glpk/") | |
79c311b8 | 228 | (synopsis "GNU Linear Programming Kit, supporting the MathProg language") |
b92eee75 AE |
229 | (description |
230 | "GLPK is a C library for solving large-scale linear programming (LP), | |
231 | mixed integer programming (MIP), and other related problems. It supports the | |
232 | GNU MathProg modeling language, a subset of the AMPL language, and features a | |
233 | translator for the language. In addition to the C library, a stand-alone | |
234 | LP/MIP solver is included in the package.") | |
235 | (license license:gpl3+))) | |
236 | ||
b146763a AE |
237 | (define-public 4ti2 |
238 | (package | |
239 | (name "4ti2") | |
240 | (version "1.6.7") | |
241 | (source | |
242 | (origin | |
243 | (method url-fetch) | |
244 | (uri (string-append "http://www.4ti2.de/version_" version | |
245 | "/4ti2-" version ".tar.gz")) | |
246 | (sha256 | |
247 | (base32 | |
248 | "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl")))) | |
249 | (build-system gnu-build-system) | |
250 | (native-inputs | |
251 | `(("which" ,(@ (gnu packages base) which)))) ; for the tests | |
252 | (inputs | |
253 | `(("glpk" ,glpk) | |
254 | ("gmp" ,gmp))) | |
255 | (home-page "http://www.4ti2.de/") | |
256 | (synopsis "Mathematical tool suite for problems on linear spaces") | |
257 | (description | |
258 | "4ti2 implements algorithms for solving algebraic, geometric and | |
259 | combinatorial problems on linear spaces. Among others, it solves systems | |
260 | of linear equations, computes extreme rays of polyhedral cones, solves | |
261 | integer programming problems and computes Markov bases for statistics.") | |
262 | (license license:gpl2+))) | |
263 | ||
53696f10 AE |
264 | (define-public cddlib |
265 | (package | |
266 | (name "cddlib") | |
267 | (version "0.94h") | |
268 | (source | |
269 | (origin | |
270 | (method url-fetch) | |
271 | (uri (string-append "ftp://ftp.ifor.math.ethz.ch/pub/fukuda/cdd/cddlib-" | |
272 | (string-delete #\. version) ".tar.gz")) | |
273 | (sha256 | |
274 | (base32 | |
275 | "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy")))) | |
276 | (build-system gnu-build-system) | |
277 | (inputs | |
278 | `(("gmp" ,gmp))) | |
279 | (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html") | |
280 | (synopsis "Library for convex hulls and extreme rays of polyhedra") | |
281 | (description | |
282 | "The C-library cddlib implements the Double Description Method of | |
283 | Motzkin et al. for generating all vertices (i.e. extreme points) and extreme | |
284 | rays of a general convex polyhedron given by a system of linear inequalities | |
285 | in arbitrary dimension. It can also be used for the converse operation of | |
286 | computing convex hulls.") | |
287 | (license license:gpl2+))) | |
288 | ||
865a69dd RW |
289 | (define-public arpack-ng |
290 | (package | |
291 | (name "arpack-ng") | |
292 | (version "3.2.0") | |
293 | (source | |
294 | (origin | |
295 | (method url-fetch) | |
296 | (uri (string-append "https://github.com/opencollab/arpack-ng/archive/" | |
297 | version ".tar.gz")) | |
f586c877 | 298 | (file-name (string-append name "-" version ".tar.gz")) |
865a69dd RW |
299 | (sha256 |
300 | (base32 | |
301 | "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff")))) | |
302 | (build-system gnu-build-system) | |
303 | (home-page "https://github.com/opencollab/arpack-ng") | |
304 | (inputs | |
305 | `(("lapack" ,lapack) | |
19afbea1 | 306 | ("fortran" ,gfortran))) |
865a69dd RW |
307 | (synopsis "Fortran subroutines for solving eigenvalue problems") |
308 | (description | |
309 | "ARPACK-NG is a collection of Fortran77 subroutines designed to solve | |
310 | large scale eigenvalue problems.") | |
166191b3 | 311 | (license (license:non-copyleft "file://COPYING" |
865a69dd RW |
312 | "See COPYING in the distribution.")))) |
313 | ||
8c94c886 EB |
314 | (define-public arpack-ng-openmpi |
315 | (package (inherit arpack-ng) | |
316 | (name "arpack-ng-openmpi") | |
317 | (inputs | |
318 | `(("mpi" ,openmpi) | |
319 | ,@(package-inputs arpack-ng))) | |
320 | (arguments `(#:configure-flags '("--enable-mpi"))) | |
321 | (synopsis "Fortran subroutines for solving eigenvalue problems with MPI"))) | |
322 | ||
da95c817 NK |
323 | (define-public lapack |
324 | (package | |
325 | (name "lapack") | |
566146ab | 326 | (version "3.5.0") |
da95c817 NK |
327 | (source |
328 | (origin | |
329 | (method url-fetch) | |
330 | (uri (string-append "http://www.netlib.org/lapack/lapack-" | |
331 | version ".tgz")) | |
332 | (sha256 | |
333 | (base32 | |
566146ab | 334 | "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s")))) |
da95c817 NK |
335 | (build-system cmake-build-system) |
336 | (home-page "http://www.netlib.org/lapack/") | |
19afbea1 | 337 | (inputs `(("fortran" ,gfortran) |
da95c817 NK |
338 | ("python" ,python-2))) |
339 | (arguments | |
7b569b01 RW |
340 | `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES" |
341 | "-DLAPACKE=ON") | |
da95c817 | 342 | #:phases (alist-cons-before |
6a995754 LC |
343 | 'check 'patch-python |
344 | (lambda* (#:key inputs #:allow-other-keys) | |
345 | (let ((python (assoc-ref inputs "python"))) | |
346 | (substitute* "lapack_testing.py" | |
347 | (("/usr/bin/env python") python)))) | |
06ed5982 | 348 | %standard-phases))) |
da95c817 NK |
349 | (synopsis "Library for numerical linear algebra") |
350 | (description | |
351 | "LAPACK is a Fortran 90 library for solving the most commonly occurring | |
352 | problems in numerical linear algebra.") | |
166191b3 | 353 | (license (license:non-copyleft "file://LICENSE" |
da95c817 | 354 | "See LICENSE in the distribution.")))) |
73fed4f8 | 355 | |
e1ff597a EB |
356 | (define-public scalapack |
357 | (package | |
358 | (name "scalapack") | |
359 | (version "2.0.2") | |
360 | (source | |
361 | (origin | |
362 | (method url-fetch) | |
363 | (uri (string-append "http://www.netlib.org/scalapack/scalapack-" | |
364 | version ".tgz")) | |
365 | (sha256 | |
366 | (base32 | |
367 | "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c")))) | |
368 | (build-system cmake-build-system) | |
369 | (inputs | |
370 | `(("mpi" ,openmpi) | |
371 | ("fortran" ,gfortran) | |
372 | ("lapack" ,lapack))) ;for testing only | |
373 | (arguments | |
374 | `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES"))) | |
375 | (home-page "http://www.netlib.org/scalapack/") | |
376 | (synopsis "Library for scalable numerical linear algebra") | |
377 | (description | |
378 | "ScaLAPACK is a Fortran 90 library of high-performance linear algebra | |
379 | routines on parallel distributed memory machines. ScaLAPACK solves dense and | |
380 | banded linear systems, least squares problems, eigenvalue problems, and | |
381 | singular value problems.") | |
382 | (license (license:bsd-style "file://LICENSE" | |
383 | "See LICENSE in the distribution.")))) | |
384 | ||
73fed4f8 | 385 | (define-public gnuplot |
430e67a4 EF |
386 | ;; Gnuplot version 5.0.4 was updated in-place, resulting in a hash mismatch. |
387 | ;; This can be removed at the next version update. | |
388 | (let ((upstream-version "5.0.4") | |
389 | (guix-revision "1")) | |
390 | (package | |
391 | (name "gnuplot") | |
392 | (version (string-append upstream-version "-" guix-revision)) | |
393 | (source | |
394 | (origin | |
395 | (method url-fetch) | |
396 | (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" | |
397 | upstream-version "/gnuplot-" | |
398 | upstream-version ".tar.gz")) | |
399 | (sha256 | |
400 | (base32 | |
401 | "07n3w12dkcxjnhsvsliaqnkhajhi818v6q8mkpmpbplbf92vh70m")))) | |
402 | (build-system gnu-build-system) | |
403 | (inputs `(("readline" ,readline) | |
404 | ("cairo" ,cairo) | |
405 | ("pango" ,pango) | |
406 | ("gd" ,gd))) | |
407 | (native-inputs `(("pkg-config" ,pkg-config) | |
408 | ("texlive" ,texlive-minimal))) | |
409 | (home-page "http://www.gnuplot.info") | |
410 | (synopsis "Command-line driven graphing utility") | |
411 | (description "Gnuplot is a portable command-line driven graphing | |
35b9e423 | 412 | utility. It was originally created to allow scientists and students to |
73fed4f8 | 413 | visualize mathematical functions and data interactively, but has grown to |
35b9e423 | 414 | support many non-interactive uses such as web scripting. It is also used as a |
73fed4f8 | 415 | plotting engine by third-party applications like Octave.") |
430e67a4 EF |
416 | ;; X11 Style with the additional restriction that derived works may only be |
417 | ;; distributed as patches to the original. | |
418 | (license (license:fsf-free | |
419 | "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))) | |
668c06ac | 420 | |
7ee3f1a2 JD |
421 | (define-public hdf5 |
422 | (package | |
423 | (name "hdf5") | |
04b7a7cd | 424 | (version "1.8.17") |
7ee3f1a2 JD |
425 | (source |
426 | (origin | |
427 | (method url-fetch) | |
93c3de92 AE |
428 | (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" |
429 | version "/src/hdf5-" | |
7ee3f1a2 JD |
430 | version ".tar.bz2")) |
431 | (sha256 | |
b8d9c93b EB |
432 | (base32 "0sj8x0gfs5fb28gipnynb9wpkz113h8wq9sva9mxx66kv27xsdgw")) |
433 | (patches (list (search-patch "hdf5-config-date.patch"))))) | |
7ee3f1a2 | 434 | (build-system gnu-build-system) |
12ed1216 AE |
435 | (inputs |
436 | `(("zlib" ,zlib))) | |
7ee3f1a2 JD |
437 | (arguments |
438 | `(#:phases | |
f622e212 EB |
439 | (modify-phases %standard-phases |
440 | (add-before 'configure 'patch-configure | |
441 | (lambda _ | |
442 | (substitute* "configure" | |
b8d9c93b EB |
443 | (("/bin/mv") "mv")) |
444 | #t)) | |
f622e212 EB |
445 | (add-after 'install 'patch-references |
446 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
447 | (let ((bin (string-append (assoc-ref outputs "out") "/bin")) | |
448 | (zlib (assoc-ref inputs "zlib"))) | |
449 | (substitute* (find-files bin "h5p?cc") | |
450 | (("-lz" lib) | |
451 | (string-append "-L" zlib "/lib " lib))) | |
452 | #t)))))) | |
7ee3f1a2 | 453 | (home-page "http://www.hdfgroup.org") |
516e93f8 | 454 | (synopsis "Management suite for extremely large and complex data") |
7ee3f1a2 JD |
455 | (description "HDF5 is a suite that makes possible the management of |
456 | extremely large and complex data collections.") | |
d4bf49b1 EB |
457 | (license (license:x11-style |
458 | "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) | |
7ee3f1a2 | 459 | |
c8378eea EB |
460 | (define-public hdf5-parallel-openmpi |
461 | (package (inherit hdf5) | |
462 | (name "hdf5-parallel-openmpi") | |
463 | (inputs | |
464 | `(("mpi" ,openmpi) | |
465 | ,@(package-inputs hdf5))) | |
466 | (arguments | |
467 | (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel") | |
468 | ,@(package-arguments hdf5)) | |
469 | ((#:phases phases) | |
470 | `(modify-phases ,phases | |
471 | (add-before 'check 'patch-tests | |
472 | (lambda _ | |
473 | ;; OpenMPI's mpirun will exit with non-zero status if it | |
474 | ;; detects an "abnormal termination", i.e. any process not | |
475 | ;; calling MPI_Finalize(). Since the test is explicitely | |
476 | ;; avoiding MPI_Finalize so as not to have at_exit and thus | |
477 | ;; H5C_flush_cache from being called, mpirun will always | |
478 | ;; complain, so turn this test off. | |
479 | (substitute* "testpar/Makefile" | |
480 | (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back) | |
481 | (string-append front back "\n"))) | |
482 | (substitute* "tools/h5diff/testph5diff.sh" | |
483 | (("/bin/sh") (which "sh"))) | |
484 | #t)))))) | |
485 | (synopsis "Management suite for data with parallel IO support"))) | |
486 | ||
00775104 EB |
487 | (define-public h5check |
488 | (package | |
489 | (name "h5check") | |
490 | (version "2.0.1") | |
491 | (source | |
492 | (origin | |
493 | (method url-fetch) | |
494 | (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/" | |
495 | "h5check/src/h5check-" version ".tar.gz")) | |
496 | (sha256 | |
497 | (base32 | |
498 | "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj")))) | |
499 | (build-system gnu-build-system) | |
500 | (inputs `(("hdf5" ,hdf5))) ;h5cc for tests | |
501 | (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html") | |
502 | (synopsis "HDF5 format checker") | |
503 | (description "@code{h5check} is a validation tool for verifying that an | |
504 | HDF5 file is encoded according to the HDF File Format Specification.") | |
505 | (license (license:x11-style "file://COPYING")))) | |
506 | ||
889187a4 EB |
507 | (define-public netcdf |
508 | (package | |
509 | (name "netcdf") | |
510 | (version "4.4.0") | |
511 | (source | |
512 | (origin | |
513 | (method url-fetch) | |
514 | (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/" | |
515 | "netcdf-" version ".tar.gz")) | |
516 | (sha256 | |
517 | (base32 | |
518 | "0y6gdcplarwqqnrav2xg1xd6ih732rzzbmdw78v3rl5b8mwcnh0d")) | |
519 | (patches (list (search-patch "netcdf-config-date.patch"))))) | |
520 | (build-system gnu-build-system) | |
521 | (native-inputs | |
522 | `(("m4" ,m4) | |
523 | ("doxygen" ,doxygen) | |
524 | ("graphviz" ,graphviz))) | |
525 | (inputs | |
526 | `(("hdf5" ,hdf5) | |
527 | ("zlib" ,zlib))) | |
528 | (arguments | |
529 | `(#:configure-flags '("--enable-doxygen" "--enable-dot") | |
530 | #:parallel-tests? #f)) ;various race conditions | |
531 | (home-page "http://www.unidata.ucar.edu/software/netcdf/") | |
532 | (synopsis "Library for scientific data") | |
533 | (description "NetCDF is an interface for scientific data access and a | |
534 | software library that provides an implementation of the interface. The netCDF | |
535 | library defines a machine-independent format for representing scientific data. | |
536 | Together, the interface, library, and format support the creation, access, and | |
537 | sharing of scientific data.") | |
538 | (license (license:x11-style "file://COPYRIGHT")))) | |
539 | ||
540 | (define-public netcdf-parallel-openmpi | |
541 | (package (inherit netcdf) | |
542 | (name "netcdf-parallel-openmpi") | |
543 | (inputs | |
544 | `(("mpi" ,openmpi) | |
545 | ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi) | |
546 | (package-inputs netcdf)))) | |
547 | ;; TODO: Replace pkg-config references in nc-config with absolute references | |
548 | (arguments | |
549 | (substitute-keyword-arguments (package-arguments netcdf) | |
550 | ((#:configure-flags flags) | |
551 | `(cons* "CC=mpicc" "CXX=mpicxx" | |
552 | "--enable-parallel-tests" | |
553 | ;; Shared libraries not supported with parallel IO. | |
554 | "--disable-shared" "--with-pic" | |
555 | ,flags)))))) | |
556 | ||
1b39a196 RJ |
557 | (define-public nlopt |
558 | (package | |
559 | (name "nlopt") | |
560 | (version "2.4.2") | |
561 | (source (origin | |
562 | (method url-fetch) | |
563 | (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-" | |
564 | version ".tar.gz")) | |
565 | (sha256 | |
566 | (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0")))) | |
567 | (build-system gnu-build-system) | |
568 | (arguments | |
569 | `(;; Shared libraries are not built by default. They are required to | |
570 | ;; build the Guile, Octave, and Python bindings. | |
571 | #:configure-flags '("--enable-shared") | |
572 | ||
573 | #:phases | |
574 | (modify-phases %standard-phases | |
575 | (add-before 'configure 'set-libnlopt-file-name | |
576 | (lambda* (#:key outputs #:allow-other-keys) | |
577 | ;; Make sure the Scheme module refers to the library by its | |
578 | ;; absolute file name (we cannot do that from a snippet | |
579 | ;; because the expansion of @libdir@ contains | |
580 | ;; ${exec_prefix}.) | |
581 | (let ((out (assoc-ref outputs "out"))) | |
582 | (substitute* "swig/nlopt.scm.in" | |
583 | (("libnlopt") | |
584 | (string-append out "/lib/libnlopt"))) | |
585 | #t)))))) | |
586 | (inputs `(("guile" ,guile-2.0))) | |
587 | (native-inputs `(("pkg-config" ,pkg-config))) | |
588 | (home-page "http://ab-initio.mit.edu/wiki/") | |
589 | (synopsis "Library for nonlinear optimization") | |
590 | (description "NLopt is a library for nonlinear optimization, providing a | |
591 | common interface for a number of different free optimization routines available | |
592 | online as well as original implementations of various other algorithms.") | |
593 | (license license:lgpl2.1+))) | |
594 | ||
005c787d LC |
595 | (define-public ipopt |
596 | (package | |
597 | (name "ipopt") | |
598 | (version "3.12.5") | |
599 | (source (origin | |
600 | (method url-fetch) | |
601 | (uri (string-append | |
602 | "http://www.coin-or.org/download/source/Ipopt/Ipopt-" | |
603 | version".tgz")) | |
604 | (sha256 | |
605 | (base32 | |
606 | "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk")) | |
607 | (modules '((guix build utils))) | |
608 | (snippet | |
609 | ;; Make sure we don't use the bundled software. | |
610 | '(delete-file-recursively "ThirdParty")))) | |
611 | (build-system gnu-build-system) | |
ad1c4537 LC |
612 | (arguments |
613 | '(#:phases (modify-phases %standard-phases | |
614 | (add-after 'install 'add--L-flags-in-ipopt.pc | |
615 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
616 | ;; The '.pc' file lists '-llapack -lblas' in "Libs"; | |
617 | ;; move it to "Libs.private" where it belongs, and add a | |
618 | ;; '-L' flag for LAPACK. | |
619 | (let ((out (assoc-ref outputs "out")) | |
620 | (lapack (assoc-ref inputs "lapack"))) | |
621 | (substitute* (string-append out "/lib/pkgconfig/" | |
622 | "ipopt.pc") | |
623 | (("Libs: (.*)-llapack -lblas(.*)$" _ before after) | |
624 | (string-append "Libs: " before " " after "\n" | |
625 | "Libs.private: " before | |
626 | "-L" lapack "/lib -llapack -lblas " | |
627 | after "\n"))) | |
628 | #t)))))) | |
005c787d LC |
629 | (native-inputs |
630 | `(("gfortran" ,gfortran))) | |
631 | (inputs | |
632 | ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL. | |
ad1c4537 | 633 | `(("lapack" ,lapack))) ;for both libblas and liblapack |
005c787d LC |
634 | (home-page "http://www.coin-or.org") |
635 | (synopsis "Large-scale nonlinear optimizer") | |
636 | (description | |
637 | "The Interior Point Optimizer (IPOPT) is a software package for | |
638 | large-scale nonlinear optimization. It provides C++, C, and Fortran | |
639 | interfaces.") | |
640 | (license license:epl1.0))) | |
641 | ||
f9940ef1 LC |
642 | (define-public ceres |
643 | (package | |
644 | (name "ceres-solver") | |
645 | (version "1.11.0") | |
646 | (home-page "http://ceres-solver.org/") | |
647 | (source (origin | |
648 | (method url-fetch) | |
649 | (uri (string-append home-page "ceres-solver-" | |
650 | version ".tar.gz")) | |
651 | (sha256 | |
652 | (base32 | |
653 | "0i7qkbf8g6pd8arxzldppga26ckv93y8zldsfz6wbd4n6b1nqrjd")))) | |
654 | (build-system cmake-build-system) | |
655 | (arguments | |
656 | ;; TODO: Build HTML user documentation and install separately. | |
bc3a2e35 | 657 | '(#:configure-flags '("-DBUILD_EXAMPLES=OFF" |
f9940ef1 LC |
658 | "-DBUILD_SHARED_LIBS=ON") |
659 | ||
660 | #:phases (modify-phases %standard-phases | |
661 | (add-before 'configure 'set-library-directory | |
662 | (lambda _ | |
663 | ;; Install libraries to lib/, not lib64/. | |
664 | (substitute* "internal/ceres/CMakeLists.txt" | |
665 | (("set\\(LIB_SUFFIX \"64\"\\)") | |
666 | "set(LIB_SUFFIX \"\")")) | |
667 | #t))))) | |
668 | (native-inputs | |
669 | `(("pkg-config" ,pkg-config))) | |
468e0b18 LC |
670 | (propagated-inputs |
671 | `(("glog" ,glog))) ;for #include <glog/glog.h> | |
f9940ef1 LC |
672 | (inputs |
673 | `(("eigen" ,eigen) | |
674 | ("blas" ,openblas) | |
675 | ("lapack" ,lapack) | |
676 | ("suitesparse" ,suitesparse) | |
677 | ("gflags" ,gflags))) | |
678 | (synopsis "C++ library for solving large optimization problems") | |
679 | (description | |
680 | "Ceres Solver is a C++ library for modeling and solving large, | |
681 | complicated optimization problems. It is a feature rich, mature and | |
682 | performant library which has been used in production since 2010. Ceres Solver | |
683 | can solve two kinds of problems: | |
684 | @enumerate | |
685 | @item non-linear least squares problems with bounds constraints; | |
686 | @item general unconstrained optimization problems. | |
687 | @end enumerate\n") | |
688 | (license license:bsd-3))) | |
689 | ||
668c06ac JD |
690 | ;; For a fully featured Octave, users are strongly recommended also to install |
691 | ;; the following packages: texinfo, less, ghostscript, gnuplot. | |
692 | (define-public octave | |
693 | (package | |
694 | (name "octave") | |
b7b27a8f | 695 | (version "4.0.2") |
668c06ac JD |
696 | (source |
697 | (origin | |
698 | (method url-fetch) | |
699 | (uri (string-append "mirror://gnu/octave/octave-" | |
a124bbd2 | 700 | version ".tar.gz")) |
668c06ac JD |
701 | (sha256 |
702 | (base32 | |
b7b27a8f | 703 | "1hdxap3j88rpqjimnfhinym6z73wdi5dfa6fv85c13r1dk9qzk9r")))) |
668c06ac JD |
704 | (build-system gnu-build-system) |
705 | (inputs | |
706 | `(("lapack" ,lapack) | |
707 | ("readline" ,readline) | |
708 | ("glpk" ,glpk) | |
1ec78e9d EB |
709 | ("fftw" ,fftw) |
710 | ("fftwf" ,fftwf) | |
711 | ("arpack" ,arpack-ng) | |
668c06ac JD |
712 | ("curl" ,curl) |
713 | ("pcre" ,pcre) | |
b7b27a8f | 714 | ("cyrus-sasl" ,cyrus-sasl) |
668c06ac JD |
715 | ("fltk" ,fltk) |
716 | ("fontconfig" ,fontconfig) | |
717 | ("freetype" ,freetype) | |
40029cbe | 718 | ("hdf5" ,hdf5) |
668c06ac JD |
719 | ("libxft" ,libxft) |
720 | ("mesa" ,mesa) | |
1ec78e9d | 721 | ("glu" ,glu) |
b7b27a8f | 722 | ("openssl" ,openssl) |
668c06ac JD |
723 | ("zlib" ,zlib))) |
724 | (native-inputs | |
19afbea1 | 725 | `(("gfortran" ,gfortran) |
668c06ac JD |
726 | ("pkg-config" ,pkg-config) |
727 | ("perl" ,perl) | |
1ec78e9d EB |
728 | ;; The following inputs are not actually used in the build process. |
729 | ;; However, the ./configure gratuitously tests for their existence and | |
730 | ;; assumes that programs not present at build time are also not, and | |
731 | ;; can never be, available at run time! If these inputs are therefore | |
732 | ;; not present, support for them will be built out. However, Octave | |
733 | ;; will still run without them, albeit without the features they | |
668c06ac JD |
734 | ;; provide. |
735 | ("less" ,less) | |
736 | ("texinfo" ,texinfo) | |
737 | ("ghostscript" ,ghostscript) | |
738 | ("gnuplot" ,gnuplot))) | |
739 | (arguments | |
b7b27a8f KY |
740 | `(#:configure-flags |
741 | (list (string-append "--with-shell=" | |
742 | (assoc-ref %build-inputs "bash") | |
743 | "/bin/sh")))) | |
668c06ac JD |
744 | (home-page "http://www.gnu.org/software/octave/") |
745 | (synopsis "High-level language for numerical computation") | |
1ec78e9d EB |
746 | (description "GNU Octave is a high-level interpreted language that is |
747 | specialized for numerical computations. It can be used for both linear and | |
748 | non-linear applications and it provides great support for visualizing results. | |
749 | Work may be performed both at the interactive command-line as well as via | |
750 | script files.") | |
668c06ac | 751 | (license license:gpl3+))) |
3de01d3f EB |
752 | |
753 | (define-public gmsh | |
754 | (package | |
755 | (name "gmsh") | |
c7b08410 | 756 | (version "2.11.0") |
3de01d3f EB |
757 | (source |
758 | (origin | |
759 | (method url-fetch) | |
760 | (uri (string-append "http://www.geuz.org/gmsh/src/gmsh-" | |
761 | version "-source.tgz")) | |
762 | (sha256 | |
c7b08410 | 763 | (base32 "1ilplibvjgf7a905grpnclrvkmqy9fgrpl7xyp3w4yl1qc682v9b")) |
3de01d3f EB |
764 | (modules '((guix build utils))) |
765 | (snippet | |
766 | ;; Remove non-free METIS code | |
767 | '(delete-file-recursively "contrib/Metis")))) | |
768 | (build-system cmake-build-system) | |
3de01d3f EB |
769 | (propagated-inputs |
770 | `(("fltk" ,fltk) | |
19afbea1 | 771 | ("gfortran" ,gfortran) |
3de01d3f | 772 | ("gmp" ,gmp) |
40029cbe | 773 | ("hdf5" ,hdf5) |
3de01d3f EB |
774 | ("lapack" ,lapack) |
775 | ("mesa" ,mesa) | |
85f41902 | 776 | ("glu" ,glu) |
3de01d3f EB |
777 | ("libx11" ,libx11) |
778 | ("libxext" ,libxext))) | |
66395a61 EF |
779 | (inputs |
780 | `(("fontconfig" ,fontconfig) | |
781 | ("libxft" ,libxft))) | |
3de01d3f EB |
782 | (arguments |
783 | `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF" | |
784 | "-DENABLE_BUILD_SHARED:BOOL=ON" | |
c7b08410 EB |
785 | "-DENABLE_BUILD_DYNAMIC:BOOL=ON") |
786 | #:phases (modify-phases %standard-phases | |
787 | (replace | |
788 | 'check | |
789 | (lambda _ | |
790 | (zero? (system* "make" "test" | |
791 | ;; Disable this test. See | |
792 | ;; https://geuz.org/trac/gmsh/ticket/271 | |
793 | "ARGS=-E component8_in_a_box"))))))) | |
3de01d3f EB |
794 | (home-page "http://www.geuz.org/gmsh/") |
795 | (synopsis "3D finite element grid generator") | |
edf684ef EB |
796 | (description "Gmsh is a 3D finite element grid generator with a built-in |
797 | CAD engine and post-processor. Its design goal is to provide a fast, light | |
798 | and user-friendly meshing tool with parametric input and advanced | |
799 | visualization capabilities. Gmsh is built around four modules: geometry, | |
800 | mesh, solver and post-processing. The specification of any input to these | |
801 | modules is done either interactively using the graphical user interface or in | |
802 | ASCII text files using Gmsh's own scripting language.") | |
3de01d3f | 803 | (license license:gpl2+))) |
b9100e2f EB |
804 | |
805 | (define-public petsc | |
806 | (package | |
807 | (name "petsc") | |
fafd623e | 808 | (version "3.7.2") |
b9100e2f EB |
809 | (source |
810 | (origin | |
811 | (method url-fetch) | |
812 | ;; The *-lite-* tarball does not contain the *large* documentation | |
813 | (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" | |
814 | "petsc-lite-" version ".tar.gz")) | |
815 | (sha256 | |
fafd623e | 816 | (base32 "0jfrq6rd4zagw1iimz05m2w91k0jvz3qbik1lk8pqcxw3rvdqk5d")))) |
b9100e2f EB |
817 | (build-system gnu-build-system) |
818 | (native-inputs | |
819 | `(("python" ,python-2) | |
820 | ("perl" ,perl))) | |
821 | (inputs | |
19afbea1 | 822 | `(("gfortran" ,gfortran) |
b9100e2f | 823 | ("lapack" ,lapack) |
f258212d | 824 | ("superlu" ,superlu) |
b9100e2f EB |
825 | ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi |
826 | ;; leaving out opengl, as configuration seems to only be for mac | |
827 | )) | |
828 | (arguments | |
829 | `(#:test-target "test" | |
9a899cce | 830 | #:parallel-build? #f ;build is parallel by default |
b9100e2f EB |
831 | #:configure-flags |
832 | `("--with-mpi=0" | |
f258212d EB |
833 | "--with-openmp=1" |
834 | "--with-superlu=1" | |
835 | ,(string-append "--with-superlu-include=" | |
836 | (assoc-ref %build-inputs "superlu") "/include") | |
837 | ,(string-append "--with-superlu-lib=" | |
838 | (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a")) | |
b9100e2f | 839 | #:phases |
64dcc289 EB |
840 | (modify-phases %standard-phases |
841 | (replace 'configure | |
842 | ;; PETSc's configure script is actually a python script, so we can't | |
843 | ;; run it with bash. | |
844 | (lambda* (#:key outputs (configure-flags '()) | |
845 | #:allow-other-keys) | |
846 | (let* ((prefix (assoc-ref outputs "out")) | |
847 | (flags `(,(string-append "--prefix=" prefix) | |
848 | ,@configure-flags))) | |
849 | (format #t "build directory: ~s~%" (getcwd)) | |
850 | (format #t "configure flags: ~s~%" flags) | |
851 | (zero? (apply system* "./configure" flags))))) | |
852 | (add-after 'configure 'clean-local-references | |
64dcc289 EB |
853 | (lambda* (#:key inputs outputs #:allow-other-keys) |
854 | (let ((out (assoc-ref outputs "out"))) | |
855 | (substitute* (find-files "." "^petsc(conf|machineinfo).h$") | |
b730b437 EB |
856 | ;; Prevent build directory from leaking into compiled code |
857 | (((getcwd)) out) | |
858 | ;; Scrub timestamp for reproducibility | |
fafd623e EB |
859 | ((".*Libraries compiled on.*") "")) |
860 | #t))) | |
64dcc289 | 861 | (add-after 'install 'clean-install |
10b11968 EB |
862 | ;; Try to keep installed files from leaking build directory names. |
863 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
64dcc289 | 864 | (let ((out (assoc-ref outputs "out"))) |
10b11968 | 865 | (substitute* (map (lambda (file) |
9a899cce | 866 | (string-append out "/lib/petsc/conf/" file)) |
fafd623e | 867 | '("petscvariables")) |
10b11968 EB |
868 | (((getcwd)) out)) |
869 | ;; Make compiler references point to the store | |
9a899cce | 870 | (substitute* (string-append out "/lib/petsc/conf/petscvariables") |
dfdf5716 EB |
871 | (("= (gcc|g\\+\\+|gfortran)" _ compiler) |
872 | (string-append "= " (which compiler)))) | |
10b11968 EB |
873 | ;; PETSc installs some build logs, which aren't necessary. |
874 | (for-each (lambda (file) | |
9a899cce | 875 | (let ((f (string-append out "/lib/petsc/conf/" file))) |
10b11968 EB |
876 | (when (file-exists? f) |
877 | (delete-file f)))) | |
9a899cce EB |
878 | '("configure.log" "make.log" "gmake.log" |
879 | "test.log" "error.log" "RDict.db" | |
fafd623e | 880 | "PETScBuildInternal.cmake" |
10b11968 | 881 | ;; Once installed, should uninstall with Guix |
fafd623e EB |
882 | "uninstall.py")) |
883 | #t)))))) | |
b9100e2f | 884 | (home-page "http://www.mcs.anl.gov/petsc") |
16ecf3ff | 885 | (synopsis "Library to solve PDEs") |
b9100e2f EB |
886 | (description "PETSc, pronounced PET-see (the S is silent), is a suite of |
887 | data structures and routines for the scalable (parallel) solution of | |
888 | scientific applications modeled by partial differential equations.") | |
166191b3 | 889 | (license (license:non-copyleft |
b9100e2f EB |
890 | "http://www.mcs.anl.gov/petsc/documentation/copyright.html")))) |
891 | ||
892 | (define-public petsc-complex | |
893 | (package (inherit petsc) | |
894 | (name "petsc-complex") | |
895 | (arguments | |
896 | (substitute-keyword-arguments (package-arguments petsc) | |
897 | ((#:configure-flags cf) | |
898 | `(cons "--with-scalar-type=complex" ,cf)))) | |
16ecf3ff | 899 | (synopsis "Library to solve PDEs (with complex scalars)"))) |
183e44ae | 900 | |
d8c7eeb9 EB |
901 | (define-public petsc-openmpi |
902 | (package (inherit petsc) | |
903 | (name "petsc-openmpi") | |
904 | (inputs | |
905 | `(("openmpi" ,openmpi) | |
906 | ,@(package-inputs petsc))) | |
907 | (arguments | |
908 | (substitute-keyword-arguments (package-arguments petsc) | |
909 | ((#:configure-flags cf) | |
910 | ``("--with-mpiexec=mpirun" | |
911 | ,(string-append "--with-mpi-dir=" | |
912 | (assoc-ref %build-inputs "openmpi")) | |
913 | ,@(delete "--with-mpi=0" ,cf))))) | |
16ecf3ff | 914 | (synopsis "Library to solve PDEs (with MPI support)"))) |
d8c7eeb9 EB |
915 | |
916 | (define-public petsc-complex-openmpi | |
917 | (package (inherit petsc-complex) | |
918 | (name "petsc-complex-openmpi") | |
919 | (inputs | |
920 | `(("openmpi" ,openmpi) | |
921 | ,@(package-inputs petsc-complex))) | |
922 | (arguments | |
923 | (substitute-keyword-arguments (package-arguments petsc-complex) | |
924 | ((#:configure-flags cf) | |
925 | ``("--with-mpiexec=mpirun" | |
926 | ,(string-append "--with-mpi-dir=" | |
927 | (assoc-ref %build-inputs "openmpi")) | |
928 | ,@(delete "--with-mpi=0" ,cf))))) | |
16ecf3ff | 929 | (synopsis "Library to solve PDEs (with complex scalars and MPI support)"))) |
d8c7eeb9 | 930 | |
a7f01414 EB |
931 | (define-public slepc |
932 | (package | |
933 | (name "slepc") | |
8787c555 | 934 | (version "3.7.1") |
a7f01414 EB |
935 | (source |
936 | (origin | |
937 | (method url-fetch) | |
938 | (uri (string-append "http://slepc.upv.es/download/download.php?" | |
939 | "filename=slepc-" version ".tar.gz")) | |
d588422e | 940 | (file-name (string-append name "-" version ".tar.gz")) |
a7f01414 EB |
941 | (sha256 |
942 | (base32 | |
8787c555 | 943 | "1hijlmrvxvfqslnx8yydzw5xqbsn1yy02g32w0hln1z3cgr1c0k7")))) |
a7f01414 EB |
944 | (build-system gnu-build-system) |
945 | (native-inputs | |
946 | `(("python" ,python-2))) | |
947 | (inputs | |
948 | `(("arpack" ,arpack-ng) | |
949 | ("gfortran" ,gfortran))) | |
950 | (propagated-inputs | |
951 | `(("petsc" ,petsc))) | |
952 | (arguments | |
953 | `(#:parallel-build? #f ;build is parallel by default | |
954 | #:configure-flags | |
955 | `(,(string-append "--with-arpack-dir=" | |
9cf52454 | 956 | (assoc-ref %build-inputs "arpack") "/lib")) |
a7f01414 EB |
957 | #:phases |
958 | (modify-phases %standard-phases | |
8787c555 | 959 | (replace 'configure |
a7f01414 EB |
960 | ;; configure is a python script, so we can't run it with bash. |
961 | (lambda* (#:key inputs outputs (configure-flags '()) | |
962 | #:allow-other-keys) | |
963 | (let* ((prefix (assoc-ref outputs "out")) | |
964 | (flags `(,(string-append "--prefix=" prefix) | |
965 | ,@configure-flags))) | |
966 | (format #t "build directory: ~s~%" (getcwd)) | |
967 | (format #t "configure flags: ~s~%" flags) | |
968 | (setenv "SLEPC_DIR" (getcwd)) | |
9cf52454 | 969 | (setenv "PETSC_DIR" (assoc-ref inputs "petsc")) |
a7f01414 | 970 | (zero? (apply system* "./configure" flags))))) |
8787c555 | 971 | (add-after 'install 'delete-doc |
a7f01414 EB |
972 | ;; TODO: SLEPc installs HTML documentation alongside headers in |
973 | ;; $out/include. We'd like to move them to share/doc, but delete | |
974 | ;; them for now, as they are incomplete and installing the complete | |
975 | ;; documentation is difficult. | |
976 | (lambda* (#:key outputs #:allow-other-keys) | |
977 | (let* ((out (assoc-ref outputs "out"))) | |
978 | (for-each delete-file (find-files out "\\.html$"))))) | |
8787c555 | 979 | (add-after 'install 'clean-install |
a7f01414 EB |
980 | ;; Clean up unnecessary build logs from installation. |
981 | (lambda* (#:key outputs #:allow-other-keys) | |
982 | (let ((out (assoc-ref outputs "out"))) | |
983 | (for-each (lambda (file) | |
984 | (let ((f (string-append out "/lib/slepc/conf/" file))) | |
985 | (when (file-exists? f) | |
986 | (delete-file f)))) | |
987 | '("configure.log" "make.log" "gmake.log" | |
988 | "test.log" "error.log" "RDict.db" | |
989 | "uninstall.py")))))))) | |
990 | (home-page "http://slepc.upv.es") | |
991 | (synopsis "Scalable library for eigenproblems") | |
992 | (description "SLEPc is a software library for the solution of large sparse | |
993 | eigenproblems on parallel computers. It can be used for the solution of | |
994 | linear eigenvalue problems formulated in either standard or generalized form, | |
995 | as well as other related problems such as the singular value decomposition. | |
996 | The emphasis of the software is on methods and techniques appropriate for | |
997 | problems in which the associated matrices are sparse, for example, those | |
998 | arising after the discretization of partial differential equations.") | |
999 | (license license:lgpl3))) | |
1000 | ||
1001 | (define-public slepc-complex | |
1002 | (package (inherit slepc) | |
1003 | (name "slepc-complex") | |
1004 | (propagated-inputs | |
1005 | `(("petsc" ,petsc-complex) | |
1006 | ,@(alist-delete "petsc" (package-propagated-inputs slepc)))) | |
1007 | (synopsis "Scalable library for eigenproblems (with complex scalars)"))) | |
1008 | ||
1009 | (define-public slepc-openmpi | |
1010 | (package (inherit slepc) | |
1011 | (name "slepc-openmpi") | |
1012 | (inputs | |
1013 | `(("mpi" ,openmpi) | |
1014 | ("arpack" ,arpack-ng-openmpi) | |
1015 | ,@(alist-delete "arpack" (package-inputs slepc)))) | |
1016 | (propagated-inputs | |
1017 | `(("petsc" ,petsc-openmpi) | |
1018 | ,@(alist-delete "petsc" (package-propagated-inputs slepc)))) | |
1019 | (synopsis "Scalable library for eigenproblems (with MPI support)"))) | |
1020 | ||
1021 | (define-public slepc-complex-openmpi | |
1022 | (package (inherit slepc-openmpi) | |
1023 | (name "slepc-complex-openmpi") | |
1024 | (propagated-inputs | |
1025 | `(("petsc" ,petsc-complex-openmpi) | |
1026 | ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi)))) | |
1027 | (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)"))) | |
1028 | ||
cec86422 EB |
1029 | (define-public mumps |
1030 | (package | |
1031 | (name "mumps") | |
c69fa438 | 1032 | (version "5.0.1") |
cec86422 EB |
1033 | (source |
1034 | (origin | |
1035 | (method url-fetch) | |
1036 | (uri (string-append "http://mumps.enseeiht.fr/MUMPS_" | |
1037 | version ".tar.gz")) | |
1038 | (sha256 | |
1039 | (base32 | |
c69fa438 | 1040 | "1820jfp3mbl7n85765v5mp6p0gzqpgr4d2lrnhwj4gl7cwp5ndah")) |
fc1adab1 | 1041 | (patches (search-patches "mumps-build-parallelism.patch")))) |
cec86422 EB |
1042 | (build-system gnu-build-system) |
1043 | (inputs | |
1044 | `(("fortran" ,gfortran) | |
1045 | ;; These are required for linking against mumps, but we let the user | |
1046 | ;; declare the dependency. | |
1047 | ("blas" ,openblas) | |
1048 | ("metis" ,metis) | |
1049 | ("scotch" ,scotch))) | |
1050 | (arguments | |
1051 | `(#:modules ((ice-9 match) | |
1052 | (ice-9 popen) | |
1053 | (srfi srfi-1) | |
1054 | ,@%gnu-build-system-modules) | |
1055 | #:phases | |
1056 | (modify-phases %standard-phases | |
1057 | (replace | |
1058 | 'configure | |
1059 | (lambda* (#:key inputs #:allow-other-keys) | |
1060 | (call-with-output-file "Makefile.inc" | |
1061 | (lambda (port) | |
1062 | (format port " | |
1063 | PLAT = | |
1064 | LIBEXT = .a | |
1065 | OUTC = -o | |
1066 | OUTF = -o | |
1067 | RM = rm -f~:[ | |
1068 | CC = gcc | |
1069 | FC = gfortran | |
1070 | FL = gfortran | |
1071 | INCSEQ = -I$(topdir)/libseq | |
1072 | LIBSEQ = -L$(topdir)/libseq -lmpiseq | |
1073 | LIBSEQNEEDED = libseqneeded~; | |
1074 | CC = mpicc | |
1075 | FC = mpifort | |
1076 | FL = mpifort~] | |
1077 | AR = ar vr # rules require trailing space, ugh... | |
1078 | RANLIB = ranlib | |
1079 | LIBBLAS = -L~a -lopenblas~@[ | |
1080 | SCALAP = -L~a -lscalapack~] | |
1081 | LIBOTHERS = -pthread | |
1082 | CDEFS = -DAdd_ | |
1083 | PIC = -fPIC | |
1084 | OPTF = -O2 -DALLOW_NON_INIT $(PIC) | |
1085 | OPTL = -O2 $(PIC) | |
1086 | OPTC = -O2 $(PIC) | |
1087 | INCS = $(INCSEQ) | |
1088 | LIBS = $(SCALAP) $(LIBSEQ) | |
1089 | LPORDDIR = $(topdir)/PORD/lib | |
1090 | IPORD = -I$(topdir)/PORD/include | |
1091 | LPORD = -L$(LPORDDIR) -lpord | |
1092 | ORDERINGSF = -Dpord~@[ | |
1093 | METISDIR = ~a | |
1094 | IMETIS = -I$(METISDIR)/include | |
1095 | LMETIS = -L$(METISDIR)/lib -lmetis | |
1096 | ORDERINGSF += -Dmetis~]~@[~:{ | |
1097 | SCOTCHDIR = ~a | |
1098 | ISCOTCH = -I$(SCOTCHDIR)/include | |
1099 | LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr | |
1100 | ORDERINGSF += ~a~}~] | |
1101 | ORDERINGSC = $(ORDERINGSF) | |
1102 | LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) | |
1103 | IORDERINGSF = $(ISCOTCH) | |
1104 | IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)" | |
1105 | (assoc-ref inputs "mpi") | |
1106 | (assoc-ref inputs "blas") | |
1107 | (assoc-ref inputs "scalapack") | |
1108 | (assoc-ref inputs "metis") | |
1109 | (match (list (assoc-ref inputs "pt-scotch") | |
1110 | (assoc-ref inputs "scotch")) | |
1111 | ((#f #f) | |
1112 | #f) | |
1113 | ((#f scotch) | |
1114 | `((,scotch "" "-Dscotch"))) | |
1115 | ((ptscotch _) | |
1116 | `((,ptscotch | |
1117 | "-lptesmumps -lptscotch -lptscotcherr " | |
1118 | "-Dptscotch"))))))))) | |
1119 | (replace | |
1120 | 'build | |
1121 | ;; By default only the d-precision library is built. Make with "all" | |
1122 | ;; target so that all precision libraries and examples are built. | |
1123 | (lambda _ | |
1124 | (zero? (system* "make" "all" | |
1125 | (format #f "-j~a" (parallel-job-count)))))) | |
1126 | (replace | |
1127 | 'check | |
1128 | ;; Run the simple test drivers, which read test input from stdin: | |
1129 | ;; from the "real" input for the single- and double-precision | |
1130 | ;; testers, and from the "cmplx" input for complex-precision | |
1131 | ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi | |
1132 | ;; package to prefix execution with "mpirun". | |
1133 | (lambda* (#:key (exec-prefix '()) #:allow-other-keys) | |
1134 | (with-directory-excursion "examples" | |
1135 | (every | |
1136 | (lambda (prec type) | |
1137 | (let ((tester (apply open-pipe* | |
1138 | `(,OPEN_WRITE | |
1139 | ,@exec-prefix | |
1140 | ,(string-append "./" prec | |
1141 | "simpletest")))) | |
1142 | (input (open-input-file | |
1143 | (string-append "input_simpletest_" type)))) | |
1144 | (begin | |
1145 | (dump-port input tester) | |
1146 | (close-port input) | |
1147 | (zero? (close-pipe tester))))) | |
1148 | '("s" "d" "c" "z") | |
1149 | '("real" "real" "cmplx" "cmplx"))))) | |
1150 | (replace | |
1151 | 'install | |
1152 | (lambda* (#:key outputs #:allow-other-keys) | |
1153 | (let ((out (assoc-ref outputs "out"))) | |
1154 | (copy-recursively "lib" (string-append out "/lib")) | |
1155 | (copy-recursively "include" (string-append out "/include")) | |
1156 | (when (file-exists? "libseq/libmpiseq.a") | |
1157 | (copy-file "libseq/libmpiseq.a" | |
1158 | (string-append out "/lib/libmpiseq.a"))))))))) | |
1159 | (home-page "http://mumps.enseeiht.fr") | |
1160 | (synopsis "Multifrontal sparse direct solver") | |
1161 | (description | |
1162 | "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a | |
1163 | sparse system of linear equations A x = b using Guassian elimination.") | |
1164 | (license license:cecill-c))) | |
1165 | ||
1166 | (define-public mumps-metis | |
1167 | (package (inherit mumps) | |
1168 | (name "mumps-metis") | |
1169 | (inputs | |
1170 | (alist-delete "scotch" (package-inputs mumps))))) | |
1171 | ||
1172 | (define-public mumps-openmpi | |
1173 | (package (inherit mumps) | |
1174 | (name "mumps-openmpi") | |
1175 | (inputs | |
1176 | `(("mpi" ,openmpi) | |
1177 | ("scalapack" ,scalapack) | |
1178 | ("pt-scotch" ,pt-scotch) | |
1179 | ,@(alist-delete "scotch" (package-inputs mumps)))) | |
1180 | (arguments | |
1181 | (substitute-keyword-arguments (package-arguments mumps) | |
1182 | ((#:phases phases) | |
1183 | `(modify-phases ,phases | |
1184 | (replace | |
1185 | 'check | |
1186 | (lambda _ | |
1187 | ((assoc-ref ,phases 'check) | |
1188 | #:exec-prefix '("mpirun" "-n" "2")))))))) | |
1189 | (synopsis "Multifrontal sparse direct solver (with MPI)"))) | |
1190 | ||
1191 | (define-public mumps-metis-openmpi | |
1192 | (package (inherit mumps-openmpi) | |
1193 | (name "mumps-metis-openmpi") | |
1194 | (inputs | |
1195 | (alist-delete "pt-scotch" (package-inputs mumps-openmpi))))) | |
1196 | ||
ec8c7e47 RJ |
1197 | (define-public r-pracma |
1198 | (package | |
1199 | (name "r-pracma") | |
1200 | (version "1.8.8") | |
1201 | (source (origin | |
1202 | (method url-fetch) | |
1203 | (uri (cran-uri "pracma" version)) | |
1204 | (sha256 | |
1205 | (base32 "0ans9l5rrb7a38gyi4qx4258sd5r5668vyrk02yzjpg9k3h8l165")))) | |
1206 | (build-system r-build-system) | |
1207 | (home-page "http://cran.r-project.org/web/packages/pracma") | |
1208 | (synopsis "Practical numerical math functions") | |
1209 | (description "This package provides functions for numerical analysis and | |
1210 | linear algebra, numerical optimization, differential equations, plus some | |
1211 | special functions. It uses Matlab function names where appropriate to simplify | |
1212 | porting.") | |
1213 | (license license:gpl3+))) | |
1214 | ||
183e44ae EB |
1215 | (define-public superlu |
1216 | (package | |
1217 | (name "superlu") | |
995a09e0 | 1218 | (version "5.2.1") |
183e44ae EB |
1219 | (source |
1220 | (origin | |
1221 | (method url-fetch) | |
1222 | (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" | |
1223 | "superlu_" version ".tar.gz")) | |
1224 | (sha256 | |
995a09e0 EB |
1225 | (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8")) |
1226 | (modules '((guix build utils))) | |
1227 | (snippet | |
1228 | ;; Replace the non-free implementation of MC64 with a stub adapted | |
1229 | ;; from Debian | |
1230 | '(begin | |
1231 | (use-modules (ice-9 regex) | |
1232 | (ice-9 rdelim)) | |
1233 | (call-with-output-file "SRC/mc64ad.c" | |
1234 | (lambda (port) | |
1235 | (display " | |
1236 | #include <stdio.h> | |
1237 | #include <stdlib.h> | |
1238 | void mc64id_(int *a) { | |
1239 | fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\"); | |
1240 | abort (); | |
1241 | } | |
1242 | void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g, | |
1243 | int *h, int *i, int *j, int *k, double *l, int *m, int *n) { | |
1244 | fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\"); | |
1245 | abort (); | |
1246 | }\n" port))) | |
1247 | ;; Remove the corresponding license verbiage. MC64 license follows | |
1248 | ;; a "------" line separator. | |
1249 | (with-atomic-file-replacement "License.txt" | |
1250 | (let ((rx (make-regexp "-{8}"))) | |
1251 | (lambda (in out) | |
1252 | (let loop () | |
1253 | (let ((line (read-line in 'concat))) | |
1254 | (unless (regexp-exec rx line) | |
1255 | (display line out) | |
1256 | (loop))))))))))) | |
1257 | (build-system cmake-build-system) | |
183e44ae EB |
1258 | (native-inputs |
1259 | `(("tcsh" ,tcsh))) | |
1260 | (inputs | |
995a09e0 | 1261 | `(("blas" ,openblas) |
19afbea1 | 1262 | ("gfortran" ,gfortran))) |
183e44ae | 1263 | (arguments |
995a09e0 EB |
1264 | `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas |
1265 | "-DTPL_BLAS_LIBRARIES=openblas" | |
1266 | "-DBUILD_SHARED_LIBS:BOOL=YES" | |
1267 | "-DCMAKE_INSTALL_LIBDIR=lib"))) | |
183e44ae EB |
1268 | (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/") |
1269 | (synopsis "Supernodal direct solver for sparse linear systems") | |
1270 | (description | |
1271 | "SuperLU is a general purpose library for the direct solution of large, | |
1272 | sparse, nonsymmetric systems of linear equations on high performance machines. | |
1273 | The library is written in C and is callable from either C or Fortran. The | |
1274 | library routines perform an LU decomposition with partial pivoting and | |
1275 | triangular system solves through forward and back substitution. The library | |
1276 | also provides threshold-based ILU factorization preconditioners.") | |
995a09e0 EB |
1277 | (license (list license:bsd-3 |
1278 | license:gpl2+ ;EXAMPLE/*fgmr.c | |
1279 | (license:fsf-free "file://SRC/colamd.h"))))) | |
f8ed036a | 1280 | |
a54aefea EB |
1281 | (define-public superlu-dist |
1282 | (package | |
1283 | (name "superlu-dist") | |
1284 | (version "3.3") | |
1285 | (source | |
1286 | (origin | |
1287 | (method url-fetch) | |
1288 | (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" | |
1289 | "superlu_dist_" version ".tar.gz")) | |
1290 | (sha256 | |
1291 | (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj")) | |
29080870 EB |
1292 | (modules '((guix build utils))) |
1293 | (snippet | |
1294 | ;; Replace the non-free implementation of MC64 with a stub | |
1295 | '(begin | |
1296 | (use-modules (ice-9 regex) | |
1297 | (ice-9 rdelim)) | |
1298 | (call-with-output-file "SRC/mc64ad.c" | |
1299 | (lambda (port) | |
1300 | (display " | |
1301 | #include <stdio.h> | |
1302 | #include <stdlib.h> | |
1303 | void mc64id_(int *a) { | |
1304 | fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\"); | |
1305 | abort (); | |
1306 | } | |
1307 | void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g, | |
1308 | int *h, int *i, int *j, int *k, double *l, int *m, int *n) { | |
1309 | fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\"); | |
1310 | abort (); | |
1311 | }\n" port))) | |
1312 | (delete-file "SRC/mc64ad.f.bak") | |
1313 | (substitute* "SRC/util.c" ;adjust default algorithm | |
1314 | (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag") | |
1315 | "RowPerm = NOROWPERM")))) | |
fc1adab1 | 1316 | (patches (search-patches "superlu-dist-scotchmetis.patch")))) |
a54aefea EB |
1317 | (build-system gnu-build-system) |
1318 | (native-inputs | |
1319 | `(("tcsh" ,tcsh))) | |
1320 | (inputs | |
19afbea1 | 1321 | `(("gfortran" ,gfortran))) |
a54aefea EB |
1322 | (propagated-inputs |
1323 | `(("openmpi" ,openmpi) ;headers include MPI heades | |
1324 | ("lapack" ,lapack) ;required to link with output library | |
1325 | ("pt-scotch" ,pt-scotch))) ;same | |
1326 | (arguments | |
1327 | `(#:parallel-build? #f ;race conditions using ar | |
1328 | #:phases | |
1329 | (alist-replace | |
1330 | 'configure | |
1331 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1332 | (call-with-output-file "make.inc" | |
1333 | (lambda (port) | |
1334 | (format port " | |
1335 | PLAT = | |
1336 | DSuperLUroot = ~a | |
1337 | DSUPERLULIB = ~a/lib/libsuperlu_dist.a | |
1338 | BLASDEF = -DUSE_VENDOR_BLAS | |
1339 | BLASLIB = -L~a/lib -lblas | |
1340 | PARMETISLIB = -L~a/lib \ | |
1341 | -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \ | |
1342 | -lscotch -lscotcherr -lscotcherrexit | |
1343 | METISLIB = -L~:*~a/lib \ | |
1344 | -lscotchmetis -lscotch -lscotcherr -lscotcherrexit | |
1345 | LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB) | |
1346 | ARCH = ar | |
1347 | ARCHFLAGS = cr | |
1348 | RANLIB = ranlib | |
1349 | CC = mpicc | |
1350 | PIC = -fPIC | |
1351 | CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC) | |
1352 | NOOPTS = -O0 -g $(PIC) | |
1353 | FORTRAN = mpifort | |
1354 | FFLAGS = -O2 -g $(PIC) | |
1355 | LOADER = $(CC) | |
1356 | CDEFS = -DAdd_" | |
1357 | (getcwd) | |
1358 | (assoc-ref outputs "out") | |
1359 | (assoc-ref inputs "lapack") | |
1360 | (assoc-ref inputs "pt-scotch"))))) | |
1361 | (alist-cons-after | |
1362 | 'unpack 'remove-broken-symlinks | |
1363 | (lambda _ | |
1364 | (for-each delete-file | |
1365 | (find-files "MAKE_INC" "\\.#make\\..*"))) | |
1366 | (alist-cons-before | |
1367 | 'build 'create-install-directories | |
1368 | (lambda* (#:key outputs #:allow-other-keys) | |
1369 | (for-each | |
1370 | (lambda (dir) | |
1371 | (mkdir-p (string-append (assoc-ref outputs "out") | |
1372 | "/" dir))) | |
1373 | '("lib" "include"))) | |
1374 | (alist-replace | |
1375 | 'check | |
1376 | (lambda _ | |
1377 | (with-directory-excursion "EXAMPLE" | |
1378 | (and | |
1379 | (zero? (system* "mpirun" "-n" "2" | |
1380 | "./pddrive" "-r" "1" "-c" "2" "g20.rua")) | |
1381 | (zero? (system* "mpirun" "-n" "2" | |
1382 | "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))))) | |
1383 | (alist-replace | |
1384 | 'install | |
1385 | (lambda* (#:key outputs #:allow-other-keys) | |
1386 | ;; Library is placed in lib during the build phase. Copy over | |
1387 | ;; headers to include. | |
1388 | (let* ((out (assoc-ref outputs "out")) | |
1389 | (incdir (string-append out "/include"))) | |
1390 | (for-each (lambda (file) | |
1391 | (let ((base (basename file))) | |
1392 | (format #t "installing `~a' to `~a'~%" | |
1393 | base incdir) | |
1394 | (copy-file file | |
1395 | (string-append incdir "/" base)))) | |
1396 | (find-files "SRC" ".*\\.h$")))) | |
1397 | %standard-phases))))))) | |
1398 | (home-page (package-home-page superlu)) | |
1399 | (synopsis "Parallel supernodal direct solver") | |
1400 | (description | |
1401 | "SuperLU_DIST is a parallel extension to the serial SuperLU library. | |
1402 | It is targeted for distributed memory parallel machines. SuperLU_DIST is | |
1403 | implemented in ANSI C, and MPI for communications.") | |
1404 | (license license:bsd-3))) | |
1405 | ||
f8ed036a EB |
1406 | (define-public scotch |
1407 | (package | |
1408 | (name "scotch") | |
6c798540 | 1409 | (version "6.0.4") |
f8ed036a EB |
1410 | (source |
1411 | (origin | |
1412 | (method url-fetch) | |
6c798540 | 1413 | (uri (string-append "https://gforge.inria.fr/frs/download.php/34618/" |
f8ed036a EB |
1414 | "scotch_" version ".tar.gz")) |
1415 | (sha256 | |
6c798540 | 1416 | (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm")) |
fc1adab1 AK |
1417 | (patches (search-patches "scotch-test-threading.patch" |
1418 | "pt-scotch-build-parallelism.patch")))) | |
f8ed036a EB |
1419 | (build-system gnu-build-system) |
1420 | (inputs | |
1421 | `(("zlib" ,zlib) | |
1422 | ("flex" ,flex) | |
1423 | ("bison" ,bison))) | |
1424 | (arguments | |
1425 | `(#:phases | |
d6602ee9 EB |
1426 | (modify-phases %standard-phases |
1427 | (add-after | |
1428 | 'unpack 'chdir-to-src | |
1429 | (lambda _ (chdir "src"))) | |
1430 | (replace | |
1431 | 'configure | |
1432 | (lambda _ | |
1433 | (call-with-output-file "Makefile.inc" | |
1434 | (lambda (port) | |
1435 | (format port " | |
f8ed036a EB |
1436 | EXE = |
1437 | LIB = .a | |
1438 | OBJ = .o | |
1439 | MAKE = make | |
1440 | AR = ar | |
1441 | ARFLAGS = -ruv | |
cf0ec6c4 | 1442 | CAT = cat |
f8ed036a EB |
1443 | CCS = gcc |
1444 | CCP = mpicc | |
1445 | CCD = gcc | |
1446 | CPPFLAGS =~{ -D~a~} | |
6c798540 | 1447 | CFLAGS = -O2 -g -fPIC $(CPPFLAGS) |
f8ed036a EB |
1448 | LDFLAGS = -lz -lm -lrt -lpthread |
1449 | CP = cp | |
1450 | LEX = flex -Pscotchyy -olex.yy.c | |
1451 | LN = ln | |
1452 | MKDIR = mkdir | |
1453 | MV = mv | |
1454 | RANLIB = ranlib | |
1455 | YACC = bison -pscotchyy -y -b y | |
1456 | " | |
d6602ee9 EB |
1457 | '("COMMON_FILE_COMPRESS_GZ" |
1458 | "COMMON_PTHREAD" | |
1459 | "COMMON_RANDOM_FIXED_SEED" | |
cf0ec6c4 EB |
1460 | ;; Prevents symbolc clashes with libesmumps |
1461 | "SCOTCH_RENAME" | |
d6602ee9 EB |
1462 | ;; XXX: Causes invalid frees in superlu-dist tests |
1463 | ;; "SCOTCH_PTHREAD" | |
1464 | ;; "SCOTCH_PTHREAD_NUMBER=2" | |
1465 | "restrict=__restrict")))))) | |
cf0ec6c4 EB |
1466 | (add-after |
1467 | 'build 'build-esmumps | |
1468 | (lambda _ | |
1469 | (zero? (system* "make" | |
1470 | (format #f "-j~a" (parallel-job-count)) | |
1471 | "esmumps")))) | |
d6602ee9 | 1472 | (replace |
f8ed036a EB |
1473 | 'install |
1474 | (lambda* (#:key outputs #:allow-other-keys) | |
1475 | (let ((out (assoc-ref outputs "out"))) | |
1476 | (mkdir out) | |
1477 | (zero? (system* "make" | |
1478 | (string-append "prefix=" out) | |
cf0ec6c4 EB |
1479 | "install")) |
1480 | ;; esmumps files are not installed with the above | |
1481 | (for-each (lambda (f) | |
1482 | (copy-file f (string-append out "/include/" f))) | |
1483 | (find-files "../include" ".*esmumps.h$")) | |
1484 | (for-each (lambda (f) | |
1485 | (copy-file f (string-append out "/lib/" f))) | |
1486 | (find-files "../lib" "^lib.*esmumps.*")))))))) | |
f8ed036a EB |
1487 | (home-page "http://www.labri.fr/perso/pelegrin/scotch/") |
1488 | (synopsis "Programs and libraries for graph algorithms") | |
1489 | (description "SCOTCH is a set of programs and libraries which implement | |
1490 | the static mapping and sparse matrix reordering algorithms developed within | |
1491 | the SCOTCH project. Its purpose is to apply graph theory, with a divide and | |
1492 | conquer approach, to scientific computing problems such as graph and mesh | |
1493 | partitioning, static mapping, and sparse matrix ordering, in application | |
1494 | domains ranging from structural mechanics to operating systems or | |
1495 | bio-chemistry.") | |
1496 | ;; See LICENSE_en.txt | |
1497 | (license license:cecill-c))) | |
6acb4adb EB |
1498 | |
1499 | (define-public pt-scotch | |
1500 | (package (inherit scotch) | |
1501 | (name "pt-scotch") | |
1502 | (propagated-inputs | |
1503 | `(("openmpi" ,openmpi))) ;Headers include MPI headers | |
1504 | (arguments | |
1505 | (substitute-keyword-arguments (package-arguments scotch) | |
1506 | ((#:phases scotch-phases) | |
d6602ee9 EB |
1507 | `(modify-phases ,scotch-phases |
1508 | (replace | |
1509 | 'build | |
d6602ee9 EB |
1510 | (lambda _ |
1511 | (and | |
cf0ec6c4 EB |
1512 | (zero? (system* "make" |
1513 | (format #f "-j~a" (parallel-job-count)) | |
1514 | "ptscotch" "ptesmumps")) | |
d6602ee9 EB |
1515 | ;; Install the serial metis compatibility library |
1516 | (zero? (system* "make" "-C" "libscotchmetis" "install"))))) | |
1517 | (replace | |
1518 | 'check | |
1519 | (lambda _ (zero? (system* "make" "ptcheck")))))))) | |
6acb4adb | 1520 | (synopsis "Programs and libraries for graph algorithms (with MPI)"))) |
5698b8b8 | 1521 | |
aa75ad00 EB |
1522 | (define-public metis |
1523 | (package | |
1524 | (name "metis") | |
1525 | (version "5.1.0") | |
1526 | (source | |
1527 | (origin | |
1528 | (method url-fetch) | |
1529 | (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/" | |
1530 | "metis-" version ".tar.gz")) | |
1531 | (sha256 | |
1532 | (base32 | |
1533 | "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn")))) | |
1534 | (build-system cmake-build-system) | |
1535 | (inputs | |
1536 | `(("blas" ,openblas))) | |
1537 | (arguments | |
1538 | `(#:tests? #f ;no tests | |
1539 | #:configure-flags `("-DSHARED=ON" | |
1540 | ,(string-append "-DGKLIB_PATH=" (getcwd) | |
1541 | "/metis-" ,version "/GKlib")))) | |
1542 | (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview") | |
1543 | (synopsis "Graph partitioning and fill-reducing matrix ordering library") | |
1544 | (description | |
1545 | "METIS is a set of serial programs for partitioning graphs, partitioning | |
1546 | finite element meshes, and producing fill-reducing orderings for sparse | |
1547 | matrices. The algorithms implemented in METIS are based on the multilevel | |
1548 | recursive-bisection, multilevel k-way, and multi-constraint partitioning | |
1549 | schemes.") | |
1550 | (license license:asl2.0))) ;As of version 5.0.3 | |
1551 | ||
700ff222 EB |
1552 | (define-public p4est |
1553 | (package | |
1554 | (name "p4est") | |
1555 | (version "1.1") | |
1556 | (source | |
1557 | (origin | |
1558 | (method url-fetch) | |
1559 | (uri (string-append "http://p4est.github.io/release/p4est-" | |
1560 | version ".tar.gz")) | |
1561 | (sha256 | |
1562 | (base32 | |
1563 | "0faina2h5qsx3m2izbzaj9bbakma1krbbjmq43wrp1hcbyijflqb")))) | |
1564 | (build-system gnu-build-system) | |
1565 | (inputs | |
1566 | `(("fortran" ,gfortran) | |
1567 | ("blas" ,openblas) | |
1568 | ("lapack" ,lapack) | |
1569 | ("zlib" ,zlib))) | |
1570 | (arguments | |
1571 | `(#:configure-flags `(,(string-append "BLAS_LIBS=-L" | |
1572 | (assoc-ref %build-inputs "blas") | |
1573 | " -lopenblas") | |
1574 | ,(string-append "LAPACK_LIBS=-L" | |
1575 | (assoc-ref %build-inputs "lapack") | |
1576 | " -llapack")))) | |
1577 | (home-page "http://www.p4est.org") | |
1578 | (synopsis "Adaptive mesh refinement on forests of octrees") | |
1579 | (description | |
1580 | "The p4est software library enables the dynamic management of a | |
1581 | collection of adaptive octrees, conveniently called a forest of octrees. | |
1582 | p4est is designed to work in parallel and scales to hundreds of thousands of | |
1583 | processor cores.") | |
1584 | (license license:gpl2+))) | |
1585 | ||
1586 | (define-public p4est-openmpi | |
1587 | (package (inherit p4est) | |
1588 | (name "p4est-openmpi") | |
1589 | (inputs | |
1590 | `(("mpi" ,openmpi) | |
1591 | ,@(package-inputs p4est))) | |
1592 | (arguments | |
1593 | (substitute-keyword-arguments (package-arguments p4est) | |
1594 | ((#:configure-flags cf) | |
1595 | ``("--enable-mpi" ,@,cf)))) | |
1596 | (synopsis "Parallel adaptive mesh refinement on forests of octrees"))) | |
1597 | ||
5698b8b8 JD |
1598 | (define-public gsegrafix |
1599 | (package | |
1600 | (name "gsegrafix") | |
1601 | (version "1.0.6") | |
1602 | (source | |
1603 | (origin | |
1604 | (method url-fetch) | |
1605 | (uri (string-append "mirror://gnu/" name "/" name "-" | |
1606 | version ".tar.gz")) | |
1607 | (sha256 | |
1608 | (base32 | |
1609 | "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda")))) | |
1610 | (build-system gnu-build-system) | |
1611 | (arguments | |
1612 | `(#:configure-flags '("LDFLAGS=-lm"))) | |
1613 | (inputs | |
1614 | `(("libgnomecanvas" ,libgnomecanvas) | |
1615 | ("libbonoboui" ,libbonoboui) | |
1616 | ("libgnomeui" ,libgnomeui) | |
1617 | ("libgnomeprintui" ,libgnomeprintui) | |
1618 | ("popt" ,popt))) | |
1619 | (native-inputs | |
1620 | `(("pkg-config" ,pkg-config))) | |
1621 | (home-page "http://www.gnu.org/software/gsegrafix/") | |
1622 | (synopsis "GNOME application to create scientific and engineering plots") | |
1623 | (description "GSEGrafix is an application which produces high-quality graphical | |
1624 | plots for science and engineering. Plots are specified via simple ASCII | |
1625 | parameter files and data files and are presented in an anti-aliased GNOME | |
1626 | canvas. The program supports rectangular two-dimensional plots, histograms, | |
1627 | polar-axis plots and three-dimensional plots. Plots can be printed or saved | |
1628 | to BMP, JPEG or PNG image formats.") | |
1629 | (license license:gpl3+))) | |
8731e527 JD |
1630 | |
1631 | (define-public maxima | |
1632 | (package | |
1633 | (name "maxima") | |
77af7b24 | 1634 | (version "5.36.1") |
8731e527 JD |
1635 | (source |
1636 | (origin | |
1637 | (method url-fetch) | |
1638 | (uri (string-append "mirror://sourceforge/maxima/Maxima-source/" | |
1639 | version "-source/" name "-" version ".tar.gz")) | |
1640 | (sha256 | |
1641 | (base32 | |
77af7b24 | 1642 | "0x1rk659sn3cq0n5c90848ilzr1gb1wf0072fl6jhkdq00qgh2s0")) |
fc1adab1 | 1643 | (patches (search-patches "maxima-defsystem-mkdir.patch")))) |
8731e527 | 1644 | (build-system gnu-build-system) |
df354a77 FB |
1645 | (inputs |
1646 | `(("gcl" ,gcl) | |
1647 | ("gnuplot" ,gnuplot) ;for plots | |
f36afe4d | 1648 | ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima' |
df354a77 FB |
1649 | (native-inputs |
1650 | `(("texinfo" ,texinfo) | |
1651 | ("perl" ,perl))) | |
8731e527 | 1652 | (arguments |
df354a77 FB |
1653 | `(#:configure-flags |
1654 | (list "--enable-gcl" | |
1655 | (string-append "--with-posix-shell=" | |
1656 | (assoc-ref %build-inputs "bash") | |
1657 | "/bin/sh") | |
1658 | (string-append "--with-wish=" | |
1659 | (assoc-ref %build-inputs "tk") | |
1660 | "/bin/wish" | |
1661 | (let ((v ,(package-version tk))) | |
1662 | (string-take v (string-index-right v #\.))))) | |
df354a77 | 1663 | ;; By default Maxima attempts to write temporary files to |
77af7b24 MW |
1664 | ;; '/tmp/nix-build-maxima-*', which won't exist at run time. |
1665 | ;; Work around that. | |
df354a77 | 1666 | #:make-flags (list "TMPDIR=/tmp") |
df354a77 | 1667 | #:phases (alist-cons-before |
8731e527 | 1668 | 'check 'pre-check |
df354a77 | 1669 | (lambda _ |
8731e527 | 1670 | (chmod "src/maxima" #o555)) |
f36afe4d FB |
1671 | ;; Make sure the doc and emacs files are found in the |
1672 | ;; standard location. Also configure maxima to find gnuplot | |
1673 | ;; without having it on the PATH. | |
1674 | (alist-cons-after | |
1675 | 'install 'post-install | |
1676 | (lambda* (#:key outputs inputs #:allow-other-keys) | |
1677 | (let* ((gnuplot (assoc-ref inputs "gnuplot")) | |
1678 | (out (assoc-ref outputs "out")) | |
1679 | (datadir (string-append out "/share/maxima/" ,version))) | |
1680 | (with-directory-excursion out | |
1681 | (mkdir-p "share/emacs") | |
1682 | (mkdir-p "share/doc") | |
1683 | (symlink | |
1684 | (string-append datadir "/emacs/") | |
1685 | (string-append out "/share/emacs/site-lisp")) | |
1686 | (symlink | |
1687 | (string-append datadir "/doc/") | |
1688 | (string-append out "/share/doc/maxima")) | |
1689 | (with-atomic-file-replacement | |
1690 | (string-append datadir "/share/maxima-init.lisp") | |
1691 | (lambda (in out) | |
1692 | (format out "~a ~s~a~%" | |
1693 | "(setf $gnuplot_command " | |
1694 | (string-append gnuplot "/bin/gnuplot") ")") | |
1695 | (dump-port in out)))))) | |
1696 | %standard-phases)))) | |
8731e527 JD |
1697 | (home-page "http://maxima.sourceforge.net") |
1698 | (synopsis "Numeric and symbolic expression manipulation") | |
1699 | (description "Maxima is a system for the manipulation of symbolic and | |
1700 | numerical expressions. It yields high precision numeric results by using | |
1701 | exact fractions, arbitrary precision integers, and variable precision floating | |
e881752c | 1702 | point numbers.") |
8731e527 JD |
1703 | ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+. |
1704 | ;; Others simply say "GNU General Public License" without stating a | |
1705 | ;; version (which implicitly means gpl1+). | |
1706 | ;; At least one file (src/maxima.asd) says "version 2." | |
1707 | ;; GPLv2 only is therefore the smallest subset. | |
f36afe4d | 1708 | (license license:gpl2))) |
ec322be2 | 1709 | |
9aafbc0c MW |
1710 | (define-public wxmaxima |
1711 | (package | |
1712 | (name "wxmaxima") | |
e6a90507 | 1713 | (version "16.04.2") |
9aafbc0c MW |
1714 | (source |
1715 | (origin | |
1716 | (method url-fetch) | |
1717 | (uri (string-append "mirror://sourceforge/wxmaxima/wxMaxima/" | |
1718 | version "/" name "-" version ".tar.gz")) | |
1719 | (sha256 | |
1720 | (base32 | |
e6a90507 | 1721 | "1fpqzk1921isiqrpgpf433ldq41924qs9sy99fl1zn5661b2l73n")))) |
9aafbc0c MW |
1722 | (build-system gnu-build-system) |
1723 | (inputs | |
1724 | `(("wxwidgets" ,wxwidgets) | |
de477809 SB |
1725 | ("maxima" ,maxima) |
1726 | ;; Runtime support. | |
1727 | ("adwaita-icon-theme" ,adwaita-icon-theme) | |
1728 | ("gtk+" ,gtk+) | |
1729 | ("shared-mime-info" ,shared-mime-info))) | |
9aafbc0c MW |
1730 | (arguments |
1731 | `(#:phases (modify-phases %standard-phases | |
1732 | (add-after | |
1733 | 'install 'wrap-program | |
1734 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
1735 | (wrap-program (string-append (assoc-ref outputs "out") | |
1736 | "/bin/wxmaxima") | |
1737 | `("PATH" ":" prefix | |
1738 | (,(string-append (assoc-ref inputs "maxima") | |
de477809 SB |
1739 | "/bin"))) |
1740 | ;; For GtkFileChooserDialog. | |
1741 | `("GSETTINGS_SCHEMA_DIR" = | |
1742 | (,(string-append (assoc-ref inputs "gtk+") | |
1743 | "/share/glib-2.0/schemas"))) | |
1744 | `("XDG_DATA_DIRS" ":" prefix | |
1745 | (;; Needed by gdk-pixbuf to know supported icon formats. | |
1746 | ,(string-append | |
1747 | (assoc-ref inputs "shared-mime-info") "/share") | |
1748 | ;; The default icon theme of GTK+. | |
1749 | ,(string-append | |
1750 | (assoc-ref inputs "adwaita-icon-theme") "/share")))) | |
9aafbc0c MW |
1751 | #t))))) |
1752 | (home-page "https://andrejv.github.io/wxmaxima/") | |
1753 | (synopsis "Graphical user interface for the Maxima computer algebra system") | |
1754 | (description | |
1755 | "wxMaxima is a graphical user interface for the Maxima computer algebra | |
1756 | system. It eases the use of Maxima by making most of its commands available | |
1757 | through a menu system and by providing input dialogs for commands that require | |
1758 | more than one argument. It also implements its own display engine that | |
1759 | outputs mathematical symbols directly instead of depicting them with ASCII | |
1760 | characters. | |
1761 | ||
1762 | wxMaxima also features 2D and 3D inline plots, simple animations, mixing of | |
1763 | text and mathematical calculations to create documents, exporting of input and | |
1764 | output to TeX, and a browser for Maxima's manual including command index and | |
1765 | full text searching.") | |
1766 | (license license:gpl2+))) | |
1767 | ||
b15e47f9 RW |
1768 | (define-public armadillo |
1769 | (package | |
1770 | (name "armadillo") | |
945eef85 | 1771 | (version "6.700.7") |
b15e47f9 RW |
1772 | (source (origin |
1773 | (method url-fetch) | |
1774 | (uri (string-append "mirror://sourceforge/arma/armadillo-" | |
1775 | version ".tar.gz")) | |
1776 | (sha256 | |
1777 | (base32 | |
945eef85 | 1778 | "0xbidcxrvbq33xf7iysg2nic2ai9a043psl33kiv6ifkk7p8hcra")))) |
b15e47f9 RW |
1779 | (build-system cmake-build-system) |
1780 | (arguments `(#:tests? #f)) ;no test target | |
1781 | (inputs | |
1782 | `(("openblas" ,openblas) | |
1783 | ("lapack" ,lapack) | |
1784 | ("arpack" ,arpack-ng))) | |
1785 | (home-page "http://arma.sourceforge.net/") | |
1786 | (synopsis "C++ linear algebra library") | |
1787 | (description | |
1788 | "Armadillo is a C++ linear algebra library, aiming towards a good balance | |
1789 | between speed and ease of use. It is useful for algorithm development | |
1790 | directly in C++, or quick conversion of research code into production | |
1791 | environments. It can be used for machine learning, pattern recognition, | |
1792 | signal processing, bioinformatics, statistics, econometrics, etc. The library | |
1793 | provides efficient classes for vectors, matrices and cubes, as well as 150+ | |
1794 | associated functions (eg. contiguous and non-contiguous submatrix views).") | |
1795 | (license license:mpl2.0))) | |
1796 | ||
e22d4ca4 RW |
1797 | (define-public armadillo-for-rcpparmadillo |
1798 | (package (inherit armadillo) | |
813efdde | 1799 | (version "6.700.6") |
e22d4ca4 RW |
1800 | (source (origin |
1801 | (method url-fetch) | |
1802 | (uri (string-append "mirror://sourceforge/arma/armadillo-" | |
1803 | version ".tar.gz")) | |
1804 | (sha256 | |
1805 | (base32 | |
813efdde | 1806 | "1cdpjxb0fz5f28y5qrqgpw53s7qi8s2v3al9lfdldqxngb21vpx8")))))) |
e22d4ca4 | 1807 | |
279663ef | 1808 | (define-public muparser |
d7cff656 LF |
1809 | ;; When switching download sites, muparser re-issued a 2.2.5 release with a |
1810 | ;; different hash. In order to make `guix package --upgrade` work correctly, | |
1811 | ;; we set a Guix packaging revision. | |
1812 | ;; When the next version of muparser is released, we can remove | |
1813 | ;; UPSTREAM-VERSION and REVISION and use the plain VERSION. | |
1814 | (let ((upstream-version "2.2.5") | |
1815 | (revision "2")) | |
1816 | (package | |
1817 | (name "muparser") | |
1818 | (version (string-append upstream-version "-" revision)) | |
1819 | (source | |
1820 | (origin | |
1821 | (method url-fetch) | |
1822 | (uri (string-append "https://github.com/beltoforion/muparser/archive/v" | |
1823 | upstream-version ".tar.gz")) | |
1824 | (file-name (string-append name "-" version ".tar.gz")) | |
1825 | (sha256 | |
1826 | (base32 | |
1827 | "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6")))) | |
1828 | (build-system gnu-build-system) | |
1829 | (arguments | |
1830 | `(#:configure-flags '("--enable-samples=no") | |
1831 | #:tests? #f)) ;no "check" target | |
1832 | (home-page "http://muparser.beltoforion.de/") | |
1833 | (synopsis "Fast parser library for mathematical expressions") | |
1834 | (description | |
1835 | "muParser is an extensible high performance math parser library. It is | |
1836 | based on transforming an expression into a bytecode and precalculating constant | |
1837 | parts of it.") | |
1838 | (license license:expat)))) | |
279663ef | 1839 | |
e73b49fb RW |
1840 | (define-public openblas |
1841 | (package | |
1842 | (name "openblas") | |
69851c59 | 1843 | (version "0.2.15") |
e73b49fb RW |
1844 | (source |
1845 | (origin | |
1846 | (method url-fetch) | |
1847 | (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v" | |
1848 | version)) | |
1849 | (file-name (string-append name "-" version ".tar.gz")) | |
1850 | (sha256 | |
1851 | (base32 | |
69851c59 | 1852 | "1k5f6vjlk54qlplk5m7xkbaw6g2y7dl50lwwdv6xsbcsgsbxfcpy")))) |
e73b49fb RW |
1853 | (build-system gnu-build-system) |
1854 | (arguments | |
5b5ea159 | 1855 | `(#:tests? #f ;no "check" target |
bd0b4379 RW |
1856 | ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no |
1857 | ;; TARGET is specified, OpenBLAS will tune itself to the build host, so | |
1858 | ;; we need to disable substitutions. | |
71923a91 AE |
1859 | #:substitutable? |
1860 | ,(let ((system (or (%current-target-system) (%current-system)))) | |
1861 | (or (string-prefix? "x86_64" system) | |
bd0b4379 RW |
1862 | (string-prefix? "i686" system) |
1863 | (string-prefix? "mips" system))) | |
e73b49fb RW |
1864 | #:make-flags |
1865 | (list (string-append "PREFIX=" (assoc-ref %outputs "out")) | |
1866 | "SHELL=bash" | |
af5b817e RW |
1867 | "NO_LAPACK=1" |
1868 | ;; Build the library for all supported CPUs. This allows | |
1869 | ;; switching CPU targets at runtime with the environment variable | |
1870 | ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type. | |
71923a91 AE |
1871 | ;; Unfortunately, this is not supported on non-x86 architectures, |
1872 | ;; where it leads to failed builds. | |
1873 | ,@(let ((system (or (%current-target-system) (%current-system)))) | |
8a637e79 RW |
1874 | (cond |
1875 | ((or (string-prefix? "x86_64" system) | |
71923a91 | 1876 | (string-prefix? "i686" system)) |
8a637e79 RW |
1877 | '("DYNAMIC_ARCH=1")) |
1878 | ;; On MIPS we force the "SICORTEX" TARGET, as for the other | |
1879 | ;; two available MIPS targets special extended instructions | |
1880 | ;; for Loongson cores are used. | |
1881 | ((string-prefix? "mips" system) | |
1882 | '("TARGET=SICORTEX")) | |
1883 | (else '())))) | |
e73b49fb RW |
1884 | ;; no configure script |
1885 | #:phases (alist-delete 'configure %standard-phases))) | |
1886 | (inputs | |
19afbea1 | 1887 | `(("fortran" ,gfortran))) |
e73b49fb RW |
1888 | (native-inputs |
1889 | `(("cunit" ,cunit) | |
1890 | ("perl" ,perl))) | |
1891 | (home-page "http://www.openblas.net/") | |
1892 | (synopsis "Optimized BLAS library based on GotoBLAS") | |
1893 | (description | |
1894 | "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.") | |
1895 | (license license:bsd-3))) | |
1896 | ||
e1605e36 RW |
1897 | (define-public openlibm |
1898 | (package | |
1899 | (name "openlibm") | |
26f6e565 | 1900 | (version "0.5.1") |
e1605e36 RW |
1901 | (source |
1902 | (origin | |
1903 | (method url-fetch) | |
1904 | (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v" | |
1905 | version ".tar.gz")) | |
1906 | (file-name (string-append name "-" version ".tar.gz")) | |
1907 | (sha256 | |
1908 | (base32 | |
26f6e565 | 1909 | "11czx2z7nh6dfpz45s3xl7v38hw36jxzxfvny454bk3if14pfakq")))) |
e1605e36 RW |
1910 | (build-system gnu-build-system) |
1911 | (arguments | |
1912 | `(#:make-flags | |
1913 | (list (string-append "prefix=" (assoc-ref %outputs "out"))) | |
1914 | #:phases | |
1915 | ;; no configure script | |
1916 | (alist-delete 'configure %standard-phases) | |
1917 | #:tests? #f)) ;the tests are part of the default target | |
1918 | (home-page "http://openlibm.org/") | |
1919 | (synopsis "Portable C mathematical library (libm)") | |
1920 | (description | |
1921 | "OpenLibm is an effort to have a high quality, portable, standalone C | |
1922 | mathematical library (libm). It can be used standalone in applications and | |
1923 | programming language implementations. The project was born out of a need to | |
e881752c | 1924 | have a good libm for the Julia programming language that worked consistently |
e1605e36 RW |
1925 | across compilers and operating systems, and in 32-bit and 64-bit |
1926 | environments.") | |
1927 | ;; See LICENSE.md for details. | |
1928 | (license (list license:expat | |
1929 | license:isc | |
1930 | license:bsd-2 | |
1931 | license:public-domain | |
1932 | license:lgpl2.1+)))) | |
1933 | ||
e62be58f RW |
1934 | (define-public openspecfun |
1935 | (package | |
1936 | (name "openspecfun") | |
49f54a74 | 1937 | (version "0.5.2") |
e62be58f RW |
1938 | (source |
1939 | (origin | |
1940 | (method url-fetch) | |
1941 | (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v" | |
1942 | version ".tar.gz")) | |
1943 | (file-name (string-append name "-" version ".tar.gz")) | |
1944 | (sha256 | |
1945 | (base32 | |
49f54a74 | 1946 | "1y5b2h6f2k72536kym3vzy3li3bhpd23x463g7hdmjdi3cncavz1")))) |
e62be58f RW |
1947 | (build-system gnu-build-system) |
1948 | (arguments | |
1949 | '(#:tests? #f ;no "check" target | |
1950 | #:make-flags | |
1951 | (list (string-append "prefix=" (assoc-ref %outputs "out"))) | |
1952 | ;; no configure script | |
1953 | #:phases (alist-delete 'configure %standard-phases))) | |
1954 | (inputs | |
19afbea1 | 1955 | `(("fortran" ,gfortran))) |
e62be58f RW |
1956 | (home-page "https://github.com/JuliaLang/openspecfun") |
1957 | (synopsis "Collection of special mathematical functions") | |
1958 | (description | |
1959 | "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a | |
1960 | portable package for Bessel Functions of a Complex Argument and Nonnegative | |
1961 | Order; it contains subroutines for computing Bessel functions and Airy | |
1962 | functions. Faddeeva allows computing the various error functions of arbitrary | |
1963 | complex arguments (Faddeeva function, error function, complementary error | |
1964 | function, scaled complementary error function, imaginary error function, and | |
1965 | Dawson function); given these, one can also easily compute Voigt functions, | |
1966 | Fresnel integrals, and similar related functions as well.") | |
1967 | ;; Faddeeva is released under the Expat license; AMOS is included as | |
1968 | ;; public domain software. | |
1969 | (license (list license:expat license:public-domain)))) | |
1970 | ||
2742f87e RW |
1971 | (define-public suitesparse |
1972 | (package | |
1973 | (name "suitesparse") | |
1974 | (version "4.4.3") | |
1975 | (source | |
1976 | (origin | |
1977 | (method url-fetch) | |
1978 | (uri (string-append | |
1979 | "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-" | |
1980 | version ".tar.gz")) | |
1981 | (sha256 | |
1982 | (base32 | |
1983 | "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5")))) | |
1984 | (build-system gnu-build-system) | |
1985 | (arguments | |
1986 | '(#:parallel-build? #f ;cholmod build fails otherwise | |
1987 | #:tests? #f ;no "check" target | |
1988 | #:make-flags | |
1989 | (list "CC=gcc" | |
1990 | "BLAS=-lblas" | |
1991 | "TBB=-ltbb" | |
1992 | "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used | |
1993 | (string-append "INSTALL_LIB=" | |
1994 | (assoc-ref %outputs "out") "/lib") | |
1995 | (string-append "INSTALL_INCLUDE=" | |
1996 | (assoc-ref %outputs "out") "/include")) | |
1997 | #:phases | |
1998 | (alist-cons-before | |
1999 | 'install 'prepare-out | |
2000 | ;; README.txt states that the target directories must exist prior to | |
2001 | ;; running "make install". | |
2002 | (lambda _ | |
2003 | (mkdir-p (string-append (assoc-ref %outputs "out") "/lib")) | |
2004 | (mkdir-p (string-append (assoc-ref %outputs "out") "/include"))) | |
2005 | ;; no configure script | |
2006 | (alist-delete 'configure %standard-phases)))) | |
2007 | (inputs | |
2008 | `(("tbb" ,tbb) | |
2009 | ("lapack" ,lapack))) | |
2010 | (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html") | |
2011 | (synopsis "Suite of sparse matrix software") | |
2012 | (description | |
2013 | "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK, | |
2014 | multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR, | |
2015 | multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit | |
2016 | simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and | |
2017 | CXSparse, a concise sparse Cholesky factorization package; and many other | |
2018 | packages.") | |
2019 | ;; LGPLv2.1+: | |
2020 | ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL | |
2021 | ;; GPLv2+: | |
2022 | ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK | |
2023 | (license (list license:gpl2+ license:lgpl2.1+)))) | |
2024 | ||
ec322be2 FB |
2025 | (define-public atlas |
2026 | (package | |
2027 | (name "atlas") | |
2028 | (version "3.10.2") | |
2029 | (source (origin | |
2030 | (method url-fetch) | |
de67e922 LF |
2031 | (uri (string-append "mirror://sourceforge/math-atlas/Stable/" |
2032 | version "/atlas" version ".tar.bz2")) | |
ec322be2 FB |
2033 | (sha256 |
2034 | (base32 | |
2035 | "0bqh4bdnjdyww4mcpg6kn0x7338mfqbdgysn97dzrwwb26di7ars")))) | |
2036 | (build-system gnu-build-system) | |
2037 | (home-page "http://math-atlas.sourceforge.net/") | |
19afbea1 | 2038 | (inputs `(("gfortran" ,gfortran) |
ec322be2 FB |
2039 | ("lapack-tar" ,(package-source lapack)))) |
2040 | (outputs '("out" "doc")) | |
01480b9e FB |
2041 | ;; For the moment we drop support for MIPS at it fails to compile. See |
2042 | ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html | |
2043 | (supported-systems (delete "mips64el-linux" %supported-systems)) | |
ec322be2 FB |
2044 | (arguments |
2045 | `(#:parallel-build? #f | |
2046 | #:parallel-tests? #f | |
f15615b1 LC |
2047 | |
2048 | ;; ATLAS tunes itself for the machine it is built on, as explained at | |
2049 | ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>. | |
2050 | ;; For this reason, we want users to build it locally instead of using | |
2051 | ;; substitutes. | |
2052 | #:substitutable? #f | |
2053 | ||
ec322be2 FB |
2054 | #:modules ((srfi srfi-26) |
2055 | (srfi srfi-1) | |
2056 | (guix build gnu-build-system) | |
2057 | (guix build utils)) | |
40029cbe | 2058 | #:configure-flags |
ec322be2 FB |
2059 | `(;; Generate position independent code suitable for dynamic libraries |
2060 | ;; and use WALL timer to get more accurate timing. | |
2061 | "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL" | |
2062 | ;; Set word width. | |
2063 | "-b" | |
2064 | ,,(if (string-match "64" (%current-system)) | |
2065 | "64" | |
2066 | "32") | |
2067 | ;; Disable parallel build as it gives errors: atlas_pthread.h is | |
2068 | ;; needed to compile C files before it is generated. | |
2069 | "-Ss" "pmake" "make -j 1" | |
af89a667 FB |
2070 | ;; Probe is failing for MIPS. We therefore define the system |
2071 | ;; architecture explicitly by setting (-A) MACHINETYPE = 49 | |
2072 | ;; 'MIPSR1xK' and (-V) ISA = 1 'none'. | |
2073 | ,,@(if (string-prefix? "mips" (%current-system)) | |
2074 | (list "-A" "49" "-V" "1") | |
2075 | (list)) | |
ec322be2 FB |
2076 | ;; Generate shared libraries. |
2077 | "--shared" | |
2078 | ;; Build a full LAPACK library. | |
2079 | ,(string-append "--with-netlib-lapack-tarfile=" | |
2080 | (assoc-ref %build-inputs "lapack-tar"))) | |
2081 | #:phases | |
e5b4b96b EF |
2082 | (modify-phases %standard-phases |
2083 | (add-after 'install 'install-doc | |
2084 | (lambda* (#:key outputs inputs #:allow-other-keys) | |
2085 | (let ((doc (string-append (assoc-ref outputs "doc") | |
2086 | "/share/doc/atlas"))) | |
2087 | (mkdir-p doc) | |
2088 | (fold (lambda (file previous) | |
2089 | (and previous (zero? (system* "cp" file doc)))) | |
2090 | #t (find-files "../ATLAS/doc" ".*"))))) | |
2091 | (add-after 'check 'check-pt | |
2092 | (lambda _ (zero? (system* "make" "ptcheck")))) | |
2093 | ;; Fix files required to run configure. | |
2094 | (add-before 'configure 'fix-/bin/sh | |
ec322be2 FB |
2095 | (lambda _ |
2096 | ;; Use `sh', not `/bin/sh'. | |
2097 | (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c") | |
2098 | (("/bin/sh") | |
e5b4b96b EF |
2099 | "sh")))) |
2100 | ;; Fix /bin/sh in generated make files. | |
2101 | (add-after 'configure 'fix-/bin/sh-in-generated-files | |
2102 | (lambda _ | |
2103 | (substitute* (find-files "." "^[Mm]ake\\.inc.*") | |
2104 | (("/bin/sh") | |
2105 | "sh")))) | |
2106 | ;; ATLAS configure program does not accepts the default flags | |
2107 | ;; passed by the 'gnu-build-system'. | |
2108 | (replace 'configure | |
2109 | (lambda* (#:key native-inputs inputs outputs | |
2110 | (configure-flags '()) | |
2111 | #:allow-other-keys #:rest args) | |
2112 | (let* ((prefix (assoc-ref outputs "out")) | |
2113 | (bash (or (and=> (assoc-ref | |
2114 | (or native-inputs inputs) "bash") | |
2115 | (cut string-append <> "/bin/bash")) | |
2116 | "/bin/sh")) | |
2117 | (flags `(,(string-append "--prefix=" prefix) | |
2118 | ,@configure-flags)) | |
2119 | (abs-srcdir (getcwd)) | |
2120 | (srcdir (string-append "../" (basename abs-srcdir)))) | |
2121 | (format #t "source directory: ~s (relative from build: ~s)~%" | |
2122 | abs-srcdir srcdir) | |
2123 | (mkdir "../build") | |
2124 | (chdir "../build") | |
2125 | (format #t "build directory: ~s~%" (getcwd)) | |
2126 | (format #t "configure flags: ~s~%" flags) | |
2127 | (zero? (apply system* bash | |
2128 | (string-append srcdir "/configure") | |
2129 | flags)))))))) | |
ec322be2 FB |
2130 | (synopsis "Automatically Tuned Linear Algebra Software") |
2131 | (description | |
2132 | "ATLAS is an automatically tuned linear algebra software library | |
2133 | providing C and Fortran77 interfaces to a portably efficient BLAS | |
2134 | implementation, as well as a few routines from LAPACK. | |
2135 | ||
f15615b1 LC |
2136 | Optimization occurs at build time. For this reason, the library is built on |
2137 | the machine where it is installed, without resorting to pre-built substitutes. | |
ec322be2 | 2138 | |
f15615b1 | 2139 | Before building the library, CPU throttling should be disabled. This can be |
d97c429a | 2140 | done in the BIOS, or, on GNU/Linux, with the following command: |
ec322be2 | 2141 | |
8e9ba611 | 2142 | @example |
d97c429a | 2143 | # cpupower --governor performance |
8e9ba611 | 2144 | @end example |
ec322be2 | 2145 | |
d97c429a | 2146 | Failure to do so will result in a library with poor performance.") |
ec322be2 | 2147 | (license license:bsd-3))) |
c12efc72 AE |
2148 | |
2149 | (define-public glm | |
2150 | (package | |
2151 | (name "glm") | |
2152 | (version "0.9.6.3") | |
2153 | (source | |
2154 | (origin | |
2155 | (method url-fetch) | |
de67e922 LF |
2156 | (uri (string-append "mirror://sourceforge/ogl-math/glm-" version |
2157 | "/glm-" version ".zip")) | |
c12efc72 AE |
2158 | (sha256 |
2159 | (base32 | |
2160 | "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l")))) | |
2161 | (build-system cmake-build-system) | |
2162 | (native-inputs | |
2163 | `(("unzip" ,unzip))) | |
2164 | (home-page "http://glm.g-truc.net") | |
2165 | (synopsis "OpenGL Mathematics library") | |
2166 | (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics | |
2167 | library for graphics software based on the OpenGL Shading Language (GLSL) | |
2168 | specifications.") | |
2169 | (license license:expat))) | |
7f18257b AE |
2170 | |
2171 | (define-public lpsolve | |
2172 | (package | |
2173 | (name "lpsolve") | |
2174 | (version "5.5.2.0") | |
2175 | (source | |
2176 | (origin | |
2177 | (method url-fetch) | |
2178 | (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version | |
2179 | "/lp_solve_" version "_source.tar.gz")) | |
2180 | (sha256 | |
2181 | (base32 | |
2182 | "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq")) | |
2183 | (modules '((guix build utils))) | |
2184 | (snippet | |
2185 | '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc") | |
2186 | (("^c=cc") "c=gcc") | |
2187 | ;; Pretend to be on a 64 bit platform to obtain a common directory | |
2188 | ;; name for the build results on all architectures; nothing else | |
2189 | ;; seems to depend on it. | |
5dbfbef7 LC |
2190 | (("^PLATFORM=.*$") "PLATFORM=ux64\n") |
2191 | ||
2192 | ;; The check for 'isnan' as it is written fails with | |
2193 | ;; "non-floating-point argument in call to function | |
2194 | ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro | |
2195 | ;; definition, which in turn leads to bad things. Fix the feature | |
2196 | ;; test. | |
2197 | (("isnan\\(0\\)") "isnan(0.)"))))) | |
7f18257b AE |
2198 | (build-system gnu-build-system) |
2199 | (arguments | |
2200 | `(#:tests? #f ; no check target | |
2201 | #:phases | |
2202 | (modify-phases %standard-phases | |
2203 | (delete 'configure) | |
2204 | (replace 'build | |
2205 | (lambda _ | |
6689d094 LC |
2206 | (and (with-directory-excursion "lpsolve55" |
2207 | (zero? (system* "bash" "ccc"))) | |
2208 | (with-directory-excursion "lp_solve" | |
2209 | (zero? (system* "bash" "ccc")))))) | |
7f18257b AE |
2210 | (replace 'install |
2211 | (lambda* (#:key outputs #:allow-other-keys) | |
2212 | (let* ((out (assoc-ref outputs "out")) | |
2213 | (bin (string-append out "/bin")) | |
2214 | (lib (string-append out "/lib")) | |
2215 | ;; This is where LibreOffice expects to find the header | |
2216 | ;; files, and where they are installed by Debian. | |
2217 | (include (string-append out "/include/lpsolve"))) | |
2218 | (mkdir-p lib) | |
2219 | (copy-file "lpsolve55/bin/ux64/liblpsolve55.a" | |
2220 | (string-append lib "/liblpsolve55.a")) | |
2221 | (copy-file "lpsolve55/bin/ux64/liblpsolve55.so" | |
2222 | (string-append lib "/liblpsolve55.so")) | |
96c46210 LC |
2223 | (install-file "lp_solve/bin/ux64/lp_solve" bin) |
2224 | ||
7f18257b AE |
2225 | ;; Install a subset of the header files as on Debian |
2226 | ;; (plus lp_bit.h, which matches the regular expression). | |
96c46210 LC |
2227 | (for-each (lambda (name) |
2228 | (install-file name include)) | |
2229 | (find-files "." "lp_[HMSa-z].*\\.h$")) | |
7f18257b | 2230 | (with-directory-excursion "shared" |
96c46210 LC |
2231 | (for-each (lambda (name) |
2232 | (install-file name include)) | |
2233 | (find-files "." "\\.h$"))) | |
7f18257b AE |
2234 | #t)))))) |
2235 | (home-page "http://lpsolve.sourceforge.net/") | |
2236 | (synopsis "Mixed integer linear programming (MILP) solver") | |
2237 | (description | |
2238 | "lp_solve is a mixed integer linear programming solver based on the | |
2239 | revised simplex and the branch-and-bound methods.") | |
2240 | (license license:lgpl2.1+))) | |
a17d4564 EB |
2241 | |
2242 | (define-public dealii | |
2243 | (package | |
2244 | (name "dealii") | |
101e8472 | 2245 | (version "8.4.1") |
a17d4564 EB |
2246 | (source |
2247 | (origin | |
2248 | (method url-fetch) | |
2249 | (uri (string-append "https://github.com/dealii/dealii/releases/" | |
2250 | "download/v" version "/dealii-" version ".tar.gz")) | |
2251 | (sha256 | |
2252 | (base32 | |
101e8472 | 2253 | "1bdksvvyp1rj37df1ndh8j3x9nzpc3sazw8nd0hzvnlw0qnyk800")) |
a17d4564 EB |
2254 | (modules '((guix build utils))) |
2255 | (snippet | |
2256 | ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost | |
2257 | '(delete-file-recursively "bundled")))) | |
2258 | (build-system cmake-build-system) | |
2259 | (inputs | |
2260 | `(("tbb" ,tbb) | |
2261 | ("zlib" ,zlib) | |
2262 | ("boost" ,boost) | |
2263 | ("p4est" ,p4est) | |
2264 | ("blas" ,openblas) | |
2265 | ("lapack" ,lapack) | |
2266 | ("arpack" ,arpack-ng) | |
2267 | ("muparser" ,muparser) | |
2268 | ("gfortran" ,gfortran) | |
2269 | ("suitesparse" ,suitesparse))) ;for UMFPACK | |
2270 | (arguments | |
2271 | `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease | |
2272 | #:configure-flags '("-DCOMPAT_FILES=OFF") ;Follow new directory structure | |
2273 | #:phases (modify-phases %standard-phases | |
2274 | (add-after | |
2275 | 'install 'hint-example-prefix | |
2276 | ;; Set Cmake hints in examples so that they can find this | |
2277 | ;; deal.II when configuring. | |
2278 | (lambda* (#:key outputs #:allow-other-keys) | |
2279 | (let* ((out (assoc-ref %outputs "out")) | |
2280 | (exmpl (string-append out "/share/doc" | |
2281 | "/dealii/examples"))) | |
2282 | (substitute* (find-files exmpl "CMakeLists.txt") | |
2283 | (("([[:space:]]*HINTS.*)\n" _ line) | |
2284 | (string-append line " $ENV{HOME}/.guix-profile " | |
2285 | out "\n"))) | |
2286 | #t)))))) | |
2287 | (home-page "https://www.dealii.org") | |
2288 | (synopsis "Finite element library") | |
2289 | (description | |
2290 | "Deal.II is a C++ program library targeted at the computational solution | |
2291 | of partial differential equations using adaptive finite elements. The main | |
2292 | aim of deal.II is to enable rapid development of modern finite element codes, | |
2293 | using among other aspects adaptive meshes and a wide array of tools often used | |
2294 | in finite element programs.") | |
2295 | (license license:lgpl2.1+))) | |
2296 | ||
2297 | (define-public dealii-openmpi | |
2298 | (package (inherit dealii) | |
2299 | (name "dealii-openmpi") | |
2300 | (inputs | |
2301 | `(("mpi" ,openmpi) | |
2302 | ;;Supported only with MPI: | |
2303 | ("p4est" ,p4est-openmpi) | |
2304 | ("petsc" ,petsc-openmpi) | |
2305 | ("slepc" ,slepc-openmpi) | |
2306 | ("metis" ,metis) ;for MUMPS | |
2307 | ("scalapack" ,scalapack) ;for MUMPS | |
2308 | ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings | |
2309 | ("arpack" ,arpack-ng-openmpi) | |
2310 | ,@(fold alist-delete (package-inputs dealii) | |
2311 | '("p4est" "arpack")))) | |
2312 | (arguments | |
2313 | (substitute-keyword-arguments (package-arguments dealii) | |
2314 | ((#:configure-flags cf) | |
2315 | ``("-DMPI_C_COMPILER=mpicc" | |
2316 | "-DMPI_CXX_COMPILER=mpicxx" | |
2317 | "-DMPI_Fortran_COMPILER=mpifort" | |
2318 | ,@,cf)))) | |
2319 | (synopsis "Finite element library (with MPI support)"))) | |
194c7f95 AE |
2320 | |
2321 | (define-public flann | |
2322 | (package | |
2323 | (name "flann") | |
2324 | (version "1.8.4") | |
2325 | (source | |
2326 | (origin | |
2327 | (method url-fetch) | |
2328 | (uri | |
2329 | (string-append | |
2330 | "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-" | |
2331 | version "-src.zip")) | |
2332 | (sha256 | |
2333 | (base32 | |
2334 | "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz")))) | |
2335 | (build-system cmake-build-system) | |
2336 | (native-inputs | |
2337 | `(("unzip" ,unzip))) | |
2338 | (inputs | |
2339 | `(("hdf5" ,hdf5) | |
2340 | ("octave" ,octave) | |
2341 | ("python" ,python-2) ; print syntax | |
2342 | ;; ("python2-numpy" ,python2-numpy) ; only required for the tests | |
2343 | ("zlib" ,zlib))) | |
2344 | (arguments | |
39b30337 LC |
2345 | `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file |
2346 | ;; taken 46 MiB unstripped, and 6 MiB stripped. | |
2347 | #:strip-directories '("lib" "lib64" "libexec" | |
2348 | "bin" "sbin" "share/flann/octave") | |
2349 | ||
9684e30b LC |
2350 | ;; Save 12 MiB by not installing .a files. Passing |
2351 | ;; '-DBUILD_STATIC_LIBS=OFF' has no effect. | |
2352 | #:phases (modify-phases %standard-phases | |
2353 | (add-after 'install 'remove-static-libraries | |
2354 | (lambda* (#:key outputs #:allow-other-keys) | |
2355 | (let* ((out (assoc-ref outputs "out")) | |
2356 | (lib (string-append out "/lib"))) | |
2357 | (for-each delete-file | |
2358 | (find-files lib "\\.a$")) | |
2359 | #t)))) | |
2360 | ||
39b30337 | 2361 | #:tests? #f)) ; The test data are downloaded from the Internet. |
194c7f95 AE |
2362 | (home-page "http://www.cs.ubc.ca/research/flann/") |
2363 | (synopsis "Library for approximate nearest neighbors computation") | |
2364 | (description "FLANN is a library for performing fast approximate | |
2365 | nearest neighbor searches in high dimensional spaces. It implements a | |
2366 | collection of algorithms and a system for automatically choosing the best | |
2367 | algorithm and optimum parameters depending on the dataset. | |
2368 | ||
2369 | FLANN is written in C++ and contains bindings for C, Octave and Python.") | |
2370 | (license (license:non-copyleft "file://COPYING" | |
2371 | "See COPYING in the distribution.")))) | |
d8c97beb EF |
2372 | |
2373 | (define-public wcalc | |
2374 | (package | |
2375 | (name "wcalc") | |
2376 | (version "2.5") | |
2377 | (source | |
2378 | (origin | |
2379 | (method url-fetch) | |
de67e922 LF |
2380 | (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/" |
2381 | "wcalc-" version ".tar.bz2")) | |
d8c97beb EF |
2382 | (sha256 |
2383 | (base32 | |
2384 | "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f")))) | |
2385 | (build-system gnu-build-system) | |
2386 | (inputs | |
2387 | `(("mpfr" ,mpfr) | |
2388 | ("readline" ,readline))) | |
2389 | (home-page "http://w-calc.sourceforge.net/index.php") | |
2390 | (synopsis "Flexible command-line scientific calculator") | |
2391 | (description "Wcalc is a very capable calculator. It has standard functions | |
2392 | (sin, asin, and sinh for example, in either radians or degrees), many | |
2393 | pre-defined constants (pi, e, c, etc.), support for using variables, \"active\" | |
2394 | variables, a command history, hex/octal/binary input and output, unit | |
2395 | conversions, embedded comments, and an expandable expression entry field. It | |
2396 | evaluates expressions using the standard order of operations.") | |
2397 | (license license:gpl2+))) | |
45147b0c FH |
2398 | |
2399 | (define-public xaos | |
2400 | (package | |
2401 | (name "xaos") | |
2402 | (version "3.6") | |
2403 | (source (origin | |
2404 | (method url-fetch) | |
de67e922 LF |
2405 | (uri (string-append "mirror://sourceforge/xaos/XaoS/" version |
2406 | "/xaos-" version ".tar.gz")) | |
45147b0c FH |
2407 | (sha256 |
2408 | (base32 | |
2409 | "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq")))) | |
2410 | (build-system gnu-build-system) | |
2411 | (native-inputs `(("gettext" ,gnu-gettext))) | |
2412 | (inputs `(("libx11" ,libx11) | |
2413 | ("zlib" ,zlib) | |
2414 | ("libpng" ,libpng) | |
2415 | ("gsl" ,gsl))) | |
2416 | (arguments | |
2417 | `(#:tests? #f ;no "check" target | |
2418 | #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale"))) | |
2419 | (synopsis "Real-time fractal zoomer") | |
2420 | (description "GNU XaoS is a graphical program that generates fractal | |
2421 | patterns and allows you to zoom in and out of them infinitely in a fluid, | |
2422 | continuous manner. It also includes tutorials that help to explain how fractals | |
2423 | are built. It can generate many different fractal types such as the Mandelbrot | |
2424 | set.") | |
2425 | (home-page "http://www.gnu.org/software/xaos/") | |
2426 | (license license:gpl2+))) | |
528bb464 EB |
2427 | |
2428 | (define-public hypre | |
2429 | (package | |
2430 | (name "hypre") | |
2431 | (version "2.11.0") | |
2432 | (source (origin | |
2433 | (method url-fetch) | |
2434 | (uri (string-append "https://github.com/LLNL/hypre/archive/" | |
2435 | "v" version ".tar.gz")) | |
2436 | (file-name (string-append name "-" version ".tar.gz")) | |
2437 | (sha256 | |
2438 | (base32 | |
2439 | "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m")) | |
2440 | (modules '((guix build utils))) | |
2441 | (snippet | |
2442 | '(begin | |
2443 | ;; Remove use of __DATE__ and __TIME__ for reproducibility; | |
2444 | ;; substitute the tarball creation time. | |
2445 | (substitute* "src/utilities/HYPRE_utilities.h" | |
2446 | (("Date Compiled: .*$") | |
2447 | "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n")) | |
2448 | #t)))) | |
2449 | (build-system gnu-build-system) | |
2450 | (outputs '("out" ;6.1 MiB of headers and libraries | |
2451 | "doc")) ;4.8 MiB of documentation | |
2452 | (native-inputs | |
2453 | `(("doc++" ,doc++) | |
2454 | ("netpbm" ,netpbm) | |
2455 | ("texlive" ,texlive) ;full package required for fonts | |
2456 | ("ghostscript" ,ghostscript))) | |
2457 | (inputs | |
2458 | `(("blas" ,openblas) | |
2459 | ("lapack" ,lapack))) | |
2460 | (arguments | |
2461 | `(#:modules ((srfi srfi-1) | |
2462 | ,@%gnu-build-system-modules) | |
2463 | #:configure-flags '("--enable-shared" | |
2464 | "--disable-fortran" | |
2465 | "--without-MPI" | |
2466 | "--with-openmp" | |
2467 | "--with-fei" | |
2468 | "--with-lapack" | |
2469 | "--with-blas") | |
2470 | #:phases | |
2471 | (modify-phases %standard-phases | |
2472 | (add-before 'configure 'chdir-src | |
2473 | (lambda _ (chdir "src"))) | |
2474 | (replace 'configure | |
2475 | (lambda* (#:key build target configure-flags | |
2476 | #:allow-other-keys #:rest args) | |
2477 | (let* ((configure (assoc-ref %standard-phases 'configure))) | |
2478 | (apply configure | |
2479 | (append args | |
2480 | (list #:configure-flags | |
2481 | (cons (string-append | |
2482 | "--host=" (or target build)) | |
2483 | configure-flags))))))) | |
2484 | (add-after 'build 'build-docs | |
2485 | (lambda _ | |
2486 | (zero? (system* "make" "-Cdocs" "pdf" "html")))) | |
2487 | (replace 'check | |
2488 | (lambda _ | |
2489 | (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib")) | |
2490 | (setenv "PATH" (string-append "." ":" (getenv "PATH"))) | |
2491 | (and (system* "make" "check" "CHECKRUN=") | |
2492 | (fold (lambda (filename result) | |
2493 | (and result | |
2494 | (let ((size (stat:size (stat filename)))) | |
2495 | (when (not (zero? size)) | |
2496 | (format #t "~a size ~d; error indication~%" | |
2497 | filename size)) | |
2498 | (zero? size)))) | |
2499 | #t | |
2500 | (find-files "test" ".*\\.err$"))))) | |
2501 | (add-after 'install 'install-docs | |
2502 | (lambda* (#:key outputs #:allow-other-keys) | |
2503 | ;; Custom install because docs/Makefile doesn't honor ${docdir}. | |
2504 | (let* ((doc (assoc-ref outputs "doc")) | |
2505 | (docdir (string-append doc "/share/doc/hypre-" ,version))) | |
2506 | (mkdir-p docdir) | |
2507 | (with-directory-excursion "docs" | |
2508 | (for-each (lambda (base) | |
2509 | (install-file (string-append base ".pdf") docdir) | |
2510 | (copy-recursively base docdir)) ;html docs | |
2511 | '("HYPRE_usr_manual" | |
2512 | "HYPRE_ref_manual"))) | |
2513 | #t)))))) | |
2514 | (home-page "http://www.llnl.gov/casc/hypre/") | |
2515 | (synopsis "Library of solvers and preconditioners for linear equations") | |
2516 | (description | |
2517 | "HYPRE is a software library of high performance preconditioners and | |
2518 | solvers for the solution of large, sparse linear systems of equations. It | |
2519 | features multigrid solvers for both structured and unstructured grid | |
2520 | problems.") | |
2521 | (license license:lgpl2.1))) | |
2522 | ||
2523 | (define-public hypre-openmpi | |
2524 | (package (inherit hypre) | |
2525 | (name "hypre-openmpi") | |
2526 | (inputs | |
2527 | `(("mpi" ,openmpi) | |
2528 | ,@(package-inputs hypre))) | |
2529 | (arguments | |
2530 | (substitute-keyword-arguments (package-arguments hypre) | |
2531 | ((#:configure-flags flags) | |
2532 | ``("--with-MPI" | |
2533 | ,@(delete "--without-MPI" ,flags))))) | |
2534 | (synopsis "Parallel solvers and preconditioners for linear equations") | |
2535 | (description | |
2536 | "HYPRE is a software library of high performance preconditioners and | |
2537 | solvers for the solution of large, sparse linear systems of equations on | |
2538 | parallel computers. It features parallel multigrid solvers for both | |
2539 | structured and unstructured grid problems."))) | |
6c90e183 EB |
2540 | |
2541 | (define-public matio | |
2542 | (package | |
2543 | (name "matio") | |
2544 | (version "1.5.6") | |
2545 | (source | |
2546 | (origin | |
2547 | (method url-fetch) | |
de67e922 | 2548 | (uri (string-append "mirror://sourceforge/matio/matio/" version "/" |
6c90e183 EB |
2549 | "matio-" version ".tar.gz")) |
2550 | (sha256 | |
2551 | (base32 | |
2552 | "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir")))) | |
2553 | (build-system gnu-build-system) | |
2554 | (inputs | |
2555 | `(("zlib" ,zlib) | |
2556 | ("hdf5" ,hdf5))) | |
2557 | (home-page "http://matio.sourceforge.net/") | |
2558 | (synopsis "Library for reading and writing MAT files") | |
2559 | (description "Matio is a library for reading and writing MAT files. It | |
2560 | supports compressed MAT files, as well as newer (version 7.3) MAT files.") | |
2561 | (license license:bsd-2))) | |
d721c83a EB |
2562 | |
2563 | (define-public libhilbert | |
2564 | (package | |
2565 | (name "libhilbert") | |
2566 | (version "0.2-1") | |
2567 | (source | |
2568 | (origin | |
2569 | (method url-fetch) | |
2570 | (uri (string-append "http://web.cs.dal.ca/~chamilto/hilbert/" | |
2571 | "libhilbert-" version ".tar.gz")) | |
2572 | (sha256 | |
2573 | (base32 | |
2574 | "0v48x8405dj95gjn2saja4bzhw86d6zl6d3dg8h7dzac2qr97s34")))) | |
2575 | (build-system gnu-build-system) | |
2576 | (home-page "http://web.cs.dal.ca/~chamilto/hilbert") | |
2577 | (synopsis "Hilbert indices for multidimensional data") | |
2578 | (description "The libhilbert library can efficiently calculate Hilbert | |
2579 | curves and order-preserving representations of Hilbert curve indices that use | |
2580 | the same amount of space as the original point representation. This is useful | |
2581 | when using the Gilbert curve as a space filling curve through a | |
2582 | high-dimensional space where not all demensions have the same cardinality.") | |
2583 | (license license:lgpl2.1+))) |