Commit | Line | Data |
---|---|---|
8f8b2451 | 1 | ;;; GNU Guix --- Functional package management for GNU |
06ed5982 | 2 | ;;; Copyright © 2013, 2014 Andreas Enge <andreas@enge.fr> |
da95c817 | 3 | ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org> |
668c06ac | 4 | ;;; Copyright © 2014 John Darrington <jmd@gnu.org> |
f5d5a346 | 5 | ;;; Copyright © 2014 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> |
865a69dd | 8 | ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net> |
8f8b2451 AE |
9 | ;;; |
10 | ;;; This file is part of GNU Guix. | |
11 | ;;; | |
12 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
13 | ;;; under the terms of the GNU General Public License as published by | |
14 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
15 | ;;; your option) any later version. | |
16 | ;;; | |
17 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
18 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
19 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
20 | ;;; GNU General Public License for more details. | |
21 | ;;; | |
22 | ;;; You should have received a copy of the GNU General Public License | |
23 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
24 | ||
25 | (define-module (gnu packages maths) | |
ec322be2 | 26 | #:use-module (ice-9 regex) |
8f8b2451 | 27 | #:use-module (gnu packages) |
b5b73a82 | 28 | #:use-module ((guix licenses) #:prefix license:) |
8f8b2451 AE |
29 | #:use-module (guix packages) |
30 | #:use-module (guix download) | |
0e2672ae | 31 | #:use-module (guix utils) |
da95c817 | 32 | #:use-module (guix build-system cmake) |
c9dfa3c7 | 33 | #:use-module (guix build-system gnu) |
3de01d3f EB |
34 | #:use-module (gnu packages algebra) |
35 | #:use-module (gnu packages bison) | |
36 | #:use-module (gnu packages cmake) | |
c9dfa3c7 | 37 | #:use-module (gnu packages compression) |
668c06ac | 38 | #:use-module (gnu packages curl) |
57e544e8 | 39 | #:use-module (gnu packages elf) |
3de01d3f | 40 | #:use-module (gnu packages flex) |
668c06ac | 41 | #:use-module (gnu packages fltk) |
f3929800 | 42 | #:use-module (gnu packages fontutils) |
1dba6407 | 43 | #:use-module (gnu packages gettext) |
da95c817 | 44 | #:use-module (gnu packages gcc) |
73fed4f8 | 45 | #:use-module (gnu packages gd) |
668c06ac | 46 | #:use-module (gnu packages ghostscript) |
221ed17a | 47 | #:use-module (gnu packages glib) |
f3929800 | 48 | #:use-module (gnu packages gtk) |
668c06ac | 49 | #:use-module (gnu packages less) |
8731e527 | 50 | #:use-module (gnu packages lisp) |
5698b8b8 | 51 | #:use-module (gnu packages gnome) |
668c06ac JD |
52 | #:use-module (gnu packages xorg) |
53 | #:use-module (gnu packages gl) | |
8731e527 | 54 | #:use-module (gnu packages m4) |
d8c7eeb9 | 55 | #:use-module (gnu packages mpi) |
b92eee75 | 56 | #:use-module (gnu packages multiprecision) |
668c06ac | 57 | #:use-module (gnu packages pcre) |
5698b8b8 | 58 | #:use-module (gnu packages popt) |
c9dfa3c7 AE |
59 | #:use-module (gnu packages perl) |
60 | #:use-module (gnu packages pkg-config) | |
da95c817 | 61 | #:use-module (gnu packages python) |
c9dfa3c7 | 62 | #:use-module (gnu packages readline) |
183e44ae | 63 | #:use-module (gnu packages tcsh) |
df354a77 | 64 | #:use-module (gnu packages tcl) |
668c06ac | 65 | #:use-module (gnu packages texinfo) |
73fed4f8 | 66 | #:use-module (gnu packages texlive) |
c9dfa3c7 | 67 | #:use-module (gnu packages xml)) |
8f8b2451 AE |
68 | |
69 | (define-public units | |
70 | (package | |
71 | (name "units") | |
983815c8 | 72 | (version "2.11") |
8f8b2451 AE |
73 | (source (origin |
74 | (method url-fetch) | |
75 | (uri (string-append "mirror://gnu/units/units-" version | |
76 | ".tar.gz")) | |
77 | (sha256 (base32 | |
983815c8 | 78 | "1gjs3wc212aaiq4r76hx9nl1h3fa39n0ljwl9420d6ixl3rdmdjk")))) |
8f8b2451 AE |
79 | (build-system gnu-build-system) |
80 | (synopsis "Conversion between thousands of scales") | |
81 | (description | |
574e86f9 LC |
82 | "GNU Units converts numeric quantities between units of measure. It |
83 | can handle scale changes through adaptive usage of standard scale prefixes | |
84 | (micro-, kilo-, etc.). It can also handle nonlinear conversions such as | |
85 | Fahrenheit to Celsius. Its interpreter is powerful enough to be used | |
86 | effectively as a scientific calculator.") | |
8f8b2451 AE |
87 | (license license:gpl3+) |
88 | (home-page "http://www.gnu.org/software/units/"))) | |
c9dfa3c7 | 89 | |
182d6311 ML |
90 | (define-public dionysus |
91 | (package | |
92 | (name "dionysus") | |
93 | (version "1.3.0") | |
94 | (source (origin | |
95 | (method url-fetch) | |
96 | (uri (string-append "mirror://gnu/dionysus/dionysus-" version | |
97 | ".tar.gz")) | |
98 | (sha256 | |
99 | (base32 | |
100 | "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs")))) | |
101 | (build-system gnu-build-system) | |
102 | (inputs `(("tcl" ,tcl))) ;for 'tclsh' | |
103 | (synopsis "Local search for universal constants and scientific values") | |
104 | (description | |
105 | "GNU Dionysus is a convenient system for quickly retrieving the values of | |
106 | mathematical constants used in science and engineering. Values can be | |
107 | searched using a simple command-line tool, choosing from three databases: | |
108 | universal constants, atomic numbers, and constants related to | |
109 | semiconductors.") | |
110 | (license license:gpl3+) | |
111 | (home-page "http://www.gnu.org/software/dionysus/"))) | |
112 | ||
88bd1804 AE |
113 | (define-public gsl |
114 | (package | |
115 | (name "gsl") | |
487da565 | 116 | (version "1.16") |
88bd1804 AE |
117 | (source |
118 | (origin | |
119 | (method url-fetch) | |
120 | (uri (string-append "mirror://gnu/gsl/gsl-" | |
121 | version ".tar.gz")) | |
122 | (sha256 | |
123 | (base32 | |
487da565 | 124 | "0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k")))) |
88bd1804 | 125 | (build-system gnu-build-system) |
71e0f288 | 126 | (arguments |
487da565 AE |
127 | `(#:parallel-tests? #f |
128 | #:phases | |
71e0f288 AE |
129 | (alist-replace |
130 | 'configure | |
131 | (lambda* (#:key target system outputs #:allow-other-keys #:rest args) | |
132 | (let ((configure (assoc-ref %standard-phases 'configure))) | |
133 | ;; disable numerically unstable test on i686, see thread at | |
134 | ;; http://lists.gnu.org/archive/html/bug-gsl/2011-11/msg00019.html | |
135 | (if (string=? (or target system) "i686-linux") | |
136 | (substitute* "ode-initval2/Makefile.in" | |
137 | (("TESTS = \\$\\(check_PROGRAMS\\)") "TESTS ="))) | |
138 | (apply configure args))) | |
139 | %standard-phases))) | |
88bd1804 AE |
140 | (home-page "http://www.gnu.org/software/gsl/") |
141 | (synopsis "Numerical library for C and C++") | |
142 | (description | |
a22dc0c4 LC |
143 | "The GNU Scientific Library is a library for numerical analysis in C |
144 | and C++. It includes a wide range of mathematical routines, with over 1000 | |
145 | functions in total. Subject areas covered by the library include: | |
146 | differential equations, linear algebra, Fast Fourier Transforms and random | |
147 | numbers.") | |
88bd1804 AE |
148 | (license license:gpl3+))) |
149 | ||
b92eee75 AE |
150 | (define-public glpk |
151 | (package | |
152 | (name "glpk") | |
66fdf545 | 153 | (version "4.55") |
b92eee75 AE |
154 | (source |
155 | (origin | |
156 | (method url-fetch) | |
157 | (uri (string-append "mirror://gnu/glpk/glpk-" | |
158 | version ".tar.gz")) | |
159 | (sha256 | |
160 | (base32 | |
66fdf545 | 161 | "1rqx5fzj1mhkifilip5mkxybpj2wkniq5qcn8h1w2vkr2rzhs29p")))) |
b92eee75 AE |
162 | (build-system gnu-build-system) |
163 | (inputs | |
164 | `(("gmp" ,gmp))) | |
165 | (arguments | |
166 | `(#:configure-flags '("--with-gmp"))) | |
167 | (home-page "http://www.gnu.org/software/glpk/") | |
79c311b8 | 168 | (synopsis "GNU Linear Programming Kit, supporting the MathProg language") |
b92eee75 AE |
169 | (description |
170 | "GLPK is a C library for solving large-scale linear programming (LP), | |
171 | mixed integer programming (MIP), and other related problems. It supports the | |
172 | GNU MathProg modeling language, a subset of the AMPL language, and features a | |
173 | translator for the language. In addition to the C library, a stand-alone | |
174 | LP/MIP solver is included in the package.") | |
175 | (license license:gpl3+))) | |
176 | ||
c9dfa3c7 AE |
177 | (define-public pspp |
178 | (package | |
179 | (name "pspp") | |
3dcd7810 | 180 | (version "0.8.4") |
c9dfa3c7 AE |
181 | (source |
182 | (origin | |
183 | (method url-fetch) | |
184 | (uri (string-append "mirror://gnu/pspp/pspp-" | |
185 | version ".tar.gz")) | |
186 | (sha256 | |
187 | (base32 | |
3dcd7810 | 188 | "0b65q45x05ps95pph6glbg7ymdr638nfb0rk9x5x9qm5k073pk5z")))) |
c9dfa3c7 AE |
189 | (build-system gnu-build-system) |
190 | (inputs | |
f3929800 AE |
191 | `(("cairo" ,cairo) |
192 | ("fontconfig" ,fontconfig) | |
1dba6407 | 193 | ("gettext" ,gnu-gettext) |
c9dfa3c7 AE |
194 | ("gsl" ,gsl) |
195 | ("libxml2" ,libxml2) | |
f3929800 | 196 | ("pango" ,pango) |
c9dfa3c7 | 197 | ("readline" ,readline) |
e6a5ce8e JD |
198 | ("gtk" ,gtk+-2) |
199 | ("gtksourceview" ,gtksourceview) | |
c9dfa3c7 AE |
200 | ("zlib" ,zlib))) |
201 | (native-inputs | |
221ed17a EB |
202 | `(("glib" ,glib "bin") ;for glib-genmarshal |
203 | ("perl" ,perl) | |
c9dfa3c7 | 204 | ("pkg-config" ,pkg-config))) |
c9dfa3c7 AE |
205 | (home-page "http://www.gnu.org/software/pspp/") |
206 | (synopsis "Statistical analysis") | |
207 | (description | |
79c311b8 | 208 | "GNU PSPP is a statistical analysis program. It can perform |
c5779c93 LC |
209 | descriptive statistics, T-tests, linear regression and non-parametric tests. |
210 | It features both a graphical interface as well as command-line input. PSPP | |
211 | is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data | |
212 | can be imported from spreadsheets, text files and database sources and it can | |
213 | be output in text, PostScript, PDF or HTML.") | |
c9dfa3c7 | 214 | (license license:gpl3+))) |
da95c817 | 215 | |
865a69dd RW |
216 | (define-public arpack-ng |
217 | (package | |
218 | (name "arpack-ng") | |
219 | (version "3.2.0") | |
220 | (source | |
221 | (origin | |
222 | (method url-fetch) | |
223 | (uri (string-append "https://github.com/opencollab/arpack-ng/archive/" | |
224 | version ".tar.gz")) | |
225 | (sha256 | |
226 | (base32 | |
227 | "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff")))) | |
228 | (build-system gnu-build-system) | |
229 | (home-page "https://github.com/opencollab/arpack-ng") | |
230 | (inputs | |
231 | `(("lapack" ,lapack) | |
232 | ("fortran" ,gfortran-4.8))) | |
233 | (synopsis "Fortran subroutines for solving eigenvalue problems") | |
234 | (description | |
235 | "ARPACK-NG is a collection of Fortran77 subroutines designed to solve | |
236 | large scale eigenvalue problems.") | |
237 | (license (license:bsd-style "file://COPYING" | |
238 | "See COPYING in the distribution.")))) | |
239 | ||
da95c817 NK |
240 | (define-public lapack |
241 | (package | |
242 | (name "lapack") | |
566146ab | 243 | (version "3.5.0") |
da95c817 NK |
244 | (source |
245 | (origin | |
246 | (method url-fetch) | |
247 | (uri (string-append "http://www.netlib.org/lapack/lapack-" | |
248 | version ".tgz")) | |
249 | (sha256 | |
250 | (base32 | |
566146ab | 251 | "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s")))) |
da95c817 NK |
252 | (build-system cmake-build-system) |
253 | (home-page "http://www.netlib.org/lapack/") | |
57e544e8 | 254 | (native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath |
da95c817 NK |
255 | (inputs `(("fortran" ,gfortran-4.8) |
256 | ("python" ,python-2))) | |
257 | (arguments | |
06ed5982 | 258 | `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES") |
da95c817 | 259 | #:phases (alist-cons-before |
6a995754 LC |
260 | 'check 'patch-python |
261 | (lambda* (#:key inputs #:allow-other-keys) | |
262 | (let ((python (assoc-ref inputs "python"))) | |
263 | (substitute* "lapack_testing.py" | |
264 | (("/usr/bin/env python") python)))) | |
06ed5982 | 265 | %standard-phases))) |
da95c817 NK |
266 | (synopsis "Library for numerical linear algebra") |
267 | (description | |
268 | "LAPACK is a Fortran 90 library for solving the most commonly occurring | |
269 | problems in numerical linear algebra.") | |
270 | (license (license:bsd-style "file://LICENSE" | |
271 | "See LICENSE in the distribution.")))) | |
73fed4f8 JD |
272 | |
273 | (define-public gnuplot | |
274 | (package | |
275 | (name "gnuplot") | |
276 | (version "4.6.3") | |
277 | (source | |
278 | (origin | |
279 | (method url-fetch) | |
280 | (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" | |
281 | version "/gnuplot-" version ".tar.gz")) | |
282 | (sha256 | |
283 | (base32 | |
284 | "1xd7gqdhlk7k1p9yyqf9vkk811nadc7m4si0q3nb6cpv4pxglpyz")))) | |
285 | (build-system gnu-build-system) | |
286 | (inputs `(("readline" ,readline) | |
287 | ("cairo" ,cairo) | |
288 | ("pango" ,pango) | |
289 | ("gd" ,gd))) | |
290 | (native-inputs `(("texlive" ,texlive) | |
291 | ("pkg-config" ,pkg-config))) | |
292 | (home-page "http://www.gnuplot.info") | |
293 | (synopsis "Command-line driven graphing utility") | |
294 | (description "Gnuplot is a portable command-line driven graphing | |
35b9e423 | 295 | utility. It was originally created to allow scientists and students to |
73fed4f8 | 296 | visualize mathematical functions and data interactively, but has grown to |
35b9e423 | 297 | support many non-interactive uses such as web scripting. It is also used as a |
73fed4f8 JD |
298 | plotting engine by third-party applications like Octave.") |
299 | ;; X11 Style with the additional restriction that derived works may only be | |
300 | ;; distributed as patches to the original. | |
301 | (license (license:fsf-free | |
668c06ac JD |
302 | "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright")))) |
303 | ||
7ee3f1a2 JD |
304 | (define-public hdf5 |
305 | (package | |
306 | (name "hdf5") | |
307 | (version "1.8.12") | |
308 | (source | |
309 | (origin | |
310 | (method url-fetch) | |
93c3de92 AE |
311 | (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" |
312 | version "/src/hdf5-" | |
7ee3f1a2 JD |
313 | version ".tar.bz2")) |
314 | (sha256 | |
315 | (base32 "0f9n0v3p3lwc7564791a39c6cn1d3dbrn7d1j3ikqsi27a8hy23d")))) | |
316 | (build-system gnu-build-system) | |
317 | (arguments | |
318 | `(#:phases | |
d4bf49b1 EB |
319 | (alist-cons-before |
320 | 'configure 'patch-configure | |
321 | (lambda _ | |
322 | (substitute* "configure" | |
323 | (("/bin/mv") "mv"))) | |
7ee3f1a2 JD |
324 | %standard-phases))) |
325 | (outputs '("out" "bin" "lib" "include")) | |
326 | (home-page "http://www.hdfgroup.org") | |
516e93f8 | 327 | (synopsis "Management suite for extremely large and complex data") |
7ee3f1a2 JD |
328 | (description "HDF5 is a suite that makes possible the management of |
329 | extremely large and complex data collections.") | |
d4bf49b1 EB |
330 | (license (license:x11-style |
331 | "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) | |
7ee3f1a2 JD |
332 | |
333 | ||
668c06ac JD |
334 | ;; For a fully featured Octave, users are strongly recommended also to install |
335 | ;; the following packages: texinfo, less, ghostscript, gnuplot. | |
336 | (define-public octave | |
337 | (package | |
338 | (name "octave") | |
339 | (version "3.8.0") | |
340 | (source | |
341 | (origin | |
342 | (method url-fetch) | |
343 | (uri (string-append "mirror://gnu/octave/octave-" | |
344 | version ".tar.gz")) | |
345 | (sha256 | |
346 | (base32 | |
347 | "0ks9pr154syw0vb3jn6xsnrkkrbvf9y7i7gaxa28rz6ngxbxvq9l")))) | |
348 | (build-system gnu-build-system) | |
349 | (inputs | |
350 | `(("lapack" ,lapack) | |
351 | ("readline" ,readline) | |
352 | ("glpk" ,glpk) | |
353 | ("curl" ,curl) | |
354 | ("pcre" ,pcre) | |
355 | ("fltk" ,fltk) | |
356 | ("fontconfig" ,fontconfig) | |
357 | ("freetype" ,freetype) | |
7ee3f1a2 JD |
358 | ("hdf5-lib" ,hdf5 "lib") |
359 | ("hdf5-include" ,hdf5 "include") | |
668c06ac JD |
360 | ("libxft" ,libxft) |
361 | ("mesa" ,mesa) | |
362 | ("zlib" ,zlib))) | |
363 | (native-inputs | |
364 | `(("gfortran" ,gfortran-4.8) | |
365 | ("pkg-config" ,pkg-config) | |
366 | ("perl" ,perl) | |
367 | ;; The following inputs are not actually used in the build process. However, the | |
368 | ;; ./configure gratuitously tests for their existence and assumes that programs not | |
369 | ;; present at build time are also not, and can never be, available at run time! | |
370 | ;; If these inputs are therefore not present, support for them will be built out. | |
371 | ;; However, Octave will still run without them, albeit without the features they | |
372 | ;; provide. | |
373 | ("less" ,less) | |
374 | ("texinfo" ,texinfo) | |
375 | ("ghostscript" ,ghostscript) | |
376 | ("gnuplot" ,gnuplot))) | |
377 | (arguments | |
378 | `(#:configure-flags (list (string-append "--with-shell=" | |
379 | (assoc-ref %build-inputs "bash") | |
380 | "/bin/sh")))) | |
381 | (home-page "http://www.gnu.org/software/octave/") | |
382 | (synopsis "High-level language for numerical computation") | |
383 | (description "GNU Octave is a high-level interpreted language that is specialized | |
384 | for numerical computations. It can be used for both linear and non-linear | |
385 | applications and it provides great support for visualizing results. Work may | |
386 | be performed both at the interactive command-line as well as via script | |
387 | files.") | |
388 | (license license:gpl3+))) | |
3de01d3f EB |
389 | |
390 | (define-public gmsh | |
391 | (package | |
392 | (name "gmsh") | |
393 | (version "2.8.4") | |
394 | (source | |
395 | (origin | |
396 | (method url-fetch) | |
397 | (uri (string-append "http://www.geuz.org/gmsh/src/gmsh-" | |
398 | version "-source.tgz")) | |
399 | (sha256 | |
400 | (base32 "0jv2yvk28w86rx5mvjkb0w12ff2jxih7axnpvznpd295lg5jg7hr")) | |
401 | (modules '((guix build utils))) | |
402 | (snippet | |
403 | ;; Remove non-free METIS code | |
404 | '(delete-file-recursively "contrib/Metis")))) | |
405 | (build-system cmake-build-system) | |
406 | (native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath | |
407 | (propagated-inputs | |
408 | `(("fltk" ,fltk) | |
409 | ("gfortran" ,gfortran-4.8) | |
410 | ("gmp" ,gmp) | |
411 | ("hdf5-lib" ,hdf5 "lib") | |
412 | ("hdf5-include" ,hdf5 "include") | |
413 | ("lapack" ,lapack) | |
414 | ("mesa" ,mesa) | |
85f41902 | 415 | ("glu" ,glu) |
3de01d3f EB |
416 | ("libx11" ,libx11) |
417 | ("libxext" ,libxext))) | |
418 | (arguments | |
419 | `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF" | |
420 | "-DENABLE_BUILD_SHARED:BOOL=ON" | |
421 | "-DENABLE_BUILD_DYNAMIC:BOOL=ON"))) | |
422 | (home-page "http://www.geuz.org/gmsh/") | |
423 | (synopsis "3D finite element grid generator") | |
edf684ef EB |
424 | (description "Gmsh is a 3D finite element grid generator with a built-in |
425 | CAD engine and post-processor. Its design goal is to provide a fast, light | |
426 | and user-friendly meshing tool with parametric input and advanced | |
427 | visualization capabilities. Gmsh is built around four modules: geometry, | |
428 | mesh, solver and post-processing. The specification of any input to these | |
429 | modules is done either interactively using the graphical user interface or in | |
430 | ASCII text files using Gmsh's own scripting language.") | |
3de01d3f | 431 | (license license:gpl2+))) |
b9100e2f EB |
432 | |
433 | (define-public petsc | |
434 | (package | |
435 | (name "petsc") | |
436 | (version "3.4.4") | |
437 | (source | |
438 | (origin | |
439 | (method url-fetch) | |
440 | ;; The *-lite-* tarball does not contain the *large* documentation | |
441 | (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" | |
442 | "petsc-lite-" version ".tar.gz")) | |
443 | (sha256 | |
444 | (base32 "0v5dg6dhdjpi5ianvd4mm6hsvxzv1bsxwnh9f9myag0a0d9xk9iv")) | |
445 | (patches | |
446 | (list (search-patch "petsc-fix-threadcomm.patch"))))) | |
447 | (build-system gnu-build-system) | |
448 | (native-inputs | |
449 | `(("python" ,python-2) | |
450 | ("perl" ,perl))) | |
451 | (inputs | |
452 | `(("gfortran" ,gfortran-4.8) | |
453 | ("lapack" ,lapack) | |
f258212d | 454 | ("superlu" ,superlu) |
b9100e2f EB |
455 | ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi |
456 | ;; leaving out opengl, as configuration seems to only be for mac | |
457 | )) | |
458 | (arguments | |
459 | `(#:test-target "test" | |
460 | #:parallel-build? #f | |
461 | #:configure-flags | |
462 | `("--with-mpi=0" | |
f258212d EB |
463 | "--with-openmp=1" |
464 | "--with-superlu=1" | |
465 | ,(string-append "--with-superlu-include=" | |
466 | (assoc-ref %build-inputs "superlu") "/include") | |
467 | ,(string-append "--with-superlu-lib=" | |
468 | (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a")) | |
b9100e2f EB |
469 | #:phases |
470 | (alist-replace | |
471 | 'configure | |
472 | ;; PETSc's configure script is actually a python script, so we can't | |
473 | ;; run it with bash. | |
474 | (lambda* (#:key outputs (configure-flags '()) | |
475 | #:allow-other-keys) | |
476 | (let* ((prefix (assoc-ref outputs "out")) | |
477 | (flags `(,(string-append "--prefix=" prefix) | |
478 | ,@configure-flags))) | |
479 | (format #t "build directory: ~s~%" (getcwd)) | |
480 | (format #t "configure flags: ~s~%" flags) | |
481 | (zero? (apply system* "./configure" flags)))) | |
482 | (alist-cons-after | |
10b11968 EB |
483 | 'configure 'clean-local-references |
484 | ;; Try to keep build directory names from leaking into compiled code | |
b9100e2f | 485 | (lambda* (#:key inputs outputs #:allow-other-keys) |
10b11968 EB |
486 | (let ((out (assoc-ref outputs "out"))) |
487 | (substitute* (find-files "." "^petsc(conf|machineinfo).h$") | |
488 | (((getcwd)) out)))) | |
489 | (alist-cons-after | |
490 | 'install 'clean-install | |
491 | ;; Try to keep installed files from leaking build directory names. | |
492 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
493 | (let ((out (assoc-ref outputs "out")) | |
494 | (fortran (assoc-ref inputs "gfortran"))) | |
495 | (substitute* (map (lambda (file) | |
496 | (string-append out "/" file)) | |
497 | '("conf/petscvariables" | |
498 | "conf/PETScConfig.cmake")) | |
499 | (((getcwd)) out)) | |
500 | ;; Make compiler references point to the store | |
501 | (substitute* (string-append out "/conf/petscvariables") | |
502 | (("= g(cc|\\+\\+|fortran)" _ suffix) | |
503 | (string-append "= " fortran "/bin/g" suffix))) | |
504 | ;; PETSc installs some build logs, which aren't necessary. | |
505 | (for-each (lambda (file) | |
506 | (let ((f (string-append out "/" file))) | |
507 | (when (file-exists? f) | |
508 | (delete-file f)))) | |
509 | '("conf/configure.log" | |
510 | "conf/make.log" | |
511 | "conf/test.log" | |
512 | "conf/error.log" | |
513 | "conf/RDict.db" | |
514 | ;; Once installed, should uninstall with Guix | |
515 | "conf/uninstall.py")))) | |
516 | %standard-phases))))) | |
b9100e2f | 517 | (home-page "http://www.mcs.anl.gov/petsc") |
16ecf3ff | 518 | (synopsis "Library to solve PDEs") |
b9100e2f EB |
519 | (description "PETSc, pronounced PET-see (the S is silent), is a suite of |
520 | data structures and routines for the scalable (parallel) solution of | |
521 | scientific applications modeled by partial differential equations.") | |
522 | (license (license:bsd-style | |
523 | "http://www.mcs.anl.gov/petsc/documentation/copyright.html")))) | |
524 | ||
525 | (define-public petsc-complex | |
526 | (package (inherit petsc) | |
9e771e3b | 527 | (location (source-properties->location (current-source-location))) |
b9100e2f EB |
528 | (name "petsc-complex") |
529 | (arguments | |
530 | (substitute-keyword-arguments (package-arguments petsc) | |
531 | ((#:configure-flags cf) | |
532 | `(cons "--with-scalar-type=complex" ,cf)))) | |
16ecf3ff | 533 | (synopsis "Library to solve PDEs (with complex scalars)"))) |
183e44ae | 534 | |
d8c7eeb9 EB |
535 | (define-public petsc-openmpi |
536 | (package (inherit petsc) | |
537 | (name "petsc-openmpi") | |
538 | (inputs | |
539 | `(("openmpi" ,openmpi) | |
540 | ,@(package-inputs petsc))) | |
541 | (arguments | |
542 | (substitute-keyword-arguments (package-arguments petsc) | |
543 | ((#:configure-flags cf) | |
544 | ``("--with-mpiexec=mpirun" | |
545 | ,(string-append "--with-mpi-dir=" | |
546 | (assoc-ref %build-inputs "openmpi")) | |
547 | ,@(delete "--with-mpi=0" ,cf))))) | |
16ecf3ff | 548 | (synopsis "Library to solve PDEs (with MPI support)"))) |
d8c7eeb9 EB |
549 | |
550 | (define-public petsc-complex-openmpi | |
551 | (package (inherit petsc-complex) | |
552 | (name "petsc-complex-openmpi") | |
553 | (inputs | |
554 | `(("openmpi" ,openmpi) | |
555 | ,@(package-inputs petsc-complex))) | |
556 | (arguments | |
557 | (substitute-keyword-arguments (package-arguments petsc-complex) | |
558 | ((#:configure-flags cf) | |
559 | ``("--with-mpiexec=mpirun" | |
560 | ,(string-append "--with-mpi-dir=" | |
561 | (assoc-ref %build-inputs "openmpi")) | |
562 | ,@(delete "--with-mpi=0" ,cf))))) | |
16ecf3ff | 563 | (synopsis "Library to solve PDEs (with complex scalars and MPI support)"))) |
d8c7eeb9 | 564 | |
183e44ae EB |
565 | (define-public superlu |
566 | (package | |
567 | (name "superlu") | |
568 | (version "4.3") | |
569 | (source | |
570 | (origin | |
571 | (method url-fetch) | |
572 | (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" | |
573 | "superlu_" version ".tar.gz")) | |
574 | (sha256 | |
575 | (base32 "10b785s9s4x0m9q7ihap09275pq4km3k2hk76jiwdfdr5qr2168n")))) | |
576 | (build-system gnu-build-system) | |
577 | (native-inputs | |
578 | `(("tcsh" ,tcsh))) | |
579 | (inputs | |
580 | `(("lapack" ,lapack) | |
581 | ("gfortran" ,gfortran-4.8))) | |
582 | (arguments | |
583 | `(#:parallel-build? #f | |
584 | #:tests? #f ;tests are run as part of `make all` | |
585 | #:phases | |
586 | (alist-replace | |
587 | 'configure | |
588 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
589 | (call-with-output-file "make.inc" | |
590 | (lambda (port) | |
591 | (format port " | |
592 | PLAT = | |
593 | SuperLUroot = ~a | |
594 | SUPERLULIB = ~a/lib/libsuperlu.a | |
595 | TMGLIB = libtmglib.a | |
596 | BLASDEF = -DUSE_VENDOR_BLAS | |
597 | BLASLIB = -L~a/lib -lblas | |
598 | LIBS = $(SUPERLULIB) $(BLASLIB) | |
599 | ARCH = ar | |
600 | ARCHFLAGS = cr | |
601 | RANLIB = ranlib | |
602 | CC = gcc | |
603 | PIC = -fPIC | |
604 | CFLAGS = -O3 -DPRNTlevel=0 $(PIC) | |
605 | NOOPTS = -O0 $(PIC) | |
606 | FORTRAN = gfortran | |
607 | FFLAGS = -O2 $(PIC) | |
608 | LOADER = $(CC) | |
609 | CDEFS = -DAdd_" | |
610 | (getcwd) | |
611 | (assoc-ref outputs "out") | |
612 | (assoc-ref inputs "lapack"))))) | |
613 | (alist-cons-before | |
614 | 'build 'create-install-directories | |
615 | (lambda* (#:key outputs #:allow-other-keys) | |
616 | (for-each | |
617 | (lambda (dir) | |
618 | (mkdir-p (string-append (assoc-ref outputs "out") | |
619 | "/" dir))) | |
620 | '("lib" "include"))) | |
621 | (alist-replace | |
622 | 'install | |
623 | (lambda* (#:key outputs #:allow-other-keys) | |
624 | ;; Library is placed in lib during the build phase. Copy over | |
625 | ;; headers to include. | |
626 | (let* ((out (assoc-ref outputs "out")) | |
627 | (incdir (string-append out "/include"))) | |
628 | (for-each (lambda (file) | |
629 | (let ((base (basename file))) | |
630 | (format #t "installing `~a' to `~a'~%" | |
631 | base incdir) | |
632 | (copy-file file | |
633 | (string-append incdir "/" base)))) | |
634 | (find-files "SRC" ".*\\.h$")))) | |
635 | %standard-phases))))) | |
636 | (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/") | |
637 | (synopsis "Supernodal direct solver for sparse linear systems") | |
638 | (description | |
639 | "SuperLU is a general purpose library for the direct solution of large, | |
640 | sparse, nonsymmetric systems of linear equations on high performance machines. | |
641 | The library is written in C and is callable from either C or Fortran. The | |
642 | library routines perform an LU decomposition with partial pivoting and | |
643 | triangular system solves through forward and back substitution. The library | |
644 | also provides threshold-based ILU factorization preconditioners.") | |
645 | (license license:bsd-3))) | |
f8ed036a | 646 | |
a54aefea EB |
647 | (define-public superlu-dist |
648 | (package | |
649 | (name "superlu-dist") | |
650 | (version "3.3") | |
651 | (source | |
652 | (origin | |
653 | (method url-fetch) | |
654 | (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" | |
655 | "superlu_dist_" version ".tar.gz")) | |
656 | (sha256 | |
657 | (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj")) | |
658 | (patches (list (search-patch "superlu-dist-scotchmetis.patch"))))) | |
659 | (build-system gnu-build-system) | |
660 | (native-inputs | |
661 | `(("tcsh" ,tcsh))) | |
662 | (inputs | |
663 | `(("gfortran" ,gfortran-4.8))) | |
664 | (propagated-inputs | |
665 | `(("openmpi" ,openmpi) ;headers include MPI heades | |
666 | ("lapack" ,lapack) ;required to link with output library | |
667 | ("pt-scotch" ,pt-scotch))) ;same | |
668 | (arguments | |
669 | `(#:parallel-build? #f ;race conditions using ar | |
670 | #:phases | |
671 | (alist-replace | |
672 | 'configure | |
673 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
674 | (call-with-output-file "make.inc" | |
675 | (lambda (port) | |
676 | (format port " | |
677 | PLAT = | |
678 | DSuperLUroot = ~a | |
679 | DSUPERLULIB = ~a/lib/libsuperlu_dist.a | |
680 | BLASDEF = -DUSE_VENDOR_BLAS | |
681 | BLASLIB = -L~a/lib -lblas | |
682 | PARMETISLIB = -L~a/lib \ | |
683 | -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \ | |
684 | -lscotch -lscotcherr -lscotcherrexit | |
685 | METISLIB = -L~:*~a/lib \ | |
686 | -lscotchmetis -lscotch -lscotcherr -lscotcherrexit | |
687 | LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB) | |
688 | ARCH = ar | |
689 | ARCHFLAGS = cr | |
690 | RANLIB = ranlib | |
691 | CC = mpicc | |
692 | PIC = -fPIC | |
693 | CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC) | |
694 | NOOPTS = -O0 -g $(PIC) | |
695 | FORTRAN = mpifort | |
696 | FFLAGS = -O2 -g $(PIC) | |
697 | LOADER = $(CC) | |
698 | CDEFS = -DAdd_" | |
699 | (getcwd) | |
700 | (assoc-ref outputs "out") | |
701 | (assoc-ref inputs "lapack") | |
702 | (assoc-ref inputs "pt-scotch"))))) | |
703 | (alist-cons-after | |
704 | 'unpack 'remove-broken-symlinks | |
705 | (lambda _ | |
706 | (for-each delete-file | |
707 | (find-files "MAKE_INC" "\\.#make\\..*"))) | |
708 | (alist-cons-before | |
709 | 'build 'create-install-directories | |
710 | (lambda* (#:key outputs #:allow-other-keys) | |
711 | (for-each | |
712 | (lambda (dir) | |
713 | (mkdir-p (string-append (assoc-ref outputs "out") | |
714 | "/" dir))) | |
715 | '("lib" "include"))) | |
716 | (alist-replace | |
717 | 'check | |
718 | (lambda _ | |
719 | (with-directory-excursion "EXAMPLE" | |
720 | (and | |
721 | (zero? (system* "mpirun" "-n" "2" | |
722 | "./pddrive" "-r" "1" "-c" "2" "g20.rua")) | |
723 | (zero? (system* "mpirun" "-n" "2" | |
724 | "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))))) | |
725 | (alist-replace | |
726 | 'install | |
727 | (lambda* (#:key outputs #:allow-other-keys) | |
728 | ;; Library is placed in lib during the build phase. Copy over | |
729 | ;; headers to include. | |
730 | (let* ((out (assoc-ref outputs "out")) | |
731 | (incdir (string-append out "/include"))) | |
732 | (for-each (lambda (file) | |
733 | (let ((base (basename file))) | |
734 | (format #t "installing `~a' to `~a'~%" | |
735 | base incdir) | |
736 | (copy-file file | |
737 | (string-append incdir "/" base)))) | |
738 | (find-files "SRC" ".*\\.h$")))) | |
739 | %standard-phases))))))) | |
740 | (home-page (package-home-page superlu)) | |
741 | (synopsis "Parallel supernodal direct solver") | |
742 | (description | |
743 | "SuperLU_DIST is a parallel extension to the serial SuperLU library. | |
744 | It is targeted for distributed memory parallel machines. SuperLU_DIST is | |
745 | implemented in ANSI C, and MPI for communications.") | |
746 | (license license:bsd-3))) | |
747 | ||
f8ed036a EB |
748 | (define-public scotch |
749 | (package | |
750 | (name "scotch") | |
751 | (version "6.0.0") | |
752 | (source | |
753 | (origin | |
754 | (method url-fetch) | |
755 | (uri (string-append "https://gforge.inria.fr/frs/download.php/31831/" | |
756 | "scotch_" version ".tar.gz")) | |
757 | (sha256 | |
758 | (base32 "0yfqf9lk7chb3h42777x42x4adx0v3n0b41q0cdqrdmscp4iczp5")) | |
759 | (patches (list (search-patch "scotch-test-threading.patch"))))) | |
760 | (build-system gnu-build-system) | |
761 | (inputs | |
762 | `(("zlib" ,zlib) | |
763 | ("flex" ,flex) | |
764 | ("bison" ,bison))) | |
765 | (arguments | |
766 | `(#:phases | |
767 | (alist-cons-after | |
768 | 'unpack 'chdir-to-src | |
769 | (lambda _ (chdir "src")) | |
770 | (alist-replace | |
771 | 'configure | |
772 | (lambda _ | |
773 | (call-with-output-file "Makefile.inc" | |
774 | (lambda (port) | |
775 | (format port " | |
776 | EXE = | |
777 | LIB = .a | |
778 | OBJ = .o | |
779 | MAKE = make | |
780 | AR = ar | |
781 | ARFLAGS = -ruv | |
782 | CCS = gcc | |
783 | CCP = mpicc | |
784 | CCD = gcc | |
785 | CPPFLAGS =~{ -D~a~} | |
786 | CFLAGS = -O2 -g $(CPPFLAGS) | |
787 | LDFLAGS = -lz -lm -lrt -lpthread | |
788 | CP = cp | |
789 | LEX = flex -Pscotchyy -olex.yy.c | |
790 | LN = ln | |
791 | MKDIR = mkdir | |
792 | MV = mv | |
793 | RANLIB = ranlib | |
794 | YACC = bison -pscotchyy -y -b y | |
795 | " | |
796 | '("COMMON_FILE_COMPRESS_GZ" | |
797 | "COMMON_PTHREAD" | |
798 | "COMMON_RANDOM_FIXED_SEED" | |
799 | ;; TODO: Define once our MPI supports | |
800 | ;; MPI_THREAD_MULTIPLE | |
801 | ;; "SCOTCH_PTHREAD" | |
802 | ;; "SCOTCH_PTHREAD_NUMBER=2" | |
803 | "restrict=__restrict"))))) | |
804 | (alist-replace | |
805 | 'install | |
806 | (lambda* (#:key outputs #:allow-other-keys) | |
807 | (let ((out (assoc-ref outputs "out"))) | |
808 | (mkdir out) | |
809 | (zero? (system* "make" | |
810 | (string-append "prefix=" out) | |
811 | "install")))) | |
812 | %standard-phases))))) | |
813 | (home-page "http://www.labri.fr/perso/pelegrin/scotch/") | |
814 | (synopsis "Programs and libraries for graph algorithms") | |
815 | (description "SCOTCH is a set of programs and libraries which implement | |
816 | the static mapping and sparse matrix reordering algorithms developed within | |
817 | the SCOTCH project. Its purpose is to apply graph theory, with a divide and | |
818 | conquer approach, to scientific computing problems such as graph and mesh | |
819 | partitioning, static mapping, and sparse matrix ordering, in application | |
820 | domains ranging from structural mechanics to operating systems or | |
821 | bio-chemistry.") | |
822 | ;; See LICENSE_en.txt | |
823 | (license license:cecill-c))) | |
6acb4adb EB |
824 | |
825 | (define-public pt-scotch | |
826 | (package (inherit scotch) | |
827 | (name "pt-scotch") | |
828 | (propagated-inputs | |
829 | `(("openmpi" ,openmpi))) ;Headers include MPI headers | |
830 | (arguments | |
831 | (substitute-keyword-arguments (package-arguments scotch) | |
832 | ((#:phases scotch-phases) | |
833 | `(alist-replace | |
834 | 'build | |
835 | ;; TODO: Would like to add parallelism here | |
836 | (lambda _ | |
837 | (and | |
838 | (zero? (system* "make" "ptscotch")) | |
839 | ;; Install the serial metis compatibility library | |
840 | (zero? (system* "make" "-C" "libscotchmetis" "install")))) | |
841 | (alist-replace | |
842 | 'check | |
843 | (lambda _ (zero? (system* "make" "ptcheck"))) | |
844 | (alist-replace | |
845 | 'install | |
846 | (lambda* (#:key outputs #:allow-other-keys) | |
847 | (let ((out (assoc-ref outputs "out"))) | |
848 | (mkdir out) | |
849 | (zero? (system* "make" | |
850 | (string-append "prefix=" out) | |
851 | "install")))) | |
852 | ,scotch-phases)))))) | |
853 | (synopsis "Programs and libraries for graph algorithms (with MPI)"))) | |
5698b8b8 JD |
854 | |
855 | (define-public gsegrafix | |
856 | (package | |
857 | (name "gsegrafix") | |
858 | (version "1.0.6") | |
859 | (source | |
860 | (origin | |
861 | (method url-fetch) | |
862 | (uri (string-append "mirror://gnu/" name "/" name "-" | |
863 | version ".tar.gz")) | |
864 | (sha256 | |
865 | (base32 | |
866 | "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda")))) | |
867 | (build-system gnu-build-system) | |
868 | (arguments | |
869 | `(#:configure-flags '("LDFLAGS=-lm"))) | |
870 | (inputs | |
871 | `(("libgnomecanvas" ,libgnomecanvas) | |
872 | ("libbonoboui" ,libbonoboui) | |
873 | ("libgnomeui" ,libgnomeui) | |
874 | ("libgnomeprintui" ,libgnomeprintui) | |
875 | ("popt" ,popt))) | |
876 | (native-inputs | |
877 | `(("pkg-config" ,pkg-config))) | |
878 | (home-page "http://www.gnu.org/software/gsegrafix/") | |
879 | (synopsis "GNOME application to create scientific and engineering plots") | |
880 | (description "GSEGrafix is an application which produces high-quality graphical | |
881 | plots for science and engineering. Plots are specified via simple ASCII | |
882 | parameter files and data files and are presented in an anti-aliased GNOME | |
883 | canvas. The program supports rectangular two-dimensional plots, histograms, | |
884 | polar-axis plots and three-dimensional plots. Plots can be printed or saved | |
885 | to BMP, JPEG or PNG image formats.") | |
886 | (license license:gpl3+))) | |
8731e527 JD |
887 | |
888 | (define-public maxima | |
889 | (package | |
890 | (name "maxima") | |
df354a77 | 891 | (version "5.34.1") |
8731e527 JD |
892 | (source |
893 | (origin | |
894 | (method url-fetch) | |
895 | (uri (string-append "mirror://sourceforge/maxima/Maxima-source/" | |
896 | version "-source/" name "-" version ".tar.gz")) | |
897 | (sha256 | |
898 | (base32 | |
df354a77 | 899 | "1dw9vfzldpj7lv303xbw0wpyn6ra6i2yzwlrjbcx7j0jm5n43ji0")))) |
8731e527 | 900 | (build-system gnu-build-system) |
df354a77 FB |
901 | (inputs |
902 | `(("gcl" ,gcl) | |
903 | ("gnuplot" ,gnuplot) ;for plots | |
f36afe4d | 904 | ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima' |
df354a77 FB |
905 | (native-inputs |
906 | `(("texinfo" ,texinfo) | |
907 | ("perl" ,perl))) | |
8731e527 | 908 | (arguments |
df354a77 FB |
909 | `(#:configure-flags |
910 | (list "--enable-gcl" | |
911 | (string-append "--with-posix-shell=" | |
912 | (assoc-ref %build-inputs "bash") | |
913 | "/bin/sh") | |
914 | (string-append "--with-wish=" | |
915 | (assoc-ref %build-inputs "tk") | |
916 | "/bin/wish" | |
917 | (let ((v ,(package-version tk))) | |
918 | (string-take v (string-index-right v #\.))))) | |
df354a77 FB |
919 | ;; By default Maxima attempts to write temporary files to |
920 | ;; '/tmp/nix-build-maxima-5.34.1', which doesn't exist. Work around | |
921 | ;; that. | |
922 | #:make-flags (list "TMPDIR=/tmp") | |
df354a77 | 923 | #:phases (alist-cons-before |
8731e527 | 924 | 'check 'pre-check |
df354a77 | 925 | (lambda _ |
8731e527 | 926 | (chmod "src/maxima" #o555)) |
f36afe4d FB |
927 | ;; Make sure the doc and emacs files are found in the |
928 | ;; standard location. Also configure maxima to find gnuplot | |
929 | ;; without having it on the PATH. | |
930 | (alist-cons-after | |
931 | 'install 'post-install | |
932 | (lambda* (#:key outputs inputs #:allow-other-keys) | |
933 | (let* ((gnuplot (assoc-ref inputs "gnuplot")) | |
934 | (out (assoc-ref outputs "out")) | |
935 | (datadir (string-append out "/share/maxima/" ,version))) | |
936 | (with-directory-excursion out | |
937 | (mkdir-p "share/emacs") | |
938 | (mkdir-p "share/doc") | |
939 | (symlink | |
940 | (string-append datadir "/emacs/") | |
941 | (string-append out "/share/emacs/site-lisp")) | |
942 | (symlink | |
943 | (string-append datadir "/doc/") | |
944 | (string-append out "/share/doc/maxima")) | |
945 | (with-atomic-file-replacement | |
946 | (string-append datadir "/share/maxima-init.lisp") | |
947 | (lambda (in out) | |
948 | (format out "~a ~s~a~%" | |
949 | "(setf $gnuplot_command " | |
950 | (string-append gnuplot "/bin/gnuplot") ")") | |
951 | (dump-port in out)))))) | |
952 | %standard-phases)))) | |
8731e527 JD |
953 | (home-page "http://maxima.sourceforge.net") |
954 | (synopsis "Numeric and symbolic expression manipulation") | |
955 | (description "Maxima is a system for the manipulation of symbolic and | |
956 | numerical expressions. It yields high precision numeric results by using | |
957 | exact fractions, arbitrary precision integers, and variable precision floating | |
958 | point numbers") | |
959 | ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+. | |
960 | ;; Others simply say "GNU General Public License" without stating a | |
961 | ;; version (which implicitly means gpl1+). | |
962 | ;; At least one file (src/maxima.asd) says "version 2." | |
963 | ;; GPLv2 only is therefore the smallest subset. | |
f36afe4d | 964 | (license license:gpl2))) |
ec322be2 FB |
965 | |
966 | (define-public atlas | |
967 | (package | |
968 | (name "atlas") | |
969 | (version "3.10.2") | |
970 | (source (origin | |
971 | (method url-fetch) | |
972 | (uri (string-append "mirror://sourceforge/math-atlas/atlas" | |
973 | version ".tar.bz2")) | |
974 | (sha256 | |
975 | (base32 | |
976 | "0bqh4bdnjdyww4mcpg6kn0x7338mfqbdgysn97dzrwwb26di7ars")))) | |
977 | (build-system gnu-build-system) | |
978 | (home-page "http://math-atlas.sourceforge.net/") | |
979 | (inputs `(("gfortran" ,gfortran-4.8) | |
980 | ("lapack-tar" ,(package-source lapack)))) | |
981 | (outputs '("out" "doc")) | |
01480b9e FB |
982 | ;; For the moment we drop support for MIPS at it fails to compile. See |
983 | ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html | |
984 | (supported-systems (delete "mips64el-linux" %supported-systems)) | |
ec322be2 FB |
985 | (arguments |
986 | `(#:parallel-build? #f | |
987 | #:parallel-tests? #f | |
f15615b1 LC |
988 | |
989 | ;; ATLAS tunes itself for the machine it is built on, as explained at | |
990 | ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>. | |
991 | ;; For this reason, we want users to build it locally instead of using | |
992 | ;; substitutes. | |
993 | #:substitutable? #f | |
994 | ||
ec322be2 FB |
995 | #:modules ((srfi srfi-26) |
996 | (srfi srfi-1) | |
997 | (guix build gnu-build-system) | |
998 | (guix build utils)) | |
999 | #:configure-flags | |
1000 | `(;; Generate position independent code suitable for dynamic libraries | |
1001 | ;; and use WALL timer to get more accurate timing. | |
1002 | "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL" | |
1003 | ;; Set word width. | |
1004 | "-b" | |
1005 | ,,(if (string-match "64" (%current-system)) | |
1006 | "64" | |
1007 | "32") | |
1008 | ;; Disable parallel build as it gives errors: atlas_pthread.h is | |
1009 | ;; needed to compile C files before it is generated. | |
1010 | "-Ss" "pmake" "make -j 1" | |
af89a667 FB |
1011 | ;; Probe is failing for MIPS. We therefore define the system |
1012 | ;; architecture explicitly by setting (-A) MACHINETYPE = 49 | |
1013 | ;; 'MIPSR1xK' and (-V) ISA = 1 'none'. | |
1014 | ,,@(if (string-prefix? "mips" (%current-system)) | |
1015 | (list "-A" "49" "-V" "1") | |
1016 | (list)) | |
ec322be2 FB |
1017 | ;; Generate shared libraries. |
1018 | "--shared" | |
1019 | ;; Build a full LAPACK library. | |
1020 | ,(string-append "--with-netlib-lapack-tarfile=" | |
1021 | (assoc-ref %build-inputs "lapack-tar"))) | |
1022 | #:phases | |
1023 | (alist-cons-after | |
1024 | 'install 'install-doc | |
1025 | (lambda* (#:key outputs inputs #:allow-other-keys) | |
1026 | (let ((doc (string-append (assoc-ref outputs "doc") | |
1027 | "/share/doc/atlas"))) | |
1028 | (mkdir-p doc) | |
1029 | (fold (lambda (file previous) | |
1030 | (and previous (zero? (system* "cp" file doc)))) | |
1031 | #t (find-files "../ATLAS/doc" ".*")))) | |
1032 | (alist-cons-after | |
1033 | 'check 'check-pt | |
1034 | (lambda _ (zero? (system* "make" "ptcheck"))) | |
1035 | ;; Fix files required to run configure. | |
1036 | (alist-cons-before | |
1037 | 'configure 'fix-/bin/sh | |
1038 | (lambda _ | |
1039 | ;; Use `sh', not `/bin/sh'. | |
1040 | (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c") | |
1041 | (("/bin/sh") | |
1042 | "sh"))) | |
1043 | ;; Fix /bin/sh in generated make files. | |
1044 | (alist-cons-after | |
1045 | 'configure 'fix-/bin/sh-in-generated-files | |
1046 | (lambda _ | |
1047 | (substitute* (find-files "." "^[Mm]ake\\.inc.*") | |
1048 | (("/bin/sh") | |
1049 | "sh"))) | |
1050 | ;; ATLAS configure program does not accepts the default flags | |
1051 | ;; passed by the 'gnu-build-system'. | |
1052 | (alist-replace | |
1053 | 'configure | |
1054 | (lambda* (#:key native-inputs inputs outputs | |
1055 | (configure-flags '()) | |
1056 | #:allow-other-keys #:rest args) | |
1057 | (let* ((prefix (assoc-ref outputs "out")) | |
1058 | (bash (or (and=> (assoc-ref | |
1059 | (or native-inputs inputs) "bash") | |
1060 | (cut string-append <> "/bin/bash")) | |
1061 | "/bin/sh")) | |
1062 | (flags `(,(string-append "--prefix=" prefix) | |
1063 | ,@configure-flags)) | |
1064 | (abs-srcdir (getcwd)) | |
1065 | (srcdir (string-append "../" (basename abs-srcdir)))) | |
1066 | (format #t "source directory: ~s (relative from build: ~s)~%" | |
1067 | abs-srcdir srcdir) | |
1068 | (mkdir "../build") | |
1069 | (chdir "../build") | |
1070 | (format #t "build directory: ~s~%" (getcwd)) | |
1071 | (format #t "configure flags: ~s~%" flags) | |
1072 | (zero? (apply system* bash | |
1073 | (string-append srcdir "/configure") | |
1074 | flags)))) | |
1075 | %standard-phases))))))) | |
1076 | (synopsis "Automatically Tuned Linear Algebra Software") | |
1077 | (description | |
1078 | "ATLAS is an automatically tuned linear algebra software library | |
1079 | providing C and Fortran77 interfaces to a portably efficient BLAS | |
1080 | implementation, as well as a few routines from LAPACK. | |
1081 | ||
f15615b1 LC |
1082 | Optimization occurs at build time. For this reason, the library is built on |
1083 | the machine where it is installed, without resorting to pre-built substitutes. | |
ec322be2 | 1084 | |
f15615b1 LC |
1085 | Before building the library, CPU throttling should be disabled. This can be |
1086 | done in the BIOS, or, on GNU/Linux, with the following commands: | |
ec322be2 FB |
1087 | |
1088 | cpufreq-selector -g performance -c 0 | |
1089 | ... | |
1090 | cpufreq-selector -g performance -c N-1 | |
1091 | ||
1092 | where N is the number of cores of your CPU. Failure to do so will result in a | |
1093 | library with poor performance.") | |
1094 | (license license:bsd-3))) |