Commit | Line | Data |
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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> |
8f8b2451 AE |
6 | ;;; |
7 | ;;; This file is part of GNU Guix. | |
8 | ;;; | |
9 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
10 | ;;; under the terms of the GNU General Public License as published by | |
11 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
12 | ;;; your option) any later version. | |
13 | ;;; | |
14 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
15 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
16 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
17 | ;;; GNU General Public License for more details. | |
18 | ;;; | |
19 | ;;; You should have received a copy of the GNU General Public License | |
20 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
21 | ||
22 | (define-module (gnu packages maths) | |
23 | #:use-module (gnu packages) | |
24 | #:use-module ((guix licenses) | |
25 | #:renamer (symbol-prefix-proc 'license:)) | |
26 | #:use-module (guix packages) | |
27 | #:use-module (guix download) | |
0e2672ae | 28 | #:use-module (guix utils) |
da95c817 | 29 | #:use-module (guix build-system cmake) |
c9dfa3c7 | 30 | #:use-module (guix build-system gnu) |
3de01d3f EB |
31 | #:use-module (gnu packages algebra) |
32 | #:use-module (gnu packages bison) | |
33 | #:use-module (gnu packages cmake) | |
c9dfa3c7 | 34 | #:use-module (gnu packages compression) |
668c06ac | 35 | #:use-module (gnu packages curl) |
57e544e8 | 36 | #:use-module (gnu packages elf) |
3de01d3f | 37 | #:use-module (gnu packages flex) |
668c06ac | 38 | #:use-module (gnu packages fltk) |
f3929800 | 39 | #:use-module (gnu packages fontutils) |
1dba6407 | 40 | #:use-module (gnu packages gettext) |
da95c817 | 41 | #:use-module (gnu packages gcc) |
73fed4f8 | 42 | #:use-module (gnu packages gd) |
668c06ac | 43 | #:use-module (gnu packages ghostscript) |
f3929800 | 44 | #:use-module (gnu packages gtk) |
668c06ac JD |
45 | #:use-module (gnu packages less) |
46 | #:use-module (gnu packages xorg) | |
47 | #:use-module (gnu packages gl) | |
d8c7eeb9 | 48 | #:use-module (gnu packages mpi) |
b92eee75 | 49 | #:use-module (gnu packages multiprecision) |
668c06ac | 50 | #:use-module (gnu packages pcre) |
c9dfa3c7 AE |
51 | #:use-module (gnu packages perl) |
52 | #:use-module (gnu packages pkg-config) | |
da95c817 | 53 | #:use-module (gnu packages python) |
c9dfa3c7 | 54 | #:use-module (gnu packages readline) |
183e44ae | 55 | #:use-module (gnu packages tcsh) |
668c06ac | 56 | #:use-module (gnu packages texinfo) |
73fed4f8 | 57 | #:use-module (gnu packages texlive) |
c9dfa3c7 | 58 | #:use-module (gnu packages xml)) |
8f8b2451 AE |
59 | |
60 | (define-public units | |
61 | (package | |
62 | (name "units") | |
983815c8 | 63 | (version "2.11") |
8f8b2451 AE |
64 | (source (origin |
65 | (method url-fetch) | |
66 | (uri (string-append "mirror://gnu/units/units-" version | |
67 | ".tar.gz")) | |
68 | (sha256 (base32 | |
983815c8 | 69 | "1gjs3wc212aaiq4r76hx9nl1h3fa39n0ljwl9420d6ixl3rdmdjk")))) |
8f8b2451 AE |
70 | (build-system gnu-build-system) |
71 | (synopsis "Conversion between thousands of scales") | |
72 | (description | |
574e86f9 LC |
73 | "GNU Units converts numeric quantities between units of measure. It |
74 | can handle scale changes through adaptive usage of standard scale prefixes | |
75 | (micro-, kilo-, etc.). It can also handle nonlinear conversions such as | |
76 | Fahrenheit to Celsius. Its interpreter is powerful enough to be used | |
77 | effectively as a scientific calculator.") | |
8f8b2451 AE |
78 | (license license:gpl3+) |
79 | (home-page "http://www.gnu.org/software/units/"))) | |
c9dfa3c7 | 80 | |
88bd1804 AE |
81 | (define-public gsl |
82 | (package | |
83 | (name "gsl") | |
487da565 | 84 | (version "1.16") |
88bd1804 AE |
85 | (source |
86 | (origin | |
87 | (method url-fetch) | |
88 | (uri (string-append "mirror://gnu/gsl/gsl-" | |
89 | version ".tar.gz")) | |
90 | (sha256 | |
91 | (base32 | |
487da565 | 92 | "0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k")))) |
88bd1804 | 93 | (build-system gnu-build-system) |
71e0f288 | 94 | (arguments |
487da565 AE |
95 | `(#:parallel-tests? #f |
96 | #:phases | |
71e0f288 AE |
97 | (alist-replace |
98 | 'configure | |
99 | (lambda* (#:key target system outputs #:allow-other-keys #:rest args) | |
100 | (let ((configure (assoc-ref %standard-phases 'configure))) | |
101 | ;; disable numerically unstable test on i686, see thread at | |
102 | ;; http://lists.gnu.org/archive/html/bug-gsl/2011-11/msg00019.html | |
103 | (if (string=? (or target system) "i686-linux") | |
104 | (substitute* "ode-initval2/Makefile.in" | |
105 | (("TESTS = \\$\\(check_PROGRAMS\\)") "TESTS ="))) | |
106 | (apply configure args))) | |
107 | %standard-phases))) | |
88bd1804 AE |
108 | (home-page "http://www.gnu.org/software/gsl/") |
109 | (synopsis "Numerical library for C and C++") | |
110 | (description | |
a22dc0c4 LC |
111 | "The GNU Scientific Library is a library for numerical analysis in C |
112 | and C++. It includes a wide range of mathematical routines, with over 1000 | |
113 | functions in total. Subject areas covered by the library include: | |
114 | differential equations, linear algebra, Fast Fourier Transforms and random | |
115 | numbers.") | |
88bd1804 AE |
116 | (license license:gpl3+))) |
117 | ||
b92eee75 AE |
118 | (define-public glpk |
119 | (package | |
120 | (name "glpk") | |
1f1c0aff | 121 | (version "4.54") |
b92eee75 AE |
122 | (source |
123 | (origin | |
124 | (method url-fetch) | |
125 | (uri (string-append "mirror://gnu/glpk/glpk-" | |
126 | version ".tar.gz")) | |
127 | (sha256 | |
128 | (base32 | |
1f1c0aff | 129 | "18gr2anv8gyps6j9f22k7li6w07glvww666sdqblvlq2hh3whwmb")))) |
b92eee75 AE |
130 | (build-system gnu-build-system) |
131 | (inputs | |
132 | `(("gmp" ,gmp))) | |
133 | (arguments | |
134 | `(#:configure-flags '("--with-gmp"))) | |
135 | (home-page "http://www.gnu.org/software/glpk/") | |
79c311b8 | 136 | (synopsis "GNU Linear Programming Kit, supporting the MathProg language") |
b92eee75 AE |
137 | (description |
138 | "GLPK is a C library for solving large-scale linear programming (LP), | |
139 | mixed integer programming (MIP), and other related problems. It supports the | |
140 | GNU MathProg modeling language, a subset of the AMPL language, and features a | |
141 | translator for the language. In addition to the C library, a stand-alone | |
142 | LP/MIP solver is included in the package.") | |
143 | (license license:gpl3+))) | |
144 | ||
c9dfa3c7 AE |
145 | (define-public pspp |
146 | (package | |
147 | (name "pspp") | |
7e0c23fb | 148 | (version "0.8.3") |
c9dfa3c7 AE |
149 | (source |
150 | (origin | |
151 | (method url-fetch) | |
152 | (uri (string-append "mirror://gnu/pspp/pspp-" | |
153 | version ".tar.gz")) | |
154 | (sha256 | |
155 | (base32 | |
7e0c23fb | 156 | "0vri2pzvmm38qaihfvwlry30f40lcnps4blg59ixic4q20ldxf5d")))) |
c9dfa3c7 AE |
157 | (build-system gnu-build-system) |
158 | (inputs | |
f3929800 AE |
159 | `(("cairo" ,cairo) |
160 | ("fontconfig" ,fontconfig) | |
1dba6407 | 161 | ("gettext" ,gnu-gettext) |
c9dfa3c7 AE |
162 | ("gsl" ,gsl) |
163 | ("libxml2" ,libxml2) | |
f3929800 | 164 | ("pango" ,pango) |
c9dfa3c7 | 165 | ("readline" ,readline) |
e6a5ce8e JD |
166 | ("gtk" ,gtk+-2) |
167 | ("gtksourceview" ,gtksourceview) | |
c9dfa3c7 AE |
168 | ("zlib" ,zlib))) |
169 | (native-inputs | |
170 | `(("perl" ,perl) | |
171 | ("pkg-config" ,pkg-config))) | |
c9dfa3c7 AE |
172 | (home-page "http://www.gnu.org/software/pspp/") |
173 | (synopsis "Statistical analysis") | |
174 | (description | |
79c311b8 LC |
175 | "GNU PSPP is a statistical analysis program. It can perform |
176 | descriptive statistics, T-tests, linear regression and non-parametric tests. | |
177 | It features both a graphical interface as well as command-line input. PSPP is | |
178 | designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data can | |
179 | be imported from spreadsheets, text files and database sources and it can be | |
180 | output in text, PostScript, PDF or HTML.") | |
c9dfa3c7 | 181 | (license license:gpl3+))) |
da95c817 NK |
182 | |
183 | (define-public lapack | |
184 | (package | |
185 | (name "lapack") | |
566146ab | 186 | (version "3.5.0") |
da95c817 NK |
187 | (source |
188 | (origin | |
189 | (method url-fetch) | |
190 | (uri (string-append "http://www.netlib.org/lapack/lapack-" | |
191 | version ".tgz")) | |
192 | (sha256 | |
193 | (base32 | |
566146ab | 194 | "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s")))) |
da95c817 NK |
195 | (build-system cmake-build-system) |
196 | (home-page "http://www.netlib.org/lapack/") | |
57e544e8 | 197 | (native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath |
da95c817 NK |
198 | (inputs `(("fortran" ,gfortran-4.8) |
199 | ("python" ,python-2))) | |
200 | (arguments | |
06ed5982 | 201 | `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES") |
da95c817 | 202 | #:phases (alist-cons-before |
6a995754 LC |
203 | 'check 'patch-python |
204 | (lambda* (#:key inputs #:allow-other-keys) | |
205 | (let ((python (assoc-ref inputs "python"))) | |
206 | (substitute* "lapack_testing.py" | |
207 | (("/usr/bin/env python") python)))) | |
06ed5982 | 208 | %standard-phases))) |
da95c817 NK |
209 | (synopsis "Library for numerical linear algebra") |
210 | (description | |
211 | "LAPACK is a Fortran 90 library for solving the most commonly occurring | |
212 | problems in numerical linear algebra.") | |
213 | (license (license:bsd-style "file://LICENSE" | |
214 | "See LICENSE in the distribution.")))) | |
73fed4f8 JD |
215 | |
216 | (define-public gnuplot | |
217 | (package | |
218 | (name "gnuplot") | |
219 | (version "4.6.3") | |
220 | (source | |
221 | (origin | |
222 | (method url-fetch) | |
223 | (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" | |
224 | version "/gnuplot-" version ".tar.gz")) | |
225 | (sha256 | |
226 | (base32 | |
227 | "1xd7gqdhlk7k1p9yyqf9vkk811nadc7m4si0q3nb6cpv4pxglpyz")))) | |
228 | (build-system gnu-build-system) | |
229 | (inputs `(("readline" ,readline) | |
230 | ("cairo" ,cairo) | |
231 | ("pango" ,pango) | |
232 | ("gd" ,gd))) | |
233 | (native-inputs `(("texlive" ,texlive) | |
234 | ("pkg-config" ,pkg-config))) | |
235 | (home-page "http://www.gnuplot.info") | |
236 | (synopsis "Command-line driven graphing utility") | |
237 | (description "Gnuplot is a portable command-line driven graphing | |
238 | utility. It was originally created to allow scientists and students to | |
239 | visualize mathematical functions and data interactively, but has grown to | |
240 | support many non-interactive uses such as web scripting. It is also used as a | |
241 | plotting engine by third-party applications like Octave.") | |
242 | ;; X11 Style with the additional restriction that derived works may only be | |
243 | ;; distributed as patches to the original. | |
244 | (license (license:fsf-free | |
668c06ac JD |
245 | "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright")))) |
246 | ||
7ee3f1a2 JD |
247 | (define-public hdf5 |
248 | (package | |
249 | (name "hdf5") | |
250 | (version "1.8.12") | |
251 | (source | |
252 | (origin | |
253 | (method url-fetch) | |
254 | (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-" | |
255 | version ".tar.bz2")) | |
256 | (sha256 | |
257 | (base32 "0f9n0v3p3lwc7564791a39c6cn1d3dbrn7d1j3ikqsi27a8hy23d")))) | |
258 | (build-system gnu-build-system) | |
259 | (arguments | |
260 | `(#:phases | |
d4bf49b1 EB |
261 | (alist-cons-before |
262 | 'configure 'patch-configure | |
263 | (lambda _ | |
264 | (substitute* "configure" | |
265 | (("/bin/mv") "mv"))) | |
7ee3f1a2 JD |
266 | %standard-phases))) |
267 | (outputs '("out" "bin" "lib" "include")) | |
268 | (home-page "http://www.hdfgroup.org") | |
269 | (synopsis "Management suite for extremely large and complex data") | |
270 | (description "HDF5 is a suite that makes possible the management of | |
271 | extremely large and complex data collections.") | |
d4bf49b1 EB |
272 | (license (license:x11-style |
273 | "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) | |
7ee3f1a2 JD |
274 | |
275 | ||
668c06ac JD |
276 | ;; For a fully featured Octave, users are strongly recommended also to install |
277 | ;; the following packages: texinfo, less, ghostscript, gnuplot. | |
278 | (define-public octave | |
279 | (package | |
280 | (name "octave") | |
281 | (version "3.8.0") | |
282 | (source | |
283 | (origin | |
284 | (method url-fetch) | |
285 | (uri (string-append "mirror://gnu/octave/octave-" | |
286 | version ".tar.gz")) | |
287 | (sha256 | |
288 | (base32 | |
289 | "0ks9pr154syw0vb3jn6xsnrkkrbvf9y7i7gaxa28rz6ngxbxvq9l")))) | |
290 | (build-system gnu-build-system) | |
291 | (inputs | |
292 | `(("lapack" ,lapack) | |
293 | ("readline" ,readline) | |
294 | ("glpk" ,glpk) | |
295 | ("curl" ,curl) | |
296 | ("pcre" ,pcre) | |
297 | ("fltk" ,fltk) | |
298 | ("fontconfig" ,fontconfig) | |
299 | ("freetype" ,freetype) | |
7ee3f1a2 JD |
300 | ("hdf5-lib" ,hdf5 "lib") |
301 | ("hdf5-include" ,hdf5 "include") | |
668c06ac JD |
302 | ("libxft" ,libxft) |
303 | ("mesa" ,mesa) | |
304 | ("zlib" ,zlib))) | |
305 | (native-inputs | |
306 | `(("gfortran" ,gfortran-4.8) | |
307 | ("pkg-config" ,pkg-config) | |
308 | ("perl" ,perl) | |
309 | ;; The following inputs are not actually used in the build process. However, the | |
310 | ;; ./configure gratuitously tests for their existence and assumes that programs not | |
311 | ;; present at build time are also not, and can never be, available at run time! | |
312 | ;; If these inputs are therefore not present, support for them will be built out. | |
313 | ;; However, Octave will still run without them, albeit without the features they | |
314 | ;; provide. | |
315 | ("less" ,less) | |
316 | ("texinfo" ,texinfo) | |
317 | ("ghostscript" ,ghostscript) | |
318 | ("gnuplot" ,gnuplot))) | |
319 | (arguments | |
320 | `(#:configure-flags (list (string-append "--with-shell=" | |
321 | (assoc-ref %build-inputs "bash") | |
322 | "/bin/sh")))) | |
323 | (home-page "http://www.gnu.org/software/octave/") | |
324 | (synopsis "High-level language for numerical computation") | |
325 | (description "GNU Octave is a high-level interpreted language that is specialized | |
326 | for numerical computations. It can be used for both linear and non-linear | |
327 | applications and it provides great support for visualizing results. Work may | |
328 | be performed both at the interactive command-line as well as via script | |
329 | files.") | |
330 | (license license:gpl3+))) | |
3de01d3f EB |
331 | |
332 | (define-public gmsh | |
333 | (package | |
334 | (name "gmsh") | |
335 | (version "2.8.4") | |
336 | (source | |
337 | (origin | |
338 | (method url-fetch) | |
339 | (uri (string-append "http://www.geuz.org/gmsh/src/gmsh-" | |
340 | version "-source.tgz")) | |
341 | (sha256 | |
342 | (base32 "0jv2yvk28w86rx5mvjkb0w12ff2jxih7axnpvznpd295lg5jg7hr")) | |
343 | (modules '((guix build utils))) | |
344 | (snippet | |
345 | ;; Remove non-free METIS code | |
346 | '(delete-file-recursively "contrib/Metis")))) | |
347 | (build-system cmake-build-system) | |
348 | (native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath | |
349 | (propagated-inputs | |
350 | `(("fltk" ,fltk) | |
351 | ("gfortran" ,gfortran-4.8) | |
352 | ("gmp" ,gmp) | |
353 | ("hdf5-lib" ,hdf5 "lib") | |
354 | ("hdf5-include" ,hdf5 "include") | |
355 | ("lapack" ,lapack) | |
356 | ("mesa" ,mesa) | |
357 | ("libx11" ,libx11) | |
358 | ("libxext" ,libxext))) | |
359 | (arguments | |
360 | `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF" | |
361 | "-DENABLE_BUILD_SHARED:BOOL=ON" | |
362 | "-DENABLE_BUILD_DYNAMIC:BOOL=ON"))) | |
363 | (home-page "http://www.geuz.org/gmsh/") | |
364 | (synopsis "3D finite element grid generator") | |
edf684ef EB |
365 | (description "Gmsh is a 3D finite element grid generator with a built-in |
366 | CAD engine and post-processor. Its design goal is to provide a fast, light | |
367 | and user-friendly meshing tool with parametric input and advanced | |
368 | visualization capabilities. Gmsh is built around four modules: geometry, | |
369 | mesh, solver and post-processing. The specification of any input to these | |
370 | modules is done either interactively using the graphical user interface or in | |
371 | ASCII text files using Gmsh's own scripting language.") | |
3de01d3f | 372 | (license license:gpl2+))) |
b9100e2f EB |
373 | |
374 | (define-public petsc | |
375 | (package | |
376 | (name "petsc") | |
377 | (version "3.4.4") | |
378 | (source | |
379 | (origin | |
380 | (method url-fetch) | |
381 | ;; The *-lite-* tarball does not contain the *large* documentation | |
382 | (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" | |
383 | "petsc-lite-" version ".tar.gz")) | |
384 | (sha256 | |
385 | (base32 "0v5dg6dhdjpi5ianvd4mm6hsvxzv1bsxwnh9f9myag0a0d9xk9iv")) | |
386 | (patches | |
387 | (list (search-patch "petsc-fix-threadcomm.patch"))))) | |
388 | (build-system gnu-build-system) | |
389 | (native-inputs | |
390 | `(("python" ,python-2) | |
391 | ("perl" ,perl))) | |
392 | (inputs | |
393 | `(("gfortran" ,gfortran-4.8) | |
394 | ("lapack" ,lapack) | |
f258212d | 395 | ("superlu" ,superlu) |
b9100e2f EB |
396 | ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi |
397 | ;; leaving out opengl, as configuration seems to only be for mac | |
398 | )) | |
399 | (arguments | |
400 | `(#:test-target "test" | |
401 | #:parallel-build? #f | |
402 | #:configure-flags | |
403 | `("--with-mpi=0" | |
f258212d EB |
404 | "--with-openmp=1" |
405 | "--with-superlu=1" | |
406 | ,(string-append "--with-superlu-include=" | |
407 | (assoc-ref %build-inputs "superlu") "/include") | |
408 | ,(string-append "--with-superlu-lib=" | |
409 | (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a")) | |
b9100e2f EB |
410 | #:phases |
411 | (alist-replace | |
412 | 'configure | |
413 | ;; PETSc's configure script is actually a python script, so we can't | |
414 | ;; run it with bash. | |
415 | (lambda* (#:key outputs (configure-flags '()) | |
416 | #:allow-other-keys) | |
417 | (let* ((prefix (assoc-ref outputs "out")) | |
418 | (flags `(,(string-append "--prefix=" prefix) | |
419 | ,@configure-flags))) | |
420 | (format #t "build directory: ~s~%" (getcwd)) | |
421 | (format #t "configure flags: ~s~%" flags) | |
422 | (zero? (apply system* "./configure" flags)))) | |
423 | (alist-cons-after | |
10b11968 EB |
424 | 'configure 'clean-local-references |
425 | ;; Try to keep build directory names from leaking into compiled code | |
b9100e2f | 426 | (lambda* (#:key inputs outputs #:allow-other-keys) |
10b11968 EB |
427 | (let ((out (assoc-ref outputs "out"))) |
428 | (substitute* (find-files "." "^petsc(conf|machineinfo).h$") | |
429 | (((getcwd)) out)))) | |
430 | (alist-cons-after | |
431 | 'install 'clean-install | |
432 | ;; Try to keep installed files from leaking build directory names. | |
433 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
434 | (let ((out (assoc-ref outputs "out")) | |
435 | (fortran (assoc-ref inputs "gfortran"))) | |
436 | (substitute* (map (lambda (file) | |
437 | (string-append out "/" file)) | |
438 | '("conf/petscvariables" | |
439 | "conf/PETScConfig.cmake")) | |
440 | (((getcwd)) out)) | |
441 | ;; Make compiler references point to the store | |
442 | (substitute* (string-append out "/conf/petscvariables") | |
443 | (("= g(cc|\\+\\+|fortran)" _ suffix) | |
444 | (string-append "= " fortran "/bin/g" suffix))) | |
445 | ;; PETSc installs some build logs, which aren't necessary. | |
446 | (for-each (lambda (file) | |
447 | (let ((f (string-append out "/" file))) | |
448 | (when (file-exists? f) | |
449 | (delete-file f)))) | |
450 | '("conf/configure.log" | |
451 | "conf/make.log" | |
452 | "conf/test.log" | |
453 | "conf/error.log" | |
454 | "conf/RDict.db" | |
455 | ;; Once installed, should uninstall with Guix | |
456 | "conf/uninstall.py")))) | |
457 | %standard-phases))))) | |
b9100e2f | 458 | (home-page "http://www.mcs.anl.gov/petsc") |
16ecf3ff | 459 | (synopsis "Library to solve PDEs") |
b9100e2f EB |
460 | (description "PETSc, pronounced PET-see (the S is silent), is a suite of |
461 | data structures and routines for the scalable (parallel) solution of | |
462 | scientific applications modeled by partial differential equations.") | |
463 | (license (license:bsd-style | |
464 | "http://www.mcs.anl.gov/petsc/documentation/copyright.html")))) | |
465 | ||
466 | (define-public petsc-complex | |
467 | (package (inherit petsc) | |
468 | (name "petsc-complex") | |
469 | (arguments | |
470 | (substitute-keyword-arguments (package-arguments petsc) | |
471 | ((#:configure-flags cf) | |
472 | `(cons "--with-scalar-type=complex" ,cf)))) | |
16ecf3ff | 473 | (synopsis "Library to solve PDEs (with complex scalars)"))) |
183e44ae | 474 | |
d8c7eeb9 EB |
475 | (define-public petsc-openmpi |
476 | (package (inherit petsc) | |
477 | (name "petsc-openmpi") | |
478 | (inputs | |
479 | `(("openmpi" ,openmpi) | |
480 | ,@(package-inputs petsc))) | |
481 | (arguments | |
482 | (substitute-keyword-arguments (package-arguments petsc) | |
483 | ((#:configure-flags cf) | |
484 | ``("--with-mpiexec=mpirun" | |
485 | ,(string-append "--with-mpi-dir=" | |
486 | (assoc-ref %build-inputs "openmpi")) | |
487 | ,@(delete "--with-mpi=0" ,cf))))) | |
16ecf3ff | 488 | (synopsis "Library to solve PDEs (with MPI support)"))) |
d8c7eeb9 EB |
489 | |
490 | (define-public petsc-complex-openmpi | |
491 | (package (inherit petsc-complex) | |
492 | (name "petsc-complex-openmpi") | |
493 | (inputs | |
494 | `(("openmpi" ,openmpi) | |
495 | ,@(package-inputs petsc-complex))) | |
496 | (arguments | |
497 | (substitute-keyword-arguments (package-arguments petsc-complex) | |
498 | ((#:configure-flags cf) | |
499 | ``("--with-mpiexec=mpirun" | |
500 | ,(string-append "--with-mpi-dir=" | |
501 | (assoc-ref %build-inputs "openmpi")) | |
502 | ,@(delete "--with-mpi=0" ,cf))))) | |
16ecf3ff | 503 | (synopsis "Library to solve PDEs (with complex scalars and MPI support)"))) |
d8c7eeb9 | 504 | |
183e44ae EB |
505 | (define-public superlu |
506 | (package | |
507 | (name "superlu") | |
508 | (version "4.3") | |
509 | (source | |
510 | (origin | |
511 | (method url-fetch) | |
512 | (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" | |
513 | "superlu_" version ".tar.gz")) | |
514 | (sha256 | |
515 | (base32 "10b785s9s4x0m9q7ihap09275pq4km3k2hk76jiwdfdr5qr2168n")))) | |
516 | (build-system gnu-build-system) | |
517 | (native-inputs | |
518 | `(("tcsh" ,tcsh))) | |
519 | (inputs | |
520 | `(("lapack" ,lapack) | |
521 | ("gfortran" ,gfortran-4.8))) | |
522 | (arguments | |
523 | `(#:parallel-build? #f | |
524 | #:tests? #f ;tests are run as part of `make all` | |
525 | #:phases | |
526 | (alist-replace | |
527 | 'configure | |
528 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
529 | (call-with-output-file "make.inc" | |
530 | (lambda (port) | |
531 | (format port " | |
532 | PLAT = | |
533 | SuperLUroot = ~a | |
534 | SUPERLULIB = ~a/lib/libsuperlu.a | |
535 | TMGLIB = libtmglib.a | |
536 | BLASDEF = -DUSE_VENDOR_BLAS | |
537 | BLASLIB = -L~a/lib -lblas | |
538 | LIBS = $(SUPERLULIB) $(BLASLIB) | |
539 | ARCH = ar | |
540 | ARCHFLAGS = cr | |
541 | RANLIB = ranlib | |
542 | CC = gcc | |
543 | PIC = -fPIC | |
544 | CFLAGS = -O3 -DPRNTlevel=0 $(PIC) | |
545 | NOOPTS = -O0 $(PIC) | |
546 | FORTRAN = gfortran | |
547 | FFLAGS = -O2 $(PIC) | |
548 | LOADER = $(CC) | |
549 | CDEFS = -DAdd_" | |
550 | (getcwd) | |
551 | (assoc-ref outputs "out") | |
552 | (assoc-ref inputs "lapack"))))) | |
553 | (alist-cons-before | |
554 | 'build 'create-install-directories | |
555 | (lambda* (#:key outputs #:allow-other-keys) | |
556 | (for-each | |
557 | (lambda (dir) | |
558 | (mkdir-p (string-append (assoc-ref outputs "out") | |
559 | "/" dir))) | |
560 | '("lib" "include"))) | |
561 | (alist-replace | |
562 | 'install | |
563 | (lambda* (#:key outputs #:allow-other-keys) | |
564 | ;; Library is placed in lib during the build phase. Copy over | |
565 | ;; headers to include. | |
566 | (let* ((out (assoc-ref outputs "out")) | |
567 | (incdir (string-append out "/include"))) | |
568 | (for-each (lambda (file) | |
569 | (let ((base (basename file))) | |
570 | (format #t "installing `~a' to `~a'~%" | |
571 | base incdir) | |
572 | (copy-file file | |
573 | (string-append incdir "/" base)))) | |
574 | (find-files "SRC" ".*\\.h$")))) | |
575 | %standard-phases))))) | |
576 | (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/") | |
577 | (synopsis "Supernodal direct solver for sparse linear systems") | |
578 | (description | |
579 | "SuperLU is a general purpose library for the direct solution of large, | |
580 | sparse, nonsymmetric systems of linear equations on high performance machines. | |
581 | The library is written in C and is callable from either C or Fortran. The | |
582 | library routines perform an LU decomposition with partial pivoting and | |
583 | triangular system solves through forward and back substitution. The library | |
584 | also provides threshold-based ILU factorization preconditioners.") | |
585 | (license license:bsd-3))) | |
f8ed036a | 586 | |
a54aefea EB |
587 | (define-public superlu-dist |
588 | (package | |
589 | (name "superlu-dist") | |
590 | (version "3.3") | |
591 | (source | |
592 | (origin | |
593 | (method url-fetch) | |
594 | (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" | |
595 | "superlu_dist_" version ".tar.gz")) | |
596 | (sha256 | |
597 | (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj")) | |
598 | (patches (list (search-patch "superlu-dist-scotchmetis.patch"))))) | |
599 | (build-system gnu-build-system) | |
600 | (native-inputs | |
601 | `(("tcsh" ,tcsh))) | |
602 | (inputs | |
603 | `(("gfortran" ,gfortran-4.8))) | |
604 | (propagated-inputs | |
605 | `(("openmpi" ,openmpi) ;headers include MPI heades | |
606 | ("lapack" ,lapack) ;required to link with output library | |
607 | ("pt-scotch" ,pt-scotch))) ;same | |
608 | (arguments | |
609 | `(#:parallel-build? #f ;race conditions using ar | |
610 | #:phases | |
611 | (alist-replace | |
612 | 'configure | |
613 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
614 | (call-with-output-file "make.inc" | |
615 | (lambda (port) | |
616 | (format port " | |
617 | PLAT = | |
618 | DSuperLUroot = ~a | |
619 | DSUPERLULIB = ~a/lib/libsuperlu_dist.a | |
620 | BLASDEF = -DUSE_VENDOR_BLAS | |
621 | BLASLIB = -L~a/lib -lblas | |
622 | PARMETISLIB = -L~a/lib \ | |
623 | -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \ | |
624 | -lscotch -lscotcherr -lscotcherrexit | |
625 | METISLIB = -L~:*~a/lib \ | |
626 | -lscotchmetis -lscotch -lscotcherr -lscotcherrexit | |
627 | LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB) | |
628 | ARCH = ar | |
629 | ARCHFLAGS = cr | |
630 | RANLIB = ranlib | |
631 | CC = mpicc | |
632 | PIC = -fPIC | |
633 | CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC) | |
634 | NOOPTS = -O0 -g $(PIC) | |
635 | FORTRAN = mpifort | |
636 | FFLAGS = -O2 -g $(PIC) | |
637 | LOADER = $(CC) | |
638 | CDEFS = -DAdd_" | |
639 | (getcwd) | |
640 | (assoc-ref outputs "out") | |
641 | (assoc-ref inputs "lapack") | |
642 | (assoc-ref inputs "pt-scotch"))))) | |
643 | (alist-cons-after | |
644 | 'unpack 'remove-broken-symlinks | |
645 | (lambda _ | |
646 | (for-each delete-file | |
647 | (find-files "MAKE_INC" "\\.#make\\..*"))) | |
648 | (alist-cons-before | |
649 | 'build 'create-install-directories | |
650 | (lambda* (#:key outputs #:allow-other-keys) | |
651 | (for-each | |
652 | (lambda (dir) | |
653 | (mkdir-p (string-append (assoc-ref outputs "out") | |
654 | "/" dir))) | |
655 | '("lib" "include"))) | |
656 | (alist-replace | |
657 | 'check | |
658 | (lambda _ | |
659 | (with-directory-excursion "EXAMPLE" | |
660 | (and | |
661 | (zero? (system* "mpirun" "-n" "2" | |
662 | "./pddrive" "-r" "1" "-c" "2" "g20.rua")) | |
663 | (zero? (system* "mpirun" "-n" "2" | |
664 | "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))))) | |
665 | (alist-replace | |
666 | 'install | |
667 | (lambda* (#:key outputs #:allow-other-keys) | |
668 | ;; Library is placed in lib during the build phase. Copy over | |
669 | ;; headers to include. | |
670 | (let* ((out (assoc-ref outputs "out")) | |
671 | (incdir (string-append out "/include"))) | |
672 | (for-each (lambda (file) | |
673 | (let ((base (basename file))) | |
674 | (format #t "installing `~a' to `~a'~%" | |
675 | base incdir) | |
676 | (copy-file file | |
677 | (string-append incdir "/" base)))) | |
678 | (find-files "SRC" ".*\\.h$")))) | |
679 | %standard-phases))))))) | |
680 | (home-page (package-home-page superlu)) | |
681 | (synopsis "Parallel supernodal direct solver") | |
682 | (description | |
683 | "SuperLU_DIST is a parallel extension to the serial SuperLU library. | |
684 | It is targeted for distributed memory parallel machines. SuperLU_DIST is | |
685 | implemented in ANSI C, and MPI for communications.") | |
686 | (license license:bsd-3))) | |
687 | ||
f8ed036a EB |
688 | (define-public scotch |
689 | (package | |
690 | (name "scotch") | |
691 | (version "6.0.0") | |
692 | (source | |
693 | (origin | |
694 | (method url-fetch) | |
695 | (uri (string-append "https://gforge.inria.fr/frs/download.php/31831/" | |
696 | "scotch_" version ".tar.gz")) | |
697 | (sha256 | |
698 | (base32 "0yfqf9lk7chb3h42777x42x4adx0v3n0b41q0cdqrdmscp4iczp5")) | |
699 | (patches (list (search-patch "scotch-test-threading.patch"))))) | |
700 | (build-system gnu-build-system) | |
701 | (inputs | |
702 | `(("zlib" ,zlib) | |
703 | ("flex" ,flex) | |
704 | ("bison" ,bison))) | |
705 | (arguments | |
706 | `(#:phases | |
707 | (alist-cons-after | |
708 | 'unpack 'chdir-to-src | |
709 | (lambda _ (chdir "src")) | |
710 | (alist-replace | |
711 | 'configure | |
712 | (lambda _ | |
713 | (call-with-output-file "Makefile.inc" | |
714 | (lambda (port) | |
715 | (format port " | |
716 | EXE = | |
717 | LIB = .a | |
718 | OBJ = .o | |
719 | MAKE = make | |
720 | AR = ar | |
721 | ARFLAGS = -ruv | |
722 | CCS = gcc | |
723 | CCP = mpicc | |
724 | CCD = gcc | |
725 | CPPFLAGS =~{ -D~a~} | |
726 | CFLAGS = -O2 -g $(CPPFLAGS) | |
727 | LDFLAGS = -lz -lm -lrt -lpthread | |
728 | CP = cp | |
729 | LEX = flex -Pscotchyy -olex.yy.c | |
730 | LN = ln | |
731 | MKDIR = mkdir | |
732 | MV = mv | |
733 | RANLIB = ranlib | |
734 | YACC = bison -pscotchyy -y -b y | |
735 | " | |
736 | '("COMMON_FILE_COMPRESS_GZ" | |
737 | "COMMON_PTHREAD" | |
738 | "COMMON_RANDOM_FIXED_SEED" | |
739 | ;; TODO: Define once our MPI supports | |
740 | ;; MPI_THREAD_MULTIPLE | |
741 | ;; "SCOTCH_PTHREAD" | |
742 | ;; "SCOTCH_PTHREAD_NUMBER=2" | |
743 | "restrict=__restrict"))))) | |
744 | (alist-replace | |
745 | 'install | |
746 | (lambda* (#:key outputs #:allow-other-keys) | |
747 | (let ((out (assoc-ref outputs "out"))) | |
748 | (mkdir out) | |
749 | (zero? (system* "make" | |
750 | (string-append "prefix=" out) | |
751 | "install")))) | |
752 | %standard-phases))))) | |
753 | (home-page "http://www.labri.fr/perso/pelegrin/scotch/") | |
754 | (synopsis "Programs and libraries for graph algorithms") | |
755 | (description "SCOTCH is a set of programs and libraries which implement | |
756 | the static mapping and sparse matrix reordering algorithms developed within | |
757 | the SCOTCH project. Its purpose is to apply graph theory, with a divide and | |
758 | conquer approach, to scientific computing problems such as graph and mesh | |
759 | partitioning, static mapping, and sparse matrix ordering, in application | |
760 | domains ranging from structural mechanics to operating systems or | |
761 | bio-chemistry.") | |
762 | ;; See LICENSE_en.txt | |
763 | (license license:cecill-c))) | |
6acb4adb EB |
764 | |
765 | (define-public pt-scotch | |
766 | (package (inherit scotch) | |
767 | (name "pt-scotch") | |
768 | (propagated-inputs | |
769 | `(("openmpi" ,openmpi))) ;Headers include MPI headers | |
770 | (arguments | |
771 | (substitute-keyword-arguments (package-arguments scotch) | |
772 | ((#:phases scotch-phases) | |
773 | `(alist-replace | |
774 | 'build | |
775 | ;; TODO: Would like to add parallelism here | |
776 | (lambda _ | |
777 | (and | |
778 | (zero? (system* "make" "ptscotch")) | |
779 | ;; Install the serial metis compatibility library | |
780 | (zero? (system* "make" "-C" "libscotchmetis" "install")))) | |
781 | (alist-replace | |
782 | 'check | |
783 | (lambda _ (zero? (system* "make" "ptcheck"))) | |
784 | (alist-replace | |
785 | 'install | |
786 | (lambda* (#:key outputs #:allow-other-keys) | |
787 | (let ((out (assoc-ref outputs "out"))) | |
788 | (mkdir out) | |
789 | (zero? (system* "make" | |
790 | (string-append "prefix=" out) | |
791 | "install")))) | |
792 | ,scotch-phases)))))) | |
793 | (synopsis "Programs and libraries for graph algorithms (with MPI)"))) |