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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>
0f43f835 17;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be>
8f8b2451
AE		 18;;;
19;;; This file is part of GNU Guix.
20;;;
21;;; GNU Guix is free software; you can redistribute it and/or modify it
22;;; under the terms of the GNU General Public License as published by
23;;; the Free Software Foundation; either version 3 of the License, or (at
24;;; your option) any later version.
25;;;
26;;; GNU Guix is distributed in the hope that it will be useful, but
27;;; WITHOUT ANY WARRANTY; without even the implied warranty of
28;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
29;;; GNU General Public License for more details.
30;;;
31;;; You should have received a copy of the GNU General Public License
32;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
33
34(define-module (gnu packages maths)
ec322be2 35 #:use-module (ice-9 regex)
8f8b2451 36 #:use-module (gnu packages)
b5b73a82 37 #:use-module ((guix licenses) #:prefix license:)
8f8b2451
AE		 38 #:use-module (guix packages)
39 #:use-module (guix download)
0e2672ae 40 #:use-module (guix utils)
cec86422 41 #:use-module (guix build utils)
da95c817 42 #:use-module (guix build-system cmake)
c9dfa3c7 43 #:use-module (guix build-system gnu)
ec8c7e47 44 #:use-module (guix build-system r)
3de01d3f
EB		 45 #:use-module (gnu packages algebra)
46 #:use-module (gnu packages bison)
a17d4564 47 #:use-module (gnu packages boost)
e73b49fb 48 #:use-module (gnu packages check)
3de01d3f 49 #:use-module (gnu packages cmake)
c9dfa3c7 50 #:use-module (gnu packages compression)
668c06ac 51 #:use-module (gnu packages curl)
b7b27a8f 52 #:use-module (gnu packages cyrus-sasl)
528bb464 53 #:use-module (gnu packages documentation)
57e544e8 54 #:use-module (gnu packages elf)
3de01d3f 55 #:use-module (gnu packages flex)
668c06ac 56 #:use-module (gnu packages fltk)
f3929800 57 #:use-module (gnu packages fontutils)
1dba6407 58 #:use-module (gnu packages gettext)
da95c817 59 #:use-module (gnu packages gcc)
73fed4f8 60 #:use-module (gnu packages gd)
668c06ac 61 #:use-module (gnu packages ghostscript)
889187a4 62 #:use-module (gnu packages graphviz)
f3929800 63 #:use-module (gnu packages gtk)
45147b0c 64 #:use-module (gnu packages image)
668c06ac 65 #:use-module (gnu packages less)
8731e527 66 #:use-module (gnu packages lisp)
bc3a2e35 67 #:use-module (gnu packages logging)
5698b8b8 68 #:use-module (gnu packages gnome)
1b39a196 69 #:use-module (gnu packages guile)
668c06ac
JD		 70 #:use-module (gnu packages xorg)
71 #:use-module (gnu packages gl)
8731e527 72 #:use-module (gnu packages m4)
d8c7eeb9 73 #:use-module (gnu packages mpi)
b92eee75 74 #:use-module (gnu packages multiprecision)
528bb464 75 #:use-module (gnu packages netpbm)
668c06ac 76 #:use-module (gnu packages pcre)
5698b8b8 77 #:use-module (gnu packages popt)
c9dfa3c7
AE		 78 #:use-module (gnu packages perl)
79 #:use-module (gnu packages pkg-config)
da95c817 80 #:use-module (gnu packages python)
c9dfa3c7 81 #:use-module (gnu packages readline)
2742f87e 82 #:use-module (gnu packages tbb)
b7194849 83 #:use-module (gnu packages shells)
df354a77 84 #:use-module (gnu packages tcl)
668c06ac 85 #:use-module (gnu packages texinfo)
8f9ac901 86 #:use-module (gnu packages tex)
b7b27a8f 87 #:use-module (gnu packages tls)
9aafbc0c 88 #:use-module (gnu packages wxwidgets)
c12efc72 89 #:use-module (gnu packages xml)
a17d4564
EB		 90 #:use-module (gnu packages zip)
91 #:use-module (srfi srfi-1))
8f8b2451 92
9c45c519
JD		 93(define-public c-graph
94 (package
95 (name "c-graph")
96 (version "2.0")
97 (source (origin
98 (method url-fetch)
99 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
100 ".tar.gz"))
101 (sha256 (base32
102 "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
103 (build-system gnu-build-system)
104 (inputs
105 `(("fortran" ,gfortran)))
a3947cb1 106 (synopsis "Visualizing and demonstrating convolution")
9c45c519 107 (description
a3947cb1
LC		 108 "GNU C-Graph is a tool for demonstrating the theory of convolution.
109Thus, it can serve as an excellent aid to students of signal and systems
110theory in visualizing the convolution process. Rather than forcing the
111student to write code, the program offers an intuitive interface with
112interactive dialogs to guide them.")
9c45c519
JD		 113 (license license:gpl3+)
114 (home-page "http://www.gnu.org/software/c-graph/")))
115
d91025e3
TD		 116(define-public coda
117 (package
118 (name "coda")
119 (version "2.17.3")
120 (source
121 (origin
122 (method url-fetch)
123 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
124 version "/coda-" version ".tar.gz"))
125 (sha256
4b12fe5c
TD		 126 (base32 "04b9l3wzcix0mnfq77mwnil6cbr8h2mki8myvy0lzn236qcwaq1h"))
127 (patches (search-patches "coda-use-system-libs.patch"))
128 (modules '((guix build utils)))
129 (snippet
130 ;; Make sure we don't use the bundled software.
131 '(for-each (lambda (d)
132 (delete-file-recursively (string-append "libcoda/" d)))
133 '("zlib" "pcre" "expat")))))
d91025e3
TD		 134 (native-inputs
135 `(("fortran" ,gfortran)
136 ("python" ,python)
137 ("python-numpy" ,python-numpy)))
138 (inputs
139 `(("zlib" ,zlib)
4b12fe5c
TD		 140 ("pcre" ,pcre)
141 ("expat" ,expat)
d91025e3
TD		 142 ("hdf4" ,hdf4-alt)
143 ("hdf5" ,hdf5)))
144 (build-system gnu-build-system)
145 (arguments
4b12fe5c
TD		 146 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
147 "LIBS= -lz -lpcre -lexpat")))
d91025e3
TD		 148 (synopsis "A common interface to various earth observation data formats")
149 (description
150 "The Common Data Access toolbox (CODA) provides a set of interfaces for
151reading remote sensing data from earth observation data files. It consists of
152command line applications and interfaces to the C, Fortran, Python, and Java
153programming languages.")
154 (home-page "https://stcorp.nl/coda")
155 (license license:gpl2+)))
156
8f8b2451
AE		 157(define-public units
158 (package
159 (name "units")
5e745292 160 (version "2.13")
8f8b2451
AE		 161 (source (origin
162 (method url-fetch)
163 (uri (string-append "mirror://gnu/units/units-" version
164 ".tar.gz"))
165 (sha256 (base32
5e745292 166 "1awhjw9zjlfb8s5g3yyx63f7ddfcr1sanlbxpqifmrgq24ql198b"))))
8f8b2451
AE		 167 (build-system gnu-build-system)
168 (synopsis "Conversion between thousands of scales")
169 (description
574e86f9 170 "GNU Units converts numeric quantities between units of measure. It
7c125ce0
AK		 171can handle scale changes through adaptive usage of standard scale
172prefixes (micro-, kilo-, etc.). It can also handle nonlinear
173conversions such as Fahrenheit to Celsius. Its interpreter is powerful
174enough to be used effectively as a scientific calculator.")
8f8b2451
AE		 175 (license license:gpl3+)
176 (home-page "http://www.gnu.org/software/units/")))
c9dfa3c7 177
61a529b4
RW		 178(define-public double-conversion
179 (package
180 (name "double-conversion")
181 (version "1.1.5")
182 (source (origin
183 (method url-fetch)
184 (uri (string-append
185 "https://github.com/floitsch/double-conversion/archive/v"
186 version ".tar.gz"))
187 (file-name (string-append name "-" version ".tar.gz"))
188 (sha256
189 (base32
190 "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83"))))
191 (build-system cmake-build-system)
192 (arguments
193 '(#:test-target "test"
194 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
195 "-DBUILD_TESTING=ON")))
196 (home-page "https://github.com/floitsch/double-conversion")
197 (synopsis "Conversion routines for IEEE doubles")
198 (description
199 "The double-conversion library provides binary-decimal and decimal-binary
200routines for IEEE doubles. The library consists of efficient conversion
201routines that have been extracted from the V8 JavaScript engine.")
202 (license license:bsd-3)))
203
182d6311
ML		 204(define-public dionysus
205 (package
206 (name "dionysus")
207 (version "1.3.0")
208 (source (origin
209 (method url-fetch)
210 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
211 ".tar.gz"))
212 (sha256
213 (base32
214 "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs"))))
215 (build-system gnu-build-system)
216 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
217 (synopsis "Local search for universal constants and scientific values")
218 (description
219 "GNU Dionysus is a convenient system for quickly retrieving the values of
220mathematical constants used in science and engineering. Values can be
221searched using a simple command-line tool, choosing from three databases:
222universal constants, atomic numbers, and constants related to
223semiconductors.")
224 (license license:gpl3+)
225 (home-page "http://www.gnu.org/software/dionysus/")))
226
88bd1804
AE		 227(define-public gsl
228 (package
229 (name "gsl")
8c82e1c9 230 (version "2.2.1")
ab2cc5cd
LC		 231 (source (origin
232 (method url-fetch)
233 (uri (string-append "mirror://gnu/gsl/gsl-"
234 version ".tar.gz"))
235 (sha256
236 (base32
237 "095hp01d8lkqdvv0p1k25kvbisgfdmvx1rzpyc2i8kl2n33kvlhk"))
238 (patches (search-patches "gsl-test-i686.patch"))))
88bd1804 239 (build-system gnu-build-system)
71e0f288 240 (arguments
5adbe65f 241 `(#:parallel-tests? #f))
88bd1804
AE		 242 (home-page "http://www.gnu.org/software/gsl/")
243 (synopsis "Numerical library for C and C++")
244 (description
a22dc0c4
LC		 245 "The GNU Scientific Library is a library for numerical analysis in C
246and C++. It includes a wide range of mathematical routines, with over 1000
247functions in total. Subject areas covered by the library include:
248differential equations, linear algebra, Fast Fourier Transforms and random
249numbers.")
88bd1804
AE		 250 (license license:gpl3+)))
251
b92eee75
AE		 252(define-public glpk
253 (package
254 (name "glpk")
f0443377 255 (version "4.60")
b92eee75
AE		 256 (source
257 (origin
258 (method url-fetch)
259 (uri (string-append "mirror://gnu/glpk/glpk-"
260 version ".tar.gz"))
261 (sha256
262 (base32
f0443377 263 "15z2ymzqhxwss6wgdj5f7vkyqlqdsjgrvm0x871kmlx0n0664mhk"))))
b92eee75
AE		 264 (build-system gnu-build-system)
265 (inputs
266 `(("gmp" ,gmp)))
267 (arguments
268 `(#:configure-flags '("--with-gmp")))
269 (home-page "http://www.gnu.org/software/glpk/")
79c311b8 270 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
b92eee75
AE		 271 (description
272 "GLPK is a C library for solving large-scale linear programming (LP),
273mixed integer programming (MIP), and other related problems. It supports the
274GNU MathProg modeling language, a subset of the AMPL language, and features a
275translator for the language. In addition to the C library, a stand-alone
276LP/MIP solver is included in the package.")
277 (license license:gpl3+)))
278
b146763a
AE		 279(define-public 4ti2
280 (package
281 (name "4ti2")
282 (version "1.6.7")
283 (source
284 (origin
285 (method url-fetch)
286 (uri (string-append "http://www.4ti2.de/version_" version
287 "/4ti2-" version ".tar.gz"))
288 (sha256
289 (base32
290 "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
291 (build-system gnu-build-system)
292 (native-inputs
293 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
294 (inputs
295 `(("glpk" ,glpk)
296 ("gmp" ,gmp)))
297 (home-page "http://www.4ti2.de/")
298 (synopsis "Mathematical tool suite for problems on linear spaces")
299 (description
300 "4ti2 implements algorithms for solving algebraic, geometric and
301combinatorial problems on linear spaces. Among others, it solves systems
302of linear equations, computes extreme rays of polyhedral cones, solves
303integer programming problems and computes Markov bases for statistics.")
304 (license license:gpl2+)))
305
53696f10
AE		 306(define-public cddlib
307 (package
308 (name "cddlib")
309 (version "0.94h")
310 (source
311 (origin
312 (method url-fetch)
313 (uri (string-append "ftp://ftp.ifor.math.ethz.ch/pub/fukuda/cdd/cddlib-"
314 (string-delete #\. version) ".tar.gz"))
315 (sha256
316 (base32
317 "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy"))))
318 (build-system gnu-build-system)
319 (inputs
320 `(("gmp" ,gmp)))
321 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
322 (synopsis "Library for convex hulls and extreme rays of polyhedra")
323 (description
324 "The C-library cddlib implements the Double Description Method of
325Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
326rays of a general convex polyhedron given by a system of linear inequalities
327in arbitrary dimension. It can also be used for the converse operation of
328computing convex hulls.")
329 (license license:gpl2+)))
330
865a69dd
RW		 331(define-public arpack-ng
332 (package
333 (name "arpack-ng")
334 (version "3.2.0")
335 (source
336 (origin
337 (method url-fetch)
338 (uri (string-append "https://github.com/opencollab/arpack-ng/archive/"
339 version ".tar.gz"))
f586c877 340 (file-name (string-append name "-" version ".tar.gz"))
865a69dd
RW		 341 (sha256
342 (base32
343 "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff"))))
344 (build-system gnu-build-system)
345 (home-page "https://github.com/opencollab/arpack-ng")
346 (inputs
347 `(("lapack" ,lapack)
19afbea1 348 ("fortran" ,gfortran)))
865a69dd
RW		 349 (synopsis "Fortran subroutines for solving eigenvalue problems")
350 (description
351 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
352large scale eigenvalue problems.")
166191b3 353 (license (license:non-copyleft "file://COPYING"
865a69dd
RW		 354 "See COPYING in the distribution."))))
355
8c94c886
EB		 356(define-public arpack-ng-openmpi
357 (package (inherit arpack-ng)
358 (name "arpack-ng-openmpi")
359 (inputs
360 `(("mpi" ,openmpi)
361 ,@(package-inputs arpack-ng)))
362 (arguments `(#:configure-flags '("--enable-mpi")))
363 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
364
da95c817
NK		 365(define-public lapack
366 (package
367 (name "lapack")
566146ab 368 (version "3.5.0")
da95c817
NK		 369 (source
370 (origin
371 (method url-fetch)
372 (uri (string-append "http://www.netlib.org/lapack/lapack-"
373 version ".tgz"))
374 (sha256
375 (base32
566146ab 376 "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s"))))
da95c817
NK		 377 (build-system cmake-build-system)
378 (home-page "http://www.netlib.org/lapack/")
19afbea1 379 (inputs `(("fortran" ,gfortran)
da95c817
NK		 380 ("python" ,python-2)))
381 (arguments
7b569b01
RW		 382 `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
383 "-DLAPACKE=ON")
da95c817 384 #:phases (alist-cons-before
6a995754
LC		 385 'check 'patch-python
386 (lambda* (#:key inputs #:allow-other-keys)
387 (let ((python (assoc-ref inputs "python")))
388 (substitute* "lapack_testing.py"
389 (("/usr/bin/env python") python))))
06ed5982 390 %standard-phases)))
da95c817
NK		 391 (synopsis "Library for numerical linear algebra")
392 (description
393 "LAPACK is a Fortran 90 library for solving the most commonly occurring
394problems in numerical linear algebra.")
166191b3 395 (license (license:non-copyleft "file://LICENSE"
da95c817 396 "See LICENSE in the distribution."))))
73fed4f8 397
e1ff597a
EB		 398(define-public scalapack
399 (package
400 (name "scalapack")
401 (version "2.0.2")
402 (source
403 (origin
404 (method url-fetch)
405 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
406 version ".tgz"))
407 (sha256
408 (base32
409 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
410 (build-system cmake-build-system)
411 (inputs
412 `(("mpi" ,openmpi)
413 ("fortran" ,gfortran)
414 ("lapack" ,lapack))) ;for testing only
415 (arguments
416 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")))
417 (home-page "http://www.netlib.org/scalapack/")
418 (synopsis "Library for scalable numerical linear algebra")
419 (description
420 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
421routines on parallel distributed memory machines. ScaLAPACK solves dense and
422banded linear systems, least squares problems, eigenvalue problems, and
423singular value problems.")
424 (license (license:bsd-style "file://LICENSE"
425 "See LICENSE in the distribution."))))
426
73fed4f8 427(define-public gnuplot
430e67a4
EF		 428 ;; Gnuplot version 5.0.4 was updated in-place, resulting in a hash mismatch.
429 ;; This can be removed at the next version update.
430 (let ((upstream-version "5.0.4")
431 (guix-revision "1"))
432 (package
433 (name "gnuplot")
434 (version (string-append upstream-version "-" guix-revision))
435 (source
436 (origin
437 (method url-fetch)
438 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
439 upstream-version "/gnuplot-"
440 upstream-version ".tar.gz"))
441 (sha256
442 (base32
443 "07n3w12dkcxjnhsvsliaqnkhajhi818v6q8mkpmpbplbf92vh70m"))))
444 (build-system gnu-build-system)
445 (inputs `(("readline" ,readline)
446 ("cairo" ,cairo)
447 ("pango" ,pango)
448 ("gd" ,gd)))
449 (native-inputs `(("pkg-config" ,pkg-config)
450 ("texlive" ,texlive-minimal)))
451 (home-page "http://www.gnuplot.info")
452 (synopsis "Command-line driven graphing utility")
453 (description "Gnuplot is a portable command-line driven graphing
35b9e423 454utility. It was originally created to allow scientists and students to
73fed4f8 455visualize mathematical functions and data interactively, but has grown to
35b9e423 456support many non-interactive uses such as web scripting. It is also used as a
73fed4f8 457plotting engine by third-party applications like Octave.")
430e67a4
EF		 458 ;; X11 Style with the additional restriction that derived works may only be
459 ;; distributed as patches to the original.
460 (license (license:fsf-free
461 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright")))))
668c06ac 462
32f70e1f
TD		 463(define-public gctp
464 (package
465 (name "gctp")
466 (version "2.0.0")
467 (source
468 (origin
469 (method url-fetch)
470 (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
471 version ".tar.gz"))
472 (file-name (string-append name "-" version ".tar.gz"))
473 (sha256
474 (base32
475 "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
476 (native-inputs
477 `(("fortran" ,gfortran)))
478 (build-system gnu-build-system)
479 (synopsis "General Cartographic Transformation Package (GCTP)")
480 (description
481 "The General Cartographic Transformation Package (GCTP) is a system of
482software routines designed to permit the transformation of coordinate pairs
483from one map projection to another. The GCTP is the standard computer
484software used by the National Mapping Division for map projection
485computations.")
486 (home-page "https://github.com/OkoSanto/GCTP")
0f7cd95b 487 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
32f70e1f 488
becbbefc
TD		 489(define-public hdf4
490 (package
491 (name "hdf4")
492 (version "4.2.11")
493 (source
494 (origin
495 (method url-fetch)
496 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
497 version "/src/hdf-" version ".tar.bz2"))
498 (sha256
499 (base32 "16yr50j845zlfx20skmw3y75ww77akk9gg0affjqkg66ih5r03mv"))
15ca49b2
AE		 500 (patches (search-patches "hdf4-architectures.patch"
501 "hdf4-reproducibility.patch"
becbbefc
TD		 502 "hdf4-shared-fortran.patch"))))
503
504 (build-system gnu-build-system)
505 (native-inputs
506 `(("gfortran" ,gfortran)
507 ("bison" ,bison)
508 ("flex" ,flex)))
509 (inputs
510 `(("zlib" ,zlib)
511 ("libjpeg" ,libjpeg)))
512 (arguments
513 `(#:parallel-tests? #f
514 #:configure-flags '("--enable-shared")
515 #:phases
516 (modify-phases %standard-phases
517 (add-before 'configure 'patchbuild
518 (lambda _
519 (substitute*
520 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
521 (("/bin/rm") "rm")
522 (("/bin/mkdir") "mkdir"))
523 (substitute* (find-files "." "^Makefile\\.in$")
524 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
525-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
526 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
527-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
528-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")))))))
529 (home-page "https://www.hdfgroup.org/products/hdf4/")
530 (synopsis
531 "Library and multi-object file format for storing and managing data")
532 (description "HDF4 is a library and multi-object file format for storing
533and managing data between machines. HDF4 is an older hierarchical data format,
534incompatible with HDF5.")
535 (license
536 (license:non-copyleft
537 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
538
539(define-public hdf4-alt
540 (package
541 (inherit hdf4)
542 (name "hdf4-alt")
543 (arguments
544 (substitute-keyword-arguments (package-arguments hdf4)
545 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
546 (synopsis
547 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
548
7ee3f1a2
JD		 549(define-public hdf5
550 (package
551 (name "hdf5")
04b7a7cd 552 (version "1.8.17")
7ee3f1a2
JD		 553 (source
554 (origin
555 (method url-fetch)
93c3de92
AE		 556 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-"
557 version "/src/hdf5-"
7ee3f1a2
JD		 558 version ".tar.bz2"))
559 (sha256
b8d9c93b
EB		 560 (base32 "0sj8x0gfs5fb28gipnynb9wpkz113h8wq9sva9mxx66kv27xsdgw"))
561 (patches (list (search-patch "hdf5-config-date.patch")))))
7ee3f1a2 562 (build-system gnu-build-system)
12ed1216
AE		 563 (inputs
564 `(("zlib" ,zlib)))
7ee3f1a2
JD		 565 (arguments
566 `(#:phases
f622e212
EB		 567 (modify-phases %standard-phases
568 (add-before 'configure 'patch-configure
569 (lambda _
570 (substitute* "configure"
b8d9c93b
EB		 571 (("/bin/mv") "mv"))
572 #t))
f622e212
EB		 573 (add-after 'install 'patch-references
574 (lambda* (#:key inputs outputs #:allow-other-keys)
575 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
576 (zlib (assoc-ref inputs "zlib")))
577 (substitute* (find-files bin "h5p?cc")
578 (("-lz" lib)
579 (string-append "-L" zlib "/lib " lib)))
580 #t))))))
7ee3f1a2 581 (home-page "http://www.hdfgroup.org")
516e93f8 582 (synopsis "Management suite for extremely large and complex data")
7ee3f1a2
JD		 583 (description "HDF5 is a suite that makes possible the management of
584extremely large and complex data collections.")
d4bf49b1
EB		 585 (license (license:x11-style
586 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
7ee3f1a2 587
d3c4f3bb
TD		 588(define-public hdf-eos2
589 (package
590 (name "hdf-eos2")
591 (version "19.1.0")
592 (source
593 (origin
594 (method url-fetch)
595 (uri "ftp://edhs1.gsfc.nasa.gov\
596/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
597 (sha256
598 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
599 (patches (search-patches "hdf-eos2-remove-gctp.patch"
600 "hdf-eos2-build-shared.patch"
601 "hdf-eos2-fortrantests.patch"))))
602 (build-system gnu-build-system)
603 (native-inputs
604 `(("gfortran" ,gfortran)))
605 (inputs
606 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
607 ("zlib" ,zlib)
608 ("libjpeg" ,libjpeg)
609 ("gctp" ,gctp)))
610 (arguments
611 `( #:configure-flags '("--enable-install-include" "--enable-shared"
612 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
613 #:parallel-tests? #f))
614 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
615 (synopsis "HDF4-based data format for NASA's Earth Observing System")
616 (description "HDF-EOS2 is a software library built on HDF4 which supports
617the construction of data structures used in NASA's Earth Observing
618System (Grid, Point and Swath).")
619
620 ;; Source files carry a permissive license header.
621 (license (license:non-copyleft home-page))))
622
0f43f835
TD		 623(define-public hdf-eos5
624 (package
625 (name "hdf-eos5")
626 (version "1.15")
627 (source (origin
628 (method url-fetch)
629 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
630/edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
631 (sha256
632 (base32
633 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
634 (patches (search-patches "hdf-eos5-build-shared.patch"
635 "hdf-eos5-remove-gctp.patch"
636 "hdf-eos5-fix-szip.patch"
637 "hdf-eos5-fortrantests.patch"))))
638 (native-inputs
639 `(("gfortran" ,gfortran)))
640 (build-system gnu-build-system)
641 (inputs
642 `(("hdf5" ,hdf5)
643 ("zlib" ,zlib)
644 ("gctp" ,gctp)))
645 (arguments
646 `(#:configure-flags '("--enable-install-include" "--enable-shared"
647 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
648 #:parallel-tests? #f))
649 (synopsis "HDF5-based data format for NASA's Earth Observing System")
650 (description
651 "HDF-EOS5 is a software library built on HDF5 to support the construction
652of data structures used in NASA's Earth Observing System (Grid, Point and
653Swath).")
654 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
655
656 ;; Source files carry a permissive license header.
657 (license (license:non-copyleft home-page))))
658
c8378eea
EB		 659(define-public hdf5-parallel-openmpi
660 (package (inherit hdf5)
661 (name "hdf5-parallel-openmpi")
662 (inputs
663 `(("mpi" ,openmpi)
664 ,@(package-inputs hdf5)))
665 (arguments
666 (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
667 ,@(package-arguments hdf5))
668 ((#:phases phases)
669 `(modify-phases ,phases
670 (add-before 'check 'patch-tests
671 (lambda _
672 ;; OpenMPI's mpirun will exit with non-zero status if it
673 ;; detects an "abnormal termination", i.e. any process not
674 ;; calling MPI_Finalize(). Since the test is explicitely
675 ;; avoiding MPI_Finalize so as not to have at_exit and thus
676 ;; H5C_flush_cache from being called, mpirun will always
677 ;; complain, so turn this test off.
678 (substitute* "testpar/Makefile"
679 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
680 (string-append front back "\n")))
681 (substitute* "tools/h5diff/testph5diff.sh"
682 (("/bin/sh") (which "sh")))
683 #t))))))
684 (synopsis "Management suite for data with parallel IO support")))
685
00775104
EB		 686(define-public h5check
687 (package
688 (name "h5check")
689 (version "2.0.1")
690 (source
691 (origin
692 (method url-fetch)
693 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
694 "h5check/src/h5check-" version ".tar.gz"))
695 (sha256
696 (base32
697 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
698 (build-system gnu-build-system)
699 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
700 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
701 (synopsis "HDF5 format checker")
702 (description "@code{h5check} is a validation tool for verifying that an
703HDF5 file is encoded according to the HDF File Format Specification.")
704 (license (license:x11-style "file://COPYING"))))
705
889187a4
EB		 706(define-public netcdf
707 (package
708 (name "netcdf")
709 (version "4.4.0")
710 (source
711 (origin
712 (method url-fetch)
713 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
714 "netcdf-" version ".tar.gz"))
715 (sha256
716 (base32
717 "0y6gdcplarwqqnrav2xg1xd6ih732rzzbmdw78v3rl5b8mwcnh0d"))
718 (patches (list (search-patch "netcdf-config-date.patch")))))
719 (build-system gnu-build-system)
720 (native-inputs
721 `(("m4" ,m4)
722 ("doxygen" ,doxygen)
723 ("graphviz" ,graphviz)))
724 (inputs
725 `(("hdf5" ,hdf5)
726 ("zlib" ,zlib)))
727 (arguments
728 `(#:configure-flags '("--enable-doxygen" "--enable-dot")
729 #:parallel-tests? #f)) ;various race conditions
730 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
731 (synopsis "Library for scientific data")
732 (description "NetCDF is an interface for scientific data access and a
733software library that provides an implementation of the interface. The netCDF
734library defines a machine-independent format for representing scientific data.
735Together, the interface, library, and format support the creation, access, and
736sharing of scientific data.")
737 (license (license:x11-style "file://COPYRIGHT"))))
738
739(define-public netcdf-parallel-openmpi
740 (package (inherit netcdf)
741 (name "netcdf-parallel-openmpi")
742 (inputs
743 `(("mpi" ,openmpi)
744 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
745 (package-inputs netcdf))))
746 ;; TODO: Replace pkg-config references in nc-config with absolute references
747 (arguments
748 (substitute-keyword-arguments (package-arguments netcdf)
749 ((#:configure-flags flags)
750 `(cons* "CC=mpicc" "CXX=mpicxx"
751 "--enable-parallel-tests"
752 ;; Shared libraries not supported with parallel IO.
753 "--disable-shared" "--with-pic"
754 ,flags))))))
755
1b39a196
RJ		 756(define-public nlopt
757 (package
758 (name "nlopt")
759 (version "2.4.2")
760 (source (origin
761 (method url-fetch)
762 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
763 version ".tar.gz"))
764 (sha256
765 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
766 (build-system gnu-build-system)
767 (arguments
768 `(;; Shared libraries are not built by default. They are required to
769 ;; build the Guile, Octave, and Python bindings.
770 #:configure-flags '("--enable-shared")
771
772 #:phases
773 (modify-phases %standard-phases
774 (add-before 'configure 'set-libnlopt-file-name
775 (lambda* (#:key outputs #:allow-other-keys)
776 ;; Make sure the Scheme module refers to the library by its
777 ;; absolute file name (we cannot do that from a snippet
778 ;; because the expansion of @libdir@ contains
779 ;; ${exec_prefix}.)
780 (let ((out (assoc-ref outputs "out")))
781 (substitute* "swig/nlopt.scm.in"
782 (("libnlopt")
783 (string-append out "/lib/libnlopt")))
784 #t))))))
785 (inputs `(("guile" ,guile-2.0)))
786 (native-inputs `(("pkg-config" ,pkg-config)))
787 (home-page "http://ab-initio.mit.edu/wiki/")
788 (synopsis "Library for nonlinear optimization")
789 (description "NLopt is a library for nonlinear optimization, providing a
790common interface for a number of different free optimization routines available
791online as well as original implementations of various other algorithms.")
792 (license license:lgpl2.1+)))
793
005c787d
LC		 794(define-public ipopt
795 (package
796 (name "ipopt")
797 (version "3.12.5")
798 (source (origin
799 (method url-fetch)
800 (uri (string-append
801 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
802 version".tgz"))
803 (sha256
804 (base32
805 "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
806 (modules '((guix build utils)))
807 (snippet
808 ;; Make sure we don't use the bundled software.
809 '(delete-file-recursively "ThirdParty"))))
810 (build-system gnu-build-system)
ad1c4537
LC		 811 (arguments
812 '(#:phases (modify-phases %standard-phases
813 (add-after 'install 'add--L-flags-in-ipopt.pc
814 (lambda* (#:key inputs outputs #:allow-other-keys)
815 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
816 ;; move it to "Libs.private" where it belongs, and add a
817 ;; '-L' flag for LAPACK.
818 (let ((out (assoc-ref outputs "out"))
819 (lapack (assoc-ref inputs "lapack")))
820 (substitute* (string-append out "/lib/pkgconfig/"
821 "ipopt.pc")
822 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
823 (string-append "Libs: " before " " after "\n"
824 "Libs.private: " before
825 "-L" lapack "/lib -llapack -lblas "
826 after "\n")))
827 #t))))))
005c787d
LC		 828 (native-inputs
829 `(("gfortran" ,gfortran)))
830 (inputs
831 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
ad1c4537 832 `(("lapack" ,lapack))) ;for both libblas and liblapack
005c787d
LC		 833 (home-page "http://www.coin-or.org")
834 (synopsis "Large-scale nonlinear optimizer")
835 (description
836 "The Interior Point Optimizer (IPOPT) is a software package for
837large-scale nonlinear optimization. It provides C++, C, and Fortran
838interfaces.")
839 (license license:epl1.0)))
840
f9940ef1
LC		 841(define-public ceres
842 (package
843 (name "ceres-solver")
844 (version "1.11.0")
845 (home-page "http://ceres-solver.org/")
846 (source (origin
847 (method url-fetch)
848 (uri (string-append home-page "ceres-solver-"
849 version ".tar.gz"))
850 (sha256
851 (base32
852 "0i7qkbf8g6pd8arxzldppga26ckv93y8zldsfz6wbd4n6b1nqrjd"))))
853 (build-system cmake-build-system)
854 (arguments
855 ;; TODO: Build HTML user documentation and install separately.
bc3a2e35 856 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
f9940ef1
LC		 857 "-DBUILD_SHARED_LIBS=ON")
858
859 #:phases (modify-phases %standard-phases
860 (add-before 'configure 'set-library-directory
861 (lambda _
862 ;; Install libraries to lib/, not lib64/.
863 (substitute* "internal/ceres/CMakeLists.txt"
864 (("set\\(LIB_SUFFIX \"64\"\\)")
865 "set(LIB_SUFFIX \"\")"))
866 #t)))))
867 (native-inputs
868 `(("pkg-config" ,pkg-config)))
468e0b18
LC		 869 (propagated-inputs
870 `(("glog" ,glog))) ;for #include <glog/glog.h>
f9940ef1
LC		 871 (inputs
872 `(("eigen" ,eigen)
873 ("blas" ,openblas)
874 ("lapack" ,lapack)
875 ("suitesparse" ,suitesparse)
876 ("gflags" ,gflags)))
877 (synopsis "C++ library for solving large optimization problems")
878 (description
879 "Ceres Solver is a C++ library for modeling and solving large,
880complicated optimization problems. It is a feature rich, mature and
881performant library which has been used in production since 2010. Ceres Solver
882can solve two kinds of problems:
883@enumerate
884@item non-linear least squares problems with bounds constraints;
885@item general unconstrained optimization problems.
886@end enumerate\n")
887 (license license:bsd-3)))
888
668c06ac
JD		 889;; For a fully featured Octave, users are strongly recommended also to install
890;; the following packages: texinfo, less, ghostscript, gnuplot.
891(define-public octave
892 (package
893 (name "octave")
aa127019 894 (version "4.0.3")
668c06ac
JD		 895 (source
896 (origin
897 (method url-fetch)
898 (uri (string-append "mirror://gnu/octave/octave-"
aa127019 899 version ".tar.xz"))
668c06ac
JD		 900 (sha256
901 (base32
aa127019 902 "11day29k4yfvxh4101x5yf26ld992x5n6qvmhjjk6mzsd26fqayw"))))
668c06ac
JD		 903 (build-system gnu-build-system)
904 (inputs
905 `(("lapack" ,lapack)
906 ("readline" ,readline)
907 ("glpk" ,glpk)
1ec78e9d
EB		 908 ("fftw" ,fftw)
909 ("fftwf" ,fftwf)
910 ("arpack" ,arpack-ng)
668c06ac
JD		 911 ("pcre" ,pcre)
912 ("fltk" ,fltk)
913 ("fontconfig" ,fontconfig)
914 ("freetype" ,freetype)
40029cbe 915 ("hdf5" ,hdf5)
668c06ac
JD		 916 ("libxft" ,libxft)
917 ("mesa" ,mesa)
1ec78e9d 918 ("glu" ,glu)
668c06ac
JD		 919 ("zlib" ,zlib)))
920 (native-inputs
19afbea1 921 `(("gfortran" ,gfortran)
668c06ac
JD		 922 ("pkg-config" ,pkg-config)
923 ("perl" ,perl)
1ec78e9d
EB		 924 ;; The following inputs are not actually used in the build process.
925 ;; However, the ./configure gratuitously tests for their existence and
926 ;; assumes that programs not present at build time are also not, and
927 ;; can never be, available at run time! If these inputs are therefore
928 ;; not present, support for them will be built out. However, Octave
929 ;; will still run without them, albeit without the features they
668c06ac
JD		 930 ;; provide.
931 ("less" ,less)
932 ("texinfo" ,texinfo)
933 ("ghostscript" ,ghostscript)
934 ("gnuplot" ,gnuplot)))
935 (arguments
b7b27a8f
KY		 936 `(#:configure-flags
937 (list (string-append "--with-shell="
938 (assoc-ref %build-inputs "bash")
939 "/bin/sh"))))
668c06ac
JD		 940 (home-page "http://www.gnu.org/software/octave/")
941 (synopsis "High-level language for numerical computation")
1ec78e9d
EB		 942 (description "GNU Octave is a high-level interpreted language that is
943specialized for numerical computations. It can be used for both linear and
944non-linear applications and it provides great support for visualizing results.
945Work may be performed both at the interactive command-line as well as via
946script files.")
668c06ac 947 (license license:gpl3+)))
3de01d3f
EB		 948
949(define-public gmsh
950 (package
951 (name "gmsh")
c7b08410 952 (version "2.11.0")
3de01d3f
EB		 953 (source
954 (origin
955 (method url-fetch)
956 (uri (string-append "http://www.geuz.org/gmsh/src/gmsh-"
957 version "-source.tgz"))
958 (sha256
c7b08410 959 (base32 "1ilplibvjgf7a905grpnclrvkmqy9fgrpl7xyp3w4yl1qc682v9b"))
3de01d3f
EB		 960 (modules '((guix build utils)))
961 (snippet
962 ;; Remove non-free METIS code
963 '(delete-file-recursively "contrib/Metis"))))
964 (build-system cmake-build-system)
3de01d3f
EB		 965 (propagated-inputs
966 `(("fltk" ,fltk)
19afbea1 967 ("gfortran" ,gfortran)
3de01d3f 968 ("gmp" ,gmp)
40029cbe 969 ("hdf5" ,hdf5)
3de01d3f
EB		 970 ("lapack" ,lapack)
971 ("mesa" ,mesa)
85f41902 972 ("glu" ,glu)
3de01d3f
EB		 973 ("libx11" ,libx11)
974 ("libxext" ,libxext)))
66395a61
EF		 975 (inputs
976 `(("fontconfig" ,fontconfig)
977 ("libxft" ,libxft)))
3de01d3f
EB		 978 (arguments
979 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
980 "-DENABLE_BUILD_SHARED:BOOL=ON"
c7b08410
EB		 981 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")
982 #:phases (modify-phases %standard-phases
983 (replace
984 'check
985 (lambda _
986 (zero? (system* "make" "test"
987 ;; Disable this test. See
988 ;; https://geuz.org/trac/gmsh/ticket/271
989 "ARGS=-E component8_in_a_box")))))))
3de01d3f
EB		 990 (home-page "http://www.geuz.org/gmsh/")
991 (synopsis "3D finite element grid generator")
edf684ef
EB		 992 (description "Gmsh is a 3D finite element grid generator with a built-in
993CAD engine and post-processor. Its design goal is to provide a fast, light
994and user-friendly meshing tool with parametric input and advanced
995visualization capabilities. Gmsh is built around four modules: geometry,
996mesh, solver and post-processing. The specification of any input to these
997modules is done either interactively using the graphical user interface or in
998ASCII text files using Gmsh's own scripting language.")
3de01d3f 999 (license license:gpl2+)))
b9100e2f
EB		 1000
1001(define-public petsc
1002 (package
1003 (name "petsc")
fafd623e 1004 (version "3.7.2")
b9100e2f
EB		 1005 (source
1006 (origin
1007 (method url-fetch)
1008 ;; The *-lite-* tarball does not contain the *large* documentation
1009 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1010 "petsc-lite-" version ".tar.gz"))
1011 (sha256
fafd623e 1012 (base32 "0jfrq6rd4zagw1iimz05m2w91k0jvz3qbik1lk8pqcxw3rvdqk5d"))))
b9100e2f
EB		 1013 (build-system gnu-build-system)
1014 (native-inputs
1015 `(("python" ,python-2)
1016 ("perl" ,perl)))
1017 (inputs
19afbea1 1018 `(("gfortran" ,gfortran)
b9100e2f 1019 ("lapack" ,lapack)
f258212d 1020 ("superlu" ,superlu)
b9100e2f
EB		 1021 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1022 ;; leaving out opengl, as configuration seems to only be for mac
1023 ))
1024 (arguments
1025 `(#:test-target "test"
9a899cce 1026 #:parallel-build? #f ;build is parallel by default
b9100e2f
EB		 1027 #:configure-flags
1028 `("--with-mpi=0"
f258212d
EB		 1029 "--with-openmp=1"
1030 "--with-superlu=1"
1031 ,(string-append "--with-superlu-include="
1032 (assoc-ref %build-inputs "superlu") "/include")
1033 ,(string-append "--with-superlu-lib="
1034 (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
b9100e2f 1035 #:phases
64dcc289
EB		 1036 (modify-phases %standard-phases
1037 (replace 'configure
1038 ;; PETSc's configure script is actually a python script, so we can't
1039 ;; run it with bash.
1040 (lambda* (#:key outputs (configure-flags '())
1041 #:allow-other-keys)
1042 (let* ((prefix (assoc-ref outputs "out"))
1043 (flags `(,(string-append "--prefix=" prefix)
1044 ,@configure-flags)))
1045 (format #t "build directory: ~s~%" (getcwd))
1046 (format #t "configure flags: ~s~%" flags)
1047 (zero? (apply system* "./configure" flags)))))
1048 (add-after 'configure 'clean-local-references
64dcc289
EB		 1049 (lambda* (#:key inputs outputs #:allow-other-keys)
1050 (let ((out (assoc-ref outputs "out")))
1051 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
b730b437
EB		 1052 ;; Prevent build directory from leaking into compiled code
1053 (((getcwd)) out)
1054 ;; Scrub timestamp for reproducibility
fafd623e
EB		 1055 ((".*Libraries compiled on.*") ""))
1056 #t)))
64dcc289 1057 (add-after 'install 'clean-install
10b11968
EB		 1058 ;; Try to keep installed files from leaking build directory names.
1059 (lambda* (#:key inputs outputs #:allow-other-keys)
64dcc289 1060 (let ((out (assoc-ref outputs "out")))
10b11968 1061 (substitute* (map (lambda (file)
9a899cce 1062 (string-append out "/lib/petsc/conf/" file))
fafd623e 1063 '("petscvariables"))
10b11968
EB		 1064 (((getcwd)) out))
1065 ;; Make compiler references point to the store
9a899cce 1066 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
dfdf5716
EB		 1067 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1068 (string-append "= " (which compiler))))
10b11968
EB		 1069 ;; PETSc installs some build logs, which aren't necessary.
1070 (for-each (lambda (file)
9a899cce 1071 (let ((f (string-append out "/lib/petsc/conf/" file)))
10b11968
EB		 1072 (when (file-exists? f)
1073 (delete-file f))))
9a899cce
EB		 1074 '("configure.log" "make.log" "gmake.log"
1075 "test.log" "error.log" "RDict.db"
fafd623e 1076 "PETScBuildInternal.cmake"
10b11968 1077 ;; Once installed, should uninstall with Guix
fafd623e
EB		 1078 "uninstall.py"))
1079 #t))))))
b9100e2f 1080 (home-page "http://www.mcs.anl.gov/petsc")
16ecf3ff 1081 (synopsis "Library to solve PDEs")
b9100e2f
EB		 1082 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1083data structures and routines for the scalable (parallel) solution of
1084scientific applications modeled by partial differential equations.")
166191b3 1085 (license (license:non-copyleft
b9100e2f
EB		 1086 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1087
1088(define-public petsc-complex
1089 (package (inherit petsc)
1090 (name "petsc-complex")
1091 (arguments
1092 (substitute-keyword-arguments (package-arguments petsc)
1093 ((#:configure-flags cf)
1094 `(cons "--with-scalar-type=complex" ,cf))))
16ecf3ff 1095 (synopsis "Library to solve PDEs (with complex scalars)")))
183e44ae 1096
d8c7eeb9
EB		 1097(define-public petsc-openmpi
1098 (package (inherit petsc)
1099 (name "petsc-openmpi")
1100 (inputs
1101 `(("openmpi" ,openmpi)
1102 ,@(package-inputs petsc)))
1103 (arguments
1104 (substitute-keyword-arguments (package-arguments petsc)
1105 ((#:configure-flags cf)
1106 ``("--with-mpiexec=mpirun"
1107 ,(string-append "--with-mpi-dir="
1108 (assoc-ref %build-inputs "openmpi"))
1109 ,@(delete "--with-mpi=0" ,cf)))))
16ecf3ff 1110 (synopsis "Library to solve PDEs (with MPI support)")))
d8c7eeb9
EB		 1111
1112(define-public petsc-complex-openmpi
1113 (package (inherit petsc-complex)
1114 (name "petsc-complex-openmpi")
1115 (inputs
1116 `(("openmpi" ,openmpi)
1117 ,@(package-inputs petsc-complex)))
1118 (arguments
1119 (substitute-keyword-arguments (package-arguments petsc-complex)
1120 ((#:configure-flags cf)
1121 ``("--with-mpiexec=mpirun"
1122 ,(string-append "--with-mpi-dir="
1123 (assoc-ref %build-inputs "openmpi"))
1124 ,@(delete "--with-mpi=0" ,cf)))))
16ecf3ff 1125 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
d8c7eeb9 1126
a7f01414
EB		 1127(define-public slepc
1128 (package
1129 (name "slepc")
8787c555 1130 (version "3.7.1")
a7f01414
EB		 1131 (source
1132 (origin
1133 (method url-fetch)
1134 (uri (string-append "http://slepc.upv.es/download/download.php?"
1135 "filename=slepc-" version ".tar.gz"))
d588422e 1136 (file-name (string-append name "-" version ".tar.gz"))
a7f01414
EB		 1137 (sha256
1138 (base32
8787c555 1139 "1hijlmrvxvfqslnx8yydzw5xqbsn1yy02g32w0hln1z3cgr1c0k7"))))
a7f01414
EB		 1140 (build-system gnu-build-system)
1141 (native-inputs
1142 `(("python" ,python-2)))
1143 (inputs
1144 `(("arpack" ,arpack-ng)
1145 ("gfortran" ,gfortran)))
1146 (propagated-inputs
1147 `(("petsc" ,petsc)))
1148 (arguments
1149 `(#:parallel-build? #f ;build is parallel by default
1150 #:configure-flags
1151 `(,(string-append "--with-arpack-dir="
9cf52454 1152 (assoc-ref %build-inputs "arpack") "/lib"))
a7f01414
EB		 1153 #:phases
1154 (modify-phases %standard-phases
8787c555 1155 (replace 'configure
a7f01414
EB		 1156 ;; configure is a python script, so we can't run it with bash.
1157 (lambda* (#:key inputs outputs (configure-flags '())
1158 #:allow-other-keys)
1159 (let* ((prefix (assoc-ref outputs "out"))
1160 (flags `(,(string-append "--prefix=" prefix)
1161 ,@configure-flags)))
1162 (format #t "build directory: ~s~%" (getcwd))
1163 (format #t "configure flags: ~s~%" flags)
1164 (setenv "SLEPC_DIR" (getcwd))
9cf52454 1165 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
a7f01414 1166 (zero? (apply system* "./configure" flags)))))
8787c555 1167 (add-after 'install 'delete-doc
a7f01414
EB		 1168 ;; TODO: SLEPc installs HTML documentation alongside headers in
1169 ;; $out/include. We'd like to move them to share/doc, but delete
1170 ;; them for now, as they are incomplete and installing the complete
1171 ;; documentation is difficult.
1172 (lambda* (#:key outputs #:allow-other-keys)
1173 (let* ((out (assoc-ref outputs "out")))
1174 (for-each delete-file (find-files out "\\.html$")))))
8787c555 1175 (add-after 'install 'clean-install
a7f01414
EB		 1176 ;; Clean up unnecessary build logs from installation.
1177 (lambda* (#:key outputs #:allow-other-keys)
1178 (let ((out (assoc-ref outputs "out")))
1179 (for-each (lambda (file)
1180 (let ((f (string-append out "/lib/slepc/conf/" file)))
1181 (when (file-exists? f)
1182 (delete-file f))))
1183 '("configure.log" "make.log" "gmake.log"
1184 "test.log" "error.log" "RDict.db"
1185 "uninstall.py"))))))))
1186 (home-page "http://slepc.upv.es")
1187 (synopsis "Scalable library for eigenproblems")
1188 (description "SLEPc is a software library for the solution of large sparse
1189eigenproblems on parallel computers. It can be used for the solution of
1190linear eigenvalue problems formulated in either standard or generalized form,
1191as well as other related problems such as the singular value decomposition.
1192The emphasis of the software is on methods and techniques appropriate for
1193problems in which the associated matrices are sparse, for example, those
1194arising after the discretization of partial differential equations.")
1195 (license license:lgpl3)))
1196
1197(define-public slepc-complex
1198 (package (inherit slepc)
1199 (name "slepc-complex")
1200 (propagated-inputs
1201 `(("petsc" ,petsc-complex)
1202 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1203 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1204
1205(define-public slepc-openmpi
1206 (package (inherit slepc)
1207 (name "slepc-openmpi")
1208 (inputs
1209 `(("mpi" ,openmpi)
1210 ("arpack" ,arpack-ng-openmpi)
1211 ,@(alist-delete "arpack" (package-inputs slepc))))
1212 (propagated-inputs
1213 `(("petsc" ,petsc-openmpi)
1214 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1215 (synopsis "Scalable library for eigenproblems (with MPI support)")))
1216
1217(define-public slepc-complex-openmpi
1218 (package (inherit slepc-openmpi)
1219 (name "slepc-complex-openmpi")
1220 (propagated-inputs
1221 `(("petsc" ,petsc-complex-openmpi)
1222 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1223 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1224
cec86422
EB		 1225(define-public mumps
1226 (package
1227 (name "mumps")
c69fa438 1228 (version "5.0.1")
cec86422
EB		 1229 (source
1230 (origin
1231 (method url-fetch)
1232 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
1233 version ".tar.gz"))
1234 (sha256
1235 (base32
c69fa438 1236 "1820jfp3mbl7n85765v5mp6p0gzqpgr4d2lrnhwj4gl7cwp5ndah"))
fc1adab1 1237 (patches (search-patches "mumps-build-parallelism.patch"))))
cec86422
EB		 1238 (build-system gnu-build-system)
1239 (inputs
1240 `(("fortran" ,gfortran)
1241 ;; These are required for linking against mumps, but we let the user
1242 ;; declare the dependency.
1243 ("blas" ,openblas)
1244 ("metis" ,metis)
1245 ("scotch" ,scotch)))
1246 (arguments
1247 `(#:modules ((ice-9 match)
1248 (ice-9 popen)
1249 (srfi srfi-1)
1250 ,@%gnu-build-system-modules)
1251 #:phases
1252 (modify-phases %standard-phases
1253 (replace
1254 'configure
1255 (lambda* (#:key inputs #:allow-other-keys)
1256 (call-with-output-file "Makefile.inc"
1257 (lambda (port)
1258 (format port "
1259PLAT =
1260LIBEXT = .a
1261OUTC = -o
1262OUTF = -o
1263RM = rm -f~:[
1264CC = gcc
1265FC = gfortran
1266FL = gfortran
1267INCSEQ = -I$(topdir)/libseq
1268LIBSEQ = -L$(topdir)/libseq -lmpiseq
1269LIBSEQNEEDED = libseqneeded~;
1270CC = mpicc
1271FC = mpifort
1272FL = mpifort~]
1273AR = ar vr # rules require trailing space, ugh...
1274RANLIB = ranlib
1275LIBBLAS = -L~a -lopenblas~@[
1276SCALAP = -L~a -lscalapack~]
1277LIBOTHERS = -pthread
1278CDEFS = -DAdd_
1279PIC = -fPIC
1280OPTF = -O2 -DALLOW_NON_INIT $(PIC)
1281OPTL = -O2 $(PIC)
1282OPTC = -O2 $(PIC)
1283INCS = $(INCSEQ)
1284LIBS = $(SCALAP) $(LIBSEQ)
1285LPORDDIR = $(topdir)/PORD/lib
1286IPORD = -I$(topdir)/PORD/include
1287LPORD = -L$(LPORDDIR) -lpord
1288ORDERINGSF = -Dpord~@[
1289METISDIR = ~a
1290IMETIS = -I$(METISDIR)/include
1291LMETIS = -L$(METISDIR)/lib -lmetis
1292ORDERINGSF += -Dmetis~]~@[~:{
1293SCOTCHDIR = ~a
1294ISCOTCH = -I$(SCOTCHDIR)/include
1295LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
1296ORDERINGSF += ~a~}~]
1297ORDERINGSC = $(ORDERINGSF)
1298LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
1299IORDERINGSF = $(ISCOTCH)
1300IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
1301 (assoc-ref inputs "mpi")
1302 (assoc-ref inputs "blas")
1303 (assoc-ref inputs "scalapack")
1304 (assoc-ref inputs "metis")
1305 (match (list (assoc-ref inputs "pt-scotch")
1306 (assoc-ref inputs "scotch"))
1307 ((#f #f)
1308 #f)
1309 ((#f scotch)
1310 `((,scotch "" "-Dscotch")))
1311 ((ptscotch _)
1312 `((,ptscotch
1313 "-lptesmumps -lptscotch -lptscotcherr "
1314 "-Dptscotch")))))))))
1315 (replace
1316 'build
1317 ;; By default only the d-precision library is built. Make with "all"
1318 ;; target so that all precision libraries and examples are built.
1319 (lambda _
1320 (zero? (system* "make" "all"
1321 (format #f "-j~a" (parallel-job-count))))))
1322 (replace
1323 'check
1324 ;; Run the simple test drivers, which read test input from stdin:
1325 ;; from the "real" input for the single- and double-precision
1326 ;; testers, and from the "cmplx" input for complex-precision
1327 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
1328 ;; package to prefix execution with "mpirun".
1329 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
1330 (with-directory-excursion "examples"
1331 (every
1332 (lambda (prec type)
1333 (let ((tester (apply open-pipe*
1334 `(,OPEN_WRITE
1335 ,@exec-prefix
1336 ,(string-append "./" prec
1337 "simpletest"))))
1338 (input (open-input-file
1339 (string-append "input_simpletest_" type))))
1340 (begin
1341 (dump-port input tester)
1342 (close-port input)
1343 (zero? (close-pipe tester)))))
1344 '("s" "d" "c" "z")
1345 '("real" "real" "cmplx" "cmplx")))))
1346 (replace
1347 'install
1348 (lambda* (#:key outputs #:allow-other-keys)
1349 (let ((out (assoc-ref outputs "out")))
1350 (copy-recursively "lib" (string-append out "/lib"))
1351 (copy-recursively "include" (string-append out "/include"))
1352 (when (file-exists? "libseq/libmpiseq.a")
1353 (copy-file "libseq/libmpiseq.a"
1354 (string-append out "/lib/libmpiseq.a")))))))))
1355 (home-page "http://mumps.enseeiht.fr")
1356 (synopsis "Multifrontal sparse direct solver")
1357 (description
1358 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
1359sparse system of linear equations A x = b using Guassian elimination.")
1360 (license license:cecill-c)))
1361
1362(define-public mumps-metis
1363 (package (inherit mumps)
1364 (name "mumps-metis")
1365 (inputs
1366 (alist-delete "scotch" (package-inputs mumps)))))
1367
1368(define-public mumps-openmpi
1369 (package (inherit mumps)
1370 (name "mumps-openmpi")
1371 (inputs
1372 `(("mpi" ,openmpi)
1373 ("scalapack" ,scalapack)
1374 ("pt-scotch" ,pt-scotch)
1375 ,@(alist-delete "scotch" (package-inputs mumps))))
1376 (arguments
1377 (substitute-keyword-arguments (package-arguments mumps)
1378 ((#:phases phases)
1379 `(modify-phases ,phases
1380 (replace
1381 'check
1382 (lambda _
1383 ((assoc-ref ,phases 'check)
1384 #:exec-prefix '("mpirun" "-n" "2"))))))))
1385 (synopsis "Multifrontal sparse direct solver (with MPI)")))
1386
1387(define-public mumps-metis-openmpi
1388 (package (inherit mumps-openmpi)
1389 (name "mumps-metis-openmpi")
1390 (inputs
1391 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
1392
2d047896
RW		 1393(define-public r-quadprog
1394 (package
1395 (name "r-quadprog")
1396 (version "1.5-5")
1397 (source
1398 (origin
1399 (method url-fetch)
1400 (uri (cran-uri "quadprog" version))
1401 (sha256
1402 (base32
1403 "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
1404 (build-system r-build-system)
1405 (native-inputs
1406 `(("gfortran" ,gfortran)))
1407 (home-page "http://cran.r-project.org/web/packages/quadprog")
1408 (synopsis "Functions to solve quadratic programming problems")
1409 (description
1410 "This package contains routines and documentation for solving quadratic
1411programming problems.")
1412 (license license:gpl3+)))
1413
ec8c7e47
RJ		 1414(define-public r-pracma
1415 (package
1416 (name "r-pracma")
ccd9b151 1417 (version "1.9.5")
ec8c7e47
RJ		 1418 (source (origin
1419 (method url-fetch)
1420 (uri (cran-uri "pracma" version))
1421 (sha256
ccd9b151 1422 (base32 "19nr2jlkbcdgvw3gx5hry12av565lmvqd5q4h7zlch3q13avwwl2"))))
ec8c7e47 1423 (build-system r-build-system)
ccd9b151
RW		 1424 (propagated-inputs
1425 `(("r-quadprog" ,r-quadprog)))
ec8c7e47
RJ		 1426 (home-page "http://cran.r-project.org/web/packages/pracma")
1427 (synopsis "Practical numerical math functions")
1428 (description "This package provides functions for numerical analysis and
1429linear algebra, numerical optimization, differential equations, plus some
1430special functions. It uses Matlab function names where appropriate to simplify
1431porting.")
1432 (license license:gpl3+)))
1433
183e44ae
EB		 1434(define-public superlu
1435 (package
1436 (name "superlu")
995a09e0 1437 (version "5.2.1")
183e44ae
EB		 1438 (source
1439 (origin
1440 (method url-fetch)
1441 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1442 "superlu_" version ".tar.gz"))
1443 (sha256
995a09e0
EB		 1444 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
1445 (modules '((guix build utils)))
1446 (snippet
1447 ;; Replace the non-free implementation of MC64 with a stub adapted
1448 ;; from Debian
1449 '(begin
1450 (use-modules (ice-9 regex)
1451 (ice-9 rdelim))
1452 (call-with-output-file "SRC/mc64ad.c"
1453 (lambda (port)
1454 (display "
1455#include <stdio.h>
1456#include <stdlib.h>
1457void mc64id_(int *a) {
1458 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
1459 abort ();
1460}
1461void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
1462 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
1463 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
1464 abort ();
1465}\n" port)))
1466 ;; Remove the corresponding license verbiage. MC64 license follows
1467 ;; a "------" line separator.
1468 (with-atomic-file-replacement "License.txt"
1469 (let ((rx (make-regexp "-{8}")))
1470 (lambda (in out)
1471 (let loop ()
1472 (let ((line (read-line in 'concat)))
1473 (unless (regexp-exec rx line)
1474 (display line out)
1475 (loop)))))))))))
1476 (build-system cmake-build-system)
183e44ae
EB		 1477 (native-inputs
1478 `(("tcsh" ,tcsh)))
1479 (inputs
995a09e0 1480 `(("blas" ,openblas)
19afbea1 1481 ("gfortran" ,gfortran)))
183e44ae 1482 (arguments
995a09e0
EB		 1483 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
1484 "-DTPL_BLAS_LIBRARIES=openblas"
1485 "-DBUILD_SHARED_LIBS:BOOL=YES"
1486 "-DCMAKE_INSTALL_LIBDIR=lib")))
183e44ae
EB		 1487 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
1488 (synopsis "Supernodal direct solver for sparse linear systems")
1489 (description
1490 "SuperLU is a general purpose library for the direct solution of large,
1491sparse, nonsymmetric systems of linear equations on high performance machines.
1492The library is written in C and is callable from either C or Fortran. The
1493library routines perform an LU decomposition with partial pivoting and
1494triangular system solves through forward and back substitution. The library
1495also provides threshold-based ILU factorization preconditioners.")
995a09e0
EB		 1496 (license (list license:bsd-3
1497 license:gpl2+ ;EXAMPLE/*fgmr.c
1498 (license:fsf-free "file://SRC/colamd.h")))))
f8ed036a 1499
a54aefea
EB		 1500(define-public superlu-dist
1501 (package
1502 (name "superlu-dist")
1503 (version "3.3")
1504 (source
1505 (origin
1506 (method url-fetch)
1507 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1508 "superlu_dist_" version ".tar.gz"))
1509 (sha256
1510 (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj"))
29080870
EB		 1511 (modules '((guix build utils)))
1512 (snippet
1513 ;; Replace the non-free implementation of MC64 with a stub
1514 '(begin
1515 (use-modules (ice-9 regex)
1516 (ice-9 rdelim))
1517 (call-with-output-file "SRC/mc64ad.c"
1518 (lambda (port)
1519 (display "
1520#include <stdio.h>
1521#include <stdlib.h>
1522void mc64id_(int *a) {
1523 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
1524 abort ();
1525}
1526void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
1527 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
1528 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
1529 abort ();
1530}\n" port)))
1531 (delete-file "SRC/mc64ad.f.bak")
1532 (substitute* "SRC/util.c" ;adjust default algorithm
1533 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
1534 "RowPerm = NOROWPERM"))))
fc1adab1 1535 (patches (search-patches "superlu-dist-scotchmetis.patch"))))
a54aefea
EB		 1536 (build-system gnu-build-system)
1537 (native-inputs
1538 `(("tcsh" ,tcsh)))
1539 (inputs
19afbea1 1540 `(("gfortran" ,gfortran)))
a54aefea
EB		 1541 (propagated-inputs
1542 `(("openmpi" ,openmpi) ;headers include MPI heades
1543 ("lapack" ,lapack) ;required to link with output library
1544 ("pt-scotch" ,pt-scotch))) ;same
1545 (arguments
1546 `(#:parallel-build? #f ;race conditions using ar
1547 #:phases
1548 (alist-replace
1549 'configure
1550 (lambda* (#:key inputs outputs #:allow-other-keys)
1551 (call-with-output-file "make.inc"
1552 (lambda (port)
1553 (format port "
1554PLAT =
1555DSuperLUroot = ~a
1556DSUPERLULIB = ~a/lib/libsuperlu_dist.a
1557BLASDEF = -DUSE_VENDOR_BLAS
1558BLASLIB = -L~a/lib -lblas
1559PARMETISLIB = -L~a/lib \
1560 -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
1561 -lscotch -lscotcherr -lscotcherrexit
1562METISLIB = -L~:*~a/lib \
1563 -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
1564LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
1565ARCH = ar
1566ARCHFLAGS = cr
1567RANLIB = ranlib
1568CC = mpicc
1569PIC = -fPIC
1570CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC)
1571NOOPTS = -O0 -g $(PIC)
1572FORTRAN = mpifort
1573FFLAGS = -O2 -g $(PIC)
1574LOADER = $(CC)
1575CDEFS = -DAdd_"
1576 (getcwd)
1577 (assoc-ref outputs "out")
1578 (assoc-ref inputs "lapack")
1579 (assoc-ref inputs "pt-scotch")))))
1580 (alist-cons-after
1581 'unpack 'remove-broken-symlinks
1582 (lambda _
1583 (for-each delete-file
1584 (find-files "MAKE_INC" "\\.#make\\..*")))
1585 (alist-cons-before
1586 'build 'create-install-directories
1587 (lambda* (#:key outputs #:allow-other-keys)
1588 (for-each
1589 (lambda (dir)
1590 (mkdir-p (string-append (assoc-ref outputs "out")
1591 "/" dir)))
1592 '("lib" "include")))
1593 (alist-replace
1594 'check
1595 (lambda _
1596 (with-directory-excursion "EXAMPLE"
1597 (and
1598 (zero? (system* "mpirun" "-n" "2"
1599 "./pddrive" "-r" "1" "-c" "2" "g20.rua"))
1600 (zero? (system* "mpirun" "-n" "2"
1601 "./pzdrive" "-r" "1" "-c" "2" "cg20.cua")))))
1602 (alist-replace
1603 'install
1604 (lambda* (#:key outputs #:allow-other-keys)
1605 ;; Library is placed in lib during the build phase. Copy over
1606 ;; headers to include.
1607 (let* ((out (assoc-ref outputs "out"))
1608 (incdir (string-append out "/include")))
1609 (for-each (lambda (file)
1610 (let ((base (basename file)))
1611 (format #t "installing `~a' to `~a'~%"
1612 base incdir)
1613 (copy-file file
1614 (string-append incdir "/" base))))
1615 (find-files "SRC" ".*\\.h$"))))
1616 %standard-phases)))))))
1617 (home-page (package-home-page superlu))
1618 (synopsis "Parallel supernodal direct solver")
1619 (description
1620 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
1621It is targeted for distributed memory parallel machines. SuperLU_DIST is
1622implemented in ANSI C, and MPI for communications.")
1623 (license license:bsd-3)))
1624
f8ed036a
EB		 1625(define-public scotch
1626 (package
1627 (name "scotch")
6c798540 1628 (version "6.0.4")
f8ed036a
EB		 1629 (source
1630 (origin
1631 (method url-fetch)
6c798540 1632 (uri (string-append "https://gforge.inria.fr/frs/download.php/34618/"
f8ed036a
EB		 1633 "scotch_" version ".tar.gz"))
1634 (sha256
6c798540 1635 (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm"))
fc1adab1
AK		 1636 (patches (search-patches "scotch-test-threading.patch"
1637 "pt-scotch-build-parallelism.patch"))))
f8ed036a
EB		 1638 (build-system gnu-build-system)
1639 (inputs
1640 `(("zlib" ,zlib)
1641 ("flex" ,flex)
1642 ("bison" ,bison)))
1643 (arguments
1644 `(#:phases
d6602ee9
EB		 1645 (modify-phases %standard-phases
1646 (add-after
1647 'unpack 'chdir-to-src
1648 (lambda _ (chdir "src")))
1649 (replace
1650 'configure
1651 (lambda _
1652 (call-with-output-file "Makefile.inc"
1653 (lambda (port)
1654 (format port "
f8ed036a
EB		 1655EXE =
1656LIB = .a
1657OBJ = .o
1658MAKE = make
1659AR = ar
1660ARFLAGS = -ruv
cf0ec6c4 1661CAT = cat
f8ed036a
EB		 1662CCS = gcc
1663CCP = mpicc
1664CCD = gcc
1665CPPFLAGS =~{ -D~a~}
6c798540 1666CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
f8ed036a
EB		 1667LDFLAGS = -lz -lm -lrt -lpthread
1668CP = cp
1669LEX = flex -Pscotchyy -olex.yy.c
1670LN = ln
1671MKDIR = mkdir
1672MV = mv
1673RANLIB = ranlib
1674YACC = bison -pscotchyy -y -b y
1675"
d6602ee9
EB		 1676 '("COMMON_FILE_COMPRESS_GZ"
1677 "COMMON_PTHREAD"
1678 "COMMON_RANDOM_FIXED_SEED"
cf0ec6c4
EB		 1679 ;; Prevents symbolc clashes with libesmumps
1680 "SCOTCH_RENAME"
d6602ee9
EB		 1681 ;; XXX: Causes invalid frees in superlu-dist tests
1682 ;; "SCOTCH_PTHREAD"
1683 ;; "SCOTCH_PTHREAD_NUMBER=2"
1684 "restrict=__restrict"))))))
cf0ec6c4
EB		 1685 (add-after
1686 'build 'build-esmumps
1687 (lambda _
1688 (zero? (system* "make"
1689 (format #f "-j~a" (parallel-job-count))
1690 "esmumps"))))
d6602ee9 1691 (replace
f8ed036a
EB		 1692 'install
1693 (lambda* (#:key outputs #:allow-other-keys)
1694 (let ((out (assoc-ref outputs "out")))
1695 (mkdir out)
1696 (zero? (system* "make"
1697 (string-append "prefix=" out)
cf0ec6c4
EB		 1698 "install"))
1699 ;; esmumps files are not installed with the above
1700 (for-each (lambda (f)
1701 (copy-file f (string-append out "/include/" f)))
1702 (find-files "../include" ".*esmumps.h$"))
1703 (for-each (lambda (f)
1704 (copy-file f (string-append out "/lib/" f)))
1705 (find-files "../lib" "^lib.*esmumps.*"))))))))
f8ed036a
EB		 1706 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
1707 (synopsis "Programs and libraries for graph algorithms")
1708 (description "SCOTCH is a set of programs and libraries which implement
1709the static mapping and sparse matrix reordering algorithms developed within
1710the SCOTCH project. Its purpose is to apply graph theory, with a divide and
1711conquer approach, to scientific computing problems such as graph and mesh
1712partitioning, static mapping, and sparse matrix ordering, in application
1713domains ranging from structural mechanics to operating systems or
1714bio-chemistry.")
1715 ;; See LICENSE_en.txt
1716 (license license:cecill-c)))
6acb4adb
EB		 1717
1718(define-public pt-scotch
1719 (package (inherit scotch)
1720 (name "pt-scotch")
1721 (propagated-inputs
1722 `(("openmpi" ,openmpi))) ;Headers include MPI headers
1723 (arguments
1724 (substitute-keyword-arguments (package-arguments scotch)
1725 ((#:phases scotch-phases)
d6602ee9
EB		 1726 `(modify-phases ,scotch-phases
1727 (replace
1728 'build
d6602ee9
EB		 1729 (lambda _
1730 (and
cf0ec6c4
EB		 1731 (zero? (system* "make"
1732 (format #f "-j~a" (parallel-job-count))
1733 "ptscotch" "ptesmumps"))
d6602ee9
EB		 1734 ;; Install the serial metis compatibility library
1735 (zero? (system* "make" "-C" "libscotchmetis" "install")))))
1736 (replace
1737 'check
1738 (lambda _ (zero? (system* "make" "ptcheck"))))))))
6acb4adb 1739 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
5698b8b8 1740
aa75ad00
EB		 1741(define-public metis
1742 (package
1743 (name "metis")
1744 (version "5.1.0")
1745 (source
1746 (origin
1747 (method url-fetch)
1748 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
1749 "metis-" version ".tar.gz"))
1750 (sha256
1751 (base32
1752 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
1753 (build-system cmake-build-system)
1754 (inputs
1755 `(("blas" ,openblas)))
1756 (arguments
1757 `(#:tests? #f ;no tests
1758 #:configure-flags `("-DSHARED=ON"
1759 ,(string-append "-DGKLIB_PATH=" (getcwd)
1760 "/metis-" ,version "/GKlib"))))
1761 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
1762 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
1763 (description
1764 "METIS is a set of serial programs for partitioning graphs, partitioning
1765finite element meshes, and producing fill-reducing orderings for sparse
1766matrices. The algorithms implemented in METIS are based on the multilevel
1767recursive-bisection, multilevel k-way, and multi-constraint partitioning
1768schemes.")
1769 (license license:asl2.0))) ;As of version 5.0.3
1770
700ff222
EB		 1771(define-public p4est
1772 (package
1773 (name "p4est")
1774 (version "1.1")
1775 (source
1776 (origin
1777 (method url-fetch)
1778 (uri (string-append "http://p4est.github.io/release/p4est-"
1779 version ".tar.gz"))
1780 (sha256
1781 (base32
1782 "0faina2h5qsx3m2izbzaj9bbakma1krbbjmq43wrp1hcbyijflqb"))))
1783 (build-system gnu-build-system)
1784 (inputs
1785 `(("fortran" ,gfortran)
1786 ("blas" ,openblas)
1787 ("lapack" ,lapack)
1788 ("zlib" ,zlib)))
1789 (arguments
1790 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
1791 (assoc-ref %build-inputs "blas")
1792 " -lopenblas")
1793 ,(string-append "LAPACK_LIBS=-L"
1794 (assoc-ref %build-inputs "lapack")
1795 " -llapack"))))
1796 (home-page "http://www.p4est.org")
1797 (synopsis "Adaptive mesh refinement on forests of octrees")
1798 (description
1799 "The p4est software library enables the dynamic management of a
1800collection of adaptive octrees, conveniently called a forest of octrees.
1801p4est is designed to work in parallel and scales to hundreds of thousands of
1802processor cores.")
1803 (license license:gpl2+)))
1804
1805(define-public p4est-openmpi
1806 (package (inherit p4est)
1807 (name "p4est-openmpi")
1808 (inputs
1809 `(("mpi" ,openmpi)
1810 ,@(package-inputs p4est)))
1811 (arguments
1812 (substitute-keyword-arguments (package-arguments p4est)
1813 ((#:configure-flags cf)
1814 ``("--enable-mpi" ,@,cf))))
1815 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
1816
5698b8b8
JD		 1817(define-public gsegrafix
1818 (package
1819 (name "gsegrafix")
1820 (version "1.0.6")
1821 (source
1822 (origin
1823 (method url-fetch)
1824 (uri (string-append "mirror://gnu/" name "/" name "-"
1825 version ".tar.gz"))
1826 (sha256
1827 (base32
1828 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
1829 (build-system gnu-build-system)
1830 (arguments
1831 `(#:configure-flags '("LDFLAGS=-lm")))
1832 (inputs
1833 `(("libgnomecanvas" ,libgnomecanvas)
1834 ("libbonoboui" ,libbonoboui)
1835 ("libgnomeui" ,libgnomeui)
1836 ("libgnomeprintui" ,libgnomeprintui)
1837 ("popt" ,popt)))
1838 (native-inputs
1839 `(("pkg-config" ,pkg-config)))
1840 (home-page "http://www.gnu.org/software/gsegrafix/")
1841 (synopsis "GNOME application to create scientific and engineering plots")
1842 (description "GSEGrafix is an application which produces high-quality graphical
1843plots for science and engineering. Plots are specified via simple ASCII
1844parameter files and data files and are presented in an anti-aliased GNOME
1845canvas. The program supports rectangular two-dimensional plots, histograms,
1846polar-axis plots and three-dimensional plots. Plots can be printed or saved
1847to BMP, JPEG or PNG image formats.")
1848 (license license:gpl3+)))
8731e527
JD		 1849
1850(define-public maxima
1851 (package
1852 (name "maxima")
77af7b24 1853 (version "5.36.1")
8731e527
JD		 1854 (source
1855 (origin
1856 (method url-fetch)
1857 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
1858 version "-source/" name "-" version ".tar.gz"))
1859 (sha256
1860 (base32
77af7b24 1861 "0x1rk659sn3cq0n5c90848ilzr1gb1wf0072fl6jhkdq00qgh2s0"))
fc1adab1 1862 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
8731e527 1863 (build-system gnu-build-system)
df354a77
FB		 1864 (inputs
1865 `(("gcl" ,gcl)
1866 ("gnuplot" ,gnuplot) ;for plots
f36afe4d 1867 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
df354a77
FB		 1868 (native-inputs
1869 `(("texinfo" ,texinfo)
1870 ("perl" ,perl)))
8731e527 1871 (arguments
df354a77
FB		 1872 `(#:configure-flags
1873 (list "--enable-gcl"
1874 (string-append "--with-posix-shell="
1875 (assoc-ref %build-inputs "bash")
1876 "/bin/sh")
1877 (string-append "--with-wish="
1878 (assoc-ref %build-inputs "tk")
1879 "/bin/wish"
1880 (let ((v ,(package-version tk)))
1881 (string-take v (string-index-right v #\.)))))
df354a77 1882 ;; By default Maxima attempts to write temporary files to
77af7b24
MW		 1883 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
1884 ;; Work around that.
df354a77 1885 #:make-flags (list "TMPDIR=/tmp")
df354a77 1886 #:phases (alist-cons-before
8731e527 1887 'check 'pre-check
df354a77 1888 (lambda _
8731e527 1889 (chmod "src/maxima" #o555))
f36afe4d
FB		 1890 ;; Make sure the doc and emacs files are found in the
1891 ;; standard location. Also configure maxima to find gnuplot
1892 ;; without having it on the PATH.
1893 (alist-cons-after
1894 'install 'post-install
1895 (lambda* (#:key outputs inputs #:allow-other-keys)
1896 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
1897 (out (assoc-ref outputs "out"))
1898 (datadir (string-append out "/share/maxima/" ,version)))
1899 (with-directory-excursion out
1900 (mkdir-p "share/emacs")
1901 (mkdir-p "share/doc")
1902 (symlink
1903 (string-append datadir "/emacs/")
1904 (string-append out "/share/emacs/site-lisp"))
1905 (symlink
1906 (string-append datadir "/doc/")
1907 (string-append out "/share/doc/maxima"))
1908 (with-atomic-file-replacement
1909 (string-append datadir "/share/maxima-init.lisp")
1910 (lambda (in out)
1911 (format out "~a ~s~a~%"
1912 "(setf $gnuplot_command "
1913 (string-append gnuplot "/bin/gnuplot") ")")
1914 (dump-port in out))))))
1915 %standard-phases))))
8731e527
JD		 1916 (home-page "http://maxima.sourceforge.net")
1917 (synopsis "Numeric and symbolic expression manipulation")
1918 (description "Maxima is a system for the manipulation of symbolic and
1919numerical expressions. It yields high precision numeric results by using
1920exact fractions, arbitrary precision integers, and variable precision floating
e881752c 1921point numbers.")
8731e527
JD		 1922 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
1923 ;; Others simply say "GNU General Public License" without stating a
1924 ;; version (which implicitly means gpl1+).
1925 ;; At least one file (src/maxima.asd) says "version 2."
1926 ;; GPLv2 only is therefore the smallest subset.
f36afe4d 1927 (license license:gpl2)))
ec322be2 1928
9aafbc0c
MW		 1929(define-public wxmaxima
1930 (package
1931 (name "wxmaxima")
e6a90507 1932 (version "16.04.2")
9aafbc0c
MW		 1933 (source
1934 (origin
1935 (method url-fetch)
1936 (uri (string-append "mirror://sourceforge/wxmaxima/wxMaxima/"
1937 version "/" name "-" version ".tar.gz"))
1938 (sha256
1939 (base32
e6a90507 1940 "1fpqzk1921isiqrpgpf433ldq41924qs9sy99fl1zn5661b2l73n"))))
9aafbc0c
MW		 1941 (build-system gnu-build-system)
1942 (inputs
1943 `(("wxwidgets" ,wxwidgets)
de477809
SB		 1944 ("maxima" ,maxima)
1945 ;; Runtime support.
1946 ("adwaita-icon-theme" ,adwaita-icon-theme)
1947 ("gtk+" ,gtk+)
1948 ("shared-mime-info" ,shared-mime-info)))
9aafbc0c
MW		 1949 (arguments
1950 `(#:phases (modify-phases %standard-phases
1951 (add-after
1952 'install 'wrap-program
1953 (lambda* (#:key inputs outputs #:allow-other-keys)
1954 (wrap-program (string-append (assoc-ref outputs "out")
1955 "/bin/wxmaxima")
1956 `("PATH" ":" prefix
1957 (,(string-append (assoc-ref inputs "maxima")
de477809
SB		 1958 "/bin")))
1959 ;; For GtkFileChooserDialog.
1960 `("GSETTINGS_SCHEMA_DIR" =
1961 (,(string-append (assoc-ref inputs "gtk+")
1962 "/share/glib-2.0/schemas")))
1963 `("XDG_DATA_DIRS" ":" prefix
1964 (;; Needed by gdk-pixbuf to know supported icon formats.
1965 ,(string-append
1966 (assoc-ref inputs "shared-mime-info") "/share")
1967 ;; The default icon theme of GTK+.
1968 ,(string-append
1969 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
9aafbc0c
MW		 1970 #t)))))
1971 (home-page "https://andrejv.github.io/wxmaxima/")
1972 (synopsis "Graphical user interface for the Maxima computer algebra system")
1973 (description
1974 "wxMaxima is a graphical user interface for the Maxima computer algebra
1975system. It eases the use of Maxima by making most of its commands available
1976through a menu system and by providing input dialogs for commands that require
1977more than one argument. It also implements its own display engine that
1978outputs mathematical symbols directly instead of depicting them with ASCII
1979characters.
1980
1981wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
1982text and mathematical calculations to create documents, exporting of input and
1983output to TeX, and a browser for Maxima's manual including command index and
1984full text searching.")
1985 (license license:gpl2+)))
1986
b15e47f9
RW		 1987(define-public armadillo
1988 (package
1989 (name "armadillo")
7397cd9e 1990 (version "7.500.0")
b15e47f9
RW		 1991 (source (origin
1992 (method url-fetch)
1993 (uri (string-append "mirror://sourceforge/arma/armadillo-"
7397cd9e 1994 version ".tar.xz"))
b15e47f9
RW		 1995 (sha256
1996 (base32
7397cd9e 1997 "1x98d32cgxbzbbma2ak6c37wnbpq13xxyxyd6jjvflv748mzi9ks"))))
b15e47f9
RW		 1998 (build-system cmake-build-system)
1999 (arguments `(#:tests? #f)) ;no test target
2000 (inputs
2001 `(("openblas" ,openblas)
2002 ("lapack" ,lapack)
2003 ("arpack" ,arpack-ng)))
2004 (home-page "http://arma.sourceforge.net/")
2005 (synopsis "C++ linear algebra library")
2006 (description
2007 "Armadillo is a C++ linear algebra library, aiming towards a good balance
2008between speed and ease of use. It is useful for algorithm development
2009directly in C++, or quick conversion of research code into production
2010environments. It can be used for machine learning, pattern recognition,
2011signal processing, bioinformatics, statistics, econometrics, etc. The library
2012provides efficient classes for vectors, matrices and cubes, as well as 150+
2013associated functions (eg. contiguous and non-contiguous submatrix views).")
2014 (license license:mpl2.0)))
2015
e22d4ca4
RW		 2016(define-public armadillo-for-rcpparmadillo
2017 (package (inherit armadillo)
062737a1 2018 (version "7.500.0")
e22d4ca4
RW		 2019 (source (origin
2020 (method url-fetch)
2021 (uri (string-append "mirror://sourceforge/arma/armadillo-"
5e675072 2022 version ".tar.xz"))
e22d4ca4
RW		 2023 (sha256
2024 (base32
062737a1 2025 "1x98d32cgxbzbbma2ak6c37wnbpq13xxyxyd6jjvflv748mzi9ks"))))))
e22d4ca4 2026
279663ef 2027(define-public muparser
d7cff656
LF		 2028 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2029 ;; different hash. In order to make `guix package --upgrade` work correctly,
2030 ;; we set a Guix packaging revision.
2031 ;; When the next version of muparser is released, we can remove
2032 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2033 (let ((upstream-version "2.2.5")
2034 (revision "2"))
2035 (package
2036 (name "muparser")
2037 (version (string-append upstream-version "-" revision))
2038 (source
2039 (origin
2040 (method url-fetch)
2041 (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
2042 upstream-version ".tar.gz"))
2043 (file-name (string-append name "-" version ".tar.gz"))
2044 (sha256
2045 (base32
2046 "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
2047 (build-system gnu-build-system)
2048 (arguments
2049 `(#:configure-flags '("--enable-samples=no")
2050 #:tests? #f)) ;no "check" target
2051 (home-page "http://muparser.beltoforion.de/")
2052 (synopsis "Fast parser library for mathematical expressions")
2053 (description
2054 "muParser is an extensible high performance math parser library. It is
2055based on transforming an expression into a bytecode and precalculating constant
2056parts of it.")
2057 (license license:expat))))
279663ef 2058
e73b49fb
RW		 2059(define-public openblas
2060 (package
2061 (name "openblas")
69851c59 2062 (version "0.2.15")
e73b49fb
RW		 2063 (source
2064 (origin
2065 (method url-fetch)
2066 (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
2067 version))
2068 (file-name (string-append name "-" version ".tar.gz"))
2069 (sha256
2070 (base32
69851c59 2071 "1k5f6vjlk54qlplk5m7xkbaw6g2y7dl50lwwdv6xsbcsgsbxfcpy"))))
e73b49fb
RW		 2072 (build-system gnu-build-system)
2073 (arguments
5b5ea159 2074 `(#:tests? #f ;no "check" target
bd0b4379
RW		 2075 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
2076 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2077 ;; we need to disable substitutions.
71923a91
AE		 2078 #:substitutable?
2079 ,(let ((system (or (%current-target-system) (%current-system))))
2080 (or (string-prefix? "x86_64" system)
bd0b4379
RW		 2081 (string-prefix? "i686" system)
2082 (string-prefix? "mips" system)))
e73b49fb
RW		 2083 #:make-flags
2084 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
2085 "SHELL=bash"
af5b817e
RW		 2086 "NO_LAPACK=1"
2087 ;; Build the library for all supported CPUs. This allows
2088 ;; switching CPU targets at runtime with the environment variable
2089 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
71923a91
AE		 2090 ;; Unfortunately, this is not supported on non-x86 architectures,
2091 ;; where it leads to failed builds.
2092 ,@(let ((system (or (%current-target-system) (%current-system))))
8a637e79
RW		 2093 (cond
2094 ((or (string-prefix? "x86_64" system)
71923a91 2095 (string-prefix? "i686" system))
8a637e79
RW		 2096 '("DYNAMIC_ARCH=1"))
2097 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
2098 ;; two available MIPS targets special extended instructions
2099 ;; for Loongson cores are used.
2100 ((string-prefix? "mips" system)
2101 '("TARGET=SICORTEX"))
2102 (else '()))))
e73b49fb
RW		 2103 ;; no configure script
2104 #:phases (alist-delete 'configure %standard-phases)))
2105 (inputs
19afbea1 2106 `(("fortran" ,gfortran)))
e73b49fb
RW		 2107 (native-inputs
2108 `(("cunit" ,cunit)
2109 ("perl" ,perl)))
2110 (home-page "http://www.openblas.net/")
2111 (synopsis "Optimized BLAS library based on GotoBLAS")
2112 (description
2113 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
2114 (license license:bsd-3)))
2115
e1605e36
RW		 2116(define-public openlibm
2117 (package
2118 (name "openlibm")
26f6e565 2119 (version "0.5.1")
e1605e36
RW		 2120 (source
2121 (origin
2122 (method url-fetch)
2123 (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
2124 version ".tar.gz"))
2125 (file-name (string-append name "-" version ".tar.gz"))
2126 (sha256
2127 (base32
26f6e565 2128 "11czx2z7nh6dfpz45s3xl7v38hw36jxzxfvny454bk3if14pfakq"))))
e1605e36
RW		 2129 (build-system gnu-build-system)
2130 (arguments
2131 `(#:make-flags
2132 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2133 #:phases
2134 ;; no configure script
2135 (alist-delete 'configure %standard-phases)
2136 #:tests? #f)) ;the tests are part of the default target
2137 (home-page "http://openlibm.org/")
2138 (synopsis "Portable C mathematical library (libm)")
2139 (description
2140 "OpenLibm is an effort to have a high quality, portable, standalone C
2141mathematical library (libm). It can be used standalone in applications and
2142programming language implementations. The project was born out of a need to
e881752c 2143have a good libm for the Julia programming language that worked consistently
e1605e36
RW		 2144across compilers and operating systems, and in 32-bit and 64-bit
2145environments.")
538c0e3b
EF		 2146 ;; Each architecture has its own make target, and there is none for mips.
2147 (supported-systems (delete "mips64el-linux" %supported-systems))
e1605e36
RW		 2148 ;; See LICENSE.md for details.
2149 (license (list license:expat
2150 license:isc
2151 license:bsd-2
2152 license:public-domain
2153 license:lgpl2.1+))))
2154
e62be58f
RW		 2155(define-public openspecfun
2156 (package
2157 (name "openspecfun")
49f54a74 2158 (version "0.5.2")
e62be58f
RW		 2159 (source
2160 (origin
2161 (method url-fetch)
2162 (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
2163 version ".tar.gz"))
2164 (file-name (string-append name "-" version ".tar.gz"))
2165 (sha256
2166 (base32
49f54a74 2167 "1y5b2h6f2k72536kym3vzy3li3bhpd23x463g7hdmjdi3cncavz1"))))
e62be58f
RW		 2168 (build-system gnu-build-system)
2169 (arguments
2170 '(#:tests? #f ;no "check" target
2171 #:make-flags
2172 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2173 ;; no configure script
2174 #:phases (alist-delete 'configure %standard-phases)))
2175 (inputs
19afbea1 2176 `(("fortran" ,gfortran)))
e62be58f
RW		 2177 (home-page "https://github.com/JuliaLang/openspecfun")
2178 (synopsis "Collection of special mathematical functions")
2179 (description
2180 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
2181portable package for Bessel Functions of a Complex Argument and Nonnegative
2182Order; it contains subroutines for computing Bessel functions and Airy
2183functions. Faddeeva allows computing the various error functions of arbitrary
2184complex arguments (Faddeeva function, error function, complementary error
2185function, scaled complementary error function, imaginary error function, and
2186Dawson function); given these, one can also easily compute Voigt functions,
2187Fresnel integrals, and similar related functions as well.")
2188 ;; Faddeeva is released under the Expat license; AMOS is included as
2189 ;; public domain software.
2190 (license (list license:expat license:public-domain))))
2191
2742f87e
RW		 2192(define-public suitesparse
2193 (package
2194 (name "suitesparse")
2195 (version "4.4.3")
2196 (source
2197 (origin
2198 (method url-fetch)
2199 (uri (string-append
2200 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
2201 version ".tar.gz"))
2202 (sha256
2203 (base32
2204 "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5"))))
2205 (build-system gnu-build-system)
2206 (arguments
2207 '(#:parallel-build? #f ;cholmod build fails otherwise
2208 #:tests? #f ;no "check" target
2209 #:make-flags
2210 (list "CC=gcc"
2211 "BLAS=-lblas"
2212 "TBB=-ltbb"
2213 "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used
2214 (string-append "INSTALL_LIB="
2215 (assoc-ref %outputs "out") "/lib")
2216 (string-append "INSTALL_INCLUDE="
2217 (assoc-ref %outputs "out") "/include"))
2218 #:phases
2219 (alist-cons-before
2220 'install 'prepare-out
2221 ;; README.txt states that the target directories must exist prior to
2222 ;; running "make install".
2223 (lambda _
2224 (mkdir-p (string-append (assoc-ref %outputs "out") "/lib"))
2225 (mkdir-p (string-append (assoc-ref %outputs "out") "/include")))
2226 ;; no configure script
2227 (alist-delete 'configure %standard-phases))))
2228 (inputs
2229 `(("tbb" ,tbb)
2230 ("lapack" ,lapack)))
2231 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
2232 (synopsis "Suite of sparse matrix software")
2233 (description
2234 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
2235multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
2236multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
2237simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
2238CXSparse, a concise sparse Cholesky factorization package; and many other
2239packages.")
2240 ;; LGPLv2.1+:
2241 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
2242 ;; GPLv2+:
2243 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
2244 (license (list license:gpl2+ license:lgpl2.1+))))
2245
ec322be2
FB		 2246(define-public atlas
2247 (package
2248 (name "atlas")
3c98ac02 2249 (version "3.10.3")
ec322be2
FB		 2250 (source (origin
2251 (method url-fetch)
de67e922
LF		 2252 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
2253 version "/atlas" version ".tar.bz2"))
ec322be2
FB		 2254 (sha256
2255 (base32
3c98ac02 2256 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
ec322be2
FB		 2257 (build-system gnu-build-system)
2258 (home-page "http://math-atlas.sourceforge.net/")
19afbea1 2259 (inputs `(("gfortran" ,gfortran)
ec322be2
FB		 2260 ("lapack-tar" ,(package-source lapack))))
2261 (outputs '("out" "doc"))
01480b9e
FB		 2262 ;; For the moment we drop support for MIPS at it fails to compile. See
2263 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
2264 (supported-systems (delete "mips64el-linux" %supported-systems))
ec322be2
FB		 2265 (arguments
2266 `(#:parallel-build? #f
2267 #:parallel-tests? #f
f15615b1
LC		 2268
2269 ;; ATLAS tunes itself for the machine it is built on, as explained at
2270 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
2271 ;; For this reason, we want users to build it locally instead of using
2272 ;; substitutes.
2273 #:substitutable? #f
2274
ec322be2
FB		 2275 #:modules ((srfi srfi-26)
2276 (srfi srfi-1)
2277 (guix build gnu-build-system)
2278 (guix build utils))
40029cbe 2279 #:configure-flags
ec322be2
FB		 2280 `(;; Generate position independent code suitable for dynamic libraries
2281 ;; and use WALL timer to get more accurate timing.
2282 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
2283 ;; Set word width.
2284 "-b"
2285 ,,(if (string-match "64" (%current-system))
2286 "64"
2287 "32")
2288 ;; Disable parallel build as it gives errors: atlas_pthread.h is
2289 ;; needed to compile C files before it is generated.
2290 "-Ss" "pmake" "make -j 1"
af89a667
FB		 2291 ;; Probe is failing for MIPS. We therefore define the system
2292 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
2293 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
2294 ,,@(if (string-prefix? "mips" (%current-system))
2295 (list "-A" "49" "-V" "1")
2296 (list))
ec322be2
FB		 2297 ;; Generate shared libraries.
2298 "--shared"
2299 ;; Build a full LAPACK library.
2300 ,(string-append "--with-netlib-lapack-tarfile="
2301 (assoc-ref %build-inputs "lapack-tar")))
2302 #:phases
e5b4b96b
EF		 2303 (modify-phases %standard-phases
2304 (add-after 'install 'install-doc
2305 (lambda* (#:key outputs inputs #:allow-other-keys)
2306 (let ((doc (string-append (assoc-ref outputs "doc")
2307 "/share/doc/atlas")))
2308 (mkdir-p doc)
2309 (fold (lambda (file previous)
2310 (and previous (zero? (system* "cp" file doc))))
2311 #t (find-files "../ATLAS/doc" ".*")))))
2312 (add-after 'check 'check-pt
2313 (lambda _ (zero? (system* "make" "ptcheck"))))
2314 ;; Fix files required to run configure.
2315 (add-before 'configure 'fix-/bin/sh
ec322be2
FB		 2316 (lambda _
2317 ;; Use `sh', not `/bin/sh'.
2318 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
2319 (("/bin/sh")
e5b4b96b
EF		 2320 "sh"))))
2321 ;; Fix /bin/sh in generated make files.
2322 (add-after 'configure 'fix-/bin/sh-in-generated-files
2323 (lambda _
2324 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
2325 (("/bin/sh")
2326 "sh"))))
2327 ;; ATLAS configure program does not accepts the default flags
2328 ;; passed by the 'gnu-build-system'.
2329 (replace 'configure
2330 (lambda* (#:key native-inputs inputs outputs
2331 (configure-flags '())
2332 #:allow-other-keys #:rest args)
2333 (let* ((prefix (assoc-ref outputs "out"))
2334 (bash (or (and=> (assoc-ref
2335 (or native-inputs inputs) "bash")
2336 (cut string-append <> "/bin/bash"))
2337 "/bin/sh"))
2338 (flags `(,(string-append "--prefix=" prefix)
2339 ,@configure-flags))
2340 (abs-srcdir (getcwd))
2341 (srcdir (string-append "../" (basename abs-srcdir))))
2342 (format #t "source directory: ~s (relative from build: ~s)~%"
2343 abs-srcdir srcdir)
2344 (mkdir "../build")
2345 (chdir "../build")
2346 (format #t "build directory: ~s~%" (getcwd))
2347 (format #t "configure flags: ~s~%" flags)
2348 (zero? (apply system* bash
2349 (string-append srcdir "/configure")
2350 flags))))))))
ec322be2
FB		 2351 (synopsis "Automatically Tuned Linear Algebra Software")
2352 (description
2353 "ATLAS is an automatically tuned linear algebra software library
2354providing C and Fortran77 interfaces to a portably efficient BLAS
2355implementation, as well as a few routines from LAPACK.
2356
f15615b1
LC		 2357Optimization occurs at build time. For this reason, the library is built on
2358the machine where it is installed, without resorting to pre-built substitutes.
ec322be2 2359
f15615b1 2360Before building the library, CPU throttling should be disabled. This can be
d97c429a 2361done in the BIOS, or, on GNU/Linux, with the following command:
ec322be2 2362
8e9ba611 2363@example
d97c429a 2364# cpupower --governor performance
8e9ba611 2365@end example
ec322be2 2366
d97c429a 2367Failure to do so will result in a library with poor performance.")
ec322be2 2368 (license license:bsd-3)))
c12efc72
AE		 2369
2370(define-public glm
2371 (package
2372 (name "glm")
2373 (version "0.9.6.3")
2374 (source
2375 (origin
2376 (method url-fetch)
de67e922
LF		 2377 (uri (string-append "mirror://sourceforge/ogl-math/glm-" version
2378 "/glm-" version ".zip"))
c12efc72
AE		 2379 (sha256
2380 (base32
2381 "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l"))))
2382 (build-system cmake-build-system)
2383 (native-inputs
2384 `(("unzip" ,unzip)))
2385 (home-page "http://glm.g-truc.net")
2386 (synopsis "OpenGL Mathematics library")
2387 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
2388library for graphics software based on the OpenGL Shading Language (GLSL)
2389specifications.")
2390 (license license:expat)))
7f18257b
AE		 2391
2392(define-public lpsolve
2393 (package
2394 (name "lpsolve")
2395 (version "5.5.2.0")
2396 (source
2397 (origin
2398 (method url-fetch)
2399 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
2400 "/lp_solve_" version "_source.tar.gz"))
2401 (sha256
2402 (base32
2403 "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq"))
2404 (modules '((guix build utils)))
2405 (snippet
2406 '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
2407 (("^c=cc") "c=gcc")
2408 ;; Pretend to be on a 64 bit platform to obtain a common directory
2409 ;; name for the build results on all architectures; nothing else
2410 ;; seems to depend on it.
5dbfbef7
LC		 2411 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
2412
2413 ;; The check for 'isnan' as it is written fails with
2414 ;; "non-floating-point argument in call to function
2415 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
2416 ;; definition, which in turn leads to bad things. Fix the feature
2417 ;; test.
2418 (("isnan\\(0\\)") "isnan(0.)")))))
7f18257b
AE		 2419 (build-system gnu-build-system)
2420 (arguments
2421 `(#:tests? #f ; no check target
2422 #:phases
2423 (modify-phases %standard-phases
2424 (delete 'configure)
2425 (replace 'build
2426 (lambda _
6689d094
LC		 2427 (and (with-directory-excursion "lpsolve55"
2428 (zero? (system* "bash" "ccc")))
2429 (with-directory-excursion "lp_solve"
2430 (zero? (system* "bash" "ccc"))))))
7f18257b
AE		 2431 (replace 'install
2432 (lambda* (#:key outputs #:allow-other-keys)
2433 (let* ((out (assoc-ref outputs "out"))
2434 (bin (string-append out "/bin"))
2435 (lib (string-append out "/lib"))
2436 ;; This is where LibreOffice expects to find the header
2437 ;; files, and where they are installed by Debian.
2438 (include (string-append out "/include/lpsolve")))
2439 (mkdir-p lib)
2440 (copy-file "lpsolve55/bin/ux64/liblpsolve55.a"
2441 (string-append lib "/liblpsolve55.a"))
2442 (copy-file "lpsolve55/bin/ux64/liblpsolve55.so"
2443 (string-append lib "/liblpsolve55.so"))
96c46210
LC		 2444 (install-file "lp_solve/bin/ux64/lp_solve" bin)
2445
7f18257b
AE		 2446 ;; Install a subset of the header files as on Debian
2447 ;; (plus lp_bit.h, which matches the regular expression).
96c46210
LC		 2448 (for-each (lambda (name)
2449 (install-file name include))
2450 (find-files "." "lp_[HMSa-z].*\\.h$"))
7f18257b 2451 (with-directory-excursion "shared"
96c46210
LC		 2452 (for-each (lambda (name)
2453 (install-file name include))
2454 (find-files "." "\\.h$")))
7f18257b
AE		 2455 #t))))))
2456 (home-page "http://lpsolve.sourceforge.net/")
2457 (synopsis "Mixed integer linear programming (MILP) solver")
2458 (description
2459 "lp_solve is a mixed integer linear programming solver based on the
2460revised simplex and the branch-and-bound methods.")
2461 (license license:lgpl2.1+)))
a17d4564
EB		 2462
2463(define-public dealii
2464 (package
2465 (name "dealii")
101e8472 2466 (version "8.4.1")
a17d4564
EB		 2467 (source
2468 (origin
2469 (method url-fetch)
2470 (uri (string-append "https://github.com/dealii/dealii/releases/"
2471 "download/v" version "/dealii-" version ".tar.gz"))
2472 (sha256
2473 (base32
101e8472 2474 "1bdksvvyp1rj37df1ndh8j3x9nzpc3sazw8nd0hzvnlw0qnyk800"))
a17d4564
EB		 2475 (modules '((guix build utils)))
2476 (snippet
2477 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
2478 '(delete-file-recursively "bundled"))))
2479 (build-system cmake-build-system)
2480 (inputs
2481 `(("tbb" ,tbb)
2482 ("zlib" ,zlib)
2483 ("boost" ,boost)
2484 ("p4est" ,p4est)
2485 ("blas" ,openblas)
2486 ("lapack" ,lapack)
2487 ("arpack" ,arpack-ng)
2488 ("muparser" ,muparser)
2489 ("gfortran" ,gfortran)
2490 ("suitesparse" ,suitesparse))) ;for UMFPACK
2491 (arguments
2492 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
2493 #:configure-flags '("-DCOMPAT_FILES=OFF") ;Follow new directory structure
2494 #:phases (modify-phases %standard-phases
2495 (add-after
2496 'install 'hint-example-prefix
2497 ;; Set Cmake hints in examples so that they can find this
2498 ;; deal.II when configuring.
2499 (lambda* (#:key outputs #:allow-other-keys)
2500 (let* ((out (assoc-ref %outputs "out"))
2501 (exmpl (string-append out "/share/doc"
2502 "/dealii/examples")))
2503 (substitute* (find-files exmpl "CMakeLists.txt")
2504 (("([[:space:]]*HINTS.*)\n" _ line)
2505 (string-append line " $ENV{HOME}/.guix-profile "
2506 out "\n")))
2507 #t))))))
2508 (home-page "https://www.dealii.org")
2509 (synopsis "Finite element library")
2510 (description
2511 "Deal.II is a C++ program library targeted at the computational solution
2512of partial differential equations using adaptive finite elements. The main
2513aim of deal.II is to enable rapid development of modern finite element codes,
2514using among other aspects adaptive meshes and a wide array of tools often used
2515in finite element programs.")
2516 (license license:lgpl2.1+)))
2517
2518(define-public dealii-openmpi
2519 (package (inherit dealii)
2520 (name "dealii-openmpi")
2521 (inputs
2522 `(("mpi" ,openmpi)
2523 ;;Supported only with MPI:
2524 ("p4est" ,p4est-openmpi)
2525 ("petsc" ,petsc-openmpi)
2526 ("slepc" ,slepc-openmpi)
2527 ("metis" ,metis) ;for MUMPS
2528 ("scalapack" ,scalapack) ;for MUMPS
2529 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
2530 ("arpack" ,arpack-ng-openmpi)
2531 ,@(fold alist-delete (package-inputs dealii)
2532 '("p4est" "arpack"))))
2533 (arguments
2534 (substitute-keyword-arguments (package-arguments dealii)
2535 ((#:configure-flags cf)
2536 ``("-DMPI_C_COMPILER=mpicc"
2537 "-DMPI_CXX_COMPILER=mpicxx"
2538 "-DMPI_Fortran_COMPILER=mpifort"
2539 ,@,cf))))
2540 (synopsis "Finite element library (with MPI support)")))
194c7f95
AE		 2541
2542(define-public flann
2543 (package
2544 (name "flann")
2545 (version "1.8.4")
2546 (source
2547 (origin
2548 (method url-fetch)
2549 (uri
2550 (string-append
2551 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
2552 version "-src.zip"))
2553 (sha256
2554 (base32
2555 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))))
2556 (build-system cmake-build-system)
2557 (native-inputs
2558 `(("unzip" ,unzip)))
2559 (inputs
2560 `(("hdf5" ,hdf5)
2561 ("octave" ,octave)
2562 ("python" ,python-2) ; print syntax
2563 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
2564 ("zlib" ,zlib)))
2565 (arguments
39b30337
LC		 2566 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
2567 ;; taken 46 MiB unstripped, and 6 MiB stripped.
2568 #:strip-directories '("lib" "lib64" "libexec"
2569 "bin" "sbin" "share/flann/octave")
2570
9684e30b
LC		 2571 ;; Save 12 MiB by not installing .a files. Passing
2572 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
2573 #:phases (modify-phases %standard-phases
2574 (add-after 'install 'remove-static-libraries
2575 (lambda* (#:key outputs #:allow-other-keys)
2576 (let* ((out (assoc-ref outputs "out"))
2577 (lib (string-append out "/lib")))
2578 (for-each delete-file
2579 (find-files lib "\\.a$"))
2580 #t))))
2581
39b30337 2582 #:tests? #f)) ; The test data are downloaded from the Internet.
194c7f95
AE		 2583 (home-page "http://www.cs.ubc.ca/research/flann/")
2584 (synopsis "Library for approximate nearest neighbors computation")
2585 (description "FLANN is a library for performing fast approximate
2586nearest neighbor searches in high dimensional spaces. It implements a
2587collection of algorithms and a system for automatically choosing the best
2588algorithm and optimum parameters depending on the dataset.
2589
2590FLANN is written in C++ and contains bindings for C, Octave and Python.")
2591 (license (license:non-copyleft "file://COPYING"
2592 "See COPYING in the distribution."))))
d8c97beb
EF		 2593
2594(define-public wcalc
2595 (package
2596 (name "wcalc")
2597 (version "2.5")
2598 (source
2599 (origin
2600 (method url-fetch)
de67e922
LF		 2601 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
2602 "wcalc-" version ".tar.bz2"))
d8c97beb
EF		 2603 (sha256
2604 (base32
2605 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
2606 (build-system gnu-build-system)
2607 (inputs
2608 `(("mpfr" ,mpfr)
2609 ("readline" ,readline)))
2610 (home-page "http://w-calc.sourceforge.net/index.php")
2611 (synopsis "Flexible command-line scientific calculator")
2612 (description "Wcalc is a very capable calculator. It has standard functions
2613(sin, asin, and sinh for example, in either radians or degrees), many
2614pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
2615variables, a command history, hex/octal/binary input and output, unit
2616conversions, embedded comments, and an expandable expression entry field. It
2617evaluates expressions using the standard order of operations.")
2618 (license license:gpl2+)))
45147b0c
FH		 2619
2620(define-public xaos
2621 (package
2622 (name "xaos")
2623 (version "3.6")
2624 (source (origin
2625 (method url-fetch)
de67e922
LF		 2626 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
2627 "/xaos-" version ".tar.gz"))
45147b0c
FH		 2628 (sha256
2629 (base32
2630 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
2631 (build-system gnu-build-system)
2632 (native-inputs `(("gettext" ,gnu-gettext)))
2633 (inputs `(("libx11" ,libx11)
2634 ("zlib" ,zlib)
2635 ("libpng" ,libpng)
2636 ("gsl" ,gsl)))
2637 (arguments
2638 `(#:tests? #f ;no "check" target
2639 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
2640 (synopsis "Real-time fractal zoomer")
2641 (description "GNU XaoS is a graphical program that generates fractal
2642patterns and allows you to zoom in and out of them infinitely in a fluid,
2643continuous manner. It also includes tutorials that help to explain how fractals
2644are built. It can generate many different fractal types such as the Mandelbrot
2645set.")
2646 (home-page "http://www.gnu.org/software/xaos/")
2647 (license license:gpl2+)))
528bb464
EB		 2648
2649(define-public hypre
2650 (package
2651 (name "hypre")
2652 (version "2.11.0")
2653 (source (origin
2654 (method url-fetch)
2655 (uri (string-append "https://github.com/LLNL/hypre/archive/"
2656 "v" version ".tar.gz"))
2657 (file-name (string-append name "-" version ".tar.gz"))
2658 (sha256
2659 (base32
2660 "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m"))
2661 (modules '((guix build utils)))
2662 (snippet
2663 '(begin
2664 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
2665 ;; substitute the tarball creation time.
2666 (substitute* "src/utilities/HYPRE_utilities.h"
2667 (("Date Compiled: .*$")
2668 "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n"))
2669 #t))))
2670 (build-system gnu-build-system)
2671 (outputs '("out" ;6.1 MiB of headers and libraries
2672 "doc")) ;4.8 MiB of documentation
2673 (native-inputs
2674 `(("doc++" ,doc++)
2675 ("netpbm" ,netpbm)
2676 ("texlive" ,texlive) ;full package required for fonts
2677 ("ghostscript" ,ghostscript)))
2678 (inputs
2679 `(("blas" ,openblas)
2680 ("lapack" ,lapack)))
2681 (arguments
2682 `(#:modules ((srfi srfi-1)
2683 ,@%gnu-build-system-modules)
2684 #:configure-flags '("--enable-shared"
2685 "--disable-fortran"
2686 "--without-MPI"
2687 "--with-openmp"
2688 "--with-fei"
2689 "--with-lapack"
2690 "--with-blas")
2691 #:phases
2692 (modify-phases %standard-phases
2693 (add-before 'configure 'chdir-src
2694 (lambda _ (chdir "src")))
2695 (replace 'configure
2696 (lambda* (#:key build target configure-flags
2697 #:allow-other-keys #:rest args)
2698 (let* ((configure (assoc-ref %standard-phases 'configure)))
2699 (apply configure
2700 (append args
2701 (list #:configure-flags
2702 (cons (string-append
2703 "--host=" (or target build))
2704 configure-flags)))))))
2705 (add-after 'build 'build-docs
2706 (lambda _
2707 (zero? (system* "make" "-Cdocs" "pdf" "html"))))
2708 (replace 'check
2709 (lambda _
2710 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
2711 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
2712 (and (system* "make" "check" "CHECKRUN=")
2713 (fold (lambda (filename result)
2714 (and result
2715 (let ((size (stat:size (stat filename))))
2716 (when (not (zero? size))
2717 (format #t "~a size ~d; error indication~%"
2718 filename size))
2719 (zero? size))))
2720 #t
2721 (find-files "test" ".*\\.err$")))))
2722 (add-after 'install 'install-docs
2723 (lambda* (#:key outputs #:allow-other-keys)
2724 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
2725 (let* ((doc (assoc-ref outputs "doc"))
2726 (docdir (string-append doc "/share/doc/hypre-" ,version)))
2727 (mkdir-p docdir)
2728 (with-directory-excursion "docs"
2729 (for-each (lambda (base)
2730 (install-file (string-append base ".pdf") docdir)
2731 (copy-recursively base docdir)) ;html docs
2732 '("HYPRE_usr_manual"
2733 "HYPRE_ref_manual")))
2734 #t))))))
2735 (home-page "http://www.llnl.gov/casc/hypre/")
2736 (synopsis "Library of solvers and preconditioners for linear equations")
2737 (description
2738 "HYPRE is a software library of high performance preconditioners and
2739solvers for the solution of large, sparse linear systems of equations. It
2740features multigrid solvers for both structured and unstructured grid
2741problems.")
2742 (license license:lgpl2.1)))
2743
2744(define-public hypre-openmpi
2745 (package (inherit hypre)
2746 (name "hypre-openmpi")
2747 (inputs
2748 `(("mpi" ,openmpi)
2749 ,@(package-inputs hypre)))
2750 (arguments
2751 (substitute-keyword-arguments (package-arguments hypre)
2752 ((#:configure-flags flags)
2753 ``("--with-MPI"
2754 ,@(delete "--without-MPI" ,flags)))))
2755 (synopsis "Parallel solvers and preconditioners for linear equations")
2756 (description
2757 "HYPRE is a software library of high performance preconditioners and
2758solvers for the solution of large, sparse linear systems of equations on
2759parallel computers. It features parallel multigrid solvers for both
2760structured and unstructured grid problems.")))
6c90e183
EB		 2761
2762(define-public matio
2763 (package
2764 (name "matio")
2765 (version "1.5.6")
2766 (source
2767 (origin
2768 (method url-fetch)
de67e922 2769 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
6c90e183
EB		 2770 "matio-" version ".tar.gz"))
2771 (sha256
2772 (base32
2773 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
2774 (build-system gnu-build-system)
2775 (inputs
2776 `(("zlib" ,zlib)
2777 ("hdf5" ,hdf5)))
2778 (home-page "http://matio.sourceforge.net/")
2779 (synopsis "Library for reading and writing MAT files")
2780 (description "Matio is a library for reading and writing MAT files. It
2781supports compressed MAT files, as well as newer (version 7.3) MAT files.")
2782 (license license:bsd-2)))
d721c83a
EB		 2783
2784(define-public libhilbert
2785 (package
2786 (name "libhilbert")
2787 (version "0.2-1")
2788 (source
2789 (origin
2790 (method url-fetch)
2791 (uri (string-append "http://web.cs.dal.ca/~chamilto/hilbert/"
2792 "libhilbert-" version ".tar.gz"))
2793 (sha256
2794 (base32
2795 "0v48x8405dj95gjn2saja4bzhw86d6zl6d3dg8h7dzac2qr97s34"))))
2796 (build-system gnu-build-system)
2797 (home-page "http://web.cs.dal.ca/~chamilto/hilbert")
2798 (synopsis "Hilbert indices for multidimensional data")
2799 (description "The libhilbert library can efficiently calculate Hilbert
2800curves and order-preserving representations of Hilbert curve indices that use
2801the same amount of space as the original point representation. This is useful
2802when using the Gilbert curve as a space filling curve through a
2803high-dimensional space where not all demensions have the same cardinality.")
2804 (license license:lgpl2.1+)))
517318ad
LF		 2805
2806(define-public vc
2807 (package
2808 (name "vc")
2809 (version "1.2.0")
2810 (source
2811 (origin (method url-fetch)
2812 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
2813 "download/" version "/Vc-" version ".tar.gz"))
2814 (sha256
2815 (base32
2816 "1rh6dhqar3y07n4xqyml0sa0v48qv3ch9dc3yc2in855hlh4vnqi"))))
2817 (build-system cmake-build-system)
2818 (arguments
2819 '(#:configure-flags
2820 '("-DBUILD_TESTING=ON")))
2821 (synopsis "SIMD vector classes for C++")
2822 (description "Vc provides portable, zero-overhead C++ types for explicitly
2823data-parallel programming. It is a library designed to ease explicit
2824vectorization of C++ code. Its types enable explicitly stating data-parallel
2825operations on multiple values. The parallelism is therefore added via the type
2826system. Vc has an intuitive API and provides portability between different
2827compilers and compiler versions as well as portability between different vector
2828instruction sets. Thus, an application written with Vc can be compiled for:
2829@enumerate
2830@item AVX and AVX2
2831@item SSE2 upto SSE4.2 or SSE4a
2832@item Scalar
2833@item MIC
2834@item NEON (in development)
2835@item NVIDIA GPUs / CUDA (in development)
2836@end enumerate\n")
2837 (home-page "https://github.com/VcDevel/Vc")
2838 (license license:bsd-3)))
jackhill's copy of GNU Guix: https://guix.gnu.org/