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gnu: Add python-parted.
[jackhill/guix/guix.git] / gnu / packages / maths.scm
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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>
a53d6719 4;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
e01397b4 5;;; Copyright © 2014, 2015, 2016, 2017, 2018 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>
4dba441c 8;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
32158110 9;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
9aafbc0c 10;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
bd041e7f 11;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
45147b0c 12;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
ec8c7e47 13;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
3c8ba11a 14;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
c0edb5b5 15;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
d7cff656 16;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
2fd26d05 17;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
5d4bd4cc 18;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>
4a78fd46 19;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
ba1be533 20;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
d109b1e8 21;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
5ca4fe96 22;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
59cd0ba4 23;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
dc7d6d4e 24;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
5b05dce7 25;;; Copyright © 2018 Jan Nieuwenhuizen <janneke@gnu.org>
41835f94 26;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
8f8b2451
AE		 27;;;
28;;; This file is part of GNU Guix.
29;;;
30;;; GNU Guix is free software; you can redistribute it and/or modify it
31;;; under the terms of the GNU General Public License as published by
32;;; the Free Software Foundation; either version 3 of the License, or (at
33;;; your option) any later version.
34;;;
35;;; GNU Guix is distributed in the hope that it will be useful, but
36;;; WITHOUT ANY WARRANTY; without even the implied warranty of
37;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
38;;; GNU General Public License for more details.
39;;;
40;;; You should have received a copy of the GNU General Public License
41;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
42
43(define-module (gnu packages maths)
ec322be2 44 #:use-module (ice-9 regex)
8f8b2451 45 #:use-module (gnu packages)
b5b73a82 46 #:use-module ((guix licenses) #:prefix license:)
8f8b2451
AE		 47 #:use-module (guix packages)
48 #:use-module (guix download)
54052a54 49 #:use-module (guix git-download)
0e2672ae 50 #:use-module (guix utils)
cec86422 51 #:use-module (guix build utils)
da95c817 52 #:use-module (guix build-system cmake)
c9dfa3c7 53 #:use-module (guix build-system gnu)
ba1be533 54 #:use-module (guix build-system ocaml)
ec8c7e47 55 #:use-module (guix build-system r)
63e07468 56 #:use-module (guix build-system ruby)
3de01d3f 57 #:use-module (gnu packages algebra)
5143517c 58 #:use-module (gnu packages autotools)
3de01d3f 59 #:use-module (gnu packages bison)
a17d4564 60 #:use-module (gnu packages boost)
e73b49fb 61 #:use-module (gnu packages check)
3de01d3f 62 #:use-module (gnu packages cmake)
c9dfa3c7 63 #:use-module (gnu packages compression)
668c06ac 64 #:use-module (gnu packages curl)
b7b27a8f 65 #:use-module (gnu packages cyrus-sasl)
528bb464 66 #:use-module (gnu packages documentation)
57e544e8 67 #:use-module (gnu packages elf)
3de01d3f 68 #:use-module (gnu packages flex)
668c06ac 69 #:use-module (gnu packages fltk)
f3929800 70 #:use-module (gnu packages fontutils)
1dba6407 71 #:use-module (gnu packages gettext)
da95c817 72 #:use-module (gnu packages gcc)
73fed4f8 73 #:use-module (gnu packages gd)
668c06ac 74 #:use-module (gnu packages ghostscript)
889187a4 75 #:use-module (gnu packages graphviz)
f3929800 76 #:use-module (gnu packages gtk)
45147b0c 77 #:use-module (gnu packages image)
2fd26d05 78 #:use-module (gnu packages java)
668c06ac 79 #:use-module (gnu packages less)
8731e527 80 #:use-module (gnu packages lisp)
bc3a2e35 81 #:use-module (gnu packages logging)
6e64766a 82 #:use-module (gnu packages lua)
5698b8b8 83 #:use-module (gnu packages gnome)
1b39a196 84 #:use-module (gnu packages guile)
668c06ac
JD		 85 #:use-module (gnu packages xorg)
86 #:use-module (gnu packages gl)
9f913401 87 #:use-module (gnu packages imagemagick)
8731e527 88 #:use-module (gnu packages m4)
d8c7eeb9 89 #:use-module (gnu packages mpi)
b92eee75 90 #:use-module (gnu packages multiprecision)
528bb464 91 #:use-module (gnu packages netpbm)
ba1be533 92 #:use-module (gnu packages ocaml)
668c06ac 93 #:use-module (gnu packages pcre)
5698b8b8 94 #:use-module (gnu packages popt)
c9dfa3c7
AE		 95 #:use-module (gnu packages perl)
96 #:use-module (gnu packages pkg-config)
da95c817 97 #:use-module (gnu packages python)
589e3f4e 98 #:use-module (gnu packages python-web)
5b05dce7 99 #:use-module (gnu packages qt)
c9dfa3c7 100 #:use-module (gnu packages readline)
63e07468 101 #:use-module (gnu packages ruby)
2742f87e 102 #:use-module (gnu packages tbb)
479c4273 103 #:use-module (gnu packages scheme)
b7194849 104 #:use-module (gnu packages shells)
df354a77 105 #:use-module (gnu packages tcl)
668c06ac 106 #:use-module (gnu packages texinfo)
8f9ac901 107 #:use-module (gnu packages tex)
b7b27a8f 108 #:use-module (gnu packages tls)
5b05dce7 109 #:use-module (gnu packages version-control)
9aafbc0c 110 #:use-module (gnu packages wxwidgets)
c12efc72 111 #:use-module (gnu packages xml)
a17d4564 112 #:use-module (srfi srfi-1))
8f8b2451 113
193abc82
JD		 114(define-public aris
115 (package
1f45f18a
JD		 116 (name "aris")
117 (version "2.2")
118 (source (origin
119 (method url-fetch)
120 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
121 (sha256 (base32
122 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
123 (build-system gnu-build-system)
124 (inputs `(("gtk+" ,gtk+)
125 ("libxml2" ,libxml2)))
126 (native-inputs `(("pkg-config" ,pkg-config)))
127 (synopsis "Natural deduction first-order logic interface")
128 (description "Aris is a program for performing logical proofs. It supports
129propositional and predicate logic, as well as Boolean algebra and
130arithmetical logic. In addition to its predefined inference and equivalence
131rules, Aris also supports references to older proofs. Its use of standard
132logical symbols and its natural deduction interface make it easy to use for
133beginners.")
134 (license license:gpl3+)
6fd52309 135 (home-page "https://www.gnu.org/software/aris/")))
193abc82 136
9c45c519
JD		 137(define-public c-graph
138 (package
139 (name "c-graph")
140 (version "2.0")
141 (source (origin
142 (method url-fetch)
143 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
144 ".tar.gz"))
145 (sha256 (base32
146 "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
147 (build-system gnu-build-system)
148 (inputs
149 `(("fortran" ,gfortran)))
a3947cb1 150 (synopsis "Visualizing and demonstrating convolution")
9c45c519 151 (description
a3947cb1
LC		 152 "GNU C-Graph is a tool for demonstrating the theory of convolution.
153Thus, it can serve as an excellent aid to students of signal and systems
154theory in visualizing the convolution process. Rather than forcing the
155student to write code, the program offers an intuitive interface with
156interactive dialogs to guide them.")
9c45c519 157 (license license:gpl3+)
6fd52309 158 (home-page "https://www.gnu.org/software/c-graph/")))
9c45c519 159
d91025e3
TD		 160(define-public coda
161 (package
162 (name "coda")
440c4273 163 (version "2.18.3")
d91025e3
TD		 164 (source
165 (origin
166 (method url-fetch)
167 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
168 version "/coda-" version ".tar.gz"))
169 (sha256
440c4273 170 (base32 "1zlzgcvwmmjm8mw8w4rg2rqy0pjilz7kyyxm0y4p8cbljbbjxxz0"))
4b12fe5c
TD		 171 (patches (search-patches "coda-use-system-libs.patch"))
172 (modules '((guix build utils)))
173 (snippet
174 ;; Make sure we don't use the bundled software.
175 '(for-each (lambda (d)
176 (delete-file-recursively (string-append "libcoda/" d)))
177 '("zlib" "pcre" "expat")))))
d91025e3
TD		 178 (native-inputs
179 `(("fortran" ,gfortran)
180 ("python" ,python)
181 ("python-numpy" ,python-numpy)))
182 (inputs
183 `(("zlib" ,zlib)
4b12fe5c
TD		 184 ("pcre" ,pcre)
185 ("expat" ,expat)
d91025e3
TD		 186 ("hdf4" ,hdf4-alt)
187 ("hdf5" ,hdf5)))
188 (build-system gnu-build-system)
189 (arguments
4b12fe5c
TD		 190 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
191 "LIBS= -lz -lpcre -lexpat")))
d91025e3
TD		 192 (synopsis "A common interface to various earth observation data formats")
193 (description
194 "The Common Data Access toolbox (CODA) provides a set of interfaces for
195reading remote sensing data from earth observation data files. It consists of
196command line applications and interfaces to the C, Fortran, Python, and Java
197programming languages.")
198 (home-page "https://stcorp.nl/coda")
199 (license license:gpl2+)))
200
8f8b2451
AE		 201(define-public units
202 (package
203 (name "units")
f11d2849 204 (version "2.16")
8f8b2451
AE		 205 (source (origin
206 (method url-fetch)
207 (uri (string-append "mirror://gnu/units/units-" version
208 ".tar.gz"))
209 (sha256 (base32
f11d2849 210 "11hnp3gcmcc5kci2caxw4hs6m08h2mhqs3xzqq7iafx1ha2ggwyw"))))
8f8b2451 211 (build-system gnu-build-system)
0498d248 212 (inputs
a2549713
EB		 213 `(("readline" ,readline)
214 ("python" ,python-wrapper) ;for 'units_cur' script
0498d248
EB		 215 ("python-requests" ,python-requests)))
216 (arguments
217 `(#:phases (modify-phases %standard-phases
218 (add-after 'install 'wrap-units_cur
219 (lambda* (#:key outputs #:allow-other-keys)
220 (let* ((out (assoc-ref outputs "out"))
221 (bin (string-append out "/bin")))
222 (wrap-program (string-append bin "/units_cur")
223 `("PYTHONPATH" ":" prefix
224 ,(search-path-as-string->list (getenv "PYTHONPATH"))))
225 #t))))))
8f8b2451
AE		 226 (synopsis "Conversion between thousands of scales")
227 (description
574e86f9 228 "GNU Units converts numeric quantities between units of measure. It
7c125ce0
AK		 229can handle scale changes through adaptive usage of standard scale
230prefixes (micro-, kilo-, etc.). It can also handle nonlinear
231conversions such as Fahrenheit to Celsius. Its interpreter is powerful
232enough to be used effectively as a scientific calculator.")
8f8b2451 233 (license license:gpl3+)
6fd52309 234 (home-page "https://www.gnu.org/software/units/")))
c9dfa3c7 235
61a529b4
RW		 236(define-public double-conversion
237 (package
238 (name "double-conversion")
239 (version "1.1.5")
240 (source (origin
241 (method url-fetch)
242 (uri (string-append
243 "https://github.com/floitsch/double-conversion/archive/v"
244 version ".tar.gz"))
245 (file-name (string-append name "-" version ".tar.gz"))
246 (sha256
247 (base32
248 "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83"))))
249 (build-system cmake-build-system)
250 (arguments
251 '(#:test-target "test"
252 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
253 "-DBUILD_TESTING=ON")))
254 (home-page "https://github.com/floitsch/double-conversion")
255 (synopsis "Conversion routines for IEEE doubles")
256 (description
257 "The double-conversion library provides binary-decimal and decimal-binary
258routines for IEEE doubles. The library consists of efficient conversion
259routines that have been extracted from the V8 JavaScript engine.")
260 (license license:bsd-3)))
261
182d6311
ML		 262(define-public dionysus
263 (package
264 (name "dionysus")
bd041e7f 265 (version "1.4.0")
182d6311
ML		 266 (source (origin
267 (method url-fetch)
268 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
bd041e7f 269 ".tar.xz"))
182d6311
ML		 270 (sha256
271 (base32
bd041e7f 272 "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
182d6311
ML		 273 (build-system gnu-build-system)
274 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
275 (synopsis "Local search for universal constants and scientific values")
276 (description
277 "GNU Dionysus is a convenient system for quickly retrieving the values of
278mathematical constants used in science and engineering. Values can be
279searched using a simple command-line tool, choosing from three databases:
280universal constants, atomic numbers, and constants related to
281semiconductors.")
282 (license license:gpl3+)
6fd52309 283 (home-page "https://www.gnu.org/software/dionysus/")))
182d6311 284
88bd1804
AE		 285(define-public gsl
286 (package
287 (name "gsl")
f885fc05 288 (version "2.4")
ab2cc5cd
LC		 289 (source (origin
290 (method url-fetch)
291 (uri (string-append "mirror://gnu/gsl/gsl-"
292 version ".tar.gz"))
293 (sha256
294 (base32
f885fc05 295 "16yfs5n444s03np1naj6yp1fsysd42kdscxzkg0k2yvfjixx0ijd"))
ab2cc5cd 296 (patches (search-patches "gsl-test-i686.patch"))))
88bd1804 297 (build-system gnu-build-system)
71e0f288 298 (arguments
f885fc05 299 `(;; Currently there are numerous tests that fail on "exotic"
6f766069
EF		 300 ;; architectures such as aarch64 and ppc64le.
301 ,@(if (string-prefix? "aarch64-linux"
302 (or (%current-target-system) (%current-system)))
303 '(#:tests? #f)
304 '())))
305 (home-page "https://www.gnu.org/software/gsl/")
88bd1804
AE		 306 (synopsis "Numerical library for C and C++")
307 (description
a22dc0c4
LC		 308 "The GNU Scientific Library is a library for numerical analysis in C
309and C++. It includes a wide range of mathematical routines, with over 1000
310functions in total. Subject areas covered by the library include:
311differential equations, linear algebra, Fast Fourier Transforms and random
312numbers.")
88bd1804
AE		 313 (license license:gpl3+)))
314
ba1be533
BW		 315(define-public ocaml-gsl
316 (package
317 (name "ocaml-gsl")
318 (version "1.19.3")
319 (source
320 (origin
321 (method url-fetch)
322 (uri
323 (string-append
324 "https://github.com/mmottl/gsl-ocaml/releases/download/v"
325 version"/gsl-ocaml-" version ".tar.gz"))
326 (sha256
327 (base32
328 "0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh"))))
329 (build-system ocaml-build-system)
330 (inputs
331 `(("gsl" ,gsl)))
332 (home-page "https://mmottl.github.io/gsl-ocaml")
333 (synopsis "Bindings to the GNU Scientific Library")
334 (description
335 "GSL-OCaml is an interface to the @dfn{GNU scientific library} (GSL) for
336the OCaml language.")
337 (license license:gpl3+)))
338
7adaab9f
BW		 339(define-public ocaml4.01-gsl
340 (package-with-ocaml4.01 ocaml-gsl))
341
b92eee75
AE		 342(define-public glpk
343 (package
344 (name "glpk")
445929e0 345 (version "4.65")
b92eee75
AE		 346 (source
347 (origin
348 (method url-fetch)
349 (uri (string-append "mirror://gnu/glpk/glpk-"
350 version ".tar.gz"))
351 (sha256
352 (base32
445929e0 353 "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
b92eee75
AE		 354 (build-system gnu-build-system)
355 (inputs
356 `(("gmp" ,gmp)))
357 (arguments
358 `(#:configure-flags '("--with-gmp")))
82110ef6 359 (home-page "https://www.gnu.org/software/glpk/")
79c311b8 360 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
b92eee75
AE		 361 (description
362 "GLPK is a C library for solving large-scale linear programming (LP),
363mixed integer programming (MIP), and other related problems. It supports the
364GNU MathProg modeling language, a subset of the AMPL language, and features a
365translator for the language. In addition to the C library, a stand-alone
366LP/MIP solver is included in the package.")
367 (license license:gpl3+)))
368
b146763a
AE		 369(define-public 4ti2
370 (package
371 (name "4ti2")
372 (version "1.6.7")
373 (source
374 (origin
375 (method url-fetch)
376 (uri (string-append "http://www.4ti2.de/version_" version
377 "/4ti2-" version ".tar.gz"))
378 (sha256
379 (base32
380 "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
381 (build-system gnu-build-system)
382 (native-inputs
383 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
384 (inputs
385 `(("glpk" ,glpk)
386 ("gmp" ,gmp)))
387 (home-page "http://www.4ti2.de/")
388 (synopsis "Mathematical tool suite for problems on linear spaces")
389 (description
390 "4ti2 implements algorithms for solving algebraic, geometric and
391combinatorial problems on linear spaces. Among others, it solves systems
392of linear equations, computes extreme rays of polyhedral cones, solves
393integer programming problems and computes Markov bases for statistics.")
394 (license license:gpl2+)))
395
53696f10
AE		 396(define-public cddlib
397 (package
398 (name "cddlib")
399 (version "0.94h")
400 (source
401 (origin
402 (method url-fetch)
182dde82 403 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
53696f10
AE		 404 (string-delete #\. version) ".tar.gz"))
405 (sha256
406 (base32
407 "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy"))))
408 (build-system gnu-build-system)
409 (inputs
410 `(("gmp" ,gmp)))
411 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
412 (synopsis "Library for convex hulls and extreme rays of polyhedra")
413 (description
414 "The C-library cddlib implements the Double Description Method of
415Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
416rays of a general convex polyhedron given by a system of linear inequalities
417in arbitrary dimension. It can also be used for the converse operation of
418computing convex hulls.")
419 (license license:gpl2+)))
420
865a69dd
RW		 421(define-public arpack-ng
422 (package
423 (name "arpack-ng")
c0edb5b5
LC		 424 (version "3.5.0")
425 (home-page "https://github.com/opencollab/arpack-ng")
865a69dd
RW		 426 (source
427 (origin
428 (method url-fetch)
c0edb5b5 429 (uri (string-append home-page "/archive/" version ".tar.gz"))
f586c877 430 (file-name (string-append name "-" version ".tar.gz"))
865a69dd
RW		 431 (sha256
432 (base32
c0edb5b5 433 "0f8jx3fifmj9qdp289zr7r651y1q48k1jya859rqxq62mvis7xsh"))))
865a69dd 434 (build-system gnu-build-system)
c0edb5b5
LC		 435 (arguments
436 '(#:phases (modify-phases %standard-phases
437 (add-after 'unpack 'autoreconf
438 (lambda _
439 (invoke "autoreconf" "-vfi"))))))
440 (native-inputs
441 `(("autoconf" ,autoconf)
442 ("automake" ,automake)
443 ("libtool" ,libtool)))
865a69dd
RW		 444 (inputs
445 `(("lapack" ,lapack)
19afbea1 446 ("fortran" ,gfortran)))
865a69dd
RW		 447 (synopsis "Fortran subroutines for solving eigenvalue problems")
448 (description
449 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
450large scale eigenvalue problems.")
166191b3 451 (license (license:non-copyleft "file://COPYING"
865a69dd
RW		 452 "See COPYING in the distribution."))))
453
c0edb5b5
LC		 454(define-public arpack-ng-3.3.0
455 (package
456 (inherit arpack-ng)
457 (version "3.3.0")
458 (name (package-name arpack-ng))
459 (home-page (package-home-page arpack-ng))
460 (source
461 (origin
462 (method url-fetch)
463 (uri (string-append home-page "/archive/" version ".tar.gz"))
464 (file-name (string-append name "-" version ".tar.gz"))
465 (sha256
466 (base32
467 "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
468
8c94c886
EB		 469(define-public arpack-ng-openmpi
470 (package (inherit arpack-ng)
471 (name "arpack-ng-openmpi")
472 (inputs
473 `(("mpi" ,openmpi)
474 ,@(package-inputs arpack-ng)))
475 (arguments `(#:configure-flags '("--enable-mpi")))
476 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
477
da95c817
NK		 478(define-public lapack
479 (package
480 (name "lapack")
ef39a177 481 (version "3.7.1")
da95c817
NK		 482 (source
483 (origin
484 (method url-fetch)
485 (uri (string-append "http://www.netlib.org/lapack/lapack-"
486 version ".tgz"))
487 (sha256
488 (base32
7c0d4c3a 489 "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
da95c817
NK		 490 (build-system cmake-build-system)
491 (home-page "http://www.netlib.org/lapack/")
19afbea1 492 (inputs `(("fortran" ,gfortran)
da95c817
NK		 493 ("python" ,python-2)))
494 (arguments
3ab869b6 495 `(#:configure-flags (list
3ab869b6
LC		 496 "-DBUILD_SHARED_LIBS:BOOL=YES"
497 "-DLAPACKE=ON"
498
499 ;; Build the 'LAPACKE_clatms' functions.
500 "-DLAPACKE_WITH_TMG=ON")
dc1d3cde
KK		 501 #:phases
502 (modify-phases %standard-phases
503 (add-before 'check 'patch-python
504 (lambda* (#:key inputs #:allow-other-keys)
505 (let ((python (assoc-ref inputs "python")))
506 (substitute* "lapack_testing.py"
507 (("/usr/bin/env python") python)))
508 #t)))))
da95c817
NK		 509 (synopsis "Library for numerical linear algebra")
510 (description
511 "LAPACK is a Fortran 90 library for solving the most commonly occurring
512problems in numerical linear algebra.")
166191b3 513 (license (license:non-copyleft "file://LICENSE"
da95c817 514 "See LICENSE in the distribution."))))
73fed4f8 515
b509efb3
TF		 516(define-public lapack-3.5
517 (package
518 (inherit lapack)
519 (version "3.5.0")
520 (source
521 (origin
522 (method url-fetch)
523 (uri (string-append "http://www.netlib.org/lapack/lapack-"
524 version ".tgz"))
525 (sha256
526 (base32
527 "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s"))))))
528
e1ff597a
EB		 529(define-public scalapack
530 (package
531 (name "scalapack")
532 (version "2.0.2")
533 (source
534 (origin
535 (method url-fetch)
536 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
537 version ".tgz"))
538 (sha256
539 (base32
540 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
541 (build-system cmake-build-system)
542 (inputs
543 `(("mpi" ,openmpi)
544 ("fortran" ,gfortran)
545 ("lapack" ,lapack))) ;for testing only
546 (arguments
547 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")))
548 (home-page "http://www.netlib.org/scalapack/")
549 (synopsis "Library for scalable numerical linear algebra")
550 (description
551 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
552routines on parallel distributed memory machines. ScaLAPACK solves dense and
553banded linear systems, least squares problems, eigenvalue problems, and
554singular value problems.")
555 (license (license:bsd-style "file://LICENSE"
556 "See LICENSE in the distribution."))))
557
73fed4f8 558(define-public gnuplot
5f800540
KK		 559 (package
560 (name "gnuplot")
7d873e0c 561 (version "5.0.6")
5f800540
KK		 562 (source (origin
563 (method url-fetch)
564 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
565 version "/gnuplot-"
566 version ".tar.gz"))
567 (sha256
568 (base32
7d873e0c 569 "0q5lr6nala3ln6f3yp6g17ziymb9r9gx9zylnw1y3hjmwl9lggjv"))))
5f800540
KK		 570 (build-system gnu-build-system)
571 (inputs `(("readline" ,readline)
572 ("cairo" ,cairo)
573 ("pango" ,pango)
6e64766a
DM		 574 ("gd" ,gd)
575 ("lua" ,lua)))
612a387f
RW		 576 (native-inputs
577 `(("pkg-config" ,pkg-config)
578 ("texlive" ,texlive-tiny)))
5f800540
KK		 579 (home-page "http://www.gnuplot.info")
580 (synopsis "Command-line driven graphing utility")
581 (description "Gnuplot is a portable command-line driven graphing
35b9e423 582utility. It was originally created to allow scientists and students to
73fed4f8 583visualize mathematical functions and data interactively, but has grown to
35b9e423 584support many non-interactive uses such as web scripting. It is also used as a
73fed4f8 585plotting engine by third-party applications like Octave.")
5f800540
KK		 586 ;; X11 Style with the additional restriction that derived works may only be
587 ;; distributed as patches to the original.
588 (license (license:fsf-free
589 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
668c06ac 590
32f70e1f
TD		 591(define-public gctp
592 (package
593 (name "gctp")
594 (version "2.0.0")
595 (source
596 (origin
597 (method url-fetch)
598 (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
599 version ".tar.gz"))
600 (file-name (string-append name "-" version ".tar.gz"))
601 (sha256
602 (base32
603 "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
604 (native-inputs
605 `(("fortran" ,gfortran)))
606 (build-system gnu-build-system)
607 (synopsis "General Cartographic Transformation Package (GCTP)")
608 (description
609 "The General Cartographic Transformation Package (GCTP) is a system of
610software routines designed to permit the transformation of coordinate pairs
611from one map projection to another. The GCTP is the standard computer
612software used by the National Mapping Division for map projection
613computations.")
614 (home-page "https://github.com/OkoSanto/GCTP")
0f7cd95b 615 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
32f70e1f 616
becbbefc
TD		 617(define-public hdf4
618 (package
619 (name "hdf4")
0abf5264 620 (version "4.2.13")
becbbefc
TD		 621 (source
622 (origin
623 (method url-fetch)
624 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
625 version "/src/hdf-" version ".tar.bz2"))
626 (sha256
0abf5264 627 (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
15ca49b2
AE		 628 (patches (search-patches "hdf4-architectures.patch"
629 "hdf4-reproducibility.patch"
becbbefc 630 "hdf4-shared-fortran.patch"))))
becbbefc
TD		 631 (build-system gnu-build-system)
632 (native-inputs
633 `(("gfortran" ,gfortran)
634 ("bison" ,bison)
635 ("flex" ,flex)))
636 (inputs
637 `(("zlib" ,zlib)
638 ("libjpeg" ,libjpeg)))
639 (arguments
640 `(#:parallel-tests? #f
641 #:configure-flags '("--enable-shared")
642 #:phases
643 (modify-phases %standard-phases
953a12fa
EF		 644 ;; This is inspired by two of Debian's patches.
645 (add-before 'configure 'add-more-aarch64-support
646 (lambda _
647 (substitute* '("mfhdf/ncgen/ncgen.l"
648 "mfhdf/ncgen/ncgenyy.c"
649 "mfhdf/libsrc/netcdf.h.in")
650 (("AIX5L64") "__aarch64__"))
651 #t))
becbbefc
TD		 652 (add-before 'configure 'patchbuild
653 (lambda _
654 (substitute*
655 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
656 (("/bin/rm") "rm")
657 (("/bin/mkdir") "mkdir"))
658 (substitute* (find-files "." "^Makefile\\.in$")
659 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
660-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
661 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
662-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
953a12fa 663-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
e464b455
TD		 664 #t))
665 (add-after 'configure 'patch-settings
666 (lambda _
667 ;; libhdf4.settings contains the full path of the
668 ;; compilers used, and its contents are included in
669 ;; .so-files. We truncate the hashes to avoid
670 ;; unnecessary store references to those compilers:
671 (substitute* "libhdf4.settings"
672 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
673 (string-append prefix (string-take hash 10) "...")))
674 #t))
675 )))
becbbefc
TD		 676 (home-page "https://www.hdfgroup.org/products/hdf4/")
677 (synopsis
678 "Library and multi-object file format for storing and managing data")
679 (description "HDF4 is a library and multi-object file format for storing
680and managing data between machines. HDF4 is an older hierarchical data format,
681incompatible with HDF5.")
682 (license
683 (license:non-copyleft
684 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
685
686(define-public hdf4-alt
687 (package
688 (inherit hdf4)
689 (name "hdf4-alt")
690 (arguments
691 (substitute-keyword-arguments (package-arguments hdf4)
692 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
693 (synopsis
694 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
695
7ee3f1a2
JD		 696(define-public hdf5
697 (package
698 (name "hdf5")
2da63064 699 (version "1.8.19")
7ee3f1a2
JD		 700 (source
701 (origin
702 (method url-fetch)
2da63064
TD		 703 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
704 "hdf5-" (version-major+minor version)
705 "/hdf5-" version "/src/hdf5-"
dcd9d163
LF		 706 version ".tar.bz2")
707 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
708 "current"
709 (apply string-append
710 (take (string-split version #\.) 2))
711 "/src/hdf5-" version ".tar.bz2")))
7ee3f1a2 712 (sha256
2da63064 713 (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
b8d9c93b 714 (patches (list (search-patch "hdf5-config-date.patch")))))
7ee3f1a2 715 (build-system gnu-build-system)
12ed1216
AE		 716 (inputs
717 `(("zlib" ,zlib)))
e3a1a1de
TD		 718 (native-inputs
719 `(("gfortran" ,gfortran)))
720 (outputs '("out" ; core library
721 "fortran")) ; fortran interface
7ee3f1a2 722 (arguments
62126576 723 `(;; Some of the users, notably Flann, need the C++ interface.
e3a1a1de
TD		 724 #:configure-flags '("--enable-cxx"
725 "--enable-fortran"
726 "--enable-fortran2003")
4dba441c
RW		 727 ;; Use -fPIC to allow the R bindings to link with the static libraries
728 #:make-flags (list "CFLAGS=-fPIC"
729 "CXXFLAGS=-fPIC")
62126576 730 #:phases
f622e212
EB		 731 (modify-phases %standard-phases
732 (add-before 'configure 'patch-configure
e3a1a1de 733 (lambda* (#:key outputs #:allow-other-keys)
f622e212 734 (substitute* "configure"
b8d9c93b 735 (("/bin/mv") "mv"))
e3a1a1de
TD		 736 (substitute* "fortran/src/Makefile.in"
737 (("libhdf5_fortran_la_LDFLAGS =")
738 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
739 (assoc-ref outputs "fortran") "/lib")))
740 (substitute* "hl/fortran/src/Makefile.in"
741 (("libhdf5hl_fortran_la_LDFLAGS =")
742 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
743 (assoc-ref outputs "fortran") "/lib")))
b8d9c93b 744 #t))
fd0378a1
TD		 745 (add-after 'configure 'patch-settings
746 (lambda _
747 ;; libhdf5.settings contains the full path of the
748 ;; compilers used, and its contents are included in
749 ;; libhdf5.so. We truncate the hashes to avoid
750 ;; unnecessary store references to those compilers:
751 (substitute* "src/libhdf5.settings"
752 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
d8f46d52
RW		 753 (string-append prefix (string-take hash 10) "..."))
754 ;; Don't record the build-time kernel version to make the
755 ;; settings file reproducible.
756 (("Uname information:.*")
757 "Uname information: Linux\n"))
b8d9c93b 758 #t))
f622e212
EB		 759 (add-after 'install 'patch-references
760 (lambda* (#:key inputs outputs #:allow-other-keys)
761 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
762 (zlib (assoc-ref inputs "zlib")))
763 (substitute* (find-files bin "h5p?cc")
764 (("-lz" lib)
765 (string-append "-L" zlib "/lib " lib)))
e3a1a1de
TD		 766 #t)))
767 (add-after 'install 'split
768 (lambda* (#:key inputs outputs #:allow-other-keys)
769 ;; Move all fortran-related files
770 (let* ((out (assoc-ref outputs "out"))
771 (bin (string-append out "/bin"))
772 (lib (string-append out "/lib"))
773 (inc (string-append out "/include"))
774 (ex (string-append out "/share/hdf5_examples/fortran"))
775 (fort (assoc-ref outputs "fortran"))
776 (fbin (string-append fort "/bin"))
777 (flib (string-append fort "/lib"))
778 (finc (string-append fort "/include"))
779 (fex (string-append fort "/share/hdf5_examples/fortran")))
780 (mkdir-p fbin)
781 (mkdir-p flib)
782 (mkdir-p finc)
783 (mkdir-p fex)
784 (rename-file (string-append bin "/h5fc")
785 (string-append fbin "/h5fc"))
786 (for-each (lambda (file)
787 (rename-file file
788 (string-append flib "/" (basename file))))
789 (find-files lib ".*fortran.*"))
790 (for-each (lambda (file)
791 (rename-file file
792 (string-append finc "/" (basename file))))
793 (find-files inc ".*mod"))
794 (for-each (lambda (file)
795 (rename-file file
796 (string-append fex "/" (basename file))))
797 (find-files ex ".*"))
798 (delete-file-recursively ex))
799 #t)))))
7ee3f1a2 800 (home-page "http://www.hdfgroup.org")
516e93f8 801 (synopsis "Management suite for extremely large and complex data")
7ee3f1a2
JD		 802 (description "HDF5 is a suite that makes possible the management of
803extremely large and complex data collections.")
d4bf49b1
EB		 804 (license (license:x11-style
805 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
7ee3f1a2 806
2fd26d05
TD		 807(define-public hdf-java
808 (package
809 (name "hdf-java")
810 (version "3.3.2")
811 (source
812 (origin
813 (method url-fetch)
814 (uri (string-append
815 "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
816 version "/src/CMake-hdfjava-" version ".tar.gz"))
817 (sha256
818 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
819 (modules '((guix build utils)))
820 (snippet ; Make sure we don't use the bundled sources and binaries.
821 `(begin
822 (for-each delete-file
823 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
824 "HDF4.tar.gz" "HDF5.tar.gz"))
825 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))))))
826 (build-system gnu-build-system)
827 (native-inputs
828 `(("jdk" ,icedtea "jdk")
829 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
830 ;; For tests:
831 ("hamcrest-core" ,java-hamcrest-core)
832 ("junit" ,java-junit)
833 ("slf4j-simple" ,java-slf4j-simple)))
834 (inputs
835 `(("hdf4" ,hdf4)
836 ("hdf5" ,hdf5)
837 ("zlib" ,zlib)
838 ("libjpeg" ,libjpeg)
839 ("slf4j-api" ,java-slf4j-api)))
840 (arguments
841 `(#:configure-flags
842 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
843 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
844 (assoc-ref %build-inputs "jdk") "/lib" )
845 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
846 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
847
848 #:make-flags
849 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
850 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
851 (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
852 (string-append "JPEGLIB="
853 (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
854 "LLEXT=so")
855
856 #:phases
857 (modify-phases %standard-phases
858 (add-before 'configure 'chdir-to-source
859 (lambda _ (chdir ,(string-append "hdfjava-" version))))
860 (add-before 'configure 'patch-build
861 (lambda* (#:key inputs outputs #:allow-other-keys)
862 (substitute* "configure"
863 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
864 (("/bin/cat") (which "cat")))
865 ;; Set classpath for compilation
866 (substitute* '("hdf/hdf5lib/Makefile.in"
867 "hdf/hdf5lib/exceptions/Makefile.in"
868 "hdf/hdflib/Makefile.in")
869 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
870 (string-append (assoc-ref inputs "slf4j-api")
871 "/share/java/slf4j-api.jar")))
872 ;; Replace outdated config.sub and config.guess:
873 (with-directory-excursion "config"
874 (for-each (lambda (file)
875 (copy-file
876 (string-append (assoc-ref inputs "automake")
877 "/share/automake-1.15/" file) file))
878 '("config.sub" "config.guess")))
879 (mkdir-p (string-append (assoc-ref outputs "out")))
880 ;; Set classpath for tests
881 (let* ((build-dir (getcwd))
882 (lib (string-append build-dir "/lib"))
883 (jhdf (string-append lib "/jhdf.jar"))
884 (jhdf5 (string-append lib "/jhdf5.jar"))
885 (testjars
886 (map (lambda (i)
887 (string-append (assoc-ref inputs i)
888 "/share/java/" i ".jar"))
889 '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
890 (class-path
891 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
892
893 (substitute* '("test/hdf5lib/Makefile.in"
894 "test/hdf5lib/junit.sh.in"
895 "examples/runExample.sh.in")
896 (("/usr/bin/test")
897 (string-append (assoc-ref inputs "coreutils")
898 "/bin/test"))
899 (("/usr/bin/uname")
900 (string-append (assoc-ref inputs "coreutils")
901 "/bin/uname"))
902 (("CLASSPATH=[^\n]*")
903 (string-append "CLASSPATH=" class-path)))
904 (setenv "CLASSPATH" class-path))
905 #t))
906 (add-before 'check 'build-examples
907 (lambda _
908 (zero? (apply system* `("javac"
909 ,@(find-files "examples" ".*\\.java")))))))
910
911 #:parallel-build? #f
912
913 #:parallel-tests? #f ))
914 (home-page "https://support.hdfgroup.org/products/java")
915 (synopsis "Java interface for the HDF4 and HDF5 libraries")
916 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
917the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
918implemented in C.")
919
920 ;; BSD-style license:
921 (license (license:x11-style
922 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
923/current/src/unpacked/COPYING"))))
924
d3c4f3bb
TD		 925(define-public hdf-eos2
926 (package
927 (name "hdf-eos2")
928 (version "19.1.0")
929 (source
930 (origin
931 (method url-fetch)
932 (uri "ftp://edhs1.gsfc.nasa.gov\
933/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
934 (sha256
935 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
936 (patches (search-patches "hdf-eos2-remove-gctp.patch"
937 "hdf-eos2-build-shared.patch"
938 "hdf-eos2-fortrantests.patch"))))
939 (build-system gnu-build-system)
940 (native-inputs
941 `(("gfortran" ,gfortran)))
942 (inputs
943 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
944 ("zlib" ,zlib)
945 ("libjpeg" ,libjpeg)
946 ("gctp" ,gctp)))
947 (arguments
948 `( #:configure-flags '("--enable-install-include" "--enable-shared"
949 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
950 #:parallel-tests? #f))
951 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
952 (synopsis "HDF4-based data format for NASA's Earth Observing System")
953 (description "HDF-EOS2 is a software library built on HDF4 which supports
954the construction of data structures used in NASA's Earth Observing
955System (Grid, Point and Swath).")
956
957 ;; Source files carry a permissive license header.
958 (license (license:non-copyleft home-page))))
959
0f43f835
TD		 960(define-public hdf-eos5
961 (package
962 (name "hdf-eos5")
963 (version "1.15")
964 (source (origin
965 (method url-fetch)
966 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
967/edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
968 (sha256
969 (base32
970 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
971 (patches (search-patches "hdf-eos5-build-shared.patch"
972 "hdf-eos5-remove-gctp.patch"
973 "hdf-eos5-fix-szip.patch"
974 "hdf-eos5-fortrantests.patch"))))
975 (native-inputs
976 `(("gfortran" ,gfortran)))
977 (build-system gnu-build-system)
978 (inputs
979 `(("hdf5" ,hdf5)
980 ("zlib" ,zlib)
981 ("gctp" ,gctp)))
982 (arguments
983 `(#:configure-flags '("--enable-install-include" "--enable-shared"
984 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
985 #:parallel-tests? #f))
986 (synopsis "HDF5-based data format for NASA's Earth Observing System")
987 (description
988 "HDF-EOS5 is a software library built on HDF5 to support the construction
989of data structures used in NASA's Earth Observing System (Grid, Point and
990Swath).")
991 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
992
993 ;; Source files carry a permissive license header.
994 (license (license:non-copyleft home-page))))
995
c8378eea
EB		 996(define-public hdf5-parallel-openmpi
997 (package (inherit hdf5)
998 (name "hdf5-parallel-openmpi")
999 (inputs
1000 `(("mpi" ,openmpi)
1001 ,@(package-inputs hdf5)))
1002 (arguments
1003 (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
1004 ,@(package-arguments hdf5))
1005 ((#:phases phases)
1006 `(modify-phases ,phases
1007 (add-before 'check 'patch-tests
1008 (lambda _
1009 ;; OpenMPI's mpirun will exit with non-zero status if it
1010 ;; detects an "abnormal termination", i.e. any process not
1011 ;; calling MPI_Finalize(). Since the test is explicitely
1012 ;; avoiding MPI_Finalize so as not to have at_exit and thus
1013 ;; H5C_flush_cache from being called, mpirun will always
1014 ;; complain, so turn this test off.
1015 (substitute* "testpar/Makefile"
1016 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1017 (string-append front back "\n")))
1018 (substitute* "tools/h5diff/testph5diff.sh"
1019 (("/bin/sh") (which "sh")))
1020 #t))))))
1021 (synopsis "Management suite for data with parallel IO support")))
1022
00775104
EB		 1023(define-public h5check
1024 (package
1025 (name "h5check")
1026 (version "2.0.1")
1027 (source
1028 (origin
1029 (method url-fetch)
1030 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
1031 "h5check/src/h5check-" version ".tar.gz"))
1032 (sha256
1033 (base32
1034 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1035 (build-system gnu-build-system)
1036 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
1037 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1038 (synopsis "HDF5 format checker")
1039 (description "@code{h5check} is a validation tool for verifying that an
1040HDF5 file is encoded according to the HDF File Format Specification.")
1041 (license (license:x11-style "file://COPYING"))))
1042
a53d6719
JD		 1043(define-public itpp
1044 (package
1045 (name "itpp")
1046 (version "4.3.1")
1047 (source (origin
1048 (method url-fetch)
1049 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1050 version "/itpp-"
1051 version ".tar.gz"))
1052 (sha256
1053 (base32
1054 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1055 (build-system cmake-build-system)
1056 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1057 (inputs `(("lapack" ,lapack)
1058 ("fftw" ,fftw)))
3a4d5df2
RW		 1059 ;; FIXME: Even though the fonts are available dvips complains:
1060 ;; "Font cmmi10 not found; characters will be left blank."
1061 (native-inputs
1062 `(("texlive" ,texlive-tiny)
1063 ("ghostscript" ,ghostscript)
1064 ("doxygen" ,doxygen)))
a53d6719
JD		 1065 (home-page "http://itpp.sourceforge.net")
1066 (synopsis "C++ library of maths, signal processing and communication classes")
1067 (description "IT++ is a C++ library of mathematical, signal processing and
1068communication classes and functions. Its main use is in simulation of
1069communication systems and for performing research in the area of
1070communications. The kernel of the library consists of generic vector and
1071matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1072similar to MATLAB, GNU Octave or SciPy.")
1073 (license license:gpl3+)))
1074
889187a4
EB		 1075(define-public netcdf
1076 (package
1077 (name "netcdf")
a4b0bfb1 1078 (version "4.4.1.1")
889187a4
EB		 1079 (source
1080 (origin
1081 (method url-fetch)
1082 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1083 "netcdf-" version ".tar.gz"))
1084 (sha256
1085 (base32
a4b0bfb1
EB		 1086 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1087 (patches (search-patches "netcdf-date-time.patch"
1088 "netcdf-tst_h_par.patch"))))
889187a4
EB		 1089 (build-system gnu-build-system)
1090 (native-inputs
1091 `(("m4" ,m4)
1092 ("doxygen" ,doxygen)
1093 ("graphviz" ,graphviz)))
1094 (inputs
db825570
TD		 1095 `(("hdf4" ,hdf4-alt)
1096 ("hdf5" ,hdf5)
1097 ("zlib" ,zlib)
1098 ("libjpeg" ,libjpeg)))
889187a4 1099 (arguments
db825570 1100 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
43d01672
TD		 1101
1102 #:phases (modify-phases %standard-phases
1103 (add-before 'configure 'fix-source-date
1104 (lambda _
1105 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1106 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1107 ;; to '1st hour of the current day', and therefore makes the
1108 ;; package not reproducible.
1109 (substitute* "./configure"
1110 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1111 "date --date='@0'"))
1112 #t))
1113 (add-after 'configure 'patch-settings
1114 (lambda _
1115 ;; libnetcdf.settings contains the full filename of the compilers
1116 ;; used to build the library. We truncate the hashes of those
1117 ;; filenames to avoid unnecessary references to the corresponding
1118 ;; store items.
1119 (substitute* "libnetcdf.settings"
1120 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1121 (string-append prefix (string-take hash 10) "...")))
1122 #t)))
1123
889187a4
EB		 1124 #:parallel-tests? #f)) ;various race conditions
1125 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
1126 (synopsis "Library for scientific data")
1127 (description "NetCDF is an interface for scientific data access and a
1128software library that provides an implementation of the interface. The netCDF
1129library defines a machine-independent format for representing scientific data.
1130Together, the interface, library, and format support the creation, access, and
1131sharing of scientific data.")
1132 (license (license:x11-style "file://COPYRIGHT"))))
1133
1134(define-public netcdf-parallel-openmpi
1135 (package (inherit netcdf)
1136 (name "netcdf-parallel-openmpi")
1137 (inputs
1138 `(("mpi" ,openmpi)
1139 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1140 (package-inputs netcdf))))
1141 ;; TODO: Replace pkg-config references in nc-config with absolute references
1142 (arguments
1143 (substitute-keyword-arguments (package-arguments netcdf)
1144 ((#:configure-flags flags)
1145 `(cons* "CC=mpicc" "CXX=mpicxx"
1146 "--enable-parallel-tests"
1147 ;; Shared libraries not supported with parallel IO.
1148 "--disable-shared" "--with-pic"
1149 ,flags))))))
1150
300200b6
TD		 1151(define-public netcdf-fortran
1152 (package
1153 (name "netcdf-fortran")
1154 (version "4.4.4")
1155 (source (origin
1156 (method url-fetch)
1157 (uri (string-append
1158 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1159 version ".tar.gz"))
1160 (sha256
1161 (base32
1162 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1163 (build-system gnu-build-system)
1164 (arguments
1165 `(#:parallel-tests? #f))
1166 (inputs
1167 `(("netcdf" ,netcdf)))
1168 (native-inputs
1169 `(("gfortran" ,gfortran)))
1170 (synopsis "Fortran interface for the netCDF library")
1171 (description (package-description netcdf))
1172 (home-page (package-home-page netcdf))
1173 (license (package-license netcdf))))
1174
1b39a196
RJ		 1175(define-public nlopt
1176 (package
1177 (name "nlopt")
1178 (version "2.4.2")
1179 (source (origin
1180 (method url-fetch)
1181 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1182 version ".tar.gz"))
1183 (sha256
1184 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1185 (build-system gnu-build-system)
1186 (arguments
1187 `(;; Shared libraries are not built by default. They are required to
1188 ;; build the Guile, Octave, and Python bindings.
1189 #:configure-flags '("--enable-shared")
1190
1191 #:phases
1192 (modify-phases %standard-phases
1193 (add-before 'configure 'set-libnlopt-file-name
1194 (lambda* (#:key outputs #:allow-other-keys)
1195 ;; Make sure the Scheme module refers to the library by its
1196 ;; absolute file name (we cannot do that from a snippet
1197 ;; because the expansion of @libdir@ contains
1198 ;; ${exec_prefix}.)
1199 (let ((out (assoc-ref outputs "out")))
1200 (substitute* "swig/nlopt.scm.in"
1201 (("libnlopt")
1202 (string-append out "/lib/libnlopt")))
1203 #t))))))
1204 (inputs `(("guile" ,guile-2.0)))
1205 (native-inputs `(("pkg-config" ,pkg-config)))
1206 (home-page "http://ab-initio.mit.edu/wiki/")
1207 (synopsis "Library for nonlinear optimization")
1208 (description "NLopt is a library for nonlinear optimization, providing a
1209common interface for a number of different free optimization routines available
1210online as well as original implementations of various other algorithms.")
1211 (license license:lgpl2.1+)))
1212
005c787d
LC		 1213(define-public ipopt
1214 (package
1215 (name "ipopt")
1216 (version "3.12.5")
1217 (source (origin
1218 (method url-fetch)
1219 (uri (string-append
1220 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1221 version".tgz"))
1222 (sha256
1223 (base32
1224 "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
1225 (modules '((guix build utils)))
1226 (snippet
1227 ;; Make sure we don't use the bundled software.
1228 '(delete-file-recursively "ThirdParty"))))
1229 (build-system gnu-build-system)
ad1c4537
LC		 1230 (arguments
1231 '(#:phases (modify-phases %standard-phases
1232 (add-after 'install 'add--L-flags-in-ipopt.pc
1233 (lambda* (#:key inputs outputs #:allow-other-keys)
1234 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1235 ;; move it to "Libs.private" where it belongs, and add a
1236 ;; '-L' flag for LAPACK.
1237 (let ((out (assoc-ref outputs "out"))
1238 (lapack (assoc-ref inputs "lapack")))
1239 (substitute* (string-append out "/lib/pkgconfig/"
1240 "ipopt.pc")
1241 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1242 (string-append "Libs: " before " " after "\n"
1243 "Libs.private: " before
1244 "-L" lapack "/lib -llapack -lblas "
1245 after "\n")))
1246 #t))))))
005c787d
LC		 1247 (native-inputs
1248 `(("gfortran" ,gfortran)))
1249 (inputs
1250 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
ad1c4537 1251 `(("lapack" ,lapack))) ;for both libblas and liblapack
005c787d
LC		 1252 (home-page "http://www.coin-or.org")
1253 (synopsis "Large-scale nonlinear optimizer")
1254 (description
1255 "The Interior Point Optimizer (IPOPT) is a software package for
1256large-scale nonlinear optimization. It provides C++, C, and Fortran
1257interfaces.")
1258 (license license:epl1.0)))
1259
f9940ef1
LC		 1260(define-public ceres
1261 (package
1262 (name "ceres-solver")
e0bee0de 1263 (version "1.14.0")
f9940ef1
LC		 1264 (home-page "http://ceres-solver.org/")
1265 (source (origin
1266 (method url-fetch)
1267 (uri (string-append home-page "ceres-solver-"
1268 version ".tar.gz"))
1269 (sha256
1270 (base32
e0bee0de 1271 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
f9940ef1
LC		 1272 (build-system cmake-build-system)
1273 (arguments
1274 ;; TODO: Build HTML user documentation and install separately.
bc3a2e35 1275 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
f9940ef1
LC		 1276 "-DBUILD_SHARED_LIBS=ON")
1277
1278 #:phases (modify-phases %standard-phases
1279 (add-before 'configure 'set-library-directory
1280 (lambda _
1281 ;; Install libraries to lib/, not lib64/.
1282 (substitute* "internal/ceres/CMakeLists.txt"
1283 (("set\\(LIB_SUFFIX \"64\"\\)")
1284 "set(LIB_SUFFIX \"\")"))
1285 #t)))))
1286 (native-inputs
1287 `(("pkg-config" ,pkg-config)))
468e0b18
LC		 1288 (propagated-inputs
1289 `(("glog" ,glog))) ;for #include <glog/glog.h>
f9940ef1
LC		 1290 (inputs
1291 `(("eigen" ,eigen)
1292 ("blas" ,openblas)
1293 ("lapack" ,lapack)
1294 ("suitesparse" ,suitesparse)
1295 ("gflags" ,gflags)))
1296 (synopsis "C++ library for solving large optimization problems")
1297 (description
1298 "Ceres Solver is a C++ library for modeling and solving large,
1299complicated optimization problems. It is a feature rich, mature and
1300performant library which has been used in production since 2010. Ceres Solver
1301can solve two kinds of problems:
1302@enumerate
1303@item non-linear least squares problems with bounds constraints;
1304@item general unconstrained optimization problems.
1305@end enumerate\n")
1306 (license license:bsd-3)))
1307
668c06ac 1308;; For a fully featured Octave, users are strongly recommended also to install
5ca4fe96 1309;; the following packages: less, ghostscript, gnuplot.
668c06ac
JD		 1310(define-public octave
1311 (package
1312 (name "octave")
47653b39 1313 (version "4.2.2")
668c06ac
JD		 1314 (source
1315 (origin
1316 (method url-fetch)
1317 (uri (string-append "mirror://gnu/octave/octave-"
f5a077b1 1318 version ".tar.lz"))
668c06ac
JD		 1319 (sha256
1320 (base32
47653b39 1321 "0pkkz1vazsh7ipffb09q0nc2jgx6q27pkkngygjij6jrpcly5zsp"))))
668c06ac
JD		 1322 (build-system gnu-build-system)
1323 (inputs
1324 `(("lapack" ,lapack)
1325 ("readline" ,readline)
181170c6 1326 ("gl2ps" ,gl2ps)
668c06ac 1327 ("glpk" ,glpk)
1ec78e9d
EB		 1328 ("fftw" ,fftw)
1329 ("fftwf" ,fftwf)
1330 ("arpack" ,arpack-ng)
668c06ac
JD		 1331 ("pcre" ,pcre)
1332 ("fltk" ,fltk)
1333 ("fontconfig" ,fontconfig)
1334 ("freetype" ,freetype)
40029cbe 1335 ("hdf5" ,hdf5)
668c06ac
JD		 1336 ("libxft" ,libxft)
1337 ("mesa" ,mesa)
1ec78e9d 1338 ("glu" ,glu)
9f913401
AI		 1339 ("zlib" ,zlib)
1340 ("curl" ,curl)
5ca4fe96 1341 ("texinfo" ,texinfo)
9f913401 1342 ("graphicsmagick" ,graphicsmagick)))
668c06ac 1343 (native-inputs
f5a077b1
EF		 1344 `(("lzip" ,lzip)
1345 ("gfortran" ,gfortran)
668c06ac
JD		 1346 ("pkg-config" ,pkg-config)
1347 ("perl" ,perl)
1ec78e9d
EB		 1348 ;; The following inputs are not actually used in the build process.
1349 ;; However, the ./configure gratuitously tests for their existence and
1350 ;; assumes that programs not present at build time are also not, and
1351 ;; can never be, available at run time! If these inputs are therefore
1352 ;; not present, support for them will be built out. However, Octave
1353 ;; will still run without them, albeit without the features they
668c06ac
JD		 1354 ;; provide.
1355 ("less" ,less)
668c06ac
JD		 1356 ("ghostscript" ,ghostscript)
1357 ("gnuplot" ,gnuplot)))
1358 (arguments
b7b27a8f
KY		 1359 `(#:configure-flags
1360 (list (string-append "--with-shell="
1361 (assoc-ref %build-inputs "bash")
5ca4fe96
AI		 1362 "/bin/sh"))
1363 #:phases
1364 (modify-phases %standard-phases
1365 (add-after 'configure 'configure-makeinfo
1366 (lambda* (#:key inputs #:allow-other-keys)
1367 (substitute* "libinterp/corefcn/help.cc"
1368 (("Vmakeinfo_program = \"makeinfo\"")
1369 (string-append "Vmakeinfo_program = \""
1370 (assoc-ref inputs "texinfo")
1371 "/bin/makeinfo\"")))
1372 #t)))))
f5a077b1 1373 (home-page "https://www.gnu.org/software/octave/")
668c06ac 1374 (synopsis "High-level language for numerical computation")
1ec78e9d
EB		 1375 (description "GNU Octave is a high-level interpreted language that is
1376specialized for numerical computations. It can be used for both linear and
1377non-linear applications and it provides great support for visualizing results.
1378Work may be performed both at the interactive command-line as well as via
1379script files.")
668c06ac 1380 (license license:gpl3+)))
3de01d3f 1381
5d4bd4cc
PG		 1382(define-public opencascade-oce
1383 (package
1384 (name "opencascade-oce")
1385 (version "0.17.2")
1386 (source
1387 (origin
1388 (method url-fetch)
1389 (uri (string-append
1390 "https://github.com/tpaviot/oce/archive/OCE-"
1391 version
1392 ".tar.gz"))
a4f393b7 1393 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
5d4bd4cc
PG		 1394 (sha256
1395 (base32
1396 "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
1397 (build-system cmake-build-system)
1398 (arguments
1399 '(#:configure-flags
1400 (list "-DOCE_TESTING:BOOL=ON"
1401 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1402 "-DOCE_DRAW:BOOL=ON"
1403 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1404 (assoc-ref %outputs "out"))
1405 "-UCMAKE_INSTALL_RPATH")))
1406 (inputs
1407 `(("freetype" ,freetype)
1408 ("glu" ,glu)
1409 ("libxmu" ,libxmu)
1410 ("mesa" ,mesa)
1411 ("tcl" ,tcl)
1412 ("tk" ,tk)))
1413 (native-inputs
1414 `(("python" ,python-wrapper)))
1415 (home-page "https://github.com/tpaviot/oce")
1416 (synopsis "Libraries for 3D modeling and numerical simulation")
1417 (description
1418 "Open CASCADE is a set of libraries for the development of applications
1419dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1420C++ class libraries providing services for 3D surface and solid modeling, CAD
1421data exchange, and visualization. It is used for development of specialized
1422software dealing with 3D models in design (CAD), manufacturing (CAM),
1423numerical simulation (CAE), measurement equipment (CMM), and quality
1424control (CAQ) domains.
1425
1426This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1427patches, improvements, and experiments contributed by users over the official
1428Open CASCADE library.")
1429 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1430 ; use of header files; see
1431 ; OCCT_LGPL_EXCEPTION.txt
1432 license:public-domain; files
1433 ; src/Standard/Standard_StdAllocator.hxx and
1434 ; src/NCollection/NCollection_StdAllocator.hxx
1435 license:expat; file src/OpenGl/OpenGl_glext.h
1436 license:bsd-3)))); test framework gtest
1437
3de01d3f
EB		 1438(define-public gmsh
1439 (package
1440 (name "gmsh")
8a4d14fa 1441 (version "2.16.0")
3de01d3f
EB		 1442 (source
1443 (origin
1444 (method url-fetch)
1c79e086 1445 (uri (string-append "http://gmsh.info/src/gmsh-"
3de01d3f
EB		 1446 version "-source.tgz"))
1447 (sha256
8a4d14fa 1448 (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
3de01d3f
EB		 1449 (modules '((guix build utils)))
1450 (snippet
1451 ;; Remove non-free METIS code
1452 '(delete-file-recursively "contrib/Metis"))))
1453 (build-system cmake-build-system)
3de01d3f
EB		 1454 (propagated-inputs
1455 `(("fltk" ,fltk)
19afbea1 1456 ("gfortran" ,gfortran)
3de01d3f 1457 ("gmp" ,gmp)
40029cbe 1458 ("hdf5" ,hdf5)
3de01d3f
EB		 1459 ("lapack" ,lapack)
1460 ("mesa" ,mesa)
85f41902 1461 ("glu" ,glu)
45548139 1462 ("opencascade-oce" ,opencascade-oce)
3de01d3f
EB		 1463 ("libx11" ,libx11)
1464 ("libxext" ,libxext)))
66395a61
EF		 1465 (inputs
1466 `(("fontconfig" ,fontconfig)
1467 ("libxft" ,libxft)))
3de01d3f
EB		 1468 (arguments
1469 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1470 "-DENABLE_BUILD_SHARED:BOOL=ON"
45548139 1471 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
3de01d3f
EB		 1472 (home-page "http://www.geuz.org/gmsh/")
1473 (synopsis "3D finite element grid generator")
edf684ef
EB		 1474 (description "Gmsh is a 3D finite element grid generator with a built-in
1475CAD engine and post-processor. Its design goal is to provide a fast, light
1476and user-friendly meshing tool with parametric input and advanced
1477visualization capabilities. Gmsh is built around four modules: geometry,
1478mesh, solver and post-processing. The specification of any input to these
1479modules is done either interactively using the graphical user interface or in
1480ASCII text files using Gmsh's own scripting language.")
3de01d3f 1481 (license license:gpl2+)))
b9100e2f 1482
6d5f63b6
JD		 1483(define-public maxflow
1484 (package
1485 (name "maxflow")
1486 (version "3.04")
1487 (source (origin
1488 (method git-fetch)
1489 (uri (git-reference
1490 (url "https://github.com/gerddie/maxflow.git")
1491 (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
1492 (file-name (string-append name "-" version "-checkout"))
1493 (sha256
1494 (base32
1495 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1496 (build-system cmake-build-system)
1497 (home-page "http://pub.ist.ac.at/~vnk/software.html")
1498 (synopsis "Library implementing Maxflow algorithm")
1499 (description "An implementation of the maxflow algorithm described in
1500@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1501Energy Minimization in Computer Vision.\n
1502Yuri Boykov and Vladimir Kolmogorov.\n
1503In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1504September 2004}")
1505 (license license:gpl3+)))
1506
b9100e2f
EB		 1507(define-public petsc
1508 (package
1509 (name "petsc")
6fec298d 1510 (version "3.8.0")
b9100e2f
EB		 1511 (source
1512 (origin
1513 (method url-fetch)
1514 ;; The *-lite-* tarball does not contain the *large* documentation
1515 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1516 "petsc-lite-" version ".tar.gz"))
1517 (sha256
6fec298d 1518 (base32 "1lajbk3c29hnh83v6cbmm3a8wv6bdykh0p70kwrr4vrnizalk88s"))))
b9100e2f
EB		 1519 (build-system gnu-build-system)
1520 (native-inputs
6fec298d 1521 `(("python" ,python-2)))
b9100e2f 1522 (inputs
19afbea1 1523 `(("gfortran" ,gfortran)
b9100e2f 1524 ("lapack" ,lapack)
f258212d 1525 ("superlu" ,superlu)
b9100e2f
EB		 1526 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1527 ;; leaving out opengl, as configuration seems to only be for mac
1528 ))
1529 (arguments
1530 `(#:test-target "test"
9a899cce 1531 #:parallel-build? #f ;build is parallel by default
b9100e2f
EB		 1532 #:configure-flags
1533 `("--with-mpi=0"
f258212d
EB		 1534 "--with-openmp=1"
1535 "--with-superlu=1"
1536 ,(string-append "--with-superlu-include="
1537 (assoc-ref %build-inputs "superlu") "/include")
1538 ,(string-append "--with-superlu-lib="
1539 (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
9731c412
EB		 1540 #:make-flags
1541 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1542 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1543 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
b9100e2f 1544 #:phases
64dcc289
EB		 1545 (modify-phases %standard-phases
1546 (replace 'configure
1547 ;; PETSc's configure script is actually a python script, so we can't
1548 ;; run it with bash.
1549 (lambda* (#:key outputs (configure-flags '())
1550 #:allow-other-keys)
1551 (let* ((prefix (assoc-ref outputs "out"))
1552 (flags `(,(string-append "--prefix=" prefix)
1553 ,@configure-flags)))
1554 (format #t "build directory: ~s~%" (getcwd))
1555 (format #t "configure flags: ~s~%" flags)
1556 (zero? (apply system* "./configure" flags)))))
1557 (add-after 'configure 'clean-local-references
9731c412 1558 (lambda* (#:key outputs #:allow-other-keys)
64dcc289
EB		 1559 (let ((out (assoc-ref outputs "out")))
1560 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
b730b437
EB		 1561 ;; Prevent build directory from leaking into compiled code
1562 (((getcwd)) out)
1563 ;; Scrub timestamp for reproducibility
fafd623e 1564 ((".*Libraries compiled on.*") ""))
9731c412
EB		 1565 (substitute* (find-files "." "petscvariables")
1566 ;; Do not expose build machine characteristics, set to defaults.
1567 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1568 (("NPMAX = [:digit:]+") "NPMAX = 2"))
fafd623e 1569 #t)))
64dcc289 1570 (add-after 'install 'clean-install
10b11968
EB		 1571 ;; Try to keep installed files from leaking build directory names.
1572 (lambda* (#:key inputs outputs #:allow-other-keys)
64dcc289 1573 (let ((out (assoc-ref outputs "out")))
10b11968 1574 (substitute* (map (lambda (file)
9a899cce 1575 (string-append out "/lib/petsc/conf/" file))
fafd623e 1576 '("petscvariables"))
10b11968
EB		 1577 (((getcwd)) out))
1578 ;; Make compiler references point to the store
9a899cce 1579 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
dfdf5716
EB		 1580 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1581 (string-append "= " (which compiler))))
10b11968
EB		 1582 ;; PETSc installs some build logs, which aren't necessary.
1583 (for-each (lambda (file)
9a899cce 1584 (let ((f (string-append out "/lib/petsc/conf/" file)))
10b11968
EB		 1585 (when (file-exists? f)
1586 (delete-file f))))
9a899cce
EB		 1587 '("configure.log" "make.log" "gmake.log"
1588 "test.log" "error.log" "RDict.db"
fafd623e 1589 "PETScBuildInternal.cmake"
10b11968 1590 ;; Once installed, should uninstall with Guix
fafd623e
EB		 1591 "uninstall.py"))
1592 #t))))))
b9100e2f 1593 (home-page "http://www.mcs.anl.gov/petsc")
16ecf3ff 1594 (synopsis "Library to solve PDEs")
b9100e2f
EB		 1595 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1596data structures and routines for the scalable (parallel) solution of
1597scientific applications modeled by partial differential equations.")
166191b3 1598 (license (license:non-copyleft
b9100e2f
EB		 1599 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1600
1601(define-public petsc-complex
1602 (package (inherit petsc)
1603 (name "petsc-complex")
1604 (arguments
1605 (substitute-keyword-arguments (package-arguments petsc)
1606 ((#:configure-flags cf)
1607 `(cons "--with-scalar-type=complex" ,cf))))
16ecf3ff 1608 (synopsis "Library to solve PDEs (with complex scalars)")))
183e44ae 1609
d8c7eeb9
EB		 1610(define-public petsc-openmpi
1611 (package (inherit petsc)
1612 (name "petsc-openmpi")
1613 (inputs
1614 `(("openmpi" ,openmpi)
1615 ,@(package-inputs petsc)))
1616 (arguments
1617 (substitute-keyword-arguments (package-arguments petsc)
1618 ((#:configure-flags cf)
1619 ``("--with-mpiexec=mpirun"
1620 ,(string-append "--with-mpi-dir="
1621 (assoc-ref %build-inputs "openmpi"))
1622 ,@(delete "--with-mpi=0" ,cf)))))
16ecf3ff 1623 (synopsis "Library to solve PDEs (with MPI support)")))
d8c7eeb9
EB		 1624
1625(define-public petsc-complex-openmpi
1626 (package (inherit petsc-complex)
1627 (name "petsc-complex-openmpi")
1628 (inputs
1629 `(("openmpi" ,openmpi)
1630 ,@(package-inputs petsc-complex)))
1631 (arguments
1632 (substitute-keyword-arguments (package-arguments petsc-complex)
1633 ((#:configure-flags cf)
1634 ``("--with-mpiexec=mpirun"
1635 ,(string-append "--with-mpi-dir="
1636 (assoc-ref %build-inputs "openmpi"))
1637 ,@(delete "--with-mpi=0" ,cf)))))
16ecf3ff 1638 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
d8c7eeb9 1639
a7f01414
EB		 1640(define-public slepc
1641 (package
1642 (name "slepc")
cc809f16 1643 (version "3.8.2")
a7f01414
EB		 1644 (source
1645 (origin
1646 (method url-fetch)
baeaf882
EB		 1647 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
1648 version ".tar.gz"))
a7f01414
EB		 1649 (sha256
1650 (base32
cc809f16 1651 "04zd48p43rnvg68p6cp28zll0px5whglc5v0sc3s6vdj1v920z8y"))))
a7f01414
EB		 1652 (build-system gnu-build-system)
1653 (native-inputs
1654 `(("python" ,python-2)))
1655 (inputs
1656 `(("arpack" ,arpack-ng)
1657 ("gfortran" ,gfortran)))
1658 (propagated-inputs
1659 `(("petsc" ,petsc)))
1660 (arguments
1661 `(#:parallel-build? #f ;build is parallel by default
1662 #:configure-flags
1663 `(,(string-append "--with-arpack-dir="
9cf52454 1664 (assoc-ref %build-inputs "arpack") "/lib"))
9731c412
EB		 1665 #:make-flags ;honor (parallel-job-count)
1666 `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
a7f01414
EB		 1667 #:phases
1668 (modify-phases %standard-phases
8787c555 1669 (replace 'configure
a7f01414
EB		 1670 ;; configure is a python script, so we can't run it with bash.
1671 (lambda* (#:key inputs outputs (configure-flags '())
1672 #:allow-other-keys)
1673 (let* ((prefix (assoc-ref outputs "out"))
1674 (flags `(,(string-append "--prefix=" prefix)
1675 ,@configure-flags)))
1676 (format #t "build directory: ~s~%" (getcwd))
1677 (format #t "configure flags: ~s~%" flags)
1678 (setenv "SLEPC_DIR" (getcwd))
9cf52454 1679 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
c6840089 1680 (apply invoke "./configure" flags))))
8787c555 1681 (add-after 'install 'delete-doc
a7f01414
EB		 1682 ;; TODO: SLEPc installs HTML documentation alongside headers in
1683 ;; $out/include. We'd like to move them to share/doc, but delete
1684 ;; them for now, as they are incomplete and installing the complete
1685 ;; documentation is difficult.
1686 (lambda* (#:key outputs #:allow-other-keys)
1687 (let* ((out (assoc-ref outputs "out")))
1688 (for-each delete-file (find-files out "\\.html$")))))
8787c555 1689 (add-after 'install 'clean-install
a7f01414
EB		 1690 ;; Clean up unnecessary build logs from installation.
1691 (lambda* (#:key outputs #:allow-other-keys)
1692 (let ((out (assoc-ref outputs "out")))
1693 (for-each (lambda (file)
1694 (let ((f (string-append out "/lib/slepc/conf/" file)))
1695 (when (file-exists? f)
1696 (delete-file f))))
1697 '("configure.log" "make.log" "gmake.log"
1698 "test.log" "error.log" "RDict.db"
1699 "uninstall.py"))))))))
1700 (home-page "http://slepc.upv.es")
1701 (synopsis "Scalable library for eigenproblems")
1702 (description "SLEPc is a software library for the solution of large sparse
1703eigenproblems on parallel computers. It can be used for the solution of
1704linear eigenvalue problems formulated in either standard or generalized form,
1705as well as other related problems such as the singular value decomposition.
1706The emphasis of the software is on methods and techniques appropriate for
1707problems in which the associated matrices are sparse, for example, those
1708arising after the discretization of partial differential equations.")
3c524f21 1709 (license license:bsd-2)))
a7f01414
EB		 1710
1711(define-public slepc-complex
1712 (package (inherit slepc)
1713 (name "slepc-complex")
1714 (propagated-inputs
1715 `(("petsc" ,petsc-complex)
1716 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1717 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1718
1719(define-public slepc-openmpi
1720 (package (inherit slepc)
1721 (name "slepc-openmpi")
1722 (inputs
1723 `(("mpi" ,openmpi)
1724 ("arpack" ,arpack-ng-openmpi)
1725 ,@(alist-delete "arpack" (package-inputs slepc))))
1726 (propagated-inputs
1727 `(("petsc" ,petsc-openmpi)
1728 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1729 (synopsis "Scalable library for eigenproblems (with MPI support)")))
1730
1731(define-public slepc-complex-openmpi
1732 (package (inherit slepc-openmpi)
1733 (name "slepc-complex-openmpi")
1734 (propagated-inputs
1735 `(("petsc" ,petsc-complex-openmpi)
1736 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1737 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1738
cec86422
EB		 1739(define-public mumps
1740 (package
1741 (name "mumps")
fba78d18 1742 (version "5.0.2")
cec86422
EB		 1743 (source
1744 (origin
1745 (method url-fetch)
1746 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
1747 version ".tar.gz"))
1748 (sha256
1749 (base32
fba78d18 1750 "0igyc1pfzxdhpbad3v3lb86ixkdbqa1a8gbs15b04r2294h2nabp"))
fc1adab1 1751 (patches (search-patches "mumps-build-parallelism.patch"))))
cec86422
EB		 1752 (build-system gnu-build-system)
1753 (inputs
1754 `(("fortran" ,gfortran)
1755 ;; These are required for linking against mumps, but we let the user
1756 ;; declare the dependency.
1757 ("blas" ,openblas)
1758 ("metis" ,metis)
1759 ("scotch" ,scotch)))
1760 (arguments
1761 `(#:modules ((ice-9 match)
1762 (ice-9 popen)
1763 (srfi srfi-1)
1764 ,@%gnu-build-system-modules)
1765 #:phases
1766 (modify-phases %standard-phases
fba78d18 1767 (replace 'configure
cec86422
EB		 1768 (lambda* (#:key inputs #:allow-other-keys)
1769 (call-with-output-file "Makefile.inc"
1770 (lambda (port)
1771 (format port "
1772PLAT =
1773LIBEXT = .a
1774OUTC = -o
1775OUTF = -o
1776RM = rm -f~:[
1777CC = gcc
1778FC = gfortran
1779FL = gfortran
1780INCSEQ = -I$(topdir)/libseq
1781LIBSEQ = -L$(topdir)/libseq -lmpiseq
1782LIBSEQNEEDED = libseqneeded~;
1783CC = mpicc
1784FC = mpifort
1785FL = mpifort~]
1786AR = ar vr # rules require trailing space, ugh...
1787RANLIB = ranlib
1788LIBBLAS = -L~a -lopenblas~@[
1789SCALAP = -L~a -lscalapack~]
1790LIBOTHERS = -pthread
1791CDEFS = -DAdd_
1792PIC = -fPIC
1793OPTF = -O2 -DALLOW_NON_INIT $(PIC)
1794OPTL = -O2 $(PIC)
1795OPTC = -O2 $(PIC)
1796INCS = $(INCSEQ)
1797LIBS = $(SCALAP) $(LIBSEQ)
1798LPORDDIR = $(topdir)/PORD/lib
1799IPORD = -I$(topdir)/PORD/include
1800LPORD = -L$(LPORDDIR) -lpord
1801ORDERINGSF = -Dpord~@[
1802METISDIR = ~a
1803IMETIS = -I$(METISDIR)/include
1804LMETIS = -L$(METISDIR)/lib -lmetis
1805ORDERINGSF += -Dmetis~]~@[~:{
1806SCOTCHDIR = ~a
1807ISCOTCH = -I$(SCOTCHDIR)/include
1808LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
1809ORDERINGSF += ~a~}~]
1810ORDERINGSC = $(ORDERINGSF)
1811LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
1812IORDERINGSF = $(ISCOTCH)
1813IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
1814 (assoc-ref inputs "mpi")
1815 (assoc-ref inputs "blas")
1816 (assoc-ref inputs "scalapack")
1817 (assoc-ref inputs "metis")
1818 (match (list (assoc-ref inputs "pt-scotch")
1819 (assoc-ref inputs "scotch"))
1820 ((#f #f)
1821 #f)
1822 ((#f scotch)
1823 `((,scotch "" "-Dscotch")))
1824 ((ptscotch _)
1825 `((,ptscotch
1826 "-lptesmumps -lptscotch -lptscotcherr "
1827 "-Dptscotch")))))))))
fba78d18 1828 (replace 'build
cec86422
EB		 1829 ;; By default only the d-precision library is built. Make with "all"
1830 ;; target so that all precision libraries and examples are built.
1831 (lambda _
1832 (zero? (system* "make" "all"
1833 (format #f "-j~a" (parallel-job-count))))))
fba78d18 1834 (replace 'check
cec86422
EB		 1835 ;; Run the simple test drivers, which read test input from stdin:
1836 ;; from the "real" input for the single- and double-precision
1837 ;; testers, and from the "cmplx" input for complex-precision
1838 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
1839 ;; package to prefix execution with "mpirun".
1840 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
1841 (with-directory-excursion "examples"
1842 (every
1843 (lambda (prec type)
1844 (let ((tester (apply open-pipe*
1845 `(,OPEN_WRITE
1846 ,@exec-prefix
1847 ,(string-append "./" prec
1848 "simpletest"))))
1849 (input (open-input-file
1850 (string-append "input_simpletest_" type))))
1851 (begin
1852 (dump-port input tester)
1853 (close-port input)
1854 (zero? (close-pipe tester)))))
1855 '("s" "d" "c" "z")
1856 '("real" "real" "cmplx" "cmplx")))))
fba78d18
EB		 1857 (replace 'install
1858 (lambda* (#:key outputs #:allow-other-keys)
1859 (let* ((out (assoc-ref outputs "out"))
1860 (libdir (string-append out "/lib")))
1861 (copy-recursively "lib" libdir)
1862 (copy-recursively "include" (string-append out "/include"))
1863 (when (file-exists? "libseq/libmpiseq.a")
1864 (install-file "libseq/libmpiseq.a" libdir))
1865 #t))))))
cec86422
EB		 1866 (home-page "http://mumps.enseeiht.fr")
1867 (synopsis "Multifrontal sparse direct solver")
1868 (description
1869 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
1870sparse system of linear equations A x = b using Guassian elimination.")
1871 (license license:cecill-c)))
1872
1873(define-public mumps-metis
1874 (package (inherit mumps)
1875 (name "mumps-metis")
1876 (inputs
1877 (alist-delete "scotch" (package-inputs mumps)))))
1878
1879(define-public mumps-openmpi
1880 (package (inherit mumps)
1881 (name "mumps-openmpi")
1882 (inputs
1883 `(("mpi" ,openmpi)
1884 ("scalapack" ,scalapack)
1885 ("pt-scotch" ,pt-scotch)
1886 ,@(alist-delete "scotch" (package-inputs mumps))))
1887 (arguments
1888 (substitute-keyword-arguments (package-arguments mumps)
1889 ((#:phases phases)
1890 `(modify-phases ,phases
1891 (replace
1892 'check
1893 (lambda _
1894 ((assoc-ref ,phases 'check)
1895 #:exec-prefix '("mpirun" "-n" "2"))))))))
1896 (synopsis "Multifrontal sparse direct solver (with MPI)")))
1897
1898(define-public mumps-metis-openmpi
1899 (package (inherit mumps-openmpi)
1900 (name "mumps-metis-openmpi")
1901 (inputs
1902 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
1903
2d047896
RW		 1904(define-public r-quadprog
1905 (package
1906 (name "r-quadprog")
1907 (version "1.5-5")
1908 (source
1909 (origin
1910 (method url-fetch)
1911 (uri (cran-uri "quadprog" version))
1912 (sha256
1913 (base32
1914 "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
1915 (build-system r-build-system)
1916 (native-inputs
1917 `(("gfortran" ,gfortran)))
e9960d8c 1918 (home-page "https://cran.r-project.org/web/packages/quadprog")
2d047896
RW		 1919 (synopsis "Functions to solve quadratic programming problems")
1920 (description
1921 "This package contains routines and documentation for solving quadratic
1922programming problems.")
1923 (license license:gpl3+)))
1924
ec8c7e47
RJ		 1925(define-public r-pracma
1926 (package
1927 (name "r-pracma")
63758425 1928 (version "2.1.4")
ec8c7e47
RJ		 1929 (source (origin
1930 (method url-fetch)
1931 (uri (cran-uri "pracma" version))
1932 (sha256
63758425 1933 (base32 "1ygm81i7mqvh229dp9935djjyb120p3bqvaf4k572sa4q63fzjhc"))))
ec8c7e47 1934 (build-system r-build-system)
ccd9b151
RW		 1935 (propagated-inputs
1936 `(("r-quadprog" ,r-quadprog)))
e9960d8c 1937 (home-page "https://cran.r-project.org/web/packages/pracma")
ec8c7e47
RJ		 1938 (synopsis "Practical numerical math functions")
1939 (description "This package provides functions for numerical analysis and
1940linear algebra, numerical optimization, differential equations, plus some
1941special functions. It uses Matlab function names where appropriate to simplify
1942porting.")
1943 (license license:gpl3+)))
1944
63e07468
BW		 1945(define-public ruby-asciimath
1946 (package
1947 (name "ruby-asciimath")
1948 (version "1.0.4")
1949 (source
1950 (origin
1951 (method url-fetch)
1952 (uri (rubygems-uri "asciimath" version))
1953 (sha256
1954 (base32
1955 "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
1956 (build-system ruby-build-system)
1957 (arguments
1958 '(#:phases
1959 (modify-phases %standard-phases
1960 ;; Apply this patch
1961 ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
1962 (add-after 'unpack 'patch-remove-spurious-backslashes
1963 (lambda _
1964 (substitute* "spec/parser_spec.rb"
1965 (("\\\\\"")
1966 "\"")))))))
1967 (native-inputs
1968 `(("bundler" ,bundler)
1969 ("ruby-rspec" ,ruby-rspec)))
1970 (synopsis "AsciiMath parsing and conversion library")
1971 (description
1972 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
1973easy-to-write markup language for mathematics.")
1974 (home-page "https://github.com/asciidoctor/asciimath")
1975 (license license:expat)))
1976
183e44ae
EB		 1977(define-public superlu
1978 (package
1979 (name "superlu")
995a09e0 1980 (version "5.2.1")
183e44ae
EB		 1981 (source
1982 (origin
1983 (method url-fetch)
1984 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1985 "superlu_" version ".tar.gz"))
1986 (sha256
995a09e0
EB		 1987 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
1988 (modules '((guix build utils)))
1989 (snippet
1990 ;; Replace the non-free implementation of MC64 with a stub adapted
1991 ;; from Debian
1992 '(begin
1993 (use-modules (ice-9 regex)
1994 (ice-9 rdelim))
1995 (call-with-output-file "SRC/mc64ad.c"
1996 (lambda (port)
1997 (display "
1998#include <stdio.h>
1999#include <stdlib.h>
2000void mc64id_(int *a) {
2001 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2002 abort ();
2003}
2004void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2005 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2006 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2007 abort ();
2008}\n" port)))
2009 ;; Remove the corresponding license verbiage. MC64 license follows
2010 ;; a "------" line separator.
2011 (with-atomic-file-replacement "License.txt"
2012 (let ((rx (make-regexp "-{8}")))
2013 (lambda (in out)
2014 (let loop ()
2015 (let ((line (read-line in 'concat)))
2016 (unless (regexp-exec rx line)
2017 (display line out)
2018 (loop)))))))))))
2019 (build-system cmake-build-system)
183e44ae
EB		 2020 (native-inputs
2021 `(("tcsh" ,tcsh)))
2022 (inputs
995a09e0 2023 `(("blas" ,openblas)
19afbea1 2024 ("gfortran" ,gfortran)))
183e44ae 2025 (arguments
995a09e0
EB		 2026 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2027 "-DTPL_BLAS_LIBRARIES=openblas"
677bc34d 2028 "-DBUILD_SHARED_LIBS:BOOL=YES")))
183e44ae
EB		 2029 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
2030 (synopsis "Supernodal direct solver for sparse linear systems")
2031 (description
2032 "SuperLU is a general purpose library for the direct solution of large,
2033sparse, nonsymmetric systems of linear equations on high performance machines.
2034The library is written in C and is callable from either C or Fortran. The
2035library routines perform an LU decomposition with partial pivoting and
2036triangular system solves through forward and back substitution. The library
2037also provides threshold-based ILU factorization preconditioners.")
995a09e0
EB		 2038 (license (list license:bsd-3
2039 license:gpl2+ ;EXAMPLE/*fgmr.c
2040 (license:fsf-free "file://SRC/colamd.h")))))
f8ed036a 2041
a54aefea
EB		 2042(define-public superlu-dist
2043 (package
2044 (name "superlu-dist")
2045 (version "3.3")
2046 (source
2047 (origin
2048 (method url-fetch)
2049 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2050 "superlu_dist_" version ".tar.gz"))
2051 (sha256
2052 (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj"))
29080870
EB		 2053 (modules '((guix build utils)))
2054 (snippet
2055 ;; Replace the non-free implementation of MC64 with a stub
2056 '(begin
2057 (use-modules (ice-9 regex)
2058 (ice-9 rdelim))
2059 (call-with-output-file "SRC/mc64ad.c"
2060 (lambda (port)
2061 (display "
2062#include <stdio.h>
2063#include <stdlib.h>
2064void mc64id_(int *a) {
2065 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2066 abort ();
2067}
2068void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2069 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2070 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2071 abort ();
2072}\n" port)))
2073 (delete-file "SRC/mc64ad.f.bak")
2074 (substitute* "SRC/util.c" ;adjust default algorithm
2075 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
2076 "RowPerm = NOROWPERM"))))
fc1adab1 2077 (patches (search-patches "superlu-dist-scotchmetis.patch"))))
a54aefea
EB		 2078 (build-system gnu-build-system)
2079 (native-inputs
2080 `(("tcsh" ,tcsh)))
2081 (inputs
19afbea1 2082 `(("gfortran" ,gfortran)))
a54aefea
EB		 2083 (propagated-inputs
2084 `(("openmpi" ,openmpi) ;headers include MPI heades
2085 ("lapack" ,lapack) ;required to link with output library
2086 ("pt-scotch" ,pt-scotch))) ;same
2087 (arguments
2088 `(#:parallel-build? #f ;race conditions using ar
2089 #:phases
dc1d3cde
KK		 2090 (modify-phases %standard-phases
2091 (replace 'configure
2092 (lambda* (#:key inputs outputs #:allow-other-keys)
2093 (call-with-output-file "make.inc"
2094 (lambda (port)
2095 (format port "
a54aefea
EB		 2096PLAT =
2097DSuperLUroot = ~a
2098DSUPERLULIB = ~a/lib/libsuperlu_dist.a
2099BLASDEF = -DUSE_VENDOR_BLAS
2100BLASLIB = -L~a/lib -lblas
2101PARMETISLIB = -L~a/lib \
2102 -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
2103 -lscotch -lscotcherr -lscotcherrexit
2104METISLIB = -L~:*~a/lib \
2105 -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
2106LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
2107ARCH = ar
2108ARCHFLAGS = cr
2109RANLIB = ranlib
2110CC = mpicc
2111PIC = -fPIC
2112CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC)
2113NOOPTS = -O0 -g $(PIC)
2114FORTRAN = mpifort
2115FFLAGS = -O2 -g $(PIC)
2116LOADER = $(CC)
2117CDEFS = -DAdd_"
dc1d3cde
KK		 2118 (getcwd)
2119 (assoc-ref outputs "out")
2120 (assoc-ref inputs "lapack")
2121 (assoc-ref inputs "pt-scotch"))))
2122 #t))
2123 (add-after 'unpack 'remove-broken-symlinks
2124 (lambda _
2125 (for-each delete-file
2126 (find-files "MAKE_INC" "\\.#make\\..*"))
2127 #t))
2128 (add-before 'build 'create-install-directories
2129 (lambda* (#:key outputs #:allow-other-keys)
2130 (for-each
2131 (lambda (dir)
2132 (mkdir-p (string-append (assoc-ref outputs "out")
2133 "/" dir)))
2134 '("lib" "include"))
2135 #t))
2136 (replace 'check
a54aefea
EB		 2137 (lambda _
2138 (with-directory-excursion "EXAMPLE"
2139 (and
2140 (zero? (system* "mpirun" "-n" "2"
2141 "./pddrive" "-r" "1" "-c" "2" "g20.rua"))
2142 (zero? (system* "mpirun" "-n" "2"
dc1d3cde
KK		 2143 "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))))))
2144 (replace 'install
2145 (lambda* (#:key outputs #:allow-other-keys)
2146 ;; Library is placed in lib during the build phase. Copy over
2147 ;; headers to include.
2148 (let* ((out (assoc-ref outputs "out"))
2149 (incdir (string-append out "/include")))
2150 (for-each (lambda (file)
2151 (let ((base (basename file)))
2152 (format #t "installing `~a' to `~a'~%"
2153 base incdir)
2154 (copy-file file
2155 (string-append incdir "/" base))))
2156 (find-files "SRC" ".*\\.h$")))
2157 #t)))))
a54aefea
EB		 2158 (home-page (package-home-page superlu))
2159 (synopsis "Parallel supernodal direct solver")
2160 (description
2161 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2162It is targeted for distributed memory parallel machines. SuperLU_DIST is
2163implemented in ANSI C, and MPI for communications.")
2164 (license license:bsd-3)))
2165
f8ed036a
EB		 2166(define-public scotch
2167 (package
2168 (name "scotch")
6c798540 2169 (version "6.0.4")
f8ed036a
EB		 2170 (source
2171 (origin
2172 (method url-fetch)
6c798540 2173 (uri (string-append "https://gforge.inria.fr/frs/download.php/34618/"
f8ed036a
EB		 2174 "scotch_" version ".tar.gz"))
2175 (sha256
6c798540 2176 (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm"))
fc1adab1
AK		 2177 (patches (search-patches "scotch-test-threading.patch"
2178 "pt-scotch-build-parallelism.patch"))))
f8ed036a
EB		 2179 (build-system gnu-build-system)
2180 (inputs
2181 `(("zlib" ,zlib)
5e54f4ad 2182 ("flex" ,flex)
f8ed036a
EB		 2183 ("bison" ,bison)))
2184 (arguments
2185 `(#:phases
d6602ee9
EB		 2186 (modify-phases %standard-phases
2187 (add-after
2188 'unpack 'chdir-to-src
2189 (lambda _ (chdir "src")))
2190 (replace
2191 'configure
2192 (lambda _
2193 (call-with-output-file "Makefile.inc"
2194 (lambda (port)
2195 (format port "
f8ed036a
EB		 2196EXE =
2197LIB = .a
2198OBJ = .o
2199MAKE = make
2200AR = ar
2201ARFLAGS = -ruv
cf0ec6c4 2202CAT = cat
f8ed036a
EB		 2203CCS = gcc
2204CCP = mpicc
2205CCD = gcc
2206CPPFLAGS =~{ -D~a~}
6c798540 2207CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
f8ed036a
EB		 2208LDFLAGS = -lz -lm -lrt -lpthread
2209CP = cp
2210LEX = flex -Pscotchyy -olex.yy.c
2211LN = ln
2212MKDIR = mkdir
2213MV = mv
2214RANLIB = ranlib
2215YACC = bison -pscotchyy -y -b y
2216"
d6602ee9
EB		 2217 '("COMMON_FILE_COMPRESS_GZ"
2218 "COMMON_PTHREAD"
2219 "COMMON_RANDOM_FIXED_SEED"
26599d69 2220 "INTSIZE64" ;use 'long' instead of 'int'
cf0ec6c4
EB		 2221 ;; Prevents symbolc clashes with libesmumps
2222 "SCOTCH_RENAME"
d6602ee9
EB		 2223 ;; XXX: Causes invalid frees in superlu-dist tests
2224 ;; "SCOTCH_PTHREAD"
2225 ;; "SCOTCH_PTHREAD_NUMBER=2"
2226 "restrict=__restrict"))))))
cf0ec6c4
EB		 2227 (add-after
2228 'build 'build-esmumps
2229 (lambda _
2230 (zero? (system* "make"
2231 (format #f "-j~a" (parallel-job-count))
2232 "esmumps"))))
d6602ee9 2233 (replace
f8ed036a
EB		 2234 'install
2235 (lambda* (#:key outputs #:allow-other-keys)
2236 (let ((out (assoc-ref outputs "out")))
2237 (mkdir out)
2238 (zero? (system* "make"
2239 (string-append "prefix=" out)
cf0ec6c4
EB		 2240 "install"))
2241 ;; esmumps files are not installed with the above
2242 (for-each (lambda (f)
2243 (copy-file f (string-append out "/include/" f)))
2244 (find-files "../include" ".*esmumps.h$"))
2245 (for-each (lambda (f)
2246 (copy-file f (string-append out "/lib/" f)))
2247 (find-files "../lib" "^lib.*esmumps.*"))))))))
f8ed036a
EB		 2248 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
2249 (synopsis "Programs and libraries for graph algorithms")
2250 (description "SCOTCH is a set of programs and libraries which implement
2251the static mapping and sparse matrix reordering algorithms developed within
2252the SCOTCH project. Its purpose is to apply graph theory, with a divide and
2253conquer approach, to scientific computing problems such as graph and mesh
2254partitioning, static mapping, and sparse matrix ordering, in application
2255domains ranging from structural mechanics to operating systems or
2256bio-chemistry.")
2257 ;; See LICENSE_en.txt
2258 (license license:cecill-c)))
6acb4adb 2259
1c39f3b8
PG		 2260(define-public scotch32
2261 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2262 ;; some applications.
2263 (package (inherit scotch)
2264 (name "scotch32")
2265 (arguments
2266 (substitute-keyword-arguments (package-arguments scotch)
2267 ((#:phases scotch-phases)
2268 `(modify-phases ,scotch-phases
2269 (replace
2270 'configure
2271 (lambda _
2272 (call-with-output-file "Makefile.inc"
2273 (lambda (port)
2274 (format port "
2275EXE =
2276LIB = .a
2277OBJ = .o
2278MAKE = make
2279AR = ar
2280ARFLAGS = -ruv
2281CAT = cat
2282CCS = gcc
2283CCP = mpicc
2284CCD = gcc
2285CPPFLAGS =~{ -D~a~}
2286CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2287LDFLAGS = -lz -lm -lrt -lpthread
2288CP = cp
2289LEX = flex -Pscotchyy -olex.yy.c
2290LN = ln
2291MKDIR = mkdir
2292MV = mv
2293RANLIB = ranlib
2294YACC = bison -pscotchyy -y -b y
2295"
2296 '("COMMON_FILE_COMPRESS_GZ"
2297 "COMMON_PTHREAD"
2298 "COMMON_RANDOM_FIXED_SEED"
2299 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
2300 ;; Prevents symbolc clashes with libesmumps
2301 "SCOTCH_RENAME"
2302 ;; XXX: Causes invalid frees in superlu-dist tests
2303 ;; "SCOTCH_PTHREAD"
2304 ;; "SCOTCH_PTHREAD_NUMBER=2"
2305 "restrict=__restrict"))))))))))
2306 (synopsis
2307 "Programs and libraries for graph algorithms (32-bit integers)")))
2308
6acb4adb
EB		 2309(define-public pt-scotch
2310 (package (inherit scotch)
2311 (name "pt-scotch")
2312 (propagated-inputs
2313 `(("openmpi" ,openmpi))) ;Headers include MPI headers
2314 (arguments
2315 (substitute-keyword-arguments (package-arguments scotch)
2316 ((#:phases scotch-phases)
d6602ee9
EB		 2317 `(modify-phases ,scotch-phases
2318 (replace
2319 'build
d6602ee9
EB		 2320 (lambda _
2321 (and
cf0ec6c4
EB		 2322 (zero? (system* "make"
2323 (format #f "-j~a" (parallel-job-count))
2324 "ptscotch" "ptesmumps"))
d6602ee9
EB		 2325 ;; Install the serial metis compatibility library
2326 (zero? (system* "make" "-C" "libscotchmetis" "install")))))
2327 (replace
2328 'check
2329 (lambda _ (zero? (system* "make" "ptcheck"))))))))
6acb4adb 2330 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
5698b8b8 2331
1c25a52c
PG		 2332(define-public pt-scotch32
2333 (package (inherit scotch32)
2334 (name "pt-scotch32")
2335 (propagated-inputs
2336 `(("openmpi" ,openmpi))) ;headers include MPI headers
2337 (arguments
c4d4a779
PG		 2338 (substitute-keyword-arguments (package-arguments scotch32)
2339 ((#:phases scotch32-phases)
2340 `(modify-phases ,scotch32-phases
1c25a52c
PG		 2341 (replace 'build
2342 (lambda _
2343 (and
2344 (zero? (system* "make"
2345 (format #f "-j~a" (parallel-job-count))
2346 "ptscotch" "ptesmumps"))
2347 ;; Install the serial metis compatibility library
2348 (zero? (system* "make" "-C" "libscotchmetis" "install")))))
2349 (replace 'check
2350 (lambda _
2351 (zero? (system* "make" "ptcheck"))))))))
2352 (synopsis
2353 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2354
aa75ad00
EB		 2355(define-public metis
2356 (package
2357 (name "metis")
2358 (version "5.1.0")
2359 (source
2360 (origin
2361 (method url-fetch)
2362 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2363 "metis-" version ".tar.gz"))
2364 (sha256
2365 (base32
2366 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2367 (build-system cmake-build-system)
2368 (inputs
2369 `(("blas" ,openblas)))
2370 (arguments
2371 `(#:tests? #f ;no tests
2372 #:configure-flags `("-DSHARED=ON"
2373 ,(string-append "-DGKLIB_PATH=" (getcwd)
2374 "/metis-" ,version "/GKlib"))))
2375 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2376 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2377 (description
2378 "METIS is a set of serial programs for partitioning graphs, partitioning
2379finite element meshes, and producing fill-reducing orderings for sparse
2380matrices. The algorithms implemented in METIS are based on the multilevel
2381recursive-bisection, multilevel k-way, and multi-constraint partitioning
2382schemes.")
2383 (license license:asl2.0))) ;As of version 5.0.3
2384
700ff222
EB		 2385(define-public p4est
2386 (package
2387 (name "p4est")
4150da63 2388 (version "2.0")
700ff222
EB		 2389 (source
2390 (origin
2391 (method url-fetch)
2392 (uri (string-append "http://p4est.github.io/release/p4est-"
2393 version ".tar.gz"))
2394 (sha256
2395 (base32
4150da63 2396 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
700ff222
EB		 2397 (build-system gnu-build-system)
2398 (inputs
2399 `(("fortran" ,gfortran)
2400 ("blas" ,openblas)
2401 ("lapack" ,lapack)
2402 ("zlib" ,zlib)))
2403 (arguments
2404 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2405 (assoc-ref %build-inputs "blas")
2406 " -lopenblas")
2407 ,(string-append "LAPACK_LIBS=-L"
2408 (assoc-ref %build-inputs "lapack")
2409 " -llapack"))))
2410 (home-page "http://www.p4est.org")
2411 (synopsis "Adaptive mesh refinement on forests of octrees")
2412 (description
2413 "The p4est software library enables the dynamic management of a
2414collection of adaptive octrees, conveniently called a forest of octrees.
2415p4est is designed to work in parallel and scales to hundreds of thousands of
2416processor cores.")
2417 (license license:gpl2+)))
2418
2419(define-public p4est-openmpi
2420 (package (inherit p4est)
2421 (name "p4est-openmpi")
2422 (inputs
2423 `(("mpi" ,openmpi)
2424 ,@(package-inputs p4est)))
2425 (arguments
2426 (substitute-keyword-arguments (package-arguments p4est)
2427 ((#:configure-flags cf)
2428 ``("--enable-mpi" ,@,cf))))
2429 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2430
5698b8b8
JD		 2431(define-public gsegrafix
2432 (package
2433 (name "gsegrafix")
2434 (version "1.0.6")
2435 (source
2436 (origin
2437 (method url-fetch)
2438 (uri (string-append "mirror://gnu/" name "/" name "-"
2439 version ".tar.gz"))
2440 (sha256
2441 (base32
2442 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2443 (build-system gnu-build-system)
2444 (arguments
2445 `(#:configure-flags '("LDFLAGS=-lm")))
2446 (inputs
2447 `(("libgnomecanvas" ,libgnomecanvas)
2448 ("libbonoboui" ,libbonoboui)
2449 ("libgnomeui" ,libgnomeui)
2450 ("libgnomeprintui" ,libgnomeprintui)
2451 ("popt" ,popt)))
2452 (native-inputs
2453 `(("pkg-config" ,pkg-config)))
6fd52309 2454 (home-page "https://www.gnu.org/software/gsegrafix/")
5698b8b8
JD		 2455 (synopsis "GNOME application to create scientific and engineering plots")
2456 (description "GSEGrafix is an application which produces high-quality graphical
2457plots for science and engineering. Plots are specified via simple ASCII
2458parameter files and data files and are presented in an anti-aliased GNOME
2459canvas. The program supports rectangular two-dimensional plots, histograms,
2460polar-axis plots and three-dimensional plots. Plots can be printed or saved
2461to BMP, JPEG or PNG image formats.")
2462 (license license:gpl3+)))
8731e527
JD		 2463
2464(define-public maxima
2465 (package
2466 (name "maxima")
b3b2efc8 2467 (version "5.41.0")
8731e527
JD		 2468 (source
2469 (origin
2470 (method url-fetch)
2471 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2472 version "-source/" name "-" version ".tar.gz"))
2473 (sha256
2474 (base32
b3b2efc8 2475 "0x0n81z0s4pl8nwpf7ivlsbvsdphm9w42250g7qdkizl0132by6s"))
fc1adab1 2476 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
8731e527 2477 (build-system gnu-build-system)
df354a77 2478 (inputs
6b2eafaa 2479 `(("gcl" ,gcl)
df354a77 2480 ("gnuplot" ,gnuplot) ;for plots
f36afe4d 2481 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
df354a77
FB		 2482 (native-inputs
2483 `(("texinfo" ,texinfo)
ccbc5758
KK		 2484 ("perl" ,perl)
2485 ("python" ,python)))
8731e527 2486 (arguments
df354a77
FB		 2487 `(#:configure-flags
2488 (list "--enable-gcl"
2489 (string-append "--with-posix-shell="
2490 (assoc-ref %build-inputs "bash")
2491 "/bin/sh")
2492 (string-append "--with-wish="
2493 (assoc-ref %build-inputs "tk")
2494 "/bin/wish"
2495 (let ((v ,(package-version tk)))
2496 (string-take v (string-index-right v #\.)))))
df354a77 2497 ;; By default Maxima attempts to write temporary files to
77af7b24
MW		 2498 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2499 ;; Work around that.
df354a77 2500 #:make-flags (list "TMPDIR=/tmp")
0093b126
KK		 2501 #:phases
2502 (modify-phases %standard-phases
2503 (add-before 'check 'pre-check
2504 (lambda _
2505 (chmod "src/maxima" #o555)
2506 #t))
2507 ;; Make sure the doc and emacs files are found in the
2508 ;; standard location. Also configure maxima to find gnuplot
2509 ;; without having it on the PATH.
2510 (add-after 'install 'post-install
2511 (lambda* (#:key outputs inputs #:allow-other-keys)
2512 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2513 (out (assoc-ref outputs "out"))
2514 (datadir (string-append out "/share/maxima/" ,version))
2515 (binutils (string-append (assoc-ref inputs "binutils")
2516 "/bin")))
2517 (with-directory-excursion out
2518 (mkdir-p "share/emacs")
2519 (mkdir-p "share/doc")
2520 (symlink
2521 (string-append datadir "/emacs/")
2522 (string-append out "/share/emacs/site-lisp"))
2523 (symlink
2524 (string-append datadir "/doc/")
2525 (string-append out "/share/doc/maxima"))
2526 (with-atomic-file-replacement
2527 (string-append datadir "/share/maxima-init.lisp")
2528 (lambda (in out)
2529 (format out "~a ~s~a~%"
2530 "(setf $gnuplot_command "
2531 (string-append gnuplot "/bin/gnuplot") ")")
2532 (dump-port in out))))
2533 ;; Ensure that Maxima will have access to the GNU binutils
2534 ;; components at runtime.
2535 (wrap-program (string-append out "/bin/maxima")
2536 `("PATH" prefix (,binutils))))
2537 #t)))))
8731e527
JD		 2538 (home-page "http://maxima.sourceforge.net")
2539 (synopsis "Numeric and symbolic expression manipulation")
2540 (description "Maxima is a system for the manipulation of symbolic and
2541numerical expressions. It yields high precision numeric results by using
2542exact fractions, arbitrary precision integers, and variable precision floating
e881752c 2543point numbers.")
8731e527
JD		 2544 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2545 ;; Others simply say "GNU General Public License" without stating a
2546 ;; version (which implicitly means gpl1+).
2547 ;; At least one file (src/maxima.asd) says "version 2."
2548 ;; GPLv2 only is therefore the smallest subset.
f36afe4d 2549 (license license:gpl2)))
ec322be2 2550
9aafbc0c
MW		 2551(define-public wxmaxima
2552 (package
2553 (name "wxmaxima")
0181df53 2554 (version "18.02.0")
9aafbc0c
MW		 2555 (source
2556 (origin
2557 (method url-fetch)
5143517c
KK		 2558 (uri (string-append "https://github.com/andrejv/" name "/archive"
2559 "/Version-" version ".tar.gz"))
2560 (file-name (string-append name "-" version ".tar.gz"))
9aafbc0c
MW		 2561 (sha256
2562 (base32
0181df53
KK		 2563 "03kr2rgfp4hcf3is8m8d8f9hj660c3xgrc50vrrfpixx4syh6wvj"))
2564 (patches
2565 (search-patches "wxmaxima-do-not-use-old-gnuplot-parameters.patch"))))
2566 (build-system cmake-build-system)
5143517c 2567 (native-inputs
0181df53 2568 `(("gettext" ,gettext-minimal)))
9aafbc0c
MW		 2569 (inputs
2570 `(("wxwidgets" ,wxwidgets)
de477809
SB		 2571 ("maxima" ,maxima)
2572 ;; Runtime support.
2573 ("adwaita-icon-theme" ,adwaita-icon-theme)
2574 ("gtk+" ,gtk+)
2575 ("shared-mime-info" ,shared-mime-info)))
9aafbc0c 2576 (arguments
0181df53
KK		 2577 `(#:tests? #f ; no check target
2578 #:phases
ac2ddcc6 2579 (modify-phases %standard-phases
ac2ddcc6
KK		 2580 (add-after 'install 'wrap-program
2581 (lambda* (#:key inputs outputs #:allow-other-keys)
2582 (wrap-program (string-append (assoc-ref outputs "out")
2583 "/bin/wxmaxima")
2584 `("PATH" ":" prefix
2585 (,(string-append (assoc-ref inputs "maxima")
2586 "/bin")))
2587 ;; For GtkFileChooserDialog.
2588 `("GSETTINGS_SCHEMA_DIR" =
2589 (,(string-append (assoc-ref inputs "gtk+")
2590 "/share/glib-2.0/schemas")))
2591 `("XDG_DATA_DIRS" ":" prefix
2592 (;; Needed by gdk-pixbuf to know supported icon formats.
2593 ,(string-append
2594 (assoc-ref inputs "shared-mime-info") "/share")
2595 ;; The default icon theme of GTK+.
2596 ,(string-append
2597 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
2598 #t)))))
9aafbc0c
MW		 2599 (home-page "https://andrejv.github.io/wxmaxima/")
2600 (synopsis "Graphical user interface for the Maxima computer algebra system")
2601 (description
2602 "wxMaxima is a graphical user interface for the Maxima computer algebra
2603system. It eases the use of Maxima by making most of its commands available
2604through a menu system and by providing input dialogs for commands that require
2605more than one argument. It also implements its own display engine that
2606outputs mathematical symbols directly instead of depicting them with ASCII
2607characters.
2608
2609wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
2610text and mathematical calculations to create documents, exporting of input and
2611output to TeX, and a browser for Maxima's manual including command index and
2612full text searching.")
2613 (license license:gpl2+)))
2614
b15e47f9
RW		 2615(define-public armadillo
2616 (package
2617 (name "armadillo")
133cba8c 2618 (version "7.800.2")
b15e47f9
RW		 2619 (source (origin
2620 (method url-fetch)
2621 (uri (string-append "mirror://sourceforge/arma/armadillo-"
7397cd9e 2622 version ".tar.xz"))
b15e47f9
RW		 2623 (sha256
2624 (base32
133cba8c 2625 "1qqzy7dp891j9v7062mv1599hdwr97vqzrd3j2fl8c3gmc00dmzg"))))
b15e47f9
RW		 2626 (build-system cmake-build-system)
2627 (arguments `(#:tests? #f)) ;no test target
2628 (inputs
2629 `(("openblas" ,openblas)
2630 ("lapack" ,lapack)
2631 ("arpack" ,arpack-ng)))
2632 (home-page "http://arma.sourceforge.net/")
2633 (synopsis "C++ linear algebra library")
2634 (description
2635 "Armadillo is a C++ linear algebra library, aiming towards a good balance
2636between speed and ease of use. It is useful for algorithm development
2637directly in C++, or quick conversion of research code into production
2638environments. It can be used for machine learning, pattern recognition,
2639signal processing, bioinformatics, statistics, econometrics, etc. The library
2640provides efficient classes for vectors, matrices and cubes, as well as 150+
2641associated functions (eg. contiguous and non-contiguous submatrix views).")
fe418cc5 2642 (license license:asl2.0)))
b15e47f9 2643
279663ef 2644(define-public muparser
d7cff656
LF		 2645 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2646 ;; different hash. In order to make `guix package --upgrade` work correctly,
2647 ;; we set a Guix packaging revision.
2648 ;; When the next version of muparser is released, we can remove
2649 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2650 (let ((upstream-version "2.2.5")
2651 (revision "2"))
2652 (package
2653 (name "muparser")
2654 (version (string-append upstream-version "-" revision))
2655 (source
2656 (origin
2657 (method url-fetch)
2658 (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
2659 upstream-version ".tar.gz"))
2660 (file-name (string-append name "-" version ".tar.gz"))
2661 (sha256
2662 (base32
2663 "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
2664 (build-system gnu-build-system)
2665 (arguments
2666 `(#:configure-flags '("--enable-samples=no")
2667 #:tests? #f)) ;no "check" target
2668 (home-page "http://muparser.beltoforion.de/")
2669 (synopsis "Fast parser library for mathematical expressions")
2670 (description
2671 "muParser is an extensible high performance math parser library. It is
2672based on transforming an expression into a bytecode and precalculating constant
2673parts of it.")
2674 (license license:expat))))
279663ef 2675
e73b49fb
RW		 2676(define-public openblas
2677 (package
2678 (name "openblas")
1b8de87c 2679 (version "0.2.20")
e73b49fb
RW		 2680 (source
2681 (origin
2682 (method url-fetch)
2683 (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
2684 version))
2685 (file-name (string-append name "-" version ".tar.gz"))
2686 (sha256
2687 (base32
1b8de87c 2688 "1bd03c5xni0bla0wg1wba841b36b0sg13sjja955kn5xzvy4i61a"))))
e73b49fb
RW		 2689 (build-system gnu-build-system)
2690 (arguments
5789566a 2691 `(#:test-target "test"
bd0b4379
RW		 2692 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
2693 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2694 ;; we need to disable substitutions.
71923a91
AE		 2695 #:substitutable?
2696 ,(let ((system (or (%current-target-system) (%current-system))))
2697 (or (string-prefix? "x86_64" system)
bd0b4379 2698 (string-prefix? "i686" system)
83a34647
EF		 2699 (string-prefix? "mips" system)
2700 (string-prefix? "aarch64" system)))
e73b49fb
RW		 2701 #:make-flags
2702 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
2703 "SHELL=bash"
af5b817e
RW		 2704 ;; Build the library for all supported CPUs. This allows
2705 ;; switching CPU targets at runtime with the environment variable
2706 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
71923a91
AE		 2707 ;; Unfortunately, this is not supported on non-x86 architectures,
2708 ;; where it leads to failed builds.
2709 ,@(let ((system (or (%current-target-system) (%current-system))))
8a637e79
RW		 2710 (cond
2711 ((or (string-prefix? "x86_64" system)
71923a91 2712 (string-prefix? "i686" system))
8a637e79
RW		 2713 '("DYNAMIC_ARCH=1"))
2714 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
2715 ;; two available MIPS targets special extended instructions
2716 ;; for Loongson cores are used.
2717 ((string-prefix? "mips" system)
2718 '("TARGET=SICORTEX"))
83a34647
EF		 2719 ;; On aarch64 force the generic 'armv8-a' target
2720 ((string-prefix? "aarch64" system)
2721 '("TARGET=ARMV8"))
8a637e79 2722 (else '()))))
e73b49fb 2723 ;; no configure script
493937ae
DL		 2724 #:phases
2725 (modify-phases %standard-phases
2726 (delete 'configure)
2727 (add-before 'build 'set-extralib
2728 (lambda* (#:key inputs #:allow-other-keys)
2729 ;; Get libgfortran found when building in utest.
2730 (setenv "FEXTRALIB"
2731 (string-append "-L" (assoc-ref inputs "fortran-lib")
2732 "/lib"))
2733 #t)))))
e73b49fb 2734 (inputs
493937ae 2735 `(("fortran-lib" ,gfortran "lib")))
e73b49fb
RW		 2736 (native-inputs
2737 `(("cunit" ,cunit)
493937ae 2738 ("fortran" ,gfortran)
e73b49fb
RW		 2739 ("perl" ,perl)))
2740 (home-page "http://www.openblas.net/")
2741 (synopsis "Optimized BLAS library based on GotoBLAS")
2742 (description
2743 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
2744 (license license:bsd-3)))
2745
5a7deb11
LC		 2746(define* (make-blis implementation #:optional substitutable?)
2747 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
2748source tree for a list of implementations.)
2749
2750SUBSTITUTABLE? determines whether the package is made available as a
2751substitute.
2752
2753Currently the specialization must be selected at configure-time, but work is
2754underway to allow BLIS to select the right optimized kernels at run time:
2755<https://github.com/flame/blis/issues/129>."
2756 (package
2757 (name (if (string=? implementation "reference")
2758 "blis"
2759 (string-append "blis-" implementation)))
2760 (version "0.2.2")
2761 (home-page "https://github.com/flame/blis")
2762 (source (origin
2763 (method git-fetch)
2764 (uri (git-reference (url home-page) (commit version)))
2765 (sha256
2766 (base32
2767 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
2768 (file-name (git-file-name "blis" version))))
2769 (build-system gnu-build-system)
2770 (arguments
2771 `(#:test-target "test"
2772
2773 #:substitutable? ,substitutable?
2774
2775 #:phases (modify-phases %standard-phases
2776 (replace 'configure
2777 (lambda* (#:key outputs #:allow-other-keys)
2778 ;; This is a home-made 'configure' script.
2779 (let ((out (assoc-ref outputs "out")))
2780 (zero? (system* "./configure" "-p" out
2781 "-d" "opt"
2782 "--disable-static"
2783 "--enable-shared"
2784 "--enable-threading=openmp"
2785
2786 ,implementation)))))
2787 (add-before 'check 'show-test-output
2788 (lambda _
2789 ;; By default "make check" is silent. Make it verbose.
2790 (system "tail -F output.testsuite &")
2791 #t)))))
2792 (synopsis "High-performance basic linear algebra (BLAS) routines")
2793 (description
2794 "BLIS is a portable software framework for instantiating high-performance
2795BLAS-like dense linear algebra libraries. The framework was designed to
2796isolate essential kernels of computation that, when optimized, immediately
2797enable optimized implementations of most of its commonly used and
2798computationally intensive operations. While BLIS exports a new BLAS-like API,
2799it also includes a BLAS compatibility layer which gives application developers
2800access to BLIS implementations via traditional BLAS routine calls.")
2801 (license license:bsd-3)))
2802
2803(define-public blis
2804 ;; This is the "reference" implementation, which is the non-optimized but
2805 ;; portable variant (no assembly).
2806 (make-blis "reference" #t))
2807
2808(define ignorance blis)
2809
2810(define-syntax-rule (blis/x86_64 processor)
2811 "Expand to a package specialized for PROCESSOR."
2812 (package
2813 (inherit (make-blis processor))
2814 (supported-systems '("x86_64-linux"))))
2815
2816(define-public blis-sandybridge
2817 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
2818 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
2819 (blis/x86_64 "sandybridge"))
2820
2821(define-public blis-haswell
2822 ;; BLIS specialized for Haswell processors (launched 2013):
2823 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
2824 (blis/x86_64 "haswell"))
2825
2826(define-public blis-knl
2827 ;; BLIS specialized for Knights Landing processor (launched 2016):
2828 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
2829 (blis/x86_64 "knl"))
2830
2831
e1605e36
RW		 2832(define-public openlibm
2833 (package
2834 (name "openlibm")
26f6e565 2835 (version "0.5.1")
e1605e36
RW		 2836 (source
2837 (origin
2838 (method url-fetch)
2839 (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
2840 version ".tar.gz"))
2841 (file-name (string-append name "-" version ".tar.gz"))
2842 (sha256
2843 (base32
26f6e565 2844 "11czx2z7nh6dfpz45s3xl7v38hw36jxzxfvny454bk3if14pfakq"))))
e1605e36
RW		 2845 (build-system gnu-build-system)
2846 (arguments
2847 `(#:make-flags
2848 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2849 #:phases
2850 ;; no configure script
dc1d3cde 2851 (modify-phases %standard-phases (delete 'configure))
e1605e36
RW		 2852 #:tests? #f)) ;the tests are part of the default target
2853 (home-page "http://openlibm.org/")
2854 (synopsis "Portable C mathematical library (libm)")
2855 (description
2856 "OpenLibm is an effort to have a high quality, portable, standalone C
2857mathematical library (libm). It can be used standalone in applications and
2858programming language implementations. The project was born out of a need to
e881752c 2859have a good libm for the Julia programming language that worked consistently
e1605e36
RW		 2860across compilers and operating systems, and in 32-bit and 64-bit
2861environments.")
538c0e3b
EF		 2862 ;; Each architecture has its own make target, and there is none for mips.
2863 (supported-systems (delete "mips64el-linux" %supported-systems))
e1605e36
RW		 2864 ;; See LICENSE.md for details.
2865 (license (list license:expat
2866 license:isc
2867 license:bsd-2
2868 license:public-domain
2869 license:lgpl2.1+))))
2870
e62be58f
RW		 2871(define-public openspecfun
2872 (package
2873 (name "openspecfun")
59cd0ba4 2874 (version "0.5.3")
e62be58f
RW		 2875 (source
2876 (origin
2877 (method url-fetch)
2878 (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
2879 version ".tar.gz"))
2880 (file-name (string-append name "-" version ".tar.gz"))
2881 (sha256
2882 (base32
59cd0ba4 2883 "1rs1bv8jq751fv9vq79890wqf9xlbjc7lvz3ighzyfczbyjcf18m"))))
e62be58f
RW		 2884 (build-system gnu-build-system)
2885 (arguments
59cd0ba4 2886 '(#:tests? #f ; no "check" target
e62be58f
RW		 2887 #:make-flags
2888 (list (string-append "prefix=" (assoc-ref %outputs "out")))
59cd0ba4
TGR		 2889 #:phases
2890 (modify-phases %standard-phases
2891 (delete 'configure)))) ; no configure script
e62be58f 2892 (inputs
19afbea1 2893 `(("fortran" ,gfortran)))
e62be58f
RW		 2894 (home-page "https://github.com/JuliaLang/openspecfun")
2895 (synopsis "Collection of special mathematical functions")
2896 (description
2897 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
2898portable package for Bessel Functions of a Complex Argument and Nonnegative
2899Order; it contains subroutines for computing Bessel functions and Airy
2900functions. Faddeeva allows computing the various error functions of arbitrary
2901complex arguments (Faddeeva function, error function, complementary error
2902function, scaled complementary error function, imaginary error function, and
2903Dawson function); given these, one can also easily compute Voigt functions,
2904Fresnel integrals, and similar related functions as well.")
2905 ;; Faddeeva is released under the Expat license; AMOS is included as
2906 ;; public domain software.
2907 (license (list license:expat license:public-domain))))
2908
2742f87e
RW		 2909(define-public suitesparse
2910 (package
2911 (name "suitesparse")
bd5b5ac0 2912 (version "4.5.5")
2742f87e
RW		 2913 (source
2914 (origin
2915 (method url-fetch)
2916 (uri (string-append
2917 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
2918 version ".tar.gz"))
2919 (sha256
2920 (base32
bd5b5ac0
EB		 2921 "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
2922 (modules '((guix build utils)))
2923 (snippet
2924 ;; Remove bundled metis source
2925 '(delete-file-recursively "metis-5.1.0"))))
2742f87e
RW		 2926 (build-system gnu-build-system)
2927 (arguments
bd5b5ac0 2928 '(#:tests? #f ;no "check" target
2742f87e
RW		 2929 #:make-flags
2930 (list "CC=gcc"
2931 "BLAS=-lblas"
2932 "TBB=-ltbb"
bd5b5ac0 2933 "MY_METIS_LIB=-lmetis"
2742f87e
RW		 2934 (string-append "INSTALL_LIB="
2935 (assoc-ref %outputs "out") "/lib")
2936 (string-append "INSTALL_INCLUDE="
bd5b5ac0
EB		 2937 (assoc-ref %outputs "out") "/include")
2938 "library")
2742f87e 2939 #:phases
2509522c 2940 (modify-phases %standard-phases
bd5b5ac0 2941 (delete 'configure)))) ;no configure script
2742f87e
RW		 2942 (inputs
2943 `(("tbb" ,tbb)
bd5b5ac0
EB		 2944 ("lapack" ,lapack)
2945 ("metis" ,metis)))
2742f87e
RW		 2946 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
2947 (synopsis "Suite of sparse matrix software")
2948 (description
2949 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
2950multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
2951multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
2952simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
2953CXSparse, a concise sparse Cholesky factorization package; and many other
2954packages.")
2955 ;; LGPLv2.1+:
2956 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
2957 ;; GPLv2+:
2958 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
2959 (license (list license:gpl2+ license:lgpl2.1+))))
2960
ec322be2
FB		 2961(define-public atlas
2962 (package
2963 (name "atlas")
3c98ac02 2964 (version "3.10.3")
ec322be2
FB		 2965 (source (origin
2966 (method url-fetch)
de67e922
LF		 2967 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
2968 version "/atlas" version ".tar.bz2"))
ec322be2
FB		 2969 (sha256
2970 (base32
3c98ac02 2971 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
ec322be2
FB		 2972 (build-system gnu-build-system)
2973 (home-page "http://math-atlas.sourceforge.net/")
19afbea1 2974 (inputs `(("gfortran" ,gfortran)
ec322be2
FB		 2975 ("lapack-tar" ,(package-source lapack))))
2976 (outputs '("out" "doc"))
01480b9e
FB		 2977 ;; For the moment we drop support for MIPS at it fails to compile. See
2978 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
2979 (supported-systems (delete "mips64el-linux" %supported-systems))
ec322be2
FB		 2980 (arguments
2981 `(#:parallel-build? #f
2982 #:parallel-tests? #f
f15615b1
LC		 2983
2984 ;; ATLAS tunes itself for the machine it is built on, as explained at
2985 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
2986 ;; For this reason, we want users to build it locally instead of using
2987 ;; substitutes.
2988 #:substitutable? #f
2989
ec322be2
FB		 2990 #:modules ((srfi srfi-26)
2991 (srfi srfi-1)
2992 (guix build gnu-build-system)
2993 (guix build utils))
40029cbe 2994 #:configure-flags
ec322be2
FB		 2995 `(;; Generate position independent code suitable for dynamic libraries
2996 ;; and use WALL timer to get more accurate timing.
2997 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
2998 ;; Set word width.
2999 "-b"
3000 ,,(if (string-match "64" (%current-system))
3001 "64"
3002 "32")
3003 ;; Disable parallel build as it gives errors: atlas_pthread.h is
3004 ;; needed to compile C files before it is generated.
3005 "-Ss" "pmake" "make -j 1"
af89a667
FB		 3006 ;; Probe is failing for MIPS. We therefore define the system
3007 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3008 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3009 ,,@(if (string-prefix? "mips" (%current-system))
3010 (list "-A" "49" "-V" "1")
3011 (list))
ec322be2
FB		 3012 ;; Generate shared libraries.
3013 "--shared"
3014 ;; Build a full LAPACK library.
3015 ,(string-append "--with-netlib-lapack-tarfile="
3016 (assoc-ref %build-inputs "lapack-tar")))
3017 #:phases
e5b4b96b
EF		 3018 (modify-phases %standard-phases
3019 (add-after 'install 'install-doc
3020 (lambda* (#:key outputs inputs #:allow-other-keys)
3021 (let ((doc (string-append (assoc-ref outputs "doc")
3022 "/share/doc/atlas")))
3023 (mkdir-p doc)
3024 (fold (lambda (file previous)
3025 (and previous (zero? (system* "cp" file doc))))
3026 #t (find-files "../ATLAS/doc" ".*")))))
3027 (add-after 'check 'check-pt
3028 (lambda _ (zero? (system* "make" "ptcheck"))))
3029 ;; Fix files required to run configure.
3030 (add-before 'configure 'fix-/bin/sh
ec322be2
FB		 3031 (lambda _
3032 ;; Use `sh', not `/bin/sh'.
3033 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3034 (("/bin/sh")
e5b4b96b
EF		 3035 "sh"))))
3036 ;; Fix /bin/sh in generated make files.
3037 (add-after 'configure 'fix-/bin/sh-in-generated-files
3038 (lambda _
3039 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3040 (("/bin/sh")
3041 "sh"))))
3042 ;; ATLAS configure program does not accepts the default flags
3043 ;; passed by the 'gnu-build-system'.
3044 (replace 'configure
3045 (lambda* (#:key native-inputs inputs outputs
3046 (configure-flags '())
3047 #:allow-other-keys #:rest args)
3048 (let* ((prefix (assoc-ref outputs "out"))
3049 (bash (or (and=> (assoc-ref
3050 (or native-inputs inputs) "bash")
3051 (cut string-append <> "/bin/bash"))
3052 "/bin/sh"))
3053 (flags `(,(string-append "--prefix=" prefix)
3054 ,@configure-flags))
3055 (abs-srcdir (getcwd))
3056 (srcdir (string-append "../" (basename abs-srcdir))))
3057 (format #t "source directory: ~s (relative from build: ~s)~%"
3058 abs-srcdir srcdir)
3059 (mkdir "../build")
3060 (chdir "../build")
3061 (format #t "build directory: ~s~%" (getcwd))
3062 (format #t "configure flags: ~s~%" flags)
3063 (zero? (apply system* bash
3064 (string-append srcdir "/configure")
3065 flags))))))))
ec322be2
FB		 3066 (synopsis "Automatically Tuned Linear Algebra Software")
3067 (description
3068 "ATLAS is an automatically tuned linear algebra software library
3069providing C and Fortran77 interfaces to a portably efficient BLAS
3070implementation, as well as a few routines from LAPACK.
3071
f15615b1
LC		 3072Optimization occurs at build time. For this reason, the library is built on
3073the machine where it is installed, without resorting to pre-built substitutes.
ec322be2 3074
f15615b1 3075Before building the library, CPU throttling should be disabled. This can be
d97c429a 3076done in the BIOS, or, on GNU/Linux, with the following command:
ec322be2 3077
8e9ba611 3078@example
d97c429a 3079# cpupower --governor performance
8e9ba611 3080@end example
ec322be2 3081
d97c429a 3082Failure to do so will result in a library with poor performance.")
ec322be2 3083 (license license:bsd-3)))
c12efc72
AE		 3084
3085(define-public glm
3086 (package
3087 (name "glm")
3088 (version "0.9.6.3")
3089 (source
3090 (origin
3091 (method url-fetch)
de67e922
LF		 3092 (uri (string-append "mirror://sourceforge/ogl-math/glm-" version
3093 "/glm-" version ".zip"))
c12efc72
AE		 3094 (sha256
3095 (base32
3096 "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l"))))
3097 (build-system cmake-build-system)
3098 (native-inputs
3099 `(("unzip" ,unzip)))
3100 (home-page "http://glm.g-truc.net")
3101 (synopsis "OpenGL Mathematics library")
3102 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3103library for graphics software based on the OpenGL Shading Language (GLSL)
3104specifications.")
3105 (license license:expat)))
7f18257b
AE		 3106
3107(define-public lpsolve
3108 (package
3109 (name "lpsolve")
a89e0cf5 3110 (version "5.5.2.5")
7f18257b
AE		 3111 (source
3112 (origin
3113 (method url-fetch)
3114 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3115 "/lp_solve_" version "_source.tar.gz"))
3116 (sha256
3117 (base32
a89e0cf5 3118 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
7f18257b
AE		 3119 (modules '((guix build utils)))
3120 (snippet
3121 '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3122 (("^c=cc") "c=gcc")
3123 ;; Pretend to be on a 64 bit platform to obtain a common directory
3124 ;; name for the build results on all architectures; nothing else
3125 ;; seems to depend on it.
5dbfbef7
LC		 3126 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3127
3128 ;; The check for 'isnan' as it is written fails with
3129 ;; "non-floating-point argument in call to function
3130 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3131 ;; definition, which in turn leads to bad things. Fix the feature
3132 ;; test.
3133 (("isnan\\(0\\)") "isnan(0.)")))))
7f18257b
AE		 3134 (build-system gnu-build-system)
3135 (arguments
6c96b545 3136 `(#:tests? #f ; no check target
7f18257b
AE		 3137 #:phases
3138 (modify-phases %standard-phases
6c96b545 3139 (delete 'configure) ; no configure script
7f18257b
AE		 3140 (replace 'build
3141 (lambda _
6c96b545
TGR		 3142 (with-directory-excursion "lpsolve55"
3143 (invoke "bash" "ccc"))
3144 (with-directory-excursion "lp_solve"
3145 (invoke "bash" "ccc"))
3146 #t))
7f18257b
AE		 3147 (replace 'install
3148 (lambda* (#:key outputs #:allow-other-keys)
3149 (let* ((out (assoc-ref outputs "out"))
3150 (bin (string-append out "/bin"))
3151 (lib (string-append out "/lib"))
3152 ;; This is where LibreOffice expects to find the header
3153 ;; files, and where they are installed by Debian.
3154 (include (string-append out "/include/lpsolve")))
6c96b545
TGR		 3155 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3156 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
96c46210
LC		 3157 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3158
7f18257b
AE		 3159 ;; Install a subset of the header files as on Debian
3160 ;; (plus lp_bit.h, which matches the regular expression).
96c46210
LC		 3161 (for-each (lambda (name)
3162 (install-file name include))
3163 (find-files "." "lp_[HMSa-z].*\\.h$"))
7f18257b 3164 (with-directory-excursion "shared"
96c46210
LC		 3165 (for-each (lambda (name)
3166 (install-file name include))
3167 (find-files "." "\\.h$")))
7f18257b
AE		 3168 #t))))))
3169 (home-page "http://lpsolve.sourceforge.net/")
3170 (synopsis "Mixed integer linear programming (MILP) solver")
3171 (description
3172 "lp_solve is a mixed integer linear programming solver based on the
3173revised simplex and the branch-and-bound methods.")
3174 (license license:lgpl2.1+)))
a17d4564
EB		 3175
3176(define-public dealii
3177 (package
3178 (name "dealii")
24404eaf 3179 (version "8.5.1")
a17d4564
EB		 3180 (source
3181 (origin
3182 (method url-fetch)
3183 (uri (string-append "https://github.com/dealii/dealii/releases/"
3184 "download/v" version "/dealii-" version ".tar.gz"))
3185 (sha256
3186 (base32
24404eaf 3187 "1bh9rsmkrg0zi70n27b11djmac9lximghsiy7mg7w7x544n82gnk"))
a17d4564
EB		 3188 (modules '((guix build utils)))
3189 (snippet
3190 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
3191 '(delete-file-recursively "bundled"))))
3192 (build-system cmake-build-system)
3193 (inputs
3194 `(("tbb" ,tbb)
3195 ("zlib" ,zlib)
3196 ("boost" ,boost)
3197 ("p4est" ,p4est)
3198 ("blas" ,openblas)
3199 ("lapack" ,lapack)
3200 ("arpack" ,arpack-ng)
3201 ("muparser" ,muparser)
3202 ("gfortran" ,gfortran)
3203 ("suitesparse" ,suitesparse))) ;for UMFPACK
3204 (arguments
3205 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
d84b09e9
EB		 3206 #:configure-flags
3207 ;; Work around a bug in libsuitesparseconfig linking
3208 ;; see https://github.com/dealii/dealii/issues/4745
3209 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
a17d4564
EB		 3210 (home-page "https://www.dealii.org")
3211 (synopsis "Finite element library")
3212 (description
3213 "Deal.II is a C++ program library targeted at the computational solution
3214of partial differential equations using adaptive finite elements. The main
3215aim of deal.II is to enable rapid development of modern finite element codes,
3216using among other aspects adaptive meshes and a wide array of tools often used
3217in finite element programs.")
3218 (license license:lgpl2.1+)))
3219
3220(define-public dealii-openmpi
3221 (package (inherit dealii)
3222 (name "dealii-openmpi")
3223 (inputs
3224 `(("mpi" ,openmpi)
3225 ;;Supported only with MPI:
3226 ("p4est" ,p4est-openmpi)
3227 ("petsc" ,petsc-openmpi)
3228 ("slepc" ,slepc-openmpi)
3229 ("metis" ,metis) ;for MUMPS
3230 ("scalapack" ,scalapack) ;for MUMPS
3231 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3232 ("arpack" ,arpack-ng-openmpi)
3233 ,@(fold alist-delete (package-inputs dealii)
3234 '("p4est" "arpack"))))
3235 (arguments
3236 (substitute-keyword-arguments (package-arguments dealii)
3237 ((#:configure-flags cf)
3238 ``("-DMPI_C_COMPILER=mpicc"
3239 "-DMPI_CXX_COMPILER=mpicxx"
3240 "-DMPI_Fortran_COMPILER=mpifort"
3241 ,@,cf))))
3242 (synopsis "Finite element library (with MPI support)")))
194c7f95
AE		 3243
3244(define-public flann
3245 (package
3246 (name "flann")
3247 (version "1.8.4")
3248 (source
3249 (origin
3250 (method url-fetch)
3251 (uri
3252 (string-append
3253 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3254 version "-src.zip"))
3255 (sha256
3256 (base32
3257 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))))
3258 (build-system cmake-build-system)
6b6aca9b
LC		 3259 (outputs '("out"
3260 "octave")) ;46 MiB .mex file that pulls Octave
194c7f95
AE		 3261 (native-inputs
3262 `(("unzip" ,unzip)))
3263 (inputs
3264 `(("hdf5" ,hdf5)
3265 ("octave" ,octave)
3266 ("python" ,python-2) ; print syntax
3267 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3268 ("zlib" ,zlib)))
3269 (arguments
39b30337
LC		 3270 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3271 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3272 #:strip-directories '("lib" "lib64" "libexec"
3273 "bin" "sbin" "share/flann/octave")
3274
9684e30b
LC		 3275 ;; Save 12 MiB by not installing .a files. Passing
3276 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3277 #:phases (modify-phases %standard-phases
6b6aca9b
LC		 3278 (add-before 'configure 'set-octave-directory
3279 (lambda* (#:key outputs #:allow-other-keys)
3280 ;; Install the .mex file in the "octave" output.
3281 (let ((out (assoc-ref outputs "octave")))
3282 (substitute* "src/matlab/CMakeLists.txt"
3283 (("share/flann/octave")
3284 (string-append out "/share/flann/octave")))
3285 #t)))
9684e30b
LC		 3286 (add-after 'install 'remove-static-libraries
3287 (lambda* (#:key outputs #:allow-other-keys)
3288 (let* ((out (assoc-ref outputs "out"))
3289 (lib (string-append out "/lib")))
3290 (for-each delete-file
3291 (find-files lib "\\.a$"))
3292 #t))))
3293
39b30337 3294 #:tests? #f)) ; The test data are downloaded from the Internet.
194c7f95
AE		 3295 (home-page "http://www.cs.ubc.ca/research/flann/")
3296 (synopsis "Library for approximate nearest neighbors computation")
3297 (description "FLANN is a library for performing fast approximate
3298nearest neighbor searches in high dimensional spaces. It implements a
3299collection of algorithms and a system for automatically choosing the best
3300algorithm and optimum parameters depending on the dataset.
3301
3302FLANN is written in C++ and contains bindings for C, Octave and Python.")
3303 (license (license:non-copyleft "file://COPYING"
3304 "See COPYING in the distribution."))))
d8c97beb
EF		 3305
3306(define-public wcalc
3307 (package
3308 (name "wcalc")
3309 (version "2.5")
3310 (source
3311 (origin
3312 (method url-fetch)
de67e922
LF		 3313 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3314 "wcalc-" version ".tar.bz2"))
d8c97beb
EF		 3315 (sha256
3316 (base32
3317 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3318 (build-system gnu-build-system)
3319 (inputs
3320 `(("mpfr" ,mpfr)
3321 ("readline" ,readline)))
3322 (home-page "http://w-calc.sourceforge.net/index.php")
3323 (synopsis "Flexible command-line scientific calculator")
3324 (description "Wcalc is a very capable calculator. It has standard functions
3325(sin, asin, and sinh for example, in either radians or degrees), many
3326pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3327variables, a command history, hex/octal/binary input and output, unit
3328conversions, embedded comments, and an expandable expression entry field. It
3329evaluates expressions using the standard order of operations.")
3330 (license license:gpl2+)))
45147b0c
FH		 3331
3332(define-public xaos
3333 (package
3334 (name "xaos")
3335 (version "3.6")
3336 (source (origin
3337 (method url-fetch)
de67e922
LF		 3338 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3339 "/xaos-" version ".tar.gz"))
45147b0c
FH		 3340 (sha256
3341 (base32
3342 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3343 (build-system gnu-build-system)
b94a6ca0 3344 (native-inputs `(("gettext" ,gettext-minimal)))
45147b0c
FH		 3345 (inputs `(("libx11" ,libx11)
3346 ("zlib" ,zlib)
3347 ("libpng" ,libpng)
3348 ("gsl" ,gsl)))
3349 (arguments
3350 `(#:tests? #f ;no "check" target
3351 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3352 (synopsis "Real-time fractal zoomer")
3353 (description "GNU XaoS is a graphical program that generates fractal
3354patterns and allows you to zoom in and out of them infinitely in a fluid,
3355continuous manner. It also includes tutorials that help to explain how fractals
3356are built. It can generate many different fractal types such as the Mandelbrot
3357set.")
6fd52309 3358 (home-page "https://www.gnu.org/software/xaos/")
45147b0c 3359 (license license:gpl2+)))
528bb464
EB		 3360
3361(define-public hypre
3362 (package
3363 (name "hypre")
3364 (version "2.11.0")
3365 (source (origin
3366 (method url-fetch)
3367 (uri (string-append "https://github.com/LLNL/hypre/archive/"
3368 "v" version ".tar.gz"))
3369 (file-name (string-append name "-" version ".tar.gz"))
3370 (sha256
3371 (base32
3372 "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m"))
3373 (modules '((guix build utils)))
3374 (snippet
3375 '(begin
3376 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
3377 ;; substitute the tarball creation time.
3378 (substitute* "src/utilities/HYPRE_utilities.h"
3379 (("Date Compiled: .*$")
3380 "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n"))
3381 #t))))
3382 (build-system gnu-build-system)
3383 (outputs '("out" ;6.1 MiB of headers and libraries
3384 "doc")) ;4.8 MiB of documentation
3385 (native-inputs
3386 `(("doc++" ,doc++)
3387 ("netpbm" ,netpbm)
3388 ("texlive" ,texlive) ;full package required for fonts
3389 ("ghostscript" ,ghostscript)))
3390 (inputs
3391 `(("blas" ,openblas)
3392 ("lapack" ,lapack)))
3393 (arguments
3394 `(#:modules ((srfi srfi-1)
3395 ,@%gnu-build-system-modules)
3396 #:configure-flags '("--enable-shared"
3397 "--disable-fortran"
3398 "--without-MPI"
3399 "--with-openmp"
3400 "--with-fei"
3401 "--with-lapack"
3402 "--with-blas")
3403 #:phases
3404 (modify-phases %standard-phases
3405 (add-before 'configure 'chdir-src
3406 (lambda _ (chdir "src")))
3407 (replace 'configure
3408 (lambda* (#:key build target configure-flags
3409 #:allow-other-keys #:rest args)
3410 (let* ((configure (assoc-ref %standard-phases 'configure)))
3411 (apply configure
3412 (append args
3413 (list #:configure-flags
3414 (cons (string-append
3415 "--host=" (or target build))
3416 configure-flags)))))))
3417 (add-after 'build 'build-docs
3418 (lambda _
3419 (zero? (system* "make" "-Cdocs" "pdf" "html"))))
3420 (replace 'check
3421 (lambda _
3422 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3423 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
3424 (and (system* "make" "check" "CHECKRUN=")
3425 (fold (lambda (filename result)
3426 (and result
3427 (let ((size (stat:size (stat filename))))
3428 (when (not (zero? size))
3429 (format #t "~a size ~d; error indication~%"
3430 filename size))
3431 (zero? size))))
3432 #t
3433 (find-files "test" ".*\\.err$")))))
3434 (add-after 'install 'install-docs
3435 (lambda* (#:key outputs #:allow-other-keys)
3436 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3437 (let* ((doc (assoc-ref outputs "doc"))
3438 (docdir (string-append doc "/share/doc/hypre-" ,version)))
528bb464
EB		 3439 (with-directory-excursion "docs"
3440 (for-each (lambda (base)
3441 (install-file (string-append base ".pdf") docdir)
3442 (copy-recursively base docdir)) ;html docs
3443 '("HYPRE_usr_manual"
3444 "HYPRE_ref_manual")))
3445 #t))))))
3446 (home-page "http://www.llnl.gov/casc/hypre/")
3447 (synopsis "Library of solvers and preconditioners for linear equations")
3448 (description
3449 "HYPRE is a software library of high performance preconditioners and
3450solvers for the solution of large, sparse linear systems of equations. It
3451features multigrid solvers for both structured and unstructured grid
3452problems.")
3453 (license license:lgpl2.1)))
3454
3455(define-public hypre-openmpi
3456 (package (inherit hypre)
3457 (name "hypre-openmpi")
3458 (inputs
3459 `(("mpi" ,openmpi)
3460 ,@(package-inputs hypre)))
3461 (arguments
3462 (substitute-keyword-arguments (package-arguments hypre)
3463 ((#:configure-flags flags)
3464 ``("--with-MPI"
3465 ,@(delete "--without-MPI" ,flags)))))
3466 (synopsis "Parallel solvers and preconditioners for linear equations")
3467 (description
3468 "HYPRE is a software library of high performance preconditioners and
3469solvers for the solution of large, sparse linear systems of equations on
3470parallel computers. It features parallel multigrid solvers for both
3471structured and unstructured grid problems.")))
6c90e183
EB		 3472
3473(define-public matio
3474 (package
3475 (name "matio")
3476 (version "1.5.6")
3477 (source
3478 (origin
3479 (method url-fetch)
de67e922 3480 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
6c90e183
EB		 3481 "matio-" version ".tar.gz"))
3482 (sha256
3483 (base32
3484 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3485 (build-system gnu-build-system)
3486 (inputs
3487 `(("zlib" ,zlib)
3488 ("hdf5" ,hdf5)))
3489 (home-page "http://matio.sourceforge.net/")
3490 (synopsis "Library for reading and writing MAT files")
3491 (description "Matio is a library for reading and writing MAT files. It
3492supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3493 (license license:bsd-2)))
d721c83a 3494
517318ad
LF		 3495(define-public vc
3496 (package
3497 (name "vc")
853b0292 3498 (version "1.3.3")
517318ad
LF		 3499 (source
3500 (origin (method url-fetch)
3501 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3502 "download/" version "/Vc-" version ".tar.gz"))
3503 (sha256
3504 (base32
853b0292 3505 "1zmlpn32jzb38smp3j834llmbix3whsrbw0h397qxysbw792kih8"))))
517318ad
LF		 3506 (build-system cmake-build-system)
3507 (arguments
3508 '(#:configure-flags
3509 '("-DBUILD_TESTING=ON")))
3510 (synopsis "SIMD vector classes for C++")
3511 (description "Vc provides portable, zero-overhead C++ types for explicitly
3512data-parallel programming. It is a library designed to ease explicit
3513vectorization of C++ code. Its types enable explicitly stating data-parallel
3514operations on multiple values. The parallelism is therefore added via the type
3515system. Vc has an intuitive API and provides portability between different
3516compilers and compiler versions as well as portability between different vector
3517instruction sets. Thus, an application written with Vc can be compiled for:
3518@enumerate
3519@item AVX and AVX2
d1e4ad1b 3520@item SSE2 up to SSE4.2 or SSE4a
517318ad
LF		 3521@item Scalar
3522@item MIC
3523@item NEON (in development)
3524@item NVIDIA GPUs / CUDA (in development)
3525@end enumerate\n")
3526 (home-page "https://github.com/VcDevel/Vc")
a8ead6f9
EF		 3527 ;; "No support_???.cpp file exists for this architecture."
3528 (supported-systems '("x86_64-linux" "i686-linux"))
517318ad 3529 (license license:bsd-3)))
54052a54 3530
3531(define-public reducelcs
3532 ;; This is the last commit which is available upstream, no
3533 ;; release happened since 2010.
3534 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
3535 (revision "1"))
3536 (package
3537 (name "reducelcs")
3538 (version (string-append "1.0-" revision "." (string-take commit 7)))
3539 (source
3540 (origin
3541 (method git-fetch)
3542 (uri (git-reference
3543 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
3544 (commit commit)))
3545 (file-name (string-append name "-" version "-checkout"))
3546 (sha256
3547 (base32
3548 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
3549 (build-system gnu-build-system)
3550 (inputs
3551 `(("openlibm" ,openlibm)))
3552 (arguments
3553 `(#:tests? #f ; no tests
3554 #:phases
3555 (modify-phases %standard-phases
3556 (delete 'configure) ; No configure script exists.
3557 (replace 'install ; No install phase exists.
3558 (lambda* (#:key outputs #:allow-other-keys)
3559 (let* ((out (assoc-ref outputs "out"))
3560 (bin (string-append out "/bin")))
3561 (install-file "Approximation" bin)
3562 (install-file "CollectResults" bin)
3563 (install-file "GenerateInstances" bin)
3564 #t))))))
3565 (synopsis "Approximate Longest Commons Subsequence computation tool")
3566 (description
3567 "@code{reduceLCS} is an implementation of the Reduce-Expand
3568algorithm for LCS. It is a fast program to compute the approximate
3569Longest Commons Subsequence of a set of strings.")
3570 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
c000b6b1 3571 (license license:gpl3+))))
479c4273
JD		 3572
3573(define-public jacal
3574 (package
3575 (name "jacal")
3576 (version "1c4")
3577 (source (origin
3578 (method url-fetch)
3579 (uri (string-append
3580 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
3581 version ".zip"))
3582 (sha256 (base32
3583 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
3584 (patches (search-patches "jacal-fix-texinfo.patch"))))
3585 (build-system gnu-build-system)
3586 (arguments
3587 `(#:phases
3588 (modify-phases %standard-phases
3589 (add-before 'build 'pre-build
3590 ;; Don't use upstream's script - it really doesn't fit into
3591 ;; Guix's functional paradigm.
3592 (lambda* (#:key inputs outputs #:allow-other-keys)
3593 (substitute* "Makefile"
3594 (("^install: install-script") "install: "))))
3595 (add-after 'install 'post-install
3596 ;; Instead, we provide our own simplified script.
3597 (lambda* (#:key inputs outputs #:allow-other-keys)
3598 (let ((wrapper (string-append (assoc-ref outputs "out")
3599 "/bin/jacal")))
3600 (format (open wrapper (logior O_WRONLY O_CREAT))
3601 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
3602 "-e '(slib:load \"~a/lib/jacal/math\") "
3603 "(math)' \"$@\"\n")
3604 (which "bash")
3605 (assoc-ref inputs "scm")
3606 (assoc-ref outputs "out"))
3607 (chmod wrapper #o555))))
3608 (replace 'configure
3609 (lambda* (#:key inputs outputs #:allow-other-keys)
3610 (zero? (system* "./configure"
3611 (string-append "--prefix="
3612 (assoc-ref outputs "out")))))))))
3613 (inputs `(("scm" ,scm)))
3614 (native-inputs `(("unzip" ,unzip)
3615 ("texinfo" ,texinfo)))
3616 (synopsis "Symbolic mathematics system")
3617 (description "GNU JACAL is an interactive symbolic mathematics program based on
3618Scheme. It manipulate and simplify a range of mathematical expressions such
3619as equations, scalars, vectors, and matrices.")
6fd52309 3620 (home-page "https://www.gnu.org/software/jacal/")
479c4273
JD		 3621 (license license:gpl3+)))
3622
313844d9
TF		 3623(define-public z3
3624 (package
3625 (name "z3")
3626 (version "4.5.0")
3627 (source (origin
3628 (method url-fetch)
3629 (uri (string-append
3630 "https://github.com/Z3Prover/z3/archive/z3-"
3631 version ".tar.gz"))
3632 (sha256
3633 (base32
3634 "032a5lvji2liwmc25jv52bdrhimqflvqbpg77ccaq1jykhiivbmf"))))
cf684d87 3635 (build-system cmake-build-system)
313844d9 3636 (arguments
cf684d87
TF		 3637 `(#:configure-flags
3638 (list "-DBUILD_PYTHON_BINDINGS=true"
3639 "-DINSTALL_PYTHON_BINDINGS=true"
3640 (string-append "-DCMAKE_INSTALL_PYTHON_PKG_DIR="
3641 %output
677bc34d 3642 "/lib/python2.7/site-packages"))
313844d9
TF		 3643 #:phases
3644 (modify-phases %standard-phases
cf684d87
TF		 3645 (add-before 'configure 'bootstrap
3646 (lambda _
313844d9 3647 (zero?
cf684d87
TF		 3648 (system* "python" "contrib/cmake/bootstrap.py" "create"))))
3649 (add-before 'check 'make-test-z3
313844d9 3650 (lambda _
cf684d87
TF		 3651 ;; Build the test suite executable.
3652 (zero? (system* "make" "test-z3" "-j"
3653 (number->string (parallel-job-count))))))
3654 (replace 'check
3655 (lambda _
3656 ;; Run all the tests that don't require arguments.
3657 (zero? (system* "./test-z3" "/a")))))))
313844d9
TF		 3658 (native-inputs
3659 `(("python" ,python-2)))
3660 (synopsis "Theorem prover")
3661 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
cf684d87 3662theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
313844d9
TF		 3663 (home-page "https://github.com/Z3Prover/z3")
3664 (license license:expat)))
3d5d87a3
JL		 3665
3666(define-public cubicle
3667 (package
3668 (name "cubicle")
3669 (version "1.1.1")
3670 (source (origin
3671 (method url-fetch)
3672 (uri (string-append "http://cubicle.lri.fr/cubicle-"
3673 version ".tar.gz"))
3674 (sha256
3675 (base32
3676 "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h"))))
3677 (build-system gnu-build-system)
3678 (native-inputs
3679 `(("ocaml" ,ocaml)
83fef82b 3680 ("which" ,(@@ (gnu packages base) which))))
3d5d87a3
JL		 3681 (propagated-inputs
3682 `(("z3" ,z3)))
3683 (arguments
3684 `(#:configure-flags (list "--with-z3")
3685 #:tests? #f
3686 #:phases
3687 (modify-phases %standard-phases
3688 (add-before 'configure 'configure-for-release
3689 (lambda _
3690 (substitute* "Makefile.in"
3691 (("SVNREV=") "#SVNREV="))))
3692 (add-before 'configure 'fix-/bin/sh
3693 (lambda _
3694 (substitute* "configure"
3695 (("/bin/sh") (which "sh")))))
3696 (add-before 'configure 'fix-smt-z3wrapper.ml
3697 (lambda _
3698 (substitute* "Makefile.in"
3699 (("\\\\n") "")))))))
3700 (home-page "http://cubicle.lri.fr/")
3701 (synopsis "Model checker for array-based systems")
5a80c15c
RW		 3702 (description "Cubicle is a model checker for verifying safety properties
3703of array-based systems. This is a syntactically restricted class of
3704parametrized transition systems with states represented as arrays indexed by
3705an arbitrary number of processes. Cache coherence protocols and mutual
3706exclusion algorithms are typical examples of such systems.")
3d5d87a3 3707 (license license:asl2.0)))
e01397b4
EB		 3708
3709(define-public elemental
3710 (package
3711 (name "elemental")
3712 (version "0.87.7")
3713 (source (origin
3714 (method url-fetch)
3715 (uri (string-append "https://github.com/elemental/Elemental/"
3716 "archive/v" version ".tar.gz"))
3717 (file-name (string-append name "-" version ".tar.gz"))
3718 (sha256
3719 (base32
3720 "1nfp82w22pi8x8fg9sc37z8kf84dqi1dhxp8bbk7571y4aygvv3v"))))
3721 (build-system cmake-build-system)
3722 (home-page "http://libelemental.org")
3723 (native-inputs
3724 `(("gfortran" ,gfortran)))
3725 (inputs
3726 `(("blas" ,openblas)
3727 ("gfortran:lib" ,gfortran "lib")
3728 ("gmp" ,gmp)
3729 ("lapack" ,lapack)
3730 ("metis" ,metis)
3731 ("mpc" ,mpc)
3732 ("mpfr" ,mpfr)
3733 ("mpi" ,openmpi)
3734 ("qd" ,qd)))
3735 (arguments
3736 `(#:build-type "Release" ;default RelWithDebInfo not supported
3737 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
3738 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
3739 "-DEL_CACHE_WARNINGS:BOOL=YES"
3740 "-DEL_TESTS:BOOL=YES"
3741 "-DCMAKE_INSTALL_LIBDIR=lib"
3742 "-DGFORTRAN_LIB=gfortran")
3743 #:phases (modify-phases %standard-phases
3744 (add-before 'check 'setup-tests
3745 (lambda _
3746 ;; Parallelism is done at the MPI layer.
3747 (setenv "OMP_NUM_THREADS" "1")
3748 #t))
3749 (add-after 'install 'remove-tests
3750 (lambda* (#:key outputs #:allow-other-keys)
3751 ;; Tests are installed, with no easy configuration
3752 ;; switch to prevent this, so delete them.
3753 (delete-file-recursively
3754 (string-append (assoc-ref outputs "out") "/bin"))
3755 #t)))))
3756 (synopsis "Dense and sparse-direct linear algebra and optimization")
3757 (description "Elemental is a modern C++ library for distributed-memory
3758dense and sparse-direct linear algebra, conic optimization, and lattice
3759reduction.")
3760 (license license:bsd-2)))
5b05dce7
JN		 3761
3762(define-public mcrl2
3763 (package
3764 (name "mcrl2")
3765 (version "201707.1.15162")
3766 (source (origin
3767 (method url-fetch)
3768 (uri (string-append "http://www.mcrl2.org/download/devel/mcrl2-"
3769 version
3770 ".tar.gz"))
3771 (sha256
3772 (base32
3773 "1ziww2fchsklm25hl9p2mngssxfh9w07nc114cncqaxfibqp2p8f"))))
3774 (native-inputs
3775 `(("subversion" ,subversion)))
3776 (inputs
3777 `(("boost" ,boost)
3778 ("glu" ,glu)
3779 ("mesa" ,mesa)
3780 ("qt" ,qt)))
3781 (build-system cmake-build-system)
ed0c5d3c 3782 (synopsis "Toolset for the mCRL2 formal specification language")
5b05dce7 3783 (description
ed0c5d3c
TGR		 3784 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
3785specification language for describing concurrent discrete event systems. Its
3786toolset supports analysis and automatic verification, linearisation, simulation,
3787state-space exploration and generation, and tools to optimise and analyse
5b05dce7
JN		 3788specifications. Also, state spaces can be manipulated, visualised and
3789analysed.")
3790 (home-page "http://mcrl2.org")
3791 (license license:boost1.0)))
41835f94
LF		 3792
3793(define-public r-subplex
3794 (package
3795 (name "r-subplex")
3796 (version "1.5-2")
3797 (source
3798 (origin
3799 (method url-fetch)
3800 (uri (cran-uri "subplex" version))
3801 (sha256
3802 (base32
3803 "1v9xrnkapnq7v1jbhlg32ignklzf2vn8rqpayc8pzk8wvz53r33g"))))
3804 (build-system r-build-system)
3805 (native-inputs
3806 `(("gfortran" ,gfortran)))
3807 (home-page "https://cran.r-project.org/web/packages/subplex")
3808 (synopsis "Unconstrained optimization using the subplex algorithm")
3809 (description "This package implements the Subplex optimization algorithm.
3810It solves unconstrained optimization problems using a simplex method on
3811subspaces. The method is well suited for optimizing objective functions that
3812are noisy or are discontinuous at the solution.")
3813 (license license:gpl3+)))
799ad71b
LF		 3814
3815(define-public r-desolve
3816 (package
3817 (name "r-desolve")
3818 (version "1.20")
3819 (source
3820 (origin
3821 (method url-fetch)
3822 (uri (cran-uri "deSolve" version))
3823 (sha256
3824 (base32
3825 "18nx3maww979a8p8ly4hv63y65mnjx8vbj2fpipd6rhcbf1lbsan"))))
3826 (properties `((upstream-name . "deSolve")))
3827 (build-system r-build-system)
3828 (native-inputs
3829 `(("gfortran" ,gfortran)))
3830 (home-page "https://desolve.r-forge.r-project.org/")
3831 (synopsis "Solvers for initial value problems of differential equations")
3832 (description "This package provides functions that solve initial
3833value problems of a system of first-order ordinary differential equations (ODE),
3834of partial differential equations (PDE), of differential algebraic equations
3835(DAE), and of delay differential equations. The functions provide an interface
3836to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
3837to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
3838the Runge-Kutta family with fixed or variable time steps. The package contains
3839routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
3840differential equations (PDE) that have been converted to ODEs by numerical
3841differencing.")
3842 (license license:gpl2+)))
jackhill's copy of GNU Guix: https://guix.gnu.org/