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gnu: clang-from-llvm: Fix install for clang-3.*.
[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>
ab5f3f21 14;;; Copyright © 2016, 2018 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>
71ca16b5 18;;; Copyright © 2017, 2018 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>
910deec6 27;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
07254d8b 28;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
560acf25 29;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
daa6036f 30;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
564cf93f 31;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
8f8b2451
AE		 32;;;
33;;; This file is part of GNU Guix.
34;;;
35;;; GNU Guix is free software; you can redistribute it and/or modify it
36;;; under the terms of the GNU General Public License as published by
37;;; the Free Software Foundation; either version 3 of the License, or (at
38;;; your option) any later version.
39;;;
40;;; GNU Guix is distributed in the hope that it will be useful, but
41;;; WITHOUT ANY WARRANTY; without even the implied warranty of
42;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
43;;; GNU General Public License for more details.
44;;;
45;;; You should have received a copy of the GNU General Public License
46;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
47
48(define-module (gnu packages maths)
ec322be2 49 #:use-module (ice-9 regex)
8f8b2451 50 #:use-module (gnu packages)
b5b73a82 51 #:use-module ((guix licenses) #:prefix license:)
8f8b2451
AE		 52 #:use-module (guix packages)
53 #:use-module (guix download)
54052a54 54 #:use-module (guix git-download)
0e2672ae 55 #:use-module (guix utils)
cec86422 56 #:use-module (guix build utils)
da95c817 57 #:use-module (guix build-system cmake)
c9dfa3c7 58 #:use-module (guix build-system gnu)
ba1be533 59 #:use-module (guix build-system ocaml)
560acf25 60 #:use-module (guix build-system python)
ec8c7e47 61 #:use-module (guix build-system r)
63e07468 62 #:use-module (guix build-system ruby)
3de01d3f 63 #:use-module (gnu packages algebra)
ab5f3f21 64 #:use-module (gnu packages audio)
5143517c 65 #:use-module (gnu packages autotools)
3de01d3f 66 #:use-module (gnu packages bison)
a17d4564 67 #:use-module (gnu packages boost)
e73b49fb 68 #:use-module (gnu packages check)
3de01d3f 69 #:use-module (gnu packages cmake)
c9dfa3c7 70 #:use-module (gnu packages compression)
668c06ac 71 #:use-module (gnu packages curl)
b7b27a8f 72 #:use-module (gnu packages cyrus-sasl)
528bb464 73 #:use-module (gnu packages documentation)
57e544e8 74 #:use-module (gnu packages elf)
3de01d3f 75 #:use-module (gnu packages flex)
668c06ac 76 #:use-module (gnu packages fltk)
f3929800 77 #:use-module (gnu packages fontutils)
1dba6407 78 #:use-module (gnu packages gettext)
da95c817 79 #:use-module (gnu packages gcc)
73fed4f8 80 #:use-module (gnu packages gd)
668c06ac 81 #:use-module (gnu packages ghostscript)
889187a4 82 #:use-module (gnu packages graphviz)
f3929800 83 #:use-module (gnu packages gtk)
45147b0c 84 #:use-module (gnu packages image)
2fd26d05 85 #:use-module (gnu packages java)
668c06ac 86 #:use-module (gnu packages less)
8731e527 87 #:use-module (gnu packages lisp)
ab5f3f21 88 #:use-module (gnu packages linux)
bc3a2e35 89 #:use-module (gnu packages logging)
6e64766a 90 #:use-module (gnu packages lua)
5698b8b8 91 #:use-module (gnu packages gnome)
1b39a196 92 #:use-module (gnu packages guile)
668c06ac
JD		 93 #:use-module (gnu packages xorg)
94 #:use-module (gnu packages gl)
9f913401 95 #:use-module (gnu packages imagemagick)
8731e527 96 #:use-module (gnu packages m4)
d8c7eeb9 97 #:use-module (gnu packages mpi)
b92eee75 98 #:use-module (gnu packages multiprecision)
528bb464 99 #:use-module (gnu packages netpbm)
ba1be533 100 #:use-module (gnu packages ocaml)
668c06ac 101 #:use-module (gnu packages pcre)
5698b8b8 102 #:use-module (gnu packages popt)
c9dfa3c7
AE		 103 #:use-module (gnu packages perl)
104 #:use-module (gnu packages pkg-config)
ab5f3f21 105 #:use-module (gnu packages pulseaudio)
da95c817 106 #:use-module (gnu packages python)
589e3f4e 107 #:use-module (gnu packages python-web)
5b05dce7 108 #:use-module (gnu packages qt)
c9dfa3c7 109 #:use-module (gnu packages readline)
63e07468 110 #:use-module (gnu packages ruby)
2742f87e 111 #:use-module (gnu packages tbb)
479c4273 112 #:use-module (gnu packages scheme)
b7194849 113 #:use-module (gnu packages shells)
df354a77 114 #:use-module (gnu packages tcl)
668c06ac 115 #:use-module (gnu packages texinfo)
8f9ac901 116 #:use-module (gnu packages tex)
b7b27a8f 117 #:use-module (gnu packages tls)
5b05dce7 118 #:use-module (gnu packages version-control)
9aafbc0c 119 #:use-module (gnu packages wxwidgets)
c12efc72 120 #:use-module (gnu packages xml)
a17d4564 121 #:use-module (srfi srfi-1))
8f8b2451 122
193abc82
JD		 123(define-public aris
124 (package
1f45f18a
JD		 125 (name "aris")
126 (version "2.2")
127 (source (origin
128 (method url-fetch)
129 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
130 (sha256 (base32
131 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
132 (build-system gnu-build-system)
133 (inputs `(("gtk+" ,gtk+)
134 ("libxml2" ,libxml2)))
135 (native-inputs `(("pkg-config" ,pkg-config)))
136 (synopsis "Natural deduction first-order logic interface")
137 (description "Aris is a program for performing logical proofs. It supports
138propositional and predicate logic, as well as Boolean algebra and
139arithmetical logic. In addition to its predefined inference and equivalence
140rules, Aris also supports references to older proofs. Its use of standard
141logical symbols and its natural deduction interface make it easy to use for
142beginners.")
143 (license license:gpl3+)
6fd52309 144 (home-page "https://www.gnu.org/software/aris/")))
193abc82 145
9c45c519
JD		 146(define-public c-graph
147 (package
148 (name "c-graph")
149 (version "2.0")
150 (source (origin
151 (method url-fetch)
152 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
153 ".tar.gz"))
154 (sha256 (base32
155 "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
156 (build-system gnu-build-system)
157 (inputs
158 `(("fortran" ,gfortran)))
a3947cb1 159 (synopsis "Visualizing and demonstrating convolution")
9c45c519 160 (description
a3947cb1
LC		 161 "GNU C-Graph is a tool for demonstrating the theory of convolution.
162Thus, it can serve as an excellent aid to students of signal and systems
163theory in visualizing the convolution process. Rather than forcing the
164student to write code, the program offers an intuitive interface with
165interactive dialogs to guide them.")
9c45c519 166 (license license:gpl3+)
6fd52309 167 (home-page "https://www.gnu.org/software/c-graph/")))
9c45c519 168
d91025e3
TD		 169(define-public coda
170 (package
171 (name "coda")
9285f8bb 172 (version "2.19")
d91025e3
TD		 173 (source
174 (origin
175 (method url-fetch)
176 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
177 version "/coda-" version ".tar.gz"))
178 (sha256
9285f8bb 179 (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245"))
4b12fe5c
TD		 180 (patches (search-patches "coda-use-system-libs.patch"))
181 (modules '((guix build utils)))
182 (snippet
183 ;; Make sure we don't use the bundled software.
6cbee49d
MW		 184 '(begin
185 (for-each (lambda (d)
186 (delete-file-recursively (string-append "libcoda/" d)))
187 '("zlib" "pcre" "expat"))
188 #t))))
d91025e3
TD		 189 (native-inputs
190 `(("fortran" ,gfortran)
191 ("python" ,python)
192 ("python-numpy" ,python-numpy)))
193 (inputs
194 `(("zlib" ,zlib)
4b12fe5c
TD		 195 ("pcre" ,pcre)
196 ("expat" ,expat)
d91025e3
TD		 197 ("hdf4" ,hdf4-alt)
198 ("hdf5" ,hdf5)))
199 (build-system gnu-build-system)
200 (arguments
4b12fe5c
TD		 201 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
202 "LIBS= -lz -lpcre -lexpat")))
d91025e3
TD		 203 (synopsis "A common interface to various earth observation data formats")
204 (description
205 "The Common Data Access toolbox (CODA) provides a set of interfaces for
206reading remote sensing data from earth observation data files. It consists of
207command line applications and interfaces to the C, Fortran, Python, and Java
208programming languages.")
209 (home-page "https://stcorp.nl/coda")
210 (license license:gpl2+)))
211
d65f0661
KK		 212(define-public qhull
213 (package
214 (name "qhull")
215 (version "2015.2")
216 (source (origin
217 (method url-fetch)
218 (uri (string-append "http://www.qhull.org/download/qhull-"
219 (car (string-split version #\.))
220 "-src-7.2.0.tgz"))
221 (sha256
222 (base32
223 "0dm4b2xr3asy6w74khq2zg4gf26zsy3qf9sq7pf7lmrvbj911c3q"))))
224 (build-system cmake-build-system)
225 (synopsis "Calculate convex hulls and related structures")
226 (description
227 "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
228diagram, halfspace intersection about a point, furthest-site Delaunay
229triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d,
2303-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull
231algorithm for computing the convex hull. It handles roundoff errors from
232floating point arithmetic. It computes volumes, surface areas, and
233approximations to the convex hull.
234
235@code{Qhull} does not support triangulation of non-convex surfaces, mesh
236generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
237shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
238triangulations.")
239 (home-page "http://qhull.org")
240 (license (license:non-copyleft "file://COPYING.txt"
241 "See COPYING in the distribution."))))
242
a8fa86c4
RW		 243(define-public python-cvxopt
244 (package
245 (name "python-cvxopt")
246 (version "1.2.1")
247 (source (origin
248 (method git-fetch)
249 (uri (git-reference
250 (url "https://github.com/cvxopt/cvxopt.git")
251 (commit version)))
252 (file-name (git-file-name name version))
253 (sha256
254 (base32
255 "05mnjil9palaa48xafdfh4f5pr4z7aqjr995rwl08qfyxs8y0crf"))))
256 (build-system python-build-system)
257 (arguments
258 `(#:phases
259 (modify-phases %standard-phases
260 (add-after 'unpack 'find-libraries
261 (lambda* (#:key inputs #:allow-other-keys)
262 (setenv "CVXOPT_BLAS_LIB" "openblas")
263 (setenv "CVXOPT_BUILD_FFTW" "1")
264 (setenv "CVXOPT_BUILD_GLPK" "1")
265 (setenv "CVXOPT_BUILD_GSL" "1")
266 #t)))))
267 (inputs
268 `(("fftw" ,fftw)
269 ("glpk" ,glpk)
270 ("gsl" ,gsl)
271 ("lapack" ,lapack)
272 ("openblas" ,openblas)
273 ("suitesparse" ,suitesparse)))
274 (home-page "https://www.cvxopt.org")
275 (synopsis "Python library for convex optimization")
276 (description
277 "CVXOPT is a package for convex optimization based on the Python
278programming language. Its main purpose is to make the development of software
279for convex optimization applications straightforward by building on Python’s
280extensive standard library and on the strengths of Python as a high-level
281programming language.")
282 (license license:gpl3+)))
283
284(define-public python2-cvxopt
285 (package-with-python2 python-cvxopt))
286
8f8b2451
AE		 287(define-public units
288 (package
289 (name "units")
4795e5e1 290 (version "2.18")
8f8b2451
AE		 291 (source (origin
292 (method url-fetch)
293 (uri (string-append "mirror://gnu/units/units-" version
294 ".tar.gz"))
295 (sha256 (base32
4795e5e1 296 "0y26kj349i048y4z3xrk90bvciw2j6ds3rka7r7yn3183hirr5b4"))))
8f8b2451 297 (build-system gnu-build-system)
0498d248 298 (inputs
a2549713
EB		 299 `(("readline" ,readline)
300 ("python" ,python-wrapper) ;for 'units_cur' script
0498d248
EB		 301 ("python-requests" ,python-requests)))
302 (arguments
303 `(#:phases (modify-phases %standard-phases
304 (add-after 'install 'wrap-units_cur
305 (lambda* (#:key outputs #:allow-other-keys)
306 (let* ((out (assoc-ref outputs "out"))
307 (bin (string-append out "/bin")))
308 (wrap-program (string-append bin "/units_cur")
309 `("PYTHONPATH" ":" prefix
310 ,(search-path-as-string->list (getenv "PYTHONPATH"))))
311 #t))))))
8f8b2451
AE		 312 (synopsis "Conversion between thousands of scales")
313 (description
574e86f9 314 "GNU Units converts numeric quantities between units of measure. It
7c125ce0
AK		 315can handle scale changes through adaptive usage of standard scale
316prefixes (micro-, kilo-, etc.). It can also handle nonlinear
317conversions such as Fahrenheit to Celsius. Its interpreter is powerful
318enough to be used effectively as a scientific calculator.")
8f8b2451 319 (license license:gpl3+)
6fd52309 320 (home-page "https://www.gnu.org/software/units/")))
c9dfa3c7 321
61a529b4
RW		 322(define-public double-conversion
323 (package
324 (name "double-conversion")
57ba8d06 325 (version "3.0.0")
b343850e 326 (home-page "https://github.com/google/double-conversion")
61a529b4
RW		 327 (source (origin
328 (method url-fetch)
b343850e 329 (uri (string-append home-page "/archive/v" version ".tar.gz"))
61a529b4
RW		 330 (file-name (string-append name "-" version ".tar.gz"))
331 (sha256
332 (base32
57ba8d06 333 "059r1czs28ljjd388pn6l3njg1ghbf1cv3q9nkxv3dj2a8siabqm"))))
61a529b4
RW		 334 (build-system cmake-build-system)
335 (arguments
336 '(#:test-target "test"
337 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
338 "-DBUILD_TESTING=ON")))
61a529b4
RW		 339 (synopsis "Conversion routines for IEEE doubles")
340 (description
341 "The double-conversion library provides binary-decimal and decimal-binary
342routines for IEEE doubles. The library consists of efficient conversion
343routines that have been extracted from the V8 JavaScript engine.")
344 (license license:bsd-3)))
345
182d6311
ML		 346(define-public dionysus
347 (package
348 (name "dionysus")
bd041e7f 349 (version "1.4.0")
182d6311
ML		 350 (source (origin
351 (method url-fetch)
352 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
bd041e7f 353 ".tar.xz"))
182d6311
ML		 354 (sha256
355 (base32
bd041e7f 356 "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
182d6311
ML		 357 (build-system gnu-build-system)
358 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
359 (synopsis "Local search for universal constants and scientific values")
360 (description
361 "GNU Dionysus is a convenient system for quickly retrieving the values of
362mathematical constants used in science and engineering. Values can be
363searched using a simple command-line tool, choosing from three databases:
364universal constants, atomic numbers, and constants related to
365semiconductors.")
366 (license license:gpl3+)
6fd52309 367 (home-page "https://www.gnu.org/software/dionysus/")))
182d6311 368
88bd1804
AE		 369(define-public gsl
370 (package
371 (name "gsl")
f3a34b9d 372 (version "2.5")
ab2cc5cd
LC		 373 (source (origin
374 (method url-fetch)
375 (uri (string-append "mirror://gnu/gsl/gsl-"
376 version ".tar.gz"))
377 (sha256
378 (base32
f3a34b9d 379 "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
ab2cc5cd 380 (patches (search-patches "gsl-test-i686.patch"))))
88bd1804 381 (build-system gnu-build-system)
71e0f288 382 (arguments
f885fc05 383 `(;; Currently there are numerous tests that fail on "exotic"
6f766069
EF		 384 ;; architectures such as aarch64 and ppc64le.
385 ,@(if (string-prefix? "aarch64-linux"
386 (or (%current-target-system) (%current-system)))
387 '(#:tests? #f)
388 '())))
389 (home-page "https://www.gnu.org/software/gsl/")
88bd1804
AE		 390 (synopsis "Numerical library for C and C++")
391 (description
a22dc0c4
LC		 392 "The GNU Scientific Library is a library for numerical analysis in C
393and C++. It includes a wide range of mathematical routines, with over 1000
394functions in total. Subject areas covered by the library include:
395differential equations, linear algebra, Fast Fourier Transforms and random
396numbers.")
88bd1804
AE		 397 (license license:gpl3+)))
398
ba1be533
BW		 399(define-public ocaml-gsl
400 (package
401 (name "ocaml-gsl")
df1bc82b 402 (version "1.22.0")
ba1be533
BW		 403 (source
404 (origin
405 (method url-fetch)
406 (uri
407 (string-append
df1bc82b
KK		 408 "https://github.com/mmottl/gsl-ocaml/releases/download/"
409 version "/gsl-" version ".tbz"))
ba1be533
BW		 410 (sha256
411 (base32
df1bc82b 412 "17vcswipliq1b2idbzx1z95kskn1a4q4s5v04igilg0f7lnkaarb"))))
ba1be533
BW		 413 (build-system ocaml-build-system)
414 (inputs
415 `(("gsl" ,gsl)))
416 (home-page "https://mmottl.github.io/gsl-ocaml")
417 (synopsis "Bindings to the GNU Scientific Library")
418 (description
419 "GSL-OCaml is an interface to the @dfn{GNU scientific library} (GSL) for
420the OCaml language.")
421 (license license:gpl3+)))
422
7adaab9f
BW		 423(define-public ocaml4.01-gsl
424 (package-with-ocaml4.01 ocaml-gsl))
425
b92eee75
AE		 426(define-public glpk
427 (package
428 (name "glpk")
445929e0 429 (version "4.65")
b92eee75
AE		 430 (source
431 (origin
432 (method url-fetch)
433 (uri (string-append "mirror://gnu/glpk/glpk-"
434 version ".tar.gz"))
435 (sha256
436 (base32
445929e0 437 "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
b92eee75
AE		 438 (build-system gnu-build-system)
439 (inputs
440 `(("gmp" ,gmp)))
441 (arguments
442 `(#:configure-flags '("--with-gmp")))
82110ef6 443 (home-page "https://www.gnu.org/software/glpk/")
79c311b8 444 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
b92eee75
AE		 445 (description
446 "GLPK is a C library for solving large-scale linear programming (LP),
447mixed integer programming (MIP), and other related problems. It supports the
448GNU MathProg modeling language, a subset of the AMPL language, and features a
449translator for the language. In addition to the C library, a stand-alone
450LP/MIP solver is included in the package.")
451 (license license:gpl3+)))
452
b146763a
AE		 453(define-public 4ti2
454 (package
455 (name "4ti2")
456 (version "1.6.7")
457 (source
458 (origin
459 (method url-fetch)
460 (uri (string-append "http://www.4ti2.de/version_" version
461 "/4ti2-" version ".tar.gz"))
462 (sha256
463 (base32
464 "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
465 (build-system gnu-build-system)
466 (native-inputs
467 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
468 (inputs
469 `(("glpk" ,glpk)
470 ("gmp" ,gmp)))
471 (home-page "http://www.4ti2.de/")
472 (synopsis "Mathematical tool suite for problems on linear spaces")
473 (description
474 "4ti2 implements algorithms for solving algebraic, geometric and
475combinatorial problems on linear spaces. Among others, it solves systems
476of linear equations, computes extreme rays of polyhedral cones, solves
477integer programming problems and computes Markov bases for statistics.")
478 (license license:gpl2+)))
479
53696f10
AE		 480(define-public cddlib
481 (package
482 (name "cddlib")
7fe491fb 483 (version "0.94i")
53696f10
AE		 484 (source
485 (origin
486 (method url-fetch)
182dde82 487 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
53696f10
AE		 488 (string-delete #\. version) ".tar.gz"))
489 (sha256
490 (base32
7fe491fb 491 "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
53696f10
AE		 492 (build-system gnu-build-system)
493 (inputs
494 `(("gmp" ,gmp)))
495 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
496 (synopsis "Library for convex hulls and extreme rays of polyhedra")
497 (description
498 "The C-library cddlib implements the Double Description Method of
499Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
500rays of a general convex polyhedron given by a system of linear inequalities
501in arbitrary dimension. It can also be used for the converse operation of
502computing convex hulls.")
503 (license license:gpl2+)))
504
865a69dd
RW		 505(define-public arpack-ng
506 (package
507 (name "arpack-ng")
f03c4ec6 508 (version "3.6.3")
c0edb5b5 509 (home-page "https://github.com/opencollab/arpack-ng")
622ef2b9
MB		 510 (source (origin
511 (method git-fetch)
512 (uri (git-reference (url home-page) (commit version)))
513 (file-name (git-file-name name version))
514 (sha256
515 (base32
f03c4ec6 516 "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
865a69dd 517 (build-system gnu-build-system)
c0edb5b5
LC		 518 (native-inputs
519 `(("autoconf" ,autoconf)
520 ("automake" ,automake)
521 ("libtool" ,libtool)))
865a69dd
RW		 522 (inputs
523 `(("lapack" ,lapack)
19afbea1 524 ("fortran" ,gfortran)))
865a69dd
RW		 525 (synopsis "Fortran subroutines for solving eigenvalue problems")
526 (description
527 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
528large scale eigenvalue problems.")
166191b3 529 (license (license:non-copyleft "file://COPYING"
865a69dd
RW		 530 "See COPYING in the distribution."))))
531
c0edb5b5
LC		 532(define-public arpack-ng-3.3.0
533 (package
534 (inherit arpack-ng)
535 (version "3.3.0")
536 (name (package-name arpack-ng))
537 (home-page (package-home-page arpack-ng))
538 (source
539 (origin
540 (method url-fetch)
541 (uri (string-append home-page "/archive/" version ".tar.gz"))
542 (file-name (string-append name "-" version ".tar.gz"))
543 (sha256
544 (base32
545 "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
546
8c94c886
EB		 547(define-public arpack-ng-openmpi
548 (package (inherit arpack-ng)
549 (name "arpack-ng-openmpi")
550 (inputs
551 `(("mpi" ,openmpi)
552 ,@(package-inputs arpack-ng)))
4f387541
LC		 553 (arguments
554 (substitute-keyword-arguments (package-arguments arpack-ng)
555 ((#:configure-flags _ '())
aa82260b
PG		 556 ''("--enable-mpi"))
557 ((#:phases phases '%standard-phases)
558 `(modify-phases ,phases
bbe46a4a
EB		 559 (add-before 'check 'mpi-setup
560 ,%openmpi-setup)))))
8c94c886
EB		 561 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
562
da95c817
NK		 563(define-public lapack
564 (package
565 (name "lapack")
ef39a177 566 (version "3.7.1")
da95c817
NK		 567 (source
568 (origin
569 (method url-fetch)
570 (uri (string-append "http://www.netlib.org/lapack/lapack-"
571 version ".tgz"))
572 (sha256
573 (base32
7c0d4c3a 574 "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
da95c817
NK		 575 (build-system cmake-build-system)
576 (home-page "http://www.netlib.org/lapack/")
19afbea1 577 (inputs `(("fortran" ,gfortran)
da95c817
NK		 578 ("python" ,python-2)))
579 (arguments
3ab869b6 580 `(#:configure-flags (list
3ab869b6
LC		 581 "-DBUILD_SHARED_LIBS:BOOL=YES"
582 "-DLAPACKE=ON"
583
584 ;; Build the 'LAPACKE_clatms' functions.
585 "-DLAPACKE_WITH_TMG=ON")
dc1d3cde
KK		 586 #:phases
587 (modify-phases %standard-phases
588 (add-before 'check 'patch-python
589 (lambda* (#:key inputs #:allow-other-keys)
590 (let ((python (assoc-ref inputs "python")))
591 (substitute* "lapack_testing.py"
592 (("/usr/bin/env python") python)))
593 #t)))))
da95c817
NK		 594 (synopsis "Library for numerical linear algebra")
595 (description
596 "LAPACK is a Fortran 90 library for solving the most commonly occurring
597problems in numerical linear algebra.")
166191b3 598 (license (license:non-copyleft "file://LICENSE"
da95c817 599 "See LICENSE in the distribution."))))
73fed4f8 600
e1ff597a
EB		 601(define-public scalapack
602 (package
603 (name "scalapack")
604 (version "2.0.2")
605 (source
606 (origin
607 (method url-fetch)
608 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
609 version ".tgz"))
610 (sha256
611 (base32
612 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
613 (build-system cmake-build-system)
614 (inputs
615 `(("mpi" ,openmpi)
616 ("fortran" ,gfortran)
617 ("lapack" ,lapack))) ;for testing only
618 (arguments
6df2a50a
LC		 619 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
620 #:phases (modify-phases %standard-phases
bbe46a4a
EB		 621 (add-before 'check 'mpi-setup
622 ,%openmpi-setup))))
e1ff597a
EB		 623 (home-page "http://www.netlib.org/scalapack/")
624 (synopsis "Library for scalable numerical linear algebra")
625 (description
626 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
627routines on parallel distributed memory machines. ScaLAPACK solves dense and
628banded linear systems, least squares problems, eigenvalue problems, and
629singular value problems.")
630 (license (license:bsd-style "file://LICENSE"
631 "See LICENSE in the distribution."))))
632
73fed4f8 633(define-public gnuplot
5f800540
KK		 634 (package
635 (name "gnuplot")
b13ba3f1 636 (version "5.2.4")
5f800540
KK		 637 (source (origin
638 (method url-fetch)
639 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
640 version "/gnuplot-"
641 version ".tar.gz"))
642 (sha256
643 (base32
b13ba3f1 644 "1jvh8xmd2cvrhlsg88kxwh55wkwx31sg50v1n59slfippl0g058m"))))
5f800540
KK		 645 (build-system gnu-build-system)
646 (inputs `(("readline" ,readline)
647 ("cairo" ,cairo)
648 ("pango" ,pango)
6e64766a
DM		 649 ("gd" ,gd)
650 ("lua" ,lua)))
612a387f
RW		 651 (native-inputs
652 `(("pkg-config" ,pkg-config)
653 ("texlive" ,texlive-tiny)))
07254d8b
AM		 654 (arguments `(#:configure-flags (list (string-append
655 "--with-texdir=" %output
656 "/texmf-local/tex/latex/gnuplot"))))
5f800540
KK		 657 (home-page "http://www.gnuplot.info")
658 (synopsis "Command-line driven graphing utility")
659 (description "Gnuplot is a portable command-line driven graphing
35b9e423 660utility. It was originally created to allow scientists and students to
73fed4f8 661visualize mathematical functions and data interactively, but has grown to
35b9e423 662support many non-interactive uses such as web scripting. It is also used as a
73fed4f8 663plotting engine by third-party applications like Octave.")
5f800540
KK		 664 ;; X11 Style with the additional restriction that derived works may only be
665 ;; distributed as patches to the original.
666 (license (license:fsf-free
667 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
668c06ac 668
32f70e1f
TD		 669(define-public gctp
670 (package
671 (name "gctp")
672 (version "2.0.0")
673 (source
674 (origin
675 (method url-fetch)
676 (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
677 version ".tar.gz"))
678 (file-name (string-append name "-" version ".tar.gz"))
679 (sha256
680 (base32
681 "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
682 (native-inputs
683 `(("fortran" ,gfortran)))
684 (build-system gnu-build-system)
685 (synopsis "General Cartographic Transformation Package (GCTP)")
686 (description
687 "The General Cartographic Transformation Package (GCTP) is a system of
688software routines designed to permit the transformation of coordinate pairs
689from one map projection to another. The GCTP is the standard computer
690software used by the National Mapping Division for map projection
691computations.")
692 (home-page "https://github.com/OkoSanto/GCTP")
0f7cd95b 693 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
32f70e1f 694
becbbefc
TD		 695(define-public hdf4
696 (package
697 (name "hdf4")
0abf5264 698 (version "4.2.13")
becbbefc
TD		 699 (source
700 (origin
701 (method url-fetch)
702 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
703 version "/src/hdf-" version ".tar.bz2"))
704 (sha256
0abf5264 705 (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
15ca49b2
AE		 706 (patches (search-patches "hdf4-architectures.patch"
707 "hdf4-reproducibility.patch"
becbbefc 708 "hdf4-shared-fortran.patch"))))
becbbefc
TD		 709 (build-system gnu-build-system)
710 (native-inputs
711 `(("gfortran" ,gfortran)
712 ("bison" ,bison)
713 ("flex" ,flex)))
714 (inputs
715 `(("zlib" ,zlib)
716 ("libjpeg" ,libjpeg)))
717 (arguments
718 `(#:parallel-tests? #f
719 #:configure-flags '("--enable-shared")
720 #:phases
721 (modify-phases %standard-phases
953a12fa
EF		 722 ;; This is inspired by two of Debian's patches.
723 (add-before 'configure 'add-more-aarch64-support
724 (lambda _
725 (substitute* '("mfhdf/ncgen/ncgen.l"
726 "mfhdf/ncgen/ncgenyy.c"
727 "mfhdf/libsrc/netcdf.h.in")
728 (("AIX5L64") "__aarch64__"))
729 #t))
becbbefc
TD		 730 (add-before 'configure 'patchbuild
731 (lambda _
732 (substitute*
733 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
734 (("/bin/rm") "rm")
735 (("/bin/mkdir") "mkdir"))
736 (substitute* (find-files "." "^Makefile\\.in$")
737 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
738-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
739 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
740-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
953a12fa 741-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
e464b455
TD		 742 #t))
743 (add-after 'configure 'patch-settings
744 (lambda _
745 ;; libhdf4.settings contains the full path of the
746 ;; compilers used, and its contents are included in
747 ;; .so-files. We truncate the hashes to avoid
748 ;; unnecessary store references to those compilers:
749 (substitute* "libhdf4.settings"
750 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
751 (string-append prefix (string-take hash 10) "...")))
752 #t))
753 )))
becbbefc
TD		 754 (home-page "https://www.hdfgroup.org/products/hdf4/")
755 (synopsis
756 "Library and multi-object file format for storing and managing data")
757 (description "HDF4 is a library and multi-object file format for storing
758and managing data between machines. HDF4 is an older hierarchical data format,
759incompatible with HDF5.")
760 (license
761 (license:non-copyleft
762 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
763
764(define-public hdf4-alt
765 (package
766 (inherit hdf4)
767 (name "hdf4-alt")
768 (arguments
769 (substitute-keyword-arguments (package-arguments hdf4)
770 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
771 (synopsis
772 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
773
7ee3f1a2
JD		 774(define-public hdf5
775 (package
776 (name "hdf5")
2da63064 777 (version "1.8.19")
7ee3f1a2
JD		 778 (source
779 (origin
780 (method url-fetch)
2da63064
TD		 781 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
782 "hdf5-" (version-major+minor version)
783 "/hdf5-" version "/src/hdf5-"
dcd9d163
LF		 784 version ".tar.bz2")
785 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
786 "current"
787 (apply string-append
788 (take (string-split version #\.) 2))
789 "/src/hdf5-" version ".tar.bz2")))
7ee3f1a2 790 (sha256
2da63064 791 (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
b8d9c93b 792 (patches (list (search-patch "hdf5-config-date.patch")))))
7ee3f1a2 793 (build-system gnu-build-system)
12ed1216
AE		 794 (inputs
795 `(("zlib" ,zlib)))
e3a1a1de
TD		 796 (native-inputs
797 `(("gfortran" ,gfortran)))
798 (outputs '("out" ; core library
799 "fortran")) ; fortran interface
7ee3f1a2 800 (arguments
62126576 801 `(;; Some of the users, notably Flann, need the C++ interface.
e3a1a1de
TD		 802 #:configure-flags '("--enable-cxx"
803 "--enable-fortran"
804 "--enable-fortran2003")
4dba441c
RW		 805 ;; Use -fPIC to allow the R bindings to link with the static libraries
806 #:make-flags (list "CFLAGS=-fPIC"
807 "CXXFLAGS=-fPIC")
62126576 808 #:phases
f622e212
EB		 809 (modify-phases %standard-phases
810 (add-before 'configure 'patch-configure
e3a1a1de 811 (lambda* (#:key outputs #:allow-other-keys)
f622e212 812 (substitute* "configure"
b8d9c93b 813 (("/bin/mv") "mv"))
e3a1a1de
TD		 814 (substitute* "fortran/src/Makefile.in"
815 (("libhdf5_fortran_la_LDFLAGS =")
816 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
817 (assoc-ref outputs "fortran") "/lib")))
818 (substitute* "hl/fortran/src/Makefile.in"
819 (("libhdf5hl_fortran_la_LDFLAGS =")
820 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
821 (assoc-ref outputs "fortran") "/lib")))
b8d9c93b 822 #t))
fd0378a1
TD		 823 (add-after 'configure 'patch-settings
824 (lambda _
825 ;; libhdf5.settings contains the full path of the
826 ;; compilers used, and its contents are included in
827 ;; libhdf5.so. We truncate the hashes to avoid
828 ;; unnecessary store references to those compilers:
829 (substitute* "src/libhdf5.settings"
830 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
d8f46d52
RW		 831 (string-append prefix (string-take hash 10) "..."))
832 ;; Don't record the build-time kernel version to make the
833 ;; settings file reproducible.
834 (("Uname information:.*")
835 "Uname information: Linux\n"))
b8d9c93b 836 #t))
f622e212
EB		 837 (add-after 'install 'patch-references
838 (lambda* (#:key inputs outputs #:allow-other-keys)
839 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
840 (zlib (assoc-ref inputs "zlib")))
841 (substitute* (find-files bin "h5p?cc")
842 (("-lz" lib)
843 (string-append "-L" zlib "/lib " lib)))
e3a1a1de
TD		 844 #t)))
845 (add-after 'install 'split
846 (lambda* (#:key inputs outputs #:allow-other-keys)
847 ;; Move all fortran-related files
848 (let* ((out (assoc-ref outputs "out"))
849 (bin (string-append out "/bin"))
850 (lib (string-append out "/lib"))
851 (inc (string-append out "/include"))
852 (ex (string-append out "/share/hdf5_examples/fortran"))
853 (fort (assoc-ref outputs "fortran"))
854 (fbin (string-append fort "/bin"))
855 (flib (string-append fort "/lib"))
856 (finc (string-append fort "/include"))
857 (fex (string-append fort "/share/hdf5_examples/fortran")))
858 (mkdir-p fbin)
859 (mkdir-p flib)
860 (mkdir-p finc)
861 (mkdir-p fex)
b0d1e60f
PG		 862 ;; Note: When built with --enable-parallel, the 'h5fc' file
863 ;; doesn't exist, hence this condition.
864 (when (file-exists? (string-append bin "/h5fc"))
865 (rename-file (string-append bin "/h5fc")
866 (string-append fbin "/h5fc")))
e3a1a1de
TD		 867 (for-each (lambda (file)
868 (rename-file file
869 (string-append flib "/" (basename file))))
870 (find-files lib ".*fortran.*"))
871 (for-each (lambda (file)
872 (rename-file file
873 (string-append finc "/" (basename file))))
874 (find-files inc ".*mod"))
875 (for-each (lambda (file)
876 (rename-file file
877 (string-append fex "/" (basename file))))
878 (find-files ex ".*"))
879 (delete-file-recursively ex))
880 #t)))))
7ee3f1a2 881 (home-page "http://www.hdfgroup.org")
516e93f8 882 (synopsis "Management suite for extremely large and complex data")
7ee3f1a2
JD		 883 (description "HDF5 is a suite that makes possible the management of
884extremely large and complex data collections.")
d4bf49b1
EB		 885 (license (license:x11-style
886 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
7ee3f1a2 887
bb47aca5
RW		 888(define-public hdf5-1.10
889 (package (inherit hdf5)
890 (version "1.10.4")
891 (source
892 (origin
893 (method url-fetch)
894 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
895 "hdf5-" (version-major+minor version)
896 "/hdf5-" version "/src/hdf5-"
897 version ".tar.bz2")
898 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
899 "current"
900 (apply string-append
901 (take (string-split version #\.) 2))
902 "/src/hdf5-" version ".tar.bz2")))
903 (sha256
904 (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
905 (patches (list (search-patch "hdf5-config-date.patch")))))))
906
2fd26d05
TD		 907(define-public hdf-java
908 (package
909 (name "hdf-java")
910 (version "3.3.2")
911 (source
912 (origin
913 (method url-fetch)
914 (uri (string-append
915 "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
916 version "/src/CMake-hdfjava-" version ".tar.gz"))
917 (sha256
918 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
919 (modules '((guix build utils)))
920 (snippet ; Make sure we don't use the bundled sources and binaries.
921 `(begin
922 (for-each delete-file
923 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
924 "HDF4.tar.gz" "HDF5.tar.gz"))
6cbee49d
MW		 925 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
926 #t))))
2fd26d05
TD		 927 (build-system gnu-build-system)
928 (native-inputs
929 `(("jdk" ,icedtea "jdk")
930 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
931 ;; For tests:
932 ("hamcrest-core" ,java-hamcrest-core)
933 ("junit" ,java-junit)
934 ("slf4j-simple" ,java-slf4j-simple)))
935 (inputs
936 `(("hdf4" ,hdf4)
937 ("hdf5" ,hdf5)
938 ("zlib" ,zlib)
939 ("libjpeg" ,libjpeg)
940 ("slf4j-api" ,java-slf4j-api)))
941 (arguments
942 `(#:configure-flags
943 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
944 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
945 (assoc-ref %build-inputs "jdk") "/lib" )
946 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
947 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
948
949 #:make-flags
950 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
951 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
952 (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
953 (string-append "JPEGLIB="
954 (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
955 "LLEXT=so")
956
957 #:phases
958 (modify-phases %standard-phases
959 (add-before 'configure 'chdir-to-source
960 (lambda _ (chdir ,(string-append "hdfjava-" version))))
961 (add-before 'configure 'patch-build
962 (lambda* (#:key inputs outputs #:allow-other-keys)
963 (substitute* "configure"
964 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
965 (("/bin/cat") (which "cat")))
966 ;; Set classpath for compilation
967 (substitute* '("hdf/hdf5lib/Makefile.in"
968 "hdf/hdf5lib/exceptions/Makefile.in"
969 "hdf/hdflib/Makefile.in")
970 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
971 (string-append (assoc-ref inputs "slf4j-api")
972 "/share/java/slf4j-api.jar")))
973 ;; Replace outdated config.sub and config.guess:
974 (with-directory-excursion "config"
975 (for-each (lambda (file)
976 (copy-file
977 (string-append (assoc-ref inputs "automake")
978 "/share/automake-1.15/" file) file))
979 '("config.sub" "config.guess")))
980 (mkdir-p (string-append (assoc-ref outputs "out")))
981 ;; Set classpath for tests
982 (let* ((build-dir (getcwd))
983 (lib (string-append build-dir "/lib"))
984 (jhdf (string-append lib "/jhdf.jar"))
985 (jhdf5 (string-append lib "/jhdf5.jar"))
986 (testjars
987 (map (lambda (i)
988 (string-append (assoc-ref inputs i)
989 "/share/java/" i ".jar"))
990 '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
991 (class-path
992 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
993
994 (substitute* '("test/hdf5lib/Makefile.in"
995 "test/hdf5lib/junit.sh.in"
996 "examples/runExample.sh.in")
997 (("/usr/bin/test")
998 (string-append (assoc-ref inputs "coreutils")
999 "/bin/test"))
1000 (("/usr/bin/uname")
1001 (string-append (assoc-ref inputs "coreutils")
1002 "/bin/uname"))
1003 (("CLASSPATH=[^\n]*")
1004 (string-append "CLASSPATH=" class-path)))
1005 (setenv "CLASSPATH" class-path))
1006 #t))
1007 (add-before 'check 'build-examples
1008 (lambda _
1009 (zero? (apply system* `("javac"
1010 ,@(find-files "examples" ".*\\.java")))))))
1011
1012 #:parallel-build? #f
1013
1014 #:parallel-tests? #f ))
1015 (home-page "https://support.hdfgroup.org/products/java")
1016 (synopsis "Java interface for the HDF4 and HDF5 libraries")
1017 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
1018the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
1019implemented in C.")
1020
1021 ;; BSD-style license:
1022 (license (license:x11-style
1023 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
1024/current/src/unpacked/COPYING"))))
1025
d3c4f3bb
TD		 1026(define-public hdf-eos2
1027 (package
1028 (name "hdf-eos2")
1029 (version "19.1.0")
1030 (source
1031 (origin
1032 (method url-fetch)
1033 (uri "ftp://edhs1.gsfc.nasa.gov\
1034/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
1035 (sha256
1036 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
1037 (patches (search-patches "hdf-eos2-remove-gctp.patch"
1038 "hdf-eos2-build-shared.patch"
1039 "hdf-eos2-fortrantests.patch"))))
1040 (build-system gnu-build-system)
1041 (native-inputs
1042 `(("gfortran" ,gfortran)))
1043 (inputs
1044 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
1045 ("zlib" ,zlib)
1046 ("libjpeg" ,libjpeg)
1047 ("gctp" ,gctp)))
1048 (arguments
1049 `( #:configure-flags '("--enable-install-include" "--enable-shared"
1050 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
1051 #:parallel-tests? #f))
1052 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
1053 (synopsis "HDF4-based data format for NASA's Earth Observing System")
1054 (description "HDF-EOS2 is a software library built on HDF4 which supports
1055the construction of data structures used in NASA's Earth Observing
1056System (Grid, Point and Swath).")
1057
1058 ;; Source files carry a permissive license header.
1059 (license (license:non-copyleft home-page))))
1060
0f43f835
TD		 1061(define-public hdf-eos5
1062 (package
1063 (name "hdf-eos5")
1064 (version "1.15")
1065 (source (origin
1066 (method url-fetch)
1067 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1068/edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1069 (sha256
1070 (base32
1071 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1072 (patches (search-patches "hdf-eos5-build-shared.patch"
1073 "hdf-eos5-remove-gctp.patch"
1074 "hdf-eos5-fix-szip.patch"
1075 "hdf-eos5-fortrantests.patch"))))
1076 (native-inputs
1077 `(("gfortran" ,gfortran)))
1078 (build-system gnu-build-system)
1079 (inputs
1080 `(("hdf5" ,hdf5)
1081 ("zlib" ,zlib)
1082 ("gctp" ,gctp)))
1083 (arguments
1084 `(#:configure-flags '("--enable-install-include" "--enable-shared"
1085 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1086 #:parallel-tests? #f))
1087 (synopsis "HDF5-based data format for NASA's Earth Observing System")
1088 (description
1089 "HDF-EOS5 is a software library built on HDF5 to support the construction
1090of data structures used in NASA's Earth Observing System (Grid, Point and
1091Swath).")
1092 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1093
1094 ;; Source files carry a permissive license header.
1095 (license (license:non-copyleft home-page))))
1096
c8378eea
EB		 1097(define-public hdf5-parallel-openmpi
1098 (package (inherit hdf5)
1099 (name "hdf5-parallel-openmpi")
1100 (inputs
1101 `(("mpi" ,openmpi)
1102 ,@(package-inputs hdf5)))
1103 (arguments
45201bf2
PG		 1104 (substitute-keyword-arguments (package-arguments hdf5)
1105 ((#:configure-flags flags)
1106 ``("--enable-parallel" ,@(delete "--enable-cxx" ,flags)))
c8378eea
EB		 1107 ((#:phases phases)
1108 `(modify-phases ,phases
45201bf2
PG		 1109 (add-after 'build 'mpi-setup
1110 ,%openmpi-setup)
c8378eea
EB		 1111 (add-before 'check 'patch-tests
1112 (lambda _
1113 ;; OpenMPI's mpirun will exit with non-zero status if it
1114 ;; detects an "abnormal termination", i.e. any process not
1115 ;; calling MPI_Finalize(). Since the test is explicitely
1116 ;; avoiding MPI_Finalize so as not to have at_exit and thus
1117 ;; H5C_flush_cache from being called, mpirun will always
1118 ;; complain, so turn this test off.
1119 (substitute* "testpar/Makefile"
1120 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1121 (string-append front back "\n")))
1122 (substitute* "tools/h5diff/testph5diff.sh"
1123 (("/bin/sh") (which "sh")))
1124 #t))))))
1125 (synopsis "Management suite for data with parallel IO support")))
1126
00775104
EB		 1127(define-public h5check
1128 (package
1129 (name "h5check")
1130 (version "2.0.1")
1131 (source
1132 (origin
1133 (method url-fetch)
1134 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
1135 "h5check/src/h5check-" version ".tar.gz"))
1136 (sha256
1137 (base32
1138 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1139 (build-system gnu-build-system)
1140 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
1141 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1142 (synopsis "HDF5 format checker")
1143 (description "@code{h5check} is a validation tool for verifying that an
1144HDF5 file is encoded according to the HDF File Format Specification.")
1145 (license (license:x11-style "file://COPYING"))))
1146
a53d6719
JD		 1147(define-public itpp
1148 (package
1149 (name "itpp")
1150 (version "4.3.1")
1151 (source (origin
1152 (method url-fetch)
1153 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1154 version "/itpp-"
1155 version ".tar.gz"))
1156 (sha256
1157 (base32
1158 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1159 (build-system cmake-build-system)
1160 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1161 (inputs `(("lapack" ,lapack)
1162 ("fftw" ,fftw)))
3a4d5df2
RW		 1163 ;; FIXME: Even though the fonts are available dvips complains:
1164 ;; "Font cmmi10 not found; characters will be left blank."
1165 (native-inputs
1166 `(("texlive" ,texlive-tiny)
1167 ("ghostscript" ,ghostscript)
1168 ("doxygen" ,doxygen)))
a53d6719
JD		 1169 (home-page "http://itpp.sourceforge.net")
1170 (synopsis "C++ library of maths, signal processing and communication classes")
1171 (description "IT++ is a C++ library of mathematical, signal processing and
1172communication classes and functions. Its main use is in simulation of
1173communication systems and for performing research in the area of
1174communications. The kernel of the library consists of generic vector and
1175matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1176similar to MATLAB, GNU Octave or SciPy.")
1177 (license license:gpl3+)))
1178
889187a4
EB		 1179(define-public netcdf
1180 (package
1181 (name "netcdf")
a4b0bfb1 1182 (version "4.4.1.1")
889187a4
EB		 1183 (source
1184 (origin
1185 (method url-fetch)
1186 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1187 "netcdf-" version ".tar.gz"))
1188 (sha256
1189 (base32
a4b0bfb1
EB		 1190 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1191 (patches (search-patches "netcdf-date-time.patch"
1192 "netcdf-tst_h_par.patch"))))
889187a4
EB		 1193 (build-system gnu-build-system)
1194 (native-inputs
1195 `(("m4" ,m4)
1196 ("doxygen" ,doxygen)
1197 ("graphviz" ,graphviz)))
1198 (inputs
db825570
TD		 1199 `(("hdf4" ,hdf4-alt)
1200 ("hdf5" ,hdf5)
1201 ("zlib" ,zlib)
1202 ("libjpeg" ,libjpeg)))
889187a4 1203 (arguments
db825570 1204 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
43d01672
TD		 1205
1206 #:phases (modify-phases %standard-phases
1207 (add-before 'configure 'fix-source-date
1208 (lambda _
1209 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1210 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1211 ;; to '1st hour of the current day', and therefore makes the
1212 ;; package not reproducible.
1213 (substitute* "./configure"
1214 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1215 "date --date='@0'"))
1216 #t))
1217 (add-after 'configure 'patch-settings
1218 (lambda _
1219 ;; libnetcdf.settings contains the full filename of the compilers
1220 ;; used to build the library. We truncate the hashes of those
1221 ;; filenames to avoid unnecessary references to the corresponding
1222 ;; store items.
1223 (substitute* "libnetcdf.settings"
1224 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1225 (string-append prefix (string-take hash 10) "...")))
1226 #t)))
1227
889187a4
EB		 1228 #:parallel-tests? #f)) ;various race conditions
1229 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
1230 (synopsis "Library for scientific data")
1231 (description "NetCDF is an interface for scientific data access and a
1232software library that provides an implementation of the interface. The netCDF
1233library defines a machine-independent format for representing scientific data.
1234Together, the interface, library, and format support the creation, access, and
1235sharing of scientific data.")
1236 (license (license:x11-style "file://COPYRIGHT"))))
1237
1238(define-public netcdf-parallel-openmpi
1239 (package (inherit netcdf)
1240 (name "netcdf-parallel-openmpi")
1241 (inputs
1242 `(("mpi" ,openmpi)
1243 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1244 (package-inputs netcdf))))
1245 ;; TODO: Replace pkg-config references in nc-config with absolute references
1246 (arguments
1247 (substitute-keyword-arguments (package-arguments netcdf)
1248 ((#:configure-flags flags)
1249 `(cons* "CC=mpicc" "CXX=mpicxx"
1250 "--enable-parallel-tests"
1251 ;; Shared libraries not supported with parallel IO.
1252 "--disable-shared" "--with-pic"
1253 ,flags))))))
1254
300200b6
TD		 1255(define-public netcdf-fortran
1256 (package
1257 (name "netcdf-fortran")
1258 (version "4.4.4")
1259 (source (origin
1260 (method url-fetch)
1261 (uri (string-append
1262 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1263 version ".tar.gz"))
1264 (sha256
1265 (base32
1266 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1267 (build-system gnu-build-system)
1268 (arguments
1269 `(#:parallel-tests? #f))
1270 (inputs
1271 `(("netcdf" ,netcdf)))
1272 (native-inputs
1273 `(("gfortran" ,gfortran)))
1274 (synopsis "Fortran interface for the netCDF library")
1275 (description (package-description netcdf))
1276 (home-page (package-home-page netcdf))
1277 (license (package-license netcdf))))
1278
1b39a196
RJ		 1279(define-public nlopt
1280 (package
1281 (name "nlopt")
1282 (version "2.4.2")
1283 (source (origin
1284 (method url-fetch)
1285 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1286 version ".tar.gz"))
1287 (sha256
1288 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1289 (build-system gnu-build-system)
1290 (arguments
1291 `(;; Shared libraries are not built by default. They are required to
1292 ;; build the Guile, Octave, and Python bindings.
1293 #:configure-flags '("--enable-shared")
1294
1295 #:phases
1296 (modify-phases %standard-phases
1297 (add-before 'configure 'set-libnlopt-file-name
1298 (lambda* (#:key outputs #:allow-other-keys)
1299 ;; Make sure the Scheme module refers to the library by its
1300 ;; absolute file name (we cannot do that from a snippet
1301 ;; because the expansion of @libdir@ contains
1302 ;; ${exec_prefix}.)
1303 (let ((out (assoc-ref outputs "out")))
1304 (substitute* "swig/nlopt.scm.in"
1305 (("libnlopt")
1306 (string-append out "/lib/libnlopt")))
1307 #t))))))
1308 (inputs `(("guile" ,guile-2.0)))
1309 (native-inputs `(("pkg-config" ,pkg-config)))
1310 (home-page "http://ab-initio.mit.edu/wiki/")
1311 (synopsis "Library for nonlinear optimization")
1312 (description "NLopt is a library for nonlinear optimization, providing a
1313common interface for a number of different free optimization routines available
1314online as well as original implementations of various other algorithms.")
1315 (license license:lgpl2.1+)))
1316
005c787d
LC		 1317(define-public ipopt
1318 (package
1319 (name "ipopt")
1320 (version "3.12.5")
1321 (source (origin
1322 (method url-fetch)
1323 (uri (string-append
1324 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1325 version".tgz"))
1326 (sha256
1327 (base32
1328 "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
1329 (modules '((guix build utils)))
1330 (snippet
1331 ;; Make sure we don't use the bundled software.
6cbee49d
MW		 1332 '(begin
1333 (delete-file-recursively "ThirdParty")
1334 #t))))
005c787d 1335 (build-system gnu-build-system)
ad1c4537
LC		 1336 (arguments
1337 '(#:phases (modify-phases %standard-phases
1338 (add-after 'install 'add--L-flags-in-ipopt.pc
1339 (lambda* (#:key inputs outputs #:allow-other-keys)
1340 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1341 ;; move it to "Libs.private" where it belongs, and add a
1342 ;; '-L' flag for LAPACK.
1343 (let ((out (assoc-ref outputs "out"))
1344 (lapack (assoc-ref inputs "lapack")))
1345 (substitute* (string-append out "/lib/pkgconfig/"
1346 "ipopt.pc")
1347 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1348 (string-append "Libs: " before " " after "\n"
1349 "Libs.private: " before
1350 "-L" lapack "/lib -llapack -lblas "
1351 after "\n")))
1352 #t))))))
005c787d
LC		 1353 (native-inputs
1354 `(("gfortran" ,gfortran)))
1355 (inputs
1356 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
ad1c4537 1357 `(("lapack" ,lapack))) ;for both libblas and liblapack
005c787d
LC		 1358 (home-page "http://www.coin-or.org")
1359 (synopsis "Large-scale nonlinear optimizer")
1360 (description
1361 "The Interior Point Optimizer (IPOPT) is a software package for
1362large-scale nonlinear optimization. It provides C++, C, and Fortran
1363interfaces.")
1364 (license license:epl1.0)))
1365
f9940ef1
LC		 1366(define-public ceres
1367 (package
1368 (name "ceres-solver")
e0bee0de 1369 (version "1.14.0")
f9940ef1
LC		 1370 (home-page "http://ceres-solver.org/")
1371 (source (origin
1372 (method url-fetch)
1373 (uri (string-append home-page "ceres-solver-"
1374 version ".tar.gz"))
1375 (sha256
1376 (base32
e0bee0de 1377 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
f9940ef1
LC		 1378 (build-system cmake-build-system)
1379 (arguments
1380 ;; TODO: Build HTML user documentation and install separately.
bc3a2e35 1381 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
f9940ef1
LC		 1382 "-DBUILD_SHARED_LIBS=ON")
1383
1384 #:phases (modify-phases %standard-phases
1385 (add-before 'configure 'set-library-directory
1386 (lambda _
1387 ;; Install libraries to lib/, not lib64/.
1388 (substitute* "internal/ceres/CMakeLists.txt"
1389 (("set\\(LIB_SUFFIX \"64\"\\)")
1390 "set(LIB_SUFFIX \"\")"))
1391 #t)))))
1392 (native-inputs
1393 `(("pkg-config" ,pkg-config)))
468e0b18
LC		 1394 (propagated-inputs
1395 `(("glog" ,glog))) ;for #include <glog/glog.h>
f9940ef1
LC		 1396 (inputs
1397 `(("eigen" ,eigen)
1398 ("blas" ,openblas)
1399 ("lapack" ,lapack)
1400 ("suitesparse" ,suitesparse)
1401 ("gflags" ,gflags)))
1402 (synopsis "C++ library for solving large optimization problems")
1403 (description
1404 "Ceres Solver is a C++ library for modeling and solving large,
1405complicated optimization problems. It is a feature rich, mature and
1406performant library which has been used in production since 2010. Ceres Solver
1407can solve two kinds of problems:
1408@enumerate
1409@item non-linear least squares problems with bounds constraints;
1410@item general unconstrained optimization problems.
1411@end enumerate\n")
1412 (license license:bsd-3)))
1413
b66741ed 1414;; For a fully featured Octave, users are strongly recommended also to install
5ca4fe96 1415;; the following packages: less, ghostscript, gnuplot.
668c06ac
JD		 1416(define-public octave
1417 (package
1418 (name "octave")
b66741ed 1419 (version "4.4.1")
668c06ac
JD		 1420 (source
1421 (origin
1422 (method url-fetch)
1423 (uri (string-append "mirror://gnu/octave/octave-"
f5a077b1 1424 version ".tar.lz"))
668c06ac
JD		 1425 (sha256
1426 (base32
b66741ed 1427 "0jsdgizlv02an2ppfjwk5qf209zpwi3317yb7jvlsjzxnir3lvhy"))))
668c06ac
JD		 1428 (build-system gnu-build-system)
1429 (inputs
1430 `(("lapack" ,lapack)
c215fa21 1431 ("qhull" ,qhull)
668c06ac 1432 ("readline" ,readline)
181170c6 1433 ("gl2ps" ,gl2ps)
668c06ac 1434 ("glpk" ,glpk)
1ec78e9d
EB		 1435 ("fftw" ,fftw)
1436 ("fftwf" ,fftwf)
1437 ("arpack" ,arpack-ng)
668c06ac
JD		 1438 ("pcre" ,pcre)
1439 ("fltk" ,fltk)
1440 ("fontconfig" ,fontconfig)
1441 ("freetype" ,freetype)
40029cbe 1442 ("hdf5" ,hdf5)
668c06ac
JD		 1443 ("libxft" ,libxft)
1444 ("mesa" ,mesa)
1ec78e9d 1445 ("glu" ,glu)
9f913401
AI		 1446 ("zlib" ,zlib)
1447 ("curl" ,curl)
5ca4fe96 1448 ("texinfo" ,texinfo)
ab5f3f21
KK		 1449 ("graphicsmagick" ,graphicsmagick)
1450 ("suitesparse" ,suitesparse)
1451 ("libsndfile" ,libsndfile)
1452 ("portaudio" ,portaudio)
1453 ("alsa-lib" ,alsa-lib)))
668c06ac 1454 (native-inputs
f5a077b1
EF		 1455 `(("lzip" ,lzip)
1456 ("gfortran" ,gfortran)
668c06ac
JD		 1457 ("pkg-config" ,pkg-config)
1458 ("perl" ,perl)
1ec78e9d
EB		 1459 ;; The following inputs are not actually used in the build process.
1460 ;; However, the ./configure gratuitously tests for their existence and
1461 ;; assumes that programs not present at build time are also not, and
1462 ;; can never be, available at run time! If these inputs are therefore
1463 ;; not present, support for them will be built out. However, Octave
1464 ;; will still run without them, albeit without the features they
668c06ac
JD		 1465 ;; provide.
1466 ("less" ,less)
668c06ac
JD		 1467 ("ghostscript" ,ghostscript)
1468 ("gnuplot" ,gnuplot)))
116af86f
KK		 1469 ;; Octave code uses this variable to detect directories holding multiple CA
1470 ;; certificates to verify peers with. This is required for the networking
1471 ;; functions that require encryption to work properly.
1472 (native-search-paths
1473 (list (search-path-specification
1474 (variable "CURLOPT_CAPATH")
1475 (files '("etc/ssl/certs")))))
668c06ac 1476 (arguments
b7b27a8f
KY		 1477 `(#:configure-flags
1478 (list (string-append "--with-shell="
1479 (assoc-ref %build-inputs "bash")
5ca4fe96
AI		 1480 "/bin/sh"))
1481 #:phases
1482 (modify-phases %standard-phases
1483 (add-after 'configure 'configure-makeinfo
1484 (lambda* (#:key inputs #:allow-other-keys)
1485 (substitute* "libinterp/corefcn/help.cc"
1486 (("Vmakeinfo_program = \"makeinfo\"")
1487 (string-append "Vmakeinfo_program = \""
1488 (assoc-ref inputs "texinfo")
1489 "/bin/makeinfo\"")))
1490 #t)))))
f5a077b1 1491 (home-page "https://www.gnu.org/software/octave/")
668c06ac 1492 (synopsis "High-level language for numerical computation")
1ec78e9d
EB		 1493 (description "GNU Octave is a high-level interpreted language that is
1494specialized for numerical computations. It can be used for both linear and
1495non-linear applications and it provides great support for visualizing results.
1496Work may be performed both at the interactive command-line as well as via
1497script files.")
668c06ac 1498 (license license:gpl3+)))
3de01d3f 1499
36ce25f0
KK		 1500(define-public qtoctave
1501 (package (inherit octave)
1502 (name "qtoctave")
7a3772b3 1503 (source (origin
b66741ed 1504 (inherit (package-source octave))))
36ce25f0
KK		 1505 (inputs
1506 `(("qscintilla" ,qscintilla)
1507 ("qt" ,qtbase)
1508 ,@(package-inputs octave)))
1509 (native-inputs
1510 `(("qttools" , qttools) ;for lrelease
7a3772b3 1511 ("texlive" ,texlive) ;for texi2dvi
36ce25f0
KK		 1512 ,@(package-native-inputs octave)))
1513 (arguments
1514 (substitute-keyword-arguments (package-arguments octave)
1515 ((#:phases phases)
1516 `(modify-phases ,phases
1517 (add-before 'configure 'patch-qscintilla-library-name
1518 (lambda* (#:key inputs #:allow-other-keys)
1519 ;; The QScintilla library that the Octave configure script tries
1520 ;; to link with should be named libqscintilla-qt5.so, but the
1521 ;; QScintilla input provides the shared library as
1522 ;; libqscintilla2_qt5.so.
1523 (substitute* "configure"
1524 (("qscintilla2-qt5")
1525 "qscintilla2_qt5"))
1526 #t))))))))
1527
5d4bd4cc
PG		 1528(define-public opencascade-oce
1529 (package
1530 (name "opencascade-oce")
1531 (version "0.17.2")
1532 (source
1533 (origin
1534 (method url-fetch)
1535 (uri (string-append
1536 "https://github.com/tpaviot/oce/archive/OCE-"
1537 version
1538 ".tar.gz"))
a4f393b7 1539 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
5d4bd4cc
PG		 1540 (sha256
1541 (base32
1542 "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
1543 (build-system cmake-build-system)
1544 (arguments
1545 '(#:configure-flags
1546 (list "-DOCE_TESTING:BOOL=ON"
1547 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1548 "-DOCE_DRAW:BOOL=ON"
1549 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1550 (assoc-ref %outputs "out"))
1551 "-UCMAKE_INSTALL_RPATH")))
1552 (inputs
1553 `(("freetype" ,freetype)
1554 ("glu" ,glu)
1555 ("libxmu" ,libxmu)
1556 ("mesa" ,mesa)
1557 ("tcl" ,tcl)
1558 ("tk" ,tk)))
1559 (native-inputs
1560 `(("python" ,python-wrapper)))
1561 (home-page "https://github.com/tpaviot/oce")
1562 (synopsis "Libraries for 3D modeling and numerical simulation")
1563 (description
1564 "Open CASCADE is a set of libraries for the development of applications
1565dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1566C++ class libraries providing services for 3D surface and solid modeling, CAD
1567data exchange, and visualization. It is used for development of specialized
1568software dealing with 3D models in design (CAD), manufacturing (CAM),
1569numerical simulation (CAE), measurement equipment (CMM), and quality
1570control (CAQ) domains.
1571
1572This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1573patches, improvements, and experiments contributed by users over the official
1574Open CASCADE library.")
1575 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1576 ; use of header files; see
1577 ; OCCT_LGPL_EXCEPTION.txt
1578 license:public-domain; files
1579 ; src/Standard/Standard_StdAllocator.hxx and
1580 ; src/NCollection/NCollection_StdAllocator.hxx
1581 license:expat; file src/OpenGl/OpenGl_glext.h
1582 license:bsd-3)))); test framework gtest
1583
3de01d3f
EB		 1584(define-public gmsh
1585 (package
1586 (name "gmsh")
8a4d14fa 1587 (version "2.16.0")
3de01d3f
EB		 1588 (source
1589 (origin
1590 (method url-fetch)
1c79e086 1591 (uri (string-append "http://gmsh.info/src/gmsh-"
3de01d3f
EB		 1592 version "-source.tgz"))
1593 (sha256
8a4d14fa 1594 (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
3de01d3f
EB		 1595 (modules '((guix build utils)))
1596 (snippet
1597 ;; Remove non-free METIS code
6cbee49d
MW		 1598 '(begin
1599 (delete-file-recursively "contrib/Metis")
1600 #t))))
3de01d3f 1601 (build-system cmake-build-system)
3de01d3f
EB		 1602 (propagated-inputs
1603 `(("fltk" ,fltk)
19afbea1 1604 ("gfortran" ,gfortran)
3de01d3f 1605 ("gmp" ,gmp)
40029cbe 1606 ("hdf5" ,hdf5)
3de01d3f
EB		 1607 ("lapack" ,lapack)
1608 ("mesa" ,mesa)
85f41902 1609 ("glu" ,glu)
45548139 1610 ("opencascade-oce" ,opencascade-oce)
3de01d3f
EB		 1611 ("libx11" ,libx11)
1612 ("libxext" ,libxext)))
66395a61
EF		 1613 (inputs
1614 `(("fontconfig" ,fontconfig)
1615 ("libxft" ,libxft)))
3de01d3f
EB		 1616 (arguments
1617 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1618 "-DENABLE_BUILD_SHARED:BOOL=ON"
45548139 1619 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
3de01d3f
EB		 1620 (home-page "http://www.geuz.org/gmsh/")
1621 (synopsis "3D finite element grid generator")
edf684ef
EB		 1622 (description "Gmsh is a 3D finite element grid generator with a built-in
1623CAD engine and post-processor. Its design goal is to provide a fast, light
1624and user-friendly meshing tool with parametric input and advanced
1625visualization capabilities. Gmsh is built around four modules: geometry,
1626mesh, solver and post-processing. The specification of any input to these
1627modules is done either interactively using the graphical user interface or in
1628ASCII text files using Gmsh's own scripting language.")
3de01d3f 1629 (license license:gpl2+)))
b9100e2f 1630
6d5f63b6
JD		 1631(define-public maxflow
1632 (package
1633 (name "maxflow")
1634 (version "3.04")
1635 (source (origin
1636 (method git-fetch)
1637 (uri (git-reference
1638 (url "https://github.com/gerddie/maxflow.git")
1639 (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
1640 (file-name (string-append name "-" version "-checkout"))
1641 (sha256
1642 (base32
1643 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1644 (build-system cmake-build-system)
1645 (home-page "http://pub.ist.ac.at/~vnk/software.html")
1646 (synopsis "Library implementing Maxflow algorithm")
1647 (description "An implementation of the maxflow algorithm described in
1648@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1649Energy Minimization in Computer Vision.\n
1650Yuri Boykov and Vladimir Kolmogorov.\n
1651In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1652September 2004}")
1653 (license license:gpl3+)))
1654
b9100e2f
EB		 1655(define-public petsc
1656 (package
1657 (name "petsc")
e6951e4e 1658 (version "3.10.2")
b9100e2f
EB		 1659 (source
1660 (origin
1661 (method url-fetch)
1662 ;; The *-lite-* tarball does not contain the *large* documentation
1663 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1664 "petsc-lite-" version ".tar.gz"))
1665 (sha256
e6951e4e 1666 (base32 "0bl64pydak3rblnjffi482r8bin4xim9sb37ksl2jkcxf0i0irsi"))))
a3a99e27 1667 (outputs '("out" ;libraries and headers
c15be128 1668 "examples")) ;~30MiB of examples
b9100e2f
EB		 1669 (build-system gnu-build-system)
1670 (native-inputs
6fec298d 1671 `(("python" ,python-2)))
b9100e2f 1672 (inputs
19afbea1 1673 `(("gfortran" ,gfortran)
b9100e2f 1674 ("lapack" ,lapack)
f258212d 1675 ("superlu" ,superlu)
b9100e2f
EB		 1676 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1677 ;; leaving out opengl, as configuration seems to only be for mac
1678 ))
1679 (arguments
1680 `(#:test-target "test"
9a899cce 1681 #:parallel-build? #f ;build is parallel by default
b9100e2f
EB		 1682 #:configure-flags
1683 `("--with-mpi=0"
f258212d 1684 "--with-openmp=1"
c15be128 1685 "--with-superlu=1")
9731c412
EB		 1686 #:make-flags
1687 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1688 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1689 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
b9100e2f 1690 #:phases
64dcc289
EB		 1691 (modify-phases %standard-phases
1692 (replace 'configure
1693 ;; PETSc's configure script is actually a python script, so we can't
1694 ;; run it with bash.
1695 (lambda* (#:key outputs (configure-flags '())
1696 #:allow-other-keys)
1697 (let* ((prefix (assoc-ref outputs "out"))
1698 (flags `(,(string-append "--prefix=" prefix)
1699 ,@configure-flags)))
1700 (format #t "build directory: ~s~%" (getcwd))
1701 (format #t "configure flags: ~s~%" flags)
49fdd357 1702 (apply invoke "./configure" flags))))
64dcc289 1703 (add-after 'configure 'clean-local-references
9731c412 1704 (lambda* (#:key outputs #:allow-other-keys)
64dcc289
EB		 1705 (let ((out (assoc-ref outputs "out")))
1706 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
b730b437
EB		 1707 ;; Prevent build directory from leaking into compiled code
1708 (((getcwd)) out)
1709 ;; Scrub timestamp for reproducibility
fafd623e 1710 ((".*Libraries compiled on.*") ""))
9731c412
EB		 1711 (substitute* (find-files "." "petscvariables")
1712 ;; Do not expose build machine characteristics, set to defaults.
1713 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1714 (("NPMAX = [:digit:]+") "NPMAX = 2"))
fafd623e 1715 #t)))
64dcc289 1716 (add-after 'install 'clean-install
10b11968
EB		 1717 ;; Try to keep installed files from leaking build directory names.
1718 (lambda* (#:key inputs outputs #:allow-other-keys)
64dcc289 1719 (let ((out (assoc-ref outputs "out")))
10b11968 1720 (substitute* (map (lambda (file)
9a899cce 1721 (string-append out "/lib/petsc/conf/" file))
fafd623e 1722 '("petscvariables"))
10b11968
EB		 1723 (((getcwd)) out))
1724 ;; Make compiler references point to the store
9a899cce 1725 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
dfdf5716
EB		 1726 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1727 (string-append "= " (which compiler))))
10b11968
EB		 1728 ;; PETSc installs some build logs, which aren't necessary.
1729 (for-each (lambda (file)
9a899cce 1730 (let ((f (string-append out "/lib/petsc/conf/" file)))
10b11968
EB		 1731 (when (file-exists? f)
1732 (delete-file f))))
9a899cce
EB		 1733 '("configure.log" "make.log" "gmake.log"
1734 "test.log" "error.log" "RDict.db"
fafd623e 1735 "PETScBuildInternal.cmake"
10b11968 1736 ;; Once installed, should uninstall with Guix
fafd623e 1737 "uninstall.py"))
a3a99e27
EB		 1738 #t)))
1739 (add-after 'install 'move-examples
1740 (lambda* (#:key outputs #:allow-other-keys)
1741 (let* ((out (assoc-ref outputs "out"))
1742 (examples (assoc-ref outputs "examples"))
1743 (exdir (string-append out "/share/petsc/examples"))
1744 (exdir' (string-append examples "/share/petsc/examples")))
1745 (copy-recursively exdir exdir')
1746 (delete-file-recursively exdir)
fafd623e 1747 #t))))))
b9100e2f 1748 (home-page "http://www.mcs.anl.gov/petsc")
16ecf3ff 1749 (synopsis "Library to solve PDEs")
b9100e2f
EB		 1750 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1751data structures and routines for the scalable (parallel) solution of
1752scientific applications modeled by partial differential equations.")
166191b3 1753 (license (license:non-copyleft
b9100e2f
EB		 1754 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1755
1756(define-public petsc-complex
1757 (package (inherit petsc)
1758 (name "petsc-complex")
1759 (arguments
1760 (substitute-keyword-arguments (package-arguments petsc)
1761 ((#:configure-flags cf)
1762 `(cons "--with-scalar-type=complex" ,cf))))
16ecf3ff 1763 (synopsis "Library to solve PDEs (with complex scalars)")))
183e44ae 1764
d8c7eeb9
EB		 1765(define-public petsc-openmpi
1766 (package (inherit petsc)
1767 (name "petsc-openmpi")
1768 (inputs
9e2aa70b
PG		 1769 `(("hdf5" ,hdf5-parallel-openmpi)
1770 ("metis" ,metis)
1771 ("mumps" ,mumps-openmpi)
1772 ("openmpi" ,openmpi)
1773 ("scalapack" ,scalapack)
1774 ("scotch" ,pt-scotch)
d8c7eeb9
EB		 1775 ,@(package-inputs petsc)))
1776 (arguments
1777 (substitute-keyword-arguments (package-arguments petsc)
1778 ((#:configure-flags cf)
1779 ``("--with-mpiexec=mpirun"
9e2aa70b
PG		 1780 "--with-metis=1"
1781 "--with-mumps=1"
1782 "--with-scalapack=1"
1783 "--with-ptscotch=1"
d8c7eeb9
EB		 1784 ,(string-append "--with-mpi-dir="
1785 (assoc-ref %build-inputs "openmpi"))
71ca16b5
PG		 1786 ,(string-append "--with-hdf5-include="
1787 (assoc-ref %build-inputs "hdf5") "/include")
1788 ,(string-append "--with-hdf5-lib="
1789 (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
1790 ,@(delete "--with-mpi=0" ,cf)))
1791 ((#:phases phases)
1792 `(modify-phases ,phases
9e2aa70b 1793 (add-before 'configure 'mpi-setup
bbe46a4a 1794 ,%openmpi-setup)))))
9e2aa70b 1795 (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
d8c7eeb9
EB		 1796
1797(define-public petsc-complex-openmpi
1798 (package (inherit petsc-complex)
1799 (name "petsc-complex-openmpi")
1800 (inputs
1801 `(("openmpi" ,openmpi)
1802 ,@(package-inputs petsc-complex)))
1803 (arguments
1804 (substitute-keyword-arguments (package-arguments petsc-complex)
1805 ((#:configure-flags cf)
1806 ``("--with-mpiexec=mpirun"
1807 ,(string-append "--with-mpi-dir="
1808 (assoc-ref %build-inputs "openmpi"))
1809 ,@(delete "--with-mpi=0" ,cf)))))
16ecf3ff 1810 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
d8c7eeb9 1811
90ff2874
PG		 1812(define-public python-petsc4py
1813 (package
1814 (name "python-petsc4py")
cd3681a2 1815 (version "3.10.0")
90ff2874
PG		 1816 (source
1817 (origin
1818 (method url-fetch)
1819 (uri (pypi-uri "petsc4py" version))
1820 (sha256
1821 (base32
cd3681a2 1822 "0ch3g6dsvxl7qi984fcssv7cxfbif4bw04gkvxl2l1b8wrmvrm25"))))
90ff2874
PG		 1823 (build-system python-build-system)
1824 (arguments
1825 `(#:phases
1826 (modify-phases %standard-phases
1827 (add-before 'build 'pre-build
1828 (lambda _
1829 ;; Define path to PETSc installation.
1830 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
1831 #t))
1832 (add-before 'check 'mpi-setup
1833 ,%openmpi-setup))))
1834 (inputs
1835 `(("petsc" ,petsc-openmpi)
1836 ("python-numpy" ,python-numpy)))
1837 (home-page "https://bitbucket.org/petsc/petsc4py/")
1838 (synopsis "Python bindings for PETSc")
1839 (description "PETSc, the Portable, Extensible Toolkit for
1840Scientific Computation, is a suite of data structures and routines for
1841the scalable (parallel) solution of scientific applications modeled by
1842partial differential equations. It employs the MPI standard for all
1843message-passing communication. @code{petsc4py} provides Python
1844bindings to almost all functions of PETSc.")
1845 (license license:bsd-3)))
1846
560acf25
MB		 1847(define-public python-kiwisolver
1848 (package
1849 (name "python-kiwisolver")
1850 (version "1.0.1")
1851 (source (origin
1852 (method url-fetch)
1853 (uri (pypi-uri "kiwisolver" version))
1854 (sha256
1855 (base32
1856 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
1857 (build-system python-build-system)
1858 (home-page "https://github.com/nucleic/kiwi")
1859 (synopsis "Fast implementation of the Cassowary constraint solver")
1860 (description
1861 "Kiwi is an efficient C++ implementation of the Cassowary constraint
1862solving algorithm. Kiwi has been designed from the ground up to be
1863lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
1864Cassowary solver with typical use cases gaining a 40x improvement. Memory
1865savings are consistently > 5x.")
1866 (license license:bsd-3)))
1867
1868(define-public python2-kiwisolver
1869 (package-with-python2 python-kiwisolver))
1870
a7f01414
EB		 1871(define-public slepc
1872 (package
1873 (name "slepc")
e93da160 1874 (version "3.10.1")
a7f01414
EB		 1875 (source
1876 (origin
1877 (method url-fetch)
baeaf882
EB		 1878 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
1879 version ".tar.gz"))
a7f01414
EB		 1880 (sha256
1881 (base32
e93da160 1882 "188j1a133q91h8pivpnzwcf78kz8dvz2nzf6ndnjygdbqb48fizn"))))
a7f01414
EB		 1883 (build-system gnu-build-system)
1884 (native-inputs
1885 `(("python" ,python-2)))
1886 (inputs
1887 `(("arpack" ,arpack-ng)
1888 ("gfortran" ,gfortran)))
1889 (propagated-inputs
1890 `(("petsc" ,petsc)))
1891 (arguments
1892 `(#:parallel-build? #f ;build is parallel by default
1893 #:configure-flags
1894 `(,(string-append "--with-arpack-dir="
9cf52454 1895 (assoc-ref %build-inputs "arpack") "/lib"))
9731c412
EB		 1896 #:make-flags ;honor (parallel-job-count)
1897 `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
a7f01414
EB		 1898 #:phases
1899 (modify-phases %standard-phases
8787c555 1900 (replace 'configure
a7f01414
EB		 1901 ;; configure is a python script, so we can't run it with bash.
1902 (lambda* (#:key inputs outputs (configure-flags '())
1903 #:allow-other-keys)
1904 (let* ((prefix (assoc-ref outputs "out"))
1905 (flags `(,(string-append "--prefix=" prefix)
1906 ,@configure-flags)))
1907 (format #t "build directory: ~s~%" (getcwd))
1908 (format #t "configure flags: ~s~%" flags)
1909 (setenv "SLEPC_DIR" (getcwd))
9cf52454 1910 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
c6840089 1911 (apply invoke "./configure" flags))))
8787c555 1912 (add-after 'install 'delete-doc
a7f01414
EB		 1913 ;; TODO: SLEPc installs HTML documentation alongside headers in
1914 ;; $out/include. We'd like to move them to share/doc, but delete
1915 ;; them for now, as they are incomplete and installing the complete
1916 ;; documentation is difficult.
1917 (lambda* (#:key outputs #:allow-other-keys)
1918 (let* ((out (assoc-ref outputs "out")))
0f6dc120
TGR		 1919 (for-each delete-file (find-files out "\\.html$"))
1920 #t)))
8787c555 1921 (add-after 'install 'clean-install
a7f01414
EB		 1922 ;; Clean up unnecessary build logs from installation.
1923 (lambda* (#:key outputs #:allow-other-keys)
1924 (let ((out (assoc-ref outputs "out")))
1925 (for-each (lambda (file)
1926 (let ((f (string-append out "/lib/slepc/conf/" file)))
1927 (when (file-exists? f)
1928 (delete-file f))))
1929 '("configure.log" "make.log" "gmake.log"
1930 "test.log" "error.log" "RDict.db"
0f6dc120
TGR		 1931 "uninstall.py"))
1932 #t))))))
a7f01414
EB		 1933 (home-page "http://slepc.upv.es")
1934 (synopsis "Scalable library for eigenproblems")
1935 (description "SLEPc is a software library for the solution of large sparse
1936eigenproblems on parallel computers. It can be used for the solution of
1937linear eigenvalue problems formulated in either standard or generalized form,
1938as well as other related problems such as the singular value decomposition.
1939The emphasis of the software is on methods and techniques appropriate for
1940problems in which the associated matrices are sparse, for example, those
1941arising after the discretization of partial differential equations.")
3c524f21 1942 (license license:bsd-2)))
a7f01414
EB		 1943
1944(define-public slepc-complex
1945 (package (inherit slepc)
1946 (name "slepc-complex")
1947 (propagated-inputs
1948 `(("petsc" ,petsc-complex)
1949 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1950 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1951
1952(define-public slepc-openmpi
1953 (package (inherit slepc)
1954 (name "slepc-openmpi")
6df2a50a
LC		 1955 (arguments
1956 (substitute-keyword-arguments (package-arguments slepc)
1957 ((#:phases phases '%standard-phases)
1958 `(modify-phases ,phases
bbe46a4a
EB		 1959 (add-before 'check 'mpi-setup
1960 ,%openmpi-setup)))))
a7f01414
EB		 1961 (inputs
1962 `(("mpi" ,openmpi)
1963 ("arpack" ,arpack-ng-openmpi)
1964 ,@(alist-delete "arpack" (package-inputs slepc))))
1965 (propagated-inputs
1966 `(("petsc" ,petsc-openmpi)
1967 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1968 (synopsis "Scalable library for eigenproblems (with MPI support)")))
1969
1970(define-public slepc-complex-openmpi
1971 (package (inherit slepc-openmpi)
1972 (name "slepc-complex-openmpi")
1973 (propagated-inputs
1974 `(("petsc" ,petsc-complex-openmpi)
1975 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1976 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1977
6b5687d0
PG		 1978(define-public python-slepc4py
1979 (package
1980 (name "python-slepc4py")
57d30004 1981 (version "3.10.0")
6b5687d0
PG		 1982 (source
1983 (origin
1984 (method url-fetch)
1985 (uri (pypi-uri "slepc4py" version))
1986 (sha256
1987 (base32
57d30004 1988 "0x049dyc8frgh79fvvavf4vlbqp4mgm61nsaivzdav4316vvlv1j"))))
6b5687d0
PG		 1989 (build-system python-build-system)
1990 (arguments
1991 `(#:phases
1992 (modify-phases %standard-phases
1993 (add-before 'build 'pre-build
1994 (lambda _
1995 ;; Define path to PETSc installation.
1996 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
1997 ;; Define path to SLEPc installation.
1998 (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
1999 #t))
2000 (add-before 'check 'mpi-setup
2001 ,%openmpi-setup))))
2002 (inputs
2003 `(("python-numpy" ,python-numpy)
2004 ("python-petsc4py" ,python-petsc4py)
2005 ("slepc" ,slepc-openmpi)))
2006 (home-page "https://bitbucket.org/slepc/slepc4py/")
2007 (synopsis "Python bindings for SLEPc")
2008 (description "SLEPc, the Scalable Library for Eigenvalue Problem
2009Computations, is based on PETSc, the Portable, Extensible Toolkit for
2010Scientific Computation. It employs the MPI standard for all
2011message-passing communication. @code{slepc4py} provides Python
2012bindings to almost all functions of SLEPc.")
2013 (license license:bsd-3)))
2014
cec86422
EB		 2015(define-public mumps
2016 (package
2017 (name "mumps")
e7323f4c 2018 (version "5.1.2")
cec86422
EB		 2019 (source
2020 (origin
2021 (method url-fetch)
2022 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
2023 version ".tar.gz"))
2024 (sha256
2025 (base32
e7323f4c 2026 "1s9asin08zqzmh08257sdghhivvy9vjif7c53fhaxaax2kd5qd7b"))
fc1adab1 2027 (patches (search-patches "mumps-build-parallelism.patch"))))
cec86422
EB		 2028 (build-system gnu-build-system)
2029 (inputs
2030 `(("fortran" ,gfortran)
2031 ;; These are required for linking against mumps, but we let the user
2032 ;; declare the dependency.
2033 ("blas" ,openblas)
2034 ("metis" ,metis)
2035 ("scotch" ,scotch)))
2036 (arguments
2037 `(#:modules ((ice-9 match)
2038 (ice-9 popen)
2039 (srfi srfi-1)
2040 ,@%gnu-build-system-modules)
2041 #:phases
2042 (modify-phases %standard-phases
fba78d18 2043 (replace 'configure
cec86422
EB		 2044 (lambda* (#:key inputs #:allow-other-keys)
2045 (call-with-output-file "Makefile.inc"
2046 (lambda (port)
2047 (format port "
2048PLAT =
2049LIBEXT = .a
2050OUTC = -o
2051OUTF = -o
2052RM = rm -f~:[
2053CC = gcc
2054FC = gfortran
2055FL = gfortran
2056INCSEQ = -I$(topdir)/libseq
2057LIBSEQ = -L$(topdir)/libseq -lmpiseq
2058LIBSEQNEEDED = libseqneeded~;
2059CC = mpicc
2060FC = mpifort
2061FL = mpifort~]
2062AR = ar vr # rules require trailing space, ugh...
2063RANLIB = ranlib
2064LIBBLAS = -L~a -lopenblas~@[
2065SCALAP = -L~a -lscalapack~]
2066LIBOTHERS = -pthread
2067CDEFS = -DAdd_
2068PIC = -fPIC
2069OPTF = -O2 -DALLOW_NON_INIT $(PIC)
2070OPTL = -O2 $(PIC)
2071OPTC = -O2 $(PIC)
2072INCS = $(INCSEQ)
2073LIBS = $(SCALAP) $(LIBSEQ)
2074LPORDDIR = $(topdir)/PORD/lib
2075IPORD = -I$(topdir)/PORD/include
2076LPORD = -L$(LPORDDIR) -lpord
2077ORDERINGSF = -Dpord~@[
2078METISDIR = ~a
2079IMETIS = -I$(METISDIR)/include
2080LMETIS = -L$(METISDIR)/lib -lmetis
2081ORDERINGSF += -Dmetis~]~@[~:{
2082SCOTCHDIR = ~a
2083ISCOTCH = -I$(SCOTCHDIR)/include
2084LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
2085ORDERINGSF += ~a~}~]
2086ORDERINGSC = $(ORDERINGSF)
2087LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
2088IORDERINGSF = $(ISCOTCH)
2089IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
2090 (assoc-ref inputs "mpi")
2091 (assoc-ref inputs "blas")
2092 (assoc-ref inputs "scalapack")
2093 (assoc-ref inputs "metis")
2094 (match (list (assoc-ref inputs "pt-scotch")
2095 (assoc-ref inputs "scotch"))
2096 ((#f #f)
2097 #f)
2098 ((#f scotch)
2099 `((,scotch "" "-Dscotch")))
2100 ((ptscotch _)
2101 `((,ptscotch
2102 "-lptesmumps -lptscotch -lptscotcherr "
2103 "-Dptscotch")))))))))
fba78d18 2104 (replace 'build
cec86422
EB		 2105 ;; By default only the d-precision library is built. Make with "all"
2106 ;; target so that all precision libraries and examples are built.
2107 (lambda _
b414cf52
TGR		 2108 (invoke "make" "all"
2109 (format #f "-j~a" (parallel-job-count)))))
fba78d18 2110 (replace 'check
cec86422
EB		 2111 ;; Run the simple test drivers, which read test input from stdin:
2112 ;; from the "real" input for the single- and double-precision
2113 ;; testers, and from the "cmplx" input for complex-precision
2114 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
2115 ;; package to prefix execution with "mpirun".
2116 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
2117 (with-directory-excursion "examples"
2118 (every
2119 (lambda (prec type)
2120 (let ((tester (apply open-pipe*
2121 `(,OPEN_WRITE
2122 ,@exec-prefix
2123 ,(string-append "./" prec
2124 "simpletest"))))
2125 (input (open-input-file
2126 (string-append "input_simpletest_" type))))
2127 (begin
2128 (dump-port input tester)
2129 (close-port input)
2130 (zero? (close-pipe tester)))))
2131 '("s" "d" "c" "z")
2132 '("real" "real" "cmplx" "cmplx")))))
fba78d18
EB		 2133 (replace 'install
2134 (lambda* (#:key outputs #:allow-other-keys)
2135 (let* ((out (assoc-ref outputs "out"))
2136 (libdir (string-append out "/lib")))
2137 (copy-recursively "lib" libdir)
2138 (copy-recursively "include" (string-append out "/include"))
2139 (when (file-exists? "libseq/libmpiseq.a")
2140 (install-file "libseq/libmpiseq.a" libdir))
2141 #t))))))
cec86422
EB		 2142 (home-page "http://mumps.enseeiht.fr")
2143 (synopsis "Multifrontal sparse direct solver")
2144 (description
2145 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
2146sparse system of linear equations A x = b using Guassian elimination.")
2147 (license license:cecill-c)))
2148
2149(define-public mumps-metis
2150 (package (inherit mumps)
2151 (name "mumps-metis")
2152 (inputs
2153 (alist-delete "scotch" (package-inputs mumps)))))
2154
2155(define-public mumps-openmpi
2156 (package (inherit mumps)
2157 (name "mumps-openmpi")
2158 (inputs
2159 `(("mpi" ,openmpi)
2160 ("scalapack" ,scalapack)
2161 ("pt-scotch" ,pt-scotch)
2162 ,@(alist-delete "scotch" (package-inputs mumps))))
2163 (arguments
2164 (substitute-keyword-arguments (package-arguments mumps)
2165 ((#:phases phases)
2166 `(modify-phases ,phases
bbe46a4a
EB		 2167 (add-before 'check 'mpi-setup
2168 ,%openmpi-setup)
6df2a50a
LC		 2169 (replace 'check
2170 (lambda _
2171 ((assoc-ref ,phases 'check)
2172 #:exec-prefix '("mpirun" "-n" "2"))))))))
cec86422
EB		 2173 (synopsis "Multifrontal sparse direct solver (with MPI)")))
2174
2175(define-public mumps-metis-openmpi
2176 (package (inherit mumps-openmpi)
2177 (name "mumps-metis-openmpi")
2178 (inputs
2179 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
2180
2d047896
RW		 2181(define-public r-quadprog
2182 (package
2183 (name "r-quadprog")
2184 (version "1.5-5")
2185 (source
2186 (origin
2187 (method url-fetch)
2188 (uri (cran-uri "quadprog" version))
2189 (sha256
2190 (base32
2191 "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
2192 (build-system r-build-system)
2193 (native-inputs
2194 `(("gfortran" ,gfortran)))
e9960d8c 2195 (home-page "https://cran.r-project.org/web/packages/quadprog")
2d047896
RW		 2196 (synopsis "Functions to solve quadratic programming problems")
2197 (description
2198 "This package contains routines and documentation for solving quadratic
2199programming problems.")
2200 (license license:gpl3+)))
2201
ec8c7e47
RJ		 2202(define-public r-pracma
2203 (package
2204 (name "r-pracma")
39528a5e 2205 (version "2.1.8")
ec8c7e47
RJ		 2206 (source (origin
2207 (method url-fetch)
2208 (uri (cran-uri "pracma" version))
2209 (sha256
39528a5e 2210 (base32 "0m8ladhrfyxwybblkcdgg4xv1mk5kibmwarpj2k0c2y34zzcix4z"))))
ec8c7e47 2211 (build-system r-build-system)
39528a5e 2212 (home-page "https://cran.r-project.org/web/packages/pracma/")
ec8c7e47
RJ		 2213 (synopsis "Practical numerical math functions")
2214 (description "This package provides functions for numerical analysis and
2215linear algebra, numerical optimization, differential equations, plus some
2216special functions. It uses Matlab function names where appropriate to simplify
2217porting.")
2218 (license license:gpl3+)))
2219
63e07468
BW		 2220(define-public ruby-asciimath
2221 (package
2222 (name "ruby-asciimath")
2223 (version "1.0.4")
2224 (source
2225 (origin
2226 (method url-fetch)
2227 (uri (rubygems-uri "asciimath" version))
2228 (sha256
2229 (base32
2230 "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
2231 (build-system ruby-build-system)
2232 (arguments
2233 '(#:phases
2234 (modify-phases %standard-phases
2235 ;; Apply this patch
2236 ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
2237 (add-after 'unpack 'patch-remove-spurious-backslashes
2238 (lambda _
2239 (substitute* "spec/parser_spec.rb"
2240 (("\\\\\"")
9923d5a4
TGR		 2241 "\""))
2242 #t)))))
63e07468
BW		 2243 (native-inputs
2244 `(("bundler" ,bundler)
2245 ("ruby-rspec" ,ruby-rspec)))
2246 (synopsis "AsciiMath parsing and conversion library")
2247 (description
2248 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
2249easy-to-write markup language for mathematics.")
2250 (home-page "https://github.com/asciidoctor/asciimath")
2251 (license license:expat)))
2252
183e44ae
EB		 2253(define-public superlu
2254 (package
2255 (name "superlu")
995a09e0 2256 (version "5.2.1")
183e44ae
EB		 2257 (source
2258 (origin
2259 (method url-fetch)
2260 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2261 "superlu_" version ".tar.gz"))
2262 (sha256
995a09e0
EB		 2263 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
2264 (modules '((guix build utils)))
2265 (snippet
2266 ;; Replace the non-free implementation of MC64 with a stub adapted
2267 ;; from Debian
2268 '(begin
2269 (use-modules (ice-9 regex)
2270 (ice-9 rdelim))
2271 (call-with-output-file "SRC/mc64ad.c"
2272 (lambda (port)
2273 (display "
2274#include <stdio.h>
2275#include <stdlib.h>
2276void mc64id_(int *a) {
2277 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2278 abort ();
2279}
2280void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2281 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2282 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2283 abort ();
2284}\n" port)))
2285 ;; Remove the corresponding license verbiage. MC64 license follows
2286 ;; a "------" line separator.
2287 (with-atomic-file-replacement "License.txt"
2288 (let ((rx (make-regexp "-{8}")))
2289 (lambda (in out)
2290 (let loop ()
2291 (let ((line (read-line in 'concat)))
2292 (unless (regexp-exec rx line)
2293 (display line out)
6cbee49d
MW		 2294 (loop))))
2295 #t)))))))
995a09e0 2296 (build-system cmake-build-system)
183e44ae
EB		 2297 (native-inputs
2298 `(("tcsh" ,tcsh)))
2299 (inputs
995a09e0 2300 `(("blas" ,openblas)
19afbea1 2301 ("gfortran" ,gfortran)))
183e44ae 2302 (arguments
995a09e0
EB		 2303 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2304 "-DTPL_BLAS_LIBRARIES=openblas"
677bc34d 2305 "-DBUILD_SHARED_LIBS:BOOL=YES")))
183e44ae
EB		 2306 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
2307 (synopsis "Supernodal direct solver for sparse linear systems")
2308 (description
2309 "SuperLU is a general purpose library for the direct solution of large,
2310sparse, nonsymmetric systems of linear equations on high performance machines.
2311The library is written in C and is callable from either C or Fortran. The
2312library routines perform an LU decomposition with partial pivoting and
2313triangular system solves through forward and back substitution. The library
2314also provides threshold-based ILU factorization preconditioners.")
995a09e0
EB		 2315 (license (list license:bsd-3
2316 license:gpl2+ ;EXAMPLE/*fgmr.c
2317 (license:fsf-free "file://SRC/colamd.h")))))
f8ed036a 2318
a54aefea
EB		 2319(define-public superlu-dist
2320 (package
2321 (name "superlu-dist")
0921eff2 2322 (version "5.3.0")
a54aefea
EB		 2323 (source
2324 (origin
2325 (method url-fetch)
2326 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2327 "superlu_dist_" version ".tar.gz"))
2328 (sha256
0921eff2
LC		 2329 (base32 "0ja5ihqivkda1wd58y4lmzvmwssm9g91f70c5q0fzwhng6580h6y"))
2330 (modules '((guix build utils)))
29080870
EB		 2331 (snippet
2332 ;; Replace the non-free implementation of MC64 with a stub
2333 '(begin
2334 (use-modules (ice-9 regex)
2335 (ice-9 rdelim))
0921eff2 2336 (call-with-output-file "SRC/mc64ad_dist.c"
29080870
EB		 2337 (lambda (port)
2338 (display "
2339#include <stdio.h>
2340#include <stdlib.h>
0921eff2 2341void mc64id_dist(int *a) {
29080870
EB		 2342 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2343 abort ();
2344}
0921eff2 2345void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
29080870
EB		 2346 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2347 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2348 abort ();
2349}\n" port)))
29080870
EB		 2350 (substitute* "SRC/util.c" ;adjust default algorithm
2351 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
6cbee49d
MW		 2352 "RowPerm = NOROWPERM"))
2353 #t))
fc1adab1 2354 (patches (search-patches "superlu-dist-scotchmetis.patch"))))
a54aefea
EB		 2355 (build-system gnu-build-system)
2356 (native-inputs
2357 `(("tcsh" ,tcsh)))
2358 (inputs
19afbea1 2359 `(("gfortran" ,gfortran)))
a54aefea
EB		 2360 (propagated-inputs
2361 `(("openmpi" ,openmpi) ;headers include MPI heades
2362 ("lapack" ,lapack) ;required to link with output library
2363 ("pt-scotch" ,pt-scotch))) ;same
2364 (arguments
2365 `(#:parallel-build? #f ;race conditions using ar
2366 #:phases
dc1d3cde
KK		 2367 (modify-phases %standard-phases
2368 (replace 'configure
2369 (lambda* (#:key inputs outputs #:allow-other-keys)
2370 (call-with-output-file "make.inc"
2371 (lambda (port)
2372 (format port "
a54aefea
EB		 2373PLAT =
2374DSuperLUroot = ~a
2375DSUPERLULIB = ~a/lib/libsuperlu_dist.a
2376BLASDEF = -DUSE_VENDOR_BLAS
2377BLASLIB = -L~a/lib -lblas
2378PARMETISLIB = -L~a/lib \
2379 -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
2380 -lscotch -lscotcherr -lscotcherrexit
2381METISLIB = -L~:*~a/lib \
2382 -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
2383LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
2384ARCH = ar
2385ARCHFLAGS = cr
2386RANLIB = ranlib
2387CC = mpicc
2388PIC = -fPIC
2389CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC)
2390NOOPTS = -O0 -g $(PIC)
2391FORTRAN = mpifort
2392FFLAGS = -O2 -g $(PIC)
2393LOADER = $(CC)
2394CDEFS = -DAdd_"
dc1d3cde
KK		 2395 (getcwd)
2396 (assoc-ref outputs "out")
2397 (assoc-ref inputs "lapack")
2398 (assoc-ref inputs "pt-scotch"))))
2399 #t))
2400 (add-after 'unpack 'remove-broken-symlinks
2401 (lambda _
2402 (for-each delete-file
2403 (find-files "MAKE_INC" "\\.#make\\..*"))
2404 #t))
2405 (add-before 'build 'create-install-directories
2406 (lambda* (#:key outputs #:allow-other-keys)
2407 (for-each
2408 (lambda (dir)
2409 (mkdir-p (string-append (assoc-ref outputs "out")
2410 "/" dir)))
2411 '("lib" "include"))
2412 #t))
bbe46a4a
EB		 2413 (add-before 'check 'mpi-setup
2414 ,%openmpi-setup)
dc1d3cde 2415 (replace 'check
a54aefea
EB		 2416 (lambda _
2417 (with-directory-excursion "EXAMPLE"
e02a9975
TGR		 2418 (invoke "mpirun" "-n" "2"
2419 "./pddrive" "-r" "1" "-c" "2" "g20.rua")
2420 (invoke "mpirun" "-n" "2"
2421 "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))
2422 #t))
dc1d3cde
KK		 2423 (replace 'install
2424 (lambda* (#:key outputs #:allow-other-keys)
2425 ;; Library is placed in lib during the build phase. Copy over
2426 ;; headers to include.
2427 (let* ((out (assoc-ref outputs "out"))
2428 (incdir (string-append out "/include")))
2429 (for-each (lambda (file)
2430 (let ((base (basename file)))
2431 (format #t "installing `~a' to `~a'~%"
2432 base incdir)
2433 (copy-file file
2434 (string-append incdir "/" base))))
2435 (find-files "SRC" ".*\\.h$")))
2436 #t)))))
a54aefea
EB		 2437 (home-page (package-home-page superlu))
2438 (synopsis "Parallel supernodal direct solver")
2439 (description
2440 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2441It is targeted for distributed memory parallel machines. SuperLU_DIST is
2442implemented in ANSI C, and MPI for communications.")
2443 (license license:bsd-3)))
2444
f8ed036a
EB		 2445(define-public scotch
2446 (package
2447 (name "scotch")
d98e9009 2448 (version "6.0.5a")
f8ed036a
EB		 2449 (source
2450 (origin
2451 (method url-fetch)
1dc31097
TGR		 2452 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
2453 "latestfile/298/scotch_" version ".tar.gz"))
f8ed036a 2454 (sha256
d98e9009 2455 (base32 "0vsmgjz8qv80di3ljmc7hbdsizxxxwy2b9rgd2fl1mdc6dgbj8av"))
fc1adab1 2456 (patches (search-patches "scotch-test-threading.patch"
d98e9009
EB		 2457 "scotch-build-parallelism.patch"
2458 "scotch-graph-induce-type-64.patch"
2459 "scotch-graph-diam-64.patch"))))
f8ed036a
EB		 2460 (build-system gnu-build-system)
2461 (inputs
2462 `(("zlib" ,zlib)
5e54f4ad 2463 ("flex" ,flex)
f8ed036a
EB		 2464 ("bison" ,bison)))
2465 (arguments
2466 `(#:phases
d6602ee9
EB		 2467 (modify-phases %standard-phases
2468 (add-after
2469 'unpack 'chdir-to-src
d67a7e9e 2470 (lambda _ (chdir "src") #t))
d6602ee9
EB		 2471 (replace
2472 'configure
2473 (lambda _
2474 (call-with-output-file "Makefile.inc"
2475 (lambda (port)
2476 (format port "
f8ed036a
EB		 2477EXE =
2478LIB = .a
2479OBJ = .o
2480MAKE = make
2481AR = ar
2482ARFLAGS = -ruv
cf0ec6c4 2483CAT = cat
f8ed036a
EB		 2484CCS = gcc
2485CCP = mpicc
2486CCD = gcc
2487CPPFLAGS =~{ -D~a~}
6c798540 2488CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
f8ed036a
EB		 2489LDFLAGS = -lz -lm -lrt -lpthread
2490CP = cp
2491LEX = flex -Pscotchyy -olex.yy.c
2492LN = ln
2493MKDIR = mkdir
2494MV = mv
2495RANLIB = ranlib
2496YACC = bison -pscotchyy -y -b y
2497"
d6602ee9
EB		 2498 '("COMMON_FILE_COMPRESS_GZ"
2499 "COMMON_PTHREAD"
2500 "COMMON_RANDOM_FIXED_SEED"
26599d69 2501 "INTSIZE64" ;use 'long' instead of 'int'
cf0ec6c4
EB		 2502 ;; Prevents symbolc clashes with libesmumps
2503 "SCOTCH_RENAME"
d6602ee9
EB		 2504 ;; XXX: Causes invalid frees in superlu-dist tests
2505 ;; "SCOTCH_PTHREAD"
2506 ;; "SCOTCH_PTHREAD_NUMBER=2"
d67a7e9e
TGR		 2507 "restrict=__restrict"))))
2508 #t))
bbe46a4a 2509 (add-after 'build 'build-esmumps
cf0ec6c4 2510 (lambda _
d67a7e9e
TGR		 2511 (invoke "make"
2512 (format #f "-j~a" (parallel-job-count))
2513 "esmumps")))
d6602ee9 2514 (replace
f8ed036a
EB		 2515 'install
2516 (lambda* (#:key outputs #:allow-other-keys)
2517 (let ((out (assoc-ref outputs "out")))
2518 (mkdir out)
d67a7e9e
TGR		 2519 (invoke "make"
2520 (string-append "prefix=" out)
2521 "install")
cf0ec6c4
EB		 2522 ;; esmumps files are not installed with the above
2523 (for-each (lambda (f)
2524 (copy-file f (string-append out "/include/" f)))
2525 (find-files "../include" ".*esmumps.h$"))
2526 (for-each (lambda (f)
2527 (copy-file f (string-append out "/lib/" f)))
d67a7e9e
TGR		 2528 (find-files "../lib" "^lib.*esmumps.*"))
2529 #t))))))
f8ed036a
EB		 2530 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
2531 (synopsis "Programs and libraries for graph algorithms")
2532 (description "SCOTCH is a set of programs and libraries which implement
2533the static mapping and sparse matrix reordering algorithms developed within
2534the SCOTCH project. Its purpose is to apply graph theory, with a divide and
2535conquer approach, to scientific computing problems such as graph and mesh
2536partitioning, static mapping, and sparse matrix ordering, in application
2537domains ranging from structural mechanics to operating systems or
2538bio-chemistry.")
2539 ;; See LICENSE_en.txt
2540 (license license:cecill-c)))
6acb4adb 2541
1c39f3b8
PG		 2542(define-public scotch32
2543 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2544 ;; some applications.
2545 (package (inherit scotch)
2546 (name "scotch32")
2547 (arguments
2548 (substitute-keyword-arguments (package-arguments scotch)
2549 ((#:phases scotch-phases)
2550 `(modify-phases ,scotch-phases
2551 (replace
2552 'configure
2553 (lambda _
2554 (call-with-output-file "Makefile.inc"
2555 (lambda (port)
2556 (format port "
2557EXE =
2558LIB = .a
2559OBJ = .o
2560MAKE = make
2561AR = ar
2562ARFLAGS = -ruv
2563CAT = cat
2564CCS = gcc
2565CCP = mpicc
2566CCD = gcc
2567CPPFLAGS =~{ -D~a~}
2568CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2569LDFLAGS = -lz -lm -lrt -lpthread
2570CP = cp
2571LEX = flex -Pscotchyy -olex.yy.c
2572LN = ln
2573MKDIR = mkdir
2574MV = mv
2575RANLIB = ranlib
2576YACC = bison -pscotchyy -y -b y
2577"
2578 '("COMMON_FILE_COMPRESS_GZ"
2579 "COMMON_PTHREAD"
2580 "COMMON_RANDOM_FIXED_SEED"
2581 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
2582 ;; Prevents symbolc clashes with libesmumps
2583 "SCOTCH_RENAME"
2584 ;; XXX: Causes invalid frees in superlu-dist tests
2585 ;; "SCOTCH_PTHREAD"
2586 ;; "SCOTCH_PTHREAD_NUMBER=2"
2587 "restrict=__restrict"))))))))))
2588 (synopsis
2589 "Programs and libraries for graph algorithms (32-bit integers)")))
2590
6acb4adb
EB		 2591(define-public pt-scotch
2592 (package (inherit scotch)
2593 (name "pt-scotch")
2594 (propagated-inputs
2595 `(("openmpi" ,openmpi))) ;Headers include MPI headers
2596 (arguments
2597 (substitute-keyword-arguments (package-arguments scotch)
2598 ((#:phases scotch-phases)
d6602ee9
EB		 2599 `(modify-phases ,scotch-phases
2600 (replace
2601 'build
d6602ee9
EB		 2602 (lambda _
2603 (and
cf0ec6c4
EB		 2604 (zero? (system* "make"
2605 (format #f "-j~a" (parallel-job-count))
2606 "ptscotch" "ptesmumps"))
d6602ee9
EB		 2607 ;; Install the serial metis compatibility library
2608 (zero? (system* "make" "-C" "libscotchmetis" "install")))))
2609 (replace
2610 'check
2611 (lambda _ (zero? (system* "make" "ptcheck"))))))))
6acb4adb 2612 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
5698b8b8 2613
1c25a52c
PG		 2614(define-public pt-scotch32
2615 (package (inherit scotch32)
2616 (name "pt-scotch32")
2617 (propagated-inputs
2618 `(("openmpi" ,openmpi))) ;headers include MPI headers
2619 (arguments
c4d4a779
PG		 2620 (substitute-keyword-arguments (package-arguments scotch32)
2621 ((#:phases scotch32-phases)
2622 `(modify-phases ,scotch32-phases
1c25a52c
PG		 2623 (replace 'build
2624 (lambda _
2625 (and
2626 (zero? (system* "make"
2627 (format #f "-j~a" (parallel-job-count))
2628 "ptscotch" "ptesmumps"))
2629 ;; Install the serial metis compatibility library
2630 (zero? (system* "make" "-C" "libscotchmetis" "install")))))
2631 (replace 'check
2632 (lambda _
2633 (zero? (system* "make" "ptcheck"))))))))
2634 (synopsis
2635 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2636
aa75ad00
EB		 2637(define-public metis
2638 (package
2639 (name "metis")
2640 (version "5.1.0")
2641 (source
2642 (origin
2643 (method url-fetch)
2644 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2645 "metis-" version ".tar.gz"))
2646 (sha256
2647 (base32
2648 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2649 (build-system cmake-build-system)
2650 (inputs
2651 `(("blas" ,openblas)))
2652 (arguments
2653 `(#:tests? #f ;no tests
2654 #:configure-flags `("-DSHARED=ON"
2655 ,(string-append "-DGKLIB_PATH=" (getcwd)
2656 "/metis-" ,version "/GKlib"))))
2657 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2658 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2659 (description
2660 "METIS is a set of serial programs for partitioning graphs, partitioning
2661finite element meshes, and producing fill-reducing orderings for sparse
2662matrices. The algorithms implemented in METIS are based on the multilevel
2663recursive-bisection, multilevel k-way, and multi-constraint partitioning
2664schemes.")
2665 (license license:asl2.0))) ;As of version 5.0.3
2666
700ff222
EB		 2667(define-public p4est
2668 (package
2669 (name "p4est")
4150da63 2670 (version "2.0")
700ff222
EB		 2671 (source
2672 (origin
2673 (method url-fetch)
2674 (uri (string-append "http://p4est.github.io/release/p4est-"
2675 version ".tar.gz"))
2676 (sha256
2677 (base32
4150da63 2678 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
700ff222
EB		 2679 (build-system gnu-build-system)
2680 (inputs
2681 `(("fortran" ,gfortran)
2682 ("blas" ,openblas)
2683 ("lapack" ,lapack)
2684 ("zlib" ,zlib)))
2685 (arguments
2686 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2687 (assoc-ref %build-inputs "blas")
2688 " -lopenblas")
2689 ,(string-append "LAPACK_LIBS=-L"
2690 (assoc-ref %build-inputs "lapack")
6df2a50a
LC		 2691 " -llapack"))
2692 #:phases (modify-phases %standard-phases
bbe46a4a
EB		 2693 (add-before 'check 'mpi-setup
2694 ,%openmpi-setup))))
700ff222
EB		 2695 (home-page "http://www.p4est.org")
2696 (synopsis "Adaptive mesh refinement on forests of octrees")
2697 (description
2698 "The p4est software library enables the dynamic management of a
2699collection of adaptive octrees, conveniently called a forest of octrees.
2700p4est is designed to work in parallel and scales to hundreds of thousands of
2701processor cores.")
2702 (license license:gpl2+)))
2703
2704(define-public p4est-openmpi
2705 (package (inherit p4est)
2706 (name "p4est-openmpi")
2707 (inputs
2708 `(("mpi" ,openmpi)
2709 ,@(package-inputs p4est)))
2710 (arguments
2711 (substitute-keyword-arguments (package-arguments p4est)
2712 ((#:configure-flags cf)
2713 ``("--enable-mpi" ,@,cf))))
2714 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2715
5698b8b8
JD		 2716(define-public gsegrafix
2717 (package
2718 (name "gsegrafix")
2719 (version "1.0.6")
2720 (source
2721 (origin
2722 (method url-fetch)
2723 (uri (string-append "mirror://gnu/" name "/" name "-"
2724 version ".tar.gz"))
2725 (sha256
2726 (base32
2727 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2728 (build-system gnu-build-system)
2729 (arguments
2730 `(#:configure-flags '("LDFLAGS=-lm")))
2731 (inputs
2732 `(("libgnomecanvas" ,libgnomecanvas)
2733 ("libbonoboui" ,libbonoboui)
2734 ("libgnomeui" ,libgnomeui)
2735 ("libgnomeprintui" ,libgnomeprintui)
2736 ("popt" ,popt)))
2737 (native-inputs
2738 `(("pkg-config" ,pkg-config)))
6fd52309 2739 (home-page "https://www.gnu.org/software/gsegrafix/")
5698b8b8
JD		 2740 (synopsis "GNOME application to create scientific and engineering plots")
2741 (description "GSEGrafix is an application which produces high-quality graphical
2742plots for science and engineering. Plots are specified via simple ASCII
2743parameter files and data files and are presented in an anti-aliased GNOME
2744canvas. The program supports rectangular two-dimensional plots, histograms,
2745polar-axis plots and three-dimensional plots. Plots can be printed or saved
2746to BMP, JPEG or PNG image formats.")
2747 (license license:gpl3+)))
8731e527
JD		 2748
2749(define-public maxima
2750 (package
2751 (name "maxima")
82cbe4e0 2752 (version "5.42.0")
8731e527
JD		 2753 (source
2754 (origin
2755 (method url-fetch)
2756 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2757 version "-source/" name "-" version ".tar.gz"))
2758 (sha256
2759 (base32
82cbe4e0 2760 "0d5pdihvcbwb7r4i4qs5qqgsz46hxlq33qj8is053llrgn9ylpyn"))
fc1adab1 2761 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
8731e527 2762 (build-system gnu-build-system)
df354a77 2763 (inputs
6b2eafaa 2764 `(("gcl" ,gcl)
df354a77 2765 ("gnuplot" ,gnuplot) ;for plots
f36afe4d 2766 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
df354a77
FB		 2767 (native-inputs
2768 `(("texinfo" ,texinfo)
ccbc5758
KK		 2769 ("perl" ,perl)
2770 ("python" ,python)))
8731e527 2771 (arguments
df354a77
FB		 2772 `(#:configure-flags
2773 (list "--enable-gcl"
2774 (string-append "--with-posix-shell="
2775 (assoc-ref %build-inputs "bash")
2776 "/bin/sh")
2777 (string-append "--with-wish="
2778 (assoc-ref %build-inputs "tk")
2779 "/bin/wish"
2780 (let ((v ,(package-version tk)))
2781 (string-take v (string-index-right v #\.)))))
df354a77 2782 ;; By default Maxima attempts to write temporary files to
77af7b24
MW		 2783 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2784 ;; Work around that.
df354a77 2785 #:make-flags (list "TMPDIR=/tmp")
0093b126
KK		 2786 #:phases
2787 (modify-phases %standard-phases
2788 (add-before 'check 'pre-check
2789 (lambda _
2790 (chmod "src/maxima" #o555)
2791 #t))
1472d19a
KK		 2792 (replace 'check
2793 (lambda _
2794 ;; This is derived from the testing code in the "debian/rules" file
2795 ;; of Debian's Maxima package.
2796 ;; If Maxima can successfully run this, the binary to be installed
2797 ;; should be fine.
2798 (zero?
2799 (system
2800 (string-append "./maxima-local "
2801 "--lisp=gcl "
2802 "--batch-string=\"run_testsuite();\" "
2803 "| grep -q \"No unexpected errors found\"")))))
0093b126
KK		 2804 ;; Make sure the doc and emacs files are found in the
2805 ;; standard location. Also configure maxima to find gnuplot
2806 ;; without having it on the PATH.
2807 (add-after 'install 'post-install
2808 (lambda* (#:key outputs inputs #:allow-other-keys)
2809 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2810 (out (assoc-ref outputs "out"))
2811 (datadir (string-append out "/share/maxima/" ,version))
2812 (binutils (string-append (assoc-ref inputs "binutils")
2813 "/bin")))
2814 (with-directory-excursion out
2815 (mkdir-p "share/emacs")
2816 (mkdir-p "share/doc")
2817 (symlink
2818 (string-append datadir "/emacs/")
2819 (string-append out "/share/emacs/site-lisp"))
2820 (symlink
2821 (string-append datadir "/doc/")
2822 (string-append out "/share/doc/maxima"))
2823 (with-atomic-file-replacement
2824 (string-append datadir "/share/maxima-init.lisp")
2825 (lambda (in out)
2826 (format out "~a ~s~a~%"
2827 "(setf $gnuplot_command "
2828 (string-append gnuplot "/bin/gnuplot") ")")
2829 (dump-port in out))))
2830 ;; Ensure that Maxima will have access to the GNU binutils
2831 ;; components at runtime.
2832 (wrap-program (string-append out "/bin/maxima")
2833 `("PATH" prefix (,binutils))))
2834 #t)))))
8731e527
JD		 2835 (home-page "http://maxima.sourceforge.net")
2836 (synopsis "Numeric and symbolic expression manipulation")
2837 (description "Maxima is a system for the manipulation of symbolic and
2838numerical expressions. It yields high precision numeric results by using
2839exact fractions, arbitrary precision integers, and variable precision floating
e881752c 2840point numbers.")
8731e527
JD		 2841 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2842 ;; Others simply say "GNU General Public License" without stating a
2843 ;; version (which implicitly means gpl1+).
2844 ;; At least one file (src/maxima.asd) says "version 2."
2845 ;; GPLv2 only is therefore the smallest subset.
f36afe4d 2846 (license license:gpl2)))
ec322be2 2847
9aafbc0c
MW		 2848(define-public wxmaxima
2849 (package
2850 (name "wxmaxima")
c93b77ad 2851 (version "18.11.4")
9aafbc0c
MW		 2852 (source
2853 (origin
c93b77ad
KK		 2854 (method git-fetch)
2855 (uri (git-reference
2856 (url "https://github.com/wxMaxima-developers/wxmaxima.git")
2857 (commit (string-append "Version-" version))))
2858 (file-name (git-file-name name version))
9aafbc0c
MW		 2859 (sha256
2860 (base32
c93b77ad 2861 "1sz8n9v23q442l7yjj67pjh0dk78rl4cbcc3j8m1bm88anlfxl9r"))))
0181df53 2862 (build-system cmake-build-system)
5143517c 2863 (native-inputs
0181df53 2864 `(("gettext" ,gettext-minimal)))
9aafbc0c
MW		 2865 (inputs
2866 `(("wxwidgets" ,wxwidgets)
de477809
SB		 2867 ("maxima" ,maxima)
2868 ;; Runtime support.
2869 ("adwaita-icon-theme" ,adwaita-icon-theme)
2870 ("gtk+" ,gtk+)
2871 ("shared-mime-info" ,shared-mime-info)))
9aafbc0c 2872 (arguments
0181df53
KK		 2873 `(#:tests? #f ; no check target
2874 #:phases
ac2ddcc6 2875 (modify-phases %standard-phases
ac2ddcc6
KK		 2876 (add-after 'install 'wrap-program
2877 (lambda* (#:key inputs outputs #:allow-other-keys)
2878 (wrap-program (string-append (assoc-ref outputs "out")
2879 "/bin/wxmaxima")
2880 `("PATH" ":" prefix
2881 (,(string-append (assoc-ref inputs "maxima")
2882 "/bin")))
2883 ;; For GtkFileChooserDialog.
2884 `("GSETTINGS_SCHEMA_DIR" =
2885 (,(string-append (assoc-ref inputs "gtk+")
2886 "/share/glib-2.0/schemas")))
2887 `("XDG_DATA_DIRS" ":" prefix
2888 (;; Needed by gdk-pixbuf to know supported icon formats.
2889 ,(string-append
2890 (assoc-ref inputs "shared-mime-info") "/share")
2891 ;; The default icon theme of GTK+.
2892 ,(string-append
2893 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
2894 #t)))))
9aafbc0c
MW		 2895 (home-page "https://andrejv.github.io/wxmaxima/")
2896 (synopsis "Graphical user interface for the Maxima computer algebra system")
2897 (description
2898 "wxMaxima is a graphical user interface for the Maxima computer algebra
2899system. It eases the use of Maxima by making most of its commands available
2900through a menu system and by providing input dialogs for commands that require
2901more than one argument. It also implements its own display engine that
2902outputs mathematical symbols directly instead of depicting them with ASCII
2903characters.
2904
2905wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
2906text and mathematical calculations to create documents, exporting of input and
2907output to TeX, and a browser for Maxima's manual including command index and
2908full text searching.")
2909 (license license:gpl2+)))
2910
b15e47f9
RW		 2911(define-public armadillo
2912 (package
2913 (name "armadillo")
f133e244 2914 (version "9.100.5")
b15e47f9
RW		 2915 (source (origin
2916 (method url-fetch)
2917 (uri (string-append "mirror://sourceforge/arma/armadillo-"
7397cd9e 2918 version ".tar.xz"))
b15e47f9
RW		 2919 (sha256
2920 (base32
f133e244 2921 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
b15e47f9 2922 (build-system cmake-build-system)
e405c0bc 2923 (arguments `(#:tests? #f)) ; no test target
b15e47f9
RW		 2924 (inputs
2925 `(("openblas" ,openblas)
2926 ("lapack" ,lapack)
2927 ("arpack" ,arpack-ng)))
2928 (home-page "http://arma.sourceforge.net/")
2929 (synopsis "C++ linear algebra library")
2930 (description
2931 "Armadillo is a C++ linear algebra library, aiming towards a good balance
2932between speed and ease of use. It is useful for algorithm development
2933directly in C++, or quick conversion of research code into production
2934environments. It can be used for machine learning, pattern recognition,
2935signal processing, bioinformatics, statistics, econometrics, etc. The library
2936provides efficient classes for vectors, matrices and cubes, as well as 150+
2937associated functions (eg. contiguous and non-contiguous submatrix views).")
fe418cc5 2938 (license license:asl2.0)))
b15e47f9 2939
279663ef 2940(define-public muparser
d7cff656
LF		 2941 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2942 ;; different hash. In order to make `guix package --upgrade` work correctly,
2943 ;; we set a Guix packaging revision.
2944 ;; When the next version of muparser is released, we can remove
2945 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2946 (let ((upstream-version "2.2.5")
2947 (revision "2"))
2948 (package
2949 (name "muparser")
2950 (version (string-append upstream-version "-" revision))
2951 (source
2952 (origin
2953 (method url-fetch)
2954 (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
2955 upstream-version ".tar.gz"))
2956 (file-name (string-append name "-" version ".tar.gz"))
2957 (sha256
2958 (base32
2959 "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
2960 (build-system gnu-build-system)
2961 (arguments
2962 `(#:configure-flags '("--enable-samples=no")
2963 #:tests? #f)) ;no "check" target
2964 (home-page "http://muparser.beltoforion.de/")
2965 (synopsis "Fast parser library for mathematical expressions")
2966 (description
2967 "muParser is an extensible high performance math parser library. It is
2968based on transforming an expression into a bytecode and precalculating constant
2969parts of it.")
2970 (license license:expat))))
279663ef 2971
e73b49fb
RW		 2972(define-public openblas
2973 (package
2974 (name "openblas")
f419abea 2975 (version "0.3.2")
e73b49fb
RW		 2976 (source
2977 (origin
2978 (method url-fetch)
a617fd55
MB		 2979 (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
2980 version "%20version.tar.gz"))
e73b49fb
RW		 2981 (file-name (string-append name "-" version ".tar.gz"))
2982 (sha256
2983 (base32
f419abea 2984 "0b20km2jv7m6qiylrlvhq2vnmkmilb633mr8rhqmgbn1wqrp58jq"))))
e73b49fb
RW		 2985 (build-system gnu-build-system)
2986 (arguments
5789566a 2987 `(#:test-target "test"
bd0b4379
RW		 2988 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
2989 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2990 ;; we need to disable substitutions.
71923a91
AE		 2991 #:substitutable?
2992 ,(let ((system (or (%current-target-system) (%current-system))))
2993 (or (string-prefix? "x86_64" system)
bd0b4379 2994 (string-prefix? "i686" system)
83a34647
EF		 2995 (string-prefix? "mips" system)
2996 (string-prefix? "aarch64" system)))
e73b49fb
RW		 2997 #:make-flags
2998 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
2999 "SHELL=bash"
af5b817e
RW		 3000 ;; Build the library for all supported CPUs. This allows
3001 ;; switching CPU targets at runtime with the environment variable
3002 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
71923a91
AE		 3003 ;; Unfortunately, this is not supported on non-x86 architectures,
3004 ;; where it leads to failed builds.
3005 ,@(let ((system (or (%current-target-system) (%current-system))))
8a637e79
RW		 3006 (cond
3007 ((or (string-prefix? "x86_64" system)
71923a91 3008 (string-prefix? "i686" system))
8a637e79
RW		 3009 '("DYNAMIC_ARCH=1"))
3010 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
3011 ;; two available MIPS targets special extended instructions
3012 ;; for Loongson cores are used.
3013 ((string-prefix? "mips" system)
3014 '("TARGET=SICORTEX"))
83a34647
EF		 3015 ;; On aarch64 force the generic 'armv8-a' target
3016 ((string-prefix? "aarch64" system)
3017 '("TARGET=ARMV8"))
8a637e79 3018 (else '()))))
e73b49fb 3019 ;; no configure script
493937ae
DL		 3020 #:phases
3021 (modify-phases %standard-phases
3022 (delete 'configure)
3023 (add-before 'build 'set-extralib
3024 (lambda* (#:key inputs #:allow-other-keys)
3025 ;; Get libgfortran found when building in utest.
3026 (setenv "FEXTRALIB"
3027 (string-append "-L" (assoc-ref inputs "fortran-lib")
3028 "/lib"))
3029 #t)))))
e73b49fb 3030 (inputs
493937ae 3031 `(("fortran-lib" ,gfortran "lib")))
e73b49fb
RW		 3032 (native-inputs
3033 `(("cunit" ,cunit)
493937ae 3034 ("fortran" ,gfortran)
e73b49fb
RW		 3035 ("perl" ,perl)))
3036 (home-page "http://www.openblas.net/")
3037 (synopsis "Optimized BLAS library based on GotoBLAS")
3038 (description
3039 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
3040 (license license:bsd-3)))
3041
daa6036f
EB		 3042(define-public openblas-ilp64
3043 (package (inherit openblas)
3044 (name "openblas-ilp64")
3045 (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
3046 (arguments
3047 (substitute-keyword-arguments (package-arguments openblas)
3048 ((#:make-flags flags '())
3049 `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
3050 ,flags))))
3051 (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
3052 (license license:bsd-3)))
3053
5a7deb11
LC		 3054(define* (make-blis implementation #:optional substitutable?)
3055 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
3056source tree for a list of implementations.)
3057
3058SUBSTITUTABLE? determines whether the package is made available as a
3059substitute.
3060
3061Currently the specialization must be selected at configure-time, but work is
3062underway to allow BLIS to select the right optimized kernels at run time:
3063<https://github.com/flame/blis/issues/129>."
3064 (package
3065 (name (if (string=? implementation "reference")
3066 "blis"
3067 (string-append "blis-" implementation)))
3068 (version "0.2.2")
3069 (home-page "https://github.com/flame/blis")
3070 (source (origin
3071 (method git-fetch)
3072 (uri (git-reference (url home-page) (commit version)))
3073 (sha256
3074 (base32
3075 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
3076 (file-name (git-file-name "blis" version))))
3077 (build-system gnu-build-system)
3078 (arguments
3079 `(#:test-target "test"
3080
3081 #:substitutable? ,substitutable?
3082
3083 #:phases (modify-phases %standard-phases
3084 (replace 'configure
3085 (lambda* (#:key outputs #:allow-other-keys)
3086 ;; This is a home-made 'configure' script.
3087 (let ((out (assoc-ref outputs "out")))
3088 (zero? (system* "./configure" "-p" out
3089 "-d" "opt"
3090 "--disable-static"
3091 "--enable-shared"
3092 "--enable-threading=openmp"
3093
3094 ,implementation)))))
3095 (add-before 'check 'show-test-output
3096 (lambda _
3097 ;; By default "make check" is silent. Make it verbose.
3098 (system "tail -F output.testsuite &")
3099 #t)))))
3100 (synopsis "High-performance basic linear algebra (BLAS) routines")
3101 (description
3102 "BLIS is a portable software framework for instantiating high-performance
3103BLAS-like dense linear algebra libraries. The framework was designed to
3104isolate essential kernels of computation that, when optimized, immediately
3105enable optimized implementations of most of its commonly used and
3106computationally intensive operations. While BLIS exports a new BLAS-like API,
3107it also includes a BLAS compatibility layer which gives application developers
3108access to BLIS implementations via traditional BLAS routine calls.")
3109 (license license:bsd-3)))
3110
3111(define-public blis
3112 ;; This is the "reference" implementation, which is the non-optimized but
3113 ;; portable variant (no assembly).
3114 (make-blis "reference" #t))
3115
3116(define ignorance blis)
3117
3118(define-syntax-rule (blis/x86_64 processor)
3119 "Expand to a package specialized for PROCESSOR."
3120 (package
3121 (inherit (make-blis processor))
3122 (supported-systems '("x86_64-linux"))))
3123
3124(define-public blis-sandybridge
3125 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
3126 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
3127 (blis/x86_64 "sandybridge"))
3128
3129(define-public blis-haswell
3130 ;; BLIS specialized for Haswell processors (launched 2013):
3131 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
3132 (blis/x86_64 "haswell"))
3133
3134(define-public blis-knl
3135 ;; BLIS specialized for Knights Landing processor (launched 2016):
3136 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
3137 (blis/x86_64 "knl"))
3138
3139
e1605e36
RW		 3140(define-public openlibm
3141 (package
3142 (name "openlibm")
48d7ac17 3143 (version "0.6.0")
e1605e36
RW		 3144 (source
3145 (origin
3146 (method url-fetch)
3147 (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
3148 version ".tar.gz"))
3149 (file-name (string-append name "-" version ".tar.gz"))
3150 (sha256
3151 (base32
48d7ac17 3152 "0a5fpm8nra5ldhjk0cqd2rx1qh32wiarkxmcqcm5xl8z7l4kjm6l"))))
e1605e36
RW		 3153 (build-system gnu-build-system)
3154 (arguments
3155 `(#:make-flags
3156 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3157 #:phases
3158 ;; no configure script
dc1d3cde 3159 (modify-phases %standard-phases (delete 'configure))
e1605e36
RW		 3160 #:tests? #f)) ;the tests are part of the default target
3161 (home-page "http://openlibm.org/")
3162 (synopsis "Portable C mathematical library (libm)")
3163 (description
3164 "OpenLibm is an effort to have a high quality, portable, standalone C
3165mathematical library (libm). It can be used standalone in applications and
3166programming language implementations. The project was born out of a need to
e881752c 3167have a good libm for the Julia programming language that worked consistently
e1605e36
RW		 3168across compilers and operating systems, and in 32-bit and 64-bit
3169environments.")
538c0e3b
EF		 3170 ;; Each architecture has its own make target, and there is none for mips.
3171 (supported-systems (delete "mips64el-linux" %supported-systems))
e1605e36
RW		 3172 ;; See LICENSE.md for details.
3173 (license (list license:expat
3174 license:isc
3175 license:bsd-2
3176 license:public-domain
3177 license:lgpl2.1+))))
3178
e62be58f
RW		 3179(define-public openspecfun
3180 (package
3181 (name "openspecfun")
59cd0ba4 3182 (version "0.5.3")
e62be58f
RW		 3183 (source
3184 (origin
3185 (method url-fetch)
3186 (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
3187 version ".tar.gz"))
3188 (file-name (string-append name "-" version ".tar.gz"))
3189 (sha256
3190 (base32
59cd0ba4 3191 "1rs1bv8jq751fv9vq79890wqf9xlbjc7lvz3ighzyfczbyjcf18m"))))
e62be58f
RW		 3192 (build-system gnu-build-system)
3193 (arguments
59cd0ba4 3194 '(#:tests? #f ; no "check" target
e62be58f
RW		 3195 #:make-flags
3196 (list (string-append "prefix=" (assoc-ref %outputs "out")))
59cd0ba4
TGR		 3197 #:phases
3198 (modify-phases %standard-phases
3199 (delete 'configure)))) ; no configure script
e62be58f 3200 (inputs
19afbea1 3201 `(("fortran" ,gfortran)))
e62be58f
RW		 3202 (home-page "https://github.com/JuliaLang/openspecfun")
3203 (synopsis "Collection of special mathematical functions")
3204 (description
3205 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
3206portable package for Bessel Functions of a Complex Argument and Nonnegative
3207Order; it contains subroutines for computing Bessel functions and Airy
3208functions. Faddeeva allows computing the various error functions of arbitrary
3209complex arguments (Faddeeva function, error function, complementary error
3210function, scaled complementary error function, imaginary error function, and
3211Dawson function); given these, one can also easily compute Voigt functions,
3212Fresnel integrals, and similar related functions as well.")
3213 ;; Faddeeva is released under the Expat license; AMOS is included as
3214 ;; public domain software.
3215 (license (list license:expat license:public-domain))))
3216
2742f87e
RW		 3217(define-public suitesparse
3218 (package
3219 (name "suitesparse")
bd5b5ac0 3220 (version "4.5.5")
2742f87e
RW		 3221 (source
3222 (origin
3223 (method url-fetch)
3224 (uri (string-append
3225 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
3226 version ".tar.gz"))
3227 (sha256
3228 (base32
bd5b5ac0
EB		 3229 "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
3230 (modules '((guix build utils)))
3231 (snippet
3232 ;; Remove bundled metis source
6cbee49d
MW		 3233 '(begin
3234 (delete-file-recursively "metis-5.1.0")
3235 #t))))
2742f87e
RW		 3236 (build-system gnu-build-system)
3237 (arguments
bd5b5ac0 3238 '(#:tests? #f ;no "check" target
2742f87e
RW		 3239 #:make-flags
3240 (list "CC=gcc"
3241 "BLAS=-lblas"
3242 "TBB=-ltbb"
bd5b5ac0 3243 "MY_METIS_LIB=-lmetis"
2742f87e
RW		 3244 (string-append "INSTALL_LIB="
3245 (assoc-ref %outputs "out") "/lib")
3246 (string-append "INSTALL_INCLUDE="
bd5b5ac0
EB		 3247 (assoc-ref %outputs "out") "/include")
3248 "library")
2742f87e 3249 #:phases
2509522c 3250 (modify-phases %standard-phases
bd5b5ac0 3251 (delete 'configure)))) ;no configure script
2742f87e
RW		 3252 (inputs
3253 `(("tbb" ,tbb)
bd5b5ac0
EB		 3254 ("lapack" ,lapack)
3255 ("metis" ,metis)))
2742f87e
RW		 3256 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
3257 (synopsis "Suite of sparse matrix software")
3258 (description
3259 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
3260multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
3261multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
3262simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
3263CXSparse, a concise sparse Cholesky factorization package; and many other
3264packages.")
3265 ;; LGPLv2.1+:
3266 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
3267 ;; GPLv2+:
3268 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
3269 (license (list license:gpl2+ license:lgpl2.1+))))
3270
ec322be2
FB		 3271(define-public atlas
3272 (package
3273 (name "atlas")
3c98ac02 3274 (version "3.10.3")
ec322be2
FB		 3275 (source (origin
3276 (method url-fetch)
de67e922
LF		 3277 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
3278 version "/atlas" version ".tar.bz2"))
ec322be2
FB		 3279 (sha256
3280 (base32
3c98ac02 3281 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
ec322be2
FB		 3282 (build-system gnu-build-system)
3283 (home-page "http://math-atlas.sourceforge.net/")
19afbea1 3284 (inputs `(("gfortran" ,gfortran)
ec322be2
FB		 3285 ("lapack-tar" ,(package-source lapack))))
3286 (outputs '("out" "doc"))
01480b9e
FB		 3287 ;; For the moment we drop support for MIPS at it fails to compile. See
3288 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
3289 (supported-systems (delete "mips64el-linux" %supported-systems))
ec322be2
FB		 3290 (arguments
3291 `(#:parallel-build? #f
3292 #:parallel-tests? #f
f15615b1
LC		 3293
3294 ;; ATLAS tunes itself for the machine it is built on, as explained at
3295 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
3296 ;; For this reason, we want users to build it locally instead of using
3297 ;; substitutes.
3298 #:substitutable? #f
3299
ec322be2
FB		 3300 #:modules ((srfi srfi-26)
3301 (srfi srfi-1)
3302 (guix build gnu-build-system)
3303 (guix build utils))
40029cbe 3304 #:configure-flags
ec322be2
FB		 3305 `(;; Generate position independent code suitable for dynamic libraries
3306 ;; and use WALL timer to get more accurate timing.
3307 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
3308 ;; Set word width.
3309 "-b"
3310 ,,(if (string-match "64" (%current-system))
3311 "64"
3312 "32")
3313 ;; Disable parallel build as it gives errors: atlas_pthread.h is
3314 ;; needed to compile C files before it is generated.
3315 "-Ss" "pmake" "make -j 1"
af89a667
FB		 3316 ;; Probe is failing for MIPS. We therefore define the system
3317 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3318 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3319 ,,@(if (string-prefix? "mips" (%current-system))
3320 (list "-A" "49" "-V" "1")
3321 (list))
ec322be2
FB		 3322 ;; Generate shared libraries.
3323 "--shared"
3324 ;; Build a full LAPACK library.
3325 ,(string-append "--with-netlib-lapack-tarfile="
3326 (assoc-ref %build-inputs "lapack-tar")))
3327 #:phases
e5b4b96b
EF		 3328 (modify-phases %standard-phases
3329 (add-after 'install 'install-doc
3330 (lambda* (#:key outputs inputs #:allow-other-keys)
3331 (let ((doc (string-append (assoc-ref outputs "doc")
3332 "/share/doc/atlas")))
3333 (mkdir-p doc)
3334 (fold (lambda (file previous)
3335 (and previous (zero? (system* "cp" file doc))))
3336 #t (find-files "../ATLAS/doc" ".*")))))
3337 (add-after 'check 'check-pt
3338 (lambda _ (zero? (system* "make" "ptcheck"))))
3339 ;; Fix files required to run configure.
3340 (add-before 'configure 'fix-/bin/sh
ec322be2
FB		 3341 (lambda _
3342 ;; Use `sh', not `/bin/sh'.
3343 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3344 (("/bin/sh")
e5b4b96b
EF		 3345 "sh"))))
3346 ;; Fix /bin/sh in generated make files.
3347 (add-after 'configure 'fix-/bin/sh-in-generated-files
3348 (lambda _
3349 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3350 (("/bin/sh")
3351 "sh"))))
3352 ;; ATLAS configure program does not accepts the default flags
3353 ;; passed by the 'gnu-build-system'.
3354 (replace 'configure
3355 (lambda* (#:key native-inputs inputs outputs
3356 (configure-flags '())
3357 #:allow-other-keys #:rest args)
3358 (let* ((prefix (assoc-ref outputs "out"))
3359 (bash (or (and=> (assoc-ref
3360 (or native-inputs inputs) "bash")
3361 (cut string-append <> "/bin/bash"))
3362 "/bin/sh"))
3363 (flags `(,(string-append "--prefix=" prefix)
3364 ,@configure-flags))
3365 (abs-srcdir (getcwd))
3366 (srcdir (string-append "../" (basename abs-srcdir))))
3367 (format #t "source directory: ~s (relative from build: ~s)~%"
3368 abs-srcdir srcdir)
3369 (mkdir "../build")
3370 (chdir "../build")
3371 (format #t "build directory: ~s~%" (getcwd))
3372 (format #t "configure flags: ~s~%" flags)
3373 (zero? (apply system* bash
3374 (string-append srcdir "/configure")
3375 flags))))))))
ec322be2
FB		 3376 (synopsis "Automatically Tuned Linear Algebra Software")
3377 (description
3378 "ATLAS is an automatically tuned linear algebra software library
3379providing C and Fortran77 interfaces to a portably efficient BLAS
3380implementation, as well as a few routines from LAPACK.
3381
f15615b1
LC		 3382Optimization occurs at build time. For this reason, the library is built on
3383the machine where it is installed, without resorting to pre-built substitutes.
ec322be2 3384
f15615b1 3385Before building the library, CPU throttling should be disabled. This can be
d97c429a 3386done in the BIOS, or, on GNU/Linux, with the following command:
ec322be2 3387
8e9ba611 3388@example
d97c429a 3389# cpupower --governor performance
8e9ba611 3390@end example
ec322be2 3391
d97c429a 3392Failure to do so will result in a library with poor performance.")
ec322be2 3393 (license license:bsd-3)))
c12efc72
AE		 3394
3395(define-public glm
3396 (package
3397 (name "glm")
66044a36 3398 (version "0.9.9.3")
c12efc72
AE		 3399 (source
3400 (origin
3401 (method url-fetch)
5ea4b594
MB		 3402 (uri (string-append "https://github.com/g-truc/glm/releases/download/"
3403 version "/glm-" version ".zip"))
c12efc72
AE		 3404 (sha256
3405 (base32
66044a36 3406 "0yqk5r3qh60d4r2iab5q7wq0fryn8p3pz6s28y1i7amqj1aqavj9"))))
c12efc72
AE		 3407 (build-system cmake-build-system)
3408 (native-inputs
3409 `(("unzip" ,unzip)))
46bda5eb 3410 (home-page "https://glm.g-truc.net/")
c12efc72
AE		 3411 (synopsis "OpenGL Mathematics library")
3412 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3413library for graphics software based on the OpenGL Shading Language (GLSL)
3414specifications.")
3415 (license license:expat)))
7f18257b
AE		 3416
3417(define-public lpsolve
3418 (package
3419 (name "lpsolve")
a89e0cf5 3420 (version "5.5.2.5")
7f18257b
AE		 3421 (source
3422 (origin
3423 (method url-fetch)
3424 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3425 "/lp_solve_" version "_source.tar.gz"))
3426 (sha256
3427 (base32
a89e0cf5 3428 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
7f18257b
AE		 3429 (modules '((guix build utils)))
3430 (snippet
6cbee49d
MW		 3431 '(begin
3432 (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3433 (("^c=cc") "c=gcc")
3434 ;; Pretend to be on a 64 bit platform to obtain a common directory
3435 ;; name for the build results on all architectures; nothing else
3436 ;; seems to depend on it.
3437 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3438
3439 ;; The check for 'isnan' as it is written fails with
3440 ;; "non-floating-point argument in call to function
3441 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3442 ;; definition, which in turn leads to bad things. Fix the feature
3443 ;; test.
3444 (("isnan\\(0\\)") "isnan(0.)"))
3445 #t))))
7f18257b
AE		 3446 (build-system gnu-build-system)
3447 (arguments
6c96b545 3448 `(#:tests? #f ; no check target
7f18257b
AE		 3449 #:phases
3450 (modify-phases %standard-phases
6c96b545 3451 (delete 'configure) ; no configure script
7f18257b
AE		 3452 (replace 'build
3453 (lambda _
6c96b545
TGR		 3454 (with-directory-excursion "lpsolve55"
3455 (invoke "bash" "ccc"))
3456 (with-directory-excursion "lp_solve"
3457 (invoke "bash" "ccc"))
3458 #t))
7f18257b
AE		 3459 (replace 'install
3460 (lambda* (#:key outputs #:allow-other-keys)
3461 (let* ((out (assoc-ref outputs "out"))
3462 (bin (string-append out "/bin"))
3463 (lib (string-append out "/lib"))
3464 ;; This is where LibreOffice expects to find the header
3465 ;; files, and where they are installed by Debian.
3466 (include (string-append out "/include/lpsolve")))
6c96b545
TGR		 3467 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3468 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
96c46210
LC		 3469 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3470
7f18257b
AE		 3471 ;; Install a subset of the header files as on Debian
3472 ;; (plus lp_bit.h, which matches the regular expression).
96c46210
LC		 3473 (for-each (lambda (name)
3474 (install-file name include))
3475 (find-files "." "lp_[HMSa-z].*\\.h$"))
7f18257b 3476 (with-directory-excursion "shared"
96c46210
LC		 3477 (for-each (lambda (name)
3478 (install-file name include))
3479 (find-files "." "\\.h$")))
7f18257b
AE		 3480 #t))))))
3481 (home-page "http://lpsolve.sourceforge.net/")
3482 (synopsis "Mixed integer linear programming (MILP) solver")
3483 (description
3484 "lp_solve is a mixed integer linear programming solver based on the
3485revised simplex and the branch-and-bound methods.")
3486 (license license:lgpl2.1+)))
a17d4564
EB		 3487
3488(define-public dealii
3489 (package
3490 (name "dealii")
24404eaf 3491 (version "8.5.1")
a17d4564
EB		 3492 (source
3493 (origin
3494 (method url-fetch)
3495 (uri (string-append "https://github.com/dealii/dealii/releases/"
3496 "download/v" version "/dealii-" version ".tar.gz"))
3497 (sha256
3498 (base32
24404eaf 3499 "1bh9rsmkrg0zi70n27b11djmac9lximghsiy7mg7w7x544n82gnk"))
a17d4564
EB		 3500 (modules '((guix build utils)))
3501 (snippet
3502 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
6cbee49d
MW		 3503 '(begin
3504 (delete-file-recursively "bundled")
3505 #t))))
a17d4564
EB		 3506 (build-system cmake-build-system)
3507 (inputs
3508 `(("tbb" ,tbb)
3509 ("zlib" ,zlib)
3510 ("boost" ,boost)
3511 ("p4est" ,p4est)
3512 ("blas" ,openblas)
3513 ("lapack" ,lapack)
3514 ("arpack" ,arpack-ng)
3515 ("muparser" ,muparser)
3516 ("gfortran" ,gfortran)
3517 ("suitesparse" ,suitesparse))) ;for UMFPACK
3518 (arguments
3519 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
d84b09e9
EB		 3520 #:configure-flags
3521 ;; Work around a bug in libsuitesparseconfig linking
3522 ;; see https://github.com/dealii/dealii/issues/4745
3523 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
a17d4564
EB		 3524 (home-page "https://www.dealii.org")
3525 (synopsis "Finite element library")
3526 (description
3527 "Deal.II is a C++ program library targeted at the computational solution
3528of partial differential equations using adaptive finite elements. The main
3529aim of deal.II is to enable rapid development of modern finite element codes,
3530using among other aspects adaptive meshes and a wide array of tools often used
3531in finite element programs.")
3532 (license license:lgpl2.1+)))
3533
3534(define-public dealii-openmpi
3535 (package (inherit dealii)
3536 (name "dealii-openmpi")
3537 (inputs
3538 `(("mpi" ,openmpi)
3539 ;;Supported only with MPI:
3540 ("p4est" ,p4est-openmpi)
3541 ("petsc" ,petsc-openmpi)
3542 ("slepc" ,slepc-openmpi)
3543 ("metis" ,metis) ;for MUMPS
3544 ("scalapack" ,scalapack) ;for MUMPS
3545 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3546 ("arpack" ,arpack-ng-openmpi)
3547 ,@(fold alist-delete (package-inputs dealii)
3548 '("p4est" "arpack"))))
3549 (arguments
3550 (substitute-keyword-arguments (package-arguments dealii)
3551 ((#:configure-flags cf)
3552 ``("-DMPI_C_COMPILER=mpicc"
3553 "-DMPI_CXX_COMPILER=mpicxx"
3554 "-DMPI_Fortran_COMPILER=mpifort"
3555 ,@,cf))))
3556 (synopsis "Finite element library (with MPI support)")))
194c7f95
AE		 3557
3558(define-public flann
3559 (package
3560 (name "flann")
3561 (version "1.8.4")
3562 (source
3563 (origin
3564 (method url-fetch)
3565 (uri
3566 (string-append
3567 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3568 version "-src.zip"))
3569 (sha256
3570 (base32
b5edc479
LC		 3571 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
3572 (patches (search-patches "flann-cmake-3.11.patch"))))
194c7f95 3573 (build-system cmake-build-system)
6b6aca9b
LC		 3574 (outputs '("out"
3575 "octave")) ;46 MiB .mex file that pulls Octave
194c7f95
AE		 3576 (native-inputs
3577 `(("unzip" ,unzip)))
3578 (inputs
3579 `(("hdf5" ,hdf5)
3580 ("octave" ,octave)
3581 ("python" ,python-2) ; print syntax
3582 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3583 ("zlib" ,zlib)))
3584 (arguments
39b30337
LC		 3585 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3586 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3587 #:strip-directories '("lib" "lib64" "libexec"
3588 "bin" "sbin" "share/flann/octave")
3589
9684e30b
LC		 3590 ;; Save 12 MiB by not installing .a files. Passing
3591 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3592 #:phases (modify-phases %standard-phases
6b6aca9b
LC		 3593 (add-before 'configure 'set-octave-directory
3594 (lambda* (#:key outputs #:allow-other-keys)
3595 ;; Install the .mex file in the "octave" output.
3596 (let ((out (assoc-ref outputs "octave")))
3597 (substitute* "src/matlab/CMakeLists.txt"
3598 (("share/flann/octave")
3599 (string-append out "/share/flann/octave")))
3600 #t)))
9684e30b
LC		 3601 (add-after 'install 'remove-static-libraries
3602 (lambda* (#:key outputs #:allow-other-keys)
3603 (let* ((out (assoc-ref outputs "out"))
3604 (lib (string-append out "/lib")))
3605 (for-each delete-file
3606 (find-files lib "\\.a$"))
3607 #t))))
3608
39b30337 3609 #:tests? #f)) ; The test data are downloaded from the Internet.
194c7f95
AE		 3610 (home-page "http://www.cs.ubc.ca/research/flann/")
3611 (synopsis "Library for approximate nearest neighbors computation")
3612 (description "FLANN is a library for performing fast approximate
3613nearest neighbor searches in high dimensional spaces. It implements a
3614collection of algorithms and a system for automatically choosing the best
3615algorithm and optimum parameters depending on the dataset.
3616
3617FLANN is written in C++ and contains bindings for C, Octave and Python.")
3618 (license (license:non-copyleft "file://COPYING"
3619 "See COPYING in the distribution."))))
d8c97beb
EF		 3620
3621(define-public wcalc
3622 (package
3623 (name "wcalc")
3624 (version "2.5")
3625 (source
3626 (origin
3627 (method url-fetch)
de67e922
LF		 3628 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3629 "wcalc-" version ".tar.bz2"))
d8c97beb
EF		 3630 (sha256
3631 (base32
3632 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3633 (build-system gnu-build-system)
3634 (inputs
3635 `(("mpfr" ,mpfr)
3636 ("readline" ,readline)))
3637 (home-page "http://w-calc.sourceforge.net/index.php")
3638 (synopsis "Flexible command-line scientific calculator")
3639 (description "Wcalc is a very capable calculator. It has standard functions
3640(sin, asin, and sinh for example, in either radians or degrees), many
3641pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3642variables, a command history, hex/octal/binary input and output, unit
3643conversions, embedded comments, and an expandable expression entry field. It
3644evaluates expressions using the standard order of operations.")
3645 (license license:gpl2+)))
45147b0c
FH		 3646
3647(define-public xaos
3648 (package
3649 (name "xaos")
3650 (version "3.6")
3651 (source (origin
3652 (method url-fetch)
de67e922
LF		 3653 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3654 "/xaos-" version ".tar.gz"))
45147b0c
FH		 3655 (sha256
3656 (base32
3657 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3658 (build-system gnu-build-system)
b94a6ca0 3659 (native-inputs `(("gettext" ,gettext-minimal)))
45147b0c
FH		 3660 (inputs `(("libx11" ,libx11)
3661 ("zlib" ,zlib)
3662 ("libpng" ,libpng)
3663 ("gsl" ,gsl)))
3664 (arguments
3665 `(#:tests? #f ;no "check" target
3666 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3667 (synopsis "Real-time fractal zoomer")
3668 (description "GNU XaoS is a graphical program that generates fractal
3669patterns and allows you to zoom in and out of them infinitely in a fluid,
3670continuous manner. It also includes tutorials that help to explain how fractals
3671are built. It can generate many different fractal types such as the Mandelbrot
3672set.")
6fd52309 3673 (home-page "https://www.gnu.org/software/xaos/")
45147b0c 3674 (license license:gpl2+)))
528bb464
EB		 3675
3676(define-public hypre
3677 (package
3678 (name "hypre")
220458b0 3679 (version "2.14.0")
528bb464
EB		 3680 (source (origin
3681 (method url-fetch)
3682 (uri (string-append "https://github.com/LLNL/hypre/archive/"
3683 "v" version ".tar.gz"))
3684 (file-name (string-append name "-" version ".tar.gz"))
3685 (sha256
3686 (base32
220458b0 3687 "0v515i73bvaz378h5465b1dy9v2gf924zy2q94cpq4qqarawvkqh"))
528bb464
EB		 3688 (modules '((guix build utils)))
3689 (snippet
3690 '(begin
3691 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
3692 ;; substitute the tarball creation time.
3693 (substitute* "src/utilities/HYPRE_utilities.h"
3694 (("Date Compiled: .*$")
220458b0 3695 "Date Compiled: Apr 11 2018 16:24:59 +0000\"\n"))
528bb464
EB		 3696 #t))))
3697 (build-system gnu-build-system)
3698 (outputs '("out" ;6.1 MiB of headers and libraries
3699 "doc")) ;4.8 MiB of documentation
3700 (native-inputs
3701 `(("doc++" ,doc++)
3702 ("netpbm" ,netpbm)
e18e7cb9 3703 ("perl" ,perl) ;needed to run 'ppmquant' during tests
528bb464
EB		 3704 ("texlive" ,texlive) ;full package required for fonts
3705 ("ghostscript" ,ghostscript)))
3706 (inputs
3707 `(("blas" ,openblas)
3708 ("lapack" ,lapack)))
3709 (arguments
3710 `(#:modules ((srfi srfi-1)
3711 ,@%gnu-build-system-modules)
3712 #:configure-flags '("--enable-shared"
3713 "--disable-fortran"
3714 "--without-MPI"
3715 "--with-openmp"
3716 "--with-fei"
3717 "--with-lapack"
3718 "--with-blas")
3719 #:phases
3720 (modify-phases %standard-phases
3721 (add-before 'configure 'chdir-src
3722 (lambda _ (chdir "src")))
3723 (replace 'configure
3724 (lambda* (#:key build target configure-flags
3725 #:allow-other-keys #:rest args)
3726 (let* ((configure (assoc-ref %standard-phases 'configure)))
3727 (apply configure
3728 (append args
3729 (list #:configure-flags
3730 (cons (string-append
3731 "--host=" (or target build))
3732 configure-flags)))))))
3733 (add-after 'build 'build-docs
3734 (lambda _
3735 (zero? (system* "make" "-Cdocs" "pdf" "html"))))
3736 (replace 'check
3737 (lambda _
3738 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3739 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
3740 (and (system* "make" "check" "CHECKRUN=")
3741 (fold (lambda (filename result)
3742 (and result
3743 (let ((size (stat:size (stat filename))))
3744 (when (not (zero? size))
3745 (format #t "~a size ~d; error indication~%"
3746 filename size))
3747 (zero? size))))
3748 #t
3749 (find-files "test" ".*\\.err$")))))
3750 (add-after 'install 'install-docs
3751 (lambda* (#:key outputs #:allow-other-keys)
3752 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3753 (let* ((doc (assoc-ref outputs "doc"))
3754 (docdir (string-append doc "/share/doc/hypre-" ,version)))
528bb464
EB		 3755 (with-directory-excursion "docs"
3756 (for-each (lambda (base)
3757 (install-file (string-append base ".pdf") docdir)
3758 (copy-recursively base docdir)) ;html docs
3759 '("HYPRE_usr_manual"
3760 "HYPRE_ref_manual")))
3761 #t))))))
3762 (home-page "http://www.llnl.gov/casc/hypre/")
3763 (synopsis "Library of solvers and preconditioners for linear equations")
3764 (description
3765 "HYPRE is a software library of high performance preconditioners and
3766solvers for the solution of large, sparse linear systems of equations. It
3767features multigrid solvers for both structured and unstructured grid
3768problems.")
3769 (license license:lgpl2.1)))
3770
3771(define-public hypre-openmpi
3772 (package (inherit hypre)
3773 (name "hypre-openmpi")
3774 (inputs
3775 `(("mpi" ,openmpi)
3776 ,@(package-inputs hypre)))
3777 (arguments
3778 (substitute-keyword-arguments (package-arguments hypre)
3779 ((#:configure-flags flags)
3780 ``("--with-MPI"
6df2a50a
LC		 3781 ,@(delete "--without-MPI" ,flags)))
3782 ((#:phases phases)
3783 `(modify-phases ,phases
bbe46a4a
EB		 3784 (add-before 'check 'mpi-setup
3785 ,%openmpi-setup)))))
528bb464
EB		 3786 (synopsis "Parallel solvers and preconditioners for linear equations")
3787 (description
3788 "HYPRE is a software library of high performance preconditioners and
3789solvers for the solution of large, sparse linear systems of equations on
3790parallel computers. It features parallel multigrid solvers for both
3791structured and unstructured grid problems.")))
6c90e183
EB		 3792
3793(define-public matio
3794 (package
3795 (name "matio")
3796 (version "1.5.6")
3797 (source
3798 (origin
3799 (method url-fetch)
de67e922 3800 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
6c90e183
EB		 3801 "matio-" version ".tar.gz"))
3802 (sha256
3803 (base32
3804 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3805 (build-system gnu-build-system)
3806 (inputs
3807 `(("zlib" ,zlib)
3808 ("hdf5" ,hdf5)))
3809 (home-page "http://matio.sourceforge.net/")
3810 (synopsis "Library for reading and writing MAT files")
3811 (description "Matio is a library for reading and writing MAT files. It
3812supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3813 (license license:bsd-2)))
d721c83a 3814
517318ad
LF		 3815(define-public vc
3816 (package
3817 (name "vc")
853b0292 3818 (version "1.3.3")
517318ad
LF		 3819 (source
3820 (origin (method url-fetch)
3821 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3822 "download/" version "/Vc-" version ".tar.gz"))
3823 (sha256
3824 (base32
853b0292 3825 "1zmlpn32jzb38smp3j834llmbix3whsrbw0h397qxysbw792kih8"))))
517318ad
LF		 3826 (build-system cmake-build-system)
3827 (arguments
3828 '(#:configure-flags
33d82486
MB		 3829 '("-DBUILD_TESTING=ON"
3830 ;; By default, Vc will optimize for the CPU of the build machine.
3831 ;; Setting this to "none" makes it create portable binaries. See
3832 ;; "cmake/OptimizeForArchitecture.cmake".
3833 "-DTARGET_ARCHITECTURE=none")))
517318ad
LF		 3834 (synopsis "SIMD vector classes for C++")
3835 (description "Vc provides portable, zero-overhead C++ types for explicitly
3836data-parallel programming. It is a library designed to ease explicit
3837vectorization of C++ code. Its types enable explicitly stating data-parallel
3838operations on multiple values. The parallelism is therefore added via the type
3839system. Vc has an intuitive API and provides portability between different
3840compilers and compiler versions as well as portability between different vector
3841instruction sets. Thus, an application written with Vc can be compiled for:
3842@enumerate
3843@item AVX and AVX2
d1e4ad1b 3844@item SSE2 up to SSE4.2 or SSE4a
517318ad
LF		 3845@item Scalar
3846@item MIC
3847@item NEON (in development)
3848@item NVIDIA GPUs / CUDA (in development)
3849@end enumerate\n")
3850 (home-page "https://github.com/VcDevel/Vc")
a8ead6f9
EF		 3851 ;; "No support_???.cpp file exists for this architecture."
3852 (supported-systems '("x86_64-linux" "i686-linux"))
517318ad 3853 (license license:bsd-3)))
54052a54 3854
3855(define-public reducelcs
3856 ;; This is the last commit which is available upstream, no
3857 ;; release happened since 2010.
3858 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
3859 (revision "1"))
3860 (package
3861 (name "reducelcs")
3862 (version (string-append "1.0-" revision "." (string-take commit 7)))
3863 (source
3864 (origin
3865 (method git-fetch)
3866 (uri (git-reference
3867 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
3868 (commit commit)))
3869 (file-name (string-append name "-" version "-checkout"))
3870 (sha256
3871 (base32
3872 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
3873 (build-system gnu-build-system)
3874 (inputs
3875 `(("openlibm" ,openlibm)))
3876 (arguments
3877 `(#:tests? #f ; no tests
3878 #:phases
3879 (modify-phases %standard-phases
3880 (delete 'configure) ; No configure script exists.
3881 (replace 'install ; No install phase exists.
3882 (lambda* (#:key outputs #:allow-other-keys)
3883 (let* ((out (assoc-ref outputs "out"))
3884 (bin (string-append out "/bin")))
3885 (install-file "Approximation" bin)
3886 (install-file "CollectResults" bin)
3887 (install-file "GenerateInstances" bin)
3888 #t))))))
3889 (synopsis "Approximate Longest Commons Subsequence computation tool")
3890 (description
3891 "@code{reduceLCS} is an implementation of the Reduce-Expand
3892algorithm for LCS. It is a fast program to compute the approximate
3893Longest Commons Subsequence of a set of strings.")
3894 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
c000b6b1 3895 (license license:gpl3+))))
479c4273
JD		 3896
3897(define-public jacal
3898 (package
3899 (name "jacal")
3900 (version "1c4")
3901 (source (origin
3902 (method url-fetch)
3903 (uri (string-append
3904 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
3905 version ".zip"))
3906 (sha256 (base32
3907 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
3908 (patches (search-patches "jacal-fix-texinfo.patch"))))
3909 (build-system gnu-build-system)
3910 (arguments
3911 `(#:phases
3912 (modify-phases %standard-phases
3913 (add-before 'build 'pre-build
3914 ;; Don't use upstream's script - it really doesn't fit into
3915 ;; Guix's functional paradigm.
3916 (lambda* (#:key inputs outputs #:allow-other-keys)
3917 (substitute* "Makefile"
3918 (("^install: install-script") "install: "))))
3919 (add-after 'install 'post-install
3920 ;; Instead, we provide our own simplified script.
3921 (lambda* (#:key inputs outputs #:allow-other-keys)
3922 (let ((wrapper (string-append (assoc-ref outputs "out")
3923 "/bin/jacal")))
3924 (format (open wrapper (logior O_WRONLY O_CREAT))
3925 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
3926 "-e '(slib:load \"~a/lib/jacal/math\") "
3927 "(math)' \"$@\"\n")
3928 (which "bash")
3929 (assoc-ref inputs "scm")
3930 (assoc-ref outputs "out"))
3931 (chmod wrapper #o555))))
3932 (replace 'configure
3933 (lambda* (#:key inputs outputs #:allow-other-keys)
3934 (zero? (system* "./configure"
3935 (string-append "--prefix="
3936 (assoc-ref outputs "out")))))))))
3937 (inputs `(("scm" ,scm)))
3938 (native-inputs `(("unzip" ,unzip)
3939 ("texinfo" ,texinfo)))
3940 (synopsis "Symbolic mathematics system")
3941 (description "GNU JACAL is an interactive symbolic mathematics program based on
3942Scheme. It manipulate and simplify a range of mathematical expressions such
3943as equations, scalars, vectors, and matrices.")
6fd52309 3944 (home-page "https://www.gnu.org/software/jacal/")
479c4273
JD		 3945 (license license:gpl3+)))
3946
313844d9
TF		 3947(define-public z3
3948 (package
3949 (name "z3")
4a4f3e77 3950 (version "4.8.1")
fb525bfd 3951 (home-page "https://github.com/Z3Prover/z3")
313844d9 3952 (source (origin
fb525bfd
MB		 3953 (method git-fetch)
3954 (uri (git-reference (url home-page)
3955 (commit (string-append "z3-" version))))
313844d9
TF		 3956 (sha256
3957 (base32
4a4f3e77 3958 "1vr57bwx40sd5riijyrhy70i2wnv9xrdihf6y5zdz56yq88rl48f"))))
cf684d87 3959 (build-system cmake-build-system)
313844d9 3960 (arguments
cf684d87
TF		 3961 `(#:configure-flags
3962 (list "-DBUILD_PYTHON_BINDINGS=true"
3963 "-DINSTALL_PYTHON_BINDINGS=true"
3964 (string-append "-DCMAKE_INSTALL_PYTHON_PKG_DIR="
3965 %output
677bc34d 3966 "/lib/python2.7/site-packages"))
313844d9
TF		 3967 #:phases
3968 (modify-phases %standard-phases
cf684d87
TF		 3969 (add-before 'configure 'bootstrap
3970 (lambda _
313844d9 3971 (zero?
cf684d87
TF		 3972 (system* "python" "contrib/cmake/bootstrap.py" "create"))))
3973 (add-before 'check 'make-test-z3
313844d9 3974 (lambda _
cf684d87
TF		 3975 ;; Build the test suite executable.
3976 (zero? (system* "make" "test-z3" "-j"
3977 (number->string (parallel-job-count))))))
3978 (replace 'check
3979 (lambda _
3980 ;; Run all the tests that don't require arguments.
3981 (zero? (system* "./test-z3" "/a")))))))
313844d9
TF		 3982 (native-inputs
3983 `(("python" ,python-2)))
3984 (synopsis "Theorem prover")
3985 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
cf684d87 3986theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
313844d9 3987 (license license:expat)))
3d5d87a3
JL		 3988
3989(define-public cubicle
3990 (package
3991 (name "cubicle")
564cf93f 3992 (version "1.1.2")
3d5d87a3
JL		 3993 (source (origin
3994 (method url-fetch)
3995 (uri (string-append "http://cubicle.lri.fr/cubicle-"
3996 version ".tar.gz"))
3997 (sha256
3998 (base32
564cf93f 3999 "10kk80jdmpdvql88sdjsh7vqzlpaphd8vip2lp47aarxjkwjlz1q"))))
3d5d87a3
JL		 4000 (build-system gnu-build-system)
4001 (native-inputs
564cf93f
JL		 4002 `(("automake" ,automake)
4003 ("ocaml" ,ocaml)
83fef82b 4004 ("which" ,(@@ (gnu packages base) which))))
3d5d87a3 4005 (propagated-inputs
564cf93f
JL		 4006 `(("ocaml-num" ,ocaml-num)
4007 ("z3" ,z3)))
3d5d87a3
JL		 4008 (arguments
4009 `(#:configure-flags (list "--with-z3")
564cf93f 4010 #:make-flags (list "QUIET=")
3d5d87a3
JL		 4011 #:tests? #f
4012 #:phases
4013 (modify-phases %standard-phases
4014 (add-before 'configure 'configure-for-release
4015 (lambda _
4016 (substitute* "Makefile.in"
564cf93f
JL		 4017 (("SVNREV=") "#SVNREV="))
4018 #t))
3d5d87a3
JL		 4019 (add-before 'configure 'fix-/bin/sh
4020 (lambda _
4021 (substitute* "configure"
564cf93f
JL		 4022 (("-/bin/sh") (string-append "-" (which "sh"))))
4023 #t))
3d5d87a3
JL		 4024 (add-before 'configure 'fix-smt-z3wrapper.ml
4025 (lambda _
4026 (substitute* "Makefile.in"
564cf93f
JL		 4027 (("\\\\n") ""))
4028 #t))
4029 (add-before 'configure 'fix-ocaml-num
4030 (lambda* (#:key inputs #:allow-other-keys)
4031 (substitute* "Makefile.in"
4032 (("= \\$\\(FUNCTORYLIB\\)")
4033 (string-append "= -I "
4034 (assoc-ref inputs "ocaml-num")
4035 "/lib/ocaml/site-lib"
4036 " $(FUNCTORYLIB)")))
4037 #t)))))
3d5d87a3
JL		 4038 (home-page "http://cubicle.lri.fr/")
4039 (synopsis "Model checker for array-based systems")
5a80c15c
RW		 4040 (description "Cubicle is a model checker for verifying safety properties
4041of array-based systems. This is a syntactically restricted class of
4042parametrized transition systems with states represented as arrays indexed by
4043an arbitrary number of processes. Cache coherence protocols and mutual
4044exclusion algorithms are typical examples of such systems.")
3d5d87a3 4045 (license license:asl2.0)))
e01397b4
EB		 4046
4047(define-public elemental
4048 (package
4049 (name "elemental")
4050 (version "0.87.7")
4051 (source (origin
4052 (method url-fetch)
4053 (uri (string-append "https://github.com/elemental/Elemental/"
4054 "archive/v" version ".tar.gz"))
4055 (file-name (string-append name "-" version ".tar.gz"))
4056 (sha256
4057 (base32
4058 "1nfp82w22pi8x8fg9sc37z8kf84dqi1dhxp8bbk7571y4aygvv3v"))))
4059 (build-system cmake-build-system)
4060 (home-page "http://libelemental.org")
4061 (native-inputs
4062 `(("gfortran" ,gfortran)))
4063 (inputs
4064 `(("blas" ,openblas)
4065 ("gfortran:lib" ,gfortran "lib")
4066 ("gmp" ,gmp)
4067 ("lapack" ,lapack)
4068 ("metis" ,metis)
4069 ("mpc" ,mpc)
4070 ("mpfr" ,mpfr)
4071 ("mpi" ,openmpi)
4072 ("qd" ,qd)))
4073 (arguments
4074 `(#:build-type "Release" ;default RelWithDebInfo not supported
4075 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
4076 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
4077 "-DEL_CACHE_WARNINGS:BOOL=YES"
4078 "-DEL_TESTS:BOOL=YES"
4079 "-DCMAKE_INSTALL_LIBDIR=lib"
4080 "-DGFORTRAN_LIB=gfortran")
4081 #:phases (modify-phases %standard-phases
bbe46a4a
EB		 4082 (add-before 'check 'mpi-setup
4083 ,%openmpi-setup)
e01397b4
EB		 4084 (add-before 'check 'setup-tests
4085 (lambda _
4086 ;; Parallelism is done at the MPI layer.
4087 (setenv "OMP_NUM_THREADS" "1")
4088 #t))
4089 (add-after 'install 'remove-tests
4090 (lambda* (#:key outputs #:allow-other-keys)
4091 ;; Tests are installed, with no easy configuration
4092 ;; switch to prevent this, so delete them.
4093 (delete-file-recursively
4094 (string-append (assoc-ref outputs "out") "/bin"))
4095 #t)))))
4096 (synopsis "Dense and sparse-direct linear algebra and optimization")
4097 (description "Elemental is a modern C++ library for distributed-memory
4098dense and sparse-direct linear algebra, conic optimization, and lattice
4099reduction.")
4100 (license license:bsd-2)))
5b05dce7
JN		 4101
4102(define-public mcrl2
4103 (package
4104 (name "mcrl2")
4105 (version "201707.1.15162")
4106 (source (origin
4107 (method url-fetch)
4108 (uri (string-append "http://www.mcrl2.org/download/devel/mcrl2-"
4109 version
4110 ".tar.gz"))
4111 (sha256
4112 (base32
4113 "1ziww2fchsklm25hl9p2mngssxfh9w07nc114cncqaxfibqp2p8f"))))
4114 (native-inputs
4115 `(("subversion" ,subversion)))
4116 (inputs
4117 `(("boost" ,boost)
4118 ("glu" ,glu)
4119 ("mesa" ,mesa)
077d66ed 4120 ("qtbase" ,qtbase)))
5b05dce7 4121 (build-system cmake-build-system)
ed0c5d3c 4122 (synopsis "Toolset for the mCRL2 formal specification language")
5b05dce7 4123 (description
ed0c5d3c
TGR		 4124 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
4125specification language for describing concurrent discrete event systems. Its
4126toolset supports analysis and automatic verification, linearisation, simulation,
4127state-space exploration and generation, and tools to optimise and analyse
5b05dce7
JN		 4128specifications. Also, state spaces can be manipulated, visualised and
4129analysed.")
b3882709 4130 (home-page "https://mcrl2.org")
5b05dce7 4131 (license license:boost1.0)))
41835f94
LF		 4132
4133(define-public r-subplex
4134 (package
4135 (name "r-subplex")
2bcf5fd3 4136 (version "1.5-4")
41835f94
LF		 4137 (source
4138 (origin
4139 (method url-fetch)
4140 (uri (cran-uri "subplex" version))
4141 (sha256
4142 (base32
2bcf5fd3 4143 "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
41835f94
LF		 4144 (build-system r-build-system)
4145 (native-inputs
4146 `(("gfortran" ,gfortran)))
4147 (home-page "https://cran.r-project.org/web/packages/subplex")
4148 (synopsis "Unconstrained optimization using the subplex algorithm")
4149 (description "This package implements the Subplex optimization algorithm.
4150It solves unconstrained optimization problems using a simplex method on
4151subspaces. The method is well suited for optimizing objective functions that
4152are noisy or are discontinuous at the solution.")
4153 (license license:gpl3+)))
799ad71b
LF		 4154
4155(define-public r-desolve
4156 (package
4157 (name "r-desolve")
9a2ac95d 4158 (version "1.21")
799ad71b
LF		 4159 (source
4160 (origin
4161 (method url-fetch)
4162 (uri (cran-uri "deSolve" version))
4163 (sha256
4164 (base32
9a2ac95d 4165 "0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"))))
799ad71b
LF		 4166 (properties `((upstream-name . "deSolve")))
4167 (build-system r-build-system)
4168 (native-inputs
4169 `(("gfortran" ,gfortran)))
4170 (home-page "https://desolve.r-forge.r-project.org/")
4171 (synopsis "Solvers for initial value problems of differential equations")
4172 (description "This package provides functions that solve initial
4173value problems of a system of first-order ordinary differential equations (ODE),
4174of partial differential equations (PDE), of differential algebraic equations
4175(DAE), and of delay differential equations. The functions provide an interface
4176to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
4177to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
4178the Runge-Kutta family with fixed or variable time steps. The package contains
4179routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
4180differential equations (PDE) that have been converted to ODEs by numerical
4181differencing.")
4182 (license license:gpl2+)))
910deec6
NV		 4183
4184(define-public tcalc
4185 (package
4186 (name "tcalc")
4187 (version "2.0")
4188 (source
4189 (origin
4190 (method url-fetch)
4191 (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
4192 version ".tar.gz"))
4193 (sha256
4194 (base32
4195 "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
4196 (build-system gnu-build-system)
4197 (synopsis "The terminal calculator")
4198 (description
4199 "The terminal calculator is a small program to help users of the GNU/Linux
4200terminal do calculations simply and quickly. The formula to be calculated can
4201be fed to @command{tcalc} through the command line.")
4202 (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
4203 (license license:gpl3+)))
b26e4f26
EB		 4204
4205(define-public sundials
4206 (package
4207 (name "sundials")
4208 (version "3.1.1")
4209 (source
4210 (origin
4211 (method url-fetch)
4212 (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
4213 "sundials-" version ".tar.gz"))
4214 (sha256
4215 (base32
4216 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
4217 (build-system cmake-build-system)
4218 (native-inputs
4219 `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
4220 (inputs
4221 `(("fortran" ,gfortran) ;for fcmix
4222 ("blas" ,openblas)
4223 ("suitesparse" ,suitesparse))) ;TODO: Add hypre
4224 (arguments
4225 `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
4226 "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
4227 "-DEXAMPLES_ENABLE_F77:BOOL=ON"
4228 "-DEXAMPLES_ENABLE_F90:BOOL=ON"
4229 "-DEXAMPLES_INSTALL:BOOL=OFF"
4230
4231 "-DFCMIX_ENABLE:BOOL=ON"
4232
4233 "-DKLU_ENABLE:BOOL=ON"
4234 ,(string-append "-DKLU_INCLUDE_DIR="
4235 (assoc-ref %build-inputs "suitesparse")
4236 "/include")
4237 ,(string-append "-DKLU_LIBRARY_DIR="
4238 (assoc-ref %build-inputs "suitesparse")
4239 "/lib"))))
4240 (home-page "https://computation.llnl.gov/projects/sundials")
4241 (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
4242 (description "SUNDIALS is a family of software packages implemented with
4243the goal of providing robust time integrators and nonlinear solvers that can
4244easily be incorporated into existing simulation codes.")
4245 (license license:bsd-3)))
4246
4247(define-public sundials-openmpi
4248 (package (inherit sundials)
4249 (name "sundials-openmpi")
4250 (inputs
4251 `(("mpi" ,openmpi)
4252 ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
4253 ,@(package-inputs sundials)))
4254 (arguments
4255 (substitute-keyword-arguments (package-arguments sundials)
4256 ((#:configure-flags flags '())
4257 `(cons* "-DMPI_ENABLE:BOOL=ON"
4258 "-DPETSC_ENABLE:BOOL=ON"
4259 (string-append "-DPETSC_INCLUDE_DIR="
4260 (assoc-ref %build-inputs "petsc")
4261 "/include")
4262 (string-append "-DPETSC_LIBRARY_DIR="
4263 (assoc-ref %build-inputs "petsc")
4264 "/lib")
4265 ,flags))
4266 ((#:phases phases '%standard-phases)
4267 `(modify-phases ,phases
bbe46a4a
EB		 4268 (add-before 'check 'mpi-setup
4269 ,%openmpi-setup)))))
b26e4f26 4270 (synopsis "SUNDIALS with OpenMPI support")))
jackhill's copy of GNU Guix: https://guix.gnu.org/