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[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")
02107081 325 (version "3.1.0")
b343850e 326 (home-page "https://github.com/google/double-conversion")
61a529b4 327 (source (origin
2bdc73fb 328 (method git-fetch)
02107081 329 (uri (git-reference (url home-page) (commit version)))
2bdc73fb 330 (file-name (git-file-name name version))
61a529b4
RW		 331 (sha256
332 (base32
02107081 333 "123rb2p4snqagrybw66vnapchqdwn2rfpr1wcq0ya9gwbyl7xccx"))))
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.
5537603f 1416(define-public octave-cli
668c06ac 1417 (package
5537603f 1418 (name "octave-cli")
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
e0ae7e73 1500(define-public octave
5537603f 1501 (package (inherit octave-cli)
e0ae7e73 1502 (name "octave")
7a3772b3 1503 (source (origin
5537603f 1504 (inherit (package-source octave-cli))))
36ce25f0
KK		 1505 (inputs
1506 `(("qscintilla" ,qscintilla)
1507 ("qt" ,qtbase)
5537603f 1508 ,@(package-inputs octave-cli)))
36ce25f0
KK		 1509 (native-inputs
1510 `(("qttools" , qttools) ;for lrelease
7a3772b3 1511 ("texlive" ,texlive) ;for texi2dvi
5537603f 1512 ,@(package-native-inputs octave-cli)))
36ce25f0 1513 (arguments
5537603f 1514 (substitute-keyword-arguments (package-arguments octave-cli)
36ce25f0
KK		 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
e0ae7e73
KK		 1528(define-public qtoctave
1529 (deprecated-package "qtoctave" octave))
1530
5d4bd4cc
PG		 1531(define-public opencascade-oce
1532 (package
1533 (name "opencascade-oce")
1534 (version "0.17.2")
1535 (source
1536 (origin
1537 (method url-fetch)
1538 (uri (string-append
1539 "https://github.com/tpaviot/oce/archive/OCE-"
1540 version
1541 ".tar.gz"))
a4f393b7 1542 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
5d4bd4cc
PG		 1543 (sha256
1544 (base32
1545 "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
1546 (build-system cmake-build-system)
1547 (arguments
1548 '(#:configure-flags
1549 (list "-DOCE_TESTING:BOOL=ON"
1550 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1551 "-DOCE_DRAW:BOOL=ON"
1552 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1553 (assoc-ref %outputs "out"))
1554 "-UCMAKE_INSTALL_RPATH")))
1555 (inputs
1556 `(("freetype" ,freetype)
1557 ("glu" ,glu)
1558 ("libxmu" ,libxmu)
1559 ("mesa" ,mesa)
1560 ("tcl" ,tcl)
1561 ("tk" ,tk)))
1562 (native-inputs
1563 `(("python" ,python-wrapper)))
1564 (home-page "https://github.com/tpaviot/oce")
1565 (synopsis "Libraries for 3D modeling and numerical simulation")
1566 (description
1567 "Open CASCADE is a set of libraries for the development of applications
1568dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1569C++ class libraries providing services for 3D surface and solid modeling, CAD
1570data exchange, and visualization. It is used for development of specialized
1571software dealing with 3D models in design (CAD), manufacturing (CAM),
1572numerical simulation (CAE), measurement equipment (CMM), and quality
1573control (CAQ) domains.
1574
1575This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1576patches, improvements, and experiments contributed by users over the official
1577Open CASCADE library.")
1578 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1579 ; use of header files; see
1580 ; OCCT_LGPL_EXCEPTION.txt
1581 license:public-domain; files
1582 ; src/Standard/Standard_StdAllocator.hxx and
1583 ; src/NCollection/NCollection_StdAllocator.hxx
1584 license:expat; file src/OpenGl/OpenGl_glext.h
1585 license:bsd-3)))); test framework gtest
1586
3de01d3f
EB		 1587(define-public gmsh
1588 (package
1589 (name "gmsh")
8a4d14fa 1590 (version "2.16.0")
3de01d3f
EB		 1591 (source
1592 (origin
1593 (method url-fetch)
1c79e086 1594 (uri (string-append "http://gmsh.info/src/gmsh-"
3de01d3f
EB		 1595 version "-source.tgz"))
1596 (sha256
8a4d14fa 1597 (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
3de01d3f
EB		 1598 (modules '((guix build utils)))
1599 (snippet
1600 ;; Remove non-free METIS code
6cbee49d
MW		 1601 '(begin
1602 (delete-file-recursively "contrib/Metis")
1603 #t))))
3de01d3f 1604 (build-system cmake-build-system)
3de01d3f
EB		 1605 (propagated-inputs
1606 `(("fltk" ,fltk)
19afbea1 1607 ("gfortran" ,gfortran)
3de01d3f 1608 ("gmp" ,gmp)
40029cbe 1609 ("hdf5" ,hdf5)
3de01d3f
EB		 1610 ("lapack" ,lapack)
1611 ("mesa" ,mesa)
85f41902 1612 ("glu" ,glu)
45548139 1613 ("opencascade-oce" ,opencascade-oce)
3de01d3f
EB		 1614 ("libx11" ,libx11)
1615 ("libxext" ,libxext)))
66395a61
EF		 1616 (inputs
1617 `(("fontconfig" ,fontconfig)
1618 ("libxft" ,libxft)))
3de01d3f
EB		 1619 (arguments
1620 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1621 "-DENABLE_BUILD_SHARED:BOOL=ON"
45548139 1622 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
3de01d3f
EB		 1623 (home-page "http://www.geuz.org/gmsh/")
1624 (synopsis "3D finite element grid generator")
edf684ef
EB		 1625 (description "Gmsh is a 3D finite element grid generator with a built-in
1626CAD engine and post-processor. Its design goal is to provide a fast, light
1627and user-friendly meshing tool with parametric input and advanced
1628visualization capabilities. Gmsh is built around four modules: geometry,
1629mesh, solver and post-processing. The specification of any input to these
1630modules is done either interactively using the graphical user interface or in
1631ASCII text files using Gmsh's own scripting language.")
3de01d3f 1632 (license license:gpl2+)))
b9100e2f 1633
6d5f63b6
JD		 1634(define-public maxflow
1635 (package
1636 (name "maxflow")
1637 (version "3.04")
1638 (source (origin
1639 (method git-fetch)
1640 (uri (git-reference
1641 (url "https://github.com/gerddie/maxflow.git")
1642 (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
1643 (file-name (string-append name "-" version "-checkout"))
1644 (sha256
1645 (base32
1646 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1647 (build-system cmake-build-system)
1648 (home-page "http://pub.ist.ac.at/~vnk/software.html")
1649 (synopsis "Library implementing Maxflow algorithm")
1650 (description "An implementation of the maxflow algorithm described in
1651@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1652Energy Minimization in Computer Vision.\n
1653Yuri Boykov and Vladimir Kolmogorov.\n
1654In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1655September 2004}")
1656 (license license:gpl3+)))
1657
b9100e2f
EB		 1658(define-public petsc
1659 (package
1660 (name "petsc")
e6951e4e 1661 (version "3.10.2")
b9100e2f
EB		 1662 (source
1663 (origin
1664 (method url-fetch)
1665 ;; The *-lite-* tarball does not contain the *large* documentation
1666 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1667 "petsc-lite-" version ".tar.gz"))
1668 (sha256
e6951e4e 1669 (base32 "0bl64pydak3rblnjffi482r8bin4xim9sb37ksl2jkcxf0i0irsi"))))
a3a99e27 1670 (outputs '("out" ;libraries and headers
c15be128 1671 "examples")) ;~30MiB of examples
b9100e2f
EB		 1672 (build-system gnu-build-system)
1673 (native-inputs
6fec298d 1674 `(("python" ,python-2)))
b9100e2f 1675 (inputs
19afbea1 1676 `(("gfortran" ,gfortran)
b9100e2f 1677 ("lapack" ,lapack)
f258212d 1678 ("superlu" ,superlu)
b9100e2f
EB		 1679 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1680 ;; leaving out opengl, as configuration seems to only be for mac
1681 ))
1682 (arguments
1683 `(#:test-target "test"
9a899cce 1684 #:parallel-build? #f ;build is parallel by default
b9100e2f
EB		 1685 #:configure-flags
1686 `("--with-mpi=0"
f258212d 1687 "--with-openmp=1"
c15be128 1688 "--with-superlu=1")
9731c412
EB		 1689 #:make-flags
1690 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1691 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1692 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
b9100e2f 1693 #:phases
64dcc289
EB		 1694 (modify-phases %standard-phases
1695 (replace 'configure
1696 ;; PETSc's configure script is actually a python script, so we can't
1697 ;; run it with bash.
1698 (lambda* (#:key outputs (configure-flags '())
1699 #:allow-other-keys)
1700 (let* ((prefix (assoc-ref outputs "out"))
1701 (flags `(,(string-append "--prefix=" prefix)
1702 ,@configure-flags)))
1703 (format #t "build directory: ~s~%" (getcwd))
1704 (format #t "configure flags: ~s~%" flags)
49fdd357 1705 (apply invoke "./configure" flags))))
64dcc289 1706 (add-after 'configure 'clean-local-references
9731c412 1707 (lambda* (#:key outputs #:allow-other-keys)
64dcc289
EB		 1708 (let ((out (assoc-ref outputs "out")))
1709 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
b730b437
EB		 1710 ;; Prevent build directory from leaking into compiled code
1711 (((getcwd)) out)
1712 ;; Scrub timestamp for reproducibility
fafd623e 1713 ((".*Libraries compiled on.*") ""))
9731c412
EB		 1714 (substitute* (find-files "." "petscvariables")
1715 ;; Do not expose build machine characteristics, set to defaults.
1716 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1717 (("NPMAX = [:digit:]+") "NPMAX = 2"))
fafd623e 1718 #t)))
64dcc289 1719 (add-after 'install 'clean-install
10b11968
EB		 1720 ;; Try to keep installed files from leaking build directory names.
1721 (lambda* (#:key inputs outputs #:allow-other-keys)
64dcc289 1722 (let ((out (assoc-ref outputs "out")))
10b11968 1723 (substitute* (map (lambda (file)
9a899cce 1724 (string-append out "/lib/petsc/conf/" file))
fafd623e 1725 '("petscvariables"))
10b11968
EB		 1726 (((getcwd)) out))
1727 ;; Make compiler references point to the store
9a899cce 1728 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
dfdf5716
EB		 1729 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1730 (string-append "= " (which compiler))))
10b11968
EB		 1731 ;; PETSc installs some build logs, which aren't necessary.
1732 (for-each (lambda (file)
9a899cce 1733 (let ((f (string-append out "/lib/petsc/conf/" file)))
10b11968
EB		 1734 (when (file-exists? f)
1735 (delete-file f))))
9a899cce
EB		 1736 '("configure.log" "make.log" "gmake.log"
1737 "test.log" "error.log" "RDict.db"
fafd623e 1738 "PETScBuildInternal.cmake"
10b11968 1739 ;; Once installed, should uninstall with Guix
fafd623e 1740 "uninstall.py"))
a3a99e27
EB		 1741 #t)))
1742 (add-after 'install 'move-examples
1743 (lambda* (#:key outputs #:allow-other-keys)
1744 (let* ((out (assoc-ref outputs "out"))
1745 (examples (assoc-ref outputs "examples"))
1746 (exdir (string-append out "/share/petsc/examples"))
1747 (exdir' (string-append examples "/share/petsc/examples")))
1748 (copy-recursively exdir exdir')
1749 (delete-file-recursively exdir)
fafd623e 1750 #t))))))
b9100e2f 1751 (home-page "http://www.mcs.anl.gov/petsc")
16ecf3ff 1752 (synopsis "Library to solve PDEs")
b9100e2f
EB		 1753 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1754data structures and routines for the scalable (parallel) solution of
1755scientific applications modeled by partial differential equations.")
166191b3 1756 (license (license:non-copyleft
b9100e2f
EB		 1757 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1758
1759(define-public petsc-complex
1760 (package (inherit petsc)
1761 (name "petsc-complex")
1762 (arguments
1763 (substitute-keyword-arguments (package-arguments petsc)
1764 ((#:configure-flags cf)
1765 `(cons "--with-scalar-type=complex" ,cf))))
16ecf3ff 1766 (synopsis "Library to solve PDEs (with complex scalars)")))
183e44ae 1767
d8c7eeb9
EB		 1768(define-public petsc-openmpi
1769 (package (inherit petsc)
1770 (name "petsc-openmpi")
1771 (inputs
9e2aa70b 1772 `(("hdf5" ,hdf5-parallel-openmpi)
af523673 1773 ("hypre" ,hypre-openmpi)
9e2aa70b
PG		 1774 ("metis" ,metis)
1775 ("mumps" ,mumps-openmpi)
1776 ("openmpi" ,openmpi)
1777 ("scalapack" ,scalapack)
72f95783 1778 ("scotch" ,pt-scotch32)
d8c7eeb9
EB		 1779 ,@(package-inputs petsc)))
1780 (arguments
1781 (substitute-keyword-arguments (package-arguments petsc)
1782 ((#:configure-flags cf)
af523673
PG		 1783 ``("--with-hypre=1"
1784 "--with-mpiexec=mpirun"
9e2aa70b
PG		 1785 "--with-metis=1"
1786 "--with-mumps=1"
1787 "--with-scalapack=1"
1788 "--with-ptscotch=1"
d8c7eeb9
EB		 1789 ,(string-append "--with-mpi-dir="
1790 (assoc-ref %build-inputs "openmpi"))
71ca16b5
PG		 1791 ,(string-append "--with-hdf5-include="
1792 (assoc-ref %build-inputs "hdf5") "/include")
1793 ,(string-append "--with-hdf5-lib="
1794 (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
1795 ,@(delete "--with-mpi=0" ,cf)))
1796 ((#:phases phases)
1797 `(modify-phases ,phases
9e2aa70b 1798 (add-before 'configure 'mpi-setup
bbe46a4a 1799 ,%openmpi-setup)))))
9e2aa70b 1800 (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
d8c7eeb9
EB		 1801
1802(define-public petsc-complex-openmpi
1803 (package (inherit petsc-complex)
1804 (name "petsc-complex-openmpi")
1805 (inputs
1806 `(("openmpi" ,openmpi)
1807 ,@(package-inputs petsc-complex)))
1808 (arguments
1809 (substitute-keyword-arguments (package-arguments petsc-complex)
1810 ((#:configure-flags cf)
1811 ``("--with-mpiexec=mpirun"
1812 ,(string-append "--with-mpi-dir="
1813 (assoc-ref %build-inputs "openmpi"))
1814 ,@(delete "--with-mpi=0" ,cf)))))
16ecf3ff 1815 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
d8c7eeb9 1816
90ff2874
PG		 1817(define-public python-petsc4py
1818 (package
1819 (name "python-petsc4py")
cd3681a2 1820 (version "3.10.0")
90ff2874
PG		 1821 (source
1822 (origin
1823 (method url-fetch)
1824 (uri (pypi-uri "petsc4py" version))
1825 (sha256
1826 (base32
cd3681a2 1827 "0ch3g6dsvxl7qi984fcssv7cxfbif4bw04gkvxl2l1b8wrmvrm25"))))
90ff2874
PG		 1828 (build-system python-build-system)
1829 (arguments
1830 `(#:phases
1831 (modify-phases %standard-phases
1832 (add-before 'build 'pre-build
1833 (lambda _
1834 ;; Define path to PETSc installation.
1835 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
1836 #t))
1837 (add-before 'check 'mpi-setup
1838 ,%openmpi-setup))))
1839 (inputs
1840 `(("petsc" ,petsc-openmpi)
1841 ("python-numpy" ,python-numpy)))
1842 (home-page "https://bitbucket.org/petsc/petsc4py/")
1843 (synopsis "Python bindings for PETSc")
1844 (description "PETSc, the Portable, Extensible Toolkit for
1845Scientific Computation, is a suite of data structures and routines for
1846the scalable (parallel) solution of scientific applications modeled by
1847partial differential equations. It employs the MPI standard for all
1848message-passing communication. @code{petsc4py} provides Python
1849bindings to almost all functions of PETSc.")
1850 (license license:bsd-3)))
1851
560acf25
MB		 1852(define-public python-kiwisolver
1853 (package
1854 (name "python-kiwisolver")
1855 (version "1.0.1")
1856 (source (origin
1857 (method url-fetch)
1858 (uri (pypi-uri "kiwisolver" version))
1859 (sha256
1860 (base32
1861 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
1862 (build-system python-build-system)
1863 (home-page "https://github.com/nucleic/kiwi")
1864 (synopsis "Fast implementation of the Cassowary constraint solver")
1865 (description
1866 "Kiwi is an efficient C++ implementation of the Cassowary constraint
1867solving algorithm. Kiwi has been designed from the ground up to be
1868lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
1869Cassowary solver with typical use cases gaining a 40x improvement. Memory
1870savings are consistently > 5x.")
1871 (license license:bsd-3)))
1872
1873(define-public python2-kiwisolver
1874 (package-with-python2 python-kiwisolver))
1875
a7f01414
EB		 1876(define-public slepc
1877 (package
1878 (name "slepc")
e93da160 1879 (version "3.10.1")
a7f01414
EB		 1880 (source
1881 (origin
1882 (method url-fetch)
baeaf882
EB		 1883 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
1884 version ".tar.gz"))
a7f01414
EB		 1885 (sha256
1886 (base32
e93da160 1887 "188j1a133q91h8pivpnzwcf78kz8dvz2nzf6ndnjygdbqb48fizn"))))
a7f01414
EB		 1888 (build-system gnu-build-system)
1889 (native-inputs
1890 `(("python" ,python-2)))
1891 (inputs
1892 `(("arpack" ,arpack-ng)
1893 ("gfortran" ,gfortran)))
1894 (propagated-inputs
1895 `(("petsc" ,petsc)))
1896 (arguments
1897 `(#:parallel-build? #f ;build is parallel by default
1898 #:configure-flags
1899 `(,(string-append "--with-arpack-dir="
9cf52454 1900 (assoc-ref %build-inputs "arpack") "/lib"))
9731c412
EB		 1901 #:make-flags ;honor (parallel-job-count)
1902 `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
a7f01414
EB		 1903 #:phases
1904 (modify-phases %standard-phases
8787c555 1905 (replace 'configure
a7f01414
EB		 1906 ;; configure is a python script, so we can't run it with bash.
1907 (lambda* (#:key inputs outputs (configure-flags '())
1908 #:allow-other-keys)
1909 (let* ((prefix (assoc-ref outputs "out"))
1910 (flags `(,(string-append "--prefix=" prefix)
1911 ,@configure-flags)))
1912 (format #t "build directory: ~s~%" (getcwd))
1913 (format #t "configure flags: ~s~%" flags)
1914 (setenv "SLEPC_DIR" (getcwd))
9cf52454 1915 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
c6840089 1916 (apply invoke "./configure" flags))))
8787c555 1917 (add-after 'install 'delete-doc
a7f01414
EB		 1918 ;; TODO: SLEPc installs HTML documentation alongside headers in
1919 ;; $out/include. We'd like to move them to share/doc, but delete
1920 ;; them for now, as they are incomplete and installing the complete
1921 ;; documentation is difficult.
1922 (lambda* (#:key outputs #:allow-other-keys)
1923 (let* ((out (assoc-ref outputs "out")))
0f6dc120
TGR		 1924 (for-each delete-file (find-files out "\\.html$"))
1925 #t)))
8787c555 1926 (add-after 'install 'clean-install
a7f01414
EB		 1927 ;; Clean up unnecessary build logs from installation.
1928 (lambda* (#:key outputs #:allow-other-keys)
1929 (let ((out (assoc-ref outputs "out")))
1930 (for-each (lambda (file)
1931 (let ((f (string-append out "/lib/slepc/conf/" file)))
1932 (when (file-exists? f)
1933 (delete-file f))))
1934 '("configure.log" "make.log" "gmake.log"
1935 "test.log" "error.log" "RDict.db"
0f6dc120
TGR		 1936 "uninstall.py"))
1937 #t))))))
a7f01414
EB		 1938 (home-page "http://slepc.upv.es")
1939 (synopsis "Scalable library for eigenproblems")
1940 (description "SLEPc is a software library for the solution of large sparse
1941eigenproblems on parallel computers. It can be used for the solution of
1942linear eigenvalue problems formulated in either standard or generalized form,
1943as well as other related problems such as the singular value decomposition.
1944The emphasis of the software is on methods and techniques appropriate for
1945problems in which the associated matrices are sparse, for example, those
1946arising after the discretization of partial differential equations.")
3c524f21 1947 (license license:bsd-2)))
a7f01414
EB		 1948
1949(define-public slepc-complex
1950 (package (inherit slepc)
1951 (name "slepc-complex")
1952 (propagated-inputs
1953 `(("petsc" ,petsc-complex)
1954 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1955 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1956
1957(define-public slepc-openmpi
1958 (package (inherit slepc)
1959 (name "slepc-openmpi")
6df2a50a
LC		 1960 (arguments
1961 (substitute-keyword-arguments (package-arguments slepc)
1962 ((#:phases phases '%standard-phases)
1963 `(modify-phases ,phases
bbe46a4a
EB		 1964 (add-before 'check 'mpi-setup
1965 ,%openmpi-setup)))))
a7f01414
EB		 1966 (inputs
1967 `(("mpi" ,openmpi)
1968 ("arpack" ,arpack-ng-openmpi)
1969 ,@(alist-delete "arpack" (package-inputs slepc))))
1970 (propagated-inputs
1971 `(("petsc" ,petsc-openmpi)
1972 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1973 (synopsis "Scalable library for eigenproblems (with MPI support)")))
1974
1975(define-public slepc-complex-openmpi
1976 (package (inherit slepc-openmpi)
1977 (name "slepc-complex-openmpi")
1978 (propagated-inputs
1979 `(("petsc" ,petsc-complex-openmpi)
1980 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1981 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1982
6b5687d0
PG		 1983(define-public python-slepc4py
1984 (package
1985 (name "python-slepc4py")
57d30004 1986 (version "3.10.0")
6b5687d0
PG		 1987 (source
1988 (origin
1989 (method url-fetch)
1990 (uri (pypi-uri "slepc4py" version))
1991 (sha256
1992 (base32
57d30004 1993 "0x049dyc8frgh79fvvavf4vlbqp4mgm61nsaivzdav4316vvlv1j"))))
6b5687d0
PG		 1994 (build-system python-build-system)
1995 (arguments
1996 `(#:phases
1997 (modify-phases %standard-phases
1998 (add-before 'build 'pre-build
1999 (lambda _
2000 ;; Define path to PETSc installation.
2001 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
2002 ;; Define path to SLEPc installation.
2003 (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
2004 #t))
2005 (add-before 'check 'mpi-setup
2006 ,%openmpi-setup))))
2007 (inputs
2008 `(("python-numpy" ,python-numpy)
2009 ("python-petsc4py" ,python-petsc4py)
2010 ("slepc" ,slepc-openmpi)))
2011 (home-page "https://bitbucket.org/slepc/slepc4py/")
2012 (synopsis "Python bindings for SLEPc")
2013 (description "SLEPc, the Scalable Library for Eigenvalue Problem
2014Computations, is based on PETSc, the Portable, Extensible Toolkit for
2015Scientific Computation. It employs the MPI standard for all
2016message-passing communication. @code{slepc4py} provides Python
2017bindings to almost all functions of SLEPc.")
2018 (license license:bsd-3)))
2019
cec86422
EB		 2020(define-public mumps
2021 (package
2022 (name "mumps")
e7323f4c 2023 (version "5.1.2")
cec86422
EB		 2024 (source
2025 (origin
2026 (method url-fetch)
2027 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
2028 version ".tar.gz"))
2029 (sha256
2030 (base32
e7323f4c 2031 "1s9asin08zqzmh08257sdghhivvy9vjif7c53fhaxaax2kd5qd7b"))
fc1adab1 2032 (patches (search-patches "mumps-build-parallelism.patch"))))
cec86422
EB		 2033 (build-system gnu-build-system)
2034 (inputs
2035 `(("fortran" ,gfortran)
2036 ;; These are required for linking against mumps, but we let the user
2037 ;; declare the dependency.
2038 ("blas" ,openblas)
2039 ("metis" ,metis)
2040 ("scotch" ,scotch)))
2041 (arguments
2042 `(#:modules ((ice-9 match)
2043 (ice-9 popen)
2044 (srfi srfi-1)
2045 ,@%gnu-build-system-modules)
2046 #:phases
2047 (modify-phases %standard-phases
fba78d18 2048 (replace 'configure
cec86422
EB		 2049 (lambda* (#:key inputs #:allow-other-keys)
2050 (call-with-output-file "Makefile.inc"
2051 (lambda (port)
2052 (format port "
2053PLAT =
2054LIBEXT = .a
2055OUTC = -o
2056OUTF = -o
2057RM = rm -f~:[
2058CC = gcc
2059FC = gfortran
2060FL = gfortran
2061INCSEQ = -I$(topdir)/libseq
2062LIBSEQ = -L$(topdir)/libseq -lmpiseq
2063LIBSEQNEEDED = libseqneeded~;
2064CC = mpicc
2065FC = mpifort
2066FL = mpifort~]
2067AR = ar vr # rules require trailing space, ugh...
2068RANLIB = ranlib
2069LIBBLAS = -L~a -lopenblas~@[
2070SCALAP = -L~a -lscalapack~]
2071LIBOTHERS = -pthread
2072CDEFS = -DAdd_
2073PIC = -fPIC
2074OPTF = -O2 -DALLOW_NON_INIT $(PIC)
2075OPTL = -O2 $(PIC)
2076OPTC = -O2 $(PIC)
2077INCS = $(INCSEQ)
2078LIBS = $(SCALAP) $(LIBSEQ)
2079LPORDDIR = $(topdir)/PORD/lib
2080IPORD = -I$(topdir)/PORD/include
2081LPORD = -L$(LPORDDIR) -lpord
2082ORDERINGSF = -Dpord~@[
2083METISDIR = ~a
2084IMETIS = -I$(METISDIR)/include
2085LMETIS = -L$(METISDIR)/lib -lmetis
2086ORDERINGSF += -Dmetis~]~@[~:{
2087SCOTCHDIR = ~a
2088ISCOTCH = -I$(SCOTCHDIR)/include
2089LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
2090ORDERINGSF += ~a~}~]
2091ORDERINGSC = $(ORDERINGSF)
2092LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
2093IORDERINGSF = $(ISCOTCH)
2094IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
2095 (assoc-ref inputs "mpi")
2096 (assoc-ref inputs "blas")
2097 (assoc-ref inputs "scalapack")
2098 (assoc-ref inputs "metis")
2099 (match (list (assoc-ref inputs "pt-scotch")
2100 (assoc-ref inputs "scotch"))
2101 ((#f #f)
2102 #f)
2103 ((#f scotch)
2104 `((,scotch "" "-Dscotch")))
2105 ((ptscotch _)
2106 `((,ptscotch
2107 "-lptesmumps -lptscotch -lptscotcherr "
2108 "-Dptscotch")))))))))
fba78d18 2109 (replace 'build
cec86422
EB		 2110 ;; By default only the d-precision library is built. Make with "all"
2111 ;; target so that all precision libraries and examples are built.
2112 (lambda _
b414cf52
TGR		 2113 (invoke "make" "all"
2114 (format #f "-j~a" (parallel-job-count)))))
fba78d18 2115 (replace 'check
cec86422
EB		 2116 ;; Run the simple test drivers, which read test input from stdin:
2117 ;; from the "real" input for the single- and double-precision
2118 ;; testers, and from the "cmplx" input for complex-precision
2119 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
2120 ;; package to prefix execution with "mpirun".
2121 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
2122 (with-directory-excursion "examples"
2123 (every
2124 (lambda (prec type)
2125 (let ((tester (apply open-pipe*
2126 `(,OPEN_WRITE
2127 ,@exec-prefix
2128 ,(string-append "./" prec
2129 "simpletest"))))
2130 (input (open-input-file
2131 (string-append "input_simpletest_" type))))
2132 (begin
2133 (dump-port input tester)
2134 (close-port input)
2135 (zero? (close-pipe tester)))))
2136 '("s" "d" "c" "z")
2137 '("real" "real" "cmplx" "cmplx")))))
fba78d18
EB		 2138 (replace 'install
2139 (lambda* (#:key outputs #:allow-other-keys)
2140 (let* ((out (assoc-ref outputs "out"))
2141 (libdir (string-append out "/lib")))
2142 (copy-recursively "lib" libdir)
2143 (copy-recursively "include" (string-append out "/include"))
2144 (when (file-exists? "libseq/libmpiseq.a")
2145 (install-file "libseq/libmpiseq.a" libdir))
2146 #t))))))
cec86422
EB		 2147 (home-page "http://mumps.enseeiht.fr")
2148 (synopsis "Multifrontal sparse direct solver")
2149 (description
2150 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
2151sparse system of linear equations A x = b using Guassian elimination.")
2152 (license license:cecill-c)))
2153
2154(define-public mumps-metis
2155 (package (inherit mumps)
2156 (name "mumps-metis")
2157 (inputs
2158 (alist-delete "scotch" (package-inputs mumps)))))
2159
2160(define-public mumps-openmpi
2161 (package (inherit mumps)
2162 (name "mumps-openmpi")
2163 (inputs
2164 `(("mpi" ,openmpi)
2165 ("scalapack" ,scalapack)
2166 ("pt-scotch" ,pt-scotch)
2167 ,@(alist-delete "scotch" (package-inputs mumps))))
2168 (arguments
2169 (substitute-keyword-arguments (package-arguments mumps)
2170 ((#:phases phases)
2171 `(modify-phases ,phases
bbe46a4a
EB		 2172 (add-before 'check 'mpi-setup
2173 ,%openmpi-setup)
6df2a50a
LC		 2174 (replace 'check
2175 (lambda _
2176 ((assoc-ref ,phases 'check)
2177 #:exec-prefix '("mpirun" "-n" "2"))))))))
cec86422
EB		 2178 (synopsis "Multifrontal sparse direct solver (with MPI)")))
2179
2180(define-public mumps-metis-openmpi
2181 (package (inherit mumps-openmpi)
2182 (name "mumps-metis-openmpi")
2183 (inputs
2184 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
2185
2d047896
RW		 2186(define-public r-quadprog
2187 (package
2188 (name "r-quadprog")
2189 (version "1.5-5")
2190 (source
2191 (origin
2192 (method url-fetch)
2193 (uri (cran-uri "quadprog" version))
2194 (sha256
2195 (base32
2196 "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
2197 (build-system r-build-system)
2198 (native-inputs
2199 `(("gfortran" ,gfortran)))
e9960d8c 2200 (home-page "https://cran.r-project.org/web/packages/quadprog")
2d047896
RW		 2201 (synopsis "Functions to solve quadratic programming problems")
2202 (description
2203 "This package contains routines and documentation for solving quadratic
2204programming problems.")
2205 (license license:gpl3+)))
2206
ec8c7e47
RJ		 2207(define-public r-pracma
2208 (package
2209 (name "r-pracma")
39528a5e 2210 (version "2.1.8")
ec8c7e47
RJ		 2211 (source (origin
2212 (method url-fetch)
2213 (uri (cran-uri "pracma" version))
2214 (sha256
39528a5e 2215 (base32 "0m8ladhrfyxwybblkcdgg4xv1mk5kibmwarpj2k0c2y34zzcix4z"))))
ec8c7e47 2216 (build-system r-build-system)
39528a5e 2217 (home-page "https://cran.r-project.org/web/packages/pracma/")
ec8c7e47
RJ		 2218 (synopsis "Practical numerical math functions")
2219 (description "This package provides functions for numerical analysis and
2220linear algebra, numerical optimization, differential equations, plus some
2221special functions. It uses Matlab function names where appropriate to simplify
2222porting.")
2223 (license license:gpl3+)))
2224
63e07468
BW		 2225(define-public ruby-asciimath
2226 (package
2227 (name "ruby-asciimath")
2228 (version "1.0.4")
2229 (source
2230 (origin
2231 (method url-fetch)
2232 (uri (rubygems-uri "asciimath" version))
2233 (sha256
2234 (base32
2235 "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
2236 (build-system ruby-build-system)
2237 (arguments
2238 '(#:phases
2239 (modify-phases %standard-phases
2240 ;; Apply this patch
2241 ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
2242 (add-after 'unpack 'patch-remove-spurious-backslashes
2243 (lambda _
2244 (substitute* "spec/parser_spec.rb"
2245 (("\\\\\"")
9923d5a4
TGR		 2246 "\""))
2247 #t)))))
63e07468
BW		 2248 (native-inputs
2249 `(("bundler" ,bundler)
2250 ("ruby-rspec" ,ruby-rspec)))
2251 (synopsis "AsciiMath parsing and conversion library")
2252 (description
2253 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
2254easy-to-write markup language for mathematics.")
2255 (home-page "https://github.com/asciidoctor/asciimath")
2256 (license license:expat)))
2257
183e44ae
EB		 2258(define-public superlu
2259 (package
2260 (name "superlu")
995a09e0 2261 (version "5.2.1")
183e44ae
EB		 2262 (source
2263 (origin
2264 (method url-fetch)
2265 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2266 "superlu_" version ".tar.gz"))
2267 (sha256
995a09e0
EB		 2268 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
2269 (modules '((guix build utils)))
2270 (snippet
2271 ;; Replace the non-free implementation of MC64 with a stub adapted
2272 ;; from Debian
2273 '(begin
2274 (use-modules (ice-9 regex)
2275 (ice-9 rdelim))
2276 (call-with-output-file "SRC/mc64ad.c"
2277 (lambda (port)
2278 (display "
2279#include <stdio.h>
2280#include <stdlib.h>
2281void mc64id_(int *a) {
2282 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2283 abort ();
2284}
2285void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2286 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2287 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2288 abort ();
2289}\n" port)))
2290 ;; Remove the corresponding license verbiage. MC64 license follows
2291 ;; a "------" line separator.
2292 (with-atomic-file-replacement "License.txt"
2293 (let ((rx (make-regexp "-{8}")))
2294 (lambda (in out)
2295 (let loop ()
2296 (let ((line (read-line in 'concat)))
2297 (unless (regexp-exec rx line)
2298 (display line out)
6cbee49d
MW		 2299 (loop))))
2300 #t)))))))
995a09e0 2301 (build-system cmake-build-system)
183e44ae
EB		 2302 (native-inputs
2303 `(("tcsh" ,tcsh)))
2304 (inputs
995a09e0 2305 `(("blas" ,openblas)
19afbea1 2306 ("gfortran" ,gfortran)))
183e44ae 2307 (arguments
995a09e0
EB		 2308 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2309 "-DTPL_BLAS_LIBRARIES=openblas"
677bc34d 2310 "-DBUILD_SHARED_LIBS:BOOL=YES")))
183e44ae
EB		 2311 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
2312 (synopsis "Supernodal direct solver for sparse linear systems")
2313 (description
2314 "SuperLU is a general purpose library for the direct solution of large,
2315sparse, nonsymmetric systems of linear equations on high performance machines.
2316The library is written in C and is callable from either C or Fortran. The
2317library routines perform an LU decomposition with partial pivoting and
2318triangular system solves through forward and back substitution. The library
2319also provides threshold-based ILU factorization preconditioners.")
995a09e0
EB		 2320 (license (list license:bsd-3
2321 license:gpl2+ ;EXAMPLE/*fgmr.c
2322 (license:fsf-free "file://SRC/colamd.h")))))
f8ed036a 2323
a54aefea
EB		 2324(define-public superlu-dist
2325 (package
2326 (name "superlu-dist")
0921eff2 2327 (version "5.3.0")
a54aefea
EB		 2328 (source
2329 (origin
2330 (method url-fetch)
2331 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2332 "superlu_dist_" version ".tar.gz"))
2333 (sha256
0921eff2
LC		 2334 (base32 "0ja5ihqivkda1wd58y4lmzvmwssm9g91f70c5q0fzwhng6580h6y"))
2335 (modules '((guix build utils)))
29080870
EB		 2336 (snippet
2337 ;; Replace the non-free implementation of MC64 with a stub
2338 '(begin
2339 (use-modules (ice-9 regex)
2340 (ice-9 rdelim))
0921eff2 2341 (call-with-output-file "SRC/mc64ad_dist.c"
29080870
EB		 2342 (lambda (port)
2343 (display "
2344#include <stdio.h>
2345#include <stdlib.h>
0921eff2 2346void mc64id_dist(int *a) {
29080870
EB		 2347 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2348 abort ();
2349}
0921eff2 2350void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
29080870
EB		 2351 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2352 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2353 abort ();
2354}\n" port)))
29080870
EB		 2355 (substitute* "SRC/util.c" ;adjust default algorithm
2356 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
6cbee49d
MW		 2357 "RowPerm = NOROWPERM"))
2358 #t))
fc1adab1 2359 (patches (search-patches "superlu-dist-scotchmetis.patch"))))
a54aefea
EB		 2360 (build-system gnu-build-system)
2361 (native-inputs
2362 `(("tcsh" ,tcsh)))
2363 (inputs
19afbea1 2364 `(("gfortran" ,gfortran)))
a54aefea
EB		 2365 (propagated-inputs
2366 `(("openmpi" ,openmpi) ;headers include MPI heades
2367 ("lapack" ,lapack) ;required to link with output library
2368 ("pt-scotch" ,pt-scotch))) ;same
2369 (arguments
2370 `(#:parallel-build? #f ;race conditions using ar
2371 #:phases
dc1d3cde
KK		 2372 (modify-phases %standard-phases
2373 (replace 'configure
2374 (lambda* (#:key inputs outputs #:allow-other-keys)
2375 (call-with-output-file "make.inc"
2376 (lambda (port)
2377 (format port "
a54aefea
EB		 2378PLAT =
2379DSuperLUroot = ~a
2380DSUPERLULIB = ~a/lib/libsuperlu_dist.a
2381BLASDEF = -DUSE_VENDOR_BLAS
2382BLASLIB = -L~a/lib -lblas
2383PARMETISLIB = -L~a/lib \
2384 -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
2385 -lscotch -lscotcherr -lscotcherrexit
2386METISLIB = -L~:*~a/lib \
2387 -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
2388LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
2389ARCH = ar
2390ARCHFLAGS = cr
2391RANLIB = ranlib
2392CC = mpicc
2393PIC = -fPIC
2394CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC)
2395NOOPTS = -O0 -g $(PIC)
2396FORTRAN = mpifort
2397FFLAGS = -O2 -g $(PIC)
2398LOADER = $(CC)
2399CDEFS = -DAdd_"
dc1d3cde
KK		 2400 (getcwd)
2401 (assoc-ref outputs "out")
2402 (assoc-ref inputs "lapack")
2403 (assoc-ref inputs "pt-scotch"))))
2404 #t))
2405 (add-after 'unpack 'remove-broken-symlinks
2406 (lambda _
2407 (for-each delete-file
2408 (find-files "MAKE_INC" "\\.#make\\..*"))
2409 #t))
2410 (add-before 'build 'create-install-directories
2411 (lambda* (#:key outputs #:allow-other-keys)
2412 (for-each
2413 (lambda (dir)
2414 (mkdir-p (string-append (assoc-ref outputs "out")
2415 "/" dir)))
2416 '("lib" "include"))
2417 #t))
bbe46a4a
EB		 2418 (add-before 'check 'mpi-setup
2419 ,%openmpi-setup)
dc1d3cde 2420 (replace 'check
a54aefea
EB		 2421 (lambda _
2422 (with-directory-excursion "EXAMPLE"
e02a9975
TGR		 2423 (invoke "mpirun" "-n" "2"
2424 "./pddrive" "-r" "1" "-c" "2" "g20.rua")
2425 (invoke "mpirun" "-n" "2"
2426 "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))
2427 #t))
dc1d3cde
KK		 2428 (replace 'install
2429 (lambda* (#:key outputs #:allow-other-keys)
2430 ;; Library is placed in lib during the build phase. Copy over
2431 ;; headers to include.
2432 (let* ((out (assoc-ref outputs "out"))
2433 (incdir (string-append out "/include")))
2434 (for-each (lambda (file)
2435 (let ((base (basename file)))
2436 (format #t "installing `~a' to `~a'~%"
2437 base incdir)
2438 (copy-file file
2439 (string-append incdir "/" base))))
2440 (find-files "SRC" ".*\\.h$")))
2441 #t)))))
a54aefea
EB		 2442 (home-page (package-home-page superlu))
2443 (synopsis "Parallel supernodal direct solver")
2444 (description
2445 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2446It is targeted for distributed memory parallel machines. SuperLU_DIST is
2447implemented in ANSI C, and MPI for communications.")
2448 (license license:bsd-3)))
2449
f8ed036a
EB		 2450(define-public scotch
2451 (package
2452 (name "scotch")
d98e9009 2453 (version "6.0.5a")
f8ed036a
EB		 2454 (source
2455 (origin
2456 (method url-fetch)
1dc31097
TGR		 2457 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
2458 "latestfile/298/scotch_" version ".tar.gz"))
f8ed036a 2459 (sha256
d98e9009 2460 (base32 "0vsmgjz8qv80di3ljmc7hbdsizxxxwy2b9rgd2fl1mdc6dgbj8av"))
fc1adab1 2461 (patches (search-patches "scotch-test-threading.patch"
d98e9009
EB		 2462 "scotch-build-parallelism.patch"
2463 "scotch-graph-induce-type-64.patch"
2464 "scotch-graph-diam-64.patch"))))
f8ed036a
EB		 2465 (build-system gnu-build-system)
2466 (inputs
2467 `(("zlib" ,zlib)
5e54f4ad 2468 ("flex" ,flex)
f8ed036a
EB		 2469 ("bison" ,bison)))
2470 (arguments
2471 `(#:phases
d6602ee9
EB		 2472 (modify-phases %standard-phases
2473 (add-after
2474 'unpack 'chdir-to-src
d67a7e9e 2475 (lambda _ (chdir "src") #t))
d6602ee9
EB		 2476 (replace
2477 'configure
2478 (lambda _
2479 (call-with-output-file "Makefile.inc"
2480 (lambda (port)
2481 (format port "
f8ed036a
EB		 2482EXE =
2483LIB = .a
2484OBJ = .o
2485MAKE = make
2486AR = ar
2487ARFLAGS = -ruv
cf0ec6c4 2488CAT = cat
f8ed036a
EB		 2489CCS = gcc
2490CCP = mpicc
2491CCD = gcc
2492CPPFLAGS =~{ -D~a~}
6c798540 2493CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
f8ed036a
EB		 2494LDFLAGS = -lz -lm -lrt -lpthread
2495CP = cp
2496LEX = flex -Pscotchyy -olex.yy.c
2497LN = ln
2498MKDIR = mkdir
2499MV = mv
2500RANLIB = ranlib
2501YACC = bison -pscotchyy -y -b y
2502"
d6602ee9
EB		 2503 '("COMMON_FILE_COMPRESS_GZ"
2504 "COMMON_PTHREAD"
2505 "COMMON_RANDOM_FIXED_SEED"
26599d69 2506 "INTSIZE64" ;use 'long' instead of 'int'
cf0ec6c4
EB		 2507 ;; Prevents symbolc clashes with libesmumps
2508 "SCOTCH_RENAME"
d6602ee9
EB		 2509 ;; XXX: Causes invalid frees in superlu-dist tests
2510 ;; "SCOTCH_PTHREAD"
2511 ;; "SCOTCH_PTHREAD_NUMBER=2"
d67a7e9e
TGR		 2512 "restrict=__restrict"))))
2513 #t))
bbe46a4a 2514 (add-after 'build 'build-esmumps
cf0ec6c4 2515 (lambda _
d67a7e9e
TGR		 2516 (invoke "make"
2517 (format #f "-j~a" (parallel-job-count))
2518 "esmumps")))
d6602ee9 2519 (replace
f8ed036a
EB		 2520 'install
2521 (lambda* (#:key outputs #:allow-other-keys)
2522 (let ((out (assoc-ref outputs "out")))
2523 (mkdir out)
d67a7e9e
TGR		 2524 (invoke "make"
2525 (string-append "prefix=" out)
2526 "install")
cf0ec6c4
EB		 2527 ;; esmumps files are not installed with the above
2528 (for-each (lambda (f)
2529 (copy-file f (string-append out "/include/" f)))
2530 (find-files "../include" ".*esmumps.h$"))
2531 (for-each (lambda (f)
2532 (copy-file f (string-append out "/lib/" f)))
d67a7e9e
TGR		 2533 (find-files "../lib" "^lib.*esmumps.*"))
2534 #t))))))
f8ed036a
EB		 2535 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
2536 (synopsis "Programs and libraries for graph algorithms")
2537 (description "SCOTCH is a set of programs and libraries which implement
2538the static mapping and sparse matrix reordering algorithms developed within
2539the SCOTCH project. Its purpose is to apply graph theory, with a divide and
2540conquer approach, to scientific computing problems such as graph and mesh
2541partitioning, static mapping, and sparse matrix ordering, in application
2542domains ranging from structural mechanics to operating systems or
2543bio-chemistry.")
2544 ;; See LICENSE_en.txt
2545 (license license:cecill-c)))
6acb4adb 2546
1c39f3b8
PG		 2547(define-public scotch32
2548 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2549 ;; some applications.
2550 (package (inherit scotch)
2551 (name "scotch32")
2552 (arguments
2553 (substitute-keyword-arguments (package-arguments scotch)
2554 ((#:phases scotch-phases)
2555 `(modify-phases ,scotch-phases
2556 (replace
2557 'configure
2558 (lambda _
2559 (call-with-output-file "Makefile.inc"
2560 (lambda (port)
2561 (format port "
2562EXE =
2563LIB = .a
2564OBJ = .o
2565MAKE = make
2566AR = ar
2567ARFLAGS = -ruv
2568CAT = cat
2569CCS = gcc
2570CCP = mpicc
2571CCD = gcc
2572CPPFLAGS =~{ -D~a~}
2573CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2574LDFLAGS = -lz -lm -lrt -lpthread
2575CP = cp
2576LEX = flex -Pscotchyy -olex.yy.c
2577LN = ln
2578MKDIR = mkdir
2579MV = mv
2580RANLIB = ranlib
2581YACC = bison -pscotchyy -y -b y
2582"
2583 '("COMMON_FILE_COMPRESS_GZ"
2584 "COMMON_PTHREAD"
2585 "COMMON_RANDOM_FIXED_SEED"
2586 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
2587 ;; Prevents symbolc clashes with libesmumps
2588 "SCOTCH_RENAME"
2589 ;; XXX: Causes invalid frees in superlu-dist tests
2590 ;; "SCOTCH_PTHREAD"
2591 ;; "SCOTCH_PTHREAD_NUMBER=2"
2592 "restrict=__restrict"))))))))))
2593 (synopsis
2594 "Programs and libraries for graph algorithms (32-bit integers)")))
2595
6acb4adb
EB		 2596(define-public pt-scotch
2597 (package (inherit scotch)
2598 (name "pt-scotch")
2599 (propagated-inputs
2600 `(("openmpi" ,openmpi))) ;Headers include MPI headers
2601 (arguments
2602 (substitute-keyword-arguments (package-arguments scotch)
2603 ((#:phases scotch-phases)
d6602ee9
EB		 2604 `(modify-phases ,scotch-phases
2605 (replace
2606 'build
d6602ee9 2607 (lambda _
c491f7f8
LC		 2608 (invoke "make" (format #f "-j~a" (parallel-job-count))
2609 "ptscotch" "ptesmumps")
2610
2611 ;; Install the serial metis compatibility library
2612 (invoke "make" "-C" "libscotchmetis" "install")))
2613 (add-before 'check 'mpi-setup
2614 ,%openmpi-setup)
2615 (replace 'check
2616 (lambda _
2617 (invoke "make" "ptcheck")))))))
6acb4adb 2618 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
5698b8b8 2619
1c25a52c
PG		 2620(define-public pt-scotch32
2621 (package (inherit scotch32)
2622 (name "pt-scotch32")
2623 (propagated-inputs
2624 `(("openmpi" ,openmpi))) ;headers include MPI headers
2625 (arguments
c4d4a779
PG		 2626 (substitute-keyword-arguments (package-arguments scotch32)
2627 ((#:phases scotch32-phases)
2628 `(modify-phases ,scotch32-phases
1c25a52c
PG		 2629 (replace 'build
2630 (lambda _
c491f7f8
LC		 2631 (invoke "make" (format #f "-j~a" (parallel-job-count))
2632 "ptscotch" "ptesmumps")
2633 ;; Install the serial metis compatibility library
2634 (invoke "make" "-C" "libscotchmetis" "install")))
2635 (add-before 'check 'mpi-setup
2636 ,%openmpi-setup)
1c25a52c
PG		 2637 (replace 'check
2638 (lambda _
c491f7f8 2639 (invoke "make" "ptcheck")))))))
1c25a52c
PG		 2640 (synopsis
2641 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2642
aa75ad00
EB		 2643(define-public metis
2644 (package
2645 (name "metis")
2646 (version "5.1.0")
2647 (source
2648 (origin
2649 (method url-fetch)
2650 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2651 "metis-" version ".tar.gz"))
2652 (sha256
2653 (base32
2654 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2655 (build-system cmake-build-system)
2656 (inputs
2657 `(("blas" ,openblas)))
2658 (arguments
2659 `(#:tests? #f ;no tests
2660 #:configure-flags `("-DSHARED=ON"
2661 ,(string-append "-DGKLIB_PATH=" (getcwd)
2662 "/metis-" ,version "/GKlib"))))
2663 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2664 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2665 (description
2666 "METIS is a set of serial programs for partitioning graphs, partitioning
2667finite element meshes, and producing fill-reducing orderings for sparse
2668matrices. The algorithms implemented in METIS are based on the multilevel
2669recursive-bisection, multilevel k-way, and multi-constraint partitioning
2670schemes.")
2671 (license license:asl2.0))) ;As of version 5.0.3
2672
700ff222
EB		 2673(define-public p4est
2674 (package
2675 (name "p4est")
4150da63 2676 (version "2.0")
700ff222
EB		 2677 (source
2678 (origin
2679 (method url-fetch)
2680 (uri (string-append "http://p4est.github.io/release/p4est-"
2681 version ".tar.gz"))
2682 (sha256
2683 (base32
4150da63 2684 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
700ff222
EB		 2685 (build-system gnu-build-system)
2686 (inputs
2687 `(("fortran" ,gfortran)
2688 ("blas" ,openblas)
2689 ("lapack" ,lapack)
2690 ("zlib" ,zlib)))
2691 (arguments
2692 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2693 (assoc-ref %build-inputs "blas")
2694 " -lopenblas")
2695 ,(string-append "LAPACK_LIBS=-L"
2696 (assoc-ref %build-inputs "lapack")
6df2a50a
LC		 2697 " -llapack"))
2698 #:phases (modify-phases %standard-phases
bbe46a4a
EB		 2699 (add-before 'check 'mpi-setup
2700 ,%openmpi-setup))))
700ff222
EB		 2701 (home-page "http://www.p4est.org")
2702 (synopsis "Adaptive mesh refinement on forests of octrees")
2703 (description
2704 "The p4est software library enables the dynamic management of a
2705collection of adaptive octrees, conveniently called a forest of octrees.
2706p4est is designed to work in parallel and scales to hundreds of thousands of
2707processor cores.")
2708 (license license:gpl2+)))
2709
2710(define-public p4est-openmpi
2711 (package (inherit p4est)
2712 (name "p4est-openmpi")
2713 (inputs
2714 `(("mpi" ,openmpi)
2715 ,@(package-inputs p4est)))
2716 (arguments
2717 (substitute-keyword-arguments (package-arguments p4est)
2718 ((#:configure-flags cf)
2719 ``("--enable-mpi" ,@,cf))))
2720 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2721
5698b8b8
JD		 2722(define-public gsegrafix
2723 (package
2724 (name "gsegrafix")
2725 (version "1.0.6")
2726 (source
2727 (origin
2728 (method url-fetch)
2729 (uri (string-append "mirror://gnu/" name "/" name "-"
2730 version ".tar.gz"))
2731 (sha256
2732 (base32
2733 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2734 (build-system gnu-build-system)
2735 (arguments
2736 `(#:configure-flags '("LDFLAGS=-lm")))
2737 (inputs
2738 `(("libgnomecanvas" ,libgnomecanvas)
2739 ("libbonoboui" ,libbonoboui)
2740 ("libgnomeui" ,libgnomeui)
2741 ("libgnomeprintui" ,libgnomeprintui)
2742 ("popt" ,popt)))
2743 (native-inputs
2744 `(("pkg-config" ,pkg-config)))
6fd52309 2745 (home-page "https://www.gnu.org/software/gsegrafix/")
5698b8b8
JD		 2746 (synopsis "GNOME application to create scientific and engineering plots")
2747 (description "GSEGrafix is an application which produces high-quality graphical
2748plots for science and engineering. Plots are specified via simple ASCII
2749parameter files and data files and are presented in an anti-aliased GNOME
2750canvas. The program supports rectangular two-dimensional plots, histograms,
2751polar-axis plots and three-dimensional plots. Plots can be printed or saved
2752to BMP, JPEG or PNG image formats.")
2753 (license license:gpl3+)))
8731e527
JD		 2754
2755(define-public maxima
2756 (package
2757 (name "maxima")
a5d474d7 2758 (version "5.42.1")
8731e527
JD		 2759 (source
2760 (origin
2761 (method url-fetch)
2762 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2763 version "-source/" name "-" version ".tar.gz"))
2764 (sha256
2765 (base32
a5d474d7 2766 "1ka0xf70a55ndgmyrq7p5xxbd78pq7bfkqhgxsivaqdw6gn5lmcg"))
fc1adab1 2767 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
8731e527 2768 (build-system gnu-build-system)
df354a77 2769 (inputs
6b2eafaa 2770 `(("gcl" ,gcl)
df354a77 2771 ("gnuplot" ,gnuplot) ;for plots
f36afe4d 2772 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
df354a77
FB		 2773 (native-inputs
2774 `(("texinfo" ,texinfo)
ccbc5758
KK		 2775 ("perl" ,perl)
2776 ("python" ,python)))
8731e527 2777 (arguments
df354a77
FB		 2778 `(#:configure-flags
2779 (list "--enable-gcl"
2780 (string-append "--with-posix-shell="
2781 (assoc-ref %build-inputs "bash")
2782 "/bin/sh")
2783 (string-append "--with-wish="
2784 (assoc-ref %build-inputs "tk")
2785 "/bin/wish"
2786 (let ((v ,(package-version tk)))
2787 (string-take v (string-index-right v #\.)))))
df354a77 2788 ;; By default Maxima attempts to write temporary files to
77af7b24
MW		 2789 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2790 ;; Work around that.
df354a77 2791 #:make-flags (list "TMPDIR=/tmp")
0093b126
KK		 2792 #:phases
2793 (modify-phases %standard-phases
2794 (add-before 'check 'pre-check
2795 (lambda _
2796 (chmod "src/maxima" #o555)
2797 #t))
1472d19a
KK		 2798 (replace 'check
2799 (lambda _
2800 ;; This is derived from the testing code in the "debian/rules" file
2801 ;; of Debian's Maxima package.
2802 ;; If Maxima can successfully run this, the binary to be installed
2803 ;; should be fine.
2804 (zero?
2805 (system
2806 (string-append "./maxima-local "
2807 "--lisp=gcl "
2808 "--batch-string=\"run_testsuite();\" "
2809 "| grep -q \"No unexpected errors found\"")))))
0093b126
KK		 2810 ;; Make sure the doc and emacs files are found in the
2811 ;; standard location. Also configure maxima to find gnuplot
2812 ;; without having it on the PATH.
2813 (add-after 'install 'post-install
2814 (lambda* (#:key outputs inputs #:allow-other-keys)
2815 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2816 (out (assoc-ref outputs "out"))
2817 (datadir (string-append out "/share/maxima/" ,version))
2818 (binutils (string-append (assoc-ref inputs "binutils")
2819 "/bin")))
2820 (with-directory-excursion out
2821 (mkdir-p "share/emacs")
2822 (mkdir-p "share/doc")
2823 (symlink
2824 (string-append datadir "/emacs/")
2825 (string-append out "/share/emacs/site-lisp"))
2826 (symlink
2827 (string-append datadir "/doc/")
2828 (string-append out "/share/doc/maxima"))
2829 (with-atomic-file-replacement
2830 (string-append datadir "/share/maxima-init.lisp")
2831 (lambda (in out)
2832 (format out "~a ~s~a~%"
2833 "(setf $gnuplot_command "
2834 (string-append gnuplot "/bin/gnuplot") ")")
2835 (dump-port in out))))
2836 ;; Ensure that Maxima will have access to the GNU binutils
2837 ;; components at runtime.
2838 (wrap-program (string-append out "/bin/maxima")
2839 `("PATH" prefix (,binutils))))
2840 #t)))))
8731e527
JD		 2841 (home-page "http://maxima.sourceforge.net")
2842 (synopsis "Numeric and symbolic expression manipulation")
2843 (description "Maxima is a system for the manipulation of symbolic and
2844numerical expressions. It yields high precision numeric results by using
2845exact fractions, arbitrary precision integers, and variable precision floating
e881752c 2846point numbers.")
8731e527
JD		 2847 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2848 ;; Others simply say "GNU General Public License" without stating a
2849 ;; version (which implicitly means gpl1+).
2850 ;; At least one file (src/maxima.asd) says "version 2."
2851 ;; GPLv2 only is therefore the smallest subset.
f36afe4d 2852 (license license:gpl2)))
ec322be2 2853
9aafbc0c
MW		 2854(define-public wxmaxima
2855 (package
2856 (name "wxmaxima")
c93b77ad 2857 (version "18.11.4")
9aafbc0c
MW		 2858 (source
2859 (origin
c93b77ad
KK		 2860 (method git-fetch)
2861 (uri (git-reference
2862 (url "https://github.com/wxMaxima-developers/wxmaxima.git")
2863 (commit (string-append "Version-" version))))
2864 (file-name (git-file-name name version))
9aafbc0c
MW		 2865 (sha256
2866 (base32
c93b77ad 2867 "1sz8n9v23q442l7yjj67pjh0dk78rl4cbcc3j8m1bm88anlfxl9r"))))
0181df53 2868 (build-system cmake-build-system)
5143517c 2869 (native-inputs
0181df53 2870 `(("gettext" ,gettext-minimal)))
9aafbc0c
MW		 2871 (inputs
2872 `(("wxwidgets" ,wxwidgets)
de477809
SB		 2873 ("maxima" ,maxima)
2874 ;; Runtime support.
2875 ("adwaita-icon-theme" ,adwaita-icon-theme)
2876 ("gtk+" ,gtk+)
2877 ("shared-mime-info" ,shared-mime-info)))
9aafbc0c 2878 (arguments
0181df53
KK		 2879 `(#:tests? #f ; no check target
2880 #:phases
ac2ddcc6 2881 (modify-phases %standard-phases
ac2ddcc6
KK		 2882 (add-after 'install 'wrap-program
2883 (lambda* (#:key inputs outputs #:allow-other-keys)
2884 (wrap-program (string-append (assoc-ref outputs "out")
2885 "/bin/wxmaxima")
2886 `("PATH" ":" prefix
2887 (,(string-append (assoc-ref inputs "maxima")
2888 "/bin")))
2889 ;; For GtkFileChooserDialog.
2890 `("GSETTINGS_SCHEMA_DIR" =
2891 (,(string-append (assoc-ref inputs "gtk+")
2892 "/share/glib-2.0/schemas")))
2893 `("XDG_DATA_DIRS" ":" prefix
2894 (;; Needed by gdk-pixbuf to know supported icon formats.
2895 ,(string-append
2896 (assoc-ref inputs "shared-mime-info") "/share")
2897 ;; The default icon theme of GTK+.
2898 ,(string-append
2899 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
2900 #t)))))
9aafbc0c
MW		 2901 (home-page "https://andrejv.github.io/wxmaxima/")
2902 (synopsis "Graphical user interface for the Maxima computer algebra system")
2903 (description
2904 "wxMaxima is a graphical user interface for the Maxima computer algebra
2905system. It eases the use of Maxima by making most of its commands available
2906through a menu system and by providing input dialogs for commands that require
2907more than one argument. It also implements its own display engine that
2908outputs mathematical symbols directly instead of depicting them with ASCII
2909characters.
2910
2911wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
2912text and mathematical calculations to create documents, exporting of input and
2913output to TeX, and a browser for Maxima's manual including command index and
2914full text searching.")
2915 (license license:gpl2+)))
2916
b15e47f9
RW		 2917(define-public armadillo
2918 (package
2919 (name "armadillo")
f133e244 2920 (version "9.100.5")
b15e47f9
RW		 2921 (source (origin
2922 (method url-fetch)
2923 (uri (string-append "mirror://sourceforge/arma/armadillo-"
7397cd9e 2924 version ".tar.xz"))
b15e47f9
RW		 2925 (sha256
2926 (base32
f133e244 2927 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
b15e47f9 2928 (build-system cmake-build-system)
e405c0bc 2929 (arguments `(#:tests? #f)) ; no test target
b15e47f9
RW		 2930 (inputs
2931 `(("openblas" ,openblas)
2932 ("lapack" ,lapack)
2933 ("arpack" ,arpack-ng)))
2934 (home-page "http://arma.sourceforge.net/")
2935 (synopsis "C++ linear algebra library")
2936 (description
2937 "Armadillo is a C++ linear algebra library, aiming towards a good balance
2938between speed and ease of use. It is useful for algorithm development
2939directly in C++, or quick conversion of research code into production
2940environments. It can be used for machine learning, pattern recognition,
2941signal processing, bioinformatics, statistics, econometrics, etc. The library
2942provides efficient classes for vectors, matrices and cubes, as well as 150+
2943associated functions (eg. contiguous and non-contiguous submatrix views).")
fe418cc5 2944 (license license:asl2.0)))
b15e47f9 2945
279663ef 2946(define-public muparser
d7cff656
LF		 2947 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2948 ;; different hash. In order to make `guix package --upgrade` work correctly,
2949 ;; we set a Guix packaging revision.
2950 ;; When the next version of muparser is released, we can remove
2951 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2952 (let ((upstream-version "2.2.5")
2953 (revision "2"))
2954 (package
2955 (name "muparser")
2956 (version (string-append upstream-version "-" revision))
2957 (source
2958 (origin
2959 (method url-fetch)
2960 (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
2961 upstream-version ".tar.gz"))
2962 (file-name (string-append name "-" version ".tar.gz"))
2963 (sha256
2964 (base32
2965 "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
2966 (build-system gnu-build-system)
2967 (arguments
2968 `(#:configure-flags '("--enable-samples=no")
2969 #:tests? #f)) ;no "check" target
2970 (home-page "http://muparser.beltoforion.de/")
2971 (synopsis "Fast parser library for mathematical expressions")
2972 (description
2973 "muParser is an extensible high performance math parser library. It is
2974based on transforming an expression into a bytecode and precalculating constant
2975parts of it.")
2976 (license license:expat))))
279663ef 2977
e73b49fb
RW		 2978(define-public openblas
2979 (package
2980 (name "openblas")
9adaf1f4 2981 (version "0.3.3")
e73b49fb
RW		 2982 (source
2983 (origin
2984 (method url-fetch)
a617fd55
MB		 2985 (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
2986 version "%20version.tar.gz"))
e73b49fb
RW		 2987 (file-name (string-append name "-" version ".tar.gz"))
2988 (sha256
2989 (base32
9adaf1f4 2990 "0cvlixnpc3cdvvn3f30phfvsgnqljqix6wn72ps9rj7xdhvw06jg"))))
e73b49fb
RW		 2991 (build-system gnu-build-system)
2992 (arguments
5789566a 2993 `(#:test-target "test"
bd0b4379
RW		 2994 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
2995 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2996 ;; we need to disable substitutions.
71923a91
AE		 2997 #:substitutable?
2998 ,(let ((system (or (%current-target-system) (%current-system))))
2999 (or (string-prefix? "x86_64" system)
bd0b4379 3000 (string-prefix? "i686" system)
83a34647
EF		 3001 (string-prefix? "mips" system)
3002 (string-prefix? "aarch64" system)))
e73b49fb
RW		 3003 #:make-flags
3004 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
3005 "SHELL=bash"
af5b817e
RW		 3006 ;; Build the library for all supported CPUs. This allows
3007 ;; switching CPU targets at runtime with the environment variable
3008 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
71923a91
AE		 3009 ;; Unfortunately, this is not supported on non-x86 architectures,
3010 ;; where it leads to failed builds.
3011 ,@(let ((system (or (%current-target-system) (%current-system))))
8a637e79
RW		 3012 (cond
3013 ((or (string-prefix? "x86_64" system)
71923a91 3014 (string-prefix? "i686" system))
8a637e79
RW		 3015 '("DYNAMIC_ARCH=1"))
3016 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
3017 ;; two available MIPS targets special extended instructions
3018 ;; for Loongson cores are used.
3019 ((string-prefix? "mips" system)
3020 '("TARGET=SICORTEX"))
83a34647
EF		 3021 ;; On aarch64 force the generic 'armv8-a' target
3022 ((string-prefix? "aarch64" system)
3023 '("TARGET=ARMV8"))
8a637e79 3024 (else '()))))
e73b49fb 3025 ;; no configure script
493937ae
DL		 3026 #:phases
3027 (modify-phases %standard-phases
3028 (delete 'configure)
3029 (add-before 'build 'set-extralib
3030 (lambda* (#:key inputs #:allow-other-keys)
3031 ;; Get libgfortran found when building in utest.
3032 (setenv "FEXTRALIB"
3033 (string-append "-L" (assoc-ref inputs "fortran-lib")
3034 "/lib"))
3035 #t)))))
e73b49fb 3036 (inputs
493937ae 3037 `(("fortran-lib" ,gfortran "lib")))
e73b49fb
RW		 3038 (native-inputs
3039 `(("cunit" ,cunit)
493937ae 3040 ("fortran" ,gfortran)
e73b49fb
RW		 3041 ("perl" ,perl)))
3042 (home-page "http://www.openblas.net/")
3043 (synopsis "Optimized BLAS library based on GotoBLAS")
3044 (description
3045 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
3046 (license license:bsd-3)))
3047
daa6036f
EB		 3048(define-public openblas-ilp64
3049 (package (inherit openblas)
3050 (name "openblas-ilp64")
3051 (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
3052 (arguments
3053 (substitute-keyword-arguments (package-arguments openblas)
3054 ((#:make-flags flags '())
3055 `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
3056 ,flags))))
3057 (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
3058 (license license:bsd-3)))
3059
5a7deb11
LC		 3060(define* (make-blis implementation #:optional substitutable?)
3061 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
3062source tree for a list of implementations.)
3063
3064SUBSTITUTABLE? determines whether the package is made available as a
3065substitute.
3066
3067Currently the specialization must be selected at configure-time, but work is
3068underway to allow BLIS to select the right optimized kernels at run time:
3069<https://github.com/flame/blis/issues/129>."
3070 (package
3071 (name (if (string=? implementation "reference")
3072 "blis"
3073 (string-append "blis-" implementation)))
3074 (version "0.2.2")
3075 (home-page "https://github.com/flame/blis")
3076 (source (origin
3077 (method git-fetch)
3078 (uri (git-reference (url home-page) (commit version)))
3079 (sha256
3080 (base32
3081 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
3082 (file-name (git-file-name "blis" version))))
3083 (build-system gnu-build-system)
3084 (arguments
3085 `(#:test-target "test"
3086
3087 #:substitutable? ,substitutable?
3088
3089 #:phases (modify-phases %standard-phases
3090 (replace 'configure
3091 (lambda* (#:key outputs #:allow-other-keys)
3092 ;; This is a home-made 'configure' script.
3093 (let ((out (assoc-ref outputs "out")))
3094 (zero? (system* "./configure" "-p" out
3095 "-d" "opt"
3096 "--disable-static"
3097 "--enable-shared"
3098 "--enable-threading=openmp"
3099
3100 ,implementation)))))
3101 (add-before 'check 'show-test-output
3102 (lambda _
3103 ;; By default "make check" is silent. Make it verbose.
3104 (system "tail -F output.testsuite &")
3105 #t)))))
3106 (synopsis "High-performance basic linear algebra (BLAS) routines")
3107 (description
3108 "BLIS is a portable software framework for instantiating high-performance
3109BLAS-like dense linear algebra libraries. The framework was designed to
3110isolate essential kernels of computation that, when optimized, immediately
3111enable optimized implementations of most of its commonly used and
3112computationally intensive operations. While BLIS exports a new BLAS-like API,
3113it also includes a BLAS compatibility layer which gives application developers
3114access to BLIS implementations via traditional BLAS routine calls.")
3115 (license license:bsd-3)))
3116
3117(define-public blis
3118 ;; This is the "reference" implementation, which is the non-optimized but
3119 ;; portable variant (no assembly).
3120 (make-blis "reference" #t))
3121
3122(define ignorance blis)
3123
3124(define-syntax-rule (blis/x86_64 processor)
3125 "Expand to a package specialized for PROCESSOR."
3126 (package
3127 (inherit (make-blis processor))
3128 (supported-systems '("x86_64-linux"))))
3129
3130(define-public blis-sandybridge
3131 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
3132 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
3133 (blis/x86_64 "sandybridge"))
3134
3135(define-public blis-haswell
3136 ;; BLIS specialized for Haswell processors (launched 2013):
3137 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
3138 (blis/x86_64 "haswell"))
3139
3140(define-public blis-knl
3141 ;; BLIS specialized for Knights Landing processor (launched 2016):
3142 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
3143 (blis/x86_64 "knl"))
3144
3145
e1605e36
RW		 3146(define-public openlibm
3147 (package
3148 (name "openlibm")
48d7ac17 3149 (version "0.6.0")
e1605e36
RW		 3150 (source
3151 (origin
3152 (method url-fetch)
3153 (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
3154 version ".tar.gz"))
3155 (file-name (string-append name "-" version ".tar.gz"))
3156 (sha256
3157 (base32
48d7ac17 3158 "0a5fpm8nra5ldhjk0cqd2rx1qh32wiarkxmcqcm5xl8z7l4kjm6l"))))
e1605e36
RW		 3159 (build-system gnu-build-system)
3160 (arguments
3161 `(#:make-flags
3162 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3163 #:phases
3164 ;; no configure script
dc1d3cde 3165 (modify-phases %standard-phases (delete 'configure))
e1605e36
RW		 3166 #:tests? #f)) ;the tests are part of the default target
3167 (home-page "http://openlibm.org/")
3168 (synopsis "Portable C mathematical library (libm)")
3169 (description
3170 "OpenLibm is an effort to have a high quality, portable, standalone C
3171mathematical library (libm). It can be used standalone in applications and
3172programming language implementations. The project was born out of a need to
e881752c 3173have a good libm for the Julia programming language that worked consistently
e1605e36
RW		 3174across compilers and operating systems, and in 32-bit and 64-bit
3175environments.")
538c0e3b
EF		 3176 ;; Each architecture has its own make target, and there is none for mips.
3177 (supported-systems (delete "mips64el-linux" %supported-systems))
e1605e36
RW		 3178 ;; See LICENSE.md for details.
3179 (license (list license:expat
3180 license:isc
3181 license:bsd-2
3182 license:public-domain
3183 license:lgpl2.1+))))
3184
e62be58f
RW		 3185(define-public openspecfun
3186 (package
3187 (name "openspecfun")
59cd0ba4 3188 (version "0.5.3")
e62be58f
RW		 3189 (source
3190 (origin
3191 (method url-fetch)
3192 (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
3193 version ".tar.gz"))
3194 (file-name (string-append name "-" version ".tar.gz"))
3195 (sha256
3196 (base32
59cd0ba4 3197 "1rs1bv8jq751fv9vq79890wqf9xlbjc7lvz3ighzyfczbyjcf18m"))))
e62be58f
RW		 3198 (build-system gnu-build-system)
3199 (arguments
59cd0ba4 3200 '(#:tests? #f ; no "check" target
e62be58f
RW		 3201 #:make-flags
3202 (list (string-append "prefix=" (assoc-ref %outputs "out")))
59cd0ba4
TGR		 3203 #:phases
3204 (modify-phases %standard-phases
3205 (delete 'configure)))) ; no configure script
e62be58f 3206 (inputs
19afbea1 3207 `(("fortran" ,gfortran)))
e62be58f
RW		 3208 (home-page "https://github.com/JuliaLang/openspecfun")
3209 (synopsis "Collection of special mathematical functions")
3210 (description
3211 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
3212portable package for Bessel Functions of a Complex Argument and Nonnegative
3213Order; it contains subroutines for computing Bessel functions and Airy
3214functions. Faddeeva allows computing the various error functions of arbitrary
3215complex arguments (Faddeeva function, error function, complementary error
3216function, scaled complementary error function, imaginary error function, and
3217Dawson function); given these, one can also easily compute Voigt functions,
3218Fresnel integrals, and similar related functions as well.")
3219 ;; Faddeeva is released under the Expat license; AMOS is included as
3220 ;; public domain software.
3221 (license (list license:expat license:public-domain))))
3222
2742f87e
RW		 3223(define-public suitesparse
3224 (package
3225 (name "suitesparse")
bd5b5ac0 3226 (version "4.5.5")
2742f87e
RW		 3227 (source
3228 (origin
3229 (method url-fetch)
3230 (uri (string-append
3231 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
3232 version ".tar.gz"))
3233 (sha256
3234 (base32
bd5b5ac0
EB		 3235 "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
3236 (modules '((guix build utils)))
3237 (snippet
3238 ;; Remove bundled metis source
6cbee49d
MW		 3239 '(begin
3240 (delete-file-recursively "metis-5.1.0")
3241 #t))))
2742f87e
RW		 3242 (build-system gnu-build-system)
3243 (arguments
bd5b5ac0 3244 '(#:tests? #f ;no "check" target
2742f87e
RW		 3245 #:make-flags
3246 (list "CC=gcc"
3247 "BLAS=-lblas"
3248 "TBB=-ltbb"
bd5b5ac0 3249 "MY_METIS_LIB=-lmetis"
2742f87e
RW		 3250 (string-append "INSTALL_LIB="
3251 (assoc-ref %outputs "out") "/lib")
3252 (string-append "INSTALL_INCLUDE="
bd5b5ac0
EB		 3253 (assoc-ref %outputs "out") "/include")
3254 "library")
2742f87e 3255 #:phases
2509522c 3256 (modify-phases %standard-phases
bd5b5ac0 3257 (delete 'configure)))) ;no configure script
2742f87e
RW		 3258 (inputs
3259 `(("tbb" ,tbb)
bd5b5ac0
EB		 3260 ("lapack" ,lapack)
3261 ("metis" ,metis)))
2742f87e
RW		 3262 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
3263 (synopsis "Suite of sparse matrix software")
3264 (description
3265 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
3266multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
3267multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
3268simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
3269CXSparse, a concise sparse Cholesky factorization package; and many other
3270packages.")
3271 ;; LGPLv2.1+:
3272 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
3273 ;; GPLv2+:
3274 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
3275 (license (list license:gpl2+ license:lgpl2.1+))))
3276
ec322be2
FB		 3277(define-public atlas
3278 (package
3279 (name "atlas")
3c98ac02 3280 (version "3.10.3")
ec322be2
FB		 3281 (source (origin
3282 (method url-fetch)
de67e922
LF		 3283 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
3284 version "/atlas" version ".tar.bz2"))
ec322be2
FB		 3285 (sha256
3286 (base32
3c98ac02 3287 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
ec322be2
FB		 3288 (build-system gnu-build-system)
3289 (home-page "http://math-atlas.sourceforge.net/")
19afbea1 3290 (inputs `(("gfortran" ,gfortran)
ec322be2
FB		 3291 ("lapack-tar" ,(package-source lapack))))
3292 (outputs '("out" "doc"))
01480b9e
FB		 3293 ;; For the moment we drop support for MIPS at it fails to compile. See
3294 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
3295 (supported-systems (delete "mips64el-linux" %supported-systems))
ec322be2
FB		 3296 (arguments
3297 `(#:parallel-build? #f
3298 #:parallel-tests? #f
f15615b1
LC		 3299
3300 ;; ATLAS tunes itself for the machine it is built on, as explained at
3301 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
3302 ;; For this reason, we want users to build it locally instead of using
3303 ;; substitutes.
3304 #:substitutable? #f
3305
ec322be2
FB		 3306 #:modules ((srfi srfi-26)
3307 (srfi srfi-1)
3308 (guix build gnu-build-system)
3309 (guix build utils))
40029cbe 3310 #:configure-flags
ec322be2
FB		 3311 `(;; Generate position independent code suitable for dynamic libraries
3312 ;; and use WALL timer to get more accurate timing.
3313 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
3314 ;; Set word width.
3315 "-b"
3316 ,,(if (string-match "64" (%current-system))
3317 "64"
3318 "32")
3319 ;; Disable parallel build as it gives errors: atlas_pthread.h is
3320 ;; needed to compile C files before it is generated.
3321 "-Ss" "pmake" "make -j 1"
af89a667
FB		 3322 ;; Probe is failing for MIPS. We therefore define the system
3323 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3324 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3325 ,,@(if (string-prefix? "mips" (%current-system))
3326 (list "-A" "49" "-V" "1")
3327 (list))
ec322be2
FB		 3328 ;; Generate shared libraries.
3329 "--shared"
3330 ;; Build a full LAPACK library.
3331 ,(string-append "--with-netlib-lapack-tarfile="
3332 (assoc-ref %build-inputs "lapack-tar")))
3333 #:phases
e5b4b96b
EF		 3334 (modify-phases %standard-phases
3335 (add-after 'install 'install-doc
3336 (lambda* (#:key outputs inputs #:allow-other-keys)
3337 (let ((doc (string-append (assoc-ref outputs "doc")
3338 "/share/doc/atlas")))
3339 (mkdir-p doc)
3340 (fold (lambda (file previous)
3341 (and previous (zero? (system* "cp" file doc))))
3342 #t (find-files "../ATLAS/doc" ".*")))))
3343 (add-after 'check 'check-pt
3344 (lambda _ (zero? (system* "make" "ptcheck"))))
3345 ;; Fix files required to run configure.
3346 (add-before 'configure 'fix-/bin/sh
ec322be2
FB		 3347 (lambda _
3348 ;; Use `sh', not `/bin/sh'.
3349 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3350 (("/bin/sh")
e5b4b96b
EF		 3351 "sh"))))
3352 ;; Fix /bin/sh in generated make files.
3353 (add-after 'configure 'fix-/bin/sh-in-generated-files
3354 (lambda _
3355 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3356 (("/bin/sh")
3357 "sh"))))
3358 ;; ATLAS configure program does not accepts the default flags
3359 ;; passed by the 'gnu-build-system'.
3360 (replace 'configure
3361 (lambda* (#:key native-inputs inputs outputs
3362 (configure-flags '())
3363 #:allow-other-keys #:rest args)
3364 (let* ((prefix (assoc-ref outputs "out"))
3365 (bash (or (and=> (assoc-ref
3366 (or native-inputs inputs) "bash")
3367 (cut string-append <> "/bin/bash"))
3368 "/bin/sh"))
3369 (flags `(,(string-append "--prefix=" prefix)
3370 ,@configure-flags))
3371 (abs-srcdir (getcwd))
3372 (srcdir (string-append "../" (basename abs-srcdir))))
3373 (format #t "source directory: ~s (relative from build: ~s)~%"
3374 abs-srcdir srcdir)
3375 (mkdir "../build")
3376 (chdir "../build")
3377 (format #t "build directory: ~s~%" (getcwd))
3378 (format #t "configure flags: ~s~%" flags)
3379 (zero? (apply system* bash
3380 (string-append srcdir "/configure")
3381 flags))))))))
ec322be2
FB		 3382 (synopsis "Automatically Tuned Linear Algebra Software")
3383 (description
3384 "ATLAS is an automatically tuned linear algebra software library
3385providing C and Fortran77 interfaces to a portably efficient BLAS
3386implementation, as well as a few routines from LAPACK.
3387
f15615b1
LC		 3388Optimization occurs at build time. For this reason, the library is built on
3389the machine where it is installed, without resorting to pre-built substitutes.
ec322be2 3390
f15615b1 3391Before building the library, CPU throttling should be disabled. This can be
d97c429a 3392done in the BIOS, or, on GNU/Linux, with the following command:
ec322be2 3393
8e9ba611 3394@example
d97c429a 3395# cpupower --governor performance
8e9ba611 3396@end example
ec322be2 3397
d97c429a 3398Failure to do so will result in a library with poor performance.")
ec322be2 3399 (license license:bsd-3)))
c12efc72
AE		 3400
3401(define-public glm
3402 (package
3403 (name "glm")
66044a36 3404 (version "0.9.9.3")
c12efc72
AE		 3405 (source
3406 (origin
3407 (method url-fetch)
5ea4b594
MB		 3408 (uri (string-append "https://github.com/g-truc/glm/releases/download/"
3409 version "/glm-" version ".zip"))
c12efc72
AE		 3410 (sha256
3411 (base32
66044a36 3412 "0yqk5r3qh60d4r2iab5q7wq0fryn8p3pz6s28y1i7amqj1aqavj9"))))
c12efc72
AE		 3413 (build-system cmake-build-system)
3414 (native-inputs
3415 `(("unzip" ,unzip)))
46bda5eb 3416 (home-page "https://glm.g-truc.net/")
c12efc72
AE		 3417 (synopsis "OpenGL Mathematics library")
3418 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3419library for graphics software based on the OpenGL Shading Language (GLSL)
3420specifications.")
3421 (license license:expat)))
7f18257b
AE		 3422
3423(define-public lpsolve
3424 (package
3425 (name "lpsolve")
a89e0cf5 3426 (version "5.5.2.5")
7f18257b
AE		 3427 (source
3428 (origin
3429 (method url-fetch)
3430 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3431 "/lp_solve_" version "_source.tar.gz"))
3432 (sha256
3433 (base32
a89e0cf5 3434 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
7f18257b
AE		 3435 (modules '((guix build utils)))
3436 (snippet
6cbee49d
MW		 3437 '(begin
3438 (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3439 (("^c=cc") "c=gcc")
3440 ;; Pretend to be on a 64 bit platform to obtain a common directory
3441 ;; name for the build results on all architectures; nothing else
3442 ;; seems to depend on it.
3443 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3444
3445 ;; The check for 'isnan' as it is written fails with
3446 ;; "non-floating-point argument in call to function
3447 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3448 ;; definition, which in turn leads to bad things. Fix the feature
3449 ;; test.
3450 (("isnan\\(0\\)") "isnan(0.)"))
3451 #t))))
7f18257b
AE		 3452 (build-system gnu-build-system)
3453 (arguments
6c96b545 3454 `(#:tests? #f ; no check target
7f18257b
AE		 3455 #:phases
3456 (modify-phases %standard-phases
6c96b545 3457 (delete 'configure) ; no configure script
7f18257b
AE		 3458 (replace 'build
3459 (lambda _
6c96b545
TGR		 3460 (with-directory-excursion "lpsolve55"
3461 (invoke "bash" "ccc"))
3462 (with-directory-excursion "lp_solve"
3463 (invoke "bash" "ccc"))
3464 #t))
7f18257b
AE		 3465 (replace 'install
3466 (lambda* (#:key outputs #:allow-other-keys)
3467 (let* ((out (assoc-ref outputs "out"))
3468 (bin (string-append out "/bin"))
3469 (lib (string-append out "/lib"))
3470 ;; This is where LibreOffice expects to find the header
3471 ;; files, and where they are installed by Debian.
3472 (include (string-append out "/include/lpsolve")))
6c96b545
TGR		 3473 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3474 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
96c46210
LC		 3475 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3476
7f18257b
AE		 3477 ;; Install a subset of the header files as on Debian
3478 ;; (plus lp_bit.h, which matches the regular expression).
96c46210
LC		 3479 (for-each (lambda (name)
3480 (install-file name include))
3481 (find-files "." "lp_[HMSa-z].*\\.h$"))
7f18257b 3482 (with-directory-excursion "shared"
96c46210
LC		 3483 (for-each (lambda (name)
3484 (install-file name include))
3485 (find-files "." "\\.h$")))
7f18257b
AE		 3486 #t))))))
3487 (home-page "http://lpsolve.sourceforge.net/")
3488 (synopsis "Mixed integer linear programming (MILP) solver")
3489 (description
3490 "lp_solve is a mixed integer linear programming solver based on the
3491revised simplex and the branch-and-bound methods.")
3492 (license license:lgpl2.1+)))
a17d4564
EB		 3493
3494(define-public dealii
3495 (package
3496 (name "dealii")
24404eaf 3497 (version "8.5.1")
a17d4564
EB		 3498 (source
3499 (origin
3500 (method url-fetch)
3501 (uri (string-append "https://github.com/dealii/dealii/releases/"
3502 "download/v" version "/dealii-" version ".tar.gz"))
3503 (sha256
3504 (base32
24404eaf 3505 "1bh9rsmkrg0zi70n27b11djmac9lximghsiy7mg7w7x544n82gnk"))
a17d4564
EB		 3506 (modules '((guix build utils)))
3507 (snippet
3508 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
6cbee49d
MW		 3509 '(begin
3510 (delete-file-recursively "bundled")
3511 #t))))
a17d4564
EB		 3512 (build-system cmake-build-system)
3513 (inputs
3514 `(("tbb" ,tbb)
3515 ("zlib" ,zlib)
3516 ("boost" ,boost)
3517 ("p4est" ,p4est)
3518 ("blas" ,openblas)
3519 ("lapack" ,lapack)
3520 ("arpack" ,arpack-ng)
3521 ("muparser" ,muparser)
3522 ("gfortran" ,gfortran)
3523 ("suitesparse" ,suitesparse))) ;for UMFPACK
3524 (arguments
3525 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
d84b09e9
EB		 3526 #:configure-flags
3527 ;; Work around a bug in libsuitesparseconfig linking
3528 ;; see https://github.com/dealii/dealii/issues/4745
3529 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
a17d4564
EB		 3530 (home-page "https://www.dealii.org")
3531 (synopsis "Finite element library")
3532 (description
3533 "Deal.II is a C++ program library targeted at the computational solution
3534of partial differential equations using adaptive finite elements. The main
3535aim of deal.II is to enable rapid development of modern finite element codes,
3536using among other aspects adaptive meshes and a wide array of tools often used
3537in finite element programs.")
3538 (license license:lgpl2.1+)))
3539
3540(define-public dealii-openmpi
3541 (package (inherit dealii)
3542 (name "dealii-openmpi")
3543 (inputs
3544 `(("mpi" ,openmpi)
3545 ;;Supported only with MPI:
3546 ("p4est" ,p4est-openmpi)
3547 ("petsc" ,petsc-openmpi)
3548 ("slepc" ,slepc-openmpi)
3549 ("metis" ,metis) ;for MUMPS
3550 ("scalapack" ,scalapack) ;for MUMPS
3551 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3552 ("arpack" ,arpack-ng-openmpi)
3553 ,@(fold alist-delete (package-inputs dealii)
3554 '("p4est" "arpack"))))
3555 (arguments
3556 (substitute-keyword-arguments (package-arguments dealii)
3557 ((#:configure-flags cf)
3558 ``("-DMPI_C_COMPILER=mpicc"
3559 "-DMPI_CXX_COMPILER=mpicxx"
3560 "-DMPI_Fortran_COMPILER=mpifort"
3561 ,@,cf))))
3562 (synopsis "Finite element library (with MPI support)")))
194c7f95
AE		 3563
3564(define-public flann
3565 (package
3566 (name "flann")
3567 (version "1.8.4")
3568 (source
3569 (origin
3570 (method url-fetch)
3571 (uri
3572 (string-append
3573 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3574 version "-src.zip"))
3575 (sha256
3576 (base32
b5edc479
LC		 3577 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
3578 (patches (search-patches "flann-cmake-3.11.patch"))))
194c7f95 3579 (build-system cmake-build-system)
6b6aca9b
LC		 3580 (outputs '("out"
3581 "octave")) ;46 MiB .mex file that pulls Octave
194c7f95
AE		 3582 (native-inputs
3583 `(("unzip" ,unzip)))
3584 (inputs
3585 `(("hdf5" ,hdf5)
5537603f 3586 ("octave" ,octave-cli)
194c7f95
AE		 3587 ("python" ,python-2) ; print syntax
3588 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3589 ("zlib" ,zlib)))
3590 (arguments
39b30337
LC		 3591 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3592 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3593 #:strip-directories '("lib" "lib64" "libexec"
3594 "bin" "sbin" "share/flann/octave")
3595
9684e30b
LC		 3596 ;; Save 12 MiB by not installing .a files. Passing
3597 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3598 #:phases (modify-phases %standard-phases
6b6aca9b
LC		 3599 (add-before 'configure 'set-octave-directory
3600 (lambda* (#:key outputs #:allow-other-keys)
3601 ;; Install the .mex file in the "octave" output.
3602 (let ((out (assoc-ref outputs "octave")))
3603 (substitute* "src/matlab/CMakeLists.txt"
3604 (("share/flann/octave")
3605 (string-append out "/share/flann/octave")))
3606 #t)))
9684e30b
LC		 3607 (add-after 'install 'remove-static-libraries
3608 (lambda* (#:key outputs #:allow-other-keys)
3609 (let* ((out (assoc-ref outputs "out"))
3610 (lib (string-append out "/lib")))
3611 (for-each delete-file
3612 (find-files lib "\\.a$"))
3613 #t))))
3614
39b30337 3615 #:tests? #f)) ; The test data are downloaded from the Internet.
194c7f95
AE		 3616 (home-page "http://www.cs.ubc.ca/research/flann/")
3617 (synopsis "Library for approximate nearest neighbors computation")
3618 (description "FLANN is a library for performing fast approximate
3619nearest neighbor searches in high dimensional spaces. It implements a
3620collection of algorithms and a system for automatically choosing the best
3621algorithm and optimum parameters depending on the dataset.
3622
3623FLANN is written in C++ and contains bindings for C, Octave and Python.")
3624 (license (license:non-copyleft "file://COPYING"
3625 "See COPYING in the distribution."))))
d8c97beb
EF		 3626
3627(define-public wcalc
3628 (package
3629 (name "wcalc")
3630 (version "2.5")
3631 (source
3632 (origin
3633 (method url-fetch)
de67e922
LF		 3634 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3635 "wcalc-" version ".tar.bz2"))
d8c97beb
EF		 3636 (sha256
3637 (base32
3638 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3639 (build-system gnu-build-system)
3640 (inputs
3641 `(("mpfr" ,mpfr)
3642 ("readline" ,readline)))
3643 (home-page "http://w-calc.sourceforge.net/index.php")
3644 (synopsis "Flexible command-line scientific calculator")
3645 (description "Wcalc is a very capable calculator. It has standard functions
3646(sin, asin, and sinh for example, in either radians or degrees), many
3647pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3648variables, a command history, hex/octal/binary input and output, unit
3649conversions, embedded comments, and an expandable expression entry field. It
3650evaluates expressions using the standard order of operations.")
3651 (license license:gpl2+)))
45147b0c
FH		 3652
3653(define-public xaos
3654 (package
3655 (name "xaos")
3656 (version "3.6")
3657 (source (origin
3658 (method url-fetch)
de67e922
LF		 3659 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3660 "/xaos-" version ".tar.gz"))
45147b0c
FH		 3661 (sha256
3662 (base32
3663 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3664 (build-system gnu-build-system)
b94a6ca0 3665 (native-inputs `(("gettext" ,gettext-minimal)))
45147b0c
FH		 3666 (inputs `(("libx11" ,libx11)
3667 ("zlib" ,zlib)
3668 ("libpng" ,libpng)
3669 ("gsl" ,gsl)))
3670 (arguments
3671 `(#:tests? #f ;no "check" target
3672 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3673 (synopsis "Real-time fractal zoomer")
3674 (description "GNU XaoS is a graphical program that generates fractal
3675patterns and allows you to zoom in and out of them infinitely in a fluid,
3676continuous manner. It also includes tutorials that help to explain how fractals
3677are built. It can generate many different fractal types such as the Mandelbrot
3678set.")
6fd52309 3679 (home-page "https://www.gnu.org/software/xaos/")
45147b0c 3680 (license license:gpl2+)))
528bb464
EB		 3681
3682(define-public hypre
3683 (package
3684 (name "hypre")
220458b0 3685 (version "2.14.0")
528bb464
EB		 3686 (source (origin
3687 (method url-fetch)
3688 (uri (string-append "https://github.com/LLNL/hypre/archive/"
3689 "v" version ".tar.gz"))
3690 (file-name (string-append name "-" version ".tar.gz"))
3691 (sha256
3692 (base32
220458b0 3693 "0v515i73bvaz378h5465b1dy9v2gf924zy2q94cpq4qqarawvkqh"))
528bb464
EB		 3694 (modules '((guix build utils)))
3695 (snippet
3696 '(begin
3697 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
3698 ;; substitute the tarball creation time.
3699 (substitute* "src/utilities/HYPRE_utilities.h"
3700 (("Date Compiled: .*$")
220458b0 3701 "Date Compiled: Apr 11 2018 16:24:59 +0000\"\n"))
528bb464
EB		 3702 #t))))
3703 (build-system gnu-build-system)
3704 (outputs '("out" ;6.1 MiB of headers and libraries
3705 "doc")) ;4.8 MiB of documentation
3706 (native-inputs
3707 `(("doc++" ,doc++)
3708 ("netpbm" ,netpbm)
e18e7cb9 3709 ("perl" ,perl) ;needed to run 'ppmquant' during tests
9b405aea
PN		 3710 ("texlive" ,(texlive-union (list texlive-generic-xypic
3711 texlive-fonts-xypic
3712 texlive-latex-hyperref
3713 texlive-latex-oberdiek
3714 texlive-generic-ifxetex
3715 texlive-latex-url
3716 texlive-bibtex)))
528bb464
EB		 3717 ("ghostscript" ,ghostscript)))
3718 (inputs
3719 `(("blas" ,openblas)
3720 ("lapack" ,lapack)))
3721 (arguments
3722 `(#:modules ((srfi srfi-1)
3723 ,@%gnu-build-system-modules)
3724 #:configure-flags '("--enable-shared"
3725 "--disable-fortran"
3726 "--without-MPI"
3727 "--with-openmp"
3728 "--with-fei"
3729 "--with-lapack"
3730 "--with-blas")
3731 #:phases
3732 (modify-phases %standard-phases
9b405aea
PN		 3733 (add-before 'build 'set-HOME
3734 (lambda _
3735 ;; FIXME: texlive-union does not find the built
3736 ;; metafonts, so it tries to generate them in HOME.
3737 (setenv "HOME" "/tmp")
3738 #t))
528bb464
EB		 3739 (add-before 'configure 'chdir-src
3740 (lambda _ (chdir "src")))
3741 (replace 'configure
3742 (lambda* (#:key build target configure-flags
3743 #:allow-other-keys #:rest args)
3744 (let* ((configure (assoc-ref %standard-phases 'configure)))
3745 (apply configure
3746 (append args
3747 (list #:configure-flags
3748 (cons (string-append
3749 "--host=" (or target build))
3750 configure-flags)))))))
3751 (add-after 'build 'build-docs
3752 (lambda _
9b405aea 3753 (invoke "make" "-Cdocs" "pdf" "html")))
528bb464
EB		 3754 (replace 'check
3755 (lambda _
3756 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3757 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
3758 (and (system* "make" "check" "CHECKRUN=")
3759 (fold (lambda (filename result)
3760 (and result
3761 (let ((size (stat:size (stat filename))))
3762 (when (not (zero? size))
3763 (format #t "~a size ~d; error indication~%"
3764 filename size))
3765 (zero? size))))
3766 #t
3767 (find-files "test" ".*\\.err$")))))
3768 (add-after 'install 'install-docs
3769 (lambda* (#:key outputs #:allow-other-keys)
3770 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3771 (let* ((doc (assoc-ref outputs "doc"))
3772 (docdir (string-append doc "/share/doc/hypre-" ,version)))
528bb464
EB		 3773 (with-directory-excursion "docs"
3774 (for-each (lambda (base)
3775 (install-file (string-append base ".pdf") docdir)
3776 (copy-recursively base docdir)) ;html docs
3777 '("HYPRE_usr_manual"
3778 "HYPRE_ref_manual")))
3779 #t))))))
3780 (home-page "http://www.llnl.gov/casc/hypre/")
3781 (synopsis "Library of solvers and preconditioners for linear equations")
3782 (description
3783 "HYPRE is a software library of high performance preconditioners and
3784solvers for the solution of large, sparse linear systems of equations. It
3785features multigrid solvers for both structured and unstructured grid
3786problems.")
3787 (license license:lgpl2.1)))
3788
3789(define-public hypre-openmpi
3790 (package (inherit hypre)
3791 (name "hypre-openmpi")
3792 (inputs
3793 `(("mpi" ,openmpi)
3794 ,@(package-inputs hypre)))
3795 (arguments
3796 (substitute-keyword-arguments (package-arguments hypre)
3797 ((#:configure-flags flags)
3798 ``("--with-MPI"
6df2a50a
LC		 3799 ,@(delete "--without-MPI" ,flags)))
3800 ((#:phases phases)
3801 `(modify-phases ,phases
bbe46a4a
EB		 3802 (add-before 'check 'mpi-setup
3803 ,%openmpi-setup)))))
528bb464
EB		 3804 (synopsis "Parallel solvers and preconditioners for linear equations")
3805 (description
3806 "HYPRE is a software library of high performance preconditioners and
3807solvers for the solution of large, sparse linear systems of equations on
3808parallel computers. It features parallel multigrid solvers for both
3809structured and unstructured grid problems.")))
6c90e183
EB		 3810
3811(define-public matio
3812 (package
3813 (name "matio")
3814 (version "1.5.6")
3815 (source
3816 (origin
3817 (method url-fetch)
de67e922 3818 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
6c90e183
EB		 3819 "matio-" version ".tar.gz"))
3820 (sha256
3821 (base32
3822 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3823 (build-system gnu-build-system)
3824 (inputs
3825 `(("zlib" ,zlib)
3826 ("hdf5" ,hdf5)))
3827 (home-page "http://matio.sourceforge.net/")
3828 (synopsis "Library for reading and writing MAT files")
3829 (description "Matio is a library for reading and writing MAT files. It
3830supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3831 (license license:bsd-2)))
d721c83a 3832
517318ad
LF		 3833(define-public vc
3834 (package
3835 (name "vc")
853b0292 3836 (version "1.3.3")
517318ad
LF		 3837 (source
3838 (origin (method url-fetch)
3839 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3840 "download/" version "/Vc-" version ".tar.gz"))
3841 (sha256
3842 (base32
853b0292 3843 "1zmlpn32jzb38smp3j834llmbix3whsrbw0h397qxysbw792kih8"))))
517318ad
LF		 3844 (build-system cmake-build-system)
3845 (arguments
3846 '(#:configure-flags
33d82486
MB		 3847 '("-DBUILD_TESTING=ON"
3848 ;; By default, Vc will optimize for the CPU of the build machine.
3849 ;; Setting this to "none" makes it create portable binaries. See
3850 ;; "cmake/OptimizeForArchitecture.cmake".
3851 "-DTARGET_ARCHITECTURE=none")))
517318ad
LF		 3852 (synopsis "SIMD vector classes for C++")
3853 (description "Vc provides portable, zero-overhead C++ types for explicitly
3854data-parallel programming. It is a library designed to ease explicit
3855vectorization of C++ code. Its types enable explicitly stating data-parallel
3856operations on multiple values. The parallelism is therefore added via the type
3857system. Vc has an intuitive API and provides portability between different
3858compilers and compiler versions as well as portability between different vector
3859instruction sets. Thus, an application written with Vc can be compiled for:
3860@enumerate
3861@item AVX and AVX2
d1e4ad1b 3862@item SSE2 up to SSE4.2 or SSE4a
517318ad
LF		 3863@item Scalar
3864@item MIC
3865@item NEON (in development)
3866@item NVIDIA GPUs / CUDA (in development)
3867@end enumerate\n")
3868 (home-page "https://github.com/VcDevel/Vc")
a8ead6f9
EF		 3869 ;; "No support_???.cpp file exists for this architecture."
3870 (supported-systems '("x86_64-linux" "i686-linux"))
517318ad 3871 (license license:bsd-3)))
54052a54 3872
3873(define-public reducelcs
3874 ;; This is the last commit which is available upstream, no
3875 ;; release happened since 2010.
3876 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
3877 (revision "1"))
3878 (package
3879 (name "reducelcs")
3880 (version (string-append "1.0-" revision "." (string-take commit 7)))
3881 (source
3882 (origin
3883 (method git-fetch)
3884 (uri (git-reference
3885 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
3886 (commit commit)))
3887 (file-name (string-append name "-" version "-checkout"))
3888 (sha256
3889 (base32
3890 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
3891 (build-system gnu-build-system)
3892 (inputs
3893 `(("openlibm" ,openlibm)))
3894 (arguments
3895 `(#:tests? #f ; no tests
3896 #:phases
3897 (modify-phases %standard-phases
3898 (delete 'configure) ; No configure script exists.
3899 (replace 'install ; No install phase exists.
3900 (lambda* (#:key outputs #:allow-other-keys)
3901 (let* ((out (assoc-ref outputs "out"))
3902 (bin (string-append out "/bin")))
3903 (install-file "Approximation" bin)
3904 (install-file "CollectResults" bin)
3905 (install-file "GenerateInstances" bin)
3906 #t))))))
3907 (synopsis "Approximate Longest Commons Subsequence computation tool")
3908 (description
3909 "@code{reduceLCS} is an implementation of the Reduce-Expand
3910algorithm for LCS. It is a fast program to compute the approximate
3911Longest Commons Subsequence of a set of strings.")
3912 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
c000b6b1 3913 (license license:gpl3+))))
479c4273
JD		 3914
3915(define-public jacal
3916 (package
3917 (name "jacal")
3918 (version "1c4")
3919 (source (origin
3920 (method url-fetch)
3921 (uri (string-append
3922 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
3923 version ".zip"))
3924 (sha256 (base32
3925 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
3926 (patches (search-patches "jacal-fix-texinfo.patch"))))
3927 (build-system gnu-build-system)
3928 (arguments
3929 `(#:phases
3930 (modify-phases %standard-phases
3931 (add-before 'build 'pre-build
3932 ;; Don't use upstream's script - it really doesn't fit into
3933 ;; Guix's functional paradigm.
3934 (lambda* (#:key inputs outputs #:allow-other-keys)
3935 (substitute* "Makefile"
3936 (("^install: install-script") "install: "))))
3937 (add-after 'install 'post-install
3938 ;; Instead, we provide our own simplified script.
3939 (lambda* (#:key inputs outputs #:allow-other-keys)
3940 (let ((wrapper (string-append (assoc-ref outputs "out")
3941 "/bin/jacal")))
3942 (format (open wrapper (logior O_WRONLY O_CREAT))
3943 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
3944 "-e '(slib:load \"~a/lib/jacal/math\") "
3945 "(math)' \"$@\"\n")
3946 (which "bash")
3947 (assoc-ref inputs "scm")
3948 (assoc-ref outputs "out"))
3949 (chmod wrapper #o555))))
3950 (replace 'configure
3951 (lambda* (#:key inputs outputs #:allow-other-keys)
3952 (zero? (system* "./configure"
3953 (string-append "--prefix="
3954 (assoc-ref outputs "out")))))))))
3955 (inputs `(("scm" ,scm)))
3956 (native-inputs `(("unzip" ,unzip)
3957 ("texinfo" ,texinfo)))
3958 (synopsis "Symbolic mathematics system")
3959 (description "GNU JACAL is an interactive symbolic mathematics program based on
3960Scheme. It manipulate and simplify a range of mathematical expressions such
3961as equations, scalars, vectors, and matrices.")
6fd52309 3962 (home-page "https://www.gnu.org/software/jacal/")
479c4273
JD		 3963 (license license:gpl3+)))
3964
313844d9
TF		 3965(define-public z3
3966 (package
3967 (name "z3")
4a4f3e77 3968 (version "4.8.1")
fb525bfd 3969 (home-page "https://github.com/Z3Prover/z3")
313844d9 3970 (source (origin
fb525bfd
MB		 3971 (method git-fetch)
3972 (uri (git-reference (url home-page)
3973 (commit (string-append "z3-" version))))
2d7b99b3 3974 (file-name (git-file-name name version))
313844d9
TF		 3975 (sha256
3976 (base32
4a4f3e77 3977 "1vr57bwx40sd5riijyrhy70i2wnv9xrdihf6y5zdz56yq88rl48f"))))
cf684d87 3978 (build-system cmake-build-system)
313844d9 3979 (arguments
cf684d87
TF		 3980 `(#:configure-flags
3981 (list "-DBUILD_PYTHON_BINDINGS=true"
3982 "-DINSTALL_PYTHON_BINDINGS=true"
3983 (string-append "-DCMAKE_INSTALL_PYTHON_PKG_DIR="
3984 %output
677bc34d 3985 "/lib/python2.7/site-packages"))
313844d9
TF		 3986 #:phases
3987 (modify-phases %standard-phases
ad6c6a5b
EF		 3988 (add-after 'unpack 'fix-compatability
3989 ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
3990 (lambda _
3991 (substitute* "src/util/mpz.cpp"
3992 (("#include <immintrin.h>") ""))
3993 #t))
cf684d87
TF		 3994 (add-before 'configure 'bootstrap
3995 (lambda _
313844d9 3996 (zero?
cf684d87
TF		 3997 (system* "python" "contrib/cmake/bootstrap.py" "create"))))
3998 (add-before 'check 'make-test-z3
313844d9 3999 (lambda _
cf684d87
TF		 4000 ;; Build the test suite executable.
4001 (zero? (system* "make" "test-z3" "-j"
4002 (number->string (parallel-job-count))))))
4003 (replace 'check
4004 (lambda _
4005 ;; Run all the tests that don't require arguments.
4006 (zero? (system* "./test-z3" "/a")))))))
313844d9
TF		 4007 (native-inputs
4008 `(("python" ,python-2)))
4009 (synopsis "Theorem prover")
4010 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
cf684d87 4011theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
313844d9 4012 (license license:expat)))
3d5d87a3
JL		 4013
4014(define-public cubicle
4015 (package
4016 (name "cubicle")
564cf93f 4017 (version "1.1.2")
3d5d87a3
JL		 4018 (source (origin
4019 (method url-fetch)
4020 (uri (string-append "http://cubicle.lri.fr/cubicle-"
4021 version ".tar.gz"))
4022 (sha256
4023 (base32
564cf93f 4024 "10kk80jdmpdvql88sdjsh7vqzlpaphd8vip2lp47aarxjkwjlz1q"))))
3d5d87a3
JL		 4025 (build-system gnu-build-system)
4026 (native-inputs
564cf93f
JL		 4027 `(("automake" ,automake)
4028 ("ocaml" ,ocaml)
83fef82b 4029 ("which" ,(@@ (gnu packages base) which))))
3d5d87a3 4030 (propagated-inputs
564cf93f
JL		 4031 `(("ocaml-num" ,ocaml-num)
4032 ("z3" ,z3)))
3d5d87a3
JL		 4033 (arguments
4034 `(#:configure-flags (list "--with-z3")
564cf93f 4035 #:make-flags (list "QUIET=")
3d5d87a3
JL		 4036 #:tests? #f
4037 #:phases
4038 (modify-phases %standard-phases
4039 (add-before 'configure 'configure-for-release
4040 (lambda _
4041 (substitute* "Makefile.in"
564cf93f
JL		 4042 (("SVNREV=") "#SVNREV="))
4043 #t))
3d5d87a3
JL		 4044 (add-before 'configure 'fix-/bin/sh
4045 (lambda _
4046 (substitute* "configure"
564cf93f
JL		 4047 (("-/bin/sh") (string-append "-" (which "sh"))))
4048 #t))
3d5d87a3
JL		 4049 (add-before 'configure 'fix-smt-z3wrapper.ml
4050 (lambda _
4051 (substitute* "Makefile.in"
564cf93f
JL		 4052 (("\\\\n") ""))
4053 #t))
4054 (add-before 'configure 'fix-ocaml-num
4055 (lambda* (#:key inputs #:allow-other-keys)
4056 (substitute* "Makefile.in"
4057 (("= \\$\\(FUNCTORYLIB\\)")
4058 (string-append "= -I "
4059 (assoc-ref inputs "ocaml-num")
4060 "/lib/ocaml/site-lib"
4061 " $(FUNCTORYLIB)")))
4062 #t)))))
3d5d87a3
JL		 4063 (home-page "http://cubicle.lri.fr/")
4064 (synopsis "Model checker for array-based systems")
5a80c15c
RW		 4065 (description "Cubicle is a model checker for verifying safety properties
4066of array-based systems. This is a syntactically restricted class of
4067parametrized transition systems with states represented as arrays indexed by
4068an arbitrary number of processes. Cache coherence protocols and mutual
4069exclusion algorithms are typical examples of such systems.")
3d5d87a3 4070 (license license:asl2.0)))
e01397b4
EB		 4071
4072(define-public elemental
4073 (package
4074 (name "elemental")
4075 (version "0.87.7")
4076 (source (origin
5c0b6d1b
EF		 4077 (method git-fetch)
4078 (uri (git-reference
4079 (url "https://github.com/elemental/Elemental.git")
4080 (commit (string-append "v" version))))
4081 (file-name (git-file-name name version))
e01397b4
EB		 4082 (sha256
4083 (base32
5c0b6d1b 4084 "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
e01397b4
EB		 4085 (build-system cmake-build-system)
4086 (home-page "http://libelemental.org")
4087 (native-inputs
4088 `(("gfortran" ,gfortran)))
4089 (inputs
4090 `(("blas" ,openblas)
4091 ("gfortran:lib" ,gfortran "lib")
4092 ("gmp" ,gmp)
4093 ("lapack" ,lapack)
4094 ("metis" ,metis)
4095 ("mpc" ,mpc)
4096 ("mpfr" ,mpfr)
4097 ("mpi" ,openmpi)
4098 ("qd" ,qd)))
4099 (arguments
4100 `(#:build-type "Release" ;default RelWithDebInfo not supported
4101 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
4102 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
4103 "-DEL_CACHE_WARNINGS:BOOL=YES"
4104 "-DEL_TESTS:BOOL=YES"
4105 "-DCMAKE_INSTALL_LIBDIR=lib"
4106 "-DGFORTRAN_LIB=gfortran")
4107 #:phases (modify-phases %standard-phases
3b42e2be
EF		 4108 (add-before 'check 'mpi-setup
4109 ,%openmpi-setup)
e01397b4
EB		 4110 (add-before 'check 'setup-tests
4111 (lambda _
4112 ;; Parallelism is done at the MPI layer.
4113 (setenv "OMP_NUM_THREADS" "1")
4114 #t))
4115 (add-after 'install 'remove-tests
4116 (lambda* (#:key outputs #:allow-other-keys)
4117 ;; Tests are installed, with no easy configuration
4118 ;; switch to prevent this, so delete them.
4119 (delete-file-recursively
3b42e2be 4120 (string-append (assoc-ref outputs "out") "/bin"))
e01397b4
EB		 4121 #t)))))
4122 (synopsis "Dense and sparse-direct linear algebra and optimization")
4123 (description "Elemental is a modern C++ library for distributed-memory
4124dense and sparse-direct linear algebra, conic optimization, and lattice
4125reduction.")
4126 (license license:bsd-2)))
5b05dce7
JN		 4127
4128(define-public mcrl2
4129 (package
4130 (name "mcrl2")
4131 (version "201707.1.15162")
4132 (source (origin
4133 (method url-fetch)
4134 (uri (string-append "http://www.mcrl2.org/download/devel/mcrl2-"
4135 version
4136 ".tar.gz"))
4137 (sha256
4138 (base32
4139 "1ziww2fchsklm25hl9p2mngssxfh9w07nc114cncqaxfibqp2p8f"))))
4140 (native-inputs
4141 `(("subversion" ,subversion)))
4142 (inputs
4143 `(("boost" ,boost)
4144 ("glu" ,glu)
4145 ("mesa" ,mesa)
077d66ed 4146 ("qtbase" ,qtbase)))
5b05dce7 4147 (build-system cmake-build-system)
ed0c5d3c 4148 (synopsis "Toolset for the mCRL2 formal specification language")
5b05dce7 4149 (description
ed0c5d3c
TGR		 4150 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
4151specification language for describing concurrent discrete event systems. Its
4152toolset supports analysis and automatic verification, linearisation, simulation,
4153state-space exploration and generation, and tools to optimise and analyse
5b05dce7
JN		 4154specifications. Also, state spaces can be manipulated, visualised and
4155analysed.")
b3882709 4156 (home-page "https://mcrl2.org")
5b05dce7 4157 (license license:boost1.0)))
41835f94
LF		 4158
4159(define-public r-subplex
4160 (package
4161 (name "r-subplex")
2bcf5fd3 4162 (version "1.5-4")
41835f94
LF		 4163 (source
4164 (origin
4165 (method url-fetch)
4166 (uri (cran-uri "subplex" version))
4167 (sha256
4168 (base32
2bcf5fd3 4169 "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
41835f94
LF		 4170 (build-system r-build-system)
4171 (native-inputs
4172 `(("gfortran" ,gfortran)))
4173 (home-page "https://cran.r-project.org/web/packages/subplex")
4174 (synopsis "Unconstrained optimization using the subplex algorithm")
4175 (description "This package implements the Subplex optimization algorithm.
4176It solves unconstrained optimization problems using a simplex method on
4177subspaces. The method is well suited for optimizing objective functions that
4178are noisy or are discontinuous at the solution.")
4179 (license license:gpl3+)))
799ad71b
LF		 4180
4181(define-public r-desolve
4182 (package
4183 (name "r-desolve")
9a2ac95d 4184 (version "1.21")
799ad71b
LF		 4185 (source
4186 (origin
4187 (method url-fetch)
4188 (uri (cran-uri "deSolve" version))
4189 (sha256
4190 (base32
9a2ac95d 4191 "0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"))))
799ad71b
LF		 4192 (properties `((upstream-name . "deSolve")))
4193 (build-system r-build-system)
4194 (native-inputs
4195 `(("gfortran" ,gfortran)))
4196 (home-page "https://desolve.r-forge.r-project.org/")
4197 (synopsis "Solvers for initial value problems of differential equations")
4198 (description "This package provides functions that solve initial
4199value problems of a system of first-order ordinary differential equations (ODE),
4200of partial differential equations (PDE), of differential algebraic equations
4201(DAE), and of delay differential equations. The functions provide an interface
4202to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
4203to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
4204the Runge-Kutta family with fixed or variable time steps. The package contains
4205routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
4206differential equations (PDE) that have been converted to ODEs by numerical
4207differencing.")
4208 (license license:gpl2+)))
910deec6
NV		 4209
4210(define-public tcalc
4211 (package
4212 (name "tcalc")
4213 (version "2.0")
4214 (source
4215 (origin
4216 (method url-fetch)
4217 (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
4218 version ".tar.gz"))
4219 (sha256
4220 (base32
4221 "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
4222 (build-system gnu-build-system)
4223 (synopsis "The terminal calculator")
4224 (description
4225 "The terminal calculator is a small program to help users of the GNU/Linux
4226terminal do calculations simply and quickly. The formula to be calculated can
4227be fed to @command{tcalc} through the command line.")
4228 (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
4229 (license license:gpl3+)))
b26e4f26
EB		 4230
4231(define-public sundials
4232 (package
4233 (name "sundials")
4234 (version "3.1.1")
4235 (source
4236 (origin
4237 (method url-fetch)
4238 (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
4239 "sundials-" version ".tar.gz"))
4240 (sha256
4241 (base32
4242 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
4243 (build-system cmake-build-system)
4244 (native-inputs
4245 `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
4246 (inputs
4247 `(("fortran" ,gfortran) ;for fcmix
4248 ("blas" ,openblas)
4249 ("suitesparse" ,suitesparse))) ;TODO: Add hypre
4250 (arguments
4251 `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
4252 "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
4253 "-DEXAMPLES_ENABLE_F77:BOOL=ON"
4254 "-DEXAMPLES_ENABLE_F90:BOOL=ON"
4255 "-DEXAMPLES_INSTALL:BOOL=OFF"
4256
4257 "-DFCMIX_ENABLE:BOOL=ON"
4258
4259 "-DKLU_ENABLE:BOOL=ON"
4260 ,(string-append "-DKLU_INCLUDE_DIR="
4261 (assoc-ref %build-inputs "suitesparse")
4262 "/include")
4263 ,(string-append "-DKLU_LIBRARY_DIR="
4264 (assoc-ref %build-inputs "suitesparse")
4265 "/lib"))))
4266 (home-page "https://computation.llnl.gov/projects/sundials")
4267 (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
4268 (description "SUNDIALS is a family of software packages implemented with
4269the goal of providing robust time integrators and nonlinear solvers that can
4270easily be incorporated into existing simulation codes.")
4271 (license license:bsd-3)))
4272
4273(define-public sundials-openmpi
4274 (package (inherit sundials)
4275 (name "sundials-openmpi")
4276 (inputs
4277 `(("mpi" ,openmpi)
4278 ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
4279 ,@(package-inputs sundials)))
4280 (arguments
4281 (substitute-keyword-arguments (package-arguments sundials)
4282 ((#:configure-flags flags '())
4283 `(cons* "-DMPI_ENABLE:BOOL=ON"
4284 "-DPETSC_ENABLE:BOOL=ON"
4285 (string-append "-DPETSC_INCLUDE_DIR="
4286 (assoc-ref %build-inputs "petsc")
4287 "/include")
4288 (string-append "-DPETSC_LIBRARY_DIR="
4289 (assoc-ref %build-inputs "petsc")
4290 "/lib")
4291 ,flags))
4292 ((#:phases phases '%standard-phases)
4293 `(modify-phases ,phases
bbe46a4a
EB		 4294 (add-before 'check 'mpi-setup
4295 ,%openmpi-setup)))))
b26e4f26 4296 (synopsis "SUNDIALS with OpenMPI support")))
jackhill's copy of GNU Guix: https://guix.gnu.org/