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gnu: libqalculate: Fix libcurl gnutls CA cert bundle file.
[jackhill/guix/guix.git] / gnu / packages / maths.scm
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8f8b2451 1;;; GNU Guix --- Functional package management for GNU
b457f3cc 2;;; Copyright © 2013, 2014, 2015, 2016, 2019, 2020 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>
aa2e83cc 5;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Eric Bavier <bavier@posteo.net>
df354a77 6;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
182d6311 7;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
0aad198e 8;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
32158110 9;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
df129041 10;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
0ef54303 11;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
45147b0c 12;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
ec8c7e47 13;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
1d3c6a31 14;;; Copyright © 2016, 2018, 2020 Kei Kebreau <kkebreau@posteo.net>
59a07504 15;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
d7cff656 16;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
2fd26d05 17;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
f1cc312e 18;;; Copyright © 2017, 2018, 2019, 2020 Paul Garlick <pgarlick@tourbillion-technology.com>
47956fa0 19;;; Copyright © 2017 ng0 <ng0@n0.is>
ba1be533 20;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
d109b1e8 21;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
b18b9d20 22;;; Copyright © 2017, 2019 Arun Isaac <arunisaac@systemreboot.net>
98a5cd51 23;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
dc7d6d4e 24;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
3bc74090 25;;; Copyright © 2018, 2019 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>
c2cf286c 32;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
6f8c4195 33;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
4cb5d251 34;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
3b7828cc 35;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net>
f6b4d395 36;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
aac148a8 37;;; Copyright © 2020 Felix Gruber <felgru@posteo.net>
70c98efa 38;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in>
525e83ec 39;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
b60e2d48 40;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
8f8b2451
AE		 41;;;
42;;; This file is part of GNU Guix.
43;;;
44;;; GNU Guix is free software; you can redistribute it and/or modify it
45;;; under the terms of the GNU General Public License as published by
46;;; the Free Software Foundation; either version 3 of the License, or (at
47;;; your option) any later version.
48;;;
49;;; GNU Guix is distributed in the hope that it will be useful, but
50;;; WITHOUT ANY WARRANTY; without even the implied warranty of
51;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
52;;; GNU General Public License for more details.
53;;;
54;;; You should have received a copy of the GNU General Public License
55;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
56
57(define-module (gnu packages maths)
ec322be2 58 #:use-module (ice-9 regex)
a6b9ebc2 59 #:use-module (ice-9 match)
8f8b2451 60 #:use-module (gnu packages)
b5b73a82 61 #:use-module ((guix licenses) #:prefix license:)
8f8b2451
AE		 62 #:use-module (guix packages)
63 #:use-module (guix download)
54052a54 64 #:use-module (guix git-download)
0e2672ae 65 #:use-module (guix utils)
fa574a6d 66 #:use-module ((guix build utils) #:select (alist-replace))
da95c817 67 #:use-module (guix build-system cmake)
72c71d24 68 #:use-module (guix build-system glib-or-gtk)
c9dfa3c7 69 #:use-module (guix build-system gnu)
560acf25 70 #:use-module (guix build-system python)
63e07468 71 #:use-module (guix build-system ruby)
3de01d3f 72 #:use-module (gnu packages algebra)
ab5f3f21 73 #:use-module (gnu packages audio)
5143517c 74 #:use-module (gnu packages autotools)
fa574a6d 75 #:use-module (gnu packages base)
3de01d3f 76 #:use-module (gnu packages bison)
a17d4564 77 #:use-module (gnu packages boost)
e73b49fb 78 #:use-module (gnu packages check)
3de01d3f 79 #:use-module (gnu packages cmake)
c9dfa3c7 80 #:use-module (gnu packages compression)
668c06ac 81 #:use-module (gnu packages curl)
b7b27a8f 82 #:use-module (gnu packages cyrus-sasl)
8a0dd289 83 #:use-module (gnu packages dbm)
528bb464 84 #:use-module (gnu packages documentation)
57e544e8 85 #:use-module (gnu packages elf)
70c98efa 86 #:use-module (gnu packages file)
3de01d3f 87 #:use-module (gnu packages flex)
668c06ac 88 #:use-module (gnu packages fltk)
f3929800 89 #:use-module (gnu packages fontutils)
1dba6407 90 #:use-module (gnu packages gettext)
da95c817 91 #:use-module (gnu packages gcc)
73fed4f8 92 #:use-module (gnu packages gd)
668c06ac 93 #:use-module (gnu packages ghostscript)
70c98efa 94 #:use-module (gnu packages glib)
889187a4 95 #:use-module (gnu packages graphviz)
f3929800 96 #:use-module (gnu packages gtk)
70c98efa 97 #:use-module (gnu packages icu4c)
45147b0c 98 #:use-module (gnu packages image)
2fd26d05 99 #:use-module (gnu packages java)
668c06ac 100 #:use-module (gnu packages less)
8731e527 101 #:use-module (gnu packages lisp)
ab5f3f21 102 #:use-module (gnu packages linux)
bc3a2e35 103 #:use-module (gnu packages logging)
6e64766a 104 #:use-module (gnu packages lua)
5698b8b8 105 #:use-module (gnu packages gnome)
1b39a196 106 #:use-module (gnu packages guile)
668c06ac
JD		 107 #:use-module (gnu packages xorg)
108 #:use-module (gnu packages gl)
9f913401 109 #:use-module (gnu packages imagemagick)
8731e527 110 #:use-module (gnu packages m4)
d8c7eeb9 111 #:use-module (gnu packages mpi)
b92eee75 112 #:use-module (gnu packages multiprecision)
528bb464 113 #:use-module (gnu packages netpbm)
bd3d71cb 114 #:use-module (gnu packages onc-rpc)
668c06ac 115 #:use-module (gnu packages pcre)
5698b8b8 116 #:use-module (gnu packages popt)
c9dfa3c7
AE		 117 #:use-module (gnu packages perl)
118 #:use-module (gnu packages pkg-config)
ab5f3f21 119 #:use-module (gnu packages pulseaudio)
da95c817 120 #:use-module (gnu packages python)
589e3f4e 121 #:use-module (gnu packages python-web)
44d10b1f 122 #:use-module (gnu packages python-xyz)
5b05dce7 123 #:use-module (gnu packages qt)
c9dfa3c7 124 #:use-module (gnu packages readline)
63e07468 125 #:use-module (gnu packages ruby)
2742f87e 126 #:use-module (gnu packages tbb)
479c4273 127 #:use-module (gnu packages scheme)
b7194849 128 #:use-module (gnu packages shells)
df354a77 129 #:use-module (gnu packages tcl)
668c06ac 130 #:use-module (gnu packages texinfo)
8f9ac901 131 #:use-module (gnu packages tex)
b7b27a8f 132 #:use-module (gnu packages tls)
5b05dce7 133 #:use-module (gnu packages version-control)
9aafbc0c 134 #:use-module (gnu packages wxwidgets)
c12efc72 135 #:use-module (gnu packages xml)
a17d4564 136 #:use-module (srfi srfi-1))
8f8b2451 137
193abc82
JD		 138(define-public aris
139 (package
1f45f18a
JD		 140 (name "aris")
141 (version "2.2")
142 (source (origin
143 (method url-fetch)
144 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
145 (sha256 (base32
146 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
147 (build-system gnu-build-system)
148 (inputs `(("gtk+" ,gtk+)
149 ("libxml2" ,libxml2)))
150 (native-inputs `(("pkg-config" ,pkg-config)))
151 (synopsis "Natural deduction first-order logic interface")
152 (description "Aris is a program for performing logical proofs. It supports
153propositional and predicate logic, as well as Boolean algebra and
154arithmetical logic. In addition to its predefined inference and equivalence
155rules, Aris also supports references to older proofs. Its use of standard
156logical symbols and its natural deduction interface make it easy to use for
157beginners.")
158 (license license:gpl3+)
6fd52309 159 (home-page "https://www.gnu.org/software/aris/")))
193abc82 160
9c45c519
JD		 161(define-public c-graph
162 (package
163 (name "c-graph")
0ef54303 164 (version "2.0.1")
9c45c519
JD		 165 (source (origin
166 (method url-fetch)
167 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
168 ".tar.gz"))
169 (sha256 (base32
0ef54303 170 "092412jzxy6wdvpk96pfj499hpmaww8xllavbvlqspfpr7ips9id"))))
9c45c519
JD		 171 (build-system gnu-build-system)
172 (inputs
0ef54303 173 `(("fortran" ,gfortran)))
a3947cb1 174 (synopsis "Visualizing and demonstrating convolution")
9c45c519 175 (description
0ef54303 176 "GNU C-Graph is a tool for demonstrating the theory of convolution.
a3947cb1
LC		 177Thus, it can serve as an excellent aid to students of signal and systems
178theory in visualizing the convolution process. Rather than forcing the
179student to write code, the program offers an intuitive interface with
180interactive dialogs to guide them.")
9c45c519 181 (license license:gpl3+)
6fd52309 182 (home-page "https://www.gnu.org/software/c-graph/")))
9c45c519 183
d91025e3
TD		 184(define-public coda
185 (package
186 (name "coda")
9285f8bb 187 (version "2.19")
d91025e3
TD		 188 (source
189 (origin
190 (method url-fetch)
191 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
192 version "/coda-" version ".tar.gz"))
193 (sha256
9285f8bb 194 (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245"))
4b12fe5c
TD		 195 (patches (search-patches "coda-use-system-libs.patch"))
196 (modules '((guix build utils)))
197 (snippet
198 ;; Make sure we don't use the bundled software.
6cbee49d
MW		 199 '(begin
200 (for-each (lambda (d)
201 (delete-file-recursively (string-append "libcoda/" d)))
202 '("zlib" "pcre" "expat"))
203 #t))))
d91025e3
TD		 204 (native-inputs
205 `(("fortran" ,gfortran)
206 ("python" ,python)
207 ("python-numpy" ,python-numpy)))
208 (inputs
209 `(("zlib" ,zlib)
4b12fe5c
TD		 210 ("pcre" ,pcre)
211 ("expat" ,expat)
d91025e3
TD		 212 ("hdf4" ,hdf4-alt)
213 ("hdf5" ,hdf5)))
214 (build-system gnu-build-system)
215 (arguments
4b12fe5c
TD		 216 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
217 "LIBS= -lz -lpcre -lexpat")))
d91025e3
TD		 218 (synopsis "A common interface to various earth observation data formats")
219 (description
220 "The Common Data Access toolbox (CODA) provides a set of interfaces for
221reading remote sensing data from earth observation data files. It consists of
222command line applications and interfaces to the C, Fortran, Python, and Java
223programming languages.")
224 (home-page "https://stcorp.nl/coda")
225 (license license:gpl2+)))
226
d65f0661
KK		 227(define-public qhull
228 (package
229 (name "qhull")
230 (version "2015.2")
231 (source (origin
232 (method url-fetch)
233 (uri (string-append "http://www.qhull.org/download/qhull-"
234 (car (string-split version #\.))
235 "-src-7.2.0.tgz"))
236 (sha256
237 (base32
238 "0dm4b2xr3asy6w74khq2zg4gf26zsy3qf9sq7pf7lmrvbj911c3q"))))
239 (build-system cmake-build-system)
240 (synopsis "Calculate convex hulls and related structures")
241 (description
242 "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
243diagram, halfspace intersection about a point, furthest-site Delaunay
244triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d,
2453-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull
246algorithm for computing the convex hull. It handles roundoff errors from
247floating point arithmetic. It computes volumes, surface areas, and
248approximations to the convex hull.
249
250@code{Qhull} does not support triangulation of non-convex surfaces, mesh
251generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
252shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
253triangulations.")
254 (home-page "http://qhull.org")
255 (license (license:non-copyleft "file://COPYING.txt"
256 "See COPYING in the distribution."))))
257
a8fa86c4
RW		 258(define-public python-cvxopt
259 (package
260 (name "python-cvxopt")
a7c7015a 261 (version "1.2.3")
a8fa86c4
RW		 262 (source (origin
263 (method git-fetch)
264 (uri (git-reference
265 (url "https://github.com/cvxopt/cvxopt.git")
266 (commit version)))
267 (file-name (git-file-name name version))
268 (sha256
269 (base32
a7c7015a 270 "1kiy2m62xgs2d5id6dnnwy4vap85cd70p7pgkb9nh23qf9xnak7b"))))
a8fa86c4
RW		 271 (build-system python-build-system)
272 (arguments
273 `(#:phases
274 (modify-phases %standard-phases
275 (add-after 'unpack 'find-libraries
276 (lambda* (#:key inputs #:allow-other-keys)
277 (setenv "CVXOPT_BLAS_LIB" "openblas")
278 (setenv "CVXOPT_BUILD_FFTW" "1")
279 (setenv "CVXOPT_BUILD_GLPK" "1")
280 (setenv "CVXOPT_BUILD_GSL" "1")
281 #t)))))
282 (inputs
283 `(("fftw" ,fftw)
284 ("glpk" ,glpk)
285 ("gsl" ,gsl)
286 ("lapack" ,lapack)
287 ("openblas" ,openblas)
288 ("suitesparse" ,suitesparse)))
289 (home-page "https://www.cvxopt.org")
290 (synopsis "Python library for convex optimization")
291 (description
292 "CVXOPT is a package for convex optimization based on the Python
293programming language. Its main purpose is to make the development of software
294for convex optimization applications straightforward by building on Python’s
295extensive standard library and on the strengths of Python as a high-level
296programming language.")
297 (license license:gpl3+)))
298
299(define-public python2-cvxopt
300 (package-with-python2 python-cvxopt))
301
8f8b2451
AE		 302(define-public units
303 (package
304 (name "units")
494a8cd0 305 (version "2.19")
8f8b2451
AE		 306 (source (origin
307 (method url-fetch)
308 (uri (string-append "mirror://gnu/units/units-" version
309 ".tar.gz"))
310 (sha256 (base32
494a8cd0 311 "0mk562g7dnidjgfgvkxxpvlba66fh1ykmfd9ylzvcln1vxmi6qj2"))))
8f8b2451 312 (build-system gnu-build-system)
0498d248 313 (inputs
a2549713
EB		 314 `(("readline" ,readline)
315 ("python" ,python-wrapper) ;for 'units_cur' script
0498d248
EB		 316 ("python-requests" ,python-requests)))
317 (arguments
318 `(#:phases (modify-phases %standard-phases
319 (add-after 'install 'wrap-units_cur
320 (lambda* (#:key outputs #:allow-other-keys)
321 (let* ((out (assoc-ref outputs "out"))
322 (bin (string-append out "/bin")))
323 (wrap-program (string-append bin "/units_cur")
324 `("PYTHONPATH" ":" prefix
325 ,(search-path-as-string->list (getenv "PYTHONPATH"))))
326 #t))))))
8f8b2451
AE		 327 (synopsis "Conversion between thousands of scales")
328 (description
574e86f9 329 "GNU Units converts numeric quantities between units of measure. It
7c125ce0
AK		 330can handle scale changes through adaptive usage of standard scale
331prefixes (micro-, kilo-, etc.). It can also handle nonlinear
332conversions such as Fahrenheit to Celsius. Its interpreter is powerful
333enough to be used effectively as a scientific calculator.")
8f8b2451 334 (license license:gpl3+)
6fd52309 335 (home-page "https://www.gnu.org/software/units/")))
c9dfa3c7 336
61a529b4
RW		 337(define-public double-conversion
338 (package
339 (name "double-conversion")
1c7d7f3f 340 (version "3.1.5")
b343850e 341 (home-page "https://github.com/google/double-conversion")
61a529b4 342 (source (origin
2bdc73fb 343 (method git-fetch)
a4de1a65
MB		 344 (uri (git-reference (url home-page)
345 (commit (string-append "v" version))))
2bdc73fb 346 (file-name (git-file-name name version))
61a529b4
RW		 347 (sha256
348 (base32
1c7d7f3f 349 "0csy4pjw1p8rp6g5qxi2h0ychhhp1fldv7gb761627fs2mclw9gv"))))
61a529b4
RW		 350 (build-system cmake-build-system)
351 (arguments
352 '(#:test-target "test"
353 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
354 "-DBUILD_TESTING=ON")))
61a529b4
RW		 355 (synopsis "Conversion routines for IEEE doubles")
356 (description
357 "The double-conversion library provides binary-decimal and decimal-binary
358routines for IEEE doubles. The library consists of efficient conversion
359routines that have been extracted from the V8 JavaScript engine.")
360 (license license:bsd-3)))
361
182d6311
ML		 362(define-public dionysus
363 (package
364 (name "dionysus")
bd041e7f 365 (version "1.4.0")
182d6311
ML		 366 (source (origin
367 (method url-fetch)
368 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
bd041e7f 369 ".tar.xz"))
182d6311
ML		 370 (sha256
371 (base32
bd041e7f 372 "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
182d6311
ML		 373 (build-system gnu-build-system)
374 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
375 (synopsis "Local search for universal constants and scientific values")
376 (description
377 "GNU Dionysus is a convenient system for quickly retrieving the values of
378mathematical constants used in science and engineering. Values can be
379searched using a simple command-line tool, choosing from three databases:
380universal constants, atomic numbers, and constants related to
381semiconductors.")
382 (license license:gpl3+)
6fd52309 383 (home-page "https://www.gnu.org/software/dionysus/")))
182d6311 384
b60e2d48
NB		 385(define-public dsfmt
386 (package
387 (name "dsfmt")
388 (version "2.2.3")
389 (source
390 (origin
391 (method url-fetch)
392 (uri
393 (string-append
394 "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/"
395 "dSFMT-src-" version ".tar.gz"))
396 (sha256
397 (base32
398 "03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))
399 (modules '((guix build utils)))
400 ;; Don't distribute html documentation with bundled jquery.
401 (snippet
402 '(begin
403 (delete-file-recursively "html") #t))
404 ;; Add patches borrowed from Julia.
405 (patches
406 (list
407 (origin
408 (method url-fetch)
409 (uri (string-append
410 "https://raw.githubusercontent.com/JuliaLang/julia/"
411 "v1.3.0/deps/patches/dSFMT.c.patch"))
412 (sha256 (base32
413 "09mhv11bms8jsmkmdqvlcgljwhzw3b6n9nncpi2b6dla9798hw2y"))
414 (file-name "dSFMT.c.patch"))
415 (origin
416 (method url-fetch)
417 (uri (string-append
418 "https://raw.githubusercontent.com/JuliaLang/julia/"
419 "v1.3.0/deps/patches/dSFMT.h.patch"))
420 (sha256 (base32
421 "1py5rd0yxic335lzka23f6x2dhncrpizpyrk57gi2f28c0p98y5n"))
422 (file-name "dSFMT.h.patch"))))))
423 (build-system gnu-build-system)
424 (arguments
425 `(#:phases
426 (modify-phases %standard-phases
427 (delete 'configure) ; no configure script
428 (replace 'build
429 ;; Upstream Makefile does not build a shared library. Borrow from Julia
430 ;; https://github.com/JuliaLang/julia/blob/v1.3.0/deps/dsfmt.mk
431 (lambda _
432 (invoke
433 "gcc" "-DNDEBUG" "-DDSFMT_MEXP=19937"
434 "-fPIC" "-DDSFMT_DO_NOT_USE_OLD_NAMES"
435 "-O3" "-finline-functions" "-fomit-frame-pointer"
436 "-fno-strict-aliasing" "--param" "max-inline-insns-single=1800"
437 "-Wmissing-prototypes" "-Wall" "-std=c99" "-shared" "dSFMT.c"
438 "-o" "libdSFMT.so")))
439 (replace 'install ; no "install" target
440 (lambda* (#:key outputs #:allow-other-keys)
441 (let* ((out (assoc-ref outputs "out"))
442 (lib (string-append out "/lib"))
443 (inc (string-append out "/include"))
444 (doc (string-append out "/share/doc/" ,name "-" ,version)))
445 (install-file "libdSFMT.so" lib)
446 (install-file "dSFMT.h" inc)
447 (install-file "LICENSE.txt" doc)
448 #t))))))
449 (synopsis "Double precision SIMD-oriented Fast Mersenne Twister")
450 (description
451 "The dSMFT package speeds up Fast Mersenne Twister generation by avoiding
452the expensive conversion of integer to double (floating point). dSFMT directly
453generates double precision floating point pseudorandom numbers which have the
454IEEE Standard for Binary Floating-Point Arithmetic (ANSI/IEEE Std 754-1985)
455format. dSFMT is only available on the CPUs which use IEEE 754 format double
456precision floating point numbers.")
457 (home-page "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/")
458 (license license:bsd-3)))
459
88bd1804
AE		 460(define-public gsl
461 (package
462 (name "gsl")
f3a34b9d 463 (version "2.5")
ab2cc5cd
LC		 464 (source (origin
465 (method url-fetch)
466 (uri (string-append "mirror://gnu/gsl/gsl-"
467 version ".tar.gz"))
468 (sha256
469 (base32
f3a34b9d 470 "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
ab2cc5cd 471 (patches (search-patches "gsl-test-i686.patch"))))
88bd1804 472 (build-system gnu-build-system)
71e0f288 473 (arguments
f885fc05 474 `(;; Currently there are numerous tests that fail on "exotic"
6f766069
EF		 475 ;; architectures such as aarch64 and ppc64le.
476 ,@(if (string-prefix? "aarch64-linux"
477 (or (%current-target-system) (%current-system)))
478 '(#:tests? #f)
479 '())))
480 (home-page "https://www.gnu.org/software/gsl/")
88bd1804
AE		 481 (synopsis "Numerical library for C and C++")
482 (description
a22dc0c4
LC		 483 "The GNU Scientific Library is a library for numerical analysis in C
484and C++. It includes a wide range of mathematical routines, with over 1000
485functions in total. Subject areas covered by the library include:
486differential equations, linear algebra, Fast Fourier Transforms and random
487numbers.")
88bd1804
AE		 488 (license license:gpl3+)))
489
b92eee75
AE		 490(define-public glpk
491 (package
492 (name "glpk")
445929e0 493 (version "4.65")
b92eee75
AE		 494 (source
495 (origin
496 (method url-fetch)
497 (uri (string-append "mirror://gnu/glpk/glpk-"
498 version ".tar.gz"))
499 (sha256
500 (base32
445929e0 501 "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
b92eee75
AE		 502 (build-system gnu-build-system)
503 (inputs
504 `(("gmp" ,gmp)))
505 (arguments
506 `(#:configure-flags '("--with-gmp")))
82110ef6 507 (home-page "https://www.gnu.org/software/glpk/")
79c311b8 508 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
b92eee75
AE		 509 (description
510 "GLPK is a C library for solving large-scale linear programming (LP),
511mixed integer programming (MIP), and other related problems. It supports the
512GNU MathProg modeling language, a subset of the AMPL language, and features a
513translator for the language. In addition to the C library, a stand-alone
514LP/MIP solver is included in the package.")
515 (license license:gpl3+)))
516
b146763a
AE		 517(define-public 4ti2
518 (package
519 (name "4ti2")
eea4a091 520 (version "1.6.9")
b146763a
AE		 521 (source
522 (origin
eea4a091
TGR		 523 (method url-fetch)
524 (uri (string-append "https://github.com/4ti2/4ti2/releases/download/"
525 "Release_"
526 (string-map (lambda (c) (if (char=? c #\.) #\_ c))
527 version)
528 "/4ti2-" version ".tar.gz"))
529 (sha256
530 (base32 "0rj92x6p9m3la5gasjbj7sa569im527ffmka5y2sv1amgd3fflrh"))))
b146763a
AE		 531 (build-system gnu-build-system)
532 (native-inputs
533 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
534 (inputs
535 `(("glpk" ,glpk)
536 ("gmp" ,gmp)))
537 (home-page "http://www.4ti2.de/")
538 (synopsis "Mathematical tool suite for problems on linear spaces")
539 (description
540 "4ti2 implements algorithms for solving algebraic, geometric and
541combinatorial problems on linear spaces. Among others, it solves systems
542of linear equations, computes extreme rays of polyhedral cones, solves
543integer programming problems and computes Markov bases for statistics.")
544 (license license:gpl2+)))
545
53696f10
AE		 546(define-public cddlib
547 (package
548 (name "cddlib")
7fe491fb 549 (version "0.94i")
53696f10
AE		 550 (source
551 (origin
552 (method url-fetch)
182dde82 553 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
53696f10
AE		 554 (string-delete #\. version) ".tar.gz"))
555 (sha256
556 (base32
7fe491fb 557 "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
53696f10
AE		 558 (build-system gnu-build-system)
559 (inputs
560 `(("gmp" ,gmp)))
561 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
562 (synopsis "Library for convex hulls and extreme rays of polyhedra")
563 (description
564 "The C-library cddlib implements the Double Description Method of
565Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
566rays of a general convex polyhedron given by a system of linear inequalities
567in arbitrary dimension. It can also be used for the converse operation of
568computing convex hulls.")
569 (license license:gpl2+)))
570
0ffc2d53
AE		 571(define-public lrslib
572 (package
573 (name "lrslib")
574 (version "7.0a")
575 (source
576 (origin
577 (method url-fetch)
578 (uri (string-append "http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/"
579 "lrslib-0"
580 (string-delete #\. version) ".tar.gz"))
581 (sha256
582 (base32
583 "034fa45r9hwx6ljmgpxk2872q34nklkalpdkc6s9hqw57rivi36k"))))
584 (build-system gnu-build-system)
585 (inputs
586 `(("gmp" ,gmp)))
587 (arguments
588 `(#:tests? #f ; no check phase
589 #:make-flags `("CC=gcc"
590 ,(string-append "prefix=" (assoc-ref %outputs "out"))
591 "all-shared")
592 #:phases
593 (modify-phases %standard-phases
594 (replace 'configure
595 (lambda _
596 (substitute* "makefile"
597 (("-L \\.") "-L . -Wl,-rpath='$$ORIGIN/../lib'"))
598 #t)))))
599 (home-page "http://cgm.cs.mcgill.ca/~avis/C/lrs.html")
600 (synopsis "Convex hulls of polyhedra with exact arithmetic")
601 (description
602 "The C code of lrslib implements the reverse search algorithm for
603vertex enumeration and convex hull problems. Its input file format is
604compatible with cddlib. All computations are done exactly in either
605multiple precision or fixed integer arithmetic. Output is not stored
606in memory, so even problems with very large output sizes can sometimes
607be solved.")
608 (license license:gpl2+)))
609
b457f3cc
AE		 610(define-public vinci
611 (package
612 (name "vinci")
613 (version "1.0.5")
614 (source
615 (origin
616 (method url-fetch)
617 (uri (string-append "https://www.math.u-bordeaux.fr/~aenge/software/"
618 "vinci/vinci-" version ".tar.gz"))
619 (sha256
620 (base32
621 "1aq0qc1y27iw9grhgnyji3290wwfznsrk3sg6ynqpxwjdda53h4m"))))
622 (build-system gnu-build-system)
623 (inputs
624 `(("lrslib" ,lrslib)))
625 (arguments
626 `(#:tests? #f ; no check phase
627 #:phases
628 (modify-phases %standard-phases
629 (replace 'configure
630 ;; register the lrs location in the config file
631 (lambda* (#:key inputs #:allow-other-keys)
632 (let* ((lrs (assoc-ref inputs "lrslib"))
633 (lrsexec (string-append lrs "/bin/lrs")))
634 (substitute* "vinci.h"
635 (("#define LRS_EXEC \"lrs\"")
636 (string-append "#define LRS_EXEC \"" lrsexec "\""))))
637 #t))
638 (replace 'install
639 (lambda* (#:key outputs #:allow-other-keys)
640 (let* ((out (assoc-ref outputs "out"))
641 (bin (string-append out "/bin")))
642 (install-file "vinci" bin))
643 #t)))))
644 (home-page
645 "https://www.math.u-bordeaux.fr/~aenge/?category=software&page=vinci")
646 (synopsis "Volume computation for polytopes")
647 (description
648 "Vinci implements a number of volume computation algorithms for convex
649polytopes in arbitrary dimension. The polytopes can be given by their
650V-representation (as the convex hull of a finite number of vertices), by
651their H-representation (as the bounded intersection of a finite number of
652halfspaces) or by their double description with both representations.")
653 (license license:gpl2+)))
654
865a69dd
RW		 655(define-public arpack-ng
656 (package
657 (name "arpack-ng")
f03c4ec6 658 (version "3.6.3")
c0edb5b5 659 (home-page "https://github.com/opencollab/arpack-ng")
622ef2b9
MB		 660 (source (origin
661 (method git-fetch)
662 (uri (git-reference (url home-page) (commit version)))
663 (file-name (git-file-name name version))
664 (sha256
665 (base32
f03c4ec6 666 "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
865a69dd 667 (build-system gnu-build-system)
c0edb5b5
LC		 668 (native-inputs
669 `(("autoconf" ,autoconf)
670 ("automake" ,automake)
671 ("libtool" ,libtool)))
865a69dd
RW		 672 (inputs
673 `(("lapack" ,lapack)
19afbea1 674 ("fortran" ,gfortran)))
865a69dd
RW		 675 (synopsis "Fortran subroutines for solving eigenvalue problems")
676 (description
677 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
678large scale eigenvalue problems.")
166191b3 679 (license (license:non-copyleft "file://COPYING"
865a69dd
RW		 680 "See COPYING in the distribution."))))
681
c0edb5b5
LC		 682(define-public arpack-ng-3.3.0
683 (package
684 (inherit arpack-ng)
685 (version "3.3.0")
686 (name (package-name arpack-ng))
687 (home-page (package-home-page arpack-ng))
688 (source
689 (origin
690 (method url-fetch)
691 (uri (string-append home-page "/archive/" version ".tar.gz"))
692 (file-name (string-append name "-" version ".tar.gz"))
693 (sha256
694 (base32
695 "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
696
8c94c886
EB		 697(define-public arpack-ng-openmpi
698 (package (inherit arpack-ng)
699 (name "arpack-ng-openmpi")
700 (inputs
701 `(("mpi" ,openmpi)
702 ,@(package-inputs arpack-ng)))
4f387541
LC		 703 (arguments
704 (substitute-keyword-arguments (package-arguments arpack-ng)
705 ((#:configure-flags _ '())
aa82260b
PG		 706 ''("--enable-mpi"))
707 ((#:phases phases '%standard-phases)
708 `(modify-phases ,phases
bbe46a4a
EB		 709 (add-before 'check 'mpi-setup
710 ,%openmpi-setup)))))
8c94c886
EB		 711 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
712
da95c817
NK		 713(define-public lapack
714 (package
715 (name "lapack")
e6de152d 716 (version "3.9.0")
da95c817
NK		 717 (source
718 (origin
719 (method url-fetch)
720 (uri (string-append "http://www.netlib.org/lapack/lapack-"
721 version ".tgz"))
722 (sha256
723 (base32
e6de152d 724 "1155qixp26c12yrxc76z9mlfw2h3xxymxxv5znpgzh5gaykpndgj"))))
da95c817
NK		 725 (build-system cmake-build-system)
726 (home-page "http://www.netlib.org/lapack/")
19afbea1 727 (inputs `(("fortran" ,gfortran)
e6de152d 728 ("python" ,python-wrapper)))
da95c817 729 (arguments
3ab869b6 730 `(#:configure-flags (list
3ab869b6
LC		 731 "-DBUILD_SHARED_LIBS:BOOL=YES"
732 "-DLAPACKE=ON"
3ab869b6 733 ;; Build the 'LAPACKE_clatms' functions.
e6de152d
KH		 734 "-DLAPACKE_WITH_TMG=ON"
735 "-DBUILD_TESTING=ON")))
da95c817
NK		 736 (synopsis "Library for numerical linear algebra")
737 (description
738 "LAPACK is a Fortran 90 library for solving the most commonly occurring
739problems in numerical linear algebra.")
166191b3 740 (license (license:non-copyleft "file://LICENSE"
da95c817 741 "See LICENSE in the distribution."))))
73fed4f8 742
e1ff597a
EB		 743(define-public scalapack
744 (package
745 (name "scalapack")
746 (version "2.0.2")
747 (source
748 (origin
749 (method url-fetch)
750 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
751 version ".tgz"))
752 (sha256
753 (base32
f73750e6
EB		 754 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))
755 (patches (search-patches "scalapack-blacs-mpi-deprecations.patch"))))
e1ff597a
EB		 756 (build-system cmake-build-system)
757 (inputs
758 `(("mpi" ,openmpi)
759 ("fortran" ,gfortran)
760 ("lapack" ,lapack))) ;for testing only
761 (arguments
6df2a50a
LC		 762 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
763 #:phases (modify-phases %standard-phases
bbe46a4a
EB		 764 (add-before 'check 'mpi-setup
765 ,%openmpi-setup))))
e1ff597a
EB		 766 (home-page "http://www.netlib.org/scalapack/")
767 (synopsis "Library for scalable numerical linear algebra")
768 (description
769 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
770routines on parallel distributed memory machines. ScaLAPACK solves dense and
771banded linear systems, least squares problems, eigenvalue problems, and
772singular value problems.")
adb223b8
LC		 773 (license (license:non-copyleft "file://LICENSE"
774 "See LICENSE in the distribution."))))
e1ff597a 775
73fed4f8 776(define-public gnuplot
5f800540
KK		 777 (package
778 (name "gnuplot")
cb1d8aee 779 (version "5.2.7")
5f800540
KK		 780 (source (origin
781 (method url-fetch)
782 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
783 version "/gnuplot-"
784 version ".tar.gz"))
785 (sha256
cb1d8aee 786 (base32 "1vglp4la40f5dpj0zdj63zprrkyjgzy068p35bz5dqxjyczm1zlp"))))
5f800540
KK		 787 (build-system gnu-build-system)
788 (inputs `(("readline" ,readline)
789 ("cairo" ,cairo)
790 ("pango" ,pango)
6e64766a
DM		 791 ("gd" ,gd)
792 ("lua" ,lua)))
612a387f
RW		 793 (native-inputs
794 `(("pkg-config" ,pkg-config)
795 ("texlive" ,texlive-tiny)))
07254d8b
AM		 796 (arguments `(#:configure-flags (list (string-append
797 "--with-texdir=" %output
798 "/texmf-local/tex/latex/gnuplot"))))
5f800540
KK		 799 (home-page "http://www.gnuplot.info")
800 (synopsis "Command-line driven graphing utility")
801 (description "Gnuplot is a portable command-line driven graphing
35b9e423 802utility. It was originally created to allow scientists and students to
73fed4f8 803visualize mathematical functions and data interactively, but has grown to
35b9e423 804support many non-interactive uses such as web scripting. It is also used as a
73fed4f8 805plotting engine by third-party applications like Octave.")
5f800540
KK		 806 ;; X11 Style with the additional restriction that derived works may only be
807 ;; distributed as patches to the original.
808 (license (license:fsf-free
809 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
668c06ac 810
32f70e1f
TD		 811(define-public gctp
812 (package
813 (name "gctp")
814 (version "2.0.0")
815 (source
816 (origin
5db874d1
TGR		 817 (method git-fetch)
818 (uri (git-reference
819 (url "https://github.com/OkoSanto/GCTP.git")
820 (commit (string-append "v" version))))
821 (file-name (git-file-name name version))
32f70e1f 822 (sha256
5db874d1 823 (base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
32f70e1f
TD		 824 (native-inputs
825 `(("fortran" ,gfortran)))
826 (build-system gnu-build-system)
827 (synopsis "General Cartographic Transformation Package (GCTP)")
828 (description
829 "The General Cartographic Transformation Package (GCTP) is a system of
830software routines designed to permit the transformation of coordinate pairs
831from one map projection to another. The GCTP is the standard computer
832software used by the National Mapping Division for map projection
833computations.")
834 (home-page "https://github.com/OkoSanto/GCTP")
0f7cd95b 835 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
32f70e1f 836
becbbefc
TD		 837(define-public hdf4
838 (package
839 (name "hdf4")
c959d99f 840 (version "4.2.14")
becbbefc
TD		 841 (source
842 (origin
843 (method url-fetch)
844 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
845 version "/src/hdf-" version ".tar.bz2"))
846 (sha256
c959d99f 847 (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l"))
15ca49b2
AE		 848 (patches (search-patches "hdf4-architectures.patch"
849 "hdf4-reproducibility.patch"
bd3d71cb
MB		 850 "hdf4-shared-fortran.patch"
851 "hdf4-tirpc.patch"))))
becbbefc
TD		 852 (build-system gnu-build-system)
853 (native-inputs
854 `(("gfortran" ,gfortran)
855 ("bison" ,bison)
856 ("flex" ,flex)))
857 (inputs
858 `(("zlib" ,zlib)
bd3d71cb
MB		 859 ("libjpeg" ,libjpeg)
860 ("libtirpc" ,libtirpc)))
becbbefc
TD		 861 (arguments
862 `(#:parallel-tests? #f
bd3d71cb
MB		 863 #:configure-flags (list "--enable-shared"
864 (string-append "CPPFLAGS=-I"
865 (assoc-ref %build-inputs "libtirpc")
866 "/include/tirpc"))
becbbefc
TD		 867 #:phases
868 (modify-phases %standard-phases
953a12fa
EF		 869 ;; This is inspired by two of Debian's patches.
870 (add-before 'configure 'add-more-aarch64-support
871 (lambda _
872 (substitute* '("mfhdf/ncgen/ncgen.l"
873 "mfhdf/ncgen/ncgenyy.c"
874 "mfhdf/libsrc/netcdf.h.in")
875 (("AIX5L64") "__aarch64__"))
876 #t))
becbbefc
TD		 877 (add-before 'configure 'patchbuild
878 (lambda _
879 (substitute*
880 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
881 (("/bin/rm") "rm")
882 (("/bin/mkdir") "mkdir"))
883 (substitute* (find-files "." "^Makefile\\.in$")
884 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
885-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
886 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
887-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
953a12fa 888-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
e464b455
TD		 889 #t))
890 (add-after 'configure 'patch-settings
891 (lambda _
892 ;; libhdf4.settings contains the full path of the
893 ;; compilers used, and its contents are included in
894 ;; .so-files. We truncate the hashes to avoid
895 ;; unnecessary store references to those compilers:
896 (substitute* "libhdf4.settings"
897 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
898 (string-append prefix (string-take hash 10) "...")))
899 #t))
900 )))
becbbefc
TD		 901 (home-page "https://www.hdfgroup.org/products/hdf4/")
902 (synopsis
903 "Library and multi-object file format for storing and managing data")
904 (description "HDF4 is a library and multi-object file format for storing
905and managing data between machines. HDF4 is an older hierarchical data format,
906incompatible with HDF5.")
907 (license
908 (license:non-copyleft
909 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
910
911(define-public hdf4-alt
912 (package
913 (inherit hdf4)
914 (name "hdf4-alt")
915 (arguments
916 (substitute-keyword-arguments (package-arguments hdf4)
917 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
918 (synopsis
919 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
920
7ee3f1a2
JD		 921(define-public hdf5
922 (package
923 (name "hdf5")
7b84610e 924 (version "1.8.21")
7ee3f1a2
JD		 925 (source
926 (origin
927 (method url-fetch)
2da63064
TD		 928 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
929 "hdf5-" (version-major+minor version)
930 "/hdf5-" version "/src/hdf5-"
dcd9d163
LF		 931 version ".tar.bz2")
932 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
933 "current"
7b84610e
EB		 934 (match (string-split version #\.)
935 ((major minor _ ...)
936 (string-append major minor)))
dcd9d163 937 "/src/hdf5-" version ".tar.bz2")))
7ee3f1a2 938 (sha256
7b84610e 939 (base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5"))
7fedc3fd
EB		 940 (patches (search-patches "hdf5-config-date.patch"
941 "hdf5-1.8-mpi-deprecations.patch"))))
7ee3f1a2 942 (build-system gnu-build-system)
12ed1216
AE		 943 (inputs
944 `(("zlib" ,zlib)))
e3a1a1de 945 (native-inputs
3ea420f3
LC		 946 `(("gfortran" ,gfortran)
947 ("perl" ,perl))) ;part of the test machinery needs Perl
e3a1a1de
TD		 948 (outputs '("out" ; core library
949 "fortran")) ; fortran interface
7ee3f1a2 950 (arguments
62126576 951 `(;; Some of the users, notably Flann, need the C++ interface.
e3a1a1de
TD		 952 #:configure-flags '("--enable-cxx"
953 "--enable-fortran"
549d1571
LC		 954 "--enable-fortran2003"
955
956 ;; Build a thread-safe library. Unfortunately,
957 ;; 'configure' invites you to either turn off C++,
958 ;; Fortran, and the high-level interface (HL), or
959 ;; to pass '--enable-unsupported'. Debian
960 ;; packagers chose to pass '--enable-unsupported'
961 ;; and we follow their lead here.
962 "--enable-threadsafe"
963 "--with-pthread"
964 "--enable-unsupported")
4dba441c
RW		 965 ;; Use -fPIC to allow the R bindings to link with the static libraries
966 #:make-flags (list "CFLAGS=-fPIC"
967 "CXXFLAGS=-fPIC")
62126576 968 #:phases
f622e212
EB		 969 (modify-phases %standard-phases
970 (add-before 'configure 'patch-configure
e3a1a1de 971 (lambda* (#:key outputs #:allow-other-keys)
f622e212 972 (substitute* "configure"
b8d9c93b 973 (("/bin/mv") "mv"))
e3a1a1de
TD		 974 (substitute* "fortran/src/Makefile.in"
975 (("libhdf5_fortran_la_LDFLAGS =")
976 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
977 (assoc-ref outputs "fortran") "/lib")))
978 (substitute* "hl/fortran/src/Makefile.in"
979 (("libhdf5hl_fortran_la_LDFLAGS =")
980 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
981 (assoc-ref outputs "fortran") "/lib")))
b8d9c93b 982 #t))
fd0378a1
TD		 983 (add-after 'configure 'patch-settings
984 (lambda _
985 ;; libhdf5.settings contains the full path of the
986 ;; compilers used, and its contents are included in
987 ;; libhdf5.so. We truncate the hashes to avoid
988 ;; unnecessary store references to those compilers:
989 (substitute* "src/libhdf5.settings"
990 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
d8f46d52
RW		 991 (string-append prefix (string-take hash 10) "..."))
992 ;; Don't record the build-time kernel version to make the
993 ;; settings file reproducible.
994 (("Uname information:.*")
995 "Uname information: Linux\n"))
b8d9c93b 996 #t))
f622e212
EB		 997 (add-after 'install 'patch-references
998 (lambda* (#:key inputs outputs #:allow-other-keys)
999 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
1000 (zlib (assoc-ref inputs "zlib")))
1001 (substitute* (find-files bin "h5p?cc")
1002 (("-lz" lib)
1003 (string-append "-L" zlib "/lib " lib)))
e3a1a1de
TD		 1004 #t)))
1005 (add-after 'install 'split
1006 (lambda* (#:key inputs outputs #:allow-other-keys)
1007 ;; Move all fortran-related files
1008 (let* ((out (assoc-ref outputs "out"))
1009 (bin (string-append out "/bin"))
1010 (lib (string-append out "/lib"))
1011 (inc (string-append out "/include"))
1012 (ex (string-append out "/share/hdf5_examples/fortran"))
1013 (fort (assoc-ref outputs "fortran"))
1014 (fbin (string-append fort "/bin"))
1015 (flib (string-append fort "/lib"))
1016 (finc (string-append fort "/include"))
1017 (fex (string-append fort "/share/hdf5_examples/fortran")))
1018 (mkdir-p fbin)
1019 (mkdir-p flib)
1020 (mkdir-p finc)
1021 (mkdir-p fex)
b0d1e60f
PG		 1022 ;; Note: When built with --enable-parallel, the 'h5fc' file
1023 ;; doesn't exist, hence this condition.
1024 (when (file-exists? (string-append bin "/h5fc"))
1025 (rename-file (string-append bin "/h5fc")
1026 (string-append fbin "/h5fc")))
e3a1a1de
TD		 1027 (for-each (lambda (file)
1028 (rename-file file
1029 (string-append flib "/" (basename file))))
1030 (find-files lib ".*fortran.*"))
1031 (for-each (lambda (file)
1032 (rename-file file
1033 (string-append finc "/" (basename file))))
1034 (find-files inc ".*mod"))
1035 (for-each (lambda (file)
1036 (rename-file file
1037 (string-append fex "/" (basename file))))
1038 (find-files ex ".*"))
1039 (delete-file-recursively ex))
1040 #t)))))
0a44f9c4 1041 (home-page "https://www.hdfgroup.org")
516e93f8 1042 (synopsis "Management suite for extremely large and complex data")
7ee3f1a2
JD		 1043 (description "HDF5 is a suite that makes possible the management of
1044extremely large and complex data collections.")
d4bf49b1 1045 (license (license:x11-style
0a44f9c4 1046 "https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
7ee3f1a2 1047
bb47aca5
RW		 1048(define-public hdf5-1.10
1049 (package (inherit hdf5)
cb169aae 1050 (version "1.10.6")
bb47aca5
RW		 1051 (source
1052 (origin
1053 (method url-fetch)
1054 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
1055 "hdf5-" (version-major+minor version)
1056 "/hdf5-" version "/src/hdf5-"
1057 version ".tar.bz2")
1058 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
1059 "current"
1060 (apply string-append
1061 (take (string-split version #\.) 2))
1062 "/src/hdf5-" version ".tar.bz2")))
1063 (sha256
cb169aae 1064 (base32 "1gf38x51128hn00744358w27xgzjk0ff4wra4yxh2lk804ck1mh9"))
94fea21b 1065 (patches (search-patches "hdf5-config-date.patch"))))))
bb47aca5 1066
2fd26d05
TD		 1067(define-public hdf-java
1068 (package
2a509880
RW		 1069 (name "hdf-java")
1070 (version "3.3.2")
1071 (source
1072 (origin
1073 (method url-fetch)
1074 (uri (string-append
0a44f9c4 1075 "https://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
2a509880
RW		 1076 version "/src/CMake-hdfjava-" version ".tar.gz"))
1077 (sha256
1078 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
1079 (modules '((guix build utils)))
1080 (snippet ; Make sure we don't use the bundled sources and binaries.
1081 `(begin
1082 (for-each delete-file
1083 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
1084 "HDF4.tar.gz" "HDF5.tar.gz"))
1085 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
1086 #t))))
1087 (build-system gnu-build-system)
1088 (native-inputs
1089 `(("jdk" ,icedtea "jdk")
1090 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
1091 ;; For tests:
1092 ("hamcrest-core" ,java-hamcrest-core)
1093 ("junit" ,java-junit)
1094 ("slf4j-simple" ,java-slf4j-simple)))
1095 (inputs
1096 `(("hdf4" ,hdf4)
1097 ("hdf5" ,hdf5)
1098 ("zlib" ,zlib)
1099 ("libjpeg" ,libjpeg)
1100 ("slf4j-api" ,java-slf4j-api)))
1101 (arguments
1102 `(#:configure-flags
1103 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
1104 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
1105 (assoc-ref %build-inputs "jdk") "/lib" )
1106 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
1107 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
2fd26d05 1108
2a509880
RW		 1109 #:make-flags
1110 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
1111 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
1112 (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
1113 (string-append "JPEGLIB="
1114 (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
1115 "LLEXT=so")
2fd26d05 1116
2a509880
RW		 1117 #:phases
1118 (modify-phases %standard-phases
1119 (add-before 'configure 'chdir-to-source
1120 (lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
1121 (add-before 'configure 'patch-build
1122 (lambda* (#:key inputs outputs #:allow-other-keys)
1123 (substitute* "configure"
1124 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
1125 (("/bin/cat") (which "cat")))
1126 ;; Set classpath for compilation
1127 (substitute* '("hdf/hdf5lib/Makefile.in"
1128 "hdf/hdf5lib/exceptions/Makefile.in"
1129 "hdf/hdflib/Makefile.in")
1130 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
1131 (string-append (assoc-ref inputs "slf4j-api")
1132 "/share/java/slf4j-api.jar")))
1133 ;; Replace outdated config.sub and config.guess:
1134 (with-directory-excursion "config"
1135 (for-each (lambda (file)
1136 (install-file
1137 (string-append (assoc-ref inputs "automake")
1138 "/share/automake-"
1139 ,(version-major+minor (package-version automake))
1140 "/" file) "."))
1141 '("config.sub" "config.guess")))
64dc8b0b 1142
2a509880
RW		 1143 ;; Fix embedded version number
1144 (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
1145 (substitute* "hdf/hdf5lib/H5.java"
1146 (("1, 8, 19")
1147 (string-join hdf5version ", "))))
64dc8b0b 1148
2a509880
RW		 1149 (mkdir-p (string-append (assoc-ref outputs "out")))
1150 ;; Set classpath for tests
1151 (let* ((build-dir (getcwd))
1152 (lib (string-append build-dir "/lib"))
1153 (jhdf (string-append lib "/jhdf.jar"))
1154 (jhdf5 (string-append lib "/jhdf5.jar"))
1155 (testjars
1156 (map (lambda (i)
1157 (string-append (assoc-ref inputs i)
1158 "/share/java/" i ".jar"))
1159 '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
1160 (class-path
1161 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
2fd26d05 1162
2a509880
RW		 1163 (substitute* '("test/hdf5lib/Makefile.in"
1164 "test/hdf5lib/junit.sh.in"
1165 "examples/runExample.sh.in")
1166 (("/usr/bin/test")
1167 (string-append (assoc-ref inputs "coreutils")
1168 "/bin/test"))
1169 (("/usr/bin/uname")
1170 (string-append (assoc-ref inputs "coreutils")
1171 "/bin/uname"))
1172 (("CLASSPATH=[^\n]*")
1173 (string-append "CLASSPATH=" class-path)))
1174 (setenv "CLASSPATH" class-path))
1175 #t))
1176 (add-before 'check 'build-examples
1177 (lambda _
1178 (apply invoke `("javac"
1179 ,@(find-files "examples" ".*\\.java"))))))
2fd26d05 1180
2a509880 1181 #:parallel-build? #f
2fd26d05 1182
2a509880
RW		 1183 #:parallel-tests? #f ))
1184 (home-page "https://support.hdfgroup.org/products/java")
1185 (synopsis "Java interface for the HDF4 and HDF5 libraries")
1186 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
2fd26d05
TD		 1187the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
1188implemented in C.")
1189
2a509880
RW		 1190 ;; BSD-style license:
1191 (license (license:x11-style
1192 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
2fd26d05
TD		 1193/current/src/unpacked/COPYING"))))
1194
d3c4f3bb
TD		 1195(define-public hdf-eos2
1196 (package
1197 (name "hdf-eos2")
1198 (version "19.1.0")
1199 (source
1200 (origin
1201 (method url-fetch)
1202 (uri "ftp://edhs1.gsfc.nasa.gov\
1203/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
1204 (sha256
1205 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
1206 (patches (search-patches "hdf-eos2-remove-gctp.patch"
1207 "hdf-eos2-build-shared.patch"
1208 "hdf-eos2-fortrantests.patch"))))
1209 (build-system gnu-build-system)
1210 (native-inputs
1211 `(("gfortran" ,gfortran)))
1212 (inputs
1213 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
25bdbb61 1214 ;; XXX: These inputs are really dependencies of hdf4.
d3c4f3bb
TD		 1215 ("zlib" ,zlib)
1216 ("libjpeg" ,libjpeg)
25bdbb61
MB		 1217 ("libtirpc" ,libtirpc)
1218
d3c4f3bb
TD		 1219 ("gctp" ,gctp)))
1220 (arguments
1221 `( #:configure-flags '("--enable-install-include" "--enable-shared"
1222 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
1223 #:parallel-tests? #f))
2aaa09f1 1224 (home-page "https://hdfeos.org/software/library.php#HDF-EOS2")
d3c4f3bb
TD		 1225 (synopsis "HDF4-based data format for NASA's Earth Observing System")
1226 (description "HDF-EOS2 is a software library built on HDF4 which supports
1227the construction of data structures used in NASA's Earth Observing
1228System (Grid, Point and Swath).")
1229
1230 ;; Source files carry a permissive license header.
1231 (license (license:non-copyleft home-page))))
1232
0f43f835
TD		 1233(define-public hdf-eos5
1234 (package
1235 (name "hdf-eos5")
1236 (version "1.15")
1237 (source (origin
1238 (method url-fetch)
1239 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1240/edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1241 (sha256
1242 (base32
1243 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1244 (patches (search-patches "hdf-eos5-build-shared.patch"
1245 "hdf-eos5-remove-gctp.patch"
1246 "hdf-eos5-fix-szip.patch"
1247 "hdf-eos5-fortrantests.patch"))))
1248 (native-inputs
1249 `(("gfortran" ,gfortran)))
1250 (build-system gnu-build-system)
1251 (inputs
1252 `(("hdf5" ,hdf5)
1253 ("zlib" ,zlib)
1254 ("gctp" ,gctp)))
1255 (arguments
1256 `(#:configure-flags '("--enable-install-include" "--enable-shared"
1257 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1258 #:parallel-tests? #f))
1259 (synopsis "HDF5-based data format for NASA's Earth Observing System")
1260 (description
1261 "HDF-EOS5 is a software library built on HDF5 to support the construction
1262of data structures used in NASA's Earth Observing System (Grid, Point and
1263Swath).")
1264 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1265
1266 ;; Source files carry a permissive license header.
1267 (license (license:non-copyleft home-page))))
1268
c8378eea
EB		 1269(define-public hdf5-parallel-openmpi
1270 (package (inherit hdf5)
1271 (name "hdf5-parallel-openmpi")
1272 (inputs
1273 `(("mpi" ,openmpi)
1274 ,@(package-inputs hdf5)))
1275 (arguments
45201bf2
PG		 1276 (substitute-keyword-arguments (package-arguments hdf5)
1277 ((#:configure-flags flags)
549d1571
LC		 1278 ``("--enable-parallel"
1279 ,@(delete "--enable-cxx"
1280 (delete "--enable-threadsafe" ,flags))))
c8378eea
EB		 1281 ((#:phases phases)
1282 `(modify-phases ,phases
45201bf2
PG		 1283 (add-after 'build 'mpi-setup
1284 ,%openmpi-setup)
c8378eea
EB		 1285 (add-before 'check 'patch-tests
1286 (lambda _
1287 ;; OpenMPI's mpirun will exit with non-zero status if it
1288 ;; detects an "abnormal termination", i.e. any process not
784c3da1 1289 ;; calling MPI_Finalize(). Since the test is explicitly
c8378eea
EB		 1290 ;; avoiding MPI_Finalize so as not to have at_exit and thus
1291 ;; H5C_flush_cache from being called, mpirun will always
1292 ;; complain, so turn this test off.
1293 (substitute* "testpar/Makefile"
1294 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1295 (string-append front back "\n")))
1296 (substitute* "tools/h5diff/testph5diff.sh"
1297 (("/bin/sh") (which "sh")))
1298 #t))))))
1299 (synopsis "Management suite for data with parallel IO support")))
1300
00775104
EB		 1301(define-public h5check
1302 (package
1303 (name "h5check")
1304 (version "2.0.1")
1305 (source
1306 (origin
1307 (method url-fetch)
0a44f9c4 1308 (uri (string-append "https://www.hdfgroup.org/ftp/HDF5/tools/"
00775104
EB		 1309 "h5check/src/h5check-" version ".tar.gz"))
1310 (sha256
1311 (base32
1312 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1313 (build-system gnu-build-system)
1314 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
1315 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1316 (synopsis "HDF5 format checker")
1317 (description "@code{h5check} is a validation tool for verifying that an
1318HDF5 file is encoded according to the HDF File Format Specification.")
1319 (license (license:x11-style "file://COPYING"))))
1320
a53d6719
JD		 1321(define-public itpp
1322 (package
1323 (name "itpp")
1324 (version "4.3.1")
1325 (source (origin
1326 (method url-fetch)
1327 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1328 version "/itpp-"
1329 version ".tar.gz"))
1330 (sha256
1331 (base32
1332 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1333 (build-system cmake-build-system)
1334 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1335 (inputs `(("lapack" ,lapack)
1336 ("fftw" ,fftw)))
3a4d5df2
RW		 1337 ;; FIXME: Even though the fonts are available dvips complains:
1338 ;; "Font cmmi10 not found; characters will be left blank."
1339 (native-inputs
1340 `(("texlive" ,texlive-tiny)
1341 ("ghostscript" ,ghostscript)
1342 ("doxygen" ,doxygen)))
a53d6719
JD		 1343 (home-page "http://itpp.sourceforge.net")
1344 (synopsis "C++ library of maths, signal processing and communication classes")
1345 (description "IT++ is a C++ library of mathematical, signal processing and
1346communication classes and functions. Its main use is in simulation of
1347communication systems and for performing research in the area of
1348communications. The kernel of the library consists of generic vector and
1349matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1350similar to MATLAB, GNU Octave or SciPy.")
1351 (license license:gpl3+)))
1352
889187a4
EB		 1353(define-public netcdf
1354 (package
1355 (name "netcdf")
a4b0bfb1 1356 (version "4.4.1.1")
889187a4
EB		 1357 (source
1358 (origin
1359 (method url-fetch)
1360 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1361 "netcdf-" version ".tar.gz"))
1362 (sha256
1363 (base32
a4b0bfb1
EB		 1364 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1365 (patches (search-patches "netcdf-date-time.patch"
1366 "netcdf-tst_h_par.patch"))))
889187a4
EB		 1367 (build-system gnu-build-system)
1368 (native-inputs
1369 `(("m4" ,m4)
1370 ("doxygen" ,doxygen)
1371 ("graphviz" ,graphviz)))
1372 (inputs
db825570
TD		 1373 `(("hdf4" ,hdf4-alt)
1374 ("hdf5" ,hdf5)
1375 ("zlib" ,zlib)
1376 ("libjpeg" ,libjpeg)))
889187a4 1377 (arguments
db825570 1378 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
43d01672
TD		 1379
1380 #:phases (modify-phases %standard-phases
1381 (add-before 'configure 'fix-source-date
1382 (lambda _
1383 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1384 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1385 ;; to '1st hour of the current day', and therefore makes the
1386 ;; package not reproducible.
1387 (substitute* "./configure"
1388 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1389 "date --date='@0'"))
1390 #t))
1391 (add-after 'configure 'patch-settings
1392 (lambda _
1393 ;; libnetcdf.settings contains the full filename of the compilers
1394 ;; used to build the library. We truncate the hashes of those
1395 ;; filenames to avoid unnecessary references to the corresponding
1396 ;; store items.
1397 (substitute* "libnetcdf.settings"
1398 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1399 (string-append prefix (string-take hash 10) "...")))
1400 #t)))
1401
889187a4 1402 #:parallel-tests? #f)) ;various race conditions
821aa687 1403 (home-page "https://www.unidata.ucar.edu/software/netcdf/")
889187a4
EB		 1404 (synopsis "Library for scientific data")
1405 (description "NetCDF is an interface for scientific data access and a
1406software library that provides an implementation of the interface. The netCDF
1407library defines a machine-independent format for representing scientific data.
1408Together, the interface, library, and format support the creation, access, and
1409sharing of scientific data.")
1410 (license (license:x11-style "file://COPYRIGHT"))))
1411
1412(define-public netcdf-parallel-openmpi
1413 (package (inherit netcdf)
1414 (name "netcdf-parallel-openmpi")
1415 (inputs
1416 `(("mpi" ,openmpi)
1417 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1418 (package-inputs netcdf))))
1419 ;; TODO: Replace pkg-config references in nc-config with absolute references
1420 (arguments
1421 (substitute-keyword-arguments (package-arguments netcdf)
1422 ((#:configure-flags flags)
1423 `(cons* "CC=mpicc" "CXX=mpicxx"
1424 "--enable-parallel-tests"
1425 ;; Shared libraries not supported with parallel IO.
1426 "--disable-shared" "--with-pic"
1427 ,flags))))))
1428
300200b6
TD		 1429(define-public netcdf-fortran
1430 (package
1431 (name "netcdf-fortran")
1432 (version "4.4.4")
1433 (source (origin
1434 (method url-fetch)
1435 (uri (string-append
1436 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1437 version ".tar.gz"))
1438 (sha256
1439 (base32
1440 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1441 (build-system gnu-build-system)
1442 (arguments
1443 `(#:parallel-tests? #f))
1444 (inputs
1445 `(("netcdf" ,netcdf)))
1446 (native-inputs
1447 `(("gfortran" ,gfortran)))
1448 (synopsis "Fortran interface for the netCDF library")
1449 (description (package-description netcdf))
1450 (home-page (package-home-page netcdf))
1451 (license (package-license netcdf))))
1452
1b39a196
RJ		 1453(define-public nlopt
1454 (package
1455 (name "nlopt")
1456 (version "2.4.2")
1457 (source (origin
1458 (method url-fetch)
1459 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1460 version ".tar.gz"))
1461 (sha256
1462 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1463 (build-system gnu-build-system)
1464 (arguments
1465 `(;; Shared libraries are not built by default. They are required to
1466 ;; build the Guile, Octave, and Python bindings.
1467 #:configure-flags '("--enable-shared")
1468
1469 #:phases
1470 (modify-phases %standard-phases
1471 (add-before 'configure 'set-libnlopt-file-name
1472 (lambda* (#:key outputs #:allow-other-keys)
1473 ;; Make sure the Scheme module refers to the library by its
1474 ;; absolute file name (we cannot do that from a snippet
1475 ;; because the expansion of @libdir@ contains
1476 ;; ${exec_prefix}.)
1477 (let ((out (assoc-ref outputs "out")))
1478 (substitute* "swig/nlopt.scm.in"
1479 (("libnlopt")
1480 (string-append out "/lib/libnlopt")))
1481 #t))))))
1482 (inputs `(("guile" ,guile-2.0)))
1483 (native-inputs `(("pkg-config" ,pkg-config)))
1484 (home-page "http://ab-initio.mit.edu/wiki/")
1485 (synopsis "Library for nonlinear optimization")
1486 (description "NLopt is a library for nonlinear optimization, providing a
1487common interface for a number of different free optimization routines available
1488online as well as original implementations of various other algorithms.")
1489 (license license:lgpl2.1+)))
1490
005c787d
LC		 1491(define-public ipopt
1492 (package
1493 (name "ipopt")
98a5cd51 1494 (version "3.12.12")
005c787d
LC		 1495 (source (origin
1496 (method url-fetch)
1497 (uri (string-append
1498 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1499 version".tgz"))
1500 (sha256
1501 (base32
98a5cd51 1502 "07yn9rzdswjk8n246qq6ci9ssf2bcplkifcpsfz9j6cdxw9vgbkv"))
005c787d
LC		 1503 (modules '((guix build utils)))
1504 (snippet
1505 ;; Make sure we don't use the bundled software.
6cbee49d
MW		 1506 '(begin
1507 (delete-file-recursively "ThirdParty")
1508 #t))))
005c787d 1509 (build-system gnu-build-system)
ad1c4537
LC		 1510 (arguments
1511 '(#:phases (modify-phases %standard-phases
1512 (add-after 'install 'add--L-flags-in-ipopt.pc
1513 (lambda* (#:key inputs outputs #:allow-other-keys)
1514 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1515 ;; move it to "Libs.private" where it belongs, and add a
1516 ;; '-L' flag for LAPACK.
1517 (let ((out (assoc-ref outputs "out"))
1518 (lapack (assoc-ref inputs "lapack")))
1519 (substitute* (string-append out "/lib/pkgconfig/"
1520 "ipopt.pc")
1521 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1522 (string-append "Libs: " before " " after "\n"
1523 "Libs.private: " before
1524 "-L" lapack "/lib -llapack -lblas "
1525 after "\n")))
1526 #t))))))
005c787d
LC		 1527 (native-inputs
1528 `(("gfortran" ,gfortran)))
1529 (inputs
1530 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
ad1c4537 1531 `(("lapack" ,lapack))) ;for both libblas and liblapack
005c787d
LC		 1532 (home-page "http://www.coin-or.org")
1533 (synopsis "Large-scale nonlinear optimizer")
1534 (description
1535 "The Interior Point Optimizer (IPOPT) is a software package for
1536large-scale nonlinear optimization. It provides C++, C, and Fortran
1537interfaces.")
1538 (license license:epl1.0)))
1539
ecfbc51f
RW		 1540(define-public clp
1541 (package
1542 (name "clp")
1543 (version "1.17.1")
1544 (source (origin
1545 (method url-fetch)
1546 (uri (string-append "https://www.coin-or.org/download/source/"
1547 "Clp/Clp-" version ".tgz"))
1548 (sha256
1549 (base32
1550 "1wdg820g3iikf9344ijwsc8sy6c0m6im42bzzizm6rlmkvnmxhk9"))
1551 (modules '((guix build utils)))
1552 (snippet
1553 ;; Make sure we don't use the bundled software.
1554 '(begin
1555 (delete-file-recursively "ThirdParty")
1556 #t))))
1557 (build-system gnu-build-system)
1558 (native-inputs
1559 `(("gfortran" ,gfortran)
1560 ("pkg-config" ,pkg-config)))
1561 (inputs
1562 `(("openblas" ,openblas)))
1563 (home-page "https://www.coin-or.org")
1564 (synopsis "Linear programming solver")
1565 (description
1566 "CLP is a high quality linear programming solver. Its main strengths are
1567its dual and primal Simplex algorithms. It also has a barrier algorithm for
1568linear and quadratic objectives. There are limited facilities for nonlinear
1569and quadratic objectives using the Simplex algorithm.")
1570 (license license:epl1.0)))
1571
f9940ef1
LC		 1572(define-public ceres
1573 (package
1574 (name "ceres-solver")
e0bee0de 1575 (version "1.14.0")
f9940ef1
LC		 1576 (home-page "http://ceres-solver.org/")
1577 (source (origin
1578 (method url-fetch)
1579 (uri (string-append home-page "ceres-solver-"
1580 version ".tar.gz"))
1581 (sha256
1582 (base32
e0bee0de 1583 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
f9940ef1
LC		 1584 (build-system cmake-build-system)
1585 (arguments
1586 ;; TODO: Build HTML user documentation and install separately.
bc3a2e35 1587 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
f9940ef1
LC		 1588 "-DBUILD_SHARED_LIBS=ON")
1589
1590 #:phases (modify-phases %standard-phases
1591 (add-before 'configure 'set-library-directory
1592 (lambda _
1593 ;; Install libraries to lib/, not lib64/.
1594 (substitute* "internal/ceres/CMakeLists.txt"
1595 (("set\\(LIB_SUFFIX \"64\"\\)")
1596 "set(LIB_SUFFIX \"\")"))
1597 #t)))))
1598 (native-inputs
1599 `(("pkg-config" ,pkg-config)))
468e0b18
LC		 1600 (propagated-inputs
1601 `(("glog" ,glog))) ;for #include <glog/glog.h>
f9940ef1
LC		 1602 (inputs
1603 `(("eigen" ,eigen)
1604 ("blas" ,openblas)
1605 ("lapack" ,lapack)
1606 ("suitesparse" ,suitesparse)
1607 ("gflags" ,gflags)))
1608 (synopsis "C++ library for solving large optimization problems")
1609 (description
1610 "Ceres Solver is a C++ library for modeling and solving large,
1611complicated optimization problems. It is a feature rich, mature and
1612performant library which has been used in production since 2010. Ceres Solver
1613can solve two kinds of problems:
1614@enumerate
1615@item non-linear least squares problems with bounds constraints;
1616@item general unconstrained optimization problems.
1617@end enumerate\n")
1618 (license license:bsd-3)))
1619
b66741ed 1620;; For a fully featured Octave, users are strongly recommended also to install
5ca4fe96 1621;; the following packages: less, ghostscript, gnuplot.
5537603f 1622(define-public octave-cli
668c06ac 1623 (package
5537603f 1624 (name "octave-cli")
8a0dd289 1625 (version "5.2.0")
668c06ac
JD		 1626 (source
1627 (origin
1628 (method url-fetch)
1629 (uri (string-append "mirror://gnu/octave/octave-"
f5a077b1 1630 version ".tar.lz"))
668c06ac
JD		 1631 (sha256
1632 (base32
8a0dd289 1633 "1848dq6nxzal8gwjrcp6xhi5gq96w89nss9d9rz75q408gb3mbl6"))))
668c06ac
JD		 1634 (build-system gnu-build-system)
1635 (inputs
697df13f
EF		 1636 `(("alsa-lib" ,alsa-lib)
1637 ("arpack" ,arpack-ng)
8a0dd289 1638 ("bdb" ,bdb)
697df13f 1639 ("curl" ,curl)
1ec78e9d
EB		 1640 ("fftw" ,fftw)
1641 ("fftwf" ,fftwf)
668c06ac
JD		 1642 ("fltk" ,fltk)
1643 ("fontconfig" ,fontconfig)
1644 ("freetype" ,freetype)
697df13f
EF		 1645 ("gl2ps" ,gl2ps)
1646 ("glpk" ,glpk)
1ec78e9d 1647 ("glu" ,glu)
ab5f3f21 1648 ("graphicsmagick" ,graphicsmagick)
697df13f
EF		 1649 ("hdf5" ,hdf5)
1650 ("lapack" ,lapack)
ab5f3f21 1651 ("libsndfile" ,libsndfile)
697df13f
EF		 1652 ("libxft" ,libxft)
1653 ("mesa" ,mesa)
1654 ("pcre" ,pcre)
ab5f3f21 1655 ("portaudio" ,portaudio)
697df13f
EF		 1656 ("qhull" ,qhull)
1657 ("readline" ,readline)
1658 ("suitesparse" ,suitesparse)
1659 ("texinfo" ,texinfo)
1660 ("zlib" ,zlib)))
668c06ac 1661 (native-inputs
f5a077b1
EF		 1662 `(("lzip" ,lzip)
1663 ("gfortran" ,gfortran)
668c06ac
JD		 1664 ("pkg-config" ,pkg-config)
1665 ("perl" ,perl)
1ec78e9d
EB		 1666 ;; The following inputs are not actually used in the build process.
1667 ;; However, the ./configure gratuitously tests for their existence and
1668 ;; assumes that programs not present at build time are also not, and
1669 ;; can never be, available at run time! If these inputs are therefore
1670 ;; not present, support for them will be built out. However, Octave
1671 ;; will still run without them, albeit without the features they
668c06ac
JD		 1672 ;; provide.
1673 ("less" ,less)
668c06ac
JD		 1674 ("ghostscript" ,ghostscript)
1675 ("gnuplot" ,gnuplot)))
116af86f
KK		 1676 ;; Octave code uses this variable to detect directories holding multiple CA
1677 ;; certificates to verify peers with. This is required for the networking
1678 ;; functions that require encryption to work properly.
1679 (native-search-paths
1680 (list (search-path-specification
1681 (variable "CURLOPT_CAPATH")
1682 (files '("etc/ssl/certs")))))
668c06ac 1683 (arguments
b7b27a8f
KY		 1684 `(#:configure-flags
1685 (list (string-append "--with-shell="
1686 (assoc-ref %build-inputs "bash")
5ca4fe96
AI		 1687 "/bin/sh"))
1688 #:phases
1689 (modify-phases %standard-phases
1690 (add-after 'configure 'configure-makeinfo
1691 (lambda* (#:key inputs #:allow-other-keys)
b18b9d20
AI		 1692 (substitute* "libinterp/corefcn/help.h"
1693 (("\"makeinfo\"")
1694 (string-append
1695 "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
5ca4fe96 1696 #t)))))
f5a077b1 1697 (home-page "https://www.gnu.org/software/octave/")
668c06ac 1698 (synopsis "High-level language for numerical computation")
1ec78e9d
EB		 1699 (description "GNU Octave is a high-level interpreted language that is
1700specialized for numerical computations. It can be used for both linear and
1701non-linear applications and it provides great support for visualizing results.
1702Work may be performed both at the interactive command-line as well as via
1703script files.")
668c06ac 1704 (license license:gpl3+)))
3de01d3f 1705
e0ae7e73 1706(define-public octave
5537603f 1707 (package (inherit octave-cli)
e0ae7e73 1708 (name "octave")
7a3772b3 1709 (source (origin
5537603f 1710 (inherit (package-source octave-cli))))
36ce25f0
KK		 1711 (inputs
1712 `(("qscintilla" ,qscintilla)
1713 ("qt" ,qtbase)
5537603f 1714 ,@(package-inputs octave-cli)))
36ce25f0
KK		 1715 (native-inputs
1716 `(("qttools" , qttools) ;for lrelease
70bb5d88 1717 ("texlive" ,(texlive-union (list texlive-epsf))) ; for texi2dvi
5537603f 1718 ,@(package-native-inputs octave-cli)))
36ce25f0 1719 (arguments
5537603f 1720 (substitute-keyword-arguments (package-arguments octave-cli)
36ce25f0
KK		 1721 ((#:phases phases)
1722 `(modify-phases ,phases
1723 (add-before 'configure 'patch-qscintilla-library-name
1724 (lambda* (#:key inputs #:allow-other-keys)
1725 ;; The QScintilla library that the Octave configure script tries
1726 ;; to link with should be named libqscintilla-qt5.so, but the
1727 ;; QScintilla input provides the shared library as
1728 ;; libqscintilla2_qt5.so.
1729 (substitute* "configure"
1730 (("qscintilla2-qt5")
1731 "qscintilla2_qt5"))
1732 #t))))))))
1733
5d4bd4cc
PG		 1734(define-public opencascade-oce
1735 (package
1736 (name "opencascade-oce")
1737 (version "0.17.2")
1738 (source
1739 (origin
830971bf
TGR		 1740 (method git-fetch)
1741 (uri (git-reference
1742 (url "https://github.com/tpaviot/oce.git")
1743 (commit (string-append "OCE-" version))))
1744 (file-name (git-file-name name version))
a4f393b7 1745 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
5d4bd4cc 1746 (sha256
830971bf 1747 (base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69"))))
5d4bd4cc
PG		 1748 (build-system cmake-build-system)
1749 (arguments
1750 '(#:configure-flags
1751 (list "-DOCE_TESTING:BOOL=ON"
1752 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1753 "-DOCE_DRAW:BOOL=ON"
1754 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1755 (assoc-ref %outputs "out"))
1756 "-UCMAKE_INSTALL_RPATH")))
1757 (inputs
1758 `(("freetype" ,freetype)
1759 ("glu" ,glu)
1760 ("libxmu" ,libxmu)
1761 ("mesa" ,mesa)
1762 ("tcl" ,tcl)
1763 ("tk" ,tk)))
1764 (native-inputs
1765 `(("python" ,python-wrapper)))
1766 (home-page "https://github.com/tpaviot/oce")
1767 (synopsis "Libraries for 3D modeling and numerical simulation")
1768 (description
1769 "Open CASCADE is a set of libraries for the development of applications
1770dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1771C++ class libraries providing services for 3D surface and solid modeling, CAD
1772data exchange, and visualization. It is used for development of specialized
1773software dealing with 3D models in design (CAD), manufacturing (CAM),
1774numerical simulation (CAE), measurement equipment (CMM), and quality
1775control (CAQ) domains.
1776
1777This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1778patches, improvements, and experiments contributed by users over the official
1779Open CASCADE library.")
1780 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1781 ; use of header files; see
1782 ; OCCT_LGPL_EXCEPTION.txt
1783 license:public-domain; files
1784 ; src/Standard/Standard_StdAllocator.hxx and
1785 ; src/NCollection/NCollection_StdAllocator.hxx
1786 license:expat; file src/OpenGl/OpenGl_glext.h
1787 license:bsd-3)))); test framework gtest
1788
37dc2920
PG		 1789(define-public opencascade-occt
1790 (package
1791 (name "opencascade-occt")
1792 (version "7.3.0p3")
1793 (source
1794 (origin
1795 (method git-fetch)
1796 (uri (git-reference
1797 (url "https://git.dev.opencascade.org/repos/occt.git")
1798 (commit
1799 (string-append "V"
1800 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
1801 version)))))
1802 (file-name (git-file-name name version))
1803 (sha256
1804 (base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4"))
1805 (modules '((guix build utils)))
1806 (snippet
1807 '(begin
1808 ;; Remove files specific to non-free operating systems.
1809 (delete-file-recursively "samples/ios")
1810 (delete-file-recursively "samples/mfc")
1811 (delete-file-recursively "samples/qt/FuncDemo")
1812 (delete-file "genconf.bat")
1813 (delete-file "gendoc.bat")
1814 (delete-file "genproj.bat")
1815 (delete-file "upgrade.bat")
1816 ;; Remove references to deleted files.
1817 (substitute* "dox/FILES_HTML.txt"
1818 ((".*standard.*") "" )
1819 ((".*UIKitSample.*") ""))
1820 #t))))
1821 (build-system cmake-build-system)
1822 (arguments
1823 '(;; There is no test target for make. OCCT provides an
1824 ;; 'Automated Testing System', which may be accessed after
1825 ;; installation via the draw.sh script. draw.sh is located in
1826 ;; the bin directory. For details see:
1827 ;; https://www.opencascade.com/doc/occt-7.3.0/overview/html/\
1828 ;; occt_dev_guides__tests.html
1829 #:tests? #f
1830 ;; Configure without freeimage: attempting to link against the
1831 ;; freeimage version 3.17 library leads to 'undefined
1832 ;; reference' errors.
1833 #:configure-flags
1834 (list "-DUSE_FREEIMAGE:BOOL=OFF"
1835 "-DUSE_TBB:BOOL=ON"
1836 "-DUSE_VTK:BOOL=OFF"
1837 "-DBUILD_DOC_Overview:BOOL=OFF"
1838 "-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON"
1839 "-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON"
1840 "-UCMAKE_INSTALL_LIBDIR")))
1841 (inputs
1842 `(("doxygen" ,doxygen)
1843 ;("freeimage" ,freeimage)
1844 ("freetype" ,freetype)
1845 ("glu" ,glu)
1846 ("libxext" ,libxext)
1847 ("libxi" ,libxi)
1848 ("libxmu" ,libxmu)
1849 ("mesa" ,mesa)
1850 ("tbb" ,tbb)
1851 ("tcl" ,tcl)
1852 ("tk" ,tk)))
1853 ;; TODO: build Overview documentation and add 'doc' output.
1854 (home-page "https://www.opencascade.com")
1855 (synopsis "Libraries for 3D modeling and numerical simulation")
1856 (description
1857 "Open CASCADE is a set of libraries for the development of applications
1858dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1859C++ class libraries providing services for 3D surface and solid modeling, CAD
1860data exchange, and visualization. It is used for development of specialized
1861software dealing with 3D models in design (CAD), manufacturing (CAM),
1862numerical simulation (CAE), measurement equipment (CMM), and quality
1863control (CAQ) domains.
1864
1865This is the certified version of the Open Cascade Technology (OCCT) library.")
1866 (license (list ;; OCCT library:
1867 license:lgpl2.1; with an exception for the use of header
1868 ; files, see OCCT_LGPL_EXCEPTION.txt.
1869 ;; Files src/OpenGl/glext.h, adm/cmake/cotire.cmake and
1870 ;; src/OpenGl/OpenGl_HaltonSampler.hxx:
1871 license:expat
1872 ;; Files src/ExprIntrp/ExprIntrp.tab.* and
1873 ;; src/StepFile/step.tab.*:
1874 license:gpl3+ ; with Bison 2.2 exception.
1875 ;; File src/NCollection/NCollection_UtfIterator.lxx:
1876 (license:non-copyleft
1877 "https://www.unicode.org/license.html")
1878 ;; File src/NCollection/NCollection_StdAllocator.hxx:
1879 license:public-domain))))
1880
3de01d3f
EB		 1881(define-public gmsh
1882 (package
1883 (name "gmsh")
8a4d14fa 1884 (version "2.16.0")
3de01d3f
EB		 1885 (source
1886 (origin
abed5df7
PG		 1887 (method git-fetch)
1888 (uri (git-reference
1889 (url "https://gitlab.onelab.info/gmsh/gmsh.git")
1890 (commit
1891 (string-append "gmsh_"
1892 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
1893 version)))))
1894 (file-name (git-file-name name version))
3de01d3f 1895 (sha256
abed5df7 1896 (base32 "08rq4jajwmlpivnm9yifz2jhaivnz065lnk0h2zv773nwl9wf162"))
3de01d3f
EB		 1897 (modules '((guix build utils)))
1898 (snippet
1899 ;; Remove non-free METIS code
6cbee49d
MW		 1900 '(begin
1901 (delete-file-recursively "contrib/Metis")
1902 #t))))
3de01d3f 1903 (build-system cmake-build-system)
3de01d3f
EB		 1904 (propagated-inputs
1905 `(("fltk" ,fltk)
19afbea1 1906 ("gfortran" ,gfortran)
3de01d3f 1907 ("gmp" ,gmp)
40029cbe 1908 ("hdf5" ,hdf5)
3de01d3f
EB		 1909 ("lapack" ,lapack)
1910 ("mesa" ,mesa)
85f41902 1911 ("glu" ,glu)
45548139 1912 ("opencascade-oce" ,opencascade-oce)
3de01d3f
EB		 1913 ("libx11" ,libx11)
1914 ("libxext" ,libxext)))
66395a61
EF		 1915 (inputs
1916 `(("fontconfig" ,fontconfig)
1917 ("libxft" ,libxft)))
3de01d3f
EB		 1918 (arguments
1919 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1920 "-DENABLE_BUILD_SHARED:BOOL=ON"
45548139 1921 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
0746c33e 1922 (home-page "http://gmsh.info/")
3de01d3f 1923 (synopsis "3D finite element grid generator")
edf684ef
EB		 1924 (description "Gmsh is a 3D finite element grid generator with a built-in
1925CAD engine and post-processor. Its design goal is to provide a fast, light
1926and user-friendly meshing tool with parametric input and advanced
1927visualization capabilities. Gmsh is built around four modules: geometry,
1928mesh, solver and post-processing. The specification of any input to these
1929modules is done either interactively using the graphical user interface or in
1930ASCII text files using Gmsh's own scripting language.")
3de01d3f 1931 (license license:gpl2+)))
b9100e2f 1932
6d5f63b6
JD		 1933(define-public maxflow
1934 (package
1935 (name "maxflow")
0af12a13
TGR		 1936 ;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’,
1937 ;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’.
1938 (version "3.0.5")
6d5f63b6
JD		 1939 (source (origin
1940 (method git-fetch)
1941 (uri (git-reference
1942 (url "https://github.com/gerddie/maxflow.git")
0af12a13 1943 (commit version)))
2dc0a6cf 1944 (file-name (git-file-name name version))
6d5f63b6
JD		 1945 (sha256
1946 (base32
1947 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1948 (build-system cmake-build-system)
0be9038c 1949 (home-page "https://pub.ist.ac.at/~vnk/software.html")
6d5f63b6
JD		 1950 (synopsis "Library implementing Maxflow algorithm")
1951 (description "An implementation of the maxflow algorithm described in
1952@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1953Energy Minimization in Computer Vision.\n
1954Yuri Boykov and Vladimir Kolmogorov.\n
1955In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1956September 2004}")
1957 (license license:gpl3+)))
1958
b9100e2f
EB		 1959(define-public petsc
1960 (package
1961 (name "petsc")
4f7a4a06 1962 (version "3.11.2")
b9100e2f
EB		 1963 (source
1964 (origin
1965 (method url-fetch)
1966 ;; The *-lite-* tarball does not contain the *large* documentation
1967 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1968 "petsc-lite-" version ".tar.gz"))
1969 (sha256
4f7a4a06 1970 (base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx"))))
b2c52fc9
TGR		 1971 (outputs '("out" ; libraries and headers
1972 "examples")) ; ~30MiB of examples
b9100e2f
EB		 1973 (build-system gnu-build-system)
1974 (native-inputs
6fec298d 1975 `(("python" ,python-2)))
b9100e2f 1976 (inputs
19afbea1 1977 `(("gfortran" ,gfortran)
b9100e2f 1978 ("lapack" ,lapack)
f258212d 1979 ("superlu" ,superlu)
b9100e2f
EB		 1980 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1981 ;; leaving out opengl, as configuration seems to only be for mac
1982 ))
1983 (arguments
1984 `(#:test-target "test"
b2c52fc9 1985 #:parallel-build? #f ; build is parallel by default
b9100e2f
EB		 1986 #:configure-flags
1987 `("--with-mpi=0"
f258212d 1988 "--with-openmp=1"
c15be128 1989 "--with-superlu=1")
9731c412
EB		 1990 #:make-flags
1991 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1992 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1993 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
b9100e2f 1994 #:phases
64dcc289
EB		 1995 (modify-phases %standard-phases
1996 (replace 'configure
1997 ;; PETSc's configure script is actually a python script, so we can't
1998 ;; run it with bash.
1999 (lambda* (#:key outputs (configure-flags '())
2000 #:allow-other-keys)
2001 (let* ((prefix (assoc-ref outputs "out"))
2002 (flags `(,(string-append "--prefix=" prefix)
2003 ,@configure-flags)))
2004 (format #t "build directory: ~s~%" (getcwd))
2005 (format #t "configure flags: ~s~%" flags)
49fdd357 2006 (apply invoke "./configure" flags))))
64dcc289 2007 (add-after 'configure 'clean-local-references
9731c412 2008 (lambda* (#:key outputs #:allow-other-keys)
64dcc289
EB		 2009 (let ((out (assoc-ref outputs "out")))
2010 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
b730b437
EB		 2011 ;; Prevent build directory from leaking into compiled code
2012 (((getcwd)) out)
2013 ;; Scrub timestamp for reproducibility
fafd623e 2014 ((".*Libraries compiled on.*") ""))
9731c412
EB		 2015 (substitute* (find-files "." "petscvariables")
2016 ;; Do not expose build machine characteristics, set to defaults.
2017 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
2018 (("NPMAX = [:digit:]+") "NPMAX = 2"))
fafd623e 2019 #t)))
64dcc289 2020 (add-after 'install 'clean-install
10b11968
EB		 2021 ;; Try to keep installed files from leaking build directory names.
2022 (lambda* (#:key inputs outputs #:allow-other-keys)
64dcc289 2023 (let ((out (assoc-ref outputs "out")))
10b11968 2024 (substitute* (map (lambda (file)
9a899cce 2025 (string-append out "/lib/petsc/conf/" file))
fafd623e 2026 '("petscvariables"))
10b11968
EB		 2027 (((getcwd)) out))
2028 ;; Make compiler references point to the store
9a899cce 2029 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
dfdf5716
EB		 2030 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
2031 (string-append "= " (which compiler))))
10b11968
EB		 2032 ;; PETSc installs some build logs, which aren't necessary.
2033 (for-each (lambda (file)
9a899cce 2034 (let ((f (string-append out "/lib/petsc/conf/" file)))
10b11968
EB		 2035 (when (file-exists? f)
2036 (delete-file f))))
9a899cce
EB		 2037 '("configure.log" "make.log" "gmake.log"
2038 "test.log" "error.log" "RDict.db"
fafd623e 2039 "PETScBuildInternal.cmake"
10b11968 2040 ;; Once installed, should uninstall with Guix
fafd623e 2041 "uninstall.py"))
a3a99e27
EB		 2042 #t)))
2043 (add-after 'install 'move-examples
2044 (lambda* (#:key outputs #:allow-other-keys)
2045 (let* ((out (assoc-ref outputs "out"))
2046 (examples (assoc-ref outputs "examples"))
2047 (exdir (string-append out "/share/petsc/examples"))
2048 (exdir' (string-append examples "/share/petsc/examples")))
2049 (copy-recursively exdir exdir')
2050 (delete-file-recursively exdir)
fafd623e 2051 #t))))))
2299d83e 2052 (home-page "https://www.mcs.anl.gov/petsc")
16ecf3ff 2053 (synopsis "Library to solve PDEs")
b9100e2f
EB		 2054 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
2055data structures and routines for the scalable (parallel) solution of
2056scientific applications modeled by partial differential equations.")
166191b3 2057 (license (license:non-copyleft
2299d83e 2058 "https://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
b9100e2f
EB		 2059
2060(define-public petsc-complex
2061 (package (inherit petsc)
2062 (name "petsc-complex")
2063 (arguments
2064 (substitute-keyword-arguments (package-arguments petsc)
2065 ((#:configure-flags cf)
2066 `(cons "--with-scalar-type=complex" ,cf))))
16ecf3ff 2067 (synopsis "Library to solve PDEs (with complex scalars)")))
183e44ae 2068
d8c7eeb9
EB		 2069(define-public petsc-openmpi
2070 (package (inherit petsc)
2071 (name "petsc-openmpi")
2072 (inputs
9e2aa70b 2073 `(("hdf5" ,hdf5-parallel-openmpi)
af523673 2074 ("hypre" ,hypre-openmpi)
9e2aa70b
PG		 2075 ("metis" ,metis)
2076 ("mumps" ,mumps-openmpi)
2077 ("openmpi" ,openmpi)
2078 ("scalapack" ,scalapack)
72f95783 2079 ("scotch" ,pt-scotch32)
d8c7eeb9
EB		 2080 ,@(package-inputs petsc)))
2081 (arguments
2082 (substitute-keyword-arguments (package-arguments petsc)
2083 ((#:configure-flags cf)
af523673
PG		 2084 ``("--with-hypre=1"
2085 "--with-mpiexec=mpirun"
9e2aa70b
PG		 2086 "--with-metis=1"
2087 "--with-mumps=1"
2088 "--with-scalapack=1"
2089 "--with-ptscotch=1"
d8c7eeb9
EB		 2090 ,(string-append "--with-mpi-dir="
2091 (assoc-ref %build-inputs "openmpi"))
71ca16b5
PG		 2092 ,(string-append "--with-hdf5-include="
2093 (assoc-ref %build-inputs "hdf5") "/include")
2094 ,(string-append "--with-hdf5-lib="
2095 (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
2096 ,@(delete "--with-mpi=0" ,cf)))
2097 ((#:phases phases)
2098 `(modify-phases ,phases
9e2aa70b 2099 (add-before 'configure 'mpi-setup
bbe46a4a 2100 ,%openmpi-setup)))))
9e2aa70b 2101 (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
d8c7eeb9
EB		 2102
2103(define-public petsc-complex-openmpi
2104 (package (inherit petsc-complex)
2105 (name "petsc-complex-openmpi")
2106 (inputs
2107 `(("openmpi" ,openmpi)
2108 ,@(package-inputs petsc-complex)))
2109 (arguments
2110 (substitute-keyword-arguments (package-arguments petsc-complex)
2111 ((#:configure-flags cf)
2112 ``("--with-mpiexec=mpirun"
2113 ,(string-append "--with-mpi-dir="
2114 (assoc-ref %build-inputs "openmpi"))
e586c6fa
EB		 2115 ,@(delete "--with-mpi=0" ,cf)))
2116 ((#:phases phases)
2117 `(modify-phases ,phases
2118 (add-before 'configure 'mpi-setup
2119 ,%openmpi-setup)))))
16ecf3ff 2120 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
d8c7eeb9 2121
90ff2874
PG		 2122(define-public python-petsc4py
2123 (package
2124 (name "python-petsc4py")
f1cc312e 2125 (version "3.11.0")
90ff2874
PG		 2126 (source
2127 (origin
2128 (method url-fetch)
2129 (uri (pypi-uri "petsc4py" version))
2130 (sha256
2131 (base32
f1cc312e 2132 "1rm1qj5wlkhxl39by9n78lh3gbmii31wsnb8j1rr5hvfr5xgbx2q"))))
90ff2874
PG		 2133 (build-system python-build-system)
2134 (arguments
2135 `(#:phases
2136 (modify-phases %standard-phases
2137 (add-before 'build 'pre-build
2138 (lambda _
2139 ;; Define path to PETSc installation.
2140 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
2141 #t))
2142 (add-before 'check 'mpi-setup
2143 ,%openmpi-setup))))
2144 (inputs
2145 `(("petsc" ,petsc-openmpi)
2146 ("python-numpy" ,python-numpy)))
2147 (home-page "https://bitbucket.org/petsc/petsc4py/")
2148 (synopsis "Python bindings for PETSc")
2149 (description "PETSc, the Portable, Extensible Toolkit for
2150Scientific Computation, is a suite of data structures and routines for
2151the scalable (parallel) solution of scientific applications modeled by
2152partial differential equations. It employs the MPI standard for all
2153message-passing communication. @code{petsc4py} provides Python
2154bindings to almost all functions of PETSc.")
2155 (license license:bsd-3)))
2156
560acf25
MB		 2157(define-public python-kiwisolver
2158 (package
2159 (name "python-kiwisolver")
2160 (version "1.0.1")
2161 (source (origin
2162 (method url-fetch)
2163 (uri (pypi-uri "kiwisolver" version))
2164 (sha256
2165 (base32
2166 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
2167 (build-system python-build-system)
2168 (home-page "https://github.com/nucleic/kiwi")
2169 (synopsis "Fast implementation of the Cassowary constraint solver")
2170 (description
2171 "Kiwi is an efficient C++ implementation of the Cassowary constraint
2172solving algorithm. Kiwi has been designed from the ground up to be
2173lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
2174Cassowary solver with typical use cases gaining a 40x improvement. Memory
2175savings are consistently > 5x.")
2176 (license license:bsd-3)))
2177
2178(define-public python2-kiwisolver
2179 (package-with-python2 python-kiwisolver))
2180
a7f01414
EB		 2181(define-public slepc
2182 (package
2183 (name "slepc")
a13e0f3d 2184 (version "3.11.1")
a7f01414
EB		 2185 (source
2186 (origin
2187 (method url-fetch)
baeaf882
EB		 2188 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
2189 version ".tar.gz"))
a7f01414
EB		 2190 (sha256
2191 (base32
a13e0f3d 2192 "1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8"))))
a7f01414
EB		 2193 (build-system gnu-build-system)
2194 (native-inputs
a13e0f3d
EB		 2195 `(("python" ,python-2)
2196 ("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
a7f01414
EB		 2197 (inputs
2198 `(("arpack" ,arpack-ng)
2199 ("gfortran" ,gfortran)))
2200 (propagated-inputs
2201 `(("petsc" ,petsc)))
2202 (arguments
2203 `(#:parallel-build? #f ;build is parallel by default
2204 #:configure-flags
2205 `(,(string-append "--with-arpack-dir="
9cf52454 2206 (assoc-ref %build-inputs "arpack") "/lib"))
9731c412 2207 #:make-flags ;honor (parallel-job-count)
a13e0f3d
EB		 2208 `(,(format #f "MAKE_NP=~a" (parallel-job-count))
2209 ,(string-append "PETSCCONFIGDIR="
2210 (assoc-ref %build-inputs "petsc:examples")
2211 "/share/petsc/examples/config"))
a7f01414
EB		 2212 #:phases
2213 (modify-phases %standard-phases
8787c555 2214 (replace 'configure
a7f01414
EB		 2215 ;; configure is a python script, so we can't run it with bash.
2216 (lambda* (#:key inputs outputs (configure-flags '())
2217 #:allow-other-keys)
2218 (let* ((prefix (assoc-ref outputs "out"))
2219 (flags `(,(string-append "--prefix=" prefix)
2220 ,@configure-flags)))
2221 (format #t "build directory: ~s~%" (getcwd))
2222 (format #t "configure flags: ~s~%" flags)
2223 (setenv "SLEPC_DIR" (getcwd))
9cf52454 2224 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
c6840089 2225 (apply invoke "./configure" flags))))
8787c555 2226 (add-after 'install 'delete-doc
a7f01414
EB		 2227 ;; TODO: SLEPc installs HTML documentation alongside headers in
2228 ;; $out/include. We'd like to move them to share/doc, but delete
2229 ;; them for now, as they are incomplete and installing the complete
2230 ;; documentation is difficult.
2231 (lambda* (#:key outputs #:allow-other-keys)
2232 (let* ((out (assoc-ref outputs "out")))
0f6dc120
TGR		 2233 (for-each delete-file (find-files out "\\.html$"))
2234 #t)))
8787c555 2235 (add-after 'install 'clean-install
a7f01414
EB		 2236 ;; Clean up unnecessary build logs from installation.
2237 (lambda* (#:key outputs #:allow-other-keys)
2238 (let ((out (assoc-ref outputs "out")))
2239 (for-each (lambda (file)
2240 (let ((f (string-append out "/lib/slepc/conf/" file)))
2241 (when (file-exists? f)
2242 (delete-file f))))
2243 '("configure.log" "make.log" "gmake.log"
2244 "test.log" "error.log" "RDict.db"
0f6dc120
TGR		 2245 "uninstall.py"))
2246 #t))))))
a7f01414
EB		 2247 (home-page "http://slepc.upv.es")
2248 (synopsis "Scalable library for eigenproblems")
2249 (description "SLEPc is a software library for the solution of large sparse
2250eigenproblems on parallel computers. It can be used for the solution of
2251linear eigenvalue problems formulated in either standard or generalized form,
2252as well as other related problems such as the singular value decomposition.
2253The emphasis of the software is on methods and techniques appropriate for
2254problems in which the associated matrices are sparse, for example, those
2255arising after the discretization of partial differential equations.")
3c524f21 2256 (license license:bsd-2)))
a7f01414
EB		 2257
2258(define-public slepc-complex
2259 (package (inherit slepc)
2260 (name "slepc-complex")
2261 (propagated-inputs
2262 `(("petsc" ,petsc-complex)
2263 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
2264 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
2265
2266(define-public slepc-openmpi
2267 (package (inherit slepc)
2268 (name "slepc-openmpi")
6df2a50a
LC		 2269 (arguments
2270 (substitute-keyword-arguments (package-arguments slepc)
2271 ((#:phases phases '%standard-phases)
2272 `(modify-phases ,phases
bbe46a4a
EB		 2273 (add-before 'check 'mpi-setup
2274 ,%openmpi-setup)))))
a7f01414
EB		 2275 (inputs
2276 `(("mpi" ,openmpi)
2277 ("arpack" ,arpack-ng-openmpi)
2278 ,@(alist-delete "arpack" (package-inputs slepc))))
2279 (propagated-inputs
2280 `(("petsc" ,petsc-openmpi)
2281 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
2282 (synopsis "Scalable library for eigenproblems (with MPI support)")))
2283
2284(define-public slepc-complex-openmpi
2285 (package (inherit slepc-openmpi)
2286 (name "slepc-complex-openmpi")
2287 (propagated-inputs
2288 `(("petsc" ,petsc-complex-openmpi)
2289 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
2290 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
2291
6b5687d0
PG		 2292(define-public python-slepc4py
2293 (package
2294 (name "python-slepc4py")
09bad3cd 2295 (version "3.11.0")
6b5687d0
PG		 2296 (source
2297 (origin
2298 (method url-fetch)
2299 (uri (pypi-uri "slepc4py" version))
2300 (sha256
2301 (base32
09bad3cd 2302 "1ksp08kxf4wg408b9nn39z3qfhy643j22d4rfbl30vzxk2rxh4lq"))))
6b5687d0
PG		 2303 (build-system python-build-system)
2304 (arguments
2305 `(#:phases
2306 (modify-phases %standard-phases
2307 (add-before 'build 'pre-build
2308 (lambda _
2309 ;; Define path to PETSc installation.
2310 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
2311 ;; Define path to SLEPc installation.
2312 (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
2313 #t))
2314 (add-before 'check 'mpi-setup
2315 ,%openmpi-setup))))
2316 (inputs
2317 `(("python-numpy" ,python-numpy)
2318 ("python-petsc4py" ,python-petsc4py)
2319 ("slepc" ,slepc-openmpi)))
2320 (home-page "https://bitbucket.org/slepc/slepc4py/")
2321 (synopsis "Python bindings for SLEPc")
2322 (description "SLEPc, the Scalable Library for Eigenvalue Problem
2323Computations, is based on PETSc, the Portable, Extensible Toolkit for
2324Scientific Computation. It employs the MPI standard for all
2325message-passing communication. @code{slepc4py} provides Python
2326bindings to almost all functions of SLEPc.")
2327 (license license:bsd-3)))
2328
cec86422
EB		 2329(define-public mumps
2330 (package
2331 (name "mumps")
5dbc79eb 2332 (version "5.2.1")
cec86422
EB		 2333 (source
2334 (origin
2335 (method url-fetch)
2336 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
2337 version ".tar.gz"))
2338 (sha256
2339 (base32
5dbc79eb 2340 "0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r"))
06e12395
MB		 2341 (patches (search-patches "mumps-build-parallelism.patch"
2342 "mumps-shared-libseq.patch"
2343 "mumps-shared-mumps.patch"
2344 "mumps-shared-pord.patch"))))
cec86422
EB		 2345 (build-system gnu-build-system)
2346 (inputs
2347 `(("fortran" ,gfortran)
2348 ;; These are required for linking against mumps, but we let the user
2349 ;; declare the dependency.
2350 ("blas" ,openblas)
2351 ("metis" ,metis)
2352 ("scotch" ,scotch)))
2353 (arguments
2354 `(#:modules ((ice-9 match)
2355 (ice-9 popen)
2356 (srfi srfi-1)
2357 ,@%gnu-build-system-modules)
2358 #:phases
2359 (modify-phases %standard-phases
fba78d18 2360 (replace 'configure
cec86422
EB		 2361 (lambda* (#:key inputs #:allow-other-keys)
2362 (call-with-output-file "Makefile.inc"
2363 (lambda (port)
2364 (format port "
2365PLAT =
2366LIBEXT = .a
2367OUTC = -o
2368OUTF = -o
2369RM = rm -f~:[
2370CC = gcc
2371FC = gfortran
2372FL = gfortran
2373INCSEQ = -I$(topdir)/libseq
06e12395 2374LIBSEQ = $(topdir)/libseq/libmpiseq.a
cec86422
EB		 2375LIBSEQNEEDED = libseqneeded~;
2376CC = mpicc
2377FC = mpifort
2378FL = mpifort~]
2379AR = ar vr # rules require trailing space, ugh...
2380RANLIB = ranlib
06e12395
MB		 2381BLASDIR = ~a
2382LIBBLAS = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[
2383SCALAPDIR = ~a
2384SCALAP = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~]
cec86422
EB		 2385LIBOTHERS = -pthread
2386CDEFS = -DAdd_
2387PIC = -fPIC
2388OPTF = -O2 -DALLOW_NON_INIT $(PIC)
2389OPTL = -O2 $(PIC)
2390OPTC = -O2 $(PIC)
2391INCS = $(INCSEQ)
2392LIBS = $(SCALAP) $(LIBSEQ)
2393LPORDDIR = $(topdir)/PORD/lib
2394IPORD = -I$(topdir)/PORD/include
06e12395 2395LPORD = $(LPORDDIR)/libpord.a
cec86422
EB		 2396ORDERINGSF = -Dpord~@[
2397METISDIR = ~a
2398IMETIS = -I$(METISDIR)/include
06e12395 2399LMETIS = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
cec86422
EB		 2400ORDERINGSF += -Dmetis~]~@[~:{
2401SCOTCHDIR = ~a
2402ISCOTCH = -I$(SCOTCHDIR)/include
06e12395 2403LSCOTCH = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
cec86422
EB		 2404ORDERINGSF += ~a~}~]
2405ORDERINGSC = $(ORDERINGSF)
06e12395 2406LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
cec86422
EB		 2407IORDERINGSF = $(ISCOTCH)
2408IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
2409 (assoc-ref inputs "mpi")
2410 (assoc-ref inputs "blas")
2411 (assoc-ref inputs "scalapack")
2412 (assoc-ref inputs "metis")
2413 (match (list (assoc-ref inputs "pt-scotch")
2414 (assoc-ref inputs "scotch"))
2415 ((#f #f)
2416 #f)
2417 ((#f scotch)
2418 `((,scotch "" "-Dscotch")))
2419 ((ptscotch _)
2420 `((,ptscotch
2421 "-lptesmumps -lptscotch -lptscotcherr "
2422 "-Dptscotch")))))))))
fba78d18 2423 (replace 'build
cec86422
EB		 2424 ;; By default only the d-precision library is built. Make with "all"
2425 ;; target so that all precision libraries and examples are built.
2426 (lambda _
b414cf52
TGR		 2427 (invoke "make" "all"
2428 (format #f "-j~a" (parallel-job-count)))))
fba78d18 2429 (replace 'check
cec86422
EB		 2430 ;; Run the simple test drivers, which read test input from stdin:
2431 ;; from the "real" input for the single- and double-precision
2432 ;; testers, and from the "cmplx" input for complex-precision
2433 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
2434 ;; package to prefix execution with "mpirun".
2435 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
2436 (with-directory-excursion "examples"
2437 (every
2438 (lambda (prec type)
2439 (let ((tester (apply open-pipe*
2440 `(,OPEN_WRITE
2441 ,@exec-prefix
2442 ,(string-append "./" prec
2443 "simpletest"))))
2444 (input (open-input-file
2445 (string-append "input_simpletest_" type))))
2446 (begin
2447 (dump-port input tester)
2448 (close-port input)
2449 (zero? (close-pipe tester)))))
2450 '("s" "d" "c" "z")
2451 '("real" "real" "cmplx" "cmplx")))))
fba78d18
EB		 2452 (replace 'install
2453 (lambda* (#:key outputs #:allow-other-keys)
2454 (let* ((out (assoc-ref outputs "out"))
2455 (libdir (string-append out "/lib")))
2456 (copy-recursively "lib" libdir)
2457 (copy-recursively "include" (string-append out "/include"))
2458 (when (file-exists? "libseq/libmpiseq.a")
2459 (install-file "libseq/libmpiseq.a" libdir))
06e12395
MB		 2460 (when (file-exists? "libseq/libmpiseq.so")
2461 (install-file "libseq/libmpiseq.so" libdir))
fba78d18 2462 #t))))))
cec86422
EB		 2463 (home-page "http://mumps.enseeiht.fr")
2464 (synopsis "Multifrontal sparse direct solver")
2465 (description
2466 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
57e69c1d 2467sparse system of linear equations A x = b using Gaussian elimination.")
cec86422
EB		 2468 (license license:cecill-c)))
2469
2470(define-public mumps-metis
2471 (package (inherit mumps)
2472 (name "mumps-metis")
2473 (inputs
2474 (alist-delete "scotch" (package-inputs mumps)))))
2475
2476(define-public mumps-openmpi
2477 (package (inherit mumps)
2478 (name "mumps-openmpi")
2479 (inputs
2480 `(("mpi" ,openmpi)
2481 ("scalapack" ,scalapack)
2482 ("pt-scotch" ,pt-scotch)
2483 ,@(alist-delete "scotch" (package-inputs mumps))))
2484 (arguments
2485 (substitute-keyword-arguments (package-arguments mumps)
2486 ((#:phases phases)
2487 `(modify-phases ,phases
bbe46a4a
EB		 2488 (add-before 'check 'mpi-setup
2489 ,%openmpi-setup)
6df2a50a
LC		 2490 (replace 'check
2491 (lambda _
2492 ((assoc-ref ,phases 'check)
2493 #:exec-prefix '("mpirun" "-n" "2"))))))))
cec86422
EB		 2494 (synopsis "Multifrontal sparse direct solver (with MPI)")))
2495
2496(define-public mumps-metis-openmpi
2497 (package (inherit mumps-openmpi)
2498 (name "mumps-metis-openmpi")
2499 (inputs
2500 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
2501
63e07468
BW		 2502(define-public ruby-asciimath
2503 (package
2504 (name "ruby-asciimath")
2505 (version "1.0.4")
2506 (source
2507 (origin
2508 (method url-fetch)
2509 (uri (rubygems-uri "asciimath" version))
2510 (sha256
2511 (base32
2512 "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
2513 (build-system ruby-build-system)
2514 (arguments
2515 '(#:phases
2516 (modify-phases %standard-phases
2517 ;; Apply this patch
2518 ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
2519 (add-after 'unpack 'patch-remove-spurious-backslashes
2520 (lambda _
2521 (substitute* "spec/parser_spec.rb"
2522 (("\\\\\"")
9923d5a4
TGR		 2523 "\""))
2524 #t)))))
63e07468
BW		 2525 (native-inputs
2526 `(("bundler" ,bundler)
2527 ("ruby-rspec" ,ruby-rspec)))
2528 (synopsis "AsciiMath parsing and conversion library")
2529 (description
2530 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
2531easy-to-write markup language for mathematics.")
2532 (home-page "https://github.com/asciidoctor/asciimath")
2533 (license license:expat)))
2534
183e44ae
EB		 2535(define-public superlu
2536 (package
2537 (name "superlu")
995a09e0 2538 (version "5.2.1")
183e44ae
EB		 2539 (source
2540 (origin
2541 (method url-fetch)
48fe5c36 2542 (uri (string-append "https://portal.nersc.gov/project/sparse/superlu/"
183e44ae
EB		 2543 "superlu_" version ".tar.gz"))
2544 (sha256
995a09e0
EB		 2545 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
2546 (modules '((guix build utils)))
2547 (snippet
2548 ;; Replace the non-free implementation of MC64 with a stub adapted
2549 ;; from Debian
2550 '(begin
2551 (use-modules (ice-9 regex)
2552 (ice-9 rdelim))
2553 (call-with-output-file "SRC/mc64ad.c"
2554 (lambda (port)
2555 (display "
2556#include <stdio.h>
2557#include <stdlib.h>
2558void mc64id_(int *a) {
2559 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2560 abort ();
2561}
2562void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2563 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2564 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2565 abort ();
2566}\n" port)))
2567 ;; Remove the corresponding license verbiage. MC64 license follows
2568 ;; a "------" line separator.
2569 (with-atomic-file-replacement "License.txt"
2570 (let ((rx (make-regexp "-{8}")))
2571 (lambda (in out)
2572 (let loop ()
2573 (let ((line (read-line in 'concat)))
2574 (unless (regexp-exec rx line)
2575 (display line out)
6cbee49d
MW		 2576 (loop))))
2577 #t)))))))
995a09e0 2578 (build-system cmake-build-system)
183e44ae
EB		 2579 (native-inputs
2580 `(("tcsh" ,tcsh)))
2581 (inputs
995a09e0 2582 `(("blas" ,openblas)
19afbea1 2583 ("gfortran" ,gfortran)))
183e44ae 2584 (arguments
995a09e0
EB		 2585 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2586 "-DTPL_BLAS_LIBRARIES=openblas"
677bc34d 2587 "-DBUILD_SHARED_LIBS:BOOL=YES")))
48fe5c36 2588 (home-page "https://portal.nersc.gov/project/sparse/superlu/")
183e44ae
EB		 2589 (synopsis "Supernodal direct solver for sparse linear systems")
2590 (description
2591 "SuperLU is a general purpose library for the direct solution of large,
2592sparse, nonsymmetric systems of linear equations on high performance machines.
2593The library is written in C and is callable from either C or Fortran. The
2594library routines perform an LU decomposition with partial pivoting and
2595triangular system solves through forward and back substitution. The library
2596also provides threshold-based ILU factorization preconditioners.")
995a09e0
EB		 2597 (license (list license:bsd-3
2598 license:gpl2+ ;EXAMPLE/*fgmr.c
2599 (license:fsf-free "file://SRC/colamd.h")))))
f8ed036a 2600
a54aefea
EB		 2601(define-public superlu-dist
2602 (package
2603 (name "superlu-dist")
aa2e83cc 2604 (version "6.2.0")
a54aefea
EB		 2605 (source
2606 (origin
2607 (method url-fetch)
aa2e83cc 2608 (uri (string-append "https://portal.nersc.gov/project/sparse/superlu/"
a54aefea
EB		 2609 "superlu_dist_" version ".tar.gz"))
2610 (sha256
aa2e83cc 2611 (base32 "1ynmwqajc9sc3my2hssa5k9s58ggvizqv9rdss0j7w99pbh5mnvw"))
0921eff2 2612 (modules '((guix build utils)))
29080870
EB		 2613 (snippet
2614 ;; Replace the non-free implementation of MC64 with a stub
2615 '(begin
0921eff2 2616 (call-with-output-file "SRC/mc64ad_dist.c"
29080870
EB		 2617 (lambda (port)
2618 (display "
2619#include <stdio.h>
2620#include <stdlib.h>
0921eff2 2621void mc64id_dist(int *a) {
29080870
EB		 2622 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2623 abort ();
2624}
0921eff2 2625void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
29080870
EB		 2626 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2627 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2628 abort ();
2629}\n" port)))
29080870 2630 (substitute* "SRC/util.c" ;adjust default algorithm
6161141e
EB		 2631 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
2632 ;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
2633 ;; general (i.e. non-square) processor-grid support.
2634 "RowPerm = NOROWPERM;"))
6cbee49d 2635 #t))
6161141e 2636 (patches (search-patches "superlu-dist-scotchmetis.patch"
aa2e83cc 2637 "superlu-dist-awpm-grid.patch"))))
6161141e 2638 (build-system cmake-build-system)
a54aefea
EB		 2639 (native-inputs
2640 `(("tcsh" ,tcsh)))
2641 (inputs
6161141e
EB		 2642 `(("gfortran" ,gfortran)
2643 ("blas" ,openblas)
2644 ("lapack" ,lapack)
2645 ("combblas" ,combinatorial-blas)))
a54aefea 2646 (propagated-inputs
6161141e
EB		 2647 `(("mpi" ,openmpi) ;headers include MPI heades
2648 ("parmetis" ,pt-scotch32 "metis")
2649 ("pt-scotch" ,pt-scotch32)))
a54aefea 2650 (arguments
6161141e
EB		 2651 `(#:parallel-tests? #f ;tests use MPI and OpenMP
2652 #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
2653 "-DTPL_ENABLE_COMBBLASLIB=YES"
2654 "-DTPL_BLAS_LIBRARIES=-lopenblas"
2655 "-DTPL_LAPACK_LIBRARIES=-llapack"
2656 (string-append "-DTPL_PARMETIS_LIBRARIES="
2657 (string-join
2658 '("ptscotchparmetis" "ptscotch" "ptscotcherr"
2659 "scotchmetis" "scotch" "scotcherr")
2660 ";"))
2661 (string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
2662 (assoc-ref %build-inputs "parmetis")
2663 "/include")
2664 "-DTPL_ENABLE_COMBBLASLIB=ON"
2665 (string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
2666 (assoc-ref %build-inputs "combblas")
2667 "/include/CombBLAS;"
2668 (assoc-ref %build-inputs "combblas")
2669 "/include/BipartiteMatchings")
2670 "-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
a54aefea 2671 #:phases
dc1d3cde 2672 (modify-phases %standard-phases
6161141e 2673 (add-before 'configure 'set-c++-standard
dc1d3cde 2674 (lambda _
6161141e
EB		 2675 (substitute* "CMakeLists.txt"
2676 ;; AWPM headers require C++14
2677 (("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
bbe46a4a
EB		 2678 (add-before 'check 'mpi-setup
2679 ,%openmpi-setup)
6161141e
EB		 2680 (add-before 'check 'omp-setup
2681 (lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
a54aefea
EB		 2682 (home-page (package-home-page superlu))
2683 (synopsis "Parallel supernodal direct solver")
2684 (description
2685 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2686It is targeted for distributed memory parallel machines. SuperLU_DIST is
2687implemented in ANSI C, and MPI for communications.")
2688 (license license:bsd-3)))
2689
f8ed036a
EB		 2690(define-public scotch
2691 (package
2692 (name "scotch")
fd373343 2693 (version "6.0.6")
f8ed036a
EB		 2694 (source
2695 (origin
2696 (method url-fetch)
1dc31097
TGR		 2697 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
2698 "latestfile/298/scotch_" version ".tar.gz"))
f8ed036a 2699 (sha256
fd373343
EB		 2700 (base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8"))
2701 (patches (search-patches "scotch-build-parallelism.patch"
2702 "scotch-integer-declarations.patch"))))
f8ed036a
EB		 2703 (build-system gnu-build-system)
2704 (inputs
525e83ec
VL		 2705 `(("zlib" ,zlib)))
2706 (native-inputs
2707 `(("flex" ,flex)
f8ed036a 2708 ("bison" ,bison)))
fd373343 2709 (outputs '("out" "metis"))
f8ed036a 2710 (arguments
fd373343
EB		 2711 `(#:make-flags (list (string-append "prefix=" %output))
2712 #:phases
d6602ee9
EB		 2713 (modify-phases %standard-phases
2714 (add-after
2715 'unpack 'chdir-to-src
d67a7e9e 2716 (lambda _ (chdir "src") #t))
d6602ee9
EB		 2717 (replace
2718 'configure
2719 (lambda _
2720 (call-with-output-file "Makefile.inc"
2721 (lambda (port)
2722 (format port "
f8ed036a
EB		 2723EXE =
2724LIB = .a
2725OBJ = .o
2726MAKE = make
2727AR = ar
2728ARFLAGS = -ruv
cf0ec6c4 2729CAT = cat
f8ed036a
EB		 2730CCS = gcc
2731CCP = mpicc
2732CCD = gcc
2733CPPFLAGS =~{ -D~a~}
6c798540 2734CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
f8ed036a
EB		 2735LDFLAGS = -lz -lm -lrt -lpthread
2736CP = cp
2737LEX = flex -Pscotchyy -olex.yy.c
2738LN = ln
2739MKDIR = mkdir
2740MV = mv
2741RANLIB = ranlib
2742YACC = bison -pscotchyy -y -b y
2743"
d6602ee9
EB		 2744 '("COMMON_FILE_COMPRESS_GZ"
2745 "COMMON_PTHREAD"
2746 "COMMON_RANDOM_FIXED_SEED"
fd373343 2747 "INTSIZE64" ;use 'int64_t'
cf0ec6c4
EB		 2748 ;; Prevents symbolc clashes with libesmumps
2749 "SCOTCH_RENAME"
d6602ee9
EB		 2750 ;; XXX: Causes invalid frees in superlu-dist tests
2751 ;; "SCOTCH_PTHREAD"
2752 ;; "SCOTCH_PTHREAD_NUMBER=2"
d67a7e9e
TGR		 2753 "restrict=__restrict"))))
2754 #t))
bbe46a4a 2755 (add-after 'build 'build-esmumps
cf0ec6c4 2756 (lambda _
d67a7e9e
TGR		 2757 (invoke "make"
2758 (format #f "-j~a" (parallel-job-count))
2759 "esmumps")))
fd373343
EB		 2760 (add-before 'install 'make-install-dirs
2761 (lambda* (#:key outputs #:allow-other-keys)
2762 (mkdir (assoc-ref outputs "out"))))
2763 (add-after 'install 'install-metis
2764 (lambda* (#:key outputs #:allow-other-keys)
2765 (let ((out (assoc-ref outputs "metis")))
2766 (mkdir out)
2767 ;; metis files are not installed with 'make install'
2768 (for-each (lambda (f)
2769 (install-file f (string-append out "/include")))
2770 (find-files "../include/" ".*metis\\.h"))
2771 (for-each (lambda (f)
2772 (install-file f (string-append out "/lib")))
2773 (find-files "../lib/" ".*metis\\..*"))
2774 #t))))))
d5730000 2775 (home-page "https://www.labri.fr/perso/pelegrin/scotch/")
f8ed036a
EB		 2776 (synopsis "Programs and libraries for graph algorithms")
2777 (description "SCOTCH is a set of programs and libraries which implement
2778the static mapping and sparse matrix reordering algorithms developed within
2779the SCOTCH project. Its purpose is to apply graph theory, with a divide and
2780conquer approach, to scientific computing problems such as graph and mesh
2781partitioning, static mapping, and sparse matrix ordering, in application
2782domains ranging from structural mechanics to operating systems or
2783bio-chemistry.")
2784 ;; See LICENSE_en.txt
2785 (license license:cecill-c)))
6acb4adb 2786
1c39f3b8
PG		 2787(define-public scotch32
2788 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2789 ;; some applications.
2790 (package (inherit scotch)
2791 (name "scotch32")
2792 (arguments
2793 (substitute-keyword-arguments (package-arguments scotch)
2794 ((#:phases scotch-phases)
2795 `(modify-phases ,scotch-phases
2796 (replace
2797 'configure
2798 (lambda _
2799 (call-with-output-file "Makefile.inc"
2800 (lambda (port)
2801 (format port "
2802EXE =
2803LIB = .a
2804OBJ = .o
2805MAKE = make
2806AR = ar
2807ARFLAGS = -ruv
2808CAT = cat
2809CCS = gcc
2810CCP = mpicc
2811CCD = gcc
2812CPPFLAGS =~{ -D~a~}
2813CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2814LDFLAGS = -lz -lm -lrt -lpthread
2815CP = cp
2816LEX = flex -Pscotchyy -olex.yy.c
2817LN = ln
2818MKDIR = mkdir
2819MV = mv
2820RANLIB = ranlib
2821YACC = bison -pscotchyy -y -b y
2822"
2823 '("COMMON_FILE_COMPRESS_GZ"
2824 "COMMON_PTHREAD"
2825 "COMMON_RANDOM_FIXED_SEED"
2826 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
2827 ;; Prevents symbolc clashes with libesmumps
2828 "SCOTCH_RENAME"
2829 ;; XXX: Causes invalid frees in superlu-dist tests
2830 ;; "SCOTCH_PTHREAD"
2831 ;; "SCOTCH_PTHREAD_NUMBER=2"
2832 "restrict=__restrict"))))))))))
2833 (synopsis
2834 "Programs and libraries for graph algorithms (32-bit integers)")))
2835
6acb4adb
EB		 2836(define-public pt-scotch
2837 (package (inherit scotch)
2838 (name "pt-scotch")
2839 (propagated-inputs
2840 `(("openmpi" ,openmpi))) ;Headers include MPI headers
2841 (arguments
2842 (substitute-keyword-arguments (package-arguments scotch)
2843 ((#:phases scotch-phases)
d6602ee9
EB		 2844 `(modify-phases ,scotch-phases
2845 (replace
2846 'build
d6602ee9 2847 (lambda _
c491f7f8
LC		 2848 (invoke "make" (format #f "-j~a" (parallel-job-count))
2849 "ptscotch" "ptesmumps")
2850
2851 ;; Install the serial metis compatibility library
2852 (invoke "make" "-C" "libscotchmetis" "install")))
2853 (add-before 'check 'mpi-setup
2854 ,%openmpi-setup)
2855 (replace 'check
2856 (lambda _
2857 (invoke "make" "ptcheck")))))))
6acb4adb 2858 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
5698b8b8 2859
1c25a52c
PG		 2860(define-public pt-scotch32
2861 (package (inherit scotch32)
2862 (name "pt-scotch32")
2863 (propagated-inputs
2864 `(("openmpi" ,openmpi))) ;headers include MPI headers
2865 (arguments
c4d4a779
PG		 2866 (substitute-keyword-arguments (package-arguments scotch32)
2867 ((#:phases scotch32-phases)
2868 `(modify-phases ,scotch32-phases
1c25a52c
PG		 2869 (replace 'build
2870 (lambda _
c491f7f8
LC		 2871 (invoke "make" (format #f "-j~a" (parallel-job-count))
2872 "ptscotch" "ptesmumps")
2873 ;; Install the serial metis compatibility library
2874 (invoke "make" "-C" "libscotchmetis" "install")))
2875 (add-before 'check 'mpi-setup
2876 ,%openmpi-setup)
1c25a52c
PG		 2877 (replace 'check
2878 (lambda _
c491f7f8 2879 (invoke "make" "ptcheck")))))))
1c25a52c
PG		 2880 (synopsis
2881 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2882
aa75ad00
EB		 2883(define-public metis
2884 (package
2885 (name "metis")
2886 (version "5.1.0")
2887 (source
2888 (origin
2889 (method url-fetch)
2890 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2891 "metis-" version ".tar.gz"))
2892 (sha256
2893 (base32
2894 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2895 (build-system cmake-build-system)
2896 (inputs
2897 `(("blas" ,openblas)))
2898 (arguments
2899 `(#:tests? #f ;no tests
2900 #:configure-flags `("-DSHARED=ON"
2901 ,(string-append "-DGKLIB_PATH=" (getcwd)
2902 "/metis-" ,version "/GKlib"))))
2903 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2904 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2905 (description
2906 "METIS is a set of serial programs for partitioning graphs, partitioning
2907finite element meshes, and producing fill-reducing orderings for sparse
2908matrices. The algorithms implemented in METIS are based on the multilevel
2909recursive-bisection, multilevel k-way, and multi-constraint partitioning
2910schemes.")
2911 (license license:asl2.0))) ;As of version 5.0.3
2912
700ff222
EB		 2913(define-public p4est
2914 (package
2915 (name "p4est")
4150da63 2916 (version "2.0")
700ff222
EB		 2917 (source
2918 (origin
2919 (method url-fetch)
2920 (uri (string-append "http://p4est.github.io/release/p4est-"
2921 version ".tar.gz"))
2922 (sha256
2923 (base32
4150da63 2924 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
700ff222
EB		 2925 (build-system gnu-build-system)
2926 (inputs
2927 `(("fortran" ,gfortran)
2928 ("blas" ,openblas)
2929 ("lapack" ,lapack)
2930 ("zlib" ,zlib)))
2931 (arguments
2932 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2933 (assoc-ref %build-inputs "blas")
2934 " -lopenblas")
2935 ,(string-append "LAPACK_LIBS=-L"
2936 (assoc-ref %build-inputs "lapack")
6df2a50a
LC		 2937 " -llapack"))
2938 #:phases (modify-phases %standard-phases
bbe46a4a
EB		 2939 (add-before 'check 'mpi-setup
2940 ,%openmpi-setup))))
700ff222
EB		 2941 (home-page "http://www.p4est.org")
2942 (synopsis "Adaptive mesh refinement on forests of octrees")
2943 (description
2944 "The p4est software library enables the dynamic management of a
2945collection of adaptive octrees, conveniently called a forest of octrees.
2946p4est is designed to work in parallel and scales to hundreds of thousands of
2947processor cores.")
2948 (license license:gpl2+)))
2949
2950(define-public p4est-openmpi
2951 (package (inherit p4est)
2952 (name "p4est-openmpi")
2953 (inputs
2954 `(("mpi" ,openmpi)
2955 ,@(package-inputs p4est)))
2956 (arguments
2957 (substitute-keyword-arguments (package-arguments p4est)
2958 ((#:configure-flags cf)
2959 ``("--enable-mpi" ,@,cf))))
2960 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2961
5698b8b8
JD		 2962(define-public gsegrafix
2963 (package
2964 (name "gsegrafix")
2965 (version "1.0.6")
2966 (source
2967 (origin
2968 (method url-fetch)
2969 (uri (string-append "mirror://gnu/" name "/" name "-"
2970 version ".tar.gz"))
2971 (sha256
2972 (base32
2973 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2974 (build-system gnu-build-system)
2975 (arguments
2976 `(#:configure-flags '("LDFLAGS=-lm")))
2977 (inputs
2978 `(("libgnomecanvas" ,libgnomecanvas)
2979 ("libbonoboui" ,libbonoboui)
2980 ("libgnomeui" ,libgnomeui)
2981 ("libgnomeprintui" ,libgnomeprintui)
2982 ("popt" ,popt)))
2983 (native-inputs
2984 `(("pkg-config" ,pkg-config)))
6fd52309 2985 (home-page "https://www.gnu.org/software/gsegrafix/")
5698b8b8
JD		 2986 (synopsis "GNOME application to create scientific and engineering plots")
2987 (description "GSEGrafix is an application which produces high-quality graphical
2988plots for science and engineering. Plots are specified via simple ASCII
2989parameter files and data files and are presented in an anti-aliased GNOME
2990canvas. The program supports rectangular two-dimensional plots, histograms,
2991polar-axis plots and three-dimensional plots. Plots can be printed or saved
2992to BMP, JPEG or PNG image formats.")
2993 (license license:gpl3+)))
8731e527
JD		 2994
2995(define-public maxima
2996 (package
2997 (name "maxima")
ccc963d5 2998 (version "5.43.0")
8731e527
JD		 2999 (source
3000 (origin
3001 (method url-fetch)
3002 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
3003 version "-source/" name "-" version ".tar.gz"))
3004 (sha256
3005 (base32
ccc963d5 3006 "0xyahp4c6509haxh4n1swiqm3421gplkdisa0zypclh3252sbzfw"))
fc1adab1 3007 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
8731e527 3008 (build-system gnu-build-system)
df354a77 3009 (inputs
6b2eafaa 3010 `(("gcl" ,gcl)
df354a77 3011 ("gnuplot" ,gnuplot) ;for plots
fc9c47bd 3012 ("sed" ,sed)
f36afe4d 3013 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
df354a77
FB		 3014 (native-inputs
3015 `(("texinfo" ,texinfo)
ccbc5758
KK		 3016 ("perl" ,perl)
3017 ("python" ,python)))
8731e527 3018 (arguments
df354a77
FB		 3019 `(#:configure-flags
3020 (list "--enable-gcl"
3021 (string-append "--with-posix-shell="
3022 (assoc-ref %build-inputs "bash")
3023 "/bin/sh")
3024 (string-append "--with-wish="
3025 (assoc-ref %build-inputs "tk")
3026 "/bin/wish"
3027 (let ((v ,(package-version tk)))
3028 (string-take v (string-index-right v #\.)))))
df354a77 3029 ;; By default Maxima attempts to write temporary files to
77af7b24
MW		 3030 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
3031 ;; Work around that.
df354a77 3032 #:make-flags (list "TMPDIR=/tmp")
0093b126
KK		 3033 #:phases
3034 (modify-phases %standard-phases
fc9c47bd
KK		 3035 (add-after 'unpack 'patch-paths
3036 (lambda* (#:key inputs #:allow-other-keys)
3037 (let* ((sed (string-append (assoc-ref inputs "sed") "/bin/sed"))
3038 (coreutils (assoc-ref inputs "coreutils"))
3039 (dirname (string-append coreutils "/bin/dirname"))
ccc963d5
KK		 3040 (head (string-append coreutils "/bin/head"))
3041 (perl (string-append (assoc-ref inputs "perl") "/bin/perl"))
3042 (python (string-append (assoc-ref inputs "python")
3043 "/bin/python3")))
fc9c47bd
KK		 3044 (substitute* "src/maxima.in"
3045 (("sed ") (string-append sed " "))
3046 (("dirname") dirname)
3047 (("head") head))
ccc963d5
KK		 3048 (substitute* "doc/info/Makefile.in"
3049 (("/usr/bin/env perl") perl))
3050 (substitute* "doc/info/build_html.sh.in"
3051 (("python") python))
fc9c47bd 3052 #t)))
0093b126
KK		 3053 (add-before 'check 'pre-check
3054 (lambda _
3055 (chmod "src/maxima" #o555)
3056 #t))
1472d19a
KK		 3057 (replace 'check
3058 (lambda _
3059 ;; This is derived from the testing code in the "debian/rules" file
3060 ;; of Debian's Maxima package.
3061 ;; If Maxima can successfully run this, the binary to be installed
3062 ;; should be fine.
df129041
MW		 3063 (invoke "sh" "-c"
3064 (string-append
3065 "./maxima-local "
3066 "--lisp=gcl "
3067 "--batch-string=\"run_testsuite();\" "
3068 "| grep -q \"No unexpected errors found\""))))
0093b126
KK		 3069 ;; Make sure the doc and emacs files are found in the
3070 ;; standard location. Also configure maxima to find gnuplot
3071 ;; without having it on the PATH.
3072 (add-after 'install 'post-install
3073 (lambda* (#:key outputs inputs #:allow-other-keys)
3074 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
3075 (out (assoc-ref outputs "out"))
3076 (datadir (string-append out "/share/maxima/" ,version))
3077 (binutils (string-append (assoc-ref inputs "binutils")
3078 "/bin")))
3079 (with-directory-excursion out
3080 (mkdir-p "share/emacs")
3081 (mkdir-p "share/doc")
0093b126
KK		 3082 (symlink
3083 (string-append datadir "/doc/")
3084 (string-append out "/share/doc/maxima"))
3085 (with-atomic-file-replacement
3086 (string-append datadir "/share/maxima-init.lisp")
3087 (lambda (in out)
3088 (format out "~a ~s~a~%"
3089 "(setf $gnuplot_command "
3090 (string-append gnuplot "/bin/gnuplot") ")")
3091 (dump-port in out))))
3092 ;; Ensure that Maxima will have access to the GNU binutils
3093 ;; components at runtime.
3094 (wrap-program (string-append out "/bin/maxima")
3095 `("PATH" prefix (,binutils))))
3096 #t)))))
8731e527
JD		 3097 (home-page "http://maxima.sourceforge.net")
3098 (synopsis "Numeric and symbolic expression manipulation")
3099 (description "Maxima is a system for the manipulation of symbolic and
3100numerical expressions. It yields high precision numeric results by using
3101exact fractions, arbitrary precision integers, and variable precision floating
e881752c 3102point numbers.")
8731e527
JD		 3103 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
3104 ;; Others simply say "GNU General Public License" without stating a
3105 ;; version (which implicitly means gpl1+).
3106 ;; At least one file (src/maxima.asd) says "version 2."
3107 ;; GPLv2 only is therefore the smallest subset.
f36afe4d 3108 (license license:gpl2)))
ec322be2 3109
9aafbc0c
MW		 3110(define-public wxmaxima
3111 (package
3112 (name "wxmaxima")
6607aad5 3113 (version "20.03.1")
9aafbc0c
MW		 3114 (source
3115 (origin
c93b77ad
KK		 3116 (method git-fetch)
3117 (uri (git-reference
3118 (url "https://github.com/wxMaxima-developers/wxmaxima.git")
3119 (commit (string-append "Version-" version))))
3120 (file-name (git-file-name name version))
9aafbc0c 3121 (sha256
6607aad5 3122 (base32 "09ciip0wkahps5jdsqqr72bwjrd15bacw38zp23v3hm71xfk8hky"))))
0181df53 3123 (build-system cmake-build-system)
5143517c 3124 (native-inputs
1d3c6a31
KK		 3125 `(("gettext" ,gettext-minimal)
3126 ("xorg-server" ,xorg-server-for-tests)))
3127 ;; TODO: Add libomp for multithreading support.
3128 ;; As of right now, enabling libomp causes the imageCells.wxm test to fail.
9aafbc0c
MW		 3129 (inputs
3130 `(("wxwidgets" ,wxwidgets)
de477809
SB		 3131 ("maxima" ,maxima)
3132 ;; Runtime support.
3133 ("adwaita-icon-theme" ,adwaita-icon-theme)
3134 ("gtk+" ,gtk+)
3135 ("shared-mime-info" ,shared-mime-info)))
9aafbc0c 3136 (arguments
1d3c6a31 3137 `(#:test-target "test"
0181df53 3138 #:phases
ac2ddcc6 3139 (modify-phases %standard-phases
1d3c6a31
KK		 3140 (add-before 'check 'pre-check
3141 (lambda _
3142 ;; Tests require a running X server.
3143 (system "Xvfb :1 &")
3144 (setenv "DISPLAY" ":1")
3145 (setenv "HOME" (getcwd))
3146 #t))
ac2ddcc6
KK		 3147 (add-after 'install 'wrap-program
3148 (lambda* (#:key inputs outputs #:allow-other-keys)
3149 (wrap-program (string-append (assoc-ref outputs "out")
3150 "/bin/wxmaxima")
3151 `("PATH" ":" prefix
3152 (,(string-append (assoc-ref inputs "maxima")
3153 "/bin")))
3154 ;; For GtkFileChooserDialog.
3155 `("GSETTINGS_SCHEMA_DIR" =
3156 (,(string-append (assoc-ref inputs "gtk+")
3157 "/share/glib-2.0/schemas")))
3158 `("XDG_DATA_DIRS" ":" prefix
3159 (;; Needed by gdk-pixbuf to know supported icon formats.
3160 ,(string-append
3161 (assoc-ref inputs "shared-mime-info") "/share")
3162 ;; The default icon theme of GTK+.
3163 ,(string-append
3164 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
3165 #t)))))
48446f0f 3166 (home-page "https://wxmaxima-developers.github.io/wxmaxima/")
9aafbc0c
MW		 3167 (synopsis "Graphical user interface for the Maxima computer algebra system")
3168 (description
3169 "wxMaxima is a graphical user interface for the Maxima computer algebra
3170system. It eases the use of Maxima by making most of its commands available
3171through a menu system and by providing input dialogs for commands that require
3172more than one argument. It also implements its own display engine that
3173outputs mathematical symbols directly instead of depicting them with ASCII
3174characters.
3175
3176wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
3177text and mathematical calculations to create documents, exporting of input and
3178output to TeX, and a browser for Maxima's manual including command index and
3179full text searching.")
3180 (license license:gpl2+)))
3181
b15e47f9
RW		 3182(define-public armadillo
3183 (package
3184 (name "armadillo")
f133e244 3185 (version "9.100.5")
b15e47f9
RW		 3186 (source (origin
3187 (method url-fetch)
3188 (uri (string-append "mirror://sourceforge/arma/armadillo-"
7397cd9e 3189 version ".tar.xz"))
b15e47f9
RW		 3190 (sha256
3191 (base32
f133e244 3192 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
b15e47f9 3193 (build-system cmake-build-system)
e405c0bc 3194 (arguments `(#:tests? #f)) ; no test target
b15e47f9
RW		 3195 (inputs
3196 `(("openblas" ,openblas)
3197 ("lapack" ,lapack)
3198 ("arpack" ,arpack-ng)))
3199 (home-page "http://arma.sourceforge.net/")
3200 (synopsis "C++ linear algebra library")
3201 (description
3202 "Armadillo is a C++ linear algebra library, aiming towards a good balance
3203between speed and ease of use. It is useful for algorithm development
3204directly in C++, or quick conversion of research code into production
3205environments. It can be used for machine learning, pattern recognition,
3206signal processing, bioinformatics, statistics, econometrics, etc. The library
3207provides efficient classes for vectors, matrices and cubes, as well as 150+
255fb17b 3208associated functions (e.g., contiguous and non-contiguous submatrix views).")
fe418cc5 3209 (license license:asl2.0)))
b15e47f9 3210
279663ef 3211(define-public muparser
d7cff656
LF		 3212 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
3213 ;; different hash. In order to make `guix package --upgrade` work correctly,
3214 ;; we set a Guix packaging revision.
3215 ;; When the next version of muparser is released, we can remove
3216 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
3217 (let ((upstream-version "2.2.5")
3218 (revision "2"))
3219 (package
3220 (name "muparser")
3221 (version (string-append upstream-version "-" revision))
3222 (source
3223 (origin
67f1db38
TGR		 3224 (method git-fetch)
3225 (uri (git-reference
3226 (url "https://github.com/beltoforion/muparser.git")
3227 (commit (string-append "v" upstream-version))))
3228 (file-name (git-file-name name version))
d7cff656 3229 (sha256
67f1db38 3230 (base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24"))))
d7cff656
LF		 3231 (build-system gnu-build-system)
3232 (arguments
3233 `(#:configure-flags '("--enable-samples=no")
3234 #:tests? #f)) ;no "check" target
3235 (home-page "http://muparser.beltoforion.de/")
3236 (synopsis "Fast parser library for mathematical expressions")
3237 (description
3238 "muParser is an extensible high performance math parser library. It is
3239based on transforming an expression into a bytecode and precalculating constant
3240parts of it.")
3241 (license license:expat))))
279663ef 3242
e73b49fb
RW		 3243(define-public openblas
3244 (package
3245 (name "openblas")
2ea09530 3246 (version "0.3.7")
e73b49fb
RW		 3247 (source
3248 (origin
3249 (method url-fetch)
a617fd55
MB		 3250 (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
3251 version "%20version.tar.gz"))
e73b49fb
RW		 3252 (file-name (string-append name "-" version ".tar.gz"))
3253 (sha256
3254 (base32
2ea09530 3255 "0jbdjsi0qsxahdcm42agnn1y7xpmg0hrhwjsxg0zbhs9wwy3p568"))))
e73b49fb
RW		 3256 (build-system gnu-build-system)
3257 (arguments
5789566a 3258 `(#:test-target "test"
bd0b4379
RW		 3259 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
3260 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
3261 ;; we need to disable substitutions.
71923a91
AE		 3262 #:substitutable?
3263 ,(let ((system (or (%current-target-system) (%current-system))))
3264 (or (string-prefix? "x86_64" system)
bd0b4379 3265 (string-prefix? "i686" system)
83a34647
EF		 3266 (string-prefix? "mips" system)
3267 (string-prefix? "aarch64" system)))
e73b49fb
RW		 3268 #:make-flags
3269 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
3270 "SHELL=bash"
5855756c 3271 "MAKE_NB_JOBS=0" ;use jobserver for submakes
a4384dc9
MB		 3272
3273 ;; This is the maximum number of threads OpenBLAS will ever use (that
3274 ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS
3275 ;; is used.) If we don't set it, the makefile sets it to the number
3276 ;; of cores of the build machine, which is obviously wrong.
3277 "NUM_THREADS=128"
3278
af5b817e
RW		 3279 ;; Build the library for all supported CPUs. This allows
3280 ;; switching CPU targets at runtime with the environment variable
3281 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
71923a91
AE		 3282 ;; Unfortunately, this is not supported on non-x86 architectures,
3283 ;; where it leads to failed builds.
3284 ,@(let ((system (or (%current-target-system) (%current-system))))
8a637e79
RW		 3285 (cond
3286 ((or (string-prefix? "x86_64" system)
71923a91 3287 (string-prefix? "i686" system))
8a637e79
RW		 3288 '("DYNAMIC_ARCH=1"))
3289 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
3290 ;; two available MIPS targets special extended instructions
3291 ;; for Loongson cores are used.
3292 ((string-prefix? "mips" system)
3293 '("TARGET=SICORTEX"))
83a34647
EF		 3294 ;; On aarch64 force the generic 'armv8-a' target
3295 ((string-prefix? "aarch64" system)
3296 '("TARGET=ARMV8"))
8a637e79 3297 (else '()))))
e73b49fb 3298 ;; no configure script
493937ae
DL		 3299 #:phases
3300 (modify-phases %standard-phases
3301 (delete 'configure)
3302 (add-before 'build 'set-extralib
3303 (lambda* (#:key inputs #:allow-other-keys)
3304 ;; Get libgfortran found when building in utest.
3305 (setenv "FEXTRALIB"
3306 (string-append "-L" (assoc-ref inputs "fortran-lib")
3307 "/lib"))
3308 #t)))))
e73b49fb 3309 (inputs
493937ae 3310 `(("fortran-lib" ,gfortran "lib")))
e73b49fb
RW		 3311 (native-inputs
3312 `(("cunit" ,cunit)
493937ae 3313 ("fortran" ,gfortran)
e73b49fb 3314 ("perl" ,perl)))
59695981 3315 (home-page "https://www.openblas.net/")
e73b49fb
RW		 3316 (synopsis "Optimized BLAS library based on GotoBLAS")
3317 (description
3318 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
3319 (license license:bsd-3)))
3320
daa6036f 3321(define-public openblas-ilp64
ba05be22 3322 (package/inherit openblas
daa6036f
EB		 3323 (name "openblas-ilp64")
3324 (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
3325 (arguments
3326 (substitute-keyword-arguments (package-arguments openblas)
3327 ((#:make-flags flags '())
3328 `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
3329 ,flags))))
3330 (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
3331 (license license:bsd-3)))
3332
5a7deb11
LC		 3333(define* (make-blis implementation #:optional substitutable?)
3334 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
3335source tree for a list of implementations.)
3336
3337SUBSTITUTABLE? determines whether the package is made available as a
3338substitute.
3339
3340Currently the specialization must be selected at configure-time, but work is
3341underway to allow BLIS to select the right optimized kernels at run time:
3342<https://github.com/flame/blis/issues/129>."
3343 (package
3344 (name (if (string=? implementation "reference")
3345 "blis"
3346 (string-append "blis-" implementation)))
3347 (version "0.2.2")
3348 (home-page "https://github.com/flame/blis")
3349 (source (origin
3350 (method git-fetch)
3351 (uri (git-reference (url home-page) (commit version)))
3352 (sha256
3353 (base32
3354 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
3355 (file-name (git-file-name "blis" version))))
3356 (build-system gnu-build-system)
3357 (arguments
3358 `(#:test-target "test"
3359
3360 #:substitutable? ,substitutable?
3361
3362 #:phases (modify-phases %standard-phases
3363 (replace 'configure
3364 (lambda* (#:key outputs #:allow-other-keys)
3365 ;; This is a home-made 'configure' script.
3366 (let ((out (assoc-ref outputs "out")))
1ec17821
RW		 3367 (invoke "./configure" "-p" out
3368 "-d" "opt"
3369 "--disable-static"
3370 "--enable-shared"
3371 "--enable-threading=openmp"
5a7deb11 3372
1ec17821 3373 ,implementation))))
5a7deb11
LC		 3374 (add-before 'check 'show-test-output
3375 (lambda _
3376 ;; By default "make check" is silent. Make it verbose.
3377 (system "tail -F output.testsuite &")
3378 #t)))))
3379 (synopsis "High-performance basic linear algebra (BLAS) routines")
3380 (description
3381 "BLIS is a portable software framework for instantiating high-performance
3382BLAS-like dense linear algebra libraries. The framework was designed to
3383isolate essential kernels of computation that, when optimized, immediately
3384enable optimized implementations of most of its commonly used and
3385computationally intensive operations. While BLIS exports a new BLAS-like API,
3386it also includes a BLAS compatibility layer which gives application developers
3387access to BLIS implementations via traditional BLAS routine calls.")
3388 (license license:bsd-3)))
3389
3390(define-public blis
3391 ;; This is the "reference" implementation, which is the non-optimized but
3392 ;; portable variant (no assembly).
3393 (make-blis "reference" #t))
3394
3395(define ignorance blis)
3396
3397(define-syntax-rule (blis/x86_64 processor)
3398 "Expand to a package specialized for PROCESSOR."
3399 (package
3400 (inherit (make-blis processor))
3401 (supported-systems '("x86_64-linux"))))
3402
3403(define-public blis-sandybridge
3404 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
3405 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
3406 (blis/x86_64 "sandybridge"))
3407
3408(define-public blis-haswell
3409 ;; BLIS specialized for Haswell processors (launched 2013):
3410 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
3411 (blis/x86_64 "haswell"))
3412
3413(define-public blis-knl
3414 ;; BLIS specialized for Knights Landing processor (launched 2016):
3415 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
3416 (blis/x86_64 "knl"))
3417
3418
e1605e36
RW		 3419(define-public openlibm
3420 (package
3421 (name "openlibm")
48d7ac17 3422 (version "0.6.0")
e1605e36
RW		 3423 (source
3424 (origin
ca72dd2c
TGR		 3425 (method git-fetch)
3426 (uri (git-reference
3427 (url "https://github.com/JuliaLang/openlibm.git")
3428 (commit (string-append "v" version))))
3429 (file-name (git-file-name name version))
e1605e36 3430 (sha256
ca72dd2c 3431 (base32 "08wfchmmr5200fvmn1kwq9byc1fhsq46hn0y5k8scdl74771c7gh"))))
e1605e36
RW		 3432 (build-system gnu-build-system)
3433 (arguments
3434 `(#:make-flags
3435 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3436 #:phases
3437 ;; no configure script
dc1d3cde 3438 (modify-phases %standard-phases (delete 'configure))
e1605e36 3439 #:tests? #f)) ;the tests are part of the default target
d3be5220 3440 (home-page "https://openlibm.org/")
e1605e36
RW		 3441 (synopsis "Portable C mathematical library (libm)")
3442 (description
3443 "OpenLibm is an effort to have a high quality, portable, standalone C
3444mathematical library (libm). It can be used standalone in applications and
3445programming language implementations. The project was born out of a need to
e881752c 3446have a good libm for the Julia programming language that worked consistently
e1605e36
RW		 3447across compilers and operating systems, and in 32-bit and 64-bit
3448environments.")
538c0e3b
EF		 3449 ;; Each architecture has its own make target, and there is none for mips.
3450 (supported-systems (delete "mips64el-linux" %supported-systems))
e1605e36
RW		 3451 ;; See LICENSE.md for details.
3452 (license (list license:expat
3453 license:isc
3454 license:bsd-2
3455 license:public-domain
3456 license:lgpl2.1+))))
3457
e62be58f
RW		 3458(define-public openspecfun
3459 (package
3460 (name "openspecfun")
59cd0ba4 3461 (version "0.5.3")
e62be58f
RW		 3462 (source
3463 (origin
90cea671
TGR		 3464 (method git-fetch)
3465 (uri (git-reference
3466 (url "https://github.com/JuliaLang/openspecfun.git")
3467 (commit (string-append "v" version))))
3468 (file-name (git-file-name name version))
e62be58f 3469 (sha256
90cea671 3470 (base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh"))))
e62be58f
RW		 3471 (build-system gnu-build-system)
3472 (arguments
59cd0ba4 3473 '(#:tests? #f ; no "check" target
e62be58f
RW		 3474 #:make-flags
3475 (list (string-append "prefix=" (assoc-ref %outputs "out")))
59cd0ba4
TGR		 3476 #:phases
3477 (modify-phases %standard-phases
3478 (delete 'configure)))) ; no configure script
e62be58f 3479 (inputs
19afbea1 3480 `(("fortran" ,gfortran)))
e62be58f
RW		 3481 (home-page "https://github.com/JuliaLang/openspecfun")
3482 (synopsis "Collection of special mathematical functions")
3483 (description
3484 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
3485portable package for Bessel Functions of a Complex Argument and Nonnegative
3486Order; it contains subroutines for computing Bessel functions and Airy
3487functions. Faddeeva allows computing the various error functions of arbitrary
3488complex arguments (Faddeeva function, error function, complementary error
3489function, scaled complementary error function, imaginary error function, and
3490Dawson function); given these, one can also easily compute Voigt functions,
3491Fresnel integrals, and similar related functions as well.")
3492 ;; Faddeeva is released under the Expat license; AMOS is included as
3493 ;; public domain software.
3494 (license (list license:expat license:public-domain))))
3495
2742f87e
RW		 3496(define-public suitesparse
3497 (package
3498 (name "suitesparse")
aac148a8 3499 (version "5.7.1")
2742f87e
RW		 3500 (source
3501 (origin
aac148a8
FG		 3502 (method git-fetch)
3503 (uri (git-reference
3504 (url "https://github.com/DrTimothyAldenDavis/SuiteSparse.git")
3505 (commit (string-append "v" version))))
3506 (file-name (git-file-name name version))
2742f87e
RW		 3507 (sha256
3508 (base32
aac148a8
FG		 3509 "174p3l78kv9gaa0i5hflyai2ydwnjzh34k9938sl4aa3li0543s8"))
3510 (patches (search-patches "suitesparse-mongoose-cmake.patch"))
bd5b5ac0
EB		 3511 (modules '((guix build utils)))
3512 (snippet
3513 ;; Remove bundled metis source
6cbee49d
MW		 3514 '(begin
3515 (delete-file-recursively "metis-5.1.0")
3516 #t))))
2742f87e
RW		 3517 (build-system gnu-build-system)
3518 (arguments
bd5b5ac0 3519 '(#:tests? #f ;no "check" target
2742f87e
RW		 3520 #:make-flags
3521 (list "CC=gcc"
3522 "BLAS=-lblas"
3523 "TBB=-ltbb"
bd5b5ac0 3524 "MY_METIS_LIB=-lmetis"
aac148a8
FG		 3525 ;; Flags for cmake (required to build GraphBLAS and Mongoose)
3526 (string-append "CMAKE_OPTIONS=-DCMAKE_INSTALL_PREFIX="
3527 (assoc-ref %outputs "out")
3528 " -DCMAKE_VERBOSE_MAKEFILE=ON"
3529 " -DCMAKE_C_FLAGS_RELEASE=\"$(CFLAGS) $(CPPFLAGS)\""
3530 " -DCMAKE_CXX_FLAGS_RELEASE=\"$(CXXFLAGS) $(CPPFLAGS)\""
3531 " -DCMAKE_SKIP_RPATH=TRUE"
3532 " -DCMAKE_BUILD_TYPE=Release")
2742f87e
RW		 3533 (string-append "INSTALL_LIB="
3534 (assoc-ref %outputs "out") "/lib")
3535 (string-append "INSTALL_INCLUDE="
bd5b5ac0
EB		 3536 (assoc-ref %outputs "out") "/include")
3537 "library")
2742f87e 3538 #:phases
2509522c 3539 (modify-phases %standard-phases
bd5b5ac0 3540 (delete 'configure)))) ;no configure script
2742f87e
RW		 3541 (inputs
3542 `(("tbb" ,tbb)
bd5b5ac0
EB		 3543 ("lapack" ,lapack)
3544 ("metis" ,metis)))
aac148a8 3545 (native-inputs
b471337d 3546 `(("cmake" ,cmake-minimal)
aac148a8 3547 ("m4" ,m4)))
2742f87e
RW		 3548 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
3549 (synopsis "Suite of sparse matrix software")
3550 (description
3551 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
3552multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
3553multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
3554simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
3555CXSparse, a concise sparse Cholesky factorization package; and many other
3556packages.")
3557 ;; LGPLv2.1+:
3558 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
3559 ;; GPLv2+:
3560 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
3561 (license (list license:gpl2+ license:lgpl2.1+))))
3562
ec322be2
FB		 3563(define-public atlas
3564 (package
3565 (name "atlas")
3c98ac02 3566 (version "3.10.3")
ec322be2
FB		 3567 (source (origin
3568 (method url-fetch)
de67e922
LF		 3569 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
3570 version "/atlas" version ".tar.bz2"))
ec322be2
FB		 3571 (sha256
3572 (base32
3c98ac02 3573 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
ec322be2
FB		 3574 (build-system gnu-build-system)
3575 (home-page "http://math-atlas.sourceforge.net/")
19afbea1 3576 (inputs `(("gfortran" ,gfortran)
ec322be2
FB		 3577 ("lapack-tar" ,(package-source lapack))))
3578 (outputs '("out" "doc"))
01480b9e
FB		 3579 ;; For the moment we drop support for MIPS at it fails to compile. See
3580 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
3581 (supported-systems (delete "mips64el-linux" %supported-systems))
ec322be2
FB		 3582 (arguments
3583 `(#:parallel-build? #f
3584 #:parallel-tests? #f
f15615b1
LC		 3585
3586 ;; ATLAS tunes itself for the machine it is built on, as explained at
3587 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
3588 ;; For this reason, we want users to build it locally instead of using
3589 ;; substitutes.
3590 #:substitutable? #f
3591
ec322be2 3592 #:modules ((srfi srfi-26)
ec322be2
FB		 3593 (guix build gnu-build-system)
3594 (guix build utils))
40029cbe 3595 #:configure-flags
ec322be2
FB		 3596 `(;; Generate position independent code suitable for dynamic libraries
3597 ;; and use WALL timer to get more accurate timing.
3598 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
3599 ;; Set word width.
3600 "-b"
3601 ,,(if (string-match "64" (%current-system))
3602 "64"
3603 "32")
3604 ;; Disable parallel build as it gives errors: atlas_pthread.h is
3605 ;; needed to compile C files before it is generated.
3606 "-Ss" "pmake" "make -j 1"
af89a667
FB		 3607 ;; Probe is failing for MIPS. We therefore define the system
3608 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3609 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3610 ,,@(if (string-prefix? "mips" (%current-system))
3611 (list "-A" "49" "-V" "1")
3612 (list))
ec322be2
FB		 3613 ;; Generate shared libraries.
3614 "--shared"
3615 ;; Build a full LAPACK library.
3616 ,(string-append "--with-netlib-lapack-tarfile="
3617 (assoc-ref %build-inputs "lapack-tar")))
3618 #:phases
e5b4b96b
EF		 3619 (modify-phases %standard-phases
3620 (add-after 'install 'install-doc
3621 (lambda* (#:key outputs inputs #:allow-other-keys)
3622 (let ((doc (string-append (assoc-ref outputs "doc")
3623 "/share/doc/atlas")))
3624 (mkdir-p doc)
cb6f44d4
RW		 3625 (for-each (cut install-file <> doc)
3626 (find-files "../ATLAS/doc" ".*"))
3627 #t)))
e5b4b96b 3628 (add-after 'check 'check-pt
cb6f44d4 3629 (lambda _ (invoke "make" "ptcheck")))
e5b4b96b
EF		 3630 ;; Fix files required to run configure.
3631 (add-before 'configure 'fix-/bin/sh
ec322be2
FB		 3632 (lambda _
3633 ;; Use `sh', not `/bin/sh'.
3634 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3635 (("/bin/sh")
5b786db8
EF		 3636 "sh"))
3637 #t))
e5b4b96b
EF		 3638 ;; Fix /bin/sh in generated make files.
3639 (add-after 'configure 'fix-/bin/sh-in-generated-files
3640 (lambda _
3641 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3642 (("/bin/sh")
5b786db8
EF		 3643 "sh"))
3644 #t))
e5b4b96b
EF		 3645 ;; ATLAS configure program does not accepts the default flags
3646 ;; passed by the 'gnu-build-system'.
3647 (replace 'configure
3648 (lambda* (#:key native-inputs inputs outputs
3649 (configure-flags '())
3650 #:allow-other-keys #:rest args)
3651 (let* ((prefix (assoc-ref outputs "out"))
3652 (bash (or (and=> (assoc-ref
3653 (or native-inputs inputs) "bash")
3654 (cut string-append <> "/bin/bash"))
3655 "/bin/sh"))
3656 (flags `(,(string-append "--prefix=" prefix)
3657 ,@configure-flags))
3658 (abs-srcdir (getcwd))
3659 (srcdir (string-append "../" (basename abs-srcdir))))
3660 (format #t "source directory: ~s (relative from build: ~s)~%"
3661 abs-srcdir srcdir)
3662 (mkdir "../build")
3663 (chdir "../build")
3664 (format #t "build directory: ~s~%" (getcwd))
3665 (format #t "configure flags: ~s~%" flags)
cb6f44d4
RW		 3666 (apply invoke bash
3667 (string-append srcdir "/configure")
3668 flags)))))))
ec322be2
FB		 3669 (synopsis "Automatically Tuned Linear Algebra Software")
3670 (description
3671 "ATLAS is an automatically tuned linear algebra software library
3672providing C and Fortran77 interfaces to a portably efficient BLAS
3673implementation, as well as a few routines from LAPACK.
3674
f15615b1
LC		 3675Optimization occurs at build time. For this reason, the library is built on
3676the machine where it is installed, without resorting to pre-built substitutes.
ec322be2 3677
f15615b1 3678Before building the library, CPU throttling should be disabled. This can be
d97c429a 3679done in the BIOS, or, on GNU/Linux, with the following command:
ec322be2 3680
8e9ba611 3681@example
d97c429a 3682# cpupower --governor performance
8e9ba611 3683@end example
ec322be2 3684
d97c429a 3685Failure to do so will result in a library with poor performance.")
ec322be2 3686 (license license:bsd-3)))
c12efc72
AE		 3687
3688(define-public glm
3689 (package
3690 (name "glm")
3f55b7be 3691 (version "0.9.9.6")
c12efc72
AE		 3692 (source
3693 (origin
3694 (method url-fetch)
5ea4b594
MB		 3695 (uri (string-append "https://github.com/g-truc/glm/releases/download/"
3696 version "/glm-" version ".zip"))
c12efc72 3697 (sha256
3f55b7be
TGR		 3698 (base32 "1l0pi1qi37mk6s0yrkrw07lspv4gcqnr9ryg3521hrl77ff37dwx"))
3699 (patches (search-patches "glm-restore-install-target.patch"))))
c12efc72
AE		 3700 (build-system cmake-build-system)
3701 (native-inputs
3702 `(("unzip" ,unzip)))
46bda5eb 3703 (home-page "https://glm.g-truc.net/")
c12efc72
AE		 3704 (synopsis "OpenGL Mathematics library")
3705 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3706library for graphics software based on the OpenGL Shading Language (GLSL)
3707specifications.")
3708 (license license:expat)))
7f18257b
AE		 3709
3710(define-public lpsolve
3711 (package
3712 (name "lpsolve")
a89e0cf5 3713 (version "5.5.2.5")
7f18257b
AE		 3714 (source
3715 (origin
3716 (method url-fetch)
3717 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3718 "/lp_solve_" version "_source.tar.gz"))
3719 (sha256
3720 (base32
a89e0cf5 3721 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
7f18257b
AE		 3722 (modules '((guix build utils)))
3723 (snippet
6cbee49d
MW		 3724 '(begin
3725 (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3726 (("^c=cc") "c=gcc")
3727 ;; Pretend to be on a 64 bit platform to obtain a common directory
3728 ;; name for the build results on all architectures; nothing else
3729 ;; seems to depend on it.
3730 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3731
3732 ;; The check for 'isnan' as it is written fails with
3733 ;; "non-floating-point argument in call to function
3734 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3735 ;; definition, which in turn leads to bad things. Fix the feature
3736 ;; test.
3737 (("isnan\\(0\\)") "isnan(0.)"))
3738 #t))))
7f18257b
AE		 3739 (build-system gnu-build-system)
3740 (arguments
6c96b545 3741 `(#:tests? #f ; no check target
7f18257b
AE		 3742 #:phases
3743 (modify-phases %standard-phases
6c96b545 3744 (delete 'configure) ; no configure script
7f18257b
AE		 3745 (replace 'build
3746 (lambda _
6c96b545
TGR		 3747 (with-directory-excursion "lpsolve55"
3748 (invoke "bash" "ccc"))
3749 (with-directory-excursion "lp_solve"
3750 (invoke "bash" "ccc"))
3751 #t))
7f18257b
AE		 3752 (replace 'install
3753 (lambda* (#:key outputs #:allow-other-keys)
3754 (let* ((out (assoc-ref outputs "out"))
3755 (bin (string-append out "/bin"))
3756 (lib (string-append out "/lib"))
3757 ;; This is where LibreOffice expects to find the header
3758 ;; files, and where they are installed by Debian.
3759 (include (string-append out "/include/lpsolve")))
6c96b545
TGR		 3760 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3761 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
96c46210
LC		 3762 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3763
7f18257b
AE		 3764 ;; Install a subset of the header files as on Debian
3765 ;; (plus lp_bit.h, which matches the regular expression).
96c46210
LC		 3766 (for-each (lambda (name)
3767 (install-file name include))
3768 (find-files "." "lp_[HMSa-z].*\\.h$"))
7f18257b 3769 (with-directory-excursion "shared"
96c46210
LC		 3770 (for-each (lambda (name)
3771 (install-file name include))
3772 (find-files "." "\\.h$")))
7f18257b
AE		 3773 #t))))))
3774 (home-page "http://lpsolve.sourceforge.net/")
3775 (synopsis "Mixed integer linear programming (MILP) solver")
3776 (description
3777 "lp_solve is a mixed integer linear programming solver based on the
3778revised simplex and the branch-and-bound methods.")
3779 (license license:lgpl2.1+)))
a17d4564
EB		 3780
3781(define-public dealii
3782 (package
3783 (name "dealii")
ba567cae 3784 (version "9.1.1")
a17d4564
EB		 3785 (source
3786 (origin
3787 (method url-fetch)
3788 (uri (string-append "https://github.com/dealii/dealii/releases/"
3789 "download/v" version "/dealii-" version ".tar.gz"))
3790 (sha256
3791 (base32
ba567cae 3792 "0xhjv0gzswpjbc43xbrpwfc5848g508l01855nszx3g5gwzlhnzw"))
a17d4564
EB		 3793 (modules '((guix build utils)))
3794 (snippet
3795 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
6cbee49d
MW		 3796 '(begin
3797 (delete-file-recursively "bundled")
3798 #t))))
a17d4564
EB		 3799 (build-system cmake-build-system)
3800 (inputs
3801 `(("tbb" ,tbb)
3802 ("zlib" ,zlib)
3803 ("boost" ,boost)
3804 ("p4est" ,p4est)
3805 ("blas" ,openblas)
3806 ("lapack" ,lapack)
3807 ("arpack" ,arpack-ng)
3808 ("muparser" ,muparser)
3809 ("gfortran" ,gfortran)
3810 ("suitesparse" ,suitesparse))) ;for UMFPACK
3811 (arguments
3812 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
d84b09e9
EB		 3813 #:configure-flags
3814 ;; Work around a bug in libsuitesparseconfig linking
3815 ;; see https://github.com/dealii/dealii/issues/4745
3816 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
a17d4564
EB		 3817 (home-page "https://www.dealii.org")
3818 (synopsis "Finite element library")
3819 (description
3820 "Deal.II is a C++ program library targeted at the computational solution
3821of partial differential equations using adaptive finite elements. The main
3822aim of deal.II is to enable rapid development of modern finite element codes,
3823using among other aspects adaptive meshes and a wide array of tools often used
3824in finite element programs.")
3825 (license license:lgpl2.1+)))
3826
3827(define-public dealii-openmpi
3828 (package (inherit dealii)
3829 (name "dealii-openmpi")
3830 (inputs
3831 `(("mpi" ,openmpi)
3832 ;;Supported only with MPI:
4d44bcad 3833 ("hdf5" ,hdf5-parallel-openmpi) ;TODO: have petsc-openmpi propagate?
a17d4564
EB		 3834 ("p4est" ,p4est-openmpi)
3835 ("petsc" ,petsc-openmpi)
3836 ("slepc" ,slepc-openmpi)
3837 ("metis" ,metis) ;for MUMPS
3838 ("scalapack" ,scalapack) ;for MUMPS
3839 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3840 ("arpack" ,arpack-ng-openmpi)
3841 ,@(fold alist-delete (package-inputs dealii)
3842 '("p4est" "arpack"))))
3843 (arguments
3844 (substitute-keyword-arguments (package-arguments dealii)
3845 ((#:configure-flags cf)
40b114c0
EB		 3846 `(cons "-DDEAL_II_WITH_MPI:BOOL=ON"
3847 ,cf))
7e309e8a
EB		 3848 ((#:phases phases '%standard-phases)
3849 `(modify-phases ,phases
3850 (add-before 'check 'mpi-setup
3851 ,%openmpi-setup)))))
a17d4564 3852 (synopsis "Finite element library (with MPI support)")))
194c7f95
AE		 3853
3854(define-public flann
3855 (package
3856 (name "flann")
3857 (version "1.8.4")
3858 (source
3859 (origin
3860 (method url-fetch)
3861 (uri
3862 (string-append
3863 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3864 version "-src.zip"))
3865 (sha256
3866 (base32
b5edc479
LC		 3867 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
3868 (patches (search-patches "flann-cmake-3.11.patch"))))
194c7f95 3869 (build-system cmake-build-system)
6b6aca9b
LC		 3870 (outputs '("out"
3871 "octave")) ;46 MiB .mex file that pulls Octave
194c7f95
AE		 3872 (native-inputs
3873 `(("unzip" ,unzip)))
3874 (inputs
3875 `(("hdf5" ,hdf5)
5537603f 3876 ("octave" ,octave-cli)
194c7f95
AE		 3877 ("python" ,python-2) ; print syntax
3878 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3879 ("zlib" ,zlib)))
3880 (arguments
39b30337
LC		 3881 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3882 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3883 #:strip-directories '("lib" "lib64" "libexec"
3884 "bin" "sbin" "share/flann/octave")
3885
9684e30b
LC		 3886 ;; Save 12 MiB by not installing .a files. Passing
3887 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3888 #:phases (modify-phases %standard-phases
6b6aca9b
LC		 3889 (add-before 'configure 'set-octave-directory
3890 (lambda* (#:key outputs #:allow-other-keys)
3891 ;; Install the .mex file in the "octave" output.
3892 (let ((out (assoc-ref outputs "octave")))
3893 (substitute* "src/matlab/CMakeLists.txt"
3894 (("share/flann/octave")
3895 (string-append out "/share/flann/octave")))
3896 #t)))
9684e30b
LC		 3897 (add-after 'install 'remove-static-libraries
3898 (lambda* (#:key outputs #:allow-other-keys)
3899 (let* ((out (assoc-ref outputs "out"))
3900 (lib (string-append out "/lib")))
3901 (for-each delete-file
3902 (find-files lib "\\.a$"))
3903 #t))))
3904
39b30337 3905 #:tests? #f)) ; The test data are downloaded from the Internet.
194c7f95
AE		 3906 (home-page "http://www.cs.ubc.ca/research/flann/")
3907 (synopsis "Library for approximate nearest neighbors computation")
3908 (description "FLANN is a library for performing fast approximate
3909nearest neighbor searches in high dimensional spaces. It implements a
3910collection of algorithms and a system for automatically choosing the best
3911algorithm and optimum parameters depending on the dataset.
3912
3913FLANN is written in C++ and contains bindings for C, Octave and Python.")
3914 (license (license:non-copyleft "file://COPYING"
3915 "See COPYING in the distribution."))))
d8c97beb
EF		 3916
3917(define-public wcalc
3918 (package
3919 (name "wcalc")
3920 (version "2.5")
3921 (source
3922 (origin
3923 (method url-fetch)
de67e922
LF		 3924 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3925 "wcalc-" version ".tar.bz2"))
d8c97beb
EF		 3926 (sha256
3927 (base32
3928 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3929 (build-system gnu-build-system)
3930 (inputs
3931 `(("mpfr" ,mpfr)
3932 ("readline" ,readline)))
3933 (home-page "http://w-calc.sourceforge.net/index.php")
3934 (synopsis "Flexible command-line scientific calculator")
3935 (description "Wcalc is a very capable calculator. It has standard functions
3936(sin, asin, and sinh for example, in either radians or degrees), many
3937pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3938variables, a command history, hex/octal/binary input and output, unit
3939conversions, embedded comments, and an expandable expression entry field. It
3940evaluates expressions using the standard order of operations.")
3941 (license license:gpl2+)))
45147b0c
FH		 3942
3943(define-public xaos
3944 (package
3945 (name "xaos")
3946 (version "3.6")
3947 (source (origin
3948 (method url-fetch)
de67e922
LF		 3949 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3950 "/xaos-" version ".tar.gz"))
45147b0c
FH		 3951 (sha256
3952 (base32
3953 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3954 (build-system gnu-build-system)
b94a6ca0 3955 (native-inputs `(("gettext" ,gettext-minimal)))
45147b0c
FH		 3956 (inputs `(("libx11" ,libx11)
3957 ("zlib" ,zlib)
3958 ("libpng" ,libpng)
3959 ("gsl" ,gsl)))
3960 (arguments
3961 `(#:tests? #f ;no "check" target
3962 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3963 (synopsis "Real-time fractal zoomer")
3964 (description "GNU XaoS is a graphical program that generates fractal
3965patterns and allows you to zoom in and out of them infinitely in a fluid,
3966continuous manner. It also includes tutorials that help to explain how fractals
3967are built. It can generate many different fractal types such as the Mandelbrot
3968set.")
6fd52309 3969 (home-page "https://www.gnu.org/software/xaos/")
45147b0c 3970 (license license:gpl2+)))
528bb464
EB		 3971
3972(define-public hypre
3973 (package
3974 (name "hypre")
be099727 3975 (version "2.15.1")
fabcbf32
TGR		 3976 (source
3977 (origin
3978 (method git-fetch)
3979 (uri (git-reference
3980 (url "https://github.com/LLNL/hypre.git")
3981 (commit (string-append "v" version))))
3982 (file-name (git-file-name name version))
3983 (sha256
be099727 3984 (base32 "1lvh4ybqkriyqfg2zmic6mrg1981qv1i9vry1fdgsabn81hb71g4"))
fabcbf32
TGR		 3985 (modules '((guix build utils)))
3986 (snippet
3987 '(begin
3988 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
be099727 3989 ;; substitute the release date.
fabcbf32
TGR		 3990 (substitute* "src/utilities/HYPRE_utilities.h"
3991 (("Date Compiled: .*$")
be099727 3992 "Date Compiled: Oct 19 2018 15:23:00 +0000\"\n"))
fabcbf32 3993 #t))))
528bb464 3994 (build-system gnu-build-system)
be099727
TGR		 3995 (outputs '("out" ; 6.1 MiB of headers and libraries
3996 "doc")) ; 4.8 MiB of documentation
528bb464
EB		 3997 (native-inputs
3998 `(("doc++" ,doc++)
3999 ("netpbm" ,netpbm)
be099727 4000 ("perl" ,perl) ; needed to run 'ppmquant' during tests
8b35c8cd
RW		 4001 ("texlive" ,(texlive-union (list texlive-xypic
4002 texlive-cm
9b405aea 4003 texlive-latex-hyperref
9b405aea 4004 texlive-bibtex)))
528bb464
EB		 4005 ("ghostscript" ,ghostscript)))
4006 (inputs
4007 `(("blas" ,openblas)
4008 ("lapack" ,lapack)))
4009 (arguments
4010 `(#:modules ((srfi srfi-1)
4011 ,@%gnu-build-system-modules)
4012 #:configure-flags '("--enable-shared"
4013 "--disable-fortran"
4014 "--without-MPI"
4015 "--with-openmp"
4016 "--with-fei"
4017 "--with-lapack"
4018 "--with-blas")
4019 #:phases
4020 (modify-phases %standard-phases
9b405aea
PN		 4021 (add-before 'build 'set-HOME
4022 (lambda _
4023 ;; FIXME: texlive-union does not find the built
4024 ;; metafonts, so it tries to generate them in HOME.
4025 (setenv "HOME" "/tmp")
4026 #t))
528bb464
EB		 4027 (add-before 'configure 'chdir-src
4028 (lambda _ (chdir "src")))
4029 (replace 'configure
4030 (lambda* (#:key build target configure-flags
4031 #:allow-other-keys #:rest args)
4032 (let* ((configure (assoc-ref %standard-phases 'configure)))
4033 (apply configure
4034 (append args
4035 (list #:configure-flags
4036 (cons (string-append
4037 "--host=" (or target build))
4038 configure-flags)))))))
4039 (add-after 'build 'build-docs
4040 (lambda _
9b405aea 4041 (invoke "make" "-Cdocs" "pdf" "html")))
528bb464
EB		 4042 (replace 'check
4043 (lambda _
4044 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
4045 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
6b1c7ac8
RW		 4046 (invoke "make" "check" "CHECKRUN=")
4047 (for-each (lambda (filename)
4048 (let ((size (stat:size (stat filename))))
4049 (when (positive? size)
4050 (error (format #f "~a size ~d; error indication~%"
4051 filename size)))))
4052 (find-files "test" ".*\\.err$"))
4053 #t))
528bb464
EB		 4054 (add-after 'install 'install-docs
4055 (lambda* (#:key outputs #:allow-other-keys)
4056 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
4057 (let* ((doc (assoc-ref outputs "doc"))
4058 (docdir (string-append doc "/share/doc/hypre-" ,version)))
528bb464
EB		 4059 (with-directory-excursion "docs"
4060 (for-each (lambda (base)
4061 (install-file (string-append base ".pdf") docdir)
be099727 4062 (copy-recursively base docdir)) ; html docs
528bb464
EB		 4063 '("HYPRE_usr_manual"
4064 "HYPRE_ref_manual")))
4065 #t))))))
4066 (home-page "http://www.llnl.gov/casc/hypre/")
4067 (synopsis "Library of solvers and preconditioners for linear equations")
4068 (description
4069 "HYPRE is a software library of high performance preconditioners and
4070solvers for the solution of large, sparse linear systems of equations. It
4071features multigrid solvers for both structured and unstructured grid
4072problems.")
4073 (license license:lgpl2.1)))
4074
4075(define-public hypre-openmpi
4076 (package (inherit hypre)
4077 (name "hypre-openmpi")
4078 (inputs
4079 `(("mpi" ,openmpi)
4080 ,@(package-inputs hypre)))
4081 (arguments
4082 (substitute-keyword-arguments (package-arguments hypre)
4083 ((#:configure-flags flags)
4084 ``("--with-MPI"
6df2a50a
LC		 4085 ,@(delete "--without-MPI" ,flags)))
4086 ((#:phases phases)
4087 `(modify-phases ,phases
bbe46a4a
EB		 4088 (add-before 'check 'mpi-setup
4089 ,%openmpi-setup)))))
528bb464
EB		 4090 (synopsis "Parallel solvers and preconditioners for linear equations")
4091 (description
4092 "HYPRE is a software library of high performance preconditioners and
4093solvers for the solution of large, sparse linear systems of equations on
4094parallel computers. It features parallel multigrid solvers for both
4095structured and unstructured grid problems.")))
6c90e183
EB		 4096
4097(define-public matio
4098 (package
4099 (name "matio")
4100 (version "1.5.6")
4101 (source
4102 (origin
4103 (method url-fetch)
de67e922 4104 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
6c90e183
EB		 4105 "matio-" version ".tar.gz"))
4106 (sha256
4107 (base32
4108 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
4109 (build-system gnu-build-system)
4110 (inputs
4111 `(("zlib" ,zlib)
4112 ("hdf5" ,hdf5)))
4113 (home-page "http://matio.sourceforge.net/")
4114 (synopsis "Library for reading and writing MAT files")
4115 (description "Matio is a library for reading and writing MAT files. It
4116supports compressed MAT files, as well as newer (version 7.3) MAT files.")
4117 (license license:bsd-2)))
d721c83a 4118
517318ad
LF		 4119(define-public vc
4120 (package
4121 (name "vc")
9d731fb6 4122 (version "1.4.1")
517318ad
LF		 4123 (source
4124 (origin (method url-fetch)
4125 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
4126 "download/" version "/Vc-" version ".tar.gz"))
4127 (sha256
4128 (base32
9d731fb6 4129 "17qili8bf8r78cng65yf4qmgna8kiqjqbgcqbric6v9j6nkhkrk8"))))
517318ad
LF		 4130 (build-system cmake-build-system)
4131 (arguments
4132 '(#:configure-flags
33d82486
MB		 4133 '("-DBUILD_TESTING=ON"
4134 ;; By default, Vc will optimize for the CPU of the build machine.
4135 ;; Setting this to "none" makes it create portable binaries. See
4136 ;; "cmake/OptimizeForArchitecture.cmake".
9d731fb6
MB		 4137 "-DTARGET_ARCHITECTURE=none")
4138 #:phases (modify-phases %standard-phases
4139 (add-after 'unpack 'copy-testdata
4140 (lambda* (#:key inputs native-inputs #:allow-other-keys)
4141 (let ((testdata (assoc-ref (or native-inputs inputs)
4142 "testdata")))
4143 (copy-recursively testdata "tests/testdata")
4144 #t))))))
4145 (native-inputs
4146 `(("virtest" ,virtest)
4147
4148 ;; This is a submodule in the git project, but not part of the
4149 ;; released sources. See the git branch for the commit to take.
4150 ("testdata" ,(let ((commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3"))
4151 (origin
4152 (method git-fetch)
4153 (uri (git-reference
4154 (url "https://github.com/VcDevel/vc-testdata")
4155 (commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3")))
4156 (file-name (git-file-name "vc-testdata"
4157 (string-take commit 7)))
4158 (sha256
4159 (base32
4160 "1hkhqib03qlcq412ym2dciynfxcdr2ygqhnplz4l1vissr1wnqn2")))))))
517318ad
LF		 4161 (synopsis "SIMD vector classes for C++")
4162 (description "Vc provides portable, zero-overhead C++ types for explicitly
4163data-parallel programming. It is a library designed to ease explicit
4164vectorization of C++ code. Its types enable explicitly stating data-parallel
4165operations on multiple values. The parallelism is therefore added via the type
4166system. Vc has an intuitive API and provides portability between different
4167compilers and compiler versions as well as portability between different vector
4168instruction sets. Thus, an application written with Vc can be compiled for:
4169@enumerate
4170@item AVX and AVX2
d1e4ad1b 4171@item SSE2 up to SSE4.2 or SSE4a
517318ad
LF		 4172@item Scalar
4173@item MIC
4174@item NEON (in development)
4175@item NVIDIA GPUs / CUDA (in development)
4176@end enumerate\n")
4177 (home-page "https://github.com/VcDevel/Vc")
a8ead6f9
EF		 4178 ;; "No support_???.cpp file exists for this architecture."
4179 (supported-systems '("x86_64-linux" "i686-linux"))
517318ad 4180 (license license:bsd-3)))
54052a54 4181
4182(define-public reducelcs
4183 ;; This is the last commit which is available upstream, no
4184 ;; release happened since 2010.
4185 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
4186 (revision "1"))
4187 (package
4188 (name "reducelcs")
4189 (version (string-append "1.0-" revision "." (string-take commit 7)))
4190 (source
4191 (origin
4192 (method git-fetch)
4193 (uri (git-reference
4194 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
4195 (commit commit)))
4196 (file-name (string-append name "-" version "-checkout"))
4197 (sha256
4198 (base32
4199 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
4200 (build-system gnu-build-system)
4201 (inputs
4202 `(("openlibm" ,openlibm)))
4203 (arguments
4204 `(#:tests? #f ; no tests
4205 #:phases
4206 (modify-phases %standard-phases
4207 (delete 'configure) ; No configure script exists.
4208 (replace 'install ; No install phase exists.
4209 (lambda* (#:key outputs #:allow-other-keys)
4210 (let* ((out (assoc-ref outputs "out"))
4211 (bin (string-append out "/bin")))
4212 (install-file "Approximation" bin)
4213 (install-file "CollectResults" bin)
4214 (install-file "GenerateInstances" bin)
4215 #t))))))
4216 (synopsis "Approximate Longest Commons Subsequence computation tool")
4217 (description
4218 "@code{reduceLCS} is an implementation of the Reduce-Expand
4219algorithm for LCS. It is a fast program to compute the approximate
4220Longest Commons Subsequence of a set of strings.")
4221 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
c000b6b1 4222 (license license:gpl3+))))
479c4273
JD		 4223
4224(define-public jacal
4225 (package
4226 (name "jacal")
4227 (version "1c4")
4228 (source (origin
4229 (method url-fetch)
4230 (uri (string-append
4231 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
4232 version ".zip"))
4233 (sha256 (base32
4234 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
4235 (patches (search-patches "jacal-fix-texinfo.patch"))))
4236 (build-system gnu-build-system)
4237 (arguments
4238 `(#:phases
4239 (modify-phases %standard-phases
4240 (add-before 'build 'pre-build
4241 ;; Don't use upstream's script - it really doesn't fit into
4242 ;; Guix's functional paradigm.
4243 (lambda* (#:key inputs outputs #:allow-other-keys)
4244 (substitute* "Makefile"
4245 (("^install: install-script") "install: "))))
4246 (add-after 'install 'post-install
4247 ;; Instead, we provide our own simplified script.
4248 (lambda* (#:key inputs outputs #:allow-other-keys)
4249 (let ((wrapper (string-append (assoc-ref outputs "out")
4250 "/bin/jacal")))
4251 (format (open wrapper (logior O_WRONLY O_CREAT))
4252 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
4253 "-e '(slib:load \"~a/lib/jacal/math\") "
4254 "(math)' \"$@\"\n")
4255 (which "bash")
4256 (assoc-ref inputs "scm")
4257 (assoc-ref outputs "out"))
4258 (chmod wrapper #o555))))
4259 (replace 'configure
9cd82b1c
RW		 4260 (lambda* (#:key outputs #:allow-other-keys)
4261 (invoke "./configure"
4262 (string-append "--prefix="
4263 (assoc-ref outputs "out"))))))))
479c4273
JD		 4264 (inputs `(("scm" ,scm)))
4265 (native-inputs `(("unzip" ,unzip)
4266 ("texinfo" ,texinfo)))
4267 (synopsis "Symbolic mathematics system")
4268 (description "GNU JACAL is an interactive symbolic mathematics program based on
4269Scheme. It manipulate and simplify a range of mathematical expressions such
4270as equations, scalars, vectors, and matrices.")
6fd52309 4271 (home-page "https://www.gnu.org/software/jacal/")
479c4273
JD		 4272 (license license:gpl3+)))
4273
313844d9
TF		 4274(define-public z3
4275 (package
4276 (name "z3")
dbef037f 4277 (version "4.8.7")
fb525bfd 4278 (home-page "https://github.com/Z3Prover/z3")
313844d9 4279 (source (origin
fb525bfd
MB		 4280 (method git-fetch)
4281 (uri (git-reference (url home-page)
4282 (commit (string-append "z3-" version))))
2d7b99b3 4283 (file-name (git-file-name name version))
313844d9
TF		 4284 (sha256
4285 (base32
dbef037f 4286 "0hprcdwhhyjigmhhk6514m71bnmvqci9r8gglrqilgx424r6ff7q"))))
fa574a6d 4287 (build-system gnu-build-system)
313844d9 4288 (arguments
f6b4d395
JK		 4289 `(#:imported-modules ((guix build python-build-system)
4290 ,@%gnu-build-system-modules)
4291 #:modules (((guix build python-build-system) #:select (site-packages))
4292 (guix build gnu-build-system)
4293 (guix build utils))
4294 #:phases
313844d9 4295 (modify-phases %standard-phases
8b87d095
JK		 4296 (add-after 'unpack 'enable-bytecode-determinism
4297 (lambda _
4298 (setenv "PYTHONHASHSEED" "0")
4299 #t))
ad6c6a5b
EF		 4300 (add-after 'unpack 'fix-compatability
4301 ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
4302 (lambda _
4303 (substitute* "src/util/mpz.cpp"
4304 (("#include <immintrin.h>") ""))
4305 #t))
cf684d87
TF		 4306 (add-before 'configure 'bootstrap
4307 (lambda _
32d5360f 4308 (invoke "python" "scripts/mk_make.py")))
fa574a6d
AB		 4309 ;; work around gnu-build-system's setting --enable-fast-install
4310 ;; (z3's `configure' is a wrapper around the above python file,
4311 ;; which fails when passed --enable-fast-install)
4312 (replace 'configure
4313 (lambda* (#:key inputs outputs #:allow-other-keys)
4314 (invoke "./configure"
f6b4d395
JK		 4315 "--python"
4316 (string-append "--prefix=" (assoc-ref outputs "out"))
4317 (string-append "--pypkgdir=" (site-packages inputs outputs)))))
fa574a6d
AB		 4318 (add-after 'configure 'change-directory
4319 (lambda _
4320 (chdir "build")
4321 #t))
cf684d87 4322 (add-before 'check 'make-test-z3
313844d9 4323 (lambda _
cf684d87 4324 ;; Build the test suite executable.
32d5360f
RW		 4325 (invoke "make" "test-z3" "-j"
4326 (number->string (parallel-job-count)))))
cf684d87
TF		 4327 (replace 'check
4328 (lambda _
4329 ;; Run all the tests that don't require arguments.
32d5360f 4330 (invoke "./test-z3" "/a"))))))
313844d9 4331 (native-inputs
fa574a6d
AB		 4332 `(("which" ,which)
4333 ("python" ,python-wrapper)))
313844d9
TF		 4334 (synopsis "Theorem prover")
4335 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
cf684d87 4336theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
313844d9 4337 (license license:expat)))
3d5d87a3 4338
6d433d6e
EB		 4339(define-public elpa
4340 (package
4341 (name "elpa")
4342 (version "2018.11.001")
4343 (source (origin
4344 (method url-fetch)
4345 (uri (string-append "http://elpa.mpcdf.mpg.de/html/Releases/"
4346 version "/elpa-" version ".tar.gz"))
4347 (sha256
4348 (base32
4349 "05hv3v5i6xmziaizw350ff72y1c3k662r85fm3xfdrkclj5zw9yc"))))
4350 (build-system gnu-build-system)
4351 (native-inputs
4352 `(("fortran" ,gfortran)
4353 ("perl" ,perl))) ;for configure and deps
4354 (inputs
4355 `(("blas" ,openblas)))
4356 (arguments
4357 `(#:configure-flags
4358 `("--enable-openmp"
4359 "--with-mpi=no"
4360 ;; ELPA unfortunately does not support runtime dispatch, so we can
4361 ;; only enable the "generic" kernels. See the "Cross compilation"
4362 ;; section of INSTALL.md.
4363 "--enable-generic"
4364 "--disable-sse" "--disable-sse-assembly" ;Require SSE3
4365 "--disable-avx" "--disable-avx2" "--disable-avx512"
4366 ,(string-append "CFLAGS=-O3 "
4367 "-funsafe-loop-optimizations -funsafe-math-optimizations "
4368 "-ftree-vect-loop-version -ftree-vectorize "
4369 ,(let ((system (or (%current-target-system)
4370 (%current-system))))
4371 (cond
4372 ((or (string-prefix? "x86_64" system)
4373 (string-prefix? "i686" system))
4374 "-msse2")
4375 (else "")))))
4376 #:parallel-tests? #f ;tests are multi-threaded, via BLAS
4377 #:phases
4378 (modify-phases %standard-phases
4379 (add-before 'configure 'patch-header-generation
4380 (lambda _
4381 (substitute* "configure"
4382 (("^ *make.*top_srcdir=\"\\$srcdir\"" &)
4383 (string-append & " CPP=\"$CPP\"")))
4384 #t))
4385 (add-before 'check 'setup-tests
4386 (lambda _
4387 ;; Decrease test time and RAM use by computing fewer eigenvalues.
4388 ;; The flags are (MATRIX-SIZE, EIGENVALUES, BLOCK-SIZE), where
4389 ;; the default is (500, 250, 16) for C tests and (5000, 150, 16)
4390 ;; for Fortran. This also causes several tests to pass that
4391 ;; otherwise would otherwise fail with matrix size 5000; possibly
4392 ;; due to floating point tolerances that are too tight.
4393 (setenv "TEST_FLAGS" "1500 50 16") ;from elpa.spec
4394 (setenv "OMP_NUM_THREADS" (number->string (parallel-job-count)))
4395 (substitute* "Makefile"
4396 ;; Test scripts are generated, patch the shebang
4397 (("#!/bin/bash") (string-append "#!" (which "sh"))))
4398 #t)))))
4399 (home-page "http://elpa.mpcdf.mpg.de")
4400 (synopsis "Eigenvalue solvers for symmetric matrices")
4401 (description
4402 "The ELPA library provides efficient and scalable direct eigensolvers for
4403symmetric matrices.")
4404 (license license:lgpl3)))
4405
4406(define-public elpa-openmpi
4407 (package (inherit elpa)
4408 (name "elpa-openmpi")
4409 (inputs
4410 `(("mpi" ,openmpi)
4411 ("scalapack" ,scalapack)
4412 ,@(package-inputs elpa)))
4413 (arguments
4414 (substitute-keyword-arguments (package-arguments elpa)
4415 ((#:configure-flags cf '())
4416 `(cons "--with-mpi=yes" (delete "--with-mpi=no" ,cf)))
4417 ((#:phases phases '%standard-phases)
4418 `(modify-phases ,phases
4419 (add-before 'check 'mpi-setup
4420 (lambda _
4421 ;; Tests use 2 mpi tasks by default, use our remaining build
4422 ;; cores as OpenMP threads.
4423 (setenv "OMP_NUM_THREADS" (number->string
4424 (max (quotient (parallel-job-count) 2)
4425 1)))
4426 (,%openmpi-setup)))))))
4427 (synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)")))
4428
e01397b4
EB		 4429(define-public elemental
4430 (package
4431 (name "elemental")
4432 (version "0.87.7")
4433 (source (origin
5c0b6d1b
EF		 4434 (method git-fetch)
4435 (uri (git-reference
4436 (url "https://github.com/elemental/Elemental.git")
4437 (commit (string-append "v" version))))
4438 (file-name (git-file-name name version))
e01397b4
EB		 4439 (sha256
4440 (base32
5c0b6d1b 4441 "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
e01397b4 4442 (build-system cmake-build-system)
1e05e837 4443 (home-page "https://github.com/elemental/Elemental")
e01397b4
EB		 4444 (native-inputs
4445 `(("gfortran" ,gfortran)))
4446 (inputs
4447 `(("blas" ,openblas)
4448 ("gfortran:lib" ,gfortran "lib")
4449 ("gmp" ,gmp)
4450 ("lapack" ,lapack)
4451 ("metis" ,metis)
4452 ("mpc" ,mpc)
4453 ("mpfr" ,mpfr)
4454 ("mpi" ,openmpi)
4455 ("qd" ,qd)))
4456 (arguments
4457 `(#:build-type "Release" ;default RelWithDebInfo not supported
4458 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
4459 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
4460 "-DEL_CACHE_WARNINGS:BOOL=YES"
4461 "-DEL_TESTS:BOOL=YES"
4462 "-DCMAKE_INSTALL_LIBDIR=lib"
4463 "-DGFORTRAN_LIB=gfortran")
4464 #:phases (modify-phases %standard-phases
3b42e2be
EF		 4465 (add-before 'check 'mpi-setup
4466 ,%openmpi-setup)
e01397b4
EB		 4467 (add-before 'check 'setup-tests
4468 (lambda _
4469 ;; Parallelism is done at the MPI layer.
4470 (setenv "OMP_NUM_THREADS" "1")
4471 #t))
4472 (add-after 'install 'remove-tests
4473 (lambda* (#:key outputs #:allow-other-keys)
4474 ;; Tests are installed, with no easy configuration
4475 ;; switch to prevent this, so delete them.
4476 (delete-file-recursively
3b42e2be 4477 (string-append (assoc-ref outputs "out") "/bin"))
e01397b4
EB		 4478 #t)))))
4479 (synopsis "Dense and sparse-direct linear algebra and optimization")
4480 (description "Elemental is a modern C++ library for distributed-memory
4481dense and sparse-direct linear algebra, conic optimization, and lattice
4482reduction.")
4483 (license license:bsd-2)))
5b05dce7
JN		 4484
4485(define-public mcrl2
4486 (package
4487 (name "mcrl2")
3bc74090 4488 (version "201908.0")
5b05dce7
JN		 4489 (source (origin
4490 (method url-fetch)
185152e3
JN		 4491 (uri (string-append
4492 "https://www.mcrl2.org/download/release/mcrl2-"
4493 version ".tar.gz"))
5b05dce7
JN		 4494 (sha256
4495 (base32
3bc74090 4496 "1i4xgl2d5fgiz1mwi50cyfkrrcpm8nxfayfjgmhq7chs58wlhfsz"))))
5b05dce7
JN		 4497 (inputs
4498 `(("boost" ,boost)
4499 ("glu" ,glu)
4500 ("mesa" ,mesa)
077d66ed 4501 ("qtbase" ,qtbase)))
5b05dce7 4502 (build-system cmake-build-system)
ed0c5d3c 4503 (synopsis "Toolset for the mCRL2 formal specification language")
5b05dce7 4504 (description
ed0c5d3c
TGR		 4505 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
4506specification language for describing concurrent discrete event systems. Its
4507toolset supports analysis and automatic verification, linearisation, simulation,
4508state-space exploration and generation, and tools to optimise and analyse
5b05dce7
JN		 4509specifications. Also, state spaces can be manipulated, visualised and
4510analysed.")
b3882709 4511 (home-page "https://mcrl2.org")
5b05dce7 4512 (license license:boost1.0)))
41835f94 4513
e03b9126
JN		 4514(define-public mcrl2-minimal
4515 (package
4516 (inherit mcrl2)
4517 (name "mcrl2-minimal")
4518 (inputs
4519 `(("boost" ,boost)))
4520 (arguments
4521 '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
4522
910deec6
NV		 4523(define-public tcalc
4524 (package
4525 (name "tcalc")
4526 (version "2.0")
4527 (source
4528 (origin
4529 (method url-fetch)
4530 (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
4531 version ".tar.gz"))
4532 (sha256
4533 (base32
4534 "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
4535 (build-system gnu-build-system)
4536 (synopsis "The terminal calculator")
4537 (description
4538 "The terminal calculator is a small program to help users of the GNU/Linux
4539terminal do calculations simply and quickly. The formula to be calculated can
4540be fed to @command{tcalc} through the command line.")
4541 (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
4542 (license license:gpl3+)))
b26e4f26
EB		 4543
4544(define-public sundials
4545 (package
4546 (name "sundials")
4547 (version "3.1.1")
4548 (source
4549 (origin
4550 (method url-fetch)
4551 (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
4552 "sundials-" version ".tar.gz"))
4553 (sha256
4554 (base32
4555 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
4556 (build-system cmake-build-system)
4557 (native-inputs
4558 `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
4559 (inputs
4560 `(("fortran" ,gfortran) ;for fcmix
4561 ("blas" ,openblas)
4562 ("suitesparse" ,suitesparse))) ;TODO: Add hypre
4563 (arguments
4564 `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
4565 "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
4566 "-DEXAMPLES_ENABLE_F77:BOOL=ON"
4567 "-DEXAMPLES_ENABLE_F90:BOOL=ON"
4568 "-DEXAMPLES_INSTALL:BOOL=OFF"
4569
4570 "-DFCMIX_ENABLE:BOOL=ON"
4571
4572 "-DKLU_ENABLE:BOOL=ON"
4573 ,(string-append "-DKLU_INCLUDE_DIR="
4574 (assoc-ref %build-inputs "suitesparse")
4575 "/include")
4576 ,(string-append "-DKLU_LIBRARY_DIR="
4577 (assoc-ref %build-inputs "suitesparse")
4578 "/lib"))))
4579 (home-page "https://computation.llnl.gov/projects/sundials")
4580 (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
4581 (description "SUNDIALS is a family of software packages implemented with
4582the goal of providing robust time integrators and nonlinear solvers that can
4583easily be incorporated into existing simulation codes.")
4584 (license license:bsd-3)))
4585
4586(define-public sundials-openmpi
4587 (package (inherit sundials)
4588 (name "sundials-openmpi")
4589 (inputs
4590 `(("mpi" ,openmpi)
4591 ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
4592 ,@(package-inputs sundials)))
4593 (arguments
4594 (substitute-keyword-arguments (package-arguments sundials)
4595 ((#:configure-flags flags '())
4596 `(cons* "-DMPI_ENABLE:BOOL=ON"
4597 "-DPETSC_ENABLE:BOOL=ON"
4598 (string-append "-DPETSC_INCLUDE_DIR="
4599 (assoc-ref %build-inputs "petsc")
4600 "/include")
4601 (string-append "-DPETSC_LIBRARY_DIR="
4602 (assoc-ref %build-inputs "petsc")
4603 "/lib")
4604 ,flags))
4605 ((#:phases phases '%standard-phases)
4606 `(modify-phases ,phases
bbe46a4a
EB		 4607 (add-before 'check 'mpi-setup
4608 ,%openmpi-setup)))))
b26e4f26 4609 (synopsis "SUNDIALS with OpenMPI support")))
a6b9ebc2
EB		 4610
4611(define-public combinatorial-blas
4612 (package
4613 (name "combinatorial-blas")
4614 (version "1.6.2")
4615 (source
4616 (origin
4617 (method url-fetch)
4618 (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/"
4619 "CombBLAS_beta_"
4620 (match (string-split version #\.)
4621 ((major minor patch)
4622 (string-append major minor "_" patch))) ;e.g. "16_2"
4623 ".tgz"))
4624 (sha256
4625 (base32
4626 "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a"))
4627 (patches (search-patches "combinatorial-blas-awpm.patch"
4628 "combinatorial-blas-io-fix.patch"))))
4629 (build-system cmake-build-system)
4630 (inputs
4631 `(("mpi" ,openmpi)
4632 ("test-data" ,(origin
4633 (method url-fetch)
4634 (uri (string-append "https://people.eecs.berkeley.edu/~aydin/"
4635 "CombBLAS_FILES/testdata_combblas1.6.1.tgz"))
4636 (sha256
4637 (base32
4638 "01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87"))))))
4639 (arguments
4640 `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
4641 "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL")
4642 #:parallel-tests? #f ;tests use 'mpiexec -n4'
4643 #:phases
4644 (modify-phases %standard-phases
4645 (add-before 'check 'mpi-setup
4646 ,%openmpi-setup)
4647 (add-before 'check 'test-setup
4648 (lambda* (#:key inputs #:allow-other-keys)
4649 (setenv "OMP_NUM_THREADS" "2")
4650 (invoke "tar" "xf" (assoc-ref inputs "test-data")))))))
4651 (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/")
4652 (synopsis "Linear algebra primitives for graph analytics")
4653 (description "The Combinatorial BLAS (CombBLAS) is an extensible
4654distributed-memory parallel graph library offering a small but powerful set of
4655linear algebra primitives specifically targeting graph analytics.")
4656 (license (list
4657 license:gpl2+ ;include/psort/(funnel|sort)*.h
4658 license:x11 ;usort and psort
4659 license:bsd-3)))) ;CombBLAS and MersenneTwister.h
3847d1f2
RW		 4660
4661(define-public dune-common
4662 (package
4663 (name "dune-common")
4664 (version "2.6.0")
4665 (source
4666 (origin
4667 (method url-fetch)
4668 (uri (string-append "https://dune-project.org/download/"
4669 version "/dune-common-" version ".tar.gz"))
4670 (sha256
4671 (base32
4672 "019wcr1qf7jwyxx1y5y290wdlglylskvbb2m01ljkzcza2xnlmhw"))))
4673 (build-system cmake-build-system)
4674 (arguments
4675 `(#:phases
4676 (modify-phases %standard-phases
4677 (add-after 'build 'build-tests
4678 (lambda* (#:key make-flags #:allow-other-keys)
393dc1cc 4679 (apply invoke "make" "build_tests" make-flags))))))
3847d1f2
RW		 4680 (inputs
4681 `(("gmp" ,gmp)
4682 ("metis" ,metis)
3847d1f2
RW		 4683 ("openblas" ,openblas)
4684 ("python" ,python)
4685 ("superlu" ,superlu)))
4686 (native-inputs
4687 `(("gfortran" ,gfortran)
4688 ("pkg-config" ,pkg-config)))
4689 (home-page "https://dune-project.org/")
4690 (synopsis "Distributed and Unified Numerics Environment")
4691 (description "DUNE, the Distributed and Unified Numerics Environment is a
4692modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4693grid-based methods. It supports the easy implementation of methods like
4694@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4695Differences} (FD).")
4696 ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2.
4697 (license license:gpl2)))
242dbd8e
RW		 4698
4699(define-public dune-geometry
4700 (package
4701 (name "dune-geometry")
4702 (version "2.6.0")
4703 (source
4704 (origin
4705 (method url-fetch)
4706 (uri (string-append "https://dune-project.org/download/"
4707 version "/dune-geometry-" version ".tar.gz"))
4708 (sha256
4709 (base32
4710 "0hlaaxjyv9j05blasvb67sy02hd0w4g9znf68gdh3l731dd1aqbn"))))
4711 (build-system cmake-build-system)
4712 (arguments
4713 `(#:phases
4714 (modify-phases %standard-phases
4715 (add-after 'build 'build-tests
4716 (lambda* (#:key make-flags #:allow-other-keys)
4717 (apply invoke "make" "build_tests" make-flags))))))
4718 (inputs
4719 `(("dune-common" ,dune-common)
242dbd8e
RW		 4720 ;; Optional
4721 ("openblas" ,openblas)
4722 ("gmp" ,gmp)
4723 ("python" ,python)))
4724 (native-inputs
4725 `(("gfortran" ,gfortran)
4726 ("pkg-config" ,pkg-config)))
4727 (home-page "https://dune-project.org/")
4728 (synopsis "Distributed and Unified Numerics Environment")
4729 (description "DUNE, the Distributed and Unified Numerics Environment is a
4730modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4731grid-based methods. It supports the easy implementation of methods like
4732@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4733Differences} (FD).
4734
4735This package contains the basic DUNE geometry classes.")
4736 ;; GPL version 2 with "runtime exception"
4737 (license license:gpl2)))
ef6e69fd 4738
07ebb75d
FG		 4739(define-public dune-uggrid
4740 (package
4741 (name "dune-uggrid")
4742 (version "2.6.0")
4743 (source
4744 (origin
4745 (method url-fetch)
4746 (uri (string-append "https://dune-project.org/download/"
4747 version "/dune-uggrid-" version ".tar.gz"))
4748 (sha256
4749 (base32
4750 "05l7a1gb78mny49anyxk6rjvn66rhgm30y72v5cjg0m5kfgr1a1f"))))
4751 (build-system cmake-build-system)
4752 (arguments
4753 `(#:phases
4754 (modify-phases %standard-phases
4755 (add-after 'build 'build-tests
4756 (lambda* (#:key make-flags #:allow-other-keys)
4757 (apply invoke "make" "build_tests" make-flags))))))
4758 (inputs
393dc1cc 4759 `(("dune-common" ,dune-common)))
07ebb75d
FG		 4760 (native-inputs
4761 `(("gfortran" ,gfortran)
4762 ("pkg-config" ,pkg-config)))
4763 (home-page "https://dune-project.org/")
4764 (synopsis "Distributed and Unified Numerics Environment")
4765 (description "DUNE, the Distributed and Unified Numerics Environment is a
4766modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4767grid-based methods. It supports the easy implementation of methods like
4768@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4769Differences} (FD).
4770
4771This package contains the DUNE UG grid classes.")
4772 (license license:lgpl2.1)))
4773
ef6e69fd
RW		 4774(define-public dune-grid
4775 (package
4776 (name "dune-grid")
4777 (version "2.6.0")
4778 (source
4779 (origin
4780 (method url-fetch)
4781 (uri (string-append "https://dune-project.org/download/"
4782 version "/dune-grid-" version ".tar.gz"))
4783 (sha256
4784 (base32
4785 "1jp4vscm9yb9xg0lh7apzccfkhvgbnk652yahigmh3cvzpl4acd0"))))
4786 (build-system cmake-build-system)
4787 (arguments
4788 `(#:phases
4789 (modify-phases %standard-phases
4790 (add-after 'build 'build-tests
4791 (lambda* (#:key make-flags #:allow-other-keys)
393dc1cc 4792 (apply invoke "make" "build_tests" make-flags))))))
ef6e69fd
RW		 4793 (inputs
4794 `(("dune-common" ,dune-common)
4795 ("dune-geometry" ,dune-geometry)
4796 ("gmp" ,gmp)
4797 ("metis" ,metis)
4798 ("openblas" ,openblas)
ef6e69fd 4799 ("python" ,python)))
07ebb75d
FG		 4800 (propagated-inputs
4801 `(("dune-uggrid" ,dune-uggrid)))
ef6e69fd
RW		 4802 (native-inputs
4803 `(("gfortran" ,gfortran)
4804 ("pkg-config" ,pkg-config)))
4805 (home-page "https://dune-project.org/")
4806 (synopsis "Distributed and Unified Numerics Environment")
4807 (description "DUNE, the Distributed and Unified Numerics Environment is a
4808modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4809grid-based methods. It supports the easy implementation of methods like
4810@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4811Differences} (FD).
4812
4813This package contains the basic DUNE grid classes.")
4814 ;; GPL version 2 with "runtime exception"
4815 (license license:gpl2)))
ea51d357
RW		 4816
4817(define-public dune-istl
4818 (package
4819 (name "dune-istl")
4820 (version "2.6.0")
4821 (source
4822 (origin
4823 (method url-fetch)
4824 (uri (string-append "https://dune-project.org/download/"
4825 version "/dune-istl-" version ".tar.gz"))
4826 (sha256
4827 (base32
4828 "0l2gyrvys5w6wsmk0ckbb7295s80b7yk7qrl7x66akv2jv1nzq2w"))))
4829 (build-system cmake-build-system)
4830 (arguments
4831 `(#:phases
4832 (modify-phases %standard-phases
4833 (add-after 'build 'build-tests
4834 (lambda* (#:key make-flags #:allow-other-keys)
393dc1cc 4835 (apply invoke "make" "build_tests" make-flags))))))
ea51d357
RW		 4836 (inputs
4837 `(("dune-common" ,dune-common)
ea51d357
RW		 4838 ;; Optional
4839 ("metis" ,metis)
0a703c04 4840 ("suitesparse" ,suitesparse)
ea51d357
RW		 4841 ("superlu" ,superlu)
4842 ("openblas" ,openblas)
4843 ("gmp" ,gmp)
4844 ("python" ,python)))
4845 (native-inputs
4846 `(("gfortran" ,gfortran)
4847 ("pkg-config" ,pkg-config)))
4848 (home-page "https://dune-project.org/")
4849 (synopsis "Distributed and Unified Numerics Environment")
4850 (description "DUNE, the Distributed and Unified Numerics Environment is a
4851modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4852grid-based methods.
4853
4854This is the iterative solver template library which provides generic sparse
4855matrix/vector classes and a variety of solvers based on these classes. A
4856special feature is the use of templates to exploit the recursive block
4857structure of finite element matrices at compile time. Available solvers
4858include Krylov methods, (block-) incomplete decompositions and
4859aggregation-based algebraic multigrid.")
4860 ;; GPL version 2 with "runtime exception"
4861 (license license:gpl2)))
5a70aa7d
RW		 4862
4863(define-public dune-localfunctions
4864 (package
4865 (name "dune-localfunctions")
4866 (version "2.6.0")
4867 (source
4868 (origin
4869 (method url-fetch)
4870 (uri (string-append "https://dune-project.org/download/"
4871 version "/dune-localfunctions-" version ".tar.gz"))
4872 (sha256
4873 (base32
4874 "19c6zjinwwpy8jh4v4prhphyd438rapd4x80fj93apmwgw04nrhl"))))
4875 (build-system cmake-build-system)
4876 (arguments
4877 `(#:phases
4878 (modify-phases %standard-phases
4879 (add-after 'build 'build-tests
4880 (lambda* (#:key make-flags #:allow-other-keys)
4881 (apply invoke "make" "build_tests" make-flags))))))
4882 (inputs
4883 `(("dune-common" ,dune-common)
4884 ("dune-geometry" ,dune-geometry)
5a70aa7d
RW		 4885 ;; Optional
4886 ("metis" ,metis)
4887 ("superlu" ,superlu)
4888 ("gmp" ,gmp)))
4889 (native-inputs
4890 `(("gfortran" ,gfortran)
4891 ("pkg-config" ,pkg-config)))
4892 (home-page "https://dune-project.org/")
4893 (synopsis "Distributed and Unified Numerics Environment") ; TODO
4894 (description "This DUNE module provides interface and implementation for
4895shape functions defined on the DUNE reference elements. In addition to the
4896shape function, interpolation operators and special keys are provided which
4897can be used to assemble global function spaces on finite-element grids.
4898
4899This package provides an interface and implementation for shape functions
4900defined on the DUNE reference elements. In addition to the shape function,
4901interpolation operators and special keys are provided which can be used to
4902assemble global function spaces on finite-element grids.")
4903 ;; GPL version 2 with "runtime exception"
4904 (license license:gpl2)))
ab03d899
RW		 4905
4906(define-public dune-alugrid
4907 (package
4908 (name "dune-alugrid")
4909 (version "2.6.0")
4910 (source
4911 (origin
4912 (method url-fetch)
4913 (uri (string-append "https://dune-project.org/download/"
4914 version "/dune-alugrid-" version ".tar.gz"))
4915 (sha256
4916 (base32
4917 "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj"))))
4918 (build-system cmake-build-system)
4919 (arguments
a669f6e2 4920 `(#:phases
ab03d899
RW		 4921 (modify-phases %standard-phases
4922 (add-after 'unpack 'patch-include
4923 (lambda _
4924 (substitute* "dune/alugrid/test/test-alugrid.cc"
4925 (("doc/grids/gridfactory/testgrids")
4926 "doc/dune-grid/grids/gridfactory/testgrids"))
4927 #t))
4928 (add-after 'build 'build-tests
4929 (lambda* (#:key inputs make-flags #:allow-other-keys)
4930 (setenv "CPLUS_INCLUDE_PATH"
97149c57 4931 (string-append (assoc-ref inputs "dune-grid") "/share"))
393dc1cc 4932 (apply invoke "make" "build_tests" make-flags))))))
ab03d899
RW		 4933 (inputs
4934 `(("dune-common" ,dune-common)
4935 ("dune-geometry" ,dune-geometry)
4936 ("dune-grid" ,dune-grid)
ab03d899
RW		 4937 ;; Optional
4938 ("metis" ,metis)
4939 ("openblas" ,openblas)
4940 ("python" ,python)
4941 ("superlu" ,superlu)
4942 ("gmp" ,gmp)
4943 ("zlib" ,zlib)))
4944 (native-inputs
4945 `(("gfortran" ,gfortran)
4946 ("pkg-config" ,pkg-config)))
4947 (home-page "https://dune-project.org/")
4948 (synopsis "Distributed and Unified Numerics Environment")
4949 (description "ALUGrid is an adaptive, loadbalancing, unstructured
4950implementation of the DUNE grid interface supporting either simplices or
4951cubes.")
4952 (license license:gpl2+)))
0e50630f 4953
f1f9466e
FG		 4954(define-public dune-subgrid
4955 (package
4956 (name "dune-subgrid")
4957 (version "2.6.0")
4958 (source
4959 (origin
4960 (method git-fetch)
4961 (uri (git-reference
4962 (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid")
4963 (commit "releases/2.6-1")))
4964 (file-name (git-file-name name version))
4965 (sha256
4966 (base32
4967 "1gcv35rx3knqd54r4pp9rzd639db4j8w2r2ibq43w1mgwdcqhs64"))))
4968 (build-system cmake-build-system)
4969 (arguments
4970 `(#:phases
4971 (modify-phases %standard-phases
4972 (add-after 'build 'build-tests
4973 (lambda* (#:key make-flags #:allow-other-keys)
393dc1cc 4974 (apply invoke "make" "build_tests" make-flags))))))
f1f9466e
FG		 4975 (inputs
4976 `(("dune-common" ,dune-common)
4977 ("dune-geometry" ,dune-geometry)
4978 ("dune-grid" ,dune-grid)
f1f9466e
FG		 4979 ;; Optional
4980 ("metis" ,metis)
4981 ("openblas" ,openblas)
4982 ("gmp" ,gmp)))
4983 (native-inputs
4984 `(("gfortran" ,gfortran)
4985 ("pkg-config" ,pkg-config)))
4986 (home-page "http://numerik.mi.fu-berlin.de/dune-subgrid/index.php")
4987 (synopsis "Distributed and Unified Numerics Environment")
48b0d9c0 4988 (description "The dune-subgrid module marks elements of
f1f9466e
FG		 4989another hierarchical dune grid. The set of marked elements can then be
4990accessed as a hierarchical dune grid in its own right. Dune-Subgrid
4991provides the full grid interface including adaptive mesh refinement.")
4992 (license license:gpl2+)))
4993
0e50630f
RW		 4994(define-public dune-typetree
4995 (package
4996 (name "dune-typetree")
4997 (version "2.6.0")
4998 (source
4999 (origin
5000 (method git-fetch)
5001 (uri (git-reference
5002 (url "https://gitlab.dune-project.org/staging/dune-typetree.git")
5003 (commit (string-append "v" version))))
5004 (file-name (git-file-name name version))
5005 (sha256
5006 (base32
5007 "0mnv6w2f22lz3j4bdpdjq55vjm8xxfx9v4vvhg9bd36xpsbjpjp9"))))
5008 (build-system cmake-build-system)
5009 (arguments
5010 `(#:phases
5011 (modify-phases %standard-phases
5012 (add-after 'build 'build-tests
5013 (lambda* (#:key make-flags #:allow-other-keys)
5014 (apply invoke "make" "build_tests" make-flags))))))
5015 (inputs
5016 `(("dune-common" ,dune-common)
0e50630f
RW		 5017 ;; Optional
5018 ("openblas" ,openblas)
5019 ("python" ,python)
5020 ("metis" ,metis)
5021 ("superlu" ,superlu)
5022 ("gmp" ,gmp)))
5023 (native-inputs
5024 `(("gfortran" ,gfortran)
5025 ("pkg-config" ,pkg-config)))
5026 (home-page "https://dune-project.org/")
5027 (synopsis "Distributed and Unified Numerics Environment")
5028 (description "TypeTree is a template library for constructing and
5029operating on statically typed trees of objects.")
5030 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
5031 (license (list license:lgpl3+ license:gpl2))))
85b9371c
RW		 5032
5033(define-public dune-functions
5034 (package
5035 (name "dune-functions")
5036 (version "2.6.0")
5037 (source
5038 (origin
5039 (method git-fetch)
5040 (uri (git-reference
5041 (url "https://gitlab.dune-project.org/staging/dune-functions.git")
5042 (commit (string-append "v" version))))
5043 (file-name (git-file-name name version))
5044 (sha256
5045 (base32
5046 "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200"))))
5047 (build-system cmake-build-system)
07ebb75d
FG		 5048 (arguments
5049 `(#:phases
5050 (modify-phases %standard-phases
5051 (add-after 'unpack 'disable-failing-tests
5052 (lambda _
5053 (setenv "ARGS"
5054 ;; unable to load GMSH file in this test
5055 "--exclude-regex gridviewfunctionspacebasistest")
5056 #t))
5057 (add-after 'build 'build-tests
5058 (lambda* (#:key make-flags #:allow-other-keys)
393dc1cc 5059 (apply invoke "make" "build_tests" make-flags))))))
85b9371c
RW		 5060 (inputs
5061 `(("dune-common" ,dune-common)
5062 ("dune-istl" ,dune-istl)
5063 ("dune-localfunctions" ,dune-localfunctions)
5064 ("dune-grid" ,dune-grid)
5065 ("dune-geometry" ,dune-geometry)
5066 ("dune-typetree" ,dune-typetree)
85b9371c
RW		 5067 ("openblas" ,openblas)
5068 ("metis" ,metis)
5069 ("python" ,python)
5070 ("superlu" ,superlu)
5071 ("gmp" ,gmp)))
5072 (native-inputs
5073 `(("gfortran" ,gfortran)
5074 ("pkg-config" ,pkg-config)))
5075 (home-page "https://dune-project.org/")
5076 (synopsis "Distributed and Unified Numerics Environment")
5077 (description "The dune-functions module provides an abstraction layer for
5078global finite element functions. Its two main concepts are functions
5079implemented as callable objects, and bases of finite element spaces.")
5080 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
5081 (license (list license:lgpl3+ license:gpl2))))
4714b00e
RW		 5082
5083(define-public dune-pdelab
5084 (package
5085 (name "dune-pdelab")
5086 (version "2.6.0-rc1")
5087 (source
5088 (origin
5089 (method git-fetch)
5090 (uri (git-reference
5091 (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
5092 (commit (string-append "v" version))))
5093 (file-name (git-file-name name version))
5094 (sha256
5095 (base32
5096 "07g0s9448z65vjrq88g5rv3340iifil85k170n8kbqchsvi4ny5v"))))
5097 (build-system cmake-build-system)
5098 (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
5099 (inputs
5100 `(("dune-common" ,dune-common)
5101 ("dune-istl" ,dune-istl)
5102 ("dune-localfunctions" ,dune-localfunctions)
5103 ("dune-geometry" ,dune-geometry)
5104 ("dune-grid" ,dune-grid)
5105 ("dune-typetree" ,dune-typetree)
5106 ("dune-functions" ,dune-functions)
4714b00e
RW		 5107 ;; Optional
5108 ("openblas" ,openblas)
5109 ("eigen" ,eigen)
5110 ("metis" ,metis)
5111 ("python" ,python)
5112 ("superlu" ,superlu)
5113 ("gmp" ,gmp)))
5114 (native-inputs
5115 `(("gfortran" ,gfortran)
5116 ("pkg-config" ,pkg-config)))
5117 (home-page "https://dune-project.org/")
5118 (synopsis "Differential equations solver toolbox")
5119 (description "PDELab is a partial differential equations solver toolbox
5120built on top of DUNE, the Distributed and Unified Numerics Environment.")
5121 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
5122 (license (list license:lgpl3+ license:gpl2))))
413f6126 5123
6ceb7716
FG		 5124(define add-openmpi-to-dune-package
5125 (let ((dune-package?
5126 (lambda (p) (string-prefix? "dune-" (package-name p)))))
5127 (package-mapping
5128 (lambda (p)
5129 (if (dune-package? p)
5130 (package (inherit p)
5131 (name (string-append (package-name p) "-openmpi"))
5132 (inputs `(,@(package-inputs p)
5133 ("openmpi" ,openmpi)))
5134 (arguments
5135 (substitute-keyword-arguments (package-arguments p)
5136 ((#:phases phases '%standard-phases)
5137 `(modify-phases ,phases
5138 (add-before 'check 'mpi-setup
5139 ,%openmpi-setup)))))
5140 (synopsis (string-append (package-synopsis p) " (with MPI support)")))
5141 p))
5142 (negate dune-package?))))
5143
5144(define-public dune-common-openmpi
5145 (add-openmpi-to-dune-package dune-common))
5146
5147(define-public dune-geometry-openmpi
5148 (add-openmpi-to-dune-package dune-geometry))
5149
5150(define-public dune-istl-openmpi
5151 (add-openmpi-to-dune-package dune-istl))
5152
5153(define-public dune-typetree-openmpi
5154 (add-openmpi-to-dune-package dune-typetree))
5155
5156(define-public dune-uggrid-openmpi
5157 (add-openmpi-to-dune-package dune-uggrid))
5158
5159(define-public dune-grid-openmpi
5160 (add-openmpi-to-dune-package dune-grid))
5161
5162(define-public dune-alugrid-openmpi
5163 (add-openmpi-to-dune-package dune-alugrid))
5164
5165(define-public dune-subgrid-openmpi
5166 (add-openmpi-to-dune-package dune-subgrid))
5167
5168(define-public dune-localfunctions-openmpi
5169 (add-openmpi-to-dune-package dune-localfunctions))
5170
5171(define-public dune-functions-openmpi
5172 (add-openmpi-to-dune-package dune-functions))
5173
5174(define-public dune-pdelab-openmpi
5175 (add-openmpi-to-dune-package dune-pdelab))
5176
413f6126
AI		 5177(define-public mlucas
5178 (package
5179 (name "mlucas")
5180 (version "18")
5181 (source
5182 (origin
5183 (method url-fetch)
5184 (uri (string-append
5185 "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz"))
5186 (sha256
a36efdbc 5187 (base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447"))))
413f6126
AI		 5188 (build-system gnu-build-system)
5189 (inputs
5190 `(("python2" ,python-2)))
5191 (arguments
a36efdbc 5192 `(#:tests? #f ; no tests
413f6126
AI		 5193 #:phases
5194 (modify-phases %standard-phases
5195 (replace 'configure
5196 (lambda _
5197 (chdir "src")
5198 (call-with-output-file "Makefile"
5199 (lambda (port)
5200 (format port "CC = gcc
5201CFLAGS = -O3 ~a -DUSE_THREADS
5202LDLIBS = -lm -lpthread -lrt
5203Mlucas: $(addsuffix .o,$(basename $(wildcard *.c)))
5204"
5205 ,(let ((system (or (%current-target-system)
5206 (%current-system))))
5207 (cond
5208 ((string-prefix? "x86_64" system) "-DUSE_SSE2")
5209 (else ""))))))
5210 #t))
5211 (replace 'install
5212 (lambda* (#:key outputs #:allow-other-keys)
5213 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
5214 (install-file "Mlucas" bin)
5215 (install-file "primenet.py" bin))
5216 #t)))))
5217 (home-page "https://www.mersenne.org")
5218 (synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client")
5219 (description "Mlucas performs Lucas-Lehmer primality testing of Mersenne
5220numbers in search of a world-record prime. You may use it to test any
5221suitable number as you wish, but it is preferable that you do so in a
5222coordinated fashion, as part of the Great Internet Mersenne Prime
5223Search (GIMPS). Mlucas also includes a simple Python script for assignment
5224management via the GIMPS project's Primenet server.")
5225 (license license:gpl2+)))
6f8c4195
NG		 5226
5227(define-public nauty
5228 (package
5229 (name "nauty")
1ff64c50 5230 (version "2.6r12")
6f8c4195
NG		 5231 (source (origin
5232 (method url-fetch)
5233 (uri (string-append
5234 "https://pallini.di.uniroma1.it/"
5235 "nauty" (string-join (string-split version #\.) "")
5236 ".tar.gz"))
5237 (sha256
5238 (base32
1ff64c50 5239 "1p4mxf8q5wm47nxyskxbqwa5p1vvkycv1zgswvnk9nsn6vff0al6"))))
6f8c4195
NG		 5240 (build-system gnu-build-system)
5241 (outputs '("out" "lib"))
5242 (arguments
5243 `(#:test-target "checks"
5244 #:phases
5245 (modify-phases %standard-phases
5246 ;; Default make target does not build all available
5247 ;; executables. Create them now.
5248 (add-after 'build 'build-extra-programs
5249 (lambda _
5250 (for-each (lambda (target) (invoke "make" target))
5251 '("blisstog" "bliss2dre" "checks6" "sumlines"))
5252 #t))
5253 ;; Upstream does not provide any install target.
5254 (replace 'install
5255 (lambda* (#:key outputs #:allow-other-keys)
5256 (let* ((out (assoc-ref outputs "out"))
5257 (lib-output (assoc-ref outputs "lib"))
5258 (bin (string-append out "/bin"))
5259 (doc (string-append out "/share/doc/nauty/"))
5260 (include (string-append lib-output "/include/nauty"))
5261 (lib (string-append lib-output "/lib/nauty")))
5262 (for-each (lambda (f) (install-file f bin))
5263 '("dreadnaut" "NRswitchg" "addedgeg" "amtog" "biplabg"
5264 "blisstog" "bliss2dre" "catg" "checks6" "complg"
5265 "converseg" "copyg" "countg" "cubhamg" "deledgeg"
5266 "delptg" "directg" "dretodot" "dretog" "genbg"
5267 "genbgL" "geng" "genquarticg" "genrang" "genspecialg"
5268 "gentourng" "gentreeg" "hamheuristic" "labelg"
5269 "linegraphg" "listg" "multig" "newedgeg" "pickg"
5270 "planarg" "ranlabg" "shortg" "showg" "subdivideg"
5271 "sumlines" "twohamg" "vcolg" "watercluster2"))
5272 (for-each (lambda (f) (install-file f include))
5273 (find-files "." "\\.h$"))
5274 (for-each (lambda (f) (install-file f lib))
5275 (find-files "." "\\.a$"))
5276 (for-each (lambda (f) (install-file f doc))
5277 (append '("formats.txt" "README" "schreier.txt")
5278 (find-files "." "\\.pdf$")))))))))
5279 (inputs
5280 `(("gmp" ,gmp))) ;for sumlines
5281 (home-page "https://pallini.di.uniroma1.it/")
5282 (synopsis "Library for graph automorphisms")
5283 (description "@code{nauty} (No AUTomorphisms, Yes?) is a set of
5284procedures for computing automorphism groups of graphs and digraphs.
5285
5286@code{nauty} computes graph information in the form of a set of
5287generators, the size of the group, and the orbits of the group; it can
5288also produce a canonical label. The @code{nauty} suite is written in
5289C and comes with a command-line interface, a collection of
5290command-line tools, and an Application Programming Interface (API).
5291
5292This package provides the static libraries required to run programs
5293compiled against the nauty library.")
5294 (license license:asl2.0)))
26433471
AE		 5295
5296(define-public ppl
5297 (package
5298 (name "ppl")
5299 (version "1.2")
5300 (source
5301 (origin
5302 (method url-fetch)
5303 (uri (string-append "https://www.bugseng.com/products/ppl/download/"
5304 "ftp/releases/" version
5305 "/ppl-" version ".tar.gz"))
5306 (sha256
5307 (base32
5308 "1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb"))))
5309 (build-system gnu-build-system)
5310 (native-inputs
5311 `(("m4", m4)))
5312 (inputs
5313 `(("glpk" ,glpk)
5314 ("gmp", gmp)))
5315 (home-page "https://www.bugseng.com/parma-polyhedra-library")
5316 (synopsis
5317 "Parma Polyhedra Library for computations with polyhedra")
5318 (description
5319 "The Parma Polyhedra Library (PPL) provides numerical abstractions
5320especially targeted at applications in the field of analysis and
5321verification of complex systems. These abstractions include convex
5322polyhedra, defined as the intersection of a finite number of (open or
5323closed) halfspaces, each described by a linear inequality (strict or
5324non-strict) with rational coefficients; some special classes of polyhedra
5325shapes that offer interesting complexity/precision tradeoffs; and grids
5326which represent regularly spaced points that satisfy a set of linear
5327congruence relations. The library also supports finite powersets and
5328products of (any kind of) polyhedra and grids, a mixed integer linear
5329programming problem solver using an exact-arithmetic version of the simplex
5330algorithm, a parametric integer programming solver, and primitives for
5331termination analysis via the automatic synthesis of linear ranking
5332functions.")
5333 (license license:gpl3+)))
4cb5d251
SS		 5334
5335(define-public speedcrunch
5336 (package
5337 (name "speedcrunch")
5338 (version "0.12.0")
5339 (source
5340 (origin
5341 (method git-fetch)
5342 (uri (git-reference
5343 (url "https://bitbucket.org/heldercorreia/speedcrunch.git")
5344 (commit (string-append "release-" version))))
5345 (file-name (git-file-name name version))
5346 (sha256
5347 (base32
5348 "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"))))
5349 (build-system cmake-build-system)
5350 (inputs `(("qtbase" ,qtbase)))
5351 (native-inputs `(("qttools" ,qttools)))
5352 (arguments
5353 `(#:phases
5354 (modify-phases %standard-phases
5355 (add-after 'unpack 'chdir-to-src
5356 (lambda _ (chdir "src") #t)))))
5357 (synopsis "High-precision scientific calculator")
5358 (description
5359 "SpeedCrunch is a high-precision scientific calculator. It features a
5360syntax-highlighted scrollable display and is designed to be fully used via
5361keyboard. Some distinctive features are auto-completion of functions and
5362variables, a formula book, and quick insertion of constants from various
5363fields of knowledge.")
80fafdba 5364 (home-page "https://speedcrunch.org/")
4cb5d251
SS		 5365 (license license:gpl2+)))
5366
3b7828cc
RS		 5367(define-public minisat
5368 ;; This is the last commit which is available upstream, no
5369 ;; release happened since 2010.
5370 (let ((commit "37dc6c67e2af26379d88ce349eb9c4c6160e8543")
5371 (revision "1"))
5372 (package
5373 (name "minisat")
5374 (version (string-append "2.2.0-" revision "." (string-take commit 7)))
5375 (source
5376 (origin
5377 (method git-fetch)
5378 (uri (git-reference
5379 (url "https://github.com/niklasso/minisat.git")
5380 (commit commit)))
5381 (file-name (string-append name "-" version "-checkout"))
5382 (sha256
5383 (base32
5384 "091hf3qkm197s5r7xcr3m07xsdwyz2rqk1hc9kj0hn13imz09irq"))
5385 (patches
5386 (search-patches "minisat-friend-declaration.patch"
5387 "minisat-install.patch"))))
5388 (build-system gnu-build-system)
5389 (arguments
5390 '(#:make-flags (list (string-append "prefix=" %output))
5391 #:tests? #f ;no check target
5392 #:phases
5393 (modify-phases %standard-phases
5394 (delete 'configure))))
5395 (inputs
5396 `(("zlib:static" ,zlib "static")
5397 ("zlib" ,zlib)))
5398 (synopsis
5399 "Small, yet efficient, SAT solver")
5400 (description
5401 "MiniSat is a minimalistic, open-source SAT solver, developed to help
5402researchers and developers alike to get started on SAT.")
5403 (home-page
5404 "http://minisat.se/MiniSat.html")
5405 (license license:expat))))
70c98efa
VK		 5406
5407(define-public libqalculate
5408 (package
5409 (name "libqalculate")
5410 (version "3.8.0")
5411 (source
5412 (origin
5413 (method git-fetch)
5414 (uri (git-reference
5415 (url "https://github.com/Qalculate/libqalculate/")
5416 (commit (string-append "v" version))))
5417 (file-name (git-file-name name version))
5418 (sha256
9b3c231e
VK		 5419 (base32 "1vbaza9c7159xf2ym90l0xkyj2mp6c3hbghhsqn29yvz08fda9df"))
5420 (patches
5421 (search-patches "libqalculate-3.8.0-libcurl-ssl-fix.patch"))))
70c98efa
VK		 5422 (build-system gnu-build-system)
5423 (native-inputs
5424 `(("pkg-config" ,pkg-config)
5425 ("gettext" ,gettext-minimal)
5426 ("intltool" ,intltool)
5427 ("automake" ,automake)
5428 ("autoconf" ,autoconf)
5429 ("libtool" ,libtool)
5430 ("doxygen" ,doxygen)
5431 ("file" ,file)))
5432 (inputs
5433 `(("gmp" ,gmp)
5434 ("mpfr" ,mpfr)
5435 ("libxml2" ,libxml2)
5436 ("curl" ,curl)
5437 ("icu4c" ,icu4c)
5438 ("gnuplot" ,gnuplot)
5439 ("readline" ,readline)
5440 ("libiconv" ,libiconv)))
5441 (arguments
5442 `(#:phases
5443 (modify-phases %standard-phases
5444 (add-before 'bootstrap 'setenv
5445 ;; Prevent the autogen.sh script to carry out the configure
5446 ;; script, which has not yet been patched to replace /bin/sh.
5447 (lambda _
5448 (setenv "NOCONFIGURE" "TRUE")
5449 #t)))))
5450 (home-page "https://qalculate.github.io/")
5451 (synopsis "Multi-purpose cli desktop calculator and library")
5452 (description
5453 "Libqalculate is a multi-purpose cli desktop calculator and library.
5454It provides basic and advanced functionality. Features include customizable
5455functions, unit calculations, and conversions, physical constants, symbolic
5456calculations (including integrals and equations), arbitrary precision,
67e2e171 5457uncertainty propagation, interval arithmetic, plotting and a user-friendly
70c98efa
VK		 5458cli.")
5459 (license license:gpl2+)))
72c71d24
VK		 5460
5461(define-public qalculate-gtk
5462 (package
5463 (name "qalculate-gtk")
5464 (version "3.8.0")
5465 (source
5466 (origin
5467 (method git-fetch)
5468 (uri (git-reference
5469 (url "https://github.com/Qalculate/qalculate-gtk/")
5470 (commit (string-append "v" version))))
5471 (file-name (git-file-name name version))
5472 (sha256
5473 (base32 "0nsg6dzg5r7rzqr671nvrf1c50rjwpz7bxv5f20i4s7agizgv840"))))
5474 (build-system glib-or-gtk-build-system)
5475 (native-inputs
5476 `(("pkg-config" ,pkg-config)
5477 ("intltool" ,intltool)
5478 ("automake" ,automake)
5479 ("autoconf" ,autoconf)
5480 ("libtool" ,libtool)
5481 ("file" ,file)))
5482 (inputs
5483 `(("gmp" ,gmp)
5484 ("mpfr" ,mpfr)
5485 ("libqalculate" ,libqalculate)
5486 ("libxml2" ,libxml2)
5487 ("glib" ,glib)
5488 ("gtk+" ,gtk+)))
5489 (arguments
5490 `(#:phases
5491 (modify-phases %standard-phases
5492 (add-before 'bootstrap 'setenv
5493 ;; Prevent the autogen.sh script to carry out the configure
5494 ;; script, which has not yet been patched to replace /bin/sh.
5495 (lambda _
5496 (setenv "NOCONFIGURE" "TRUE")
5497 #t))
5498 (add-before 'check 'add-pot-file
5499 ;; the file contains translations and are currently not in use
5500 ;; left out on purpose so add it to POTFILES.skip
5501 (lambda _
5502 (with-output-to-file "po/POTFILES.skip"
5503 (lambda _
5504 (format #t "data/shortcuts.ui~%")
5505 #t))
5506 #t)))))
5507 (home-page "https://qalculate.github.io/")
5508 (synopsis "Multi-purpose graphical desktop calculator")
5509 (description
5510 "Qalculate-gtk is the GTK frontend for libqalculate. It is a
5511multi-purpose GUI desktop calculator. It provides basic and advanced
5512functionality. Features include customizable functions, unit calculations,
5513and conversions, physical constants, symbolic calculations (including
5514integrals and equations), arbitrary precision, uncertainity propagation,
5515interval arithmetic, plotting.")
5516 (license license:gpl2+)))
jackhill's copy of GNU Guix: https://guix.gnu.org/