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8f8b2451 1;;; GNU Guix --- Functional package management for GNU
b146763a 2;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
da95c817 3;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
a53d6719 4;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
e01397b4 5;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org>
df354a77 6;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
182d6311 7;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
4dba441c 8;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
32158110 9;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
9aafbc0c 10;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
83a34647 11;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
45147b0c 12;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
ec8c7e47 13;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
3c8ba11a 14;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
5d4bd4cc 15;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
d7cff656 16;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
2fd26d05 17;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
5d4bd4cc 18;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>
54052a54 19;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net>
ba1be533 20;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
d109b1e8 21;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
5ca4fe96 22;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
59cd0ba4 23;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
dc7d6d4e 24;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
5b05dce7 25;;; Copyright © 2018 Jan Nieuwenhuizen <janneke@gnu.org>
8f8b2451
AE		 26;;;
27;;; This file is part of GNU Guix.
28;;;
29;;; GNU Guix is free software; you can redistribute it and/or modify it
30;;; under the terms of the GNU General Public License as published by
31;;; the Free Software Foundation; either version 3 of the License, or (at
32;;; your option) any later version.
33;;;
34;;; GNU Guix is distributed in the hope that it will be useful, but
35;;; WITHOUT ANY WARRANTY; without even the implied warranty of
36;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
37;;; GNU General Public License for more details.
38;;;
39;;; You should have received a copy of the GNU General Public License
40;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
41
42(define-module (gnu packages maths)
ec322be2 43 #:use-module (ice-9 regex)
8f8b2451 44 #:use-module (gnu packages)
b5b73a82 45 #:use-module ((guix licenses) #:prefix license:)
8f8b2451
AE		 46 #:use-module (guix packages)
47 #:use-module (guix download)
54052a54 48 #:use-module (guix git-download)
0e2672ae 49 #:use-module (guix utils)
cec86422 50 #:use-module (guix build utils)
da95c817 51 #:use-module (guix build-system cmake)
c9dfa3c7 52 #:use-module (guix build-system gnu)
ba1be533 53 #:use-module (guix build-system ocaml)
ec8c7e47 54 #:use-module (guix build-system r)
3de01d3f 55 #:use-module (gnu packages algebra)
5143517c 56 #:use-module (gnu packages autotools)
3de01d3f 57 #:use-module (gnu packages bison)
a17d4564 58 #:use-module (gnu packages boost)
e73b49fb 59 #:use-module (gnu packages check)
3de01d3f 60 #:use-module (gnu packages cmake)
c9dfa3c7 61 #:use-module (gnu packages compression)
668c06ac 62 #:use-module (gnu packages curl)
b7b27a8f 63 #:use-module (gnu packages cyrus-sasl)
528bb464 64 #:use-module (gnu packages documentation)
57e544e8 65 #:use-module (gnu packages elf)
3de01d3f 66 #:use-module (gnu packages flex)
668c06ac 67 #:use-module (gnu packages fltk)
f3929800 68 #:use-module (gnu packages fontutils)
1dba6407 69 #:use-module (gnu packages gettext)
da95c817 70 #:use-module (gnu packages gcc)
73fed4f8 71 #:use-module (gnu packages gd)
668c06ac 72 #:use-module (gnu packages ghostscript)
889187a4 73 #:use-module (gnu packages graphviz)
f3929800 74 #:use-module (gnu packages gtk)
45147b0c 75 #:use-module (gnu packages image)
2fd26d05 76 #:use-module (gnu packages java)
668c06ac 77 #:use-module (gnu packages less)
8731e527 78 #:use-module (gnu packages lisp)
bc3a2e35 79 #:use-module (gnu packages logging)
6e64766a 80 #:use-module (gnu packages lua)
5698b8b8 81 #:use-module (gnu packages gnome)
1b39a196 82 #:use-module (gnu packages guile)
668c06ac
JD		 83 #:use-module (gnu packages xorg)
84 #:use-module (gnu packages gl)
9f913401 85 #:use-module (gnu packages imagemagick)
8731e527 86 #:use-module (gnu packages m4)
d8c7eeb9 87 #:use-module (gnu packages mpi)
b92eee75 88 #:use-module (gnu packages multiprecision)
528bb464 89 #:use-module (gnu packages netpbm)
ba1be533 90 #:use-module (gnu packages ocaml)
668c06ac 91 #:use-module (gnu packages pcre)
5698b8b8 92 #:use-module (gnu packages popt)
c9dfa3c7
AE		 93 #:use-module (gnu packages perl)
94 #:use-module (gnu packages pkg-config)
da95c817 95 #:use-module (gnu packages python)
589e3f4e 96 #:use-module (gnu packages python-web)
5b05dce7 97 #:use-module (gnu packages qt)
c9dfa3c7 98 #:use-module (gnu packages readline)
2742f87e 99 #:use-module (gnu packages tbb)
479c4273 100 #:use-module (gnu packages scheme)
b7194849 101 #:use-module (gnu packages shells)
df354a77 102 #:use-module (gnu packages tcl)
668c06ac 103 #:use-module (gnu packages texinfo)
8f9ac901 104 #:use-module (gnu packages tex)
b7b27a8f 105 #:use-module (gnu packages tls)
5b05dce7 106 #:use-module (gnu packages version-control)
9aafbc0c 107 #:use-module (gnu packages wxwidgets)
c12efc72 108 #:use-module (gnu packages xml)
a17d4564 109 #:use-module (srfi srfi-1))
8f8b2451 110
193abc82
JD		 111(define-public aris
112 (package
1f45f18a
JD		 113 (name "aris")
114 (version "2.2")
115 (source (origin
116 (method url-fetch)
117 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
118 (sha256 (base32
119 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
120 (build-system gnu-build-system)
121 (inputs `(("gtk+" ,gtk+)
122 ("libxml2" ,libxml2)))
123 (native-inputs `(("pkg-config" ,pkg-config)))
124 (synopsis "Natural deduction first-order logic interface")
125 (description "Aris is a program for performing logical proofs. It supports
126propositional and predicate logic, as well as Boolean algebra and
127arithmetical logic. In addition to its predefined inference and equivalence
128rules, Aris also supports references to older proofs. Its use of standard
129logical symbols and its natural deduction interface make it easy to use for
130beginners.")
131 (license license:gpl3+)
6fd52309 132 (home-page "https://www.gnu.org/software/aris/")))
193abc82 133
9c45c519
JD		 134(define-public c-graph
135 (package
136 (name "c-graph")
137 (version "2.0")
138 (source (origin
139 (method url-fetch)
140 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
141 ".tar.gz"))
142 (sha256 (base32
143 "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
144 (build-system gnu-build-system)
145 (inputs
146 `(("fortran" ,gfortran)))
a3947cb1 147 (synopsis "Visualizing and demonstrating convolution")
9c45c519 148 (description
a3947cb1
LC		 149 "GNU C-Graph is a tool for demonstrating the theory of convolution.
150Thus, it can serve as an excellent aid to students of signal and systems
151theory in visualizing the convolution process. Rather than forcing the
152student to write code, the program offers an intuitive interface with
153interactive dialogs to guide them.")
9c45c519 154 (license license:gpl3+)
6fd52309 155 (home-page "https://www.gnu.org/software/c-graph/")))
9c45c519 156
d91025e3
TD		 157(define-public coda
158 (package
159 (name "coda")
440c4273 160 (version "2.18.3")
d91025e3
TD		 161 (source
162 (origin
163 (method url-fetch)
164 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
165 version "/coda-" version ".tar.gz"))
166 (sha256
440c4273 167 (base32 "1zlzgcvwmmjm8mw8w4rg2rqy0pjilz7kyyxm0y4p8cbljbbjxxz0"))
4b12fe5c
TD		 168 (patches (search-patches "coda-use-system-libs.patch"))
169 (modules '((guix build utils)))
170 (snippet
171 ;; Make sure we don't use the bundled software.
172 '(for-each (lambda (d)
173 (delete-file-recursively (string-append "libcoda/" d)))
174 '("zlib" "pcre" "expat")))))
d91025e3
TD		 175 (native-inputs
176 `(("fortran" ,gfortran)
177 ("python" ,python)
178 ("python-numpy" ,python-numpy)))
179 (inputs
180 `(("zlib" ,zlib)
4b12fe5c
TD		 181 ("pcre" ,pcre)
182 ("expat" ,expat)
d91025e3
TD		 183 ("hdf4" ,hdf4-alt)
184 ("hdf5" ,hdf5)))
185 (build-system gnu-build-system)
186 (arguments
4b12fe5c
TD		 187 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
188 "LIBS= -lz -lpcre -lexpat")))
d91025e3
TD		 189 (synopsis "A common interface to various earth observation data formats")
190 (description
191 "The Common Data Access toolbox (CODA) provides a set of interfaces for
192reading remote sensing data from earth observation data files. It consists of
193command line applications and interfaces to the C, Fortran, Python, and Java
194programming languages.")
195 (home-page "https://stcorp.nl/coda")
196 (license license:gpl2+)))
197
8f8b2451
AE		 198(define-public units
199 (package
200 (name "units")
f11d2849 201 (version "2.16")
8f8b2451
AE		 202 (source (origin
203 (method url-fetch)
204 (uri (string-append "mirror://gnu/units/units-" version
205 ".tar.gz"))
206 (sha256 (base32
f11d2849 207 "11hnp3gcmcc5kci2caxw4hs6m08h2mhqs3xzqq7iafx1ha2ggwyw"))))
8f8b2451 208 (build-system gnu-build-system)
0498d248 209 (inputs
a2549713
EB		 210 `(("readline" ,readline)
211 ("python" ,python-wrapper) ;for 'units_cur' script
0498d248
EB		 212 ("python-requests" ,python-requests)))
213 (arguments
214 `(#:phases (modify-phases %standard-phases
215 (add-after 'install 'wrap-units_cur
216 (lambda* (#:key outputs #:allow-other-keys)
217 (let* ((out (assoc-ref outputs "out"))
218 (bin (string-append out "/bin")))
219 (wrap-program (string-append bin "/units_cur")
220 `("PYTHONPATH" ":" prefix
221 ,(search-path-as-string->list (getenv "PYTHONPATH"))))
222 #t))))))
8f8b2451
AE		 223 (synopsis "Conversion between thousands of scales")
224 (description
574e86f9 225 "GNU Units converts numeric quantities between units of measure. It
7c125ce0
AK		 226can handle scale changes through adaptive usage of standard scale
227prefixes (micro-, kilo-, etc.). It can also handle nonlinear
228conversions such as Fahrenheit to Celsius. Its interpreter is powerful
229enough to be used effectively as a scientific calculator.")
8f8b2451 230 (license license:gpl3+)
6fd52309 231 (home-page "https://www.gnu.org/software/units/")))
c9dfa3c7 232
61a529b4
RW		 233(define-public double-conversion
234 (package
235 (name "double-conversion")
236 (version "1.1.5")
237 (source (origin
238 (method url-fetch)
239 (uri (string-append
240 "https://github.com/floitsch/double-conversion/archive/v"
241 version ".tar.gz"))
242 (file-name (string-append name "-" version ".tar.gz"))
243 (sha256
244 (base32
245 "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83"))))
246 (build-system cmake-build-system)
247 (arguments
248 '(#:test-target "test"
249 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
250 "-DBUILD_TESTING=ON")))
251 (home-page "https://github.com/floitsch/double-conversion")
252 (synopsis "Conversion routines for IEEE doubles")
253 (description
254 "The double-conversion library provides binary-decimal and decimal-binary
255routines for IEEE doubles. The library consists of efficient conversion
256routines that have been extracted from the V8 JavaScript engine.")
257 (license license:bsd-3)))
258
182d6311
ML		 259(define-public dionysus
260 (package
261 (name "dionysus")
262 (version "1.3.0")
263 (source (origin
264 (method url-fetch)
265 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
266 ".tar.gz"))
267 (sha256
268 (base32
269 "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs"))))
270 (build-system gnu-build-system)
271 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
272 (synopsis "Local search for universal constants and scientific values")
273 (description
274 "GNU Dionysus is a convenient system for quickly retrieving the values of
275mathematical constants used in science and engineering. Values can be
276searched using a simple command-line tool, choosing from three databases:
277universal constants, atomic numbers, and constants related to
278semiconductors.")
279 (license license:gpl3+)
6fd52309 280 (home-page "https://www.gnu.org/software/dionysus/")))
182d6311 281
88bd1804
AE		 282(define-public gsl
283 (package
284 (name "gsl")
f885fc05 285 (version "2.4")
ab2cc5cd
LC		 286 (source (origin
287 (method url-fetch)
288 (uri (string-append "mirror://gnu/gsl/gsl-"
289 version ".tar.gz"))
290 (sha256
291 (base32
f885fc05 292 "16yfs5n444s03np1naj6yp1fsysd42kdscxzkg0k2yvfjixx0ijd"))
ab2cc5cd 293 (patches (search-patches "gsl-test-i686.patch"))))
88bd1804 294 (build-system gnu-build-system)
71e0f288 295 (arguments
f885fc05 296 `(;; Currently there are numerous tests that fail on "exotic"
6f766069
EF		 297 ;; architectures such as aarch64 and ppc64le.
298 ,@(if (string-prefix? "aarch64-linux"
299 (or (%current-target-system) (%current-system)))
300 '(#:tests? #f)
301 '())))
302 (home-page "https://www.gnu.org/software/gsl/")
88bd1804
AE		 303 (synopsis "Numerical library for C and C++")
304 (description
a22dc0c4
LC		 305 "The GNU Scientific Library is a library for numerical analysis in C
306and C++. It includes a wide range of mathematical routines, with over 1000
307functions in total. Subject areas covered by the library include:
308differential equations, linear algebra, Fast Fourier Transforms and random
309numbers.")
88bd1804
AE		 310 (license license:gpl3+)))
311
ba1be533
BW		 312(define-public ocaml-gsl
313 (package
314 (name "ocaml-gsl")
315 (version "1.19.3")
316 (source
317 (origin
318 (method url-fetch)
319 (uri
320 (string-append
321 "https://github.com/mmottl/gsl-ocaml/releases/download/v"
322 version"/gsl-ocaml-" version ".tar.gz"))
323 (sha256
324 (base32
325 "0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh"))))
326 (build-system ocaml-build-system)
327 (inputs
328 `(("gsl" ,gsl)))
329 (home-page "https://mmottl.github.io/gsl-ocaml")
330 (synopsis "Bindings to the GNU Scientific Library")
331 (description
332 "GSL-OCaml is an interface to the @dfn{GNU scientific library} (GSL) for
333the OCaml language.")
334 (license license:gpl3+)))
335
7adaab9f
BW		 336(define-public ocaml4.01-gsl
337 (package-with-ocaml4.01 ocaml-gsl))
338
b92eee75
AE		 339(define-public glpk
340 (package
341 (name "glpk")
445929e0 342 (version "4.65")
b92eee75
AE		 343 (source
344 (origin
345 (method url-fetch)
346 (uri (string-append "mirror://gnu/glpk/glpk-"
347 version ".tar.gz"))
348 (sha256
349 (base32
445929e0 350 "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
b92eee75
AE		 351 (build-system gnu-build-system)
352 (inputs
353 `(("gmp" ,gmp)))
354 (arguments
355 `(#:configure-flags '("--with-gmp")))
82110ef6 356 (home-page "https://www.gnu.org/software/glpk/")
79c311b8 357 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
b92eee75
AE		 358 (description
359 "GLPK is a C library for solving large-scale linear programming (LP),
360mixed integer programming (MIP), and other related problems. It supports the
361GNU MathProg modeling language, a subset of the AMPL language, and features a
362translator for the language. In addition to the C library, a stand-alone
363LP/MIP solver is included in the package.")
364 (license license:gpl3+)))
365
b146763a
AE		 366(define-public 4ti2
367 (package
368 (name "4ti2")
369 (version "1.6.7")
370 (source
371 (origin
372 (method url-fetch)
373 (uri (string-append "http://www.4ti2.de/version_" version
374 "/4ti2-" version ".tar.gz"))
375 (sha256
376 (base32
377 "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
378 (build-system gnu-build-system)
379 (native-inputs
380 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
381 (inputs
382 `(("glpk" ,glpk)
383 ("gmp" ,gmp)))
384 (home-page "http://www.4ti2.de/")
385 (synopsis "Mathematical tool suite for problems on linear spaces")
386 (description
387 "4ti2 implements algorithms for solving algebraic, geometric and
388combinatorial problems on linear spaces. Among others, it solves systems
389of linear equations, computes extreme rays of polyhedral cones, solves
390integer programming problems and computes Markov bases for statistics.")
391 (license license:gpl2+)))
392
53696f10
AE		 393(define-public cddlib
394 (package
395 (name "cddlib")
396 (version "0.94h")
397 (source
398 (origin
399 (method url-fetch)
182dde82 400 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
53696f10
AE		 401 (string-delete #\. version) ".tar.gz"))
402 (sha256
403 (base32
404 "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy"))))
405 (build-system gnu-build-system)
406 (inputs
407 `(("gmp" ,gmp)))
408 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
409 (synopsis "Library for convex hulls and extreme rays of polyhedra")
410 (description
411 "The C-library cddlib implements the Double Description Method of
412Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
413rays of a general convex polyhedron given by a system of linear inequalities
414in arbitrary dimension. It can also be used for the converse operation of
415computing convex hulls.")
416 (license license:gpl2+)))
417
865a69dd
RW		 418(define-public arpack-ng
419 (package
420 (name "arpack-ng")
421 (version "3.2.0")
422 (source
423 (origin
424 (method url-fetch)
425 (uri (string-append "https://github.com/opencollab/arpack-ng/archive/"
426 version ".tar.gz"))
f586c877 427 (file-name (string-append name "-" version ".tar.gz"))
865a69dd
RW		 428 (sha256
429 (base32
430 "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff"))))
431 (build-system gnu-build-system)
432 (home-page "https://github.com/opencollab/arpack-ng")
433 (inputs
434 `(("lapack" ,lapack)
19afbea1 435 ("fortran" ,gfortran)))
865a69dd
RW		 436 (synopsis "Fortran subroutines for solving eigenvalue problems")
437 (description
438 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
439large scale eigenvalue problems.")
166191b3 440 (license (license:non-copyleft "file://COPYING"
865a69dd
RW		 441 "See COPYING in the distribution."))))
442
8c94c886
EB		 443(define-public arpack-ng-openmpi
444 (package (inherit arpack-ng)
445 (name "arpack-ng-openmpi")
446 (inputs
447 `(("mpi" ,openmpi)
448 ,@(package-inputs arpack-ng)))
449 (arguments `(#:configure-flags '("--enable-mpi")))
450 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
451
da95c817
NK		 452(define-public lapack
453 (package
454 (name "lapack")
ef39a177 455 (version "3.7.1")
da95c817
NK		 456 (source
457 (origin
458 (method url-fetch)
459 (uri (string-append "http://www.netlib.org/lapack/lapack-"
460 version ".tgz"))
461 (sha256
462 (base32
7c0d4c3a 463 "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
da95c817
NK		 464 (build-system cmake-build-system)
465 (home-page "http://www.netlib.org/lapack/")
19afbea1 466 (inputs `(("fortran" ,gfortran)
da95c817
NK		 467 ("python" ,python-2)))
468 (arguments
3ab869b6 469 `(#:configure-flags (list
3ab869b6
LC		 470 "-DBUILD_SHARED_LIBS:BOOL=YES"
471 "-DLAPACKE=ON"
472
473 ;; Build the 'LAPACKE_clatms' functions.
474 "-DLAPACKE_WITH_TMG=ON")
dc1d3cde
KK		 475 #:phases
476 (modify-phases %standard-phases
477 (add-before 'check 'patch-python
478 (lambda* (#:key inputs #:allow-other-keys)
479 (let ((python (assoc-ref inputs "python")))
480 (substitute* "lapack_testing.py"
481 (("/usr/bin/env python") python)))
482 #t)))))
da95c817
NK		 483 (synopsis "Library for numerical linear algebra")
484 (description
485 "LAPACK is a Fortran 90 library for solving the most commonly occurring
486problems in numerical linear algebra.")
166191b3 487 (license (license:non-copyleft "file://LICENSE"
da95c817 488 "See LICENSE in the distribution."))))
73fed4f8 489
b509efb3
TF		 490(define-public lapack-3.5
491 (package
492 (inherit lapack)
493 (version "3.5.0")
494 (source
495 (origin
496 (method url-fetch)
497 (uri (string-append "http://www.netlib.org/lapack/lapack-"
498 version ".tgz"))
499 (sha256
500 (base32
501 "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s"))))))
502
e1ff597a
EB		 503(define-public scalapack
504 (package
505 (name "scalapack")
506 (version "2.0.2")
507 (source
508 (origin
509 (method url-fetch)
510 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
511 version ".tgz"))
512 (sha256
513 (base32
514 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
515 (build-system cmake-build-system)
516 (inputs
517 `(("mpi" ,openmpi)
518 ("fortran" ,gfortran)
519 ("lapack" ,lapack))) ;for testing only
520 (arguments
521 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")))
522 (home-page "http://www.netlib.org/scalapack/")
523 (synopsis "Library for scalable numerical linear algebra")
524 (description
525 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
526routines on parallel distributed memory machines. ScaLAPACK solves dense and
527banded linear systems, least squares problems, eigenvalue problems, and
528singular value problems.")
529 (license (license:bsd-style "file://LICENSE"
530 "See LICENSE in the distribution."))))
531
73fed4f8 532(define-public gnuplot
5f800540
KK		 533 (package
534 (name "gnuplot")
7d873e0c 535 (version "5.0.6")
5f800540
KK		 536 (source (origin
537 (method url-fetch)
538 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
539 version "/gnuplot-"
540 version ".tar.gz"))
541 (sha256
542 (base32
7d873e0c 543 "0q5lr6nala3ln6f3yp6g17ziymb9r9gx9zylnw1y3hjmwl9lggjv"))))
5f800540
KK		 544 (build-system gnu-build-system)
545 (inputs `(("readline" ,readline)
546 ("cairo" ,cairo)
547 ("pango" ,pango)
6e64766a
DM		 548 ("gd" ,gd)
549 ("lua" ,lua)))
612a387f
RW		 550 (native-inputs
551 `(("pkg-config" ,pkg-config)
552 ("texlive" ,texlive-tiny)))
5f800540
KK		 553 (home-page "http://www.gnuplot.info")
554 (synopsis "Command-line driven graphing utility")
555 (description "Gnuplot is a portable command-line driven graphing
35b9e423 556utility. It was originally created to allow scientists and students to
73fed4f8 557visualize mathematical functions and data interactively, but has grown to
35b9e423 558support many non-interactive uses such as web scripting. It is also used as a
73fed4f8 559plotting engine by third-party applications like Octave.")
5f800540
KK		 560 ;; X11 Style with the additional restriction that derived works may only be
561 ;; distributed as patches to the original.
562 (license (license:fsf-free
563 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
668c06ac 564
32f70e1f
TD		 565(define-public gctp
566 (package
567 (name "gctp")
568 (version "2.0.0")
569 (source
570 (origin
571 (method url-fetch)
572 (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
573 version ".tar.gz"))
574 (file-name (string-append name "-" version ".tar.gz"))
575 (sha256
576 (base32
577 "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
578 (native-inputs
579 `(("fortran" ,gfortran)))
580 (build-system gnu-build-system)
581 (synopsis "General Cartographic Transformation Package (GCTP)")
582 (description
583 "The General Cartographic Transformation Package (GCTP) is a system of
584software routines designed to permit the transformation of coordinate pairs
585from one map projection to another. The GCTP is the standard computer
586software used by the National Mapping Division for map projection
587computations.")
588 (home-page "https://github.com/OkoSanto/GCTP")
0f7cd95b 589 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
32f70e1f 590
becbbefc
TD		 591(define-public hdf4
592 (package
593 (name "hdf4")
0abf5264 594 (version "4.2.13")
becbbefc
TD		 595 (source
596 (origin
597 (method url-fetch)
598 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
599 version "/src/hdf-" version ".tar.bz2"))
600 (sha256
0abf5264 601 (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
15ca49b2
AE		 602 (patches (search-patches "hdf4-architectures.patch"
603 "hdf4-reproducibility.patch"
becbbefc 604 "hdf4-shared-fortran.patch"))))
becbbefc
TD		 605 (build-system gnu-build-system)
606 (native-inputs
607 `(("gfortran" ,gfortran)
608 ("bison" ,bison)
609 ("flex" ,flex)))
610 (inputs
611 `(("zlib" ,zlib)
612 ("libjpeg" ,libjpeg)))
613 (arguments
614 `(#:parallel-tests? #f
615 #:configure-flags '("--enable-shared")
616 #:phases
617 (modify-phases %standard-phases
953a12fa
EF		 618 ;; This is inspired by two of Debian's patches.
619 (add-before 'configure 'add-more-aarch64-support
620 (lambda _
621 (substitute* '("mfhdf/ncgen/ncgen.l"
622 "mfhdf/ncgen/ncgenyy.c"
623 "mfhdf/libsrc/netcdf.h.in")
624 (("AIX5L64") "__aarch64__"))
625 #t))
becbbefc
TD		 626 (add-before 'configure 'patchbuild
627 (lambda _
628 (substitute*
629 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
630 (("/bin/rm") "rm")
631 (("/bin/mkdir") "mkdir"))
632 (substitute* (find-files "." "^Makefile\\.in$")
633 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
634-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
635 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
636-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
953a12fa 637-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
e464b455
TD		 638 #t))
639 (add-after 'configure 'patch-settings
640 (lambda _
641 ;; libhdf4.settings contains the full path of the
642 ;; compilers used, and its contents are included in
643 ;; .so-files. We truncate the hashes to avoid
644 ;; unnecessary store references to those compilers:
645 (substitute* "libhdf4.settings"
646 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
647 (string-append prefix (string-take hash 10) "...")))
648 #t))
649 )))
becbbefc
TD		 650 (home-page "https://www.hdfgroup.org/products/hdf4/")
651 (synopsis
652 "Library and multi-object file format for storing and managing data")
653 (description "HDF4 is a library and multi-object file format for storing
654and managing data between machines. HDF4 is an older hierarchical data format,
655incompatible with HDF5.")
656 (license
657 (license:non-copyleft
658 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
659
660(define-public hdf4-alt
661 (package
662 (inherit hdf4)
663 (name "hdf4-alt")
664 (arguments
665 (substitute-keyword-arguments (package-arguments hdf4)
666 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
667 (synopsis
668 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
669
7ee3f1a2
JD		 670(define-public hdf5
671 (package
672 (name "hdf5")
2da63064 673 (version "1.8.19")
7ee3f1a2
JD		 674 (source
675 (origin
676 (method url-fetch)
2da63064
TD		 677 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
678 "hdf5-" (version-major+minor version)
679 "/hdf5-" version "/src/hdf5-"
dcd9d163
LF		 680 version ".tar.bz2")
681 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
682 "current"
683 (apply string-append
684 (take (string-split version #\.) 2))
685 "/src/hdf5-" version ".tar.bz2")))
7ee3f1a2 686 (sha256
2da63064 687 (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
b8d9c93b 688 (patches (list (search-patch "hdf5-config-date.patch")))))
7ee3f1a2 689 (build-system gnu-build-system)
12ed1216
AE		 690 (inputs
691 `(("zlib" ,zlib)))
e3a1a1de
TD		 692 (native-inputs
693 `(("gfortran" ,gfortran)))
694 (outputs '("out" ; core library
695 "fortran")) ; fortran interface
7ee3f1a2 696 (arguments
62126576 697 `(;; Some of the users, notably Flann, need the C++ interface.
e3a1a1de
TD		 698 #:configure-flags '("--enable-cxx"
699 "--enable-fortran"
700 "--enable-fortran2003")
4dba441c
RW		 701 ;; Use -fPIC to allow the R bindings to link with the static libraries
702 #:make-flags (list "CFLAGS=-fPIC"
703 "CXXFLAGS=-fPIC")
62126576 704 #:phases
f622e212
EB		 705 (modify-phases %standard-phases
706 (add-before 'configure 'patch-configure
e3a1a1de 707 (lambda* (#:key outputs #:allow-other-keys)
f622e212 708 (substitute* "configure"
b8d9c93b 709 (("/bin/mv") "mv"))
e3a1a1de
TD		 710 (substitute* "fortran/src/Makefile.in"
711 (("libhdf5_fortran_la_LDFLAGS =")
712 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
713 (assoc-ref outputs "fortran") "/lib")))
714 (substitute* "hl/fortran/src/Makefile.in"
715 (("libhdf5hl_fortran_la_LDFLAGS =")
716 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
717 (assoc-ref outputs "fortran") "/lib")))
b8d9c93b 718 #t))
fd0378a1
TD		 719 (add-after 'configure 'patch-settings
720 (lambda _
721 ;; libhdf5.settings contains the full path of the
722 ;; compilers used, and its contents are included in
723 ;; libhdf5.so. We truncate the hashes to avoid
724 ;; unnecessary store references to those compilers:
725 (substitute* "src/libhdf5.settings"
726 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
727 (string-append prefix (string-take hash 10) "...")))
b8d9c93b 728 #t))
f622e212
EB		 729 (add-after 'install 'patch-references
730 (lambda* (#:key inputs outputs #:allow-other-keys)
731 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
732 (zlib (assoc-ref inputs "zlib")))
733 (substitute* (find-files bin "h5p?cc")
734 (("-lz" lib)
735 (string-append "-L" zlib "/lib " lib)))
e3a1a1de
TD		 736 #t)))
737 (add-after 'install 'split
738 (lambda* (#:key inputs outputs #:allow-other-keys)
739 ;; Move all fortran-related files
740 (let* ((out (assoc-ref outputs "out"))
741 (bin (string-append out "/bin"))
742 (lib (string-append out "/lib"))
743 (inc (string-append out "/include"))
744 (ex (string-append out "/share/hdf5_examples/fortran"))
745 (fort (assoc-ref outputs "fortran"))
746 (fbin (string-append fort "/bin"))
747 (flib (string-append fort "/lib"))
748 (finc (string-append fort "/include"))
749 (fex (string-append fort "/share/hdf5_examples/fortran")))
750 (mkdir-p fbin)
751 (mkdir-p flib)
752 (mkdir-p finc)
753 (mkdir-p fex)
754 (rename-file (string-append bin "/h5fc")
755 (string-append fbin "/h5fc"))
756 (for-each (lambda (file)
757 (rename-file file
758 (string-append flib "/" (basename file))))
759 (find-files lib ".*fortran.*"))
760 (for-each (lambda (file)
761 (rename-file file
762 (string-append finc "/" (basename file))))
763 (find-files inc ".*mod"))
764 (for-each (lambda (file)
765 (rename-file file
766 (string-append fex "/" (basename file))))
767 (find-files ex ".*"))
768 (delete-file-recursively ex))
769 #t)))))
7ee3f1a2 770 (home-page "http://www.hdfgroup.org")
516e93f8 771 (synopsis "Management suite for extremely large and complex data")
7ee3f1a2
JD		 772 (description "HDF5 is a suite that makes possible the management of
773extremely large and complex data collections.")
d4bf49b1
EB		 774 (license (license:x11-style
775 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
7ee3f1a2 776
2fd26d05
TD		 777(define-public hdf-java
778 (package
779 (name "hdf-java")
780 (version "3.3.2")
781 (source
782 (origin
783 (method url-fetch)
784 (uri (string-append
785 "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
786 version "/src/CMake-hdfjava-" version ".tar.gz"))
787 (sha256
788 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
789 (modules '((guix build utils)))
790 (snippet ; Make sure we don't use the bundled sources and binaries.
791 `(begin
792 (for-each delete-file
793 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
794 "HDF4.tar.gz" "HDF5.tar.gz"))
795 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))))))
796 (build-system gnu-build-system)
797 (native-inputs
798 `(("jdk" ,icedtea "jdk")
799 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
800 ;; For tests:
801 ("hamcrest-core" ,java-hamcrest-core)
802 ("junit" ,java-junit)
803 ("slf4j-simple" ,java-slf4j-simple)))
804 (inputs
805 `(("hdf4" ,hdf4)
806 ("hdf5" ,hdf5)
807 ("zlib" ,zlib)
808 ("libjpeg" ,libjpeg)
809 ("slf4j-api" ,java-slf4j-api)))
810 (arguments
811 `(#:configure-flags
812 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
813 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
814 (assoc-ref %build-inputs "jdk") "/lib" )
815 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
816 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
817
818 #:make-flags
819 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
820 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
821 (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
822 (string-append "JPEGLIB="
823 (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
824 "LLEXT=so")
825
826 #:phases
827 (modify-phases %standard-phases
828 (add-before 'configure 'chdir-to-source
829 (lambda _ (chdir ,(string-append "hdfjava-" version))))
830 (add-before 'configure 'patch-build
831 (lambda* (#:key inputs outputs #:allow-other-keys)
832 (substitute* "configure"
833 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
834 (("/bin/cat") (which "cat")))
835 ;; Set classpath for compilation
836 (substitute* '("hdf/hdf5lib/Makefile.in"
837 "hdf/hdf5lib/exceptions/Makefile.in"
838 "hdf/hdflib/Makefile.in")
839 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
840 (string-append (assoc-ref inputs "slf4j-api")
841 "/share/java/slf4j-api.jar")))
842 ;; Replace outdated config.sub and config.guess:
843 (with-directory-excursion "config"
844 (for-each (lambda (file)
845 (copy-file
846 (string-append (assoc-ref inputs "automake")
847 "/share/automake-1.15/" file) file))
848 '("config.sub" "config.guess")))
849 (mkdir-p (string-append (assoc-ref outputs "out")))
850 ;; Set classpath for tests
851 (let* ((build-dir (getcwd))
852 (lib (string-append build-dir "/lib"))
853 (jhdf (string-append lib "/jhdf.jar"))
854 (jhdf5 (string-append lib "/jhdf5.jar"))
855 (testjars
856 (map (lambda (i)
857 (string-append (assoc-ref inputs i)
858 "/share/java/" i ".jar"))
859 '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
860 (class-path
861 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
862
863 (substitute* '("test/hdf5lib/Makefile.in"
864 "test/hdf5lib/junit.sh.in"
865 "examples/runExample.sh.in")
866 (("/usr/bin/test")
867 (string-append (assoc-ref inputs "coreutils")
868 "/bin/test"))
869 (("/usr/bin/uname")
870 (string-append (assoc-ref inputs "coreutils")
871 "/bin/uname"))
872 (("CLASSPATH=[^\n]*")
873 (string-append "CLASSPATH=" class-path)))
874 (setenv "CLASSPATH" class-path))
875 #t))
876 (add-before 'check 'build-examples
877 (lambda _
878 (zero? (apply system* `("javac"
879 ,@(find-files "examples" ".*\\.java")))))))
880
881 #:parallel-build? #f
882
883 #:parallel-tests? #f ))
884 (home-page "https://support.hdfgroup.org/products/java")
885 (synopsis "Java interface for the HDF4 and HDF5 libraries")
886 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
887the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
888implemented in C.")
889
890 ;; BSD-style license:
891 (license (license:x11-style
892 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
893/current/src/unpacked/COPYING"))))
894
d3c4f3bb
TD		 895(define-public hdf-eos2
896 (package
897 (name "hdf-eos2")
898 (version "19.1.0")
899 (source
900 (origin
901 (method url-fetch)
902 (uri "ftp://edhs1.gsfc.nasa.gov\
903/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
904 (sha256
905 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
906 (patches (search-patches "hdf-eos2-remove-gctp.patch"
907 "hdf-eos2-build-shared.patch"
908 "hdf-eos2-fortrantests.patch"))))
909 (build-system gnu-build-system)
910 (native-inputs
911 `(("gfortran" ,gfortran)))
912 (inputs
913 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
914 ("zlib" ,zlib)
915 ("libjpeg" ,libjpeg)
916 ("gctp" ,gctp)))
917 (arguments
918 `( #:configure-flags '("--enable-install-include" "--enable-shared"
919 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
920 #:parallel-tests? #f))
921 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
922 (synopsis "HDF4-based data format for NASA's Earth Observing System")
923 (description "HDF-EOS2 is a software library built on HDF4 which supports
924the construction of data structures used in NASA's Earth Observing
925System (Grid, Point and Swath).")
926
927 ;; Source files carry a permissive license header.
928 (license (license:non-copyleft home-page))))
929
0f43f835
TD		 930(define-public hdf-eos5
931 (package
932 (name "hdf-eos5")
933 (version "1.15")
934 (source (origin
935 (method url-fetch)
936 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
937/edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
938 (sha256
939 (base32
940 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
941 (patches (search-patches "hdf-eos5-build-shared.patch"
942 "hdf-eos5-remove-gctp.patch"
943 "hdf-eos5-fix-szip.patch"
944 "hdf-eos5-fortrantests.patch"))))
945 (native-inputs
946 `(("gfortran" ,gfortran)))
947 (build-system gnu-build-system)
948 (inputs
949 `(("hdf5" ,hdf5)
950 ("zlib" ,zlib)
951 ("gctp" ,gctp)))
952 (arguments
953 `(#:configure-flags '("--enable-install-include" "--enable-shared"
954 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
955 #:parallel-tests? #f))
956 (synopsis "HDF5-based data format for NASA's Earth Observing System")
957 (description
958 "HDF-EOS5 is a software library built on HDF5 to support the construction
959of data structures used in NASA's Earth Observing System (Grid, Point and
960Swath).")
961 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
962
963 ;; Source files carry a permissive license header.
964 (license (license:non-copyleft home-page))))
965
c8378eea
EB		 966(define-public hdf5-parallel-openmpi
967 (package (inherit hdf5)
968 (name "hdf5-parallel-openmpi")
969 (inputs
970 `(("mpi" ,openmpi)
971 ,@(package-inputs hdf5)))
972 (arguments
973 (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
974 ,@(package-arguments hdf5))
975 ((#:phases phases)
976 `(modify-phases ,phases
977 (add-before 'check 'patch-tests
978 (lambda _
979 ;; OpenMPI's mpirun will exit with non-zero status if it
980 ;; detects an "abnormal termination", i.e. any process not
981 ;; calling MPI_Finalize(). Since the test is explicitely
982 ;; avoiding MPI_Finalize so as not to have at_exit and thus
983 ;; H5C_flush_cache from being called, mpirun will always
984 ;; complain, so turn this test off.
985 (substitute* "testpar/Makefile"
986 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
987 (string-append front back "\n")))
988 (substitute* "tools/h5diff/testph5diff.sh"
989 (("/bin/sh") (which "sh")))
990 #t))))))
991 (synopsis "Management suite for data with parallel IO support")))
992
00775104
EB		 993(define-public h5check
994 (package
995 (name "h5check")
996 (version "2.0.1")
997 (source
998 (origin
999 (method url-fetch)
1000 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
1001 "h5check/src/h5check-" version ".tar.gz"))
1002 (sha256
1003 (base32
1004 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1005 (build-system gnu-build-system)
1006 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
1007 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1008 (synopsis "HDF5 format checker")
1009 (description "@code{h5check} is a validation tool for verifying that an
1010HDF5 file is encoded according to the HDF File Format Specification.")
1011 (license (license:x11-style "file://COPYING"))))
1012
a53d6719
JD		 1013(define-public itpp
1014 (package
1015 (name "itpp")
1016 (version "4.3.1")
1017 (source (origin
1018 (method url-fetch)
1019 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1020 version "/itpp-"
1021 version ".tar.gz"))
1022 (sha256
1023 (base32
1024 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1025 (build-system cmake-build-system)
1026 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1027 (inputs `(("lapack" ,lapack)
1028 ("fftw" ,fftw)))
3a4d5df2
RW		 1029 ;; FIXME: Even though the fonts are available dvips complains:
1030 ;; "Font cmmi10 not found; characters will be left blank."
1031 (native-inputs
1032 `(("texlive" ,texlive-tiny)
1033 ("ghostscript" ,ghostscript)
1034 ("doxygen" ,doxygen)))
a53d6719
JD		 1035 (home-page "http://itpp.sourceforge.net")
1036 (synopsis "C++ library of maths, signal processing and communication classes")
1037 (description "IT++ is a C++ library of mathematical, signal processing and
1038communication classes and functions. Its main use is in simulation of
1039communication systems and for performing research in the area of
1040communications. The kernel of the library consists of generic vector and
1041matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1042similar to MATLAB, GNU Octave or SciPy.")
1043 (license license:gpl3+)))
1044
889187a4
EB		 1045(define-public netcdf
1046 (package
1047 (name "netcdf")
a4b0bfb1 1048 (version "4.4.1.1")
889187a4
EB		 1049 (source
1050 (origin
1051 (method url-fetch)
1052 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1053 "netcdf-" version ".tar.gz"))
1054 (sha256
1055 (base32
a4b0bfb1
EB		 1056 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1057 (patches (search-patches "netcdf-date-time.patch"
1058 "netcdf-tst_h_par.patch"))))
889187a4
EB		 1059 (build-system gnu-build-system)
1060 (native-inputs
1061 `(("m4" ,m4)
1062 ("doxygen" ,doxygen)
1063 ("graphviz" ,graphviz)))
1064 (inputs
db825570
TD		 1065 `(("hdf4" ,hdf4-alt)
1066 ("hdf5" ,hdf5)
1067 ("zlib" ,zlib)
1068 ("libjpeg" ,libjpeg)))
889187a4 1069 (arguments
db825570 1070 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
43d01672
TD		 1071
1072 #:phases (modify-phases %standard-phases
1073 (add-before 'configure 'fix-source-date
1074 (lambda _
1075 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1076 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1077 ;; to '1st hour of the current day', and therefore makes the
1078 ;; package not reproducible.
1079 (substitute* "./configure"
1080 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1081 "date --date='@0'"))
1082 #t))
1083 (add-after 'configure 'patch-settings
1084 (lambda _
1085 ;; libnetcdf.settings contains the full filename of the compilers
1086 ;; used to build the library. We truncate the hashes of those
1087 ;; filenames to avoid unnecessary references to the corresponding
1088 ;; store items.
1089 (substitute* "libnetcdf.settings"
1090 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1091 (string-append prefix (string-take hash 10) "...")))
1092 #t)))
1093
889187a4
EB		 1094 #:parallel-tests? #f)) ;various race conditions
1095 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
1096 (synopsis "Library for scientific data")
1097 (description "NetCDF is an interface for scientific data access and a
1098software library that provides an implementation of the interface. The netCDF
1099library defines a machine-independent format for representing scientific data.
1100Together, the interface, library, and format support the creation, access, and
1101sharing of scientific data.")
1102 (license (license:x11-style "file://COPYRIGHT"))))
1103
1104(define-public netcdf-parallel-openmpi
1105 (package (inherit netcdf)
1106 (name "netcdf-parallel-openmpi")
1107 (inputs
1108 `(("mpi" ,openmpi)
1109 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1110 (package-inputs netcdf))))
1111 ;; TODO: Replace pkg-config references in nc-config with absolute references
1112 (arguments
1113 (substitute-keyword-arguments (package-arguments netcdf)
1114 ((#:configure-flags flags)
1115 `(cons* "CC=mpicc" "CXX=mpicxx"
1116 "--enable-parallel-tests"
1117 ;; Shared libraries not supported with parallel IO.
1118 "--disable-shared" "--with-pic"
1119 ,flags))))))
1120
300200b6
TD		 1121(define-public netcdf-fortran
1122 (package
1123 (name "netcdf-fortran")
1124 (version "4.4.4")
1125 (source (origin
1126 (method url-fetch)
1127 (uri (string-append
1128 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1129 version ".tar.gz"))
1130 (sha256
1131 (base32
1132 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1133 (build-system gnu-build-system)
1134 (arguments
1135 `(#:parallel-tests? #f))
1136 (inputs
1137 `(("netcdf" ,netcdf)))
1138 (native-inputs
1139 `(("gfortran" ,gfortran)))
1140 (synopsis "Fortran interface for the netCDF library")
1141 (description (package-description netcdf))
1142 (home-page (package-home-page netcdf))
1143 (license (package-license netcdf))))
1144
1b39a196
RJ		 1145(define-public nlopt
1146 (package
1147 (name "nlopt")
1148 (version "2.4.2")
1149 (source (origin
1150 (method url-fetch)
1151 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1152 version ".tar.gz"))
1153 (sha256
1154 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1155 (build-system gnu-build-system)
1156 (arguments
1157 `(;; Shared libraries are not built by default. They are required to
1158 ;; build the Guile, Octave, and Python bindings.
1159 #:configure-flags '("--enable-shared")
1160
1161 #:phases
1162 (modify-phases %standard-phases
1163 (add-before 'configure 'set-libnlopt-file-name
1164 (lambda* (#:key outputs #:allow-other-keys)
1165 ;; Make sure the Scheme module refers to the library by its
1166 ;; absolute file name (we cannot do that from a snippet
1167 ;; because the expansion of @libdir@ contains
1168 ;; ${exec_prefix}.)
1169 (let ((out (assoc-ref outputs "out")))
1170 (substitute* "swig/nlopt.scm.in"
1171 (("libnlopt")
1172 (string-append out "/lib/libnlopt")))
1173 #t))))))
1174 (inputs `(("guile" ,guile-2.0)))
1175 (native-inputs `(("pkg-config" ,pkg-config)))
1176 (home-page "http://ab-initio.mit.edu/wiki/")
1177 (synopsis "Library for nonlinear optimization")
1178 (description "NLopt is a library for nonlinear optimization, providing a
1179common interface for a number of different free optimization routines available
1180online as well as original implementations of various other algorithms.")
1181 (license license:lgpl2.1+)))
1182
005c787d
LC		 1183(define-public ipopt
1184 (package
1185 (name "ipopt")
1186 (version "3.12.5")
1187 (source (origin
1188 (method url-fetch)
1189 (uri (string-append
1190 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1191 version".tgz"))
1192 (sha256
1193 (base32
1194 "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
1195 (modules '((guix build utils)))
1196 (snippet
1197 ;; Make sure we don't use the bundled software.
1198 '(delete-file-recursively "ThirdParty"))))
1199 (build-system gnu-build-system)
ad1c4537
LC		 1200 (arguments
1201 '(#:phases (modify-phases %standard-phases
1202 (add-after 'install 'add--L-flags-in-ipopt.pc
1203 (lambda* (#:key inputs outputs #:allow-other-keys)
1204 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1205 ;; move it to "Libs.private" where it belongs, and add a
1206 ;; '-L' flag for LAPACK.
1207 (let ((out (assoc-ref outputs "out"))
1208 (lapack (assoc-ref inputs "lapack")))
1209 (substitute* (string-append out "/lib/pkgconfig/"
1210 "ipopt.pc")
1211 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1212 (string-append "Libs: " before " " after "\n"
1213 "Libs.private: " before
1214 "-L" lapack "/lib -llapack -lblas "
1215 after "\n")))
1216 #t))))))
005c787d
LC		 1217 (native-inputs
1218 `(("gfortran" ,gfortran)))
1219 (inputs
1220 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
ad1c4537 1221 `(("lapack" ,lapack))) ;for both libblas and liblapack
005c787d
LC		 1222 (home-page "http://www.coin-or.org")
1223 (synopsis "Large-scale nonlinear optimizer")
1224 (description
1225 "The Interior Point Optimizer (IPOPT) is a software package for
1226large-scale nonlinear optimization. It provides C++, C, and Fortran
1227interfaces.")
1228 (license license:epl1.0)))
1229
f9940ef1
LC		 1230(define-public ceres
1231 (package
1232 (name "ceres-solver")
6ad0c92d 1233 (version "1.13.0")
f9940ef1
LC		 1234 (home-page "http://ceres-solver.org/")
1235 (source (origin
1236 (method url-fetch)
1237 (uri (string-append home-page "ceres-solver-"
1238 version ".tar.gz"))
1239 (sha256
1240 (base32
6ad0c92d 1241 "1kbxgab3q1vgyq7hjqasr1lji4b2sgn7ss351amklkb3jyhr1x0x"))))
f9940ef1
LC		 1242 (build-system cmake-build-system)
1243 (arguments
1244 ;; TODO: Build HTML user documentation and install separately.
bc3a2e35 1245 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
f9940ef1
LC		 1246 "-DBUILD_SHARED_LIBS=ON")
1247
1248 #:phases (modify-phases %standard-phases
1249 (add-before 'configure 'set-library-directory
1250 (lambda _
1251 ;; Install libraries to lib/, not lib64/.
1252 (substitute* "internal/ceres/CMakeLists.txt"
1253 (("set\\(LIB_SUFFIX \"64\"\\)")
1254 "set(LIB_SUFFIX \"\")"))
1255 #t)))))
1256 (native-inputs
1257 `(("pkg-config" ,pkg-config)))
468e0b18
LC		 1258 (propagated-inputs
1259 `(("glog" ,glog))) ;for #include <glog/glog.h>
f9940ef1
LC		 1260 (inputs
1261 `(("eigen" ,eigen)
1262 ("blas" ,openblas)
1263 ("lapack" ,lapack)
1264 ("suitesparse" ,suitesparse)
1265 ("gflags" ,gflags)))
1266 (synopsis "C++ library for solving large optimization problems")
1267 (description
1268 "Ceres Solver is a C++ library for modeling and solving large,
1269complicated optimization problems. It is a feature rich, mature and
1270performant library which has been used in production since 2010. Ceres Solver
1271can solve two kinds of problems:
1272@enumerate
1273@item non-linear least squares problems with bounds constraints;
1274@item general unconstrained optimization problems.
1275@end enumerate\n")
1276 (license license:bsd-3)))
1277
668c06ac 1278;; For a fully featured Octave, users are strongly recommended also to install
5ca4fe96 1279;; the following packages: less, ghostscript, gnuplot.
668c06ac
JD		 1280(define-public octave
1281 (package
1282 (name "octave")
e9d60eba 1283 (version "4.2.1")
668c06ac
JD		 1284 (source
1285 (origin
1286 (method url-fetch)
1287 (uri (string-append "mirror://gnu/octave/octave-"
f5a077b1 1288 version ".tar.lz"))
668c06ac
JD		 1289 (sha256
1290 (base32
e9d60eba 1291 "09zhhch79jw3ynw39vizx0i2cbd2bjz3sp38pjdzraqrbivpwp92"))))
668c06ac
JD		 1292 (build-system gnu-build-system)
1293 (inputs
1294 `(("lapack" ,lapack)
1295 ("readline" ,readline)
181170c6 1296 ("gl2ps" ,gl2ps)
668c06ac 1297 ("glpk" ,glpk)
1ec78e9d
EB		 1298 ("fftw" ,fftw)
1299 ("fftwf" ,fftwf)
1300 ("arpack" ,arpack-ng)
668c06ac
JD		 1301 ("pcre" ,pcre)
1302 ("fltk" ,fltk)
1303 ("fontconfig" ,fontconfig)
1304 ("freetype" ,freetype)
40029cbe 1305 ("hdf5" ,hdf5)
668c06ac
JD		 1306 ("libxft" ,libxft)
1307 ("mesa" ,mesa)
1ec78e9d 1308 ("glu" ,glu)
9f913401
AI		 1309 ("zlib" ,zlib)
1310 ("curl" ,curl)
5ca4fe96 1311 ("texinfo" ,texinfo)
9f913401 1312 ("graphicsmagick" ,graphicsmagick)))
668c06ac 1313 (native-inputs
f5a077b1
EF		 1314 `(("lzip" ,lzip)
1315 ("gfortran" ,gfortran)
668c06ac
JD		 1316 ("pkg-config" ,pkg-config)
1317 ("perl" ,perl)
1ec78e9d
EB		 1318 ;; The following inputs are not actually used in the build process.
1319 ;; However, the ./configure gratuitously tests for their existence and
1320 ;; assumes that programs not present at build time are also not, and
1321 ;; can never be, available at run time! If these inputs are therefore
1322 ;; not present, support for them will be built out. However, Octave
1323 ;; will still run without them, albeit without the features they
668c06ac
JD		 1324 ;; provide.
1325 ("less" ,less)
668c06ac
JD		 1326 ("ghostscript" ,ghostscript)
1327 ("gnuplot" ,gnuplot)))
1328 (arguments
b7b27a8f
KY		 1329 `(#:configure-flags
1330 (list (string-append "--with-shell="
1331 (assoc-ref %build-inputs "bash")
5ca4fe96
AI		 1332 "/bin/sh"))
1333 #:phases
1334 (modify-phases %standard-phases
1335 (add-after 'configure 'configure-makeinfo
1336 (lambda* (#:key inputs #:allow-other-keys)
1337 (substitute* "libinterp/corefcn/help.cc"
1338 (("Vmakeinfo_program = \"makeinfo\"")
1339 (string-append "Vmakeinfo_program = \""
1340 (assoc-ref inputs "texinfo")
1341 "/bin/makeinfo\"")))
1342 #t)))))
f5a077b1 1343 (home-page "https://www.gnu.org/software/octave/")
668c06ac 1344 (synopsis "High-level language for numerical computation")
1ec78e9d
EB		 1345 (description "GNU Octave is a high-level interpreted language that is
1346specialized for numerical computations. It can be used for both linear and
1347non-linear applications and it provides great support for visualizing results.
1348Work may be performed both at the interactive command-line as well as via
1349script files.")
668c06ac 1350 (license license:gpl3+)))
3de01d3f 1351
5d4bd4cc
PG		 1352(define-public opencascade-oce
1353 (package
1354 (name "opencascade-oce")
1355 (version "0.17.2")
1356 (source
1357 (origin
1358 (method url-fetch)
1359 (uri (string-append
1360 "https://github.com/tpaviot/oce/archive/OCE-"
1361 version
1362 ".tar.gz"))
a4f393b7 1363 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
5d4bd4cc
PG		 1364 (sha256
1365 (base32
1366 "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
1367 (build-system cmake-build-system)
1368 (arguments
1369 '(#:configure-flags
1370 (list "-DOCE_TESTING:BOOL=ON"
1371 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1372 "-DOCE_DRAW:BOOL=ON"
1373 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1374 (assoc-ref %outputs "out"))
1375 "-UCMAKE_INSTALL_RPATH")))
1376 (inputs
1377 `(("freetype" ,freetype)
1378 ("glu" ,glu)
1379 ("libxmu" ,libxmu)
1380 ("mesa" ,mesa)
1381 ("tcl" ,tcl)
1382 ("tk" ,tk)))
1383 (native-inputs
1384 `(("python" ,python-wrapper)))
1385 (home-page "https://github.com/tpaviot/oce")
1386 (synopsis "Libraries for 3D modeling and numerical simulation")
1387 (description
1388 "Open CASCADE is a set of libraries for the development of applications
1389dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1390C++ class libraries providing services for 3D surface and solid modeling, CAD
1391data exchange, and visualization. It is used for development of specialized
1392software dealing with 3D models in design (CAD), manufacturing (CAM),
1393numerical simulation (CAE), measurement equipment (CMM), and quality
1394control (CAQ) domains.
1395
1396This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1397patches, improvements, and experiments contributed by users over the official
1398Open CASCADE library.")
1399 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1400 ; use of header files; see
1401 ; OCCT_LGPL_EXCEPTION.txt
1402 license:public-domain; files
1403 ; src/Standard/Standard_StdAllocator.hxx and
1404 ; src/NCollection/NCollection_StdAllocator.hxx
1405 license:expat; file src/OpenGl/OpenGl_glext.h
1406 license:bsd-3)))); test framework gtest
1407
3de01d3f
EB		 1408(define-public gmsh
1409 (package
1410 (name "gmsh")
8a4d14fa 1411 (version "2.16.0")
3de01d3f
EB		 1412 (source
1413 (origin
1414 (method url-fetch)
1c79e086 1415 (uri (string-append "http://gmsh.info/src/gmsh-"
3de01d3f
EB		 1416 version "-source.tgz"))
1417 (sha256
8a4d14fa 1418 (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
3de01d3f
EB		 1419 (modules '((guix build utils)))
1420 (snippet
1421 ;; Remove non-free METIS code
1422 '(delete-file-recursively "contrib/Metis"))))
1423 (build-system cmake-build-system)
3de01d3f
EB		 1424 (propagated-inputs
1425 `(("fltk" ,fltk)
19afbea1 1426 ("gfortran" ,gfortran)
3de01d3f 1427 ("gmp" ,gmp)
40029cbe 1428 ("hdf5" ,hdf5)
3de01d3f
EB		 1429 ("lapack" ,lapack)
1430 ("mesa" ,mesa)
85f41902 1431 ("glu" ,glu)
45548139 1432 ("opencascade-oce" ,opencascade-oce)
3de01d3f
EB		 1433 ("libx11" ,libx11)
1434 ("libxext" ,libxext)))
66395a61
EF		 1435 (inputs
1436 `(("fontconfig" ,fontconfig)
1437 ("libxft" ,libxft)))
3de01d3f
EB		 1438 (arguments
1439 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1440 "-DENABLE_BUILD_SHARED:BOOL=ON"
45548139 1441 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
3de01d3f
EB		 1442 (home-page "http://www.geuz.org/gmsh/")
1443 (synopsis "3D finite element grid generator")
edf684ef
EB		 1444 (description "Gmsh is a 3D finite element grid generator with a built-in
1445CAD engine and post-processor. Its design goal is to provide a fast, light
1446and user-friendly meshing tool with parametric input and advanced
1447visualization capabilities. Gmsh is built around four modules: geometry,
1448mesh, solver and post-processing. The specification of any input to these
1449modules is done either interactively using the graphical user interface or in
1450ASCII text files using Gmsh's own scripting language.")
3de01d3f 1451 (license license:gpl2+)))
b9100e2f 1452
6d5f63b6
JD		 1453(define-public maxflow
1454 (package
1455 (name "maxflow")
1456 (version "3.04")
1457 (source (origin
1458 (method git-fetch)
1459 (uri (git-reference
1460 (url "https://github.com/gerddie/maxflow.git")
1461 (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
1462 (file-name (string-append name "-" version "-checkout"))
1463 (sha256
1464 (base32
1465 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1466 (build-system cmake-build-system)
1467 (home-page "http://pub.ist.ac.at/~vnk/software.html")
1468 (synopsis "Library implementing Maxflow algorithm")
1469 (description "An implementation of the maxflow algorithm described in
1470@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1471Energy Minimization in Computer Vision.\n
1472Yuri Boykov and Vladimir Kolmogorov.\n
1473In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1474September 2004}")
1475 (license license:gpl3+)))
1476
b9100e2f
EB		 1477(define-public petsc
1478 (package
1479 (name "petsc")
6fec298d 1480 (version "3.8.0")
b9100e2f
EB		 1481 (source
1482 (origin
1483 (method url-fetch)
1484 ;; The *-lite-* tarball does not contain the *large* documentation
1485 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1486 "petsc-lite-" version ".tar.gz"))
1487 (sha256
6fec298d 1488 (base32 "1lajbk3c29hnh83v6cbmm3a8wv6bdykh0p70kwrr4vrnizalk88s"))))
b9100e2f
EB		 1489 (build-system gnu-build-system)
1490 (native-inputs
6fec298d 1491 `(("python" ,python-2)))
b9100e2f 1492 (inputs
19afbea1 1493 `(("gfortran" ,gfortran)
b9100e2f 1494 ("lapack" ,lapack)
f258212d 1495 ("superlu" ,superlu)
b9100e2f
EB		 1496 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1497 ;; leaving out opengl, as configuration seems to only be for mac
1498 ))
1499 (arguments
1500 `(#:test-target "test"
9a899cce 1501 #:parallel-build? #f ;build is parallel by default
b9100e2f
EB		 1502 #:configure-flags
1503 `("--with-mpi=0"
f258212d
EB		 1504 "--with-openmp=1"
1505 "--with-superlu=1"
1506 ,(string-append "--with-superlu-include="
1507 (assoc-ref %build-inputs "superlu") "/include")
1508 ,(string-append "--with-superlu-lib="
1509 (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
9731c412
EB		 1510 #:make-flags
1511 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1512 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1513 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
b9100e2f 1514 #:phases
64dcc289
EB		 1515 (modify-phases %standard-phases
1516 (replace 'configure
1517 ;; PETSc's configure script is actually a python script, so we can't
1518 ;; run it with bash.
1519 (lambda* (#:key outputs (configure-flags '())
1520 #:allow-other-keys)
1521 (let* ((prefix (assoc-ref outputs "out"))
1522 (flags `(,(string-append "--prefix=" prefix)
1523 ,@configure-flags)))
1524 (format #t "build directory: ~s~%" (getcwd))
1525 (format #t "configure flags: ~s~%" flags)
1526 (zero? (apply system* "./configure" flags)))))
1527 (add-after 'configure 'clean-local-references
9731c412 1528 (lambda* (#:key outputs #:allow-other-keys)
64dcc289
EB		 1529 (let ((out (assoc-ref outputs "out")))
1530 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
b730b437
EB		 1531 ;; Prevent build directory from leaking into compiled code
1532 (((getcwd)) out)
1533 ;; Scrub timestamp for reproducibility
fafd623e 1534 ((".*Libraries compiled on.*") ""))
9731c412
EB		 1535 (substitute* (find-files "." "petscvariables")
1536 ;; Do not expose build machine characteristics, set to defaults.
1537 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1538 (("NPMAX = [:digit:]+") "NPMAX = 2"))
fafd623e 1539 #t)))
64dcc289 1540 (add-after 'install 'clean-install
10b11968
EB		 1541 ;; Try to keep installed files from leaking build directory names.
1542 (lambda* (#:key inputs outputs #:allow-other-keys)
64dcc289 1543 (let ((out (assoc-ref outputs "out")))
10b11968 1544 (substitute* (map (lambda (file)
9a899cce 1545 (string-append out "/lib/petsc/conf/" file))
fafd623e 1546 '("petscvariables"))
10b11968
EB		 1547 (((getcwd)) out))
1548 ;; Make compiler references point to the store
9a899cce 1549 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
dfdf5716
EB		 1550 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1551 (string-append "= " (which compiler))))
10b11968
EB		 1552 ;; PETSc installs some build logs, which aren't necessary.
1553 (for-each (lambda (file)
9a899cce 1554 (let ((f (string-append out "/lib/petsc/conf/" file)))
10b11968
EB		 1555 (when (file-exists? f)
1556 (delete-file f))))
9a899cce
EB		 1557 '("configure.log" "make.log" "gmake.log"
1558 "test.log" "error.log" "RDict.db"
fafd623e 1559 "PETScBuildInternal.cmake"
10b11968 1560 ;; Once installed, should uninstall with Guix
fafd623e
EB		 1561 "uninstall.py"))
1562 #t))))))
b9100e2f 1563 (home-page "http://www.mcs.anl.gov/petsc")
16ecf3ff 1564 (synopsis "Library to solve PDEs")
b9100e2f
EB		 1565 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1566data structures and routines for the scalable (parallel) solution of
1567scientific applications modeled by partial differential equations.")
166191b3 1568 (license (license:non-copyleft
b9100e2f
EB		 1569 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1570
1571(define-public petsc-complex
1572 (package (inherit petsc)
1573 (name "petsc-complex")
1574 (arguments
1575 (substitute-keyword-arguments (package-arguments petsc)
1576 ((#:configure-flags cf)
1577 `(cons "--with-scalar-type=complex" ,cf))))
16ecf3ff 1578 (synopsis "Library to solve PDEs (with complex scalars)")))
183e44ae 1579
d8c7eeb9
EB		 1580(define-public petsc-openmpi
1581 (package (inherit petsc)
1582 (name "petsc-openmpi")
1583 (inputs
1584 `(("openmpi" ,openmpi)
1585 ,@(package-inputs petsc)))
1586 (arguments
1587 (substitute-keyword-arguments (package-arguments petsc)
1588 ((#:configure-flags cf)
1589 ``("--with-mpiexec=mpirun"
1590 ,(string-append "--with-mpi-dir="
1591 (assoc-ref %build-inputs "openmpi"))
1592 ,@(delete "--with-mpi=0" ,cf)))))
16ecf3ff 1593 (synopsis "Library to solve PDEs (with MPI support)")))
d8c7eeb9
EB		 1594
1595(define-public petsc-complex-openmpi
1596 (package (inherit petsc-complex)
1597 (name "petsc-complex-openmpi")
1598 (inputs
1599 `(("openmpi" ,openmpi)
1600 ,@(package-inputs petsc-complex)))
1601 (arguments
1602 (substitute-keyword-arguments (package-arguments petsc-complex)
1603 ((#:configure-flags cf)
1604 ``("--with-mpiexec=mpirun"
1605 ,(string-append "--with-mpi-dir="
1606 (assoc-ref %build-inputs "openmpi"))
1607 ,@(delete "--with-mpi=0" ,cf)))))
16ecf3ff 1608 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
d8c7eeb9 1609
a7f01414
EB		 1610(define-public slepc
1611 (package
1612 (name "slepc")
cc809f16 1613 (version "3.8.2")
a7f01414
EB		 1614 (source
1615 (origin
1616 (method url-fetch)
baeaf882
EB		 1617 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
1618 version ".tar.gz"))
a7f01414
EB		 1619 (sha256
1620 (base32
cc809f16 1621 "04zd48p43rnvg68p6cp28zll0px5whglc5v0sc3s6vdj1v920z8y"))))
a7f01414
EB		 1622 (build-system gnu-build-system)
1623 (native-inputs
1624 `(("python" ,python-2)))
1625 (inputs
1626 `(("arpack" ,arpack-ng)
1627 ("gfortran" ,gfortran)))
1628 (propagated-inputs
1629 `(("petsc" ,petsc)))
1630 (arguments
1631 `(#:parallel-build? #f ;build is parallel by default
1632 #:configure-flags
1633 `(,(string-append "--with-arpack-dir="
9cf52454 1634 (assoc-ref %build-inputs "arpack") "/lib"))
9731c412
EB		 1635 #:make-flags ;honor (parallel-job-count)
1636 `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
a7f01414
EB		 1637 #:phases
1638 (modify-phases %standard-phases
8787c555 1639 (replace 'configure
a7f01414
EB		 1640 ;; configure is a python script, so we can't run it with bash.
1641 (lambda* (#:key inputs outputs (configure-flags '())
1642 #:allow-other-keys)
1643 (let* ((prefix (assoc-ref outputs "out"))
1644 (flags `(,(string-append "--prefix=" prefix)
1645 ,@configure-flags)))
1646 (format #t "build directory: ~s~%" (getcwd))
1647 (format #t "configure flags: ~s~%" flags)
1648 (setenv "SLEPC_DIR" (getcwd))
9cf52454 1649 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
c6840089 1650 (apply invoke "./configure" flags))))
8787c555 1651 (add-after 'install 'delete-doc
a7f01414
EB		 1652 ;; TODO: SLEPc installs HTML documentation alongside headers in
1653 ;; $out/include. We'd like to move them to share/doc, but delete
1654 ;; them for now, as they are incomplete and installing the complete
1655 ;; documentation is difficult.
1656 (lambda* (#:key outputs #:allow-other-keys)
1657 (let* ((out (assoc-ref outputs "out")))
1658 (for-each delete-file (find-files out "\\.html$")))))
8787c555 1659 (add-after 'install 'clean-install
a7f01414
EB		 1660 ;; Clean up unnecessary build logs from installation.
1661 (lambda* (#:key outputs #:allow-other-keys)
1662 (let ((out (assoc-ref outputs "out")))
1663 (for-each (lambda (file)
1664 (let ((f (string-append out "/lib/slepc/conf/" file)))
1665 (when (file-exists? f)
1666 (delete-file f))))
1667 '("configure.log" "make.log" "gmake.log"
1668 "test.log" "error.log" "RDict.db"
1669 "uninstall.py"))))))))
1670 (home-page "http://slepc.upv.es")
1671 (synopsis "Scalable library for eigenproblems")
1672 (description "SLEPc is a software library for the solution of large sparse
1673eigenproblems on parallel computers. It can be used for the solution of
1674linear eigenvalue problems formulated in either standard or generalized form,
1675as well as other related problems such as the singular value decomposition.
1676The emphasis of the software is on methods and techniques appropriate for
1677problems in which the associated matrices are sparse, for example, those
1678arising after the discretization of partial differential equations.")
3c524f21 1679 (license license:bsd-2)))
a7f01414
EB		 1680
1681(define-public slepc-complex
1682 (package (inherit slepc)
1683 (name "slepc-complex")
1684 (propagated-inputs
1685 `(("petsc" ,petsc-complex)
1686 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1687 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1688
1689(define-public slepc-openmpi
1690 (package (inherit slepc)
1691 (name "slepc-openmpi")
1692 (inputs
1693 `(("mpi" ,openmpi)
1694 ("arpack" ,arpack-ng-openmpi)
1695 ,@(alist-delete "arpack" (package-inputs slepc))))
1696 (propagated-inputs
1697 `(("petsc" ,petsc-openmpi)
1698 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1699 (synopsis "Scalable library for eigenproblems (with MPI support)")))
1700
1701(define-public slepc-complex-openmpi
1702 (package (inherit slepc-openmpi)
1703 (name "slepc-complex-openmpi")
1704 (propagated-inputs
1705 `(("petsc" ,petsc-complex-openmpi)
1706 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1707 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1708
cec86422
EB		 1709(define-public mumps
1710 (package
1711 (name "mumps")
fba78d18 1712 (version "5.0.2")
cec86422
EB		 1713 (source
1714 (origin
1715 (method url-fetch)
1716 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
1717 version ".tar.gz"))
1718 (sha256
1719 (base32
fba78d18 1720 "0igyc1pfzxdhpbad3v3lb86ixkdbqa1a8gbs15b04r2294h2nabp"))
fc1adab1 1721 (patches (search-patches "mumps-build-parallelism.patch"))))
cec86422
EB		 1722 (build-system gnu-build-system)
1723 (inputs
1724 `(("fortran" ,gfortran)
1725 ;; These are required for linking against mumps, but we let the user
1726 ;; declare the dependency.
1727 ("blas" ,openblas)
1728 ("metis" ,metis)
1729 ("scotch" ,scotch)))
1730 (arguments
1731 `(#:modules ((ice-9 match)
1732 (ice-9 popen)
1733 (srfi srfi-1)
1734 ,@%gnu-build-system-modules)
1735 #:phases
1736 (modify-phases %standard-phases
fba78d18 1737 (replace 'configure
cec86422
EB		 1738 (lambda* (#:key inputs #:allow-other-keys)
1739 (call-with-output-file "Makefile.inc"
1740 (lambda (port)
1741 (format port "
1742PLAT =
1743LIBEXT = .a
1744OUTC = -o
1745OUTF = -o
1746RM = rm -f~:[
1747CC = gcc
1748FC = gfortran
1749FL = gfortran
1750INCSEQ = -I$(topdir)/libseq
1751LIBSEQ = -L$(topdir)/libseq -lmpiseq
1752LIBSEQNEEDED = libseqneeded~;
1753CC = mpicc
1754FC = mpifort
1755FL = mpifort~]
1756AR = ar vr # rules require trailing space, ugh...
1757RANLIB = ranlib
1758LIBBLAS = -L~a -lopenblas~@[
1759SCALAP = -L~a -lscalapack~]
1760LIBOTHERS = -pthread
1761CDEFS = -DAdd_
1762PIC = -fPIC
1763OPTF = -O2 -DALLOW_NON_INIT $(PIC)
1764OPTL = -O2 $(PIC)
1765OPTC = -O2 $(PIC)
1766INCS = $(INCSEQ)
1767LIBS = $(SCALAP) $(LIBSEQ)
1768LPORDDIR = $(topdir)/PORD/lib
1769IPORD = -I$(topdir)/PORD/include
1770LPORD = -L$(LPORDDIR) -lpord
1771ORDERINGSF = -Dpord~@[
1772METISDIR = ~a
1773IMETIS = -I$(METISDIR)/include
1774LMETIS = -L$(METISDIR)/lib -lmetis
1775ORDERINGSF += -Dmetis~]~@[~:{
1776SCOTCHDIR = ~a
1777ISCOTCH = -I$(SCOTCHDIR)/include
1778LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
1779ORDERINGSF += ~a~}~]
1780ORDERINGSC = $(ORDERINGSF)
1781LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
1782IORDERINGSF = $(ISCOTCH)
1783IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
1784 (assoc-ref inputs "mpi")
1785 (assoc-ref inputs "blas")
1786 (assoc-ref inputs "scalapack")
1787 (assoc-ref inputs "metis")
1788 (match (list (assoc-ref inputs "pt-scotch")
1789 (assoc-ref inputs "scotch"))
1790 ((#f #f)
1791 #f)
1792 ((#f scotch)
1793 `((,scotch "" "-Dscotch")))
1794 ((ptscotch _)
1795 `((,ptscotch
1796 "-lptesmumps -lptscotch -lptscotcherr "
1797 "-Dptscotch")))))))))
fba78d18 1798 (replace 'build
cec86422
EB		 1799 ;; By default only the d-precision library is built. Make with "all"
1800 ;; target so that all precision libraries and examples are built.
1801 (lambda _
1802 (zero? (system* "make" "all"
1803 (format #f "-j~a" (parallel-job-count))))))
fba78d18 1804 (replace 'check
cec86422
EB		 1805 ;; Run the simple test drivers, which read test input from stdin:
1806 ;; from the "real" input for the single- and double-precision
1807 ;; testers, and from the "cmplx" input for complex-precision
1808 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
1809 ;; package to prefix execution with "mpirun".
1810 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
1811 (with-directory-excursion "examples"
1812 (every
1813 (lambda (prec type)
1814 (let ((tester (apply open-pipe*
1815 `(,OPEN_WRITE
1816 ,@exec-prefix
1817 ,(string-append "./" prec
1818 "simpletest"))))
1819 (input (open-input-file
1820 (string-append "input_simpletest_" type))))
1821 (begin
1822 (dump-port input tester)
1823 (close-port input)
1824 (zero? (close-pipe tester)))))
1825 '("s" "d" "c" "z")
1826 '("real" "real" "cmplx" "cmplx")))))
fba78d18
EB		 1827 (replace 'install
1828 (lambda* (#:key outputs #:allow-other-keys)
1829 (let* ((out (assoc-ref outputs "out"))
1830 (libdir (string-append out "/lib")))
1831 (copy-recursively "lib" libdir)
1832 (copy-recursively "include" (string-append out "/include"))
1833 (when (file-exists? "libseq/libmpiseq.a")
1834 (install-file "libseq/libmpiseq.a" libdir))
1835 #t))))))
cec86422
EB		 1836 (home-page "http://mumps.enseeiht.fr")
1837 (synopsis "Multifrontal sparse direct solver")
1838 (description
1839 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
1840sparse system of linear equations A x = b using Guassian elimination.")
1841 (license license:cecill-c)))
1842
1843(define-public mumps-metis
1844 (package (inherit mumps)
1845 (name "mumps-metis")
1846 (inputs
1847 (alist-delete "scotch" (package-inputs mumps)))))
1848
1849(define-public mumps-openmpi
1850 (package (inherit mumps)
1851 (name "mumps-openmpi")
1852 (inputs
1853 `(("mpi" ,openmpi)
1854 ("scalapack" ,scalapack)
1855 ("pt-scotch" ,pt-scotch)
1856 ,@(alist-delete "scotch" (package-inputs mumps))))
1857 (arguments
1858 (substitute-keyword-arguments (package-arguments mumps)
1859 ((#:phases phases)
1860 `(modify-phases ,phases
1861 (replace
1862 'check
1863 (lambda _
1864 ((assoc-ref ,phases 'check)
1865 #:exec-prefix '("mpirun" "-n" "2"))))))))
1866 (synopsis "Multifrontal sparse direct solver (with MPI)")))
1867
1868(define-public mumps-metis-openmpi
1869 (package (inherit mumps-openmpi)
1870 (name "mumps-metis-openmpi")
1871 (inputs
1872 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
1873
2d047896
RW		 1874(define-public r-quadprog
1875 (package
1876 (name "r-quadprog")
1877 (version "1.5-5")
1878 (source
1879 (origin
1880 (method url-fetch)
1881 (uri (cran-uri "quadprog" version))
1882 (sha256
1883 (base32
1884 "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
1885 (build-system r-build-system)
1886 (native-inputs
1887 `(("gfortran" ,gfortran)))
e9960d8c 1888 (home-page "https://cran.r-project.org/web/packages/quadprog")
2d047896
RW		 1889 (synopsis "Functions to solve quadratic programming problems")
1890 (description
1891 "This package contains routines and documentation for solving quadratic
1892programming problems.")
1893 (license license:gpl3+)))
1894
ec8c7e47
RJ		 1895(define-public r-pracma
1896 (package
1897 (name "r-pracma")
63758425 1898 (version "2.1.4")
ec8c7e47
RJ		 1899 (source (origin
1900 (method url-fetch)
1901 (uri (cran-uri "pracma" version))
1902 (sha256
63758425 1903 (base32 "1ygm81i7mqvh229dp9935djjyb120p3bqvaf4k572sa4q63fzjhc"))))
ec8c7e47 1904 (build-system r-build-system)
ccd9b151
RW		 1905 (propagated-inputs
1906 `(("r-quadprog" ,r-quadprog)))
e9960d8c 1907 (home-page "https://cran.r-project.org/web/packages/pracma")
ec8c7e47
RJ		 1908 (synopsis "Practical numerical math functions")
1909 (description "This package provides functions for numerical analysis and
1910linear algebra, numerical optimization, differential equations, plus some
1911special functions. It uses Matlab function names where appropriate to simplify
1912porting.")
1913 (license license:gpl3+)))
1914
183e44ae
EB		 1915(define-public superlu
1916 (package
1917 (name "superlu")
995a09e0 1918 (version "5.2.1")
183e44ae
EB		 1919 (source
1920 (origin
1921 (method url-fetch)
1922 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1923 "superlu_" version ".tar.gz"))
1924 (sha256
995a09e0
EB		 1925 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
1926 (modules '((guix build utils)))
1927 (snippet
1928 ;; Replace the non-free implementation of MC64 with a stub adapted
1929 ;; from Debian
1930 '(begin
1931 (use-modules (ice-9 regex)
1932 (ice-9 rdelim))
1933 (call-with-output-file "SRC/mc64ad.c"
1934 (lambda (port)
1935 (display "
1936#include <stdio.h>
1937#include <stdlib.h>
1938void mc64id_(int *a) {
1939 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
1940 abort ();
1941}
1942void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
1943 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
1944 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
1945 abort ();
1946}\n" port)))
1947 ;; Remove the corresponding license verbiage. MC64 license follows
1948 ;; a "------" line separator.
1949 (with-atomic-file-replacement "License.txt"
1950 (let ((rx (make-regexp "-{8}")))
1951 (lambda (in out)
1952 (let loop ()
1953 (let ((line (read-line in 'concat)))
1954 (unless (regexp-exec rx line)
1955 (display line out)
1956 (loop)))))))))))
1957 (build-system cmake-build-system)
183e44ae
EB		 1958 (native-inputs
1959 `(("tcsh" ,tcsh)))
1960 (inputs
995a09e0 1961 `(("blas" ,openblas)
19afbea1 1962 ("gfortran" ,gfortran)))
183e44ae 1963 (arguments
995a09e0
EB		 1964 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
1965 "-DTPL_BLAS_LIBRARIES=openblas"
677bc34d 1966 "-DBUILD_SHARED_LIBS:BOOL=YES")))
183e44ae
EB		 1967 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
1968 (synopsis "Supernodal direct solver for sparse linear systems")
1969 (description
1970 "SuperLU is a general purpose library for the direct solution of large,
1971sparse, nonsymmetric systems of linear equations on high performance machines.
1972The library is written in C and is callable from either C or Fortran. The
1973library routines perform an LU decomposition with partial pivoting and
1974triangular system solves through forward and back substitution. The library
1975also provides threshold-based ILU factorization preconditioners.")
995a09e0
EB		 1976 (license (list license:bsd-3
1977 license:gpl2+ ;EXAMPLE/*fgmr.c
1978 (license:fsf-free "file://SRC/colamd.h")))))
f8ed036a 1979
a54aefea
EB		 1980(define-public superlu-dist
1981 (package
1982 (name "superlu-dist")
1983 (version "3.3")
1984 (source
1985 (origin
1986 (method url-fetch)
1987 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1988 "superlu_dist_" version ".tar.gz"))
1989 (sha256
1990 (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj"))
29080870
EB		 1991 (modules '((guix build utils)))
1992 (snippet
1993 ;; Replace the non-free implementation of MC64 with a stub
1994 '(begin
1995 (use-modules (ice-9 regex)
1996 (ice-9 rdelim))
1997 (call-with-output-file "SRC/mc64ad.c"
1998 (lambda (port)
1999 (display "
2000#include <stdio.h>
2001#include <stdlib.h>
2002void mc64id_(int *a) {
2003 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2004 abort ();
2005}
2006void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2007 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2008 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2009 abort ();
2010}\n" port)))
2011 (delete-file "SRC/mc64ad.f.bak")
2012 (substitute* "SRC/util.c" ;adjust default algorithm
2013 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
2014 "RowPerm = NOROWPERM"))))
fc1adab1 2015 (patches (search-patches "superlu-dist-scotchmetis.patch"))))
a54aefea
EB		 2016 (build-system gnu-build-system)
2017 (native-inputs
2018 `(("tcsh" ,tcsh)))
2019 (inputs
19afbea1 2020 `(("gfortran" ,gfortran)))
a54aefea
EB		 2021 (propagated-inputs
2022 `(("openmpi" ,openmpi) ;headers include MPI heades
2023 ("lapack" ,lapack) ;required to link with output library
2024 ("pt-scotch" ,pt-scotch))) ;same
2025 (arguments
2026 `(#:parallel-build? #f ;race conditions using ar
2027 #:phases
dc1d3cde
KK		 2028 (modify-phases %standard-phases
2029 (replace 'configure
2030 (lambda* (#:key inputs outputs #:allow-other-keys)
2031 (call-with-output-file "make.inc"
2032 (lambda (port)
2033 (format port "
a54aefea
EB		 2034PLAT =
2035DSuperLUroot = ~a
2036DSUPERLULIB = ~a/lib/libsuperlu_dist.a
2037BLASDEF = -DUSE_VENDOR_BLAS
2038BLASLIB = -L~a/lib -lblas
2039PARMETISLIB = -L~a/lib \
2040 -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
2041 -lscotch -lscotcherr -lscotcherrexit
2042METISLIB = -L~:*~a/lib \
2043 -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
2044LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
2045ARCH = ar
2046ARCHFLAGS = cr
2047RANLIB = ranlib
2048CC = mpicc
2049PIC = -fPIC
2050CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC)
2051NOOPTS = -O0 -g $(PIC)
2052FORTRAN = mpifort
2053FFLAGS = -O2 -g $(PIC)
2054LOADER = $(CC)
2055CDEFS = -DAdd_"
dc1d3cde
KK		 2056 (getcwd)
2057 (assoc-ref outputs "out")
2058 (assoc-ref inputs "lapack")
2059 (assoc-ref inputs "pt-scotch"))))
2060 #t))
2061 (add-after 'unpack 'remove-broken-symlinks
2062 (lambda _
2063 (for-each delete-file
2064 (find-files "MAKE_INC" "\\.#make\\..*"))
2065 #t))
2066 (add-before 'build 'create-install-directories
2067 (lambda* (#:key outputs #:allow-other-keys)
2068 (for-each
2069 (lambda (dir)
2070 (mkdir-p (string-append (assoc-ref outputs "out")
2071 "/" dir)))
2072 '("lib" "include"))
2073 #t))
2074 (replace 'check
a54aefea
EB		 2075 (lambda _
2076 (with-directory-excursion "EXAMPLE"
2077 (and
2078 (zero? (system* "mpirun" "-n" "2"
2079 "./pddrive" "-r" "1" "-c" "2" "g20.rua"))
2080 (zero? (system* "mpirun" "-n" "2"
dc1d3cde
KK		 2081 "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))))))
2082 (replace 'install
2083 (lambda* (#:key outputs #:allow-other-keys)
2084 ;; Library is placed in lib during the build phase. Copy over
2085 ;; headers to include.
2086 (let* ((out (assoc-ref outputs "out"))
2087 (incdir (string-append out "/include")))
2088 (for-each (lambda (file)
2089 (let ((base (basename file)))
2090 (format #t "installing `~a' to `~a'~%"
2091 base incdir)
2092 (copy-file file
2093 (string-append incdir "/" base))))
2094 (find-files "SRC" ".*\\.h$")))
2095 #t)))))
a54aefea
EB		 2096 (home-page (package-home-page superlu))
2097 (synopsis "Parallel supernodal direct solver")
2098 (description
2099 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2100It is targeted for distributed memory parallel machines. SuperLU_DIST is
2101implemented in ANSI C, and MPI for communications.")
2102 (license license:bsd-3)))
2103
f8ed036a
EB		 2104(define-public scotch
2105 (package
2106 (name "scotch")
6c798540 2107 (version "6.0.4")
f8ed036a
EB		 2108 (source
2109 (origin
2110 (method url-fetch)
6c798540 2111 (uri (string-append "https://gforge.inria.fr/frs/download.php/34618/"
f8ed036a
EB		 2112 "scotch_" version ".tar.gz"))
2113 (sha256
6c798540 2114 (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm"))
fc1adab1
AK		 2115 (patches (search-patches "scotch-test-threading.patch"
2116 "pt-scotch-build-parallelism.patch"))))
f8ed036a
EB		 2117 (build-system gnu-build-system)
2118 (inputs
2119 `(("zlib" ,zlib)
5e54f4ad 2120 ("flex" ,flex)
f8ed036a
EB		 2121 ("bison" ,bison)))
2122 (arguments
2123 `(#:phases
d6602ee9
EB		 2124 (modify-phases %standard-phases
2125 (add-after
2126 'unpack 'chdir-to-src
2127 (lambda _ (chdir "src")))
2128 (replace
2129 'configure
2130 (lambda _
2131 (call-with-output-file "Makefile.inc"
2132 (lambda (port)
2133 (format port "
f8ed036a
EB		 2134EXE =
2135LIB = .a
2136OBJ = .o
2137MAKE = make
2138AR = ar
2139ARFLAGS = -ruv
cf0ec6c4 2140CAT = cat
f8ed036a
EB		 2141CCS = gcc
2142CCP = mpicc
2143CCD = gcc
2144CPPFLAGS =~{ -D~a~}
6c798540 2145CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
f8ed036a
EB		 2146LDFLAGS = -lz -lm -lrt -lpthread
2147CP = cp
2148LEX = flex -Pscotchyy -olex.yy.c
2149LN = ln
2150MKDIR = mkdir
2151MV = mv
2152RANLIB = ranlib
2153YACC = bison -pscotchyy -y -b y
2154"
d6602ee9
EB		 2155 '("COMMON_FILE_COMPRESS_GZ"
2156 "COMMON_PTHREAD"
2157 "COMMON_RANDOM_FIXED_SEED"
26599d69 2158 "INTSIZE64" ;use 'long' instead of 'int'
cf0ec6c4
EB		 2159 ;; Prevents symbolc clashes with libesmumps
2160 "SCOTCH_RENAME"
d6602ee9
EB		 2161 ;; XXX: Causes invalid frees in superlu-dist tests
2162 ;; "SCOTCH_PTHREAD"
2163 ;; "SCOTCH_PTHREAD_NUMBER=2"
2164 "restrict=__restrict"))))))
cf0ec6c4
EB		 2165 (add-after
2166 'build 'build-esmumps
2167 (lambda _
2168 (zero? (system* "make"
2169 (format #f "-j~a" (parallel-job-count))
2170 "esmumps"))))
d6602ee9 2171 (replace
f8ed036a
EB		 2172 'install
2173 (lambda* (#:key outputs #:allow-other-keys)
2174 (let ((out (assoc-ref outputs "out")))
2175 (mkdir out)
2176 (zero? (system* "make"
2177 (string-append "prefix=" out)
cf0ec6c4
EB		 2178 "install"))
2179 ;; esmumps files are not installed with the above
2180 (for-each (lambda (f)
2181 (copy-file f (string-append out "/include/" f)))
2182 (find-files "../include" ".*esmumps.h$"))
2183 (for-each (lambda (f)
2184 (copy-file f (string-append out "/lib/" f)))
2185 (find-files "../lib" "^lib.*esmumps.*"))))))))
f8ed036a
EB		 2186 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
2187 (synopsis "Programs and libraries for graph algorithms")
2188 (description "SCOTCH is a set of programs and libraries which implement
2189the static mapping and sparse matrix reordering algorithms developed within
2190the SCOTCH project. Its purpose is to apply graph theory, with a divide and
2191conquer approach, to scientific computing problems such as graph and mesh
2192partitioning, static mapping, and sparse matrix ordering, in application
2193domains ranging from structural mechanics to operating systems or
2194bio-chemistry.")
2195 ;; See LICENSE_en.txt
2196 (license license:cecill-c)))
6acb4adb 2197
1c39f3b8
PG		 2198(define-public scotch32
2199 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2200 ;; some applications.
2201 (package (inherit scotch)
2202 (name "scotch32")
2203 (arguments
2204 (substitute-keyword-arguments (package-arguments scotch)
2205 ((#:phases scotch-phases)
2206 `(modify-phases ,scotch-phases
2207 (replace
2208 'configure
2209 (lambda _
2210 (call-with-output-file "Makefile.inc"
2211 (lambda (port)
2212 (format port "
2213EXE =
2214LIB = .a
2215OBJ = .o
2216MAKE = make
2217AR = ar
2218ARFLAGS = -ruv
2219CAT = cat
2220CCS = gcc
2221CCP = mpicc
2222CCD = gcc
2223CPPFLAGS =~{ -D~a~}
2224CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2225LDFLAGS = -lz -lm -lrt -lpthread
2226CP = cp
2227LEX = flex -Pscotchyy -olex.yy.c
2228LN = ln
2229MKDIR = mkdir
2230MV = mv
2231RANLIB = ranlib
2232YACC = bison -pscotchyy -y -b y
2233"
2234 '("COMMON_FILE_COMPRESS_GZ"
2235 "COMMON_PTHREAD"
2236 "COMMON_RANDOM_FIXED_SEED"
2237 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
2238 ;; Prevents symbolc clashes with libesmumps
2239 "SCOTCH_RENAME"
2240 ;; XXX: Causes invalid frees in superlu-dist tests
2241 ;; "SCOTCH_PTHREAD"
2242 ;; "SCOTCH_PTHREAD_NUMBER=2"
2243 "restrict=__restrict"))))))))))
2244 (synopsis
2245 "Programs and libraries for graph algorithms (32-bit integers)")))
2246
6acb4adb
EB		 2247(define-public pt-scotch
2248 (package (inherit scotch)
2249 (name "pt-scotch")
2250 (propagated-inputs
2251 `(("openmpi" ,openmpi))) ;Headers include MPI headers
2252 (arguments
2253 (substitute-keyword-arguments (package-arguments scotch)
2254 ((#:phases scotch-phases)
d6602ee9
EB		 2255 `(modify-phases ,scotch-phases
2256 (replace
2257 'build
d6602ee9
EB		 2258 (lambda _
2259 (and
cf0ec6c4
EB		 2260 (zero? (system* "make"
2261 (format #f "-j~a" (parallel-job-count))
2262 "ptscotch" "ptesmumps"))
d6602ee9
EB		 2263 ;; Install the serial metis compatibility library
2264 (zero? (system* "make" "-C" "libscotchmetis" "install")))))
2265 (replace
2266 'check
2267 (lambda _ (zero? (system* "make" "ptcheck"))))))))
6acb4adb 2268 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
5698b8b8 2269
1c25a52c
PG		 2270(define-public pt-scotch32
2271 (package (inherit scotch32)
2272 (name "pt-scotch32")
2273 (propagated-inputs
2274 `(("openmpi" ,openmpi))) ;headers include MPI headers
2275 (arguments
c4d4a779
PG		 2276 (substitute-keyword-arguments (package-arguments scotch32)
2277 ((#:phases scotch32-phases)
2278 `(modify-phases ,scotch32-phases
1c25a52c
PG		 2279 (replace 'build
2280 (lambda _
2281 (and
2282 (zero? (system* "make"
2283 (format #f "-j~a" (parallel-job-count))
2284 "ptscotch" "ptesmumps"))
2285 ;; Install the serial metis compatibility library
2286 (zero? (system* "make" "-C" "libscotchmetis" "install")))))
2287 (replace 'check
2288 (lambda _
2289 (zero? (system* "make" "ptcheck"))))))))
2290 (synopsis
2291 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2292
aa75ad00
EB		 2293(define-public metis
2294 (package
2295 (name "metis")
2296 (version "5.1.0")
2297 (source
2298 (origin
2299 (method url-fetch)
2300 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2301 "metis-" version ".tar.gz"))
2302 (sha256
2303 (base32
2304 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2305 (build-system cmake-build-system)
2306 (inputs
2307 `(("blas" ,openblas)))
2308 (arguments
2309 `(#:tests? #f ;no tests
2310 #:configure-flags `("-DSHARED=ON"
2311 ,(string-append "-DGKLIB_PATH=" (getcwd)
2312 "/metis-" ,version "/GKlib"))))
2313 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2314 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2315 (description
2316 "METIS is a set of serial programs for partitioning graphs, partitioning
2317finite element meshes, and producing fill-reducing orderings for sparse
2318matrices. The algorithms implemented in METIS are based on the multilevel
2319recursive-bisection, multilevel k-way, and multi-constraint partitioning
2320schemes.")
2321 (license license:asl2.0))) ;As of version 5.0.3
2322
700ff222
EB		 2323(define-public p4est
2324 (package
2325 (name "p4est")
4150da63 2326 (version "2.0")
700ff222
EB		 2327 (source
2328 (origin
2329 (method url-fetch)
2330 (uri (string-append "http://p4est.github.io/release/p4est-"
2331 version ".tar.gz"))
2332 (sha256
2333 (base32
4150da63 2334 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
700ff222
EB		 2335 (build-system gnu-build-system)
2336 (inputs
2337 `(("fortran" ,gfortran)
2338 ("blas" ,openblas)
2339 ("lapack" ,lapack)
2340 ("zlib" ,zlib)))
2341 (arguments
2342 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2343 (assoc-ref %build-inputs "blas")
2344 " -lopenblas")
2345 ,(string-append "LAPACK_LIBS=-L"
2346 (assoc-ref %build-inputs "lapack")
2347 " -llapack"))))
2348 (home-page "http://www.p4est.org")
2349 (synopsis "Adaptive mesh refinement on forests of octrees")
2350 (description
2351 "The p4est software library enables the dynamic management of a
2352collection of adaptive octrees, conveniently called a forest of octrees.
2353p4est is designed to work in parallel and scales to hundreds of thousands of
2354processor cores.")
2355 (license license:gpl2+)))
2356
2357(define-public p4est-openmpi
2358 (package (inherit p4est)
2359 (name "p4est-openmpi")
2360 (inputs
2361 `(("mpi" ,openmpi)
2362 ,@(package-inputs p4est)))
2363 (arguments
2364 (substitute-keyword-arguments (package-arguments p4est)
2365 ((#:configure-flags cf)
2366 ``("--enable-mpi" ,@,cf))))
2367 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2368
5698b8b8
JD		 2369(define-public gsegrafix
2370 (package
2371 (name "gsegrafix")
2372 (version "1.0.6")
2373 (source
2374 (origin
2375 (method url-fetch)
2376 (uri (string-append "mirror://gnu/" name "/" name "-"
2377 version ".tar.gz"))
2378 (sha256
2379 (base32
2380 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2381 (build-system gnu-build-system)
2382 (arguments
2383 `(#:configure-flags '("LDFLAGS=-lm")))
2384 (inputs
2385 `(("libgnomecanvas" ,libgnomecanvas)
2386 ("libbonoboui" ,libbonoboui)
2387 ("libgnomeui" ,libgnomeui)
2388 ("libgnomeprintui" ,libgnomeprintui)
2389 ("popt" ,popt)))
2390 (native-inputs
2391 `(("pkg-config" ,pkg-config)))
6fd52309 2392 (home-page "https://www.gnu.org/software/gsegrafix/")
5698b8b8
JD		 2393 (synopsis "GNOME application to create scientific and engineering plots")
2394 (description "GSEGrafix is an application which produces high-quality graphical
2395plots for science and engineering. Plots are specified via simple ASCII
2396parameter files and data files and are presented in an anti-aliased GNOME
2397canvas. The program supports rectangular two-dimensional plots, histograms,
2398polar-axis plots and three-dimensional plots. Plots can be printed or saved
2399to BMP, JPEG or PNG image formats.")
2400 (license license:gpl3+)))
8731e527
JD		 2401
2402(define-public maxima
2403 (package
2404 (name "maxima")
b3b2efc8 2405 (version "5.41.0")
8731e527
JD		 2406 (source
2407 (origin
2408 (method url-fetch)
2409 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2410 version "-source/" name "-" version ".tar.gz"))
2411 (sha256
2412 (base32
b3b2efc8 2413 "0x0n81z0s4pl8nwpf7ivlsbvsdphm9w42250g7qdkizl0132by6s"))
fc1adab1 2414 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
8731e527 2415 (build-system gnu-build-system)
df354a77 2416 (inputs
6b2eafaa 2417 `(("gcl" ,gcl)
df354a77 2418 ("gnuplot" ,gnuplot) ;for plots
f36afe4d 2419 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
df354a77
FB		 2420 (native-inputs
2421 `(("texinfo" ,texinfo)
ccbc5758
KK		 2422 ("perl" ,perl)
2423 ("python" ,python)))
8731e527 2424 (arguments
df354a77
FB		 2425 `(#:configure-flags
2426 (list "--enable-gcl"
2427 (string-append "--with-posix-shell="
2428 (assoc-ref %build-inputs "bash")
2429 "/bin/sh")
2430 (string-append "--with-wish="
2431 (assoc-ref %build-inputs "tk")
2432 "/bin/wish"
2433 (let ((v ,(package-version tk)))
2434 (string-take v (string-index-right v #\.)))))
df354a77 2435 ;; By default Maxima attempts to write temporary files to
77af7b24
MW		 2436 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2437 ;; Work around that.
df354a77 2438 #:make-flags (list "TMPDIR=/tmp")
0093b126
KK		 2439 #:phases
2440 (modify-phases %standard-phases
2441 (add-before 'check 'pre-check
2442 (lambda _
2443 (chmod "src/maxima" #o555)
2444 #t))
2445 ;; Make sure the doc and emacs files are found in the
2446 ;; standard location. Also configure maxima to find gnuplot
2447 ;; without having it on the PATH.
2448 (add-after 'install 'post-install
2449 (lambda* (#:key outputs inputs #:allow-other-keys)
2450 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2451 (out (assoc-ref outputs "out"))
2452 (datadir (string-append out "/share/maxima/" ,version))
2453 (binutils (string-append (assoc-ref inputs "binutils")
2454 "/bin")))
2455 (with-directory-excursion out
2456 (mkdir-p "share/emacs")
2457 (mkdir-p "share/doc")
2458 (symlink
2459 (string-append datadir "/emacs/")
2460 (string-append out "/share/emacs/site-lisp"))
2461 (symlink
2462 (string-append datadir "/doc/")
2463 (string-append out "/share/doc/maxima"))
2464 (with-atomic-file-replacement
2465 (string-append datadir "/share/maxima-init.lisp")
2466 (lambda (in out)
2467 (format out "~a ~s~a~%"
2468 "(setf $gnuplot_command "
2469 (string-append gnuplot "/bin/gnuplot") ")")
2470 (dump-port in out))))
2471 ;; Ensure that Maxima will have access to the GNU binutils
2472 ;; components at runtime.
2473 (wrap-program (string-append out "/bin/maxima")
2474 `("PATH" prefix (,binutils))))
2475 #t)))))
8731e527
JD		 2476 (home-page "http://maxima.sourceforge.net")
2477 (synopsis "Numeric and symbolic expression manipulation")
2478 (description "Maxima is a system for the manipulation of symbolic and
2479numerical expressions. It yields high precision numeric results by using
2480exact fractions, arbitrary precision integers, and variable precision floating
e881752c 2481point numbers.")
8731e527
JD		 2482 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2483 ;; Others simply say "GNU General Public License" without stating a
2484 ;; version (which implicitly means gpl1+).
2485 ;; At least one file (src/maxima.asd) says "version 2."
2486 ;; GPLv2 only is therefore the smallest subset.
f36afe4d 2487 (license license:gpl2)))
ec322be2 2488
9aafbc0c
MW		 2489(define-public wxmaxima
2490 (package
2491 (name "wxmaxima")
a8db968f 2492 (version "17.10.1")
9aafbc0c
MW		 2493 (source
2494 (origin
2495 (method url-fetch)
5143517c
KK		 2496 (uri (string-append "https://github.com/andrejv/" name "/archive"
2497 "/Version-" version ".tar.gz"))
2498 (file-name (string-append name "-" version ".tar.gz"))
9aafbc0c
MW		 2499 (sha256
2500 (base32
a8db968f 2501 "0qlzc31cqkwpfgrb9cif9bcnkj3rq487plg4rns7jxv6pq4609v1"))))
9aafbc0c 2502 (build-system gnu-build-system)
5143517c
KK		 2503 (native-inputs
2504 `(("autoconf" ,autoconf)
2505 ("automake" ,automake)
2506 ("gettext" ,gettext-minimal)))
9aafbc0c
MW		 2507 (inputs
2508 `(("wxwidgets" ,wxwidgets)
de477809
SB		 2509 ("maxima" ,maxima)
2510 ;; Runtime support.
2511 ("adwaita-icon-theme" ,adwaita-icon-theme)
2512 ("gtk+" ,gtk+)
2513 ("shared-mime-info" ,shared-mime-info)))
9aafbc0c 2514 (arguments
ac2ddcc6
KK		 2515 `(#:phases
2516 (modify-phases %standard-phases
2517 (add-after 'unpack 'autoconf
2518 (lambda _
2519 (zero? (system* "sh" "bootstrap"))))
2520 (add-after 'install 'wrap-program
2521 (lambda* (#:key inputs outputs #:allow-other-keys)
2522 (wrap-program (string-append (assoc-ref outputs "out")
2523 "/bin/wxmaxima")
2524 `("PATH" ":" prefix
2525 (,(string-append (assoc-ref inputs "maxima")
2526 "/bin")))
2527 ;; For GtkFileChooserDialog.
2528 `("GSETTINGS_SCHEMA_DIR" =
2529 (,(string-append (assoc-ref inputs "gtk+")
2530 "/share/glib-2.0/schemas")))
2531 `("XDG_DATA_DIRS" ":" prefix
2532 (;; Needed by gdk-pixbuf to know supported icon formats.
2533 ,(string-append
2534 (assoc-ref inputs "shared-mime-info") "/share")
2535 ;; The default icon theme of GTK+.
2536 ,(string-append
2537 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
2538 #t)))))
9aafbc0c
MW		 2539 (home-page "https://andrejv.github.io/wxmaxima/")
2540 (synopsis "Graphical user interface for the Maxima computer algebra system")
2541 (description
2542 "wxMaxima is a graphical user interface for the Maxima computer algebra
2543system. It eases the use of Maxima by making most of its commands available
2544through a menu system and by providing input dialogs for commands that require
2545more than one argument. It also implements its own display engine that
2546outputs mathematical symbols directly instead of depicting them with ASCII
2547characters.
2548
2549wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
2550text and mathematical calculations to create documents, exporting of input and
2551output to TeX, and a browser for Maxima's manual including command index and
2552full text searching.")
2553 (license license:gpl2+)))
2554
b15e47f9
RW		 2555(define-public armadillo
2556 (package
2557 (name "armadillo")
133cba8c 2558 (version "7.800.2")
b15e47f9
RW		 2559 (source (origin
2560 (method url-fetch)
2561 (uri (string-append "mirror://sourceforge/arma/armadillo-"
7397cd9e 2562 version ".tar.xz"))
b15e47f9
RW		 2563 (sha256
2564 (base32
133cba8c 2565 "1qqzy7dp891j9v7062mv1599hdwr97vqzrd3j2fl8c3gmc00dmzg"))))
b15e47f9
RW		 2566 (build-system cmake-build-system)
2567 (arguments `(#:tests? #f)) ;no test target
2568 (inputs
2569 `(("openblas" ,openblas)
2570 ("lapack" ,lapack)
2571 ("arpack" ,arpack-ng)))
2572 (home-page "http://arma.sourceforge.net/")
2573 (synopsis "C++ linear algebra library")
2574 (description
2575 "Armadillo is a C++ linear algebra library, aiming towards a good balance
2576between speed and ease of use. It is useful for algorithm development
2577directly in C++, or quick conversion of research code into production
2578environments. It can be used for machine learning, pattern recognition,
2579signal processing, bioinformatics, statistics, econometrics, etc. The library
2580provides efficient classes for vectors, matrices and cubes, as well as 150+
2581associated functions (eg. contiguous and non-contiguous submatrix views).")
fe418cc5 2582 (license license:asl2.0)))
b15e47f9 2583
279663ef 2584(define-public muparser
d7cff656
LF		 2585 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2586 ;; different hash. In order to make `guix package --upgrade` work correctly,
2587 ;; we set a Guix packaging revision.
2588 ;; When the next version of muparser is released, we can remove
2589 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2590 (let ((upstream-version "2.2.5")
2591 (revision "2"))
2592 (package
2593 (name "muparser")
2594 (version (string-append upstream-version "-" revision))
2595 (source
2596 (origin
2597 (method url-fetch)
2598 (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
2599 upstream-version ".tar.gz"))
2600 (file-name (string-append name "-" version ".tar.gz"))
2601 (sha256
2602 (base32
2603 "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
2604 (build-system gnu-build-system)
2605 (arguments
2606 `(#:configure-flags '("--enable-samples=no")
2607 #:tests? #f)) ;no "check" target
2608 (home-page "http://muparser.beltoforion.de/")
2609 (synopsis "Fast parser library for mathematical expressions")
2610 (description
2611 "muParser is an extensible high performance math parser library. It is
2612based on transforming an expression into a bytecode and precalculating constant
2613parts of it.")
2614 (license license:expat))))
279663ef 2615
e73b49fb
RW		 2616(define-public openblas
2617 (package
2618 (name "openblas")
1b8de87c 2619 (version "0.2.20")
e73b49fb
RW		 2620 (source
2621 (origin
2622 (method url-fetch)
2623 (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
2624 version))
2625 (file-name (string-append name "-" version ".tar.gz"))
2626 (sha256
2627 (base32
1b8de87c 2628 "1bd03c5xni0bla0wg1wba841b36b0sg13sjja955kn5xzvy4i61a"))))
e73b49fb
RW		 2629 (build-system gnu-build-system)
2630 (arguments
5789566a 2631 `(#:test-target "test"
bd0b4379
RW		 2632 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
2633 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2634 ;; we need to disable substitutions.
71923a91
AE		 2635 #:substitutable?
2636 ,(let ((system (or (%current-target-system) (%current-system))))
2637 (or (string-prefix? "x86_64" system)
bd0b4379 2638 (string-prefix? "i686" system)
83a34647
EF		 2639 (string-prefix? "mips" system)
2640 (string-prefix? "aarch64" system)))
e73b49fb
RW		 2641 #:make-flags
2642 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
2643 "SHELL=bash"
af5b817e
RW		 2644 ;; Build the library for all supported CPUs. This allows
2645 ;; switching CPU targets at runtime with the environment variable
2646 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
71923a91
AE		 2647 ;; Unfortunately, this is not supported on non-x86 architectures,
2648 ;; where it leads to failed builds.
2649 ,@(let ((system (or (%current-target-system) (%current-system))))
8a637e79
RW		 2650 (cond
2651 ((or (string-prefix? "x86_64" system)
71923a91 2652 (string-prefix? "i686" system))
8a637e79
RW		 2653 '("DYNAMIC_ARCH=1"))
2654 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
2655 ;; two available MIPS targets special extended instructions
2656 ;; for Loongson cores are used.
2657 ((string-prefix? "mips" system)
2658 '("TARGET=SICORTEX"))
83a34647
EF		 2659 ;; On aarch64 force the generic 'armv8-a' target
2660 ((string-prefix? "aarch64" system)
2661 '("TARGET=ARMV8"))
8a637e79 2662 (else '()))))
e73b49fb 2663 ;; no configure script
493937ae
DL		 2664 #:phases
2665 (modify-phases %standard-phases
2666 (delete 'configure)
2667 (add-before 'build 'set-extralib
2668 (lambda* (#:key inputs #:allow-other-keys)
2669 ;; Get libgfortran found when building in utest.
2670 (setenv "FEXTRALIB"
2671 (string-append "-L" (assoc-ref inputs "fortran-lib")
2672 "/lib"))
2673 #t)))))
e73b49fb 2674 (inputs
493937ae 2675 `(("fortran-lib" ,gfortran "lib")))
e73b49fb
RW		 2676 (native-inputs
2677 `(("cunit" ,cunit)
493937ae 2678 ("fortran" ,gfortran)
e73b49fb
RW		 2679 ("perl" ,perl)))
2680 (home-page "http://www.openblas.net/")
2681 (synopsis "Optimized BLAS library based on GotoBLAS")
2682 (description
2683 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
2684 (license license:bsd-3)))
2685
5a7deb11
LC		 2686(define* (make-blis implementation #:optional substitutable?)
2687 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
2688source tree for a list of implementations.)
2689
2690SUBSTITUTABLE? determines whether the package is made available as a
2691substitute.
2692
2693Currently the specialization must be selected at configure-time, but work is
2694underway to allow BLIS to select the right optimized kernels at run time:
2695<https://github.com/flame/blis/issues/129>."
2696 (package
2697 (name (if (string=? implementation "reference")
2698 "blis"
2699 (string-append "blis-" implementation)))
2700 (version "0.2.2")
2701 (home-page "https://github.com/flame/blis")
2702 (source (origin
2703 (method git-fetch)
2704 (uri (git-reference (url home-page) (commit version)))
2705 (sha256
2706 (base32
2707 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
2708 (file-name (git-file-name "blis" version))))
2709 (build-system gnu-build-system)
2710 (arguments
2711 `(#:test-target "test"
2712
2713 #:substitutable? ,substitutable?
2714
2715 #:phases (modify-phases %standard-phases
2716 (replace 'configure
2717 (lambda* (#:key outputs #:allow-other-keys)
2718 ;; This is a home-made 'configure' script.
2719 (let ((out (assoc-ref outputs "out")))
2720 (zero? (system* "./configure" "-p" out
2721 "-d" "opt"
2722 "--disable-static"
2723 "--enable-shared"
2724 "--enable-threading=openmp"
2725
2726 ,implementation)))))
2727 (add-before 'check 'show-test-output
2728 (lambda _
2729 ;; By default "make check" is silent. Make it verbose.
2730 (system "tail -F output.testsuite &")
2731 #t)))))
2732 (synopsis "High-performance basic linear algebra (BLAS) routines")
2733 (description
2734 "BLIS is a portable software framework for instantiating high-performance
2735BLAS-like dense linear algebra libraries. The framework was designed to
2736isolate essential kernels of computation that, when optimized, immediately
2737enable optimized implementations of most of its commonly used and
2738computationally intensive operations. While BLIS exports a new BLAS-like API,
2739it also includes a BLAS compatibility layer which gives application developers
2740access to BLIS implementations via traditional BLAS routine calls.")
2741 (license license:bsd-3)))
2742
2743(define-public blis
2744 ;; This is the "reference" implementation, which is the non-optimized but
2745 ;; portable variant (no assembly).
2746 (make-blis "reference" #t))
2747
2748(define ignorance blis)
2749
2750(define-syntax-rule (blis/x86_64 processor)
2751 "Expand to a package specialized for PROCESSOR."
2752 (package
2753 (inherit (make-blis processor))
2754 (supported-systems '("x86_64-linux"))))
2755
2756(define-public blis-sandybridge
2757 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
2758 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
2759 (blis/x86_64 "sandybridge"))
2760
2761(define-public blis-haswell
2762 ;; BLIS specialized for Haswell processors (launched 2013):
2763 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
2764 (blis/x86_64 "haswell"))
2765
2766(define-public blis-knl
2767 ;; BLIS specialized for Knights Landing processor (launched 2016):
2768 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
2769 (blis/x86_64 "knl"))
2770
2771
e1605e36
RW		 2772(define-public openlibm
2773 (package
2774 (name "openlibm")
26f6e565 2775 (version "0.5.1")
e1605e36
RW		 2776 (source
2777 (origin
2778 (method url-fetch)
2779 (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
2780 version ".tar.gz"))
2781 (file-name (string-append name "-" version ".tar.gz"))
2782 (sha256
2783 (base32
26f6e565 2784 "11czx2z7nh6dfpz45s3xl7v38hw36jxzxfvny454bk3if14pfakq"))))
e1605e36
RW		 2785 (build-system gnu-build-system)
2786 (arguments
2787 `(#:make-flags
2788 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2789 #:phases
2790 ;; no configure script
dc1d3cde 2791 (modify-phases %standard-phases (delete 'configure))
e1605e36
RW		 2792 #:tests? #f)) ;the tests are part of the default target
2793 (home-page "http://openlibm.org/")
2794 (synopsis "Portable C mathematical library (libm)")
2795 (description
2796 "OpenLibm is an effort to have a high quality, portable, standalone C
2797mathematical library (libm). It can be used standalone in applications and
2798programming language implementations. The project was born out of a need to
e881752c 2799have a good libm for the Julia programming language that worked consistently
e1605e36
RW		 2800across compilers and operating systems, and in 32-bit and 64-bit
2801environments.")
538c0e3b
EF		 2802 ;; Each architecture has its own make target, and there is none for mips.
2803 (supported-systems (delete "mips64el-linux" %supported-systems))
e1605e36
RW		 2804 ;; See LICENSE.md for details.
2805 (license (list license:expat
2806 license:isc
2807 license:bsd-2
2808 license:public-domain
2809 license:lgpl2.1+))))
2810
e62be58f
RW		 2811(define-public openspecfun
2812 (package
2813 (name "openspecfun")
59cd0ba4 2814 (version "0.5.3")
e62be58f
RW		 2815 (source
2816 (origin
2817 (method url-fetch)
2818 (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
2819 version ".tar.gz"))
2820 (file-name (string-append name "-" version ".tar.gz"))
2821 (sha256
2822 (base32
59cd0ba4 2823 "1rs1bv8jq751fv9vq79890wqf9xlbjc7lvz3ighzyfczbyjcf18m"))))
e62be58f
RW		 2824 (build-system gnu-build-system)
2825 (arguments
59cd0ba4 2826 '(#:tests? #f ; no "check" target
e62be58f
RW		 2827 #:make-flags
2828 (list (string-append "prefix=" (assoc-ref %outputs "out")))
59cd0ba4
TGR		 2829 #:phases
2830 (modify-phases %standard-phases
2831 (delete 'configure)))) ; no configure script
e62be58f 2832 (inputs
19afbea1 2833 `(("fortran" ,gfortran)))
e62be58f
RW		 2834 (home-page "https://github.com/JuliaLang/openspecfun")
2835 (synopsis "Collection of special mathematical functions")
2836 (description
2837 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
2838portable package for Bessel Functions of a Complex Argument and Nonnegative
2839Order; it contains subroutines for computing Bessel functions and Airy
2840functions. Faddeeva allows computing the various error functions of arbitrary
2841complex arguments (Faddeeva function, error function, complementary error
2842function, scaled complementary error function, imaginary error function, and
2843Dawson function); given these, one can also easily compute Voigt functions,
2844Fresnel integrals, and similar related functions as well.")
2845 ;; Faddeeva is released under the Expat license; AMOS is included as
2846 ;; public domain software.
2847 (license (list license:expat license:public-domain))))
2848
2742f87e
RW		 2849(define-public suitesparse
2850 (package
2851 (name "suitesparse")
bd5b5ac0 2852 (version "4.5.5")
2742f87e
RW		 2853 (source
2854 (origin
2855 (method url-fetch)
2856 (uri (string-append
2857 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
2858 version ".tar.gz"))
2859 (sha256
2860 (base32
bd5b5ac0
EB		 2861 "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
2862 (modules '((guix build utils)))
2863 (snippet
2864 ;; Remove bundled metis source
2865 '(delete-file-recursively "metis-5.1.0"))))
2742f87e
RW		 2866 (build-system gnu-build-system)
2867 (arguments
bd5b5ac0 2868 '(#:tests? #f ;no "check" target
2742f87e
RW		 2869 #:make-flags
2870 (list "CC=gcc"
2871 "BLAS=-lblas"
2872 "TBB=-ltbb"
bd5b5ac0 2873 "MY_METIS_LIB=-lmetis"
2742f87e
RW		 2874 (string-append "INSTALL_LIB="
2875 (assoc-ref %outputs "out") "/lib")
2876 (string-append "INSTALL_INCLUDE="
bd5b5ac0
EB		 2877 (assoc-ref %outputs "out") "/include")
2878 "library")
2742f87e 2879 #:phases
2509522c 2880 (modify-phases %standard-phases
bd5b5ac0 2881 (delete 'configure)))) ;no configure script
2742f87e
RW		 2882 (inputs
2883 `(("tbb" ,tbb)
bd5b5ac0
EB		 2884 ("lapack" ,lapack)
2885 ("metis" ,metis)))
2742f87e
RW		 2886 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
2887 (synopsis "Suite of sparse matrix software")
2888 (description
2889 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
2890multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
2891multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
2892simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
2893CXSparse, a concise sparse Cholesky factorization package; and many other
2894packages.")
2895 ;; LGPLv2.1+:
2896 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
2897 ;; GPLv2+:
2898 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
2899 (license (list license:gpl2+ license:lgpl2.1+))))
2900
ec322be2
FB		 2901(define-public atlas
2902 (package
2903 (name "atlas")
3c98ac02 2904 (version "3.10.3")
ec322be2
FB		 2905 (source (origin
2906 (method url-fetch)
de67e922
LF		 2907 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
2908 version "/atlas" version ".tar.bz2"))
ec322be2
FB		 2909 (sha256
2910 (base32
3c98ac02 2911 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
ec322be2
FB		 2912 (build-system gnu-build-system)
2913 (home-page "http://math-atlas.sourceforge.net/")
19afbea1 2914 (inputs `(("gfortran" ,gfortran)
ec322be2
FB		 2915 ("lapack-tar" ,(package-source lapack))))
2916 (outputs '("out" "doc"))
01480b9e
FB		 2917 ;; For the moment we drop support for MIPS at it fails to compile. See
2918 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
2919 (supported-systems (delete "mips64el-linux" %supported-systems))
ec322be2
FB		 2920 (arguments
2921 `(#:parallel-build? #f
2922 #:parallel-tests? #f
f15615b1
LC		 2923
2924 ;; ATLAS tunes itself for the machine it is built on, as explained at
2925 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
2926 ;; For this reason, we want users to build it locally instead of using
2927 ;; substitutes.
2928 #:substitutable? #f
2929
ec322be2
FB		 2930 #:modules ((srfi srfi-26)
2931 (srfi srfi-1)
2932 (guix build gnu-build-system)
2933 (guix build utils))
40029cbe 2934 #:configure-flags
ec322be2
FB		 2935 `(;; Generate position independent code suitable for dynamic libraries
2936 ;; and use WALL timer to get more accurate timing.
2937 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
2938 ;; Set word width.
2939 "-b"
2940 ,,(if (string-match "64" (%current-system))
2941 "64"
2942 "32")
2943 ;; Disable parallel build as it gives errors: atlas_pthread.h is
2944 ;; needed to compile C files before it is generated.
2945 "-Ss" "pmake" "make -j 1"
af89a667
FB		 2946 ;; Probe is failing for MIPS. We therefore define the system
2947 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
2948 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
2949 ,,@(if (string-prefix? "mips" (%current-system))
2950 (list "-A" "49" "-V" "1")
2951 (list))
ec322be2
FB		 2952 ;; Generate shared libraries.
2953 "--shared"
2954 ;; Build a full LAPACK library.
2955 ,(string-append "--with-netlib-lapack-tarfile="
2956 (assoc-ref %build-inputs "lapack-tar")))
2957 #:phases
e5b4b96b
EF		 2958 (modify-phases %standard-phases
2959 (add-after 'install 'install-doc
2960 (lambda* (#:key outputs inputs #:allow-other-keys)
2961 (let ((doc (string-append (assoc-ref outputs "doc")
2962 "/share/doc/atlas")))
2963 (mkdir-p doc)
2964 (fold (lambda (file previous)
2965 (and previous (zero? (system* "cp" file doc))))
2966 #t (find-files "../ATLAS/doc" ".*")))))
2967 (add-after 'check 'check-pt
2968 (lambda _ (zero? (system* "make" "ptcheck"))))
2969 ;; Fix files required to run configure.
2970 (add-before 'configure 'fix-/bin/sh
ec322be2
FB		 2971 (lambda _
2972 ;; Use `sh', not `/bin/sh'.
2973 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
2974 (("/bin/sh")
e5b4b96b
EF		 2975 "sh"))))
2976 ;; Fix /bin/sh in generated make files.
2977 (add-after 'configure 'fix-/bin/sh-in-generated-files
2978 (lambda _
2979 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
2980 (("/bin/sh")
2981 "sh"))))
2982 ;; ATLAS configure program does not accepts the default flags
2983 ;; passed by the 'gnu-build-system'.
2984 (replace 'configure
2985 (lambda* (#:key native-inputs inputs outputs
2986 (configure-flags '())
2987 #:allow-other-keys #:rest args)
2988 (let* ((prefix (assoc-ref outputs "out"))
2989 (bash (or (and=> (assoc-ref
2990 (or native-inputs inputs) "bash")
2991 (cut string-append <> "/bin/bash"))
2992 "/bin/sh"))
2993 (flags `(,(string-append "--prefix=" prefix)
2994 ,@configure-flags))
2995 (abs-srcdir (getcwd))
2996 (srcdir (string-append "../" (basename abs-srcdir))))
2997 (format #t "source directory: ~s (relative from build: ~s)~%"
2998 abs-srcdir srcdir)
2999 (mkdir "../build")
3000 (chdir "../build")
3001 (format #t "build directory: ~s~%" (getcwd))
3002 (format #t "configure flags: ~s~%" flags)
3003 (zero? (apply system* bash
3004 (string-append srcdir "/configure")
3005 flags))))))))
ec322be2
FB		 3006 (synopsis "Automatically Tuned Linear Algebra Software")
3007 (description
3008 "ATLAS is an automatically tuned linear algebra software library
3009providing C and Fortran77 interfaces to a portably efficient BLAS
3010implementation, as well as a few routines from LAPACK.
3011
f15615b1
LC		 3012Optimization occurs at build time. For this reason, the library is built on
3013the machine where it is installed, without resorting to pre-built substitutes.
ec322be2 3014
f15615b1 3015Before building the library, CPU throttling should be disabled. This can be
d97c429a 3016done in the BIOS, or, on GNU/Linux, with the following command:
ec322be2 3017
8e9ba611 3018@example
d97c429a 3019# cpupower --governor performance
8e9ba611 3020@end example
ec322be2 3021
d97c429a 3022Failure to do so will result in a library with poor performance.")
ec322be2 3023 (license license:bsd-3)))
c12efc72
AE		 3024
3025(define-public glm
3026 (package
3027 (name "glm")
3028 (version "0.9.6.3")
3029 (source
3030 (origin
3031 (method url-fetch)
de67e922
LF		 3032 (uri (string-append "mirror://sourceforge/ogl-math/glm-" version
3033 "/glm-" version ".zip"))
c12efc72
AE		 3034 (sha256
3035 (base32
3036 "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l"))))
3037 (build-system cmake-build-system)
3038 (native-inputs
3039 `(("unzip" ,unzip)))
3040 (home-page "http://glm.g-truc.net")
3041 (synopsis "OpenGL Mathematics library")
3042 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3043library for graphics software based on the OpenGL Shading Language (GLSL)
3044specifications.")
3045 (license license:expat)))
7f18257b
AE		 3046
3047(define-public lpsolve
3048 (package
3049 (name "lpsolve")
3050 (version "5.5.2.0")
3051 (source
3052 (origin
3053 (method url-fetch)
3054 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3055 "/lp_solve_" version "_source.tar.gz"))
3056 (sha256
3057 (base32
3058 "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq"))
3059 (modules '((guix build utils)))
3060 (snippet
3061 '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3062 (("^c=cc") "c=gcc")
3063 ;; Pretend to be on a 64 bit platform to obtain a common directory
3064 ;; name for the build results on all architectures; nothing else
3065 ;; seems to depend on it.
5dbfbef7
LC		 3066 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3067
3068 ;; The check for 'isnan' as it is written fails with
3069 ;; "non-floating-point argument in call to function
3070 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3071 ;; definition, which in turn leads to bad things. Fix the feature
3072 ;; test.
3073 (("isnan\\(0\\)") "isnan(0.)")))))
7f18257b
AE		 3074 (build-system gnu-build-system)
3075 (arguments
6c96b545 3076 `(#:tests? #f ; no check target
7f18257b
AE		 3077 #:phases
3078 (modify-phases %standard-phases
6c96b545 3079 (delete 'configure) ; no configure script
7f18257b
AE		 3080 (replace 'build
3081 (lambda _
6c96b545
TGR		 3082 (with-directory-excursion "lpsolve55"
3083 (invoke "bash" "ccc"))
3084 (with-directory-excursion "lp_solve"
3085 (invoke "bash" "ccc"))
3086 #t))
7f18257b
AE		 3087 (replace 'install
3088 (lambda* (#:key outputs #:allow-other-keys)
3089 (let* ((out (assoc-ref outputs "out"))
3090 (bin (string-append out "/bin"))
3091 (lib (string-append out "/lib"))
3092 ;; This is where LibreOffice expects to find the header
3093 ;; files, and where they are installed by Debian.
3094 (include (string-append out "/include/lpsolve")))
6c96b545
TGR		 3095 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3096 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
96c46210
LC		 3097 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3098
7f18257b
AE		 3099 ;; Install a subset of the header files as on Debian
3100 ;; (plus lp_bit.h, which matches the regular expression).
96c46210
LC		 3101 (for-each (lambda (name)
3102 (install-file name include))
3103 (find-files "." "lp_[HMSa-z].*\\.h$"))
7f18257b 3104 (with-directory-excursion "shared"
96c46210
LC		 3105 (for-each (lambda (name)
3106 (install-file name include))
3107 (find-files "." "\\.h$")))
7f18257b
AE		 3108 #t))))))
3109 (home-page "http://lpsolve.sourceforge.net/")
3110 (synopsis "Mixed integer linear programming (MILP) solver")
3111 (description
3112 "lp_solve is a mixed integer linear programming solver based on the
3113revised simplex and the branch-and-bound methods.")
3114 (license license:lgpl2.1+)))
a17d4564
EB		 3115
3116(define-public dealii
3117 (package
3118 (name "dealii")
24404eaf 3119 (version "8.5.1")
a17d4564
EB		 3120 (source
3121 (origin
3122 (method url-fetch)
3123 (uri (string-append "https://github.com/dealii/dealii/releases/"
3124 "download/v" version "/dealii-" version ".tar.gz"))
3125 (sha256
3126 (base32
24404eaf 3127 "1bh9rsmkrg0zi70n27b11djmac9lximghsiy7mg7w7x544n82gnk"))
a17d4564
EB		 3128 (modules '((guix build utils)))
3129 (snippet
3130 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
3131 '(delete-file-recursively "bundled"))))
3132 (build-system cmake-build-system)
3133 (inputs
3134 `(("tbb" ,tbb)
3135 ("zlib" ,zlib)
3136 ("boost" ,boost)
3137 ("p4est" ,p4est)
3138 ("blas" ,openblas)
3139 ("lapack" ,lapack)
3140 ("arpack" ,arpack-ng)
3141 ("muparser" ,muparser)
3142 ("gfortran" ,gfortran)
3143 ("suitesparse" ,suitesparse))) ;for UMFPACK
3144 (arguments
3145 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
d84b09e9
EB		 3146 #:configure-flags
3147 ;; Work around a bug in libsuitesparseconfig linking
3148 ;; see https://github.com/dealii/dealii/issues/4745
3149 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
a17d4564
EB		 3150 (home-page "https://www.dealii.org")
3151 (synopsis "Finite element library")
3152 (description
3153 "Deal.II is a C++ program library targeted at the computational solution
3154of partial differential equations using adaptive finite elements. The main
3155aim of deal.II is to enable rapid development of modern finite element codes,
3156using among other aspects adaptive meshes and a wide array of tools often used
3157in finite element programs.")
3158 (license license:lgpl2.1+)))
3159
3160(define-public dealii-openmpi
3161 (package (inherit dealii)
3162 (name "dealii-openmpi")
3163 (inputs
3164 `(("mpi" ,openmpi)
3165 ;;Supported only with MPI:
3166 ("p4est" ,p4est-openmpi)
3167 ("petsc" ,petsc-openmpi)
3168 ("slepc" ,slepc-openmpi)
3169 ("metis" ,metis) ;for MUMPS
3170 ("scalapack" ,scalapack) ;for MUMPS
3171 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3172 ("arpack" ,arpack-ng-openmpi)
3173 ,@(fold alist-delete (package-inputs dealii)
3174 '("p4est" "arpack"))))
3175 (arguments
3176 (substitute-keyword-arguments (package-arguments dealii)
3177 ((#:configure-flags cf)
3178 ``("-DMPI_C_COMPILER=mpicc"
3179 "-DMPI_CXX_COMPILER=mpicxx"
3180 "-DMPI_Fortran_COMPILER=mpifort"
3181 ,@,cf))))
3182 (synopsis "Finite element library (with MPI support)")))
194c7f95
AE		 3183
3184(define-public flann
3185 (package
3186 (name "flann")
3187 (version "1.8.4")
3188 (source
3189 (origin
3190 (method url-fetch)
3191 (uri
3192 (string-append
3193 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3194 version "-src.zip"))
3195 (sha256
3196 (base32
3197 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))))
3198 (build-system cmake-build-system)
6b6aca9b
LC		 3199 (outputs '("out"
3200 "octave")) ;46 MiB .mex file that pulls Octave
194c7f95
AE		 3201 (native-inputs
3202 `(("unzip" ,unzip)))
3203 (inputs
3204 `(("hdf5" ,hdf5)
3205 ("octave" ,octave)
3206 ("python" ,python-2) ; print syntax
3207 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3208 ("zlib" ,zlib)))
3209 (arguments
39b30337
LC		 3210 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3211 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3212 #:strip-directories '("lib" "lib64" "libexec"
3213 "bin" "sbin" "share/flann/octave")
3214
9684e30b
LC		 3215 ;; Save 12 MiB by not installing .a files. Passing
3216 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3217 #:phases (modify-phases %standard-phases
6b6aca9b
LC		 3218 (add-before 'configure 'set-octave-directory
3219 (lambda* (#:key outputs #:allow-other-keys)
3220 ;; Install the .mex file in the "octave" output.
3221 (let ((out (assoc-ref outputs "octave")))
3222 (substitute* "src/matlab/CMakeLists.txt"
3223 (("share/flann/octave")
3224 (string-append out "/share/flann/octave")))
3225 #t)))
9684e30b
LC		 3226 (add-after 'install 'remove-static-libraries
3227 (lambda* (#:key outputs #:allow-other-keys)
3228 (let* ((out (assoc-ref outputs "out"))
3229 (lib (string-append out "/lib")))
3230 (for-each delete-file
3231 (find-files lib "\\.a$"))
3232 #t))))
3233
39b30337 3234 #:tests? #f)) ; The test data are downloaded from the Internet.
194c7f95
AE		 3235 (home-page "http://www.cs.ubc.ca/research/flann/")
3236 (synopsis "Library for approximate nearest neighbors computation")
3237 (description "FLANN is a library for performing fast approximate
3238nearest neighbor searches in high dimensional spaces. It implements a
3239collection of algorithms and a system for automatically choosing the best
3240algorithm and optimum parameters depending on the dataset.
3241
3242FLANN is written in C++ and contains bindings for C, Octave and Python.")
3243 (license (license:non-copyleft "file://COPYING"
3244 "See COPYING in the distribution."))))
d8c97beb
EF		 3245
3246(define-public wcalc
3247 (package
3248 (name "wcalc")
3249 (version "2.5")
3250 (source
3251 (origin
3252 (method url-fetch)
de67e922
LF		 3253 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3254 "wcalc-" version ".tar.bz2"))
d8c97beb
EF		 3255 (sha256
3256 (base32
3257 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3258 (build-system gnu-build-system)
3259 (inputs
3260 `(("mpfr" ,mpfr)
3261 ("readline" ,readline)))
3262 (home-page "http://w-calc.sourceforge.net/index.php")
3263 (synopsis "Flexible command-line scientific calculator")
3264 (description "Wcalc is a very capable calculator. It has standard functions
3265(sin, asin, and sinh for example, in either radians or degrees), many
3266pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3267variables, a command history, hex/octal/binary input and output, unit
3268conversions, embedded comments, and an expandable expression entry field. It
3269evaluates expressions using the standard order of operations.")
3270 (license license:gpl2+)))
45147b0c
FH		 3271
3272(define-public xaos
3273 (package
3274 (name "xaos")
3275 (version "3.6")
3276 (source (origin
3277 (method url-fetch)
de67e922
LF		 3278 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3279 "/xaos-" version ".tar.gz"))
45147b0c
FH		 3280 (sha256
3281 (base32
3282 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3283 (build-system gnu-build-system)
b94a6ca0 3284 (native-inputs `(("gettext" ,gettext-minimal)))
45147b0c
FH		 3285 (inputs `(("libx11" ,libx11)
3286 ("zlib" ,zlib)
3287 ("libpng" ,libpng)
3288 ("gsl" ,gsl)))
3289 (arguments
3290 `(#:tests? #f ;no "check" target
3291 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3292 (synopsis "Real-time fractal zoomer")
3293 (description "GNU XaoS is a graphical program that generates fractal
3294patterns and allows you to zoom in and out of them infinitely in a fluid,
3295continuous manner. It also includes tutorials that help to explain how fractals
3296are built. It can generate many different fractal types such as the Mandelbrot
3297set.")
6fd52309 3298 (home-page "https://www.gnu.org/software/xaos/")
45147b0c 3299 (license license:gpl2+)))
528bb464
EB		 3300
3301(define-public hypre
3302 (package
3303 (name "hypre")
3304 (version "2.11.0")
3305 (source (origin
3306 (method url-fetch)
3307 (uri (string-append "https://github.com/LLNL/hypre/archive/"
3308 "v" version ".tar.gz"))
3309 (file-name (string-append name "-" version ".tar.gz"))
3310 (sha256
3311 (base32
3312 "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m"))
3313 (modules '((guix build utils)))
3314 (snippet
3315 '(begin
3316 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
3317 ;; substitute the tarball creation time.
3318 (substitute* "src/utilities/HYPRE_utilities.h"
3319 (("Date Compiled: .*$")
3320 "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n"))
3321 #t))))
3322 (build-system gnu-build-system)
3323 (outputs '("out" ;6.1 MiB of headers and libraries
3324 "doc")) ;4.8 MiB of documentation
3325 (native-inputs
3326 `(("doc++" ,doc++)
3327 ("netpbm" ,netpbm)
3328 ("texlive" ,texlive) ;full package required for fonts
3329 ("ghostscript" ,ghostscript)))
3330 (inputs
3331 `(("blas" ,openblas)
3332 ("lapack" ,lapack)))
3333 (arguments
3334 `(#:modules ((srfi srfi-1)
3335 ,@%gnu-build-system-modules)
3336 #:configure-flags '("--enable-shared"
3337 "--disable-fortran"
3338 "--without-MPI"
3339 "--with-openmp"
3340 "--with-fei"
3341 "--with-lapack"
3342 "--with-blas")
3343 #:phases
3344 (modify-phases %standard-phases
3345 (add-before 'configure 'chdir-src
3346 (lambda _ (chdir "src")))
3347 (replace 'configure
3348 (lambda* (#:key build target configure-flags
3349 #:allow-other-keys #:rest args)
3350 (let* ((configure (assoc-ref %standard-phases 'configure)))
3351 (apply configure
3352 (append args
3353 (list #:configure-flags
3354 (cons (string-append
3355 "--host=" (or target build))
3356 configure-flags)))))))
3357 (add-after 'build 'build-docs
3358 (lambda _
3359 (zero? (system* "make" "-Cdocs" "pdf" "html"))))
3360 (replace 'check
3361 (lambda _
3362 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3363 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
3364 (and (system* "make" "check" "CHECKRUN=")
3365 (fold (lambda (filename result)
3366 (and result
3367 (let ((size (stat:size (stat filename))))
3368 (when (not (zero? size))
3369 (format #t "~a size ~d; error indication~%"
3370 filename size))
3371 (zero? size))))
3372 #t
3373 (find-files "test" ".*\\.err$")))))
3374 (add-after 'install 'install-docs
3375 (lambda* (#:key outputs #:allow-other-keys)
3376 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3377 (let* ((doc (assoc-ref outputs "doc"))
3378 (docdir (string-append doc "/share/doc/hypre-" ,version)))
528bb464
EB		 3379 (with-directory-excursion "docs"
3380 (for-each (lambda (base)
3381 (install-file (string-append base ".pdf") docdir)
3382 (copy-recursively base docdir)) ;html docs
3383 '("HYPRE_usr_manual"
3384 "HYPRE_ref_manual")))
3385 #t))))))
3386 (home-page "http://www.llnl.gov/casc/hypre/")
3387 (synopsis "Library of solvers and preconditioners for linear equations")
3388 (description
3389 "HYPRE is a software library of high performance preconditioners and
3390solvers for the solution of large, sparse linear systems of equations. It
3391features multigrid solvers for both structured and unstructured grid
3392problems.")
3393 (license license:lgpl2.1)))
3394
3395(define-public hypre-openmpi
3396 (package (inherit hypre)
3397 (name "hypre-openmpi")
3398 (inputs
3399 `(("mpi" ,openmpi)
3400 ,@(package-inputs hypre)))
3401 (arguments
3402 (substitute-keyword-arguments (package-arguments hypre)
3403 ((#:configure-flags flags)
3404 ``("--with-MPI"
3405 ,@(delete "--without-MPI" ,flags)))))
3406 (synopsis "Parallel solvers and preconditioners for linear equations")
3407 (description
3408 "HYPRE is a software library of high performance preconditioners and
3409solvers for the solution of large, sparse linear systems of equations on
3410parallel computers. It features parallel multigrid solvers for both
3411structured and unstructured grid problems.")))
6c90e183
EB		 3412
3413(define-public matio
3414 (package
3415 (name "matio")
3416 (version "1.5.6")
3417 (source
3418 (origin
3419 (method url-fetch)
de67e922 3420 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
6c90e183
EB		 3421 "matio-" version ".tar.gz"))
3422 (sha256
3423 (base32
3424 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3425 (build-system gnu-build-system)
3426 (inputs
3427 `(("zlib" ,zlib)
3428 ("hdf5" ,hdf5)))
3429 (home-page "http://matio.sourceforge.net/")
3430 (synopsis "Library for reading and writing MAT files")
3431 (description "Matio is a library for reading and writing MAT files. It
3432supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3433 (license license:bsd-2)))
d721c83a 3434
517318ad
LF		 3435(define-public vc
3436 (package
3437 (name "vc")
3438 (version "1.2.0")
3439 (source
3440 (origin (method url-fetch)
3441 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3442 "download/" version "/Vc-" version ".tar.gz"))
3443 (sha256
3444 (base32
3445 "1rh6dhqar3y07n4xqyml0sa0v48qv3ch9dc3yc2in855hlh4vnqi"))))
3446 (build-system cmake-build-system)
3447 (arguments
3448 '(#:configure-flags
3449 '("-DBUILD_TESTING=ON")))
3450 (synopsis "SIMD vector classes for C++")
3451 (description "Vc provides portable, zero-overhead C++ types for explicitly
3452data-parallel programming. It is a library designed to ease explicit
3453vectorization of C++ code. Its types enable explicitly stating data-parallel
3454operations on multiple values. The parallelism is therefore added via the type
3455system. Vc has an intuitive API and provides portability between different
3456compilers and compiler versions as well as portability between different vector
3457instruction sets. Thus, an application written with Vc can be compiled for:
3458@enumerate
3459@item AVX and AVX2
d1e4ad1b 3460@item SSE2 up to SSE4.2 or SSE4a
517318ad
LF		 3461@item Scalar
3462@item MIC
3463@item NEON (in development)
3464@item NVIDIA GPUs / CUDA (in development)
3465@end enumerate\n")
3466 (home-page "https://github.com/VcDevel/Vc")
a8ead6f9
EF		 3467 ;; "No support_???.cpp file exists for this architecture."
3468 (supported-systems '("x86_64-linux" "i686-linux"))
517318ad 3469 (license license:bsd-3)))
54052a54 3470
3471(define-public reducelcs
3472 ;; This is the last commit which is available upstream, no
3473 ;; release happened since 2010.
3474 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
3475 (revision "1"))
3476 (package
3477 (name "reducelcs")
3478 (version (string-append "1.0-" revision "." (string-take commit 7)))
3479 (source
3480 (origin
3481 (method git-fetch)
3482 (uri (git-reference
3483 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
3484 (commit commit)))
3485 (file-name (string-append name "-" version "-checkout"))
3486 (sha256
3487 (base32
3488 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
3489 (build-system gnu-build-system)
3490 (inputs
3491 `(("openlibm" ,openlibm)))
3492 (arguments
3493 `(#:tests? #f ; no tests
3494 #:phases
3495 (modify-phases %standard-phases
3496 (delete 'configure) ; No configure script exists.
3497 (replace 'install ; No install phase exists.
3498 (lambda* (#:key outputs #:allow-other-keys)
3499 (let* ((out (assoc-ref outputs "out"))
3500 (bin (string-append out "/bin")))
3501 (install-file "Approximation" bin)
3502 (install-file "CollectResults" bin)
3503 (install-file "GenerateInstances" bin)
3504 #t))))))
3505 (synopsis "Approximate Longest Commons Subsequence computation tool")
3506 (description
3507 "@code{reduceLCS} is an implementation of the Reduce-Expand
3508algorithm for LCS. It is a fast program to compute the approximate
3509Longest Commons Subsequence of a set of strings.")
3510 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
c000b6b1 3511 (license license:gpl3+))))
479c4273
JD		 3512
3513(define-public jacal
3514 (package
3515 (name "jacal")
3516 (version "1c4")
3517 (source (origin
3518 (method url-fetch)
3519 (uri (string-append
3520 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
3521 version ".zip"))
3522 (sha256 (base32
3523 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
3524 (patches (search-patches "jacal-fix-texinfo.patch"))))
3525 (build-system gnu-build-system)
3526 (arguments
3527 `(#:phases
3528 (modify-phases %standard-phases
3529 (add-before 'build 'pre-build
3530 ;; Don't use upstream's script - it really doesn't fit into
3531 ;; Guix's functional paradigm.
3532 (lambda* (#:key inputs outputs #:allow-other-keys)
3533 (substitute* "Makefile"
3534 (("^install: install-script") "install: "))))
3535 (add-after 'install 'post-install
3536 ;; Instead, we provide our own simplified script.
3537 (lambda* (#:key inputs outputs #:allow-other-keys)
3538 (let ((wrapper (string-append (assoc-ref outputs "out")
3539 "/bin/jacal")))
3540 (format (open wrapper (logior O_WRONLY O_CREAT))
3541 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
3542 "-e '(slib:load \"~a/lib/jacal/math\") "
3543 "(math)' \"$@\"\n")
3544 (which "bash")
3545 (assoc-ref inputs "scm")
3546 (assoc-ref outputs "out"))
3547 (chmod wrapper #o555))))
3548 (replace 'configure
3549 (lambda* (#:key inputs outputs #:allow-other-keys)
3550 (zero? (system* "./configure"
3551 (string-append "--prefix="
3552 (assoc-ref outputs "out")))))))))
3553 (inputs `(("scm" ,scm)))
3554 (native-inputs `(("unzip" ,unzip)
3555 ("texinfo" ,texinfo)))
3556 (synopsis "Symbolic mathematics system")
3557 (description "GNU JACAL is an interactive symbolic mathematics program based on
3558Scheme. It manipulate and simplify a range of mathematical expressions such
3559as equations, scalars, vectors, and matrices.")
6fd52309 3560 (home-page "https://www.gnu.org/software/jacal/")
479c4273
JD		 3561 (license license:gpl3+)))
3562
313844d9
TF		 3563(define-public z3
3564 (package
3565 (name "z3")
3566 (version "4.5.0")
3567 (source (origin
3568 (method url-fetch)
3569 (uri (string-append
3570 "https://github.com/Z3Prover/z3/archive/z3-"
3571 version ".tar.gz"))
3572 (sha256
3573 (base32
3574 "032a5lvji2liwmc25jv52bdrhimqflvqbpg77ccaq1jykhiivbmf"))))
cf684d87 3575 (build-system cmake-build-system)
313844d9 3576 (arguments
cf684d87
TF		 3577 `(#:configure-flags
3578 (list "-DBUILD_PYTHON_BINDINGS=true"
3579 "-DINSTALL_PYTHON_BINDINGS=true"
3580 (string-append "-DCMAKE_INSTALL_PYTHON_PKG_DIR="
3581 %output
677bc34d 3582 "/lib/python2.7/site-packages"))
313844d9
TF		 3583 #:phases
3584 (modify-phases %standard-phases
cf684d87
TF		 3585 (add-before 'configure 'bootstrap
3586 (lambda _
313844d9 3587 (zero?
cf684d87
TF		 3588 (system* "python" "contrib/cmake/bootstrap.py" "create"))))
3589 (add-before 'check 'make-test-z3
313844d9 3590 (lambda _
cf684d87
TF		 3591 ;; Build the test suite executable.
3592 (zero? (system* "make" "test-z3" "-j"
3593 (number->string (parallel-job-count))))))
3594 (replace 'check
3595 (lambda _
3596 ;; Run all the tests that don't require arguments.
3597 (zero? (system* "./test-z3" "/a")))))))
313844d9
TF		 3598 (native-inputs
3599 `(("python" ,python-2)))
3600 (synopsis "Theorem prover")
3601 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
cf684d87 3602theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
313844d9
TF		 3603 (home-page "https://github.com/Z3Prover/z3")
3604 (license license:expat)))
3d5d87a3
JL		 3605
3606(define-public cubicle
3607 (package
3608 (name "cubicle")
3609 (version "1.1.1")
3610 (source (origin
3611 (method url-fetch)
3612 (uri (string-append "http://cubicle.lri.fr/cubicle-"
3613 version ".tar.gz"))
3614 (sha256
3615 (base32
3616 "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h"))))
3617 (build-system gnu-build-system)
3618 (native-inputs
3619 `(("ocaml" ,ocaml)
83fef82b 3620 ("which" ,(@@ (gnu packages base) which))))
3d5d87a3
JL		 3621 (propagated-inputs
3622 `(("z3" ,z3)))
3623 (arguments
3624 `(#:configure-flags (list "--with-z3")
3625 #:tests? #f
3626 #:phases
3627 (modify-phases %standard-phases
3628 (add-before 'configure 'configure-for-release
3629 (lambda _
3630 (substitute* "Makefile.in"
3631 (("SVNREV=") "#SVNREV="))))
3632 (add-before 'configure 'fix-/bin/sh
3633 (lambda _
3634 (substitute* "configure"
3635 (("/bin/sh") (which "sh")))))
3636 (add-before 'configure 'fix-smt-z3wrapper.ml
3637 (lambda _
3638 (substitute* "Makefile.in"
3639 (("\\\\n") "")))))))
3640 (home-page "http://cubicle.lri.fr/")
3641 (synopsis "Model checker for array-based systems")
5a80c15c
RW		 3642 (description "Cubicle is a model checker for verifying safety properties
3643of array-based systems. This is a syntactically restricted class of
3644parametrized transition systems with states represented as arrays indexed by
3645an arbitrary number of processes. Cache coherence protocols and mutual
3646exclusion algorithms are typical examples of such systems.")
3d5d87a3 3647 (license license:asl2.0)))
e01397b4
EB		 3648
3649(define-public elemental
3650 (package
3651 (name "elemental")
3652 (version "0.87.7")
3653 (source (origin
3654 (method url-fetch)
3655 (uri (string-append "https://github.com/elemental/Elemental/"
3656 "archive/v" version ".tar.gz"))
3657 (file-name (string-append name "-" version ".tar.gz"))
3658 (sha256
3659 (base32
3660 "1nfp82w22pi8x8fg9sc37z8kf84dqi1dhxp8bbk7571y4aygvv3v"))))
3661 (build-system cmake-build-system)
3662 (home-page "http://libelemental.org")
3663 (native-inputs
3664 `(("gfortran" ,gfortran)))
3665 (inputs
3666 `(("blas" ,openblas)
3667 ("gfortran:lib" ,gfortran "lib")
3668 ("gmp" ,gmp)
3669 ("lapack" ,lapack)
3670 ("metis" ,metis)
3671 ("mpc" ,mpc)
3672 ("mpfr" ,mpfr)
3673 ("mpi" ,openmpi)
3674 ("qd" ,qd)))
3675 (arguments
3676 `(#:build-type "Release" ;default RelWithDebInfo not supported
3677 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
3678 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
3679 "-DEL_CACHE_WARNINGS:BOOL=YES"
3680 "-DEL_TESTS:BOOL=YES"
3681 "-DCMAKE_INSTALL_LIBDIR=lib"
3682 "-DGFORTRAN_LIB=gfortran")
3683 #:phases (modify-phases %standard-phases
3684 (add-before 'check 'setup-tests
3685 (lambda _
3686 ;; Parallelism is done at the MPI layer.
3687 (setenv "OMP_NUM_THREADS" "1")
3688 #t))
3689 (add-after 'install 'remove-tests
3690 (lambda* (#:key outputs #:allow-other-keys)
3691 ;; Tests are installed, with no easy configuration
3692 ;; switch to prevent this, so delete them.
3693 (delete-file-recursively
3694 (string-append (assoc-ref outputs "out") "/bin"))
3695 #t)))))
3696 (synopsis "Dense and sparse-direct linear algebra and optimization")
3697 (description "Elemental is a modern C++ library for distributed-memory
3698dense and sparse-direct linear algebra, conic optimization, and lattice
3699reduction.")
3700 (license license:bsd-2)))
5b05dce7
JN		 3701
3702(define-public mcrl2
3703 (package
3704 (name "mcrl2")
3705 (version "201707.1.15162")
3706 (source (origin
3707 (method url-fetch)
3708 (uri (string-append "http://www.mcrl2.org/download/devel/mcrl2-"
3709 version
3710 ".tar.gz"))
3711 (sha256
3712 (base32
3713 "1ziww2fchsklm25hl9p2mngssxfh9w07nc114cncqaxfibqp2p8f"))))
3714 (native-inputs
3715 `(("subversion" ,subversion)))
3716 (inputs
3717 `(("boost" ,boost)
3718 ("glu" ,glu)
3719 ("mesa" ,mesa)
3720 ("qt" ,qt)))
3721 (build-system cmake-build-system)
ed0c5d3c 3722 (synopsis "Toolset for the mCRL2 formal specification language")
5b05dce7 3723 (description
ed0c5d3c
TGR		 3724 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
3725specification language for describing concurrent discrete event systems. Its
3726toolset supports analysis and automatic verification, linearisation, simulation,
3727state-space exploration and generation, and tools to optimise and analyse
5b05dce7
JN		 3728specifications. Also, state spaces can be manipulated, visualised and
3729analysed.")
3730 (home-page "http://mcrl2.org")
3731 (license license:boost1.0)))
jackhill's copy of GNU Guix: https://guix.gnu.org/