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gnu: Add quakespasm.
[jackhill/guix/guix.git] / gnu / packages / maths.scm
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8f8b2451 1;;; GNU Guix --- Functional package management for GNU
b146763a 2;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
da95c817 3;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
a53d6719 4;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
41a46a50 5;;; Copyright © 2014, 2015, 2016, 2017 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>
612a387f 8;;; Copyright © 2015, 2016, 2017 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>
440c4273 23;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
8f8b2451
AE		 24;;;
25;;; This file is part of GNU Guix.
26;;;
27;;; GNU Guix is free software; you can redistribute it and/or modify it
28;;; under the terms of the GNU General Public License as published by
29;;; the Free Software Foundation; either version 3 of the License, or (at
30;;; your option) any later version.
31;;;
32;;; GNU Guix is distributed in the hope that it will be useful, but
33;;; WITHOUT ANY WARRANTY; without even the implied warranty of
34;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
35;;; GNU General Public License for more details.
36;;;
37;;; You should have received a copy of the GNU General Public License
38;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
39
40(define-module (gnu packages maths)
ec322be2 41 #:use-module (ice-9 regex)
8f8b2451 42 #:use-module (gnu packages)
b5b73a82 43 #:use-module ((guix licenses) #:prefix license:)
8f8b2451
AE		 44 #:use-module (guix packages)
45 #:use-module (guix download)
54052a54 46 #:use-module (guix git-download)
0e2672ae 47 #:use-module (guix utils)
cec86422 48 #:use-module (guix build utils)
da95c817 49 #:use-module (guix build-system cmake)
c9dfa3c7 50 #:use-module (guix build-system gnu)
ba1be533 51 #:use-module (guix build-system ocaml)
ec8c7e47 52 #:use-module (guix build-system r)
3de01d3f 53 #:use-module (gnu packages algebra)
5143517c 54 #:use-module (gnu packages autotools)
3de01d3f 55 #:use-module (gnu packages bison)
a17d4564 56 #:use-module (gnu packages boost)
e73b49fb 57 #:use-module (gnu packages check)
3de01d3f 58 #:use-module (gnu packages cmake)
c9dfa3c7 59 #:use-module (gnu packages compression)
668c06ac 60 #:use-module (gnu packages curl)
b7b27a8f 61 #:use-module (gnu packages cyrus-sasl)
528bb464 62 #:use-module (gnu packages documentation)
57e544e8 63 #:use-module (gnu packages elf)
3de01d3f 64 #:use-module (gnu packages flex)
668c06ac 65 #:use-module (gnu packages fltk)
f3929800 66 #:use-module (gnu packages fontutils)
1dba6407 67 #:use-module (gnu packages gettext)
da95c817 68 #:use-module (gnu packages gcc)
73fed4f8 69 #:use-module (gnu packages gd)
668c06ac 70 #:use-module (gnu packages ghostscript)
889187a4 71 #:use-module (gnu packages graphviz)
f3929800 72 #:use-module (gnu packages gtk)
45147b0c 73 #:use-module (gnu packages image)
2fd26d05 74 #:use-module (gnu packages java)
668c06ac 75 #:use-module (gnu packages less)
8731e527 76 #:use-module (gnu packages lisp)
bc3a2e35 77 #:use-module (gnu packages logging)
6e64766a 78 #:use-module (gnu packages lua)
5698b8b8 79 #:use-module (gnu packages gnome)
1b39a196 80 #:use-module (gnu packages guile)
668c06ac
JD		 81 #:use-module (gnu packages xorg)
82 #:use-module (gnu packages gl)
9f913401 83 #:use-module (gnu packages imagemagick)
8731e527 84 #:use-module (gnu packages m4)
d8c7eeb9 85 #:use-module (gnu packages mpi)
b92eee75 86 #:use-module (gnu packages multiprecision)
528bb464 87 #:use-module (gnu packages netpbm)
ba1be533 88 #:use-module (gnu packages ocaml)
668c06ac 89 #:use-module (gnu packages pcre)
5698b8b8 90 #:use-module (gnu packages popt)
c9dfa3c7
AE		 91 #:use-module (gnu packages perl)
92 #:use-module (gnu packages pkg-config)
da95c817 93 #:use-module (gnu packages python)
589e3f4e 94 #:use-module (gnu packages python-web)
c9dfa3c7 95 #:use-module (gnu packages readline)
2742f87e 96 #:use-module (gnu packages tbb)
479c4273 97 #:use-module (gnu packages scheme)
b7194849 98 #:use-module (gnu packages shells)
df354a77 99 #:use-module (gnu packages tcl)
668c06ac 100 #:use-module (gnu packages texinfo)
8f9ac901 101 #:use-module (gnu packages tex)
b7b27a8f 102 #:use-module (gnu packages tls)
9aafbc0c 103 #:use-module (gnu packages wxwidgets)
c12efc72 104 #:use-module (gnu packages xml)
a17d4564 105 #:use-module (srfi srfi-1))
8f8b2451 106
193abc82
JD		 107(define-public aris
108 (package
1f45f18a
JD		 109 (name "aris")
110 (version "2.2")
111 (source (origin
112 (method url-fetch)
113 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
114 (sha256 (base32
115 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
116 (build-system gnu-build-system)
117 (inputs `(("gtk+" ,gtk+)
118 ("libxml2" ,libxml2)))
119 (native-inputs `(("pkg-config" ,pkg-config)))
120 (synopsis "Natural deduction first-order logic interface")
121 (description "Aris is a program for performing logical proofs. It supports
122propositional and predicate logic, as well as Boolean algebra and
123arithmetical logic. In addition to its predefined inference and equivalence
124rules, Aris also supports references to older proofs. Its use of standard
125logical symbols and its natural deduction interface make it easy to use for
126beginners.")
127 (license license:gpl3+)
6fd52309 128 (home-page "https://www.gnu.org/software/aris/")))
193abc82 129
9c45c519
JD		 130(define-public c-graph
131 (package
132 (name "c-graph")
133 (version "2.0")
134 (source (origin
135 (method url-fetch)
136 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
137 ".tar.gz"))
138 (sha256 (base32
139 "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
140 (build-system gnu-build-system)
141 (inputs
142 `(("fortran" ,gfortran)))
a3947cb1 143 (synopsis "Visualizing and demonstrating convolution")
9c45c519 144 (description
a3947cb1
LC		 145 "GNU C-Graph is a tool for demonstrating the theory of convolution.
146Thus, it can serve as an excellent aid to students of signal and systems
147theory in visualizing the convolution process. Rather than forcing the
148student to write code, the program offers an intuitive interface with
149interactive dialogs to guide them.")
9c45c519 150 (license license:gpl3+)
6fd52309 151 (home-page "https://www.gnu.org/software/c-graph/")))
9c45c519 152
d91025e3
TD		 153(define-public coda
154 (package
155 (name "coda")
440c4273 156 (version "2.18.3")
d91025e3
TD		 157 (source
158 (origin
159 (method url-fetch)
160 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
161 version "/coda-" version ".tar.gz"))
162 (sha256
440c4273 163 (base32 "1zlzgcvwmmjm8mw8w4rg2rqy0pjilz7kyyxm0y4p8cbljbbjxxz0"))
4b12fe5c
TD		 164 (patches (search-patches "coda-use-system-libs.patch"))
165 (modules '((guix build utils)))
166 (snippet
167 ;; Make sure we don't use the bundled software.
168 '(for-each (lambda (d)
169 (delete-file-recursively (string-append "libcoda/" d)))
170 '("zlib" "pcre" "expat")))))
d91025e3
TD		 171 (native-inputs
172 `(("fortran" ,gfortran)
173 ("python" ,python)
174 ("python-numpy" ,python-numpy)))
175 (inputs
176 `(("zlib" ,zlib)
4b12fe5c
TD		 177 ("pcre" ,pcre)
178 ("expat" ,expat)
d91025e3
TD		 179 ("hdf4" ,hdf4-alt)
180 ("hdf5" ,hdf5)))
181 (build-system gnu-build-system)
182 (arguments
4b12fe5c
TD		 183 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
184 "LIBS= -lz -lpcre -lexpat")))
d91025e3
TD		 185 (synopsis "A common interface to various earth observation data formats")
186 (description
187 "The Common Data Access toolbox (CODA) provides a set of interfaces for
188reading remote sensing data from earth observation data files. It consists of
189command line applications and interfaces to the C, Fortran, Python, and Java
190programming languages.")
191 (home-page "https://stcorp.nl/coda")
192 (license license:gpl2+)))
193
8f8b2451
AE		 194(define-public units
195 (package
196 (name "units")
f11d2849 197 (version "2.16")
8f8b2451
AE		 198 (source (origin
199 (method url-fetch)
200 (uri (string-append "mirror://gnu/units/units-" version
201 ".tar.gz"))
202 (sha256 (base32
f11d2849 203 "11hnp3gcmcc5kci2caxw4hs6m08h2mhqs3xzqq7iafx1ha2ggwyw"))))
8f8b2451 204 (build-system gnu-build-system)
0498d248 205 (inputs
a2549713
EB		 206 `(("readline" ,readline)
207 ("python" ,python-wrapper) ;for 'units_cur' script
0498d248
EB		 208 ("python-requests" ,python-requests)))
209 (arguments
210 `(#:phases (modify-phases %standard-phases
211 (add-after 'install 'wrap-units_cur
212 (lambda* (#:key outputs #:allow-other-keys)
213 (let* ((out (assoc-ref outputs "out"))
214 (bin (string-append out "/bin")))
215 (wrap-program (string-append bin "/units_cur")
216 `("PYTHONPATH" ":" prefix
217 ,(search-path-as-string->list (getenv "PYTHONPATH"))))
218 #t))))))
8f8b2451
AE		 219 (synopsis "Conversion between thousands of scales")
220 (description
574e86f9 221 "GNU Units converts numeric quantities between units of measure. It
7c125ce0
AK		 222can handle scale changes through adaptive usage of standard scale
223prefixes (micro-, kilo-, etc.). It can also handle nonlinear
224conversions such as Fahrenheit to Celsius. Its interpreter is powerful
225enough to be used effectively as a scientific calculator.")
8f8b2451 226 (license license:gpl3+)
6fd52309 227 (home-page "https://www.gnu.org/software/units/")))
c9dfa3c7 228
61a529b4
RW		 229(define-public double-conversion
230 (package
231 (name "double-conversion")
232 (version "1.1.5")
233 (source (origin
234 (method url-fetch)
235 (uri (string-append
236 "https://github.com/floitsch/double-conversion/archive/v"
237 version ".tar.gz"))
238 (file-name (string-append name "-" version ".tar.gz"))
239 (sha256
240 (base32
241 "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83"))))
242 (build-system cmake-build-system)
243 (arguments
244 '(#:test-target "test"
245 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
246 "-DBUILD_TESTING=ON")))
247 (home-page "https://github.com/floitsch/double-conversion")
248 (synopsis "Conversion routines for IEEE doubles")
249 (description
250 "The double-conversion library provides binary-decimal and decimal-binary
251routines for IEEE doubles. The library consists of efficient conversion
252routines that have been extracted from the V8 JavaScript engine.")
253 (license license:bsd-3)))
254
182d6311
ML		 255(define-public dionysus
256 (package
257 (name "dionysus")
258 (version "1.3.0")
259 (source (origin
260 (method url-fetch)
261 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
262 ".tar.gz"))
263 (sha256
264 (base32
265 "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs"))))
266 (build-system gnu-build-system)
267 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
268 (synopsis "Local search for universal constants and scientific values")
269 (description
270 "GNU Dionysus is a convenient system for quickly retrieving the values of
271mathematical constants used in science and engineering. Values can be
272searched using a simple command-line tool, choosing from three databases:
273universal constants, atomic numbers, and constants related to
274semiconductors.")
275 (license license:gpl3+)
6fd52309 276 (home-page "https://www.gnu.org/software/dionysus/")))
182d6311 277
88bd1804
AE		 278(define-public gsl
279 (package
280 (name "gsl")
f885fc05 281 (version "2.4")
ab2cc5cd
LC		 282 (source (origin
283 (method url-fetch)
284 (uri (string-append "mirror://gnu/gsl/gsl-"
285 version ".tar.gz"))
286 (sha256
287 (base32
f885fc05 288 "16yfs5n444s03np1naj6yp1fsysd42kdscxzkg0k2yvfjixx0ijd"))
ab2cc5cd 289 (patches (search-patches "gsl-test-i686.patch"))))
88bd1804 290 (build-system gnu-build-system)
71e0f288 291 (arguments
f885fc05 292 `(;; Currently there are numerous tests that fail on "exotic"
6f766069
EF		 293 ;; architectures such as aarch64 and ppc64le.
294 ,@(if (string-prefix? "aarch64-linux"
295 (or (%current-target-system) (%current-system)))
296 '(#:tests? #f)
297 '())))
298 (home-page "https://www.gnu.org/software/gsl/")
88bd1804
AE		 299 (synopsis "Numerical library for C and C++")
300 (description
a22dc0c4
LC		 301 "The GNU Scientific Library is a library for numerical analysis in C
302and C++. It includes a wide range of mathematical routines, with over 1000
303functions in total. Subject areas covered by the library include:
304differential equations, linear algebra, Fast Fourier Transforms and random
305numbers.")
88bd1804
AE		 306 (license license:gpl3+)))
307
ba1be533
BW		 308(define-public ocaml-gsl
309 (package
310 (name "ocaml-gsl")
311 (version "1.19.3")
312 (source
313 (origin
314 (method url-fetch)
315 (uri
316 (string-append
317 "https://github.com/mmottl/gsl-ocaml/releases/download/v"
318 version"/gsl-ocaml-" version ".tar.gz"))
319 (sha256
320 (base32
321 "0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh"))))
322 (build-system ocaml-build-system)
323 (inputs
324 `(("gsl" ,gsl)))
325 (home-page "https://mmottl.github.io/gsl-ocaml")
326 (synopsis "Bindings to the GNU Scientific Library")
327 (description
328 "GSL-OCaml is an interface to the @dfn{GNU scientific library} (GSL) for
329the OCaml language.")
330 (license license:gpl3+)))
331
7adaab9f
BW		 332(define-public ocaml4.01-gsl
333 (package-with-ocaml4.01 ocaml-gsl))
334
b92eee75
AE		 335(define-public glpk
336 (package
337 (name "glpk")
dec2ade1 338 (version "4.64")
b92eee75
AE		 339 (source
340 (origin
341 (method url-fetch)
342 (uri (string-append "mirror://gnu/glpk/glpk-"
343 version ".tar.gz"))
344 (sha256
345 (base32
dec2ade1 346 "096cqgjc7vkq6wd8znhcxjbs1s2rym3qf753fqxrrq531vs6g4jk"))))
b92eee75
AE		 347 (build-system gnu-build-system)
348 (inputs
349 `(("gmp" ,gmp)))
350 (arguments
351 `(#:configure-flags '("--with-gmp")))
82110ef6 352 (home-page "https://www.gnu.org/software/glpk/")
79c311b8 353 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
b92eee75
AE		 354 (description
355 "GLPK is a C library for solving large-scale linear programming (LP),
356mixed integer programming (MIP), and other related problems. It supports the
357GNU MathProg modeling language, a subset of the AMPL language, and features a
358translator for the language. In addition to the C library, a stand-alone
359LP/MIP solver is included in the package.")
360 (license license:gpl3+)))
361
b146763a
AE		 362(define-public 4ti2
363 (package
364 (name "4ti2")
365 (version "1.6.7")
366 (source
367 (origin
368 (method url-fetch)
369 (uri (string-append "http://www.4ti2.de/version_" version
370 "/4ti2-" version ".tar.gz"))
371 (sha256
372 (base32
373 "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
374 (build-system gnu-build-system)
375 (native-inputs
376 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
377 (inputs
378 `(("glpk" ,glpk)
379 ("gmp" ,gmp)))
380 (home-page "http://www.4ti2.de/")
381 (synopsis "Mathematical tool suite for problems on linear spaces")
382 (description
383 "4ti2 implements algorithms for solving algebraic, geometric and
384combinatorial problems on linear spaces. Among others, it solves systems
385of linear equations, computes extreme rays of polyhedral cones, solves
386integer programming problems and computes Markov bases for statistics.")
387 (license license:gpl2+)))
388
53696f10
AE		 389(define-public cddlib
390 (package
391 (name "cddlib")
392 (version "0.94h")
393 (source
394 (origin
395 (method url-fetch)
182dde82 396 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
53696f10
AE		 397 (string-delete #\. version) ".tar.gz"))
398 (sha256
399 (base32
400 "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy"))))
401 (build-system gnu-build-system)
402 (inputs
403 `(("gmp" ,gmp)))
404 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
405 (synopsis "Library for convex hulls and extreme rays of polyhedra")
406 (description
407 "The C-library cddlib implements the Double Description Method of
408Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
409rays of a general convex polyhedron given by a system of linear inequalities
410in arbitrary dimension. It can also be used for the converse operation of
411computing convex hulls.")
412 (license license:gpl2+)))
413
865a69dd
RW		 414(define-public arpack-ng
415 (package
416 (name "arpack-ng")
417 (version "3.2.0")
418 (source
419 (origin
420 (method url-fetch)
421 (uri (string-append "https://github.com/opencollab/arpack-ng/archive/"
422 version ".tar.gz"))
f586c877 423 (file-name (string-append name "-" version ".tar.gz"))
865a69dd
RW		 424 (sha256
425 (base32
426 "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff"))))
427 (build-system gnu-build-system)
428 (home-page "https://github.com/opencollab/arpack-ng")
429 (inputs
430 `(("lapack" ,lapack)
19afbea1 431 ("fortran" ,gfortran)))
865a69dd
RW		 432 (synopsis "Fortran subroutines for solving eigenvalue problems")
433 (description
434 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
435large scale eigenvalue problems.")
166191b3 436 (license (license:non-copyleft "file://COPYING"
865a69dd
RW		 437 "See COPYING in the distribution."))))
438
8c94c886
EB		 439(define-public arpack-ng-openmpi
440 (package (inherit arpack-ng)
441 (name "arpack-ng-openmpi")
442 (inputs
443 `(("mpi" ,openmpi)
444 ,@(package-inputs arpack-ng)))
445 (arguments `(#:configure-flags '("--enable-mpi")))
446 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
447
da95c817
NK		 448(define-public lapack
449 (package
450 (name "lapack")
ef39a177 451 (version "3.7.1")
da95c817
NK		 452 (source
453 (origin
454 (method url-fetch)
455 (uri (string-append "http://www.netlib.org/lapack/lapack-"
456 version ".tgz"))
457 (sha256
458 (base32
7c0d4c3a 459 "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
da95c817
NK		 460 (build-system cmake-build-system)
461 (home-page "http://www.netlib.org/lapack/")
19afbea1 462 (inputs `(("fortran" ,gfortran)
da95c817
NK		 463 ("python" ,python-2)))
464 (arguments
3ab869b6
LC		 465 `(#:configure-flags (list
466 ;; Install to PREFIX/lib (the default is
467 ;; PREFIX/lib64).
468 (string-append "-DCMAKE_INSTALL_LIBDIR="
469 (assoc-ref %outputs "out")
470 "/lib")
11f0c4e8 471
3ab869b6
LC		 472 "-DBUILD_SHARED_LIBS:BOOL=YES"
473 "-DLAPACKE=ON"
474
475 ;; Build the 'LAPACKE_clatms' functions.
476 "-DLAPACKE_WITH_TMG=ON")
dc1d3cde
KK		 477 #:phases
478 (modify-phases %standard-phases
479 (add-before 'check 'patch-python
480 (lambda* (#:key inputs #:allow-other-keys)
481 (let ((python (assoc-ref inputs "python")))
482 (substitute* "lapack_testing.py"
483 (("/usr/bin/env python") python)))
484 #t)))))
da95c817
NK		 485 (synopsis "Library for numerical linear algebra")
486 (description
487 "LAPACK is a Fortran 90 library for solving the most commonly occurring
488problems in numerical linear algebra.")
166191b3 489 (license (license:non-copyleft "file://LICENSE"
da95c817 490 "See LICENSE in the distribution."))))
73fed4f8 491
b509efb3
TF		 492(define-public lapack-3.5
493 (package
494 (inherit lapack)
495 (version "3.5.0")
496 (source
497 (origin
498 (method url-fetch)
499 (uri (string-append "http://www.netlib.org/lapack/lapack-"
500 version ".tgz"))
501 (sha256
502 (base32
503 "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s"))))))
504
e1ff597a
EB		 505(define-public scalapack
506 (package
507 (name "scalapack")
508 (version "2.0.2")
509 (source
510 (origin
511 (method url-fetch)
512 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
513 version ".tgz"))
514 (sha256
515 (base32
516 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
517 (build-system cmake-build-system)
518 (inputs
519 `(("mpi" ,openmpi)
520 ("fortran" ,gfortran)
521 ("lapack" ,lapack))) ;for testing only
522 (arguments
523 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")))
524 (home-page "http://www.netlib.org/scalapack/")
525 (synopsis "Library for scalable numerical linear algebra")
526 (description
527 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
528routines on parallel distributed memory machines. ScaLAPACK solves dense and
529banded linear systems, least squares problems, eigenvalue problems, and
530singular value problems.")
531 (license (license:bsd-style "file://LICENSE"
532 "See LICENSE in the distribution."))))
533
73fed4f8 534(define-public gnuplot
5f800540
KK		 535 (package
536 (name "gnuplot")
7d873e0c 537 (version "5.0.6")
5f800540
KK		 538 (source (origin
539 (method url-fetch)
540 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
541 version "/gnuplot-"
542 version ".tar.gz"))
543 (sha256
544 (base32
7d873e0c 545 "0q5lr6nala3ln6f3yp6g17ziymb9r9gx9zylnw1y3hjmwl9lggjv"))))
5f800540
KK		 546 (build-system gnu-build-system)
547 (inputs `(("readline" ,readline)
548 ("cairo" ,cairo)
549 ("pango" ,pango)
6e64766a
DM		 550 ("gd" ,gd)
551 ("lua" ,lua)))
612a387f
RW		 552 (native-inputs
553 `(("pkg-config" ,pkg-config)
554 ("texlive" ,texlive-tiny)))
5f800540
KK		 555 (home-page "http://www.gnuplot.info")
556 (synopsis "Command-line driven graphing utility")
557 (description "Gnuplot is a portable command-line driven graphing
35b9e423 558utility. It was originally created to allow scientists and students to
73fed4f8 559visualize mathematical functions and data interactively, but has grown to
35b9e423 560support many non-interactive uses such as web scripting. It is also used as a
73fed4f8 561plotting engine by third-party applications like Octave.")
5f800540
KK		 562 ;; X11 Style with the additional restriction that derived works may only be
563 ;; distributed as patches to the original.
564 (license (license:fsf-free
565 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
668c06ac 566
32f70e1f
TD		 567(define-public gctp
568 (package
569 (name "gctp")
570 (version "2.0.0")
571 (source
572 (origin
573 (method url-fetch)
574 (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
575 version ".tar.gz"))
576 (file-name (string-append name "-" version ".tar.gz"))
577 (sha256
578 (base32
579 "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
580 (native-inputs
581 `(("fortran" ,gfortran)))
582 (build-system gnu-build-system)
583 (synopsis "General Cartographic Transformation Package (GCTP)")
584 (description
585 "The General Cartographic Transformation Package (GCTP) is a system of
586software routines designed to permit the transformation of coordinate pairs
587from one map projection to another. The GCTP is the standard computer
588software used by the National Mapping Division for map projection
589computations.")
590 (home-page "https://github.com/OkoSanto/GCTP")
0f7cd95b 591 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
32f70e1f 592
becbbefc
TD		 593(define-public hdf4
594 (package
595 (name "hdf4")
0abf5264 596 (version "4.2.13")
becbbefc
TD		 597 (source
598 (origin
599 (method url-fetch)
600 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
601 version "/src/hdf-" version ".tar.bz2"))
602 (sha256
0abf5264 603 (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
15ca49b2
AE		 604 (patches (search-patches "hdf4-architectures.patch"
605 "hdf4-reproducibility.patch"
becbbefc 606 "hdf4-shared-fortran.patch"))))
becbbefc
TD		 607 (build-system gnu-build-system)
608 (native-inputs
609 `(("gfortran" ,gfortran)
610 ("bison" ,bison)
611 ("flex" ,flex)))
612 (inputs
613 `(("zlib" ,zlib)
614 ("libjpeg" ,libjpeg)))
615 (arguments
616 `(#:parallel-tests? #f
617 #:configure-flags '("--enable-shared")
618 #:phases
619 (modify-phases %standard-phases
953a12fa
EF		 620 ;; This is inspired by two of Debian's patches.
621 (add-before 'configure 'add-more-aarch64-support
622 (lambda _
623 (substitute* '("mfhdf/ncgen/ncgen.l"
624 "mfhdf/ncgen/ncgenyy.c"
625 "mfhdf/libsrc/netcdf.h.in")
626 (("AIX5L64") "__aarch64__"))
627 #t))
becbbefc
TD		 628 (add-before 'configure 'patchbuild
629 (lambda _
630 (substitute*
631 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
632 (("/bin/rm") "rm")
633 (("/bin/mkdir") "mkdir"))
634 (substitute* (find-files "." "^Makefile\\.in$")
635 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
636-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
637 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
638-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
953a12fa 639-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
e464b455
TD		 640 #t))
641 (add-after 'configure 'patch-settings
642 (lambda _
643 ;; libhdf4.settings contains the full path of the
644 ;; compilers used, and its contents are included in
645 ;; .so-files. We truncate the hashes to avoid
646 ;; unnecessary store references to those compilers:
647 (substitute* "libhdf4.settings"
648 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
649 (string-append prefix (string-take hash 10) "...")))
650 #t))
651 )))
becbbefc
TD		 652 (home-page "https://www.hdfgroup.org/products/hdf4/")
653 (synopsis
654 "Library and multi-object file format for storing and managing data")
655 (description "HDF4 is a library and multi-object file format for storing
656and managing data between machines. HDF4 is an older hierarchical data format,
657incompatible with HDF5.")
658 (license
659 (license:non-copyleft
660 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
661
662(define-public hdf4-alt
663 (package
664 (inherit hdf4)
665 (name "hdf4-alt")
666 (arguments
667 (substitute-keyword-arguments (package-arguments hdf4)
668 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
669 (synopsis
670 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
671
7ee3f1a2
JD		 672(define-public hdf5
673 (package
674 (name "hdf5")
2da63064 675 (version "1.8.19")
7ee3f1a2
JD		 676 (source
677 (origin
678 (method url-fetch)
2da63064
TD		 679 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
680 "hdf5-" (version-major+minor version)
681 "/hdf5-" version "/src/hdf5-"
dcd9d163
LF		 682 version ".tar.bz2")
683 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
684 "current"
685 (apply string-append
686 (take (string-split version #\.) 2))
687 "/src/hdf5-" version ".tar.bz2")))
7ee3f1a2 688 (sha256
2da63064 689 (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
b8d9c93b 690 (patches (list (search-patch "hdf5-config-date.patch")))))
7ee3f1a2 691 (build-system gnu-build-system)
12ed1216
AE		 692 (inputs
693 `(("zlib" ,zlib)))
e3a1a1de
TD		 694 (native-inputs
695 `(("gfortran" ,gfortran)))
696 (outputs '("out" ; core library
697 "fortran")) ; fortran interface
7ee3f1a2 698 (arguments
62126576 699 `(;; Some of the users, notably Flann, need the C++ interface.
e3a1a1de
TD		 700 #:configure-flags '("--enable-cxx"
701 "--enable-fortran"
702 "--enable-fortran2003")
62126576
LC		 703
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) "...")))
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"))
1363 (sha256
1364 (base32
1365 "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
1366 (build-system cmake-build-system)
1367 (arguments
1368 '(#:configure-flags
1369 (list "-DOCE_TESTING:BOOL=ON"
1370 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1371 "-DOCE_DRAW:BOOL=ON"
1372 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1373 (assoc-ref %outputs "out"))
1374 "-UCMAKE_INSTALL_RPATH")))
1375 (inputs
1376 `(("freetype" ,freetype)
1377 ("glu" ,glu)
1378 ("libxmu" ,libxmu)
1379 ("mesa" ,mesa)
1380 ("tcl" ,tcl)
1381 ("tk" ,tk)))
1382 (native-inputs
1383 `(("python" ,python-wrapper)))
1384 (home-page "https://github.com/tpaviot/oce")
1385 (synopsis "Libraries for 3D modeling and numerical simulation")
1386 (description
1387 "Open CASCADE is a set of libraries for the development of applications
1388dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1389C++ class libraries providing services for 3D surface and solid modeling, CAD
1390data exchange, and visualization. It is used for development of specialized
1391software dealing with 3D models in design (CAD), manufacturing (CAM),
1392numerical simulation (CAE), measurement equipment (CMM), and quality
1393control (CAQ) domains.
1394
1395This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1396patches, improvements, and experiments contributed by users over the official
1397Open CASCADE library.")
1398 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1399 ; use of header files; see
1400 ; OCCT_LGPL_EXCEPTION.txt
1401 license:public-domain; files
1402 ; src/Standard/Standard_StdAllocator.hxx and
1403 ; src/NCollection/NCollection_StdAllocator.hxx
1404 license:expat; file src/OpenGl/OpenGl_glext.h
1405 license:bsd-3)))); test framework gtest
1406
3de01d3f
EB		 1407(define-public gmsh
1408 (package
1409 (name "gmsh")
8a4d14fa 1410 (version "2.16.0")
3de01d3f
EB		 1411 (source
1412 (origin
1413 (method url-fetch)
1c79e086 1414 (uri (string-append "http://gmsh.info/src/gmsh-"
3de01d3f
EB		 1415 version "-source.tgz"))
1416 (sha256
8a4d14fa 1417 (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
3de01d3f
EB		 1418 (modules '((guix build utils)))
1419 (snippet
1420 ;; Remove non-free METIS code
1421 '(delete-file-recursively "contrib/Metis"))))
1422 (build-system cmake-build-system)
3de01d3f
EB		 1423 (propagated-inputs
1424 `(("fltk" ,fltk)
19afbea1 1425 ("gfortran" ,gfortran)
3de01d3f 1426 ("gmp" ,gmp)
40029cbe 1427 ("hdf5" ,hdf5)
3de01d3f
EB		 1428 ("lapack" ,lapack)
1429 ("mesa" ,mesa)
85f41902 1430 ("glu" ,glu)
45548139 1431 ("opencascade-oce" ,opencascade-oce)
3de01d3f
EB		 1432 ("libx11" ,libx11)
1433 ("libxext" ,libxext)))
66395a61
EF		 1434 (inputs
1435 `(("fontconfig" ,fontconfig)
1436 ("libxft" ,libxft)))
3de01d3f
EB		 1437 (arguments
1438 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1439 "-DENABLE_BUILD_SHARED:BOOL=ON"
45548139 1440 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
3de01d3f
EB		 1441 (home-page "http://www.geuz.org/gmsh/")
1442 (synopsis "3D finite element grid generator")
edf684ef
EB		 1443 (description "Gmsh is a 3D finite element grid generator with a built-in
1444CAD engine and post-processor. Its design goal is to provide a fast, light
1445and user-friendly meshing tool with parametric input and advanced
1446visualization capabilities. Gmsh is built around four modules: geometry,
1447mesh, solver and post-processing. The specification of any input to these
1448modules is done either interactively using the graphical user interface or in
1449ASCII text files using Gmsh's own scripting language.")
3de01d3f 1450 (license license:gpl2+)))
b9100e2f 1451
6d5f63b6
JD		 1452(define-public maxflow
1453 (package
1454 (name "maxflow")
1455 (version "3.04")
1456 (source (origin
1457 (method git-fetch)
1458 (uri (git-reference
1459 (url "https://github.com/gerddie/maxflow.git")
1460 (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
1461 (file-name (string-append name "-" version "-checkout"))
1462 (sha256
1463 (base32
1464 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1465 (build-system cmake-build-system)
1466 (home-page "http://pub.ist.ac.at/~vnk/software.html")
1467 (synopsis "Library implementing Maxflow algorithm")
1468 (description "An implementation of the maxflow algorithm described in
1469@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1470Energy Minimization in Computer Vision.\n
1471Yuri Boykov and Vladimir Kolmogorov.\n
1472In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1473September 2004}")
1474 (license license:gpl3+)))
1475
b9100e2f
EB		 1476(define-public petsc
1477 (package
1478 (name "petsc")
6fec298d 1479 (version "3.8.0")
b9100e2f
EB		 1480 (source
1481 (origin
1482 (method url-fetch)
1483 ;; The *-lite-* tarball does not contain the *large* documentation
1484 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1485 "petsc-lite-" version ".tar.gz"))
1486 (sha256
6fec298d 1487 (base32 "1lajbk3c29hnh83v6cbmm3a8wv6bdykh0p70kwrr4vrnizalk88s"))))
b9100e2f
EB		 1488 (build-system gnu-build-system)
1489 (native-inputs
6fec298d 1490 `(("python" ,python-2)))
b9100e2f 1491 (inputs
19afbea1 1492 `(("gfortran" ,gfortran)
b9100e2f 1493 ("lapack" ,lapack)
f258212d 1494 ("superlu" ,superlu)
b9100e2f
EB		 1495 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1496 ;; leaving out opengl, as configuration seems to only be for mac
1497 ))
1498 (arguments
1499 `(#:test-target "test"
9a899cce 1500 #:parallel-build? #f ;build is parallel by default
b9100e2f
EB		 1501 #:configure-flags
1502 `("--with-mpi=0"
f258212d
EB		 1503 "--with-openmp=1"
1504 "--with-superlu=1"
1505 ,(string-append "--with-superlu-include="
1506 (assoc-ref %build-inputs "superlu") "/include")
1507 ,(string-append "--with-superlu-lib="
1508 (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
9731c412
EB		 1509 #:make-flags
1510 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1511 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1512 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
b9100e2f 1513 #:phases
64dcc289
EB		 1514 (modify-phases %standard-phases
1515 (replace 'configure
1516 ;; PETSc's configure script is actually a python script, so we can't
1517 ;; run it with bash.
1518 (lambda* (#:key outputs (configure-flags '())
1519 #:allow-other-keys)
1520 (let* ((prefix (assoc-ref outputs "out"))
1521 (flags `(,(string-append "--prefix=" prefix)
1522 ,@configure-flags)))
1523 (format #t "build directory: ~s~%" (getcwd))
1524 (format #t "configure flags: ~s~%" flags)
1525 (zero? (apply system* "./configure" flags)))))
1526 (add-after 'configure 'clean-local-references
9731c412 1527 (lambda* (#:key outputs #:allow-other-keys)
64dcc289
EB		 1528 (let ((out (assoc-ref outputs "out")))
1529 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
b730b437
EB		 1530 ;; Prevent build directory from leaking into compiled code
1531 (((getcwd)) out)
1532 ;; Scrub timestamp for reproducibility
fafd623e 1533 ((".*Libraries compiled on.*") ""))
9731c412
EB		 1534 (substitute* (find-files "." "petscvariables")
1535 ;; Do not expose build machine characteristics, set to defaults.
1536 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1537 (("NPMAX = [:digit:]+") "NPMAX = 2"))
fafd623e 1538 #t)))
64dcc289 1539 (add-after 'install 'clean-install
10b11968
EB		 1540 ;; Try to keep installed files from leaking build directory names.
1541 (lambda* (#:key inputs outputs #:allow-other-keys)
64dcc289 1542 (let ((out (assoc-ref outputs "out")))
10b11968 1543 (substitute* (map (lambda (file)
9a899cce 1544 (string-append out "/lib/petsc/conf/" file))
fafd623e 1545 '("petscvariables"))
10b11968
EB		 1546 (((getcwd)) out))
1547 ;; Make compiler references point to the store
9a899cce 1548 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
dfdf5716
EB		 1549 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1550 (string-append "= " (which compiler))))
10b11968
EB		 1551 ;; PETSc installs some build logs, which aren't necessary.
1552 (for-each (lambda (file)
9a899cce 1553 (let ((f (string-append out "/lib/petsc/conf/" file)))
10b11968
EB		 1554 (when (file-exists? f)
1555 (delete-file f))))
9a899cce
EB		 1556 '("configure.log" "make.log" "gmake.log"
1557 "test.log" "error.log" "RDict.db"
fafd623e 1558 "PETScBuildInternal.cmake"
10b11968 1559 ;; Once installed, should uninstall with Guix
fafd623e
EB		 1560 "uninstall.py"))
1561 #t))))))
b9100e2f 1562 (home-page "http://www.mcs.anl.gov/petsc")
16ecf3ff 1563 (synopsis "Library to solve PDEs")
b9100e2f
EB		 1564 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1565data structures and routines for the scalable (parallel) solution of
1566scientific applications modeled by partial differential equations.")
166191b3 1567 (license (license:non-copyleft
b9100e2f
EB		 1568 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1569
1570(define-public petsc-complex
1571 (package (inherit petsc)
1572 (name "petsc-complex")
1573 (arguments
1574 (substitute-keyword-arguments (package-arguments petsc)
1575 ((#:configure-flags cf)
1576 `(cons "--with-scalar-type=complex" ,cf))))
16ecf3ff 1577 (synopsis "Library to solve PDEs (with complex scalars)")))
183e44ae 1578
d8c7eeb9
EB		 1579(define-public petsc-openmpi
1580 (package (inherit petsc)
1581 (name "petsc-openmpi")
1582 (inputs
1583 `(("openmpi" ,openmpi)
1584 ,@(package-inputs petsc)))
1585 (arguments
1586 (substitute-keyword-arguments (package-arguments petsc)
1587 ((#:configure-flags cf)
1588 ``("--with-mpiexec=mpirun"
1589 ,(string-append "--with-mpi-dir="
1590 (assoc-ref %build-inputs "openmpi"))
1591 ,@(delete "--with-mpi=0" ,cf)))))
16ecf3ff 1592 (synopsis "Library to solve PDEs (with MPI support)")))
d8c7eeb9
EB		 1593
1594(define-public petsc-complex-openmpi
1595 (package (inherit petsc-complex)
1596 (name "petsc-complex-openmpi")
1597 (inputs
1598 `(("openmpi" ,openmpi)
1599 ,@(package-inputs petsc-complex)))
1600 (arguments
1601 (substitute-keyword-arguments (package-arguments petsc-complex)
1602 ((#:configure-flags cf)
1603 ``("--with-mpiexec=mpirun"
1604 ,(string-append "--with-mpi-dir="
1605 (assoc-ref %build-inputs "openmpi"))
1606 ,@(delete "--with-mpi=0" ,cf)))))
16ecf3ff 1607 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
d8c7eeb9 1608
a7f01414
EB		 1609(define-public slepc
1610 (package
1611 (name "slepc")
958b5a1c 1612 (version "3.8.0")
a7f01414
EB		 1613 (source
1614 (origin
1615 (method url-fetch)
baeaf882
EB		 1616 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
1617 version ".tar.gz"))
a7f01414
EB		 1618 (sha256
1619 (base32
958b5a1c 1620 "0qyrsdndfdw2g0jmj9iskxj3j20zlkplhv26288s079dhm7cr365"))))
a7f01414
EB		 1621 (build-system gnu-build-system)
1622 (native-inputs
1623 `(("python" ,python-2)))
1624 (inputs
1625 `(("arpack" ,arpack-ng)
1626 ("gfortran" ,gfortran)))
1627 (propagated-inputs
1628 `(("petsc" ,petsc)))
1629 (arguments
1630 `(#:parallel-build? #f ;build is parallel by default
1631 #:configure-flags
1632 `(,(string-append "--with-arpack-dir="
9cf52454 1633 (assoc-ref %build-inputs "arpack") "/lib"))
9731c412
EB		 1634 #:make-flags ;honor (parallel-job-count)
1635 `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
a7f01414
EB		 1636 #:phases
1637 (modify-phases %standard-phases
8787c555 1638 (replace 'configure
a7f01414
EB		 1639 ;; configure is a python script, so we can't run it with bash.
1640 (lambda* (#:key inputs outputs (configure-flags '())
1641 #:allow-other-keys)
1642 (let* ((prefix (assoc-ref outputs "out"))
1643 (flags `(,(string-append "--prefix=" prefix)
1644 ,@configure-flags)))
1645 (format #t "build directory: ~s~%" (getcwd))
1646 (format #t "configure flags: ~s~%" flags)
1647 (setenv "SLEPC_DIR" (getcwd))
9cf52454 1648 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
a7f01414 1649 (zero? (apply system* "./configure" flags)))))
8787c555 1650 (add-after 'install 'delete-doc
a7f01414
EB		 1651 ;; TODO: SLEPc installs HTML documentation alongside headers in
1652 ;; $out/include. We'd like to move them to share/doc, but delete
1653 ;; them for now, as they are incomplete and installing the complete
1654 ;; documentation is difficult.
1655 (lambda* (#:key outputs #:allow-other-keys)
1656 (let* ((out (assoc-ref outputs "out")))
1657 (for-each delete-file (find-files out "\\.html$")))))
8787c555 1658 (add-after 'install 'clean-install
a7f01414
EB		 1659 ;; Clean up unnecessary build logs from installation.
1660 (lambda* (#:key outputs #:allow-other-keys)
1661 (let ((out (assoc-ref outputs "out")))
1662 (for-each (lambda (file)
1663 (let ((f (string-append out "/lib/slepc/conf/" file)))
1664 (when (file-exists? f)
1665 (delete-file f))))
1666 '("configure.log" "make.log" "gmake.log"
1667 "test.log" "error.log" "RDict.db"
1668 "uninstall.py"))))))))
1669 (home-page "http://slepc.upv.es")
1670 (synopsis "Scalable library for eigenproblems")
1671 (description "SLEPc is a software library for the solution of large sparse
1672eigenproblems on parallel computers. It can be used for the solution of
1673linear eigenvalue problems formulated in either standard or generalized form,
1674as well as other related problems such as the singular value decomposition.
1675The emphasis of the software is on methods and techniques appropriate for
1676problems in which the associated matrices are sparse, for example, those
1677arising after the discretization of partial differential equations.")
1678 (license license:lgpl3)))
1679
1680(define-public slepc-complex
1681 (package (inherit slepc)
1682 (name "slepc-complex")
1683 (propagated-inputs
1684 `(("petsc" ,petsc-complex)
1685 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1686 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1687
1688(define-public slepc-openmpi
1689 (package (inherit slepc)
1690 (name "slepc-openmpi")
1691 (inputs
1692 `(("mpi" ,openmpi)
1693 ("arpack" ,arpack-ng-openmpi)
1694 ,@(alist-delete "arpack" (package-inputs slepc))))
1695 (propagated-inputs
1696 `(("petsc" ,petsc-openmpi)
1697 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1698 (synopsis "Scalable library for eigenproblems (with MPI support)")))
1699
1700(define-public slepc-complex-openmpi
1701 (package (inherit slepc-openmpi)
1702 (name "slepc-complex-openmpi")
1703 (propagated-inputs
1704 `(("petsc" ,petsc-complex-openmpi)
1705 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1706 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1707
cec86422
EB		 1708(define-public mumps
1709 (package
1710 (name "mumps")
fba78d18 1711 (version "5.0.2")
cec86422
EB		 1712 (source
1713 (origin
1714 (method url-fetch)
1715 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
1716 version ".tar.gz"))
1717 (sha256
1718 (base32
fba78d18 1719 "0igyc1pfzxdhpbad3v3lb86ixkdbqa1a8gbs15b04r2294h2nabp"))
fc1adab1 1720 (patches (search-patches "mumps-build-parallelism.patch"))))
cec86422
EB		 1721 (build-system gnu-build-system)
1722 (inputs
1723 `(("fortran" ,gfortran)
1724 ;; These are required for linking against mumps, but we let the user
1725 ;; declare the dependency.
1726 ("blas" ,openblas)
1727 ("metis" ,metis)
1728 ("scotch" ,scotch)))
1729 (arguments
1730 `(#:modules ((ice-9 match)
1731 (ice-9 popen)
1732 (srfi srfi-1)
1733 ,@%gnu-build-system-modules)
1734 #:phases
1735 (modify-phases %standard-phases
fba78d18 1736 (replace 'configure
cec86422
EB		 1737 (lambda* (#:key inputs #:allow-other-keys)
1738 (call-with-output-file "Makefile.inc"
1739 (lambda (port)
1740 (format port "
1741PLAT =
1742LIBEXT = .a
1743OUTC = -o
1744OUTF = -o
1745RM = rm -f~:[
1746CC = gcc
1747FC = gfortran
1748FL = gfortran
1749INCSEQ = -I$(topdir)/libseq
1750LIBSEQ = -L$(topdir)/libseq -lmpiseq
1751LIBSEQNEEDED = libseqneeded~;
1752CC = mpicc
1753FC = mpifort
1754FL = mpifort~]
1755AR = ar vr # rules require trailing space, ugh...
1756RANLIB = ranlib
1757LIBBLAS = -L~a -lopenblas~@[
1758SCALAP = -L~a -lscalapack~]
1759LIBOTHERS = -pthread
1760CDEFS = -DAdd_
1761PIC = -fPIC
1762OPTF = -O2 -DALLOW_NON_INIT $(PIC)
1763OPTL = -O2 $(PIC)
1764OPTC = -O2 $(PIC)
1765INCS = $(INCSEQ)
1766LIBS = $(SCALAP) $(LIBSEQ)
1767LPORDDIR = $(topdir)/PORD/lib
1768IPORD = -I$(topdir)/PORD/include
1769LPORD = -L$(LPORDDIR) -lpord
1770ORDERINGSF = -Dpord~@[
1771METISDIR = ~a
1772IMETIS = -I$(METISDIR)/include
1773LMETIS = -L$(METISDIR)/lib -lmetis
1774ORDERINGSF += -Dmetis~]~@[~:{
1775SCOTCHDIR = ~a
1776ISCOTCH = -I$(SCOTCHDIR)/include
1777LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
1778ORDERINGSF += ~a~}~]
1779ORDERINGSC = $(ORDERINGSF)
1780LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
1781IORDERINGSF = $(ISCOTCH)
1782IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
1783 (assoc-ref inputs "mpi")
1784 (assoc-ref inputs "blas")
1785 (assoc-ref inputs "scalapack")
1786 (assoc-ref inputs "metis")
1787 (match (list (assoc-ref inputs "pt-scotch")
1788 (assoc-ref inputs "scotch"))
1789 ((#f #f)
1790 #f)
1791 ((#f scotch)
1792 `((,scotch "" "-Dscotch")))
1793 ((ptscotch _)
1794 `((,ptscotch
1795 "-lptesmumps -lptscotch -lptscotcherr "
1796 "-Dptscotch")))))))))
fba78d18 1797 (replace 'build
cec86422
EB		 1798 ;; By default only the d-precision library is built. Make with "all"
1799 ;; target so that all precision libraries and examples are built.
1800 (lambda _
1801 (zero? (system* "make" "all"
1802 (format #f "-j~a" (parallel-job-count))))))
fba78d18 1803 (replace 'check
cec86422
EB		 1804 ;; Run the simple test drivers, which read test input from stdin:
1805 ;; from the "real" input for the single- and double-precision
1806 ;; testers, and from the "cmplx" input for complex-precision
1807 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
1808 ;; package to prefix execution with "mpirun".
1809 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
1810 (with-directory-excursion "examples"
1811 (every
1812 (lambda (prec type)
1813 (let ((tester (apply open-pipe*
1814 `(,OPEN_WRITE
1815 ,@exec-prefix
1816 ,(string-append "./" prec
1817 "simpletest"))))
1818 (input (open-input-file
1819 (string-append "input_simpletest_" type))))
1820 (begin
1821 (dump-port input tester)
1822 (close-port input)
1823 (zero? (close-pipe tester)))))
1824 '("s" "d" "c" "z")
1825 '("real" "real" "cmplx" "cmplx")))))
fba78d18
EB		 1826 (replace 'install
1827 (lambda* (#:key outputs #:allow-other-keys)
1828 (let* ((out (assoc-ref outputs "out"))
1829 (libdir (string-append out "/lib")))
1830 (copy-recursively "lib" libdir)
1831 (copy-recursively "include" (string-append out "/include"))
1832 (when (file-exists? "libseq/libmpiseq.a")
1833 (install-file "libseq/libmpiseq.a" libdir))
1834 #t))))))
cec86422
EB		 1835 (home-page "http://mumps.enseeiht.fr")
1836 (synopsis "Multifrontal sparse direct solver")
1837 (description
1838 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
1839sparse system of linear equations A x = b using Guassian elimination.")
1840 (license license:cecill-c)))
1841
1842(define-public mumps-metis
1843 (package (inherit mumps)
1844 (name "mumps-metis")
1845 (inputs
1846 (alist-delete "scotch" (package-inputs mumps)))))
1847
1848(define-public mumps-openmpi
1849 (package (inherit mumps)
1850 (name "mumps-openmpi")
1851 (inputs
1852 `(("mpi" ,openmpi)
1853 ("scalapack" ,scalapack)
1854 ("pt-scotch" ,pt-scotch)
1855 ,@(alist-delete "scotch" (package-inputs mumps))))
1856 (arguments
1857 (substitute-keyword-arguments (package-arguments mumps)
1858 ((#:phases phases)
1859 `(modify-phases ,phases
1860 (replace
1861 'check
1862 (lambda _
1863 ((assoc-ref ,phases 'check)
1864 #:exec-prefix '("mpirun" "-n" "2"))))))))
1865 (synopsis "Multifrontal sparse direct solver (with MPI)")))
1866
1867(define-public mumps-metis-openmpi
1868 (package (inherit mumps-openmpi)
1869 (name "mumps-metis-openmpi")
1870 (inputs
1871 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
1872
2d047896
RW		 1873(define-public r-quadprog
1874 (package
1875 (name "r-quadprog")
1876 (version "1.5-5")
1877 (source
1878 (origin
1879 (method url-fetch)
1880 (uri (cran-uri "quadprog" version))
1881 (sha256
1882 (base32
1883 "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
1884 (build-system r-build-system)
1885 (native-inputs
1886 `(("gfortran" ,gfortran)))
1887 (home-page "http://cran.r-project.org/web/packages/quadprog")
1888 (synopsis "Functions to solve quadratic programming problems")
1889 (description
1890 "This package contains routines and documentation for solving quadratic
1891programming problems.")
1892 (license license:gpl3+)))
1893
ec8c7e47
RJ		 1894(define-public r-pracma
1895 (package
1896 (name "r-pracma")
05fd8e6b 1897 (version "2.1.1")
ec8c7e47
RJ		 1898 (source (origin
1899 (method url-fetch)
1900 (uri (cran-uri "pracma" version))
1901 (sha256
05fd8e6b 1902 (base32 "1mylrrkyycaw9m01mmg6xkn5wgdlabs5l0qyws60r0n2ycblp897"))))
ec8c7e47 1903 (build-system r-build-system)
ccd9b151
RW		 1904 (propagated-inputs
1905 `(("r-quadprog" ,r-quadprog)))
ec8c7e47
RJ		 1906 (home-page "http://cran.r-project.org/web/packages/pracma")
1907 (synopsis "Practical numerical math functions")
1908 (description "This package provides functions for numerical analysis and
1909linear algebra, numerical optimization, differential equations, plus some
1910special functions. It uses Matlab function names where appropriate to simplify
1911porting.")
1912 (license license:gpl3+)))
1913
183e44ae
EB		 1914(define-public superlu
1915 (package
1916 (name "superlu")
995a09e0 1917 (version "5.2.1")
183e44ae
EB		 1918 (source
1919 (origin
1920 (method url-fetch)
1921 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1922 "superlu_" version ".tar.gz"))
1923 (sha256
995a09e0
EB		 1924 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
1925 (modules '((guix build utils)))
1926 (snippet
1927 ;; Replace the non-free implementation of MC64 with a stub adapted
1928 ;; from Debian
1929 '(begin
1930 (use-modules (ice-9 regex)
1931 (ice-9 rdelim))
1932 (call-with-output-file "SRC/mc64ad.c"
1933 (lambda (port)
1934 (display "
1935#include <stdio.h>
1936#include <stdlib.h>
1937void mc64id_(int *a) {
1938 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
1939 abort ();
1940}
1941void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
1942 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
1943 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
1944 abort ();
1945}\n" port)))
1946 ;; Remove the corresponding license verbiage. MC64 license follows
1947 ;; a "------" line separator.
1948 (with-atomic-file-replacement "License.txt"
1949 (let ((rx (make-regexp "-{8}")))
1950 (lambda (in out)
1951 (let loop ()
1952 (let ((line (read-line in 'concat)))
1953 (unless (regexp-exec rx line)
1954 (display line out)
1955 (loop)))))))))))
1956 (build-system cmake-build-system)
183e44ae
EB		 1957 (native-inputs
1958 `(("tcsh" ,tcsh)))
1959 (inputs
995a09e0 1960 `(("blas" ,openblas)
19afbea1 1961 ("gfortran" ,gfortran)))
183e44ae 1962 (arguments
995a09e0
EB		 1963 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
1964 "-DTPL_BLAS_LIBRARIES=openblas"
1965 "-DBUILD_SHARED_LIBS:BOOL=YES"
1966 "-DCMAKE_INSTALL_LIBDIR=lib")))
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")
ac2ddcc6 2492 (version "17.05.1")
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
ac2ddcc6 2501 "0dv0cy0cf46v0cbw32izscpkdmpxg1qhwq1f4cz46kkqd8k4yfbj"))))
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")
883d0a7d 2619 (version "0.2.19")
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
883d0a7d 2628 "071zqnmnxhh0c9phzyn3f198yxa0hjxda7016azdbq2056sm70w7"))))
e73b49fb
RW		 2629 (build-system gnu-build-system)
2630 (arguments
5b5ea159 2631 `(#:tests? #f ;no "check" target
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 "NO_LAPACK=1"
2645 ;; Build the library for all supported CPUs. This allows
2646 ;; switching CPU targets at runtime with the environment variable
2647 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
71923a91
AE		 2648 ;; Unfortunately, this is not supported on non-x86 architectures,
2649 ;; where it leads to failed builds.
2650 ,@(let ((system (or (%current-target-system) (%current-system))))
8a637e79
RW		 2651 (cond
2652 ((or (string-prefix? "x86_64" system)
71923a91 2653 (string-prefix? "i686" system))
8a637e79
RW		 2654 '("DYNAMIC_ARCH=1"))
2655 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
2656 ;; two available MIPS targets special extended instructions
2657 ;; for Loongson cores are used.
2658 ((string-prefix? "mips" system)
2659 '("TARGET=SICORTEX"))
83a34647
EF		 2660 ;; On aarch64 force the generic 'armv8-a' target
2661 ((string-prefix? "aarch64" system)
2662 '("TARGET=ARMV8"))
8a637e79 2663 (else '()))))
e73b49fb
RW		 2664 ;; no configure script
2665 #:phases (alist-delete 'configure %standard-phases)))
2666 (inputs
19afbea1 2667 `(("fortran" ,gfortran)))
e73b49fb
RW		 2668 (native-inputs
2669 `(("cunit" ,cunit)
2670 ("perl" ,perl)))
2671 (home-page "http://www.openblas.net/")
2672 (synopsis "Optimized BLAS library based on GotoBLAS")
2673 (description
2674 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
2675 (license license:bsd-3)))
2676
5a7deb11
LC		 2677(define* (make-blis implementation #:optional substitutable?)
2678 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
2679source tree for a list of implementations.)
2680
2681SUBSTITUTABLE? determines whether the package is made available as a
2682substitute.
2683
2684Currently the specialization must be selected at configure-time, but work is
2685underway to allow BLIS to select the right optimized kernels at run time:
2686<https://github.com/flame/blis/issues/129>."
2687 (package
2688 (name (if (string=? implementation "reference")
2689 "blis"
2690 (string-append "blis-" implementation)))
2691 (version "0.2.2")
2692 (home-page "https://github.com/flame/blis")
2693 (source (origin
2694 (method git-fetch)
2695 (uri (git-reference (url home-page) (commit version)))
2696 (sha256
2697 (base32
2698 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
2699 (file-name (git-file-name "blis" version))))
2700 (build-system gnu-build-system)
2701 (arguments
2702 `(#:test-target "test"
2703
2704 #:substitutable? ,substitutable?
2705
2706 #:phases (modify-phases %standard-phases
2707 (replace 'configure
2708 (lambda* (#:key outputs #:allow-other-keys)
2709 ;; This is a home-made 'configure' script.
2710 (let ((out (assoc-ref outputs "out")))
2711 (zero? (system* "./configure" "-p" out
2712 "-d" "opt"
2713 "--disable-static"
2714 "--enable-shared"
2715 "--enable-threading=openmp"
2716
2717 ,implementation)))))
2718 (add-before 'check 'show-test-output
2719 (lambda _
2720 ;; By default "make check" is silent. Make it verbose.
2721 (system "tail -F output.testsuite &")
2722 #t)))))
2723 (synopsis "High-performance basic linear algebra (BLAS) routines")
2724 (description
2725 "BLIS is a portable software framework for instantiating high-performance
2726BLAS-like dense linear algebra libraries. The framework was designed to
2727isolate essential kernels of computation that, when optimized, immediately
2728enable optimized implementations of most of its commonly used and
2729computationally intensive operations. While BLIS exports a new BLAS-like API,
2730it also includes a BLAS compatibility layer which gives application developers
2731access to BLIS implementations via traditional BLAS routine calls.")
2732 (license license:bsd-3)))
2733
2734(define-public blis
2735 ;; This is the "reference" implementation, which is the non-optimized but
2736 ;; portable variant (no assembly).
2737 (make-blis "reference" #t))
2738
2739(define ignorance blis)
2740
2741(define-syntax-rule (blis/x86_64 processor)
2742 "Expand to a package specialized for PROCESSOR."
2743 (package
2744 (inherit (make-blis processor))
2745 (supported-systems '("x86_64-linux"))))
2746
2747(define-public blis-sandybridge
2748 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
2749 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
2750 (blis/x86_64 "sandybridge"))
2751
2752(define-public blis-haswell
2753 ;; BLIS specialized for Haswell processors (launched 2013):
2754 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
2755 (blis/x86_64 "haswell"))
2756
2757(define-public blis-knl
2758 ;; BLIS specialized for Knights Landing processor (launched 2016):
2759 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
2760 (blis/x86_64 "knl"))
2761
2762
e1605e36
RW		 2763(define-public openlibm
2764 (package
2765 (name "openlibm")
26f6e565 2766 (version "0.5.1")
e1605e36
RW		 2767 (source
2768 (origin
2769 (method url-fetch)
2770 (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
2771 version ".tar.gz"))
2772 (file-name (string-append name "-" version ".tar.gz"))
2773 (sha256
2774 (base32
26f6e565 2775 "11czx2z7nh6dfpz45s3xl7v38hw36jxzxfvny454bk3if14pfakq"))))
e1605e36
RW		 2776 (build-system gnu-build-system)
2777 (arguments
2778 `(#:make-flags
2779 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2780 #:phases
2781 ;; no configure script
dc1d3cde 2782 (modify-phases %standard-phases (delete 'configure))
e1605e36
RW		 2783 #:tests? #f)) ;the tests are part of the default target
2784 (home-page "http://openlibm.org/")
2785 (synopsis "Portable C mathematical library (libm)")
2786 (description
2787 "OpenLibm is an effort to have a high quality, portable, standalone C
2788mathematical library (libm). It can be used standalone in applications and
2789programming language implementations. The project was born out of a need to
e881752c 2790have a good libm for the Julia programming language that worked consistently
e1605e36
RW		 2791across compilers and operating systems, and in 32-bit and 64-bit
2792environments.")
538c0e3b
EF		 2793 ;; Each architecture has its own make target, and there is none for mips.
2794 (supported-systems (delete "mips64el-linux" %supported-systems))
e1605e36
RW		 2795 ;; See LICENSE.md for details.
2796 (license (list license:expat
2797 license:isc
2798 license:bsd-2
2799 license:public-domain
2800 license:lgpl2.1+))))
2801
e62be58f
RW		 2802(define-public openspecfun
2803 (package
2804 (name "openspecfun")
49f54a74 2805 (version "0.5.2")
e62be58f
RW		 2806 (source
2807 (origin
2808 (method url-fetch)
2809 (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
2810 version ".tar.gz"))
2811 (file-name (string-append name "-" version ".tar.gz"))
2812 (sha256
2813 (base32
49f54a74 2814 "1y5b2h6f2k72536kym3vzy3li3bhpd23x463g7hdmjdi3cncavz1"))))
e62be58f
RW		 2815 (build-system gnu-build-system)
2816 (arguments
2817 '(#:tests? #f ;no "check" target
2818 #:make-flags
2819 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2820 ;; no configure script
dc1d3cde 2821 #:phases (modify-phases %standard-phases (delete 'configure))))
e62be58f 2822 (inputs
19afbea1 2823 `(("fortran" ,gfortran)))
e62be58f
RW		 2824 (home-page "https://github.com/JuliaLang/openspecfun")
2825 (synopsis "Collection of special mathematical functions")
2826 (description
2827 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
2828portable package for Bessel Functions of a Complex Argument and Nonnegative
2829Order; it contains subroutines for computing Bessel functions and Airy
2830functions. Faddeeva allows computing the various error functions of arbitrary
2831complex arguments (Faddeeva function, error function, complementary error
2832function, scaled complementary error function, imaginary error function, and
2833Dawson function); given these, one can also easily compute Voigt functions,
2834Fresnel integrals, and similar related functions as well.")
2835 ;; Faddeeva is released under the Expat license; AMOS is included as
2836 ;; public domain software.
2837 (license (list license:expat license:public-domain))))
2838
2742f87e
RW		 2839(define-public suitesparse
2840 (package
2841 (name "suitesparse")
bd5b5ac0 2842 (version "4.5.5")
2742f87e
RW		 2843 (source
2844 (origin
2845 (method url-fetch)
2846 (uri (string-append
2847 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
2848 version ".tar.gz"))
2849 (sha256
2850 (base32
bd5b5ac0
EB		 2851 "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
2852 (modules '((guix build utils)))
2853 (snippet
2854 ;; Remove bundled metis source
2855 '(delete-file-recursively "metis-5.1.0"))))
2742f87e
RW		 2856 (build-system gnu-build-system)
2857 (arguments
bd5b5ac0 2858 '(#:tests? #f ;no "check" target
2742f87e
RW		 2859 #:make-flags
2860 (list "CC=gcc"
2861 "BLAS=-lblas"
2862 "TBB=-ltbb"
bd5b5ac0 2863 "MY_METIS_LIB=-lmetis"
2742f87e
RW		 2864 (string-append "INSTALL_LIB="
2865 (assoc-ref %outputs "out") "/lib")
2866 (string-append "INSTALL_INCLUDE="
bd5b5ac0
EB		 2867 (assoc-ref %outputs "out") "/include")
2868 "library")
2742f87e 2869 #:phases
2509522c 2870 (modify-phases %standard-phases
bd5b5ac0 2871 (delete 'configure)))) ;no configure script
2742f87e
RW		 2872 (inputs
2873 `(("tbb" ,tbb)
bd5b5ac0
EB		 2874 ("lapack" ,lapack)
2875 ("metis" ,metis)))
2742f87e
RW		 2876 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
2877 (synopsis "Suite of sparse matrix software")
2878 (description
2879 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
2880multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
2881multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
2882simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
2883CXSparse, a concise sparse Cholesky factorization package; and many other
2884packages.")
2885 ;; LGPLv2.1+:
2886 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
2887 ;; GPLv2+:
2888 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
2889 (license (list license:gpl2+ license:lgpl2.1+))))
2890
ec322be2
FB		 2891(define-public atlas
2892 (package
2893 (name "atlas")
3c98ac02 2894 (version "3.10.3")
ec322be2
FB		 2895 (source (origin
2896 (method url-fetch)
de67e922
LF		 2897 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
2898 version "/atlas" version ".tar.bz2"))
ec322be2
FB		 2899 (sha256
2900 (base32
3c98ac02 2901 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
ec322be2
FB		 2902 (build-system gnu-build-system)
2903 (home-page "http://math-atlas.sourceforge.net/")
19afbea1 2904 (inputs `(("gfortran" ,gfortran)
ec322be2
FB		 2905 ("lapack-tar" ,(package-source lapack))))
2906 (outputs '("out" "doc"))
01480b9e
FB		 2907 ;; For the moment we drop support for MIPS at it fails to compile. See
2908 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
2909 (supported-systems (delete "mips64el-linux" %supported-systems))
ec322be2
FB		 2910 (arguments
2911 `(#:parallel-build? #f
2912 #:parallel-tests? #f
f15615b1
LC		 2913
2914 ;; ATLAS tunes itself for the machine it is built on, as explained at
2915 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
2916 ;; For this reason, we want users to build it locally instead of using
2917 ;; substitutes.
2918 #:substitutable? #f
2919
ec322be2
FB		 2920 #:modules ((srfi srfi-26)
2921 (srfi srfi-1)
2922 (guix build gnu-build-system)
2923 (guix build utils))
40029cbe 2924 #:configure-flags
ec322be2
FB		 2925 `(;; Generate position independent code suitable for dynamic libraries
2926 ;; and use WALL timer to get more accurate timing.
2927 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
2928 ;; Set word width.
2929 "-b"
2930 ,,(if (string-match "64" (%current-system))
2931 "64"
2932 "32")
2933 ;; Disable parallel build as it gives errors: atlas_pthread.h is
2934 ;; needed to compile C files before it is generated.
2935 "-Ss" "pmake" "make -j 1"
af89a667
FB		 2936 ;; Probe is failing for MIPS. We therefore define the system
2937 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
2938 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
2939 ,,@(if (string-prefix? "mips" (%current-system))
2940 (list "-A" "49" "-V" "1")
2941 (list))
ec322be2
FB		 2942 ;; Generate shared libraries.
2943 "--shared"
2944 ;; Build a full LAPACK library.
2945 ,(string-append "--with-netlib-lapack-tarfile="
2946 (assoc-ref %build-inputs "lapack-tar")))
2947 #:phases
e5b4b96b
EF		 2948 (modify-phases %standard-phases
2949 (add-after 'install 'install-doc
2950 (lambda* (#:key outputs inputs #:allow-other-keys)
2951 (let ((doc (string-append (assoc-ref outputs "doc")
2952 "/share/doc/atlas")))
2953 (mkdir-p doc)
2954 (fold (lambda (file previous)
2955 (and previous (zero? (system* "cp" file doc))))
2956 #t (find-files "../ATLAS/doc" ".*")))))
2957 (add-after 'check 'check-pt
2958 (lambda _ (zero? (system* "make" "ptcheck"))))
2959 ;; Fix files required to run configure.
2960 (add-before 'configure 'fix-/bin/sh
ec322be2
FB		 2961 (lambda _
2962 ;; Use `sh', not `/bin/sh'.
2963 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
2964 (("/bin/sh")
e5b4b96b
EF		 2965 "sh"))))
2966 ;; Fix /bin/sh in generated make files.
2967 (add-after 'configure 'fix-/bin/sh-in-generated-files
2968 (lambda _
2969 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
2970 (("/bin/sh")
2971 "sh"))))
2972 ;; ATLAS configure program does not accepts the default flags
2973 ;; passed by the 'gnu-build-system'.
2974 (replace 'configure
2975 (lambda* (#:key native-inputs inputs outputs
2976 (configure-flags '())
2977 #:allow-other-keys #:rest args)
2978 (let* ((prefix (assoc-ref outputs "out"))
2979 (bash (or (and=> (assoc-ref
2980 (or native-inputs inputs) "bash")
2981 (cut string-append <> "/bin/bash"))
2982 "/bin/sh"))
2983 (flags `(,(string-append "--prefix=" prefix)
2984 ,@configure-flags))
2985 (abs-srcdir (getcwd))
2986 (srcdir (string-append "../" (basename abs-srcdir))))
2987 (format #t "source directory: ~s (relative from build: ~s)~%"
2988 abs-srcdir srcdir)
2989 (mkdir "../build")
2990 (chdir "../build")
2991 (format #t "build directory: ~s~%" (getcwd))
2992 (format #t "configure flags: ~s~%" flags)
2993 (zero? (apply system* bash
2994 (string-append srcdir "/configure")
2995 flags))))))))
ec322be2
FB		 2996 (synopsis "Automatically Tuned Linear Algebra Software")
2997 (description
2998 "ATLAS is an automatically tuned linear algebra software library
2999providing C and Fortran77 interfaces to a portably efficient BLAS
3000implementation, as well as a few routines from LAPACK.
3001
f15615b1
LC		 3002Optimization occurs at build time. For this reason, the library is built on
3003the machine where it is installed, without resorting to pre-built substitutes.
ec322be2 3004
f15615b1 3005Before building the library, CPU throttling should be disabled. This can be
d97c429a 3006done in the BIOS, or, on GNU/Linux, with the following command:
ec322be2 3007
8e9ba611 3008@example
d97c429a 3009# cpupower --governor performance
8e9ba611 3010@end example
ec322be2 3011
d97c429a 3012Failure to do so will result in a library with poor performance.")
ec322be2 3013 (license license:bsd-3)))
c12efc72
AE		 3014
3015(define-public glm
3016 (package
3017 (name "glm")
3018 (version "0.9.6.3")
3019 (source
3020 (origin
3021 (method url-fetch)
de67e922
LF		 3022 (uri (string-append "mirror://sourceforge/ogl-math/glm-" version
3023 "/glm-" version ".zip"))
c12efc72
AE		 3024 (sha256
3025 (base32
3026 "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l"))))
3027 (build-system cmake-build-system)
3028 (native-inputs
3029 `(("unzip" ,unzip)))
3030 (home-page "http://glm.g-truc.net")
3031 (synopsis "OpenGL Mathematics library")
3032 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3033library for graphics software based on the OpenGL Shading Language (GLSL)
3034specifications.")
3035 (license license:expat)))
7f18257b
AE		 3036
3037(define-public lpsolve
3038 (package
3039 (name "lpsolve")
3040 (version "5.5.2.0")
3041 (source
3042 (origin
3043 (method url-fetch)
3044 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3045 "/lp_solve_" version "_source.tar.gz"))
3046 (sha256
3047 (base32
3048 "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq"))
3049 (modules '((guix build utils)))
3050 (snippet
3051 '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3052 (("^c=cc") "c=gcc")
3053 ;; Pretend to be on a 64 bit platform to obtain a common directory
3054 ;; name for the build results on all architectures; nothing else
3055 ;; seems to depend on it.
5dbfbef7
LC		 3056 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3057
3058 ;; The check for 'isnan' as it is written fails with
3059 ;; "non-floating-point argument in call to function
3060 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3061 ;; definition, which in turn leads to bad things. Fix the feature
3062 ;; test.
3063 (("isnan\\(0\\)") "isnan(0.)")))))
7f18257b
AE		 3064 (build-system gnu-build-system)
3065 (arguments
3066 `(#:tests? #f ; no check target
3067 #:phases
3068 (modify-phases %standard-phases
3069 (delete 'configure)
3070 (replace 'build
3071 (lambda _
6689d094
LC		 3072 (and (with-directory-excursion "lpsolve55"
3073 (zero? (system* "bash" "ccc")))
3074 (with-directory-excursion "lp_solve"
3075 (zero? (system* "bash" "ccc"))))))
7f18257b
AE		 3076 (replace 'install
3077 (lambda* (#:key outputs #:allow-other-keys)
3078 (let* ((out (assoc-ref outputs "out"))
3079 (bin (string-append out "/bin"))
3080 (lib (string-append out "/lib"))
3081 ;; This is where LibreOffice expects to find the header
3082 ;; files, and where they are installed by Debian.
3083 (include (string-append out "/include/lpsolve")))
3084 (mkdir-p lib)
3085 (copy-file "lpsolve55/bin/ux64/liblpsolve55.a"
3086 (string-append lib "/liblpsolve55.a"))
3087 (copy-file "lpsolve55/bin/ux64/liblpsolve55.so"
3088 (string-append lib "/liblpsolve55.so"))
96c46210
LC		 3089 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3090
7f18257b
AE		 3091 ;; Install a subset of the header files as on Debian
3092 ;; (plus lp_bit.h, which matches the regular expression).
96c46210
LC		 3093 (for-each (lambda (name)
3094 (install-file name include))
3095 (find-files "." "lp_[HMSa-z].*\\.h$"))
7f18257b 3096 (with-directory-excursion "shared"
96c46210
LC		 3097 (for-each (lambda (name)
3098 (install-file name include))
3099 (find-files "." "\\.h$")))
7f18257b
AE		 3100 #t))))))
3101 (home-page "http://lpsolve.sourceforge.net/")
3102 (synopsis "Mixed integer linear programming (MILP) solver")
3103 (description
3104 "lp_solve is a mixed integer linear programming solver based on the
3105revised simplex and the branch-and-bound methods.")
3106 (license license:lgpl2.1+)))
a17d4564
EB		 3107
3108(define-public dealii
3109 (package
3110 (name "dealii")
24404eaf 3111 (version "8.5.1")
a17d4564
EB		 3112 (source
3113 (origin
3114 (method url-fetch)
3115 (uri (string-append "https://github.com/dealii/dealii/releases/"
3116 "download/v" version "/dealii-" version ".tar.gz"))
3117 (sha256
3118 (base32
24404eaf 3119 "1bh9rsmkrg0zi70n27b11djmac9lximghsiy7mg7w7x544n82gnk"))
a17d4564
EB		 3120 (modules '((guix build utils)))
3121 (snippet
3122 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
3123 '(delete-file-recursively "bundled"))))
3124 (build-system cmake-build-system)
3125 (inputs
3126 `(("tbb" ,tbb)
3127 ("zlib" ,zlib)
3128 ("boost" ,boost)
3129 ("p4est" ,p4est)
3130 ("blas" ,openblas)
3131 ("lapack" ,lapack)
3132 ("arpack" ,arpack-ng)
3133 ("muparser" ,muparser)
3134 ("gfortran" ,gfortran)
3135 ("suitesparse" ,suitesparse))) ;for UMFPACK
3136 (arguments
3137 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
d84b09e9
EB		 3138 #:configure-flags
3139 ;; Work around a bug in libsuitesparseconfig linking
3140 ;; see https://github.com/dealii/dealii/issues/4745
3141 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
a17d4564
EB		 3142 (home-page "https://www.dealii.org")
3143 (synopsis "Finite element library")
3144 (description
3145 "Deal.II is a C++ program library targeted at the computational solution
3146of partial differential equations using adaptive finite elements. The main
3147aim of deal.II is to enable rapid development of modern finite element codes,
3148using among other aspects adaptive meshes and a wide array of tools often used
3149in finite element programs.")
3150 (license license:lgpl2.1+)))
3151
3152(define-public dealii-openmpi
3153 (package (inherit dealii)
3154 (name "dealii-openmpi")
3155 (inputs
3156 `(("mpi" ,openmpi)
3157 ;;Supported only with MPI:
3158 ("p4est" ,p4est-openmpi)
3159 ("petsc" ,petsc-openmpi)
3160 ("slepc" ,slepc-openmpi)
3161 ("metis" ,metis) ;for MUMPS
3162 ("scalapack" ,scalapack) ;for MUMPS
3163 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3164 ("arpack" ,arpack-ng-openmpi)
3165 ,@(fold alist-delete (package-inputs dealii)
3166 '("p4est" "arpack"))))
3167 (arguments
3168 (substitute-keyword-arguments (package-arguments dealii)
3169 ((#:configure-flags cf)
3170 ``("-DMPI_C_COMPILER=mpicc"
3171 "-DMPI_CXX_COMPILER=mpicxx"
3172 "-DMPI_Fortran_COMPILER=mpifort"
3173 ,@,cf))))
3174 (synopsis "Finite element library (with MPI support)")))
194c7f95
AE		 3175
3176(define-public flann
3177 (package
3178 (name "flann")
3179 (version "1.8.4")
3180 (source
3181 (origin
3182 (method url-fetch)
3183 (uri
3184 (string-append
3185 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3186 version "-src.zip"))
3187 (sha256
3188 (base32
3189 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))))
3190 (build-system cmake-build-system)
6b6aca9b
LC		 3191 (outputs '("out"
3192 "octave")) ;46 MiB .mex file that pulls Octave
194c7f95
AE		 3193 (native-inputs
3194 `(("unzip" ,unzip)))
3195 (inputs
3196 `(("hdf5" ,hdf5)
3197 ("octave" ,octave)
3198 ("python" ,python-2) ; print syntax
3199 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3200 ("zlib" ,zlib)))
3201 (arguments
39b30337
LC		 3202 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3203 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3204 #:strip-directories '("lib" "lib64" "libexec"
3205 "bin" "sbin" "share/flann/octave")
3206
9684e30b
LC		 3207 ;; Save 12 MiB by not installing .a files. Passing
3208 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3209 #:phases (modify-phases %standard-phases
6b6aca9b
LC		 3210 (add-before 'configure 'set-octave-directory
3211 (lambda* (#:key outputs #:allow-other-keys)
3212 ;; Install the .mex file in the "octave" output.
3213 (let ((out (assoc-ref outputs "octave")))
3214 (substitute* "src/matlab/CMakeLists.txt"
3215 (("share/flann/octave")
3216 (string-append out "/share/flann/octave")))
3217 #t)))
9684e30b
LC		 3218 (add-after 'install 'remove-static-libraries
3219 (lambda* (#:key outputs #:allow-other-keys)
3220 (let* ((out (assoc-ref outputs "out"))
3221 (lib (string-append out "/lib")))
3222 (for-each delete-file
3223 (find-files lib "\\.a$"))
3224 #t))))
3225
39b30337 3226 #:tests? #f)) ; The test data are downloaded from the Internet.
194c7f95
AE		 3227 (home-page "http://www.cs.ubc.ca/research/flann/")
3228 (synopsis "Library for approximate nearest neighbors computation")
3229 (description "FLANN is a library for performing fast approximate
3230nearest neighbor searches in high dimensional spaces. It implements a
3231collection of algorithms and a system for automatically choosing the best
3232algorithm and optimum parameters depending on the dataset.
3233
3234FLANN is written in C++ and contains bindings for C, Octave and Python.")
3235 (license (license:non-copyleft "file://COPYING"
3236 "See COPYING in the distribution."))))
d8c97beb
EF		 3237
3238(define-public wcalc
3239 (package
3240 (name "wcalc")
3241 (version "2.5")
3242 (source
3243 (origin
3244 (method url-fetch)
de67e922
LF		 3245 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3246 "wcalc-" version ".tar.bz2"))
d8c97beb
EF		 3247 (sha256
3248 (base32
3249 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3250 (build-system gnu-build-system)
3251 (inputs
3252 `(("mpfr" ,mpfr)
3253 ("readline" ,readline)))
3254 (home-page "http://w-calc.sourceforge.net/index.php")
3255 (synopsis "Flexible command-line scientific calculator")
3256 (description "Wcalc is a very capable calculator. It has standard functions
3257(sin, asin, and sinh for example, in either radians or degrees), many
3258pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3259variables, a command history, hex/octal/binary input and output, unit
3260conversions, embedded comments, and an expandable expression entry field. It
3261evaluates expressions using the standard order of operations.")
3262 (license license:gpl2+)))
45147b0c
FH		 3263
3264(define-public xaos
3265 (package
3266 (name "xaos")
3267 (version "3.6")
3268 (source (origin
3269 (method url-fetch)
de67e922
LF		 3270 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3271 "/xaos-" version ".tar.gz"))
45147b0c
FH		 3272 (sha256
3273 (base32
3274 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3275 (build-system gnu-build-system)
b94a6ca0 3276 (native-inputs `(("gettext" ,gettext-minimal)))
45147b0c
FH		 3277 (inputs `(("libx11" ,libx11)
3278 ("zlib" ,zlib)
3279 ("libpng" ,libpng)
3280 ("gsl" ,gsl)))
3281 (arguments
3282 `(#:tests? #f ;no "check" target
3283 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3284 (synopsis "Real-time fractal zoomer")
3285 (description "GNU XaoS is a graphical program that generates fractal
3286patterns and allows you to zoom in and out of them infinitely in a fluid,
3287continuous manner. It also includes tutorials that help to explain how fractals
3288are built. It can generate many different fractal types such as the Mandelbrot
3289set.")
6fd52309 3290 (home-page "https://www.gnu.org/software/xaos/")
45147b0c 3291 (license license:gpl2+)))
528bb464
EB		 3292
3293(define-public hypre
3294 (package
3295 (name "hypre")
3296 (version "2.11.0")
3297 (source (origin
3298 (method url-fetch)
3299 (uri (string-append "https://github.com/LLNL/hypre/archive/"
3300 "v" version ".tar.gz"))
3301 (file-name (string-append name "-" version ".tar.gz"))
3302 (sha256
3303 (base32
3304 "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m"))
3305 (modules '((guix build utils)))
3306 (snippet
3307 '(begin
3308 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
3309 ;; substitute the tarball creation time.
3310 (substitute* "src/utilities/HYPRE_utilities.h"
3311 (("Date Compiled: .*$")
3312 "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n"))
3313 #t))))
3314 (build-system gnu-build-system)
3315 (outputs '("out" ;6.1 MiB of headers and libraries
3316 "doc")) ;4.8 MiB of documentation
3317 (native-inputs
3318 `(("doc++" ,doc++)
3319 ("netpbm" ,netpbm)
3320 ("texlive" ,texlive) ;full package required for fonts
3321 ("ghostscript" ,ghostscript)))
3322 (inputs
3323 `(("blas" ,openblas)
3324 ("lapack" ,lapack)))
3325 (arguments
3326 `(#:modules ((srfi srfi-1)
3327 ,@%gnu-build-system-modules)
3328 #:configure-flags '("--enable-shared"
3329 "--disable-fortran"
3330 "--without-MPI"
3331 "--with-openmp"
3332 "--with-fei"
3333 "--with-lapack"
3334 "--with-blas")
3335 #:phases
3336 (modify-phases %standard-phases
3337 (add-before 'configure 'chdir-src
3338 (lambda _ (chdir "src")))
3339 (replace 'configure
3340 (lambda* (#:key build target configure-flags
3341 #:allow-other-keys #:rest args)
3342 (let* ((configure (assoc-ref %standard-phases 'configure)))
3343 (apply configure
3344 (append args
3345 (list #:configure-flags
3346 (cons (string-append
3347 "--host=" (or target build))
3348 configure-flags)))))))
3349 (add-after 'build 'build-docs
3350 (lambda _
3351 (zero? (system* "make" "-Cdocs" "pdf" "html"))))
3352 (replace 'check
3353 (lambda _
3354 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3355 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
3356 (and (system* "make" "check" "CHECKRUN=")
3357 (fold (lambda (filename result)
3358 (and result
3359 (let ((size (stat:size (stat filename))))
3360 (when (not (zero? size))
3361 (format #t "~a size ~d; error indication~%"
3362 filename size))
3363 (zero? size))))
3364 #t
3365 (find-files "test" ".*\\.err$")))))
3366 (add-after 'install 'install-docs
3367 (lambda* (#:key outputs #:allow-other-keys)
3368 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3369 (let* ((doc (assoc-ref outputs "doc"))
3370 (docdir (string-append doc "/share/doc/hypre-" ,version)))
528bb464
EB		 3371 (with-directory-excursion "docs"
3372 (for-each (lambda (base)
3373 (install-file (string-append base ".pdf") docdir)
3374 (copy-recursively base docdir)) ;html docs
3375 '("HYPRE_usr_manual"
3376 "HYPRE_ref_manual")))
3377 #t))))))
3378 (home-page "http://www.llnl.gov/casc/hypre/")
3379 (synopsis "Library of solvers and preconditioners for linear equations")
3380 (description
3381 "HYPRE is a software library of high performance preconditioners and
3382solvers for the solution of large, sparse linear systems of equations. It
3383features multigrid solvers for both structured and unstructured grid
3384problems.")
3385 (license license:lgpl2.1)))
3386
3387(define-public hypre-openmpi
3388 (package (inherit hypre)
3389 (name "hypre-openmpi")
3390 (inputs
3391 `(("mpi" ,openmpi)
3392 ,@(package-inputs hypre)))
3393 (arguments
3394 (substitute-keyword-arguments (package-arguments hypre)
3395 ((#:configure-flags flags)
3396 ``("--with-MPI"
3397 ,@(delete "--without-MPI" ,flags)))))
3398 (synopsis "Parallel solvers and preconditioners for linear equations")
3399 (description
3400 "HYPRE is a software library of high performance preconditioners and
3401solvers for the solution of large, sparse linear systems of equations on
3402parallel computers. It features parallel multigrid solvers for both
3403structured and unstructured grid problems.")))
6c90e183
EB		 3404
3405(define-public matio
3406 (package
3407 (name "matio")
3408 (version "1.5.6")
3409 (source
3410 (origin
3411 (method url-fetch)
de67e922 3412 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
6c90e183
EB		 3413 "matio-" version ".tar.gz"))
3414 (sha256
3415 (base32
3416 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3417 (build-system gnu-build-system)
3418 (inputs
3419 `(("zlib" ,zlib)
3420 ("hdf5" ,hdf5)))
3421 (home-page "http://matio.sourceforge.net/")
3422 (synopsis "Library for reading and writing MAT files")
3423 (description "Matio is a library for reading and writing MAT files. It
3424supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3425 (license license:bsd-2)))
d721c83a 3426
517318ad
LF		 3427(define-public vc
3428 (package
3429 (name "vc")
3430 (version "1.2.0")
3431 (source
3432 (origin (method url-fetch)
3433 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3434 "download/" version "/Vc-" version ".tar.gz"))
3435 (sha256
3436 (base32
3437 "1rh6dhqar3y07n4xqyml0sa0v48qv3ch9dc3yc2in855hlh4vnqi"))))
3438 (build-system cmake-build-system)
3439 (arguments
3440 '(#:configure-flags
3441 '("-DBUILD_TESTING=ON")))
3442 (synopsis "SIMD vector classes for C++")
3443 (description "Vc provides portable, zero-overhead C++ types for explicitly
3444data-parallel programming. It is a library designed to ease explicit
3445vectorization of C++ code. Its types enable explicitly stating data-parallel
3446operations on multiple values. The parallelism is therefore added via the type
3447system. Vc has an intuitive API and provides portability between different
3448compilers and compiler versions as well as portability between different vector
3449instruction sets. Thus, an application written with Vc can be compiled for:
3450@enumerate
3451@item AVX and AVX2
d1e4ad1b 3452@item SSE2 up to SSE4.2 or SSE4a
517318ad
LF		 3453@item Scalar
3454@item MIC
3455@item NEON (in development)
3456@item NVIDIA GPUs / CUDA (in development)
3457@end enumerate\n")
3458 (home-page "https://github.com/VcDevel/Vc")
a8ead6f9
EF		 3459 ;; "No support_???.cpp file exists for this architecture."
3460 (supported-systems '("x86_64-linux" "i686-linux"))
517318ad 3461 (license license:bsd-3)))
54052a54 3462
3463(define-public reducelcs
3464 ;; This is the last commit which is available upstream, no
3465 ;; release happened since 2010.
3466 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
3467 (revision "1"))
3468 (package
3469 (name "reducelcs")
3470 (version (string-append "1.0-" revision "." (string-take commit 7)))
3471 (source
3472 (origin
3473 (method git-fetch)
3474 (uri (git-reference
3475 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
3476 (commit commit)))
3477 (file-name (string-append name "-" version "-checkout"))
3478 (sha256
3479 (base32
3480 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
3481 (build-system gnu-build-system)
3482 (inputs
3483 `(("openlibm" ,openlibm)))
3484 (arguments
3485 `(#:tests? #f ; no tests
3486 #:phases
3487 (modify-phases %standard-phases
3488 (delete 'configure) ; No configure script exists.
3489 (replace 'install ; No install phase exists.
3490 (lambda* (#:key outputs #:allow-other-keys)
3491 (let* ((out (assoc-ref outputs "out"))
3492 (bin (string-append out "/bin")))
3493 (install-file "Approximation" bin)
3494 (install-file "CollectResults" bin)
3495 (install-file "GenerateInstances" bin)
3496 #t))))))
3497 (synopsis "Approximate Longest Commons Subsequence computation tool")
3498 (description
3499 "@code{reduceLCS} is an implementation of the Reduce-Expand
3500algorithm for LCS. It is a fast program to compute the approximate
3501Longest Commons Subsequence of a set of strings.")
3502 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
c000b6b1 3503 (license license:gpl3+))))
479c4273
JD		 3504
3505(define-public jacal
3506 (package
3507 (name "jacal")
3508 (version "1c4")
3509 (source (origin
3510 (method url-fetch)
3511 (uri (string-append
3512 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
3513 version ".zip"))
3514 (sha256 (base32
3515 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
3516 (patches (search-patches "jacal-fix-texinfo.patch"))))
3517 (build-system gnu-build-system)
3518 (arguments
3519 `(#:phases
3520 (modify-phases %standard-phases
3521 (add-before 'build 'pre-build
3522 ;; Don't use upstream's script - it really doesn't fit into
3523 ;; Guix's functional paradigm.
3524 (lambda* (#:key inputs outputs #:allow-other-keys)
3525 (substitute* "Makefile"
3526 (("^install: install-script") "install: "))))
3527 (add-after 'install 'post-install
3528 ;; Instead, we provide our own simplified script.
3529 (lambda* (#:key inputs outputs #:allow-other-keys)
3530 (let ((wrapper (string-append (assoc-ref outputs "out")
3531 "/bin/jacal")))
3532 (format (open wrapper (logior O_WRONLY O_CREAT))
3533 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
3534 "-e '(slib:load \"~a/lib/jacal/math\") "
3535 "(math)' \"$@\"\n")
3536 (which "bash")
3537 (assoc-ref inputs "scm")
3538 (assoc-ref outputs "out"))
3539 (chmod wrapper #o555))))
3540 (replace 'configure
3541 (lambda* (#:key inputs outputs #:allow-other-keys)
3542 (zero? (system* "./configure"
3543 (string-append "--prefix="
3544 (assoc-ref outputs "out")))))))))
3545 (inputs `(("scm" ,scm)))
3546 (native-inputs `(("unzip" ,unzip)
3547 ("texinfo" ,texinfo)))
3548 (synopsis "Symbolic mathematics system")
3549 (description "GNU JACAL is an interactive symbolic mathematics program based on
3550Scheme. It manipulate and simplify a range of mathematical expressions such
3551as equations, scalars, vectors, and matrices.")
6fd52309 3552 (home-page "https://www.gnu.org/software/jacal/")
479c4273
JD		 3553 (license license:gpl3+)))
3554
313844d9
TF		 3555(define-public z3
3556 (package
3557 (name "z3")
3558 (version "4.5.0")
3559 (source (origin
3560 (method url-fetch)
3561 (uri (string-append
3562 "https://github.com/Z3Prover/z3/archive/z3-"
3563 version ".tar.gz"))
3564 (sha256
3565 (base32
3566 "032a5lvji2liwmc25jv52bdrhimqflvqbpg77ccaq1jykhiivbmf"))))
cf684d87 3567 (build-system cmake-build-system)
313844d9 3568 (arguments
cf684d87
TF		 3569 `(#:configure-flags
3570 (list "-DBUILD_PYTHON_BINDINGS=true"
3571 "-DINSTALL_PYTHON_BINDINGS=true"
3572 (string-append "-DCMAKE_INSTALL_PYTHON_PKG_DIR="
3573 %output
3574 "/lib/python2.7/site-packages")
3575 (string-append "-DCMAKE_INSTALL_LIBDIR="
3576 %output
3577 "/lib"))
3578
313844d9
TF		 3579 #:phases
3580 (modify-phases %standard-phases
cf684d87
TF		 3581 (add-before 'configure 'bootstrap
3582 (lambda _
313844d9 3583 (zero?
cf684d87
TF		 3584 (system* "python" "contrib/cmake/bootstrap.py" "create"))))
3585 (add-before 'check 'make-test-z3
313844d9 3586 (lambda _
cf684d87
TF		 3587 ;; Build the test suite executable.
3588 (zero? (system* "make" "test-z3" "-j"
3589 (number->string (parallel-job-count))))))
3590 (replace 'check
3591 (lambda _
3592 ;; Run all the tests that don't require arguments.
3593 (zero? (system* "./test-z3" "/a")))))))
313844d9
TF		 3594 (native-inputs
3595 `(("python" ,python-2)))
3596 (synopsis "Theorem prover")
3597 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
cf684d87 3598theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
313844d9
TF		 3599 (home-page "https://github.com/Z3Prover/z3")
3600 (license license:expat)))
3d5d87a3
JL		 3601
3602(define-public cubicle
3603 (package
3604 (name "cubicle")
3605 (version "1.1.1")
3606 (source (origin
3607 (method url-fetch)
3608 (uri (string-append "http://cubicle.lri.fr/cubicle-"
3609 version ".tar.gz"))
3610 (sha256
3611 (base32
3612 "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h"))))
3613 (build-system gnu-build-system)
3614 (native-inputs
3615 `(("ocaml" ,ocaml)
83fef82b 3616 ("which" ,(@@ (gnu packages base) which))))
3d5d87a3
JL		 3617 (propagated-inputs
3618 `(("z3" ,z3)))
3619 (arguments
3620 `(#:configure-flags (list "--with-z3")
3621 #:tests? #f
3622 #:phases
3623 (modify-phases %standard-phases
3624 (add-before 'configure 'configure-for-release
3625 (lambda _
3626 (substitute* "Makefile.in"
3627 (("SVNREV=") "#SVNREV="))))
3628 (add-before 'configure 'fix-/bin/sh
3629 (lambda _
3630 (substitute* "configure"
3631 (("/bin/sh") (which "sh")))))
3632 (add-before 'configure 'fix-smt-z3wrapper.ml
3633 (lambda _
3634 (substitute* "Makefile.in"
3635 (("\\\\n") "")))))))
3636 (home-page "http://cubicle.lri.fr/")
3637 (synopsis "Model checker for array-based systems")
5a80c15c
RW		 3638 (description "Cubicle is a model checker for verifying safety properties
3639of array-based systems. This is a syntactically restricted class of
3640parametrized transition systems with states represented as arrays indexed by
3641an arbitrary number of processes. Cache coherence protocols and mutual
3642exclusion algorithms are typical examples of such systems.")
3d5d87a3 3643 (license license:asl2.0)))
jackhill's copy of GNU Guix: https://guix.gnu.org/