1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2013, 2014, 2015, 2016, 2019, 2020 Andreas Enge <andreas@enge.fr>
3 ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
4 ;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
5 ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Eric Bavier <bavier@posteo.net>
6 ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
7 ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
8 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
9 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
10 ;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
11 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
12 ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
13 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
14 ;;; Copyright © 2016, 2018, 2020, 2021 Kei Kebreau <kkebreau@posteo.net>
15 ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès <ludo@gnu.org>
16 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
17 ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
18 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
19 ;;; Copyright © 2017 Nikita <nikita@n0.is>
20 ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
21 ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
22 ;;; Copyright © 2017, 2019 Arun Isaac <arunisaac@systemreboot.net>
23 ;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr>
24 ;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
25 ;;; Copyright © 2018, 2019, 2020, 2021 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
26 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
27 ;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
28 ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
29 ;;; Copyright © 2018, 2020, 2021 Marius Bakke <marius@gnu.org>
30 ;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
31 ;;; Copyright © 2018, 2021 Julien Lepiller <julien@lepiller.eu>
32 ;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
33 ;;; Copyright © 2019, 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr>
34 ;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
35 ;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net>
36 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
37 ;;; Copyright © 2020, 2021 Felix Gruber <felgru@posteo.net>
38 ;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in>
39 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
40 ;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
41 ;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com>
42 ;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
43 ;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com>
44 ;;; Copyright © 2020 Martin Becze <mjbecze@riseup.net>
45 ;;; Copyright © 2021 Gerd Heber <gerd.heber@gmail.com>
46 ;;; Copyright © 2021 Franck Pérignon <franck.perignon@univ-grenoble-alpes.fr>
47 ;;; Copyright © 2021 Philip McGrath <philip@philipmcgrath.com>
48 ;;; Copyright © 2021 Paul A. Patience <paul@apatience.com>
49 ;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru>
50 ;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
51 ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
53 ;;; This file is part of GNU Guix.
55 ;;; GNU Guix is free software; you can redistribute it and/or modify it
56 ;;; under the terms of the GNU General Public License as published by
57 ;;; the Free Software Foundation; either version 3 of the License, or (at
58 ;;; your option) any later version.
60 ;;; GNU Guix is distributed in the hope that it will be useful, but
61 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
62 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
63 ;;; GNU General Public License for more details.
65 ;;; You should have received a copy of the GNU General Public License
66 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
68 (define-module (gnu packages maths)
69 #:use-module (ice-9 regex)
70 #:use-module (ice-9 match)
71 #:use-module (gnu packages)
72 #:use-module ((guix licenses) #:prefix license:)
73 #:use-module (guix packages)
74 #:use-module (guix download)
75 #:use-module (guix git-download)
76 #:use-module (guix gexp)
77 #:use-module (guix utils)
78 #:use-module ((guix build utils) #:select (alist-replace))
79 #:use-module (guix build-system cmake)
80 #:use-module (guix build-system glib-or-gtk)
81 #:use-module (guix build-system gnu)
82 #:use-module (guix build-system ocaml)
83 #:use-module (guix build-system python)
84 #:use-module (guix build-system ruby)
85 #:use-module (gnu packages algebra)
86 #:use-module (gnu packages audio)
87 #:use-module (gnu packages autotools)
88 #:use-module (gnu packages base)
89 #:use-module (gnu packages bash)
90 #:use-module (gnu packages bison)
91 #:use-module (gnu packages boost)
92 #:use-module (gnu packages check)
93 #:use-module (gnu packages cmake)
94 #:use-module (gnu packages compression)
95 #:use-module (gnu packages coq)
96 #:use-module (gnu packages curl)
97 #:use-module (gnu packages cyrus-sasl)
98 #:use-module (gnu packages dbm)
99 #:use-module (gnu packages documentation)
100 #:use-module (gnu packages elf)
101 #:use-module (gnu packages emacs)
102 #:use-module (gnu packages file)
103 #:use-module (gnu packages flex)
104 #:use-module (gnu packages fltk)
105 #:use-module (gnu packages fontutils)
106 #:use-module (gnu packages gettext)
107 #:use-module (gnu packages gcc)
108 #:use-module (gnu packages gd)
109 #:use-module (gnu packages ghostscript)
110 #:use-module (gnu packages glib)
111 #:use-module (gnu packages graphviz)
112 #:use-module (gnu packages gtk)
113 #:use-module (gnu packages icu4c)
114 #:use-module (gnu packages image)
115 #:use-module (gnu packages java)
116 #:use-module (gnu packages less)
117 #:use-module (gnu packages lisp)
118 #:use-module (gnu packages linux)
119 #:use-module (gnu packages llvm)
120 #:use-module (gnu packages logging)
121 #:use-module (gnu packages lua)
122 #:use-module (gnu packages gnome)
123 #:use-module (gnu packages guile)
124 #:use-module (gnu packages xorg)
125 #:use-module (gnu packages gl)
126 #:use-module (gnu packages imagemagick)
127 #:use-module (gnu packages m4)
128 #:use-module (gnu packages mpi)
129 #:use-module (gnu packages multiprecision)
130 #:use-module (gnu packages ncurses)
131 #:use-module (gnu packages netpbm)
132 #:use-module (gnu packages ocaml)
133 #:use-module (gnu packages onc-rpc)
134 #:use-module (gnu packages parallel)
135 #:use-module (gnu packages pcre)
136 #:use-module (gnu packages popt)
137 #:use-module (gnu packages perl)
138 #:use-module (gnu packages pkg-config)
139 #:use-module (gnu packages pulseaudio)
140 #:use-module (gnu packages python)
141 #:use-module (gnu packages python-web)
142 #:use-module (gnu packages python-xyz)
143 #:use-module (gnu packages qt)
144 #:use-module (gnu packages readline)
145 #:use-module (gnu packages ruby)
146 #:use-module (gnu packages tbb)
147 #:use-module (gnu packages scheme)
148 #:use-module (gnu packages serialization)
149 #:use-module (gnu packages shells)
150 #:use-module (gnu packages sphinx)
151 #:use-module (gnu packages tcl)
152 #:use-module (gnu packages texinfo)
153 #:use-module (gnu packages tex)
154 #:use-module (gnu packages tls)
155 #:use-module (gnu packages version-control)
156 #:use-module (gnu packages wxwidgets)
157 #:use-module (gnu packages xml)
158 #:use-module (srfi srfi-1)
159 #:use-module (srfi srfi-26))
167 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
169 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
170 (build-system gnu-build-system)
171 (inputs `(("gtk+" ,gtk+)
172 ("libxml2" ,libxml2)))
173 (native-inputs `(("pkg-config" ,pkg-config)))
175 `(#:configure-flags '("CFLAGS=-fcommon")))
176 (synopsis "Natural deduction first-order logic interface")
177 (description "Aris is a program for performing logical proofs. It supports
178 propositional and predicate logic, as well as Boolean algebra and
179 arithmetical logic. In addition to its predefined inference and equivalence
180 rules, Aris also supports references to older proofs. Its use of standard
181 logical symbols and its natural deduction interface make it easy to use for
183 (license license:gpl3+)
184 (home-page "https://www.gnu.org/software/aris/")))
186 (define-public bitwise
192 (uri (string-append "https://github.com/mellowcandle/bitwise"
193 "/releases/download/v" version
194 "/bitwise-v" version ".tar.gz"))
196 (base32 "1lniw4bsb5qs5ybf018qllf95pzixb1q3lvybzl4k3xz8zpkrm6k"))))
197 (build-system gnu-build-system)
199 `(("ncurses" ,ncurses)
200 ("readline" ,readline)))
203 ("pkg-config" ,pkg-config)))
204 (synopsis "Terminal based bit manipulator in ncurses")
205 (description "Bitwise is a multi base interactive calculator supporting
206 dynamic base conversion and bit manipulation. It's a handy tool for low level
207 hackers, kernel developers and device drivers developers.
209 Some of the features include:
211 @item Interactive ncurses interface.
212 @item Command line calculator supporting all bitwise operations.
213 @item Individual bit manipulator.
214 @item Bitwise operations such as NOT, OR, AND, XOR, and shifts.
216 (license license:gpl3+)
217 (home-page "https://github.com/mellowcandle/bitwise/")))
219 (define-public c-graph
225 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
228 "092412jzxy6wdvpk96pfj499hpmaww8xllavbvlqspfpr7ips9id"))))
229 (build-system gnu-build-system)
231 `(("fortran" ,gfortran)))
232 (synopsis "Visualizing and demonstrating convolution")
234 "GNU C-Graph is a tool for demonstrating the theory of convolution.
235 Thus, it can serve as an excellent aid to students of signal and systems
236 theory in visualizing the convolution process. Rather than forcing the
237 student to write code, the program offers an intuitive interface with
238 interactive dialogs to guide them.")
239 (license license:gpl3+)
240 (home-page "https://www.gnu.org/software/c-graph/")))
249 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
250 version "/coda-" version ".tar.gz"))
252 (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245"))
253 (patches (search-patches "coda-use-system-libs.patch"))
254 (modules '((guix build utils)))
256 ;; Make sure we don't use the bundled software.
258 (for-each (lambda (d)
259 (delete-file-recursively (string-append "libcoda/" d)))
260 '("zlib" "pcre" "expat"))
263 `(("fortran" ,gfortran)
265 ("python-numpy" ,python-numpy)))
272 (build-system gnu-build-system)
274 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
275 "LIBS= -lz -lpcre -lexpat")))
276 (synopsis "A common interface to various earth observation data formats")
278 "The Common Data Access toolbox (CODA) provides a set of interfaces for
279 reading remote sensing data from earth observation data files. It consists of
280 command line applications and interfaces to the C, Fortran, Python, and Java
281 programming languages.")
282 (home-page "https://stcorp.nl/coda")
283 (license license:gpl2+)))
291 (uri (string-append "http://www.qhull.org/download/qhull-"
292 (car (string-split version #\.))
296 "0zlbhg0lb6j60188c2xhcrvviskr079552icjldqhy1jhgmxghmm"))))
297 (build-system cmake-build-system)
299 `(#:configure-flags '("-DLINK_APPS_SHARED=ON"
300 "-DCMAKE_POSITION_INDEPENDENT_CODE=ON")))
301 (synopsis "Calculate convex hulls and related structures")
303 "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
304 diagram, halfspace intersection about a point, furthest-site Delaunay
305 triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d,
306 3-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull
307 algorithm for computing the convex hull. It handles roundoff errors from
308 floating point arithmetic. It computes volumes, surface areas, and
309 approximations to the convex hull.
311 @code{Qhull} does not support triangulation of non-convex surfaces, mesh
312 generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
313 shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
315 (home-page "http://qhull.org")
316 (license (license:non-copyleft "file://COPYING.txt"
317 "See COPYING in the distribution."))))
319 (define-public python-cvxopt
321 (name "python-cvxopt")
326 (url "https://github.com/cvxopt/cvxopt")
328 (file-name (git-file-name name version))
331 "1kiy2m62xgs2d5id6dnnwy4vap85cd70p7pgkb9nh23qf9xnak7b"))))
332 (build-system python-build-system)
335 (modify-phases %standard-phases
336 (add-after 'unpack 'find-libraries
337 (lambda* (#:key inputs #:allow-other-keys)
338 (setenv "CVXOPT_BLAS_LIB" "openblas")
339 (setenv "CVXOPT_BUILD_FFTW" "1")
340 (setenv "CVXOPT_BUILD_GLPK" "1")
341 (setenv "CVXOPT_BUILD_GSL" "1")
348 ("openblas" ,openblas)
349 ("suitesparse" ,suitesparse)))
350 (home-page "https://www.cvxopt.org")
351 (synopsis "Python library for convex optimization")
353 "CVXOPT is a package for convex optimization based on the Python
354 programming language. Its main purpose is to make the development of software
355 for convex optimization applications straightforward by building on Python’s
356 extensive standard library and on the strengths of Python as a high-level
357 programming language.")
358 (license license:gpl3+)))
360 (define-public python2-cvxopt
361 (package-with-python2 python-cvxopt))
369 (uri (string-append "mirror://gnu/units/units-" version
372 "1bybhqs4yrly9myb5maz3kdmf8k4fhk2m1d5cbcryn40z6lq0gkc"))))
373 (build-system gnu-build-system)
375 `(("readline" ,readline)
376 ("python" ,python-wrapper) ;for 'units_cur' script
377 ("python-requests" ,python-requests)))
379 `(#:phases (modify-phases %standard-phases
380 (add-after 'install 'wrap-units_cur
381 (lambda* (#:key outputs #:allow-other-keys)
382 (let* ((out (assoc-ref outputs "out"))
383 (bin (string-append out "/bin")))
384 (wrap-program (string-append bin "/units_cur")
385 `("GUIX_PYTHONPATH" ":" prefix
386 ,(search-path-as-string->list (getenv "GUIX_PYTHONPATH"))))
388 (synopsis "Conversion between thousands of scales")
390 "GNU Units converts numeric quantities between units of measure. It
391 can handle scale changes through adaptive usage of standard scale
392 prefixes (micro-, kilo-, etc.). It can also handle nonlinear
393 conversions such as Fahrenheit to Celsius. Its interpreter is powerful
394 enough to be used effectively as a scientific calculator.")
395 (license license:gpl3+)
396 (home-page "https://www.gnu.org/software/units/")))
398 (define-public double-conversion
400 (name "double-conversion")
402 (home-page "https://github.com/google/double-conversion")
405 (uri (git-reference (url home-page)
406 (commit (string-append "v" version))))
407 (file-name (git-file-name name version))
410 "0csy4pjw1p8rp6g5qxi2h0ychhhp1fldv7gb761627fs2mclw9gv"))))
411 (build-system cmake-build-system)
413 '(#:test-target "test"
414 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
415 "-DBUILD_TESTING=ON")))
416 (synopsis "Conversion routines for IEEE doubles")
418 "The double-conversion library provides binary-decimal and decimal-binary
419 routines for IEEE doubles. The library consists of efficient conversion
420 routines that have been extracted from the V8 JavaScript engine.")
421 (license license:bsd-3)))
423 (define-public dionysus
429 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
433 "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
434 (build-system gnu-build-system)
435 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
436 (synopsis "Local search for universal constants and scientific values")
438 "GNU Dionysus is a convenient system for quickly retrieving the values of
439 mathematical constants used in science and engineering. Values can be
440 searched using a simple command-line tool, choosing from three databases:
441 universal constants, atomic numbers, and constants related to
443 (license license:gpl3+)
444 (home-page "https://www.gnu.org/software/dionysus/")))
455 "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/"
456 "dSFMT-src-" version ".tar.gz"))
459 "03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))
460 (modules '((guix build utils)))
461 ;; Don't distribute html documentation with bundled jquery.
464 (delete-file-recursively "html") #t))
465 ;; Add patches borrowed from Julia.
471 "https://raw.githubusercontent.com/JuliaLang/julia/"
472 "v1.3.0/deps/patches/dSFMT.c.patch"))
474 "09mhv11bms8jsmkmdqvlcgljwhzw3b6n9nncpi2b6dla9798hw2y"))
475 (file-name "dSFMT.c.patch"))
479 "https://raw.githubusercontent.com/JuliaLang/julia/"
480 "v1.3.0/deps/patches/dSFMT.h.patch"))
482 "1py5rd0yxic335lzka23f6x2dhncrpizpyrk57gi2f28c0p98y5n"))
483 (file-name "dSFMT.h.patch"))))))
484 (build-system gnu-build-system)
487 (modify-phases %standard-phases
488 (delete 'configure) ; no configure script
490 ;; Upstream Makefile does not build a shared library. Borrow from Julia
491 ;; https://github.com/JuliaLang/julia/blob/v1.3.0/deps/dsfmt.mk
494 "gcc" "-DNDEBUG" "-DDSFMT_MEXP=19937"
495 "-fPIC" "-DDSFMT_DO_NOT_USE_OLD_NAMES"
496 "-O3" "-finline-functions" "-fomit-frame-pointer"
497 "-fno-strict-aliasing" "--param" "max-inline-insns-single=1800"
498 "-Wmissing-prototypes" "-Wall" "-std=c99" "-shared" "dSFMT.c"
499 "-o" "libdSFMT.so")))
500 (replace 'install ; no "install" target
501 (lambda* (#:key outputs #:allow-other-keys)
502 (let* ((out (assoc-ref outputs "out"))
503 (lib (string-append out "/lib"))
504 (inc (string-append out "/include"))
505 (doc (string-append out "/share/doc/" ,name "-" ,version)))
506 (install-file "libdSFMT.so" lib)
507 (install-file "dSFMT.h" inc)
508 (install-file "LICENSE.txt" doc)
510 (synopsis "Double precision SIMD-oriented Fast Mersenne Twister")
512 "The dSMFT package speeds up Fast Mersenne Twister generation by avoiding
513 the expensive conversion of integer to double (floating point). dSFMT directly
514 generates double precision floating point pseudorandom numbers which have the
515 IEEE Standard for Binary Floating-Point Arithmetic (ANSI/IEEE Std 754-1985)
516 format. dSFMT is only available on the CPUs which use IEEE 754 format double
517 precision floating point numbers.")
518 (home-page "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/")
519 (license license:bsd-3)))
527 (uri (string-append "mirror://gnu/gsl/gsl-"
531 "0av04cpblphvvs3kl5rwphniarml503501vrpqw31rd0bmwg7fzg"))))
532 (build-system gnu-build-system)
534 (let ((system (%current-system)))
535 `(#:configure-flags (list "--disable-static") ;halves package size
537 (modify-phases %standard-phases
539 ((or (string-prefix? "aarch64" system)
540 (string-prefix? "powerpc" system))
541 ;; Some sparse matrix tests are failing on AArch64 and PowerPC:
542 ;; https://lists.gnu.org/archive/html/bug-gsl/2020-04/msg00001.html
543 '((add-before 'check 'disable-failing-tests
545 (substitute* "spmatrix/test.c"
546 ((".*test_complex.*") "\n"))))))
548 ((string-prefix? "i686" system)
549 ;; There are rounding issues with these tests on i686:
550 ;; https://lists.gnu.org/archive/html/bug-gsl/2016-10/msg00000.html
551 ;; https://lists.gnu.org/archive/html/bug-gsl/2020-04/msg00000.html
552 '((add-before 'check 'disable-failing-tests
554 (substitute* "linalg/test.c"
555 ((".*gsl_test\\(test_LU_decomp.*") "\n")
556 ((".*gsl_test\\(test_LUc_decomp.*") "\n")
557 ((".*gsl_test\\(test_QR_decomp_r.*") "\n")
558 ((".*gsl_test\\(test_cholesky_decomp.*") "\n")
559 ((".*gsl_test\\(test_pcholesky_solve.*") "\n")
560 ((".*gsl_test\\(test_COD_lssolve2.*") "\n"))
561 (substitute* "spmatrix/test.c"
562 ((".*test_all.*") "\n")
563 ((".*test_float.*") "\n")
564 ((".*test_complex.*") "\n"))
566 ;; XXX: These tests abort with:
567 ;; gsl: cholesky.c:645: ERROR: matrix is not positive definite
568 (substitute* '("multifit_nlinear/test.c"
569 "multilarge_nlinear/test.c")
570 (("gsl_ieee_env_setup.*" all)
571 (string-append "exit (77);\n" all)))))))
574 (home-page "https://www.gnu.org/software/gsl/")
575 (synopsis "Numerical library for C and C++")
577 "The GNU Scientific Library is a library for numerical analysis in C
578 and C++. It includes a wide range of mathematical routines, with over 1000
579 functions in total. Subject areas covered by the library include:
580 differential equations, linear algebra, Fast Fourier Transforms and random
582 (license license:gpl3+)))
592 (url "https://github.com/shibatch/sleef")
594 (file-name (git-file-name name version))
596 (base32 "1jybqrl2dvjxzg30xrhh847s375n2jr1pix644wi6hb5wh5mx3f7"))))
597 (build-system cmake-build-system)
599 '(#:configure-flags (list "-DCMAKE_BUILD_TYPE=Release"
600 (string-append "-DCMAKE_INSTALL_LIBDIR="
601 (assoc-ref %outputs "out")
603 (string-append "-DCMAKE_INSTALL_PREFIX="
604 (assoc-ref %outputs "out")))
606 (modify-phases %standard-phases
607 ;; SLEEF generates a header library during the build process and writes
608 ;; to it via shell redirection. Make the checkout writable so the
609 ;; build can succeed.
610 (add-after 'unpack 'make-git-checkout-writable
612 (for-each make-file-writable (find-files "."))
618 ("openssl" ,openssl)))
619 (home-page "https://sleef.org/")
620 (synopsis "SIMD library for evaluating elementary functions and DFT")
622 "SLEEF (SIMD Library for Evaluating Elementary Functions) is a library that
623 implements vectorized versions of all C99 real floating point math functions.
624 It can utilize SIMD instructions that are available on modern processors.")
625 (license (list license:boost1.0 ;sleef
626 license:cc-by4.0)))) ;simplex algorithm
635 (uri (string-append "mirror://gnu/glpk/glpk-"
639 "05bgxidxj8d9xdp82niy7cy36w181cxq7p8vc3y2ixshpgp1642a"))))
640 (build-system gnu-build-system)
644 `(#:configure-flags '("--with-gmp"
645 "--disable-static")))
646 (home-page "https://www.gnu.org/software/glpk/")
647 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
649 "GLPK is a C library for solving large-scale linear programming (LP),
650 mixed integer programming (MIP), and other related problems. It supports the
651 GNU MathProg modeling language, a subset of the AMPL language, and features a
652 translator for the language. In addition to the C library, a stand-alone
653 LP/MIP solver is included in the package.")
654 (license license:gpl3+)))
656 (define-public glpk-4
664 (uri (string-append "mirror://gnu/glpk/glpk-"
668 "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))))
677 (uri (string-append "https://github.com/4ti2/4ti2/releases/download/"
679 (string-map (lambda (c) (if (char=? c #\.) #\_ c))
681 "/4ti2-" version ".tar.gz"))
683 (base32 "0rj92x6p9m3la5gasjbj7sa569im527ffmka5y2sv1amgd3fflrh"))))
684 (build-system gnu-build-system)
686 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
690 (home-page "http://www.4ti2.de/")
691 (synopsis "Mathematical tool suite for problems on linear spaces")
693 "4ti2 implements algorithms for solving algebraic, geometric and
694 combinatorial problems on linear spaces. Among others, it solves systems
695 of linear equations, computes extreme rays of polyhedral cones, solves
696 integer programming problems and computes Markov bases for statistics.")
697 (license license:gpl2+)))
699 (define-public cddlib
706 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
707 (string-delete #\. version) ".tar.gz"))
710 "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
711 (build-system gnu-build-system)
714 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
715 (synopsis "Library for convex hulls and extreme rays of polyhedra")
717 "The C-library cddlib implements the Double Description Method of
718 Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
719 rays of a general convex polyhedron given by a system of linear inequalities
720 in arbitrary dimension. It can also be used for the converse operation of
721 computing convex hulls.")
722 (license license:gpl2+)))
724 (define-public lrslib
731 (uri (string-append "http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/"
733 (string-delete #\. version) ".tar.gz"))
736 "05kq3hzam31dlmkccv3v358r478kpvx76mw37ka12c6ypwv5dsnk"))))
737 (build-system gnu-build-system)
741 `(#:tests? #f ; no check phase
742 #:make-flags `("CC=gcc"
743 ,(string-append "prefix=" (assoc-ref %outputs "out"))
746 (modify-phases %standard-phases
749 (substitute* "makefile"
750 (("-L \\.") "-L . -Wl,-rpath='$$ORIGIN/../lib'"))
752 (home-page "http://cgm.cs.mcgill.ca/~avis/C/lrs.html")
753 (synopsis "Convex hulls of polyhedra with exact arithmetic")
755 "The C code of lrslib implements the reverse search algorithm for
756 vertex enumeration and convex hull problems. Its input file format is
757 compatible with cddlib. All computations are done exactly in either
758 multiple precision or fixed integer arithmetic. Output is not stored
759 in memory, so even problems with very large output sizes can sometimes
761 (license license:gpl2+)))
763 (define-public libcerf
771 (url "https://jugit.fz-juelich.de/mlz/libcerf")
772 (commit (string-append "v" version))))
773 (file-name (git-file-name name version))
775 (base32 "1ic2q7kvxpqmgxlishygvx8d00i4wn51vkq4fyac44ahhf6c3kwd"))))
776 (build-system cmake-build-system)
779 (home-page "https://jugit.fz-juelich.de/mlz/libcerf")
780 (synopsis "Library for complex error functions")
782 "@code{libcerf} is a self-contained numeric library that provides an
783 efficient and accurate implementation of complex error functions, along with
784 Dawson, Faddeeva, and Voigt functions.")
785 (license license:expat)))
794 (uri (string-append "https://www.math.u-bordeaux.fr/~aenge/software/"
795 "vinci/vinci-" version ".tar.gz"))
798 "1aq0qc1y27iw9grhgnyji3290wwfznsrk3sg6ynqpxwjdda53h4m"))))
799 (build-system gnu-build-system)
801 `(("lrslib" ,lrslib)))
803 `(#:tests? #f ; no check phase
805 (modify-phases %standard-phases
807 ;; register the lrs location in the config file
808 (lambda* (#:key inputs #:allow-other-keys)
809 (let* ((lrs (assoc-ref inputs "lrslib"))
810 (lrsexec (string-append lrs "/bin/lrs")))
811 (substitute* "vinci.h"
812 (("#define LRS_EXEC \"lrs\"")
813 (string-append "#define LRS_EXEC \"" lrsexec "\""))))
816 (lambda* (#:key outputs #:allow-other-keys)
817 (let* ((out (assoc-ref outputs "out"))
818 (bin (string-append out "/bin")))
819 (install-file "vinci" bin))
822 "https://www.math.u-bordeaux.fr/~aenge/?category=software&page=vinci")
823 (synopsis "Volume computation for polytopes")
825 "Vinci implements a number of volume computation algorithms for convex
826 polytopes in arbitrary dimension. The polytopes can be given by their
827 V-representation (as the convex hull of a finite number of vertices), by
828 their H-representation (as the bounded intersection of a finite number of
829 halfspaces) or by their double description with both representations.")
830 (license license:gpl2+)))
832 (define-public arpack-ng
836 (home-page "https://github.com/opencollab/arpack-ng")
839 (uri (git-reference (url home-page) (commit version)))
840 (file-name (git-file-name name version))
843 "0l7as5z6xvbxly8alam9s4kws70952qq35a6vkljzayi4b9gbklx"))))
844 (build-system gnu-build-system)
846 `(("autoconf" ,autoconf)
847 ("automake" ,automake)
849 ("pkg-config" ,pkg-config)))
853 ("fortran" ,gfortran)))
854 (synopsis "Fortran subroutines for solving eigenvalue problems")
856 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
857 large scale eigenvalue problems.")
858 (license (license:non-copyleft "file://COPYING"
859 "See COPYING in the distribution."))))
861 (define-public arpack-ng-3.3.0
868 (uri (git-reference (url (package-home-page arpack-ng))
870 (file-name (git-file-name (package-name arpack-ng) version))
873 "00h6bjvxjq7bv0b8pwnc0gw33ns6brlqv00xx2rh3w9b5n205918"))))))
875 (define-public arpack-ng-openmpi
876 (package (inherit arpack-ng)
877 (name "arpack-ng-openmpi")
880 ,@(package-inputs arpack-ng)))
882 (substitute-keyword-arguments (package-arguments arpack-ng)
883 ((#:configure-flags _ '())
885 ((#:phases phases '%standard-phases)
886 `(modify-phases ,phases
887 (add-before 'check 'mpi-setup
889 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
891 (define-public lapack
898 (uri (string-append "http://www.netlib.org/lapack/lapack-"
902 "1155qixp26c12yrxc76z9mlfw2h3xxymxxv5znpgzh5gaykpndgj"))))
903 (build-system cmake-build-system)
904 (home-page "http://www.netlib.org/lapack/")
905 (inputs `(("fortran" ,gfortran)
906 ("python" ,python-wrapper)))
908 `(#:configure-flags (list
909 "-DBUILD_SHARED_LIBS:BOOL=YES"
911 ;; Build the 'LAPACKE_clatms' functions.
912 "-DLAPACKE_WITH_TMG=ON"
913 "-DBUILD_TESTING=ON")))
914 (synopsis "Library for numerical linear algebra")
916 "LAPACK is a Fortran 90 library for solving the most commonly occurring
917 problems in numerical linear algebra.")
918 (license (license:non-copyleft "file://LICENSE"
919 "See LICENSE in the distribution."))))
921 (define-public clapack
928 (uri (string-append "http://www.netlib.org/clapack/clapack-"
929 version "-CMAKE.tgz"))
932 "0nnap9q1mv14g57dl3vkvxrdr10k5w7zzyxs6rgxhia8q8mphgqb"))))
933 (build-system cmake-build-system)
936 (modify-phases %standard-phases
937 ;; These tests use a lot of stack variables and segfault without
938 ;; lifting resource limits.
939 (add-after 'unpack 'disable-broken-tests
941 (substitute* "TESTING/CMakeLists.txt"
942 (("add_lapack_test.* xeigtstz\\)") ""))
945 (lambda* (#:key outputs #:allow-other-keys)
946 (let* ((out (assoc-ref outputs "out"))
947 (libdir (string-append out "/lib"))
948 (f2cinc (string-append out "/include/libf2c")))
951 (for-each (lambda (file)
952 (install-file file libdir))
954 "F2CLIBS/libf2c/libf2c.a"
955 "TESTING/MATGEN/libtmglib.a"
956 "BLAS/SRC/libblas.a"))
957 (for-each (lambda (file)
958 (install-file file f2cinc))
959 (cons "F2CLIBS/libf2c/arith.h"
960 (find-files (string-append "../clapack-"
961 ,version "-CMAKE/F2CLIBS/libf2c")
963 (copy-recursively (string-append "../clapack-"
964 ,version "-CMAKE/INCLUDE")
965 (string-append out "/include"))
967 (home-page "https://www.netlib.org/clapack/")
968 (synopsis "Numerical linear algebra library for C")
970 "The CLAPACK library was built using a Fortran to C conversion utility
971 called f2c. The entire Fortran 77 LAPACK library is run through f2c to obtain
972 C code, and then modified to improve readability. CLAPACK's goal is to
973 provide LAPACK for someone who does not have access to a Fortran compiler.")
974 (license (license:non-copyleft "file://LICENSE"
975 "See LICENSE in the distribution."))))
977 (define-public scalapack
984 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
988 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))
989 (patches (search-patches "scalapack-blacs-mpi-deprecations.patch"))))
990 (build-system cmake-build-system)
993 ("fortran" ,gfortran)
994 ("lapack" ,lapack))) ;for testing only
996 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
997 #:phases (modify-phases %standard-phases
998 (add-before 'check 'mpi-setup
1000 (home-page "http://www.netlib.org/scalapack/")
1001 (synopsis "Library for scalable numerical linear algebra")
1003 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
1004 routines on parallel distributed memory machines. ScaLAPACK solves dense and
1005 banded linear systems, least squares problems, eigenvalue problems, and
1006 singular value problems.")
1007 (license (license:non-copyleft "file://LICENSE"
1008 "See LICENSE in the distribution."))))
1010 (define-public gnuplot
1016 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
1020 (base32 "1fp7rbhjmz2w63r72kicf8lfszzimz2csfx868fracw167hpaz75"))))
1021 (build-system gnu-build-system)
1022 (inputs `(("readline" ,readline)
1028 `(("pkg-config" ,pkg-config)
1029 ("texlive" ,texlive-tiny)))
1030 (arguments `(#:configure-flags (list (string-append
1031 "--with-texdir=" %output
1032 "/texmf-local/tex/latex/gnuplot"))
1033 ;; Plot on a dumb terminal during tests.
1034 #:make-flags '("GNUTERM=dumb")))
1035 (home-page "http://www.gnuplot.info")
1036 (synopsis "Command-line driven graphing utility")
1037 (description "Gnuplot is a portable command-line driven graphing
1038 utility. It was originally created to allow scientists and students to
1039 visualize mathematical functions and data interactively, but has grown to
1040 support many non-interactive uses such as web scripting. It is also used as a
1041 plotting engine by third-party applications like Octave.")
1042 ;; X11 Style with the additional restriction that derived works may only be
1043 ;; distributed as patches to the original.
1044 (license (license:fsf-free
1045 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
1055 (url "https://github.com/OkoSanto/GCTP")
1056 (commit (string-append "v" version))))
1057 (file-name (git-file-name name version))
1059 (base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
1061 `(("fortran" ,gfortran)))
1062 (build-system gnu-build-system)
1063 (synopsis "General Cartographic Transformation Package (GCTP)")
1065 "The General Cartographic Transformation Package (GCTP) is a system of
1066 software routines designed to permit the transformation of coordinate pairs
1067 from one map projection to another. The GCTP is the standard computer
1068 software used by the National Mapping Division for map projection
1070 (home-page "https://github.com/OkoSanto/GCTP")
1071 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
1080 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
1081 version "/src/hdf-" version ".tar.bz2"))
1083 (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l"))
1084 (patches (search-patches "hdf4-architectures.patch"
1085 "hdf4-reproducibility.patch"
1086 "hdf4-shared-fortran.patch"
1087 "hdf4-tirpc.patch"))))
1088 (build-system gnu-build-system)
1090 `(("gfortran" ,gfortran)
1095 ("libjpeg" ,libjpeg-turbo)
1096 ("libtirpc" ,libtirpc)))
1098 `(#:parallel-tests? #f
1099 #:configure-flags (list "--enable-shared"
1100 "FCFLAGS=-fallow-argument-mismatch"
1101 "FFLAGS=-fallow-argument-mismatch"
1102 (string-append "CPPFLAGS=-I"
1103 (assoc-ref %build-inputs "libtirpc")
1106 (modify-phases %standard-phases
1107 ;; This is inspired by two of Debian's patches.
1108 (add-before 'configure 'add-more-aarch64-support
1110 (substitute* '("mfhdf/ncgen/ncgen.l"
1111 "mfhdf/ncgen/ncgenyy.c"
1112 "mfhdf/libsrc/netcdf.h.in")
1113 (("AIX5L64") "__aarch64__"))
1115 (add-before 'configure 'patchbuild
1118 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
1120 (("/bin/mkdir") "mkdir"))
1121 (substitute* (find-files "." "^Makefile\\.in$")
1122 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
1123 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
1124 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
1125 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
1126 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
1128 (add-after 'configure 'patch-settings
1130 ;; libhdf4.settings contains the full path of the
1131 ;; compilers used, and its contents are included in
1132 ;; .so-files. We truncate the hashes to avoid
1133 ;; unnecessary store references to those compilers:
1134 (substitute* "libhdf4.settings"
1135 (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash)
1136 (string-append prefix (string-take hash 10) "...")))
1138 (add-after 'install 'provide-absolute-libjpeg-reference
1139 (lambda* (#:key inputs outputs #:allow-other-keys)
1140 (let ((out (assoc-ref outputs "out"))
1141 (libjpeg (assoc-ref inputs "libjpeg")))
1142 ;; libjpeg-turbo does not provide a .la file, so libtool is
1143 ;; unable to add an absolute reference for -ljpeg in the .la
1144 ;; files. Fix it manually to avoid having to propagate it.
1145 (substitute* (find-files (string-append out "/lib") "\\.la$")
1147 (string-append "-L" libjpeg "/lib -ljpeg")))
1149 (home-page "https://www.hdfgroup.org/products/hdf4/")
1151 "Library and multi-object file format for storing and managing data")
1152 (description "HDF4 is a library and multi-object file format for storing
1153 and managing data between machines. HDF4 is an older hierarchical data format,
1154 incompatible with HDF5.")
1156 (license:non-copyleft
1157 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
1159 (define-public hdf4-alt
1164 (substitute-keyword-arguments (package-arguments hdf4)
1165 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
1167 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
1169 (define-public hdf5-1.8
1176 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
1177 "hdf5-" (version-major+minor version)
1178 "/hdf5-" version "/src/hdf5-"
1180 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
1182 (match (string-split version #\.)
1183 ((major minor _ ...)
1184 (string-append major minor)))
1185 "/src/hdf5-" version ".tar.bz2")))
1187 (base32 "194ki2s5jrgl4czkvy5nc9nwjyapah0fj72l0gb0aysplp38i6v8"))
1188 (patches (search-patches "hdf5-config-date.patch"))))
1189 (build-system gnu-build-system)
1193 `(("gfortran" ,gfortran)
1194 ("perl" ,perl))) ;part of the test machinery needs Perl
1195 (outputs '("out" ; core library
1196 "fortran")) ; fortran interface
1198 `(;; Some of the users, notably Flann, need the C++ interface.
1199 #:configure-flags '("--enable-cxx"
1201 "--enable-fortran2003"
1203 ;; Build a thread-safe library. Unfortunately,
1204 ;; 'configure' invites you to either turn off C++,
1205 ;; Fortran, and the high-level interface (HL), or
1206 ;; to pass '--enable-unsupported'. Debian
1207 ;; packagers chose to pass '--enable-unsupported'
1208 ;; and we follow their lead here.
1209 "--enable-threadsafe"
1211 "--enable-unsupported")
1212 ;; Use -fPIC to allow the R bindings to link with the static libraries
1213 #:make-flags (list "CFLAGS=-fPIC"
1216 (modify-phases %standard-phases
1217 (add-before 'configure 'patch-configure
1218 (lambda* (#:key outputs #:allow-other-keys)
1219 (substitute* "configure"
1221 (substitute* "fortran/src/Makefile.in"
1222 (("libhdf5_fortran_la_LDFLAGS =")
1223 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
1224 (assoc-ref outputs "fortran") "/lib")))
1225 (substitute* "hl/fortran/src/Makefile.in"
1226 (("libhdf5hl_fortran_la_LDFLAGS =")
1227 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
1228 (assoc-ref outputs "fortran") "/lib")))
1230 (add-after 'configure 'patch-settings
1232 ;; libhdf5.settings contains the full path of the
1233 ;; compilers used, and its contents are included in
1234 ;; libhdf5.so. We truncate the hashes to avoid
1235 ;; unnecessary store references to those compilers:
1236 (substitute* "src/libhdf5.settings"
1237 (("(/gnu/store/)([a-zA-Z0-9]*)" all prefix hash)
1238 (string-append prefix (string-take hash 10) "..."))
1239 ;; Don't record the build-time kernel version to make the
1240 ;; settings file reproducible.
1241 (("Uname information:.*")
1242 "Uname information: Linux\n"))
1244 (add-after 'install 'patch-references
1245 (lambda* (#:key inputs outputs #:allow-other-keys)
1246 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
1247 (zlib (assoc-ref inputs "zlib")))
1248 (substitute* (find-files bin "h5p?cc")
1250 (string-append "-L" zlib "/lib " lib)))
1252 (add-after 'install 'split
1253 (lambda* (#:key inputs outputs #:allow-other-keys)
1254 ;; Move all fortran-related files
1255 (let* ((out (assoc-ref outputs "out"))
1256 (bin (string-append out "/bin"))
1257 (lib (string-append out "/lib"))
1258 (inc (string-append out "/include"))
1259 (ex (string-append out "/share/hdf5_examples/fortran"))
1260 (fort (assoc-ref outputs "fortran"))
1261 (fbin (string-append fort "/bin"))
1262 (flib (string-append fort "/lib"))
1263 (finc (string-append fort "/include"))
1264 (fex (string-append fort "/share/hdf5_examples/fortran")))
1269 ;; Note: When built with --enable-parallel, the 'h5fc' file
1270 ;; doesn't exist, hence this condition.
1271 (when (file-exists? (string-append bin "/h5fc"))
1272 (rename-file (string-append bin "/h5fc")
1273 (string-append fbin "/h5fc")))
1274 (for-each (lambda (file)
1276 (string-append flib "/" (basename file))))
1277 (find-files lib ".*fortran.*"))
1278 (for-each (lambda (file)
1280 (string-append finc "/" (basename file))))
1281 (find-files inc ".*mod"))
1282 (for-each (lambda (file)
1284 (string-append fex "/" (basename file))))
1285 (find-files ex ".*"))
1286 (delete-file-recursively ex))
1288 (home-page "https://www.hdfgroup.org")
1289 (synopsis "Management suite for extremely large and complex data")
1290 (description "HDF5 is a suite that makes possible the management of
1291 extremely large and complex data collections.")
1292 (license (license:x11-style
1293 "https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
1295 (define-public hdf5-1.10
1302 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
1303 "hdf5-" (version-major+minor version)
1304 "/hdf5-" version "/src/hdf5-"
1306 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
1308 (apply string-append
1309 (take (string-split version #\.) 2))
1310 "/src/hdf5-" version ".tar.bz2")))
1312 (base32 "0pm5xxry55i0h7wmvc7svzdaa90rnk7h78rrjmnlkz2ygsn8y082"))
1313 (patches (search-patches "hdf5-config-date.patch"))))))
1315 (define-public hdf5-1.12
1322 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
1323 "hdf5-" (version-major+minor version)
1324 "/hdf5-" version "/src/hdf5-"
1326 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
1328 (apply string-append
1329 (take (string-split version #\.) 2))
1330 "/src/hdf5-" version ".tar.bz2")))
1332 (base32 "0qazfslkqbmzg495jafpvqp0khws3jkxa0z7rph9qvhacil6544p"))
1333 (patches (search-patches "hdf5-config-date.patch"))))))
1336 ;; Default version of HDF5.
1339 (define-public hdf-java
1347 "https://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
1348 version "/src/CMake-hdfjava-" version ".tar.gz"))
1350 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
1351 (modules '((guix build utils)))
1352 (snippet ; Make sure we don't use the bundled sources and binaries.
1354 (for-each delete-file
1355 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
1356 "HDF4.tar.gz" "HDF5.tar.gz"))
1357 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
1359 (build-system gnu-build-system)
1361 `(("jdk" ,icedtea "jdk")
1362 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
1364 ("hamcrest-core" ,java-hamcrest-core)
1365 ("junit" ,java-junit)
1366 ("slf4j-simple" ,java-slf4j-simple)))
1371 ("libjpeg" ,libjpeg-turbo)
1372 ("slf4j-api" ,java-slf4j-api)))
1375 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
1376 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
1377 (assoc-ref %build-inputs "jdk") "/lib" )
1378 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
1379 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
1382 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
1383 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
1384 (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
1385 (string-append "JPEGLIB="
1386 (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
1390 (modify-phases %standard-phases
1391 (add-before 'configure 'chdir-to-source
1392 (lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
1393 (add-before 'configure 'patch-build
1394 (lambda* (#:key inputs outputs #:allow-other-keys)
1395 (substitute* "configure"
1396 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
1397 (("/bin/cat") (which "cat")))
1398 ;; Set classpath for compilation
1399 (substitute* '("hdf/hdf5lib/Makefile.in"
1400 "hdf/hdf5lib/exceptions/Makefile.in"
1401 "hdf/hdflib/Makefile.in")
1402 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
1403 (search-input-file inputs "/share/java/slf4j-api.jar")))
1404 ;; Replace outdated config.sub and config.guess:
1405 (with-directory-excursion "config"
1406 (for-each (lambda (file)
1408 (search-input-file inputs
1411 ,(version-major+minor (package-version automake))
1414 '("config.sub" "config.guess")))
1416 ;; Fix embedded version number
1417 (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
1418 (substitute* "hdf/hdf5lib/H5.java"
1420 (string-join hdf5version ", "))))
1422 (mkdir-p (string-append (assoc-ref outputs "out")))
1423 ;; Set classpath for tests
1424 (let* ((build-dir (getcwd))
1425 (lib (string-append build-dir "/lib"))
1426 (jhdf (string-append lib "/jhdf.jar"))
1427 (jhdf5 (string-append lib "/jhdf5.jar"))
1431 (string-append (assoc-ref inputs i)
1432 "/share/java/" i ".jar"))
1433 '("slf4j-api" "slf4j-simple"))
1435 (car (find-files (assoc-ref inputs "junit") "jar$"))
1436 (car (find-files (assoc-ref inputs "hamcrest-core")
1439 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
1441 (substitute* '("test/hdf5lib/Makefile.in"
1442 "test/hdf5lib/junit.sh.in"
1443 "examples/runExample.sh.in")
1445 (search-input-file inputs "/bin/test"))
1447 (search-input-file inputs "/bin/uname"))
1448 (("CLASSPATH=[^\n]*")
1449 (string-append "CLASSPATH=" class-path)))
1450 (setenv "CLASSPATH" class-path))
1452 (add-before 'check 'build-examples
1454 (apply invoke `("javac"
1455 ,@(find-files "examples" ".*\\.java"))))))
1457 #:parallel-build? #f
1459 #:parallel-tests? #f ))
1460 (home-page "https://support.hdfgroup.org/products/java")
1461 (synopsis "Java interface for the HDF4 and HDF5 libraries")
1462 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
1463 the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
1466 ;; BSD-style license:
1467 (license (license:x11-style
1468 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
1469 /current/src/unpacked/COPYING"))))
1471 (define-public hdf-eos2
1478 (uri "ftp://edhs1.gsfc.nasa.gov\
1479 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
1481 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
1482 (patches (search-patches "hdf-eos2-remove-gctp.patch"
1483 "hdf-eos2-build-shared.patch"
1484 "hdf-eos2-fortrantests.patch"))))
1485 (build-system gnu-build-system)
1487 `(("gfortran" ,gfortran)))
1489 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
1490 ;; XXX: These inputs are really dependencies of hdf4.
1492 ("libjpeg" ,libjpeg-turbo)
1493 ("libtirpc" ,libtirpc)
1497 `( #:configure-flags '("--enable-install-include" "--enable-shared"
1498 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
1499 #:parallel-tests? #f))
1500 (home-page "https://hdfeos.org/software/library.php#HDF-EOS2")
1501 (synopsis "HDF4-based data format for NASA's Earth Observing System")
1502 (description "HDF-EOS2 is a software library built on HDF4 which supports
1503 the construction of data structures used in NASA's Earth Observing
1504 System (Grid, Point and Swath).")
1506 ;; Source files carry a permissive license header.
1507 (license (license:non-copyleft home-page))))
1509 (define-public hdf-eos5
1515 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1516 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1519 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1520 (patches (search-patches "hdf-eos5-build-shared.patch"
1521 "hdf-eos5-remove-gctp.patch"
1522 "hdf-eos5-fix-szip.patch"
1523 "hdf-eos5-fortrantests.patch"))))
1525 `(("gfortran" ,gfortran)))
1526 (build-system gnu-build-system)
1528 `(("hdf5" ,hdf5-1.8)
1532 `(#:configure-flags '("--enable-install-include" "--enable-shared"
1533 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1534 #:parallel-tests? #f))
1535 (synopsis "HDF5-based data format for NASA's Earth Observing System")
1537 "HDF-EOS5 is a software library built on HDF5 to support the construction
1538 of data structures used in NASA's Earth Observing System (Grid, Point and
1540 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1542 ;; Source files carry a permissive license header.
1543 (license (license:non-copyleft home-page))))
1545 (define-public hdf5-parallel-openmpi
1546 (package/inherit hdf5-1.10 ;use the latest
1547 (name "hdf5-parallel-openmpi")
1550 ,@(package-inputs hdf5)))
1552 (substitute-keyword-arguments (package-arguments hdf5)
1553 ((#:configure-flags flags)
1554 ``("--enable-parallel"
1555 ,@(delete "--enable-cxx"
1556 (delete "--enable-threadsafe" ,flags))))
1558 `(modify-phases ,phases
1559 (add-after 'build 'mpi-setup
1561 (add-before 'check 'patch-tests
1563 ;; OpenMPI's mpirun will exit with non-zero status if it
1564 ;; detects an "abnormal termination", i.e. any process not
1565 ;; calling MPI_Finalize(). Since the test is explicitly
1566 ;; avoiding MPI_Finalize so as not to have at_exit and thus
1567 ;; H5C_flush_cache from being called, mpirun will always
1568 ;; complain, so turn this test off.
1569 (substitute* "testpar/Makefile"
1570 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1571 (string-append front back "\n")))
1572 (substitute* "tools/test/h5diff/testph5diff.sh"
1573 (("/bin/sh") (which "sh")))
1575 (synopsis "Management suite for data with parallel IO support")))
1577 (define-public hdf5-blosc
1585 (url "https://github.com/Blosc/hdf5-blosc")
1586 (commit (string-append "v" version))))
1587 (file-name (git-file-name name version))
1589 (base32 "1nj2bm1v6ymm3fmyvhbn6ih5fgdiapavlfghh1pvbmhw71cysyqs"))))
1590 (build-system cmake-build-system)
1593 (list (string-append "-DBLOSC_INSTALL_DIR="
1594 (assoc-ref %build-inputs "c-blosc"))
1595 (string-append "-DPLUGIN_INSTALL_PATH="
1596 (assoc-ref %outputs "out")
1597 "/hdf5/lib/plugin"))
1599 (modify-phases %standard-phases
1600 (add-after 'unpack 'do-not-build-blosc
1602 (substitute* "CMakeLists.txt"
1603 (("set\\(BLOSC_INSTALL_DIR.*") "")
1604 (("ExternalProject_Add\\(project_blosc") "message("))
1607 `(("c-blosc" ,c-blosc)
1608 ("hdf5" ,hdf5-1.10)))
1609 (home-page "https://github.com/Blosc/hdf5-blosc")
1610 (synopsis "Filter for HDF5 using the Blosc compressor")
1611 (description "This is a filter for HDF5 that uses the Blosc compressor; by
1612 installing this filter, you can read and write HDF5 files with
1613 Blosc-compressed datasets.")
1614 (license license:expat)))
1616 (define-public h5check
1623 (uri (string-append "https://www.hdfgroup.org/ftp/HDF5/tools/"
1624 "h5check/src/h5check-" version ".tar.gz"))
1627 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1628 (build-system gnu-build-system)
1629 (inputs `(("hdf5" ,hdf5-1.8))) ;h5cc for tests
1630 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1631 (synopsis "HDF5 format checker")
1632 (description "@code{h5check} is a validation tool for verifying that an
1633 HDF5 file is encoded according to the HDF File Format Specification.")
1634 (license (license:x11-style "file://COPYING"))))
1642 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1647 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1648 (build-system cmake-build-system)
1649 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1650 (inputs `(("lapack" ,lapack)
1652 ;; FIXME: Even though the fonts are available dvips complains:
1653 ;; "Font cmmi10 not found; characters will be left blank."
1655 `(("texlive" ,texlive-tiny)
1656 ("ghostscript" ,ghostscript)
1657 ("doxygen" ,doxygen)))
1658 (home-page "http://itpp.sourceforge.net")
1659 (synopsis "C++ library of maths, signal processing and communication classes")
1660 (description "IT++ is a C++ library of mathematical, signal processing and
1661 communication classes and functions. Its main use is in simulation of
1662 communication systems and for performing research in the area of
1663 communications. The kernel of the library consists of generic vector and
1664 matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1665 similar to MATLAB, GNU Octave or SciPy.")
1666 (license license:gpl3+)))
1668 (define-public netcdf
1676 "https://www.unidata.ucar.edu/downloads/netcdf/ftp/"
1677 "netcdf-c-" version ".tar.gz"))
1680 "1a2fpp15a2rl1m50gcvvzd9y6bavl6vjf9zzf63sz5gdmq06yiqf"))
1681 (modules '((guix build utils)))
1683 ;; Make sure this variable is defined only once. Failing to do so
1684 ;; would break builds of 'netcdf-parallel-openmpi' with a
1685 ;; multiple-definition link error with GCC 10.
1686 '(substitute* "ncdump/ocprint.c"
1687 (("^int ocdebug") "static int ocdebug")))
1688 (patches (search-patches "netcdf-date-time.patch"))))
1689 (build-system gnu-build-system)
1692 ("doxygen" ,doxygen)
1693 ("graphviz" ,graphviz)))
1695 `(("hdf4" ,hdf4-alt)
1699 ("libjpeg" ,libjpeg-turbo)))
1701 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
1703 #:phases (modify-phases %standard-phases
1704 (add-before 'configure 'fix-source-date
1706 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1707 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1708 ;; to '1st hour of the current day', and therefore makes the
1709 ;; package not reproducible.
1710 (substitute* "./configure"
1711 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1712 "date --date='@0'"))
1714 (add-after 'configure 'patch-settings
1716 ;; libnetcdf.settings contains the full filename of the compilers
1717 ;; used to build the library. We truncate the hashes of those
1718 ;; filenames to avoid unnecessary references to the corresponding
1720 (substitute* "libnetcdf.settings"
1721 (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash)
1722 (string-append prefix (string-take hash 10) "...")))
1725 #:parallel-tests? #f)) ;various race conditions
1726 (home-page "https://www.unidata.ucar.edu/software/netcdf/")
1727 (synopsis "Library for scientific data")
1728 (description "NetCDF is an interface for scientific data access and a
1729 software library that provides an implementation of the interface. The netCDF
1730 library defines a machine-independent format for representing scientific data.
1731 Together, the interface, library, and format support the creation, access, and
1732 sharing of scientific data.")
1733 (license (license:x11-style "file://COPYRIGHT"))))
1735 (define-public netcdf-parallel-openmpi
1736 (package (inherit netcdf)
1737 (name "netcdf-parallel-openmpi")
1740 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1741 (package-inputs netcdf))))
1742 ;; TODO: Replace pkg-config references in nc-config with absolute references
1744 (substitute-keyword-arguments (package-arguments netcdf)
1745 ((#:configure-flags flags)
1746 `(cons* "CC=mpicc" "CXX=mpicxx"
1747 "--enable-parallel-tests"
1748 ;; Shared libraries not supported with parallel IO.
1749 "--disable-shared" "--with-pic"
1751 ((#:phases phases '%standard-phases)
1752 `(modify-phases ,phases
1753 (add-after 'build 'mpi-setup
1754 ,%openmpi-setup)))))))
1756 (define-public netcdf-fortran
1758 (name "netcdf-fortran")
1763 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1767 "0x4acvfhbsx1q79dkkwrwbgfhm0w5ngnp4zj5kk92s1khihmqfhj"))))
1768 (build-system gnu-build-system)
1770 `(#:configure-flags '("FCFLAGS=-fallow-argument-mismatch"
1771 "FFLAGS=-fallow-argument-mismatch")
1772 #:parallel-tests? #f))
1774 `(("netcdf" ,netcdf)))
1776 `(("gfortran" ,gfortran)))
1777 (synopsis "Fortran interface for the netCDF library")
1778 (description (package-description netcdf))
1779 (home-page (package-home-page netcdf))
1780 (license (package-license netcdf))))
1782 (define-public nlopt
1788 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1791 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1792 (build-system gnu-build-system)
1794 `(;; Shared libraries are not built by default. They are required to
1795 ;; build the Guile, Octave, and Python bindings.
1796 #:configure-flags '("--enable-shared")
1799 (modify-phases %standard-phases
1800 (add-before 'configure 'set-libnlopt-file-name
1801 (lambda* (#:key outputs #:allow-other-keys)
1802 ;; Make sure the Scheme module refers to the library by its
1803 ;; absolute file name (we cannot do that from a snippet
1804 ;; because the expansion of @libdir@ contains
1806 (let ((out (assoc-ref outputs "out")))
1807 (substitute* "swig/nlopt.scm.in"
1809 (string-append out "/lib/libnlopt")))
1811 (inputs `(("guile" ,guile-2.0)))
1812 (native-inputs `(("pkg-config" ,pkg-config)))
1813 (home-page "http://ab-initio.mit.edu/wiki/")
1814 (synopsis "Library for nonlinear optimization")
1815 (description "NLopt is a library for nonlinear optimization, providing a
1816 common interface for a number of different free optimization routines available
1817 online as well as original implementations of various other algorithms.")
1818 (license license:lgpl2.1+)))
1820 (define-public ipopt
1827 (url "https://github.com/coin-or/Ipopt")
1828 (commit (string-append "releases/" version))))
1829 (file-name (git-file-name name version))
1832 "08gznhwhqv1x4baksz350ih8q16r5rd0k8vals6078m3h94khr4b"))))
1833 (build-system gnu-build-system)
1835 '(#:phases (modify-phases %standard-phases
1836 (add-after 'install 'add--L-flags-in-ipopt.pc
1837 (lambda* (#:key inputs outputs #:allow-other-keys)
1838 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1839 ;; move it to "Libs.private" where it belongs, and add a
1840 ;; '-L' flag for LAPACK.
1841 (let ((out (assoc-ref outputs "out"))
1842 (lapack (assoc-ref inputs "lapack")))
1843 (substitute* (string-append out "/lib/pkgconfig/"
1845 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1846 (string-append "Libs: " before " " after "\n"
1847 "Libs.private: " before
1848 "-L" lapack "/lib -llapack -lblas "
1852 `(("gfortran" ,gfortran)
1853 ("pkg-config" ,pkg-config)))
1855 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
1856 `(("lapack" ,lapack))) ;for both libblas and liblapack
1857 (home-page "https://www.coin-or.org")
1858 (synopsis "Large-scale nonlinear optimizer")
1860 "The Interior Point Optimizer (IPOPT) is a software package for
1861 large-scale nonlinear optimization. It provides C++, C, and Fortran
1863 (license license:epl2.0)))
1865 (define-public nomad-optimizer
1867 (name "nomad-optimizer")
1873 (url "https://github.com/bbopt/nomad/")
1874 (commit (string-append "v" version))))
1875 (file-name (git-file-name name version))
1878 "0w386d8r5ldbvnv0c0g7vz95pfpvwdxis26vaalk2amsa5akl775"))))
1879 (build-system cmake-build-system)
1881 `(("python" ,python-wrapper)
1882 ("python-cython" ,python-cython)))
1884 `(#:imported-modules ((guix build python-build-system)
1885 ,@%cmake-build-system-modules)
1886 #:modules (((guix build python-build-system)
1887 #:select (python-version site-packages))
1888 (guix build cmake-build-system)
1891 '("-DBUILD_INTERFACES=ON"
1894 (modify-phases %standard-phases
1895 (add-after 'unpack 'fix-sources-for-build
1896 (lambda* (#:key outputs #:allow-other-keys)
1897 (substitute* "CMakeLists.txt"
1898 ;; CMAKE_INSTALL_PREFIX is accidentally hardcoded.
1899 (("set\\(CMAKE_INSTALL_PREFIX .* FORCE\\)") "")
1900 ;; Requiring GCC version 8 or later is unwarranted.
1901 (("message\\(FATAL_ERROR \"GCC version < 8")
1902 "message(STATUS \"GCC version < 8"))
1904 (let ((out (assoc-ref outputs "out")))
1905 (substitute* "interfaces/PyNomad/CMakeLists.txt"
1906 ;; We don't want to build in-place, and anyway the install
1907 ;; command further below runs build_ext as a prerequisite.
1908 (("COMMAND python setup_PyNomad\\.py .* build_ext --inplace\n")
1910 ;; Don't install locally.
1911 (("COMMAND python (setup_PyNomad\\.py .* install) --user\n"
1913 (string-append "COMMAND ${CMAKE_COMMAND} -E env"
1914 " CC=" ,(cc-for-target)
1915 " CXX=" ,(cxx-for-target)
1916 " " (which "python")
1920 ;; Fix erroneous assumptions about the paths of the include and
1921 ;; library directories.
1922 (substitute* "interfaces/PyNomad/setup_PyNomad.py"
1923 (("^( +os_include_dirs = ).*" _ prefix)
1924 (string-append prefix "[\"../../src\"]\n"))
1925 (("^(installed_lib_dir = ).*" _ prefix)
1926 (string-append prefix "\"" out "/lib\"\n"))))
1929 ;; Fix the tests so they run in out-of-source builds.
1930 (add-after 'fix-sources-for-build 'fix-sources-for-tests
1933 (map (lambda (d) (string-append "examples/" d "/CMakeLists.txt"))
1935 (map (lambda (d) (string-append "basic/library/" d))
1936 '("example1" "example2" "example3"
1937 "single_obj_parallel"))
1938 (map (lambda (d) (string-append "advanced/library/" d))
1939 '("FixedVariable" "NMonly" "PSDMads" "Restart"
1940 "c_api/example1" "c_api/example2"
1941 "exampleSuggestAndObserve"))))
1942 ;; The built examples are assumed to be in the source tree
1943 ;; (which isn't the case here).
1944 (("(COMMAND \\$\\{CMAKE_BINARY_DIR\\}/examples/runExampleTest\\.sh )\\.(/.*)"
1946 (string-append command "${CMAKE_CURRENT_BINARY_DIR}" test)))
1947 ;; (Unrelated to support for out-of-source testing.)
1949 "examples/advanced/library/exampleSuggestAndObserve/cache0.txt")
1951 (let* ((builddir (string-append (getcwd) "/../build"))
1952 ;; The BB_EXE and SURROGATE_EXE paths are interpreted
1953 ;; relative to the configuration file provided to NOMAD.
1954 ;; However, the configuration files are all in the source
1955 ;; tree rather than in the build tree (unlike the compiled
1957 (fix-exe-path (lambda* (dir #:optional
1960 (substitute* (string-append dir "/" file)
1961 (((string-append "^" exe-opt " +"))
1962 ;; The $ prevents NOMAD from prefixing
1963 ;; the executable with the path of the
1964 ;; parent directory of the configuration
1965 ;; file NOMAD was provided with as
1966 ;; argument (param.txt or some such).
1967 (string-append exe-opt " $"
1968 builddir "/" dir "/"))))))
1971 (let ((dir (string-append "examples/" dir)))
1972 (substitute* (string-append dir "/CMakeLists.txt")
1973 ;; The install phase has not yet run.
1974 (("COMMAND \\$\\{CMAKE_INSTALL_PREFIX\\}/bin/nomad ")
1975 "COMMAND ${CMAKE_BINARY_DIR}/src/nomad "))
1977 (when (equal? dir "examples/basic/batch/surrogate_sort")
1978 (fix-exe-path dir "param.txt" "SURROGATE_EXE"))))
1979 (append (map (lambda (d) (string-append "basic/batch/" d))
1980 '("example1" "example2"
1981 "single_obj" "single_obj_parallel"
1983 '("advanced/batch/LHonly")))
1985 (let ((dir "examples/advanced/batch/FixedVariable"))
1986 (substitute* (string-append dir "/runFixed.sh")
1987 ;; Hardcoded path to NOMAD executable.
1988 (("^\\.\\./\\.\\./\\.\\./\\.\\./bin/nomad ")
1989 (string-append builddir "/src/nomad ")))
1991 (lambda (f) (fix-exe-path dir f))
1992 '("param1.txt" "param2.txt" "param3.txt" "param10.txt"))))
1995 ;; The information in the .egg-info file is not kept up to date.
1996 (add-after 'install 'delete-superfluous-egg-info
1997 (lambda* (#:key inputs outputs #:allow-other-keys)
1998 (delete-file (string-append
1999 (site-packages inputs outputs)
2001 (python-version (assoc-ref inputs "python"))
2004 (home-page "https://www.gerad.ca/nomad/")
2005 (synopsis "Nonlinear optimization by mesh-adaptive direct search")
2007 "NOMAD is a C++ implementation of the mesh-adaptive direct search (MADS)
2008 algorithm, designed for difficult blackbox optimization problems. These
2009 problems occur when the functions defining the objective and constraints are
2010 the result of costly computer simulations.")
2011 (license license:lgpl3+)))
2019 (uri (string-append "https://www.coin-or.org/download/source/"
2020 "Cbc/Cbc-" version ".tgz"))
2023 "0wk9vr6zc62gw71v7gnra5wxqlcljcgbhm5lasx236v791b986ns"))
2024 (modules '((guix build utils)))
2026 ;; Make sure we don't use the bundled software.
2027 '(delete-file-recursively "ThirdParty"))))
2028 (build-system gnu-build-system)
2030 `(("gfortran" ,gfortran)
2031 ("pkg-config" ,pkg-config)))
2033 `(("openblas" ,openblas)))
2034 (home-page "https://www.coin-or.org")
2035 (synopsis "Branch-and-cut solver")
2037 "Cbc (Coin-or branch and cut) is a mixed integer linear programming
2038 solver written in C++. It can be used as a library or as a standalone
2040 (license license:epl1.0)))
2048 (uri (string-append "https://www.coin-or.org/download/source/"
2049 "Clp/Clp-" version ".tgz"))
2052 "0ap1f0lxppa6pnbc4bg7ih7a96avwaki482nig8w5fr3vg9wvkzr"))
2053 (modules '((guix build utils)))
2055 ;; Make sure we don't use the bundled software.
2057 (delete-file-recursively "ThirdParty")
2059 (build-system gnu-build-system)
2061 `(("gfortran" ,gfortran)
2062 ("pkg-config" ,pkg-config)))
2064 `(("openblas" ,openblas)))
2065 (home-page "https://www.coin-or.org")
2066 (synopsis "Linear programming solver")
2068 "CLP is a high quality linear programming solver. Its main strengths are
2069 its dual and primal Simplex algorithms. It also has a barrier algorithm for
2070 linear and quadratic objectives. There are limited facilities for nonlinear
2071 and quadratic objectives using the Simplex algorithm.")
2072 (license license:epl1.0)))
2074 (define-public gecode
2081 (url "https://github.com/Gecode/gecode")
2082 (commit (string-append "release-" version))))
2083 (file-name (git-file-name name version))
2086 "0b1cq0c810j1xr2x9y9996p894571sdxng5h74py17c6nr8c6dmk"))
2087 (modules '((guix build utils)))
2090 ;; delete generated sources
2091 (for-each delete-file
2092 '("gecode/kernel/var-imp.hpp"
2093 "gecode/kernel/var-type.hpp"))))))
2094 (outputs '("out" "examples"))
2095 (build-system gnu-build-system)
2098 (list (string-append "GLDFLAGS=-Wl,-rpath="
2099 (assoc-ref %outputs "out")
2101 "--enable-examples=no")
2102 #:modules ((guix build gnu-build-system)
2107 (modify-phases %standard-phases
2108 (add-after 'build 'build-examples
2109 (lambda* (#:key outputs #:allow-other-keys)
2110 (invoke "make" "compileexamples")))
2111 ;; The Makefile disrespects GLDFLAGS for some reason, so we have to
2112 ;; patch it ourselves... *sigh*
2113 (add-after 'install 'fix-rpath
2114 (lambda* (#:key outputs #:allow-other-keys)
2115 (let ((libdir (string-append (assoc-ref outputs "out") "/lib")))
2118 (let* ((pipe (open-pipe* OPEN_READ "patchelf"
2119 "--print-rpath" file))
2120 (line (read-line pipe)))
2121 (and (zero? (close-pipe pipe))
2122 (invoke "patchelf" "--set-rpath"
2123 (string-append libdir ":" line)
2125 (find-files libdir ".*\\.so$")))))
2126 (add-after 'install 'install-examples
2127 (lambda* (#:key outputs #:allow-other-keys)
2128 (invoke "make" "installexamples"
2129 (string-append "bindir=" (assoc-ref outputs "examples")
2131 ;; Tests depend on installed libraries.
2133 (add-after 'fix-rpath 'check
2134 (assoc-ref %standard-phases 'check)))))
2136 `(("patchelf" ,patchelf)
2139 (home-page "https://www.gecode.org")
2140 (synopsis "Toolkit for developing constraint-based systems")
2141 (description "Gecode is a C++ toolkit for developing constraint-based
2142 systems and applications. It provides a modular and extensible solver.")
2143 (license license:expat)))
2145 (define-public libflame
2149 (outputs '("out" "static"))
2154 (url "https://github.com/flame/libflame")
2156 (file-name (git-file-name name version))
2159 "1n6lf0wvpp77lxqlr721h2jbfbzigphdp19wq8ajiccilcksh7ay"))))
2160 (build-system gnu-build-system)
2163 ;; Sensible defaults: https://github.com/flame/libflame/issues/28
2164 (list "--enable-dynamic-build"
2165 "--enable-max-arg-list-hack"
2166 "--enable-lapack2flame"
2167 "--enable-verbose-make-output"
2168 "--enable-multithreading=pthreads" ; Openblas isn't built with openmp.
2169 ,@(if (any (cute string-prefix? <> (or (%current-target-system)
2172 '("--enable-vector-intrinsics=sse")
2174 "--enable-supermatrix"
2175 "--enable-memory-alignment=16"
2176 "--enable-ldim-alignment")
2178 (modify-phases %standard-phases
2179 (add-after 'unpack 'patch-/usr/bin/env-bash
2181 (substitute* "build/config.mk.in"
2182 (("/usr/bin/env bash") (which "bash")))
2185 (lambda* (#:key tests? #:allow-other-keys)
2186 (substitute* "test/Makefile"
2187 (("LIBBLAS .*") "LIBBLAS = -lblas\n")
2188 (("LIBLAPACK .*") "LIBLAPACK = -llapack\n"))
2190 (with-directory-excursion "test"
2193 (invoke "./test_libflame.x"))
2195 (add-after 'install 'install-static
2196 (lambda* (#:key outputs #:allow-other-keys)
2197 (let ((out (assoc-ref outputs "out"))
2198 (static (assoc-ref outputs "static")))
2199 (mkdir-p (string-append static "/lib"))
2200 (rename-file (string-append out "/lib/libflame.a")
2201 (string-append static "/lib/libflame.a"))
2202 (install-file (string-append out "/include/FLAME.h")
2203 (string-append static "/include"))
2206 `(("gfortran" ,gfortran)))
2208 `(("lapack" ,lapack)
2209 ("openblas" ,openblas)
2211 ("python" ,python-wrapper)))
2212 (home-page "https://github.com/flame/libflame")
2213 (synopsis "High-performance object-based library for DLA computations")
2214 (description "@code{libflame} is a portable library for dense matrix
2215 computations, providing much of the functionality present in LAPACK, developed
2216 by current and former members of the @acronym{SHPC, Science of High-Performance
2217 Computing} group in the @url{https://www.ices.utexas.edu/, Institute for
2218 Computational Engineering and Sciences} at The University of Texas at Austin.
2219 @code{libflame} includes a compatibility layer, @code{lapack2flame}, which
2220 includes a complete LAPACK implementation.")
2221 (license license:bsd-3)))
2223 (define-public ceres
2225 (name "ceres-solver")
2227 (home-page "http://ceres-solver.org/")
2230 (uri (string-append home-page "ceres-solver-"
2234 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
2235 (build-system cmake-build-system)
2237 ;; TODO: Build HTML user documentation and install separately.
2238 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
2239 "-DBUILD_SHARED_LIBS=ON")
2241 #:phases (modify-phases %standard-phases
2242 (add-before 'configure 'set-library-directory
2244 ;; Install libraries to lib/, not lib64/.
2245 (substitute* "internal/ceres/CMakeLists.txt"
2246 (("set\\(LIB_SUFFIX \"64\"\\)")
2247 "set(LIB_SUFFIX \"\")"))
2250 `(("pkg-config" ,pkg-config)))
2252 `(("glog" ,glog))) ;for #include <glog/glog.h>
2257 ("suitesparse" ,suitesparse)
2258 ("gflags" ,gflags)))
2259 (synopsis "C++ library for solving large optimization problems")
2261 "Ceres Solver is a C++ library for modeling and solving large,
2262 complicated optimization problems. It is a feature rich, mature and
2263 performant library which has been used in production since 2010. Ceres Solver
2264 can solve two kinds of problems:
2266 @item non-linear least squares problems with bounds constraints;
2267 @item general unconstrained optimization problems.
2269 (license license:bsd-3)))
2271 ;; For a fully featured Octave, users are strongly recommended also to install
2272 ;; the following packages: less, ghostscript, gnuplot.
2273 (define-public octave-cli
2280 (uri (string-append "mirror://gnu/octave/octave-"
2284 "06id09zspya24gshcwgp039cp35c06150mdlxysawgnbrhj16wkv"))))
2285 (build-system gnu-build-system)
2287 `(("alsa-lib" ,alsa-lib)
2288 ("arpack" ,arpack-ng)
2294 ("fontconfig" ,fontconfig)
2295 ("freetype" ,freetype)
2299 ("graphicsmagick" ,graphicsmagick)
2301 ;; TODO: libjpeg-turbo is indirectly required through libtiff. In
2302 ;; the next rebuild cycle, add an absolute reference for -ljpeg in
2303 ;; libtiff.la instead of having to provide it here.
2304 ("libjpeg" ,libjpeg-turbo)
2308 ("libsndfile" ,libsndfile)
2312 ("portaudio" ,portaudio)
2314 ("readline" ,readline)
2315 ("suitesparse" ,suitesparse)
2316 ("texinfo" ,texinfo)
2319 `(("gfortran" ,gfortran)
2320 ("pkg-config" ,pkg-config)
2322 ;; The following inputs are not actually used in the build process.
2323 ;; However, the ./configure gratuitously tests for their existence and
2324 ;; assumes that programs not present at build time are also not, and
2325 ;; can never be, available at run time! If these inputs are therefore
2326 ;; not present, support for them will be built out. However, Octave
2327 ;; will still run without them, albeit without the features they
2330 ("ghostscript" ,ghostscript)
2331 ("gnuplot" ,gnuplot)))
2332 ;; Octave code uses this variable to detect directories holding multiple CA
2333 ;; certificates to verify peers with. This is required for the networking
2334 ;; functions that require encryption to work properly.
2335 (native-search-paths
2336 (list (search-path-specification
2337 (variable "CURLOPT_CAPATH")
2338 (files '("etc/ssl/certs")))))
2341 (list (string-append "--with-shell="
2342 (assoc-ref %build-inputs "bash")
2345 ;; XXX: Without this flag, linking octave-cli fails with
2346 ;; undefined references to 'logf@GLIBCXX_3.4' et.al. due to
2347 ;; not pulling in liboctinterp.la for -lstdc++.
2348 "--enable-link-all-dependencies")
2350 (modify-phases %standard-phases
2351 (add-after 'configure 'configure-makeinfo
2352 (lambda* (#:key inputs #:allow-other-keys)
2353 (substitute* "libinterp/corefcn/help.h"
2356 "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
2358 (home-page "https://www.gnu.org/software/octave/")
2359 (synopsis "High-level language for numerical computation (no GUI)")
2360 (description "GNU Octave is a high-level interpreted language that is
2361 specialized for numerical computations. It can be used for both linear and
2362 non-linear applications and it provides great support for visualizing results.
2363 Work may be performed both at the interactive command-line as well as via
2365 (license license:gpl3+)))
2367 (define-public octave
2368 (package (inherit octave-cli)
2371 `(("qscintilla" ,qscintilla)
2373 ,@(package-inputs octave-cli)))
2375 `(("qttools" , qttools) ;for lrelease
2376 ("texlive" ,(texlive-updmap.cfg (list texlive-epsf))) ; for texi2dvi
2377 ,@(package-native-inputs octave-cli)))
2379 (substitute-keyword-arguments (package-arguments octave-cli)
2381 `(modify-phases ,phases
2382 (add-before 'configure 'patch-qscintilla-library-name
2383 (lambda* (#:key inputs #:allow-other-keys)
2384 ;; The QScintilla library that the Octave configure script tries
2385 ;; to link with should be named libqscintilla-qt5.so, but the
2386 ;; QScintilla input provides the shared library as
2387 ;; libqscintilla2_qt5.so.
2388 (substitute* "configure"
2389 (("qscintilla2-qt5")
2392 (synopsis "High-level language for numerical computation (with GUI)")))
2394 (define-public opencascade-oce
2396 (name "opencascade-oce")
2402 (url "https://github.com/tpaviot/oce")
2403 (commit (string-append "OCE-" version))))
2404 (file-name (git-file-name name version))
2405 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
2407 (base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69"))))
2408 (build-system cmake-build-system)
2411 (list "-DOCE_TESTING:BOOL=ON"
2412 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
2413 "-DOCE_DRAW:BOOL=ON"
2414 (string-append "-DOCE_INSTALL_PREFIX:PATH="
2415 (assoc-ref %outputs "out"))
2416 "-UCMAKE_INSTALL_RPATH")))
2418 `(("freetype" ,freetype)
2425 `(("python" ,python-wrapper)))
2426 (home-page "https://github.com/tpaviot/oce")
2427 (synopsis "Libraries for 3D modeling and numerical simulation")
2429 "Open CASCADE is a set of libraries for the development of applications
2430 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
2431 C++ class libraries providing services for 3D surface and solid modeling, CAD
2432 data exchange, and visualization. It is used for development of specialized
2433 software dealing with 3D models in design (CAD), manufacturing (CAM),
2434 numerical simulation (CAE), measurement equipment (CMM), and quality
2435 control (CAQ) domains.
2437 This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
2438 patches, improvements, and experiments contributed by users over the official
2439 Open CASCADE library.")
2440 (license (list license:lgpl2.1; OCE libraries, with an exception for the
2441 ; use of header files; see
2442 ; OCCT_LGPL_EXCEPTION.txt
2443 license:public-domain; files
2444 ; src/Standard/Standard_StdAllocator.hxx and
2445 ; src/NCollection/NCollection_StdAllocator.hxx
2446 license:expat; file src/OpenGl/OpenGl_glext.h
2447 license:bsd-3)))); test framework gtest
2449 (define-public opencascade-occt
2451 (name "opencascade-occt")
2457 (url "https://git.dev.opencascade.org/repos/occt.git")
2460 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
2462 (file-name (git-file-name name version))
2464 (base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4"))
2465 (modules '((guix build utils)))
2468 ;; Remove files specific to non-free operating systems.
2469 (delete-file-recursively "samples/ios")
2470 (delete-file-recursively "samples/mfc")
2471 (delete-file-recursively "samples/qt/FuncDemo")
2472 (delete-file "genconf.bat")
2473 (delete-file "gendoc.bat")
2474 (delete-file "genproj.bat")
2475 (delete-file "upgrade.bat")
2476 ;; Remove references to deleted files.
2477 (substitute* "dox/FILES_HTML.txt"
2478 ((".*standard.*") "" )
2479 ((".*UIKitSample.*") ""))
2481 (build-system cmake-build-system)
2483 '(;; There is no test target for make. OCCT provides an
2484 ;; 'Automated Testing System', which may be accessed after
2485 ;; installation via the draw.sh script. draw.sh is located in
2486 ;; the bin directory. For details see:
2487 ;; https://www.opencascade.com/doc/occt-7.3.0/overview/html/\
2488 ;; occt_dev_guides__tests.html
2490 ;; Configure without freeimage: attempting to link against the
2491 ;; freeimage version 3.17 library leads to 'undefined
2492 ;; reference' errors.
2494 (list "-DUSE_FREEIMAGE:BOOL=OFF"
2496 "-DUSE_VTK:BOOL=OFF"
2497 "-DBUILD_DOC_Overview:BOOL=OFF"
2498 "-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON"
2499 "-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON"
2500 "-UCMAKE_INSTALL_LIBDIR")))
2502 `(("doxygen" ,doxygen)
2503 ;("freeimage" ,freeimage)
2504 ("freetype" ,freetype)
2506 ("libxext" ,libxext)
2513 ;; TODO: build Overview documentation and add 'doc' output.
2514 (home-page "https://www.opencascade.com")
2515 (synopsis "Libraries for 3D modeling and numerical simulation")
2517 "Open CASCADE is a set of libraries for the development of applications
2518 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
2519 C++ class libraries providing services for 3D surface and solid modeling, CAD
2520 data exchange, and visualization. It is used for development of specialized
2521 software dealing with 3D models in design (CAD), manufacturing (CAM),
2522 numerical simulation (CAE), measurement equipment (CMM), and quality
2523 control (CAQ) domains.
2525 This is the certified version of the Open Cascade Technology (OCCT) library.")
2526 (license (list ;; OCCT library:
2527 license:lgpl2.1; with an exception for the use of header
2528 ; files, see OCCT_LGPL_EXCEPTION.txt.
2529 ;; Files src/OpenGl/glext.h, adm/cmake/cotire.cmake and
2530 ;; src/OpenGl/OpenGl_HaltonSampler.hxx:
2532 ;; Files src/ExprIntrp/ExprIntrp.tab.* and
2533 ;; src/StepFile/step.tab.*:
2534 license:gpl3+ ; with Bison 2.2 exception.
2535 ;; File src/NCollection/NCollection_UtfIterator.lxx:
2536 (license:non-copyleft
2537 "https://www.unicode.org/license.html")
2538 ;; File src/NCollection/NCollection_StdAllocator.hxx:
2539 license:public-domain))))
2549 (url "https://gitlab.onelab.info/gmsh/gmsh.git")
2551 (string-append "gmsh_"
2552 (string-replace-substring version "." "_")))))
2553 (file-name (git-file-name name version))
2555 (base32 "07mi6ja3b9libgcdp2b4dwnkap1b9ha2wi2zdn9mhmwvp3g1pxhp"))
2556 (modules '((guix build utils)))
2559 (delete-file-recursively "contrib/metis")
2561 (build-system cmake-build-system)
2564 ("gfortran" ,gfortran)
2570 ("libxext" ,libxext)
2573 ("opencascade-occt" ,opencascade-occt)))
2575 `(("fontconfig" ,fontconfig)
2577 ("python" ,python)))
2579 `(#:configure-flags `("-DENABLE_SYSTEM_CONTRIB:BOOL=ON"
2580 "-DENABLE_BUILD_SHARED:BOOL=ON"
2581 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")
2582 #:imported-modules (,@%cmake-build-system-modules
2583 (guix build python-build-system))
2584 #:modules (((guix build python-build-system) #:select (site-packages))
2585 (guix build cmake-build-system)
2588 (modify-phases %standard-phases
2589 (add-after 'unpack 'patch-paths
2590 (lambda* (#:key inputs outputs #:allow-other-keys)
2591 ;; Use the standard Guix site-package path for
2592 ;; installation of the Python API.
2593 (substitute* "CMakeLists.txt"
2594 (("include\\(GNUInstallDirs\\)\n")
2595 (string-append "include(GNUInstallDirs)\n"
2597 (site-packages inputs outputs) ")\n"))
2598 (("\\$\\{GMSH\\_PY\\} DESTINATION \\$\\{GMSH\\_LIB\\}")
2599 "${GMSH_PY} DESTINATION ${GMSH_PY_LIB}"))
2600 ;; Find the shared library.
2601 (let ((libgmsh (string-append (assoc-ref outputs "out")
2602 "/lib/libgmsh.so")))
2603 (substitute* "api/gmsh.py"
2604 (("find_library\\(\"gmsh\"\\)")
2605 (simple-format #f "\"~a\"" libgmsh))))
2607 (home-page "http://gmsh.info/")
2608 (synopsis "3D finite element grid generator")
2609 (description "Gmsh is a 3D finite element grid generator with a built-in
2610 CAD engine and post-processor. Its design goal is to provide a fast, light
2611 and user-friendly meshing tool with parametric input and advanced
2612 visualization capabilities. Gmsh is built around four modules: geometry,
2613 mesh, solver and post-processing. The specification of any input to these
2614 modules is done either interactively using the graphical user interface or in
2615 ASCII text files using Gmsh's own scripting language.")
2616 (license license:gpl2+)))
2618 (define-public veusz
2625 (uri (pypi-uri "veusz" version))
2627 (base32 "1q7hi1qwwg4pgiz62isvv1pia85m13bspdpp1q3mrnwl11in0ag0"))))
2628 (build-system python-build-system)
2630 `(;; Tests will fail because they depend on optional packages like
2631 ;; python-astropy, which is not packaged.
2634 (modify-phases %standard-phases
2635 ;; Veusz will append 'PyQt5' to sip_dir by default. That is not how
2636 ;; the path is defined in Guix, therefore we have to change it.
2637 (add-after 'unpack 'fix-sip-dir
2639 (substitute* "pyqtdistutils.py"
2640 (("os.path.join\\(sip_dir, 'PyQt5'\\)") "sip_dir"))
2642 ;; Now we have to pass the correct sip_dir to setup.py.
2644 (lambda* (#:key inputs #:allow-other-keys)
2645 ;; We need to tell setup.py where to locate QtCoremod.sip
2646 ((@@ (guix build python-build-system) call-setuppy)
2648 (list (string-append "--sip-dir="
2649 (assoc-ref inputs "python-pyqt")
2652 ;; Ensure that icons are found at runtime.
2653 (add-after 'install 'wrap-executable
2654 (lambda* (#:key inputs outputs #:allow-other-keys)
2655 (let ((out (assoc-ref outputs "out")))
2656 (wrap-program (string-append out "/bin/veusz")
2657 `("QT_PLUGIN_PATH" prefix
2658 ,(list (string-append (assoc-ref inputs "qtsvg")
2659 "/lib/qt5/plugins/"))))))))))
2661 `(("pkg-config" ,pkg-config)
2662 ;;("python-astropy" ,python-astropy) ;; FIXME: Package this.
2663 ("qttools" ,qttools)
2664 ("python-sip" ,python-sip-4)))
2666 `(("ghostscript" ,ghostscript) ;optional, for EPS/PS output
2667 ("python-dbus" ,python-dbus)
2668 ("python-h5py" ,python-h5py) ;optional, for HDF5 data
2669 ("python-pyqt" ,python-pyqt)
2670 ("qtbase" ,qtbase-5)
2673 `(("python-numpy" ,python-numpy)))
2674 (home-page "https://veusz.github.io/")
2675 (synopsis "Scientific plotting package")
2677 "Veusz is a scientific plotting and graphing program with a graphical
2678 user interface, designed to produce publication-ready 2D and 3D plots. In
2679 addition it can be used as a module in Python for plotting. It supports
2680 vector and bitmap output, including PDF, Postscript, SVG and EMF.")
2681 (license license:gpl2+)))
2683 (define-public maxflow
2686 ;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’,
2687 ;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’.
2692 (url "https://github.com/gerddie/maxflow")
2694 (file-name (git-file-name name version))
2697 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
2698 (build-system cmake-build-system)
2699 (home-page "https://pub.ist.ac.at/~vnk/software.html")
2700 (synopsis "Library implementing Maxflow algorithm")
2701 (description "An implementation of the maxflow algorithm described in
2702 @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
2703 Energy Minimization in Computer Vision.\n
2704 Yuri Boykov and Vladimir Kolmogorov.\n
2705 In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
2707 (license license:gpl3+)))
2709 (define-public petsc
2716 ;; The *-lite-* tarball does not contain the *large* documentation
2717 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
2718 "petsc-lite-" version ".tar.gz"))
2720 (base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx"))))
2721 (outputs '("out" ; libraries and headers
2722 "examples")) ; ~30MiB of examples
2723 (build-system gnu-build-system)
2725 `(("python" ,python-2)))
2727 `(("gfortran" ,gfortran)
2728 ("openblas" ,openblas)
2729 ("superlu" ,superlu)
2730 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
2731 ;; leaving out opengl, as configuration seems to only be for mac
2734 `(#:test-target "test"
2735 #:parallel-build? #f ; build is parallel by default
2742 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
2743 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
2744 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
2746 (modify-phases %standard-phases
2748 ;; PETSc's configure script is actually a python script, so we can't
2749 ;; run it with bash.
2750 (lambda* (#:key outputs (configure-flags '())
2752 (let* ((prefix (assoc-ref outputs "out"))
2753 (flags `(,(string-append "--prefix=" prefix)
2754 ,@configure-flags)))
2755 (format #t "build directory: ~s~%" (getcwd))
2756 (format #t "configure flags: ~s~%" flags)
2757 (apply invoke "./configure" flags))))
2758 (add-after 'configure 'clean-local-references
2759 (lambda* (#:key outputs #:allow-other-keys)
2760 (let ((out (assoc-ref outputs "out")))
2761 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
2762 ;; Prevent build directory from leaking into compiled code
2764 ;; Scrub timestamp for reproducibility
2765 ((".*Libraries compiled on.*") ""))
2766 (substitute* (find-files "." "petscvariables")
2767 ;; Do not expose build machine characteristics, set to defaults.
2768 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
2769 (("NPMAX = [:digit:]+") "NPMAX = 2"))
2771 (add-after 'install 'clean-install
2772 ;; Try to keep installed files from leaking build directory names.
2773 (lambda* (#:key inputs outputs #:allow-other-keys)
2774 (let ((out (assoc-ref outputs "out")))
2775 (substitute* (map (lambda (file)
2776 (string-append out "/lib/petsc/conf/" file))
2777 '("petscvariables"))
2779 ;; Make compiler references point to the store
2780 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
2781 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
2782 (string-append "= " (which compiler))))
2783 ;; PETSc installs some build logs, which aren't necessary.
2784 (for-each (lambda (file)
2785 (let ((f (string-append out "/lib/petsc/conf/" file)))
2786 (when (file-exists? f)
2788 '("configure.log" "make.log" "gmake.log"
2789 "test.log" "error.log" "RDict.db"
2790 "PETScBuildInternal.cmake"
2791 ;; Once installed, should uninstall with Guix
2794 (add-after 'install 'move-examples
2795 (lambda* (#:key outputs #:allow-other-keys)
2796 (let* ((out (assoc-ref outputs "out"))
2797 (examples (assoc-ref outputs "examples"))
2798 (exdir (string-append out "/share/petsc/examples"))
2799 (exdir' (string-append examples "/share/petsc/examples")))
2800 (copy-recursively exdir exdir')
2801 (delete-file-recursively exdir)
2803 (home-page "https://www.mcs.anl.gov/petsc")
2804 (synopsis "Library to solve PDEs")
2805 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
2806 data structures and routines for the scalable (parallel) solution of
2807 scientific applications modeled by partial differential equations.")
2808 (license (license:non-copyleft
2809 "https://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
2811 (define-public petsc-complex
2812 (package (inherit petsc)
2813 (name "petsc-complex")
2815 (substitute-keyword-arguments (package-arguments petsc)
2816 ((#:configure-flags cf)
2817 `(cons "--with-scalar-type=complex" ,cf))))
2818 (synopsis "Library to solve PDEs (with complex scalars)")))
2820 (define-public petsc-openmpi
2821 (package (inherit petsc)
2822 (name "petsc-openmpi")
2824 `(("hdf5" ,hdf5-parallel-openmpi)
2825 ("hypre" ,hypre-openmpi)
2827 ("mumps" ,mumps-openmpi)
2828 ("openmpi" ,openmpi)
2829 ("scalapack" ,scalapack)
2830 ("scotch" ,pt-scotch32)
2831 ,@(package-inputs petsc)))
2833 (substitute-keyword-arguments (package-arguments petsc)
2834 ((#:configure-flags cf)
2836 "--with-mpiexec=mpirun"
2839 "--with-scalapack=1"
2841 ,(string-append "--with-mpi-dir="
2842 (assoc-ref %build-inputs "openmpi"))
2843 ,(string-append "--with-hdf5-include="
2844 (assoc-ref %build-inputs "hdf5") "/include")
2845 ,(string-append "--with-hdf5-lib="
2846 (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
2847 ,@(delete "--with-mpi=0" ,cf)))
2849 `(modify-phases ,phases
2850 (add-before 'configure 'mpi-setup
2851 ,%openmpi-setup)))))
2852 (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
2854 (define-public petsc-complex-openmpi
2855 (package (inherit petsc-complex)
2856 (name "petsc-complex-openmpi")
2858 `(("openmpi" ,openmpi)
2859 ,@(package-inputs petsc-complex)))
2861 (substitute-keyword-arguments (package-arguments petsc-complex)
2862 ((#:configure-flags cf)
2863 ``("--with-mpiexec=mpirun"
2864 ,(string-append "--with-mpi-dir="
2865 (assoc-ref %build-inputs "openmpi"))
2866 ,@(delete "--with-mpi=0" ,cf)))
2868 `(modify-phases ,phases
2869 (add-before 'configure 'mpi-setup
2870 ,%openmpi-setup)))))
2871 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
2873 (define-public python-petsc4py
2875 (name "python-petsc4py")
2880 (uri (pypi-uri "petsc4py" version))
2883 "1rm1qj5wlkhxl39by9n78lh3gbmii31wsnb8j1rr5hvfr5xgbx2q"))
2884 (modules '((guix build utils)))
2887 ;; Ensure source file is regenerated in the build phase.
2888 (delete-file "src/petsc4py.PETSc.c")
2889 ;; Remove legacy GC code. See
2890 ;; https://bitbucket.org/petsc/petsc4py/issues/125.
2891 (substitute* "src/PETSc/cyclicgc.pxi"
2892 ((".*gc_refs.*") "" )
2893 ((".*PyGC_Head.*") ""))
2895 (build-system python-build-system)
2898 (modify-phases %standard-phases
2899 (add-before 'build 'pre-build
2901 ;; Define path to PETSc installation.
2902 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
2904 (add-before 'check 'mpi-setup
2907 `(("python-cython" ,python-cython)))
2909 `(("petsc" ,petsc-openmpi)
2910 ("python-numpy" ,python-numpy)))
2911 (home-page "https://bitbucket.org/petsc/petsc4py/")
2912 (synopsis "Python bindings for PETSc")
2913 (description "PETSc, the Portable, Extensible Toolkit for
2914 Scientific Computation, is a suite of data structures and routines for
2915 the scalable (parallel) solution of scientific applications modeled by
2916 partial differential equations. It employs the MPI standard for all
2917 message-passing communication. @code{petsc4py} provides Python
2918 bindings to almost all functions of PETSc.")
2919 (license license:bsd-3)))
2921 (define-public python-kiwisolver
2923 (name "python-kiwisolver")
2927 (uri (pypi-uri "kiwisolver" version))
2930 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
2931 (build-system python-build-system)
2932 (home-page "https://github.com/nucleic/kiwi")
2933 (synopsis "Fast implementation of the Cassowary constraint solver")
2935 "Kiwi is an efficient C++ implementation of the Cassowary constraint
2936 solving algorithm. Kiwi has been designed from the ground up to be
2937 lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
2938 Cassowary solver with typical use cases gaining a 40x improvement. Memory
2939 savings are consistently > 5x.")
2940 (license license:bsd-3)))
2942 (define-public python2-kiwisolver
2943 (package-with-python2 python-kiwisolver))
2945 (define-public slepc
2952 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
2956 "1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8"))))
2957 (build-system gnu-build-system)
2959 `(("python" ,python-2)
2960 ("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
2962 `(("arpack" ,arpack-ng)
2963 ("gfortran" ,gfortran)))
2965 `(("petsc" ,petsc)))
2967 `(#:parallel-build? #f ;build is parallel by default
2969 `(,(string-append "--with-arpack-dir="
2970 (assoc-ref %build-inputs "arpack") "/lib"))
2971 #:make-flags ;honor (parallel-job-count)
2972 `(,(format #f "MAKE_NP=~a" (parallel-job-count))
2973 ,(string-append "PETSCCONFIGDIR="
2974 (assoc-ref %build-inputs "petsc:examples")
2975 "/share/petsc/examples/config"))
2977 (modify-phases %standard-phases
2979 ;; configure is a python script, so we can't run it with bash.
2980 (lambda* (#:key inputs outputs (configure-flags '())
2982 (let* ((prefix (assoc-ref outputs "out"))
2983 (flags `(,(string-append "--prefix=" prefix)
2984 ,@configure-flags)))
2985 (format #t "build directory: ~s~%" (getcwd))
2986 (format #t "configure flags: ~s~%" flags)
2987 (setenv "SLEPC_DIR" (getcwd))
2988 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
2989 (apply invoke "./configure" flags))))
2990 (add-after 'install 'delete-doc
2991 ;; TODO: SLEPc installs HTML documentation alongside headers in
2992 ;; $out/include. We'd like to move them to share/doc, but delete
2993 ;; them for now, as they are incomplete and installing the complete
2994 ;; documentation is difficult.
2995 (lambda* (#:key outputs #:allow-other-keys)
2996 (let* ((out (assoc-ref outputs "out")))
2997 (for-each delete-file (find-files out "\\.html$"))
2999 (add-after 'install 'clean-install
3000 ;; Clean up unnecessary build logs from installation.
3001 (lambda* (#:key outputs #:allow-other-keys)
3002 (let ((out (assoc-ref outputs "out")))
3003 (for-each (lambda (file)
3004 (let ((f (string-append out "/lib/slepc/conf/" file)))
3005 (when (file-exists? f)
3007 '("configure.log" "make.log" "gmake.log"
3008 "test.log" "error.log" "RDict.db"
3011 (home-page "https://slepc.upv.es")
3012 (synopsis "Scalable library for eigenproblems")
3013 (description "SLEPc is a software library for the solution of large sparse
3014 eigenproblems on parallel computers. It can be used for the solution of
3015 linear eigenvalue problems formulated in either standard or generalized form,
3016 as well as other related problems such as the singular value decomposition.
3017 The emphasis of the software is on methods and techniques appropriate for
3018 problems in which the associated matrices are sparse, for example, those
3019 arising after the discretization of partial differential equations.")
3020 (license license:bsd-2)))
3022 (define-public slepc-complex
3023 (package (inherit slepc)
3024 (name "slepc-complex")
3026 `(("petsc" ,petsc-complex)
3027 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
3028 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
3030 (define-public slepc-openmpi
3031 (package (inherit slepc)
3032 (name "slepc-openmpi")
3034 (substitute-keyword-arguments (package-arguments slepc)
3035 ((#:phases phases '%standard-phases)
3036 `(modify-phases ,phases
3037 (add-before 'check 'mpi-setup
3038 ,%openmpi-setup)))))
3041 ("arpack" ,arpack-ng-openmpi)
3042 ,@(alist-delete "arpack" (package-inputs slepc))))
3044 `(("petsc" ,petsc-openmpi)
3045 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
3046 (synopsis "Scalable library for eigenproblems (with MPI support)")))
3048 (define-public slepc-complex-openmpi
3049 (package (inherit slepc-openmpi)
3050 (name "slepc-complex-openmpi")
3052 `(("petsc" ,petsc-complex-openmpi)
3053 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
3054 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
3056 (define-public python-slepc4py
3058 (name "python-slepc4py")
3063 (uri (pypi-uri "slepc4py" version))
3066 "1ksp08kxf4wg408b9nn39z3qfhy643j22d4rfbl30vzxk2rxh4lq"))))
3067 (build-system python-build-system)
3070 (modify-phases %standard-phases
3071 (add-before 'build 'pre-build
3073 ;; Define path to PETSc installation.
3074 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
3075 ;; Define path to SLEPc installation.
3076 (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
3078 (add-before 'check 'mpi-setup
3081 `(("python-numpy" ,python-numpy)
3082 ("python-petsc4py" ,python-petsc4py)
3083 ("slepc" ,slepc-openmpi)))
3084 (home-page "https://bitbucket.org/slepc/slepc4py/")
3085 (synopsis "Python bindings for SLEPc")
3086 (description "SLEPc, the Scalable Library for Eigenvalue Problem
3087 Computations, is based on PETSc, the Portable, Extensible Toolkit for
3088 Scientific Computation. It employs the MPI standard for all
3089 message-passing communication. @code{slepc4py} provides Python
3090 bindings to almost all functions of SLEPc.")
3091 (license license:bsd-3)))
3093 (define-public metamath
3101 (url "https://github.com/metamath/metamath-exe")
3102 (commit (string-append "v" version))))
3103 (file-name (git-file-name name version))
3105 (base32 "1s9hyknfvhj86g3giayyf3dxzg23iij0rs7bdvj075v9qbyhqn9b"))))
3106 (build-system gnu-build-system)
3108 `(("autoconf" ,autoconf)
3109 ("automake" ,automake)))
3110 (home-page "http://us.metamath.org/")
3111 (synopsis "Proof verifier based on a minimalistic formalism")
3113 "Metamath is a tiny formal language and that can express theorems in
3114 abstract mathematics, with an accompyaning @command{metamath} executable that
3115 verifies databases of these proofs. There is a public database,
3116 @url{https://github.com/metamath/set.mm, set.mm}, implementing first-order
3117 logic and Zermelo-Frenkel set theory with Choice, along with a large swath of
3118 associated, high-level theorems, e.g.@: the fundamental theorem of arithmetic,
3119 the Cauchy-Schwarz inequality, Stirling's formula, etc. See the Metamath
3121 (license license:gpl2+)))
3123 (define-public minizinc
3130 (url "https://github.com/MiniZinc/libminizinc")
3132 (file-name (git-file-name name version))
3135 "10b2hsl1fx9psh0iagmp8ki3f60f3qg5hmvra5aczjlfmbl88ggp"))
3136 (modules '((guix build utils)
3141 ;; Do not advertise proprietary solvers
3142 (with-directory-excursion "cmake/targets"
3143 (let ((targets '("libminizinc_fzn.cmake"
3144 "libminizinc_gecode.cmake"
3145 "libminizinc_mip.cmake"
3146 "libminizinc_nl.cmake"
3147 "libminizinc_osicbc.cmake"
3148 "libminizinc_parser.cmake"
3152 (for-each delete-file
3155 (member file (cons* "." ".." targets)))
3157 (substitute* "libmzn.cmake"
3158 (("include\\(cmake/targets/(.*)\\)" all target)
3159 (if (member target targets) all "")))))
3160 (with-directory-excursion "include/minizinc/solvers/MIP"
3161 (for-each delete-file
3164 (member file '("." ".."
3165 "MIP_osicbc_solverfactory.hh"
3166 "MIP_osicbc_wrap.hh"
3167 "MIP_solverinstance.hh"
3168 "MIP_solverinstance.hpp"
3171 (with-directory-excursion "solvers/MIP"
3172 (for-each delete-file
3175 (member file '("." ".."
3176 "MIP_osicbc_solverfactory.cpp"
3177 "MIP_osicbc_wrap.cpp"
3178 "MIP_solverinstance.cpp"
3181 (substitute* "CMakeLists.txt"
3182 (("find_package\\(([^ ]*).*\\)" all pkg)
3183 (if (member pkg '("Gecode" "OsiCBC" "Threads"))
3186 ;; TODO: swap out miniz for zlib
3188 (build-system cmake-build-system)
3190 `(#:tests? #f ; no ‘check’ target
3191 #:modules ((guix build cmake-build-system)
3195 (modify-phases %standard-phases
3196 (add-after 'install 'install-solver-configs
3197 (lambda* (#:key inputs outputs #:allow-other-keys)
3198 (let ((gecode (assoc-ref inputs "gecode"))
3199 (pkgdatadir (string-append (assoc-ref outputs "out")
3200 "/share/minizinc")))
3201 (call-with-output-file (string-append pkgdatadir
3202 "/Preferences.json")
3207 [\"\", \"org.gecode.gecode\"],
3208 [\"gecode\", \"org.gecode.gecode\"]
3210 \"solverDefaults\": []
3215 (mkdir-p (string-append pkgdatadir "/solvers"))
3216 (call-with-output-file (string-append pkgdatadir
3217 "/solvers/gecode.msc")
3222 \"id\": \"org.gecode.gecode\",
3223 \"name\": \"Gecode\",
3224 \"description\": \"Gecode FlatZinc executable\",
3228 \"supportsMzn\": false,
3229 \"supportsFzn\": true,
3230 \"needsSolns2Out\": true,
3231 \"needsMznExecutable\": false,
3232 \"needsStdlibDir\": false,
3233 \"isGUIApplication\": false
3235 (last (string-split gecode #\-))
3236 (string-append gecode "/share/gecode/mznlib")
3237 (string-append gecode "/bin/fzn-gecode"))
3238 (newline port)))))))))
3246 (home-page "https://www.minizinc.org")
3247 (synopsis "High-level constraint modeling language")
3248 (description "MiniZinc is a high-level modeling language for constraint
3249 satisfaction and optimization problems. Models are compiled to FlatZinc, a
3250 language understood by many solvers.")
3251 (license license:mpl2.0)))
3253 (define-public mumps
3260 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
3264 "0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r"))
3265 (patches (search-patches "mumps-build-parallelism.patch"
3266 "mumps-shared-libseq.patch"
3267 "mumps-shared-mumps.patch"
3268 "mumps-shared-pord.patch"))))
3269 (build-system gnu-build-system)
3271 `(("fortran" ,gfortran)
3272 ;; These are required for linking against mumps, but we let the user
3273 ;; declare the dependency.
3276 ("scotch" ,scotch)))
3278 `(#:modules ((ice-9 match)
3281 ,@%gnu-build-system-modules)
3283 (modify-phases %standard-phases
3285 (lambda* (#:key inputs #:allow-other-keys)
3286 (call-with-output-file "Makefile.inc"
3297 INCSEQ = -I$(topdir)/libseq
3298 LIBSEQ = $(topdir)/libseq/libmpiseq.a
3299 LIBSEQNEEDED = libseqneeded~;
3303 AR = ar vr # rules require trailing space, ugh...
3306 LIBBLAS = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[
3308 SCALAP = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~]
3309 LIBOTHERS = -pthread
3312 OPTF = -O2 -DALLOW_NON_INIT $(PIC)
3316 LIBS = $(SCALAP) $(LIBSEQ)
3317 LPORDDIR = $(topdir)/PORD/lib
3318 IPORD = -I$(topdir)/PORD/include
3319 LPORD = $(LPORDDIR)/libpord.a
3320 ORDERINGSF = -Dpord~@[
3322 IMETIS = -I$(METISDIR)/include
3323 LMETIS = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
3324 ORDERINGSF += -Dmetis~]~@[~:{
3326 ISCOTCH = -I$(SCOTCHDIR)/include
3327 LSCOTCH = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
3328 ORDERINGSF += ~a~}~]
3329 ORDERINGSC = $(ORDERINGSF)
3330 LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
3331 IORDERINGSF = $(ISCOTCH)
3332 IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
3333 (assoc-ref inputs "mpi")
3334 (assoc-ref inputs "blas")
3335 (assoc-ref inputs "scalapack")
3336 (assoc-ref inputs "metis")
3337 (match (list (assoc-ref inputs "pt-scotch")
3338 (assoc-ref inputs "scotch"))
3342 `((,scotch "" "-Dscotch")))
3345 "-lptesmumps -lptscotch -lptscotcherr "
3346 "-Dptscotch")))))))))
3348 ;; By default only the d-precision library is built. Make with "all"
3349 ;; target so that all precision libraries and examples are built.
3351 (invoke "make" "all"
3352 (format #f "-j~a" (parallel-job-count)))))
3354 ;; Run the simple test drivers, which read test input from stdin:
3355 ;; from the "real" input for the single- and double-precision
3356 ;; testers, and from the "cmplx" input for complex-precision
3357 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
3358 ;; package to prefix execution with "mpirun".
3359 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
3360 (with-directory-excursion "examples"
3363 (let ((tester (apply open-pipe*
3366 ,(string-append "./" prec
3368 (input (open-input-file
3369 (string-append "input_simpletest_" type))))
3371 (dump-port input tester)
3373 (zero? (close-pipe tester)))))
3375 '("real" "real" "cmplx" "cmplx")))))
3377 (lambda* (#:key outputs #:allow-other-keys)
3378 (let* ((out (assoc-ref outputs "out"))
3379 (libdir (string-append out "/lib")))
3380 (copy-recursively "lib" libdir)
3381 (copy-recursively "include" (string-append out "/include"))
3382 (when (file-exists? "libseq/libmpiseq.a")
3383 (install-file "libseq/libmpiseq.a" libdir))
3384 (when (file-exists? "libseq/libmpiseq.so")
3385 (install-file "libseq/libmpiseq.so" libdir))
3387 (home-page "http://mumps.enseeiht.fr")
3388 (synopsis "Multifrontal sparse direct solver")
3390 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
3391 sparse system of linear equations A x = b using Gaussian elimination.")
3392 (license license:cecill-c)))
3394 (define-public mumps-metis
3395 (package (inherit mumps)
3396 (name "mumps-metis")
3398 (alist-delete "scotch" (package-inputs mumps)))))
3400 (define-public mumps-openmpi
3401 (package (inherit mumps)
3402 (name "mumps-openmpi")
3405 ("scalapack" ,scalapack)
3406 ("pt-scotch" ,pt-scotch)
3407 ,@(alist-delete "scotch" (package-inputs mumps))))
3409 (substitute-keyword-arguments (package-arguments mumps)
3411 `(modify-phases ,phases
3412 (add-before 'check 'mpi-setup
3416 ((assoc-ref ,phases 'check)
3417 #:exec-prefix '("mpirun" "-n" "2"))))))))
3418 (synopsis "Multifrontal sparse direct solver (with MPI)")))
3420 (define-public mumps-metis-openmpi
3421 (package (inherit mumps-openmpi)
3422 (name "mumps-metis-openmpi")
3424 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
3426 (define-public ruby-asciimath
3428 (name "ruby-asciimath")
3433 (uri (rubygems-uri "asciimath" version))
3436 "1aapydwwkydbwgz07n7ma3a5jy9n3v0shy6q6j8mi4wr3crhx45a"))))
3437 (build-system ruby-build-system)
3439 `(("ruby-nokogiri" ,ruby-nokogiri)
3440 ("ruby-rspec" ,ruby-rspec)))
3441 (synopsis "AsciiMath parsing and conversion library")
3443 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
3444 easy-to-write markup language for mathematics.")
3445 (home-page "https://github.com/asciidoctor/asciimath")
3446 (license license:expat)))
3448 (define-public superlu
3455 (uri (string-append "https://portal.nersc.gov/project/sparse/superlu/"
3456 "superlu_" version ".tar.gz"))
3458 (base32 "13520vk6fqspyl22cq4ak2jh3rlmhja4czq56j75fdx65fkk80s7"))
3459 (modules '((guix build utils)))
3461 ;; Replace the non-free implementation of MC64 with a stub adapted
3464 (use-modules (ice-9 regex)
3466 (call-with-output-file "SRC/mc64ad.c"
3471 void mc64id_(int *a) {
3472 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
3475 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
3476 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
3477 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
3480 ;; Remove the corresponding license verbiage. MC64 license follows
3481 ;; a "------" line separator.
3482 (with-atomic-file-replacement "License.txt"
3483 (let ((rx (make-regexp "-{8}")))
3486 (let ((line (read-line in 'concat)))
3487 (unless (regexp-exec rx line)
3491 (build-system cmake-build-system)
3495 `(("blas" ,openblas)
3496 ("gfortran" ,gfortran)))
3498 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
3499 "-DTPL_BLAS_LIBRARIES=openblas"
3500 "-DBUILD_SHARED_LIBS:BOOL=YES")))
3501 (home-page "https://portal.nersc.gov/project/sparse/superlu/")
3502 (synopsis "Supernodal direct solver for sparse linear systems")
3504 "SuperLU is a general purpose library for the direct solution of large,
3505 sparse, nonsymmetric systems of linear equations on high performance machines.
3506 The library is written in C and is callable from either C or Fortran. The
3507 library routines perform an LU decomposition with partial pivoting and
3508 triangular system solves through forward and back substitution. The library
3509 also provides threshold-based ILU factorization preconditioners.")
3510 (license (list license:bsd-3
3511 license:gpl2+ ;EXAMPLE/*fgmr.c
3512 (license:fsf-free "file://SRC/colamd.h")))))
3514 (define-public superlu-dist
3516 (name "superlu-dist")
3522 (url "https://github.com/xiaoyeli/superlu_dist")
3523 (commit (string-append "v" version))))
3524 (file-name (git-file-name name version))
3526 (base32 "0fa29yr72p4yq5ln4rgfsawmi5935n4qcr5niz6864bjladz4lql"))
3527 (modules '((guix build utils)))
3529 ;; Replace the non-free implementation of MC64 with a stub
3531 (make-file-writable "SRC/mc64ad_dist.c")
3532 (call-with-output-file "SRC/mc64ad_dist.c"
3537 void mc64id_dist(int *a) {
3538 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
3541 void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
3542 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
3543 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
3546 (substitute* "SRC/util.c" ;adjust default algorithm
3547 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
3548 ;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
3549 ;; general (i.e. non-square) processor-grid support.
3550 "RowPerm = NOROWPERM;"))
3552 (patches (search-patches "superlu-dist-scotchmetis.patch"
3553 "superlu-dist-awpm-grid.patch"))))
3554 (build-system cmake-build-system)
3558 `(("gfortran" ,gfortran)
3561 ("combblas" ,combinatorial-blas)))
3563 `(("mpi" ,openmpi) ;headers include MPI heades
3564 ("parmetis" ,pt-scotch32 "metis")
3565 ("pt-scotch" ,pt-scotch32)))
3567 `(#:parallel-tests? #f ;tests use MPI and OpenMP
3568 #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
3569 "-DTPL_ENABLE_COMBBLASLIB=YES"
3570 "-DTPL_BLAS_LIBRARIES=-lopenblas"
3571 "-DTPL_LAPACK_LIBRARIES=-llapack"
3572 (string-append "-DTPL_PARMETIS_LIBRARIES="
3574 '("ptscotchparmetis" "ptscotch" "ptscotcherr"
3575 "scotchmetis" "scotch" "scotcherr")
3577 (string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
3578 (assoc-ref %build-inputs "parmetis")
3580 "-DTPL_ENABLE_COMBBLASLIB=ON"
3581 (string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
3582 (assoc-ref %build-inputs "combblas")
3583 "/include/CombBLAS;"
3584 (assoc-ref %build-inputs "combblas")
3585 "/include/BipartiteMatchings")
3586 "-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
3588 (modify-phases %standard-phases
3589 (add-before 'configure 'set-c++-standard
3591 (substitute* "CMakeLists.txt"
3592 ;; AWPM headers require C++14
3593 (("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
3594 (add-before 'check 'mpi-setup
3596 (add-before 'check 'omp-setup
3597 (lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
3598 (home-page (package-home-page superlu))
3599 (synopsis "Parallel supernodal direct solver")
3601 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
3602 It is targeted for distributed memory parallel machines. SuperLU_DIST is
3603 implemented in ANSI C, and MPI for communications.")
3604 (license license:bsd-3)))
3606 (define-public scotch
3613 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
3614 "latestfile/298/scotch_" version ".tar.gz"))
3616 (base32 "04dkz24a2g20wq703fnyi4440ac4mwycy9gwrrllljj7zxcjy19r"))
3617 (patches (search-patches "scotch-build-parallelism.patch"
3618 "scotch-integer-declarations.patch"))))
3619 (build-system gnu-build-system)
3625 ("gfortran" ,gfortran)))
3626 (outputs '("out" "metis"))
3628 `(#:make-flags (list (string-append "prefix=" %output))
3630 (modify-phases %standard-phases
3632 'unpack 'chdir-to-src
3633 (lambda _ (chdir "src") #t))
3637 (call-with-output-file "Makefile.inc"
3652 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
3653 LDFLAGS = -lz -lm -lrt -lpthread
3655 LEX = flex -Pscotchyy -olex.yy.c
3660 YACC = bison -pscotchyy -y -b y
3662 '("COMMON_FILE_COMPRESS_GZ"
3664 "COMMON_RANDOM_FIXED_SEED"
3665 "INTSIZE64" ;use 'int64_t'
3666 ;; Prevents symbol clashes with libesmumps
3668 ;; XXX: Causes invalid frees in superlu-dist tests
3670 ;; "SCOTCH_PTHREAD_NUMBER=2"
3671 "restrict=__restrict"))))
3673 (add-after 'build 'build-esmumps
3676 (format #f "-j~a" (parallel-job-count))
3678 (add-before 'install 'make-install-dirs
3679 (lambda* (#:key outputs #:allow-other-keys)
3680 (mkdir (assoc-ref outputs "out"))))
3681 (add-after 'install 'install-metis
3682 (lambda* (#:key outputs #:allow-other-keys)
3683 (let ((out (assoc-ref outputs "metis")))
3685 ;; metis files are not installed with 'make install'
3686 (for-each (lambda (f)
3687 (install-file f (string-append out "/include")))
3688 (find-files "../include/" ".*metis\\.h"))
3689 (for-each (lambda (f)
3690 (install-file f (string-append out "/lib")))
3691 (find-files "../lib/" ".*metis\\..*"))
3693 (home-page "https://www.labri.fr/perso/pelegrin/scotch/")
3695 `((release-monitoring-url . "https://gforge.inria.fr/frs/?group_id=248")))
3696 (synopsis "Programs and libraries for graph algorithms")
3697 (description "SCOTCH is a set of programs and libraries which implement
3698 the static mapping and sparse matrix reordering algorithms developed within
3699 the SCOTCH project. Its purpose is to apply graph theory, with a divide and
3700 conquer approach, to scientific computing problems such as graph and mesh
3701 partitioning, static mapping, and sparse matrix ordering, in application
3702 domains ranging from structural mechanics to operating systems or
3704 ;; See LICENSE_en.txt
3705 (license license:cecill-c)))
3707 (define-public scotch32
3708 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
3709 ;; some applications.
3710 (package (inherit scotch)
3713 (substitute-keyword-arguments (package-arguments scotch)
3714 ((#:phases scotch-phases)
3715 `(modify-phases ,scotch-phases
3719 (call-with-output-file "Makefile.inc"
3734 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
3735 LDFLAGS = -lz -lm -lrt -lpthread
3737 LEX = flex -Pscotchyy -olex.yy.c
3742 YACC = bison -pscotchyy -y -b y
3744 '("COMMON_FILE_COMPRESS_GZ"
3746 "COMMON_RANDOM_FIXED_SEED"
3747 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
3748 ;; Prevents symbolc clashes with libesmumps
3750 ;; XXX: Causes invalid frees in superlu-dist tests
3752 ;; "SCOTCH_PTHREAD_NUMBER=2"
3753 "restrict=__restrict"))))))))))
3755 "Programs and libraries for graph algorithms (32-bit integers)")))
3757 (define-public scotch-shared
3758 (package (inherit scotch)
3759 (name "scotch-shared")
3765 (substitute-keyword-arguments (package-arguments scotch)
3766 ((#:phases scotch-shared-phases)
3767 `(modify-phases ,scotch-shared-phases
3771 ;; Otherwise, the RUNPATH will lack the final path component.
3772 (setenv "RPATHFLAGS" (string-append "-Wl,-rpath="
3773 (assoc-ref %outputs "out") "/lib"))
3774 (call-with-output-file "Makefile.inc"
3782 ARFLAGS = -shared -o
3789 CFLAGS = -O2 -g -fPIC $(CPPFLAGS) $(RPATHFLAGS)
3790 CLIBFLAGS = -shared -fPIC
3791 LDFLAGS = -lz -lm -lrt -lpthread -Xlinker --no-as-needed
3793 LEX = flex -Pscotchyy -olex.yy.c
3798 YACC = bison -pscotchyy -y -b y
3800 '("COMMON_FILE_COMPRESS_GZ"
3802 "COMMON_RANDOM_FIXED_SEED"
3803 "INTSIZE64" ;use 'int64_t'
3804 ;; Prevents symbolc clashes with libesmumps
3806 ;; XXX: Causes invalid frees in superlu-dist tests
3808 ;; "SCOTCH_PTHREAD_NUMBER=2"
3809 "restrict=__restrict"
3813 "Programs and libraries for graph algorithms (shared libraries version)")))
3815 (define-public pt-scotch
3816 (package (inherit scotch)
3819 `(("openmpi" ,openmpi))) ;Headers include MPI headers
3821 (substitute-keyword-arguments (package-arguments scotch)
3822 ((#:phases scotch-phases)
3823 `(modify-phases ,scotch-phases
3827 (invoke "make" (format #f "-j~a" (parallel-job-count))
3828 "ptscotch" "ptesmumps")
3830 ;; Install the serial metis compatibility library
3831 (invoke "make" "-C" "libscotchmetis" "install")))
3832 (add-before 'check 'mpi-setup
3836 (invoke "make" "ptcheck")))))))
3837 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
3839 (define-public pt-scotch32
3840 (package (inherit scotch32)
3841 (name "pt-scotch32")
3843 `(("openmpi" ,openmpi))) ;headers include MPI headers
3845 (substitute-keyword-arguments (package-arguments scotch32)
3846 ((#:phases scotch32-phases)
3847 `(modify-phases ,scotch32-phases
3850 (invoke "make" (format #f "-j~a" (parallel-job-count))
3851 "ptscotch" "ptesmumps")
3852 ;; Install the serial metis compatibility library
3853 (invoke "make" "-C" "libscotchmetis" "install")))
3854 (add-before 'check 'mpi-setup
3858 (invoke "make" "ptcheck")))))))
3860 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
3862 (define-public pt-scotch-shared
3863 (package (inherit scotch-shared)
3864 (name "pt-scotch-shared")
3866 `(("openmpi" ,openmpi))) ;Headers include MPI headers
3868 (substitute-keyword-arguments (package-arguments scotch-shared)
3869 ((#:phases scotch-shared-phases)
3870 `(modify-phases ,scotch-shared-phases
3874 (invoke "make" (format #f "-j~a" (parallel-job-count))
3875 "ptscotch" "ptesmumps")
3877 ;; Install the serial metis compatibility library
3878 (invoke "make" "-C" "libscotchmetis" "install")))
3879 (add-before 'check 'mpi-setup
3880 ,%openmpi-setup)))))
3881 (synopsis "Graph algorithms (shared libraries version, with MPI)")))
3884 (define-public metis
3891 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
3892 "metis-" version ".tar.gz"))
3895 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
3897 `((release-monitoring-url
3898 . "http://glaros.dtc.umn.edu/gkhome/metis/metis/download")))
3899 (build-system cmake-build-system)
3901 `(("blas" ,openblas)))
3903 `(#:tests? #f ;no tests
3904 #:configure-flags `("-DSHARED=ON"
3905 ,(string-append "-DGKLIB_PATH=" (getcwd)
3906 "/metis-" ,version "/GKlib"))))
3907 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
3908 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
3910 "METIS is a set of serial programs for partitioning graphs, partitioning
3911 finite element meshes, and producing fill-reducing orderings for sparse
3912 matrices. The algorithms implemented in METIS are based on the multilevel
3913 recursive-bisection, multilevel k-way, and multi-constraint partitioning
3915 (license license:asl2.0))) ;As of version 5.0.3
3917 (define-public p4est
3924 (uri (string-append "http://p4est.github.io/release/p4est-"
3928 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
3929 (build-system gnu-build-system)
3931 `(("fortran" ,gfortran)
3936 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
3937 (assoc-ref %build-inputs "blas")
3939 ,(string-append "LAPACK_LIBS=-L"
3940 (assoc-ref %build-inputs "lapack")
3942 #:phases (modify-phases %standard-phases
3943 (add-before 'check 'mpi-setup
3945 (home-page "http://www.p4est.org")
3946 (synopsis "Adaptive mesh refinement on forests of octrees")
3948 "The p4est software library enables the dynamic management of a
3949 collection of adaptive octrees, conveniently called a forest of octrees.
3950 p4est is designed to work in parallel and scales to hundreds of thousands of
3952 (license license:gpl2+)))
3954 (define-public p4est-openmpi
3955 (package (inherit p4est)
3956 (name "p4est-openmpi")
3959 ,@(package-inputs p4est)))
3961 (substitute-keyword-arguments (package-arguments p4est)
3962 ((#:configure-flags cf)
3963 ``("--enable-mpi" ,@,cf))))
3964 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
3966 (define-public gsegrafix
3967 ;; This is an old and equally dead "experimental fork" of the longer-dead
3968 ;; original. At least it no longer requires the even-deader libgnomeprint{,ui}
3969 ;; libraries, instead rendering plots with Pango.
3976 (uri (string-append "mirror://savannah/gsegrafix-experimental/"
3977 "gsegrafix-experimental-" version ".tar.gz"))
3979 (base32 "0fwh6719xy2zasmqlp0vdx6kzm45hn37ga88xmw5cz0yx7xw4j6f"))))
3980 (build-system gnu-build-system)
3983 (list "--disable-static")))
3988 `(("pkg-config" ,pkg-config)))
3989 (home-page "https://www.gnu.org/software/gsegrafix/")
3990 (synopsis "GNOME application to create scientific and engineering plots")
3992 "GSEGrafix is an application which produces high-quality graphical
3993 plots for science and engineering. Plots are specified via simple ASCII
3994 parameter files and data files and are presented in an anti-aliased GNOME
3995 canvas. The program supports rectangular two-dimensional plots, histograms,
3996 polar-axis plots and three-dimensional plots. Plots can be printed or saved
3997 to BMP, JPEG or PNG image formats.")
3998 (license license:gpl3+)))
4000 (define-public maxima
4007 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
4008 version "-source/" name "-" version ".tar.gz"))
4011 "1p77nk5sz1qfkn5zr97szpbi8ib4b22k8i52l4ag5gkhd4kid47y"))
4012 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
4013 (build-system gnu-build-system)
4015 `(("bash" ,bash-minimal)
4016 ("gnuplot" ,gnuplot) ;for plots
4019 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
4021 `(("texinfo" ,texinfo)
4023 ("python" ,python)))
4026 ,#~(list "--enable-sbcl"
4027 (string-append "--with-sbcl=" #$sbcl "/bin/sbcl")
4028 (string-append "--with-posix-shell=" #$bash-minimal "/bin/sh")
4029 (string-append "--with-wish=" #$tk "/bin/wish"
4030 #$(version-major+minor (package-version tk))))
4031 ;; By default Maxima attempts to write temporary files to
4032 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
4033 ;; Work around that.
4034 #:make-flags (list "TMPDIR=/tmp")
4036 (modify-phases %standard-phases
4037 (add-after 'unpack 'patch-paths
4038 (lambda* (#:key inputs #:allow-other-keys)
4039 (let* ((sed (search-input-file inputs "/bin/sed"))
4040 (coreutils (assoc-ref inputs "coreutils"))
4041 (dirname (string-append coreutils "/bin/dirname"))
4042 (head (string-append coreutils "/bin/head"))
4043 (perl (search-input-file inputs "/bin/perl"))
4044 (python (search-input-file inputs "/bin/python3")))
4045 (substitute* "src/maxima.in"
4046 (("sed ") (string-append sed " "))
4047 (("dirname") dirname)
4049 (substitute* "doc/info/Makefile.in"
4050 (("/usr/bin/env perl") perl))
4051 (substitute* "doc/info/build_html.sh.in"
4052 (("python") python))
4054 (add-before 'check 'pre-check
4056 (chmod "src/maxima" #o555)
4060 ;; This is derived from the testing code in the "debian/rules" file
4061 ;; of Debian's Maxima package.
4062 ;; If Maxima can successfully run this, the binary to be installed
4068 "--batch-string=\"run_testsuite();\" "
4069 "| grep -q \"No unexpected errors found\""))))
4070 ;; Make sure the doc and emacs files are found in the
4071 ;; standard location. Also configure maxima to find gnuplot
4072 ;; without having it on the PATH.
4073 (add-after 'install 'post-install
4074 (lambda* (#:key outputs inputs #:allow-other-keys)
4075 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
4076 (out (assoc-ref outputs "out"))
4077 (datadir (string-append out "/share/maxima/" ,version))
4078 (binutils (dirname (search-input-file inputs "/bin/as"))))
4079 (with-directory-excursion out
4080 (mkdir-p "share/emacs")
4081 (mkdir-p "share/doc")
4083 (string-append datadir "/doc/")
4084 (string-append out "/share/doc/maxima"))
4085 (with-atomic-file-replacement
4086 (string-append datadir "/share/maxima-init.lisp")
4088 (format out "~a ~s~a~%"
4089 "(setf $gnuplot_command "
4090 (string-append gnuplot "/bin/gnuplot") ")")
4091 (dump-port in out))))
4092 ;; Ensure that Maxima will have access to the GNU binutils
4093 ;; components at runtime.
4094 (wrap-program (string-append out "/bin/maxima")
4095 `("PATH" prefix (,binutils))))
4097 (home-page "https://maxima.sourceforge.io")
4098 (synopsis "Numeric and symbolic expression manipulation")
4099 (description "Maxima is a system for the manipulation of symbolic and
4100 numerical expressions. It yields high precision numeric results by using
4101 exact fractions, arbitrary precision integers, and variable precision floating
4103 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
4104 ;; Others simply say "GNU General Public License" without stating a
4105 ;; version (which implicitly means gpl1+).
4106 ;; At least one file (src/maxima.asd) says "version 2."
4107 ;; GPLv2 only is therefore the smallest subset.
4108 (license license:gpl2)))
4110 (define-public wxmaxima
4118 (url "https://github.com/wxMaxima-developers/wxmaxima")
4119 (commit (string-append "Version-" version))))
4120 (file-name (git-file-name name version))
4122 (base32 "0h7ryykh2dapcyvpp4f1j1b3vrrz80x9k8nkci2yxifgdb29vyhw"))))
4123 (build-system cmake-build-system)
4125 `(("gettext" ,gettext-minimal)))
4127 `(("wxwidgets" ,wxwidgets)
4130 ("adwaita-icon-theme" ,adwaita-icon-theme)
4132 ("shared-mime-info" ,shared-mime-info)))
4134 `(#:tests? #f ; tests fail non-deterministically
4136 (modify-phases %standard-phases
4137 (add-after 'unpack 'patch-doc-path
4139 ;; Don't look in share/doc/wxmaxima-xx.xx.x for the
4140 ;; documentation. Only licensing information is placed there by
4142 (substitute* "src/Dirstructure.cpp"
4143 (("/doc/wxmaxima-\\%s") "/doc/wxmaxima"))
4145 (add-after 'install 'wrap-program
4146 (lambda* (#:key inputs outputs #:allow-other-keys)
4147 (wrap-program (string-append (assoc-ref outputs "out")
4150 (,(string-append (assoc-ref inputs "maxima")
4152 ;; For GtkFileChooserDialog.
4153 `("GSETTINGS_SCHEMA_DIR" =
4154 (,(string-append (assoc-ref inputs "gtk+")
4155 "/share/glib-2.0/schemas")))
4156 `("XDG_DATA_DIRS" ":" prefix
4157 (;; Needed by gdk-pixbuf to know supported icon formats.
4159 (assoc-ref inputs "shared-mime-info") "/share")
4160 ;; The default icon theme of GTK+.
4162 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
4164 (home-page "https://wxmaxima-developers.github.io/wxmaxima/")
4165 (synopsis "Graphical user interface for the Maxima computer algebra system")
4167 "wxMaxima is a graphical user interface for the Maxima computer algebra
4168 system. It eases the use of Maxima by making most of its commands available
4169 through a menu system and by providing input dialogs for commands that require
4170 more than one argument. It also implements its own display engine that
4171 outputs mathematical symbols directly instead of depicting them with ASCII
4174 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
4175 text and mathematical calculations to create documents, exporting of input and
4176 output to TeX, and a browser for Maxima's manual including command index and
4177 full text searching.")
4178 (license license:gpl2+)))
4180 (define-public armadillo
4186 (uri (string-append "mirror://sourceforge/arma/armadillo-"
4190 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
4191 (build-system cmake-build-system)
4192 (arguments `(#:tests? #f)) ; no test target
4194 `(("openblas" ,openblas)
4196 ("arpack" ,arpack-ng)))
4197 (home-page "http://arma.sourceforge.net/")
4198 (synopsis "C++ linear algebra library")
4200 "Armadillo is a C++ linear algebra library, aiming towards a good balance
4201 between speed and ease of use. It is useful for algorithm development
4202 directly in C++, or quick conversion of research code into production
4203 environments. It can be used for machine learning, pattern recognition,
4204 signal processing, bioinformatics, statistics, econometrics, etc. The library
4205 provides efficient classes for vectors, matrices and cubes, as well as 150+
4206 associated functions (e.g., contiguous and non-contiguous submatrix views).")
4207 (license license:asl2.0)))
4209 (define-public muparser
4210 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
4211 ;; different hash. In order to make `guix package --upgrade` work correctly,
4212 ;; we set a Guix packaging revision.
4213 ;; When the next version of muparser is released, we can remove
4214 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
4215 (let ((upstream-version "2.2.5")
4219 (version (string-append upstream-version "-" revision))
4224 (url "https://github.com/beltoforion/muparser")
4225 (commit (string-append "v" upstream-version))))
4226 (file-name (git-file-name name version))
4228 (base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24"))))
4229 (build-system gnu-build-system)
4231 `(#:configure-flags '("--enable-samples=no")
4232 #:tests? #f)) ;no "check" target
4233 (home-page "http://muparser.beltoforion.de/")
4234 (synopsis "Fast parser library for mathematical expressions")
4236 "muParser is an extensible high performance math parser library. It is
4237 based on transforming an expression into a bytecode and precalculating constant
4239 (license license:expat))))
4241 (define-public openblas
4249 (url "https://github.com/xianyi/OpenBLAS")
4250 (commit (string-append "v" version))))
4251 (file-name (git-file-name name version))
4254 "14jxh0v3jfbw4mfjx4mcz4dd51lyq7pqvh9k8dg94539ypzjr2lj"))))
4255 (build-system gnu-build-system)
4257 `(#:test-target "test"
4258 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
4259 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
4260 ;; we need to disable substitutions.
4262 ,(let ((system (or (%current-target-system) (%current-system))))
4263 (or (string-prefix? "x86_64" system)
4264 (string-prefix? "i686" system)
4265 (string-prefix? "mips" system)
4266 (string-prefix? "aarch64" system)))
4268 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
4270 "MAKE_NB_JOBS=0" ;use jobserver for submakes
4272 ;; This is the maximum number of threads OpenBLAS will ever use (that
4273 ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS
4274 ;; is used.) If we don't set it, the makefile sets it to the number
4275 ;; of cores of the build machine, which is obviously wrong.
4278 ;; Build the library for all supported CPUs. This allows
4279 ;; switching CPU targets at runtime with the environment variable
4280 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
4281 ;; Unfortunately, this is not supported on all architectures,
4282 ;; where it leads to failed builds.
4283 ,@(let ((system (or (%current-target-system) (%current-system))))
4285 ((or (string-prefix? "x86_64" system)
4286 (string-prefix? "i686" system))
4287 '("DYNAMIC_ARCH=1"))
4288 ;; On some of these architectures the CPU can't be detected.
4289 ((or (string-prefix? "powerpc64le" system)
4290 (string-prefix? "aarch64" system))
4293 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
4294 ;; two available MIPS targets special extended instructions
4295 ;; for Loongson cores are used.
4296 ((string-prefix? "mips" system)
4297 '("TARGET=SICORTEX"))
4298 ;; Failed to detect CPU.
4299 ((string-prefix? "armhf" system)
4302 ;; no configure script
4304 (modify-phases %standard-phases
4306 (add-before 'build 'set-extralib
4307 (lambda* (#:key inputs #:allow-other-keys)
4308 ;; Get libgfortran found when building in utest.
4310 (string-append "-L" (assoc-ref inputs "fortran-lib")
4314 `(("fortran-lib" ,gfortran "lib")))
4317 ("fortran" ,gfortran)
4319 (home-page "https://www.openblas.net/")
4320 (synopsis "Optimized BLAS library based on GotoBLAS")
4322 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
4323 (license license:bsd-3)))
4325 (define-public openblas-ilp64
4326 (package/inherit openblas
4327 (name "openblas-ilp64")
4328 (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
4330 (substitute-keyword-arguments (package-arguments openblas)
4331 ((#:make-flags flags '())
4332 `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
4334 (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
4335 (license license:bsd-3)))
4341 (home-page "https://github.com/flame/blis")
4344 (uri (git-reference (url home-page) (commit version)))
4347 "05ifil6jj9424sr8kmircl8k4bmxnl3y12a79vwj1kxxva5gz50g"))
4348 (file-name (git-file-name "blis" version))))
4350 `(("python" ,python)
4352 (build-system gnu-build-system)
4355 ((guix build gnu-build-system)
4358 #:test-target "test"
4360 (modify-phases %standard-phases
4362 (lambda* (#:key outputs
4365 (configure-flags '())
4367 ;; This is a home-made 'configure' script.
4368 (let* ((out (assoc-ref outputs "out"))
4369 ;; Guix-specific support for choosing the configuration
4370 ;; via #:configure-flags: see below for details.
4371 (config-flag-prefix "--blis-config=")
4372 (maybe-config-flag (find
4374 (string-prefix? config-flag-prefix s))
4376 (configure-flags (if maybe-config-flag
4377 (delete maybe-config-flag
4380 ;; Select the "configuration" to build.
4381 ;; The "generic" configuration is non-optimized but
4382 ;; portable (no assembly).
4383 ;; The "x86_64" configuration family includes
4384 ;; sub-configurations for all supported
4385 ;; x86_64 microarchitectures.
4386 ;; BLIS currently lacks runtime hardware detection
4387 ;; for other architectures: see
4388 ;; <https://github.com/flame/blis/commit/c534da6>.
4389 ;; Conservatively, we stick to "generic" on armhf,
4390 ;; aarch64, and ppc64le for now. (But perhaps
4391 ;; "power9", "cortexa9", and "cortexa57" might be
4392 ;; general enough to use?)
4393 ;; Another approach would be to use the "auto"
4394 ;; configuration and make this package
4395 ;; non-substitutable.
4396 ;; The build is fairly intensive, though.
4400 (substring maybe-config-flag
4401 (string-length config-flag-prefix)))
4402 ((string-prefix? "x86_64" (or target system))
4411 "--enable-threading=openmp"
4412 "--enable-verbose-make"
4415 (format #t "configure args: ~s~%" configure-args)
4420 (add-before 'check 'show-test-output
4422 ;; By default "make check" is silent. Make it verbose.
4423 (system "tail -F output.testsuite &")
4425 (synopsis "High-performance basic linear algebra (BLAS) routines")
4427 "BLIS is a portable software framework for instantiating high-performance
4428 BLAS-like dense linear algebra libraries. The framework was designed to
4429 isolate essential kernels of computation that, when optimized, immediately
4430 enable optimized implementations of most of its commonly used and
4431 computationally intensive operations. While BLIS exports a new BLAS-like API,
4432 it also includes a BLAS compatibility layer which gives application developers
4433 access to BLIS implementations via traditional BLAS routine calls.")
4434 (license license:bsd-3)))
4436 (define-public blis-sandybridge (deprecated-package "blis-sandybridge" blis))
4437 (define-public blis-haswell (deprecated-package "blis-haswell" blis))
4438 (define-public blis-knl (deprecated-package "blis-knl" blis))
4440 (define ignorance blis)
4442 (define-public openlibm
4450 (url "https://github.com/JuliaLang/openlibm")
4451 (commit (string-append "v" version))))
4452 (file-name (git-file-name name version))
4454 (base32 "1azms0lpxb7vxb3bln5lyz0wpwx6jnzbffkclclpq2v5aiw8d14i"))))
4455 (build-system gnu-build-system)
4458 (list (string-append "prefix=" (assoc-ref %outputs "out"))
4459 ,(string-append "CC=" (cc-for-target)))
4461 ;; no configure script
4462 (modify-phases %standard-phases (delete 'configure))
4463 #:tests? #f)) ;the tests are part of the default target
4464 (home-page "https://openlibm.org/")
4465 (synopsis "Portable C mathematical library (libm)")
4467 "OpenLibm is an effort to have a high quality, portable, standalone C
4468 mathematical library (libm). It can be used standalone in applications and
4469 programming language implementations. The project was born out of a need to
4470 have a good libm for the Julia programming language that worked consistently
4471 across compilers and operating systems, and in 32-bit and 64-bit
4473 ;; Each architecture has its own make target, and there is none for mips.
4474 (supported-systems (delete "mips64el-linux" %supported-systems))
4475 ;; See LICENSE.md for details.
4476 (license (list license:expat
4479 license:public-domain
4480 license:lgpl2.1+))))
4482 (define-public openspecfun
4484 (name "openspecfun")
4490 (url "https://github.com/JuliaLang/openspecfun")
4491 (commit (string-append "v" version))))
4492 (file-name (git-file-name name version))
4494 (base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh"))))
4495 (build-system gnu-build-system)
4497 '(#:tests? #f ; no "check" target
4499 (list (string-append "prefix=" (assoc-ref %outputs "out")))
4501 (modify-phases %standard-phases
4502 (delete 'configure)))) ; no configure script
4504 `(("fortran" ,gfortran)))
4505 (home-page "https://github.com/JuliaLang/openspecfun")
4506 (synopsis "Collection of special mathematical functions")
4508 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
4509 portable package for Bessel Functions of a Complex Argument and Nonnegative
4510 Order; it contains subroutines for computing Bessel functions and Airy
4511 functions. Faddeeva allows computing the various error functions of arbitrary
4512 complex arguments (Faddeeva function, error function, complementary error
4513 function, scaled complementary error function, imaginary error function, and
4514 Dawson function); given these, one can also easily compute Voigt functions,
4515 Fresnel integrals, and similar related functions as well.")
4516 ;; Faddeeva is released under the Expat license; AMOS is included as
4517 ;; public domain software.
4518 (license (list license:expat license:public-domain))))
4520 (define-public suitesparse
4522 (name "suitesparse")
4528 (url "https://github.com/DrTimothyAldenDavis/SuiteSparse")
4529 (commit (string-append "v" version))))
4530 (file-name (git-file-name name version))
4533 "19gx5wlgqnqpgz6mvam9lalyzpbfwgqhppps8z3np9sh0mgaiyw9"))
4534 (patches (search-patches "suitesparse-mongoose-cmake.patch"))
4535 (modules '((guix build utils)))
4537 ;; Remove bundled metis source
4539 (delete-file-recursively "metis-5.1.0")
4541 (build-system gnu-build-system)
4543 `(#:tests? #f ;no "check" target
4545 (list (string-append "CC=" ,(cc-for-target))
4547 "MY_METIS_LIB=-lmetis"
4549 ;; The default is to link against netlib lapack. Use OpenBLAS
4551 "BLAS=-lopenblas" "LAPACK=-lopenblas"
4553 ;; Flags for cmake (required to build GraphBLAS and Mongoose)
4554 (string-append "CMAKE_OPTIONS=-DCMAKE_INSTALL_PREFIX="
4555 (assoc-ref %outputs "out")
4556 " -DCMAKE_VERBOSE_MAKEFILE=ON"
4557 " -DCMAKE_C_FLAGS_RELEASE=\"$(CFLAGS) $(CPPFLAGS)\""
4558 " -DCMAKE_CXX_FLAGS_RELEASE=\"$(CXXFLAGS) $(CPPFLAGS)\""
4559 " -DCMAKE_SKIP_RPATH=TRUE"
4560 " -DCMAKE_BUILD_TYPE=Release"
4561 " -DCMAKE_INSTALL_LIBDIR=lib")
4562 (string-append "INSTALL_LIB="
4563 (assoc-ref %outputs "out") "/lib")
4564 (string-append "INSTALL_INCLUDE="
4565 (assoc-ref %outputs "out") "/include")
4568 (modify-phases %standard-phases
4569 (delete 'configure)))) ;no configure script
4572 ("openblas" ,openblas)
4577 `(("cmake" ,cmake-minimal)
4579 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
4580 (synopsis "Suite of sparse matrix software")
4582 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
4583 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
4584 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
4585 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
4586 CXSparse, a concise sparse Cholesky factorization package; and many other
4589 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
4591 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
4592 (license (list license:gpl2+ license:lgpl2.1+))))
4594 (define-public atlas
4600 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
4601 version "/atlas" version ".tar.bz2"))
4602 (patches (search-patches "atlas-gfortran-compat.patch"))
4605 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
4606 (build-system gnu-build-system)
4607 (home-page "http://math-atlas.sourceforge.net/")
4608 (inputs `(("gfortran" ,gfortran)
4609 ("lapack-tar" ,(package-source lapack))))
4610 (outputs '("out" "doc"))
4611 ;; For the moment we drop support for MIPS at it fails to compile. See
4612 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
4613 (supported-systems (delete "mips64el-linux" %supported-systems))
4615 `(#:parallel-build? #f
4616 #:parallel-tests? #f
4618 ;; ATLAS tunes itself for the machine it is built on, as explained at
4619 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
4620 ;; For this reason, we want users to build it locally instead of using
4624 #:modules ((srfi srfi-26)
4625 (guix build gnu-build-system)
4628 `(;; Generate position independent code suitable for dynamic libraries
4629 ;; and use WALL timer to get more accurate timing.
4630 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
4633 ,,(if (string-match "64" (%current-system))
4636 ;; Disable parallel build as it gives errors: atlas_pthread.h is
4637 ;; needed to compile C files before it is generated.
4638 "-Ss" "pmake" "make -j 1"
4639 ;; Probe is failing for MIPS. We therefore define the system
4640 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
4641 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
4642 ,,@(if (string-prefix? "mips" (%current-system))
4643 (list "-A" "49" "-V" "1")
4645 ;; Generate shared libraries.
4647 ;; Build a full LAPACK library.
4648 ,(string-append "--with-netlib-lapack-tarfile="
4649 (assoc-ref %build-inputs "lapack-tar")))
4651 (modify-phases %standard-phases
4652 (add-after 'install 'install-doc
4653 (lambda* (#:key outputs inputs #:allow-other-keys)
4654 (let ((doc (string-append (assoc-ref outputs "doc")
4655 "/share/doc/atlas")))
4657 (for-each (cut install-file <> doc)
4658 (find-files "../ATLAS/doc" ".*"))
4660 (add-after 'check 'check-pt
4661 (lambda _ (invoke "make" "ptcheck")))
4662 ;; Fix files required to run configure.
4663 (add-before 'configure 'fix-/bin/sh
4665 ;; Use `sh', not `/bin/sh'.
4666 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
4670 ;; Fix /bin/sh in generated make files.
4671 (add-after 'configure 'fix-/bin/sh-in-generated-files
4673 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
4677 ;; ATLAS configure program does not accepts the default flags
4678 ;; passed by the 'gnu-build-system'.
4680 (lambda* (#:key native-inputs inputs outputs
4681 (configure-flags '())
4682 #:allow-other-keys #:rest args)
4683 (let* ((prefix (assoc-ref outputs "out"))
4684 (bash (or (and=> (assoc-ref
4685 (or native-inputs inputs) "bash")
4686 (cut string-append <> "/bin/bash"))
4688 (flags `(,(string-append "--prefix=" prefix)
4690 (abs-srcdir (getcwd))
4691 (srcdir (string-append "../" (basename abs-srcdir))))
4692 (format #t "source directory: ~s (relative from build: ~s)~%"
4696 (format #t "build directory: ~s~%" (getcwd))
4697 (format #t "configure flags: ~s~%" flags)
4699 (string-append srcdir "/configure")
4701 (synopsis "Automatically Tuned Linear Algebra Software")
4703 "ATLAS is an automatically tuned linear algebra software library
4704 providing C and Fortran77 interfaces to a portably efficient BLAS
4705 implementation, as well as a few routines from LAPACK.
4707 Optimization occurs at build time. For this reason, the library is built on
4708 the machine where it is installed, without resorting to pre-built substitutes.
4710 Before building the library, CPU throttling should be disabled. This can be
4711 done in the BIOS, or, on GNU/Linux, with the following command:
4714 # cpupower --governor performance
4717 Failure to do so will result in a library with poor performance.")
4718 ;; The test suite is notoriously lengthy and routinely exceeds the default
4719 ;; timeout of 21600 seconds on the not unbeefy berlin build nodes.
4720 (properties '((timeout . 86400))) ; 1 day
4721 (license license:bsd-3)))
4731 (url "https://github.com/recp/cglm")
4732 (commit (string-append "v" version))))
4733 (file-name (git-file-name name version))
4735 (base32 "1lcfl9ph4bnl3hckpx4hzwh8r4llnw94ik75igc5qy38wk468gmk"))))
4736 (build-system cmake-build-system)
4739 (list "-DCGLM_USE_TEST=ON")))
4740 (home-page "https://github.com/recp/cglm")
4741 (synopsis "Mathematics C library for graphics programming")
4743 "@acronym{CGLM, C OpenGL Mathematics} is an optimised 3D maths library
4744 for graphics software based on the @acronym{GLSL, OpenGL Shading Language}
4747 It's similar to the original C++ GLM library but written in C99 and compatible
4749 (license license:expat)))
4758 (uri (string-append "https://github.com/g-truc/glm/releases/download/"
4759 version "/glm-" version ".zip"))
4761 (base32 "0k6yk9v46h690rshdx49x98y5qspkzibld1wb51jwcm35vba7qip"))))
4762 (build-system cmake-build-system)
4764 `(#:phases (modify-phases %standard-phases
4766 (lambda* (#:key outputs #:allow-other-keys)
4767 ;; Since version 0.9.9.6, 'make install' is not supported
4768 ;; and we have to do it "manually". Upstream discussion:
4769 ;; <https://github.com/g-truc/glm/pull/968>.
4770 (let* ((source (string-append "../glm"))
4771 (out (assoc-ref outputs "out"))
4772 (inc (string-append out "/include"))
4773 (lib (string-append out "/lib"))
4774 (pkgconfig (string-append lib "/pkgconfig")))
4775 (with-directory-excursion source
4778 (copy-recursively "glm" (string-append inc "/glm"))
4779 (copy-recursively "cmake" (string-append lib "/cmake"))
4780 (call-with-output-file (string-append pkgconfig "/glm.pc")
4784 includedir=${prefix}/include
4787 Description: OpenGL Mathematics
4789 Cflags: -I${includedir}~%" out ,(version-prefix version 3)))))
4792 `(("unzip" ,unzip)))
4793 (home-page "https://glm.g-truc.net/")
4794 (synopsis "OpenGL Mathematics library")
4795 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
4796 library for graphics software based on the OpenGL Shading Language (GLSL)
4798 (license license:expat)))
4800 (define-public lpsolve
4807 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
4808 "/lp_solve_" version "_source.tar.gz"))
4811 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
4812 (modules '((guix build utils)))
4815 (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
4817 ;; Pretend to be on a 64 bit platform to obtain a common directory
4818 ;; name for the build results on all architectures; nothing else
4819 ;; seems to depend on it.
4820 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
4822 ;; The check for 'isnan' as it is written fails with
4823 ;; "non-floating-point argument in call to function
4824 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
4825 ;; definition, which in turn leads to bad things. Fix the feature
4827 (("isnan\\(0\\)") "isnan(0.)"))
4829 (build-system gnu-build-system)
4831 `(#:tests? #f ; no check target
4833 (modify-phases %standard-phases
4834 (delete 'configure) ; no configure script
4837 (with-directory-excursion "lpsolve55"
4838 (invoke "bash" "ccc"))
4839 (with-directory-excursion "lp_solve"
4840 (invoke "bash" "ccc"))
4843 (lambda* (#:key outputs #:allow-other-keys)
4844 (let* ((out (assoc-ref outputs "out"))
4845 (bin (string-append out "/bin"))
4846 (lib (string-append out "/lib"))
4847 ;; This is where LibreOffice expects to find the header
4848 ;; files, and where they are installed by Debian.
4849 (include (string-append out "/include/lpsolve")))
4850 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
4851 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
4852 (install-file "lp_solve/bin/ux64/lp_solve" bin)
4854 ;; Install a subset of the header files as on Debian
4855 ;; (plus lp_bit.h, which matches the regular expression).
4856 (for-each (lambda (name)
4857 (install-file name include))
4858 (find-files "." "lp_[HMSa-z].*\\.h$"))
4859 (with-directory-excursion "shared"
4860 (for-each (lambda (name)
4861 (install-file name include))
4862 (find-files "." "\\.h$")))
4864 (home-page "http://lpsolve.sourceforge.net/")
4865 (synopsis "Mixed integer linear programming (MILP) solver")
4867 "lp_solve is a mixed integer linear programming solver based on the
4868 revised simplex and the branch-and-bound methods.")
4869 (license license:lgpl2.1+)))
4871 ;; Private Trilinos package for dealii-openmpi (similar to
4872 ;; trilinos-serial-xyce and trilinos-parallel-xyce).
4873 ;; This version is the latest known to be compatible with deal.II [1].
4874 ;; Since the latest version of Trilinos is not necessarily supported by
4875 ;; deal.II, it may be worth keeping this package even if and when Trilinos
4876 ;; gets packaged separately for Guix (unless various versions of Trilinos are
4879 ;; An insightful source of information for building Trilinos for deal.II lies
4880 ;; in the Trilinos package for candi [2], which is a source-based installer
4881 ;; for deal.II and its dependencies.
4883 ;; [1]: https://www.dealii.org/current/external-libs/trilinos.html
4884 ;; [2]: https://github.com/dealii/candi/blob/master/deal.II-toolchain/packages/trilinos.package
4885 (define trilinos-for-dealii-openmpi
4887 (name "trilinos-for-dealii-openmpi")
4893 (url "https://github.com/trilinos/Trilinos/")
4895 (string-append "trilinos-release-"
4896 (string-replace-substring version "." "-")))))
4897 (file-name (git-file-name "trilinos" version))
4899 (base32 "0fnwlhzsh85qj38cq3igbs8nm1b2jdgr2z734sapmyyzsy21mkgp"))))
4900 (build-system cmake-build-system)
4902 `(("gfortran" ,gfortran)
4903 ;; Trilinos's repository contains several C-shell scripts, but adding
4904 ;; tcsh to the native inputs does not result in the check phase running
4905 ;; any more tests than without it (nor is tcsh required to build
4907 ;; It seems that Trilinos has replaced its use of C-shell test scripts
4908 ;; with CMake's testing facilities.
4910 ;; packages/zoltan/doc/Zoltan_html/dev_html/dev_test_script.html [1]
4911 ;; states that Zoltan's C-shell test script
4912 ;; packages/zoltan/test/test_zoltan has been obsoleted by the tests now
4913 ;; performed through CMake.
4915 ;; Perl is required for some Zoltan tests and Python 2 for one ML test.
4917 ;; [1]: https://cs.sandia.gov/zoltan/dev_html/dev_test_script.html
4919 ("python" ,python-2)))
4921 `(("blas" ,openblas)
4923 ("mumps" ,mumps-openmpi)
4924 ("scalapack" ,scalapack)))
4926 `(("mpi" ,openmpi)))
4928 `(#:build-type "Release"
4930 `("-DBUILD_SHARED_LIBS=ON"
4931 ;; Obtain the equivalent of RelWithDebInfo but with -O3 (the Release
4932 ;; default) rather than -O2 (the RelWithDebInfo default), to conform
4933 ;; to candi's trilinos.package's compilation flags, which are -g -O3.
4934 "-DCMAKE_C_FLAGS=-g"
4935 "-DCMAKE_CXX_FLAGS=-g"
4936 "-DCMAKE_Fortran_FLAGS=-g"
4938 ;; Trilinos libraries that deal.II can interface with.
4939 "-DTrilinos_ENABLE_Amesos=ON"
4940 "-DTrilinos_ENABLE_AztecOO=ON"
4941 "-DTrilinos_ENABLE_Epetra=ON"
4942 "-DTrilinos_ENABLE_EpetraExt=ON"
4943 "-DTrilinos_ENABLE_Ifpack=ON"
4944 "-DTrilinos_ENABLE_ML=ON"
4945 "-DTrilinos_ENABLE_MueLu=ON"
4946 "-DTrilinos_ENABLE_ROL=ON"
4947 ;; Optional; required for deal.II's GridIn::read_exodusii, but
4948 ;; depends on netcdf.
4949 ;; Enable if and when someone needs it.
4950 ;;"-DTrilinos_ENABLE_SEACAS=ON"
4951 "-DTrilinos_ENABLE_Sacado=ON"
4952 "-DTrilinos_ENABLE_Teuchos=ON"
4953 "-DTrilinos_ENABLE_Tpetra=ON"
4954 "-DTrilinos_ENABLE_Zoltan=ON"
4956 ;; Third-party libraries (TPLs) that Trilinos can interface with.
4957 "-DBLAS_LIBRARY_NAMES=openblas"
4958 "-DTPL_ENABLE_MPI=ON"
4959 "-DTPL_ENABLE_MUMPS=ON"
4960 "-DTPL_ENABLE_SCALAPACK=ON"
4962 ;; Enable the tests but not the examples (which are enabled by
4963 ;; default when enabling tests).
4964 ;; Although some examples are run as tests, they are otherwise
4965 ;; unnecessary since this is a private package meant for
4967 ;; Besides, some MueLu and ROL examples require a lot of memory to
4970 ;; (For future reference, note that some ROL and SEACAS examples
4971 ;; require removing gfortran from CPLUS_INCLUDE_PATH as in the
4972 ;; dune-istl, dune-localfunctions and dune-alugrid packages.)
4973 "-DTrilinos_ENABLE_TESTS=ON"
4974 "-DTrilinos_ENABLE_EXAMPLES=OFF"
4975 ;; MueLu tests require considerably more time and memory to compile
4976 ;; than the rest of the tests.
4977 "-DMueLu_ENABLE_TESTS=OFF"
4979 ;; The following options were gleaned from candi's trilinos.package.
4980 ;; (We do not enable the complex instantiations, which are anyway
4981 ;; provided only as an option in trilinos.package, because they are
4982 ;; costly in compilation time and memory usage, and disk space [1].)
4984 ;; [1]: https://www.docs.trilinos.org/files/TrilinosBuildReference.html#enabling-float-and-complex-scalar-types
4985 "-DTrilinos_ENABLE_Ifpack2=OFF"
4986 "-DTeuchos_ENABLE_FLOAT=ON"
4987 "-DTpetra_INST_INT_LONG=ON"
4988 "-DTPL_ENABLE_Boost=OFF")
4990 (modify-phases %standard-phases
4991 (add-after 'configure 'fix-kokkos-config
4993 ;; GNU Make 4.3 accidentally leaves the backslash preceding the
4994 ;; number sign in strings containing a literal backslash–number
4995 ;; sign (\#) [1, 2].
4996 ;; This is still an issue in Trilinos 13.0.1, but should be fixed
4997 ;; in the following version.
4998 ;; (The latest versions of Kokkos incorporate the fix [2].)
5000 ;; [1]: https://github.com/GEOSX/thirdPartyLibs/issues/136
5001 ;; [2]: https://github.com/kokkos/kokkos/blob/3.4.00/Makefile.kokkos#L441
5002 (substitute* "KokkosCore_config.h"
5005 (add-before 'check 'mpi-setup
5007 (home-page "https://trilinos.github.io/")
5008 (synopsis "Algorithms for engineering and scientific problems")
5010 "The Trilinos Project is an effort to develop algorithms and enabling
5011 technologies within an object-oriented software framework for the solution of
5012 large-scale, complex multi-physics engineering and scientific problems.
5013 A unique design feature of Trilinos is its focus on packages.")
5014 ;; The packages are variously licensed under more than just BSD-3 and
5015 ;; LGPL-2.1+, but all the licenses are either BSD- or LGPL-compatible.
5016 ;; See https://trilinos.github.io/license.html.
5017 (license (list license:bsd-3 license:lgpl2.1+))))
5019 (define-public dealii
5026 (uri (string-append "https://github.com/dealii/dealii/releases/"
5027 "download/v" version "/dealii-" version ".tar.gz"))
5029 (base32 "1f0sqvlxvl0myqcn0q6xrn1vnp5pgx143lai4a4jkh1dmdv4cbx6"))
5030 (modules '((guix build utils)))
5033 ;; Remove bundled boost, muparser, TBB and UMFPACK.
5034 (delete-file-recursively "bundled")
5036 (build-system cmake-build-system)
5037 (outputs '("out" "doc"))
5039 ;; Required to build the documentation.
5041 ("doxygen" ,doxygen)
5044 `(("arpack" ,arpack-ng)
5046 ("gfortran" ,gfortran)
5048 ("muparser" ,muparser)
5051 ;; Some scripts are installed into share/deal.II/scripts that require
5052 ;; perl and python, but they are not executable (and some are missing the
5053 ;; shebang line) and therefore must be explicitly passed to the
5055 ;; Anyway, they are meant to be used at build time, so rather than adding
5056 ;; the interpreters here, any package depending on them should just add
5057 ;; the requisite interpreter to its native inputs.
5060 ("suitesparse" ,suitesparse) ; For UMFPACK.
5063 `(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease.
5064 ;; The tests take too long and must be explicitly enabled with "make
5066 ;; See https://www.dealii.org/developer/developers/testsuite.html.
5067 ;; (They can also be run for an already installed deal.II.)
5070 (let ((doc (string-append (assoc-ref %outputs "doc")
5071 "/share/doc/" ,name "-" ,version)))
5072 `("-DDEAL_II_COMPONENT_DOCUMENTATION=ON"
5073 ,(string-append "-DDEAL_II_DOCREADME_RELDIR=" doc)
5074 ,(string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html")
5075 ;; Don't compile the examples because the source and CMakeLists.txt
5076 ;; are installed anyway, allowing users to do so for themselves.
5077 "-DDEAL_II_COMPILE_EXAMPLES=OFF"
5078 ,(string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc "/examples")))
5080 (modify-phases %standard-phases
5081 (add-after 'install 'remove-build-logs
5082 ;; These build logs leak the name of the build directory by storing
5083 ;; the values of CMAKE_SOURCE_DIR and CMAKE_BINARY_DIR.
5084 (lambda* (#:key outputs #:allow-other-keys)
5085 (let ((doc (string-append (assoc-ref outputs "doc")
5086 "/share/doc/" ,name "-" ,version)))
5087 (for-each delete-file (map (lambda (f) (string-append doc "/" f))
5088 '("detailed.log" "summary.log"))))
5090 (home-page "https://www.dealii.org/")
5091 (synopsis "Finite element library")
5093 "Deal.II is a C++ program library targeted at the computational solution
5094 of partial differential equations using adaptive finite elements. The main
5095 aim of deal.II is to enable rapid development of modern finite element codes,
5096 using among other aspects adaptive meshes and a wide array of tools often used
5097 in finite element programs.")
5098 (license license:lgpl2.1+)))
5100 (define-public dealii-openmpi
5101 (package/inherit dealii
5102 (name "dealii-openmpi")
5104 `(("arpack" ,arpack-ng-openmpi)
5106 ("scalapack" ,scalapack)
5107 ,@(alist-delete "arpack" (package-inputs dealii))))
5109 `(("hdf5" ,hdf5-parallel-openmpi)
5111 ("p4est" ,p4est-openmpi)
5112 ("petsc" ,petsc-openmpi)
5113 ("slepc" ,slepc-openmpi)
5114 ("trilinos" ,trilinos-for-dealii-openmpi)
5115 ,@(alist-delete "hdf5" (package-propagated-inputs dealii))))
5117 (substitute-keyword-arguments (package-arguments dealii)
5118 ((#:configure-flags flags)
5119 `(cons "-DDEAL_II_WITH_MPI=ON" ,flags))))
5120 (synopsis "Finite element library (with MPI support)")))
5122 (define-public flann
5126 (home-page "https://github.com/mariusmuja/flann/")
5130 (uri (git-reference (url home-page) (commit version)))
5131 (file-name (git-file-name name version))
5134 "0p56fl2yx1r86ds1mgjq40926jdcgq3hka7p3l1hv2acv9jxp15x"))
5135 (patches (search-patches "flann-cmake-3.11.patch"))))
5136 (build-system cmake-build-system)
5139 `(("unzip" ,unzip)))
5142 ;; FIXME: 'mkoctfile' fails with a linker error:
5143 ;; ld: cannot find -loctinterp
5144 ;; ld: cannot find -loctave
5145 ;; Disable it for now.
5146 ;;("octave" ,octave-cli)
5147 ("python" ,python-2) ; print syntax
5148 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
5151 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
5152 ;; taken 46 MiB unstripped, and 6 MiB stripped.
5153 #:strip-directories '("lib" "lib64" "libexec"
5154 "bin" "sbin" "share/flann/octave")
5156 ;; Save 12 MiB by not installing .a files. Passing
5157 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
5158 #:phases (modify-phases %standard-phases
5159 (add-after 'install 'remove-static-libraries
5160 (lambda* (#:key outputs #:allow-other-keys)
5161 (let* ((out (assoc-ref outputs "out"))
5162 (lib (string-append out "/lib")))
5163 (for-each delete-file
5164 (find-files lib "\\.a$"))
5167 #:tests? #f)) ; The test data are downloaded from the Internet.
5168 (synopsis "Library for approximate nearest neighbors computation")
5169 (description "FLANN is a library for performing fast approximate
5170 nearest neighbor searches in high dimensional spaces. It implements a
5171 collection of algorithms and a system for automatically choosing the best
5172 algorithm and optimum parameters depending on the dataset.
5174 FLANN is written in C++ and contains bindings for C, Octave and Python.")
5175 (license (license:non-copyleft "file://COPYING"
5176 "See COPYING in the distribution."))))
5178 (define-public wcalc
5185 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
5186 "wcalc-" version ".tar.bz2"))
5189 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
5190 (build-system gnu-build-system)
5193 ("readline" ,readline)))
5194 (home-page "http://w-calc.sourceforge.net/index.php")
5195 (synopsis "Flexible command-line scientific calculator")
5196 (description "Wcalc is a very capable calculator. It has standard functions
5197 (sin, asin, and sinh for example, in either radians or degrees), many
5198 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
5199 variables, a command history, hex/octal/binary input and output, unit
5200 conversions, embedded comments, and an expandable expression entry field. It
5201 evaluates expressions using the standard order of operations.")
5202 (license license:gpl2+)))
5211 (url "https://github.com/xaos-project/XaoS")
5212 (commit (string-append "release-" version))))
5213 (file-name (git-file-name name version))
5216 "0maw5am6rrkyjrprfg113zjq37mqj0iaznkg4h2927ff7wrprc94"))))
5217 (build-system gnu-build-system)
5218 (native-inputs `(("gettext" ,gettext-minimal)
5219 ("qtbase" ,qtbase-5)
5220 ("qttools" ,qttools)))
5221 (inputs `(("libx11" ,libx11)
5225 ;; The upstream project file ("XaoS.pro") and the Makefile it generates are
5226 ;; not enough for this package to install properly. These phases fix that.
5228 `(#:tests? #f ;no "check" target
5230 (modify-phases %standard-phases
5231 (add-before 'configure 'make-qt-deterministic
5233 ;; Make Qt deterministic.
5234 (setenv "QT_RCC_SOURCE_DATE_OVERRIDE" "1")
5237 (lambda* (#:key outputs #:allow-other-keys)
5238 (let ((out (assoc-ref outputs "out")))
5239 (substitute* "XaoS.pro"
5240 ;; The DESTDIR is originally set to install the xaos binary to
5241 ;; the "bin" folder inside the build directory. Setting make
5242 ;; flags doesn't seem to change this.
5244 (string-append "DESTDIR=" out "/bin"))
5245 ;; Set the correct path to the lrelease binary.
5246 (("lrelease-qt5") "lrelease"))
5247 (substitute* "src/include/config.h"
5248 (("/usr/share/XaoS")
5249 (string-append out "/share/XaoS")))
5251 (add-after 'install 'install-data
5252 (lambda* (#:key outputs #:allow-other-keys)
5253 (let* ((out (assoc-ref outputs "out"))
5254 (share (string-append out "/share")))
5258 (copy-recursively folder
5259 (string-append share "/XaoS/" folder)))
5260 '("catalogs" "examples" "tutorial"))
5261 (install-file "xdg/xaos.png"
5262 (string-append share "/pixmaps"))
5263 (install-file "xdg/xaos.desktop"
5264 (string-append share "/applications")))
5266 (synopsis "Real-time fractal zoomer")
5267 (description "GNU XaoS is a graphical program that generates fractal
5268 patterns and allows you to zoom in and out of them infinitely in a fluid,
5269 continuous manner. It also includes tutorials that help to explain how fractals
5270 are built. It can generate many different fractal types such as the Mandelbrot
5272 (home-page "https://xaos-project.github.io/")
5273 (license license:gpl2+)))
5275 (define-public hypre
5283 (url "https://github.com/hypre-space/hypre")
5284 (commit (string-append "v" version))))
5285 (file-name (git-file-name name version))
5287 (base32 "14iqjwg5sv1qjn7c2cfv0xxmn9rwamjrhh9hgs8fjbywcbvrkjdi"))))
5288 (build-system gnu-build-system)
5289 (outputs '("out" ;5.3 MiB of headers and libraries
5290 "doc")) ;12 MiB of documentation
5293 ("doxygen" ,doxygen)
5295 ("python-breathe" ,python-breathe)
5296 ("python-sphinx" ,python-sphinx)
5297 ("texlive" ,(texlive-updmap.cfg (list texlive-adjustbox
5309 texlive-generic-listofitems
5310 texlive-generic-ulem
5311 texlive-latex-capt-of
5313 texlive-latex-colortbl
5315 texlive-latex-fancyhdr
5316 texlive-latex-fancyvrb
5318 texlive-latex-fncychap
5319 texlive-latex-framed
5320 texlive-latex-geometry
5321 texlive-latex-hanging
5323 texlive-latex-multirow
5324 texlive-latex-natbib
5325 texlive-latex-needspace
5326 texlive-latex-newunicodechar
5327 texlive-latex-parskip
5328 texlive-latex-stackengine
5329 texlive-latex-tabulary
5330 texlive-latex-titlesec
5331 texlive-latex-tocloft
5332 texlive-latex-upquote
5333 texlive-latex-varwidth
5335 texlive-latex-wrapfig)))))
5337 `(("blas" ,openblas)
5338 ("lapack" ,lapack)))
5340 `(#:modules ((srfi srfi-1)
5341 ,@%gnu-build-system-modules)
5342 #:configure-flags '("--enable-shared"
5350 (modify-phases %standard-phases
5351 (add-before 'configure 'chdir-src
5352 (lambda _ (chdir "src")))
5354 (lambda* (#:key build target configure-flags
5355 #:allow-other-keys #:rest args)
5356 (let* ((configure (assoc-ref %standard-phases 'configure)))
5359 (list #:configure-flags
5360 (cons (string-append
5361 "--host=" (or target build))
5362 configure-flags)))))))
5363 (add-after 'build 'build-docs
5365 (invoke "make" "-C" "docs")))
5368 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
5369 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
5370 (invoke "make" "check" "CHECKRUN=")
5371 (for-each (lambda (filename)
5372 (let ((size (stat:size (stat filename))))
5373 (when (positive? size)
5374 (error (format #f "~a size ~d; error indication~%"
5376 (find-files "test" ".*\\.err$"))))
5377 (add-after 'install 'install-docs
5378 (lambda* (#:key outputs #:allow-other-keys)
5379 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
5380 (let* ((doc (assoc-ref outputs "doc"))
5381 (docdir (string-append doc "/share/doc/hypre-" ,version)))
5382 (with-directory-excursion "docs"
5383 (for-each (lambda (base)
5384 (install-file (string-append base ".pdf") docdir)
5385 (copy-recursively (string-append base "-html")
5386 (string-append docdir "/" base)))
5387 '("usr-manual" "ref-manual")))))))))
5388 (home-page "https://computing.llnl.gov/projects\
5389 /hypre-scalable-linear-solvers-multigrid-methods")
5390 (synopsis "Library of solvers and preconditioners for linear equations")
5392 "HYPRE is a software library of high performance preconditioners and
5393 solvers for the solution of large, sparse linear systems of equations. It
5394 features multigrid solvers for both structured and unstructured grid
5396 (license license:lgpl2.1)))
5398 (define-public hypre-openmpi
5399 (package (inherit hypre)
5400 (name "hypre-openmpi")
5403 ,@(package-inputs hypre)))
5405 (substitute-keyword-arguments (package-arguments hypre)
5406 ((#:configure-flags flags)
5408 ,@(delete "--without-MPI" ,flags)))
5410 `(modify-phases ,phases
5411 (add-before 'check 'mpi-setup
5412 ,%openmpi-setup)))))
5413 (synopsis "Parallel solvers and preconditioners for linear equations")
5415 "HYPRE is a software library of high performance preconditioners and
5416 solvers for the solution of large, sparse linear systems of equations on
5417 parallel computers. It features parallel multigrid solvers for both
5418 structured and unstructured grid problems.")))
5420 (define-public matio
5427 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
5428 "matio-" version ".tar.gz"))
5431 "0vr8c1mz1k6mz0sgh6n3scl5c3a71iqmy5fnydrgq504icj4vym4"))))
5432 (build-system gnu-build-system)
5435 ("hdf5" ,hdf5-1.8)))
5436 (home-page "http://matio.sourceforge.net/")
5437 (synopsis "Library for reading and writing MAT files")
5438 (description "Matio is a library for reading and writing MAT files. It
5439 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
5440 (license license:bsd-2)))
5447 (origin (method url-fetch)
5448 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
5449 "download/" version "/Vc-" version ".tar.gz"))
5452 "0lirdqzcxys9walz04bllsphydynk7973aimd5k1h1qbwi8z3lsh"))))
5453 (build-system cmake-build-system)
5456 '("-DBUILD_TESTING=ON"
5457 ;; By default, Vc will optimize for the CPU of the build machine.
5458 ;; Setting this to "none" makes it create portable binaries. See
5459 ;; "cmake/OptimizeForArchitecture.cmake".
5460 "-DTARGET_ARCHITECTURE=none")
5461 #:phases (modify-phases %standard-phases
5462 (add-after 'unpack 'copy-testdata
5463 (lambda* (#:key inputs native-inputs #:allow-other-keys)
5464 (let ((testdata (assoc-ref (or native-inputs inputs)
5466 (copy-recursively testdata "tests/testdata")
5469 `(("virtest" ,virtest)
5471 ;; This is a submodule in the git project, but not part of the
5472 ;; released sources. See the git branch for the commit to take.
5473 ("testdata" ,(let ((commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3"))
5477 (url "https://github.com/VcDevel/vc-testdata")
5478 (commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3")))
5479 (file-name (git-file-name "vc-testdata"
5480 (string-take commit 7)))
5483 "1hkhqib03qlcq412ym2dciynfxcdr2ygqhnplz4l1vissr1wnqn2")))))))
5484 (synopsis "SIMD vector classes for C++")
5485 (description "Vc provides portable, zero-overhead C++ types for explicitly
5486 data-parallel programming. It is a library designed to ease explicit
5487 vectorization of C++ code. Its types enable explicitly stating data-parallel
5488 operations on multiple values. The parallelism is therefore added via the type
5489 system. Vc has an intuitive API and provides portability between different
5490 compilers and compiler versions as well as portability between different vector
5491 instruction sets. Thus, an application written with Vc can be compiled for:
5494 @item SSE2 up to SSE4.2 or SSE4a
5497 @item NEON (in development)
5498 @item NVIDIA GPUs / CUDA (in development)
5500 (home-page "https://github.com/VcDevel/Vc")
5501 ;; "No support_???.cpp file exists for this architecture."
5502 (supported-systems '("x86_64-linux" "i686-linux"))
5503 (license license:bsd-3)))
5505 (define-public reducelcs
5506 ;; This is the last commit which is available upstream, no
5507 ;; release happened since 2010.
5508 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
5512 (version (string-append "1.0-" revision "." (string-take commit 7)))
5517 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
5519 (file-name (string-append name "-" version "-checkout"))
5522 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
5523 (build-system gnu-build-system)
5525 `(("openlibm" ,openlibm)))
5527 `(#:tests? #f ; no tests
5529 (modify-phases %standard-phases
5530 (delete 'configure) ; No configure script exists.
5531 (replace 'install ; No install phase exists.
5532 (lambda* (#:key outputs #:allow-other-keys)
5533 (let* ((out (assoc-ref outputs "out"))
5534 (bin (string-append out "/bin")))
5535 (install-file "Approximation" bin)
5536 (install-file "CollectResults" bin)
5537 (install-file "GenerateInstances" bin)
5539 (synopsis "Approximate Longest Commons Subsequence computation tool")
5541 "@code{reduceLCS} is an implementation of the Reduce-Expand
5542 algorithm for LCS. It is a fast program to compute the approximate
5543 Longest Commons Subsequence of a set of strings.")
5544 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
5545 (license license:gpl3+))))
5547 (define-public jacal
5554 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
5557 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
5558 (patches (search-patches "jacal-fix-texinfo.patch"))))
5559 (build-system gnu-build-system)
5562 (modify-phases %standard-phases
5563 (add-before 'build 'pre-build
5564 ;; Don't use upstream's script - it really doesn't fit into
5565 ;; Guix's functional paradigm.
5566 (lambda* (#:key inputs outputs #:allow-other-keys)
5567 (substitute* "Makefile"
5568 (("^install: install-script") "install: "))))
5569 (add-after 'install 'post-install
5570 ;; Instead, we provide our own simplified script.
5571 (lambda* (#:key inputs outputs #:allow-other-keys)
5572 (let ((wrapper (string-append (assoc-ref outputs "out")
5574 (format (open wrapper (logior O_WRONLY O_CREAT))
5575 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
5576 "-e '(slib:load \"~a/lib/jacal/math\") "
5579 (assoc-ref inputs "scm")
5580 (assoc-ref outputs "out"))
5581 (chmod wrapper #o555))))
5583 (lambda* (#:key outputs #:allow-other-keys)
5584 (invoke "./configure"
5585 (string-append "--prefix="
5586 (assoc-ref outputs "out"))))))))
5587 (inputs `(("scm" ,scm)))
5588 (native-inputs `(("unzip" ,unzip)
5589 ("texinfo" ,texinfo)))
5590 (synopsis "Symbolic mathematics system")
5591 (description "GNU JACAL is an interactive symbolic mathematics program based on
5592 Scheme. It manipulate and simplify a range of mathematical expressions such
5593 as equations, scalars, vectors, and matrices.")
5594 (home-page "https://www.gnu.org/software/jacal/")
5595 (license license:gpl3+)))
5601 (home-page "https://github.com/Z3Prover/z3")
5604 (uri (git-reference (url home-page)
5605 (commit (string-append "z3-" version))))
5606 (file-name (git-file-name name version))
5609 "1hnbzq10d23drd7ksm3c1n2611c3kd0q0yxgz8y78zaafwczvwxx"))))
5610 (build-system gnu-build-system)
5612 `(#:imported-modules ((guix build python-build-system)
5613 ,@%gnu-build-system-modules)
5614 #:modules (((guix build python-build-system) #:select (site-packages))
5615 (guix build gnu-build-system)
5618 (modify-phases %standard-phases
5619 (add-after 'unpack 'enable-bytecode-determinism
5621 (setenv "PYTHONHASHSEED" "0")
5623 (add-after 'unpack 'fix-compatability
5624 ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
5626 (substitute* "src/util/mpz.cpp"
5627 (("#include <immintrin.h>") ""))
5629 (add-before 'configure 'bootstrap
5631 (invoke "python" "scripts/mk_make.py")))
5632 ;; work around gnu-build-system's setting --enable-fast-install
5633 ;; (z3's `configure' is a wrapper around the above python file,
5634 ;; which fails when passed --enable-fast-install)
5636 (lambda* (#:key inputs outputs #:allow-other-keys)
5637 (invoke "./configure"
5639 (string-append "--prefix=" (assoc-ref outputs "out"))
5640 (string-append "--pypkgdir=" (site-packages inputs outputs)))))
5641 (add-after 'configure 'change-directory
5645 (add-before 'check 'make-test-z3
5647 ;; Build the test suite executable.
5648 (invoke "make" "test-z3" "-j"
5649 (number->string (parallel-job-count)))))
5652 ;; Run all the tests that don't require arguments.
5653 (invoke "./test-z3" "/a"))))))
5656 ("python" ,python-wrapper)))
5657 (synopsis "Theorem prover")
5658 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
5659 theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
5660 (license license:expat)))
5665 (version "2018.11.001")
5668 (uri (string-append "http://elpa.mpcdf.mpg.de/html/Releases/"
5669 version "/elpa-" version ".tar.gz"))
5672 "05hv3v5i6xmziaizw350ff72y1c3k662r85fm3xfdrkclj5zw9yc"))))
5673 (build-system gnu-build-system)
5675 `(("fortran" ,gfortran)
5676 ("perl" ,perl))) ;for configure and deps
5678 `(("blas" ,openblas)))
5683 ;; ELPA unfortunately does not support runtime dispatch, so we can
5684 ;; only enable the "generic" kernels. See the "Cross compilation"
5685 ;; section of INSTALL.md.
5687 "--disable-sse" "--disable-sse-assembly" ;Require SSE3
5688 "--disable-avx" "--disable-avx2" "--disable-avx512"
5689 ,(string-append "CFLAGS=-O3 "
5690 "-funsafe-loop-optimizations -funsafe-math-optimizations "
5691 "-ftree-vect-loop-version -ftree-vectorize "
5692 ,(let ((system (or (%current-target-system)
5693 (%current-system))))
5695 ((or (string-prefix? "x86_64" system)
5696 (string-prefix? "i686" system))
5699 #:parallel-tests? #f ;tests are multi-threaded, via BLAS
5701 (modify-phases %standard-phases
5702 (add-before 'configure 'patch-header-generation
5704 (substitute* "configure"
5705 (("^ *make.*top_srcdir=\"\\$srcdir\"" &)
5706 (string-append & " CPP=\"$CPP\"")))
5708 (add-before 'check 'setup-tests
5710 ;; Decrease test time and RAM use by computing fewer eigenvalues.
5711 ;; The flags are (MATRIX-SIZE, EIGENVALUES, BLOCK-SIZE), where
5712 ;; the default is (500, 250, 16) for C tests and (5000, 150, 16)
5713 ;; for Fortran. This also causes several tests to pass that
5714 ;; otherwise would otherwise fail with matrix size 5000; possibly
5715 ;; due to floating point tolerances that are too tight.
5716 (setenv "TEST_FLAGS" "1500 50 16") ;from elpa.spec
5717 (setenv "OMP_NUM_THREADS" (number->string (parallel-job-count)))
5718 (substitute* "Makefile"
5719 ;; Test scripts are generated, patch the shebang
5720 (("#!/bin/bash") (string-append "#!" (which "sh"))))
5722 (home-page "https://elpa.mpcdf.mpg.de")
5723 (synopsis "Eigenvalue solvers for symmetric matrices")
5725 "The ELPA library provides efficient and scalable direct eigensolvers for
5726 symmetric matrices.")
5727 (license license:lgpl3)))
5729 (define-public elpa-openmpi
5730 (package (inherit elpa)
5731 (name "elpa-openmpi")
5734 ("scalapack" ,scalapack)
5735 ,@(package-inputs elpa)))
5737 (substitute-keyword-arguments (package-arguments elpa)
5738 ((#:configure-flags cf '())
5739 `(cons "--with-mpi=yes" (delete "--with-mpi=no" ,cf)))
5740 ((#:phases phases '%standard-phases)
5741 `(modify-phases ,phases
5742 (add-before 'check 'mpi-setup
5744 ;; Tests use 2 mpi tasks by default, use our remaining build
5745 ;; cores as OpenMP threads.
5746 (setenv "OMP_NUM_THREADS" (number->string
5747 (max (quotient (parallel-job-count) 2)
5749 (,%openmpi-setup)))))))
5750 (synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)")))
5752 (define-public elemental
5759 (url "https://github.com/elemental/Elemental")
5760 (commit (string-append "v" version))))
5761 (file-name (git-file-name name version))
5764 "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
5765 (build-system cmake-build-system)
5766 (home-page "https://github.com/elemental/Elemental")
5768 `(("gfortran" ,gfortran)))
5770 `(("blas" ,openblas)
5771 ("gfortran:lib" ,gfortran "lib")
5780 `(#:build-type "Release" ;default RelWithDebInfo not supported
5781 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
5782 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
5783 "-DEL_CACHE_WARNINGS:BOOL=YES"
5784 "-DEL_TESTS:BOOL=YES"
5785 "-DCMAKE_INSTALL_LIBDIR=lib"
5786 "-DGFORTRAN_LIB=gfortran")
5787 #:phases (modify-phases %standard-phases
5788 (add-before 'check 'mpi-setup
5790 (add-before 'check 'setup-tests
5792 ;; Parallelism is done at the MPI layer.
5793 (setenv "OMP_NUM_THREADS" "1")
5795 (add-after 'install 'remove-tests
5796 (lambda* (#:key outputs #:allow-other-keys)
5797 ;; Tests are installed, with no easy configuration
5798 ;; switch to prevent this, so delete them.
5799 (delete-file-recursively
5800 (string-append (assoc-ref outputs "out") "/bin"))
5802 (synopsis "Dense and sparse-direct linear algebra and optimization")
5803 (description "Elemental is a modern C++ library for distributed-memory
5804 dense and sparse-direct linear algebra, conic optimization, and lattice
5806 (license license:bsd-2)))
5808 (define-public mcrl2
5811 (version "202106.0")
5815 "https://www.mcrl2.org/download/release/mcrl2-"
5819 "1xgx3cd57vc7gbjic24j1q2za6j3ybz6nk4afvvpbwsf33xnlf4v"))))
5824 ("qtbase" ,qtbase-5)))
5825 (build-system cmake-build-system)
5826 (synopsis "Toolset for the mCRL2 formal specification language")
5828 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
5829 specification language for describing concurrent discrete event systems. Its
5830 toolset supports analysis and automatic verification, linearisation, simulation,
5831 state-space exploration and generation, and tools to optimise and analyse
5832 specifications. Also, state spaces can be manipulated, visualised and
5834 (home-page "https://mcrl2.org")
5835 (license license:boost1.0)))
5837 (define-public mcrl2-minimal
5840 (name "mcrl2-minimal")
5842 `(("boost" ,boost)))
5844 '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
5846 (define-public tcalc
5853 (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
5857 "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
5858 (build-system gnu-build-system)
5859 (synopsis "The terminal calculator")
5861 "The terminal calculator is a small program to help users of the GNU/Linux
5862 terminal do calculations simply and quickly. The formula to be calculated can
5863 be fed to @command{tcalc} through the command line.")
5864 (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
5865 (license license:gpl3+)))
5867 (define-public tiny-bignum
5868 (let ((commit "1d7a1f9b8e77316187a6b3eae8e68d60a6f9a4d4"))
5870 (name "tiny-bignum")
5871 (version (git-version "0" "0" commit))
5876 (url "https://github.com/kokke/tiny-bignum-c")
5878 (file-name (git-file-name "tiny-bignum" commit))
5880 (base32 "0vj71qlhlaa7d92bfar1kwqv6582dqrby8x3kdw0yzh82k2023g6"))))
5881 (build-system gnu-build-system)
5884 (modify-phases %standard-phases
5886 (add-after 'unpack 'patch-tests
5888 (substitute* "scripts/test_rand.py"
5890 (("\" % (\\w+)" _ symbol) (string-append "\" % int(" symbol ")")))
5893 (lambda* (#:key tests? #:allow-other-keys)
5895 (invoke "make" "test"))
5898 (lambda* (#:key outputs #:allow-other-keys)
5899 (let ((share (string-append (assoc-ref outputs "out") "/share"))
5900 (doc (string-append (assoc-ref outputs "out") "/doc")))
5902 (install-file "bn.c" share)
5903 (install-file "bn.h" share)
5905 (install-file "LICENSE" doc)
5906 (install-file "README.md" doc))
5909 `(("python" ,python-wrapper)))
5910 (home-page "https://github.com/kokke/tiny-bignum-c")
5911 (synopsis "Small portable multiple-precision unsigned integer arithmetic in C")
5913 "This library provides portable Arbitrary-precision unsigned integer
5914 arithmetic in C, for calculating with large numbers. Basic arithmetic (+, -,
5915 *, /, %) and bitwise operations (&, |, ^. <<, >>) plus increments, decrements
5916 and comparisons are supported.")
5917 (license license:unlicense))))
5919 (define-public sundials
5926 (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
5927 "sundials-" version ".tar.gz"))
5930 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
5931 (build-system cmake-build-system)
5933 `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
5935 `(("fortran" ,gfortran) ;for fcmix
5937 ("suitesparse" ,suitesparse))) ;TODO: Add hypre
5939 `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
5940 "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
5941 "-DEXAMPLES_ENABLE_F77:BOOL=ON"
5942 "-DEXAMPLES_ENABLE_F90:BOOL=ON"
5943 "-DEXAMPLES_INSTALL:BOOL=OFF"
5945 "-DFCMIX_ENABLE:BOOL=ON"
5947 "-DKLU_ENABLE:BOOL=ON"
5948 ,(string-append "-DKLU_INCLUDE_DIR="
5949 (assoc-ref %build-inputs "suitesparse")
5951 ,(string-append "-DKLU_LIBRARY_DIR="
5952 (assoc-ref %build-inputs "suitesparse")
5954 (home-page "https://computation.llnl.gov/projects/sundials")
5955 (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
5956 (description "SUNDIALS is a family of software packages implemented with
5957 the goal of providing robust time integrators and nonlinear solvers that can
5958 easily be incorporated into existing simulation codes.")
5959 (license license:bsd-3)))
5961 (define-public sundials-openmpi
5962 (package (inherit sundials)
5963 (name "sundials-openmpi")
5966 ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
5967 ,@(package-inputs sundials)))
5969 (substitute-keyword-arguments (package-arguments sundials)
5970 ((#:configure-flags flags '())
5971 `(cons* "-DMPI_ENABLE:BOOL=ON"
5972 "-DPETSC_ENABLE:BOOL=ON"
5973 (string-append "-DPETSC_INCLUDE_DIR="
5974 (assoc-ref %build-inputs "petsc")
5976 (string-append "-DPETSC_LIBRARY_DIR="
5977 (assoc-ref %build-inputs "petsc")
5980 ((#:phases phases '%standard-phases)
5981 `(modify-phases ,phases
5982 (add-before 'check 'mpi-setup
5983 ,%openmpi-setup)))))
5984 (synopsis "SUNDIALS with OpenMPI support")))
5986 (define-public combinatorial-blas
5988 (name "combinatorial-blas")
5993 (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/"
5995 (match (string-split version #\.)
5996 ((major minor patch)
5997 (string-append major minor "_" patch))) ;e.g. "16_2"
6001 "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a"))
6002 (patches (search-patches "combinatorial-blas-awpm.patch"
6003 "combinatorial-blas-io-fix.patch"))))
6004 (build-system cmake-build-system)
6007 ("test-data" ,(origin
6009 (uri (string-append "https://people.eecs.berkeley.edu/~aydin/"
6010 "CombBLAS_FILES/testdata_combblas1.6.1.tgz"))
6013 "01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87"))))))
6015 `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
6016 "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL")
6017 #:parallel-tests? #f ;tests use 'mpiexec -n4'
6019 (modify-phases %standard-phases
6020 (add-before 'check 'mpi-setup
6022 (add-before 'check 'test-setup
6023 (lambda* (#:key inputs #:allow-other-keys)
6024 (setenv "OMP_NUM_THREADS" "2")
6025 (invoke "tar" "xf" (assoc-ref inputs "test-data")))))))
6026 (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/")
6027 (synopsis "Linear algebra primitives for graph analytics")
6028 (description "The Combinatorial BLAS (CombBLAS) is an extensible
6029 distributed-memory parallel graph library offering a small but powerful set of
6030 linear algebra primitives specifically targeting graph analytics.")
6032 license:gpl2+ ;include/psort/(funnel|sort)*.h
6033 license:x11 ;usort and psort
6034 license:bsd-3)))) ;CombBLAS and MersenneTwister.h
6036 (define-public dune-common
6038 (name "dune-common")
6043 (uri (string-append "https://dune-project.org/download/"
6044 version "/dune-common-" version ".tar.gz"))
6047 "140q1zh44cr5yrjwg4b5ga803rkqv55vk30l2cqm29aklj1wb0rw"))))
6048 (build-system cmake-build-system)
6051 (modify-phases %standard-phases
6052 (add-after 'build 'build-tests
6053 (lambda* (#:key make-flags #:allow-other-keys)
6054 (apply invoke "make" "build_tests" make-flags))))))
6058 ("openblas" ,openblas)
6060 ("superlu" ,superlu)))
6062 `(("gfortran" ,gfortran)
6063 ("pkg-config" ,pkg-config)))
6064 (home-page "https://dune-project.org/")
6065 (synopsis "Distributed and Unified Numerics Environment")
6066 (description "DUNE, the Distributed and Unified Numerics Environment is a
6067 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
6068 grid-based methods. It supports the easy implementation of methods like
6069 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
6070 Differences} (FD).")
6071 ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2.
6072 (license license:gpl2)))
6074 (define-public dune-geometry
6076 (name "dune-geometry")
6081 (uri (string-append "https://dune-project.org/download/"
6082 version "/dune-geometry-" version ".tar.gz"))
6085 "1cicvlwbyyw76npicnblxckyvhbfn3ip8isydiv3hlrlz8zcg5nr"))))
6086 (build-system cmake-build-system)
6089 (modify-phases %standard-phases
6090 (add-after 'build 'build-tests
6091 (lambda* (#:key make-flags #:allow-other-keys)
6092 (apply invoke "make" "build_tests" make-flags))))))
6094 `(("dune-common" ,dune-common)
6096 ("openblas" ,openblas)
6098 ("python" ,python)))
6100 `(("gfortran" ,gfortran)
6101 ("pkg-config" ,pkg-config)))
6102 (home-page "https://dune-project.org/")
6103 (synopsis "Distributed and Unified Numerics Environment")
6104 (description "DUNE, the Distributed and Unified Numerics Environment is a
6105 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
6106 grid-based methods. It supports the easy implementation of methods like
6107 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
6110 This package contains the basic DUNE geometry classes.")
6111 ;; GPL version 2 with "runtime exception"
6112 (license license:gpl2)))
6114 (define-public dune-uggrid
6116 (name "dune-uggrid")
6122 (url "https://gitlab.dune-project.org/staging/dune-uggrid.git")
6123 (commit (string-append "v" version))))
6124 (file-name (git-file-name name version))
6127 "192miqgmfj6jwk969gydzpbv9ki7jg5nky3ydnrwa2nq29b5xkh0"))))
6128 (build-system cmake-build-system)
6131 (modify-phases %standard-phases
6132 (add-after 'build 'build-tests
6133 (lambda* (#:key make-flags #:allow-other-keys)
6134 (apply invoke "make" "build_tests" make-flags))))))
6136 `(("dune-common" ,dune-common)))
6138 `(("gfortran" ,gfortran)
6139 ("pkg-config" ,pkg-config)))
6140 (home-page "https://dune-project.org/")
6141 (synopsis "Distributed and Unified Numerics Environment")
6142 (description "DUNE, the Distributed and Unified Numerics Environment is a
6143 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
6144 grid-based methods. It supports the easy implementation of methods like
6145 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
6148 This package contains the DUNE UG grid classes.")
6149 (license license:lgpl2.1)))
6151 (define-public dune-grid
6158 (uri (string-append "https://dune-project.org/download/"
6159 version "/dune-grid-" version ".tar.gz"))
6162 "17fjz30qazjgl11sryyxnw9klai4yz1ji4bs68013xcxc5hdv27s"))))
6163 (build-system cmake-build-system)
6166 (modify-phases %standard-phases
6167 (add-after 'build 'build-tests
6168 (lambda* (#:key make-flags #:allow-other-keys)
6169 (apply invoke "make" "build_tests" make-flags))))))
6171 `(("dune-common" ,dune-common)
6172 ("dune-geometry" ,dune-geometry)
6175 ("openblas" ,openblas)
6176 ("python" ,python)))
6178 `(("dune-uggrid" ,dune-uggrid)))
6180 `(("gfortran" ,gfortran)
6181 ("pkg-config" ,pkg-config)))
6182 (home-page "https://dune-project.org/")
6183 (synopsis "Distributed and Unified Numerics Environment")
6184 (description "DUNE, the Distributed and Unified Numerics Environment is a
6185 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
6186 grid-based methods. It supports the easy implementation of methods like
6187 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
6190 This package contains the basic DUNE grid classes.")
6191 ;; GPL version 2 with "runtime exception"
6192 (license license:gpl2)))
6194 (define-public dune-istl
6201 (uri (string-append "https://dune-project.org/download/"
6202 version "/dune-istl-" version ".tar.gz"))
6205 "0gl3wgz5rs6sb4m83440ny45sbx7z7lnbi3gx6r9nm3rvy5j33f9"))
6206 (patches (search-patches "dune-istl-2.7-fix-non-mpi-tests.patch"))))
6207 (build-system cmake-build-system)
6210 (modify-phases %standard-phases
6211 ;; XXX: istl/test/matrixtest.cc includes <fenv.h> and fails to find
6212 ;; the stdlib types when the gfortran header is used. Remove gfortran
6213 ;; from CPLUS_INCLUDE_PATH as a workaround.
6214 (add-after 'set-paths 'hide-gfortran
6215 (lambda* (#:key inputs #:allow-other-keys)
6216 (let ((gfortran (assoc-ref inputs "gfortran")))
6217 (setenv "CPLUS_INCLUDE_PATH"
6219 (delete (string-append gfortran "/include/c++")
6220 (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
6223 (add-after 'build 'build-tests
6224 (lambda* (#:key make-flags #:allow-other-keys)
6225 (apply invoke "make" "build_tests" make-flags))))))
6227 `(("dune-common" ,dune-common)
6230 ("suitesparse" ,suitesparse)
6231 ("superlu" ,superlu)
6232 ("openblas" ,openblas)
6234 ("python" ,python)))
6236 `(("gfortran" ,gfortran)
6237 ("pkg-config" ,pkg-config)))
6238 (home-page "https://dune-project.org/")
6239 (synopsis "Distributed and Unified Numerics Environment")
6240 (description "DUNE, the Distributed and Unified Numerics Environment is a
6241 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
6244 This is the iterative solver template library which provides generic sparse
6245 matrix/vector classes and a variety of solvers based on these classes. A
6246 special feature is the use of templates to exploit the recursive block
6247 structure of finite element matrices at compile time. Available solvers
6248 include Krylov methods, (block-) incomplete decompositions and
6249 aggregation-based algebraic multigrid.")
6250 ;; GPL version 2 with "runtime exception"
6251 (license license:gpl2)))
6253 (define-public dune-localfunctions
6255 (name "dune-localfunctions")
6260 (uri (string-append "https://dune-project.org/download/"
6261 version "/dune-localfunctions-" version ".tar.gz"))
6264 "1yih59h6vngii696bx1c2vil02lriij4kz0nc583mjn9kiaqxfqd"))))
6265 (build-system cmake-build-system)
6268 (modify-phases %standard-phases
6269 ;; XXX: localfunctions/test/lagrangeshapefunctiontest.cc includes <fenv.h>
6270 ;; and fails to find the stdlib types when the gfortran header is used.
6271 ;; Hide gfortran from CPLUS_INCLUDE_PATH to ensure we get the GCC header.
6272 (add-after 'set-paths 'hide-gfortran
6273 (lambda* (#:key inputs #:allow-other-keys)
6274 (let ((gfortran (assoc-ref inputs "gfortran")))
6275 (setenv "CPLUS_INCLUDE_PATH"
6277 (delete (string-append gfortran "/include/c++")
6278 (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
6281 (add-after 'build 'build-tests
6282 (lambda* (#:key make-flags #:allow-other-keys)
6283 (apply invoke "make" "build_tests" make-flags))))))
6285 `(("dune-common" ,dune-common)
6286 ("dune-geometry" ,dune-geometry)
6289 ("superlu" ,superlu)
6292 `(("gfortran" ,gfortran)
6293 ("pkg-config" ,pkg-config)))
6294 (home-page "https://dune-project.org/")
6295 (synopsis "Distributed and Unified Numerics Environment") ; TODO
6296 (description "This DUNE module provides interface and implementation for
6297 shape functions defined on the DUNE reference elements. In addition to the
6298 shape function, interpolation operators and special keys are provided which
6299 can be used to assemble global function spaces on finite-element grids.
6301 This package provides an interface and implementation for shape functions
6302 defined on the DUNE reference elements. In addition to the shape function,
6303 interpolation operators and special keys are provided which can be used to
6304 assemble global function spaces on finite-element grids.")
6305 ;; GPL version 2 with "runtime exception"
6306 (license license:gpl2)))
6308 (define-public dune-alugrid
6310 (name "dune-alugrid")
6311 (version "2.7.0-git-81d35682")
6316 (url "https://gitlab.dune-project.org/extensions/dune-alugrid.git")
6317 (commit "81d356827c84454b971937db02c02b90bbcd7fe5")))
6318 (file-name (git-file-name name version))
6321 "0z54lwfp53prcrs94k8gwh047l9z642jll3l56xlyfr69z0b2zz1"))))
6322 (build-system cmake-build-system)
6325 (modify-phases %standard-phases
6326 (add-after 'unpack 'patch-include
6328 (substitute* "dune/alugrid/test/test-alugrid.cc"
6329 (("doc/grids/gridfactory/testgrids")
6330 "doc/dune-grid/grids/gridfactory/testgrids"))
6332 (add-after 'build 'build-tests
6333 (lambda* (#:key inputs make-flags #:allow-other-keys)
6334 (setenv "CPLUS_INCLUDE_PATH"
6335 (string-append (assoc-ref inputs "dune-grid") "/share"))
6336 (apply invoke "make" "build_tests" make-flags))))))
6338 `(("dune-common" ,dune-common)
6339 ("dune-geometry" ,dune-geometry)
6340 ("dune-grid" ,dune-grid)
6343 ("openblas" ,openblas)
6345 ("superlu" ,superlu)
6349 `(("gfortran" ,gfortran)
6350 ("pkg-config" ,pkg-config)))
6351 (home-page "https://dune-project.org/")
6352 (synopsis "Distributed and Unified Numerics Environment")
6353 (description "ALUGrid is an adaptive, loadbalancing, unstructured
6354 implementation of the DUNE grid interface supporting either simplices or
6356 (license license:gpl2+)))
6358 (define-public dune-subgrid
6360 (name "dune-subgrid")
6361 (version "2.7.0-git-2103a363")
6366 (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid")
6367 (commit "2103a363f32e8d7b60e66eee7ddecf969f6cf762")))
6368 (file-name (git-file-name name version))
6371 "1wsjlypd3835c3arqjkw836cxx5q67zy447wa65q634lf6f6v9ia"))))
6372 (build-system cmake-build-system)
6375 (modify-phases %standard-phases
6376 (add-after 'build 'build-tests
6377 (lambda* (#:key make-flags #:allow-other-keys)
6378 (apply invoke "make" "build_tests" make-flags))))))
6380 `(("dune-common" ,dune-common)
6381 ("dune-geometry" ,dune-geometry)
6382 ("dune-grid" ,dune-grid)
6385 ("openblas" ,openblas)
6388 `(("gfortran" ,gfortran)
6389 ("pkg-config" ,pkg-config)))
6390 (home-page "http://numerik.mi.fu-berlin.de/dune-subgrid/index.php")
6391 (synopsis "Distributed and Unified Numerics Environment")
6392 (description "The dune-subgrid module marks elements of
6393 another hierarchical dune grid. The set of marked elements can then be
6394 accessed as a hierarchical dune grid in its own right. Dune-Subgrid
6395 provides the full grid interface including adaptive mesh refinement.")
6396 (license license:gpl2+)))
6398 (define-public dune-typetree
6400 (name "dune-typetree")
6406 (url "https://gitlab.dune-project.org/staging/dune-typetree.git")
6407 (commit (string-append "v" version))))
6408 (file-name (git-file-name name version))
6411 "1rhv25yg0q1hw50c8wlfqhgwrjl4mh62zq9v14ilwgzbfgxmpiy7"))))
6412 (build-system cmake-build-system)
6415 (modify-phases %standard-phases
6416 (add-after 'build 'build-tests
6417 (lambda* (#:key make-flags #:allow-other-keys)
6418 (apply invoke "make" "build_tests" make-flags))))))
6420 `(("dune-common" ,dune-common)
6422 ("openblas" ,openblas)
6425 ("superlu" ,superlu)
6428 `(("gfortran" ,gfortran)
6429 ("pkg-config" ,pkg-config)))
6430 (home-page "https://dune-project.org/")
6431 (synopsis "Distributed and Unified Numerics Environment")
6432 (description "TypeTree is a template library for constructing and
6433 operating on statically typed trees of objects.")
6434 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
6435 (license (list license:lgpl3+ license:gpl2))))
6437 (define-public dune-functions
6439 (name "dune-functions")
6445 (url "https://gitlab.dune-project.org/staging/dune-functions.git")
6446 (commit (string-append "v" version))))
6447 (file-name (git-file-name name version))
6450 "1na4gcih0kin37ksj2xj07ds04v7zx53pjdhm1hzy55jjfqdjk8h"))))
6451 (build-system cmake-build-system)
6454 (modify-phases %standard-phases
6455 (add-after 'unpack 'disable-failing-tests
6458 ;; unable to load GMSH file in this test
6459 "--exclude-regex gridviewfunctionspacebasistest")
6461 (add-after 'build 'build-tests
6462 (lambda* (#:key make-flags #:allow-other-keys)
6463 (apply invoke "make" "build_tests" make-flags))))))
6465 `(("dune-common" ,dune-common)
6466 ("dune-istl" ,dune-istl)
6467 ("dune-localfunctions" ,dune-localfunctions)
6468 ("dune-grid" ,dune-grid)
6469 ("dune-geometry" ,dune-geometry)
6470 ("dune-typetree" ,dune-typetree)
6471 ("openblas" ,openblas)
6474 ("superlu" ,superlu)
6477 `(("gfortran" ,gfortran)
6478 ("pkg-config" ,pkg-config)))
6479 (home-page "https://dune-project.org/")
6480 (synopsis "Distributed and Unified Numerics Environment")
6481 (description "The dune-functions module provides an abstraction layer for
6482 global finite element functions. Its two main concepts are functions
6483 implemented as callable objects, and bases of finite element spaces.")
6484 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
6485 (license (list license:lgpl3+ license:gpl2))))
6487 (define-public dune-pdelab
6489 (name "dune-pdelab")
6490 (version "2.7.0-git-476fe437")
6495 (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
6496 (commit "476fe43763fa6f459c5e4658e2a2b4b5582db834")))
6497 (file-name (git-file-name name version))
6500 "0cs36piqzn6rq0j2ih3ab3q3q9yg199wk72k5qi86pkzh7i7fdn1"))))
6501 (build-system cmake-build-system)
6502 (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
6504 `(("dune-common" ,dune-common)
6505 ("dune-istl" ,dune-istl)
6506 ("dune-localfunctions" ,dune-localfunctions)
6507 ("dune-geometry" ,dune-geometry)
6508 ("dune-grid" ,dune-grid)
6509 ("dune-typetree" ,dune-typetree)
6510 ("dune-functions" ,dune-functions)
6512 ("openblas" ,openblas)
6516 ("superlu" ,superlu)
6519 `(("gfortran" ,gfortran)
6520 ("pkg-config" ,pkg-config)))
6521 (home-page "https://dune-project.org/")
6522 (synopsis "Differential equations solver toolbox")
6523 (description "PDELab is a partial differential equations solver toolbox
6524 built on top of DUNE, the Distributed and Unified Numerics Environment.")
6525 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
6526 (license (list license:lgpl3+ license:gpl2))))
6528 (define add-openmpi-to-dune-package
6529 (let ((dune-package?
6530 (lambda (p) (string-prefix? "dune-" (package-name p)))))
6533 (if (dune-package? p)
6534 (package (inherit p)
6535 (name (string-append (package-name p) "-openmpi"))
6536 (inputs `(,@(package-inputs p)
6537 ("openmpi" ,openmpi)))
6539 (substitute-keyword-arguments (package-arguments p)
6540 ((#:phases phases '%standard-phases)
6541 `(modify-phases ,phases
6542 (add-before 'check 'mpi-setup
6543 ,%openmpi-setup)))))
6544 (synopsis (string-append (package-synopsis p) " (with MPI support)")))
6546 (negate dune-package?))))
6548 (define-public dune-common-openmpi
6549 (add-openmpi-to-dune-package dune-common))
6551 (define-public dune-geometry-openmpi
6552 (add-openmpi-to-dune-package dune-geometry))
6554 (define-public dune-istl-openmpi
6555 (add-openmpi-to-dune-package dune-istl))
6557 (define-public dune-typetree-openmpi
6558 (add-openmpi-to-dune-package dune-typetree))
6560 (define-public dune-uggrid-openmpi
6561 (add-openmpi-to-dune-package dune-uggrid))
6563 (define-public dune-grid-openmpi
6564 (add-openmpi-to-dune-package dune-grid))
6566 (define-public dune-alugrid-openmpi
6567 (add-openmpi-to-dune-package dune-alugrid))
6569 (define-public dune-subgrid-openmpi
6570 (add-openmpi-to-dune-package dune-subgrid))
6572 (define-public dune-localfunctions-openmpi
6573 (add-openmpi-to-dune-package dune-localfunctions))
6575 (define-public dune-functions-openmpi
6576 (add-openmpi-to-dune-package dune-functions))
6578 (define-public dune-pdelab-openmpi
6579 (add-openmpi-to-dune-package dune-pdelab))
6581 (define-public mlucas
6589 "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz"))
6591 (base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447"))))
6592 (build-system gnu-build-system)
6594 `(("python2" ,python-2)))
6596 `(#:tests? #f ; no tests
6598 (modify-phases %standard-phases
6602 (call-with-output-file "Makefile"
6604 (format port "CC = gcc
6605 CFLAGS = -O3 ~a -DUSE_THREADS
6606 LDLIBS = -lm -lpthread -lrt
6607 Mlucas: $(addsuffix .o,$(basename $(wildcard *.c)))
6609 ,(let ((system (or (%current-target-system)
6610 (%current-system))))
6612 ((string-prefix? "x86_64" system) "-DUSE_SSE2")
6616 (lambda* (#:key outputs #:allow-other-keys)
6617 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
6618 (install-file "Mlucas" bin)
6619 (install-file "primenet.py" bin))
6621 (home-page "https://www.mersenne.org")
6622 (synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client")
6623 (description "Mlucas performs Lucas-Lehmer primality testing of Mersenne
6624 numbers in search of a world-record prime. You may use it to test any
6625 suitable number as you wish, but it is preferable that you do so in a
6626 coordinated fashion, as part of the Great Internet Mersenne Prime
6627 Search (GIMPS). Mlucas also includes a simple Python script for assignment
6628 management via the GIMPS project's Primenet server.")
6629 (license license:gpl2+)))
6631 (define-public nauty
6639 "https://pallini.di.uniroma1.it/"
6640 "nauty" (string-join (string-split version #\.) "") ".tar.gz"))
6642 (base32 "1hl81gpf3xjf809w04jczvilq1ixy9ch1qrax8a7lgx52svna1jg"))))
6643 (build-system gnu-build-system)
6644 (outputs '("out" "lib"))
6646 `(#:test-target "checks"
6647 #:configure-flags '("--enable-generic") ;prevent -march-native
6649 (modify-phases %standard-phases
6650 ;; Default make target does not build all available
6651 ;; executables. Create them now.
6652 (add-after 'build 'build-extra-programs
6654 (for-each (lambda (target) (invoke "make" target))
6655 '("blisstog" "bliss2dre" "checks6" "sumlines"))
6657 ;; Upstream does not provide any install target.
6659 (lambda* (#:key outputs #:allow-other-keys)
6660 (let* ((out (assoc-ref outputs "out"))
6661 (lib-output (assoc-ref outputs "lib"))
6662 (bin (string-append out "/bin"))
6663 (doc (string-append out "/share/doc/nauty/"))
6664 (include (string-append lib-output "/include/nauty"))
6665 (lib (string-append lib-output "/lib/nauty")))
6666 (for-each (lambda (f) (install-file f bin))
6667 '("addedgeg" "amtog" "assembleg" "biplabg" "blisstog"
6668 "bliss2dre" "catg" "checks6" "complg" "converseg"
6669 "copyg" "countg" "cubhamg" "deledgeg" "delptg"
6670 "directg" "dreadnaut" "dretodot" "dretog" "genbg"
6671 "genbgL" "geng" "genquarticg" "genrang" "genspecialg"
6672 "gentourng" "gentreeg" "hamheuristic" "labelg"
6673 "linegraphg" "listg" "multig" "newedgeg" "pickg"
6674 "planarg" "ranlabg" "shortg" "showg" "subdivideg"
6675 "sumlines" "twohamg" "underlyingg" "vcolg"
6676 "watercluster2" "NRswitchg"))
6677 (for-each (lambda (f) (install-file f include))
6678 (find-files "." "\\.h$"))
6679 (for-each (lambda (f) (install-file f lib))
6680 (find-files "." "\\.a$"))
6681 (for-each (lambda (f) (install-file f doc))
6682 (append '("formats.txt" "README" "schreier.txt")
6683 (find-files "." "\\.pdf$")))))))))
6685 `(("gmp" ,gmp))) ;for sumlines
6686 (home-page "https://pallini.di.uniroma1.it/")
6687 (synopsis "Library for graph automorphisms")
6688 (description "@code{nauty} (No AUTomorphisms, Yes?) is a set of
6689 procedures for computing automorphism groups of graphs and digraphs.
6691 @code{nauty} computes graph information in the form of a set of
6692 generators, the size of the group, and the orbits of the group; it can
6693 also produce a canonical label. The @code{nauty} suite is written in
6694 C and comes with a command-line interface, a collection of
6695 command-line tools, and an Application Programming Interface (API).
6697 This package provides the static libraries required to run programs
6698 compiled against the nauty library.")
6699 (license license:asl2.0)))
6708 (uri (string-append "https://www.bugseng.com/products/ppl/download/"
6709 "ftp/releases/" version
6710 "/ppl-" version ".tar.gz"))
6713 "1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb"))))
6714 (build-system gnu-build-system)
6720 (home-page "https://www.bugseng.com/parma-polyhedra-library")
6722 "Parma Polyhedra Library for computations with polyhedra")
6724 "The Parma Polyhedra Library (PPL) provides numerical abstractions
6725 especially targeted at applications in the field of analysis and
6726 verification of complex systems. These abstractions include convex
6727 polyhedra, defined as the intersection of a finite number of (open or
6728 closed) halfspaces, each described by a linear inequality (strict or
6729 non-strict) with rational coefficients; some special classes of polyhedra
6730 shapes that offer interesting complexity/precision tradeoffs; and grids
6731 which represent regularly spaced points that satisfy a set of linear
6732 congruence relations. The library also supports finite powersets and
6733 products of (any kind of) polyhedra and grids, a mixed integer linear
6734 programming problem solver using an exact-arithmetic version of the simplex
6735 algorithm, a parametric integer programming solver, and primitives for
6736 termination analysis via the automatic synthesis of linear ranking
6738 (license license:gpl3+)))
6740 (define-public speedcrunch
6742 (name "speedcrunch")
6748 (url "https://bitbucket.org/heldercorreia/speedcrunch.git")
6749 (commit (string-append "release-" version))))
6750 (file-name (git-file-name name version))
6753 "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"))))
6754 (build-system cmake-build-system)
6755 (inputs `(("qtbase" ,qtbase-5)))
6756 (native-inputs `(("qttools" ,qttools)))
6759 (modify-phases %standard-phases
6760 (add-after 'unpack 'chdir-to-src
6761 (lambda _ (chdir "src") #t)))))
6762 (synopsis "High-precision scientific calculator")
6764 "SpeedCrunch is a high-precision scientific calculator. It features a
6765 syntax-highlighted scrollable display and is designed to be fully used via
6766 keyboard. Some distinctive features are auto-completion of functions and
6767 variables, a formula book, and quick insertion of constants from various
6768 fields of knowledge.")
6769 (home-page "https://speedcrunch.org/")
6770 (license license:gpl2+)))
6772 (define-public minisat
6773 ;; This is the last commit which is available upstream, no
6774 ;; release happened since 2010.
6775 (let ((commit "37dc6c67e2af26379d88ce349eb9c4c6160e8543")
6779 (version (string-append "2.2.0-" revision "." (string-take commit 7)))
6784 (url "https://github.com/niklasso/minisat")
6786 (file-name (string-append name "-" version "-checkout"))
6789 "091hf3qkm197s5r7xcr3m07xsdwyz2rqk1hc9kj0hn13imz09irq"))
6791 (search-patches "minisat-friend-declaration.patch"
6792 "minisat-install.patch"))))
6793 (build-system gnu-build-system)
6795 '(#:make-flags (list (string-append "prefix=" %output))
6796 #:tests? #f ;no check target
6798 (modify-phases %standard-phases
6799 (delete 'configure))))
6801 `(("zlib:static" ,zlib "static")
6804 "Small, yet efficient, SAT solver")
6806 "MiniSat is a minimalistic, open-source SAT solver, developed to help
6807 researchers and developers alike to get started on SAT.")
6809 "http://minisat.se/MiniSat.html")
6810 (license license:expat))))
6812 (define-public libqalculate
6814 (name "libqalculate")
6820 (url "https://github.com/Qalculate/libqalculate/")
6821 (commit (string-append "v" version))))
6822 (file-name (git-file-name name version))
6824 (base32 "1w44407wb552q21dz4m2nwwdi8b9hzjb2w1l3ffsikzqckc7wbyj"))
6826 (search-patches "libqalculate-3.8.0-libcurl-ssl-fix.patch"))))
6827 (build-system gnu-build-system)
6829 `(("pkg-config" ,pkg-config)
6830 ("gettext" ,gettext-minimal)
6831 ("intltool" ,intltool)
6832 ("automake" ,automake)
6833 ("autoconf" ,autoconf)
6834 ("libtool" ,libtool)
6835 ("doxygen" ,doxygen)
6840 ("libxml2" ,libxml2)
6843 ("gnuplot" ,gnuplot)
6844 ("readline" ,readline)
6845 ("libiconv" ,libiconv)))
6848 (modify-phases %standard-phases
6849 (add-before 'bootstrap 'setenv
6850 ;; Prevent the autogen.sh script to carry out the configure
6851 ;; script, which has not yet been patched to replace /bin/sh.
6853 (setenv "NOCONFIGURE" "TRUE")
6855 (home-page "https://qalculate.github.io/")
6856 (synopsis "Multi-purpose cli desktop calculator and library")
6858 "Libqalculate is a multi-purpose cli desktop calculator and library.
6859 It provides basic and advanced functionality. Features include customizable
6860 functions, unit calculations, and conversions, physical constants, symbolic
6861 calculations (including integrals and equations), arbitrary precision,
6862 uncertainty propagation, interval arithmetic, plotting and a user-friendly
6864 (license license:gpl2+)))
6866 (define-public qalculate-gtk
6868 (name "qalculate-gtk")
6874 (url "https://github.com/Qalculate/qalculate-gtk/")
6875 (commit (string-append "v" version))))
6876 (file-name (git-file-name name version))
6878 (base32 "1nrx7gp6f1yalbdda1gb97azhbr4xclq2xf08vvbvsk8jfd6fd2v"))))
6879 (build-system glib-or-gtk-build-system)
6881 `(("pkg-config" ,pkg-config)
6882 ("intltool" ,intltool)
6883 ("automake" ,automake)
6884 ("autoconf" ,autoconf)
6885 ("libtool" ,libtool)
6890 ("libqalculate" ,libqalculate)
6891 ("libxml2" ,libxml2)
6896 (modify-phases %standard-phases
6897 (add-before 'bootstrap 'setenv
6898 ;; Prevent the autogen.sh script to carry out the configure
6899 ;; script, which has not yet been patched to replace /bin/sh.
6901 (setenv "NOCONFIGURE" "TRUE")
6903 (home-page "https://qalculate.github.io/")
6904 (synopsis "Multi-purpose graphical desktop calculator")
6906 "Qalculate-gtk is the GTK frontend for libqalculate. It is a
6907 multi-purpose GUI desktop calculator. It provides basic and advanced
6908 functionality. Features include customizable functions, unit calculations,
6909 and conversions, physical constants, symbolic calculations (including
6910 integrals and equations), arbitrary precision, uncertainty propagation,
6911 interval arithmetic, plotting.")
6912 (license license:gpl2+)))
6914 (define-public numdiff
6921 (uri (string-append "mirror://savannah/numdiff/numdiff-"
6925 "1vzmjh8mhwwysn4x4m2vif7q2k8i19x8azq7pzmkwwj4g48lla47"))))
6926 (build-system gnu-build-system)
6928 '(#:tests? #f ; There are no tests.
6930 (modify-phases %standard-phases
6931 (add-before 'compress-documentation 'delete-precompressed-info-file
6933 (delete-file (string-append (assoc-ref %outputs "out")
6934 "/share/info/numdiff.info.gz"))
6936 (home-page "https://nongnu.org/numdiff/")
6937 (synopsis "Compare files with numeric fields")
6939 "Numdiff compares files line by line and field by field, ignoring small
6940 numeric differences and differences in numeric formats.")
6941 (license license:gpl3+)))
6950 (url "https://gitlab.inria.fr/why3/why3")
6952 (file-name (git-file-name name version))
6955 "0pfsiddnk26f384wbazfpgzh1n1ibf3xq101q74mxvczi7z0a791"))))
6956 (build-system ocaml-build-system)
6958 `(("autoconf" ,autoconf)
6959 ("automake" ,automake)
6964 `(("camlzip" ,camlzip)
6965 ("ocaml-graph" ,ocaml-graph)
6966 ("ocaml-menhir" ,ocaml-menhir)
6967 ("ocaml-num" ,ocaml-num)
6968 ("ocaml-zarith" ,ocaml-zarith)))
6970 `(("coq-flocq" ,coq-flocq)
6971 ("emacs-minimal" ,emacs-minimal)
6975 (modify-phases %standard-phases
6976 (add-before 'configure 'bootstrap
6978 (invoke "./autogen.sh")
6979 (setenv "CONFIG_SHELL" (which "sh"))
6980 (substitute* "configure"
6981 (("#! /bin/sh") (string-append "#!" (which "sh")))
6982 ;; find ocaml-num in the correct directory
6983 (("\\$DIR/nums.cma") "$DIR/num.cma")
6984 (("\\$DIR/num.cmi") "$DIR/core/num.cmi"))
6986 (add-after 'configure 'fix-makefile
6988 (substitute* "Makefile"
6989 ;; find ocaml-num in the correct directory
6990 (("site-lib/num") "site-lib"))
6992 (add-after 'install 'install-lib
6994 (invoke "make" "byte")
6995 (invoke "make" "install-lib")
6997 (home-page "http://why3.lri.fr")
6998 (synopsis "Deductive program verification")
6999 (description "Why3 provides a language for specification and programming,
7000 called WhyML, and relies on external theorem provers, both automated and
7001 interactive, to discharge verification conditions. Why3 comes with a standard
7002 library of logical theories (integer and real arithmetic, Boolean operations,
7003 sets and maps, etc.) and basic programming data structures (arrays, queues,
7004 hash tables, etc.). A user can write WhyML programs directly and get
7005 correct-by-construction OCaml programs through an automated extraction
7006 mechanism. WhyML is also used as an intermediate language for the verification
7007 of C, Java, or Ada programs.")
7008 (license license:lgpl2.1)))
7010 (define-public frama-c
7016 (uri (string-append "http://frama-c.com/download/frama-c-"
7017 version "-Vanadium.tar.gz"))
7020 "1rgkq9sg436smw005ag0j6y3xryhjn18a07m5wjfrfp0s1438nnj"))))
7021 (build-system ocaml-build-system)
7023 `(#:tests? #f; no test target in Makefile
7025 (modify-phases %standard-phases
7026 (add-before 'configure 'export-shell
7027 (lambda* (#:key inputs #:allow-other-keys)
7028 (setenv "CONFIG_SHELL"
7029 (search-input-file inputs "/bin/sh")))))))
7033 `(("ocaml-biniou" ,ocaml-biniou)
7034 ("ocaml-easy-format" ,ocaml-easy-format)
7035 ("ocaml-graph" ,ocaml-graph)
7036 ("ocaml-yojson" ,ocaml-yojson)
7037 ("ocaml-zarith" ,ocaml-zarith)
7039 (native-search-paths
7040 (list (search-path-specification
7041 (variable "FRAMAC_SHARE")
7042 (files '("share/frama-c"))
7044 (search-path-specification
7045 (variable "FRAMAC_LIB")
7046 (files '("lib/frama-c"))
7048 (home-page "http://frama-c.com")
7049 (synopsis "C source code analysis platform")
7050 (description "Frama-C is an extensible and collaborative platform dedicated
7051 to source-code analysis of C software. The Frama-C analyzers assist you in
7052 various source-code-related activities, from the navigation through unfamiliar
7053 projects up to the certification of critical software.")
7054 (license license:lgpl2.1+)))
7056 (define-public blitz
7064 (url "https://github.com/blitzpp/blitz")
7066 (file-name (git-file-name name version))
7068 (base32 "0c88gc72j3zggyk4yrrip6i0v7xkx97l140vpy3xhxs2i7xy1461"))))
7069 (build-system cmake-build-system)
7071 `(#:configure-flags '("-DBUILD_DOC=ON"
7072 "-DBUILD_TESTING=ON")
7073 ;; The default "check" target also includes examples and benchmarks.
7074 #:test-target "check-testsuite"
7076 (modify-phases %standard-phases
7077 (add-after 'build 'build-doc
7079 (invoke "make" "-j" (number->string (parallel-job-count))
7082 `(("python" ,python)
7083 ("texinfo" ,texinfo)))
7084 (synopsis "C++ template class library for multidimensional arrays")
7085 (description "Blitz++ is a C++ template class library that provides
7086 high-performance multidimensional array containers for scientific computing.")
7087 (home-page "https://github.com/blitzpp/blitz")
7088 (license (list license:artistic2.0
7092 (define-public fxdiv
7093 ;; There is currently no tag in this repo.
7094 (let ((commit "63058eff77e11aa15bf531df5dd34395ec3017c8")
7099 (version (git-version version revision commit))
7100 (home-page "https://github.com/Maratyszcza/FXdiv")
7103 (uri (git-reference (url home-page) (commit commit)))
7104 (file-name (git-file-name name version))
7107 "0zwzh8gmbx4m6b18s5nf13b0dk5yjkd1fs8f421bl7fz5f9gjd9f"))
7108 (patches (search-patches "fxdiv-system-libraries.patch"))))
7109 (build-system cmake-build-system)
7111 `(("googletest" ,googletest)
7112 ("googlebenchmark" ,googlebenchmark)))
7114 "C++ library for division via fixed-point multiplication by inverse")
7116 "On modern CPUs and GPUs, integer division is several times slower than
7117 multiplication. FXdiv implements an algorithm to replace an integer division
7118 with a multiplication and two shifts. This algorithm improves performance
7119 when an application performs repeated divisions by the same divisor.")
7120 (license license:expat))))
7123 ;; There is currently no tag in this repo.
7124 (let ((commit "0a92994d729ff76a58f692d3028ca1b64b145d91")
7129 (version (git-version version revision commit))
7130 (home-page "https://github.com/Maratyszcza/FP16")
7133 (uri (git-reference (url home-page) (commit commit)))
7134 (file-name (git-file-name name version))
7137 "05mm4vrxsac35hjf5djif9r6rdxj9ippg97ia3p6q6b8lrp7srwv"))
7138 (patches (search-patches "fp16-system-libraries.patch"))))
7139 (build-system cmake-build-system)
7141 `(#:imported-modules ((guix build python-build-system)
7142 ,@%cmake-build-system-modules)
7143 #:modules (((guix build python-build-system)
7144 #:select (site-packages))
7145 (guix build cmake-build-system)
7147 #:phases (modify-phases %standard-phases
7148 (add-after 'install 'move-python-files
7149 (lambda* (#:key inputs outputs #:allow-other-keys)
7150 ;; Python files get installed to $includedir (!).
7151 ;; Move them to the usual Python site directory.
7152 (let* ((out (assoc-ref outputs "out"))
7153 (include (string-append out "/include"))
7154 (site (site-packages inputs outputs))
7155 (target (string-append site "/fp16")))
7157 (for-each (lambda (file)
7159 (string-append target "/"
7162 (find-files include "\\.py$"))))))))
7164 `(("python-wrapper" ,python-wrapper)))
7167 ("googletest" ,googletest)
7168 ("googlebenchmark" ,googlebenchmark)))
7169 (synopsis "C++ library for half-precision floating point formats")
7171 "This header-only C++ library implements conversion to and from
7172 half-precision floating point formats.")
7173 (license license:expat))))
7175 (define-public optizelle
7176 (let ((commit "ed4160b5287518448caeb34789d92dc6a0b7e2cc"))
7179 (version (git-version "1.3.0" "0" commit))
7184 (url "https://github.com/OptimoJoe/Optizelle")
7186 (file-name (git-file-name "optizelle" commit))
7189 "0rjrs5sdmd33a9f4xm8an7p0953aa0bxsmr4hs3ss1aad9k181vq"))
7190 (modules '((guix build utils)))
7193 ;; Reduce the stopping tolerance in one test so that the
7194 ;; convergence check returns the correct stopping
7197 "src/unit/linear_algebra/tcg_loss_of_orthogonality.cpp"
7198 (("1e-13") "5e-14"))
7199 ;; Skip one set of python tests. See
7200 ;; https://github.com/OptimoJoe/Optizelle/issues/2.
7202 "src/examples/inequality_scaling/CMakeLists.txt"
7203 (("add_unit(.*)\\$\\{interfaces\\}(.*)$" all middle end)
7204 (string-append "add_unit" middle "\"cpp\"" end)))
7205 ;; Install the licence for Optizelle, without also
7206 ;; including the licences for the dependencies.
7207 (substitute* "licenses/CMakeLists.txt"
7208 (("file.*package.*$" all)
7209 (string-append "# " all))
7210 ((".*[^l].[.]txt\\)\n") "")
7211 (("add_license.*\"\n") ""))
7213 (build-system cmake-build-system)
7215 `(#:imported-modules ((guix build python-build-system)
7216 ,@%cmake-build-system-modules)
7217 #:modules (((guix build python-build-system) #:select
7219 (guix build cmake-build-system)
7221 #:configure-flags `("-DCMAKE_CXX_FLAGS:STRING=-pthread"
7222 "-DENABLE_CPP_UNIT:BOOL=ON"
7223 "-DENABLE_CPP_EXAMPLES:BOOL=ON"
7224 "-DENABLE_PYTHON:BOOL=ON"
7225 "-DENABLE_PYTHON_UNIT:BOOL=ON"
7226 "-DENABLE_PYTHON_EXAMPLES:BOOL=ON"
7227 ,(string-append "-DBLAS_LIBRARY:FILEPATH="
7228 (assoc-ref %build-inputs
7230 "/lib/libopenblas.so")
7231 ,(string-append "-DLAPACK_LIBRARY:FILEPATH="
7232 (assoc-ref %build-inputs
7234 "/lib/libgfortran.so;"
7235 (assoc-ref %build-inputs
7237 "/lib/libquadmath.so"))
7239 (modify-phases %standard-phases
7240 (add-after 'unpack 'set-numpy-path ; Needed for the unit tests.
7241 (lambda* (#:key inputs #:allow-other-keys)
7242 (let* ((pyver (python-version (assoc-ref inputs "python")))
7243 (npdir (string-append (assoc-ref inputs "numpy")
7246 (substitute* "src/cmake/Modules/Optizelle.cmake"
7248 (string-append "LD_LIBRARY_PATH=$ENV{LIBRARY_PATH};"
7249 "PYTHONPATH=" npdir ":"))))))
7250 (delete 'install-license-files)))) ; LICENSE.txt is installed.
7252 `(("blas/lapack" ,openblas)
7253 ("fortran:lib" ,gfortran "lib")
7254 ("jsoncpp" ,jsoncpp)
7255 ("numpy" ,python-numpy)
7256 ("python" ,python)))
7258 `(("fortran" ,gfortran)
7259 ("pkg-config" ,pkg-config)))
7260 (home-page "https://www.optimojoe.com/products/optizelle/")
7261 (synopsis "Mathematical optimization library")
7262 (description "@code{optizelle} is a software library designed to
7263 solve nonlinear optimization problems. Four types of problem are
7264 considered: unconstrained, equality constrained, inequality
7265 constrained and constrained. Constraints may be applied as values of
7266 functions or sets of partial differential equations (PDEs).
7268 Solution algorithms such as the preconditioned nonlinear conjugate
7269 gradient method, sequential quadratic programming (SQP) and the
7270 primal-dual interior-point method are made available. Interfaces are
7271 provided for applications written in C++ and Python. Parallel
7272 computation is supported via MPI.")
7273 (license license:bsd-2))))