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 © 2015–2021 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=-O2 -g -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 "19i0h9vdc3zsy58r6fy1vs2kz2l7amifkz0cf926j90xz1n23nb1"))
989 (patches (search-patches "scalapack-gcc-10-compilation.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 (add-after 'unpack 'skip-faulty-test
1002 ;; FIXME: Skip these two tests that fail to complete for
1004 ;; <https://github.com/Reference-ScaLAPACK/scalapack/issues/43>.
1005 (substitute* "TESTING/CMakeLists.txt"
1006 (("^add_test\\(x[sd]hseqr.*" all)
1007 (string-append "# " all "\n"))))))))
1008 (home-page "http://www.netlib.org/scalapack/")
1009 (synopsis "Library for scalable numerical linear algebra")
1011 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
1012 routines on parallel distributed memory machines. ScaLAPACK solves dense and
1013 banded linear systems, least squares problems, eigenvalue problems, and
1014 singular value problems.")
1015 (license (license:non-copyleft "file://LICENSE"
1016 "See LICENSE in the distribution."))))
1018 (define-public gnuplot
1024 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
1028 (base32 "1fp7rbhjmz2w63r72kicf8lfszzimz2csfx868fracw167hpaz75"))))
1029 (build-system gnu-build-system)
1030 (inputs `(("readline" ,readline)
1036 `(("pkg-config" ,pkg-config)
1037 ("texlive" ,texlive-tiny)))
1038 (arguments `(#:configure-flags (list (string-append
1039 "--with-texdir=" %output
1040 "/texmf-local/tex/latex/gnuplot"))
1041 ;; Plot on a dumb terminal during tests.
1042 #:make-flags '("GNUTERM=dumb")))
1043 (home-page "http://www.gnuplot.info")
1044 (synopsis "Command-line driven graphing utility")
1045 (description "Gnuplot is a portable command-line driven graphing
1046 utility. It was originally created to allow scientists and students to
1047 visualize mathematical functions and data interactively, but has grown to
1048 support many non-interactive uses such as web scripting. It is also used as a
1049 plotting engine by third-party applications like Octave.")
1050 ;; X11 Style with the additional restriction that derived works may only be
1051 ;; distributed as patches to the original.
1052 (license (license:fsf-free
1053 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
1063 (url "https://github.com/OkoSanto/GCTP")
1064 (commit (string-append "v" version))))
1065 (file-name (git-file-name name version))
1067 (base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
1069 `(("fortran" ,gfortran)))
1070 (build-system gnu-build-system)
1071 (synopsis "General Cartographic Transformation Package (GCTP)")
1073 "The General Cartographic Transformation Package (GCTP) is a system of
1074 software routines designed to permit the transformation of coordinate pairs
1075 from one map projection to another. The GCTP is the standard computer
1076 software used by the National Mapping Division for map projection
1078 (home-page "https://github.com/OkoSanto/GCTP")
1079 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
1088 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
1089 version "/src/hdf-" version ".tar.bz2"))
1091 (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l"))
1092 (patches (search-patches "hdf4-architectures.patch"
1093 "hdf4-reproducibility.patch"
1094 "hdf4-shared-fortran.patch"
1095 "hdf4-tirpc.patch"))))
1096 (build-system gnu-build-system)
1098 `(("gfortran" ,gfortran)
1103 ("libjpeg" ,libjpeg-turbo)
1104 ("libtirpc" ,libtirpc)))
1106 `(#:parallel-tests? #f
1107 #:configure-flags (list "--enable-shared"
1108 "FCFLAGS=-fallow-argument-mismatch"
1109 "FFLAGS=-fallow-argument-mismatch"
1110 (string-append "CPPFLAGS=-I"
1111 (assoc-ref %build-inputs "libtirpc")
1114 (modify-phases %standard-phases
1115 ;; This is inspired by two of Debian's patches.
1116 (add-before 'configure 'add-more-aarch64-support
1118 (substitute* '("mfhdf/ncgen/ncgen.l"
1119 "mfhdf/ncgen/ncgenyy.c"
1120 "mfhdf/libsrc/netcdf.h.in")
1121 (("AIX5L64") "__aarch64__"))
1123 (add-before 'configure 'patchbuild
1126 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
1128 (("/bin/mkdir") "mkdir"))
1129 (substitute* (find-files "." "^Makefile\\.in$")
1130 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
1131 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
1132 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
1133 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
1134 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
1136 (add-after 'configure 'patch-settings
1138 ;; libhdf4.settings contains the full path of the
1139 ;; compilers used, and its contents are included in
1140 ;; .so-files. We truncate the hashes to avoid
1141 ;; unnecessary store references to those compilers:
1142 (substitute* "libhdf4.settings"
1143 (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash)
1144 (string-append prefix (string-take hash 10) "...")))
1146 (add-after 'install 'provide-absolute-libjpeg-reference
1147 (lambda* (#:key inputs outputs #:allow-other-keys)
1148 (let ((out (assoc-ref outputs "out"))
1149 (libjpeg (assoc-ref inputs "libjpeg")))
1150 ;; libjpeg-turbo does not provide a .la file, so libtool is
1151 ;; unable to add an absolute reference for -ljpeg in the .la
1152 ;; files. Fix it manually to avoid having to propagate it.
1153 (substitute* (find-files (string-append out "/lib") "\\.la$")
1155 (string-append "-L" libjpeg "/lib -ljpeg")))
1157 (home-page "https://www.hdfgroup.org/products/hdf4/")
1159 "Library and multi-object file format for storing and managing data")
1160 (description "HDF4 is a library and multi-object file format for storing
1161 and managing data between machines. HDF4 is an older hierarchical data format,
1162 incompatible with HDF5.")
1164 (license:non-copyleft
1165 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
1167 (define-public hdf4-alt
1172 (substitute-keyword-arguments (package-arguments hdf4)
1173 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
1175 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
1177 (define-public hdf5-1.8
1184 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
1185 "hdf5-" (version-major+minor version)
1186 "/hdf5-" version "/src/hdf5-"
1188 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
1190 (match (string-split version #\.)
1191 ((major minor _ ...)
1192 (string-append major minor)))
1193 "/src/hdf5-" version ".tar.bz2")))
1195 (base32 "194ki2s5jrgl4czkvy5nc9nwjyapah0fj72l0gb0aysplp38i6v8"))
1196 (patches (search-patches "hdf5-config-date.patch"))))
1197 (build-system gnu-build-system)
1201 `(("gfortran" ,gfortran)
1202 ("perl" ,perl))) ;part of the test machinery needs Perl
1203 (outputs '("out" ; core library
1204 "fortran")) ; fortran interface
1206 `(;; Some of the users, notably Flann, need the C++ interface.
1207 #:configure-flags '("--enable-cxx"
1209 "--enable-fortran2003"
1211 ;; Build a thread-safe library. Unfortunately,
1212 ;; 'configure' invites you to either turn off C++,
1213 ;; Fortran, and the high-level interface (HL), or
1214 ;; to pass '--enable-unsupported'. Debian
1215 ;; packagers chose to pass '--enable-unsupported'
1216 ;; and we follow their lead here.
1217 "--enable-threadsafe"
1219 "--enable-unsupported")
1220 ;; Use -fPIC to allow the R bindings to link with the static libraries
1221 #:make-flags (list "CFLAGS=-fPIC"
1224 (modify-phases %standard-phases
1225 (add-before 'configure 'patch-configure
1226 (lambda* (#:key outputs #:allow-other-keys)
1227 (substitute* "configure"
1229 (substitute* "fortran/src/Makefile.in"
1230 (("libhdf5_fortran_la_LDFLAGS =")
1231 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
1232 (assoc-ref outputs "fortran") "/lib")))
1233 (substitute* "hl/fortran/src/Makefile.in"
1234 (("libhdf5hl_fortran_la_LDFLAGS =")
1235 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
1236 (assoc-ref outputs "fortran") "/lib")))
1238 (add-after 'configure 'patch-settings
1240 ;; libhdf5.settings contains the full path of the
1241 ;; compilers used, and its contents are included in
1242 ;; libhdf5.so. We truncate the hashes to avoid
1243 ;; unnecessary store references to those compilers:
1244 (substitute* "src/libhdf5.settings"
1245 (("(/gnu/store/)([a-zA-Z0-9]*)" all prefix hash)
1246 (string-append prefix (string-take hash 10) "..."))
1247 ;; Don't record the build-time kernel version to make the
1248 ;; settings file reproducible.
1249 (("Uname information:.*")
1250 "Uname information: Linux\n"))
1252 (add-after 'install 'patch-references
1253 (lambda* (#:key inputs outputs #:allow-other-keys)
1254 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
1255 (zlib (assoc-ref inputs "zlib")))
1256 (substitute* (find-files bin "h5p?cc")
1258 (string-append "-L" zlib "/lib " lib)))
1260 (add-after 'install 'split
1261 (lambda* (#:key inputs outputs #:allow-other-keys)
1262 ;; Move all fortran-related files
1263 (let* ((out (assoc-ref outputs "out"))
1264 (bin (string-append out "/bin"))
1265 (lib (string-append out "/lib"))
1266 (inc (string-append out "/include"))
1267 (ex (string-append out "/share/hdf5_examples/fortran"))
1268 (fort (assoc-ref outputs "fortran"))
1269 (fbin (string-append fort "/bin"))
1270 (flib (string-append fort "/lib"))
1271 (finc (string-append fort "/include"))
1272 (fex (string-append fort "/share/hdf5_examples/fortran")))
1277 ;; Note: When built with --enable-parallel, the 'h5fc' file
1278 ;; doesn't exist, hence this condition.
1279 (when (file-exists? (string-append bin "/h5fc"))
1280 (rename-file (string-append bin "/h5fc")
1281 (string-append fbin "/h5fc")))
1282 (for-each (lambda (file)
1284 (string-append flib "/" (basename file))))
1285 (find-files lib ".*fortran.*"))
1286 (for-each (lambda (file)
1288 (string-append finc "/" (basename file))))
1289 (find-files inc ".*mod"))
1290 (for-each (lambda (file)
1292 (string-append fex "/" (basename file))))
1293 (find-files ex ".*"))
1294 (delete-file-recursively ex))
1296 (home-page "https://www.hdfgroup.org")
1297 (synopsis "Management suite for extremely large and complex data")
1298 (description "HDF5 is a suite that makes possible the management of
1299 extremely large and complex data collections.")
1300 (license (license:x11-style
1301 "https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
1303 (define-public hdf5-1.10
1310 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
1311 "hdf5-" (version-major+minor version)
1312 "/hdf5-" version "/src/hdf5-"
1314 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
1316 (apply string-append
1317 (take (string-split version #\.) 2))
1318 "/src/hdf5-" version ".tar.bz2")))
1320 (base32 "0pm5xxry55i0h7wmvc7svzdaa90rnk7h78rrjmnlkz2ygsn8y082"))
1321 (patches (search-patches "hdf5-config-date.patch"))))))
1323 (define-public hdf5-1.12
1330 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
1331 "hdf5-" (version-major+minor version)
1332 "/hdf5-" version "/src/hdf5-"
1334 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
1336 (apply string-append
1337 (take (string-split version #\.) 2))
1338 "/src/hdf5-" version ".tar.bz2")))
1340 (base32 "074g3z504xf77ff38igs30i1aqxpm508p7yw78ykva7dncrgbyda"))
1341 (patches (search-patches "hdf5-config-date.patch"))))))
1344 ;; Default version of HDF5.
1347 (define-public hdf-java
1355 "https://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
1356 version "/src/CMake-hdfjava-" version ".tar.gz"))
1358 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
1359 (modules '((guix build utils)))
1360 (snippet ; Make sure we don't use the bundled sources and binaries.
1362 (for-each delete-file
1363 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
1364 "HDF4.tar.gz" "HDF5.tar.gz"))
1365 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
1367 (build-system gnu-build-system)
1369 `(("jdk" ,icedtea "jdk")
1370 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
1372 ("hamcrest-core" ,java-hamcrest-core)
1373 ("junit" ,java-junit)
1374 ("slf4j-simple" ,java-slf4j-simple)))
1379 ("libjpeg" ,libjpeg-turbo)
1380 ("slf4j-api" ,java-slf4j-api)))
1383 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
1384 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
1385 (assoc-ref %build-inputs "jdk") "/lib" )
1386 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
1387 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
1390 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
1391 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
1392 (string-append "ZLIB=" (search-input-file %build-inputs "/lib/libz.so"))
1393 (string-append "JPEGLIB="
1394 (search-input-file %build-inputs "/lib/libjpeg.so"))
1398 (modify-phases %standard-phases
1399 (add-before 'configure 'chdir-to-source
1400 (lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
1401 (add-before 'configure 'patch-build
1402 (lambda* (#:key inputs outputs #:allow-other-keys)
1403 (substitute* "configure"
1404 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
1405 (("/bin/cat") (which "cat")))
1406 ;; Set classpath for compilation
1407 (substitute* '("hdf/hdf5lib/Makefile.in"
1408 "hdf/hdf5lib/exceptions/Makefile.in"
1409 "hdf/hdflib/Makefile.in")
1410 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
1411 ;; 'slf4j-api-X.Y.Z.jar' is installed in a Maven-style
1412 ;; directory, so use 'find-files' to find it.
1413 (car (find-files (assoc-ref inputs "slf4j-api")
1414 "^slf4j-api.*\\.jar$"))))
1415 ;; Replace outdated config.sub and config.guess:
1416 (with-directory-excursion "config"
1417 (for-each (lambda (file)
1419 (search-input-file inputs
1422 ,(version-major+minor (package-version automake))
1425 '("config.sub" "config.guess")))
1427 ;; Fix embedded version number
1428 (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
1429 (substitute* "hdf/hdf5lib/H5.java"
1431 (string-join hdf5version ", "))))
1433 (mkdir-p (string-append (assoc-ref outputs "out")))
1434 ;; Set classpath for tests
1435 (let* ((build-dir (getcwd))
1436 (lib (string-append build-dir "/lib"))
1437 (jhdf (string-append lib "/jhdf.jar"))
1438 (jhdf5 (string-append lib "/jhdf5.jar"))
1442 (car (find-files (assoc-ref inputs i)
1443 (string-append "^" i
1445 '("slf4j-api" "slf4j-simple"))
1447 (car (find-files (assoc-ref inputs "junit") "jar$"))
1448 (car (find-files (assoc-ref inputs "hamcrest-core")
1451 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
1453 (substitute* '("test/hdf5lib/Makefile.in"
1454 "test/hdf5lib/junit.sh.in"
1455 "examples/runExample.sh.in")
1457 (search-input-file inputs "/bin/test"))
1459 (search-input-file inputs "/bin/uname"))
1460 (("CLASSPATH=[^\n]*")
1461 (string-append "CLASSPATH=" class-path)))
1462 (setenv "CLASSPATH" class-path))
1464 (add-before 'check 'build-examples
1466 (apply invoke `("javac"
1467 ,@(find-files "examples" ".*\\.java"))))))
1469 #:parallel-build? #f
1471 #:parallel-tests? #f ))
1472 (home-page "https://support.hdfgroup.org/products/java")
1473 (synopsis "Java interface for the HDF4 and HDF5 libraries")
1474 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
1475 the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
1478 ;; BSD-style license:
1479 (license (license:x11-style
1480 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
1481 /current/src/unpacked/COPYING"))))
1483 (define-public hdf-eos2
1490 (uri "ftp://edhs1.gsfc.nasa.gov\
1491 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
1493 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
1494 (patches (search-patches "hdf-eos2-remove-gctp.patch"
1495 "hdf-eos2-build-shared.patch"
1496 "hdf-eos2-fortrantests.patch"))))
1497 (build-system gnu-build-system)
1499 `(("gfortran" ,gfortran)))
1501 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
1502 ;; XXX: These inputs are really dependencies of hdf4.
1504 ("libjpeg" ,libjpeg-turbo)
1505 ("libtirpc" ,libtirpc)
1509 `( #:configure-flags '("--enable-install-include" "--enable-shared"
1510 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
1511 #:parallel-tests? #f))
1512 (home-page "https://hdfeos.org/software/library.php#HDF-EOS2")
1513 (synopsis "HDF4-based data format for NASA's Earth Observing System")
1514 (description "HDF-EOS2 is a software library built on HDF4 which supports
1515 the construction of data structures used in NASA's Earth Observing
1516 System (Grid, Point and Swath).")
1518 ;; Source files carry a permissive license header.
1519 (license (license:non-copyleft home-page))))
1521 (define-public hdf-eos5
1527 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1528 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1531 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1532 (patches (search-patches "hdf-eos5-build-shared.patch"
1533 "hdf-eos5-remove-gctp.patch"
1534 "hdf-eos5-fix-szip.patch"
1535 "hdf-eos5-fortrantests.patch"))))
1537 `(("gfortran" ,gfortran)))
1538 (build-system gnu-build-system)
1540 `(("hdf5" ,hdf5-1.8)
1544 `(#:configure-flags '("--enable-install-include" "--enable-shared"
1545 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1546 #:parallel-tests? #f))
1547 (synopsis "HDF5-based data format for NASA's Earth Observing System")
1549 "HDF-EOS5 is a software library built on HDF5 to support the construction
1550 of data structures used in NASA's Earth Observing System (Grid, Point and
1552 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1554 ;; Source files carry a permissive license header.
1555 (license (license:non-copyleft home-page))))
1557 (define-public hdf5-parallel-openmpi
1558 (package/inherit hdf5-1.10 ;use the latest
1559 (name "hdf5-parallel-openmpi")
1562 ,@(package-inputs hdf5)))
1564 (substitute-keyword-arguments (package-arguments hdf5)
1565 ((#:configure-flags flags)
1566 ``("--enable-parallel"
1567 ,@(delete "--enable-cxx"
1568 (delete "--enable-threadsafe" ,flags))))
1570 `(modify-phases ,phases
1571 (add-after 'build 'mpi-setup
1573 (add-before 'check 'patch-tests
1575 ;; OpenMPI's mpirun will exit with non-zero status if it
1576 ;; detects an "abnormal termination", i.e. any process not
1577 ;; calling MPI_Finalize(). Since the test is explicitly
1578 ;; avoiding MPI_Finalize so as not to have at_exit and thus
1579 ;; H5C_flush_cache from being called, mpirun will always
1580 ;; complain, so turn this test off.
1581 (substitute* "testpar/Makefile"
1582 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1583 (string-append front back "\n")))
1584 (substitute* "tools/test/h5diff/testph5diff.sh"
1585 (("/bin/sh") (which "sh")))
1587 (synopsis "Management suite for data with parallel IO support")))
1589 (define-public hdf5-blosc
1597 (url "https://github.com/Blosc/hdf5-blosc")
1598 (commit (string-append "v" version))))
1599 (file-name (git-file-name name version))
1601 (base32 "1nj2bm1v6ymm3fmyvhbn6ih5fgdiapavlfghh1pvbmhw71cysyqs"))))
1602 (build-system cmake-build-system)
1605 (list (string-append "-DBLOSC_INSTALL_DIR="
1606 (assoc-ref %build-inputs "c-blosc"))
1607 (string-append "-DPLUGIN_INSTALL_PATH="
1608 (assoc-ref %outputs "out")
1609 "/hdf5/lib/plugin"))
1611 (modify-phases %standard-phases
1612 (add-after 'unpack 'do-not-build-blosc
1614 (substitute* "CMakeLists.txt"
1615 (("set\\(BLOSC_INSTALL_DIR.*") "")
1616 (("ExternalProject_Add\\(project_blosc") "message("))
1619 `(("c-blosc" ,c-blosc)
1620 ("hdf5" ,hdf5-1.10)))
1621 (home-page "https://github.com/Blosc/hdf5-blosc")
1622 (synopsis "Filter for HDF5 using the Blosc compressor")
1623 (description "This is a filter for HDF5 that uses the Blosc compressor; by
1624 installing this filter, you can read and write HDF5 files with
1625 Blosc-compressed datasets.")
1626 (license license:expat)))
1628 (define-public h5check
1635 (uri (string-append "https://www.hdfgroup.org/ftp/HDF5/tools/"
1636 "h5check/src/h5check-" version ".tar.gz"))
1639 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1640 (build-system gnu-build-system)
1641 (inputs `(("hdf5" ,hdf5-1.8))) ;h5cc for tests
1642 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1643 (synopsis "HDF5 format checker")
1644 (description "@code{h5check} is a validation tool for verifying that an
1645 HDF5 file is encoded according to the HDF File Format Specification.")
1646 (license (license:x11-style "file://COPYING"))))
1654 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1659 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1660 (build-system cmake-build-system)
1661 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1662 (inputs `(("lapack" ,lapack)
1664 ;; FIXME: Even though the fonts are available dvips complains:
1665 ;; "Font cmmi10 not found; characters will be left blank."
1667 `(("texlive" ,texlive-tiny)
1668 ("ghostscript" ,ghostscript)
1669 ("doxygen" ,doxygen)))
1670 (home-page "http://itpp.sourceforge.net")
1671 (synopsis "C++ library of maths, signal processing and communication classes")
1672 (description "IT++ is a C++ library of mathematical, signal processing and
1673 communication classes and functions. Its main use is in simulation of
1674 communication systems and for performing research in the area of
1675 communications. The kernel of the library consists of generic vector and
1676 matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1677 similar to MATLAB, GNU Octave or SciPy.")
1678 (license license:gpl3+)))
1680 (define-public netcdf
1688 "https://www.unidata.ucar.edu/downloads/netcdf/ftp/"
1689 "netcdf-c-" version ".tar.gz"))
1692 "1a2fpp15a2rl1m50gcvvzd9y6bavl6vjf9zzf63sz5gdmq06yiqf"))
1693 (modules '((guix build utils)))
1695 ;; Make sure this variable is defined only once. Failing to do so
1696 ;; would break builds of 'netcdf-parallel-openmpi' with a
1697 ;; multiple-definition link error with GCC 10.
1698 '(substitute* "ncdump/ocprint.c"
1699 (("^int ocdebug") "static int ocdebug")))
1700 (patches (search-patches "netcdf-date-time.patch"))))
1701 (build-system gnu-build-system)
1704 ("doxygen" ,doxygen)
1705 ("graphviz" ,graphviz)))
1707 `(("hdf4" ,hdf4-alt)
1711 ("libjpeg" ,libjpeg-turbo)))
1713 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
1715 #:phases (modify-phases %standard-phases
1716 (add-before 'configure 'fix-source-date
1718 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1719 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1720 ;; to '1st hour of the current day', and therefore makes the
1721 ;; package not reproducible.
1722 (substitute* "./configure"
1723 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1724 "date --date='@0'"))
1726 (add-after 'configure 'patch-settings
1728 ;; libnetcdf.settings contains the full filename of the compilers
1729 ;; used to build the library. We truncate the hashes of those
1730 ;; filenames to avoid unnecessary references to the corresponding
1732 (substitute* "libnetcdf.settings"
1733 (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash)
1734 (string-append prefix (string-take hash 10) "...")))
1737 #:parallel-tests? #f)) ;various race conditions
1738 (home-page "https://www.unidata.ucar.edu/software/netcdf/")
1739 (synopsis "Library for scientific data")
1740 (description "NetCDF is an interface for scientific data access and a
1741 software library that provides an implementation of the interface. The netCDF
1742 library defines a machine-independent format for representing scientific data.
1743 Together, the interface, library, and format support the creation, access, and
1744 sharing of scientific data.")
1745 (license (license:x11-style "file://COPYRIGHT"))))
1747 (define-public netcdf-parallel-openmpi
1748 (package (inherit netcdf)
1749 (name "netcdf-parallel-openmpi")
1752 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1753 (package-inputs netcdf))))
1754 ;; TODO: Replace pkg-config references in nc-config with absolute references
1756 (substitute-keyword-arguments (package-arguments netcdf)
1757 ((#:configure-flags flags)
1758 `(cons* "CC=mpicc" "CXX=mpicxx"
1759 "--enable-parallel-tests"
1760 ;; Shared libraries not supported with parallel IO.
1761 "--disable-shared" "--with-pic"
1763 ((#:phases phases '%standard-phases)
1764 `(modify-phases ,phases
1765 (add-after 'build 'mpi-setup
1766 ,%openmpi-setup)))))))
1768 (define-public netcdf-fortran
1770 (name "netcdf-fortran")
1775 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1779 "0x4acvfhbsx1q79dkkwrwbgfhm0w5ngnp4zj5kk92s1khihmqfhj"))))
1780 (build-system gnu-build-system)
1782 `(#:configure-flags '("FCFLAGS=-fallow-argument-mismatch"
1783 "FFLAGS=-fallow-argument-mismatch")
1784 #:parallel-tests? #f))
1786 `(("netcdf" ,netcdf)))
1788 `(("gfortran" ,gfortran)))
1789 (synopsis "Fortran interface for the netCDF library")
1790 (description (package-description netcdf))
1791 (home-page (package-home-page netcdf))
1792 (license (package-license netcdf))))
1794 (define-public nlopt
1800 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1803 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1804 (build-system gnu-build-system)
1806 `(;; Shared libraries are not built by default. They are required to
1807 ;; build the Guile, Octave, and Python bindings.
1808 #:configure-flags '("--enable-shared")
1811 (modify-phases %standard-phases
1812 (add-before 'configure 'set-libnlopt-file-name
1813 (lambda* (#:key outputs #:allow-other-keys)
1814 ;; Make sure the Scheme module refers to the library by its
1815 ;; absolute file name (we cannot do that from a snippet
1816 ;; because the expansion of @libdir@ contains
1818 (let ((out (assoc-ref outputs "out")))
1819 (substitute* "swig/nlopt.scm.in"
1821 (string-append out "/lib/libnlopt")))
1823 (inputs `(("guile" ,guile-2.0)))
1824 (native-inputs `(("pkg-config" ,pkg-config)))
1825 (home-page "http://ab-initio.mit.edu/wiki/")
1826 (synopsis "Library for nonlinear optimization")
1827 (description "NLopt is a library for nonlinear optimization, providing a
1828 common interface for a number of different free optimization routines available
1829 online as well as original implementations of various other algorithms.")
1830 (license license:lgpl2.1+)))
1832 (define-public ipopt
1839 (url "https://github.com/coin-or/Ipopt")
1840 (commit (string-append "releases/" version))))
1841 (file-name (git-file-name name version))
1844 "08gznhwhqv1x4baksz350ih8q16r5rd0k8vals6078m3h94khr4b"))))
1845 (build-system gnu-build-system)
1847 '(#:phases (modify-phases %standard-phases
1848 (add-after 'install 'add--L-flags-in-ipopt.pc
1849 (lambda* (#:key inputs outputs #:allow-other-keys)
1850 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1851 ;; move it to "Libs.private" where it belongs, and add a
1852 ;; '-L' flag for LAPACK.
1853 (let ((out (assoc-ref outputs "out"))
1854 (lapack (assoc-ref inputs "lapack")))
1855 (substitute* (string-append out "/lib/pkgconfig/"
1857 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1858 (string-append "Libs: " before " " after "\n"
1859 "Libs.private: " before
1860 "-L" lapack "/lib -llapack -lblas "
1864 `(("gfortran" ,gfortran)
1865 ("pkg-config" ,pkg-config)))
1867 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
1868 `(("lapack" ,lapack))) ;for both libblas and liblapack
1869 (home-page "https://www.coin-or.org")
1870 (synopsis "Large-scale nonlinear optimizer")
1872 "The Interior Point Optimizer (IPOPT) is a software package for
1873 large-scale nonlinear optimization. It provides C++, C, and Fortran
1875 (license license:epl2.0)))
1877 (define-public nomad-optimizer
1879 (name "nomad-optimizer")
1885 (url "https://github.com/bbopt/nomad/")
1886 (commit (string-append "v" version))))
1887 (file-name (git-file-name name version))
1890 "0w386d8r5ldbvnv0c0g7vz95pfpvwdxis26vaalk2amsa5akl775"))))
1891 (build-system cmake-build-system)
1893 `(("python" ,python-wrapper)
1894 ("python-cython" ,python-cython)))
1896 `(#:imported-modules ((guix build python-build-system)
1897 ,@%cmake-build-system-modules)
1898 #:modules (((guix build python-build-system)
1899 #:select (python-version site-packages))
1900 (guix build cmake-build-system)
1903 '("-DBUILD_INTERFACES=ON"
1906 (modify-phases %standard-phases
1907 (add-after 'unpack 'fix-sources-for-build
1908 (lambda* (#:key outputs #:allow-other-keys)
1909 (substitute* "CMakeLists.txt"
1910 ;; CMAKE_INSTALL_PREFIX is accidentally hardcoded.
1911 (("set\\(CMAKE_INSTALL_PREFIX .* FORCE\\)") "")
1912 ;; Requiring GCC version 8 or later is unwarranted.
1913 (("message\\(FATAL_ERROR \"GCC version < 8")
1914 "message(STATUS \"GCC version < 8"))
1916 (let ((out (assoc-ref outputs "out")))
1917 (substitute* "interfaces/PyNomad/CMakeLists.txt"
1918 ;; We don't want to build in-place, and anyway the install
1919 ;; command further below runs build_ext as a prerequisite.
1920 (("COMMAND python setup_PyNomad\\.py .* build_ext --inplace\n")
1922 ;; Don't install locally.
1923 (("COMMAND python (setup_PyNomad\\.py .* install) --user\n"
1925 (string-append "COMMAND ${CMAKE_COMMAND} -E env"
1926 " CC=" ,(cc-for-target)
1927 " CXX=" ,(cxx-for-target)
1928 " " (which "python")
1932 ;; Fix erroneous assumptions about the paths of the include and
1933 ;; library directories.
1934 (substitute* "interfaces/PyNomad/setup_PyNomad.py"
1935 (("^( +os_include_dirs = ).*" _ prefix)
1936 (string-append prefix "[\"../../src\"]\n"))
1937 (("^(installed_lib_dir = ).*" _ prefix)
1938 (string-append prefix "\"" out "/lib\"\n"))))
1941 ;; Fix the tests so they run in out-of-source builds.
1942 (add-after 'fix-sources-for-build 'fix-sources-for-tests
1945 (map (lambda (d) (string-append "examples/" d "/CMakeLists.txt"))
1947 (map (lambda (d) (string-append "basic/library/" d))
1948 '("example1" "example2" "example3"
1949 "single_obj_parallel"))
1950 (map (lambda (d) (string-append "advanced/library/" d))
1951 '("FixedVariable" "NMonly" "PSDMads" "Restart"
1952 "c_api/example1" "c_api/example2"
1953 "exampleSuggestAndObserve"))))
1954 ;; The built examples are assumed to be in the source tree
1955 ;; (which isn't the case here).
1956 (("(COMMAND \\$\\{CMAKE_BINARY_DIR\\}/examples/runExampleTest\\.sh )\\.(/.*)"
1958 (string-append command "${CMAKE_CURRENT_BINARY_DIR}" test)))
1959 ;; (Unrelated to support for out-of-source testing.)
1961 "examples/advanced/library/exampleSuggestAndObserve/cache0.txt")
1963 (let* ((builddir (string-append (getcwd) "/../build"))
1964 ;; The BB_EXE and SURROGATE_EXE paths are interpreted
1965 ;; relative to the configuration file provided to NOMAD.
1966 ;; However, the configuration files are all in the source
1967 ;; tree rather than in the build tree (unlike the compiled
1969 (fix-exe-path (lambda* (dir #:optional
1972 (substitute* (string-append dir "/" file)
1973 (((string-append "^" exe-opt " +"))
1974 ;; The $ prevents NOMAD from prefixing
1975 ;; the executable with the path of the
1976 ;; parent directory of the configuration
1977 ;; file NOMAD was provided with as
1978 ;; argument (param.txt or some such).
1979 (string-append exe-opt " $"
1980 builddir "/" dir "/"))))))
1983 (let ((dir (string-append "examples/" dir)))
1984 (substitute* (string-append dir "/CMakeLists.txt")
1985 ;; The install phase has not yet run.
1986 (("COMMAND \\$\\{CMAKE_INSTALL_PREFIX\\}/bin/nomad ")
1987 "COMMAND ${CMAKE_BINARY_DIR}/src/nomad "))
1989 (when (equal? dir "examples/basic/batch/surrogate_sort")
1990 (fix-exe-path dir "param.txt" "SURROGATE_EXE"))))
1991 (append (map (lambda (d) (string-append "basic/batch/" d))
1992 '("example1" "example2"
1993 "single_obj" "single_obj_parallel"
1995 '("advanced/batch/LHonly")))
1997 (let ((dir "examples/advanced/batch/FixedVariable"))
1998 (substitute* (string-append dir "/runFixed.sh")
1999 ;; Hardcoded path to NOMAD executable.
2000 (("^\\.\\./\\.\\./\\.\\./\\.\\./bin/nomad ")
2001 (string-append builddir "/src/nomad ")))
2003 (lambda (f) (fix-exe-path dir f))
2004 '("param1.txt" "param2.txt" "param3.txt" "param10.txt"))))
2007 ;; The information in the .egg-info file is not kept up to date.
2008 (add-after 'install 'delete-superfluous-egg-info
2009 (lambda* (#:key inputs outputs #:allow-other-keys)
2010 (delete-file (string-append
2011 (site-packages inputs outputs)
2013 (python-version (assoc-ref inputs "python"))
2016 (home-page "https://www.gerad.ca/nomad/")
2017 (synopsis "Nonlinear optimization by mesh-adaptive direct search")
2019 "NOMAD is a C++ implementation of the mesh-adaptive direct search (MADS)
2020 algorithm, designed for difficult blackbox optimization problems. These
2021 problems occur when the functions defining the objective and constraints are
2022 the result of costly computer simulations.")
2023 (license license:lgpl3+)))
2031 (uri (string-append "https://www.coin-or.org/download/source/"
2032 "Cbc/Cbc-" version ".tgz"))
2035 "0wk9vr6zc62gw71v7gnra5wxqlcljcgbhm5lasx236v791b986ns"))
2036 (modules '((guix build utils)))
2038 ;; Make sure we don't use the bundled software.
2039 '(delete-file-recursively "ThirdParty"))))
2040 (build-system gnu-build-system)
2042 `(("gfortran" ,gfortran)
2043 ("pkg-config" ,pkg-config)))
2045 `(("openblas" ,openblas)))
2046 (home-page "https://www.coin-or.org")
2047 (synopsis "Branch-and-cut solver")
2049 "Cbc (Coin-or branch and cut) is a mixed integer linear programming
2050 solver written in C++. It can be used as a library or as a standalone
2052 (license license:epl1.0)))
2060 (uri (string-append "https://www.coin-or.org/download/source/"
2061 "Clp/Clp-" version ".tgz"))
2064 "0ap1f0lxppa6pnbc4bg7ih7a96avwaki482nig8w5fr3vg9wvkzr"))
2065 (modules '((guix build utils)))
2067 ;; Make sure we don't use the bundled software.
2069 (delete-file-recursively "ThirdParty")
2071 (build-system gnu-build-system)
2073 `(("gfortran" ,gfortran)
2074 ("pkg-config" ,pkg-config)))
2076 `(("openblas" ,openblas)))
2077 (home-page "https://www.coin-or.org")
2078 (synopsis "Linear programming solver")
2080 "CLP is a high quality linear programming solver. Its main strengths are
2081 its dual and primal Simplex algorithms. It also has a barrier algorithm for
2082 linear and quadratic objectives. There are limited facilities for nonlinear
2083 and quadratic objectives using the Simplex algorithm.")
2084 (license license:epl1.0)))
2086 (define-public gecode
2093 (url "https://github.com/Gecode/gecode")
2094 (commit (string-append "release-" version))))
2095 (file-name (git-file-name name version))
2098 "0b1cq0c810j1xr2x9y9996p894571sdxng5h74py17c6nr8c6dmk"))
2099 (modules '((guix build utils)))
2102 ;; delete generated sources
2103 (for-each delete-file
2104 '("gecode/kernel/var-imp.hpp"
2105 "gecode/kernel/var-type.hpp"))))))
2106 (outputs '("out" "examples"))
2107 (build-system gnu-build-system)
2110 (list (string-append "GLDFLAGS=-Wl,-rpath="
2111 (assoc-ref %outputs "out")
2113 "--enable-examples=no")
2114 #:modules ((guix build gnu-build-system)
2119 (modify-phases %standard-phases
2120 (add-after 'build 'build-examples
2121 (lambda* (#:key outputs #:allow-other-keys)
2122 (invoke "make" "compileexamples")))
2123 ;; The Makefile disrespects GLDFLAGS for some reason, so we have to
2124 ;; patch it ourselves... *sigh*
2125 (add-after 'install 'fix-rpath
2126 (lambda* (#:key outputs #:allow-other-keys)
2127 (let ((libdir (string-append (assoc-ref outputs "out") "/lib")))
2130 (let* ((pipe (open-pipe* OPEN_READ "patchelf"
2131 "--print-rpath" file))
2132 (line (read-line pipe)))
2133 (and (zero? (close-pipe pipe))
2134 (invoke "patchelf" "--set-rpath"
2135 (string-append libdir ":" line)
2137 (find-files libdir ".*\\.so$")))))
2138 (add-after 'install 'install-examples
2139 (lambda* (#:key outputs #:allow-other-keys)
2140 (invoke "make" "installexamples"
2141 (string-append "bindir=" (assoc-ref outputs "examples")
2143 ;; Tests depend on installed libraries.
2145 (add-after 'fix-rpath 'check
2146 (assoc-ref %standard-phases 'check)))))
2148 `(("patchelf" ,patchelf)
2151 (home-page "https://www.gecode.org")
2152 (synopsis "Toolkit for developing constraint-based systems")
2153 (description "Gecode is a C++ toolkit for developing constraint-based
2154 systems and applications. It provides a modular and extensible solver.")
2155 (license license:expat)))
2157 (define-public libflame
2161 (outputs '("out" "static"))
2166 (url "https://github.com/flame/libflame")
2168 (file-name (git-file-name name version))
2171 "1n6lf0wvpp77lxqlr721h2jbfbzigphdp19wq8ajiccilcksh7ay"))))
2172 (build-system gnu-build-system)
2175 ;; Sensible defaults: https://github.com/flame/libflame/issues/28
2176 (list "--enable-dynamic-build"
2177 "--enable-max-arg-list-hack"
2178 "--enable-lapack2flame"
2179 "--enable-verbose-make-output"
2180 "--enable-multithreading=pthreads" ; Openblas isn't built with openmp.
2181 ,@(if (any (cute string-prefix? <> (or (%current-target-system)
2184 '("--enable-vector-intrinsics=sse")
2186 "--enable-supermatrix"
2187 "--enable-memory-alignment=16"
2188 "--enable-ldim-alignment")
2190 (modify-phases %standard-phases
2191 (add-after 'unpack 'patch-/usr/bin/env-bash
2193 (substitute* "build/config.mk.in"
2194 (("/usr/bin/env bash") (which "bash")))
2197 (lambda* (#:key tests? #:allow-other-keys)
2198 (substitute* "test/Makefile"
2199 (("LIBBLAS .*") "LIBBLAS = -lblas\n")
2200 (("LIBLAPACK .*") "LIBLAPACK = -llapack\n"))
2202 (with-directory-excursion "test"
2205 (invoke "./test_libflame.x"))
2207 (add-after 'install 'install-static
2208 (lambda* (#:key outputs #:allow-other-keys)
2209 (let ((out (assoc-ref outputs "out"))
2210 (static (assoc-ref outputs "static")))
2211 (mkdir-p (string-append static "/lib"))
2212 (rename-file (string-append out "/lib/libflame.a")
2213 (string-append static "/lib/libflame.a"))
2214 (install-file (string-append out "/include/FLAME.h")
2215 (string-append static "/include"))
2218 `(("gfortran" ,gfortran)))
2220 `(("lapack" ,lapack)
2221 ("openblas" ,openblas)
2223 ("python" ,python-wrapper)))
2224 (home-page "https://github.com/flame/libflame")
2225 (synopsis "High-performance object-based library for DLA computations")
2226 (description "@code{libflame} is a portable library for dense matrix
2227 computations, providing much of the functionality present in LAPACK, developed
2228 by current and former members of the @acronym{SHPC, Science of High-Performance
2229 Computing} group in the @url{https://www.ices.utexas.edu/, Institute for
2230 Computational Engineering and Sciences} at The University of Texas at Austin.
2231 @code{libflame} includes a compatibility layer, @code{lapack2flame}, which
2232 includes a complete LAPACK implementation.")
2233 (license license:bsd-3)))
2235 (define-public libpotassco
2236 ;; No public release, update together with clasp
2237 (let ((revision "1")
2238 (commit "2f9fb7ca2c202f1b47643aa414054f2f4f9c1821"))
2240 (name "libpotassco")
2241 (version (git-version "0.0" revision commit))
2245 (url "https://github.com/potassco/libpotassco")
2247 (file-name (git-file-name name version))
2250 "1c32f9gqclf7qx07lpx8wd720vfhkjqhzc6nyy8mjmgwpmb3iyyn"))))
2252 `(#:configure-flags '("-DLIB_POTASSCO_BUILD_TESTS=on"
2253 "-DLIB_POTASSCO_INSTALL_LIB=on"
2254 "-DBUILD_SHARED_LIBS=on")
2256 (modify-phases %standard-phases
2257 (add-after 'unpack 'patch-cmake
2259 (substitute* "CMakeLists.txt"
2260 ;; clasp expects lowercase potassco and include directory is
2261 ;; lowercase as well, so let's use that
2262 (("\"cmake/Potassco\"") "\"cmake/potassco\"")
2263 (("PotasscoConfig\\.cmake") "potassco-config.cmake")
2264 (("PotasscoConfigVersion\\.cmake")
2265 "potassco-config-version.cmake"))
2266 (rename-file "cmake/PotasscoConfig.cmake.in"
2267 "cmake/potassco-config.cmake.in"))))))
2268 (build-system cmake-build-system)
2269 (home-page "https://potassco.org/")
2270 (synopsis "Utility library for Potassco's projects")
2271 (description "@code{libpotassco} is a utility library providing functions
2274 @item parsing, writing, and converting logic programs in aspif and smodels
2276 @item passing information between a grounder and a solver,
2277 @item and defining and parsing command-line options and for creating
2278 command-line applications.
2280 Furthermore, it comes with the tool @command{lpconvert} that converts either
2281 between aspif and smodels format or to a human-readable text format.")
2282 (license license:expat))))
2284 (define-public clasp
2291 (url "https://github.com/potassco/clasp")
2292 (commit (string-append "v" version))))
2293 (file-name (git-file-name name version))
2296 "0rahqiq530jckvx717858h1q5p8znp1kb6sjm95p8blkr4n3pvmj"))))
2297 (build-system cmake-build-system)
2299 `(#:configure-flags '("-DCLASP_BUILD_TESTS=on"
2300 "-DCLASP_INSTALL_LIB=on"
2301 "-DCLASP_USE_LOCAL_LIB_POTASSCO=off"
2302 "-DBUILD_SHARED_LIBS=on")
2304 (modify-phases %standard-phases
2305 (add-after 'unpack 'patch-cmake
2307 (substitute* "CMakeLists.txt"
2308 ;; Use lowercase to be consistent with libpotassco
2309 (("\"cmake/Clasp\"") "\"cmake/clasp\"")
2310 (("ClaspConfig\\.cmake") "clasp-config.cmake")
2311 (("ClaspConfigVersion\\.cmake")
2312 "clasp-config-version.cmake"))
2313 (substitute* "cmake/ClaspConfig.cmake.in"
2314 (("find_package\\(Potassco") "find_package(potassco"))
2315 (rename-file "cmake/ClaspConfig.cmake.in"
2316 "cmake/clasp-config.cmake.in"))))))
2318 `(("libpotassco" ,libpotassco)))
2319 (home-page "https://potassco.org/")
2320 (synopsis "Answer set solver")
2321 (description "clasp is an answer set solver for (extended) normal and
2322 disjunctive logic programs. The primary algorithm of clasp relies on
2323 conflict-driven nogood learning, a technique that proved very successful for
2324 satisfiability checking (SAT).")
2325 (license license:expat)))
2327 (define-public clingo
2334 (url "https://github.com/potassco/clingo")
2335 (commit (string-append "v" version))))
2336 (file-name (git-file-name name version))
2339 "0rfjwkcwm0mmf3r4i7asyjwb6cia4i7px7fn2kdbi9j85qvas4pb"))))
2340 (build-system cmake-build-system)
2342 `(#:configure-flags `("-DCLINGO_BUILD_TESTS=on"
2343 "-DCLINGO_INSTALL_LIB=on"
2344 "-DCLINGO_BUILD_STATIC=off"
2345 "-DCLINGO_BUILD_SHARED=on"
2346 ;; XXX: Clingo requries private headers and
2347 ;; sources from clasp
2349 "-DCLASP_SOURCE_DIR="
2350 (assoc-ref %build-inputs "clasp-src")))
2352 (modify-phases %standard-phases
2353 (add-after 'unpack 'patch-cmake
2355 (substitute* "CMakeLists.txt"
2356 (("add_subdirectory\\(clasp\\)")
2357 "find_package(clasp REQUIRED)"))
2358 (substitute* "libclingo/CMakeLists.txt"
2359 (("\"cmake/Clingo\"") "\"cmake/clingo\"")
2360 (("ClingoConfig\\.cmake") "clingo-config.cmake")
2361 (("ClingoConfigVersion\\.cmake")
2362 "clingo-config-version.cmake"))
2363 (substitute* "cmake/ClingoConfig.cmake.in"
2364 (("find_package\\(Clasp") "find_package(clasp"))
2365 (rename-file "cmake/ClingoConfig.cmake.in"
2366 "cmake/clingo-config.cmake.in")))
2367 (add-after 'unpack 'skip-failing-tests
2369 (with-directory-excursion "libclingo/tests"
2370 (substitute* "CMakeLists.txt"
2371 (("COMMAND test_clingo" all)
2374 "\"${CMAKE_CURRENT_SOURCE_DIR}/good.txt\"")))
2375 (call-with-output-file "good.txt"
2377 (for-each (lambda (test) (format port "~s~%" test))
2378 '("parse-ast-v2" "add-ast-v2" "build-ast-v2"
2379 "unpool-ast-v2" "parse_term"
2380 "propagator" "propgator-sequence-mining"
2381 "symbol" "visitor"))))))))))
2384 ("libpotassco" ,libpotassco)))
2386 `(("clasp-src" ,(package-source clasp))))
2387 (home-page "https://potassco.org/")
2388 (synopsis "Grounder and solver for logic programs")
2389 (description "Clingo computes answer sets for a given logic program.")
2390 (license license:expat)))
2392 (define-public ceres
2394 (name "ceres-solver")
2396 (home-page "http://ceres-solver.org/")
2399 (uri (string-append home-page "ceres-solver-"
2403 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
2404 (build-system cmake-build-system)
2406 ;; TODO: Build HTML user documentation and install separately.
2407 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
2408 "-DBUILD_SHARED_LIBS=ON")
2410 #:phases (modify-phases %standard-phases
2411 (add-before 'configure 'set-library-directory
2413 ;; Install libraries to lib/, not lib64/.
2414 (substitute* "internal/ceres/CMakeLists.txt"
2415 (("set\\(LIB_SUFFIX \"64\"\\)")
2416 "set(LIB_SUFFIX \"\")"))
2419 `(("pkg-config" ,pkg-config)))
2421 `(("glog" ,glog))) ;for #include <glog/glog.h>
2426 ("suitesparse" ,suitesparse)
2427 ("gflags" ,gflags)))
2428 (synopsis "C++ library for solving large optimization problems")
2430 "Ceres Solver is a C++ library for modeling and solving large,
2431 complicated optimization problems. It is a feature rich, mature and
2432 performant library which has been used in production since 2010. Ceres Solver
2433 can solve two kinds of problems:
2435 @item non-linear least squares problems with bounds constraints;
2436 @item general unconstrained optimization problems.
2438 (license license:bsd-3)))
2440 ;; For a fully featured Octave, users are strongly recommended also to install
2441 ;; the following packages: less, ghostscript, gnuplot.
2442 (define-public octave-cli
2449 (uri (string-append "mirror://gnu/octave/octave-"
2453 "06id09zspya24gshcwgp039cp35c06150mdlxysawgnbrhj16wkv"))))
2454 (build-system gnu-build-system)
2456 `(("alsa-lib" ,alsa-lib)
2457 ("arpack" ,arpack-ng)
2463 ("fontconfig" ,fontconfig)
2464 ("freetype" ,freetype)
2468 ("graphicsmagick" ,graphicsmagick)
2470 ;; TODO: libjpeg-turbo is indirectly required through libtiff. In
2471 ;; the next rebuild cycle, add an absolute reference for -ljpeg in
2472 ;; libtiff.la instead of having to provide it here.
2473 ("libjpeg" ,libjpeg-turbo)
2477 ("libsndfile" ,libsndfile)
2481 ("portaudio" ,portaudio)
2483 ("readline" ,readline)
2484 ("suitesparse" ,suitesparse)
2485 ("texinfo" ,texinfo)
2488 `(("gfortran" ,gfortran)
2489 ("pkg-config" ,pkg-config)
2491 ;; The following inputs are not actually used in the build process.
2492 ;; However, the ./configure gratuitously tests for their existence and
2493 ;; assumes that programs not present at build time are also not, and
2494 ;; can never be, available at run time! If these inputs are therefore
2495 ;; not present, support for them will be built out. However, Octave
2496 ;; will still run without them, albeit without the features they
2499 ("ghostscript" ,ghostscript)
2500 ("gnuplot" ,gnuplot)))
2501 ;; Octave code uses this variable to detect directories holding multiple CA
2502 ;; certificates to verify peers with. This is required for the networking
2503 ;; functions that require encryption to work properly.
2504 (native-search-paths
2505 (list (search-path-specification
2506 (variable "CURLOPT_CAPATH")
2507 (files '("etc/ssl/certs")))))
2510 (list (string-append "--with-shell="
2511 (assoc-ref %build-inputs "bash")
2514 ;; XXX: Without this flag, linking octave-cli fails with
2515 ;; undefined references to 'logf@GLIBCXX_3.4' et.al. due to
2516 ;; not pulling in liboctinterp.la for -lstdc++.
2517 "--enable-link-all-dependencies")
2519 (modify-phases %standard-phases
2520 (add-after 'configure 'configure-makeinfo
2521 (lambda* (#:key inputs #:allow-other-keys)
2522 (substitute* "libinterp/corefcn/help.h"
2525 "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
2527 (home-page "https://www.gnu.org/software/octave/")
2528 (synopsis "High-level language for numerical computation (no GUI)")
2529 (description "GNU Octave is a high-level interpreted language that is
2530 specialized for numerical computations. It can be used for both linear and
2531 non-linear applications and it provides great support for visualizing results.
2532 Work may be performed both at the interactive command-line as well as via
2534 (license license:gpl3+)))
2536 (define-public octave
2537 (package (inherit octave-cli)
2540 `(("qscintilla" ,qscintilla)
2542 ,@(package-inputs octave-cli)))
2544 `(("qttools" , qttools) ;for lrelease
2545 ("texlive" ,(texlive-updmap.cfg (list texlive-epsf))) ; for texi2dvi
2546 ,@(package-native-inputs octave-cli)))
2548 (substitute-keyword-arguments (package-arguments octave-cli)
2550 `(modify-phases ,phases
2551 (add-before 'configure 'patch-qscintilla-library-name
2552 (lambda* (#:key inputs #:allow-other-keys)
2553 ;; The QScintilla library that the Octave configure script tries
2554 ;; to link with should be named libqscintilla-qt5.so, but the
2555 ;; QScintilla input provides the shared library as
2556 ;; libqscintilla2_qt5.so.
2557 (substitute* "configure"
2558 (("qscintilla2-qt5")
2561 (synopsis "High-level language for numerical computation (with GUI)")))
2563 (define-public opencascade-oce
2565 (name "opencascade-oce")
2571 (url "https://github.com/tpaviot/oce")
2572 (commit (string-append "OCE-" version))))
2573 (file-name (git-file-name name version))
2574 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
2576 (base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69"))))
2577 (build-system cmake-build-system)
2580 (list "-DOCE_TESTING:BOOL=ON"
2581 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
2582 "-DOCE_DRAW:BOOL=ON"
2583 (string-append "-DOCE_INSTALL_PREFIX:PATH="
2584 (assoc-ref %outputs "out"))
2585 "-UCMAKE_INSTALL_RPATH")))
2587 `(("freetype" ,freetype)
2594 `(("python" ,python-wrapper)))
2595 (home-page "https://github.com/tpaviot/oce")
2596 (synopsis "Libraries for 3D modeling and numerical simulation")
2598 "Open CASCADE is a set of libraries for the development of applications
2599 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
2600 C++ class libraries providing services for 3D surface and solid modeling, CAD
2601 data exchange, and visualization. It is used for development of specialized
2602 software dealing with 3D models in design (CAD), manufacturing (CAM),
2603 numerical simulation (CAE), measurement equipment (CMM), and quality
2604 control (CAQ) domains.
2606 This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
2607 patches, improvements, and experiments contributed by users over the official
2608 Open CASCADE library.")
2609 (license (list license:lgpl2.1; OCE libraries, with an exception for the
2610 ; use of header files; see
2611 ; OCCT_LGPL_EXCEPTION.txt
2612 license:public-domain; files
2613 ; src/Standard/Standard_StdAllocator.hxx and
2614 ; src/NCollection/NCollection_StdAllocator.hxx
2615 license:expat; file src/OpenGl/OpenGl_glext.h
2616 license:bsd-3)))); test framework gtest
2618 (define-public opencascade-occt
2620 (name "opencascade-occt")
2626 (url "https://git.dev.opencascade.org/repos/occt.git")
2629 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
2631 (file-name (git-file-name name version))
2633 (base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4"))
2634 (modules '((guix build utils)))
2637 ;; Remove files specific to non-free operating systems.
2638 (delete-file-recursively "samples/ios")
2639 (delete-file-recursively "samples/mfc")
2640 (delete-file-recursively "samples/qt/FuncDemo")
2641 (delete-file "genconf.bat")
2642 (delete-file "gendoc.bat")
2643 (delete-file "genproj.bat")
2644 (delete-file "upgrade.bat")
2645 ;; Remove references to deleted files.
2646 (substitute* "dox/FILES_HTML.txt"
2647 ((".*standard.*") "" )
2648 ((".*UIKitSample.*") ""))
2650 (build-system cmake-build-system)
2652 '(;; There is no test target for make. OCCT provides an
2653 ;; 'Automated Testing System', which may be accessed after
2654 ;; installation via the draw.sh script. draw.sh is located in
2655 ;; the bin directory. For details see:
2656 ;; https://www.opencascade.com/doc/occt-7.3.0/overview/html/\
2657 ;; occt_dev_guides__tests.html
2659 ;; Configure without freeimage: attempting to link against the
2660 ;; freeimage version 3.17 library leads to 'undefined
2661 ;; reference' errors.
2663 (list "-DUSE_FREEIMAGE:BOOL=OFF"
2665 "-DUSE_VTK:BOOL=OFF"
2666 "-DBUILD_DOC_Overview:BOOL=OFF"
2667 "-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON"
2668 "-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON"
2669 "-UCMAKE_INSTALL_LIBDIR")))
2671 `(("doxygen" ,doxygen)
2672 ;("freeimage" ,freeimage)
2673 ("freetype" ,freetype)
2675 ("libxext" ,libxext)
2682 ;; TODO: build Overview documentation and add 'doc' output.
2683 (home-page "https://www.opencascade.com")
2684 (synopsis "Libraries for 3D modeling and numerical simulation")
2686 "Open CASCADE is a set of libraries for the development of applications
2687 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
2688 C++ class libraries providing services for 3D surface and solid modeling, CAD
2689 data exchange, and visualization. It is used for development of specialized
2690 software dealing with 3D models in design (CAD), manufacturing (CAM),
2691 numerical simulation (CAE), measurement equipment (CMM), and quality
2692 control (CAQ) domains.
2694 This is the certified version of the Open Cascade Technology (OCCT) library.")
2695 (license (list ;; OCCT library:
2696 license:lgpl2.1; with an exception for the use of header
2697 ; files, see OCCT_LGPL_EXCEPTION.txt.
2698 ;; Files src/OpenGl/glext.h, adm/cmake/cotire.cmake and
2699 ;; src/OpenGl/OpenGl_HaltonSampler.hxx:
2701 ;; Files src/ExprIntrp/ExprIntrp.tab.* and
2702 ;; src/StepFile/step.tab.*:
2703 license:gpl3+ ; with Bison 2.2 exception.
2704 ;; File src/NCollection/NCollection_UtfIterator.lxx:
2705 (license:non-copyleft
2706 "https://www.unicode.org/license.html")
2707 ;; File src/NCollection/NCollection_StdAllocator.hxx:
2708 license:public-domain))))
2718 (url "https://gitlab.onelab.info/gmsh/gmsh.git")
2720 (string-append "gmsh_"
2721 (string-replace-substring version "." "_")))))
2722 (file-name (git-file-name name version))
2724 (base32 "07mi6ja3b9libgcdp2b4dwnkap1b9ha2wi2zdn9mhmwvp3g1pxhp"))
2725 (modules '((guix build utils)))
2728 (delete-file-recursively "contrib/metis")
2730 (build-system cmake-build-system)
2733 ("gfortran" ,gfortran)
2739 ("libxext" ,libxext)
2742 ("opencascade-occt" ,opencascade-occt)))
2744 `(("fontconfig" ,fontconfig)
2746 ("python" ,python)))
2748 `(#:configure-flags `("-DENABLE_SYSTEM_CONTRIB:BOOL=ON"
2749 "-DENABLE_BUILD_SHARED:BOOL=ON"
2750 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")
2751 #:imported-modules (,@%cmake-build-system-modules
2752 (guix build python-build-system))
2753 #:modules (((guix build python-build-system) #:select (site-packages))
2754 (guix build cmake-build-system)
2757 (modify-phases %standard-phases
2758 (add-after 'unpack 'patch-paths
2759 (lambda* (#:key inputs outputs #:allow-other-keys)
2760 ;; Use the standard Guix site-package path for
2761 ;; installation of the Python API.
2762 (substitute* "CMakeLists.txt"
2763 (("include\\(GNUInstallDirs\\)\n")
2764 (string-append "include(GNUInstallDirs)\n"
2766 (site-packages inputs outputs) ")\n"))
2767 (("\\$\\{GMSH\\_PY\\} DESTINATION \\$\\{GMSH\\_LIB\\}")
2768 "${GMSH_PY} DESTINATION ${GMSH_PY_LIB}"))
2769 ;; Find the shared library.
2770 (let ((libgmsh (string-append (assoc-ref outputs "out")
2771 "/lib/libgmsh.so")))
2772 (substitute* "api/gmsh.py"
2773 (("find_library\\(\"gmsh\"\\)")
2774 (simple-format #f "\"~a\"" libgmsh))))
2776 (home-page "http://gmsh.info/")
2777 (synopsis "3D finite element grid generator")
2778 (description "Gmsh is a 3D finite element grid generator with a built-in
2779 CAD engine and post-processor. Its design goal is to provide a fast, light
2780 and user-friendly meshing tool with parametric input and advanced
2781 visualization capabilities. Gmsh is built around four modules: geometry,
2782 mesh, solver and post-processing. The specification of any input to these
2783 modules is done either interactively using the graphical user interface or in
2784 ASCII text files using Gmsh's own scripting language.")
2785 (license license:gpl2+)))
2787 (define-public veusz
2794 (uri (pypi-uri "veusz" version))
2796 (base32 "1q7hi1qwwg4pgiz62isvv1pia85m13bspdpp1q3mrnwl11in0ag0"))))
2797 (build-system python-build-system)
2799 `(;; Tests will fail because they depend on optional packages like
2800 ;; python-astropy, which is not packaged.
2803 (modify-phases %standard-phases
2804 ;; Veusz will append 'PyQt5' to sip_dir by default. That is not how
2805 ;; the path is defined in Guix, therefore we have to change it.
2806 (add-after 'unpack 'fix-sip-dir
2808 (substitute* "pyqtdistutils.py"
2809 (("os.path.join\\(sip_dir, 'PyQt5'\\)") "sip_dir"))
2811 ;; Now we have to pass the correct sip_dir to setup.py.
2813 (lambda* (#:key inputs #:allow-other-keys)
2814 ;; We need to tell setup.py where to locate QtCoremod.sip
2815 ((@@ (guix build python-build-system) call-setuppy)
2817 (list (string-append "--sip-dir="
2818 (assoc-ref inputs "python-pyqt")
2821 ;; Ensure that icons are found at runtime.
2822 (add-after 'install 'wrap-executable
2823 (lambda* (#:key inputs outputs #:allow-other-keys)
2824 (let ((out (assoc-ref outputs "out")))
2825 (wrap-program (string-append out "/bin/veusz")
2826 `("QT_PLUGIN_PATH" prefix
2827 ,(list (string-append (assoc-ref inputs "qtsvg")
2828 "/lib/qt5/plugins/"))))))))))
2830 `(("pkg-config" ,pkg-config)
2831 ;;("python-astropy" ,python-astropy) ;; FIXME: Package this.
2832 ("qttools" ,qttools)
2833 ("python-sip" ,python-sip-4)))
2835 `(("ghostscript" ,ghostscript) ;optional, for EPS/PS output
2836 ("python-dbus" ,python-dbus)
2837 ("python-h5py" ,python-h5py) ;optional, for HDF5 data
2838 ("python-pyqt" ,python-pyqt)
2839 ("qtbase" ,qtbase-5)
2842 `(("python-numpy" ,python-numpy)))
2843 (home-page "https://veusz.github.io/")
2844 (synopsis "Scientific plotting package")
2846 "Veusz is a scientific plotting and graphing program with a graphical
2847 user interface, designed to produce publication-ready 2D and 3D plots. In
2848 addition it can be used as a module in Python for plotting. It supports
2849 vector and bitmap output, including PDF, Postscript, SVG and EMF.")
2850 (license license:gpl2+)))
2852 (define-public maxflow
2855 ;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’,
2856 ;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’.
2861 (url "https://github.com/gerddie/maxflow")
2863 (file-name (git-file-name name version))
2866 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
2867 (build-system cmake-build-system)
2868 (home-page "https://pub.ist.ac.at/~vnk/software.html")
2869 (synopsis "Library implementing Maxflow algorithm")
2870 (description "An implementation of the maxflow algorithm described in
2871 @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
2872 Energy Minimization in Computer Vision.\n
2873 Yuri Boykov and Vladimir Kolmogorov.\n
2874 In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
2876 (license license:gpl3+)))
2878 (define-public petsc
2885 ;; The *-lite-* tarball does not contain the *large* documentation
2886 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
2887 "petsc-lite-" version ".tar.gz"))
2889 (base32 "0sm03vpg010q9icidiq587n325m0598cj6hab2rdv85nwyygg74h"))))
2890 (outputs '("out" ; libraries and headers
2891 "examples")) ; ~30MiB of examples
2892 (build-system gnu-build-system)
2894 `(("python" ,python)
2897 `(("gfortran" ,gfortran)
2898 ("openblas" ,openblas)
2899 ("superlu" ,superlu)
2900 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
2901 ;; leaving out opengl, as configuration seems to only be for mac
2905 #:test-target "test"
2906 #:parallel-build? #f ; build is parallel by default
2908 #~(list "--with-mpi=0"
2911 (string-append "--with-openblas-dir="
2912 #$(this-package-input "openblas"))
2915 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
2916 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
2917 #~(list (format #f "MAKE_NP=~a" (parallel-job-count)))
2919 #~(modify-phases %standard-phases
2921 ;; PETSc's configure script is actually a python script, so we can't
2922 ;; run it with bash.
2923 (lambda* (#:key outputs (configure-flags '())
2925 (let* ((prefix (assoc-ref outputs "out"))
2926 (flags `(,(string-append "--prefix=" prefix)
2927 ,@configure-flags)))
2928 (format #t "build directory: ~s~%" (getcwd))
2929 (format #t "configure flags: ~s~%" flags)
2930 (apply invoke "./configure" flags)
2932 ;; Generate test scripts with the right shebang.
2933 (substitute* "config/example_template.py"
2934 (("#!/usr/bin/env bash")
2935 (string-append "#!" (which "bash")))))))
2936 (add-after 'configure 'clean-local-references
2937 (lambda* (#:key outputs #:allow-other-keys)
2938 (let ((out (assoc-ref outputs "out")))
2939 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
2940 ;; Prevent build directory from leaking into compiled code
2942 ;; Scrub timestamp for reproducibility
2943 ((".*Libraries compiled on.*") ""))
2944 (substitute* (find-files "." "petscvariables")
2945 ;; Do not expose build machine characteristics, set to defaults.
2946 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
2947 (("NPMAX = [:digit:]+") "NPMAX = 2")))))
2948 (add-after 'install 'clean-install
2949 ;; Try to keep installed files from leaking build directory names.
2950 (lambda* (#:key inputs outputs #:allow-other-keys)
2951 (let ((out (assoc-ref outputs "out")))
2952 (substitute* (map (lambda (file)
2953 (string-append out "/lib/petsc/conf/" file))
2954 '("petscvariables"))
2956 ;; Make compiler references point to the store
2957 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
2958 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
2959 (string-append "= " (which compiler))))
2960 ;; PETSc installs some build logs, which aren't necessary.
2961 (for-each (lambda (file)
2962 (let ((f (string-append out "/lib/petsc/conf/" file)))
2963 (when (file-exists? f)
2965 '("configure.log" "make.log" "gmake.log"
2966 "test.log" "error.log" "RDict.db"
2967 "PETScBuildInternal.cmake"
2968 ;; Once installed, should uninstall with Guix
2970 (add-after 'install 'move-examples
2971 (lambda* (#:key outputs #:allow-other-keys)
2972 (let* ((out (assoc-ref outputs "out"))
2973 (examples (assoc-ref outputs "examples"))
2974 (exdir (string-append out "/share/petsc/examples"))
2975 (exdir' (string-append examples "/share/petsc/examples")))
2976 (copy-recursively exdir exdir')
2977 (delete-file-recursively exdir)))))))
2978 (home-page "https://www.mcs.anl.gov/petsc")
2979 (synopsis "Library to solve PDEs")
2980 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
2981 data structures and routines for the scalable (parallel) solution of
2982 scientific applications modeled by partial differential equations.")
2983 (license (license:non-copyleft
2984 "https://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
2986 (define-public petsc-complex
2987 (package (inherit petsc)
2988 (name "petsc-complex")
2990 (substitute-keyword-arguments (package-arguments petsc)
2991 ((#:configure-flags cf)
2992 `(cons "--with-scalar-type=complex" ,cf))))
2993 (synopsis "Library to solve PDEs (with complex scalars)")))
2995 (define-public petsc-openmpi
2996 (package (inherit petsc)
2997 (name "petsc-openmpi")
2999 `(("hdf5" ,hdf5-parallel-openmpi)
3000 ("hypre" ,hypre-openmpi)
3002 ("mumps" ,mumps-openmpi)
3003 ("openmpi" ,openmpi)
3004 ("scalapack" ,scalapack)
3005 ("scotch" ,pt-scotch32)
3006 ,@(package-inputs petsc)))
3008 (substitute-keyword-arguments (package-arguments petsc)
3009 ((#:configure-flags cf)
3011 "--with-mpiexec=mpirun"
3014 "--with-scalapack=1"
3016 ,(string-append "--with-mpi-dir="
3017 (assoc-ref %build-inputs "openmpi"))
3018 ,(string-append "--with-hdf5-include="
3019 (assoc-ref %build-inputs "hdf5") "/include")
3020 ,(string-append "--with-hdf5-lib="
3021 (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
3022 ,@(delete "--with-mpi=0" ,cf)))
3024 `(modify-phases ,phases
3025 (add-before 'configure 'mpi-setup
3026 ,%openmpi-setup)))))
3027 (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
3029 (define-public petsc-complex-openmpi
3030 (package (inherit petsc-complex)
3031 (name "petsc-complex-openmpi")
3033 `(("openmpi" ,openmpi)
3034 ,@(package-inputs petsc-complex)))
3036 (substitute-keyword-arguments (package-arguments petsc-complex)
3037 ((#:configure-flags cf)
3038 ``("--with-mpiexec=mpirun"
3039 ,(string-append "--with-mpi-dir="
3040 (assoc-ref %build-inputs "openmpi"))
3041 ,@(delete "--with-mpi=0" ,cf)))
3043 `(modify-phases ,phases
3044 (add-before 'configure 'mpi-setup
3045 ,%openmpi-setup)))))
3046 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
3048 (define-public python-petsc4py
3050 (name "python-petsc4py")
3055 (uri (pypi-uri "petsc4py" version))
3058 "1rm1qj5wlkhxl39by9n78lh3gbmii31wsnb8j1rr5hvfr5xgbx2q"))
3059 (modules '((guix build utils)))
3062 ;; Ensure source file is regenerated in the build phase.
3063 (delete-file "src/petsc4py.PETSc.c")
3064 ;; Remove legacy GC code. See
3065 ;; https://bitbucket.org/petsc/petsc4py/issues/125.
3066 (substitute* "src/PETSc/cyclicgc.pxi"
3067 ((".*gc_refs.*") "" )
3068 ((".*PyGC_Head.*") ""))
3070 (build-system python-build-system)
3073 (modify-phases %standard-phases
3074 (add-before 'build 'pre-build
3076 ;; Define path to PETSc installation.
3077 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
3079 (add-before 'check 'mpi-setup
3082 `(("python-cython" ,python-cython)))
3084 `(("petsc" ,petsc-openmpi)
3085 ("python-numpy" ,python-numpy)))
3086 (home-page "https://bitbucket.org/petsc/petsc4py/")
3087 (synopsis "Python bindings for PETSc")
3088 (description "PETSc, the Portable, Extensible Toolkit for
3089 Scientific Computation, is a suite of data structures and routines for
3090 the scalable (parallel) solution of scientific applications modeled by
3091 partial differential equations. It employs the MPI standard for all
3092 message-passing communication. @code{petsc4py} provides Python
3093 bindings to almost all functions of PETSc.")
3094 (license license:bsd-3)))
3096 (define-public python-kiwisolver
3098 (name "python-kiwisolver")
3102 (uri (pypi-uri "kiwisolver" version))
3105 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
3106 (build-system python-build-system)
3107 (home-page "https://github.com/nucleic/kiwi")
3108 (synopsis "Fast implementation of the Cassowary constraint solver")
3110 "Kiwi is an efficient C++ implementation of the Cassowary constraint
3111 solving algorithm. Kiwi has been designed from the ground up to be
3112 lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
3113 Cassowary solver with typical use cases gaining a 40x improvement. Memory
3114 savings are consistently > 5x.")
3115 (license license:bsd-3)))
3117 (define-public python2-kiwisolver
3118 (package-with-python2 python-kiwisolver))
3120 (define-public slepc
3127 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
3131 "1ysfm77s5fcissv3q0k5d65mlp93zi4anqg62q3cd25dn66sva5i"))))
3132 (build-system gnu-build-system)
3134 `(("python" ,python)
3136 ("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
3138 `(("arpack" ,arpack-ng)
3139 ("gfortran" ,gfortran)))
3141 `(("petsc" ,petsc)))
3143 `(#:parallel-build? #f ;build is parallel by default
3145 `(,(string-append "--with-arpack-dir="
3146 (assoc-ref %build-inputs "arpack") "/lib"))
3147 #:make-flags ;honor (parallel-job-count)
3148 `(,(format #f "MAKE_NP=~a" (parallel-job-count))
3149 ,(string-append "PETSCCONFIGDIR="
3150 (assoc-ref %build-inputs "petsc:examples")
3151 "/share/petsc/examples/config"))
3153 (modify-phases %standard-phases
3155 ;; configure is a python script, so we can't run it with bash.
3156 (lambda* (#:key inputs outputs (configure-flags '())
3158 (let* ((prefix (assoc-ref outputs "out"))
3159 (flags `(,(string-append "--prefix=" prefix)
3160 ,@configure-flags)))
3161 (format #t "build directory: ~s~%" (getcwd))
3162 (format #t "configure flags: ~s~%" flags)
3163 (setenv "SLEPC_DIR" (getcwd))
3164 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
3165 (apply invoke "./configure" flags))))
3166 (add-after 'install 'delete-doc
3167 ;; TODO: SLEPc installs HTML documentation alongside headers in
3168 ;; $out/include. We'd like to move them to share/doc, but delete
3169 ;; them for now, as they are incomplete and installing the complete
3170 ;; documentation is difficult.
3171 (lambda* (#:key outputs #:allow-other-keys)
3172 (let* ((out (assoc-ref outputs "out")))
3173 (for-each delete-file (find-files out "\\.html$"))
3175 (add-after 'install 'clean-install
3176 ;; Clean up unnecessary build logs from installation.
3177 (lambda* (#:key outputs #:allow-other-keys)
3178 (let ((out (assoc-ref outputs "out")))
3179 (for-each (lambda (file)
3180 (let ((f (string-append out "/lib/slepc/conf/" file)))
3181 (when (file-exists? f)
3183 '("configure.log" "make.log" "gmake.log"
3184 "test.log" "error.log" "RDict.db"
3187 (home-page "https://slepc.upv.es")
3188 (synopsis "Scalable library for eigenproblems")
3189 (description "SLEPc is a software library for the solution of large sparse
3190 eigenproblems on parallel computers. It can be used for the solution of
3191 linear eigenvalue problems formulated in either standard or generalized form,
3192 as well as other related problems such as the singular value decomposition.
3193 The emphasis of the software is on methods and techniques appropriate for
3194 problems in which the associated matrices are sparse, for example, those
3195 arising after the discretization of partial differential equations.")
3196 (license license:bsd-2)
3198 `((release-monitoring-url . "http://slepc.upv.es/download/")))))
3200 (define-public slepc-complex
3201 (package (inherit slepc)
3202 (name "slepc-complex")
3204 `(("petsc" ,petsc-complex)
3205 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
3206 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
3208 (define-public slepc-openmpi
3209 (package (inherit slepc)
3210 (name "slepc-openmpi")
3212 (substitute-keyword-arguments (package-arguments slepc)
3213 ((#:phases phases '%standard-phases)
3214 `(modify-phases ,phases
3215 (add-before 'check 'mpi-setup
3216 ,%openmpi-setup)))))
3219 ("arpack" ,arpack-ng-openmpi)
3220 ,@(alist-delete "arpack" (package-inputs slepc))))
3222 `(("petsc" ,petsc-openmpi)
3223 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
3224 (synopsis "Scalable library for eigenproblems (with MPI support)")))
3226 (define-public slepc-complex-openmpi
3227 (package (inherit slepc-openmpi)
3228 (name "slepc-complex-openmpi")
3230 `(("petsc" ,petsc-complex-openmpi)
3231 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
3232 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
3234 (define-public python-slepc4py
3236 (name "python-slepc4py")
3241 (uri (pypi-uri "slepc4py" version))
3244 "1ksp08kxf4wg408b9nn39z3qfhy643j22d4rfbl30vzxk2rxh4lq"))))
3245 (build-system python-build-system)
3248 (modify-phases %standard-phases
3249 (add-before 'build 'pre-build
3251 ;; Define path to PETSc installation.
3252 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
3253 ;; Define path to SLEPc installation.
3254 (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
3256 (add-before 'check 'mpi-setup
3259 `(("python-numpy" ,python-numpy)
3260 ("python-petsc4py" ,python-petsc4py)
3261 ("slepc" ,slepc-openmpi)))
3262 (home-page "https://bitbucket.org/slepc/slepc4py/")
3263 (synopsis "Python bindings for SLEPc")
3264 (description "SLEPc, the Scalable Library for Eigenvalue Problem
3265 Computations, is based on PETSc, the Portable, Extensible Toolkit for
3266 Scientific Computation. It employs the MPI standard for all
3267 message-passing communication. @code{slepc4py} provides Python
3268 bindings to almost all functions of SLEPc.")
3269 (license license:bsd-3)))
3271 (define-public metamath
3279 (url "https://github.com/metamath/metamath-exe")
3280 (commit (string-append "v" version))))
3281 (file-name (git-file-name name version))
3283 (base32 "1s9hyknfvhj86g3giayyf3dxzg23iij0rs7bdvj075v9qbyhqn9b"))))
3284 (build-system gnu-build-system)
3286 `(("autoconf" ,autoconf)
3287 ("automake" ,automake)))
3288 (home-page "http://us.metamath.org/")
3289 (synopsis "Proof verifier based on a minimalistic formalism")
3291 "Metamath is a tiny formal language and that can express theorems in
3292 abstract mathematics, with an accompyaning @command{metamath} executable that
3293 verifies databases of these proofs. There is a public database,
3294 @url{https://github.com/metamath/set.mm, set.mm}, implementing first-order
3295 logic and Zermelo-Frenkel set theory with Choice, along with a large swath of
3296 associated, high-level theorems, e.g.@: the fundamental theorem of arithmetic,
3297 the Cauchy-Schwarz inequality, Stirling's formula, etc. See the Metamath
3299 (license license:gpl2+)))
3301 (define-public minizinc
3308 (url "https://github.com/MiniZinc/libminizinc")
3310 (file-name (git-file-name name version))
3313 "10b2hsl1fx9psh0iagmp8ki3f60f3qg5hmvra5aczjlfmbl88ggp"))
3314 (modules '((guix build utils)
3319 ;; Do not advertise proprietary solvers
3320 (with-directory-excursion "cmake/targets"
3321 (let ((targets '("libminizinc_fzn.cmake"
3322 "libminizinc_gecode.cmake"
3323 "libminizinc_mip.cmake"
3324 "libminizinc_nl.cmake"
3325 "libminizinc_osicbc.cmake"
3326 "libminizinc_parser.cmake"
3330 (for-each delete-file
3333 (member file (cons* "." ".." targets)))
3335 (substitute* "libmzn.cmake"
3336 (("include\\(cmake/targets/(.*)\\)" all target)
3337 (if (member target targets) all "")))))
3338 (with-directory-excursion "include/minizinc/solvers/MIP"
3339 (for-each delete-file
3342 (member file '("." ".."
3343 "MIP_osicbc_solverfactory.hh"
3344 "MIP_osicbc_wrap.hh"
3345 "MIP_solverinstance.hh"
3346 "MIP_solverinstance.hpp"
3349 (with-directory-excursion "solvers/MIP"
3350 (for-each delete-file
3353 (member file '("." ".."
3354 "MIP_osicbc_solverfactory.cpp"
3355 "MIP_osicbc_wrap.cpp"
3356 "MIP_solverinstance.cpp"
3359 (substitute* "CMakeLists.txt"
3360 (("find_package\\(([^ ]*).*\\)" all pkg)
3361 (if (member pkg '("Gecode" "OsiCBC" "Threads"))
3364 ;; TODO: swap out miniz for zlib
3366 (build-system cmake-build-system)
3368 `(#:tests? #f ; no ‘check’ target
3369 #:modules ((guix build cmake-build-system)
3373 (modify-phases %standard-phases
3374 (add-after 'install 'install-solver-configs
3375 (lambda* (#:key inputs outputs #:allow-other-keys)
3376 (let ((gecode (assoc-ref inputs "gecode"))
3377 (pkgdatadir (string-append (assoc-ref outputs "out")
3378 "/share/minizinc")))
3379 (call-with-output-file (string-append pkgdatadir
3380 "/Preferences.json")
3385 [\"\", \"org.gecode.gecode\"],
3386 [\"gecode\", \"org.gecode.gecode\"]
3388 \"solverDefaults\": []
3393 (mkdir-p (string-append pkgdatadir "/solvers"))
3394 (call-with-output-file (string-append pkgdatadir
3395 "/solvers/gecode.msc")
3400 \"id\": \"org.gecode.gecode\",
3401 \"name\": \"Gecode\",
3402 \"description\": \"Gecode FlatZinc executable\",
3406 \"supportsMzn\": false,
3407 \"supportsFzn\": true,
3408 \"needsSolns2Out\": true,
3409 \"needsMznExecutable\": false,
3410 \"needsStdlibDir\": false,
3411 \"isGUIApplication\": false
3413 (last (string-split gecode #\-))
3414 (string-append gecode "/share/gecode/mznlib")
3415 (string-append gecode "/bin/fzn-gecode"))
3416 (newline port)))))))))
3424 (home-page "https://www.minizinc.org")
3425 (synopsis "High-level constraint modeling language")
3426 (description "MiniZinc is a high-level modeling language for constraint
3427 satisfaction and optimization problems. Models are compiled to FlatZinc, a
3428 language understood by many solvers.")
3429 (license license:mpl2.0)))
3431 (define-public mumps
3438 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
3442 "0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r"))
3443 (patches (search-patches "mumps-build-parallelism.patch"
3444 "mumps-shared-libseq.patch"
3445 "mumps-shared-mumps.patch"
3446 "mumps-shared-pord.patch"))))
3447 (build-system gnu-build-system)
3449 `(("fortran" ,gfortran)
3450 ;; These are required for linking against mumps, but we let the user
3451 ;; declare the dependency.
3454 ("scotch" ,scotch)))
3456 `(#:modules ((ice-9 match)
3459 ,@%gnu-build-system-modules)
3461 (modify-phases %standard-phases
3463 (lambda* (#:key inputs #:allow-other-keys)
3464 (call-with-output-file "Makefile.inc"
3475 INCSEQ = -I$(topdir)/libseq
3476 LIBSEQ = $(topdir)/libseq/libmpiseq.a
3477 LIBSEQNEEDED = libseqneeded~;
3481 AR = ar vr # rules require trailing space, ugh...
3484 LIBBLAS = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[
3486 SCALAP = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~]
3487 LIBOTHERS = -pthread
3490 OPTF = -O2 -DALLOW_NON_INIT $(PIC)
3494 LIBS = $(SCALAP) $(LIBSEQ)
3495 LPORDDIR = $(topdir)/PORD/lib
3496 IPORD = -I$(topdir)/PORD/include
3497 LPORD = $(LPORDDIR)/libpord.a
3498 ORDERINGSF = -Dpord~@[
3500 IMETIS = -I$(METISDIR)/include
3501 LMETIS = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
3502 ORDERINGSF += -Dmetis~]~@[~:{
3504 ISCOTCH = -I$(SCOTCHDIR)/include
3505 LSCOTCH = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
3506 ORDERINGSF += ~a~}~]
3507 ORDERINGSC = $(ORDERINGSF)
3508 LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
3509 IORDERINGSF = $(ISCOTCH)
3510 IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
3511 (assoc-ref inputs "mpi")
3512 (assoc-ref inputs "blas")
3513 (assoc-ref inputs "scalapack")
3514 (assoc-ref inputs "metis")
3515 (match (list (assoc-ref inputs "pt-scotch")
3516 (assoc-ref inputs "scotch"))
3520 `((,scotch "" "-Dscotch")))
3523 "-lptesmumps -lptscotch -lptscotcherr "
3524 "-Dptscotch")))))))))
3526 ;; By default only the d-precision library is built. Make with "all"
3527 ;; target so that all precision libraries and examples are built.
3529 (invoke "make" "all"
3530 (format #f "-j~a" (parallel-job-count)))))
3532 ;; Run the simple test drivers, which read test input from stdin:
3533 ;; from the "real" input for the single- and double-precision
3534 ;; testers, and from the "cmplx" input for complex-precision
3535 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
3536 ;; package to prefix execution with "mpirun".
3537 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
3538 (with-directory-excursion "examples"
3541 (let ((tester (apply open-pipe*
3544 ,(string-append "./" prec
3546 (input (open-input-file
3547 (string-append "input_simpletest_" type))))
3549 (dump-port input tester)
3551 (zero? (close-pipe tester)))))
3553 '("real" "real" "cmplx" "cmplx")))))
3555 (lambda* (#:key outputs #:allow-other-keys)
3556 (let* ((out (assoc-ref outputs "out"))
3557 (libdir (string-append out "/lib")))
3558 (copy-recursively "lib" libdir)
3559 (copy-recursively "include" (string-append out "/include"))
3560 (when (file-exists? "libseq/libmpiseq.a")
3561 (install-file "libseq/libmpiseq.a" libdir))
3562 (when (file-exists? "libseq/libmpiseq.so")
3563 (install-file "libseq/libmpiseq.so" libdir))
3565 (home-page "http://mumps.enseeiht.fr")
3566 (synopsis "Multifrontal sparse direct solver")
3568 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
3569 sparse system of linear equations A x = b using Gaussian elimination.")
3570 (license license:cecill-c)))
3572 (define-public mumps-metis
3573 (package (inherit mumps)
3574 (name "mumps-metis")
3576 (alist-delete "scotch" (package-inputs mumps)))))
3578 (define-public mumps-openmpi
3579 (package (inherit mumps)
3580 (name "mumps-openmpi")
3583 ("scalapack" ,scalapack)
3584 ("pt-scotch" ,pt-scotch)
3585 ,@(alist-delete "scotch" (package-inputs mumps))))
3587 (substitute-keyword-arguments (package-arguments mumps)
3589 `(modify-phases ,phases
3590 (add-before 'check 'mpi-setup
3594 ((assoc-ref ,phases 'check)
3595 #:exec-prefix '("mpirun" "-n" "2"))))))))
3596 (synopsis "Multifrontal sparse direct solver (with MPI)")))
3598 (define-public mumps-metis-openmpi
3599 (package (inherit mumps-openmpi)
3600 (name "mumps-metis-openmpi")
3602 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
3604 (define-public ruby-asciimath
3606 (name "ruby-asciimath")
3611 (uri (rubygems-uri "asciimath" version))
3614 "1aapydwwkydbwgz07n7ma3a5jy9n3v0shy6q6j8mi4wr3crhx45a"))))
3615 (build-system ruby-build-system)
3617 `(("ruby-nokogiri" ,ruby-nokogiri)
3618 ("ruby-rspec" ,ruby-rspec)))
3619 (synopsis "AsciiMath parsing and conversion library")
3621 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
3622 easy-to-write markup language for mathematics.")
3623 (home-page "https://github.com/asciidoctor/asciimath")
3624 (license license:expat)))
3626 (define-public superlu
3633 (uri (string-append "https://portal.nersc.gov/project/sparse/superlu/"
3634 "superlu_" version ".tar.gz"))
3636 (base32 "13520vk6fqspyl22cq4ak2jh3rlmhja4czq56j75fdx65fkk80s7"))
3637 (modules '((guix build utils)))
3639 ;; Replace the non-free implementation of MC64 with a stub adapted
3642 (use-modules (ice-9 regex)
3644 (call-with-output-file "SRC/mc64ad.c"
3649 void mc64id_(int *a) {
3650 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
3653 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
3654 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
3655 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
3658 ;; Remove the corresponding license verbiage. MC64 license follows
3659 ;; a "------" line separator.
3660 (with-atomic-file-replacement "License.txt"
3661 (let ((rx (make-regexp "-{8}")))
3664 (let ((line (read-line in 'concat)))
3665 (unless (regexp-exec rx line)
3669 (build-system cmake-build-system)
3673 `(("blas" ,openblas)
3674 ("gfortran" ,gfortran)))
3676 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
3677 "-DTPL_BLAS_LIBRARIES=openblas"
3678 "-DBUILD_SHARED_LIBS:BOOL=YES")))
3679 (home-page "https://portal.nersc.gov/project/sparse/superlu/")
3680 (synopsis "Supernodal direct solver for sparse linear systems")
3682 "SuperLU is a general purpose library for the direct solution of large,
3683 sparse, nonsymmetric systems of linear equations on high performance machines.
3684 The library is written in C and is callable from either C or Fortran. The
3685 library routines perform an LU decomposition with partial pivoting and
3686 triangular system solves through forward and back substitution. The library
3687 also provides threshold-based ILU factorization preconditioners.")
3688 (license (list license:bsd-3
3689 license:gpl2+ ;EXAMPLE/*fgmr.c
3690 (license:fsf-free "file://SRC/colamd.h")))))
3692 (define-public superlu-dist
3694 (name "superlu-dist")
3700 (url "https://github.com/xiaoyeli/superlu_dist")
3701 (commit (string-append "v" version))))
3702 (file-name (git-file-name name version))
3704 (base32 "0fa29yr72p4yq5ln4rgfsawmi5935n4qcr5niz6864bjladz4lql"))
3705 (modules '((guix build utils)))
3707 ;; Replace the non-free implementation of MC64 with a stub
3709 (make-file-writable "SRC/mc64ad_dist.c")
3710 (call-with-output-file "SRC/mc64ad_dist.c"
3715 void mc64id_dist(int *a) {
3716 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
3719 void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
3720 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
3721 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
3724 (substitute* "SRC/util.c" ;adjust default algorithm
3725 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
3726 ;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
3727 ;; general (i.e. non-square) processor-grid support.
3728 "RowPerm = NOROWPERM;"))
3730 (patches (search-patches "superlu-dist-scotchmetis.patch"
3731 "superlu-dist-awpm-grid.patch"))))
3732 (build-system cmake-build-system)
3736 `(("gfortran" ,gfortran)
3739 ("combblas" ,combinatorial-blas)))
3741 `(("mpi" ,openmpi) ;headers include MPI heades
3742 ("parmetis" ,pt-scotch32 "metis")
3743 ("pt-scotch" ,pt-scotch32)))
3745 `(#:parallel-tests? #f ;tests use MPI and OpenMP
3746 #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
3747 "-DTPL_ENABLE_COMBBLASLIB=YES"
3748 "-DTPL_BLAS_LIBRARIES=-lopenblas"
3749 "-DTPL_LAPACK_LIBRARIES=-llapack"
3750 (string-append "-DTPL_PARMETIS_LIBRARIES="
3752 '("ptscotchparmetis" "ptscotch" "ptscotcherr"
3753 "scotchmetis" "scotch" "scotcherr")
3755 (string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
3756 (assoc-ref %build-inputs "parmetis")
3758 "-DTPL_ENABLE_COMBBLASLIB=ON"
3759 (string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
3760 (assoc-ref %build-inputs "combblas")
3761 "/include/CombBLAS;"
3762 (assoc-ref %build-inputs "combblas")
3763 "/include/BipartiteMatchings")
3764 "-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
3766 (modify-phases %standard-phases
3767 (add-before 'configure 'set-c++-standard
3769 (substitute* "CMakeLists.txt"
3770 ;; AWPM headers require C++14
3771 (("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
3772 (add-before 'check 'mpi-setup
3774 (add-before 'check 'omp-setup
3775 (lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
3776 (home-page (package-home-page superlu))
3777 (synopsis "Parallel supernodal direct solver")
3779 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
3780 It is targeted for distributed memory parallel machines. SuperLU_DIST is
3781 implemented in ANSI C, and MPI for communications.")
3782 (license license:bsd-3)))
3784 (define-public scotch
3791 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
3792 "latestfile/298/scotch_" version ".tar.gz"))
3794 (base32 "04dkz24a2g20wq703fnyi4440ac4mwycy9gwrrllljj7zxcjy19r"))
3795 (patches (search-patches "scotch-build-parallelism.patch"
3796 "scotch-integer-declarations.patch"))))
3797 (build-system gnu-build-system)
3803 ("gfortran" ,gfortran)))
3804 (outputs '("out" "metis"))
3806 `(#:make-flags (list (string-append "prefix=" %output))
3808 (modify-phases %standard-phases
3810 'unpack 'chdir-to-src
3811 (lambda _ (chdir "src") #t))
3815 (call-with-output-file "Makefile.inc"
3830 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
3831 LDFLAGS = -lz -lm -lrt -lpthread
3833 LEX = flex -Pscotchyy -olex.yy.c
3838 YACC = bison -pscotchyy -y -b y
3840 '("COMMON_FILE_COMPRESS_GZ"
3842 "COMMON_RANDOM_FIXED_SEED"
3843 "INTSIZE64" ;use 'int64_t'
3844 ;; Prevents symbol clashes with libesmumps
3846 ;; XXX: Causes invalid frees in superlu-dist tests
3848 ;; "SCOTCH_PTHREAD_NUMBER=2"
3849 "restrict=__restrict"))))
3851 (add-after 'build 'build-esmumps
3854 (format #f "-j~a" (parallel-job-count))
3856 (add-before 'install 'make-install-dirs
3857 (lambda* (#:key outputs #:allow-other-keys)
3858 (mkdir (assoc-ref outputs "out"))))
3859 (add-after 'install 'install-metis
3860 (lambda* (#:key outputs #:allow-other-keys)
3861 (let ((out (assoc-ref outputs "metis")))
3863 ;; metis files are not installed with 'make install'
3864 (for-each (lambda (f)
3865 (install-file f (string-append out "/include")))
3866 (find-files "../include/" ".*metis\\.h"))
3867 (for-each (lambda (f)
3868 (install-file f (string-append out "/lib")))
3869 (find-files "../lib/" ".*metis\\..*"))
3871 (home-page "https://www.labri.fr/perso/pelegrin/scotch/")
3873 `((release-monitoring-url . "https://gforge.inria.fr/frs/?group_id=248")))
3874 (synopsis "Programs and libraries for graph algorithms")
3875 (description "SCOTCH is a set of programs and libraries which implement
3876 the static mapping and sparse matrix reordering algorithms developed within
3877 the SCOTCH project. Its purpose is to apply graph theory, with a divide and
3878 conquer approach, to scientific computing problems such as graph and mesh
3879 partitioning, static mapping, and sparse matrix ordering, in application
3880 domains ranging from structural mechanics to operating systems or
3882 ;; See LICENSE_en.txt
3883 (license license:cecill-c)))
3885 (define-public scotch32
3886 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
3887 ;; some applications.
3888 (package (inherit scotch)
3891 (substitute-keyword-arguments (package-arguments scotch)
3892 ((#:phases scotch-phases)
3893 `(modify-phases ,scotch-phases
3897 (call-with-output-file "Makefile.inc"
3912 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
3913 LDFLAGS = -lz -lm -lrt -lpthread
3915 LEX = flex -Pscotchyy -olex.yy.c
3920 YACC = bison -pscotchyy -y -b y
3922 '("COMMON_FILE_COMPRESS_GZ"
3924 "COMMON_RANDOM_FIXED_SEED"
3925 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
3926 ;; Prevents symbolc clashes with libesmumps
3928 ;; XXX: Causes invalid frees in superlu-dist tests
3930 ;; "SCOTCH_PTHREAD_NUMBER=2"
3931 "restrict=__restrict"))))))))))
3933 "Programs and libraries for graph algorithms (32-bit integers)")))
3935 (define-public scotch-shared
3936 (package (inherit scotch)
3937 (name "scotch-shared")
3943 (substitute-keyword-arguments (package-arguments scotch)
3944 ((#:phases scotch-shared-phases)
3945 `(modify-phases ,scotch-shared-phases
3949 ;; Otherwise, the RUNPATH will lack the final path component.
3950 (setenv "RPATHFLAGS" (string-append "-Wl,-rpath="
3951 (assoc-ref %outputs "out") "/lib"))
3952 (call-with-output-file "Makefile.inc"
3960 ARFLAGS = -shared -o
3967 CFLAGS = -O2 -g -fPIC $(CPPFLAGS) $(RPATHFLAGS)
3968 CLIBFLAGS = -shared -fPIC
3969 LDFLAGS = -lz -lm -lrt -lpthread -Xlinker --no-as-needed
3971 LEX = flex -Pscotchyy -olex.yy.c
3976 YACC = bison -pscotchyy -y -b y
3978 '("COMMON_FILE_COMPRESS_GZ"
3980 "COMMON_RANDOM_FIXED_SEED"
3981 "INTSIZE64" ;use 'int64_t'
3982 ;; Prevents symbolc clashes with libesmumps
3984 ;; XXX: Causes invalid frees in superlu-dist tests
3986 ;; "SCOTCH_PTHREAD_NUMBER=2"
3987 "restrict=__restrict"
3991 "Programs and libraries for graph algorithms (shared libraries version)")))
3993 (define-public pt-scotch
3994 (package (inherit scotch)
3997 `(("openmpi" ,openmpi))) ;Headers include MPI headers
3999 (substitute-keyword-arguments (package-arguments scotch)
4000 ((#:phases scotch-phases)
4001 `(modify-phases ,scotch-phases
4005 (invoke "make" (format #f "-j~a" (parallel-job-count))
4006 "ptscotch" "ptesmumps")
4008 ;; Install the serial metis compatibility library
4009 (invoke "make" "-C" "libscotchmetis" "install")))
4010 (add-before 'check 'mpi-setup
4014 (invoke "make" "ptcheck")))))))
4015 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
4017 (define-public pt-scotch32
4018 (package (inherit scotch32)
4019 (name "pt-scotch32")
4021 `(("openmpi" ,openmpi))) ;headers include MPI headers
4023 (substitute-keyword-arguments (package-arguments scotch32)
4024 ((#:phases scotch32-phases)
4025 `(modify-phases ,scotch32-phases
4028 (invoke "make" (format #f "-j~a" (parallel-job-count))
4029 "ptscotch" "ptesmumps")
4030 ;; Install the serial metis compatibility library
4031 (invoke "make" "-C" "libscotchmetis" "install")))
4032 (add-before 'check 'mpi-setup
4036 (invoke "make" "ptcheck")))))))
4038 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
4040 (define-public pt-scotch-shared
4041 (package (inherit scotch-shared)
4042 (name "pt-scotch-shared")
4044 `(("openmpi" ,openmpi))) ;Headers include MPI headers
4046 (substitute-keyword-arguments (package-arguments scotch-shared)
4047 ((#:phases scotch-shared-phases)
4048 `(modify-phases ,scotch-shared-phases
4052 (invoke "make" (format #f "-j~a" (parallel-job-count))
4053 "ptscotch" "ptesmumps")
4055 ;; Install the serial metis compatibility library
4056 (invoke "make" "-C" "libscotchmetis" "install")))
4057 (add-before 'check 'mpi-setup
4058 ,%openmpi-setup)))))
4059 (synopsis "Graph algorithms (shared libraries version, with MPI)")))
4062 (define-public metis
4069 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
4070 "metis-" version ".tar.gz"))
4073 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
4075 `((release-monitoring-url
4076 . "http://glaros.dtc.umn.edu/gkhome/metis/metis/download")))
4077 (build-system cmake-build-system)
4079 `(("blas" ,openblas)))
4081 `(#:tests? #f ;no tests
4082 #:configure-flags `("-DSHARED=ON"
4083 ,(string-append "-DGKLIB_PATH=" (getcwd)
4084 "/metis-" ,version "/GKlib"))))
4085 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
4086 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
4088 "METIS is a set of serial programs for partitioning graphs, partitioning
4089 finite element meshes, and producing fill-reducing orderings for sparse
4090 matrices. The algorithms implemented in METIS are based on the multilevel
4091 recursive-bisection, multilevel k-way, and multi-constraint partitioning
4093 (license license:asl2.0))) ;As of version 5.0.3
4095 (define-public p4est
4102 (uri (string-append "http://p4est.github.io/release/p4est-"
4106 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
4107 (build-system gnu-build-system)
4109 `(("fortran" ,gfortran)
4114 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
4115 (assoc-ref %build-inputs "blas")
4117 ,(string-append "LAPACK_LIBS=-L"
4118 (assoc-ref %build-inputs "lapack")
4120 #:phases (modify-phases %standard-phases
4121 (add-before 'check 'mpi-setup
4123 (home-page "http://www.p4est.org")
4124 (synopsis "Adaptive mesh refinement on forests of octrees")
4126 "The p4est software library enables the dynamic management of a
4127 collection of adaptive octrees, conveniently called a forest of octrees.
4128 p4est is designed to work in parallel and scales to hundreds of thousands of
4130 (license license:gpl2+)))
4132 (define-public p4est-openmpi
4133 (package (inherit p4est)
4134 (name "p4est-openmpi")
4137 ,@(package-inputs p4est)))
4139 (substitute-keyword-arguments (package-arguments p4est)
4140 ((#:configure-flags cf)
4141 ``("--enable-mpi" ,@,cf))))
4142 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
4144 (define-public gsegrafix
4145 ;; This is an old and equally dead "experimental fork" of the longer-dead
4146 ;; original. At least it no longer requires the even-deader libgnomeprint{,ui}
4147 ;; libraries, instead rendering plots with Pango.
4154 (uri (string-append "mirror://savannah/gsegrafix-experimental/"
4155 "gsegrafix-experimental-" version ".tar.gz"))
4157 (base32 "0fwh6719xy2zasmqlp0vdx6kzm45hn37ga88xmw5cz0yx7xw4j6f"))))
4158 (build-system gnu-build-system)
4161 (list "--disable-static")))
4166 `(("pkg-config" ,pkg-config)))
4167 (home-page "https://www.gnu.org/software/gsegrafix/")
4168 (synopsis "GNOME application to create scientific and engineering plots")
4170 "GSEGrafix is an application which produces high-quality graphical
4171 plots for science and engineering. Plots are specified via simple ASCII
4172 parameter files and data files and are presented in an anti-aliased GNOME
4173 canvas. The program supports rectangular two-dimensional plots, histograms,
4174 polar-axis plots and three-dimensional plots. Plots can be printed or saved
4175 to BMP, JPEG or PNG image formats.")
4176 (license license:gpl3+)))
4178 (define-public maxima
4185 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
4186 version "-source/" name "-" version ".tar.gz"))
4189 "1p77nk5sz1qfkn5zr97szpbi8ib4b22k8i52l4ag5gkhd4kid47y"))
4190 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
4191 (build-system gnu-build-system)
4193 `(("bash" ,bash-minimal)
4194 ("gnuplot" ,gnuplot) ;for plots
4197 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
4199 `(("texinfo" ,texinfo)
4201 ("python" ,python)))
4204 ,#~(list "--enable-sbcl"
4205 (string-append "--with-sbcl=" #$sbcl "/bin/sbcl")
4206 (string-append "--with-posix-shell=" #$bash-minimal "/bin/sh")
4207 (string-append "--with-wish=" #$tk "/bin/wish"
4208 #$(version-major+minor (package-version tk))))
4209 ;; By default Maxima attempts to write temporary files to
4210 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
4211 ;; Work around that.
4212 #:make-flags (list "TMPDIR=/tmp")
4214 (modify-phases %standard-phases
4215 (add-after 'unpack 'patch-paths
4216 (lambda* (#:key inputs #:allow-other-keys)
4217 (let* ((sed (search-input-file inputs "/bin/sed"))
4218 (coreutils (assoc-ref inputs "coreutils"))
4219 (dirname (string-append coreutils "/bin/dirname"))
4220 (head (string-append coreutils "/bin/head"))
4221 (perl (search-input-file inputs "/bin/perl"))
4222 (python (search-input-file inputs "/bin/python3")))
4223 (substitute* "src/maxima.in"
4224 (("sed ") (string-append sed " "))
4225 (("dirname") dirname)
4227 (substitute* "doc/info/Makefile.in"
4228 (("/usr/bin/env perl") perl))
4229 (substitute* "doc/info/build_html.sh.in"
4230 (("python") python))
4232 (add-before 'check 'pre-check
4234 (chmod "src/maxima" #o555)
4238 ;; This is derived from the testing code in the "debian/rules" file
4239 ;; of Debian's Maxima package.
4240 ;; If Maxima can successfully run this, the binary to be installed
4246 "--batch-string=\"run_testsuite();\" "
4247 "| grep -q \"No unexpected errors found\""))))
4248 ;; Make sure the doc and emacs files are found in the
4249 ;; standard location. Also configure maxima to find gnuplot
4250 ;; without having it on the PATH.
4251 (add-after 'install 'post-install
4252 (lambda* (#:key outputs inputs #:allow-other-keys)
4253 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
4254 (out (assoc-ref outputs "out"))
4255 (datadir (string-append out "/share/maxima/" ,version))
4256 (binutils (dirname (search-input-file inputs "/bin/as"))))
4257 (with-directory-excursion out
4258 (mkdir-p "share/emacs")
4259 (mkdir-p "share/doc")
4261 (string-append datadir "/doc/")
4262 (string-append out "/share/doc/maxima"))
4263 (with-atomic-file-replacement
4264 (string-append datadir "/share/maxima-init.lisp")
4266 (format out "~a ~s~a~%"
4267 "(setf $gnuplot_command "
4268 (string-append gnuplot "/bin/gnuplot") ")")
4269 (dump-port in out))))
4270 ;; Ensure that Maxima will have access to the GNU binutils
4271 ;; components at runtime.
4272 (wrap-program (string-append out "/bin/maxima")
4273 `("PATH" prefix (,binutils))))
4275 (home-page "https://maxima.sourceforge.io")
4276 (synopsis "Numeric and symbolic expression manipulation")
4277 (description "Maxima is a system for the manipulation of symbolic and
4278 numerical expressions. It yields high precision numeric results by using
4279 exact fractions, arbitrary precision integers, and variable precision floating
4281 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
4282 ;; Others simply say "GNU General Public License" without stating a
4283 ;; version (which implicitly means gpl1+).
4284 ;; At least one file (src/maxima.asd) says "version 2."
4285 ;; GPLv2 only is therefore the smallest subset.
4286 (license license:gpl2)))
4288 (define-public wxmaxima
4296 (url "https://github.com/wxMaxima-developers/wxmaxima")
4297 (commit (string-append "Version-" version))))
4298 (file-name (git-file-name name version))
4300 (base32 "0h7ryykh2dapcyvpp4f1j1b3vrrz80x9k8nkci2yxifgdb29vyhw"))))
4301 (build-system cmake-build-system)
4303 `(("gettext" ,gettext-minimal)))
4305 `(("wxwidgets" ,wxwidgets)
4308 ("adwaita-icon-theme" ,adwaita-icon-theme)
4310 ("shared-mime-info" ,shared-mime-info)))
4312 `(#:tests? #f ; tests fail non-deterministically
4314 (modify-phases %standard-phases
4315 (add-after 'unpack 'patch-doc-path
4317 ;; Don't look in share/doc/wxmaxima-xx.xx.x for the
4318 ;; documentation. Only licensing information is placed there by
4320 (substitute* "src/Dirstructure.cpp"
4321 (("/doc/wxmaxima-\\%s") "/doc/wxmaxima"))
4323 (add-after 'install 'wrap-program
4324 (lambda* (#:key inputs outputs #:allow-other-keys)
4325 (wrap-program (string-append (assoc-ref outputs "out")
4328 (,(string-append (assoc-ref inputs "maxima")
4330 ;; For GtkFileChooserDialog.
4331 `("GSETTINGS_SCHEMA_DIR" =
4332 (,(string-append (assoc-ref inputs "gtk+")
4333 "/share/glib-2.0/schemas")))
4334 `("XDG_DATA_DIRS" ":" prefix
4335 (;; Needed by gdk-pixbuf to know supported icon formats.
4337 (assoc-ref inputs "shared-mime-info") "/share")
4338 ;; The default icon theme of GTK+.
4340 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
4342 (home-page "https://wxmaxima-developers.github.io/wxmaxima/")
4343 (synopsis "Graphical user interface for the Maxima computer algebra system")
4345 "wxMaxima is a graphical user interface for the Maxima computer algebra
4346 system. It eases the use of Maxima by making most of its commands available
4347 through a menu system and by providing input dialogs for commands that require
4348 more than one argument. It also implements its own display engine that
4349 outputs mathematical symbols directly instead of depicting them with ASCII
4352 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
4353 text and mathematical calculations to create documents, exporting of input and
4354 output to TeX, and a browser for Maxima's manual including command index and
4355 full text searching.")
4356 (license license:gpl2+)))
4358 (define-public armadillo
4364 (uri (string-append "mirror://sourceforge/arma/armadillo-"
4368 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
4369 (build-system cmake-build-system)
4370 (arguments `(#:tests? #f)) ; no test target
4372 `(("openblas" ,openblas)
4374 ("arpack" ,arpack-ng)))
4375 (home-page "http://arma.sourceforge.net/")
4376 (synopsis "C++ linear algebra library")
4378 "Armadillo is a C++ linear algebra library, aiming towards a good balance
4379 between speed and ease of use. It is useful for algorithm development
4380 directly in C++, or quick conversion of research code into production
4381 environments. It can be used for machine learning, pattern recognition,
4382 signal processing, bioinformatics, statistics, econometrics, etc. The library
4383 provides efficient classes for vectors, matrices and cubes, as well as 150+
4384 associated functions (e.g., contiguous and non-contiguous submatrix views).")
4385 (license license:asl2.0)))
4387 (define-public muparser
4388 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
4389 ;; different hash. In order to make `guix package --upgrade` work correctly,
4390 ;; we set a Guix packaging revision.
4391 ;; When the next version of muparser is released, we can remove
4392 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
4393 (let ((upstream-version "2.2.5")
4397 (version (string-append upstream-version "-" revision))
4402 (url "https://github.com/beltoforion/muparser")
4403 (commit (string-append "v" upstream-version))))
4404 (file-name (git-file-name name version))
4406 (base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24"))))
4407 (build-system gnu-build-system)
4409 `(#:configure-flags '("--enable-samples=no")
4410 #:tests? #f)) ;no "check" target
4411 (home-page "http://muparser.beltoforion.de/")
4412 (synopsis "Fast parser library for mathematical expressions")
4414 "muParser is an extensible high performance math parser library. It is
4415 based on transforming an expression into a bytecode and precalculating constant
4417 (license license:expat))))
4419 (define-public openblas
4427 (url "https://github.com/xianyi/OpenBLAS")
4428 (commit (string-append "v" version))))
4429 (file-name (git-file-name name version))
4432 "17zdd8asylz2w71hczrz5y344p6d5ds1jn4901maw7zcp3dbk63g"))))
4433 (build-system gnu-build-system)
4435 `(#:test-target "test"
4436 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
4437 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
4438 ;; we need to disable substitutions.
4440 ,(let ((system (or (%current-target-system) (%current-system))))
4441 (or (string-prefix? "x86_64" system)
4442 (string-prefix? "i686" system)
4443 (string-prefix? "mips" system)
4444 (string-prefix? "aarch64" system)))
4446 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
4448 "MAKE_NB_JOBS=0" ;use jobserver for submakes
4449 "NO_STATIC=1" ;avoid a 67 MiB static archive
4451 ;; This is the maximum number of threads OpenBLAS will ever use (that
4452 ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS
4453 ;; is used.) If we don't set it, the makefile sets it to the number
4454 ;; of cores of the build machine, which is obviously wrong.
4457 ;; Build the library for all supported CPUs. This allows
4458 ;; switching CPU targets at runtime with the environment variable
4459 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
4460 ;; Unfortunately, this is not supported on all architectures,
4461 ;; where it leads to failed builds.
4462 ,@(let ((system (or (%current-target-system) (%current-system))))
4464 ((or (string-prefix? "x86_64" system)
4465 (string-prefix? "i686" system)
4466 (string-prefix? "powerpc64le" system)
4467 (string-prefix? "aarch64" system))
4468 ;; Dynamic older enables a few extra CPU architectures that
4469 ;; were released before 2010.
4470 '("DYNAMIC_ARCH=1" "DYNAMIC_OLDER=1" "TARGET=GENERIC"))
4471 ;; On some of these architectures the CPU can't be detected.
4472 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
4473 ;; two available MIPS targets special extended instructions
4474 ;; for Loongson cores are used.
4475 ((string-prefix? "mips" system)
4476 '("TARGET=SICORTEX"))
4477 ;; Failed to detect CPU.
4478 ((string-prefix? "armhf" system)
4481 ;; no configure script
4483 (modify-phases %standard-phases
4485 (add-before 'build 'set-extralib
4486 (lambda* (#:key inputs #:allow-other-keys)
4487 ;; Get libgfortran found when building in utest.
4489 (string-append "-L" (assoc-ref inputs "fortran-lib")
4492 `(("fortran-lib" ,gfortran "lib")))
4495 ("fortran" ,gfortran)
4497 (home-page "https://www.openblas.net/")
4498 (synopsis "Optimized BLAS library based on GotoBLAS")
4500 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
4501 (license license:bsd-3)))
4503 (define-public openblas-ilp64
4504 (package/inherit openblas
4505 (name "openblas-ilp64")
4506 (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
4508 (substitute-keyword-arguments (package-arguments openblas)
4509 ((#:make-flags flags '())
4510 `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
4512 (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
4513 (license license:bsd-3)))
4519 (home-page "https://github.com/flame/blis")
4522 (uri (git-reference (url home-page) (commit version)))
4525 "05ifil6jj9424sr8kmircl8k4bmxnl3y12a79vwj1kxxva5gz50g"))
4526 (file-name (git-file-name "blis" version))))
4528 `(("python" ,python)
4530 (build-system gnu-build-system)
4533 ((guix build gnu-build-system)
4536 #:test-target "test"
4538 (modify-phases %standard-phases
4540 (lambda* (#:key outputs
4543 (configure-flags '())
4545 ;; This is a home-made 'configure' script.
4546 (let* ((out (assoc-ref outputs "out"))
4547 ;; Guix-specific support for choosing the configuration
4548 ;; via #:configure-flags: see below for details.
4549 (config-flag-prefix "--blis-config=")
4550 (maybe-config-flag (find
4552 (string-prefix? config-flag-prefix s))
4554 (configure-flags (if maybe-config-flag
4555 (delete maybe-config-flag
4558 ;; Select the "configuration" to build.
4559 ;; The "generic" configuration is non-optimized but
4560 ;; portable (no assembly).
4561 ;; The "x86_64" configuration family includes
4562 ;; sub-configurations for all supported
4563 ;; x86_64 microarchitectures.
4564 ;; BLIS currently lacks runtime hardware detection
4565 ;; for other architectures: see
4566 ;; <https://github.com/flame/blis/commit/c534da6>.
4567 ;; Conservatively, we stick to "generic" on armhf,
4568 ;; aarch64, and ppc64le for now. (But perhaps
4569 ;; "power9", "cortexa9", and "cortexa57" might be
4570 ;; general enough to use?)
4571 ;; Another approach would be to use the "auto"
4572 ;; configuration and make this package
4573 ;; non-substitutable.
4574 ;; The build is fairly intensive, though.
4578 (substring maybe-config-flag
4579 (string-length config-flag-prefix)))
4580 ((string-prefix? "x86_64" (or target system))
4589 "--enable-threading=openmp"
4590 "--enable-verbose-make"
4593 (format #t "configure args: ~s~%" configure-args)
4598 (add-before 'check 'show-test-output
4600 ;; By default "make check" is silent. Make it verbose.
4601 (system "tail -F output.testsuite &")
4603 (synopsis "High-performance basic linear algebra (BLAS) routines")
4605 "BLIS is a portable software framework for instantiating high-performance
4606 BLAS-like dense linear algebra libraries. The framework was designed to
4607 isolate essential kernels of computation that, when optimized, immediately
4608 enable optimized implementations of most of its commonly used and
4609 computationally intensive operations. While BLIS exports a new BLAS-like API,
4610 it also includes a BLAS compatibility layer which gives application developers
4611 access to BLIS implementations via traditional BLAS routine calls.")
4612 (license license:bsd-3)))
4614 (define-public blis-sandybridge (deprecated-package "blis-sandybridge" blis))
4615 (define-public blis-haswell (deprecated-package "blis-haswell" blis))
4616 (define-public blis-knl (deprecated-package "blis-knl" blis))
4618 (define ignorance blis)
4620 (define-public openlibm
4628 (url "https://github.com/JuliaLang/openlibm")
4629 (commit (string-append "v" version))))
4630 (file-name (git-file-name name version))
4632 (base32 "1azms0lpxb7vxb3bln5lyz0wpwx6jnzbffkclclpq2v5aiw8d14i"))))
4633 (build-system gnu-build-system)
4636 (list (string-append "prefix=" (assoc-ref %outputs "out"))
4637 ,(string-append "CC=" (cc-for-target)))
4639 ;; no configure script
4640 (modify-phases %standard-phases (delete 'configure))
4641 #:tests? #f)) ;the tests are part of the default target
4642 (home-page "https://openlibm.org/")
4643 (synopsis "Portable C mathematical library (libm)")
4645 "OpenLibm is an effort to have a high quality, portable, standalone C
4646 mathematical library (libm). It can be used standalone in applications and
4647 programming language implementations. The project was born out of a need to
4648 have a good libm for the Julia programming language that worked consistently
4649 across compilers and operating systems, and in 32-bit and 64-bit
4651 ;; Each architecture has its own make target, and there is none for mips.
4652 (supported-systems (delete "mips64el-linux" %supported-systems))
4653 ;; See LICENSE.md for details.
4654 (license (list license:expat
4657 license:public-domain
4658 license:lgpl2.1+))))
4660 (define-public openspecfun
4662 (name "openspecfun")
4668 (url "https://github.com/JuliaLang/openspecfun")
4669 (commit (string-append "v" version))))
4670 (file-name (git-file-name name version))
4672 (base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh"))))
4673 (build-system gnu-build-system)
4675 '(#:tests? #f ; no "check" target
4677 (list (string-append "prefix=" (assoc-ref %outputs "out")))
4679 (modify-phases %standard-phases
4680 (delete 'configure)))) ; no configure script
4682 `(("fortran" ,gfortran)))
4683 (home-page "https://github.com/JuliaLang/openspecfun")
4684 (synopsis "Collection of special mathematical functions")
4686 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
4687 portable package for Bessel Functions of a Complex Argument and Nonnegative
4688 Order; it contains subroutines for computing Bessel functions and Airy
4689 functions. Faddeeva allows computing the various error functions of arbitrary
4690 complex arguments (Faddeeva function, error function, complementary error
4691 function, scaled complementary error function, imaginary error function, and
4692 Dawson function); given these, one can also easily compute Voigt functions,
4693 Fresnel integrals, and similar related functions as well.")
4694 ;; Faddeeva is released under the Expat license; AMOS is included as
4695 ;; public domain software.
4696 (license (list license:expat license:public-domain))))
4698 (define-public suitesparse
4700 (name "suitesparse")
4706 (url "https://github.com/DrTimothyAldenDavis/SuiteSparse")
4707 (commit (string-append "v" version))))
4708 (file-name (git-file-name name version))
4711 "19gx5wlgqnqpgz6mvam9lalyzpbfwgqhppps8z3np9sh0mgaiyw9"))
4712 (patches (search-patches "suitesparse-mongoose-cmake.patch"))
4713 (modules '((guix build utils)))
4715 ;; Remove bundled metis source
4717 (delete-file-recursively "metis-5.1.0")
4719 (build-system gnu-build-system)
4721 `(#:tests? #f ;no "check" target
4723 (list (string-append "CC=" ,(cc-for-target))
4725 "MY_METIS_LIB=-lmetis"
4727 ;; The default is to link against netlib lapack. Use OpenBLAS
4729 "BLAS=-lopenblas" "LAPACK=-lopenblas"
4731 ;; Flags for cmake (required to build GraphBLAS and Mongoose)
4732 (string-append "CMAKE_OPTIONS=-DCMAKE_INSTALL_PREFIX="
4733 (assoc-ref %outputs "out")
4734 " -DCMAKE_VERBOSE_MAKEFILE=ON"
4735 " -DCMAKE_C_FLAGS_RELEASE=\"$(CFLAGS) $(CPPFLAGS)\""
4736 " -DCMAKE_CXX_FLAGS_RELEASE=\"$(CXXFLAGS) $(CPPFLAGS)\""
4737 " -DCMAKE_SKIP_RPATH=TRUE"
4738 " -DCMAKE_BUILD_TYPE=Release"
4739 " -DCMAKE_INSTALL_LIBDIR=lib")
4740 (string-append "INSTALL_LIB="
4741 (assoc-ref %outputs "out") "/lib")
4742 (string-append "INSTALL_INCLUDE="
4743 (assoc-ref %outputs "out") "/include")
4746 (modify-phases %standard-phases
4747 (delete 'configure)))) ;no configure script
4750 ("openblas" ,openblas)
4755 `(("cmake" ,cmake-minimal)
4757 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
4758 (synopsis "Suite of sparse matrix software")
4760 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
4761 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
4762 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
4763 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
4764 CXSparse, a concise sparse Cholesky factorization package; and many other
4767 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
4769 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
4770 (license (list license:gpl2+ license:lgpl2.1+))))
4772 (define-public atlas
4778 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
4779 version "/atlas" version ".tar.bz2"))
4780 (patches (search-patches "atlas-gfortran-compat.patch"))
4783 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
4784 (build-system gnu-build-system)
4785 (home-page "http://math-atlas.sourceforge.net/")
4786 (inputs `(("gfortran" ,gfortran)
4787 ("lapack-tar" ,(package-source lapack))))
4788 (outputs '("out" "doc"))
4789 ;; For the moment we drop support for MIPS at it fails to compile. See
4790 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
4791 (supported-systems (delete "mips64el-linux" %supported-systems))
4793 `(#:parallel-build? #f
4794 #:parallel-tests? #f
4796 ;; ATLAS tunes itself for the machine it is built on, as explained at
4797 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
4798 ;; For this reason, we want users to build it locally instead of using
4802 #:modules ((srfi srfi-26)
4803 (guix build gnu-build-system)
4806 `(;; Generate position independent code suitable for dynamic libraries
4807 ;; and use WALL timer to get more accurate timing.
4808 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
4811 ,,(if (string-match "64" (%current-system))
4814 ;; Disable parallel build as it gives errors: atlas_pthread.h is
4815 ;; needed to compile C files before it is generated.
4816 "-Ss" "pmake" "make -j 1"
4817 ;; Probe is failing for MIPS. We therefore define the system
4818 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
4819 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
4820 ,,@(if (string-prefix? "mips" (%current-system))
4821 (list "-A" "49" "-V" "1")
4823 ;; Generate shared libraries.
4825 ;; Build a full LAPACK library.
4826 ,(string-append "--with-netlib-lapack-tarfile="
4827 (assoc-ref %build-inputs "lapack-tar")))
4829 (modify-phases %standard-phases
4830 (add-after 'install 'install-doc
4831 (lambda* (#:key outputs inputs #:allow-other-keys)
4832 (let ((doc (string-append (assoc-ref outputs "doc")
4833 "/share/doc/atlas")))
4835 (for-each (cut install-file <> doc)
4836 (find-files "../ATLAS/doc" ".*"))
4838 (add-after 'check 'check-pt
4839 (lambda _ (invoke "make" "ptcheck")))
4840 ;; Fix files required to run configure.
4841 (add-before 'configure 'fix-/bin/sh
4843 ;; Use `sh', not `/bin/sh'.
4844 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
4848 ;; Fix /bin/sh in generated make files.
4849 (add-after 'configure 'fix-/bin/sh-in-generated-files
4851 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
4855 ;; ATLAS configure program does not accepts the default flags
4856 ;; passed by the 'gnu-build-system'.
4858 (lambda* (#:key native-inputs inputs outputs
4859 (configure-flags '())
4860 #:allow-other-keys #:rest args)
4861 (let* ((prefix (assoc-ref outputs "out"))
4862 (bash (or (and=> (assoc-ref
4863 (or native-inputs inputs) "bash")
4864 (cut string-append <> "/bin/bash"))
4866 (flags `(,(string-append "--prefix=" prefix)
4868 (abs-srcdir (getcwd))
4869 (srcdir (string-append "../" (basename abs-srcdir))))
4870 (format #t "source directory: ~s (relative from build: ~s)~%"
4874 (format #t "build directory: ~s~%" (getcwd))
4875 (format #t "configure flags: ~s~%" flags)
4877 (string-append srcdir "/configure")
4879 (synopsis "Automatically Tuned Linear Algebra Software")
4881 "ATLAS is an automatically tuned linear algebra software library
4882 providing C and Fortran77 interfaces to a portably efficient BLAS
4883 implementation, as well as a few routines from LAPACK.
4885 Optimization occurs at build time. For this reason, the library is built on
4886 the machine where it is installed, without resorting to pre-built substitutes.
4888 Before building the library, CPU throttling should be disabled. This can be
4889 done in the BIOS, or, on GNU/Linux, with the following command:
4892 # cpupower --governor performance
4895 Failure to do so will result in a library with poor performance.")
4896 ;; The test suite is notoriously lengthy and routinely exceeds the default
4897 ;; timeout of 21600 seconds on the not unbeefy berlin build nodes.
4898 (properties '((timeout . 86400))) ; 1 day
4899 (license license:bsd-3)))
4909 (url "https://github.com/recp/cglm")
4910 (commit (string-append "v" version))))
4911 (file-name (git-file-name name version))
4913 (base32 "1lcfl9ph4bnl3hckpx4hzwh8r4llnw94ik75igc5qy38wk468gmk"))))
4914 (build-system cmake-build-system)
4917 (list "-DCGLM_USE_TEST=ON")))
4918 (home-page "https://github.com/recp/cglm")
4919 (synopsis "Mathematics C library for graphics programming")
4921 "@acronym{CGLM, C OpenGL Mathematics} is an optimised 3D maths library
4922 for graphics software based on the @acronym{GLSL, OpenGL Shading Language}
4925 It's similar to the original C++ GLM library but written in C99 and compatible
4927 (license license:expat)))
4936 (uri (string-append "https://github.com/g-truc/glm/releases/download/"
4937 version "/glm-" version ".zip"))
4939 (base32 "0k6yk9v46h690rshdx49x98y5qspkzibld1wb51jwcm35vba7qip"))))
4940 (build-system cmake-build-system)
4942 `(#:phases (modify-phases %standard-phases
4944 (lambda* (#:key outputs #:allow-other-keys)
4945 ;; Since version 0.9.9.6, 'make install' is not supported
4946 ;; and we have to do it "manually". Upstream discussion:
4947 ;; <https://github.com/g-truc/glm/pull/968>.
4948 (let* ((source (string-append "../glm"))
4949 (out (assoc-ref outputs "out"))
4950 (inc (string-append out "/include"))
4951 (lib (string-append out "/lib"))
4952 (pkgconfig (string-append lib "/pkgconfig")))
4953 (with-directory-excursion source
4956 (copy-recursively "glm" (string-append inc "/glm"))
4957 (copy-recursively "cmake" (string-append lib "/cmake"))
4958 (call-with-output-file (string-append pkgconfig "/glm.pc")
4962 includedir=${prefix}/include
4965 Description: OpenGL Mathematics
4967 Cflags: -I${includedir}~%" out ,(version-prefix version 3)))))
4970 `(("unzip" ,unzip)))
4971 (home-page "https://glm.g-truc.net/")
4972 (synopsis "OpenGL Mathematics library")
4973 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
4974 library for graphics software based on the OpenGL Shading Language (GLSL)
4976 (license license:expat)))
4978 (define-public lpsolve
4985 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
4986 "/lp_solve_" version "_source.tar.gz"))
4989 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
4990 (modules '((guix build utils)))
4993 (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
4995 ;; Pretend to be on a 64 bit platform to obtain a common directory
4996 ;; name for the build results on all architectures; nothing else
4997 ;; seems to depend on it.
4998 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
5000 ;; The check for 'isnan' as it is written fails with
5001 ;; "non-floating-point argument in call to function
5002 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
5003 ;; definition, which in turn leads to bad things. Fix the feature
5005 (("isnan\\(0\\)") "isnan(0.)"))
5007 (build-system gnu-build-system)
5009 `(#:tests? #f ; no check target
5011 (modify-phases %standard-phases
5012 (delete 'configure) ; no configure script
5015 (with-directory-excursion "lpsolve55"
5016 (invoke "bash" "ccc"))
5017 (with-directory-excursion "lp_solve"
5018 (invoke "bash" "ccc"))
5021 (lambda* (#:key outputs #:allow-other-keys)
5022 (let* ((out (assoc-ref outputs "out"))
5023 (bin (string-append out "/bin"))
5024 (lib (string-append out "/lib"))
5025 ;; This is where LibreOffice expects to find the header
5026 ;; files, and where they are installed by Debian.
5027 (include (string-append out "/include/lpsolve")))
5028 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
5029 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
5030 (install-file "lp_solve/bin/ux64/lp_solve" bin)
5032 ;; Install a subset of the header files as on Debian
5033 ;; (plus lp_bit.h, which matches the regular expression).
5034 (for-each (lambda (name)
5035 (install-file name include))
5036 (find-files "." "lp_[HMSa-z].*\\.h$"))
5037 (with-directory-excursion "shared"
5038 (for-each (lambda (name)
5039 (install-file name include))
5040 (find-files "." "\\.h$")))
5042 (home-page "http://lpsolve.sourceforge.net/")
5043 (synopsis "Mixed integer linear programming (MILP) solver")
5045 "lp_solve is a mixed integer linear programming solver based on the
5046 revised simplex and the branch-and-bound methods.")
5047 (license license:lgpl2.1+)))
5049 ;; Private Trilinos package for dealii-openmpi (similar to
5050 ;; trilinos-serial-xyce and trilinos-parallel-xyce).
5051 ;; This version is the latest known to be compatible with deal.II [1].
5052 ;; Since the latest version of Trilinos is not necessarily supported by
5053 ;; deal.II, it may be worth keeping this package even if and when Trilinos
5054 ;; gets packaged separately for Guix (unless various versions of Trilinos are
5057 ;; An insightful source of information for building Trilinos for deal.II lies
5058 ;; in the Trilinos package for candi [2], which is a source-based installer
5059 ;; for deal.II and its dependencies.
5061 ;; [1]: https://www.dealii.org/current/external-libs/trilinos.html
5062 ;; [2]: https://github.com/dealii/candi/blob/master/deal.II-toolchain/packages/trilinos.package
5063 (define trilinos-for-dealii-openmpi
5065 (name "trilinos-for-dealii-openmpi")
5071 (url "https://github.com/trilinos/Trilinos/")
5073 (string-append "trilinos-release-"
5074 (string-replace-substring version "." "-")))))
5075 (file-name (git-file-name "trilinos" version))
5077 (base32 "0fnwlhzsh85qj38cq3igbs8nm1b2jdgr2z734sapmyyzsy21mkgp"))))
5078 (build-system cmake-build-system)
5080 `(("gfortran" ,gfortran)
5081 ;; Trilinos's repository contains several C-shell scripts, but adding
5082 ;; tcsh to the native inputs does not result in the check phase running
5083 ;; any more tests than without it (nor is tcsh required to build
5085 ;; It seems that Trilinos has replaced its use of C-shell test scripts
5086 ;; with CMake's testing facilities.
5088 ;; packages/zoltan/doc/Zoltan_html/dev_html/dev_test_script.html [1]
5089 ;; states that Zoltan's C-shell test script
5090 ;; packages/zoltan/test/test_zoltan has been obsoleted by the tests now
5091 ;; performed through CMake.
5093 ;; Perl is required for some Zoltan tests and Python 2 for one ML test.
5095 ;; [1]: https://cs.sandia.gov/zoltan/dev_html/dev_test_script.html
5097 ("python" ,python-2)))
5099 `(("blas" ,openblas)
5101 ("mumps" ,mumps-openmpi)
5102 ("scalapack" ,scalapack)))
5104 `(("mpi" ,openmpi)))
5106 `(#:build-type "Release"
5108 `("-DBUILD_SHARED_LIBS=ON"
5109 ;; Obtain the equivalent of RelWithDebInfo but with -O3 (the Release
5110 ;; default) rather than -O2 (the RelWithDebInfo default), to conform
5111 ;; to candi's trilinos.package's compilation flags, which are -g -O3.
5112 "-DCMAKE_C_FLAGS=-g"
5113 "-DCMAKE_CXX_FLAGS=-g"
5114 "-DCMAKE_Fortran_FLAGS=-g"
5116 ;; Trilinos libraries that deal.II can interface with.
5117 "-DTrilinos_ENABLE_Amesos=ON"
5118 "-DTrilinos_ENABLE_AztecOO=ON"
5119 "-DTrilinos_ENABLE_Epetra=ON"
5120 "-DTrilinos_ENABLE_EpetraExt=ON"
5121 "-DTrilinos_ENABLE_Ifpack=ON"
5122 "-DTrilinos_ENABLE_ML=ON"
5123 "-DTrilinos_ENABLE_MueLu=ON"
5124 "-DTrilinos_ENABLE_ROL=ON"
5125 ;; Optional; required for deal.II's GridIn::read_exodusii, but
5126 ;; depends on netcdf.
5127 ;; Enable if and when someone needs it.
5128 ;;"-DTrilinos_ENABLE_SEACAS=ON"
5129 "-DTrilinos_ENABLE_Sacado=ON"
5130 "-DTrilinos_ENABLE_Teuchos=ON"
5131 "-DTrilinos_ENABLE_Tpetra=ON"
5132 "-DTrilinos_ENABLE_Zoltan=ON"
5134 ;; Third-party libraries (TPLs) that Trilinos can interface with.
5135 "-DBLAS_LIBRARY_NAMES=openblas"
5136 "-DTPL_ENABLE_MPI=ON"
5137 "-DTPL_ENABLE_MUMPS=ON"
5138 "-DTPL_ENABLE_SCALAPACK=ON"
5140 ;; Enable the tests but not the examples (which are enabled by
5141 ;; default when enabling tests).
5142 ;; Although some examples are run as tests, they are otherwise
5143 ;; unnecessary since this is a private package meant for
5145 ;; Besides, some MueLu and ROL examples require a lot of memory to
5148 ;; (For future reference, note that some ROL and SEACAS examples
5149 ;; require removing gfortran from CPLUS_INCLUDE_PATH as in the
5150 ;; dune-istl, dune-localfunctions and dune-alugrid packages.)
5151 "-DTrilinos_ENABLE_TESTS=ON"
5152 "-DTrilinos_ENABLE_EXAMPLES=OFF"
5153 ;; MueLu tests require considerably more time and memory to compile
5154 ;; than the rest of the tests.
5155 "-DMueLu_ENABLE_TESTS=OFF"
5157 ;; The following options were gleaned from candi's trilinos.package.
5158 ;; (We do not enable the complex instantiations, which are anyway
5159 ;; provided only as an option in trilinos.package, because they are
5160 ;; costly in compilation time and memory usage, and disk space [1].)
5162 ;; [1]: https://www.docs.trilinos.org/files/TrilinosBuildReference.html#enabling-float-and-complex-scalar-types
5163 "-DTrilinos_ENABLE_Ifpack2=OFF"
5164 "-DTeuchos_ENABLE_FLOAT=ON"
5165 "-DTpetra_INST_INT_LONG=ON"
5166 "-DTPL_ENABLE_Boost=OFF")
5168 (modify-phases %standard-phases
5169 (add-after 'configure 'fix-kokkos-config
5171 ;; GNU Make 4.3 accidentally leaves the backslash preceding the
5172 ;; number sign in strings containing a literal backslash–number
5173 ;; sign (\#) [1, 2].
5174 ;; This is still an issue in Trilinos 13.0.1, but should be fixed
5175 ;; in the following version.
5176 ;; (The latest versions of Kokkos incorporate the fix [2].)
5178 ;; [1]: https://github.com/GEOSX/thirdPartyLibs/issues/136
5179 ;; [2]: https://github.com/kokkos/kokkos/blob/3.4.00/Makefile.kokkos#L441
5180 (substitute* "KokkosCore_config.h"
5183 (add-before 'check 'mpi-setup
5185 (home-page "https://trilinos.github.io/")
5186 (synopsis "Algorithms for engineering and scientific problems")
5188 "The Trilinos Project is an effort to develop algorithms and enabling
5189 technologies within an object-oriented software framework for the solution of
5190 large-scale, complex multi-physics engineering and scientific problems.
5191 A unique design feature of Trilinos is its focus on packages.")
5192 ;; The packages are variously licensed under more than just BSD-3 and
5193 ;; LGPL-2.1+, but all the licenses are either BSD- or LGPL-compatible.
5194 ;; See https://trilinos.github.io/license.html.
5195 (license (list license:bsd-3 license:lgpl2.1+))))
5197 (define-public dealii
5204 (uri (string-append "https://github.com/dealii/dealii/releases/"
5205 "download/v" version "/dealii-" version ".tar.gz"))
5207 (base32 "1f0sqvlxvl0myqcn0q6xrn1vnp5pgx143lai4a4jkh1dmdv4cbx6"))
5208 (modules '((guix build utils)))
5211 ;; Remove bundled boost, muparser, TBB and UMFPACK.
5212 (delete-file-recursively "bundled")
5214 (build-system cmake-build-system)
5215 (outputs '("out" "doc"))
5217 ;; Required to build the documentation.
5219 ("doxygen" ,doxygen)
5222 `(("arpack" ,arpack-ng)
5224 ("gfortran" ,gfortran)
5226 ("muparser" ,muparser)
5229 ;; Some scripts are installed into share/deal.II/scripts that require
5230 ;; perl and python, but they are not executable (and some are missing the
5231 ;; shebang line) and therefore must be explicitly passed to the
5233 ;; Anyway, they are meant to be used at build time, so rather than adding
5234 ;; the interpreters here, any package depending on them should just add
5235 ;; the requisite interpreter to its native inputs.
5238 ("suitesparse" ,suitesparse) ; For UMFPACK.
5241 `(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease.
5242 ;; The tests take too long and must be explicitly enabled with "make
5244 ;; See https://www.dealii.org/developer/developers/testsuite.html.
5245 ;; (They can also be run for an already installed deal.II.)
5248 (let ((doc (string-append (assoc-ref %outputs "doc")
5249 "/share/doc/" ,name "-" ,version)))
5250 `("-DDEAL_II_COMPONENT_DOCUMENTATION=ON"
5251 ,(string-append "-DDEAL_II_DOCREADME_RELDIR=" doc)
5252 ,(string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html")
5253 ;; Don't compile the examples because the source and CMakeLists.txt
5254 ;; are installed anyway, allowing users to do so for themselves.
5255 "-DDEAL_II_COMPILE_EXAMPLES=OFF"
5256 ,(string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc "/examples")))
5258 (modify-phases %standard-phases
5259 (add-after 'install 'remove-build-logs
5260 ;; These build logs leak the name of the build directory by storing
5261 ;; the values of CMAKE_SOURCE_DIR and CMAKE_BINARY_DIR.
5262 (lambda* (#:key outputs #:allow-other-keys)
5263 (let ((doc (string-append (assoc-ref outputs "doc")
5264 "/share/doc/" ,name "-" ,version)))
5265 (for-each delete-file (map (lambda (f) (string-append doc "/" f))
5266 '("detailed.log" "summary.log"))))
5268 (home-page "https://www.dealii.org/")
5269 (synopsis "Finite element library")
5271 "Deal.II is a C++ program library targeted at the computational solution
5272 of partial differential equations using adaptive finite elements. The main
5273 aim of deal.II is to enable rapid development of modern finite element codes,
5274 using among other aspects adaptive meshes and a wide array of tools often used
5275 in finite element programs.")
5276 (license license:lgpl2.1+)))
5278 (define-public dealii-openmpi
5279 (package/inherit dealii
5280 (name "dealii-openmpi")
5282 `(("arpack" ,arpack-ng-openmpi)
5284 ("scalapack" ,scalapack)
5285 ,@(alist-delete "arpack" (package-inputs dealii))))
5287 `(("hdf5" ,hdf5-parallel-openmpi)
5289 ("p4est" ,p4est-openmpi)
5290 ("petsc" ,petsc-openmpi)
5291 ("slepc" ,slepc-openmpi)
5292 ("trilinos" ,trilinos-for-dealii-openmpi)
5293 ,@(alist-delete "hdf5" (package-propagated-inputs dealii))))
5295 (substitute-keyword-arguments (package-arguments dealii)
5296 ((#:configure-flags flags)
5297 `(cons "-DDEAL_II_WITH_MPI=ON" ,flags))))
5298 (synopsis "Finite element library (with MPI support)")))
5300 (define-public flann
5304 (home-page "https://github.com/mariusmuja/flann/")
5308 (uri (git-reference (url home-page) (commit version)))
5309 (file-name (git-file-name name version))
5312 "0p56fl2yx1r86ds1mgjq40926jdcgq3hka7p3l1hv2acv9jxp15x"))
5313 (patches (search-patches "flann-cmake-3.11.patch"))))
5314 (build-system cmake-build-system)
5317 `(("unzip" ,unzip)))
5320 ;; FIXME: 'mkoctfile' fails with a linker error:
5321 ;; ld: cannot find -loctinterp
5322 ;; ld: cannot find -loctave
5323 ;; Disable it for now.
5324 ;;("octave" ,octave-cli)
5325 ("python" ,python-2) ; print syntax
5326 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
5329 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
5330 ;; taken 46 MiB unstripped, and 6 MiB stripped.
5331 #:strip-directories '("lib" "lib64" "libexec"
5332 "bin" "sbin" "share/flann/octave")
5334 ;; Save 12 MiB by not installing .a files. Passing
5335 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
5336 #:phases (modify-phases %standard-phases
5337 (add-after 'install 'remove-static-libraries
5338 (lambda* (#:key outputs #:allow-other-keys)
5339 (let* ((out (assoc-ref outputs "out"))
5340 (lib (string-append out "/lib")))
5341 (for-each delete-file
5342 (find-files lib "\\.a$"))
5345 #:tests? #f)) ; The test data are downloaded from the Internet.
5346 (synopsis "Library for approximate nearest neighbors computation")
5347 (description "FLANN is a library for performing fast approximate
5348 nearest neighbor searches in high dimensional spaces. It implements a
5349 collection of algorithms and a system for automatically choosing the best
5350 algorithm and optimum parameters depending on the dataset.
5352 FLANN is written in C++ and contains bindings for C, Octave and Python.")
5353 (license (license:non-copyleft "file://COPYING"
5354 "See COPYING in the distribution."))))
5356 (define-public wcalc
5363 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
5364 "wcalc-" version ".tar.bz2"))
5367 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
5368 (build-system gnu-build-system)
5371 ("readline" ,readline)))
5372 (home-page "http://w-calc.sourceforge.net/index.php")
5373 (synopsis "Flexible command-line scientific calculator")
5374 (description "Wcalc is a very capable calculator. It has standard functions
5375 (sin, asin, and sinh for example, in either radians or degrees), many
5376 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
5377 variables, a command history, hex/octal/binary input and output, unit
5378 conversions, embedded comments, and an expandable expression entry field. It
5379 evaluates expressions using the standard order of operations.")
5380 (license license:gpl2+)))
5389 (url "https://github.com/xaos-project/XaoS")
5390 (commit (string-append "release-" version))))
5391 (file-name (git-file-name name version))
5394 "0maw5am6rrkyjrprfg113zjq37mqj0iaznkg4h2927ff7wrprc94"))))
5395 (build-system gnu-build-system)
5396 (native-inputs `(("gettext" ,gettext-minimal)
5397 ("qtbase" ,qtbase-5)
5398 ("qttools" ,qttools)))
5399 (inputs `(("libx11" ,libx11)
5403 ;; The upstream project file ("XaoS.pro") and the Makefile it generates are
5404 ;; not enough for this package to install properly. These phases fix that.
5406 `(#:tests? #f ;no "check" target
5408 (modify-phases %standard-phases
5409 (add-before 'configure 'make-qt-deterministic
5411 ;; Make Qt deterministic.
5412 (setenv "QT_RCC_SOURCE_DATE_OVERRIDE" "1")
5415 (lambda* (#:key outputs #:allow-other-keys)
5416 (let ((out (assoc-ref outputs "out")))
5417 (substitute* "XaoS.pro"
5418 ;; The DESTDIR is originally set to install the xaos binary to
5419 ;; the "bin" folder inside the build directory. Setting make
5420 ;; flags doesn't seem to change this.
5422 (string-append "DESTDIR=" out "/bin"))
5423 ;; Set the correct path to the lrelease binary.
5424 (("lrelease-qt5") "lrelease"))
5425 (substitute* "src/include/config.h"
5426 (("/usr/share/XaoS")
5427 (string-append out "/share/XaoS")))
5429 (add-after 'install 'install-data
5430 (lambda* (#:key outputs #:allow-other-keys)
5431 (let* ((out (assoc-ref outputs "out"))
5432 (share (string-append out "/share")))
5436 (copy-recursively folder
5437 (string-append share "/XaoS/" folder)))
5438 '("catalogs" "examples" "tutorial"))
5439 (install-file "xdg/xaos.png"
5440 (string-append share "/pixmaps"))
5441 (install-file "xdg/xaos.desktop"
5442 (string-append share "/applications")))
5444 (synopsis "Real-time fractal zoomer")
5445 (description "GNU XaoS is a graphical program that generates fractal
5446 patterns and allows you to zoom in and out of them infinitely in a fluid,
5447 continuous manner. It also includes tutorials that help to explain how fractals
5448 are built. It can generate many different fractal types such as the Mandelbrot
5450 (home-page "https://xaos-project.github.io/")
5451 (license license:gpl2+)))
5453 (define-public hypre
5461 (url "https://github.com/hypre-space/hypre")
5462 (commit (string-append "v" version))))
5463 (file-name (git-file-name name version))
5465 (base32 "14iqjwg5sv1qjn7c2cfv0xxmn9rwamjrhh9hgs8fjbywcbvrkjdi"))))
5466 (build-system gnu-build-system)
5467 (outputs '("out" ;5.3 MiB of headers and libraries
5468 "doc")) ;12 MiB of documentation
5471 ("doxygen" ,doxygen)
5473 ("python-breathe" ,python-breathe)
5474 ("python-sphinx" ,python-sphinx)
5475 ("texlive" ,(texlive-updmap.cfg (list texlive-adjustbox
5487 texlive-generic-listofitems
5488 texlive-generic-ulem
5489 texlive-latex-capt-of
5491 texlive-latex-colortbl
5493 texlive-latex-fancyhdr
5494 texlive-latex-fancyvrb
5496 texlive-latex-fncychap
5497 texlive-latex-framed
5498 texlive-latex-geometry
5499 texlive-latex-hanging
5501 texlive-latex-multirow
5502 texlive-latex-natbib
5503 texlive-latex-needspace
5504 texlive-latex-newunicodechar
5505 texlive-latex-parskip
5506 texlive-latex-stackengine
5507 texlive-latex-tabulary
5508 texlive-latex-titlesec
5509 texlive-latex-tocloft
5510 texlive-latex-upquote
5511 texlive-latex-varwidth
5513 texlive-latex-wrapfig)))))
5515 `(("blas" ,openblas)
5516 ("lapack" ,lapack)))
5518 `(#:modules ((srfi srfi-1)
5519 ,@%gnu-build-system-modules)
5520 #:configure-flags '("--enable-shared"
5528 (modify-phases %standard-phases
5529 (add-before 'configure 'chdir-src
5530 (lambda _ (chdir "src")))
5532 (lambda* (#:key build target configure-flags
5533 #:allow-other-keys #:rest args)
5534 (let* ((configure (assoc-ref %standard-phases 'configure)))
5537 (list #:configure-flags
5538 (cons (string-append
5539 "--host=" (or target build))
5540 configure-flags)))))))
5541 (add-after 'build 'build-docs
5543 (invoke "make" "-C" "docs")))
5546 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
5547 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
5548 (invoke "make" "check" "CHECKRUN=")
5549 (for-each (lambda (filename)
5550 (let ((size (stat:size (stat filename))))
5551 (when (positive? size)
5552 (error (format #f "~a size ~d; error indication~%"
5554 (find-files "test" ".*\\.err$"))))
5555 (add-after 'install 'install-docs
5556 (lambda* (#:key outputs #:allow-other-keys)
5557 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
5558 (let* ((doc (assoc-ref outputs "doc"))
5559 (docdir (string-append doc "/share/doc/hypre-" ,version)))
5560 (with-directory-excursion "docs"
5561 (for-each (lambda (base)
5562 (install-file (string-append base ".pdf") docdir)
5563 (copy-recursively (string-append base "-html")
5564 (string-append docdir "/" base)))
5565 '("usr-manual" "ref-manual")))))))))
5566 (home-page "https://computing.llnl.gov/projects\
5567 /hypre-scalable-linear-solvers-multigrid-methods")
5568 (synopsis "Library of solvers and preconditioners for linear equations")
5570 "HYPRE is a software library of high performance preconditioners and
5571 solvers for the solution of large, sparse linear systems of equations. It
5572 features multigrid solvers for both structured and unstructured grid
5574 (license license:lgpl2.1)))
5576 (define-public hypre-openmpi
5577 (package (inherit hypre)
5578 (name "hypre-openmpi")
5581 ,@(package-inputs hypre)))
5583 (substitute-keyword-arguments (package-arguments hypre)
5584 ((#:configure-flags flags)
5586 ,@(delete "--without-MPI" ,flags)))
5588 `(modify-phases ,phases
5589 (add-before 'check 'mpi-setup
5590 ,%openmpi-setup)))))
5591 (synopsis "Parallel solvers and preconditioners for linear equations")
5593 "HYPRE is a software library of high performance preconditioners and
5594 solvers for the solution of large, sparse linear systems of equations on
5595 parallel computers. It features parallel multigrid solvers for both
5596 structured and unstructured grid problems.")))
5598 (define-public matio
5605 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
5606 "matio-" version ".tar.gz"))
5609 "0vr8c1mz1k6mz0sgh6n3scl5c3a71iqmy5fnydrgq504icj4vym4"))))
5610 (build-system gnu-build-system)
5613 ("hdf5" ,hdf5-1.8)))
5614 (home-page "http://matio.sourceforge.net/")
5615 (synopsis "Library for reading and writing MAT files")
5616 (description "Matio is a library for reading and writing MAT files. It
5617 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
5618 (license license:bsd-2)))
5625 (origin (method url-fetch)
5626 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
5627 "download/" version "/Vc-" version ".tar.gz"))
5630 "0lirdqzcxys9walz04bllsphydynk7973aimd5k1h1qbwi8z3lsh"))))
5631 (build-system cmake-build-system)
5634 '("-DBUILD_TESTING=ON"
5635 ;; By default, Vc will optimize for the CPU of the build machine.
5636 ;; Setting this to "none" makes it create portable binaries. See
5637 ;; "cmake/OptimizeForArchitecture.cmake".
5638 "-DTARGET_ARCHITECTURE=none")
5639 #:phases (modify-phases %standard-phases
5640 (add-after 'unpack 'copy-testdata
5641 (lambda* (#:key inputs native-inputs #:allow-other-keys)
5642 (let ((testdata (assoc-ref (or native-inputs inputs)
5644 (copy-recursively testdata "tests/testdata")
5647 `(("virtest" ,virtest)
5649 ;; This is a submodule in the git project, but not part of the
5650 ;; released sources. See the git branch for the commit to take.
5651 ("testdata" ,(let ((commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3"))
5655 (url "https://github.com/VcDevel/vc-testdata")
5656 (commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3")))
5657 (file-name (git-file-name "vc-testdata"
5658 (string-take commit 7)))
5661 "1hkhqib03qlcq412ym2dciynfxcdr2ygqhnplz4l1vissr1wnqn2")))))))
5662 (synopsis "SIMD vector classes for C++")
5663 (description "Vc provides portable, zero-overhead C++ types for explicitly
5664 data-parallel programming. It is a library designed to ease explicit
5665 vectorization of C++ code. Its types enable explicitly stating data-parallel
5666 operations on multiple values. The parallelism is therefore added via the type
5667 system. Vc has an intuitive API and provides portability between different
5668 compilers and compiler versions as well as portability between different vector
5669 instruction sets. Thus, an application written with Vc can be compiled for:
5672 @item SSE2 up to SSE4.2 or SSE4a
5675 @item NEON (in development)
5676 @item NVIDIA GPUs / CUDA (in development)
5678 (home-page "https://github.com/VcDevel/Vc")
5679 ;; "No support_???.cpp file exists for this architecture."
5680 (supported-systems '("x86_64-linux" "i686-linux"))
5681 (license license:bsd-3)))
5683 (define-public reducelcs
5684 ;; This is the last commit which is available upstream, no
5685 ;; release happened since 2010.
5686 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
5690 (version (string-append "1.0-" revision "." (string-take commit 7)))
5695 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
5697 (file-name (string-append name "-" version "-checkout"))
5700 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
5701 (build-system gnu-build-system)
5703 `(("openlibm" ,openlibm)))
5705 `(#:tests? #f ; no tests
5707 (modify-phases %standard-phases
5708 (delete 'configure) ; No configure script exists.
5709 (replace 'install ; No install phase exists.
5710 (lambda* (#:key outputs #:allow-other-keys)
5711 (let* ((out (assoc-ref outputs "out"))
5712 (bin (string-append out "/bin")))
5713 (install-file "Approximation" bin)
5714 (install-file "CollectResults" bin)
5715 (install-file "GenerateInstances" bin)
5717 (synopsis "Approximate Longest Commons Subsequence computation tool")
5719 "@code{reduceLCS} is an implementation of the Reduce-Expand
5720 algorithm for LCS. It is a fast program to compute the approximate
5721 Longest Commons Subsequence of a set of strings.")
5722 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
5723 (license license:gpl3+))))
5725 (define-public jacal
5732 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
5735 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
5736 (patches (search-patches "jacal-fix-texinfo.patch"))))
5737 (build-system gnu-build-system)
5740 (modify-phases %standard-phases
5741 (add-before 'build 'pre-build
5742 ;; Don't use upstream's script - it really doesn't fit into
5743 ;; Guix's functional paradigm.
5744 (lambda* (#:key inputs outputs #:allow-other-keys)
5745 (substitute* "Makefile"
5746 (("^install: install-script") "install: "))))
5747 (add-after 'install 'post-install
5748 ;; Instead, we provide our own simplified script.
5749 (lambda* (#:key inputs outputs #:allow-other-keys)
5750 (let ((wrapper (string-append (assoc-ref outputs "out")
5752 (format (open wrapper (logior O_WRONLY O_CREAT))
5753 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
5754 "-e '(slib:load \"~a/lib/jacal/math\") "
5757 (assoc-ref inputs "scm")
5758 (assoc-ref outputs "out"))
5759 (chmod wrapper #o555))))
5761 (lambda* (#:key outputs #:allow-other-keys)
5762 (invoke "./configure"
5763 (string-append "--prefix="
5764 (assoc-ref outputs "out"))))))))
5765 (inputs `(("scm" ,scm)))
5766 (native-inputs `(("unzip" ,unzip)
5767 ("texinfo" ,texinfo)))
5768 (synopsis "Symbolic mathematics system")
5769 (description "GNU JACAL is an interactive symbolic mathematics program based on
5770 Scheme. It manipulate and simplify a range of mathematical expressions such
5771 as equations, scalars, vectors, and matrices.")
5772 (home-page "https://www.gnu.org/software/jacal/")
5773 (license license:gpl3+)))
5779 (home-page "https://github.com/Z3Prover/z3")
5782 (uri (git-reference (url home-page)
5783 (commit (string-append "z3-" version))))
5784 (file-name (git-file-name name version))
5787 "1hnbzq10d23drd7ksm3c1n2611c3kd0q0yxgz8y78zaafwczvwxx"))))
5788 (build-system gnu-build-system)
5790 `(#:imported-modules ((guix build python-build-system)
5791 ,@%gnu-build-system-modules)
5792 #:modules (((guix build python-build-system) #:select (site-packages))
5793 (guix build gnu-build-system)
5796 (modify-phases %standard-phases
5797 (add-after 'unpack 'enable-bytecode-determinism
5799 (setenv "PYTHONHASHSEED" "0")
5801 (add-after 'unpack 'fix-compatability
5802 ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
5804 (substitute* "src/util/mpz.cpp"
5805 (("#include <immintrin.h>") ""))
5807 (add-before 'configure 'bootstrap
5809 (invoke "python" "scripts/mk_make.py")))
5810 ;; work around gnu-build-system's setting --enable-fast-install
5811 ;; (z3's `configure' is a wrapper around the above python file,
5812 ;; which fails when passed --enable-fast-install)
5814 (lambda* (#:key inputs outputs #:allow-other-keys)
5815 (invoke "./configure"
5817 (string-append "--prefix=" (assoc-ref outputs "out"))
5818 (string-append "--pypkgdir=" (site-packages inputs outputs)))))
5819 (add-after 'configure 'change-directory
5823 (add-before 'check 'make-test-z3
5825 ;; Build the test suite executable.
5826 (invoke "make" "test-z3" "-j"
5827 (number->string (parallel-job-count)))))
5830 ;; Run all the tests that don't require arguments.
5831 (invoke "./test-z3" "/a"))))))
5834 ("python" ,python-wrapper)))
5835 (synopsis "Theorem prover")
5836 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
5837 theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
5838 (license license:expat)))
5840 (define-public ocaml-z3
5845 `(#:imported-modules ((guix build python-build-system)
5846 ,@%gnu-build-system-modules)
5847 #:modules (((guix build python-build-system) #:select (site-packages))
5848 (guix build gnu-build-system)
5850 #:tests? #f; no ml tests
5852 (modify-phases %standard-phases
5853 (add-before 'configure 'bootstrap
5854 (lambda* (#:key outputs #:allow-other-keys)
5855 (let ((out (assoc-ref outputs "out")))
5856 (setenv "OCAMLFIND_LDCONF" "ignore")
5857 (setenv "OCAMLFIND_DESTDIR" (string-append out "/lib/ocaml/site-lib"))
5858 (mkdir-p (string-append out "/lib/ocaml/site-lib"))
5859 (substitute* "scripts/mk_util.py"
5861 (string-append "LIBZ3 = LIBZ3 + ' -dllpath " out "/lib'"))
5862 ;; Do not build z3 again, use the library passed as input
5864 (("z3linkdep,") "\"\",")
5865 (("z3linkdep)") "\"\")"))
5866 (invoke "python" "scripts/mk_make.py"))))
5868 (lambda* (#:key inputs outputs #:allow-other-keys)
5869 (invoke "./configure"
5871 (string-append "--prefix=" (assoc-ref outputs "out")))))
5872 (add-after 'configure 'change-directory
5878 (invoke "make" "ml")))
5880 (lambda* (#:key outputs #:allow-other-keys)
5881 (invoke "ocamlfind" "install" "-destdir"
5882 (string-append (assoc-ref outputs "out") "/lib/ocaml/site-lib")
5883 "z3" "api/ml/META" "api/ml/z3enums.mli" "api/ml/z3enums.cmi"
5884 "api/ml/z3enums.cmx" "api/ml/z3native.mli"
5885 "api/ml/z3native.cmi" "api/ml/z3native.cmx"
5886 "../src/api/ml/z3.mli" "api/ml/z3.cmi" "api/ml/z3.cmx"
5887 "api/ml/libz3ml.a" "api/ml/z3ml.a" "api/ml/z3ml.cma"
5888 "api/ml/z3ml.cmxa" "api/ml/z3ml.cmxs" "api/ml/dllz3ml.so"))))))
5891 ("python" ,python-wrapper)
5893 ("ocaml-findlib" ,ocaml-findlib)))
5895 `(("ocaml-zarith" ,ocaml-zarith)))
5902 (version "2018.11.001")
5905 (uri (string-append "http://elpa.mpcdf.mpg.de/html/Releases/"
5906 version "/elpa-" version ".tar.gz"))
5909 "05hv3v5i6xmziaizw350ff72y1c3k662r85fm3xfdrkclj5zw9yc"))))
5910 (build-system gnu-build-system)
5912 `(("fortran" ,gfortran)
5913 ("perl" ,perl))) ;for configure and deps
5915 `(("blas" ,openblas)))
5920 ;; ELPA unfortunately does not support runtime dispatch, so we can
5921 ;; only enable the "generic" kernels. See the "Cross compilation"
5922 ;; section of INSTALL.md.
5924 "--disable-sse" "--disable-sse-assembly" ;Require SSE3
5925 "--disable-avx" "--disable-avx2" "--disable-avx512"
5926 ,(string-append "CFLAGS=-O3 "
5927 "-funsafe-loop-optimizations -funsafe-math-optimizations "
5928 "-ftree-vect-loop-version -ftree-vectorize "
5929 ,(let ((system (or (%current-target-system)
5930 (%current-system))))
5932 ((or (string-prefix? "x86_64" system)
5933 (string-prefix? "i686" system))
5936 #:parallel-tests? #f ;tests are multi-threaded, via BLAS
5938 (modify-phases %standard-phases
5939 (add-before 'configure 'patch-header-generation
5941 (substitute* "configure"
5942 (("^ *make.*top_srcdir=\"\\$srcdir\"" &)
5943 (string-append & " CPP=\"$CPP\"")))
5945 (add-before 'check 'setup-tests
5947 ;; Decrease test time and RAM use by computing fewer eigenvalues.
5948 ;; The flags are (MATRIX-SIZE, EIGENVALUES, BLOCK-SIZE), where
5949 ;; the default is (500, 250, 16) for C tests and (5000, 150, 16)
5950 ;; for Fortran. This also causes several tests to pass that
5951 ;; otherwise would otherwise fail with matrix size 5000; possibly
5952 ;; due to floating point tolerances that are too tight.
5953 (setenv "TEST_FLAGS" "1500 50 16") ;from elpa.spec
5954 (setenv "OMP_NUM_THREADS" (number->string (parallel-job-count)))
5955 (substitute* "Makefile"
5956 ;; Test scripts are generated, patch the shebang
5957 (("#!/bin/bash") (string-append "#!" (which "sh"))))
5959 (home-page "https://elpa.mpcdf.mpg.de")
5960 (synopsis "Eigenvalue solvers for symmetric matrices")
5962 "The ELPA library provides efficient and scalable direct eigensolvers for
5963 symmetric matrices.")
5964 (license license:lgpl3)))
5966 (define-public elpa-openmpi
5967 (package (inherit elpa)
5968 (name "elpa-openmpi")
5971 ("scalapack" ,scalapack)
5972 ,@(package-inputs elpa)))
5974 (substitute-keyword-arguments (package-arguments elpa)
5975 ((#:configure-flags cf '())
5976 `(cons "--with-mpi=yes" (delete "--with-mpi=no" ,cf)))
5977 ((#:phases phases '%standard-phases)
5978 `(modify-phases ,phases
5979 (add-before 'check 'mpi-setup
5981 ;; Tests use 2 mpi tasks by default, use our remaining build
5982 ;; cores as OpenMP threads.
5983 (setenv "OMP_NUM_THREADS" (number->string
5984 (max (quotient (parallel-job-count) 2)
5986 (,%openmpi-setup)))))))
5987 (synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)")))
5989 (define-public elemental
5996 (url "https://github.com/elemental/Elemental")
5997 (commit (string-append "v" version))))
5998 (file-name (git-file-name name version))
6001 "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
6002 (build-system cmake-build-system)
6003 (home-page "https://github.com/elemental/Elemental")
6005 `(("gfortran" ,gfortran)))
6007 `(("blas" ,openblas)
6008 ("gfortran:lib" ,gfortran "lib")
6017 `(#:build-type "Release" ;default RelWithDebInfo not supported
6018 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
6019 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
6020 "-DEL_CACHE_WARNINGS:BOOL=YES"
6021 "-DEL_TESTS:BOOL=YES"
6022 "-DCMAKE_INSTALL_LIBDIR=lib"
6023 "-DGFORTRAN_LIB=gfortran")
6024 #:phases (modify-phases %standard-phases
6025 (add-before 'check 'mpi-setup
6027 (add-before 'check 'setup-tests
6029 ;; Parallelism is done at the MPI layer.
6030 (setenv "OMP_NUM_THREADS" "1")
6032 (add-after 'install 'remove-tests
6033 (lambda* (#:key outputs #:allow-other-keys)
6034 ;; Tests are installed, with no easy configuration
6035 ;; switch to prevent this, so delete them.
6036 (delete-file-recursively
6037 (string-append (assoc-ref outputs "out") "/bin"))
6039 (synopsis "Dense and sparse-direct linear algebra and optimization")
6040 (description "Elemental is a modern C++ library for distributed-memory
6041 dense and sparse-direct linear algebra, conic optimization, and lattice
6043 (license license:bsd-2)))
6045 (define-public mcrl2
6048 (version "202106.0")
6052 "https://www.mcrl2.org/download/release/mcrl2-"
6056 "1xgx3cd57vc7gbjic24j1q2za6j3ybz6nk4afvvpbwsf33xnlf4v"))))
6061 ("qtbase" ,qtbase-5)))
6062 (build-system cmake-build-system)
6063 (synopsis "Toolset for the mCRL2 formal specification language")
6065 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
6066 specification language for describing concurrent discrete event systems. Its
6067 toolset supports analysis and automatic verification, linearisation, simulation,
6068 state-space exploration and generation, and tools to optimise and analyse
6069 specifications. Also, state spaces can be manipulated, visualised and
6071 (home-page "https://mcrl2.org")
6072 (license license:boost1.0)))
6074 (define-public mcrl2-minimal
6077 (name "mcrl2-minimal")
6079 `(("boost" ,boost)))
6081 '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
6083 (define-public tcalc
6090 (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
6094 "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
6095 (build-system gnu-build-system)
6096 (synopsis "The terminal calculator")
6098 "The terminal calculator is a small program to help users of the GNU/Linux
6099 terminal do calculations simply and quickly. The formula to be calculated can
6100 be fed to @command{tcalc} through the command line.")
6101 (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
6102 (license license:gpl3+)))
6104 (define-public tiny-bignum
6105 (let ((commit "1d7a1f9b8e77316187a6b3eae8e68d60a6f9a4d4"))
6107 (name "tiny-bignum")
6108 (version (git-version "0" "0" commit))
6113 (url "https://github.com/kokke/tiny-bignum-c")
6115 (file-name (git-file-name "tiny-bignum" commit))
6117 (base32 "0vj71qlhlaa7d92bfar1kwqv6582dqrby8x3kdw0yzh82k2023g6"))))
6118 (build-system gnu-build-system)
6121 (modify-phases %standard-phases
6123 (add-after 'unpack 'patch-tests
6125 (substitute* "scripts/test_rand.py"
6127 (("\" % (\\w+)" _ symbol) (string-append "\" % int(" symbol ")")))
6130 (lambda* (#:key tests? #:allow-other-keys)
6132 (invoke "make" "test"))
6135 (lambda* (#:key outputs #:allow-other-keys)
6136 (let ((share (string-append (assoc-ref outputs "out") "/share"))
6137 (doc (string-append (assoc-ref outputs "out") "/doc")))
6139 (install-file "bn.c" share)
6140 (install-file "bn.h" share)
6142 (install-file "LICENSE" doc)
6143 (install-file "README.md" doc))
6146 `(("python" ,python-wrapper)))
6147 (home-page "https://github.com/kokke/tiny-bignum-c")
6148 (synopsis "Small portable multiple-precision unsigned integer arithmetic in C")
6150 "This library provides portable Arbitrary-precision unsigned integer
6151 arithmetic in C, for calculating with large numbers. Basic arithmetic (+, -,
6152 *, /, %) and bitwise operations (&, |, ^. <<, >>) plus increments, decrements
6153 and comparisons are supported.")
6154 (license license:unlicense))))
6156 (define-public sundials
6163 (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
6164 "sundials-" version ".tar.gz"))
6167 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
6168 (build-system cmake-build-system)
6170 `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
6172 `(("fortran" ,gfortran) ;for fcmix
6174 ("suitesparse" ,suitesparse))) ;TODO: Add hypre
6176 `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
6177 "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
6178 "-DEXAMPLES_ENABLE_F77:BOOL=ON"
6179 "-DEXAMPLES_ENABLE_F90:BOOL=ON"
6180 "-DEXAMPLES_INSTALL:BOOL=OFF"
6182 "-DFCMIX_ENABLE:BOOL=ON"
6184 "-DKLU_ENABLE:BOOL=ON"
6185 ,(string-append "-DKLU_INCLUDE_DIR="
6186 (assoc-ref %build-inputs "suitesparse")
6188 ,(string-append "-DKLU_LIBRARY_DIR="
6189 (assoc-ref %build-inputs "suitesparse")
6191 (home-page "https://computation.llnl.gov/projects/sundials")
6192 (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
6193 (description "SUNDIALS is a family of software packages implemented with
6194 the goal of providing robust time integrators and nonlinear solvers that can
6195 easily be incorporated into existing simulation codes.")
6196 (license license:bsd-3)))
6198 (define-public sundials-openmpi
6199 (package (inherit sundials)
6200 (name "sundials-openmpi")
6203 ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
6204 ,@(package-inputs sundials)))
6206 (substitute-keyword-arguments (package-arguments sundials)
6207 ((#:configure-flags flags '())
6208 `(cons* "-DMPI_ENABLE:BOOL=ON"
6209 "-DPETSC_ENABLE:BOOL=ON"
6210 (string-append "-DPETSC_INCLUDE_DIR="
6211 (assoc-ref %build-inputs "petsc")
6213 (string-append "-DPETSC_LIBRARY_DIR="
6214 (assoc-ref %build-inputs "petsc")
6217 ((#:phases phases '%standard-phases)
6218 `(modify-phases ,phases
6219 (add-before 'check 'mpi-setup
6220 ,%openmpi-setup)))))
6221 (synopsis "SUNDIALS with OpenMPI support")))
6223 (define-public sundials-julia
6226 (name "sundials-julia")
6232 (url "https://github.com/LLNL/sundials")
6233 (commit (string-append "v" version))))
6234 (file-name (git-file-name name version))
6237 "0nx4sqhmi126m14myzm7syv2053harav9snl0a247wnkcgs5rxrv"))))
6239 `(("lapack" ,lapack)
6240 ,@(package-inputs sundials)))
6242 (substitute-keyword-arguments (package-arguments sundials)
6243 ((#:configure-flags flags '())
6244 `(cons* "-DLAPACK_ENABLE:BOOL=ON"
6246 (synopsis "SUNDIALS with lapack support as required by julia-sundials-jll")))
6248 (define-public combinatorial-blas
6250 (name "combinatorial-blas")
6255 (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/"
6257 (match (string-split version #\.)
6258 ((major minor patch)
6259 (string-append major minor "_" patch))) ;e.g. "16_2"
6263 "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a"))
6264 (patches (search-patches "combinatorial-blas-awpm.patch"
6265 "combinatorial-blas-io-fix.patch"))))
6266 (build-system cmake-build-system)
6269 ("test-data" ,(origin
6271 (uri (string-append "https://people.eecs.berkeley.edu/~aydin/"
6272 "CombBLAS_FILES/testdata_combblas1.6.1.tgz"))
6275 "01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87"))))))
6277 `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
6278 "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL")
6279 #:parallel-tests? #f ;tests use 'mpiexec -n4'
6281 (modify-phases %standard-phases
6282 (add-before 'check 'mpi-setup
6284 (add-before 'check 'test-setup
6285 (lambda* (#:key inputs #:allow-other-keys)
6286 (setenv "OMP_NUM_THREADS" "2")
6287 (invoke "tar" "xf" (assoc-ref inputs "test-data")))))))
6288 (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/")
6289 (synopsis "Linear algebra primitives for graph analytics")
6290 (description "The Combinatorial BLAS (CombBLAS) is an extensible
6291 distributed-memory parallel graph library offering a small but powerful set of
6292 linear algebra primitives specifically targeting graph analytics.")
6294 license:gpl2+ ;include/psort/(funnel|sort)*.h
6295 license:x11 ;usort and psort
6296 license:bsd-3)))) ;CombBLAS and MersenneTwister.h
6298 (define-public dune-common
6300 (name "dune-common")
6305 (uri (string-append "https://dune-project.org/download/"
6306 version "/dune-common-" version ".tar.gz"))
6309 "140q1zh44cr5yrjwg4b5ga803rkqv55vk30l2cqm29aklj1wb0rw"))))
6310 (build-system cmake-build-system)
6313 (modify-phases %standard-phases
6314 (add-after 'build 'build-tests
6315 (lambda* (#:key make-flags #:allow-other-keys)
6316 (apply invoke "make" "build_tests" make-flags))))))
6320 ("openblas" ,openblas)
6322 ("superlu" ,superlu)))
6324 `(("gfortran" ,gfortran)
6325 ("pkg-config" ,pkg-config)))
6326 (home-page "https://dune-project.org/")
6327 (synopsis "Distributed and Unified Numerics Environment")
6328 (description "DUNE, the Distributed and Unified Numerics Environment is a
6329 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
6330 grid-based methods. It supports the easy implementation of methods like
6331 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
6332 Differences} (FD).")
6333 ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2.
6334 (license license:gpl2)))
6336 (define-public dune-geometry
6338 (name "dune-geometry")
6343 (uri (string-append "https://dune-project.org/download/"
6344 version "/dune-geometry-" version ".tar.gz"))
6347 "1cicvlwbyyw76npicnblxckyvhbfn3ip8isydiv3hlrlz8zcg5nr"))))
6348 (build-system cmake-build-system)
6351 (modify-phases %standard-phases
6352 (add-after 'build 'build-tests
6353 (lambda* (#:key make-flags #:allow-other-keys)
6354 (apply invoke "make" "build_tests" make-flags))))))
6356 `(("dune-common" ,dune-common)
6358 ("openblas" ,openblas)
6360 ("python" ,python)))
6362 `(("gfortran" ,gfortran)
6363 ("pkg-config" ,pkg-config)))
6364 (home-page "https://dune-project.org/")
6365 (synopsis "Distributed and Unified Numerics Environment")
6366 (description "DUNE, the Distributed and Unified Numerics Environment is a
6367 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
6368 grid-based methods. It supports the easy implementation of methods like
6369 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
6372 This package contains the basic DUNE geometry classes.")
6373 ;; GPL version 2 with "runtime exception"
6374 (license license:gpl2)))
6376 (define-public dune-uggrid
6378 (name "dune-uggrid")
6384 (url "https://gitlab.dune-project.org/staging/dune-uggrid.git")
6385 (commit (string-append "v" version))))
6386 (file-name (git-file-name name version))
6389 "192miqgmfj6jwk969gydzpbv9ki7jg5nky3ydnrwa2nq29b5xkh0"))))
6390 (build-system cmake-build-system)
6393 (modify-phases %standard-phases
6394 (add-after 'build 'build-tests
6395 (lambda* (#:key make-flags #:allow-other-keys)
6396 (apply invoke "make" "build_tests" make-flags))))))
6398 `(("dune-common" ,dune-common)))
6400 `(("gfortran" ,gfortran)
6401 ("pkg-config" ,pkg-config)))
6402 (home-page "https://dune-project.org/")
6403 (synopsis "Distributed and Unified Numerics Environment")
6404 (description "DUNE, the Distributed and Unified Numerics Environment is a
6405 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
6406 grid-based methods. It supports the easy implementation of methods like
6407 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
6410 This package contains the DUNE UG grid classes.")
6411 (license license:lgpl2.1)))
6413 (define-public dune-grid
6420 (uri (string-append "https://dune-project.org/download/"
6421 version "/dune-grid-" version ".tar.gz"))
6424 "17fjz30qazjgl11sryyxnw9klai4yz1ji4bs68013xcxc5hdv27s"))))
6425 (build-system cmake-build-system)
6428 (modify-phases %standard-phases
6429 (add-after 'build 'build-tests
6430 (lambda* (#:key make-flags #:allow-other-keys)
6431 (apply invoke "make" "build_tests" make-flags))))))
6433 `(("dune-common" ,dune-common)
6434 ("dune-geometry" ,dune-geometry)
6437 ("openblas" ,openblas)
6438 ("python" ,python)))
6440 `(("dune-uggrid" ,dune-uggrid)))
6442 `(("gfortran" ,gfortran)
6443 ("pkg-config" ,pkg-config)))
6444 (home-page "https://dune-project.org/")
6445 (synopsis "Distributed and Unified Numerics Environment")
6446 (description "DUNE, the Distributed and Unified Numerics Environment is a
6447 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
6448 grid-based methods. It supports the easy implementation of methods like
6449 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
6452 This package contains the basic DUNE grid classes.")
6453 ;; GPL version 2 with "runtime exception"
6454 (license license:gpl2)))
6456 (define-public dune-istl
6463 (uri (string-append "https://dune-project.org/download/"
6464 version "/dune-istl-" version ".tar.gz"))
6467 "0gl3wgz5rs6sb4m83440ny45sbx7z7lnbi3gx6r9nm3rvy5j33f9"))
6468 (patches (search-patches "dune-istl-2.7-fix-non-mpi-tests.patch"))))
6469 (build-system cmake-build-system)
6472 (modify-phases %standard-phases
6473 ;; XXX: istl/test/matrixtest.cc includes <fenv.h> and fails to find
6474 ;; the stdlib types when the gfortran header is used. Remove gfortran
6475 ;; from CPLUS_INCLUDE_PATH as a workaround.
6476 (add-after 'set-paths 'hide-gfortran
6477 (lambda* (#:key inputs #:allow-other-keys)
6478 (let ((gfortran (assoc-ref inputs "gfortran")))
6479 (setenv "CPLUS_INCLUDE_PATH"
6481 (delete (string-append gfortran "/include/c++")
6482 (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
6485 (add-after 'build 'build-tests
6486 (lambda* (#:key make-flags #:allow-other-keys)
6487 (apply invoke "make" "build_tests" make-flags))))))
6489 `(("dune-common" ,dune-common)
6492 ("suitesparse" ,suitesparse)
6493 ("superlu" ,superlu)
6494 ("openblas" ,openblas)
6496 ("python" ,python)))
6498 `(("gfortran" ,gfortran)
6499 ("pkg-config" ,pkg-config)))
6500 (home-page "https://dune-project.org/")
6501 (synopsis "Distributed and Unified Numerics Environment")
6502 (description "DUNE, the Distributed and Unified Numerics Environment is a
6503 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
6506 This is the iterative solver template library which provides generic sparse
6507 matrix/vector classes and a variety of solvers based on these classes. A
6508 special feature is the use of templates to exploit the recursive block
6509 structure of finite element matrices at compile time. Available solvers
6510 include Krylov methods, (block-) incomplete decompositions and
6511 aggregation-based algebraic multigrid.")
6512 ;; GPL version 2 with "runtime exception"
6513 (license license:gpl2)))
6515 (define-public dune-localfunctions
6517 (name "dune-localfunctions")
6522 (uri (string-append "https://dune-project.org/download/"
6523 version "/dune-localfunctions-" version ".tar.gz"))
6526 "1yih59h6vngii696bx1c2vil02lriij4kz0nc583mjn9kiaqxfqd"))))
6527 (build-system cmake-build-system)
6530 (modify-phases %standard-phases
6531 ;; XXX: localfunctions/test/lagrangeshapefunctiontest.cc includes <fenv.h>
6532 ;; and fails to find the stdlib types when the gfortran header is used.
6533 ;; Hide gfortran from CPLUS_INCLUDE_PATH to ensure we get the GCC header.
6534 (add-after 'set-paths 'hide-gfortran
6535 (lambda* (#:key inputs #:allow-other-keys)
6536 (let ((gfortran (assoc-ref inputs "gfortran")))
6537 (setenv "CPLUS_INCLUDE_PATH"
6539 (delete (string-append gfortran "/include/c++")
6540 (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
6543 (add-after 'build 'build-tests
6544 (lambda* (#:key make-flags #:allow-other-keys)
6545 (apply invoke "make" "build_tests" make-flags))))))
6547 `(("dune-common" ,dune-common)
6548 ("dune-geometry" ,dune-geometry)
6551 ("superlu" ,superlu)
6554 `(("gfortran" ,gfortran)
6555 ("pkg-config" ,pkg-config)))
6556 (home-page "https://dune-project.org/")
6557 (synopsis "Distributed and Unified Numerics Environment") ; TODO
6558 (description "This DUNE module provides interface and implementation for
6559 shape functions defined on the DUNE reference elements. In addition to the
6560 shape function, interpolation operators and special keys are provided which
6561 can be used to assemble global function spaces on finite-element grids.
6563 This package provides an interface and implementation for shape functions
6564 defined on the DUNE reference elements. In addition to the shape function,
6565 interpolation operators and special keys are provided which can be used to
6566 assemble global function spaces on finite-element grids.")
6567 ;; GPL version 2 with "runtime exception"
6568 (license license:gpl2)))
6570 (define-public dune-alugrid
6572 (name "dune-alugrid")
6573 (version "2.7.0-git-81d35682")
6578 (url "https://gitlab.dune-project.org/extensions/dune-alugrid.git")
6579 (commit "81d356827c84454b971937db02c02b90bbcd7fe5")))
6580 (file-name (git-file-name name version))
6583 "0z54lwfp53prcrs94k8gwh047l9z642jll3l56xlyfr69z0b2zz1"))))
6584 (build-system cmake-build-system)
6587 (modify-phases %standard-phases
6588 (add-after 'unpack 'patch-include
6590 (substitute* "dune/alugrid/test/test-alugrid.cc"
6591 (("doc/grids/gridfactory/testgrids")
6592 "doc/dune-grid/grids/gridfactory/testgrids"))
6594 (add-after 'build 'build-tests
6595 (lambda* (#:key inputs make-flags #:allow-other-keys)
6596 (setenv "CPLUS_INCLUDE_PATH"
6597 (string-append (assoc-ref inputs "dune-grid") "/share"))
6598 (apply invoke "make" "build_tests" make-flags))))))
6600 `(("dune-common" ,dune-common)
6601 ("dune-geometry" ,dune-geometry)
6602 ("dune-grid" ,dune-grid)
6605 ("openblas" ,openblas)
6607 ("superlu" ,superlu)
6611 `(("gfortran" ,gfortran)
6612 ("pkg-config" ,pkg-config)))
6613 (home-page "https://dune-project.org/")
6614 (synopsis "Distributed and Unified Numerics Environment")
6615 (description "ALUGrid is an adaptive, loadbalancing, unstructured
6616 implementation of the DUNE grid interface supporting either simplices or
6618 (license license:gpl2+)))
6620 (define-public dune-subgrid
6622 (name "dune-subgrid")
6623 (version "2.7.0-git-2103a363")
6628 (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid")
6629 (commit "2103a363f32e8d7b60e66eee7ddecf969f6cf762")))
6630 (file-name (git-file-name name version))
6633 "1wsjlypd3835c3arqjkw836cxx5q67zy447wa65q634lf6f6v9ia"))))
6634 (build-system cmake-build-system)
6637 (modify-phases %standard-phases
6638 (add-after 'build 'build-tests
6639 (lambda* (#:key make-flags #:allow-other-keys)
6640 (apply invoke "make" "build_tests" make-flags))))))
6642 `(("dune-common" ,dune-common)
6643 ("dune-geometry" ,dune-geometry)
6644 ("dune-grid" ,dune-grid)
6647 ("openblas" ,openblas)
6650 `(("gfortran" ,gfortran)
6651 ("pkg-config" ,pkg-config)))
6652 (home-page "http://numerik.mi.fu-berlin.de/dune-subgrid/index.php")
6653 (synopsis "Distributed and Unified Numerics Environment")
6654 (description "The dune-subgrid module marks elements of
6655 another hierarchical dune grid. The set of marked elements can then be
6656 accessed as a hierarchical dune grid in its own right. Dune-Subgrid
6657 provides the full grid interface including adaptive mesh refinement.")
6658 (license license:gpl2+)))
6660 (define-public dune-typetree
6662 (name "dune-typetree")
6668 (url "https://gitlab.dune-project.org/staging/dune-typetree.git")
6669 (commit (string-append "v" version))))
6670 (file-name (git-file-name name version))
6673 "1rhv25yg0q1hw50c8wlfqhgwrjl4mh62zq9v14ilwgzbfgxmpiy7"))))
6674 (build-system cmake-build-system)
6677 (modify-phases %standard-phases
6678 (add-after 'build 'build-tests
6679 (lambda* (#:key make-flags #:allow-other-keys)
6680 (apply invoke "make" "build_tests" make-flags))))))
6682 `(("dune-common" ,dune-common)
6684 ("openblas" ,openblas)
6687 ("superlu" ,superlu)
6690 `(("gfortran" ,gfortran)
6691 ("pkg-config" ,pkg-config)))
6692 (home-page "https://dune-project.org/")
6693 (synopsis "Distributed and Unified Numerics Environment")
6694 (description "TypeTree is a template library for constructing and
6695 operating on statically typed trees of objects.")
6696 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
6697 (license (list license:lgpl3+ license:gpl2))))
6699 (define-public dune-functions
6701 (name "dune-functions")
6707 (url "https://gitlab.dune-project.org/staging/dune-functions.git")
6708 (commit (string-append "v" version))))
6709 (file-name (git-file-name name version))
6712 "1na4gcih0kin37ksj2xj07ds04v7zx53pjdhm1hzy55jjfqdjk8h"))))
6713 (build-system cmake-build-system)
6716 (modify-phases %standard-phases
6717 (add-after 'unpack 'disable-failing-tests
6720 ;; unable to load GMSH file in this test
6721 "--exclude-regex gridviewfunctionspacebasistest")
6723 (add-after 'build 'build-tests
6724 (lambda* (#:key make-flags #:allow-other-keys)
6725 (apply invoke "make" "build_tests" make-flags))))))
6727 `(("dune-common" ,dune-common)
6728 ("dune-istl" ,dune-istl)
6729 ("dune-localfunctions" ,dune-localfunctions)
6730 ("dune-grid" ,dune-grid)
6731 ("dune-geometry" ,dune-geometry)
6732 ("dune-typetree" ,dune-typetree)
6733 ("openblas" ,openblas)
6736 ("superlu" ,superlu)
6739 `(("gfortran" ,gfortran)
6740 ("pkg-config" ,pkg-config)))
6741 (home-page "https://dune-project.org/")
6742 (synopsis "Distributed and Unified Numerics Environment")
6743 (description "The dune-functions module provides an abstraction layer for
6744 global finite element functions. Its two main concepts are functions
6745 implemented as callable objects, and bases of finite element spaces.")
6746 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
6747 (license (list license:lgpl3+ license:gpl2))))
6749 (define-public dune-pdelab
6751 (name "dune-pdelab")
6752 (version "2.7.0-git-476fe437")
6757 (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
6758 (commit "476fe43763fa6f459c5e4658e2a2b4b5582db834")))
6759 (file-name (git-file-name name version))
6762 "0cs36piqzn6rq0j2ih3ab3q3q9yg199wk72k5qi86pkzh7i7fdn1"))))
6763 (build-system cmake-build-system)
6764 (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
6766 `(("dune-common" ,dune-common)
6767 ("dune-istl" ,dune-istl)
6768 ("dune-localfunctions" ,dune-localfunctions)
6769 ("dune-geometry" ,dune-geometry)
6770 ("dune-grid" ,dune-grid)
6771 ("dune-typetree" ,dune-typetree)
6772 ("dune-functions" ,dune-functions)
6774 ("openblas" ,openblas)
6778 ("superlu" ,superlu)
6781 `(("gfortran" ,gfortran)
6782 ("pkg-config" ,pkg-config)))
6783 (home-page "https://dune-project.org/")
6784 (synopsis "Differential equations solver toolbox")
6785 (description "PDELab is a partial differential equations solver toolbox
6786 built on top of DUNE, the Distributed and Unified Numerics Environment.")
6787 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
6788 (license (list license:lgpl3+ license:gpl2))))
6790 (define add-openmpi-to-dune-package
6791 (let ((dune-package?
6792 (lambda (p) (string-prefix? "dune-" (package-name p)))))
6795 (if (dune-package? p)
6796 (package (inherit p)
6797 (name (string-append (package-name p) "-openmpi"))
6798 (inputs `(,@(package-inputs p)
6799 ("openmpi" ,openmpi)))
6801 (substitute-keyword-arguments (package-arguments p)
6802 ((#:phases phases '%standard-phases)
6803 `(modify-phases ,phases
6804 (add-before 'check 'mpi-setup
6805 ,%openmpi-setup)))))
6806 (synopsis (string-append (package-synopsis p) " (with MPI support)")))
6808 (negate dune-package?))))
6810 (define-public dune-common-openmpi
6811 (add-openmpi-to-dune-package dune-common))
6813 (define-public dune-geometry-openmpi
6814 (add-openmpi-to-dune-package dune-geometry))
6816 (define-public dune-istl-openmpi
6817 (add-openmpi-to-dune-package dune-istl))
6819 (define-public dune-typetree-openmpi
6820 (add-openmpi-to-dune-package dune-typetree))
6822 (define-public dune-uggrid-openmpi
6823 (add-openmpi-to-dune-package dune-uggrid))
6825 (define-public dune-grid-openmpi
6826 (add-openmpi-to-dune-package dune-grid))
6828 (define-public dune-alugrid-openmpi
6829 (add-openmpi-to-dune-package dune-alugrid))
6831 (define-public dune-subgrid-openmpi
6832 (add-openmpi-to-dune-package dune-subgrid))
6834 (define-public dune-localfunctions-openmpi
6835 (add-openmpi-to-dune-package dune-localfunctions))
6837 (define-public dune-functions-openmpi
6838 (add-openmpi-to-dune-package dune-functions))
6840 (define-public dune-pdelab-openmpi
6841 (add-openmpi-to-dune-package dune-pdelab))
6843 (define-public mlucas
6851 "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz"))
6853 (base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447"))))
6854 (build-system gnu-build-system)
6856 `(("python2" ,python-2)))
6858 `(#:tests? #f ; no tests
6860 (modify-phases %standard-phases
6864 (call-with-output-file "Makefile"
6866 (format port "CC = gcc
6867 CFLAGS = -O3 ~a -DUSE_THREADS
6868 LDLIBS = -lm -lpthread -lrt
6869 Mlucas: $(addsuffix .o,$(basename $(wildcard *.c)))
6871 ,(let ((system (or (%current-target-system)
6872 (%current-system))))
6874 ((string-prefix? "x86_64" system) "-DUSE_SSE2")
6878 (lambda* (#:key outputs #:allow-other-keys)
6879 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
6880 (install-file "Mlucas" bin)
6881 (install-file "primenet.py" bin))
6883 (home-page "https://www.mersenne.org")
6884 (synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client")
6885 (description "Mlucas performs Lucas-Lehmer primality testing of Mersenne
6886 numbers in search of a world-record prime. You may use it to test any
6887 suitable number as you wish, but it is preferable that you do so in a
6888 coordinated fashion, as part of the Great Internet Mersenne Prime
6889 Search (GIMPS). Mlucas also includes a simple Python script for assignment
6890 management via the GIMPS project's Primenet server.")
6891 (license license:gpl2+)))
6893 (define-public nauty
6901 "https://pallini.di.uniroma1.it/"
6902 "nauty" (string-join (string-split version #\.) "") ".tar.gz"))
6904 (base32 "1hl81gpf3xjf809w04jczvilq1ixy9ch1qrax8a7lgx52svna1jg"))))
6905 (build-system gnu-build-system)
6906 (outputs '("out" "lib"))
6908 `(#:test-target "checks"
6909 #:configure-flags '("--enable-generic") ;prevent -march-native
6911 (modify-phases %standard-phases
6912 ;; Default make target does not build all available
6913 ;; executables. Create them now.
6914 (add-after 'build 'build-extra-programs
6916 (for-each (lambda (target) (invoke "make" target))
6917 '("blisstog" "bliss2dre" "checks6" "sumlines"))
6919 ;; Upstream does not provide any install target.
6921 (lambda* (#:key outputs #:allow-other-keys)
6922 (let* ((out (assoc-ref outputs "out"))
6923 (lib-output (assoc-ref outputs "lib"))
6924 (bin (string-append out "/bin"))
6925 (doc (string-append out "/share/doc/nauty/"))
6926 (include (string-append lib-output "/include/nauty"))
6927 (lib (string-append lib-output "/lib/nauty")))
6928 (for-each (lambda (f) (install-file f bin))
6929 '("addedgeg" "amtog" "assembleg" "biplabg" "blisstog"
6930 "bliss2dre" "catg" "checks6" "complg" "converseg"
6931 "copyg" "countg" "cubhamg" "deledgeg" "delptg"
6932 "directg" "dreadnaut" "dretodot" "dretog" "genbg"
6933 "genbgL" "geng" "genquarticg" "genrang" "genspecialg"
6934 "gentourng" "gentreeg" "hamheuristic" "labelg"
6935 "linegraphg" "listg" "multig" "newedgeg" "pickg"
6936 "planarg" "ranlabg" "shortg" "showg" "subdivideg"
6937 "sumlines" "twohamg" "underlyingg" "vcolg"
6938 "watercluster2" "NRswitchg"))
6939 (for-each (lambda (f) (install-file f include))
6940 (find-files "." "\\.h$"))
6941 (for-each (lambda (f) (install-file f lib))
6942 (find-files "." "\\.a$"))
6943 (for-each (lambda (f) (install-file f doc))
6944 (append '("formats.txt" "README" "schreier.txt")
6945 (find-files "." "\\.pdf$")))))))))
6947 `(("gmp" ,gmp))) ;for sumlines
6948 (home-page "https://pallini.di.uniroma1.it/")
6949 (synopsis "Library for graph automorphisms")
6950 (description "@code{nauty} (No AUTomorphisms, Yes?) is a set of
6951 procedures for computing automorphism groups of graphs and digraphs.
6953 @code{nauty} computes graph information in the form of a set of
6954 generators, the size of the group, and the orbits of the group; it can
6955 also produce a canonical label. The @code{nauty} suite is written in
6956 C and comes with a command-line interface, a collection of
6957 command-line tools, and an Application Programming Interface (API).
6959 This package provides the static libraries required to run programs
6960 compiled against the nauty library.")
6961 (license license:asl2.0)))
6970 (uri (string-append "https://www.bugseng.com/products/ppl/download/"
6971 "ftp/releases/" version
6972 "/ppl-" version ".tar.gz"))
6975 "1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb"))))
6976 (build-system gnu-build-system)
6982 (home-page "https://www.bugseng.com/parma-polyhedra-library")
6984 "Parma Polyhedra Library for computations with polyhedra")
6986 "The Parma Polyhedra Library (PPL) provides numerical abstractions
6987 especially targeted at applications in the field of analysis and
6988 verification of complex systems. These abstractions include convex
6989 polyhedra, defined as the intersection of a finite number of (open or
6990 closed) halfspaces, each described by a linear inequality (strict or
6991 non-strict) with rational coefficients; some special classes of polyhedra
6992 shapes that offer interesting complexity/precision tradeoffs; and grids
6993 which represent regularly spaced points that satisfy a set of linear
6994 congruence relations. The library also supports finite powersets and
6995 products of (any kind of) polyhedra and grids, a mixed integer linear
6996 programming problem solver using an exact-arithmetic version of the simplex
6997 algorithm, a parametric integer programming solver, and primitives for
6998 termination analysis via the automatic synthesis of linear ranking
7000 (license license:gpl3+)))
7002 (define-public speedcrunch
7004 (name "speedcrunch")
7010 (url "https://bitbucket.org/heldercorreia/speedcrunch.git")
7011 (commit (string-append "release-" version))))
7012 (file-name (git-file-name name version))
7015 "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"))))
7016 (build-system cmake-build-system)
7017 (inputs `(("qtbase" ,qtbase-5)))
7018 (native-inputs `(("qttools" ,qttools)))
7021 (modify-phases %standard-phases
7022 (add-after 'unpack 'chdir-to-src
7023 (lambda _ (chdir "src") #t)))))
7024 (synopsis "High-precision scientific calculator")
7026 "SpeedCrunch is a high-precision scientific calculator. It features a
7027 syntax-highlighted scrollable display and is designed to be fully used via
7028 keyboard. Some distinctive features are auto-completion of functions and
7029 variables, a formula book, and quick insertion of constants from various
7030 fields of knowledge.")
7031 (home-page "https://speedcrunch.org/")
7032 (license license:gpl2+)))
7034 (define-public minisat
7035 ;; This is the last commit which is available upstream, no
7036 ;; release happened since 2010.
7037 (let ((commit "37dc6c67e2af26379d88ce349eb9c4c6160e8543")
7041 (version (string-append "2.2.0-" revision "." (string-take commit 7)))
7046 (url "https://github.com/niklasso/minisat")
7048 (file-name (string-append name "-" version "-checkout"))
7051 "091hf3qkm197s5r7xcr3m07xsdwyz2rqk1hc9kj0hn13imz09irq"))
7053 (search-patches "minisat-friend-declaration.patch"
7054 "minisat-install.patch"))))
7055 (build-system gnu-build-system)
7057 '(#:make-flags (list (string-append "prefix=" %output))
7058 #:tests? #f ;no check target
7060 (modify-phases %standard-phases
7061 (delete 'configure))))
7063 `(("zlib:static" ,zlib "static")
7066 "Small, yet efficient, SAT solver")
7068 "MiniSat is a minimalistic, open-source SAT solver, developed to help
7069 researchers and developers alike to get started on SAT.")
7071 "http://minisat.se/MiniSat.html")
7072 (license license:expat))))
7074 (define-public libqalculate
7076 (name "libqalculate")
7082 (url "https://github.com/Qalculate/libqalculate/")
7083 (commit (string-append "v" version))))
7084 (file-name (git-file-name name version))
7086 (base32 "1w44407wb552q21dz4m2nwwdi8b9hzjb2w1l3ffsikzqckc7wbyj"))
7088 (search-patches "libqalculate-3.8.0-libcurl-ssl-fix.patch"))))
7089 (build-system gnu-build-system)
7091 `(("pkg-config" ,pkg-config)
7092 ("gettext" ,gettext-minimal)
7093 ("intltool" ,intltool)
7094 ("automake" ,automake)
7095 ("autoconf" ,autoconf)
7096 ("libtool" ,libtool)
7097 ("doxygen" ,doxygen)
7102 ("libxml2" ,libxml2)
7105 ("gnuplot" ,gnuplot)
7106 ("readline" ,readline)
7107 ("libiconv" ,libiconv)))
7110 (modify-phases %standard-phases
7111 (add-before 'bootstrap 'setenv
7112 ;; Prevent the autogen.sh script to carry out the configure
7113 ;; script, which has not yet been patched to replace /bin/sh.
7115 (setenv "NOCONFIGURE" "TRUE")
7117 (home-page "https://qalculate.github.io/")
7118 (synopsis "Multi-purpose cli desktop calculator and library")
7120 "Libqalculate is a multi-purpose cli desktop calculator and library.
7121 It provides basic and advanced functionality. Features include customizable
7122 functions, unit calculations, and conversions, physical constants, symbolic
7123 calculations (including integrals and equations), arbitrary precision,
7124 uncertainty propagation, interval arithmetic, plotting and a user-friendly
7126 (license license:gpl2+)))
7128 (define-public qalculate-gtk
7130 (name "qalculate-gtk")
7136 (url "https://github.com/Qalculate/qalculate-gtk/")
7137 (commit (string-append "v" version))))
7138 (file-name (git-file-name name version))
7140 (base32 "1nrx7gp6f1yalbdda1gb97azhbr4xclq2xf08vvbvsk8jfd6fd2v"))))
7141 (build-system glib-or-gtk-build-system)
7143 `(("pkg-config" ,pkg-config)
7144 ("intltool" ,intltool)
7145 ("automake" ,automake)
7146 ("autoconf" ,autoconf)
7147 ("libtool" ,libtool)
7152 ("libqalculate" ,libqalculate)
7153 ("libxml2" ,libxml2)
7158 (modify-phases %standard-phases
7159 (add-before 'bootstrap 'setenv
7160 ;; Prevent the autogen.sh script to carry out the configure
7161 ;; script, which has not yet been patched to replace /bin/sh.
7163 (setenv "NOCONFIGURE" "TRUE")
7165 (home-page "https://qalculate.github.io/")
7166 (synopsis "Multi-purpose graphical desktop calculator")
7168 "Qalculate-gtk is the GTK frontend for libqalculate. It is a
7169 multi-purpose GUI desktop calculator. It provides basic and advanced
7170 functionality. Features include customizable functions, unit calculations,
7171 and conversions, physical constants, symbolic calculations (including
7172 integrals and equations), arbitrary precision, uncertainty propagation,
7173 interval arithmetic, plotting.")
7174 (license license:gpl2+)))
7176 (define-public numdiff
7183 (uri (string-append "mirror://savannah/numdiff/numdiff-"
7187 "1vzmjh8mhwwysn4x4m2vif7q2k8i19x8azq7pzmkwwj4g48lla47"))))
7188 (build-system gnu-build-system)
7190 '(#:tests? #f ; There are no tests.
7192 (modify-phases %standard-phases
7193 (add-before 'compress-documentation 'delete-precompressed-info-file
7195 (delete-file (string-append (assoc-ref %outputs "out")
7196 "/share/info/numdiff.info.gz"))
7198 (home-page "https://nongnu.org/numdiff/")
7199 (synopsis "Compare files with numeric fields")
7201 "Numdiff compares files line by line and field by field, ignoring small
7202 numeric differences and differences in numeric formats.")
7203 (license license:gpl3+)))
7212 (url "https://gitlab.inria.fr/why3/why3")
7214 (file-name (git-file-name name version))
7217 "0pfsiddnk26f384wbazfpgzh1n1ibf3xq101q74mxvczi7z0a791"))))
7218 (build-system ocaml-build-system)
7220 `(("autoconf" ,autoconf)
7221 ("automake" ,automake)
7226 `(("camlzip" ,camlzip)
7227 ("ocaml-graph" ,ocaml-graph)
7228 ("ocaml-menhir" ,ocaml-menhir)
7229 ("ocaml-num" ,ocaml-num)
7230 ("ocaml-zarith" ,ocaml-zarith)))
7232 `(("coq-flocq" ,coq-flocq)
7233 ("emacs-minimal" ,emacs-minimal)
7237 (modify-phases %standard-phases
7238 (add-before 'configure 'bootstrap
7240 (invoke "./autogen.sh")
7241 (setenv "CONFIG_SHELL" (which "sh"))
7242 (substitute* "configure"
7243 (("#! /bin/sh") (string-append "#!" (which "sh")))
7244 ;; find ocaml-num in the correct directory
7245 (("\\$DIR/nums.cma") "$DIR/num.cma")
7246 (("\\$DIR/num.cmi") "$DIR/core/num.cmi"))
7248 (add-after 'configure 'fix-makefile
7250 (substitute* "Makefile"
7251 ;; find ocaml-num in the correct directory
7252 (("site-lib/num") "site-lib"))
7254 (add-after 'install 'install-lib
7256 (invoke "make" "byte")
7257 (invoke "make" "install-lib")
7259 (home-page "http://why3.lri.fr")
7260 (synopsis "Deductive program verification")
7261 (description "Why3 provides a language for specification and programming,
7262 called WhyML, and relies on external theorem provers, both automated and
7263 interactive, to discharge verification conditions. Why3 comes with a standard
7264 library of logical theories (integer and real arithmetic, Boolean operations,
7265 sets and maps, etc.) and basic programming data structures (arrays, queues,
7266 hash tables, etc.). A user can write WhyML programs directly and get
7267 correct-by-construction OCaml programs through an automated extraction
7268 mechanism. WhyML is also used as an intermediate language for the verification
7269 of C, Java, or Ada programs.")
7270 (license license:lgpl2.1)))
7272 (define-public frama-c
7278 (uri (string-append "http://frama-c.com/download/frama-c-"
7279 version "-Vanadium.tar.gz"))
7282 "1rgkq9sg436smw005ag0j6y3xryhjn18a07m5wjfrfp0s1438nnj"))))
7283 (build-system ocaml-build-system)
7285 `(#:tests? #f; no test target in Makefile
7287 (modify-phases %standard-phases
7288 (add-before 'configure 'export-shell
7289 (lambda* (#:key inputs #:allow-other-keys)
7290 (setenv "CONFIG_SHELL"
7291 (search-input-file inputs "/bin/sh")))))))
7295 `(("ocaml-biniou" ,ocaml-biniou)
7296 ("ocaml-easy-format" ,ocaml-easy-format)
7297 ("ocaml-graph" ,ocaml-graph)
7298 ("ocaml-yojson" ,ocaml-yojson)
7299 ("ocaml-zarith" ,ocaml-zarith)
7301 (native-search-paths
7302 (list (search-path-specification
7303 (variable "FRAMAC_SHARE")
7304 (files '("share/frama-c"))
7306 (search-path-specification
7307 (variable "FRAMAC_LIB")
7308 (files '("lib/frama-c"))
7310 (home-page "http://frama-c.com")
7311 (synopsis "C source code analysis platform")
7312 (description "Frama-C is an extensible and collaborative platform dedicated
7313 to source-code analysis of C software. The Frama-C analyzers assist you in
7314 various source-code-related activities, from the navigation through unfamiliar
7315 projects up to the certification of critical software.")
7316 (license license:lgpl2.1+)))
7318 (define-public blitz
7326 (url "https://github.com/blitzpp/blitz")
7328 (file-name (git-file-name name version))
7330 (base32 "0c88gc72j3zggyk4yrrip6i0v7xkx97l140vpy3xhxs2i7xy1461"))))
7331 (build-system cmake-build-system)
7333 `(#:configure-flags '("-DBUILD_DOC=ON"
7334 "-DBUILD_TESTING=ON")
7335 ;; The default "check" target also includes examples and benchmarks.
7336 #:test-target "check-testsuite"
7338 (modify-phases %standard-phases
7339 (add-after 'build 'build-doc
7341 (invoke "make" "-j" (number->string (parallel-job-count))
7344 `(("python" ,python)
7345 ("texinfo" ,texinfo)))
7346 (synopsis "C++ template class library for multidimensional arrays")
7347 (description "Blitz++ is a C++ template class library that provides
7348 high-performance multidimensional array containers for scientific computing.")
7349 (home-page "https://github.com/blitzpp/blitz")
7350 (license (list license:artistic2.0
7354 (define-public fxdiv
7355 ;; There is currently no tag in this repo.
7356 (let ((commit "63058eff77e11aa15bf531df5dd34395ec3017c8")
7361 (version (git-version version revision commit))
7362 (home-page "https://github.com/Maratyszcza/FXdiv")
7365 (uri (git-reference (url home-page) (commit commit)))
7366 (file-name (git-file-name name version))
7369 "0zwzh8gmbx4m6b18s5nf13b0dk5yjkd1fs8f421bl7fz5f9gjd9f"))
7370 (patches (search-patches "fxdiv-system-libraries.patch"))))
7371 (build-system cmake-build-system)
7373 `(("googletest" ,googletest)
7374 ("googlebenchmark" ,googlebenchmark)))
7376 "C++ library for division via fixed-point multiplication by inverse")
7378 "On modern CPUs and GPUs, integer division is several times slower than
7379 multiplication. FXdiv implements an algorithm to replace an integer division
7380 with a multiplication and two shifts. This algorithm improves performance
7381 when an application performs repeated divisions by the same divisor.")
7382 (license license:expat))))
7385 ;; There is currently no tag in this repo.
7386 (let ((commit "0a92994d729ff76a58f692d3028ca1b64b145d91")
7391 (version (git-version version revision commit))
7392 (home-page "https://github.com/Maratyszcza/FP16")
7395 (uri (git-reference (url home-page) (commit commit)))
7396 (file-name (git-file-name name version))
7399 "05mm4vrxsac35hjf5djif9r6rdxj9ippg97ia3p6q6b8lrp7srwv"))
7400 (patches (search-patches "fp16-system-libraries.patch"))))
7401 (build-system cmake-build-system)
7403 `(#:imported-modules ((guix build python-build-system)
7404 ,@%cmake-build-system-modules)
7405 #:modules (((guix build python-build-system)
7406 #:select (site-packages))
7407 (guix build cmake-build-system)
7409 #:phases (modify-phases %standard-phases
7410 (add-after 'install 'move-python-files
7411 (lambda* (#:key inputs outputs #:allow-other-keys)
7412 ;; Python files get installed to $includedir (!).
7413 ;; Move them to the usual Python site directory.
7414 (let* ((out (assoc-ref outputs "out"))
7415 (include (string-append out "/include"))
7416 (site (site-packages inputs outputs))
7417 (target (string-append site "/fp16")))
7419 (for-each (lambda (file)
7421 (string-append target "/"
7424 (find-files include "\\.py$"))))))))
7426 `(("python-wrapper" ,python-wrapper)))
7429 ("googletest" ,googletest)
7430 ("googlebenchmark" ,googlebenchmark)))
7431 (synopsis "C++ library for half-precision floating point formats")
7433 "This header-only C++ library implements conversion to and from
7434 half-precision floating point formats.")
7435 (license license:expat))))
7437 (define-public optizelle
7438 (let ((commit "ed4160b5287518448caeb34789d92dc6a0b7e2cc"))
7441 (version (git-version "1.3.0" "0" commit))
7446 (url "https://github.com/OptimoJoe/Optizelle")
7448 (file-name (git-file-name "optizelle" commit))
7451 "0rjrs5sdmd33a9f4xm8an7p0953aa0bxsmr4hs3ss1aad9k181vq"))
7452 (modules '((guix build utils)))
7455 ;; Reduce the stopping tolerance in one test so that the
7456 ;; convergence check returns the correct stopping
7459 "src/unit/linear_algebra/tcg_loss_of_orthogonality.cpp"
7460 (("1e-13") "5e-14"))
7461 ;; Skip one set of python tests. See
7462 ;; https://github.com/OptimoJoe/Optizelle/issues/2.
7464 "src/examples/inequality_scaling/CMakeLists.txt"
7465 (("add_unit(.*)\\$\\{interfaces\\}(.*)$" all middle end)
7466 (string-append "add_unit" middle "\"cpp\"" end)))
7467 ;; Install the licence for Optizelle, without also
7468 ;; including the licences for the dependencies.
7469 (substitute* "licenses/CMakeLists.txt"
7470 (("file.*package.*$" all)
7471 (string-append "# " all))
7472 ((".*[^l].[.]txt\\)\n") "")
7473 (("add_license.*\"\n") ""))
7475 (build-system cmake-build-system)
7477 `(#:imported-modules ((guix build python-build-system)
7478 ,@%cmake-build-system-modules)
7479 #:modules (((guix build python-build-system) #:select
7481 (guix build cmake-build-system)
7483 #:configure-flags `("-DCMAKE_CXX_FLAGS:STRING=-pthread"
7484 "-DENABLE_CPP_UNIT:BOOL=ON"
7485 "-DENABLE_CPP_EXAMPLES:BOOL=ON"
7486 "-DENABLE_PYTHON:BOOL=ON"
7487 "-DENABLE_PYTHON_UNIT:BOOL=ON"
7488 "-DENABLE_PYTHON_EXAMPLES:BOOL=ON"
7489 ,(string-append "-DBLAS_LIBRARY:FILEPATH="
7490 (assoc-ref %build-inputs
7492 "/lib/libopenblas.so")
7493 ,(string-append "-DLAPACK_LIBRARY:FILEPATH="
7494 (assoc-ref %build-inputs
7496 "/lib/libgfortran.so;"
7497 (assoc-ref %build-inputs
7499 "/lib/libquadmath.so"))
7501 (modify-phases %standard-phases
7502 (add-after 'unpack 'set-numpy-path ; Needed for the unit tests.
7503 (lambda* (#:key inputs #:allow-other-keys)
7504 (let* ((pyver (python-version (assoc-ref inputs "python")))
7505 (npdir (string-append (assoc-ref inputs "numpy")
7508 (substitute* "src/cmake/Modules/Optizelle.cmake"
7510 (string-append "LD_LIBRARY_PATH=$ENV{LIBRARY_PATH};"
7511 "PYTHONPATH=" npdir ":"))))))
7512 (delete 'install-license-files)))) ; LICENSE.txt is installed.
7514 `(("blas/lapack" ,openblas)
7515 ("fortran:lib" ,gfortran "lib")
7516 ("jsoncpp" ,jsoncpp)
7517 ("numpy" ,python-numpy)
7518 ("python" ,python)))
7520 `(("fortran" ,gfortran)
7521 ("pkg-config" ,pkg-config)))
7522 (home-page "https://www.optimojoe.com/products/optizelle/")
7523 (synopsis "Mathematical optimization library")
7524 (description "@code{optizelle} is a software library designed to
7525 solve nonlinear optimization problems. Four types of problem are
7526 considered: unconstrained, equality constrained, inequality
7527 constrained and constrained. Constraints may be applied as values of
7528 functions or sets of partial differential equations (PDEs).
7530 Solution algorithms such as the preconditioned nonlinear conjugate
7531 gradient method, sequential quadratic programming (SQP) and the
7532 primal-dual interior-point method are made available. Interfaces are
7533 provided for applications written in C++ and Python. Parallel
7534 computation is supported via MPI.")
7535 (license license:bsd-2))))