1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2013, 2014, 2015, 2016, 2019 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 Eric Bavier <bavier@member.fsf.org>
6 ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
7 ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
8 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 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 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 Kei Kebreau <kkebreau@posteo.net>
15 ;;; Copyright © 2016, 2017, 2018, 2019 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 Paul Garlick <pgarlick@tourbillion-technology.com>
19 ;;; Copyright © 2017 ng0 <ng0@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, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
24 ;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
25 ;;; Copyright © 2018, 2019 Jan 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 Marius Bakke <mbakke@fastmail.com>
30 ;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
31 ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
32 ;;; Copyright © 2018 Amin Bandali <mab@gnu.org>
33 ;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
34 ;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
35 ;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net>
37 ;;; This file is part of GNU Guix.
39 ;;; GNU Guix is free software; you can redistribute it and/or modify it
40 ;;; under the terms of the GNU General Public License as published by
41 ;;; the Free Software Foundation; either version 3 of the License, or (at
42 ;;; your option) any later version.
44 ;;; GNU Guix is distributed in the hope that it will be useful, but
45 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
46 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
47 ;;; GNU General Public License for more details.
49 ;;; You should have received a copy of the GNU General Public License
50 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
52 (define-module (gnu packages maths)
53 #:use-module (ice-9 regex)
54 #:use-module (ice-9 match)
55 #:use-module (gnu packages)
56 #:use-module ((guix licenses) #:prefix license:)
57 #:use-module (guix packages)
58 #:use-module (guix download)
59 #:use-module (guix git-download)
60 #:use-module (guix utils)
61 #:use-module ((guix build utils) #:select (alist-replace))
62 #:use-module (guix build-system cmake)
63 #:use-module (guix build-system gnu)
64 #:use-module (guix build-system python)
65 #:use-module (guix build-system ruby)
66 #:use-module (gnu packages algebra)
67 #:use-module (gnu packages audio)
68 #:use-module (gnu packages autotools)
69 #:use-module (gnu packages base)
70 #:use-module (gnu packages bison)
71 #:use-module (gnu packages boost)
72 #:use-module (gnu packages check)
73 #:use-module (gnu packages cmake)
74 #:use-module (gnu packages compression)
75 #:use-module (gnu packages curl)
76 #:use-module (gnu packages cyrus-sasl)
77 #:use-module (gnu packages documentation)
78 #:use-module (gnu packages elf)
79 #:use-module (gnu packages flex)
80 #:use-module (gnu packages fltk)
81 #:use-module (gnu packages fontutils)
82 #:use-module (gnu packages gettext)
83 #:use-module (gnu packages gcc)
84 #:use-module (gnu packages gd)
85 #:use-module (gnu packages ghostscript)
86 #:use-module (gnu packages graphviz)
87 #:use-module (gnu packages gtk)
88 #:use-module (gnu packages image)
89 #:use-module (gnu packages java)
90 #:use-module (gnu packages less)
91 #:use-module (gnu packages lisp)
92 #:use-module (gnu packages linux)
93 #:use-module (gnu packages logging)
94 #:use-module (gnu packages lua)
95 #:use-module (gnu packages gnome)
96 #:use-module (gnu packages guile)
97 #:use-module (gnu packages xorg)
98 #:use-module (gnu packages gl)
99 #:use-module (gnu packages imagemagick)
100 #:use-module (gnu packages m4)
101 #:use-module (gnu packages mpi)
102 #:use-module (gnu packages multiprecision)
103 #:use-module (gnu packages netpbm)
104 #:use-module (gnu packages onc-rpc)
105 #:use-module (gnu packages pcre)
106 #:use-module (gnu packages popt)
107 #:use-module (gnu packages perl)
108 #:use-module (gnu packages pkg-config)
109 #:use-module (gnu packages pulseaudio)
110 #:use-module (gnu packages python)
111 #:use-module (gnu packages python-web)
112 #:use-module (gnu packages python-xyz)
113 #:use-module (gnu packages qt)
114 #:use-module (gnu packages readline)
115 #:use-module (gnu packages ruby)
116 #:use-module (gnu packages tbb)
117 #:use-module (gnu packages scheme)
118 #:use-module (gnu packages shells)
119 #:use-module (gnu packages tcl)
120 #:use-module (gnu packages texinfo)
121 #:use-module (gnu packages tex)
122 #:use-module (gnu packages tls)
123 #:use-module (gnu packages version-control)
124 #:use-module (gnu packages wxwidgets)
125 #:use-module (gnu packages xml)
126 #:use-module (srfi srfi-1))
134 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
136 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
137 (build-system gnu-build-system)
138 (inputs `(("gtk+" ,gtk+)
139 ("libxml2" ,libxml2)))
140 (native-inputs `(("pkg-config" ,pkg-config)))
141 (synopsis "Natural deduction first-order logic interface")
142 (description "Aris is a program for performing logical proofs. It supports
143 propositional and predicate logic, as well as Boolean algebra and
144 arithmetical logic. In addition to its predefined inference and equivalence
145 rules, Aris also supports references to older proofs. Its use of standard
146 logical symbols and its natural deduction interface make it easy to use for
148 (license license:gpl3+)
149 (home-page "https://www.gnu.org/software/aris/")))
151 (define-public c-graph
157 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
160 "092412jzxy6wdvpk96pfj499hpmaww8xllavbvlqspfpr7ips9id"))))
161 (build-system gnu-build-system)
163 `(("fortran" ,gfortran)))
164 (synopsis "Visualizing and demonstrating convolution")
166 "GNU C-Graph is a tool for demonstrating the theory of convolution.
167 Thus, it can serve as an excellent aid to students of signal and systems
168 theory in visualizing the convolution process. Rather than forcing the
169 student to write code, the program offers an intuitive interface with
170 interactive dialogs to guide them.")
171 (license license:gpl3+)
172 (home-page "https://www.gnu.org/software/c-graph/")))
181 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
182 version "/coda-" version ".tar.gz"))
184 (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245"))
185 (patches (search-patches "coda-use-system-libs.patch"))
186 (modules '((guix build utils)))
188 ;; Make sure we don't use the bundled software.
190 (for-each (lambda (d)
191 (delete-file-recursively (string-append "libcoda/" d)))
192 '("zlib" "pcre" "expat"))
195 `(("fortran" ,gfortran)
197 ("python-numpy" ,python-numpy)))
204 (build-system gnu-build-system)
206 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
207 "LIBS= -lz -lpcre -lexpat")))
208 (synopsis "A common interface to various earth observation data formats")
210 "The Common Data Access toolbox (CODA) provides a set of interfaces for
211 reading remote sensing data from earth observation data files. It consists of
212 command line applications and interfaces to the C, Fortran, Python, and Java
213 programming languages.")
214 (home-page "https://stcorp.nl/coda")
215 (license license:gpl2+)))
223 (uri (string-append "http://www.qhull.org/download/qhull-"
224 (car (string-split version #\.))
228 "0dm4b2xr3asy6w74khq2zg4gf26zsy3qf9sq7pf7lmrvbj911c3q"))))
229 (build-system cmake-build-system)
230 (synopsis "Calculate convex hulls and related structures")
232 "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
233 diagram, halfspace intersection about a point, furthest-site Delaunay
234 triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d,
235 3-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull
236 algorithm for computing the convex hull. It handles roundoff errors from
237 floating point arithmetic. It computes volumes, surface areas, and
238 approximations to the convex hull.
240 @code{Qhull} does not support triangulation of non-convex surfaces, mesh
241 generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
242 shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
244 (home-page "http://qhull.org")
245 (license (license:non-copyleft "file://COPYING.txt"
246 "See COPYING in the distribution."))))
248 (define-public python-cvxopt
250 (name "python-cvxopt")
255 (url "https://github.com/cvxopt/cvxopt.git")
257 (file-name (git-file-name name version))
260 "1kiy2m62xgs2d5id6dnnwy4vap85cd70p7pgkb9nh23qf9xnak7b"))))
261 (build-system python-build-system)
264 (modify-phases %standard-phases
265 (add-after 'unpack 'find-libraries
266 (lambda* (#:key inputs #:allow-other-keys)
267 (setenv "CVXOPT_BLAS_LIB" "openblas")
268 (setenv "CVXOPT_BUILD_FFTW" "1")
269 (setenv "CVXOPT_BUILD_GLPK" "1")
270 (setenv "CVXOPT_BUILD_GSL" "1")
277 ("openblas" ,openblas)
278 ("suitesparse" ,suitesparse)))
279 (home-page "https://www.cvxopt.org")
280 (synopsis "Python library for convex optimization")
282 "CVXOPT is a package for convex optimization based on the Python
283 programming language. Its main purpose is to make the development of software
284 for convex optimization applications straightforward by building on Python’s
285 extensive standard library and on the strengths of Python as a high-level
286 programming language.")
287 (license license:gpl3+)))
289 (define-public python2-cvxopt
290 (package-with-python2 python-cvxopt))
298 (uri (string-append "mirror://gnu/units/units-" version
301 "0mk562g7dnidjgfgvkxxpvlba66fh1ykmfd9ylzvcln1vxmi6qj2"))))
302 (build-system gnu-build-system)
304 `(("readline" ,readline)
305 ("python" ,python-wrapper) ;for 'units_cur' script
306 ("python-requests" ,python-requests)))
308 `(#:phases (modify-phases %standard-phases
309 (add-after 'install 'wrap-units_cur
310 (lambda* (#:key outputs #:allow-other-keys)
311 (let* ((out (assoc-ref outputs "out"))
312 (bin (string-append out "/bin")))
313 (wrap-program (string-append bin "/units_cur")
314 `("PYTHONPATH" ":" prefix
315 ,(search-path-as-string->list (getenv "PYTHONPATH"))))
317 (synopsis "Conversion between thousands of scales")
319 "GNU Units converts numeric quantities between units of measure. It
320 can handle scale changes through adaptive usage of standard scale
321 prefixes (micro-, kilo-, etc.). It can also handle nonlinear
322 conversions such as Fahrenheit to Celsius. Its interpreter is powerful
323 enough to be used effectively as a scientific calculator.")
324 (license license:gpl3+)
325 (home-page "https://www.gnu.org/software/units/")))
327 (define-public double-conversion
329 (name "double-conversion")
331 (home-page "https://github.com/google/double-conversion")
334 (uri (git-reference (url home-page)
335 (commit (string-append "v" version))))
336 (file-name (git-file-name name version))
339 "0csy4pjw1p8rp6g5qxi2h0ychhhp1fldv7gb761627fs2mclw9gv"))))
340 (build-system cmake-build-system)
342 '(#:test-target "test"
343 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
344 "-DBUILD_TESTING=ON")))
345 (synopsis "Conversion routines for IEEE doubles")
347 "The double-conversion library provides binary-decimal and decimal-binary
348 routines for IEEE doubles. The library consists of efficient conversion
349 routines that have been extracted from the V8 JavaScript engine.")
350 (license license:bsd-3)))
352 (define-public dionysus
358 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
362 "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
363 (build-system gnu-build-system)
364 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
365 (synopsis "Local search for universal constants and scientific values")
367 "GNU Dionysus is a convenient system for quickly retrieving the values of
368 mathematical constants used in science and engineering. Values can be
369 searched using a simple command-line tool, choosing from three databases:
370 universal constants, atomic numbers, and constants related to
372 (license license:gpl3+)
373 (home-page "https://www.gnu.org/software/dionysus/")))
381 (uri (string-append "mirror://gnu/gsl/gsl-"
385 "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
386 (patches (search-patches "gsl-test-i686.patch"))))
387 (build-system gnu-build-system)
389 `(;; Currently there are numerous tests that fail on "exotic"
390 ;; architectures such as aarch64 and ppc64le.
391 ,@(if (string-prefix? "aarch64-linux"
392 (or (%current-target-system) (%current-system)))
395 (home-page "https://www.gnu.org/software/gsl/")
396 (synopsis "Numerical library for C and C++")
398 "The GNU Scientific Library is a library for numerical analysis in C
399 and C++. It includes a wide range of mathematical routines, with over 1000
400 functions in total. Subject areas covered by the library include:
401 differential equations, linear algebra, Fast Fourier Transforms and random
403 (license license:gpl3+)))
412 (uri (string-append "mirror://gnu/glpk/glpk-"
416 "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
417 (build-system gnu-build-system)
421 `(#:configure-flags '("--with-gmp")))
422 (home-page "https://www.gnu.org/software/glpk/")
423 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
425 "GLPK is a C library for solving large-scale linear programming (LP),
426 mixed integer programming (MIP), and other related problems. It supports the
427 GNU MathProg modeling language, a subset of the AMPL language, and features a
428 translator for the language. In addition to the C library, a stand-alone
429 LP/MIP solver is included in the package.")
430 (license license:gpl3+)))
439 (uri (string-append "https://github.com/4ti2/4ti2/releases/download/"
441 (string-map (lambda (c) (if (char=? c #\.) #\_ c))
443 "/4ti2-" version ".tar.gz"))
445 (base32 "0rj92x6p9m3la5gasjbj7sa569im527ffmka5y2sv1amgd3fflrh"))))
446 (build-system gnu-build-system)
448 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
452 (home-page "http://www.4ti2.de/")
453 (synopsis "Mathematical tool suite for problems on linear spaces")
455 "4ti2 implements algorithms for solving algebraic, geometric and
456 combinatorial problems on linear spaces. Among others, it solves systems
457 of linear equations, computes extreme rays of polyhedral cones, solves
458 integer programming problems and computes Markov bases for statistics.")
459 (license license:gpl2+)))
461 (define-public cddlib
468 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
469 (string-delete #\. version) ".tar.gz"))
472 "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
473 (build-system gnu-build-system)
476 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
477 (synopsis "Library for convex hulls and extreme rays of polyhedra")
479 "The C-library cddlib implements the Double Description Method of
480 Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
481 rays of a general convex polyhedron given by a system of linear inequalities
482 in arbitrary dimension. It can also be used for the converse operation of
483 computing convex hulls.")
484 (license license:gpl2+)))
486 (define-public lrslib
493 (uri (string-append "http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/"
495 (string-delete #\. version) ".tar.gz"))
498 "034fa45r9hwx6ljmgpxk2872q34nklkalpdkc6s9hqw57rivi36k"))))
499 (build-system gnu-build-system)
503 `(#:tests? #f ; no check phase
504 #:make-flags `("CC=gcc"
505 ,(string-append "prefix=" (assoc-ref %outputs "out"))
508 (modify-phases %standard-phases
511 (substitute* "makefile"
512 (("-L \\.") "-L . -Wl,-rpath='$$ORIGIN/../lib'"))
514 (home-page "http://cgm.cs.mcgill.ca/~avis/C/lrs.html")
515 (synopsis "Convex hulls of polyhedra with exact arithmetic")
517 "The C code of lrslib implements the reverse search algorithm for
518 vertex enumeration and convex hull problems. Its input file format is
519 compatible with cddlib. All computations are done exactly in either
520 multiple precision or fixed integer arithmetic. Output is not stored
521 in memory, so even problems with very large output sizes can sometimes
523 (license license:gpl2+)))
525 (define-public arpack-ng
529 (home-page "https://github.com/opencollab/arpack-ng")
532 (uri (git-reference (url home-page) (commit version)))
533 (file-name (git-file-name name version))
536 "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
537 (build-system gnu-build-system)
539 `(("autoconf" ,autoconf)
540 ("automake" ,automake)
541 ("libtool" ,libtool)))
544 ("fortran" ,gfortran)))
545 (synopsis "Fortran subroutines for solving eigenvalue problems")
547 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
548 large scale eigenvalue problems.")
549 (license (license:non-copyleft "file://COPYING"
550 "See COPYING in the distribution."))))
552 (define-public arpack-ng-3.3.0
556 (name (package-name arpack-ng))
557 (home-page (package-home-page arpack-ng))
561 (uri (string-append home-page "/archive/" version ".tar.gz"))
562 (file-name (string-append name "-" version ".tar.gz"))
565 "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
567 (define-public arpack-ng-openmpi
568 (package (inherit arpack-ng)
569 (name "arpack-ng-openmpi")
572 ,@(package-inputs arpack-ng)))
574 (substitute-keyword-arguments (package-arguments arpack-ng)
575 ((#:configure-flags _ '())
577 ((#:phases phases '%standard-phases)
578 `(modify-phases ,phases
579 (add-before 'check 'mpi-setup
581 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
583 (define-public lapack
590 (uri (string-append "http://www.netlib.org/lapack/lapack-"
594 "1155qixp26c12yrxc76z9mlfw2h3xxymxxv5znpgzh5gaykpndgj"))))
595 (build-system cmake-build-system)
596 (home-page "http://www.netlib.org/lapack/")
597 (inputs `(("fortran" ,gfortran)
598 ("python" ,python-wrapper)))
600 `(#:configure-flags (list
601 "-DBUILD_SHARED_LIBS:BOOL=YES"
603 ;; Build the 'LAPACKE_clatms' functions.
604 "-DLAPACKE_WITH_TMG=ON"
605 "-DBUILD_TESTING=ON")))
606 (synopsis "Library for numerical linear algebra")
608 "LAPACK is a Fortran 90 library for solving the most commonly occurring
609 problems in numerical linear algebra.")
610 (license (license:non-copyleft "file://LICENSE"
611 "See LICENSE in the distribution."))))
613 (define-public scalapack
620 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
624 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))
625 (patches (search-patches "scalapack-blacs-mpi-deprecations.patch"))))
626 (build-system cmake-build-system)
629 ("fortran" ,gfortran)
630 ("lapack" ,lapack))) ;for testing only
632 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
633 #:phases (modify-phases %standard-phases
634 (add-before 'check 'mpi-setup
636 (home-page "http://www.netlib.org/scalapack/")
637 (synopsis "Library for scalable numerical linear algebra")
639 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
640 routines on parallel distributed memory machines. ScaLAPACK solves dense and
641 banded linear systems, least squares problems, eigenvalue problems, and
642 singular value problems.")
643 (license (license:non-copyleft "file://LICENSE"
644 "See LICENSE in the distribution."))))
646 (define-public gnuplot
652 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
656 (base32 "1vglp4la40f5dpj0zdj63zprrkyjgzy068p35bz5dqxjyczm1zlp"))))
657 (build-system gnu-build-system)
658 (inputs `(("readline" ,readline)
664 `(("pkg-config" ,pkg-config)
665 ("texlive" ,texlive-tiny)))
666 (arguments `(#:configure-flags (list (string-append
667 "--with-texdir=" %output
668 "/texmf-local/tex/latex/gnuplot"))))
669 (home-page "http://www.gnuplot.info")
670 (synopsis "Command-line driven graphing utility")
671 (description "Gnuplot is a portable command-line driven graphing
672 utility. It was originally created to allow scientists and students to
673 visualize mathematical functions and data interactively, but has grown to
674 support many non-interactive uses such as web scripting. It is also used as a
675 plotting engine by third-party applications like Octave.")
676 ;; X11 Style with the additional restriction that derived works may only be
677 ;; distributed as patches to the original.
678 (license (license:fsf-free
679 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
689 (url "https://github.com/OkoSanto/GCTP.git")
690 (commit (string-append "v" version))))
691 (file-name (git-file-name name version))
693 (base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
695 `(("fortran" ,gfortran)))
696 (build-system gnu-build-system)
697 (synopsis "General Cartographic Transformation Package (GCTP)")
699 "The General Cartographic Transformation Package (GCTP) is a system of
700 software routines designed to permit the transformation of coordinate pairs
701 from one map projection to another. The GCTP is the standard computer
702 software used by the National Mapping Division for map projection
704 (home-page "https://github.com/OkoSanto/GCTP")
705 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
714 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
715 version "/src/hdf-" version ".tar.bz2"))
717 (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l"))
718 (patches (search-patches "hdf4-architectures.patch"
719 "hdf4-reproducibility.patch"
720 "hdf4-shared-fortran.patch"
721 "hdf4-tirpc.patch"))))
722 (build-system gnu-build-system)
724 `(("gfortran" ,gfortran)
730 ("libtirpc" ,libtirpc)))
732 `(#:parallel-tests? #f
733 #:configure-flags (list "--enable-shared"
734 (string-append "CPPFLAGS=-I"
735 (assoc-ref %build-inputs "libtirpc")
738 (modify-phases %standard-phases
739 ;; This is inspired by two of Debian's patches.
740 (add-before 'configure 'add-more-aarch64-support
742 (substitute* '("mfhdf/ncgen/ncgen.l"
743 "mfhdf/ncgen/ncgenyy.c"
744 "mfhdf/libsrc/netcdf.h.in")
745 (("AIX5L64") "__aarch64__"))
747 (add-before 'configure 'patchbuild
750 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
752 (("/bin/mkdir") "mkdir"))
753 (substitute* (find-files "." "^Makefile\\.in$")
754 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
755 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
756 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
757 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
758 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
760 (add-after 'configure 'patch-settings
762 ;; libhdf4.settings contains the full path of the
763 ;; compilers used, and its contents are included in
764 ;; .so-files. We truncate the hashes to avoid
765 ;; unnecessary store references to those compilers:
766 (substitute* "libhdf4.settings"
767 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
768 (string-append prefix (string-take hash 10) "...")))
771 (home-page "https://www.hdfgroup.org/products/hdf4/")
773 "Library and multi-object file format for storing and managing data")
774 (description "HDF4 is a library and multi-object file format for storing
775 and managing data between machines. HDF4 is an older hierarchical data format,
776 incompatible with HDF5.")
778 (license:non-copyleft
779 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
781 (define-public hdf4-alt
786 (substitute-keyword-arguments (package-arguments hdf4)
787 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
789 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
798 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
799 "hdf5-" (version-major+minor version)
800 "/hdf5-" version "/src/hdf5-"
802 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
804 (match (string-split version #\.)
806 (string-append major minor)))
807 "/src/hdf5-" version ".tar.bz2")))
809 (base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5"))
810 (patches (search-patches "hdf5-config-date.patch"
811 "hdf5-1.8-mpi-deprecations.patch"))))
812 (build-system gnu-build-system)
816 `(("gfortran" ,gfortran)
817 ("perl" ,perl))) ;part of the test machinery needs Perl
818 (outputs '("out" ; core library
819 "fortran")) ; fortran interface
821 `(;; Some of the users, notably Flann, need the C++ interface.
822 #:configure-flags '("--enable-cxx"
824 "--enable-fortran2003"
826 ;; Build a thread-safe library. Unfortunately,
827 ;; 'configure' invites you to either turn off C++,
828 ;; Fortran, and the high-level interface (HL), or
829 ;; to pass '--enable-unsupported'. Debian
830 ;; packagers chose to pass '--enable-unsupported'
831 ;; and we follow their lead here.
832 "--enable-threadsafe"
834 "--enable-unsupported")
835 ;; Use -fPIC to allow the R bindings to link with the static libraries
836 #:make-flags (list "CFLAGS=-fPIC"
839 (modify-phases %standard-phases
840 (add-before 'configure 'patch-configure
841 (lambda* (#:key outputs #:allow-other-keys)
842 (substitute* "configure"
844 (substitute* "fortran/src/Makefile.in"
845 (("libhdf5_fortran_la_LDFLAGS =")
846 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
847 (assoc-ref outputs "fortran") "/lib")))
848 (substitute* "hl/fortran/src/Makefile.in"
849 (("libhdf5hl_fortran_la_LDFLAGS =")
850 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
851 (assoc-ref outputs "fortran") "/lib")))
853 (add-after 'configure 'patch-settings
855 ;; libhdf5.settings contains the full path of the
856 ;; compilers used, and its contents are included in
857 ;; libhdf5.so. We truncate the hashes to avoid
858 ;; unnecessary store references to those compilers:
859 (substitute* "src/libhdf5.settings"
860 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
861 (string-append prefix (string-take hash 10) "..."))
862 ;; Don't record the build-time kernel version to make the
863 ;; settings file reproducible.
864 (("Uname information:.*")
865 "Uname information: Linux\n"))
867 (add-after 'install 'patch-references
868 (lambda* (#:key inputs outputs #:allow-other-keys)
869 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
870 (zlib (assoc-ref inputs "zlib")))
871 (substitute* (find-files bin "h5p?cc")
873 (string-append "-L" zlib "/lib " lib)))
875 (add-after 'install 'split
876 (lambda* (#:key inputs outputs #:allow-other-keys)
877 ;; Move all fortran-related files
878 (let* ((out (assoc-ref outputs "out"))
879 (bin (string-append out "/bin"))
880 (lib (string-append out "/lib"))
881 (inc (string-append out "/include"))
882 (ex (string-append out "/share/hdf5_examples/fortran"))
883 (fort (assoc-ref outputs "fortran"))
884 (fbin (string-append fort "/bin"))
885 (flib (string-append fort "/lib"))
886 (finc (string-append fort "/include"))
887 (fex (string-append fort "/share/hdf5_examples/fortran")))
892 ;; Note: When built with --enable-parallel, the 'h5fc' file
893 ;; doesn't exist, hence this condition.
894 (when (file-exists? (string-append bin "/h5fc"))
895 (rename-file (string-append bin "/h5fc")
896 (string-append fbin "/h5fc")))
897 (for-each (lambda (file)
899 (string-append flib "/" (basename file))))
900 (find-files lib ".*fortran.*"))
901 (for-each (lambda (file)
903 (string-append finc "/" (basename file))))
904 (find-files inc ".*mod"))
905 (for-each (lambda (file)
907 (string-append fex "/" (basename file))))
908 (find-files ex ".*"))
909 (delete-file-recursively ex))
911 (home-page "https://www.hdfgroup.org")
912 (synopsis "Management suite for extremely large and complex data")
913 (description "HDF5 is a suite that makes possible the management of
914 extremely large and complex data collections.")
915 (license (license:x11-style
916 "https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
918 (define-public hdf5-1.10
919 (package (inherit hdf5)
924 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
925 "hdf5-" (version-major+minor version)
926 "/hdf5-" version "/src/hdf5-"
928 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
931 (take (string-split version #\.) 2))
932 "/src/hdf5-" version ".tar.bz2")))
934 (base32 "1gf38x51128hn00744358w27xgzjk0ff4wra4yxh2lk804ck1mh9"))
935 (patches (search-patches "hdf5-config-date.patch"))))))
937 (define-public hdf-java
945 "https://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
946 version "/src/CMake-hdfjava-" version ".tar.gz"))
948 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
949 (modules '((guix build utils)))
950 (snippet ; Make sure we don't use the bundled sources and binaries.
952 (for-each delete-file
953 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
954 "HDF4.tar.gz" "HDF5.tar.gz"))
955 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
957 (build-system gnu-build-system)
959 `(("jdk" ,icedtea "jdk")
960 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
962 ("hamcrest-core" ,java-hamcrest-core)
963 ("junit" ,java-junit)
964 ("slf4j-simple" ,java-slf4j-simple)))
970 ("slf4j-api" ,java-slf4j-api)))
973 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
974 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
975 (assoc-ref %build-inputs "jdk") "/lib" )
976 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
977 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
980 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
981 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
982 (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
983 (string-append "JPEGLIB="
984 (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
988 (modify-phases %standard-phases
989 (add-before 'configure 'chdir-to-source
990 (lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
991 (add-before 'configure 'patch-build
992 (lambda* (#:key inputs outputs #:allow-other-keys)
993 (substitute* "configure"
994 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
995 (("/bin/cat") (which "cat")))
996 ;; Set classpath for compilation
997 (substitute* '("hdf/hdf5lib/Makefile.in"
998 "hdf/hdf5lib/exceptions/Makefile.in"
999 "hdf/hdflib/Makefile.in")
1000 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
1001 (string-append (assoc-ref inputs "slf4j-api")
1002 "/share/java/slf4j-api.jar")))
1003 ;; Replace outdated config.sub and config.guess:
1004 (with-directory-excursion "config"
1005 (for-each (lambda (file)
1007 (string-append (assoc-ref inputs "automake")
1009 ,(version-major+minor (package-version automake))
1011 '("config.sub" "config.guess")))
1013 ;; Fix embedded version number
1014 (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
1015 (substitute* "hdf/hdf5lib/H5.java"
1017 (string-join hdf5version ", "))))
1019 (mkdir-p (string-append (assoc-ref outputs "out")))
1020 ;; Set classpath for tests
1021 (let* ((build-dir (getcwd))
1022 (lib (string-append build-dir "/lib"))
1023 (jhdf (string-append lib "/jhdf.jar"))
1024 (jhdf5 (string-append lib "/jhdf5.jar"))
1027 (string-append (assoc-ref inputs i)
1028 "/share/java/" i ".jar"))
1029 '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
1031 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
1033 (substitute* '("test/hdf5lib/Makefile.in"
1034 "test/hdf5lib/junit.sh.in"
1035 "examples/runExample.sh.in")
1037 (string-append (assoc-ref inputs "coreutils")
1040 (string-append (assoc-ref inputs "coreutils")
1042 (("CLASSPATH=[^\n]*")
1043 (string-append "CLASSPATH=" class-path)))
1044 (setenv "CLASSPATH" class-path))
1046 (add-before 'check 'build-examples
1048 (apply invoke `("javac"
1049 ,@(find-files "examples" ".*\\.java"))))))
1051 #:parallel-build? #f
1053 #:parallel-tests? #f ))
1054 (home-page "https://support.hdfgroup.org/products/java")
1055 (synopsis "Java interface for the HDF4 and HDF5 libraries")
1056 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
1057 the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
1060 ;; BSD-style license:
1061 (license (license:x11-style
1062 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
1063 /current/src/unpacked/COPYING"))))
1065 (define-public hdf-eos2
1072 (uri "ftp://edhs1.gsfc.nasa.gov\
1073 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
1075 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
1076 (patches (search-patches "hdf-eos2-remove-gctp.patch"
1077 "hdf-eos2-build-shared.patch"
1078 "hdf-eos2-fortrantests.patch"))))
1079 (build-system gnu-build-system)
1081 `(("gfortran" ,gfortran)))
1083 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
1084 ;; XXX: These inputs are really dependencies of hdf4.
1086 ("libjpeg" ,libjpeg)
1087 ("libtirpc" ,libtirpc)
1091 `( #:configure-flags '("--enable-install-include" "--enable-shared"
1092 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
1093 #:parallel-tests? #f))
1094 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
1095 (synopsis "HDF4-based data format for NASA's Earth Observing System")
1096 (description "HDF-EOS2 is a software library built on HDF4 which supports
1097 the construction of data structures used in NASA's Earth Observing
1098 System (Grid, Point and Swath).")
1100 ;; Source files carry a permissive license header.
1101 (license (license:non-copyleft home-page))))
1103 (define-public hdf-eos5
1109 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1110 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1113 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1114 (patches (search-patches "hdf-eos5-build-shared.patch"
1115 "hdf-eos5-remove-gctp.patch"
1116 "hdf-eos5-fix-szip.patch"
1117 "hdf-eos5-fortrantests.patch"))))
1119 `(("gfortran" ,gfortran)))
1120 (build-system gnu-build-system)
1126 `(#:configure-flags '("--enable-install-include" "--enable-shared"
1127 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1128 #:parallel-tests? #f))
1129 (synopsis "HDF5-based data format for NASA's Earth Observing System")
1131 "HDF-EOS5 is a software library built on HDF5 to support the construction
1132 of data structures used in NASA's Earth Observing System (Grid, Point and
1134 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1136 ;; Source files carry a permissive license header.
1137 (license (license:non-copyleft home-page))))
1139 (define-public hdf5-parallel-openmpi
1140 (package (inherit hdf5)
1141 (name "hdf5-parallel-openmpi")
1144 ,@(package-inputs hdf5)))
1146 (substitute-keyword-arguments (package-arguments hdf5)
1147 ((#:configure-flags flags)
1148 ``("--enable-parallel"
1149 ,@(delete "--enable-cxx"
1150 (delete "--enable-threadsafe" ,flags))))
1152 `(modify-phases ,phases
1153 (add-after 'build 'mpi-setup
1155 (add-before 'check 'patch-tests
1157 ;; OpenMPI's mpirun will exit with non-zero status if it
1158 ;; detects an "abnormal termination", i.e. any process not
1159 ;; calling MPI_Finalize(). Since the test is explicitly
1160 ;; avoiding MPI_Finalize so as not to have at_exit and thus
1161 ;; H5C_flush_cache from being called, mpirun will always
1162 ;; complain, so turn this test off.
1163 (substitute* "testpar/Makefile"
1164 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1165 (string-append front back "\n")))
1166 (substitute* "tools/h5diff/testph5diff.sh"
1167 (("/bin/sh") (which "sh")))
1169 (synopsis "Management suite for data with parallel IO support")))
1171 (define-public h5check
1178 (uri (string-append "https://www.hdfgroup.org/ftp/HDF5/tools/"
1179 "h5check/src/h5check-" version ".tar.gz"))
1182 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1183 (build-system gnu-build-system)
1184 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
1185 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1186 (synopsis "HDF5 format checker")
1187 (description "@code{h5check} is a validation tool for verifying that an
1188 HDF5 file is encoded according to the HDF File Format Specification.")
1189 (license (license:x11-style "file://COPYING"))))
1197 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1202 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1203 (build-system cmake-build-system)
1204 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1205 (inputs `(("lapack" ,lapack)
1207 ;; FIXME: Even though the fonts are available dvips complains:
1208 ;; "Font cmmi10 not found; characters will be left blank."
1210 `(("texlive" ,texlive-tiny)
1211 ("ghostscript" ,ghostscript)
1212 ("doxygen" ,doxygen)))
1213 (home-page "http://itpp.sourceforge.net")
1214 (synopsis "C++ library of maths, signal processing and communication classes")
1215 (description "IT++ is a C++ library of mathematical, signal processing and
1216 communication classes and functions. Its main use is in simulation of
1217 communication systems and for performing research in the area of
1218 communications. The kernel of the library consists of generic vector and
1219 matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1220 similar to MATLAB, GNU Octave or SciPy.")
1221 (license license:gpl3+)))
1223 (define-public netcdf
1230 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1231 "netcdf-" version ".tar.gz"))
1234 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1235 (patches (search-patches "netcdf-date-time.patch"
1236 "netcdf-tst_h_par.patch"))))
1237 (build-system gnu-build-system)
1240 ("doxygen" ,doxygen)
1241 ("graphviz" ,graphviz)))
1243 `(("hdf4" ,hdf4-alt)
1246 ("libjpeg" ,libjpeg)))
1248 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
1250 #:phases (modify-phases %standard-phases
1251 (add-before 'configure 'fix-source-date
1253 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1254 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1255 ;; to '1st hour of the current day', and therefore makes the
1256 ;; package not reproducible.
1257 (substitute* "./configure"
1258 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1259 "date --date='@0'"))
1261 (add-after 'configure 'patch-settings
1263 ;; libnetcdf.settings contains the full filename of the compilers
1264 ;; used to build the library. We truncate the hashes of those
1265 ;; filenames to avoid unnecessary references to the corresponding
1267 (substitute* "libnetcdf.settings"
1268 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1269 (string-append prefix (string-take hash 10) "...")))
1272 #:parallel-tests? #f)) ;various race conditions
1273 (home-page "https://www.unidata.ucar.edu/software/netcdf/")
1274 (synopsis "Library for scientific data")
1275 (description "NetCDF is an interface for scientific data access and a
1276 software library that provides an implementation of the interface. The netCDF
1277 library defines a machine-independent format for representing scientific data.
1278 Together, the interface, library, and format support the creation, access, and
1279 sharing of scientific data.")
1280 (license (license:x11-style "file://COPYRIGHT"))))
1282 (define-public netcdf-parallel-openmpi
1283 (package (inherit netcdf)
1284 (name "netcdf-parallel-openmpi")
1287 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1288 (package-inputs netcdf))))
1289 ;; TODO: Replace pkg-config references in nc-config with absolute references
1291 (substitute-keyword-arguments (package-arguments netcdf)
1292 ((#:configure-flags flags)
1293 `(cons* "CC=mpicc" "CXX=mpicxx"
1294 "--enable-parallel-tests"
1295 ;; Shared libraries not supported with parallel IO.
1296 "--disable-shared" "--with-pic"
1299 (define-public netcdf-fortran
1301 (name "netcdf-fortran")
1306 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1310 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1311 (build-system gnu-build-system)
1313 `(#:parallel-tests? #f))
1315 `(("netcdf" ,netcdf)))
1317 `(("gfortran" ,gfortran)))
1318 (synopsis "Fortran interface for the netCDF library")
1319 (description (package-description netcdf))
1320 (home-page (package-home-page netcdf))
1321 (license (package-license netcdf))))
1323 (define-public nlopt
1329 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1332 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1333 (build-system gnu-build-system)
1335 `(;; Shared libraries are not built by default. They are required to
1336 ;; build the Guile, Octave, and Python bindings.
1337 #:configure-flags '("--enable-shared")
1340 (modify-phases %standard-phases
1341 (add-before 'configure 'set-libnlopt-file-name
1342 (lambda* (#:key outputs #:allow-other-keys)
1343 ;; Make sure the Scheme module refers to the library by its
1344 ;; absolute file name (we cannot do that from a snippet
1345 ;; because the expansion of @libdir@ contains
1347 (let ((out (assoc-ref outputs "out")))
1348 (substitute* "swig/nlopt.scm.in"
1350 (string-append out "/lib/libnlopt")))
1352 (inputs `(("guile" ,guile-2.0)))
1353 (native-inputs `(("pkg-config" ,pkg-config)))
1354 (home-page "http://ab-initio.mit.edu/wiki/")
1355 (synopsis "Library for nonlinear optimization")
1356 (description "NLopt is a library for nonlinear optimization, providing a
1357 common interface for a number of different free optimization routines available
1358 online as well as original implementations of various other algorithms.")
1359 (license license:lgpl2.1+)))
1361 (define-public ipopt
1368 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1372 "07yn9rzdswjk8n246qq6ci9ssf2bcplkifcpsfz9j6cdxw9vgbkv"))
1373 (modules '((guix build utils)))
1375 ;; Make sure we don't use the bundled software.
1377 (delete-file-recursively "ThirdParty")
1379 (build-system gnu-build-system)
1381 '(#:phases (modify-phases %standard-phases
1382 (add-after 'install 'add--L-flags-in-ipopt.pc
1383 (lambda* (#:key inputs outputs #:allow-other-keys)
1384 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1385 ;; move it to "Libs.private" where it belongs, and add a
1386 ;; '-L' flag for LAPACK.
1387 (let ((out (assoc-ref outputs "out"))
1388 (lapack (assoc-ref inputs "lapack")))
1389 (substitute* (string-append out "/lib/pkgconfig/"
1391 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1392 (string-append "Libs: " before " " after "\n"
1393 "Libs.private: " before
1394 "-L" lapack "/lib -llapack -lblas "
1398 `(("gfortran" ,gfortran)))
1400 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
1401 `(("lapack" ,lapack))) ;for both libblas and liblapack
1402 (home-page "http://www.coin-or.org")
1403 (synopsis "Large-scale nonlinear optimizer")
1405 "The Interior Point Optimizer (IPOPT) is a software package for
1406 large-scale nonlinear optimization. It provides C++, C, and Fortran
1408 (license license:epl1.0)))
1416 (uri (string-append "https://www.coin-or.org/download/source/"
1417 "Clp/Clp-" version ".tgz"))
1420 "1wdg820g3iikf9344ijwsc8sy6c0m6im42bzzizm6rlmkvnmxhk9"))
1421 (modules '((guix build utils)))
1423 ;; Make sure we don't use the bundled software.
1425 (delete-file-recursively "ThirdParty")
1427 (build-system gnu-build-system)
1429 `(("gfortran" ,gfortran)
1430 ("pkg-config" ,pkg-config)))
1432 `(("openblas" ,openblas)))
1433 (home-page "https://www.coin-or.org")
1434 (synopsis "Linear programming solver")
1436 "CLP is a high quality linear programming solver. Its main strengths are
1437 its dual and primal Simplex algorithms. It also has a barrier algorithm for
1438 linear and quadratic objectives. There are limited facilities for nonlinear
1439 and quadratic objectives using the Simplex algorithm.")
1440 (license license:epl1.0)))
1442 (define-public ceres
1444 (name "ceres-solver")
1446 (home-page "http://ceres-solver.org/")
1449 (uri (string-append home-page "ceres-solver-"
1453 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
1454 (build-system cmake-build-system)
1456 ;; TODO: Build HTML user documentation and install separately.
1457 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
1458 "-DBUILD_SHARED_LIBS=ON")
1460 #:phases (modify-phases %standard-phases
1461 (add-before 'configure 'set-library-directory
1463 ;; Install libraries to lib/, not lib64/.
1464 (substitute* "internal/ceres/CMakeLists.txt"
1465 (("set\\(LIB_SUFFIX \"64\"\\)")
1466 "set(LIB_SUFFIX \"\")"))
1469 `(("pkg-config" ,pkg-config)))
1471 `(("glog" ,glog))) ;for #include <glog/glog.h>
1476 ("suitesparse" ,suitesparse)
1477 ("gflags" ,gflags)))
1478 (synopsis "C++ library for solving large optimization problems")
1480 "Ceres Solver is a C++ library for modeling and solving large,
1481 complicated optimization problems. It is a feature rich, mature and
1482 performant library which has been used in production since 2010. Ceres Solver
1483 can solve two kinds of problems:
1485 @item non-linear least squares problems with bounds constraints;
1486 @item general unconstrained optimization problems.
1488 (license license:bsd-3)))
1490 ;; For a fully featured Octave, users are strongly recommended also to install
1491 ;; the following packages: less, ghostscript, gnuplot.
1492 (define-public octave-cli
1499 (uri (string-append "mirror://gnu/octave/octave-"
1503 "11wwxpy2q1bhxs2v41bqn05i2sb0905cj1xil6mg8l4k2kka4cq6"))))
1504 (build-system gnu-build-system)
1506 `(("alsa-lib" ,alsa-lib)
1507 ("arpack" ,arpack-ng)
1512 ("fontconfig" ,fontconfig)
1513 ("freetype" ,freetype)
1517 ("graphicsmagick" ,graphicsmagick)
1520 ("libsndfile" ,libsndfile)
1524 ("portaudio" ,portaudio)
1526 ("readline" ,readline)
1527 ("suitesparse" ,suitesparse)
1528 ("texinfo" ,texinfo)
1532 ("gfortran" ,gfortran)
1533 ("pkg-config" ,pkg-config)
1535 ;; The following inputs are not actually used in the build process.
1536 ;; However, the ./configure gratuitously tests for their existence and
1537 ;; assumes that programs not present at build time are also not, and
1538 ;; can never be, available at run time! If these inputs are therefore
1539 ;; not present, support for them will be built out. However, Octave
1540 ;; will still run without them, albeit without the features they
1543 ("ghostscript" ,ghostscript)
1544 ("gnuplot" ,gnuplot)))
1545 ;; Octave code uses this variable to detect directories holding multiple CA
1546 ;; certificates to verify peers with. This is required for the networking
1547 ;; functions that require encryption to work properly.
1548 (native-search-paths
1549 (list (search-path-specification
1550 (variable "CURLOPT_CAPATH")
1551 (files '("etc/ssl/certs")))))
1554 (list (string-append "--with-shell="
1555 (assoc-ref %build-inputs "bash")
1558 (modify-phases %standard-phases
1559 (add-after 'configure 'configure-makeinfo
1560 (lambda* (#:key inputs #:allow-other-keys)
1561 (substitute* "libinterp/corefcn/help.h"
1564 "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
1566 (home-page "https://www.gnu.org/software/octave/")
1567 (synopsis "High-level language for numerical computation")
1568 (description "GNU Octave is a high-level interpreted language that is
1569 specialized for numerical computations. It can be used for both linear and
1570 non-linear applications and it provides great support for visualizing results.
1571 Work may be performed both at the interactive command-line as well as via
1573 (license license:gpl3+)))
1575 (define-public octave
1576 (package (inherit octave-cli)
1579 (inherit (package-source octave-cli))))
1581 `(("qscintilla" ,qscintilla)
1583 ,@(package-inputs octave-cli)))
1585 `(("qttools" , qttools) ;for lrelease
1586 ("texlive" ,(texlive-union (list texlive-epsf))) ; for texi2dvi
1587 ,@(package-native-inputs octave-cli)))
1589 (substitute-keyword-arguments (package-arguments octave-cli)
1591 `(modify-phases ,phases
1592 (add-before 'configure 'patch-qscintilla-library-name
1593 (lambda* (#:key inputs #:allow-other-keys)
1594 ;; The QScintilla library that the Octave configure script tries
1595 ;; to link with should be named libqscintilla-qt5.so, but the
1596 ;; QScintilla input provides the shared library as
1597 ;; libqscintilla2_qt5.so.
1598 (substitute* "configure"
1599 (("qscintilla2-qt5")
1603 (define-public qtoctave
1604 (deprecated-package "qtoctave" octave))
1606 (define-public opencascade-oce
1608 (name "opencascade-oce")
1614 (url "https://github.com/tpaviot/oce.git")
1615 (commit (string-append "OCE-" version))))
1616 (file-name (git-file-name name version))
1617 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
1619 (base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69"))))
1620 (build-system cmake-build-system)
1623 (list "-DOCE_TESTING:BOOL=ON"
1624 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1625 "-DOCE_DRAW:BOOL=ON"
1626 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1627 (assoc-ref %outputs "out"))
1628 "-UCMAKE_INSTALL_RPATH")))
1630 `(("freetype" ,freetype)
1637 `(("python" ,python-wrapper)))
1638 (home-page "https://github.com/tpaviot/oce")
1639 (synopsis "Libraries for 3D modeling and numerical simulation")
1641 "Open CASCADE is a set of libraries for the development of applications
1642 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1643 C++ class libraries providing services for 3D surface and solid modeling, CAD
1644 data exchange, and visualization. It is used for development of specialized
1645 software dealing with 3D models in design (CAD), manufacturing (CAM),
1646 numerical simulation (CAE), measurement equipment (CMM), and quality
1647 control (CAQ) domains.
1649 This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1650 patches, improvements, and experiments contributed by users over the official
1651 Open CASCADE library.")
1652 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1653 ; use of header files; see
1654 ; OCCT_LGPL_EXCEPTION.txt
1655 license:public-domain; files
1656 ; src/Standard/Standard_StdAllocator.hxx and
1657 ; src/NCollection/NCollection_StdAllocator.hxx
1658 license:expat; file src/OpenGl/OpenGl_glext.h
1659 license:bsd-3)))); test framework gtest
1661 (define-public opencascade-occt
1663 (name "opencascade-occt")
1669 (url "https://git.dev.opencascade.org/repos/occt.git")
1672 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
1674 (file-name (git-file-name name version))
1676 (base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4"))
1677 (modules '((guix build utils)))
1680 ;; Remove files specific to non-free operating systems.
1681 (delete-file-recursively "samples/ios")
1682 (delete-file-recursively "samples/mfc")
1683 (delete-file-recursively "samples/qt/FuncDemo")
1684 (delete-file "genconf.bat")
1685 (delete-file "gendoc.bat")
1686 (delete-file "genproj.bat")
1687 (delete-file "upgrade.bat")
1688 ;; Remove references to deleted files.
1689 (substitute* "dox/FILES_HTML.txt"
1690 ((".*standard.*") "" )
1691 ((".*UIKitSample.*") ""))
1693 (build-system cmake-build-system)
1695 '(;; There is no test target for make. OCCT provides an
1696 ;; 'Automated Testing System', which may be accessed after
1697 ;; installation via the draw.sh script. draw.sh is located in
1698 ;; the bin directory. For details see:
1699 ;; https://www.opencascade.com/doc/occt-7.3.0/overview/html/\
1700 ;; occt_dev_guides__tests.html
1702 ;; Configure without freeimage: attempting to link against the
1703 ;; freeimage version 3.17 library leads to 'undefined
1704 ;; reference' errors.
1706 (list "-DUSE_FREEIMAGE:BOOL=OFF"
1708 "-DUSE_VTK:BOOL=OFF"
1709 "-DBUILD_DOC_Overview:BOOL=OFF"
1710 "-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON"
1711 "-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON"
1712 "-UCMAKE_INSTALL_LIBDIR")))
1714 `(("doxygen" ,doxygen)
1715 ;("freeimage" ,freeimage)
1716 ("freetype" ,freetype)
1718 ("libxext" ,libxext)
1725 ;; TODO: build Overview documentation and add 'doc' output.
1726 (home-page "https://www.opencascade.com")
1727 (synopsis "Libraries for 3D modeling and numerical simulation")
1729 "Open CASCADE is a set of libraries for the development of applications
1730 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1731 C++ class libraries providing services for 3D surface and solid modeling, CAD
1732 data exchange, and visualization. It is used for development of specialized
1733 software dealing with 3D models in design (CAD), manufacturing (CAM),
1734 numerical simulation (CAE), measurement equipment (CMM), and quality
1735 control (CAQ) domains.
1737 This is the certified version of the Open Cascade Technology (OCCT) library.")
1738 (license (list ;; OCCT library:
1739 license:lgpl2.1; with an exception for the use of header
1740 ; files, see OCCT_LGPL_EXCEPTION.txt.
1741 ;; Files src/OpenGl/glext.h, adm/cmake/cotire.cmake and
1742 ;; src/OpenGl/OpenGl_HaltonSampler.hxx:
1744 ;; Files src/ExprIntrp/ExprIntrp.tab.* and
1745 ;; src/StepFile/step.tab.*:
1746 license:gpl3+ ; with Bison 2.2 exception.
1747 ;; File src/NCollection/NCollection_UtfIterator.lxx:
1748 (license:non-copyleft
1749 "https://www.unicode.org/license.html")
1750 ;; File src/NCollection/NCollection_StdAllocator.hxx:
1751 license:public-domain))))
1761 (url "https://gitlab.onelab.info/gmsh/gmsh.git")
1763 (string-append "gmsh_"
1764 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
1766 (file-name (git-file-name name version))
1768 (base32 "08rq4jajwmlpivnm9yifz2jhaivnz065lnk0h2zv773nwl9wf162"))
1769 (modules '((guix build utils)))
1771 ;; Remove non-free METIS code
1773 (delete-file-recursively "contrib/Metis")
1775 (build-system cmake-build-system)
1778 ("gfortran" ,gfortran)
1784 ("opencascade-oce" ,opencascade-oce)
1786 ("libxext" ,libxext)))
1788 `(("fontconfig" ,fontconfig)
1789 ("libxft" ,libxft)))
1791 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1792 "-DENABLE_BUILD_SHARED:BOOL=ON"
1793 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
1794 (home-page "http://gmsh.info/")
1795 (synopsis "3D finite element grid generator")
1796 (description "Gmsh is a 3D finite element grid generator with a built-in
1797 CAD engine and post-processor. Its design goal is to provide a fast, light
1798 and user-friendly meshing tool with parametric input and advanced
1799 visualization capabilities. Gmsh is built around four modules: geometry,
1800 mesh, solver and post-processing. The specification of any input to these
1801 modules is done either interactively using the graphical user interface or in
1802 ASCII text files using Gmsh's own scripting language.")
1803 (license license:gpl2+)))
1805 (define-public maxflow
1808 ;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’,
1809 ;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’.
1814 (url "https://github.com/gerddie/maxflow.git")
1816 (file-name (git-file-name name version))
1819 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1820 (build-system cmake-build-system)
1821 (home-page "https://pub.ist.ac.at/~vnk/software.html")
1822 (synopsis "Library implementing Maxflow algorithm")
1823 (description "An implementation of the maxflow algorithm described in
1824 @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1825 Energy Minimization in Computer Vision.\n
1826 Yuri Boykov and Vladimir Kolmogorov.\n
1827 In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1829 (license license:gpl3+)))
1831 (define-public petsc
1838 ;; The *-lite-* tarball does not contain the *large* documentation
1839 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1840 "petsc-lite-" version ".tar.gz"))
1842 (base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx"))))
1843 (outputs '("out" ; libraries and headers
1844 "examples")) ; ~30MiB of examples
1845 (build-system gnu-build-system)
1847 `(("python" ,python-2)))
1849 `(("gfortran" ,gfortran)
1851 ("superlu" ,superlu)
1852 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1853 ;; leaving out opengl, as configuration seems to only be for mac
1856 `(#:test-target "test"
1857 #:parallel-build? #f ; build is parallel by default
1863 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1864 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1865 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
1867 (modify-phases %standard-phases
1869 ;; PETSc's configure script is actually a python script, so we can't
1870 ;; run it with bash.
1871 (lambda* (#:key outputs (configure-flags '())
1873 (let* ((prefix (assoc-ref outputs "out"))
1874 (flags `(,(string-append "--prefix=" prefix)
1875 ,@configure-flags)))
1876 (format #t "build directory: ~s~%" (getcwd))
1877 (format #t "configure flags: ~s~%" flags)
1878 (apply invoke "./configure" flags))))
1879 (add-after 'configure 'clean-local-references
1880 (lambda* (#:key outputs #:allow-other-keys)
1881 (let ((out (assoc-ref outputs "out")))
1882 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
1883 ;; Prevent build directory from leaking into compiled code
1885 ;; Scrub timestamp for reproducibility
1886 ((".*Libraries compiled on.*") ""))
1887 (substitute* (find-files "." "petscvariables")
1888 ;; Do not expose build machine characteristics, set to defaults.
1889 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1890 (("NPMAX = [:digit:]+") "NPMAX = 2"))
1892 (add-after 'install 'clean-install
1893 ;; Try to keep installed files from leaking build directory names.
1894 (lambda* (#:key inputs outputs #:allow-other-keys)
1895 (let ((out (assoc-ref outputs "out")))
1896 (substitute* (map (lambda (file)
1897 (string-append out "/lib/petsc/conf/" file))
1898 '("petscvariables"))
1900 ;; Make compiler references point to the store
1901 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
1902 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1903 (string-append "= " (which compiler))))
1904 ;; PETSc installs some build logs, which aren't necessary.
1905 (for-each (lambda (file)
1906 (let ((f (string-append out "/lib/petsc/conf/" file)))
1907 (when (file-exists? f)
1909 '("configure.log" "make.log" "gmake.log"
1910 "test.log" "error.log" "RDict.db"
1911 "PETScBuildInternal.cmake"
1912 ;; Once installed, should uninstall with Guix
1915 (add-after 'install 'move-examples
1916 (lambda* (#:key outputs #:allow-other-keys)
1917 (let* ((out (assoc-ref outputs "out"))
1918 (examples (assoc-ref outputs "examples"))
1919 (exdir (string-append out "/share/petsc/examples"))
1920 (exdir' (string-append examples "/share/petsc/examples")))
1921 (copy-recursively exdir exdir')
1922 (delete-file-recursively exdir)
1924 (home-page "https://www.mcs.anl.gov/petsc")
1925 (synopsis "Library to solve PDEs")
1926 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1927 data structures and routines for the scalable (parallel) solution of
1928 scientific applications modeled by partial differential equations.")
1929 (license (license:non-copyleft
1930 "https://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1932 (define-public petsc-complex
1933 (package (inherit petsc)
1934 (name "petsc-complex")
1936 (substitute-keyword-arguments (package-arguments petsc)
1937 ((#:configure-flags cf)
1938 `(cons "--with-scalar-type=complex" ,cf))))
1939 (synopsis "Library to solve PDEs (with complex scalars)")))
1941 (define-public petsc-openmpi
1942 (package (inherit petsc)
1943 (name "petsc-openmpi")
1945 `(("hdf5" ,hdf5-parallel-openmpi)
1946 ("hypre" ,hypre-openmpi)
1948 ("mumps" ,mumps-openmpi)
1949 ("openmpi" ,openmpi)
1950 ("scalapack" ,scalapack)
1951 ("scotch" ,pt-scotch32)
1952 ,@(package-inputs petsc)))
1954 (substitute-keyword-arguments (package-arguments petsc)
1955 ((#:configure-flags cf)
1957 "--with-mpiexec=mpirun"
1960 "--with-scalapack=1"
1962 ,(string-append "--with-mpi-dir="
1963 (assoc-ref %build-inputs "openmpi"))
1964 ,(string-append "--with-hdf5-include="
1965 (assoc-ref %build-inputs "hdf5") "/include")
1966 ,(string-append "--with-hdf5-lib="
1967 (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
1968 ,@(delete "--with-mpi=0" ,cf)))
1970 `(modify-phases ,phases
1971 (add-before 'configure 'mpi-setup
1972 ,%openmpi-setup)))))
1973 (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
1975 (define-public petsc-complex-openmpi
1976 (package (inherit petsc-complex)
1977 (name "petsc-complex-openmpi")
1979 `(("openmpi" ,openmpi)
1980 ,@(package-inputs petsc-complex)))
1982 (substitute-keyword-arguments (package-arguments petsc-complex)
1983 ((#:configure-flags cf)
1984 ``("--with-mpiexec=mpirun"
1985 ,(string-append "--with-mpi-dir="
1986 (assoc-ref %build-inputs "openmpi"))
1987 ,@(delete "--with-mpi=0" ,cf)))
1989 `(modify-phases ,phases
1990 (add-before 'configure 'mpi-setup
1991 ,%openmpi-setup)))))
1992 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
1994 (define-public python-petsc4py
1996 (name "python-petsc4py")
2001 (uri (pypi-uri "petsc4py" version))
2004 "1rm1qj5wlkhxl39by9n78lh3gbmii31wsnb8j1rr5hvfr5xgbx2q"))))
2005 (build-system python-build-system)
2008 (modify-phases %standard-phases
2009 (add-before 'build 'pre-build
2011 ;; Define path to PETSc installation.
2012 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
2014 (add-before 'check 'mpi-setup
2017 `(("petsc" ,petsc-openmpi)
2018 ("python-numpy" ,python-numpy)))
2019 (home-page "https://bitbucket.org/petsc/petsc4py/")
2020 (synopsis "Python bindings for PETSc")
2021 (description "PETSc, the Portable, Extensible Toolkit for
2022 Scientific Computation, is a suite of data structures and routines for
2023 the scalable (parallel) solution of scientific applications modeled by
2024 partial differential equations. It employs the MPI standard for all
2025 message-passing communication. @code{petsc4py} provides Python
2026 bindings to almost all functions of PETSc.")
2027 (license license:bsd-3)))
2029 (define-public python-kiwisolver
2031 (name "python-kiwisolver")
2035 (uri (pypi-uri "kiwisolver" version))
2038 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
2039 (build-system python-build-system)
2040 (home-page "https://github.com/nucleic/kiwi")
2041 (synopsis "Fast implementation of the Cassowary constraint solver")
2043 "Kiwi is an efficient C++ implementation of the Cassowary constraint
2044 solving algorithm. Kiwi has been designed from the ground up to be
2045 lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
2046 Cassowary solver with typical use cases gaining a 40x improvement. Memory
2047 savings are consistently > 5x.")
2048 (license license:bsd-3)))
2050 (define-public python2-kiwisolver
2051 (package-with-python2 python-kiwisolver))
2053 (define-public slepc
2060 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
2064 "1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8"))))
2065 (build-system gnu-build-system)
2067 `(("python" ,python-2)
2068 ("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
2070 `(("arpack" ,arpack-ng)
2071 ("gfortran" ,gfortran)))
2073 `(("petsc" ,petsc)))
2075 `(#:parallel-build? #f ;build is parallel by default
2077 `(,(string-append "--with-arpack-dir="
2078 (assoc-ref %build-inputs "arpack") "/lib"))
2079 #:make-flags ;honor (parallel-job-count)
2080 `(,(format #f "MAKE_NP=~a" (parallel-job-count))
2081 ,(string-append "PETSCCONFIGDIR="
2082 (assoc-ref %build-inputs "petsc:examples")
2083 "/share/petsc/examples/config"))
2085 (modify-phases %standard-phases
2087 ;; configure is a python script, so we can't run it with bash.
2088 (lambda* (#:key inputs outputs (configure-flags '())
2090 (let* ((prefix (assoc-ref outputs "out"))
2091 (flags `(,(string-append "--prefix=" prefix)
2092 ,@configure-flags)))
2093 (format #t "build directory: ~s~%" (getcwd))
2094 (format #t "configure flags: ~s~%" flags)
2095 (setenv "SLEPC_DIR" (getcwd))
2096 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
2097 (apply invoke "./configure" flags))))
2098 (add-after 'install 'delete-doc
2099 ;; TODO: SLEPc installs HTML documentation alongside headers in
2100 ;; $out/include. We'd like to move them to share/doc, but delete
2101 ;; them for now, as they are incomplete and installing the complete
2102 ;; documentation is difficult.
2103 (lambda* (#:key outputs #:allow-other-keys)
2104 (let* ((out (assoc-ref outputs "out")))
2105 (for-each delete-file (find-files out "\\.html$"))
2107 (add-after 'install 'clean-install
2108 ;; Clean up unnecessary build logs from installation.
2109 (lambda* (#:key outputs #:allow-other-keys)
2110 (let ((out (assoc-ref outputs "out")))
2111 (for-each (lambda (file)
2112 (let ((f (string-append out "/lib/slepc/conf/" file)))
2113 (when (file-exists? f)
2115 '("configure.log" "make.log" "gmake.log"
2116 "test.log" "error.log" "RDict.db"
2119 (home-page "http://slepc.upv.es")
2120 (synopsis "Scalable library for eigenproblems")
2121 (description "SLEPc is a software library for the solution of large sparse
2122 eigenproblems on parallel computers. It can be used for the solution of
2123 linear eigenvalue problems formulated in either standard or generalized form,
2124 as well as other related problems such as the singular value decomposition.
2125 The emphasis of the software is on methods and techniques appropriate for
2126 problems in which the associated matrices are sparse, for example, those
2127 arising after the discretization of partial differential equations.")
2128 (license license:bsd-2)))
2130 (define-public slepc-complex
2131 (package (inherit slepc)
2132 (name "slepc-complex")
2134 `(("petsc" ,petsc-complex)
2135 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
2136 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
2138 (define-public slepc-openmpi
2139 (package (inherit slepc)
2140 (name "slepc-openmpi")
2142 (substitute-keyword-arguments (package-arguments slepc)
2143 ((#:phases phases '%standard-phases)
2144 `(modify-phases ,phases
2145 (add-before 'check 'mpi-setup
2146 ,%openmpi-setup)))))
2149 ("arpack" ,arpack-ng-openmpi)
2150 ,@(alist-delete "arpack" (package-inputs slepc))))
2152 `(("petsc" ,petsc-openmpi)
2153 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
2154 (synopsis "Scalable library for eigenproblems (with MPI support)")))
2156 (define-public slepc-complex-openmpi
2157 (package (inherit slepc-openmpi)
2158 (name "slepc-complex-openmpi")
2160 `(("petsc" ,petsc-complex-openmpi)
2161 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
2162 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
2164 (define-public python-slepc4py
2166 (name "python-slepc4py")
2171 (uri (pypi-uri "slepc4py" version))
2174 "1ksp08kxf4wg408b9nn39z3qfhy643j22d4rfbl30vzxk2rxh4lq"))))
2175 (build-system python-build-system)
2178 (modify-phases %standard-phases
2179 (add-before 'build 'pre-build
2181 ;; Define path to PETSc installation.
2182 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
2183 ;; Define path to SLEPc installation.
2184 (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
2186 (add-before 'check 'mpi-setup
2189 `(("python-numpy" ,python-numpy)
2190 ("python-petsc4py" ,python-petsc4py)
2191 ("slepc" ,slepc-openmpi)))
2192 (home-page "https://bitbucket.org/slepc/slepc4py/")
2193 (synopsis "Python bindings for SLEPc")
2194 (description "SLEPc, the Scalable Library for Eigenvalue Problem
2195 Computations, is based on PETSc, the Portable, Extensible Toolkit for
2196 Scientific Computation. It employs the MPI standard for all
2197 message-passing communication. @code{slepc4py} provides Python
2198 bindings to almost all functions of SLEPc.")
2199 (license license:bsd-3)))
2201 (define-public mumps
2208 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
2212 "0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r"))
2213 (patches (search-patches "mumps-build-parallelism.patch"
2214 "mumps-shared-libseq.patch"
2215 "mumps-shared-mumps.patch"
2216 "mumps-shared-pord.patch"))))
2217 (build-system gnu-build-system)
2219 `(("fortran" ,gfortran)
2220 ;; These are required for linking against mumps, but we let the user
2221 ;; declare the dependency.
2224 ("scotch" ,scotch)))
2226 `(#:modules ((ice-9 match)
2229 ,@%gnu-build-system-modules)
2231 (modify-phases %standard-phases
2233 (lambda* (#:key inputs #:allow-other-keys)
2234 (call-with-output-file "Makefile.inc"
2245 INCSEQ = -I$(topdir)/libseq
2246 LIBSEQ = $(topdir)/libseq/libmpiseq.a
2247 LIBSEQNEEDED = libseqneeded~;
2251 AR = ar vr # rules require trailing space, ugh...
2254 LIBBLAS = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[
2256 SCALAP = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~]
2257 LIBOTHERS = -pthread
2260 OPTF = -O2 -DALLOW_NON_INIT $(PIC)
2264 LIBS = $(SCALAP) $(LIBSEQ)
2265 LPORDDIR = $(topdir)/PORD/lib
2266 IPORD = -I$(topdir)/PORD/include
2267 LPORD = $(LPORDDIR)/libpord.a
2268 ORDERINGSF = -Dpord~@[
2270 IMETIS = -I$(METISDIR)/include
2271 LMETIS = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
2272 ORDERINGSF += -Dmetis~]~@[~:{
2274 ISCOTCH = -I$(SCOTCHDIR)/include
2275 LSCOTCH = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
2276 ORDERINGSF += ~a~}~]
2277 ORDERINGSC = $(ORDERINGSF)
2278 LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
2279 IORDERINGSF = $(ISCOTCH)
2280 IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
2281 (assoc-ref inputs "mpi")
2282 (assoc-ref inputs "blas")
2283 (assoc-ref inputs "scalapack")
2284 (assoc-ref inputs "metis")
2285 (match (list (assoc-ref inputs "pt-scotch")
2286 (assoc-ref inputs "scotch"))
2290 `((,scotch "" "-Dscotch")))
2293 "-lptesmumps -lptscotch -lptscotcherr "
2294 "-Dptscotch")))))))))
2296 ;; By default only the d-precision library is built. Make with "all"
2297 ;; target so that all precision libraries and examples are built.
2299 (invoke "make" "all"
2300 (format #f "-j~a" (parallel-job-count)))))
2302 ;; Run the simple test drivers, which read test input from stdin:
2303 ;; from the "real" input for the single- and double-precision
2304 ;; testers, and from the "cmplx" input for complex-precision
2305 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
2306 ;; package to prefix execution with "mpirun".
2307 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
2308 (with-directory-excursion "examples"
2311 (let ((tester (apply open-pipe*
2314 ,(string-append "./" prec
2316 (input (open-input-file
2317 (string-append "input_simpletest_" type))))
2319 (dump-port input tester)
2321 (zero? (close-pipe tester)))))
2323 '("real" "real" "cmplx" "cmplx")))))
2325 (lambda* (#:key outputs #:allow-other-keys)
2326 (let* ((out (assoc-ref outputs "out"))
2327 (libdir (string-append out "/lib")))
2328 (copy-recursively "lib" libdir)
2329 (copy-recursively "include" (string-append out "/include"))
2330 (when (file-exists? "libseq/libmpiseq.a")
2331 (install-file "libseq/libmpiseq.a" libdir))
2332 (when (file-exists? "libseq/libmpiseq.so")
2333 (install-file "libseq/libmpiseq.so" libdir))
2335 (home-page "http://mumps.enseeiht.fr")
2336 (synopsis "Multifrontal sparse direct solver")
2338 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
2339 sparse system of linear equations A x = b using Gaussian elimination.")
2340 (license license:cecill-c)))
2342 (define-public mumps-metis
2343 (package (inherit mumps)
2344 (name "mumps-metis")
2346 (alist-delete "scotch" (package-inputs mumps)))))
2348 (define-public mumps-openmpi
2349 (package (inherit mumps)
2350 (name "mumps-openmpi")
2353 ("scalapack" ,scalapack)
2354 ("pt-scotch" ,pt-scotch)
2355 ,@(alist-delete "scotch" (package-inputs mumps))))
2357 (substitute-keyword-arguments (package-arguments mumps)
2359 `(modify-phases ,phases
2360 (add-before 'check 'mpi-setup
2364 ((assoc-ref ,phases 'check)
2365 #:exec-prefix '("mpirun" "-n" "2"))))))))
2366 (synopsis "Multifrontal sparse direct solver (with MPI)")))
2368 (define-public mumps-metis-openmpi
2369 (package (inherit mumps-openmpi)
2370 (name "mumps-metis-openmpi")
2372 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
2374 (define-public ruby-asciimath
2376 (name "ruby-asciimath")
2381 (uri (rubygems-uri "asciimath" version))
2384 "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
2385 (build-system ruby-build-system)
2388 (modify-phases %standard-phases
2390 ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
2391 (add-after 'unpack 'patch-remove-spurious-backslashes
2393 (substitute* "spec/parser_spec.rb"
2398 `(("bundler" ,bundler)
2399 ("ruby-rspec" ,ruby-rspec)))
2400 (synopsis "AsciiMath parsing and conversion library")
2402 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
2403 easy-to-write markup language for mathematics.")
2404 (home-page "https://github.com/asciidoctor/asciimath")
2405 (license license:expat)))
2407 (define-public superlu
2414 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2415 "superlu_" version ".tar.gz"))
2417 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
2418 (modules '((guix build utils)))
2420 ;; Replace the non-free implementation of MC64 with a stub adapted
2423 (use-modules (ice-9 regex)
2425 (call-with-output-file "SRC/mc64ad.c"
2430 void mc64id_(int *a) {
2431 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2434 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2435 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2436 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2439 ;; Remove the corresponding license verbiage. MC64 license follows
2440 ;; a "------" line separator.
2441 (with-atomic-file-replacement "License.txt"
2442 (let ((rx (make-regexp "-{8}")))
2445 (let ((line (read-line in 'concat)))
2446 (unless (regexp-exec rx line)
2450 (build-system cmake-build-system)
2454 `(("blas" ,openblas)
2455 ("gfortran" ,gfortran)))
2457 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2458 "-DTPL_BLAS_LIBRARIES=openblas"
2459 "-DBUILD_SHARED_LIBS:BOOL=YES")))
2460 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
2461 (synopsis "Supernodal direct solver for sparse linear systems")
2463 "SuperLU is a general purpose library for the direct solution of large,
2464 sparse, nonsymmetric systems of linear equations on high performance machines.
2465 The library is written in C and is callable from either C or Fortran. The
2466 library routines perform an LU decomposition with partial pivoting and
2467 triangular system solves through forward and back substitution. The library
2468 also provides threshold-based ILU factorization preconditioners.")
2469 (license (list license:bsd-3
2470 license:gpl2+ ;EXAMPLE/*fgmr.c
2471 (license:fsf-free "file://SRC/colamd.h")))))
2473 (define-public superlu-dist
2475 (name "superlu-dist")
2480 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2481 "superlu_dist_" version ".tar.gz"))
2483 (base32 "0pqgcgh1yxhfzs99fas3mggajzd5wca3nbyp878rziy74gfk03dl"))
2484 (modules '((guix build utils)))
2486 ;; Replace the non-free implementation of MC64 with a stub
2488 (call-with-output-file "SRC/mc64ad_dist.c"
2493 void mc64id_dist(int *a) {
2494 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2497 void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2498 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2499 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2502 (substitute* "SRC/util.c" ;adjust default algorithm
2503 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
2504 ;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
2505 ;; general (i.e. non-square) processor-grid support.
2506 "RowPerm = NOROWPERM;"))
2508 (patches (search-patches "superlu-dist-scotchmetis.patch"
2509 "superlu-dist-awpm-grid.patch"
2510 "superlu-dist-fix-mpi-deprecations.patch"))))
2511 (build-system cmake-build-system)
2515 `(("gfortran" ,gfortran)
2518 ("combblas" ,combinatorial-blas)))
2520 `(("mpi" ,openmpi) ;headers include MPI heades
2521 ("parmetis" ,pt-scotch32 "metis")
2522 ("pt-scotch" ,pt-scotch32)))
2524 `(#:parallel-tests? #f ;tests use MPI and OpenMP
2525 #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
2526 "-DTPL_ENABLE_COMBBLASLIB=YES"
2527 "-DTPL_BLAS_LIBRARIES=-lopenblas"
2528 "-DTPL_LAPACK_LIBRARIES=-llapack"
2529 (string-append "-DTPL_PARMETIS_LIBRARIES="
2531 '("ptscotchparmetis" "ptscotch" "ptscotcherr"
2532 "scotchmetis" "scotch" "scotcherr")
2534 (string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
2535 (assoc-ref %build-inputs "parmetis")
2537 "-DTPL_ENABLE_COMBBLASLIB=ON"
2538 (string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
2539 (assoc-ref %build-inputs "combblas")
2540 "/include/CombBLAS;"
2541 (assoc-ref %build-inputs "combblas")
2542 "/include/BipartiteMatchings")
2543 "-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
2545 (modify-phases %standard-phases
2546 (add-before 'configure 'set-c++-standard
2548 (substitute* "CMakeLists.txt"
2549 ;; AWPM headers require C++14
2550 (("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
2551 (add-before 'check 'mpi-setup
2553 (add-before 'check 'omp-setup
2554 (lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
2555 (home-page (package-home-page superlu))
2556 (synopsis "Parallel supernodal direct solver")
2558 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2559 It is targeted for distributed memory parallel machines. SuperLU_DIST is
2560 implemented in ANSI C, and MPI for communications.")
2561 (license license:bsd-3)))
2563 (define-public scotch
2570 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
2571 "latestfile/298/scotch_" version ".tar.gz"))
2573 (base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8"))
2574 (patches (search-patches "scotch-build-parallelism.patch"
2575 "scotch-integer-declarations.patch"))))
2576 (build-system gnu-build-system)
2581 (outputs '("out" "metis"))
2583 `(#:make-flags (list (string-append "prefix=" %output))
2585 (modify-phases %standard-phases
2587 'unpack 'chdir-to-src
2588 (lambda _ (chdir "src") #t))
2592 (call-with-output-file "Makefile.inc"
2606 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2607 LDFLAGS = -lz -lm -lrt -lpthread
2609 LEX = flex -Pscotchyy -olex.yy.c
2614 YACC = bison -pscotchyy -y -b y
2616 '("COMMON_FILE_COMPRESS_GZ"
2618 "COMMON_RANDOM_FIXED_SEED"
2619 "INTSIZE64" ;use 'int64_t'
2620 ;; Prevents symbolc clashes with libesmumps
2622 ;; XXX: Causes invalid frees in superlu-dist tests
2624 ;; "SCOTCH_PTHREAD_NUMBER=2"
2625 "restrict=__restrict"))))
2627 (add-after 'build 'build-esmumps
2630 (format #f "-j~a" (parallel-job-count))
2632 (add-before 'install 'make-install-dirs
2633 (lambda* (#:key outputs #:allow-other-keys)
2634 (mkdir (assoc-ref outputs "out"))))
2635 (add-after 'install 'install-metis
2636 (lambda* (#:key outputs #:allow-other-keys)
2637 (let ((out (assoc-ref outputs "metis")))
2639 ;; metis files are not installed with 'make install'
2640 (for-each (lambda (f)
2641 (install-file f (string-append out "/include")))
2642 (find-files "../include/" ".*metis\\.h"))
2643 (for-each (lambda (f)
2644 (install-file f (string-append out "/lib")))
2645 (find-files "../lib/" ".*metis\\..*"))
2647 (home-page "https://www.labri.fr/perso/pelegrin/scotch/")
2648 (synopsis "Programs and libraries for graph algorithms")
2649 (description "SCOTCH is a set of programs and libraries which implement
2650 the static mapping and sparse matrix reordering algorithms developed within
2651 the SCOTCH project. Its purpose is to apply graph theory, with a divide and
2652 conquer approach, to scientific computing problems such as graph and mesh
2653 partitioning, static mapping, and sparse matrix ordering, in application
2654 domains ranging from structural mechanics to operating systems or
2656 ;; See LICENSE_en.txt
2657 (license license:cecill-c)))
2659 (define-public scotch32
2660 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2661 ;; some applications.
2662 (package (inherit scotch)
2665 (substitute-keyword-arguments (package-arguments scotch)
2666 ((#:phases scotch-phases)
2667 `(modify-phases ,scotch-phases
2671 (call-with-output-file "Makefile.inc"
2685 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2686 LDFLAGS = -lz -lm -lrt -lpthread
2688 LEX = flex -Pscotchyy -olex.yy.c
2693 YACC = bison -pscotchyy -y -b y
2695 '("COMMON_FILE_COMPRESS_GZ"
2697 "COMMON_RANDOM_FIXED_SEED"
2698 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
2699 ;; Prevents symbolc clashes with libesmumps
2701 ;; XXX: Causes invalid frees in superlu-dist tests
2703 ;; "SCOTCH_PTHREAD_NUMBER=2"
2704 "restrict=__restrict"))))))))))
2706 "Programs and libraries for graph algorithms (32-bit integers)")))
2708 (define-public pt-scotch
2709 (package (inherit scotch)
2712 `(("openmpi" ,openmpi))) ;Headers include MPI headers
2714 (substitute-keyword-arguments (package-arguments scotch)
2715 ((#:phases scotch-phases)
2716 `(modify-phases ,scotch-phases
2720 (invoke "make" (format #f "-j~a" (parallel-job-count))
2721 "ptscotch" "ptesmumps")
2723 ;; Install the serial metis compatibility library
2724 (invoke "make" "-C" "libscotchmetis" "install")))
2725 (add-before 'check 'mpi-setup
2729 (invoke "make" "ptcheck")))))))
2730 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
2732 (define-public pt-scotch32
2733 (package (inherit scotch32)
2734 (name "pt-scotch32")
2736 `(("openmpi" ,openmpi))) ;headers include MPI headers
2738 (substitute-keyword-arguments (package-arguments scotch32)
2739 ((#:phases scotch32-phases)
2740 `(modify-phases ,scotch32-phases
2743 (invoke "make" (format #f "-j~a" (parallel-job-count))
2744 "ptscotch" "ptesmumps")
2745 ;; Install the serial metis compatibility library
2746 (invoke "make" "-C" "libscotchmetis" "install")))
2747 (add-before 'check 'mpi-setup
2751 (invoke "make" "ptcheck")))))))
2753 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2755 (define-public metis
2762 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2763 "metis-" version ".tar.gz"))
2766 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2767 (build-system cmake-build-system)
2769 `(("blas" ,openblas)))
2771 `(#:tests? #f ;no tests
2772 #:configure-flags `("-DSHARED=ON"
2773 ,(string-append "-DGKLIB_PATH=" (getcwd)
2774 "/metis-" ,version "/GKlib"))))
2775 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2776 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2778 "METIS is a set of serial programs for partitioning graphs, partitioning
2779 finite element meshes, and producing fill-reducing orderings for sparse
2780 matrices. The algorithms implemented in METIS are based on the multilevel
2781 recursive-bisection, multilevel k-way, and multi-constraint partitioning
2783 (license license:asl2.0))) ;As of version 5.0.3
2785 (define-public p4est
2792 (uri (string-append "http://p4est.github.io/release/p4est-"
2796 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
2797 (build-system gnu-build-system)
2799 `(("fortran" ,gfortran)
2804 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2805 (assoc-ref %build-inputs "blas")
2807 ,(string-append "LAPACK_LIBS=-L"
2808 (assoc-ref %build-inputs "lapack")
2810 #:phases (modify-phases %standard-phases
2811 (add-before 'check 'mpi-setup
2813 (home-page "http://www.p4est.org")
2814 (synopsis "Adaptive mesh refinement on forests of octrees")
2816 "The p4est software library enables the dynamic management of a
2817 collection of adaptive octrees, conveniently called a forest of octrees.
2818 p4est is designed to work in parallel and scales to hundreds of thousands of
2820 (license license:gpl2+)))
2822 (define-public p4est-openmpi
2823 (package (inherit p4est)
2824 (name "p4est-openmpi")
2827 ,@(package-inputs p4est)))
2829 (substitute-keyword-arguments (package-arguments p4est)
2830 ((#:configure-flags cf)
2831 ``("--enable-mpi" ,@,cf))))
2832 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2834 (define-public gsegrafix
2841 (uri (string-append "mirror://gnu/" name "/" name "-"
2845 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2846 (build-system gnu-build-system)
2848 `(#:configure-flags '("LDFLAGS=-lm")))
2850 `(("libgnomecanvas" ,libgnomecanvas)
2851 ("libbonoboui" ,libbonoboui)
2852 ("libgnomeui" ,libgnomeui)
2853 ("libgnomeprintui" ,libgnomeprintui)
2856 `(("pkg-config" ,pkg-config)))
2857 (home-page "https://www.gnu.org/software/gsegrafix/")
2858 (synopsis "GNOME application to create scientific and engineering plots")
2859 (description "GSEGrafix is an application which produces high-quality graphical
2860 plots for science and engineering. Plots are specified via simple ASCII
2861 parameter files and data files and are presented in an anti-aliased GNOME
2862 canvas. The program supports rectangular two-dimensional plots, histograms,
2863 polar-axis plots and three-dimensional plots. Plots can be printed or saved
2864 to BMP, JPEG or PNG image formats.")
2865 (license license:gpl3+)))
2867 (define-public maxima
2874 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2875 version "-source/" name "-" version ".tar.gz"))
2878 "0xyahp4c6509haxh4n1swiqm3421gplkdisa0zypclh3252sbzfw"))
2879 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
2880 (build-system gnu-build-system)
2883 ("gnuplot" ,gnuplot) ;for plots
2885 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
2887 `(("texinfo" ,texinfo)
2889 ("python" ,python)))
2892 (list "--enable-gcl"
2893 (string-append "--with-posix-shell="
2894 (assoc-ref %build-inputs "bash")
2896 (string-append "--with-wish="
2897 (assoc-ref %build-inputs "tk")
2899 (let ((v ,(package-version tk)))
2900 (string-take v (string-index-right v #\.)))))
2901 ;; By default Maxima attempts to write temporary files to
2902 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2903 ;; Work around that.
2904 #:make-flags (list "TMPDIR=/tmp")
2906 (modify-phases %standard-phases
2907 (add-after 'unpack 'patch-paths
2908 (lambda* (#:key inputs #:allow-other-keys)
2909 (let* ((sed (string-append (assoc-ref inputs "sed") "/bin/sed"))
2910 (coreutils (assoc-ref inputs "coreutils"))
2911 (dirname (string-append coreutils "/bin/dirname"))
2912 (head (string-append coreutils "/bin/head"))
2913 (perl (string-append (assoc-ref inputs "perl") "/bin/perl"))
2914 (python (string-append (assoc-ref inputs "python")
2916 (substitute* "src/maxima.in"
2917 (("sed ") (string-append sed " "))
2918 (("dirname") dirname)
2920 (substitute* "doc/info/Makefile.in"
2921 (("/usr/bin/env perl") perl))
2922 (substitute* "doc/info/build_html.sh.in"
2923 (("python") python))
2925 (add-before 'check 'pre-check
2927 (chmod "src/maxima" #o555)
2931 ;; This is derived from the testing code in the "debian/rules" file
2932 ;; of Debian's Maxima package.
2933 ;; If Maxima can successfully run this, the binary to be installed
2939 "--batch-string=\"run_testsuite();\" "
2940 "| grep -q \"No unexpected errors found\""))))
2941 ;; Make sure the doc and emacs files are found in the
2942 ;; standard location. Also configure maxima to find gnuplot
2943 ;; without having it on the PATH.
2944 (add-after 'install 'post-install
2945 (lambda* (#:key outputs inputs #:allow-other-keys)
2946 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2947 (out (assoc-ref outputs "out"))
2948 (datadir (string-append out "/share/maxima/" ,version))
2949 (binutils (string-append (assoc-ref inputs "binutils")
2951 (with-directory-excursion out
2952 (mkdir-p "share/emacs")
2953 (mkdir-p "share/doc")
2955 (string-append datadir "/doc/")
2956 (string-append out "/share/doc/maxima"))
2957 (with-atomic-file-replacement
2958 (string-append datadir "/share/maxima-init.lisp")
2960 (format out "~a ~s~a~%"
2961 "(setf $gnuplot_command "
2962 (string-append gnuplot "/bin/gnuplot") ")")
2963 (dump-port in out))))
2964 ;; Ensure that Maxima will have access to the GNU binutils
2965 ;; components at runtime.
2966 (wrap-program (string-append out "/bin/maxima")
2967 `("PATH" prefix (,binutils))))
2969 (home-page "http://maxima.sourceforge.net")
2970 (synopsis "Numeric and symbolic expression manipulation")
2971 (description "Maxima is a system for the manipulation of symbolic and
2972 numerical expressions. It yields high precision numeric results by using
2973 exact fractions, arbitrary precision integers, and variable precision floating
2975 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2976 ;; Others simply say "GNU General Public License" without stating a
2977 ;; version (which implicitly means gpl1+).
2978 ;; At least one file (src/maxima.asd) says "version 2."
2979 ;; GPLv2 only is therefore the smallest subset.
2980 (license license:gpl2)))
2982 (define-public wxmaxima
2990 (url "https://github.com/wxMaxima-developers/wxmaxima.git")
2991 (commit (string-append "Version-" version))))
2992 (file-name (git-file-name name version))
2994 (base32 "16xizaddb27432n1083y89ir5zdqvllsgbwrzzk4jc2rw1ldxfsv"))))
2995 (build-system cmake-build-system)
2997 `(("gettext" ,gettext-minimal)))
2999 `(("wxwidgets" ,wxwidgets)
3002 ("adwaita-icon-theme" ,adwaita-icon-theme)
3004 ("shared-mime-info" ,shared-mime-info)))
3006 `(#:tests? #f ; no check target
3008 (modify-phases %standard-phases
3009 (add-after 'install 'wrap-program
3010 (lambda* (#:key inputs outputs #:allow-other-keys)
3011 (wrap-program (string-append (assoc-ref outputs "out")
3014 (,(string-append (assoc-ref inputs "maxima")
3016 ;; For GtkFileChooserDialog.
3017 `("GSETTINGS_SCHEMA_DIR" =
3018 (,(string-append (assoc-ref inputs "gtk+")
3019 "/share/glib-2.0/schemas")))
3020 `("XDG_DATA_DIRS" ":" prefix
3021 (;; Needed by gdk-pixbuf to know supported icon formats.
3023 (assoc-ref inputs "shared-mime-info") "/share")
3024 ;; The default icon theme of GTK+.
3026 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
3028 (home-page "https://andrejv.github.io/wxmaxima/")
3029 (synopsis "Graphical user interface for the Maxima computer algebra system")
3031 "wxMaxima is a graphical user interface for the Maxima computer algebra
3032 system. It eases the use of Maxima by making most of its commands available
3033 through a menu system and by providing input dialogs for commands that require
3034 more than one argument. It also implements its own display engine that
3035 outputs mathematical symbols directly instead of depicting them with ASCII
3038 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
3039 text and mathematical calculations to create documents, exporting of input and
3040 output to TeX, and a browser for Maxima's manual including command index and
3041 full text searching.")
3042 (license license:gpl2+)))
3044 (define-public armadillo
3050 (uri (string-append "mirror://sourceforge/arma/armadillo-"
3054 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
3055 (build-system cmake-build-system)
3056 (arguments `(#:tests? #f)) ; no test target
3058 `(("openblas" ,openblas)
3060 ("arpack" ,arpack-ng)))
3061 (home-page "http://arma.sourceforge.net/")
3062 (synopsis "C++ linear algebra library")
3064 "Armadillo is a C++ linear algebra library, aiming towards a good balance
3065 between speed and ease of use. It is useful for algorithm development
3066 directly in C++, or quick conversion of research code into production
3067 environments. It can be used for machine learning, pattern recognition,
3068 signal processing, bioinformatics, statistics, econometrics, etc. The library
3069 provides efficient classes for vectors, matrices and cubes, as well as 150+
3070 associated functions (eg. contiguous and non-contiguous submatrix views).")
3071 (license license:asl2.0)))
3073 (define-public muparser
3074 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
3075 ;; different hash. In order to make `guix package --upgrade` work correctly,
3076 ;; we set a Guix packaging revision.
3077 ;; When the next version of muparser is released, we can remove
3078 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
3079 (let ((upstream-version "2.2.5")
3083 (version (string-append upstream-version "-" revision))
3088 (url "https://github.com/beltoforion/muparser.git")
3089 (commit (string-append "v" upstream-version))))
3090 (file-name (git-file-name name version))
3092 (base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24"))))
3093 (build-system gnu-build-system)
3095 `(#:configure-flags '("--enable-samples=no")
3096 #:tests? #f)) ;no "check" target
3097 (home-page "http://muparser.beltoforion.de/")
3098 (synopsis "Fast parser library for mathematical expressions")
3100 "muParser is an extensible high performance math parser library. It is
3101 based on transforming an expression into a bytecode and precalculating constant
3103 (license license:expat))))
3105 (define-public openblas
3112 (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
3113 version "%20version.tar.gz"))
3114 (file-name (string-append name "-" version ".tar.gz"))
3117 "0jbdjsi0qsxahdcm42agnn1y7xpmg0hrhwjsxg0zbhs9wwy3p568"))))
3118 (build-system gnu-build-system)
3120 `(#:test-target "test"
3121 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
3122 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
3123 ;; we need to disable substitutions.
3125 ,(let ((system (or (%current-target-system) (%current-system))))
3126 (or (string-prefix? "x86_64" system)
3127 (string-prefix? "i686" system)
3128 (string-prefix? "mips" system)
3129 (string-prefix? "aarch64" system)))
3131 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
3133 "MAKE_NB_JOBS=0" ;use jobserver for submakes
3135 ;; This is the maximum number of threads OpenBLAS will ever use (that
3136 ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS
3137 ;; is used.) If we don't set it, the makefile sets it to the number
3138 ;; of cores of the build machine, which is obviously wrong.
3141 ;; Build the library for all supported CPUs. This allows
3142 ;; switching CPU targets at runtime with the environment variable
3143 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
3144 ;; Unfortunately, this is not supported on non-x86 architectures,
3145 ;; where it leads to failed builds.
3146 ,@(let ((system (or (%current-target-system) (%current-system))))
3148 ((or (string-prefix? "x86_64" system)
3149 (string-prefix? "i686" system))
3150 '("DYNAMIC_ARCH=1"))
3151 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
3152 ;; two available MIPS targets special extended instructions
3153 ;; for Loongson cores are used.
3154 ((string-prefix? "mips" system)
3155 '("TARGET=SICORTEX"))
3156 ;; On aarch64 force the generic 'armv8-a' target
3157 ((string-prefix? "aarch64" system)
3160 ;; no configure script
3162 (modify-phases %standard-phases
3164 (add-before 'build 'set-extralib
3165 (lambda* (#:key inputs #:allow-other-keys)
3166 ;; Get libgfortran found when building in utest.
3168 (string-append "-L" (assoc-ref inputs "fortran-lib")
3172 `(("fortran-lib" ,gfortran "lib")))
3175 ("fortran" ,gfortran)
3177 (home-page "http://www.openblas.net/")
3178 (synopsis "Optimized BLAS library based on GotoBLAS")
3180 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
3181 (license license:bsd-3)))
3183 (define-public openblas-ilp64
3184 (package/inherit openblas
3185 (name "openblas-ilp64")
3186 (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
3188 (substitute-keyword-arguments (package-arguments openblas)
3189 ((#:make-flags flags '())
3190 `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
3192 (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
3193 (license license:bsd-3)))
3195 (define* (make-blis implementation #:optional substitutable?)
3196 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
3197 source tree for a list of implementations.)
3199 SUBSTITUTABLE? determines whether the package is made available as a
3202 Currently the specialization must be selected at configure-time, but work is
3203 underway to allow BLIS to select the right optimized kernels at run time:
3204 <https://github.com/flame/blis/issues/129>."
3206 (name (if (string=? implementation "reference")
3208 (string-append "blis-" implementation)))
3210 (home-page "https://github.com/flame/blis")
3213 (uri (git-reference (url home-page) (commit version)))
3216 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
3217 (file-name (git-file-name "blis" version))))
3218 (build-system gnu-build-system)
3220 `(#:test-target "test"
3222 #:substitutable? ,substitutable?
3224 #:phases (modify-phases %standard-phases
3226 (lambda* (#:key outputs #:allow-other-keys)
3227 ;; This is a home-made 'configure' script.
3228 (let ((out (assoc-ref outputs "out")))
3229 (invoke "./configure" "-p" out
3233 "--enable-threading=openmp"
3236 (add-before 'check 'show-test-output
3238 ;; By default "make check" is silent. Make it verbose.
3239 (system "tail -F output.testsuite &")
3241 (synopsis "High-performance basic linear algebra (BLAS) routines")
3243 "BLIS is a portable software framework for instantiating high-performance
3244 BLAS-like dense linear algebra libraries. The framework was designed to
3245 isolate essential kernels of computation that, when optimized, immediately
3246 enable optimized implementations of most of its commonly used and
3247 computationally intensive operations. While BLIS exports a new BLAS-like API,
3248 it also includes a BLAS compatibility layer which gives application developers
3249 access to BLIS implementations via traditional BLAS routine calls.")
3250 (license license:bsd-3)))
3253 ;; This is the "reference" implementation, which is the non-optimized but
3254 ;; portable variant (no assembly).
3255 (make-blis "reference" #t))
3257 (define ignorance blis)
3259 (define-syntax-rule (blis/x86_64 processor)
3260 "Expand to a package specialized for PROCESSOR."
3262 (inherit (make-blis processor))
3263 (supported-systems '("x86_64-linux"))))
3265 (define-public blis-sandybridge
3266 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
3267 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
3268 (blis/x86_64 "sandybridge"))
3270 (define-public blis-haswell
3271 ;; BLIS specialized for Haswell processors (launched 2013):
3272 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
3273 (blis/x86_64 "haswell"))
3275 (define-public blis-knl
3276 ;; BLIS specialized for Knights Landing processor (launched 2016):
3277 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
3278 (blis/x86_64 "knl"))
3281 (define-public openlibm
3289 (url "https://github.com/JuliaLang/openlibm.git")
3290 (commit (string-append "v" version))))
3291 (file-name (git-file-name name version))
3293 (base32 "08wfchmmr5200fvmn1kwq9byc1fhsq46hn0y5k8scdl74771c7gh"))))
3294 (build-system gnu-build-system)
3297 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3299 ;; no configure script
3300 (modify-phases %standard-phases (delete 'configure))
3301 #:tests? #f)) ;the tests are part of the default target
3302 (home-page "http://openlibm.org/")
3303 (synopsis "Portable C mathematical library (libm)")
3305 "OpenLibm is an effort to have a high quality, portable, standalone C
3306 mathematical library (libm). It can be used standalone in applications and
3307 programming language implementations. The project was born out of a need to
3308 have a good libm for the Julia programming language that worked consistently
3309 across compilers and operating systems, and in 32-bit and 64-bit
3311 ;; Each architecture has its own make target, and there is none for mips.
3312 (supported-systems (delete "mips64el-linux" %supported-systems))
3313 ;; See LICENSE.md for details.
3314 (license (list license:expat
3317 license:public-domain
3318 license:lgpl2.1+))))
3320 (define-public openspecfun
3322 (name "openspecfun")
3328 (url "https://github.com/JuliaLang/openspecfun.git")
3329 (commit (string-append "v" version))))
3330 (file-name (git-file-name name version))
3332 (base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh"))))
3333 (build-system gnu-build-system)
3335 '(#:tests? #f ; no "check" target
3337 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3339 (modify-phases %standard-phases
3340 (delete 'configure)))) ; no configure script
3342 `(("fortran" ,gfortran)))
3343 (home-page "https://github.com/JuliaLang/openspecfun")
3344 (synopsis "Collection of special mathematical functions")
3346 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
3347 portable package for Bessel Functions of a Complex Argument and Nonnegative
3348 Order; it contains subroutines for computing Bessel functions and Airy
3349 functions. Faddeeva allows computing the various error functions of arbitrary
3350 complex arguments (Faddeeva function, error function, complementary error
3351 function, scaled complementary error function, imaginary error function, and
3352 Dawson function); given these, one can also easily compute Voigt functions,
3353 Fresnel integrals, and similar related functions as well.")
3354 ;; Faddeeva is released under the Expat license; AMOS is included as
3355 ;; public domain software.
3356 (license (list license:expat license:public-domain))))
3358 (define-public suitesparse
3360 (name "suitesparse")
3366 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
3370 "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
3371 (modules '((guix build utils)))
3373 ;; Remove bundled metis source
3375 (delete-file-recursively "metis-5.1.0")
3377 (build-system gnu-build-system)
3379 '(#:tests? #f ;no "check" target
3384 "MY_METIS_LIB=-lmetis"
3385 (string-append "INSTALL_LIB="
3386 (assoc-ref %outputs "out") "/lib")
3387 (string-append "INSTALL_INCLUDE="
3388 (assoc-ref %outputs "out") "/include")
3391 (modify-phases %standard-phases
3392 (delete 'configure)))) ;no configure script
3397 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
3398 (synopsis "Suite of sparse matrix software")
3400 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
3401 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
3402 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
3403 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
3404 CXSparse, a concise sparse Cholesky factorization package; and many other
3407 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
3409 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
3410 (license (list license:gpl2+ license:lgpl2.1+))))
3412 (define-public atlas
3418 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
3419 version "/atlas" version ".tar.bz2"))
3422 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
3423 (build-system gnu-build-system)
3424 (home-page "http://math-atlas.sourceforge.net/")
3425 (inputs `(("gfortran" ,gfortran)
3426 ("lapack-tar" ,(package-source lapack))))
3427 (outputs '("out" "doc"))
3428 ;; For the moment we drop support for MIPS at it fails to compile. See
3429 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
3430 (supported-systems (delete "mips64el-linux" %supported-systems))
3432 `(#:parallel-build? #f
3433 #:parallel-tests? #f
3435 ;; ATLAS tunes itself for the machine it is built on, as explained at
3436 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
3437 ;; For this reason, we want users to build it locally instead of using
3441 #:modules ((srfi srfi-26)
3442 (guix build gnu-build-system)
3445 `(;; Generate position independent code suitable for dynamic libraries
3446 ;; and use WALL timer to get more accurate timing.
3447 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
3450 ,,(if (string-match "64" (%current-system))
3453 ;; Disable parallel build as it gives errors: atlas_pthread.h is
3454 ;; needed to compile C files before it is generated.
3455 "-Ss" "pmake" "make -j 1"
3456 ;; Probe is failing for MIPS. We therefore define the system
3457 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3458 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3459 ,,@(if (string-prefix? "mips" (%current-system))
3460 (list "-A" "49" "-V" "1")
3462 ;; Generate shared libraries.
3464 ;; Build a full LAPACK library.
3465 ,(string-append "--with-netlib-lapack-tarfile="
3466 (assoc-ref %build-inputs "lapack-tar")))
3468 (modify-phases %standard-phases
3469 (add-after 'install 'install-doc
3470 (lambda* (#:key outputs inputs #:allow-other-keys)
3471 (let ((doc (string-append (assoc-ref outputs "doc")
3472 "/share/doc/atlas")))
3474 (for-each (cut install-file <> doc)
3475 (find-files "../ATLAS/doc" ".*"))
3477 (add-after 'check 'check-pt
3478 (lambda _ (invoke "make" "ptcheck")))
3479 ;; Fix files required to run configure.
3480 (add-before 'configure 'fix-/bin/sh
3482 ;; Use `sh', not `/bin/sh'.
3483 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3487 ;; Fix /bin/sh in generated make files.
3488 (add-after 'configure 'fix-/bin/sh-in-generated-files
3490 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3494 ;; ATLAS configure program does not accepts the default flags
3495 ;; passed by the 'gnu-build-system'.
3497 (lambda* (#:key native-inputs inputs outputs
3498 (configure-flags '())
3499 #:allow-other-keys #:rest args)
3500 (let* ((prefix (assoc-ref outputs "out"))
3501 (bash (or (and=> (assoc-ref
3502 (or native-inputs inputs) "bash")
3503 (cut string-append <> "/bin/bash"))
3505 (flags `(,(string-append "--prefix=" prefix)
3507 (abs-srcdir (getcwd))
3508 (srcdir (string-append "../" (basename abs-srcdir))))
3509 (format #t "source directory: ~s (relative from build: ~s)~%"
3513 (format #t "build directory: ~s~%" (getcwd))
3514 (format #t "configure flags: ~s~%" flags)
3516 (string-append srcdir "/configure")
3518 (synopsis "Automatically Tuned Linear Algebra Software")
3520 "ATLAS is an automatically tuned linear algebra software library
3521 providing C and Fortran77 interfaces to a portably efficient BLAS
3522 implementation, as well as a few routines from LAPACK.
3524 Optimization occurs at build time. For this reason, the library is built on
3525 the machine where it is installed, without resorting to pre-built substitutes.
3527 Before building the library, CPU throttling should be disabled. This can be
3528 done in the BIOS, or, on GNU/Linux, with the following command:
3531 # cpupower --governor performance
3534 Failure to do so will result in a library with poor performance.")
3535 (license license:bsd-3)))
3544 (uri (string-append "https://github.com/g-truc/glm/releases/download/"
3545 version "/glm-" version ".zip"))
3547 (base32 "1l0pi1qi37mk6s0yrkrw07lspv4gcqnr9ryg3521hrl77ff37dwx"))
3548 (patches (search-patches "glm-restore-install-target.patch"))))
3549 (build-system cmake-build-system)
3551 `(("unzip" ,unzip)))
3552 (home-page "https://glm.g-truc.net/")
3553 (synopsis "OpenGL Mathematics library")
3554 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3555 library for graphics software based on the OpenGL Shading Language (GLSL)
3557 (license license:expat)))
3559 (define-public lpsolve
3566 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3567 "/lp_solve_" version "_source.tar.gz"))
3570 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
3571 (modules '((guix build utils)))
3574 (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3576 ;; Pretend to be on a 64 bit platform to obtain a common directory
3577 ;; name for the build results on all architectures; nothing else
3578 ;; seems to depend on it.
3579 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3581 ;; The check for 'isnan' as it is written fails with
3582 ;; "non-floating-point argument in call to function
3583 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3584 ;; definition, which in turn leads to bad things. Fix the feature
3586 (("isnan\\(0\\)") "isnan(0.)"))
3588 (build-system gnu-build-system)
3590 `(#:tests? #f ; no check target
3592 (modify-phases %standard-phases
3593 (delete 'configure) ; no configure script
3596 (with-directory-excursion "lpsolve55"
3597 (invoke "bash" "ccc"))
3598 (with-directory-excursion "lp_solve"
3599 (invoke "bash" "ccc"))
3602 (lambda* (#:key outputs #:allow-other-keys)
3603 (let* ((out (assoc-ref outputs "out"))
3604 (bin (string-append out "/bin"))
3605 (lib (string-append out "/lib"))
3606 ;; This is where LibreOffice expects to find the header
3607 ;; files, and where they are installed by Debian.
3608 (include (string-append out "/include/lpsolve")))
3609 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3610 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
3611 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3613 ;; Install a subset of the header files as on Debian
3614 ;; (plus lp_bit.h, which matches the regular expression).
3615 (for-each (lambda (name)
3616 (install-file name include))
3617 (find-files "." "lp_[HMSa-z].*\\.h$"))
3618 (with-directory-excursion "shared"
3619 (for-each (lambda (name)
3620 (install-file name include))
3621 (find-files "." "\\.h$")))
3623 (home-page "http://lpsolve.sourceforge.net/")
3624 (synopsis "Mixed integer linear programming (MILP) solver")
3626 "lp_solve is a mixed integer linear programming solver based on the
3627 revised simplex and the branch-and-bound methods.")
3628 (license license:lgpl2.1+)))
3630 (define-public dealii
3637 (uri (string-append "https://github.com/dealii/dealii/releases/"
3638 "download/v" version "/dealii-" version ".tar.gz"))
3641 "0xhjv0gzswpjbc43xbrpwfc5848g508l01855nszx3g5gwzlhnzw"))
3642 (modules '((guix build utils)))
3644 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
3646 (delete-file-recursively "bundled")
3648 (build-system cmake-build-system)
3656 ("arpack" ,arpack-ng)
3657 ("muparser" ,muparser)
3658 ("gfortran" ,gfortran)
3659 ("suitesparse" ,suitesparse))) ;for UMFPACK
3661 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
3663 ;; Work around a bug in libsuitesparseconfig linking
3664 ;; see https://github.com/dealii/dealii/issues/4745
3665 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
3666 (home-page "https://www.dealii.org")
3667 (synopsis "Finite element library")
3669 "Deal.II is a C++ program library targeted at the computational solution
3670 of partial differential equations using adaptive finite elements. The main
3671 aim of deal.II is to enable rapid development of modern finite element codes,
3672 using among other aspects adaptive meshes and a wide array of tools often used
3673 in finite element programs.")
3674 (license license:lgpl2.1+)))
3676 (define-public dealii-openmpi
3677 (package (inherit dealii)
3678 (name "dealii-openmpi")
3681 ;;Supported only with MPI:
3682 ("hdf5" ,hdf5-parallel-openmpi) ;TODO: have petsc-openmpi propagate?
3683 ("p4est" ,p4est-openmpi)
3684 ("petsc" ,petsc-openmpi)
3685 ("slepc" ,slepc-openmpi)
3686 ("metis" ,metis) ;for MUMPS
3687 ("scalapack" ,scalapack) ;for MUMPS
3688 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3689 ("arpack" ,arpack-ng-openmpi)
3690 ,@(fold alist-delete (package-inputs dealii)
3691 '("p4est" "arpack"))))
3693 (substitute-keyword-arguments (package-arguments dealii)
3694 ((#:configure-flags cf)
3695 `(cons "-DDEAL_II_WITH_MPI:BOOL=ON"
3697 ((#:phases phases '%standard-phases)
3698 `(modify-phases ,phases
3699 (add-before 'check 'mpi-setup
3700 ,%openmpi-setup)))))
3701 (synopsis "Finite element library (with MPI support)")))
3703 (define-public flann
3712 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3713 version "-src.zip"))
3716 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
3717 (patches (search-patches "flann-cmake-3.11.patch"))))
3718 (build-system cmake-build-system)
3720 "octave")) ;46 MiB .mex file that pulls Octave
3722 `(("unzip" ,unzip)))
3725 ("octave" ,octave-cli)
3726 ("python" ,python-2) ; print syntax
3727 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3730 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3731 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3732 #:strip-directories '("lib" "lib64" "libexec"
3733 "bin" "sbin" "share/flann/octave")
3735 ;; Save 12 MiB by not installing .a files. Passing
3736 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3737 #:phases (modify-phases %standard-phases
3738 (add-before 'configure 'set-octave-directory
3739 (lambda* (#:key outputs #:allow-other-keys)
3740 ;; Install the .mex file in the "octave" output.
3741 (let ((out (assoc-ref outputs "octave")))
3742 (substitute* "src/matlab/CMakeLists.txt"
3743 (("share/flann/octave")
3744 (string-append out "/share/flann/octave")))
3746 (add-after 'install 'remove-static-libraries
3747 (lambda* (#:key outputs #:allow-other-keys)
3748 (let* ((out (assoc-ref outputs "out"))
3749 (lib (string-append out "/lib")))
3750 (for-each delete-file
3751 (find-files lib "\\.a$"))
3754 #:tests? #f)) ; The test data are downloaded from the Internet.
3755 (home-page "http://www.cs.ubc.ca/research/flann/")
3756 (synopsis "Library for approximate nearest neighbors computation")
3757 (description "FLANN is a library for performing fast approximate
3758 nearest neighbor searches in high dimensional spaces. It implements a
3759 collection of algorithms and a system for automatically choosing the best
3760 algorithm and optimum parameters depending on the dataset.
3762 FLANN is written in C++ and contains bindings for C, Octave and Python.")
3763 (license (license:non-copyleft "file://COPYING"
3764 "See COPYING in the distribution."))))
3766 (define-public wcalc
3773 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3774 "wcalc-" version ".tar.bz2"))
3777 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3778 (build-system gnu-build-system)
3781 ("readline" ,readline)))
3782 (home-page "http://w-calc.sourceforge.net/index.php")
3783 (synopsis "Flexible command-line scientific calculator")
3784 (description "Wcalc is a very capable calculator. It has standard functions
3785 (sin, asin, and sinh for example, in either radians or degrees), many
3786 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3787 variables, a command history, hex/octal/binary input and output, unit
3788 conversions, embedded comments, and an expandable expression entry field. It
3789 evaluates expressions using the standard order of operations.")
3790 (license license:gpl2+)))
3798 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3799 "/xaos-" version ".tar.gz"))
3802 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3803 (build-system gnu-build-system)
3804 (native-inputs `(("gettext" ,gettext-minimal)))
3805 (inputs `(("libx11" ,libx11)
3810 `(#:tests? #f ;no "check" target
3811 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3812 (synopsis "Real-time fractal zoomer")
3813 (description "GNU XaoS is a graphical program that generates fractal
3814 patterns and allows you to zoom in and out of them infinitely in a fluid,
3815 continuous manner. It also includes tutorials that help to explain how fractals
3816 are built. It can generate many different fractal types such as the Mandelbrot
3818 (home-page "https://www.gnu.org/software/xaos/")
3819 (license license:gpl2+)))
3821 (define-public hypre
3829 (url "https://github.com/LLNL/hypre.git")
3830 (commit (string-append "v" version))))
3831 (file-name (git-file-name name version))
3833 (base32 "1lvh4ybqkriyqfg2zmic6mrg1981qv1i9vry1fdgsabn81hb71g4"))
3834 (modules '((guix build utils)))
3837 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
3838 ;; substitute the release date.
3839 (substitute* "src/utilities/HYPRE_utilities.h"
3840 (("Date Compiled: .*$")
3841 "Date Compiled: Oct 19 2018 15:23:00 +0000\"\n"))
3843 (build-system gnu-build-system)
3844 (outputs '("out" ; 6.1 MiB of headers and libraries
3845 "doc")) ; 4.8 MiB of documentation
3849 ("perl" ,perl) ; needed to run 'ppmquant' during tests
3850 ("texlive" ,(texlive-union (list texlive-xypic
3852 texlive-latex-hyperref
3854 ("ghostscript" ,ghostscript)))
3856 `(("blas" ,openblas)
3857 ("lapack" ,lapack)))
3859 `(#:modules ((srfi srfi-1)
3860 ,@%gnu-build-system-modules)
3861 #:configure-flags '("--enable-shared"
3869 (modify-phases %standard-phases
3870 (add-before 'build 'set-HOME
3872 ;; FIXME: texlive-union does not find the built
3873 ;; metafonts, so it tries to generate them in HOME.
3874 (setenv "HOME" "/tmp")
3876 (add-before 'configure 'chdir-src
3877 (lambda _ (chdir "src")))
3879 (lambda* (#:key build target configure-flags
3880 #:allow-other-keys #:rest args)
3881 (let* ((configure (assoc-ref %standard-phases 'configure)))
3884 (list #:configure-flags
3885 (cons (string-append
3886 "--host=" (or target build))
3887 configure-flags)))))))
3888 (add-after 'build 'build-docs
3890 (invoke "make" "-Cdocs" "pdf" "html")))
3893 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3894 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
3895 (invoke "make" "check" "CHECKRUN=")
3896 (for-each (lambda (filename)
3897 (let ((size (stat:size (stat filename))))
3898 (when (positive? size)
3899 (error (format #f "~a size ~d; error indication~%"
3901 (find-files "test" ".*\\.err$"))
3903 (add-after 'install 'install-docs
3904 (lambda* (#:key outputs #:allow-other-keys)
3905 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3906 (let* ((doc (assoc-ref outputs "doc"))
3907 (docdir (string-append doc "/share/doc/hypre-" ,version)))
3908 (with-directory-excursion "docs"
3909 (for-each (lambda (base)
3910 (install-file (string-append base ".pdf") docdir)
3911 (copy-recursively base docdir)) ; html docs
3912 '("HYPRE_usr_manual"
3913 "HYPRE_ref_manual")))
3915 (home-page "http://www.llnl.gov/casc/hypre/")
3916 (synopsis "Library of solvers and preconditioners for linear equations")
3918 "HYPRE is a software library of high performance preconditioners and
3919 solvers for the solution of large, sparse linear systems of equations. It
3920 features multigrid solvers for both structured and unstructured grid
3922 (license license:lgpl2.1)))
3924 (define-public hypre-openmpi
3925 (package (inherit hypre)
3926 (name "hypre-openmpi")
3929 ,@(package-inputs hypre)))
3931 (substitute-keyword-arguments (package-arguments hypre)
3932 ((#:configure-flags flags)
3934 ,@(delete "--without-MPI" ,flags)))
3936 `(modify-phases ,phases
3937 (add-before 'check 'mpi-setup
3938 ,%openmpi-setup)))))
3939 (synopsis "Parallel solvers and preconditioners for linear equations")
3941 "HYPRE is a software library of high performance preconditioners and
3942 solvers for the solution of large, sparse linear systems of equations on
3943 parallel computers. It features parallel multigrid solvers for both
3944 structured and unstructured grid problems.")))
3946 (define-public matio
3953 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
3954 "matio-" version ".tar.gz"))
3957 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3958 (build-system gnu-build-system)
3962 (home-page "http://matio.sourceforge.net/")
3963 (synopsis "Library for reading and writing MAT files")
3964 (description "Matio is a library for reading and writing MAT files. It
3965 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3966 (license license:bsd-2)))
3973 (origin (method url-fetch)
3974 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3975 "download/" version "/Vc-" version ".tar.gz"))
3978 "17qili8bf8r78cng65yf4qmgna8kiqjqbgcqbric6v9j6nkhkrk8"))))
3979 (build-system cmake-build-system)
3982 '("-DBUILD_TESTING=ON"
3983 ;; By default, Vc will optimize for the CPU of the build machine.
3984 ;; Setting this to "none" makes it create portable binaries. See
3985 ;; "cmake/OptimizeForArchitecture.cmake".
3986 "-DTARGET_ARCHITECTURE=none")
3987 #:phases (modify-phases %standard-phases
3988 (add-after 'unpack 'copy-testdata
3989 (lambda* (#:key inputs native-inputs #:allow-other-keys)
3990 (let ((testdata (assoc-ref (or native-inputs inputs)
3992 (copy-recursively testdata "tests/testdata")
3995 `(("virtest" ,virtest)
3997 ;; This is a submodule in the git project, but not part of the
3998 ;; released sources. See the git branch for the commit to take.
3999 ("testdata" ,(let ((commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3"))
4003 (url "https://github.com/VcDevel/vc-testdata")
4004 (commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3")))
4005 (file-name (git-file-name "vc-testdata"
4006 (string-take commit 7)))
4009 "1hkhqib03qlcq412ym2dciynfxcdr2ygqhnplz4l1vissr1wnqn2")))))))
4010 (synopsis "SIMD vector classes for C++")
4011 (description "Vc provides portable, zero-overhead C++ types for explicitly
4012 data-parallel programming. It is a library designed to ease explicit
4013 vectorization of C++ code. Its types enable explicitly stating data-parallel
4014 operations on multiple values. The parallelism is therefore added via the type
4015 system. Vc has an intuitive API and provides portability between different
4016 compilers and compiler versions as well as portability between different vector
4017 instruction sets. Thus, an application written with Vc can be compiled for:
4020 @item SSE2 up to SSE4.2 or SSE4a
4023 @item NEON (in development)
4024 @item NVIDIA GPUs / CUDA (in development)
4026 (home-page "https://github.com/VcDevel/Vc")
4027 ;; "No support_???.cpp file exists for this architecture."
4028 (supported-systems '("x86_64-linux" "i686-linux"))
4029 (license license:bsd-3)))
4031 (define-public reducelcs
4032 ;; This is the last commit which is available upstream, no
4033 ;; release happened since 2010.
4034 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
4038 (version (string-append "1.0-" revision "." (string-take commit 7)))
4043 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
4045 (file-name (string-append name "-" version "-checkout"))
4048 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
4049 (build-system gnu-build-system)
4051 `(("openlibm" ,openlibm)))
4053 `(#:tests? #f ; no tests
4055 (modify-phases %standard-phases
4056 (delete 'configure) ; No configure script exists.
4057 (replace 'install ; No install phase exists.
4058 (lambda* (#:key outputs #:allow-other-keys)
4059 (let* ((out (assoc-ref outputs "out"))
4060 (bin (string-append out "/bin")))
4061 (install-file "Approximation" bin)
4062 (install-file "CollectResults" bin)
4063 (install-file "GenerateInstances" bin)
4065 (synopsis "Approximate Longest Commons Subsequence computation tool")
4067 "@code{reduceLCS} is an implementation of the Reduce-Expand
4068 algorithm for LCS. It is a fast program to compute the approximate
4069 Longest Commons Subsequence of a set of strings.")
4070 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
4071 (license license:gpl3+))))
4073 (define-public jacal
4080 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
4083 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
4084 (patches (search-patches "jacal-fix-texinfo.patch"))))
4085 (build-system gnu-build-system)
4088 (modify-phases %standard-phases
4089 (add-before 'build 'pre-build
4090 ;; Don't use upstream's script - it really doesn't fit into
4091 ;; Guix's functional paradigm.
4092 (lambda* (#:key inputs outputs #:allow-other-keys)
4093 (substitute* "Makefile"
4094 (("^install: install-script") "install: "))))
4095 (add-after 'install 'post-install
4096 ;; Instead, we provide our own simplified script.
4097 (lambda* (#:key inputs outputs #:allow-other-keys)
4098 (let ((wrapper (string-append (assoc-ref outputs "out")
4100 (format (open wrapper (logior O_WRONLY O_CREAT))
4101 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
4102 "-e '(slib:load \"~a/lib/jacal/math\") "
4105 (assoc-ref inputs "scm")
4106 (assoc-ref outputs "out"))
4107 (chmod wrapper #o555))))
4109 (lambda* (#:key outputs #:allow-other-keys)
4110 (invoke "./configure"
4111 (string-append "--prefix="
4112 (assoc-ref outputs "out"))))))))
4113 (inputs `(("scm" ,scm)))
4114 (native-inputs `(("unzip" ,unzip)
4115 ("texinfo" ,texinfo)))
4116 (synopsis "Symbolic mathematics system")
4117 (description "GNU JACAL is an interactive symbolic mathematics program based on
4118 Scheme. It manipulate and simplify a range of mathematical expressions such
4119 as equations, scalars, vectors, and matrices.")
4120 (home-page "https://www.gnu.org/software/jacal/")
4121 (license license:gpl3+)))
4127 (home-page "https://github.com/Z3Prover/z3")
4130 (uri (git-reference (url home-page)
4131 (commit (string-append "z3-" version))))
4132 (file-name (git-file-name name version))
4135 "0hprcdwhhyjigmhhk6514m71bnmvqci9r8gglrqilgx424r6ff7q"))))
4136 (build-system gnu-build-system)
4139 (modify-phases %standard-phases
4140 (add-after 'unpack 'fix-compatability
4141 ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
4143 (substitute* "src/util/mpz.cpp"
4144 (("#include <immintrin.h>") ""))
4146 (add-before 'configure 'bootstrap
4148 (invoke "python" "scripts/mk_make.py")))
4149 ;; work around gnu-build-system's setting --enable-fast-install
4150 ;; (z3's `configure' is a wrapper around the above python file,
4151 ;; which fails when passed --enable-fast-install)
4153 (lambda* (#:key inputs outputs #:allow-other-keys)
4154 (invoke "./configure"
4155 (string-append "--prefix=" (assoc-ref outputs "out")))))
4156 (add-after 'configure 'change-directory
4160 (add-before 'check 'make-test-z3
4162 ;; Build the test suite executable.
4163 (invoke "make" "test-z3" "-j"
4164 (number->string (parallel-job-count)))))
4167 ;; Run all the tests that don't require arguments.
4168 (invoke "./test-z3" "/a"))))))
4171 ("python" ,python-wrapper)))
4172 (synopsis "Theorem prover")
4173 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
4174 theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
4175 (license license:expat)))
4180 (version "2018.11.001")
4183 (uri (string-append "http://elpa.mpcdf.mpg.de/html/Releases/"
4184 version "/elpa-" version ".tar.gz"))
4187 "05hv3v5i6xmziaizw350ff72y1c3k662r85fm3xfdrkclj5zw9yc"))))
4188 (build-system gnu-build-system)
4190 `(("fortran" ,gfortran)
4191 ("perl" ,perl))) ;for configure and deps
4193 `(("blas" ,openblas)))
4198 ;; ELPA unfortunately does not support runtime dispatch, so we can
4199 ;; only enable the "generic" kernels. See the "Cross compilation"
4200 ;; section of INSTALL.md.
4202 "--disable-sse" "--disable-sse-assembly" ;Require SSE3
4203 "--disable-avx" "--disable-avx2" "--disable-avx512"
4204 ,(string-append "CFLAGS=-O3 "
4205 "-funsafe-loop-optimizations -funsafe-math-optimizations "
4206 "-ftree-vect-loop-version -ftree-vectorize "
4207 ,(let ((system (or (%current-target-system)
4208 (%current-system))))
4210 ((or (string-prefix? "x86_64" system)
4211 (string-prefix? "i686" system))
4214 #:parallel-tests? #f ;tests are multi-threaded, via BLAS
4216 (modify-phases %standard-phases
4217 (add-before 'configure 'patch-header-generation
4219 (substitute* "configure"
4220 (("^ *make.*top_srcdir=\"\\$srcdir\"" &)
4221 (string-append & " CPP=\"$CPP\"")))
4223 (add-before 'check 'setup-tests
4225 ;; Decrease test time and RAM use by computing fewer eigenvalues.
4226 ;; The flags are (MATRIX-SIZE, EIGENVALUES, BLOCK-SIZE), where
4227 ;; the default is (500, 250, 16) for C tests and (5000, 150, 16)
4228 ;; for Fortran. This also causes several tests to pass that
4229 ;; otherwise would otherwise fail with matrix size 5000; possibly
4230 ;; due to floating point tolerances that are too tight.
4231 (setenv "TEST_FLAGS" "1500 50 16") ;from elpa.spec
4232 (setenv "OMP_NUM_THREADS" (number->string (parallel-job-count)))
4233 (substitute* "Makefile"
4234 ;; Test scripts are generated, patch the shebang
4235 (("#!/bin/bash") (string-append "#!" (which "sh"))))
4237 (home-page "http://elpa.mpcdf.mpg.de")
4238 (synopsis "Eigenvalue solvers for symmetric matrices")
4240 "The ELPA library provides efficient and scalable direct eigensolvers for
4241 symmetric matrices.")
4242 (license license:lgpl3)))
4244 (define-public elpa-openmpi
4245 (package (inherit elpa)
4246 (name "elpa-openmpi")
4249 ("scalapack" ,scalapack)
4250 ,@(package-inputs elpa)))
4252 (substitute-keyword-arguments (package-arguments elpa)
4253 ((#:configure-flags cf '())
4254 `(cons "--with-mpi=yes" (delete "--with-mpi=no" ,cf)))
4255 ((#:phases phases '%standard-phases)
4256 `(modify-phases ,phases
4257 (add-before 'check 'mpi-setup
4259 ;; Tests use 2 mpi tasks by default, use our remaining build
4260 ;; cores as OpenMP threads.
4261 (setenv "OMP_NUM_THREADS" (number->string
4262 (max (quotient (parallel-job-count) 2)
4264 (,%openmpi-setup)))))))
4265 (synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)")))
4267 (define-public elemental
4274 (url "https://github.com/elemental/Elemental.git")
4275 (commit (string-append "v" version))))
4276 (file-name (git-file-name name version))
4279 "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
4280 (build-system cmake-build-system)
4281 (home-page "https://github.com/elemental/Elemental")
4283 `(("gfortran" ,gfortran)))
4285 `(("blas" ,openblas)
4286 ("gfortran:lib" ,gfortran "lib")
4295 `(#:build-type "Release" ;default RelWithDebInfo not supported
4296 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
4297 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
4298 "-DEL_CACHE_WARNINGS:BOOL=YES"
4299 "-DEL_TESTS:BOOL=YES"
4300 "-DCMAKE_INSTALL_LIBDIR=lib"
4301 "-DGFORTRAN_LIB=gfortran")
4302 #:phases (modify-phases %standard-phases
4303 (add-before 'check 'mpi-setup
4305 (add-before 'check 'setup-tests
4307 ;; Parallelism is done at the MPI layer.
4308 (setenv "OMP_NUM_THREADS" "1")
4310 (add-after 'install 'remove-tests
4311 (lambda* (#:key outputs #:allow-other-keys)
4312 ;; Tests are installed, with no easy configuration
4313 ;; switch to prevent this, so delete them.
4314 (delete-file-recursively
4315 (string-append (assoc-ref outputs "out") "/bin"))
4317 (synopsis "Dense and sparse-direct linear algebra and optimization")
4318 (description "Elemental is a modern C++ library for distributed-memory
4319 dense and sparse-direct linear algebra, conic optimization, and lattice
4321 (license license:bsd-2)))
4323 (define-public mcrl2
4326 (version "201908.0")
4330 "https://www.mcrl2.org/download/release/mcrl2-"
4334 "1i4xgl2d5fgiz1mwi50cyfkrrcpm8nxfayfjgmhq7chs58wlhfsz"))))
4339 ("qtbase" ,qtbase)))
4340 (build-system cmake-build-system)
4341 (synopsis "Toolset for the mCRL2 formal specification language")
4343 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
4344 specification language for describing concurrent discrete event systems. Its
4345 toolset supports analysis and automatic verification, linearisation, simulation,
4346 state-space exploration and generation, and tools to optimise and analyse
4347 specifications. Also, state spaces can be manipulated, visualised and
4349 (home-page "https://mcrl2.org")
4350 (license license:boost1.0)))
4352 (define-public mcrl2-minimal
4355 (name "mcrl2-minimal")
4357 `(("boost" ,boost)))
4359 '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
4361 (define-public tcalc
4368 (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
4372 "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
4373 (build-system gnu-build-system)
4374 (synopsis "The terminal calculator")
4376 "The terminal calculator is a small program to help users of the GNU/Linux
4377 terminal do calculations simply and quickly. The formula to be calculated can
4378 be fed to @command{tcalc} through the command line.")
4379 (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
4380 (license license:gpl3+)))
4382 (define-public sundials
4389 (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
4390 "sundials-" version ".tar.gz"))
4393 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
4394 (build-system cmake-build-system)
4396 `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
4398 `(("fortran" ,gfortran) ;for fcmix
4400 ("suitesparse" ,suitesparse))) ;TODO: Add hypre
4402 `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
4403 "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
4404 "-DEXAMPLES_ENABLE_F77:BOOL=ON"
4405 "-DEXAMPLES_ENABLE_F90:BOOL=ON"
4406 "-DEXAMPLES_INSTALL:BOOL=OFF"
4408 "-DFCMIX_ENABLE:BOOL=ON"
4410 "-DKLU_ENABLE:BOOL=ON"
4411 ,(string-append "-DKLU_INCLUDE_DIR="
4412 (assoc-ref %build-inputs "suitesparse")
4414 ,(string-append "-DKLU_LIBRARY_DIR="
4415 (assoc-ref %build-inputs "suitesparse")
4417 (home-page "https://computation.llnl.gov/projects/sundials")
4418 (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
4419 (description "SUNDIALS is a family of software packages implemented with
4420 the goal of providing robust time integrators and nonlinear solvers that can
4421 easily be incorporated into existing simulation codes.")
4422 (license license:bsd-3)))
4424 (define-public sundials-openmpi
4425 (package (inherit sundials)
4426 (name "sundials-openmpi")
4429 ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
4430 ,@(package-inputs sundials)))
4432 (substitute-keyword-arguments (package-arguments sundials)
4433 ((#:configure-flags flags '())
4434 `(cons* "-DMPI_ENABLE:BOOL=ON"
4435 "-DPETSC_ENABLE:BOOL=ON"
4436 (string-append "-DPETSC_INCLUDE_DIR="
4437 (assoc-ref %build-inputs "petsc")
4439 (string-append "-DPETSC_LIBRARY_DIR="
4440 (assoc-ref %build-inputs "petsc")
4443 ((#:phases phases '%standard-phases)
4444 `(modify-phases ,phases
4445 (add-before 'check 'mpi-setup
4446 ,%openmpi-setup)))))
4447 (synopsis "SUNDIALS with OpenMPI support")))
4449 (define-public combinatorial-blas
4451 (name "combinatorial-blas")
4456 (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/"
4458 (match (string-split version #\.)
4459 ((major minor patch)
4460 (string-append major minor "_" patch))) ;e.g. "16_2"
4464 "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a"))
4465 (patches (search-patches "combinatorial-blas-awpm.patch"
4466 "combinatorial-blas-io-fix.patch"))))
4467 (build-system cmake-build-system)
4470 ("test-data" ,(origin
4472 (uri (string-append "https://people.eecs.berkeley.edu/~aydin/"
4473 "CombBLAS_FILES/testdata_combblas1.6.1.tgz"))
4476 "01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87"))))))
4478 `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
4479 "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL")
4480 #:parallel-tests? #f ;tests use 'mpiexec -n4'
4482 (modify-phases %standard-phases
4483 (add-before 'check 'mpi-setup
4485 (add-before 'check 'test-setup
4486 (lambda* (#:key inputs #:allow-other-keys)
4487 (setenv "OMP_NUM_THREADS" "2")
4488 (invoke "tar" "xf" (assoc-ref inputs "test-data")))))))
4489 (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/")
4490 (synopsis "Linear algebra primitives for graph analytics")
4491 (description "The Combinatorial BLAS (CombBLAS) is an extensible
4492 distributed-memory parallel graph library offering a small but powerful set of
4493 linear algebra primitives specifically targeting graph analytics.")
4495 license:gpl2+ ;include/psort/(funnel|sort)*.h
4496 license:x11 ;usort and psort
4497 license:bsd-3)))) ;CombBLAS and MersenneTwister.h
4499 (define-public dune-common
4501 (name "dune-common")
4506 (uri (string-append "https://dune-project.org/download/"
4507 version "/dune-common-" version ".tar.gz"))
4510 "019wcr1qf7jwyxx1y5y290wdlglylskvbb2m01ljkzcza2xnlmhw"))))
4511 (build-system cmake-build-system)
4514 (modify-phases %standard-phases
4515 (add-after 'build 'build-tests
4516 (lambda* (#:key make-flags #:allow-other-keys)
4517 (apply invoke "make" "build_tests" make-flags)))
4518 ;; These tests fail because they require a fully functional MPI
4520 (add-after 'unpack 'disable-failing-tests
4523 (string-append "--exclude-regex '("
4527 "remoteindicestest-mpi-2"
4530 "variablesizecommunicatortest"
4531 "variablesizecommunicatortest-mpi-2"
4532 "arithmetictestsuitetest"
4533 "assertandreturntest"
4534 "assertandreturntest_ndebug"
4537 "mpicollectivecommunication"
4538 "mpicollectivecommunication-mpi-2"
4540 "mpiguardtest-mpi-2"
4542 "mpihelpertest-mpi-2"
4544 "mpihelpertest2-mpi-2")
4551 ("openmpi" ,openmpi)
4552 ("openblas" ,openblas)
4554 ("superlu" ,superlu)))
4556 `(("gfortran" ,gfortran)
4557 ("pkg-config" ,pkg-config)))
4558 (home-page "https://dune-project.org/")
4559 (synopsis "Distributed and Unified Numerics Environment")
4560 (description "DUNE, the Distributed and Unified Numerics Environment is a
4561 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4562 grid-based methods. It supports the easy implementation of methods like
4563 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4564 Differences} (FD).")
4565 ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2.
4566 (license license:gpl2)))
4568 (define-public dune-geometry
4570 (name "dune-geometry")
4575 (uri (string-append "https://dune-project.org/download/"
4576 version "/dune-geometry-" version ".tar.gz"))
4579 "0hlaaxjyv9j05blasvb67sy02hd0w4g9znf68gdh3l731dd1aqbn"))))
4580 (build-system cmake-build-system)
4583 (modify-phases %standard-phases
4584 (add-after 'build 'build-tests
4585 (lambda* (#:key make-flags #:allow-other-keys)
4586 (apply invoke "make" "build_tests" make-flags))))))
4588 `(("dune-common" ,dune-common)
4589 ("openmpi" ,openmpi)
4591 ("openblas" ,openblas)
4593 ("python" ,python)))
4595 `(("gfortran" ,gfortran)
4596 ("pkg-config" ,pkg-config)))
4597 (home-page "https://dune-project.org/")
4598 (synopsis "Distributed and Unified Numerics Environment")
4599 (description "DUNE, the Distributed and Unified Numerics Environment is a
4600 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4601 grid-based methods. It supports the easy implementation of methods like
4602 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4605 This package contains the basic DUNE geometry classes.")
4606 ;; GPL version 2 with "runtime exception"
4607 (license license:gpl2)))
4609 (define-public dune-grid
4616 (uri (string-append "https://dune-project.org/download/"
4617 version "/dune-grid-" version ".tar.gz"))
4620 "1jp4vscm9yb9xg0lh7apzccfkhvgbnk652yahigmh3cvzpl4acd0"))))
4621 (build-system cmake-build-system)
4624 (modify-phases %standard-phases
4625 (add-after 'build 'build-tests
4626 (lambda* (#:key make-flags #:allow-other-keys)
4627 (apply invoke "make" "build_tests" make-flags)))
4628 ;; These tests fail because they require a fully functional MPI
4630 (add-after 'unpack 'disable-failing-tests
4633 (string-append "--exclude-regex '("
4637 "conformvolumevtktest"
4639 "nonconformboundaryvtktest"
4640 "subsamplingvtktest"
4646 "test-dgf-yasp-offset"
4648 "test-geogrid-yaspgrid"
4651 "testiteratorranges"
4652 "test-hierarchicsearch"
4653 "test-parallel-ug-mpi-2"
4654 "test-yaspgrid-backuprestore-equidistant"
4655 "test-yaspgrid-backuprestore-equidistant-mpi-2"
4656 "test-yaspgrid-backuprestore-equidistantoffset"
4657 "test-yaspgrid-backuprestore-equidistantoffset-mpi-2"
4658 "test-yaspgrid-backuprestore-tensor"
4659 "test-yaspgrid-backuprestore-tensor-mpi-2"
4660 "test-yaspgrid-tensorgridfactory"
4661 "test-yaspgrid-tensorgridfactory-mpi-2"
4662 "test-yaspgrid-yaspfactory-1d"
4663 "test-yaspgrid-yaspfactory-1d-mpi-2"
4664 "test-yaspgrid-yaspfactory-2d"
4665 "test-yaspgrid-yaspfactory-2d-mpi-2"
4666 "test-yaspgrid-yaspfactory-3d"
4667 "test-yaspgrid-yaspfactory-3d-mpi-2"
4668 "globalindexsettest"
4669 "persistentcontainertest"
4670 "structuredgridfactorytest"
4671 "tensorgridfactorytest"
4677 `(("dune-common" ,dune-common)
4678 ("dune-geometry" ,dune-geometry)
4681 ("openblas" ,openblas)
4682 ("openmpi" ,openmpi)
4683 ("python" ,python)))
4685 `(("gfortran" ,gfortran)
4686 ("pkg-config" ,pkg-config)))
4687 (home-page "https://dune-project.org/")
4688 (synopsis "Distributed and Unified Numerics Environment")
4689 (description "DUNE, the Distributed and Unified Numerics Environment is a
4690 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4691 grid-based methods. It supports the easy implementation of methods like
4692 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4695 This package contains the basic DUNE grid classes.")
4696 ;; GPL version 2 with "runtime exception"
4697 (license license:gpl2)))
4699 (define-public dune-istl
4706 (uri (string-append "https://dune-project.org/download/"
4707 version "/dune-istl-" version ".tar.gz"))
4710 "0l2gyrvys5w6wsmk0ckbb7295s80b7yk7qrl7x66akv2jv1nzq2w"))))
4711 (build-system cmake-build-system)
4714 (modify-phases %standard-phases
4715 (add-after 'build 'build-tests
4716 (lambda* (#:key make-flags #:allow-other-keys)
4717 (apply invoke "make" "build_tests" make-flags)))
4718 ;; These tests fail because they require a fully functional MPI
4720 (add-after 'unpack 'disable-failing-tests
4723 (string-append "--exclude-regex '("
4729 "pamg_comm_repart_test"
4737 `(("dune-common" ,dune-common)
4738 ("openmpi" ,openmpi)
4741 ("superlu" ,superlu)
4742 ("openblas" ,openblas)
4744 ("python" ,python)))
4746 `(("gfortran" ,gfortran)
4747 ("pkg-config" ,pkg-config)))
4748 (home-page "https://dune-project.org/")
4749 (synopsis "Distributed and Unified Numerics Environment")
4750 (description "DUNE, the Distributed and Unified Numerics Environment is a
4751 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4754 This is the iterative solver template library which provides generic sparse
4755 matrix/vector classes and a variety of solvers based on these classes. A
4756 special feature is the use of templates to exploit the recursive block
4757 structure of finite element matrices at compile time. Available solvers
4758 include Krylov methods, (block-) incomplete decompositions and
4759 aggregation-based algebraic multigrid.")
4760 ;; GPL version 2 with "runtime exception"
4761 (license license:gpl2)))
4763 (define-public dune-localfunctions
4765 (name "dune-localfunctions")
4770 (uri (string-append "https://dune-project.org/download/"
4771 version "/dune-localfunctions-" version ".tar.gz"))
4774 "19c6zjinwwpy8jh4v4prhphyd438rapd4x80fj93apmwgw04nrhl"))))
4775 (build-system cmake-build-system)
4778 (modify-phases %standard-phases
4779 (add-after 'build 'build-tests
4780 (lambda* (#:key make-flags #:allow-other-keys)
4781 (apply invoke "make" "build_tests" make-flags))))))
4783 `(("dune-common" ,dune-common)
4784 ("dune-geometry" ,dune-geometry)
4785 ("openmpi" ,openmpi)
4788 ("superlu" ,superlu)
4791 `(("gfortran" ,gfortran)
4792 ("pkg-config" ,pkg-config)))
4793 (home-page "https://dune-project.org/")
4794 (synopsis "Distributed and Unified Numerics Environment") ; TODO
4795 (description "This DUNE module provides interface and implementation for
4796 shape functions defined on the DUNE reference elements. In addition to the
4797 shape function, interpolation operators and special keys are provided which
4798 can be used to assemble global function spaces on finite-element grids.
4800 This package provides an interface and implementation for shape functions
4801 defined on the DUNE reference elements. In addition to the shape function,
4802 interpolation operators and special keys are provided which can be used to
4803 assemble global function spaces on finite-element grids.")
4804 ;; GPL version 2 with "runtime exception"
4805 (license license:gpl2)))
4807 (define-public dune-alugrid
4809 (name "dune-alugrid")
4814 (uri (string-append "https://dune-project.org/download/"
4815 version "/dune-alugrid-" version ".tar.gz"))
4818 "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj"))))
4819 (build-system cmake-build-system)
4821 `(#:tests? #f ; 7 of 8 tests fail because they need a full MPI
4824 (modify-phases %standard-phases
4825 (add-after 'unpack 'patch-include
4827 (substitute* "dune/alugrid/test/test-alugrid.cc"
4828 (("doc/grids/gridfactory/testgrids")
4829 "doc/dune-grid/grids/gridfactory/testgrids"))
4831 (add-after 'build 'build-tests
4832 (lambda* (#:key inputs make-flags #:allow-other-keys)
4833 (setenv "CPLUS_INCLUDE_PATH"
4834 (string-append (assoc-ref inputs "dune-grid") "/share"))
4835 (apply invoke "make" "build_tests" make-flags))))))
4837 `(("dune-common" ,dune-common)
4838 ("dune-geometry" ,dune-geometry)
4839 ("dune-grid" ,dune-grid)
4840 ("openmpi" ,openmpi)
4843 ("openblas" ,openblas)
4845 ("superlu" ,superlu)
4849 `(("gfortran" ,gfortran)
4850 ("pkg-config" ,pkg-config)))
4851 (home-page "https://dune-project.org/")
4852 (synopsis "Distributed and Unified Numerics Environment")
4853 (description "ALUGrid is an adaptive, loadbalancing, unstructured
4854 implementation of the DUNE grid interface supporting either simplices or
4856 (license license:gpl2+)))
4858 (define-public dune-typetree
4860 (name "dune-typetree")
4866 (url "https://gitlab.dune-project.org/staging/dune-typetree.git")
4867 (commit (string-append "v" version))))
4868 (file-name (git-file-name name version))
4871 "0mnv6w2f22lz3j4bdpdjq55vjm8xxfx9v4vvhg9bd36xpsbjpjp9"))))
4872 (build-system cmake-build-system)
4875 (modify-phases %standard-phases
4876 (add-after 'build 'build-tests
4877 (lambda* (#:key make-flags #:allow-other-keys)
4878 (apply invoke "make" "build_tests" make-flags))))))
4880 `(("dune-common" ,dune-common)
4881 ("openmpi" ,openmpi)
4883 ("openblas" ,openblas)
4886 ("superlu" ,superlu)
4889 `(("gfortran" ,gfortran)
4890 ("pkg-config" ,pkg-config)))
4891 (home-page "https://dune-project.org/")
4892 (synopsis "Distributed and Unified Numerics Environment")
4893 (description "TypeTree is a template library for constructing and
4894 operating on statically typed trees of objects.")
4895 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4896 (license (list license:lgpl3+ license:gpl2))))
4898 (define-public dune-functions
4900 (name "dune-functions")
4906 (url "https://gitlab.dune-project.org/staging/dune-functions.git")
4907 (commit (string-append "v" version))))
4908 (file-name (git-file-name name version))
4911 "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200"))))
4912 (build-system cmake-build-system)
4913 (arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid
4915 `(("dune-common" ,dune-common)
4916 ("dune-istl" ,dune-istl)
4917 ("dune-localfunctions" ,dune-localfunctions)
4918 ("dune-grid" ,dune-grid)
4919 ("dune-geometry" ,dune-geometry)
4920 ("dune-typetree" ,dune-typetree)
4921 ("openmpi" ,openmpi)
4922 ("openblas" ,openblas)
4925 ("superlu" ,superlu)
4928 `(("gfortran" ,gfortran)
4929 ("pkg-config" ,pkg-config)))
4930 (home-page "https://dune-project.org/")
4931 (synopsis "Distributed and Unified Numerics Environment")
4932 (description "The dune-functions module provides an abstraction layer for
4933 global finite element functions. Its two main concepts are functions
4934 implemented as callable objects, and bases of finite element spaces.")
4935 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4936 (license (list license:lgpl3+ license:gpl2))))
4938 (define-public dune-pdelab
4940 (name "dune-pdelab")
4941 (version "2.6.0-rc1")
4946 (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
4947 (commit (string-append "v" version))))
4948 (file-name (git-file-name name version))
4951 "07g0s9448z65vjrq88g5rv3340iifil85k170n8kbqchsvi4ny5v"))))
4952 (build-system cmake-build-system)
4953 (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
4955 `(("dune-common" ,dune-common)
4956 ("dune-istl" ,dune-istl)
4957 ("dune-localfunctions" ,dune-localfunctions)
4958 ("dune-geometry" ,dune-geometry)
4959 ("dune-grid" ,dune-grid)
4960 ("dune-typetree" ,dune-typetree)
4961 ("dune-functions" ,dune-functions)
4962 ("openmpi" ,openmpi)
4964 ("openblas" ,openblas)
4968 ("superlu" ,superlu)
4971 `(("gfortran" ,gfortran)
4972 ("pkg-config" ,pkg-config)))
4973 (home-page "https://dune-project.org/")
4974 (synopsis "Differential equations solver toolbox")
4975 (description "PDELab is a partial differential equations solver toolbox
4976 built on top of DUNE, the Distributed and Unified Numerics Environment.")
4977 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4978 (license (list license:lgpl3+ license:gpl2))))
4980 (define-public mlucas
4988 "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz"))
4990 (base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447"))))
4991 (build-system gnu-build-system)
4993 `(("python2" ,python-2)))
4995 `(#:tests? #f ; no tests
4997 (modify-phases %standard-phases
5001 (call-with-output-file "Makefile"
5003 (format port "CC = gcc
5004 CFLAGS = -O3 ~a -DUSE_THREADS
5005 LDLIBS = -lm -lpthread -lrt
5006 Mlucas: $(addsuffix .o,$(basename $(wildcard *.c)))
5008 ,(let ((system (or (%current-target-system)
5009 (%current-system))))
5011 ((string-prefix? "x86_64" system) "-DUSE_SSE2")
5015 (lambda* (#:key outputs #:allow-other-keys)
5016 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
5017 (install-file "Mlucas" bin)
5018 (install-file "primenet.py" bin))
5020 (home-page "https://www.mersenne.org")
5021 (synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client")
5022 (description "Mlucas performs Lucas-Lehmer primality testing of Mersenne
5023 numbers in search of a world-record prime. You may use it to test any
5024 suitable number as you wish, but it is preferable that you do so in a
5025 coordinated fashion, as part of the Great Internet Mersenne Prime
5026 Search (GIMPS). Mlucas also includes a simple Python script for assignment
5027 management via the GIMPS project's Primenet server.")
5028 (license license:gpl2+)))
5030 (define-public nauty
5037 "https://pallini.di.uniroma1.it/"
5038 "nauty" (string-join (string-split version #\.) "")
5042 "1p4mxf8q5wm47nxyskxbqwa5p1vvkycv1zgswvnk9nsn6vff0al6"))))
5043 (build-system gnu-build-system)
5044 (outputs '("out" "lib"))
5046 `(#:test-target "checks"
5048 (modify-phases %standard-phases
5049 ;; Default make target does not build all available
5050 ;; executables. Create them now.
5051 (add-after 'build 'build-extra-programs
5053 (for-each (lambda (target) (invoke "make" target))
5054 '("blisstog" "bliss2dre" "checks6" "sumlines"))
5056 ;; Upstream does not provide any install target.
5058 (lambda* (#:key outputs #:allow-other-keys)
5059 (let* ((out (assoc-ref outputs "out"))
5060 (lib-output (assoc-ref outputs "lib"))
5061 (bin (string-append out "/bin"))
5062 (doc (string-append out "/share/doc/nauty/"))
5063 (include (string-append lib-output "/include/nauty"))
5064 (lib (string-append lib-output "/lib/nauty")))
5065 (for-each (lambda (f) (install-file f bin))
5066 '("dreadnaut" "NRswitchg" "addedgeg" "amtog" "biplabg"
5067 "blisstog" "bliss2dre" "catg" "checks6" "complg"
5068 "converseg" "copyg" "countg" "cubhamg" "deledgeg"
5069 "delptg" "directg" "dretodot" "dretog" "genbg"
5070 "genbgL" "geng" "genquarticg" "genrang" "genspecialg"
5071 "gentourng" "gentreeg" "hamheuristic" "labelg"
5072 "linegraphg" "listg" "multig" "newedgeg" "pickg"
5073 "planarg" "ranlabg" "shortg" "showg" "subdivideg"
5074 "sumlines" "twohamg" "vcolg" "watercluster2"))
5075 (for-each (lambda (f) (install-file f include))
5076 (find-files "." "\\.h$"))
5077 (for-each (lambda (f) (install-file f lib))
5078 (find-files "." "\\.a$"))
5079 (for-each (lambda (f) (install-file f doc))
5080 (append '("formats.txt" "README" "schreier.txt")
5081 (find-files "." "\\.pdf$")))))))))
5083 `(("gmp" ,gmp))) ;for sumlines
5084 (home-page "https://pallini.di.uniroma1.it/")
5085 (synopsis "Library for graph automorphisms")
5086 (description "@code{nauty} (No AUTomorphisms, Yes?) is a set of
5087 procedures for computing automorphism groups of graphs and digraphs.
5089 @code{nauty} computes graph information in the form of a set of
5090 generators, the size of the group, and the orbits of the group; it can
5091 also produce a canonical label. The @code{nauty} suite is written in
5092 C and comes with a command-line interface, a collection of
5093 command-line tools, and an Application Programming Interface (API).
5095 This package provides the static libraries required to run programs
5096 compiled against the nauty library.")
5097 (license license:asl2.0)))
5106 (uri (string-append "https://www.bugseng.com/products/ppl/download/"
5107 "ftp/releases/" version
5108 "/ppl-" version ".tar.gz"))
5111 "1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb"))))
5112 (build-system gnu-build-system)
5118 (home-page "https://www.bugseng.com/parma-polyhedra-library")
5120 "Parma Polyhedra Library for computations with polyhedra")
5122 "The Parma Polyhedra Library (PPL) provides numerical abstractions
5123 especially targeted at applications in the field of analysis and
5124 verification of complex systems. These abstractions include convex
5125 polyhedra, defined as the intersection of a finite number of (open or
5126 closed) halfspaces, each described by a linear inequality (strict or
5127 non-strict) with rational coefficients; some special classes of polyhedra
5128 shapes that offer interesting complexity/precision tradeoffs; and grids
5129 which represent regularly spaced points that satisfy a set of linear
5130 congruence relations. The library also supports finite powersets and
5131 products of (any kind of) polyhedra and grids, a mixed integer linear
5132 programming problem solver using an exact-arithmetic version of the simplex
5133 algorithm, a parametric integer programming solver, and primitives for
5134 termination analysis via the automatic synthesis of linear ranking
5136 (license license:gpl3+)))
5138 (define-public speedcrunch
5140 (name "speedcrunch")
5146 (url "https://bitbucket.org/heldercorreia/speedcrunch.git")
5147 (commit (string-append "release-" version))))
5148 (file-name (git-file-name name version))
5151 "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"))))
5152 (build-system cmake-build-system)
5153 (inputs `(("qtbase" ,qtbase)))
5154 (native-inputs `(("qttools" ,qttools)))
5157 (modify-phases %standard-phases
5158 (add-after 'unpack 'chdir-to-src
5159 (lambda _ (chdir "src") #t)))))
5160 (synopsis "High-precision scientific calculator")
5162 "SpeedCrunch is a high-precision scientific calculator. It features a
5163 syntax-highlighted scrollable display and is designed to be fully used via
5164 keyboard. Some distinctive features are auto-completion of functions and
5165 variables, a formula book, and quick insertion of constants from various
5166 fields of knowledge.")
5167 (home-page "http://speedcrunch.org/")
5168 (license license:gpl2+)))
5170 (define-public minisat
5171 ;; This is the last commit which is available upstream, no
5172 ;; release happened since 2010.
5173 (let ((commit "37dc6c67e2af26379d88ce349eb9c4c6160e8543")
5177 (version (string-append "2.2.0-" revision "." (string-take commit 7)))
5182 (url "https://github.com/niklasso/minisat.git")
5184 (file-name (string-append name "-" version "-checkout"))
5187 "091hf3qkm197s5r7xcr3m07xsdwyz2rqk1hc9kj0hn13imz09irq"))
5189 (search-patches "minisat-friend-declaration.patch"
5190 "minisat-install.patch"))))
5191 (build-system gnu-build-system)
5193 '(#:make-flags (list (string-append "prefix=" %output))
5194 #:tests? #f ;no check target
5196 (modify-phases %standard-phases
5197 (delete 'configure))))
5199 `(("zlib:static" ,zlib "static")
5202 "Small, yet efficient, SAT solver")
5204 "MiniSat is a minimalistic, open-source SAT solver, developed to help
5205 researchers and developers alike to get started on SAT.")
5207 "http://minisat.se/MiniSat.html")
5208 (license license:expat))))