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 "1a460zj9xmbgvcymkdhqh313c4l29mn9cffbi5vf33x3qygk70mp"))))
386 (build-system gnu-build-system)
388 `(;; Currently there are numerous tests that fail on "exotic"
389 ;; architectures such as aarch64 and ppc64le.
390 ,@(if (string-prefix? "aarch64-linux"
391 (or (%current-target-system) (%current-system)))
394 (home-page "https://www.gnu.org/software/gsl/")
395 (synopsis "Numerical library for C and C++")
397 "The GNU Scientific Library is a library for numerical analysis in C
398 and C++. It includes a wide range of mathematical routines, with over 1000
399 functions in total. Subject areas covered by the library include:
400 differential equations, linear algebra, Fast Fourier Transforms and random
402 (license license:gpl3+)))
411 (uri (string-append "mirror://gnu/glpk/glpk-"
415 "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
416 (build-system gnu-build-system)
420 `(#:configure-flags '("--with-gmp")))
421 (home-page "https://www.gnu.org/software/glpk/")
422 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
424 "GLPK is a C library for solving large-scale linear programming (LP),
425 mixed integer programming (MIP), and other related problems. It supports the
426 GNU MathProg modeling language, a subset of the AMPL language, and features a
427 translator for the language. In addition to the C library, a stand-alone
428 LP/MIP solver is included in the package.")
429 (license license:gpl3+)))
438 (uri (string-append "https://github.com/4ti2/4ti2/releases/download/"
440 (string-map (lambda (c) (if (char=? c #\.) #\_ c))
442 "/4ti2-" version ".tar.gz"))
444 (base32 "0rj92x6p9m3la5gasjbj7sa569im527ffmka5y2sv1amgd3fflrh"))))
445 (build-system gnu-build-system)
447 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
451 (home-page "http://www.4ti2.de/")
452 (synopsis "Mathematical tool suite for problems on linear spaces")
454 "4ti2 implements algorithms for solving algebraic, geometric and
455 combinatorial problems on linear spaces. Among others, it solves systems
456 of linear equations, computes extreme rays of polyhedral cones, solves
457 integer programming problems and computes Markov bases for statistics.")
458 (license license:gpl2+)))
460 (define-public cddlib
467 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
468 (string-delete #\. version) ".tar.gz"))
471 "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
472 (build-system gnu-build-system)
475 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
476 (synopsis "Library for convex hulls and extreme rays of polyhedra")
478 "The C-library cddlib implements the Double Description Method of
479 Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
480 rays of a general convex polyhedron given by a system of linear inequalities
481 in arbitrary dimension. It can also be used for the converse operation of
482 computing convex hulls.")
483 (license license:gpl2+)))
485 (define-public lrslib
492 (uri (string-append "http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/"
494 (string-delete #\. version) ".tar.gz"))
497 "034fa45r9hwx6ljmgpxk2872q34nklkalpdkc6s9hqw57rivi36k"))))
498 (build-system gnu-build-system)
502 `(#:tests? #f ; no check phase
503 #:make-flags `("CC=gcc"
504 ,(string-append "prefix=" (assoc-ref %outputs "out"))
507 (modify-phases %standard-phases
510 (substitute* "makefile"
511 (("-L \\.") "-L . -Wl,-rpath='$$ORIGIN/../lib'"))
513 (home-page "http://cgm.cs.mcgill.ca/~avis/C/lrs.html")
514 (synopsis "Convex hulls of polyhedra with exact arithmetic")
516 "The C code of lrslib implements the reverse search algorithm for
517 vertex enumeration and convex hull problems. Its input file format is
518 compatible with cddlib. All computations are done exactly in either
519 multiple precision or fixed integer arithmetic. Output is not stored
520 in memory, so even problems with very large output sizes can sometimes
522 (license license:gpl2+)))
524 (define-public arpack-ng
528 (home-page "https://github.com/opencollab/arpack-ng")
531 (uri (git-reference (url home-page) (commit version)))
532 (file-name (git-file-name name version))
535 "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
536 (build-system gnu-build-system)
538 `(("autoconf" ,autoconf)
539 ("automake" ,automake)
540 ("libtool" ,libtool)))
543 ("fortran" ,gfortran)))
544 (synopsis "Fortran subroutines for solving eigenvalue problems")
546 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
547 large scale eigenvalue problems.")
548 (license (license:non-copyleft "file://COPYING"
549 "See COPYING in the distribution."))))
551 (define-public arpack-ng-3.3.0
555 (name (package-name arpack-ng))
556 (home-page (package-home-page arpack-ng))
560 (uri (string-append home-page "/archive/" version ".tar.gz"))
561 (file-name (string-append name "-" version ".tar.gz"))
564 "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
566 (define-public arpack-ng-openmpi
567 (package (inherit arpack-ng)
568 (name "arpack-ng-openmpi")
571 ,@(package-inputs arpack-ng)))
573 (substitute-keyword-arguments (package-arguments arpack-ng)
574 ((#:configure-flags _ '())
576 ((#:phases phases '%standard-phases)
577 `(modify-phases ,phases
578 (add-before 'check 'mpi-setup
580 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
582 (define-public lapack
589 (uri (string-append "http://www.netlib.org/lapack/lapack-"
593 "1155qixp26c12yrxc76z9mlfw2h3xxymxxv5znpgzh5gaykpndgj"))))
594 (build-system cmake-build-system)
595 (home-page "http://www.netlib.org/lapack/")
596 (inputs `(("fortran" ,gfortran)
597 ("python" ,python-wrapper)))
599 `(#:configure-flags (list
600 "-DBUILD_SHARED_LIBS:BOOL=YES"
602 ;; Build the 'LAPACKE_clatms' functions.
603 "-DLAPACKE_WITH_TMG=ON"
604 "-DBUILD_TESTING=ON")))
605 (synopsis "Library for numerical linear algebra")
607 "LAPACK is a Fortran 90 library for solving the most commonly occurring
608 problems in numerical linear algebra.")
609 (license (license:non-copyleft "file://LICENSE"
610 "See LICENSE in the distribution."))))
612 (define-public scalapack
619 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
623 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))
624 (patches (search-patches "scalapack-blacs-mpi-deprecations.patch"))))
625 (build-system cmake-build-system)
628 ("fortran" ,gfortran)
629 ("lapack" ,lapack))) ;for testing only
631 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
632 #:phases (modify-phases %standard-phases
633 (add-before 'check 'mpi-setup
635 (home-page "http://www.netlib.org/scalapack/")
636 (synopsis "Library for scalable numerical linear algebra")
638 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
639 routines on parallel distributed memory machines. ScaLAPACK solves dense and
640 banded linear systems, least squares problems, eigenvalue problems, and
641 singular value problems.")
642 (license (license:non-copyleft "file://LICENSE"
643 "See LICENSE in the distribution."))))
645 (define-public gnuplot
651 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
655 (base32 "1vglp4la40f5dpj0zdj63zprrkyjgzy068p35bz5dqxjyczm1zlp"))))
656 (build-system gnu-build-system)
657 (inputs `(("readline" ,readline)
663 `(("pkg-config" ,pkg-config)
664 ("texlive" ,texlive-tiny)))
665 (arguments `(#:configure-flags (list (string-append
666 "--with-texdir=" %output
667 "/texmf-local/tex/latex/gnuplot"))))
668 (home-page "http://www.gnuplot.info")
669 (synopsis "Command-line driven graphing utility")
670 (description "Gnuplot is a portable command-line driven graphing
671 utility. It was originally created to allow scientists and students to
672 visualize mathematical functions and data interactively, but has grown to
673 support many non-interactive uses such as web scripting. It is also used as a
674 plotting engine by third-party applications like Octave.")
675 ;; X11 Style with the additional restriction that derived works may only be
676 ;; distributed as patches to the original.
677 (license (license:fsf-free
678 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
688 (url "https://github.com/OkoSanto/GCTP.git")
689 (commit (string-append "v" version))))
690 (file-name (git-file-name name version))
692 (base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
694 `(("fortran" ,gfortran)))
695 (build-system gnu-build-system)
696 (synopsis "General Cartographic Transformation Package (GCTP)")
698 "The General Cartographic Transformation Package (GCTP) is a system of
699 software routines designed to permit the transformation of coordinate pairs
700 from one map projection to another. The GCTP is the standard computer
701 software used by the National Mapping Division for map projection
703 (home-page "https://github.com/OkoSanto/GCTP")
704 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
713 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
714 version "/src/hdf-" version ".tar.bz2"))
716 (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l"))
717 (patches (search-patches "hdf4-architectures.patch"
718 "hdf4-reproducibility.patch"
719 "hdf4-shared-fortran.patch"
720 "hdf4-tirpc.patch"))))
721 (build-system gnu-build-system)
723 `(("gfortran" ,gfortran)
729 ("libtirpc" ,libtirpc)))
731 `(#:parallel-tests? #f
732 #:configure-flags (list "--enable-shared"
733 (string-append "CPPFLAGS=-I"
734 (assoc-ref %build-inputs "libtirpc")
737 (modify-phases %standard-phases
738 ;; This is inspired by two of Debian's patches.
739 (add-before 'configure 'add-more-aarch64-support
741 (substitute* '("mfhdf/ncgen/ncgen.l"
742 "mfhdf/ncgen/ncgenyy.c"
743 "mfhdf/libsrc/netcdf.h.in")
744 (("AIX5L64") "__aarch64__"))
746 (add-before 'configure 'patchbuild
749 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
751 (("/bin/mkdir") "mkdir"))
752 (substitute* (find-files "." "^Makefile\\.in$")
753 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
754 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
755 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
756 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
757 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
759 (add-after 'configure 'patch-settings
761 ;; libhdf4.settings contains the full path of the
762 ;; compilers used, and its contents are included in
763 ;; .so-files. We truncate the hashes to avoid
764 ;; unnecessary store references to those compilers:
765 (substitute* "libhdf4.settings"
766 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
767 (string-append prefix (string-take hash 10) "...")))
770 (home-page "https://www.hdfgroup.org/products/hdf4/")
772 "Library and multi-object file format for storing and managing data")
773 (description "HDF4 is a library and multi-object file format for storing
774 and managing data between machines. HDF4 is an older hierarchical data format,
775 incompatible with HDF5.")
777 (license:non-copyleft
778 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
780 (define-public hdf4-alt
785 (substitute-keyword-arguments (package-arguments hdf4)
786 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
788 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
797 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
798 "hdf5-" (version-major+minor version)
799 "/hdf5-" version "/src/hdf5-"
801 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
803 (match (string-split version #\.)
805 (string-append major minor)))
806 "/src/hdf5-" version ".tar.bz2")))
808 (base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5"))
809 (patches (search-patches "hdf5-config-date.patch"
810 "hdf5-1.8-mpi-deprecations.patch"))))
811 (build-system gnu-build-system)
815 `(("gfortran" ,gfortran)
816 ("perl" ,perl))) ;part of the test machinery needs Perl
817 (outputs '("out" ; core library
818 "fortran")) ; fortran interface
820 `(;; Some of the users, notably Flann, need the C++ interface.
821 #:configure-flags '("--enable-cxx"
823 "--enable-fortran2003"
825 ;; Build a thread-safe library. Unfortunately,
826 ;; 'configure' invites you to either turn off C++,
827 ;; Fortran, and the high-level interface (HL), or
828 ;; to pass '--enable-unsupported'. Debian
829 ;; packagers chose to pass '--enable-unsupported'
830 ;; and we follow their lead here.
831 "--enable-threadsafe"
833 "--enable-unsupported")
834 ;; Use -fPIC to allow the R bindings to link with the static libraries
835 #:make-flags (list "CFLAGS=-fPIC"
838 (modify-phases %standard-phases
839 (add-before 'configure 'patch-configure
840 (lambda* (#:key outputs #:allow-other-keys)
841 (substitute* "configure"
843 (substitute* "fortran/src/Makefile.in"
844 (("libhdf5_fortran_la_LDFLAGS =")
845 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
846 (assoc-ref outputs "fortran") "/lib")))
847 (substitute* "hl/fortran/src/Makefile.in"
848 (("libhdf5hl_fortran_la_LDFLAGS =")
849 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
850 (assoc-ref outputs "fortran") "/lib")))
852 (add-after 'configure 'patch-settings
854 ;; libhdf5.settings contains the full path of the
855 ;; compilers used, and its contents are included in
856 ;; libhdf5.so. We truncate the hashes to avoid
857 ;; unnecessary store references to those compilers:
858 (substitute* "src/libhdf5.settings"
859 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
860 (string-append prefix (string-take hash 10) "..."))
861 ;; Don't record the build-time kernel version to make the
862 ;; settings file reproducible.
863 (("Uname information:.*")
864 "Uname information: Linux\n"))
866 (add-after 'install 'patch-references
867 (lambda* (#:key inputs outputs #:allow-other-keys)
868 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
869 (zlib (assoc-ref inputs "zlib")))
870 (substitute* (find-files bin "h5p?cc")
872 (string-append "-L" zlib "/lib " lib)))
874 (add-after 'install 'split
875 (lambda* (#:key inputs outputs #:allow-other-keys)
876 ;; Move all fortran-related files
877 (let* ((out (assoc-ref outputs "out"))
878 (bin (string-append out "/bin"))
879 (lib (string-append out "/lib"))
880 (inc (string-append out "/include"))
881 (ex (string-append out "/share/hdf5_examples/fortran"))
882 (fort (assoc-ref outputs "fortran"))
883 (fbin (string-append fort "/bin"))
884 (flib (string-append fort "/lib"))
885 (finc (string-append fort "/include"))
886 (fex (string-append fort "/share/hdf5_examples/fortran")))
891 ;; Note: When built with --enable-parallel, the 'h5fc' file
892 ;; doesn't exist, hence this condition.
893 (when (file-exists? (string-append bin "/h5fc"))
894 (rename-file (string-append bin "/h5fc")
895 (string-append fbin "/h5fc")))
896 (for-each (lambda (file)
898 (string-append flib "/" (basename file))))
899 (find-files lib ".*fortran.*"))
900 (for-each (lambda (file)
902 (string-append finc "/" (basename file))))
903 (find-files inc ".*mod"))
904 (for-each (lambda (file)
906 (string-append fex "/" (basename file))))
907 (find-files ex ".*"))
908 (delete-file-recursively ex))
910 (home-page "https://www.hdfgroup.org")
911 (synopsis "Management suite for extremely large and complex data")
912 (description "HDF5 is a suite that makes possible the management of
913 extremely large and complex data collections.")
914 (license (license:x11-style
915 "https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
917 (define-public hdf5-1.10
918 (package (inherit hdf5)
923 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
924 "hdf5-" (version-major+minor version)
925 "/hdf5-" version "/src/hdf5-"
927 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
930 (take (string-split version #\.) 2))
931 "/src/hdf5-" version ".tar.bz2")))
933 (base32 "1gf38x51128hn00744358w27xgzjk0ff4wra4yxh2lk804ck1mh9"))
934 (patches (search-patches "hdf5-config-date.patch"))))))
936 (define-public hdf-java
944 "https://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
945 version "/src/CMake-hdfjava-" version ".tar.gz"))
947 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
948 (modules '((guix build utils)))
949 (snippet ; Make sure we don't use the bundled sources and binaries.
951 (for-each delete-file
952 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
953 "HDF4.tar.gz" "HDF5.tar.gz"))
954 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
956 (build-system gnu-build-system)
958 `(("jdk" ,icedtea "jdk")
959 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
961 ("hamcrest-core" ,java-hamcrest-core)
962 ("junit" ,java-junit)
963 ("slf4j-simple" ,java-slf4j-simple)))
969 ("slf4j-api" ,java-slf4j-api)))
972 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
973 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
974 (assoc-ref %build-inputs "jdk") "/lib" )
975 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
976 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
979 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
980 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
981 (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
982 (string-append "JPEGLIB="
983 (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
987 (modify-phases %standard-phases
988 (add-before 'configure 'chdir-to-source
989 (lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
990 (add-before 'configure 'patch-build
991 (lambda* (#:key inputs outputs #:allow-other-keys)
992 (substitute* "configure"
993 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
994 (("/bin/cat") (which "cat")))
995 ;; Set classpath for compilation
996 (substitute* '("hdf/hdf5lib/Makefile.in"
997 "hdf/hdf5lib/exceptions/Makefile.in"
998 "hdf/hdflib/Makefile.in")
999 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
1000 (string-append (assoc-ref inputs "slf4j-api")
1001 "/share/java/slf4j-api.jar")))
1002 ;; Replace outdated config.sub and config.guess:
1003 (with-directory-excursion "config"
1004 (for-each (lambda (file)
1006 (string-append (assoc-ref inputs "automake")
1008 ,(version-major+minor (package-version automake))
1010 '("config.sub" "config.guess")))
1012 ;; Fix embedded version number
1013 (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
1014 (substitute* "hdf/hdf5lib/H5.java"
1016 (string-join hdf5version ", "))))
1018 (mkdir-p (string-append (assoc-ref outputs "out")))
1019 ;; Set classpath for tests
1020 (let* ((build-dir (getcwd))
1021 (lib (string-append build-dir "/lib"))
1022 (jhdf (string-append lib "/jhdf.jar"))
1023 (jhdf5 (string-append lib "/jhdf5.jar"))
1026 (string-append (assoc-ref inputs i)
1027 "/share/java/" i ".jar"))
1028 '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
1030 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
1032 (substitute* '("test/hdf5lib/Makefile.in"
1033 "test/hdf5lib/junit.sh.in"
1034 "examples/runExample.sh.in")
1036 (string-append (assoc-ref inputs "coreutils")
1039 (string-append (assoc-ref inputs "coreutils")
1041 (("CLASSPATH=[^\n]*")
1042 (string-append "CLASSPATH=" class-path)))
1043 (setenv "CLASSPATH" class-path))
1045 (add-before 'check 'build-examples
1047 (apply invoke `("javac"
1048 ,@(find-files "examples" ".*\\.java"))))))
1050 #:parallel-build? #f
1052 #:parallel-tests? #f ))
1053 (home-page "https://support.hdfgroup.org/products/java")
1054 (synopsis "Java interface for the HDF4 and HDF5 libraries")
1055 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
1056 the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
1059 ;; BSD-style license:
1060 (license (license:x11-style
1061 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
1062 /current/src/unpacked/COPYING"))))
1064 (define-public hdf-eos2
1071 (uri "ftp://edhs1.gsfc.nasa.gov\
1072 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
1074 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
1075 (patches (search-patches "hdf-eos2-remove-gctp.patch"
1076 "hdf-eos2-build-shared.patch"
1077 "hdf-eos2-fortrantests.patch"))))
1078 (build-system gnu-build-system)
1080 `(("gfortran" ,gfortran)))
1082 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
1083 ;; XXX: These inputs are really dependencies of hdf4.
1085 ("libjpeg" ,libjpeg)
1086 ("libtirpc" ,libtirpc)
1090 `( #:configure-flags '("--enable-install-include" "--enable-shared"
1091 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
1092 #:parallel-tests? #f))
1093 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
1094 (synopsis "HDF4-based data format for NASA's Earth Observing System")
1095 (description "HDF-EOS2 is a software library built on HDF4 which supports
1096 the construction of data structures used in NASA's Earth Observing
1097 System (Grid, Point and Swath).")
1099 ;; Source files carry a permissive license header.
1100 (license (license:non-copyleft home-page))))
1102 (define-public hdf-eos5
1108 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1109 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1112 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1113 (patches (search-patches "hdf-eos5-build-shared.patch"
1114 "hdf-eos5-remove-gctp.patch"
1115 "hdf-eos5-fix-szip.patch"
1116 "hdf-eos5-fortrantests.patch"))))
1118 `(("gfortran" ,gfortran)))
1119 (build-system gnu-build-system)
1125 `(#:configure-flags '("--enable-install-include" "--enable-shared"
1126 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1127 #:parallel-tests? #f))
1128 (synopsis "HDF5-based data format for NASA's Earth Observing System")
1130 "HDF-EOS5 is a software library built on HDF5 to support the construction
1131 of data structures used in NASA's Earth Observing System (Grid, Point and
1133 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1135 ;; Source files carry a permissive license header.
1136 (license (license:non-copyleft home-page))))
1138 (define-public hdf5-parallel-openmpi
1139 (package (inherit hdf5)
1140 (name "hdf5-parallel-openmpi")
1143 ,@(package-inputs hdf5)))
1145 (substitute-keyword-arguments (package-arguments hdf5)
1146 ((#:configure-flags flags)
1147 ``("--enable-parallel"
1148 ,@(delete "--enable-cxx"
1149 (delete "--enable-threadsafe" ,flags))))
1151 `(modify-phases ,phases
1152 (add-after 'build 'mpi-setup
1154 (add-before 'check 'patch-tests
1156 ;; OpenMPI's mpirun will exit with non-zero status if it
1157 ;; detects an "abnormal termination", i.e. any process not
1158 ;; calling MPI_Finalize(). Since the test is explicitly
1159 ;; avoiding MPI_Finalize so as not to have at_exit and thus
1160 ;; H5C_flush_cache from being called, mpirun will always
1161 ;; complain, so turn this test off.
1162 (substitute* "testpar/Makefile"
1163 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1164 (string-append front back "\n")))
1165 (substitute* "tools/h5diff/testph5diff.sh"
1166 (("/bin/sh") (which "sh")))
1168 (synopsis "Management suite for data with parallel IO support")))
1170 (define-public h5check
1177 (uri (string-append "https://www.hdfgroup.org/ftp/HDF5/tools/"
1178 "h5check/src/h5check-" version ".tar.gz"))
1181 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1182 (build-system gnu-build-system)
1183 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
1184 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1185 (synopsis "HDF5 format checker")
1186 (description "@code{h5check} is a validation tool for verifying that an
1187 HDF5 file is encoded according to the HDF File Format Specification.")
1188 (license (license:x11-style "file://COPYING"))))
1196 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1201 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1202 (build-system cmake-build-system)
1203 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1204 (inputs `(("lapack" ,lapack)
1206 ;; FIXME: Even though the fonts are available dvips complains:
1207 ;; "Font cmmi10 not found; characters will be left blank."
1209 `(("texlive" ,texlive-tiny)
1210 ("ghostscript" ,ghostscript)
1211 ("doxygen" ,doxygen)))
1212 (home-page "http://itpp.sourceforge.net")
1213 (synopsis "C++ library of maths, signal processing and communication classes")
1214 (description "IT++ is a C++ library of mathematical, signal processing and
1215 communication classes and functions. Its main use is in simulation of
1216 communication systems and for performing research in the area of
1217 communications. The kernel of the library consists of generic vector and
1218 matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1219 similar to MATLAB, GNU Octave or SciPy.")
1220 (license license:gpl3+)))
1222 (define-public netcdf
1229 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1230 "netcdf-" version ".tar.gz"))
1233 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1234 (patches (search-patches "netcdf-date-time.patch"
1235 "netcdf-tst_h_par.patch"))))
1236 (build-system gnu-build-system)
1239 ("doxygen" ,doxygen)
1240 ("graphviz" ,graphviz)))
1242 `(("hdf4" ,hdf4-alt)
1245 ("libjpeg" ,libjpeg)))
1247 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
1249 #:phases (modify-phases %standard-phases
1250 (add-before 'configure 'fix-source-date
1252 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1253 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1254 ;; to '1st hour of the current day', and therefore makes the
1255 ;; package not reproducible.
1256 (substitute* "./configure"
1257 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1258 "date --date='@0'"))
1260 (add-after 'configure 'patch-settings
1262 ;; libnetcdf.settings contains the full filename of the compilers
1263 ;; used to build the library. We truncate the hashes of those
1264 ;; filenames to avoid unnecessary references to the corresponding
1266 (substitute* "libnetcdf.settings"
1267 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1268 (string-append prefix (string-take hash 10) "...")))
1271 #:parallel-tests? #f)) ;various race conditions
1272 (home-page "https://www.unidata.ucar.edu/software/netcdf/")
1273 (synopsis "Library for scientific data")
1274 (description "NetCDF is an interface for scientific data access and a
1275 software library that provides an implementation of the interface. The netCDF
1276 library defines a machine-independent format for representing scientific data.
1277 Together, the interface, library, and format support the creation, access, and
1278 sharing of scientific data.")
1279 (license (license:x11-style "file://COPYRIGHT"))))
1281 (define-public netcdf-parallel-openmpi
1282 (package (inherit netcdf)
1283 (name "netcdf-parallel-openmpi")
1286 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1287 (package-inputs netcdf))))
1288 ;; TODO: Replace pkg-config references in nc-config with absolute references
1290 (substitute-keyword-arguments (package-arguments netcdf)
1291 ((#:configure-flags flags)
1292 `(cons* "CC=mpicc" "CXX=mpicxx"
1293 "--enable-parallel-tests"
1294 ;; Shared libraries not supported with parallel IO.
1295 "--disable-shared" "--with-pic"
1298 (define-public netcdf-fortran
1300 (name "netcdf-fortran")
1305 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1309 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1310 (build-system gnu-build-system)
1312 `(#:parallel-tests? #f))
1314 `(("netcdf" ,netcdf)))
1316 `(("gfortran" ,gfortran)))
1317 (synopsis "Fortran interface for the netCDF library")
1318 (description (package-description netcdf))
1319 (home-page (package-home-page netcdf))
1320 (license (package-license netcdf))))
1322 (define-public nlopt
1328 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1331 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1332 (build-system gnu-build-system)
1334 `(;; Shared libraries are not built by default. They are required to
1335 ;; build the Guile, Octave, and Python bindings.
1336 #:configure-flags '("--enable-shared")
1339 (modify-phases %standard-phases
1340 (add-before 'configure 'set-libnlopt-file-name
1341 (lambda* (#:key outputs #:allow-other-keys)
1342 ;; Make sure the Scheme module refers to the library by its
1343 ;; absolute file name (we cannot do that from a snippet
1344 ;; because the expansion of @libdir@ contains
1346 (let ((out (assoc-ref outputs "out")))
1347 (substitute* "swig/nlopt.scm.in"
1349 (string-append out "/lib/libnlopt")))
1351 (inputs `(("guile" ,guile-2.0)))
1352 (native-inputs `(("pkg-config" ,pkg-config)))
1353 (home-page "http://ab-initio.mit.edu/wiki/")
1354 (synopsis "Library for nonlinear optimization")
1355 (description "NLopt is a library for nonlinear optimization, providing a
1356 common interface for a number of different free optimization routines available
1357 online as well as original implementations of various other algorithms.")
1358 (license license:lgpl2.1+)))
1360 (define-public ipopt
1367 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1371 "07yn9rzdswjk8n246qq6ci9ssf2bcplkifcpsfz9j6cdxw9vgbkv"))
1372 (modules '((guix build utils)))
1374 ;; Make sure we don't use the bundled software.
1376 (delete-file-recursively "ThirdParty")
1378 (build-system gnu-build-system)
1380 '(#:phases (modify-phases %standard-phases
1381 (add-after 'install 'add--L-flags-in-ipopt.pc
1382 (lambda* (#:key inputs outputs #:allow-other-keys)
1383 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1384 ;; move it to "Libs.private" where it belongs, and add a
1385 ;; '-L' flag for LAPACK.
1386 (let ((out (assoc-ref outputs "out"))
1387 (lapack (assoc-ref inputs "lapack")))
1388 (substitute* (string-append out "/lib/pkgconfig/"
1390 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1391 (string-append "Libs: " before " " after "\n"
1392 "Libs.private: " before
1393 "-L" lapack "/lib -llapack -lblas "
1397 `(("gfortran" ,gfortran)))
1399 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
1400 `(("lapack" ,lapack))) ;for both libblas and liblapack
1401 (home-page "http://www.coin-or.org")
1402 (synopsis "Large-scale nonlinear optimizer")
1404 "The Interior Point Optimizer (IPOPT) is a software package for
1405 large-scale nonlinear optimization. It provides C++, C, and Fortran
1407 (license license:epl1.0)))
1415 (uri (string-append "https://www.coin-or.org/download/source/"
1416 "Clp/Clp-" version ".tgz"))
1419 "1wdg820g3iikf9344ijwsc8sy6c0m6im42bzzizm6rlmkvnmxhk9"))
1420 (modules '((guix build utils)))
1422 ;; Make sure we don't use the bundled software.
1424 (delete-file-recursively "ThirdParty")
1426 (build-system gnu-build-system)
1428 `(("gfortran" ,gfortran)
1429 ("pkg-config" ,pkg-config)))
1431 `(("openblas" ,openblas)))
1432 (home-page "https://www.coin-or.org")
1433 (synopsis "Linear programming solver")
1435 "CLP is a high quality linear programming solver. Its main strengths are
1436 its dual and primal Simplex algorithms. It also has a barrier algorithm for
1437 linear and quadratic objectives. There are limited facilities for nonlinear
1438 and quadratic objectives using the Simplex algorithm.")
1439 (license license:epl1.0)))
1441 (define-public ceres
1443 (name "ceres-solver")
1445 (home-page "http://ceres-solver.org/")
1448 (uri (string-append home-page "ceres-solver-"
1452 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
1453 (build-system cmake-build-system)
1455 ;; TODO: Build HTML user documentation and install separately.
1456 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
1457 "-DBUILD_SHARED_LIBS=ON")
1459 #:phases (modify-phases %standard-phases
1460 (add-before 'configure 'set-library-directory
1462 ;; Install libraries to lib/, not lib64/.
1463 (substitute* "internal/ceres/CMakeLists.txt"
1464 (("set\\(LIB_SUFFIX \"64\"\\)")
1465 "set(LIB_SUFFIX \"\")"))
1468 `(("pkg-config" ,pkg-config)))
1470 `(("glog" ,glog))) ;for #include <glog/glog.h>
1475 ("suitesparse" ,suitesparse)
1476 ("gflags" ,gflags)))
1477 (synopsis "C++ library for solving large optimization problems")
1479 "Ceres Solver is a C++ library for modeling and solving large,
1480 complicated optimization problems. It is a feature rich, mature and
1481 performant library which has been used in production since 2010. Ceres Solver
1482 can solve two kinds of problems:
1484 @item non-linear least squares problems with bounds constraints;
1485 @item general unconstrained optimization problems.
1487 (license license:bsd-3)))
1489 ;; For a fully featured Octave, users are strongly recommended also to install
1490 ;; the following packages: less, ghostscript, gnuplot.
1491 (define-public octave-cli
1498 (uri (string-append "mirror://gnu/octave/octave-"
1502 "11wwxpy2q1bhxs2v41bqn05i2sb0905cj1xil6mg8l4k2kka4cq6"))))
1503 (build-system gnu-build-system)
1505 `(("alsa-lib" ,alsa-lib)
1506 ("arpack" ,arpack-ng)
1511 ("fontconfig" ,fontconfig)
1512 ("freetype" ,freetype)
1516 ("graphicsmagick" ,graphicsmagick)
1519 ("libsndfile" ,libsndfile)
1523 ("portaudio" ,portaudio)
1525 ("readline" ,readline)
1526 ("suitesparse" ,suitesparse)
1527 ("texinfo" ,texinfo)
1531 ("gfortran" ,gfortran)
1532 ("pkg-config" ,pkg-config)
1534 ;; The following inputs are not actually used in the build process.
1535 ;; However, the ./configure gratuitously tests for their existence and
1536 ;; assumes that programs not present at build time are also not, and
1537 ;; can never be, available at run time! If these inputs are therefore
1538 ;; not present, support for them will be built out. However, Octave
1539 ;; will still run without them, albeit without the features they
1542 ("ghostscript" ,ghostscript)
1543 ("gnuplot" ,gnuplot)))
1544 ;; Octave code uses this variable to detect directories holding multiple CA
1545 ;; certificates to verify peers with. This is required for the networking
1546 ;; functions that require encryption to work properly.
1547 (native-search-paths
1548 (list (search-path-specification
1549 (variable "CURLOPT_CAPATH")
1550 (files '("etc/ssl/certs")))))
1553 (list (string-append "--with-shell="
1554 (assoc-ref %build-inputs "bash")
1557 (modify-phases %standard-phases
1558 (add-after 'configure 'configure-makeinfo
1559 (lambda* (#:key inputs #:allow-other-keys)
1560 (substitute* "libinterp/corefcn/help.h"
1563 "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
1565 (home-page "https://www.gnu.org/software/octave/")
1566 (synopsis "High-level language for numerical computation")
1567 (description "GNU Octave is a high-level interpreted language that is
1568 specialized for numerical computations. It can be used for both linear and
1569 non-linear applications and it provides great support for visualizing results.
1570 Work may be performed both at the interactive command-line as well as via
1572 (license license:gpl3+)))
1574 (define-public octave
1575 (package (inherit octave-cli)
1578 (inherit (package-source octave-cli))))
1580 `(("qscintilla" ,qscintilla)
1582 ,@(package-inputs octave-cli)))
1584 `(("qttools" , qttools) ;for lrelease
1585 ("texlive" ,(texlive-union (list texlive-epsf))) ; for texi2dvi
1586 ,@(package-native-inputs octave-cli)))
1588 (substitute-keyword-arguments (package-arguments octave-cli)
1590 `(modify-phases ,phases
1591 (add-before 'configure 'patch-qscintilla-library-name
1592 (lambda* (#:key inputs #:allow-other-keys)
1593 ;; The QScintilla library that the Octave configure script tries
1594 ;; to link with should be named libqscintilla-qt5.so, but the
1595 ;; QScintilla input provides the shared library as
1596 ;; libqscintilla2_qt5.so.
1597 (substitute* "configure"
1598 (("qscintilla2-qt5")
1602 (define-public qtoctave
1603 (deprecated-package "qtoctave" octave))
1605 (define-public opencascade-oce
1607 (name "opencascade-oce")
1613 (url "https://github.com/tpaviot/oce.git")
1614 (commit (string-append "OCE-" version))))
1615 (file-name (git-file-name name version))
1616 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
1618 (base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69"))))
1619 (build-system cmake-build-system)
1622 (list "-DOCE_TESTING:BOOL=ON"
1623 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1624 "-DOCE_DRAW:BOOL=ON"
1625 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1626 (assoc-ref %outputs "out"))
1627 "-UCMAKE_INSTALL_RPATH")))
1629 `(("freetype" ,freetype)
1636 `(("python" ,python-wrapper)))
1637 (home-page "https://github.com/tpaviot/oce")
1638 (synopsis "Libraries for 3D modeling and numerical simulation")
1640 "Open CASCADE is a set of libraries for the development of applications
1641 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1642 C++ class libraries providing services for 3D surface and solid modeling, CAD
1643 data exchange, and visualization. It is used for development of specialized
1644 software dealing with 3D models in design (CAD), manufacturing (CAM),
1645 numerical simulation (CAE), measurement equipment (CMM), and quality
1646 control (CAQ) domains.
1648 This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1649 patches, improvements, and experiments contributed by users over the official
1650 Open CASCADE library.")
1651 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1652 ; use of header files; see
1653 ; OCCT_LGPL_EXCEPTION.txt
1654 license:public-domain; files
1655 ; src/Standard/Standard_StdAllocator.hxx and
1656 ; src/NCollection/NCollection_StdAllocator.hxx
1657 license:expat; file src/OpenGl/OpenGl_glext.h
1658 license:bsd-3)))); test framework gtest
1660 (define-public opencascade-occt
1662 (name "opencascade-occt")
1668 (url "https://git.dev.opencascade.org/repos/occt.git")
1671 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
1673 (file-name (git-file-name name version))
1675 (base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4"))
1676 (modules '((guix build utils)))
1679 ;; Remove files specific to non-free operating systems.
1680 (delete-file-recursively "samples/ios")
1681 (delete-file-recursively "samples/mfc")
1682 (delete-file-recursively "samples/qt/FuncDemo")
1683 (delete-file "genconf.bat")
1684 (delete-file "gendoc.bat")
1685 (delete-file "genproj.bat")
1686 (delete-file "upgrade.bat")
1687 ;; Remove references to deleted files.
1688 (substitute* "dox/FILES_HTML.txt"
1689 ((".*standard.*") "" )
1690 ((".*UIKitSample.*") ""))
1692 (build-system cmake-build-system)
1694 '(;; There is no test target for make. OCCT provides an
1695 ;; 'Automated Testing System', which may be accessed after
1696 ;; installation via the draw.sh script. draw.sh is located in
1697 ;; the bin directory. For details see:
1698 ;; https://www.opencascade.com/doc/occt-7.3.0/overview/html/\
1699 ;; occt_dev_guides__tests.html
1701 ;; Configure without freeimage: attempting to link against the
1702 ;; freeimage version 3.17 library leads to 'undefined
1703 ;; reference' errors.
1705 (list "-DUSE_FREEIMAGE:BOOL=OFF"
1707 "-DUSE_VTK:BOOL=OFF"
1708 "-DBUILD_DOC_Overview:BOOL=OFF"
1709 "-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON"
1710 "-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON"
1711 "-UCMAKE_INSTALL_LIBDIR")))
1713 `(("doxygen" ,doxygen)
1714 ;("freeimage" ,freeimage)
1715 ("freetype" ,freetype)
1717 ("libxext" ,libxext)
1724 ;; TODO: build Overview documentation and add 'doc' output.
1725 (home-page "https://www.opencascade.com")
1726 (synopsis "Libraries for 3D modeling and numerical simulation")
1728 "Open CASCADE is a set of libraries for the development of applications
1729 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1730 C++ class libraries providing services for 3D surface and solid modeling, CAD
1731 data exchange, and visualization. It is used for development of specialized
1732 software dealing with 3D models in design (CAD), manufacturing (CAM),
1733 numerical simulation (CAE), measurement equipment (CMM), and quality
1734 control (CAQ) domains.
1736 This is the certified version of the Open Cascade Technology (OCCT) library.")
1737 (license (list ;; OCCT library:
1738 license:lgpl2.1; with an exception for the use of header
1739 ; files, see OCCT_LGPL_EXCEPTION.txt.
1740 ;; Files src/OpenGl/glext.h, adm/cmake/cotire.cmake and
1741 ;; src/OpenGl/OpenGl_HaltonSampler.hxx:
1743 ;; Files src/ExprIntrp/ExprIntrp.tab.* and
1744 ;; src/StepFile/step.tab.*:
1745 license:gpl3+ ; with Bison 2.2 exception.
1746 ;; File src/NCollection/NCollection_UtfIterator.lxx:
1747 (license:non-copyleft
1748 "https://www.unicode.org/license.html")
1749 ;; File src/NCollection/NCollection_StdAllocator.hxx:
1750 license:public-domain))))
1760 (url "https://gitlab.onelab.info/gmsh/gmsh.git")
1762 (string-append "gmsh_"
1763 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
1765 (file-name (git-file-name name version))
1767 (base32 "08rq4jajwmlpivnm9yifz2jhaivnz065lnk0h2zv773nwl9wf162"))
1768 (modules '((guix build utils)))
1770 ;; Remove non-free METIS code
1772 (delete-file-recursively "contrib/Metis")
1774 (build-system cmake-build-system)
1777 ("gfortran" ,gfortran)
1783 ("opencascade-oce" ,opencascade-oce)
1785 ("libxext" ,libxext)))
1787 `(("fontconfig" ,fontconfig)
1788 ("libxft" ,libxft)))
1790 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1791 "-DENABLE_BUILD_SHARED:BOOL=ON"
1792 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
1793 (home-page "http://gmsh.info/")
1794 (synopsis "3D finite element grid generator")
1795 (description "Gmsh is a 3D finite element grid generator with a built-in
1796 CAD engine and post-processor. Its design goal is to provide a fast, light
1797 and user-friendly meshing tool with parametric input and advanced
1798 visualization capabilities. Gmsh is built around four modules: geometry,
1799 mesh, solver and post-processing. The specification of any input to these
1800 modules is done either interactively using the graphical user interface or in
1801 ASCII text files using Gmsh's own scripting language.")
1802 (license license:gpl2+)))
1804 (define-public maxflow
1807 ;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’,
1808 ;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’.
1813 (url "https://github.com/gerddie/maxflow.git")
1815 (file-name (git-file-name name version))
1818 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1819 (build-system cmake-build-system)
1820 (home-page "https://pub.ist.ac.at/~vnk/software.html")
1821 (synopsis "Library implementing Maxflow algorithm")
1822 (description "An implementation of the maxflow algorithm described in
1823 @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1824 Energy Minimization in Computer Vision.\n
1825 Yuri Boykov and Vladimir Kolmogorov.\n
1826 In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1828 (license license:gpl3+)))
1830 (define-public petsc
1837 ;; The *-lite-* tarball does not contain the *large* documentation
1838 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1839 "petsc-lite-" version ".tar.gz"))
1841 (base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx"))))
1842 (outputs '("out" ; libraries and headers
1843 "examples")) ; ~30MiB of examples
1844 (build-system gnu-build-system)
1846 `(("python" ,python-2)))
1848 `(("gfortran" ,gfortran)
1850 ("superlu" ,superlu)
1851 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1852 ;; leaving out opengl, as configuration seems to only be for mac
1855 `(#:test-target "test"
1856 #:parallel-build? #f ; build is parallel by default
1862 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1863 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1864 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
1866 (modify-phases %standard-phases
1868 ;; PETSc's configure script is actually a python script, so we can't
1869 ;; run it with bash.
1870 (lambda* (#:key outputs (configure-flags '())
1872 (let* ((prefix (assoc-ref outputs "out"))
1873 (flags `(,(string-append "--prefix=" prefix)
1874 ,@configure-flags)))
1875 (format #t "build directory: ~s~%" (getcwd))
1876 (format #t "configure flags: ~s~%" flags)
1877 (apply invoke "./configure" flags))))
1878 (add-after 'configure 'clean-local-references
1879 (lambda* (#:key outputs #:allow-other-keys)
1880 (let ((out (assoc-ref outputs "out")))
1881 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
1882 ;; Prevent build directory from leaking into compiled code
1884 ;; Scrub timestamp for reproducibility
1885 ((".*Libraries compiled on.*") ""))
1886 (substitute* (find-files "." "petscvariables")
1887 ;; Do not expose build machine characteristics, set to defaults.
1888 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1889 (("NPMAX = [:digit:]+") "NPMAX = 2"))
1891 (add-after 'install 'clean-install
1892 ;; Try to keep installed files from leaking build directory names.
1893 (lambda* (#:key inputs outputs #:allow-other-keys)
1894 (let ((out (assoc-ref outputs "out")))
1895 (substitute* (map (lambda (file)
1896 (string-append out "/lib/petsc/conf/" file))
1897 '("petscvariables"))
1899 ;; Make compiler references point to the store
1900 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
1901 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1902 (string-append "= " (which compiler))))
1903 ;; PETSc installs some build logs, which aren't necessary.
1904 (for-each (lambda (file)
1905 (let ((f (string-append out "/lib/petsc/conf/" file)))
1906 (when (file-exists? f)
1908 '("configure.log" "make.log" "gmake.log"
1909 "test.log" "error.log" "RDict.db"
1910 "PETScBuildInternal.cmake"
1911 ;; Once installed, should uninstall with Guix
1914 (add-after 'install 'move-examples
1915 (lambda* (#:key outputs #:allow-other-keys)
1916 (let* ((out (assoc-ref outputs "out"))
1917 (examples (assoc-ref outputs "examples"))
1918 (exdir (string-append out "/share/petsc/examples"))
1919 (exdir' (string-append examples "/share/petsc/examples")))
1920 (copy-recursively exdir exdir')
1921 (delete-file-recursively exdir)
1923 (home-page "https://www.mcs.anl.gov/petsc")
1924 (synopsis "Library to solve PDEs")
1925 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1926 data structures and routines for the scalable (parallel) solution of
1927 scientific applications modeled by partial differential equations.")
1928 (license (license:non-copyleft
1929 "https://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1931 (define-public petsc-complex
1932 (package (inherit petsc)
1933 (name "petsc-complex")
1935 (substitute-keyword-arguments (package-arguments petsc)
1936 ((#:configure-flags cf)
1937 `(cons "--with-scalar-type=complex" ,cf))))
1938 (synopsis "Library to solve PDEs (with complex scalars)")))
1940 (define-public petsc-openmpi
1941 (package (inherit petsc)
1942 (name "petsc-openmpi")
1944 `(("hdf5" ,hdf5-parallel-openmpi)
1945 ("hypre" ,hypre-openmpi)
1947 ("mumps" ,mumps-openmpi)
1948 ("openmpi" ,openmpi)
1949 ("scalapack" ,scalapack)
1950 ("scotch" ,pt-scotch32)
1951 ,@(package-inputs petsc)))
1953 (substitute-keyword-arguments (package-arguments petsc)
1954 ((#:configure-flags cf)
1956 "--with-mpiexec=mpirun"
1959 "--with-scalapack=1"
1961 ,(string-append "--with-mpi-dir="
1962 (assoc-ref %build-inputs "openmpi"))
1963 ,(string-append "--with-hdf5-include="
1964 (assoc-ref %build-inputs "hdf5") "/include")
1965 ,(string-append "--with-hdf5-lib="
1966 (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
1967 ,@(delete "--with-mpi=0" ,cf)))
1969 `(modify-phases ,phases
1970 (add-before 'configure 'mpi-setup
1971 ,%openmpi-setup)))))
1972 (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
1974 (define-public petsc-complex-openmpi
1975 (package (inherit petsc-complex)
1976 (name "petsc-complex-openmpi")
1978 `(("openmpi" ,openmpi)
1979 ,@(package-inputs petsc-complex)))
1981 (substitute-keyword-arguments (package-arguments petsc-complex)
1982 ((#:configure-flags cf)
1983 ``("--with-mpiexec=mpirun"
1984 ,(string-append "--with-mpi-dir="
1985 (assoc-ref %build-inputs "openmpi"))
1986 ,@(delete "--with-mpi=0" ,cf)))
1988 `(modify-phases ,phases
1989 (add-before 'configure 'mpi-setup
1990 ,%openmpi-setup)))))
1991 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
1993 (define-public python-petsc4py
1995 (name "python-petsc4py")
2000 (uri (pypi-uri "petsc4py" version))
2003 "1rm1qj5wlkhxl39by9n78lh3gbmii31wsnb8j1rr5hvfr5xgbx2q"))))
2004 (build-system python-build-system)
2007 (modify-phases %standard-phases
2008 (add-before 'build 'pre-build
2010 ;; Define path to PETSc installation.
2011 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
2013 (add-before 'check 'mpi-setup
2016 `(("petsc" ,petsc-openmpi)
2017 ("python-numpy" ,python-numpy)))
2018 (home-page "https://bitbucket.org/petsc/petsc4py/")
2019 (synopsis "Python bindings for PETSc")
2020 (description "PETSc, the Portable, Extensible Toolkit for
2021 Scientific Computation, is a suite of data structures and routines for
2022 the scalable (parallel) solution of scientific applications modeled by
2023 partial differential equations. It employs the MPI standard for all
2024 message-passing communication. @code{petsc4py} provides Python
2025 bindings to almost all functions of PETSc.")
2026 (license license:bsd-3)))
2028 (define-public python-kiwisolver
2030 (name "python-kiwisolver")
2034 (uri (pypi-uri "kiwisolver" version))
2037 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
2038 (build-system python-build-system)
2039 (home-page "https://github.com/nucleic/kiwi")
2040 (synopsis "Fast implementation of the Cassowary constraint solver")
2042 "Kiwi is an efficient C++ implementation of the Cassowary constraint
2043 solving algorithm. Kiwi has been designed from the ground up to be
2044 lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
2045 Cassowary solver with typical use cases gaining a 40x improvement. Memory
2046 savings are consistently > 5x.")
2047 (license license:bsd-3)))
2049 (define-public python2-kiwisolver
2050 (package-with-python2 python-kiwisolver))
2052 (define-public slepc
2059 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
2063 "1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8"))))
2064 (build-system gnu-build-system)
2066 `(("python" ,python-2)
2067 ("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
2069 `(("arpack" ,arpack-ng)
2070 ("gfortran" ,gfortran)))
2072 `(("petsc" ,petsc)))
2074 `(#:parallel-build? #f ;build is parallel by default
2076 `(,(string-append "--with-arpack-dir="
2077 (assoc-ref %build-inputs "arpack") "/lib"))
2078 #:make-flags ;honor (parallel-job-count)
2079 `(,(format #f "MAKE_NP=~a" (parallel-job-count))
2080 ,(string-append "PETSCCONFIGDIR="
2081 (assoc-ref %build-inputs "petsc:examples")
2082 "/share/petsc/examples/config"))
2084 (modify-phases %standard-phases
2086 ;; configure is a python script, so we can't run it with bash.
2087 (lambda* (#:key inputs outputs (configure-flags '())
2089 (let* ((prefix (assoc-ref outputs "out"))
2090 (flags `(,(string-append "--prefix=" prefix)
2091 ,@configure-flags)))
2092 (format #t "build directory: ~s~%" (getcwd))
2093 (format #t "configure flags: ~s~%" flags)
2094 (setenv "SLEPC_DIR" (getcwd))
2095 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
2096 (apply invoke "./configure" flags))))
2097 (add-after 'install 'delete-doc
2098 ;; TODO: SLEPc installs HTML documentation alongside headers in
2099 ;; $out/include. We'd like to move them to share/doc, but delete
2100 ;; them for now, as they are incomplete and installing the complete
2101 ;; documentation is difficult.
2102 (lambda* (#:key outputs #:allow-other-keys)
2103 (let* ((out (assoc-ref outputs "out")))
2104 (for-each delete-file (find-files out "\\.html$"))
2106 (add-after 'install 'clean-install
2107 ;; Clean up unnecessary build logs from installation.
2108 (lambda* (#:key outputs #:allow-other-keys)
2109 (let ((out (assoc-ref outputs "out")))
2110 (for-each (lambda (file)
2111 (let ((f (string-append out "/lib/slepc/conf/" file)))
2112 (when (file-exists? f)
2114 '("configure.log" "make.log" "gmake.log"
2115 "test.log" "error.log" "RDict.db"
2118 (home-page "http://slepc.upv.es")
2119 (synopsis "Scalable library for eigenproblems")
2120 (description "SLEPc is a software library for the solution of large sparse
2121 eigenproblems on parallel computers. It can be used for the solution of
2122 linear eigenvalue problems formulated in either standard or generalized form,
2123 as well as other related problems such as the singular value decomposition.
2124 The emphasis of the software is on methods and techniques appropriate for
2125 problems in which the associated matrices are sparse, for example, those
2126 arising after the discretization of partial differential equations.")
2127 (license license:bsd-2)))
2129 (define-public slepc-complex
2130 (package (inherit slepc)
2131 (name "slepc-complex")
2133 `(("petsc" ,petsc-complex)
2134 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
2135 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
2137 (define-public slepc-openmpi
2138 (package (inherit slepc)
2139 (name "slepc-openmpi")
2141 (substitute-keyword-arguments (package-arguments slepc)
2142 ((#:phases phases '%standard-phases)
2143 `(modify-phases ,phases
2144 (add-before 'check 'mpi-setup
2145 ,%openmpi-setup)))))
2148 ("arpack" ,arpack-ng-openmpi)
2149 ,@(alist-delete "arpack" (package-inputs slepc))))
2151 `(("petsc" ,petsc-openmpi)
2152 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
2153 (synopsis "Scalable library for eigenproblems (with MPI support)")))
2155 (define-public slepc-complex-openmpi
2156 (package (inherit slepc-openmpi)
2157 (name "slepc-complex-openmpi")
2159 `(("petsc" ,petsc-complex-openmpi)
2160 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
2161 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
2163 (define-public python-slepc4py
2165 (name "python-slepc4py")
2170 (uri (pypi-uri "slepc4py" version))
2173 "1ksp08kxf4wg408b9nn39z3qfhy643j22d4rfbl30vzxk2rxh4lq"))))
2174 (build-system python-build-system)
2177 (modify-phases %standard-phases
2178 (add-before 'build 'pre-build
2180 ;; Define path to PETSc installation.
2181 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
2182 ;; Define path to SLEPc installation.
2183 (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
2185 (add-before 'check 'mpi-setup
2188 `(("python-numpy" ,python-numpy)
2189 ("python-petsc4py" ,python-petsc4py)
2190 ("slepc" ,slepc-openmpi)))
2191 (home-page "https://bitbucket.org/slepc/slepc4py/")
2192 (synopsis "Python bindings for SLEPc")
2193 (description "SLEPc, the Scalable Library for Eigenvalue Problem
2194 Computations, is based on PETSc, the Portable, Extensible Toolkit for
2195 Scientific Computation. It employs the MPI standard for all
2196 message-passing communication. @code{slepc4py} provides Python
2197 bindings to almost all functions of SLEPc.")
2198 (license license:bsd-3)))
2200 (define-public mumps
2207 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
2211 "0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r"))
2212 (patches (search-patches "mumps-build-parallelism.patch"
2213 "mumps-shared-libseq.patch"
2214 "mumps-shared-mumps.patch"
2215 "mumps-shared-pord.patch"))))
2216 (build-system gnu-build-system)
2218 `(("fortran" ,gfortran)
2219 ;; These are required for linking against mumps, but we let the user
2220 ;; declare the dependency.
2223 ("scotch" ,scotch)))
2225 `(#:modules ((ice-9 match)
2228 ,@%gnu-build-system-modules)
2230 (modify-phases %standard-phases
2232 (lambda* (#:key inputs #:allow-other-keys)
2233 (call-with-output-file "Makefile.inc"
2244 INCSEQ = -I$(topdir)/libseq
2245 LIBSEQ = $(topdir)/libseq/libmpiseq.a
2246 LIBSEQNEEDED = libseqneeded~;
2250 AR = ar vr # rules require trailing space, ugh...
2253 LIBBLAS = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[
2255 SCALAP = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~]
2256 LIBOTHERS = -pthread
2259 OPTF = -O2 -DALLOW_NON_INIT $(PIC)
2263 LIBS = $(SCALAP) $(LIBSEQ)
2264 LPORDDIR = $(topdir)/PORD/lib
2265 IPORD = -I$(topdir)/PORD/include
2266 LPORD = $(LPORDDIR)/libpord.a
2267 ORDERINGSF = -Dpord~@[
2269 IMETIS = -I$(METISDIR)/include
2270 LMETIS = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
2271 ORDERINGSF += -Dmetis~]~@[~:{
2273 ISCOTCH = -I$(SCOTCHDIR)/include
2274 LSCOTCH = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
2275 ORDERINGSF += ~a~}~]
2276 ORDERINGSC = $(ORDERINGSF)
2277 LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
2278 IORDERINGSF = $(ISCOTCH)
2279 IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
2280 (assoc-ref inputs "mpi")
2281 (assoc-ref inputs "blas")
2282 (assoc-ref inputs "scalapack")
2283 (assoc-ref inputs "metis")
2284 (match (list (assoc-ref inputs "pt-scotch")
2285 (assoc-ref inputs "scotch"))
2289 `((,scotch "" "-Dscotch")))
2292 "-lptesmumps -lptscotch -lptscotcherr "
2293 "-Dptscotch")))))))))
2295 ;; By default only the d-precision library is built. Make with "all"
2296 ;; target so that all precision libraries and examples are built.
2298 (invoke "make" "all"
2299 (format #f "-j~a" (parallel-job-count)))))
2301 ;; Run the simple test drivers, which read test input from stdin:
2302 ;; from the "real" input for the single- and double-precision
2303 ;; testers, and from the "cmplx" input for complex-precision
2304 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
2305 ;; package to prefix execution with "mpirun".
2306 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
2307 (with-directory-excursion "examples"
2310 (let ((tester (apply open-pipe*
2313 ,(string-append "./" prec
2315 (input (open-input-file
2316 (string-append "input_simpletest_" type))))
2318 (dump-port input tester)
2320 (zero? (close-pipe tester)))))
2322 '("real" "real" "cmplx" "cmplx")))))
2324 (lambda* (#:key outputs #:allow-other-keys)
2325 (let* ((out (assoc-ref outputs "out"))
2326 (libdir (string-append out "/lib")))
2327 (copy-recursively "lib" libdir)
2328 (copy-recursively "include" (string-append out "/include"))
2329 (when (file-exists? "libseq/libmpiseq.a")
2330 (install-file "libseq/libmpiseq.a" libdir))
2331 (when (file-exists? "libseq/libmpiseq.so")
2332 (install-file "libseq/libmpiseq.so" libdir))
2334 (home-page "http://mumps.enseeiht.fr")
2335 (synopsis "Multifrontal sparse direct solver")
2337 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
2338 sparse system of linear equations A x = b using Gaussian elimination.")
2339 (license license:cecill-c)))
2341 (define-public mumps-metis
2342 (package (inherit mumps)
2343 (name "mumps-metis")
2345 (alist-delete "scotch" (package-inputs mumps)))))
2347 (define-public mumps-openmpi
2348 (package (inherit mumps)
2349 (name "mumps-openmpi")
2352 ("scalapack" ,scalapack)
2353 ("pt-scotch" ,pt-scotch)
2354 ,@(alist-delete "scotch" (package-inputs mumps))))
2356 (substitute-keyword-arguments (package-arguments mumps)
2358 `(modify-phases ,phases
2359 (add-before 'check 'mpi-setup
2363 ((assoc-ref ,phases 'check)
2364 #:exec-prefix '("mpirun" "-n" "2"))))))))
2365 (synopsis "Multifrontal sparse direct solver (with MPI)")))
2367 (define-public mumps-metis-openmpi
2368 (package (inherit mumps-openmpi)
2369 (name "mumps-metis-openmpi")
2371 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
2373 (define-public ruby-asciimath
2375 (name "ruby-asciimath")
2380 (uri (rubygems-uri "asciimath" version))
2383 "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
2384 (build-system ruby-build-system)
2387 (modify-phases %standard-phases
2389 ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
2390 (add-after 'unpack 'patch-remove-spurious-backslashes
2392 (substitute* "spec/parser_spec.rb"
2397 `(("bundler" ,bundler)
2398 ("ruby-rspec" ,ruby-rspec)))
2399 (synopsis "AsciiMath parsing and conversion library")
2401 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
2402 easy-to-write markup language for mathematics.")
2403 (home-page "https://github.com/asciidoctor/asciimath")
2404 (license license:expat)))
2406 (define-public superlu
2413 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2414 "superlu_" version ".tar.gz"))
2416 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
2417 (modules '((guix build utils)))
2419 ;; Replace the non-free implementation of MC64 with a stub adapted
2422 (use-modules (ice-9 regex)
2424 (call-with-output-file "SRC/mc64ad.c"
2429 void mc64id_(int *a) {
2430 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2433 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2434 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2435 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2438 ;; Remove the corresponding license verbiage. MC64 license follows
2439 ;; a "------" line separator.
2440 (with-atomic-file-replacement "License.txt"
2441 (let ((rx (make-regexp "-{8}")))
2444 (let ((line (read-line in 'concat)))
2445 (unless (regexp-exec rx line)
2449 (build-system cmake-build-system)
2453 `(("blas" ,openblas)
2454 ("gfortran" ,gfortran)))
2456 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2457 "-DTPL_BLAS_LIBRARIES=openblas"
2458 "-DBUILD_SHARED_LIBS:BOOL=YES")))
2459 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
2460 (synopsis "Supernodal direct solver for sparse linear systems")
2462 "SuperLU is a general purpose library for the direct solution of large,
2463 sparse, nonsymmetric systems of linear equations on high performance machines.
2464 The library is written in C and is callable from either C or Fortran. The
2465 library routines perform an LU decomposition with partial pivoting and
2466 triangular system solves through forward and back substitution. The library
2467 also provides threshold-based ILU factorization preconditioners.")
2468 (license (list license:bsd-3
2469 license:gpl2+ ;EXAMPLE/*fgmr.c
2470 (license:fsf-free "file://SRC/colamd.h")))))
2472 (define-public superlu-dist
2474 (name "superlu-dist")
2479 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2480 "superlu_dist_" version ".tar.gz"))
2482 (base32 "0pqgcgh1yxhfzs99fas3mggajzd5wca3nbyp878rziy74gfk03dl"))
2483 (modules '((guix build utils)))
2485 ;; Replace the non-free implementation of MC64 with a stub
2487 (call-with-output-file "SRC/mc64ad_dist.c"
2492 void mc64id_dist(int *a) {
2493 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2496 void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2497 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2498 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2501 (substitute* "SRC/util.c" ;adjust default algorithm
2502 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
2503 ;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
2504 ;; general (i.e. non-square) processor-grid support.
2505 "RowPerm = NOROWPERM;"))
2507 (patches (search-patches "superlu-dist-scotchmetis.patch"
2508 "superlu-dist-awpm-grid.patch"
2509 "superlu-dist-fix-mpi-deprecations.patch"))))
2510 (build-system cmake-build-system)
2514 `(("gfortran" ,gfortran)
2517 ("combblas" ,combinatorial-blas)))
2519 `(("mpi" ,openmpi) ;headers include MPI heades
2520 ("parmetis" ,pt-scotch32 "metis")
2521 ("pt-scotch" ,pt-scotch32)))
2523 `(#:parallel-tests? #f ;tests use MPI and OpenMP
2524 #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
2525 "-DTPL_ENABLE_COMBBLASLIB=YES"
2526 "-DTPL_BLAS_LIBRARIES=-lopenblas"
2527 "-DTPL_LAPACK_LIBRARIES=-llapack"
2528 (string-append "-DTPL_PARMETIS_LIBRARIES="
2530 '("ptscotchparmetis" "ptscotch" "ptscotcherr"
2531 "scotchmetis" "scotch" "scotcherr")
2533 (string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
2534 (assoc-ref %build-inputs "parmetis")
2536 "-DTPL_ENABLE_COMBBLASLIB=ON"
2537 (string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
2538 (assoc-ref %build-inputs "combblas")
2539 "/include/CombBLAS;"
2540 (assoc-ref %build-inputs "combblas")
2541 "/include/BipartiteMatchings")
2542 "-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
2544 (modify-phases %standard-phases
2545 (add-before 'configure 'set-c++-standard
2547 (substitute* "CMakeLists.txt"
2548 ;; AWPM headers require C++14
2549 (("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
2550 (add-before 'check 'mpi-setup
2552 (add-before 'check 'omp-setup
2553 (lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
2554 (home-page (package-home-page superlu))
2555 (synopsis "Parallel supernodal direct solver")
2557 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2558 It is targeted for distributed memory parallel machines. SuperLU_DIST is
2559 implemented in ANSI C, and MPI for communications.")
2560 (license license:bsd-3)))
2562 (define-public scotch
2569 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
2570 "latestfile/298/scotch_" version ".tar.gz"))
2572 (base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8"))
2573 (patches (search-patches "scotch-build-parallelism.patch"
2574 "scotch-integer-declarations.patch"))))
2575 (build-system gnu-build-system)
2580 (outputs '("out" "metis"))
2582 `(#:make-flags (list (string-append "prefix=" %output))
2584 (modify-phases %standard-phases
2586 'unpack 'chdir-to-src
2587 (lambda _ (chdir "src") #t))
2591 (call-with-output-file "Makefile.inc"
2605 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2606 LDFLAGS = -lz -lm -lrt -lpthread
2608 LEX = flex -Pscotchyy -olex.yy.c
2613 YACC = bison -pscotchyy -y -b y
2615 '("COMMON_FILE_COMPRESS_GZ"
2617 "COMMON_RANDOM_FIXED_SEED"
2618 "INTSIZE64" ;use 'int64_t'
2619 ;; Prevents symbolc clashes with libesmumps
2621 ;; XXX: Causes invalid frees in superlu-dist tests
2623 ;; "SCOTCH_PTHREAD_NUMBER=2"
2624 "restrict=__restrict"))))
2626 (add-after 'build 'build-esmumps
2629 (format #f "-j~a" (parallel-job-count))
2631 (add-before 'install 'make-install-dirs
2632 (lambda* (#:key outputs #:allow-other-keys)
2633 (mkdir (assoc-ref outputs "out"))))
2634 (add-after 'install 'install-metis
2635 (lambda* (#:key outputs #:allow-other-keys)
2636 (let ((out (assoc-ref outputs "metis")))
2638 ;; metis files are not installed with 'make install'
2639 (for-each (lambda (f)
2640 (install-file f (string-append out "/include")))
2641 (find-files "../include/" ".*metis\\.h"))
2642 (for-each (lambda (f)
2643 (install-file f (string-append out "/lib")))
2644 (find-files "../lib/" ".*metis\\..*"))
2646 (home-page "https://www.labri.fr/perso/pelegrin/scotch/")
2647 (synopsis "Programs and libraries for graph algorithms")
2648 (description "SCOTCH is a set of programs and libraries which implement
2649 the static mapping and sparse matrix reordering algorithms developed within
2650 the SCOTCH project. Its purpose is to apply graph theory, with a divide and
2651 conquer approach, to scientific computing problems such as graph and mesh
2652 partitioning, static mapping, and sparse matrix ordering, in application
2653 domains ranging from structural mechanics to operating systems or
2655 ;; See LICENSE_en.txt
2656 (license license:cecill-c)))
2658 (define-public scotch32
2659 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2660 ;; some applications.
2661 (package (inherit scotch)
2664 (substitute-keyword-arguments (package-arguments scotch)
2665 ((#:phases scotch-phases)
2666 `(modify-phases ,scotch-phases
2670 (call-with-output-file "Makefile.inc"
2684 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2685 LDFLAGS = -lz -lm -lrt -lpthread
2687 LEX = flex -Pscotchyy -olex.yy.c
2692 YACC = bison -pscotchyy -y -b y
2694 '("COMMON_FILE_COMPRESS_GZ"
2696 "COMMON_RANDOM_FIXED_SEED"
2697 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
2698 ;; Prevents symbolc clashes with libesmumps
2700 ;; XXX: Causes invalid frees in superlu-dist tests
2702 ;; "SCOTCH_PTHREAD_NUMBER=2"
2703 "restrict=__restrict"))))))))))
2705 "Programs and libraries for graph algorithms (32-bit integers)")))
2707 (define-public pt-scotch
2708 (package (inherit scotch)
2711 `(("openmpi" ,openmpi))) ;Headers include MPI headers
2713 (substitute-keyword-arguments (package-arguments scotch)
2714 ((#:phases scotch-phases)
2715 `(modify-phases ,scotch-phases
2719 (invoke "make" (format #f "-j~a" (parallel-job-count))
2720 "ptscotch" "ptesmumps")
2722 ;; Install the serial metis compatibility library
2723 (invoke "make" "-C" "libscotchmetis" "install")))
2724 (add-before 'check 'mpi-setup
2728 (invoke "make" "ptcheck")))))))
2729 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
2731 (define-public pt-scotch32
2732 (package (inherit scotch32)
2733 (name "pt-scotch32")
2735 `(("openmpi" ,openmpi))) ;headers include MPI headers
2737 (substitute-keyword-arguments (package-arguments scotch32)
2738 ((#:phases scotch32-phases)
2739 `(modify-phases ,scotch32-phases
2742 (invoke "make" (format #f "-j~a" (parallel-job-count))
2743 "ptscotch" "ptesmumps")
2744 ;; Install the serial metis compatibility library
2745 (invoke "make" "-C" "libscotchmetis" "install")))
2746 (add-before 'check 'mpi-setup
2750 (invoke "make" "ptcheck")))))))
2752 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2754 (define-public metis
2761 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2762 "metis-" version ".tar.gz"))
2765 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2766 (build-system cmake-build-system)
2768 `(("blas" ,openblas)))
2770 `(#:tests? #f ;no tests
2771 #:configure-flags `("-DSHARED=ON"
2772 ,(string-append "-DGKLIB_PATH=" (getcwd)
2773 "/metis-" ,version "/GKlib"))))
2774 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2775 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2777 "METIS is a set of serial programs for partitioning graphs, partitioning
2778 finite element meshes, and producing fill-reducing orderings for sparse
2779 matrices. The algorithms implemented in METIS are based on the multilevel
2780 recursive-bisection, multilevel k-way, and multi-constraint partitioning
2782 (license license:asl2.0))) ;As of version 5.0.3
2784 (define-public p4est
2791 (uri (string-append "http://p4est.github.io/release/p4est-"
2795 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
2796 (build-system gnu-build-system)
2798 `(("fortran" ,gfortran)
2803 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2804 (assoc-ref %build-inputs "blas")
2806 ,(string-append "LAPACK_LIBS=-L"
2807 (assoc-ref %build-inputs "lapack")
2809 #:phases (modify-phases %standard-phases
2810 (add-before 'check 'mpi-setup
2812 (home-page "http://www.p4est.org")
2813 (synopsis "Adaptive mesh refinement on forests of octrees")
2815 "The p4est software library enables the dynamic management of a
2816 collection of adaptive octrees, conveniently called a forest of octrees.
2817 p4est is designed to work in parallel and scales to hundreds of thousands of
2819 (license license:gpl2+)))
2821 (define-public p4est-openmpi
2822 (package (inherit p4est)
2823 (name "p4est-openmpi")
2826 ,@(package-inputs p4est)))
2828 (substitute-keyword-arguments (package-arguments p4est)
2829 ((#:configure-flags cf)
2830 ``("--enable-mpi" ,@,cf))))
2831 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2833 (define-public gsegrafix
2840 (uri (string-append "mirror://gnu/" name "/" name "-"
2844 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2845 (build-system gnu-build-system)
2847 `(#:configure-flags '("LDFLAGS=-lm")))
2849 `(("libgnomecanvas" ,libgnomecanvas)
2850 ("libbonoboui" ,libbonoboui)
2851 ("libgnomeui" ,libgnomeui)
2852 ("libgnomeprintui" ,libgnomeprintui)
2855 `(("pkg-config" ,pkg-config)))
2856 (home-page "https://www.gnu.org/software/gsegrafix/")
2857 (synopsis "GNOME application to create scientific and engineering plots")
2858 (description "GSEGrafix is an application which produces high-quality graphical
2859 plots for science and engineering. Plots are specified via simple ASCII
2860 parameter files and data files and are presented in an anti-aliased GNOME
2861 canvas. The program supports rectangular two-dimensional plots, histograms,
2862 polar-axis plots and three-dimensional plots. Plots can be printed or saved
2863 to BMP, JPEG or PNG image formats.")
2864 (license license:gpl3+)))
2866 (define-public maxima
2873 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2874 version "-source/" name "-" version ".tar.gz"))
2877 "0xyahp4c6509haxh4n1swiqm3421gplkdisa0zypclh3252sbzfw"))
2878 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
2879 (build-system gnu-build-system)
2882 ("gnuplot" ,gnuplot) ;for plots
2884 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
2886 `(("texinfo" ,texinfo)
2888 ("python" ,python)))
2891 (list "--enable-gcl"
2892 (string-append "--with-posix-shell="
2893 (assoc-ref %build-inputs "bash")
2895 (string-append "--with-wish="
2896 (assoc-ref %build-inputs "tk")
2898 (let ((v ,(package-version tk)))
2899 (string-take v (string-index-right v #\.)))))
2900 ;; By default Maxima attempts to write temporary files to
2901 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2902 ;; Work around that.
2903 #:make-flags (list "TMPDIR=/tmp")
2905 (modify-phases %standard-phases
2906 (add-after 'unpack 'patch-paths
2907 (lambda* (#:key inputs #:allow-other-keys)
2908 (let* ((sed (string-append (assoc-ref inputs "sed") "/bin/sed"))
2909 (coreutils (assoc-ref inputs "coreutils"))
2910 (dirname (string-append coreutils "/bin/dirname"))
2911 (head (string-append coreutils "/bin/head"))
2912 (perl (string-append (assoc-ref inputs "perl") "/bin/perl"))
2913 (python (string-append (assoc-ref inputs "python")
2915 (substitute* "src/maxima.in"
2916 (("sed ") (string-append sed " "))
2917 (("dirname") dirname)
2919 (substitute* "doc/info/Makefile.in"
2920 (("/usr/bin/env perl") perl))
2921 (substitute* "doc/info/build_html.sh.in"
2922 (("python") python))
2924 (add-before 'check 'pre-check
2926 (chmod "src/maxima" #o555)
2930 ;; This is derived from the testing code in the "debian/rules" file
2931 ;; of Debian's Maxima package.
2932 ;; If Maxima can successfully run this, the binary to be installed
2938 "--batch-string=\"run_testsuite();\" "
2939 "| grep -q \"No unexpected errors found\""))))
2940 ;; Make sure the doc and emacs files are found in the
2941 ;; standard location. Also configure maxima to find gnuplot
2942 ;; without having it on the PATH.
2943 (add-after 'install 'post-install
2944 (lambda* (#:key outputs inputs #:allow-other-keys)
2945 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2946 (out (assoc-ref outputs "out"))
2947 (datadir (string-append out "/share/maxima/" ,version))
2948 (binutils (string-append (assoc-ref inputs "binutils")
2950 (with-directory-excursion out
2951 (mkdir-p "share/emacs")
2952 (mkdir-p "share/doc")
2954 (string-append datadir "/doc/")
2955 (string-append out "/share/doc/maxima"))
2956 (with-atomic-file-replacement
2957 (string-append datadir "/share/maxima-init.lisp")
2959 (format out "~a ~s~a~%"
2960 "(setf $gnuplot_command "
2961 (string-append gnuplot "/bin/gnuplot") ")")
2962 (dump-port in out))))
2963 ;; Ensure that Maxima will have access to the GNU binutils
2964 ;; components at runtime.
2965 (wrap-program (string-append out "/bin/maxima")
2966 `("PATH" prefix (,binutils))))
2968 (home-page "http://maxima.sourceforge.net")
2969 (synopsis "Numeric and symbolic expression manipulation")
2970 (description "Maxima is a system for the manipulation of symbolic and
2971 numerical expressions. It yields high precision numeric results by using
2972 exact fractions, arbitrary precision integers, and variable precision floating
2974 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2975 ;; Others simply say "GNU General Public License" without stating a
2976 ;; version (which implicitly means gpl1+).
2977 ;; At least one file (src/maxima.asd) says "version 2."
2978 ;; GPLv2 only is therefore the smallest subset.
2979 (license license:gpl2)))
2981 (define-public wxmaxima
2989 (url "https://github.com/wxMaxima-developers/wxmaxima.git")
2990 (commit (string-append "Version-" version))))
2991 (file-name (git-file-name name version))
2993 (base32 "16xizaddb27432n1083y89ir5zdqvllsgbwrzzk4jc2rw1ldxfsv"))))
2994 (build-system cmake-build-system)
2996 `(("gettext" ,gettext-minimal)))
2998 `(("wxwidgets" ,wxwidgets)
3001 ("adwaita-icon-theme" ,adwaita-icon-theme)
3003 ("shared-mime-info" ,shared-mime-info)))
3005 `(#:tests? #f ; no check target
3007 (modify-phases %standard-phases
3008 (add-after 'install 'wrap-program
3009 (lambda* (#:key inputs outputs #:allow-other-keys)
3010 (wrap-program (string-append (assoc-ref outputs "out")
3013 (,(string-append (assoc-ref inputs "maxima")
3015 ;; For GtkFileChooserDialog.
3016 `("GSETTINGS_SCHEMA_DIR" =
3017 (,(string-append (assoc-ref inputs "gtk+")
3018 "/share/glib-2.0/schemas")))
3019 `("XDG_DATA_DIRS" ":" prefix
3020 (;; Needed by gdk-pixbuf to know supported icon formats.
3022 (assoc-ref inputs "shared-mime-info") "/share")
3023 ;; The default icon theme of GTK+.
3025 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
3027 (home-page "https://andrejv.github.io/wxmaxima/")
3028 (synopsis "Graphical user interface for the Maxima computer algebra system")
3030 "wxMaxima is a graphical user interface for the Maxima computer algebra
3031 system. It eases the use of Maxima by making most of its commands available
3032 through a menu system and by providing input dialogs for commands that require
3033 more than one argument. It also implements its own display engine that
3034 outputs mathematical symbols directly instead of depicting them with ASCII
3037 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
3038 text and mathematical calculations to create documents, exporting of input and
3039 output to TeX, and a browser for Maxima's manual including command index and
3040 full text searching.")
3041 (license license:gpl2+)))
3043 (define-public armadillo
3049 (uri (string-append "mirror://sourceforge/arma/armadillo-"
3053 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
3054 (build-system cmake-build-system)
3055 (arguments `(#:tests? #f)) ; no test target
3057 `(("openblas" ,openblas)
3059 ("arpack" ,arpack-ng)))
3060 (home-page "http://arma.sourceforge.net/")
3061 (synopsis "C++ linear algebra library")
3063 "Armadillo is a C++ linear algebra library, aiming towards a good balance
3064 between speed and ease of use. It is useful for algorithm development
3065 directly in C++, or quick conversion of research code into production
3066 environments. It can be used for machine learning, pattern recognition,
3067 signal processing, bioinformatics, statistics, econometrics, etc. The library
3068 provides efficient classes for vectors, matrices and cubes, as well as 150+
3069 associated functions (eg. contiguous and non-contiguous submatrix views).")
3070 (license license:asl2.0)))
3072 (define-public muparser
3073 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
3074 ;; different hash. In order to make `guix package --upgrade` work correctly,
3075 ;; we set a Guix packaging revision.
3076 ;; When the next version of muparser is released, we can remove
3077 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
3078 (let ((upstream-version "2.2.5")
3082 (version (string-append upstream-version "-" revision))
3087 (url "https://github.com/beltoforion/muparser.git")
3088 (commit (string-append "v" upstream-version))))
3089 (file-name (git-file-name name version))
3091 (base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24"))))
3092 (build-system gnu-build-system)
3094 `(#:configure-flags '("--enable-samples=no")
3095 #:tests? #f)) ;no "check" target
3096 (home-page "http://muparser.beltoforion.de/")
3097 (synopsis "Fast parser library for mathematical expressions")
3099 "muParser is an extensible high performance math parser library. It is
3100 based on transforming an expression into a bytecode and precalculating constant
3102 (license license:expat))))
3104 (define-public openblas
3111 (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
3112 version "%20version.tar.gz"))
3113 (file-name (string-append name "-" version ".tar.gz"))
3116 "0jbdjsi0qsxahdcm42agnn1y7xpmg0hrhwjsxg0zbhs9wwy3p568"))))
3117 (build-system gnu-build-system)
3119 `(#:test-target "test"
3120 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
3121 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
3122 ;; we need to disable substitutions.
3124 ,(let ((system (or (%current-target-system) (%current-system))))
3125 (or (string-prefix? "x86_64" system)
3126 (string-prefix? "i686" system)
3127 (string-prefix? "mips" system)
3128 (string-prefix? "aarch64" system)))
3130 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
3132 "MAKE_NB_JOBS=0" ;use jobserver for submakes
3134 ;; This is the maximum number of threads OpenBLAS will ever use (that
3135 ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS
3136 ;; is used.) If we don't set it, the makefile sets it to the number
3137 ;; of cores of the build machine, which is obviously wrong.
3140 ;; Build the library for all supported CPUs. This allows
3141 ;; switching CPU targets at runtime with the environment variable
3142 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
3143 ;; Unfortunately, this is not supported on non-x86 architectures,
3144 ;; where it leads to failed builds.
3145 ,@(let ((system (or (%current-target-system) (%current-system))))
3147 ((or (string-prefix? "x86_64" system)
3148 (string-prefix? "i686" system))
3149 '("DYNAMIC_ARCH=1"))
3150 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
3151 ;; two available MIPS targets special extended instructions
3152 ;; for Loongson cores are used.
3153 ((string-prefix? "mips" system)
3154 '("TARGET=SICORTEX"))
3155 ;; On aarch64 force the generic 'armv8-a' target
3156 ((string-prefix? "aarch64" system)
3159 ;; no configure script
3161 (modify-phases %standard-phases
3163 (add-before 'build 'set-extralib
3164 (lambda* (#:key inputs #:allow-other-keys)
3165 ;; Get libgfortran found when building in utest.
3167 (string-append "-L" (assoc-ref inputs "fortran-lib")
3171 `(("fortran-lib" ,gfortran "lib")))
3174 ("fortran" ,gfortran)
3176 (home-page "http://www.openblas.net/")
3177 (synopsis "Optimized BLAS library based on GotoBLAS")
3179 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
3180 (license license:bsd-3)))
3182 (define-public openblas-ilp64
3183 (package/inherit openblas
3184 (name "openblas-ilp64")
3185 (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
3187 (substitute-keyword-arguments (package-arguments openblas)
3188 ((#:make-flags flags '())
3189 `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
3191 (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
3192 (license license:bsd-3)))
3194 (define* (make-blis implementation #:optional substitutable?)
3195 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
3196 source tree for a list of implementations.)
3198 SUBSTITUTABLE? determines whether the package is made available as a
3201 Currently the specialization must be selected at configure-time, but work is
3202 underway to allow BLIS to select the right optimized kernels at run time:
3203 <https://github.com/flame/blis/issues/129>."
3205 (name (if (string=? implementation "reference")
3207 (string-append "blis-" implementation)))
3209 (home-page "https://github.com/flame/blis")
3212 (uri (git-reference (url home-page) (commit version)))
3215 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
3216 (file-name (git-file-name "blis" version))))
3217 (build-system gnu-build-system)
3219 `(#:test-target "test"
3221 #:substitutable? ,substitutable?
3223 #:phases (modify-phases %standard-phases
3225 (lambda* (#:key outputs #:allow-other-keys)
3226 ;; This is a home-made 'configure' script.
3227 (let ((out (assoc-ref outputs "out")))
3228 (invoke "./configure" "-p" out
3232 "--enable-threading=openmp"
3235 (add-before 'check 'show-test-output
3237 ;; By default "make check" is silent. Make it verbose.
3238 (system "tail -F output.testsuite &")
3240 (synopsis "High-performance basic linear algebra (BLAS) routines")
3242 "BLIS is a portable software framework for instantiating high-performance
3243 BLAS-like dense linear algebra libraries. The framework was designed to
3244 isolate essential kernels of computation that, when optimized, immediately
3245 enable optimized implementations of most of its commonly used and
3246 computationally intensive operations. While BLIS exports a new BLAS-like API,
3247 it also includes a BLAS compatibility layer which gives application developers
3248 access to BLIS implementations via traditional BLAS routine calls.")
3249 (license license:bsd-3)))
3252 ;; This is the "reference" implementation, which is the non-optimized but
3253 ;; portable variant (no assembly).
3254 (make-blis "reference" #t))
3256 (define ignorance blis)
3258 (define-syntax-rule (blis/x86_64 processor)
3259 "Expand to a package specialized for PROCESSOR."
3261 (inherit (make-blis processor))
3262 (supported-systems '("x86_64-linux"))))
3264 (define-public blis-sandybridge
3265 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
3266 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
3267 (blis/x86_64 "sandybridge"))
3269 (define-public blis-haswell
3270 ;; BLIS specialized for Haswell processors (launched 2013):
3271 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
3272 (blis/x86_64 "haswell"))
3274 (define-public blis-knl
3275 ;; BLIS specialized for Knights Landing processor (launched 2016):
3276 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
3277 (blis/x86_64 "knl"))
3280 (define-public openlibm
3288 (url "https://github.com/JuliaLang/openlibm.git")
3289 (commit (string-append "v" version))))
3290 (file-name (git-file-name name version))
3292 (base32 "08wfchmmr5200fvmn1kwq9byc1fhsq46hn0y5k8scdl74771c7gh"))))
3293 (build-system gnu-build-system)
3296 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3298 ;; no configure script
3299 (modify-phases %standard-phases (delete 'configure))
3300 #:tests? #f)) ;the tests are part of the default target
3301 (home-page "http://openlibm.org/")
3302 (synopsis "Portable C mathematical library (libm)")
3304 "OpenLibm is an effort to have a high quality, portable, standalone C
3305 mathematical library (libm). It can be used standalone in applications and
3306 programming language implementations. The project was born out of a need to
3307 have a good libm for the Julia programming language that worked consistently
3308 across compilers and operating systems, and in 32-bit and 64-bit
3310 ;; Each architecture has its own make target, and there is none for mips.
3311 (supported-systems (delete "mips64el-linux" %supported-systems))
3312 ;; See LICENSE.md for details.
3313 (license (list license:expat
3316 license:public-domain
3317 license:lgpl2.1+))))
3319 (define-public openspecfun
3321 (name "openspecfun")
3327 (url "https://github.com/JuliaLang/openspecfun.git")
3328 (commit (string-append "v" version))))
3329 (file-name (git-file-name name version))
3331 (base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh"))))
3332 (build-system gnu-build-system)
3334 '(#:tests? #f ; no "check" target
3336 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3338 (modify-phases %standard-phases
3339 (delete 'configure)))) ; no configure script
3341 `(("fortran" ,gfortran)))
3342 (home-page "https://github.com/JuliaLang/openspecfun")
3343 (synopsis "Collection of special mathematical functions")
3345 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
3346 portable package for Bessel Functions of a Complex Argument and Nonnegative
3347 Order; it contains subroutines for computing Bessel functions and Airy
3348 functions. Faddeeva allows computing the various error functions of arbitrary
3349 complex arguments (Faddeeva function, error function, complementary error
3350 function, scaled complementary error function, imaginary error function, and
3351 Dawson function); given these, one can also easily compute Voigt functions,
3352 Fresnel integrals, and similar related functions as well.")
3353 ;; Faddeeva is released under the Expat license; AMOS is included as
3354 ;; public domain software.
3355 (license (list license:expat license:public-domain))))
3357 (define-public suitesparse
3359 (name "suitesparse")
3365 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
3369 "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
3370 (modules '((guix build utils)))
3372 ;; Remove bundled metis source
3374 (delete-file-recursively "metis-5.1.0")
3376 (build-system gnu-build-system)
3378 '(#:tests? #f ;no "check" target
3383 "MY_METIS_LIB=-lmetis"
3384 (string-append "INSTALL_LIB="
3385 (assoc-ref %outputs "out") "/lib")
3386 (string-append "INSTALL_INCLUDE="
3387 (assoc-ref %outputs "out") "/include")
3390 (modify-phases %standard-phases
3391 (delete 'configure)))) ;no configure script
3396 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
3397 (synopsis "Suite of sparse matrix software")
3399 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
3400 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
3401 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
3402 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
3403 CXSparse, a concise sparse Cholesky factorization package; and many other
3406 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
3408 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
3409 (license (list license:gpl2+ license:lgpl2.1+))))
3411 (define-public atlas
3417 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
3418 version "/atlas" version ".tar.bz2"))
3421 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
3422 (build-system gnu-build-system)
3423 (home-page "http://math-atlas.sourceforge.net/")
3424 (inputs `(("gfortran" ,gfortran)
3425 ("lapack-tar" ,(package-source lapack))))
3426 (outputs '("out" "doc"))
3427 ;; For the moment we drop support for MIPS at it fails to compile. See
3428 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
3429 (supported-systems (delete "mips64el-linux" %supported-systems))
3431 `(#:parallel-build? #f
3432 #:parallel-tests? #f
3434 ;; ATLAS tunes itself for the machine it is built on, as explained at
3435 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
3436 ;; For this reason, we want users to build it locally instead of using
3440 #:modules ((srfi srfi-26)
3441 (guix build gnu-build-system)
3444 `(;; Generate position independent code suitable for dynamic libraries
3445 ;; and use WALL timer to get more accurate timing.
3446 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
3449 ,,(if (string-match "64" (%current-system))
3452 ;; Disable parallel build as it gives errors: atlas_pthread.h is
3453 ;; needed to compile C files before it is generated.
3454 "-Ss" "pmake" "make -j 1"
3455 ;; Probe is failing for MIPS. We therefore define the system
3456 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3457 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3458 ,,@(if (string-prefix? "mips" (%current-system))
3459 (list "-A" "49" "-V" "1")
3461 ;; Generate shared libraries.
3463 ;; Build a full LAPACK library.
3464 ,(string-append "--with-netlib-lapack-tarfile="
3465 (assoc-ref %build-inputs "lapack-tar")))
3467 (modify-phases %standard-phases
3468 (add-after 'install 'install-doc
3469 (lambda* (#:key outputs inputs #:allow-other-keys)
3470 (let ((doc (string-append (assoc-ref outputs "doc")
3471 "/share/doc/atlas")))
3473 (for-each (cut install-file <> doc)
3474 (find-files "../ATLAS/doc" ".*"))
3476 (add-after 'check 'check-pt
3477 (lambda _ (invoke "make" "ptcheck")))
3478 ;; Fix files required to run configure.
3479 (add-before 'configure 'fix-/bin/sh
3481 ;; Use `sh', not `/bin/sh'.
3482 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3486 ;; Fix /bin/sh in generated make files.
3487 (add-after 'configure 'fix-/bin/sh-in-generated-files
3489 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3493 ;; ATLAS configure program does not accepts the default flags
3494 ;; passed by the 'gnu-build-system'.
3496 (lambda* (#:key native-inputs inputs outputs
3497 (configure-flags '())
3498 #:allow-other-keys #:rest args)
3499 (let* ((prefix (assoc-ref outputs "out"))
3500 (bash (or (and=> (assoc-ref
3501 (or native-inputs inputs) "bash")
3502 (cut string-append <> "/bin/bash"))
3504 (flags `(,(string-append "--prefix=" prefix)
3506 (abs-srcdir (getcwd))
3507 (srcdir (string-append "../" (basename abs-srcdir))))
3508 (format #t "source directory: ~s (relative from build: ~s)~%"
3512 (format #t "build directory: ~s~%" (getcwd))
3513 (format #t "configure flags: ~s~%" flags)
3515 (string-append srcdir "/configure")
3517 (synopsis "Automatically Tuned Linear Algebra Software")
3519 "ATLAS is an automatically tuned linear algebra software library
3520 providing C and Fortran77 interfaces to a portably efficient BLAS
3521 implementation, as well as a few routines from LAPACK.
3523 Optimization occurs at build time. For this reason, the library is built on
3524 the machine where it is installed, without resorting to pre-built substitutes.
3526 Before building the library, CPU throttling should be disabled. This can be
3527 done in the BIOS, or, on GNU/Linux, with the following command:
3530 # cpupower --governor performance
3533 Failure to do so will result in a library with poor performance.")
3534 (license license:bsd-3)))
3543 (uri (string-append "https://github.com/g-truc/glm/releases/download/"
3544 version "/glm-" version ".zip"))
3546 (base32 "1l0pi1qi37mk6s0yrkrw07lspv4gcqnr9ryg3521hrl77ff37dwx"))
3547 (patches (search-patches "glm-restore-install-target.patch"))))
3548 (build-system cmake-build-system)
3550 `(("unzip" ,unzip)))
3551 (home-page "https://glm.g-truc.net/")
3552 (synopsis "OpenGL Mathematics library")
3553 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3554 library for graphics software based on the OpenGL Shading Language (GLSL)
3556 (license license:expat)))
3558 (define-public lpsolve
3565 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3566 "/lp_solve_" version "_source.tar.gz"))
3569 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
3570 (modules '((guix build utils)))
3573 (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3575 ;; Pretend to be on a 64 bit platform to obtain a common directory
3576 ;; name for the build results on all architectures; nothing else
3577 ;; seems to depend on it.
3578 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3580 ;; The check for 'isnan' as it is written fails with
3581 ;; "non-floating-point argument in call to function
3582 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3583 ;; definition, which in turn leads to bad things. Fix the feature
3585 (("isnan\\(0\\)") "isnan(0.)"))
3587 (build-system gnu-build-system)
3589 `(#:tests? #f ; no check target
3591 (modify-phases %standard-phases
3592 (delete 'configure) ; no configure script
3595 (with-directory-excursion "lpsolve55"
3596 (invoke "bash" "ccc"))
3597 (with-directory-excursion "lp_solve"
3598 (invoke "bash" "ccc"))
3601 (lambda* (#:key outputs #:allow-other-keys)
3602 (let* ((out (assoc-ref outputs "out"))
3603 (bin (string-append out "/bin"))
3604 (lib (string-append out "/lib"))
3605 ;; This is where LibreOffice expects to find the header
3606 ;; files, and where they are installed by Debian.
3607 (include (string-append out "/include/lpsolve")))
3608 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3609 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
3610 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3612 ;; Install a subset of the header files as on Debian
3613 ;; (plus lp_bit.h, which matches the regular expression).
3614 (for-each (lambda (name)
3615 (install-file name include))
3616 (find-files "." "lp_[HMSa-z].*\\.h$"))
3617 (with-directory-excursion "shared"
3618 (for-each (lambda (name)
3619 (install-file name include))
3620 (find-files "." "\\.h$")))
3622 (home-page "http://lpsolve.sourceforge.net/")
3623 (synopsis "Mixed integer linear programming (MILP) solver")
3625 "lp_solve is a mixed integer linear programming solver based on the
3626 revised simplex and the branch-and-bound methods.")
3627 (license license:lgpl2.1+)))
3629 (define-public dealii
3636 (uri (string-append "https://github.com/dealii/dealii/releases/"
3637 "download/v" version "/dealii-" version ".tar.gz"))
3640 "0xhjv0gzswpjbc43xbrpwfc5848g508l01855nszx3g5gwzlhnzw"))
3641 (modules '((guix build utils)))
3643 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
3645 (delete-file-recursively "bundled")
3647 (build-system cmake-build-system)
3655 ("arpack" ,arpack-ng)
3656 ("muparser" ,muparser)
3657 ("gfortran" ,gfortran)
3658 ("suitesparse" ,suitesparse))) ;for UMFPACK
3660 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
3662 ;; Work around a bug in libsuitesparseconfig linking
3663 ;; see https://github.com/dealii/dealii/issues/4745
3664 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
3665 (home-page "https://www.dealii.org")
3666 (synopsis "Finite element library")
3668 "Deal.II is a C++ program library targeted at the computational solution
3669 of partial differential equations using adaptive finite elements. The main
3670 aim of deal.II is to enable rapid development of modern finite element codes,
3671 using among other aspects adaptive meshes and a wide array of tools often used
3672 in finite element programs.")
3673 (license license:lgpl2.1+)))
3675 (define-public dealii-openmpi
3676 (package (inherit dealii)
3677 (name "dealii-openmpi")
3680 ;;Supported only with MPI:
3681 ("hdf5" ,hdf5-parallel-openmpi) ;TODO: have petsc-openmpi propagate?
3682 ("p4est" ,p4est-openmpi)
3683 ("petsc" ,petsc-openmpi)
3684 ("slepc" ,slepc-openmpi)
3685 ("metis" ,metis) ;for MUMPS
3686 ("scalapack" ,scalapack) ;for MUMPS
3687 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3688 ("arpack" ,arpack-ng-openmpi)
3689 ,@(fold alist-delete (package-inputs dealii)
3690 '("p4est" "arpack"))))
3692 (substitute-keyword-arguments (package-arguments dealii)
3693 ((#:configure-flags cf)
3694 `(cons "-DDEAL_II_WITH_MPI:BOOL=ON"
3696 ((#:phases phases '%standard-phases)
3697 `(modify-phases ,phases
3698 (add-before 'check 'mpi-setup
3699 ,%openmpi-setup)))))
3700 (synopsis "Finite element library (with MPI support)")))
3702 (define-public flann
3711 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3712 version "-src.zip"))
3715 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
3716 (patches (search-patches "flann-cmake-3.11.patch"))))
3717 (build-system cmake-build-system)
3719 "octave")) ;46 MiB .mex file that pulls Octave
3721 `(("unzip" ,unzip)))
3724 ("octave" ,octave-cli)
3725 ("python" ,python-2) ; print syntax
3726 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3729 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3730 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3731 #:strip-directories '("lib" "lib64" "libexec"
3732 "bin" "sbin" "share/flann/octave")
3734 ;; Save 12 MiB by not installing .a files. Passing
3735 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3736 #:phases (modify-phases %standard-phases
3737 (add-before 'configure 'set-octave-directory
3738 (lambda* (#:key outputs #:allow-other-keys)
3739 ;; Install the .mex file in the "octave" output.
3740 (let ((out (assoc-ref outputs "octave")))
3741 (substitute* "src/matlab/CMakeLists.txt"
3742 (("share/flann/octave")
3743 (string-append out "/share/flann/octave")))
3745 (add-after 'install 'remove-static-libraries
3746 (lambda* (#:key outputs #:allow-other-keys)
3747 (let* ((out (assoc-ref outputs "out"))
3748 (lib (string-append out "/lib")))
3749 (for-each delete-file
3750 (find-files lib "\\.a$"))
3753 #:tests? #f)) ; The test data are downloaded from the Internet.
3754 (home-page "http://www.cs.ubc.ca/research/flann/")
3755 (synopsis "Library for approximate nearest neighbors computation")
3756 (description "FLANN is a library for performing fast approximate
3757 nearest neighbor searches in high dimensional spaces. It implements a
3758 collection of algorithms and a system for automatically choosing the best
3759 algorithm and optimum parameters depending on the dataset.
3761 FLANN is written in C++ and contains bindings for C, Octave and Python.")
3762 (license (license:non-copyleft "file://COPYING"
3763 "See COPYING in the distribution."))))
3765 (define-public wcalc
3772 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3773 "wcalc-" version ".tar.bz2"))
3776 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3777 (build-system gnu-build-system)
3780 ("readline" ,readline)))
3781 (home-page "http://w-calc.sourceforge.net/index.php")
3782 (synopsis "Flexible command-line scientific calculator")
3783 (description "Wcalc is a very capable calculator. It has standard functions
3784 (sin, asin, and sinh for example, in either radians or degrees), many
3785 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3786 variables, a command history, hex/octal/binary input and output, unit
3787 conversions, embedded comments, and an expandable expression entry field. It
3788 evaluates expressions using the standard order of operations.")
3789 (license license:gpl2+)))
3797 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3798 "/xaos-" version ".tar.gz"))
3801 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3802 (build-system gnu-build-system)
3803 (native-inputs `(("gettext" ,gettext-minimal)))
3804 (inputs `(("libx11" ,libx11)
3809 `(#:tests? #f ;no "check" target
3810 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3811 (synopsis "Real-time fractal zoomer")
3812 (description "GNU XaoS is a graphical program that generates fractal
3813 patterns and allows you to zoom in and out of them infinitely in a fluid,
3814 continuous manner. It also includes tutorials that help to explain how fractals
3815 are built. It can generate many different fractal types such as the Mandelbrot
3817 (home-page "https://www.gnu.org/software/xaos/")
3818 (license license:gpl2+)))
3820 (define-public hypre
3828 (url "https://github.com/LLNL/hypre.git")
3829 (commit (string-append "v" version))))
3830 (file-name (git-file-name name version))
3832 (base32 "1lvh4ybqkriyqfg2zmic6mrg1981qv1i9vry1fdgsabn81hb71g4"))
3833 (modules '((guix build utils)))
3836 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
3837 ;; substitute the release date.
3838 (substitute* "src/utilities/HYPRE_utilities.h"
3839 (("Date Compiled: .*$")
3840 "Date Compiled: Oct 19 2018 15:23:00 +0000\"\n"))
3842 (build-system gnu-build-system)
3843 (outputs '("out" ; 6.1 MiB of headers and libraries
3844 "doc")) ; 4.8 MiB of documentation
3848 ("perl" ,perl) ; needed to run 'ppmquant' during tests
3849 ("texlive" ,(texlive-union (list texlive-xypic
3851 texlive-latex-hyperref
3853 ("ghostscript" ,ghostscript)))
3855 `(("blas" ,openblas)
3856 ("lapack" ,lapack)))
3858 `(#:modules ((srfi srfi-1)
3859 ,@%gnu-build-system-modules)
3860 #:configure-flags '("--enable-shared"
3868 (modify-phases %standard-phases
3869 (add-before 'build 'set-HOME
3871 ;; FIXME: texlive-union does not find the built
3872 ;; metafonts, so it tries to generate them in HOME.
3873 (setenv "HOME" "/tmp")
3875 (add-before 'configure 'chdir-src
3876 (lambda _ (chdir "src")))
3878 (lambda* (#:key build target configure-flags
3879 #:allow-other-keys #:rest args)
3880 (let* ((configure (assoc-ref %standard-phases 'configure)))
3883 (list #:configure-flags
3884 (cons (string-append
3885 "--host=" (or target build))
3886 configure-flags)))))))
3887 (add-after 'build 'build-docs
3889 (invoke "make" "-Cdocs" "pdf" "html")))
3892 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3893 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
3894 (invoke "make" "check" "CHECKRUN=")
3895 (for-each (lambda (filename)
3896 (let ((size (stat:size (stat filename))))
3897 (when (positive? size)
3898 (error (format #f "~a size ~d; error indication~%"
3900 (find-files "test" ".*\\.err$"))
3902 (add-after 'install 'install-docs
3903 (lambda* (#:key outputs #:allow-other-keys)
3904 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3905 (let* ((doc (assoc-ref outputs "doc"))
3906 (docdir (string-append doc "/share/doc/hypre-" ,version)))
3907 (with-directory-excursion "docs"
3908 (for-each (lambda (base)
3909 (install-file (string-append base ".pdf") docdir)
3910 (copy-recursively base docdir)) ; html docs
3911 '("HYPRE_usr_manual"
3912 "HYPRE_ref_manual")))
3914 (home-page "http://www.llnl.gov/casc/hypre/")
3915 (synopsis "Library of solvers and preconditioners for linear equations")
3917 "HYPRE is a software library of high performance preconditioners and
3918 solvers for the solution of large, sparse linear systems of equations. It
3919 features multigrid solvers for both structured and unstructured grid
3921 (license license:lgpl2.1)))
3923 (define-public hypre-openmpi
3924 (package (inherit hypre)
3925 (name "hypre-openmpi")
3928 ,@(package-inputs hypre)))
3930 (substitute-keyword-arguments (package-arguments hypre)
3931 ((#:configure-flags flags)
3933 ,@(delete "--without-MPI" ,flags)))
3935 `(modify-phases ,phases
3936 (add-before 'check 'mpi-setup
3937 ,%openmpi-setup)))))
3938 (synopsis "Parallel solvers and preconditioners for linear equations")
3940 "HYPRE is a software library of high performance preconditioners and
3941 solvers for the solution of large, sparse linear systems of equations on
3942 parallel computers. It features parallel multigrid solvers for both
3943 structured and unstructured grid problems.")))
3945 (define-public matio
3952 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
3953 "matio-" version ".tar.gz"))
3956 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3957 (build-system gnu-build-system)
3961 (home-page "http://matio.sourceforge.net/")
3962 (synopsis "Library for reading and writing MAT files")
3963 (description "Matio is a library for reading and writing MAT files. It
3964 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3965 (license license:bsd-2)))
3972 (origin (method url-fetch)
3973 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3974 "download/" version "/Vc-" version ".tar.gz"))
3977 "17qili8bf8r78cng65yf4qmgna8kiqjqbgcqbric6v9j6nkhkrk8"))))
3978 (build-system cmake-build-system)
3981 '("-DBUILD_TESTING=ON"
3982 ;; By default, Vc will optimize for the CPU of the build machine.
3983 ;; Setting this to "none" makes it create portable binaries. See
3984 ;; "cmake/OptimizeForArchitecture.cmake".
3985 "-DTARGET_ARCHITECTURE=none")
3986 #:phases (modify-phases %standard-phases
3987 (add-after 'unpack 'copy-testdata
3988 (lambda* (#:key inputs native-inputs #:allow-other-keys)
3989 (let ((testdata (assoc-ref (or native-inputs inputs)
3991 (copy-recursively testdata "tests/testdata")
3994 `(("virtest" ,virtest)
3996 ;; This is a submodule in the git project, but not part of the
3997 ;; released sources. See the git branch for the commit to take.
3998 ("testdata" ,(let ((commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3"))
4002 (url "https://github.com/VcDevel/vc-testdata")
4003 (commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3")))
4004 (file-name (git-file-name "vc-testdata"
4005 (string-take commit 7)))
4008 "1hkhqib03qlcq412ym2dciynfxcdr2ygqhnplz4l1vissr1wnqn2")))))))
4009 (synopsis "SIMD vector classes for C++")
4010 (description "Vc provides portable, zero-overhead C++ types for explicitly
4011 data-parallel programming. It is a library designed to ease explicit
4012 vectorization of C++ code. Its types enable explicitly stating data-parallel
4013 operations on multiple values. The parallelism is therefore added via the type
4014 system. Vc has an intuitive API and provides portability between different
4015 compilers and compiler versions as well as portability between different vector
4016 instruction sets. Thus, an application written with Vc can be compiled for:
4019 @item SSE2 up to SSE4.2 or SSE4a
4022 @item NEON (in development)
4023 @item NVIDIA GPUs / CUDA (in development)
4025 (home-page "https://github.com/VcDevel/Vc")
4026 ;; "No support_???.cpp file exists for this architecture."
4027 (supported-systems '("x86_64-linux" "i686-linux"))
4028 (license license:bsd-3)))
4030 (define-public reducelcs
4031 ;; This is the last commit which is available upstream, no
4032 ;; release happened since 2010.
4033 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
4037 (version (string-append "1.0-" revision "." (string-take commit 7)))
4042 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
4044 (file-name (string-append name "-" version "-checkout"))
4047 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
4048 (build-system gnu-build-system)
4050 `(("openlibm" ,openlibm)))
4052 `(#:tests? #f ; no tests
4054 (modify-phases %standard-phases
4055 (delete 'configure) ; No configure script exists.
4056 (replace 'install ; No install phase exists.
4057 (lambda* (#:key outputs #:allow-other-keys)
4058 (let* ((out (assoc-ref outputs "out"))
4059 (bin (string-append out "/bin")))
4060 (install-file "Approximation" bin)
4061 (install-file "CollectResults" bin)
4062 (install-file "GenerateInstances" bin)
4064 (synopsis "Approximate Longest Commons Subsequence computation tool")
4066 "@code{reduceLCS} is an implementation of the Reduce-Expand
4067 algorithm for LCS. It is a fast program to compute the approximate
4068 Longest Commons Subsequence of a set of strings.")
4069 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
4070 (license license:gpl3+))))
4072 (define-public jacal
4079 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
4082 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
4083 (patches (search-patches "jacal-fix-texinfo.patch"))))
4084 (build-system gnu-build-system)
4087 (modify-phases %standard-phases
4088 (add-before 'build 'pre-build
4089 ;; Don't use upstream's script - it really doesn't fit into
4090 ;; Guix's functional paradigm.
4091 (lambda* (#:key inputs outputs #:allow-other-keys)
4092 (substitute* "Makefile"
4093 (("^install: install-script") "install: "))))
4094 (add-after 'install 'post-install
4095 ;; Instead, we provide our own simplified script.
4096 (lambda* (#:key inputs outputs #:allow-other-keys)
4097 (let ((wrapper (string-append (assoc-ref outputs "out")
4099 (format (open wrapper (logior O_WRONLY O_CREAT))
4100 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
4101 "-e '(slib:load \"~a/lib/jacal/math\") "
4104 (assoc-ref inputs "scm")
4105 (assoc-ref outputs "out"))
4106 (chmod wrapper #o555))))
4108 (lambda* (#:key outputs #:allow-other-keys)
4109 (invoke "./configure"
4110 (string-append "--prefix="
4111 (assoc-ref outputs "out"))))))))
4112 (inputs `(("scm" ,scm)))
4113 (native-inputs `(("unzip" ,unzip)
4114 ("texinfo" ,texinfo)))
4115 (synopsis "Symbolic mathematics system")
4116 (description "GNU JACAL is an interactive symbolic mathematics program based on
4117 Scheme. It manipulate and simplify a range of mathematical expressions such
4118 as equations, scalars, vectors, and matrices.")
4119 (home-page "https://www.gnu.org/software/jacal/")
4120 (license license:gpl3+)))
4126 (home-page "https://github.com/Z3Prover/z3")
4129 (uri (git-reference (url home-page)
4130 (commit (string-append "z3-" version))))
4131 (file-name (git-file-name name version))
4134 "0hprcdwhhyjigmhhk6514m71bnmvqci9r8gglrqilgx424r6ff7q"))))
4135 (build-system gnu-build-system)
4138 (modify-phases %standard-phases
4139 (add-after 'unpack 'fix-compatability
4140 ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
4142 (substitute* "src/util/mpz.cpp"
4143 (("#include <immintrin.h>") ""))
4145 (add-before 'configure 'bootstrap
4147 (invoke "python" "scripts/mk_make.py")))
4148 ;; work around gnu-build-system's setting --enable-fast-install
4149 ;; (z3's `configure' is a wrapper around the above python file,
4150 ;; which fails when passed --enable-fast-install)
4152 (lambda* (#:key inputs outputs #:allow-other-keys)
4153 (invoke "./configure"
4154 (string-append "--prefix=" (assoc-ref outputs "out")))))
4155 (add-after 'configure 'change-directory
4159 (add-before 'check 'make-test-z3
4161 ;; Build the test suite executable.
4162 (invoke "make" "test-z3" "-j"
4163 (number->string (parallel-job-count)))))
4166 ;; Run all the tests that don't require arguments.
4167 (invoke "./test-z3" "/a"))))))
4170 ("python" ,python-wrapper)))
4171 (synopsis "Theorem prover")
4172 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
4173 theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
4174 (license license:expat)))
4179 (version "2018.11.001")
4182 (uri (string-append "http://elpa.mpcdf.mpg.de/html/Releases/"
4183 version "/elpa-" version ".tar.gz"))
4186 "05hv3v5i6xmziaizw350ff72y1c3k662r85fm3xfdrkclj5zw9yc"))))
4187 (build-system gnu-build-system)
4189 `(("fortran" ,gfortran)
4190 ("perl" ,perl))) ;for configure and deps
4192 `(("blas" ,openblas)))
4197 ;; ELPA unfortunately does not support runtime dispatch, so we can
4198 ;; only enable the "generic" kernels. See the "Cross compilation"
4199 ;; section of INSTALL.md.
4201 "--disable-sse" "--disable-sse-assembly" ;Require SSE3
4202 "--disable-avx" "--disable-avx2" "--disable-avx512"
4203 ,(string-append "CFLAGS=-O3 "
4204 "-funsafe-loop-optimizations -funsafe-math-optimizations "
4205 "-ftree-vect-loop-version -ftree-vectorize "
4206 ,(let ((system (or (%current-target-system)
4207 (%current-system))))
4209 ((or (string-prefix? "x86_64" system)
4210 (string-prefix? "i686" system))
4213 #:parallel-tests? #f ;tests are multi-threaded, via BLAS
4215 (modify-phases %standard-phases
4216 (add-before 'configure 'patch-header-generation
4218 (substitute* "configure"
4219 (("^ *make.*top_srcdir=\"\\$srcdir\"" &)
4220 (string-append & " CPP=\"$CPP\"")))
4222 (add-before 'check 'setup-tests
4224 ;; Decrease test time and RAM use by computing fewer eigenvalues.
4225 ;; The flags are (MATRIX-SIZE, EIGENVALUES, BLOCK-SIZE), where
4226 ;; the default is (500, 250, 16) for C tests and (5000, 150, 16)
4227 ;; for Fortran. This also causes several tests to pass that
4228 ;; otherwise would otherwise fail with matrix size 5000; possibly
4229 ;; due to floating point tolerances that are too tight.
4230 (setenv "TEST_FLAGS" "1500 50 16") ;from elpa.spec
4231 (setenv "OMP_NUM_THREADS" (number->string (parallel-job-count)))
4232 (substitute* "Makefile"
4233 ;; Test scripts are generated, patch the shebang
4234 (("#!/bin/bash") (string-append "#!" (which "sh"))))
4236 (home-page "http://elpa.mpcdf.mpg.de")
4237 (synopsis "Eigenvalue solvers for symmetric matrices")
4239 "The ELPA library provides efficient and scalable direct eigensolvers for
4240 symmetric matrices.")
4241 (license license:lgpl3)))
4243 (define-public elpa-openmpi
4244 (package (inherit elpa)
4245 (name "elpa-openmpi")
4248 ("scalapack" ,scalapack)
4249 ,@(package-inputs elpa)))
4251 (substitute-keyword-arguments (package-arguments elpa)
4252 ((#:configure-flags cf '())
4253 `(cons "--with-mpi=yes" (delete "--with-mpi=no" ,cf)))
4254 ((#:phases phases '%standard-phases)
4255 `(modify-phases ,phases
4256 (add-before 'check 'mpi-setup
4258 ;; Tests use 2 mpi tasks by default, use our remaining build
4259 ;; cores as OpenMP threads.
4260 (setenv "OMP_NUM_THREADS" (number->string
4261 (max (quotient (parallel-job-count) 2)
4263 (,%openmpi-setup)))))))
4264 (synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)")))
4266 (define-public elemental
4273 (url "https://github.com/elemental/Elemental.git")
4274 (commit (string-append "v" version))))
4275 (file-name (git-file-name name version))
4278 "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
4279 (build-system cmake-build-system)
4280 (home-page "https://github.com/elemental/Elemental")
4282 `(("gfortran" ,gfortran)))
4284 `(("blas" ,openblas)
4285 ("gfortran:lib" ,gfortran "lib")
4294 `(#:build-type "Release" ;default RelWithDebInfo not supported
4295 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
4296 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
4297 "-DEL_CACHE_WARNINGS:BOOL=YES"
4298 "-DEL_TESTS:BOOL=YES"
4299 "-DCMAKE_INSTALL_LIBDIR=lib"
4300 "-DGFORTRAN_LIB=gfortran")
4301 #:phases (modify-phases %standard-phases
4302 (add-before 'check 'mpi-setup
4304 (add-before 'check 'setup-tests
4306 ;; Parallelism is done at the MPI layer.
4307 (setenv "OMP_NUM_THREADS" "1")
4309 (add-after 'install 'remove-tests
4310 (lambda* (#:key outputs #:allow-other-keys)
4311 ;; Tests are installed, with no easy configuration
4312 ;; switch to prevent this, so delete them.
4313 (delete-file-recursively
4314 (string-append (assoc-ref outputs "out") "/bin"))
4316 (synopsis "Dense and sparse-direct linear algebra and optimization")
4317 (description "Elemental is a modern C++ library for distributed-memory
4318 dense and sparse-direct linear algebra, conic optimization, and lattice
4320 (license license:bsd-2)))
4322 (define-public mcrl2
4325 (version "201908.0")
4329 "https://www.mcrl2.org/download/release/mcrl2-"
4333 "1i4xgl2d5fgiz1mwi50cyfkrrcpm8nxfayfjgmhq7chs58wlhfsz"))))
4338 ("qtbase" ,qtbase)))
4339 (build-system cmake-build-system)
4340 (synopsis "Toolset for the mCRL2 formal specification language")
4342 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
4343 specification language for describing concurrent discrete event systems. Its
4344 toolset supports analysis and automatic verification, linearisation, simulation,
4345 state-space exploration and generation, and tools to optimise and analyse
4346 specifications. Also, state spaces can be manipulated, visualised and
4348 (home-page "https://mcrl2.org")
4349 (license license:boost1.0)))
4351 (define-public mcrl2-minimal
4354 (name "mcrl2-minimal")
4356 `(("boost" ,boost)))
4358 '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
4360 (define-public tcalc
4367 (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
4371 "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
4372 (build-system gnu-build-system)
4373 (synopsis "The terminal calculator")
4375 "The terminal calculator is a small program to help users of the GNU/Linux
4376 terminal do calculations simply and quickly. The formula to be calculated can
4377 be fed to @command{tcalc} through the command line.")
4378 (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
4379 (license license:gpl3+)))
4381 (define-public sundials
4388 (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
4389 "sundials-" version ".tar.gz"))
4392 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
4393 (build-system cmake-build-system)
4395 `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
4397 `(("fortran" ,gfortran) ;for fcmix
4399 ("suitesparse" ,suitesparse))) ;TODO: Add hypre
4401 `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
4402 "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
4403 "-DEXAMPLES_ENABLE_F77:BOOL=ON"
4404 "-DEXAMPLES_ENABLE_F90:BOOL=ON"
4405 "-DEXAMPLES_INSTALL:BOOL=OFF"
4407 "-DFCMIX_ENABLE:BOOL=ON"
4409 "-DKLU_ENABLE:BOOL=ON"
4410 ,(string-append "-DKLU_INCLUDE_DIR="
4411 (assoc-ref %build-inputs "suitesparse")
4413 ,(string-append "-DKLU_LIBRARY_DIR="
4414 (assoc-ref %build-inputs "suitesparse")
4416 (home-page "https://computation.llnl.gov/projects/sundials")
4417 (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
4418 (description "SUNDIALS is a family of software packages implemented with
4419 the goal of providing robust time integrators and nonlinear solvers that can
4420 easily be incorporated into existing simulation codes.")
4421 (license license:bsd-3)))
4423 (define-public sundials-openmpi
4424 (package (inherit sundials)
4425 (name "sundials-openmpi")
4428 ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
4429 ,@(package-inputs sundials)))
4431 (substitute-keyword-arguments (package-arguments sundials)
4432 ((#:configure-flags flags '())
4433 `(cons* "-DMPI_ENABLE:BOOL=ON"
4434 "-DPETSC_ENABLE:BOOL=ON"
4435 (string-append "-DPETSC_INCLUDE_DIR="
4436 (assoc-ref %build-inputs "petsc")
4438 (string-append "-DPETSC_LIBRARY_DIR="
4439 (assoc-ref %build-inputs "petsc")
4442 ((#:phases phases '%standard-phases)
4443 `(modify-phases ,phases
4444 (add-before 'check 'mpi-setup
4445 ,%openmpi-setup)))))
4446 (synopsis "SUNDIALS with OpenMPI support")))
4448 (define-public combinatorial-blas
4450 (name "combinatorial-blas")
4455 (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/"
4457 (match (string-split version #\.)
4458 ((major minor patch)
4459 (string-append major minor "_" patch))) ;e.g. "16_2"
4463 "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a"))
4464 (patches (search-patches "combinatorial-blas-awpm.patch"
4465 "combinatorial-blas-io-fix.patch"))))
4466 (build-system cmake-build-system)
4469 ("test-data" ,(origin
4471 (uri (string-append "https://people.eecs.berkeley.edu/~aydin/"
4472 "CombBLAS_FILES/testdata_combblas1.6.1.tgz"))
4475 "01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87"))))))
4477 `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
4478 "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL")
4479 #:parallel-tests? #f ;tests use 'mpiexec -n4'
4481 (modify-phases %standard-phases
4482 (add-before 'check 'mpi-setup
4484 (add-before 'check 'test-setup
4485 (lambda* (#:key inputs #:allow-other-keys)
4486 (setenv "OMP_NUM_THREADS" "2")
4487 (invoke "tar" "xf" (assoc-ref inputs "test-data")))))))
4488 (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/")
4489 (synopsis "Linear algebra primitives for graph analytics")
4490 (description "The Combinatorial BLAS (CombBLAS) is an extensible
4491 distributed-memory parallel graph library offering a small but powerful set of
4492 linear algebra primitives specifically targeting graph analytics.")
4494 license:gpl2+ ;include/psort/(funnel|sort)*.h
4495 license:x11 ;usort and psort
4496 license:bsd-3)))) ;CombBLAS and MersenneTwister.h
4498 (define-public dune-common
4500 (name "dune-common")
4505 (uri (string-append "https://dune-project.org/download/"
4506 version "/dune-common-" version ".tar.gz"))
4509 "019wcr1qf7jwyxx1y5y290wdlglylskvbb2m01ljkzcza2xnlmhw"))))
4510 (build-system cmake-build-system)
4513 (modify-phases %standard-phases
4514 (add-after 'build 'build-tests
4515 (lambda* (#:key make-flags #:allow-other-keys)
4516 (apply invoke "make" "build_tests" make-flags)))
4517 ;; These tests fail because they require a fully functional MPI
4519 (add-after 'unpack 'disable-failing-tests
4522 (string-append "--exclude-regex '("
4526 "remoteindicestest-mpi-2"
4529 "variablesizecommunicatortest"
4530 "variablesizecommunicatortest-mpi-2"
4531 "arithmetictestsuitetest"
4532 "assertandreturntest"
4533 "assertandreturntest_ndebug"
4536 "mpicollectivecommunication"
4537 "mpicollectivecommunication-mpi-2"
4539 "mpiguardtest-mpi-2"
4541 "mpihelpertest-mpi-2"
4543 "mpihelpertest2-mpi-2")
4550 ("openmpi" ,openmpi)
4551 ("openblas" ,openblas)
4553 ("superlu" ,superlu)))
4555 `(("gfortran" ,gfortran)
4556 ("pkg-config" ,pkg-config)))
4557 (home-page "https://dune-project.org/")
4558 (synopsis "Distributed and Unified Numerics Environment")
4559 (description "DUNE, the Distributed and Unified Numerics Environment is a
4560 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4561 grid-based methods. It supports the easy implementation of methods like
4562 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4563 Differences} (FD).")
4564 ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2.
4565 (license license:gpl2)))
4567 (define-public dune-geometry
4569 (name "dune-geometry")
4574 (uri (string-append "https://dune-project.org/download/"
4575 version "/dune-geometry-" version ".tar.gz"))
4578 "0hlaaxjyv9j05blasvb67sy02hd0w4g9znf68gdh3l731dd1aqbn"))))
4579 (build-system cmake-build-system)
4582 (modify-phases %standard-phases
4583 (add-after 'build 'build-tests
4584 (lambda* (#:key make-flags #:allow-other-keys)
4585 (apply invoke "make" "build_tests" make-flags))))))
4587 `(("dune-common" ,dune-common)
4588 ("openmpi" ,openmpi)
4590 ("openblas" ,openblas)
4592 ("python" ,python)))
4594 `(("gfortran" ,gfortran)
4595 ("pkg-config" ,pkg-config)))
4596 (home-page "https://dune-project.org/")
4597 (synopsis "Distributed and Unified Numerics Environment")
4598 (description "DUNE, the Distributed and Unified Numerics Environment is a
4599 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4600 grid-based methods. It supports the easy implementation of methods like
4601 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4604 This package contains the basic DUNE geometry classes.")
4605 ;; GPL version 2 with "runtime exception"
4606 (license license:gpl2)))
4608 (define-public dune-grid
4615 (uri (string-append "https://dune-project.org/download/"
4616 version "/dune-grid-" version ".tar.gz"))
4619 "1jp4vscm9yb9xg0lh7apzccfkhvgbnk652yahigmh3cvzpl4acd0"))))
4620 (build-system cmake-build-system)
4623 (modify-phases %standard-phases
4624 (add-after 'build 'build-tests
4625 (lambda* (#:key make-flags #:allow-other-keys)
4626 (apply invoke "make" "build_tests" make-flags)))
4627 ;; These tests fail because they require a fully functional MPI
4629 (add-after 'unpack 'disable-failing-tests
4632 (string-append "--exclude-regex '("
4636 "conformvolumevtktest"
4638 "nonconformboundaryvtktest"
4639 "subsamplingvtktest"
4645 "test-dgf-yasp-offset"
4647 "test-geogrid-yaspgrid"
4650 "testiteratorranges"
4651 "test-hierarchicsearch"
4652 "test-parallel-ug-mpi-2"
4653 "test-yaspgrid-backuprestore-equidistant"
4654 "test-yaspgrid-backuprestore-equidistant-mpi-2"
4655 "test-yaspgrid-backuprestore-equidistantoffset"
4656 "test-yaspgrid-backuprestore-equidistantoffset-mpi-2"
4657 "test-yaspgrid-backuprestore-tensor"
4658 "test-yaspgrid-backuprestore-tensor-mpi-2"
4659 "test-yaspgrid-tensorgridfactory"
4660 "test-yaspgrid-tensorgridfactory-mpi-2"
4661 "test-yaspgrid-yaspfactory-1d"
4662 "test-yaspgrid-yaspfactory-1d-mpi-2"
4663 "test-yaspgrid-yaspfactory-2d"
4664 "test-yaspgrid-yaspfactory-2d-mpi-2"
4665 "test-yaspgrid-yaspfactory-3d"
4666 "test-yaspgrid-yaspfactory-3d-mpi-2"
4667 "globalindexsettest"
4668 "persistentcontainertest"
4669 "structuredgridfactorytest"
4670 "tensorgridfactorytest"
4676 `(("dune-common" ,dune-common)
4677 ("dune-geometry" ,dune-geometry)
4680 ("openblas" ,openblas)
4681 ("openmpi" ,openmpi)
4682 ("python" ,python)))
4684 `(("gfortran" ,gfortran)
4685 ("pkg-config" ,pkg-config)))
4686 (home-page "https://dune-project.org/")
4687 (synopsis "Distributed and Unified Numerics Environment")
4688 (description "DUNE, the Distributed and Unified Numerics Environment is a
4689 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4690 grid-based methods. It supports the easy implementation of methods like
4691 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4694 This package contains the basic DUNE grid classes.")
4695 ;; GPL version 2 with "runtime exception"
4696 (license license:gpl2)))
4698 (define-public dune-istl
4705 (uri (string-append "https://dune-project.org/download/"
4706 version "/dune-istl-" version ".tar.gz"))
4709 "0l2gyrvys5w6wsmk0ckbb7295s80b7yk7qrl7x66akv2jv1nzq2w"))))
4710 (build-system cmake-build-system)
4713 (modify-phases %standard-phases
4714 (add-after 'build 'build-tests
4715 (lambda* (#:key make-flags #:allow-other-keys)
4716 (apply invoke "make" "build_tests" make-flags)))
4717 ;; These tests fail because they require a fully functional MPI
4719 (add-after 'unpack 'disable-failing-tests
4722 (string-append "--exclude-regex '("
4728 "pamg_comm_repart_test"
4736 `(("dune-common" ,dune-common)
4737 ("openmpi" ,openmpi)
4740 ("superlu" ,superlu)
4741 ("openblas" ,openblas)
4743 ("python" ,python)))
4745 `(("gfortran" ,gfortran)
4746 ("pkg-config" ,pkg-config)))
4747 (home-page "https://dune-project.org/")
4748 (synopsis "Distributed and Unified Numerics Environment")
4749 (description "DUNE, the Distributed and Unified Numerics Environment is a
4750 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4753 This is the iterative solver template library which provides generic sparse
4754 matrix/vector classes and a variety of solvers based on these classes. A
4755 special feature is the use of templates to exploit the recursive block
4756 structure of finite element matrices at compile time. Available solvers
4757 include Krylov methods, (block-) incomplete decompositions and
4758 aggregation-based algebraic multigrid.")
4759 ;; GPL version 2 with "runtime exception"
4760 (license license:gpl2)))
4762 (define-public dune-localfunctions
4764 (name "dune-localfunctions")
4769 (uri (string-append "https://dune-project.org/download/"
4770 version "/dune-localfunctions-" version ".tar.gz"))
4773 "19c6zjinwwpy8jh4v4prhphyd438rapd4x80fj93apmwgw04nrhl"))))
4774 (build-system cmake-build-system)
4777 (modify-phases %standard-phases
4778 (add-after 'build 'build-tests
4779 (lambda* (#:key make-flags #:allow-other-keys)
4780 (apply invoke "make" "build_tests" make-flags))))))
4782 `(("dune-common" ,dune-common)
4783 ("dune-geometry" ,dune-geometry)
4784 ("openmpi" ,openmpi)
4787 ("superlu" ,superlu)
4790 `(("gfortran" ,gfortran)
4791 ("pkg-config" ,pkg-config)))
4792 (home-page "https://dune-project.org/")
4793 (synopsis "Distributed and Unified Numerics Environment") ; TODO
4794 (description "This DUNE module provides interface and implementation for
4795 shape functions defined on the DUNE reference elements. In addition to the
4796 shape function, interpolation operators and special keys are provided which
4797 can be used to assemble global function spaces on finite-element grids.
4799 This package provides an interface and implementation for shape functions
4800 defined on the DUNE reference elements. In addition to the shape function,
4801 interpolation operators and special keys are provided which can be used to
4802 assemble global function spaces on finite-element grids.")
4803 ;; GPL version 2 with "runtime exception"
4804 (license license:gpl2)))
4806 (define-public dune-alugrid
4808 (name "dune-alugrid")
4813 (uri (string-append "https://dune-project.org/download/"
4814 version "/dune-alugrid-" version ".tar.gz"))
4817 "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj"))))
4818 (build-system cmake-build-system)
4820 `(#:tests? #f ; 7 of 8 tests fail because they need a full MPI
4823 (modify-phases %standard-phases
4824 (add-after 'unpack 'patch-include
4826 (substitute* "dune/alugrid/test/test-alugrid.cc"
4827 (("doc/grids/gridfactory/testgrids")
4828 "doc/dune-grid/grids/gridfactory/testgrids"))
4830 (add-after 'build 'build-tests
4831 (lambda* (#:key inputs make-flags #:allow-other-keys)
4832 (setenv "CPLUS_INCLUDE_PATH"
4833 (string-append (assoc-ref inputs "dune-grid") "/share"))
4834 (apply invoke "make" "build_tests" make-flags))))))
4836 `(("dune-common" ,dune-common)
4837 ("dune-geometry" ,dune-geometry)
4838 ("dune-grid" ,dune-grid)
4839 ("openmpi" ,openmpi)
4842 ("openblas" ,openblas)
4844 ("superlu" ,superlu)
4848 `(("gfortran" ,gfortran)
4849 ("pkg-config" ,pkg-config)))
4850 (home-page "https://dune-project.org/")
4851 (synopsis "Distributed and Unified Numerics Environment")
4852 (description "ALUGrid is an adaptive, loadbalancing, unstructured
4853 implementation of the DUNE grid interface supporting either simplices or
4855 (license license:gpl2+)))
4857 (define-public dune-typetree
4859 (name "dune-typetree")
4865 (url "https://gitlab.dune-project.org/staging/dune-typetree.git")
4866 (commit (string-append "v" version))))
4867 (file-name (git-file-name name version))
4870 "0mnv6w2f22lz3j4bdpdjq55vjm8xxfx9v4vvhg9bd36xpsbjpjp9"))))
4871 (build-system cmake-build-system)
4874 (modify-phases %standard-phases
4875 (add-after 'build 'build-tests
4876 (lambda* (#:key make-flags #:allow-other-keys)
4877 (apply invoke "make" "build_tests" make-flags))))))
4879 `(("dune-common" ,dune-common)
4880 ("openmpi" ,openmpi)
4882 ("openblas" ,openblas)
4885 ("superlu" ,superlu)
4888 `(("gfortran" ,gfortran)
4889 ("pkg-config" ,pkg-config)))
4890 (home-page "https://dune-project.org/")
4891 (synopsis "Distributed and Unified Numerics Environment")
4892 (description "TypeTree is a template library for constructing and
4893 operating on statically typed trees of objects.")
4894 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4895 (license (list license:lgpl3+ license:gpl2))))
4897 (define-public dune-functions
4899 (name "dune-functions")
4905 (url "https://gitlab.dune-project.org/staging/dune-functions.git")
4906 (commit (string-append "v" version))))
4907 (file-name (git-file-name name version))
4910 "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200"))))
4911 (build-system cmake-build-system)
4912 (arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid
4914 `(("dune-common" ,dune-common)
4915 ("dune-istl" ,dune-istl)
4916 ("dune-localfunctions" ,dune-localfunctions)
4917 ("dune-grid" ,dune-grid)
4918 ("dune-geometry" ,dune-geometry)
4919 ("dune-typetree" ,dune-typetree)
4920 ("openmpi" ,openmpi)
4921 ("openblas" ,openblas)
4924 ("superlu" ,superlu)
4927 `(("gfortran" ,gfortran)
4928 ("pkg-config" ,pkg-config)))
4929 (home-page "https://dune-project.org/")
4930 (synopsis "Distributed and Unified Numerics Environment")
4931 (description "The dune-functions module provides an abstraction layer for
4932 global finite element functions. Its two main concepts are functions
4933 implemented as callable objects, and bases of finite element spaces.")
4934 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4935 (license (list license:lgpl3+ license:gpl2))))
4937 (define-public dune-pdelab
4939 (name "dune-pdelab")
4940 (version "2.6.0-rc1")
4945 (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
4946 (commit (string-append "v" version))))
4947 (file-name (git-file-name name version))
4950 "07g0s9448z65vjrq88g5rv3340iifil85k170n8kbqchsvi4ny5v"))))
4951 (build-system cmake-build-system)
4952 (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
4954 `(("dune-common" ,dune-common)
4955 ("dune-istl" ,dune-istl)
4956 ("dune-localfunctions" ,dune-localfunctions)
4957 ("dune-geometry" ,dune-geometry)
4958 ("dune-grid" ,dune-grid)
4959 ("dune-typetree" ,dune-typetree)
4960 ("dune-functions" ,dune-functions)
4961 ("openmpi" ,openmpi)
4963 ("openblas" ,openblas)
4967 ("superlu" ,superlu)
4970 `(("gfortran" ,gfortran)
4971 ("pkg-config" ,pkg-config)))
4972 (home-page "https://dune-project.org/")
4973 (synopsis "Differential equations solver toolbox")
4974 (description "PDELab is a partial differential equations solver toolbox
4975 built on top of DUNE, the Distributed and Unified Numerics Environment.")
4976 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4977 (license (list license:lgpl3+ license:gpl2))))
4979 (define-public mlucas
4987 "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz"))
4989 (base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447"))))
4990 (build-system gnu-build-system)
4992 `(("python2" ,python-2)))
4994 `(#:tests? #f ; no tests
4996 (modify-phases %standard-phases
5000 (call-with-output-file "Makefile"
5002 (format port "CC = gcc
5003 CFLAGS = -O3 ~a -DUSE_THREADS
5004 LDLIBS = -lm -lpthread -lrt
5005 Mlucas: $(addsuffix .o,$(basename $(wildcard *.c)))
5007 ,(let ((system (or (%current-target-system)
5008 (%current-system))))
5010 ((string-prefix? "x86_64" system) "-DUSE_SSE2")
5014 (lambda* (#:key outputs #:allow-other-keys)
5015 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
5016 (install-file "Mlucas" bin)
5017 (install-file "primenet.py" bin))
5019 (home-page "https://www.mersenne.org")
5020 (synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client")
5021 (description "Mlucas performs Lucas-Lehmer primality testing of Mersenne
5022 numbers in search of a world-record prime. You may use it to test any
5023 suitable number as you wish, but it is preferable that you do so in a
5024 coordinated fashion, as part of the Great Internet Mersenne Prime
5025 Search (GIMPS). Mlucas also includes a simple Python script for assignment
5026 management via the GIMPS project's Primenet server.")
5027 (license license:gpl2+)))
5029 (define-public nauty
5036 "https://pallini.di.uniroma1.it/"
5037 "nauty" (string-join (string-split version #\.) "")
5041 "1p4mxf8q5wm47nxyskxbqwa5p1vvkycv1zgswvnk9nsn6vff0al6"))))
5042 (build-system gnu-build-system)
5043 (outputs '("out" "lib"))
5045 `(#:test-target "checks"
5047 (modify-phases %standard-phases
5048 ;; Default make target does not build all available
5049 ;; executables. Create them now.
5050 (add-after 'build 'build-extra-programs
5052 (for-each (lambda (target) (invoke "make" target))
5053 '("blisstog" "bliss2dre" "checks6" "sumlines"))
5055 ;; Upstream does not provide any install target.
5057 (lambda* (#:key outputs #:allow-other-keys)
5058 (let* ((out (assoc-ref outputs "out"))
5059 (lib-output (assoc-ref outputs "lib"))
5060 (bin (string-append out "/bin"))
5061 (doc (string-append out "/share/doc/nauty/"))
5062 (include (string-append lib-output "/include/nauty"))
5063 (lib (string-append lib-output "/lib/nauty")))
5064 (for-each (lambda (f) (install-file f bin))
5065 '("dreadnaut" "NRswitchg" "addedgeg" "amtog" "biplabg"
5066 "blisstog" "bliss2dre" "catg" "checks6" "complg"
5067 "converseg" "copyg" "countg" "cubhamg" "deledgeg"
5068 "delptg" "directg" "dretodot" "dretog" "genbg"
5069 "genbgL" "geng" "genquarticg" "genrang" "genspecialg"
5070 "gentourng" "gentreeg" "hamheuristic" "labelg"
5071 "linegraphg" "listg" "multig" "newedgeg" "pickg"
5072 "planarg" "ranlabg" "shortg" "showg" "subdivideg"
5073 "sumlines" "twohamg" "vcolg" "watercluster2"))
5074 (for-each (lambda (f) (install-file f include))
5075 (find-files "." "\\.h$"))
5076 (for-each (lambda (f) (install-file f lib))
5077 (find-files "." "\\.a$"))
5078 (for-each (lambda (f) (install-file f doc))
5079 (append '("formats.txt" "README" "schreier.txt")
5080 (find-files "." "\\.pdf$")))))))))
5082 `(("gmp" ,gmp))) ;for sumlines
5083 (home-page "https://pallini.di.uniroma1.it/")
5084 (synopsis "Library for graph automorphisms")
5085 (description "@code{nauty} (No AUTomorphisms, Yes?) is a set of
5086 procedures for computing automorphism groups of graphs and digraphs.
5088 @code{nauty} computes graph information in the form of a set of
5089 generators, the size of the group, and the orbits of the group; it can
5090 also produce a canonical label. The @code{nauty} suite is written in
5091 C and comes with a command-line interface, a collection of
5092 command-line tools, and an Application Programming Interface (API).
5094 This package provides the static libraries required to run programs
5095 compiled against the nauty library.")
5096 (license license:asl2.0)))
5105 (uri (string-append "https://www.bugseng.com/products/ppl/download/"
5106 "ftp/releases/" version
5107 "/ppl-" version ".tar.gz"))
5110 "1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb"))))
5111 (build-system gnu-build-system)
5117 (home-page "https://www.bugseng.com/parma-polyhedra-library")
5119 "Parma Polyhedra Library for computations with polyhedra")
5121 "The Parma Polyhedra Library (PPL) provides numerical abstractions
5122 especially targeted at applications in the field of analysis and
5123 verification of complex systems. These abstractions include convex
5124 polyhedra, defined as the intersection of a finite number of (open or
5125 closed) halfspaces, each described by a linear inequality (strict or
5126 non-strict) with rational coefficients; some special classes of polyhedra
5127 shapes that offer interesting complexity/precision tradeoffs; and grids
5128 which represent regularly spaced points that satisfy a set of linear
5129 congruence relations. The library also supports finite powersets and
5130 products of (any kind of) polyhedra and grids, a mixed integer linear
5131 programming problem solver using an exact-arithmetic version of the simplex
5132 algorithm, a parametric integer programming solver, and primitives for
5133 termination analysis via the automatic synthesis of linear ranking
5135 (license license:gpl3+)))
5137 (define-public speedcrunch
5139 (name "speedcrunch")
5145 (url "https://bitbucket.org/heldercorreia/speedcrunch.git")
5146 (commit (string-append "release-" version))))
5147 (file-name (git-file-name name version))
5150 "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"))))
5151 (build-system cmake-build-system)
5152 (inputs `(("qtbase" ,qtbase)))
5153 (native-inputs `(("qttools" ,qttools)))
5156 (modify-phases %standard-phases
5157 (add-after 'unpack 'chdir-to-src
5158 (lambda _ (chdir "src") #t)))))
5159 (synopsis "High-precision scientific calculator")
5161 "SpeedCrunch is a high-precision scientific calculator. It features a
5162 syntax-highlighted scrollable display and is designed to be fully used via
5163 keyboard. Some distinctive features are auto-completion of functions and
5164 variables, a formula book, and quick insertion of constants from various
5165 fields of knowledge.")
5166 (home-page "http://speedcrunch.org/")
5167 (license license:gpl2+)))
5169 (define-public minisat
5170 ;; This is the last commit which is available upstream, no
5171 ;; release happened since 2010.
5172 (let ((commit "37dc6c67e2af26379d88ce349eb9c4c6160e8543")
5176 (version (string-append "2.2.0-" revision "." (string-take commit 7)))
5181 (url "https://github.com/niklasso/minisat.git")
5183 (file-name (string-append name "-" version "-checkout"))
5186 "091hf3qkm197s5r7xcr3m07xsdwyz2rqk1hc9kj0hn13imz09irq"))
5188 (search-patches "minisat-friend-declaration.patch"
5189 "minisat-install.patch"))))
5190 (build-system gnu-build-system)
5192 '(#:make-flags (list (string-append "prefix=" %output))
5193 #:tests? #f ;no check target
5195 (modify-phases %standard-phases
5196 (delete 'configure))))
5198 `(("zlib:static" ,zlib "static")
5201 "Small, yet efficient, SAT solver")
5203 "MiniSat is a minimalistic, open-source SAT solver, developed to help
5204 researchers and developers alike to get started on SAT.")
5206 "http://minisat.se/MiniSat.html")
5207 (license license:expat))))