1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2013, 2014, 2015, 2016 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 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 Ricardo Wurmus <rekado@elephly.net>
9 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
10 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
11 ;;; Copyright © 2015, 2016, 2017, 2018 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 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 Paul Garlick <pgarlick@tourbillion-technology.com>
19 ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
20 ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
21 ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
22 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
23 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
24 ;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
25 ;;; Copyright © 2018 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>
33 ;;; This file is part of GNU Guix.
35 ;;; GNU Guix is free software; you can redistribute it and/or modify it
36 ;;; under the terms of the GNU General Public License as published by
37 ;;; the Free Software Foundation; either version 3 of the License, or (at
38 ;;; your option) any later version.
40 ;;; GNU Guix is distributed in the hope that it will be useful, but
41 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
42 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
43 ;;; GNU General Public License for more details.
45 ;;; You should have received a copy of the GNU General Public License
46 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
48 (define-module (gnu packages maths)
49 #:use-module (ice-9 regex)
50 #:use-module (gnu packages)
51 #:use-module ((guix licenses) #:prefix license:)
52 #:use-module (guix packages)
53 #:use-module (guix download)
54 #:use-module (guix git-download)
55 #:use-module (guix utils)
56 #:use-module (guix build utils)
57 #:use-module (guix build-system cmake)
58 #:use-module (guix build-system gnu)
59 #:use-module (guix build-system ocaml)
60 #:use-module (guix build-system python)
61 #:use-module (guix build-system r)
62 #:use-module (guix build-system ruby)
63 #:use-module (gnu packages algebra)
64 #:use-module (gnu packages audio)
65 #:use-module (gnu packages autotools)
66 #:use-module (gnu packages bison)
67 #:use-module (gnu packages boost)
68 #:use-module (gnu packages check)
69 #:use-module (gnu packages cmake)
70 #:use-module (gnu packages compression)
71 #:use-module (gnu packages curl)
72 #:use-module (gnu packages cyrus-sasl)
73 #:use-module (gnu packages documentation)
74 #:use-module (gnu packages elf)
75 #:use-module (gnu packages flex)
76 #:use-module (gnu packages fltk)
77 #:use-module (gnu packages fontutils)
78 #:use-module (gnu packages gettext)
79 #:use-module (gnu packages gcc)
80 #:use-module (gnu packages gd)
81 #:use-module (gnu packages ghostscript)
82 #:use-module (gnu packages graphviz)
83 #:use-module (gnu packages gtk)
84 #:use-module (gnu packages image)
85 #:use-module (gnu packages java)
86 #:use-module (gnu packages less)
87 #:use-module (gnu packages lisp)
88 #:use-module (gnu packages linux)
89 #:use-module (gnu packages logging)
90 #:use-module (gnu packages lua)
91 #:use-module (gnu packages gnome)
92 #:use-module (gnu packages guile)
93 #:use-module (gnu packages xorg)
94 #:use-module (gnu packages gl)
95 #:use-module (gnu packages imagemagick)
96 #:use-module (gnu packages m4)
97 #:use-module (gnu packages mpi)
98 #:use-module (gnu packages multiprecision)
99 #:use-module (gnu packages netpbm)
100 #:use-module (gnu packages ocaml)
101 #:use-module (gnu packages pcre)
102 #:use-module (gnu packages popt)
103 #:use-module (gnu packages perl)
104 #:use-module (gnu packages pkg-config)
105 #:use-module (gnu packages pulseaudio)
106 #:use-module (gnu packages python)
107 #:use-module (gnu packages python-web)
108 #:use-module (gnu packages qt)
109 #:use-module (gnu packages readline)
110 #:use-module (gnu packages ruby)
111 #:use-module (gnu packages tbb)
112 #:use-module (gnu packages scheme)
113 #:use-module (gnu packages shells)
114 #:use-module (gnu packages tcl)
115 #:use-module (gnu packages texinfo)
116 #:use-module (gnu packages tex)
117 #:use-module (gnu packages tls)
118 #:use-module (gnu packages version-control)
119 #:use-module (gnu packages wxwidgets)
120 #:use-module (gnu packages xml)
121 #:use-module (srfi srfi-1))
129 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
131 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
132 (build-system gnu-build-system)
133 (inputs `(("gtk+" ,gtk+)
134 ("libxml2" ,libxml2)))
135 (native-inputs `(("pkg-config" ,pkg-config)))
136 (synopsis "Natural deduction first-order logic interface")
137 (description "Aris is a program for performing logical proofs. It supports
138 propositional and predicate logic, as well as Boolean algebra and
139 arithmetical logic. In addition to its predefined inference and equivalence
140 rules, Aris also supports references to older proofs. Its use of standard
141 logical symbols and its natural deduction interface make it easy to use for
143 (license license:gpl3+)
144 (home-page "https://www.gnu.org/software/aris/")))
146 (define-public c-graph
152 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
155 "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
156 (build-system gnu-build-system)
158 `(("fortran" ,gfortran)))
159 (synopsis "Visualizing and demonstrating convolution")
161 "GNU C-Graph is a tool for demonstrating the theory of convolution.
162 Thus, it can serve as an excellent aid to students of signal and systems
163 theory in visualizing the convolution process. Rather than forcing the
164 student to write code, the program offers an intuitive interface with
165 interactive dialogs to guide them.")
166 (license license:gpl3+)
167 (home-page "https://www.gnu.org/software/c-graph/")))
176 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
177 version "/coda-" version ".tar.gz"))
179 (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245"))
180 (patches (search-patches "coda-use-system-libs.patch"))
181 (modules '((guix build utils)))
183 ;; Make sure we don't use the bundled software.
185 (for-each (lambda (d)
186 (delete-file-recursively (string-append "libcoda/" d)))
187 '("zlib" "pcre" "expat"))
190 `(("fortran" ,gfortran)
192 ("python-numpy" ,python-numpy)))
199 (build-system gnu-build-system)
201 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
202 "LIBS= -lz -lpcre -lexpat")))
203 (synopsis "A common interface to various earth observation data formats")
205 "The Common Data Access toolbox (CODA) provides a set of interfaces for
206 reading remote sensing data from earth observation data files. It consists of
207 command line applications and interfaces to the C, Fortran, Python, and Java
208 programming languages.")
209 (home-page "https://stcorp.nl/coda")
210 (license license:gpl2+)))
218 (uri (string-append "http://www.qhull.org/download/qhull-"
219 (car (string-split version #\.))
223 "0dm4b2xr3asy6w74khq2zg4gf26zsy3qf9sq7pf7lmrvbj911c3q"))))
224 (build-system cmake-build-system)
225 (synopsis "Calculate convex hulls and related structures")
227 "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
228 diagram, halfspace intersection about a point, furthest-site Delaunay
229 triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d,
230 3-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull
231 algorithm for computing the convex hull. It handles roundoff errors from
232 floating point arithmetic. It computes volumes, surface areas, and
233 approximations to the convex hull.
235 @code{Qhull} does not support triangulation of non-convex surfaces, mesh
236 generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
237 shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
239 (home-page "http://qhull.org")
240 (license (license:non-copyleft "file://COPYING.txt"
241 "See COPYING in the distribution."))))
243 (define-public python-cvxopt
245 (name "python-cvxopt")
250 (url "https://github.com/cvxopt/cvxopt.git")
252 (file-name (git-file-name name version))
255 "05mnjil9palaa48xafdfh4f5pr4z7aqjr995rwl08qfyxs8y0crf"))))
256 (build-system python-build-system)
259 (modify-phases %standard-phases
260 (add-after 'unpack 'find-libraries
261 (lambda* (#:key inputs #:allow-other-keys)
262 (setenv "CVXOPT_BLAS_LIB" "openblas")
263 (setenv "CVXOPT_BUILD_FFTW" "1")
264 (setenv "CVXOPT_BUILD_GLPK" "1")
265 (setenv "CVXOPT_BUILD_GSL" "1")
272 ("openblas" ,openblas)
273 ("suitesparse" ,suitesparse)))
274 (home-page "https://www.cvxopt.org")
275 (synopsis "Python library for convex optimization")
277 "CVXOPT is a package for convex optimization based on the Python
278 programming language. Its main purpose is to make the development of software
279 for convex optimization applications straightforward by building on Python’s
280 extensive standard library and on the strengths of Python as a high-level
281 programming language.")
282 (license license:gpl3+)))
284 (define-public python2-cvxopt
285 (package-with-python2 python-cvxopt))
293 (uri (string-append "mirror://gnu/units/units-" version
296 "0y26kj349i048y4z3xrk90bvciw2j6ds3rka7r7yn3183hirr5b4"))))
297 (build-system gnu-build-system)
299 `(("readline" ,readline)
300 ("python" ,python-wrapper) ;for 'units_cur' script
301 ("python-requests" ,python-requests)))
303 `(#:phases (modify-phases %standard-phases
304 (add-after 'install 'wrap-units_cur
305 (lambda* (#:key outputs #:allow-other-keys)
306 (let* ((out (assoc-ref outputs "out"))
307 (bin (string-append out "/bin")))
308 (wrap-program (string-append bin "/units_cur")
309 `("PYTHONPATH" ":" prefix
310 ,(search-path-as-string->list (getenv "PYTHONPATH"))))
312 (synopsis "Conversion between thousands of scales")
314 "GNU Units converts numeric quantities between units of measure. It
315 can handle scale changes through adaptive usage of standard scale
316 prefixes (micro-, kilo-, etc.). It can also handle nonlinear
317 conversions such as Fahrenheit to Celsius. Its interpreter is powerful
318 enough to be used effectively as a scientific calculator.")
319 (license license:gpl3+)
320 (home-page "https://www.gnu.org/software/units/")))
322 (define-public double-conversion
324 (name "double-conversion")
326 (home-page "https://github.com/google/double-conversion")
329 (uri (git-reference (url home-page) (commit version)))
330 (file-name (git-file-name name version))
333 "123rb2p4snqagrybw66vnapchqdwn2rfpr1wcq0ya9gwbyl7xccx"))))
334 (build-system cmake-build-system)
336 '(#:test-target "test"
337 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
338 "-DBUILD_TESTING=ON")))
339 (synopsis "Conversion routines for IEEE doubles")
341 "The double-conversion library provides binary-decimal and decimal-binary
342 routines for IEEE doubles. The library consists of efficient conversion
343 routines that have been extracted from the V8 JavaScript engine.")
344 (license license:bsd-3)))
346 (define-public dionysus
352 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
356 "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
357 (build-system gnu-build-system)
358 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
359 (synopsis "Local search for universal constants and scientific values")
361 "GNU Dionysus is a convenient system for quickly retrieving the values of
362 mathematical constants used in science and engineering. Values can be
363 searched using a simple command-line tool, choosing from three databases:
364 universal constants, atomic numbers, and constants related to
366 (license license:gpl3+)
367 (home-page "https://www.gnu.org/software/dionysus/")))
375 (uri (string-append "mirror://gnu/gsl/gsl-"
379 "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
380 (patches (search-patches "gsl-test-i686.patch"))))
381 (build-system gnu-build-system)
383 `(;; Currently there are numerous tests that fail on "exotic"
384 ;; architectures such as aarch64 and ppc64le.
385 ,@(if (string-prefix? "aarch64-linux"
386 (or (%current-target-system) (%current-system)))
389 (home-page "https://www.gnu.org/software/gsl/")
390 (synopsis "Numerical library for C and C++")
392 "The GNU Scientific Library is a library for numerical analysis in C
393 and C++. It includes a wide range of mathematical routines, with over 1000
394 functions in total. Subject areas covered by the library include:
395 differential equations, linear algebra, Fast Fourier Transforms and random
397 (license license:gpl3+)))
399 (define-public ocaml-gsl
408 "https://github.com/mmottl/gsl-ocaml/releases/download/"
409 version "/gsl-" version ".tbz"))
412 "17vcswipliq1b2idbzx1z95kskn1a4q4s5v04igilg0f7lnkaarb"))))
413 (build-system ocaml-build-system)
416 (home-page "https://mmottl.github.io/gsl-ocaml")
417 (synopsis "Bindings to the GNU Scientific Library")
419 "GSL-OCaml is an interface to the @dfn{GNU scientific library} (GSL) for
420 the OCaml language.")
421 (license license:gpl3+)))
423 (define-public ocaml4.01-gsl
424 (package-with-ocaml4.01 ocaml-gsl))
433 (uri (string-append "mirror://gnu/glpk/glpk-"
437 "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
438 (build-system gnu-build-system)
442 `(#:configure-flags '("--with-gmp")))
443 (home-page "https://www.gnu.org/software/glpk/")
444 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
446 "GLPK is a C library for solving large-scale linear programming (LP),
447 mixed integer programming (MIP), and other related problems. It supports the
448 GNU MathProg modeling language, a subset of the AMPL language, and features a
449 translator for the language. In addition to the C library, a stand-alone
450 LP/MIP solver is included in the package.")
451 (license license:gpl3+)))
460 (uri (string-append "http://www.4ti2.de/version_" version
461 "/4ti2-" version ".tar.gz"))
464 "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
465 (build-system gnu-build-system)
467 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
471 (home-page "http://www.4ti2.de/")
472 (synopsis "Mathematical tool suite for problems on linear spaces")
474 "4ti2 implements algorithms for solving algebraic, geometric and
475 combinatorial problems on linear spaces. Among others, it solves systems
476 of linear equations, computes extreme rays of polyhedral cones, solves
477 integer programming problems and computes Markov bases for statistics.")
478 (license license:gpl2+)))
480 (define-public cddlib
487 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
488 (string-delete #\. version) ".tar.gz"))
491 "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
492 (build-system gnu-build-system)
495 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
496 (synopsis "Library for convex hulls and extreme rays of polyhedra")
498 "The C-library cddlib implements the Double Description Method of
499 Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
500 rays of a general convex polyhedron given by a system of linear inequalities
501 in arbitrary dimension. It can also be used for the converse operation of
502 computing convex hulls.")
503 (license license:gpl2+)))
505 (define-public arpack-ng
509 (home-page "https://github.com/opencollab/arpack-ng")
512 (uri (git-reference (url home-page) (commit version)))
513 (file-name (git-file-name name version))
516 "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
517 (build-system gnu-build-system)
519 `(("autoconf" ,autoconf)
520 ("automake" ,automake)
521 ("libtool" ,libtool)))
524 ("fortran" ,gfortran)))
525 (synopsis "Fortran subroutines for solving eigenvalue problems")
527 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
528 large scale eigenvalue problems.")
529 (license (license:non-copyleft "file://COPYING"
530 "See COPYING in the distribution."))))
532 (define-public arpack-ng-3.3.0
536 (name (package-name arpack-ng))
537 (home-page (package-home-page arpack-ng))
541 (uri (string-append home-page "/archive/" version ".tar.gz"))
542 (file-name (string-append name "-" version ".tar.gz"))
545 "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
547 (define-public arpack-ng-openmpi
548 (package (inherit arpack-ng)
549 (name "arpack-ng-openmpi")
552 ,@(package-inputs arpack-ng)))
554 (substitute-keyword-arguments (package-arguments arpack-ng)
555 ((#:configure-flags _ '())
557 ((#:phases phases '%standard-phases)
558 `(modify-phases ,phases
559 (add-before 'check 'mpi-setup
561 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
563 (define-public lapack
570 (uri (string-append "http://www.netlib.org/lapack/lapack-"
574 "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
575 (build-system cmake-build-system)
576 (home-page "http://www.netlib.org/lapack/")
577 (inputs `(("fortran" ,gfortran)
578 ("python" ,python-2)))
580 `(#:configure-flags (list
581 "-DBUILD_SHARED_LIBS:BOOL=YES"
584 ;; Build the 'LAPACKE_clatms' functions.
585 "-DLAPACKE_WITH_TMG=ON")
587 (modify-phases %standard-phases
588 (add-before 'check 'patch-python
589 (lambda* (#:key inputs #:allow-other-keys)
590 (let ((python (assoc-ref inputs "python")))
591 (substitute* "lapack_testing.py"
592 (("/usr/bin/env python") python)))
594 (synopsis "Library for numerical linear algebra")
596 "LAPACK is a Fortran 90 library for solving the most commonly occurring
597 problems in numerical linear algebra.")
598 (license (license:non-copyleft "file://LICENSE"
599 "See LICENSE in the distribution."))))
601 (define-public scalapack
608 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
612 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
613 (build-system cmake-build-system)
616 ("fortran" ,gfortran)
617 ("lapack" ,lapack))) ;for testing only
619 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
620 #:phases (modify-phases %standard-phases
621 (add-before 'check 'mpi-setup
623 (home-page "http://www.netlib.org/scalapack/")
624 (synopsis "Library for scalable numerical linear algebra")
626 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
627 routines on parallel distributed memory machines. ScaLAPACK solves dense and
628 banded linear systems, least squares problems, eigenvalue problems, and
629 singular value problems.")
630 (license (license:bsd-style "file://LICENSE"
631 "See LICENSE in the distribution."))))
633 (define-public gnuplot
639 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
644 "1jvh8xmd2cvrhlsg88kxwh55wkwx31sg50v1n59slfippl0g058m"))))
645 (build-system gnu-build-system)
646 (inputs `(("readline" ,readline)
652 `(("pkg-config" ,pkg-config)
653 ("texlive" ,texlive-tiny)))
654 (arguments `(#:configure-flags (list (string-append
655 "--with-texdir=" %output
656 "/texmf-local/tex/latex/gnuplot"))))
657 (home-page "http://www.gnuplot.info")
658 (synopsis "Command-line driven graphing utility")
659 (description "Gnuplot is a portable command-line driven graphing
660 utility. It was originally created to allow scientists and students to
661 visualize mathematical functions and data interactively, but has grown to
662 support many non-interactive uses such as web scripting. It is also used as a
663 plotting engine by third-party applications like Octave.")
664 ;; X11 Style with the additional restriction that derived works may only be
665 ;; distributed as patches to the original.
666 (license (license:fsf-free
667 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
676 (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
678 (file-name (string-append name "-" version ".tar.gz"))
681 "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
683 `(("fortran" ,gfortran)))
684 (build-system gnu-build-system)
685 (synopsis "General Cartographic Transformation Package (GCTP)")
687 "The General Cartographic Transformation Package (GCTP) is a system of
688 software routines designed to permit the transformation of coordinate pairs
689 from one map projection to another. The GCTP is the standard computer
690 software used by the National Mapping Division for map projection
692 (home-page "https://github.com/OkoSanto/GCTP")
693 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
702 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
703 version "/src/hdf-" version ".tar.bz2"))
705 (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
706 (patches (search-patches "hdf4-architectures.patch"
707 "hdf4-reproducibility.patch"
708 "hdf4-shared-fortran.patch"))))
709 (build-system gnu-build-system)
711 `(("gfortran" ,gfortran)
716 ("libjpeg" ,libjpeg)))
718 `(#:parallel-tests? #f
719 #:configure-flags '("--enable-shared")
721 (modify-phases %standard-phases
722 ;; This is inspired by two of Debian's patches.
723 (add-before 'configure 'add-more-aarch64-support
725 (substitute* '("mfhdf/ncgen/ncgen.l"
726 "mfhdf/ncgen/ncgenyy.c"
727 "mfhdf/libsrc/netcdf.h.in")
728 (("AIX5L64") "__aarch64__"))
730 (add-before 'configure 'patchbuild
733 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
735 (("/bin/mkdir") "mkdir"))
736 (substitute* (find-files "." "^Makefile\\.in$")
737 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
738 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
739 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
740 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
741 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
743 (add-after 'configure 'patch-settings
745 ;; libhdf4.settings contains the full path of the
746 ;; compilers used, and its contents are included in
747 ;; .so-files. We truncate the hashes to avoid
748 ;; unnecessary store references to those compilers:
749 (substitute* "libhdf4.settings"
750 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
751 (string-append prefix (string-take hash 10) "...")))
754 (home-page "https://www.hdfgroup.org/products/hdf4/")
756 "Library and multi-object file format for storing and managing data")
757 (description "HDF4 is a library and multi-object file format for storing
758 and managing data between machines. HDF4 is an older hierarchical data format,
759 incompatible with HDF5.")
761 (license:non-copyleft
762 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
764 (define-public hdf4-alt
769 (substitute-keyword-arguments (package-arguments hdf4)
770 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
772 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
781 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
782 "hdf5-" (version-major+minor version)
783 "/hdf5-" version "/src/hdf5-"
785 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
788 (take (string-split version #\.) 2))
789 "/src/hdf5-" version ".tar.bz2")))
791 (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
792 (patches (list (search-patch "hdf5-config-date.patch")))))
793 (build-system gnu-build-system)
797 `(("gfortran" ,gfortran)))
798 (outputs '("out" ; core library
799 "fortran")) ; fortran interface
801 `(;; Some of the users, notably Flann, need the C++ interface.
802 #:configure-flags '("--enable-cxx"
804 "--enable-fortran2003")
805 ;; Use -fPIC to allow the R bindings to link with the static libraries
806 #:make-flags (list "CFLAGS=-fPIC"
809 (modify-phases %standard-phases
810 (add-before 'configure 'patch-configure
811 (lambda* (#:key outputs #:allow-other-keys)
812 (substitute* "configure"
814 (substitute* "fortran/src/Makefile.in"
815 (("libhdf5_fortran_la_LDFLAGS =")
816 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
817 (assoc-ref outputs "fortran") "/lib")))
818 (substitute* "hl/fortran/src/Makefile.in"
819 (("libhdf5hl_fortran_la_LDFLAGS =")
820 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
821 (assoc-ref outputs "fortran") "/lib")))
823 (add-after 'configure 'patch-settings
825 ;; libhdf5.settings contains the full path of the
826 ;; compilers used, and its contents are included in
827 ;; libhdf5.so. We truncate the hashes to avoid
828 ;; unnecessary store references to those compilers:
829 (substitute* "src/libhdf5.settings"
830 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
831 (string-append prefix (string-take hash 10) "..."))
832 ;; Don't record the build-time kernel version to make the
833 ;; settings file reproducible.
834 (("Uname information:.*")
835 "Uname information: Linux\n"))
837 (add-after 'install 'patch-references
838 (lambda* (#:key inputs outputs #:allow-other-keys)
839 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
840 (zlib (assoc-ref inputs "zlib")))
841 (substitute* (find-files bin "h5p?cc")
843 (string-append "-L" zlib "/lib " lib)))
845 (add-after 'install 'split
846 (lambda* (#:key inputs outputs #:allow-other-keys)
847 ;; Move all fortran-related files
848 (let* ((out (assoc-ref outputs "out"))
849 (bin (string-append out "/bin"))
850 (lib (string-append out "/lib"))
851 (inc (string-append out "/include"))
852 (ex (string-append out "/share/hdf5_examples/fortran"))
853 (fort (assoc-ref outputs "fortran"))
854 (fbin (string-append fort "/bin"))
855 (flib (string-append fort "/lib"))
856 (finc (string-append fort "/include"))
857 (fex (string-append fort "/share/hdf5_examples/fortran")))
862 ;; Note: When built with --enable-parallel, the 'h5fc' file
863 ;; doesn't exist, hence this condition.
864 (when (file-exists? (string-append bin "/h5fc"))
865 (rename-file (string-append bin "/h5fc")
866 (string-append fbin "/h5fc")))
867 (for-each (lambda (file)
869 (string-append flib "/" (basename file))))
870 (find-files lib ".*fortran.*"))
871 (for-each (lambda (file)
873 (string-append finc "/" (basename file))))
874 (find-files inc ".*mod"))
875 (for-each (lambda (file)
877 (string-append fex "/" (basename file))))
878 (find-files ex ".*"))
879 (delete-file-recursively ex))
881 (home-page "http://www.hdfgroup.org")
882 (synopsis "Management suite for extremely large and complex data")
883 (description "HDF5 is a suite that makes possible the management of
884 extremely large and complex data collections.")
885 (license (license:x11-style
886 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
888 (define-public hdf5-1.10
889 (package (inherit hdf5)
894 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
895 "hdf5-" (version-major+minor version)
896 "/hdf5-" version "/src/hdf5-"
898 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
901 (take (string-split version #\.) 2))
902 "/src/hdf5-" version ".tar.bz2")))
904 (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
905 (patches (list (search-patch "hdf5-config-date.patch")))))))
907 (define-public hdf-java
915 "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
916 version "/src/CMake-hdfjava-" version ".tar.gz"))
918 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
919 (modules '((guix build utils)))
920 (snippet ; Make sure we don't use the bundled sources and binaries.
922 (for-each delete-file
923 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
924 "HDF4.tar.gz" "HDF5.tar.gz"))
925 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
927 (build-system gnu-build-system)
929 `(("jdk" ,icedtea "jdk")
930 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
932 ("hamcrest-core" ,java-hamcrest-core)
933 ("junit" ,java-junit)
934 ("slf4j-simple" ,java-slf4j-simple)))
940 ("slf4j-api" ,java-slf4j-api)))
943 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
944 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
945 (assoc-ref %build-inputs "jdk") "/lib" )
946 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
947 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
950 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
951 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
952 (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
953 (string-append "JPEGLIB="
954 (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
958 (modify-phases %standard-phases
959 (add-before 'configure 'chdir-to-source
960 (lambda _ (chdir ,(string-append "hdfjava-" version))))
961 (add-before 'configure 'patch-build
962 (lambda* (#:key inputs outputs #:allow-other-keys)
963 (substitute* "configure"
964 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
965 (("/bin/cat") (which "cat")))
966 ;; Set classpath for compilation
967 (substitute* '("hdf/hdf5lib/Makefile.in"
968 "hdf/hdf5lib/exceptions/Makefile.in"
969 "hdf/hdflib/Makefile.in")
970 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
971 (string-append (assoc-ref inputs "slf4j-api")
972 "/share/java/slf4j-api.jar")))
973 ;; Replace outdated config.sub and config.guess:
974 (with-directory-excursion "config"
975 (for-each (lambda (file)
977 (string-append (assoc-ref inputs "automake")
978 "/share/automake-1.15/" file) file))
979 '("config.sub" "config.guess")))
980 (mkdir-p (string-append (assoc-ref outputs "out")))
981 ;; Set classpath for tests
982 (let* ((build-dir (getcwd))
983 (lib (string-append build-dir "/lib"))
984 (jhdf (string-append lib "/jhdf.jar"))
985 (jhdf5 (string-append lib "/jhdf5.jar"))
988 (string-append (assoc-ref inputs i)
989 "/share/java/" i ".jar"))
990 '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
992 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
994 (substitute* '("test/hdf5lib/Makefile.in"
995 "test/hdf5lib/junit.sh.in"
996 "examples/runExample.sh.in")
998 (string-append (assoc-ref inputs "coreutils")
1001 (string-append (assoc-ref inputs "coreutils")
1003 (("CLASSPATH=[^\n]*")
1004 (string-append "CLASSPATH=" class-path)))
1005 (setenv "CLASSPATH" class-path))
1007 (add-before 'check 'build-examples
1009 (zero? (apply system* `("javac"
1010 ,@(find-files "examples" ".*\\.java")))))))
1012 #:parallel-build? #f
1014 #:parallel-tests? #f ))
1015 (home-page "https://support.hdfgroup.org/products/java")
1016 (synopsis "Java interface for the HDF4 and HDF5 libraries")
1017 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
1018 the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
1021 ;; BSD-style license:
1022 (license (license:x11-style
1023 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
1024 /current/src/unpacked/COPYING"))))
1026 (define-public hdf-eos2
1033 (uri "ftp://edhs1.gsfc.nasa.gov\
1034 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
1036 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
1037 (patches (search-patches "hdf-eos2-remove-gctp.patch"
1038 "hdf-eos2-build-shared.patch"
1039 "hdf-eos2-fortrantests.patch"))))
1040 (build-system gnu-build-system)
1042 `(("gfortran" ,gfortran)))
1044 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
1046 ("libjpeg" ,libjpeg)
1049 `( #:configure-flags '("--enable-install-include" "--enable-shared"
1050 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
1051 #:parallel-tests? #f))
1052 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
1053 (synopsis "HDF4-based data format for NASA's Earth Observing System")
1054 (description "HDF-EOS2 is a software library built on HDF4 which supports
1055 the construction of data structures used in NASA's Earth Observing
1056 System (Grid, Point and Swath).")
1058 ;; Source files carry a permissive license header.
1059 (license (license:non-copyleft home-page))))
1061 (define-public hdf-eos5
1067 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1068 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1071 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1072 (patches (search-patches "hdf-eos5-build-shared.patch"
1073 "hdf-eos5-remove-gctp.patch"
1074 "hdf-eos5-fix-szip.patch"
1075 "hdf-eos5-fortrantests.patch"))))
1077 `(("gfortran" ,gfortran)))
1078 (build-system gnu-build-system)
1084 `(#:configure-flags '("--enable-install-include" "--enable-shared"
1085 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1086 #:parallel-tests? #f))
1087 (synopsis "HDF5-based data format for NASA's Earth Observing System")
1089 "HDF-EOS5 is a software library built on HDF5 to support the construction
1090 of data structures used in NASA's Earth Observing System (Grid, Point and
1092 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1094 ;; Source files carry a permissive license header.
1095 (license (license:non-copyleft home-page))))
1097 (define-public hdf5-parallel-openmpi
1098 (package (inherit hdf5)
1099 (name "hdf5-parallel-openmpi")
1102 ,@(package-inputs hdf5)))
1104 (substitute-keyword-arguments (package-arguments hdf5)
1105 ((#:configure-flags flags)
1106 ``("--enable-parallel" ,@(delete "--enable-cxx" ,flags)))
1108 `(modify-phases ,phases
1109 (add-after 'build 'mpi-setup
1111 (add-before 'check 'patch-tests
1113 ;; OpenMPI's mpirun will exit with non-zero status if it
1114 ;; detects an "abnormal termination", i.e. any process not
1115 ;; calling MPI_Finalize(). Since the test is explicitely
1116 ;; avoiding MPI_Finalize so as not to have at_exit and thus
1117 ;; H5C_flush_cache from being called, mpirun will always
1118 ;; complain, so turn this test off.
1119 (substitute* "testpar/Makefile"
1120 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1121 (string-append front back "\n")))
1122 (substitute* "tools/h5diff/testph5diff.sh"
1123 (("/bin/sh") (which "sh")))
1125 (synopsis "Management suite for data with parallel IO support")))
1127 (define-public h5check
1134 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
1135 "h5check/src/h5check-" version ".tar.gz"))
1138 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1139 (build-system gnu-build-system)
1140 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
1141 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1142 (synopsis "HDF5 format checker")
1143 (description "@code{h5check} is a validation tool for verifying that an
1144 HDF5 file is encoded according to the HDF File Format Specification.")
1145 (license (license:x11-style "file://COPYING"))))
1153 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1158 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1159 (build-system cmake-build-system)
1160 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1161 (inputs `(("lapack" ,lapack)
1163 ;; FIXME: Even though the fonts are available dvips complains:
1164 ;; "Font cmmi10 not found; characters will be left blank."
1166 `(("texlive" ,texlive-tiny)
1167 ("ghostscript" ,ghostscript)
1168 ("doxygen" ,doxygen)))
1169 (home-page "http://itpp.sourceforge.net")
1170 (synopsis "C++ library of maths, signal processing and communication classes")
1171 (description "IT++ is a C++ library of mathematical, signal processing and
1172 communication classes and functions. Its main use is in simulation of
1173 communication systems and for performing research in the area of
1174 communications. The kernel of the library consists of generic vector and
1175 matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1176 similar to MATLAB, GNU Octave or SciPy.")
1177 (license license:gpl3+)))
1179 (define-public netcdf
1186 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1187 "netcdf-" version ".tar.gz"))
1190 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1191 (patches (search-patches "netcdf-date-time.patch"
1192 "netcdf-tst_h_par.patch"))))
1193 (build-system gnu-build-system)
1196 ("doxygen" ,doxygen)
1197 ("graphviz" ,graphviz)))
1199 `(("hdf4" ,hdf4-alt)
1202 ("libjpeg" ,libjpeg)))
1204 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
1206 #:phases (modify-phases %standard-phases
1207 (add-before 'configure 'fix-source-date
1209 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1210 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1211 ;; to '1st hour of the current day', and therefore makes the
1212 ;; package not reproducible.
1213 (substitute* "./configure"
1214 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1215 "date --date='@0'"))
1217 (add-after 'configure 'patch-settings
1219 ;; libnetcdf.settings contains the full filename of the compilers
1220 ;; used to build the library. We truncate the hashes of those
1221 ;; filenames to avoid unnecessary references to the corresponding
1223 (substitute* "libnetcdf.settings"
1224 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1225 (string-append prefix (string-take hash 10) "...")))
1228 #:parallel-tests? #f)) ;various race conditions
1229 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
1230 (synopsis "Library for scientific data")
1231 (description "NetCDF is an interface for scientific data access and a
1232 software library that provides an implementation of the interface. The netCDF
1233 library defines a machine-independent format for representing scientific data.
1234 Together, the interface, library, and format support the creation, access, and
1235 sharing of scientific data.")
1236 (license (license:x11-style "file://COPYRIGHT"))))
1238 (define-public netcdf-parallel-openmpi
1239 (package (inherit netcdf)
1240 (name "netcdf-parallel-openmpi")
1243 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1244 (package-inputs netcdf))))
1245 ;; TODO: Replace pkg-config references in nc-config with absolute references
1247 (substitute-keyword-arguments (package-arguments netcdf)
1248 ((#:configure-flags flags)
1249 `(cons* "CC=mpicc" "CXX=mpicxx"
1250 "--enable-parallel-tests"
1251 ;; Shared libraries not supported with parallel IO.
1252 "--disable-shared" "--with-pic"
1255 (define-public netcdf-fortran
1257 (name "netcdf-fortran")
1262 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1266 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1267 (build-system gnu-build-system)
1269 `(#:parallel-tests? #f))
1271 `(("netcdf" ,netcdf)))
1273 `(("gfortran" ,gfortran)))
1274 (synopsis "Fortran interface for the netCDF library")
1275 (description (package-description netcdf))
1276 (home-page (package-home-page netcdf))
1277 (license (package-license netcdf))))
1279 (define-public nlopt
1285 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1288 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1289 (build-system gnu-build-system)
1291 `(;; Shared libraries are not built by default. They are required to
1292 ;; build the Guile, Octave, and Python bindings.
1293 #:configure-flags '("--enable-shared")
1296 (modify-phases %standard-phases
1297 (add-before 'configure 'set-libnlopt-file-name
1298 (lambda* (#:key outputs #:allow-other-keys)
1299 ;; Make sure the Scheme module refers to the library by its
1300 ;; absolute file name (we cannot do that from a snippet
1301 ;; because the expansion of @libdir@ contains
1303 (let ((out (assoc-ref outputs "out")))
1304 (substitute* "swig/nlopt.scm.in"
1306 (string-append out "/lib/libnlopt")))
1308 (inputs `(("guile" ,guile-2.0)))
1309 (native-inputs `(("pkg-config" ,pkg-config)))
1310 (home-page "http://ab-initio.mit.edu/wiki/")
1311 (synopsis "Library for nonlinear optimization")
1312 (description "NLopt is a library for nonlinear optimization, providing a
1313 common interface for a number of different free optimization routines available
1314 online as well as original implementations of various other algorithms.")
1315 (license license:lgpl2.1+)))
1317 (define-public ipopt
1324 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1328 "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
1329 (modules '((guix build utils)))
1331 ;; Make sure we don't use the bundled software.
1333 (delete-file-recursively "ThirdParty")
1335 (build-system gnu-build-system)
1337 '(#:phases (modify-phases %standard-phases
1338 (add-after 'install 'add--L-flags-in-ipopt.pc
1339 (lambda* (#:key inputs outputs #:allow-other-keys)
1340 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1341 ;; move it to "Libs.private" where it belongs, and add a
1342 ;; '-L' flag for LAPACK.
1343 (let ((out (assoc-ref outputs "out"))
1344 (lapack (assoc-ref inputs "lapack")))
1345 (substitute* (string-append out "/lib/pkgconfig/"
1347 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1348 (string-append "Libs: " before " " after "\n"
1349 "Libs.private: " before
1350 "-L" lapack "/lib -llapack -lblas "
1354 `(("gfortran" ,gfortran)))
1356 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
1357 `(("lapack" ,lapack))) ;for both libblas and liblapack
1358 (home-page "http://www.coin-or.org")
1359 (synopsis "Large-scale nonlinear optimizer")
1361 "The Interior Point Optimizer (IPOPT) is a software package for
1362 large-scale nonlinear optimization. It provides C++, C, and Fortran
1364 (license license:epl1.0)))
1366 (define-public ceres
1368 (name "ceres-solver")
1370 (home-page "http://ceres-solver.org/")
1373 (uri (string-append home-page "ceres-solver-"
1377 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
1378 (build-system cmake-build-system)
1380 ;; TODO: Build HTML user documentation and install separately.
1381 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
1382 "-DBUILD_SHARED_LIBS=ON")
1384 #:phases (modify-phases %standard-phases
1385 (add-before 'configure 'set-library-directory
1387 ;; Install libraries to lib/, not lib64/.
1388 (substitute* "internal/ceres/CMakeLists.txt"
1389 (("set\\(LIB_SUFFIX \"64\"\\)")
1390 "set(LIB_SUFFIX \"\")"))
1393 `(("pkg-config" ,pkg-config)))
1395 `(("glog" ,glog))) ;for #include <glog/glog.h>
1400 ("suitesparse" ,suitesparse)
1401 ("gflags" ,gflags)))
1402 (synopsis "C++ library for solving large optimization problems")
1404 "Ceres Solver is a C++ library for modeling and solving large,
1405 complicated optimization problems. It is a feature rich, mature and
1406 performant library which has been used in production since 2010. Ceres Solver
1407 can solve two kinds of problems:
1409 @item non-linear least squares problems with bounds constraints;
1410 @item general unconstrained optimization problems.
1412 (license license:bsd-3)))
1414 ;; For a fully featured Octave, users are strongly recommended also to install
1415 ;; the following packages: less, ghostscript, gnuplot.
1416 (define-public octave
1423 (uri (string-append "mirror://gnu/octave/octave-"
1427 "0jsdgizlv02an2ppfjwk5qf209zpwi3317yb7jvlsjzxnir3lvhy"))))
1428 (build-system gnu-build-system)
1430 `(("lapack" ,lapack)
1432 ("readline" ,readline)
1437 ("arpack" ,arpack-ng)
1440 ("fontconfig" ,fontconfig)
1441 ("freetype" ,freetype)
1448 ("texinfo" ,texinfo)
1449 ("graphicsmagick" ,graphicsmagick)
1450 ("suitesparse" ,suitesparse)
1451 ("libsndfile" ,libsndfile)
1452 ("portaudio" ,portaudio)
1453 ("alsa-lib" ,alsa-lib)))
1456 ("gfortran" ,gfortran)
1457 ("pkg-config" ,pkg-config)
1459 ;; The following inputs are not actually used in the build process.
1460 ;; However, the ./configure gratuitously tests for their existence and
1461 ;; assumes that programs not present at build time are also not, and
1462 ;; can never be, available at run time! If these inputs are therefore
1463 ;; not present, support for them will be built out. However, Octave
1464 ;; will still run without them, albeit without the features they
1467 ("ghostscript" ,ghostscript)
1468 ("gnuplot" ,gnuplot)))
1469 ;; Octave code uses this variable to detect directories holding multiple CA
1470 ;; certificates to verify peers with. This is required for the networking
1471 ;; functions that require encryption to work properly.
1472 (native-search-paths
1473 (list (search-path-specification
1474 (variable "CURLOPT_CAPATH")
1475 (files '("etc/ssl/certs")))))
1478 (list (string-append "--with-shell="
1479 (assoc-ref %build-inputs "bash")
1482 (modify-phases %standard-phases
1483 (add-after 'configure 'configure-makeinfo
1484 (lambda* (#:key inputs #:allow-other-keys)
1485 (substitute* "libinterp/corefcn/help.cc"
1486 (("Vmakeinfo_program = \"makeinfo\"")
1487 (string-append "Vmakeinfo_program = \""
1488 (assoc-ref inputs "texinfo")
1489 "/bin/makeinfo\"")))
1491 (home-page "https://www.gnu.org/software/octave/")
1492 (synopsis "High-level language for numerical computation")
1493 (description "GNU Octave is a high-level interpreted language that is
1494 specialized for numerical computations. It can be used for both linear and
1495 non-linear applications and it provides great support for visualizing results.
1496 Work may be performed both at the interactive command-line as well as via
1498 (license license:gpl3+)))
1500 (define-public qtoctave
1501 (package (inherit octave)
1504 (inherit (package-source octave))))
1506 `(("qscintilla" ,qscintilla)
1508 ,@(package-inputs octave)))
1510 `(("qttools" , qttools) ;for lrelease
1511 ("texlive" ,texlive) ;for texi2dvi
1512 ,@(package-native-inputs octave)))
1514 (substitute-keyword-arguments (package-arguments octave)
1516 `(modify-phases ,phases
1517 (add-before 'configure 'patch-qscintilla-library-name
1518 (lambda* (#:key inputs #:allow-other-keys)
1519 ;; The QScintilla library that the Octave configure script tries
1520 ;; to link with should be named libqscintilla-qt5.so, but the
1521 ;; QScintilla input provides the shared library as
1522 ;; libqscintilla2_qt5.so.
1523 (substitute* "configure"
1524 (("qscintilla2-qt5")
1528 (define-public opencascade-oce
1530 (name "opencascade-oce")
1536 "https://github.com/tpaviot/oce/archive/OCE-"
1539 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
1542 "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
1543 (build-system cmake-build-system)
1546 (list "-DOCE_TESTING:BOOL=ON"
1547 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1548 "-DOCE_DRAW:BOOL=ON"
1549 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1550 (assoc-ref %outputs "out"))
1551 "-UCMAKE_INSTALL_RPATH")))
1553 `(("freetype" ,freetype)
1560 `(("python" ,python-wrapper)))
1561 (home-page "https://github.com/tpaviot/oce")
1562 (synopsis "Libraries for 3D modeling and numerical simulation")
1564 "Open CASCADE is a set of libraries for the development of applications
1565 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1566 C++ class libraries providing services for 3D surface and solid modeling, CAD
1567 data exchange, and visualization. It is used for development of specialized
1568 software dealing with 3D models in design (CAD), manufacturing (CAM),
1569 numerical simulation (CAE), measurement equipment (CMM), and quality
1570 control (CAQ) domains.
1572 This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1573 patches, improvements, and experiments contributed by users over the official
1574 Open CASCADE library.")
1575 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1576 ; use of header files; see
1577 ; OCCT_LGPL_EXCEPTION.txt
1578 license:public-domain; files
1579 ; src/Standard/Standard_StdAllocator.hxx and
1580 ; src/NCollection/NCollection_StdAllocator.hxx
1581 license:expat; file src/OpenGl/OpenGl_glext.h
1582 license:bsd-3)))); test framework gtest
1591 (uri (string-append "http://gmsh.info/src/gmsh-"
1592 version "-source.tgz"))
1594 (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
1595 (modules '((guix build utils)))
1597 ;; Remove non-free METIS code
1599 (delete-file-recursively "contrib/Metis")
1601 (build-system cmake-build-system)
1604 ("gfortran" ,gfortran)
1610 ("opencascade-oce" ,opencascade-oce)
1612 ("libxext" ,libxext)))
1614 `(("fontconfig" ,fontconfig)
1615 ("libxft" ,libxft)))
1617 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1618 "-DENABLE_BUILD_SHARED:BOOL=ON"
1619 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
1620 (home-page "http://www.geuz.org/gmsh/")
1621 (synopsis "3D finite element grid generator")
1622 (description "Gmsh is a 3D finite element grid generator with a built-in
1623 CAD engine and post-processor. Its design goal is to provide a fast, light
1624 and user-friendly meshing tool with parametric input and advanced
1625 visualization capabilities. Gmsh is built around four modules: geometry,
1626 mesh, solver and post-processing. The specification of any input to these
1627 modules is done either interactively using the graphical user interface or in
1628 ASCII text files using Gmsh's own scripting language.")
1629 (license license:gpl2+)))
1631 (define-public maxflow
1638 (url "https://github.com/gerddie/maxflow.git")
1639 (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
1640 (file-name (string-append name "-" version "-checkout"))
1643 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1644 (build-system cmake-build-system)
1645 (home-page "http://pub.ist.ac.at/~vnk/software.html")
1646 (synopsis "Library implementing Maxflow algorithm")
1647 (description "An implementation of the maxflow algorithm described in
1648 @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1649 Energy Minimization in Computer Vision.\n
1650 Yuri Boykov and Vladimir Kolmogorov.\n
1651 In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1653 (license license:gpl3+)))
1655 (define-public petsc
1662 ;; The *-lite-* tarball does not contain the *large* documentation
1663 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1664 "petsc-lite-" version ".tar.gz"))
1666 (base32 "0bl64pydak3rblnjffi482r8bin4xim9sb37ksl2jkcxf0i0irsi"))))
1667 (outputs '("out" ;libraries and headers
1668 "examples")) ;~30MiB of examples
1669 (build-system gnu-build-system)
1671 `(("python" ,python-2)))
1673 `(("gfortran" ,gfortran)
1675 ("superlu" ,superlu)
1676 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1677 ;; leaving out opengl, as configuration seems to only be for mac
1680 `(#:test-target "test"
1681 #:parallel-build? #f ;build is parallel by default
1687 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1688 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1689 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
1691 (modify-phases %standard-phases
1693 ;; PETSc's configure script is actually a python script, so we can't
1694 ;; run it with bash.
1695 (lambda* (#:key outputs (configure-flags '())
1697 (let* ((prefix (assoc-ref outputs "out"))
1698 (flags `(,(string-append "--prefix=" prefix)
1699 ,@configure-flags)))
1700 (format #t "build directory: ~s~%" (getcwd))
1701 (format #t "configure flags: ~s~%" flags)
1702 (apply invoke "./configure" flags))))
1703 (add-after 'configure 'clean-local-references
1704 (lambda* (#:key outputs #:allow-other-keys)
1705 (let ((out (assoc-ref outputs "out")))
1706 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
1707 ;; Prevent build directory from leaking into compiled code
1709 ;; Scrub timestamp for reproducibility
1710 ((".*Libraries compiled on.*") ""))
1711 (substitute* (find-files "." "petscvariables")
1712 ;; Do not expose build machine characteristics, set to defaults.
1713 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1714 (("NPMAX = [:digit:]+") "NPMAX = 2"))
1716 (add-after 'install 'clean-install
1717 ;; Try to keep installed files from leaking build directory names.
1718 (lambda* (#:key inputs outputs #:allow-other-keys)
1719 (let ((out (assoc-ref outputs "out")))
1720 (substitute* (map (lambda (file)
1721 (string-append out "/lib/petsc/conf/" file))
1722 '("petscvariables"))
1724 ;; Make compiler references point to the store
1725 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
1726 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1727 (string-append "= " (which compiler))))
1728 ;; PETSc installs some build logs, which aren't necessary.
1729 (for-each (lambda (file)
1730 (let ((f (string-append out "/lib/petsc/conf/" file)))
1731 (when (file-exists? f)
1733 '("configure.log" "make.log" "gmake.log"
1734 "test.log" "error.log" "RDict.db"
1735 "PETScBuildInternal.cmake"
1736 ;; Once installed, should uninstall with Guix
1739 (add-after 'install 'move-examples
1740 (lambda* (#:key outputs #:allow-other-keys)
1741 (let* ((out (assoc-ref outputs "out"))
1742 (examples (assoc-ref outputs "examples"))
1743 (exdir (string-append out "/share/petsc/examples"))
1744 (exdir' (string-append examples "/share/petsc/examples")))
1745 (copy-recursively exdir exdir')
1746 (delete-file-recursively exdir)
1748 (home-page "http://www.mcs.anl.gov/petsc")
1749 (synopsis "Library to solve PDEs")
1750 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1751 data structures and routines for the scalable (parallel) solution of
1752 scientific applications modeled by partial differential equations.")
1753 (license (license:non-copyleft
1754 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1756 (define-public petsc-complex
1757 (package (inherit petsc)
1758 (name "petsc-complex")
1760 (substitute-keyword-arguments (package-arguments petsc)
1761 ((#:configure-flags cf)
1762 `(cons "--with-scalar-type=complex" ,cf))))
1763 (synopsis "Library to solve PDEs (with complex scalars)")))
1765 (define-public petsc-openmpi
1766 (package (inherit petsc)
1767 (name "petsc-openmpi")
1769 `(("hdf5" ,hdf5-parallel-openmpi)
1770 ("hypre" ,hypre-openmpi)
1772 ("mumps" ,mumps-openmpi)
1773 ("openmpi" ,openmpi)
1774 ("scalapack" ,scalapack)
1775 ("scotch" ,pt-scotch)
1776 ,@(package-inputs petsc)))
1778 (substitute-keyword-arguments (package-arguments petsc)
1779 ((#:configure-flags cf)
1781 "--with-mpiexec=mpirun"
1784 "--with-scalapack=1"
1786 ,(string-append "--with-mpi-dir="
1787 (assoc-ref %build-inputs "openmpi"))
1788 ,(string-append "--with-hdf5-include="
1789 (assoc-ref %build-inputs "hdf5") "/include")
1790 ,(string-append "--with-hdf5-lib="
1791 (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
1792 ,@(delete "--with-mpi=0" ,cf)))
1794 `(modify-phases ,phases
1795 (add-before 'configure 'mpi-setup
1796 ,%openmpi-setup)))))
1797 (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
1799 (define-public petsc-complex-openmpi
1800 (package (inherit petsc-complex)
1801 (name "petsc-complex-openmpi")
1803 `(("openmpi" ,openmpi)
1804 ,@(package-inputs petsc-complex)))
1806 (substitute-keyword-arguments (package-arguments petsc-complex)
1807 ((#:configure-flags cf)
1808 ``("--with-mpiexec=mpirun"
1809 ,(string-append "--with-mpi-dir="
1810 (assoc-ref %build-inputs "openmpi"))
1811 ,@(delete "--with-mpi=0" ,cf)))))
1812 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
1814 (define-public python-petsc4py
1816 (name "python-petsc4py")
1821 (uri (pypi-uri "petsc4py" version))
1824 "0ch3g6dsvxl7qi984fcssv7cxfbif4bw04gkvxl2l1b8wrmvrm25"))))
1825 (build-system python-build-system)
1828 (modify-phases %standard-phases
1829 (add-before 'build 'pre-build
1831 ;; Define path to PETSc installation.
1832 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
1834 (add-before 'check 'mpi-setup
1837 `(("petsc" ,petsc-openmpi)
1838 ("python-numpy" ,python-numpy)))
1839 (home-page "https://bitbucket.org/petsc/petsc4py/")
1840 (synopsis "Python bindings for PETSc")
1841 (description "PETSc, the Portable, Extensible Toolkit for
1842 Scientific Computation, is a suite of data structures and routines for
1843 the scalable (parallel) solution of scientific applications modeled by
1844 partial differential equations. It employs the MPI standard for all
1845 message-passing communication. @code{petsc4py} provides Python
1846 bindings to almost all functions of PETSc.")
1847 (license license:bsd-3)))
1849 (define-public python-kiwisolver
1851 (name "python-kiwisolver")
1855 (uri (pypi-uri "kiwisolver" version))
1858 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
1859 (build-system python-build-system)
1860 (home-page "https://github.com/nucleic/kiwi")
1861 (synopsis "Fast implementation of the Cassowary constraint solver")
1863 "Kiwi is an efficient C++ implementation of the Cassowary constraint
1864 solving algorithm. Kiwi has been designed from the ground up to be
1865 lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
1866 Cassowary solver with typical use cases gaining a 40x improvement. Memory
1867 savings are consistently > 5x.")
1868 (license license:bsd-3)))
1870 (define-public python2-kiwisolver
1871 (package-with-python2 python-kiwisolver))
1873 (define-public slepc
1880 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
1884 "188j1a133q91h8pivpnzwcf78kz8dvz2nzf6ndnjygdbqb48fizn"))))
1885 (build-system gnu-build-system)
1887 `(("python" ,python-2)))
1889 `(("arpack" ,arpack-ng)
1890 ("gfortran" ,gfortran)))
1892 `(("petsc" ,petsc)))
1894 `(#:parallel-build? #f ;build is parallel by default
1896 `(,(string-append "--with-arpack-dir="
1897 (assoc-ref %build-inputs "arpack") "/lib"))
1898 #:make-flags ;honor (parallel-job-count)
1899 `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
1901 (modify-phases %standard-phases
1903 ;; configure is a python script, so we can't run it with bash.
1904 (lambda* (#:key inputs outputs (configure-flags '())
1906 (let* ((prefix (assoc-ref outputs "out"))
1907 (flags `(,(string-append "--prefix=" prefix)
1908 ,@configure-flags)))
1909 (format #t "build directory: ~s~%" (getcwd))
1910 (format #t "configure flags: ~s~%" flags)
1911 (setenv "SLEPC_DIR" (getcwd))
1912 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
1913 (apply invoke "./configure" flags))))
1914 (add-after 'install 'delete-doc
1915 ;; TODO: SLEPc installs HTML documentation alongside headers in
1916 ;; $out/include. We'd like to move them to share/doc, but delete
1917 ;; them for now, as they are incomplete and installing the complete
1918 ;; documentation is difficult.
1919 (lambda* (#:key outputs #:allow-other-keys)
1920 (let* ((out (assoc-ref outputs "out")))
1921 (for-each delete-file (find-files out "\\.html$"))
1923 (add-after 'install 'clean-install
1924 ;; Clean up unnecessary build logs from installation.
1925 (lambda* (#:key outputs #:allow-other-keys)
1926 (let ((out (assoc-ref outputs "out")))
1927 (for-each (lambda (file)
1928 (let ((f (string-append out "/lib/slepc/conf/" file)))
1929 (when (file-exists? f)
1931 '("configure.log" "make.log" "gmake.log"
1932 "test.log" "error.log" "RDict.db"
1935 (home-page "http://slepc.upv.es")
1936 (synopsis "Scalable library for eigenproblems")
1937 (description "SLEPc is a software library for the solution of large sparse
1938 eigenproblems on parallel computers. It can be used for the solution of
1939 linear eigenvalue problems formulated in either standard or generalized form,
1940 as well as other related problems such as the singular value decomposition.
1941 The emphasis of the software is on methods and techniques appropriate for
1942 problems in which the associated matrices are sparse, for example, those
1943 arising after the discretization of partial differential equations.")
1944 (license license:bsd-2)))
1946 (define-public slepc-complex
1947 (package (inherit slepc)
1948 (name "slepc-complex")
1950 `(("petsc" ,petsc-complex)
1951 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1952 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1954 (define-public slepc-openmpi
1955 (package (inherit slepc)
1956 (name "slepc-openmpi")
1958 (substitute-keyword-arguments (package-arguments slepc)
1959 ((#:phases phases '%standard-phases)
1960 `(modify-phases ,phases
1961 (add-before 'check 'mpi-setup
1962 ,%openmpi-setup)))))
1965 ("arpack" ,arpack-ng-openmpi)
1966 ,@(alist-delete "arpack" (package-inputs slepc))))
1968 `(("petsc" ,petsc-openmpi)
1969 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1970 (synopsis "Scalable library for eigenproblems (with MPI support)")))
1972 (define-public slepc-complex-openmpi
1973 (package (inherit slepc-openmpi)
1974 (name "slepc-complex-openmpi")
1976 `(("petsc" ,petsc-complex-openmpi)
1977 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1978 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1980 (define-public python-slepc4py
1982 (name "python-slepc4py")
1987 (uri (pypi-uri "slepc4py" version))
1990 "0x049dyc8frgh79fvvavf4vlbqp4mgm61nsaivzdav4316vvlv1j"))))
1991 (build-system python-build-system)
1994 (modify-phases %standard-phases
1995 (add-before 'build 'pre-build
1997 ;; Define path to PETSc installation.
1998 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
1999 ;; Define path to SLEPc installation.
2000 (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
2002 (add-before 'check 'mpi-setup
2005 `(("python-numpy" ,python-numpy)
2006 ("python-petsc4py" ,python-petsc4py)
2007 ("slepc" ,slepc-openmpi)))
2008 (home-page "https://bitbucket.org/slepc/slepc4py/")
2009 (synopsis "Python bindings for SLEPc")
2010 (description "SLEPc, the Scalable Library for Eigenvalue Problem
2011 Computations, is based on PETSc, the Portable, Extensible Toolkit for
2012 Scientific Computation. It employs the MPI standard for all
2013 message-passing communication. @code{slepc4py} provides Python
2014 bindings to almost all functions of SLEPc.")
2015 (license license:bsd-3)))
2017 (define-public mumps
2024 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
2028 "1s9asin08zqzmh08257sdghhivvy9vjif7c53fhaxaax2kd5qd7b"))
2029 (patches (search-patches "mumps-build-parallelism.patch"))))
2030 (build-system gnu-build-system)
2032 `(("fortran" ,gfortran)
2033 ;; These are required for linking against mumps, but we let the user
2034 ;; declare the dependency.
2037 ("scotch" ,scotch)))
2039 `(#:modules ((ice-9 match)
2042 ,@%gnu-build-system-modules)
2044 (modify-phases %standard-phases
2046 (lambda* (#:key inputs #:allow-other-keys)
2047 (call-with-output-file "Makefile.inc"
2058 INCSEQ = -I$(topdir)/libseq
2059 LIBSEQ = -L$(topdir)/libseq -lmpiseq
2060 LIBSEQNEEDED = libseqneeded~;
2064 AR = ar vr # rules require trailing space, ugh...
2066 LIBBLAS = -L~a -lopenblas~@[
2067 SCALAP = -L~a -lscalapack~]
2068 LIBOTHERS = -pthread
2071 OPTF = -O2 -DALLOW_NON_INIT $(PIC)
2075 LIBS = $(SCALAP) $(LIBSEQ)
2076 LPORDDIR = $(topdir)/PORD/lib
2077 IPORD = -I$(topdir)/PORD/include
2078 LPORD = -L$(LPORDDIR) -lpord
2079 ORDERINGSF = -Dpord~@[
2081 IMETIS = -I$(METISDIR)/include
2082 LMETIS = -L$(METISDIR)/lib -lmetis
2083 ORDERINGSF += -Dmetis~]~@[~:{
2085 ISCOTCH = -I$(SCOTCHDIR)/include
2086 LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
2087 ORDERINGSF += ~a~}~]
2088 ORDERINGSC = $(ORDERINGSF)
2089 LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
2090 IORDERINGSF = $(ISCOTCH)
2091 IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
2092 (assoc-ref inputs "mpi")
2093 (assoc-ref inputs "blas")
2094 (assoc-ref inputs "scalapack")
2095 (assoc-ref inputs "metis")
2096 (match (list (assoc-ref inputs "pt-scotch")
2097 (assoc-ref inputs "scotch"))
2101 `((,scotch "" "-Dscotch")))
2104 "-lptesmumps -lptscotch -lptscotcherr "
2105 "-Dptscotch")))))))))
2107 ;; By default only the d-precision library is built. Make with "all"
2108 ;; target so that all precision libraries and examples are built.
2110 (invoke "make" "all"
2111 (format #f "-j~a" (parallel-job-count)))))
2113 ;; Run the simple test drivers, which read test input from stdin:
2114 ;; from the "real" input for the single- and double-precision
2115 ;; testers, and from the "cmplx" input for complex-precision
2116 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
2117 ;; package to prefix execution with "mpirun".
2118 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
2119 (with-directory-excursion "examples"
2122 (let ((tester (apply open-pipe*
2125 ,(string-append "./" prec
2127 (input (open-input-file
2128 (string-append "input_simpletest_" type))))
2130 (dump-port input tester)
2132 (zero? (close-pipe tester)))))
2134 '("real" "real" "cmplx" "cmplx")))))
2136 (lambda* (#:key outputs #:allow-other-keys)
2137 (let* ((out (assoc-ref outputs "out"))
2138 (libdir (string-append out "/lib")))
2139 (copy-recursively "lib" libdir)
2140 (copy-recursively "include" (string-append out "/include"))
2141 (when (file-exists? "libseq/libmpiseq.a")
2142 (install-file "libseq/libmpiseq.a" libdir))
2144 (home-page "http://mumps.enseeiht.fr")
2145 (synopsis "Multifrontal sparse direct solver")
2147 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
2148 sparse system of linear equations A x = b using Guassian elimination.")
2149 (license license:cecill-c)))
2151 (define-public mumps-metis
2152 (package (inherit mumps)
2153 (name "mumps-metis")
2155 (alist-delete "scotch" (package-inputs mumps)))))
2157 (define-public mumps-openmpi
2158 (package (inherit mumps)
2159 (name "mumps-openmpi")
2162 ("scalapack" ,scalapack)
2163 ("pt-scotch" ,pt-scotch)
2164 ,@(alist-delete "scotch" (package-inputs mumps))))
2166 (substitute-keyword-arguments (package-arguments mumps)
2168 `(modify-phases ,phases
2169 (add-before 'check 'mpi-setup
2173 ((assoc-ref ,phases 'check)
2174 #:exec-prefix '("mpirun" "-n" "2"))))))))
2175 (synopsis "Multifrontal sparse direct solver (with MPI)")))
2177 (define-public mumps-metis-openmpi
2178 (package (inherit mumps-openmpi)
2179 (name "mumps-metis-openmpi")
2181 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
2183 (define-public r-quadprog
2190 (uri (cran-uri "quadprog" version))
2193 "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
2194 (build-system r-build-system)
2196 `(("gfortran" ,gfortran)))
2197 (home-page "https://cran.r-project.org/web/packages/quadprog")
2198 (synopsis "Functions to solve quadratic programming problems")
2200 "This package contains routines and documentation for solving quadratic
2201 programming problems.")
2202 (license license:gpl3+)))
2204 (define-public r-pracma
2210 (uri (cran-uri "pracma" version))
2212 (base32 "0m8ladhrfyxwybblkcdgg4xv1mk5kibmwarpj2k0c2y34zzcix4z"))))
2213 (build-system r-build-system)
2214 (home-page "https://cran.r-project.org/web/packages/pracma/")
2215 (synopsis "Practical numerical math functions")
2216 (description "This package provides functions for numerical analysis and
2217 linear algebra, numerical optimization, differential equations, plus some
2218 special functions. It uses Matlab function names where appropriate to simplify
2220 (license license:gpl3+)))
2222 (define-public ruby-asciimath
2224 (name "ruby-asciimath")
2229 (uri (rubygems-uri "asciimath" version))
2232 "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
2233 (build-system ruby-build-system)
2236 (modify-phases %standard-phases
2238 ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
2239 (add-after 'unpack 'patch-remove-spurious-backslashes
2241 (substitute* "spec/parser_spec.rb"
2246 `(("bundler" ,bundler)
2247 ("ruby-rspec" ,ruby-rspec)))
2248 (synopsis "AsciiMath parsing and conversion library")
2250 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
2251 easy-to-write markup language for mathematics.")
2252 (home-page "https://github.com/asciidoctor/asciimath")
2253 (license license:expat)))
2255 (define-public superlu
2262 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2263 "superlu_" version ".tar.gz"))
2265 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
2266 (modules '((guix build utils)))
2268 ;; Replace the non-free implementation of MC64 with a stub adapted
2271 (use-modules (ice-9 regex)
2273 (call-with-output-file "SRC/mc64ad.c"
2278 void mc64id_(int *a) {
2279 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2282 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2283 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2284 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2287 ;; Remove the corresponding license verbiage. MC64 license follows
2288 ;; a "------" line separator.
2289 (with-atomic-file-replacement "License.txt"
2290 (let ((rx (make-regexp "-{8}")))
2293 (let ((line (read-line in 'concat)))
2294 (unless (regexp-exec rx line)
2298 (build-system cmake-build-system)
2302 `(("blas" ,openblas)
2303 ("gfortran" ,gfortran)))
2305 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2306 "-DTPL_BLAS_LIBRARIES=openblas"
2307 "-DBUILD_SHARED_LIBS:BOOL=YES")))
2308 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
2309 (synopsis "Supernodal direct solver for sparse linear systems")
2311 "SuperLU is a general purpose library for the direct solution of large,
2312 sparse, nonsymmetric systems of linear equations on high performance machines.
2313 The library is written in C and is callable from either C or Fortran. The
2314 library routines perform an LU decomposition with partial pivoting and
2315 triangular system solves through forward and back substitution. The library
2316 also provides threshold-based ILU factorization preconditioners.")
2317 (license (list license:bsd-3
2318 license:gpl2+ ;EXAMPLE/*fgmr.c
2319 (license:fsf-free "file://SRC/colamd.h")))))
2321 (define-public superlu-dist
2323 (name "superlu-dist")
2328 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2329 "superlu_dist_" version ".tar.gz"))
2331 (base32 "0ja5ihqivkda1wd58y4lmzvmwssm9g91f70c5q0fzwhng6580h6y"))
2332 (modules '((guix build utils)))
2334 ;; Replace the non-free implementation of MC64 with a stub
2336 (use-modules (ice-9 regex)
2338 (call-with-output-file "SRC/mc64ad_dist.c"
2343 void mc64id_dist(int *a) {
2344 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2347 void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2348 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2349 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2352 (substitute* "SRC/util.c" ;adjust default algorithm
2353 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
2354 "RowPerm = NOROWPERM"))
2356 (patches (search-patches "superlu-dist-scotchmetis.patch"))))
2357 (build-system gnu-build-system)
2361 `(("gfortran" ,gfortran)))
2363 `(("openmpi" ,openmpi) ;headers include MPI heades
2364 ("lapack" ,lapack) ;required to link with output library
2365 ("pt-scotch" ,pt-scotch))) ;same
2367 `(#:parallel-build? #f ;race conditions using ar
2369 (modify-phases %standard-phases
2371 (lambda* (#:key inputs outputs #:allow-other-keys)
2372 (call-with-output-file "make.inc"
2377 DSUPERLULIB = ~a/lib/libsuperlu_dist.a
2378 BLASDEF = -DUSE_VENDOR_BLAS
2379 BLASLIB = -L~a/lib -lblas
2380 PARMETISLIB = -L~a/lib \
2381 -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
2382 -lscotch -lscotcherr -lscotcherrexit
2383 METISLIB = -L~:*~a/lib \
2384 -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
2385 LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
2391 CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC)
2392 NOOPTS = -O0 -g $(PIC)
2394 FFLAGS = -O2 -g $(PIC)
2398 (assoc-ref outputs "out")
2399 (assoc-ref inputs "lapack")
2400 (assoc-ref inputs "pt-scotch"))))
2402 (add-after 'unpack 'remove-broken-symlinks
2404 (for-each delete-file
2405 (find-files "MAKE_INC" "\\.#make\\..*"))
2407 (add-before 'build 'create-install-directories
2408 (lambda* (#:key outputs #:allow-other-keys)
2411 (mkdir-p (string-append (assoc-ref outputs "out")
2415 (add-before 'check 'mpi-setup
2419 (with-directory-excursion "EXAMPLE"
2420 (invoke "mpirun" "-n" "2"
2421 "./pddrive" "-r" "1" "-c" "2" "g20.rua")
2422 (invoke "mpirun" "-n" "2"
2423 "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))
2426 (lambda* (#:key outputs #:allow-other-keys)
2427 ;; Library is placed in lib during the build phase. Copy over
2428 ;; headers to include.
2429 (let* ((out (assoc-ref outputs "out"))
2430 (incdir (string-append out "/include")))
2431 (for-each (lambda (file)
2432 (let ((base (basename file)))
2433 (format #t "installing `~a' to `~a'~%"
2436 (string-append incdir "/" base))))
2437 (find-files "SRC" ".*\\.h$")))
2439 (home-page (package-home-page superlu))
2440 (synopsis "Parallel supernodal direct solver")
2442 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2443 It is targeted for distributed memory parallel machines. SuperLU_DIST is
2444 implemented in ANSI C, and MPI for communications.")
2445 (license license:bsd-3)))
2447 (define-public scotch
2454 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
2455 "latestfile/298/scotch_" version ".tar.gz"))
2457 (base32 "0vsmgjz8qv80di3ljmc7hbdsizxxxwy2b9rgd2fl1mdc6dgbj8av"))
2458 (patches (search-patches "scotch-test-threading.patch"
2459 "scotch-build-parallelism.patch"
2460 "scotch-graph-induce-type-64.patch"
2461 "scotch-graph-diam-64.patch"))))
2462 (build-system gnu-build-system)
2469 (modify-phases %standard-phases
2471 'unpack 'chdir-to-src
2472 (lambda _ (chdir "src") #t))
2476 (call-with-output-file "Makefile.inc"
2490 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2491 LDFLAGS = -lz -lm -lrt -lpthread
2493 LEX = flex -Pscotchyy -olex.yy.c
2498 YACC = bison -pscotchyy -y -b y
2500 '("COMMON_FILE_COMPRESS_GZ"
2502 "COMMON_RANDOM_FIXED_SEED"
2503 "INTSIZE64" ;use 'long' instead of 'int'
2504 ;; Prevents symbolc clashes with libesmumps
2506 ;; XXX: Causes invalid frees in superlu-dist tests
2508 ;; "SCOTCH_PTHREAD_NUMBER=2"
2509 "restrict=__restrict"))))
2511 (add-after 'build 'build-esmumps
2514 (format #f "-j~a" (parallel-job-count))
2518 (lambda* (#:key outputs #:allow-other-keys)
2519 (let ((out (assoc-ref outputs "out")))
2522 (string-append "prefix=" out)
2524 ;; esmumps files are not installed with the above
2525 (for-each (lambda (f)
2526 (copy-file f (string-append out "/include/" f)))
2527 (find-files "../include" ".*esmumps.h$"))
2528 (for-each (lambda (f)
2529 (copy-file f (string-append out "/lib/" f)))
2530 (find-files "../lib" "^lib.*esmumps.*"))
2532 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
2533 (synopsis "Programs and libraries for graph algorithms")
2534 (description "SCOTCH is a set of programs and libraries which implement
2535 the static mapping and sparse matrix reordering algorithms developed within
2536 the SCOTCH project. Its purpose is to apply graph theory, with a divide and
2537 conquer approach, to scientific computing problems such as graph and mesh
2538 partitioning, static mapping, and sparse matrix ordering, in application
2539 domains ranging from structural mechanics to operating systems or
2541 ;; See LICENSE_en.txt
2542 (license license:cecill-c)))
2544 (define-public scotch32
2545 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2546 ;; some applications.
2547 (package (inherit scotch)
2550 (substitute-keyword-arguments (package-arguments scotch)
2551 ((#:phases scotch-phases)
2552 `(modify-phases ,scotch-phases
2556 (call-with-output-file "Makefile.inc"
2570 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2571 LDFLAGS = -lz -lm -lrt -lpthread
2573 LEX = flex -Pscotchyy -olex.yy.c
2578 YACC = bison -pscotchyy -y -b y
2580 '("COMMON_FILE_COMPRESS_GZ"
2582 "COMMON_RANDOM_FIXED_SEED"
2583 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
2584 ;; Prevents symbolc clashes with libesmumps
2586 ;; XXX: Causes invalid frees in superlu-dist tests
2588 ;; "SCOTCH_PTHREAD_NUMBER=2"
2589 "restrict=__restrict"))))))))))
2591 "Programs and libraries for graph algorithms (32-bit integers)")))
2593 (define-public pt-scotch
2594 (package (inherit scotch)
2597 `(("openmpi" ,openmpi))) ;Headers include MPI headers
2599 (substitute-keyword-arguments (package-arguments scotch)
2600 ((#:phases scotch-phases)
2601 `(modify-phases ,scotch-phases
2605 (invoke "make" (format #f "-j~a" (parallel-job-count))
2606 "ptscotch" "ptesmumps")
2608 ;; Install the serial metis compatibility library
2609 (invoke "make" "-C" "libscotchmetis" "install")))
2610 (add-before 'check 'mpi-setup
2614 (invoke "make" "ptcheck")))))))
2615 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
2617 (define-public pt-scotch32
2618 (package (inherit scotch32)
2619 (name "pt-scotch32")
2621 `(("openmpi" ,openmpi))) ;headers include MPI headers
2623 (substitute-keyword-arguments (package-arguments scotch32)
2624 ((#:phases scotch32-phases)
2625 `(modify-phases ,scotch32-phases
2628 (invoke "make" (format #f "-j~a" (parallel-job-count))
2629 "ptscotch" "ptesmumps")
2630 ;; Install the serial metis compatibility library
2631 (invoke "make" "-C" "libscotchmetis" "install")))
2632 (add-before 'check 'mpi-setup
2636 (invoke "make" "ptcheck")))))))
2638 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2640 (define-public metis
2647 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2648 "metis-" version ".tar.gz"))
2651 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2652 (build-system cmake-build-system)
2654 `(("blas" ,openblas)))
2656 `(#:tests? #f ;no tests
2657 #:configure-flags `("-DSHARED=ON"
2658 ,(string-append "-DGKLIB_PATH=" (getcwd)
2659 "/metis-" ,version "/GKlib"))))
2660 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2661 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2663 "METIS is a set of serial programs for partitioning graphs, partitioning
2664 finite element meshes, and producing fill-reducing orderings for sparse
2665 matrices. The algorithms implemented in METIS are based on the multilevel
2666 recursive-bisection, multilevel k-way, and multi-constraint partitioning
2668 (license license:asl2.0))) ;As of version 5.0.3
2670 (define-public p4est
2677 (uri (string-append "http://p4est.github.io/release/p4est-"
2681 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
2682 (build-system gnu-build-system)
2684 `(("fortran" ,gfortran)
2689 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2690 (assoc-ref %build-inputs "blas")
2692 ,(string-append "LAPACK_LIBS=-L"
2693 (assoc-ref %build-inputs "lapack")
2695 #:phases (modify-phases %standard-phases
2696 (add-before 'check 'mpi-setup
2698 (home-page "http://www.p4est.org")
2699 (synopsis "Adaptive mesh refinement on forests of octrees")
2701 "The p4est software library enables the dynamic management of a
2702 collection of adaptive octrees, conveniently called a forest of octrees.
2703 p4est is designed to work in parallel and scales to hundreds of thousands of
2705 (license license:gpl2+)))
2707 (define-public p4est-openmpi
2708 (package (inherit p4est)
2709 (name "p4est-openmpi")
2712 ,@(package-inputs p4est)))
2714 (substitute-keyword-arguments (package-arguments p4est)
2715 ((#:configure-flags cf)
2716 ``("--enable-mpi" ,@,cf))))
2717 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2719 (define-public gsegrafix
2726 (uri (string-append "mirror://gnu/" name "/" name "-"
2730 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2731 (build-system gnu-build-system)
2733 `(#:configure-flags '("LDFLAGS=-lm")))
2735 `(("libgnomecanvas" ,libgnomecanvas)
2736 ("libbonoboui" ,libbonoboui)
2737 ("libgnomeui" ,libgnomeui)
2738 ("libgnomeprintui" ,libgnomeprintui)
2741 `(("pkg-config" ,pkg-config)))
2742 (home-page "https://www.gnu.org/software/gsegrafix/")
2743 (synopsis "GNOME application to create scientific and engineering plots")
2744 (description "GSEGrafix is an application which produces high-quality graphical
2745 plots for science and engineering. Plots are specified via simple ASCII
2746 parameter files and data files and are presented in an anti-aliased GNOME
2747 canvas. The program supports rectangular two-dimensional plots, histograms,
2748 polar-axis plots and three-dimensional plots. Plots can be printed or saved
2749 to BMP, JPEG or PNG image formats.")
2750 (license license:gpl3+)))
2752 (define-public maxima
2759 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2760 version "-source/" name "-" version ".tar.gz"))
2763 "1ka0xf70a55ndgmyrq7p5xxbd78pq7bfkqhgxsivaqdw6gn5lmcg"))
2764 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
2765 (build-system gnu-build-system)
2768 ("gnuplot" ,gnuplot) ;for plots
2769 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
2771 `(("texinfo" ,texinfo)
2773 ("python" ,python)))
2776 (list "--enable-gcl"
2777 (string-append "--with-posix-shell="
2778 (assoc-ref %build-inputs "bash")
2780 (string-append "--with-wish="
2781 (assoc-ref %build-inputs "tk")
2783 (let ((v ,(package-version tk)))
2784 (string-take v (string-index-right v #\.)))))
2785 ;; By default Maxima attempts to write temporary files to
2786 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2787 ;; Work around that.
2788 #:make-flags (list "TMPDIR=/tmp")
2790 (modify-phases %standard-phases
2791 (add-before 'check 'pre-check
2793 (chmod "src/maxima" #o555)
2797 ;; This is derived from the testing code in the "debian/rules" file
2798 ;; of Debian's Maxima package.
2799 ;; If Maxima can successfully run this, the binary to be installed
2803 (string-append "./maxima-local "
2805 "--batch-string=\"run_testsuite();\" "
2806 "| grep -q \"No unexpected errors found\"")))))
2807 ;; Make sure the doc and emacs files are found in the
2808 ;; standard location. Also configure maxima to find gnuplot
2809 ;; without having it on the PATH.
2810 (add-after 'install 'post-install
2811 (lambda* (#:key outputs inputs #:allow-other-keys)
2812 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2813 (out (assoc-ref outputs "out"))
2814 (datadir (string-append out "/share/maxima/" ,version))
2815 (binutils (string-append (assoc-ref inputs "binutils")
2817 (with-directory-excursion out
2818 (mkdir-p "share/emacs")
2819 (mkdir-p "share/doc")
2821 (string-append datadir "/emacs/")
2822 (string-append out "/share/emacs/site-lisp"))
2824 (string-append datadir "/doc/")
2825 (string-append out "/share/doc/maxima"))
2826 (with-atomic-file-replacement
2827 (string-append datadir "/share/maxima-init.lisp")
2829 (format out "~a ~s~a~%"
2830 "(setf $gnuplot_command "
2831 (string-append gnuplot "/bin/gnuplot") ")")
2832 (dump-port in out))))
2833 ;; Ensure that Maxima will have access to the GNU binutils
2834 ;; components at runtime.
2835 (wrap-program (string-append out "/bin/maxima")
2836 `("PATH" prefix (,binutils))))
2838 (home-page "http://maxima.sourceforge.net")
2839 (synopsis "Numeric and symbolic expression manipulation")
2840 (description "Maxima is a system for the manipulation of symbolic and
2841 numerical expressions. It yields high precision numeric results by using
2842 exact fractions, arbitrary precision integers, and variable precision floating
2844 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2845 ;; Others simply say "GNU General Public License" without stating a
2846 ;; version (which implicitly means gpl1+).
2847 ;; At least one file (src/maxima.asd) says "version 2."
2848 ;; GPLv2 only is therefore the smallest subset.
2849 (license license:gpl2)))
2851 (define-public wxmaxima
2859 (url "https://github.com/wxMaxima-developers/wxmaxima.git")
2860 (commit (string-append "Version-" version))))
2861 (file-name (git-file-name name version))
2864 "1sz8n9v23q442l7yjj67pjh0dk78rl4cbcc3j8m1bm88anlfxl9r"))))
2865 (build-system cmake-build-system)
2867 `(("gettext" ,gettext-minimal)))
2869 `(("wxwidgets" ,wxwidgets)
2872 ("adwaita-icon-theme" ,adwaita-icon-theme)
2874 ("shared-mime-info" ,shared-mime-info)))
2876 `(#:tests? #f ; no check target
2878 (modify-phases %standard-phases
2879 (add-after 'install 'wrap-program
2880 (lambda* (#:key inputs outputs #:allow-other-keys)
2881 (wrap-program (string-append (assoc-ref outputs "out")
2884 (,(string-append (assoc-ref inputs "maxima")
2886 ;; For GtkFileChooserDialog.
2887 `("GSETTINGS_SCHEMA_DIR" =
2888 (,(string-append (assoc-ref inputs "gtk+")
2889 "/share/glib-2.0/schemas")))
2890 `("XDG_DATA_DIRS" ":" prefix
2891 (;; Needed by gdk-pixbuf to know supported icon formats.
2893 (assoc-ref inputs "shared-mime-info") "/share")
2894 ;; The default icon theme of GTK+.
2896 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
2898 (home-page "https://andrejv.github.io/wxmaxima/")
2899 (synopsis "Graphical user interface for the Maxima computer algebra system")
2901 "wxMaxima is a graphical user interface for the Maxima computer algebra
2902 system. It eases the use of Maxima by making most of its commands available
2903 through a menu system and by providing input dialogs for commands that require
2904 more than one argument. It also implements its own display engine that
2905 outputs mathematical symbols directly instead of depicting them with ASCII
2908 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
2909 text and mathematical calculations to create documents, exporting of input and
2910 output to TeX, and a browser for Maxima's manual including command index and
2911 full text searching.")
2912 (license license:gpl2+)))
2914 (define-public armadillo
2920 (uri (string-append "mirror://sourceforge/arma/armadillo-"
2924 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
2925 (build-system cmake-build-system)
2926 (arguments `(#:tests? #f)) ; no test target
2928 `(("openblas" ,openblas)
2930 ("arpack" ,arpack-ng)))
2931 (home-page "http://arma.sourceforge.net/")
2932 (synopsis "C++ linear algebra library")
2934 "Armadillo is a C++ linear algebra library, aiming towards a good balance
2935 between speed and ease of use. It is useful for algorithm development
2936 directly in C++, or quick conversion of research code into production
2937 environments. It can be used for machine learning, pattern recognition,
2938 signal processing, bioinformatics, statistics, econometrics, etc. The library
2939 provides efficient classes for vectors, matrices and cubes, as well as 150+
2940 associated functions (eg. contiguous and non-contiguous submatrix views).")
2941 (license license:asl2.0)))
2943 (define-public muparser
2944 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2945 ;; different hash. In order to make `guix package --upgrade` work correctly,
2946 ;; we set a Guix packaging revision.
2947 ;; When the next version of muparser is released, we can remove
2948 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2949 (let ((upstream-version "2.2.5")
2953 (version (string-append upstream-version "-" revision))
2957 (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
2958 upstream-version ".tar.gz"))
2959 (file-name (string-append name "-" version ".tar.gz"))
2962 "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
2963 (build-system gnu-build-system)
2965 `(#:configure-flags '("--enable-samples=no")
2966 #:tests? #f)) ;no "check" target
2967 (home-page "http://muparser.beltoforion.de/")
2968 (synopsis "Fast parser library for mathematical expressions")
2970 "muParser is an extensible high performance math parser library. It is
2971 based on transforming an expression into a bytecode and precalculating constant
2973 (license license:expat))))
2975 (define-public openblas
2982 (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
2983 version "%20version.tar.gz"))
2984 (file-name (string-append name "-" version ".tar.gz"))
2987 "0cvlixnpc3cdvvn3f30phfvsgnqljqix6wn72ps9rj7xdhvw06jg"))))
2988 (build-system gnu-build-system)
2990 `(#:test-target "test"
2991 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
2992 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2993 ;; we need to disable substitutions.
2995 ,(let ((system (or (%current-target-system) (%current-system))))
2996 (or (string-prefix? "x86_64" system)
2997 (string-prefix? "i686" system)
2998 (string-prefix? "mips" system)
2999 (string-prefix? "aarch64" system)))
3001 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
3003 ;; Build the library for all supported CPUs. This allows
3004 ;; switching CPU targets at runtime with the environment variable
3005 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
3006 ;; Unfortunately, this is not supported on non-x86 architectures,
3007 ;; where it leads to failed builds.
3008 ,@(let ((system (or (%current-target-system) (%current-system))))
3010 ((or (string-prefix? "x86_64" system)
3011 (string-prefix? "i686" system))
3012 '("DYNAMIC_ARCH=1"))
3013 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
3014 ;; two available MIPS targets special extended instructions
3015 ;; for Loongson cores are used.
3016 ((string-prefix? "mips" system)
3017 '("TARGET=SICORTEX"))
3018 ;; On aarch64 force the generic 'armv8-a' target
3019 ((string-prefix? "aarch64" system)
3022 ;; no configure script
3024 (modify-phases %standard-phases
3026 (add-before 'build 'set-extralib
3027 (lambda* (#:key inputs #:allow-other-keys)
3028 ;; Get libgfortran found when building in utest.
3030 (string-append "-L" (assoc-ref inputs "fortran-lib")
3034 `(("fortran-lib" ,gfortran "lib")))
3037 ("fortran" ,gfortran)
3039 (home-page "http://www.openblas.net/")
3040 (synopsis "Optimized BLAS library based on GotoBLAS")
3042 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
3043 (license license:bsd-3)))
3045 (define-public openblas-ilp64
3046 (package (inherit openblas)
3047 (name "openblas-ilp64")
3048 (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
3050 (substitute-keyword-arguments (package-arguments openblas)
3051 ((#:make-flags flags '())
3052 `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
3054 (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
3055 (license license:bsd-3)))
3057 (define* (make-blis implementation #:optional substitutable?)
3058 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
3059 source tree for a list of implementations.)
3061 SUBSTITUTABLE? determines whether the package is made available as a
3064 Currently the specialization must be selected at configure-time, but work is
3065 underway to allow BLIS to select the right optimized kernels at run time:
3066 <https://github.com/flame/blis/issues/129>."
3068 (name (if (string=? implementation "reference")
3070 (string-append "blis-" implementation)))
3072 (home-page "https://github.com/flame/blis")
3075 (uri (git-reference (url home-page) (commit version)))
3078 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
3079 (file-name (git-file-name "blis" version))))
3080 (build-system gnu-build-system)
3082 `(#:test-target "test"
3084 #:substitutable? ,substitutable?
3086 #:phases (modify-phases %standard-phases
3088 (lambda* (#:key outputs #:allow-other-keys)
3089 ;; This is a home-made 'configure' script.
3090 (let ((out (assoc-ref outputs "out")))
3091 (zero? (system* "./configure" "-p" out
3095 "--enable-threading=openmp"
3097 ,implementation)))))
3098 (add-before 'check 'show-test-output
3100 ;; By default "make check" is silent. Make it verbose.
3101 (system "tail -F output.testsuite &")
3103 (synopsis "High-performance basic linear algebra (BLAS) routines")
3105 "BLIS is a portable software framework for instantiating high-performance
3106 BLAS-like dense linear algebra libraries. The framework was designed to
3107 isolate essential kernels of computation that, when optimized, immediately
3108 enable optimized implementations of most of its commonly used and
3109 computationally intensive operations. While BLIS exports a new BLAS-like API,
3110 it also includes a BLAS compatibility layer which gives application developers
3111 access to BLIS implementations via traditional BLAS routine calls.")
3112 (license license:bsd-3)))
3115 ;; This is the "reference" implementation, which is the non-optimized but
3116 ;; portable variant (no assembly).
3117 (make-blis "reference" #t))
3119 (define ignorance blis)
3121 (define-syntax-rule (blis/x86_64 processor)
3122 "Expand to a package specialized for PROCESSOR."
3124 (inherit (make-blis processor))
3125 (supported-systems '("x86_64-linux"))))
3127 (define-public blis-sandybridge
3128 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
3129 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
3130 (blis/x86_64 "sandybridge"))
3132 (define-public blis-haswell
3133 ;; BLIS specialized for Haswell processors (launched 2013):
3134 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
3135 (blis/x86_64 "haswell"))
3137 (define-public blis-knl
3138 ;; BLIS specialized for Knights Landing processor (launched 2016):
3139 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
3140 (blis/x86_64 "knl"))
3143 (define-public openlibm
3150 (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
3152 (file-name (string-append name "-" version ".tar.gz"))
3155 "0a5fpm8nra5ldhjk0cqd2rx1qh32wiarkxmcqcm5xl8z7l4kjm6l"))))
3156 (build-system gnu-build-system)
3159 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3161 ;; no configure script
3162 (modify-phases %standard-phases (delete 'configure))
3163 #:tests? #f)) ;the tests are part of the default target
3164 (home-page "http://openlibm.org/")
3165 (synopsis "Portable C mathematical library (libm)")
3167 "OpenLibm is an effort to have a high quality, portable, standalone C
3168 mathematical library (libm). It can be used standalone in applications and
3169 programming language implementations. The project was born out of a need to
3170 have a good libm for the Julia programming language that worked consistently
3171 across compilers and operating systems, and in 32-bit and 64-bit
3173 ;; Each architecture has its own make target, and there is none for mips.
3174 (supported-systems (delete "mips64el-linux" %supported-systems))
3175 ;; See LICENSE.md for details.
3176 (license (list license:expat
3179 license:public-domain
3180 license:lgpl2.1+))))
3182 (define-public openspecfun
3184 (name "openspecfun")
3189 (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
3191 (file-name (string-append name "-" version ".tar.gz"))
3194 "1rs1bv8jq751fv9vq79890wqf9xlbjc7lvz3ighzyfczbyjcf18m"))))
3195 (build-system gnu-build-system)
3197 '(#:tests? #f ; no "check" target
3199 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3201 (modify-phases %standard-phases
3202 (delete 'configure)))) ; no configure script
3204 `(("fortran" ,gfortran)))
3205 (home-page "https://github.com/JuliaLang/openspecfun")
3206 (synopsis "Collection of special mathematical functions")
3208 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
3209 portable package for Bessel Functions of a Complex Argument and Nonnegative
3210 Order; it contains subroutines for computing Bessel functions and Airy
3211 functions. Faddeeva allows computing the various error functions of arbitrary
3212 complex arguments (Faddeeva function, error function, complementary error
3213 function, scaled complementary error function, imaginary error function, and
3214 Dawson function); given these, one can also easily compute Voigt functions,
3215 Fresnel integrals, and similar related functions as well.")
3216 ;; Faddeeva is released under the Expat license; AMOS is included as
3217 ;; public domain software.
3218 (license (list license:expat license:public-domain))))
3220 (define-public suitesparse
3222 (name "suitesparse")
3228 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
3232 "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
3233 (modules '((guix build utils)))
3235 ;; Remove bundled metis source
3237 (delete-file-recursively "metis-5.1.0")
3239 (build-system gnu-build-system)
3241 '(#:tests? #f ;no "check" target
3246 "MY_METIS_LIB=-lmetis"
3247 (string-append "INSTALL_LIB="
3248 (assoc-ref %outputs "out") "/lib")
3249 (string-append "INSTALL_INCLUDE="
3250 (assoc-ref %outputs "out") "/include")
3253 (modify-phases %standard-phases
3254 (delete 'configure)))) ;no configure script
3259 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
3260 (synopsis "Suite of sparse matrix software")
3262 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
3263 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
3264 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
3265 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
3266 CXSparse, a concise sparse Cholesky factorization package; and many other
3269 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
3271 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
3272 (license (list license:gpl2+ license:lgpl2.1+))))
3274 (define-public atlas
3280 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
3281 version "/atlas" version ".tar.bz2"))
3284 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
3285 (build-system gnu-build-system)
3286 (home-page "http://math-atlas.sourceforge.net/")
3287 (inputs `(("gfortran" ,gfortran)
3288 ("lapack-tar" ,(package-source lapack))))
3289 (outputs '("out" "doc"))
3290 ;; For the moment we drop support for MIPS at it fails to compile. See
3291 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
3292 (supported-systems (delete "mips64el-linux" %supported-systems))
3294 `(#:parallel-build? #f
3295 #:parallel-tests? #f
3297 ;; ATLAS tunes itself for the machine it is built on, as explained at
3298 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
3299 ;; For this reason, we want users to build it locally instead of using
3303 #:modules ((srfi srfi-26)
3305 (guix build gnu-build-system)
3308 `(;; Generate position independent code suitable for dynamic libraries
3309 ;; and use WALL timer to get more accurate timing.
3310 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
3313 ,,(if (string-match "64" (%current-system))
3316 ;; Disable parallel build as it gives errors: atlas_pthread.h is
3317 ;; needed to compile C files before it is generated.
3318 "-Ss" "pmake" "make -j 1"
3319 ;; Probe is failing for MIPS. We therefore define the system
3320 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3321 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3322 ,,@(if (string-prefix? "mips" (%current-system))
3323 (list "-A" "49" "-V" "1")
3325 ;; Generate shared libraries.
3327 ;; Build a full LAPACK library.
3328 ,(string-append "--with-netlib-lapack-tarfile="
3329 (assoc-ref %build-inputs "lapack-tar")))
3331 (modify-phases %standard-phases
3332 (add-after 'install 'install-doc
3333 (lambda* (#:key outputs inputs #:allow-other-keys)
3334 (let ((doc (string-append (assoc-ref outputs "doc")
3335 "/share/doc/atlas")))
3337 (fold (lambda (file previous)
3338 (and previous (zero? (system* "cp" file doc))))
3339 #t (find-files "../ATLAS/doc" ".*")))))
3340 (add-after 'check 'check-pt
3341 (lambda _ (zero? (system* "make" "ptcheck"))))
3342 ;; Fix files required to run configure.
3343 (add-before 'configure 'fix-/bin/sh
3345 ;; Use `sh', not `/bin/sh'.
3346 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3349 ;; Fix /bin/sh in generated make files.
3350 (add-after 'configure 'fix-/bin/sh-in-generated-files
3352 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3355 ;; ATLAS configure program does not accepts the default flags
3356 ;; passed by the 'gnu-build-system'.
3358 (lambda* (#:key native-inputs inputs outputs
3359 (configure-flags '())
3360 #:allow-other-keys #:rest args)
3361 (let* ((prefix (assoc-ref outputs "out"))
3362 (bash (or (and=> (assoc-ref
3363 (or native-inputs inputs) "bash")
3364 (cut string-append <> "/bin/bash"))
3366 (flags `(,(string-append "--prefix=" prefix)
3368 (abs-srcdir (getcwd))
3369 (srcdir (string-append "../" (basename abs-srcdir))))
3370 (format #t "source directory: ~s (relative from build: ~s)~%"
3374 (format #t "build directory: ~s~%" (getcwd))
3375 (format #t "configure flags: ~s~%" flags)
3376 (zero? (apply system* bash
3377 (string-append srcdir "/configure")
3379 (synopsis "Automatically Tuned Linear Algebra Software")
3381 "ATLAS is an automatically tuned linear algebra software library
3382 providing C and Fortran77 interfaces to a portably efficient BLAS
3383 implementation, as well as a few routines from LAPACK.
3385 Optimization occurs at build time. For this reason, the library is built on
3386 the machine where it is installed, without resorting to pre-built substitutes.
3388 Before building the library, CPU throttling should be disabled. This can be
3389 done in the BIOS, or, on GNU/Linux, with the following command:
3392 # cpupower --governor performance
3395 Failure to do so will result in a library with poor performance.")
3396 (license license:bsd-3)))
3405 (uri (string-append "https://github.com/g-truc/glm/releases/download/"
3406 version "/glm-" version ".zip"))
3409 "0yqk5r3qh60d4r2iab5q7wq0fryn8p3pz6s28y1i7amqj1aqavj9"))))
3410 (build-system cmake-build-system)
3412 `(("unzip" ,unzip)))
3413 (home-page "https://glm.g-truc.net/")
3414 (synopsis "OpenGL Mathematics library")
3415 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3416 library for graphics software based on the OpenGL Shading Language (GLSL)
3418 (license license:expat)))
3420 (define-public lpsolve
3427 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3428 "/lp_solve_" version "_source.tar.gz"))
3431 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
3432 (modules '((guix build utils)))
3435 (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3437 ;; Pretend to be on a 64 bit platform to obtain a common directory
3438 ;; name for the build results on all architectures; nothing else
3439 ;; seems to depend on it.
3440 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3442 ;; The check for 'isnan' as it is written fails with
3443 ;; "non-floating-point argument in call to function
3444 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3445 ;; definition, which in turn leads to bad things. Fix the feature
3447 (("isnan\\(0\\)") "isnan(0.)"))
3449 (build-system gnu-build-system)
3451 `(#:tests? #f ; no check target
3453 (modify-phases %standard-phases
3454 (delete 'configure) ; no configure script
3457 (with-directory-excursion "lpsolve55"
3458 (invoke "bash" "ccc"))
3459 (with-directory-excursion "lp_solve"
3460 (invoke "bash" "ccc"))
3463 (lambda* (#:key outputs #:allow-other-keys)
3464 (let* ((out (assoc-ref outputs "out"))
3465 (bin (string-append out "/bin"))
3466 (lib (string-append out "/lib"))
3467 ;; This is where LibreOffice expects to find the header
3468 ;; files, and where they are installed by Debian.
3469 (include (string-append out "/include/lpsolve")))
3470 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3471 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
3472 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3474 ;; Install a subset of the header files as on Debian
3475 ;; (plus lp_bit.h, which matches the regular expression).
3476 (for-each (lambda (name)
3477 (install-file name include))
3478 (find-files "." "lp_[HMSa-z].*\\.h$"))
3479 (with-directory-excursion "shared"
3480 (for-each (lambda (name)
3481 (install-file name include))
3482 (find-files "." "\\.h$")))
3484 (home-page "http://lpsolve.sourceforge.net/")
3485 (synopsis "Mixed integer linear programming (MILP) solver")
3487 "lp_solve is a mixed integer linear programming solver based on the
3488 revised simplex and the branch-and-bound methods.")
3489 (license license:lgpl2.1+)))
3491 (define-public dealii
3498 (uri (string-append "https://github.com/dealii/dealii/releases/"
3499 "download/v" version "/dealii-" version ".tar.gz"))
3502 "1bh9rsmkrg0zi70n27b11djmac9lximghsiy7mg7w7x544n82gnk"))
3503 (modules '((guix build utils)))
3505 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
3507 (delete-file-recursively "bundled")
3509 (build-system cmake-build-system)
3517 ("arpack" ,arpack-ng)
3518 ("muparser" ,muparser)
3519 ("gfortran" ,gfortran)
3520 ("suitesparse" ,suitesparse))) ;for UMFPACK
3522 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
3524 ;; Work around a bug in libsuitesparseconfig linking
3525 ;; see https://github.com/dealii/dealii/issues/4745
3526 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
3527 (home-page "https://www.dealii.org")
3528 (synopsis "Finite element library")
3530 "Deal.II is a C++ program library targeted at the computational solution
3531 of partial differential equations using adaptive finite elements. The main
3532 aim of deal.II is to enable rapid development of modern finite element codes,
3533 using among other aspects adaptive meshes and a wide array of tools often used
3534 in finite element programs.")
3535 (license license:lgpl2.1+)))
3537 (define-public dealii-openmpi
3538 (package (inherit dealii)
3539 (name "dealii-openmpi")
3542 ;;Supported only with MPI:
3543 ("p4est" ,p4est-openmpi)
3544 ("petsc" ,petsc-openmpi)
3545 ("slepc" ,slepc-openmpi)
3546 ("metis" ,metis) ;for MUMPS
3547 ("scalapack" ,scalapack) ;for MUMPS
3548 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3549 ("arpack" ,arpack-ng-openmpi)
3550 ,@(fold alist-delete (package-inputs dealii)
3551 '("p4est" "arpack"))))
3553 (substitute-keyword-arguments (package-arguments dealii)
3554 ((#:configure-flags cf)
3555 ``("-DMPI_C_COMPILER=mpicc"
3556 "-DMPI_CXX_COMPILER=mpicxx"
3557 "-DMPI_Fortran_COMPILER=mpifort"
3559 (synopsis "Finite element library (with MPI support)")))
3561 (define-public flann
3570 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3571 version "-src.zip"))
3574 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
3575 (patches (search-patches "flann-cmake-3.11.patch"))))
3576 (build-system cmake-build-system)
3578 "octave")) ;46 MiB .mex file that pulls Octave
3580 `(("unzip" ,unzip)))
3584 ("python" ,python-2) ; print syntax
3585 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3588 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3589 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3590 #:strip-directories '("lib" "lib64" "libexec"
3591 "bin" "sbin" "share/flann/octave")
3593 ;; Save 12 MiB by not installing .a files. Passing
3594 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3595 #:phases (modify-phases %standard-phases
3596 (add-before 'configure 'set-octave-directory
3597 (lambda* (#:key outputs #:allow-other-keys)
3598 ;; Install the .mex file in the "octave" output.
3599 (let ((out (assoc-ref outputs "octave")))
3600 (substitute* "src/matlab/CMakeLists.txt"
3601 (("share/flann/octave")
3602 (string-append out "/share/flann/octave")))
3604 (add-after 'install 'remove-static-libraries
3605 (lambda* (#:key outputs #:allow-other-keys)
3606 (let* ((out (assoc-ref outputs "out"))
3607 (lib (string-append out "/lib")))
3608 (for-each delete-file
3609 (find-files lib "\\.a$"))
3612 #:tests? #f)) ; The test data are downloaded from the Internet.
3613 (home-page "http://www.cs.ubc.ca/research/flann/")
3614 (synopsis "Library for approximate nearest neighbors computation")
3615 (description "FLANN is a library for performing fast approximate
3616 nearest neighbor searches in high dimensional spaces. It implements a
3617 collection of algorithms and a system for automatically choosing the best
3618 algorithm and optimum parameters depending on the dataset.
3620 FLANN is written in C++ and contains bindings for C, Octave and Python.")
3621 (license (license:non-copyleft "file://COPYING"
3622 "See COPYING in the distribution."))))
3624 (define-public wcalc
3631 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3632 "wcalc-" version ".tar.bz2"))
3635 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3636 (build-system gnu-build-system)
3639 ("readline" ,readline)))
3640 (home-page "http://w-calc.sourceforge.net/index.php")
3641 (synopsis "Flexible command-line scientific calculator")
3642 (description "Wcalc is a very capable calculator. It has standard functions
3643 (sin, asin, and sinh for example, in either radians or degrees), many
3644 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3645 variables, a command history, hex/octal/binary input and output, unit
3646 conversions, embedded comments, and an expandable expression entry field. It
3647 evaluates expressions using the standard order of operations.")
3648 (license license:gpl2+)))
3656 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3657 "/xaos-" version ".tar.gz"))
3660 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3661 (build-system gnu-build-system)
3662 (native-inputs `(("gettext" ,gettext-minimal)))
3663 (inputs `(("libx11" ,libx11)
3668 `(#:tests? #f ;no "check" target
3669 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3670 (synopsis "Real-time fractal zoomer")
3671 (description "GNU XaoS is a graphical program that generates fractal
3672 patterns and allows you to zoom in and out of them infinitely in a fluid,
3673 continuous manner. It also includes tutorials that help to explain how fractals
3674 are built. It can generate many different fractal types such as the Mandelbrot
3676 (home-page "https://www.gnu.org/software/xaos/")
3677 (license license:gpl2+)))
3679 (define-public hypre
3685 (uri (string-append "https://github.com/LLNL/hypre/archive/"
3686 "v" version ".tar.gz"))
3687 (file-name (string-append name "-" version ".tar.gz"))
3690 "0v515i73bvaz378h5465b1dy9v2gf924zy2q94cpq4qqarawvkqh"))
3691 (modules '((guix build utils)))
3694 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
3695 ;; substitute the tarball creation time.
3696 (substitute* "src/utilities/HYPRE_utilities.h"
3697 (("Date Compiled: .*$")
3698 "Date Compiled: Apr 11 2018 16:24:59 +0000\"\n"))
3700 (build-system gnu-build-system)
3701 (outputs '("out" ;6.1 MiB of headers and libraries
3702 "doc")) ;4.8 MiB of documentation
3706 ("perl" ,perl) ;needed to run 'ppmquant' during tests
3707 ("texlive" ,texlive) ;full package required for fonts
3708 ("ghostscript" ,ghostscript)))
3710 `(("blas" ,openblas)
3711 ("lapack" ,lapack)))
3713 `(#:modules ((srfi srfi-1)
3714 ,@%gnu-build-system-modules)
3715 #:configure-flags '("--enable-shared"
3723 (modify-phases %standard-phases
3724 (add-before 'configure 'chdir-src
3725 (lambda _ (chdir "src")))
3727 (lambda* (#:key build target configure-flags
3728 #:allow-other-keys #:rest args)
3729 (let* ((configure (assoc-ref %standard-phases 'configure)))
3732 (list #:configure-flags
3733 (cons (string-append
3734 "--host=" (or target build))
3735 configure-flags)))))))
3736 (add-after 'build 'build-docs
3738 (zero? (system* "make" "-Cdocs" "pdf" "html"))))
3741 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3742 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
3743 (and (system* "make" "check" "CHECKRUN=")
3744 (fold (lambda (filename result)
3746 (let ((size (stat:size (stat filename))))
3747 (when (not (zero? size))
3748 (format #t "~a size ~d; error indication~%"
3752 (find-files "test" ".*\\.err$")))))
3753 (add-after 'install 'install-docs
3754 (lambda* (#:key outputs #:allow-other-keys)
3755 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3756 (let* ((doc (assoc-ref outputs "doc"))
3757 (docdir (string-append doc "/share/doc/hypre-" ,version)))
3758 (with-directory-excursion "docs"
3759 (for-each (lambda (base)
3760 (install-file (string-append base ".pdf") docdir)
3761 (copy-recursively base docdir)) ;html docs
3762 '("HYPRE_usr_manual"
3763 "HYPRE_ref_manual")))
3765 (home-page "http://www.llnl.gov/casc/hypre/")
3766 (synopsis "Library of solvers and preconditioners for linear equations")
3768 "HYPRE is a software library of high performance preconditioners and
3769 solvers for the solution of large, sparse linear systems of equations. It
3770 features multigrid solvers for both structured and unstructured grid
3772 (license license:lgpl2.1)))
3774 (define-public hypre-openmpi
3775 (package (inherit hypre)
3776 (name "hypre-openmpi")
3779 ,@(package-inputs hypre)))
3781 (substitute-keyword-arguments (package-arguments hypre)
3782 ((#:configure-flags flags)
3784 ,@(delete "--without-MPI" ,flags)))
3786 `(modify-phases ,phases
3787 (add-before 'check 'mpi-setup
3788 ,%openmpi-setup)))))
3789 (synopsis "Parallel solvers and preconditioners for linear equations")
3791 "HYPRE is a software library of high performance preconditioners and
3792 solvers for the solution of large, sparse linear systems of equations on
3793 parallel computers. It features parallel multigrid solvers for both
3794 structured and unstructured grid problems.")))
3796 (define-public matio
3803 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
3804 "matio-" version ".tar.gz"))
3807 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3808 (build-system gnu-build-system)
3812 (home-page "http://matio.sourceforge.net/")
3813 (synopsis "Library for reading and writing MAT files")
3814 (description "Matio is a library for reading and writing MAT files. It
3815 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3816 (license license:bsd-2)))
3823 (origin (method url-fetch)
3824 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3825 "download/" version "/Vc-" version ".tar.gz"))
3828 "1zmlpn32jzb38smp3j834llmbix3whsrbw0h397qxysbw792kih8"))))
3829 (build-system cmake-build-system)
3832 '("-DBUILD_TESTING=ON"
3833 ;; By default, Vc will optimize for the CPU of the build machine.
3834 ;; Setting this to "none" makes it create portable binaries. See
3835 ;; "cmake/OptimizeForArchitecture.cmake".
3836 "-DTARGET_ARCHITECTURE=none")))
3837 (synopsis "SIMD vector classes for C++")
3838 (description "Vc provides portable, zero-overhead C++ types for explicitly
3839 data-parallel programming. It is a library designed to ease explicit
3840 vectorization of C++ code. Its types enable explicitly stating data-parallel
3841 operations on multiple values. The parallelism is therefore added via the type
3842 system. Vc has an intuitive API and provides portability between different
3843 compilers and compiler versions as well as portability between different vector
3844 instruction sets. Thus, an application written with Vc can be compiled for:
3847 @item SSE2 up to SSE4.2 or SSE4a
3850 @item NEON (in development)
3851 @item NVIDIA GPUs / CUDA (in development)
3853 (home-page "https://github.com/VcDevel/Vc")
3854 ;; "No support_???.cpp file exists for this architecture."
3855 (supported-systems '("x86_64-linux" "i686-linux"))
3856 (license license:bsd-3)))
3858 (define-public reducelcs
3859 ;; This is the last commit which is available upstream, no
3860 ;; release happened since 2010.
3861 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
3865 (version (string-append "1.0-" revision "." (string-take commit 7)))
3870 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
3872 (file-name (string-append name "-" version "-checkout"))
3875 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
3876 (build-system gnu-build-system)
3878 `(("openlibm" ,openlibm)))
3880 `(#:tests? #f ; no tests
3882 (modify-phases %standard-phases
3883 (delete 'configure) ; No configure script exists.
3884 (replace 'install ; No install phase exists.
3885 (lambda* (#:key outputs #:allow-other-keys)
3886 (let* ((out (assoc-ref outputs "out"))
3887 (bin (string-append out "/bin")))
3888 (install-file "Approximation" bin)
3889 (install-file "CollectResults" bin)
3890 (install-file "GenerateInstances" bin)
3892 (synopsis "Approximate Longest Commons Subsequence computation tool")
3894 "@code{reduceLCS} is an implementation of the Reduce-Expand
3895 algorithm for LCS. It is a fast program to compute the approximate
3896 Longest Commons Subsequence of a set of strings.")
3897 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
3898 (license license:gpl3+))))
3900 (define-public jacal
3907 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
3910 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
3911 (patches (search-patches "jacal-fix-texinfo.patch"))))
3912 (build-system gnu-build-system)
3915 (modify-phases %standard-phases
3916 (add-before 'build 'pre-build
3917 ;; Don't use upstream's script - it really doesn't fit into
3918 ;; Guix's functional paradigm.
3919 (lambda* (#:key inputs outputs #:allow-other-keys)
3920 (substitute* "Makefile"
3921 (("^install: install-script") "install: "))))
3922 (add-after 'install 'post-install
3923 ;; Instead, we provide our own simplified script.
3924 (lambda* (#:key inputs outputs #:allow-other-keys)
3925 (let ((wrapper (string-append (assoc-ref outputs "out")
3927 (format (open wrapper (logior O_WRONLY O_CREAT))
3928 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
3929 "-e '(slib:load \"~a/lib/jacal/math\") "
3932 (assoc-ref inputs "scm")
3933 (assoc-ref outputs "out"))
3934 (chmod wrapper #o555))))
3936 (lambda* (#:key inputs outputs #:allow-other-keys)
3937 (zero? (system* "./configure"
3938 (string-append "--prefix="
3939 (assoc-ref outputs "out")))))))))
3940 (inputs `(("scm" ,scm)))
3941 (native-inputs `(("unzip" ,unzip)
3942 ("texinfo" ,texinfo)))
3943 (synopsis "Symbolic mathematics system")
3944 (description "GNU JACAL is an interactive symbolic mathematics program based on
3945 Scheme. It manipulate and simplify a range of mathematical expressions such
3946 as equations, scalars, vectors, and matrices.")
3947 (home-page "https://www.gnu.org/software/jacal/")
3948 (license license:gpl3+)))
3954 (home-page "https://github.com/Z3Prover/z3")
3957 (uri (git-reference (url home-page)
3958 (commit (string-append "z3-" version))))
3961 "1vr57bwx40sd5riijyrhy70i2wnv9xrdihf6y5zdz56yq88rl48f"))))
3962 (build-system cmake-build-system)
3965 (list "-DBUILD_PYTHON_BINDINGS=true"
3966 "-DINSTALL_PYTHON_BINDINGS=true"
3967 (string-append "-DCMAKE_INSTALL_PYTHON_PKG_DIR="
3969 "/lib/python2.7/site-packages"))
3971 (modify-phases %standard-phases
3972 (add-before 'configure 'bootstrap
3975 (system* "python" "contrib/cmake/bootstrap.py" "create"))))
3976 (add-before 'check 'make-test-z3
3978 ;; Build the test suite executable.
3979 (zero? (system* "make" "test-z3" "-j"
3980 (number->string (parallel-job-count))))))
3983 ;; Run all the tests that don't require arguments.
3984 (zero? (system* "./test-z3" "/a")))))))
3986 `(("python" ,python-2)))
3987 (synopsis "Theorem prover")
3988 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
3989 theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
3990 (license license:expat)))
3992 (define-public cubicle
3998 (uri (string-append "http://cubicle.lri.fr/cubicle-"
4002 "10kk80jdmpdvql88sdjsh7vqzlpaphd8vip2lp47aarxjkwjlz1q"))))
4003 (build-system gnu-build-system)
4005 `(("automake" ,automake)
4007 ("which" ,(@@ (gnu packages base) which))))
4009 `(("ocaml-num" ,ocaml-num)
4012 `(#:configure-flags (list "--with-z3")
4013 #:make-flags (list "QUIET=")
4016 (modify-phases %standard-phases
4017 (add-before 'configure 'configure-for-release
4019 (substitute* "Makefile.in"
4020 (("SVNREV=") "#SVNREV="))
4022 (add-before 'configure 'fix-/bin/sh
4024 (substitute* "configure"
4025 (("-/bin/sh") (string-append "-" (which "sh"))))
4027 (add-before 'configure 'fix-smt-z3wrapper.ml
4029 (substitute* "Makefile.in"
4032 (add-before 'configure 'fix-ocaml-num
4033 (lambda* (#:key inputs #:allow-other-keys)
4034 (substitute* "Makefile.in"
4035 (("= \\$\\(FUNCTORYLIB\\)")
4036 (string-append "= -I "
4037 (assoc-ref inputs "ocaml-num")
4038 "/lib/ocaml/site-lib"
4039 " $(FUNCTORYLIB)")))
4041 (home-page "http://cubicle.lri.fr/")
4042 (synopsis "Model checker for array-based systems")
4043 (description "Cubicle is a model checker for verifying safety properties
4044 of array-based systems. This is a syntactically restricted class of
4045 parametrized transition systems with states represented as arrays indexed by
4046 an arbitrary number of processes. Cache coherence protocols and mutual
4047 exclusion algorithms are typical examples of such systems.")
4048 (license license:asl2.0)))
4050 (define-public elemental
4056 (uri (string-append "https://github.com/elemental/Elemental/"
4057 "archive/v" version ".tar.gz"))
4058 (file-name (string-append name "-" version ".tar.gz"))
4061 "1nfp82w22pi8x8fg9sc37z8kf84dqi1dhxp8bbk7571y4aygvv3v"))))
4062 (build-system cmake-build-system)
4063 (home-page "http://libelemental.org")
4065 `(("gfortran" ,gfortran)))
4067 `(("blas" ,openblas)
4068 ("gfortran:lib" ,gfortran "lib")
4077 `(#:build-type "Release" ;default RelWithDebInfo not supported
4078 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
4079 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
4080 "-DEL_CACHE_WARNINGS:BOOL=YES"
4081 "-DEL_TESTS:BOOL=YES"
4082 "-DCMAKE_INSTALL_LIBDIR=lib"
4083 "-DGFORTRAN_LIB=gfortran")
4084 #:phases (modify-phases %standard-phases
4085 (add-before 'check 'mpi-setup
4087 (add-before 'check 'setup-tests
4089 ;; Parallelism is done at the MPI layer.
4090 (setenv "OMP_NUM_THREADS" "1")
4092 (add-after 'install 'remove-tests
4093 (lambda* (#:key outputs #:allow-other-keys)
4094 ;; Tests are installed, with no easy configuration
4095 ;; switch to prevent this, so delete them.
4096 (delete-file-recursively
4097 (string-append (assoc-ref outputs "out") "/bin"))
4099 (synopsis "Dense and sparse-direct linear algebra and optimization")
4100 (description "Elemental is a modern C++ library for distributed-memory
4101 dense and sparse-direct linear algebra, conic optimization, and lattice
4103 (license license:bsd-2)))
4105 (define-public mcrl2
4108 (version "201707.1.15162")
4111 (uri (string-append "http://www.mcrl2.org/download/devel/mcrl2-"
4116 "1ziww2fchsklm25hl9p2mngssxfh9w07nc114cncqaxfibqp2p8f"))))
4118 `(("subversion" ,subversion)))
4123 ("qtbase" ,qtbase)))
4124 (build-system cmake-build-system)
4125 (synopsis "Toolset for the mCRL2 formal specification language")
4127 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
4128 specification language for describing concurrent discrete event systems. Its
4129 toolset supports analysis and automatic verification, linearisation, simulation,
4130 state-space exploration and generation, and tools to optimise and analyse
4131 specifications. Also, state spaces can be manipulated, visualised and
4133 (home-page "https://mcrl2.org")
4134 (license license:boost1.0)))
4136 (define-public r-subplex
4143 (uri (cran-uri "subplex" version))
4146 "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
4147 (build-system r-build-system)
4149 `(("gfortran" ,gfortran)))
4150 (home-page "https://cran.r-project.org/web/packages/subplex")
4151 (synopsis "Unconstrained optimization using the subplex algorithm")
4152 (description "This package implements the Subplex optimization algorithm.
4153 It solves unconstrained optimization problems using a simplex method on
4154 subspaces. The method is well suited for optimizing objective functions that
4155 are noisy or are discontinuous at the solution.")
4156 (license license:gpl3+)))
4158 (define-public r-desolve
4165 (uri (cran-uri "deSolve" version))
4168 "0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"))))
4169 (properties `((upstream-name . "deSolve")))
4170 (build-system r-build-system)
4172 `(("gfortran" ,gfortran)))
4173 (home-page "https://desolve.r-forge.r-project.org/")
4174 (synopsis "Solvers for initial value problems of differential equations")
4175 (description "This package provides functions that solve initial
4176 value problems of a system of first-order ordinary differential equations (ODE),
4177 of partial differential equations (PDE), of differential algebraic equations
4178 (DAE), and of delay differential equations. The functions provide an interface
4179 to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
4180 to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
4181 the Runge-Kutta family with fixed or variable time steps. The package contains
4182 routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
4183 differential equations (PDE) that have been converted to ODEs by numerical
4185 (license license:gpl2+)))
4187 (define-public tcalc
4194 (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
4198 "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
4199 (build-system gnu-build-system)
4200 (synopsis "The terminal calculator")
4202 "The terminal calculator is a small program to help users of the GNU/Linux
4203 terminal do calculations simply and quickly. The formula to be calculated can
4204 be fed to @command{tcalc} through the command line.")
4205 (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
4206 (license license:gpl3+)))
4208 (define-public sundials
4215 (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
4216 "sundials-" version ".tar.gz"))
4219 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
4220 (build-system cmake-build-system)
4222 `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
4224 `(("fortran" ,gfortran) ;for fcmix
4226 ("suitesparse" ,suitesparse))) ;TODO: Add hypre
4228 `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
4229 "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
4230 "-DEXAMPLES_ENABLE_F77:BOOL=ON"
4231 "-DEXAMPLES_ENABLE_F90:BOOL=ON"
4232 "-DEXAMPLES_INSTALL:BOOL=OFF"
4234 "-DFCMIX_ENABLE:BOOL=ON"
4236 "-DKLU_ENABLE:BOOL=ON"
4237 ,(string-append "-DKLU_INCLUDE_DIR="
4238 (assoc-ref %build-inputs "suitesparse")
4240 ,(string-append "-DKLU_LIBRARY_DIR="
4241 (assoc-ref %build-inputs "suitesparse")
4243 (home-page "https://computation.llnl.gov/projects/sundials")
4244 (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
4245 (description "SUNDIALS is a family of software packages implemented with
4246 the goal of providing robust time integrators and nonlinear solvers that can
4247 easily be incorporated into existing simulation codes.")
4248 (license license:bsd-3)))
4250 (define-public sundials-openmpi
4251 (package (inherit sundials)
4252 (name "sundials-openmpi")
4255 ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
4256 ,@(package-inputs sundials)))
4258 (substitute-keyword-arguments (package-arguments sundials)
4259 ((#:configure-flags flags '())
4260 `(cons* "-DMPI_ENABLE:BOOL=ON"
4261 "-DPETSC_ENABLE:BOOL=ON"
4262 (string-append "-DPETSC_INCLUDE_DIR="
4263 (assoc-ref %build-inputs "petsc")
4265 (string-append "-DPETSC_LIBRARY_DIR="
4266 (assoc-ref %build-inputs "petsc")
4269 ((#:phases phases '%standard-phases)
4270 `(modify-phases ,phases
4271 (add-before 'check 'mpi-setup
4272 ,%openmpi-setup)))))
4273 (synopsis "SUNDIALS with OpenMPI support")))