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, 2019 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, 2019 Ludovic Courtès <ludo@gnu.org>
16 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
17 ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
18 ;;; Copyright © 2017, 2018 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, 2019 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>
32 ;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
34 ;;; This file is part of GNU Guix.
36 ;;; GNU Guix is free software; you can redistribute it and/or modify it
37 ;;; under the terms of the GNU General Public License as published by
38 ;;; the Free Software Foundation; either version 3 of the License, or (at
39 ;;; your option) any later version.
41 ;;; GNU Guix is distributed in the hope that it will be useful, but
42 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
43 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
44 ;;; GNU General Public License for more details.
46 ;;; You should have received a copy of the GNU General Public License
47 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
49 (define-module (gnu packages maths)
50 #:use-module (ice-9 regex)
51 #:use-module (gnu packages)
52 #:use-module ((guix licenses) #:prefix license:)
53 #:use-module (guix packages)
54 #:use-module (guix download)
55 #:use-module (guix git-download)
56 #:use-module (guix utils)
57 #:use-module ((guix build utils) #:select (alist-replace))
58 #:use-module (guix build-system cmake)
59 #:use-module (guix build-system gnu)
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 base)
67 #:use-module (gnu packages bison)
68 #:use-module (gnu packages boost)
69 #:use-module (gnu packages check)
70 #:use-module (gnu packages cmake)
71 #:use-module (gnu packages compression)
72 #:use-module (gnu packages curl)
73 #:use-module (gnu packages cyrus-sasl)
74 #:use-module (gnu packages documentation)
75 #:use-module (gnu packages elf)
76 #:use-module (gnu packages flex)
77 #:use-module (gnu packages fltk)
78 #:use-module (gnu packages fontutils)
79 #:use-module (gnu packages gettext)
80 #:use-module (gnu packages gcc)
81 #:use-module (gnu packages gd)
82 #:use-module (gnu packages ghostscript)
83 #:use-module (gnu packages graphviz)
84 #:use-module (gnu packages gtk)
85 #:use-module (gnu packages image)
86 #:use-module (gnu packages java)
87 #:use-module (gnu packages less)
88 #:use-module (gnu packages lisp)
89 #:use-module (gnu packages linux)
90 #:use-module (gnu packages logging)
91 #:use-module (gnu packages lua)
92 #:use-module (gnu packages gnome)
93 #:use-module (gnu packages guile)
94 #:use-module (gnu packages xorg)
95 #:use-module (gnu packages gl)
96 #:use-module (gnu packages imagemagick)
97 #:use-module (gnu packages m4)
98 #:use-module (gnu packages mpi)
99 #:use-module (gnu packages multiprecision)
100 #:use-module (gnu packages netpbm)
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 python-xyz)
109 #:use-module (gnu packages qt)
110 #:use-module (gnu packages readline)
111 #:use-module (gnu packages ruby)
112 #:use-module (gnu packages tbb)
113 #:use-module (gnu packages scheme)
114 #:use-module (gnu packages shells)
115 #:use-module (gnu packages tcl)
116 #:use-module (gnu packages texinfo)
117 #:use-module (gnu packages tex)
118 #:use-module (gnu packages tls)
119 #:use-module (gnu packages version-control)
120 #:use-module (gnu packages wxwidgets)
121 #:use-module (gnu packages xml)
122 #:use-module (srfi srfi-1))
130 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
132 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
133 (build-system gnu-build-system)
134 (inputs `(("gtk+" ,gtk+)
135 ("libxml2" ,libxml2)))
136 (native-inputs `(("pkg-config" ,pkg-config)))
137 (synopsis "Natural deduction first-order logic interface")
138 (description "Aris is a program for performing logical proofs. It supports
139 propositional and predicate logic, as well as Boolean algebra and
140 arithmetical logic. In addition to its predefined inference and equivalence
141 rules, Aris also supports references to older proofs. Its use of standard
142 logical symbols and its natural deduction interface make it easy to use for
144 (license license:gpl3+)
145 (home-page "https://www.gnu.org/software/aris/")))
147 (define-public c-graph
153 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
156 "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
157 (build-system gnu-build-system)
159 `(("fortran" ,gfortran)))
160 (synopsis "Visualizing and demonstrating convolution")
162 "GNU C-Graph is a tool for demonstrating the theory of convolution.
163 Thus, it can serve as an excellent aid to students of signal and systems
164 theory in visualizing the convolution process. Rather than forcing the
165 student to write code, the program offers an intuitive interface with
166 interactive dialogs to guide them.")
167 (license license:gpl3+)
168 (home-page "https://www.gnu.org/software/c-graph/")))
177 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
178 version "/coda-" version ".tar.gz"))
180 (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245"))
181 (patches (search-patches "coda-use-system-libs.patch"))
182 (modules '((guix build utils)))
184 ;; Make sure we don't use the bundled software.
186 (for-each (lambda (d)
187 (delete-file-recursively (string-append "libcoda/" d)))
188 '("zlib" "pcre" "expat"))
191 `(("fortran" ,gfortran)
193 ("python-numpy" ,python-numpy)))
200 (build-system gnu-build-system)
202 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
203 "LIBS= -lz -lpcre -lexpat")))
204 (synopsis "A common interface to various earth observation data formats")
206 "The Common Data Access toolbox (CODA) provides a set of interfaces for
207 reading remote sensing data from earth observation data files. It consists of
208 command line applications and interfaces to the C, Fortran, Python, and Java
209 programming languages.")
210 (home-page "https://stcorp.nl/coda")
211 (license license:gpl2+)))
219 (uri (string-append "http://www.qhull.org/download/qhull-"
220 (car (string-split version #\.))
224 "0dm4b2xr3asy6w74khq2zg4gf26zsy3qf9sq7pf7lmrvbj911c3q"))))
225 (build-system cmake-build-system)
226 (synopsis "Calculate convex hulls and related structures")
228 "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
229 diagram, halfspace intersection about a point, furthest-site Delaunay
230 triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d,
231 3-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull
232 algorithm for computing the convex hull. It handles roundoff errors from
233 floating point arithmetic. It computes volumes, surface areas, and
234 approximations to the convex hull.
236 @code{Qhull} does not support triangulation of non-convex surfaces, mesh
237 generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
238 shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
240 (home-page "http://qhull.org")
241 (license (license:non-copyleft "file://COPYING.txt"
242 "See COPYING in the distribution."))))
244 (define-public python-cvxopt
246 (name "python-cvxopt")
251 (url "https://github.com/cvxopt/cvxopt.git")
253 (file-name (git-file-name name version))
256 "05mnjil9palaa48xafdfh4f5pr4z7aqjr995rwl08qfyxs8y0crf"))))
257 (build-system python-build-system)
260 (modify-phases %standard-phases
261 (add-after 'unpack 'find-libraries
262 (lambda* (#:key inputs #:allow-other-keys)
263 (setenv "CVXOPT_BLAS_LIB" "openblas")
264 (setenv "CVXOPT_BUILD_FFTW" "1")
265 (setenv "CVXOPT_BUILD_GLPK" "1")
266 (setenv "CVXOPT_BUILD_GSL" "1")
273 ("openblas" ,openblas)
274 ("suitesparse" ,suitesparse)))
275 (home-page "https://www.cvxopt.org")
276 (synopsis "Python library for convex optimization")
278 "CVXOPT is a package for convex optimization based on the Python
279 programming language. Its main purpose is to make the development of software
280 for convex optimization applications straightforward by building on Python’s
281 extensive standard library and on the strengths of Python as a high-level
282 programming language.")
283 (license license:gpl3+)))
285 (define-public python2-cvxopt
286 (package-with-python2 python-cvxopt))
294 (uri (string-append "mirror://gnu/units/units-" version
297 "0y26kj349i048y4z3xrk90bvciw2j6ds3rka7r7yn3183hirr5b4"))))
298 (build-system gnu-build-system)
300 `(("readline" ,readline)
301 ("python" ,python-wrapper) ;for 'units_cur' script
302 ("python-requests" ,python-requests)))
304 `(#:phases (modify-phases %standard-phases
305 (add-after 'install 'wrap-units_cur
306 (lambda* (#:key outputs #:allow-other-keys)
307 (let* ((out (assoc-ref outputs "out"))
308 (bin (string-append out "/bin")))
309 (wrap-program (string-append bin "/units_cur")
310 `("PYTHONPATH" ":" prefix
311 ,(search-path-as-string->list (getenv "PYTHONPATH"))))
313 (synopsis "Conversion between thousands of scales")
315 "GNU Units converts numeric quantities between units of measure. It
316 can handle scale changes through adaptive usage of standard scale
317 prefixes (micro-, kilo-, etc.). It can also handle nonlinear
318 conversions such as Fahrenheit to Celsius. Its interpreter is powerful
319 enough to be used effectively as a scientific calculator.")
320 (license license:gpl3+)
321 (home-page "https://www.gnu.org/software/units/")))
323 (define-public double-conversion
325 (name "double-conversion")
327 (home-page "https://github.com/google/double-conversion")
330 (uri (git-reference (url home-page) (commit version)))
331 (file-name (git-file-name name version))
334 "123rb2p4snqagrybw66vnapchqdwn2rfpr1wcq0ya9gwbyl7xccx"))))
335 (build-system cmake-build-system)
337 '(#:test-target "test"
338 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
339 "-DBUILD_TESTING=ON")))
340 (synopsis "Conversion routines for IEEE doubles")
342 "The double-conversion library provides binary-decimal and decimal-binary
343 routines for IEEE doubles. The library consists of efficient conversion
344 routines that have been extracted from the V8 JavaScript engine.")
345 (license license:bsd-3)))
347 (define-public dionysus
353 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
357 "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
358 (build-system gnu-build-system)
359 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
360 (synopsis "Local search for universal constants and scientific values")
362 "GNU Dionysus is a convenient system for quickly retrieving the values of
363 mathematical constants used in science and engineering. Values can be
364 searched using a simple command-line tool, choosing from three databases:
365 universal constants, atomic numbers, and constants related to
367 (license license:gpl3+)
368 (home-page "https://www.gnu.org/software/dionysus/")))
376 (uri (string-append "mirror://gnu/gsl/gsl-"
380 "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
381 (patches (search-patches "gsl-test-i686.patch"))))
382 (build-system gnu-build-system)
384 `(;; Currently there are numerous tests that fail on "exotic"
385 ;; architectures such as aarch64 and ppc64le.
386 ,@(if (string-prefix? "aarch64-linux"
387 (or (%current-target-system) (%current-system)))
390 (home-page "https://www.gnu.org/software/gsl/")
391 (synopsis "Numerical library for C and C++")
393 "The GNU Scientific Library is a library for numerical analysis in C
394 and C++. It includes a wide range of mathematical routines, with over 1000
395 functions in total. Subject areas covered by the library include:
396 differential equations, linear algebra, Fast Fourier Transforms and random
398 (license license:gpl3+)))
407 (uri (string-append "mirror://gnu/glpk/glpk-"
411 "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
412 (build-system gnu-build-system)
416 `(#:configure-flags '("--with-gmp")))
417 (home-page "https://www.gnu.org/software/glpk/")
418 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
420 "GLPK is a C library for solving large-scale linear programming (LP),
421 mixed integer programming (MIP), and other related problems. It supports the
422 GNU MathProg modeling language, a subset of the AMPL language, and features a
423 translator for the language. In addition to the C library, a stand-alone
424 LP/MIP solver is included in the package.")
425 (license license:gpl3+)))
434 (uri (string-append "http://www.4ti2.de/version_" version
435 "/4ti2-" version ".tar.gz"))
438 "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
439 (build-system gnu-build-system)
441 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
445 (home-page "http://www.4ti2.de/")
446 (synopsis "Mathematical tool suite for problems on linear spaces")
448 "4ti2 implements algorithms for solving algebraic, geometric and
449 combinatorial problems on linear spaces. Among others, it solves systems
450 of linear equations, computes extreme rays of polyhedral cones, solves
451 integer programming problems and computes Markov bases for statistics.")
452 (license license:gpl2+)))
454 (define-public cddlib
461 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
462 (string-delete #\. version) ".tar.gz"))
465 "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
466 (build-system gnu-build-system)
469 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
470 (synopsis "Library for convex hulls and extreme rays of polyhedra")
472 "The C-library cddlib implements the Double Description Method of
473 Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
474 rays of a general convex polyhedron given by a system of linear inequalities
475 in arbitrary dimension. It can also be used for the converse operation of
476 computing convex hulls.")
477 (license license:gpl2+)))
479 (define-public arpack-ng
483 (home-page "https://github.com/opencollab/arpack-ng")
486 (uri (git-reference (url home-page) (commit version)))
487 (file-name (git-file-name name version))
490 "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
491 (build-system gnu-build-system)
493 `(("autoconf" ,autoconf)
494 ("automake" ,automake)
495 ("libtool" ,libtool)))
498 ("fortran" ,gfortran)))
499 (synopsis "Fortran subroutines for solving eigenvalue problems")
501 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
502 large scale eigenvalue problems.")
503 (license (license:non-copyleft "file://COPYING"
504 "See COPYING in the distribution."))))
506 (define-public arpack-ng-3.3.0
510 (name (package-name arpack-ng))
511 (home-page (package-home-page arpack-ng))
515 (uri (string-append home-page "/archive/" version ".tar.gz"))
516 (file-name (string-append name "-" version ".tar.gz"))
519 "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
521 (define-public arpack-ng-openmpi
522 (package (inherit arpack-ng)
523 (name "arpack-ng-openmpi")
526 ,@(package-inputs arpack-ng)))
528 (substitute-keyword-arguments (package-arguments arpack-ng)
529 ((#:configure-flags _ '())
531 ((#:phases phases '%standard-phases)
532 `(modify-phases ,phases
533 (add-before 'check 'mpi-setup
535 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
537 (define-public lapack
544 (uri (string-append "http://www.netlib.org/lapack/lapack-"
548 "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
549 (build-system cmake-build-system)
550 (home-page "http://www.netlib.org/lapack/")
551 (inputs `(("fortran" ,gfortran)
552 ("python" ,python-2)))
554 `(#:configure-flags (list
555 "-DBUILD_SHARED_LIBS:BOOL=YES"
558 ;; Build the 'LAPACKE_clatms' functions.
559 "-DLAPACKE_WITH_TMG=ON")
561 (modify-phases %standard-phases
562 (add-before 'check 'patch-python
563 (lambda* (#:key inputs #:allow-other-keys)
564 (let ((python (assoc-ref inputs "python")))
565 (substitute* "lapack_testing.py"
566 (("/usr/bin/env python") python)))
568 (synopsis "Library for numerical linear algebra")
570 "LAPACK is a Fortran 90 library for solving the most commonly occurring
571 problems in numerical linear algebra.")
572 (license (license:non-copyleft "file://LICENSE"
573 "See LICENSE in the distribution."))))
575 (define-public scalapack
582 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
586 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
587 (build-system cmake-build-system)
590 ("fortran" ,gfortran)
591 ("lapack" ,lapack))) ;for testing only
593 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
594 #:phases (modify-phases %standard-phases
595 (add-before 'check 'mpi-setup
597 (home-page "http://www.netlib.org/scalapack/")
598 (synopsis "Library for scalable numerical linear algebra")
600 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
601 routines on parallel distributed memory machines. ScaLAPACK solves dense and
602 banded linear systems, least squares problems, eigenvalue problems, and
603 singular value problems.")
604 (license (license:bsd-style "file://LICENSE"
605 "See LICENSE in the distribution."))))
607 (define-public gnuplot
613 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
618 "1jvh8xmd2cvrhlsg88kxwh55wkwx31sg50v1n59slfippl0g058m"))))
619 (build-system gnu-build-system)
620 (inputs `(("readline" ,readline)
626 `(("pkg-config" ,pkg-config)
627 ("texlive" ,texlive-tiny)))
628 (arguments `(#:configure-flags (list (string-append
629 "--with-texdir=" %output
630 "/texmf-local/tex/latex/gnuplot"))))
631 (home-page "http://www.gnuplot.info")
632 (synopsis "Command-line driven graphing utility")
633 (description "Gnuplot is a portable command-line driven graphing
634 utility. It was originally created to allow scientists and students to
635 visualize mathematical functions and data interactively, but has grown to
636 support many non-interactive uses such as web scripting. It is also used as a
637 plotting engine by third-party applications like Octave.")
638 ;; X11 Style with the additional restriction that derived works may only be
639 ;; distributed as patches to the original.
640 (license (license:fsf-free
641 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
650 (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
652 (file-name (string-append name "-" version ".tar.gz"))
655 "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
657 `(("fortran" ,gfortran)))
658 (build-system gnu-build-system)
659 (synopsis "General Cartographic Transformation Package (GCTP)")
661 "The General Cartographic Transformation Package (GCTP) is a system of
662 software routines designed to permit the transformation of coordinate pairs
663 from one map projection to another. The GCTP is the standard computer
664 software used by the National Mapping Division for map projection
666 (home-page "https://github.com/OkoSanto/GCTP")
667 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
676 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
677 version "/src/hdf-" version ".tar.bz2"))
679 (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
680 (patches (search-patches "hdf4-architectures.patch"
681 "hdf4-reproducibility.patch"
682 "hdf4-shared-fortran.patch"))))
683 (build-system gnu-build-system)
685 `(("gfortran" ,gfortran)
690 ("libjpeg" ,libjpeg)))
692 `(#:parallel-tests? #f
693 #:configure-flags '("--enable-shared")
695 (modify-phases %standard-phases
696 ;; This is inspired by two of Debian's patches.
697 (add-before 'configure 'add-more-aarch64-support
699 (substitute* '("mfhdf/ncgen/ncgen.l"
700 "mfhdf/ncgen/ncgenyy.c"
701 "mfhdf/libsrc/netcdf.h.in")
702 (("AIX5L64") "__aarch64__"))
704 (add-before 'configure 'patchbuild
707 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
709 (("/bin/mkdir") "mkdir"))
710 (substitute* (find-files "." "^Makefile\\.in$")
711 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
712 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
713 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
714 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
715 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
717 (add-after 'configure 'patch-settings
719 ;; libhdf4.settings contains the full path of the
720 ;; compilers used, and its contents are included in
721 ;; .so-files. We truncate the hashes to avoid
722 ;; unnecessary store references to those compilers:
723 (substitute* "libhdf4.settings"
724 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
725 (string-append prefix (string-take hash 10) "...")))
728 (home-page "https://www.hdfgroup.org/products/hdf4/")
730 "Library and multi-object file format for storing and managing data")
731 (description "HDF4 is a library and multi-object file format for storing
732 and managing data between machines. HDF4 is an older hierarchical data format,
733 incompatible with HDF5.")
735 (license:non-copyleft
736 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
738 (define-public hdf4-alt
743 (substitute-keyword-arguments (package-arguments hdf4)
744 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
746 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
755 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
756 "hdf5-" (version-major+minor version)
757 "/hdf5-" version "/src/hdf5-"
759 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
762 (take (string-split version #\.) 2))
763 "/src/hdf5-" version ".tar.bz2")))
765 (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
766 (patches (list (search-patch "hdf5-config-date.patch")))))
767 (build-system gnu-build-system)
771 `(("gfortran" ,gfortran)))
772 (outputs '("out" ; core library
773 "fortran")) ; fortran interface
775 `(;; Some of the users, notably Flann, need the C++ interface.
776 #:configure-flags '("--enable-cxx"
778 "--enable-fortran2003")
779 ;; Use -fPIC to allow the R bindings to link with the static libraries
780 #:make-flags (list "CFLAGS=-fPIC"
783 (modify-phases %standard-phases
784 (add-before 'configure 'patch-configure
785 (lambda* (#:key outputs #:allow-other-keys)
786 (substitute* "configure"
788 (substitute* "fortran/src/Makefile.in"
789 (("libhdf5_fortran_la_LDFLAGS =")
790 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
791 (assoc-ref outputs "fortran") "/lib")))
792 (substitute* "hl/fortran/src/Makefile.in"
793 (("libhdf5hl_fortran_la_LDFLAGS =")
794 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
795 (assoc-ref outputs "fortran") "/lib")))
797 (add-after 'configure 'patch-settings
799 ;; libhdf5.settings contains the full path of the
800 ;; compilers used, and its contents are included in
801 ;; libhdf5.so. We truncate the hashes to avoid
802 ;; unnecessary store references to those compilers:
803 (substitute* "src/libhdf5.settings"
804 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
805 (string-append prefix (string-take hash 10) "..."))
806 ;; Don't record the build-time kernel version to make the
807 ;; settings file reproducible.
808 (("Uname information:.*")
809 "Uname information: Linux\n"))
811 (add-after 'install 'patch-references
812 (lambda* (#:key inputs outputs #:allow-other-keys)
813 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
814 (zlib (assoc-ref inputs "zlib")))
815 (substitute* (find-files bin "h5p?cc")
817 (string-append "-L" zlib "/lib " lib)))
819 (add-after 'install 'split
820 (lambda* (#:key inputs outputs #:allow-other-keys)
821 ;; Move all fortran-related files
822 (let* ((out (assoc-ref outputs "out"))
823 (bin (string-append out "/bin"))
824 (lib (string-append out "/lib"))
825 (inc (string-append out "/include"))
826 (ex (string-append out "/share/hdf5_examples/fortran"))
827 (fort (assoc-ref outputs "fortran"))
828 (fbin (string-append fort "/bin"))
829 (flib (string-append fort "/lib"))
830 (finc (string-append fort "/include"))
831 (fex (string-append fort "/share/hdf5_examples/fortran")))
836 ;; Note: When built with --enable-parallel, the 'h5fc' file
837 ;; doesn't exist, hence this condition.
838 (when (file-exists? (string-append bin "/h5fc"))
839 (rename-file (string-append bin "/h5fc")
840 (string-append fbin "/h5fc")))
841 (for-each (lambda (file)
843 (string-append flib "/" (basename file))))
844 (find-files lib ".*fortran.*"))
845 (for-each (lambda (file)
847 (string-append finc "/" (basename file))))
848 (find-files inc ".*mod"))
849 (for-each (lambda (file)
851 (string-append fex "/" (basename file))))
852 (find-files ex ".*"))
853 (delete-file-recursively ex))
855 (home-page "http://www.hdfgroup.org")
856 (synopsis "Management suite for extremely large and complex data")
857 (description "HDF5 is a suite that makes possible the management of
858 extremely large and complex data collections.")
859 (license (license:x11-style
860 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
862 (define-public hdf5-1.10
863 (package (inherit hdf5)
868 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
869 "hdf5-" (version-major+minor version)
870 "/hdf5-" version "/src/hdf5-"
872 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
875 (take (string-split version #\.) 2))
876 "/src/hdf5-" version ".tar.bz2")))
878 (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
879 (patches (list (search-patch "hdf5-config-date.patch")))))))
881 (define-public hdf-java
889 "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
890 version "/src/CMake-hdfjava-" version ".tar.gz"))
892 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
893 (modules '((guix build utils)))
894 (snippet ; Make sure we don't use the bundled sources and binaries.
896 (for-each delete-file
897 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
898 "HDF4.tar.gz" "HDF5.tar.gz"))
899 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
901 (build-system gnu-build-system)
903 `(("jdk" ,icedtea "jdk")
904 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
906 ("hamcrest-core" ,java-hamcrest-core)
907 ("junit" ,java-junit)
908 ("slf4j-simple" ,java-slf4j-simple)))
914 ("slf4j-api" ,java-slf4j-api)))
917 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
918 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
919 (assoc-ref %build-inputs "jdk") "/lib" )
920 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
921 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
924 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
925 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
926 (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
927 (string-append "JPEGLIB="
928 (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
932 (modify-phases %standard-phases
933 (add-before 'configure 'chdir-to-source
934 (lambda _ (chdir ,(string-append "hdfjava-" version))))
935 (add-before 'configure 'patch-build
936 (lambda* (#:key inputs outputs #:allow-other-keys)
937 (substitute* "configure"
938 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
939 (("/bin/cat") (which "cat")))
940 ;; Set classpath for compilation
941 (substitute* '("hdf/hdf5lib/Makefile.in"
942 "hdf/hdf5lib/exceptions/Makefile.in"
943 "hdf/hdflib/Makefile.in")
944 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
945 (string-append (assoc-ref inputs "slf4j-api")
946 "/share/java/slf4j-api.jar")))
947 ;; Replace outdated config.sub and config.guess:
948 (with-directory-excursion "config"
949 (for-each (lambda (file)
951 (string-append (assoc-ref inputs "automake")
952 "/share/automake-1.15/" file) file))
953 '("config.sub" "config.guess")))
954 (mkdir-p (string-append (assoc-ref outputs "out")))
955 ;; Set classpath for tests
956 (let* ((build-dir (getcwd))
957 (lib (string-append build-dir "/lib"))
958 (jhdf (string-append lib "/jhdf.jar"))
959 (jhdf5 (string-append lib "/jhdf5.jar"))
962 (string-append (assoc-ref inputs i)
963 "/share/java/" i ".jar"))
964 '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
966 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
968 (substitute* '("test/hdf5lib/Makefile.in"
969 "test/hdf5lib/junit.sh.in"
970 "examples/runExample.sh.in")
972 (string-append (assoc-ref inputs "coreutils")
975 (string-append (assoc-ref inputs "coreutils")
977 (("CLASSPATH=[^\n]*")
978 (string-append "CLASSPATH=" class-path)))
979 (setenv "CLASSPATH" class-path))
981 (add-before 'check 'build-examples
983 (zero? (apply system* `("javac"
984 ,@(find-files "examples" ".*\\.java")))))))
988 #:parallel-tests? #f ))
989 (home-page "https://support.hdfgroup.org/products/java")
990 (synopsis "Java interface for the HDF4 and HDF5 libraries")
991 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
992 the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
995 ;; BSD-style license:
996 (license (license:x11-style
997 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
998 /current/src/unpacked/COPYING"))))
1000 (define-public hdf-eos2
1007 (uri "ftp://edhs1.gsfc.nasa.gov\
1008 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
1010 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
1011 (patches (search-patches "hdf-eos2-remove-gctp.patch"
1012 "hdf-eos2-build-shared.patch"
1013 "hdf-eos2-fortrantests.patch"))))
1014 (build-system gnu-build-system)
1016 `(("gfortran" ,gfortran)))
1018 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
1020 ("libjpeg" ,libjpeg)
1023 `( #:configure-flags '("--enable-install-include" "--enable-shared"
1024 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
1025 #:parallel-tests? #f))
1026 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
1027 (synopsis "HDF4-based data format for NASA's Earth Observing System")
1028 (description "HDF-EOS2 is a software library built on HDF4 which supports
1029 the construction of data structures used in NASA's Earth Observing
1030 System (Grid, Point and Swath).")
1032 ;; Source files carry a permissive license header.
1033 (license (license:non-copyleft home-page))))
1035 (define-public hdf-eos5
1041 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1042 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1045 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1046 (patches (search-patches "hdf-eos5-build-shared.patch"
1047 "hdf-eos5-remove-gctp.patch"
1048 "hdf-eos5-fix-szip.patch"
1049 "hdf-eos5-fortrantests.patch"))))
1051 `(("gfortran" ,gfortran)))
1052 (build-system gnu-build-system)
1058 `(#:configure-flags '("--enable-install-include" "--enable-shared"
1059 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1060 #:parallel-tests? #f))
1061 (synopsis "HDF5-based data format for NASA's Earth Observing System")
1063 "HDF-EOS5 is a software library built on HDF5 to support the construction
1064 of data structures used in NASA's Earth Observing System (Grid, Point and
1066 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1068 ;; Source files carry a permissive license header.
1069 (license (license:non-copyleft home-page))))
1071 (define-public hdf5-parallel-openmpi
1072 (package (inherit hdf5)
1073 (name "hdf5-parallel-openmpi")
1076 ,@(package-inputs hdf5)))
1078 (substitute-keyword-arguments (package-arguments hdf5)
1079 ((#:configure-flags flags)
1080 ``("--enable-parallel" ,@(delete "--enable-cxx" ,flags)))
1082 `(modify-phases ,phases
1083 (add-after 'build 'mpi-setup
1085 (add-before 'check 'patch-tests
1087 ;; OpenMPI's mpirun will exit with non-zero status if it
1088 ;; detects an "abnormal termination", i.e. any process not
1089 ;; calling MPI_Finalize(). Since the test is explicitely
1090 ;; avoiding MPI_Finalize so as not to have at_exit and thus
1091 ;; H5C_flush_cache from being called, mpirun will always
1092 ;; complain, so turn this test off.
1093 (substitute* "testpar/Makefile"
1094 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1095 (string-append front back "\n")))
1096 (substitute* "tools/h5diff/testph5diff.sh"
1097 (("/bin/sh") (which "sh")))
1099 (synopsis "Management suite for data with parallel IO support")))
1101 (define-public h5check
1108 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
1109 "h5check/src/h5check-" version ".tar.gz"))
1112 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1113 (build-system gnu-build-system)
1114 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
1115 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1116 (synopsis "HDF5 format checker")
1117 (description "@code{h5check} is a validation tool for verifying that an
1118 HDF5 file is encoded according to the HDF File Format Specification.")
1119 (license (license:x11-style "file://COPYING"))))
1127 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1132 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1133 (build-system cmake-build-system)
1134 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1135 (inputs `(("lapack" ,lapack)
1137 ;; FIXME: Even though the fonts are available dvips complains:
1138 ;; "Font cmmi10 not found; characters will be left blank."
1140 `(("texlive" ,texlive-tiny)
1141 ("ghostscript" ,ghostscript)
1142 ("doxygen" ,doxygen)))
1143 (home-page "http://itpp.sourceforge.net")
1144 (synopsis "C++ library of maths, signal processing and communication classes")
1145 (description "IT++ is a C++ library of mathematical, signal processing and
1146 communication classes and functions. Its main use is in simulation of
1147 communication systems and for performing research in the area of
1148 communications. The kernel of the library consists of generic vector and
1149 matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1150 similar to MATLAB, GNU Octave or SciPy.")
1151 (license license:gpl3+)))
1153 (define-public netcdf
1160 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1161 "netcdf-" version ".tar.gz"))
1164 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1165 (patches (search-patches "netcdf-date-time.patch"
1166 "netcdf-tst_h_par.patch"))))
1167 (build-system gnu-build-system)
1170 ("doxygen" ,doxygen)
1171 ("graphviz" ,graphviz)))
1173 `(("hdf4" ,hdf4-alt)
1176 ("libjpeg" ,libjpeg)))
1178 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
1180 #:phases (modify-phases %standard-phases
1181 (add-before 'configure 'fix-source-date
1183 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1184 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1185 ;; to '1st hour of the current day', and therefore makes the
1186 ;; package not reproducible.
1187 (substitute* "./configure"
1188 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1189 "date --date='@0'"))
1191 (add-after 'configure 'patch-settings
1193 ;; libnetcdf.settings contains the full filename of the compilers
1194 ;; used to build the library. We truncate the hashes of those
1195 ;; filenames to avoid unnecessary references to the corresponding
1197 (substitute* "libnetcdf.settings"
1198 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1199 (string-append prefix (string-take hash 10) "...")))
1202 #:parallel-tests? #f)) ;various race conditions
1203 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
1204 (synopsis "Library for scientific data")
1205 (description "NetCDF is an interface for scientific data access and a
1206 software library that provides an implementation of the interface. The netCDF
1207 library defines a machine-independent format for representing scientific data.
1208 Together, the interface, library, and format support the creation, access, and
1209 sharing of scientific data.")
1210 (license (license:x11-style "file://COPYRIGHT"))))
1212 (define-public netcdf-parallel-openmpi
1213 (package (inherit netcdf)
1214 (name "netcdf-parallel-openmpi")
1217 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1218 (package-inputs netcdf))))
1219 ;; TODO: Replace pkg-config references in nc-config with absolute references
1221 (substitute-keyword-arguments (package-arguments netcdf)
1222 ((#:configure-flags flags)
1223 `(cons* "CC=mpicc" "CXX=mpicxx"
1224 "--enable-parallel-tests"
1225 ;; Shared libraries not supported with parallel IO.
1226 "--disable-shared" "--with-pic"
1229 (define-public netcdf-fortran
1231 (name "netcdf-fortran")
1236 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1240 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1241 (build-system gnu-build-system)
1243 `(#:parallel-tests? #f))
1245 `(("netcdf" ,netcdf)))
1247 `(("gfortran" ,gfortran)))
1248 (synopsis "Fortran interface for the netCDF library")
1249 (description (package-description netcdf))
1250 (home-page (package-home-page netcdf))
1251 (license (package-license netcdf))))
1253 (define-public nlopt
1259 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1262 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1263 (build-system gnu-build-system)
1265 `(;; Shared libraries are not built by default. They are required to
1266 ;; build the Guile, Octave, and Python bindings.
1267 #:configure-flags '("--enable-shared")
1270 (modify-phases %standard-phases
1271 (add-before 'configure 'set-libnlopt-file-name
1272 (lambda* (#:key outputs #:allow-other-keys)
1273 ;; Make sure the Scheme module refers to the library by its
1274 ;; absolute file name (we cannot do that from a snippet
1275 ;; because the expansion of @libdir@ contains
1277 (let ((out (assoc-ref outputs "out")))
1278 (substitute* "swig/nlopt.scm.in"
1280 (string-append out "/lib/libnlopt")))
1282 (inputs `(("guile" ,guile-2.0)))
1283 (native-inputs `(("pkg-config" ,pkg-config)))
1284 (home-page "http://ab-initio.mit.edu/wiki/")
1285 (synopsis "Library for nonlinear optimization")
1286 (description "NLopt is a library for nonlinear optimization, providing a
1287 common interface for a number of different free optimization routines available
1288 online as well as original implementations of various other algorithms.")
1289 (license license:lgpl2.1+)))
1291 (define-public ipopt
1298 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1302 "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
1303 (modules '((guix build utils)))
1305 ;; Make sure we don't use the bundled software.
1307 (delete-file-recursively "ThirdParty")
1309 (build-system gnu-build-system)
1311 '(#:phases (modify-phases %standard-phases
1312 (add-after 'install 'add--L-flags-in-ipopt.pc
1313 (lambda* (#:key inputs outputs #:allow-other-keys)
1314 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1315 ;; move it to "Libs.private" where it belongs, and add a
1316 ;; '-L' flag for LAPACK.
1317 (let ((out (assoc-ref outputs "out"))
1318 (lapack (assoc-ref inputs "lapack")))
1319 (substitute* (string-append out "/lib/pkgconfig/"
1321 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1322 (string-append "Libs: " before " " after "\n"
1323 "Libs.private: " before
1324 "-L" lapack "/lib -llapack -lblas "
1328 `(("gfortran" ,gfortran)))
1330 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
1331 `(("lapack" ,lapack))) ;for both libblas and liblapack
1332 (home-page "http://www.coin-or.org")
1333 (synopsis "Large-scale nonlinear optimizer")
1335 "The Interior Point Optimizer (IPOPT) is a software package for
1336 large-scale nonlinear optimization. It provides C++, C, and Fortran
1338 (license license:epl1.0)))
1340 (define-public ceres
1342 (name "ceres-solver")
1344 (home-page "http://ceres-solver.org/")
1347 (uri (string-append home-page "ceres-solver-"
1351 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
1352 (build-system cmake-build-system)
1354 ;; TODO: Build HTML user documentation and install separately.
1355 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
1356 "-DBUILD_SHARED_LIBS=ON")
1358 #:phases (modify-phases %standard-phases
1359 (add-before 'configure 'set-library-directory
1361 ;; Install libraries to lib/, not lib64/.
1362 (substitute* "internal/ceres/CMakeLists.txt"
1363 (("set\\(LIB_SUFFIX \"64\"\\)")
1364 "set(LIB_SUFFIX \"\")"))
1367 `(("pkg-config" ,pkg-config)))
1369 `(("glog" ,glog))) ;for #include <glog/glog.h>
1374 ("suitesparse" ,suitesparse)
1375 ("gflags" ,gflags)))
1376 (synopsis "C++ library for solving large optimization problems")
1378 "Ceres Solver is a C++ library for modeling and solving large,
1379 complicated optimization problems. It is a feature rich, mature and
1380 performant library which has been used in production since 2010. Ceres Solver
1381 can solve two kinds of problems:
1383 @item non-linear least squares problems with bounds constraints;
1384 @item general unconstrained optimization problems.
1386 (license license:bsd-3)))
1388 ;; For a fully featured Octave, users are strongly recommended also to install
1389 ;; the following packages: less, ghostscript, gnuplot.
1390 (define-public octave-cli
1397 (uri (string-append "mirror://gnu/octave/octave-"
1401 "0jsdgizlv02an2ppfjwk5qf209zpwi3317yb7jvlsjzxnir3lvhy"))))
1402 (build-system gnu-build-system)
1404 `(("lapack" ,lapack)
1406 ("readline" ,readline)
1411 ("arpack" ,arpack-ng)
1414 ("fontconfig" ,fontconfig)
1415 ("freetype" ,freetype)
1422 ("texinfo" ,texinfo)
1423 ("graphicsmagick" ,graphicsmagick)
1424 ("suitesparse" ,suitesparse)
1425 ("libsndfile" ,libsndfile)
1426 ("portaudio" ,portaudio)
1427 ("alsa-lib" ,alsa-lib)))
1430 ("gfortran" ,gfortran)
1431 ("pkg-config" ,pkg-config)
1433 ;; The following inputs are not actually used in the build process.
1434 ;; However, the ./configure gratuitously tests for their existence and
1435 ;; assumes that programs not present at build time are also not, and
1436 ;; can never be, available at run time! If these inputs are therefore
1437 ;; not present, support for them will be built out. However, Octave
1438 ;; will still run without them, albeit without the features they
1441 ("ghostscript" ,ghostscript)
1442 ("gnuplot" ,gnuplot)))
1443 ;; Octave code uses this variable to detect directories holding multiple CA
1444 ;; certificates to verify peers with. This is required for the networking
1445 ;; functions that require encryption to work properly.
1446 (native-search-paths
1447 (list (search-path-specification
1448 (variable "CURLOPT_CAPATH")
1449 (files '("etc/ssl/certs")))))
1452 (list (string-append "--with-shell="
1453 (assoc-ref %build-inputs "bash")
1456 (modify-phases %standard-phases
1457 (add-after 'configure 'configure-makeinfo
1458 (lambda* (#:key inputs #:allow-other-keys)
1459 (substitute* "libinterp/corefcn/help.h"
1462 "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
1464 (home-page "https://www.gnu.org/software/octave/")
1465 (synopsis "High-level language for numerical computation")
1466 (description "GNU Octave is a high-level interpreted language that is
1467 specialized for numerical computations. It can be used for both linear and
1468 non-linear applications and it provides great support for visualizing results.
1469 Work may be performed both at the interactive command-line as well as via
1471 (license license:gpl3+)))
1473 (define-public octave
1474 (package (inherit octave-cli)
1477 (inherit (package-source octave-cli))))
1479 `(("qscintilla" ,qscintilla)
1481 ,@(package-inputs octave-cli)))
1483 `(("qttools" , qttools) ;for lrelease
1484 ("texlive" ,texlive) ;for texi2dvi
1485 ,@(package-native-inputs octave-cli)))
1487 (substitute-keyword-arguments (package-arguments octave-cli)
1489 `(modify-phases ,phases
1490 (add-before 'configure 'patch-qscintilla-library-name
1491 (lambda* (#:key inputs #:allow-other-keys)
1492 ;; The QScintilla library that the Octave configure script tries
1493 ;; to link with should be named libqscintilla-qt5.so, but the
1494 ;; QScintilla input provides the shared library as
1495 ;; libqscintilla2_qt5.so.
1496 (substitute* "configure"
1497 (("qscintilla2-qt5")
1501 (define-public qtoctave
1502 (deprecated-package "qtoctave" octave))
1504 (define-public opencascade-oce
1506 (name "opencascade-oce")
1512 "https://github.com/tpaviot/oce/archive/OCE-"
1515 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
1518 "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
1519 (build-system cmake-build-system)
1522 (list "-DOCE_TESTING:BOOL=ON"
1523 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1524 "-DOCE_DRAW:BOOL=ON"
1525 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1526 (assoc-ref %outputs "out"))
1527 "-UCMAKE_INSTALL_RPATH")))
1529 `(("freetype" ,freetype)
1536 `(("python" ,python-wrapper)))
1537 (home-page "https://github.com/tpaviot/oce")
1538 (synopsis "Libraries for 3D modeling and numerical simulation")
1540 "Open CASCADE is a set of libraries for the development of applications
1541 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1542 C++ class libraries providing services for 3D surface and solid modeling, CAD
1543 data exchange, and visualization. It is used for development of specialized
1544 software dealing with 3D models in design (CAD), manufacturing (CAM),
1545 numerical simulation (CAE), measurement equipment (CMM), and quality
1546 control (CAQ) domains.
1548 This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1549 patches, improvements, and experiments contributed by users over the official
1550 Open CASCADE library.")
1551 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1552 ; use of header files; see
1553 ; OCCT_LGPL_EXCEPTION.txt
1554 license:public-domain; files
1555 ; src/Standard/Standard_StdAllocator.hxx and
1556 ; src/NCollection/NCollection_StdAllocator.hxx
1557 license:expat; file src/OpenGl/OpenGl_glext.h
1558 license:bsd-3)))); test framework gtest
1567 (uri (string-append "http://gmsh.info/src/gmsh-"
1568 version "-source.tgz"))
1570 (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
1571 (modules '((guix build utils)))
1573 ;; Remove non-free METIS code
1575 (delete-file-recursively "contrib/Metis")
1577 (build-system cmake-build-system)
1580 ("gfortran" ,gfortran)
1586 ("opencascade-oce" ,opencascade-oce)
1588 ("libxext" ,libxext)))
1590 `(("fontconfig" ,fontconfig)
1591 ("libxft" ,libxft)))
1593 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1594 "-DENABLE_BUILD_SHARED:BOOL=ON"
1595 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
1596 (home-page "http://www.geuz.org/gmsh/")
1597 (synopsis "3D finite element grid generator")
1598 (description "Gmsh is a 3D finite element grid generator with a built-in
1599 CAD engine and post-processor. Its design goal is to provide a fast, light
1600 and user-friendly meshing tool with parametric input and advanced
1601 visualization capabilities. Gmsh is built around four modules: geometry,
1602 mesh, solver and post-processing. The specification of any input to these
1603 modules is done either interactively using the graphical user interface or in
1604 ASCII text files using Gmsh's own scripting language.")
1605 (license license:gpl2+)))
1607 (define-public maxflow
1614 (url "https://github.com/gerddie/maxflow.git")
1615 (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
1616 (file-name (string-append name "-" version "-checkout"))
1619 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1620 (build-system cmake-build-system)
1621 (home-page "http://pub.ist.ac.at/~vnk/software.html")
1622 (synopsis "Library implementing Maxflow algorithm")
1623 (description "An implementation of the maxflow algorithm described in
1624 @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1625 Energy Minimization in Computer Vision.\n
1626 Yuri Boykov and Vladimir Kolmogorov.\n
1627 In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1629 (license license:gpl3+)))
1631 (define-public petsc
1638 ;; The *-lite-* tarball does not contain the *large* documentation
1639 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1640 "petsc-lite-" version ".tar.gz"))
1642 (base32 "0bl64pydak3rblnjffi482r8bin4xim9sb37ksl2jkcxf0i0irsi"))))
1643 (outputs '("out" ;libraries and headers
1644 "examples")) ;~30MiB of examples
1645 (build-system gnu-build-system)
1647 `(("python" ,python-2)))
1649 `(("gfortran" ,gfortran)
1651 ("superlu" ,superlu)
1652 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1653 ;; leaving out opengl, as configuration seems to only be for mac
1656 `(#:test-target "test"
1657 #:parallel-build? #f ;build is parallel by default
1663 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1664 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1665 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
1667 (modify-phases %standard-phases
1669 ;; PETSc's configure script is actually a python script, so we can't
1670 ;; run it with bash.
1671 (lambda* (#:key outputs (configure-flags '())
1673 (let* ((prefix (assoc-ref outputs "out"))
1674 (flags `(,(string-append "--prefix=" prefix)
1675 ,@configure-flags)))
1676 (format #t "build directory: ~s~%" (getcwd))
1677 (format #t "configure flags: ~s~%" flags)
1678 (apply invoke "./configure" flags))))
1679 (add-after 'configure 'clean-local-references
1680 (lambda* (#:key outputs #:allow-other-keys)
1681 (let ((out (assoc-ref outputs "out")))
1682 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
1683 ;; Prevent build directory from leaking into compiled code
1685 ;; Scrub timestamp for reproducibility
1686 ((".*Libraries compiled on.*") ""))
1687 (substitute* (find-files "." "petscvariables")
1688 ;; Do not expose build machine characteristics, set to defaults.
1689 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1690 (("NPMAX = [:digit:]+") "NPMAX = 2"))
1692 (add-after 'install 'clean-install
1693 ;; Try to keep installed files from leaking build directory names.
1694 (lambda* (#:key inputs outputs #:allow-other-keys)
1695 (let ((out (assoc-ref outputs "out")))
1696 (substitute* (map (lambda (file)
1697 (string-append out "/lib/petsc/conf/" file))
1698 '("petscvariables"))
1700 ;; Make compiler references point to the store
1701 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
1702 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1703 (string-append "= " (which compiler))))
1704 ;; PETSc installs some build logs, which aren't necessary.
1705 (for-each (lambda (file)
1706 (let ((f (string-append out "/lib/petsc/conf/" file)))
1707 (when (file-exists? f)
1709 '("configure.log" "make.log" "gmake.log"
1710 "test.log" "error.log" "RDict.db"
1711 "PETScBuildInternal.cmake"
1712 ;; Once installed, should uninstall with Guix
1715 (add-after 'install 'move-examples
1716 (lambda* (#:key outputs #:allow-other-keys)
1717 (let* ((out (assoc-ref outputs "out"))
1718 (examples (assoc-ref outputs "examples"))
1719 (exdir (string-append out "/share/petsc/examples"))
1720 (exdir' (string-append examples "/share/petsc/examples")))
1721 (copy-recursively exdir exdir')
1722 (delete-file-recursively exdir)
1724 (home-page "http://www.mcs.anl.gov/petsc")
1725 (synopsis "Library to solve PDEs")
1726 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1727 data structures and routines for the scalable (parallel) solution of
1728 scientific applications modeled by partial differential equations.")
1729 (license (license:non-copyleft
1730 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1732 (define-public petsc-complex
1733 (package (inherit petsc)
1734 (name "petsc-complex")
1736 (substitute-keyword-arguments (package-arguments petsc)
1737 ((#:configure-flags cf)
1738 `(cons "--with-scalar-type=complex" ,cf))))
1739 (synopsis "Library to solve PDEs (with complex scalars)")))
1741 (define-public petsc-openmpi
1742 (package (inherit petsc)
1743 (name "petsc-openmpi")
1745 `(("hdf5" ,hdf5-parallel-openmpi)
1746 ("hypre" ,hypre-openmpi)
1748 ("mumps" ,mumps-openmpi)
1749 ("openmpi" ,openmpi)
1750 ("scalapack" ,scalapack)
1751 ("scotch" ,pt-scotch32)
1752 ,@(package-inputs petsc)))
1754 (substitute-keyword-arguments (package-arguments petsc)
1755 ((#:configure-flags cf)
1757 "--with-mpiexec=mpirun"
1760 "--with-scalapack=1"
1762 ,(string-append "--with-mpi-dir="
1763 (assoc-ref %build-inputs "openmpi"))
1764 ,(string-append "--with-hdf5-include="
1765 (assoc-ref %build-inputs "hdf5") "/include")
1766 ,(string-append "--with-hdf5-lib="
1767 (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
1768 ,@(delete "--with-mpi=0" ,cf)))
1770 `(modify-phases ,phases
1771 (add-before 'configure 'mpi-setup
1772 ,%openmpi-setup)))))
1773 (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
1775 (define-public petsc-complex-openmpi
1776 (package (inherit petsc-complex)
1777 (name "petsc-complex-openmpi")
1779 `(("openmpi" ,openmpi)
1780 ,@(package-inputs petsc-complex)))
1782 (substitute-keyword-arguments (package-arguments petsc-complex)
1783 ((#:configure-flags cf)
1784 ``("--with-mpiexec=mpirun"
1785 ,(string-append "--with-mpi-dir="
1786 (assoc-ref %build-inputs "openmpi"))
1787 ,@(delete "--with-mpi=0" ,cf)))))
1788 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
1790 (define-public python-petsc4py
1792 (name "python-petsc4py")
1797 (uri (pypi-uri "petsc4py" version))
1800 "0ch3g6dsvxl7qi984fcssv7cxfbif4bw04gkvxl2l1b8wrmvrm25"))))
1801 (build-system python-build-system)
1804 (modify-phases %standard-phases
1805 (add-before 'build 'pre-build
1807 ;; Define path to PETSc installation.
1808 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
1810 (add-before 'check 'mpi-setup
1813 `(("petsc" ,petsc-openmpi)
1814 ("python-numpy" ,python-numpy)))
1815 (home-page "https://bitbucket.org/petsc/petsc4py/")
1816 (synopsis "Python bindings for PETSc")
1817 (description "PETSc, the Portable, Extensible Toolkit for
1818 Scientific Computation, is a suite of data structures and routines for
1819 the scalable (parallel) solution of scientific applications modeled by
1820 partial differential equations. It employs the MPI standard for all
1821 message-passing communication. @code{petsc4py} provides Python
1822 bindings to almost all functions of PETSc.")
1823 (license license:bsd-3)))
1825 (define-public python-kiwisolver
1827 (name "python-kiwisolver")
1831 (uri (pypi-uri "kiwisolver" version))
1834 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
1835 (build-system python-build-system)
1836 (home-page "https://github.com/nucleic/kiwi")
1837 (synopsis "Fast implementation of the Cassowary constraint solver")
1839 "Kiwi is an efficient C++ implementation of the Cassowary constraint
1840 solving algorithm. Kiwi has been designed from the ground up to be
1841 lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
1842 Cassowary solver with typical use cases gaining a 40x improvement. Memory
1843 savings are consistently > 5x.")
1844 (license license:bsd-3)))
1846 (define-public python2-kiwisolver
1847 (package-with-python2 python-kiwisolver))
1849 (define-public slepc
1856 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
1860 "188j1a133q91h8pivpnzwcf78kz8dvz2nzf6ndnjygdbqb48fizn"))))
1861 (build-system gnu-build-system)
1863 `(("python" ,python-2)))
1865 `(("arpack" ,arpack-ng)
1866 ("gfortran" ,gfortran)))
1868 `(("petsc" ,petsc)))
1870 `(#:parallel-build? #f ;build is parallel by default
1872 `(,(string-append "--with-arpack-dir="
1873 (assoc-ref %build-inputs "arpack") "/lib"))
1874 #:make-flags ;honor (parallel-job-count)
1875 `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
1877 (modify-phases %standard-phases
1879 ;; configure is a python script, so we can't run it with bash.
1880 (lambda* (#:key inputs outputs (configure-flags '())
1882 (let* ((prefix (assoc-ref outputs "out"))
1883 (flags `(,(string-append "--prefix=" prefix)
1884 ,@configure-flags)))
1885 (format #t "build directory: ~s~%" (getcwd))
1886 (format #t "configure flags: ~s~%" flags)
1887 (setenv "SLEPC_DIR" (getcwd))
1888 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
1889 (apply invoke "./configure" flags))))
1890 (add-after 'install 'delete-doc
1891 ;; TODO: SLEPc installs HTML documentation alongside headers in
1892 ;; $out/include. We'd like to move them to share/doc, but delete
1893 ;; them for now, as they are incomplete and installing the complete
1894 ;; documentation is difficult.
1895 (lambda* (#:key outputs #:allow-other-keys)
1896 (let* ((out (assoc-ref outputs "out")))
1897 (for-each delete-file (find-files out "\\.html$"))
1899 (add-after 'install 'clean-install
1900 ;; Clean up unnecessary build logs from installation.
1901 (lambda* (#:key outputs #:allow-other-keys)
1902 (let ((out (assoc-ref outputs "out")))
1903 (for-each (lambda (file)
1904 (let ((f (string-append out "/lib/slepc/conf/" file)))
1905 (when (file-exists? f)
1907 '("configure.log" "make.log" "gmake.log"
1908 "test.log" "error.log" "RDict.db"
1911 (home-page "http://slepc.upv.es")
1912 (synopsis "Scalable library for eigenproblems")
1913 (description "SLEPc is a software library for the solution of large sparse
1914 eigenproblems on parallel computers. It can be used for the solution of
1915 linear eigenvalue problems formulated in either standard or generalized form,
1916 as well as other related problems such as the singular value decomposition.
1917 The emphasis of the software is on methods and techniques appropriate for
1918 problems in which the associated matrices are sparse, for example, those
1919 arising after the discretization of partial differential equations.")
1920 (license license:bsd-2)))
1922 (define-public slepc-complex
1923 (package (inherit slepc)
1924 (name "slepc-complex")
1926 `(("petsc" ,petsc-complex)
1927 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1928 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1930 (define-public slepc-openmpi
1931 (package (inherit slepc)
1932 (name "slepc-openmpi")
1934 (substitute-keyword-arguments (package-arguments slepc)
1935 ((#:phases phases '%standard-phases)
1936 `(modify-phases ,phases
1937 (add-before 'check 'mpi-setup
1938 ,%openmpi-setup)))))
1941 ("arpack" ,arpack-ng-openmpi)
1942 ,@(alist-delete "arpack" (package-inputs slepc))))
1944 `(("petsc" ,petsc-openmpi)
1945 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1946 (synopsis "Scalable library for eigenproblems (with MPI support)")))
1948 (define-public slepc-complex-openmpi
1949 (package (inherit slepc-openmpi)
1950 (name "slepc-complex-openmpi")
1952 `(("petsc" ,petsc-complex-openmpi)
1953 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1954 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1956 (define-public python-slepc4py
1958 (name "python-slepc4py")
1963 (uri (pypi-uri "slepc4py" version))
1966 "0x049dyc8frgh79fvvavf4vlbqp4mgm61nsaivzdav4316vvlv1j"))))
1967 (build-system python-build-system)
1970 (modify-phases %standard-phases
1971 (add-before 'build 'pre-build
1973 ;; Define path to PETSc installation.
1974 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
1975 ;; Define path to SLEPc installation.
1976 (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
1978 (add-before 'check 'mpi-setup
1981 `(("python-numpy" ,python-numpy)
1982 ("python-petsc4py" ,python-petsc4py)
1983 ("slepc" ,slepc-openmpi)))
1984 (home-page "https://bitbucket.org/slepc/slepc4py/")
1985 (synopsis "Python bindings for SLEPc")
1986 (description "SLEPc, the Scalable Library for Eigenvalue Problem
1987 Computations, is based on PETSc, the Portable, Extensible Toolkit for
1988 Scientific Computation. It employs the MPI standard for all
1989 message-passing communication. @code{slepc4py} provides Python
1990 bindings to almost all functions of SLEPc.")
1991 (license license:bsd-3)))
1993 (define-public mumps
2000 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
2004 "1s9asin08zqzmh08257sdghhivvy9vjif7c53fhaxaax2kd5qd7b"))
2005 (patches (search-patches "mumps-build-parallelism.patch"))))
2006 (build-system gnu-build-system)
2008 `(("fortran" ,gfortran)
2009 ;; These are required for linking against mumps, but we let the user
2010 ;; declare the dependency.
2013 ("scotch" ,scotch)))
2015 `(#:modules ((ice-9 match)
2018 ,@%gnu-build-system-modules)
2020 (modify-phases %standard-phases
2022 (lambda* (#:key inputs #:allow-other-keys)
2023 (call-with-output-file "Makefile.inc"
2034 INCSEQ = -I$(topdir)/libseq
2035 LIBSEQ = -L$(topdir)/libseq -lmpiseq
2036 LIBSEQNEEDED = libseqneeded~;
2040 AR = ar vr # rules require trailing space, ugh...
2042 LIBBLAS = -L~a -lopenblas~@[
2043 SCALAP = -L~a -lscalapack~]
2044 LIBOTHERS = -pthread
2047 OPTF = -O2 -DALLOW_NON_INIT $(PIC)
2051 LIBS = $(SCALAP) $(LIBSEQ)
2052 LPORDDIR = $(topdir)/PORD/lib
2053 IPORD = -I$(topdir)/PORD/include
2054 LPORD = -L$(LPORDDIR) -lpord
2055 ORDERINGSF = -Dpord~@[
2057 IMETIS = -I$(METISDIR)/include
2058 LMETIS = -L$(METISDIR)/lib -lmetis
2059 ORDERINGSF += -Dmetis~]~@[~:{
2061 ISCOTCH = -I$(SCOTCHDIR)/include
2062 LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
2063 ORDERINGSF += ~a~}~]
2064 ORDERINGSC = $(ORDERINGSF)
2065 LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
2066 IORDERINGSF = $(ISCOTCH)
2067 IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
2068 (assoc-ref inputs "mpi")
2069 (assoc-ref inputs "blas")
2070 (assoc-ref inputs "scalapack")
2071 (assoc-ref inputs "metis")
2072 (match (list (assoc-ref inputs "pt-scotch")
2073 (assoc-ref inputs "scotch"))
2077 `((,scotch "" "-Dscotch")))
2080 "-lptesmumps -lptscotch -lptscotcherr "
2081 "-Dptscotch")))))))))
2083 ;; By default only the d-precision library is built. Make with "all"
2084 ;; target so that all precision libraries and examples are built.
2086 (invoke "make" "all"
2087 (format #f "-j~a" (parallel-job-count)))))
2089 ;; Run the simple test drivers, which read test input from stdin:
2090 ;; from the "real" input for the single- and double-precision
2091 ;; testers, and from the "cmplx" input for complex-precision
2092 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
2093 ;; package to prefix execution with "mpirun".
2094 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
2095 (with-directory-excursion "examples"
2098 (let ((tester (apply open-pipe*
2101 ,(string-append "./" prec
2103 (input (open-input-file
2104 (string-append "input_simpletest_" type))))
2106 (dump-port input tester)
2108 (zero? (close-pipe tester)))))
2110 '("real" "real" "cmplx" "cmplx")))))
2112 (lambda* (#:key outputs #:allow-other-keys)
2113 (let* ((out (assoc-ref outputs "out"))
2114 (libdir (string-append out "/lib")))
2115 (copy-recursively "lib" libdir)
2116 (copy-recursively "include" (string-append out "/include"))
2117 (when (file-exists? "libseq/libmpiseq.a")
2118 (install-file "libseq/libmpiseq.a" libdir))
2120 (home-page "http://mumps.enseeiht.fr")
2121 (synopsis "Multifrontal sparse direct solver")
2123 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
2124 sparse system of linear equations A x = b using Guassian elimination.")
2125 (license license:cecill-c)))
2127 (define-public mumps-metis
2128 (package (inherit mumps)
2129 (name "mumps-metis")
2131 (alist-delete "scotch" (package-inputs mumps)))))
2133 (define-public mumps-openmpi
2134 (package (inherit mumps)
2135 (name "mumps-openmpi")
2138 ("scalapack" ,scalapack)
2139 ("pt-scotch" ,pt-scotch)
2140 ,@(alist-delete "scotch" (package-inputs mumps))))
2142 (substitute-keyword-arguments (package-arguments mumps)
2144 `(modify-phases ,phases
2145 (add-before 'check 'mpi-setup
2149 ((assoc-ref ,phases 'check)
2150 #:exec-prefix '("mpirun" "-n" "2"))))))))
2151 (synopsis "Multifrontal sparse direct solver (with MPI)")))
2153 (define-public mumps-metis-openmpi
2154 (package (inherit mumps-openmpi)
2155 (name "mumps-metis-openmpi")
2157 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
2159 (define-public r-quadprog
2166 (uri (cran-uri "quadprog" version))
2169 "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
2170 (build-system r-build-system)
2172 `(("gfortran" ,gfortran)))
2173 (home-page "https://cran.r-project.org/web/packages/quadprog")
2174 (synopsis "Functions to solve quadratic programming problems")
2176 "This package contains routines and documentation for solving quadratic
2177 programming problems.")
2178 (license license:gpl3+)))
2180 (define-public r-pracma
2186 (uri (cran-uri "pracma" version))
2188 (base32 "18zhni05gwnxbphl6bmjjxmsgg5wwnnkwlb4g971cqyw3dsd83ki"))))
2189 (build-system r-build-system)
2190 (home-page "https://cran.r-project.org/web/packages/pracma/")
2191 (synopsis "Practical numerical math functions")
2192 (description "This package provides functions for numerical analysis and
2193 linear algebra, numerical optimization, differential equations, plus some
2194 special functions. It uses Matlab function names where appropriate to simplify
2196 (license license:gpl3+)))
2198 (define-public ruby-asciimath
2200 (name "ruby-asciimath")
2205 (uri (rubygems-uri "asciimath" version))
2208 "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
2209 (build-system ruby-build-system)
2212 (modify-phases %standard-phases
2214 ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
2215 (add-after 'unpack 'patch-remove-spurious-backslashes
2217 (substitute* "spec/parser_spec.rb"
2222 `(("bundler" ,bundler)
2223 ("ruby-rspec" ,ruby-rspec)))
2224 (synopsis "AsciiMath parsing and conversion library")
2226 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
2227 easy-to-write markup language for mathematics.")
2228 (home-page "https://github.com/asciidoctor/asciimath")
2229 (license license:expat)))
2231 (define-public superlu
2238 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2239 "superlu_" version ".tar.gz"))
2241 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
2242 (modules '((guix build utils)))
2244 ;; Replace the non-free implementation of MC64 with a stub adapted
2247 (use-modules (ice-9 regex)
2249 (call-with-output-file "SRC/mc64ad.c"
2254 void mc64id_(int *a) {
2255 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2258 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2259 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2260 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2263 ;; Remove the corresponding license verbiage. MC64 license follows
2264 ;; a "------" line separator.
2265 (with-atomic-file-replacement "License.txt"
2266 (let ((rx (make-regexp "-{8}")))
2269 (let ((line (read-line in 'concat)))
2270 (unless (regexp-exec rx line)
2274 (build-system cmake-build-system)
2278 `(("blas" ,openblas)
2279 ("gfortran" ,gfortran)))
2281 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2282 "-DTPL_BLAS_LIBRARIES=openblas"
2283 "-DBUILD_SHARED_LIBS:BOOL=YES")))
2284 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
2285 (synopsis "Supernodal direct solver for sparse linear systems")
2287 "SuperLU is a general purpose library for the direct solution of large,
2288 sparse, nonsymmetric systems of linear equations on high performance machines.
2289 The library is written in C and is callable from either C or Fortran. The
2290 library routines perform an LU decomposition with partial pivoting and
2291 triangular system solves through forward and back substitution. The library
2292 also provides threshold-based ILU factorization preconditioners.")
2293 (license (list license:bsd-3
2294 license:gpl2+ ;EXAMPLE/*fgmr.c
2295 (license:fsf-free "file://SRC/colamd.h")))))
2297 (define-public superlu-dist
2299 (name "superlu-dist")
2304 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2305 "superlu_dist_" version ".tar.gz"))
2307 (base32 "0ja5ihqivkda1wd58y4lmzvmwssm9g91f70c5q0fzwhng6580h6y"))
2308 (modules '((guix build utils)))
2310 ;; Replace the non-free implementation of MC64 with a stub
2312 (use-modules (ice-9 regex)
2314 (call-with-output-file "SRC/mc64ad_dist.c"
2319 void mc64id_dist(int *a) {
2320 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2323 void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2324 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2325 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2328 (substitute* "SRC/util.c" ;adjust default algorithm
2329 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
2330 "RowPerm = NOROWPERM"))
2332 (patches (search-patches "superlu-dist-scotchmetis.patch"))))
2333 (build-system gnu-build-system)
2337 `(("gfortran" ,gfortran)))
2339 `(("openmpi" ,openmpi) ;headers include MPI heades
2340 ("lapack" ,lapack) ;required to link with output library
2341 ("pt-scotch" ,pt-scotch))) ;same
2343 `(#:parallel-build? #f ;race conditions using ar
2345 (modify-phases %standard-phases
2347 (lambda* (#:key inputs outputs #:allow-other-keys)
2348 (call-with-output-file "make.inc"
2353 DSUPERLULIB = ~a/lib/libsuperlu_dist.a
2354 BLASDEF = -DUSE_VENDOR_BLAS
2355 BLASLIB = -L~a/lib -lblas
2356 PARMETISLIB = -L~a/lib \
2357 -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
2358 -lscotch -lscotcherr -lscotcherrexit
2359 METISLIB = -L~:*~a/lib \
2360 -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
2361 LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
2367 CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC)
2368 NOOPTS = -O0 -g $(PIC)
2370 FFLAGS = -O2 -g $(PIC)
2374 (assoc-ref outputs "out")
2375 (assoc-ref inputs "lapack")
2376 (assoc-ref inputs "pt-scotch"))))
2378 (add-after 'unpack 'remove-broken-symlinks
2380 (for-each delete-file
2381 (find-files "MAKE_INC" "\\.#make\\..*"))
2383 (add-before 'build 'create-install-directories
2384 (lambda* (#:key outputs #:allow-other-keys)
2387 (mkdir-p (string-append (assoc-ref outputs "out")
2391 (add-before 'check 'mpi-setup
2395 (with-directory-excursion "EXAMPLE"
2396 (invoke "mpirun" "-n" "2"
2397 "./pddrive" "-r" "1" "-c" "2" "g20.rua")
2398 (invoke "mpirun" "-n" "2"
2399 "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))
2402 (lambda* (#:key outputs #:allow-other-keys)
2403 ;; Library is placed in lib during the build phase. Copy over
2404 ;; headers to include.
2405 (let* ((out (assoc-ref outputs "out"))
2406 (incdir (string-append out "/include")))
2407 (for-each (lambda (file)
2408 (let ((base (basename file)))
2409 (format #t "installing `~a' to `~a'~%"
2412 (string-append incdir "/" base))))
2413 (find-files "SRC" ".*\\.h$")))
2415 (home-page (package-home-page superlu))
2416 (synopsis "Parallel supernodal direct solver")
2418 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2419 It is targeted for distributed memory parallel machines. SuperLU_DIST is
2420 implemented in ANSI C, and MPI for communications.")
2421 (license license:bsd-3)))
2423 (define-public scotch
2430 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
2431 "latestfile/298/scotch_" version ".tar.gz"))
2433 (base32 "0vsmgjz8qv80di3ljmc7hbdsizxxxwy2b9rgd2fl1mdc6dgbj8av"))
2434 (patches (search-patches "scotch-test-threading.patch"
2435 "scotch-build-parallelism.patch"
2436 "scotch-graph-induce-type-64.patch"
2437 "scotch-graph-diam-64.patch"))))
2438 (build-system gnu-build-system)
2445 (modify-phases %standard-phases
2447 'unpack 'chdir-to-src
2448 (lambda _ (chdir "src") #t))
2452 (call-with-output-file "Makefile.inc"
2466 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2467 LDFLAGS = -lz -lm -lrt -lpthread
2469 LEX = flex -Pscotchyy -olex.yy.c
2474 YACC = bison -pscotchyy -y -b y
2476 '("COMMON_FILE_COMPRESS_GZ"
2478 "COMMON_RANDOM_FIXED_SEED"
2479 "INTSIZE64" ;use 'long' instead of 'int'
2480 ;; Prevents symbolc clashes with libesmumps
2482 ;; XXX: Causes invalid frees in superlu-dist tests
2484 ;; "SCOTCH_PTHREAD_NUMBER=2"
2485 "restrict=__restrict"))))
2487 (add-after 'build 'build-esmumps
2490 (format #f "-j~a" (parallel-job-count))
2494 (lambda* (#:key outputs #:allow-other-keys)
2495 (let ((out (assoc-ref outputs "out")))
2498 (string-append "prefix=" out)
2500 ;; esmumps files are not installed with the above
2501 (for-each (lambda (f)
2502 (copy-file f (string-append out "/include/" f)))
2503 (find-files "../include" ".*esmumps.h$"))
2504 (for-each (lambda (f)
2505 (copy-file f (string-append out "/lib/" f)))
2506 (find-files "../lib" "^lib.*esmumps.*"))
2508 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
2509 (synopsis "Programs and libraries for graph algorithms")
2510 (description "SCOTCH is a set of programs and libraries which implement
2511 the static mapping and sparse matrix reordering algorithms developed within
2512 the SCOTCH project. Its purpose is to apply graph theory, with a divide and
2513 conquer approach, to scientific computing problems such as graph and mesh
2514 partitioning, static mapping, and sparse matrix ordering, in application
2515 domains ranging from structural mechanics to operating systems or
2517 ;; See LICENSE_en.txt
2518 (license license:cecill-c)))
2520 (define-public scotch32
2521 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2522 ;; some applications.
2523 (package (inherit scotch)
2526 (substitute-keyword-arguments (package-arguments scotch)
2527 ((#:phases scotch-phases)
2528 `(modify-phases ,scotch-phases
2532 (call-with-output-file "Makefile.inc"
2546 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2547 LDFLAGS = -lz -lm -lrt -lpthread
2549 LEX = flex -Pscotchyy -olex.yy.c
2554 YACC = bison -pscotchyy -y -b y
2556 '("COMMON_FILE_COMPRESS_GZ"
2558 "COMMON_RANDOM_FIXED_SEED"
2559 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
2560 ;; Prevents symbolc clashes with libesmumps
2562 ;; XXX: Causes invalid frees in superlu-dist tests
2564 ;; "SCOTCH_PTHREAD_NUMBER=2"
2565 "restrict=__restrict"))))))))))
2567 "Programs and libraries for graph algorithms (32-bit integers)")))
2569 (define-public pt-scotch
2570 (package (inherit scotch)
2573 `(("openmpi" ,openmpi))) ;Headers include MPI headers
2575 (substitute-keyword-arguments (package-arguments scotch)
2576 ((#:phases scotch-phases)
2577 `(modify-phases ,scotch-phases
2581 (invoke "make" (format #f "-j~a" (parallel-job-count))
2582 "ptscotch" "ptesmumps")
2584 ;; Install the serial metis compatibility library
2585 (invoke "make" "-C" "libscotchmetis" "install")))
2586 (add-before 'check 'mpi-setup
2590 (invoke "make" "ptcheck")))))))
2591 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
2593 (define-public pt-scotch32
2594 (package (inherit scotch32)
2595 (name "pt-scotch32")
2597 `(("openmpi" ,openmpi))) ;headers include MPI headers
2599 (substitute-keyword-arguments (package-arguments scotch32)
2600 ((#:phases scotch32-phases)
2601 `(modify-phases ,scotch32-phases
2604 (invoke "make" (format #f "-j~a" (parallel-job-count))
2605 "ptscotch" "ptesmumps")
2606 ;; Install the serial metis compatibility library
2607 (invoke "make" "-C" "libscotchmetis" "install")))
2608 (add-before 'check 'mpi-setup
2612 (invoke "make" "ptcheck")))))))
2614 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2616 (define-public metis
2623 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2624 "metis-" version ".tar.gz"))
2627 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2628 (build-system cmake-build-system)
2630 `(("blas" ,openblas)))
2632 `(#:tests? #f ;no tests
2633 #:configure-flags `("-DSHARED=ON"
2634 ,(string-append "-DGKLIB_PATH=" (getcwd)
2635 "/metis-" ,version "/GKlib"))))
2636 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2637 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2639 "METIS is a set of serial programs for partitioning graphs, partitioning
2640 finite element meshes, and producing fill-reducing orderings for sparse
2641 matrices. The algorithms implemented in METIS are based on the multilevel
2642 recursive-bisection, multilevel k-way, and multi-constraint partitioning
2644 (license license:asl2.0))) ;As of version 5.0.3
2646 (define-public p4est
2653 (uri (string-append "http://p4est.github.io/release/p4est-"
2657 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
2658 (build-system gnu-build-system)
2660 `(("fortran" ,gfortran)
2665 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2666 (assoc-ref %build-inputs "blas")
2668 ,(string-append "LAPACK_LIBS=-L"
2669 (assoc-ref %build-inputs "lapack")
2671 #:phases (modify-phases %standard-phases
2672 (add-before 'check 'mpi-setup
2674 (home-page "http://www.p4est.org")
2675 (synopsis "Adaptive mesh refinement on forests of octrees")
2677 "The p4est software library enables the dynamic management of a
2678 collection of adaptive octrees, conveniently called a forest of octrees.
2679 p4est is designed to work in parallel and scales to hundreds of thousands of
2681 (license license:gpl2+)))
2683 (define-public p4est-openmpi
2684 (package (inherit p4est)
2685 (name "p4est-openmpi")
2688 ,@(package-inputs p4est)))
2690 (substitute-keyword-arguments (package-arguments p4est)
2691 ((#:configure-flags cf)
2692 ``("--enable-mpi" ,@,cf))))
2693 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2695 (define-public gsegrafix
2702 (uri (string-append "mirror://gnu/" name "/" name "-"
2706 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2707 (build-system gnu-build-system)
2709 `(#:configure-flags '("LDFLAGS=-lm")))
2711 `(("libgnomecanvas" ,libgnomecanvas)
2712 ("libbonoboui" ,libbonoboui)
2713 ("libgnomeui" ,libgnomeui)
2714 ("libgnomeprintui" ,libgnomeprintui)
2717 `(("pkg-config" ,pkg-config)))
2718 (home-page "https://www.gnu.org/software/gsegrafix/")
2719 (synopsis "GNOME application to create scientific and engineering plots")
2720 (description "GSEGrafix is an application which produces high-quality graphical
2721 plots for science and engineering. Plots are specified via simple ASCII
2722 parameter files and data files and are presented in an anti-aliased GNOME
2723 canvas. The program supports rectangular two-dimensional plots, histograms,
2724 polar-axis plots and three-dimensional plots. Plots can be printed or saved
2725 to BMP, JPEG or PNG image formats.")
2726 (license license:gpl3+)))
2728 (define-public maxima
2735 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2736 version "-source/" name "-" version ".tar.gz"))
2739 "1ka0xf70a55ndgmyrq7p5xxbd78pq7bfkqhgxsivaqdw6gn5lmcg"))
2740 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
2741 (build-system gnu-build-system)
2744 ("gnuplot" ,gnuplot) ;for plots
2745 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
2747 `(("texinfo" ,texinfo)
2749 ("python" ,python)))
2752 (list "--enable-gcl"
2753 (string-append "--with-posix-shell="
2754 (assoc-ref %build-inputs "bash")
2756 (string-append "--with-wish="
2757 (assoc-ref %build-inputs "tk")
2759 (let ((v ,(package-version tk)))
2760 (string-take v (string-index-right v #\.)))))
2761 ;; By default Maxima attempts to write temporary files to
2762 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2763 ;; Work around that.
2764 #:make-flags (list "TMPDIR=/tmp")
2766 (modify-phases %standard-phases
2767 (add-before 'check 'pre-check
2769 (chmod "src/maxima" #o555)
2773 ;; This is derived from the testing code in the "debian/rules" file
2774 ;; of Debian's Maxima package.
2775 ;; If Maxima can successfully run this, the binary to be installed
2779 (string-append "./maxima-local "
2781 "--batch-string=\"run_testsuite();\" "
2782 "| grep -q \"No unexpected errors found\"")))))
2783 ;; Make sure the doc and emacs files are found in the
2784 ;; standard location. Also configure maxima to find gnuplot
2785 ;; without having it on the PATH.
2786 (add-after 'install 'post-install
2787 (lambda* (#:key outputs inputs #:allow-other-keys)
2788 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2789 (out (assoc-ref outputs "out"))
2790 (datadir (string-append out "/share/maxima/" ,version))
2791 (binutils (string-append (assoc-ref inputs "binutils")
2793 (with-directory-excursion out
2794 (mkdir-p "share/emacs")
2795 (mkdir-p "share/doc")
2797 (string-append datadir "/emacs/")
2798 (string-append out "/share/emacs/site-lisp"))
2800 (string-append datadir "/doc/")
2801 (string-append out "/share/doc/maxima"))
2802 (with-atomic-file-replacement
2803 (string-append datadir "/share/maxima-init.lisp")
2805 (format out "~a ~s~a~%"
2806 "(setf $gnuplot_command "
2807 (string-append gnuplot "/bin/gnuplot") ")")
2808 (dump-port in out))))
2809 ;; Ensure that Maxima will have access to the GNU binutils
2810 ;; components at runtime.
2811 (wrap-program (string-append out "/bin/maxima")
2812 `("PATH" prefix (,binutils))))
2814 (home-page "http://maxima.sourceforge.net")
2815 (synopsis "Numeric and symbolic expression manipulation")
2816 (description "Maxima is a system for the manipulation of symbolic and
2817 numerical expressions. It yields high precision numeric results by using
2818 exact fractions, arbitrary precision integers, and variable precision floating
2820 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2821 ;; Others simply say "GNU General Public License" without stating a
2822 ;; version (which implicitly means gpl1+).
2823 ;; At least one file (src/maxima.asd) says "version 2."
2824 ;; GPLv2 only is therefore the smallest subset.
2825 (license license:gpl2)))
2827 (define-public wxmaxima
2835 (url "https://github.com/wxMaxima-developers/wxmaxima.git")
2836 (commit (string-append "Version-" version))))
2837 (file-name (git-file-name name version))
2840 "1sz8n9v23q442l7yjj67pjh0dk78rl4cbcc3j8m1bm88anlfxl9r"))))
2841 (build-system cmake-build-system)
2843 `(("gettext" ,gettext-minimal)))
2845 `(("wxwidgets" ,wxwidgets)
2848 ("adwaita-icon-theme" ,adwaita-icon-theme)
2850 ("shared-mime-info" ,shared-mime-info)))
2852 `(#:tests? #f ; no check target
2854 (modify-phases %standard-phases
2855 (add-after 'install 'wrap-program
2856 (lambda* (#:key inputs outputs #:allow-other-keys)
2857 (wrap-program (string-append (assoc-ref outputs "out")
2860 (,(string-append (assoc-ref inputs "maxima")
2862 ;; For GtkFileChooserDialog.
2863 `("GSETTINGS_SCHEMA_DIR" =
2864 (,(string-append (assoc-ref inputs "gtk+")
2865 "/share/glib-2.0/schemas")))
2866 `("XDG_DATA_DIRS" ":" prefix
2867 (;; Needed by gdk-pixbuf to know supported icon formats.
2869 (assoc-ref inputs "shared-mime-info") "/share")
2870 ;; The default icon theme of GTK+.
2872 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
2874 (home-page "https://andrejv.github.io/wxmaxima/")
2875 (synopsis "Graphical user interface for the Maxima computer algebra system")
2877 "wxMaxima is a graphical user interface for the Maxima computer algebra
2878 system. It eases the use of Maxima by making most of its commands available
2879 through a menu system and by providing input dialogs for commands that require
2880 more than one argument. It also implements its own display engine that
2881 outputs mathematical symbols directly instead of depicting them with ASCII
2884 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
2885 text and mathematical calculations to create documents, exporting of input and
2886 output to TeX, and a browser for Maxima's manual including command index and
2887 full text searching.")
2888 (license license:gpl2+)))
2890 (define-public armadillo
2896 (uri (string-append "mirror://sourceforge/arma/armadillo-"
2900 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
2901 (build-system cmake-build-system)
2902 (arguments `(#:tests? #f)) ; no test target
2904 `(("openblas" ,openblas)
2906 ("arpack" ,arpack-ng)))
2907 (home-page "http://arma.sourceforge.net/")
2908 (synopsis "C++ linear algebra library")
2910 "Armadillo is a C++ linear algebra library, aiming towards a good balance
2911 between speed and ease of use. It is useful for algorithm development
2912 directly in C++, or quick conversion of research code into production
2913 environments. It can be used for machine learning, pattern recognition,
2914 signal processing, bioinformatics, statistics, econometrics, etc. The library
2915 provides efficient classes for vectors, matrices and cubes, as well as 150+
2916 associated functions (eg. contiguous and non-contiguous submatrix views).")
2917 (license license:asl2.0)))
2919 (define-public muparser
2920 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2921 ;; different hash. In order to make `guix package --upgrade` work correctly,
2922 ;; we set a Guix packaging revision.
2923 ;; When the next version of muparser is released, we can remove
2924 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2925 (let ((upstream-version "2.2.5")
2929 (version (string-append upstream-version "-" revision))
2933 (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
2934 upstream-version ".tar.gz"))
2935 (file-name (string-append name "-" version ".tar.gz"))
2938 "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
2939 (build-system gnu-build-system)
2941 `(#:configure-flags '("--enable-samples=no")
2942 #:tests? #f)) ;no "check" target
2943 (home-page "http://muparser.beltoforion.de/")
2944 (synopsis "Fast parser library for mathematical expressions")
2946 "muParser is an extensible high performance math parser library. It is
2947 based on transforming an expression into a bytecode and precalculating constant
2949 (license license:expat))))
2951 (define-public openblas
2958 (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
2959 version "%20version.tar.gz"))
2960 (file-name (string-append name "-" version ".tar.gz"))
2963 "1s56lgilyyw86dzmj3jkci9zsg24n60wq4d0zri1hrxlxb6ihimj"))))
2964 (build-system gnu-build-system)
2966 `(#:test-target "test"
2967 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
2968 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2969 ;; we need to disable substitutions.
2971 ,(let ((system (or (%current-target-system) (%current-system))))
2972 (or (string-prefix? "x86_64" system)
2973 (string-prefix? "i686" system)
2974 (string-prefix? "mips" system)
2975 (string-prefix? "aarch64" system)))
2977 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
2979 ;; Build the library for all supported CPUs. This allows
2980 ;; switching CPU targets at runtime with the environment variable
2981 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
2982 ;; Unfortunately, this is not supported on non-x86 architectures,
2983 ;; where it leads to failed builds.
2984 ,@(let ((system (or (%current-target-system) (%current-system))))
2986 ((or (string-prefix? "x86_64" system)
2987 (string-prefix? "i686" system))
2988 '("DYNAMIC_ARCH=1"))
2989 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
2990 ;; two available MIPS targets special extended instructions
2991 ;; for Loongson cores are used.
2992 ((string-prefix? "mips" system)
2993 '("TARGET=SICORTEX"))
2994 ;; On aarch64 force the generic 'armv8-a' target
2995 ((string-prefix? "aarch64" system)
2998 ;; no configure script
3000 (modify-phases %standard-phases
3002 (add-before 'build 'set-extralib
3003 (lambda* (#:key inputs #:allow-other-keys)
3004 ;; Get libgfortran found when building in utest.
3006 (string-append "-L" (assoc-ref inputs "fortran-lib")
3010 `(("fortran-lib" ,gfortran "lib")))
3013 ("fortran" ,gfortran)
3015 (home-page "http://www.openblas.net/")
3016 (synopsis "Optimized BLAS library based on GotoBLAS")
3018 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
3019 (license license:bsd-3)))
3021 (define-public openblas-ilp64
3022 (package (inherit openblas)
3023 (name "openblas-ilp64")
3024 (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
3026 (substitute-keyword-arguments (package-arguments openblas)
3027 ((#:make-flags flags '())
3028 `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
3030 (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
3031 (license license:bsd-3)))
3033 (define* (make-blis implementation #:optional substitutable?)
3034 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
3035 source tree for a list of implementations.)
3037 SUBSTITUTABLE? determines whether the package is made available as a
3040 Currently the specialization must be selected at configure-time, but work is
3041 underway to allow BLIS to select the right optimized kernels at run time:
3042 <https://github.com/flame/blis/issues/129>."
3044 (name (if (string=? implementation "reference")
3046 (string-append "blis-" implementation)))
3048 (home-page "https://github.com/flame/blis")
3051 (uri (git-reference (url home-page) (commit version)))
3054 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
3055 (file-name (git-file-name "blis" version))))
3056 (build-system gnu-build-system)
3058 `(#:test-target "test"
3060 #:substitutable? ,substitutable?
3062 #:phases (modify-phases %standard-phases
3064 (lambda* (#:key outputs #:allow-other-keys)
3065 ;; This is a home-made 'configure' script.
3066 (let ((out (assoc-ref outputs "out")))
3067 (zero? (system* "./configure" "-p" out
3071 "--enable-threading=openmp"
3073 ,implementation)))))
3074 (add-before 'check 'show-test-output
3076 ;; By default "make check" is silent. Make it verbose.
3077 (system "tail -F output.testsuite &")
3079 (synopsis "High-performance basic linear algebra (BLAS) routines")
3081 "BLIS is a portable software framework for instantiating high-performance
3082 BLAS-like dense linear algebra libraries. The framework was designed to
3083 isolate essential kernels of computation that, when optimized, immediately
3084 enable optimized implementations of most of its commonly used and
3085 computationally intensive operations. While BLIS exports a new BLAS-like API,
3086 it also includes a BLAS compatibility layer which gives application developers
3087 access to BLIS implementations via traditional BLAS routine calls.")
3088 (license license:bsd-3)))
3091 ;; This is the "reference" implementation, which is the non-optimized but
3092 ;; portable variant (no assembly).
3093 (make-blis "reference" #t))
3095 (define ignorance blis)
3097 (define-syntax-rule (blis/x86_64 processor)
3098 "Expand to a package specialized for PROCESSOR."
3100 (inherit (make-blis processor))
3101 (supported-systems '("x86_64-linux"))))
3103 (define-public blis-sandybridge
3104 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
3105 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
3106 (blis/x86_64 "sandybridge"))
3108 (define-public blis-haswell
3109 ;; BLIS specialized for Haswell processors (launched 2013):
3110 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
3111 (blis/x86_64 "haswell"))
3113 (define-public blis-knl
3114 ;; BLIS specialized for Knights Landing processor (launched 2016):
3115 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
3116 (blis/x86_64 "knl"))
3119 (define-public openlibm
3126 (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
3128 (file-name (string-append name "-" version ".tar.gz"))
3131 "0a5fpm8nra5ldhjk0cqd2rx1qh32wiarkxmcqcm5xl8z7l4kjm6l"))))
3132 (build-system gnu-build-system)
3135 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3137 ;; no configure script
3138 (modify-phases %standard-phases (delete 'configure))
3139 #:tests? #f)) ;the tests are part of the default target
3140 (home-page "http://openlibm.org/")
3141 (synopsis "Portable C mathematical library (libm)")
3143 "OpenLibm is an effort to have a high quality, portable, standalone C
3144 mathematical library (libm). It can be used standalone in applications and
3145 programming language implementations. The project was born out of a need to
3146 have a good libm for the Julia programming language that worked consistently
3147 across compilers and operating systems, and in 32-bit and 64-bit
3149 ;; Each architecture has its own make target, and there is none for mips.
3150 (supported-systems (delete "mips64el-linux" %supported-systems))
3151 ;; See LICENSE.md for details.
3152 (license (list license:expat
3155 license:public-domain
3156 license:lgpl2.1+))))
3158 (define-public openspecfun
3160 (name "openspecfun")
3165 (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
3167 (file-name (string-append name "-" version ".tar.gz"))
3170 "1rs1bv8jq751fv9vq79890wqf9xlbjc7lvz3ighzyfczbyjcf18m"))))
3171 (build-system gnu-build-system)
3173 '(#:tests? #f ; no "check" target
3175 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3177 (modify-phases %standard-phases
3178 (delete 'configure)))) ; no configure script
3180 `(("fortran" ,gfortran)))
3181 (home-page "https://github.com/JuliaLang/openspecfun")
3182 (synopsis "Collection of special mathematical functions")
3184 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
3185 portable package for Bessel Functions of a Complex Argument and Nonnegative
3186 Order; it contains subroutines for computing Bessel functions and Airy
3187 functions. Faddeeva allows computing the various error functions of arbitrary
3188 complex arguments (Faddeeva function, error function, complementary error
3189 function, scaled complementary error function, imaginary error function, and
3190 Dawson function); given these, one can also easily compute Voigt functions,
3191 Fresnel integrals, and similar related functions as well.")
3192 ;; Faddeeva is released under the Expat license; AMOS is included as
3193 ;; public domain software.
3194 (license (list license:expat license:public-domain))))
3196 (define-public suitesparse
3198 (name "suitesparse")
3204 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
3208 "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
3209 (modules '((guix build utils)))
3211 ;; Remove bundled metis source
3213 (delete-file-recursively "metis-5.1.0")
3215 (build-system gnu-build-system)
3217 '(#:tests? #f ;no "check" target
3222 "MY_METIS_LIB=-lmetis"
3223 (string-append "INSTALL_LIB="
3224 (assoc-ref %outputs "out") "/lib")
3225 (string-append "INSTALL_INCLUDE="
3226 (assoc-ref %outputs "out") "/include")
3229 (modify-phases %standard-phases
3230 (delete 'configure)))) ;no configure script
3235 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
3236 (synopsis "Suite of sparse matrix software")
3238 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
3239 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
3240 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
3241 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
3242 CXSparse, a concise sparse Cholesky factorization package; and many other
3245 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
3247 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
3248 (license (list license:gpl2+ license:lgpl2.1+))))
3250 (define-public atlas
3256 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
3257 version "/atlas" version ".tar.bz2"))
3260 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
3261 (build-system gnu-build-system)
3262 (home-page "http://math-atlas.sourceforge.net/")
3263 (inputs `(("gfortran" ,gfortran)
3264 ("lapack-tar" ,(package-source lapack))))
3265 (outputs '("out" "doc"))
3266 ;; For the moment we drop support for MIPS at it fails to compile. See
3267 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
3268 (supported-systems (delete "mips64el-linux" %supported-systems))
3270 `(#:parallel-build? #f
3271 #:parallel-tests? #f
3273 ;; ATLAS tunes itself for the machine it is built on, as explained at
3274 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
3275 ;; For this reason, we want users to build it locally instead of using
3279 #:modules ((srfi srfi-26)
3281 (guix build gnu-build-system)
3284 `(;; Generate position independent code suitable for dynamic libraries
3285 ;; and use WALL timer to get more accurate timing.
3286 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
3289 ,,(if (string-match "64" (%current-system))
3292 ;; Disable parallel build as it gives errors: atlas_pthread.h is
3293 ;; needed to compile C files before it is generated.
3294 "-Ss" "pmake" "make -j 1"
3295 ;; Probe is failing for MIPS. We therefore define the system
3296 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3297 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3298 ,,@(if (string-prefix? "mips" (%current-system))
3299 (list "-A" "49" "-V" "1")
3301 ;; Generate shared libraries.
3303 ;; Build a full LAPACK library.
3304 ,(string-append "--with-netlib-lapack-tarfile="
3305 (assoc-ref %build-inputs "lapack-tar")))
3307 (modify-phases %standard-phases
3308 (add-after 'install 'install-doc
3309 (lambda* (#:key outputs inputs #:allow-other-keys)
3310 (let ((doc (string-append (assoc-ref outputs "doc")
3311 "/share/doc/atlas")))
3313 (fold (lambda (file previous)
3314 (and previous (zero? (system* "cp" file doc))))
3315 #t (find-files "../ATLAS/doc" ".*")))))
3316 (add-after 'check 'check-pt
3317 (lambda _ (zero? (system* "make" "ptcheck"))))
3318 ;; Fix files required to run configure.
3319 (add-before 'configure 'fix-/bin/sh
3321 ;; Use `sh', not `/bin/sh'.
3322 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3325 ;; Fix /bin/sh in generated make files.
3326 (add-after 'configure 'fix-/bin/sh-in-generated-files
3328 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3331 ;; ATLAS configure program does not accepts the default flags
3332 ;; passed by the 'gnu-build-system'.
3334 (lambda* (#:key native-inputs inputs outputs
3335 (configure-flags '())
3336 #:allow-other-keys #:rest args)
3337 (let* ((prefix (assoc-ref outputs "out"))
3338 (bash (or (and=> (assoc-ref
3339 (or native-inputs inputs) "bash")
3340 (cut string-append <> "/bin/bash"))
3342 (flags `(,(string-append "--prefix=" prefix)
3344 (abs-srcdir (getcwd))
3345 (srcdir (string-append "../" (basename abs-srcdir))))
3346 (format #t "source directory: ~s (relative from build: ~s)~%"
3350 (format #t "build directory: ~s~%" (getcwd))
3351 (format #t "configure flags: ~s~%" flags)
3352 (zero? (apply system* bash
3353 (string-append srcdir "/configure")
3355 (synopsis "Automatically Tuned Linear Algebra Software")
3357 "ATLAS is an automatically tuned linear algebra software library
3358 providing C and Fortran77 interfaces to a portably efficient BLAS
3359 implementation, as well as a few routines from LAPACK.
3361 Optimization occurs at build time. For this reason, the library is built on
3362 the machine where it is installed, without resorting to pre-built substitutes.
3364 Before building the library, CPU throttling should be disabled. This can be
3365 done in the BIOS, or, on GNU/Linux, with the following command:
3368 # cpupower --governor performance
3371 Failure to do so will result in a library with poor performance.")
3372 (license license:bsd-3)))
3381 (uri (string-append "https://github.com/g-truc/glm/releases/download/"
3382 version "/glm-" version ".zip"))
3385 "0yqk5r3qh60d4r2iab5q7wq0fryn8p3pz6s28y1i7amqj1aqavj9"))))
3386 (build-system cmake-build-system)
3388 `(("unzip" ,unzip)))
3389 (home-page "https://glm.g-truc.net/")
3390 (synopsis "OpenGL Mathematics library")
3391 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3392 library for graphics software based on the OpenGL Shading Language (GLSL)
3394 (license license:expat)))
3396 (define-public lpsolve
3403 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3404 "/lp_solve_" version "_source.tar.gz"))
3407 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
3408 (modules '((guix build utils)))
3411 (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3413 ;; Pretend to be on a 64 bit platform to obtain a common directory
3414 ;; name for the build results on all architectures; nothing else
3415 ;; seems to depend on it.
3416 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3418 ;; The check for 'isnan' as it is written fails with
3419 ;; "non-floating-point argument in call to function
3420 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3421 ;; definition, which in turn leads to bad things. Fix the feature
3423 (("isnan\\(0\\)") "isnan(0.)"))
3425 (build-system gnu-build-system)
3427 `(#:tests? #f ; no check target
3429 (modify-phases %standard-phases
3430 (delete 'configure) ; no configure script
3433 (with-directory-excursion "lpsolve55"
3434 (invoke "bash" "ccc"))
3435 (with-directory-excursion "lp_solve"
3436 (invoke "bash" "ccc"))
3439 (lambda* (#:key outputs #:allow-other-keys)
3440 (let* ((out (assoc-ref outputs "out"))
3441 (bin (string-append out "/bin"))
3442 (lib (string-append out "/lib"))
3443 ;; This is where LibreOffice expects to find the header
3444 ;; files, and where they are installed by Debian.
3445 (include (string-append out "/include/lpsolve")))
3446 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3447 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
3448 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3450 ;; Install a subset of the header files as on Debian
3451 ;; (plus lp_bit.h, which matches the regular expression).
3452 (for-each (lambda (name)
3453 (install-file name include))
3454 (find-files "." "lp_[HMSa-z].*\\.h$"))
3455 (with-directory-excursion "shared"
3456 (for-each (lambda (name)
3457 (install-file name include))
3458 (find-files "." "\\.h$")))
3460 (home-page "http://lpsolve.sourceforge.net/")
3461 (synopsis "Mixed integer linear programming (MILP) solver")
3463 "lp_solve is a mixed integer linear programming solver based on the
3464 revised simplex and the branch-and-bound methods.")
3465 (license license:lgpl2.1+)))
3467 (define-public dealii
3474 (uri (string-append "https://github.com/dealii/dealii/releases/"
3475 "download/v" version "/dealii-" version ".tar.gz"))
3478 "1bh9rsmkrg0zi70n27b11djmac9lximghsiy7mg7w7x544n82gnk"))
3479 (modules '((guix build utils)))
3481 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
3483 (delete-file-recursively "bundled")
3485 (build-system cmake-build-system)
3493 ("arpack" ,arpack-ng)
3494 ("muparser" ,muparser)
3495 ("gfortran" ,gfortran)
3496 ("suitesparse" ,suitesparse))) ;for UMFPACK
3498 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
3500 ;; Work around a bug in libsuitesparseconfig linking
3501 ;; see https://github.com/dealii/dealii/issues/4745
3502 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
3503 (home-page "https://www.dealii.org")
3504 (synopsis "Finite element library")
3506 "Deal.II is a C++ program library targeted at the computational solution
3507 of partial differential equations using adaptive finite elements. The main
3508 aim of deal.II is to enable rapid development of modern finite element codes,
3509 using among other aspects adaptive meshes and a wide array of tools often used
3510 in finite element programs.")
3511 (license license:lgpl2.1+)))
3513 (define-public dealii-openmpi
3514 (package (inherit dealii)
3515 (name "dealii-openmpi")
3518 ;;Supported only with MPI:
3519 ("p4est" ,p4est-openmpi)
3520 ("petsc" ,petsc-openmpi)
3521 ("slepc" ,slepc-openmpi)
3522 ("metis" ,metis) ;for MUMPS
3523 ("scalapack" ,scalapack) ;for MUMPS
3524 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3525 ("arpack" ,arpack-ng-openmpi)
3526 ,@(fold alist-delete (package-inputs dealii)
3527 '("p4est" "arpack"))))
3529 (substitute-keyword-arguments (package-arguments dealii)
3530 ((#:configure-flags cf)
3531 ``("-DMPI_C_COMPILER=mpicc"
3532 "-DMPI_CXX_COMPILER=mpicxx"
3533 "-DMPI_Fortran_COMPILER=mpifort"
3535 (synopsis "Finite element library (with MPI support)")))
3537 (define-public flann
3546 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3547 version "-src.zip"))
3550 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
3551 (patches (search-patches "flann-cmake-3.11.patch"))))
3552 (build-system cmake-build-system)
3554 "octave")) ;46 MiB .mex file that pulls Octave
3556 `(("unzip" ,unzip)))
3559 ("octave" ,octave-cli)
3560 ("python" ,python-2) ; print syntax
3561 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3564 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3565 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3566 #:strip-directories '("lib" "lib64" "libexec"
3567 "bin" "sbin" "share/flann/octave")
3569 ;; Save 12 MiB by not installing .a files. Passing
3570 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3571 #:phases (modify-phases %standard-phases
3572 (add-before 'configure 'set-octave-directory
3573 (lambda* (#:key outputs #:allow-other-keys)
3574 ;; Install the .mex file in the "octave" output.
3575 (let ((out (assoc-ref outputs "octave")))
3576 (substitute* "src/matlab/CMakeLists.txt"
3577 (("share/flann/octave")
3578 (string-append out "/share/flann/octave")))
3580 (add-after 'install 'remove-static-libraries
3581 (lambda* (#:key outputs #:allow-other-keys)
3582 (let* ((out (assoc-ref outputs "out"))
3583 (lib (string-append out "/lib")))
3584 (for-each delete-file
3585 (find-files lib "\\.a$"))
3588 #:tests? #f)) ; The test data are downloaded from the Internet.
3589 (home-page "http://www.cs.ubc.ca/research/flann/")
3590 (synopsis "Library for approximate nearest neighbors computation")
3591 (description "FLANN is a library for performing fast approximate
3592 nearest neighbor searches in high dimensional spaces. It implements a
3593 collection of algorithms and a system for automatically choosing the best
3594 algorithm and optimum parameters depending on the dataset.
3596 FLANN is written in C++ and contains bindings for C, Octave and Python.")
3597 (license (license:non-copyleft "file://COPYING"
3598 "See COPYING in the distribution."))))
3600 (define-public wcalc
3607 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3608 "wcalc-" version ".tar.bz2"))
3611 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3612 (build-system gnu-build-system)
3615 ("readline" ,readline)))
3616 (home-page "http://w-calc.sourceforge.net/index.php")
3617 (synopsis "Flexible command-line scientific calculator")
3618 (description "Wcalc is a very capable calculator. It has standard functions
3619 (sin, asin, and sinh for example, in either radians or degrees), many
3620 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3621 variables, a command history, hex/octal/binary input and output, unit
3622 conversions, embedded comments, and an expandable expression entry field. It
3623 evaluates expressions using the standard order of operations.")
3624 (license license:gpl2+)))
3632 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3633 "/xaos-" version ".tar.gz"))
3636 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3637 (build-system gnu-build-system)
3638 (native-inputs `(("gettext" ,gettext-minimal)))
3639 (inputs `(("libx11" ,libx11)
3644 `(#:tests? #f ;no "check" target
3645 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3646 (synopsis "Real-time fractal zoomer")
3647 (description "GNU XaoS is a graphical program that generates fractal
3648 patterns and allows you to zoom in and out of them infinitely in a fluid,
3649 continuous manner. It also includes tutorials that help to explain how fractals
3650 are built. It can generate many different fractal types such as the Mandelbrot
3652 (home-page "https://www.gnu.org/software/xaos/")
3653 (license license:gpl2+)))
3655 (define-public hypre
3661 (uri (string-append "https://github.com/LLNL/hypre/archive/"
3662 "v" version ".tar.gz"))
3663 (file-name (string-append name "-" version ".tar.gz"))
3666 "0v515i73bvaz378h5465b1dy9v2gf924zy2q94cpq4qqarawvkqh"))
3667 (modules '((guix build utils)))
3670 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
3671 ;; substitute the tarball creation time.
3672 (substitute* "src/utilities/HYPRE_utilities.h"
3673 (("Date Compiled: .*$")
3674 "Date Compiled: Apr 11 2018 16:24:59 +0000\"\n"))
3676 (build-system gnu-build-system)
3677 (outputs '("out" ;6.1 MiB of headers and libraries
3678 "doc")) ;4.8 MiB of documentation
3682 ("perl" ,perl) ;needed to run 'ppmquant' during tests
3683 ("texlive" ,(texlive-union (list texlive-generic-xypic
3685 texlive-latex-hyperref
3686 texlive-latex-oberdiek
3687 texlive-generic-ifxetex
3690 ("ghostscript" ,ghostscript)))
3692 `(("blas" ,openblas)
3693 ("lapack" ,lapack)))
3695 `(#:modules ((srfi srfi-1)
3696 ,@%gnu-build-system-modules)
3697 #:configure-flags '("--enable-shared"
3705 (modify-phases %standard-phases
3706 (add-before 'build 'set-HOME
3708 ;; FIXME: texlive-union does not find the built
3709 ;; metafonts, so it tries to generate them in HOME.
3710 (setenv "HOME" "/tmp")
3712 (add-before 'configure 'chdir-src
3713 (lambda _ (chdir "src")))
3715 (lambda* (#:key build target configure-flags
3716 #:allow-other-keys #:rest args)
3717 (let* ((configure (assoc-ref %standard-phases 'configure)))
3720 (list #:configure-flags
3721 (cons (string-append
3722 "--host=" (or target build))
3723 configure-flags)))))))
3724 (add-after 'build 'build-docs
3726 (invoke "make" "-Cdocs" "pdf" "html")))
3729 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3730 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
3731 (and (system* "make" "check" "CHECKRUN=")
3732 (fold (lambda (filename result)
3734 (let ((size (stat:size (stat filename))))
3735 (when (not (zero? size))
3736 (format #t "~a size ~d; error indication~%"
3740 (find-files "test" ".*\\.err$")))))
3741 (add-after 'install 'install-docs
3742 (lambda* (#:key outputs #:allow-other-keys)
3743 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3744 (let* ((doc (assoc-ref outputs "doc"))
3745 (docdir (string-append doc "/share/doc/hypre-" ,version)))
3746 (with-directory-excursion "docs"
3747 (for-each (lambda (base)
3748 (install-file (string-append base ".pdf") docdir)
3749 (copy-recursively base docdir)) ;html docs
3750 '("HYPRE_usr_manual"
3751 "HYPRE_ref_manual")))
3753 (home-page "http://www.llnl.gov/casc/hypre/")
3754 (synopsis "Library of solvers and preconditioners for linear equations")
3756 "HYPRE is a software library of high performance preconditioners and
3757 solvers for the solution of large, sparse linear systems of equations. It
3758 features multigrid solvers for both structured and unstructured grid
3760 (license license:lgpl2.1)))
3762 (define-public hypre-openmpi
3763 (package (inherit hypre)
3764 (name "hypre-openmpi")
3767 ,@(package-inputs hypre)))
3769 (substitute-keyword-arguments (package-arguments hypre)
3770 ((#:configure-flags flags)
3772 ,@(delete "--without-MPI" ,flags)))
3774 `(modify-phases ,phases
3775 (add-before 'check 'mpi-setup
3776 ,%openmpi-setup)))))
3777 (synopsis "Parallel solvers and preconditioners for linear equations")
3779 "HYPRE is a software library of high performance preconditioners and
3780 solvers for the solution of large, sparse linear systems of equations on
3781 parallel computers. It features parallel multigrid solvers for both
3782 structured and unstructured grid problems.")))
3784 (define-public matio
3791 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
3792 "matio-" version ".tar.gz"))
3795 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3796 (build-system gnu-build-system)
3800 (home-page "http://matio.sourceforge.net/")
3801 (synopsis "Library for reading and writing MAT files")
3802 (description "Matio is a library for reading and writing MAT files. It
3803 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3804 (license license:bsd-2)))
3811 (origin (method url-fetch)
3812 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3813 "download/" version "/Vc-" version ".tar.gz"))
3816 "1zmlpn32jzb38smp3j834llmbix3whsrbw0h397qxysbw792kih8"))))
3817 (build-system cmake-build-system)
3820 '("-DBUILD_TESTING=ON"
3821 ;; By default, Vc will optimize for the CPU of the build machine.
3822 ;; Setting this to "none" makes it create portable binaries. See
3823 ;; "cmake/OptimizeForArchitecture.cmake".
3824 "-DTARGET_ARCHITECTURE=none")))
3825 (synopsis "SIMD vector classes for C++")
3826 (description "Vc provides portable, zero-overhead C++ types for explicitly
3827 data-parallel programming. It is a library designed to ease explicit
3828 vectorization of C++ code. Its types enable explicitly stating data-parallel
3829 operations on multiple values. The parallelism is therefore added via the type
3830 system. Vc has an intuitive API and provides portability between different
3831 compilers and compiler versions as well as portability between different vector
3832 instruction sets. Thus, an application written with Vc can be compiled for:
3835 @item SSE2 up to SSE4.2 or SSE4a
3838 @item NEON (in development)
3839 @item NVIDIA GPUs / CUDA (in development)
3841 (home-page "https://github.com/VcDevel/Vc")
3842 ;; "No support_???.cpp file exists for this architecture."
3843 (supported-systems '("x86_64-linux" "i686-linux"))
3844 (license license:bsd-3)))
3846 (define-public reducelcs
3847 ;; This is the last commit which is available upstream, no
3848 ;; release happened since 2010.
3849 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
3853 (version (string-append "1.0-" revision "." (string-take commit 7)))
3858 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
3860 (file-name (string-append name "-" version "-checkout"))
3863 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
3864 (build-system gnu-build-system)
3866 `(("openlibm" ,openlibm)))
3868 `(#:tests? #f ; no tests
3870 (modify-phases %standard-phases
3871 (delete 'configure) ; No configure script exists.
3872 (replace 'install ; No install phase exists.
3873 (lambda* (#:key outputs #:allow-other-keys)
3874 (let* ((out (assoc-ref outputs "out"))
3875 (bin (string-append out "/bin")))
3876 (install-file "Approximation" bin)
3877 (install-file "CollectResults" bin)
3878 (install-file "GenerateInstances" bin)
3880 (synopsis "Approximate Longest Commons Subsequence computation tool")
3882 "@code{reduceLCS} is an implementation of the Reduce-Expand
3883 algorithm for LCS. It is a fast program to compute the approximate
3884 Longest Commons Subsequence of a set of strings.")
3885 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
3886 (license license:gpl3+))))
3888 (define-public jacal
3895 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
3898 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
3899 (patches (search-patches "jacal-fix-texinfo.patch"))))
3900 (build-system gnu-build-system)
3903 (modify-phases %standard-phases
3904 (add-before 'build 'pre-build
3905 ;; Don't use upstream's script - it really doesn't fit into
3906 ;; Guix's functional paradigm.
3907 (lambda* (#:key inputs outputs #:allow-other-keys)
3908 (substitute* "Makefile"
3909 (("^install: install-script") "install: "))))
3910 (add-after 'install 'post-install
3911 ;; Instead, we provide our own simplified script.
3912 (lambda* (#:key inputs outputs #:allow-other-keys)
3913 (let ((wrapper (string-append (assoc-ref outputs "out")
3915 (format (open wrapper (logior O_WRONLY O_CREAT))
3916 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
3917 "-e '(slib:load \"~a/lib/jacal/math\") "
3920 (assoc-ref inputs "scm")
3921 (assoc-ref outputs "out"))
3922 (chmod wrapper #o555))))
3924 (lambda* (#:key inputs outputs #:allow-other-keys)
3925 (zero? (system* "./configure"
3926 (string-append "--prefix="
3927 (assoc-ref outputs "out")))))))))
3928 (inputs `(("scm" ,scm)))
3929 (native-inputs `(("unzip" ,unzip)
3930 ("texinfo" ,texinfo)))
3931 (synopsis "Symbolic mathematics system")
3932 (description "GNU JACAL is an interactive symbolic mathematics program based on
3933 Scheme. It manipulate and simplify a range of mathematical expressions such
3934 as equations, scalars, vectors, and matrices.")
3935 (home-page "https://www.gnu.org/software/jacal/")
3936 (license license:gpl3+)))
3942 (home-page "https://github.com/Z3Prover/z3")
3945 (uri (git-reference (url home-page)
3946 (commit (string-append "z3-" version))))
3947 (file-name (git-file-name name version))
3950 "014igqm5vwswz0yhz0cdxsj3a6dh7i79hvhgc3jmmmz3z0xm1gyn"))))
3951 (build-system gnu-build-system)
3954 (modify-phases %standard-phases
3955 (add-after 'unpack 'fix-compatability
3956 ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
3958 (substitute* "src/util/mpz.cpp"
3959 (("#include <immintrin.h>") ""))
3961 (add-before 'configure 'bootstrap
3964 (system* "python" "scripts/mk_make.py"))))
3965 ;; work around gnu-build-system's setting --enable-fast-install
3966 ;; (z3's `configure' is a wrapper around the above python file,
3967 ;; which fails when passed --enable-fast-install)
3969 (lambda* (#:key inputs outputs #:allow-other-keys)
3970 (invoke "./configure"
3971 (string-append "--prefix=" (assoc-ref outputs "out")))))
3972 (add-after 'configure 'change-directory
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")))))))
3987 ("python" ,python-wrapper)))
3988 (synopsis "Theorem prover")
3989 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
3990 theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
3991 (license license:expat)))
3993 (define-public elemental
4000 (url "https://github.com/elemental/Elemental.git")
4001 (commit (string-append "v" version))))
4002 (file-name (git-file-name name version))
4005 "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
4006 (build-system cmake-build-system)
4007 (home-page "http://libelemental.org")
4009 `(("gfortran" ,gfortran)))
4011 `(("blas" ,openblas)
4012 ("gfortran:lib" ,gfortran "lib")
4021 `(#:build-type "Release" ;default RelWithDebInfo not supported
4022 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
4023 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
4024 "-DEL_CACHE_WARNINGS:BOOL=YES"
4025 "-DEL_TESTS:BOOL=YES"
4026 "-DCMAKE_INSTALL_LIBDIR=lib"
4027 "-DGFORTRAN_LIB=gfortran")
4028 #:phases (modify-phases %standard-phases
4029 (add-before 'check 'mpi-setup
4031 (add-before 'check 'setup-tests
4033 ;; Parallelism is done at the MPI layer.
4034 (setenv "OMP_NUM_THREADS" "1")
4036 (add-after 'install 'remove-tests
4037 (lambda* (#:key outputs #:allow-other-keys)
4038 ;; Tests are installed, with no easy configuration
4039 ;; switch to prevent this, so delete them.
4040 (delete-file-recursively
4041 (string-append (assoc-ref outputs "out") "/bin"))
4043 (synopsis "Dense and sparse-direct linear algebra and optimization")
4044 (description "Elemental is a modern C++ library for distributed-memory
4045 dense and sparse-direct linear algebra, conic optimization, and lattice
4047 (license license:bsd-2)))
4049 (define-public mcrl2
4052 (version "201707.1.15162")
4055 (uri (string-append "http://www.mcrl2.org/download/devel/mcrl2-"
4060 "1ziww2fchsklm25hl9p2mngssxfh9w07nc114cncqaxfibqp2p8f"))))
4062 `(("subversion" ,subversion)))
4067 ("qtbase" ,qtbase)))
4068 (build-system cmake-build-system)
4069 (synopsis "Toolset for the mCRL2 formal specification language")
4071 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
4072 specification language for describing concurrent discrete event systems. Its
4073 toolset supports analysis and automatic verification, linearisation, simulation,
4074 state-space exploration and generation, and tools to optimise and analyse
4075 specifications. Also, state spaces can be manipulated, visualised and
4077 (home-page "https://mcrl2.org")
4078 (license license:boost1.0)))
4080 (define-public r-subplex
4087 (uri (cran-uri "subplex" version))
4090 "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
4091 (build-system r-build-system)
4093 `(("gfortran" ,gfortran)))
4094 (home-page "https://cran.r-project.org/web/packages/subplex")
4095 (synopsis "Unconstrained optimization using the subplex algorithm")
4096 (description "This package implements the Subplex optimization algorithm.
4097 It solves unconstrained optimization problems using a simplex method on
4098 subspaces. The method is well suited for optimizing objective functions that
4099 are noisy or are discontinuous at the solution.")
4100 (license license:gpl3+)))
4102 (define-public r-desolve
4109 (uri (cran-uri "deSolve" version))
4112 "0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"))))
4113 (properties `((upstream-name . "deSolve")))
4114 (build-system r-build-system)
4116 `(("gfortran" ,gfortran)))
4117 (home-page "https://desolve.r-forge.r-project.org/")
4118 (synopsis "Solvers for initial value problems of differential equations")
4119 (description "This package provides functions that solve initial
4120 value problems of a system of first-order ordinary differential equations (ODE),
4121 of partial differential equations (PDE), of differential algebraic equations
4122 (DAE), and of delay differential equations. The functions provide an interface
4123 to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
4124 to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
4125 the Runge-Kutta family with fixed or variable time steps. The package contains
4126 routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
4127 differential equations (PDE) that have been converted to ODEs by numerical
4129 (license license:gpl2+)))
4131 (define-public tcalc
4138 (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
4142 "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
4143 (build-system gnu-build-system)
4144 (synopsis "The terminal calculator")
4146 "The terminal calculator is a small program to help users of the GNU/Linux
4147 terminal do calculations simply and quickly. The formula to be calculated can
4148 be fed to @command{tcalc} through the command line.")
4149 (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
4150 (license license:gpl3+)))
4152 (define-public sundials
4159 (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
4160 "sundials-" version ".tar.gz"))
4163 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
4164 (build-system cmake-build-system)
4166 `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
4168 `(("fortran" ,gfortran) ;for fcmix
4170 ("suitesparse" ,suitesparse))) ;TODO: Add hypre
4172 `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
4173 "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
4174 "-DEXAMPLES_ENABLE_F77:BOOL=ON"
4175 "-DEXAMPLES_ENABLE_F90:BOOL=ON"
4176 "-DEXAMPLES_INSTALL:BOOL=OFF"
4178 "-DFCMIX_ENABLE:BOOL=ON"
4180 "-DKLU_ENABLE:BOOL=ON"
4181 ,(string-append "-DKLU_INCLUDE_DIR="
4182 (assoc-ref %build-inputs "suitesparse")
4184 ,(string-append "-DKLU_LIBRARY_DIR="
4185 (assoc-ref %build-inputs "suitesparse")
4187 (home-page "https://computation.llnl.gov/projects/sundials")
4188 (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
4189 (description "SUNDIALS is a family of software packages implemented with
4190 the goal of providing robust time integrators and nonlinear solvers that can
4191 easily be incorporated into existing simulation codes.")
4192 (license license:bsd-3)))
4194 (define-public sundials-openmpi
4195 (package (inherit sundials)
4196 (name "sundials-openmpi")
4199 ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
4200 ,@(package-inputs sundials)))
4202 (substitute-keyword-arguments (package-arguments sundials)
4203 ((#:configure-flags flags '())
4204 `(cons* "-DMPI_ENABLE:BOOL=ON"
4205 "-DPETSC_ENABLE:BOOL=ON"
4206 (string-append "-DPETSC_INCLUDE_DIR="
4207 (assoc-ref %build-inputs "petsc")
4209 (string-append "-DPETSC_LIBRARY_DIR="
4210 (assoc-ref %build-inputs "petsc")
4213 ((#:phases phases '%standard-phases)
4214 `(modify-phases ,phases
4215 (add-before 'check 'mpi-setup
4216 ,%openmpi-setup)))))
4217 (synopsis "SUNDIALS with OpenMPI support")))
HCoop / jackhill / guix / guix.git / blob