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 (ice-9 match)
52 #:use-module (gnu packages)
53 #:use-module ((guix licenses) #:prefix license:)
54 #:use-module (guix packages)
55 #:use-module (guix download)
56 #:use-module (guix git-download)
57 #:use-module (guix utils)
58 #:use-module ((guix build utils) #:select (alist-replace))
59 #:use-module (guix build-system cmake)
60 #:use-module (guix build-system gnu)
61 #:use-module (guix build-system python)
62 #:use-module (guix build-system r)
63 #:use-module (guix build-system ruby)
64 #:use-module (gnu packages algebra)
65 #:use-module (gnu packages audio)
66 #:use-module (gnu packages autotools)
67 #:use-module (gnu packages base)
68 #:use-module (gnu packages bison)
69 #:use-module (gnu packages boost)
70 #:use-module (gnu packages check)
71 #:use-module (gnu packages cmake)
72 #:use-module (gnu packages compression)
73 #:use-module (gnu packages curl)
74 #:use-module (gnu packages cyrus-sasl)
75 #:use-module (gnu packages documentation)
76 #:use-module (gnu packages elf)
77 #:use-module (gnu packages flex)
78 #:use-module (gnu packages fltk)
79 #:use-module (gnu packages fontutils)
80 #:use-module (gnu packages gettext)
81 #:use-module (gnu packages gcc)
82 #:use-module (gnu packages gd)
83 #:use-module (gnu packages ghostscript)
84 #:use-module (gnu packages graphviz)
85 #:use-module (gnu packages gtk)
86 #:use-module (gnu packages image)
87 #:use-module (gnu packages java)
88 #:use-module (gnu packages less)
89 #:use-module (gnu packages lisp)
90 #:use-module (gnu packages linux)
91 #:use-module (gnu packages logging)
92 #:use-module (gnu packages lua)
93 #:use-module (gnu packages gnome)
94 #:use-module (gnu packages guile)
95 #:use-module (gnu packages xorg)
96 #:use-module (gnu packages gl)
97 #:use-module (gnu packages imagemagick)
98 #:use-module (gnu packages m4)
99 #:use-module (gnu packages mpi)
100 #:use-module (gnu packages multiprecision)
101 #:use-module (gnu packages netpbm)
102 #:use-module (gnu packages pcre)
103 #:use-module (gnu packages popt)
104 #:use-module (gnu packages perl)
105 #:use-module (gnu packages pkg-config)
106 #:use-module (gnu packages pulseaudio)
107 #:use-module (gnu packages python)
108 #:use-module (gnu packages python-web)
109 #:use-module (gnu packages python-xyz)
110 #:use-module (gnu packages qt)
111 #:use-module (gnu packages readline)
112 #:use-module (gnu packages ruby)
113 #:use-module (gnu packages tbb)
114 #:use-module (gnu packages scheme)
115 #:use-module (gnu packages shells)
116 #:use-module (gnu packages tcl)
117 #:use-module (gnu packages texinfo)
118 #:use-module (gnu packages tex)
119 #:use-module (gnu packages tls)
120 #:use-module (gnu packages version-control)
121 #:use-module (gnu packages wxwidgets)
122 #:use-module (gnu packages xml)
123 #:use-module (srfi srfi-1))
131 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
133 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
134 (build-system gnu-build-system)
135 (inputs `(("gtk+" ,gtk+)
136 ("libxml2" ,libxml2)))
137 (native-inputs `(("pkg-config" ,pkg-config)))
138 (synopsis "Natural deduction first-order logic interface")
139 (description "Aris is a program for performing logical proofs. It supports
140 propositional and predicate logic, as well as Boolean algebra and
141 arithmetical logic. In addition to its predefined inference and equivalence
142 rules, Aris also supports references to older proofs. Its use of standard
143 logical symbols and its natural deduction interface make it easy to use for
145 (license license:gpl3+)
146 (home-page "https://www.gnu.org/software/aris/")))
148 (define-public c-graph
154 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
157 "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
158 (build-system gnu-build-system)
160 `(("fortran" ,gfortran)))
161 (synopsis "Visualizing and demonstrating convolution")
163 "GNU C-Graph is a tool for demonstrating the theory of convolution.
164 Thus, it can serve as an excellent aid to students of signal and systems
165 theory in visualizing the convolution process. Rather than forcing the
166 student to write code, the program offers an intuitive interface with
167 interactive dialogs to guide them.")
168 (license license:gpl3+)
169 (home-page "https://www.gnu.org/software/c-graph/")))
178 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
179 version "/coda-" version ".tar.gz"))
181 (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245"))
182 (patches (search-patches "coda-use-system-libs.patch"))
183 (modules '((guix build utils)))
185 ;; Make sure we don't use the bundled software.
187 (for-each (lambda (d)
188 (delete-file-recursively (string-append "libcoda/" d)))
189 '("zlib" "pcre" "expat"))
192 `(("fortran" ,gfortran)
194 ("python-numpy" ,python-numpy)))
201 (build-system gnu-build-system)
203 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
204 "LIBS= -lz -lpcre -lexpat")))
205 (synopsis "A common interface to various earth observation data formats")
207 "The Common Data Access toolbox (CODA) provides a set of interfaces for
208 reading remote sensing data from earth observation data files. It consists of
209 command line applications and interfaces to the C, Fortran, Python, and Java
210 programming languages.")
211 (home-page "https://stcorp.nl/coda")
212 (license license:gpl2+)))
220 (uri (string-append "http://www.qhull.org/download/qhull-"
221 (car (string-split version #\.))
225 "0dm4b2xr3asy6w74khq2zg4gf26zsy3qf9sq7pf7lmrvbj911c3q"))))
226 (build-system cmake-build-system)
227 (synopsis "Calculate convex hulls and related structures")
229 "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
230 diagram, halfspace intersection about a point, furthest-site Delaunay
231 triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d,
232 3-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull
233 algorithm for computing the convex hull. It handles roundoff errors from
234 floating point arithmetic. It computes volumes, surface areas, and
235 approximations to the convex hull.
237 @code{Qhull} does not support triangulation of non-convex surfaces, mesh
238 generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
239 shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
241 (home-page "http://qhull.org")
242 (license (license:non-copyleft "file://COPYING.txt"
243 "See COPYING in the distribution."))))
245 (define-public python-cvxopt
247 (name "python-cvxopt")
252 (url "https://github.com/cvxopt/cvxopt.git")
254 (file-name (git-file-name name version))
257 "05mnjil9palaa48xafdfh4f5pr4z7aqjr995rwl08qfyxs8y0crf"))))
258 (build-system python-build-system)
261 (modify-phases %standard-phases
262 (add-after 'unpack 'find-libraries
263 (lambda* (#:key inputs #:allow-other-keys)
264 (setenv "CVXOPT_BLAS_LIB" "openblas")
265 (setenv "CVXOPT_BUILD_FFTW" "1")
266 (setenv "CVXOPT_BUILD_GLPK" "1")
267 (setenv "CVXOPT_BUILD_GSL" "1")
274 ("openblas" ,openblas)
275 ("suitesparse" ,suitesparse)))
276 (home-page "https://www.cvxopt.org")
277 (synopsis "Python library for convex optimization")
279 "CVXOPT is a package for convex optimization based on the Python
280 programming language. Its main purpose is to make the development of software
281 for convex optimization applications straightforward by building on Python’s
282 extensive standard library and on the strengths of Python as a high-level
283 programming language.")
284 (license license:gpl3+)))
286 (define-public python2-cvxopt
287 (package-with-python2 python-cvxopt))
295 (uri (string-append "mirror://gnu/units/units-" version
298 "0y26kj349i048y4z3xrk90bvciw2j6ds3rka7r7yn3183hirr5b4"))))
299 (build-system gnu-build-system)
301 `(("readline" ,readline)
302 ("python" ,python-wrapper) ;for 'units_cur' script
303 ("python-requests" ,python-requests)))
305 `(#:phases (modify-phases %standard-phases
306 (add-after 'install 'wrap-units_cur
307 (lambda* (#:key outputs #:allow-other-keys)
308 (let* ((out (assoc-ref outputs "out"))
309 (bin (string-append out "/bin")))
310 (wrap-program (string-append bin "/units_cur")
311 `("PYTHONPATH" ":" prefix
312 ,(search-path-as-string->list (getenv "PYTHONPATH"))))
314 (synopsis "Conversion between thousands of scales")
316 "GNU Units converts numeric quantities between units of measure. It
317 can handle scale changes through adaptive usage of standard scale
318 prefixes (micro-, kilo-, etc.). It can also handle nonlinear
319 conversions such as Fahrenheit to Celsius. Its interpreter is powerful
320 enough to be used effectively as a scientific calculator.")
321 (license license:gpl3+)
322 (home-page "https://www.gnu.org/software/units/")))
324 (define-public double-conversion
326 (name "double-conversion")
328 (home-page "https://github.com/google/double-conversion")
331 (uri (git-reference (url home-page) (commit version)))
332 (file-name (git-file-name name version))
335 "123rb2p4snqagrybw66vnapchqdwn2rfpr1wcq0ya9gwbyl7xccx"))))
336 (build-system cmake-build-system)
338 '(#:test-target "test"
339 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
340 "-DBUILD_TESTING=ON")))
341 (synopsis "Conversion routines for IEEE doubles")
343 "The double-conversion library provides binary-decimal and decimal-binary
344 routines for IEEE doubles. The library consists of efficient conversion
345 routines that have been extracted from the V8 JavaScript engine.")
346 (license license:bsd-3)))
348 (define-public dionysus
354 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
358 "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
359 (build-system gnu-build-system)
360 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
361 (synopsis "Local search for universal constants and scientific values")
363 "GNU Dionysus is a convenient system for quickly retrieving the values of
364 mathematical constants used in science and engineering. Values can be
365 searched using a simple command-line tool, choosing from three databases:
366 universal constants, atomic numbers, and constants related to
368 (license license:gpl3+)
369 (home-page "https://www.gnu.org/software/dionysus/")))
377 (uri (string-append "mirror://gnu/gsl/gsl-"
381 "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
382 (patches (search-patches "gsl-test-i686.patch"))))
383 (build-system gnu-build-system)
385 `(;; Currently there are numerous tests that fail on "exotic"
386 ;; architectures such as aarch64 and ppc64le.
387 ,@(if (string-prefix? "aarch64-linux"
388 (or (%current-target-system) (%current-system)))
391 (home-page "https://www.gnu.org/software/gsl/")
392 (synopsis "Numerical library for C and C++")
394 "The GNU Scientific Library is a library for numerical analysis in C
395 and C++. It includes a wide range of mathematical routines, with over 1000
396 functions in total. Subject areas covered by the library include:
397 differential equations, linear algebra, Fast Fourier Transforms and random
399 (license license:gpl3+)))
408 (uri (string-append "mirror://gnu/glpk/glpk-"
412 "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
413 (build-system gnu-build-system)
417 `(#:configure-flags '("--with-gmp")))
418 (home-page "https://www.gnu.org/software/glpk/")
419 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
421 "GLPK is a C library for solving large-scale linear programming (LP),
422 mixed integer programming (MIP), and other related problems. It supports the
423 GNU MathProg modeling language, a subset of the AMPL language, and features a
424 translator for the language. In addition to the C library, a stand-alone
425 LP/MIP solver is included in the package.")
426 (license license:gpl3+)))
435 (uri (string-append "http://www.4ti2.de/version_" version
436 "/4ti2-" version ".tar.gz"))
439 "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
440 (build-system gnu-build-system)
442 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
446 (home-page "http://www.4ti2.de/")
447 (synopsis "Mathematical tool suite for problems on linear spaces")
449 "4ti2 implements algorithms for solving algebraic, geometric and
450 combinatorial problems on linear spaces. Among others, it solves systems
451 of linear equations, computes extreme rays of polyhedral cones, solves
452 integer programming problems and computes Markov bases for statistics.")
453 (license license:gpl2+)))
455 (define-public cddlib
462 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
463 (string-delete #\. version) ".tar.gz"))
466 "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
467 (build-system gnu-build-system)
470 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
471 (synopsis "Library for convex hulls and extreme rays of polyhedra")
473 "The C-library cddlib implements the Double Description Method of
474 Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
475 rays of a general convex polyhedron given by a system of linear inequalities
476 in arbitrary dimension. It can also be used for the converse operation of
477 computing convex hulls.")
478 (license license:gpl2+)))
480 (define-public arpack-ng
484 (home-page "https://github.com/opencollab/arpack-ng")
487 (uri (git-reference (url home-page) (commit version)))
488 (file-name (git-file-name name version))
491 "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
492 (build-system gnu-build-system)
494 `(("autoconf" ,autoconf)
495 ("automake" ,automake)
496 ("libtool" ,libtool)))
499 ("fortran" ,gfortran)))
500 (synopsis "Fortran subroutines for solving eigenvalue problems")
502 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
503 large scale eigenvalue problems.")
504 (license (license:non-copyleft "file://COPYING"
505 "See COPYING in the distribution."))))
507 (define-public arpack-ng-3.3.0
511 (name (package-name arpack-ng))
512 (home-page (package-home-page arpack-ng))
516 (uri (string-append home-page "/archive/" version ".tar.gz"))
517 (file-name (string-append name "-" version ".tar.gz"))
520 "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
522 (define-public arpack-ng-openmpi
523 (package (inherit arpack-ng)
524 (name "arpack-ng-openmpi")
527 ,@(package-inputs arpack-ng)))
529 (substitute-keyword-arguments (package-arguments arpack-ng)
530 ((#:configure-flags _ '())
532 ((#:phases phases '%standard-phases)
533 `(modify-phases ,phases
534 (add-before 'check 'mpi-setup
536 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
538 (define-public lapack
545 (uri (string-append "http://www.netlib.org/lapack/lapack-"
549 "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
550 (build-system cmake-build-system)
551 (home-page "http://www.netlib.org/lapack/")
552 (inputs `(("fortran" ,gfortran)
553 ("python" ,python-2)))
555 `(#:configure-flags (list
556 "-DBUILD_SHARED_LIBS:BOOL=YES"
559 ;; Build the 'LAPACKE_clatms' functions.
560 "-DLAPACKE_WITH_TMG=ON")
562 (modify-phases %standard-phases
563 (add-before 'check 'patch-python
564 (lambda* (#:key inputs #:allow-other-keys)
565 (let ((python (assoc-ref inputs "python")))
566 (substitute* "lapack_testing.py"
567 (("/usr/bin/env python") python)))
569 (synopsis "Library for numerical linear algebra")
571 "LAPACK is a Fortran 90 library for solving the most commonly occurring
572 problems in numerical linear algebra.")
573 (license (license:non-copyleft "file://LICENSE"
574 "See LICENSE in the distribution."))))
576 (define-public scalapack
583 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
587 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
588 (build-system cmake-build-system)
591 ("fortran" ,gfortran)
592 ("lapack" ,lapack))) ;for testing only
594 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
595 #:phases (modify-phases %standard-phases
596 (add-before 'check 'mpi-setup
598 (home-page "http://www.netlib.org/scalapack/")
599 (synopsis "Library for scalable numerical linear algebra")
601 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
602 routines on parallel distributed memory machines. ScaLAPACK solves dense and
603 banded linear systems, least squares problems, eigenvalue problems, and
604 singular value problems.")
605 (license (license:bsd-style "file://LICENSE"
606 "See LICENSE in the distribution."))))
608 (define-public gnuplot
614 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
619 "1jvh8xmd2cvrhlsg88kxwh55wkwx31sg50v1n59slfippl0g058m"))))
620 (build-system gnu-build-system)
621 (inputs `(("readline" ,readline)
627 `(("pkg-config" ,pkg-config)
628 ("texlive" ,texlive-tiny)))
629 (arguments `(#:configure-flags (list (string-append
630 "--with-texdir=" %output
631 "/texmf-local/tex/latex/gnuplot"))))
632 (home-page "http://www.gnuplot.info")
633 (synopsis "Command-line driven graphing utility")
634 (description "Gnuplot is a portable command-line driven graphing
635 utility. It was originally created to allow scientists and students to
636 visualize mathematical functions and data interactively, but has grown to
637 support many non-interactive uses such as web scripting. It is also used as a
638 plotting engine by third-party applications like Octave.")
639 ;; X11 Style with the additional restriction that derived works may only be
640 ;; distributed as patches to the original.
641 (license (license:fsf-free
642 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
651 (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
653 (file-name (string-append name "-" version ".tar.gz"))
656 "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
658 `(("fortran" ,gfortran)))
659 (build-system gnu-build-system)
660 (synopsis "General Cartographic Transformation Package (GCTP)")
662 "The General Cartographic Transformation Package (GCTP) is a system of
663 software routines designed to permit the transformation of coordinate pairs
664 from one map projection to another. The GCTP is the standard computer
665 software used by the National Mapping Division for map projection
667 (home-page "https://github.com/OkoSanto/GCTP")
668 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
677 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
678 version "/src/hdf-" version ".tar.bz2"))
680 (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
681 (patches (search-patches "hdf4-architectures.patch"
682 "hdf4-reproducibility.patch"
683 "hdf4-shared-fortran.patch"))))
684 (build-system gnu-build-system)
686 `(("gfortran" ,gfortran)
691 ("libjpeg" ,libjpeg)))
693 `(#:parallel-tests? #f
694 #:configure-flags '("--enable-shared")
696 (modify-phases %standard-phases
697 ;; This is inspired by two of Debian's patches.
698 (add-before 'configure 'add-more-aarch64-support
700 (substitute* '("mfhdf/ncgen/ncgen.l"
701 "mfhdf/ncgen/ncgenyy.c"
702 "mfhdf/libsrc/netcdf.h.in")
703 (("AIX5L64") "__aarch64__"))
705 (add-before 'configure 'patchbuild
708 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
710 (("/bin/mkdir") "mkdir"))
711 (substitute* (find-files "." "^Makefile\\.in$")
712 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
713 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
714 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
715 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
716 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
718 (add-after 'configure 'patch-settings
720 ;; libhdf4.settings contains the full path of the
721 ;; compilers used, and its contents are included in
722 ;; .so-files. We truncate the hashes to avoid
723 ;; unnecessary store references to those compilers:
724 (substitute* "libhdf4.settings"
725 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
726 (string-append prefix (string-take hash 10) "...")))
729 (home-page "https://www.hdfgroup.org/products/hdf4/")
731 "Library and multi-object file format for storing and managing data")
732 (description "HDF4 is a library and multi-object file format for storing
733 and managing data between machines. HDF4 is an older hierarchical data format,
734 incompatible with HDF5.")
736 (license:non-copyleft
737 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
739 (define-public hdf4-alt
744 (substitute-keyword-arguments (package-arguments hdf4)
745 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
747 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
756 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
757 "hdf5-" (version-major+minor version)
758 "/hdf5-" version "/src/hdf5-"
760 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
762 (match (string-split version #\.)
764 (string-append major minor)))
765 "/src/hdf5-" version ".tar.bz2")))
767 (base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5"))
768 (patches (search-patches "hdf5-config-date.patch"
769 "hdf5-1.8-mpi-deprecations.patch"))))
770 (build-system gnu-build-system)
774 `(("gfortran" ,gfortran)))
775 (outputs '("out" ; core library
776 "fortran")) ; fortran interface
778 `(;; Some of the users, notably Flann, need the C++ interface.
779 #:configure-flags '("--enable-cxx"
781 "--enable-fortran2003")
782 ;; Use -fPIC to allow the R bindings to link with the static libraries
783 #:make-flags (list "CFLAGS=-fPIC"
786 (modify-phases %standard-phases
787 (add-before 'configure 'patch-configure
788 (lambda* (#:key outputs #:allow-other-keys)
789 (substitute* "configure"
791 (substitute* "fortran/src/Makefile.in"
792 (("libhdf5_fortran_la_LDFLAGS =")
793 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
794 (assoc-ref outputs "fortran") "/lib")))
795 (substitute* "hl/fortran/src/Makefile.in"
796 (("libhdf5hl_fortran_la_LDFLAGS =")
797 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
798 (assoc-ref outputs "fortran") "/lib")))
800 (add-after 'configure 'patch-settings
802 ;; libhdf5.settings contains the full path of the
803 ;; compilers used, and its contents are included in
804 ;; libhdf5.so. We truncate the hashes to avoid
805 ;; unnecessary store references to those compilers:
806 (substitute* "src/libhdf5.settings"
807 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
808 (string-append prefix (string-take hash 10) "..."))
809 ;; Don't record the build-time kernel version to make the
810 ;; settings file reproducible.
811 (("Uname information:.*")
812 "Uname information: Linux\n"))
814 (add-after 'install 'patch-references
815 (lambda* (#:key inputs outputs #:allow-other-keys)
816 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
817 (zlib (assoc-ref inputs "zlib")))
818 (substitute* (find-files bin "h5p?cc")
820 (string-append "-L" zlib "/lib " lib)))
822 (add-after 'install 'split
823 (lambda* (#:key inputs outputs #:allow-other-keys)
824 ;; Move all fortran-related files
825 (let* ((out (assoc-ref outputs "out"))
826 (bin (string-append out "/bin"))
827 (lib (string-append out "/lib"))
828 (inc (string-append out "/include"))
829 (ex (string-append out "/share/hdf5_examples/fortran"))
830 (fort (assoc-ref outputs "fortran"))
831 (fbin (string-append fort "/bin"))
832 (flib (string-append fort "/lib"))
833 (finc (string-append fort "/include"))
834 (fex (string-append fort "/share/hdf5_examples/fortran")))
839 ;; Note: When built with --enable-parallel, the 'h5fc' file
840 ;; doesn't exist, hence this condition.
841 (when (file-exists? (string-append bin "/h5fc"))
842 (rename-file (string-append bin "/h5fc")
843 (string-append fbin "/h5fc")))
844 (for-each (lambda (file)
846 (string-append flib "/" (basename file))))
847 (find-files lib ".*fortran.*"))
848 (for-each (lambda (file)
850 (string-append finc "/" (basename file))))
851 (find-files inc ".*mod"))
852 (for-each (lambda (file)
854 (string-append fex "/" (basename file))))
855 (find-files ex ".*"))
856 (delete-file-recursively ex))
858 (home-page "http://www.hdfgroup.org")
859 (synopsis "Management suite for extremely large and complex data")
860 (description "HDF5 is a suite that makes possible the management of
861 extremely large and complex data collections.")
862 (license (license:x11-style
863 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
865 (define-public hdf5-1.10
866 (package (inherit hdf5)
871 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
872 "hdf5-" (version-major+minor version)
873 "/hdf5-" version "/src/hdf5-"
875 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
878 (take (string-split version #\.) 2))
879 "/src/hdf5-" version ".tar.bz2")))
881 (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
882 (patches (search-patches "hdf5-config-date.patch"
883 "hdf5-mpi-deprecations.patch"))))))
885 (define-public hdf-java
893 "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
894 version "/src/CMake-hdfjava-" version ".tar.gz"))
896 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
897 (modules '((guix build utils)))
898 (snippet ; Make sure we don't use the bundled sources and binaries.
900 (for-each delete-file
901 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
902 "HDF4.tar.gz" "HDF5.tar.gz"))
903 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
905 (build-system gnu-build-system)
907 `(("jdk" ,icedtea "jdk")
908 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
910 ("hamcrest-core" ,java-hamcrest-core)
911 ("junit" ,java-junit)
912 ("slf4j-simple" ,java-slf4j-simple)))
918 ("slf4j-api" ,java-slf4j-api)))
921 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
922 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
923 (assoc-ref %build-inputs "jdk") "/lib" )
924 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
925 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
928 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
929 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
930 (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
931 (string-append "JPEGLIB="
932 (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
936 (modify-phases %standard-phases
937 (add-before 'configure 'chdir-to-source
938 (lambda _ (chdir ,(string-append "hdfjava-" version))))
939 (add-before 'configure 'patch-build
940 (lambda* (#:key inputs outputs #:allow-other-keys)
941 (substitute* "configure"
942 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
943 (("/bin/cat") (which "cat")))
944 ;; Set classpath for compilation
945 (substitute* '("hdf/hdf5lib/Makefile.in"
946 "hdf/hdf5lib/exceptions/Makefile.in"
947 "hdf/hdflib/Makefile.in")
948 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
949 (string-append (assoc-ref inputs "slf4j-api")
950 "/share/java/slf4j-api.jar")))
951 ;; Replace outdated config.sub and config.guess:
952 (with-directory-excursion "config"
953 (for-each (lambda (file)
955 (string-append (assoc-ref inputs "automake")
956 "/share/automake-1.15/" file) file))
957 '("config.sub" "config.guess")))
958 (mkdir-p (string-append (assoc-ref outputs "out")))
959 ;; Set classpath for tests
960 (let* ((build-dir (getcwd))
961 (lib (string-append build-dir "/lib"))
962 (jhdf (string-append lib "/jhdf.jar"))
963 (jhdf5 (string-append lib "/jhdf5.jar"))
966 (string-append (assoc-ref inputs i)
967 "/share/java/" i ".jar"))
968 '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
970 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
972 (substitute* '("test/hdf5lib/Makefile.in"
973 "test/hdf5lib/junit.sh.in"
974 "examples/runExample.sh.in")
976 (string-append (assoc-ref inputs "coreutils")
979 (string-append (assoc-ref inputs "coreutils")
981 (("CLASSPATH=[^\n]*")
982 (string-append "CLASSPATH=" class-path)))
983 (setenv "CLASSPATH" class-path))
985 (add-before 'check 'build-examples
987 (zero? (apply system* `("javac"
988 ,@(find-files "examples" ".*\\.java")))))))
992 #:parallel-tests? #f ))
993 (home-page "https://support.hdfgroup.org/products/java")
994 (synopsis "Java interface for the HDF4 and HDF5 libraries")
995 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
996 the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
999 ;; BSD-style license:
1000 (license (license:x11-style
1001 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
1002 /current/src/unpacked/COPYING"))))
1004 (define-public hdf-eos2
1011 (uri "ftp://edhs1.gsfc.nasa.gov\
1012 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
1014 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
1015 (patches (search-patches "hdf-eos2-remove-gctp.patch"
1016 "hdf-eos2-build-shared.patch"
1017 "hdf-eos2-fortrantests.patch"))))
1018 (build-system gnu-build-system)
1020 `(("gfortran" ,gfortran)))
1022 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
1024 ("libjpeg" ,libjpeg)
1027 `( #:configure-flags '("--enable-install-include" "--enable-shared"
1028 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
1029 #:parallel-tests? #f))
1030 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
1031 (synopsis "HDF4-based data format for NASA's Earth Observing System")
1032 (description "HDF-EOS2 is a software library built on HDF4 which supports
1033 the construction of data structures used in NASA's Earth Observing
1034 System (Grid, Point and Swath).")
1036 ;; Source files carry a permissive license header.
1037 (license (license:non-copyleft home-page))))
1039 (define-public hdf-eos5
1045 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1046 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1049 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1050 (patches (search-patches "hdf-eos5-build-shared.patch"
1051 "hdf-eos5-remove-gctp.patch"
1052 "hdf-eos5-fix-szip.patch"
1053 "hdf-eos5-fortrantests.patch"))))
1055 `(("gfortran" ,gfortran)))
1056 (build-system gnu-build-system)
1062 `(#:configure-flags '("--enable-install-include" "--enable-shared"
1063 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1064 #:parallel-tests? #f))
1065 (synopsis "HDF5-based data format for NASA's Earth Observing System")
1067 "HDF-EOS5 is a software library built on HDF5 to support the construction
1068 of data structures used in NASA's Earth Observing System (Grid, Point and
1070 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1072 ;; Source files carry a permissive license header.
1073 (license (license:non-copyleft home-page))))
1075 (define-public hdf5-parallel-openmpi
1076 (package (inherit hdf5)
1077 (name "hdf5-parallel-openmpi")
1080 ,@(package-inputs hdf5)))
1082 (substitute-keyword-arguments (package-arguments hdf5)
1083 ((#:configure-flags flags)
1084 ``("--enable-parallel" ,@(delete "--enable-cxx" ,flags)))
1086 `(modify-phases ,phases
1087 (add-after 'build 'mpi-setup
1089 (add-before 'check 'patch-tests
1091 ;; OpenMPI's mpirun will exit with non-zero status if it
1092 ;; detects an "abnormal termination", i.e. any process not
1093 ;; calling MPI_Finalize(). Since the test is explicitely
1094 ;; avoiding MPI_Finalize so as not to have at_exit and thus
1095 ;; H5C_flush_cache from being called, mpirun will always
1096 ;; complain, so turn this test off.
1097 (substitute* "testpar/Makefile"
1098 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1099 (string-append front back "\n")))
1100 (substitute* "tools/h5diff/testph5diff.sh"
1101 (("/bin/sh") (which "sh")))
1103 (synopsis "Management suite for data with parallel IO support")))
1105 (define-public h5check
1112 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
1113 "h5check/src/h5check-" version ".tar.gz"))
1116 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1117 (build-system gnu-build-system)
1118 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
1119 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1120 (synopsis "HDF5 format checker")
1121 (description "@code{h5check} is a validation tool for verifying that an
1122 HDF5 file is encoded according to the HDF File Format Specification.")
1123 (license (license:x11-style "file://COPYING"))))
1131 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1136 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1137 (build-system cmake-build-system)
1138 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1139 (inputs `(("lapack" ,lapack)
1141 ;; FIXME: Even though the fonts are available dvips complains:
1142 ;; "Font cmmi10 not found; characters will be left blank."
1144 `(("texlive" ,texlive-tiny)
1145 ("ghostscript" ,ghostscript)
1146 ("doxygen" ,doxygen)))
1147 (home-page "http://itpp.sourceforge.net")
1148 (synopsis "C++ library of maths, signal processing and communication classes")
1149 (description "IT++ is a C++ library of mathematical, signal processing and
1150 communication classes and functions. Its main use is in simulation of
1151 communication systems and for performing research in the area of
1152 communications. The kernel of the library consists of generic vector and
1153 matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1154 similar to MATLAB, GNU Octave or SciPy.")
1155 (license license:gpl3+)))
1157 (define-public netcdf
1164 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1165 "netcdf-" version ".tar.gz"))
1168 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1169 (patches (search-patches "netcdf-date-time.patch"
1170 "netcdf-tst_h_par.patch"))))
1171 (build-system gnu-build-system)
1174 ("doxygen" ,doxygen)
1175 ("graphviz" ,graphviz)))
1177 `(("hdf4" ,hdf4-alt)
1180 ("libjpeg" ,libjpeg)))
1182 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
1184 #:phases (modify-phases %standard-phases
1185 (add-before 'configure 'fix-source-date
1187 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1188 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1189 ;; to '1st hour of the current day', and therefore makes the
1190 ;; package not reproducible.
1191 (substitute* "./configure"
1192 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1193 "date --date='@0'"))
1195 (add-after 'configure 'patch-settings
1197 ;; libnetcdf.settings contains the full filename of the compilers
1198 ;; used to build the library. We truncate the hashes of those
1199 ;; filenames to avoid unnecessary references to the corresponding
1201 (substitute* "libnetcdf.settings"
1202 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1203 (string-append prefix (string-take hash 10) "...")))
1206 #:parallel-tests? #f)) ;various race conditions
1207 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
1208 (synopsis "Library for scientific data")
1209 (description "NetCDF is an interface for scientific data access and a
1210 software library that provides an implementation of the interface. The netCDF
1211 library defines a machine-independent format for representing scientific data.
1212 Together, the interface, library, and format support the creation, access, and
1213 sharing of scientific data.")
1214 (license (license:x11-style "file://COPYRIGHT"))))
1216 (define-public netcdf-parallel-openmpi
1217 (package (inherit netcdf)
1218 (name "netcdf-parallel-openmpi")
1221 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1222 (package-inputs netcdf))))
1223 ;; TODO: Replace pkg-config references in nc-config with absolute references
1225 (substitute-keyword-arguments (package-arguments netcdf)
1226 ((#:configure-flags flags)
1227 `(cons* "CC=mpicc" "CXX=mpicxx"
1228 "--enable-parallel-tests"
1229 ;; Shared libraries not supported with parallel IO.
1230 "--disable-shared" "--with-pic"
1233 (define-public netcdf-fortran
1235 (name "netcdf-fortran")
1240 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1244 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1245 (build-system gnu-build-system)
1247 `(#:parallel-tests? #f))
1249 `(("netcdf" ,netcdf)))
1251 `(("gfortran" ,gfortran)))
1252 (synopsis "Fortran interface for the netCDF library")
1253 (description (package-description netcdf))
1254 (home-page (package-home-page netcdf))
1255 (license (package-license netcdf))))
1257 (define-public nlopt
1263 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1266 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1267 (build-system gnu-build-system)
1269 `(;; Shared libraries are not built by default. They are required to
1270 ;; build the Guile, Octave, and Python bindings.
1271 #:configure-flags '("--enable-shared")
1274 (modify-phases %standard-phases
1275 (add-before 'configure 'set-libnlopt-file-name
1276 (lambda* (#:key outputs #:allow-other-keys)
1277 ;; Make sure the Scheme module refers to the library by its
1278 ;; absolute file name (we cannot do that from a snippet
1279 ;; because the expansion of @libdir@ contains
1281 (let ((out (assoc-ref outputs "out")))
1282 (substitute* "swig/nlopt.scm.in"
1284 (string-append out "/lib/libnlopt")))
1286 (inputs `(("guile" ,guile-2.0)))
1287 (native-inputs `(("pkg-config" ,pkg-config)))
1288 (home-page "http://ab-initio.mit.edu/wiki/")
1289 (synopsis "Library for nonlinear optimization")
1290 (description "NLopt is a library for nonlinear optimization, providing a
1291 common interface for a number of different free optimization routines available
1292 online as well as original implementations of various other algorithms.")
1293 (license license:lgpl2.1+)))
1295 (define-public ipopt
1302 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1306 "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
1307 (modules '((guix build utils)))
1309 ;; Make sure we don't use the bundled software.
1311 (delete-file-recursively "ThirdParty")
1313 (build-system gnu-build-system)
1315 '(#:phases (modify-phases %standard-phases
1316 (add-after 'install 'add--L-flags-in-ipopt.pc
1317 (lambda* (#:key inputs outputs #:allow-other-keys)
1318 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1319 ;; move it to "Libs.private" where it belongs, and add a
1320 ;; '-L' flag for LAPACK.
1321 (let ((out (assoc-ref outputs "out"))
1322 (lapack (assoc-ref inputs "lapack")))
1323 (substitute* (string-append out "/lib/pkgconfig/"
1325 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1326 (string-append "Libs: " before " " after "\n"
1327 "Libs.private: " before
1328 "-L" lapack "/lib -llapack -lblas "
1332 `(("gfortran" ,gfortran)))
1334 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
1335 `(("lapack" ,lapack))) ;for both libblas and liblapack
1336 (home-page "http://www.coin-or.org")
1337 (synopsis "Large-scale nonlinear optimizer")
1339 "The Interior Point Optimizer (IPOPT) is a software package for
1340 large-scale nonlinear optimization. It provides C++, C, and Fortran
1342 (license license:epl1.0)))
1344 (define-public ceres
1346 (name "ceres-solver")
1348 (home-page "http://ceres-solver.org/")
1351 (uri (string-append home-page "ceres-solver-"
1355 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
1356 (build-system cmake-build-system)
1358 ;; TODO: Build HTML user documentation and install separately.
1359 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
1360 "-DBUILD_SHARED_LIBS=ON")
1362 #:phases (modify-phases %standard-phases
1363 (add-before 'configure 'set-library-directory
1365 ;; Install libraries to lib/, not lib64/.
1366 (substitute* "internal/ceres/CMakeLists.txt"
1367 (("set\\(LIB_SUFFIX \"64\"\\)")
1368 "set(LIB_SUFFIX \"\")"))
1371 `(("pkg-config" ,pkg-config)))
1373 `(("glog" ,glog))) ;for #include <glog/glog.h>
1378 ("suitesparse" ,suitesparse)
1379 ("gflags" ,gflags)))
1380 (synopsis "C++ library for solving large optimization problems")
1382 "Ceres Solver is a C++ library for modeling and solving large,
1383 complicated optimization problems. It is a feature rich, mature and
1384 performant library which has been used in production since 2010. Ceres Solver
1385 can solve two kinds of problems:
1387 @item non-linear least squares problems with bounds constraints;
1388 @item general unconstrained optimization problems.
1390 (license license:bsd-3)))
1392 ;; For a fully featured Octave, users are strongly recommended also to install
1393 ;; the following packages: less, ghostscript, gnuplot.
1394 (define-public octave-cli
1401 (uri (string-append "mirror://gnu/octave/octave-"
1405 "0jsdgizlv02an2ppfjwk5qf209zpwi3317yb7jvlsjzxnir3lvhy"))))
1406 (build-system gnu-build-system)
1408 `(("lapack" ,lapack)
1410 ("readline" ,readline)
1415 ("arpack" ,arpack-ng)
1418 ("fontconfig" ,fontconfig)
1419 ("freetype" ,freetype)
1426 ("texinfo" ,texinfo)
1427 ("graphicsmagick" ,graphicsmagick)
1428 ("suitesparse" ,suitesparse)
1429 ("libsndfile" ,libsndfile)
1430 ("portaudio" ,portaudio)
1431 ("alsa-lib" ,alsa-lib)))
1434 ("gfortran" ,gfortran)
1435 ("pkg-config" ,pkg-config)
1437 ;; The following inputs are not actually used in the build process.
1438 ;; However, the ./configure gratuitously tests for their existence and
1439 ;; assumes that programs not present at build time are also not, and
1440 ;; can never be, available at run time! If these inputs are therefore
1441 ;; not present, support for them will be built out. However, Octave
1442 ;; will still run without them, albeit without the features they
1445 ("ghostscript" ,ghostscript)
1446 ("gnuplot" ,gnuplot)))
1447 ;; Octave code uses this variable to detect directories holding multiple CA
1448 ;; certificates to verify peers with. This is required for the networking
1449 ;; functions that require encryption to work properly.
1450 (native-search-paths
1451 (list (search-path-specification
1452 (variable "CURLOPT_CAPATH")
1453 (files '("etc/ssl/certs")))))
1456 (list (string-append "--with-shell="
1457 (assoc-ref %build-inputs "bash")
1460 (modify-phases %standard-phases
1461 (add-after 'configure 'configure-makeinfo
1462 (lambda* (#:key inputs #:allow-other-keys)
1463 (substitute* "libinterp/corefcn/help.h"
1466 "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
1468 (home-page "https://www.gnu.org/software/octave/")
1469 (synopsis "High-level language for numerical computation")
1470 (description "GNU Octave is a high-level interpreted language that is
1471 specialized for numerical computations. It can be used for both linear and
1472 non-linear applications and it provides great support for visualizing results.
1473 Work may be performed both at the interactive command-line as well as via
1475 (license license:gpl3+)))
1477 (define-public octave
1478 (package (inherit octave-cli)
1481 (inherit (package-source octave-cli))))
1483 `(("qscintilla" ,qscintilla)
1485 ,@(package-inputs octave-cli)))
1487 `(("qttools" , qttools) ;for lrelease
1488 ("texlive" ,texlive) ;for texi2dvi
1489 ,@(package-native-inputs octave-cli)))
1491 (substitute-keyword-arguments (package-arguments octave-cli)
1493 `(modify-phases ,phases
1494 (add-before 'configure 'patch-qscintilla-library-name
1495 (lambda* (#:key inputs #:allow-other-keys)
1496 ;; The QScintilla library that the Octave configure script tries
1497 ;; to link with should be named libqscintilla-qt5.so, but the
1498 ;; QScintilla input provides the shared library as
1499 ;; libqscintilla2_qt5.so.
1500 (substitute* "configure"
1501 (("qscintilla2-qt5")
1505 (define-public qtoctave
1506 (deprecated-package "qtoctave" octave))
1508 (define-public opencascade-oce
1510 (name "opencascade-oce")
1516 "https://github.com/tpaviot/oce/archive/OCE-"
1519 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
1522 "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
1523 (build-system cmake-build-system)
1526 (list "-DOCE_TESTING:BOOL=ON"
1527 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1528 "-DOCE_DRAW:BOOL=ON"
1529 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1530 (assoc-ref %outputs "out"))
1531 "-UCMAKE_INSTALL_RPATH")))
1533 `(("freetype" ,freetype)
1540 `(("python" ,python-wrapper)))
1541 (home-page "https://github.com/tpaviot/oce")
1542 (synopsis "Libraries for 3D modeling and numerical simulation")
1544 "Open CASCADE is a set of libraries for the development of applications
1545 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1546 C++ class libraries providing services for 3D surface and solid modeling, CAD
1547 data exchange, and visualization. It is used for development of specialized
1548 software dealing with 3D models in design (CAD), manufacturing (CAM),
1549 numerical simulation (CAE), measurement equipment (CMM), and quality
1550 control (CAQ) domains.
1552 This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1553 patches, improvements, and experiments contributed by users over the official
1554 Open CASCADE library.")
1555 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1556 ; use of header files; see
1557 ; OCCT_LGPL_EXCEPTION.txt
1558 license:public-domain; files
1559 ; src/Standard/Standard_StdAllocator.hxx and
1560 ; src/NCollection/NCollection_StdAllocator.hxx
1561 license:expat; file src/OpenGl/OpenGl_glext.h
1562 license:bsd-3)))); test framework gtest
1571 (uri (string-append "http://gmsh.info/src/gmsh-"
1572 version "-source.tgz"))
1574 (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
1575 (modules '((guix build utils)))
1577 ;; Remove non-free METIS code
1579 (delete-file-recursively "contrib/Metis")
1581 (build-system cmake-build-system)
1584 ("gfortran" ,gfortran)
1590 ("opencascade-oce" ,opencascade-oce)
1592 ("libxext" ,libxext)))
1594 `(("fontconfig" ,fontconfig)
1595 ("libxft" ,libxft)))
1597 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1598 "-DENABLE_BUILD_SHARED:BOOL=ON"
1599 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
1600 (home-page "http://www.geuz.org/gmsh/")
1601 (synopsis "3D finite element grid generator")
1602 (description "Gmsh is a 3D finite element grid generator with a built-in
1603 CAD engine and post-processor. Its design goal is to provide a fast, light
1604 and user-friendly meshing tool with parametric input and advanced
1605 visualization capabilities. Gmsh is built around four modules: geometry,
1606 mesh, solver and post-processing. The specification of any input to these
1607 modules is done either interactively using the graphical user interface or in
1608 ASCII text files using Gmsh's own scripting language.")
1609 (license license:gpl2+)))
1611 (define-public maxflow
1618 (url "https://github.com/gerddie/maxflow.git")
1619 (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
1620 (file-name (string-append name "-" version "-checkout"))
1623 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1624 (build-system cmake-build-system)
1625 (home-page "http://pub.ist.ac.at/~vnk/software.html")
1626 (synopsis "Library implementing Maxflow algorithm")
1627 (description "An implementation of the maxflow algorithm described in
1628 @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1629 Energy Minimization in Computer Vision.\n
1630 Yuri Boykov and Vladimir Kolmogorov.\n
1631 In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1633 (license license:gpl3+)))
1635 (define-public petsc
1642 ;; The *-lite-* tarball does not contain the *large* documentation
1643 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1644 "petsc-lite-" version ".tar.gz"))
1646 (base32 "0bl64pydak3rblnjffi482r8bin4xim9sb37ksl2jkcxf0i0irsi"))))
1647 (outputs '("out" ;libraries and headers
1648 "examples")) ;~30MiB of examples
1649 (build-system gnu-build-system)
1651 `(("python" ,python-2)))
1653 `(("gfortran" ,gfortran)
1655 ("superlu" ,superlu)
1656 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1657 ;; leaving out opengl, as configuration seems to only be for mac
1660 `(#:test-target "test"
1661 #:parallel-build? #f ;build is parallel by default
1667 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1668 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1669 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
1671 (modify-phases %standard-phases
1673 ;; PETSc's configure script is actually a python script, so we can't
1674 ;; run it with bash.
1675 (lambda* (#:key outputs (configure-flags '())
1677 (let* ((prefix (assoc-ref outputs "out"))
1678 (flags `(,(string-append "--prefix=" prefix)
1679 ,@configure-flags)))
1680 (format #t "build directory: ~s~%" (getcwd))
1681 (format #t "configure flags: ~s~%" flags)
1682 (apply invoke "./configure" flags))))
1683 (add-after 'configure 'clean-local-references
1684 (lambda* (#:key outputs #:allow-other-keys)
1685 (let ((out (assoc-ref outputs "out")))
1686 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
1687 ;; Prevent build directory from leaking into compiled code
1689 ;; Scrub timestamp for reproducibility
1690 ((".*Libraries compiled on.*") ""))
1691 (substitute* (find-files "." "petscvariables")
1692 ;; Do not expose build machine characteristics, set to defaults.
1693 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1694 (("NPMAX = [:digit:]+") "NPMAX = 2"))
1696 (add-after 'install 'clean-install
1697 ;; Try to keep installed files from leaking build directory names.
1698 (lambda* (#:key inputs outputs #:allow-other-keys)
1699 (let ((out (assoc-ref outputs "out")))
1700 (substitute* (map (lambda (file)
1701 (string-append out "/lib/petsc/conf/" file))
1702 '("petscvariables"))
1704 ;; Make compiler references point to the store
1705 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
1706 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1707 (string-append "= " (which compiler))))
1708 ;; PETSc installs some build logs, which aren't necessary.
1709 (for-each (lambda (file)
1710 (let ((f (string-append out "/lib/petsc/conf/" file)))
1711 (when (file-exists? f)
1713 '("configure.log" "make.log" "gmake.log"
1714 "test.log" "error.log" "RDict.db"
1715 "PETScBuildInternal.cmake"
1716 ;; Once installed, should uninstall with Guix
1719 (add-after 'install 'move-examples
1720 (lambda* (#:key outputs #:allow-other-keys)
1721 (let* ((out (assoc-ref outputs "out"))
1722 (examples (assoc-ref outputs "examples"))
1723 (exdir (string-append out "/share/petsc/examples"))
1724 (exdir' (string-append examples "/share/petsc/examples")))
1725 (copy-recursively exdir exdir')
1726 (delete-file-recursively exdir)
1728 (home-page "http://www.mcs.anl.gov/petsc")
1729 (synopsis "Library to solve PDEs")
1730 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1731 data structures and routines for the scalable (parallel) solution of
1732 scientific applications modeled by partial differential equations.")
1733 (license (license:non-copyleft
1734 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1736 (define-public petsc-complex
1737 (package (inherit petsc)
1738 (name "petsc-complex")
1740 (substitute-keyword-arguments (package-arguments petsc)
1741 ((#:configure-flags cf)
1742 `(cons "--with-scalar-type=complex" ,cf))))
1743 (synopsis "Library to solve PDEs (with complex scalars)")))
1745 (define-public petsc-openmpi
1746 (package (inherit petsc)
1747 (name "petsc-openmpi")
1749 `(("hdf5" ,hdf5-parallel-openmpi)
1750 ("hypre" ,hypre-openmpi)
1752 ("mumps" ,mumps-openmpi)
1753 ("openmpi" ,openmpi)
1754 ("scalapack" ,scalapack)
1755 ("scotch" ,pt-scotch32)
1756 ,@(package-inputs petsc)))
1758 (substitute-keyword-arguments (package-arguments petsc)
1759 ((#:configure-flags cf)
1761 "--with-mpiexec=mpirun"
1764 "--with-scalapack=1"
1766 ,(string-append "--with-mpi-dir="
1767 (assoc-ref %build-inputs "openmpi"))
1768 ,(string-append "--with-hdf5-include="
1769 (assoc-ref %build-inputs "hdf5") "/include")
1770 ,(string-append "--with-hdf5-lib="
1771 (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
1772 ,@(delete "--with-mpi=0" ,cf)))
1774 `(modify-phases ,phases
1775 (add-before 'configure 'mpi-setup
1776 ,%openmpi-setup)))))
1777 (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
1779 (define-public petsc-complex-openmpi
1780 (package (inherit petsc-complex)
1781 (name "petsc-complex-openmpi")
1783 `(("openmpi" ,openmpi)
1784 ,@(package-inputs petsc-complex)))
1786 (substitute-keyword-arguments (package-arguments petsc-complex)
1787 ((#:configure-flags cf)
1788 ``("--with-mpiexec=mpirun"
1789 ,(string-append "--with-mpi-dir="
1790 (assoc-ref %build-inputs "openmpi"))
1791 ,@(delete "--with-mpi=0" ,cf)))))
1792 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
1794 (define-public python-petsc4py
1796 (name "python-petsc4py")
1801 (uri (pypi-uri "petsc4py" version))
1804 "0ch3g6dsvxl7qi984fcssv7cxfbif4bw04gkvxl2l1b8wrmvrm25"))))
1805 (build-system python-build-system)
1808 (modify-phases %standard-phases
1809 (add-before 'build 'pre-build
1811 ;; Define path to PETSc installation.
1812 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
1814 (add-before 'check 'mpi-setup
1817 `(("petsc" ,petsc-openmpi)
1818 ("python-numpy" ,python-numpy)))
1819 (home-page "https://bitbucket.org/petsc/petsc4py/")
1820 (synopsis "Python bindings for PETSc")
1821 (description "PETSc, the Portable, Extensible Toolkit for
1822 Scientific Computation, is a suite of data structures and routines for
1823 the scalable (parallel) solution of scientific applications modeled by
1824 partial differential equations. It employs the MPI standard for all
1825 message-passing communication. @code{petsc4py} provides Python
1826 bindings to almost all functions of PETSc.")
1827 (license license:bsd-3)))
1829 (define-public python-kiwisolver
1831 (name "python-kiwisolver")
1835 (uri (pypi-uri "kiwisolver" version))
1838 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
1839 (build-system python-build-system)
1840 (home-page "https://github.com/nucleic/kiwi")
1841 (synopsis "Fast implementation of the Cassowary constraint solver")
1843 "Kiwi is an efficient C++ implementation of the Cassowary constraint
1844 solving algorithm. Kiwi has been designed from the ground up to be
1845 lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
1846 Cassowary solver with typical use cases gaining a 40x improvement. Memory
1847 savings are consistently > 5x.")
1848 (license license:bsd-3)))
1850 (define-public python2-kiwisolver
1851 (package-with-python2 python-kiwisolver))
1853 (define-public slepc
1860 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
1864 "188j1a133q91h8pivpnzwcf78kz8dvz2nzf6ndnjygdbqb48fizn"))))
1865 (build-system gnu-build-system)
1867 `(("python" ,python-2)))
1869 `(("arpack" ,arpack-ng)
1870 ("gfortran" ,gfortran)))
1872 `(("petsc" ,petsc)))
1874 `(#:parallel-build? #f ;build is parallel by default
1876 `(,(string-append "--with-arpack-dir="
1877 (assoc-ref %build-inputs "arpack") "/lib"))
1878 #:make-flags ;honor (parallel-job-count)
1879 `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
1881 (modify-phases %standard-phases
1883 ;; configure is a python script, so we can't run it with bash.
1884 (lambda* (#:key inputs outputs (configure-flags '())
1886 (let* ((prefix (assoc-ref outputs "out"))
1887 (flags `(,(string-append "--prefix=" prefix)
1888 ,@configure-flags)))
1889 (format #t "build directory: ~s~%" (getcwd))
1890 (format #t "configure flags: ~s~%" flags)
1891 (setenv "SLEPC_DIR" (getcwd))
1892 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
1893 (apply invoke "./configure" flags))))
1894 (add-after 'install 'delete-doc
1895 ;; TODO: SLEPc installs HTML documentation alongside headers in
1896 ;; $out/include. We'd like to move them to share/doc, but delete
1897 ;; them for now, as they are incomplete and installing the complete
1898 ;; documentation is difficult.
1899 (lambda* (#:key outputs #:allow-other-keys)
1900 (let* ((out (assoc-ref outputs "out")))
1901 (for-each delete-file (find-files out "\\.html$"))
1903 (add-after 'install 'clean-install
1904 ;; Clean up unnecessary build logs from installation.
1905 (lambda* (#:key outputs #:allow-other-keys)
1906 (let ((out (assoc-ref outputs "out")))
1907 (for-each (lambda (file)
1908 (let ((f (string-append out "/lib/slepc/conf/" file)))
1909 (when (file-exists? f)
1911 '("configure.log" "make.log" "gmake.log"
1912 "test.log" "error.log" "RDict.db"
1915 (home-page "http://slepc.upv.es")
1916 (synopsis "Scalable library for eigenproblems")
1917 (description "SLEPc is a software library for the solution of large sparse
1918 eigenproblems on parallel computers. It can be used for the solution of
1919 linear eigenvalue problems formulated in either standard or generalized form,
1920 as well as other related problems such as the singular value decomposition.
1921 The emphasis of the software is on methods and techniques appropriate for
1922 problems in which the associated matrices are sparse, for example, those
1923 arising after the discretization of partial differential equations.")
1924 (license license:bsd-2)))
1926 (define-public slepc-complex
1927 (package (inherit slepc)
1928 (name "slepc-complex")
1930 `(("petsc" ,petsc-complex)
1931 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1932 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1934 (define-public slepc-openmpi
1935 (package (inherit slepc)
1936 (name "slepc-openmpi")
1938 (substitute-keyword-arguments (package-arguments slepc)
1939 ((#:phases phases '%standard-phases)
1940 `(modify-phases ,phases
1941 (add-before 'check 'mpi-setup
1942 ,%openmpi-setup)))))
1945 ("arpack" ,arpack-ng-openmpi)
1946 ,@(alist-delete "arpack" (package-inputs slepc))))
1948 `(("petsc" ,petsc-openmpi)
1949 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1950 (synopsis "Scalable library for eigenproblems (with MPI support)")))
1952 (define-public slepc-complex-openmpi
1953 (package (inherit slepc-openmpi)
1954 (name "slepc-complex-openmpi")
1956 `(("petsc" ,petsc-complex-openmpi)
1957 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1958 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1960 (define-public python-slepc4py
1962 (name "python-slepc4py")
1967 (uri (pypi-uri "slepc4py" version))
1970 "0x049dyc8frgh79fvvavf4vlbqp4mgm61nsaivzdav4316vvlv1j"))))
1971 (build-system python-build-system)
1974 (modify-phases %standard-phases
1975 (add-before 'build 'pre-build
1977 ;; Define path to PETSc installation.
1978 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
1979 ;; Define path to SLEPc installation.
1980 (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
1982 (add-before 'check 'mpi-setup
1985 `(("python-numpy" ,python-numpy)
1986 ("python-petsc4py" ,python-petsc4py)
1987 ("slepc" ,slepc-openmpi)))
1988 (home-page "https://bitbucket.org/slepc/slepc4py/")
1989 (synopsis "Python bindings for SLEPc")
1990 (description "SLEPc, the Scalable Library for Eigenvalue Problem
1991 Computations, is based on PETSc, the Portable, Extensible Toolkit for
1992 Scientific Computation. It employs the MPI standard for all
1993 message-passing communication. @code{slepc4py} provides Python
1994 bindings to almost all functions of SLEPc.")
1995 (license license:bsd-3)))
1997 (define-public mumps
2004 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
2008 "1s9asin08zqzmh08257sdghhivvy9vjif7c53fhaxaax2kd5qd7b"))
2009 (patches (search-patches "mumps-build-parallelism.patch"))))
2010 (build-system gnu-build-system)
2012 `(("fortran" ,gfortran)
2013 ;; These are required for linking against mumps, but we let the user
2014 ;; declare the dependency.
2017 ("scotch" ,scotch)))
2019 `(#:modules ((ice-9 match)
2022 ,@%gnu-build-system-modules)
2024 (modify-phases %standard-phases
2026 (lambda* (#:key inputs #:allow-other-keys)
2027 (call-with-output-file "Makefile.inc"
2038 INCSEQ = -I$(topdir)/libseq
2039 LIBSEQ = -L$(topdir)/libseq -lmpiseq
2040 LIBSEQNEEDED = libseqneeded~;
2044 AR = ar vr # rules require trailing space, ugh...
2046 LIBBLAS = -L~a -lopenblas~@[
2047 SCALAP = -L~a -lscalapack~]
2048 LIBOTHERS = -pthread
2051 OPTF = -O2 -DALLOW_NON_INIT $(PIC)
2055 LIBS = $(SCALAP) $(LIBSEQ)
2056 LPORDDIR = $(topdir)/PORD/lib
2057 IPORD = -I$(topdir)/PORD/include
2058 LPORD = -L$(LPORDDIR) -lpord
2059 ORDERINGSF = -Dpord~@[
2061 IMETIS = -I$(METISDIR)/include
2062 LMETIS = -L$(METISDIR)/lib -lmetis
2063 ORDERINGSF += -Dmetis~]~@[~:{
2065 ISCOTCH = -I$(SCOTCHDIR)/include
2066 LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
2067 ORDERINGSF += ~a~}~]
2068 ORDERINGSC = $(ORDERINGSF)
2069 LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
2070 IORDERINGSF = $(ISCOTCH)
2071 IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
2072 (assoc-ref inputs "mpi")
2073 (assoc-ref inputs "blas")
2074 (assoc-ref inputs "scalapack")
2075 (assoc-ref inputs "metis")
2076 (match (list (assoc-ref inputs "pt-scotch")
2077 (assoc-ref inputs "scotch"))
2081 `((,scotch "" "-Dscotch")))
2084 "-lptesmumps -lptscotch -lptscotcherr "
2085 "-Dptscotch")))))))))
2087 ;; By default only the d-precision library is built. Make with "all"
2088 ;; target so that all precision libraries and examples are built.
2090 (invoke "make" "all"
2091 (format #f "-j~a" (parallel-job-count)))))
2093 ;; Run the simple test drivers, which read test input from stdin:
2094 ;; from the "real" input for the single- and double-precision
2095 ;; testers, and from the "cmplx" input for complex-precision
2096 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
2097 ;; package to prefix execution with "mpirun".
2098 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
2099 (with-directory-excursion "examples"
2102 (let ((tester (apply open-pipe*
2105 ,(string-append "./" prec
2107 (input (open-input-file
2108 (string-append "input_simpletest_" type))))
2110 (dump-port input tester)
2112 (zero? (close-pipe tester)))))
2114 '("real" "real" "cmplx" "cmplx")))))
2116 (lambda* (#:key outputs #:allow-other-keys)
2117 (let* ((out (assoc-ref outputs "out"))
2118 (libdir (string-append out "/lib")))
2119 (copy-recursively "lib" libdir)
2120 (copy-recursively "include" (string-append out "/include"))
2121 (when (file-exists? "libseq/libmpiseq.a")
2122 (install-file "libseq/libmpiseq.a" libdir))
2124 (home-page "http://mumps.enseeiht.fr")
2125 (synopsis "Multifrontal sparse direct solver")
2127 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
2128 sparse system of linear equations A x = b using Guassian elimination.")
2129 (license license:cecill-c)))
2131 (define-public mumps-metis
2132 (package (inherit mumps)
2133 (name "mumps-metis")
2135 (alist-delete "scotch" (package-inputs mumps)))))
2137 (define-public mumps-openmpi
2138 (package (inherit mumps)
2139 (name "mumps-openmpi")
2142 ("scalapack" ,scalapack)
2143 ("pt-scotch" ,pt-scotch)
2144 ,@(alist-delete "scotch" (package-inputs mumps))))
2146 (substitute-keyword-arguments (package-arguments mumps)
2148 `(modify-phases ,phases
2149 (add-before 'check 'mpi-setup
2153 ((assoc-ref ,phases 'check)
2154 #:exec-prefix '("mpirun" "-n" "2"))))))))
2155 (synopsis "Multifrontal sparse direct solver (with MPI)")))
2157 (define-public mumps-metis-openmpi
2158 (package (inherit mumps-openmpi)
2159 (name "mumps-metis-openmpi")
2161 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
2163 (define-public r-quadprog
2170 (uri (cran-uri "quadprog" version))
2173 "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
2174 (build-system r-build-system)
2176 `(("gfortran" ,gfortran)))
2177 (home-page "https://cran.r-project.org/web/packages/quadprog")
2178 (synopsis "Functions to solve quadratic programming problems")
2180 "This package contains routines and documentation for solving quadratic
2181 programming problems.")
2182 (license license:gpl3+)))
2184 (define-public r-pracma
2190 (uri (cran-uri "pracma" version))
2192 (base32 "18zhni05gwnxbphl6bmjjxmsgg5wwnnkwlb4g971cqyw3dsd83ki"))))
2193 (build-system r-build-system)
2194 (home-page "https://cran.r-project.org/web/packages/pracma/")
2195 (synopsis "Practical numerical math functions")
2196 (description "This package provides functions for numerical analysis and
2197 linear algebra, numerical optimization, differential equations, plus some
2198 special functions. It uses Matlab function names where appropriate to simplify
2200 (license license:gpl3+)))
2202 (define-public ruby-asciimath
2204 (name "ruby-asciimath")
2209 (uri (rubygems-uri "asciimath" version))
2212 "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
2213 (build-system ruby-build-system)
2216 (modify-phases %standard-phases
2218 ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
2219 (add-after 'unpack 'patch-remove-spurious-backslashes
2221 (substitute* "spec/parser_spec.rb"
2226 `(("bundler" ,bundler)
2227 ("ruby-rspec" ,ruby-rspec)))
2228 (synopsis "AsciiMath parsing and conversion library")
2230 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
2231 easy-to-write markup language for mathematics.")
2232 (home-page "https://github.com/asciidoctor/asciimath")
2233 (license license:expat)))
2235 (define-public superlu
2242 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2243 "superlu_" version ".tar.gz"))
2245 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
2246 (modules '((guix build utils)))
2248 ;; Replace the non-free implementation of MC64 with a stub adapted
2251 (use-modules (ice-9 regex)
2253 (call-with-output-file "SRC/mc64ad.c"
2258 void mc64id_(int *a) {
2259 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2262 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2263 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2264 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2267 ;; Remove the corresponding license verbiage. MC64 license follows
2268 ;; a "------" line separator.
2269 (with-atomic-file-replacement "License.txt"
2270 (let ((rx (make-regexp "-{8}")))
2273 (let ((line (read-line in 'concat)))
2274 (unless (regexp-exec rx line)
2278 (build-system cmake-build-system)
2282 `(("blas" ,openblas)
2283 ("gfortran" ,gfortran)))
2285 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2286 "-DTPL_BLAS_LIBRARIES=openblas"
2287 "-DBUILD_SHARED_LIBS:BOOL=YES")))
2288 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
2289 (synopsis "Supernodal direct solver for sparse linear systems")
2291 "SuperLU is a general purpose library for the direct solution of large,
2292 sparse, nonsymmetric systems of linear equations on high performance machines.
2293 The library is written in C and is callable from either C or Fortran. The
2294 library routines perform an LU decomposition with partial pivoting and
2295 triangular system solves through forward and back substitution. The library
2296 also provides threshold-based ILU factorization preconditioners.")
2297 (license (list license:bsd-3
2298 license:gpl2+ ;EXAMPLE/*fgmr.c
2299 (license:fsf-free "file://SRC/colamd.h")))))
2301 (define-public superlu-dist
2303 (name "superlu-dist")
2308 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2309 "superlu_dist_" version ".tar.gz"))
2311 (base32 "0pqgcgh1yxhfzs99fas3mggajzd5wca3nbyp878rziy74gfk03dl"))
2312 (modules '((guix build utils)))
2314 ;; Replace the non-free implementation of MC64 with a stub
2316 (call-with-output-file "SRC/mc64ad_dist.c"
2321 void mc64id_dist(int *a) {
2322 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2325 void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2326 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2327 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2330 (substitute* "SRC/util.c" ;adjust default algorithm
2331 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
2332 ;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
2333 ;; general (i.e. non-square) processor-grid support.
2334 "RowPerm = NOROWPERM;"))
2336 (patches (search-patches "superlu-dist-scotchmetis.patch"
2337 "superlu-dist-awpm-grid.patch"
2338 "superlu-dist-fix-mpi-deprecations.patch"))))
2339 (build-system cmake-build-system)
2343 `(("gfortran" ,gfortran)
2346 ("combblas" ,combinatorial-blas)))
2348 `(("mpi" ,openmpi) ;headers include MPI heades
2349 ("parmetis" ,pt-scotch32 "metis")
2350 ("pt-scotch" ,pt-scotch32)))
2352 `(#:parallel-tests? #f ;tests use MPI and OpenMP
2353 #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
2354 "-DTPL_ENABLE_COMBBLASLIB=YES"
2355 "-DTPL_BLAS_LIBRARIES=-lopenblas"
2356 "-DTPL_LAPACK_LIBRARIES=-llapack"
2357 (string-append "-DTPL_PARMETIS_LIBRARIES="
2359 '("ptscotchparmetis" "ptscotch" "ptscotcherr"
2360 "scotchmetis" "scotch" "scotcherr")
2362 (string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
2363 (assoc-ref %build-inputs "parmetis")
2365 "-DTPL_ENABLE_COMBBLASLIB=ON"
2366 (string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
2367 (assoc-ref %build-inputs "combblas")
2368 "/include/CombBLAS;"
2369 (assoc-ref %build-inputs "combblas")
2370 "/include/BipartiteMatchings")
2371 "-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
2373 (modify-phases %standard-phases
2374 (add-before 'configure 'set-c++-standard
2376 (substitute* "CMakeLists.txt"
2377 ;; AWPM headers require C++14
2378 (("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
2379 (add-before 'check 'mpi-setup
2381 (add-before 'check 'omp-setup
2382 (lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
2383 (home-page (package-home-page superlu))
2384 (synopsis "Parallel supernodal direct solver")
2386 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2387 It is targeted for distributed memory parallel machines. SuperLU_DIST is
2388 implemented in ANSI C, and MPI for communications.")
2389 (license license:bsd-3)))
2391 (define-public scotch
2398 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
2399 "latestfile/298/scotch_" version ".tar.gz"))
2401 (base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8"))
2402 (patches (search-patches "scotch-build-parallelism.patch"
2403 "scotch-integer-declarations.patch"))))
2404 (build-system gnu-build-system)
2409 (outputs '("out" "metis"))
2411 `(#:make-flags (list (string-append "prefix=" %output))
2413 (modify-phases %standard-phases
2415 'unpack 'chdir-to-src
2416 (lambda _ (chdir "src") #t))
2420 (call-with-output-file "Makefile.inc"
2434 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2435 LDFLAGS = -lz -lm -lrt -lpthread
2437 LEX = flex -Pscotchyy -olex.yy.c
2442 YACC = bison -pscotchyy -y -b y
2444 '("COMMON_FILE_COMPRESS_GZ"
2446 "COMMON_RANDOM_FIXED_SEED"
2447 "INTSIZE64" ;use 'int64_t'
2448 ;; Prevents symbolc clashes with libesmumps
2450 ;; XXX: Causes invalid frees in superlu-dist tests
2452 ;; "SCOTCH_PTHREAD_NUMBER=2"
2453 "restrict=__restrict"))))
2455 (add-after 'build 'build-esmumps
2458 (format #f "-j~a" (parallel-job-count))
2460 (add-before 'install 'make-install-dirs
2461 (lambda* (#:key outputs #:allow-other-keys)
2462 (mkdir (assoc-ref outputs "out"))))
2463 (add-after 'install 'install-metis
2464 (lambda* (#:key outputs #:allow-other-keys)
2465 (let ((out (assoc-ref outputs "metis")))
2467 ;; metis files are not installed with 'make install'
2468 (for-each (lambda (f)
2469 (install-file f (string-append out "/include")))
2470 (find-files "../include/" ".*metis\\.h"))
2471 (for-each (lambda (f)
2472 (install-file f (string-append out "/lib")))
2473 (find-files "../lib/" ".*metis\\..*"))
2475 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
2476 (synopsis "Programs and libraries for graph algorithms")
2477 (description "SCOTCH is a set of programs and libraries which implement
2478 the static mapping and sparse matrix reordering algorithms developed within
2479 the SCOTCH project. Its purpose is to apply graph theory, with a divide and
2480 conquer approach, to scientific computing problems such as graph and mesh
2481 partitioning, static mapping, and sparse matrix ordering, in application
2482 domains ranging from structural mechanics to operating systems or
2484 ;; See LICENSE_en.txt
2485 (license license:cecill-c)))
2487 (define-public scotch32
2488 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2489 ;; some applications.
2490 (package (inherit scotch)
2493 (substitute-keyword-arguments (package-arguments scotch)
2494 ((#:phases scotch-phases)
2495 `(modify-phases ,scotch-phases
2499 (call-with-output-file "Makefile.inc"
2513 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2514 LDFLAGS = -lz -lm -lrt -lpthread
2516 LEX = flex -Pscotchyy -olex.yy.c
2521 YACC = bison -pscotchyy -y -b y
2523 '("COMMON_FILE_COMPRESS_GZ"
2525 "COMMON_RANDOM_FIXED_SEED"
2526 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
2527 ;; Prevents symbolc clashes with libesmumps
2529 ;; XXX: Causes invalid frees in superlu-dist tests
2531 ;; "SCOTCH_PTHREAD_NUMBER=2"
2532 "restrict=__restrict"))))))))))
2534 "Programs and libraries for graph algorithms (32-bit integers)")))
2536 (define-public pt-scotch
2537 (package (inherit scotch)
2540 `(("openmpi" ,openmpi))) ;Headers include MPI headers
2542 (substitute-keyword-arguments (package-arguments scotch)
2543 ((#:phases scotch-phases)
2544 `(modify-phases ,scotch-phases
2548 (invoke "make" (format #f "-j~a" (parallel-job-count))
2549 "ptscotch" "ptesmumps")
2551 ;; Install the serial metis compatibility library
2552 (invoke "make" "-C" "libscotchmetis" "install")))
2553 (add-before 'check 'mpi-setup
2557 (invoke "make" "ptcheck")))))))
2558 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
2560 (define-public pt-scotch32
2561 (package (inherit scotch32)
2562 (name "pt-scotch32")
2564 `(("openmpi" ,openmpi))) ;headers include MPI headers
2566 (substitute-keyword-arguments (package-arguments scotch32)
2567 ((#:phases scotch32-phases)
2568 `(modify-phases ,scotch32-phases
2571 (invoke "make" (format #f "-j~a" (parallel-job-count))
2572 "ptscotch" "ptesmumps")
2573 ;; Install the serial metis compatibility library
2574 (invoke "make" "-C" "libscotchmetis" "install")))
2575 (add-before 'check 'mpi-setup
2579 (invoke "make" "ptcheck")))))))
2581 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2583 (define-public metis
2590 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2591 "metis-" version ".tar.gz"))
2594 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2595 (build-system cmake-build-system)
2597 `(("blas" ,openblas)))
2599 `(#:tests? #f ;no tests
2600 #:configure-flags `("-DSHARED=ON"
2601 ,(string-append "-DGKLIB_PATH=" (getcwd)
2602 "/metis-" ,version "/GKlib"))))
2603 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2604 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2606 "METIS is a set of serial programs for partitioning graphs, partitioning
2607 finite element meshes, and producing fill-reducing orderings for sparse
2608 matrices. The algorithms implemented in METIS are based on the multilevel
2609 recursive-bisection, multilevel k-way, and multi-constraint partitioning
2611 (license license:asl2.0))) ;As of version 5.0.3
2613 (define-public p4est
2620 (uri (string-append "http://p4est.github.io/release/p4est-"
2624 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
2625 (build-system gnu-build-system)
2627 `(("fortran" ,gfortran)
2632 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2633 (assoc-ref %build-inputs "blas")
2635 ,(string-append "LAPACK_LIBS=-L"
2636 (assoc-ref %build-inputs "lapack")
2638 #:phases (modify-phases %standard-phases
2639 (add-before 'check 'mpi-setup
2641 (home-page "http://www.p4est.org")
2642 (synopsis "Adaptive mesh refinement on forests of octrees")
2644 "The p4est software library enables the dynamic management of a
2645 collection of adaptive octrees, conveniently called a forest of octrees.
2646 p4est is designed to work in parallel and scales to hundreds of thousands of
2648 (license license:gpl2+)))
2650 (define-public p4est-openmpi
2651 (package (inherit p4est)
2652 (name "p4est-openmpi")
2655 ,@(package-inputs p4est)))
2657 (substitute-keyword-arguments (package-arguments p4est)
2658 ((#:configure-flags cf)
2659 ``("--enable-mpi" ,@,cf))))
2660 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2662 (define-public gsegrafix
2669 (uri (string-append "mirror://gnu/" name "/" name "-"
2673 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2674 (build-system gnu-build-system)
2676 `(#:configure-flags '("LDFLAGS=-lm")))
2678 `(("libgnomecanvas" ,libgnomecanvas)
2679 ("libbonoboui" ,libbonoboui)
2680 ("libgnomeui" ,libgnomeui)
2681 ("libgnomeprintui" ,libgnomeprintui)
2684 `(("pkg-config" ,pkg-config)))
2685 (home-page "https://www.gnu.org/software/gsegrafix/")
2686 (synopsis "GNOME application to create scientific and engineering plots")
2687 (description "GSEGrafix is an application which produces high-quality graphical
2688 plots for science and engineering. Plots are specified via simple ASCII
2689 parameter files and data files and are presented in an anti-aliased GNOME
2690 canvas. The program supports rectangular two-dimensional plots, histograms,
2691 polar-axis plots and three-dimensional plots. Plots can be printed or saved
2692 to BMP, JPEG or PNG image formats.")
2693 (license license:gpl3+)))
2695 (define-public maxima
2702 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2703 version "-source/" name "-" version ".tar.gz"))
2706 "0kdncy6137sg3rradirxzj10mkcvafxd892zlclwhr9sa7b12zhn"))
2707 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
2708 (build-system gnu-build-system)
2711 ("gnuplot" ,gnuplot) ;for plots
2713 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
2715 `(("texinfo" ,texinfo)
2717 ("python" ,python)))
2720 (list "--enable-gcl"
2721 (string-append "--with-posix-shell="
2722 (assoc-ref %build-inputs "bash")
2724 (string-append "--with-wish="
2725 (assoc-ref %build-inputs "tk")
2727 (let ((v ,(package-version tk)))
2728 (string-take v (string-index-right v #\.)))))
2729 ;; By default Maxima attempts to write temporary files to
2730 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2731 ;; Work around that.
2732 #:make-flags (list "TMPDIR=/tmp")
2734 (modify-phases %standard-phases
2735 (add-after 'unpack 'patch-paths
2736 (lambda* (#:key inputs #:allow-other-keys)
2737 (let* ((sed (string-append (assoc-ref inputs "sed") "/bin/sed"))
2738 (coreutils (assoc-ref inputs "coreutils"))
2739 (dirname (string-append coreutils "/bin/dirname"))
2740 (head (string-append coreutils "/bin/head")))
2741 (substitute* "src/maxima.in"
2742 (("sed ") (string-append sed " "))
2743 (("dirname") dirname)
2746 (add-before 'check 'pre-check
2748 (chmod "src/maxima" #o555)
2752 ;; This is derived from the testing code in the "debian/rules" file
2753 ;; of Debian's Maxima package.
2754 ;; If Maxima can successfully run this, the binary to be installed
2758 (string-append "./maxima-local "
2760 "--batch-string=\"run_testsuite();\" "
2761 "| grep -q \"No unexpected errors found\"")))))
2762 ;; Make sure the doc and emacs files are found in the
2763 ;; standard location. Also configure maxima to find gnuplot
2764 ;; without having it on the PATH.
2765 (add-after 'install 'post-install
2766 (lambda* (#:key outputs inputs #:allow-other-keys)
2767 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2768 (out (assoc-ref outputs "out"))
2769 (datadir (string-append out "/share/maxima/" ,version))
2770 (binutils (string-append (assoc-ref inputs "binutils")
2772 (with-directory-excursion out
2773 (mkdir-p "share/emacs")
2774 (mkdir-p "share/doc")
2776 (string-append datadir "/emacs/")
2777 (string-append out "/share/emacs/site-lisp"))
2779 (string-append datadir "/doc/")
2780 (string-append out "/share/doc/maxima"))
2781 (with-atomic-file-replacement
2782 (string-append datadir "/share/maxima-init.lisp")
2784 (format out "~a ~s~a~%"
2785 "(setf $gnuplot_command "
2786 (string-append gnuplot "/bin/gnuplot") ")")
2787 (dump-port in out))))
2788 ;; Ensure that Maxima will have access to the GNU binutils
2789 ;; components at runtime.
2790 (wrap-program (string-append out "/bin/maxima")
2791 `("PATH" prefix (,binutils))))
2793 (home-page "http://maxima.sourceforge.net")
2794 (synopsis "Numeric and symbolic expression manipulation")
2795 (description "Maxima is a system for the manipulation of symbolic and
2796 numerical expressions. It yields high precision numeric results by using
2797 exact fractions, arbitrary precision integers, and variable precision floating
2799 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2800 ;; Others simply say "GNU General Public License" without stating a
2801 ;; version (which implicitly means gpl1+).
2802 ;; At least one file (src/maxima.asd) says "version 2."
2803 ;; GPLv2 only is therefore the smallest subset.
2804 (license license:gpl2)))
2806 (define-public wxmaxima
2814 (url "https://github.com/wxMaxima-developers/wxmaxima.git")
2815 (commit (string-append "Version-" version))))
2816 (file-name (git-file-name name version))
2819 "1vwahx3zxkn3qlv4z0fm7v8wh0wspvs026alrh7ff7s0c2dcy95x"))))
2820 (build-system cmake-build-system)
2822 `(("gettext" ,gettext-minimal)))
2824 `(("wxwidgets" ,wxwidgets)
2827 ("adwaita-icon-theme" ,adwaita-icon-theme)
2829 ("shared-mime-info" ,shared-mime-info)))
2831 `(#:tests? #f ; no check target
2833 (modify-phases %standard-phases
2834 (add-after 'install 'wrap-program
2835 (lambda* (#:key inputs outputs #:allow-other-keys)
2836 (wrap-program (string-append (assoc-ref outputs "out")
2839 (,(string-append (assoc-ref inputs "maxima")
2841 ;; For GtkFileChooserDialog.
2842 `("GSETTINGS_SCHEMA_DIR" =
2843 (,(string-append (assoc-ref inputs "gtk+")
2844 "/share/glib-2.0/schemas")))
2845 `("XDG_DATA_DIRS" ":" prefix
2846 (;; Needed by gdk-pixbuf to know supported icon formats.
2848 (assoc-ref inputs "shared-mime-info") "/share")
2849 ;; The default icon theme of GTK+.
2851 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
2853 (home-page "https://andrejv.github.io/wxmaxima/")
2854 (synopsis "Graphical user interface for the Maxima computer algebra system")
2856 "wxMaxima is a graphical user interface for the Maxima computer algebra
2857 system. It eases the use of Maxima by making most of its commands available
2858 through a menu system and by providing input dialogs for commands that require
2859 more than one argument. It also implements its own display engine that
2860 outputs mathematical symbols directly instead of depicting them with ASCII
2863 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
2864 text and mathematical calculations to create documents, exporting of input and
2865 output to TeX, and a browser for Maxima's manual including command index and
2866 full text searching.")
2867 (license license:gpl2+)))
2869 (define-public armadillo
2875 (uri (string-append "mirror://sourceforge/arma/armadillo-"
2879 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
2880 (build-system cmake-build-system)
2881 (arguments `(#:tests? #f)) ; no test target
2883 `(("openblas" ,openblas)
2885 ("arpack" ,arpack-ng)))
2886 (home-page "http://arma.sourceforge.net/")
2887 (synopsis "C++ linear algebra library")
2889 "Armadillo is a C++ linear algebra library, aiming towards a good balance
2890 between speed and ease of use. It is useful for algorithm development
2891 directly in C++, or quick conversion of research code into production
2892 environments. It can be used for machine learning, pattern recognition,
2893 signal processing, bioinformatics, statistics, econometrics, etc. The library
2894 provides efficient classes for vectors, matrices and cubes, as well as 150+
2895 associated functions (eg. contiguous and non-contiguous submatrix views).")
2896 (license license:asl2.0)))
2898 (define-public muparser
2899 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2900 ;; different hash. In order to make `guix package --upgrade` work correctly,
2901 ;; we set a Guix packaging revision.
2902 ;; When the next version of muparser is released, we can remove
2903 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2904 (let ((upstream-version "2.2.5")
2908 (version (string-append upstream-version "-" revision))
2912 (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
2913 upstream-version ".tar.gz"))
2914 (file-name (string-append name "-" version ".tar.gz"))
2917 "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
2918 (build-system gnu-build-system)
2920 `(#:configure-flags '("--enable-samples=no")
2921 #:tests? #f)) ;no "check" target
2922 (home-page "http://muparser.beltoforion.de/")
2923 (synopsis "Fast parser library for mathematical expressions")
2925 "muParser is an extensible high performance math parser library. It is
2926 based on transforming an expression into a bytecode and precalculating constant
2928 (license license:expat))))
2930 (define-public openblas
2937 (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
2938 version "%20version.tar.gz"))
2939 (file-name (string-append name "-" version ".tar.gz"))
2942 "0cvlixnpc3cdvvn3f30phfvsgnqljqix6wn72ps9rj7xdhvw06jg"))))
2943 (build-system gnu-build-system)
2945 `(#:test-target "test"
2946 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
2947 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2948 ;; we need to disable substitutions.
2950 ,(let ((system (or (%current-target-system) (%current-system))))
2951 (or (string-prefix? "x86_64" system)
2952 (string-prefix? "i686" system)
2953 (string-prefix? "mips" system)
2954 (string-prefix? "aarch64" system)))
2956 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
2958 ;; Build the library for all supported CPUs. This allows
2959 ;; switching CPU targets at runtime with the environment variable
2960 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
2961 ;; Unfortunately, this is not supported on non-x86 architectures,
2962 ;; where it leads to failed builds.
2963 ,@(let ((system (or (%current-target-system) (%current-system))))
2965 ((or (string-prefix? "x86_64" system)
2966 (string-prefix? "i686" system))
2967 '("DYNAMIC_ARCH=1"))
2968 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
2969 ;; two available MIPS targets special extended instructions
2970 ;; for Loongson cores are used.
2971 ((string-prefix? "mips" system)
2972 '("TARGET=SICORTEX"))
2973 ;; On aarch64 force the generic 'armv8-a' target
2974 ((string-prefix? "aarch64" system)
2977 ;; no configure script
2979 (modify-phases %standard-phases
2981 (add-before 'build 'set-extralib
2982 (lambda* (#:key inputs #:allow-other-keys)
2983 ;; Get libgfortran found when building in utest.
2985 (string-append "-L" (assoc-ref inputs "fortran-lib")
2989 `(("fortran-lib" ,gfortran "lib")))
2992 ("fortran" ,gfortran)
2994 (home-page "http://www.openblas.net/")
2995 (synopsis "Optimized BLAS library based on GotoBLAS")
2997 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
2998 (license license:bsd-3)))
3000 (define-public openblas-ilp64
3001 (package (inherit openblas)
3002 (name "openblas-ilp64")
3003 (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
3005 (substitute-keyword-arguments (package-arguments openblas)
3006 ((#:make-flags flags '())
3007 `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
3009 (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
3010 (license license:bsd-3)))
3012 (define* (make-blis implementation #:optional substitutable?)
3013 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
3014 source tree for a list of implementations.)
3016 SUBSTITUTABLE? determines whether the package is made available as a
3019 Currently the specialization must be selected at configure-time, but work is
3020 underway to allow BLIS to select the right optimized kernels at run time:
3021 <https://github.com/flame/blis/issues/129>."
3023 (name (if (string=? implementation "reference")
3025 (string-append "blis-" implementation)))
3027 (home-page "https://github.com/flame/blis")
3030 (uri (git-reference (url home-page) (commit version)))
3033 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
3034 (file-name (git-file-name "blis" version))))
3035 (build-system gnu-build-system)
3037 `(#:test-target "test"
3039 #:substitutable? ,substitutable?
3041 #:phases (modify-phases %standard-phases
3043 (lambda* (#:key outputs #:allow-other-keys)
3044 ;; This is a home-made 'configure' script.
3045 (let ((out (assoc-ref outputs "out")))
3046 (zero? (system* "./configure" "-p" out
3050 "--enable-threading=openmp"
3052 ,implementation)))))
3053 (add-before 'check 'show-test-output
3055 ;; By default "make check" is silent. Make it verbose.
3056 (system "tail -F output.testsuite &")
3058 (synopsis "High-performance basic linear algebra (BLAS) routines")
3060 "BLIS is a portable software framework for instantiating high-performance
3061 BLAS-like dense linear algebra libraries. The framework was designed to
3062 isolate essential kernels of computation that, when optimized, immediately
3063 enable optimized implementations of most of its commonly used and
3064 computationally intensive operations. While BLIS exports a new BLAS-like API,
3065 it also includes a BLAS compatibility layer which gives application developers
3066 access to BLIS implementations via traditional BLAS routine calls.")
3067 (license license:bsd-3)))
3070 ;; This is the "reference" implementation, which is the non-optimized but
3071 ;; portable variant (no assembly).
3072 (make-blis "reference" #t))
3074 (define ignorance blis)
3076 (define-syntax-rule (blis/x86_64 processor)
3077 "Expand to a package specialized for PROCESSOR."
3079 (inherit (make-blis processor))
3080 (supported-systems '("x86_64-linux"))))
3082 (define-public blis-sandybridge
3083 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
3084 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
3085 (blis/x86_64 "sandybridge"))
3087 (define-public blis-haswell
3088 ;; BLIS specialized for Haswell processors (launched 2013):
3089 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
3090 (blis/x86_64 "haswell"))
3092 (define-public blis-knl
3093 ;; BLIS specialized for Knights Landing processor (launched 2016):
3094 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
3095 (blis/x86_64 "knl"))
3098 (define-public openlibm
3105 (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
3107 (file-name (string-append name "-" version ".tar.gz"))
3110 "0a5fpm8nra5ldhjk0cqd2rx1qh32wiarkxmcqcm5xl8z7l4kjm6l"))))
3111 (build-system gnu-build-system)
3114 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3116 ;; no configure script
3117 (modify-phases %standard-phases (delete 'configure))
3118 #:tests? #f)) ;the tests are part of the default target
3119 (home-page "http://openlibm.org/")
3120 (synopsis "Portable C mathematical library (libm)")
3122 "OpenLibm is an effort to have a high quality, portable, standalone C
3123 mathematical library (libm). It can be used standalone in applications and
3124 programming language implementations. The project was born out of a need to
3125 have a good libm for the Julia programming language that worked consistently
3126 across compilers and operating systems, and in 32-bit and 64-bit
3128 ;; Each architecture has its own make target, and there is none for mips.
3129 (supported-systems (delete "mips64el-linux" %supported-systems))
3130 ;; See LICENSE.md for details.
3131 (license (list license:expat
3134 license:public-domain
3135 license:lgpl2.1+))))
3137 (define-public openspecfun
3139 (name "openspecfun")
3144 (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
3146 (file-name (string-append name "-" version ".tar.gz"))
3149 "1rs1bv8jq751fv9vq79890wqf9xlbjc7lvz3ighzyfczbyjcf18m"))))
3150 (build-system gnu-build-system)
3152 '(#:tests? #f ; no "check" target
3154 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3156 (modify-phases %standard-phases
3157 (delete 'configure)))) ; no configure script
3159 `(("fortran" ,gfortran)))
3160 (home-page "https://github.com/JuliaLang/openspecfun")
3161 (synopsis "Collection of special mathematical functions")
3163 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
3164 portable package for Bessel Functions of a Complex Argument and Nonnegative
3165 Order; it contains subroutines for computing Bessel functions and Airy
3166 functions. Faddeeva allows computing the various error functions of arbitrary
3167 complex arguments (Faddeeva function, error function, complementary error
3168 function, scaled complementary error function, imaginary error function, and
3169 Dawson function); given these, one can also easily compute Voigt functions,
3170 Fresnel integrals, and similar related functions as well.")
3171 ;; Faddeeva is released under the Expat license; AMOS is included as
3172 ;; public domain software.
3173 (license (list license:expat license:public-domain))))
3175 (define-public suitesparse
3177 (name "suitesparse")
3183 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
3187 "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
3188 (modules '((guix build utils)))
3190 ;; Remove bundled metis source
3192 (delete-file-recursively "metis-5.1.0")
3194 (build-system gnu-build-system)
3196 '(#:tests? #f ;no "check" target
3201 "MY_METIS_LIB=-lmetis"
3202 (string-append "INSTALL_LIB="
3203 (assoc-ref %outputs "out") "/lib")
3204 (string-append "INSTALL_INCLUDE="
3205 (assoc-ref %outputs "out") "/include")
3208 (modify-phases %standard-phases
3209 (delete 'configure)))) ;no configure script
3214 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
3215 (synopsis "Suite of sparse matrix software")
3217 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
3218 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
3219 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
3220 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
3221 CXSparse, a concise sparse Cholesky factorization package; and many other
3224 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
3226 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
3227 (license (list license:gpl2+ license:lgpl2.1+))))
3229 (define-public atlas
3235 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
3236 version "/atlas" version ".tar.bz2"))
3239 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
3240 (build-system gnu-build-system)
3241 (home-page "http://math-atlas.sourceforge.net/")
3242 (inputs `(("gfortran" ,gfortran)
3243 ("lapack-tar" ,(package-source lapack))))
3244 (outputs '("out" "doc"))
3245 ;; For the moment we drop support for MIPS at it fails to compile. See
3246 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
3247 (supported-systems (delete "mips64el-linux" %supported-systems))
3249 `(#:parallel-build? #f
3250 #:parallel-tests? #f
3252 ;; ATLAS tunes itself for the machine it is built on, as explained at
3253 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
3254 ;; For this reason, we want users to build it locally instead of using
3258 #:modules ((srfi srfi-26)
3260 (guix build gnu-build-system)
3263 `(;; Generate position independent code suitable for dynamic libraries
3264 ;; and use WALL timer to get more accurate timing.
3265 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
3268 ,,(if (string-match "64" (%current-system))
3271 ;; Disable parallel build as it gives errors: atlas_pthread.h is
3272 ;; needed to compile C files before it is generated.
3273 "-Ss" "pmake" "make -j 1"
3274 ;; Probe is failing for MIPS. We therefore define the system
3275 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3276 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3277 ,,@(if (string-prefix? "mips" (%current-system))
3278 (list "-A" "49" "-V" "1")
3280 ;; Generate shared libraries.
3282 ;; Build a full LAPACK library.
3283 ,(string-append "--with-netlib-lapack-tarfile="
3284 (assoc-ref %build-inputs "lapack-tar")))
3286 (modify-phases %standard-phases
3287 (add-after 'install 'install-doc
3288 (lambda* (#:key outputs inputs #:allow-other-keys)
3289 (let ((doc (string-append (assoc-ref outputs "doc")
3290 "/share/doc/atlas")))
3292 (fold (lambda (file previous)
3293 (and previous (zero? (system* "cp" file doc))))
3294 #t (find-files "../ATLAS/doc" ".*")))))
3295 (add-after 'check 'check-pt
3296 (lambda _ (zero? (system* "make" "ptcheck"))))
3297 ;; Fix files required to run configure.
3298 (add-before 'configure 'fix-/bin/sh
3300 ;; Use `sh', not `/bin/sh'.
3301 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3304 ;; Fix /bin/sh in generated make files.
3305 (add-after 'configure 'fix-/bin/sh-in-generated-files
3307 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3310 ;; ATLAS configure program does not accepts the default flags
3311 ;; passed by the 'gnu-build-system'.
3313 (lambda* (#:key native-inputs inputs outputs
3314 (configure-flags '())
3315 #:allow-other-keys #:rest args)
3316 (let* ((prefix (assoc-ref outputs "out"))
3317 (bash (or (and=> (assoc-ref
3318 (or native-inputs inputs) "bash")
3319 (cut string-append <> "/bin/bash"))
3321 (flags `(,(string-append "--prefix=" prefix)
3323 (abs-srcdir (getcwd))
3324 (srcdir (string-append "../" (basename abs-srcdir))))
3325 (format #t "source directory: ~s (relative from build: ~s)~%"
3329 (format #t "build directory: ~s~%" (getcwd))
3330 (format #t "configure flags: ~s~%" flags)
3331 (zero? (apply system* bash
3332 (string-append srcdir "/configure")
3334 (synopsis "Automatically Tuned Linear Algebra Software")
3336 "ATLAS is an automatically tuned linear algebra software library
3337 providing C and Fortran77 interfaces to a portably efficient BLAS
3338 implementation, as well as a few routines from LAPACK.
3340 Optimization occurs at build time. For this reason, the library is built on
3341 the machine where it is installed, without resorting to pre-built substitutes.
3343 Before building the library, CPU throttling should be disabled. This can be
3344 done in the BIOS, or, on GNU/Linux, with the following command:
3347 # cpupower --governor performance
3350 Failure to do so will result in a library with poor performance.")
3351 (license license:bsd-3)))
3360 (uri (string-append "https://github.com/g-truc/glm/releases/download/"
3361 version "/glm-" version ".zip"))
3364 "0yqk5r3qh60d4r2iab5q7wq0fryn8p3pz6s28y1i7amqj1aqavj9"))))
3365 (build-system cmake-build-system)
3367 `(("unzip" ,unzip)))
3368 (home-page "https://glm.g-truc.net/")
3369 (synopsis "OpenGL Mathematics library")
3370 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3371 library for graphics software based on the OpenGL Shading Language (GLSL)
3373 (license license:expat)))
3375 (define-public lpsolve
3382 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3383 "/lp_solve_" version "_source.tar.gz"))
3386 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
3387 (modules '((guix build utils)))
3390 (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3392 ;; Pretend to be on a 64 bit platform to obtain a common directory
3393 ;; name for the build results on all architectures; nothing else
3394 ;; seems to depend on it.
3395 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3397 ;; The check for 'isnan' as it is written fails with
3398 ;; "non-floating-point argument in call to function
3399 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3400 ;; definition, which in turn leads to bad things. Fix the feature
3402 (("isnan\\(0\\)") "isnan(0.)"))
3404 (build-system gnu-build-system)
3406 `(#:tests? #f ; no check target
3408 (modify-phases %standard-phases
3409 (delete 'configure) ; no configure script
3412 (with-directory-excursion "lpsolve55"
3413 (invoke "bash" "ccc"))
3414 (with-directory-excursion "lp_solve"
3415 (invoke "bash" "ccc"))
3418 (lambda* (#:key outputs #:allow-other-keys)
3419 (let* ((out (assoc-ref outputs "out"))
3420 (bin (string-append out "/bin"))
3421 (lib (string-append out "/lib"))
3422 ;; This is where LibreOffice expects to find the header
3423 ;; files, and where they are installed by Debian.
3424 (include (string-append out "/include/lpsolve")))
3425 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3426 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
3427 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3429 ;; Install a subset of the header files as on Debian
3430 ;; (plus lp_bit.h, which matches the regular expression).
3431 (for-each (lambda (name)
3432 (install-file name include))
3433 (find-files "." "lp_[HMSa-z].*\\.h$"))
3434 (with-directory-excursion "shared"
3435 (for-each (lambda (name)
3436 (install-file name include))
3437 (find-files "." "\\.h$")))
3439 (home-page "http://lpsolve.sourceforge.net/")
3440 (synopsis "Mixed integer linear programming (MILP) solver")
3442 "lp_solve is a mixed integer linear programming solver based on the
3443 revised simplex and the branch-and-bound methods.")
3444 (license license:lgpl2.1+)))
3446 (define-public dealii
3453 (uri (string-append "https://github.com/dealii/dealii/releases/"
3454 "download/v" version "/dealii-" version ".tar.gz"))
3457 "1bh9rsmkrg0zi70n27b11djmac9lximghsiy7mg7w7x544n82gnk"))
3458 (modules '((guix build utils)))
3460 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
3462 (delete-file-recursively "bundled")
3464 (build-system cmake-build-system)
3472 ("arpack" ,arpack-ng)
3473 ("muparser" ,muparser)
3474 ("gfortran" ,gfortran)
3475 ("suitesparse" ,suitesparse))) ;for UMFPACK
3477 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
3479 ;; Work around a bug in libsuitesparseconfig linking
3480 ;; see https://github.com/dealii/dealii/issues/4745
3481 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
3482 (home-page "https://www.dealii.org")
3483 (synopsis "Finite element library")
3485 "Deal.II is a C++ program library targeted at the computational solution
3486 of partial differential equations using adaptive finite elements. The main
3487 aim of deal.II is to enable rapid development of modern finite element codes,
3488 using among other aspects adaptive meshes and a wide array of tools often used
3489 in finite element programs.")
3490 (license license:lgpl2.1+)))
3492 (define-public dealii-openmpi
3493 (package (inherit dealii)
3494 (name "dealii-openmpi")
3497 ;;Supported only with MPI:
3498 ("p4est" ,p4est-openmpi)
3499 ("petsc" ,petsc-openmpi)
3500 ("slepc" ,slepc-openmpi)
3501 ("metis" ,metis) ;for MUMPS
3502 ("scalapack" ,scalapack) ;for MUMPS
3503 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3504 ("arpack" ,arpack-ng-openmpi)
3505 ,@(fold alist-delete (package-inputs dealii)
3506 '("p4est" "arpack"))))
3508 (substitute-keyword-arguments (package-arguments dealii)
3509 ((#:configure-flags cf)
3510 ``("-DMPI_C_COMPILER=mpicc"
3511 "-DMPI_CXX_COMPILER=mpicxx"
3512 "-DMPI_Fortran_COMPILER=mpifort"
3514 ((#:phases phases '%standard-phases)
3515 `(modify-phases ,phases
3516 (add-before 'check 'mpi-setup
3517 ,%openmpi-setup)))))
3518 (synopsis "Finite element library (with MPI support)")))
3520 (define-public flann
3529 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3530 version "-src.zip"))
3533 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
3534 (patches (search-patches "flann-cmake-3.11.patch"))))
3535 (build-system cmake-build-system)
3537 "octave")) ;46 MiB .mex file that pulls Octave
3539 `(("unzip" ,unzip)))
3542 ("octave" ,octave-cli)
3543 ("python" ,python-2) ; print syntax
3544 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3547 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3548 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3549 #:strip-directories '("lib" "lib64" "libexec"
3550 "bin" "sbin" "share/flann/octave")
3552 ;; Save 12 MiB by not installing .a files. Passing
3553 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3554 #:phases (modify-phases %standard-phases
3555 (add-before 'configure 'set-octave-directory
3556 (lambda* (#:key outputs #:allow-other-keys)
3557 ;; Install the .mex file in the "octave" output.
3558 (let ((out (assoc-ref outputs "octave")))
3559 (substitute* "src/matlab/CMakeLists.txt"
3560 (("share/flann/octave")
3561 (string-append out "/share/flann/octave")))
3563 (add-after 'install 'remove-static-libraries
3564 (lambda* (#:key outputs #:allow-other-keys)
3565 (let* ((out (assoc-ref outputs "out"))
3566 (lib (string-append out "/lib")))
3567 (for-each delete-file
3568 (find-files lib "\\.a$"))
3571 #:tests? #f)) ; The test data are downloaded from the Internet.
3572 (home-page "http://www.cs.ubc.ca/research/flann/")
3573 (synopsis "Library for approximate nearest neighbors computation")
3574 (description "FLANN is a library for performing fast approximate
3575 nearest neighbor searches in high dimensional spaces. It implements a
3576 collection of algorithms and a system for automatically choosing the best
3577 algorithm and optimum parameters depending on the dataset.
3579 FLANN is written in C++ and contains bindings for C, Octave and Python.")
3580 (license (license:non-copyleft "file://COPYING"
3581 "See COPYING in the distribution."))))
3583 (define-public wcalc
3590 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3591 "wcalc-" version ".tar.bz2"))
3594 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3595 (build-system gnu-build-system)
3598 ("readline" ,readline)))
3599 (home-page "http://w-calc.sourceforge.net/index.php")
3600 (synopsis "Flexible command-line scientific calculator")
3601 (description "Wcalc is a very capable calculator. It has standard functions
3602 (sin, asin, and sinh for example, in either radians or degrees), many
3603 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3604 variables, a command history, hex/octal/binary input and output, unit
3605 conversions, embedded comments, and an expandable expression entry field. It
3606 evaluates expressions using the standard order of operations.")
3607 (license license:gpl2+)))
3615 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3616 "/xaos-" version ".tar.gz"))
3619 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3620 (build-system gnu-build-system)
3621 (native-inputs `(("gettext" ,gettext-minimal)))
3622 (inputs `(("libx11" ,libx11)
3627 `(#:tests? #f ;no "check" target
3628 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3629 (synopsis "Real-time fractal zoomer")
3630 (description "GNU XaoS is a graphical program that generates fractal
3631 patterns and allows you to zoom in and out of them infinitely in a fluid,
3632 continuous manner. It also includes tutorials that help to explain how fractals
3633 are built. It can generate many different fractal types such as the Mandelbrot
3635 (home-page "https://www.gnu.org/software/xaos/")
3636 (license license:gpl2+)))
3638 (define-public hypre
3644 (uri (string-append "https://github.com/LLNL/hypre/archive/"
3645 "v" version ".tar.gz"))
3646 (file-name (string-append name "-" version ".tar.gz"))
3649 "0v515i73bvaz378h5465b1dy9v2gf924zy2q94cpq4qqarawvkqh"))
3650 (modules '((guix build utils)))
3653 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
3654 ;; substitute the tarball creation time.
3655 (substitute* "src/utilities/HYPRE_utilities.h"
3656 (("Date Compiled: .*$")
3657 "Date Compiled: Apr 11 2018 16:24:59 +0000\"\n"))
3659 (build-system gnu-build-system)
3660 (outputs '("out" ;6.1 MiB of headers and libraries
3661 "doc")) ;4.8 MiB of documentation
3665 ("perl" ,perl) ;needed to run 'ppmquant' during tests
3666 ("texlive" ,(texlive-union (list texlive-generic-xypic
3668 texlive-latex-hyperref
3669 texlive-latex-oberdiek
3670 texlive-generic-ifxetex
3673 ("ghostscript" ,ghostscript)))
3675 `(("blas" ,openblas)
3676 ("lapack" ,lapack)))
3678 `(#:modules ((srfi srfi-1)
3679 ,@%gnu-build-system-modules)
3680 #:configure-flags '("--enable-shared"
3688 (modify-phases %standard-phases
3689 (add-before 'build 'set-HOME
3691 ;; FIXME: texlive-union does not find the built
3692 ;; metafonts, so it tries to generate them in HOME.
3693 (setenv "HOME" "/tmp")
3695 (add-before 'configure 'chdir-src
3696 (lambda _ (chdir "src")))
3698 (lambda* (#:key build target configure-flags
3699 #:allow-other-keys #:rest args)
3700 (let* ((configure (assoc-ref %standard-phases 'configure)))
3703 (list #:configure-flags
3704 (cons (string-append
3705 "--host=" (or target build))
3706 configure-flags)))))))
3707 (add-after 'build 'build-docs
3709 (invoke "make" "-Cdocs" "pdf" "html")))
3712 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3713 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
3714 (and (system* "make" "check" "CHECKRUN=")
3715 (fold (lambda (filename result)
3717 (let ((size (stat:size (stat filename))))
3718 (when (not (zero? size))
3719 (format #t "~a size ~d; error indication~%"
3723 (find-files "test" ".*\\.err$")))))
3724 (add-after 'install 'install-docs
3725 (lambda* (#:key outputs #:allow-other-keys)
3726 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3727 (let* ((doc (assoc-ref outputs "doc"))
3728 (docdir (string-append doc "/share/doc/hypre-" ,version)))
3729 (with-directory-excursion "docs"
3730 (for-each (lambda (base)
3731 (install-file (string-append base ".pdf") docdir)
3732 (copy-recursively base docdir)) ;html docs
3733 '("HYPRE_usr_manual"
3734 "HYPRE_ref_manual")))
3736 (home-page "http://www.llnl.gov/casc/hypre/")
3737 (synopsis "Library of solvers and preconditioners for linear equations")
3739 "HYPRE is a software library of high performance preconditioners and
3740 solvers for the solution of large, sparse linear systems of equations. It
3741 features multigrid solvers for both structured and unstructured grid
3743 (license license:lgpl2.1)))
3745 (define-public hypre-openmpi
3746 (package (inherit hypre)
3747 (name "hypre-openmpi")
3750 ,@(package-inputs hypre)))
3752 (substitute-keyword-arguments (package-arguments hypre)
3753 ((#:configure-flags flags)
3755 ,@(delete "--without-MPI" ,flags)))
3757 `(modify-phases ,phases
3758 (add-before 'check 'mpi-setup
3759 ,%openmpi-setup)))))
3760 (synopsis "Parallel solvers and preconditioners for linear equations")
3762 "HYPRE is a software library of high performance preconditioners and
3763 solvers for the solution of large, sparse linear systems of equations on
3764 parallel computers. It features parallel multigrid solvers for both
3765 structured and unstructured grid problems.")))
3767 (define-public matio
3774 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
3775 "matio-" version ".tar.gz"))
3778 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3779 (build-system gnu-build-system)
3783 (home-page "http://matio.sourceforge.net/")
3784 (synopsis "Library for reading and writing MAT files")
3785 (description "Matio is a library for reading and writing MAT files. It
3786 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3787 (license license:bsd-2)))
3794 (origin (method url-fetch)
3795 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3796 "download/" version "/Vc-" version ".tar.gz"))
3799 "1zmlpn32jzb38smp3j834llmbix3whsrbw0h397qxysbw792kih8"))))
3800 (build-system cmake-build-system)
3803 '("-DBUILD_TESTING=ON"
3804 ;; By default, Vc will optimize for the CPU of the build machine.
3805 ;; Setting this to "none" makes it create portable binaries. See
3806 ;; "cmake/OptimizeForArchitecture.cmake".
3807 "-DTARGET_ARCHITECTURE=none")))
3808 (synopsis "SIMD vector classes for C++")
3809 (description "Vc provides portable, zero-overhead C++ types for explicitly
3810 data-parallel programming. It is a library designed to ease explicit
3811 vectorization of C++ code. Its types enable explicitly stating data-parallel
3812 operations on multiple values. The parallelism is therefore added via the type
3813 system. Vc has an intuitive API and provides portability between different
3814 compilers and compiler versions as well as portability between different vector
3815 instruction sets. Thus, an application written with Vc can be compiled for:
3818 @item SSE2 up to SSE4.2 or SSE4a
3821 @item NEON (in development)
3822 @item NVIDIA GPUs / CUDA (in development)
3824 (home-page "https://github.com/VcDevel/Vc")
3825 ;; "No support_???.cpp file exists for this architecture."
3826 (supported-systems '("x86_64-linux" "i686-linux"))
3827 (license license:bsd-3)))
3829 (define-public reducelcs
3830 ;; This is the last commit which is available upstream, no
3831 ;; release happened since 2010.
3832 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
3836 (version (string-append "1.0-" revision "." (string-take commit 7)))
3841 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
3843 (file-name (string-append name "-" version "-checkout"))
3846 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
3847 (build-system gnu-build-system)
3849 `(("openlibm" ,openlibm)))
3851 `(#:tests? #f ; no tests
3853 (modify-phases %standard-phases
3854 (delete 'configure) ; No configure script exists.
3855 (replace 'install ; No install phase exists.
3856 (lambda* (#:key outputs #:allow-other-keys)
3857 (let* ((out (assoc-ref outputs "out"))
3858 (bin (string-append out "/bin")))
3859 (install-file "Approximation" bin)
3860 (install-file "CollectResults" bin)
3861 (install-file "GenerateInstances" bin)
3863 (synopsis "Approximate Longest Commons Subsequence computation tool")
3865 "@code{reduceLCS} is an implementation of the Reduce-Expand
3866 algorithm for LCS. It is a fast program to compute the approximate
3867 Longest Commons Subsequence of a set of strings.")
3868 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
3869 (license license:gpl3+))))
3871 (define-public jacal
3878 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
3881 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
3882 (patches (search-patches "jacal-fix-texinfo.patch"))))
3883 (build-system gnu-build-system)
3886 (modify-phases %standard-phases
3887 (add-before 'build 'pre-build
3888 ;; Don't use upstream's script - it really doesn't fit into
3889 ;; Guix's functional paradigm.
3890 (lambda* (#:key inputs outputs #:allow-other-keys)
3891 (substitute* "Makefile"
3892 (("^install: install-script") "install: "))))
3893 (add-after 'install 'post-install
3894 ;; Instead, we provide our own simplified script.
3895 (lambda* (#:key inputs outputs #:allow-other-keys)
3896 (let ((wrapper (string-append (assoc-ref outputs "out")
3898 (format (open wrapper (logior O_WRONLY O_CREAT))
3899 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
3900 "-e '(slib:load \"~a/lib/jacal/math\") "
3903 (assoc-ref inputs "scm")
3904 (assoc-ref outputs "out"))
3905 (chmod wrapper #o555))))
3907 (lambda* (#:key inputs outputs #:allow-other-keys)
3908 (zero? (system* "./configure"
3909 (string-append "--prefix="
3910 (assoc-ref outputs "out")))))))))
3911 (inputs `(("scm" ,scm)))
3912 (native-inputs `(("unzip" ,unzip)
3913 ("texinfo" ,texinfo)))
3914 (synopsis "Symbolic mathematics system")
3915 (description "GNU JACAL is an interactive symbolic mathematics program based on
3916 Scheme. It manipulate and simplify a range of mathematical expressions such
3917 as equations, scalars, vectors, and matrices.")
3918 (home-page "https://www.gnu.org/software/jacal/")
3919 (license license:gpl3+)))
3925 (home-page "https://github.com/Z3Prover/z3")
3928 (uri (git-reference (url home-page)
3929 (commit (string-append "z3-" version))))
3930 (file-name (git-file-name name version))
3933 "014igqm5vwswz0yhz0cdxsj3a6dh7i79hvhgc3jmmmz3z0xm1gyn"))))
3934 (build-system gnu-build-system)
3937 (modify-phases %standard-phases
3938 (add-after 'unpack 'fix-compatability
3939 ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
3941 (substitute* "src/util/mpz.cpp"
3942 (("#include <immintrin.h>") ""))
3944 (add-before 'configure 'bootstrap
3947 (system* "python" "scripts/mk_make.py"))))
3948 ;; work around gnu-build-system's setting --enable-fast-install
3949 ;; (z3's `configure' is a wrapper around the above python file,
3950 ;; which fails when passed --enable-fast-install)
3952 (lambda* (#:key inputs outputs #:allow-other-keys)
3953 (invoke "./configure"
3954 (string-append "--prefix=" (assoc-ref outputs "out")))))
3955 (add-after 'configure 'change-directory
3959 (add-before 'check 'make-test-z3
3961 ;; Build the test suite executable.
3962 (zero? (system* "make" "test-z3" "-j"
3963 (number->string (parallel-job-count))))))
3966 ;; Run all the tests that don't require arguments.
3967 (zero? (system* "./test-z3" "/a")))))))
3970 ("python" ,python-wrapper)))
3971 (synopsis "Theorem prover")
3972 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
3973 theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
3974 (license license:expat)))
3976 (define-public elemental
3983 (url "https://github.com/elemental/Elemental.git")
3984 (commit (string-append "v" version))))
3985 (file-name (git-file-name name version))
3988 "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
3989 (build-system cmake-build-system)
3990 (home-page "http://libelemental.org")
3992 `(("gfortran" ,gfortran)))
3994 `(("blas" ,openblas)
3995 ("gfortran:lib" ,gfortran "lib")
4004 `(#:build-type "Release" ;default RelWithDebInfo not supported
4005 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
4006 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
4007 "-DEL_CACHE_WARNINGS:BOOL=YES"
4008 "-DEL_TESTS:BOOL=YES"
4009 "-DCMAKE_INSTALL_LIBDIR=lib"
4010 "-DGFORTRAN_LIB=gfortran")
4011 #:phases (modify-phases %standard-phases
4012 (add-before 'check 'mpi-setup
4014 (add-before 'check 'setup-tests
4016 ;; Parallelism is done at the MPI layer.
4017 (setenv "OMP_NUM_THREADS" "1")
4019 (add-after 'install 'remove-tests
4020 (lambda* (#:key outputs #:allow-other-keys)
4021 ;; Tests are installed, with no easy configuration
4022 ;; switch to prevent this, so delete them.
4023 (delete-file-recursively
4024 (string-append (assoc-ref outputs "out") "/bin"))
4026 (synopsis "Dense and sparse-direct linear algebra and optimization")
4027 (description "Elemental is a modern C++ library for distributed-memory
4028 dense and sparse-direct linear algebra, conic optimization, and lattice
4030 (license license:bsd-2)))
4032 (define-public mcrl2
4035 (version "201707.1.15162")
4038 (uri (string-append "http://www.mcrl2.org/download/devel/mcrl2-"
4043 "1ziww2fchsklm25hl9p2mngssxfh9w07nc114cncqaxfibqp2p8f"))))
4045 `(("subversion" ,subversion)))
4050 ("qtbase" ,qtbase)))
4051 (build-system cmake-build-system)
4052 (synopsis "Toolset for the mCRL2 formal specification language")
4054 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
4055 specification language for describing concurrent discrete event systems. Its
4056 toolset supports analysis and automatic verification, linearisation, simulation,
4057 state-space exploration and generation, and tools to optimise and analyse
4058 specifications. Also, state spaces can be manipulated, visualised and
4060 (home-page "https://mcrl2.org")
4061 (license license:boost1.0)))
4063 (define-public r-subplex
4070 (uri (cran-uri "subplex" version))
4073 "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
4074 (build-system r-build-system)
4076 `(("gfortran" ,gfortran)))
4077 (home-page "https://cran.r-project.org/web/packages/subplex")
4078 (synopsis "Unconstrained optimization using the subplex algorithm")
4079 (description "This package implements the Subplex optimization algorithm.
4080 It solves unconstrained optimization problems using a simplex method on
4081 subspaces. The method is well suited for optimizing objective functions that
4082 are noisy or are discontinuous at the solution.")
4083 (license license:gpl3+)))
4085 (define-public r-desolve
4092 (uri (cran-uri "deSolve" version))
4095 "0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"))))
4096 (properties `((upstream-name . "deSolve")))
4097 (build-system r-build-system)
4099 `(("gfortran" ,gfortran)))
4100 (home-page "https://desolve.r-forge.r-project.org/")
4101 (synopsis "Solvers for initial value problems of differential equations")
4102 (description "This package provides functions that solve initial
4103 value problems of a system of first-order ordinary differential equations (ODE),
4104 of partial differential equations (PDE), of differential algebraic equations
4105 (DAE), and of delay differential equations. The functions provide an interface
4106 to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
4107 to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
4108 the Runge-Kutta family with fixed or variable time steps. The package contains
4109 routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
4110 differential equations (PDE) that have been converted to ODEs by numerical
4112 (license license:gpl2+)))
4114 (define-public tcalc
4121 (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
4125 "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
4126 (build-system gnu-build-system)
4127 (synopsis "The terminal calculator")
4129 "The terminal calculator is a small program to help users of the GNU/Linux
4130 terminal do calculations simply and quickly. The formula to be calculated can
4131 be fed to @command{tcalc} through the command line.")
4132 (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
4133 (license license:gpl3+)))
4135 (define-public sundials
4142 (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
4143 "sundials-" version ".tar.gz"))
4146 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
4147 (build-system cmake-build-system)
4149 `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
4151 `(("fortran" ,gfortran) ;for fcmix
4153 ("suitesparse" ,suitesparse))) ;TODO: Add hypre
4155 `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
4156 "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
4157 "-DEXAMPLES_ENABLE_F77:BOOL=ON"
4158 "-DEXAMPLES_ENABLE_F90:BOOL=ON"
4159 "-DEXAMPLES_INSTALL:BOOL=OFF"
4161 "-DFCMIX_ENABLE:BOOL=ON"
4163 "-DKLU_ENABLE:BOOL=ON"
4164 ,(string-append "-DKLU_INCLUDE_DIR="
4165 (assoc-ref %build-inputs "suitesparse")
4167 ,(string-append "-DKLU_LIBRARY_DIR="
4168 (assoc-ref %build-inputs "suitesparse")
4170 (home-page "https://computation.llnl.gov/projects/sundials")
4171 (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
4172 (description "SUNDIALS is a family of software packages implemented with
4173 the goal of providing robust time integrators and nonlinear solvers that can
4174 easily be incorporated into existing simulation codes.")
4175 (license license:bsd-3)))
4177 (define-public sundials-openmpi
4178 (package (inherit sundials)
4179 (name "sundials-openmpi")
4182 ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
4183 ,@(package-inputs sundials)))
4185 (substitute-keyword-arguments (package-arguments sundials)
4186 ((#:configure-flags flags '())
4187 `(cons* "-DMPI_ENABLE:BOOL=ON"
4188 "-DPETSC_ENABLE:BOOL=ON"
4189 (string-append "-DPETSC_INCLUDE_DIR="
4190 (assoc-ref %build-inputs "petsc")
4192 (string-append "-DPETSC_LIBRARY_DIR="
4193 (assoc-ref %build-inputs "petsc")
4196 ((#:phases phases '%standard-phases)
4197 `(modify-phases ,phases
4198 (add-before 'check 'mpi-setup
4199 ,%openmpi-setup)))))
4200 (synopsis "SUNDIALS with OpenMPI support")))
4202 (define-public combinatorial-blas
4204 (name "combinatorial-blas")
4209 (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/"
4211 (match (string-split version #\.)
4212 ((major minor patch)
4213 (string-append major minor "_" patch))) ;e.g. "16_2"
4217 "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a"))
4218 (patches (search-patches "combinatorial-blas-awpm.patch"
4219 "combinatorial-blas-io-fix.patch"))))
4220 (build-system cmake-build-system)
4223 ("test-data" ,(origin
4225 (uri (string-append "https://people.eecs.berkeley.edu/~aydin/"
4226 "CombBLAS_FILES/testdata_combblas1.6.1.tgz"))
4229 "01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87"))))))
4231 `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
4232 "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL")
4233 #:parallel-tests? #f ;tests use 'mpiexec -n4'
4235 (modify-phases %standard-phases
4236 (add-before 'check 'mpi-setup
4238 (add-before 'check 'test-setup
4239 (lambda* (#:key inputs #:allow-other-keys)
4240 (setenv "OMP_NUM_THREADS" "2")
4241 (invoke "tar" "xf" (assoc-ref inputs "test-data")))))))
4242 (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/")
4243 (synopsis "Linear algebra primitives for graph analytics")
4244 (description "The Combinatorial BLAS (CombBLAS) is an extensible
4245 distributed-memory parallel graph library offering a small but powerful set of
4246 linear algebra primitives specifically targeting graph analytics.")
4248 license:gpl2+ ;include/psort/(funnel|sort)*.h
4249 license:x11 ;usort and psort
4250 license:bsd-3)))) ;CombBLAS and MersenneTwister.h
4252 (define-public dune-common
4254 (name "dune-common")
4259 (uri (string-append "https://dune-project.org/download/"
4260 version "/dune-common-" version ".tar.gz"))
4263 "019wcr1qf7jwyxx1y5y290wdlglylskvbb2m01ljkzcza2xnlmhw"))))
4264 (build-system cmake-build-system)
4267 (modify-phases %standard-phases
4268 (add-after 'build 'build-tests
4269 (lambda* (#:key make-flags #:allow-other-keys)
4270 (apply invoke "make" "build_tests" make-flags)))
4271 ;; These tests fail because they require a fully functional MPI
4273 (add-after 'unpack 'disable-failing-tests
4276 (string-append "--exclude-regex '("
4280 "remoteindicestest-mpi-2"
4283 "variablesizecommunicatortest"
4284 "variablesizecommunicatortest-mpi-2"
4285 "arithmetictestsuitetest"
4286 "assertandreturntest"
4287 "assertandreturntest_ndebug"
4290 "mpicollectivecommunication"
4291 "mpicollectivecommunication-mpi-2"
4293 "mpiguardtest-mpi-2"
4295 "mpihelpertest-mpi-2"
4297 "mpihelpertest2-mpi-2")
4304 ("openmpi" ,openmpi)
4305 ("openblas" ,openblas)
4307 ("superlu" ,superlu)))
4309 `(("gfortran" ,gfortran)
4310 ("pkg-config" ,pkg-config)))
4311 (home-page "https://dune-project.org/")
4312 (synopsis "Distributed and Unified Numerics Environment")
4313 (description "DUNE, the Distributed and Unified Numerics Environment is a
4314 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4315 grid-based methods. It supports the easy implementation of methods like
4316 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4317 Differences} (FD).")
4318 ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2.
4319 (license license:gpl2)))
4321 (define-public dune-geometry
4323 (name "dune-geometry")
4328 (uri (string-append "https://dune-project.org/download/"
4329 version "/dune-geometry-" version ".tar.gz"))
4332 "0hlaaxjyv9j05blasvb67sy02hd0w4g9znf68gdh3l731dd1aqbn"))))
4333 (build-system cmake-build-system)
4336 (modify-phases %standard-phases
4337 (add-after 'build 'build-tests
4338 (lambda* (#:key make-flags #:allow-other-keys)
4339 (apply invoke "make" "build_tests" make-flags))))))
4341 `(("dune-common" ,dune-common)
4342 ("openmpi" ,openmpi)
4344 ("openblas" ,openblas)
4346 ("python" ,python)))
4348 `(("gfortran" ,gfortran)
4349 ("pkg-config" ,pkg-config)))
4350 (home-page "https://dune-project.org/")
4351 (synopsis "Distributed and Unified Numerics Environment")
4352 (description "DUNE, the Distributed and Unified Numerics Environment is a
4353 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4354 grid-based methods. It supports the easy implementation of methods like
4355 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4358 This package contains the basic DUNE geometry classes.")
4359 ;; GPL version 2 with "runtime exception"
4360 (license license:gpl2)))
4362 (define-public dune-grid
4369 (uri (string-append "https://dune-project.org/download/"
4370 version "/dune-grid-" version ".tar.gz"))
4373 "1jp4vscm9yb9xg0lh7apzccfkhvgbnk652yahigmh3cvzpl4acd0"))))
4374 (build-system cmake-build-system)
4377 (modify-phases %standard-phases
4378 (add-after 'build 'build-tests
4379 (lambda* (#:key make-flags #:allow-other-keys)
4380 (apply invoke "make" "build_tests" make-flags)))
4381 ;; These tests fail because they require a fully functional MPI
4383 (add-after 'unpack 'disable-failing-tests
4386 (string-append "--exclude-regex '("
4390 "conformvolumevtktest"
4392 "nonconformboundaryvtktest"
4393 "subsamplingvtktest"
4399 "test-dgf-yasp-offset"
4401 "test-geogrid-yaspgrid"
4404 "testiteratorranges"
4405 "test-hierarchicsearch"
4406 "test-parallel-ug-mpi-2"
4407 "test-yaspgrid-backuprestore-equidistant"
4408 "test-yaspgrid-backuprestore-equidistant-mpi-2"
4409 "test-yaspgrid-backuprestore-equidistantoffset"
4410 "test-yaspgrid-backuprestore-equidistantoffset-mpi-2"
4411 "test-yaspgrid-backuprestore-tensor"
4412 "test-yaspgrid-backuprestore-tensor-mpi-2"
4413 "test-yaspgrid-tensorgridfactory"
4414 "test-yaspgrid-tensorgridfactory-mpi-2"
4415 "test-yaspgrid-yaspfactory-1d"
4416 "test-yaspgrid-yaspfactory-1d-mpi-2"
4417 "test-yaspgrid-yaspfactory-2d"
4418 "test-yaspgrid-yaspfactory-2d-mpi-2"
4419 "test-yaspgrid-yaspfactory-3d"
4420 "test-yaspgrid-yaspfactory-3d-mpi-2"
4421 "globalindexsettest"
4422 "persistentcontainertest"
4423 "structuredgridfactorytest"
4424 "tensorgridfactorytest"
4430 `(("dune-common" ,dune-common)
4431 ("dune-geometry" ,dune-geometry)
4434 ("openblas" ,openblas)
4435 ("openmpi" ,openmpi)
4436 ("python" ,python)))
4438 `(("gfortran" ,gfortran)
4439 ("pkg-config" ,pkg-config)))
4440 (home-page "https://dune-project.org/")
4441 (synopsis "Distributed and Unified Numerics Environment")
4442 (description "DUNE, the Distributed and Unified Numerics Environment is a
4443 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4444 grid-based methods. It supports the easy implementation of methods like
4445 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4448 This package contains the basic DUNE grid classes.")
4449 ;; GPL version 2 with "runtime exception"
4450 (license license:gpl2)))