1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2013, 2014, 2015, 2016, 2019 Andreas Enge <andreas@enge.fr>
3 ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
4 ;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
5 ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Eric Bavier <bavier@member.fsf.org>
6 ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
7 ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
8 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
9 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
10 ;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
11 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
12 ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
13 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
14 ;;; Copyright © 2016, 2018 Kei Kebreau <kkebreau@posteo.net>
15 ;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
16 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
17 ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
18 ;;; Copyright © 2017, 2018, 2019 Paul Garlick <pgarlick@tourbillion-technology.com>
19 ;;; Copyright © 2017 ng0 <ng0@n0.is>
20 ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
21 ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
22 ;;; Copyright © 2017, 2019 Arun Isaac <arunisaac@systemreboot.net>
23 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
24 ;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
25 ;;; Copyright © 2018, 2019 Jan Nieuwenhuizen <janneke@gnu.org>
26 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
27 ;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
28 ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
29 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
30 ;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
31 ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
32 ;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
33 ;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
34 ;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
35 ;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net>
37 ;;; This file is part of GNU Guix.
39 ;;; GNU Guix is free software; you can redistribute it and/or modify it
40 ;;; under the terms of the GNU General Public License as published by
41 ;;; the Free Software Foundation; either version 3 of the License, or (at
42 ;;; your option) any later version.
44 ;;; GNU Guix is distributed in the hope that it will be useful, but
45 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
46 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
47 ;;; GNU General Public License for more details.
49 ;;; You should have received a copy of the GNU General Public License
50 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
52 (define-module (gnu packages maths)
53 #:use-module (ice-9 regex)
54 #:use-module (ice-9 match)
55 #:use-module (gnu packages)
56 #:use-module ((guix licenses) #:prefix license:)
57 #:use-module (guix packages)
58 #:use-module (guix download)
59 #:use-module (guix git-download)
60 #:use-module (guix utils)
61 #:use-module ((guix build utils) #:select (alist-replace))
62 #:use-module (guix build-system cmake)
63 #:use-module (guix build-system gnu)
64 #:use-module (guix build-system python)
65 #:use-module (guix build-system r)
66 #:use-module (guix build-system ruby)
67 #:use-module (gnu packages algebra)
68 #:use-module (gnu packages audio)
69 #:use-module (gnu packages autotools)
70 #:use-module (gnu packages base)
71 #:use-module (gnu packages bison)
72 #:use-module (gnu packages boost)
73 #:use-module (gnu packages check)
74 #:use-module (gnu packages cmake)
75 #:use-module (gnu packages compression)
76 #:use-module (gnu packages curl)
77 #:use-module (gnu packages cyrus-sasl)
78 #:use-module (gnu packages documentation)
79 #:use-module (gnu packages elf)
80 #:use-module (gnu packages flex)
81 #:use-module (gnu packages fltk)
82 #:use-module (gnu packages fontutils)
83 #:use-module (gnu packages gettext)
84 #:use-module (gnu packages gcc)
85 #:use-module (gnu packages gd)
86 #:use-module (gnu packages ghostscript)
87 #:use-module (gnu packages graphviz)
88 #:use-module (gnu packages gtk)
89 #:use-module (gnu packages image)
90 #:use-module (gnu packages java)
91 #:use-module (gnu packages less)
92 #:use-module (gnu packages lisp)
93 #:use-module (gnu packages linux)
94 #:use-module (gnu packages logging)
95 #:use-module (gnu packages lua)
96 #:use-module (gnu packages gnome)
97 #:use-module (gnu packages guile)
98 #:use-module (gnu packages xorg)
99 #:use-module (gnu packages gl)
100 #:use-module (gnu packages imagemagick)
101 #:use-module (gnu packages m4)
102 #:use-module (gnu packages mpi)
103 #:use-module (gnu packages multiprecision)
104 #:use-module (gnu packages netpbm)
105 #:use-module (gnu packages onc-rpc)
106 #:use-module (gnu packages pcre)
107 #:use-module (gnu packages popt)
108 #:use-module (gnu packages perl)
109 #:use-module (gnu packages pkg-config)
110 #:use-module (gnu packages pulseaudio)
111 #:use-module (gnu packages python)
112 #:use-module (gnu packages python-web)
113 #:use-module (gnu packages python-xyz)
114 #:use-module (gnu packages qt)
115 #:use-module (gnu packages readline)
116 #:use-module (gnu packages ruby)
117 #:use-module (gnu packages tbb)
118 #:use-module (gnu packages scheme)
119 #:use-module (gnu packages shells)
120 #:use-module (gnu packages tcl)
121 #:use-module (gnu packages texinfo)
122 #:use-module (gnu packages tex)
123 #:use-module (gnu packages tls)
124 #:use-module (gnu packages version-control)
125 #:use-module (gnu packages wxwidgets)
126 #:use-module (gnu packages xml)
127 #:use-module (srfi srfi-1))
135 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
137 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
138 (build-system gnu-build-system)
139 (inputs `(("gtk+" ,gtk+)
140 ("libxml2" ,libxml2)))
141 (native-inputs `(("pkg-config" ,pkg-config)))
142 (synopsis "Natural deduction first-order logic interface")
143 (description "Aris is a program for performing logical proofs. It supports
144 propositional and predicate logic, as well as Boolean algebra and
145 arithmetical logic. In addition to its predefined inference and equivalence
146 rules, Aris also supports references to older proofs. Its use of standard
147 logical symbols and its natural deduction interface make it easy to use for
149 (license license:gpl3+)
150 (home-page "https://www.gnu.org/software/aris/")))
152 (define-public c-graph
158 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
161 "092412jzxy6wdvpk96pfj499hpmaww8xllavbvlqspfpr7ips9id"))))
162 (build-system gnu-build-system)
164 `(("fortran" ,gfortran)))
165 (synopsis "Visualizing and demonstrating convolution")
167 "GNU C-Graph is a tool for demonstrating the theory of convolution.
168 Thus, it can serve as an excellent aid to students of signal and systems
169 theory in visualizing the convolution process. Rather than forcing the
170 student to write code, the program offers an intuitive interface with
171 interactive dialogs to guide them.")
172 (license license:gpl3+)
173 (home-page "https://www.gnu.org/software/c-graph/")))
182 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
183 version "/coda-" version ".tar.gz"))
185 (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245"))
186 (patches (search-patches "coda-use-system-libs.patch"))
187 (modules '((guix build utils)))
189 ;; Make sure we don't use the bundled software.
191 (for-each (lambda (d)
192 (delete-file-recursively (string-append "libcoda/" d)))
193 '("zlib" "pcre" "expat"))
196 `(("fortran" ,gfortran)
198 ("python-numpy" ,python-numpy)))
205 (build-system gnu-build-system)
207 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
208 "LIBS= -lz -lpcre -lexpat")))
209 (synopsis "A common interface to various earth observation data formats")
211 "The Common Data Access toolbox (CODA) provides a set of interfaces for
212 reading remote sensing data from earth observation data files. It consists of
213 command line applications and interfaces to the C, Fortran, Python, and Java
214 programming languages.")
215 (home-page "https://stcorp.nl/coda")
216 (license license:gpl2+)))
224 (uri (string-append "http://www.qhull.org/download/qhull-"
225 (car (string-split version #\.))
229 "0dm4b2xr3asy6w74khq2zg4gf26zsy3qf9sq7pf7lmrvbj911c3q"))))
230 (build-system cmake-build-system)
231 (synopsis "Calculate convex hulls and related structures")
233 "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
234 diagram, halfspace intersection about a point, furthest-site Delaunay
235 triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d,
236 3-d, 4-d, and higher dimensions. @code{Qhull} implements the Quickhull
237 algorithm for computing the convex hull. It handles roundoff errors from
238 floating point arithmetic. It computes volumes, surface areas, and
239 approximations to the convex hull.
241 @code{Qhull} does not support triangulation of non-convex surfaces, mesh
242 generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
243 shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
245 (home-page "http://qhull.org")
246 (license (license:non-copyleft "file://COPYING.txt"
247 "See COPYING in the distribution."))))
249 (define-public python-cvxopt
251 (name "python-cvxopt")
256 (url "https://github.com/cvxopt/cvxopt.git")
258 (file-name (git-file-name name version))
261 "1kiy2m62xgs2d5id6dnnwy4vap85cd70p7pgkb9nh23qf9xnak7b"))))
262 (build-system python-build-system)
265 (modify-phases %standard-phases
266 (add-after 'unpack 'find-libraries
267 (lambda* (#:key inputs #:allow-other-keys)
268 (setenv "CVXOPT_BLAS_LIB" "openblas")
269 (setenv "CVXOPT_BUILD_FFTW" "1")
270 (setenv "CVXOPT_BUILD_GLPK" "1")
271 (setenv "CVXOPT_BUILD_GSL" "1")
278 ("openblas" ,openblas)
279 ("suitesparse" ,suitesparse)))
280 (home-page "https://www.cvxopt.org")
281 (synopsis "Python library for convex optimization")
283 "CVXOPT is a package for convex optimization based on the Python
284 programming language. Its main purpose is to make the development of software
285 for convex optimization applications straightforward by building on Python’s
286 extensive standard library and on the strengths of Python as a high-level
287 programming language.")
288 (license license:gpl3+)))
290 (define-public python2-cvxopt
291 (package-with-python2 python-cvxopt))
299 (uri (string-append "mirror://gnu/units/units-" version
302 "0mk562g7dnidjgfgvkxxpvlba66fh1ykmfd9ylzvcln1vxmi6qj2"))))
303 (build-system gnu-build-system)
305 `(("readline" ,readline)
306 ("python" ,python-wrapper) ;for 'units_cur' script
307 ("python-requests" ,python-requests)))
309 `(#:phases (modify-phases %standard-phases
310 (add-after 'install 'wrap-units_cur
311 (lambda* (#:key outputs #:allow-other-keys)
312 (let* ((out (assoc-ref outputs "out"))
313 (bin (string-append out "/bin")))
314 (wrap-program (string-append bin "/units_cur")
315 `("PYTHONPATH" ":" prefix
316 ,(search-path-as-string->list (getenv "PYTHONPATH"))))
318 (synopsis "Conversion between thousands of scales")
320 "GNU Units converts numeric quantities between units of measure. It
321 can handle scale changes through adaptive usage of standard scale
322 prefixes (micro-, kilo-, etc.). It can also handle nonlinear
323 conversions such as Fahrenheit to Celsius. Its interpreter is powerful
324 enough to be used effectively as a scientific calculator.")
325 (license license:gpl3+)
326 (home-page "https://www.gnu.org/software/units/")))
328 (define-public double-conversion
330 (name "double-conversion")
332 (home-page "https://github.com/google/double-conversion")
335 (uri (git-reference (url home-page)
336 (commit (string-append "v" version))))
337 (file-name (git-file-name name version))
340 "0csy4pjw1p8rp6g5qxi2h0ychhhp1fldv7gb761627fs2mclw9gv"))))
341 (build-system cmake-build-system)
343 '(#:test-target "test"
344 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
345 "-DBUILD_TESTING=ON")))
346 (synopsis "Conversion routines for IEEE doubles")
348 "The double-conversion library provides binary-decimal and decimal-binary
349 routines for IEEE doubles. The library consists of efficient conversion
350 routines that have been extracted from the V8 JavaScript engine.")
351 (license license:bsd-3)))
353 (define-public dionysus
359 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
363 "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
364 (build-system gnu-build-system)
365 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
366 (synopsis "Local search for universal constants and scientific values")
368 "GNU Dionysus is a convenient system for quickly retrieving the values of
369 mathematical constants used in science and engineering. Values can be
370 searched using a simple command-line tool, choosing from three databases:
371 universal constants, atomic numbers, and constants related to
373 (license license:gpl3+)
374 (home-page "https://www.gnu.org/software/dionysus/")))
382 (uri (string-append "mirror://gnu/gsl/gsl-"
386 "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
387 (patches (search-patches "gsl-test-i686.patch"))))
388 (build-system gnu-build-system)
390 `(;; Currently there are numerous tests that fail on "exotic"
391 ;; architectures such as aarch64 and ppc64le.
392 ,@(if (string-prefix? "aarch64-linux"
393 (or (%current-target-system) (%current-system)))
396 (home-page "https://www.gnu.org/software/gsl/")
397 (synopsis "Numerical library for C and C++")
399 "The GNU Scientific Library is a library for numerical analysis in C
400 and C++. It includes a wide range of mathematical routines, with over 1000
401 functions in total. Subject areas covered by the library include:
402 differential equations, linear algebra, Fast Fourier Transforms and random
404 (license license:gpl3+)))
413 (uri (string-append "mirror://gnu/glpk/glpk-"
417 "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
418 (build-system gnu-build-system)
422 `(#:configure-flags '("--with-gmp")))
423 (home-page "https://www.gnu.org/software/glpk/")
424 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
426 "GLPK is a C library for solving large-scale linear programming (LP),
427 mixed integer programming (MIP), and other related problems. It supports the
428 GNU MathProg modeling language, a subset of the AMPL language, and features a
429 translator for the language. In addition to the C library, a stand-alone
430 LP/MIP solver is included in the package.")
431 (license license:gpl3+)))
440 (uri (string-append "https://github.com/4ti2/4ti2/releases/download/"
442 (string-map (lambda (c) (if (char=? c #\.) #\_ c))
444 "/4ti2-" version ".tar.gz"))
446 (base32 "0rj92x6p9m3la5gasjbj7sa569im527ffmka5y2sv1amgd3fflrh"))))
447 (build-system gnu-build-system)
449 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
453 (home-page "http://www.4ti2.de/")
454 (synopsis "Mathematical tool suite for problems on linear spaces")
456 "4ti2 implements algorithms for solving algebraic, geometric and
457 combinatorial problems on linear spaces. Among others, it solves systems
458 of linear equations, computes extreme rays of polyhedral cones, solves
459 integer programming problems and computes Markov bases for statistics.")
460 (license license:gpl2+)))
462 (define-public cddlib
469 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
470 (string-delete #\. version) ".tar.gz"))
473 "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
474 (build-system gnu-build-system)
477 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
478 (synopsis "Library for convex hulls and extreme rays of polyhedra")
480 "The C-library cddlib implements the Double Description Method of
481 Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
482 rays of a general convex polyhedron given by a system of linear inequalities
483 in arbitrary dimension. It can also be used for the converse operation of
484 computing convex hulls.")
485 (license license:gpl2+)))
487 (define-public arpack-ng
491 (home-page "https://github.com/opencollab/arpack-ng")
494 (uri (git-reference (url home-page) (commit version)))
495 (file-name (git-file-name name version))
498 "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
499 (build-system gnu-build-system)
501 `(("autoconf" ,autoconf)
502 ("automake" ,automake)
503 ("libtool" ,libtool)))
506 ("fortran" ,gfortran)))
507 (synopsis "Fortran subroutines for solving eigenvalue problems")
509 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
510 large scale eigenvalue problems.")
511 (license (license:non-copyleft "file://COPYING"
512 "See COPYING in the distribution."))))
514 (define-public arpack-ng-3.3.0
518 (name (package-name arpack-ng))
519 (home-page (package-home-page arpack-ng))
523 (uri (string-append home-page "/archive/" version ".tar.gz"))
524 (file-name (string-append name "-" version ".tar.gz"))
527 "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
529 (define-public arpack-ng-openmpi
530 (package (inherit arpack-ng)
531 (name "arpack-ng-openmpi")
534 ,@(package-inputs arpack-ng)))
536 (substitute-keyword-arguments (package-arguments arpack-ng)
537 ((#:configure-flags _ '())
539 ((#:phases phases '%standard-phases)
540 `(modify-phases ,phases
541 (add-before 'check 'mpi-setup
543 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
545 (define-public lapack
552 (uri (string-append "http://www.netlib.org/lapack/lapack-"
556 "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
557 (build-system cmake-build-system)
558 (home-page "http://www.netlib.org/lapack/")
559 (inputs `(("fortran" ,gfortran)
560 ("python" ,python-2)))
562 `(#:configure-flags (list
563 "-DBUILD_SHARED_LIBS:BOOL=YES"
566 ;; Build the 'LAPACKE_clatms' functions.
567 "-DLAPACKE_WITH_TMG=ON")
569 (modify-phases %standard-phases
570 (add-before 'check 'patch-python
571 (lambda* (#:key inputs #:allow-other-keys)
572 (let ((python (assoc-ref inputs "python")))
573 (substitute* "lapack_testing.py"
574 (("/usr/bin/env python") python)))
576 (synopsis "Library for numerical linear algebra")
578 "LAPACK is a Fortran 90 library for solving the most commonly occurring
579 problems in numerical linear algebra.")
580 (license (license:non-copyleft "file://LICENSE"
581 "See LICENSE in the distribution."))))
583 (define-public scalapack
590 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
594 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))
595 (patches (search-patches "scalapack-blacs-mpi-deprecations.patch"))))
596 (build-system cmake-build-system)
599 ("fortran" ,gfortran)
600 ("lapack" ,lapack))) ;for testing only
602 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
603 #:phases (modify-phases %standard-phases
604 (add-before 'check 'mpi-setup
606 (home-page "http://www.netlib.org/scalapack/")
607 (synopsis "Library for scalable numerical linear algebra")
609 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
610 routines on parallel distributed memory machines. ScaLAPACK solves dense and
611 banded linear systems, least squares problems, eigenvalue problems, and
612 singular value problems.")
613 (license (license:non-copyleft "file://LICENSE"
614 "See LICENSE in the distribution."))))
616 (define-public gnuplot
622 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
626 (base32 "1vglp4la40f5dpj0zdj63zprrkyjgzy068p35bz5dqxjyczm1zlp"))))
627 (build-system gnu-build-system)
628 (inputs `(("readline" ,readline)
634 `(("pkg-config" ,pkg-config)
635 ("texlive" ,texlive-tiny)))
636 (arguments `(#:configure-flags (list (string-append
637 "--with-texdir=" %output
638 "/texmf-local/tex/latex/gnuplot"))))
639 (home-page "http://www.gnuplot.info")
640 (synopsis "Command-line driven graphing utility")
641 (description "Gnuplot is a portable command-line driven graphing
642 utility. It was originally created to allow scientists and students to
643 visualize mathematical functions and data interactively, but has grown to
644 support many non-interactive uses such as web scripting. It is also used as a
645 plotting engine by third-party applications like Octave.")
646 ;; X11 Style with the additional restriction that derived works may only be
647 ;; distributed as patches to the original.
648 (license (license:fsf-free
649 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
659 (url "https://github.com/OkoSanto/GCTP.git")
660 (commit (string-append "v" version))))
661 (file-name (git-file-name name version))
663 (base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
665 `(("fortran" ,gfortran)))
666 (build-system gnu-build-system)
667 (synopsis "General Cartographic Transformation Package (GCTP)")
669 "The General Cartographic Transformation Package (GCTP) is a system of
670 software routines designed to permit the transformation of coordinate pairs
671 from one map projection to another. The GCTP is the standard computer
672 software used by the National Mapping Division for map projection
674 (home-page "https://github.com/OkoSanto/GCTP")
675 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
684 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
685 version "/src/hdf-" version ".tar.bz2"))
687 (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l"))
688 (patches (search-patches "hdf4-architectures.patch"
689 "hdf4-reproducibility.patch"
690 "hdf4-shared-fortran.patch"
691 "hdf4-tirpc.patch"))))
692 (build-system gnu-build-system)
694 `(("gfortran" ,gfortran)
700 ("libtirpc" ,libtirpc)))
702 `(#:parallel-tests? #f
703 #:configure-flags (list "--enable-shared"
704 (string-append "CPPFLAGS=-I"
705 (assoc-ref %build-inputs "libtirpc")
708 (modify-phases %standard-phases
709 ;; This is inspired by two of Debian's patches.
710 (add-before 'configure 'add-more-aarch64-support
712 (substitute* '("mfhdf/ncgen/ncgen.l"
713 "mfhdf/ncgen/ncgenyy.c"
714 "mfhdf/libsrc/netcdf.h.in")
715 (("AIX5L64") "__aarch64__"))
717 (add-before 'configure 'patchbuild
720 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
722 (("/bin/mkdir") "mkdir"))
723 (substitute* (find-files "." "^Makefile\\.in$")
724 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
725 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
726 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
727 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
728 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
730 (add-after 'configure 'patch-settings
732 ;; libhdf4.settings contains the full path of the
733 ;; compilers used, and its contents are included in
734 ;; .so-files. We truncate the hashes to avoid
735 ;; unnecessary store references to those compilers:
736 (substitute* "libhdf4.settings"
737 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
738 (string-append prefix (string-take hash 10) "...")))
741 (home-page "https://www.hdfgroup.org/products/hdf4/")
743 "Library and multi-object file format for storing and managing data")
744 (description "HDF4 is a library and multi-object file format for storing
745 and managing data between machines. HDF4 is an older hierarchical data format,
746 incompatible with HDF5.")
748 (license:non-copyleft
749 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
751 (define-public hdf4-alt
756 (substitute-keyword-arguments (package-arguments hdf4)
757 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
759 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
768 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
769 "hdf5-" (version-major+minor version)
770 "/hdf5-" version "/src/hdf5-"
772 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
774 (match (string-split version #\.)
776 (string-append major minor)))
777 "/src/hdf5-" version ".tar.bz2")))
779 (base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5"))
780 (patches (search-patches "hdf5-config-date.patch"
781 "hdf5-1.8-mpi-deprecations.patch"))))
782 (build-system gnu-build-system)
786 `(("gfortran" ,gfortran)
787 ("perl" ,perl))) ;part of the test machinery needs Perl
788 (outputs '("out" ; core library
789 "fortran")) ; fortran interface
791 `(;; Some of the users, notably Flann, need the C++ interface.
792 #:configure-flags '("--enable-cxx"
794 "--enable-fortran2003"
796 ;; Build a thread-safe library. Unfortunately,
797 ;; 'configure' invites you to either turn off C++,
798 ;; Fortran, and the high-level interface (HL), or
799 ;; to pass '--enable-unsupported'. Debian
800 ;; packagers chose to pass '--enable-unsupported'
801 ;; and we follow their lead here.
802 "--enable-threadsafe"
804 "--enable-unsupported")
805 ;; Use -fPIC to allow the R bindings to link with the static libraries
806 #:make-flags (list "CFLAGS=-fPIC"
809 (modify-phases %standard-phases
810 (add-before 'configure 'patch-configure
811 (lambda* (#:key outputs #:allow-other-keys)
812 (substitute* "configure"
814 (substitute* "fortran/src/Makefile.in"
815 (("libhdf5_fortran_la_LDFLAGS =")
816 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
817 (assoc-ref outputs "fortran") "/lib")))
818 (substitute* "hl/fortran/src/Makefile.in"
819 (("libhdf5hl_fortran_la_LDFLAGS =")
820 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
821 (assoc-ref outputs "fortran") "/lib")))
823 (add-after 'configure 'patch-settings
825 ;; libhdf5.settings contains the full path of the
826 ;; compilers used, and its contents are included in
827 ;; libhdf5.so. We truncate the hashes to avoid
828 ;; unnecessary store references to those compilers:
829 (substitute* "src/libhdf5.settings"
830 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
831 (string-append prefix (string-take hash 10) "..."))
832 ;; Don't record the build-time kernel version to make the
833 ;; settings file reproducible.
834 (("Uname information:.*")
835 "Uname information: Linux\n"))
837 (add-after 'install 'patch-references
838 (lambda* (#:key inputs outputs #:allow-other-keys)
839 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
840 (zlib (assoc-ref inputs "zlib")))
841 (substitute* (find-files bin "h5p?cc")
843 (string-append "-L" zlib "/lib " lib)))
845 (add-after 'install 'split
846 (lambda* (#:key inputs outputs #:allow-other-keys)
847 ;; Move all fortran-related files
848 (let* ((out (assoc-ref outputs "out"))
849 (bin (string-append out "/bin"))
850 (lib (string-append out "/lib"))
851 (inc (string-append out "/include"))
852 (ex (string-append out "/share/hdf5_examples/fortran"))
853 (fort (assoc-ref outputs "fortran"))
854 (fbin (string-append fort "/bin"))
855 (flib (string-append fort "/lib"))
856 (finc (string-append fort "/include"))
857 (fex (string-append fort "/share/hdf5_examples/fortran")))
862 ;; Note: When built with --enable-parallel, the 'h5fc' file
863 ;; doesn't exist, hence this condition.
864 (when (file-exists? (string-append bin "/h5fc"))
865 (rename-file (string-append bin "/h5fc")
866 (string-append fbin "/h5fc")))
867 (for-each (lambda (file)
869 (string-append flib "/" (basename file))))
870 (find-files lib ".*fortran.*"))
871 (for-each (lambda (file)
873 (string-append finc "/" (basename file))))
874 (find-files inc ".*mod"))
875 (for-each (lambda (file)
877 (string-append fex "/" (basename file))))
878 (find-files ex ".*"))
879 (delete-file-recursively ex))
881 (home-page "http://www.hdfgroup.org")
882 (synopsis "Management suite for extremely large and complex data")
883 (description "HDF5 is a suite that makes possible the management of
884 extremely large and complex data collections.")
885 (license (license:x11-style
886 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
888 (define-public hdf5-1.10
889 (package (inherit hdf5)
894 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
895 "hdf5-" (version-major+minor version)
896 "/hdf5-" version "/src/hdf5-"
898 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
901 (take (string-split version #\.) 2))
902 "/src/hdf5-" version ".tar.bz2")))
904 (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
905 (patches (search-patches "hdf5-config-date.patch"
906 "hdf5-mpi-deprecations.patch"))))))
908 (define-public hdf-java
916 "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
917 version "/src/CMake-hdfjava-" version ".tar.gz"))
919 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
920 (modules '((guix build utils)))
921 (snippet ; Make sure we don't use the bundled sources and binaries.
923 (for-each delete-file
924 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
925 "HDF4.tar.gz" "HDF5.tar.gz"))
926 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
928 (build-system gnu-build-system)
930 `(("jdk" ,icedtea "jdk")
931 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
933 ("hamcrest-core" ,java-hamcrest-core)
934 ("junit" ,java-junit)
935 ("slf4j-simple" ,java-slf4j-simple)))
941 ("slf4j-api" ,java-slf4j-api)))
944 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
945 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
946 (assoc-ref %build-inputs "jdk") "/lib" )
947 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
948 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
951 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
952 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
953 (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
954 (string-append "JPEGLIB="
955 (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
959 (modify-phases %standard-phases
960 (add-before 'configure 'chdir-to-source
961 (lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
962 (add-before 'configure 'patch-build
963 (lambda* (#:key inputs outputs #:allow-other-keys)
964 (substitute* "configure"
965 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
966 (("/bin/cat") (which "cat")))
967 ;; Set classpath for compilation
968 (substitute* '("hdf/hdf5lib/Makefile.in"
969 "hdf/hdf5lib/exceptions/Makefile.in"
970 "hdf/hdflib/Makefile.in")
971 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
972 (string-append (assoc-ref inputs "slf4j-api")
973 "/share/java/slf4j-api.jar")))
974 ;; Replace outdated config.sub and config.guess:
975 (with-directory-excursion "config"
976 (for-each (lambda (file)
978 (string-append (assoc-ref inputs "automake")
980 ,(version-major+minor (package-version automake))
982 '("config.sub" "config.guess")))
984 ;; Fix embedded version number
985 (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
986 (substitute* "hdf/hdf5lib/H5.java"
988 (string-join hdf5version ", "))))
990 (mkdir-p (string-append (assoc-ref outputs "out")))
991 ;; Set classpath for tests
992 (let* ((build-dir (getcwd))
993 (lib (string-append build-dir "/lib"))
994 (jhdf (string-append lib "/jhdf.jar"))
995 (jhdf5 (string-append lib "/jhdf5.jar"))
998 (string-append (assoc-ref inputs i)
999 "/share/java/" i ".jar"))
1000 '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
1002 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
1004 (substitute* '("test/hdf5lib/Makefile.in"
1005 "test/hdf5lib/junit.sh.in"
1006 "examples/runExample.sh.in")
1008 (string-append (assoc-ref inputs "coreutils")
1011 (string-append (assoc-ref inputs "coreutils")
1013 (("CLASSPATH=[^\n]*")
1014 (string-append "CLASSPATH=" class-path)))
1015 (setenv "CLASSPATH" class-path))
1017 (add-before 'check 'build-examples
1019 (apply invoke `("javac"
1020 ,@(find-files "examples" ".*\\.java"))))))
1022 #:parallel-build? #f
1024 #:parallel-tests? #f ))
1025 (home-page "https://support.hdfgroup.org/products/java")
1026 (synopsis "Java interface for the HDF4 and HDF5 libraries")
1027 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
1028 the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
1031 ;; BSD-style license:
1032 (license (license:x11-style
1033 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
1034 /current/src/unpacked/COPYING"))))
1036 (define-public hdf-eos2
1043 (uri "ftp://edhs1.gsfc.nasa.gov\
1044 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
1046 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
1047 (patches (search-patches "hdf-eos2-remove-gctp.patch"
1048 "hdf-eos2-build-shared.patch"
1049 "hdf-eos2-fortrantests.patch"))))
1050 (build-system gnu-build-system)
1052 `(("gfortran" ,gfortran)))
1054 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
1055 ;; XXX: These inputs are really dependencies of hdf4.
1057 ("libjpeg" ,libjpeg)
1058 ("libtirpc" ,libtirpc)
1062 `( #:configure-flags '("--enable-install-include" "--enable-shared"
1063 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
1064 #:parallel-tests? #f))
1065 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
1066 (synopsis "HDF4-based data format for NASA's Earth Observing System")
1067 (description "HDF-EOS2 is a software library built on HDF4 which supports
1068 the construction of data structures used in NASA's Earth Observing
1069 System (Grid, Point and Swath).")
1071 ;; Source files carry a permissive license header.
1072 (license (license:non-copyleft home-page))))
1074 (define-public hdf-eos5
1080 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1081 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1084 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1085 (patches (search-patches "hdf-eos5-build-shared.patch"
1086 "hdf-eos5-remove-gctp.patch"
1087 "hdf-eos5-fix-szip.patch"
1088 "hdf-eos5-fortrantests.patch"))))
1090 `(("gfortran" ,gfortran)))
1091 (build-system gnu-build-system)
1097 `(#:configure-flags '("--enable-install-include" "--enable-shared"
1098 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1099 #:parallel-tests? #f))
1100 (synopsis "HDF5-based data format for NASA's Earth Observing System")
1102 "HDF-EOS5 is a software library built on HDF5 to support the construction
1103 of data structures used in NASA's Earth Observing System (Grid, Point and
1105 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1107 ;; Source files carry a permissive license header.
1108 (license (license:non-copyleft home-page))))
1110 (define-public hdf5-parallel-openmpi
1111 (package (inherit hdf5)
1112 (name "hdf5-parallel-openmpi")
1115 ,@(package-inputs hdf5)))
1117 (substitute-keyword-arguments (package-arguments hdf5)
1118 ((#:configure-flags flags)
1119 ``("--enable-parallel"
1120 ,@(delete "--enable-cxx"
1121 (delete "--enable-threadsafe" ,flags))))
1123 `(modify-phases ,phases
1124 (add-after 'build 'mpi-setup
1126 (add-before 'check 'patch-tests
1128 ;; OpenMPI's mpirun will exit with non-zero status if it
1129 ;; detects an "abnormal termination", i.e. any process not
1130 ;; calling MPI_Finalize(). Since the test is explicitly
1131 ;; avoiding MPI_Finalize so as not to have at_exit and thus
1132 ;; H5C_flush_cache from being called, mpirun will always
1133 ;; complain, so turn this test off.
1134 (substitute* "testpar/Makefile"
1135 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1136 (string-append front back "\n")))
1137 (substitute* "tools/h5diff/testph5diff.sh"
1138 (("/bin/sh") (which "sh")))
1140 (synopsis "Management suite for data with parallel IO support")))
1142 (define-public h5check
1149 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
1150 "h5check/src/h5check-" version ".tar.gz"))
1153 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1154 (build-system gnu-build-system)
1155 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
1156 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1157 (synopsis "HDF5 format checker")
1158 (description "@code{h5check} is a validation tool for verifying that an
1159 HDF5 file is encoded according to the HDF File Format Specification.")
1160 (license (license:x11-style "file://COPYING"))))
1168 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1173 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1174 (build-system cmake-build-system)
1175 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1176 (inputs `(("lapack" ,lapack)
1178 ;; FIXME: Even though the fonts are available dvips complains:
1179 ;; "Font cmmi10 not found; characters will be left blank."
1181 `(("texlive" ,texlive-tiny)
1182 ("ghostscript" ,ghostscript)
1183 ("doxygen" ,doxygen)))
1184 (home-page "http://itpp.sourceforge.net")
1185 (synopsis "C++ library of maths, signal processing and communication classes")
1186 (description "IT++ is a C++ library of mathematical, signal processing and
1187 communication classes and functions. Its main use is in simulation of
1188 communication systems and for performing research in the area of
1189 communications. The kernel of the library consists of generic vector and
1190 matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1191 similar to MATLAB, GNU Octave or SciPy.")
1192 (license license:gpl3+)))
1194 (define-public netcdf
1201 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1202 "netcdf-" version ".tar.gz"))
1205 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1206 (patches (search-patches "netcdf-date-time.patch"
1207 "netcdf-tst_h_par.patch"))))
1208 (build-system gnu-build-system)
1211 ("doxygen" ,doxygen)
1212 ("graphviz" ,graphviz)))
1214 `(("hdf4" ,hdf4-alt)
1217 ("libjpeg" ,libjpeg)))
1219 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
1221 #:phases (modify-phases %standard-phases
1222 (add-before 'configure 'fix-source-date
1224 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1225 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1226 ;; to '1st hour of the current day', and therefore makes the
1227 ;; package not reproducible.
1228 (substitute* "./configure"
1229 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1230 "date --date='@0'"))
1232 (add-after 'configure 'patch-settings
1234 ;; libnetcdf.settings contains the full filename of the compilers
1235 ;; used to build the library. We truncate the hashes of those
1236 ;; filenames to avoid unnecessary references to the corresponding
1238 (substitute* "libnetcdf.settings"
1239 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1240 (string-append prefix (string-take hash 10) "...")))
1243 #:parallel-tests? #f)) ;various race conditions
1244 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
1245 (synopsis "Library for scientific data")
1246 (description "NetCDF is an interface for scientific data access and a
1247 software library that provides an implementation of the interface. The netCDF
1248 library defines a machine-independent format for representing scientific data.
1249 Together, the interface, library, and format support the creation, access, and
1250 sharing of scientific data.")
1251 (license (license:x11-style "file://COPYRIGHT"))))
1253 (define-public netcdf-parallel-openmpi
1254 (package (inherit netcdf)
1255 (name "netcdf-parallel-openmpi")
1258 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1259 (package-inputs netcdf))))
1260 ;; TODO: Replace pkg-config references in nc-config with absolute references
1262 (substitute-keyword-arguments (package-arguments netcdf)
1263 ((#:configure-flags flags)
1264 `(cons* "CC=mpicc" "CXX=mpicxx"
1265 "--enable-parallel-tests"
1266 ;; Shared libraries not supported with parallel IO.
1267 "--disable-shared" "--with-pic"
1270 (define-public netcdf-fortran
1272 (name "netcdf-fortran")
1277 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1281 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1282 (build-system gnu-build-system)
1284 `(#:parallel-tests? #f))
1286 `(("netcdf" ,netcdf)))
1288 `(("gfortran" ,gfortran)))
1289 (synopsis "Fortran interface for the netCDF library")
1290 (description (package-description netcdf))
1291 (home-page (package-home-page netcdf))
1292 (license (package-license netcdf))))
1294 (define-public nlopt
1300 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1303 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1304 (build-system gnu-build-system)
1306 `(;; Shared libraries are not built by default. They are required to
1307 ;; build the Guile, Octave, and Python bindings.
1308 #:configure-flags '("--enable-shared")
1311 (modify-phases %standard-phases
1312 (add-before 'configure 'set-libnlopt-file-name
1313 (lambda* (#:key outputs #:allow-other-keys)
1314 ;; Make sure the Scheme module refers to the library by its
1315 ;; absolute file name (we cannot do that from a snippet
1316 ;; because the expansion of @libdir@ contains
1318 (let ((out (assoc-ref outputs "out")))
1319 (substitute* "swig/nlopt.scm.in"
1321 (string-append out "/lib/libnlopt")))
1323 (inputs `(("guile" ,guile-2.0)))
1324 (native-inputs `(("pkg-config" ,pkg-config)))
1325 (home-page "http://ab-initio.mit.edu/wiki/")
1326 (synopsis "Library for nonlinear optimization")
1327 (description "NLopt is a library for nonlinear optimization, providing a
1328 common interface for a number of different free optimization routines available
1329 online as well as original implementations of various other algorithms.")
1330 (license license:lgpl2.1+)))
1332 (define-public ipopt
1339 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1343 "07yn9rzdswjk8n246qq6ci9ssf2bcplkifcpsfz9j6cdxw9vgbkv"))
1344 (modules '((guix build utils)))
1346 ;; Make sure we don't use the bundled software.
1348 (delete-file-recursively "ThirdParty")
1350 (build-system gnu-build-system)
1352 '(#:phases (modify-phases %standard-phases
1353 (add-after 'install 'add--L-flags-in-ipopt.pc
1354 (lambda* (#:key inputs outputs #:allow-other-keys)
1355 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1356 ;; move it to "Libs.private" where it belongs, and add a
1357 ;; '-L' flag for LAPACK.
1358 (let ((out (assoc-ref outputs "out"))
1359 (lapack (assoc-ref inputs "lapack")))
1360 (substitute* (string-append out "/lib/pkgconfig/"
1362 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1363 (string-append "Libs: " before " " after "\n"
1364 "Libs.private: " before
1365 "-L" lapack "/lib -llapack -lblas "
1369 `(("gfortran" ,gfortran)))
1371 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
1372 `(("lapack" ,lapack))) ;for both libblas and liblapack
1373 (home-page "http://www.coin-or.org")
1374 (synopsis "Large-scale nonlinear optimizer")
1376 "The Interior Point Optimizer (IPOPT) is a software package for
1377 large-scale nonlinear optimization. It provides C++, C, and Fortran
1379 (license license:epl1.0)))
1387 (uri (string-append "https://www.coin-or.org/download/source/"
1388 "Clp/Clp-" version ".tgz"))
1391 "1wdg820g3iikf9344ijwsc8sy6c0m6im42bzzizm6rlmkvnmxhk9"))
1392 (modules '((guix build utils)))
1394 ;; Make sure we don't use the bundled software.
1396 (delete-file-recursively "ThirdParty")
1398 (build-system gnu-build-system)
1400 `(("gfortran" ,gfortran)
1401 ("pkg-config" ,pkg-config)))
1403 `(("openblas" ,openblas)))
1404 (home-page "https://www.coin-or.org")
1405 (synopsis "Linear programming solver")
1407 "CLP is a high quality linear programming solver. Its main strengths are
1408 its dual and primal Simplex algorithms. It also has a barrier algorithm for
1409 linear and quadratic objectives. There are limited facilities for nonlinear
1410 and quadratic objectives using the Simplex algorithm.")
1411 (license license:epl1.0)))
1413 (define-public ceres
1415 (name "ceres-solver")
1417 (home-page "http://ceres-solver.org/")
1420 (uri (string-append home-page "ceres-solver-"
1424 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
1425 (build-system cmake-build-system)
1427 ;; TODO: Build HTML user documentation and install separately.
1428 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
1429 "-DBUILD_SHARED_LIBS=ON")
1431 #:phases (modify-phases %standard-phases
1432 (add-before 'configure 'set-library-directory
1434 ;; Install libraries to lib/, not lib64/.
1435 (substitute* "internal/ceres/CMakeLists.txt"
1436 (("set\\(LIB_SUFFIX \"64\"\\)")
1437 "set(LIB_SUFFIX \"\")"))
1440 `(("pkg-config" ,pkg-config)))
1442 `(("glog" ,glog))) ;for #include <glog/glog.h>
1447 ("suitesparse" ,suitesparse)
1448 ("gflags" ,gflags)))
1449 (synopsis "C++ library for solving large optimization problems")
1451 "Ceres Solver is a C++ library for modeling and solving large,
1452 complicated optimization problems. It is a feature rich, mature and
1453 performant library which has been used in production since 2010. Ceres Solver
1454 can solve two kinds of problems:
1456 @item non-linear least squares problems with bounds constraints;
1457 @item general unconstrained optimization problems.
1459 (license license:bsd-3)))
1461 ;; For a fully featured Octave, users are strongly recommended also to install
1462 ;; the following packages: less, ghostscript, gnuplot.
1463 (define-public octave-cli
1470 (uri (string-append "mirror://gnu/octave/octave-"
1474 "11wwxpy2q1bhxs2v41bqn05i2sb0905cj1xil6mg8l4k2kka4cq6"))))
1475 (build-system gnu-build-system)
1477 `(("alsa-lib" ,alsa-lib)
1478 ("arpack" ,arpack-ng)
1483 ("fontconfig" ,fontconfig)
1484 ("freetype" ,freetype)
1488 ("graphicsmagick" ,graphicsmagick)
1491 ("libsndfile" ,libsndfile)
1495 ("portaudio" ,portaudio)
1497 ("readline" ,readline)
1498 ("suitesparse" ,suitesparse)
1499 ("texinfo" ,texinfo)
1503 ("gfortran" ,gfortran)
1504 ("pkg-config" ,pkg-config)
1506 ;; The following inputs are not actually used in the build process.
1507 ;; However, the ./configure gratuitously tests for their existence and
1508 ;; assumes that programs not present at build time are also not, and
1509 ;; can never be, available at run time! If these inputs are therefore
1510 ;; not present, support for them will be built out. However, Octave
1511 ;; will still run without them, albeit without the features they
1514 ("ghostscript" ,ghostscript)
1515 ("gnuplot" ,gnuplot)))
1516 ;; Octave code uses this variable to detect directories holding multiple CA
1517 ;; certificates to verify peers with. This is required for the networking
1518 ;; functions that require encryption to work properly.
1519 (native-search-paths
1520 (list (search-path-specification
1521 (variable "CURLOPT_CAPATH")
1522 (files '("etc/ssl/certs")))))
1525 (list (string-append "--with-shell="
1526 (assoc-ref %build-inputs "bash")
1529 (modify-phases %standard-phases
1530 (add-after 'configure 'configure-makeinfo
1531 (lambda* (#:key inputs #:allow-other-keys)
1532 (substitute* "libinterp/corefcn/help.h"
1535 "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
1537 (home-page "https://www.gnu.org/software/octave/")
1538 (synopsis "High-level language for numerical computation")
1539 (description "GNU Octave is a high-level interpreted language that is
1540 specialized for numerical computations. It can be used for both linear and
1541 non-linear applications and it provides great support for visualizing results.
1542 Work may be performed both at the interactive command-line as well as via
1544 (license license:gpl3+)))
1546 (define-public octave
1547 (package (inherit octave-cli)
1550 (inherit (package-source octave-cli))))
1552 `(("qscintilla" ,qscintilla)
1554 ,@(package-inputs octave-cli)))
1556 `(("qttools" , qttools) ;for lrelease
1557 ("texlive" ,(texlive-union (list texlive-epsf))) ; for texi2dvi
1558 ,@(package-native-inputs octave-cli)))
1560 (substitute-keyword-arguments (package-arguments octave-cli)
1562 `(modify-phases ,phases
1563 (add-before 'configure 'patch-qscintilla-library-name
1564 (lambda* (#:key inputs #:allow-other-keys)
1565 ;; The QScintilla library that the Octave configure script tries
1566 ;; to link with should be named libqscintilla-qt5.so, but the
1567 ;; QScintilla input provides the shared library as
1568 ;; libqscintilla2_qt5.so.
1569 (substitute* "configure"
1570 (("qscintilla2-qt5")
1574 (define-public qtoctave
1575 (deprecated-package "qtoctave" octave))
1577 (define-public opencascade-oce
1579 (name "opencascade-oce")
1585 (url "https://github.com/tpaviot/oce.git")
1586 (commit (string-append "OCE-" version))))
1587 (file-name (git-file-name name version))
1588 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
1590 (base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69"))))
1591 (build-system cmake-build-system)
1594 (list "-DOCE_TESTING:BOOL=ON"
1595 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1596 "-DOCE_DRAW:BOOL=ON"
1597 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1598 (assoc-ref %outputs "out"))
1599 "-UCMAKE_INSTALL_RPATH")))
1601 `(("freetype" ,freetype)
1608 `(("python" ,python-wrapper)))
1609 (home-page "https://github.com/tpaviot/oce")
1610 (synopsis "Libraries for 3D modeling and numerical simulation")
1612 "Open CASCADE is a set of libraries for the development of applications
1613 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1614 C++ class libraries providing services for 3D surface and solid modeling, CAD
1615 data exchange, and visualization. It is used for development of specialized
1616 software dealing with 3D models in design (CAD), manufacturing (CAM),
1617 numerical simulation (CAE), measurement equipment (CMM), and quality
1618 control (CAQ) domains.
1620 This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1621 patches, improvements, and experiments contributed by users over the official
1622 Open CASCADE library.")
1623 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1624 ; use of header files; see
1625 ; OCCT_LGPL_EXCEPTION.txt
1626 license:public-domain; files
1627 ; src/Standard/Standard_StdAllocator.hxx and
1628 ; src/NCollection/NCollection_StdAllocator.hxx
1629 license:expat; file src/OpenGl/OpenGl_glext.h
1630 license:bsd-3)))); test framework gtest
1632 (define-public opencascade-occt
1634 (name "opencascade-occt")
1640 (url "https://git.dev.opencascade.org/repos/occt.git")
1643 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
1645 (file-name (git-file-name name version))
1647 (base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4"))
1648 (modules '((guix build utils)))
1651 ;; Remove files specific to non-free operating systems.
1652 (delete-file-recursively "samples/ios")
1653 (delete-file-recursively "samples/mfc")
1654 (delete-file-recursively "samples/qt/FuncDemo")
1655 (delete-file "genconf.bat")
1656 (delete-file "gendoc.bat")
1657 (delete-file "genproj.bat")
1658 (delete-file "upgrade.bat")
1659 ;; Remove references to deleted files.
1660 (substitute* "dox/FILES_HTML.txt"
1661 ((".*standard.*") "" )
1662 ((".*UIKitSample.*") ""))
1664 (build-system cmake-build-system)
1666 '(;; There is no test target for make. OCCT provides an
1667 ;; 'Automated Testing System', which may be accessed after
1668 ;; installation via the draw.sh script. draw.sh is located in
1669 ;; the bin directory. For details see:
1670 ;; https://www.opencascade.com/doc/occt-7.3.0/overview/html/\
1671 ;; occt_dev_guides__tests.html
1673 ;; Configure without freeimage: attempting to link against the
1674 ;; freeimage version 3.17 library leads to 'undefined
1675 ;; reference' errors.
1677 (list "-DUSE_FREEIMAGE:BOOL=OFF"
1679 "-DUSE_VTK:BOOL=OFF"
1680 "-DBUILD_DOC_Overview:BOOL=OFF"
1681 "-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON"
1682 "-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON"
1683 "-UCMAKE_INSTALL_LIBDIR")))
1685 `(("doxygen" ,doxygen)
1686 ;("freeimage" ,freeimage)
1687 ("freetype" ,freetype)
1689 ("libxext" ,libxext)
1696 ;; TODO: build Overview documentation and add 'doc' output.
1697 (home-page "https://www.opencascade.com")
1698 (synopsis "Libraries for 3D modeling and numerical simulation")
1700 "Open CASCADE is a set of libraries for the development of applications
1701 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1702 C++ class libraries providing services for 3D surface and solid modeling, CAD
1703 data exchange, and visualization. It is used for development of specialized
1704 software dealing with 3D models in design (CAD), manufacturing (CAM),
1705 numerical simulation (CAE), measurement equipment (CMM), and quality
1706 control (CAQ) domains.
1708 This is the certified version of the Open Cascade Technology (OCCT) library.")
1709 (license (list ;; OCCT library:
1710 license:lgpl2.1; with an exception for the use of header
1711 ; files, see OCCT_LGPL_EXCEPTION.txt.
1712 ;; Files src/OpenGl/glext.h, adm/cmake/cotire.cmake and
1713 ;; src/OpenGl/OpenGl_HaltonSampler.hxx:
1715 ;; Files src/ExprIntrp/ExprIntrp.tab.* and
1716 ;; src/StepFile/step.tab.*:
1717 license:gpl3+ ; with Bison 2.2 exception.
1718 ;; File src/NCollection/NCollection_UtfIterator.lxx:
1719 (license:non-copyleft
1720 "https://www.unicode.org/license.html")
1721 ;; File src/NCollection/NCollection_StdAllocator.hxx:
1722 license:public-domain))))
1732 (url "https://gitlab.onelab.info/gmsh/gmsh.git")
1734 (string-append "gmsh_"
1735 (string-map (lambda (x) (if (eq? x #\.) #\_ x))
1737 (file-name (git-file-name name version))
1739 (base32 "08rq4jajwmlpivnm9yifz2jhaivnz065lnk0h2zv773nwl9wf162"))
1740 (modules '((guix build utils)))
1742 ;; Remove non-free METIS code
1744 (delete-file-recursively "contrib/Metis")
1746 (build-system cmake-build-system)
1749 ("gfortran" ,gfortran)
1755 ("opencascade-oce" ,opencascade-oce)
1757 ("libxext" ,libxext)))
1759 `(("fontconfig" ,fontconfig)
1760 ("libxft" ,libxft)))
1762 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1763 "-DENABLE_BUILD_SHARED:BOOL=ON"
1764 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
1765 (home-page "http://gmsh.info/")
1766 (synopsis "3D finite element grid generator")
1767 (description "Gmsh is a 3D finite element grid generator with a built-in
1768 CAD engine and post-processor. Its design goal is to provide a fast, light
1769 and user-friendly meshing tool with parametric input and advanced
1770 visualization capabilities. Gmsh is built around four modules: geometry,
1771 mesh, solver and post-processing. The specification of any input to these
1772 modules is done either interactively using the graphical user interface or in
1773 ASCII text files using Gmsh's own scripting language.")
1774 (license license:gpl2+)))
1776 (define-public maxflow
1779 ;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’,
1780 ;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’.
1785 (url "https://github.com/gerddie/maxflow.git")
1787 (file-name (git-file-name name version))
1790 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1791 (build-system cmake-build-system)
1792 (home-page "https://pub.ist.ac.at/~vnk/software.html")
1793 (synopsis "Library implementing Maxflow algorithm")
1794 (description "An implementation of the maxflow algorithm described in
1795 @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1796 Energy Minimization in Computer Vision.\n
1797 Yuri Boykov and Vladimir Kolmogorov.\n
1798 In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1800 (license license:gpl3+)))
1802 (define-public petsc
1809 ;; The *-lite-* tarball does not contain the *large* documentation
1810 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1811 "petsc-lite-" version ".tar.gz"))
1813 (base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx"))))
1814 (outputs '("out" ; libraries and headers
1815 "examples")) ; ~30MiB of examples
1816 (build-system gnu-build-system)
1818 `(("python" ,python-2)))
1820 `(("gfortran" ,gfortran)
1822 ("superlu" ,superlu)
1823 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1824 ;; leaving out opengl, as configuration seems to only be for mac
1827 `(#:test-target "test"
1828 #:parallel-build? #f ; build is parallel by default
1834 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1835 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1836 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
1838 (modify-phases %standard-phases
1840 ;; PETSc's configure script is actually a python script, so we can't
1841 ;; run it with bash.
1842 (lambda* (#:key outputs (configure-flags '())
1844 (let* ((prefix (assoc-ref outputs "out"))
1845 (flags `(,(string-append "--prefix=" prefix)
1846 ,@configure-flags)))
1847 (format #t "build directory: ~s~%" (getcwd))
1848 (format #t "configure flags: ~s~%" flags)
1849 (apply invoke "./configure" flags))))
1850 (add-after 'configure 'clean-local-references
1851 (lambda* (#:key outputs #:allow-other-keys)
1852 (let ((out (assoc-ref outputs "out")))
1853 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
1854 ;; Prevent build directory from leaking into compiled code
1856 ;; Scrub timestamp for reproducibility
1857 ((".*Libraries compiled on.*") ""))
1858 (substitute* (find-files "." "petscvariables")
1859 ;; Do not expose build machine characteristics, set to defaults.
1860 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1861 (("NPMAX = [:digit:]+") "NPMAX = 2"))
1863 (add-after 'install 'clean-install
1864 ;; Try to keep installed files from leaking build directory names.
1865 (lambda* (#:key inputs outputs #:allow-other-keys)
1866 (let ((out (assoc-ref outputs "out")))
1867 (substitute* (map (lambda (file)
1868 (string-append out "/lib/petsc/conf/" file))
1869 '("petscvariables"))
1871 ;; Make compiler references point to the store
1872 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
1873 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1874 (string-append "= " (which compiler))))
1875 ;; PETSc installs some build logs, which aren't necessary.
1876 (for-each (lambda (file)
1877 (let ((f (string-append out "/lib/petsc/conf/" file)))
1878 (when (file-exists? f)
1880 '("configure.log" "make.log" "gmake.log"
1881 "test.log" "error.log" "RDict.db"
1882 "PETScBuildInternal.cmake"
1883 ;; Once installed, should uninstall with Guix
1886 (add-after 'install 'move-examples
1887 (lambda* (#:key outputs #:allow-other-keys)
1888 (let* ((out (assoc-ref outputs "out"))
1889 (examples (assoc-ref outputs "examples"))
1890 (exdir (string-append out "/share/petsc/examples"))
1891 (exdir' (string-append examples "/share/petsc/examples")))
1892 (copy-recursively exdir exdir')
1893 (delete-file-recursively exdir)
1895 (home-page "http://www.mcs.anl.gov/petsc")
1896 (synopsis "Library to solve PDEs")
1897 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1898 data structures and routines for the scalable (parallel) solution of
1899 scientific applications modeled by partial differential equations.")
1900 (license (license:non-copyleft
1901 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1903 (define-public petsc-complex
1904 (package (inherit petsc)
1905 (name "petsc-complex")
1907 (substitute-keyword-arguments (package-arguments petsc)
1908 ((#:configure-flags cf)
1909 `(cons "--with-scalar-type=complex" ,cf))))
1910 (synopsis "Library to solve PDEs (with complex scalars)")))
1912 (define-public petsc-openmpi
1913 (package (inherit petsc)
1914 (name "petsc-openmpi")
1916 `(("hdf5" ,hdf5-parallel-openmpi)
1917 ("hypre" ,hypre-openmpi)
1919 ("mumps" ,mumps-openmpi)
1920 ("openmpi" ,openmpi)
1921 ("scalapack" ,scalapack)
1922 ("scotch" ,pt-scotch32)
1923 ,@(package-inputs petsc)))
1925 (substitute-keyword-arguments (package-arguments petsc)
1926 ((#:configure-flags cf)
1928 "--with-mpiexec=mpirun"
1931 "--with-scalapack=1"
1933 ,(string-append "--with-mpi-dir="
1934 (assoc-ref %build-inputs "openmpi"))
1935 ,(string-append "--with-hdf5-include="
1936 (assoc-ref %build-inputs "hdf5") "/include")
1937 ,(string-append "--with-hdf5-lib="
1938 (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
1939 ,@(delete "--with-mpi=0" ,cf)))
1941 `(modify-phases ,phases
1942 (add-before 'configure 'mpi-setup
1943 ,%openmpi-setup)))))
1944 (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
1946 (define-public petsc-complex-openmpi
1947 (package (inherit petsc-complex)
1948 (name "petsc-complex-openmpi")
1950 `(("openmpi" ,openmpi)
1951 ,@(package-inputs petsc-complex)))
1953 (substitute-keyword-arguments (package-arguments petsc-complex)
1954 ((#:configure-flags cf)
1955 ``("--with-mpiexec=mpirun"
1956 ,(string-append "--with-mpi-dir="
1957 (assoc-ref %build-inputs "openmpi"))
1958 ,@(delete "--with-mpi=0" ,cf)))
1960 `(modify-phases ,phases
1961 (add-before 'configure 'mpi-setup
1962 ,%openmpi-setup)))))
1963 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
1965 (define-public python-petsc4py
1967 (name "python-petsc4py")
1972 (uri (pypi-uri "petsc4py" version))
1975 "094hcnran0r2z1wlvmjswsz3ski1m9kqrl5l0ax8jjhnk55x0flh"))))
1976 (build-system python-build-system)
1979 (modify-phases %standard-phases
1980 (add-before 'build 'pre-build
1982 ;; Define path to PETSc installation.
1983 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
1985 (add-before 'check 'mpi-setup
1988 `(("petsc" ,petsc-openmpi)
1989 ("python-numpy" ,python-numpy)))
1990 (home-page "https://bitbucket.org/petsc/petsc4py/")
1991 (synopsis "Python bindings for PETSc")
1992 (description "PETSc, the Portable, Extensible Toolkit for
1993 Scientific Computation, is a suite of data structures and routines for
1994 the scalable (parallel) solution of scientific applications modeled by
1995 partial differential equations. It employs the MPI standard for all
1996 message-passing communication. @code{petsc4py} provides Python
1997 bindings to almost all functions of PETSc.")
1998 (license license:bsd-3)))
2000 (define-public python-kiwisolver
2002 (name "python-kiwisolver")
2006 (uri (pypi-uri "kiwisolver" version))
2009 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
2010 (build-system python-build-system)
2011 (home-page "https://github.com/nucleic/kiwi")
2012 (synopsis "Fast implementation of the Cassowary constraint solver")
2014 "Kiwi is an efficient C++ implementation of the Cassowary constraint
2015 solving algorithm. Kiwi has been designed from the ground up to be
2016 lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
2017 Cassowary solver with typical use cases gaining a 40x improvement. Memory
2018 savings are consistently > 5x.")
2019 (license license:bsd-3)))
2021 (define-public python2-kiwisolver
2022 (package-with-python2 python-kiwisolver))
2024 (define-public slepc
2031 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
2035 "1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8"))))
2036 (build-system gnu-build-system)
2038 `(("python" ,python-2)
2039 ("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
2041 `(("arpack" ,arpack-ng)
2042 ("gfortran" ,gfortran)))
2044 `(("petsc" ,petsc)))
2046 `(#:parallel-build? #f ;build is parallel by default
2048 `(,(string-append "--with-arpack-dir="
2049 (assoc-ref %build-inputs "arpack") "/lib"))
2050 #:make-flags ;honor (parallel-job-count)
2051 `(,(format #f "MAKE_NP=~a" (parallel-job-count))
2052 ,(string-append "PETSCCONFIGDIR="
2053 (assoc-ref %build-inputs "petsc:examples")
2054 "/share/petsc/examples/config"))
2056 (modify-phases %standard-phases
2058 ;; configure is a python script, so we can't run it with bash.
2059 (lambda* (#:key inputs outputs (configure-flags '())
2061 (let* ((prefix (assoc-ref outputs "out"))
2062 (flags `(,(string-append "--prefix=" prefix)
2063 ,@configure-flags)))
2064 (format #t "build directory: ~s~%" (getcwd))
2065 (format #t "configure flags: ~s~%" flags)
2066 (setenv "SLEPC_DIR" (getcwd))
2067 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
2068 (apply invoke "./configure" flags))))
2069 (add-after 'install 'delete-doc
2070 ;; TODO: SLEPc installs HTML documentation alongside headers in
2071 ;; $out/include. We'd like to move them to share/doc, but delete
2072 ;; them for now, as they are incomplete and installing the complete
2073 ;; documentation is difficult.
2074 (lambda* (#:key outputs #:allow-other-keys)
2075 (let* ((out (assoc-ref outputs "out")))
2076 (for-each delete-file (find-files out "\\.html$"))
2078 (add-after 'install 'clean-install
2079 ;; Clean up unnecessary build logs from installation.
2080 (lambda* (#:key outputs #:allow-other-keys)
2081 (let ((out (assoc-ref outputs "out")))
2082 (for-each (lambda (file)
2083 (let ((f (string-append out "/lib/slepc/conf/" file)))
2084 (when (file-exists? f)
2086 '("configure.log" "make.log" "gmake.log"
2087 "test.log" "error.log" "RDict.db"
2090 (home-page "http://slepc.upv.es")
2091 (synopsis "Scalable library for eigenproblems")
2092 (description "SLEPc is a software library for the solution of large sparse
2093 eigenproblems on parallel computers. It can be used for the solution of
2094 linear eigenvalue problems formulated in either standard or generalized form,
2095 as well as other related problems such as the singular value decomposition.
2096 The emphasis of the software is on methods and techniques appropriate for
2097 problems in which the associated matrices are sparse, for example, those
2098 arising after the discretization of partial differential equations.")
2099 (license license:bsd-2)))
2101 (define-public slepc-complex
2102 (package (inherit slepc)
2103 (name "slepc-complex")
2105 `(("petsc" ,petsc-complex)
2106 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
2107 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
2109 (define-public slepc-openmpi
2110 (package (inherit slepc)
2111 (name "slepc-openmpi")
2113 (substitute-keyword-arguments (package-arguments slepc)
2114 ((#:phases phases '%standard-phases)
2115 `(modify-phases ,phases
2116 (add-before 'check 'mpi-setup
2117 ,%openmpi-setup)))))
2120 ("arpack" ,arpack-ng-openmpi)
2121 ,@(alist-delete "arpack" (package-inputs slepc))))
2123 `(("petsc" ,petsc-openmpi)
2124 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
2125 (synopsis "Scalable library for eigenproblems (with MPI support)")))
2127 (define-public slepc-complex-openmpi
2128 (package (inherit slepc-openmpi)
2129 (name "slepc-complex-openmpi")
2131 `(("petsc" ,petsc-complex-openmpi)
2132 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
2133 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
2135 (define-public python-slepc4py
2137 (name "python-slepc4py")
2142 (uri (pypi-uri "slepc4py" version))
2145 "0x049dyc8frgh79fvvavf4vlbqp4mgm61nsaivzdav4316vvlv1j"))))
2146 (build-system python-build-system)
2149 (modify-phases %standard-phases
2150 (add-before 'build 'pre-build
2152 ;; Define path to PETSc installation.
2153 (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
2154 ;; Define path to SLEPc installation.
2155 (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
2157 (add-before 'check 'mpi-setup
2160 `(("python-numpy" ,python-numpy)
2161 ("python-petsc4py" ,python-petsc4py)
2162 ("slepc" ,slepc-openmpi)))
2163 (home-page "https://bitbucket.org/slepc/slepc4py/")
2164 (synopsis "Python bindings for SLEPc")
2165 (description "SLEPc, the Scalable Library for Eigenvalue Problem
2166 Computations, is based on PETSc, the Portable, Extensible Toolkit for
2167 Scientific Computation. It employs the MPI standard for all
2168 message-passing communication. @code{slepc4py} provides Python
2169 bindings to almost all functions of SLEPc.")
2170 (license license:bsd-3)))
2172 (define-public mumps
2179 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
2183 "0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r"))
2184 (patches (search-patches "mumps-build-parallelism.patch"
2185 "mumps-shared-libseq.patch"
2186 "mumps-shared-mumps.patch"
2187 "mumps-shared-pord.patch"))))
2188 (build-system gnu-build-system)
2190 `(("fortran" ,gfortran)
2191 ;; These are required for linking against mumps, but we let the user
2192 ;; declare the dependency.
2195 ("scotch" ,scotch)))
2197 `(#:modules ((ice-9 match)
2200 ,@%gnu-build-system-modules)
2202 (modify-phases %standard-phases
2204 (lambda* (#:key inputs #:allow-other-keys)
2205 (call-with-output-file "Makefile.inc"
2216 INCSEQ = -I$(topdir)/libseq
2217 LIBSEQ = $(topdir)/libseq/libmpiseq.a
2218 LIBSEQNEEDED = libseqneeded~;
2222 AR = ar vr # rules require trailing space, ugh...
2225 LIBBLAS = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[
2227 SCALAP = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~]
2228 LIBOTHERS = -pthread
2231 OPTF = -O2 -DALLOW_NON_INIT $(PIC)
2235 LIBS = $(SCALAP) $(LIBSEQ)
2236 LPORDDIR = $(topdir)/PORD/lib
2237 IPORD = -I$(topdir)/PORD/include
2238 LPORD = $(LPORDDIR)/libpord.a
2239 ORDERINGSF = -Dpord~@[
2241 IMETIS = -I$(METISDIR)/include
2242 LMETIS = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
2243 ORDERINGSF += -Dmetis~]~@[~:{
2245 ISCOTCH = -I$(SCOTCHDIR)/include
2246 LSCOTCH = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
2247 ORDERINGSF += ~a~}~]
2248 ORDERINGSC = $(ORDERINGSF)
2249 LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
2250 IORDERINGSF = $(ISCOTCH)
2251 IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
2252 (assoc-ref inputs "mpi")
2253 (assoc-ref inputs "blas")
2254 (assoc-ref inputs "scalapack")
2255 (assoc-ref inputs "metis")
2256 (match (list (assoc-ref inputs "pt-scotch")
2257 (assoc-ref inputs "scotch"))
2261 `((,scotch "" "-Dscotch")))
2264 "-lptesmumps -lptscotch -lptscotcherr "
2265 "-Dptscotch")))))))))
2267 ;; By default only the d-precision library is built. Make with "all"
2268 ;; target so that all precision libraries and examples are built.
2270 (invoke "make" "all"
2271 (format #f "-j~a" (parallel-job-count)))))
2273 ;; Run the simple test drivers, which read test input from stdin:
2274 ;; from the "real" input for the single- and double-precision
2275 ;; testers, and from the "cmplx" input for complex-precision
2276 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
2277 ;; package to prefix execution with "mpirun".
2278 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
2279 (with-directory-excursion "examples"
2282 (let ((tester (apply open-pipe*
2285 ,(string-append "./" prec
2287 (input (open-input-file
2288 (string-append "input_simpletest_" type))))
2290 (dump-port input tester)
2292 (zero? (close-pipe tester)))))
2294 '("real" "real" "cmplx" "cmplx")))))
2296 (lambda* (#:key outputs #:allow-other-keys)
2297 (let* ((out (assoc-ref outputs "out"))
2298 (libdir (string-append out "/lib")))
2299 (copy-recursively "lib" libdir)
2300 (copy-recursively "include" (string-append out "/include"))
2301 (when (file-exists? "libseq/libmpiseq.a")
2302 (install-file "libseq/libmpiseq.a" libdir))
2303 (when (file-exists? "libseq/libmpiseq.so")
2304 (install-file "libseq/libmpiseq.so" libdir))
2306 (home-page "http://mumps.enseeiht.fr")
2307 (synopsis "Multifrontal sparse direct solver")
2309 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
2310 sparse system of linear equations A x = b using Gaussian elimination.")
2311 (license license:cecill-c)))
2313 (define-public mumps-metis
2314 (package (inherit mumps)
2315 (name "mumps-metis")
2317 (alist-delete "scotch" (package-inputs mumps)))))
2319 (define-public mumps-openmpi
2320 (package (inherit mumps)
2321 (name "mumps-openmpi")
2324 ("scalapack" ,scalapack)
2325 ("pt-scotch" ,pt-scotch)
2326 ,@(alist-delete "scotch" (package-inputs mumps))))
2328 (substitute-keyword-arguments (package-arguments mumps)
2330 `(modify-phases ,phases
2331 (add-before 'check 'mpi-setup
2335 ((assoc-ref ,phases 'check)
2336 #:exec-prefix '("mpirun" "-n" "2"))))))))
2337 (synopsis "Multifrontal sparse direct solver (with MPI)")))
2339 (define-public mumps-metis-openmpi
2340 (package (inherit mumps-openmpi)
2341 (name "mumps-metis-openmpi")
2343 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
2345 (define-public ruby-asciimath
2347 (name "ruby-asciimath")
2352 (uri (rubygems-uri "asciimath" version))
2355 "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
2356 (build-system ruby-build-system)
2359 (modify-phases %standard-phases
2361 ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
2362 (add-after 'unpack 'patch-remove-spurious-backslashes
2364 (substitute* "spec/parser_spec.rb"
2369 `(("bundler" ,bundler)
2370 ("ruby-rspec" ,ruby-rspec)))
2371 (synopsis "AsciiMath parsing and conversion library")
2373 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
2374 easy-to-write markup language for mathematics.")
2375 (home-page "https://github.com/asciidoctor/asciimath")
2376 (license license:expat)))
2378 (define-public superlu
2385 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2386 "superlu_" version ".tar.gz"))
2388 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
2389 (modules '((guix build utils)))
2391 ;; Replace the non-free implementation of MC64 with a stub adapted
2394 (use-modules (ice-9 regex)
2396 (call-with-output-file "SRC/mc64ad.c"
2401 void mc64id_(int *a) {
2402 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2405 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2406 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2407 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2410 ;; Remove the corresponding license verbiage. MC64 license follows
2411 ;; a "------" line separator.
2412 (with-atomic-file-replacement "License.txt"
2413 (let ((rx (make-regexp "-{8}")))
2416 (let ((line (read-line in 'concat)))
2417 (unless (regexp-exec rx line)
2421 (build-system cmake-build-system)
2425 `(("blas" ,openblas)
2426 ("gfortran" ,gfortran)))
2428 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2429 "-DTPL_BLAS_LIBRARIES=openblas"
2430 "-DBUILD_SHARED_LIBS:BOOL=YES")))
2431 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
2432 (synopsis "Supernodal direct solver for sparse linear systems")
2434 "SuperLU is a general purpose library for the direct solution of large,
2435 sparse, nonsymmetric systems of linear equations on high performance machines.
2436 The library is written in C and is callable from either C or Fortran. The
2437 library routines perform an LU decomposition with partial pivoting and
2438 triangular system solves through forward and back substitution. The library
2439 also provides threshold-based ILU factorization preconditioners.")
2440 (license (list license:bsd-3
2441 license:gpl2+ ;EXAMPLE/*fgmr.c
2442 (license:fsf-free "file://SRC/colamd.h")))))
2444 (define-public superlu-dist
2446 (name "superlu-dist")
2451 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2452 "superlu_dist_" version ".tar.gz"))
2454 (base32 "0pqgcgh1yxhfzs99fas3mggajzd5wca3nbyp878rziy74gfk03dl"))
2455 (modules '((guix build utils)))
2457 ;; Replace the non-free implementation of MC64 with a stub
2459 (call-with-output-file "SRC/mc64ad_dist.c"
2464 void mc64id_dist(int *a) {
2465 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2468 void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2469 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2470 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2473 (substitute* "SRC/util.c" ;adjust default algorithm
2474 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
2475 ;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
2476 ;; general (i.e. non-square) processor-grid support.
2477 "RowPerm = NOROWPERM;"))
2479 (patches (search-patches "superlu-dist-scotchmetis.patch"
2480 "superlu-dist-awpm-grid.patch"
2481 "superlu-dist-fix-mpi-deprecations.patch"))))
2482 (build-system cmake-build-system)
2486 `(("gfortran" ,gfortran)
2489 ("combblas" ,combinatorial-blas)))
2491 `(("mpi" ,openmpi) ;headers include MPI heades
2492 ("parmetis" ,pt-scotch32 "metis")
2493 ("pt-scotch" ,pt-scotch32)))
2495 `(#:parallel-tests? #f ;tests use MPI and OpenMP
2496 #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
2497 "-DTPL_ENABLE_COMBBLASLIB=YES"
2498 "-DTPL_BLAS_LIBRARIES=-lopenblas"
2499 "-DTPL_LAPACK_LIBRARIES=-llapack"
2500 (string-append "-DTPL_PARMETIS_LIBRARIES="
2502 '("ptscotchparmetis" "ptscotch" "ptscotcherr"
2503 "scotchmetis" "scotch" "scotcherr")
2505 (string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
2506 (assoc-ref %build-inputs "parmetis")
2508 "-DTPL_ENABLE_COMBBLASLIB=ON"
2509 (string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
2510 (assoc-ref %build-inputs "combblas")
2511 "/include/CombBLAS;"
2512 (assoc-ref %build-inputs "combblas")
2513 "/include/BipartiteMatchings")
2514 "-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
2516 (modify-phases %standard-phases
2517 (add-before 'configure 'set-c++-standard
2519 (substitute* "CMakeLists.txt"
2520 ;; AWPM headers require C++14
2521 (("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
2522 (add-before 'check 'mpi-setup
2524 (add-before 'check 'omp-setup
2525 (lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
2526 (home-page (package-home-page superlu))
2527 (synopsis "Parallel supernodal direct solver")
2529 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2530 It is targeted for distributed memory parallel machines. SuperLU_DIST is
2531 implemented in ANSI C, and MPI for communications.")
2532 (license license:bsd-3)))
2534 (define-public scotch
2541 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
2542 "latestfile/298/scotch_" version ".tar.gz"))
2544 (base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8"))
2545 (patches (search-patches "scotch-build-parallelism.patch"
2546 "scotch-integer-declarations.patch"))))
2547 (build-system gnu-build-system)
2552 (outputs '("out" "metis"))
2554 `(#:make-flags (list (string-append "prefix=" %output))
2556 (modify-phases %standard-phases
2558 'unpack 'chdir-to-src
2559 (lambda _ (chdir "src") #t))
2563 (call-with-output-file "Makefile.inc"
2577 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2578 LDFLAGS = -lz -lm -lrt -lpthread
2580 LEX = flex -Pscotchyy -olex.yy.c
2585 YACC = bison -pscotchyy -y -b y
2587 '("COMMON_FILE_COMPRESS_GZ"
2589 "COMMON_RANDOM_FIXED_SEED"
2590 "INTSIZE64" ;use 'int64_t'
2591 ;; Prevents symbolc clashes with libesmumps
2593 ;; XXX: Causes invalid frees in superlu-dist tests
2595 ;; "SCOTCH_PTHREAD_NUMBER=2"
2596 "restrict=__restrict"))))
2598 (add-after 'build 'build-esmumps
2601 (format #f "-j~a" (parallel-job-count))
2603 (add-before 'install 'make-install-dirs
2604 (lambda* (#:key outputs #:allow-other-keys)
2605 (mkdir (assoc-ref outputs "out"))))
2606 (add-after 'install 'install-metis
2607 (lambda* (#:key outputs #:allow-other-keys)
2608 (let ((out (assoc-ref outputs "metis")))
2610 ;; metis files are not installed with 'make install'
2611 (for-each (lambda (f)
2612 (install-file f (string-append out "/include")))
2613 (find-files "../include/" ".*metis\\.h"))
2614 (for-each (lambda (f)
2615 (install-file f (string-append out "/lib")))
2616 (find-files "../lib/" ".*metis\\..*"))
2618 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
2619 (synopsis "Programs and libraries for graph algorithms")
2620 (description "SCOTCH is a set of programs and libraries which implement
2621 the static mapping and sparse matrix reordering algorithms developed within
2622 the SCOTCH project. Its purpose is to apply graph theory, with a divide and
2623 conquer approach, to scientific computing problems such as graph and mesh
2624 partitioning, static mapping, and sparse matrix ordering, in application
2625 domains ranging from structural mechanics to operating systems or
2627 ;; See LICENSE_en.txt
2628 (license license:cecill-c)))
2630 (define-public scotch32
2631 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2632 ;; some applications.
2633 (package (inherit scotch)
2636 (substitute-keyword-arguments (package-arguments scotch)
2637 ((#:phases scotch-phases)
2638 `(modify-phases ,scotch-phases
2642 (call-with-output-file "Makefile.inc"
2656 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2657 LDFLAGS = -lz -lm -lrt -lpthread
2659 LEX = flex -Pscotchyy -olex.yy.c
2664 YACC = bison -pscotchyy -y -b y
2666 '("COMMON_FILE_COMPRESS_GZ"
2668 "COMMON_RANDOM_FIXED_SEED"
2669 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
2670 ;; Prevents symbolc clashes with libesmumps
2672 ;; XXX: Causes invalid frees in superlu-dist tests
2674 ;; "SCOTCH_PTHREAD_NUMBER=2"
2675 "restrict=__restrict"))))))))))
2677 "Programs and libraries for graph algorithms (32-bit integers)")))
2679 (define-public pt-scotch
2680 (package (inherit scotch)
2683 `(("openmpi" ,openmpi))) ;Headers include MPI headers
2685 (substitute-keyword-arguments (package-arguments scotch)
2686 ((#:phases scotch-phases)
2687 `(modify-phases ,scotch-phases
2691 (invoke "make" (format #f "-j~a" (parallel-job-count))
2692 "ptscotch" "ptesmumps")
2694 ;; Install the serial metis compatibility library
2695 (invoke "make" "-C" "libscotchmetis" "install")))
2696 (add-before 'check 'mpi-setup
2700 (invoke "make" "ptcheck")))))))
2701 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
2703 (define-public pt-scotch32
2704 (package (inherit scotch32)
2705 (name "pt-scotch32")
2707 `(("openmpi" ,openmpi))) ;headers include MPI headers
2709 (substitute-keyword-arguments (package-arguments scotch32)
2710 ((#:phases scotch32-phases)
2711 `(modify-phases ,scotch32-phases
2714 (invoke "make" (format #f "-j~a" (parallel-job-count))
2715 "ptscotch" "ptesmumps")
2716 ;; Install the serial metis compatibility library
2717 (invoke "make" "-C" "libscotchmetis" "install")))
2718 (add-before 'check 'mpi-setup
2722 (invoke "make" "ptcheck")))))))
2724 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2726 (define-public metis
2733 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2734 "metis-" version ".tar.gz"))
2737 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2738 (build-system cmake-build-system)
2740 `(("blas" ,openblas)))
2742 `(#:tests? #f ;no tests
2743 #:configure-flags `("-DSHARED=ON"
2744 ,(string-append "-DGKLIB_PATH=" (getcwd)
2745 "/metis-" ,version "/GKlib"))))
2746 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2747 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2749 "METIS is a set of serial programs for partitioning graphs, partitioning
2750 finite element meshes, and producing fill-reducing orderings for sparse
2751 matrices. The algorithms implemented in METIS are based on the multilevel
2752 recursive-bisection, multilevel k-way, and multi-constraint partitioning
2754 (license license:asl2.0))) ;As of version 5.0.3
2756 (define-public p4est
2763 (uri (string-append "http://p4est.github.io/release/p4est-"
2767 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
2768 (build-system gnu-build-system)
2770 `(("fortran" ,gfortran)
2775 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2776 (assoc-ref %build-inputs "blas")
2778 ,(string-append "LAPACK_LIBS=-L"
2779 (assoc-ref %build-inputs "lapack")
2781 #:phases (modify-phases %standard-phases
2782 (add-before 'check 'mpi-setup
2784 (home-page "http://www.p4est.org")
2785 (synopsis "Adaptive mesh refinement on forests of octrees")
2787 "The p4est software library enables the dynamic management of a
2788 collection of adaptive octrees, conveniently called a forest of octrees.
2789 p4est is designed to work in parallel and scales to hundreds of thousands of
2791 (license license:gpl2+)))
2793 (define-public p4est-openmpi
2794 (package (inherit p4est)
2795 (name "p4est-openmpi")
2798 ,@(package-inputs p4est)))
2800 (substitute-keyword-arguments (package-arguments p4est)
2801 ((#:configure-flags cf)
2802 ``("--enable-mpi" ,@,cf))))
2803 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2805 (define-public gsegrafix
2812 (uri (string-append "mirror://gnu/" name "/" name "-"
2816 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2817 (build-system gnu-build-system)
2819 `(#:configure-flags '("LDFLAGS=-lm")))
2821 `(("libgnomecanvas" ,libgnomecanvas)
2822 ("libbonoboui" ,libbonoboui)
2823 ("libgnomeui" ,libgnomeui)
2824 ("libgnomeprintui" ,libgnomeprintui)
2827 `(("pkg-config" ,pkg-config)))
2828 (home-page "https://www.gnu.org/software/gsegrafix/")
2829 (synopsis "GNOME application to create scientific and engineering plots")
2830 (description "GSEGrafix is an application which produces high-quality graphical
2831 plots for science and engineering. Plots are specified via simple ASCII
2832 parameter files and data files and are presented in an anti-aliased GNOME
2833 canvas. The program supports rectangular two-dimensional plots, histograms,
2834 polar-axis plots and three-dimensional plots. Plots can be printed or saved
2835 to BMP, JPEG or PNG image formats.")
2836 (license license:gpl3+)))
2838 (define-public maxima
2845 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2846 version "-source/" name "-" version ".tar.gz"))
2849 "0xyahp4c6509haxh4n1swiqm3421gplkdisa0zypclh3252sbzfw"))
2850 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
2851 (build-system gnu-build-system)
2854 ("gnuplot" ,gnuplot) ;for plots
2856 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
2858 `(("texinfo" ,texinfo)
2860 ("python" ,python)))
2863 (list "--enable-gcl"
2864 (string-append "--with-posix-shell="
2865 (assoc-ref %build-inputs "bash")
2867 (string-append "--with-wish="
2868 (assoc-ref %build-inputs "tk")
2870 (let ((v ,(package-version tk)))
2871 (string-take v (string-index-right v #\.)))))
2872 ;; By default Maxima attempts to write temporary files to
2873 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2874 ;; Work around that.
2875 #:make-flags (list "TMPDIR=/tmp")
2877 (modify-phases %standard-phases
2878 (add-after 'unpack 'patch-paths
2879 (lambda* (#:key inputs #:allow-other-keys)
2880 (let* ((sed (string-append (assoc-ref inputs "sed") "/bin/sed"))
2881 (coreutils (assoc-ref inputs "coreutils"))
2882 (dirname (string-append coreutils "/bin/dirname"))
2883 (head (string-append coreutils "/bin/head"))
2884 (perl (string-append (assoc-ref inputs "perl") "/bin/perl"))
2885 (python (string-append (assoc-ref inputs "python")
2887 (substitute* "src/maxima.in"
2888 (("sed ") (string-append sed " "))
2889 (("dirname") dirname)
2891 (substitute* "doc/info/Makefile.in"
2892 (("/usr/bin/env perl") perl))
2893 (substitute* "doc/info/build_html.sh.in"
2894 (("python") python))
2896 (add-before 'check 'pre-check
2898 (chmod "src/maxima" #o555)
2902 ;; This is derived from the testing code in the "debian/rules" file
2903 ;; of Debian's Maxima package.
2904 ;; If Maxima can successfully run this, the binary to be installed
2910 "--batch-string=\"run_testsuite();\" "
2911 "| grep -q \"No unexpected errors found\""))))
2912 ;; Make sure the doc and emacs files are found in the
2913 ;; standard location. Also configure maxima to find gnuplot
2914 ;; without having it on the PATH.
2915 (add-after 'install 'post-install
2916 (lambda* (#:key outputs inputs #:allow-other-keys)
2917 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2918 (out (assoc-ref outputs "out"))
2919 (datadir (string-append out "/share/maxima/" ,version))
2920 (binutils (string-append (assoc-ref inputs "binutils")
2922 (with-directory-excursion out
2923 (mkdir-p "share/emacs")
2924 (mkdir-p "share/doc")
2926 (string-append datadir "/doc/")
2927 (string-append out "/share/doc/maxima"))
2928 (with-atomic-file-replacement
2929 (string-append datadir "/share/maxima-init.lisp")
2931 (format out "~a ~s~a~%"
2932 "(setf $gnuplot_command "
2933 (string-append gnuplot "/bin/gnuplot") ")")
2934 (dump-port in out))))
2935 ;; Ensure that Maxima will have access to the GNU binutils
2936 ;; components at runtime.
2937 (wrap-program (string-append out "/bin/maxima")
2938 `("PATH" prefix (,binutils))))
2940 (home-page "http://maxima.sourceforge.net")
2941 (synopsis "Numeric and symbolic expression manipulation")
2942 (description "Maxima is a system for the manipulation of symbolic and
2943 numerical expressions. It yields high precision numeric results by using
2944 exact fractions, arbitrary precision integers, and variable precision floating
2946 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2947 ;; Others simply say "GNU General Public License" without stating a
2948 ;; version (which implicitly means gpl1+).
2949 ;; At least one file (src/maxima.asd) says "version 2."
2950 ;; GPLv2 only is therefore the smallest subset.
2951 (license license:gpl2)))
2953 (define-public wxmaxima
2961 (url "https://github.com/wxMaxima-developers/wxmaxima.git")
2962 (commit (string-append "Version-" version))))
2963 (file-name (git-file-name name version))
2965 (base32 "16xizaddb27432n1083y89ir5zdqvllsgbwrzzk4jc2rw1ldxfsv"))))
2966 (build-system cmake-build-system)
2968 `(("gettext" ,gettext-minimal)))
2970 `(("wxwidgets" ,wxwidgets)
2973 ("adwaita-icon-theme" ,adwaita-icon-theme)
2975 ("shared-mime-info" ,shared-mime-info)))
2977 `(#:tests? #f ; no check target
2979 (modify-phases %standard-phases
2980 (add-after 'install 'wrap-program
2981 (lambda* (#:key inputs outputs #:allow-other-keys)
2982 (wrap-program (string-append (assoc-ref outputs "out")
2985 (,(string-append (assoc-ref inputs "maxima")
2987 ;; For GtkFileChooserDialog.
2988 `("GSETTINGS_SCHEMA_DIR" =
2989 (,(string-append (assoc-ref inputs "gtk+")
2990 "/share/glib-2.0/schemas")))
2991 `("XDG_DATA_DIRS" ":" prefix
2992 (;; Needed by gdk-pixbuf to know supported icon formats.
2994 (assoc-ref inputs "shared-mime-info") "/share")
2995 ;; The default icon theme of GTK+.
2997 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
2999 (home-page "https://andrejv.github.io/wxmaxima/")
3000 (synopsis "Graphical user interface for the Maxima computer algebra system")
3002 "wxMaxima is a graphical user interface for the Maxima computer algebra
3003 system. It eases the use of Maxima by making most of its commands available
3004 through a menu system and by providing input dialogs for commands that require
3005 more than one argument. It also implements its own display engine that
3006 outputs mathematical symbols directly instead of depicting them with ASCII
3009 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
3010 text and mathematical calculations to create documents, exporting of input and
3011 output to TeX, and a browser for Maxima's manual including command index and
3012 full text searching.")
3013 (license license:gpl2+)))
3015 (define-public armadillo
3021 (uri (string-append "mirror://sourceforge/arma/armadillo-"
3025 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
3026 (build-system cmake-build-system)
3027 (arguments `(#:tests? #f)) ; no test target
3029 `(("openblas" ,openblas)
3031 ("arpack" ,arpack-ng)))
3032 (home-page "http://arma.sourceforge.net/")
3033 (synopsis "C++ linear algebra library")
3035 "Armadillo is a C++ linear algebra library, aiming towards a good balance
3036 between speed and ease of use. It is useful for algorithm development
3037 directly in C++, or quick conversion of research code into production
3038 environments. It can be used for machine learning, pattern recognition,
3039 signal processing, bioinformatics, statistics, econometrics, etc. The library
3040 provides efficient classes for vectors, matrices and cubes, as well as 150+
3041 associated functions (eg. contiguous and non-contiguous submatrix views).")
3042 (license license:asl2.0)))
3044 (define-public muparser
3045 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
3046 ;; different hash. In order to make `guix package --upgrade` work correctly,
3047 ;; we set a Guix packaging revision.
3048 ;; When the next version of muparser is released, we can remove
3049 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
3050 (let ((upstream-version "2.2.5")
3054 (version (string-append upstream-version "-" revision))
3059 (url "https://github.com/beltoforion/muparser.git")
3060 (commit (string-append "v" upstream-version))))
3061 (file-name (git-file-name name version))
3063 (base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24"))))
3064 (build-system gnu-build-system)
3066 `(#:configure-flags '("--enable-samples=no")
3067 #:tests? #f)) ;no "check" target
3068 (home-page "http://muparser.beltoforion.de/")
3069 (synopsis "Fast parser library for mathematical expressions")
3071 "muParser is an extensible high performance math parser library. It is
3072 based on transforming an expression into a bytecode and precalculating constant
3074 (license license:expat))))
3076 (define-public openblas
3078 ;; TODO: Incorporate 'openblas/fixed-num-threads' changes on the next
3080 (replacement openblas/fixed-num-threads)
3087 (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
3088 version "%20version.tar.gz"))
3089 (file-name (string-append name "-" version ".tar.gz"))
3092 "1r2g9zzwq5dm8vjd19pxwggfvfzy56cvkmpmp5d014qr3svgmsap"))))
3093 (build-system gnu-build-system)
3095 `(#:test-target "test"
3096 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
3097 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
3098 ;; we need to disable substitutions.
3100 ,(let ((system (or (%current-target-system) (%current-system))))
3101 (or (string-prefix? "x86_64" system)
3102 (string-prefix? "i686" system)
3103 (string-prefix? "mips" system)
3104 (string-prefix? "aarch64" system)))
3106 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
3108 "MAKE_NB_JOBS=0" ;use jobserver for submakes
3109 ;; Build the library for all supported CPUs. This allows
3110 ;; switching CPU targets at runtime with the environment variable
3111 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
3112 ;; Unfortunately, this is not supported on non-x86 architectures,
3113 ;; where it leads to failed builds.
3114 ,@(let ((system (or (%current-target-system) (%current-system))))
3116 ((or (string-prefix? "x86_64" system)
3117 (string-prefix? "i686" system))
3118 '("DYNAMIC_ARCH=1"))
3119 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
3120 ;; two available MIPS targets special extended instructions
3121 ;; for Loongson cores are used.
3122 ((string-prefix? "mips" system)
3123 '("TARGET=SICORTEX"))
3124 ;; On aarch64 force the generic 'armv8-a' target
3125 ((string-prefix? "aarch64" system)
3128 ;; no configure script
3130 (modify-phases %standard-phases
3132 (add-before 'build 'set-extralib
3133 (lambda* (#:key inputs #:allow-other-keys)
3134 ;; Get libgfortran found when building in utest.
3136 (string-append "-L" (assoc-ref inputs "fortran-lib")
3140 `(("fortran-lib" ,gfortran "lib")))
3143 ("fortran" ,gfortran)
3145 (home-page "http://www.openblas.net/")
3146 (synopsis "Optimized BLAS library based on GotoBLAS")
3148 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
3149 (license license:bsd-3)))
3151 (define-public openblas-ilp64
3152 (package/inherit openblas
3153 (name "openblas-ilp64")
3154 (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
3156 (substitute-keyword-arguments (package-arguments openblas)
3157 ((#:make-flags flags '())
3158 `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
3160 (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
3161 (license license:bsd-3)))
3163 (define openblas/fixed-num-threads
3164 ;; TODO: Move that to 'openblas' proper on the next rebuild cycle.
3167 (version (match (string-split (package-version openblas) #\.)
3168 ((numbers ... (= string-length len))
3169 (string-join (append numbers
3170 (list (make-string len #\a)))
3173 (substitute-keyword-arguments (package-arguments openblas)
3174 ((#:make-flags flags ''())
3175 ;; This is the maximum number of threads OpenBLAS will ever use (that
3176 ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS
3177 ;; is used.) If we don't set it, the makefile sets it to the number
3178 ;; of cores of the build machine, which is obviously wrong.
3179 `(cons "NUM_THREADS=128" ,flags))))))
3181 (define* (make-blis implementation #:optional substitutable?)
3182 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
3183 source tree for a list of implementations.)
3185 SUBSTITUTABLE? determines whether the package is made available as a
3188 Currently the specialization must be selected at configure-time, but work is
3189 underway to allow BLIS to select the right optimized kernels at run time:
3190 <https://github.com/flame/blis/issues/129>."
3192 (name (if (string=? implementation "reference")
3194 (string-append "blis-" implementation)))
3196 (home-page "https://github.com/flame/blis")
3199 (uri (git-reference (url home-page) (commit version)))
3202 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
3203 (file-name (git-file-name "blis" version))))
3204 (build-system gnu-build-system)
3206 `(#:test-target "test"
3208 #:substitutable? ,substitutable?
3210 #:phases (modify-phases %standard-phases
3212 (lambda* (#:key outputs #:allow-other-keys)
3213 ;; This is a home-made 'configure' script.
3214 (let ((out (assoc-ref outputs "out")))
3215 (invoke "./configure" "-p" out
3219 "--enable-threading=openmp"
3222 (add-before 'check 'show-test-output
3224 ;; By default "make check" is silent. Make it verbose.
3225 (system "tail -F output.testsuite &")
3227 (synopsis "High-performance basic linear algebra (BLAS) routines")
3229 "BLIS is a portable software framework for instantiating high-performance
3230 BLAS-like dense linear algebra libraries. The framework was designed to
3231 isolate essential kernels of computation that, when optimized, immediately
3232 enable optimized implementations of most of its commonly used and
3233 computationally intensive operations. While BLIS exports a new BLAS-like API,
3234 it also includes a BLAS compatibility layer which gives application developers
3235 access to BLIS implementations via traditional BLAS routine calls.")
3236 (license license:bsd-3)))
3239 ;; This is the "reference" implementation, which is the non-optimized but
3240 ;; portable variant (no assembly).
3241 (make-blis "reference" #t))
3243 (define ignorance blis)
3245 (define-syntax-rule (blis/x86_64 processor)
3246 "Expand to a package specialized for PROCESSOR."
3248 (inherit (make-blis processor))
3249 (supported-systems '("x86_64-linux"))))
3251 (define-public blis-sandybridge
3252 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
3253 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
3254 (blis/x86_64 "sandybridge"))
3256 (define-public blis-haswell
3257 ;; BLIS specialized for Haswell processors (launched 2013):
3258 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
3259 (blis/x86_64 "haswell"))
3261 (define-public blis-knl
3262 ;; BLIS specialized for Knights Landing processor (launched 2016):
3263 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
3264 (blis/x86_64 "knl"))
3267 (define-public openlibm
3275 (url "https://github.com/JuliaLang/openlibm.git")
3276 (commit (string-append "v" version))))
3277 (file-name (git-file-name name version))
3279 (base32 "08wfchmmr5200fvmn1kwq9byc1fhsq46hn0y5k8scdl74771c7gh"))))
3280 (build-system gnu-build-system)
3283 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3285 ;; no configure script
3286 (modify-phases %standard-phases (delete 'configure))
3287 #:tests? #f)) ;the tests are part of the default target
3288 (home-page "http://openlibm.org/")
3289 (synopsis "Portable C mathematical library (libm)")
3291 "OpenLibm is an effort to have a high quality, portable, standalone C
3292 mathematical library (libm). It can be used standalone in applications and
3293 programming language implementations. The project was born out of a need to
3294 have a good libm for the Julia programming language that worked consistently
3295 across compilers and operating systems, and in 32-bit and 64-bit
3297 ;; Each architecture has its own make target, and there is none for mips.
3298 (supported-systems (delete "mips64el-linux" %supported-systems))
3299 ;; See LICENSE.md for details.
3300 (license (list license:expat
3303 license:public-domain
3304 license:lgpl2.1+))))
3306 (define-public openspecfun
3308 (name "openspecfun")
3314 (url "https://github.com/JuliaLang/openspecfun.git")
3315 (commit (string-append "v" version))))
3316 (file-name (git-file-name name version))
3318 (base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh"))))
3319 (build-system gnu-build-system)
3321 '(#:tests? #f ; no "check" target
3323 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3325 (modify-phases %standard-phases
3326 (delete 'configure)))) ; no configure script
3328 `(("fortran" ,gfortran)))
3329 (home-page "https://github.com/JuliaLang/openspecfun")
3330 (synopsis "Collection of special mathematical functions")
3332 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
3333 portable package for Bessel Functions of a Complex Argument and Nonnegative
3334 Order; it contains subroutines for computing Bessel functions and Airy
3335 functions. Faddeeva allows computing the various error functions of arbitrary
3336 complex arguments (Faddeeva function, error function, complementary error
3337 function, scaled complementary error function, imaginary error function, and
3338 Dawson function); given these, one can also easily compute Voigt functions,
3339 Fresnel integrals, and similar related functions as well.")
3340 ;; Faddeeva is released under the Expat license; AMOS is included as
3341 ;; public domain software.
3342 (license (list license:expat license:public-domain))))
3344 (define-public suitesparse
3346 (name "suitesparse")
3352 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
3356 "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
3357 (modules '((guix build utils)))
3359 ;; Remove bundled metis source
3361 (delete-file-recursively "metis-5.1.0")
3363 (build-system gnu-build-system)
3365 '(#:tests? #f ;no "check" target
3370 "MY_METIS_LIB=-lmetis"
3371 (string-append "INSTALL_LIB="
3372 (assoc-ref %outputs "out") "/lib")
3373 (string-append "INSTALL_INCLUDE="
3374 (assoc-ref %outputs "out") "/include")
3377 (modify-phases %standard-phases
3378 (delete 'configure)))) ;no configure script
3383 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
3384 (synopsis "Suite of sparse matrix software")
3386 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
3387 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
3388 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
3389 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
3390 CXSparse, a concise sparse Cholesky factorization package; and many other
3393 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
3395 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
3396 (license (list license:gpl2+ license:lgpl2.1+))))
3398 (define-public atlas
3404 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
3405 version "/atlas" version ".tar.bz2"))
3408 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
3409 (build-system gnu-build-system)
3410 (home-page "http://math-atlas.sourceforge.net/")
3411 (inputs `(("gfortran" ,gfortran)
3412 ("lapack-tar" ,(package-source lapack))))
3413 (outputs '("out" "doc"))
3414 ;; For the moment we drop support for MIPS at it fails to compile. See
3415 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
3416 (supported-systems (delete "mips64el-linux" %supported-systems))
3418 `(#:parallel-build? #f
3419 #:parallel-tests? #f
3421 ;; ATLAS tunes itself for the machine it is built on, as explained at
3422 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
3423 ;; For this reason, we want users to build it locally instead of using
3427 #:modules ((srfi srfi-26)
3428 (guix build gnu-build-system)
3431 `(;; Generate position independent code suitable for dynamic libraries
3432 ;; and use WALL timer to get more accurate timing.
3433 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
3436 ,,(if (string-match "64" (%current-system))
3439 ;; Disable parallel build as it gives errors: atlas_pthread.h is
3440 ;; needed to compile C files before it is generated.
3441 "-Ss" "pmake" "make -j 1"
3442 ;; Probe is failing for MIPS. We therefore define the system
3443 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3444 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3445 ,,@(if (string-prefix? "mips" (%current-system))
3446 (list "-A" "49" "-V" "1")
3448 ;; Generate shared libraries.
3450 ;; Build a full LAPACK library.
3451 ,(string-append "--with-netlib-lapack-tarfile="
3452 (assoc-ref %build-inputs "lapack-tar")))
3454 (modify-phases %standard-phases
3455 (add-after 'install 'install-doc
3456 (lambda* (#:key outputs inputs #:allow-other-keys)
3457 (let ((doc (string-append (assoc-ref outputs "doc")
3458 "/share/doc/atlas")))
3460 (for-each (cut install-file <> doc)
3461 (find-files "../ATLAS/doc" ".*"))
3463 (add-after 'check 'check-pt
3464 (lambda _ (invoke "make" "ptcheck")))
3465 ;; Fix files required to run configure.
3466 (add-before 'configure 'fix-/bin/sh
3468 ;; Use `sh', not `/bin/sh'.
3469 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3473 ;; Fix /bin/sh in generated make files.
3474 (add-after 'configure 'fix-/bin/sh-in-generated-files
3476 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3480 ;; ATLAS configure program does not accepts the default flags
3481 ;; passed by the 'gnu-build-system'.
3483 (lambda* (#:key native-inputs inputs outputs
3484 (configure-flags '())
3485 #:allow-other-keys #:rest args)
3486 (let* ((prefix (assoc-ref outputs "out"))
3487 (bash (or (and=> (assoc-ref
3488 (or native-inputs inputs) "bash")
3489 (cut string-append <> "/bin/bash"))
3491 (flags `(,(string-append "--prefix=" prefix)
3493 (abs-srcdir (getcwd))
3494 (srcdir (string-append "../" (basename abs-srcdir))))
3495 (format #t "source directory: ~s (relative from build: ~s)~%"
3499 (format #t "build directory: ~s~%" (getcwd))
3500 (format #t "configure flags: ~s~%" flags)
3502 (string-append srcdir "/configure")
3504 (synopsis "Automatically Tuned Linear Algebra Software")
3506 "ATLAS is an automatically tuned linear algebra software library
3507 providing C and Fortran77 interfaces to a portably efficient BLAS
3508 implementation, as well as a few routines from LAPACK.
3510 Optimization occurs at build time. For this reason, the library is built on
3511 the machine where it is installed, without resorting to pre-built substitutes.
3513 Before building the library, CPU throttling should be disabled. This can be
3514 done in the BIOS, or, on GNU/Linux, with the following command:
3517 # cpupower --governor performance
3520 Failure to do so will result in a library with poor performance.")
3521 (license license:bsd-3)))
3530 (uri (string-append "https://github.com/g-truc/glm/releases/download/"
3531 version "/glm-" version ".zip"))
3533 (base32 "1l0pi1qi37mk6s0yrkrw07lspv4gcqnr9ryg3521hrl77ff37dwx"))
3534 (patches (search-patches "glm-restore-install-target.patch"))))
3535 (build-system cmake-build-system)
3537 `(("unzip" ,unzip)))
3538 (home-page "https://glm.g-truc.net/")
3539 (synopsis "OpenGL Mathematics library")
3540 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3541 library for graphics software based on the OpenGL Shading Language (GLSL)
3543 (license license:expat)))
3545 (define-public lpsolve
3552 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3553 "/lp_solve_" version "_source.tar.gz"))
3556 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
3557 (modules '((guix build utils)))
3560 (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3562 ;; Pretend to be on a 64 bit platform to obtain a common directory
3563 ;; name for the build results on all architectures; nothing else
3564 ;; seems to depend on it.
3565 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3567 ;; The check for 'isnan' as it is written fails with
3568 ;; "non-floating-point argument in call to function
3569 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3570 ;; definition, which in turn leads to bad things. Fix the feature
3572 (("isnan\\(0\\)") "isnan(0.)"))
3574 (build-system gnu-build-system)
3576 `(#:tests? #f ; no check target
3578 (modify-phases %standard-phases
3579 (delete 'configure) ; no configure script
3582 (with-directory-excursion "lpsolve55"
3583 (invoke "bash" "ccc"))
3584 (with-directory-excursion "lp_solve"
3585 (invoke "bash" "ccc"))
3588 (lambda* (#:key outputs #:allow-other-keys)
3589 (let* ((out (assoc-ref outputs "out"))
3590 (bin (string-append out "/bin"))
3591 (lib (string-append out "/lib"))
3592 ;; This is where LibreOffice expects to find the header
3593 ;; files, and where they are installed by Debian.
3594 (include (string-append out "/include/lpsolve")))
3595 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3596 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
3597 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3599 ;; Install a subset of the header files as on Debian
3600 ;; (plus lp_bit.h, which matches the regular expression).
3601 (for-each (lambda (name)
3602 (install-file name include))
3603 (find-files "." "lp_[HMSa-z].*\\.h$"))
3604 (with-directory-excursion "shared"
3605 (for-each (lambda (name)
3606 (install-file name include))
3607 (find-files "." "\\.h$")))
3609 (home-page "http://lpsolve.sourceforge.net/")
3610 (synopsis "Mixed integer linear programming (MILP) solver")
3612 "lp_solve is a mixed integer linear programming solver based on the
3613 revised simplex and the branch-and-bound methods.")
3614 (license license:lgpl2.1+)))
3616 (define-public dealii
3623 (uri (string-append "https://github.com/dealii/dealii/releases/"
3624 "download/v" version "/dealii-" version ".tar.gz"))
3627 "0xhjv0gzswpjbc43xbrpwfc5848g508l01855nszx3g5gwzlhnzw"))
3628 (modules '((guix build utils)))
3630 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
3632 (delete-file-recursively "bundled")
3634 (build-system cmake-build-system)
3642 ("arpack" ,arpack-ng)
3643 ("muparser" ,muparser)
3644 ("gfortran" ,gfortran)
3645 ("suitesparse" ,suitesparse))) ;for UMFPACK
3647 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
3649 ;; Work around a bug in libsuitesparseconfig linking
3650 ;; see https://github.com/dealii/dealii/issues/4745
3651 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
3652 (home-page "https://www.dealii.org")
3653 (synopsis "Finite element library")
3655 "Deal.II is a C++ program library targeted at the computational solution
3656 of partial differential equations using adaptive finite elements. The main
3657 aim of deal.II is to enable rapid development of modern finite element codes,
3658 using among other aspects adaptive meshes and a wide array of tools often used
3659 in finite element programs.")
3660 (license license:lgpl2.1+)))
3662 (define-public dealii-openmpi
3663 (package (inherit dealii)
3664 (name "dealii-openmpi")
3667 ;;Supported only with MPI:
3668 ("hdf5" ,hdf5-parallel-openmpi) ;TODO: have petsc-openmpi propagate?
3669 ("p4est" ,p4est-openmpi)
3670 ("petsc" ,petsc-openmpi)
3671 ("slepc" ,slepc-openmpi)
3672 ("metis" ,metis) ;for MUMPS
3673 ("scalapack" ,scalapack) ;for MUMPS
3674 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3675 ("arpack" ,arpack-ng-openmpi)
3676 ,@(fold alist-delete (package-inputs dealii)
3677 '("p4est" "arpack"))))
3679 (substitute-keyword-arguments (package-arguments dealii)
3680 ((#:configure-flags cf)
3681 `(cons "-DDEAL_II_WITH_MPI:BOOL=ON"
3683 ((#:phases phases '%standard-phases)
3684 `(modify-phases ,phases
3685 (add-before 'check 'mpi-setup
3686 ,%openmpi-setup)))))
3687 (synopsis "Finite element library (with MPI support)")))
3689 (define-public flann
3698 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3699 version "-src.zip"))
3702 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
3703 (patches (search-patches "flann-cmake-3.11.patch"))))
3704 (build-system cmake-build-system)
3706 "octave")) ;46 MiB .mex file that pulls Octave
3708 `(("unzip" ,unzip)))
3711 ("octave" ,octave-cli)
3712 ("python" ,python-2) ; print syntax
3713 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3716 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3717 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3718 #:strip-directories '("lib" "lib64" "libexec"
3719 "bin" "sbin" "share/flann/octave")
3721 ;; Save 12 MiB by not installing .a files. Passing
3722 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3723 #:phases (modify-phases %standard-phases
3724 (add-before 'configure 'set-octave-directory
3725 (lambda* (#:key outputs #:allow-other-keys)
3726 ;; Install the .mex file in the "octave" output.
3727 (let ((out (assoc-ref outputs "octave")))
3728 (substitute* "src/matlab/CMakeLists.txt"
3729 (("share/flann/octave")
3730 (string-append out "/share/flann/octave")))
3732 (add-after 'install 'remove-static-libraries
3733 (lambda* (#:key outputs #:allow-other-keys)
3734 (let* ((out (assoc-ref outputs "out"))
3735 (lib (string-append out "/lib")))
3736 (for-each delete-file
3737 (find-files lib "\\.a$"))
3740 #:tests? #f)) ; The test data are downloaded from the Internet.
3741 (home-page "http://www.cs.ubc.ca/research/flann/")
3742 (synopsis "Library for approximate nearest neighbors computation")
3743 (description "FLANN is a library for performing fast approximate
3744 nearest neighbor searches in high dimensional spaces. It implements a
3745 collection of algorithms and a system for automatically choosing the best
3746 algorithm and optimum parameters depending on the dataset.
3748 FLANN is written in C++ and contains bindings for C, Octave and Python.")
3749 (license (license:non-copyleft "file://COPYING"
3750 "See COPYING in the distribution."))))
3752 (define-public wcalc
3759 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3760 "wcalc-" version ".tar.bz2"))
3763 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3764 (build-system gnu-build-system)
3767 ("readline" ,readline)))
3768 (home-page "http://w-calc.sourceforge.net/index.php")
3769 (synopsis "Flexible command-line scientific calculator")
3770 (description "Wcalc is a very capable calculator. It has standard functions
3771 (sin, asin, and sinh for example, in either radians or degrees), many
3772 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3773 variables, a command history, hex/octal/binary input and output, unit
3774 conversions, embedded comments, and an expandable expression entry field. It
3775 evaluates expressions using the standard order of operations.")
3776 (license license:gpl2+)))
3784 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3785 "/xaos-" version ".tar.gz"))
3788 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3789 (build-system gnu-build-system)
3790 (native-inputs `(("gettext" ,gettext-minimal)))
3791 (inputs `(("libx11" ,libx11)
3796 `(#:tests? #f ;no "check" target
3797 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3798 (synopsis "Real-time fractal zoomer")
3799 (description "GNU XaoS is a graphical program that generates fractal
3800 patterns and allows you to zoom in and out of them infinitely in a fluid,
3801 continuous manner. It also includes tutorials that help to explain how fractals
3802 are built. It can generate many different fractal types such as the Mandelbrot
3804 (home-page "https://www.gnu.org/software/xaos/")
3805 (license license:gpl2+)))
3807 (define-public hypre
3815 (url "https://github.com/LLNL/hypre.git")
3816 (commit (string-append "v" version))))
3817 (file-name (git-file-name name version))
3819 (base32 "1lvh4ybqkriyqfg2zmic6mrg1981qv1i9vry1fdgsabn81hb71g4"))
3820 (modules '((guix build utils)))
3823 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
3824 ;; substitute the release date.
3825 (substitute* "src/utilities/HYPRE_utilities.h"
3826 (("Date Compiled: .*$")
3827 "Date Compiled: Oct 19 2018 15:23:00 +0000\"\n"))
3829 (build-system gnu-build-system)
3830 (outputs '("out" ; 6.1 MiB of headers and libraries
3831 "doc")) ; 4.8 MiB of documentation
3835 ("perl" ,perl) ; needed to run 'ppmquant' during tests
3836 ("texlive" ,(texlive-union (list texlive-xypic
3838 texlive-latex-hyperref
3840 ("ghostscript" ,ghostscript)))
3842 `(("blas" ,openblas)
3843 ("lapack" ,lapack)))
3845 `(#:modules ((srfi srfi-1)
3846 ,@%gnu-build-system-modules)
3847 #:configure-flags '("--enable-shared"
3855 (modify-phases %standard-phases
3856 (add-before 'build 'set-HOME
3858 ;; FIXME: texlive-union does not find the built
3859 ;; metafonts, so it tries to generate them in HOME.
3860 (setenv "HOME" "/tmp")
3862 (add-before 'configure 'chdir-src
3863 (lambda _ (chdir "src")))
3865 (lambda* (#:key build target configure-flags
3866 #:allow-other-keys #:rest args)
3867 (let* ((configure (assoc-ref %standard-phases 'configure)))
3870 (list #:configure-flags
3871 (cons (string-append
3872 "--host=" (or target build))
3873 configure-flags)))))))
3874 (add-after 'build 'build-docs
3876 (invoke "make" "-Cdocs" "pdf" "html")))
3879 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3880 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
3881 (invoke "make" "check" "CHECKRUN=")
3882 (for-each (lambda (filename)
3883 (let ((size (stat:size (stat filename))))
3884 (when (positive? size)
3885 (error (format #f "~a size ~d; error indication~%"
3887 (find-files "test" ".*\\.err$"))
3889 (add-after 'install 'install-docs
3890 (lambda* (#:key outputs #:allow-other-keys)
3891 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3892 (let* ((doc (assoc-ref outputs "doc"))
3893 (docdir (string-append doc "/share/doc/hypre-" ,version)))
3894 (with-directory-excursion "docs"
3895 (for-each (lambda (base)
3896 (install-file (string-append base ".pdf") docdir)
3897 (copy-recursively base docdir)) ; html docs
3898 '("HYPRE_usr_manual"
3899 "HYPRE_ref_manual")))
3901 (home-page "http://www.llnl.gov/casc/hypre/")
3902 (synopsis "Library of solvers and preconditioners for linear equations")
3904 "HYPRE is a software library of high performance preconditioners and
3905 solvers for the solution of large, sparse linear systems of equations. It
3906 features multigrid solvers for both structured and unstructured grid
3908 (license license:lgpl2.1)))
3910 (define-public hypre-openmpi
3911 (package (inherit hypre)
3912 (name "hypre-openmpi")
3915 ,@(package-inputs hypre)))
3917 (substitute-keyword-arguments (package-arguments hypre)
3918 ((#:configure-flags flags)
3920 ,@(delete "--without-MPI" ,flags)))
3922 `(modify-phases ,phases
3923 (add-before 'check 'mpi-setup
3924 ,%openmpi-setup)))))
3925 (synopsis "Parallel solvers and preconditioners for linear equations")
3927 "HYPRE is a software library of high performance preconditioners and
3928 solvers for the solution of large, sparse linear systems of equations on
3929 parallel computers. It features parallel multigrid solvers for both
3930 structured and unstructured grid problems.")))
3932 (define-public matio
3939 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
3940 "matio-" version ".tar.gz"))
3943 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3944 (build-system gnu-build-system)
3948 (home-page "http://matio.sourceforge.net/")
3949 (synopsis "Library for reading and writing MAT files")
3950 (description "Matio is a library for reading and writing MAT files. It
3951 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3952 (license license:bsd-2)))
3959 (origin (method url-fetch)
3960 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3961 "download/" version "/Vc-" version ".tar.gz"))
3964 "17qili8bf8r78cng65yf4qmgna8kiqjqbgcqbric6v9j6nkhkrk8"))))
3965 (build-system cmake-build-system)
3968 '("-DBUILD_TESTING=ON"
3969 ;; By default, Vc will optimize for the CPU of the build machine.
3970 ;; Setting this to "none" makes it create portable binaries. See
3971 ;; "cmake/OptimizeForArchitecture.cmake".
3972 "-DTARGET_ARCHITECTURE=none")
3973 #:phases (modify-phases %standard-phases
3974 (add-after 'unpack 'copy-testdata
3975 (lambda* (#:key inputs native-inputs #:allow-other-keys)
3976 (let ((testdata (assoc-ref (or native-inputs inputs)
3978 (copy-recursively testdata "tests/testdata")
3981 `(("virtest" ,virtest)
3983 ;; This is a submodule in the git project, but not part of the
3984 ;; released sources. See the git branch for the commit to take.
3985 ("testdata" ,(let ((commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3"))
3989 (url "https://github.com/VcDevel/vc-testdata")
3990 (commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3")))
3991 (file-name (git-file-name "vc-testdata"
3992 (string-take commit 7)))
3995 "1hkhqib03qlcq412ym2dciynfxcdr2ygqhnplz4l1vissr1wnqn2")))))))
3996 (synopsis "SIMD vector classes for C++")
3997 (description "Vc provides portable, zero-overhead C++ types for explicitly
3998 data-parallel programming. It is a library designed to ease explicit
3999 vectorization of C++ code. Its types enable explicitly stating data-parallel
4000 operations on multiple values. The parallelism is therefore added via the type
4001 system. Vc has an intuitive API and provides portability between different
4002 compilers and compiler versions as well as portability between different vector
4003 instruction sets. Thus, an application written with Vc can be compiled for:
4006 @item SSE2 up to SSE4.2 or SSE4a
4009 @item NEON (in development)
4010 @item NVIDIA GPUs / CUDA (in development)
4012 (home-page "https://github.com/VcDevel/Vc")
4013 ;; "No support_???.cpp file exists for this architecture."
4014 (supported-systems '("x86_64-linux" "i686-linux"))
4015 (license license:bsd-3)))
4017 (define-public reducelcs
4018 ;; This is the last commit which is available upstream, no
4019 ;; release happened since 2010.
4020 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
4024 (version (string-append "1.0-" revision "." (string-take commit 7)))
4029 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
4031 (file-name (string-append name "-" version "-checkout"))
4034 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
4035 (build-system gnu-build-system)
4037 `(("openlibm" ,openlibm)))
4039 `(#:tests? #f ; no tests
4041 (modify-phases %standard-phases
4042 (delete 'configure) ; No configure script exists.
4043 (replace 'install ; No install phase exists.
4044 (lambda* (#:key outputs #:allow-other-keys)
4045 (let* ((out (assoc-ref outputs "out"))
4046 (bin (string-append out "/bin")))
4047 (install-file "Approximation" bin)
4048 (install-file "CollectResults" bin)
4049 (install-file "GenerateInstances" bin)
4051 (synopsis "Approximate Longest Commons Subsequence computation tool")
4053 "@code{reduceLCS} is an implementation of the Reduce-Expand
4054 algorithm for LCS. It is a fast program to compute the approximate
4055 Longest Commons Subsequence of a set of strings.")
4056 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
4057 (license license:gpl3+))))
4059 (define-public jacal
4066 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
4069 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
4070 (patches (search-patches "jacal-fix-texinfo.patch"))))
4071 (build-system gnu-build-system)
4074 (modify-phases %standard-phases
4075 (add-before 'build 'pre-build
4076 ;; Don't use upstream's script - it really doesn't fit into
4077 ;; Guix's functional paradigm.
4078 (lambda* (#:key inputs outputs #:allow-other-keys)
4079 (substitute* "Makefile"
4080 (("^install: install-script") "install: "))))
4081 (add-after 'install 'post-install
4082 ;; Instead, we provide our own simplified script.
4083 (lambda* (#:key inputs outputs #:allow-other-keys)
4084 (let ((wrapper (string-append (assoc-ref outputs "out")
4086 (format (open wrapper (logior O_WRONLY O_CREAT))
4087 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
4088 "-e '(slib:load \"~a/lib/jacal/math\") "
4091 (assoc-ref inputs "scm")
4092 (assoc-ref outputs "out"))
4093 (chmod wrapper #o555))))
4095 (lambda* (#:key outputs #:allow-other-keys)
4096 (invoke "./configure"
4097 (string-append "--prefix="
4098 (assoc-ref outputs "out"))))))))
4099 (inputs `(("scm" ,scm)))
4100 (native-inputs `(("unzip" ,unzip)
4101 ("texinfo" ,texinfo)))
4102 (synopsis "Symbolic mathematics system")
4103 (description "GNU JACAL is an interactive symbolic mathematics program based on
4104 Scheme. It manipulate and simplify a range of mathematical expressions such
4105 as equations, scalars, vectors, and matrices.")
4106 (home-page "https://www.gnu.org/software/jacal/")
4107 (license license:gpl3+)))
4113 (home-page "https://github.com/Z3Prover/z3")
4116 (uri (git-reference (url home-page)
4117 (commit (string-append "z3-" version))))
4118 (file-name (git-file-name name version))
4121 "1sywcqj5y8yp28m4cdvzsgw74kd6zr1s3y1x17ky8pr9prvpvl6x"))))
4122 (build-system gnu-build-system)
4125 (modify-phases %standard-phases
4126 (add-after 'unpack 'fix-compatability
4127 ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
4129 (substitute* "src/util/mpz.cpp"
4130 (("#include <immintrin.h>") ""))
4132 (add-before 'configure 'bootstrap
4134 (invoke "python" "scripts/mk_make.py")))
4135 ;; work around gnu-build-system's setting --enable-fast-install
4136 ;; (z3's `configure' is a wrapper around the above python file,
4137 ;; which fails when passed --enable-fast-install)
4139 (lambda* (#:key inputs outputs #:allow-other-keys)
4140 (invoke "./configure"
4141 (string-append "--prefix=" (assoc-ref outputs "out")))))
4142 (add-after 'configure 'change-directory
4146 (add-before 'check 'make-test-z3
4148 ;; Build the test suite executable.
4149 (invoke "make" "test-z3" "-j"
4150 (number->string (parallel-job-count)))))
4153 ;; Run all the tests that don't require arguments.
4154 (invoke "./test-z3" "/a"))))))
4157 ("python" ,python-wrapper)))
4158 (synopsis "Theorem prover")
4159 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
4160 theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
4161 (license license:expat)))
4166 (version "2018.11.001")
4169 (uri (string-append "http://elpa.mpcdf.mpg.de/html/Releases/"
4170 version "/elpa-" version ".tar.gz"))
4173 "05hv3v5i6xmziaizw350ff72y1c3k662r85fm3xfdrkclj5zw9yc"))))
4174 (build-system gnu-build-system)
4176 `(("fortran" ,gfortran)
4177 ("perl" ,perl))) ;for configure and deps
4179 `(("blas" ,openblas)))
4184 ;; ELPA unfortunately does not support runtime dispatch, so we can
4185 ;; only enable the "generic" kernels. See the "Cross compilation"
4186 ;; section of INSTALL.md.
4188 "--disable-sse" "--disable-sse-assembly" ;Require SSE3
4189 "--disable-avx" "--disable-avx2" "--disable-avx512"
4190 ,(string-append "CFLAGS=-O3 "
4191 "-funsafe-loop-optimizations -funsafe-math-optimizations "
4192 "-ftree-vect-loop-version -ftree-vectorize "
4193 ,(let ((system (or (%current-target-system)
4194 (%current-system))))
4196 ((or (string-prefix? "x86_64" system)
4197 (string-prefix? "i686" system))
4200 #:parallel-tests? #f ;tests are multi-threaded, via BLAS
4202 (modify-phases %standard-phases
4203 (add-before 'configure 'patch-header-generation
4205 (substitute* "configure"
4206 (("^ *make.*top_srcdir=\"\\$srcdir\"" &)
4207 (string-append & " CPP=\"$CPP\"")))
4209 (add-before 'check 'setup-tests
4211 ;; Decrease test time and RAM use by computing fewer eigenvalues.
4212 ;; The flags are (MATRIX-SIZE, EIGENVALUES, BLOCK-SIZE), where
4213 ;; the default is (500, 250, 16) for C tests and (5000, 150, 16)
4214 ;; for Fortran. This also causes several tests to pass that
4215 ;; otherwise would otherwise fail with matrix size 5000; possibly
4216 ;; due to floating point tolerances that are too tight.
4217 (setenv "TEST_FLAGS" "1500 50 16") ;from elpa.spec
4218 (setenv "OMP_NUM_THREADS" (number->string (parallel-job-count)))
4219 (substitute* "Makefile"
4220 ;; Test scripts are generated, patch the shebang
4221 (("#!/bin/bash") (string-append "#!" (which "sh"))))
4223 (home-page "http://elpa.mpcdf.mpg.de")
4224 (synopsis "Eigenvalue solvers for symmetric matrices")
4226 "The ELPA library provides efficient and scalable direct eigensolvers for
4227 symmetric matrices.")
4228 (license license:lgpl3)))
4230 (define-public elpa-openmpi
4231 (package (inherit elpa)
4232 (name "elpa-openmpi")
4235 ("scalapack" ,scalapack)
4236 ,@(package-inputs elpa)))
4238 (substitute-keyword-arguments (package-arguments elpa)
4239 ((#:configure-flags cf '())
4240 `(cons "--with-mpi=yes" (delete "--with-mpi=no" ,cf)))
4241 ((#:phases phases '%standard-phases)
4242 `(modify-phases ,phases
4243 (add-before 'check 'mpi-setup
4245 ;; Tests use 2 mpi tasks by default, use our remaining build
4246 ;; cores as OpenMP threads.
4247 (setenv "OMP_NUM_THREADS" (number->string
4248 (max (quotient (parallel-job-count) 2)
4250 (,%openmpi-setup)))))))
4251 (synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)")))
4253 (define-public elemental
4260 (url "https://github.com/elemental/Elemental.git")
4261 (commit (string-append "v" version))))
4262 (file-name (git-file-name name version))
4265 "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
4266 (build-system cmake-build-system)
4267 (home-page "http://libelemental.org")
4269 `(("gfortran" ,gfortran)))
4271 `(("blas" ,openblas)
4272 ("gfortran:lib" ,gfortran "lib")
4281 `(#:build-type "Release" ;default RelWithDebInfo not supported
4282 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
4283 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
4284 "-DEL_CACHE_WARNINGS:BOOL=YES"
4285 "-DEL_TESTS:BOOL=YES"
4286 "-DCMAKE_INSTALL_LIBDIR=lib"
4287 "-DGFORTRAN_LIB=gfortran")
4288 #:phases (modify-phases %standard-phases
4289 (add-before 'check 'mpi-setup
4291 (add-before 'check 'setup-tests
4293 ;; Parallelism is done at the MPI layer.
4294 (setenv "OMP_NUM_THREADS" "1")
4296 (add-after 'install 'remove-tests
4297 (lambda* (#:key outputs #:allow-other-keys)
4298 ;; Tests are installed, with no easy configuration
4299 ;; switch to prevent this, so delete them.
4300 (delete-file-recursively
4301 (string-append (assoc-ref outputs "out") "/bin"))
4303 (synopsis "Dense and sparse-direct linear algebra and optimization")
4304 (description "Elemental is a modern C++ library for distributed-memory
4305 dense and sparse-direct linear algebra, conic optimization, and lattice
4307 (license license:bsd-2)))
4309 (define-public mcrl2
4312 (version "201908.0")
4316 "https://www.mcrl2.org/download/release/mcrl2-"
4320 "1i4xgl2d5fgiz1mwi50cyfkrrcpm8nxfayfjgmhq7chs58wlhfsz"))))
4325 ("qtbase" ,qtbase)))
4326 (build-system cmake-build-system)
4327 (synopsis "Toolset for the mCRL2 formal specification language")
4329 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
4330 specification language for describing concurrent discrete event systems. Its
4331 toolset supports analysis and automatic verification, linearisation, simulation,
4332 state-space exploration and generation, and tools to optimise and analyse
4333 specifications. Also, state spaces can be manipulated, visualised and
4335 (home-page "https://mcrl2.org")
4336 (license license:boost1.0)))
4338 (define-public mcrl2-minimal
4341 (name "mcrl2-minimal")
4343 `(("boost" ,boost)))
4345 '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
4347 (define-public tcalc
4354 (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
4358 "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
4359 (build-system gnu-build-system)
4360 (synopsis "The terminal calculator")
4362 "The terminal calculator is a small program to help users of the GNU/Linux
4363 terminal do calculations simply and quickly. The formula to be calculated can
4364 be fed to @command{tcalc} through the command line.")
4365 (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
4366 (license license:gpl3+)))
4368 (define-public sundials
4375 (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
4376 "sundials-" version ".tar.gz"))
4379 "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
4380 (build-system cmake-build-system)
4382 `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
4384 `(("fortran" ,gfortran) ;for fcmix
4386 ("suitesparse" ,suitesparse))) ;TODO: Add hypre
4388 `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
4389 "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
4390 "-DEXAMPLES_ENABLE_F77:BOOL=ON"
4391 "-DEXAMPLES_ENABLE_F90:BOOL=ON"
4392 "-DEXAMPLES_INSTALL:BOOL=OFF"
4394 "-DFCMIX_ENABLE:BOOL=ON"
4396 "-DKLU_ENABLE:BOOL=ON"
4397 ,(string-append "-DKLU_INCLUDE_DIR="
4398 (assoc-ref %build-inputs "suitesparse")
4400 ,(string-append "-DKLU_LIBRARY_DIR="
4401 (assoc-ref %build-inputs "suitesparse")
4403 (home-page "https://computation.llnl.gov/projects/sundials")
4404 (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
4405 (description "SUNDIALS is a family of software packages implemented with
4406 the goal of providing robust time integrators and nonlinear solvers that can
4407 easily be incorporated into existing simulation codes.")
4408 (license license:bsd-3)))
4410 (define-public sundials-openmpi
4411 (package (inherit sundials)
4412 (name "sundials-openmpi")
4415 ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
4416 ,@(package-inputs sundials)))
4418 (substitute-keyword-arguments (package-arguments sundials)
4419 ((#:configure-flags flags '())
4420 `(cons* "-DMPI_ENABLE:BOOL=ON"
4421 "-DPETSC_ENABLE:BOOL=ON"
4422 (string-append "-DPETSC_INCLUDE_DIR="
4423 (assoc-ref %build-inputs "petsc")
4425 (string-append "-DPETSC_LIBRARY_DIR="
4426 (assoc-ref %build-inputs "petsc")
4429 ((#:phases phases '%standard-phases)
4430 `(modify-phases ,phases
4431 (add-before 'check 'mpi-setup
4432 ,%openmpi-setup)))))
4433 (synopsis "SUNDIALS with OpenMPI support")))
4435 (define-public combinatorial-blas
4437 (name "combinatorial-blas")
4442 (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/"
4444 (match (string-split version #\.)
4445 ((major minor patch)
4446 (string-append major minor "_" patch))) ;e.g. "16_2"
4450 "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a"))
4451 (patches (search-patches "combinatorial-blas-awpm.patch"
4452 "combinatorial-blas-io-fix.patch"))))
4453 (build-system cmake-build-system)
4456 ("test-data" ,(origin
4458 (uri (string-append "https://people.eecs.berkeley.edu/~aydin/"
4459 "CombBLAS_FILES/testdata_combblas1.6.1.tgz"))
4462 "01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87"))))))
4464 `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
4465 "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL")
4466 #:parallel-tests? #f ;tests use 'mpiexec -n4'
4468 (modify-phases %standard-phases
4469 (add-before 'check 'mpi-setup
4471 (add-before 'check 'test-setup
4472 (lambda* (#:key inputs #:allow-other-keys)
4473 (setenv "OMP_NUM_THREADS" "2")
4474 (invoke "tar" "xf" (assoc-ref inputs "test-data")))))))
4475 (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/")
4476 (synopsis "Linear algebra primitives for graph analytics")
4477 (description "The Combinatorial BLAS (CombBLAS) is an extensible
4478 distributed-memory parallel graph library offering a small but powerful set of
4479 linear algebra primitives specifically targeting graph analytics.")
4481 license:gpl2+ ;include/psort/(funnel|sort)*.h
4482 license:x11 ;usort and psort
4483 license:bsd-3)))) ;CombBLAS and MersenneTwister.h
4485 (define-public dune-common
4487 (name "dune-common")
4492 (uri (string-append "https://dune-project.org/download/"
4493 version "/dune-common-" version ".tar.gz"))
4496 "019wcr1qf7jwyxx1y5y290wdlglylskvbb2m01ljkzcza2xnlmhw"))))
4497 (build-system cmake-build-system)
4500 (modify-phases %standard-phases
4501 (add-after 'build 'build-tests
4502 (lambda* (#:key make-flags #:allow-other-keys)
4503 (apply invoke "make" "build_tests" make-flags)))
4504 ;; These tests fail because they require a fully functional MPI
4506 (add-after 'unpack 'disable-failing-tests
4509 (string-append "--exclude-regex '("
4513 "remoteindicestest-mpi-2"
4516 "variablesizecommunicatortest"
4517 "variablesizecommunicatortest-mpi-2"
4518 "arithmetictestsuitetest"
4519 "assertandreturntest"
4520 "assertandreturntest_ndebug"
4523 "mpicollectivecommunication"
4524 "mpicollectivecommunication-mpi-2"
4526 "mpiguardtest-mpi-2"
4528 "mpihelpertest-mpi-2"
4530 "mpihelpertest2-mpi-2")
4537 ("openmpi" ,openmpi)
4538 ("openblas" ,openblas)
4540 ("superlu" ,superlu)))
4542 `(("gfortran" ,gfortran)
4543 ("pkg-config" ,pkg-config)))
4544 (home-page "https://dune-project.org/")
4545 (synopsis "Distributed and Unified Numerics Environment")
4546 (description "DUNE, the Distributed and Unified Numerics Environment is a
4547 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4548 grid-based methods. It supports the easy implementation of methods like
4549 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4550 Differences} (FD).")
4551 ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2.
4552 (license license:gpl2)))
4554 (define-public dune-geometry
4556 (name "dune-geometry")
4561 (uri (string-append "https://dune-project.org/download/"
4562 version "/dune-geometry-" version ".tar.gz"))
4565 "0hlaaxjyv9j05blasvb67sy02hd0w4g9znf68gdh3l731dd1aqbn"))))
4566 (build-system cmake-build-system)
4569 (modify-phases %standard-phases
4570 (add-after 'build 'build-tests
4571 (lambda* (#:key make-flags #:allow-other-keys)
4572 (apply invoke "make" "build_tests" make-flags))))))
4574 `(("dune-common" ,dune-common)
4575 ("openmpi" ,openmpi)
4577 ("openblas" ,openblas)
4579 ("python" ,python)))
4581 `(("gfortran" ,gfortran)
4582 ("pkg-config" ,pkg-config)))
4583 (home-page "https://dune-project.org/")
4584 (synopsis "Distributed and Unified Numerics Environment")
4585 (description "DUNE, the Distributed and Unified Numerics Environment is a
4586 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4587 grid-based methods. It supports the easy implementation of methods like
4588 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4591 This package contains the basic DUNE geometry classes.")
4592 ;; GPL version 2 with "runtime exception"
4593 (license license:gpl2)))
4595 (define-public dune-grid
4602 (uri (string-append "https://dune-project.org/download/"
4603 version "/dune-grid-" version ".tar.gz"))
4606 "1jp4vscm9yb9xg0lh7apzccfkhvgbnk652yahigmh3cvzpl4acd0"))))
4607 (build-system cmake-build-system)
4610 (modify-phases %standard-phases
4611 (add-after 'build 'build-tests
4612 (lambda* (#:key make-flags #:allow-other-keys)
4613 (apply invoke "make" "build_tests" make-flags)))
4614 ;; These tests fail because they require a fully functional MPI
4616 (add-after 'unpack 'disable-failing-tests
4619 (string-append "--exclude-regex '("
4623 "conformvolumevtktest"
4625 "nonconformboundaryvtktest"
4626 "subsamplingvtktest"
4632 "test-dgf-yasp-offset"
4634 "test-geogrid-yaspgrid"
4637 "testiteratorranges"
4638 "test-hierarchicsearch"
4639 "test-parallel-ug-mpi-2"
4640 "test-yaspgrid-backuprestore-equidistant"
4641 "test-yaspgrid-backuprestore-equidistant-mpi-2"
4642 "test-yaspgrid-backuprestore-equidistantoffset"
4643 "test-yaspgrid-backuprestore-equidistantoffset-mpi-2"
4644 "test-yaspgrid-backuprestore-tensor"
4645 "test-yaspgrid-backuprestore-tensor-mpi-2"
4646 "test-yaspgrid-tensorgridfactory"
4647 "test-yaspgrid-tensorgridfactory-mpi-2"
4648 "test-yaspgrid-yaspfactory-1d"
4649 "test-yaspgrid-yaspfactory-1d-mpi-2"
4650 "test-yaspgrid-yaspfactory-2d"
4651 "test-yaspgrid-yaspfactory-2d-mpi-2"
4652 "test-yaspgrid-yaspfactory-3d"
4653 "test-yaspgrid-yaspfactory-3d-mpi-2"
4654 "globalindexsettest"
4655 "persistentcontainertest"
4656 "structuredgridfactorytest"
4657 "tensorgridfactorytest"
4663 `(("dune-common" ,dune-common)
4664 ("dune-geometry" ,dune-geometry)
4667 ("openblas" ,openblas)
4668 ("openmpi" ,openmpi)
4669 ("python" ,python)))
4671 `(("gfortran" ,gfortran)
4672 ("pkg-config" ,pkg-config)))
4673 (home-page "https://dune-project.org/")
4674 (synopsis "Distributed and Unified Numerics Environment")
4675 (description "DUNE, the Distributed and Unified Numerics Environment is a
4676 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4677 grid-based methods. It supports the easy implementation of methods like
4678 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4681 This package contains the basic DUNE grid classes.")
4682 ;; GPL version 2 with "runtime exception"
4683 (license license:gpl2)))
4685 (define-public dune-istl
4692 (uri (string-append "https://dune-project.org/download/"
4693 version "/dune-istl-" version ".tar.gz"))
4696 "0l2gyrvys5w6wsmk0ckbb7295s80b7yk7qrl7x66akv2jv1nzq2w"))))
4697 (build-system cmake-build-system)
4700 (modify-phases %standard-phases
4701 (add-after 'build 'build-tests
4702 (lambda* (#:key make-flags #:allow-other-keys)
4703 (apply invoke "make" "build_tests" make-flags)))
4704 ;; These tests fail because they require a fully functional MPI
4706 (add-after 'unpack 'disable-failing-tests
4709 (string-append "--exclude-regex '("
4715 "pamg_comm_repart_test"
4723 `(("dune-common" ,dune-common)
4724 ("openmpi" ,openmpi)
4727 ("superlu" ,superlu)
4728 ("openblas" ,openblas)
4730 ("python" ,python)))
4732 `(("gfortran" ,gfortran)
4733 ("pkg-config" ,pkg-config)))
4734 (home-page "https://dune-project.org/")
4735 (synopsis "Distributed and Unified Numerics Environment")
4736 (description "DUNE, the Distributed and Unified Numerics Environment is a
4737 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4740 This is the iterative solver template library which provides generic sparse
4741 matrix/vector classes and a variety of solvers based on these classes. A
4742 special feature is the use of templates to exploit the recursive block
4743 structure of finite element matrices at compile time. Available solvers
4744 include Krylov methods, (block-) incomplete decompositions and
4745 aggregation-based algebraic multigrid.")
4746 ;; GPL version 2 with "runtime exception"
4747 (license license:gpl2)))
4749 (define-public dune-localfunctions
4751 (name "dune-localfunctions")
4756 (uri (string-append "https://dune-project.org/download/"
4757 version "/dune-localfunctions-" version ".tar.gz"))
4760 "19c6zjinwwpy8jh4v4prhphyd438rapd4x80fj93apmwgw04nrhl"))))
4761 (build-system cmake-build-system)
4764 (modify-phases %standard-phases
4765 (add-after 'build 'build-tests
4766 (lambda* (#:key make-flags #:allow-other-keys)
4767 (apply invoke "make" "build_tests" make-flags))))))
4769 `(("dune-common" ,dune-common)
4770 ("dune-geometry" ,dune-geometry)
4771 ("openmpi" ,openmpi)
4774 ("superlu" ,superlu)
4777 `(("gfortran" ,gfortran)
4778 ("pkg-config" ,pkg-config)))
4779 (home-page "https://dune-project.org/")
4780 (synopsis "Distributed and Unified Numerics Environment") ; TODO
4781 (description "This DUNE module provides interface and implementation for
4782 shape functions defined on the DUNE reference elements. In addition to the
4783 shape function, interpolation operators and special keys are provided which
4784 can be used to assemble global function spaces on finite-element grids.
4786 This package provides an interface and implementation for shape functions
4787 defined on the DUNE reference elements. In addition to the shape function,
4788 interpolation operators and special keys are provided which can be used to
4789 assemble global function spaces on finite-element grids.")
4790 ;; GPL version 2 with "runtime exception"
4791 (license license:gpl2)))
4793 (define-public dune-alugrid
4795 (name "dune-alugrid")
4800 (uri (string-append "https://dune-project.org/download/"
4801 version "/dune-alugrid-" version ".tar.gz"))
4804 "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj"))))
4805 (build-system cmake-build-system)
4807 `(#:tests? #f ; 7 of 8 tests fail because they need a full MPI
4810 (modify-phases %standard-phases
4811 (add-after 'unpack 'patch-include
4813 (substitute* "dune/alugrid/test/test-alugrid.cc"
4814 (("doc/grids/gridfactory/testgrids")
4815 "doc/dune-grid/grids/gridfactory/testgrids"))
4817 (add-after 'build 'build-tests
4818 (lambda* (#:key inputs make-flags #:allow-other-keys)
4819 (setenv "CPLUS_INCLUDE_PATH"
4820 (string-append (assoc-ref inputs "dune-grid") "/share"))
4821 (apply invoke "make" "build_tests" make-flags))))))
4823 `(("dune-common" ,dune-common)
4824 ("dune-geometry" ,dune-geometry)
4825 ("dune-grid" ,dune-grid)
4826 ("openmpi" ,openmpi)
4829 ("openblas" ,openblas)
4831 ("superlu" ,superlu)
4835 `(("gfortran" ,gfortran)
4836 ("pkg-config" ,pkg-config)))
4837 (home-page "https://dune-project.org/")
4838 (synopsis "Distributed and Unified Numerics Environment")
4839 (description "ALUGrid is an adaptive, loadbalancing, unstructured
4840 implementation of the DUNE grid interface supporting either simplices or
4842 (license license:gpl2+)))
4844 (define-public dune-typetree
4846 (name "dune-typetree")
4852 (url "https://gitlab.dune-project.org/staging/dune-typetree.git")
4853 (commit (string-append "v" version))))
4854 (file-name (git-file-name name version))
4857 "0mnv6w2f22lz3j4bdpdjq55vjm8xxfx9v4vvhg9bd36xpsbjpjp9"))))
4858 (build-system cmake-build-system)
4861 (modify-phases %standard-phases
4862 (add-after 'build 'build-tests
4863 (lambda* (#:key make-flags #:allow-other-keys)
4864 (apply invoke "make" "build_tests" make-flags))))))
4866 `(("dune-common" ,dune-common)
4867 ("openmpi" ,openmpi)
4869 ("openblas" ,openblas)
4872 ("superlu" ,superlu)
4875 `(("gfortran" ,gfortran)
4876 ("pkg-config" ,pkg-config)))
4877 (home-page "https://dune-project.org/")
4878 (synopsis "Distributed and Unified Numerics Environment")
4879 (description "TypeTree is a template library for constructing and
4880 operating on statically typed trees of objects.")
4881 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4882 (license (list license:lgpl3+ license:gpl2))))
4884 (define-public dune-functions
4886 (name "dune-functions")
4892 (url "https://gitlab.dune-project.org/staging/dune-functions.git")
4893 (commit (string-append "v" version))))
4894 (file-name (git-file-name name version))
4897 "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200"))))
4898 (build-system cmake-build-system)
4899 (arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid
4901 `(("dune-common" ,dune-common)
4902 ("dune-istl" ,dune-istl)
4903 ("dune-localfunctions" ,dune-localfunctions)
4904 ("dune-grid" ,dune-grid)
4905 ("dune-geometry" ,dune-geometry)
4906 ("dune-typetree" ,dune-typetree)
4907 ("openmpi" ,openmpi)
4908 ("openblas" ,openblas)
4911 ("superlu" ,superlu)
4914 `(("gfortran" ,gfortran)
4915 ("pkg-config" ,pkg-config)))
4916 (home-page "https://dune-project.org/")
4917 (synopsis "Distributed and Unified Numerics Environment")
4918 (description "The dune-functions module provides an abstraction layer for
4919 global finite element functions. Its two main concepts are functions
4920 implemented as callable objects, and bases of finite element spaces.")
4921 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4922 (license (list license:lgpl3+ license:gpl2))))
4924 (define-public dune-pdelab
4926 (name "dune-pdelab")
4927 (version "2.6.0-rc1")
4932 (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
4933 (commit (string-append "v" version))))
4934 (file-name (git-file-name name version))
4937 "07g0s9448z65vjrq88g5rv3340iifil85k170n8kbqchsvi4ny5v"))))
4938 (build-system cmake-build-system)
4939 (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
4941 `(("dune-common" ,dune-common)
4942 ("dune-istl" ,dune-istl)
4943 ("dune-localfunctions" ,dune-localfunctions)
4944 ("dune-geometry" ,dune-geometry)
4945 ("dune-grid" ,dune-grid)
4946 ("dune-typetree" ,dune-typetree)
4947 ("dune-functions" ,dune-functions)
4948 ("openmpi" ,openmpi)
4950 ("openblas" ,openblas)
4954 ("superlu" ,superlu)
4957 `(("gfortran" ,gfortran)
4958 ("pkg-config" ,pkg-config)))
4959 (home-page "https://dune-project.org/")
4960 (synopsis "Differential equations solver toolbox")
4961 (description "PDELab is a partial differential equations solver toolbox
4962 built on top of DUNE, the Distributed and Unified Numerics Environment.")
4963 ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4964 (license (list license:lgpl3+ license:gpl2))))
4966 (define-public mlucas
4974 "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz"))
4976 (base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447"))))
4977 (build-system gnu-build-system)
4979 `(("python2" ,python-2)))
4981 `(#:tests? #f ; no tests
4983 (modify-phases %standard-phases
4987 (call-with-output-file "Makefile"
4989 (format port "CC = gcc
4990 CFLAGS = -O3 ~a -DUSE_THREADS
4991 LDLIBS = -lm -lpthread -lrt
4992 Mlucas: $(addsuffix .o,$(basename $(wildcard *.c)))
4994 ,(let ((system (or (%current-target-system)
4995 (%current-system))))
4997 ((string-prefix? "x86_64" system) "-DUSE_SSE2")
5001 (lambda* (#:key outputs #:allow-other-keys)
5002 (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
5003 (install-file "Mlucas" bin)
5004 (install-file "primenet.py" bin))
5006 (home-page "https://www.mersenne.org")
5007 (synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client")
5008 (description "Mlucas performs Lucas-Lehmer primality testing of Mersenne
5009 numbers in search of a world-record prime. You may use it to test any
5010 suitable number as you wish, but it is preferable that you do so in a
5011 coordinated fashion, as part of the Great Internet Mersenne Prime
5012 Search (GIMPS). Mlucas also includes a simple Python script for assignment
5013 management via the GIMPS project's Primenet server.")
5014 (license license:gpl2+)))
5016 (define-public nauty
5023 "https://pallini.di.uniroma1.it/"
5024 "nauty" (string-join (string-split version #\.) "")
5028 "05z6mk7c31j70md83396cdjmvzzip1hqb88pfszzc6k4gy8h3m2y"))))
5029 (build-system gnu-build-system)
5030 (outputs '("out" "lib"))
5032 `(#:test-target "checks"
5034 (modify-phases %standard-phases
5035 ;; Default make target does not build all available
5036 ;; executables. Create them now.
5037 (add-after 'build 'build-extra-programs
5039 (for-each (lambda (target) (invoke "make" target))
5040 '("blisstog" "bliss2dre" "checks6" "sumlines"))
5042 ;; Upstream does not provide any install target.
5044 (lambda* (#:key outputs #:allow-other-keys)
5045 (let* ((out (assoc-ref outputs "out"))
5046 (lib-output (assoc-ref outputs "lib"))
5047 (bin (string-append out "/bin"))
5048 (doc (string-append out "/share/doc/nauty/"))
5049 (include (string-append lib-output "/include/nauty"))
5050 (lib (string-append lib-output "/lib/nauty")))
5051 (for-each (lambda (f) (install-file f bin))
5052 '("dreadnaut" "NRswitchg" "addedgeg" "amtog" "biplabg"
5053 "blisstog" "bliss2dre" "catg" "checks6" "complg"
5054 "converseg" "copyg" "countg" "cubhamg" "deledgeg"
5055 "delptg" "directg" "dretodot" "dretog" "genbg"
5056 "genbgL" "geng" "genquarticg" "genrang" "genspecialg"
5057 "gentourng" "gentreeg" "hamheuristic" "labelg"
5058 "linegraphg" "listg" "multig" "newedgeg" "pickg"
5059 "planarg" "ranlabg" "shortg" "showg" "subdivideg"
5060 "sumlines" "twohamg" "vcolg" "watercluster2"))
5061 (for-each (lambda (f) (install-file f include))
5062 (find-files "." "\\.h$"))
5063 (for-each (lambda (f) (install-file f lib))
5064 (find-files "." "\\.a$"))
5065 (for-each (lambda (f) (install-file f doc))
5066 (append '("formats.txt" "README" "schreier.txt")
5067 (find-files "." "\\.pdf$")))))))))
5069 `(("gmp" ,gmp))) ;for sumlines
5070 (home-page "https://pallini.di.uniroma1.it/")
5071 (synopsis "Library for graph automorphisms")
5072 (description "@code{nauty} (No AUTomorphisms, Yes?) is a set of
5073 procedures for computing automorphism groups of graphs and digraphs.
5075 @code{nauty} computes graph information in the form of a set of
5076 generators, the size of the group, and the orbits of the group; it can
5077 also produce a canonical label. The @code{nauty} suite is written in
5078 C and comes with a command-line interface, a collection of
5079 command-line tools, and an Application Programming Interface (API).
5081 This package provides the static libraries required to run programs
5082 compiled against the nauty library.")
5083 (license license:asl2.0)))
5092 (uri (string-append "https://www.bugseng.com/products/ppl/download/"
5093 "ftp/releases/" version
5094 "/ppl-" version ".tar.gz"))
5097 "1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb"))))
5098 (build-system gnu-build-system)
5104 (home-page "https://www.bugseng.com/parma-polyhedra-library")
5106 "Parma Polyhedra Library for computations with polyhedra")
5108 "The Parma Polyhedra Library (PPL) provides numerical abstractions
5109 especially targeted at applications in the field of analysis and
5110 verification of complex systems. These abstractions include convex
5111 polyhedra, defined as the intersection of a finite number of (open or
5112 closed) halfspaces, each described by a linear inequality (strict or
5113 non-strict) with rational coefficients; some special classes of polyhedra
5114 shapes that offer interesting complexity/precision tradeoffs; and grids
5115 which represent regularly spaced points that satisfy a set of linear
5116 congruence relations. The library also supports finite powersets and
5117 products of (any kind of) polyhedra and grids, a mixed integer linear
5118 programming problem solver using an exact-arithmetic version of the simplex
5119 algorithm, a parametric integer programming solver, and primitives for
5120 termination analysis via the automatic synthesis of linear ranking
5122 (license license:gpl3+)))
5124 (define-public speedcrunch
5126 (name "speedcrunch")
5132 (url "https://bitbucket.org/heldercorreia/speedcrunch.git")
5133 (commit (string-append "release-" version))))
5134 (file-name (git-file-name name version))
5137 "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"))))
5138 (build-system cmake-build-system)
5139 (inputs `(("qtbase" ,qtbase)))
5140 (native-inputs `(("qttools" ,qttools)))
5143 (modify-phases %standard-phases
5144 (add-after 'unpack 'chdir-to-src
5145 (lambda _ (chdir "src") #t)))))
5146 (synopsis "High-precision scientific calculator")
5148 "SpeedCrunch is a high-precision scientific calculator. It features a
5149 syntax-highlighted scrollable display and is designed to be fully used via
5150 keyboard. Some distinctive features are auto-completion of functions and
5151 variables, a formula book, and quick insertion of constants from various
5152 fields of knowledge.")
5153 (home-page "http://speedcrunch.org/")
5154 (license license:gpl2+)))
5156 (define-public minisat
5157 ;; This is the last commit which is available upstream, no
5158 ;; release happened since 2010.
5159 (let ((commit "37dc6c67e2af26379d88ce349eb9c4c6160e8543")
5163 (version (string-append "2.2.0-" revision "." (string-take commit 7)))
5168 (url "https://github.com/niklasso/minisat.git")
5170 (file-name (string-append name "-" version "-checkout"))
5173 "091hf3qkm197s5r7xcr3m07xsdwyz2rqk1hc9kj0hn13imz09irq"))
5175 (search-patches "minisat-friend-declaration.patch"
5176 "minisat-install.patch"))))
5177 (build-system gnu-build-system)
5179 '(#:make-flags (list (string-append "prefix=" %output))
5180 #:tests? #f ;no check target
5182 (modify-phases %standard-phases
5183 (delete 'configure))))
5185 `(("zlib:static" ,zlib "static")
5188 "Small, yet efficient, SAT solver")
5190 "MiniSat is a minimalistic, open-source SAT solver, developed to help
5191 researchers and developers alike to get started on SAT.")
5193 "http://minisat.se/MiniSat.html")
5194 (license license:expat))))
HCoop / jackhill / guix / guix.git / blob