1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
3 ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
4 ;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
5 ;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org>
6 ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
7 ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
8 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
9 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
10 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
11 ;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
12 ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
13 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
14 ;;; Copyright © 2016, 2018 Kei Kebreau <kkebreau@posteo.net>
15 ;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
16 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
17 ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
18 ;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>
19 ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
20 ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
21 ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
22 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
23 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
24 ;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
25 ;;; Copyright © 2018 Jan Nieuwenhuizen <janneke@gnu.org>
26 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
27 ;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
28 ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
29 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
31 ;;; This file is part of GNU Guix.
33 ;;; GNU Guix is free software; you can redistribute it and/or modify it
34 ;;; under the terms of the GNU General Public License as published by
35 ;;; the Free Software Foundation; either version 3 of the License, or (at
36 ;;; your option) any later version.
38 ;;; GNU Guix is distributed in the hope that it will be useful, but
39 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
40 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
41 ;;; GNU General Public License for more details.
43 ;;; You should have received a copy of the GNU General Public License
44 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
46 (define-module (gnu packages maths)
47 #:use-module (ice-9 regex)
48 #:use-module (gnu packages)
49 #:use-module ((guix licenses) #:prefix license:)
50 #:use-module (guix packages)
51 #:use-module (guix download)
52 #:use-module (guix git-download)
53 #:use-module (guix utils)
54 #:use-module (guix build utils)
55 #:use-module (guix build-system cmake)
56 #:use-module (guix build-system gnu)
57 #:use-module (guix build-system ocaml)
58 #:use-module (guix build-system python)
59 #:use-module (guix build-system r)
60 #:use-module (guix build-system ruby)
61 #:use-module (gnu packages algebra)
62 #:use-module (gnu packages audio)
63 #:use-module (gnu packages autotools)
64 #:use-module (gnu packages bison)
65 #:use-module (gnu packages boost)
66 #:use-module (gnu packages check)
67 #:use-module (gnu packages cmake)
68 #:use-module (gnu packages compression)
69 #:use-module (gnu packages curl)
70 #:use-module (gnu packages cyrus-sasl)
71 #:use-module (gnu packages documentation)
72 #:use-module (gnu packages elf)
73 #:use-module (gnu packages flex)
74 #:use-module (gnu packages fltk)
75 #:use-module (gnu packages fontutils)
76 #:use-module (gnu packages gettext)
77 #:use-module (gnu packages gcc)
78 #:use-module (gnu packages gd)
79 #:use-module (gnu packages ghostscript)
80 #:use-module (gnu packages graphviz)
81 #:use-module (gnu packages gtk)
82 #:use-module (gnu packages image)
83 #:use-module (gnu packages java)
84 #:use-module (gnu packages less)
85 #:use-module (gnu packages lisp)
86 #:use-module (gnu packages linux)
87 #:use-module (gnu packages logging)
88 #:use-module (gnu packages lua)
89 #:use-module (gnu packages gnome)
90 #:use-module (gnu packages guile)
91 #:use-module (gnu packages xorg)
92 #:use-module (gnu packages gl)
93 #:use-module (gnu packages imagemagick)
94 #:use-module (gnu packages m4)
95 #:use-module (gnu packages mpi)
96 #:use-module (gnu packages multiprecision)
97 #:use-module (gnu packages netpbm)
98 #:use-module (gnu packages ocaml)
99 #:use-module (gnu packages pcre)
100 #:use-module (gnu packages popt)
101 #:use-module (gnu packages perl)
102 #:use-module (gnu packages pkg-config)
103 #:use-module (gnu packages pulseaudio)
104 #:use-module (gnu packages python)
105 #:use-module (gnu packages python-web)
106 #:use-module (gnu packages qt)
107 #:use-module (gnu packages readline)
108 #:use-module (gnu packages ruby)
109 #:use-module (gnu packages tbb)
110 #:use-module (gnu packages scheme)
111 #:use-module (gnu packages shells)
112 #:use-module (gnu packages tcl)
113 #:use-module (gnu packages texinfo)
114 #:use-module (gnu packages tex)
115 #:use-module (gnu packages tls)
116 #:use-module (gnu packages version-control)
117 #:use-module (gnu packages wxwidgets)
118 #:use-module (gnu packages xml)
119 #:use-module (srfi srfi-1))
127 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
129 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
130 (build-system gnu-build-system)
131 (inputs `(("gtk+" ,gtk+)
132 ("libxml2" ,libxml2)))
133 (native-inputs `(("pkg-config" ,pkg-config)))
134 (synopsis "Natural deduction first-order logic interface")
135 (description "Aris is a program for performing logical proofs. It supports
136 propositional and predicate logic, as well as Boolean algebra and
137 arithmetical logic. In addition to its predefined inference and equivalence
138 rules, Aris also supports references to older proofs. Its use of standard
139 logical symbols and its natural deduction interface make it easy to use for
141 (license license:gpl3+)
142 (home-page "https://www.gnu.org/software/aris/")))
144 (define-public c-graph
150 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
153 "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
154 (build-system gnu-build-system)
156 `(("fortran" ,gfortran)))
157 (synopsis "Visualizing and demonstrating convolution")
159 "GNU C-Graph is a tool for demonstrating the theory of convolution.
160 Thus, it can serve as an excellent aid to students of signal and systems
161 theory in visualizing the convolution process. Rather than forcing the
162 student to write code, the program offers an intuitive interface with
163 interactive dialogs to guide them.")
164 (license license:gpl3+)
165 (home-page "https://www.gnu.org/software/c-graph/")))
174 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
175 version "/coda-" version ".tar.gz"))
177 (base32 "1zlzgcvwmmjm8mw8w4rg2rqy0pjilz7kyyxm0y4p8cbljbbjxxz0"))
178 (patches (search-patches "coda-use-system-libs.patch"))
179 (modules '((guix build utils)))
181 ;; Make sure we don't use the bundled software.
182 '(for-each (lambda (d)
183 (delete-file-recursively (string-append "libcoda/" d)))
184 '("zlib" "pcre" "expat")))))
186 `(("fortran" ,gfortran)
188 ("python-numpy" ,python-numpy)))
195 (build-system gnu-build-system)
197 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
198 "LIBS= -lz -lpcre -lexpat")))
199 (synopsis "A common interface to various earth observation data formats")
201 "The Common Data Access toolbox (CODA) provides a set of interfaces for
202 reading remote sensing data from earth observation data files. It consists of
203 command line applications and interfaces to the C, Fortran, Python, and Java
204 programming languages.")
205 (home-page "https://stcorp.nl/coda")
206 (license license:gpl2+)))
214 (uri (string-append "mirror://gnu/units/units-" version
217 "11hnp3gcmcc5kci2caxw4hs6m08h2mhqs3xzqq7iafx1ha2ggwyw"))))
218 (build-system gnu-build-system)
220 `(("readline" ,readline)
221 ("python" ,python-wrapper) ;for 'units_cur' script
222 ("python-requests" ,python-requests)))
224 `(#:phases (modify-phases %standard-phases
225 (add-after 'install 'wrap-units_cur
226 (lambda* (#:key outputs #:allow-other-keys)
227 (let* ((out (assoc-ref outputs "out"))
228 (bin (string-append out "/bin")))
229 (wrap-program (string-append bin "/units_cur")
230 `("PYTHONPATH" ":" prefix
231 ,(search-path-as-string->list (getenv "PYTHONPATH"))))
233 (synopsis "Conversion between thousands of scales")
235 "GNU Units converts numeric quantities between units of measure. It
236 can handle scale changes through adaptive usage of standard scale
237 prefixes (micro-, kilo-, etc.). It can also handle nonlinear
238 conversions such as Fahrenheit to Celsius. Its interpreter is powerful
239 enough to be used effectively as a scientific calculator.")
240 (license license:gpl3+)
241 (home-page "https://www.gnu.org/software/units/")))
243 (define-public double-conversion
245 (name "double-conversion")
250 "https://github.com/floitsch/double-conversion/archive/v"
252 (file-name (string-append name "-" version ".tar.gz"))
255 "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83"))))
256 (build-system cmake-build-system)
258 '(#:test-target "test"
259 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
260 "-DBUILD_TESTING=ON")))
261 (home-page "https://github.com/floitsch/double-conversion")
262 (synopsis "Conversion routines for IEEE doubles")
264 "The double-conversion library provides binary-decimal and decimal-binary
265 routines for IEEE doubles. The library consists of efficient conversion
266 routines that have been extracted from the V8 JavaScript engine.")
267 (license license:bsd-3)))
269 (define-public dionysus
275 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
279 "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
280 (build-system gnu-build-system)
281 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
282 (synopsis "Local search for universal constants and scientific values")
284 "GNU Dionysus is a convenient system for quickly retrieving the values of
285 mathematical constants used in science and engineering. Values can be
286 searched using a simple command-line tool, choosing from three databases:
287 universal constants, atomic numbers, and constants related to
289 (license license:gpl3+)
290 (home-page "https://www.gnu.org/software/dionysus/")))
298 (uri (string-append "mirror://gnu/gsl/gsl-"
302 "16yfs5n444s03np1naj6yp1fsysd42kdscxzkg0k2yvfjixx0ijd"))
303 (patches (search-patches "gsl-test-i686.patch"))))
304 (build-system gnu-build-system)
306 `(;; Currently there are numerous tests that fail on "exotic"
307 ;; architectures such as aarch64 and ppc64le.
308 ,@(if (string-prefix? "aarch64-linux"
309 (or (%current-target-system) (%current-system)))
312 (home-page "https://www.gnu.org/software/gsl/")
313 (synopsis "Numerical library for C and C++")
315 "The GNU Scientific Library is a library for numerical analysis in C
316 and C++. It includes a wide range of mathematical routines, with over 1000
317 functions in total. Subject areas covered by the library include:
318 differential equations, linear algebra, Fast Fourier Transforms and random
320 (license license:gpl3+)))
322 (define-public ocaml-gsl
331 "https://github.com/mmottl/gsl-ocaml/releases/download/v"
332 version"/gsl-ocaml-" version ".tar.gz"))
335 "0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh"))))
336 (build-system ocaml-build-system)
339 (home-page "https://mmottl.github.io/gsl-ocaml")
340 (synopsis "Bindings to the GNU Scientific Library")
342 "GSL-OCaml is an interface to the @dfn{GNU scientific library} (GSL) for
343 the OCaml language.")
344 (license license:gpl3+)))
346 (define-public ocaml4.01-gsl
347 (package-with-ocaml4.01 ocaml-gsl))
356 (uri (string-append "mirror://gnu/glpk/glpk-"
360 "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
361 (build-system gnu-build-system)
365 `(#:configure-flags '("--with-gmp")))
366 (home-page "https://www.gnu.org/software/glpk/")
367 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
369 "GLPK is a C library for solving large-scale linear programming (LP),
370 mixed integer programming (MIP), and other related problems. It supports the
371 GNU MathProg modeling language, a subset of the AMPL language, and features a
372 translator for the language. In addition to the C library, a stand-alone
373 LP/MIP solver is included in the package.")
374 (license license:gpl3+)))
383 (uri (string-append "http://www.4ti2.de/version_" version
384 "/4ti2-" version ".tar.gz"))
387 "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
388 (build-system gnu-build-system)
390 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
394 (home-page "http://www.4ti2.de/")
395 (synopsis "Mathematical tool suite for problems on linear spaces")
397 "4ti2 implements algorithms for solving algebraic, geometric and
398 combinatorial problems on linear spaces. Among others, it solves systems
399 of linear equations, computes extreme rays of polyhedral cones, solves
400 integer programming problems and computes Markov bases for statistics.")
401 (license license:gpl2+)))
403 (define-public cddlib
410 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
411 (string-delete #\. version) ".tar.gz"))
414 "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy"))))
415 (build-system gnu-build-system)
418 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
419 (synopsis "Library for convex hulls and extreme rays of polyhedra")
421 "The C-library cddlib implements the Double Description Method of
422 Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
423 rays of a general convex polyhedron given by a system of linear inequalities
424 in arbitrary dimension. It can also be used for the converse operation of
425 computing convex hulls.")
426 (license license:gpl2+)))
428 (define-public arpack-ng
432 (home-page "https://github.com/opencollab/arpack-ng")
436 (uri (string-append home-page "/archive/" version ".tar.gz"))
437 (file-name (string-append name "-" version ".tar.gz"))
440 "0f8jx3fifmj9qdp289zr7r651y1q48k1jya859rqxq62mvis7xsh"))))
441 (build-system gnu-build-system)
443 '(#:phases (modify-phases %standard-phases
444 (add-after 'unpack 'autoreconf
446 (invoke "autoreconf" "-vfi"))))))
448 `(("autoconf" ,autoconf)
449 ("automake" ,automake)
450 ("libtool" ,libtool)))
453 ("fortran" ,gfortran)))
454 (synopsis "Fortran subroutines for solving eigenvalue problems")
456 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
457 large scale eigenvalue problems.")
458 (license (license:non-copyleft "file://COPYING"
459 "See COPYING in the distribution."))))
461 (define-public arpack-ng-3.3.0
465 (name (package-name arpack-ng))
466 (home-page (package-home-page arpack-ng))
470 (uri (string-append home-page "/archive/" version ".tar.gz"))
471 (file-name (string-append name "-" version ".tar.gz"))
474 "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
476 (define-public arpack-ng-openmpi
477 (package (inherit arpack-ng)
478 (name "arpack-ng-openmpi")
481 ,@(package-inputs arpack-ng)))
483 (substitute-keyword-arguments (package-arguments arpack-ng)
484 ((#:configure-flags _ '())
485 ''("--enable-mpi"))))
486 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
488 (define-public lapack
495 (uri (string-append "http://www.netlib.org/lapack/lapack-"
499 "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
500 (build-system cmake-build-system)
501 (home-page "http://www.netlib.org/lapack/")
502 (inputs `(("fortran" ,gfortran)
503 ("python" ,python-2)))
505 `(#:configure-flags (list
506 "-DBUILD_SHARED_LIBS:BOOL=YES"
509 ;; Build the 'LAPACKE_clatms' functions.
510 "-DLAPACKE_WITH_TMG=ON")
512 (modify-phases %standard-phases
513 (add-before 'check 'patch-python
514 (lambda* (#:key inputs #:allow-other-keys)
515 (let ((python (assoc-ref inputs "python")))
516 (substitute* "lapack_testing.py"
517 (("/usr/bin/env python") python)))
519 (synopsis "Library for numerical linear algebra")
521 "LAPACK is a Fortran 90 library for solving the most commonly occurring
522 problems in numerical linear algebra.")
523 (license (license:non-copyleft "file://LICENSE"
524 "See LICENSE in the distribution."))))
526 (define-public lapack-3.5
533 (uri (string-append "http://www.netlib.org/lapack/lapack-"
537 "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s"))))))
539 (define-public scalapack
546 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
550 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
551 (build-system cmake-build-system)
554 ("fortran" ,gfortran)
555 ("lapack" ,lapack))) ;for testing only
557 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
558 #:phases (modify-phases %standard-phases
559 (add-before 'check 'set-test-environment
561 ;; By default, running the test suite would fail because
562 ;; 'ssh' could not be found in $PATH. Define this
563 ;; variable to placate Open MPI without adding a
564 ;; dependency on OpenSSH (the agent isn't used anyway.)
565 (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
567 (home-page "http://www.netlib.org/scalapack/")
568 (synopsis "Library for scalable numerical linear algebra")
570 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
571 routines on parallel distributed memory machines. ScaLAPACK solves dense and
572 banded linear systems, least squares problems, eigenvalue problems, and
573 singular value problems.")
574 (license (license:bsd-style "file://LICENSE"
575 "See LICENSE in the distribution."))))
577 (define-public gnuplot
583 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
588 "18diyy7aib9mn098x07g25c7jij1x7wbfpicz0z8gwxx08px45m4"))))
589 (build-system gnu-build-system)
590 (inputs `(("readline" ,readline)
596 `(("pkg-config" ,pkg-config)
597 ("texlive" ,texlive-tiny)))
598 (arguments `(#:configure-flags (list (string-append
599 "--with-texdir=" %output
600 "/texmf-local/tex/latex/gnuplot"))))
601 (home-page "http://www.gnuplot.info")
602 (synopsis "Command-line driven graphing utility")
603 (description "Gnuplot is a portable command-line driven graphing
604 utility. It was originally created to allow scientists and students to
605 visualize mathematical functions and data interactively, but has grown to
606 support many non-interactive uses such as web scripting. It is also used as a
607 plotting engine by third-party applications like Octave.")
608 ;; X11 Style with the additional restriction that derived works may only be
609 ;; distributed as patches to the original.
610 (license (license:fsf-free
611 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
620 (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
622 (file-name (string-append name "-" version ".tar.gz"))
625 "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
627 `(("fortran" ,gfortran)))
628 (build-system gnu-build-system)
629 (synopsis "General Cartographic Transformation Package (GCTP)")
631 "The General Cartographic Transformation Package (GCTP) is a system of
632 software routines designed to permit the transformation of coordinate pairs
633 from one map projection to another. The GCTP is the standard computer
634 software used by the National Mapping Division for map projection
636 (home-page "https://github.com/OkoSanto/GCTP")
637 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
646 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
647 version "/src/hdf-" version ".tar.bz2"))
649 (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
650 (patches (search-patches "hdf4-architectures.patch"
651 "hdf4-reproducibility.patch"
652 "hdf4-shared-fortran.patch"))))
653 (build-system gnu-build-system)
655 `(("gfortran" ,gfortran)
660 ("libjpeg" ,libjpeg)))
662 `(#:parallel-tests? #f
663 #:configure-flags '("--enable-shared")
665 (modify-phases %standard-phases
666 ;; This is inspired by two of Debian's patches.
667 (add-before 'configure 'add-more-aarch64-support
669 (substitute* '("mfhdf/ncgen/ncgen.l"
670 "mfhdf/ncgen/ncgenyy.c"
671 "mfhdf/libsrc/netcdf.h.in")
672 (("AIX5L64") "__aarch64__"))
674 (add-before 'configure 'patchbuild
677 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
679 (("/bin/mkdir") "mkdir"))
680 (substitute* (find-files "." "^Makefile\\.in$")
681 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
682 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
683 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
684 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
685 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
687 (add-after 'configure 'patch-settings
689 ;; libhdf4.settings contains the full path of the
690 ;; compilers used, and its contents are included in
691 ;; .so-files. We truncate the hashes to avoid
692 ;; unnecessary store references to those compilers:
693 (substitute* "libhdf4.settings"
694 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
695 (string-append prefix (string-take hash 10) "...")))
698 (home-page "https://www.hdfgroup.org/products/hdf4/")
700 "Library and multi-object file format for storing and managing data")
701 (description "HDF4 is a library and multi-object file format for storing
702 and managing data between machines. HDF4 is an older hierarchical data format,
703 incompatible with HDF5.")
705 (license:non-copyleft
706 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
708 (define-public hdf4-alt
713 (substitute-keyword-arguments (package-arguments hdf4)
714 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
716 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
725 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
726 "hdf5-" (version-major+minor version)
727 "/hdf5-" version "/src/hdf5-"
729 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
732 (take (string-split version #\.) 2))
733 "/src/hdf5-" version ".tar.bz2")))
735 (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
736 (patches (list (search-patch "hdf5-config-date.patch")))))
737 (build-system gnu-build-system)
741 `(("gfortran" ,gfortran)))
742 (outputs '("out" ; core library
743 "fortran")) ; fortran interface
745 `(;; Some of the users, notably Flann, need the C++ interface.
746 #:configure-flags '("--enable-cxx"
748 "--enable-fortran2003")
749 ;; Use -fPIC to allow the R bindings to link with the static libraries
750 #:make-flags (list "CFLAGS=-fPIC"
753 (modify-phases %standard-phases
754 (add-before 'configure 'patch-configure
755 (lambda* (#:key outputs #:allow-other-keys)
756 (substitute* "configure"
758 (substitute* "fortran/src/Makefile.in"
759 (("libhdf5_fortran_la_LDFLAGS =")
760 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
761 (assoc-ref outputs "fortran") "/lib")))
762 (substitute* "hl/fortran/src/Makefile.in"
763 (("libhdf5hl_fortran_la_LDFLAGS =")
764 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
765 (assoc-ref outputs "fortran") "/lib")))
767 (add-after 'configure 'patch-settings
769 ;; libhdf5.settings contains the full path of the
770 ;; compilers used, and its contents are included in
771 ;; libhdf5.so. We truncate the hashes to avoid
772 ;; unnecessary store references to those compilers:
773 (substitute* "src/libhdf5.settings"
774 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
775 (string-append prefix (string-take hash 10) "..."))
776 ;; Don't record the build-time kernel version to make the
777 ;; settings file reproducible.
778 (("Uname information:.*")
779 "Uname information: Linux\n"))
781 (add-after 'install 'patch-references
782 (lambda* (#:key inputs outputs #:allow-other-keys)
783 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
784 (zlib (assoc-ref inputs "zlib")))
785 (substitute* (find-files bin "h5p?cc")
787 (string-append "-L" zlib "/lib " lib)))
789 (add-after 'install 'split
790 (lambda* (#:key inputs outputs #:allow-other-keys)
791 ;; Move all fortran-related files
792 (let* ((out (assoc-ref outputs "out"))
793 (bin (string-append out "/bin"))
794 (lib (string-append out "/lib"))
795 (inc (string-append out "/include"))
796 (ex (string-append out "/share/hdf5_examples/fortran"))
797 (fort (assoc-ref outputs "fortran"))
798 (fbin (string-append fort "/bin"))
799 (flib (string-append fort "/lib"))
800 (finc (string-append fort "/include"))
801 (fex (string-append fort "/share/hdf5_examples/fortran")))
806 (rename-file (string-append bin "/h5fc")
807 (string-append fbin "/h5fc"))
808 (for-each (lambda (file)
810 (string-append flib "/" (basename file))))
811 (find-files lib ".*fortran.*"))
812 (for-each (lambda (file)
814 (string-append finc "/" (basename file))))
815 (find-files inc ".*mod"))
816 (for-each (lambda (file)
818 (string-append fex "/" (basename file))))
819 (find-files ex ".*"))
820 (delete-file-recursively ex))
822 (home-page "http://www.hdfgroup.org")
823 (synopsis "Management suite for extremely large and complex data")
824 (description "HDF5 is a suite that makes possible the management of
825 extremely large and complex data collections.")
826 (license (license:x11-style
827 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
829 (define-public hdf-java
837 "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
838 version "/src/CMake-hdfjava-" version ".tar.gz"))
840 (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
841 (modules '((guix build utils)))
842 (snippet ; Make sure we don't use the bundled sources and binaries.
844 (for-each delete-file
845 (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
846 "HDF4.tar.gz" "HDF5.tar.gz"))
847 (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))))))
848 (build-system gnu-build-system)
850 `(("jdk" ,icedtea "jdk")
851 ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
853 ("hamcrest-core" ,java-hamcrest-core)
854 ("junit" ,java-junit)
855 ("slf4j-simple" ,java-slf4j-simple)))
861 ("slf4j-api" ,java-slf4j-api)))
864 (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
865 (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
866 (assoc-ref %build-inputs "jdk") "/lib" )
867 (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
868 (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
871 (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
872 (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
873 (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
874 (string-append "JPEGLIB="
875 (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
879 (modify-phases %standard-phases
880 (add-before 'configure 'chdir-to-source
881 (lambda _ (chdir ,(string-append "hdfjava-" version))))
882 (add-before 'configure 'patch-build
883 (lambda* (#:key inputs outputs #:allow-other-keys)
884 (substitute* "configure"
885 (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
886 (("/bin/cat") (which "cat")))
887 ;; Set classpath for compilation
888 (substitute* '("hdf/hdf5lib/Makefile.in"
889 "hdf/hdf5lib/exceptions/Makefile.in"
890 "hdf/hdflib/Makefile.in")
891 (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
892 (string-append (assoc-ref inputs "slf4j-api")
893 "/share/java/slf4j-api.jar")))
894 ;; Replace outdated config.sub and config.guess:
895 (with-directory-excursion "config"
896 (for-each (lambda (file)
898 (string-append (assoc-ref inputs "automake")
899 "/share/automake-1.15/" file) file))
900 '("config.sub" "config.guess")))
901 (mkdir-p (string-append (assoc-ref outputs "out")))
902 ;; Set classpath for tests
903 (let* ((build-dir (getcwd))
904 (lib (string-append build-dir "/lib"))
905 (jhdf (string-append lib "/jhdf.jar"))
906 (jhdf5 (string-append lib "/jhdf5.jar"))
909 (string-append (assoc-ref inputs i)
910 "/share/java/" i ".jar"))
911 '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
913 (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
915 (substitute* '("test/hdf5lib/Makefile.in"
916 "test/hdf5lib/junit.sh.in"
917 "examples/runExample.sh.in")
919 (string-append (assoc-ref inputs "coreutils")
922 (string-append (assoc-ref inputs "coreutils")
924 (("CLASSPATH=[^\n]*")
925 (string-append "CLASSPATH=" class-path)))
926 (setenv "CLASSPATH" class-path))
928 (add-before 'check 'build-examples
930 (zero? (apply system* `("javac"
931 ,@(find-files "examples" ".*\\.java")))))))
935 #:parallel-tests? #f ))
936 (home-page "https://support.hdfgroup.org/products/java")
937 (synopsis "Java interface for the HDF4 and HDF5 libraries")
938 (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
939 the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
942 ;; BSD-style license:
943 (license (license:x11-style
944 "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
945 /current/src/unpacked/COPYING"))))
947 (define-public hdf-eos2
954 (uri "ftp://edhs1.gsfc.nasa.gov\
955 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
957 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
958 (patches (search-patches "hdf-eos2-remove-gctp.patch"
959 "hdf-eos2-build-shared.patch"
960 "hdf-eos2-fortrantests.patch"))))
961 (build-system gnu-build-system)
963 `(("gfortran" ,gfortran)))
965 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
970 `( #:configure-flags '("--enable-install-include" "--enable-shared"
971 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
972 #:parallel-tests? #f))
973 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
974 (synopsis "HDF4-based data format for NASA's Earth Observing System")
975 (description "HDF-EOS2 is a software library built on HDF4 which supports
976 the construction of data structures used in NASA's Earth Observing
977 System (Grid, Point and Swath).")
979 ;; Source files carry a permissive license header.
980 (license (license:non-copyleft home-page))))
982 (define-public hdf-eos5
988 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
989 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
992 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
993 (patches (search-patches "hdf-eos5-build-shared.patch"
994 "hdf-eos5-remove-gctp.patch"
995 "hdf-eos5-fix-szip.patch"
996 "hdf-eos5-fortrantests.patch"))))
998 `(("gfortran" ,gfortran)))
999 (build-system gnu-build-system)
1005 `(#:configure-flags '("--enable-install-include" "--enable-shared"
1006 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1007 #:parallel-tests? #f))
1008 (synopsis "HDF5-based data format for NASA's Earth Observing System")
1010 "HDF-EOS5 is a software library built on HDF5 to support the construction
1011 of data structures used in NASA's Earth Observing System (Grid, Point and
1013 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1015 ;; Source files carry a permissive license header.
1016 (license (license:non-copyleft home-page))))
1018 (define-public hdf5-parallel-openmpi
1019 (package (inherit hdf5)
1020 (name "hdf5-parallel-openmpi")
1023 ,@(package-inputs hdf5)))
1025 (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
1026 ,@(package-arguments hdf5))
1028 `(modify-phases ,phases
1029 (add-before 'check 'patch-tests
1031 ;; OpenMPI's mpirun will exit with non-zero status if it
1032 ;; detects an "abnormal termination", i.e. any process not
1033 ;; calling MPI_Finalize(). Since the test is explicitely
1034 ;; avoiding MPI_Finalize so as not to have at_exit and thus
1035 ;; H5C_flush_cache from being called, mpirun will always
1036 ;; complain, so turn this test off.
1037 (substitute* "testpar/Makefile"
1038 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1039 (string-append front back "\n")))
1040 (substitute* "tools/h5diff/testph5diff.sh"
1041 (("/bin/sh") (which "sh")))
1043 (synopsis "Management suite for data with parallel IO support")))
1045 (define-public h5check
1052 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
1053 "h5check/src/h5check-" version ".tar.gz"))
1056 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1057 (build-system gnu-build-system)
1058 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
1059 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1060 (synopsis "HDF5 format checker")
1061 (description "@code{h5check} is a validation tool for verifying that an
1062 HDF5 file is encoded according to the HDF File Format Specification.")
1063 (license (license:x11-style "file://COPYING"))))
1071 (uri (string-append "mirror://sourceforge/itpp/itpp/"
1076 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1077 (build-system cmake-build-system)
1078 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1079 (inputs `(("lapack" ,lapack)
1081 ;; FIXME: Even though the fonts are available dvips complains:
1082 ;; "Font cmmi10 not found; characters will be left blank."
1084 `(("texlive" ,texlive-tiny)
1085 ("ghostscript" ,ghostscript)
1086 ("doxygen" ,doxygen)))
1087 (home-page "http://itpp.sourceforge.net")
1088 (synopsis "C++ library of maths, signal processing and communication classes")
1089 (description "IT++ is a C++ library of mathematical, signal processing and
1090 communication classes and functions. Its main use is in simulation of
1091 communication systems and for performing research in the area of
1092 communications. The kernel of the library consists of generic vector and
1093 matrix classes, and a set of accompanying routines. Such a kernel makes IT++
1094 similar to MATLAB, GNU Octave or SciPy.")
1095 (license license:gpl3+)))
1097 (define-public netcdf
1104 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1105 "netcdf-" version ".tar.gz"))
1108 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1109 (patches (search-patches "netcdf-date-time.patch"
1110 "netcdf-tst_h_par.patch"))))
1111 (build-system gnu-build-system)
1114 ("doxygen" ,doxygen)
1115 ("graphviz" ,graphviz)))
1117 `(("hdf4" ,hdf4-alt)
1120 ("libjpeg" ,libjpeg)))
1122 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
1124 #:phases (modify-phases %standard-phases
1125 (add-before 'configure 'fix-source-date
1127 ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1128 ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1129 ;; to '1st hour of the current day', and therefore makes the
1130 ;; package not reproducible.
1131 (substitute* "./configure"
1132 (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1133 "date --date='@0'"))
1135 (add-after 'configure 'patch-settings
1137 ;; libnetcdf.settings contains the full filename of the compilers
1138 ;; used to build the library. We truncate the hashes of those
1139 ;; filenames to avoid unnecessary references to the corresponding
1141 (substitute* "libnetcdf.settings"
1142 (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1143 (string-append prefix (string-take hash 10) "...")))
1146 #:parallel-tests? #f)) ;various race conditions
1147 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
1148 (synopsis "Library for scientific data")
1149 (description "NetCDF is an interface for scientific data access and a
1150 software library that provides an implementation of the interface. The netCDF
1151 library defines a machine-independent format for representing scientific data.
1152 Together, the interface, library, and format support the creation, access, and
1153 sharing of scientific data.")
1154 (license (license:x11-style "file://COPYRIGHT"))))
1156 (define-public netcdf-parallel-openmpi
1157 (package (inherit netcdf)
1158 (name "netcdf-parallel-openmpi")
1161 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1162 (package-inputs netcdf))))
1163 ;; TODO: Replace pkg-config references in nc-config with absolute references
1165 (substitute-keyword-arguments (package-arguments netcdf)
1166 ((#:configure-flags flags)
1167 `(cons* "CC=mpicc" "CXX=mpicxx"
1168 "--enable-parallel-tests"
1169 ;; Shared libraries not supported with parallel IO.
1170 "--disable-shared" "--with-pic"
1173 (define-public netcdf-fortran
1175 (name "netcdf-fortran")
1180 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1184 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1185 (build-system gnu-build-system)
1187 `(#:parallel-tests? #f))
1189 `(("netcdf" ,netcdf)))
1191 `(("gfortran" ,gfortran)))
1192 (synopsis "Fortran interface for the netCDF library")
1193 (description (package-description netcdf))
1194 (home-page (package-home-page netcdf))
1195 (license (package-license netcdf))))
1197 (define-public nlopt
1203 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1206 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1207 (build-system gnu-build-system)
1209 `(;; Shared libraries are not built by default. They are required to
1210 ;; build the Guile, Octave, and Python bindings.
1211 #:configure-flags '("--enable-shared")
1214 (modify-phases %standard-phases
1215 (add-before 'configure 'set-libnlopt-file-name
1216 (lambda* (#:key outputs #:allow-other-keys)
1217 ;; Make sure the Scheme module refers to the library by its
1218 ;; absolute file name (we cannot do that from a snippet
1219 ;; because the expansion of @libdir@ contains
1221 (let ((out (assoc-ref outputs "out")))
1222 (substitute* "swig/nlopt.scm.in"
1224 (string-append out "/lib/libnlopt")))
1226 (inputs `(("guile" ,guile-2.0)))
1227 (native-inputs `(("pkg-config" ,pkg-config)))
1228 (home-page "http://ab-initio.mit.edu/wiki/")
1229 (synopsis "Library for nonlinear optimization")
1230 (description "NLopt is a library for nonlinear optimization, providing a
1231 common interface for a number of different free optimization routines available
1232 online as well as original implementations of various other algorithms.")
1233 (license license:lgpl2.1+)))
1235 (define-public ipopt
1242 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1246 "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
1247 (modules '((guix build utils)))
1249 ;; Make sure we don't use the bundled software.
1250 '(delete-file-recursively "ThirdParty"))))
1251 (build-system gnu-build-system)
1253 '(#:phases (modify-phases %standard-phases
1254 (add-after 'install 'add--L-flags-in-ipopt.pc
1255 (lambda* (#:key inputs outputs #:allow-other-keys)
1256 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1257 ;; move it to "Libs.private" where it belongs, and add a
1258 ;; '-L' flag for LAPACK.
1259 (let ((out (assoc-ref outputs "out"))
1260 (lapack (assoc-ref inputs "lapack")))
1261 (substitute* (string-append out "/lib/pkgconfig/"
1263 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1264 (string-append "Libs: " before " " after "\n"
1265 "Libs.private: " before
1266 "-L" lapack "/lib -llapack -lblas "
1270 `(("gfortran" ,gfortran)))
1272 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
1273 `(("lapack" ,lapack))) ;for both libblas and liblapack
1274 (home-page "http://www.coin-or.org")
1275 (synopsis "Large-scale nonlinear optimizer")
1277 "The Interior Point Optimizer (IPOPT) is a software package for
1278 large-scale nonlinear optimization. It provides C++, C, and Fortran
1280 (license license:epl1.0)))
1282 (define-public ceres
1284 (name "ceres-solver")
1286 (home-page "http://ceres-solver.org/")
1289 (uri (string-append home-page "ceres-solver-"
1293 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
1294 (build-system cmake-build-system)
1296 ;; TODO: Build HTML user documentation and install separately.
1297 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
1298 "-DBUILD_SHARED_LIBS=ON")
1300 #:phases (modify-phases %standard-phases
1301 (add-before 'configure 'set-library-directory
1303 ;; Install libraries to lib/, not lib64/.
1304 (substitute* "internal/ceres/CMakeLists.txt"
1305 (("set\\(LIB_SUFFIX \"64\"\\)")
1306 "set(LIB_SUFFIX \"\")"))
1309 `(("pkg-config" ,pkg-config)))
1311 `(("glog" ,glog))) ;for #include <glog/glog.h>
1316 ("suitesparse" ,suitesparse)
1317 ("gflags" ,gflags)))
1318 (synopsis "C++ library for solving large optimization problems")
1320 "Ceres Solver is a C++ library for modeling and solving large,
1321 complicated optimization problems. It is a feature rich, mature and
1322 performant library which has been used in production since 2010. Ceres Solver
1323 can solve two kinds of problems:
1325 @item non-linear least squares problems with bounds constraints;
1326 @item general unconstrained optimization problems.
1328 (license license:bsd-3)))
1330 ;; For a fully featured Octave, users are strongly recommended also to install
1331 ;; the following packages: less, ghostscript, gnuplot.
1332 (define-public octave
1339 (uri (string-append "mirror://gnu/octave/octave-"
1343 "0nm766737gbkq9wqry54a026k3dg7rb1065kngfpwgjz8b544xbp"))))
1344 (build-system gnu-build-system)
1346 `(("lapack" ,lapack)
1347 ("readline" ,readline)
1352 ("arpack" ,arpack-ng)
1355 ("fontconfig" ,fontconfig)
1356 ("freetype" ,freetype)
1363 ("texinfo" ,texinfo)
1364 ("graphicsmagick" ,graphicsmagick)
1365 ("suitesparse" ,suitesparse)
1366 ("libsndfile" ,libsndfile)
1367 ("portaudio" ,portaudio)
1368 ("alsa-lib" ,alsa-lib)))
1371 ("gfortran" ,gfortran)
1372 ("pkg-config" ,pkg-config)
1374 ;; The following inputs are not actually used in the build process.
1375 ;; However, the ./configure gratuitously tests for their existence and
1376 ;; assumes that programs not present at build time are also not, and
1377 ;; can never be, available at run time! If these inputs are therefore
1378 ;; not present, support for them will be built out. However, Octave
1379 ;; will still run without them, albeit without the features they
1382 ("ghostscript" ,ghostscript)
1383 ("gnuplot" ,gnuplot)))
1386 (list (string-append "--with-shell="
1387 (assoc-ref %build-inputs "bash")
1390 (modify-phases %standard-phases
1391 (add-after 'configure 'configure-makeinfo
1392 (lambda* (#:key inputs #:allow-other-keys)
1393 (substitute* "libinterp/corefcn/help.cc"
1394 (("Vmakeinfo_program = \"makeinfo\"")
1395 (string-append "Vmakeinfo_program = \""
1396 (assoc-ref inputs "texinfo")
1397 "/bin/makeinfo\"")))
1399 (home-page "https://www.gnu.org/software/octave/")
1400 (synopsis "High-level language for numerical computation")
1401 (description "GNU Octave is a high-level interpreted language that is
1402 specialized for numerical computations. It can be used for both linear and
1403 non-linear applications and it provides great support for visualizing results.
1404 Work may be performed both at the interactive command-line as well as via
1406 (license license:gpl3+)))
1408 (define-public qtoctave
1409 (package (inherit octave)
1412 `(("qscintilla" ,qscintilla)
1414 ,@(package-inputs octave)))
1416 `(("qttools" , qttools) ;for lrelease
1417 ,@(package-native-inputs octave)))
1419 (substitute-keyword-arguments (package-arguments octave)
1421 `(modify-phases ,phases
1422 (add-before 'configure 'patch-qscintilla-library-name
1423 (lambda* (#:key inputs #:allow-other-keys)
1424 ;; The QScintilla library that the Octave configure script tries
1425 ;; to link with should be named libqscintilla-qt5.so, but the
1426 ;; QScintilla input provides the shared library as
1427 ;; libqscintilla2_qt5.so.
1428 (substitute* "configure"
1429 (("qscintilla2-qt5")
1433 (define-public opencascade-oce
1435 (name "opencascade-oce")
1441 "https://github.com/tpaviot/oce/archive/OCE-"
1444 (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
1447 "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
1448 (build-system cmake-build-system)
1451 (list "-DOCE_TESTING:BOOL=ON"
1452 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1453 "-DOCE_DRAW:BOOL=ON"
1454 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1455 (assoc-ref %outputs "out"))
1456 "-UCMAKE_INSTALL_RPATH")))
1458 `(("freetype" ,freetype)
1465 `(("python" ,python-wrapper)))
1466 (home-page "https://github.com/tpaviot/oce")
1467 (synopsis "Libraries for 3D modeling and numerical simulation")
1469 "Open CASCADE is a set of libraries for the development of applications
1470 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1471 C++ class libraries providing services for 3D surface and solid modeling, CAD
1472 data exchange, and visualization. It is used for development of specialized
1473 software dealing with 3D models in design (CAD), manufacturing (CAM),
1474 numerical simulation (CAE), measurement equipment (CMM), and quality
1475 control (CAQ) domains.
1477 This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1478 patches, improvements, and experiments contributed by users over the official
1479 Open CASCADE library.")
1480 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1481 ; use of header files; see
1482 ; OCCT_LGPL_EXCEPTION.txt
1483 license:public-domain; files
1484 ; src/Standard/Standard_StdAllocator.hxx and
1485 ; src/NCollection/NCollection_StdAllocator.hxx
1486 license:expat; file src/OpenGl/OpenGl_glext.h
1487 license:bsd-3)))); test framework gtest
1496 (uri (string-append "http://gmsh.info/src/gmsh-"
1497 version "-source.tgz"))
1499 (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
1500 (modules '((guix build utils)))
1502 ;; Remove non-free METIS code
1503 '(delete-file-recursively "contrib/Metis"))))
1504 (build-system cmake-build-system)
1507 ("gfortran" ,gfortran)
1513 ("opencascade-oce" ,opencascade-oce)
1515 ("libxext" ,libxext)))
1517 `(("fontconfig" ,fontconfig)
1518 ("libxft" ,libxft)))
1520 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1521 "-DENABLE_BUILD_SHARED:BOOL=ON"
1522 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
1523 (home-page "http://www.geuz.org/gmsh/")
1524 (synopsis "3D finite element grid generator")
1525 (description "Gmsh is a 3D finite element grid generator with a built-in
1526 CAD engine and post-processor. Its design goal is to provide a fast, light
1527 and user-friendly meshing tool with parametric input and advanced
1528 visualization capabilities. Gmsh is built around four modules: geometry,
1529 mesh, solver and post-processing. The specification of any input to these
1530 modules is done either interactively using the graphical user interface or in
1531 ASCII text files using Gmsh's own scripting language.")
1532 (license license:gpl2+)))
1534 (define-public maxflow
1541 (url "https://github.com/gerddie/maxflow.git")
1542 (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
1543 (file-name (string-append name "-" version "-checkout"))
1546 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1547 (build-system cmake-build-system)
1548 (home-page "http://pub.ist.ac.at/~vnk/software.html")
1549 (synopsis "Library implementing Maxflow algorithm")
1550 (description "An implementation of the maxflow algorithm described in
1551 @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1552 Energy Minimization in Computer Vision.\n
1553 Yuri Boykov and Vladimir Kolmogorov.\n
1554 In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1556 (license license:gpl3+)))
1558 (define-public petsc
1565 ;; The *-lite-* tarball does not contain the *large* documentation
1566 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1567 "petsc-lite-" version ".tar.gz"))
1569 (base32 "1lajbk3c29hnh83v6cbmm3a8wv6bdykh0p70kwrr4vrnizalk88s"))))
1570 (build-system gnu-build-system)
1572 `(("python" ,python-2)))
1574 `(("gfortran" ,gfortran)
1576 ("superlu" ,superlu)
1577 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1578 ;; leaving out opengl, as configuration seems to only be for mac
1581 `(#:test-target "test"
1582 #:parallel-build? #f ;build is parallel by default
1587 ,(string-append "--with-superlu-include="
1588 (assoc-ref %build-inputs "superlu") "/include")
1589 ,(string-append "--with-superlu-lib="
1590 (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
1592 ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
1593 ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1594 (list (format #f "MAKE_NP=~a" (parallel-job-count)))
1596 (modify-phases %standard-phases
1598 ;; PETSc's configure script is actually a python script, so we can't
1599 ;; run it with bash.
1600 (lambda* (#:key outputs (configure-flags '())
1602 (let* ((prefix (assoc-ref outputs "out"))
1603 (flags `(,(string-append "--prefix=" prefix)
1604 ,@configure-flags)))
1605 (format #t "build directory: ~s~%" (getcwd))
1606 (format #t "configure flags: ~s~%" flags)
1607 (zero? (apply system* "./configure" flags)))))
1608 (add-after 'configure 'clean-local-references
1609 (lambda* (#:key outputs #:allow-other-keys)
1610 (let ((out (assoc-ref outputs "out")))
1611 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
1612 ;; Prevent build directory from leaking into compiled code
1614 ;; Scrub timestamp for reproducibility
1615 ((".*Libraries compiled on.*") ""))
1616 (substitute* (find-files "." "petscvariables")
1617 ;; Do not expose build machine characteristics, set to defaults.
1618 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1619 (("NPMAX = [:digit:]+") "NPMAX = 2"))
1621 (add-after 'install 'clean-install
1622 ;; Try to keep installed files from leaking build directory names.
1623 (lambda* (#:key inputs outputs #:allow-other-keys)
1624 (let ((out (assoc-ref outputs "out")))
1625 (substitute* (map (lambda (file)
1626 (string-append out "/lib/petsc/conf/" file))
1627 '("petscvariables"))
1629 ;; Make compiler references point to the store
1630 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
1631 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1632 (string-append "= " (which compiler))))
1633 ;; PETSc installs some build logs, which aren't necessary.
1634 (for-each (lambda (file)
1635 (let ((f (string-append out "/lib/petsc/conf/" file)))
1636 (when (file-exists? f)
1638 '("configure.log" "make.log" "gmake.log"
1639 "test.log" "error.log" "RDict.db"
1640 "PETScBuildInternal.cmake"
1641 ;; Once installed, should uninstall with Guix
1644 (home-page "http://www.mcs.anl.gov/petsc")
1645 (synopsis "Library to solve PDEs")
1646 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1647 data structures and routines for the scalable (parallel) solution of
1648 scientific applications modeled by partial differential equations.")
1649 (license (license:non-copyleft
1650 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1652 (define-public petsc-complex
1653 (package (inherit petsc)
1654 (name "petsc-complex")
1656 (substitute-keyword-arguments (package-arguments petsc)
1657 ((#:configure-flags cf)
1658 `(cons "--with-scalar-type=complex" ,cf))))
1659 (synopsis "Library to solve PDEs (with complex scalars)")))
1661 (define-public petsc-openmpi
1662 (package (inherit petsc)
1663 (name "petsc-openmpi")
1665 `(("openmpi" ,openmpi)
1666 ,@(package-inputs petsc)))
1668 (substitute-keyword-arguments (package-arguments petsc)
1669 ((#:configure-flags cf)
1670 ``("--with-mpiexec=mpirun"
1671 ,(string-append "--with-mpi-dir="
1672 (assoc-ref %build-inputs "openmpi"))
1673 ,@(delete "--with-mpi=0" ,cf)))))
1674 (synopsis "Library to solve PDEs (with MPI support)")))
1676 (define-public petsc-complex-openmpi
1677 (package (inherit petsc-complex)
1678 (name "petsc-complex-openmpi")
1680 `(("openmpi" ,openmpi)
1681 ,@(package-inputs petsc-complex)))
1683 (substitute-keyword-arguments (package-arguments petsc-complex)
1684 ((#:configure-flags cf)
1685 ``("--with-mpiexec=mpirun"
1686 ,(string-append "--with-mpi-dir="
1687 (assoc-ref %build-inputs "openmpi"))
1688 ,@(delete "--with-mpi=0" ,cf)))))
1689 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
1692 (define-public python-kiwisolver
1694 (name "python-kiwisolver")
1698 (uri (pypi-uri "kiwisolver" version))
1701 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
1702 (build-system python-build-system)
1703 (home-page "https://github.com/nucleic/kiwi")
1704 (synopsis "Fast implementation of the Cassowary constraint solver")
1706 "Kiwi is an efficient C++ implementation of the Cassowary constraint
1707 solving algorithm. Kiwi has been designed from the ground up to be
1708 lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
1709 Cassowary solver with typical use cases gaining a 40x improvement. Memory
1710 savings are consistently > 5x.")
1711 (license license:bsd-3)))
1713 (define-public python2-kiwisolver
1714 (package-with-python2 python-kiwisolver))
1716 (define-public slepc
1723 (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
1727 "04zd48p43rnvg68p6cp28zll0px5whglc5v0sc3s6vdj1v920z8y"))))
1728 (build-system gnu-build-system)
1730 `(("python" ,python-2)))
1732 `(("arpack" ,arpack-ng)
1733 ("gfortran" ,gfortran)))
1735 `(("petsc" ,petsc)))
1737 `(#:parallel-build? #f ;build is parallel by default
1739 `(,(string-append "--with-arpack-dir="
1740 (assoc-ref %build-inputs "arpack") "/lib"))
1741 #:make-flags ;honor (parallel-job-count)
1742 `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
1744 (modify-phases %standard-phases
1746 ;; configure is a python script, so we can't run it with bash.
1747 (lambda* (#:key inputs outputs (configure-flags '())
1749 (let* ((prefix (assoc-ref outputs "out"))
1750 (flags `(,(string-append "--prefix=" prefix)
1751 ,@configure-flags)))
1752 (format #t "build directory: ~s~%" (getcwd))
1753 (format #t "configure flags: ~s~%" flags)
1754 (setenv "SLEPC_DIR" (getcwd))
1755 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
1756 (apply invoke "./configure" flags))))
1757 (add-after 'install 'delete-doc
1758 ;; TODO: SLEPc installs HTML documentation alongside headers in
1759 ;; $out/include. We'd like to move them to share/doc, but delete
1760 ;; them for now, as they are incomplete and installing the complete
1761 ;; documentation is difficult.
1762 (lambda* (#:key outputs #:allow-other-keys)
1763 (let* ((out (assoc-ref outputs "out")))
1764 (for-each delete-file (find-files out "\\.html$")))))
1765 (add-after 'install 'clean-install
1766 ;; Clean up unnecessary build logs from installation.
1767 (lambda* (#:key outputs #:allow-other-keys)
1768 (let ((out (assoc-ref outputs "out")))
1769 (for-each (lambda (file)
1770 (let ((f (string-append out "/lib/slepc/conf/" file)))
1771 (when (file-exists? f)
1773 '("configure.log" "make.log" "gmake.log"
1774 "test.log" "error.log" "RDict.db"
1775 "uninstall.py"))))))))
1776 (home-page "http://slepc.upv.es")
1777 (synopsis "Scalable library for eigenproblems")
1778 (description "SLEPc is a software library for the solution of large sparse
1779 eigenproblems on parallel computers. It can be used for the solution of
1780 linear eigenvalue problems formulated in either standard or generalized form,
1781 as well as other related problems such as the singular value decomposition.
1782 The emphasis of the software is on methods and techniques appropriate for
1783 problems in which the associated matrices are sparse, for example, those
1784 arising after the discretization of partial differential equations.")
1785 (license license:bsd-2)))
1787 (define-public slepc-complex
1788 (package (inherit slepc)
1789 (name "slepc-complex")
1791 `(("petsc" ,petsc-complex)
1792 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1793 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1795 (define-public slepc-openmpi
1796 (package (inherit slepc)
1797 (name "slepc-openmpi")
1799 (substitute-keyword-arguments (package-arguments slepc)
1800 ((#:phases phases '%standard-phases)
1801 `(modify-phases ,phases
1802 (add-before 'check 'set-test-environment
1804 ;; By default, running the test suite would fail because 'ssh'
1805 ;; could not be found in $PATH. Define this variable to
1806 ;; placate Open MPI without adding a dependency on OpenSSH (the
1807 ;; agent isn't used anyway.)
1808 (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
1812 ("arpack" ,arpack-ng-openmpi)
1813 ,@(alist-delete "arpack" (package-inputs slepc))))
1815 `(("petsc" ,petsc-openmpi)
1816 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1817 (synopsis "Scalable library for eigenproblems (with MPI support)")))
1819 (define-public slepc-complex-openmpi
1820 (package (inherit slepc-openmpi)
1821 (name "slepc-complex-openmpi")
1823 `(("petsc" ,petsc-complex-openmpi)
1824 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1825 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1827 (define-public mumps
1834 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
1838 "1s9asin08zqzmh08257sdghhivvy9vjif7c53fhaxaax2kd5qd7b"))
1839 (patches (search-patches "mumps-build-parallelism.patch"))))
1840 (build-system gnu-build-system)
1842 `(("fortran" ,gfortran)
1843 ;; These are required for linking against mumps, but we let the user
1844 ;; declare the dependency.
1847 ("scotch" ,scotch)))
1849 `(#:modules ((ice-9 match)
1852 ,@%gnu-build-system-modules)
1854 (modify-phases %standard-phases
1856 (lambda* (#:key inputs #:allow-other-keys)
1857 (call-with-output-file "Makefile.inc"
1868 INCSEQ = -I$(topdir)/libseq
1869 LIBSEQ = -L$(topdir)/libseq -lmpiseq
1870 LIBSEQNEEDED = libseqneeded~;
1874 AR = ar vr # rules require trailing space, ugh...
1876 LIBBLAS = -L~a -lopenblas~@[
1877 SCALAP = -L~a -lscalapack~]
1878 LIBOTHERS = -pthread
1881 OPTF = -O2 -DALLOW_NON_INIT $(PIC)
1885 LIBS = $(SCALAP) $(LIBSEQ)
1886 LPORDDIR = $(topdir)/PORD/lib
1887 IPORD = -I$(topdir)/PORD/include
1888 LPORD = -L$(LPORDDIR) -lpord
1889 ORDERINGSF = -Dpord~@[
1891 IMETIS = -I$(METISDIR)/include
1892 LMETIS = -L$(METISDIR)/lib -lmetis
1893 ORDERINGSF += -Dmetis~]~@[~:{
1895 ISCOTCH = -I$(SCOTCHDIR)/include
1896 LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
1897 ORDERINGSF += ~a~}~]
1898 ORDERINGSC = $(ORDERINGSF)
1899 LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
1900 IORDERINGSF = $(ISCOTCH)
1901 IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
1902 (assoc-ref inputs "mpi")
1903 (assoc-ref inputs "blas")
1904 (assoc-ref inputs "scalapack")
1905 (assoc-ref inputs "metis")
1906 (match (list (assoc-ref inputs "pt-scotch")
1907 (assoc-ref inputs "scotch"))
1911 `((,scotch "" "-Dscotch")))
1914 "-lptesmumps -lptscotch -lptscotcherr "
1915 "-Dptscotch")))))))))
1917 ;; By default only the d-precision library is built. Make with "all"
1918 ;; target so that all precision libraries and examples are built.
1920 (zero? (system* "make" "all"
1921 (format #f "-j~a" (parallel-job-count))))))
1923 ;; Run the simple test drivers, which read test input from stdin:
1924 ;; from the "real" input for the single- and double-precision
1925 ;; testers, and from the "cmplx" input for complex-precision
1926 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
1927 ;; package to prefix execution with "mpirun".
1928 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
1929 (with-directory-excursion "examples"
1932 (let ((tester (apply open-pipe*
1935 ,(string-append "./" prec
1937 (input (open-input-file
1938 (string-append "input_simpletest_" type))))
1940 (dump-port input tester)
1942 (zero? (close-pipe tester)))))
1944 '("real" "real" "cmplx" "cmplx")))))
1946 (lambda* (#:key outputs #:allow-other-keys)
1947 (let* ((out (assoc-ref outputs "out"))
1948 (libdir (string-append out "/lib")))
1949 (copy-recursively "lib" libdir)
1950 (copy-recursively "include" (string-append out "/include"))
1951 (when (file-exists? "libseq/libmpiseq.a")
1952 (install-file "libseq/libmpiseq.a" libdir))
1954 (home-page "http://mumps.enseeiht.fr")
1955 (synopsis "Multifrontal sparse direct solver")
1957 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
1958 sparse system of linear equations A x = b using Guassian elimination.")
1959 (license license:cecill-c)))
1961 (define-public mumps-metis
1962 (package (inherit mumps)
1963 (name "mumps-metis")
1965 (alist-delete "scotch" (package-inputs mumps)))))
1967 (define-public mumps-openmpi
1968 (package (inherit mumps)
1969 (name "mumps-openmpi")
1972 ("scalapack" ,scalapack)
1973 ("pt-scotch" ,pt-scotch)
1974 ,@(alist-delete "scotch" (package-inputs mumps))))
1976 (substitute-keyword-arguments (package-arguments mumps)
1978 `(modify-phases ,phases
1979 (add-before 'check 'set-test-environment
1981 ;; By default, running the test suite would fail because 'ssh'
1982 ;; could not be found in $PATH. Define this variable to
1983 ;; placate Open MPI without adding a dependency on OpenSSH (the
1984 ;; agent isn't used anyway.)
1985 (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
1989 ((assoc-ref ,phases 'check)
1990 #:exec-prefix '("mpirun" "-n" "2"))))))))
1991 (synopsis "Multifrontal sparse direct solver (with MPI)")))
1993 (define-public mumps-metis-openmpi
1994 (package (inherit mumps-openmpi)
1995 (name "mumps-metis-openmpi")
1997 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
1999 (define-public r-quadprog
2006 (uri (cran-uri "quadprog" version))
2009 "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
2010 (build-system r-build-system)
2012 `(("gfortran" ,gfortran)))
2013 (home-page "https://cran.r-project.org/web/packages/quadprog")
2014 (synopsis "Functions to solve quadratic programming problems")
2016 "This package contains routines and documentation for solving quadratic
2017 programming problems.")
2018 (license license:gpl3+)))
2020 (define-public r-pracma
2026 (uri (cran-uri "pracma" version))
2028 (base32 "1ygm81i7mqvh229dp9935djjyb120p3bqvaf4k572sa4q63fzjhc"))))
2029 (build-system r-build-system)
2031 `(("r-quadprog" ,r-quadprog)))
2032 (home-page "https://cran.r-project.org/web/packages/pracma")
2033 (synopsis "Practical numerical math functions")
2034 (description "This package provides functions for numerical analysis and
2035 linear algebra, numerical optimization, differential equations, plus some
2036 special functions. It uses Matlab function names where appropriate to simplify
2038 (license license:gpl3+)))
2040 (define-public ruby-asciimath
2042 (name "ruby-asciimath")
2047 (uri (rubygems-uri "asciimath" version))
2050 "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
2051 (build-system ruby-build-system)
2054 (modify-phases %standard-phases
2056 ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
2057 (add-after 'unpack 'patch-remove-spurious-backslashes
2059 (substitute* "spec/parser_spec.rb"
2063 `(("bundler" ,bundler)
2064 ("ruby-rspec" ,ruby-rspec)))
2065 (synopsis "AsciiMath parsing and conversion library")
2067 "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
2068 easy-to-write markup language for mathematics.")
2069 (home-page "https://github.com/asciidoctor/asciimath")
2070 (license license:expat)))
2072 (define-public superlu
2079 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2080 "superlu_" version ".tar.gz"))
2082 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
2083 (modules '((guix build utils)))
2085 ;; Replace the non-free implementation of MC64 with a stub adapted
2088 (use-modules (ice-9 regex)
2090 (call-with-output-file "SRC/mc64ad.c"
2095 void mc64id_(int *a) {
2096 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2099 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2100 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2101 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
2104 ;; Remove the corresponding license verbiage. MC64 license follows
2105 ;; a "------" line separator.
2106 (with-atomic-file-replacement "License.txt"
2107 (let ((rx (make-regexp "-{8}")))
2110 (let ((line (read-line in 'concat)))
2111 (unless (regexp-exec rx line)
2114 (build-system cmake-build-system)
2118 `(("blas" ,openblas)
2119 ("gfortran" ,gfortran)))
2121 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2122 "-DTPL_BLAS_LIBRARIES=openblas"
2123 "-DBUILD_SHARED_LIBS:BOOL=YES")))
2124 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
2125 (synopsis "Supernodal direct solver for sparse linear systems")
2127 "SuperLU is a general purpose library for the direct solution of large,
2128 sparse, nonsymmetric systems of linear equations on high performance machines.
2129 The library is written in C and is callable from either C or Fortran. The
2130 library routines perform an LU decomposition with partial pivoting and
2131 triangular system solves through forward and back substitution. The library
2132 also provides threshold-based ILU factorization preconditioners.")
2133 (license (list license:bsd-3
2134 license:gpl2+ ;EXAMPLE/*fgmr.c
2135 (license:fsf-free "file://SRC/colamd.h")))))
2137 (define-public superlu-dist
2139 (name "superlu-dist")
2144 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2145 "superlu_dist_" version ".tar.gz"))
2147 (base32 "0ja5ihqivkda1wd58y4lmzvmwssm9g91f70c5q0fzwhng6580h6y"))
2148 (modules '((guix build utils)))
2150 ;; Replace the non-free implementation of MC64 with a stub
2152 (use-modules (ice-9 regex)
2154 (call-with-output-file "SRC/mc64ad_dist.c"
2159 void mc64id_dist(int *a) {
2160 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2163 void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2164 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2165 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
2168 (substitute* "SRC/util.c" ;adjust default algorithm
2169 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
2170 "RowPerm = NOROWPERM"))))
2171 (patches (search-patches "superlu-dist-scotchmetis.patch"))))
2172 (build-system gnu-build-system)
2176 `(("gfortran" ,gfortran)))
2178 `(("openmpi" ,openmpi) ;headers include MPI heades
2179 ("lapack" ,lapack) ;required to link with output library
2180 ("pt-scotch" ,pt-scotch))) ;same
2182 `(#:parallel-build? #f ;race conditions using ar
2184 (modify-phases %standard-phases
2186 (lambda* (#:key inputs outputs #:allow-other-keys)
2187 (call-with-output-file "make.inc"
2192 DSUPERLULIB = ~a/lib/libsuperlu_dist.a
2193 BLASDEF = -DUSE_VENDOR_BLAS
2194 BLASLIB = -L~a/lib -lblas
2195 PARMETISLIB = -L~a/lib \
2196 -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
2197 -lscotch -lscotcherr -lscotcherrexit
2198 METISLIB = -L~:*~a/lib \
2199 -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
2200 LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
2206 CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC)
2207 NOOPTS = -O0 -g $(PIC)
2209 FFLAGS = -O2 -g $(PIC)
2213 (assoc-ref outputs "out")
2214 (assoc-ref inputs "lapack")
2215 (assoc-ref inputs "pt-scotch"))))
2217 (add-after 'unpack 'remove-broken-symlinks
2219 (for-each delete-file
2220 (find-files "MAKE_INC" "\\.#make\\..*"))
2222 (add-before 'build 'create-install-directories
2223 (lambda* (#:key outputs #:allow-other-keys)
2226 (mkdir-p (string-append (assoc-ref outputs "out")
2232 ;; By default, running the test suite would fail because 'ssh'
2233 ;; could not be found in $PATH. Define this variable to placate
2234 ;; Open MPI without adding a dependency on OpenSSH (the agent
2235 ;; isn't used anyway.)
2236 (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
2237 (with-directory-excursion "EXAMPLE"
2239 (zero? (system* "mpirun" "-n" "2"
2240 "./pddrive" "-r" "1" "-c" "2" "g20.rua"))
2241 (zero? (system* "mpirun" "-n" "2"
2242 "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))))))
2244 (lambda* (#:key outputs #:allow-other-keys)
2245 ;; Library is placed in lib during the build phase. Copy over
2246 ;; headers to include.
2247 (let* ((out (assoc-ref outputs "out"))
2248 (incdir (string-append out "/include")))
2249 (for-each (lambda (file)
2250 (let ((base (basename file)))
2251 (format #t "installing `~a' to `~a'~%"
2254 (string-append incdir "/" base))))
2255 (find-files "SRC" ".*\\.h$")))
2257 (home-page (package-home-page superlu))
2258 (synopsis "Parallel supernodal direct solver")
2260 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2261 It is targeted for distributed memory parallel machines. SuperLU_DIST is
2262 implemented in ANSI C, and MPI for communications.")
2263 (license license:bsd-3)))
2265 (define-public scotch
2272 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
2273 "latestfile/298/scotch_" version ".tar.gz"))
2275 (base32 "0vsmgjz8qv80di3ljmc7hbdsizxxxwy2b9rgd2fl1mdc6dgbj8av"))
2276 (patches (search-patches "scotch-test-threading.patch"
2277 "scotch-build-parallelism.patch"
2278 "scotch-graph-induce-type-64.patch"
2279 "scotch-graph-diam-64.patch"))))
2280 (build-system gnu-build-system)
2287 (modify-phases %standard-phases
2289 'unpack 'chdir-to-src
2290 (lambda _ (chdir "src")))
2294 (call-with-output-file "Makefile.inc"
2308 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2309 LDFLAGS = -lz -lm -lrt -lpthread
2311 LEX = flex -Pscotchyy -olex.yy.c
2316 YACC = bison -pscotchyy -y -b y
2318 '("COMMON_FILE_COMPRESS_GZ"
2320 "COMMON_RANDOM_FIXED_SEED"
2321 "INTSIZE64" ;use 'long' instead of 'int'
2322 ;; Prevents symbolc clashes with libesmumps
2324 ;; XXX: Causes invalid frees in superlu-dist tests
2326 ;; "SCOTCH_PTHREAD_NUMBER=2"
2327 "restrict=__restrict"))))))
2329 'build 'build-esmumps
2331 ;; By default, running the test suite would fail because 'ssh'
2332 ;; could not be found in $PATH. Define this variable to placate
2333 ;; Open MPI without adding a dependency on OpenSSH (the agent
2334 ;; isn't used anyway.)
2335 (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
2337 (zero? (system* "make"
2338 (format #f "-j~a" (parallel-job-count))
2342 (lambda* (#:key outputs #:allow-other-keys)
2343 (let ((out (assoc-ref outputs "out")))
2345 (zero? (system* "make"
2346 (string-append "prefix=" out)
2348 ;; esmumps files are not installed with the above
2349 (for-each (lambda (f)
2350 (copy-file f (string-append out "/include/" f)))
2351 (find-files "../include" ".*esmumps.h$"))
2352 (for-each (lambda (f)
2353 (copy-file f (string-append out "/lib/" f)))
2354 (find-files "../lib" "^lib.*esmumps.*"))))))))
2355 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
2356 (synopsis "Programs and libraries for graph algorithms")
2357 (description "SCOTCH is a set of programs and libraries which implement
2358 the static mapping and sparse matrix reordering algorithms developed within
2359 the SCOTCH project. Its purpose is to apply graph theory, with a divide and
2360 conquer approach, to scientific computing problems such as graph and mesh
2361 partitioning, static mapping, and sparse matrix ordering, in application
2362 domains ranging from structural mechanics to operating systems or
2364 ;; See LICENSE_en.txt
2365 (license license:cecill-c)))
2367 (define-public scotch32
2368 ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2369 ;; some applications.
2370 (package (inherit scotch)
2373 (substitute-keyword-arguments (package-arguments scotch)
2374 ((#:phases scotch-phases)
2375 `(modify-phases ,scotch-phases
2379 (call-with-output-file "Makefile.inc"
2393 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2394 LDFLAGS = -lz -lm -lrt -lpthread
2396 LEX = flex -Pscotchyy -olex.yy.c
2401 YACC = bison -pscotchyy -y -b y
2403 '("COMMON_FILE_COMPRESS_GZ"
2405 "COMMON_RANDOM_FIXED_SEED"
2406 "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
2407 ;; Prevents symbolc clashes with libesmumps
2409 ;; XXX: Causes invalid frees in superlu-dist tests
2411 ;; "SCOTCH_PTHREAD_NUMBER=2"
2412 "restrict=__restrict"))))))))))
2414 "Programs and libraries for graph algorithms (32-bit integers)")))
2416 (define-public pt-scotch
2417 (package (inherit scotch)
2420 `(("openmpi" ,openmpi))) ;Headers include MPI headers
2422 (substitute-keyword-arguments (package-arguments scotch)
2423 ((#:phases scotch-phases)
2424 `(modify-phases ,scotch-phases
2429 (zero? (system* "make"
2430 (format #f "-j~a" (parallel-job-count))
2431 "ptscotch" "ptesmumps"))
2432 ;; Install the serial metis compatibility library
2433 (zero? (system* "make" "-C" "libscotchmetis" "install")))))
2436 (lambda _ (zero? (system* "make" "ptcheck"))))))))
2437 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
2439 (define-public pt-scotch32
2440 (package (inherit scotch32)
2441 (name "pt-scotch32")
2443 `(("openmpi" ,openmpi))) ;headers include MPI headers
2445 (substitute-keyword-arguments (package-arguments scotch32)
2446 ((#:phases scotch32-phases)
2447 `(modify-phases ,scotch32-phases
2451 (zero? (system* "make"
2452 (format #f "-j~a" (parallel-job-count))
2453 "ptscotch" "ptesmumps"))
2454 ;; Install the serial metis compatibility library
2455 (zero? (system* "make" "-C" "libscotchmetis" "install")))))
2458 (zero? (system* "make" "ptcheck"))))))))
2460 "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2462 (define-public metis
2469 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2470 "metis-" version ".tar.gz"))
2473 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2474 (build-system cmake-build-system)
2476 `(("blas" ,openblas)))
2478 `(#:tests? #f ;no tests
2479 #:configure-flags `("-DSHARED=ON"
2480 ,(string-append "-DGKLIB_PATH=" (getcwd)
2481 "/metis-" ,version "/GKlib"))))
2482 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2483 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2485 "METIS is a set of serial programs for partitioning graphs, partitioning
2486 finite element meshes, and producing fill-reducing orderings for sparse
2487 matrices. The algorithms implemented in METIS are based on the multilevel
2488 recursive-bisection, multilevel k-way, and multi-constraint partitioning
2490 (license license:asl2.0))) ;As of version 5.0.3
2492 (define-public p4est
2499 (uri (string-append "http://p4est.github.io/release/p4est-"
2503 "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
2504 (build-system gnu-build-system)
2506 `(("fortran" ,gfortran)
2511 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2512 (assoc-ref %build-inputs "blas")
2514 ,(string-append "LAPACK_LIBS=-L"
2515 (assoc-ref %build-inputs "lapack")
2517 #:phases (modify-phases %standard-phases
2518 (add-before 'check 'set-test-environment
2520 ;; By default, running the test suite would fail because
2521 ;; 'ssh' could not be found in $PATH. Define this
2522 ;; variable to placate Open MPI without adding a
2523 ;; dependency on OpenSSH (the agent isn't used anyway.)
2524 (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
2526 (home-page "http://www.p4est.org")
2527 (synopsis "Adaptive mesh refinement on forests of octrees")
2529 "The p4est software library enables the dynamic management of a
2530 collection of adaptive octrees, conveniently called a forest of octrees.
2531 p4est is designed to work in parallel and scales to hundreds of thousands of
2533 (license license:gpl2+)))
2535 (define-public p4est-openmpi
2536 (package (inherit p4est)
2537 (name "p4est-openmpi")
2540 ,@(package-inputs p4est)))
2542 (substitute-keyword-arguments (package-arguments p4est)
2543 ((#:configure-flags cf)
2544 ``("--enable-mpi" ,@,cf))))
2545 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2547 (define-public gsegrafix
2554 (uri (string-append "mirror://gnu/" name "/" name "-"
2558 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2559 (build-system gnu-build-system)
2561 `(#:configure-flags '("LDFLAGS=-lm")))
2563 `(("libgnomecanvas" ,libgnomecanvas)
2564 ("libbonoboui" ,libbonoboui)
2565 ("libgnomeui" ,libgnomeui)
2566 ("libgnomeprintui" ,libgnomeprintui)
2569 `(("pkg-config" ,pkg-config)))
2570 (home-page "https://www.gnu.org/software/gsegrafix/")
2571 (synopsis "GNOME application to create scientific and engineering plots")
2572 (description "GSEGrafix is an application which produces high-quality graphical
2573 plots for science and engineering. Plots are specified via simple ASCII
2574 parameter files and data files and are presented in an anti-aliased GNOME
2575 canvas. The program supports rectangular two-dimensional plots, histograms,
2576 polar-axis plots and three-dimensional plots. Plots can be printed or saved
2577 to BMP, JPEG or PNG image formats.")
2578 (license license:gpl3+)))
2580 (define-public maxima
2587 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2588 version "-source/" name "-" version ".tar.gz"))
2591 "0x0n81z0s4pl8nwpf7ivlsbvsdphm9w42250g7qdkizl0132by6s"))
2592 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
2593 (build-system gnu-build-system)
2596 ("gnuplot" ,gnuplot) ;for plots
2597 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
2599 `(("texinfo" ,texinfo)
2601 ("python" ,python)))
2604 (list "--enable-gcl"
2605 (string-append "--with-posix-shell="
2606 (assoc-ref %build-inputs "bash")
2608 (string-append "--with-wish="
2609 (assoc-ref %build-inputs "tk")
2611 (let ((v ,(package-version tk)))
2612 (string-take v (string-index-right v #\.)))))
2613 ;; By default Maxima attempts to write temporary files to
2614 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2615 ;; Work around that.
2616 #:make-flags (list "TMPDIR=/tmp")
2618 (modify-phases %standard-phases
2619 (add-before 'check 'pre-check
2621 (chmod "src/maxima" #o555)
2623 ;; Make sure the doc and emacs files are found in the
2624 ;; standard location. Also configure maxima to find gnuplot
2625 ;; without having it on the PATH.
2626 (add-after 'install 'post-install
2627 (lambda* (#:key outputs inputs #:allow-other-keys)
2628 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2629 (out (assoc-ref outputs "out"))
2630 (datadir (string-append out "/share/maxima/" ,version))
2631 (binutils (string-append (assoc-ref inputs "binutils")
2633 (with-directory-excursion out
2634 (mkdir-p "share/emacs")
2635 (mkdir-p "share/doc")
2637 (string-append datadir "/emacs/")
2638 (string-append out "/share/emacs/site-lisp"))
2640 (string-append datadir "/doc/")
2641 (string-append out "/share/doc/maxima"))
2642 (with-atomic-file-replacement
2643 (string-append datadir "/share/maxima-init.lisp")
2645 (format out "~a ~s~a~%"
2646 "(setf $gnuplot_command "
2647 (string-append gnuplot "/bin/gnuplot") ")")
2648 (dump-port in out))))
2649 ;; Ensure that Maxima will have access to the GNU binutils
2650 ;; components at runtime.
2651 (wrap-program (string-append out "/bin/maxima")
2652 `("PATH" prefix (,binutils))))
2654 (home-page "http://maxima.sourceforge.net")
2655 (synopsis "Numeric and symbolic expression manipulation")
2656 (description "Maxima is a system for the manipulation of symbolic and
2657 numerical expressions. It yields high precision numeric results by using
2658 exact fractions, arbitrary precision integers, and variable precision floating
2660 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2661 ;; Others simply say "GNU General Public License" without stating a
2662 ;; version (which implicitly means gpl1+).
2663 ;; At least one file (src/maxima.asd) says "version 2."
2664 ;; GPLv2 only is therefore the smallest subset.
2665 (license license:gpl2)))
2667 (define-public wxmaxima
2674 (uri (string-append "https://github.com/andrejv/" name "/archive"
2675 "/Version-" version ".tar.gz"))
2676 (file-name (string-append name "-" version ".tar.gz"))
2679 "03kr2rgfp4hcf3is8m8d8f9hj660c3xgrc50vrrfpixx4syh6wvj"))
2681 (search-patches "wxmaxima-do-not-use-old-gnuplot-parameters.patch"))))
2682 (build-system cmake-build-system)
2684 `(("gettext" ,gettext-minimal)))
2686 `(("wxwidgets" ,wxwidgets)
2689 ("adwaita-icon-theme" ,adwaita-icon-theme)
2691 ("shared-mime-info" ,shared-mime-info)))
2693 `(#:tests? #f ; no check target
2695 (modify-phases %standard-phases
2696 (add-after 'install 'wrap-program
2697 (lambda* (#:key inputs outputs #:allow-other-keys)
2698 (wrap-program (string-append (assoc-ref outputs "out")
2701 (,(string-append (assoc-ref inputs "maxima")
2703 ;; For GtkFileChooserDialog.
2704 `("GSETTINGS_SCHEMA_DIR" =
2705 (,(string-append (assoc-ref inputs "gtk+")
2706 "/share/glib-2.0/schemas")))
2707 `("XDG_DATA_DIRS" ":" prefix
2708 (;; Needed by gdk-pixbuf to know supported icon formats.
2710 (assoc-ref inputs "shared-mime-info") "/share")
2711 ;; The default icon theme of GTK+.
2713 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
2715 (home-page "https://andrejv.github.io/wxmaxima/")
2716 (synopsis "Graphical user interface for the Maxima computer algebra system")
2718 "wxMaxima is a graphical user interface for the Maxima computer algebra
2719 system. It eases the use of Maxima by making most of its commands available
2720 through a menu system and by providing input dialogs for commands that require
2721 more than one argument. It also implements its own display engine that
2722 outputs mathematical symbols directly instead of depicting them with ASCII
2725 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
2726 text and mathematical calculations to create documents, exporting of input and
2727 output to TeX, and a browser for Maxima's manual including command index and
2728 full text searching.")
2729 (license license:gpl2+)))
2731 (define-public armadillo
2737 (uri (string-append "mirror://sourceforge/arma/armadillo-"
2741 "1qqzy7dp891j9v7062mv1599hdwr97vqzrd3j2fl8c3gmc00dmzg"))))
2742 (build-system cmake-build-system)
2743 (arguments `(#:tests? #f)) ;no test target
2745 `(("openblas" ,openblas)
2747 ("arpack" ,arpack-ng)))
2748 (home-page "http://arma.sourceforge.net/")
2749 (synopsis "C++ linear algebra library")
2751 "Armadillo is a C++ linear algebra library, aiming towards a good balance
2752 between speed and ease of use. It is useful for algorithm development
2753 directly in C++, or quick conversion of research code into production
2754 environments. It can be used for machine learning, pattern recognition,
2755 signal processing, bioinformatics, statistics, econometrics, etc. The library
2756 provides efficient classes for vectors, matrices and cubes, as well as 150+
2757 associated functions (eg. contiguous and non-contiguous submatrix views).")
2758 (license license:asl2.0)))
2760 (define-public muparser
2761 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2762 ;; different hash. In order to make `guix package --upgrade` work correctly,
2763 ;; we set a Guix packaging revision.
2764 ;; When the next version of muparser is released, we can remove
2765 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2766 (let ((upstream-version "2.2.5")
2770 (version (string-append upstream-version "-" revision))
2774 (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
2775 upstream-version ".tar.gz"))
2776 (file-name (string-append name "-" version ".tar.gz"))
2779 "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
2780 (build-system gnu-build-system)
2782 `(#:configure-flags '("--enable-samples=no")
2783 #:tests? #f)) ;no "check" target
2784 (home-page "http://muparser.beltoforion.de/")
2785 (synopsis "Fast parser library for mathematical expressions")
2787 "muParser is an extensible high performance math parser library. It is
2788 based on transforming an expression into a bytecode and precalculating constant
2790 (license license:expat))))
2792 (define-public openblas
2799 (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
2801 (file-name (string-append name "-" version ".tar.gz"))
2804 "1bd03c5xni0bla0wg1wba841b36b0sg13sjja955kn5xzvy4i61a"))))
2805 (build-system gnu-build-system)
2807 `(#:test-target "test"
2808 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
2809 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2810 ;; we need to disable substitutions.
2812 ,(let ((system (or (%current-target-system) (%current-system))))
2813 (or (string-prefix? "x86_64" system)
2814 (string-prefix? "i686" system)
2815 (string-prefix? "mips" system)
2816 (string-prefix? "aarch64" system)))
2818 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
2820 ;; Build the library for all supported CPUs. This allows
2821 ;; switching CPU targets at runtime with the environment variable
2822 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
2823 ;; Unfortunately, this is not supported on non-x86 architectures,
2824 ;; where it leads to failed builds.
2825 ,@(let ((system (or (%current-target-system) (%current-system))))
2827 ((or (string-prefix? "x86_64" system)
2828 (string-prefix? "i686" system))
2829 '("DYNAMIC_ARCH=1"))
2830 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
2831 ;; two available MIPS targets special extended instructions
2832 ;; for Loongson cores are used.
2833 ((string-prefix? "mips" system)
2834 '("TARGET=SICORTEX"))
2835 ;; On aarch64 force the generic 'armv8-a' target
2836 ((string-prefix? "aarch64" system)
2839 ;; no configure script
2841 (modify-phases %standard-phases
2843 (add-before 'build 'set-extralib
2844 (lambda* (#:key inputs #:allow-other-keys)
2845 ;; Get libgfortran found when building in utest.
2847 (string-append "-L" (assoc-ref inputs "fortran-lib")
2851 `(("fortran-lib" ,gfortran "lib")))
2854 ("fortran" ,gfortran)
2856 (home-page "http://www.openblas.net/")
2857 (synopsis "Optimized BLAS library based on GotoBLAS")
2859 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
2860 (license license:bsd-3)))
2862 (define* (make-blis implementation #:optional substitutable?)
2863 "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
2864 source tree for a list of implementations.)
2866 SUBSTITUTABLE? determines whether the package is made available as a
2869 Currently the specialization must be selected at configure-time, but work is
2870 underway to allow BLIS to select the right optimized kernels at run time:
2871 <https://github.com/flame/blis/issues/129>."
2873 (name (if (string=? implementation "reference")
2875 (string-append "blis-" implementation)))
2877 (home-page "https://github.com/flame/blis")
2880 (uri (git-reference (url home-page) (commit version)))
2883 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
2884 (file-name (git-file-name "blis" version))))
2885 (build-system gnu-build-system)
2887 `(#:test-target "test"
2889 #:substitutable? ,substitutable?
2891 #:phases (modify-phases %standard-phases
2893 (lambda* (#:key outputs #:allow-other-keys)
2894 ;; This is a home-made 'configure' script.
2895 (let ((out (assoc-ref outputs "out")))
2896 (zero? (system* "./configure" "-p" out
2900 "--enable-threading=openmp"
2902 ,implementation)))))
2903 (add-before 'check 'show-test-output
2905 ;; By default "make check" is silent. Make it verbose.
2906 (system "tail -F output.testsuite &")
2908 (synopsis "High-performance basic linear algebra (BLAS) routines")
2910 "BLIS is a portable software framework for instantiating high-performance
2911 BLAS-like dense linear algebra libraries. The framework was designed to
2912 isolate essential kernels of computation that, when optimized, immediately
2913 enable optimized implementations of most of its commonly used and
2914 computationally intensive operations. While BLIS exports a new BLAS-like API,
2915 it also includes a BLAS compatibility layer which gives application developers
2916 access to BLIS implementations via traditional BLAS routine calls.")
2917 (license license:bsd-3)))
2920 ;; This is the "reference" implementation, which is the non-optimized but
2921 ;; portable variant (no assembly).
2922 (make-blis "reference" #t))
2924 (define ignorance blis)
2926 (define-syntax-rule (blis/x86_64 processor)
2927 "Expand to a package specialized for PROCESSOR."
2929 (inherit (make-blis processor))
2930 (supported-systems '("x86_64-linux"))))
2932 (define-public blis-sandybridge
2933 ;; BLIS specialized for Sandy Bridge processors (launched 2011):
2934 ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
2935 (blis/x86_64 "sandybridge"))
2937 (define-public blis-haswell
2938 ;; BLIS specialized for Haswell processors (launched 2013):
2939 ;; <http://ark.intel.com/products/codename/42174/Haswell>.
2940 (blis/x86_64 "haswell"))
2942 (define-public blis-knl
2943 ;; BLIS specialized for Knights Landing processor (launched 2016):
2944 ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
2945 (blis/x86_64 "knl"))
2948 (define-public openlibm
2955 (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
2957 (file-name (string-append name "-" version ".tar.gz"))
2960 "1z8cj5q8ca8kmrakwkpjxf8svi81waw0c568cx8v8pv9kvswbp07"))))
2961 (build-system gnu-build-system)
2964 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2966 ;; no configure script
2967 (modify-phases %standard-phases (delete 'configure))
2968 #:tests? #f)) ;the tests are part of the default target
2969 (home-page "http://openlibm.org/")
2970 (synopsis "Portable C mathematical library (libm)")
2972 "OpenLibm is an effort to have a high quality, portable, standalone C
2973 mathematical library (libm). It can be used standalone in applications and
2974 programming language implementations. The project was born out of a need to
2975 have a good libm for the Julia programming language that worked consistently
2976 across compilers and operating systems, and in 32-bit and 64-bit
2978 ;; Each architecture has its own make target, and there is none for mips.
2979 (supported-systems (delete "mips64el-linux" %supported-systems))
2980 ;; See LICENSE.md for details.
2981 (license (list license:expat
2984 license:public-domain
2985 license:lgpl2.1+))))
2987 (define-public openspecfun
2989 (name "openspecfun")
2994 (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
2996 (file-name (string-append name "-" version ".tar.gz"))
2999 "1rs1bv8jq751fv9vq79890wqf9xlbjc7lvz3ighzyfczbyjcf18m"))))
3000 (build-system gnu-build-system)
3002 '(#:tests? #f ; no "check" target
3004 (list (string-append "prefix=" (assoc-ref %outputs "out")))
3006 (modify-phases %standard-phases
3007 (delete 'configure)))) ; no configure script
3009 `(("fortran" ,gfortran)))
3010 (home-page "https://github.com/JuliaLang/openspecfun")
3011 (synopsis "Collection of special mathematical functions")
3013 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
3014 portable package for Bessel Functions of a Complex Argument and Nonnegative
3015 Order; it contains subroutines for computing Bessel functions and Airy
3016 functions. Faddeeva allows computing the various error functions of arbitrary
3017 complex arguments (Faddeeva function, error function, complementary error
3018 function, scaled complementary error function, imaginary error function, and
3019 Dawson function); given these, one can also easily compute Voigt functions,
3020 Fresnel integrals, and similar related functions as well.")
3021 ;; Faddeeva is released under the Expat license; AMOS is included as
3022 ;; public domain software.
3023 (license (list license:expat license:public-domain))))
3025 (define-public suitesparse
3027 (name "suitesparse")
3033 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
3037 "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
3038 (modules '((guix build utils)))
3040 ;; Remove bundled metis source
3041 '(delete-file-recursively "metis-5.1.0"))))
3042 (build-system gnu-build-system)
3044 '(#:tests? #f ;no "check" target
3049 "MY_METIS_LIB=-lmetis"
3050 (string-append "INSTALL_LIB="
3051 (assoc-ref %outputs "out") "/lib")
3052 (string-append "INSTALL_INCLUDE="
3053 (assoc-ref %outputs "out") "/include")
3056 (modify-phases %standard-phases
3057 (delete 'configure)))) ;no configure script
3062 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
3063 (synopsis "Suite of sparse matrix software")
3065 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
3066 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
3067 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
3068 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
3069 CXSparse, a concise sparse Cholesky factorization package; and many other
3072 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
3074 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
3075 (license (list license:gpl2+ license:lgpl2.1+))))
3077 (define-public atlas
3083 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
3084 version "/atlas" version ".tar.bz2"))
3087 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
3088 (build-system gnu-build-system)
3089 (home-page "http://math-atlas.sourceforge.net/")
3090 (inputs `(("gfortran" ,gfortran)
3091 ("lapack-tar" ,(package-source lapack))))
3092 (outputs '("out" "doc"))
3093 ;; For the moment we drop support for MIPS at it fails to compile. See
3094 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
3095 (supported-systems (delete "mips64el-linux" %supported-systems))
3097 `(#:parallel-build? #f
3098 #:parallel-tests? #f
3100 ;; ATLAS tunes itself for the machine it is built on, as explained at
3101 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
3102 ;; For this reason, we want users to build it locally instead of using
3106 #:modules ((srfi srfi-26)
3108 (guix build gnu-build-system)
3111 `(;; Generate position independent code suitable for dynamic libraries
3112 ;; and use WALL timer to get more accurate timing.
3113 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
3116 ,,(if (string-match "64" (%current-system))
3119 ;; Disable parallel build as it gives errors: atlas_pthread.h is
3120 ;; needed to compile C files before it is generated.
3121 "-Ss" "pmake" "make -j 1"
3122 ;; Probe is failing for MIPS. We therefore define the system
3123 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3124 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3125 ,,@(if (string-prefix? "mips" (%current-system))
3126 (list "-A" "49" "-V" "1")
3128 ;; Generate shared libraries.
3130 ;; Build a full LAPACK library.
3131 ,(string-append "--with-netlib-lapack-tarfile="
3132 (assoc-ref %build-inputs "lapack-tar")))
3134 (modify-phases %standard-phases
3135 (add-after 'install 'install-doc
3136 (lambda* (#:key outputs inputs #:allow-other-keys)
3137 (let ((doc (string-append (assoc-ref outputs "doc")
3138 "/share/doc/atlas")))
3140 (fold (lambda (file previous)
3141 (and previous (zero? (system* "cp" file doc))))
3142 #t (find-files "../ATLAS/doc" ".*")))))
3143 (add-after 'check 'check-pt
3144 (lambda _ (zero? (system* "make" "ptcheck"))))
3145 ;; Fix files required to run configure.
3146 (add-before 'configure 'fix-/bin/sh
3148 ;; Use `sh', not `/bin/sh'.
3149 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3152 ;; Fix /bin/sh in generated make files.
3153 (add-after 'configure 'fix-/bin/sh-in-generated-files
3155 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3158 ;; ATLAS configure program does not accepts the default flags
3159 ;; passed by the 'gnu-build-system'.
3161 (lambda* (#:key native-inputs inputs outputs
3162 (configure-flags '())
3163 #:allow-other-keys #:rest args)
3164 (let* ((prefix (assoc-ref outputs "out"))
3165 (bash (or (and=> (assoc-ref
3166 (or native-inputs inputs) "bash")
3167 (cut string-append <> "/bin/bash"))
3169 (flags `(,(string-append "--prefix=" prefix)
3171 (abs-srcdir (getcwd))
3172 (srcdir (string-append "../" (basename abs-srcdir))))
3173 (format #t "source directory: ~s (relative from build: ~s)~%"
3177 (format #t "build directory: ~s~%" (getcwd))
3178 (format #t "configure flags: ~s~%" flags)
3179 (zero? (apply system* bash
3180 (string-append srcdir "/configure")
3182 (synopsis "Automatically Tuned Linear Algebra Software")
3184 "ATLAS is an automatically tuned linear algebra software library
3185 providing C and Fortran77 interfaces to a portably efficient BLAS
3186 implementation, as well as a few routines from LAPACK.
3188 Optimization occurs at build time. For this reason, the library is built on
3189 the machine where it is installed, without resorting to pre-built substitutes.
3191 Before building the library, CPU throttling should be disabled. This can be
3192 done in the BIOS, or, on GNU/Linux, with the following command:
3195 # cpupower --governor performance
3198 Failure to do so will result in a library with poor performance.")
3199 (license license:bsd-3)))
3208 (uri (string-append "mirror://sourceforge/ogl-math/glm-" version
3209 "/glm-" version ".zip"))
3212 "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l"))))
3213 (build-system cmake-build-system)
3215 `(("unzip" ,unzip)))
3216 (home-page "http://glm.g-truc.net")
3217 (synopsis "OpenGL Mathematics library")
3218 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3219 library for graphics software based on the OpenGL Shading Language (GLSL)
3221 (license license:expat)))
3223 (define-public lpsolve
3230 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3231 "/lp_solve_" version "_source.tar.gz"))
3234 "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
3235 (modules '((guix build utils)))
3237 '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3239 ;; Pretend to be on a 64 bit platform to obtain a common directory
3240 ;; name for the build results on all architectures; nothing else
3241 ;; seems to depend on it.
3242 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3244 ;; The check for 'isnan' as it is written fails with
3245 ;; "non-floating-point argument in call to function
3246 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3247 ;; definition, which in turn leads to bad things. Fix the feature
3249 (("isnan\\(0\\)") "isnan(0.)")))))
3250 (build-system gnu-build-system)
3252 `(#:tests? #f ; no check target
3254 (modify-phases %standard-phases
3255 (delete 'configure) ; no configure script
3258 (with-directory-excursion "lpsolve55"
3259 (invoke "bash" "ccc"))
3260 (with-directory-excursion "lp_solve"
3261 (invoke "bash" "ccc"))
3264 (lambda* (#:key outputs #:allow-other-keys)
3265 (let* ((out (assoc-ref outputs "out"))
3266 (bin (string-append out "/bin"))
3267 (lib (string-append out "/lib"))
3268 ;; This is where LibreOffice expects to find the header
3269 ;; files, and where they are installed by Debian.
3270 (include (string-append out "/include/lpsolve")))
3271 (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3272 (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
3273 (install-file "lp_solve/bin/ux64/lp_solve" bin)
3275 ;; Install a subset of the header files as on Debian
3276 ;; (plus lp_bit.h, which matches the regular expression).
3277 (for-each (lambda (name)
3278 (install-file name include))
3279 (find-files "." "lp_[HMSa-z].*\\.h$"))
3280 (with-directory-excursion "shared"
3281 (for-each (lambda (name)
3282 (install-file name include))
3283 (find-files "." "\\.h$")))
3285 (home-page "http://lpsolve.sourceforge.net/")
3286 (synopsis "Mixed integer linear programming (MILP) solver")
3288 "lp_solve is a mixed integer linear programming solver based on the
3289 revised simplex and the branch-and-bound methods.")
3290 (license license:lgpl2.1+)))
3292 (define-public dealii
3299 (uri (string-append "https://github.com/dealii/dealii/releases/"
3300 "download/v" version "/dealii-" version ".tar.gz"))
3303 "1bh9rsmkrg0zi70n27b11djmac9lximghsiy7mg7w7x544n82gnk"))
3304 (modules '((guix build utils)))
3306 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
3307 '(delete-file-recursively "bundled"))))
3308 (build-system cmake-build-system)
3316 ("arpack" ,arpack-ng)
3317 ("muparser" ,muparser)
3318 ("gfortran" ,gfortran)
3319 ("suitesparse" ,suitesparse))) ;for UMFPACK
3321 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
3323 ;; Work around a bug in libsuitesparseconfig linking
3324 ;; see https://github.com/dealii/dealii/issues/4745
3325 '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
3326 (home-page "https://www.dealii.org")
3327 (synopsis "Finite element library")
3329 "Deal.II is a C++ program library targeted at the computational solution
3330 of partial differential equations using adaptive finite elements. The main
3331 aim of deal.II is to enable rapid development of modern finite element codes,
3332 using among other aspects adaptive meshes and a wide array of tools often used
3333 in finite element programs.")
3334 (license license:lgpl2.1+)))
3336 (define-public dealii-openmpi
3337 (package (inherit dealii)
3338 (name "dealii-openmpi")
3341 ;;Supported only with MPI:
3342 ("p4est" ,p4est-openmpi)
3343 ("petsc" ,petsc-openmpi)
3344 ("slepc" ,slepc-openmpi)
3345 ("metis" ,metis) ;for MUMPS
3346 ("scalapack" ,scalapack) ;for MUMPS
3347 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3348 ("arpack" ,arpack-ng-openmpi)
3349 ,@(fold alist-delete (package-inputs dealii)
3350 '("p4est" "arpack"))))
3352 (substitute-keyword-arguments (package-arguments dealii)
3353 ((#:configure-flags cf)
3354 ``("-DMPI_C_COMPILER=mpicc"
3355 "-DMPI_CXX_COMPILER=mpicxx"
3356 "-DMPI_Fortran_COMPILER=mpifort"
3358 (synopsis "Finite element library (with MPI support)")))
3360 (define-public flann
3369 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3370 version "-src.zip"))
3373 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))))
3374 (build-system cmake-build-system)
3376 "octave")) ;46 MiB .mex file that pulls Octave
3378 `(("unzip" ,unzip)))
3382 ("python" ,python-2) ; print syntax
3383 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3386 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3387 ;; taken 46 MiB unstripped, and 6 MiB stripped.
3388 #:strip-directories '("lib" "lib64" "libexec"
3389 "bin" "sbin" "share/flann/octave")
3391 ;; Save 12 MiB by not installing .a files. Passing
3392 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3393 #:phases (modify-phases %standard-phases
3394 (add-before 'configure 'set-octave-directory
3395 (lambda* (#:key outputs #:allow-other-keys)
3396 ;; Install the .mex file in the "octave" output.
3397 (let ((out (assoc-ref outputs "octave")))
3398 (substitute* "src/matlab/CMakeLists.txt"
3399 (("share/flann/octave")
3400 (string-append out "/share/flann/octave")))
3402 (add-after 'install 'remove-static-libraries
3403 (lambda* (#:key outputs #:allow-other-keys)
3404 (let* ((out (assoc-ref outputs "out"))
3405 (lib (string-append out "/lib")))
3406 (for-each delete-file
3407 (find-files lib "\\.a$"))
3410 #:tests? #f)) ; The test data are downloaded from the Internet.
3411 (home-page "http://www.cs.ubc.ca/research/flann/")
3412 (synopsis "Library for approximate nearest neighbors computation")
3413 (description "FLANN is a library for performing fast approximate
3414 nearest neighbor searches in high dimensional spaces. It implements a
3415 collection of algorithms and a system for automatically choosing the best
3416 algorithm and optimum parameters depending on the dataset.
3418 FLANN is written in C++ and contains bindings for C, Octave and Python.")
3419 (license (license:non-copyleft "file://COPYING"
3420 "See COPYING in the distribution."))))
3422 (define-public wcalc
3429 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3430 "wcalc-" version ".tar.bz2"))
3433 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3434 (build-system gnu-build-system)
3437 ("readline" ,readline)))
3438 (home-page "http://w-calc.sourceforge.net/index.php")
3439 (synopsis "Flexible command-line scientific calculator")
3440 (description "Wcalc is a very capable calculator. It has standard functions
3441 (sin, asin, and sinh for example, in either radians or degrees), many
3442 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3443 variables, a command history, hex/octal/binary input and output, unit
3444 conversions, embedded comments, and an expandable expression entry field. It
3445 evaluates expressions using the standard order of operations.")
3446 (license license:gpl2+)))
3454 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3455 "/xaos-" version ".tar.gz"))
3458 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3459 (build-system gnu-build-system)
3460 (native-inputs `(("gettext" ,gettext-minimal)))
3461 (inputs `(("libx11" ,libx11)
3466 `(#:tests? #f ;no "check" target
3467 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3468 (synopsis "Real-time fractal zoomer")
3469 (description "GNU XaoS is a graphical program that generates fractal
3470 patterns and allows you to zoom in and out of them infinitely in a fluid,
3471 continuous manner. It also includes tutorials that help to explain how fractals
3472 are built. It can generate many different fractal types such as the Mandelbrot
3474 (home-page "https://www.gnu.org/software/xaos/")
3475 (license license:gpl2+)))
3477 (define-public hypre
3483 (uri (string-append "https://github.com/LLNL/hypre/archive/"
3484 "v" version ".tar.gz"))
3485 (file-name (string-append name "-" version ".tar.gz"))
3488 "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m"))
3489 (modules '((guix build utils)))
3492 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
3493 ;; substitute the tarball creation time.
3494 (substitute* "src/utilities/HYPRE_utilities.h"
3495 (("Date Compiled: .*$")
3496 "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n"))
3498 (build-system gnu-build-system)
3499 (outputs '("out" ;6.1 MiB of headers and libraries
3500 "doc")) ;4.8 MiB of documentation
3504 ("perl" ,perl) ;needed to run 'ppmquant' during tests
3505 ("texlive" ,texlive) ;full package required for fonts
3506 ("ghostscript" ,ghostscript)))
3508 `(("blas" ,openblas)
3509 ("lapack" ,lapack)))
3511 `(#:modules ((srfi srfi-1)
3512 ,@%gnu-build-system-modules)
3513 #:configure-flags '("--enable-shared"
3521 (modify-phases %standard-phases
3522 (add-before 'configure 'chdir-src
3523 (lambda _ (chdir "src")))
3525 (lambda* (#:key build target configure-flags
3526 #:allow-other-keys #:rest args)
3527 (let* ((configure (assoc-ref %standard-phases 'configure)))
3530 (list #:configure-flags
3531 (cons (string-append
3532 "--host=" (or target build))
3533 configure-flags)))))))
3534 (add-after 'build 'build-docs
3536 (zero? (system* "make" "-Cdocs" "pdf" "html"))))
3539 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3540 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
3541 (and (system* "make" "check" "CHECKRUN=")
3542 (fold (lambda (filename result)
3544 (let ((size (stat:size (stat filename))))
3545 (when (not (zero? size))
3546 (format #t "~a size ~d; error indication~%"
3550 (find-files "test" ".*\\.err$")))))
3551 (add-after 'install 'install-docs
3552 (lambda* (#:key outputs #:allow-other-keys)
3553 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3554 (let* ((doc (assoc-ref outputs "doc"))
3555 (docdir (string-append doc "/share/doc/hypre-" ,version)))
3556 (with-directory-excursion "docs"
3557 (for-each (lambda (base)
3558 (install-file (string-append base ".pdf") docdir)
3559 (copy-recursively base docdir)) ;html docs
3560 '("HYPRE_usr_manual"
3561 "HYPRE_ref_manual")))
3563 (home-page "http://www.llnl.gov/casc/hypre/")
3564 (synopsis "Library of solvers and preconditioners for linear equations")
3566 "HYPRE is a software library of high performance preconditioners and
3567 solvers for the solution of large, sparse linear systems of equations. It
3568 features multigrid solvers for both structured and unstructured grid
3570 (license license:lgpl2.1)))
3572 (define-public hypre-openmpi
3573 (package (inherit hypre)
3574 (name "hypre-openmpi")
3577 ,@(package-inputs hypre)))
3579 (substitute-keyword-arguments (package-arguments hypre)
3580 ((#:configure-flags flags)
3582 ,@(delete "--without-MPI" ,flags)))
3584 `(modify-phases ,phases
3585 (add-before 'check 'set-test-environment
3587 ;; By default, running the test suite would fail because 'ssh'
3588 ;; could not be found in $PATH. Define this variable to
3589 ;; placate Open MPI without adding a dependency on OpenSSH (the
3590 ;; agent isn't used anyway.)
3591 (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
3593 (synopsis "Parallel solvers and preconditioners for linear equations")
3595 "HYPRE is a software library of high performance preconditioners and
3596 solvers for the solution of large, sparse linear systems of equations on
3597 parallel computers. It features parallel multigrid solvers for both
3598 structured and unstructured grid problems.")))
3600 (define-public matio
3607 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
3608 "matio-" version ".tar.gz"))
3611 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3612 (build-system gnu-build-system)
3616 (home-page "http://matio.sourceforge.net/")
3617 (synopsis "Library for reading and writing MAT files")
3618 (description "Matio is a library for reading and writing MAT files. It
3619 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3620 (license license:bsd-2)))
3627 (origin (method url-fetch)
3628 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3629 "download/" version "/Vc-" version ".tar.gz"))
3632 "1zmlpn32jzb38smp3j834llmbix3whsrbw0h397qxysbw792kih8"))))
3633 (build-system cmake-build-system)
3636 '("-DBUILD_TESTING=ON"
3637 ;; By default, Vc will optimize for the CPU of the build machine.
3638 ;; Setting this to "none" makes it create portable binaries. See
3639 ;; "cmake/OptimizeForArchitecture.cmake".
3640 "-DTARGET_ARCHITECTURE=none")))
3641 (synopsis "SIMD vector classes for C++")
3642 (description "Vc provides portable, zero-overhead C++ types for explicitly
3643 data-parallel programming. It is a library designed to ease explicit
3644 vectorization of C++ code. Its types enable explicitly stating data-parallel
3645 operations on multiple values. The parallelism is therefore added via the type
3646 system. Vc has an intuitive API and provides portability between different
3647 compilers and compiler versions as well as portability between different vector
3648 instruction sets. Thus, an application written with Vc can be compiled for:
3651 @item SSE2 up to SSE4.2 or SSE4a
3654 @item NEON (in development)
3655 @item NVIDIA GPUs / CUDA (in development)
3657 (home-page "https://github.com/VcDevel/Vc")
3658 ;; "No support_???.cpp file exists for this architecture."
3659 (supported-systems '("x86_64-linux" "i686-linux"))
3660 (license license:bsd-3)))
3662 (define-public reducelcs
3663 ;; This is the last commit which is available upstream, no
3664 ;; release happened since 2010.
3665 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
3669 (version (string-append "1.0-" revision "." (string-take commit 7)))
3674 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
3676 (file-name (string-append name "-" version "-checkout"))
3679 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
3680 (build-system gnu-build-system)
3682 `(("openlibm" ,openlibm)))
3684 `(#:tests? #f ; no tests
3686 (modify-phases %standard-phases
3687 (delete 'configure) ; No configure script exists.
3688 (replace 'install ; No install phase exists.
3689 (lambda* (#:key outputs #:allow-other-keys)
3690 (let* ((out (assoc-ref outputs "out"))
3691 (bin (string-append out "/bin")))
3692 (install-file "Approximation" bin)
3693 (install-file "CollectResults" bin)
3694 (install-file "GenerateInstances" bin)
3696 (synopsis "Approximate Longest Commons Subsequence computation tool")
3698 "@code{reduceLCS} is an implementation of the Reduce-Expand
3699 algorithm for LCS. It is a fast program to compute the approximate
3700 Longest Commons Subsequence of a set of strings.")
3701 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
3702 (license license:gpl3+))))
3704 (define-public jacal
3711 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
3714 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
3715 (patches (search-patches "jacal-fix-texinfo.patch"))))
3716 (build-system gnu-build-system)
3719 (modify-phases %standard-phases
3720 (add-before 'build 'pre-build
3721 ;; Don't use upstream's script - it really doesn't fit into
3722 ;; Guix's functional paradigm.
3723 (lambda* (#:key inputs outputs #:allow-other-keys)
3724 (substitute* "Makefile"
3725 (("^install: install-script") "install: "))))
3726 (add-after 'install 'post-install
3727 ;; Instead, we provide our own simplified script.
3728 (lambda* (#:key inputs outputs #:allow-other-keys)
3729 (let ((wrapper (string-append (assoc-ref outputs "out")
3731 (format (open wrapper (logior O_WRONLY O_CREAT))
3732 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
3733 "-e '(slib:load \"~a/lib/jacal/math\") "
3736 (assoc-ref inputs "scm")
3737 (assoc-ref outputs "out"))
3738 (chmod wrapper #o555))))
3740 (lambda* (#:key inputs outputs #:allow-other-keys)
3741 (zero? (system* "./configure"
3742 (string-append "--prefix="
3743 (assoc-ref outputs "out")))))))))
3744 (inputs `(("scm" ,scm)))
3745 (native-inputs `(("unzip" ,unzip)
3746 ("texinfo" ,texinfo)))
3747 (synopsis "Symbolic mathematics system")
3748 (description "GNU JACAL is an interactive symbolic mathematics program based on
3749 Scheme. It manipulate and simplify a range of mathematical expressions such
3750 as equations, scalars, vectors, and matrices.")
3751 (home-page "https://www.gnu.org/software/jacal/")
3752 (license license:gpl3+)))
3761 "https://github.com/Z3Prover/z3/archive/z3-"
3765 "032a5lvji2liwmc25jv52bdrhimqflvqbpg77ccaq1jykhiivbmf"))))
3766 (build-system cmake-build-system)
3769 (list "-DBUILD_PYTHON_BINDINGS=true"
3770 "-DINSTALL_PYTHON_BINDINGS=true"
3771 (string-append "-DCMAKE_INSTALL_PYTHON_PKG_DIR="
3773 "/lib/python2.7/site-packages"))
3775 (modify-phases %standard-phases
3776 (add-before 'configure 'bootstrap
3779 (system* "python" "contrib/cmake/bootstrap.py" "create"))))
3780 (add-before 'check 'make-test-z3
3782 ;; Build the test suite executable.
3783 (zero? (system* "make" "test-z3" "-j"
3784 (number->string (parallel-job-count))))))
3787 ;; Run all the tests that don't require arguments.
3788 (zero? (system* "./test-z3" "/a")))))))
3790 `(("python" ,python-2)))
3791 (synopsis "Theorem prover")
3792 (description "Z3 is a theorem prover and @dfn{satisfiability modulo
3793 theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
3794 (home-page "https://github.com/Z3Prover/z3")
3795 (license license:expat)))
3797 (define-public cubicle
3803 (uri (string-append "http://cubicle.lri.fr/cubicle-"
3807 "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h"))))
3808 (build-system gnu-build-system)
3811 ("which" ,(@@ (gnu packages base) which))))
3815 `(#:configure-flags (list "--with-z3")
3818 (modify-phases %standard-phases
3819 (add-before 'configure 'configure-for-release
3821 (substitute* "Makefile.in"
3822 (("SVNREV=") "#SVNREV="))))
3823 (add-before 'configure 'fix-/bin/sh
3825 (substitute* "configure"
3826 (("/bin/sh") (which "sh")))))
3827 (add-before 'configure 'fix-smt-z3wrapper.ml
3829 (substitute* "Makefile.in"
3830 (("\\\\n") "")))))))
3831 (home-page "http://cubicle.lri.fr/")
3832 (synopsis "Model checker for array-based systems")
3833 (description "Cubicle is a model checker for verifying safety properties
3834 of array-based systems. This is a syntactically restricted class of
3835 parametrized transition systems with states represented as arrays indexed by
3836 an arbitrary number of processes. Cache coherence protocols and mutual
3837 exclusion algorithms are typical examples of such systems.")
3838 (license license:asl2.0)))
3840 (define-public elemental
3846 (uri (string-append "https://github.com/elemental/Elemental/"
3847 "archive/v" version ".tar.gz"))
3848 (file-name (string-append name "-" version ".tar.gz"))
3851 "1nfp82w22pi8x8fg9sc37z8kf84dqi1dhxp8bbk7571y4aygvv3v"))))
3852 (build-system cmake-build-system)
3853 (home-page "http://libelemental.org")
3855 `(("gfortran" ,gfortran)))
3857 `(("blas" ,openblas)
3858 ("gfortran:lib" ,gfortran "lib")
3867 `(#:build-type "Release" ;default RelWithDebInfo not supported
3868 #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
3869 "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
3870 "-DEL_CACHE_WARNINGS:BOOL=YES"
3871 "-DEL_TESTS:BOOL=YES"
3872 "-DCMAKE_INSTALL_LIBDIR=lib"
3873 "-DGFORTRAN_LIB=gfortran")
3874 #:phases (modify-phases %standard-phases
3875 (add-before 'check 'setup-tests
3877 ;; Parallelism is done at the MPI layer.
3878 (setenv "OMP_NUM_THREADS" "1")
3880 (add-after 'install 'remove-tests
3881 (lambda* (#:key outputs #:allow-other-keys)
3882 ;; Tests are installed, with no easy configuration
3883 ;; switch to prevent this, so delete them.
3884 (delete-file-recursively
3885 (string-append (assoc-ref outputs "out") "/bin"))
3887 (synopsis "Dense and sparse-direct linear algebra and optimization")
3888 (description "Elemental is a modern C++ library for distributed-memory
3889 dense and sparse-direct linear algebra, conic optimization, and lattice
3891 (license license:bsd-2)))
3893 (define-public mcrl2
3896 (version "201707.1.15162")
3899 (uri (string-append "http://www.mcrl2.org/download/devel/mcrl2-"
3904 "1ziww2fchsklm25hl9p2mngssxfh9w07nc114cncqaxfibqp2p8f"))))
3906 `(("subversion" ,subversion)))
3912 (build-system cmake-build-system)
3913 (synopsis "Toolset for the mCRL2 formal specification language")
3915 "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
3916 specification language for describing concurrent discrete event systems. Its
3917 toolset supports analysis and automatic verification, linearisation, simulation,
3918 state-space exploration and generation, and tools to optimise and analyse
3919 specifications. Also, state spaces can be manipulated, visualised and
3921 (home-page "http://mcrl2.org")
3922 (license license:boost1.0)))
3924 (define-public r-subplex
3931 (uri (cran-uri "subplex" version))
3934 "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
3935 (build-system r-build-system)
3937 `(("gfortran" ,gfortran)))
3938 (home-page "https://cran.r-project.org/web/packages/subplex")
3939 (synopsis "Unconstrained optimization using the subplex algorithm")
3940 (description "This package implements the Subplex optimization algorithm.
3941 It solves unconstrained optimization problems using a simplex method on
3942 subspaces. The method is well suited for optimizing objective functions that
3943 are noisy or are discontinuous at the solution.")
3944 (license license:gpl3+)))
3946 (define-public r-desolve
3953 (uri (cran-uri "deSolve" version))
3956 "0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"))))
3957 (properties `((upstream-name . "deSolve")))
3958 (build-system r-build-system)
3960 `(("gfortran" ,gfortran)))
3961 (home-page "https://desolve.r-forge.r-project.org/")
3962 (synopsis "Solvers for initial value problems of differential equations")
3963 (description "This package provides functions that solve initial
3964 value problems of a system of first-order ordinary differential equations (ODE),
3965 of partial differential equations (PDE), of differential algebraic equations
3966 (DAE), and of delay differential equations. The functions provide an interface
3967 to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
3968 to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
3969 the Runge-Kutta family with fixed or variable time steps. The package contains
3970 routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
3971 differential equations (PDE) that have been converted to ODEs by numerical
3973 (license license:gpl2+)))
3975 (define-public tcalc
3982 (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
3986 "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
3987 (build-system gnu-build-system)
3988 (synopsis "The terminal calculator")
3990 "The terminal calculator is a small program to help users of the GNU/Linux
3991 terminal do calculations simply and quickly. The formula to be calculated can
3992 be fed to @command{tcalc} through the command line.")
3993 (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
3994 (license license:gpl3+)))