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 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 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 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 Kei Kebreau <kei@openmailbox.org>
15 ;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
16 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
17 ;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be>
18 ;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>
19 ;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net>
20 ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
22 ;;; This file is part of GNU Guix.
24 ;;; GNU Guix is free software; you can redistribute it and/or modify it
25 ;;; under the terms of the GNU General Public License as published by
26 ;;; the Free Software Foundation; either version 3 of the License, or (at
27 ;;; your option) any later version.
29 ;;; GNU Guix is distributed in the hope that it will be useful, but
30 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
31 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
32 ;;; GNU General Public License for more details.
34 ;;; You should have received a copy of the GNU General Public License
35 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
37 (define-module (gnu packages maths)
38 #:use-module (ice-9 regex)
39 #:use-module (gnu packages)
40 #:use-module ((guix licenses) #:prefix license:)
41 #:use-module (guix packages)
42 #:use-module (guix download)
43 #:use-module (guix git-download)
44 #:use-module (guix utils)
45 #:use-module (guix build utils)
46 #:use-module (guix build-system cmake)
47 #:use-module (guix build-system gnu)
48 #:use-module (guix build-system ocaml)
49 #:use-module (guix build-system r)
50 #:use-module (gnu packages algebra)
51 #:use-module (gnu packages autotools)
52 #:use-module (gnu packages bison)
53 #:use-module (gnu packages boost)
54 #:use-module (gnu packages check)
55 #:use-module (gnu packages cmake)
56 #:use-module (gnu packages compression)
57 #:use-module (gnu packages curl)
58 #:use-module (gnu packages cyrus-sasl)
59 #:use-module (gnu packages documentation)
60 #:use-module (gnu packages elf)
61 #:use-module (gnu packages flex)
62 #:use-module (gnu packages fltk)
63 #:use-module (gnu packages fontutils)
64 #:use-module (gnu packages gettext)
65 #:use-module (gnu packages gcc)
66 #:use-module (gnu packages gd)
67 #:use-module (gnu packages ghostscript)
68 #:use-module (gnu packages graphviz)
69 #:use-module (gnu packages gtk)
70 #:use-module (gnu packages image)
71 #:use-module (gnu packages less)
72 #:use-module (gnu packages lisp)
73 #:use-module (gnu packages logging)
74 #:use-module (gnu packages lua)
75 #:use-module (gnu packages gnome)
76 #:use-module (gnu packages guile)
77 #:use-module (gnu packages xorg)
78 #:use-module (gnu packages gl)
79 #:use-module (gnu packages imagemagick)
80 #:use-module (gnu packages m4)
81 #:use-module (gnu packages mpi)
82 #:use-module (gnu packages multiprecision)
83 #:use-module (gnu packages netpbm)
84 #:use-module (gnu packages ocaml)
85 #:use-module (gnu packages pcre)
86 #:use-module (gnu packages popt)
87 #:use-module (gnu packages perl)
88 #:use-module (gnu packages pkg-config)
89 #:use-module (gnu packages python)
90 #:use-module (gnu packages readline)
91 #:use-module (gnu packages tbb)
92 #:use-module (gnu packages scheme)
93 #:use-module (gnu packages shells)
94 #:use-module (gnu packages tcl)
95 #:use-module (gnu packages texinfo)
96 #:use-module (gnu packages tex)
97 #:use-module (gnu packages tls)
98 #:use-module (gnu packages wxwidgets)
99 #:use-module (gnu packages xml)
100 #:use-module (srfi srfi-1))
108 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
110 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
111 (build-system gnu-build-system)
112 (inputs `(("gtk+" ,gtk+)
113 ("libxml2" ,libxml2)))
114 (native-inputs `(("pkg-config" ,pkg-config)))
115 (synopsis "Natural deduction first-order logic interface")
116 (description "Aris is a program for performing logical proofs. It supports
117 propositional and predicate logic, as well as Boolean algebra and
118 arithmetical logic. In addition to its predefined inference and equivalence
119 rules, Aris also supports references to older proofs. Its use of standard
120 logical symbols and its natural deduction interface make it easy to use for
122 (license license:gpl3+)
123 (home-page "https://www.gnu.org/software/aris/")))
125 (define-public c-graph
131 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
134 "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
135 (build-system gnu-build-system)
137 `(("fortran" ,gfortran)))
138 (synopsis "Visualizing and demonstrating convolution")
140 "GNU C-Graph is a tool for demonstrating the theory of convolution.
141 Thus, it can serve as an excellent aid to students of signal and systems
142 theory in visualizing the convolution process. Rather than forcing the
143 student to write code, the program offers an intuitive interface with
144 interactive dialogs to guide them.")
145 (license license:gpl3+)
146 (home-page "https://www.gnu.org/software/c-graph/")))
155 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
156 version "/coda-" version ".tar.gz"))
158 (base32 "11asla1ap8vd73farqjlpb179sfiy0biydcwxjfcakrp9sf8v9bs"))
159 (patches (search-patches "coda-use-system-libs.patch"))
160 (modules '((guix build utils)))
162 ;; Make sure we don't use the bundled software.
163 '(for-each (lambda (d)
164 (delete-file-recursively (string-append "libcoda/" d)))
165 '("zlib" "pcre" "expat")))))
167 `(("fortran" ,gfortran)
169 ("python-numpy" ,python-numpy)))
176 (build-system gnu-build-system)
178 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
179 "LIBS= -lz -lpcre -lexpat")))
180 (synopsis "A common interface to various earth observation data formats")
182 "The Common Data Access toolbox (CODA) provides a set of interfaces for
183 reading remote sensing data from earth observation data files. It consists of
184 command line applications and interfaces to the C, Fortran, Python, and Java
185 programming languages.")
186 (home-page "https://stcorp.nl/coda")
187 (license license:gpl2+)))
195 (uri (string-append "mirror://gnu/units/units-" version
198 "1s421bxm36akjsy3qzg6da1d1g20gh094ac2slqxipgkh8yqjcwx"))))
199 (build-system gnu-build-system)
200 (synopsis "Conversion between thousands of scales")
202 "GNU Units converts numeric quantities between units of measure. It
203 can handle scale changes through adaptive usage of standard scale
204 prefixes (micro-, kilo-, etc.). It can also handle nonlinear
205 conversions such as Fahrenheit to Celsius. Its interpreter is powerful
206 enough to be used effectively as a scientific calculator.")
207 (license license:gpl3+)
208 (home-page "https://www.gnu.org/software/units/")))
210 (define-public double-conversion
212 (name "double-conversion")
217 "https://github.com/floitsch/double-conversion/archive/v"
219 (file-name (string-append name "-" version ".tar.gz"))
222 "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83"))))
223 (build-system cmake-build-system)
225 '(#:test-target "test"
226 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
227 "-DBUILD_TESTING=ON")))
228 (home-page "https://github.com/floitsch/double-conversion")
229 (synopsis "Conversion routines for IEEE doubles")
231 "The double-conversion library provides binary-decimal and decimal-binary
232 routines for IEEE doubles. The library consists of efficient conversion
233 routines that have been extracted from the V8 JavaScript engine.")
234 (license license:bsd-3)))
236 (define-public dionysus
242 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
246 "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs"))))
247 (build-system gnu-build-system)
248 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
249 (synopsis "Local search for universal constants and scientific values")
251 "GNU Dionysus is a convenient system for quickly retrieving the values of
252 mathematical constants used in science and engineering. Values can be
253 searched using a simple command-line tool, choosing from three databases:
254 universal constants, atomic numbers, and constants related to
256 (license license:gpl3+)
257 (home-page "https://www.gnu.org/software/dionysus/")))
265 (uri (string-append "mirror://gnu/gsl/gsl-"
269 "16yfs5n444s03np1naj6yp1fsysd42kdscxzkg0k2yvfjixx0ijd"))
270 (patches (search-patches "gsl-test-i686.patch"))))
271 (build-system gnu-build-system)
273 `(;; Currently there are numerous tests that fail on "exotic"
274 ;; architectures such as aarch64 and ppc64le.
275 ,@(if (string-prefix? "aarch64-linux"
276 (or (%current-target-system) (%current-system)))
279 (home-page "https://www.gnu.org/software/gsl/")
280 (synopsis "Numerical library for C and C++")
282 "The GNU Scientific Library is a library for numerical analysis in C
283 and C++. It includes a wide range of mathematical routines, with over 1000
284 functions in total. Subject areas covered by the library include:
285 differential equations, linear algebra, Fast Fourier Transforms and random
287 (license license:gpl3+)))
289 (define-public ocaml-gsl
298 "https://github.com/mmottl/gsl-ocaml/releases/download/v"
299 version"/gsl-ocaml-" version ".tar.gz"))
302 "0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh"))))
303 (build-system ocaml-build-system)
306 (home-page "https://mmottl.github.io/gsl-ocaml")
307 (synopsis "Bindings to the GNU Scientific Library")
309 "GSL-OCaml is an interface to the @dfn{GNU scientific library} (GSL) for
310 the OCaml language.")
311 (license license:gpl3+)))
313 (define-public ocaml4.01-gsl
314 (package-with-ocaml4.01 ocaml-gsl))
323 (uri (string-append "mirror://gnu/glpk/glpk-"
327 "0w7s3869ybwyq9a4490dikpib1qp3jnn5nqz1vvwqy1qz3ilnvh9"))))
328 (build-system gnu-build-system)
332 `(#:configure-flags '("--with-gmp")))
333 (home-page "https://www.gnu.org/software/glpk/")
334 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
336 "GLPK is a C library for solving large-scale linear programming (LP),
337 mixed integer programming (MIP), and other related problems. It supports the
338 GNU MathProg modeling language, a subset of the AMPL language, and features a
339 translator for the language. In addition to the C library, a stand-alone
340 LP/MIP solver is included in the package.")
341 (license license:gpl3+)))
350 (uri (string-append "http://www.4ti2.de/version_" version
351 "/4ti2-" version ".tar.gz"))
354 "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
355 (build-system gnu-build-system)
357 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
361 (home-page "http://www.4ti2.de/")
362 (synopsis "Mathematical tool suite for problems on linear spaces")
364 "4ti2 implements algorithms for solving algebraic, geometric and
365 combinatorial problems on linear spaces. Among others, it solves systems
366 of linear equations, computes extreme rays of polyhedral cones, solves
367 integer programming problems and computes Markov bases for statistics.")
368 (license license:gpl2+)))
370 (define-public cddlib
377 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
378 (string-delete #\. version) ".tar.gz"))
381 "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy"))))
382 (build-system gnu-build-system)
385 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
386 (synopsis "Library for convex hulls and extreme rays of polyhedra")
388 "The C-library cddlib implements the Double Description Method of
389 Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
390 rays of a general convex polyhedron given by a system of linear inequalities
391 in arbitrary dimension. It can also be used for the converse operation of
392 computing convex hulls.")
393 (license license:gpl2+)))
395 (define-public arpack-ng
402 (uri (string-append "https://github.com/opencollab/arpack-ng/archive/"
404 (file-name (string-append name "-" version ".tar.gz"))
407 "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff"))))
408 (build-system gnu-build-system)
409 (home-page "https://github.com/opencollab/arpack-ng")
412 ("fortran" ,gfortran)))
413 (synopsis "Fortran subroutines for solving eigenvalue problems")
415 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
416 large scale eigenvalue problems.")
417 (license (license:non-copyleft "file://COPYING"
418 "See COPYING in the distribution."))))
420 (define-public arpack-ng-openmpi
421 (package (inherit arpack-ng)
422 (name "arpack-ng-openmpi")
425 ,@(package-inputs arpack-ng)))
426 (arguments `(#:configure-flags '("--enable-mpi")))
427 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
429 (define-public lapack
436 (uri (string-append "http://www.netlib.org/lapack/lapack-"
440 "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
441 (build-system cmake-build-system)
442 (home-page "http://www.netlib.org/lapack/")
443 (inputs `(("fortran" ,gfortran)
444 ("python" ,python-2)))
446 `(#:configure-flags (list
447 ;; Install to PREFIX/lib (the default is
449 (string-append "-DCMAKE_INSTALL_LIBDIR="
450 (assoc-ref %outputs "out")
453 "-DBUILD_SHARED_LIBS:BOOL=YES"
456 ;; Build the 'LAPACKE_clatms' functions.
457 "-DLAPACKE_WITH_TMG=ON")
458 #:phases (alist-cons-before
460 (lambda* (#:key inputs #:allow-other-keys)
461 (let ((python (assoc-ref inputs "python")))
462 (substitute* "lapack_testing.py"
463 (("/usr/bin/env python") python))))
465 (synopsis "Library for numerical linear algebra")
467 "LAPACK is a Fortran 90 library for solving the most commonly occurring
468 problems in numerical linear algebra.")
469 (license (license:non-copyleft "file://LICENSE"
470 "See LICENSE in the distribution."))))
472 (define-public scalapack
479 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
483 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
484 (build-system cmake-build-system)
487 ("fortran" ,gfortran)
488 ("lapack" ,lapack))) ;for testing only
490 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")))
491 (home-page "http://www.netlib.org/scalapack/")
492 (synopsis "Library for scalable numerical linear algebra")
494 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
495 routines on parallel distributed memory machines. ScaLAPACK solves dense and
496 banded linear systems, least squares problems, eigenvalue problems, and
497 singular value problems.")
498 (license (license:bsd-style "file://LICENSE"
499 "See LICENSE in the distribution."))))
501 (define-public gnuplot
507 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
512 "0q5lr6nala3ln6f3yp6g17ziymb9r9gx9zylnw1y3hjmwl9lggjv"))))
513 (build-system gnu-build-system)
514 (inputs `(("readline" ,readline)
520 `(("pkg-config" ,pkg-config)
521 ("texlive" ,texlive-tiny)))
522 (home-page "http://www.gnuplot.info")
523 (synopsis "Command-line driven graphing utility")
524 (description "Gnuplot is a portable command-line driven graphing
525 utility. It was originally created to allow scientists and students to
526 visualize mathematical functions and data interactively, but has grown to
527 support many non-interactive uses such as web scripting. It is also used as a
528 plotting engine by third-party applications like Octave.")
529 ;; X11 Style with the additional restriction that derived works may only be
530 ;; distributed as patches to the original.
531 (license (license:fsf-free
532 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
541 (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
543 (file-name (string-append name "-" version ".tar.gz"))
546 "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
548 `(("fortran" ,gfortran)))
549 (build-system gnu-build-system)
550 (synopsis "General Cartographic Transformation Package (GCTP)")
552 "The General Cartographic Transformation Package (GCTP) is a system of
553 software routines designed to permit the transformation of coordinate pairs
554 from one map projection to another. The GCTP is the standard computer
555 software used by the National Mapping Division for map projection
557 (home-page "https://github.com/OkoSanto/GCTP")
558 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
567 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
568 version "/src/hdf-" version ".tar.bz2"))
570 (base32 "020jh563sjyxsgml8l809d2i1d4ms9shivwj3gbm7n0ilxbll8id"))
571 (patches (search-patches "hdf4-architectures.patch"
572 "hdf4-reproducibility.patch"
573 "hdf4-shared-fortran.patch"))))
575 (build-system gnu-build-system)
577 `(("gfortran" ,gfortran)
582 ("libjpeg" ,libjpeg)))
584 `(#:parallel-tests? #f
585 #:configure-flags '("--enable-shared")
587 (modify-phases %standard-phases
588 (add-before 'configure 'patchbuild
591 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
593 (("/bin/mkdir") "mkdir"))
594 (substitute* (find-files "." "^Makefile\\.in$")
595 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
596 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
597 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
598 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
599 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")))))))
600 (home-page "https://www.hdfgroup.org/products/hdf4/")
602 "Library and multi-object file format for storing and managing data")
603 (description "HDF4 is a library and multi-object file format for storing
604 and managing data between machines. HDF4 is an older hierarchical data format,
605 incompatible with HDF5.")
607 (license:non-copyleft
608 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
610 (define-public hdf4-alt
615 (substitute-keyword-arguments (package-arguments hdf4)
616 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
618 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
627 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
628 "hdf5-" (version-major+minor version)
629 "/hdf5-" version "/src/hdf5-"
631 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
634 (take (string-split version #\.) 2))
635 "/src/hdf5-" version ".tar.bz2")))
637 (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
638 (patches (list (search-patch "hdf5-config-date.patch")))))
639 (build-system gnu-build-system)
643 `(;; Some of the users, notably Flann, need the C++ interface.
644 #:configure-flags '("--enable-cxx")
647 (modify-phases %standard-phases
648 (add-before 'configure 'patch-configure
650 (substitute* "configure"
653 (add-after 'install 'patch-references
654 (lambda* (#:key inputs outputs #:allow-other-keys)
655 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
656 (zlib (assoc-ref inputs "zlib")))
657 (substitute* (find-files bin "h5p?cc")
659 (string-append "-L" zlib "/lib " lib)))
661 (home-page "http://www.hdfgroup.org")
662 (synopsis "Management suite for extremely large and complex data")
663 (description "HDF5 is a suite that makes possible the management of
664 extremely large and complex data collections.")
665 (license (license:x11-style
666 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
668 (define-public hdf-eos2
675 (uri "ftp://edhs1.gsfc.nasa.gov\
676 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
678 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
679 (patches (search-patches "hdf-eos2-remove-gctp.patch"
680 "hdf-eos2-build-shared.patch"
681 "hdf-eos2-fortrantests.patch"))))
682 (build-system gnu-build-system)
684 `(("gfortran" ,gfortran)))
686 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
691 `( #:configure-flags '("--enable-install-include" "--enable-shared"
692 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
693 #:parallel-tests? #f))
694 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
695 (synopsis "HDF4-based data format for NASA's Earth Observing System")
696 (description "HDF-EOS2 is a software library built on HDF4 which supports
697 the construction of data structures used in NASA's Earth Observing
698 System (Grid, Point and Swath).")
700 ;; Source files carry a permissive license header.
701 (license (license:non-copyleft home-page))))
703 (define-public hdf-eos5
709 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
710 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
713 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
714 (patches (search-patches "hdf-eos5-build-shared.patch"
715 "hdf-eos5-remove-gctp.patch"
716 "hdf-eos5-fix-szip.patch"
717 "hdf-eos5-fortrantests.patch"))))
719 `(("gfortran" ,gfortran)))
720 (build-system gnu-build-system)
726 `(#:configure-flags '("--enable-install-include" "--enable-shared"
727 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
728 #:parallel-tests? #f))
729 (synopsis "HDF5-based data format for NASA's Earth Observing System")
731 "HDF-EOS5 is a software library built on HDF5 to support the construction
732 of data structures used in NASA's Earth Observing System (Grid, Point and
734 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
736 ;; Source files carry a permissive license header.
737 (license (license:non-copyleft home-page))))
739 (define-public hdf5-parallel-openmpi
740 (package (inherit hdf5)
741 (name "hdf5-parallel-openmpi")
744 ,@(package-inputs hdf5)))
746 (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
747 ,@(package-arguments hdf5))
749 `(modify-phases ,phases
750 (add-before 'check 'patch-tests
752 ;; OpenMPI's mpirun will exit with non-zero status if it
753 ;; detects an "abnormal termination", i.e. any process not
754 ;; calling MPI_Finalize(). Since the test is explicitely
755 ;; avoiding MPI_Finalize so as not to have at_exit and thus
756 ;; H5C_flush_cache from being called, mpirun will always
757 ;; complain, so turn this test off.
758 (substitute* "testpar/Makefile"
759 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
760 (string-append front back "\n")))
761 (substitute* "tools/h5diff/testph5diff.sh"
762 (("/bin/sh") (which "sh")))
764 (synopsis "Management suite for data with parallel IO support")))
766 (define-public h5check
773 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
774 "h5check/src/h5check-" version ".tar.gz"))
777 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
778 (build-system gnu-build-system)
779 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
780 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
781 (synopsis "HDF5 format checker")
782 (description "@code{h5check} is a validation tool for verifying that an
783 HDF5 file is encoded according to the HDF File Format Specification.")
784 (license (license:x11-style "file://COPYING"))))
792 (uri (string-append "mirror://sourceforge/itpp/itpp/"
797 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
798 (build-system cmake-build-system)
799 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
800 (inputs `(("lapack" ,lapack)
802 ;; FIXME: Even though the fonts are available dvips complains:
803 ;; "Font cmmi10 not found; characters will be left blank."
805 `(("texlive" ,texlive-tiny)
806 ("ghostscript" ,ghostscript)
807 ("doxygen" ,doxygen)))
808 (home-page "http://itpp.sourceforge.net")
809 (synopsis "C++ library of maths, signal processing and communication classes")
810 (description "IT++ is a C++ library of mathematical, signal processing and
811 communication classes and functions. Its main use is in simulation of
812 communication systems and for performing research in the area of
813 communications. The kernel of the library consists of generic vector and
814 matrix classes, and a set of accompanying routines. Such a kernel makes IT++
815 similar to MATLAB, GNU Octave or SciPy.")
816 (license license:gpl3+)))
818 (define-public netcdf
825 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
826 "netcdf-" version ".tar.gz"))
829 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
830 (patches (search-patches "netcdf-date-time.patch"
831 "netcdf-tst_h_par.patch"))))
832 (build-system gnu-build-system)
836 ("graphviz" ,graphviz)))
841 ("libjpeg" ,libjpeg)))
843 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
844 #:parallel-tests? #f)) ;various race conditions
845 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
846 (synopsis "Library for scientific data")
847 (description "NetCDF is an interface for scientific data access and a
848 software library that provides an implementation of the interface. The netCDF
849 library defines a machine-independent format for representing scientific data.
850 Together, the interface, library, and format support the creation, access, and
851 sharing of scientific data.")
852 (license (license:x11-style "file://COPYRIGHT"))))
854 (define-public netcdf-parallel-openmpi
855 (package (inherit netcdf)
856 (name "netcdf-parallel-openmpi")
859 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
860 (package-inputs netcdf))))
861 ;; TODO: Replace pkg-config references in nc-config with absolute references
863 (substitute-keyword-arguments (package-arguments netcdf)
864 ((#:configure-flags flags)
865 `(cons* "CC=mpicc" "CXX=mpicxx"
866 "--enable-parallel-tests"
867 ;; Shared libraries not supported with parallel IO.
868 "--disable-shared" "--with-pic"
871 (define-public netcdf-fortran
873 (name "netcdf-fortran")
878 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
882 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
883 (build-system gnu-build-system)
885 `(#:parallel-tests? #f))
887 `(("netcdf" ,netcdf)))
889 `(("gfortran" ,gfortran)))
890 (synopsis "Fortran interface for the netCDF library")
891 (description (package-description netcdf))
892 (home-page (package-home-page netcdf))
893 (license (package-license netcdf))))
901 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
904 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
905 (build-system gnu-build-system)
907 `(;; Shared libraries are not built by default. They are required to
908 ;; build the Guile, Octave, and Python bindings.
909 #:configure-flags '("--enable-shared")
912 (modify-phases %standard-phases
913 (add-before 'configure 'set-libnlopt-file-name
914 (lambda* (#:key outputs #:allow-other-keys)
915 ;; Make sure the Scheme module refers to the library by its
916 ;; absolute file name (we cannot do that from a snippet
917 ;; because the expansion of @libdir@ contains
919 (let ((out (assoc-ref outputs "out")))
920 (substitute* "swig/nlopt.scm.in"
922 (string-append out "/lib/libnlopt")))
924 (inputs `(("guile" ,guile-2.0)))
925 (native-inputs `(("pkg-config" ,pkg-config)))
926 (home-page "http://ab-initio.mit.edu/wiki/")
927 (synopsis "Library for nonlinear optimization")
928 (description "NLopt is a library for nonlinear optimization, providing a
929 common interface for a number of different free optimization routines available
930 online as well as original implementations of various other algorithms.")
931 (license license:lgpl2.1+)))
940 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
944 "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
945 (modules '((guix build utils)))
947 ;; Make sure we don't use the bundled software.
948 '(delete-file-recursively "ThirdParty"))))
949 (build-system gnu-build-system)
951 '(#:phases (modify-phases %standard-phases
952 (add-after 'install 'add--L-flags-in-ipopt.pc
953 (lambda* (#:key inputs outputs #:allow-other-keys)
954 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
955 ;; move it to "Libs.private" where it belongs, and add a
956 ;; '-L' flag for LAPACK.
957 (let ((out (assoc-ref outputs "out"))
958 (lapack (assoc-ref inputs "lapack")))
959 (substitute* (string-append out "/lib/pkgconfig/"
961 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
962 (string-append "Libs: " before " " after "\n"
963 "Libs.private: " before
964 "-L" lapack "/lib -llapack -lblas "
968 `(("gfortran" ,gfortran)))
970 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
971 `(("lapack" ,lapack))) ;for both libblas and liblapack
972 (home-page "http://www.coin-or.org")
973 (synopsis "Large-scale nonlinear optimizer")
975 "The Interior Point Optimizer (IPOPT) is a software package for
976 large-scale nonlinear optimization. It provides C++, C, and Fortran
978 (license license:epl1.0)))
982 (name "ceres-solver")
984 (home-page "http://ceres-solver.org/")
987 (uri (string-append home-page "ceres-solver-"
991 "0i7qkbf8g6pd8arxzldppga26ckv93y8zldsfz6wbd4n6b1nqrjd"))))
992 (build-system cmake-build-system)
994 ;; TODO: Build HTML user documentation and install separately.
995 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
996 "-DBUILD_SHARED_LIBS=ON")
998 #:phases (modify-phases %standard-phases
999 (add-before 'configure 'set-library-directory
1001 ;; Install libraries to lib/, not lib64/.
1002 (substitute* "internal/ceres/CMakeLists.txt"
1003 (("set\\(LIB_SUFFIX \"64\"\\)")
1004 "set(LIB_SUFFIX \"\")"))
1007 `(("pkg-config" ,pkg-config)))
1009 `(("glog" ,glog))) ;for #include <glog/glog.h>
1014 ("suitesparse" ,suitesparse)
1015 ("gflags" ,gflags)))
1016 (synopsis "C++ library for solving large optimization problems")
1018 "Ceres Solver is a C++ library for modeling and solving large,
1019 complicated optimization problems. It is a feature rich, mature and
1020 performant library which has been used in production since 2010. Ceres Solver
1021 can solve two kinds of problems:
1023 @item non-linear least squares problems with bounds constraints;
1024 @item general unconstrained optimization problems.
1026 (license license:bsd-3)))
1028 ;; For a fully featured Octave, users are strongly recommended also to install
1029 ;; the following packages: texinfo, less, ghostscript, gnuplot.
1030 (define-public octave
1037 (uri (string-append "mirror://gnu/octave/octave-"
1041 "09zhhch79jw3ynw39vizx0i2cbd2bjz3sp38pjdzraqrbivpwp92"))))
1042 (build-system gnu-build-system)
1044 `(("lapack" ,lapack)
1045 ("readline" ,readline)
1050 ("arpack" ,arpack-ng)
1053 ("fontconfig" ,fontconfig)
1054 ("freetype" ,freetype)
1061 ("graphicsmagick" ,graphicsmagick)))
1064 ("gfortran" ,gfortran)
1065 ("pkg-config" ,pkg-config)
1067 ;; The following inputs are not actually used in the build process.
1068 ;; However, the ./configure gratuitously tests for their existence and
1069 ;; assumes that programs not present at build time are also not, and
1070 ;; can never be, available at run time! If these inputs are therefore
1071 ;; not present, support for them will be built out. However, Octave
1072 ;; will still run without them, albeit without the features they
1075 ("texinfo" ,texinfo)
1076 ("ghostscript" ,ghostscript)
1077 ("gnuplot" ,gnuplot)))
1080 (list (string-append "--with-shell="
1081 (assoc-ref %build-inputs "bash")
1083 (home-page "https://www.gnu.org/software/octave/")
1084 (synopsis "High-level language for numerical computation")
1085 (description "GNU Octave is a high-level interpreted language that is
1086 specialized for numerical computations. It can be used for both linear and
1087 non-linear applications and it provides great support for visualizing results.
1088 Work may be performed both at the interactive command-line as well as via
1090 (license license:gpl3+)))
1092 (define-public opencascade-oce
1094 (name "opencascade-oce")
1100 "https://github.com/tpaviot/oce/archive/OCE-"
1105 "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
1106 (build-system cmake-build-system)
1109 (list "-DOCE_TESTING:BOOL=ON"
1110 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1111 "-DOCE_DRAW:BOOL=ON"
1112 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1113 (assoc-ref %outputs "out"))
1114 "-UCMAKE_INSTALL_RPATH")))
1116 `(("freetype" ,freetype)
1123 `(("python" ,python-wrapper)))
1124 (home-page "https://github.com/tpaviot/oce")
1125 (synopsis "Libraries for 3D modeling and numerical simulation")
1127 "Open CASCADE is a set of libraries for the development of applications
1128 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1129 C++ class libraries providing services for 3D surface and solid modeling, CAD
1130 data exchange, and visualization. It is used for development of specialized
1131 software dealing with 3D models in design (CAD), manufacturing (CAM),
1132 numerical simulation (CAE), measurement equipment (CMM), and quality
1133 control (CAQ) domains.
1135 This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1136 patches, improvements, and experiments contributed by users over the official
1137 Open CASCADE library.")
1138 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1139 ; use of header files; see
1140 ; OCCT_LGPL_EXCEPTION.txt
1141 license:public-domain; files
1142 ; src/Standard/Standard_StdAllocator.hxx and
1143 ; src/NCollection/NCollection_StdAllocator.hxx
1144 license:expat; file src/OpenGl/OpenGl_glext.h
1145 license:bsd-3)))); test framework gtest
1154 (uri (string-append "http://gmsh.info/src/gmsh-"
1155 version "-source.tgz"))
1157 (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
1158 (modules '((guix build utils)))
1160 ;; Remove non-free METIS code
1161 '(delete-file-recursively "contrib/Metis"))))
1162 (build-system cmake-build-system)
1165 ("gfortran" ,gfortran)
1171 ("opencascade-oce" ,opencascade-oce)
1173 ("libxext" ,libxext)))
1175 `(("fontconfig" ,fontconfig)
1176 ("libxft" ,libxft)))
1178 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1179 "-DENABLE_BUILD_SHARED:BOOL=ON"
1180 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
1181 (home-page "http://www.geuz.org/gmsh/")
1182 (synopsis "3D finite element grid generator")
1183 (description "Gmsh is a 3D finite element grid generator with a built-in
1184 CAD engine and post-processor. Its design goal is to provide a fast, light
1185 and user-friendly meshing tool with parametric input and advanced
1186 visualization capabilities. Gmsh is built around four modules: geometry,
1187 mesh, solver and post-processing. The specification of any input to these
1188 modules is done either interactively using the graphical user interface or in
1189 ASCII text files using Gmsh's own scripting language.")
1190 (license license:gpl2+)))
1192 (define-public maxflow
1199 (url "https://github.com/gerddie/maxflow.git")
1200 (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
1201 (file-name (string-append name "-" version "-checkout"))
1204 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1205 (build-system cmake-build-system)
1206 (home-page "http://pub.ist.ac.at/~vnk/software.html")
1207 (synopsis "Library implementing Maxflow algorithm")
1208 (description "An implementation of the maxflow algorithm described in
1209 @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1210 Energy Minimization in Computer Vision.\n
1211 Yuri Boykov and Vladimir Kolmogorov.\n
1212 In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1214 (license license:gpl3+)))
1216 (define-public petsc
1223 ;; The *-lite-* tarball does not contain the *large* documentation
1224 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1225 "petsc-lite-" version ".tar.gz"))
1227 (base32 "0jfrq6rd4zagw1iimz05m2w91k0jvz3qbik1lk8pqcxw3rvdqk5d"))))
1228 (build-system gnu-build-system)
1230 `(("python" ,python-2)
1233 `(("gfortran" ,gfortran)
1235 ("superlu" ,superlu)
1236 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1237 ;; leaving out opengl, as configuration seems to only be for mac
1240 `(#:test-target "test"
1241 #:parallel-build? #f ;build is parallel by default
1246 ,(string-append "--with-superlu-include="
1247 (assoc-ref %build-inputs "superlu") "/include")
1248 ,(string-append "--with-superlu-lib="
1249 (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
1251 (modify-phases %standard-phases
1253 ;; PETSc's configure script is actually a python script, so we can't
1254 ;; run it with bash.
1255 (lambda* (#:key outputs (configure-flags '())
1257 (let* ((prefix (assoc-ref outputs "out"))
1258 (flags `(,(string-append "--prefix=" prefix)
1259 ,@configure-flags)))
1260 (format #t "build directory: ~s~%" (getcwd))
1261 (format #t "configure flags: ~s~%" flags)
1262 (zero? (apply system* "./configure" flags)))))
1263 (add-after 'configure 'clean-local-references
1264 (lambda* (#:key inputs outputs #:allow-other-keys)
1265 (let ((out (assoc-ref outputs "out")))
1266 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
1267 ;; Prevent build directory from leaking into compiled code
1269 ;; Scrub timestamp for reproducibility
1270 ((".*Libraries compiled on.*") ""))
1272 (add-after 'install 'clean-install
1273 ;; Try to keep installed files from leaking build directory names.
1274 (lambda* (#:key inputs outputs #:allow-other-keys)
1275 (let ((out (assoc-ref outputs "out")))
1276 (substitute* (map (lambda (file)
1277 (string-append out "/lib/petsc/conf/" file))
1278 '("petscvariables"))
1280 ;; Make compiler references point to the store
1281 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
1282 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1283 (string-append "= " (which compiler))))
1284 ;; PETSc installs some build logs, which aren't necessary.
1285 (for-each (lambda (file)
1286 (let ((f (string-append out "/lib/petsc/conf/" file)))
1287 (when (file-exists? f)
1289 '("configure.log" "make.log" "gmake.log"
1290 "test.log" "error.log" "RDict.db"
1291 "PETScBuildInternal.cmake"
1292 ;; Once installed, should uninstall with Guix
1295 (home-page "http://www.mcs.anl.gov/petsc")
1296 (synopsis "Library to solve PDEs")
1297 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1298 data structures and routines for the scalable (parallel) solution of
1299 scientific applications modeled by partial differential equations.")
1300 (license (license:non-copyleft
1301 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1303 (define-public petsc-complex
1304 (package (inherit petsc)
1305 (name "petsc-complex")
1307 (substitute-keyword-arguments (package-arguments petsc)
1308 ((#:configure-flags cf)
1309 `(cons "--with-scalar-type=complex" ,cf))))
1310 (synopsis "Library to solve PDEs (with complex scalars)")))
1312 (define-public petsc-openmpi
1313 (package (inherit petsc)
1314 (name "petsc-openmpi")
1316 `(("openmpi" ,openmpi)
1317 ,@(package-inputs petsc)))
1319 (substitute-keyword-arguments (package-arguments petsc)
1320 ((#:configure-flags cf)
1321 ``("--with-mpiexec=mpirun"
1322 ,(string-append "--with-mpi-dir="
1323 (assoc-ref %build-inputs "openmpi"))
1324 ,@(delete "--with-mpi=0" ,cf)))))
1325 (synopsis "Library to solve PDEs (with MPI support)")))
1327 (define-public petsc-complex-openmpi
1328 (package (inherit petsc-complex)
1329 (name "petsc-complex-openmpi")
1331 `(("openmpi" ,openmpi)
1332 ,@(package-inputs petsc-complex)))
1334 (substitute-keyword-arguments (package-arguments petsc-complex)
1335 ((#:configure-flags cf)
1336 ``("--with-mpiexec=mpirun"
1337 ,(string-append "--with-mpi-dir="
1338 (assoc-ref %build-inputs "openmpi"))
1339 ,@(delete "--with-mpi=0" ,cf)))))
1340 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
1342 (define-public slepc
1349 (uri (string-append "http://slepc.upv.es/download/download.php?"
1350 "filename=slepc-" version ".tar.gz"))
1351 (file-name (string-append name "-" version ".tar.gz"))
1354 "1hijlmrvxvfqslnx8yydzw5xqbsn1yy02g32w0hln1z3cgr1c0k7"))))
1355 (build-system gnu-build-system)
1357 `(("python" ,python-2)))
1359 `(("arpack" ,arpack-ng)
1360 ("gfortran" ,gfortran)))
1362 `(("petsc" ,petsc)))
1364 `(#:parallel-build? #f ;build is parallel by default
1366 `(,(string-append "--with-arpack-dir="
1367 (assoc-ref %build-inputs "arpack") "/lib"))
1369 (modify-phases %standard-phases
1371 ;; configure is a python script, so we can't run it with bash.
1372 (lambda* (#:key inputs outputs (configure-flags '())
1374 (let* ((prefix (assoc-ref outputs "out"))
1375 (flags `(,(string-append "--prefix=" prefix)
1376 ,@configure-flags)))
1377 (format #t "build directory: ~s~%" (getcwd))
1378 (format #t "configure flags: ~s~%" flags)
1379 (setenv "SLEPC_DIR" (getcwd))
1380 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
1381 (zero? (apply system* "./configure" flags)))))
1382 (add-after 'install 'delete-doc
1383 ;; TODO: SLEPc installs HTML documentation alongside headers in
1384 ;; $out/include. We'd like to move them to share/doc, but delete
1385 ;; them for now, as they are incomplete and installing the complete
1386 ;; documentation is difficult.
1387 (lambda* (#:key outputs #:allow-other-keys)
1388 (let* ((out (assoc-ref outputs "out")))
1389 (for-each delete-file (find-files out "\\.html$")))))
1390 (add-after 'install 'clean-install
1391 ;; Clean up unnecessary build logs from installation.
1392 (lambda* (#:key outputs #:allow-other-keys)
1393 (let ((out (assoc-ref outputs "out")))
1394 (for-each (lambda (file)
1395 (let ((f (string-append out "/lib/slepc/conf/" file)))
1396 (when (file-exists? f)
1398 '("configure.log" "make.log" "gmake.log"
1399 "test.log" "error.log" "RDict.db"
1400 "uninstall.py"))))))))
1401 (home-page "http://slepc.upv.es")
1402 (synopsis "Scalable library for eigenproblems")
1403 (description "SLEPc is a software library for the solution of large sparse
1404 eigenproblems on parallel computers. It can be used for the solution of
1405 linear eigenvalue problems formulated in either standard or generalized form,
1406 as well as other related problems such as the singular value decomposition.
1407 The emphasis of the software is on methods and techniques appropriate for
1408 problems in which the associated matrices are sparse, for example, those
1409 arising after the discretization of partial differential equations.")
1410 (license license:lgpl3)))
1412 (define-public slepc-complex
1413 (package (inherit slepc)
1414 (name "slepc-complex")
1416 `(("petsc" ,petsc-complex)
1417 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1418 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1420 (define-public slepc-openmpi
1421 (package (inherit slepc)
1422 (name "slepc-openmpi")
1425 ("arpack" ,arpack-ng-openmpi)
1426 ,@(alist-delete "arpack" (package-inputs slepc))))
1428 `(("petsc" ,petsc-openmpi)
1429 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1430 (synopsis "Scalable library for eigenproblems (with MPI support)")))
1432 (define-public slepc-complex-openmpi
1433 (package (inherit slepc-openmpi)
1434 (name "slepc-complex-openmpi")
1436 `(("petsc" ,petsc-complex-openmpi)
1437 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1438 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1440 (define-public mumps
1447 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
1451 "0igyc1pfzxdhpbad3v3lb86ixkdbqa1a8gbs15b04r2294h2nabp"))
1452 (patches (search-patches "mumps-build-parallelism.patch"))))
1453 (build-system gnu-build-system)
1455 `(("fortran" ,gfortran)
1456 ;; These are required for linking against mumps, but we let the user
1457 ;; declare the dependency.
1460 ("scotch" ,scotch)))
1462 `(#:modules ((ice-9 match)
1465 ,@%gnu-build-system-modules)
1467 (modify-phases %standard-phases
1469 (lambda* (#:key inputs #:allow-other-keys)
1470 (call-with-output-file "Makefile.inc"
1481 INCSEQ = -I$(topdir)/libseq
1482 LIBSEQ = -L$(topdir)/libseq -lmpiseq
1483 LIBSEQNEEDED = libseqneeded~;
1487 AR = ar vr # rules require trailing space, ugh...
1489 LIBBLAS = -L~a -lopenblas~@[
1490 SCALAP = -L~a -lscalapack~]
1491 LIBOTHERS = -pthread
1494 OPTF = -O2 -DALLOW_NON_INIT $(PIC)
1498 LIBS = $(SCALAP) $(LIBSEQ)
1499 LPORDDIR = $(topdir)/PORD/lib
1500 IPORD = -I$(topdir)/PORD/include
1501 LPORD = -L$(LPORDDIR) -lpord
1502 ORDERINGSF = -Dpord~@[
1504 IMETIS = -I$(METISDIR)/include
1505 LMETIS = -L$(METISDIR)/lib -lmetis
1506 ORDERINGSF += -Dmetis~]~@[~:{
1508 ISCOTCH = -I$(SCOTCHDIR)/include
1509 LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
1510 ORDERINGSF += ~a~}~]
1511 ORDERINGSC = $(ORDERINGSF)
1512 LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
1513 IORDERINGSF = $(ISCOTCH)
1514 IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
1515 (assoc-ref inputs "mpi")
1516 (assoc-ref inputs "blas")
1517 (assoc-ref inputs "scalapack")
1518 (assoc-ref inputs "metis")
1519 (match (list (assoc-ref inputs "pt-scotch")
1520 (assoc-ref inputs "scotch"))
1524 `((,scotch "" "-Dscotch")))
1527 "-lptesmumps -lptscotch -lptscotcherr "
1528 "-Dptscotch")))))))))
1530 ;; By default only the d-precision library is built. Make with "all"
1531 ;; target so that all precision libraries and examples are built.
1533 (zero? (system* "make" "all"
1534 (format #f "-j~a" (parallel-job-count))))))
1536 ;; Run the simple test drivers, which read test input from stdin:
1537 ;; from the "real" input for the single- and double-precision
1538 ;; testers, and from the "cmplx" input for complex-precision
1539 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
1540 ;; package to prefix execution with "mpirun".
1541 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
1542 (with-directory-excursion "examples"
1545 (let ((tester (apply open-pipe*
1548 ,(string-append "./" prec
1550 (input (open-input-file
1551 (string-append "input_simpletest_" type))))
1553 (dump-port input tester)
1555 (zero? (close-pipe tester)))))
1557 '("real" "real" "cmplx" "cmplx")))))
1559 (lambda* (#:key outputs #:allow-other-keys)
1560 (let* ((out (assoc-ref outputs "out"))
1561 (libdir (string-append out "/lib")))
1562 (copy-recursively "lib" libdir)
1563 (copy-recursively "include" (string-append out "/include"))
1564 (when (file-exists? "libseq/libmpiseq.a")
1565 (install-file "libseq/libmpiseq.a" libdir))
1567 (home-page "http://mumps.enseeiht.fr")
1568 (synopsis "Multifrontal sparse direct solver")
1570 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
1571 sparse system of linear equations A x = b using Guassian elimination.")
1572 (license license:cecill-c)))
1574 (define-public mumps-metis
1575 (package (inherit mumps)
1576 (name "mumps-metis")
1578 (alist-delete "scotch" (package-inputs mumps)))))
1580 (define-public mumps-openmpi
1581 (package (inherit mumps)
1582 (name "mumps-openmpi")
1585 ("scalapack" ,scalapack)
1586 ("pt-scotch" ,pt-scotch)
1587 ,@(alist-delete "scotch" (package-inputs mumps))))
1589 (substitute-keyword-arguments (package-arguments mumps)
1591 `(modify-phases ,phases
1595 ((assoc-ref ,phases 'check)
1596 #:exec-prefix '("mpirun" "-n" "2"))))))))
1597 (synopsis "Multifrontal sparse direct solver (with MPI)")))
1599 (define-public mumps-metis-openmpi
1600 (package (inherit mumps-openmpi)
1601 (name "mumps-metis-openmpi")
1603 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
1605 (define-public r-quadprog
1612 (uri (cran-uri "quadprog" version))
1615 "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
1616 (build-system r-build-system)
1618 `(("gfortran" ,gfortran)))
1619 (home-page "http://cran.r-project.org/web/packages/quadprog")
1620 (synopsis "Functions to solve quadratic programming problems")
1622 "This package contains routines and documentation for solving quadratic
1623 programming problems.")
1624 (license license:gpl3+)))
1626 (define-public r-pracma
1632 (uri (cran-uri "pracma" version))
1634 (base32 "1z3i90mkzwvp9di17caf4934z2xlb2imm3hwxllcrbwvmnmhrwyc"))))
1635 (build-system r-build-system)
1637 `(("r-quadprog" ,r-quadprog)))
1638 (home-page "http://cran.r-project.org/web/packages/pracma")
1639 (synopsis "Practical numerical math functions")
1640 (description "This package provides functions for numerical analysis and
1641 linear algebra, numerical optimization, differential equations, plus some
1642 special functions. It uses Matlab function names where appropriate to simplify
1644 (license license:gpl3+)))
1646 (define-public superlu
1653 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1654 "superlu_" version ".tar.gz"))
1656 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
1657 (modules '((guix build utils)))
1659 ;; Replace the non-free implementation of MC64 with a stub adapted
1662 (use-modules (ice-9 regex)
1664 (call-with-output-file "SRC/mc64ad.c"
1669 void mc64id_(int *a) {
1670 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
1673 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
1674 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
1675 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
1678 ;; Remove the corresponding license verbiage. MC64 license follows
1679 ;; a "------" line separator.
1680 (with-atomic-file-replacement "License.txt"
1681 (let ((rx (make-regexp "-{8}")))
1684 (let ((line (read-line in 'concat)))
1685 (unless (regexp-exec rx line)
1688 (build-system cmake-build-system)
1692 `(("blas" ,openblas)
1693 ("gfortran" ,gfortran)))
1695 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
1696 "-DTPL_BLAS_LIBRARIES=openblas"
1697 "-DBUILD_SHARED_LIBS:BOOL=YES"
1698 "-DCMAKE_INSTALL_LIBDIR=lib")))
1699 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
1700 (synopsis "Supernodal direct solver for sparse linear systems")
1702 "SuperLU is a general purpose library for the direct solution of large,
1703 sparse, nonsymmetric systems of linear equations on high performance machines.
1704 The library is written in C and is callable from either C or Fortran. The
1705 library routines perform an LU decomposition with partial pivoting and
1706 triangular system solves through forward and back substitution. The library
1707 also provides threshold-based ILU factorization preconditioners.")
1708 (license (list license:bsd-3
1709 license:gpl2+ ;EXAMPLE/*fgmr.c
1710 (license:fsf-free "file://SRC/colamd.h")))))
1712 (define-public superlu-dist
1714 (name "superlu-dist")
1719 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1720 "superlu_dist_" version ".tar.gz"))
1722 (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj"))
1723 (modules '((guix build utils)))
1725 ;; Replace the non-free implementation of MC64 with a stub
1727 (use-modules (ice-9 regex)
1729 (call-with-output-file "SRC/mc64ad.c"
1734 void mc64id_(int *a) {
1735 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
1738 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
1739 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
1740 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
1743 (delete-file "SRC/mc64ad.f.bak")
1744 (substitute* "SRC/util.c" ;adjust default algorithm
1745 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
1746 "RowPerm = NOROWPERM"))))
1747 (patches (search-patches "superlu-dist-scotchmetis.patch"))))
1748 (build-system gnu-build-system)
1752 `(("gfortran" ,gfortran)))
1754 `(("openmpi" ,openmpi) ;headers include MPI heades
1755 ("lapack" ,lapack) ;required to link with output library
1756 ("pt-scotch" ,pt-scotch))) ;same
1758 `(#:parallel-build? #f ;race conditions using ar
1762 (lambda* (#:key inputs outputs #:allow-other-keys)
1763 (call-with-output-file "make.inc"
1768 DSUPERLULIB = ~a/lib/libsuperlu_dist.a
1769 BLASDEF = -DUSE_VENDOR_BLAS
1770 BLASLIB = -L~a/lib -lblas
1771 PARMETISLIB = -L~a/lib \
1772 -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
1773 -lscotch -lscotcherr -lscotcherrexit
1774 METISLIB = -L~:*~a/lib \
1775 -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
1776 LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
1782 CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC)
1783 NOOPTS = -O0 -g $(PIC)
1785 FFLAGS = -O2 -g $(PIC)
1789 (assoc-ref outputs "out")
1790 (assoc-ref inputs "lapack")
1791 (assoc-ref inputs "pt-scotch")))))
1793 'unpack 'remove-broken-symlinks
1795 (for-each delete-file
1796 (find-files "MAKE_INC" "\\.#make\\..*")))
1798 'build 'create-install-directories
1799 (lambda* (#:key outputs #:allow-other-keys)
1802 (mkdir-p (string-append (assoc-ref outputs "out")
1804 '("lib" "include")))
1808 (with-directory-excursion "EXAMPLE"
1810 (zero? (system* "mpirun" "-n" "2"
1811 "./pddrive" "-r" "1" "-c" "2" "g20.rua"))
1812 (zero? (system* "mpirun" "-n" "2"
1813 "./pzdrive" "-r" "1" "-c" "2" "cg20.cua")))))
1816 (lambda* (#:key outputs #:allow-other-keys)
1817 ;; Library is placed in lib during the build phase. Copy over
1818 ;; headers to include.
1819 (let* ((out (assoc-ref outputs "out"))
1820 (incdir (string-append out "/include")))
1821 (for-each (lambda (file)
1822 (let ((base (basename file)))
1823 (format #t "installing `~a' to `~a'~%"
1826 (string-append incdir "/" base))))
1827 (find-files "SRC" ".*\\.h$"))))
1828 %standard-phases)))))))
1829 (home-page (package-home-page superlu))
1830 (synopsis "Parallel supernodal direct solver")
1832 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
1833 It is targeted for distributed memory parallel machines. SuperLU_DIST is
1834 implemented in ANSI C, and MPI for communications.")
1835 (license license:bsd-3)))
1837 (define-public scotch
1844 (uri (string-append "https://gforge.inria.fr/frs/download.php/34618/"
1845 "scotch_" version ".tar.gz"))
1847 (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm"))
1848 (patches (search-patches "scotch-test-threading.patch"
1849 "pt-scotch-build-parallelism.patch"))))
1850 (build-system gnu-build-system)
1853 ("flex" ,flex-2.6.1) ; A bug in flex prevents building with flex-2.6.3.
1857 (modify-phases %standard-phases
1859 'unpack 'chdir-to-src
1860 (lambda _ (chdir "src")))
1864 (call-with-output-file "Makefile.inc"
1878 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
1879 LDFLAGS = -lz -lm -lrt -lpthread
1881 LEX = flex -Pscotchyy -olex.yy.c
1886 YACC = bison -pscotchyy -y -b y
1888 '("COMMON_FILE_COMPRESS_GZ"
1890 "COMMON_RANDOM_FIXED_SEED"
1891 "INTSIZE64" ;use 'long' instead of 'int'
1892 ;; Prevents symbolc clashes with libesmumps
1894 ;; XXX: Causes invalid frees in superlu-dist tests
1896 ;; "SCOTCH_PTHREAD_NUMBER=2"
1897 "restrict=__restrict"))))))
1899 'build 'build-esmumps
1901 (zero? (system* "make"
1902 (format #f "-j~a" (parallel-job-count))
1906 (lambda* (#:key outputs #:allow-other-keys)
1907 (let ((out (assoc-ref outputs "out")))
1909 (zero? (system* "make"
1910 (string-append "prefix=" out)
1912 ;; esmumps files are not installed with the above
1913 (for-each (lambda (f)
1914 (copy-file f (string-append out "/include/" f)))
1915 (find-files "../include" ".*esmumps.h$"))
1916 (for-each (lambda (f)
1917 (copy-file f (string-append out "/lib/" f)))
1918 (find-files "../lib" "^lib.*esmumps.*"))))))))
1919 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
1920 (synopsis "Programs and libraries for graph algorithms")
1921 (description "SCOTCH is a set of programs and libraries which implement
1922 the static mapping and sparse matrix reordering algorithms developed within
1923 the SCOTCH project. Its purpose is to apply graph theory, with a divide and
1924 conquer approach, to scientific computing problems such as graph and mesh
1925 partitioning, static mapping, and sparse matrix ordering, in application
1926 domains ranging from structural mechanics to operating systems or
1928 ;; See LICENSE_en.txt
1929 (license license:cecill-c)))
1931 (define-public pt-scotch
1932 (package (inherit scotch)
1935 `(("openmpi" ,openmpi))) ;Headers include MPI headers
1937 (substitute-keyword-arguments (package-arguments scotch)
1938 ((#:phases scotch-phases)
1939 `(modify-phases ,scotch-phases
1944 (zero? (system* "make"
1945 (format #f "-j~a" (parallel-job-count))
1946 "ptscotch" "ptesmumps"))
1947 ;; Install the serial metis compatibility library
1948 (zero? (system* "make" "-C" "libscotchmetis" "install")))))
1951 (lambda _ (zero? (system* "make" "ptcheck"))))))))
1952 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
1954 (define-public metis
1961 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
1962 "metis-" version ".tar.gz"))
1965 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
1966 (build-system cmake-build-system)
1968 `(("blas" ,openblas)))
1970 `(#:tests? #f ;no tests
1971 #:configure-flags `("-DSHARED=ON"
1972 ,(string-append "-DGKLIB_PATH=" (getcwd)
1973 "/metis-" ,version "/GKlib"))))
1974 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
1975 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
1977 "METIS is a set of serial programs for partitioning graphs, partitioning
1978 finite element meshes, and producing fill-reducing orderings for sparse
1979 matrices. The algorithms implemented in METIS are based on the multilevel
1980 recursive-bisection, multilevel k-way, and multi-constraint partitioning
1982 (license license:asl2.0))) ;As of version 5.0.3
1984 (define-public p4est
1991 (uri (string-append "http://p4est.github.io/release/p4est-"
1995 "0faina2h5qsx3m2izbzaj9bbakma1krbbjmq43wrp1hcbyijflqb"))))
1996 (build-system gnu-build-system)
1998 `(("fortran" ,gfortran)
2003 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2004 (assoc-ref %build-inputs "blas")
2006 ,(string-append "LAPACK_LIBS=-L"
2007 (assoc-ref %build-inputs "lapack")
2009 (home-page "http://www.p4est.org")
2010 (synopsis "Adaptive mesh refinement on forests of octrees")
2012 "The p4est software library enables the dynamic management of a
2013 collection of adaptive octrees, conveniently called a forest of octrees.
2014 p4est is designed to work in parallel and scales to hundreds of thousands of
2016 (license license:gpl2+)))
2018 (define-public p4est-openmpi
2019 (package (inherit p4est)
2020 (name "p4est-openmpi")
2023 ,@(package-inputs p4est)))
2025 (substitute-keyword-arguments (package-arguments p4est)
2026 ((#:configure-flags cf)
2027 ``("--enable-mpi" ,@,cf))))
2028 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2030 (define-public gsegrafix
2037 (uri (string-append "mirror://gnu/" name "/" name "-"
2041 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2042 (build-system gnu-build-system)
2044 `(#:configure-flags '("LDFLAGS=-lm")))
2046 `(("libgnomecanvas" ,libgnomecanvas)
2047 ("libbonoboui" ,libbonoboui)
2048 ("libgnomeui" ,libgnomeui)
2049 ("libgnomeprintui" ,libgnomeprintui)
2052 `(("pkg-config" ,pkg-config)))
2053 (home-page "https://www.gnu.org/software/gsegrafix/")
2054 (synopsis "GNOME application to create scientific and engineering plots")
2055 (description "GSEGrafix is an application which produces high-quality graphical
2056 plots for science and engineering. Plots are specified via simple ASCII
2057 parameter files and data files and are presented in an anti-aliased GNOME
2058 canvas. The program supports rectangular two-dimensional plots, histograms,
2059 polar-axis plots and three-dimensional plots. Plots can be printed or saved
2060 to BMP, JPEG or PNG image formats.")
2061 (license license:gpl3+)))
2063 (define-public maxima
2070 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2071 version "-source/" name "-" version ".tar.gz"))
2074 "15pp35ayglv723bjbqc60gcdv2bm54s6pywsm4i4cwbjsf64dzkl"))
2075 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
2076 (build-system gnu-build-system)
2079 ("gnuplot" ,gnuplot) ;for plots
2080 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
2082 `(("texinfo" ,texinfo)
2084 ("python" ,python)))
2087 (list "--enable-gcl"
2088 (string-append "--with-posix-shell="
2089 (assoc-ref %build-inputs "bash")
2091 (string-append "--with-wish="
2092 (assoc-ref %build-inputs "tk")
2094 (let ((v ,(package-version tk)))
2095 (string-take v (string-index-right v #\.)))))
2096 ;; By default Maxima attempts to write temporary files to
2097 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2098 ;; Work around that.
2099 #:make-flags (list "TMPDIR=/tmp")
2100 #:phases (alist-cons-before
2103 (chmod "src/maxima" #o555))
2104 ;; Make sure the doc and emacs files are found in the
2105 ;; standard location. Also configure maxima to find gnuplot
2106 ;; without having it on the PATH.
2108 'install 'post-install
2109 (lambda* (#:key outputs inputs #:allow-other-keys)
2110 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2111 (out (assoc-ref outputs "out"))
2112 (datadir (string-append out "/share/maxima/" ,version)))
2113 (with-directory-excursion out
2114 (mkdir-p "share/emacs")
2115 (mkdir-p "share/doc")
2117 (string-append datadir "/emacs/")
2118 (string-append out "/share/emacs/site-lisp"))
2120 (string-append datadir "/doc/")
2121 (string-append out "/share/doc/maxima"))
2122 (with-atomic-file-replacement
2123 (string-append datadir "/share/maxima-init.lisp")
2125 (format out "~a ~s~a~%"
2126 "(setf $gnuplot_command "
2127 (string-append gnuplot "/bin/gnuplot") ")")
2128 (dump-port in out))))))
2129 %standard-phases))))
2130 (home-page "http://maxima.sourceforge.net")
2131 (synopsis "Numeric and symbolic expression manipulation")
2132 (description "Maxima is a system for the manipulation of symbolic and
2133 numerical expressions. It yields high precision numeric results by using
2134 exact fractions, arbitrary precision integers, and variable precision floating
2136 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2137 ;; Others simply say "GNU General Public License" without stating a
2138 ;; version (which implicitly means gpl1+).
2139 ;; At least one file (src/maxima.asd) says "version 2."
2140 ;; GPLv2 only is therefore the smallest subset.
2141 (license license:gpl2)))
2143 (define-public wxmaxima
2150 (uri (string-append "https://github.com/andrejv/" name "/archive"
2151 "/Version-" version ".tar.gz"))
2152 (file-name (string-append name "-" version ".tar.gz"))
2155 "1bsyd7r12xm2crpizb9iyyki3j0mbazzzwbsh871m06dv2wk97gq"))))
2156 (build-system gnu-build-system)
2158 `(("autoconf" ,autoconf)
2159 ("automake" ,automake)
2160 ("gettext" ,gettext-minimal)))
2162 `(("wxwidgets" ,wxwidgets)
2165 ("adwaita-icon-theme" ,adwaita-icon-theme)
2167 ("shared-mime-info" ,shared-mime-info)))
2169 `(#:phases (modify-phases %standard-phases
2171 'configure 'autoconf
2173 (zero? (system* "./bootstrap"))))
2175 'install 'wrap-program
2176 (lambda* (#:key inputs outputs #:allow-other-keys)
2177 (wrap-program (string-append (assoc-ref outputs "out")
2180 (,(string-append (assoc-ref inputs "maxima")
2182 ;; For GtkFileChooserDialog.
2183 `("GSETTINGS_SCHEMA_DIR" =
2184 (,(string-append (assoc-ref inputs "gtk+")
2185 "/share/glib-2.0/schemas")))
2186 `("XDG_DATA_DIRS" ":" prefix
2187 (;; Needed by gdk-pixbuf to know supported icon formats.
2189 (assoc-ref inputs "shared-mime-info") "/share")
2190 ;; The default icon theme of GTK+.
2192 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
2194 (home-page "https://andrejv.github.io/wxmaxima/")
2195 (synopsis "Graphical user interface for the Maxima computer algebra system")
2197 "wxMaxima is a graphical user interface for the Maxima computer algebra
2198 system. It eases the use of Maxima by making most of its commands available
2199 through a menu system and by providing input dialogs for commands that require
2200 more than one argument. It also implements its own display engine that
2201 outputs mathematical symbols directly instead of depicting them with ASCII
2204 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
2205 text and mathematical calculations to create documents, exporting of input and
2206 output to TeX, and a browser for Maxima's manual including command index and
2207 full text searching.")
2208 (license license:gpl2+)))
2210 (define-public armadillo
2216 (uri (string-append "mirror://sourceforge/arma/armadillo-"
2220 "1qqzy7dp891j9v7062mv1599hdwr97vqzrd3j2fl8c3gmc00dmzg"))))
2221 (build-system cmake-build-system)
2222 (arguments `(#:tests? #f)) ;no test target
2224 `(("openblas" ,openblas)
2226 ("arpack" ,arpack-ng)))
2227 (home-page "http://arma.sourceforge.net/")
2228 (synopsis "C++ linear algebra library")
2230 "Armadillo is a C++ linear algebra library, aiming towards a good balance
2231 between speed and ease of use. It is useful for algorithm development
2232 directly in C++, or quick conversion of research code into production
2233 environments. It can be used for machine learning, pattern recognition,
2234 signal processing, bioinformatics, statistics, econometrics, etc. The library
2235 provides efficient classes for vectors, matrices and cubes, as well as 150+
2236 associated functions (eg. contiguous and non-contiguous submatrix views).")
2237 (license license:asl2.0)))
2239 (define-public muparser
2240 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2241 ;; different hash. In order to make `guix package --upgrade` work correctly,
2242 ;; we set a Guix packaging revision.
2243 ;; When the next version of muparser is released, we can remove
2244 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2245 (let ((upstream-version "2.2.5")
2249 (version (string-append upstream-version "-" revision))
2253 (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
2254 upstream-version ".tar.gz"))
2255 (file-name (string-append name "-" version ".tar.gz"))
2258 "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
2259 (build-system gnu-build-system)
2261 `(#:configure-flags '("--enable-samples=no")
2262 #:tests? #f)) ;no "check" target
2263 (home-page "http://muparser.beltoforion.de/")
2264 (synopsis "Fast parser library for mathematical expressions")
2266 "muParser is an extensible high performance math parser library. It is
2267 based on transforming an expression into a bytecode and precalculating constant
2269 (license license:expat))))
2271 (define-public openblas
2278 (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
2280 (file-name (string-append name "-" version ".tar.gz"))
2283 "071zqnmnxhh0c9phzyn3f198yxa0hjxda7016azdbq2056sm70w7"))))
2284 (build-system gnu-build-system)
2286 `(#:tests? #f ;no "check" target
2287 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
2288 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2289 ;; we need to disable substitutions.
2291 ,(let ((system (or (%current-target-system) (%current-system))))
2292 (or (string-prefix? "x86_64" system)
2293 (string-prefix? "i686" system)
2294 (string-prefix? "mips" system)
2295 (string-prefix? "aarch64" system)))
2297 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
2300 ;; Build the library for all supported CPUs. This allows
2301 ;; switching CPU targets at runtime with the environment variable
2302 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
2303 ;; Unfortunately, this is not supported on non-x86 architectures,
2304 ;; where it leads to failed builds.
2305 ,@(let ((system (or (%current-target-system) (%current-system))))
2307 ((or (string-prefix? "x86_64" system)
2308 (string-prefix? "i686" system))
2309 '("DYNAMIC_ARCH=1"))
2310 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
2311 ;; two available MIPS targets special extended instructions
2312 ;; for Loongson cores are used.
2313 ((string-prefix? "mips" system)
2314 '("TARGET=SICORTEX"))
2315 ;; On aarch64 force the generic 'armv8-a' target
2316 ((string-prefix? "aarch64" system)
2319 ;; no configure script
2320 #:phases (alist-delete 'configure %standard-phases)))
2322 `(("fortran" ,gfortran)))
2326 (home-page "http://www.openblas.net/")
2327 (synopsis "Optimized BLAS library based on GotoBLAS")
2329 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
2330 (license license:bsd-3)))
2332 (define-public openlibm
2339 (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
2341 (file-name (string-append name "-" version ".tar.gz"))
2344 "11czx2z7nh6dfpz45s3xl7v38hw36jxzxfvny454bk3if14pfakq"))))
2345 (build-system gnu-build-system)
2348 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2350 ;; no configure script
2351 (alist-delete 'configure %standard-phases)
2352 #:tests? #f)) ;the tests are part of the default target
2353 (home-page "http://openlibm.org/")
2354 (synopsis "Portable C mathematical library (libm)")
2356 "OpenLibm is an effort to have a high quality, portable, standalone C
2357 mathematical library (libm). It can be used standalone in applications and
2358 programming language implementations. The project was born out of a need to
2359 have a good libm for the Julia programming language that worked consistently
2360 across compilers and operating systems, and in 32-bit and 64-bit
2362 ;; Each architecture has its own make target, and there is none for mips.
2363 (supported-systems (delete "mips64el-linux" %supported-systems))
2364 ;; See LICENSE.md for details.
2365 (license (list license:expat
2368 license:public-domain
2369 license:lgpl2.1+))))
2371 (define-public openspecfun
2373 (name "openspecfun")
2378 (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
2380 (file-name (string-append name "-" version ".tar.gz"))
2383 "1y5b2h6f2k72536kym3vzy3li3bhpd23x463g7hdmjdi3cncavz1"))))
2384 (build-system gnu-build-system)
2386 '(#:tests? #f ;no "check" target
2388 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2389 ;; no configure script
2390 #:phases (alist-delete 'configure %standard-phases)))
2392 `(("fortran" ,gfortran)))
2393 (home-page "https://github.com/JuliaLang/openspecfun")
2394 (synopsis "Collection of special mathematical functions")
2396 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
2397 portable package for Bessel Functions of a Complex Argument and Nonnegative
2398 Order; it contains subroutines for computing Bessel functions and Airy
2399 functions. Faddeeva allows computing the various error functions of arbitrary
2400 complex arguments (Faddeeva function, error function, complementary error
2401 function, scaled complementary error function, imaginary error function, and
2402 Dawson function); given these, one can also easily compute Voigt functions,
2403 Fresnel integrals, and similar related functions as well.")
2404 ;; Faddeeva is released under the Expat license; AMOS is included as
2405 ;; public domain software.
2406 (license (list license:expat license:public-domain))))
2408 (define-public suitesparse
2410 (name "suitesparse")
2416 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
2420 "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5"))))
2421 (build-system gnu-build-system)
2423 '(#:parallel-build? #f ;cholmod build fails otherwise
2424 #:tests? #f ;no "check" target
2429 "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used
2430 (string-append "INSTALL_LIB="
2431 (assoc-ref %outputs "out") "/lib")
2432 (string-append "INSTALL_INCLUDE="
2433 (assoc-ref %outputs "out") "/include"))
2436 'install 'prepare-out
2437 ;; README.txt states that the target directories must exist prior to
2438 ;; running "make install".
2440 (mkdir-p (string-append (assoc-ref %outputs "out") "/lib"))
2441 (mkdir-p (string-append (assoc-ref %outputs "out") "/include")))
2442 ;; no configure script
2443 (alist-delete 'configure %standard-phases))))
2446 ("lapack" ,lapack)))
2447 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
2448 (synopsis "Suite of sparse matrix software")
2450 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
2451 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
2452 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
2453 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
2454 CXSparse, a concise sparse Cholesky factorization package; and many other
2457 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
2459 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
2460 (license (list license:gpl2+ license:lgpl2.1+))))
2462 (define-public atlas
2468 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
2469 version "/atlas" version ".tar.bz2"))
2472 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
2473 (build-system gnu-build-system)
2474 (home-page "http://math-atlas.sourceforge.net/")
2475 (inputs `(("gfortran" ,gfortran)
2476 ("lapack-tar" ,(package-source lapack))))
2477 (outputs '("out" "doc"))
2478 ;; For the moment we drop support for MIPS at it fails to compile. See
2479 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
2480 (supported-systems (delete "mips64el-linux" %supported-systems))
2482 `(#:parallel-build? #f
2483 #:parallel-tests? #f
2485 ;; ATLAS tunes itself for the machine it is built on, as explained at
2486 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
2487 ;; For this reason, we want users to build it locally instead of using
2491 #:modules ((srfi srfi-26)
2493 (guix build gnu-build-system)
2496 `(;; Generate position independent code suitable for dynamic libraries
2497 ;; and use WALL timer to get more accurate timing.
2498 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
2501 ,,(if (string-match "64" (%current-system))
2504 ;; Disable parallel build as it gives errors: atlas_pthread.h is
2505 ;; needed to compile C files before it is generated.
2506 "-Ss" "pmake" "make -j 1"
2507 ;; Probe is failing for MIPS. We therefore define the system
2508 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
2509 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
2510 ,,@(if (string-prefix? "mips" (%current-system))
2511 (list "-A" "49" "-V" "1")
2513 ;; Generate shared libraries.
2515 ;; Build a full LAPACK library.
2516 ,(string-append "--with-netlib-lapack-tarfile="
2517 (assoc-ref %build-inputs "lapack-tar")))
2519 (modify-phases %standard-phases
2520 (add-after 'install 'install-doc
2521 (lambda* (#:key outputs inputs #:allow-other-keys)
2522 (let ((doc (string-append (assoc-ref outputs "doc")
2523 "/share/doc/atlas")))
2525 (fold (lambda (file previous)
2526 (and previous (zero? (system* "cp" file doc))))
2527 #t (find-files "../ATLAS/doc" ".*")))))
2528 (add-after 'check 'check-pt
2529 (lambda _ (zero? (system* "make" "ptcheck"))))
2530 ;; Fix files required to run configure.
2531 (add-before 'configure 'fix-/bin/sh
2533 ;; Use `sh', not `/bin/sh'.
2534 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
2537 ;; Fix /bin/sh in generated make files.
2538 (add-after 'configure 'fix-/bin/sh-in-generated-files
2540 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
2543 ;; ATLAS configure program does not accepts the default flags
2544 ;; passed by the 'gnu-build-system'.
2546 (lambda* (#:key native-inputs inputs outputs
2547 (configure-flags '())
2548 #:allow-other-keys #:rest args)
2549 (let* ((prefix (assoc-ref outputs "out"))
2550 (bash (or (and=> (assoc-ref
2551 (or native-inputs inputs) "bash")
2552 (cut string-append <> "/bin/bash"))
2554 (flags `(,(string-append "--prefix=" prefix)
2556 (abs-srcdir (getcwd))
2557 (srcdir (string-append "../" (basename abs-srcdir))))
2558 (format #t "source directory: ~s (relative from build: ~s)~%"
2562 (format #t "build directory: ~s~%" (getcwd))
2563 (format #t "configure flags: ~s~%" flags)
2564 (zero? (apply system* bash
2565 (string-append srcdir "/configure")
2567 (synopsis "Automatically Tuned Linear Algebra Software")
2569 "ATLAS is an automatically tuned linear algebra software library
2570 providing C and Fortran77 interfaces to a portably efficient BLAS
2571 implementation, as well as a few routines from LAPACK.
2573 Optimization occurs at build time. For this reason, the library is built on
2574 the machine where it is installed, without resorting to pre-built substitutes.
2576 Before building the library, CPU throttling should be disabled. This can be
2577 done in the BIOS, or, on GNU/Linux, with the following command:
2580 # cpupower --governor performance
2583 Failure to do so will result in a library with poor performance.")
2584 (license license:bsd-3)))
2593 (uri (string-append "mirror://sourceforge/ogl-math/glm-" version
2594 "/glm-" version ".zip"))
2597 "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l"))))
2598 (build-system cmake-build-system)
2600 `(("unzip" ,unzip)))
2601 (home-page "http://glm.g-truc.net")
2602 (synopsis "OpenGL Mathematics library")
2603 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
2604 library for graphics software based on the OpenGL Shading Language (GLSL)
2606 (license license:expat)))
2608 (define-public lpsolve
2615 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
2616 "/lp_solve_" version "_source.tar.gz"))
2619 "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq"))
2620 (modules '((guix build utils)))
2622 '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
2624 ;; Pretend to be on a 64 bit platform to obtain a common directory
2625 ;; name for the build results on all architectures; nothing else
2626 ;; seems to depend on it.
2627 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
2629 ;; The check for 'isnan' as it is written fails with
2630 ;; "non-floating-point argument in call to function
2631 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
2632 ;; definition, which in turn leads to bad things. Fix the feature
2634 (("isnan\\(0\\)") "isnan(0.)")))))
2635 (build-system gnu-build-system)
2637 `(#:tests? #f ; no check target
2639 (modify-phases %standard-phases
2643 (and (with-directory-excursion "lpsolve55"
2644 (zero? (system* "bash" "ccc")))
2645 (with-directory-excursion "lp_solve"
2646 (zero? (system* "bash" "ccc"))))))
2648 (lambda* (#:key outputs #:allow-other-keys)
2649 (let* ((out (assoc-ref outputs "out"))
2650 (bin (string-append out "/bin"))
2651 (lib (string-append out "/lib"))
2652 ;; This is where LibreOffice expects to find the header
2653 ;; files, and where they are installed by Debian.
2654 (include (string-append out "/include/lpsolve")))
2656 (copy-file "lpsolve55/bin/ux64/liblpsolve55.a"
2657 (string-append lib "/liblpsolve55.a"))
2658 (copy-file "lpsolve55/bin/ux64/liblpsolve55.so"
2659 (string-append lib "/liblpsolve55.so"))
2660 (install-file "lp_solve/bin/ux64/lp_solve" bin)
2662 ;; Install a subset of the header files as on Debian
2663 ;; (plus lp_bit.h, which matches the regular expression).
2664 (for-each (lambda (name)
2665 (install-file name include))
2666 (find-files "." "lp_[HMSa-z].*\\.h$"))
2667 (with-directory-excursion "shared"
2668 (for-each (lambda (name)
2669 (install-file name include))
2670 (find-files "." "\\.h$")))
2672 (home-page "http://lpsolve.sourceforge.net/")
2673 (synopsis "Mixed integer linear programming (MILP) solver")
2675 "lp_solve is a mixed integer linear programming solver based on the
2676 revised simplex and the branch-and-bound methods.")
2677 (license license:lgpl2.1+)))
2679 (define-public dealii
2686 (uri (string-append "https://github.com/dealii/dealii/releases/"
2687 "download/v" version "/dealii-" version ".tar.gz"))
2690 "1bdksvvyp1rj37df1ndh8j3x9nzpc3sazw8nd0hzvnlw0qnyk800"))
2691 (modules '((guix build utils)))
2693 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
2694 '(delete-file-recursively "bundled"))))
2695 (build-system cmake-build-system)
2703 ("arpack" ,arpack-ng)
2704 ("muparser" ,muparser)
2705 ("gfortran" ,gfortran)
2706 ("suitesparse" ,suitesparse))) ;for UMFPACK
2708 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
2709 #:configure-flags '("-DCOMPAT_FILES=OFF") ;Follow new directory structure
2710 #:phases (modify-phases %standard-phases
2712 'install 'hint-example-prefix
2713 ;; Set Cmake hints in examples so that they can find this
2714 ;; deal.II when configuring.
2715 (lambda* (#:key outputs #:allow-other-keys)
2716 (let* ((out (assoc-ref %outputs "out"))
2717 (exmpl (string-append out "/share/doc"
2718 "/dealii/examples")))
2719 (substitute* (find-files exmpl "CMakeLists.txt")
2720 (("([[:space:]]*HINTS.*)\n" _ line)
2721 (string-append line " $ENV{HOME}/.guix-profile "
2724 (home-page "https://www.dealii.org")
2725 (synopsis "Finite element library")
2727 "Deal.II is a C++ program library targeted at the computational solution
2728 of partial differential equations using adaptive finite elements. The main
2729 aim of deal.II is to enable rapid development of modern finite element codes,
2730 using among other aspects adaptive meshes and a wide array of tools often used
2731 in finite element programs.")
2732 (license license:lgpl2.1+)))
2734 (define-public dealii-openmpi
2735 (package (inherit dealii)
2736 (name "dealii-openmpi")
2739 ;;Supported only with MPI:
2740 ("p4est" ,p4est-openmpi)
2741 ("petsc" ,petsc-openmpi)
2742 ("slepc" ,slepc-openmpi)
2743 ("metis" ,metis) ;for MUMPS
2744 ("scalapack" ,scalapack) ;for MUMPS
2745 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
2746 ("arpack" ,arpack-ng-openmpi)
2747 ,@(fold alist-delete (package-inputs dealii)
2748 '("p4est" "arpack"))))
2750 (substitute-keyword-arguments (package-arguments dealii)
2751 ((#:configure-flags cf)
2752 ``("-DMPI_C_COMPILER=mpicc"
2753 "-DMPI_CXX_COMPILER=mpicxx"
2754 "-DMPI_Fortran_COMPILER=mpifort"
2756 (synopsis "Finite element library (with MPI support)")))
2758 (define-public flann
2767 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
2768 version "-src.zip"))
2771 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))))
2772 (build-system cmake-build-system)
2774 "octave")) ;46 MiB .mex file that pulls Octave
2776 `(("unzip" ,unzip)))
2780 ("python" ,python-2) ; print syntax
2781 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
2784 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
2785 ;; taken 46 MiB unstripped, and 6 MiB stripped.
2786 #:strip-directories '("lib" "lib64" "libexec"
2787 "bin" "sbin" "share/flann/octave")
2789 ;; Save 12 MiB by not installing .a files. Passing
2790 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
2791 #:phases (modify-phases %standard-phases
2792 (add-before 'configure 'set-octave-directory
2793 (lambda* (#:key outputs #:allow-other-keys)
2794 ;; Install the .mex file in the "octave" output.
2795 (let ((out (assoc-ref outputs "octave")))
2796 (substitute* "src/matlab/CMakeLists.txt"
2797 (("share/flann/octave")
2798 (string-append out "/share/flann/octave")))
2800 (add-after 'install 'remove-static-libraries
2801 (lambda* (#:key outputs #:allow-other-keys)
2802 (let* ((out (assoc-ref outputs "out"))
2803 (lib (string-append out "/lib")))
2804 (for-each delete-file
2805 (find-files lib "\\.a$"))
2808 #:tests? #f)) ; The test data are downloaded from the Internet.
2809 (home-page "http://www.cs.ubc.ca/research/flann/")
2810 (synopsis "Library for approximate nearest neighbors computation")
2811 (description "FLANN is a library for performing fast approximate
2812 nearest neighbor searches in high dimensional spaces. It implements a
2813 collection of algorithms and a system for automatically choosing the best
2814 algorithm and optimum parameters depending on the dataset.
2816 FLANN is written in C++ and contains bindings for C, Octave and Python.")
2817 (license (license:non-copyleft "file://COPYING"
2818 "See COPYING in the distribution."))))
2820 (define-public wcalc
2827 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
2828 "wcalc-" version ".tar.bz2"))
2831 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
2832 (build-system gnu-build-system)
2835 ("readline" ,readline)))
2836 (home-page "http://w-calc.sourceforge.net/index.php")
2837 (synopsis "Flexible command-line scientific calculator")
2838 (description "Wcalc is a very capable calculator. It has standard functions
2839 (sin, asin, and sinh for example, in either radians or degrees), many
2840 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
2841 variables, a command history, hex/octal/binary input and output, unit
2842 conversions, embedded comments, and an expandable expression entry field. It
2843 evaluates expressions using the standard order of operations.")
2844 (license license:gpl2+)))
2852 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
2853 "/xaos-" version ".tar.gz"))
2856 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
2857 (build-system gnu-build-system)
2858 (native-inputs `(("gettext" ,gettext-minimal)))
2859 (inputs `(("libx11" ,libx11)
2864 `(#:tests? #f ;no "check" target
2865 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
2866 (synopsis "Real-time fractal zoomer")
2867 (description "GNU XaoS is a graphical program that generates fractal
2868 patterns and allows you to zoom in and out of them infinitely in a fluid,
2869 continuous manner. It also includes tutorials that help to explain how fractals
2870 are built. It can generate many different fractal types such as the Mandelbrot
2872 (home-page "https://www.gnu.org/software/xaos/")
2873 (license license:gpl2+)))
2875 (define-public hypre
2881 (uri (string-append "https://github.com/LLNL/hypre/archive/"
2882 "v" version ".tar.gz"))
2883 (file-name (string-append name "-" version ".tar.gz"))
2886 "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m"))
2887 (modules '((guix build utils)))
2890 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
2891 ;; substitute the tarball creation time.
2892 (substitute* "src/utilities/HYPRE_utilities.h"
2893 (("Date Compiled: .*$")
2894 "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n"))
2896 (build-system gnu-build-system)
2897 (outputs '("out" ;6.1 MiB of headers and libraries
2898 "doc")) ;4.8 MiB of documentation
2902 ("texlive" ,texlive) ;full package required for fonts
2903 ("ghostscript" ,ghostscript)))
2905 `(("blas" ,openblas)
2906 ("lapack" ,lapack)))
2908 `(#:modules ((srfi srfi-1)
2909 ,@%gnu-build-system-modules)
2910 #:configure-flags '("--enable-shared"
2918 (modify-phases %standard-phases
2919 (add-before 'configure 'chdir-src
2920 (lambda _ (chdir "src")))
2922 (lambda* (#:key build target configure-flags
2923 #:allow-other-keys #:rest args)
2924 (let* ((configure (assoc-ref %standard-phases 'configure)))
2927 (list #:configure-flags
2928 (cons (string-append
2929 "--host=" (or target build))
2930 configure-flags)))))))
2931 (add-after 'build 'build-docs
2933 (zero? (system* "make" "-Cdocs" "pdf" "html"))))
2936 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
2937 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
2938 (and (system* "make" "check" "CHECKRUN=")
2939 (fold (lambda (filename result)
2941 (let ((size (stat:size (stat filename))))
2942 (when (not (zero? size))
2943 (format #t "~a size ~d; error indication~%"
2947 (find-files "test" ".*\\.err$")))))
2948 (add-after 'install 'install-docs
2949 (lambda* (#:key outputs #:allow-other-keys)
2950 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
2951 (let* ((doc (assoc-ref outputs "doc"))
2952 (docdir (string-append doc "/share/doc/hypre-" ,version)))
2953 (with-directory-excursion "docs"
2954 (for-each (lambda (base)
2955 (install-file (string-append base ".pdf") docdir)
2956 (copy-recursively base docdir)) ;html docs
2957 '("HYPRE_usr_manual"
2958 "HYPRE_ref_manual")))
2960 (home-page "http://www.llnl.gov/casc/hypre/")
2961 (synopsis "Library of solvers and preconditioners for linear equations")
2963 "HYPRE is a software library of high performance preconditioners and
2964 solvers for the solution of large, sparse linear systems of equations. It
2965 features multigrid solvers for both structured and unstructured grid
2967 (license license:lgpl2.1)))
2969 (define-public hypre-openmpi
2970 (package (inherit hypre)
2971 (name "hypre-openmpi")
2974 ,@(package-inputs hypre)))
2976 (substitute-keyword-arguments (package-arguments hypre)
2977 ((#:configure-flags flags)
2979 ,@(delete "--without-MPI" ,flags)))))
2980 (synopsis "Parallel solvers and preconditioners for linear equations")
2982 "HYPRE is a software library of high performance preconditioners and
2983 solvers for the solution of large, sparse linear systems of equations on
2984 parallel computers. It features parallel multigrid solvers for both
2985 structured and unstructured grid problems.")))
2987 (define-public matio
2994 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
2995 "matio-" version ".tar.gz"))
2998 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
2999 (build-system gnu-build-system)
3003 (home-page "http://matio.sourceforge.net/")
3004 (synopsis "Library for reading and writing MAT files")
3005 (description "Matio is a library for reading and writing MAT files. It
3006 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3007 (license license:bsd-2)))
3009 (define-public libhilbert
3016 (uri (string-append "http://web.cs.dal.ca/~chamilto/hilbert/"
3017 "libhilbert-" version ".tar.gz"))
3020 "0v48x8405dj95gjn2saja4bzhw86d6zl6d3dg8h7dzac2qr97s34"))))
3021 (build-system gnu-build-system)
3022 (home-page "http://web.cs.dal.ca/~chamilto/hilbert")
3023 (synopsis "Hilbert indices for multidimensional data")
3024 (description "The libhilbert library can efficiently calculate Hilbert
3025 curves and order-preserving representations of Hilbert curve indices that use
3026 the same amount of space as the original point representation. This is useful
3027 when using the Gilbert curve as a space filling curve through a
3028 high-dimensional space where not all demensions have the same cardinality.")
3029 (license license:lgpl2.1+)))
3036 (origin (method url-fetch)
3037 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3038 "download/" version "/Vc-" version ".tar.gz"))
3041 "1rh6dhqar3y07n4xqyml0sa0v48qv3ch9dc3yc2in855hlh4vnqi"))))
3042 (build-system cmake-build-system)
3045 '("-DBUILD_TESTING=ON")))
3046 (synopsis "SIMD vector classes for C++")
3047 (description "Vc provides portable, zero-overhead C++ types for explicitly
3048 data-parallel programming. It is a library designed to ease explicit
3049 vectorization of C++ code. Its types enable explicitly stating data-parallel
3050 operations on multiple values. The parallelism is therefore added via the type
3051 system. Vc has an intuitive API and provides portability between different
3052 compilers and compiler versions as well as portability between different vector
3053 instruction sets. Thus, an application written with Vc can be compiled for:
3056 @item SSE2 up to SSE4.2 or SSE4a
3059 @item NEON (in development)
3060 @item NVIDIA GPUs / CUDA (in development)
3062 (home-page "https://github.com/VcDevel/Vc")
3063 (license license:bsd-3)))
3065 (define-public reducelcs
3066 ;; This is the last commit which is available upstream, no
3067 ;; release happened since 2010.
3068 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
3072 (version (string-append "1.0-" revision "." (string-take commit 7)))
3077 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
3079 (file-name (string-append name "-" version "-checkout"))
3082 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
3083 (build-system gnu-build-system)
3085 `(("openlibm" ,openlibm)))
3087 `(#:tests? #f ; no tests
3089 (modify-phases %standard-phases
3090 (delete 'configure) ; No configure script exists.
3091 (replace 'install ; No install phase exists.
3092 (lambda* (#:key outputs #:allow-other-keys)
3093 (let* ((out (assoc-ref outputs "out"))
3094 (bin (string-append out "/bin")))
3095 (install-file "Approximation" bin)
3096 (install-file "CollectResults" bin)
3097 (install-file "GenerateInstances" bin)
3099 (synopsis "Approximate Longest Commons Subsequence computation tool")
3101 "@code{reduceLCS} is an implementation of the Reduce-Expand
3102 algorithm for LCS. It is a fast program to compute the approximate
3103 Longest Commons Subsequence of a set of strings.")
3104 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
3105 (license license:gpl3+))))
3107 (define-public jacal
3114 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
3117 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
3118 (patches (search-patches "jacal-fix-texinfo.patch"))))
3119 (build-system gnu-build-system)
3122 (modify-phases %standard-phases
3123 (add-before 'build 'pre-build
3124 ;; Don't use upstream's script - it really doesn't fit into
3125 ;; Guix's functional paradigm.
3126 (lambda* (#:key inputs outputs #:allow-other-keys)
3127 (substitute* "Makefile"
3128 (("^install: install-script") "install: "))))
3129 (add-after 'install 'post-install
3130 ;; Instead, we provide our own simplified script.
3131 (lambda* (#:key inputs outputs #:allow-other-keys)
3132 (let ((wrapper (string-append (assoc-ref outputs "out")
3134 (format (open wrapper (logior O_WRONLY O_CREAT))
3135 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
3136 "-e '(slib:load \"~a/lib/jacal/math\") "
3139 (assoc-ref inputs "scm")
3140 (assoc-ref outputs "out"))
3141 (chmod wrapper #o555))))
3143 (lambda* (#:key inputs outputs #:allow-other-keys)
3144 (zero? (system* "./configure"
3145 (string-append "--prefix="
3146 (assoc-ref outputs "out")))))))))
3147 (inputs `(("scm" ,scm)))
3148 (native-inputs `(("unzip" ,unzip)
3149 ("texinfo" ,texinfo)))
3150 (synopsis "Symbolic mathematics system")
3151 (description "GNU JACAL is an interactive symbolic mathematics program based on
3152 Scheme. It manipulate and simplify a range of mathematical expressions such
3153 as equations, scalars, vectors, and matrices.")
3154 (home-page "https://www.gnu.org/software/jacal/")
3155 (license license:gpl3+)))