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 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 bison)
52 #:use-module (gnu packages boost)
53 #:use-module (gnu packages check)
54 #:use-module (gnu packages cmake)
55 #:use-module (gnu packages compression)
56 #:use-module (gnu packages curl)
57 #:use-module (gnu packages cyrus-sasl)
58 #:use-module (gnu packages documentation)
59 #:use-module (gnu packages elf)
60 #:use-module (gnu packages flex)
61 #:use-module (gnu packages fltk)
62 #:use-module (gnu packages fontutils)
63 #:use-module (gnu packages gettext)
64 #:use-module (gnu packages gcc)
65 #:use-module (gnu packages gd)
66 #:use-module (gnu packages ghostscript)
67 #:use-module (gnu packages graphviz)
68 #:use-module (gnu packages gtk)
69 #:use-module (gnu packages image)
70 #:use-module (gnu packages less)
71 #:use-module (gnu packages lisp)
72 #:use-module (gnu packages logging)
73 #:use-module (gnu packages lua)
74 #:use-module (gnu packages gnome)
75 #:use-module (gnu packages guile)
76 #:use-module (gnu packages xorg)
77 #:use-module (gnu packages gl)
78 #:use-module (gnu packages imagemagick)
79 #:use-module (gnu packages m4)
80 #:use-module (gnu packages mpi)
81 #:use-module (gnu packages multiprecision)
82 #:use-module (gnu packages netpbm)
83 #:use-module (gnu packages ocaml)
84 #:use-module (gnu packages pcre)
85 #:use-module (gnu packages popt)
86 #:use-module (gnu packages perl)
87 #:use-module (gnu packages pkg-config)
88 #:use-module (gnu packages python)
89 #:use-module (gnu packages readline)
90 #:use-module (gnu packages tbb)
91 #:use-module (gnu packages scheme)
92 #:use-module (gnu packages shells)
93 #:use-module (gnu packages tcl)
94 #:use-module (gnu packages texinfo)
95 #:use-module (gnu packages tex)
96 #:use-module (gnu packages tls)
97 #:use-module (gnu packages wxwidgets)
98 #:use-module (gnu packages xml)
99 #:use-module (srfi srfi-1))
107 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
109 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
110 (build-system gnu-build-system)
111 (inputs `(("gtk+" ,gtk+)
112 ("libxml2" ,libxml2)))
113 (native-inputs `(("pkg-config" ,pkg-config)))
114 (synopsis "Natural deduction first-order logic interface")
115 (description "Aris is a program for performing logical proofs. It supports
116 propositional and predicate logic, as well as Boolean algebra and
117 arithmetical logic. In addition to its predefined inference and equivalence
118 rules, Aris also supports references to older proofs. Its use of standard
119 logical symbols and its natural deduction interface make it easy to use for
121 (license license:gpl3+)
122 (home-page "https://www.gnu.org/software/aris/")))
124 (define-public c-graph
130 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
133 "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
134 (build-system gnu-build-system)
136 `(("fortran" ,gfortran)))
137 (synopsis "Visualizing and demonstrating convolution")
139 "GNU C-Graph is a tool for demonstrating the theory of convolution.
140 Thus, it can serve as an excellent aid to students of signal and systems
141 theory in visualizing the convolution process. Rather than forcing the
142 student to write code, the program offers an intuitive interface with
143 interactive dialogs to guide them.")
144 (license license:gpl3+)
145 (home-page "https://www.gnu.org/software/c-graph/")))
154 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
155 version "/coda-" version ".tar.gz"))
157 (base32 "11asla1ap8vd73farqjlpb179sfiy0biydcwxjfcakrp9sf8v9bs"))
158 (patches (search-patches "coda-use-system-libs.patch"))
159 (modules '((guix build utils)))
161 ;; Make sure we don't use the bundled software.
162 '(for-each (lambda (d)
163 (delete-file-recursively (string-append "libcoda/" d)))
164 '("zlib" "pcre" "expat")))))
166 `(("fortran" ,gfortran)
168 ("python-numpy" ,python-numpy)))
175 (build-system gnu-build-system)
177 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
178 "LIBS= -lz -lpcre -lexpat")))
179 (synopsis "A common interface to various earth observation data formats")
181 "The Common Data Access toolbox (CODA) provides a set of interfaces for
182 reading remote sensing data from earth observation data files. It consists of
183 command line applications and interfaces to the C, Fortran, Python, and Java
184 programming languages.")
185 (home-page "https://stcorp.nl/coda")
186 (license license:gpl2+)))
194 (uri (string-append "mirror://gnu/units/units-" version
197 "1s421bxm36akjsy3qzg6da1d1g20gh094ac2slqxipgkh8yqjcwx"))))
198 (build-system gnu-build-system)
199 (synopsis "Conversion between thousands of scales")
201 "GNU Units converts numeric quantities between units of measure. It
202 can handle scale changes through adaptive usage of standard scale
203 prefixes (micro-, kilo-, etc.). It can also handle nonlinear
204 conversions such as Fahrenheit to Celsius. Its interpreter is powerful
205 enough to be used effectively as a scientific calculator.")
206 (license license:gpl3+)
207 (home-page "https://www.gnu.org/software/units/")))
209 (define-public double-conversion
211 (name "double-conversion")
216 "https://github.com/floitsch/double-conversion/archive/v"
218 (file-name (string-append name "-" version ".tar.gz"))
221 "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83"))))
222 (build-system cmake-build-system)
224 '(#:test-target "test"
225 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
226 "-DBUILD_TESTING=ON")))
227 (home-page "https://github.com/floitsch/double-conversion")
228 (synopsis "Conversion routines for IEEE doubles")
230 "The double-conversion library provides binary-decimal and decimal-binary
231 routines for IEEE doubles. The library consists of efficient conversion
232 routines that have been extracted from the V8 JavaScript engine.")
233 (license license:bsd-3)))
235 (define-public dionysus
241 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
245 "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs"))))
246 (build-system gnu-build-system)
247 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
248 (synopsis "Local search for universal constants and scientific values")
250 "GNU Dionysus is a convenient system for quickly retrieving the values of
251 mathematical constants used in science and engineering. Values can be
252 searched using a simple command-line tool, choosing from three databases:
253 universal constants, atomic numbers, and constants related to
255 (license license:gpl3+)
256 (home-page "https://www.gnu.org/software/dionysus/")))
264 (uri (string-append "mirror://gnu/gsl/gsl-"
268 "16yfs5n444s03np1naj6yp1fsysd42kdscxzkg0k2yvfjixx0ijd"))
269 (patches (search-patches "gsl-test-i686.patch"))))
270 (build-system gnu-build-system)
272 `(;; Currently there are numerous tests that fail on "exotic"
273 ;; architectures such as aarch64 and ppc64le.
274 ,@(if (string-prefix? "aarch64-linux"
275 (or (%current-target-system) (%current-system)))
278 (home-page "https://www.gnu.org/software/gsl/")
279 (synopsis "Numerical library for C and C++")
281 "The GNU Scientific Library is a library for numerical analysis in C
282 and C++. It includes a wide range of mathematical routines, with over 1000
283 functions in total. Subject areas covered by the library include:
284 differential equations, linear algebra, Fast Fourier Transforms and random
286 (license license:gpl3+)))
288 (define-public ocaml-gsl
297 "https://github.com/mmottl/gsl-ocaml/releases/download/v"
298 version"/gsl-ocaml-" version ".tar.gz"))
301 "0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh"))))
302 (build-system ocaml-build-system)
305 (home-page "https://mmottl.github.io/gsl-ocaml")
306 (synopsis "Bindings to the GNU Scientific Library")
308 "GSL-OCaml is an interface to the @dfn{GNU scientific library} (GSL) for
309 the OCaml language.")
310 (license license:gpl3+)))
312 (define-public ocaml4.01-gsl
313 (package-with-ocaml4.01 ocaml-gsl))
322 (uri (string-append "mirror://gnu/glpk/glpk-"
326 "0w7s3869ybwyq9a4490dikpib1qp3jnn5nqz1vvwqy1qz3ilnvh9"))))
327 (build-system gnu-build-system)
331 `(#:configure-flags '("--with-gmp")))
332 (home-page "https://www.gnu.org/software/glpk/")
333 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
335 "GLPK is a C library for solving large-scale linear programming (LP),
336 mixed integer programming (MIP), and other related problems. It supports the
337 GNU MathProg modeling language, a subset of the AMPL language, and features a
338 translator for the language. In addition to the C library, a stand-alone
339 LP/MIP solver is included in the package.")
340 (license license:gpl3+)))
349 (uri (string-append "http://www.4ti2.de/version_" version
350 "/4ti2-" version ".tar.gz"))
353 "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
354 (build-system gnu-build-system)
356 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
360 (home-page "http://www.4ti2.de/")
361 (synopsis "Mathematical tool suite for problems on linear spaces")
363 "4ti2 implements algorithms for solving algebraic, geometric and
364 combinatorial problems on linear spaces. Among others, it solves systems
365 of linear equations, computes extreme rays of polyhedral cones, solves
366 integer programming problems and computes Markov bases for statistics.")
367 (license license:gpl2+)))
369 (define-public cddlib
376 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
377 (string-delete #\. version) ".tar.gz"))
380 "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy"))))
381 (build-system gnu-build-system)
384 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
385 (synopsis "Library for convex hulls and extreme rays of polyhedra")
387 "The C-library cddlib implements the Double Description Method of
388 Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
389 rays of a general convex polyhedron given by a system of linear inequalities
390 in arbitrary dimension. It can also be used for the converse operation of
391 computing convex hulls.")
392 (license license:gpl2+)))
394 (define-public arpack-ng
401 (uri (string-append "https://github.com/opencollab/arpack-ng/archive/"
403 (file-name (string-append name "-" version ".tar.gz"))
406 "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff"))))
407 (build-system gnu-build-system)
408 (home-page "https://github.com/opencollab/arpack-ng")
411 ("fortran" ,gfortran)))
412 (synopsis "Fortran subroutines for solving eigenvalue problems")
414 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
415 large scale eigenvalue problems.")
416 (license (license:non-copyleft "file://COPYING"
417 "See COPYING in the distribution."))))
419 (define-public arpack-ng-openmpi
420 (package (inherit arpack-ng)
421 (name "arpack-ng-openmpi")
424 ,@(package-inputs arpack-ng)))
425 (arguments `(#:configure-flags '("--enable-mpi")))
426 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
428 (define-public lapack
435 (uri (string-append "http://www.netlib.org/lapack/lapack-"
439 "0yavf6m9l78pwlnk5g61cg8x28mr30j0g8gkai0jrdqfjjmf3whs"))))
440 (build-system cmake-build-system)
441 (home-page "http://www.netlib.org/lapack/")
442 (inputs `(("fortran" ,gfortran)
443 ("python" ,python-2)))
445 `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
448 ;; Build the 'LAPACKE_clatms' functions.
449 "-DLAPACKE_WITH_TMG=ON")
450 #:phases (alist-cons-before
452 (lambda* (#:key inputs #:allow-other-keys)
453 (let ((python (assoc-ref inputs "python")))
454 (substitute* "lapack_testing.py"
455 (("/usr/bin/env python") python))))
457 (synopsis "Library for numerical linear algebra")
459 "LAPACK is a Fortran 90 library for solving the most commonly occurring
460 problems in numerical linear algebra.")
461 (license (license:non-copyleft "file://LICENSE"
462 "See LICENSE in the distribution."))))
464 (define-public scalapack
471 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
475 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
476 (build-system cmake-build-system)
479 ("fortran" ,gfortran)
480 ("lapack" ,lapack))) ;for testing only
482 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")))
483 (home-page "http://www.netlib.org/scalapack/")
484 (synopsis "Library for scalable numerical linear algebra")
486 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
487 routines on parallel distributed memory machines. ScaLAPACK solves dense and
488 banded linear systems, least squares problems, eigenvalue problems, and
489 singular value problems.")
490 (license (license:bsd-style "file://LICENSE"
491 "See LICENSE in the distribution."))))
493 (define-public gnuplot
499 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
504 "0q5lr6nala3ln6f3yp6g17ziymb9r9gx9zylnw1y3hjmwl9lggjv"))))
505 (build-system gnu-build-system)
506 (inputs `(("readline" ,readline)
511 (native-inputs `(("pkg-config" ,pkg-config)
512 ("texlive" ,texlive-minimal)))
513 (home-page "http://www.gnuplot.info")
514 (synopsis "Command-line driven graphing utility")
515 (description "Gnuplot is a portable command-line driven graphing
516 utility. It was originally created to allow scientists and students to
517 visualize mathematical functions and data interactively, but has grown to
518 support many non-interactive uses such as web scripting. It is also used as a
519 plotting engine by third-party applications like Octave.")
520 ;; X11 Style with the additional restriction that derived works may only be
521 ;; distributed as patches to the original.
522 (license (license:fsf-free
523 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
532 (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
534 (file-name (string-append name "-" version ".tar.gz"))
537 "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
539 `(("fortran" ,gfortran)))
540 (build-system gnu-build-system)
541 (synopsis "General Cartographic Transformation Package (GCTP)")
543 "The General Cartographic Transformation Package (GCTP) is a system of
544 software routines designed to permit the transformation of coordinate pairs
545 from one map projection to another. The GCTP is the standard computer
546 software used by the National Mapping Division for map projection
548 (home-page "https://github.com/OkoSanto/GCTP")
549 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
558 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
559 version "/src/hdf-" version ".tar.bz2"))
561 (base32 "020jh563sjyxsgml8l809d2i1d4ms9shivwj3gbm7n0ilxbll8id"))
562 (patches (search-patches "hdf4-architectures.patch"
563 "hdf4-reproducibility.patch"
564 "hdf4-shared-fortran.patch"))))
566 (build-system gnu-build-system)
568 `(("gfortran" ,gfortran)
573 ("libjpeg" ,libjpeg)))
575 `(#:parallel-tests? #f
576 #:configure-flags '("--enable-shared")
578 (modify-phases %standard-phases
579 (add-before 'configure 'patchbuild
582 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
584 (("/bin/mkdir") "mkdir"))
585 (substitute* (find-files "." "^Makefile\\.in$")
586 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
587 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
588 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
589 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
590 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")))))))
591 (home-page "https://www.hdfgroup.org/products/hdf4/")
593 "Library and multi-object file format for storing and managing data")
594 (description "HDF4 is a library and multi-object file format for storing
595 and managing data between machines. HDF4 is an older hierarchical data format,
596 incompatible with HDF5.")
598 (license:non-copyleft
599 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
601 (define-public hdf4-alt
606 (substitute-keyword-arguments (package-arguments hdf4)
607 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
609 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
618 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
619 "hdf5-" (version-major+minor version)
620 "/hdf5-" version "/src/hdf5-"
622 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
625 (take (string-split version #\.) 2))
626 "/src/hdf5-" version ".tar.bz2")))
628 (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
629 (patches (list (search-patch "hdf5-config-date.patch")))))
630 (build-system gnu-build-system)
634 `(;; Some of the users, notably Flann, need the C++ interface.
635 #:configure-flags '("--enable-cxx")
638 (modify-phases %standard-phases
639 (add-before 'configure 'patch-configure
641 (substitute* "configure"
644 (add-after 'install 'patch-references
645 (lambda* (#:key inputs outputs #:allow-other-keys)
646 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
647 (zlib (assoc-ref inputs "zlib")))
648 (substitute* (find-files bin "h5p?cc")
650 (string-append "-L" zlib "/lib " lib)))
652 (home-page "http://www.hdfgroup.org")
653 (synopsis "Management suite for extremely large and complex data")
654 (description "HDF5 is a suite that makes possible the management of
655 extremely large and complex data collections.")
656 (license (license:x11-style
657 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
659 (define-public hdf-eos2
666 (uri "ftp://edhs1.gsfc.nasa.gov\
667 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
669 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
670 (patches (search-patches "hdf-eos2-remove-gctp.patch"
671 "hdf-eos2-build-shared.patch"
672 "hdf-eos2-fortrantests.patch"))))
673 (build-system gnu-build-system)
675 `(("gfortran" ,gfortran)))
677 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
682 `( #:configure-flags '("--enable-install-include" "--enable-shared"
683 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
684 #:parallel-tests? #f))
685 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
686 (synopsis "HDF4-based data format for NASA's Earth Observing System")
687 (description "HDF-EOS2 is a software library built on HDF4 which supports
688 the construction of data structures used in NASA's Earth Observing
689 System (Grid, Point and Swath).")
691 ;; Source files carry a permissive license header.
692 (license (license:non-copyleft home-page))))
694 (define-public hdf-eos5
700 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
701 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
704 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
705 (patches (search-patches "hdf-eos5-build-shared.patch"
706 "hdf-eos5-remove-gctp.patch"
707 "hdf-eos5-fix-szip.patch"
708 "hdf-eos5-fortrantests.patch"))))
710 `(("gfortran" ,gfortran)))
711 (build-system gnu-build-system)
717 `(#:configure-flags '("--enable-install-include" "--enable-shared"
718 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
719 #:parallel-tests? #f))
720 (synopsis "HDF5-based data format for NASA's Earth Observing System")
722 "HDF-EOS5 is a software library built on HDF5 to support the construction
723 of data structures used in NASA's Earth Observing System (Grid, Point and
725 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
727 ;; Source files carry a permissive license header.
728 (license (license:non-copyleft home-page))))
730 (define-public hdf5-parallel-openmpi
731 (package (inherit hdf5)
732 (name "hdf5-parallel-openmpi")
735 ,@(package-inputs hdf5)))
737 (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
738 ,@(package-arguments hdf5))
740 `(modify-phases ,phases
741 (add-before 'check 'patch-tests
743 ;; OpenMPI's mpirun will exit with non-zero status if it
744 ;; detects an "abnormal termination", i.e. any process not
745 ;; calling MPI_Finalize(). Since the test is explicitely
746 ;; avoiding MPI_Finalize so as not to have at_exit and thus
747 ;; H5C_flush_cache from being called, mpirun will always
748 ;; complain, so turn this test off.
749 (substitute* "testpar/Makefile"
750 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
751 (string-append front back "\n")))
752 (substitute* "tools/h5diff/testph5diff.sh"
753 (("/bin/sh") (which "sh")))
755 (synopsis "Management suite for data with parallel IO support")))
757 (define-public h5check
764 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
765 "h5check/src/h5check-" version ".tar.gz"))
768 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
769 (build-system gnu-build-system)
770 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
771 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
772 (synopsis "HDF5 format checker")
773 (description "@code{h5check} is a validation tool for verifying that an
774 HDF5 file is encoded according to the HDF File Format Specification.")
775 (license (license:x11-style "file://COPYING"))))
783 (uri (string-append "mirror://sourceforge/itpp/itpp/"
788 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
789 (build-system cmake-build-system)
790 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
791 (inputs `(("lapack" ,lapack)
793 (native-inputs `(("texlive-minimal" ,texlive-minimal)
794 ("doxygen" ,doxygen)))
795 (home-page "http://itpp.sourceforge.net")
796 (synopsis "C++ library of maths, signal processing and communication classes")
797 (description "IT++ is a C++ library of mathematical, signal processing and
798 communication classes and functions. Its main use is in simulation of
799 communication systems and for performing research in the area of
800 communications. The kernel of the library consists of generic vector and
801 matrix classes, and a set of accompanying routines. Such a kernel makes IT++
802 similar to MATLAB, GNU Octave or SciPy.")
803 (license license:gpl3+)))
805 (define-public netcdf
812 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
813 "netcdf-" version ".tar.gz"))
816 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
817 (patches (search-patches "netcdf-date-time.patch"
818 "netcdf-tst_h_par.patch"))))
819 (build-system gnu-build-system)
823 ("graphviz" ,graphviz)))
828 ("libjpeg" ,libjpeg)))
830 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
831 #:parallel-tests? #f)) ;various race conditions
832 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
833 (synopsis "Library for scientific data")
834 (description "NetCDF is an interface for scientific data access and a
835 software library that provides an implementation of the interface. The netCDF
836 library defines a machine-independent format for representing scientific data.
837 Together, the interface, library, and format support the creation, access, and
838 sharing of scientific data.")
839 (license (license:x11-style "file://COPYRIGHT"))))
841 (define-public netcdf-parallel-openmpi
842 (package (inherit netcdf)
843 (name "netcdf-parallel-openmpi")
846 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
847 (package-inputs netcdf))))
848 ;; TODO: Replace pkg-config references in nc-config with absolute references
850 (substitute-keyword-arguments (package-arguments netcdf)
851 ((#:configure-flags flags)
852 `(cons* "CC=mpicc" "CXX=mpicxx"
853 "--enable-parallel-tests"
854 ;; Shared libraries not supported with parallel IO.
855 "--disable-shared" "--with-pic"
858 (define-public netcdf-fortran
860 (name "netcdf-fortran")
865 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
869 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
870 (build-system gnu-build-system)
872 `(#:parallel-tests? #f))
874 `(("netcdf" ,netcdf)))
876 `(("gfortran" ,gfortran)))
877 (synopsis "Fortran interface for the netCDF library")
878 (description (package-description netcdf))
879 (home-page (package-home-page netcdf))
880 (license (package-license netcdf))))
888 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
891 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
892 (build-system gnu-build-system)
894 `(;; Shared libraries are not built by default. They are required to
895 ;; build the Guile, Octave, and Python bindings.
896 #:configure-flags '("--enable-shared")
899 (modify-phases %standard-phases
900 (add-before 'configure 'set-libnlopt-file-name
901 (lambda* (#:key outputs #:allow-other-keys)
902 ;; Make sure the Scheme module refers to the library by its
903 ;; absolute file name (we cannot do that from a snippet
904 ;; because the expansion of @libdir@ contains
906 (let ((out (assoc-ref outputs "out")))
907 (substitute* "swig/nlopt.scm.in"
909 (string-append out "/lib/libnlopt")))
911 (inputs `(("guile" ,guile-2.0)))
912 (native-inputs `(("pkg-config" ,pkg-config)))
913 (home-page "http://ab-initio.mit.edu/wiki/")
914 (synopsis "Library for nonlinear optimization")
915 (description "NLopt is a library for nonlinear optimization, providing a
916 common interface for a number of different free optimization routines available
917 online as well as original implementations of various other algorithms.")
918 (license license:lgpl2.1+)))
927 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
931 "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
932 (modules '((guix build utils)))
934 ;; Make sure we don't use the bundled software.
935 '(delete-file-recursively "ThirdParty"))))
936 (build-system gnu-build-system)
938 '(#:phases (modify-phases %standard-phases
939 (add-after 'install 'add--L-flags-in-ipopt.pc
940 (lambda* (#:key inputs outputs #:allow-other-keys)
941 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
942 ;; move it to "Libs.private" where it belongs, and add a
943 ;; '-L' flag for LAPACK.
944 (let ((out (assoc-ref outputs "out"))
945 (lapack (assoc-ref inputs "lapack")))
946 (substitute* (string-append out "/lib/pkgconfig/"
948 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
949 (string-append "Libs: " before " " after "\n"
950 "Libs.private: " before
951 "-L" lapack "/lib -llapack -lblas "
955 `(("gfortran" ,gfortran)))
957 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
958 `(("lapack" ,lapack))) ;for both libblas and liblapack
959 (home-page "http://www.coin-or.org")
960 (synopsis "Large-scale nonlinear optimizer")
962 "The Interior Point Optimizer (IPOPT) is a software package for
963 large-scale nonlinear optimization. It provides C++, C, and Fortran
965 (license license:epl1.0)))
969 (name "ceres-solver")
971 (home-page "http://ceres-solver.org/")
974 (uri (string-append home-page "ceres-solver-"
978 "0i7qkbf8g6pd8arxzldppga26ckv93y8zldsfz6wbd4n6b1nqrjd"))))
979 (build-system cmake-build-system)
981 ;; TODO: Build HTML user documentation and install separately.
982 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
983 "-DBUILD_SHARED_LIBS=ON")
985 #:phases (modify-phases %standard-phases
986 (add-before 'configure 'set-library-directory
988 ;; Install libraries to lib/, not lib64/.
989 (substitute* "internal/ceres/CMakeLists.txt"
990 (("set\\(LIB_SUFFIX \"64\"\\)")
991 "set(LIB_SUFFIX \"\")"))
994 `(("pkg-config" ,pkg-config)))
996 `(("glog" ,glog))) ;for #include <glog/glog.h>
1001 ("suitesparse" ,suitesparse)
1002 ("gflags" ,gflags)))
1003 (synopsis "C++ library for solving large optimization problems")
1005 "Ceres Solver is a C++ library for modeling and solving large,
1006 complicated optimization problems. It is a feature rich, mature and
1007 performant library which has been used in production since 2010. Ceres Solver
1008 can solve two kinds of problems:
1010 @item non-linear least squares problems with bounds constraints;
1011 @item general unconstrained optimization problems.
1013 (license license:bsd-3)))
1015 ;; For a fully featured Octave, users are strongly recommended also to install
1016 ;; the following packages: texinfo, less, ghostscript, gnuplot.
1017 (define-public octave
1024 (uri (string-append "mirror://gnu/octave/octave-"
1028 "09zhhch79jw3ynw39vizx0i2cbd2bjz3sp38pjdzraqrbivpwp92"))))
1029 (build-system gnu-build-system)
1031 `(("lapack" ,lapack)
1032 ("readline" ,readline)
1037 ("arpack" ,arpack-ng)
1040 ("fontconfig" ,fontconfig)
1041 ("freetype" ,freetype)
1048 ("graphicsmagick" ,graphicsmagick)))
1051 ("gfortran" ,gfortran)
1052 ("pkg-config" ,pkg-config)
1054 ;; The following inputs are not actually used in the build process.
1055 ;; However, the ./configure gratuitously tests for their existence and
1056 ;; assumes that programs not present at build time are also not, and
1057 ;; can never be, available at run time! If these inputs are therefore
1058 ;; not present, support for them will be built out. However, Octave
1059 ;; will still run without them, albeit without the features they
1062 ("texinfo" ,texinfo)
1063 ("ghostscript" ,ghostscript)
1064 ("gnuplot" ,gnuplot)))
1067 (list (string-append "--with-shell="
1068 (assoc-ref %build-inputs "bash")
1070 (home-page "https://www.gnu.org/software/octave/")
1071 (synopsis "High-level language for numerical computation")
1072 (description "GNU Octave is a high-level interpreted language that is
1073 specialized for numerical computations. It can be used for both linear and
1074 non-linear applications and it provides great support for visualizing results.
1075 Work may be performed both at the interactive command-line as well as via
1077 (license license:gpl3+)))
1079 (define-public opencascade-oce
1081 (name "opencascade-oce")
1087 "https://github.com/tpaviot/oce/archive/OCE-"
1092 "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
1093 (build-system cmake-build-system)
1096 (list "-DOCE_TESTING:BOOL=ON"
1097 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1098 "-DOCE_DRAW:BOOL=ON"
1099 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1100 (assoc-ref %outputs "out"))
1101 "-UCMAKE_INSTALL_RPATH")))
1103 `(("freetype" ,freetype)
1110 `(("python" ,python-wrapper)))
1111 (home-page "https://github.com/tpaviot/oce")
1112 (synopsis "Libraries for 3D modeling and numerical simulation")
1114 "Open CASCADE is a set of libraries for the development of applications
1115 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1116 C++ class libraries providing services for 3D surface and solid modeling, CAD
1117 data exchange, and visualization. It is used for development of specialized
1118 software dealing with 3D models in design (CAD), manufacturing (CAM),
1119 numerical simulation (CAE), measurement equipment (CMM), and quality
1120 control (CAQ) domains.
1122 This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1123 patches, improvements, and experiments contributed by users over the official
1124 Open CASCADE library.")
1125 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1126 ; use of header files; see
1127 ; OCCT_LGPL_EXCEPTION.txt
1128 license:public-domain; files
1129 ; src/Standard/Standard_StdAllocator.hxx and
1130 ; src/NCollection/NCollection_StdAllocator.hxx
1131 license:expat; file src/OpenGl/OpenGl_glext.h
1132 license:bsd-3)))); test framework gtest
1141 (uri (string-append "http://gmsh.info/src/gmsh-"
1142 version "-source.tgz"))
1144 (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
1145 (modules '((guix build utils)))
1147 ;; Remove non-free METIS code
1148 '(delete-file-recursively "contrib/Metis"))))
1149 (build-system cmake-build-system)
1152 ("gfortran" ,gfortran)
1158 ("opencascade-oce" ,opencascade-oce)
1160 ("libxext" ,libxext)))
1162 `(("fontconfig" ,fontconfig)
1163 ("libxft" ,libxft)))
1165 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1166 "-DENABLE_BUILD_SHARED:BOOL=ON"
1167 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
1168 (home-page "http://www.geuz.org/gmsh/")
1169 (synopsis "3D finite element grid generator")
1170 (description "Gmsh is a 3D finite element grid generator with a built-in
1171 CAD engine and post-processor. Its design goal is to provide a fast, light
1172 and user-friendly meshing tool with parametric input and advanced
1173 visualization capabilities. Gmsh is built around four modules: geometry,
1174 mesh, solver and post-processing. The specification of any input to these
1175 modules is done either interactively using the graphical user interface or in
1176 ASCII text files using Gmsh's own scripting language.")
1177 (license license:gpl2+)))
1179 (define-public maxflow
1186 (url "https://github.com/gerddie/maxflow.git")
1187 (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
1188 (file-name (string-append name "-" version "-checkout"))
1191 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1192 (build-system cmake-build-system)
1193 (home-page "http://pub.ist.ac.at/~vnk/software.html")
1194 (synopsis "Library implementing Maxflow algorithm")
1195 (description "An implementation of the maxflow algorithm described in
1196 @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1197 Energy Minimization in Computer Vision.\n
1198 Yuri Boykov and Vladimir Kolmogorov.\n
1199 In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1201 (license license:gpl3+)))
1203 (define-public petsc
1210 ;; The *-lite-* tarball does not contain the *large* documentation
1211 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1212 "petsc-lite-" version ".tar.gz"))
1214 (base32 "0jfrq6rd4zagw1iimz05m2w91k0jvz3qbik1lk8pqcxw3rvdqk5d"))))
1215 (build-system gnu-build-system)
1217 `(("python" ,python-2)
1220 `(("gfortran" ,gfortran)
1222 ("superlu" ,superlu)
1223 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1224 ;; leaving out opengl, as configuration seems to only be for mac
1227 `(#:test-target "test"
1228 #:parallel-build? #f ;build is parallel by default
1233 ,(string-append "--with-superlu-include="
1234 (assoc-ref %build-inputs "superlu") "/include")
1235 ,(string-append "--with-superlu-lib="
1236 (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
1238 (modify-phases %standard-phases
1240 ;; PETSc's configure script is actually a python script, so we can't
1241 ;; run it with bash.
1242 (lambda* (#:key outputs (configure-flags '())
1244 (let* ((prefix (assoc-ref outputs "out"))
1245 (flags `(,(string-append "--prefix=" prefix)
1246 ,@configure-flags)))
1247 (format #t "build directory: ~s~%" (getcwd))
1248 (format #t "configure flags: ~s~%" flags)
1249 (zero? (apply system* "./configure" flags)))))
1250 (add-after 'configure 'clean-local-references
1251 (lambda* (#:key inputs outputs #:allow-other-keys)
1252 (let ((out (assoc-ref outputs "out")))
1253 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
1254 ;; Prevent build directory from leaking into compiled code
1256 ;; Scrub timestamp for reproducibility
1257 ((".*Libraries compiled on.*") ""))
1259 (add-after 'install 'clean-install
1260 ;; Try to keep installed files from leaking build directory names.
1261 (lambda* (#:key inputs outputs #:allow-other-keys)
1262 (let ((out (assoc-ref outputs "out")))
1263 (substitute* (map (lambda (file)
1264 (string-append out "/lib/petsc/conf/" file))
1265 '("petscvariables"))
1267 ;; Make compiler references point to the store
1268 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
1269 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1270 (string-append "= " (which compiler))))
1271 ;; PETSc installs some build logs, which aren't necessary.
1272 (for-each (lambda (file)
1273 (let ((f (string-append out "/lib/petsc/conf/" file)))
1274 (when (file-exists? f)
1276 '("configure.log" "make.log" "gmake.log"
1277 "test.log" "error.log" "RDict.db"
1278 "PETScBuildInternal.cmake"
1279 ;; Once installed, should uninstall with Guix
1282 (home-page "http://www.mcs.anl.gov/petsc")
1283 (synopsis "Library to solve PDEs")
1284 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1285 data structures and routines for the scalable (parallel) solution of
1286 scientific applications modeled by partial differential equations.")
1287 (license (license:non-copyleft
1288 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1290 (define-public petsc-complex
1291 (package (inherit petsc)
1292 (name "petsc-complex")
1294 (substitute-keyword-arguments (package-arguments petsc)
1295 ((#:configure-flags cf)
1296 `(cons "--with-scalar-type=complex" ,cf))))
1297 (synopsis "Library to solve PDEs (with complex scalars)")))
1299 (define-public petsc-openmpi
1300 (package (inherit petsc)
1301 (name "petsc-openmpi")
1303 `(("openmpi" ,openmpi)
1304 ,@(package-inputs petsc)))
1306 (substitute-keyword-arguments (package-arguments petsc)
1307 ((#:configure-flags cf)
1308 ``("--with-mpiexec=mpirun"
1309 ,(string-append "--with-mpi-dir="
1310 (assoc-ref %build-inputs "openmpi"))
1311 ,@(delete "--with-mpi=0" ,cf)))))
1312 (synopsis "Library to solve PDEs (with MPI support)")))
1314 (define-public petsc-complex-openmpi
1315 (package (inherit petsc-complex)
1316 (name "petsc-complex-openmpi")
1318 `(("openmpi" ,openmpi)
1319 ,@(package-inputs petsc-complex)))
1321 (substitute-keyword-arguments (package-arguments petsc-complex)
1322 ((#:configure-flags cf)
1323 ``("--with-mpiexec=mpirun"
1324 ,(string-append "--with-mpi-dir="
1325 (assoc-ref %build-inputs "openmpi"))
1326 ,@(delete "--with-mpi=0" ,cf)))))
1327 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
1329 (define-public slepc
1336 (uri (string-append "http://slepc.upv.es/download/download.php?"
1337 "filename=slepc-" version ".tar.gz"))
1338 (file-name (string-append name "-" version ".tar.gz"))
1341 "1hijlmrvxvfqslnx8yydzw5xqbsn1yy02g32w0hln1z3cgr1c0k7"))))
1342 (build-system gnu-build-system)
1344 `(("python" ,python-2)))
1346 `(("arpack" ,arpack-ng)
1347 ("gfortran" ,gfortran)))
1349 `(("petsc" ,petsc)))
1351 `(#:parallel-build? #f ;build is parallel by default
1353 `(,(string-append "--with-arpack-dir="
1354 (assoc-ref %build-inputs "arpack") "/lib"))
1356 (modify-phases %standard-phases
1358 ;; configure is a python script, so we can't run it with bash.
1359 (lambda* (#:key inputs outputs (configure-flags '())
1361 (let* ((prefix (assoc-ref outputs "out"))
1362 (flags `(,(string-append "--prefix=" prefix)
1363 ,@configure-flags)))
1364 (format #t "build directory: ~s~%" (getcwd))
1365 (format #t "configure flags: ~s~%" flags)
1366 (setenv "SLEPC_DIR" (getcwd))
1367 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
1368 (zero? (apply system* "./configure" flags)))))
1369 (add-after 'install 'delete-doc
1370 ;; TODO: SLEPc installs HTML documentation alongside headers in
1371 ;; $out/include. We'd like to move them to share/doc, but delete
1372 ;; them for now, as they are incomplete and installing the complete
1373 ;; documentation is difficult.
1374 (lambda* (#:key outputs #:allow-other-keys)
1375 (let* ((out (assoc-ref outputs "out")))
1376 (for-each delete-file (find-files out "\\.html$")))))
1377 (add-after 'install 'clean-install
1378 ;; Clean up unnecessary build logs from installation.
1379 (lambda* (#:key outputs #:allow-other-keys)
1380 (let ((out (assoc-ref outputs "out")))
1381 (for-each (lambda (file)
1382 (let ((f (string-append out "/lib/slepc/conf/" file)))
1383 (when (file-exists? f)
1385 '("configure.log" "make.log" "gmake.log"
1386 "test.log" "error.log" "RDict.db"
1387 "uninstall.py"))))))))
1388 (home-page "http://slepc.upv.es")
1389 (synopsis "Scalable library for eigenproblems")
1390 (description "SLEPc is a software library for the solution of large sparse
1391 eigenproblems on parallel computers. It can be used for the solution of
1392 linear eigenvalue problems formulated in either standard or generalized form,
1393 as well as other related problems such as the singular value decomposition.
1394 The emphasis of the software is on methods and techniques appropriate for
1395 problems in which the associated matrices are sparse, for example, those
1396 arising after the discretization of partial differential equations.")
1397 (license license:lgpl3)))
1399 (define-public slepc-complex
1400 (package (inherit slepc)
1401 (name "slepc-complex")
1403 `(("petsc" ,petsc-complex)
1404 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1405 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1407 (define-public slepc-openmpi
1408 (package (inherit slepc)
1409 (name "slepc-openmpi")
1412 ("arpack" ,arpack-ng-openmpi)
1413 ,@(alist-delete "arpack" (package-inputs slepc))))
1415 `(("petsc" ,petsc-openmpi)
1416 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1417 (synopsis "Scalable library for eigenproblems (with MPI support)")))
1419 (define-public slepc-complex-openmpi
1420 (package (inherit slepc-openmpi)
1421 (name "slepc-complex-openmpi")
1423 `(("petsc" ,petsc-complex-openmpi)
1424 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1425 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1427 (define-public mumps
1434 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
1438 "0igyc1pfzxdhpbad3v3lb86ixkdbqa1a8gbs15b04r2294h2nabp"))
1439 (patches (search-patches "mumps-build-parallelism.patch"))))
1440 (build-system gnu-build-system)
1442 `(("fortran" ,gfortran)
1443 ;; These are required for linking against mumps, but we let the user
1444 ;; declare the dependency.
1447 ("scotch" ,scotch)))
1449 `(#:modules ((ice-9 match)
1452 ,@%gnu-build-system-modules)
1454 (modify-phases %standard-phases
1456 (lambda* (#:key inputs #:allow-other-keys)
1457 (call-with-output-file "Makefile.inc"
1468 INCSEQ = -I$(topdir)/libseq
1469 LIBSEQ = -L$(topdir)/libseq -lmpiseq
1470 LIBSEQNEEDED = libseqneeded~;
1474 AR = ar vr # rules require trailing space, ugh...
1476 LIBBLAS = -L~a -lopenblas~@[
1477 SCALAP = -L~a -lscalapack~]
1478 LIBOTHERS = -pthread
1481 OPTF = -O2 -DALLOW_NON_INIT $(PIC)
1485 LIBS = $(SCALAP) $(LIBSEQ)
1486 LPORDDIR = $(topdir)/PORD/lib
1487 IPORD = -I$(topdir)/PORD/include
1488 LPORD = -L$(LPORDDIR) -lpord
1489 ORDERINGSF = -Dpord~@[
1491 IMETIS = -I$(METISDIR)/include
1492 LMETIS = -L$(METISDIR)/lib -lmetis
1493 ORDERINGSF += -Dmetis~]~@[~:{
1495 ISCOTCH = -I$(SCOTCHDIR)/include
1496 LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
1497 ORDERINGSF += ~a~}~]
1498 ORDERINGSC = $(ORDERINGSF)
1499 LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
1500 IORDERINGSF = $(ISCOTCH)
1501 IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
1502 (assoc-ref inputs "mpi")
1503 (assoc-ref inputs "blas")
1504 (assoc-ref inputs "scalapack")
1505 (assoc-ref inputs "metis")
1506 (match (list (assoc-ref inputs "pt-scotch")
1507 (assoc-ref inputs "scotch"))
1511 `((,scotch "" "-Dscotch")))
1514 "-lptesmumps -lptscotch -lptscotcherr "
1515 "-Dptscotch")))))))))
1517 ;; By default only the d-precision library is built. Make with "all"
1518 ;; target so that all precision libraries and examples are built.
1520 (zero? (system* "make" "all"
1521 (format #f "-j~a" (parallel-job-count))))))
1523 ;; Run the simple test drivers, which read test input from stdin:
1524 ;; from the "real" input for the single- and double-precision
1525 ;; testers, and from the "cmplx" input for complex-precision
1526 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
1527 ;; package to prefix execution with "mpirun".
1528 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
1529 (with-directory-excursion "examples"
1532 (let ((tester (apply open-pipe*
1535 ,(string-append "./" prec
1537 (input (open-input-file
1538 (string-append "input_simpletest_" type))))
1540 (dump-port input tester)
1542 (zero? (close-pipe tester)))))
1544 '("real" "real" "cmplx" "cmplx")))))
1546 (lambda* (#:key outputs #:allow-other-keys)
1547 (let* ((out (assoc-ref outputs "out"))
1548 (libdir (string-append out "/lib")))
1549 (copy-recursively "lib" libdir)
1550 (copy-recursively "include" (string-append out "/include"))
1551 (when (file-exists? "libseq/libmpiseq.a")
1552 (install-file "libseq/libmpiseq.a" libdir))
1554 (home-page "http://mumps.enseeiht.fr")
1555 (synopsis "Multifrontal sparse direct solver")
1557 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
1558 sparse system of linear equations A x = b using Guassian elimination.")
1559 (license license:cecill-c)))
1561 (define-public mumps-metis
1562 (package (inherit mumps)
1563 (name "mumps-metis")
1565 (alist-delete "scotch" (package-inputs mumps)))))
1567 (define-public mumps-openmpi
1568 (package (inherit mumps)
1569 (name "mumps-openmpi")
1572 ("scalapack" ,scalapack)
1573 ("pt-scotch" ,pt-scotch)
1574 ,@(alist-delete "scotch" (package-inputs mumps))))
1576 (substitute-keyword-arguments (package-arguments mumps)
1578 `(modify-phases ,phases
1582 ((assoc-ref ,phases 'check)
1583 #:exec-prefix '("mpirun" "-n" "2"))))))))
1584 (synopsis "Multifrontal sparse direct solver (with MPI)")))
1586 (define-public mumps-metis-openmpi
1587 (package (inherit mumps-openmpi)
1588 (name "mumps-metis-openmpi")
1590 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
1592 (define-public r-quadprog
1599 (uri (cran-uri "quadprog" version))
1602 "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
1603 (build-system r-build-system)
1605 `(("gfortran" ,gfortran)))
1606 (home-page "http://cran.r-project.org/web/packages/quadprog")
1607 (synopsis "Functions to solve quadratic programming problems")
1609 "This package contains routines and documentation for solving quadratic
1610 programming problems.")
1611 (license license:gpl3+)))
1613 (define-public r-pracma
1619 (uri (cran-uri "pracma" version))
1621 (base32 "1z3i90mkzwvp9di17caf4934z2xlb2imm3hwxllcrbwvmnmhrwyc"))))
1622 (build-system r-build-system)
1624 `(("r-quadprog" ,r-quadprog)))
1625 (home-page "http://cran.r-project.org/web/packages/pracma")
1626 (synopsis "Practical numerical math functions")
1627 (description "This package provides functions for numerical analysis and
1628 linear algebra, numerical optimization, differential equations, plus some
1629 special functions. It uses Matlab function names where appropriate to simplify
1631 (license license:gpl3+)))
1633 (define-public superlu
1640 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1641 "superlu_" version ".tar.gz"))
1643 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
1644 (modules '((guix build utils)))
1646 ;; Replace the non-free implementation of MC64 with a stub adapted
1649 (use-modules (ice-9 regex)
1651 (call-with-output-file "SRC/mc64ad.c"
1656 void mc64id_(int *a) {
1657 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
1660 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
1661 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
1662 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
1665 ;; Remove the corresponding license verbiage. MC64 license follows
1666 ;; a "------" line separator.
1667 (with-atomic-file-replacement "License.txt"
1668 (let ((rx (make-regexp "-{8}")))
1671 (let ((line (read-line in 'concat)))
1672 (unless (regexp-exec rx line)
1675 (build-system cmake-build-system)
1679 `(("blas" ,openblas)
1680 ("gfortran" ,gfortran)))
1682 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
1683 "-DTPL_BLAS_LIBRARIES=openblas"
1684 "-DBUILD_SHARED_LIBS:BOOL=YES"
1685 "-DCMAKE_INSTALL_LIBDIR=lib")))
1686 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
1687 (synopsis "Supernodal direct solver for sparse linear systems")
1689 "SuperLU is a general purpose library for the direct solution of large,
1690 sparse, nonsymmetric systems of linear equations on high performance machines.
1691 The library is written in C and is callable from either C or Fortran. The
1692 library routines perform an LU decomposition with partial pivoting and
1693 triangular system solves through forward and back substitution. The library
1694 also provides threshold-based ILU factorization preconditioners.")
1695 (license (list license:bsd-3
1696 license:gpl2+ ;EXAMPLE/*fgmr.c
1697 (license:fsf-free "file://SRC/colamd.h")))))
1699 (define-public superlu-dist
1701 (name "superlu-dist")
1706 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1707 "superlu_dist_" version ".tar.gz"))
1709 (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj"))
1710 (modules '((guix build utils)))
1712 ;; Replace the non-free implementation of MC64 with a stub
1714 (use-modules (ice-9 regex)
1716 (call-with-output-file "SRC/mc64ad.c"
1721 void mc64id_(int *a) {
1722 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
1725 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
1726 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
1727 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
1730 (delete-file "SRC/mc64ad.f.bak")
1731 (substitute* "SRC/util.c" ;adjust default algorithm
1732 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
1733 "RowPerm = NOROWPERM"))))
1734 (patches (search-patches "superlu-dist-scotchmetis.patch"))))
1735 (build-system gnu-build-system)
1739 `(("gfortran" ,gfortran)))
1741 `(("openmpi" ,openmpi) ;headers include MPI heades
1742 ("lapack" ,lapack) ;required to link with output library
1743 ("pt-scotch" ,pt-scotch))) ;same
1745 `(#:parallel-build? #f ;race conditions using ar
1749 (lambda* (#:key inputs outputs #:allow-other-keys)
1750 (call-with-output-file "make.inc"
1755 DSUPERLULIB = ~a/lib/libsuperlu_dist.a
1756 BLASDEF = -DUSE_VENDOR_BLAS
1757 BLASLIB = -L~a/lib -lblas
1758 PARMETISLIB = -L~a/lib \
1759 -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
1760 -lscotch -lscotcherr -lscotcherrexit
1761 METISLIB = -L~:*~a/lib \
1762 -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
1763 LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
1769 CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC)
1770 NOOPTS = -O0 -g $(PIC)
1772 FFLAGS = -O2 -g $(PIC)
1776 (assoc-ref outputs "out")
1777 (assoc-ref inputs "lapack")
1778 (assoc-ref inputs "pt-scotch")))))
1780 'unpack 'remove-broken-symlinks
1782 (for-each delete-file
1783 (find-files "MAKE_INC" "\\.#make\\..*")))
1785 'build 'create-install-directories
1786 (lambda* (#:key outputs #:allow-other-keys)
1789 (mkdir-p (string-append (assoc-ref outputs "out")
1791 '("lib" "include")))
1795 (with-directory-excursion "EXAMPLE"
1797 (zero? (system* "mpirun" "-n" "2"
1798 "./pddrive" "-r" "1" "-c" "2" "g20.rua"))
1799 (zero? (system* "mpirun" "-n" "2"
1800 "./pzdrive" "-r" "1" "-c" "2" "cg20.cua")))))
1803 (lambda* (#:key outputs #:allow-other-keys)
1804 ;; Library is placed in lib during the build phase. Copy over
1805 ;; headers to include.
1806 (let* ((out (assoc-ref outputs "out"))
1807 (incdir (string-append out "/include")))
1808 (for-each (lambda (file)
1809 (let ((base (basename file)))
1810 (format #t "installing `~a' to `~a'~%"
1813 (string-append incdir "/" base))))
1814 (find-files "SRC" ".*\\.h$"))))
1815 %standard-phases)))))))
1816 (home-page (package-home-page superlu))
1817 (synopsis "Parallel supernodal direct solver")
1819 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
1820 It is targeted for distributed memory parallel machines. SuperLU_DIST is
1821 implemented in ANSI C, and MPI for communications.")
1822 (license license:bsd-3)))
1824 (define-public scotch
1831 (uri (string-append "https://gforge.inria.fr/frs/download.php/34618/"
1832 "scotch_" version ".tar.gz"))
1834 (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm"))
1835 (patches (search-patches "scotch-test-threading.patch"
1836 "pt-scotch-build-parallelism.patch"))))
1837 (build-system gnu-build-system)
1840 ("flex" ,flex-2.6.1) ; A bug in flex prevents building with flex-2.6.3.
1844 (modify-phases %standard-phases
1846 'unpack 'chdir-to-src
1847 (lambda _ (chdir "src")))
1851 (call-with-output-file "Makefile.inc"
1865 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
1866 LDFLAGS = -lz -lm -lrt -lpthread
1868 LEX = flex -Pscotchyy -olex.yy.c
1873 YACC = bison -pscotchyy -y -b y
1875 '("COMMON_FILE_COMPRESS_GZ"
1877 "COMMON_RANDOM_FIXED_SEED"
1878 "INTSIZE64" ;use 'long' instead of 'int'
1879 ;; Prevents symbolc clashes with libesmumps
1881 ;; XXX: Causes invalid frees in superlu-dist tests
1883 ;; "SCOTCH_PTHREAD_NUMBER=2"
1884 "restrict=__restrict"))))))
1886 'build 'build-esmumps
1888 (zero? (system* "make"
1889 (format #f "-j~a" (parallel-job-count))
1893 (lambda* (#:key outputs #:allow-other-keys)
1894 (let ((out (assoc-ref outputs "out")))
1896 (zero? (system* "make"
1897 (string-append "prefix=" out)
1899 ;; esmumps files are not installed with the above
1900 (for-each (lambda (f)
1901 (copy-file f (string-append out "/include/" f)))
1902 (find-files "../include" ".*esmumps.h$"))
1903 (for-each (lambda (f)
1904 (copy-file f (string-append out "/lib/" f)))
1905 (find-files "../lib" "^lib.*esmumps.*"))))))))
1906 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
1907 (synopsis "Programs and libraries for graph algorithms")
1908 (description "SCOTCH is a set of programs and libraries which implement
1909 the static mapping and sparse matrix reordering algorithms developed within
1910 the SCOTCH project. Its purpose is to apply graph theory, with a divide and
1911 conquer approach, to scientific computing problems such as graph and mesh
1912 partitioning, static mapping, and sparse matrix ordering, in application
1913 domains ranging from structural mechanics to operating systems or
1915 ;; See LICENSE_en.txt
1916 (license license:cecill-c)))
1918 (define-public pt-scotch
1919 (package (inherit scotch)
1922 `(("openmpi" ,openmpi))) ;Headers include MPI headers
1924 (substitute-keyword-arguments (package-arguments scotch)
1925 ((#:phases scotch-phases)
1926 `(modify-phases ,scotch-phases
1931 (zero? (system* "make"
1932 (format #f "-j~a" (parallel-job-count))
1933 "ptscotch" "ptesmumps"))
1934 ;; Install the serial metis compatibility library
1935 (zero? (system* "make" "-C" "libscotchmetis" "install")))))
1938 (lambda _ (zero? (system* "make" "ptcheck"))))))))
1939 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
1941 (define-public metis
1948 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
1949 "metis-" version ".tar.gz"))
1952 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
1953 (build-system cmake-build-system)
1955 `(("blas" ,openblas)))
1957 `(#:tests? #f ;no tests
1958 #:configure-flags `("-DSHARED=ON"
1959 ,(string-append "-DGKLIB_PATH=" (getcwd)
1960 "/metis-" ,version "/GKlib"))))
1961 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
1962 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
1964 "METIS is a set of serial programs for partitioning graphs, partitioning
1965 finite element meshes, and producing fill-reducing orderings for sparse
1966 matrices. The algorithms implemented in METIS are based on the multilevel
1967 recursive-bisection, multilevel k-way, and multi-constraint partitioning
1969 (license license:asl2.0))) ;As of version 5.0.3
1971 (define-public p4est
1978 (uri (string-append "http://p4est.github.io/release/p4est-"
1982 "0faina2h5qsx3m2izbzaj9bbakma1krbbjmq43wrp1hcbyijflqb"))))
1983 (build-system gnu-build-system)
1985 `(("fortran" ,gfortran)
1990 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
1991 (assoc-ref %build-inputs "blas")
1993 ,(string-append "LAPACK_LIBS=-L"
1994 (assoc-ref %build-inputs "lapack")
1996 (home-page "http://www.p4est.org")
1997 (synopsis "Adaptive mesh refinement on forests of octrees")
1999 "The p4est software library enables the dynamic management of a
2000 collection of adaptive octrees, conveniently called a forest of octrees.
2001 p4est is designed to work in parallel and scales to hundreds of thousands of
2003 (license license:gpl2+)))
2005 (define-public p4est-openmpi
2006 (package (inherit p4est)
2007 (name "p4est-openmpi")
2010 ,@(package-inputs p4est)))
2012 (substitute-keyword-arguments (package-arguments p4est)
2013 ((#:configure-flags cf)
2014 ``("--enable-mpi" ,@,cf))))
2015 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2017 (define-public gsegrafix
2024 (uri (string-append "mirror://gnu/" name "/" name "-"
2028 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2029 (build-system gnu-build-system)
2031 `(#:configure-flags '("LDFLAGS=-lm")))
2033 `(("libgnomecanvas" ,libgnomecanvas)
2034 ("libbonoboui" ,libbonoboui)
2035 ("libgnomeui" ,libgnomeui)
2036 ("libgnomeprintui" ,libgnomeprintui)
2039 `(("pkg-config" ,pkg-config)))
2040 (home-page "https://www.gnu.org/software/gsegrafix/")
2041 (synopsis "GNOME application to create scientific and engineering plots")
2042 (description "GSEGrafix is an application which produces high-quality graphical
2043 plots for science and engineering. Plots are specified via simple ASCII
2044 parameter files and data files and are presented in an anti-aliased GNOME
2045 canvas. The program supports rectangular two-dimensional plots, histograms,
2046 polar-axis plots and three-dimensional plots. Plots can be printed or saved
2047 to BMP, JPEG or PNG image formats.")
2048 (license license:gpl3+)))
2050 (define-public maxima
2057 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2058 version "-source/" name "-" version ".tar.gz"))
2061 "15pp35ayglv723bjbqc60gcdv2bm54s6pywsm4i4cwbjsf64dzkl"))
2062 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
2063 (build-system gnu-build-system)
2066 ("gnuplot" ,gnuplot) ;for plots
2067 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
2069 `(("texinfo" ,texinfo)
2071 ("python" ,python)))
2074 (list "--enable-gcl"
2075 (string-append "--with-posix-shell="
2076 (assoc-ref %build-inputs "bash")
2078 (string-append "--with-wish="
2079 (assoc-ref %build-inputs "tk")
2081 (let ((v ,(package-version tk)))
2082 (string-take v (string-index-right v #\.)))))
2083 ;; By default Maxima attempts to write temporary files to
2084 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2085 ;; Work around that.
2086 #:make-flags (list "TMPDIR=/tmp")
2087 #:phases (alist-cons-before
2090 (chmod "src/maxima" #o555))
2091 ;; Make sure the doc and emacs files are found in the
2092 ;; standard location. Also configure maxima to find gnuplot
2093 ;; without having it on the PATH.
2095 'install 'post-install
2096 (lambda* (#:key outputs inputs #:allow-other-keys)
2097 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2098 (out (assoc-ref outputs "out"))
2099 (datadir (string-append out "/share/maxima/" ,version)))
2100 (with-directory-excursion out
2101 (mkdir-p "share/emacs")
2102 (mkdir-p "share/doc")
2104 (string-append datadir "/emacs/")
2105 (string-append out "/share/emacs/site-lisp"))
2107 (string-append datadir "/doc/")
2108 (string-append out "/share/doc/maxima"))
2109 (with-atomic-file-replacement
2110 (string-append datadir "/share/maxima-init.lisp")
2112 (format out "~a ~s~a~%"
2113 "(setf $gnuplot_command "
2114 (string-append gnuplot "/bin/gnuplot") ")")
2115 (dump-port in out))))))
2116 %standard-phases))))
2117 (home-page "http://maxima.sourceforge.net")
2118 (synopsis "Numeric and symbolic expression manipulation")
2119 (description "Maxima is a system for the manipulation of symbolic and
2120 numerical expressions. It yields high precision numeric results by using
2121 exact fractions, arbitrary precision integers, and variable precision floating
2123 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2124 ;; Others simply say "GNU General Public License" without stating a
2125 ;; version (which implicitly means gpl1+).
2126 ;; At least one file (src/maxima.asd) says "version 2."
2127 ;; GPLv2 only is therefore the smallest subset.
2128 (license license:gpl2)))
2130 (define-public wxmaxima
2133 ;; Versions 16.12.0 to 16.12.2 have a bug which causes output lines to
2134 ;; overlap. See <https://debbugs.gnu.org/25793>
2139 (uri (string-append "mirror://sourceforge/wxmaxima/wxMaxima/"
2140 version "/" name "-" version ".tar.gz"))
2143 "1fpqzk1921isiqrpgpf433ldq41924qs9sy99fl1zn5661b2l73n"))))
2144 (build-system gnu-build-system)
2146 `(("wxwidgets" ,wxwidgets)
2149 ("adwaita-icon-theme" ,adwaita-icon-theme)
2151 ("shared-mime-info" ,shared-mime-info)))
2153 `(#:phases (modify-phases %standard-phases
2155 'install 'wrap-program
2156 (lambda* (#:key inputs outputs #:allow-other-keys)
2157 (wrap-program (string-append (assoc-ref outputs "out")
2160 (,(string-append (assoc-ref inputs "maxima")
2162 ;; For GtkFileChooserDialog.
2163 `("GSETTINGS_SCHEMA_DIR" =
2164 (,(string-append (assoc-ref inputs "gtk+")
2165 "/share/glib-2.0/schemas")))
2166 `("XDG_DATA_DIRS" ":" prefix
2167 (;; Needed by gdk-pixbuf to know supported icon formats.
2169 (assoc-ref inputs "shared-mime-info") "/share")
2170 ;; The default icon theme of GTK+.
2172 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
2174 (home-page "https://andrejv.github.io/wxmaxima/")
2175 (synopsis "Graphical user interface for the Maxima computer algebra system")
2177 "wxMaxima is a graphical user interface for the Maxima computer algebra
2178 system. It eases the use of Maxima by making most of its commands available
2179 through a menu system and by providing input dialogs for commands that require
2180 more than one argument. It also implements its own display engine that
2181 outputs mathematical symbols directly instead of depicting them with ASCII
2184 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
2185 text and mathematical calculations to create documents, exporting of input and
2186 output to TeX, and a browser for Maxima's manual including command index and
2187 full text searching.")
2188 (license license:gpl2+)))
2190 (define-public armadillo
2196 (uri (string-append "mirror://sourceforge/arma/armadillo-"
2200 "1qqzy7dp891j9v7062mv1599hdwr97vqzrd3j2fl8c3gmc00dmzg"))))
2201 (build-system cmake-build-system)
2202 (arguments `(#:tests? #f)) ;no test target
2204 `(("openblas" ,openblas)
2206 ("arpack" ,arpack-ng)))
2207 (home-page "http://arma.sourceforge.net/")
2208 (synopsis "C++ linear algebra library")
2210 "Armadillo is a C++ linear algebra library, aiming towards a good balance
2211 between speed and ease of use. It is useful for algorithm development
2212 directly in C++, or quick conversion of research code into production
2213 environments. It can be used for machine learning, pattern recognition,
2214 signal processing, bioinformatics, statistics, econometrics, etc. The library
2215 provides efficient classes for vectors, matrices and cubes, as well as 150+
2216 associated functions (eg. contiguous and non-contiguous submatrix views).")
2217 (license license:asl2.0)))
2219 (define-public muparser
2220 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2221 ;; different hash. In order to make `guix package --upgrade` work correctly,
2222 ;; we set a Guix packaging revision.
2223 ;; When the next version of muparser is released, we can remove
2224 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2225 (let ((upstream-version "2.2.5")
2229 (version (string-append upstream-version "-" revision))
2233 (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
2234 upstream-version ".tar.gz"))
2235 (file-name (string-append name "-" version ".tar.gz"))
2238 "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
2239 (build-system gnu-build-system)
2241 `(#:configure-flags '("--enable-samples=no")
2242 #:tests? #f)) ;no "check" target
2243 (home-page "http://muparser.beltoforion.de/")
2244 (synopsis "Fast parser library for mathematical expressions")
2246 "muParser is an extensible high performance math parser library. It is
2247 based on transforming an expression into a bytecode and precalculating constant
2249 (license license:expat))))
2251 (define-public openblas
2258 (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
2260 (file-name (string-append name "-" version ".tar.gz"))
2263 "071zqnmnxhh0c9phzyn3f198yxa0hjxda7016azdbq2056sm70w7"))))
2264 (build-system gnu-build-system)
2266 `(#:tests? #f ;no "check" target
2267 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
2268 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2269 ;; we need to disable substitutions.
2271 ,(let ((system (or (%current-target-system) (%current-system))))
2272 (or (string-prefix? "x86_64" system)
2273 (string-prefix? "i686" system)
2274 (string-prefix? "mips" system)
2275 (string-prefix? "aarch64" system)))
2277 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
2280 ;; Build the library for all supported CPUs. This allows
2281 ;; switching CPU targets at runtime with the environment variable
2282 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
2283 ;; Unfortunately, this is not supported on non-x86 architectures,
2284 ;; where it leads to failed builds.
2285 ,@(let ((system (or (%current-target-system) (%current-system))))
2287 ((or (string-prefix? "x86_64" system)
2288 (string-prefix? "i686" system))
2289 '("DYNAMIC_ARCH=1"))
2290 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
2291 ;; two available MIPS targets special extended instructions
2292 ;; for Loongson cores are used.
2293 ((string-prefix? "mips" system)
2294 '("TARGET=SICORTEX"))
2295 ;; On aarch64 force the generic 'armv8-a' target
2296 ((string-prefix? "aarch64" system)
2299 ;; no configure script
2300 #:phases (alist-delete 'configure %standard-phases)))
2302 `(("fortran" ,gfortran)))
2306 (home-page "http://www.openblas.net/")
2307 (synopsis "Optimized BLAS library based on GotoBLAS")
2309 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
2310 (license license:bsd-3)))
2312 (define-public openlibm
2319 (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
2321 (file-name (string-append name "-" version ".tar.gz"))
2324 "11czx2z7nh6dfpz45s3xl7v38hw36jxzxfvny454bk3if14pfakq"))))
2325 (build-system gnu-build-system)
2328 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2330 ;; no configure script
2331 (alist-delete 'configure %standard-phases)
2332 #:tests? #f)) ;the tests are part of the default target
2333 (home-page "http://openlibm.org/")
2334 (synopsis "Portable C mathematical library (libm)")
2336 "OpenLibm is an effort to have a high quality, portable, standalone C
2337 mathematical library (libm). It can be used standalone in applications and
2338 programming language implementations. The project was born out of a need to
2339 have a good libm for the Julia programming language that worked consistently
2340 across compilers and operating systems, and in 32-bit and 64-bit
2342 ;; Each architecture has its own make target, and there is none for mips.
2343 (supported-systems (delete "mips64el-linux" %supported-systems))
2344 ;; See LICENSE.md for details.
2345 (license (list license:expat
2348 license:public-domain
2349 license:lgpl2.1+))))
2351 (define-public openspecfun
2353 (name "openspecfun")
2358 (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
2360 (file-name (string-append name "-" version ".tar.gz"))
2363 "1y5b2h6f2k72536kym3vzy3li3bhpd23x463g7hdmjdi3cncavz1"))))
2364 (build-system gnu-build-system)
2366 '(#:tests? #f ;no "check" target
2368 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2369 ;; no configure script
2370 #:phases (alist-delete 'configure %standard-phases)))
2372 `(("fortran" ,gfortran)))
2373 (home-page "https://github.com/JuliaLang/openspecfun")
2374 (synopsis "Collection of special mathematical functions")
2376 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
2377 portable package for Bessel Functions of a Complex Argument and Nonnegative
2378 Order; it contains subroutines for computing Bessel functions and Airy
2379 functions. Faddeeva allows computing the various error functions of arbitrary
2380 complex arguments (Faddeeva function, error function, complementary error
2381 function, scaled complementary error function, imaginary error function, and
2382 Dawson function); given these, one can also easily compute Voigt functions,
2383 Fresnel integrals, and similar related functions as well.")
2384 ;; Faddeeva is released under the Expat license; AMOS is included as
2385 ;; public domain software.
2386 (license (list license:expat license:public-domain))))
2388 (define-public suitesparse
2390 (name "suitesparse")
2396 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
2400 "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5"))))
2401 (build-system gnu-build-system)
2403 '(#:parallel-build? #f ;cholmod build fails otherwise
2404 #:tests? #f ;no "check" target
2409 "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used
2410 (string-append "INSTALL_LIB="
2411 (assoc-ref %outputs "out") "/lib")
2412 (string-append "INSTALL_INCLUDE="
2413 (assoc-ref %outputs "out") "/include"))
2416 'install 'prepare-out
2417 ;; README.txt states that the target directories must exist prior to
2418 ;; running "make install".
2420 (mkdir-p (string-append (assoc-ref %outputs "out") "/lib"))
2421 (mkdir-p (string-append (assoc-ref %outputs "out") "/include")))
2422 ;; no configure script
2423 (alist-delete 'configure %standard-phases))))
2426 ("lapack" ,lapack)))
2427 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
2428 (synopsis "Suite of sparse matrix software")
2430 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
2431 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
2432 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
2433 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
2434 CXSparse, a concise sparse Cholesky factorization package; and many other
2437 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
2439 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
2440 (license (list license:gpl2+ license:lgpl2.1+))))
2442 (define-public atlas
2448 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
2449 version "/atlas" version ".tar.bz2"))
2452 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
2453 (build-system gnu-build-system)
2454 (home-page "http://math-atlas.sourceforge.net/")
2455 (inputs `(("gfortran" ,gfortran)
2456 ("lapack-tar" ,(package-source lapack))))
2457 (outputs '("out" "doc"))
2458 ;; For the moment we drop support for MIPS at it fails to compile. See
2459 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
2460 (supported-systems (delete "mips64el-linux" %supported-systems))
2462 `(#:parallel-build? #f
2463 #:parallel-tests? #f
2465 ;; ATLAS tunes itself for the machine it is built on, as explained at
2466 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
2467 ;; For this reason, we want users to build it locally instead of using
2471 #:modules ((srfi srfi-26)
2473 (guix build gnu-build-system)
2476 `(;; Generate position independent code suitable for dynamic libraries
2477 ;; and use WALL timer to get more accurate timing.
2478 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
2481 ,,(if (string-match "64" (%current-system))
2484 ;; Disable parallel build as it gives errors: atlas_pthread.h is
2485 ;; needed to compile C files before it is generated.
2486 "-Ss" "pmake" "make -j 1"
2487 ;; Probe is failing for MIPS. We therefore define the system
2488 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
2489 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
2490 ,,@(if (string-prefix? "mips" (%current-system))
2491 (list "-A" "49" "-V" "1")
2493 ;; Generate shared libraries.
2495 ;; Build a full LAPACK library.
2496 ,(string-append "--with-netlib-lapack-tarfile="
2497 (assoc-ref %build-inputs "lapack-tar")))
2499 (modify-phases %standard-phases
2500 (add-after 'install 'install-doc
2501 (lambda* (#:key outputs inputs #:allow-other-keys)
2502 (let ((doc (string-append (assoc-ref outputs "doc")
2503 "/share/doc/atlas")))
2505 (fold (lambda (file previous)
2506 (and previous (zero? (system* "cp" file doc))))
2507 #t (find-files "../ATLAS/doc" ".*")))))
2508 (add-after 'check 'check-pt
2509 (lambda _ (zero? (system* "make" "ptcheck"))))
2510 ;; Fix files required to run configure.
2511 (add-before 'configure 'fix-/bin/sh
2513 ;; Use `sh', not `/bin/sh'.
2514 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
2517 ;; Fix /bin/sh in generated make files.
2518 (add-after 'configure 'fix-/bin/sh-in-generated-files
2520 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
2523 ;; ATLAS configure program does not accepts the default flags
2524 ;; passed by the 'gnu-build-system'.
2526 (lambda* (#:key native-inputs inputs outputs
2527 (configure-flags '())
2528 #:allow-other-keys #:rest args)
2529 (let* ((prefix (assoc-ref outputs "out"))
2530 (bash (or (and=> (assoc-ref
2531 (or native-inputs inputs) "bash")
2532 (cut string-append <> "/bin/bash"))
2534 (flags `(,(string-append "--prefix=" prefix)
2536 (abs-srcdir (getcwd))
2537 (srcdir (string-append "../" (basename abs-srcdir))))
2538 (format #t "source directory: ~s (relative from build: ~s)~%"
2542 (format #t "build directory: ~s~%" (getcwd))
2543 (format #t "configure flags: ~s~%" flags)
2544 (zero? (apply system* bash
2545 (string-append srcdir "/configure")
2547 (synopsis "Automatically Tuned Linear Algebra Software")
2549 "ATLAS is an automatically tuned linear algebra software library
2550 providing C and Fortran77 interfaces to a portably efficient BLAS
2551 implementation, as well as a few routines from LAPACK.
2553 Optimization occurs at build time. For this reason, the library is built on
2554 the machine where it is installed, without resorting to pre-built substitutes.
2556 Before building the library, CPU throttling should be disabled. This can be
2557 done in the BIOS, or, on GNU/Linux, with the following command:
2560 # cpupower --governor performance
2563 Failure to do so will result in a library with poor performance.")
2564 (license license:bsd-3)))
2573 (uri (string-append "mirror://sourceforge/ogl-math/glm-" version
2574 "/glm-" version ".zip"))
2577 "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l"))))
2578 (build-system cmake-build-system)
2580 `(("unzip" ,unzip)))
2581 (home-page "http://glm.g-truc.net")
2582 (synopsis "OpenGL Mathematics library")
2583 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
2584 library for graphics software based on the OpenGL Shading Language (GLSL)
2586 (license license:expat)))
2588 (define-public lpsolve
2595 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
2596 "/lp_solve_" version "_source.tar.gz"))
2599 "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq"))
2600 (modules '((guix build utils)))
2602 '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
2604 ;; Pretend to be on a 64 bit platform to obtain a common directory
2605 ;; name for the build results on all architectures; nothing else
2606 ;; seems to depend on it.
2607 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
2609 ;; The check for 'isnan' as it is written fails with
2610 ;; "non-floating-point argument in call to function
2611 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
2612 ;; definition, which in turn leads to bad things. Fix the feature
2614 (("isnan\\(0\\)") "isnan(0.)")))))
2615 (build-system gnu-build-system)
2617 `(#:tests? #f ; no check target
2619 (modify-phases %standard-phases
2623 (and (with-directory-excursion "lpsolve55"
2624 (zero? (system* "bash" "ccc")))
2625 (with-directory-excursion "lp_solve"
2626 (zero? (system* "bash" "ccc"))))))
2628 (lambda* (#:key outputs #:allow-other-keys)
2629 (let* ((out (assoc-ref outputs "out"))
2630 (bin (string-append out "/bin"))
2631 (lib (string-append out "/lib"))
2632 ;; This is where LibreOffice expects to find the header
2633 ;; files, and where they are installed by Debian.
2634 (include (string-append out "/include/lpsolve")))
2636 (copy-file "lpsolve55/bin/ux64/liblpsolve55.a"
2637 (string-append lib "/liblpsolve55.a"))
2638 (copy-file "lpsolve55/bin/ux64/liblpsolve55.so"
2639 (string-append lib "/liblpsolve55.so"))
2640 (install-file "lp_solve/bin/ux64/lp_solve" bin)
2642 ;; Install a subset of the header files as on Debian
2643 ;; (plus lp_bit.h, which matches the regular expression).
2644 (for-each (lambda (name)
2645 (install-file name include))
2646 (find-files "." "lp_[HMSa-z].*\\.h$"))
2647 (with-directory-excursion "shared"
2648 (for-each (lambda (name)
2649 (install-file name include))
2650 (find-files "." "\\.h$")))
2652 (home-page "http://lpsolve.sourceforge.net/")
2653 (synopsis "Mixed integer linear programming (MILP) solver")
2655 "lp_solve is a mixed integer linear programming solver based on the
2656 revised simplex and the branch-and-bound methods.")
2657 (license license:lgpl2.1+)))
2659 (define-public dealii
2666 (uri (string-append "https://github.com/dealii/dealii/releases/"
2667 "download/v" version "/dealii-" version ".tar.gz"))
2670 "1bdksvvyp1rj37df1ndh8j3x9nzpc3sazw8nd0hzvnlw0qnyk800"))
2671 (modules '((guix build utils)))
2673 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
2674 '(delete-file-recursively "bundled"))))
2675 (build-system cmake-build-system)
2683 ("arpack" ,arpack-ng)
2684 ("muparser" ,muparser)
2685 ("gfortran" ,gfortran)
2686 ("suitesparse" ,suitesparse))) ;for UMFPACK
2688 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
2689 #:configure-flags '("-DCOMPAT_FILES=OFF") ;Follow new directory structure
2690 #:phases (modify-phases %standard-phases
2692 'install 'hint-example-prefix
2693 ;; Set Cmake hints in examples so that they can find this
2694 ;; deal.II when configuring.
2695 (lambda* (#:key outputs #:allow-other-keys)
2696 (let* ((out (assoc-ref %outputs "out"))
2697 (exmpl (string-append out "/share/doc"
2698 "/dealii/examples")))
2699 (substitute* (find-files exmpl "CMakeLists.txt")
2700 (("([[:space:]]*HINTS.*)\n" _ line)
2701 (string-append line " $ENV{HOME}/.guix-profile "
2704 (home-page "https://www.dealii.org")
2705 (synopsis "Finite element library")
2707 "Deal.II is a C++ program library targeted at the computational solution
2708 of partial differential equations using adaptive finite elements. The main
2709 aim of deal.II is to enable rapid development of modern finite element codes,
2710 using among other aspects adaptive meshes and a wide array of tools often used
2711 in finite element programs.")
2712 (license license:lgpl2.1+)))
2714 (define-public dealii-openmpi
2715 (package (inherit dealii)
2716 (name "dealii-openmpi")
2719 ;;Supported only with MPI:
2720 ("p4est" ,p4est-openmpi)
2721 ("petsc" ,petsc-openmpi)
2722 ("slepc" ,slepc-openmpi)
2723 ("metis" ,metis) ;for MUMPS
2724 ("scalapack" ,scalapack) ;for MUMPS
2725 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
2726 ("arpack" ,arpack-ng-openmpi)
2727 ,@(fold alist-delete (package-inputs dealii)
2728 '("p4est" "arpack"))))
2730 (substitute-keyword-arguments (package-arguments dealii)
2731 ((#:configure-flags cf)
2732 ``("-DMPI_C_COMPILER=mpicc"
2733 "-DMPI_CXX_COMPILER=mpicxx"
2734 "-DMPI_Fortran_COMPILER=mpifort"
2736 (synopsis "Finite element library (with MPI support)")))
2738 (define-public flann
2747 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
2748 version "-src.zip"))
2751 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))))
2752 (build-system cmake-build-system)
2754 "octave")) ;46 MiB .mex file that pulls Octave
2756 `(("unzip" ,unzip)))
2760 ("python" ,python-2) ; print syntax
2761 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
2764 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
2765 ;; taken 46 MiB unstripped, and 6 MiB stripped.
2766 #:strip-directories '("lib" "lib64" "libexec"
2767 "bin" "sbin" "share/flann/octave")
2769 ;; Save 12 MiB by not installing .a files. Passing
2770 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
2771 #:phases (modify-phases %standard-phases
2772 (add-before 'configure 'set-octave-directory
2773 (lambda* (#:key outputs #:allow-other-keys)
2774 ;; Install the .mex file in the "octave" output.
2775 (let ((out (assoc-ref outputs "octave")))
2776 (substitute* "src/matlab/CMakeLists.txt"
2777 (("share/flann/octave")
2778 (string-append out "/share/flann/octave")))
2780 (add-after 'install 'remove-static-libraries
2781 (lambda* (#:key outputs #:allow-other-keys)
2782 (let* ((out (assoc-ref outputs "out"))
2783 (lib (string-append out "/lib")))
2784 (for-each delete-file
2785 (find-files lib "\\.a$"))
2788 #:tests? #f)) ; The test data are downloaded from the Internet.
2789 (home-page "http://www.cs.ubc.ca/research/flann/")
2790 (synopsis "Library for approximate nearest neighbors computation")
2791 (description "FLANN is a library for performing fast approximate
2792 nearest neighbor searches in high dimensional spaces. It implements a
2793 collection of algorithms and a system for automatically choosing the best
2794 algorithm and optimum parameters depending on the dataset.
2796 FLANN is written in C++ and contains bindings for C, Octave and Python.")
2797 (license (license:non-copyleft "file://COPYING"
2798 "See COPYING in the distribution."))))
2800 (define-public wcalc
2807 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
2808 "wcalc-" version ".tar.bz2"))
2811 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
2812 (build-system gnu-build-system)
2815 ("readline" ,readline)))
2816 (home-page "http://w-calc.sourceforge.net/index.php")
2817 (synopsis "Flexible command-line scientific calculator")
2818 (description "Wcalc is a very capable calculator. It has standard functions
2819 (sin, asin, and sinh for example, in either radians or degrees), many
2820 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
2821 variables, a command history, hex/octal/binary input and output, unit
2822 conversions, embedded comments, and an expandable expression entry field. It
2823 evaluates expressions using the standard order of operations.")
2824 (license license:gpl2+)))
2832 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
2833 "/xaos-" version ".tar.gz"))
2836 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
2837 (build-system gnu-build-system)
2838 (native-inputs `(("gettext" ,gettext-minimal)))
2839 (inputs `(("libx11" ,libx11)
2844 `(#:tests? #f ;no "check" target
2845 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
2846 (synopsis "Real-time fractal zoomer")
2847 (description "GNU XaoS is a graphical program that generates fractal
2848 patterns and allows you to zoom in and out of them infinitely in a fluid,
2849 continuous manner. It also includes tutorials that help to explain how fractals
2850 are built. It can generate many different fractal types such as the Mandelbrot
2852 (home-page "https://www.gnu.org/software/xaos/")
2853 (license license:gpl2+)))
2855 (define-public hypre
2861 (uri (string-append "https://github.com/LLNL/hypre/archive/"
2862 "v" version ".tar.gz"))
2863 (file-name (string-append name "-" version ".tar.gz"))
2866 "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m"))
2867 (modules '((guix build utils)))
2870 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
2871 ;; substitute the tarball creation time.
2872 (substitute* "src/utilities/HYPRE_utilities.h"
2873 (("Date Compiled: .*$")
2874 "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n"))
2876 (build-system gnu-build-system)
2877 (outputs '("out" ;6.1 MiB of headers and libraries
2878 "doc")) ;4.8 MiB of documentation
2882 ("texlive" ,texlive) ;full package required for fonts
2883 ("ghostscript" ,ghostscript)))
2885 `(("blas" ,openblas)
2886 ("lapack" ,lapack)))
2888 `(#:modules ((srfi srfi-1)
2889 ,@%gnu-build-system-modules)
2890 #:configure-flags '("--enable-shared"
2898 (modify-phases %standard-phases
2899 (add-before 'configure 'chdir-src
2900 (lambda _ (chdir "src")))
2902 (lambda* (#:key build target configure-flags
2903 #:allow-other-keys #:rest args)
2904 (let* ((configure (assoc-ref %standard-phases 'configure)))
2907 (list #:configure-flags
2908 (cons (string-append
2909 "--host=" (or target build))
2910 configure-flags)))))))
2911 (add-after 'build 'build-docs
2913 (zero? (system* "make" "-Cdocs" "pdf" "html"))))
2916 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
2917 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
2918 (and (system* "make" "check" "CHECKRUN=")
2919 (fold (lambda (filename result)
2921 (let ((size (stat:size (stat filename))))
2922 (when (not (zero? size))
2923 (format #t "~a size ~d; error indication~%"
2927 (find-files "test" ".*\\.err$")))))
2928 (add-after 'install 'install-docs
2929 (lambda* (#:key outputs #:allow-other-keys)
2930 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
2931 (let* ((doc (assoc-ref outputs "doc"))
2932 (docdir (string-append doc "/share/doc/hypre-" ,version)))
2933 (with-directory-excursion "docs"
2934 (for-each (lambda (base)
2935 (install-file (string-append base ".pdf") docdir)
2936 (copy-recursively base docdir)) ;html docs
2937 '("HYPRE_usr_manual"
2938 "HYPRE_ref_manual")))
2940 (home-page "http://www.llnl.gov/casc/hypre/")
2941 (synopsis "Library of solvers and preconditioners for linear equations")
2943 "HYPRE is a software library of high performance preconditioners and
2944 solvers for the solution of large, sparse linear systems of equations. It
2945 features multigrid solvers for both structured and unstructured grid
2947 (license license:lgpl2.1)))
2949 (define-public hypre-openmpi
2950 (package (inherit hypre)
2951 (name "hypre-openmpi")
2954 ,@(package-inputs hypre)))
2956 (substitute-keyword-arguments (package-arguments hypre)
2957 ((#:configure-flags flags)
2959 ,@(delete "--without-MPI" ,flags)))))
2960 (synopsis "Parallel solvers and preconditioners for linear equations")
2962 "HYPRE is a software library of high performance preconditioners and
2963 solvers for the solution of large, sparse linear systems of equations on
2964 parallel computers. It features parallel multigrid solvers for both
2965 structured and unstructured grid problems.")))
2967 (define-public matio
2974 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
2975 "matio-" version ".tar.gz"))
2978 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
2979 (build-system gnu-build-system)
2983 (home-page "http://matio.sourceforge.net/")
2984 (synopsis "Library for reading and writing MAT files")
2985 (description "Matio is a library for reading and writing MAT files. It
2986 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
2987 (license license:bsd-2)))
2989 (define-public libhilbert
2996 (uri (string-append "http://web.cs.dal.ca/~chamilto/hilbert/"
2997 "libhilbert-" version ".tar.gz"))
3000 "0v48x8405dj95gjn2saja4bzhw86d6zl6d3dg8h7dzac2qr97s34"))))
3001 (build-system gnu-build-system)
3002 (home-page "http://web.cs.dal.ca/~chamilto/hilbert")
3003 (synopsis "Hilbert indices for multidimensional data")
3004 (description "The libhilbert library can efficiently calculate Hilbert
3005 curves and order-preserving representations of Hilbert curve indices that use
3006 the same amount of space as the original point representation. This is useful
3007 when using the Gilbert curve as a space filling curve through a
3008 high-dimensional space where not all demensions have the same cardinality.")
3009 (license license:lgpl2.1+)))
3016 (origin (method url-fetch)
3017 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3018 "download/" version "/Vc-" version ".tar.gz"))
3021 "1rh6dhqar3y07n4xqyml0sa0v48qv3ch9dc3yc2in855hlh4vnqi"))))
3022 (build-system cmake-build-system)
3025 '("-DBUILD_TESTING=ON")))
3026 (synopsis "SIMD vector classes for C++")
3027 (description "Vc provides portable, zero-overhead C++ types for explicitly
3028 data-parallel programming. It is a library designed to ease explicit
3029 vectorization of C++ code. Its types enable explicitly stating data-parallel
3030 operations on multiple values. The parallelism is therefore added via the type
3031 system. Vc has an intuitive API and provides portability between different
3032 compilers and compiler versions as well as portability between different vector
3033 instruction sets. Thus, an application written with Vc can be compiled for:
3036 @item SSE2 up to SSE4.2 or SSE4a
3039 @item NEON (in development)
3040 @item NVIDIA GPUs / CUDA (in development)
3042 (home-page "https://github.com/VcDevel/Vc")
3043 (license license:bsd-3)))
3045 (define-public reducelcs
3046 ;; This is the last commit which is available upstream, no
3047 ;; release happened since 2010.
3048 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
3052 (version (string-append "1.0-" revision "." (string-take commit 7)))
3057 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
3059 (file-name (string-append name "-" version "-checkout"))
3062 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
3063 (build-system gnu-build-system)
3065 `(("openlibm" ,openlibm)))
3067 `(#:tests? #f ; no tests
3069 (modify-phases %standard-phases
3070 (delete 'configure) ; No configure script exists.
3071 (replace 'install ; No install phase exists.
3072 (lambda* (#:key outputs #:allow-other-keys)
3073 (let* ((out (assoc-ref outputs "out"))
3074 (bin (string-append out "/bin")))
3075 (install-file "Approximation" bin)
3076 (install-file "CollectResults" bin)
3077 (install-file "GenerateInstances" bin)
3079 (synopsis "Approximate Longest Commons Subsequence computation tool")
3081 "@code{reduceLCS} is an implementation of the Reduce-Expand
3082 algorithm for LCS. It is a fast program to compute the approximate
3083 Longest Commons Subsequence of a set of strings.")
3084 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
3085 (license license:gpl3+))))
3087 (define-public jacal
3094 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
3097 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
3098 (patches (search-patches "jacal-fix-texinfo.patch"))))
3099 (build-system gnu-build-system)
3102 (modify-phases %standard-phases
3103 (add-before 'build 'pre-build
3104 ;; Don't use upstream's script - it really doesn't fit into
3105 ;; Guix's functional paradigm.
3106 (lambda* (#:key inputs outputs #:allow-other-keys)
3107 (substitute* "Makefile"
3108 (("^install: install-script") "install: "))))
3109 (add-after 'install 'post-install
3110 ;; Instead, we provide our own simplified script.
3111 (lambda* (#:key inputs outputs #:allow-other-keys)
3112 (let ((wrapper (string-append (assoc-ref outputs "out")
3114 (format (open wrapper (logior O_WRONLY O_CREAT))
3115 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
3116 "-e '(slib:load \"~a/lib/jacal/math\") "
3119 (assoc-ref inputs "scm")
3120 (assoc-ref outputs "out"))
3121 (chmod wrapper #o555))))
3123 (lambda* (#:key inputs outputs #:allow-other-keys)
3124 (zero? (system* "./configure"
3125 (string-append "--prefix="
3126 (assoc-ref outputs "out")))))))))
3127 (inputs `(("scm" ,scm)))
3128 (native-inputs `(("unzip" ,unzip)
3129 ("texinfo" ,texinfo)))
3130 (synopsis "Symbolic mathematics system")
3131 (description "GNU JACAL is an interactive symbolic mathematics program based on
3132 Scheme. It manipulate and simplify a range of mathematical expressions such
3133 as equations, scalars, vectors, and matrices.")
3134 (home-page "https://www.gnu.org/software/jacal/")
3135 (license license:gpl3+)))