1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
3 ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
4 ;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
5 ;;; Copyright © 2014, 2015, 2016 Eric Bavier <bavier@member.fsf.org>
6 ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
7 ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
8 ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
9 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
10 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
11 ;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
12 ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
13 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
14 ;;; Copyright © 2016 Kei Kebreau <kei@openmailbox.org>
15 ;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
16 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
17 ;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be>
18 ;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>
19 ;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net>
20 ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
22 ;;; This file is part of GNU Guix.
24 ;;; GNU Guix is free software; you can redistribute it and/or modify it
25 ;;; under the terms of the GNU General Public License as published by
26 ;;; the Free Software Foundation; either version 3 of the License, or (at
27 ;;; your option) any later version.
29 ;;; GNU Guix is distributed in the hope that it will be useful, but
30 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
31 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
32 ;;; GNU General Public License for more details.
34 ;;; You should have received a copy of the GNU General Public License
35 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
37 (define-module (gnu packages maths)
38 #:use-module (ice-9 regex)
39 #:use-module (gnu packages)
40 #:use-module ((guix licenses) #:prefix license:)
41 #:use-module (guix packages)
42 #:use-module (guix download)
43 #:use-module (guix git-download)
44 #:use-module (guix utils)
45 #:use-module (guix build utils)
46 #:use-module (guix build-system cmake)
47 #:use-module (guix build-system gnu)
48 #:use-module (guix build-system ocaml)
49 #:use-module (guix build-system r)
50 #:use-module (gnu packages algebra)
51 #:use-module (gnu packages 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 (list
446 ;; Install to PREFIX/lib (the default is
448 (string-append "-DCMAKE_INSTALL_LIBDIR="
449 (assoc-ref %outputs "out")
452 "-DBUILD_SHARED_LIBS:BOOL=YES"
455 ;; Build the 'LAPACKE_clatms' functions.
456 "-DLAPACKE_WITH_TMG=ON")
457 #:phases (alist-cons-before
459 (lambda* (#:key inputs #:allow-other-keys)
460 (let ((python (assoc-ref inputs "python")))
461 (substitute* "lapack_testing.py"
462 (("/usr/bin/env python") python))))
464 (synopsis "Library for numerical linear algebra")
466 "LAPACK is a Fortran 90 library for solving the most commonly occurring
467 problems in numerical linear algebra.")
468 (license (license:non-copyleft "file://LICENSE"
469 "See LICENSE in the distribution."))))
471 (define-public scalapack
478 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
482 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
483 (build-system cmake-build-system)
486 ("fortran" ,gfortran)
487 ("lapack" ,lapack))) ;for testing only
489 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")))
490 (home-page "http://www.netlib.org/scalapack/")
491 (synopsis "Library for scalable numerical linear algebra")
493 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
494 routines on parallel distributed memory machines. ScaLAPACK solves dense and
495 banded linear systems, least squares problems, eigenvalue problems, and
496 singular value problems.")
497 (license (license:bsd-style "file://LICENSE"
498 "See LICENSE in the distribution."))))
500 (define-public gnuplot
506 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
511 "0q5lr6nala3ln6f3yp6g17ziymb9r9gx9zylnw1y3hjmwl9lggjv"))))
512 (build-system gnu-build-system)
513 (inputs `(("readline" ,readline)
519 `(("pkg-config" ,pkg-config)
520 ("texlive" ,texlive-tiny)))
521 (home-page "http://www.gnuplot.info")
522 (synopsis "Command-line driven graphing utility")
523 (description "Gnuplot is a portable command-line driven graphing
524 utility. It was originally created to allow scientists and students to
525 visualize mathematical functions and data interactively, but has grown to
526 support many non-interactive uses such as web scripting. It is also used as a
527 plotting engine by third-party applications like Octave.")
528 ;; X11 Style with the additional restriction that derived works may only be
529 ;; distributed as patches to the original.
530 (license (license:fsf-free
531 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
540 (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
542 (file-name (string-append name "-" version ".tar.gz"))
545 "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
547 `(("fortran" ,gfortran)))
548 (build-system gnu-build-system)
549 (synopsis "General Cartographic Transformation Package (GCTP)")
551 "The General Cartographic Transformation Package (GCTP) is a system of
552 software routines designed to permit the transformation of coordinate pairs
553 from one map projection to another. The GCTP is the standard computer
554 software used by the National Mapping Division for map projection
556 (home-page "https://github.com/OkoSanto/GCTP")
557 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
566 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
567 version "/src/hdf-" version ".tar.bz2"))
569 (base32 "020jh563sjyxsgml8l809d2i1d4ms9shivwj3gbm7n0ilxbll8id"))
570 (patches (search-patches "hdf4-architectures.patch"
571 "hdf4-reproducibility.patch"
572 "hdf4-shared-fortran.patch"))))
574 (build-system gnu-build-system)
576 `(("gfortran" ,gfortran)
581 ("libjpeg" ,libjpeg)))
583 `(#:parallel-tests? #f
584 #:configure-flags '("--enable-shared")
586 (modify-phases %standard-phases
587 (add-before 'configure 'patchbuild
590 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
592 (("/bin/mkdir") "mkdir"))
593 (substitute* (find-files "." "^Makefile\\.in$")
594 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
595 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
596 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
597 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
598 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")))))))
599 (home-page "https://www.hdfgroup.org/products/hdf4/")
601 "Library and multi-object file format for storing and managing data")
602 (description "HDF4 is a library and multi-object file format for storing
603 and managing data between machines. HDF4 is an older hierarchical data format,
604 incompatible with HDF5.")
606 (license:non-copyleft
607 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
609 (define-public hdf4-alt
614 (substitute-keyword-arguments (package-arguments hdf4)
615 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
617 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
626 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
627 "hdf5-" (version-major+minor version)
628 "/hdf5-" version "/src/hdf5-"
630 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
633 (take (string-split version #\.) 2))
634 "/src/hdf5-" version ".tar.bz2")))
636 (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
637 (patches (list (search-patch "hdf5-config-date.patch")))))
638 (build-system gnu-build-system)
642 `(;; Some of the users, notably Flann, need the C++ interface.
643 #:configure-flags '("--enable-cxx")
646 (modify-phases %standard-phases
647 (add-before 'configure 'patch-configure
649 (substitute* "configure"
652 (add-after 'install 'patch-references
653 (lambda* (#:key inputs outputs #:allow-other-keys)
654 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
655 (zlib (assoc-ref inputs "zlib")))
656 (substitute* (find-files bin "h5p?cc")
658 (string-append "-L" zlib "/lib " lib)))
660 (home-page "http://www.hdfgroup.org")
661 (synopsis "Management suite for extremely large and complex data")
662 (description "HDF5 is a suite that makes possible the management of
663 extremely large and complex data collections.")
664 (license (license:x11-style
665 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
667 (define-public hdf-eos2
674 (uri "ftp://edhs1.gsfc.nasa.gov\
675 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
677 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
678 (patches (search-patches "hdf-eos2-remove-gctp.patch"
679 "hdf-eos2-build-shared.patch"
680 "hdf-eos2-fortrantests.patch"))))
681 (build-system gnu-build-system)
683 `(("gfortran" ,gfortran)))
685 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
690 `( #:configure-flags '("--enable-install-include" "--enable-shared"
691 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
692 #:parallel-tests? #f))
693 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
694 (synopsis "HDF4-based data format for NASA's Earth Observing System")
695 (description "HDF-EOS2 is a software library built on HDF4 which supports
696 the construction of data structures used in NASA's Earth Observing
697 System (Grid, Point and Swath).")
699 ;; Source files carry a permissive license header.
700 (license (license:non-copyleft home-page))))
702 (define-public hdf-eos5
708 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
709 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
712 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
713 (patches (search-patches "hdf-eos5-build-shared.patch"
714 "hdf-eos5-remove-gctp.patch"
715 "hdf-eos5-fix-szip.patch"
716 "hdf-eos5-fortrantests.patch"))))
718 `(("gfortran" ,gfortran)))
719 (build-system gnu-build-system)
725 `(#:configure-flags '("--enable-install-include" "--enable-shared"
726 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
727 #:parallel-tests? #f))
728 (synopsis "HDF5-based data format for NASA's Earth Observing System")
730 "HDF-EOS5 is a software library built on HDF5 to support the construction
731 of data structures used in NASA's Earth Observing System (Grid, Point and
733 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
735 ;; Source files carry a permissive license header.
736 (license (license:non-copyleft home-page))))
738 (define-public hdf5-parallel-openmpi
739 (package (inherit hdf5)
740 (name "hdf5-parallel-openmpi")
743 ,@(package-inputs hdf5)))
745 (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
746 ,@(package-arguments hdf5))
748 `(modify-phases ,phases
749 (add-before 'check 'patch-tests
751 ;; OpenMPI's mpirun will exit with non-zero status if it
752 ;; detects an "abnormal termination", i.e. any process not
753 ;; calling MPI_Finalize(). Since the test is explicitely
754 ;; avoiding MPI_Finalize so as not to have at_exit and thus
755 ;; H5C_flush_cache from being called, mpirun will always
756 ;; complain, so turn this test off.
757 (substitute* "testpar/Makefile"
758 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
759 (string-append front back "\n")))
760 (substitute* "tools/h5diff/testph5diff.sh"
761 (("/bin/sh") (which "sh")))
763 (synopsis "Management suite for data with parallel IO support")))
765 (define-public h5check
772 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
773 "h5check/src/h5check-" version ".tar.gz"))
776 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
777 (build-system gnu-build-system)
778 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
779 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
780 (synopsis "HDF5 format checker")
781 (description "@code{h5check} is a validation tool for verifying that an
782 HDF5 file is encoded according to the HDF File Format Specification.")
783 (license (license:x11-style "file://COPYING"))))
791 (uri (string-append "mirror://sourceforge/itpp/itpp/"
796 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
797 (build-system cmake-build-system)
798 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
799 (inputs `(("lapack" ,lapack)
801 ;; FIXME: Even though the fonts are available dvips complains:
802 ;; "Font cmmi10 not found; characters will be left blank."
804 `(("texlive" ,texlive-tiny)
805 ("ghostscript" ,ghostscript)
806 ("doxygen" ,doxygen)))
807 (home-page "http://itpp.sourceforge.net")
808 (synopsis "C++ library of maths, signal processing and communication classes")
809 (description "IT++ is a C++ library of mathematical, signal processing and
810 communication classes and functions. Its main use is in simulation of
811 communication systems and for performing research in the area of
812 communications. The kernel of the library consists of generic vector and
813 matrix classes, and a set of accompanying routines. Such a kernel makes IT++
814 similar to MATLAB, GNU Octave or SciPy.")
815 (license license:gpl3+)))
817 (define-public netcdf
824 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
825 "netcdf-" version ".tar.gz"))
828 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
829 (patches (search-patches "netcdf-date-time.patch"
830 "netcdf-tst_h_par.patch"))))
831 (build-system gnu-build-system)
835 ("graphviz" ,graphviz)))
840 ("libjpeg" ,libjpeg)))
842 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
843 #:parallel-tests? #f)) ;various race conditions
844 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
845 (synopsis "Library for scientific data")
846 (description "NetCDF is an interface for scientific data access and a
847 software library that provides an implementation of the interface. The netCDF
848 library defines a machine-independent format for representing scientific data.
849 Together, the interface, library, and format support the creation, access, and
850 sharing of scientific data.")
851 (license (license:x11-style "file://COPYRIGHT"))))
853 (define-public netcdf-parallel-openmpi
854 (package (inherit netcdf)
855 (name "netcdf-parallel-openmpi")
858 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
859 (package-inputs netcdf))))
860 ;; TODO: Replace pkg-config references in nc-config with absolute references
862 (substitute-keyword-arguments (package-arguments netcdf)
863 ((#:configure-flags flags)
864 `(cons* "CC=mpicc" "CXX=mpicxx"
865 "--enable-parallel-tests"
866 ;; Shared libraries not supported with parallel IO.
867 "--disable-shared" "--with-pic"
870 (define-public netcdf-fortran
872 (name "netcdf-fortran")
877 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
881 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
882 (build-system gnu-build-system)
884 `(#:parallel-tests? #f))
886 `(("netcdf" ,netcdf)))
888 `(("gfortran" ,gfortran)))
889 (synopsis "Fortran interface for the netCDF library")
890 (description (package-description netcdf))
891 (home-page (package-home-page netcdf))
892 (license (package-license netcdf))))
900 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
903 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
904 (build-system gnu-build-system)
906 `(;; Shared libraries are not built by default. They are required to
907 ;; build the Guile, Octave, and Python bindings.
908 #:configure-flags '("--enable-shared")
911 (modify-phases %standard-phases
912 (add-before 'configure 'set-libnlopt-file-name
913 (lambda* (#:key outputs #:allow-other-keys)
914 ;; Make sure the Scheme module refers to the library by its
915 ;; absolute file name (we cannot do that from a snippet
916 ;; because the expansion of @libdir@ contains
918 (let ((out (assoc-ref outputs "out")))
919 (substitute* "swig/nlopt.scm.in"
921 (string-append out "/lib/libnlopt")))
923 (inputs `(("guile" ,guile-2.0)))
924 (native-inputs `(("pkg-config" ,pkg-config)))
925 (home-page "http://ab-initio.mit.edu/wiki/")
926 (synopsis "Library for nonlinear optimization")
927 (description "NLopt is a library for nonlinear optimization, providing a
928 common interface for a number of different free optimization routines available
929 online as well as original implementations of various other algorithms.")
930 (license license:lgpl2.1+)))
939 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
943 "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
944 (modules '((guix build utils)))
946 ;; Make sure we don't use the bundled software.
947 '(delete-file-recursively "ThirdParty"))))
948 (build-system gnu-build-system)
950 '(#:phases (modify-phases %standard-phases
951 (add-after 'install 'add--L-flags-in-ipopt.pc
952 (lambda* (#:key inputs outputs #:allow-other-keys)
953 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
954 ;; move it to "Libs.private" where it belongs, and add a
955 ;; '-L' flag for LAPACK.
956 (let ((out (assoc-ref outputs "out"))
957 (lapack (assoc-ref inputs "lapack")))
958 (substitute* (string-append out "/lib/pkgconfig/"
960 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
961 (string-append "Libs: " before " " after "\n"
962 "Libs.private: " before
963 "-L" lapack "/lib -llapack -lblas "
967 `(("gfortran" ,gfortran)))
969 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
970 `(("lapack" ,lapack))) ;for both libblas and liblapack
971 (home-page "http://www.coin-or.org")
972 (synopsis "Large-scale nonlinear optimizer")
974 "The Interior Point Optimizer (IPOPT) is a software package for
975 large-scale nonlinear optimization. It provides C++, C, and Fortran
977 (license license:epl1.0)))
981 (name "ceres-solver")
983 (home-page "http://ceres-solver.org/")
986 (uri (string-append home-page "ceres-solver-"
990 "0i7qkbf8g6pd8arxzldppga26ckv93y8zldsfz6wbd4n6b1nqrjd"))))
991 (build-system cmake-build-system)
993 ;; TODO: Build HTML user documentation and install separately.
994 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
995 "-DBUILD_SHARED_LIBS=ON")
997 #:phases (modify-phases %standard-phases
998 (add-before 'configure 'set-library-directory
1000 ;; Install libraries to lib/, not lib64/.
1001 (substitute* "internal/ceres/CMakeLists.txt"
1002 (("set\\(LIB_SUFFIX \"64\"\\)")
1003 "set(LIB_SUFFIX \"\")"))
1006 `(("pkg-config" ,pkg-config)))
1008 `(("glog" ,glog))) ;for #include <glog/glog.h>
1013 ("suitesparse" ,suitesparse)
1014 ("gflags" ,gflags)))
1015 (synopsis "C++ library for solving large optimization problems")
1017 "Ceres Solver is a C++ library for modeling and solving large,
1018 complicated optimization problems. It is a feature rich, mature and
1019 performant library which has been used in production since 2010. Ceres Solver
1020 can solve two kinds of problems:
1022 @item non-linear least squares problems with bounds constraints;
1023 @item general unconstrained optimization problems.
1025 (license license:bsd-3)))
1027 ;; For a fully featured Octave, users are strongly recommended also to install
1028 ;; the following packages: texinfo, less, ghostscript, gnuplot.
1029 (define-public octave
1036 (uri (string-append "mirror://gnu/octave/octave-"
1040 "09zhhch79jw3ynw39vizx0i2cbd2bjz3sp38pjdzraqrbivpwp92"))))
1041 (build-system gnu-build-system)
1043 `(("lapack" ,lapack)
1044 ("readline" ,readline)
1049 ("arpack" ,arpack-ng)
1052 ("fontconfig" ,fontconfig)
1053 ("freetype" ,freetype)
1060 ("graphicsmagick" ,graphicsmagick)))
1063 ("gfortran" ,gfortran)
1064 ("pkg-config" ,pkg-config)
1066 ;; The following inputs are not actually used in the build process.
1067 ;; However, the ./configure gratuitously tests for their existence and
1068 ;; assumes that programs not present at build time are also not, and
1069 ;; can never be, available at run time! If these inputs are therefore
1070 ;; not present, support for them will be built out. However, Octave
1071 ;; will still run without them, albeit without the features they
1074 ("texinfo" ,texinfo)
1075 ("ghostscript" ,ghostscript)
1076 ("gnuplot" ,gnuplot)))
1079 (list (string-append "--with-shell="
1080 (assoc-ref %build-inputs "bash")
1082 (home-page "https://www.gnu.org/software/octave/")
1083 (synopsis "High-level language for numerical computation")
1084 (description "GNU Octave is a high-level interpreted language that is
1085 specialized for numerical computations. It can be used for both linear and
1086 non-linear applications and it provides great support for visualizing results.
1087 Work may be performed both at the interactive command-line as well as via
1089 (license license:gpl3+)))
1091 (define-public opencascade-oce
1093 (name "opencascade-oce")
1099 "https://github.com/tpaviot/oce/archive/OCE-"
1104 "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
1105 (build-system cmake-build-system)
1108 (list "-DOCE_TESTING:BOOL=ON"
1109 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1110 "-DOCE_DRAW:BOOL=ON"
1111 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1112 (assoc-ref %outputs "out"))
1113 "-UCMAKE_INSTALL_RPATH")))
1115 `(("freetype" ,freetype)
1122 `(("python" ,python-wrapper)))
1123 (home-page "https://github.com/tpaviot/oce")
1124 (synopsis "Libraries for 3D modeling and numerical simulation")
1126 "Open CASCADE is a set of libraries for the development of applications
1127 dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1128 C++ class libraries providing services for 3D surface and solid modeling, CAD
1129 data exchange, and visualization. It is used for development of specialized
1130 software dealing with 3D models in design (CAD), manufacturing (CAM),
1131 numerical simulation (CAE), measurement equipment (CMM), and quality
1132 control (CAQ) domains.
1134 This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1135 patches, improvements, and experiments contributed by users over the official
1136 Open CASCADE library.")
1137 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1138 ; use of header files; see
1139 ; OCCT_LGPL_EXCEPTION.txt
1140 license:public-domain; files
1141 ; src/Standard/Standard_StdAllocator.hxx and
1142 ; src/NCollection/NCollection_StdAllocator.hxx
1143 license:expat; file src/OpenGl/OpenGl_glext.h
1144 license:bsd-3)))); test framework gtest
1153 (uri (string-append "http://gmsh.info/src/gmsh-"
1154 version "-source.tgz"))
1156 (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
1157 (modules '((guix build utils)))
1159 ;; Remove non-free METIS code
1160 '(delete-file-recursively "contrib/Metis"))))
1161 (build-system cmake-build-system)
1164 ("gfortran" ,gfortran)
1170 ("opencascade-oce" ,opencascade-oce)
1172 ("libxext" ,libxext)))
1174 `(("fontconfig" ,fontconfig)
1175 ("libxft" ,libxft)))
1177 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1178 "-DENABLE_BUILD_SHARED:BOOL=ON"
1179 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
1180 (home-page "http://www.geuz.org/gmsh/")
1181 (synopsis "3D finite element grid generator")
1182 (description "Gmsh is a 3D finite element grid generator with a built-in
1183 CAD engine and post-processor. Its design goal is to provide a fast, light
1184 and user-friendly meshing tool with parametric input and advanced
1185 visualization capabilities. Gmsh is built around four modules: geometry,
1186 mesh, solver and post-processing. The specification of any input to these
1187 modules is done either interactively using the graphical user interface or in
1188 ASCII text files using Gmsh's own scripting language.")
1189 (license license:gpl2+)))
1191 (define-public maxflow
1198 (url "https://github.com/gerddie/maxflow.git")
1199 (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
1200 (file-name (string-append name "-" version "-checkout"))
1203 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1204 (build-system cmake-build-system)
1205 (home-page "http://pub.ist.ac.at/~vnk/software.html")
1206 (synopsis "Library implementing Maxflow algorithm")
1207 (description "An implementation of the maxflow algorithm described in
1208 @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1209 Energy Minimization in Computer Vision.\n
1210 Yuri Boykov and Vladimir Kolmogorov.\n
1211 In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1213 (license license:gpl3+)))
1215 (define-public petsc
1222 ;; The *-lite-* tarball does not contain the *large* documentation
1223 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1224 "petsc-lite-" version ".tar.gz"))
1226 (base32 "0jfrq6rd4zagw1iimz05m2w91k0jvz3qbik1lk8pqcxw3rvdqk5d"))))
1227 (build-system gnu-build-system)
1229 `(("python" ,python-2)
1232 `(("gfortran" ,gfortran)
1234 ("superlu" ,superlu)
1235 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1236 ;; leaving out opengl, as configuration seems to only be for mac
1239 `(#:test-target "test"
1240 #:parallel-build? #f ;build is parallel by default
1245 ,(string-append "--with-superlu-include="
1246 (assoc-ref %build-inputs "superlu") "/include")
1247 ,(string-append "--with-superlu-lib="
1248 (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
1250 (modify-phases %standard-phases
1252 ;; PETSc's configure script is actually a python script, so we can't
1253 ;; run it with bash.
1254 (lambda* (#:key outputs (configure-flags '())
1256 (let* ((prefix (assoc-ref outputs "out"))
1257 (flags `(,(string-append "--prefix=" prefix)
1258 ,@configure-flags)))
1259 (format #t "build directory: ~s~%" (getcwd))
1260 (format #t "configure flags: ~s~%" flags)
1261 (zero? (apply system* "./configure" flags)))))
1262 (add-after 'configure 'clean-local-references
1263 (lambda* (#:key inputs outputs #:allow-other-keys)
1264 (let ((out (assoc-ref outputs "out")))
1265 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
1266 ;; Prevent build directory from leaking into compiled code
1268 ;; Scrub timestamp for reproducibility
1269 ((".*Libraries compiled on.*") ""))
1271 (add-after 'install 'clean-install
1272 ;; Try to keep installed files from leaking build directory names.
1273 (lambda* (#:key inputs outputs #:allow-other-keys)
1274 (let ((out (assoc-ref outputs "out")))
1275 (substitute* (map (lambda (file)
1276 (string-append out "/lib/petsc/conf/" file))
1277 '("petscvariables"))
1279 ;; Make compiler references point to the store
1280 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
1281 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1282 (string-append "= " (which compiler))))
1283 ;; PETSc installs some build logs, which aren't necessary.
1284 (for-each (lambda (file)
1285 (let ((f (string-append out "/lib/petsc/conf/" file)))
1286 (when (file-exists? f)
1288 '("configure.log" "make.log" "gmake.log"
1289 "test.log" "error.log" "RDict.db"
1290 "PETScBuildInternal.cmake"
1291 ;; Once installed, should uninstall with Guix
1294 (home-page "http://www.mcs.anl.gov/petsc")
1295 (synopsis "Library to solve PDEs")
1296 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1297 data structures and routines for the scalable (parallel) solution of
1298 scientific applications modeled by partial differential equations.")
1299 (license (license:non-copyleft
1300 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1302 (define-public petsc-complex
1303 (package (inherit petsc)
1304 (name "petsc-complex")
1306 (substitute-keyword-arguments (package-arguments petsc)
1307 ((#:configure-flags cf)
1308 `(cons "--with-scalar-type=complex" ,cf))))
1309 (synopsis "Library to solve PDEs (with complex scalars)")))
1311 (define-public petsc-openmpi
1312 (package (inherit petsc)
1313 (name "petsc-openmpi")
1315 `(("openmpi" ,openmpi)
1316 ,@(package-inputs petsc)))
1318 (substitute-keyword-arguments (package-arguments petsc)
1319 ((#:configure-flags cf)
1320 ``("--with-mpiexec=mpirun"
1321 ,(string-append "--with-mpi-dir="
1322 (assoc-ref %build-inputs "openmpi"))
1323 ,@(delete "--with-mpi=0" ,cf)))))
1324 (synopsis "Library to solve PDEs (with MPI support)")))
1326 (define-public petsc-complex-openmpi
1327 (package (inherit petsc-complex)
1328 (name "petsc-complex-openmpi")
1330 `(("openmpi" ,openmpi)
1331 ,@(package-inputs petsc-complex)))
1333 (substitute-keyword-arguments (package-arguments petsc-complex)
1334 ((#:configure-flags cf)
1335 ``("--with-mpiexec=mpirun"
1336 ,(string-append "--with-mpi-dir="
1337 (assoc-ref %build-inputs "openmpi"))
1338 ,@(delete "--with-mpi=0" ,cf)))))
1339 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
1341 (define-public slepc
1348 (uri (string-append "http://slepc.upv.es/download/download.php?"
1349 "filename=slepc-" version ".tar.gz"))
1350 (file-name (string-append name "-" version ".tar.gz"))
1353 "1hijlmrvxvfqslnx8yydzw5xqbsn1yy02g32w0hln1z3cgr1c0k7"))))
1354 (build-system gnu-build-system)
1356 `(("python" ,python-2)))
1358 `(("arpack" ,arpack-ng)
1359 ("gfortran" ,gfortran)))
1361 `(("petsc" ,petsc)))
1363 `(#:parallel-build? #f ;build is parallel by default
1365 `(,(string-append "--with-arpack-dir="
1366 (assoc-ref %build-inputs "arpack") "/lib"))
1368 (modify-phases %standard-phases
1370 ;; configure is a python script, so we can't run it with bash.
1371 (lambda* (#:key inputs outputs (configure-flags '())
1373 (let* ((prefix (assoc-ref outputs "out"))
1374 (flags `(,(string-append "--prefix=" prefix)
1375 ,@configure-flags)))
1376 (format #t "build directory: ~s~%" (getcwd))
1377 (format #t "configure flags: ~s~%" flags)
1378 (setenv "SLEPC_DIR" (getcwd))
1379 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
1380 (zero? (apply system* "./configure" flags)))))
1381 (add-after 'install 'delete-doc
1382 ;; TODO: SLEPc installs HTML documentation alongside headers in
1383 ;; $out/include. We'd like to move them to share/doc, but delete
1384 ;; them for now, as they are incomplete and installing the complete
1385 ;; documentation is difficult.
1386 (lambda* (#:key outputs #:allow-other-keys)
1387 (let* ((out (assoc-ref outputs "out")))
1388 (for-each delete-file (find-files out "\\.html$")))))
1389 (add-after 'install 'clean-install
1390 ;; Clean up unnecessary build logs from installation.
1391 (lambda* (#:key outputs #:allow-other-keys)
1392 (let ((out (assoc-ref outputs "out")))
1393 (for-each (lambda (file)
1394 (let ((f (string-append out "/lib/slepc/conf/" file)))
1395 (when (file-exists? f)
1397 '("configure.log" "make.log" "gmake.log"
1398 "test.log" "error.log" "RDict.db"
1399 "uninstall.py"))))))))
1400 (home-page "http://slepc.upv.es")
1401 (synopsis "Scalable library for eigenproblems")
1402 (description "SLEPc is a software library for the solution of large sparse
1403 eigenproblems on parallel computers. It can be used for the solution of
1404 linear eigenvalue problems formulated in either standard or generalized form,
1405 as well as other related problems such as the singular value decomposition.
1406 The emphasis of the software is on methods and techniques appropriate for
1407 problems in which the associated matrices are sparse, for example, those
1408 arising after the discretization of partial differential equations.")
1409 (license license:lgpl3)))
1411 (define-public slepc-complex
1412 (package (inherit slepc)
1413 (name "slepc-complex")
1415 `(("petsc" ,petsc-complex)
1416 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1417 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1419 (define-public slepc-openmpi
1420 (package (inherit slepc)
1421 (name "slepc-openmpi")
1424 ("arpack" ,arpack-ng-openmpi)
1425 ,@(alist-delete "arpack" (package-inputs slepc))))
1427 `(("petsc" ,petsc-openmpi)
1428 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1429 (synopsis "Scalable library for eigenproblems (with MPI support)")))
1431 (define-public slepc-complex-openmpi
1432 (package (inherit slepc-openmpi)
1433 (name "slepc-complex-openmpi")
1435 `(("petsc" ,petsc-complex-openmpi)
1436 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1437 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1439 (define-public mumps
1446 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
1450 "0igyc1pfzxdhpbad3v3lb86ixkdbqa1a8gbs15b04r2294h2nabp"))
1451 (patches (search-patches "mumps-build-parallelism.patch"))))
1452 (build-system gnu-build-system)
1454 `(("fortran" ,gfortran)
1455 ;; These are required for linking against mumps, but we let the user
1456 ;; declare the dependency.
1459 ("scotch" ,scotch)))
1461 `(#:modules ((ice-9 match)
1464 ,@%gnu-build-system-modules)
1466 (modify-phases %standard-phases
1468 (lambda* (#:key inputs #:allow-other-keys)
1469 (call-with-output-file "Makefile.inc"
1480 INCSEQ = -I$(topdir)/libseq
1481 LIBSEQ = -L$(topdir)/libseq -lmpiseq
1482 LIBSEQNEEDED = libseqneeded~;
1486 AR = ar vr # rules require trailing space, ugh...
1488 LIBBLAS = -L~a -lopenblas~@[
1489 SCALAP = -L~a -lscalapack~]
1490 LIBOTHERS = -pthread
1493 OPTF = -O2 -DALLOW_NON_INIT $(PIC)
1497 LIBS = $(SCALAP) $(LIBSEQ)
1498 LPORDDIR = $(topdir)/PORD/lib
1499 IPORD = -I$(topdir)/PORD/include
1500 LPORD = -L$(LPORDDIR) -lpord
1501 ORDERINGSF = -Dpord~@[
1503 IMETIS = -I$(METISDIR)/include
1504 LMETIS = -L$(METISDIR)/lib -lmetis
1505 ORDERINGSF += -Dmetis~]~@[~:{
1507 ISCOTCH = -I$(SCOTCHDIR)/include
1508 LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
1509 ORDERINGSF += ~a~}~]
1510 ORDERINGSC = $(ORDERINGSF)
1511 LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
1512 IORDERINGSF = $(ISCOTCH)
1513 IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
1514 (assoc-ref inputs "mpi")
1515 (assoc-ref inputs "blas")
1516 (assoc-ref inputs "scalapack")
1517 (assoc-ref inputs "metis")
1518 (match (list (assoc-ref inputs "pt-scotch")
1519 (assoc-ref inputs "scotch"))
1523 `((,scotch "" "-Dscotch")))
1526 "-lptesmumps -lptscotch -lptscotcherr "
1527 "-Dptscotch")))))))))
1529 ;; By default only the d-precision library is built. Make with "all"
1530 ;; target so that all precision libraries and examples are built.
1532 (zero? (system* "make" "all"
1533 (format #f "-j~a" (parallel-job-count))))))
1535 ;; Run the simple test drivers, which read test input from stdin:
1536 ;; from the "real" input for the single- and double-precision
1537 ;; testers, and from the "cmplx" input for complex-precision
1538 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
1539 ;; package to prefix execution with "mpirun".
1540 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
1541 (with-directory-excursion "examples"
1544 (let ((tester (apply open-pipe*
1547 ,(string-append "./" prec
1549 (input (open-input-file
1550 (string-append "input_simpletest_" type))))
1552 (dump-port input tester)
1554 (zero? (close-pipe tester)))))
1556 '("real" "real" "cmplx" "cmplx")))))
1558 (lambda* (#:key outputs #:allow-other-keys)
1559 (let* ((out (assoc-ref outputs "out"))
1560 (libdir (string-append out "/lib")))
1561 (copy-recursively "lib" libdir)
1562 (copy-recursively "include" (string-append out "/include"))
1563 (when (file-exists? "libseq/libmpiseq.a")
1564 (install-file "libseq/libmpiseq.a" libdir))
1566 (home-page "http://mumps.enseeiht.fr")
1567 (synopsis "Multifrontal sparse direct solver")
1569 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
1570 sparse system of linear equations A x = b using Guassian elimination.")
1571 (license license:cecill-c)))
1573 (define-public mumps-metis
1574 (package (inherit mumps)
1575 (name "mumps-metis")
1577 (alist-delete "scotch" (package-inputs mumps)))))
1579 (define-public mumps-openmpi
1580 (package (inherit mumps)
1581 (name "mumps-openmpi")
1584 ("scalapack" ,scalapack)
1585 ("pt-scotch" ,pt-scotch)
1586 ,@(alist-delete "scotch" (package-inputs mumps))))
1588 (substitute-keyword-arguments (package-arguments mumps)
1590 `(modify-phases ,phases
1594 ((assoc-ref ,phases 'check)
1595 #:exec-prefix '("mpirun" "-n" "2"))))))))
1596 (synopsis "Multifrontal sparse direct solver (with MPI)")))
1598 (define-public mumps-metis-openmpi
1599 (package (inherit mumps-openmpi)
1600 (name "mumps-metis-openmpi")
1602 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
1604 (define-public r-quadprog
1611 (uri (cran-uri "quadprog" version))
1614 "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
1615 (build-system r-build-system)
1617 `(("gfortran" ,gfortran)))
1618 (home-page "http://cran.r-project.org/web/packages/quadprog")
1619 (synopsis "Functions to solve quadratic programming problems")
1621 "This package contains routines and documentation for solving quadratic
1622 programming problems.")
1623 (license license:gpl3+)))
1625 (define-public r-pracma
1631 (uri (cran-uri "pracma" version))
1633 (base32 "1z3i90mkzwvp9di17caf4934z2xlb2imm3hwxllcrbwvmnmhrwyc"))))
1634 (build-system r-build-system)
1636 `(("r-quadprog" ,r-quadprog)))
1637 (home-page "http://cran.r-project.org/web/packages/pracma")
1638 (synopsis "Practical numerical math functions")
1639 (description "This package provides functions for numerical analysis and
1640 linear algebra, numerical optimization, differential equations, plus some
1641 special functions. It uses Matlab function names where appropriate to simplify
1643 (license license:gpl3+)))
1645 (define-public superlu
1652 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1653 "superlu_" version ".tar.gz"))
1655 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
1656 (modules '((guix build utils)))
1658 ;; Replace the non-free implementation of MC64 with a stub adapted
1661 (use-modules (ice-9 regex)
1663 (call-with-output-file "SRC/mc64ad.c"
1668 void mc64id_(int *a) {
1669 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
1672 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
1673 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
1674 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
1677 ;; Remove the corresponding license verbiage. MC64 license follows
1678 ;; a "------" line separator.
1679 (with-atomic-file-replacement "License.txt"
1680 (let ((rx (make-regexp "-{8}")))
1683 (let ((line (read-line in 'concat)))
1684 (unless (regexp-exec rx line)
1687 (build-system cmake-build-system)
1691 `(("blas" ,openblas)
1692 ("gfortran" ,gfortran)))
1694 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
1695 "-DTPL_BLAS_LIBRARIES=openblas"
1696 "-DBUILD_SHARED_LIBS:BOOL=YES"
1697 "-DCMAKE_INSTALL_LIBDIR=lib")))
1698 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
1699 (synopsis "Supernodal direct solver for sparse linear systems")
1701 "SuperLU is a general purpose library for the direct solution of large,
1702 sparse, nonsymmetric systems of linear equations on high performance machines.
1703 The library is written in C and is callable from either C or Fortran. The
1704 library routines perform an LU decomposition with partial pivoting and
1705 triangular system solves through forward and back substitution. The library
1706 also provides threshold-based ILU factorization preconditioners.")
1707 (license (list license:bsd-3
1708 license:gpl2+ ;EXAMPLE/*fgmr.c
1709 (license:fsf-free "file://SRC/colamd.h")))))
1711 (define-public superlu-dist
1713 (name "superlu-dist")
1718 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1719 "superlu_dist_" version ".tar.gz"))
1721 (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj"))
1722 (modules '((guix build utils)))
1724 ;; Replace the non-free implementation of MC64 with a stub
1726 (use-modules (ice-9 regex)
1728 (call-with-output-file "SRC/mc64ad.c"
1733 void mc64id_(int *a) {
1734 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
1737 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
1738 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
1739 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
1742 (delete-file "SRC/mc64ad.f.bak")
1743 (substitute* "SRC/util.c" ;adjust default algorithm
1744 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
1745 "RowPerm = NOROWPERM"))))
1746 (patches (search-patches "superlu-dist-scotchmetis.patch"))))
1747 (build-system gnu-build-system)
1751 `(("gfortran" ,gfortran)))
1753 `(("openmpi" ,openmpi) ;headers include MPI heades
1754 ("lapack" ,lapack) ;required to link with output library
1755 ("pt-scotch" ,pt-scotch))) ;same
1757 `(#:parallel-build? #f ;race conditions using ar
1761 (lambda* (#:key inputs outputs #:allow-other-keys)
1762 (call-with-output-file "make.inc"
1767 DSUPERLULIB = ~a/lib/libsuperlu_dist.a
1768 BLASDEF = -DUSE_VENDOR_BLAS
1769 BLASLIB = -L~a/lib -lblas
1770 PARMETISLIB = -L~a/lib \
1771 -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
1772 -lscotch -lscotcherr -lscotcherrexit
1773 METISLIB = -L~:*~a/lib \
1774 -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
1775 LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
1781 CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC)
1782 NOOPTS = -O0 -g $(PIC)
1784 FFLAGS = -O2 -g $(PIC)
1788 (assoc-ref outputs "out")
1789 (assoc-ref inputs "lapack")
1790 (assoc-ref inputs "pt-scotch")))))
1792 'unpack 'remove-broken-symlinks
1794 (for-each delete-file
1795 (find-files "MAKE_INC" "\\.#make\\..*")))
1797 'build 'create-install-directories
1798 (lambda* (#:key outputs #:allow-other-keys)
1801 (mkdir-p (string-append (assoc-ref outputs "out")
1803 '("lib" "include")))
1807 (with-directory-excursion "EXAMPLE"
1809 (zero? (system* "mpirun" "-n" "2"
1810 "./pddrive" "-r" "1" "-c" "2" "g20.rua"))
1811 (zero? (system* "mpirun" "-n" "2"
1812 "./pzdrive" "-r" "1" "-c" "2" "cg20.cua")))))
1815 (lambda* (#:key outputs #:allow-other-keys)
1816 ;; Library is placed in lib during the build phase. Copy over
1817 ;; headers to include.
1818 (let* ((out (assoc-ref outputs "out"))
1819 (incdir (string-append out "/include")))
1820 (for-each (lambda (file)
1821 (let ((base (basename file)))
1822 (format #t "installing `~a' to `~a'~%"
1825 (string-append incdir "/" base))))
1826 (find-files "SRC" ".*\\.h$"))))
1827 %standard-phases)))))))
1828 (home-page (package-home-page superlu))
1829 (synopsis "Parallel supernodal direct solver")
1831 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
1832 It is targeted for distributed memory parallel machines. SuperLU_DIST is
1833 implemented in ANSI C, and MPI for communications.")
1834 (license license:bsd-3)))
1836 (define-public scotch
1843 (uri (string-append "https://gforge.inria.fr/frs/download.php/34618/"
1844 "scotch_" version ".tar.gz"))
1846 (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm"))
1847 (patches (search-patches "scotch-test-threading.patch"
1848 "pt-scotch-build-parallelism.patch"))))
1849 (build-system gnu-build-system)
1852 ("flex" ,flex-2.6.1) ; A bug in flex prevents building with flex-2.6.3.
1856 (modify-phases %standard-phases
1858 'unpack 'chdir-to-src
1859 (lambda _ (chdir "src")))
1863 (call-with-output-file "Makefile.inc"
1877 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
1878 LDFLAGS = -lz -lm -lrt -lpthread
1880 LEX = flex -Pscotchyy -olex.yy.c
1885 YACC = bison -pscotchyy -y -b y
1887 '("COMMON_FILE_COMPRESS_GZ"
1889 "COMMON_RANDOM_FIXED_SEED"
1890 "INTSIZE64" ;use 'long' instead of 'int'
1891 ;; Prevents symbolc clashes with libesmumps
1893 ;; XXX: Causes invalid frees in superlu-dist tests
1895 ;; "SCOTCH_PTHREAD_NUMBER=2"
1896 "restrict=__restrict"))))))
1898 'build 'build-esmumps
1900 (zero? (system* "make"
1901 (format #f "-j~a" (parallel-job-count))
1905 (lambda* (#:key outputs #:allow-other-keys)
1906 (let ((out (assoc-ref outputs "out")))
1908 (zero? (system* "make"
1909 (string-append "prefix=" out)
1911 ;; esmumps files are not installed with the above
1912 (for-each (lambda (f)
1913 (copy-file f (string-append out "/include/" f)))
1914 (find-files "../include" ".*esmumps.h$"))
1915 (for-each (lambda (f)
1916 (copy-file f (string-append out "/lib/" f)))
1917 (find-files "../lib" "^lib.*esmumps.*"))))))))
1918 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
1919 (synopsis "Programs and libraries for graph algorithms")
1920 (description "SCOTCH is a set of programs and libraries which implement
1921 the static mapping and sparse matrix reordering algorithms developed within
1922 the SCOTCH project. Its purpose is to apply graph theory, with a divide and
1923 conquer approach, to scientific computing problems such as graph and mesh
1924 partitioning, static mapping, and sparse matrix ordering, in application
1925 domains ranging from structural mechanics to operating systems or
1927 ;; See LICENSE_en.txt
1928 (license license:cecill-c)))
1930 (define-public pt-scotch
1931 (package (inherit scotch)
1934 `(("openmpi" ,openmpi))) ;Headers include MPI headers
1936 (substitute-keyword-arguments (package-arguments scotch)
1937 ((#:phases scotch-phases)
1938 `(modify-phases ,scotch-phases
1943 (zero? (system* "make"
1944 (format #f "-j~a" (parallel-job-count))
1945 "ptscotch" "ptesmumps"))
1946 ;; Install the serial metis compatibility library
1947 (zero? (system* "make" "-C" "libscotchmetis" "install")))))
1950 (lambda _ (zero? (system* "make" "ptcheck"))))))))
1951 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
1953 (define-public metis
1960 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
1961 "metis-" version ".tar.gz"))
1964 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
1965 (build-system cmake-build-system)
1967 `(("blas" ,openblas)))
1969 `(#:tests? #f ;no tests
1970 #:configure-flags `("-DSHARED=ON"
1971 ,(string-append "-DGKLIB_PATH=" (getcwd)
1972 "/metis-" ,version "/GKlib"))))
1973 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
1974 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
1976 "METIS is a set of serial programs for partitioning graphs, partitioning
1977 finite element meshes, and producing fill-reducing orderings for sparse
1978 matrices. The algorithms implemented in METIS are based on the multilevel
1979 recursive-bisection, multilevel k-way, and multi-constraint partitioning
1981 (license license:asl2.0))) ;As of version 5.0.3
1983 (define-public p4est
1990 (uri (string-append "http://p4est.github.io/release/p4est-"
1994 "0faina2h5qsx3m2izbzaj9bbakma1krbbjmq43wrp1hcbyijflqb"))))
1995 (build-system gnu-build-system)
1997 `(("fortran" ,gfortran)
2002 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2003 (assoc-ref %build-inputs "blas")
2005 ,(string-append "LAPACK_LIBS=-L"
2006 (assoc-ref %build-inputs "lapack")
2008 (home-page "http://www.p4est.org")
2009 (synopsis "Adaptive mesh refinement on forests of octrees")
2011 "The p4est software library enables the dynamic management of a
2012 collection of adaptive octrees, conveniently called a forest of octrees.
2013 p4est is designed to work in parallel and scales to hundreds of thousands of
2015 (license license:gpl2+)))
2017 (define-public p4est-openmpi
2018 (package (inherit p4est)
2019 (name "p4est-openmpi")
2022 ,@(package-inputs p4est)))
2024 (substitute-keyword-arguments (package-arguments p4est)
2025 ((#:configure-flags cf)
2026 ``("--enable-mpi" ,@,cf))))
2027 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2029 (define-public gsegrafix
2036 (uri (string-append "mirror://gnu/" name "/" name "-"
2040 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2041 (build-system gnu-build-system)
2043 `(#:configure-flags '("LDFLAGS=-lm")))
2045 `(("libgnomecanvas" ,libgnomecanvas)
2046 ("libbonoboui" ,libbonoboui)
2047 ("libgnomeui" ,libgnomeui)
2048 ("libgnomeprintui" ,libgnomeprintui)
2051 `(("pkg-config" ,pkg-config)))
2052 (home-page "https://www.gnu.org/software/gsegrafix/")
2053 (synopsis "GNOME application to create scientific and engineering plots")
2054 (description "GSEGrafix is an application which produces high-quality graphical
2055 plots for science and engineering. Plots are specified via simple ASCII
2056 parameter files and data files and are presented in an anti-aliased GNOME
2057 canvas. The program supports rectangular two-dimensional plots, histograms,
2058 polar-axis plots and three-dimensional plots. Plots can be printed or saved
2059 to BMP, JPEG or PNG image formats.")
2060 (license license:gpl3+)))
2062 (define-public maxima
2069 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2070 version "-source/" name "-" version ".tar.gz"))
2073 "15pp35ayglv723bjbqc60gcdv2bm54s6pywsm4i4cwbjsf64dzkl"))
2074 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
2075 (build-system gnu-build-system)
2078 ("gnuplot" ,gnuplot) ;for plots
2079 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
2081 `(("texinfo" ,texinfo)
2083 ("python" ,python)))
2086 (list "--enable-gcl"
2087 (string-append "--with-posix-shell="
2088 (assoc-ref %build-inputs "bash")
2090 (string-append "--with-wish="
2091 (assoc-ref %build-inputs "tk")
2093 (let ((v ,(package-version tk)))
2094 (string-take v (string-index-right v #\.)))))
2095 ;; By default Maxima attempts to write temporary files to
2096 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2097 ;; Work around that.
2098 #:make-flags (list "TMPDIR=/tmp")
2099 #:phases (alist-cons-before
2102 (chmod "src/maxima" #o555))
2103 ;; Make sure the doc and emacs files are found in the
2104 ;; standard location. Also configure maxima to find gnuplot
2105 ;; without having it on the PATH.
2107 'install 'post-install
2108 (lambda* (#:key outputs inputs #:allow-other-keys)
2109 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2110 (out (assoc-ref outputs "out"))
2111 (datadir (string-append out "/share/maxima/" ,version)))
2112 (with-directory-excursion out
2113 (mkdir-p "share/emacs")
2114 (mkdir-p "share/doc")
2116 (string-append datadir "/emacs/")
2117 (string-append out "/share/emacs/site-lisp"))
2119 (string-append datadir "/doc/")
2120 (string-append out "/share/doc/maxima"))
2121 (with-atomic-file-replacement
2122 (string-append datadir "/share/maxima-init.lisp")
2124 (format out "~a ~s~a~%"
2125 "(setf $gnuplot_command "
2126 (string-append gnuplot "/bin/gnuplot") ")")
2127 (dump-port in out))))))
2128 %standard-phases))))
2129 (home-page "http://maxima.sourceforge.net")
2130 (synopsis "Numeric and symbolic expression manipulation")
2131 (description "Maxima is a system for the manipulation of symbolic and
2132 numerical expressions. It yields high precision numeric results by using
2133 exact fractions, arbitrary precision integers, and variable precision floating
2135 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2136 ;; Others simply say "GNU General Public License" without stating a
2137 ;; version (which implicitly means gpl1+).
2138 ;; At least one file (src/maxima.asd) says "version 2."
2139 ;; GPLv2 only is therefore the smallest subset.
2140 (license license:gpl2)))
2142 (define-public wxmaxima
2145 ;; Versions 16.12.0 to 16.12.2 have a bug which causes output lines to
2146 ;; overlap. See <https://debbugs.gnu.org/25793>
2151 (uri (string-append "mirror://sourceforge/wxmaxima/wxMaxima/"
2152 version "/" name "-" version ".tar.gz"))
2155 "1fpqzk1921isiqrpgpf433ldq41924qs9sy99fl1zn5661b2l73n"))))
2156 (build-system gnu-build-system)
2158 `(("wxwidgets" ,wxwidgets)
2161 ("adwaita-icon-theme" ,adwaita-icon-theme)
2163 ("shared-mime-info" ,shared-mime-info)))
2165 `(#:phases (modify-phases %standard-phases
2167 'install 'wrap-program
2168 (lambda* (#:key inputs outputs #:allow-other-keys)
2169 (wrap-program (string-append (assoc-ref outputs "out")
2172 (,(string-append (assoc-ref inputs "maxima")
2174 ;; For GtkFileChooserDialog.
2175 `("GSETTINGS_SCHEMA_DIR" =
2176 (,(string-append (assoc-ref inputs "gtk+")
2177 "/share/glib-2.0/schemas")))
2178 `("XDG_DATA_DIRS" ":" prefix
2179 (;; Needed by gdk-pixbuf to know supported icon formats.
2181 (assoc-ref inputs "shared-mime-info") "/share")
2182 ;; The default icon theme of GTK+.
2184 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
2186 (home-page "https://andrejv.github.io/wxmaxima/")
2187 (synopsis "Graphical user interface for the Maxima computer algebra system")
2189 "wxMaxima is a graphical user interface for the Maxima computer algebra
2190 system. It eases the use of Maxima by making most of its commands available
2191 through a menu system and by providing input dialogs for commands that require
2192 more than one argument. It also implements its own display engine that
2193 outputs mathematical symbols directly instead of depicting them with ASCII
2196 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
2197 text and mathematical calculations to create documents, exporting of input and
2198 output to TeX, and a browser for Maxima's manual including command index and
2199 full text searching.")
2200 (license license:gpl2+)))
2202 (define-public armadillo
2208 (uri (string-append "mirror://sourceforge/arma/armadillo-"
2212 "1qqzy7dp891j9v7062mv1599hdwr97vqzrd3j2fl8c3gmc00dmzg"))))
2213 (build-system cmake-build-system)
2214 (arguments `(#:tests? #f)) ;no test target
2216 `(("openblas" ,openblas)
2218 ("arpack" ,arpack-ng)))
2219 (home-page "http://arma.sourceforge.net/")
2220 (synopsis "C++ linear algebra library")
2222 "Armadillo is a C++ linear algebra library, aiming towards a good balance
2223 between speed and ease of use. It is useful for algorithm development
2224 directly in C++, or quick conversion of research code into production
2225 environments. It can be used for machine learning, pattern recognition,
2226 signal processing, bioinformatics, statistics, econometrics, etc. The library
2227 provides efficient classes for vectors, matrices and cubes, as well as 150+
2228 associated functions (eg. contiguous and non-contiguous submatrix views).")
2229 (license license:asl2.0)))
2231 (define-public muparser
2232 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2233 ;; different hash. In order to make `guix package --upgrade` work correctly,
2234 ;; we set a Guix packaging revision.
2235 ;; When the next version of muparser is released, we can remove
2236 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2237 (let ((upstream-version "2.2.5")
2241 (version (string-append upstream-version "-" revision))
2245 (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
2246 upstream-version ".tar.gz"))
2247 (file-name (string-append name "-" version ".tar.gz"))
2250 "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
2251 (build-system gnu-build-system)
2253 `(#:configure-flags '("--enable-samples=no")
2254 #:tests? #f)) ;no "check" target
2255 (home-page "http://muparser.beltoforion.de/")
2256 (synopsis "Fast parser library for mathematical expressions")
2258 "muParser is an extensible high performance math parser library. It is
2259 based on transforming an expression into a bytecode and precalculating constant
2261 (license license:expat))))
2263 (define-public openblas
2270 (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
2272 (file-name (string-append name "-" version ".tar.gz"))
2275 "071zqnmnxhh0c9phzyn3f198yxa0hjxda7016azdbq2056sm70w7"))))
2276 (build-system gnu-build-system)
2278 `(#:tests? #f ;no "check" target
2279 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
2280 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2281 ;; we need to disable substitutions.
2283 ,(let ((system (or (%current-target-system) (%current-system))))
2284 (or (string-prefix? "x86_64" system)
2285 (string-prefix? "i686" system)
2286 (string-prefix? "mips" system)
2287 (string-prefix? "aarch64" system)))
2289 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
2292 ;; Build the library for all supported CPUs. This allows
2293 ;; switching CPU targets at runtime with the environment variable
2294 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
2295 ;; Unfortunately, this is not supported on non-x86 architectures,
2296 ;; where it leads to failed builds.
2297 ,@(let ((system (or (%current-target-system) (%current-system))))
2299 ((or (string-prefix? "x86_64" system)
2300 (string-prefix? "i686" system))
2301 '("DYNAMIC_ARCH=1"))
2302 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
2303 ;; two available MIPS targets special extended instructions
2304 ;; for Loongson cores are used.
2305 ((string-prefix? "mips" system)
2306 '("TARGET=SICORTEX"))
2307 ;; On aarch64 force the generic 'armv8-a' target
2308 ((string-prefix? "aarch64" system)
2311 ;; no configure script
2312 #:phases (alist-delete 'configure %standard-phases)))
2314 `(("fortran" ,gfortran)))
2318 (home-page "http://www.openblas.net/")
2319 (synopsis "Optimized BLAS library based on GotoBLAS")
2321 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
2322 (license license:bsd-3)))
2324 (define-public openlibm
2331 (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
2333 (file-name (string-append name "-" version ".tar.gz"))
2336 "11czx2z7nh6dfpz45s3xl7v38hw36jxzxfvny454bk3if14pfakq"))))
2337 (build-system gnu-build-system)
2340 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2342 ;; no configure script
2343 (alist-delete 'configure %standard-phases)
2344 #:tests? #f)) ;the tests are part of the default target
2345 (home-page "http://openlibm.org/")
2346 (synopsis "Portable C mathematical library (libm)")
2348 "OpenLibm is an effort to have a high quality, portable, standalone C
2349 mathematical library (libm). It can be used standalone in applications and
2350 programming language implementations. The project was born out of a need to
2351 have a good libm for the Julia programming language that worked consistently
2352 across compilers and operating systems, and in 32-bit and 64-bit
2354 ;; Each architecture has its own make target, and there is none for mips.
2355 (supported-systems (delete "mips64el-linux" %supported-systems))
2356 ;; See LICENSE.md for details.
2357 (license (list license:expat
2360 license:public-domain
2361 license:lgpl2.1+))))
2363 (define-public openspecfun
2365 (name "openspecfun")
2370 (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
2372 (file-name (string-append name "-" version ".tar.gz"))
2375 "1y5b2h6f2k72536kym3vzy3li3bhpd23x463g7hdmjdi3cncavz1"))))
2376 (build-system gnu-build-system)
2378 '(#:tests? #f ;no "check" target
2380 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2381 ;; no configure script
2382 #:phases (alist-delete 'configure %standard-phases)))
2384 `(("fortran" ,gfortran)))
2385 (home-page "https://github.com/JuliaLang/openspecfun")
2386 (synopsis "Collection of special mathematical functions")
2388 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
2389 portable package for Bessel Functions of a Complex Argument and Nonnegative
2390 Order; it contains subroutines for computing Bessel functions and Airy
2391 functions. Faddeeva allows computing the various error functions of arbitrary
2392 complex arguments (Faddeeva function, error function, complementary error
2393 function, scaled complementary error function, imaginary error function, and
2394 Dawson function); given these, one can also easily compute Voigt functions,
2395 Fresnel integrals, and similar related functions as well.")
2396 ;; Faddeeva is released under the Expat license; AMOS is included as
2397 ;; public domain software.
2398 (license (list license:expat license:public-domain))))
2400 (define-public suitesparse
2402 (name "suitesparse")
2408 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
2412 "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5"))))
2413 (build-system gnu-build-system)
2415 '(#:parallel-build? #f ;cholmod build fails otherwise
2416 #:tests? #f ;no "check" target
2421 "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used
2422 (string-append "INSTALL_LIB="
2423 (assoc-ref %outputs "out") "/lib")
2424 (string-append "INSTALL_INCLUDE="
2425 (assoc-ref %outputs "out") "/include"))
2428 'install 'prepare-out
2429 ;; README.txt states that the target directories must exist prior to
2430 ;; running "make install".
2432 (mkdir-p (string-append (assoc-ref %outputs "out") "/lib"))
2433 (mkdir-p (string-append (assoc-ref %outputs "out") "/include")))
2434 ;; no configure script
2435 (alist-delete 'configure %standard-phases))))
2438 ("lapack" ,lapack)))
2439 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
2440 (synopsis "Suite of sparse matrix software")
2442 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
2443 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
2444 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
2445 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
2446 CXSparse, a concise sparse Cholesky factorization package; and many other
2449 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
2451 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
2452 (license (list license:gpl2+ license:lgpl2.1+))))
2454 (define-public atlas
2460 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
2461 version "/atlas" version ".tar.bz2"))
2464 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
2465 (build-system gnu-build-system)
2466 (home-page "http://math-atlas.sourceforge.net/")
2467 (inputs `(("gfortran" ,gfortran)
2468 ("lapack-tar" ,(package-source lapack))))
2469 (outputs '("out" "doc"))
2470 ;; For the moment we drop support for MIPS at it fails to compile. See
2471 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
2472 (supported-systems (delete "mips64el-linux" %supported-systems))
2474 `(#:parallel-build? #f
2475 #:parallel-tests? #f
2477 ;; ATLAS tunes itself for the machine it is built on, as explained at
2478 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
2479 ;; For this reason, we want users to build it locally instead of using
2483 #:modules ((srfi srfi-26)
2485 (guix build gnu-build-system)
2488 `(;; Generate position independent code suitable for dynamic libraries
2489 ;; and use WALL timer to get more accurate timing.
2490 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
2493 ,,(if (string-match "64" (%current-system))
2496 ;; Disable parallel build as it gives errors: atlas_pthread.h is
2497 ;; needed to compile C files before it is generated.
2498 "-Ss" "pmake" "make -j 1"
2499 ;; Probe is failing for MIPS. We therefore define the system
2500 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
2501 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
2502 ,,@(if (string-prefix? "mips" (%current-system))
2503 (list "-A" "49" "-V" "1")
2505 ;; Generate shared libraries.
2507 ;; Build a full LAPACK library.
2508 ,(string-append "--with-netlib-lapack-tarfile="
2509 (assoc-ref %build-inputs "lapack-tar")))
2511 (modify-phases %standard-phases
2512 (add-after 'install 'install-doc
2513 (lambda* (#:key outputs inputs #:allow-other-keys)
2514 (let ((doc (string-append (assoc-ref outputs "doc")
2515 "/share/doc/atlas")))
2517 (fold (lambda (file previous)
2518 (and previous (zero? (system* "cp" file doc))))
2519 #t (find-files "../ATLAS/doc" ".*")))))
2520 (add-after 'check 'check-pt
2521 (lambda _ (zero? (system* "make" "ptcheck"))))
2522 ;; Fix files required to run configure.
2523 (add-before 'configure 'fix-/bin/sh
2525 ;; Use `sh', not `/bin/sh'.
2526 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
2529 ;; Fix /bin/sh in generated make files.
2530 (add-after 'configure 'fix-/bin/sh-in-generated-files
2532 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
2535 ;; ATLAS configure program does not accepts the default flags
2536 ;; passed by the 'gnu-build-system'.
2538 (lambda* (#:key native-inputs inputs outputs
2539 (configure-flags '())
2540 #:allow-other-keys #:rest args)
2541 (let* ((prefix (assoc-ref outputs "out"))
2542 (bash (or (and=> (assoc-ref
2543 (or native-inputs inputs) "bash")
2544 (cut string-append <> "/bin/bash"))
2546 (flags `(,(string-append "--prefix=" prefix)
2548 (abs-srcdir (getcwd))
2549 (srcdir (string-append "../" (basename abs-srcdir))))
2550 (format #t "source directory: ~s (relative from build: ~s)~%"
2554 (format #t "build directory: ~s~%" (getcwd))
2555 (format #t "configure flags: ~s~%" flags)
2556 (zero? (apply system* bash
2557 (string-append srcdir "/configure")
2559 (synopsis "Automatically Tuned Linear Algebra Software")
2561 "ATLAS is an automatically tuned linear algebra software library
2562 providing C and Fortran77 interfaces to a portably efficient BLAS
2563 implementation, as well as a few routines from LAPACK.
2565 Optimization occurs at build time. For this reason, the library is built on
2566 the machine where it is installed, without resorting to pre-built substitutes.
2568 Before building the library, CPU throttling should be disabled. This can be
2569 done in the BIOS, or, on GNU/Linux, with the following command:
2572 # cpupower --governor performance
2575 Failure to do so will result in a library with poor performance.")
2576 (license license:bsd-3)))
2585 (uri (string-append "mirror://sourceforge/ogl-math/glm-" version
2586 "/glm-" version ".zip"))
2589 "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l"))))
2590 (build-system cmake-build-system)
2592 `(("unzip" ,unzip)))
2593 (home-page "http://glm.g-truc.net")
2594 (synopsis "OpenGL Mathematics library")
2595 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
2596 library for graphics software based on the OpenGL Shading Language (GLSL)
2598 (license license:expat)))
2600 (define-public lpsolve
2607 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
2608 "/lp_solve_" version "_source.tar.gz"))
2611 "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq"))
2612 (modules '((guix build utils)))
2614 '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
2616 ;; Pretend to be on a 64 bit platform to obtain a common directory
2617 ;; name for the build results on all architectures; nothing else
2618 ;; seems to depend on it.
2619 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
2621 ;; The check for 'isnan' as it is written fails with
2622 ;; "non-floating-point argument in call to function
2623 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
2624 ;; definition, which in turn leads to bad things. Fix the feature
2626 (("isnan\\(0\\)") "isnan(0.)")))))
2627 (build-system gnu-build-system)
2629 `(#:tests? #f ; no check target
2631 (modify-phases %standard-phases
2635 (and (with-directory-excursion "lpsolve55"
2636 (zero? (system* "bash" "ccc")))
2637 (with-directory-excursion "lp_solve"
2638 (zero? (system* "bash" "ccc"))))))
2640 (lambda* (#:key outputs #:allow-other-keys)
2641 (let* ((out (assoc-ref outputs "out"))
2642 (bin (string-append out "/bin"))
2643 (lib (string-append out "/lib"))
2644 ;; This is where LibreOffice expects to find the header
2645 ;; files, and where they are installed by Debian.
2646 (include (string-append out "/include/lpsolve")))
2648 (copy-file "lpsolve55/bin/ux64/liblpsolve55.a"
2649 (string-append lib "/liblpsolve55.a"))
2650 (copy-file "lpsolve55/bin/ux64/liblpsolve55.so"
2651 (string-append lib "/liblpsolve55.so"))
2652 (install-file "lp_solve/bin/ux64/lp_solve" bin)
2654 ;; Install a subset of the header files as on Debian
2655 ;; (plus lp_bit.h, which matches the regular expression).
2656 (for-each (lambda (name)
2657 (install-file name include))
2658 (find-files "." "lp_[HMSa-z].*\\.h$"))
2659 (with-directory-excursion "shared"
2660 (for-each (lambda (name)
2661 (install-file name include))
2662 (find-files "." "\\.h$")))
2664 (home-page "http://lpsolve.sourceforge.net/")
2665 (synopsis "Mixed integer linear programming (MILP) solver")
2667 "lp_solve is a mixed integer linear programming solver based on the
2668 revised simplex and the branch-and-bound methods.")
2669 (license license:lgpl2.1+)))
2671 (define-public dealii
2678 (uri (string-append "https://github.com/dealii/dealii/releases/"
2679 "download/v" version "/dealii-" version ".tar.gz"))
2682 "1bdksvvyp1rj37df1ndh8j3x9nzpc3sazw8nd0hzvnlw0qnyk800"))
2683 (modules '((guix build utils)))
2685 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
2686 '(delete-file-recursively "bundled"))))
2687 (build-system cmake-build-system)
2695 ("arpack" ,arpack-ng)
2696 ("muparser" ,muparser)
2697 ("gfortran" ,gfortran)
2698 ("suitesparse" ,suitesparse))) ;for UMFPACK
2700 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
2701 #:configure-flags '("-DCOMPAT_FILES=OFF") ;Follow new directory structure
2702 #:phases (modify-phases %standard-phases
2704 'install 'hint-example-prefix
2705 ;; Set Cmake hints in examples so that they can find this
2706 ;; deal.II when configuring.
2707 (lambda* (#:key outputs #:allow-other-keys)
2708 (let* ((out (assoc-ref %outputs "out"))
2709 (exmpl (string-append out "/share/doc"
2710 "/dealii/examples")))
2711 (substitute* (find-files exmpl "CMakeLists.txt")
2712 (("([[:space:]]*HINTS.*)\n" _ line)
2713 (string-append line " $ENV{HOME}/.guix-profile "
2716 (home-page "https://www.dealii.org")
2717 (synopsis "Finite element library")
2719 "Deal.II is a C++ program library targeted at the computational solution
2720 of partial differential equations using adaptive finite elements. The main
2721 aim of deal.II is to enable rapid development of modern finite element codes,
2722 using among other aspects adaptive meshes and a wide array of tools often used
2723 in finite element programs.")
2724 (license license:lgpl2.1+)))
2726 (define-public dealii-openmpi
2727 (package (inherit dealii)
2728 (name "dealii-openmpi")
2731 ;;Supported only with MPI:
2732 ("p4est" ,p4est-openmpi)
2733 ("petsc" ,petsc-openmpi)
2734 ("slepc" ,slepc-openmpi)
2735 ("metis" ,metis) ;for MUMPS
2736 ("scalapack" ,scalapack) ;for MUMPS
2737 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
2738 ("arpack" ,arpack-ng-openmpi)
2739 ,@(fold alist-delete (package-inputs dealii)
2740 '("p4est" "arpack"))))
2742 (substitute-keyword-arguments (package-arguments dealii)
2743 ((#:configure-flags cf)
2744 ``("-DMPI_C_COMPILER=mpicc"
2745 "-DMPI_CXX_COMPILER=mpicxx"
2746 "-DMPI_Fortran_COMPILER=mpifort"
2748 (synopsis "Finite element library (with MPI support)")))
2750 (define-public flann
2759 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
2760 version "-src.zip"))
2763 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))))
2764 (build-system cmake-build-system)
2766 "octave")) ;46 MiB .mex file that pulls Octave
2768 `(("unzip" ,unzip)))
2772 ("python" ,python-2) ; print syntax
2773 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
2776 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
2777 ;; taken 46 MiB unstripped, and 6 MiB stripped.
2778 #:strip-directories '("lib" "lib64" "libexec"
2779 "bin" "sbin" "share/flann/octave")
2781 ;; Save 12 MiB by not installing .a files. Passing
2782 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
2783 #:phases (modify-phases %standard-phases
2784 (add-before 'configure 'set-octave-directory
2785 (lambda* (#:key outputs #:allow-other-keys)
2786 ;; Install the .mex file in the "octave" output.
2787 (let ((out (assoc-ref outputs "octave")))
2788 (substitute* "src/matlab/CMakeLists.txt"
2789 (("share/flann/octave")
2790 (string-append out "/share/flann/octave")))
2792 (add-after 'install 'remove-static-libraries
2793 (lambda* (#:key outputs #:allow-other-keys)
2794 (let* ((out (assoc-ref outputs "out"))
2795 (lib (string-append out "/lib")))
2796 (for-each delete-file
2797 (find-files lib "\\.a$"))
2800 #:tests? #f)) ; The test data are downloaded from the Internet.
2801 (home-page "http://www.cs.ubc.ca/research/flann/")
2802 (synopsis "Library for approximate nearest neighbors computation")
2803 (description "FLANN is a library for performing fast approximate
2804 nearest neighbor searches in high dimensional spaces. It implements a
2805 collection of algorithms and a system for automatically choosing the best
2806 algorithm and optimum parameters depending on the dataset.
2808 FLANN is written in C++ and contains bindings for C, Octave and Python.")
2809 (license (license:non-copyleft "file://COPYING"
2810 "See COPYING in the distribution."))))
2812 (define-public wcalc
2819 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
2820 "wcalc-" version ".tar.bz2"))
2823 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
2824 (build-system gnu-build-system)
2827 ("readline" ,readline)))
2828 (home-page "http://w-calc.sourceforge.net/index.php")
2829 (synopsis "Flexible command-line scientific calculator")
2830 (description "Wcalc is a very capable calculator. It has standard functions
2831 (sin, asin, and sinh for example, in either radians or degrees), many
2832 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
2833 variables, a command history, hex/octal/binary input and output, unit
2834 conversions, embedded comments, and an expandable expression entry field. It
2835 evaluates expressions using the standard order of operations.")
2836 (license license:gpl2+)))
2844 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
2845 "/xaos-" version ".tar.gz"))
2848 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
2849 (build-system gnu-build-system)
2850 (native-inputs `(("gettext" ,gettext-minimal)))
2851 (inputs `(("libx11" ,libx11)
2856 `(#:tests? #f ;no "check" target
2857 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
2858 (synopsis "Real-time fractal zoomer")
2859 (description "GNU XaoS is a graphical program that generates fractal
2860 patterns and allows you to zoom in and out of them infinitely in a fluid,
2861 continuous manner. It also includes tutorials that help to explain how fractals
2862 are built. It can generate many different fractal types such as the Mandelbrot
2864 (home-page "https://www.gnu.org/software/xaos/")
2865 (license license:gpl2+)))
2867 (define-public hypre
2873 (uri (string-append "https://github.com/LLNL/hypre/archive/"
2874 "v" version ".tar.gz"))
2875 (file-name (string-append name "-" version ".tar.gz"))
2878 "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m"))
2879 (modules '((guix build utils)))
2882 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
2883 ;; substitute the tarball creation time.
2884 (substitute* "src/utilities/HYPRE_utilities.h"
2885 (("Date Compiled: .*$")
2886 "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n"))
2888 (build-system gnu-build-system)
2889 (outputs '("out" ;6.1 MiB of headers and libraries
2890 "doc")) ;4.8 MiB of documentation
2894 ("texlive" ,texlive) ;full package required for fonts
2895 ("ghostscript" ,ghostscript)))
2897 `(("blas" ,openblas)
2898 ("lapack" ,lapack)))
2900 `(#:modules ((srfi srfi-1)
2901 ,@%gnu-build-system-modules)
2902 #:configure-flags '("--enable-shared"
2910 (modify-phases %standard-phases
2911 (add-before 'configure 'chdir-src
2912 (lambda _ (chdir "src")))
2914 (lambda* (#:key build target configure-flags
2915 #:allow-other-keys #:rest args)
2916 (let* ((configure (assoc-ref %standard-phases 'configure)))
2919 (list #:configure-flags
2920 (cons (string-append
2921 "--host=" (or target build))
2922 configure-flags)))))))
2923 (add-after 'build 'build-docs
2925 (zero? (system* "make" "-Cdocs" "pdf" "html"))))
2928 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
2929 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
2930 (and (system* "make" "check" "CHECKRUN=")
2931 (fold (lambda (filename result)
2933 (let ((size (stat:size (stat filename))))
2934 (when (not (zero? size))
2935 (format #t "~a size ~d; error indication~%"
2939 (find-files "test" ".*\\.err$")))))
2940 (add-after 'install 'install-docs
2941 (lambda* (#:key outputs #:allow-other-keys)
2942 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
2943 (let* ((doc (assoc-ref outputs "doc"))
2944 (docdir (string-append doc "/share/doc/hypre-" ,version)))
2945 (with-directory-excursion "docs"
2946 (for-each (lambda (base)
2947 (install-file (string-append base ".pdf") docdir)
2948 (copy-recursively base docdir)) ;html docs
2949 '("HYPRE_usr_manual"
2950 "HYPRE_ref_manual")))
2952 (home-page "http://www.llnl.gov/casc/hypre/")
2953 (synopsis "Library of solvers and preconditioners for linear equations")
2955 "HYPRE is a software library of high performance preconditioners and
2956 solvers for the solution of large, sparse linear systems of equations. It
2957 features multigrid solvers for both structured and unstructured grid
2959 (license license:lgpl2.1)))
2961 (define-public hypre-openmpi
2962 (package (inherit hypre)
2963 (name "hypre-openmpi")
2966 ,@(package-inputs hypre)))
2968 (substitute-keyword-arguments (package-arguments hypre)
2969 ((#:configure-flags flags)
2971 ,@(delete "--without-MPI" ,flags)))))
2972 (synopsis "Parallel solvers and preconditioners for linear equations")
2974 "HYPRE is a software library of high performance preconditioners and
2975 solvers for the solution of large, sparse linear systems of equations on
2976 parallel computers. It features parallel multigrid solvers for both
2977 structured and unstructured grid problems.")))
2979 (define-public matio
2986 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
2987 "matio-" version ".tar.gz"))
2990 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
2991 (build-system gnu-build-system)
2995 (home-page "http://matio.sourceforge.net/")
2996 (synopsis "Library for reading and writing MAT files")
2997 (description "Matio is a library for reading and writing MAT files. It
2998 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
2999 (license license:bsd-2)))
3001 (define-public libhilbert
3008 (uri (string-append "http://web.cs.dal.ca/~chamilto/hilbert/"
3009 "libhilbert-" version ".tar.gz"))
3012 "0v48x8405dj95gjn2saja4bzhw86d6zl6d3dg8h7dzac2qr97s34"))))
3013 (build-system gnu-build-system)
3014 (home-page "http://web.cs.dal.ca/~chamilto/hilbert")
3015 (synopsis "Hilbert indices for multidimensional data")
3016 (description "The libhilbert library can efficiently calculate Hilbert
3017 curves and order-preserving representations of Hilbert curve indices that use
3018 the same amount of space as the original point representation. This is useful
3019 when using the Gilbert curve as a space filling curve through a
3020 high-dimensional space where not all demensions have the same cardinality.")
3021 (license license:lgpl2.1+)))
3028 (origin (method url-fetch)
3029 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3030 "download/" version "/Vc-" version ".tar.gz"))
3033 "1rh6dhqar3y07n4xqyml0sa0v48qv3ch9dc3yc2in855hlh4vnqi"))))
3034 (build-system cmake-build-system)
3037 '("-DBUILD_TESTING=ON")))
3038 (synopsis "SIMD vector classes for C++")
3039 (description "Vc provides portable, zero-overhead C++ types for explicitly
3040 data-parallel programming. It is a library designed to ease explicit
3041 vectorization of C++ code. Its types enable explicitly stating data-parallel
3042 operations on multiple values. The parallelism is therefore added via the type
3043 system. Vc has an intuitive API and provides portability between different
3044 compilers and compiler versions as well as portability between different vector
3045 instruction sets. Thus, an application written with Vc can be compiled for:
3048 @item SSE2 up to SSE4.2 or SSE4a
3051 @item NEON (in development)
3052 @item NVIDIA GPUs / CUDA (in development)
3054 (home-page "https://github.com/VcDevel/Vc")
3055 (license license:bsd-3)))
3057 (define-public reducelcs
3058 ;; This is the last commit which is available upstream, no
3059 ;; release happened since 2010.
3060 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
3064 (version (string-append "1.0-" revision "." (string-take commit 7)))
3069 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
3071 (file-name (string-append name "-" version "-checkout"))
3074 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
3075 (build-system gnu-build-system)
3077 `(("openlibm" ,openlibm)))
3079 `(#:tests? #f ; no tests
3081 (modify-phases %standard-phases
3082 (delete 'configure) ; No configure script exists.
3083 (replace 'install ; No install phase exists.
3084 (lambda* (#:key outputs #:allow-other-keys)
3085 (let* ((out (assoc-ref outputs "out"))
3086 (bin (string-append out "/bin")))
3087 (install-file "Approximation" bin)
3088 (install-file "CollectResults" bin)
3089 (install-file "GenerateInstances" bin)
3091 (synopsis "Approximate Longest Commons Subsequence computation tool")
3093 "@code{reduceLCS} is an implementation of the Reduce-Expand
3094 algorithm for LCS. It is a fast program to compute the approximate
3095 Longest Commons Subsequence of a set of strings.")
3096 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
3097 (license license:gpl3+))))
3099 (define-public jacal
3106 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
3109 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
3110 (patches (search-patches "jacal-fix-texinfo.patch"))))
3111 (build-system gnu-build-system)
3114 (modify-phases %standard-phases
3115 (add-before 'build 'pre-build
3116 ;; Don't use upstream's script - it really doesn't fit into
3117 ;; Guix's functional paradigm.
3118 (lambda* (#:key inputs outputs #:allow-other-keys)
3119 (substitute* "Makefile"
3120 (("^install: install-script") "install: "))))
3121 (add-after 'install 'post-install
3122 ;; Instead, we provide our own simplified script.
3123 (lambda* (#:key inputs outputs #:allow-other-keys)
3124 (let ((wrapper (string-append (assoc-ref outputs "out")
3126 (format (open wrapper (logior O_WRONLY O_CREAT))
3127 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
3128 "-e '(slib:load \"~a/lib/jacal/math\") "
3131 (assoc-ref inputs "scm")
3132 (assoc-ref outputs "out"))
3133 (chmod wrapper #o555))))
3135 (lambda* (#:key inputs outputs #:allow-other-keys)
3136 (zero? (system* "./configure"
3137 (string-append "--prefix="
3138 (assoc-ref outputs "out")))))))))
3139 (inputs `(("scm" ,scm)))
3140 (native-inputs `(("unzip" ,unzip)
3141 ("texinfo" ,texinfo)))
3142 (synopsis "Symbolic mathematics system")
3143 (description "GNU JACAL is an interactive symbolic mathematics program based on
3144 Scheme. It manipulate and simplify a range of mathematical expressions such
3145 as equations, scalars, vectors, and matrices.")
3146 (home-page "https://www.gnu.org/software/jacal/")
3147 (license license:gpl3+)))