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 John Darrington <jmd@gnu.org>
5 ;;; Copyright © 2014, 2015, 2016 Eric Bavier <bavier@member.fsf.org>
6 ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
7 ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
8 ;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
9 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
10 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
11 ;;; Copyright © 2015, 2016 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 Ludovic Courtès <ludo@gnu.org>
16 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
17 ;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be>
19 ;;; This file is part of GNU Guix.
21 ;;; GNU Guix is free software; you can redistribute it and/or modify it
22 ;;; under the terms of the GNU General Public License as published by
23 ;;; the Free Software Foundation; either version 3 of the License, or (at
24 ;;; your option) any later version.
26 ;;; GNU Guix is distributed in the hope that it will be useful, but
27 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
28 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
29 ;;; GNU General Public License for more details.
31 ;;; You should have received a copy of the GNU General Public License
32 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
34 (define-module (gnu packages maths)
35 #:use-module (ice-9 regex)
36 #:use-module (gnu packages)
37 #:use-module ((guix licenses) #:prefix license:)
38 #:use-module (guix packages)
39 #:use-module (guix download)
40 #:use-module (guix utils)
41 #:use-module (guix build utils)
42 #:use-module (guix build-system cmake)
43 #:use-module (guix build-system gnu)
44 #:use-module (guix build-system r)
45 #:use-module (gnu packages algebra)
46 #:use-module (gnu packages bison)
47 #:use-module (gnu packages boost)
48 #:use-module (gnu packages check)
49 #:use-module (gnu packages cmake)
50 #:use-module (gnu packages compression)
51 #:use-module (gnu packages curl)
52 #:use-module (gnu packages cyrus-sasl)
53 #:use-module (gnu packages documentation)
54 #:use-module (gnu packages elf)
55 #:use-module (gnu packages flex)
56 #:use-module (gnu packages fltk)
57 #:use-module (gnu packages fontutils)
58 #:use-module (gnu packages gettext)
59 #:use-module (gnu packages gcc)
60 #:use-module (gnu packages gd)
61 #:use-module (gnu packages ghostscript)
62 #:use-module (gnu packages graphviz)
63 #:use-module (gnu packages gtk)
64 #:use-module (gnu packages image)
65 #:use-module (gnu packages less)
66 #:use-module (gnu packages lisp)
67 #:use-module (gnu packages logging)
68 #:use-module (gnu packages gnome)
69 #:use-module (gnu packages guile)
70 #:use-module (gnu packages xorg)
71 #:use-module (gnu packages gl)
72 #:use-module (gnu packages m4)
73 #:use-module (gnu packages mpi)
74 #:use-module (gnu packages multiprecision)
75 #:use-module (gnu packages netpbm)
76 #:use-module (gnu packages pcre)
77 #:use-module (gnu packages popt)
78 #:use-module (gnu packages perl)
79 #:use-module (gnu packages pkg-config)
80 #:use-module (gnu packages python)
81 #:use-module (gnu packages readline)
82 #:use-module (gnu packages tbb)
83 #:use-module (gnu packages shells)
84 #:use-module (gnu packages tcl)
85 #:use-module (gnu packages texinfo)
86 #:use-module (gnu packages tex)
87 #:use-module (gnu packages tls)
88 #:use-module (gnu packages wxwidgets)
89 #:use-module (gnu packages xml)
90 #:use-module (gnu packages zip)
91 #:use-module (srfi srfi-1))
93 (define-public c-graph
99 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
102 "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
103 (build-system gnu-build-system)
105 `(("fortran" ,gfortran)))
106 (synopsis "Visualizing and demonstrating convolution")
108 "GNU C-Graph is a tool for demonstrating the theory of convolution.
109 Thus, it can serve as an excellent aid to students of signal and systems
110 theory in visualizing the convolution process. Rather than forcing the
111 student to write code, the program offers an intuitive interface with
112 interactive dialogs to guide them.")
113 (license license:gpl3+)
114 (home-page "http://www.gnu.org/software/c-graph/")))
123 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
124 version "/coda-" version ".tar.gz"))
126 (base32 "04b9l3wzcix0mnfq77mwnil6cbr8h2mki8myvy0lzn236qcwaq1h"))
127 (patches (search-patches "coda-use-system-libs.patch"))
128 (modules '((guix build utils)))
130 ;; Make sure we don't use the bundled software.
131 '(for-each (lambda (d)
132 (delete-file-recursively (string-append "libcoda/" d)))
133 '("zlib" "pcre" "expat")))))
135 `(("fortran" ,gfortran)
137 ("python-numpy" ,python-numpy)))
144 (build-system gnu-build-system)
146 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
147 "LIBS= -lz -lpcre -lexpat")))
148 (synopsis "A common interface to various earth observation data formats")
150 "The Common Data Access toolbox (CODA) provides a set of interfaces for
151 reading remote sensing data from earth observation data files. It consists of
152 command line applications and interfaces to the C, Fortran, Python, and Java
153 programming languages.")
154 (home-page "https://stcorp.nl/coda")
155 (license license:gpl2+)))
163 (uri (string-append "mirror://gnu/units/units-" version
166 "1awhjw9zjlfb8s5g3yyx63f7ddfcr1sanlbxpqifmrgq24ql198b"))))
167 (build-system gnu-build-system)
168 (synopsis "Conversion between thousands of scales")
170 "GNU Units converts numeric quantities between units of measure. It
171 can handle scale changes through adaptive usage of standard scale
172 prefixes (micro-, kilo-, etc.). It can also handle nonlinear
173 conversions such as Fahrenheit to Celsius. Its interpreter is powerful
174 enough to be used effectively as a scientific calculator.")
175 (license license:gpl3+)
176 (home-page "http://www.gnu.org/software/units/")))
178 (define-public double-conversion
180 (name "double-conversion")
185 "https://github.com/floitsch/double-conversion/archive/v"
187 (file-name (string-append name "-" version ".tar.gz"))
190 "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83"))))
191 (build-system cmake-build-system)
193 '(#:test-target "test"
194 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
195 "-DBUILD_TESTING=ON")))
196 (home-page "https://github.com/floitsch/double-conversion")
197 (synopsis "Conversion routines for IEEE doubles")
199 "The double-conversion library provides binary-decimal and decimal-binary
200 routines for IEEE doubles. The library consists of efficient conversion
201 routines that have been extracted from the V8 JavaScript engine.")
202 (license license:bsd-3)))
204 (define-public dionysus
210 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
214 "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs"))))
215 (build-system gnu-build-system)
216 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
217 (synopsis "Local search for universal constants and scientific values")
219 "GNU Dionysus is a convenient system for quickly retrieving the values of
220 mathematical constants used in science and engineering. Values can be
221 searched using a simple command-line tool, choosing from three databases:
222 universal constants, atomic numbers, and constants related to
224 (license license:gpl3+)
225 (home-page "http://www.gnu.org/software/dionysus/")))
233 (uri (string-append "mirror://gnu/gsl/gsl-"
237 "1yxdzqjwmi2aid650fa9zyr8llw069x7lm489wx9nnfdi6vh09an"))
238 (patches (search-patches "gsl-test-i686.patch"))))
239 (build-system gnu-build-system)
241 `(#:parallel-tests? #f))
242 (home-page "http://www.gnu.org/software/gsl/")
243 (synopsis "Numerical library for C and C++")
245 "The GNU Scientific Library is a library for numerical analysis in C
246 and C++. It includes a wide range of mathematical routines, with over 1000
247 functions in total. Subject areas covered by the library include:
248 differential equations, linear algebra, Fast Fourier Transforms and random
250 (license license:gpl3+)))
259 (uri (string-append "mirror://gnu/glpk/glpk-"
263 "15z2ymzqhxwss6wgdj5f7vkyqlqdsjgrvm0x871kmlx0n0664mhk"))))
264 (build-system gnu-build-system)
268 `(#:configure-flags '("--with-gmp")))
269 (home-page "http://www.gnu.org/software/glpk/")
270 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
272 "GLPK is a C library for solving large-scale linear programming (LP),
273 mixed integer programming (MIP), and other related problems. It supports the
274 GNU MathProg modeling language, a subset of the AMPL language, and features a
275 translator for the language. In addition to the C library, a stand-alone
276 LP/MIP solver is included in the package.")
277 (license license:gpl3+)))
286 (uri (string-append "http://www.4ti2.de/version_" version
287 "/4ti2-" version ".tar.gz"))
290 "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
291 (build-system gnu-build-system)
293 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
297 (home-page "http://www.4ti2.de/")
298 (synopsis "Mathematical tool suite for problems on linear spaces")
300 "4ti2 implements algorithms for solving algebraic, geometric and
301 combinatorial problems on linear spaces. Among others, it solves systems
302 of linear equations, computes extreme rays of polyhedral cones, solves
303 integer programming problems and computes Markov bases for statistics.")
304 (license license:gpl2+)))
306 (define-public cddlib
313 (uri (string-append "ftp://ftp.ifor.math.ethz.ch/pub/fukuda/cdd/cddlib-"
314 (string-delete #\. version) ".tar.gz"))
317 "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy"))))
318 (build-system gnu-build-system)
321 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
322 (synopsis "Library for convex hulls and extreme rays of polyhedra")
324 "The C-library cddlib implements the Double Description Method of
325 Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
326 rays of a general convex polyhedron given by a system of linear inequalities
327 in arbitrary dimension. It can also be used for the converse operation of
328 computing convex hulls.")
329 (license license:gpl2+)))
331 (define-public arpack-ng
338 (uri (string-append "https://github.com/opencollab/arpack-ng/archive/"
340 (file-name (string-append name "-" version ".tar.gz"))
343 "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff"))))
344 (build-system gnu-build-system)
345 (home-page "https://github.com/opencollab/arpack-ng")
348 ("fortran" ,gfortran)))
349 (synopsis "Fortran subroutines for solving eigenvalue problems")
351 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
352 large scale eigenvalue problems.")
353 (license (license:non-copyleft "file://COPYING"
354 "See COPYING in the distribution."))))
356 (define-public arpack-ng-openmpi
357 (package (inherit arpack-ng)
358 (name "arpack-ng-openmpi")
361 ,@(package-inputs arpack-ng)))
362 (arguments `(#:configure-flags '("--enable-mpi")))
363 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
365 (define-public lapack
372 (uri (string-append "http://www.netlib.org/lapack/lapack-"
376 "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s"))))
377 (build-system cmake-build-system)
378 (home-page "http://www.netlib.org/lapack/")
379 (inputs `(("fortran" ,gfortran)
380 ("python" ,python-2)))
382 `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
384 #:phases (alist-cons-before
386 (lambda* (#:key inputs #:allow-other-keys)
387 (let ((python (assoc-ref inputs "python")))
388 (substitute* "lapack_testing.py"
389 (("/usr/bin/env python") python))))
391 (synopsis "Library for numerical linear algebra")
393 "LAPACK is a Fortran 90 library for solving the most commonly occurring
394 problems in numerical linear algebra.")
395 (license (license:non-copyleft "file://LICENSE"
396 "See LICENSE in the distribution."))))
398 (define-public scalapack
405 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
409 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
410 (build-system cmake-build-system)
413 ("fortran" ,gfortran)
414 ("lapack" ,lapack))) ;for testing only
416 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")))
417 (home-page "http://www.netlib.org/scalapack/")
418 (synopsis "Library for scalable numerical linear algebra")
420 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
421 routines on parallel distributed memory machines. ScaLAPACK solves dense and
422 banded linear systems, least squares problems, eigenvalue problems, and
423 singular value problems.")
424 (license (license:bsd-style "file://LICENSE"
425 "See LICENSE in the distribution."))))
427 (define-public gnuplot
433 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
438 "0lr065qdlgss8lmy31l7hkmnk9fp4lvqq9qgb1f1209f36zy1wr5"))))
439 (build-system gnu-build-system)
440 (inputs `(("readline" ,readline)
444 (native-inputs `(("pkg-config" ,pkg-config)
445 ("texlive" ,texlive-minimal)))
446 (home-page "http://www.gnuplot.info")
447 (synopsis "Command-line driven graphing utility")
448 (description "Gnuplot is a portable command-line driven graphing
449 utility. It was originally created to allow scientists and students to
450 visualize mathematical functions and data interactively, but has grown to
451 support many non-interactive uses such as web scripting. It is also used as a
452 plotting engine by third-party applications like Octave.")
453 ;; X11 Style with the additional restriction that derived works may only be
454 ;; distributed as patches to the original.
455 (license (license:fsf-free
456 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
465 (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
467 (file-name (string-append name "-" version ".tar.gz"))
470 "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
472 `(("fortran" ,gfortran)))
473 (build-system gnu-build-system)
474 (synopsis "General Cartographic Transformation Package (GCTP)")
476 "The General Cartographic Transformation Package (GCTP) is a system of
477 software routines designed to permit the transformation of coordinate pairs
478 from one map projection to another. The GCTP is the standard computer
479 software used by the National Mapping Division for map projection
481 (home-page "https://github.com/OkoSanto/GCTP")
482 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
491 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
492 version "/src/hdf-" version ".tar.bz2"))
494 (base32 "16yr50j845zlfx20skmw3y75ww77akk9gg0affjqkg66ih5r03mv"))
495 (patches (search-patches "hdf4-architectures.patch"
496 "hdf4-reproducibility.patch"
497 "hdf4-shared-fortran.patch"))))
499 (build-system gnu-build-system)
501 `(("gfortran" ,gfortran)
506 ("libjpeg" ,libjpeg)))
508 `(#:parallel-tests? #f
509 #:configure-flags '("--enable-shared")
511 (modify-phases %standard-phases
512 (add-before 'configure 'patchbuild
515 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
517 (("/bin/mkdir") "mkdir"))
518 (substitute* (find-files "." "^Makefile\\.in$")
519 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
520 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
521 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
522 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
523 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")))))))
524 (home-page "https://www.hdfgroup.org/products/hdf4/")
526 "Library and multi-object file format for storing and managing data")
527 (description "HDF4 is a library and multi-object file format for storing
528 and managing data between machines. HDF4 is an older hierarchical data format,
529 incompatible with HDF5.")
531 (license:non-copyleft
532 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
534 (define-public hdf4-alt
539 (substitute-keyword-arguments (package-arguments hdf4)
540 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
542 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
551 (uri (list (string-append "http://www.hdfgroup.org/ftp/HDF5/releases/"
552 "hdf5-" version "/src/hdf5-"
554 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
557 (take (string-split version #\.) 2))
558 "/src/hdf5-" version ".tar.bz2")))
560 (base32 "13542vrnl1p35n8vbq0wzk40vddmm33q5nh04j98c7r1yjnxxih1"))
561 (patches (list (search-patch "hdf5-config-date.patch")))))
562 (build-system gnu-build-system)
566 `(;; Some of the users, notably Flann, need the C++ interface.
567 #:configure-flags '("--enable-cxx")
570 (modify-phases %standard-phases
571 (add-before 'configure 'patch-configure
573 (substitute* "configure"
576 (add-after 'install 'patch-references
577 (lambda* (#:key inputs outputs #:allow-other-keys)
578 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
579 (zlib (assoc-ref inputs "zlib")))
580 (substitute* (find-files bin "h5p?cc")
582 (string-append "-L" zlib "/lib " lib)))
584 (home-page "http://www.hdfgroup.org")
585 (synopsis "Management suite for extremely large and complex data")
586 (description "HDF5 is a suite that makes possible the management of
587 extremely large and complex data collections.")
588 (license (license:x11-style
589 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
591 (define-public hdf-eos2
598 (uri "ftp://edhs1.gsfc.nasa.gov\
599 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
601 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
602 (patches (search-patches "hdf-eos2-remove-gctp.patch"
603 "hdf-eos2-build-shared.patch"
604 "hdf-eos2-fortrantests.patch"))))
605 (build-system gnu-build-system)
607 `(("gfortran" ,gfortran)))
609 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
614 `( #:configure-flags '("--enable-install-include" "--enable-shared"
615 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
616 #:parallel-tests? #f))
617 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
618 (synopsis "HDF4-based data format for NASA's Earth Observing System")
619 (description "HDF-EOS2 is a software library built on HDF4 which supports
620 the construction of data structures used in NASA's Earth Observing
621 System (Grid, Point and Swath).")
623 ;; Source files carry a permissive license header.
624 (license (license:non-copyleft home-page))))
626 (define-public hdf-eos5
632 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
633 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
636 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
637 (patches (search-patches "hdf-eos5-build-shared.patch"
638 "hdf-eos5-remove-gctp.patch"
639 "hdf-eos5-fix-szip.patch"
640 "hdf-eos5-fortrantests.patch"))))
642 `(("gfortran" ,gfortran)))
643 (build-system gnu-build-system)
649 `(#:configure-flags '("--enable-install-include" "--enable-shared"
650 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
651 #:parallel-tests? #f))
652 (synopsis "HDF5-based data format for NASA's Earth Observing System")
654 "HDF-EOS5 is a software library built on HDF5 to support the construction
655 of data structures used in NASA's Earth Observing System (Grid, Point and
657 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
659 ;; Source files carry a permissive license header.
660 (license (license:non-copyleft home-page))))
662 (define-public hdf5-parallel-openmpi
663 (package (inherit hdf5)
664 (name "hdf5-parallel-openmpi")
667 ,@(package-inputs hdf5)))
669 (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
670 ,@(package-arguments hdf5))
672 `(modify-phases ,phases
673 (add-before 'check 'patch-tests
675 ;; OpenMPI's mpirun will exit with non-zero status if it
676 ;; detects an "abnormal termination", i.e. any process not
677 ;; calling MPI_Finalize(). Since the test is explicitely
678 ;; avoiding MPI_Finalize so as not to have at_exit and thus
679 ;; H5C_flush_cache from being called, mpirun will always
680 ;; complain, so turn this test off.
681 (substitute* "testpar/Makefile"
682 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
683 (string-append front back "\n")))
684 (substitute* "tools/h5diff/testph5diff.sh"
685 (("/bin/sh") (which "sh")))
687 (synopsis "Management suite for data with parallel IO support")))
689 (define-public h5check
696 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
697 "h5check/src/h5check-" version ".tar.gz"))
700 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
701 (build-system gnu-build-system)
702 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
703 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
704 (synopsis "HDF5 format checker")
705 (description "@code{h5check} is a validation tool for verifying that an
706 HDF5 file is encoded according to the HDF File Format Specification.")
707 (license (license:x11-style "file://COPYING"))))
709 (define-public netcdf
716 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
717 "netcdf-" version ".tar.gz"))
720 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
721 (patches (search-patches "netcdf-date-time.patch"
722 "netcdf-tst_h_par.patch"))))
723 (build-system gnu-build-system)
727 ("graphviz" ,graphviz)))
732 `(#:configure-flags '("--enable-doxygen" "--enable-dot")
733 #:parallel-tests? #f)) ;various race conditions
734 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
735 (synopsis "Library for scientific data")
736 (description "NetCDF is an interface for scientific data access and a
737 software library that provides an implementation of the interface. The netCDF
738 library defines a machine-independent format for representing scientific data.
739 Together, the interface, library, and format support the creation, access, and
740 sharing of scientific data.")
741 (license (license:x11-style "file://COPYRIGHT"))))
743 (define-public netcdf-parallel-openmpi
744 (package (inherit netcdf)
745 (name "netcdf-parallel-openmpi")
748 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
749 (package-inputs netcdf))))
750 ;; TODO: Replace pkg-config references in nc-config with absolute references
752 (substitute-keyword-arguments (package-arguments netcdf)
753 ((#:configure-flags flags)
754 `(cons* "CC=mpicc" "CXX=mpicxx"
755 "--enable-parallel-tests"
756 ;; Shared libraries not supported with parallel IO.
757 "--disable-shared" "--with-pic"
766 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
769 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
770 (build-system gnu-build-system)
772 `(;; Shared libraries are not built by default. They are required to
773 ;; build the Guile, Octave, and Python bindings.
774 #:configure-flags '("--enable-shared")
777 (modify-phases %standard-phases
778 (add-before 'configure 'set-libnlopt-file-name
779 (lambda* (#:key outputs #:allow-other-keys)
780 ;; Make sure the Scheme module refers to the library by its
781 ;; absolute file name (we cannot do that from a snippet
782 ;; because the expansion of @libdir@ contains
784 (let ((out (assoc-ref outputs "out")))
785 (substitute* "swig/nlopt.scm.in"
787 (string-append out "/lib/libnlopt")))
789 (inputs `(("guile" ,guile-2.0)))
790 (native-inputs `(("pkg-config" ,pkg-config)))
791 (home-page "http://ab-initio.mit.edu/wiki/")
792 (synopsis "Library for nonlinear optimization")
793 (description "NLopt is a library for nonlinear optimization, providing a
794 common interface for a number of different free optimization routines available
795 online as well as original implementations of various other algorithms.")
796 (license license:lgpl2.1+)))
805 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
809 "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
810 (modules '((guix build utils)))
812 ;; Make sure we don't use the bundled software.
813 '(delete-file-recursively "ThirdParty"))))
814 (build-system gnu-build-system)
816 '(#:phases (modify-phases %standard-phases
817 (add-after 'install 'add--L-flags-in-ipopt.pc
818 (lambda* (#:key inputs outputs #:allow-other-keys)
819 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
820 ;; move it to "Libs.private" where it belongs, and add a
821 ;; '-L' flag for LAPACK.
822 (let ((out (assoc-ref outputs "out"))
823 (lapack (assoc-ref inputs "lapack")))
824 (substitute* (string-append out "/lib/pkgconfig/"
826 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
827 (string-append "Libs: " before " " after "\n"
828 "Libs.private: " before
829 "-L" lapack "/lib -llapack -lblas "
833 `(("gfortran" ,gfortran)))
835 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
836 `(("lapack" ,lapack))) ;for both libblas and liblapack
837 (home-page "http://www.coin-or.org")
838 (synopsis "Large-scale nonlinear optimizer")
840 "The Interior Point Optimizer (IPOPT) is a software package for
841 large-scale nonlinear optimization. It provides C++, C, and Fortran
843 (license license:epl1.0)))
847 (name "ceres-solver")
849 (home-page "http://ceres-solver.org/")
852 (uri (string-append home-page "ceres-solver-"
856 "0i7qkbf8g6pd8arxzldppga26ckv93y8zldsfz6wbd4n6b1nqrjd"))))
857 (build-system cmake-build-system)
859 ;; TODO: Build HTML user documentation and install separately.
860 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
861 "-DBUILD_SHARED_LIBS=ON")
863 #:phases (modify-phases %standard-phases
864 (add-before 'configure 'set-library-directory
866 ;; Install libraries to lib/, not lib64/.
867 (substitute* "internal/ceres/CMakeLists.txt"
868 (("set\\(LIB_SUFFIX \"64\"\\)")
869 "set(LIB_SUFFIX \"\")"))
872 `(("pkg-config" ,pkg-config)))
874 `(("glog" ,glog))) ;for #include <glog/glog.h>
879 ("suitesparse" ,suitesparse)
881 (synopsis "C++ library for solving large optimization problems")
883 "Ceres Solver is a C++ library for modeling and solving large,
884 complicated optimization problems. It is a feature rich, mature and
885 performant library which has been used in production since 2010. Ceres Solver
886 can solve two kinds of problems:
888 @item non-linear least squares problems with bounds constraints;
889 @item general unconstrained optimization problems.
891 (license license:bsd-3)))
893 ;; For a fully featured Octave, users are strongly recommended also to install
894 ;; the following packages: texinfo, less, ghostscript, gnuplot.
895 (define-public octave
902 (uri (string-append "mirror://gnu/octave/octave-"
906 "19vvliwxgip0af812vny5xy5r8kacyj7v62203mh4z2n3p14b78i"))))
907 (build-system gnu-build-system)
910 ("readline" ,readline)
914 ("arpack" ,arpack-ng)
917 ("fontconfig" ,fontconfig)
918 ("freetype" ,freetype)
926 ("gfortran" ,gfortran)
927 ("pkg-config" ,pkg-config)
929 ;; The following inputs are not actually used in the build process.
930 ;; However, the ./configure gratuitously tests for their existence and
931 ;; assumes that programs not present at build time are also not, and
932 ;; can never be, available at run time! If these inputs are therefore
933 ;; not present, support for them will be built out. However, Octave
934 ;; will still run without them, albeit without the features they
938 ("ghostscript" ,ghostscript)
939 ("gnuplot" ,gnuplot)))
942 (list (string-append "--with-shell="
943 (assoc-ref %build-inputs "bash")
945 (home-page "https://www.gnu.org/software/octave/")
946 (synopsis "High-level language for numerical computation")
947 (description "GNU Octave is a high-level interpreted language that is
948 specialized for numerical computations. It can be used for both linear and
949 non-linear applications and it provides great support for visualizing results.
950 Work may be performed both at the interactive command-line as well as via
952 (license license:gpl3+)))
961 (uri (string-append "http://gmsh.info/src/gmsh-"
962 version "-source.tgz"))
964 (base32 "02h7fk4vv8qwnq3ymm409c5sp4nksd0m9h2vkxqmy42l0ic4nalr"))
965 (modules '((guix build utils)))
967 ;; Remove non-free METIS code
968 '(delete-file-recursively "contrib/Metis"))))
969 (build-system cmake-build-system)
972 ("gfortran" ,gfortran)
979 ("libxext" ,libxext)))
981 `(("fontconfig" ,fontconfig)
984 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
985 "-DENABLE_BUILD_SHARED:BOOL=ON"
986 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")
987 #:phases (modify-phases %standard-phases
991 (zero? (system* "make" "test"
992 ;; Disable this test. See
993 ;; https://geuz.org/trac/gmsh/ticket/271
994 "ARGS=-E component8_in_a_box")))))))
995 (home-page "http://www.geuz.org/gmsh/")
996 (synopsis "3D finite element grid generator")
997 (description "Gmsh is a 3D finite element grid generator with a built-in
998 CAD engine and post-processor. Its design goal is to provide a fast, light
999 and user-friendly meshing tool with parametric input and advanced
1000 visualization capabilities. Gmsh is built around four modules: geometry,
1001 mesh, solver and post-processing. The specification of any input to these
1002 modules is done either interactively using the graphical user interface or in
1003 ASCII text files using Gmsh's own scripting language.")
1004 (license license:gpl2+)))
1006 (define-public petsc
1013 ;; The *-lite-* tarball does not contain the *large* documentation
1014 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1015 "petsc-lite-" version ".tar.gz"))
1017 (base32 "0jfrq6rd4zagw1iimz05m2w91k0jvz3qbik1lk8pqcxw3rvdqk5d"))))
1018 (build-system gnu-build-system)
1020 `(("python" ,python-2)
1023 `(("gfortran" ,gfortran)
1025 ("superlu" ,superlu)
1026 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1027 ;; leaving out opengl, as configuration seems to only be for mac
1030 `(#:test-target "test"
1031 #:parallel-build? #f ;build is parallel by default
1036 ,(string-append "--with-superlu-include="
1037 (assoc-ref %build-inputs "superlu") "/include")
1038 ,(string-append "--with-superlu-lib="
1039 (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
1041 (modify-phases %standard-phases
1043 ;; PETSc's configure script is actually a python script, so we can't
1044 ;; run it with bash.
1045 (lambda* (#:key outputs (configure-flags '())
1047 (let* ((prefix (assoc-ref outputs "out"))
1048 (flags `(,(string-append "--prefix=" prefix)
1049 ,@configure-flags)))
1050 (format #t "build directory: ~s~%" (getcwd))
1051 (format #t "configure flags: ~s~%" flags)
1052 (zero? (apply system* "./configure" flags)))))
1053 (add-after 'configure 'clean-local-references
1054 (lambda* (#:key inputs outputs #:allow-other-keys)
1055 (let ((out (assoc-ref outputs "out")))
1056 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
1057 ;; Prevent build directory from leaking into compiled code
1059 ;; Scrub timestamp for reproducibility
1060 ((".*Libraries compiled on.*") ""))
1062 (add-after 'install 'clean-install
1063 ;; Try to keep installed files from leaking build directory names.
1064 (lambda* (#:key inputs outputs #:allow-other-keys)
1065 (let ((out (assoc-ref outputs "out")))
1066 (substitute* (map (lambda (file)
1067 (string-append out "/lib/petsc/conf/" file))
1068 '("petscvariables"))
1070 ;; Make compiler references point to the store
1071 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
1072 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1073 (string-append "= " (which compiler))))
1074 ;; PETSc installs some build logs, which aren't necessary.
1075 (for-each (lambda (file)
1076 (let ((f (string-append out "/lib/petsc/conf/" file)))
1077 (when (file-exists? f)
1079 '("configure.log" "make.log" "gmake.log"
1080 "test.log" "error.log" "RDict.db"
1081 "PETScBuildInternal.cmake"
1082 ;; Once installed, should uninstall with Guix
1085 (home-page "http://www.mcs.anl.gov/petsc")
1086 (synopsis "Library to solve PDEs")
1087 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1088 data structures and routines for the scalable (parallel) solution of
1089 scientific applications modeled by partial differential equations.")
1090 (license (license:non-copyleft
1091 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1093 (define-public petsc-complex
1094 (package (inherit petsc)
1095 (name "petsc-complex")
1097 (substitute-keyword-arguments (package-arguments petsc)
1098 ((#:configure-flags cf)
1099 `(cons "--with-scalar-type=complex" ,cf))))
1100 (synopsis "Library to solve PDEs (with complex scalars)")))
1102 (define-public petsc-openmpi
1103 (package (inherit petsc)
1104 (name "petsc-openmpi")
1106 `(("openmpi" ,openmpi)
1107 ,@(package-inputs petsc)))
1109 (substitute-keyword-arguments (package-arguments petsc)
1110 ((#:configure-flags cf)
1111 ``("--with-mpiexec=mpirun"
1112 ,(string-append "--with-mpi-dir="
1113 (assoc-ref %build-inputs "openmpi"))
1114 ,@(delete "--with-mpi=0" ,cf)))))
1115 (synopsis "Library to solve PDEs (with MPI support)")))
1117 (define-public petsc-complex-openmpi
1118 (package (inherit petsc-complex)
1119 (name "petsc-complex-openmpi")
1121 `(("openmpi" ,openmpi)
1122 ,@(package-inputs petsc-complex)))
1124 (substitute-keyword-arguments (package-arguments petsc-complex)
1125 ((#:configure-flags cf)
1126 ``("--with-mpiexec=mpirun"
1127 ,(string-append "--with-mpi-dir="
1128 (assoc-ref %build-inputs "openmpi"))
1129 ,@(delete "--with-mpi=0" ,cf)))))
1130 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
1132 (define-public slepc
1139 (uri (string-append "http://slepc.upv.es/download/download.php?"
1140 "filename=slepc-" version ".tar.gz"))
1141 (file-name (string-append name "-" version ".tar.gz"))
1144 "1hijlmrvxvfqslnx8yydzw5xqbsn1yy02g32w0hln1z3cgr1c0k7"))))
1145 (build-system gnu-build-system)
1147 `(("python" ,python-2)))
1149 `(("arpack" ,arpack-ng)
1150 ("gfortran" ,gfortran)))
1152 `(("petsc" ,petsc)))
1154 `(#:parallel-build? #f ;build is parallel by default
1156 `(,(string-append "--with-arpack-dir="
1157 (assoc-ref %build-inputs "arpack") "/lib"))
1159 (modify-phases %standard-phases
1161 ;; configure is a python script, so we can't run it with bash.
1162 (lambda* (#:key inputs outputs (configure-flags '())
1164 (let* ((prefix (assoc-ref outputs "out"))
1165 (flags `(,(string-append "--prefix=" prefix)
1166 ,@configure-flags)))
1167 (format #t "build directory: ~s~%" (getcwd))
1168 (format #t "configure flags: ~s~%" flags)
1169 (setenv "SLEPC_DIR" (getcwd))
1170 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
1171 (zero? (apply system* "./configure" flags)))))
1172 (add-after 'install 'delete-doc
1173 ;; TODO: SLEPc installs HTML documentation alongside headers in
1174 ;; $out/include. We'd like to move them to share/doc, but delete
1175 ;; them for now, as they are incomplete and installing the complete
1176 ;; documentation is difficult.
1177 (lambda* (#:key outputs #:allow-other-keys)
1178 (let* ((out (assoc-ref outputs "out")))
1179 (for-each delete-file (find-files out "\\.html$")))))
1180 (add-after 'install 'clean-install
1181 ;; Clean up unnecessary build logs from installation.
1182 (lambda* (#:key outputs #:allow-other-keys)
1183 (let ((out (assoc-ref outputs "out")))
1184 (for-each (lambda (file)
1185 (let ((f (string-append out "/lib/slepc/conf/" file)))
1186 (when (file-exists? f)
1188 '("configure.log" "make.log" "gmake.log"
1189 "test.log" "error.log" "RDict.db"
1190 "uninstall.py"))))))))
1191 (home-page "http://slepc.upv.es")
1192 (synopsis "Scalable library for eigenproblems")
1193 (description "SLEPc is a software library for the solution of large sparse
1194 eigenproblems on parallel computers. It can be used for the solution of
1195 linear eigenvalue problems formulated in either standard or generalized form,
1196 as well as other related problems such as the singular value decomposition.
1197 The emphasis of the software is on methods and techniques appropriate for
1198 problems in which the associated matrices are sparse, for example, those
1199 arising after the discretization of partial differential equations.")
1200 (license license:lgpl3)))
1202 (define-public slepc-complex
1203 (package (inherit slepc)
1204 (name "slepc-complex")
1206 `(("petsc" ,petsc-complex)
1207 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1208 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1210 (define-public slepc-openmpi
1211 (package (inherit slepc)
1212 (name "slepc-openmpi")
1215 ("arpack" ,arpack-ng-openmpi)
1216 ,@(alist-delete "arpack" (package-inputs slepc))))
1218 `(("petsc" ,petsc-openmpi)
1219 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1220 (synopsis "Scalable library for eigenproblems (with MPI support)")))
1222 (define-public slepc-complex-openmpi
1223 (package (inherit slepc-openmpi)
1224 (name "slepc-complex-openmpi")
1226 `(("petsc" ,petsc-complex-openmpi)
1227 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1228 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1230 (define-public mumps
1237 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
1241 "0igyc1pfzxdhpbad3v3lb86ixkdbqa1a8gbs15b04r2294h2nabp"))
1242 (patches (search-patches "mumps-build-parallelism.patch"))))
1243 (build-system gnu-build-system)
1245 `(("fortran" ,gfortran)
1246 ;; These are required for linking against mumps, but we let the user
1247 ;; declare the dependency.
1250 ("scotch" ,scotch)))
1252 `(#:modules ((ice-9 match)
1255 ,@%gnu-build-system-modules)
1257 (modify-phases %standard-phases
1259 (lambda* (#:key inputs #:allow-other-keys)
1260 (call-with-output-file "Makefile.inc"
1271 INCSEQ = -I$(topdir)/libseq
1272 LIBSEQ = -L$(topdir)/libseq -lmpiseq
1273 LIBSEQNEEDED = libseqneeded~;
1277 AR = ar vr # rules require trailing space, ugh...
1279 LIBBLAS = -L~a -lopenblas~@[
1280 SCALAP = -L~a -lscalapack~]
1281 LIBOTHERS = -pthread
1284 OPTF = -O2 -DALLOW_NON_INIT $(PIC)
1288 LIBS = $(SCALAP) $(LIBSEQ)
1289 LPORDDIR = $(topdir)/PORD/lib
1290 IPORD = -I$(topdir)/PORD/include
1291 LPORD = -L$(LPORDDIR) -lpord
1292 ORDERINGSF = -Dpord~@[
1294 IMETIS = -I$(METISDIR)/include
1295 LMETIS = -L$(METISDIR)/lib -lmetis
1296 ORDERINGSF += -Dmetis~]~@[~:{
1298 ISCOTCH = -I$(SCOTCHDIR)/include
1299 LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
1300 ORDERINGSF += ~a~}~]
1301 ORDERINGSC = $(ORDERINGSF)
1302 LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
1303 IORDERINGSF = $(ISCOTCH)
1304 IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
1305 (assoc-ref inputs "mpi")
1306 (assoc-ref inputs "blas")
1307 (assoc-ref inputs "scalapack")
1308 (assoc-ref inputs "metis")
1309 (match (list (assoc-ref inputs "pt-scotch")
1310 (assoc-ref inputs "scotch"))
1314 `((,scotch "" "-Dscotch")))
1317 "-lptesmumps -lptscotch -lptscotcherr "
1318 "-Dptscotch")))))))))
1320 ;; By default only the d-precision library is built. Make with "all"
1321 ;; target so that all precision libraries and examples are built.
1323 (zero? (system* "make" "all"
1324 (format #f "-j~a" (parallel-job-count))))))
1326 ;; Run the simple test drivers, which read test input from stdin:
1327 ;; from the "real" input for the single- and double-precision
1328 ;; testers, and from the "cmplx" input for complex-precision
1329 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
1330 ;; package to prefix execution with "mpirun".
1331 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
1332 (with-directory-excursion "examples"
1335 (let ((tester (apply open-pipe*
1338 ,(string-append "./" prec
1340 (input (open-input-file
1341 (string-append "input_simpletest_" type))))
1343 (dump-port input tester)
1345 (zero? (close-pipe tester)))))
1347 '("real" "real" "cmplx" "cmplx")))))
1349 (lambda* (#:key outputs #:allow-other-keys)
1350 (let* ((out (assoc-ref outputs "out"))
1351 (libdir (string-append out "/lib")))
1352 (copy-recursively "lib" libdir)
1353 (copy-recursively "include" (string-append out "/include"))
1354 (when (file-exists? "libseq/libmpiseq.a")
1355 (install-file "libseq/libmpiseq.a" libdir))
1357 (home-page "http://mumps.enseeiht.fr")
1358 (synopsis "Multifrontal sparse direct solver")
1360 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
1361 sparse system of linear equations A x = b using Guassian elimination.")
1362 (license license:cecill-c)))
1364 (define-public mumps-metis
1365 (package (inherit mumps)
1366 (name "mumps-metis")
1368 (alist-delete "scotch" (package-inputs mumps)))))
1370 (define-public mumps-openmpi
1371 (package (inherit mumps)
1372 (name "mumps-openmpi")
1375 ("scalapack" ,scalapack)
1376 ("pt-scotch" ,pt-scotch)
1377 ,@(alist-delete "scotch" (package-inputs mumps))))
1379 (substitute-keyword-arguments (package-arguments mumps)
1381 `(modify-phases ,phases
1385 ((assoc-ref ,phases 'check)
1386 #:exec-prefix '("mpirun" "-n" "2"))))))))
1387 (synopsis "Multifrontal sparse direct solver (with MPI)")))
1389 (define-public mumps-metis-openmpi
1390 (package (inherit mumps-openmpi)
1391 (name "mumps-metis-openmpi")
1393 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
1395 (define-public r-quadprog
1402 (uri (cran-uri "quadprog" version))
1405 "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
1406 (build-system r-build-system)
1408 `(("gfortran" ,gfortran)))
1409 (home-page "http://cran.r-project.org/web/packages/quadprog")
1410 (synopsis "Functions to solve quadratic programming problems")
1412 "This package contains routines and documentation for solving quadratic
1413 programming problems.")
1414 (license license:gpl3+)))
1416 (define-public r-pracma
1422 (uri (cran-uri "pracma" version))
1424 (base32 "19nr2jlkbcdgvw3gx5hry12av565lmvqd5q4h7zlch3q13avwwl2"))))
1425 (build-system r-build-system)
1427 `(("r-quadprog" ,r-quadprog)))
1428 (home-page "http://cran.r-project.org/web/packages/pracma")
1429 (synopsis "Practical numerical math functions")
1430 (description "This package provides functions for numerical analysis and
1431 linear algebra, numerical optimization, differential equations, plus some
1432 special functions. It uses Matlab function names where appropriate to simplify
1434 (license license:gpl3+)))
1436 (define-public superlu
1443 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1444 "superlu_" version ".tar.gz"))
1446 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
1447 (modules '((guix build utils)))
1449 ;; Replace the non-free implementation of MC64 with a stub adapted
1452 (use-modules (ice-9 regex)
1454 (call-with-output-file "SRC/mc64ad.c"
1459 void mc64id_(int *a) {
1460 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
1463 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
1464 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
1465 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
1468 ;; Remove the corresponding license verbiage. MC64 license follows
1469 ;; a "------" line separator.
1470 (with-atomic-file-replacement "License.txt"
1471 (let ((rx (make-regexp "-{8}")))
1474 (let ((line (read-line in 'concat)))
1475 (unless (regexp-exec rx line)
1478 (build-system cmake-build-system)
1482 `(("blas" ,openblas)
1483 ("gfortran" ,gfortran)))
1485 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
1486 "-DTPL_BLAS_LIBRARIES=openblas"
1487 "-DBUILD_SHARED_LIBS:BOOL=YES"
1488 "-DCMAKE_INSTALL_LIBDIR=lib")))
1489 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
1490 (synopsis "Supernodal direct solver for sparse linear systems")
1492 "SuperLU is a general purpose library for the direct solution of large,
1493 sparse, nonsymmetric systems of linear equations on high performance machines.
1494 The library is written in C and is callable from either C or Fortran. The
1495 library routines perform an LU decomposition with partial pivoting and
1496 triangular system solves through forward and back substitution. The library
1497 also provides threshold-based ILU factorization preconditioners.")
1498 (license (list license:bsd-3
1499 license:gpl2+ ;EXAMPLE/*fgmr.c
1500 (license:fsf-free "file://SRC/colamd.h")))))
1502 (define-public superlu-dist
1504 (name "superlu-dist")
1509 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1510 "superlu_dist_" version ".tar.gz"))
1512 (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj"))
1513 (modules '((guix build utils)))
1515 ;; Replace the non-free implementation of MC64 with a stub
1517 (use-modules (ice-9 regex)
1519 (call-with-output-file "SRC/mc64ad.c"
1524 void mc64id_(int *a) {
1525 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
1528 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
1529 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
1530 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
1533 (delete-file "SRC/mc64ad.f.bak")
1534 (substitute* "SRC/util.c" ;adjust default algorithm
1535 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
1536 "RowPerm = NOROWPERM"))))
1537 (patches (search-patches "superlu-dist-scotchmetis.patch"))))
1538 (build-system gnu-build-system)
1542 `(("gfortran" ,gfortran)))
1544 `(("openmpi" ,openmpi) ;headers include MPI heades
1545 ("lapack" ,lapack) ;required to link with output library
1546 ("pt-scotch" ,pt-scotch))) ;same
1548 `(#:parallel-build? #f ;race conditions using ar
1552 (lambda* (#:key inputs outputs #:allow-other-keys)
1553 (call-with-output-file "make.inc"
1558 DSUPERLULIB = ~a/lib/libsuperlu_dist.a
1559 BLASDEF = -DUSE_VENDOR_BLAS
1560 BLASLIB = -L~a/lib -lblas
1561 PARMETISLIB = -L~a/lib \
1562 -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
1563 -lscotch -lscotcherr -lscotcherrexit
1564 METISLIB = -L~:*~a/lib \
1565 -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
1566 LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
1572 CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC)
1573 NOOPTS = -O0 -g $(PIC)
1575 FFLAGS = -O2 -g $(PIC)
1579 (assoc-ref outputs "out")
1580 (assoc-ref inputs "lapack")
1581 (assoc-ref inputs "pt-scotch")))))
1583 'unpack 'remove-broken-symlinks
1585 (for-each delete-file
1586 (find-files "MAKE_INC" "\\.#make\\..*")))
1588 'build 'create-install-directories
1589 (lambda* (#:key outputs #:allow-other-keys)
1592 (mkdir-p (string-append (assoc-ref outputs "out")
1594 '("lib" "include")))
1598 (with-directory-excursion "EXAMPLE"
1600 (zero? (system* "mpirun" "-n" "2"
1601 "./pddrive" "-r" "1" "-c" "2" "g20.rua"))
1602 (zero? (system* "mpirun" "-n" "2"
1603 "./pzdrive" "-r" "1" "-c" "2" "cg20.cua")))))
1606 (lambda* (#:key outputs #:allow-other-keys)
1607 ;; Library is placed in lib during the build phase. Copy over
1608 ;; headers to include.
1609 (let* ((out (assoc-ref outputs "out"))
1610 (incdir (string-append out "/include")))
1611 (for-each (lambda (file)
1612 (let ((base (basename file)))
1613 (format #t "installing `~a' to `~a'~%"
1616 (string-append incdir "/" base))))
1617 (find-files "SRC" ".*\\.h$"))))
1618 %standard-phases)))))))
1619 (home-page (package-home-page superlu))
1620 (synopsis "Parallel supernodal direct solver")
1622 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
1623 It is targeted for distributed memory parallel machines. SuperLU_DIST is
1624 implemented in ANSI C, and MPI for communications.")
1625 (license license:bsd-3)))
1627 (define-public scotch
1634 (uri (string-append "https://gforge.inria.fr/frs/download.php/34618/"
1635 "scotch_" version ".tar.gz"))
1637 (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm"))
1638 (patches (search-patches "scotch-test-threading.patch"
1639 "pt-scotch-build-parallelism.patch"))))
1640 (build-system gnu-build-system)
1647 (modify-phases %standard-phases
1649 'unpack 'chdir-to-src
1650 (lambda _ (chdir "src")))
1654 (call-with-output-file "Makefile.inc"
1668 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
1669 LDFLAGS = -lz -lm -lrt -lpthread
1671 LEX = flex -Pscotchyy -olex.yy.c
1676 YACC = bison -pscotchyy -y -b y
1678 '("COMMON_FILE_COMPRESS_GZ"
1680 "COMMON_RANDOM_FIXED_SEED"
1681 ;; Prevents symbolc clashes with libesmumps
1683 ;; XXX: Causes invalid frees in superlu-dist tests
1685 ;; "SCOTCH_PTHREAD_NUMBER=2"
1686 "restrict=__restrict"))))))
1688 'build 'build-esmumps
1690 (zero? (system* "make"
1691 (format #f "-j~a" (parallel-job-count))
1695 (lambda* (#:key outputs #:allow-other-keys)
1696 (let ((out (assoc-ref outputs "out")))
1698 (zero? (system* "make"
1699 (string-append "prefix=" out)
1701 ;; esmumps files are not installed with the above
1702 (for-each (lambda (f)
1703 (copy-file f (string-append out "/include/" f)))
1704 (find-files "../include" ".*esmumps.h$"))
1705 (for-each (lambda (f)
1706 (copy-file f (string-append out "/lib/" f)))
1707 (find-files "../lib" "^lib.*esmumps.*"))))))))
1708 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
1709 (synopsis "Programs and libraries for graph algorithms")
1710 (description "SCOTCH is a set of programs and libraries which implement
1711 the static mapping and sparse matrix reordering algorithms developed within
1712 the SCOTCH project. Its purpose is to apply graph theory, with a divide and
1713 conquer approach, to scientific computing problems such as graph and mesh
1714 partitioning, static mapping, and sparse matrix ordering, in application
1715 domains ranging from structural mechanics to operating systems or
1717 ;; See LICENSE_en.txt
1718 (license license:cecill-c)))
1720 (define-public pt-scotch
1721 (package (inherit scotch)
1724 `(("openmpi" ,openmpi))) ;Headers include MPI headers
1726 (substitute-keyword-arguments (package-arguments scotch)
1727 ((#:phases scotch-phases)
1728 `(modify-phases ,scotch-phases
1733 (zero? (system* "make"
1734 (format #f "-j~a" (parallel-job-count))
1735 "ptscotch" "ptesmumps"))
1736 ;; Install the serial metis compatibility library
1737 (zero? (system* "make" "-C" "libscotchmetis" "install")))))
1740 (lambda _ (zero? (system* "make" "ptcheck"))))))))
1741 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
1743 (define-public metis
1750 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
1751 "metis-" version ".tar.gz"))
1754 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
1755 (build-system cmake-build-system)
1757 `(("blas" ,openblas)))
1759 `(#:tests? #f ;no tests
1760 #:configure-flags `("-DSHARED=ON"
1761 ,(string-append "-DGKLIB_PATH=" (getcwd)
1762 "/metis-" ,version "/GKlib"))))
1763 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
1764 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
1766 "METIS is a set of serial programs for partitioning graphs, partitioning
1767 finite element meshes, and producing fill-reducing orderings for sparse
1768 matrices. The algorithms implemented in METIS are based on the multilevel
1769 recursive-bisection, multilevel k-way, and multi-constraint partitioning
1771 (license license:asl2.0))) ;As of version 5.0.3
1773 (define-public p4est
1780 (uri (string-append "http://p4est.github.io/release/p4est-"
1784 "0faina2h5qsx3m2izbzaj9bbakma1krbbjmq43wrp1hcbyijflqb"))))
1785 (build-system gnu-build-system)
1787 `(("fortran" ,gfortran)
1792 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
1793 (assoc-ref %build-inputs "blas")
1795 ,(string-append "LAPACK_LIBS=-L"
1796 (assoc-ref %build-inputs "lapack")
1798 (home-page "http://www.p4est.org")
1799 (synopsis "Adaptive mesh refinement on forests of octrees")
1801 "The p4est software library enables the dynamic management of a
1802 collection of adaptive octrees, conveniently called a forest of octrees.
1803 p4est is designed to work in parallel and scales to hundreds of thousands of
1805 (license license:gpl2+)))
1807 (define-public p4est-openmpi
1808 (package (inherit p4est)
1809 (name "p4est-openmpi")
1812 ,@(package-inputs p4est)))
1814 (substitute-keyword-arguments (package-arguments p4est)
1815 ((#:configure-flags cf)
1816 ``("--enable-mpi" ,@,cf))))
1817 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
1819 (define-public gsegrafix
1826 (uri (string-append "mirror://gnu/" name "/" name "-"
1830 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
1831 (build-system gnu-build-system)
1833 `(#:configure-flags '("LDFLAGS=-lm")))
1835 `(("libgnomecanvas" ,libgnomecanvas)
1836 ("libbonoboui" ,libbonoboui)
1837 ("libgnomeui" ,libgnomeui)
1838 ("libgnomeprintui" ,libgnomeprintui)
1841 `(("pkg-config" ,pkg-config)))
1842 (home-page "http://www.gnu.org/software/gsegrafix/")
1843 (synopsis "GNOME application to create scientific and engineering plots")
1844 (description "GSEGrafix is an application which produces high-quality graphical
1845 plots for science and engineering. Plots are specified via simple ASCII
1846 parameter files and data files and are presented in an anti-aliased GNOME
1847 canvas. The program supports rectangular two-dimensional plots, histograms,
1848 polar-axis plots and three-dimensional plots. Plots can be printed or saved
1849 to BMP, JPEG or PNG image formats.")
1850 (license license:gpl3+)))
1852 (define-public maxima
1859 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
1860 version "-source/" name "-" version ".tar.gz"))
1863 "1cvignn5y6qzrby6qb885yc8zdcdqdr1d50vcvc3gapw2f0gk3zm"))
1864 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
1865 (build-system gnu-build-system)
1868 ("gnuplot" ,gnuplot) ;for plots
1869 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
1871 `(("texinfo" ,texinfo)
1873 ("python" ,python)))
1876 (list "--enable-gcl"
1877 (string-append "--with-posix-shell="
1878 (assoc-ref %build-inputs "bash")
1880 (string-append "--with-wish="
1881 (assoc-ref %build-inputs "tk")
1883 (let ((v ,(package-version tk)))
1884 (string-take v (string-index-right v #\.)))))
1885 ;; By default Maxima attempts to write temporary files to
1886 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
1887 ;; Work around that.
1888 #:make-flags (list "TMPDIR=/tmp")
1889 #:phases (alist-cons-before
1892 (chmod "src/maxima" #o555))
1893 ;; Make sure the doc and emacs files are found in the
1894 ;; standard location. Also configure maxima to find gnuplot
1895 ;; without having it on the PATH.
1897 'install 'post-install
1898 (lambda* (#:key outputs inputs #:allow-other-keys)
1899 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
1900 (out (assoc-ref outputs "out"))
1901 (datadir (string-append out "/share/maxima/" ,version)))
1902 (with-directory-excursion out
1903 (mkdir-p "share/emacs")
1904 (mkdir-p "share/doc")
1906 (string-append datadir "/emacs/")
1907 (string-append out "/share/emacs/site-lisp"))
1909 (string-append datadir "/doc/")
1910 (string-append out "/share/doc/maxima"))
1911 (with-atomic-file-replacement
1912 (string-append datadir "/share/maxima-init.lisp")
1914 (format out "~a ~s~a~%"
1915 "(setf $gnuplot_command "
1916 (string-append gnuplot "/bin/gnuplot") ")")
1917 (dump-port in out))))))
1918 %standard-phases))))
1919 (home-page "http://maxima.sourceforge.net")
1920 (synopsis "Numeric and symbolic expression manipulation")
1921 (description "Maxima is a system for the manipulation of symbolic and
1922 numerical expressions. It yields high precision numeric results by using
1923 exact fractions, arbitrary precision integers, and variable precision floating
1925 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
1926 ;; Others simply say "GNU General Public License" without stating a
1927 ;; version (which implicitly means gpl1+).
1928 ;; At least one file (src/maxima.asd) says "version 2."
1929 ;; GPLv2 only is therefore the smallest subset.
1930 (license license:gpl2)))
1932 (define-public wxmaxima
1939 (uri (string-append "mirror://sourceforge/wxmaxima/wxMaxima/"
1940 version "/" name "-" version ".tar.gz"))
1943 "01kas9viqabw5id6crbhz8ahjimmv78gqzizs5hgnj9kngrgrm1h"))))
1944 (build-system gnu-build-system)
1946 `(("wxwidgets" ,wxwidgets)
1949 ("adwaita-icon-theme" ,adwaita-icon-theme)
1951 ("shared-mime-info" ,shared-mime-info)))
1953 `(#:phases (modify-phases %standard-phases
1955 'install 'wrap-program
1956 (lambda* (#:key inputs outputs #:allow-other-keys)
1957 (wrap-program (string-append (assoc-ref outputs "out")
1960 (,(string-append (assoc-ref inputs "maxima")
1962 ;; For GtkFileChooserDialog.
1963 `("GSETTINGS_SCHEMA_DIR" =
1964 (,(string-append (assoc-ref inputs "gtk+")
1965 "/share/glib-2.0/schemas")))
1966 `("XDG_DATA_DIRS" ":" prefix
1967 (;; Needed by gdk-pixbuf to know supported icon formats.
1969 (assoc-ref inputs "shared-mime-info") "/share")
1970 ;; The default icon theme of GTK+.
1972 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
1974 (home-page "https://andrejv.github.io/wxmaxima/")
1975 (synopsis "Graphical user interface for the Maxima computer algebra system")
1977 "wxMaxima is a graphical user interface for the Maxima computer algebra
1978 system. It eases the use of Maxima by making most of its commands available
1979 through a menu system and by providing input dialogs for commands that require
1980 more than one argument. It also implements its own display engine that
1981 outputs mathematical symbols directly instead of depicting them with ASCII
1984 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
1985 text and mathematical calculations to create documents, exporting of input and
1986 output to TeX, and a browser for Maxima's manual including command index and
1987 full text searching.")
1988 (license license:gpl2+)))
1990 (define-public armadillo
1996 (uri (string-append "mirror://sourceforge/arma/armadillo-"
2000 "1x98d32cgxbzbbma2ak6c37wnbpq13xxyxyd6jjvflv748mzi9ks"))))
2001 (build-system cmake-build-system)
2002 (arguments `(#:tests? #f)) ;no test target
2004 `(("openblas" ,openblas)
2006 ("arpack" ,arpack-ng)))
2007 (home-page "http://arma.sourceforge.net/")
2008 (synopsis "C++ linear algebra library")
2010 "Armadillo is a C++ linear algebra library, aiming towards a good balance
2011 between speed and ease of use. It is useful for algorithm development
2012 directly in C++, or quick conversion of research code into production
2013 environments. It can be used for machine learning, pattern recognition,
2014 signal processing, bioinformatics, statistics, econometrics, etc. The library
2015 provides efficient classes for vectors, matrices and cubes, as well as 150+
2016 associated functions (eg. contiguous and non-contiguous submatrix views).")
2017 (license license:mpl2.0)))
2019 (define-public armadillo-for-rcpparmadillo
2020 (package (inherit armadillo)
2024 (uri (string-append "mirror://sourceforge/arma/armadillo-"
2028 "1x98d32cgxbzbbma2ak6c37wnbpq13xxyxyd6jjvflv748mzi9ks"))))))
2030 (define-public muparser
2031 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2032 ;; different hash. In order to make `guix package --upgrade` work correctly,
2033 ;; we set a Guix packaging revision.
2034 ;; When the next version of muparser is released, we can remove
2035 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2036 (let ((upstream-version "2.2.5")
2040 (version (string-append upstream-version "-" revision))
2044 (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
2045 upstream-version ".tar.gz"))
2046 (file-name (string-append name "-" version ".tar.gz"))
2049 "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
2050 (build-system gnu-build-system)
2052 `(#:configure-flags '("--enable-samples=no")
2053 #:tests? #f)) ;no "check" target
2054 (home-page "http://muparser.beltoforion.de/")
2055 (synopsis "Fast parser library for mathematical expressions")
2057 "muParser is an extensible high performance math parser library. It is
2058 based on transforming an expression into a bytecode and precalculating constant
2060 (license license:expat))))
2062 (define-public openblas
2069 (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
2071 (file-name (string-append name "-" version ".tar.gz"))
2074 "071zqnmnxhh0c9phzyn3f198yxa0hjxda7016azdbq2056sm70w7"))))
2075 (build-system gnu-build-system)
2077 `(#:tests? #f ;no "check" target
2078 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
2079 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2080 ;; we need to disable substitutions.
2082 ,(let ((system (or (%current-target-system) (%current-system))))
2083 (or (string-prefix? "x86_64" system)
2084 (string-prefix? "i686" system)
2085 (string-prefix? "mips" system)))
2087 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
2090 ;; Build the library for all supported CPUs. This allows
2091 ;; switching CPU targets at runtime with the environment variable
2092 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
2093 ;; Unfortunately, this is not supported on non-x86 architectures,
2094 ;; where it leads to failed builds.
2095 ,@(let ((system (or (%current-target-system) (%current-system))))
2097 ((or (string-prefix? "x86_64" system)
2098 (string-prefix? "i686" system))
2099 '("DYNAMIC_ARCH=1"))
2100 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
2101 ;; two available MIPS targets special extended instructions
2102 ;; for Loongson cores are used.
2103 ((string-prefix? "mips" system)
2104 '("TARGET=SICORTEX"))
2106 ;; no configure script
2107 #:phases (alist-delete 'configure %standard-phases)))
2109 `(("fortran" ,gfortran)))
2113 (home-page "http://www.openblas.net/")
2114 (synopsis "Optimized BLAS library based on GotoBLAS")
2116 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
2117 (license license:bsd-3)))
2119 (define-public openlibm
2126 (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
2128 (file-name (string-append name "-" version ".tar.gz"))
2131 "11czx2z7nh6dfpz45s3xl7v38hw36jxzxfvny454bk3if14pfakq"))))
2132 (build-system gnu-build-system)
2135 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2137 ;; no configure script
2138 (alist-delete 'configure %standard-phases)
2139 #:tests? #f)) ;the tests are part of the default target
2140 (home-page "http://openlibm.org/")
2141 (synopsis "Portable C mathematical library (libm)")
2143 "OpenLibm is an effort to have a high quality, portable, standalone C
2144 mathematical library (libm). It can be used standalone in applications and
2145 programming language implementations. The project was born out of a need to
2146 have a good libm for the Julia programming language that worked consistently
2147 across compilers and operating systems, and in 32-bit and 64-bit
2149 ;; Each architecture has its own make target, and there is none for mips.
2150 (supported-systems (delete "mips64el-linux" %supported-systems))
2151 ;; See LICENSE.md for details.
2152 (license (list license:expat
2155 license:public-domain
2156 license:lgpl2.1+))))
2158 (define-public openspecfun
2160 (name "openspecfun")
2165 (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
2167 (file-name (string-append name "-" version ".tar.gz"))
2170 "1y5b2h6f2k72536kym3vzy3li3bhpd23x463g7hdmjdi3cncavz1"))))
2171 (build-system gnu-build-system)
2173 '(#:tests? #f ;no "check" target
2175 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2176 ;; no configure script
2177 #:phases (alist-delete 'configure %standard-phases)))
2179 `(("fortran" ,gfortran)))
2180 (home-page "https://github.com/JuliaLang/openspecfun")
2181 (synopsis "Collection of special mathematical functions")
2183 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
2184 portable package for Bessel Functions of a Complex Argument and Nonnegative
2185 Order; it contains subroutines for computing Bessel functions and Airy
2186 functions. Faddeeva allows computing the various error functions of arbitrary
2187 complex arguments (Faddeeva function, error function, complementary error
2188 function, scaled complementary error function, imaginary error function, and
2189 Dawson function); given these, one can also easily compute Voigt functions,
2190 Fresnel integrals, and similar related functions as well.")
2191 ;; Faddeeva is released under the Expat license; AMOS is included as
2192 ;; public domain software.
2193 (license (list license:expat license:public-domain))))
2195 (define-public suitesparse
2197 (name "suitesparse")
2203 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
2207 "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5"))))
2208 (build-system gnu-build-system)
2210 '(#:parallel-build? #f ;cholmod build fails otherwise
2211 #:tests? #f ;no "check" target
2216 "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used
2217 (string-append "INSTALL_LIB="
2218 (assoc-ref %outputs "out") "/lib")
2219 (string-append "INSTALL_INCLUDE="
2220 (assoc-ref %outputs "out") "/include"))
2223 'install 'prepare-out
2224 ;; README.txt states that the target directories must exist prior to
2225 ;; running "make install".
2227 (mkdir-p (string-append (assoc-ref %outputs "out") "/lib"))
2228 (mkdir-p (string-append (assoc-ref %outputs "out") "/include")))
2229 ;; no configure script
2230 (alist-delete 'configure %standard-phases))))
2233 ("lapack" ,lapack)))
2234 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
2235 (synopsis "Suite of sparse matrix software")
2237 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
2238 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
2239 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
2240 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
2241 CXSparse, a concise sparse Cholesky factorization package; and many other
2244 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
2246 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
2247 (license (list license:gpl2+ license:lgpl2.1+))))
2249 (define-public atlas
2255 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
2256 version "/atlas" version ".tar.bz2"))
2259 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
2260 (build-system gnu-build-system)
2261 (home-page "http://math-atlas.sourceforge.net/")
2262 (inputs `(("gfortran" ,gfortran)
2263 ("lapack-tar" ,(package-source lapack))))
2264 (outputs '("out" "doc"))
2265 ;; For the moment we drop support for MIPS at it fails to compile. See
2266 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
2267 (supported-systems (delete "mips64el-linux" %supported-systems))
2269 `(#:parallel-build? #f
2270 #:parallel-tests? #f
2272 ;; ATLAS tunes itself for the machine it is built on, as explained at
2273 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
2274 ;; For this reason, we want users to build it locally instead of using
2278 #:modules ((srfi srfi-26)
2280 (guix build gnu-build-system)
2283 `(;; Generate position independent code suitable for dynamic libraries
2284 ;; and use WALL timer to get more accurate timing.
2285 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
2288 ,,(if (string-match "64" (%current-system))
2291 ;; Disable parallel build as it gives errors: atlas_pthread.h is
2292 ;; needed to compile C files before it is generated.
2293 "-Ss" "pmake" "make -j 1"
2294 ;; Probe is failing for MIPS. We therefore define the system
2295 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
2296 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
2297 ,,@(if (string-prefix? "mips" (%current-system))
2298 (list "-A" "49" "-V" "1")
2300 ;; Generate shared libraries.
2302 ;; Build a full LAPACK library.
2303 ,(string-append "--with-netlib-lapack-tarfile="
2304 (assoc-ref %build-inputs "lapack-tar")))
2306 (modify-phases %standard-phases
2307 (add-after 'install 'install-doc
2308 (lambda* (#:key outputs inputs #:allow-other-keys)
2309 (let ((doc (string-append (assoc-ref outputs "doc")
2310 "/share/doc/atlas")))
2312 (fold (lambda (file previous)
2313 (and previous (zero? (system* "cp" file doc))))
2314 #t (find-files "../ATLAS/doc" ".*")))))
2315 (add-after 'check 'check-pt
2316 (lambda _ (zero? (system* "make" "ptcheck"))))
2317 ;; Fix files required to run configure.
2318 (add-before 'configure 'fix-/bin/sh
2320 ;; Use `sh', not `/bin/sh'.
2321 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
2324 ;; Fix /bin/sh in generated make files.
2325 (add-after 'configure 'fix-/bin/sh-in-generated-files
2327 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
2330 ;; ATLAS configure program does not accepts the default flags
2331 ;; passed by the 'gnu-build-system'.
2333 (lambda* (#:key native-inputs inputs outputs
2334 (configure-flags '())
2335 #:allow-other-keys #:rest args)
2336 (let* ((prefix (assoc-ref outputs "out"))
2337 (bash (or (and=> (assoc-ref
2338 (or native-inputs inputs) "bash")
2339 (cut string-append <> "/bin/bash"))
2341 (flags `(,(string-append "--prefix=" prefix)
2343 (abs-srcdir (getcwd))
2344 (srcdir (string-append "../" (basename abs-srcdir))))
2345 (format #t "source directory: ~s (relative from build: ~s)~%"
2349 (format #t "build directory: ~s~%" (getcwd))
2350 (format #t "configure flags: ~s~%" flags)
2351 (zero? (apply system* bash
2352 (string-append srcdir "/configure")
2354 (synopsis "Automatically Tuned Linear Algebra Software")
2356 "ATLAS is an automatically tuned linear algebra software library
2357 providing C and Fortran77 interfaces to a portably efficient BLAS
2358 implementation, as well as a few routines from LAPACK.
2360 Optimization occurs at build time. For this reason, the library is built on
2361 the machine where it is installed, without resorting to pre-built substitutes.
2363 Before building the library, CPU throttling should be disabled. This can be
2364 done in the BIOS, or, on GNU/Linux, with the following command:
2367 # cpupower --governor performance
2370 Failure to do so will result in a library with poor performance.")
2371 (license license:bsd-3)))
2380 (uri (string-append "mirror://sourceforge/ogl-math/glm-" version
2381 "/glm-" version ".zip"))
2384 "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l"))))
2385 (build-system cmake-build-system)
2387 `(("unzip" ,unzip)))
2388 (home-page "http://glm.g-truc.net")
2389 (synopsis "OpenGL Mathematics library")
2390 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
2391 library for graphics software based on the OpenGL Shading Language (GLSL)
2393 (license license:expat)))
2395 (define-public lpsolve
2402 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
2403 "/lp_solve_" version "_source.tar.gz"))
2406 "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq"))
2407 (modules '((guix build utils)))
2409 '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
2411 ;; Pretend to be on a 64 bit platform to obtain a common directory
2412 ;; name for the build results on all architectures; nothing else
2413 ;; seems to depend on it.
2414 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
2416 ;; The check for 'isnan' as it is written fails with
2417 ;; "non-floating-point argument in call to function
2418 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
2419 ;; definition, which in turn leads to bad things. Fix the feature
2421 (("isnan\\(0\\)") "isnan(0.)")))))
2422 (build-system gnu-build-system)
2424 `(#:tests? #f ; no check target
2426 (modify-phases %standard-phases
2430 (and (with-directory-excursion "lpsolve55"
2431 (zero? (system* "bash" "ccc")))
2432 (with-directory-excursion "lp_solve"
2433 (zero? (system* "bash" "ccc"))))))
2435 (lambda* (#:key outputs #:allow-other-keys)
2436 (let* ((out (assoc-ref outputs "out"))
2437 (bin (string-append out "/bin"))
2438 (lib (string-append out "/lib"))
2439 ;; This is where LibreOffice expects to find the header
2440 ;; files, and where they are installed by Debian.
2441 (include (string-append out "/include/lpsolve")))
2443 (copy-file "lpsolve55/bin/ux64/liblpsolve55.a"
2444 (string-append lib "/liblpsolve55.a"))
2445 (copy-file "lpsolve55/bin/ux64/liblpsolve55.so"
2446 (string-append lib "/liblpsolve55.so"))
2447 (install-file "lp_solve/bin/ux64/lp_solve" bin)
2449 ;; Install a subset of the header files as on Debian
2450 ;; (plus lp_bit.h, which matches the regular expression).
2451 (for-each (lambda (name)
2452 (install-file name include))
2453 (find-files "." "lp_[HMSa-z].*\\.h$"))
2454 (with-directory-excursion "shared"
2455 (for-each (lambda (name)
2456 (install-file name include))
2457 (find-files "." "\\.h$")))
2459 (home-page "http://lpsolve.sourceforge.net/")
2460 (synopsis "Mixed integer linear programming (MILP) solver")
2462 "lp_solve is a mixed integer linear programming solver based on the
2463 revised simplex and the branch-and-bound methods.")
2464 (license license:lgpl2.1+)))
2466 (define-public dealii
2473 (uri (string-append "https://github.com/dealii/dealii/releases/"
2474 "download/v" version "/dealii-" version ".tar.gz"))
2477 "1bdksvvyp1rj37df1ndh8j3x9nzpc3sazw8nd0hzvnlw0qnyk800"))
2478 (modules '((guix build utils)))
2480 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
2481 '(delete-file-recursively "bundled"))))
2482 (build-system cmake-build-system)
2490 ("arpack" ,arpack-ng)
2491 ("muparser" ,muparser)
2492 ("gfortran" ,gfortran)
2493 ("suitesparse" ,suitesparse))) ;for UMFPACK
2495 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
2496 #:configure-flags '("-DCOMPAT_FILES=OFF") ;Follow new directory structure
2497 #:phases (modify-phases %standard-phases
2499 'install 'hint-example-prefix
2500 ;; Set Cmake hints in examples so that they can find this
2501 ;; deal.II when configuring.
2502 (lambda* (#:key outputs #:allow-other-keys)
2503 (let* ((out (assoc-ref %outputs "out"))
2504 (exmpl (string-append out "/share/doc"
2505 "/dealii/examples")))
2506 (substitute* (find-files exmpl "CMakeLists.txt")
2507 (("([[:space:]]*HINTS.*)\n" _ line)
2508 (string-append line " $ENV{HOME}/.guix-profile "
2511 (home-page "https://www.dealii.org")
2512 (synopsis "Finite element library")
2514 "Deal.II is a C++ program library targeted at the computational solution
2515 of partial differential equations using adaptive finite elements. The main
2516 aim of deal.II is to enable rapid development of modern finite element codes,
2517 using among other aspects adaptive meshes and a wide array of tools often used
2518 in finite element programs.")
2519 (license license:lgpl2.1+)))
2521 (define-public dealii-openmpi
2522 (package (inherit dealii)
2523 (name "dealii-openmpi")
2526 ;;Supported only with MPI:
2527 ("p4est" ,p4est-openmpi)
2528 ("petsc" ,petsc-openmpi)
2529 ("slepc" ,slepc-openmpi)
2530 ("metis" ,metis) ;for MUMPS
2531 ("scalapack" ,scalapack) ;for MUMPS
2532 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
2533 ("arpack" ,arpack-ng-openmpi)
2534 ,@(fold alist-delete (package-inputs dealii)
2535 '("p4est" "arpack"))))
2537 (substitute-keyword-arguments (package-arguments dealii)
2538 ((#:configure-flags cf)
2539 ``("-DMPI_C_COMPILER=mpicc"
2540 "-DMPI_CXX_COMPILER=mpicxx"
2541 "-DMPI_Fortran_COMPILER=mpifort"
2543 (synopsis "Finite element library (with MPI support)")))
2545 (define-public flann
2554 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
2555 version "-src.zip"))
2558 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))))
2559 (build-system cmake-build-system)
2561 `(("unzip" ,unzip)))
2565 ("python" ,python-2) ; print syntax
2566 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
2569 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
2570 ;; taken 46 MiB unstripped, and 6 MiB stripped.
2571 #:strip-directories '("lib" "lib64" "libexec"
2572 "bin" "sbin" "share/flann/octave")
2574 ;; Save 12 MiB by not installing .a files. Passing
2575 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
2576 #:phases (modify-phases %standard-phases
2577 (add-after 'install 'remove-static-libraries
2578 (lambda* (#:key outputs #:allow-other-keys)
2579 (let* ((out (assoc-ref outputs "out"))
2580 (lib (string-append out "/lib")))
2581 (for-each delete-file
2582 (find-files lib "\\.a$"))
2585 #:tests? #f)) ; The test data are downloaded from the Internet.
2586 (home-page "http://www.cs.ubc.ca/research/flann/")
2587 (synopsis "Library for approximate nearest neighbors computation")
2588 (description "FLANN is a library for performing fast approximate
2589 nearest neighbor searches in high dimensional spaces. It implements a
2590 collection of algorithms and a system for automatically choosing the best
2591 algorithm and optimum parameters depending on the dataset.
2593 FLANN is written in C++ and contains bindings for C, Octave and Python.")
2594 (license (license:non-copyleft "file://COPYING"
2595 "See COPYING in the distribution."))))
2597 (define-public wcalc
2604 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
2605 "wcalc-" version ".tar.bz2"))
2608 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
2609 (build-system gnu-build-system)
2612 ("readline" ,readline)))
2613 (home-page "http://w-calc.sourceforge.net/index.php")
2614 (synopsis "Flexible command-line scientific calculator")
2615 (description "Wcalc is a very capable calculator. It has standard functions
2616 (sin, asin, and sinh for example, in either radians or degrees), many
2617 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
2618 variables, a command history, hex/octal/binary input and output, unit
2619 conversions, embedded comments, and an expandable expression entry field. It
2620 evaluates expressions using the standard order of operations.")
2621 (license license:gpl2+)))
2629 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
2630 "/xaos-" version ".tar.gz"))
2633 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
2634 (build-system gnu-build-system)
2635 (native-inputs `(("gettext" ,gettext-minimal)))
2636 (inputs `(("libx11" ,libx11)
2641 `(#:tests? #f ;no "check" target
2642 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
2643 (synopsis "Real-time fractal zoomer")
2644 (description "GNU XaoS is a graphical program that generates fractal
2645 patterns and allows you to zoom in and out of them infinitely in a fluid,
2646 continuous manner. It also includes tutorials that help to explain how fractals
2647 are built. It can generate many different fractal types such as the Mandelbrot
2649 (home-page "http://www.gnu.org/software/xaos/")
2650 (license license:gpl2+)))
2652 (define-public hypre
2658 (uri (string-append "https://github.com/LLNL/hypre/archive/"
2659 "v" version ".tar.gz"))
2660 (file-name (string-append name "-" version ".tar.gz"))
2663 "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m"))
2664 (modules '((guix build utils)))
2667 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
2668 ;; substitute the tarball creation time.
2669 (substitute* "src/utilities/HYPRE_utilities.h"
2670 (("Date Compiled: .*$")
2671 "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n"))
2673 (build-system gnu-build-system)
2674 (outputs '("out" ;6.1 MiB of headers and libraries
2675 "doc")) ;4.8 MiB of documentation
2679 ("texlive" ,texlive) ;full package required for fonts
2680 ("ghostscript" ,ghostscript)))
2682 `(("blas" ,openblas)
2683 ("lapack" ,lapack)))
2685 `(#:modules ((srfi srfi-1)
2686 ,@%gnu-build-system-modules)
2687 #:configure-flags '("--enable-shared"
2695 (modify-phases %standard-phases
2696 (add-before 'configure 'chdir-src
2697 (lambda _ (chdir "src")))
2699 (lambda* (#:key build target configure-flags
2700 #:allow-other-keys #:rest args)
2701 (let* ((configure (assoc-ref %standard-phases 'configure)))
2704 (list #:configure-flags
2705 (cons (string-append
2706 "--host=" (or target build))
2707 configure-flags)))))))
2708 (add-after 'build 'build-docs
2710 (zero? (system* "make" "-Cdocs" "pdf" "html"))))
2713 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
2714 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
2715 (and (system* "make" "check" "CHECKRUN=")
2716 (fold (lambda (filename result)
2718 (let ((size (stat:size (stat filename))))
2719 (when (not (zero? size))
2720 (format #t "~a size ~d; error indication~%"
2724 (find-files "test" ".*\\.err$")))))
2725 (add-after 'install 'install-docs
2726 (lambda* (#:key outputs #:allow-other-keys)
2727 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
2728 (let* ((doc (assoc-ref outputs "doc"))
2729 (docdir (string-append doc "/share/doc/hypre-" ,version)))
2730 (with-directory-excursion "docs"
2731 (for-each (lambda (base)
2732 (install-file (string-append base ".pdf") docdir)
2733 (copy-recursively base docdir)) ;html docs
2734 '("HYPRE_usr_manual"
2735 "HYPRE_ref_manual")))
2737 (home-page "http://www.llnl.gov/casc/hypre/")
2738 (synopsis "Library of solvers and preconditioners for linear equations")
2740 "HYPRE is a software library of high performance preconditioners and
2741 solvers for the solution of large, sparse linear systems of equations. It
2742 features multigrid solvers for both structured and unstructured grid
2744 (license license:lgpl2.1)))
2746 (define-public hypre-openmpi
2747 (package (inherit hypre)
2748 (name "hypre-openmpi")
2751 ,@(package-inputs hypre)))
2753 (substitute-keyword-arguments (package-arguments hypre)
2754 ((#:configure-flags flags)
2756 ,@(delete "--without-MPI" ,flags)))))
2757 (synopsis "Parallel solvers and preconditioners for linear equations")
2759 "HYPRE is a software library of high performance preconditioners and
2760 solvers for the solution of large, sparse linear systems of equations on
2761 parallel computers. It features parallel multigrid solvers for both
2762 structured and unstructured grid problems.")))
2764 (define-public matio
2771 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
2772 "matio-" version ".tar.gz"))
2775 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
2776 (build-system gnu-build-system)
2780 (home-page "http://matio.sourceforge.net/")
2781 (synopsis "Library for reading and writing MAT files")
2782 (description "Matio is a library for reading and writing MAT files. It
2783 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
2784 (license license:bsd-2)))
2786 (define-public libhilbert
2793 (uri (string-append "http://web.cs.dal.ca/~chamilto/hilbert/"
2794 "libhilbert-" version ".tar.gz"))
2797 "0v48x8405dj95gjn2saja4bzhw86d6zl6d3dg8h7dzac2qr97s34"))))
2798 (build-system gnu-build-system)
2799 (home-page "http://web.cs.dal.ca/~chamilto/hilbert")
2800 (synopsis "Hilbert indices for multidimensional data")
2801 (description "The libhilbert library can efficiently calculate Hilbert
2802 curves and order-preserving representations of Hilbert curve indices that use
2803 the same amount of space as the original point representation. This is useful
2804 when using the Gilbert curve as a space filling curve through a
2805 high-dimensional space where not all demensions have the same cardinality.")
2806 (license license:lgpl2.1+)))
2813 (origin (method url-fetch)
2814 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
2815 "download/" version "/Vc-" version ".tar.gz"))
2818 "1rh6dhqar3y07n4xqyml0sa0v48qv3ch9dc3yc2in855hlh4vnqi"))))
2819 (build-system cmake-build-system)
2822 '("-DBUILD_TESTING=ON")))
2823 (synopsis "SIMD vector classes for C++")
2824 (description "Vc provides portable, zero-overhead C++ types for explicitly
2825 data-parallel programming. It is a library designed to ease explicit
2826 vectorization of C++ code. Its types enable explicitly stating data-parallel
2827 operations on multiple values. The parallelism is therefore added via the type
2828 system. Vc has an intuitive API and provides portability between different
2829 compilers and compiler versions as well as portability between different vector
2830 instruction sets. Thus, an application written with Vc can be compiled for:
2833 @item SSE2 upto SSE4.2 or SSE4a
2836 @item NEON (in development)
2837 @item NVIDIA GPUs / CUDA (in development)
2839 (home-page "https://github.com/VcDevel/Vc")
2840 (license license:bsd-3)))