gnu/packages/maths.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
   3 ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
   4 ;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
   5 ;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org>
   6 ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
   7 ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
   8 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
   9 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
  10 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
  11 ;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
  12 ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
  13 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
  14 ;;; Copyright © 2016, 2018 Kei Kebreau <kkebreau@posteo.net>
  15 ;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
  16 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
  17 ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
  18 ;;; Copyright © 2017, 2018 Paul Garlick <pgarlick@tourbillion-technology.com>
  19 ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
  20 ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
  21 ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
  22 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
  23 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
  24 ;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
  25 ;;; Copyright © 2018 Jan Nieuwenhuizen <janneke@gnu.org>
  26 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
  27 ;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
  28 ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
  29 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
  30 ;;;
  31 ;;; This file is part of GNU Guix.
  32 ;;;
  33 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  34 ;;; under the terms of the GNU General Public License as published by
  35 ;;; the Free Software Foundation; either version 3 of the License, or (at
  36 ;;; your option) any later version.
  37 ;;;
  38 ;;; GNU Guix is distributed in the hope that it will be useful, but
  39 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  40 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  41 ;;; GNU General Public License for more details.
  42 ;;;
  43 ;;; You should have received a copy of the GNU General Public License
  44 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  45
  46 (define-module (gnu packages maths)
  47   #:use-module (ice-9 regex)
  48   #:use-module (gnu packages)
  49   #:use-module ((guix licenses) #:prefix license:)
  50   #:use-module (guix packages)
  51   #:use-module (guix download)
  52   #:use-module (guix git-download)
  53   #:use-module (guix utils)
  54   #:use-module (guix build utils)
  55   #:use-module (guix build-system cmake)
  56   #:use-module (guix build-system gnu)
  57   #:use-module (guix build-system ocaml)
  58   #:use-module (guix build-system python)
  59   #:use-module (guix build-system r)
  60   #:use-module (guix build-system ruby)
  61   #:use-module (gnu packages algebra)
  62   #:use-module (gnu packages audio)
  63   #:use-module (gnu packages autotools)
  64   #:use-module (gnu packages bison)
  65   #:use-module (gnu packages boost)
  66   #:use-module (gnu packages check)
  67   #:use-module (gnu packages cmake)
  68   #:use-module (gnu packages compression)
  69   #:use-module (gnu packages curl)
  70   #:use-module (gnu packages cyrus-sasl)
  71   #:use-module (gnu packages documentation)
  72   #:use-module (gnu packages elf)
  73   #:use-module (gnu packages flex)
  74   #:use-module (gnu packages fltk)
  75   #:use-module (gnu packages fontutils)
  76   #:use-module (gnu packages gettext)
  77   #:use-module (gnu packages gcc)
  78   #:use-module (gnu packages gd)
  79   #:use-module (gnu packages ghostscript)
  80   #:use-module (gnu packages graphviz)
  81   #:use-module (gnu packages gtk)
  82   #:use-module (gnu packages image)
  83   #:use-module (gnu packages java)
  84   #:use-module (gnu packages less)
  85   #:use-module (gnu packages lisp)
  86   #:use-module (gnu packages linux)
  87   #:use-module (gnu packages logging)
  88   #:use-module (gnu packages lua)
  89   #:use-module (gnu packages gnome)
  90   #:use-module (gnu packages guile)
  91   #:use-module (gnu packages xorg)
  92   #:use-module (gnu packages gl)
  93   #:use-module (gnu packages imagemagick)
  94   #:use-module (gnu packages m4)
  95   #:use-module (gnu packages mpi)
  96   #:use-module (gnu packages multiprecision)
  97   #:use-module (gnu packages netpbm)
  98   #:use-module (gnu packages ocaml)
  99   #:use-module (gnu packages pcre)
 100   #:use-module (gnu packages popt)
 101   #:use-module (gnu packages perl)
 102   #:use-module (gnu packages pkg-config)
 103   #:use-module (gnu packages pulseaudio)
 104   #:use-module (gnu packages python)
 105   #:use-module (gnu packages python-web)
 106   #:use-module (gnu packages qt)
 107   #:use-module (gnu packages readline)
 108   #:use-module (gnu packages ruby)
 109   #:use-module (gnu packages tbb)
 110   #:use-module (gnu packages scheme)
 111   #:use-module (gnu packages shells)
 112   #:use-module (gnu packages tcl)
 113   #:use-module (gnu packages texinfo)
 114   #:use-module (gnu packages tex)
 115   #:use-module (gnu packages tls)
 116   #:use-module (gnu packages version-control)
 117   #:use-module (gnu packages wxwidgets)
 118   #:use-module (gnu packages xml)
 119   #:use-module (srfi srfi-1))
 120
 121 (define-public aris
 122   (package
 123     (name "aris")
 124     (version "2.2")
 125     (source (origin
 126               (method url-fetch)
 127               (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
 128               (sha256 (base32
 129                        "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
 130     (build-system gnu-build-system)
 131     (inputs `(("gtk+" ,gtk+)
 132               ("libxml2" ,libxml2)))
 133     (native-inputs `(("pkg-config" ,pkg-config)))
 134     (synopsis "Natural deduction first-order logic interface")
 135     (description "Aris is a program for performing logical proofs.  It supports
 136 propositional and predicate logic, as well as Boolean algebra and
 137 arithmetical logic.  In addition to its predefined inference and equivalence
 138 rules, Aris also supports references to older proofs.  Its use of standard
 139 logical symbols and its natural deduction interface make it easy to use for
 140 beginners.")
 141     (license license:gpl3+)
 142     (home-page "https://www.gnu.org/software/aris/")))
 143
 144 (define-public c-graph
 145   (package
 146    (name "c-graph")
 147    (version "2.0")
 148    (source (origin
 149             (method url-fetch)
 150             (uri (string-append "mirror://gnu/c-graph/c-graph-" version
 151                                 ".tar.gz"))
 152             (sha256 (base32
 153                      "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
 154    (build-system gnu-build-system)
 155    (inputs
 156      `(("fortran" ,gfortran)))
 157    (synopsis "Visualizing and demonstrating convolution")
 158    (description
 159      "GNU C-Graph is a tool for demonstrating the theory of convolution.
 160 Thus, it can serve as an excellent aid to students of signal and systems
 161 theory in visualizing the convolution process.  Rather than forcing the
 162 student to write code, the program offers an intuitive interface with
 163 interactive dialogs to guide them.")
 164    (license license:gpl3+)
 165    (home-page "https://www.gnu.org/software/c-graph/")))
 166
 167 (define-public coda
 168   (package
 169     (name "coda")
 170     (version "2.19")
 171     (source
 172      (origin
 173        (method url-fetch)
 174        (uri (string-append "https://github.com/stcorp/coda/releases/download/"
 175                            version "/coda-" version ".tar.gz"))
 176        (sha256
 177         (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245"))
 178        (patches (search-patches "coda-use-system-libs.patch"))
 179        (modules '((guix build utils)))
 180        (snippet
 181         ;; Make sure we don't use the bundled software.
 182         '(begin
 183            (for-each (lambda (d)
 184                        (delete-file-recursively (string-append "libcoda/" d)))
 185                      '("zlib" "pcre" "expat"))
 186            #t))))
 187     (native-inputs
 188      `(("fortran" ,gfortran)
 189        ("python" ,python)
 190        ("python-numpy" ,python-numpy)))
 191     (inputs
 192      `(("zlib" ,zlib)
 193        ("pcre" ,pcre)
 194        ("expat" ,expat)
 195        ("hdf4" ,hdf4-alt)
 196        ("hdf5" ,hdf5)))
 197     (build-system gnu-build-system)
 198     (arguments
 199      '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
 200                            "LIBS= -lz -lpcre -lexpat")))
 201     (synopsis "A common interface to various earth observation data formats")
 202     (description
 203      "The Common Data Access toolbox (CODA) provides a set of interfaces for
 204 reading remote sensing data from earth observation data files.  It consists of
 205 command line applications and interfaces to the C, Fortran, Python, and Java
 206 programming languages.")
 207     (home-page "https://stcorp.nl/coda")
 208     (license license:gpl2+)))
 209
 210 (define-public qhull
 211   (package
 212     (name "qhull")
 213     (version "2015.2")
 214     (source (origin
 215               (method url-fetch)
 216               (uri (string-append "http://www.qhull.org/download/qhull-"
 217                                   (car (string-split version #\.))
 218                                   "-src-7.2.0.tgz"))
 219               (sha256
 220                (base32
 221                 "0dm4b2xr3asy6w74khq2zg4gf26zsy3qf9sq7pf7lmrvbj911c3q"))))
 222     (build-system cmake-build-system)
 223     (synopsis "Calculate convex hulls and related structures")
 224     (description
 225      "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
 226 diagram, halfspace intersection about a point, furthest-site Delaunay
 227 triangulation, and furthest-site Voronoi diagram.  The source code runs in 2-d,
 228 3-d, 4-d, and higher dimensions.  @code{Qhull} implements the Quickhull
 229 algorithm for computing the convex hull.  It handles roundoff errors from
 230 floating point arithmetic.  It computes volumes, surface areas, and
 231 approximations to the convex hull.
 232
 233 @code{Qhull} does not support triangulation of non-convex surfaces, mesh
 234 generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
 235 shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
 236 triangulations.")
 237     (home-page "http://qhull.org")
 238     (license (license:non-copyleft "file://COPYING.txt"
 239                                    "See COPYING in the distribution."))))
 240
 241 (define-public units
 242   (package
 243    (name "units")
 244    (version "2.17")
 245    (source (origin
 246             (method url-fetch)
 247             (uri (string-append "mirror://gnu/units/units-" version
 248                                 ".tar.gz"))
 249             (sha256 (base32
 250                      "1n2xzpnxfn475zkd8rzs5gg58xszjbr4bdbgvk6hryzimvwwj0qz"))))
 251    (build-system gnu-build-system)
 252    (inputs
 253     `(("readline" ,readline)
 254       ("python" ,python-wrapper)        ;for 'units_cur' script
 255       ("python-requests" ,python-requests)))
 256    (arguments
 257     `(#:phases (modify-phases %standard-phases
 258                  (add-after 'install 'wrap-units_cur
 259                    (lambda* (#:key outputs #:allow-other-keys)
 260                      (let* ((out (assoc-ref outputs "out"))
 261                             (bin (string-append out "/bin")))
 262                        (wrap-program (string-append bin "/units_cur")
 263                          `("PYTHONPATH" ":" prefix
 264                            ,(search-path-as-string->list (getenv "PYTHONPATH"))))
 265                        #t))))))
 266    (synopsis "Conversion between thousands of scales")
 267    (description
 268     "GNU Units converts numeric quantities between units of measure.  It
 269 can handle scale changes through adaptive usage of standard scale
 270 prefixes (micro-, kilo-, etc.).  It can also handle nonlinear
 271 conversions such as Fahrenheit to Celsius.  Its interpreter is powerful
 272 enough to be used effectively as a scientific calculator.")
 273    (license license:gpl3+)
 274    (home-page "https://www.gnu.org/software/units/")))
 275
 276 (define-public double-conversion
 277   (package
 278     (name "double-conversion")
 279     (version "3.0.0")
 280     (home-page "https://github.com/google/double-conversion")
 281     (source (origin
 282               (method url-fetch)
 283               (uri (string-append home-page "/archive/v" version ".tar.gz"))
 284               (file-name (string-append name "-" version ".tar.gz"))
 285               (sha256
 286                (base32
 287                 "059r1czs28ljjd388pn6l3njg1ghbf1cv3q9nkxv3dj2a8siabqm"))))
 288     (build-system cmake-build-system)
 289     (arguments
 290      '(#:test-target "test"
 291        #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
 292                            "-DBUILD_TESTING=ON")))
 293     (synopsis "Conversion routines for IEEE doubles")
 294     (description
 295      "The double-conversion library provides binary-decimal and decimal-binary
 296 routines for IEEE doubles.  The library consists of efficient conversion
 297 routines that have been extracted from the V8 JavaScript engine.")
 298     (license license:bsd-3)))
 299
 300 (define-public dionysus
 301   (package
 302     (name "dionysus")
 303     (version "1.4.0")
 304     (source (origin
 305               (method url-fetch)
 306               (uri (string-append "mirror://gnu/dionysus/dionysus-" version
 307                                   ".tar.xz"))
 308               (sha256
 309                (base32
 310                 "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
 311     (build-system gnu-build-system)
 312     (inputs `(("tcl" ,tcl)))                      ;for 'tclsh'
 313     (synopsis "Local search for universal constants and scientific values")
 314     (description
 315      "GNU Dionysus is a convenient system for quickly retrieving the values of
 316 mathematical constants used in science and engineering.  Values can be
 317 searched using a simple command-line tool, choosing from three databases:
 318 universal constants, atomic numbers, and constants related to
 319 semiconductors.")
 320     (license license:gpl3+)
 321     (home-page "https://www.gnu.org/software/dionysus/")))
 322
 323 (define-public gsl
 324   (package
 325     (name "gsl")
 326     (version "2.5")
 327     (source (origin
 328               (method url-fetch)
 329               (uri (string-append "mirror://gnu/gsl/gsl-"
 330                                   version ".tar.gz"))
 331               (sha256
 332                (base32
 333                 "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
 334               (patches (search-patches "gsl-test-i686.patch"))))
 335     (build-system gnu-build-system)
 336     (arguments
 337      `(;; Currently there are numerous tests that fail on "exotic"
 338        ;; architectures such as aarch64 and ppc64le.
 339        ,@(if (string-prefix? "aarch64-linux"
 340                              (or (%current-target-system) (%current-system)))
 341            '(#:tests? #f)
 342            '())))
 343     (home-page "https://www.gnu.org/software/gsl/")
 344     (synopsis "Numerical library for C and C++")
 345     (description
 346      "The GNU Scientific Library is a library for numerical analysis in C
 347 and C++.  It includes a wide range of mathematical routines, with over 1000
 348 functions in total.  Subject areas covered by the library include:
 349 differential equations, linear algebra, Fast Fourier Transforms and random
 350 numbers.")
 351     (license license:gpl3+)))
 352
 353 (define-public ocaml-gsl
 354   (package
 355     (name "ocaml-gsl")
 356     (version "1.22.0")
 357     (source
 358      (origin
 359        (method url-fetch)
 360        (uri
 361         (string-append
 362          "https://github.com/mmottl/gsl-ocaml/releases/download/"
 363          version "/gsl-" version ".tbz"))
 364        (sha256
 365         (base32
 366          "17vcswipliq1b2idbzx1z95kskn1a4q4s5v04igilg0f7lnkaarb"))))
 367     (build-system ocaml-build-system)
 368     (inputs
 369      `(("gsl" ,gsl)))
 370     (home-page "https://mmottl.github.io/gsl-ocaml")
 371     (synopsis "Bindings to the GNU Scientific Library")
 372     (description
 373      "GSL-OCaml is an interface to the @dfn{GNU scientific library} (GSL) for
 374 the OCaml language.")
 375     (license license:gpl3+)))
 376
 377 (define-public ocaml4.01-gsl
 378   (package-with-ocaml4.01 ocaml-gsl))
 379
 380 (define-public glpk
 381   (package
 382     (name "glpk")
 383     (version "4.65")
 384     (source
 385      (origin
 386       (method url-fetch)
 387       (uri (string-append "mirror://gnu/glpk/glpk-"
 388                           version ".tar.gz"))
 389       (sha256
 390        (base32
 391         "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
 392     (build-system gnu-build-system)
 393     (inputs
 394      `(("gmp" ,gmp)))
 395     (arguments
 396      `(#:configure-flags '("--with-gmp")))
 397     (home-page "https://www.gnu.org/software/glpk/")
 398     (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
 399     (description
 400      "GLPK is a C library for solving large-scale linear programming (LP),
 401 mixed integer programming (MIP), and other related problems.  It supports the
 402 GNU MathProg modeling language, a subset of the AMPL language, and features a
 403 translator for the language.  In addition to the C library, a stand-alone
 404 LP/MIP solver is included in the package.")
 405     (license license:gpl3+)))
 406
 407 (define-public 4ti2
 408   (package
 409     (name "4ti2")
 410     (version "1.6.7")
 411     (source
 412      (origin
 413       (method url-fetch)
 414       (uri (string-append "http://www.4ti2.de/version_" version
 415                           "/4ti2-" version ".tar.gz"))
 416       (sha256
 417        (base32
 418         "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
 419     (build-system gnu-build-system)
 420     (native-inputs
 421      `(("which" ,(@ (gnu packages base) which)))) ; for the tests
 422     (inputs
 423      `(("glpk" ,glpk)
 424        ("gmp" ,gmp)))
 425     (home-page "http://www.4ti2.de/")
 426     (synopsis "Mathematical tool suite for problems on linear spaces")
 427     (description
 428      "4ti2 implements algorithms for solving algebraic, geometric and
 429 combinatorial problems on linear spaces.  Among others, it solves systems
 430 of linear equations, computes extreme rays of polyhedral cones, solves
 431 integer programming problems and computes Markov bases for statistics.")
 432     (license license:gpl2+)))
 433
 434 (define-public cddlib
 435   (package
 436     (name "cddlib")
 437     (version "0.94i")
 438     (source
 439      (origin
 440       (method url-fetch)
 441       (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
 442                           (string-delete #\. version) ".tar.gz"))
 443       (sha256
 444        (base32
 445         "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
 446     (build-system gnu-build-system)
 447     (inputs
 448      `(("gmp" ,gmp)))
 449     (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
 450     (synopsis "Library for convex hulls and extreme rays of polyhedra")
 451     (description
 452      "The C-library cddlib implements the Double Description Method of
 453 Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
 454 rays of a general convex polyhedron given by a system of linear inequalities
 455 in arbitrary dimension.  It can also be used for the converse operation of
 456 computing convex hulls.")
 457     (license license:gpl2+)))
 458
 459 (define-public arpack-ng
 460   (package
 461     (name "arpack-ng")
 462     (version "3.6.2")
 463     (home-page "https://github.com/opencollab/arpack-ng")
 464     (source
 465      (origin
 466        (method url-fetch)
 467        (uri (string-append home-page "/archive/" version ".tar.gz"))
 468        (file-name (string-append name "-" version ".tar.gz"))
 469        (sha256
 470         (base32
 471          "16jrvdl0gh78rrfnvrcxwys4slwfh6qmwwjhfc9d6vwrvq184g37"))))
 472     (build-system gnu-build-system)
 473     (native-inputs
 474      `(("autoconf" ,autoconf)
 475        ("automake" ,automake)
 476        ("libtool" ,libtool)))
 477     (inputs
 478      `(("lapack" ,lapack)
 479        ("fortran" ,gfortran)))
 480     (synopsis "Fortran subroutines for solving eigenvalue problems")
 481     (description
 482      "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
 483 large scale eigenvalue problems.")
 484     (license (license:non-copyleft "file://COPYING"
 485                                 "See COPYING in the distribution."))))
 486
 487 (define-public arpack-ng-3.3.0
 488   (package
 489     (inherit arpack-ng)
 490     (version "3.3.0")
 491     (name (package-name arpack-ng))
 492     (home-page (package-home-page arpack-ng))
 493     (source
 494      (origin
 495        (method url-fetch)
 496        (uri (string-append home-page "/archive/" version ".tar.gz"))
 497        (file-name (string-append name "-" version ".tar.gz"))
 498        (sha256
 499         (base32
 500          "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
 501
 502 (define-public arpack-ng-openmpi
 503   (package (inherit arpack-ng)
 504     (name "arpack-ng-openmpi")
 505     (inputs
 506      `(("mpi" ,openmpi)
 507        ,@(package-inputs arpack-ng)))
 508     (arguments
 509      (substitute-keyword-arguments (package-arguments arpack-ng)
 510        ((#:configure-flags _ '())
 511         ''("--enable-mpi"))))
 512     (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
 513
 514 (define-public lapack
 515   (package
 516     (name "lapack")
 517     (version "3.7.1")
 518     (source
 519      (origin
 520       (method url-fetch)
 521       (uri (string-append "http://www.netlib.org/lapack/lapack-"
 522                           version ".tgz"))
 523       (sha256
 524        (base32
 525         "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
 526     (build-system cmake-build-system)
 527     (home-page "http://www.netlib.org/lapack/")
 528     (inputs `(("fortran" ,gfortran)
 529               ("python" ,python-2)))
 530     (arguments
 531      `(#:configure-flags (list
 532                           "-DBUILD_SHARED_LIBS:BOOL=YES"
 533                           "-DLAPACKE=ON"
 534
 535                           ;; Build the 'LAPACKE_clatms' functions.
 536                           "-DLAPACKE_WITH_TMG=ON")
 537        #:phases
 538        (modify-phases %standard-phases
 539          (add-before 'check 'patch-python
 540            (lambda* (#:key inputs #:allow-other-keys)
 541              (let ((python (assoc-ref inputs "python")))
 542                (substitute* "lapack_testing.py"
 543                  (("/usr/bin/env python") python)))
 544              #t)))))
 545     (synopsis "Library for numerical linear algebra")
 546     (description
 547      "LAPACK is a Fortran 90 library for solving the most commonly occurring
 548 problems in numerical linear algebra.")
 549     (license (license:non-copyleft "file://LICENSE"
 550                                 "See LICENSE in the distribution."))))
 551
 552 (define-public scalapack
 553   (package
 554     (name "scalapack")
 555     (version "2.0.2")
 556     (source
 557      (origin
 558        (method url-fetch)
 559        (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
 560                            version ".tgz"))
 561        (sha256
 562         (base32
 563          "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
 564     (build-system cmake-build-system)
 565     (inputs
 566      `(("mpi" ,openmpi)
 567        ("fortran" ,gfortran)
 568        ("lapack" ,lapack)))             ;for testing only
 569     (arguments
 570      `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
 571        #:phases (modify-phases %standard-phases
 572                   (add-before 'check 'set-test-environment
 573                     (lambda _
 574                       ;; By default, running the test suite would fail because
 575                       ;; 'ssh' could not be found in $PATH.  Define this
 576                       ;; variable to placate Open MPI without adding a
 577                       ;; dependency on OpenSSH (the agent isn't used anyway.)
 578                       (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
 579                       #t)))))
 580     (home-page "http://www.netlib.org/scalapack/")
 581     (synopsis "Library for scalable numerical linear algebra")
 582     (description
 583      "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
 584 routines on parallel distributed memory machines.  ScaLAPACK solves dense and
 585 banded linear systems, least squares problems, eigenvalue problems, and
 586 singular value problems.")
 587     (license (license:bsd-style "file://LICENSE"
 588                                 "See LICENSE in the distribution."))))
 589
 590 (define-public gnuplot
 591   (package
 592     (name "gnuplot")
 593     (version "5.2.4")
 594     (source (origin
 595               (method url-fetch)
 596               (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
 597                                   version "/gnuplot-"
 598                                   version ".tar.gz"))
 599        (sha256
 600         (base32
 601          "1jvh8xmd2cvrhlsg88kxwh55wkwx31sg50v1n59slfippl0g058m"))))
 602     (build-system gnu-build-system)
 603     (inputs `(("readline" ,readline)
 604               ("cairo" ,cairo)
 605               ("pango" ,pango)
 606               ("gd" ,gd)
 607               ("lua" ,lua)))
 608     (native-inputs
 609      `(("pkg-config" ,pkg-config)
 610        ("texlive" ,texlive-tiny)))
 611     (arguments `(#:configure-flags (list (string-append
 612                                           "--with-texdir=" %output
 613                                           "/texmf-local/tex/latex/gnuplot"))))
 614     (home-page "http://www.gnuplot.info")
 615     (synopsis "Command-line driven graphing utility")
 616     (description "Gnuplot is a portable command-line driven graphing
 617 utility.  It was originally created to allow scientists and students to
 618 visualize mathematical functions and data interactively, but has grown to
 619 support many non-interactive uses such as web scripting.  It is also used as a
 620 plotting engine by third-party applications like Octave.")
 621     ;;  X11 Style with the additional restriction that derived works may only be
 622     ;;  distributed as patches to the original.
 623     (license (license:fsf-free
 624               "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
 625
 626 (define-public gctp
 627   (package
 628     (name "gctp")
 629     (version "2.0.0")
 630     (source
 631      (origin
 632        (method url-fetch)
 633        (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
 634                            version ".tar.gz"))
 635        (file-name (string-append name "-" version ".tar.gz"))
 636        (sha256
 637         (base32
 638          "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
 639     (native-inputs
 640      `(("fortran" ,gfortran)))
 641     (build-system gnu-build-system)
 642     (synopsis "General Cartographic Transformation Package (GCTP)")
 643     (description
 644      "The General Cartographic Transformation Package (GCTP) is a system of
 645 software routines designed to permit the transformation of coordinate pairs
 646 from one map projection to another.  The GCTP is the standard computer
 647 software used by the National Mapping Division for map projection
 648 computations.")
 649     (home-page "https://github.com/OkoSanto/GCTP")
 650     (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
 651
 652 (define-public hdf4
 653   (package
 654     (name "hdf4")
 655     (version "4.2.13")
 656     (source
 657      (origin
 658        (method url-fetch)
 659        (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
 660                            version "/src/hdf-" version ".tar.bz2"))
 661        (sha256
 662         (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
 663        (patches (search-patches "hdf4-architectures.patch"
 664                                 "hdf4-reproducibility.patch"
 665                                 "hdf4-shared-fortran.patch"))))
 666     (build-system gnu-build-system)
 667     (native-inputs
 668      `(("gfortran" ,gfortran)
 669        ("bison" ,bison)
 670        ("flex" ,flex)))
 671     (inputs
 672      `(("zlib" ,zlib)
 673        ("libjpeg" ,libjpeg)))
 674     (arguments
 675      `(#:parallel-tests? #f
 676        #:configure-flags '("--enable-shared")
 677        #:phases
 678        (modify-phases %standard-phases
 679          ;; This is inspired by two of Debian's patches.
 680          (add-before 'configure 'add-more-aarch64-support
 681            (lambda _
 682              (substitute* '("mfhdf/ncgen/ncgen.l"
 683                             "mfhdf/ncgen/ncgenyy.c"
 684                             "mfhdf/libsrc/netcdf.h.in")
 685                (("AIX5L64") "__aarch64__"))
 686              #t))
 687          (add-before 'configure 'patchbuild
 688            (lambda _
 689              (substitute*
 690                  '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
 691                (("/bin/rm") "rm")
 692                (("/bin/mkdir") "mkdir"))
 693              (substitute* (find-files "." "^Makefile\\.in$")
 694                (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
 695 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
 696                (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
 697 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
 698 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
 699              #t))
 700          (add-after 'configure 'patch-settings
 701            (lambda _
 702              ;; libhdf4.settings contains the full path of the
 703              ;; compilers used, and its contents are included in
 704              ;; .so-files.  We truncate the hashes to avoid
 705              ;; unnecessary store references to those compilers:
 706              (substitute* "libhdf4.settings"
 707                (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
 708                 (string-append prefix (string-take hash 10) "...")))
 709              #t))
 710          )))
 711     (home-page "https://www.hdfgroup.org/products/hdf4/")
 712     (synopsis
 713      "Library and multi-object file format for storing and managing data")
 714     (description "HDF4 is a library and multi-object file format for storing
 715 and managing data between machines.  HDF4 is an older hierarchical data format,
 716 incompatible with HDF5.")
 717     (license
 718      (license:non-copyleft
 719       "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
 720
 721 (define-public hdf4-alt
 722   (package
 723     (inherit hdf4)
 724     (name "hdf4-alt")
 725     (arguments
 726      (substitute-keyword-arguments (package-arguments hdf4)
 727        ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
 728     (synopsis
 729      "HDF4 without netCDF API, can be combined with the regular netCDF library")))
 730
 731 (define-public hdf5
 732   (package
 733     (name "hdf5")
 734     (version "1.8.19")
 735     (source
 736      (origin
 737       (method url-fetch)
 738       (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
 739                                 "hdf5-" (version-major+minor version)
 740                                 "/hdf5-" version "/src/hdf5-"
 741                                 version ".tar.bz2")
 742                  (string-append "https://support.hdfgroup.org/ftp/HDF5/"
 743                                 "current"
 744                                 (apply string-append
 745                                        (take (string-split version #\.) 2))
 746                                 "/src/hdf5-" version ".tar.bz2")))
 747       (sha256
 748        (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
 749       (patches (list (search-patch "hdf5-config-date.patch")))))
 750     (build-system gnu-build-system)
 751     (inputs
 752      `(("zlib" ,zlib)))
 753     (native-inputs
 754      `(("gfortran" ,gfortran)))
 755     (outputs '("out"       ; core library
 756                "fortran")) ; fortran interface
 757     (arguments
 758      `(;; Some of the users, notably Flann, need the C++ interface.
 759        #:configure-flags '("--enable-cxx"
 760                            "--enable-fortran"
 761                            "--enable-fortran2003")
 762        ;; Use -fPIC to allow the R bindings to link with the static libraries
 763        #:make-flags (list "CFLAGS=-fPIC"
 764                           "CXXFLAGS=-fPIC")
 765        #:phases
 766        (modify-phases %standard-phases
 767          (add-before 'configure 'patch-configure
 768            (lambda* (#:key outputs #:allow-other-keys)
 769              (substitute* "configure"
 770                (("/bin/mv") "mv"))
 771              (substitute* "fortran/src/Makefile.in"
 772                (("libhdf5_fortran_la_LDFLAGS =")
 773                 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
 774                                (assoc-ref outputs "fortran") "/lib")))
 775              (substitute* "hl/fortran/src/Makefile.in"
 776                (("libhdf5hl_fortran_la_LDFLAGS =")
 777                 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
 778                                (assoc-ref outputs "fortran") "/lib")))
 779              #t))
 780          (add-after 'configure 'patch-settings
 781            (lambda _
 782              ;; libhdf5.settings contains the full path of the
 783              ;; compilers used, and its contents are included in
 784              ;; libhdf5.so.  We truncate the hashes to avoid
 785              ;; unnecessary store references to those compilers:
 786              (substitute* "src/libhdf5.settings"
 787               (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
 788                (string-append prefix (string-take hash 10) "..."))
 789               ;; Don't record the build-time kernel version to make the
 790               ;; settings file reproducible.
 791               (("Uname information:.*")
 792                "Uname information: Linux\n"))
 793              #t))
 794          (add-after 'install 'patch-references
 795            (lambda* (#:key inputs outputs #:allow-other-keys)
 796              (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
 797                    (zlib (assoc-ref inputs "zlib")))
 798                (substitute* (find-files bin "h5p?cc")
 799                  (("-lz" lib)
 800                   (string-append "-L" zlib "/lib " lib)))
 801                #t)))
 802          (add-after 'install 'split
 803             (lambda* (#:key inputs outputs #:allow-other-keys)
 804               ;; Move all fortran-related files
 805               (let* ((out (assoc-ref outputs "out"))
 806                      (bin (string-append out "/bin"))
 807                      (lib (string-append out "/lib"))
 808                      (inc (string-append out "/include"))
 809                      (ex (string-append out "/share/hdf5_examples/fortran"))
 810                      (fort (assoc-ref outputs "fortran"))
 811                      (fbin (string-append fort "/bin"))
 812                      (flib (string-append fort "/lib"))
 813                      (finc (string-append fort "/include"))
 814                      (fex (string-append fort "/share/hdf5_examples/fortran")))
 815                 (mkdir-p fbin)
 816                 (mkdir-p flib)
 817                 (mkdir-p finc)
 818                 (mkdir-p fex)
 819                 (rename-file (string-append bin "/h5fc")
 820                              (string-append fbin "/h5fc"))
 821                 (for-each (lambda (file)
 822                             (rename-file file
 823                                          (string-append flib "/" (basename file))))
 824                           (find-files lib ".*fortran.*"))
 825                 (for-each (lambda (file)
 826                             (rename-file file
 827                                          (string-append finc "/" (basename file))))
 828                           (find-files inc ".*mod"))
 829                 (for-each (lambda (file)
 830                             (rename-file file
 831                                          (string-append fex "/" (basename file))))
 832                           (find-files ex ".*"))
 833                 (delete-file-recursively ex))
 834               #t)))))
 835     (home-page "http://www.hdfgroup.org")
 836     (synopsis "Management suite for extremely large and complex data")
 837     (description "HDF5 is a suite that makes possible the management of
 838 extremely large and complex data collections.")
 839     (license (license:x11-style
 840               "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
 841
 842 (define-public hdf-java
 843   (package
 844    (name "hdf-java")
 845    (version "3.3.2")
 846    (source
 847     (origin
 848       (method url-fetch)
 849       (uri (string-append
 850             "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
 851             version "/src/CMake-hdfjava-" version ".tar.gz"))
 852       (sha256
 853        (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
 854       (modules '((guix build utils)))
 855       (snippet ; Make sure we don't use the bundled sources and binaries.
 856        `(begin
 857           (for-each delete-file
 858                     (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
 859                           "HDF4.tar.gz" "HDF5.tar.gz"))
 860           (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
 861           #t))))
 862    (build-system gnu-build-system)
 863    (native-inputs
 864     `(("jdk" ,icedtea "jdk")
 865       ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
 866       ;; For tests:
 867       ("hamcrest-core" ,java-hamcrest-core)
 868       ("junit" ,java-junit)
 869       ("slf4j-simple" ,java-slf4j-simple)))
 870    (inputs
 871     `(("hdf4" ,hdf4)
 872       ("hdf5" ,hdf5)
 873       ("zlib" ,zlib)
 874       ("libjpeg" ,libjpeg)
 875       ("slf4j-api" ,java-slf4j-api)))
 876    (arguments
 877     `(#:configure-flags
 878       (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
 879             (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
 880                            (assoc-ref %build-inputs "jdk") "/lib" )
 881             (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
 882             (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
 883
 884       #:make-flags
 885       (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
 886             (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
 887             (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
 888             (string-append "JPEGLIB="
 889                            (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
 890             "LLEXT=so")
 891
 892       #:phases
 893       (modify-phases %standard-phases
 894         (add-before 'configure 'chdir-to-source
 895           (lambda _ (chdir ,(string-append "hdfjava-" version))))
 896         (add-before 'configure 'patch-build
 897           (lambda* (#:key inputs outputs #:allow-other-keys)
 898             (substitute* "configure"
 899               (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
 900               (("/bin/cat") (which "cat")))
 901             ;; Set classpath for compilation
 902             (substitute* '("hdf/hdf5lib/Makefile.in"
 903                            "hdf/hdf5lib/exceptions/Makefile.in"
 904                            "hdf/hdflib/Makefile.in")
 905               (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
 906                (string-append (assoc-ref inputs "slf4j-api")
 907                               "/share/java/slf4j-api.jar")))
 908             ;; Replace outdated config.sub and config.guess:
 909             (with-directory-excursion "config"
 910               (for-each (lambda (file)
 911                           (copy-file
 912                            (string-append (assoc-ref inputs "automake")
 913                                           "/share/automake-1.15/" file) file))
 914                         '("config.sub" "config.guess")))
 915             (mkdir-p (string-append (assoc-ref outputs "out")))
 916             ;; Set classpath for tests
 917             (let* ((build-dir (getcwd))
 918                    (lib (string-append build-dir "/lib"))
 919                    (jhdf (string-append lib "/jhdf.jar"))
 920                    (jhdf5 (string-append lib "/jhdf5.jar"))
 921                    (testjars
 922                     (map (lambda (i)
 923                            (string-append (assoc-ref inputs i)
 924                                           "/share/java/" i ".jar"))
 925                          '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
 926                    (class-path
 927                     (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
 928
 929               (substitute* '("test/hdf5lib/Makefile.in"
 930                              "test/hdf5lib/junit.sh.in"
 931                              "examples/runExample.sh.in")
 932                 (("/usr/bin/test")
 933                  (string-append (assoc-ref inputs "coreutils")
 934                                 "/bin/test"))
 935                 (("/usr/bin/uname")
 936                  (string-append (assoc-ref inputs "coreutils")
 937                                 "/bin/uname"))
 938                 (("CLASSPATH=[^\n]*")
 939                  (string-append "CLASSPATH=" class-path)))
 940               (setenv "CLASSPATH" class-path))
 941             #t))
 942         (add-before 'check 'build-examples
 943           (lambda _
 944             (zero? (apply system* `("javac"
 945                                     ,@(find-files "examples" ".*\\.java")))))))
 946
 947       #:parallel-build? #f
 948
 949       #:parallel-tests? #f ))
 950    (home-page "https://support.hdfgroup.org/products/java")
 951    (synopsis "Java interface for the HDF4 and HDF5 libraries")
 952    (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
 953 the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
 954 implemented in C.")
 955
 956    ;; BSD-style license:
 957    (license (license:x11-style
 958              "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
 959 /current/src/unpacked/COPYING"))))
 960
 961 (define-public hdf-eos2
 962   (package
 963     (name "hdf-eos2")
 964     (version "19.1.0")
 965     (source
 966      (origin
 967        (method url-fetch)
 968        (uri "ftp://edhs1.gsfc.nasa.gov\
 969 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
 970        (sha256
 971         (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
 972        (patches (search-patches "hdf-eos2-remove-gctp.patch"
 973                                 "hdf-eos2-build-shared.patch"
 974                                 "hdf-eos2-fortrantests.patch"))))
 975     (build-system gnu-build-system)
 976     (native-inputs
 977      `(("gfortran" ,gfortran)))
 978     (inputs
 979      `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
 980        ("zlib" ,zlib)
 981        ("libjpeg" ,libjpeg)
 982        ("gctp" ,gctp)))
 983     (arguments
 984      `( #:configure-flags '("--enable-install-include" "--enable-shared"
 985                             "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
 986         #:parallel-tests? #f))
 987     (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
 988     (synopsis "HDF4-based data format for NASA's Earth Observing System")
 989     (description "HDF-EOS2 is a software library built on HDF4 which supports
 990 the construction of data structures used in NASA's Earth Observing
 991 System (Grid, Point and Swath).")
 992
 993     ;; Source files carry a permissive license header.
 994     (license (license:non-copyleft home-page))))
 995
 996 (define-public hdf-eos5
 997   (package
 998     (name "hdf-eos5")
 999     (version "1.15")
1000     (source (origin
1001               (method url-fetch)
1002               (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1003 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1004               (sha256
1005                (base32
1006                 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1007               (patches (search-patches "hdf-eos5-build-shared.patch"
1008                                        "hdf-eos5-remove-gctp.patch"
1009                                        "hdf-eos5-fix-szip.patch"
1010                                        "hdf-eos5-fortrantests.patch"))))
1011     (native-inputs
1012      `(("gfortran" ,gfortran)))
1013     (build-system gnu-build-system)
1014     (inputs
1015      `(("hdf5" ,hdf5)
1016        ("zlib" ,zlib)
1017        ("gctp" ,gctp)))
1018     (arguments
1019      `(#:configure-flags '("--enable-install-include" "--enable-shared"
1020                            "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1021        #:parallel-tests? #f))
1022     (synopsis "HDF5-based data format for NASA's Earth Observing System")
1023     (description
1024      "HDF-EOS5 is a software library built on HDF5 to support the construction
1025 of data structures used in NASA's Earth Observing System (Grid, Point and
1026 Swath).")
1027     (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1028
1029     ;; Source files carry a permissive license header.
1030     (license (license:non-copyleft home-page))))
1031
1032 (define-public hdf5-parallel-openmpi
1033   (package (inherit hdf5)
1034     (name "hdf5-parallel-openmpi")
1035     (inputs
1036      `(("mpi" ,openmpi)
1037        ,@(package-inputs hdf5)))
1038     (arguments
1039      (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
1040                                      ,@(package-arguments hdf5))
1041        ((#:phases phases)
1042         `(modify-phases ,phases
1043            (add-before 'check 'patch-tests
1044              (lambda _
1045                ;; OpenMPI's mpirun will exit with non-zero status if it
1046                ;; detects an "abnormal termination", i.e. any process not
1047                ;; calling MPI_Finalize().  Since the test is explicitely
1048                ;; avoiding MPI_Finalize so as not to have at_exit and thus
1049                ;; H5C_flush_cache from being called, mpirun will always
1050                ;; complain, so turn this test off.
1051                (substitute* "testpar/Makefile"
1052                  (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1053                   (string-append front back "\n")))
1054                (substitute* "tools/h5diff/testph5diff.sh"
1055                  (("/bin/sh") (which "sh")))
1056                #t))))))
1057     (synopsis "Management suite for data with parallel IO support")))
1058
1059 (define-public h5check
1060   (package
1061     (name "h5check")
1062     (version "2.0.1")
1063     (source
1064      (origin
1065        (method url-fetch)
1066        (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
1067                            "h5check/src/h5check-" version ".tar.gz"))
1068        (sha256
1069         (base32
1070          "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1071     (build-system gnu-build-system)
1072     (inputs `(("hdf5" ,hdf5)))                 ;h5cc for tests
1073     (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1074     (synopsis "HDF5 format checker")
1075     (description "@code{h5check} is a validation tool for verifying that an
1076 HDF5 file is encoded according to the HDF File Format Specification.")
1077     (license (license:x11-style "file://COPYING"))))
1078
1079 (define-public itpp
1080   (package
1081     (name "itpp")
1082     (version "4.3.1")
1083     (source (origin
1084               (method url-fetch)
1085               (uri (string-append "mirror://sourceforge/itpp/itpp/"
1086                                   version "/itpp-"
1087                                   version ".tar.gz"))
1088        (sha256
1089         (base32
1090          "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1091     (build-system cmake-build-system)
1092     (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1093     (inputs `(("lapack" ,lapack)
1094               ("fftw" ,fftw)))
1095     ;; FIXME: Even though the fonts are available dvips complains:
1096     ;; "Font cmmi10 not found; characters will be left blank."
1097     (native-inputs
1098      `(("texlive" ,texlive-tiny)
1099        ("ghostscript" ,ghostscript)
1100        ("doxygen" ,doxygen)))
1101     (home-page "http://itpp.sourceforge.net")
1102     (synopsis "C++ library of maths, signal processing and communication classes")
1103     (description "IT++ is a C++ library of mathematical, signal processing and
1104 communication classes and functions.  Its main use is in simulation of
1105 communication systems and for performing research in the area of
1106 communications.  The kernel of the library consists of generic vector and
1107 matrix classes, and a set of accompanying routines.  Such a kernel makes IT++
1108 similar to MATLAB, GNU Octave or SciPy.")
1109     (license license:gpl3+)))
1110
1111 (define-public netcdf
1112   (package
1113     (name "netcdf")
1114     (version "4.4.1.1")
1115     (source
1116      (origin
1117        (method url-fetch)
1118        (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1119                            "netcdf-" version ".tar.gz"))
1120        (sha256
1121         (base32
1122          "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1123        (patches (search-patches "netcdf-date-time.patch"
1124                                 "netcdf-tst_h_par.patch"))))
1125     (build-system gnu-build-system)
1126     (native-inputs
1127      `(("m4" ,m4)
1128        ("doxygen" ,doxygen)
1129        ("graphviz" ,graphviz)))
1130     (inputs
1131      `(("hdf4" ,hdf4-alt)
1132        ("hdf5" ,hdf5)
1133        ("zlib" ,zlib)
1134        ("libjpeg" ,libjpeg)))
1135     (arguments
1136      `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
1137
1138        #:phases (modify-phases %standard-phases
1139          (add-before 'configure 'fix-source-date
1140            (lambda _
1141              ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1142              ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1143              ;; to '1st hour of the current day', and therefore makes the
1144              ;; package not reproducible.
1145              (substitute* "./configure"
1146                (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1147                 "date --date='@0'"))
1148              #t))
1149          (add-after 'configure 'patch-settings
1150            (lambda _
1151              ;; libnetcdf.settings contains the full filename of the compilers
1152              ;; used to build the library.  We truncate the hashes of those
1153              ;; filenames to avoid unnecessary references to the corresponding
1154              ;; store items.
1155              (substitute* "libnetcdf.settings"
1156                (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1157                 (string-append prefix (string-take hash 10) "...")))
1158              #t)))
1159
1160        #:parallel-tests? #f))           ;various race conditions
1161     (home-page "http://www.unidata.ucar.edu/software/netcdf/")
1162     (synopsis "Library for scientific data")
1163     (description "NetCDF is an interface for scientific data access and a
1164 software library that provides an implementation of the interface.  The netCDF
1165 library defines a machine-independent format for representing scientific data.
1166 Together, the interface, library, and format support the creation, access, and
1167 sharing of scientific data.")
1168     (license (license:x11-style "file://COPYRIGHT"))))
1169
1170 (define-public netcdf-parallel-openmpi
1171   (package (inherit netcdf)
1172     (name "netcdf-parallel-openmpi")
1173     (inputs
1174      `(("mpi" ,openmpi)
1175        ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1176                         (package-inputs netcdf))))
1177     ;; TODO: Replace pkg-config references in nc-config with absolute references
1178     (arguments
1179      (substitute-keyword-arguments (package-arguments netcdf)
1180        ((#:configure-flags flags)
1181         `(cons* "CC=mpicc" "CXX=mpicxx"
1182                 "--enable-parallel-tests"
1183                 ;; Shared libraries not supported with parallel IO.
1184                 "--disable-shared" "--with-pic"
1185                 ,flags))))))
1186
1187 (define-public netcdf-fortran
1188   (package
1189     (name "netcdf-fortran")
1190     (version "4.4.4")
1191     (source (origin
1192               (method url-fetch)
1193               (uri (string-append
1194                     "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1195                     version ".tar.gz"))
1196               (sha256
1197                (base32
1198                 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1199     (build-system gnu-build-system)
1200     (arguments
1201      `(#:parallel-tests? #f))
1202     (inputs
1203      `(("netcdf" ,netcdf)))
1204     (native-inputs
1205      `(("gfortran" ,gfortran)))
1206     (synopsis "Fortran interface for the netCDF library")
1207     (description (package-description netcdf))
1208     (home-page (package-home-page netcdf))
1209     (license (package-license netcdf))))
1210
1211 (define-public nlopt
1212   (package
1213     (name "nlopt")
1214     (version "2.4.2")
1215     (source (origin
1216               (method url-fetch)
1217               (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1218                                   version ".tar.gz"))
1219               (sha256
1220                (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1221     (build-system gnu-build-system)
1222     (arguments
1223      `(;; Shared libraries are not built by default.  They are required to
1224        ;; build the Guile, Octave, and Python bindings.
1225        #:configure-flags '("--enable-shared")
1226
1227        #:phases
1228        (modify-phases %standard-phases
1229          (add-before 'configure 'set-libnlopt-file-name
1230            (lambda* (#:key outputs #:allow-other-keys)
1231              ;; Make sure the Scheme module refers to the library by its
1232              ;; absolute file name (we cannot do that from a snippet
1233              ;; because the expansion of @libdir@ contains
1234              ;; ${exec_prefix}.)
1235              (let ((out (assoc-ref outputs "out")))
1236                (substitute* "swig/nlopt.scm.in"
1237                  (("libnlopt")
1238                   (string-append out "/lib/libnlopt")))
1239                #t))))))
1240     (inputs `(("guile" ,guile-2.0)))
1241     (native-inputs `(("pkg-config" ,pkg-config)))
1242     (home-page "http://ab-initio.mit.edu/wiki/")
1243     (synopsis "Library for nonlinear optimization")
1244     (description "NLopt is a library for nonlinear optimization, providing a
1245 common interface for a number of different free optimization routines available
1246 online as well as original implementations of various other algorithms.")
1247     (license license:lgpl2.1+)))
1248
1249 (define-public ipopt
1250   (package
1251     (name "ipopt")
1252     (version "3.12.5")
1253     (source (origin
1254               (method url-fetch)
1255               (uri (string-append
1256                     "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1257                     version".tgz"))
1258               (sha256
1259                (base32
1260                 "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
1261               (modules '((guix build utils)))
1262               (snippet
1263                ;; Make sure we don't use the bundled software.
1264                '(begin
1265                   (delete-file-recursively "ThirdParty")
1266                   #t))))
1267     (build-system gnu-build-system)
1268     (arguments
1269      '(#:phases (modify-phases %standard-phases
1270                   (add-after 'install 'add--L-flags-in-ipopt.pc
1271                     (lambda* (#:key inputs outputs #:allow-other-keys)
1272                       ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1273                       ;; move it to "Libs.private" where it belongs, and add a
1274                       ;; '-L' flag for LAPACK.
1275                       (let ((out    (assoc-ref outputs "out"))
1276                             (lapack (assoc-ref inputs "lapack")))
1277                         (substitute* (string-append out "/lib/pkgconfig/"
1278                                                     "ipopt.pc")
1279                           (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1280                            (string-append "Libs: " before " " after "\n"
1281                                           "Libs.private: " before
1282                                           "-L" lapack "/lib -llapack -lblas "
1283                                           after "\n")))
1284                         #t))))))
1285     (native-inputs
1286      `(("gfortran" ,gfortran)))
1287     (inputs
1288      ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
1289      `(("lapack" ,lapack)))                    ;for both libblas and liblapack
1290     (home-page "http://www.coin-or.org")
1291     (synopsis "Large-scale nonlinear optimizer")
1292     (description
1293      "The Interior Point Optimizer (IPOPT) is a software package for
1294 large-scale nonlinear optimization.  It provides C++, C, and Fortran
1295 interfaces.")
1296     (license license:epl1.0)))
1297
1298 (define-public ceres
1299   (package
1300     (name "ceres-solver")
1301     (version "1.14.0")
1302     (home-page "http://ceres-solver.org/")
1303     (source (origin
1304               (method url-fetch)
1305               (uri (string-append home-page "ceres-solver-"
1306                                   version ".tar.gz"))
1307               (sha256
1308                (base32
1309                 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
1310     (build-system cmake-build-system)
1311     (arguments
1312      ;; TODO: Build HTML user documentation and install separately.
1313      '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
1314                            "-DBUILD_SHARED_LIBS=ON")
1315
1316        #:phases (modify-phases %standard-phases
1317                   (add-before 'configure 'set-library-directory
1318                     (lambda _
1319                       ;; Install libraries to lib/, not lib64/.
1320                       (substitute* "internal/ceres/CMakeLists.txt"
1321                         (("set\\(LIB_SUFFIX \"64\"\\)")
1322                          "set(LIB_SUFFIX \"\")"))
1323                       #t)))))
1324     (native-inputs
1325      `(("pkg-config" ,pkg-config)))
1326     (propagated-inputs
1327      `(("glog" ,glog)))                           ;for #include <glog/glog.h>
1328     (inputs
1329      `(("eigen" ,eigen)
1330        ("blas" ,openblas)
1331        ("lapack" ,lapack)
1332        ("suitesparse" ,suitesparse)
1333        ("gflags" ,gflags)))
1334     (synopsis "C++ library for solving large optimization problems")
1335     (description
1336      "Ceres Solver is a C++ library for modeling and solving large,
1337 complicated optimization problems.  It is a feature rich, mature and
1338 performant library which has been used in production since 2010.  Ceres Solver
1339 can solve two kinds of problems:
1340 @enumerate
1341 @item non-linear least squares problems with bounds constraints;
1342 @item general unconstrained optimization problems.
1343 @end enumerate\n")
1344     (license license:bsd-3)))
1345
1346 ;; For a fully featured Octave, users are strongly recommended also to install
1347 ;; the following packages: less, ghostscript, gnuplot.
1348 (define-public octave
1349   (package
1350     (name "octave")
1351     (version "4.4.1")
1352     (source
1353      (origin
1354       (method url-fetch)
1355       (uri (string-append "mirror://gnu/octave/octave-"
1356                           version ".tar.lz"))
1357       (sha256
1358        (base32
1359         "0jsdgizlv02an2ppfjwk5qf209zpwi3317yb7jvlsjzxnir3lvhy"))))
1360     (build-system gnu-build-system)
1361     (inputs
1362      `(("lapack" ,lapack)
1363        ("qhull" ,qhull)
1364        ("readline" ,readline)
1365        ("gl2ps" ,gl2ps)
1366        ("glpk" ,glpk)
1367        ("fftw" ,fftw)
1368        ("fftwf" ,fftwf)
1369        ("arpack" ,arpack-ng)
1370        ("pcre" ,pcre)
1371        ("fltk" ,fltk)
1372        ("fontconfig" ,fontconfig)
1373        ("freetype" ,freetype)
1374        ("hdf5" ,hdf5)
1375        ("libxft" ,libxft)
1376        ("mesa" ,mesa)
1377        ("glu" ,glu)
1378        ("zlib" ,zlib)
1379        ("curl" ,curl)
1380        ("texinfo" ,texinfo)
1381        ("graphicsmagick" ,graphicsmagick)
1382        ("suitesparse" ,suitesparse)
1383        ("libsndfile" ,libsndfile)
1384        ("portaudio" ,portaudio)
1385        ("alsa-lib" ,alsa-lib)))
1386     (native-inputs
1387      `(("lzip" ,lzip)
1388        ("gfortran" ,gfortran)
1389        ("pkg-config" ,pkg-config)
1390        ("perl" ,perl)
1391        ;; The following inputs are not actually used in the build process.
1392        ;; However, the ./configure gratuitously tests for their existence and
1393        ;; assumes that programs not present at build time are also not, and
1394        ;; can never be, available at run time!  If these inputs are therefore
1395        ;; not present, support for them will be built out.  However, Octave
1396        ;; will still run without them, albeit without the features they
1397        ;; provide.
1398        ("less" ,less)
1399        ("ghostscript" ,ghostscript)
1400        ("gnuplot" ,gnuplot)))
1401     (arguments
1402      `(#:configure-flags
1403        (list (string-append "--with-shell="
1404                             (assoc-ref %build-inputs "bash")
1405                             "/bin/sh"))
1406        #:phases
1407        (modify-phases %standard-phases
1408          (add-after 'configure 'configure-makeinfo
1409            (lambda* (#:key inputs #:allow-other-keys)
1410              (substitute* "libinterp/corefcn/help.cc"
1411                (("Vmakeinfo_program = \"makeinfo\"")
1412                 (string-append "Vmakeinfo_program = \""
1413                                (assoc-ref inputs "texinfo")
1414                                "/bin/makeinfo\"")))
1415              #t)))))
1416     (home-page "https://www.gnu.org/software/octave/")
1417     (synopsis "High-level language for numerical computation")
1418     (description "GNU Octave is a high-level interpreted language that is
1419 specialized for numerical computations.  It can be used for both linear and
1420 non-linear applications and it provides great support for visualizing results.
1421 Work may be performed both at the interactive command-line as well as via
1422 script files.")
1423     (license license:gpl3+)))
1424
1425 (define-public qtoctave
1426   (package (inherit octave)
1427     (name "qtoctave")
1428     (source (origin
1429               (inherit (package-source octave))))
1430     (inputs
1431      `(("qscintilla" ,qscintilla)
1432        ("qt" ,qtbase)
1433        ,@(package-inputs octave)))
1434     (native-inputs
1435      `(("qttools" , qttools) ;for lrelease
1436        ("texlive" ,texlive) ;for texi2dvi
1437        ,@(package-native-inputs octave)))
1438     (arguments
1439      (substitute-keyword-arguments (package-arguments octave)
1440        ((#:phases phases)
1441         `(modify-phases ,phases
1442            (add-before 'configure 'patch-qscintilla-library-name
1443              (lambda* (#:key inputs #:allow-other-keys)
1444                ;; The QScintilla library that the Octave configure script tries
1445                ;; to link with should be named libqscintilla-qt5.so, but the
1446                ;; QScintilla input provides the shared library as
1447                ;; libqscintilla2_qt5.so.
1448                (substitute* "configure"
1449                  (("qscintilla2-qt5")
1450                   "qscintilla2_qt5"))
1451                #t))))))))
1452
1453 (define-public opencascade-oce
1454   (package
1455     (name "opencascade-oce")
1456     (version "0.17.2")
1457     (source
1458       (origin
1459         (method url-fetch)
1460         (uri (string-append
1461                "https://github.com/tpaviot/oce/archive/OCE-"
1462                version
1463                ".tar.gz"))
1464         (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
1465         (sha256
1466           (base32
1467             "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
1468     (build-system cmake-build-system)
1469     (arguments
1470      '(#:configure-flags
1471         (list "-DOCE_TESTING:BOOL=ON"
1472               "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1473               "-DOCE_DRAW:BOOL=ON"
1474               (string-append "-DOCE_INSTALL_PREFIX:PATH="
1475                         (assoc-ref %outputs "out"))
1476               "-UCMAKE_INSTALL_RPATH")))
1477     (inputs
1478       `(("freetype" ,freetype)
1479         ("glu" ,glu)
1480         ("libxmu" ,libxmu)
1481         ("mesa" ,mesa)
1482         ("tcl" ,tcl)
1483         ("tk" ,tk)))
1484     (native-inputs
1485       `(("python" ,python-wrapper)))
1486     (home-page "https://github.com/tpaviot/oce")
1487     (synopsis "Libraries for 3D modeling and numerical simulation")
1488     (description
1489      "Open CASCADE is a set of libraries for the development of applications
1490 dealing with 3D CAD data or requiring industrial 3D capabilities.  It includes
1491 C++ class libraries providing services for 3D surface and solid modeling, CAD
1492 data exchange, and visualization.  It is used for development of specialized
1493 software dealing with 3D models in design (CAD), manufacturing (CAM),
1494 numerical simulation (CAE), measurement equipment (CMM), and quality
1495 control (CAQ) domains.
1496
1497 This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1498 patches, improvements, and experiments contributed by users over the official
1499 Open CASCADE library.")
1500     (license (list license:lgpl2.1; OCE libraries, with an exception for the
1501                                   ; use of header files; see
1502                                   ; OCCT_LGPL_EXCEPTION.txt
1503                    license:public-domain; files
1504                                   ; src/Standard/Standard_StdAllocator.hxx and
1505                                   ; src/NCollection/NCollection_StdAllocator.hxx
1506                    license:expat; file src/OpenGl/OpenGl_glext.h
1507                    license:bsd-3)))); test framework gtest
1508
1509 (define-public gmsh
1510   (package
1511     (name "gmsh")
1512     (version "2.16.0")
1513     (source
1514      (origin
1515       (method url-fetch)
1516       (uri (string-append "http://gmsh.info/src/gmsh-"
1517                           version "-source.tgz"))
1518       (sha256
1519        (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
1520       (modules '((guix build utils)))
1521       (snippet
1522        ;; Remove non-free METIS code
1523        '(begin
1524           (delete-file-recursively "contrib/Metis")
1525           #t))))
1526     (build-system cmake-build-system)
1527     (propagated-inputs
1528      `(("fltk" ,fltk)
1529        ("gfortran" ,gfortran)
1530        ("gmp" ,gmp)
1531        ("hdf5" ,hdf5)
1532        ("lapack" ,lapack)
1533        ("mesa" ,mesa)
1534        ("glu" ,glu)
1535        ("opencascade-oce" ,opencascade-oce)
1536        ("libx11" ,libx11)
1537        ("libxext" ,libxext)))
1538     (inputs
1539      `(("fontconfig" ,fontconfig)
1540        ("libxft" ,libxft)))
1541     (arguments
1542      `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1543                            "-DENABLE_BUILD_SHARED:BOOL=ON"
1544                            "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
1545     (home-page "http://www.geuz.org/gmsh/")
1546     (synopsis "3D finite element grid generator")
1547     (description "Gmsh is a 3D finite element grid generator with a built-in
1548 CAD engine and post-processor.  Its design goal is to provide a fast, light
1549 and user-friendly meshing tool with parametric input and advanced
1550 visualization capabilities.  Gmsh is built around four modules: geometry,
1551 mesh, solver and post-processing.  The specification of any input to these
1552 modules is done either interactively using the graphical user interface or in
1553 ASCII text files using Gmsh's own scripting language.")
1554     (license license:gpl2+)))
1555
1556 (define-public maxflow
1557   (package
1558     (name "maxflow")
1559     (version "3.04")
1560     (source (origin
1561               (method git-fetch)
1562               (uri (git-reference
1563                     (url "https://github.com/gerddie/maxflow.git")
1564                     (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
1565               (file-name (string-append name "-" version "-checkout"))
1566               (sha256
1567                (base32
1568                 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1569     (build-system cmake-build-system)
1570     (home-page "http://pub.ist.ac.at/~vnk/software.html")
1571     (synopsis "Library implementing Maxflow algorithm")
1572     (description "An implementation of the maxflow algorithm described in
1573 @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1574 Energy Minimization in Computer Vision.\n
1575 Yuri Boykov and Vladimir Kolmogorov.\n
1576 In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1577 September 2004}")
1578     (license license:gpl3+)))
1579
1580 (define-public petsc
1581   (package
1582     (name "petsc")
1583     (version "3.9.3")
1584     (source
1585      (origin
1586       (method url-fetch)
1587       ;; The *-lite-* tarball does not contain the *large* documentation
1588       (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1589                           "petsc-lite-" version ".tar.gz"))
1590       (sha256
1591        (base32 "1fwkbwv4g7zf2lc8fw865xd0bl9anb6jaczfis5dff7h449gwa48"))))
1592     (outputs '("out"                    ;libraries and headers
1593                "examples"))             ;~30MiB of examples
1594     (build-system gnu-build-system)
1595     (native-inputs
1596      `(("python" ,python-2)))
1597     (inputs
1598      `(("gfortran" ,gfortran)
1599        ("lapack" ,lapack)
1600        ("superlu" ,superlu)
1601        ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1602        ;; leaving out opengl, as configuration seems to only be for mac
1603        ))
1604     (arguments
1605      `(#:test-target "test"
1606        #:parallel-build? #f             ;build is parallel by default
1607        #:configure-flags
1608        `("--with-mpi=0"
1609          "--with-openmp=1"
1610          "--with-superlu=1")
1611        #:make-flags
1612        ;; Honor (parallel-job-count) for build.  Do not use --with-make-np,
1613        ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1614        (list (format #f "MAKE_NP=~a" (parallel-job-count)))
1615        #:phases
1616        (modify-phases %standard-phases
1617         (replace 'configure
1618           ;; PETSc's configure script is actually a python script, so we can't
1619           ;; run it with bash.
1620           (lambda* (#:key outputs (configure-flags '())
1621                           #:allow-other-keys)
1622             (let* ((prefix (assoc-ref outputs "out"))
1623                    (flags `(,(string-append "--prefix=" prefix)
1624                             ,@configure-flags)))
1625               (format #t "build directory: ~s~%" (getcwd))
1626               (format #t "configure flags: ~s~%" flags)
1627               (apply invoke "./configure" flags))))
1628         (add-after 'configure 'clean-local-references
1629           (lambda* (#:key outputs #:allow-other-keys)
1630             (let ((out (assoc-ref outputs "out")))
1631               (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
1632                 ;; Prevent build directory from leaking into compiled code
1633                 (((getcwd)) out)
1634                 ;; Scrub timestamp for reproducibility
1635                 ((".*Libraries compiled on.*") ""))
1636               (substitute* (find-files "." "petscvariables")
1637                 ;; Do not expose build machine characteristics, set to defaults.
1638                 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1639                 (("NPMAX = [:digit:]+") "NPMAX = 2"))
1640               #t)))
1641         (add-after 'install 'clean-install
1642           ;; Try to keep installed files from leaking build directory names.
1643           (lambda* (#:key inputs outputs #:allow-other-keys)
1644             (let ((out (assoc-ref outputs "out")))
1645               (substitute* (map (lambda (file)
1646                                   (string-append out "/lib/petsc/conf/" file))
1647                                 '("petscvariables"))
1648                 (((getcwd)) out))
1649               ;; Make compiler references point to the store
1650               (substitute* (string-append out "/lib/petsc/conf/petscvariables")
1651                 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1652                  (string-append "= " (which compiler))))
1653               ;; PETSc installs some build logs, which aren't necessary.
1654               (for-each (lambda (file)
1655                           (let ((f (string-append out "/lib/petsc/conf/" file)))
1656                             (when (file-exists? f)
1657                               (delete-file f))))
1658                         '("configure.log" "make.log" "gmake.log"
1659                           "test.log" "error.log" "RDict.db"
1660                           "PETScBuildInternal.cmake"
1661                           ;; Once installed, should uninstall with Guix
1662                           "uninstall.py"))
1663               #t)))
1664         (add-after 'install 'move-examples
1665           (lambda* (#:key outputs #:allow-other-keys)
1666             (let* ((out (assoc-ref outputs "out"))
1667                    (examples (assoc-ref outputs "examples"))
1668                    (exdir (string-append out "/share/petsc/examples"))
1669                    (exdir' (string-append examples "/share/petsc/examples")))
1670               (copy-recursively exdir exdir')
1671               (delete-file-recursively exdir)
1672               #t))))))
1673     (home-page "http://www.mcs.anl.gov/petsc")
1674     (synopsis "Library to solve PDEs")
1675     (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1676 data structures and routines for the scalable (parallel) solution of
1677 scientific applications modeled by partial differential equations.")
1678     (license (license:non-copyleft
1679               "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1680
1681 (define-public petsc-complex
1682   (package (inherit petsc)
1683     (name "petsc-complex")
1684     (arguments
1685      (substitute-keyword-arguments (package-arguments petsc)
1686        ((#:configure-flags cf)
1687         `(cons "--with-scalar-type=complex" ,cf))))
1688     (synopsis "Library to solve PDEs (with complex scalars)")))
1689
1690 (define-public petsc-openmpi
1691   (package (inherit petsc)
1692     (name "petsc-openmpi")
1693     (inputs
1694      `(("openmpi" ,openmpi)
1695        ("hdf5" ,hdf5-parallel-openmpi)
1696        ,@(package-inputs petsc)))
1697     (arguments
1698      (substitute-keyword-arguments (package-arguments petsc)
1699        ((#:configure-flags cf)
1700         ``("--with-mpiexec=mpirun"
1701            ,(string-append "--with-mpi-dir="
1702                            (assoc-ref %build-inputs "openmpi"))
1703            ,(string-append "--with-hdf5-include="
1704                            (assoc-ref %build-inputs "hdf5") "/include")
1705            ,(string-append "--with-hdf5-lib="
1706                            (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
1707            ,@(delete "--with-mpi=0" ,cf)))
1708        ((#:phases phases)
1709         `(modify-phases ,phases
1710            (add-before 'check 'set-test-environment
1711              (lambda _
1712                ;; By default, running the test suite would fail because 'ssh'
1713                ;; could not be found in $PATH.  Define this variable to
1714                ;; placate Open MPI without adding a dependency on OpenSSH (the
1715                ;; agent isn't used anyway.)
1716                (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
1717                #t))))))
1718     (synopsis "Library to solve PDEs (with MPI support)")))
1719
1720 (define-public petsc-complex-openmpi
1721   (package (inherit petsc-complex)
1722     (name "petsc-complex-openmpi")
1723     (inputs
1724      `(("openmpi" ,openmpi)
1725        ,@(package-inputs petsc-complex)))
1726     (arguments
1727      (substitute-keyword-arguments (package-arguments petsc-complex)
1728        ((#:configure-flags cf)
1729         ``("--with-mpiexec=mpirun"
1730            ,(string-append "--with-mpi-dir="
1731                            (assoc-ref %build-inputs "openmpi"))
1732            ,@(delete "--with-mpi=0" ,cf)))))
1733     (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
1734
1735
1736 (define-public python-kiwisolver
1737   (package
1738     (name "python-kiwisolver")
1739     (version "1.0.1")
1740     (source (origin
1741               (method url-fetch)
1742               (uri (pypi-uri "kiwisolver" version))
1743               (sha256
1744                (base32
1745                 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
1746     (build-system python-build-system)
1747     (home-page "https://github.com/nucleic/kiwi")
1748     (synopsis "Fast implementation of the Cassowary constraint solver")
1749     (description
1750      "Kiwi is an efficient C++ implementation of the Cassowary constraint
1751 solving algorithm.  Kiwi has been designed from the ground up to be
1752 lightweight and fast.  Kiwi ranges from 10x to 500x faster than the original
1753 Cassowary solver with typical use cases gaining a 40x improvement.  Memory
1754 savings are consistently > 5x.")
1755     (license license:bsd-3)))
1756
1757 (define-public python2-kiwisolver
1758   (package-with-python2 python-kiwisolver))
1759
1760 (define-public slepc
1761   (package
1762     (name "slepc")
1763     (version "3.9.2")
1764     (source
1765      (origin
1766        (method url-fetch)
1767        (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
1768                            version ".tar.gz"))
1769        (sha256
1770         (base32
1771          "0gmhdqac8zm3jx43h935z7bflazjnpvqxjv4jh5za2y1z2rqax94"))))
1772     (build-system gnu-build-system)
1773     (native-inputs
1774      `(("python" ,python-2)))
1775     (inputs
1776      `(("arpack" ,arpack-ng)
1777        ("gfortran" ,gfortran)))
1778     (propagated-inputs
1779      `(("petsc" ,petsc)))
1780     (arguments
1781      `(#:parallel-build? #f             ;build is parallel by default
1782        #:configure-flags
1783        `(,(string-append "--with-arpack-dir="
1784                          (assoc-ref %build-inputs "arpack") "/lib"))
1785        #:make-flags                     ;honor (parallel-job-count)
1786        `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
1787        #:phases
1788        (modify-phases %standard-phases
1789          (replace 'configure
1790           ;; configure is a python script, so we can't run it with bash.
1791           (lambda* (#:key inputs outputs (configure-flags '())
1792                     #:allow-other-keys)
1793             (let* ((prefix (assoc-ref outputs "out"))
1794                    (flags `(,(string-append "--prefix=" prefix)
1795                             ,@configure-flags)))
1796               (format #t "build directory: ~s~%" (getcwd))
1797               (format #t "configure flags: ~s~%" flags)
1798               (setenv "SLEPC_DIR" (getcwd))
1799               (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
1800               (apply invoke "./configure" flags))))
1801          (add-after 'install 'delete-doc
1802           ;; TODO: SLEPc installs HTML documentation alongside headers in
1803           ;; $out/include.  We'd like to move them to share/doc, but delete
1804           ;; them for now, as they are incomplete and installing the complete
1805           ;; documentation is difficult.
1806           (lambda* (#:key outputs #:allow-other-keys)
1807             (let* ((out (assoc-ref outputs "out")))
1808               (for-each delete-file (find-files out "\\.html$"))
1809               #t)))
1810          (add-after 'install 'clean-install
1811           ;; Clean up unnecessary build logs from installation.
1812           (lambda* (#:key outputs #:allow-other-keys)
1813             (let ((out (assoc-ref outputs "out")))
1814               (for-each (lambda (file)
1815                           (let ((f (string-append out "/lib/slepc/conf/" file)))
1816                             (when (file-exists? f)
1817                               (delete-file f))))
1818                         '("configure.log" "make.log" "gmake.log"
1819                           "test.log" "error.log" "RDict.db"
1820                           "uninstall.py"))
1821               #t))))))
1822     (home-page "http://slepc.upv.es")
1823     (synopsis "Scalable library for eigenproblems")
1824     (description "SLEPc is a software library for the solution of large sparse
1825 eigenproblems on parallel computers.  It can be used for the solution of
1826 linear eigenvalue problems formulated in either standard or generalized form,
1827 as well as other related problems such as the singular value decomposition.
1828 The emphasis of the software is on methods and techniques appropriate for
1829 problems in which the associated matrices are sparse, for example, those
1830 arising after the discretization of partial differential equations.")
1831     (license license:bsd-2)))
1832
1833 (define-public slepc-complex
1834   (package (inherit slepc)
1835     (name "slepc-complex")
1836     (propagated-inputs
1837      `(("petsc" ,petsc-complex)
1838        ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1839     (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1840
1841 (define-public slepc-openmpi
1842   (package (inherit slepc)
1843     (name "slepc-openmpi")
1844     (arguments
1845      (substitute-keyword-arguments (package-arguments slepc)
1846        ((#:phases phases '%standard-phases)
1847         `(modify-phases ,phases
1848            (add-before 'check 'set-test-environment
1849              (lambda _
1850                ;; By default, running the test suite would fail because 'ssh'
1851                ;; could not be found in $PATH.  Define this variable to
1852                ;; placate Open MPI without adding a dependency on OpenSSH (the
1853                ;; agent isn't used anyway.)
1854                (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
1855                #t))))))
1856     (inputs
1857      `(("mpi" ,openmpi)
1858        ("arpack" ,arpack-ng-openmpi)
1859        ,@(alist-delete "arpack" (package-inputs slepc))))
1860     (propagated-inputs
1861      `(("petsc" ,petsc-openmpi)
1862        ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1863     (synopsis "Scalable library for eigenproblems (with MPI support)")))
1864
1865 (define-public slepc-complex-openmpi
1866   (package (inherit slepc-openmpi)
1867     (name "slepc-complex-openmpi")
1868     (propagated-inputs
1869      `(("petsc" ,petsc-complex-openmpi)
1870        ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1871     (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1872
1873 (define-public mumps
1874   (package
1875     (name "mumps")
1876     (version "5.1.2")
1877     (source
1878      (origin
1879        (method url-fetch)
1880        (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
1881                            version ".tar.gz"))
1882        (sha256
1883         (base32
1884          "1s9asin08zqzmh08257sdghhivvy9vjif7c53fhaxaax2kd5qd7b"))
1885        (patches (search-patches "mumps-build-parallelism.patch"))))
1886     (build-system gnu-build-system)
1887     (inputs
1888      `(("fortran" ,gfortran)
1889        ;; These are required for linking against mumps, but we let the user
1890        ;; declare the dependency.
1891        ("blas" ,openblas)
1892        ("metis" ,metis)
1893        ("scotch" ,scotch)))
1894     (arguments
1895      `(#:modules ((ice-9 match)
1896                   (ice-9 popen)
1897                   (srfi srfi-1)
1898                   ,@%gnu-build-system-modules)
1899        #:phases
1900        (modify-phases %standard-phases
1901          (replace 'configure
1902           (lambda* (#:key inputs #:allow-other-keys)
1903             (call-with-output-file "Makefile.inc"
1904               (lambda (port)
1905                 (format port "
1906 PLAT         =
1907 LIBEXT       = .a
1908 OUTC         = -o
1909 OUTF         = -o
1910 RM           = rm -f~:[
1911 CC           = gcc
1912 FC           = gfortran
1913 FL           = gfortran
1914 INCSEQ       = -I$(topdir)/libseq
1915 LIBSEQ       = -L$(topdir)/libseq -lmpiseq
1916 LIBSEQNEEDED = libseqneeded~;
1917 CC           = mpicc
1918 FC           = mpifort
1919 FL           = mpifort~]
1920 AR           = ar vr # rules require trailing space, ugh...
1921 RANLIB       = ranlib
1922 LIBBLAS      = -L~a -lopenblas~@[
1923 SCALAP       = -L~a -lscalapack~]
1924 LIBOTHERS    = -pthread
1925 CDEFS        = -DAdd_
1926 PIC          = -fPIC
1927 OPTF         = -O2 -DALLOW_NON_INIT $(PIC)
1928 OPTL         = -O2 $(PIC)
1929 OPTC         = -O2 $(PIC)
1930 INCS         = $(INCSEQ)
1931 LIBS         = $(SCALAP) $(LIBSEQ)
1932 LPORDDIR     = $(topdir)/PORD/lib
1933 IPORD        = -I$(topdir)/PORD/include
1934 LPORD        = -L$(LPORDDIR) -lpord
1935 ORDERINGSF   = -Dpord~@[
1936 METISDIR     = ~a
1937 IMETIS       = -I$(METISDIR)/include
1938 LMETIS       = -L$(METISDIR)/lib -lmetis
1939 ORDERINGSF  += -Dmetis~]~@[~:{
1940 SCOTCHDIR    = ~a
1941 ISCOTCH      = -I$(SCOTCHDIR)/include
1942 LSCOTCH      = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
1943 ORDERINGSF  += ~a~}~]
1944 ORDERINGSC   = $(ORDERINGSF)
1945 LORDERINGS   = $(LPORD) $(LMETIS) $(LSCOTCH)
1946 IORDERINGSF  = $(ISCOTCH)
1947 IORDERINGSC  = $(IPORD) $(IMETIS) $(ISCOTCH)"
1948                         (assoc-ref inputs "mpi")
1949                         (assoc-ref inputs "blas")
1950                         (assoc-ref inputs "scalapack")
1951                         (assoc-ref inputs "metis")
1952                         (match (list (assoc-ref inputs "pt-scotch")
1953                                      (assoc-ref inputs "scotch"))
1954                           ((#f #f)
1955                            #f)
1956                           ((#f scotch)
1957                            `((,scotch "" "-Dscotch")))
1958                           ((ptscotch _)
1959                            `((,ptscotch
1960                               "-lptesmumps -lptscotch -lptscotcherr "
1961                               "-Dptscotch")))))))))
1962          (replace 'build
1963           ;; By default only the d-precision library is built.  Make with "all"
1964           ;; target so that all precision libraries and examples are built.
1965           (lambda _
1966             (invoke "make" "all"
1967                     (format #f "-j~a" (parallel-job-count)))))
1968          (replace 'check
1969           ;; Run the simple test drivers, which read test input from stdin:
1970           ;; from the "real" input for the single- and double-precision
1971           ;; testers, and from the "cmplx" input for complex-precision
1972           ;; testers.  The EXEC-PREFIX key is used by the mumps-openmpi
1973           ;; package to prefix execution with "mpirun".
1974           (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
1975             (with-directory-excursion "examples"
1976               (every
1977                (lambda (prec type)
1978                  (let ((tester (apply open-pipe*
1979                                       `(,OPEN_WRITE
1980                                         ,@exec-prefix
1981                                         ,(string-append "./" prec
1982                                                         "simpletest"))))
1983                        (input  (open-input-file
1984                                 (string-append "input_simpletest_" type))))
1985                    (begin
1986                      (dump-port input tester)
1987                      (close-port input)
1988                      (zero? (close-pipe tester)))))
1989                '("s" "d" "c" "z")
1990                '("real" "real" "cmplx" "cmplx")))))
1991          (replace 'install
1992            (lambda* (#:key outputs #:allow-other-keys)
1993              (let* ((out (assoc-ref outputs "out"))
1994                     (libdir (string-append out "/lib")))
1995                (copy-recursively "lib" libdir)
1996                (copy-recursively "include" (string-append out "/include"))
1997                (when (file-exists? "libseq/libmpiseq.a")
1998                  (install-file "libseq/libmpiseq.a" libdir))
1999                #t))))))
2000     (home-page "http://mumps.enseeiht.fr")
2001     (synopsis "Multifrontal sparse direct solver")
2002     (description
2003      "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
2004 sparse system of linear equations A x = b using Guassian elimination.")
2005     (license license:cecill-c)))
2006
2007 (define-public mumps-metis
2008   (package (inherit mumps)
2009     (name "mumps-metis")
2010     (inputs
2011      (alist-delete "scotch" (package-inputs mumps)))))
2012
2013 (define-public mumps-openmpi
2014   (package (inherit mumps)
2015     (name "mumps-openmpi")
2016     (inputs
2017      `(("mpi" ,openmpi)
2018        ("scalapack" ,scalapack)
2019        ("pt-scotch" ,pt-scotch)
2020        ,@(alist-delete "scotch" (package-inputs mumps))))
2021     (arguments
2022      (substitute-keyword-arguments (package-arguments mumps)
2023        ((#:phases phases)
2024         `(modify-phases ,phases
2025            (add-before 'check 'set-test-environment
2026              (lambda _
2027                ;; By default, running the test suite would fail because 'ssh'
2028                ;; could not be found in $PATH.  Define this variable to
2029                ;; placate Open MPI without adding a dependency on OpenSSH (the
2030                ;; agent isn't used anyway.)
2031                (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
2032                #t))
2033            (replace 'check
2034              (lambda _
2035                ((assoc-ref ,phases 'check)
2036                 #:exec-prefix '("mpirun" "-n" "2"))))))))
2037     (synopsis "Multifrontal sparse direct solver (with MPI)")))
2038
2039 (define-public mumps-metis-openmpi
2040   (package (inherit mumps-openmpi)
2041     (name "mumps-metis-openmpi")
2042     (inputs
2043      (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
2044
2045 (define-public r-quadprog
2046   (package
2047     (name "r-quadprog")
2048     (version "1.5-5")
2049     (source
2050      (origin
2051        (method url-fetch)
2052        (uri (cran-uri "quadprog" version))
2053        (sha256
2054         (base32
2055          "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
2056     (build-system r-build-system)
2057     (native-inputs
2058      `(("gfortran" ,gfortran)))
2059     (home-page "https://cran.r-project.org/web/packages/quadprog")
2060     (synopsis "Functions to solve quadratic programming problems")
2061     (description
2062      "This package contains routines and documentation for solving quadratic
2063 programming problems.")
2064     (license license:gpl3+)))
2065
2066 (define-public r-pracma
2067   (package
2068     (name "r-pracma")
2069     (version "2.1.5")
2070     (source (origin
2071       (method url-fetch)
2072       (uri (cran-uri "pracma" version))
2073       (sha256
2074         (base32 "18cv7c2gvagbmggfbsy2xk9bpn47izd0qrmqnc3q7afvj6pr6nf9"))))
2075     (build-system r-build-system)
2076     (propagated-inputs
2077      `(("r-quadprog" ,r-quadprog)))
2078     (home-page "https://cran.r-project.org/web/packages/pracma")
2079     (synopsis "Practical numerical math functions")
2080     (description "This package provides functions for numerical analysis and
2081 linear algebra, numerical optimization, differential equations, plus some
2082 special functions.  It uses Matlab function names where appropriate to simplify
2083 porting.")
2084     (license license:gpl3+)))
2085
2086 (define-public ruby-asciimath
2087   (package
2088     (name "ruby-asciimath")
2089     (version "1.0.4")
2090     (source
2091      (origin
2092        (method url-fetch)
2093        (uri (rubygems-uri "asciimath" version))
2094        (sha256
2095         (base32
2096          "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
2097     (build-system ruby-build-system)
2098     (arguments
2099      '(#:phases
2100        (modify-phases %standard-phases
2101          ;; Apply this patch
2102          ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
2103          (add-after 'unpack 'patch-remove-spurious-backslashes
2104            (lambda _
2105              (substitute* "spec/parser_spec.rb"
2106                (("\\\\\"")
2107                 "\"")))))))
2108     (native-inputs
2109      `(("bundler" ,bundler)
2110        ("ruby-rspec" ,ruby-rspec)))
2111     (synopsis "AsciiMath parsing and conversion library")
2112     (description
2113      "A pure Ruby AsciiMath parsing and conversion library.  AsciiMath is an
2114 easy-to-write markup language for mathematics.")
2115     (home-page "https://github.com/asciidoctor/asciimath")
2116     (license license:expat)))
2117
2118 (define-public superlu
2119   (package
2120     (name "superlu")
2121     (version "5.2.1")
2122     (source
2123      (origin
2124        (method url-fetch)
2125        (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2126                            "superlu_" version ".tar.gz"))
2127        (sha256
2128         (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
2129        (modules '((guix build utils)))
2130        (snippet
2131         ;; Replace the non-free implementation of MC64 with a stub adapted
2132         ;; from Debian
2133         '(begin
2134            (use-modules (ice-9 regex)
2135                         (ice-9 rdelim))
2136            (call-with-output-file "SRC/mc64ad.c"
2137              (lambda (port)
2138                (display "
2139 #include <stdio.h>
2140 #include <stdlib.h>
2141 void mc64id_(int *a) {
2142   fprintf (stderr, \"SuperLU: non-free MC64 not available.  Aborting.\\n\");
2143   abort ();
2144 }
2145 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2146               int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2147   fprintf (stderr, \"SuperLU: non-free MC64 not available.  Aborting.\\n\");
2148   abort ();
2149 }\n" port)))
2150            ;; Remove the corresponding license verbiage.  MC64 license follows
2151            ;; a "------" line separator.
2152            (with-atomic-file-replacement "License.txt"
2153              (let ((rx (make-regexp "-{8}")))
2154                (lambda (in out)
2155                  (let loop ()
2156                    (let ((line (read-line in 'concat)))
2157                     (unless (regexp-exec rx line)
2158                       (display line out)
2159                       (loop))))
2160                  #t)))))))
2161     (build-system cmake-build-system)
2162     (native-inputs
2163      `(("tcsh" ,tcsh)))
2164     (inputs
2165      `(("blas" ,openblas)
2166        ("gfortran" ,gfortran)))
2167     (arguments
2168      `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2169                            "-DTPL_BLAS_LIBRARIES=openblas"
2170                            "-DBUILD_SHARED_LIBS:BOOL=YES")))
2171     (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
2172     (synopsis "Supernodal direct solver for sparse linear systems")
2173     (description
2174      "SuperLU is a general purpose library for the direct solution of large,
2175 sparse, nonsymmetric systems of linear equations on high performance machines.
2176 The library is written in C and is callable from either C or Fortran.  The
2177 library routines perform an LU decomposition with partial pivoting and
2178 triangular system solves through forward and back substitution.  The library
2179 also provides threshold-based ILU factorization preconditioners.")
2180     (license (list license:bsd-3
2181                    license:gpl2+        ;EXAMPLE/*fgmr.c
2182                    (license:fsf-free "file://SRC/colamd.h")))))
2183
2184 (define-public superlu-dist
2185   (package
2186     (name "superlu-dist")
2187     (version "5.3.0")
2188     (source
2189      (origin
2190        (method url-fetch)
2191        (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2192                            "superlu_dist_" version ".tar.gz"))
2193        (sha256
2194         (base32 "0ja5ihqivkda1wd58y4lmzvmwssm9g91f70c5q0fzwhng6580h6y"))
2195        (modules '((guix build utils)))
2196        (snippet
2197         ;; Replace the non-free implementation of MC64 with a stub
2198         '(begin
2199            (use-modules (ice-9 regex)
2200                         (ice-9 rdelim))
2201            (call-with-output-file "SRC/mc64ad_dist.c"
2202              (lambda (port)
2203                (display "
2204 #include <stdio.h>
2205 #include <stdlib.h>
2206 void mc64id_dist(int *a) {
2207   fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available.  Aborting.\\n\");
2208   abort ();
2209 }
2210 void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2211               int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2212   fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available.  Aborting.\\n\");
2213   abort ();
2214 }\n" port)))
2215            (substitute* "SRC/util.c"    ;adjust default algorithm
2216              (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
2217               "RowPerm = NOROWPERM"))
2218            #t))
2219        (patches (search-patches "superlu-dist-scotchmetis.patch"))))
2220     (build-system gnu-build-system)
2221     (native-inputs
2222      `(("tcsh" ,tcsh)))
2223     (inputs
2224      `(("gfortran" ,gfortran)))
2225     (propagated-inputs
2226      `(("openmpi" ,openmpi)             ;headers include MPI heades
2227        ("lapack" ,lapack)               ;required to link with output library
2228        ("pt-scotch" ,pt-scotch)))       ;same
2229     (arguments
2230      `(#:parallel-build? #f             ;race conditions using ar
2231        #:phases
2232        (modify-phases %standard-phases
2233          (replace 'configure
2234            (lambda* (#:key inputs outputs #:allow-other-keys)
2235              (call-with-output-file "make.inc"
2236                (lambda (port)
2237                  (format port "
2238 PLAT        =
2239 DSuperLUroot = ~a
2240 DSUPERLULIB  = ~a/lib/libsuperlu_dist.a
2241 BLASDEF     = -DUSE_VENDOR_BLAS
2242 BLASLIB     = -L~a/lib -lblas
2243 PARMETISLIB = -L~a/lib \
2244               -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
2245               -lscotch -lscotcherr -lscotcherrexit
2246 METISLIB    = -L~:*~a/lib \
2247               -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
2248 LIBS        = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
2249 ARCH        = ar
2250 ARCHFLAGS   = cr
2251 RANLIB      = ranlib
2252 CC          = mpicc
2253 PIC         = -fPIC
2254 CFLAGS      = -O3 -g -DPRNTlevel=0 $(PIC)
2255 NOOPTS      = -O0 -g $(PIC)
2256 FORTRAN     = mpifort
2257 FFLAGS      = -O2 -g $(PIC)
2258 LOADER      = $(CC)
2259 CDEFS       = -DAdd_"
2260                          (getcwd)
2261                          (assoc-ref outputs "out")
2262                          (assoc-ref inputs "lapack")
2263                          (assoc-ref inputs "pt-scotch"))))
2264              #t))
2265          (add-after 'unpack 'remove-broken-symlinks
2266            (lambda _
2267              (for-each delete-file
2268                        (find-files "MAKE_INC" "\\.#make\\..*"))
2269              #t))
2270          (add-before 'build 'create-install-directories
2271            (lambda* (#:key outputs #:allow-other-keys)
2272              (for-each
2273               (lambda (dir)
2274                 (mkdir-p (string-append (assoc-ref outputs "out")
2275                                         "/" dir)))
2276               '("lib" "include"))
2277              #t))
2278          (replace 'check
2279            (lambda _
2280              ;; By default, running the test suite would fail because 'ssh'
2281              ;; could not be found in $PATH.  Define this variable to placate
2282              ;; Open MPI without adding a dependency on OpenSSH (the agent
2283              ;; isn't used anyway.)
2284              (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
2285              (with-directory-excursion "EXAMPLE"
2286                (invoke "mpirun" "-n" "2"
2287                        "./pddrive" "-r" "1" "-c" "2" "g20.rua")
2288                (invoke "mpirun" "-n" "2"
2289                        "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))
2290              #t))
2291          (replace 'install
2292            (lambda* (#:key outputs #:allow-other-keys)
2293              ;; Library is placed in lib during the build phase.  Copy over
2294              ;; headers to include.
2295              (let* ((out    (assoc-ref outputs "out"))
2296                     (incdir (string-append out "/include")))
2297                (for-each (lambda (file)
2298                            (let ((base (basename file)))
2299                              (format #t "installing `~a' to `~a'~%"
2300                                      base incdir)
2301                              (copy-file file
2302                                         (string-append incdir "/" base))))
2303                          (find-files "SRC" ".*\\.h$")))
2304              #t)))))
2305     (home-page (package-home-page superlu))
2306     (synopsis "Parallel supernodal direct solver")
2307     (description
2308      "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2309 It is targeted for distributed memory parallel machines.  SuperLU_DIST is
2310 implemented in ANSI C, and MPI for communications.")
2311     (license license:bsd-3)))
2312
2313 (define-public scotch
2314   (package
2315     (name "scotch")
2316     (version "6.0.5a")
2317     (source
2318      (origin
2319       (method url-fetch)
2320       (uri (string-append "https://gforge.inria.fr/frs/download.php/"
2321                           "latestfile/298/scotch_" version ".tar.gz"))
2322       (sha256
2323        (base32 "0vsmgjz8qv80di3ljmc7hbdsizxxxwy2b9rgd2fl1mdc6dgbj8av"))
2324       (patches (search-patches "scotch-test-threading.patch"
2325                                "scotch-build-parallelism.patch"
2326                                "scotch-graph-induce-type-64.patch"
2327                                "scotch-graph-diam-64.patch"))))
2328     (build-system gnu-build-system)
2329     (inputs
2330      `(("zlib" ,zlib)
2331        ("flex" ,flex)
2332        ("bison" ,bison)))
2333     (arguments
2334      `(#:phases
2335        (modify-phases %standard-phases
2336          (add-after
2337           'unpack 'chdir-to-src
2338           (lambda _ (chdir "src") #t))
2339          (replace
2340           'configure
2341           (lambda _
2342             (call-with-output-file "Makefile.inc"
2343               (lambda (port)
2344                 (format port "
2345 EXE =
2346 LIB = .a
2347 OBJ = .o
2348 MAKE = make
2349 AR = ar
2350 ARFLAGS = -ruv
2351 CAT = cat
2352 CCS = gcc
2353 CCP = mpicc
2354 CCD = gcc
2355 CPPFLAGS =~{ -D~a~}
2356 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2357 LDFLAGS = -lz -lm -lrt -lpthread
2358 CP = cp
2359 LEX = flex -Pscotchyy -olex.yy.c
2360 LN = ln
2361 MKDIR = mkdir
2362 MV = mv
2363 RANLIB = ranlib
2364 YACC = bison -pscotchyy -y -b y
2365 "
2366                         '("COMMON_FILE_COMPRESS_GZ"
2367                           "COMMON_PTHREAD"
2368                           "COMMON_RANDOM_FIXED_SEED"
2369                           "INTSIZE64"             ;use 'long' instead of 'int'
2370                           ;; Prevents symbolc clashes with libesmumps
2371                           "SCOTCH_RENAME"
2372                           ;; XXX: Causes invalid frees in superlu-dist tests
2373                           ;; "SCOTCH_PTHREAD"
2374                           ;; "SCOTCH_PTHREAD_NUMBER=2"
2375                           "restrict=__restrict"))))
2376             #t))
2377          (add-after
2378           'build 'build-esmumps
2379           (lambda _
2380             ;; By default, running the test suite would fail because 'ssh'
2381             ;; could not be found in $PATH.  Define this variable to placate
2382             ;; Open MPI without adding a dependency on OpenSSH (the agent
2383             ;; isn't used anyway.)
2384             (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
2385
2386             (invoke "make"
2387                     (format #f "-j~a" (parallel-job-count))
2388                     "esmumps")))
2389          (replace
2390           'install
2391           (lambda* (#:key outputs #:allow-other-keys)
2392             (let ((out (assoc-ref outputs "out")))
2393               (mkdir out)
2394               (invoke "make"
2395                       (string-append "prefix=" out)
2396                       "install")
2397               ;; esmumps files are not installed with the above
2398               (for-each (lambda (f)
2399                           (copy-file f (string-append out "/include/" f)))
2400                         (find-files "../include" ".*esmumps.h$"))
2401               (for-each (lambda (f)
2402                           (copy-file f (string-append out "/lib/" f)))
2403                         (find-files "../lib" "^lib.*esmumps.*"))
2404               #t))))))
2405     (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
2406     (synopsis "Programs and libraries for graph algorithms")
2407     (description "SCOTCH is a set of programs and libraries which implement
2408 the static mapping and sparse matrix reordering algorithms developed within
2409 the SCOTCH project.  Its purpose is to apply graph theory, with a divide and
2410 conquer approach, to scientific computing problems such as graph and mesh
2411 partitioning, static mapping, and sparse matrix ordering, in application
2412 domains ranging from structural mechanics to operating systems or
2413 bio-chemistry.")
2414     ;; See LICENSE_en.txt
2415     (license license:cecill-c)))
2416
2417 (define-public scotch32
2418   ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2419   ;; some applications.
2420   (package (inherit scotch)
2421     (name "scotch32")
2422     (arguments
2423      (substitute-keyword-arguments (package-arguments scotch)
2424        ((#:phases scotch-phases)
2425         `(modify-phases ,scotch-phases
2426           (replace
2427            'configure
2428            (lambda _
2429              (call-with-output-file "Makefile.inc"
2430                (lambda (port)
2431                  (format port "
2432 EXE =
2433 LIB = .a
2434 OBJ = .o
2435 MAKE = make
2436 AR = ar
2437 ARFLAGS = -ruv
2438 CAT = cat
2439 CCS = gcc
2440 CCP = mpicc
2441 CCD = gcc
2442 CPPFLAGS =~{ -D~a~}
2443 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2444 LDFLAGS = -lz -lm -lrt -lpthread
2445 CP = cp
2446 LEX = flex -Pscotchyy -olex.yy.c
2447 LN = ln
2448 MKDIR = mkdir
2449 MV = mv
2450 RANLIB = ranlib
2451 YACC = bison -pscotchyy -y -b y
2452 "
2453                         '("COMMON_FILE_COMPRESS_GZ"
2454                           "COMMON_PTHREAD"
2455                           "COMMON_RANDOM_FIXED_SEED"
2456                           "INTSIZE32"   ;use 32-bit integers.  See INSTALL.txt
2457                           ;; Prevents symbolc clashes with libesmumps
2458                           "SCOTCH_RENAME"
2459                           ;; XXX: Causes invalid frees in superlu-dist tests
2460                           ;; "SCOTCH_PTHREAD"
2461                           ;; "SCOTCH_PTHREAD_NUMBER=2"
2462                           "restrict=__restrict"))))))))))
2463     (synopsis
2464      "Programs and libraries for graph algorithms (32-bit integers)")))
2465
2466 (define-public pt-scotch
2467   (package (inherit scotch)
2468     (name "pt-scotch")
2469     (propagated-inputs
2470      `(("openmpi" ,openmpi)))           ;Headers include MPI headers
2471     (arguments
2472      (substitute-keyword-arguments (package-arguments scotch)
2473        ((#:phases scotch-phases)
2474         `(modify-phases ,scotch-phases
2475            (replace
2476             'build
2477             (lambda _
2478               (and
2479                (zero? (system* "make"
2480                                (format #f "-j~a" (parallel-job-count))
2481                                "ptscotch" "ptesmumps"))
2482                ;; Install the serial metis compatibility library
2483                (zero? (system* "make" "-C" "libscotchmetis" "install")))))
2484            (replace
2485             'check
2486             (lambda _ (zero? (system* "make" "ptcheck"))))))))
2487     (synopsis "Programs and libraries for graph algorithms (with MPI)")))
2488
2489 (define-public pt-scotch32
2490   (package (inherit scotch32)
2491     (name "pt-scotch32")
2492     (propagated-inputs
2493      `(("openmpi" ,openmpi)))                     ;headers include MPI headers
2494     (arguments
2495      (substitute-keyword-arguments (package-arguments scotch32)
2496        ((#:phases scotch32-phases)
2497         `(modify-phases ,scotch32-phases
2498            (replace 'build
2499              (lambda _
2500                (and
2501                 (zero? (system* "make"
2502                                 (format #f "-j~a" (parallel-job-count))
2503                                 "ptscotch" "ptesmumps"))
2504                 ;; Install the serial metis compatibility library
2505                 (zero? (system* "make" "-C" "libscotchmetis" "install")))))
2506            (replace 'check
2507              (lambda _
2508                (zero? (system* "make" "ptcheck"))))))))
2509     (synopsis
2510      "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2511
2512 (define-public metis
2513   (package
2514     (name "metis")
2515     (version "5.1.0")
2516     (source
2517      (origin
2518        (method url-fetch)
2519        (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2520                            "metis-" version ".tar.gz"))
2521        (sha256
2522         (base32
2523          "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2524     (build-system cmake-build-system)
2525     (inputs
2526      `(("blas" ,openblas)))
2527     (arguments
2528      `(#:tests? #f                      ;no tests
2529        #:configure-flags `("-DSHARED=ON"
2530                            ,(string-append "-DGKLIB_PATH=" (getcwd)
2531                                            "/metis-" ,version "/GKlib"))))
2532     (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2533     (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2534     (description
2535      "METIS is a set of serial programs for partitioning graphs, partitioning
2536 finite element meshes, and producing fill-reducing orderings for sparse
2537 matrices.  The algorithms implemented in METIS are based on the multilevel
2538 recursive-bisection, multilevel k-way, and multi-constraint partitioning
2539 schemes.")
2540     (license license:asl2.0)))          ;As of version 5.0.3
2541
2542 (define-public p4est
2543   (package
2544     (name "p4est")
2545     (version "2.0")
2546     (source
2547      (origin
2548        (method url-fetch)
2549        (uri (string-append "http://p4est.github.io/release/p4est-"
2550                            version ".tar.gz"))
2551        (sha256
2552         (base32
2553          "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
2554     (build-system gnu-build-system)
2555     (inputs
2556      `(("fortran" ,gfortran)
2557        ("blas" ,openblas)
2558        ("lapack" ,lapack)
2559        ("zlib" ,zlib)))
2560     (arguments
2561      `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2562                                            (assoc-ref %build-inputs "blas")
2563                                            " -lopenblas")
2564                            ,(string-append "LAPACK_LIBS=-L"
2565                                            (assoc-ref %build-inputs "lapack")
2566                                            " -llapack"))
2567        #:phases (modify-phases %standard-phases
2568                   (add-before 'check 'set-test-environment
2569                     (lambda _
2570                       ;; By default, running the test suite would fail because
2571                       ;; 'ssh' could not be found in $PATH.  Define this
2572                       ;; variable to placate Open MPI without adding a
2573                       ;; dependency on OpenSSH (the agent isn't used anyway.)
2574                       (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
2575                       #t)))))
2576     (home-page "http://www.p4est.org")
2577     (synopsis "Adaptive mesh refinement on forests of octrees")
2578     (description
2579      "The p4est software library enables the dynamic management of a
2580 collection of adaptive octrees, conveniently called a forest of octrees.
2581 p4est is designed to work in parallel and scales to hundreds of thousands of
2582 processor cores.")
2583     (license license:gpl2+)))
2584
2585 (define-public p4est-openmpi
2586   (package (inherit p4est)
2587     (name "p4est-openmpi")
2588     (inputs
2589      `(("mpi" ,openmpi)
2590        ,@(package-inputs p4est)))
2591     (arguments
2592      (substitute-keyword-arguments (package-arguments p4est)
2593        ((#:configure-flags cf)
2594         ``("--enable-mpi" ,@,cf))))
2595     (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2596
2597 (define-public gsegrafix
2598   (package
2599     (name "gsegrafix")
2600     (version "1.0.6")
2601     (source
2602      (origin
2603       (method url-fetch)
2604       (uri (string-append "mirror://gnu/" name "/" name "-"
2605                           version ".tar.gz"))
2606       (sha256
2607        (base32
2608         "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2609     (build-system gnu-build-system)
2610     (arguments
2611      `(#:configure-flags '("LDFLAGS=-lm")))
2612     (inputs
2613      `(("libgnomecanvas" ,libgnomecanvas)
2614        ("libbonoboui" ,libbonoboui)
2615        ("libgnomeui" ,libgnomeui)
2616        ("libgnomeprintui" ,libgnomeprintui)
2617        ("popt" ,popt)))
2618     (native-inputs
2619      `(("pkg-config" ,pkg-config)))
2620     (home-page "https://www.gnu.org/software/gsegrafix/")
2621     (synopsis "GNOME application to create scientific and engineering plots")
2622     (description  "GSEGrafix is an application which produces high-quality graphical
2623 plots for science and engineering.  Plots are specified via simple ASCII
2624 parameter files and data files and are presented in an anti-aliased GNOME
2625 canvas.  The program supports rectangular two-dimensional plots, histograms,
2626 polar-axis plots and three-dimensional plots.  Plots can be printed or saved
2627 to BMP, JPEG or PNG image formats.")
2628     (license license:gpl3+)))
2629
2630 (define-public maxima
2631   (package
2632     (name "maxima")
2633     (version "5.41.0")
2634     (source
2635      (origin
2636        (method url-fetch)
2637        (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2638                            version "-source/" name "-" version ".tar.gz"))
2639        (sha256
2640         (base32
2641          "0x0n81z0s4pl8nwpf7ivlsbvsdphm9w42250g7qdkizl0132by6s"))
2642        (patches (search-patches "maxima-defsystem-mkdir.patch"))))
2643     (build-system gnu-build-system)
2644     (inputs
2645      `(("gcl" ,gcl)
2646        ("gnuplot" ,gnuplot)                       ;for plots
2647        ("tk" ,tk)))                               ;Tcl/Tk is used by 'xmaxima'
2648     (native-inputs
2649      `(("texinfo" ,texinfo)
2650        ("perl" ,perl)
2651        ("python" ,python)))
2652     (arguments
2653      `(#:configure-flags
2654        (list "--enable-gcl"
2655              (string-append "--with-posix-shell="
2656                             (assoc-ref %build-inputs "bash")
2657                             "/bin/sh")
2658              (string-append "--with-wish="
2659                             (assoc-ref %build-inputs "tk")
2660                             "/bin/wish"
2661                             (let ((v ,(package-version tk)))
2662                               (string-take v (string-index-right v #\.)))))
2663        ;; By default Maxima attempts to write temporary files to
2664        ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2665        ;; Work around that.
2666        #:make-flags (list "TMPDIR=/tmp")
2667        #:phases
2668        (modify-phases %standard-phases
2669          (add-before 'check 'pre-check
2670            (lambda _
2671              (chmod "src/maxima" #o555)
2672              #t))
2673          ;; Make sure the doc and emacs files are found in the
2674          ;; standard location.  Also configure maxima to find gnuplot
2675          ;; without having it on the PATH.
2676          (add-after 'install 'post-install
2677            (lambda* (#:key outputs inputs #:allow-other-keys)
2678              (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2679                     (out (assoc-ref outputs "out"))
2680                     (datadir (string-append out "/share/maxima/" ,version))
2681                     (binutils (string-append (assoc-ref inputs "binutils")
2682                                              "/bin")))
2683                (with-directory-excursion out
2684                  (mkdir-p "share/emacs")
2685                  (mkdir-p "share/doc")
2686                  (symlink
2687                   (string-append datadir "/emacs/")
2688                   (string-append out "/share/emacs/site-lisp"))
2689                  (symlink
2690                   (string-append datadir "/doc/")
2691                   (string-append out "/share/doc/maxima"))
2692                  (with-atomic-file-replacement
2693                   (string-append datadir "/share/maxima-init.lisp")
2694                   (lambda (in out)
2695                     (format out "~a ~s~a~%"
2696                             "(setf $gnuplot_command "
2697                             (string-append gnuplot "/bin/gnuplot") ")")
2698                     (dump-port in out))))
2699                ;; Ensure that Maxima will have access to the GNU binutils
2700                ;; components at runtime.
2701                (wrap-program (string-append out "/bin/maxima")
2702                  `("PATH" prefix (,binutils))))
2703              #t)))))
2704     (home-page "http://maxima.sourceforge.net")
2705     (synopsis "Numeric and symbolic expression manipulation")
2706     (description "Maxima is a system for the manipulation of symbolic and
2707 numerical expressions.  It yields high precision numeric results by using
2708 exact fractions, arbitrary precision integers, and variable precision floating
2709 point numbers.")
2710     ;; Some files are lgpl2.1+. Some are gpl2+.  Some explicitly state gpl1+.
2711     ;; Others simply say "GNU General Public License" without stating a
2712     ;; version (which implicitly means gpl1+).
2713     ;; At least one file (src/maxima.asd) says "version 2."
2714     ;; GPLv2 only is therefore the smallest subset.
2715     (license license:gpl2)))
2716
2717 (define-public wxmaxima
2718   (package
2719     (name "wxmaxima")
2720     (version "18.02.0")
2721     (source
2722      (origin
2723        (method url-fetch)
2724        (uri (string-append "https://github.com/andrejv/" name "/archive"
2725                            "/Version-" version ".tar.gz"))
2726        (file-name (string-append name "-" version ".tar.gz"))
2727        (sha256
2728         (base32
2729          "03kr2rgfp4hcf3is8m8d8f9hj660c3xgrc50vrrfpixx4syh6wvj"))
2730        (patches
2731         (search-patches "wxmaxima-do-not-use-old-gnuplot-parameters.patch"))))
2732     (build-system cmake-build-system)
2733     (native-inputs
2734      `(("gettext" ,gettext-minimal)))
2735     (inputs
2736      `(("wxwidgets" ,wxwidgets)
2737        ("maxima" ,maxima)
2738        ;; Runtime support.
2739        ("adwaita-icon-theme" ,adwaita-icon-theme)
2740        ("gtk+" ,gtk+)
2741        ("shared-mime-info" ,shared-mime-info)))
2742     (arguments
2743      `(#:tests? #f ; no check target
2744        #:phases
2745        (modify-phases %standard-phases
2746          (add-after 'install 'wrap-program
2747            (lambda* (#:key inputs outputs #:allow-other-keys)
2748              (wrap-program (string-append (assoc-ref outputs "out")
2749                                           "/bin/wxmaxima")
2750                `("PATH" ":" prefix
2751                  (,(string-append (assoc-ref inputs "maxima")
2752                                   "/bin")))
2753                ;; For GtkFileChooserDialog.
2754                `("GSETTINGS_SCHEMA_DIR" =
2755                  (,(string-append (assoc-ref inputs "gtk+")
2756                                   "/share/glib-2.0/schemas")))
2757                `("XDG_DATA_DIRS" ":" prefix
2758                  (;; Needed by gdk-pixbuf to know supported icon formats.
2759                   ,(string-append
2760                     (assoc-ref inputs "shared-mime-info") "/share")
2761                   ;; The default icon theme of GTK+.
2762                   ,(string-append
2763                     (assoc-ref inputs "adwaita-icon-theme") "/share"))))
2764              #t)))))
2765     (home-page "https://andrejv.github.io/wxmaxima/")
2766     (synopsis "Graphical user interface for the Maxima computer algebra system")
2767     (description
2768      "wxMaxima is a graphical user interface for the Maxima computer algebra
2769 system.  It eases the use of Maxima by making most of its commands available
2770 through a menu system and by providing input dialogs for commands that require
2771 more than one argument.  It also implements its own display engine that
2772 outputs mathematical symbols directly instead of depicting them with ASCII
2773 characters.
2774
2775 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
2776 text and mathematical calculations to create documents, exporting of input and
2777 output to TeX, and a browser for Maxima's manual including command index and
2778 full text searching.")
2779     (license license:gpl2+)))
2780
2781 (define-public armadillo
2782   (package
2783     (name "armadillo")
2784     (version "9.100.5")
2785     (source (origin
2786               (method url-fetch)
2787               (uri (string-append "mirror://sourceforge/arma/armadillo-"
2788                                   version ".tar.xz"))
2789               (sha256
2790                (base32
2791                 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
2792     (build-system cmake-build-system)
2793     (arguments `(#:tests? #f))          ; no test target
2794     (inputs
2795      `(("openblas" ,openblas)
2796        ("lapack" ,lapack)
2797        ("arpack" ,arpack-ng)))
2798     (home-page "http://arma.sourceforge.net/")
2799     (synopsis "C++ linear algebra library")
2800     (description
2801      "Armadillo is a C++ linear algebra library, aiming towards a good balance
2802 between speed and ease of use.  It is useful for algorithm development
2803 directly in C++, or quick conversion of research code into production
2804 environments.  It can be used for machine learning, pattern recognition,
2805 signal processing, bioinformatics, statistics, econometrics, etc.  The library
2806 provides efficient classes for vectors, matrices and cubes, as well as 150+
2807 associated functions (eg. contiguous and non-contiguous submatrix views).")
2808     (license license:asl2.0)))
2809
2810 (define-public muparser
2811   ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2812   ;; different hash. In order to make `guix package --upgrade` work correctly,
2813   ;; we set a Guix packaging revision.
2814   ;; When the next version of muparser is released, we can remove
2815   ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2816   (let ((upstream-version "2.2.5")
2817         (revision "2"))
2818     (package
2819       (name "muparser")
2820       (version (string-append upstream-version "-" revision))
2821       (source
2822        (origin
2823          (method url-fetch)
2824          (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
2825                              upstream-version ".tar.gz"))
2826          (file-name (string-append name "-" version ".tar.gz"))
2827          (sha256
2828           (base32
2829            "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
2830       (build-system gnu-build-system)
2831       (arguments
2832        `(#:configure-flags '("--enable-samples=no")
2833          #:tests? #f)) ;no "check" target
2834       (home-page "http://muparser.beltoforion.de/")
2835       (synopsis "Fast parser library for mathematical expressions")
2836       (description
2837        "muParser is an extensible high performance math parser library.  It is
2838 based on transforming an expression into a bytecode and precalculating constant
2839 parts of it.")
2840       (license license:expat))))
2841
2842 (define-public openblas
2843   (package
2844     (name "openblas")
2845     (version "0.3.2")
2846     (source
2847      (origin
2848        (method url-fetch)
2849        (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
2850                            version "%20version.tar.gz"))
2851        (file-name (string-append name "-" version ".tar.gz"))
2852        (sha256
2853         (base32
2854          "0b20km2jv7m6qiylrlvhq2vnmkmilb633mr8rhqmgbn1wqrp58jq"))))
2855     (build-system gnu-build-system)
2856     (arguments
2857      `(#:test-target "test"
2858        ;; DYNAMIC_ARCH is only supported on x86.  When it is disabled and no
2859        ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2860        ;; we need to disable substitutions.
2861        #:substitutable?
2862         ,(let ((system (or (%current-target-system) (%current-system))))
2863            (or (string-prefix? "x86_64" system)
2864                (string-prefix? "i686" system)
2865                (string-prefix? "mips" system)
2866                (string-prefix? "aarch64" system)))
2867        #:make-flags
2868        (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
2869              "SHELL=bash"
2870              ;; Build the library for all supported CPUs.  This allows
2871              ;; switching CPU targets at runtime with the environment variable
2872              ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
2873              ;; Unfortunately, this is not supported on non-x86 architectures,
2874              ;; where it leads to failed builds.
2875              ,@(let ((system (or (%current-target-system) (%current-system))))
2876                  (cond
2877                   ((or (string-prefix? "x86_64" system)
2878                        (string-prefix? "i686" system))
2879                    '("DYNAMIC_ARCH=1"))
2880                   ;; On MIPS we force the "SICORTEX" TARGET, as for the other
2881                   ;; two available MIPS targets special extended instructions
2882                   ;; for Loongson cores are used.
2883                   ((string-prefix? "mips" system)
2884                    '("TARGET=SICORTEX"))
2885                   ;; On aarch64 force the generic 'armv8-a' target
2886                   ((string-prefix? "aarch64" system)
2887                    '("TARGET=ARMV8"))
2888                   (else '()))))
2889        ;; no configure script
2890        #:phases
2891        (modify-phases %standard-phases
2892          (delete 'configure)
2893          (add-before 'build 'set-extralib
2894            (lambda* (#:key inputs #:allow-other-keys)
2895              ;; Get libgfortran found when building in utest.
2896              (setenv "FEXTRALIB"
2897                      (string-append "-L" (assoc-ref inputs "fortran-lib")
2898                                     "/lib"))
2899              #t)))))
2900     (inputs
2901      `(("fortran-lib" ,gfortran "lib")))
2902     (native-inputs
2903      `(("cunit" ,cunit)
2904        ("fortran" ,gfortran)
2905        ("perl" ,perl)))
2906     (home-page "http://www.openblas.net/")
2907     (synopsis "Optimized BLAS library based on GotoBLAS")
2908     (description
2909      "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
2910     (license license:bsd-3)))
2911
2912 (define* (make-blis implementation #:optional substitutable?)
2913   "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
2914 source tree for a list of implementations.)
2915
2916 SUBSTITUTABLE? determines whether the package is made available as a
2917 substitute.
2918
2919 Currently the specialization must be selected at configure-time, but work is
2920 underway to allow BLIS to select the right optimized kernels at run time:
2921 <https://github.com/flame/blis/issues/129>."
2922   (package
2923     (name (if (string=? implementation "reference")
2924               "blis"
2925               (string-append "blis-" implementation)))
2926     (version "0.2.2")
2927     (home-page "https://github.com/flame/blis")
2928     (source (origin
2929               (method git-fetch)
2930               (uri (git-reference (url home-page) (commit version)))
2931               (sha256
2932                (base32
2933                 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
2934               (file-name (git-file-name "blis" version))))
2935     (build-system gnu-build-system)
2936     (arguments
2937      `(#:test-target "test"
2938
2939        #:substitutable? ,substitutable?
2940
2941        #:phases (modify-phases %standard-phases
2942                   (replace 'configure
2943                     (lambda* (#:key outputs #:allow-other-keys)
2944                       ;; This is a home-made 'configure' script.
2945                       (let ((out (assoc-ref outputs "out")))
2946                         (zero? (system* "./configure" "-p" out
2947                                         "-d" "opt"
2948                                         "--disable-static"
2949                                         "--enable-shared"
2950                                         "--enable-threading=openmp"
2951
2952                                         ,implementation)))))
2953                   (add-before 'check 'show-test-output
2954                     (lambda _
2955                       ;; By default "make check" is silent.  Make it verbose.
2956                       (system "tail -F output.testsuite &")
2957                       #t)))))
2958     (synopsis "High-performance basic linear algebra (BLAS) routines")
2959     (description
2960      "BLIS is a portable software framework for instantiating high-performance
2961 BLAS-like dense linear algebra libraries.  The framework was designed to
2962 isolate essential kernels of computation that, when optimized, immediately
2963 enable optimized implementations of most of its commonly used and
2964 computationally intensive operations.  While BLIS exports a new BLAS-like API,
2965 it also includes a BLAS compatibility layer which gives application developers
2966 access to BLIS implementations via traditional BLAS routine calls.")
2967     (license license:bsd-3)))
2968
2969 (define-public blis
2970   ;; This is the "reference" implementation, which is the non-optimized but
2971   ;; portable variant (no assembly).
2972   (make-blis "reference" #t))
2973
2974 (define ignorance blis)
2975
2976 (define-syntax-rule (blis/x86_64 processor)
2977   "Expand to a package specialized for PROCESSOR."
2978   (package
2979     (inherit (make-blis processor))
2980     (supported-systems '("x86_64-linux"))))
2981
2982 (define-public blis-sandybridge
2983   ;; BLIS specialized for Sandy Bridge processors (launched 2011):
2984   ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
2985   (blis/x86_64 "sandybridge"))
2986
2987 (define-public blis-haswell
2988   ;; BLIS specialized for Haswell processors (launched 2013):
2989   ;; <http://ark.intel.com/products/codename/42174/Haswell>.
2990   (blis/x86_64 "haswell"))
2991
2992 (define-public blis-knl
2993   ;; BLIS specialized for Knights Landing processor (launched 2016):
2994   ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
2995   (blis/x86_64 "knl"))
2996
2997
2998 (define-public openlibm
2999   (package
3000     (name "openlibm")
3001     (version "0.6.0")
3002     (source
3003      (origin
3004        (method url-fetch)
3005        (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
3006                            version ".tar.gz"))
3007        (file-name (string-append name "-" version ".tar.gz"))
3008        (sha256
3009         (base32
3010          "0a5fpm8nra5ldhjk0cqd2rx1qh32wiarkxmcqcm5xl8z7l4kjm6l"))))
3011     (build-system gnu-build-system)
3012     (arguments
3013      `(#:make-flags
3014        (list (string-append "prefix=" (assoc-ref %outputs "out")))
3015        #:phases
3016        ;; no configure script
3017        (modify-phases %standard-phases (delete 'configure))
3018        #:tests? #f)) ;the tests are part of the default target
3019     (home-page "http://openlibm.org/")
3020     (synopsis "Portable C mathematical library (libm)")
3021     (description
3022      "OpenLibm is an effort to have a high quality, portable, standalone C
3023 mathematical library (libm).  It can be used standalone in applications and
3024 programming language implementations.  The project was born out of a need to
3025 have a good libm for the Julia programming language that worked consistently
3026 across compilers and operating systems, and in 32-bit and 64-bit
3027 environments.")
3028     ;; Each architecture has its own make target, and there is none for mips.
3029     (supported-systems (delete "mips64el-linux" %supported-systems))
3030     ;; See LICENSE.md for details.
3031     (license (list license:expat
3032                    license:isc
3033                    license:bsd-2
3034                    license:public-domain
3035                    license:lgpl2.1+))))
3036
3037 (define-public openspecfun
3038   (package
3039     (name "openspecfun")
3040     (version "0.5.3")
3041     (source
3042      (origin
3043        (method url-fetch)
3044        (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
3045                            version ".tar.gz"))
3046        (file-name (string-append name "-" version ".tar.gz"))
3047        (sha256
3048         (base32
3049          "1rs1bv8jq751fv9vq79890wqf9xlbjc7lvz3ighzyfczbyjcf18m"))))
3050     (build-system gnu-build-system)
3051     (arguments
3052      '(#:tests? #f                      ; no "check" target
3053        #:make-flags
3054        (list (string-append "prefix=" (assoc-ref %outputs "out")))
3055        #:phases
3056        (modify-phases %standard-phases
3057          (delete 'configure))))         ; no configure script
3058     (inputs
3059      `(("fortran" ,gfortran)))
3060     (home-page "https://github.com/JuliaLang/openspecfun")
3061     (synopsis "Collection of special mathematical functions")
3062     (description
3063      "Openspecfun provides AMOS and Faddeeva.  AMOS (from Netlib) is a
3064 portable package for Bessel Functions of a Complex Argument and Nonnegative
3065 Order; it contains subroutines for computing Bessel functions and Airy
3066 functions.  Faddeeva allows computing the various error functions of arbitrary
3067 complex arguments (Faddeeva function, error function, complementary error
3068 function, scaled complementary error function, imaginary error function, and
3069 Dawson function); given these, one can also easily compute Voigt functions,
3070 Fresnel integrals, and similar related functions as well.")
3071     ;; Faddeeva is released under the Expat license; AMOS is included as
3072     ;; public domain software.
3073     (license (list license:expat license:public-domain))))
3074
3075 (define-public suitesparse
3076   (package
3077     (name "suitesparse")
3078     (version "4.5.5")
3079     (source
3080      (origin
3081        (method url-fetch)
3082        (uri (string-append
3083              "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
3084              version ".tar.gz"))
3085        (sha256
3086         (base32
3087          "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
3088        (modules '((guix build utils)))
3089        (snippet
3090         ;; Remove bundled metis source
3091         '(begin
3092            (delete-file-recursively "metis-5.1.0")
3093            #t))))
3094     (build-system gnu-build-system)
3095     (arguments
3096      '(#:tests? #f  ;no "check" target
3097        #:make-flags
3098        (list "CC=gcc"
3099              "BLAS=-lblas"
3100              "TBB=-ltbb"
3101              "MY_METIS_LIB=-lmetis"
3102              (string-append "INSTALL_LIB="
3103                             (assoc-ref %outputs "out") "/lib")
3104              (string-append "INSTALL_INCLUDE="
3105                             (assoc-ref %outputs "out") "/include")
3106              "library")
3107        #:phases
3108        (modify-phases %standard-phases
3109          (delete 'configure))))         ;no configure script
3110     (inputs
3111      `(("tbb" ,tbb)
3112        ("lapack" ,lapack)
3113        ("metis" ,metis)))
3114     (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
3115     (synopsis "Suite of sparse matrix software")
3116     (description
3117      "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
3118 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
3119 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
3120 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
3121 CXSparse, a concise sparse Cholesky factorization package; and many other
3122 packages.")
3123     ;; LGPLv2.1+:
3124     ;;   AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
3125     ;; GPLv2+:
3126     ;;  GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
3127     (license (list license:gpl2+ license:lgpl2.1+))))
3128
3129 (define-public atlas
3130   (package
3131     (name "atlas")
3132     (version "3.10.3")
3133     (source (origin
3134               (method url-fetch)
3135               (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
3136                                   version "/atlas" version ".tar.bz2"))
3137               (sha256
3138                (base32
3139                 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
3140     (build-system gnu-build-system)
3141     (home-page "http://math-atlas.sourceforge.net/")
3142     (inputs `(("gfortran" ,gfortran)
3143               ("lapack-tar" ,(package-source lapack))))
3144     (outputs '("out" "doc"))
3145     ;; For the moment we drop support for MIPS at it fails to compile. See
3146     ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
3147     (supported-systems (delete "mips64el-linux" %supported-systems))
3148     (arguments
3149      `(#:parallel-build? #f
3150        #:parallel-tests? #f
3151
3152        ;; ATLAS tunes itself for the machine it is built on, as explained at
3153        ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
3154        ;; For this reason, we want users to build it locally instead of using
3155        ;; substitutes.
3156        #:substitutable? #f
3157
3158        #:modules ((srfi srfi-26)
3159                   (srfi srfi-1)
3160                   (guix build gnu-build-system)
3161                   (guix build utils))
3162        #:configure-flags
3163        `(;; Generate position independent code suitable for dynamic libraries
3164          ;; and use WALL timer to get more accurate timing.
3165          "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
3166          ;; Set word width.
3167          "-b"
3168          ,,(if (string-match "64" (%current-system))
3169                "64"
3170                "32")
3171          ;; Disable parallel build as it gives errors: atlas_pthread.h is
3172          ;; needed to compile C files before it is generated.
3173          "-Ss" "pmake" "make -j 1"
3174          ;; Probe is failing for MIPS.  We therefore define the system
3175          ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3176          ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3177          ,,@(if (string-prefix? "mips" (%current-system))
3178               (list "-A" "49" "-V" "1")
3179               (list))
3180          ;; Generate shared libraries.
3181          "--shared"
3182          ;; Build a full LAPACK library.
3183          ,(string-append "--with-netlib-lapack-tarfile="
3184                          (assoc-ref %build-inputs "lapack-tar")))
3185        #:phases
3186        (modify-phases %standard-phases
3187          (add-after 'install 'install-doc
3188            (lambda* (#:key outputs inputs #:allow-other-keys)
3189              (let ((doc (string-append (assoc-ref outputs "doc")
3190                                        "/share/doc/atlas")))
3191                (mkdir-p doc)
3192                (fold (lambda (file previous)
3193                        (and previous (zero? (system* "cp" file doc))))
3194                      #t (find-files "../ATLAS/doc" ".*")))))
3195          (add-after 'check 'check-pt
3196            (lambda _ (zero? (system* "make" "ptcheck"))))
3197          ;; Fix files required to run configure.
3198          (add-before 'configure 'fix-/bin/sh
3199            (lambda _
3200              ;; Use `sh', not `/bin/sh'.
3201              (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3202                (("/bin/sh")
3203                 "sh"))))
3204          ;; Fix /bin/sh in generated make files.
3205          (add-after 'configure 'fix-/bin/sh-in-generated-files
3206            (lambda _
3207              (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3208                (("/bin/sh")
3209                 "sh"))))
3210          ;; ATLAS configure program does not accepts the default flags
3211          ;; passed by the 'gnu-build-system'.
3212          (replace 'configure
3213            (lambda* (#:key native-inputs inputs outputs
3214                            (configure-flags '())
3215                            #:allow-other-keys #:rest args)
3216              (let* ((prefix     (assoc-ref outputs "out"))
3217                     (bash       (or (and=> (assoc-ref
3218                                             (or native-inputs inputs) "bash")
3219                                            (cut string-append <> "/bin/bash"))
3220                                     "/bin/sh"))
3221                     (flags      `(,(string-append "--prefix=" prefix)
3222                                   ,@configure-flags))
3223                     (abs-srcdir (getcwd))
3224                     (srcdir     (string-append "../" (basename abs-srcdir))))
3225                (format #t "source directory: ~s (relative from build: ~s)~%"
3226                        abs-srcdir srcdir)
3227                (mkdir "../build")
3228                (chdir "../build")
3229                (format #t "build directory: ~s~%" (getcwd))
3230                (format #t "configure flags: ~s~%" flags)
3231                (zero? (apply system* bash
3232                              (string-append srcdir "/configure")
3233                              flags))))))))
3234     (synopsis "Automatically Tuned Linear Algebra Software")
3235     (description
3236      "ATLAS is an automatically tuned linear algebra software library
3237 providing C and Fortran77 interfaces to a portably efficient BLAS
3238 implementation, as well as a few routines from LAPACK.
3239
3240 Optimization occurs at build time.  For this reason, the library is built on
3241 the machine where it is installed, without resorting to pre-built substitutes.
3242
3243 Before building the library, CPU throttling should be disabled.  This can be
3244 done in the BIOS, or, on GNU/Linux, with the following command:
3245
3246 @example
3247 # cpupower --governor performance
3248 @end example
3249
3250 Failure to do so will result in a library with poor performance.")
3251     (license license:bsd-3)))
3252
3253 (define-public glm
3254   (package
3255     (name "glm")
3256     (version "0.9.9.1")
3257     (source
3258      (origin
3259        (method url-fetch)
3260        (uri (string-append "https://github.com/g-truc/glm/releases/download/"
3261                            version  "/glm-" version ".zip"))
3262        (sha256
3263         (base32
3264          "042a23hmxfs429czkmlg5ixf28aikzfbw18780prj2gcd4flgw8h"))))
3265     (build-system cmake-build-system)
3266     (native-inputs
3267      `(("unzip" ,unzip)))
3268     (home-page "https://glm.g-truc.net/")
3269     (synopsis "OpenGL Mathematics library")
3270     (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3271 library for graphics software based on the OpenGL Shading Language (GLSL)
3272 specifications.")
3273     (license license:expat)))
3274
3275 (define-public lpsolve
3276   (package
3277     (name "lpsolve")
3278     (version "5.5.2.5")
3279     (source
3280      (origin
3281       (method url-fetch)
3282       (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3283                           "/lp_solve_" version "_source.tar.gz"))
3284       (sha256
3285        (base32
3286         "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
3287       (modules '((guix build utils)))
3288       (snippet
3289        '(begin
3290           (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3291             (("^c=cc") "c=gcc")
3292             ;; Pretend to be on a 64 bit platform to obtain a common directory
3293             ;; name for the build results on all architectures; nothing else
3294             ;; seems to depend on it.
3295             (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3296
3297             ;; The check for 'isnan' as it is written fails with
3298             ;; "non-floating-point argument in call to function
3299             ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3300             ;; definition, which in turn leads to bad things.  Fix the feature
3301             ;; test.
3302             (("isnan\\(0\\)") "isnan(0.)"))
3303           #t))))
3304     (build-system gnu-build-system)
3305     (arguments
3306      `(#:tests? #f                      ; no check target
3307        #:phases
3308        (modify-phases %standard-phases
3309          (delete 'configure)            ; no configure script
3310          (replace 'build
3311            (lambda _
3312              (with-directory-excursion "lpsolve55"
3313                (invoke "bash" "ccc"))
3314              (with-directory-excursion "lp_solve"
3315                (invoke "bash" "ccc"))
3316              #t))
3317          (replace 'install
3318            (lambda* (#:key outputs #:allow-other-keys)
3319              (let* ((out (assoc-ref outputs "out"))
3320                     (bin (string-append out "/bin"))
3321                     (lib (string-append out "/lib"))
3322                     ;; This is where LibreOffice expects to find the header
3323                     ;; files, and where they are installed by Debian.
3324                     (include (string-append out "/include/lpsolve")))
3325                (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3326                (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
3327                (install-file "lp_solve/bin/ux64/lp_solve" bin)
3328
3329                ;; Install a subset of the header files as on Debian
3330                ;; (plus lp_bit.h, which matches the regular expression).
3331                (for-each (lambda (name)
3332                            (install-file name include))
3333                          (find-files "." "lp_[HMSa-z].*\\.h$"))
3334                (with-directory-excursion "shared"
3335                  (for-each (lambda (name)
3336                              (install-file name include))
3337                            (find-files "." "\\.h$")))
3338                #t))))))
3339     (home-page "http://lpsolve.sourceforge.net/")
3340     (synopsis "Mixed integer linear programming (MILP) solver")
3341     (description
3342      "lp_solve is a mixed integer linear programming solver based on the
3343 revised simplex and the branch-and-bound methods.")
3344     (license license:lgpl2.1+)))
3345
3346 (define-public dealii
3347   (package
3348     (name "dealii")
3349     (version "8.5.1")
3350     (source
3351      (origin
3352        (method url-fetch)
3353        (uri (string-append "https://github.com/dealii/dealii/releases/"
3354                            "download/v" version "/dealii-" version ".tar.gz"))
3355        (sha256
3356         (base32
3357          "1bh9rsmkrg0zi70n27b11djmac9lximghsiy7mg7w7x544n82gnk"))
3358        (modules '((guix build utils)))
3359        (snippet
3360         ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
3361         '(begin
3362            (delete-file-recursively "bundled")
3363            #t))))
3364     (build-system cmake-build-system)
3365     (inputs
3366      `(("tbb" ,tbb)
3367        ("zlib" ,zlib)
3368        ("boost" ,boost)
3369        ("p4est" ,p4est)
3370        ("blas" ,openblas)
3371        ("lapack" ,lapack)
3372        ("arpack" ,arpack-ng)
3373        ("muparser" ,muparser)
3374        ("gfortran" ,gfortran)
3375        ("suitesparse" ,suitesparse)))   ;for UMFPACK
3376     (arguments
3377      `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
3378        #:configure-flags
3379        ;; Work around a bug in libsuitesparseconfig linking
3380        ;; see https://github.com/dealii/dealii/issues/4745
3381        '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
3382     (home-page "https://www.dealii.org")
3383     (synopsis "Finite element library")
3384     (description
3385      "Deal.II is a C++ program library targeted at the computational solution
3386 of partial differential equations using adaptive finite elements.  The main
3387 aim of deal.II is to enable rapid development of modern finite element codes,
3388 using among other aspects adaptive meshes and a wide array of tools often used
3389 in finite element programs.")
3390     (license license:lgpl2.1+)))
3391
3392 (define-public dealii-openmpi
3393   (package (inherit dealii)
3394     (name "dealii-openmpi")
3395     (inputs
3396      `(("mpi" ,openmpi)
3397        ;;Supported only with MPI:
3398        ("p4est" ,p4est-openmpi)
3399        ("petsc" ,petsc-openmpi)
3400        ("slepc" ,slepc-openmpi)
3401        ("metis" ,metis)               ;for MUMPS
3402        ("scalapack" ,scalapack)       ;for MUMPS
3403        ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3404        ("arpack" ,arpack-ng-openmpi)
3405        ,@(fold alist-delete (package-inputs dealii)
3406                '("p4est" "arpack"))))
3407     (arguments
3408      (substitute-keyword-arguments (package-arguments dealii)
3409        ((#:configure-flags cf)
3410         ``("-DMPI_C_COMPILER=mpicc"
3411            "-DMPI_CXX_COMPILER=mpicxx"
3412            "-DMPI_Fortran_COMPILER=mpifort"
3413            ,@,cf))))
3414     (synopsis "Finite element library (with MPI support)")))
3415
3416 (define-public flann
3417   (package
3418     (name "flann")
3419     (version "1.8.4")
3420     (source
3421       (origin
3422         (method url-fetch)
3423         (uri
3424           (string-append
3425             "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3426             version "-src.zip"))
3427         (sha256
3428           (base32
3429             "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
3430         (patches (search-patches "flann-cmake-3.11.patch"))))
3431     (build-system cmake-build-system)
3432     (outputs '("out"
3433                "octave"))                  ;46 MiB .mex file that pulls Octave
3434     (native-inputs
3435      `(("unzip" ,unzip)))
3436     (inputs
3437      `(("hdf5" ,hdf5)
3438        ("octave" ,octave)
3439        ("python" ,python-2) ; print syntax
3440        ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3441        ("zlib" ,zlib)))
3442     (arguments
3443      `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3444        ;; taken 46 MiB unstripped, and 6 MiB stripped.
3445        #:strip-directories '("lib" "lib64" "libexec"
3446                              "bin" "sbin" "share/flann/octave")
3447
3448        ;; Save 12 MiB by not installing .a files.  Passing
3449        ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3450        #:phases (modify-phases %standard-phases
3451                   (add-before 'configure 'set-octave-directory
3452                     (lambda* (#:key outputs #:allow-other-keys)
3453                       ;; Install the .mex file in the "octave" output.
3454                       (let ((out (assoc-ref outputs "octave")))
3455                         (substitute* "src/matlab/CMakeLists.txt"
3456                           (("share/flann/octave")
3457                            (string-append out "/share/flann/octave")))
3458                         #t)))
3459                   (add-after 'install 'remove-static-libraries
3460                     (lambda* (#:key outputs #:allow-other-keys)
3461                       (let* ((out (assoc-ref outputs "out"))
3462                              (lib (string-append out "/lib")))
3463                         (for-each delete-file
3464                                   (find-files lib "\\.a$"))
3465                         #t))))
3466
3467        #:tests? #f)) ; The test data are downloaded from the Internet.
3468     (home-page "http://www.cs.ubc.ca/research/flann/")
3469     (synopsis "Library for approximate nearest neighbors computation")
3470     (description "FLANN is a library for performing fast approximate
3471 nearest neighbor searches in high dimensional spaces.  It implements a
3472 collection of algorithms and a system for automatically choosing the best
3473 algorithm and optimum parameters depending on the dataset.
3474
3475 FLANN is written in C++ and contains bindings for C, Octave and Python.")
3476     (license (license:non-copyleft "file://COPYING"
3477                                 "See COPYING in the distribution."))))
3478
3479 (define-public wcalc
3480   (package
3481     (name "wcalc")
3482     (version "2.5")
3483     (source
3484       (origin
3485         (method url-fetch)
3486         (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3487                             "wcalc-" version ".tar.bz2"))
3488         (sha256
3489           (base32
3490             "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3491     (build-system gnu-build-system)
3492     (inputs
3493      `(("mpfr" ,mpfr)
3494        ("readline" ,readline)))
3495     (home-page "http://w-calc.sourceforge.net/index.php")
3496     (synopsis "Flexible command-line scientific calculator")
3497     (description "Wcalc is a very capable calculator.  It has standard functions
3498 (sin, asin, and sinh for example, in either radians or degrees), many
3499 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3500 variables, a command history, hex/octal/binary input and output, unit
3501 conversions, embedded comments, and an expandable expression entry field.  It
3502 evaluates expressions using the standard order of operations.")
3503     (license license:gpl2+)))
3504
3505 (define-public xaos
3506   (package
3507     (name "xaos")
3508     (version "3.6")
3509     (source (origin
3510               (method url-fetch)
3511               (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3512                                   "/xaos-" version ".tar.gz"))
3513               (sha256
3514                (base32
3515                 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3516     (build-system gnu-build-system)
3517     (native-inputs `(("gettext" ,gettext-minimal)))
3518     (inputs `(("libx11" ,libx11)
3519               ("zlib" ,zlib)
3520               ("libpng" ,libpng)
3521               ("gsl" ,gsl)))
3522     (arguments
3523      `(#:tests? #f ;no "check" target
3524        #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3525     (synopsis "Real-time fractal zoomer")
3526     (description "GNU XaoS is a graphical program that generates fractal
3527 patterns and allows you to zoom in and out of them infinitely in a fluid,
3528 continuous manner.  It also includes tutorials that help to explain how fractals
3529 are built.  It can generate many different fractal types such as the Mandelbrot
3530 set.")
3531     (home-page "https://www.gnu.org/software/xaos/")
3532     (license license:gpl2+)))
3533
3534 (define-public hypre
3535   (package
3536     (name "hypre")
3537     (version "2.14.0")
3538     (source (origin
3539               (method url-fetch)
3540               (uri (string-append "https://github.com/LLNL/hypre/archive/"
3541                                   "v" version ".tar.gz"))
3542               (file-name (string-append name "-" version ".tar.gz"))
3543               (sha256
3544                (base32
3545                 "0v515i73bvaz378h5465b1dy9v2gf924zy2q94cpq4qqarawvkqh"))
3546               (modules '((guix build utils)))
3547               (snippet
3548                '(begin
3549                   ;; Remove use of __DATE__ and __TIME__ for reproducibility;
3550                   ;; substitute the tarball creation time.
3551                   (substitute* "src/utilities/HYPRE_utilities.h"
3552                     (("Date Compiled: .*$")
3553                      "Date Compiled: Apr 11 2018 16:24:59 +0000\"\n"))
3554                   #t))))
3555     (build-system gnu-build-system)
3556     (outputs '("out"                    ;6.1 MiB of headers and libraries
3557                "doc"))                  ;4.8 MiB of documentation
3558     (native-inputs
3559      `(("doc++" ,doc++)
3560        ("netpbm" ,netpbm)
3561        ("perl" ,perl)                   ;needed to run 'ppmquant' during tests
3562        ("texlive" ,texlive)             ;full package required for fonts
3563        ("ghostscript" ,ghostscript)))
3564     (inputs
3565      `(("blas" ,openblas)
3566        ("lapack" ,lapack)))
3567     (arguments
3568      `(#:modules ((srfi srfi-1)
3569                   ,@%gnu-build-system-modules)
3570        #:configure-flags '("--enable-shared"
3571                            "--disable-fortran"
3572                            "--without-MPI"
3573                            "--with-openmp"
3574                            "--with-fei"
3575                            "--with-lapack"
3576                            "--with-blas")
3577        #:phases
3578        (modify-phases %standard-phases
3579          (add-before 'configure 'chdir-src
3580            (lambda _ (chdir "src")))
3581          (replace 'configure
3582            (lambda* (#:key build target configure-flags
3583                            #:allow-other-keys #:rest args)
3584              (let* ((configure (assoc-ref %standard-phases 'configure)))
3585                (apply configure
3586                       (append args
3587                               (list #:configure-flags
3588                                     (cons (string-append
3589                                            "--host=" (or target build))
3590                                           configure-flags)))))))
3591          (add-after 'build 'build-docs
3592            (lambda _
3593              (zero? (system* "make" "-Cdocs" "pdf" "html"))))
3594          (replace 'check
3595            (lambda _
3596              (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3597              (setenv "PATH" (string-append "." ":" (getenv "PATH")))
3598              (and (system* "make" "check" "CHECKRUN=")
3599                   (fold (lambda (filename result)
3600                           (and result
3601                                (let ((size (stat:size (stat filename))))
3602                                  (when (not (zero? size))
3603                                    (format #t "~a size ~d; error indication~%"
3604                                            filename size))
3605                                  (zero? size))))
3606                         #t
3607                         (find-files "test" ".*\\.err$")))))
3608          (add-after 'install 'install-docs
3609            (lambda* (#:key outputs #:allow-other-keys)
3610              ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3611              (let* ((doc (assoc-ref outputs "doc"))
3612                     (docdir (string-append doc "/share/doc/hypre-" ,version)))
3613                (with-directory-excursion "docs"
3614                  (for-each (lambda (base)
3615                              (install-file (string-append base ".pdf") docdir)
3616                              (copy-recursively base docdir)) ;html docs
3617                            '("HYPRE_usr_manual"
3618                              "HYPRE_ref_manual")))
3619                #t))))))
3620     (home-page "http://www.llnl.gov/casc/hypre/")
3621     (synopsis "Library of solvers and preconditioners for linear equations")
3622     (description
3623      "HYPRE is a software library of high performance preconditioners and
3624 solvers for the solution of large, sparse linear systems of equations.  It
3625 features multigrid solvers for both structured and unstructured grid
3626 problems.")
3627     (license license:lgpl2.1)))
3628
3629 (define-public hypre-openmpi
3630   (package (inherit hypre)
3631     (name "hypre-openmpi")
3632     (inputs
3633      `(("mpi" ,openmpi)
3634        ,@(package-inputs hypre)))
3635     (arguments
3636      (substitute-keyword-arguments (package-arguments hypre)
3637        ((#:configure-flags flags)
3638         ``("--with-MPI"
3639            ,@(delete "--without-MPI" ,flags)))
3640        ((#:phases phases)
3641         `(modify-phases ,phases
3642            (add-before 'check 'set-test-environment
3643              (lambda _
3644                ;; By default, running the test suite would fail because 'ssh'
3645                ;; could not be found in $PATH.  Define this variable to
3646                ;; placate Open MPI without adding a dependency on OpenSSH (the
3647                ;; agent isn't used anyway.)
3648                (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
3649                #t))))))
3650     (synopsis "Parallel solvers and preconditioners for linear equations")
3651     (description
3652      "HYPRE is a software library of high performance preconditioners and
3653 solvers for the solution of large, sparse linear systems of equations on
3654 parallel computers.  It features parallel multigrid solvers for both
3655 structured and unstructured grid problems.")))
3656
3657 (define-public matio
3658   (package
3659     (name "matio")
3660     (version "1.5.6")
3661     (source
3662      (origin
3663        (method url-fetch)
3664        (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
3665                            "matio-" version ".tar.gz"))
3666        (sha256
3667         (base32
3668          "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3669     (build-system gnu-build-system)
3670     (inputs
3671      `(("zlib" ,zlib)
3672        ("hdf5" ,hdf5)))
3673     (home-page "http://matio.sourceforge.net/")
3674     (synopsis "Library for reading and writing MAT files")
3675     (description "Matio is a library for reading and writing MAT files.  It
3676 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3677     (license license:bsd-2)))
3678
3679 (define-public vc
3680   (package
3681     (name "vc")
3682     (version "1.3.3")
3683     (source
3684       (origin (method url-fetch)
3685               (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3686                                   "download/" version "/Vc-" version ".tar.gz"))
3687               (sha256
3688                (base32
3689                 "1zmlpn32jzb38smp3j834llmbix3whsrbw0h397qxysbw792kih8"))))
3690     (build-system cmake-build-system)
3691     (arguments
3692      '(#:configure-flags
3693        '("-DBUILD_TESTING=ON"
3694          ;; By default, Vc will optimize for the CPU of the build machine.
3695          ;; Setting this to "none" makes it create portable binaries.  See
3696          ;; "cmake/OptimizeForArchitecture.cmake".
3697          "-DTARGET_ARCHITECTURE=none")))
3698     (synopsis "SIMD vector classes for C++")
3699     (description "Vc provides portable, zero-overhead C++ types for explicitly
3700 data-parallel programming.  It is a library designed to ease explicit
3701 vectorization of C++ code.  Its types enable explicitly stating data-parallel
3702 operations on multiple values.  The parallelism is therefore added via the type
3703 system.  Vc has an intuitive API and provides portability between different
3704 compilers and compiler versions as well as portability between different vector
3705 instruction sets.  Thus, an application written with Vc can be compiled for:
3706 @enumerate
3707 @item AVX and AVX2
3708 @item SSE2 up to SSE4.2 or SSE4a
3709 @item Scalar
3710 @item MIC
3711 @item NEON (in development)
3712 @item NVIDIA GPUs / CUDA (in development)
3713 @end enumerate\n")
3714     (home-page "https://github.com/VcDevel/Vc")
3715     ;; "No support_???.cpp file exists for this architecture."
3716     (supported-systems '("x86_64-linux" "i686-linux"))
3717     (license license:bsd-3)))
3718
3719 (define-public reducelcs
3720   ;; This is the last commit which is available upstream, no
3721   ;; release happened since 2010.
3722   (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
3723         (revision "1"))
3724     (package
3725       (name "reducelcs")
3726       (version (string-append "1.0-" revision "." (string-take commit 7)))
3727       (source
3728        (origin
3729          (method git-fetch)
3730          (uri (git-reference
3731                (url "https://github.com/gdv/Reduce-Expand-for-LCS")
3732                (commit commit)))
3733          (file-name (string-append name "-" version "-checkout"))
3734          (sha256
3735           (base32
3736            "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
3737       (build-system gnu-build-system)
3738       (inputs
3739        `(("openlibm" ,openlibm)))
3740       (arguments
3741        `(#:tests? #f ; no tests
3742          #:phases
3743          (modify-phases %standard-phases
3744            (delete 'configure) ; No configure script exists.
3745            (replace 'install ; No install phase exists.
3746              (lambda* (#:key outputs #:allow-other-keys)
3747                (let* ((out (assoc-ref outputs "out"))
3748                       (bin (string-append out "/bin")))
3749                  (install-file "Approximation" bin)
3750                  (install-file "CollectResults" bin)
3751                  (install-file "GenerateInstances" bin)
3752                  #t))))))
3753       (synopsis "Approximate Longest Commons Subsequence computation tool")
3754       (description
3755        "@code{reduceLCS} is an implementation of the Reduce-Expand
3756 algorithm for LCS.  It is a fast program to compute the approximate
3757 Longest Commons Subsequence of a set of strings.")
3758       (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
3759       (license license:gpl3+))))
3760
3761 (define-public jacal
3762   (package
3763     (name "jacal")
3764     (version "1c4")
3765     (source (origin
3766               (method url-fetch)
3767               (uri (string-append
3768                     "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
3769                     version ".zip"))
3770               (sha256 (base32
3771                        "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
3772               (patches (search-patches "jacal-fix-texinfo.patch"))))
3773     (build-system gnu-build-system)
3774     (arguments
3775      `(#:phases
3776        (modify-phases %standard-phases
3777          (add-before 'build 'pre-build
3778                      ;; Don't use upstream's script - it really doesn't fit into
3779                      ;; Guix's functional paradigm.
3780                      (lambda* (#:key inputs outputs #:allow-other-keys)
3781                        (substitute* "Makefile"
3782                          (("^install: install-script") "install: "))))
3783          (add-after 'install 'post-install
3784                     ;; Instead, we provide our own simplified script.
3785                     (lambda* (#:key inputs outputs #:allow-other-keys)
3786                       (let ((wrapper (string-append (assoc-ref outputs "out")
3787                                                     "/bin/jacal")))
3788                         (format (open wrapper (logior O_WRONLY O_CREAT))
3789                                 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
3790                                 "-e '(slib:load \"~a/lib/jacal/math\") "
3791                                 "(math)' \"$@\"\n")
3792                                 (which  "bash")
3793                                 (assoc-ref inputs "scm")
3794                                 (assoc-ref outputs "out"))
3795                         (chmod wrapper #o555))))
3796          (replace 'configure
3797                   (lambda* (#:key inputs outputs #:allow-other-keys)
3798                     (zero? (system* "./configure"
3799                                     (string-append "--prefix="
3800                                                    (assoc-ref outputs "out")))))))))
3801     (inputs `(("scm" ,scm)))
3802     (native-inputs `(("unzip" ,unzip)
3803                      ("texinfo" ,texinfo)))
3804     (synopsis "Symbolic mathematics system")
3805     (description "GNU JACAL is an interactive symbolic mathematics program based on
3806 Scheme.  It manipulate and simplify a range of mathematical expressions such
3807 as equations, scalars, vectors, and matrices.")
3808     (home-page "https://www.gnu.org/software/jacal/")
3809     (license license:gpl3+)))
3810
3811 (define-public z3
3812   (package
3813     (name "z3")
3814     (version "4.5.0")
3815     (source (origin
3816               (method url-fetch)
3817               (uri (string-append
3818                     "https://github.com/Z3Prover/z3/archive/z3-"
3819                     version ".tar.gz"))
3820               (sha256
3821                (base32
3822                 "032a5lvji2liwmc25jv52bdrhimqflvqbpg77ccaq1jykhiivbmf"))))
3823     (build-system cmake-build-system)
3824     (arguments
3825      `(#:configure-flags
3826        (list "-DBUILD_PYTHON_BINDINGS=true"
3827              "-DINSTALL_PYTHON_BINDINGS=true"
3828              (string-append "-DCMAKE_INSTALL_PYTHON_PKG_DIR="
3829                             %output
3830                             "/lib/python2.7/site-packages"))
3831        #:phases
3832        (modify-phases %standard-phases
3833          (add-before 'configure 'bootstrap
3834            (lambda _
3835              (zero?
3836               (system* "python" "contrib/cmake/bootstrap.py" "create"))))
3837          (add-before 'check 'make-test-z3
3838            (lambda _
3839              ;; Build the test suite executable.
3840              (zero? (system* "make" "test-z3" "-j"
3841                              (number->string (parallel-job-count))))))
3842          (replace 'check
3843            (lambda _
3844              ;; Run all the tests that don't require arguments.
3845              (zero? (system* "./test-z3" "/a")))))))
3846     (native-inputs
3847      `(("python" ,python-2)))
3848     (synopsis "Theorem prover")
3849     (description "Z3 is a theorem prover and @dfn{satisfiability modulo
3850 theories} (SMT) solver.  It provides a C/C++ API, as well as Python bindings.")
3851     (home-page "https://github.com/Z3Prover/z3")
3852     (license license:expat)))
3853
3854 (define-public cubicle
3855   (package
3856     (name "cubicle")
3857     (version "1.1.1")
3858     (source (origin
3859               (method url-fetch)
3860               (uri (string-append "http://cubicle.lri.fr/cubicle-"
3861                                   version ".tar.gz"))
3862               (sha256
3863                (base32
3864                 "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h"))))
3865     (build-system gnu-build-system)
3866     (native-inputs
3867      `(("ocaml" ,ocaml)
3868        ("which" ,(@@ (gnu packages base) which))))
3869     (propagated-inputs
3870      `(("z3" ,z3)))
3871     (arguments
3872      `(#:configure-flags (list "--with-z3")
3873        #:tests? #f
3874        #:phases
3875        (modify-phases %standard-phases
3876          (add-before 'configure 'configure-for-release
3877            (lambda _
3878              (substitute* "Makefile.in"
3879                (("SVNREV=") "#SVNREV="))))
3880          (add-before 'configure 'fix-/bin/sh
3881            (lambda _
3882              (substitute* "configure"
3883                (("/bin/sh") (which "sh")))))
3884          (add-before 'configure 'fix-smt-z3wrapper.ml
3885            (lambda _
3886              (substitute* "Makefile.in"
3887                (("\\\\n") "")))))))
3888     (home-page "http://cubicle.lri.fr/")
3889     (synopsis "Model checker for array-based systems")
3890     (description "Cubicle is a model checker for verifying safety properties
3891 of array-based systems.  This is a syntactically restricted class of
3892 parametrized transition systems with states represented as arrays indexed by
3893 an arbitrary number of processes.  Cache coherence protocols and mutual
3894 exclusion algorithms are typical examples of such systems.")
3895     (license license:asl2.0)))
3896
3897 (define-public elemental
3898   (package
3899     (name "elemental")
3900     (version "0.87.7")
3901     (source (origin
3902               (method url-fetch)
3903               (uri (string-append "https://github.com/elemental/Elemental/"
3904                                   "archive/v" version ".tar.gz"))
3905               (file-name (string-append name "-" version ".tar.gz"))
3906               (sha256
3907                (base32
3908                 "1nfp82w22pi8x8fg9sc37z8kf84dqi1dhxp8bbk7571y4aygvv3v"))))
3909     (build-system cmake-build-system)
3910     (home-page "http://libelemental.org")
3911     (native-inputs
3912      `(("gfortran" ,gfortran)))
3913     (inputs
3914      `(("blas" ,openblas)
3915        ("gfortran:lib" ,gfortran "lib")
3916        ("gmp" ,gmp)
3917        ("lapack" ,lapack)
3918        ("metis" ,metis)
3919        ("mpc" ,mpc)
3920        ("mpfr" ,mpfr)
3921        ("mpi" ,openmpi)
3922        ("qd" ,qd)))
3923     (arguments
3924      `(#:build-type "Release"           ;default RelWithDebInfo not supported
3925        #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
3926                            "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
3927                            "-DEL_CACHE_WARNINGS:BOOL=YES"
3928                            "-DEL_TESTS:BOOL=YES"
3929                            "-DCMAKE_INSTALL_LIBDIR=lib"
3930                            "-DGFORTRAN_LIB=gfortran")
3931        #:phases (modify-phases %standard-phases
3932                   (add-before 'check 'setup-tests
3933                     (lambda _
3934                       ;; Parallelism is done at the MPI layer.
3935                       (setenv "OMP_NUM_THREADS" "1")
3936                       #t))
3937                   (add-after 'install 'remove-tests
3938                     (lambda* (#:key outputs #:allow-other-keys)
3939                       ;; Tests are installed, with no easy configuration
3940                       ;; switch to prevent this, so delete them.
3941                       (delete-file-recursively
3942                        (string-append (assoc-ref outputs "out") "/bin"))
3943                       #t)))))
3944     (synopsis "Dense and sparse-direct linear algebra and optimization")
3945     (description "Elemental is a modern C++ library for distributed-memory
3946 dense and sparse-direct linear algebra, conic optimization, and lattice
3947 reduction.")
3948     (license license:bsd-2)))
3949
3950 (define-public mcrl2
3951   (package
3952     (name "mcrl2")
3953     (version "201707.1.15162")
3954     (source (origin
3955               (method url-fetch)
3956               (uri (string-append "http://www.mcrl2.org/download/devel/mcrl2-"
3957                                   version
3958                                   ".tar.gz"))
3959               (sha256
3960                (base32
3961                 "1ziww2fchsklm25hl9p2mngssxfh9w07nc114cncqaxfibqp2p8f"))))
3962     (native-inputs
3963      `(("subversion" ,subversion)))
3964     (inputs
3965      `(("boost" ,boost)
3966        ("glu" ,glu)
3967        ("mesa" ,mesa)
3968        ("qtbase" ,qtbase)))
3969     (build-system cmake-build-system)
3970     (synopsis "Toolset for the mCRL2 formal specification language")
3971     (description
3972      "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
3973 specification language for describing concurrent discrete event systems.  Its
3974 toolset supports analysis and automatic verification, linearisation, simulation,
3975 state-space exploration and generation, and tools to optimise and analyse
3976 specifications.  Also, state spaces can be manipulated, visualised and
3977 analysed.")
3978     (home-page "https://mcrl2.org")
3979     (license license:boost1.0)))
3980
3981 (define-public r-subplex
3982   (package
3983     (name "r-subplex")
3984     (version "1.5-4")
3985     (source
3986     (origin
3987       (method url-fetch)
3988       (uri (cran-uri "subplex" version))
3989       (sha256
3990        (base32
3991         "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
3992     (build-system r-build-system)
3993     (native-inputs
3994      `(("gfortran" ,gfortran)))
3995     (home-page "https://cran.r-project.org/web/packages/subplex")
3996     (synopsis "Unconstrained optimization using the subplex algorithm")
3997     (description "This package implements the Subplex optimization algorithm.
3998 It solves unconstrained optimization problems using a simplex method on
3999 subspaces.  The method is well suited for optimizing objective functions that
4000 are noisy or are discontinuous at the solution.")
4001     (license license:gpl3+)))
4002
4003 (define-public r-desolve
4004   (package
4005     (name "r-desolve")
4006     (version "1.21")
4007     (source
4008       (origin
4009         (method url-fetch)
4010         (uri (cran-uri "deSolve" version))
4011         (sha256
4012          (base32
4013           "0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"))))
4014     (properties `((upstream-name . "deSolve")))
4015     (build-system r-build-system)
4016     (native-inputs
4017      `(("gfortran" ,gfortran)))
4018     (home-page "https://desolve.r-forge.r-project.org/")
4019     (synopsis "Solvers for initial value problems of differential equations")
4020     (description "This package provides functions that solve initial
4021 value problems of a system of first-order ordinary differential equations (ODE),
4022 of partial differential equations (PDE), of differential algebraic equations
4023 (DAE), and of delay differential equations.  The functions provide an interface
4024 to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
4025 to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
4026 the Runge-Kutta family with fixed or variable time steps.  The package contains
4027 routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
4028 differential equations (PDE) that have been converted to ODEs by numerical
4029 differencing.")
4030     (license license:gpl2+)))
4031
4032 (define-public tcalc
4033   (package
4034   (name "tcalc")
4035   (version "2.0")
4036   (source
4037     (origin
4038       (method url-fetch)
4039       (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
4040                             version ".tar.gz"))
4041       (sha256
4042         (base32
4043           "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
4044   (build-system gnu-build-system)
4045   (synopsis "The terminal calculator")
4046   (description
4047     "The terminal calculator is a small program to help users of the GNU/Linux
4048 terminal do calculations simply and quickly.  The formula to be calculated can
4049 be fed to @command{tcalc} through the command line.")
4050   (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
4051   (license license:gpl3+)))
4052
4053 (define-public sundials
4054   (package
4055     (name "sundials")
4056     (version "3.1.1")
4057     (source
4058      (origin
4059        (method url-fetch)
4060        (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
4061                            "sundials-" version ".tar.gz"))
4062        (sha256
4063         (base32
4064          "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
4065     (build-system cmake-build-system)
4066     (native-inputs
4067      `(("python" ,python-2)))    ;for tests; syntax incompatible with python 3
4068     (inputs
4069      `(("fortran" ,gfortran)            ;for fcmix
4070        ("blas" ,openblas)
4071        ("suitesparse" ,suitesparse)))   ;TODO: Add hypre
4072     (arguments
4073      `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
4074                            "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
4075                            "-DEXAMPLES_ENABLE_F77:BOOL=ON"
4076                            "-DEXAMPLES_ENABLE_F90:BOOL=ON"
4077                            "-DEXAMPLES_INSTALL:BOOL=OFF"
4078
4079                            "-DFCMIX_ENABLE:BOOL=ON"
4080
4081                            "-DKLU_ENABLE:BOOL=ON"
4082                            ,(string-append "-DKLU_INCLUDE_DIR="
4083                                            (assoc-ref %build-inputs "suitesparse")
4084                                            "/include")
4085                            ,(string-append "-DKLU_LIBRARY_DIR="
4086                                            (assoc-ref %build-inputs "suitesparse")
4087                                            "/lib"))))
4088     (home-page "https://computation.llnl.gov/projects/sundials")
4089     (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
4090     (description "SUNDIALS is a family of software packages implemented with
4091 the goal of providing robust time integrators and nonlinear solvers that can
4092 easily be incorporated into existing simulation codes.")
4093     (license license:bsd-3)))
4094
4095 (define-public sundials-openmpi
4096   (package (inherit sundials)
4097     (name "sundials-openmpi")
4098     (inputs
4099      `(("mpi" ,openmpi)
4100        ("petsc" ,petsc-openmpi)         ;support in SUNDIALS requires MPI
4101        ,@(package-inputs sundials)))
4102     (arguments
4103      (substitute-keyword-arguments (package-arguments sundials)
4104        ((#:configure-flags flags '())
4105         `(cons* "-DMPI_ENABLE:BOOL=ON"
4106                 "-DPETSC_ENABLE:BOOL=ON"
4107                 (string-append "-DPETSC_INCLUDE_DIR="
4108                                (assoc-ref %build-inputs "petsc")
4109                                "/include")
4110                 (string-append "-DPETSC_LIBRARY_DIR="
4111                                (assoc-ref %build-inputs "petsc")
4112                                "/lib")
4113                 ,flags))
4114        ((#:phases phases '%standard-phases)
4115         `(modify-phases ,phases
4116            (add-before 'check 'set-test-environment
4117              (lambda _
4118                ;; By default, running the test suite would fail because 'ssh'
4119                ;; could not be found in $PATH.  Define this variable to
4120                ;; placate Open MPI without adding a dependency on OpenSSH (the
4121                ;; agent isn't used anyway.)
4122                (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
4123                ;; Allow oversubscription in case there are less
4124                ;; physical cores available in the build environment
4125                ;; than SUNDIALS wants while testing.
4126                (setenv "OMPI_MCA_rmaps_base_oversubscribe" "yes")
4127                #t))))))
4128     (synopsis "SUNDIALS with OpenMPI support")))