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, 2019 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, 2019 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, 2019 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, 2019 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 ng0 <ng0@n0.is>
  20 ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
  21 ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
  22 ;;; Copyright © 2017, 2019 Arun Isaac <arunisaac@systemreboot.net>
  23 ;;; Copyright © 2017, 2018, 2019 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 ;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
  31 ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
  32 ;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
  33 ;;;
  34 ;;; This file is part of GNU Guix.
  35 ;;;
  36 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  37 ;;; under the terms of the GNU General Public License as published by
  38 ;;; the Free Software Foundation; either version 3 of the License, or (at
  39 ;;; your option) any later version.
  40 ;;;
  41 ;;; GNU Guix is distributed in the hope that it will be useful, but
  42 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  43 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  44 ;;; GNU General Public License for more details.
  45 ;;;
  46 ;;; You should have received a copy of the GNU General Public License
  47 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  48
  49 (define-module (gnu packages maths)
  50   #:use-module (ice-9 regex)
  51   #:use-module (ice-9 match)
  52   #:use-module (gnu packages)
  53   #:use-module ((guix licenses) #:prefix license:)
  54   #:use-module (guix packages)
  55   #:use-module (guix download)
  56   #:use-module (guix git-download)
  57   #:use-module (guix utils)
  58   #:use-module ((guix build utils) #:select (alist-replace))
  59   #:use-module (guix build-system cmake)
  60   #:use-module (guix build-system gnu)
  61   #:use-module (guix build-system python)
  62   #:use-module (guix build-system r)
  63   #:use-module (guix build-system ruby)
  64   #:use-module (gnu packages algebra)
  65   #:use-module (gnu packages audio)
  66   #:use-module (gnu packages autotools)
  67   #:use-module (gnu packages base)
  68   #:use-module (gnu packages bison)
  69   #:use-module (gnu packages boost)
  70   #:use-module (gnu packages check)
  71   #:use-module (gnu packages cmake)
  72   #:use-module (gnu packages compression)
  73   #:use-module (gnu packages curl)
  74   #:use-module (gnu packages cyrus-sasl)
  75   #:use-module (gnu packages documentation)
  76   #:use-module (gnu packages elf)
  77   #:use-module (gnu packages flex)
  78   #:use-module (gnu packages fltk)
  79   #:use-module (gnu packages fontutils)
  80   #:use-module (gnu packages gettext)
  81   #:use-module (gnu packages gcc)
  82   #:use-module (gnu packages gd)
  83   #:use-module (gnu packages ghostscript)
  84   #:use-module (gnu packages graphviz)
  85   #:use-module (gnu packages gtk)
  86   #:use-module (gnu packages image)
  87   #:use-module (gnu packages java)
  88   #:use-module (gnu packages less)
  89   #:use-module (gnu packages lisp)
  90   #:use-module (gnu packages linux)
  91   #:use-module (gnu packages logging)
  92   #:use-module (gnu packages lua)
  93   #:use-module (gnu packages gnome)
  94   #:use-module (gnu packages guile)
  95   #:use-module (gnu packages xorg)
  96   #:use-module (gnu packages gl)
  97   #:use-module (gnu packages imagemagick)
  98   #:use-module (gnu packages m4)
  99   #:use-module (gnu packages mpi)
 100   #:use-module (gnu packages multiprecision)
 101   #:use-module (gnu packages netpbm)
 102   #:use-module (gnu packages pcre)
 103   #:use-module (gnu packages popt)
 104   #:use-module (gnu packages perl)
 105   #:use-module (gnu packages pkg-config)
 106   #:use-module (gnu packages pulseaudio)
 107   #:use-module (gnu packages python)
 108   #:use-module (gnu packages python-web)
 109   #:use-module (gnu packages python-xyz)
 110   #:use-module (gnu packages qt)
 111   #:use-module (gnu packages readline)
 112   #:use-module (gnu packages ruby)
 113   #:use-module (gnu packages tbb)
 114   #:use-module (gnu packages scheme)
 115   #:use-module (gnu packages shells)
 116   #:use-module (gnu packages tcl)
 117   #:use-module (gnu packages texinfo)
 118   #:use-module (gnu packages tex)
 119   #:use-module (gnu packages tls)
 120   #:use-module (gnu packages version-control)
 121   #:use-module (gnu packages wxwidgets)
 122   #:use-module (gnu packages xml)
 123   #:use-module (srfi srfi-1))
 124
 125 (define-public aris
 126   (package
 127     (name "aris")
 128     (version "2.2")
 129     (source (origin
 130               (method url-fetch)
 131               (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
 132               (sha256 (base32
 133                        "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
 134     (build-system gnu-build-system)
 135     (inputs `(("gtk+" ,gtk+)
 136               ("libxml2" ,libxml2)))
 137     (native-inputs `(("pkg-config" ,pkg-config)))
 138     (synopsis "Natural deduction first-order logic interface")
 139     (description "Aris is a program for performing logical proofs.  It supports
 140 propositional and predicate logic, as well as Boolean algebra and
 141 arithmetical logic.  In addition to its predefined inference and equivalence
 142 rules, Aris also supports references to older proofs.  Its use of standard
 143 logical symbols and its natural deduction interface make it easy to use for
 144 beginners.")
 145     (license license:gpl3+)
 146     (home-page "https://www.gnu.org/software/aris/")))
 147
 148 (define-public c-graph
 149   (package
 150    (name "c-graph")
 151    (version "2.0.1")
 152    (source (origin
 153             (method url-fetch)
 154             (uri (string-append "mirror://gnu/c-graph/c-graph-" version
 155                                 ".tar.gz"))
 156             (sha256 (base32
 157                      "092412jzxy6wdvpk96pfj499hpmaww8xllavbvlqspfpr7ips9id"))))
 158    (build-system gnu-build-system)
 159    (inputs
 160     `(("fortran" ,gfortran)))
 161    (synopsis "Visualizing and demonstrating convolution")
 162    (description
 163     "GNU C-Graph is a tool for demonstrating the theory of convolution.
 164 Thus, it can serve as an excellent aid to students of signal and systems
 165 theory in visualizing the convolution process.  Rather than forcing the
 166 student to write code, the program offers an intuitive interface with
 167 interactive dialogs to guide them.")
 168    (license license:gpl3+)
 169    (home-page "https://www.gnu.org/software/c-graph/")))
 170
 171 (define-public coda
 172   (package
 173     (name "coda")
 174     (version "2.19")
 175     (source
 176      (origin
 177        (method url-fetch)
 178        (uri (string-append "https://github.com/stcorp/coda/releases/download/"
 179                            version "/coda-" version ".tar.gz"))
 180        (sha256
 181         (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245"))
 182        (patches (search-patches "coda-use-system-libs.patch"))
 183        (modules '((guix build utils)))
 184        (snippet
 185         ;; Make sure we don't use the bundled software.
 186         '(begin
 187            (for-each (lambda (d)
 188                        (delete-file-recursively (string-append "libcoda/" d)))
 189                      '("zlib" "pcre" "expat"))
 190            #t))))
 191     (native-inputs
 192      `(("fortran" ,gfortran)
 193        ("python" ,python)
 194        ("python-numpy" ,python-numpy)))
 195     (inputs
 196      `(("zlib" ,zlib)
 197        ("pcre" ,pcre)
 198        ("expat" ,expat)
 199        ("hdf4" ,hdf4-alt)
 200        ("hdf5" ,hdf5)))
 201     (build-system gnu-build-system)
 202     (arguments
 203      '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
 204                            "LIBS= -lz -lpcre -lexpat")))
 205     (synopsis "A common interface to various earth observation data formats")
 206     (description
 207      "The Common Data Access toolbox (CODA) provides a set of interfaces for
 208 reading remote sensing data from earth observation data files.  It consists of
 209 command line applications and interfaces to the C, Fortran, Python, and Java
 210 programming languages.")
 211     (home-page "https://stcorp.nl/coda")
 212     (license license:gpl2+)))
 213
 214 (define-public qhull
 215   (package
 216     (name "qhull")
 217     (version "2015.2")
 218     (source (origin
 219               (method url-fetch)
 220               (uri (string-append "http://www.qhull.org/download/qhull-"
 221                                   (car (string-split version #\.))
 222                                   "-src-7.2.0.tgz"))
 223               (sha256
 224                (base32
 225                 "0dm4b2xr3asy6w74khq2zg4gf26zsy3qf9sq7pf7lmrvbj911c3q"))))
 226     (build-system cmake-build-system)
 227     (synopsis "Calculate convex hulls and related structures")
 228     (description
 229      "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
 230 diagram, halfspace intersection about a point, furthest-site Delaunay
 231 triangulation, and furthest-site Voronoi diagram.  The source code runs in 2-d,
 232 3-d, 4-d, and higher dimensions.  @code{Qhull} implements the Quickhull
 233 algorithm for computing the convex hull.  It handles roundoff errors from
 234 floating point arithmetic.  It computes volumes, surface areas, and
 235 approximations to the convex hull.
 236
 237 @code{Qhull} does not support triangulation of non-convex surfaces, mesh
 238 generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
 239 shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
 240 triangulations.")
 241     (home-page "http://qhull.org")
 242     (license (license:non-copyleft "file://COPYING.txt"
 243                                    "See COPYING in the distribution."))))
 244
 245 (define-public python-cvxopt
 246   (package
 247     (name "python-cvxopt")
 248     (version "1.2.1")
 249     (source (origin
 250               (method git-fetch)
 251               (uri (git-reference
 252                     (url "https://github.com/cvxopt/cvxopt.git")
 253                     (commit version)))
 254               (file-name (git-file-name name version))
 255               (sha256
 256                (base32
 257                 "05mnjil9palaa48xafdfh4f5pr4z7aqjr995rwl08qfyxs8y0crf"))))
 258     (build-system python-build-system)
 259     (arguments
 260      `(#:phases
 261        (modify-phases %standard-phases
 262          (add-after 'unpack 'find-libraries
 263            (lambda* (#:key inputs #:allow-other-keys)
 264              (setenv "CVXOPT_BLAS_LIB" "openblas")
 265              (setenv "CVXOPT_BUILD_FFTW" "1")
 266              (setenv "CVXOPT_BUILD_GLPK" "1")
 267              (setenv "CVXOPT_BUILD_GSL" "1")
 268              #t)))))
 269     (inputs
 270      `(("fftw" ,fftw)
 271        ("glpk" ,glpk)
 272        ("gsl" ,gsl)
 273        ("lapack" ,lapack)
 274        ("openblas" ,openblas)
 275        ("suitesparse" ,suitesparse)))
 276     (home-page "https://www.cvxopt.org")
 277     (synopsis "Python library for convex optimization")
 278     (description
 279      "CVXOPT is a package for convex optimization based on the Python
 280 programming language.  Its main purpose is to make the development of software
 281 for convex optimization applications straightforward by building on Python’s
 282 extensive standard library and on the strengths of Python as a high-level
 283 programming language.")
 284     (license license:gpl3+)))
 285
 286 (define-public python2-cvxopt
 287   (package-with-python2 python-cvxopt))
 288
 289 (define-public units
 290   (package
 291    (name "units")
 292    (version "2.18")
 293    (source (origin
 294             (method url-fetch)
 295             (uri (string-append "mirror://gnu/units/units-" version
 296                                 ".tar.gz"))
 297             (sha256 (base32
 298                      "0y26kj349i048y4z3xrk90bvciw2j6ds3rka7r7yn3183hirr5b4"))))
 299    (build-system gnu-build-system)
 300    (inputs
 301     `(("readline" ,readline)
 302       ("python" ,python-wrapper)        ;for 'units_cur' script
 303       ("python-requests" ,python-requests)))
 304    (arguments
 305     `(#:phases (modify-phases %standard-phases
 306                  (add-after 'install 'wrap-units_cur
 307                    (lambda* (#:key outputs #:allow-other-keys)
 308                      (let* ((out (assoc-ref outputs "out"))
 309                             (bin (string-append out "/bin")))
 310                        (wrap-program (string-append bin "/units_cur")
 311                          `("PYTHONPATH" ":" prefix
 312                            ,(search-path-as-string->list (getenv "PYTHONPATH"))))
 313                        #t))))))
 314    (synopsis "Conversion between thousands of scales")
 315    (description
 316     "GNU Units converts numeric quantities between units of measure.  It
 317 can handle scale changes through adaptive usage of standard scale
 318 prefixes (micro-, kilo-, etc.).  It can also handle nonlinear
 319 conversions such as Fahrenheit to Celsius.  Its interpreter is powerful
 320 enough to be used effectively as a scientific calculator.")
 321    (license license:gpl3+)
 322    (home-page "https://www.gnu.org/software/units/")))
 323
 324 (define-public double-conversion
 325   (package
 326     (name "double-conversion")
 327     (version "3.1.0")
 328     (home-page "https://github.com/google/double-conversion")
 329     (source (origin
 330               (method git-fetch)
 331               (uri (git-reference (url home-page) (commit version)))
 332               (file-name (git-file-name name version))
 333               (sha256
 334                (base32
 335                 "123rb2p4snqagrybw66vnapchqdwn2rfpr1wcq0ya9gwbyl7xccx"))))
 336     (build-system cmake-build-system)
 337     (arguments
 338      '(#:test-target "test"
 339        #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
 340                            "-DBUILD_TESTING=ON")))
 341     (synopsis "Conversion routines for IEEE doubles")
 342     (description
 343      "The double-conversion library provides binary-decimal and decimal-binary
 344 routines for IEEE doubles.  The library consists of efficient conversion
 345 routines that have been extracted from the V8 JavaScript engine.")
 346     (license license:bsd-3)))
 347
 348 (define-public dionysus
 349   (package
 350     (name "dionysus")
 351     (version "1.4.0")
 352     (source (origin
 353               (method url-fetch)
 354               (uri (string-append "mirror://gnu/dionysus/dionysus-" version
 355                                   ".tar.xz"))
 356               (sha256
 357                (base32
 358                 "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
 359     (build-system gnu-build-system)
 360     (inputs `(("tcl" ,tcl)))                      ;for 'tclsh'
 361     (synopsis "Local search for universal constants and scientific values")
 362     (description
 363      "GNU Dionysus is a convenient system for quickly retrieving the values of
 364 mathematical constants used in science and engineering.  Values can be
 365 searched using a simple command-line tool, choosing from three databases:
 366 universal constants, atomic numbers, and constants related to
 367 semiconductors.")
 368     (license license:gpl3+)
 369     (home-page "https://www.gnu.org/software/dionysus/")))
 370
 371 (define-public gsl
 372   (package
 373     (name "gsl")
 374     (version "2.5")
 375     (source (origin
 376               (method url-fetch)
 377               (uri (string-append "mirror://gnu/gsl/gsl-"
 378                                   version ".tar.gz"))
 379               (sha256
 380                (base32
 381                 "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04"))
 382               (patches (search-patches "gsl-test-i686.patch"))))
 383     (build-system gnu-build-system)
 384     (arguments
 385      `(;; Currently there are numerous tests that fail on "exotic"
 386        ;; architectures such as aarch64 and ppc64le.
 387        ,@(if (string-prefix? "aarch64-linux"
 388                              (or (%current-target-system) (%current-system)))
 389            '(#:tests? #f)
 390            '())))
 391     (home-page "https://www.gnu.org/software/gsl/")
 392     (synopsis "Numerical library for C and C++")
 393     (description
 394      "The GNU Scientific Library is a library for numerical analysis in C
 395 and C++.  It includes a wide range of mathematical routines, with over 1000
 396 functions in total.  Subject areas covered by the library include:
 397 differential equations, linear algebra, Fast Fourier Transforms and random
 398 numbers.")
 399     (license license:gpl3+)))
 400
 401 (define-public glpk
 402   (package
 403     (name "glpk")
 404     (version "4.65")
 405     (source
 406      (origin
 407       (method url-fetch)
 408       (uri (string-append "mirror://gnu/glpk/glpk-"
 409                           version ".tar.gz"))
 410       (sha256
 411        (base32
 412         "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))
 413     (build-system gnu-build-system)
 414     (inputs
 415      `(("gmp" ,gmp)))
 416     (arguments
 417      `(#:configure-flags '("--with-gmp")))
 418     (home-page "https://www.gnu.org/software/glpk/")
 419     (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
 420     (description
 421      "GLPK is a C library for solving large-scale linear programming (LP),
 422 mixed integer programming (MIP), and other related problems.  It supports the
 423 GNU MathProg modeling language, a subset of the AMPL language, and features a
 424 translator for the language.  In addition to the C library, a stand-alone
 425 LP/MIP solver is included in the package.")
 426     (license license:gpl3+)))
 427
 428 (define-public 4ti2
 429   (package
 430     (name "4ti2")
 431     (version "1.6.9")
 432     (source
 433      (origin
 434        (method url-fetch)
 435        (uri (string-append "https://github.com/4ti2/4ti2/releases/download/"
 436                            "Release_"
 437                            (string-map (lambda (c) (if (char=? c #\.) #\_ c))
 438                                        version)
 439                            "/4ti2-" version ".tar.gz"))
 440        (sha256
 441         (base32 "0rj92x6p9m3la5gasjbj7sa569im527ffmka5y2sv1amgd3fflrh"))))
 442     (build-system gnu-build-system)
 443     (native-inputs
 444      `(("which" ,(@ (gnu packages base) which)))) ; for the tests
 445     (inputs
 446      `(("glpk" ,glpk)
 447        ("gmp" ,gmp)))
 448     (home-page "http://www.4ti2.de/")
 449     (synopsis "Mathematical tool suite for problems on linear spaces")
 450     (description
 451      "4ti2 implements algorithms for solving algebraic, geometric and
 452 combinatorial problems on linear spaces.  Among others, it solves systems
 453 of linear equations, computes extreme rays of polyhedral cones, solves
 454 integer programming problems and computes Markov bases for statistics.")
 455     (license license:gpl2+)))
 456
 457 (define-public cddlib
 458   (package
 459     (name "cddlib")
 460     (version "0.94i")
 461     (source
 462      (origin
 463       (method url-fetch)
 464       (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
 465                           (string-delete #\. version) ".tar.gz"))
 466       (sha256
 467        (base32
 468         "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
 469     (build-system gnu-build-system)
 470     (inputs
 471      `(("gmp" ,gmp)))
 472     (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
 473     (synopsis "Library for convex hulls and extreme rays of polyhedra")
 474     (description
 475      "The C-library cddlib implements the Double Description Method of
 476 Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
 477 rays of a general convex polyhedron given by a system of linear inequalities
 478 in arbitrary dimension.  It can also be used for the converse operation of
 479 computing convex hulls.")
 480     (license license:gpl2+)))
 481
 482 (define-public arpack-ng
 483   (package
 484     (name "arpack-ng")
 485     (version "3.6.3")
 486     (home-page "https://github.com/opencollab/arpack-ng")
 487     (source (origin
 488               (method git-fetch)
 489               (uri (git-reference (url home-page) (commit version)))
 490               (file-name (git-file-name name version))
 491               (sha256
 492                (base32
 493                 "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
 494     (build-system gnu-build-system)
 495     (native-inputs
 496      `(("autoconf" ,autoconf)
 497        ("automake" ,automake)
 498        ("libtool" ,libtool)))
 499     (inputs
 500      `(("lapack" ,lapack)
 501        ("fortran" ,gfortran)))
 502     (synopsis "Fortran subroutines for solving eigenvalue problems")
 503     (description
 504      "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
 505 large scale eigenvalue problems.")
 506     (license (license:non-copyleft "file://COPYING"
 507                                 "See COPYING in the distribution."))))
 508
 509 (define-public arpack-ng-3.3.0
 510   (package
 511     (inherit arpack-ng)
 512     (version "3.3.0")
 513     (name (package-name arpack-ng))
 514     (home-page (package-home-page arpack-ng))
 515     (source
 516      (origin
 517        (method url-fetch)
 518        (uri (string-append home-page "/archive/" version ".tar.gz"))
 519        (file-name (string-append name "-" version ".tar.gz"))
 520        (sha256
 521         (base32
 522          "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd"))))))
 523
 524 (define-public arpack-ng-openmpi
 525   (package (inherit arpack-ng)
 526     (name "arpack-ng-openmpi")
 527     (inputs
 528      `(("mpi" ,openmpi)
 529        ,@(package-inputs arpack-ng)))
 530     (arguments
 531      (substitute-keyword-arguments (package-arguments arpack-ng)
 532        ((#:configure-flags _ '())
 533         ''("--enable-mpi"))
 534        ((#:phases phases '%standard-phases)
 535         `(modify-phases ,phases
 536            (add-before 'check 'mpi-setup
 537              ,%openmpi-setup)))))
 538     (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
 539
 540 (define-public lapack
 541   (package
 542     (name "lapack")
 543     (version "3.7.1")
 544     (source
 545      (origin
 546       (method url-fetch)
 547       (uri (string-append "http://www.netlib.org/lapack/lapack-"
 548                           version ".tgz"))
 549       (sha256
 550        (base32
 551         "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
 552     (build-system cmake-build-system)
 553     (home-page "http://www.netlib.org/lapack/")
 554     (inputs `(("fortran" ,gfortran)
 555               ("python" ,python-2)))
 556     (arguments
 557      `(#:configure-flags (list
 558                           "-DBUILD_SHARED_LIBS:BOOL=YES"
 559                           "-DLAPACKE=ON"
 560
 561                           ;; Build the 'LAPACKE_clatms' functions.
 562                           "-DLAPACKE_WITH_TMG=ON")
 563        #:phases
 564        (modify-phases %standard-phases
 565          (add-before 'check 'patch-python
 566            (lambda* (#:key inputs #:allow-other-keys)
 567              (let ((python (assoc-ref inputs "python")))
 568                (substitute* "lapack_testing.py"
 569                  (("/usr/bin/env python") python)))
 570              #t)))))
 571     (synopsis "Library for numerical linear algebra")
 572     (description
 573      "LAPACK is a Fortran 90 library for solving the most commonly occurring
 574 problems in numerical linear algebra.")
 575     (license (license:non-copyleft "file://LICENSE"
 576                                 "See LICENSE in the distribution."))))
 577
 578 (define-public scalapack
 579   (package
 580     (name "scalapack")
 581     (version "2.0.2")
 582     (source
 583      (origin
 584        (method url-fetch)
 585        (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
 586                            version ".tgz"))
 587        (sha256
 588         (base32
 589          "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))
 590        (patches (search-patches "scalapack-blacs-mpi-deprecations.patch"))))
 591     (build-system cmake-build-system)
 592     (inputs
 593      `(("mpi" ,openmpi)
 594        ("fortran" ,gfortran)
 595        ("lapack" ,lapack)))             ;for testing only
 596     (arguments
 597      `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
 598        #:phases (modify-phases %standard-phases
 599                   (add-before 'check 'mpi-setup
 600                     ,%openmpi-setup))))
 601     (home-page "http://www.netlib.org/scalapack/")
 602     (synopsis "Library for scalable numerical linear algebra")
 603     (description
 604      "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
 605 routines on parallel distributed memory machines.  ScaLAPACK solves dense and
 606 banded linear systems, least squares problems, eigenvalue problems, and
 607 singular value problems.")
 608     (license (license:non-copyleft "file://LICENSE"
 609                                    "See LICENSE in the distribution."))))
 610
 611 (define-public gnuplot
 612   (package
 613     (name "gnuplot")
 614     (version "5.2.6")
 615     (source (origin
 616               (method url-fetch)
 617               (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
 618                                   version "/gnuplot-"
 619                                   version ".tar.gz"))
 620        (sha256
 621         (base32 "1vllgap08nhvdmc03idmkdnk9cfl2bp81hps50q1pqrr640qzp9m"))))
 622     (build-system gnu-build-system)
 623     (inputs `(("readline" ,readline)
 624               ("cairo" ,cairo)
 625               ("pango" ,pango)
 626               ("gd" ,gd)
 627               ("lua" ,lua)))
 628     (native-inputs
 629      `(("pkg-config" ,pkg-config)
 630        ("texlive" ,texlive-tiny)))
 631     (arguments `(#:configure-flags (list (string-append
 632                                           "--with-texdir=" %output
 633                                           "/texmf-local/tex/latex/gnuplot"))))
 634     (home-page "http://www.gnuplot.info")
 635     (synopsis "Command-line driven graphing utility")
 636     (description "Gnuplot is a portable command-line driven graphing
 637 utility.  It was originally created to allow scientists and students to
 638 visualize mathematical functions and data interactively, but has grown to
 639 support many non-interactive uses such as web scripting.  It is also used as a
 640 plotting engine by third-party applications like Octave.")
 641     ;;  X11 Style with the additional restriction that derived works may only be
 642     ;;  distributed as patches to the original.
 643     (license (license:fsf-free
 644               "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
 645
 646 (define-public gctp
 647   (package
 648     (name "gctp")
 649     (version "2.0.0")
 650     (source
 651      (origin
 652        (method git-fetch)
 653        (uri (git-reference
 654              (url "https://github.com/OkoSanto/GCTP.git")
 655              (commit (string-append "v" version))))
 656        (file-name (git-file-name name version))
 657        (sha256
 658         (base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
 659     (native-inputs
 660      `(("fortran" ,gfortran)))
 661     (build-system gnu-build-system)
 662     (synopsis "General Cartographic Transformation Package (GCTP)")
 663     (description
 664      "The General Cartographic Transformation Package (GCTP) is a system of
 665 software routines designed to permit the transformation of coordinate pairs
 666 from one map projection to another.  The GCTP is the standard computer
 667 software used by the National Mapping Division for map projection
 668 computations.")
 669     (home-page "https://github.com/OkoSanto/GCTP")
 670     (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
 671
 672 (define-public hdf4
 673   (package
 674     (name "hdf4")
 675     (version "4.2.13")
 676     (source
 677      (origin
 678        (method url-fetch)
 679        (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
 680                            version "/src/hdf-" version ".tar.bz2"))
 681        (sha256
 682         (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
 683        (patches (search-patches "hdf4-architectures.patch"
 684                                 "hdf4-reproducibility.patch"
 685                                 "hdf4-shared-fortran.patch"))))
 686     (build-system gnu-build-system)
 687     (native-inputs
 688      `(("gfortran" ,gfortran)
 689        ("bison" ,bison)
 690        ("flex" ,flex)))
 691     (inputs
 692      `(("zlib" ,zlib)
 693        ("libjpeg" ,libjpeg)))
 694     (arguments
 695      `(#:parallel-tests? #f
 696        #:configure-flags '("--enable-shared")
 697        #:phases
 698        (modify-phases %standard-phases
 699          ;; This is inspired by two of Debian's patches.
 700          (add-before 'configure 'add-more-aarch64-support
 701            (lambda _
 702              (substitute* '("mfhdf/ncgen/ncgen.l"
 703                             "mfhdf/ncgen/ncgenyy.c"
 704                             "mfhdf/libsrc/netcdf.h.in")
 705                (("AIX5L64") "__aarch64__"))
 706              #t))
 707          (add-before 'configure 'patchbuild
 708            (lambda _
 709              (substitute*
 710                  '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
 711                (("/bin/rm") "rm")
 712                (("/bin/mkdir") "mkdir"))
 713              (substitute* (find-files "." "^Makefile\\.in$")
 714                (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
 715 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
 716                (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
 717 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
 718 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
 719              #t))
 720          (add-after 'configure 'patch-settings
 721            (lambda _
 722              ;; libhdf4.settings contains the full path of the
 723              ;; compilers used, and its contents are included in
 724              ;; .so-files.  We truncate the hashes to avoid
 725              ;; unnecessary store references to those compilers:
 726              (substitute* "libhdf4.settings"
 727                (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
 728                 (string-append prefix (string-take hash 10) "...")))
 729              #t))
 730          )))
 731     (home-page "https://www.hdfgroup.org/products/hdf4/")
 732     (synopsis
 733      "Library and multi-object file format for storing and managing data")
 734     (description "HDF4 is a library and multi-object file format for storing
 735 and managing data between machines.  HDF4 is an older hierarchical data format,
 736 incompatible with HDF5.")
 737     (license
 738      (license:non-copyleft
 739       "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
 740
 741 (define-public hdf4-alt
 742   (package
 743     (inherit hdf4)
 744     (name "hdf4-alt")
 745     (arguments
 746      (substitute-keyword-arguments (package-arguments hdf4)
 747        ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
 748     (synopsis
 749      "HDF4 without netCDF API, can be combined with the regular netCDF library")))
 750
 751 (define-public hdf5
 752   (package
 753     (name "hdf5")
 754     (version "1.8.21")
 755     (source
 756      (origin
 757       (method url-fetch)
 758       (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
 759                                 "hdf5-" (version-major+minor version)
 760                                 "/hdf5-" version "/src/hdf5-"
 761                                 version ".tar.bz2")
 762                  (string-append "https://support.hdfgroup.org/ftp/HDF5/"
 763                                 "current"
 764                                 (match (string-split version #\.)
 765                                   ((major minor _ ...)
 766                                    (string-append major minor)))
 767                                 "/src/hdf5-" version ".tar.bz2")))
 768       (sha256
 769        (base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5"))
 770       (patches (search-patches "hdf5-config-date.patch"
 771                                "hdf5-1.8-mpi-deprecations.patch"))))
 772     (build-system gnu-build-system)
 773     (inputs
 774      `(("zlib" ,zlib)))
 775     (native-inputs
 776      `(("gfortran" ,gfortran)))
 777     (outputs '("out"       ; core library
 778                "fortran")) ; fortran interface
 779     (arguments
 780      `(;; Some of the users, notably Flann, need the C++ interface.
 781        #:configure-flags '("--enable-cxx"
 782                            "--enable-fortran"
 783                            "--enable-fortran2003")
 784        ;; Use -fPIC to allow the R bindings to link with the static libraries
 785        #:make-flags (list "CFLAGS=-fPIC"
 786                           "CXXFLAGS=-fPIC")
 787        #:phases
 788        (modify-phases %standard-phases
 789          (add-before 'configure 'patch-configure
 790            (lambda* (#:key outputs #:allow-other-keys)
 791              (substitute* "configure"
 792                (("/bin/mv") "mv"))
 793              (substitute* "fortran/src/Makefile.in"
 794                (("libhdf5_fortran_la_LDFLAGS =")
 795                 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
 796                                (assoc-ref outputs "fortran") "/lib")))
 797              (substitute* "hl/fortran/src/Makefile.in"
 798                (("libhdf5hl_fortran_la_LDFLAGS =")
 799                 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
 800                                (assoc-ref outputs "fortran") "/lib")))
 801              #t))
 802          (add-after 'configure 'patch-settings
 803            (lambda _
 804              ;; libhdf5.settings contains the full path of the
 805              ;; compilers used, and its contents are included in
 806              ;; libhdf5.so.  We truncate the hashes to avoid
 807              ;; unnecessary store references to those compilers:
 808              (substitute* "src/libhdf5.settings"
 809               (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
 810                (string-append prefix (string-take hash 10) "..."))
 811               ;; Don't record the build-time kernel version to make the
 812               ;; settings file reproducible.
 813               (("Uname information:.*")
 814                "Uname information: Linux\n"))
 815              #t))
 816          (add-after 'install 'patch-references
 817            (lambda* (#:key inputs outputs #:allow-other-keys)
 818              (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
 819                    (zlib (assoc-ref inputs "zlib")))
 820                (substitute* (find-files bin "h5p?cc")
 821                  (("-lz" lib)
 822                   (string-append "-L" zlib "/lib " lib)))
 823                #t)))
 824          (add-after 'install 'split
 825             (lambda* (#:key inputs outputs #:allow-other-keys)
 826               ;; Move all fortran-related files
 827               (let* ((out (assoc-ref outputs "out"))
 828                      (bin (string-append out "/bin"))
 829                      (lib (string-append out "/lib"))
 830                      (inc (string-append out "/include"))
 831                      (ex (string-append out "/share/hdf5_examples/fortran"))
 832                      (fort (assoc-ref outputs "fortran"))
 833                      (fbin (string-append fort "/bin"))
 834                      (flib (string-append fort "/lib"))
 835                      (finc (string-append fort "/include"))
 836                      (fex (string-append fort "/share/hdf5_examples/fortran")))
 837                 (mkdir-p fbin)
 838                 (mkdir-p flib)
 839                 (mkdir-p finc)
 840                 (mkdir-p fex)
 841                 ;; Note: When built with --enable-parallel, the 'h5fc' file
 842                 ;; doesn't exist, hence this condition.
 843                 (when (file-exists? (string-append bin "/h5fc"))
 844                   (rename-file (string-append bin "/h5fc")
 845                                (string-append fbin "/h5fc")))
 846                 (for-each (lambda (file)
 847                             (rename-file file
 848                                          (string-append flib "/" (basename file))))
 849                           (find-files lib ".*fortran.*"))
 850                 (for-each (lambda (file)
 851                             (rename-file file
 852                                          (string-append finc "/" (basename file))))
 853                           (find-files inc ".*mod"))
 854                 (for-each (lambda (file)
 855                             (rename-file file
 856                                          (string-append fex "/" (basename file))))
 857                           (find-files ex ".*"))
 858                 (delete-file-recursively ex))
 859               #t)))))
 860     (home-page "http://www.hdfgroup.org")
 861     (synopsis "Management suite for extremely large and complex data")
 862     (description "HDF5 is a suite that makes possible the management of
 863 extremely large and complex data collections.")
 864     (license (license:x11-style
 865               "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
 866
 867 (define-public hdf5-1.10
 868   (package (inherit hdf5)
 869     (version "1.10.4")
 870     (source
 871      (origin
 872       (method url-fetch)
 873       (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
 874                                 "hdf5-" (version-major+minor version)
 875                                 "/hdf5-" version "/src/hdf5-"
 876                                 version ".tar.bz2")
 877                  (string-append "https://support.hdfgroup.org/ftp/HDF5/"
 878                                 "current"
 879                                 (apply string-append
 880                                        (take (string-split version #\.) 2))
 881                                 "/src/hdf5-" version ".tar.bz2")))
 882       (sha256
 883        (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
 884       (patches (search-patches "hdf5-config-date.patch"
 885                                "hdf5-mpi-deprecations.patch"))))))
 886
 887 (define-public hdf-java
 888   (package
 889     (name "hdf-java")
 890     (version "3.3.2")
 891     (source
 892      (origin
 893        (method url-fetch)
 894        (uri (string-append
 895              "http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
 896              version "/src/CMake-hdfjava-" version ".tar.gz"))
 897        (sha256
 898         (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
 899        (modules '((guix build utils)))
 900        (snippet     ; Make sure we don't use the bundled sources and binaries.
 901         `(begin
 902            (for-each delete-file
 903                      (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
 904                            "HDF4.tar.gz" "HDF5.tar.gz"))
 905            (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
 906            #t))))
 907     (build-system gnu-build-system)
 908     (native-inputs
 909      `(("jdk" ,icedtea "jdk")
 910        ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
 911        ;; For tests:
 912        ("hamcrest-core" ,java-hamcrest-core)
 913        ("junit" ,java-junit)
 914        ("slf4j-simple" ,java-slf4j-simple)))
 915     (inputs
 916      `(("hdf4" ,hdf4)
 917        ("hdf5" ,hdf5)
 918        ("zlib" ,zlib)
 919        ("libjpeg" ,libjpeg)
 920        ("slf4j-api" ,java-slf4j-api)))
 921     (arguments
 922      `(#:configure-flags
 923        (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
 924              (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
 925                             (assoc-ref %build-inputs "jdk") "/lib" )
 926              (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
 927              (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
 928
 929        #:make-flags
 930        (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
 931              (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
 932              (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
 933              (string-append "JPEGLIB="
 934                             (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
 935              "LLEXT=so")
 936
 937        #:phases
 938        (modify-phases %standard-phases
 939          (add-before 'configure 'chdir-to-source
 940            (lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
 941          (add-before 'configure 'patch-build
 942            (lambda* (#:key inputs outputs #:allow-other-keys)
 943              (substitute* "configure"
 944                (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
 945                (("/bin/cat") (which "cat")))
 946              ;; Set classpath for compilation
 947              (substitute* '("hdf/hdf5lib/Makefile.in"
 948                             "hdf/hdf5lib/exceptions/Makefile.in"
 949                             "hdf/hdflib/Makefile.in")
 950                (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
 951                 (string-append (assoc-ref inputs "slf4j-api")
 952                                "/share/java/slf4j-api.jar")))
 953              ;; Replace outdated config.sub and config.guess:
 954              (with-directory-excursion "config"
 955                (for-each (lambda (file)
 956                            (install-file
 957                             (string-append (assoc-ref inputs "automake")
 958                                            "/share/automake-"
 959                                            ,(version-major+minor (package-version automake))
 960                                            "/" file) "."))
 961                          '("config.sub" "config.guess")))
 962
 963              ;; Fix embedded version number
 964              (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
 965                (substitute* "hdf/hdf5lib/H5.java"
 966                  (("1, 8, 19")
 967                   (string-join hdf5version ", "))))
 968
 969              (mkdir-p (string-append (assoc-ref outputs "out")))
 970              ;; Set classpath for tests
 971              (let* ((build-dir (getcwd))
 972                     (lib (string-append build-dir "/lib"))
 973                     (jhdf (string-append lib "/jhdf.jar"))
 974                     (jhdf5 (string-append lib "/jhdf5.jar"))
 975                     (testjars
 976                      (map (lambda (i)
 977                             (string-append (assoc-ref inputs i)
 978                                            "/share/java/" i ".jar"))
 979                           '("junit" "hamcrest-core" "slf4j-api" "slf4j-simple")))
 980                     (class-path
 981                      (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
 982
 983                (substitute* '("test/hdf5lib/Makefile.in"
 984                               "test/hdf5lib/junit.sh.in"
 985                               "examples/runExample.sh.in")
 986                  (("/usr/bin/test")
 987                   (string-append (assoc-ref inputs "coreutils")
 988                                  "/bin/test"))
 989                  (("/usr/bin/uname")
 990                   (string-append (assoc-ref inputs "coreutils")
 991                                  "/bin/uname"))
 992                  (("CLASSPATH=[^\n]*")
 993                   (string-append "CLASSPATH=" class-path)))
 994                (setenv "CLASSPATH" class-path))
 995              #t))
 996          (add-before 'check 'build-examples
 997            (lambda _
 998              (apply invoke `("javac"
 999                              ,@(find-files "examples" ".*\\.java"))))))
1000
1001        #:parallel-build? #f
1002
1003        #:parallel-tests? #f ))
1004     (home-page "https://support.hdfgroup.org/products/java")
1005     (synopsis "Java interface for the HDF4 and HDF5 libraries")
1006     (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
1007 the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
1008 implemented in C.")
1009
1010     ;; BSD-style license:
1011     (license (license:x11-style
1012               "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
1013 /current/src/unpacked/COPYING"))))
1014
1015 (define-public hdf-eos2
1016   (package
1017     (name "hdf-eos2")
1018     (version "19.1.0")
1019     (source
1020      (origin
1021        (method url-fetch)
1022        (uri "ftp://edhs1.gsfc.nasa.gov\
1023 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
1024        (sha256
1025         (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
1026        (patches (search-patches "hdf-eos2-remove-gctp.patch"
1027                                 "hdf-eos2-build-shared.patch"
1028                                 "hdf-eos2-fortrantests.patch"))))
1029     (build-system gnu-build-system)
1030     (native-inputs
1031      `(("gfortran" ,gfortran)))
1032     (inputs
1033      `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
1034        ("zlib" ,zlib)
1035        ("libjpeg" ,libjpeg)
1036        ("gctp" ,gctp)))
1037     (arguments
1038      `( #:configure-flags '("--enable-install-include" "--enable-shared"
1039                             "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
1040         #:parallel-tests? #f))
1041     (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
1042     (synopsis "HDF4-based data format for NASA's Earth Observing System")
1043     (description "HDF-EOS2 is a software library built on HDF4 which supports
1044 the construction of data structures used in NASA's Earth Observing
1045 System (Grid, Point and Swath).")
1046
1047     ;; Source files carry a permissive license header.
1048     (license (license:non-copyleft home-page))))
1049
1050 (define-public hdf-eos5
1051   (package
1052     (name "hdf-eos5")
1053     (version "1.15")
1054     (source (origin
1055               (method url-fetch)
1056               (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1057 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1058               (sha256
1059                (base32
1060                 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1061               (patches (search-patches "hdf-eos5-build-shared.patch"
1062                                        "hdf-eos5-remove-gctp.patch"
1063                                        "hdf-eos5-fix-szip.patch"
1064                                        "hdf-eos5-fortrantests.patch"))))
1065     (native-inputs
1066      `(("gfortran" ,gfortran)))
1067     (build-system gnu-build-system)
1068     (inputs
1069      `(("hdf5" ,hdf5)
1070        ("zlib" ,zlib)
1071        ("gctp" ,gctp)))
1072     (arguments
1073      `(#:configure-flags '("--enable-install-include" "--enable-shared"
1074                            "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1075        #:parallel-tests? #f))
1076     (synopsis "HDF5-based data format for NASA's Earth Observing System")
1077     (description
1078      "HDF-EOS5 is a software library built on HDF5 to support the construction
1079 of data structures used in NASA's Earth Observing System (Grid, Point and
1080 Swath).")
1081     (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1082
1083     ;; Source files carry a permissive license header.
1084     (license (license:non-copyleft home-page))))
1085
1086 (define-public hdf5-parallel-openmpi
1087   (package (inherit hdf5)
1088     (name "hdf5-parallel-openmpi")
1089     (inputs
1090      `(("mpi" ,openmpi)
1091        ,@(package-inputs hdf5)))
1092     (arguments
1093      (substitute-keyword-arguments (package-arguments hdf5)
1094        ((#:configure-flags flags)
1095         ``("--enable-parallel" ,@(delete "--enable-cxx" ,flags)))
1096        ((#:phases phases)
1097         `(modify-phases ,phases
1098            (add-after 'build 'mpi-setup
1099              ,%openmpi-setup)
1100            (add-before 'check 'patch-tests
1101              (lambda _
1102                ;; OpenMPI's mpirun will exit with non-zero status if it
1103                ;; detects an "abnormal termination", i.e. any process not
1104                ;; calling MPI_Finalize().  Since the test is explicitely
1105                ;; avoiding MPI_Finalize so as not to have at_exit and thus
1106                ;; H5C_flush_cache from being called, mpirun will always
1107                ;; complain, so turn this test off.
1108                (substitute* "testpar/Makefile"
1109                  (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1110                   (string-append front back "\n")))
1111                (substitute* "tools/h5diff/testph5diff.sh"
1112                  (("/bin/sh") (which "sh")))
1113                #t))))))
1114     (synopsis "Management suite for data with parallel IO support")))
1115
1116 (define-public h5check
1117   (package
1118     (name "h5check")
1119     (version "2.0.1")
1120     (source
1121      (origin
1122        (method url-fetch)
1123        (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
1124                            "h5check/src/h5check-" version ".tar.gz"))
1125        (sha256
1126         (base32
1127          "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1128     (build-system gnu-build-system)
1129     (inputs `(("hdf5" ,hdf5)))                 ;h5cc for tests
1130     (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1131     (synopsis "HDF5 format checker")
1132     (description "@code{h5check} is a validation tool for verifying that an
1133 HDF5 file is encoded according to the HDF File Format Specification.")
1134     (license (license:x11-style "file://COPYING"))))
1135
1136 (define-public itpp
1137   (package
1138     (name "itpp")
1139     (version "4.3.1")
1140     (source (origin
1141               (method url-fetch)
1142               (uri (string-append "mirror://sourceforge/itpp/itpp/"
1143                                   version "/itpp-"
1144                                   version ".tar.gz"))
1145        (sha256
1146         (base32
1147          "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1148     (build-system cmake-build-system)
1149     (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1150     (inputs `(("lapack" ,lapack)
1151               ("fftw" ,fftw)))
1152     ;; FIXME: Even though the fonts are available dvips complains:
1153     ;; "Font cmmi10 not found; characters will be left blank."
1154     (native-inputs
1155      `(("texlive" ,texlive-tiny)
1156        ("ghostscript" ,ghostscript)
1157        ("doxygen" ,doxygen)))
1158     (home-page "http://itpp.sourceforge.net")
1159     (synopsis "C++ library of maths, signal processing and communication classes")
1160     (description "IT++ is a C++ library of mathematical, signal processing and
1161 communication classes and functions.  Its main use is in simulation of
1162 communication systems and for performing research in the area of
1163 communications.  The kernel of the library consists of generic vector and
1164 matrix classes, and a set of accompanying routines.  Such a kernel makes IT++
1165 similar to MATLAB, GNU Octave or SciPy.")
1166     (license license:gpl3+)))
1167
1168 (define-public netcdf
1169   (package
1170     (name "netcdf")
1171     (version "4.4.1.1")
1172     (source
1173      (origin
1174        (method url-fetch)
1175        (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
1176                            "netcdf-" version ".tar.gz"))
1177        (sha256
1178         (base32
1179          "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
1180        (patches (search-patches "netcdf-date-time.patch"
1181                                 "netcdf-tst_h_par.patch"))))
1182     (build-system gnu-build-system)
1183     (native-inputs
1184      `(("m4" ,m4)
1185        ("doxygen" ,doxygen)
1186        ("graphviz" ,graphviz)))
1187     (inputs
1188      `(("hdf4" ,hdf4-alt)
1189        ("hdf5" ,hdf5)
1190        ("zlib" ,zlib)
1191        ("libjpeg" ,libjpeg)))
1192     (arguments
1193      `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
1194
1195        #:phases (modify-phases %standard-phases
1196          (add-before 'configure 'fix-source-date
1197            (lambda _
1198              ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1199              ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1200              ;; to '1st hour of the current day', and therefore makes the
1201              ;; package not reproducible.
1202              (substitute* "./configure"
1203                (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1204                 "date --date='@0'"))
1205              #t))
1206          (add-after 'configure 'patch-settings
1207            (lambda _
1208              ;; libnetcdf.settings contains the full filename of the compilers
1209              ;; used to build the library.  We truncate the hashes of those
1210              ;; filenames to avoid unnecessary references to the corresponding
1211              ;; store items.
1212              (substitute* "libnetcdf.settings"
1213                (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
1214                 (string-append prefix (string-take hash 10) "...")))
1215              #t)))
1216
1217        #:parallel-tests? #f))           ;various race conditions
1218     (home-page "http://www.unidata.ucar.edu/software/netcdf/")
1219     (synopsis "Library for scientific data")
1220     (description "NetCDF is an interface for scientific data access and a
1221 software library that provides an implementation of the interface.  The netCDF
1222 library defines a machine-independent format for representing scientific data.
1223 Together, the interface, library, and format support the creation, access, and
1224 sharing of scientific data.")
1225     (license (license:x11-style "file://COPYRIGHT"))))
1226
1227 (define-public netcdf-parallel-openmpi
1228   (package (inherit netcdf)
1229     (name "netcdf-parallel-openmpi")
1230     (inputs
1231      `(("mpi" ,openmpi)
1232        ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1233                         (package-inputs netcdf))))
1234     ;; TODO: Replace pkg-config references in nc-config with absolute references
1235     (arguments
1236      (substitute-keyword-arguments (package-arguments netcdf)
1237        ((#:configure-flags flags)
1238         `(cons* "CC=mpicc" "CXX=mpicxx"
1239                 "--enable-parallel-tests"
1240                 ;; Shared libraries not supported with parallel IO.
1241                 "--disable-shared" "--with-pic"
1242                 ,flags))))))
1243
1244 (define-public netcdf-fortran
1245   (package
1246     (name "netcdf-fortran")
1247     (version "4.4.4")
1248     (source (origin
1249               (method url-fetch)
1250               (uri (string-append
1251                     "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1252                     version ".tar.gz"))
1253               (sha256
1254                (base32
1255                 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
1256     (build-system gnu-build-system)
1257     (arguments
1258      `(#:parallel-tests? #f))
1259     (inputs
1260      `(("netcdf" ,netcdf)))
1261     (native-inputs
1262      `(("gfortran" ,gfortran)))
1263     (synopsis "Fortran interface for the netCDF library")
1264     (description (package-description netcdf))
1265     (home-page (package-home-page netcdf))
1266     (license (package-license netcdf))))
1267
1268 (define-public nlopt
1269   (package
1270     (name "nlopt")
1271     (version "2.4.2")
1272     (source (origin
1273               (method url-fetch)
1274               (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1275                                   version ".tar.gz"))
1276               (sha256
1277                (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1278     (build-system gnu-build-system)
1279     (arguments
1280      `(;; Shared libraries are not built by default.  They are required to
1281        ;; build the Guile, Octave, and Python bindings.
1282        #:configure-flags '("--enable-shared")
1283
1284        #:phases
1285        (modify-phases %standard-phases
1286          (add-before 'configure 'set-libnlopt-file-name
1287            (lambda* (#:key outputs #:allow-other-keys)
1288              ;; Make sure the Scheme module refers to the library by its
1289              ;; absolute file name (we cannot do that from a snippet
1290              ;; because the expansion of @libdir@ contains
1291              ;; ${exec_prefix}.)
1292              (let ((out (assoc-ref outputs "out")))
1293                (substitute* "swig/nlopt.scm.in"
1294                  (("libnlopt")
1295                   (string-append out "/lib/libnlopt")))
1296                #t))))))
1297     (inputs `(("guile" ,guile-2.0)))
1298     (native-inputs `(("pkg-config" ,pkg-config)))
1299     (home-page "http://ab-initio.mit.edu/wiki/")
1300     (synopsis "Library for nonlinear optimization")
1301     (description "NLopt is a library for nonlinear optimization, providing a
1302 common interface for a number of different free optimization routines available
1303 online as well as original implementations of various other algorithms.")
1304     (license license:lgpl2.1+)))
1305
1306 (define-public ipopt
1307   (package
1308     (name "ipopt")
1309     (version "3.12.12")
1310     (source (origin
1311               (method url-fetch)
1312               (uri (string-append
1313                     "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
1314                     version".tgz"))
1315               (sha256
1316                (base32
1317                 "07yn9rzdswjk8n246qq6ci9ssf2bcplkifcpsfz9j6cdxw9vgbkv"))
1318               (modules '((guix build utils)))
1319               (snippet
1320                ;; Make sure we don't use the bundled software.
1321                '(begin
1322                   (delete-file-recursively "ThirdParty")
1323                   #t))))
1324     (build-system gnu-build-system)
1325     (arguments
1326      '(#:phases (modify-phases %standard-phases
1327                   (add-after 'install 'add--L-flags-in-ipopt.pc
1328                     (lambda* (#:key inputs outputs #:allow-other-keys)
1329                       ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1330                       ;; move it to "Libs.private" where it belongs, and add a
1331                       ;; '-L' flag for LAPACK.
1332                       (let ((out    (assoc-ref outputs "out"))
1333                             (lapack (assoc-ref inputs "lapack")))
1334                         (substitute* (string-append out "/lib/pkgconfig/"
1335                                                     "ipopt.pc")
1336                           (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1337                            (string-append "Libs: " before " " after "\n"
1338                                           "Libs.private: " before
1339                                           "-L" lapack "/lib -llapack -lblas "
1340                                           after "\n")))
1341                         #t))))))
1342     (native-inputs
1343      `(("gfortran" ,gfortran)))
1344     (inputs
1345      ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
1346      `(("lapack" ,lapack)))                    ;for both libblas and liblapack
1347     (home-page "http://www.coin-or.org")
1348     (synopsis "Large-scale nonlinear optimizer")
1349     (description
1350      "The Interior Point Optimizer (IPOPT) is a software package for
1351 large-scale nonlinear optimization.  It provides C++, C, and Fortran
1352 interfaces.")
1353     (license license:epl1.0)))
1354
1355 (define-public clp
1356   (package
1357     (name "clp")
1358     (version "1.17.1")
1359     (source (origin
1360               (method url-fetch)
1361               (uri (string-append "https://www.coin-or.org/download/source/"
1362                                   "Clp/Clp-" version ".tgz"))
1363               (sha256
1364                (base32
1365                 "1wdg820g3iikf9344ijwsc8sy6c0m6im42bzzizm6rlmkvnmxhk9"))
1366               (modules '((guix build utils)))
1367               (snippet
1368                ;; Make sure we don't use the bundled software.
1369                '(begin
1370                   (delete-file-recursively "ThirdParty")
1371                   #t))))
1372     (build-system gnu-build-system)
1373     (native-inputs
1374      `(("gfortran" ,gfortran)
1375        ("pkg-config" ,pkg-config)))
1376     (inputs
1377      `(("openblas" ,openblas)))
1378     (home-page "https://www.coin-or.org")
1379     (synopsis "Linear programming solver")
1380     (description
1381      "CLP is a high quality linear programming solver.  Its main strengths are
1382 its dual and primal Simplex algorithms.  It also has a barrier algorithm for
1383 linear and quadratic objectives.  There are limited facilities for nonlinear
1384 and quadratic objectives using the Simplex algorithm.")
1385     (license license:epl1.0)))
1386
1387 (define-public ceres
1388   (package
1389     (name "ceres-solver")
1390     (version "1.14.0")
1391     (home-page "http://ceres-solver.org/")
1392     (source (origin
1393               (method url-fetch)
1394               (uri (string-append home-page "ceres-solver-"
1395                                   version ".tar.gz"))
1396               (sha256
1397                (base32
1398                 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
1399     (build-system cmake-build-system)
1400     (arguments
1401      ;; TODO: Build HTML user documentation and install separately.
1402      '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
1403                            "-DBUILD_SHARED_LIBS=ON")
1404
1405        #:phases (modify-phases %standard-phases
1406                   (add-before 'configure 'set-library-directory
1407                     (lambda _
1408                       ;; Install libraries to lib/, not lib64/.
1409                       (substitute* "internal/ceres/CMakeLists.txt"
1410                         (("set\\(LIB_SUFFIX \"64\"\\)")
1411                          "set(LIB_SUFFIX \"\")"))
1412                       #t)))))
1413     (native-inputs
1414      `(("pkg-config" ,pkg-config)))
1415     (propagated-inputs
1416      `(("glog" ,glog)))                           ;for #include <glog/glog.h>
1417     (inputs
1418      `(("eigen" ,eigen)
1419        ("blas" ,openblas)
1420        ("lapack" ,lapack)
1421        ("suitesparse" ,suitesparse)
1422        ("gflags" ,gflags)))
1423     (synopsis "C++ library for solving large optimization problems")
1424     (description
1425      "Ceres Solver is a C++ library for modeling and solving large,
1426 complicated optimization problems.  It is a feature rich, mature and
1427 performant library which has been used in production since 2010.  Ceres Solver
1428 can solve two kinds of problems:
1429 @enumerate
1430 @item non-linear least squares problems with bounds constraints;
1431 @item general unconstrained optimization problems.
1432 @end enumerate\n")
1433     (license license:bsd-3)))
1434
1435 ;; For a fully featured Octave, users are strongly recommended also to install
1436 ;; the following packages: less, ghostscript, gnuplot.
1437 (define-public octave-cli
1438   (package
1439     (name "octave-cli")
1440     (version "5.1.0")
1441     (source
1442      (origin
1443       (method url-fetch)
1444       (uri (string-append "mirror://gnu/octave/octave-"
1445                           version ".tar.lz"))
1446       (sha256
1447        (base32
1448         "11wwxpy2q1bhxs2v41bqn05i2sb0905cj1xil6mg8l4k2kka4cq6"))))
1449     (build-system gnu-build-system)
1450     (inputs
1451      `(("lapack" ,lapack)
1452        ("qhull" ,qhull)
1453        ("readline" ,readline)
1454        ("gl2ps" ,gl2ps)
1455        ("glpk" ,glpk)
1456        ("fftw" ,fftw)
1457        ("fftwf" ,fftwf)
1458        ("arpack" ,arpack-ng)
1459        ("pcre" ,pcre)
1460        ("fltk" ,fltk)
1461        ("fontconfig" ,fontconfig)
1462        ("freetype" ,freetype)
1463        ("hdf5" ,hdf5)
1464        ("libxft" ,libxft)
1465        ("mesa" ,mesa)
1466        ("glu" ,glu)
1467        ("zlib" ,zlib)
1468        ("curl" ,curl)
1469        ("texinfo" ,texinfo)
1470        ("graphicsmagick" ,graphicsmagick)
1471        ("suitesparse" ,suitesparse)
1472        ("libsndfile" ,libsndfile)
1473        ("portaudio" ,portaudio)
1474        ("alsa-lib" ,alsa-lib)))
1475     (native-inputs
1476      `(("lzip" ,lzip)
1477        ("gfortran" ,gfortran)
1478        ("pkg-config" ,pkg-config)
1479        ("perl" ,perl)
1480        ;; The following inputs are not actually used in the build process.
1481        ;; However, the ./configure gratuitously tests for their existence and
1482        ;; assumes that programs not present at build time are also not, and
1483        ;; can never be, available at run time!  If these inputs are therefore
1484        ;; not present, support for them will be built out.  However, Octave
1485        ;; will still run without them, albeit without the features they
1486        ;; provide.
1487        ("less" ,less)
1488        ("ghostscript" ,ghostscript)
1489        ("gnuplot" ,gnuplot)))
1490     ;; Octave code uses this variable to detect directories holding multiple CA
1491     ;; certificates to verify peers with.  This is required for the networking
1492     ;; functions that require encryption to work properly.
1493     (native-search-paths
1494      (list (search-path-specification
1495             (variable "CURLOPT_CAPATH")
1496             (files '("etc/ssl/certs")))))
1497     (arguments
1498      `(#:configure-flags
1499        (list (string-append "--with-shell="
1500                             (assoc-ref %build-inputs "bash")
1501                             "/bin/sh"))
1502        #:phases
1503        (modify-phases %standard-phases
1504          (add-after 'configure 'configure-makeinfo
1505            (lambda* (#:key inputs #:allow-other-keys)
1506              (substitute* "libinterp/corefcn/help.h"
1507                (("\"makeinfo\"")
1508                 (string-append
1509                  "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
1510              #t)))))
1511     (home-page "https://www.gnu.org/software/octave/")
1512     (synopsis "High-level language for numerical computation")
1513     (description "GNU Octave is a high-level interpreted language that is
1514 specialized for numerical computations.  It can be used for both linear and
1515 non-linear applications and it provides great support for visualizing results.
1516 Work may be performed both at the interactive command-line as well as via
1517 script files.")
1518     (license license:gpl3+)))
1519
1520 (define-public octave
1521   (package (inherit octave-cli)
1522     (name "octave")
1523     (source (origin
1524               (inherit (package-source octave-cli))))
1525     (inputs
1526      `(("qscintilla" ,qscintilla)
1527        ("qt" ,qtbase)
1528        ,@(package-inputs octave-cli)))
1529     (native-inputs
1530      `(("qttools" , qttools) ;for lrelease
1531        ("texlive" ,texlive) ;for texi2dvi
1532        ,@(package-native-inputs octave-cli)))
1533     (arguments
1534      (substitute-keyword-arguments (package-arguments octave-cli)
1535        ((#:phases phases)
1536         `(modify-phases ,phases
1537            (add-before 'configure 'patch-qscintilla-library-name
1538              (lambda* (#:key inputs #:allow-other-keys)
1539                ;; The QScintilla library that the Octave configure script tries
1540                ;; to link with should be named libqscintilla-qt5.so, but the
1541                ;; QScintilla input provides the shared library as
1542                ;; libqscintilla2_qt5.so.
1543                (substitute* "configure"
1544                  (("qscintilla2-qt5")
1545                   "qscintilla2_qt5"))
1546                #t))))))))
1547
1548 (define-public qtoctave
1549   (deprecated-package "qtoctave" octave))
1550
1551 (define-public opencascade-oce
1552   (package
1553     (name "opencascade-oce")
1554     (version "0.17.2")
1555     (source
1556       (origin
1557         (method git-fetch)
1558         (uri (git-reference
1559               (url "https://github.com/tpaviot/oce.git")
1560               (commit (string-append "OCE-" version))))
1561         (file-name (git-file-name name version))
1562         (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
1563         (sha256
1564           (base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69"))))
1565     (build-system cmake-build-system)
1566     (arguments
1567      '(#:configure-flags
1568         (list "-DOCE_TESTING:BOOL=ON"
1569               "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1570               "-DOCE_DRAW:BOOL=ON"
1571               (string-append "-DOCE_INSTALL_PREFIX:PATH="
1572                         (assoc-ref %outputs "out"))
1573               "-UCMAKE_INSTALL_RPATH")))
1574     (inputs
1575       `(("freetype" ,freetype)
1576         ("glu" ,glu)
1577         ("libxmu" ,libxmu)
1578         ("mesa" ,mesa)
1579         ("tcl" ,tcl)
1580         ("tk" ,tk)))
1581     (native-inputs
1582       `(("python" ,python-wrapper)))
1583     (home-page "https://github.com/tpaviot/oce")
1584     (synopsis "Libraries for 3D modeling and numerical simulation")
1585     (description
1586      "Open CASCADE is a set of libraries for the development of applications
1587 dealing with 3D CAD data or requiring industrial 3D capabilities.  It includes
1588 C++ class libraries providing services for 3D surface and solid modeling, CAD
1589 data exchange, and visualization.  It is used for development of specialized
1590 software dealing with 3D models in design (CAD), manufacturing (CAM),
1591 numerical simulation (CAE), measurement equipment (CMM), and quality
1592 control (CAQ) domains.
1593
1594 This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1595 patches, improvements, and experiments contributed by users over the official
1596 Open CASCADE library.")
1597     (license (list license:lgpl2.1; OCE libraries, with an exception for the
1598                                   ; use of header files; see
1599                                   ; OCCT_LGPL_EXCEPTION.txt
1600                    license:public-domain; files
1601                                   ; src/Standard/Standard_StdAllocator.hxx and
1602                                   ; src/NCollection/NCollection_StdAllocator.hxx
1603                    license:expat; file src/OpenGl/OpenGl_glext.h
1604                    license:bsd-3)))); test framework gtest
1605
1606 (define-public gmsh
1607   (package
1608     (name "gmsh")
1609     (version "2.16.0")
1610     (source
1611      (origin
1612       (method url-fetch)
1613       (uri (string-append "http://gmsh.info/src/gmsh-"
1614                           version "-source.tgz"))
1615       (sha256
1616        (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
1617       (modules '((guix build utils)))
1618       (snippet
1619        ;; Remove non-free METIS code
1620        '(begin
1621           (delete-file-recursively "contrib/Metis")
1622           #t))))
1623     (build-system cmake-build-system)
1624     (propagated-inputs
1625      `(("fltk" ,fltk)
1626        ("gfortran" ,gfortran)
1627        ("gmp" ,gmp)
1628        ("hdf5" ,hdf5)
1629        ("lapack" ,lapack)
1630        ("mesa" ,mesa)
1631        ("glu" ,glu)
1632        ("opencascade-oce" ,opencascade-oce)
1633        ("libx11" ,libx11)
1634        ("libxext" ,libxext)))
1635     (inputs
1636      `(("fontconfig" ,fontconfig)
1637        ("libxft" ,libxft)))
1638     (arguments
1639      `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1640                            "-DENABLE_BUILD_SHARED:BOOL=ON"
1641                            "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
1642     (home-page "http://www.geuz.org/gmsh/")
1643     (synopsis "3D finite element grid generator")
1644     (description "Gmsh is a 3D finite element grid generator with a built-in
1645 CAD engine and post-processor.  Its design goal is to provide a fast, light
1646 and user-friendly meshing tool with parametric input and advanced
1647 visualization capabilities.  Gmsh is built around four modules: geometry,
1648 mesh, solver and post-processing.  The specification of any input to these
1649 modules is done either interactively using the graphical user interface or in
1650 ASCII text files using Gmsh's own scripting language.")
1651     (license license:gpl2+)))
1652
1653 (define-public maxflow
1654   (package
1655     (name "maxflow")
1656     (version "3.04")
1657     (source (origin
1658               (method git-fetch)
1659               (uri (git-reference
1660                     (url "https://github.com/gerddie/maxflow.git")
1661                     (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
1662               (file-name (string-append name "-" version "-checkout"))
1663               (sha256
1664                (base32
1665                 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1666     (build-system cmake-build-system)
1667     (home-page "http://pub.ist.ac.at/~vnk/software.html")
1668     (synopsis "Library implementing Maxflow algorithm")
1669     (description "An implementation of the maxflow algorithm described in
1670 @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1671 Energy Minimization in Computer Vision.\n
1672 Yuri Boykov and Vladimir Kolmogorov.\n
1673 In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1674 September 2004}")
1675     (license license:gpl3+)))
1676
1677 (define-public petsc
1678   (package
1679     (name "petsc")
1680     (version "3.10.4")
1681     (source
1682      (origin
1683       (method url-fetch)
1684       ;; The *-lite-* tarball does not contain the *large* documentation
1685       (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1686                           "petsc-lite-" version ".tar.gz"))
1687       (sha256
1688        (base32 "0fk16944zh3473ra198kdkxdn08rq7b6ap838hxy1mh1i0hb488r"))))
1689     (outputs '("out"                    ; libraries and headers
1690                "examples"))             ; ~30MiB of examples
1691     (build-system gnu-build-system)
1692     (native-inputs
1693      `(("python" ,python-2)))
1694     (inputs
1695      `(("gfortran" ,gfortran)
1696        ("lapack" ,lapack)
1697        ("superlu" ,superlu)
1698        ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1699        ;; leaving out opengl, as configuration seems to only be for mac
1700        ))
1701     (arguments
1702      `(#:test-target "test"
1703        #:parallel-build? #f             ; build is parallel by default
1704        #:configure-flags
1705        `("--with-mpi=0"
1706          "--with-openmp=1"
1707          "--with-superlu=1")
1708        #:make-flags
1709        ;; Honor (parallel-job-count) for build.  Do not use --with-make-np,
1710        ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1711        (list (format #f "MAKE_NP=~a" (parallel-job-count)))
1712        #:phases
1713        (modify-phases %standard-phases
1714         (replace 'configure
1715           ;; PETSc's configure script is actually a python script, so we can't
1716           ;; run it with bash.
1717           (lambda* (#:key outputs (configure-flags '())
1718                           #:allow-other-keys)
1719             (let* ((prefix (assoc-ref outputs "out"))
1720                    (flags `(,(string-append "--prefix=" prefix)
1721                             ,@configure-flags)))
1722               (format #t "build directory: ~s~%" (getcwd))
1723               (format #t "configure flags: ~s~%" flags)
1724               (apply invoke "./configure" flags))))
1725         (add-after 'configure 'clean-local-references
1726           (lambda* (#:key outputs #:allow-other-keys)
1727             (let ((out (assoc-ref outputs "out")))
1728               (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
1729                 ;; Prevent build directory from leaking into compiled code
1730                 (((getcwd)) out)
1731                 ;; Scrub timestamp for reproducibility
1732                 ((".*Libraries compiled on.*") ""))
1733               (substitute* (find-files "." "petscvariables")
1734                 ;; Do not expose build machine characteristics, set to defaults.
1735                 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1736                 (("NPMAX = [:digit:]+") "NPMAX = 2"))
1737               #t)))
1738         (add-after 'install 'clean-install
1739           ;; Try to keep installed files from leaking build directory names.
1740           (lambda* (#:key inputs outputs #:allow-other-keys)
1741             (let ((out (assoc-ref outputs "out")))
1742               (substitute* (map (lambda (file)
1743                                   (string-append out "/lib/petsc/conf/" file))
1744                                 '("petscvariables"))
1745                 (((getcwd)) out))
1746               ;; Make compiler references point to the store
1747               (substitute* (string-append out "/lib/petsc/conf/petscvariables")
1748                 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1749                  (string-append "= " (which compiler))))
1750               ;; PETSc installs some build logs, which aren't necessary.
1751               (for-each (lambda (file)
1752                           (let ((f (string-append out "/lib/petsc/conf/" file)))
1753                             (when (file-exists? f)
1754                               (delete-file f))))
1755                         '("configure.log" "make.log" "gmake.log"
1756                           "test.log" "error.log" "RDict.db"
1757                           "PETScBuildInternal.cmake"
1758                           ;; Once installed, should uninstall with Guix
1759                           "uninstall.py"))
1760               #t)))
1761         (add-after 'install 'move-examples
1762           (lambda* (#:key outputs #:allow-other-keys)
1763             (let* ((out (assoc-ref outputs "out"))
1764                    (examples (assoc-ref outputs "examples"))
1765                    (exdir (string-append out "/share/petsc/examples"))
1766                    (exdir' (string-append examples "/share/petsc/examples")))
1767               (copy-recursively exdir exdir')
1768               (delete-file-recursively exdir)
1769               #t))))))
1770     (home-page "http://www.mcs.anl.gov/petsc")
1771     (synopsis "Library to solve PDEs")
1772     (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1773 data structures and routines for the scalable (parallel) solution of
1774 scientific applications modeled by partial differential equations.")
1775     (license (license:non-copyleft
1776               "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1777
1778 (define-public petsc-complex
1779   (package (inherit petsc)
1780     (name "petsc-complex")
1781     (arguments
1782      (substitute-keyword-arguments (package-arguments petsc)
1783        ((#:configure-flags cf)
1784         `(cons "--with-scalar-type=complex" ,cf))))
1785     (synopsis "Library to solve PDEs (with complex scalars)")))
1786
1787 (define-public petsc-openmpi
1788   (package (inherit petsc)
1789     (name "petsc-openmpi")
1790     (inputs
1791      `(("hdf5" ,hdf5-parallel-openmpi)
1792        ("hypre" ,hypre-openmpi)
1793        ("metis" ,metis)
1794        ("mumps" ,mumps-openmpi)
1795        ("openmpi" ,openmpi)
1796        ("scalapack" ,scalapack)
1797        ("scotch" ,pt-scotch32)
1798        ,@(package-inputs petsc)))
1799     (arguments
1800      (substitute-keyword-arguments (package-arguments petsc)
1801        ((#:configure-flags cf)
1802         ``("--with-hypre=1"
1803            "--with-mpiexec=mpirun"
1804            "--with-metis=1"
1805            "--with-mumps=1"
1806            "--with-scalapack=1"
1807            "--with-ptscotch=1"
1808            ,(string-append "--with-mpi-dir="
1809                            (assoc-ref %build-inputs "openmpi"))
1810            ,(string-append "--with-hdf5-include="
1811                            (assoc-ref %build-inputs "hdf5") "/include")
1812            ,(string-append "--with-hdf5-lib="
1813                            (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
1814            ,@(delete "--with-mpi=0" ,cf)))
1815        ((#:phases phases)
1816         `(modify-phases ,phases
1817            (add-before 'configure 'mpi-setup
1818              ,%openmpi-setup)))))
1819     (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
1820
1821 (define-public petsc-complex-openmpi
1822   (package (inherit petsc-complex)
1823     (name "petsc-complex-openmpi")
1824     (inputs
1825      `(("openmpi" ,openmpi)
1826        ,@(package-inputs petsc-complex)))
1827     (arguments
1828      (substitute-keyword-arguments (package-arguments petsc-complex)
1829        ((#:configure-flags cf)
1830         ``("--with-mpiexec=mpirun"
1831            ,(string-append "--with-mpi-dir="
1832                            (assoc-ref %build-inputs "openmpi"))
1833            ,@(delete "--with-mpi=0" ,cf)))))
1834     (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
1835
1836 (define-public python-petsc4py
1837   (package
1838     (name "python-petsc4py")
1839     (version "3.10.1")
1840     (source
1841       (origin
1842         (method url-fetch)
1843         (uri (pypi-uri "petsc4py" version))
1844         (sha256
1845           (base32
1846             "094hcnran0r2z1wlvmjswsz3ski1m9kqrl5l0ax8jjhnk55x0flh"))))
1847     (build-system python-build-system)
1848     (arguments
1849      `(#:phases
1850        (modify-phases %standard-phases
1851          (add-before 'build 'pre-build
1852            (lambda _
1853              ;; Define path to PETSc installation.
1854              (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
1855              #t))
1856          (add-before 'check 'mpi-setup
1857            ,%openmpi-setup))))
1858     (inputs
1859      `(("petsc" ,petsc-openmpi)
1860        ("python-numpy" ,python-numpy)))
1861     (home-page "https://bitbucket.org/petsc/petsc4py/")
1862     (synopsis "Python bindings for PETSc")
1863     (description "PETSc, the Portable, Extensible Toolkit for
1864 Scientific Computation, is a suite of data structures and routines for
1865 the scalable (parallel) solution of scientific applications modeled by
1866 partial differential equations.  It employs the MPI standard for all
1867 message-passing communication.  @code{petsc4py} provides Python
1868 bindings to almost all functions of PETSc.")
1869     (license license:bsd-3)))
1870
1871 (define-public python-kiwisolver
1872   (package
1873     (name "python-kiwisolver")
1874     (version "1.0.1")
1875     (source (origin
1876               (method url-fetch)
1877               (uri (pypi-uri "kiwisolver" version))
1878               (sha256
1879                (base32
1880                 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
1881     (build-system python-build-system)
1882     (home-page "https://github.com/nucleic/kiwi")
1883     (synopsis "Fast implementation of the Cassowary constraint solver")
1884     (description
1885      "Kiwi is an efficient C++ implementation of the Cassowary constraint
1886 solving algorithm.  Kiwi has been designed from the ground up to be
1887 lightweight and fast.  Kiwi ranges from 10x to 500x faster than the original
1888 Cassowary solver with typical use cases gaining a 40x improvement.  Memory
1889 savings are consistently > 5x.")
1890     (license license:bsd-3)))
1891
1892 (define-public python2-kiwisolver
1893   (package-with-python2 python-kiwisolver))
1894
1895 (define-public slepc
1896   (package
1897     (name "slepc")
1898     (version "3.10.1")
1899     (source
1900      (origin
1901        (method url-fetch)
1902        (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
1903                            version ".tar.gz"))
1904        (sha256
1905         (base32
1906          "188j1a133q91h8pivpnzwcf78kz8dvz2nzf6ndnjygdbqb48fizn"))))
1907     (build-system gnu-build-system)
1908     (native-inputs
1909      `(("python" ,python-2)))
1910     (inputs
1911      `(("arpack" ,arpack-ng)
1912        ("gfortran" ,gfortran)))
1913     (propagated-inputs
1914      `(("petsc" ,petsc)))
1915     (arguments
1916      `(#:parallel-build? #f             ;build is parallel by default
1917        #:configure-flags
1918        `(,(string-append "--with-arpack-dir="
1919                          (assoc-ref %build-inputs "arpack") "/lib"))
1920        #:make-flags                     ;honor (parallel-job-count)
1921        `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
1922        #:phases
1923        (modify-phases %standard-phases
1924          (replace 'configure
1925           ;; configure is a python script, so we can't run it with bash.
1926           (lambda* (#:key inputs outputs (configure-flags '())
1927                     #:allow-other-keys)
1928             (let* ((prefix (assoc-ref outputs "out"))
1929                    (flags `(,(string-append "--prefix=" prefix)
1930                             ,@configure-flags)))
1931               (format #t "build directory: ~s~%" (getcwd))
1932               (format #t "configure flags: ~s~%" flags)
1933               (setenv "SLEPC_DIR" (getcwd))
1934               (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
1935               (apply invoke "./configure" flags))))
1936          (add-after 'install 'delete-doc
1937           ;; TODO: SLEPc installs HTML documentation alongside headers in
1938           ;; $out/include.  We'd like to move them to share/doc, but delete
1939           ;; them for now, as they are incomplete and installing the complete
1940           ;; documentation is difficult.
1941           (lambda* (#:key outputs #:allow-other-keys)
1942             (let* ((out (assoc-ref outputs "out")))
1943               (for-each delete-file (find-files out "\\.html$"))
1944               #t)))
1945          (add-after 'install 'clean-install
1946           ;; Clean up unnecessary build logs from installation.
1947           (lambda* (#:key outputs #:allow-other-keys)
1948             (let ((out (assoc-ref outputs "out")))
1949               (for-each (lambda (file)
1950                           (let ((f (string-append out "/lib/slepc/conf/" file)))
1951                             (when (file-exists? f)
1952                               (delete-file f))))
1953                         '("configure.log" "make.log" "gmake.log"
1954                           "test.log" "error.log" "RDict.db"
1955                           "uninstall.py"))
1956               #t))))))
1957     (home-page "http://slepc.upv.es")
1958     (synopsis "Scalable library for eigenproblems")
1959     (description "SLEPc is a software library for the solution of large sparse
1960 eigenproblems on parallel computers.  It can be used for the solution of
1961 linear eigenvalue problems formulated in either standard or generalized form,
1962 as well as other related problems such as the singular value decomposition.
1963 The emphasis of the software is on methods and techniques appropriate for
1964 problems in which the associated matrices are sparse, for example, those
1965 arising after the discretization of partial differential equations.")
1966     (license license:bsd-2)))
1967
1968 (define-public slepc-complex
1969   (package (inherit slepc)
1970     (name "slepc-complex")
1971     (propagated-inputs
1972      `(("petsc" ,petsc-complex)
1973        ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1974     (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1975
1976 (define-public slepc-openmpi
1977   (package (inherit slepc)
1978     (name "slepc-openmpi")
1979     (arguments
1980      (substitute-keyword-arguments (package-arguments slepc)
1981        ((#:phases phases '%standard-phases)
1982         `(modify-phases ,phases
1983            (add-before 'check 'mpi-setup
1984              ,%openmpi-setup)))))
1985     (inputs
1986      `(("mpi" ,openmpi)
1987        ("arpack" ,arpack-ng-openmpi)
1988        ,@(alist-delete "arpack" (package-inputs slepc))))
1989     (propagated-inputs
1990      `(("petsc" ,petsc-openmpi)
1991        ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1992     (synopsis "Scalable library for eigenproblems (with MPI support)")))
1993
1994 (define-public slepc-complex-openmpi
1995   (package (inherit slepc-openmpi)
1996     (name "slepc-complex-openmpi")
1997     (propagated-inputs
1998      `(("petsc" ,petsc-complex-openmpi)
1999        ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
2000     (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
2001
2002 (define-public python-slepc4py
2003   (package
2004     (name "python-slepc4py")
2005     (version "3.10.0")
2006     (source
2007       (origin
2008         (method url-fetch)
2009         (uri (pypi-uri "slepc4py" version))
2010         (sha256
2011           (base32
2012             "0x049dyc8frgh79fvvavf4vlbqp4mgm61nsaivzdav4316vvlv1j"))))
2013     (build-system python-build-system)
2014     (arguments
2015      `(#:phases
2016        (modify-phases %standard-phases
2017          (add-before 'build 'pre-build
2018            (lambda _
2019              ;; Define path to PETSc installation.
2020              (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
2021              ;; Define path to SLEPc installation.
2022              (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
2023              #t))
2024          (add-before 'check 'mpi-setup
2025            ,%openmpi-setup))))
2026     (inputs
2027      `(("python-numpy" ,python-numpy)
2028        ("python-petsc4py" ,python-petsc4py)
2029        ("slepc" ,slepc-openmpi)))
2030     (home-page "https://bitbucket.org/slepc/slepc4py/")
2031     (synopsis "Python bindings for SLEPc")
2032     (description "SLEPc, the Scalable Library for Eigenvalue Problem
2033 Computations, is based on PETSc, the Portable, Extensible Toolkit for
2034 Scientific Computation.  It employs the MPI standard for all
2035 message-passing communication.  @code{slepc4py} provides Python
2036 bindings to almost all functions of SLEPc.")
2037     (license license:bsd-3)))
2038
2039 (define-public mumps
2040   (package
2041     (name "mumps")
2042     (version "5.1.2")
2043     (source
2044      (origin
2045        (method url-fetch)
2046        (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
2047                            version ".tar.gz"))
2048        (sha256
2049         (base32
2050          "1s9asin08zqzmh08257sdghhivvy9vjif7c53fhaxaax2kd5qd7b"))
2051        (patches (search-patches "mumps-build-parallelism.patch"))))
2052     (build-system gnu-build-system)
2053     (inputs
2054      `(("fortran" ,gfortran)
2055        ;; These are required for linking against mumps, but we let the user
2056        ;; declare the dependency.
2057        ("blas" ,openblas)
2058        ("metis" ,metis)
2059        ("scotch" ,scotch)))
2060     (arguments
2061      `(#:modules ((ice-9 match)
2062                   (ice-9 popen)
2063                   (srfi srfi-1)
2064                   ,@%gnu-build-system-modules)
2065        #:phases
2066        (modify-phases %standard-phases
2067          (replace 'configure
2068           (lambda* (#:key inputs #:allow-other-keys)
2069             (call-with-output-file "Makefile.inc"
2070               (lambda (port)
2071                 (format port "
2072 PLAT         =
2073 LIBEXT       = .a
2074 OUTC         = -o
2075 OUTF         = -o
2076 RM           = rm -f~:[
2077 CC           = gcc
2078 FC           = gfortran
2079 FL           = gfortran
2080 INCSEQ       = -I$(topdir)/libseq
2081 LIBSEQ       = -L$(topdir)/libseq -lmpiseq
2082 LIBSEQNEEDED = libseqneeded~;
2083 CC           = mpicc
2084 FC           = mpifort
2085 FL           = mpifort~]
2086 AR           = ar vr # rules require trailing space, ugh...
2087 RANLIB       = ranlib
2088 LIBBLAS      = -L~a -lopenblas~@[
2089 SCALAP       = -L~a -lscalapack~]
2090 LIBOTHERS    = -pthread
2091 CDEFS        = -DAdd_
2092 PIC          = -fPIC
2093 OPTF         = -O2 -DALLOW_NON_INIT $(PIC)
2094 OPTL         = -O2 $(PIC)
2095 OPTC         = -O2 $(PIC)
2096 INCS         = $(INCSEQ)
2097 LIBS         = $(SCALAP) $(LIBSEQ)
2098 LPORDDIR     = $(topdir)/PORD/lib
2099 IPORD        = -I$(topdir)/PORD/include
2100 LPORD        = -L$(LPORDDIR) -lpord
2101 ORDERINGSF   = -Dpord~@[
2102 METISDIR     = ~a
2103 IMETIS       = -I$(METISDIR)/include
2104 LMETIS       = -L$(METISDIR)/lib -lmetis
2105 ORDERINGSF  += -Dmetis~]~@[~:{
2106 SCOTCHDIR    = ~a
2107 ISCOTCH      = -I$(SCOTCHDIR)/include
2108 LSCOTCH      = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
2109 ORDERINGSF  += ~a~}~]
2110 ORDERINGSC   = $(ORDERINGSF)
2111 LORDERINGS   = $(LPORD) $(LMETIS) $(LSCOTCH)
2112 IORDERINGSF  = $(ISCOTCH)
2113 IORDERINGSC  = $(IPORD) $(IMETIS) $(ISCOTCH)"
2114                         (assoc-ref inputs "mpi")
2115                         (assoc-ref inputs "blas")
2116                         (assoc-ref inputs "scalapack")
2117                         (assoc-ref inputs "metis")
2118                         (match (list (assoc-ref inputs "pt-scotch")
2119                                      (assoc-ref inputs "scotch"))
2120                           ((#f #f)
2121                            #f)
2122                           ((#f scotch)
2123                            `((,scotch "" "-Dscotch")))
2124                           ((ptscotch _)
2125                            `((,ptscotch
2126                               "-lptesmumps -lptscotch -lptscotcherr "
2127                               "-Dptscotch")))))))))
2128          (replace 'build
2129           ;; By default only the d-precision library is built.  Make with "all"
2130           ;; target so that all precision libraries and examples are built.
2131           (lambda _
2132             (invoke "make" "all"
2133                     (format #f "-j~a" (parallel-job-count)))))
2134          (replace 'check
2135           ;; Run the simple test drivers, which read test input from stdin:
2136           ;; from the "real" input for the single- and double-precision
2137           ;; testers, and from the "cmplx" input for complex-precision
2138           ;; testers.  The EXEC-PREFIX key is used by the mumps-openmpi
2139           ;; package to prefix execution with "mpirun".
2140           (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
2141             (with-directory-excursion "examples"
2142               (every
2143                (lambda (prec type)
2144                  (let ((tester (apply open-pipe*
2145                                       `(,OPEN_WRITE
2146                                         ,@exec-prefix
2147                                         ,(string-append "./" prec
2148                                                         "simpletest"))))
2149                        (input  (open-input-file
2150                                 (string-append "input_simpletest_" type))))
2151                    (begin
2152                      (dump-port input tester)
2153                      (close-port input)
2154                      (zero? (close-pipe tester)))))
2155                '("s" "d" "c" "z")
2156                '("real" "real" "cmplx" "cmplx")))))
2157          (replace 'install
2158            (lambda* (#:key outputs #:allow-other-keys)
2159              (let* ((out (assoc-ref outputs "out"))
2160                     (libdir (string-append out "/lib")))
2161                (copy-recursively "lib" libdir)
2162                (copy-recursively "include" (string-append out "/include"))
2163                (when (file-exists? "libseq/libmpiseq.a")
2164                  (install-file "libseq/libmpiseq.a" libdir))
2165                #t))))))
2166     (home-page "http://mumps.enseeiht.fr")
2167     (synopsis "Multifrontal sparse direct solver")
2168     (description
2169      "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
2170 sparse system of linear equations A x = b using Guassian elimination.")
2171     (license license:cecill-c)))
2172
2173 (define-public mumps-metis
2174   (package (inherit mumps)
2175     (name "mumps-metis")
2176     (inputs
2177      (alist-delete "scotch" (package-inputs mumps)))))
2178
2179 (define-public mumps-openmpi
2180   (package (inherit mumps)
2181     (name "mumps-openmpi")
2182     (inputs
2183      `(("mpi" ,openmpi)
2184        ("scalapack" ,scalapack)
2185        ("pt-scotch" ,pt-scotch)
2186        ,@(alist-delete "scotch" (package-inputs mumps))))
2187     (arguments
2188      (substitute-keyword-arguments (package-arguments mumps)
2189        ((#:phases phases)
2190         `(modify-phases ,phases
2191            (add-before 'check 'mpi-setup
2192              ,%openmpi-setup)
2193            (replace 'check
2194              (lambda _
2195                ((assoc-ref ,phases 'check)
2196                 #:exec-prefix '("mpirun" "-n" "2"))))))))
2197     (synopsis "Multifrontal sparse direct solver (with MPI)")))
2198
2199 (define-public mumps-metis-openmpi
2200   (package (inherit mumps-openmpi)
2201     (name "mumps-metis-openmpi")
2202     (inputs
2203      (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
2204
2205 (define-public r-quadprog
2206   (package
2207     (name "r-quadprog")
2208     (version "1.5-5")
2209     (source
2210      (origin
2211        (method url-fetch)
2212        (uri (cran-uri "quadprog" version))
2213        (sha256
2214         (base32
2215          "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
2216     (build-system r-build-system)
2217     (native-inputs
2218      `(("gfortran" ,gfortran)))
2219     (home-page "https://cran.r-project.org/web/packages/quadprog")
2220     (synopsis "Functions to solve quadratic programming problems")
2221     (description
2222      "This package contains routines and documentation for solving quadratic
2223 programming problems.")
2224     (license license:gpl3+)))
2225
2226 (define-public r-pracma
2227   (package
2228     (name "r-pracma")
2229     (version "2.2.5")
2230     (source (origin
2231       (method url-fetch)
2232       (uri (cran-uri "pracma" version))
2233       (sha256
2234         (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g"))))
2235     (build-system r-build-system)
2236     (home-page "https://cran.r-project.org/web/packages/pracma/")
2237     (synopsis "Practical numerical math functions")
2238     (description "This package provides functions for numerical analysis and
2239 linear algebra, numerical optimization, differential equations, plus some
2240 special functions.  It uses Matlab function names where appropriate to simplify
2241 porting.")
2242     (license license:gpl3+)))
2243
2244 (define-public ruby-asciimath
2245   (package
2246     (name "ruby-asciimath")
2247     (version "1.0.4")
2248     (source
2249      (origin
2250        (method url-fetch)
2251        (uri (rubygems-uri "asciimath" version))
2252        (sha256
2253         (base32
2254          "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc"))))
2255     (build-system ruby-build-system)
2256     (arguments
2257      '(#:phases
2258        (modify-phases %standard-phases
2259          ;; Apply this patch
2260          ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948
2261          (add-after 'unpack 'patch-remove-spurious-backslashes
2262            (lambda _
2263              (substitute* "spec/parser_spec.rb"
2264                (("\\\\\"")
2265                 "\""))
2266              #t)))))
2267     (native-inputs
2268      `(("bundler" ,bundler)
2269        ("ruby-rspec" ,ruby-rspec)))
2270     (synopsis "AsciiMath parsing and conversion library")
2271     (description
2272      "A pure Ruby AsciiMath parsing and conversion library.  AsciiMath is an
2273 easy-to-write markup language for mathematics.")
2274     (home-page "https://github.com/asciidoctor/asciimath")
2275     (license license:expat)))
2276
2277 (define-public superlu
2278   (package
2279     (name "superlu")
2280     (version "5.2.1")
2281     (source
2282      (origin
2283        (method url-fetch)
2284        (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2285                            "superlu_" version ".tar.gz"))
2286        (sha256
2287         (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
2288        (modules '((guix build utils)))
2289        (snippet
2290         ;; Replace the non-free implementation of MC64 with a stub adapted
2291         ;; from Debian
2292         '(begin
2293            (use-modules (ice-9 regex)
2294                         (ice-9 rdelim))
2295            (call-with-output-file "SRC/mc64ad.c"
2296              (lambda (port)
2297                (display "
2298 #include <stdio.h>
2299 #include <stdlib.h>
2300 void mc64id_(int *a) {
2301   fprintf (stderr, \"SuperLU: non-free MC64 not available.  Aborting.\\n\");
2302   abort ();
2303 }
2304 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2305               int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2306   fprintf (stderr, \"SuperLU: non-free MC64 not available.  Aborting.\\n\");
2307   abort ();
2308 }\n" port)))
2309            ;; Remove the corresponding license verbiage.  MC64 license follows
2310            ;; a "------" line separator.
2311            (with-atomic-file-replacement "License.txt"
2312              (let ((rx (make-regexp "-{8}")))
2313                (lambda (in out)
2314                  (let loop ()
2315                    (let ((line (read-line in 'concat)))
2316                     (unless (regexp-exec rx line)
2317                       (display line out)
2318                       (loop))))
2319                  #t)))))))
2320     (build-system cmake-build-system)
2321     (native-inputs
2322      `(("tcsh" ,tcsh)))
2323     (inputs
2324      `(("blas" ,openblas)
2325        ("gfortran" ,gfortran)))
2326     (arguments
2327      `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
2328                            "-DTPL_BLAS_LIBRARIES=openblas"
2329                            "-DBUILD_SHARED_LIBS:BOOL=YES")))
2330     (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
2331     (synopsis "Supernodal direct solver for sparse linear systems")
2332     (description
2333      "SuperLU is a general purpose library for the direct solution of large,
2334 sparse, nonsymmetric systems of linear equations on high performance machines.
2335 The library is written in C and is callable from either C or Fortran.  The
2336 library routines perform an LU decomposition with partial pivoting and
2337 triangular system solves through forward and back substitution.  The library
2338 also provides threshold-based ILU factorization preconditioners.")
2339     (license (list license:bsd-3
2340                    license:gpl2+        ;EXAMPLE/*fgmr.c
2341                    (license:fsf-free "file://SRC/colamd.h")))))
2342
2343 (define-public superlu-dist
2344   (package
2345     (name "superlu-dist")
2346     (version "6.1.0")
2347     (source
2348      (origin
2349        (method url-fetch)
2350        (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
2351                            "superlu_dist_" version ".tar.gz"))
2352        (sha256
2353         (base32 "0pqgcgh1yxhfzs99fas3mggajzd5wca3nbyp878rziy74gfk03dl"))
2354        (modules '((guix build utils)))
2355        (snippet
2356         ;; Replace the non-free implementation of MC64 with a stub
2357         '(begin
2358            (call-with-output-file "SRC/mc64ad_dist.c"
2359              (lambda (port)
2360                (display "
2361 #include <stdio.h>
2362 #include <stdlib.h>
2363 void mc64id_dist(int *a) {
2364   fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available.  Aborting.\\n\");
2365   abort ();
2366 }
2367 void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
2368               int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
2369   fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available.  Aborting.\\n\");
2370   abort ();
2371 }\n" port)))
2372            (substitute* "SRC/util.c"    ;adjust default algorithm
2373              (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
2374               ;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
2375               ;; general (i.e. non-square) processor-grid support.
2376               "RowPerm = NOROWPERM;"))
2377            #t))
2378        (patches (search-patches "superlu-dist-scotchmetis.patch"
2379                                 "superlu-dist-awpm-grid.patch"
2380                                 "superlu-dist-fix-mpi-deprecations.patch"))))
2381     (build-system cmake-build-system)
2382     (native-inputs
2383      `(("tcsh" ,tcsh)))
2384     (inputs
2385      `(("gfortran" ,gfortran)
2386        ("blas" ,openblas)
2387        ("lapack" ,lapack)
2388        ("combblas" ,combinatorial-blas)))
2389     (propagated-inputs
2390      `(("mpi" ,openmpi)                 ;headers include MPI heades
2391        ("parmetis" ,pt-scotch32 "metis")
2392        ("pt-scotch" ,pt-scotch32)))
2393     (arguments
2394      `(#:parallel-tests? #f             ;tests use MPI and OpenMP
2395        #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
2396                                "-DTPL_ENABLE_COMBBLASLIB=YES"
2397                                "-DTPL_BLAS_LIBRARIES=-lopenblas"
2398                                "-DTPL_LAPACK_LIBRARIES=-llapack"
2399                                (string-append "-DTPL_PARMETIS_LIBRARIES="
2400                                               (string-join
2401                                                '("ptscotchparmetis" "ptscotch" "ptscotcherr"
2402                                                  "scotchmetis" "scotch" "scotcherr")
2403                                                ";"))
2404                                (string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
2405                                               (assoc-ref %build-inputs "parmetis")
2406                                               "/include")
2407                                "-DTPL_ENABLE_COMBBLASLIB=ON"
2408                                (string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
2409                                               (assoc-ref %build-inputs "combblas")
2410                                               "/include/CombBLAS;"
2411                                               (assoc-ref %build-inputs "combblas")
2412                                               "/include/BipartiteMatchings")
2413                                "-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
2414        #:phases
2415        (modify-phases %standard-phases
2416          (add-before 'configure 'set-c++-standard
2417            (lambda _
2418              (substitute* "CMakeLists.txt"
2419                ;; AWPM headers require C++14
2420                (("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
2421          (add-before 'check 'mpi-setup
2422            ,%openmpi-setup)
2423          (add-before 'check 'omp-setup
2424            (lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
2425     (home-page (package-home-page superlu))
2426     (synopsis "Parallel supernodal direct solver")
2427     (description
2428      "SuperLU_DIST is a parallel extension to the serial SuperLU library.
2429 It is targeted for distributed memory parallel machines.  SuperLU_DIST is
2430 implemented in ANSI C, and MPI for communications.")
2431     (license license:bsd-3)))
2432
2433 (define-public scotch
2434   (package
2435     (name "scotch")
2436     (version "6.0.6")
2437     (source
2438      (origin
2439       (method url-fetch)
2440       (uri (string-append "https://gforge.inria.fr/frs/download.php/"
2441                           "latestfile/298/scotch_" version ".tar.gz"))
2442       (sha256
2443        (base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8"))
2444       (patches (search-patches "scotch-build-parallelism.patch"
2445                                "scotch-integer-declarations.patch"))))
2446     (build-system gnu-build-system)
2447     (inputs
2448      `(("zlib" ,zlib)
2449        ("flex" ,flex)
2450        ("bison" ,bison)))
2451     (outputs '("out" "metis"))
2452     (arguments
2453      `(#:make-flags (list (string-append "prefix=" %output))
2454        #:phases
2455        (modify-phases %standard-phases
2456          (add-after
2457           'unpack 'chdir-to-src
2458           (lambda _ (chdir "src") #t))
2459          (replace
2460           'configure
2461           (lambda _
2462             (call-with-output-file "Makefile.inc"
2463               (lambda (port)
2464                 (format port "
2465 EXE =
2466 LIB = .a
2467 OBJ = .o
2468 MAKE = make
2469 AR = ar
2470 ARFLAGS = -ruv
2471 CAT = cat
2472 CCS = gcc
2473 CCP = mpicc
2474 CCD = gcc
2475 CPPFLAGS =~{ -D~a~}
2476 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2477 LDFLAGS = -lz -lm -lrt -lpthread
2478 CP = cp
2479 LEX = flex -Pscotchyy -olex.yy.c
2480 LN = ln
2481 MKDIR = mkdir
2482 MV = mv
2483 RANLIB = ranlib
2484 YACC = bison -pscotchyy -y -b y
2485 "
2486                         '("COMMON_FILE_COMPRESS_GZ"
2487                           "COMMON_PTHREAD"
2488                           "COMMON_RANDOM_FIXED_SEED"
2489                           "INTSIZE64"             ;use 'int64_t'
2490                           ;; Prevents symbolc clashes with libesmumps
2491                           "SCOTCH_RENAME"
2492                           ;; XXX: Causes invalid frees in superlu-dist tests
2493                           ;; "SCOTCH_PTHREAD"
2494                           ;; "SCOTCH_PTHREAD_NUMBER=2"
2495                           "restrict=__restrict"))))
2496             #t))
2497          (add-after 'build 'build-esmumps
2498           (lambda _
2499             (invoke "make"
2500                     (format #f "-j~a" (parallel-job-count))
2501                     "esmumps")))
2502          (add-before 'install 'make-install-dirs
2503            (lambda* (#:key outputs #:allow-other-keys)
2504              (mkdir (assoc-ref outputs "out"))))
2505          (add-after 'install 'install-metis
2506            (lambda* (#:key outputs #:allow-other-keys)
2507              (let ((out (assoc-ref outputs "metis")))
2508                (mkdir out)
2509                ;; metis files are not installed with 'make install'
2510                (for-each (lambda (f)
2511                            (install-file f (string-append out "/include")))
2512                          (find-files "../include/" ".*metis\\.h"))
2513                (for-each (lambda (f)
2514                            (install-file f (string-append out "/lib")))
2515                          (find-files "../lib/" ".*metis\\..*"))
2516                #t))))))
2517     (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
2518     (synopsis "Programs and libraries for graph algorithms")
2519     (description "SCOTCH is a set of programs and libraries which implement
2520 the static mapping and sparse matrix reordering algorithms developed within
2521 the SCOTCH project.  Its purpose is to apply graph theory, with a divide and
2522 conquer approach, to scientific computing problems such as graph and mesh
2523 partitioning, static mapping, and sparse matrix ordering, in application
2524 domains ranging from structural mechanics to operating systems or
2525 bio-chemistry.")
2526     ;; See LICENSE_en.txt
2527     (license license:cecill-c)))
2528
2529 (define-public scotch32
2530   ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
2531   ;; some applications.
2532   (package (inherit scotch)
2533     (name "scotch32")
2534     (arguments
2535      (substitute-keyword-arguments (package-arguments scotch)
2536        ((#:phases scotch-phases)
2537         `(modify-phases ,scotch-phases
2538           (replace
2539            'configure
2540            (lambda _
2541              (call-with-output-file "Makefile.inc"
2542                (lambda (port)
2543                  (format port "
2544 EXE =
2545 LIB = .a
2546 OBJ = .o
2547 MAKE = make
2548 AR = ar
2549 ARFLAGS = -ruv
2550 CAT = cat
2551 CCS = gcc
2552 CCP = mpicc
2553 CCD = gcc
2554 CPPFLAGS =~{ -D~a~}
2555 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
2556 LDFLAGS = -lz -lm -lrt -lpthread
2557 CP = cp
2558 LEX = flex -Pscotchyy -olex.yy.c
2559 LN = ln
2560 MKDIR = mkdir
2561 MV = mv
2562 RANLIB = ranlib
2563 YACC = bison -pscotchyy -y -b y
2564 "
2565                         '("COMMON_FILE_COMPRESS_GZ"
2566                           "COMMON_PTHREAD"
2567                           "COMMON_RANDOM_FIXED_SEED"
2568                           "INTSIZE32"   ;use 32-bit integers.  See INSTALL.txt
2569                           ;; Prevents symbolc clashes with libesmumps
2570                           "SCOTCH_RENAME"
2571                           ;; XXX: Causes invalid frees in superlu-dist tests
2572                           ;; "SCOTCH_PTHREAD"
2573                           ;; "SCOTCH_PTHREAD_NUMBER=2"
2574                           "restrict=__restrict"))))))))))
2575     (synopsis
2576      "Programs and libraries for graph algorithms (32-bit integers)")))
2577
2578 (define-public pt-scotch
2579   (package (inherit scotch)
2580     (name "pt-scotch")
2581     (propagated-inputs
2582      `(("openmpi" ,openmpi)))           ;Headers include MPI headers
2583     (arguments
2584      (substitute-keyword-arguments (package-arguments scotch)
2585        ((#:phases scotch-phases)
2586         `(modify-phases ,scotch-phases
2587            (replace
2588             'build
2589             (lambda _
2590               (invoke "make" (format #f "-j~a" (parallel-job-count))
2591                       "ptscotch" "ptesmumps")
2592
2593               ;; Install the serial metis compatibility library
2594               (invoke "make" "-C" "libscotchmetis" "install")))
2595            (add-before 'check 'mpi-setup
2596              ,%openmpi-setup)
2597            (replace 'check
2598              (lambda _
2599                (invoke "make" "ptcheck")))))))
2600     (synopsis "Programs and libraries for graph algorithms (with MPI)")))
2601
2602 (define-public pt-scotch32
2603   (package (inherit scotch32)
2604     (name "pt-scotch32")
2605     (propagated-inputs
2606      `(("openmpi" ,openmpi)))                     ;headers include MPI headers
2607     (arguments
2608      (substitute-keyword-arguments (package-arguments scotch32)
2609        ((#:phases scotch32-phases)
2610         `(modify-phases ,scotch32-phases
2611            (replace 'build
2612              (lambda _
2613                (invoke "make" (format #f "-j~a" (parallel-job-count))
2614                        "ptscotch" "ptesmumps")
2615                ;; Install the serial metis compatibility library
2616                (invoke "make" "-C" "libscotchmetis" "install")))
2617            (add-before 'check 'mpi-setup
2618              ,%openmpi-setup)
2619            (replace 'check
2620              (lambda _
2621                (invoke "make" "ptcheck")))))))
2622     (synopsis
2623      "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
2624
2625 (define-public metis
2626   (package
2627     (name "metis")
2628     (version "5.1.0")
2629     (source
2630      (origin
2631        (method url-fetch)
2632        (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
2633                            "metis-" version ".tar.gz"))
2634        (sha256
2635         (base32
2636          "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
2637     (build-system cmake-build-system)
2638     (inputs
2639      `(("blas" ,openblas)))
2640     (arguments
2641      `(#:tests? #f                      ;no tests
2642        #:configure-flags `("-DSHARED=ON"
2643                            ,(string-append "-DGKLIB_PATH=" (getcwd)
2644                                            "/metis-" ,version "/GKlib"))))
2645     (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
2646     (synopsis "Graph partitioning and fill-reducing matrix ordering library")
2647     (description
2648      "METIS is a set of serial programs for partitioning graphs, partitioning
2649 finite element meshes, and producing fill-reducing orderings for sparse
2650 matrices.  The algorithms implemented in METIS are based on the multilevel
2651 recursive-bisection, multilevel k-way, and multi-constraint partitioning
2652 schemes.")
2653     (license license:asl2.0)))          ;As of version 5.0.3
2654
2655 (define-public p4est
2656   (package
2657     (name "p4est")
2658     (version "2.0")
2659     (source
2660      (origin
2661        (method url-fetch)
2662        (uri (string-append "http://p4est.github.io/release/p4est-"
2663                            version ".tar.gz"))
2664        (sha256
2665         (base32
2666          "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
2667     (build-system gnu-build-system)
2668     (inputs
2669      `(("fortran" ,gfortran)
2670        ("blas" ,openblas)
2671        ("lapack" ,lapack)
2672        ("zlib" ,zlib)))
2673     (arguments
2674      `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2675                                            (assoc-ref %build-inputs "blas")
2676                                            " -lopenblas")
2677                            ,(string-append "LAPACK_LIBS=-L"
2678                                            (assoc-ref %build-inputs "lapack")
2679                                            " -llapack"))
2680        #:phases (modify-phases %standard-phases
2681                   (add-before 'check 'mpi-setup
2682                     ,%openmpi-setup))))
2683     (home-page "http://www.p4est.org")
2684     (synopsis "Adaptive mesh refinement on forests of octrees")
2685     (description
2686      "The p4est software library enables the dynamic management of a
2687 collection of adaptive octrees, conveniently called a forest of octrees.
2688 p4est is designed to work in parallel and scales to hundreds of thousands of
2689 processor cores.")
2690     (license license:gpl2+)))
2691
2692 (define-public p4est-openmpi
2693   (package (inherit p4est)
2694     (name "p4est-openmpi")
2695     (inputs
2696      `(("mpi" ,openmpi)
2697        ,@(package-inputs p4est)))
2698     (arguments
2699      (substitute-keyword-arguments (package-arguments p4est)
2700        ((#:configure-flags cf)
2701         ``("--enable-mpi" ,@,cf))))
2702     (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2703
2704 (define-public gsegrafix
2705   (package
2706     (name "gsegrafix")
2707     (version "1.0.6")
2708     (source
2709      (origin
2710       (method url-fetch)
2711       (uri (string-append "mirror://gnu/" name "/" name "-"
2712                           version ".tar.gz"))
2713       (sha256
2714        (base32
2715         "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2716     (build-system gnu-build-system)
2717     (arguments
2718      `(#:configure-flags '("LDFLAGS=-lm")))
2719     (inputs
2720      `(("libgnomecanvas" ,libgnomecanvas)
2721        ("libbonoboui" ,libbonoboui)
2722        ("libgnomeui" ,libgnomeui)
2723        ("libgnomeprintui" ,libgnomeprintui)
2724        ("popt" ,popt)))
2725     (native-inputs
2726      `(("pkg-config" ,pkg-config)))
2727     (home-page "https://www.gnu.org/software/gsegrafix/")
2728     (synopsis "GNOME application to create scientific and engineering plots")
2729     (description  "GSEGrafix is an application which produces high-quality graphical
2730 plots for science and engineering.  Plots are specified via simple ASCII
2731 parameter files and data files and are presented in an anti-aliased GNOME
2732 canvas.  The program supports rectangular two-dimensional plots, histograms,
2733 polar-axis plots and three-dimensional plots.  Plots can be printed or saved
2734 to BMP, JPEG or PNG image formats.")
2735     (license license:gpl3+)))
2736
2737 (define-public maxima
2738   (package
2739     (name "maxima")
2740     (version "5.42.2")
2741     (source
2742      (origin
2743        (method url-fetch)
2744        (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2745                            version "-source/" name "-" version ".tar.gz"))
2746        (sha256
2747         (base32
2748          "0kdncy6137sg3rradirxzj10mkcvafxd892zlclwhr9sa7b12zhn"))
2749        (patches (search-patches "maxima-defsystem-mkdir.patch"))))
2750     (build-system gnu-build-system)
2751     (inputs
2752      `(("gcl" ,gcl)
2753        ("gnuplot" ,gnuplot)                       ;for plots
2754        ("sed" ,sed)
2755        ("tk" ,tk)))                               ;Tcl/Tk is used by 'xmaxima'
2756     (native-inputs
2757      `(("texinfo" ,texinfo)
2758        ("perl" ,perl)
2759        ("python" ,python)))
2760     (arguments
2761      `(#:configure-flags
2762        (list "--enable-gcl"
2763              (string-append "--with-posix-shell="
2764                             (assoc-ref %build-inputs "bash")
2765                             "/bin/sh")
2766              (string-append "--with-wish="
2767                             (assoc-ref %build-inputs "tk")
2768                             "/bin/wish"
2769                             (let ((v ,(package-version tk)))
2770                               (string-take v (string-index-right v #\.)))))
2771        ;; By default Maxima attempts to write temporary files to
2772        ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2773        ;; Work around that.
2774        #:make-flags (list "TMPDIR=/tmp")
2775        #:phases
2776        (modify-phases %standard-phases
2777          (add-after 'unpack 'patch-paths
2778            (lambda* (#:key inputs #:allow-other-keys)
2779              (let* ((sed (string-append (assoc-ref inputs "sed") "/bin/sed"))
2780                     (coreutils (assoc-ref inputs "coreutils"))
2781                     (dirname (string-append coreutils "/bin/dirname"))
2782                     (head (string-append coreutils "/bin/head")))
2783                (substitute* "src/maxima.in"
2784                  (("sed ") (string-append sed " "))
2785                  (("dirname") dirname)
2786                  (("head") head))
2787                #t)))
2788          (add-before 'check 'pre-check
2789            (lambda _
2790              (chmod "src/maxima" #o555)
2791              #t))
2792          (replace 'check
2793            (lambda _
2794              ;; This is derived from the testing code in the "debian/rules" file
2795              ;; of Debian's Maxima package.
2796              ;; If Maxima can successfully run this, the binary to be installed
2797              ;; should be fine.
2798              (zero?
2799               (system
2800                (string-append "./maxima-local "
2801                               "--lisp=gcl "
2802                               "--batch-string=\"run_testsuite();\" "
2803                               "| grep -q \"No unexpected errors found\"")))))
2804          ;; Make sure the doc and emacs files are found in the
2805          ;; standard location.  Also configure maxima to find gnuplot
2806          ;; without having it on the PATH.
2807          (add-after 'install 'post-install
2808            (lambda* (#:key outputs inputs #:allow-other-keys)
2809              (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2810                     (out (assoc-ref outputs "out"))
2811                     (datadir (string-append out "/share/maxima/" ,version))
2812                     (binutils (string-append (assoc-ref inputs "binutils")
2813                                              "/bin")))
2814                (with-directory-excursion out
2815                  (mkdir-p "share/emacs")
2816                  (mkdir-p "share/doc")
2817                  (symlink
2818                   (string-append datadir "/emacs/")
2819                   (string-append out "/share/emacs/site-lisp"))
2820                  (symlink
2821                   (string-append datadir "/doc/")
2822                   (string-append out "/share/doc/maxima"))
2823                  (with-atomic-file-replacement
2824                   (string-append datadir "/share/maxima-init.lisp")
2825                   (lambda (in out)
2826                     (format out "~a ~s~a~%"
2827                             "(setf $gnuplot_command "
2828                             (string-append gnuplot "/bin/gnuplot") ")")
2829                     (dump-port in out))))
2830                ;; Ensure that Maxima will have access to the GNU binutils
2831                ;; components at runtime.
2832                (wrap-program (string-append out "/bin/maxima")
2833                  `("PATH" prefix (,binutils))))
2834              #t)))))
2835     (home-page "http://maxima.sourceforge.net")
2836     (synopsis "Numeric and symbolic expression manipulation")
2837     (description "Maxima is a system for the manipulation of symbolic and
2838 numerical expressions.  It yields high precision numeric results by using
2839 exact fractions, arbitrary precision integers, and variable precision floating
2840 point numbers.")
2841     ;; Some files are lgpl2.1+. Some are gpl2+.  Some explicitly state gpl1+.
2842     ;; Others simply say "GNU General Public License" without stating a
2843     ;; version (which implicitly means gpl1+).
2844     ;; At least one file (src/maxima.asd) says "version 2."
2845     ;; GPLv2 only is therefore the smallest subset.
2846     (license license:gpl2)))
2847
2848 (define-public wxmaxima
2849   (package
2850     (name "wxmaxima")
2851     (version "19.03.1")
2852     (source
2853      (origin
2854        (method git-fetch)
2855        (uri (git-reference
2856              (url "https://github.com/wxMaxima-developers/wxmaxima.git")
2857              (commit (string-append "Version-" version))))
2858        (file-name (git-file-name name version))
2859        (sha256
2860         (base32
2861          "1qkf4jg86xnn3wk3782ffmfz12axb92dkjagcz3ffzw2wi1rclml"))))
2862     (build-system cmake-build-system)
2863     (native-inputs
2864      `(("gettext" ,gettext-minimal)))
2865     (inputs
2866      `(("wxwidgets" ,wxwidgets)
2867        ("maxima" ,maxima)
2868        ;; Runtime support.
2869        ("adwaita-icon-theme" ,adwaita-icon-theme)
2870        ("gtk+" ,gtk+)
2871        ("shared-mime-info" ,shared-mime-info)))
2872     (arguments
2873      `(#:tests? #f ; no check target
2874        #:phases
2875        (modify-phases %standard-phases
2876          (add-after 'install 'wrap-program
2877            (lambda* (#:key inputs outputs #:allow-other-keys)
2878              (wrap-program (string-append (assoc-ref outputs "out")
2879                                           "/bin/wxmaxima")
2880                `("PATH" ":" prefix
2881                  (,(string-append (assoc-ref inputs "maxima")
2882                                   "/bin")))
2883                ;; For GtkFileChooserDialog.
2884                `("GSETTINGS_SCHEMA_DIR" =
2885                  (,(string-append (assoc-ref inputs "gtk+")
2886                                   "/share/glib-2.0/schemas")))
2887                `("XDG_DATA_DIRS" ":" prefix
2888                  (;; Needed by gdk-pixbuf to know supported icon formats.
2889                   ,(string-append
2890                     (assoc-ref inputs "shared-mime-info") "/share")
2891                   ;; The default icon theme of GTK+.
2892                   ,(string-append
2893                     (assoc-ref inputs "adwaita-icon-theme") "/share"))))
2894              #t)))))
2895     (home-page "https://andrejv.github.io/wxmaxima/")
2896     (synopsis "Graphical user interface for the Maxima computer algebra system")
2897     (description
2898      "wxMaxima is a graphical user interface for the Maxima computer algebra
2899 system.  It eases the use of Maxima by making most of its commands available
2900 through a menu system and by providing input dialogs for commands that require
2901 more than one argument.  It also implements its own display engine that
2902 outputs mathematical symbols directly instead of depicting them with ASCII
2903 characters.
2904
2905 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
2906 text and mathematical calculations to create documents, exporting of input and
2907 output to TeX, and a browser for Maxima's manual including command index and
2908 full text searching.")
2909     (license license:gpl2+)))
2910
2911 (define-public armadillo
2912   (package
2913     (name "armadillo")
2914     (version "9.100.5")
2915     (source (origin
2916               (method url-fetch)
2917               (uri (string-append "mirror://sourceforge/arma/armadillo-"
2918                                   version ".tar.xz"))
2919               (sha256
2920                (base32
2921                 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
2922     (build-system cmake-build-system)
2923     (arguments `(#:tests? #f))          ; no test target
2924     (inputs
2925      `(("openblas" ,openblas)
2926        ("lapack" ,lapack)
2927        ("arpack" ,arpack-ng)))
2928     (home-page "http://arma.sourceforge.net/")
2929     (synopsis "C++ linear algebra library")
2930     (description
2931      "Armadillo is a C++ linear algebra library, aiming towards a good balance
2932 between speed and ease of use.  It is useful for algorithm development
2933 directly in C++, or quick conversion of research code into production
2934 environments.  It can be used for machine learning, pattern recognition,
2935 signal processing, bioinformatics, statistics, econometrics, etc.  The library
2936 provides efficient classes for vectors, matrices and cubes, as well as 150+
2937 associated functions (eg. contiguous and non-contiguous submatrix views).")
2938     (license license:asl2.0)))
2939
2940 (define-public muparser
2941   ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2942   ;; different hash. In order to make `guix package --upgrade` work correctly,
2943   ;; we set a Guix packaging revision.
2944   ;; When the next version of muparser is released, we can remove
2945   ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2946   (let ((upstream-version "2.2.5")
2947         (revision "2"))
2948     (package
2949       (name "muparser")
2950       (version (string-append upstream-version "-" revision))
2951       (source
2952        (origin
2953          (method git-fetch)
2954          (uri (git-reference
2955                (url "https://github.com/beltoforion/muparser.git")
2956                (commit (string-append "v" upstream-version))))
2957          (file-name (git-file-name name version))
2958          (sha256
2959           (base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24"))))
2960       (build-system gnu-build-system)
2961       (arguments
2962        `(#:configure-flags '("--enable-samples=no")
2963          #:tests? #f)) ;no "check" target
2964       (home-page "http://muparser.beltoforion.de/")
2965       (synopsis "Fast parser library for mathematical expressions")
2966       (description
2967        "muParser is an extensible high performance math parser library.  It is
2968 based on transforming an expression into a bytecode and precalculating constant
2969 parts of it.")
2970       (license license:expat))))
2971
2972 (define-public openblas
2973   (package
2974     (name "openblas")
2975     (version "0.3.4")
2976     (source
2977      (origin
2978        (method url-fetch)
2979        (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
2980                            version "%20version.tar.gz"))
2981        (file-name (string-append name "-" version ".tar.gz"))
2982        (sha256
2983         (base32
2984          "1s56lgilyyw86dzmj3jkci9zsg24n60wq4d0zri1hrxlxb6ihimj"))))
2985     (build-system gnu-build-system)
2986     (arguments
2987      `(#:test-target "test"
2988        ;; DYNAMIC_ARCH is only supported on x86.  When it is disabled and no
2989        ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2990        ;; we need to disable substitutions.
2991        #:substitutable?
2992         ,(let ((system (or (%current-target-system) (%current-system))))
2993            (or (string-prefix? "x86_64" system)
2994                (string-prefix? "i686" system)
2995                (string-prefix? "mips" system)
2996                (string-prefix? "aarch64" system)))
2997        #:make-flags
2998        (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
2999              "SHELL=bash"
3000              ;; Build the library for all supported CPUs.  This allows
3001              ;; switching CPU targets at runtime with the environment variable
3002              ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
3003              ;; Unfortunately, this is not supported on non-x86 architectures,
3004              ;; where it leads to failed builds.
3005              ,@(let ((system (or (%current-target-system) (%current-system))))
3006                  (cond
3007                   ((or (string-prefix? "x86_64" system)
3008                        (string-prefix? "i686" system))
3009                    '("DYNAMIC_ARCH=1"))
3010                   ;; On MIPS we force the "SICORTEX" TARGET, as for the other
3011                   ;; two available MIPS targets special extended instructions
3012                   ;; for Loongson cores are used.
3013                   ((string-prefix? "mips" system)
3014                    '("TARGET=SICORTEX"))
3015                   ;; On aarch64 force the generic 'armv8-a' target
3016                   ((string-prefix? "aarch64" system)
3017                    '("TARGET=ARMV8"))
3018                   (else '()))))
3019        ;; no configure script
3020        #:phases
3021        (modify-phases %standard-phases
3022          (delete 'configure)
3023          (add-before 'build 'set-extralib
3024            (lambda* (#:key inputs #:allow-other-keys)
3025              ;; Get libgfortran found when building in utest.
3026              (setenv "FEXTRALIB"
3027                      (string-append "-L" (assoc-ref inputs "fortran-lib")
3028                                     "/lib"))
3029              #t)))))
3030     (inputs
3031      `(("fortran-lib" ,gfortran "lib")))
3032     (native-inputs
3033      `(("cunit" ,cunit)
3034        ("fortran" ,gfortran)
3035        ("perl" ,perl)))
3036     (home-page "http://www.openblas.net/")
3037     (synopsis "Optimized BLAS library based on GotoBLAS")
3038     (description
3039      "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
3040     (license license:bsd-3)))
3041
3042 (define-public openblas-ilp64
3043   (package (inherit openblas)
3044     (name "openblas-ilp64")
3045     (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
3046     (arguments
3047      (substitute-keyword-arguments (package-arguments openblas)
3048        ((#:make-flags flags '())
3049         `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
3050                  ,flags))))
3051     (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
3052     (license license:bsd-3)))
3053
3054 (define* (make-blis implementation #:optional substitutable?)
3055   "Return a BLIS package with the given IMPLEMENTATION (see config/ in the
3056 source tree for a list of implementations.)
3057
3058 SUBSTITUTABLE? determines whether the package is made available as a
3059 substitute.
3060
3061 Currently the specialization must be selected at configure-time, but work is
3062 underway to allow BLIS to select the right optimized kernels at run time:
3063 <https://github.com/flame/blis/issues/129>."
3064   (package
3065     (name (if (string=? implementation "reference")
3066               "blis"
3067               (string-append "blis-" implementation)))
3068     (version "0.2.2")
3069     (home-page "https://github.com/flame/blis")
3070     (source (origin
3071               (method git-fetch)
3072               (uri (git-reference (url home-page) (commit version)))
3073               (sha256
3074                (base32
3075                 "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh"))
3076               (file-name (git-file-name "blis" version))))
3077     (build-system gnu-build-system)
3078     (arguments
3079      `(#:test-target "test"
3080
3081        #:substitutable? ,substitutable?
3082
3083        #:phases (modify-phases %standard-phases
3084                   (replace 'configure
3085                     (lambda* (#:key outputs #:allow-other-keys)
3086                       ;; This is a home-made 'configure' script.
3087                       (let ((out (assoc-ref outputs "out")))
3088                         (zero? (system* "./configure" "-p" out
3089                                         "-d" "opt"
3090                                         "--disable-static"
3091                                         "--enable-shared"
3092                                         "--enable-threading=openmp"
3093
3094                                         ,implementation)))))
3095                   (add-before 'check 'show-test-output
3096                     (lambda _
3097                       ;; By default "make check" is silent.  Make it verbose.
3098                       (system "tail -F output.testsuite &")
3099                       #t)))))
3100     (synopsis "High-performance basic linear algebra (BLAS) routines")
3101     (description
3102      "BLIS is a portable software framework for instantiating high-performance
3103 BLAS-like dense linear algebra libraries.  The framework was designed to
3104 isolate essential kernels of computation that, when optimized, immediately
3105 enable optimized implementations of most of its commonly used and
3106 computationally intensive operations.  While BLIS exports a new BLAS-like API,
3107 it also includes a BLAS compatibility layer which gives application developers
3108 access to BLIS implementations via traditional BLAS routine calls.")
3109     (license license:bsd-3)))
3110
3111 (define-public blis
3112   ;; This is the "reference" implementation, which is the non-optimized but
3113   ;; portable variant (no assembly).
3114   (make-blis "reference" #t))
3115
3116 (define ignorance blis)
3117
3118 (define-syntax-rule (blis/x86_64 processor)
3119   "Expand to a package specialized for PROCESSOR."
3120   (package
3121     (inherit (make-blis processor))
3122     (supported-systems '("x86_64-linux"))))
3123
3124 (define-public blis-sandybridge
3125   ;; BLIS specialized for Sandy Bridge processors (launched 2011):
3126   ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>.
3127   (blis/x86_64 "sandybridge"))
3128
3129 (define-public blis-haswell
3130   ;; BLIS specialized for Haswell processors (launched 2013):
3131   ;; <http://ark.intel.com/products/codename/42174/Haswell>.
3132   (blis/x86_64 "haswell"))
3133
3134 (define-public blis-knl
3135   ;; BLIS specialized for Knights Landing processor (launched 2016):
3136   ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>.
3137   (blis/x86_64 "knl"))
3138
3139
3140 (define-public openlibm
3141   (package
3142     (name "openlibm")
3143     (version "0.6.0")
3144     (source
3145      (origin
3146        (method git-fetch)
3147        (uri (git-reference
3148              (url "https://github.com/JuliaLang/openlibm.git")
3149              (commit (string-append "v" version))))
3150        (file-name (git-file-name name version))
3151        (sha256
3152         (base32 "08wfchmmr5200fvmn1kwq9byc1fhsq46hn0y5k8scdl74771c7gh"))))
3153     (build-system gnu-build-system)
3154     (arguments
3155      `(#:make-flags
3156        (list (string-append "prefix=" (assoc-ref %outputs "out")))
3157        #:phases
3158        ;; no configure script
3159        (modify-phases %standard-phases (delete 'configure))
3160        #:tests? #f)) ;the tests are part of the default target
3161     (home-page "http://openlibm.org/")
3162     (synopsis "Portable C mathematical library (libm)")
3163     (description
3164      "OpenLibm is an effort to have a high quality, portable, standalone C
3165 mathematical library (libm).  It can be used standalone in applications and
3166 programming language implementations.  The project was born out of a need to
3167 have a good libm for the Julia programming language that worked consistently
3168 across compilers and operating systems, and in 32-bit and 64-bit
3169 environments.")
3170     ;; Each architecture has its own make target, and there is none for mips.
3171     (supported-systems (delete "mips64el-linux" %supported-systems))
3172     ;; See LICENSE.md for details.
3173     (license (list license:expat
3174                    license:isc
3175                    license:bsd-2
3176                    license:public-domain
3177                    license:lgpl2.1+))))
3178
3179 (define-public openspecfun
3180   (package
3181     (name "openspecfun")
3182     (version "0.5.3")
3183     (source
3184      (origin
3185        (method git-fetch)
3186        (uri (git-reference
3187              (url "https://github.com/JuliaLang/openspecfun.git")
3188              (commit (string-append "v" version))))
3189        (file-name (git-file-name name version))
3190        (sha256
3191         (base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh"))))
3192     (build-system gnu-build-system)
3193     (arguments
3194      '(#:tests? #f                      ; no "check" target
3195        #:make-flags
3196        (list (string-append "prefix=" (assoc-ref %outputs "out")))
3197        #:phases
3198        (modify-phases %standard-phases
3199          (delete 'configure))))         ; no configure script
3200     (inputs
3201      `(("fortran" ,gfortran)))
3202     (home-page "https://github.com/JuliaLang/openspecfun")
3203     (synopsis "Collection of special mathematical functions")
3204     (description
3205      "Openspecfun provides AMOS and Faddeeva.  AMOS (from Netlib) is a
3206 portable package for Bessel Functions of a Complex Argument and Nonnegative
3207 Order; it contains subroutines for computing Bessel functions and Airy
3208 functions.  Faddeeva allows computing the various error functions of arbitrary
3209 complex arguments (Faddeeva function, error function, complementary error
3210 function, scaled complementary error function, imaginary error function, and
3211 Dawson function); given these, one can also easily compute Voigt functions,
3212 Fresnel integrals, and similar related functions as well.")
3213     ;; Faddeeva is released under the Expat license; AMOS is included as
3214     ;; public domain software.
3215     (license (list license:expat license:public-domain))))
3216
3217 (define-public suitesparse
3218   (package
3219     (name "suitesparse")
3220     (version "4.5.5")
3221     (source
3222      (origin
3223        (method url-fetch)
3224        (uri (string-append
3225              "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
3226              version ".tar.gz"))
3227        (sha256
3228         (base32
3229          "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
3230        (modules '((guix build utils)))
3231        (snippet
3232         ;; Remove bundled metis source
3233         '(begin
3234            (delete-file-recursively "metis-5.1.0")
3235            #t))))
3236     (build-system gnu-build-system)
3237     (arguments
3238      '(#:tests? #f  ;no "check" target
3239        #:make-flags
3240        (list "CC=gcc"
3241              "BLAS=-lblas"
3242              "TBB=-ltbb"
3243              "MY_METIS_LIB=-lmetis"
3244              (string-append "INSTALL_LIB="
3245                             (assoc-ref %outputs "out") "/lib")
3246              (string-append "INSTALL_INCLUDE="
3247                             (assoc-ref %outputs "out") "/include")
3248              "library")
3249        #:phases
3250        (modify-phases %standard-phases
3251          (delete 'configure))))         ;no configure script
3252     (inputs
3253      `(("tbb" ,tbb)
3254        ("lapack" ,lapack)
3255        ("metis" ,metis)))
3256     (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
3257     (synopsis "Suite of sparse matrix software")
3258     (description
3259      "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
3260 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
3261 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
3262 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
3263 CXSparse, a concise sparse Cholesky factorization package; and many other
3264 packages.")
3265     ;; LGPLv2.1+:
3266     ;;   AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
3267     ;; GPLv2+:
3268     ;;  GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
3269     (license (list license:gpl2+ license:lgpl2.1+))))
3270
3271 (define-public atlas
3272   (package
3273     (name "atlas")
3274     (version "3.10.3")
3275     (source (origin
3276               (method url-fetch)
3277               (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
3278                                   version "/atlas" version ".tar.bz2"))
3279               (sha256
3280                (base32
3281                 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
3282     (build-system gnu-build-system)
3283     (home-page "http://math-atlas.sourceforge.net/")
3284     (inputs `(("gfortran" ,gfortran)
3285               ("lapack-tar" ,(package-source lapack))))
3286     (outputs '("out" "doc"))
3287     ;; For the moment we drop support for MIPS at it fails to compile. See
3288     ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
3289     (supported-systems (delete "mips64el-linux" %supported-systems))
3290     (arguments
3291      `(#:parallel-build? #f
3292        #:parallel-tests? #f
3293
3294        ;; ATLAS tunes itself for the machine it is built on, as explained at
3295        ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
3296        ;; For this reason, we want users to build it locally instead of using
3297        ;; substitutes.
3298        #:substitutable? #f
3299
3300        #:modules ((srfi srfi-26)
3301                   (srfi srfi-1)
3302                   (guix build gnu-build-system)
3303                   (guix build utils))
3304        #:configure-flags
3305        `(;; Generate position independent code suitable for dynamic libraries
3306          ;; and use WALL timer to get more accurate timing.
3307          "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
3308          ;; Set word width.
3309          "-b"
3310          ,,(if (string-match "64" (%current-system))
3311                "64"
3312                "32")
3313          ;; Disable parallel build as it gives errors: atlas_pthread.h is
3314          ;; needed to compile C files before it is generated.
3315          "-Ss" "pmake" "make -j 1"
3316          ;; Probe is failing for MIPS.  We therefore define the system
3317          ;; architecture explicitly by setting (-A) MACHINETYPE = 49
3318          ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
3319          ,,@(if (string-prefix? "mips" (%current-system))
3320               (list "-A" "49" "-V" "1")
3321               (list))
3322          ;; Generate shared libraries.
3323          "--shared"
3324          ;; Build a full LAPACK library.
3325          ,(string-append "--with-netlib-lapack-tarfile="
3326                          (assoc-ref %build-inputs "lapack-tar")))
3327        #:phases
3328        (modify-phases %standard-phases
3329          (add-after 'install 'install-doc
3330            (lambda* (#:key outputs inputs #:allow-other-keys)
3331              (let ((doc (string-append (assoc-ref outputs "doc")
3332                                        "/share/doc/atlas")))
3333                (mkdir-p doc)
3334                (fold (lambda (file previous)
3335                        (and previous (zero? (system* "cp" file doc))))
3336                      #t (find-files "../ATLAS/doc" ".*")))))
3337          (add-after 'check 'check-pt
3338            (lambda _ (zero? (system* "make" "ptcheck"))))
3339          ;; Fix files required to run configure.
3340          (add-before 'configure 'fix-/bin/sh
3341            (lambda _
3342              ;; Use `sh', not `/bin/sh'.
3343              (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
3344                (("/bin/sh")
3345                 "sh"))))
3346          ;; Fix /bin/sh in generated make files.
3347          (add-after 'configure 'fix-/bin/sh-in-generated-files
3348            (lambda _
3349              (substitute* (find-files "." "^[Mm]ake\\.inc.*")
3350                (("/bin/sh")
3351                 "sh"))))
3352          ;; ATLAS configure program does not accepts the default flags
3353          ;; passed by the 'gnu-build-system'.
3354          (replace 'configure
3355            (lambda* (#:key native-inputs inputs outputs
3356                            (configure-flags '())
3357                            #:allow-other-keys #:rest args)
3358              (let* ((prefix     (assoc-ref outputs "out"))
3359                     (bash       (or (and=> (assoc-ref
3360                                             (or native-inputs inputs) "bash")
3361                                            (cut string-append <> "/bin/bash"))
3362                                     "/bin/sh"))
3363                     (flags      `(,(string-append "--prefix=" prefix)
3364                                   ,@configure-flags))
3365                     (abs-srcdir (getcwd))
3366                     (srcdir     (string-append "../" (basename abs-srcdir))))
3367                (format #t "source directory: ~s (relative from build: ~s)~%"
3368                        abs-srcdir srcdir)
3369                (mkdir "../build")
3370                (chdir "../build")
3371                (format #t "build directory: ~s~%" (getcwd))
3372                (format #t "configure flags: ~s~%" flags)
3373                (zero? (apply system* bash
3374                              (string-append srcdir "/configure")
3375                              flags))))))))
3376     (synopsis "Automatically Tuned Linear Algebra Software")
3377     (description
3378      "ATLAS is an automatically tuned linear algebra software library
3379 providing C and Fortran77 interfaces to a portably efficient BLAS
3380 implementation, as well as a few routines from LAPACK.
3381
3382 Optimization occurs at build time.  For this reason, the library is built on
3383 the machine where it is installed, without resorting to pre-built substitutes.
3384
3385 Before building the library, CPU throttling should be disabled.  This can be
3386 done in the BIOS, or, on GNU/Linux, with the following command:
3387
3388 @example
3389 # cpupower --governor performance
3390 @end example
3391
3392 Failure to do so will result in a library with poor performance.")
3393     (license license:bsd-3)))
3394
3395 (define-public glm
3396   (package
3397     (name "glm")
3398     (version "0.9.9.5")
3399     (source
3400      (origin
3401        (method url-fetch)
3402        (uri (string-append "https://github.com/g-truc/glm/releases/download/"
3403                            version  "/glm-" version ".zip"))
3404        (sha256
3405         (base32
3406          "1vmg7hb4xvsa77zpbwiw6lqc7pyaj56dihx6xriny5b9rrh4iqsg"))))
3407     (build-system cmake-build-system)
3408     (native-inputs
3409      `(("unzip" ,unzip)))
3410     (home-page "https://glm.g-truc.net/")
3411     (synopsis "OpenGL Mathematics library")
3412     (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
3413 library for graphics software based on the OpenGL Shading Language (GLSL)
3414 specifications.")
3415     (license license:expat)))
3416
3417 (define-public lpsolve
3418   (package
3419     (name "lpsolve")
3420     (version "5.5.2.5")
3421     (source
3422      (origin
3423       (method url-fetch)
3424       (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
3425                           "/lp_solve_" version "_source.tar.gz"))
3426       (sha256
3427        (base32
3428         "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
3429       (modules '((guix build utils)))
3430       (snippet
3431        '(begin
3432           (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
3433             (("^c=cc") "c=gcc")
3434             ;; Pretend to be on a 64 bit platform to obtain a common directory
3435             ;; name for the build results on all architectures; nothing else
3436             ;; seems to depend on it.
3437             (("^PLATFORM=.*$") "PLATFORM=ux64\n")
3438
3439             ;; The check for 'isnan' as it is written fails with
3440             ;; "non-floating-point argument in call to function
3441             ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
3442             ;; definition, which in turn leads to bad things.  Fix the feature
3443             ;; test.
3444             (("isnan\\(0\\)") "isnan(0.)"))
3445           #t))))
3446     (build-system gnu-build-system)
3447     (arguments
3448      `(#:tests? #f                      ; no check target
3449        #:phases
3450        (modify-phases %standard-phases
3451          (delete 'configure)            ; no configure script
3452          (replace 'build
3453            (lambda _
3454              (with-directory-excursion "lpsolve55"
3455                (invoke "bash" "ccc"))
3456              (with-directory-excursion "lp_solve"
3457                (invoke "bash" "ccc"))
3458              #t))
3459          (replace 'install
3460            (lambda* (#:key outputs #:allow-other-keys)
3461              (let* ((out (assoc-ref outputs "out"))
3462                     (bin (string-append out "/bin"))
3463                     (lib (string-append out "/lib"))
3464                     ;; This is where LibreOffice expects to find the header
3465                     ;; files, and where they are installed by Debian.
3466                     (include (string-append out "/include/lpsolve")))
3467                (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
3468                (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
3469                (install-file "lp_solve/bin/ux64/lp_solve" bin)
3470
3471                ;; Install a subset of the header files as on Debian
3472                ;; (plus lp_bit.h, which matches the regular expression).
3473                (for-each (lambda (name)
3474                            (install-file name include))
3475                          (find-files "." "lp_[HMSa-z].*\\.h$"))
3476                (with-directory-excursion "shared"
3477                  (for-each (lambda (name)
3478                              (install-file name include))
3479                            (find-files "." "\\.h$")))
3480                #t))))))
3481     (home-page "http://lpsolve.sourceforge.net/")
3482     (synopsis "Mixed integer linear programming (MILP) solver")
3483     (description
3484      "lp_solve is a mixed integer linear programming solver based on the
3485 revised simplex and the branch-and-bound methods.")
3486     (license license:lgpl2.1+)))
3487
3488 (define-public dealii
3489   (package
3490     (name "dealii")
3491     (version "9.0.1")
3492     (source
3493      (origin
3494        (method url-fetch)
3495        (uri (string-append "https://github.com/dealii/dealii/releases/"
3496                            "download/v" version "/dealii-" version ".tar.gz"))
3497        (sha256
3498         (base32
3499          "0r7f8rhl3xr94imd372plizdcbqk0a70w73lwc3vw912dxk0sbyz"))
3500        (patches (search-patches "dealii-mpi-deprecations.patch"))
3501        (modules '((guix build utils)))
3502        (snippet
3503         ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
3504         '(begin
3505            (delete-file-recursively "bundled")
3506            #t))))
3507     (build-system cmake-build-system)
3508     (inputs
3509      `(("tbb" ,tbb)
3510        ("zlib" ,zlib)
3511        ("boost" ,boost)
3512        ("p4est" ,p4est)
3513        ("blas" ,openblas)
3514        ("lapack" ,lapack)
3515        ("arpack" ,arpack-ng)
3516        ("muparser" ,muparser)
3517        ("gfortran" ,gfortran)
3518        ("suitesparse" ,suitesparse)))   ;for UMFPACK
3519     (arguments
3520      `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
3521        #:configure-flags
3522        ;; Work around a bug in libsuitesparseconfig linking
3523        ;; see https://github.com/dealii/dealii/issues/4745
3524        '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
3525     (home-page "https://www.dealii.org")
3526     (synopsis "Finite element library")
3527     (description
3528      "Deal.II is a C++ program library targeted at the computational solution
3529 of partial differential equations using adaptive finite elements.  The main
3530 aim of deal.II is to enable rapid development of modern finite element codes,
3531 using among other aspects adaptive meshes and a wide array of tools often used
3532 in finite element programs.")
3533     (license license:lgpl2.1+)))
3534
3535 (define-public dealii-openmpi
3536   (package (inherit dealii)
3537     (name "dealii-openmpi")
3538     (inputs
3539      `(("mpi" ,openmpi)
3540        ;;Supported only with MPI:
3541        ("p4est" ,p4est-openmpi)
3542        ("petsc" ,petsc-openmpi)
3543        ("slepc" ,slepc-openmpi)
3544        ("metis" ,metis)               ;for MUMPS
3545        ("scalapack" ,scalapack)       ;for MUMPS
3546        ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
3547        ("arpack" ,arpack-ng-openmpi)
3548        ,@(fold alist-delete (package-inputs dealii)
3549                '("p4est" "arpack"))))
3550     (arguments
3551      (substitute-keyword-arguments (package-arguments dealii)
3552        ((#:configure-flags cf)
3553         `(cons "-DDEAL_II_WITH_MPI:BOOL=ON"
3554                ,cf))
3555        ((#:phases phases '%standard-phases)
3556         `(modify-phases ,phases
3557            (add-before 'check 'mpi-setup
3558              ,%openmpi-setup)))))
3559     (synopsis "Finite element library (with MPI support)")))
3560
3561 (define-public flann
3562   (package
3563     (name "flann")
3564     (version "1.8.4")
3565     (source
3566       (origin
3567         (method url-fetch)
3568         (uri
3569           (string-append
3570             "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
3571             version "-src.zip"))
3572         (sha256
3573           (base32
3574             "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))
3575         (patches (search-patches "flann-cmake-3.11.patch"))))
3576     (build-system cmake-build-system)
3577     (outputs '("out"
3578                "octave"))                  ;46 MiB .mex file that pulls Octave
3579     (native-inputs
3580      `(("unzip" ,unzip)))
3581     (inputs
3582      `(("hdf5" ,hdf5)
3583        ("octave" ,octave-cli)
3584        ("python" ,python-2) ; print syntax
3585        ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
3586        ("zlib" ,zlib)))
3587     (arguments
3588      `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
3589        ;; taken 46 MiB unstripped, and 6 MiB stripped.
3590        #:strip-directories '("lib" "lib64" "libexec"
3591                              "bin" "sbin" "share/flann/octave")
3592
3593        ;; Save 12 MiB by not installing .a files.  Passing
3594        ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
3595        #:phases (modify-phases %standard-phases
3596                   (add-before 'configure 'set-octave-directory
3597                     (lambda* (#:key outputs #:allow-other-keys)
3598                       ;; Install the .mex file in the "octave" output.
3599                       (let ((out (assoc-ref outputs "octave")))
3600                         (substitute* "src/matlab/CMakeLists.txt"
3601                           (("share/flann/octave")
3602                            (string-append out "/share/flann/octave")))
3603                         #t)))
3604                   (add-after 'install 'remove-static-libraries
3605                     (lambda* (#:key outputs #:allow-other-keys)
3606                       (let* ((out (assoc-ref outputs "out"))
3607                              (lib (string-append out "/lib")))
3608                         (for-each delete-file
3609                                   (find-files lib "\\.a$"))
3610                         #t))))
3611
3612        #:tests? #f)) ; The test data are downloaded from the Internet.
3613     (home-page "http://www.cs.ubc.ca/research/flann/")
3614     (synopsis "Library for approximate nearest neighbors computation")
3615     (description "FLANN is a library for performing fast approximate
3616 nearest neighbor searches in high dimensional spaces.  It implements a
3617 collection of algorithms and a system for automatically choosing the best
3618 algorithm and optimum parameters depending on the dataset.
3619
3620 FLANN is written in C++ and contains bindings for C, Octave and Python.")
3621     (license (license:non-copyleft "file://COPYING"
3622                                 "See COPYING in the distribution."))))
3623
3624 (define-public wcalc
3625   (package
3626     (name "wcalc")
3627     (version "2.5")
3628     (source
3629       (origin
3630         (method url-fetch)
3631         (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
3632                             "wcalc-" version ".tar.bz2"))
3633         (sha256
3634           (base32
3635             "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
3636     (build-system gnu-build-system)
3637     (inputs
3638      `(("mpfr" ,mpfr)
3639        ("readline" ,readline)))
3640     (home-page "http://w-calc.sourceforge.net/index.php")
3641     (synopsis "Flexible command-line scientific calculator")
3642     (description "Wcalc is a very capable calculator.  It has standard functions
3643 (sin, asin, and sinh for example, in either radians or degrees), many
3644 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
3645 variables, a command history, hex/octal/binary input and output, unit
3646 conversions, embedded comments, and an expandable expression entry field.  It
3647 evaluates expressions using the standard order of operations.")
3648     (license license:gpl2+)))
3649
3650 (define-public xaos
3651   (package
3652     (name "xaos")
3653     (version "3.6")
3654     (source (origin
3655               (method url-fetch)
3656               (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
3657                                   "/xaos-" version ".tar.gz"))
3658               (sha256
3659                (base32
3660                 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
3661     (build-system gnu-build-system)
3662     (native-inputs `(("gettext" ,gettext-minimal)))
3663     (inputs `(("libx11" ,libx11)
3664               ("zlib" ,zlib)
3665               ("libpng" ,libpng)
3666               ("gsl" ,gsl)))
3667     (arguments
3668      `(#:tests? #f ;no "check" target
3669        #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
3670     (synopsis "Real-time fractal zoomer")
3671     (description "GNU XaoS is a graphical program that generates fractal
3672 patterns and allows you to zoom in and out of them infinitely in a fluid,
3673 continuous manner.  It also includes tutorials that help to explain how fractals
3674 are built.  It can generate many different fractal types such as the Mandelbrot
3675 set.")
3676     (home-page "https://www.gnu.org/software/xaos/")
3677     (license license:gpl2+)))
3678
3679 (define-public hypre
3680   (package
3681     (name "hypre")
3682     (version "2.14.0")
3683     (source (origin
3684               (method url-fetch)
3685               (uri (string-append "https://github.com/LLNL/hypre/archive/"
3686                                   "v" version ".tar.gz"))
3687               (file-name (string-append name "-" version ".tar.gz"))
3688               (sha256
3689                (base32
3690                 "0v515i73bvaz378h5465b1dy9v2gf924zy2q94cpq4qqarawvkqh"))
3691               (modules '((guix build utils)))
3692               (snippet
3693                '(begin
3694                   ;; Remove use of __DATE__ and __TIME__ for reproducibility;
3695                   ;; substitute the tarball creation time.
3696                   (substitute* "src/utilities/HYPRE_utilities.h"
3697                     (("Date Compiled: .*$")
3698                      "Date Compiled: Apr 11 2018 16:24:59 +0000\"\n"))
3699                   #t))))
3700     (build-system gnu-build-system)
3701     (outputs '("out"                    ;6.1 MiB of headers and libraries
3702                "doc"))                  ;4.8 MiB of documentation
3703     (native-inputs
3704      `(("doc++" ,doc++)
3705        ("netpbm" ,netpbm)
3706        ("perl" ,perl)                   ;needed to run 'ppmquant' during tests
3707        ("texlive" ,(texlive-union (list texlive-generic-xypic
3708                                         texlive-fonts-xypic
3709                                         texlive-latex-hyperref
3710                                         texlive-bibtex)))
3711        ("ghostscript" ,ghostscript)))
3712     (inputs
3713      `(("blas" ,openblas)
3714        ("lapack" ,lapack)))
3715     (arguments
3716      `(#:modules ((srfi srfi-1)
3717                   ,@%gnu-build-system-modules)
3718        #:configure-flags '("--enable-shared"
3719                            "--disable-fortran"
3720                            "--without-MPI"
3721                            "--with-openmp"
3722                            "--with-fei"
3723                            "--with-lapack"
3724                            "--with-blas")
3725        #:phases
3726        (modify-phases %standard-phases
3727          (add-before 'build 'set-HOME
3728            (lambda _
3729              ;; FIXME: texlive-union does not find the built
3730              ;; metafonts, so it tries to generate them in HOME.
3731              (setenv "HOME" "/tmp")
3732              #t))
3733          (add-before 'configure 'chdir-src
3734            (lambda _ (chdir "src")))
3735          (replace 'configure
3736            (lambda* (#:key build target configure-flags
3737                            #:allow-other-keys #:rest args)
3738              (let* ((configure (assoc-ref %standard-phases 'configure)))
3739                (apply configure
3740                       (append args
3741                               (list #:configure-flags
3742                                     (cons (string-append
3743                                            "--host=" (or target build))
3744                                           configure-flags)))))))
3745          (add-after 'build 'build-docs
3746            (lambda _
3747              (invoke "make" "-Cdocs" "pdf" "html")))
3748          (replace 'check
3749            (lambda _
3750              (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
3751              (setenv "PATH" (string-append "." ":" (getenv "PATH")))
3752              (and (system* "make" "check" "CHECKRUN=")
3753                   (fold (lambda (filename result)
3754                           (and result
3755                                (let ((size (stat:size (stat filename))))
3756                                  (when (not (zero? size))
3757                                    (format #t "~a size ~d; error indication~%"
3758                                            filename size))
3759                                  (zero? size))))
3760                         #t
3761                         (find-files "test" ".*\\.err$")))))
3762          (add-after 'install 'install-docs
3763            (lambda* (#:key outputs #:allow-other-keys)
3764              ;; Custom install because docs/Makefile doesn't honor ${docdir}.
3765              (let* ((doc (assoc-ref outputs "doc"))
3766                     (docdir (string-append doc "/share/doc/hypre-" ,version)))
3767                (with-directory-excursion "docs"
3768                  (for-each (lambda (base)
3769                              (install-file (string-append base ".pdf") docdir)
3770                              (copy-recursively base docdir)) ;html docs
3771                            '("HYPRE_usr_manual"
3772                              "HYPRE_ref_manual")))
3773                #t))))))
3774     (home-page "http://www.llnl.gov/casc/hypre/")
3775     (synopsis "Library of solvers and preconditioners for linear equations")
3776     (description
3777      "HYPRE is a software library of high performance preconditioners and
3778 solvers for the solution of large, sparse linear systems of equations.  It
3779 features multigrid solvers for both structured and unstructured grid
3780 problems.")
3781     (license license:lgpl2.1)))
3782
3783 (define-public hypre-openmpi
3784   (package (inherit hypre)
3785     (name "hypre-openmpi")
3786     (inputs
3787      `(("mpi" ,openmpi)
3788        ,@(package-inputs hypre)))
3789     (arguments
3790      (substitute-keyword-arguments (package-arguments hypre)
3791        ((#:configure-flags flags)
3792         ``("--with-MPI"
3793            ,@(delete "--without-MPI" ,flags)))
3794        ((#:phases phases)
3795         `(modify-phases ,phases
3796            (add-before 'check 'mpi-setup
3797              ,%openmpi-setup)))))
3798     (synopsis "Parallel solvers and preconditioners for linear equations")
3799     (description
3800      "HYPRE is a software library of high performance preconditioners and
3801 solvers for the solution of large, sparse linear systems of equations on
3802 parallel computers.  It features parallel multigrid solvers for both
3803 structured and unstructured grid problems.")))
3804
3805 (define-public matio
3806   (package
3807     (name "matio")
3808     (version "1.5.6")
3809     (source
3810      (origin
3811        (method url-fetch)
3812        (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
3813                            "matio-" version ".tar.gz"))
3814        (sha256
3815         (base32
3816          "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3817     (build-system gnu-build-system)
3818     (inputs
3819      `(("zlib" ,zlib)
3820        ("hdf5" ,hdf5)))
3821     (home-page "http://matio.sourceforge.net/")
3822     (synopsis "Library for reading and writing MAT files")
3823     (description "Matio is a library for reading and writing MAT files.  It
3824 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3825     (license license:bsd-2)))
3826
3827 (define-public vc
3828   (package
3829     (name "vc")
3830     (version "1.3.3")
3831     (source
3832       (origin (method url-fetch)
3833               (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3834                                   "download/" version "/Vc-" version ".tar.gz"))
3835               (sha256
3836                (base32
3837                 "1zmlpn32jzb38smp3j834llmbix3whsrbw0h397qxysbw792kih8"))))
3838     (build-system cmake-build-system)
3839     (arguments
3840      '(#:configure-flags
3841        '("-DBUILD_TESTING=ON"
3842          ;; By default, Vc will optimize for the CPU of the build machine.
3843          ;; Setting this to "none" makes it create portable binaries.  See
3844          ;; "cmake/OptimizeForArchitecture.cmake".
3845          "-DTARGET_ARCHITECTURE=none")))
3846     (synopsis "SIMD vector classes for C++")
3847     (description "Vc provides portable, zero-overhead C++ types for explicitly
3848 data-parallel programming.  It is a library designed to ease explicit
3849 vectorization of C++ code.  Its types enable explicitly stating data-parallel
3850 operations on multiple values.  The parallelism is therefore added via the type
3851 system.  Vc has an intuitive API and provides portability between different
3852 compilers and compiler versions as well as portability between different vector
3853 instruction sets.  Thus, an application written with Vc can be compiled for:
3854 @enumerate
3855 @item AVX and AVX2
3856 @item SSE2 up to SSE4.2 or SSE4a
3857 @item Scalar
3858 @item MIC
3859 @item NEON (in development)
3860 @item NVIDIA GPUs / CUDA (in development)
3861 @end enumerate\n")
3862     (home-page "https://github.com/VcDevel/Vc")
3863     ;; "No support_???.cpp file exists for this architecture."
3864     (supported-systems '("x86_64-linux" "i686-linux"))
3865     (license license:bsd-3)))
3866
3867 (define-public reducelcs
3868   ;; This is the last commit which is available upstream, no
3869   ;; release happened since 2010.
3870   (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
3871         (revision "1"))
3872     (package
3873       (name "reducelcs")
3874       (version (string-append "1.0-" revision "." (string-take commit 7)))
3875       (source
3876        (origin
3877          (method git-fetch)
3878          (uri (git-reference
3879                (url "https://github.com/gdv/Reduce-Expand-for-LCS")
3880                (commit commit)))
3881          (file-name (string-append name "-" version "-checkout"))
3882          (sha256
3883           (base32
3884            "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
3885       (build-system gnu-build-system)
3886       (inputs
3887        `(("openlibm" ,openlibm)))
3888       (arguments
3889        `(#:tests? #f ; no tests
3890          #:phases
3891          (modify-phases %standard-phases
3892            (delete 'configure) ; No configure script exists.
3893            (replace 'install ; No install phase exists.
3894              (lambda* (#:key outputs #:allow-other-keys)
3895                (let* ((out (assoc-ref outputs "out"))
3896                       (bin (string-append out "/bin")))
3897                  (install-file "Approximation" bin)
3898                  (install-file "CollectResults" bin)
3899                  (install-file "GenerateInstances" bin)
3900                  #t))))))
3901       (synopsis "Approximate Longest Commons Subsequence computation tool")
3902       (description
3903        "@code{reduceLCS} is an implementation of the Reduce-Expand
3904 algorithm for LCS.  It is a fast program to compute the approximate
3905 Longest Commons Subsequence of a set of strings.")
3906       (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
3907       (license license:gpl3+))))
3908
3909 (define-public jacal
3910   (package
3911     (name "jacal")
3912     (version "1c4")
3913     (source (origin
3914               (method url-fetch)
3915               (uri (string-append
3916                     "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
3917                     version ".zip"))
3918               (sha256 (base32
3919                        "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
3920               (patches (search-patches "jacal-fix-texinfo.patch"))))
3921     (build-system gnu-build-system)
3922     (arguments
3923      `(#:phases
3924        (modify-phases %standard-phases
3925          (add-before 'build 'pre-build
3926                      ;; Don't use upstream's script - it really doesn't fit into
3927                      ;; Guix's functional paradigm.
3928                      (lambda* (#:key inputs outputs #:allow-other-keys)
3929                        (substitute* "Makefile"
3930                          (("^install: install-script") "install: "))))
3931          (add-after 'install 'post-install
3932                     ;; Instead, we provide our own simplified script.
3933                     (lambda* (#:key inputs outputs #:allow-other-keys)
3934                       (let ((wrapper (string-append (assoc-ref outputs "out")
3935                                                     "/bin/jacal")))
3936                         (format (open wrapper (logior O_WRONLY O_CREAT))
3937                                 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
3938                                 "-e '(slib:load \"~a/lib/jacal/math\") "
3939                                 "(math)' \"$@\"\n")
3940                                 (which  "bash")
3941                                 (assoc-ref inputs "scm")
3942                                 (assoc-ref outputs "out"))
3943                         (chmod wrapper #o555))))
3944          (replace 'configure
3945                   (lambda* (#:key inputs outputs #:allow-other-keys)
3946                     (zero? (system* "./configure"
3947                                     (string-append "--prefix="
3948                                                    (assoc-ref outputs "out")))))))))
3949     (inputs `(("scm" ,scm)))
3950     (native-inputs `(("unzip" ,unzip)
3951                      ("texinfo" ,texinfo)))
3952     (synopsis "Symbolic mathematics system")
3953     (description "GNU JACAL is an interactive symbolic mathematics program based on
3954 Scheme.  It manipulate and simplify a range of mathematical expressions such
3955 as equations, scalars, vectors, and matrices.")
3956     (home-page "https://www.gnu.org/software/jacal/")
3957     (license license:gpl3+)))
3958
3959 (define-public z3
3960   (package
3961     (name "z3")
3962     (version "4.8.4")
3963     (home-page "https://github.com/Z3Prover/z3")
3964     (source (origin
3965               (method git-fetch)
3966               (uri (git-reference (url home-page)
3967                                   (commit (string-append "z3-" version))))
3968               (file-name (git-file-name name version))
3969               (sha256
3970                (base32
3971                 "014igqm5vwswz0yhz0cdxsj3a6dh7i79hvhgc3jmmmz3z0xm1gyn"))))
3972     (build-system gnu-build-system)
3973     (arguments
3974      `(#:phases
3975        (modify-phases %standard-phases
3976          (add-after 'unpack 'fix-compatability
3977            ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
3978            (lambda _
3979              (substitute* "src/util/mpz.cpp"
3980                (("#include <immintrin.h>") ""))
3981              #t))
3982          (add-before 'configure 'bootstrap
3983            (lambda _
3984              (zero?
3985               (system* "python" "scripts/mk_make.py"))))
3986          ;; work around gnu-build-system's setting --enable-fast-install
3987          ;; (z3's `configure' is a wrapper around the above python file,
3988          ;; which fails when passed --enable-fast-install)
3989          (replace 'configure
3990            (lambda* (#:key inputs outputs #:allow-other-keys)
3991              (invoke "./configure"
3992                      (string-append "--prefix=" (assoc-ref outputs "out")))))
3993          (add-after 'configure 'change-directory
3994            (lambda _
3995              (chdir "build")
3996              #t))
3997          (add-before 'check 'make-test-z3
3998            (lambda _
3999              ;; Build the test suite executable.
4000              (zero? (system* "make" "test-z3" "-j"
4001                              (number->string (parallel-job-count))))))
4002          (replace 'check
4003            (lambda _
4004              ;; Run all the tests that don't require arguments.
4005              (zero? (system* "./test-z3" "/a")))))))
4006     (native-inputs
4007      `(("which" ,which)
4008        ("python" ,python-wrapper)))
4009     (synopsis "Theorem prover")
4010     (description "Z3 is a theorem prover and @dfn{satisfiability modulo
4011 theories} (SMT) solver.  It provides a C/C++ API, as well as Python bindings.")
4012     (license license:expat)))
4013
4014 (define-public elpa
4015   (package
4016     (name "elpa")
4017     (version "2018.11.001")
4018     (source (origin
4019               (method url-fetch)
4020               (uri (string-append "http://elpa.mpcdf.mpg.de/html/Releases/"
4021                                   version "/elpa-" version ".tar.gz"))
4022               (sha256
4023                (base32
4024                 "05hv3v5i6xmziaizw350ff72y1c3k662r85fm3xfdrkclj5zw9yc"))))
4025     (build-system gnu-build-system)
4026     (native-inputs
4027      `(("fortran" ,gfortran)
4028        ("perl" ,perl)))                 ;for configure and deps
4029     (inputs
4030      `(("blas" ,openblas)))
4031     (arguments
4032      `(#:configure-flags
4033        `("--enable-openmp"
4034          "--with-mpi=no"
4035          ;; ELPA unfortunately does not support runtime dispatch, so we can
4036          ;; only enable the "generic" kernels.  See the "Cross compilation"
4037          ;; section of INSTALL.md.
4038          "--enable-generic"
4039          "--disable-sse" "--disable-sse-assembly" ;Require SSE3
4040          "--disable-avx" "--disable-avx2" "--disable-avx512"
4041          ,(string-append "CFLAGS=-O3 "
4042                          "-funsafe-loop-optimizations -funsafe-math-optimizations "
4043                          "-ftree-vect-loop-version -ftree-vectorize "
4044                          ,(let ((system (or (%current-target-system)
4045                                             (%current-system))))
4046                             (cond
4047                              ((or (string-prefix? "x86_64" system)
4048                                   (string-prefix? "i686" system))
4049                               "-msse2")
4050                              (else "")))))
4051        #:parallel-tests? #f             ;tests are multi-threaded, via BLAS
4052        #:phases
4053        (modify-phases %standard-phases
4054          (add-before 'configure 'patch-header-generation
4055            (lambda _
4056              (substitute* "configure"
4057                (("^  *make.*top_srcdir=\"\\$srcdir\"" &)
4058                 (string-append & " CPP=\"$CPP\"")))
4059              #t))
4060          (add-before 'check 'setup-tests
4061            (lambda _
4062              ;; Decrease test time and RAM use by computing fewer eigenvalues.
4063              ;; The flags are (MATRIX-SIZE, EIGENVALUES, BLOCK-SIZE), where
4064              ;; the default is (500, 250, 16) for C tests and (5000, 150, 16)
4065              ;; for Fortran.  This also causes several tests to pass that
4066              ;; otherwise would otherwise fail with matrix size 5000; possibly
4067              ;; due to floating point tolerances that are too tight.
4068              (setenv "TEST_FLAGS" "1500 50 16") ;from elpa.spec
4069              (setenv "OMP_NUM_THREADS" (number->string (parallel-job-count)))
4070              (substitute* "Makefile"
4071                ;; Test scripts are generated, patch the shebang
4072                (("#!/bin/bash") (string-append "#!" (which "sh"))))
4073              #t)))))
4074     (home-page "http://elpa.mpcdf.mpg.de")
4075     (synopsis "Eigenvalue solvers for symmetric matrices")
4076     (description
4077      "The ELPA library provides efficient and scalable direct eigensolvers for
4078 symmetric matrices.")
4079     (license license:lgpl3)))
4080
4081 (define-public elpa-openmpi
4082   (package (inherit elpa)
4083     (name "elpa-openmpi")
4084     (inputs
4085      `(("mpi" ,openmpi)
4086        ("scalapack" ,scalapack)
4087        ,@(package-inputs elpa)))
4088     (arguments
4089      (substitute-keyword-arguments (package-arguments elpa)
4090        ((#:configure-flags cf '())
4091         `(cons "--with-mpi=yes" (delete "--with-mpi=no" ,cf)))
4092        ((#:phases phases '%standard-phases)
4093         `(modify-phases ,phases
4094            (add-before 'check 'mpi-setup
4095              (lambda _
4096                ;; Tests use 2 mpi tasks by default, use our remaining build
4097                ;; cores as OpenMP threads.
4098                (setenv "OMP_NUM_THREADS" (number->string
4099                                           (max (quotient (parallel-job-count) 2)
4100                                                1)))
4101                (,%openmpi-setup)))))))
4102     (synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)")))
4103
4104 (define-public elemental
4105   (package
4106     (name "elemental")
4107     (version "0.87.7")
4108     (source (origin
4109               (method git-fetch)
4110               (uri (git-reference
4111                      (url "https://github.com/elemental/Elemental.git")
4112                      (commit (string-append "v" version))))
4113               (file-name (git-file-name name version))
4114               (sha256
4115                (base32
4116                 "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
4117     (build-system cmake-build-system)
4118     (home-page "http://libelemental.org")
4119     (native-inputs
4120      `(("gfortran" ,gfortran)))
4121     (inputs
4122      `(("blas" ,openblas)
4123        ("gfortran:lib" ,gfortran "lib")
4124        ("gmp" ,gmp)
4125        ("lapack" ,lapack)
4126        ("metis" ,metis)
4127        ("mpc" ,mpc)
4128        ("mpfr" ,mpfr)
4129        ("mpi" ,openmpi)
4130        ("qd" ,qd)))
4131     (arguments
4132      `(#:build-type "Release"           ;default RelWithDebInfo not supported
4133        #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
4134                            "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
4135                            "-DEL_CACHE_WARNINGS:BOOL=YES"
4136                            "-DEL_TESTS:BOOL=YES"
4137                            "-DCMAKE_INSTALL_LIBDIR=lib"
4138                            "-DGFORTRAN_LIB=gfortran")
4139        #:phases (modify-phases %standard-phases
4140                   (add-before 'check 'mpi-setup
4141                     ,%openmpi-setup)
4142                   (add-before 'check 'setup-tests
4143                     (lambda _
4144                       ;; Parallelism is done at the MPI layer.
4145                       (setenv "OMP_NUM_THREADS" "1")
4146                       #t))
4147                   (add-after 'install 'remove-tests
4148                     (lambda* (#:key outputs #:allow-other-keys)
4149                       ;; Tests are installed, with no easy configuration
4150                       ;; switch to prevent this, so delete them.
4151                       (delete-file-recursively
4152                         (string-append (assoc-ref outputs "out") "/bin"))
4153                       #t)))))
4154     (synopsis "Dense and sparse-direct linear algebra and optimization")
4155     (description "Elemental is a modern C++ library for distributed-memory
4156 dense and sparse-direct linear algebra, conic optimization, and lattice
4157 reduction.")
4158     (license license:bsd-2)))
4159
4160 (define-public mcrl2
4161   (package
4162     (name "mcrl2")
4163     (version "201707.1.15162")
4164     (source (origin
4165               (method url-fetch)
4166               (uri (string-append "http://www.mcrl2.org/download/devel/mcrl2-"
4167                                   version
4168                                   ".tar.gz"))
4169               (sha256
4170                (base32
4171                 "1ziww2fchsklm25hl9p2mngssxfh9w07nc114cncqaxfibqp2p8f"))))
4172     (native-inputs
4173      `(("subversion" ,subversion)))
4174     (inputs
4175      `(("boost" ,boost)
4176        ("glu" ,glu)
4177        ("mesa" ,mesa)
4178        ("qtbase" ,qtbase)))
4179     (build-system cmake-build-system)
4180     (synopsis "Toolset for the mCRL2 formal specification language")
4181     (description
4182      "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
4183 specification language for describing concurrent discrete event systems.  Its
4184 toolset supports analysis and automatic verification, linearisation, simulation,
4185 state-space exploration and generation, and tools to optimise and analyse
4186 specifications.  Also, state spaces can be manipulated, visualised and
4187 analysed.")
4188     (home-page "https://mcrl2.org")
4189     (license license:boost1.0)))
4190
4191 (define-public r-subplex
4192   (package
4193     (name "r-subplex")
4194     (version "1.5-4")
4195     (source
4196     (origin
4197       (method url-fetch)
4198       (uri (cran-uri "subplex" version))
4199       (sha256
4200        (base32
4201         "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
4202     (build-system r-build-system)
4203     (native-inputs
4204      `(("gfortran" ,gfortran)))
4205     (home-page "https://cran.r-project.org/web/packages/subplex")
4206     (synopsis "Unconstrained optimization using the subplex algorithm")
4207     (description "This package implements the Subplex optimization algorithm.
4208 It solves unconstrained optimization problems using a simplex method on
4209 subspaces.  The method is well suited for optimizing objective functions that
4210 are noisy or are discontinuous at the solution.")
4211     (license license:gpl3+)))
4212
4213 (define-public r-desolve
4214   (package
4215     (name "r-desolve")
4216     (version "1.21")
4217     (source
4218       (origin
4219         (method url-fetch)
4220         (uri (cran-uri "deSolve" version))
4221         (sha256
4222          (base32
4223           "0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"))))
4224     (properties `((upstream-name . "deSolve")))
4225     (build-system r-build-system)
4226     (native-inputs
4227      `(("gfortran" ,gfortran)))
4228     (home-page "https://desolve.r-forge.r-project.org/")
4229     (synopsis "Solvers for initial value problems of differential equations")
4230     (description "This package provides functions that solve initial
4231 value problems of a system of first-order ordinary differential equations (ODE),
4232 of partial differential equations (PDE), of differential algebraic equations
4233 (DAE), and of delay differential equations.  The functions provide an interface
4234 to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
4235 to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
4236 the Runge-Kutta family with fixed or variable time steps.  The package contains
4237 routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
4238 differential equations (PDE) that have been converted to ODEs by numerical
4239 differencing.")
4240     (license license:gpl2+)))
4241
4242 (define-public tcalc
4243   (package
4244   (name "tcalc")
4245   (version "2.0")
4246   (source
4247     (origin
4248       (method url-fetch)
4249       (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
4250                             version ".tar.gz"))
4251       (sha256
4252         (base32
4253           "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
4254   (build-system gnu-build-system)
4255   (synopsis "The terminal calculator")
4256   (description
4257     "The terminal calculator is a small program to help users of the GNU/Linux
4258 terminal do calculations simply and quickly.  The formula to be calculated can
4259 be fed to @command{tcalc} through the command line.")
4260   (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
4261   (license license:gpl3+)))
4262
4263 (define-public sundials
4264   (package
4265     (name "sundials")
4266     (version "3.1.1")
4267     (source
4268      (origin
4269        (method url-fetch)
4270        (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
4271                            "sundials-" version ".tar.gz"))
4272        (sha256
4273         (base32
4274          "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
4275     (build-system cmake-build-system)
4276     (native-inputs
4277      `(("python" ,python-2)))    ;for tests; syntax incompatible with python 3
4278     (inputs
4279      `(("fortran" ,gfortran)            ;for fcmix
4280        ("blas" ,openblas)
4281        ("suitesparse" ,suitesparse)))   ;TODO: Add hypre
4282     (arguments
4283      `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
4284                            "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
4285                            "-DEXAMPLES_ENABLE_F77:BOOL=ON"
4286                            "-DEXAMPLES_ENABLE_F90:BOOL=ON"
4287                            "-DEXAMPLES_INSTALL:BOOL=OFF"
4288
4289                            "-DFCMIX_ENABLE:BOOL=ON"
4290
4291                            "-DKLU_ENABLE:BOOL=ON"
4292                            ,(string-append "-DKLU_INCLUDE_DIR="
4293                                            (assoc-ref %build-inputs "suitesparse")
4294                                            "/include")
4295                            ,(string-append "-DKLU_LIBRARY_DIR="
4296                                            (assoc-ref %build-inputs "suitesparse")
4297                                            "/lib"))))
4298     (home-page "https://computation.llnl.gov/projects/sundials")
4299     (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
4300     (description "SUNDIALS is a family of software packages implemented with
4301 the goal of providing robust time integrators and nonlinear solvers that can
4302 easily be incorporated into existing simulation codes.")
4303     (license license:bsd-3)))
4304
4305 (define-public sundials-openmpi
4306   (package (inherit sundials)
4307     (name "sundials-openmpi")
4308     (inputs
4309      `(("mpi" ,openmpi)
4310        ("petsc" ,petsc-openmpi)         ;support in SUNDIALS requires MPI
4311        ,@(package-inputs sundials)))
4312     (arguments
4313      (substitute-keyword-arguments (package-arguments sundials)
4314        ((#:configure-flags flags '())
4315         `(cons* "-DMPI_ENABLE:BOOL=ON"
4316                 "-DPETSC_ENABLE:BOOL=ON"
4317                 (string-append "-DPETSC_INCLUDE_DIR="
4318                                (assoc-ref %build-inputs "petsc")
4319                                "/include")
4320                 (string-append "-DPETSC_LIBRARY_DIR="
4321                                (assoc-ref %build-inputs "petsc")
4322                                "/lib")
4323                 ,flags))
4324        ((#:phases phases '%standard-phases)
4325         `(modify-phases ,phases
4326            (add-before 'check 'mpi-setup
4327              ,%openmpi-setup)))))
4328     (synopsis "SUNDIALS with OpenMPI support")))
4329
4330 (define-public combinatorial-blas
4331   (package
4332     (name "combinatorial-blas")
4333     (version "1.6.2")
4334     (source
4335      (origin
4336        (method url-fetch)
4337        (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/"
4338                            "CombBLAS_beta_"
4339                            (match (string-split version #\.)
4340                             ((major minor patch)
4341                              (string-append major minor "_" patch))) ;e.g. "16_2"
4342                            ".tgz"))
4343        (sha256
4344         (base32
4345          "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a"))
4346        (patches (search-patches "combinatorial-blas-awpm.patch"
4347                                 "combinatorial-blas-io-fix.patch"))))
4348     (build-system cmake-build-system)
4349     (inputs
4350      `(("mpi" ,openmpi)
4351        ("test-data" ,(origin
4352                        (method url-fetch)
4353                        (uri (string-append "https://people.eecs.berkeley.edu/~aydin/"
4354                                            "CombBLAS_FILES/testdata_combblas1.6.1.tgz"))
4355                        (sha256
4356                         (base32
4357                          "01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87"))))))
4358     (arguments
4359      `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
4360                            "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL")
4361        #:parallel-tests? #f             ;tests use 'mpiexec -n4'
4362        #:phases
4363        (modify-phases %standard-phases
4364          (add-before 'check 'mpi-setup
4365            ,%openmpi-setup)
4366          (add-before 'check 'test-setup
4367            (lambda* (#:key inputs #:allow-other-keys)
4368              (setenv "OMP_NUM_THREADS" "2")
4369              (invoke "tar" "xf" (assoc-ref inputs "test-data")))))))
4370     (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/")
4371     (synopsis "Linear algebra primitives for graph analytics")
4372     (description "The Combinatorial BLAS (CombBLAS) is an extensible
4373 distributed-memory parallel graph library offering a small but powerful set of
4374 linear algebra primitives specifically targeting graph analytics.")
4375     (license (list
4376               license:gpl2+             ;include/psort/(funnel|sort)*.h
4377               license:x11               ;usort and psort
4378               license:bsd-3))))         ;CombBLAS and MersenneTwister.h
4379
4380 (define-public dune-common
4381   (package
4382     (name "dune-common")
4383     (version "2.6.0")
4384     (source
4385      (origin
4386        (method url-fetch)
4387        (uri (string-append "https://dune-project.org/download/"
4388                            version "/dune-common-" version ".tar.gz"))
4389        (sha256
4390         (base32
4391          "019wcr1qf7jwyxx1y5y290wdlglylskvbb2m01ljkzcza2xnlmhw"))))
4392     (build-system cmake-build-system)
4393     (arguments
4394      `(#:phases
4395        (modify-phases %standard-phases
4396          (add-after 'build 'build-tests
4397            (lambda* (#:key make-flags #:allow-other-keys)
4398              (apply invoke "make" "build_tests" make-flags)))
4399          ;; These tests fail because they require a fully functional MPI
4400          ;; environment.
4401          (add-after 'unpack 'disable-failing-tests
4402            (lambda _
4403              (setenv "ARGS"
4404                      (string-append "--exclude-regex '("
4405                                     (string-join
4406                                      (list
4407                                       "remoteindicestest"
4408                                       "remoteindicestest-mpi-2"
4409                                       "syncertest"
4410                                       "syncertest-mpi-2"
4411                                       "variablesizecommunicatortest"
4412                                       "variablesizecommunicatortest-mpi-2"
4413                                       "arithmetictestsuitetest"
4414                                       "assertandreturntest"
4415                                       "assertandreturntest_ndebug"
4416                                       "concept"
4417                                       "debugaligntest"
4418                                       "mpicollectivecommunication"
4419                                       "mpicollectivecommunication-mpi-2"
4420                                       "mpiguardtest"
4421                                       "mpiguardtest-mpi-2"
4422                                       "mpihelpertest"
4423                                       "mpihelpertest-mpi-2"
4424                                       "mpihelpertest2"
4425                                       "mpihelpertest2-mpi-2")
4426                                      "|")
4427                                     ")'"))
4428              #t)))))
4429     (inputs
4430      `(("gmp" ,gmp)
4431        ("metis" ,metis)
4432        ("openmpi" ,openmpi)
4433        ("openblas" ,openblas)
4434        ("python" ,python)
4435        ("superlu" ,superlu)))
4436     (native-inputs
4437      `(("gfortran" ,gfortran)
4438        ("pkg-config" ,pkg-config)))
4439     (home-page "https://dune-project.org/")
4440     (synopsis "Distributed and Unified Numerics Environment")
4441     (description "DUNE, the Distributed and Unified Numerics Environment is a
4442 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4443 grid-based methods.  It supports the easy implementation of methods like
4444 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4445 Differences} (FD).")
4446     ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2.
4447     (license license:gpl2)))
4448
4449 (define-public dune-geometry
4450   (package
4451     (name "dune-geometry")
4452     (version "2.6.0")
4453     (source
4454      (origin
4455        (method url-fetch)
4456        (uri (string-append "https://dune-project.org/download/"
4457                            version "/dune-geometry-" version ".tar.gz"))
4458        (sha256
4459         (base32
4460          "0hlaaxjyv9j05blasvb67sy02hd0w4g9znf68gdh3l731dd1aqbn"))))
4461     (build-system cmake-build-system)
4462     (arguments
4463      `(#:phases
4464        (modify-phases %standard-phases
4465          (add-after 'build 'build-tests
4466            (lambda* (#:key make-flags #:allow-other-keys)
4467              (apply invoke "make" "build_tests" make-flags))))))
4468     (inputs
4469      `(("dune-common" ,dune-common)
4470        ("openmpi" ,openmpi)
4471        ;; Optional
4472        ("openblas" ,openblas)
4473        ("gmp" ,gmp)
4474        ("python" ,python)))
4475     (native-inputs
4476      `(("gfortran" ,gfortran)
4477        ("pkg-config" ,pkg-config)))
4478     (home-page "https://dune-project.org/")
4479     (synopsis "Distributed and Unified Numerics Environment")
4480     (description "DUNE, the Distributed and Unified Numerics Environment is a
4481 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4482 grid-based methods.  It supports the easy implementation of methods like
4483 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4484 Differences} (FD).
4485
4486 This package contains the basic DUNE geometry classes.")
4487     ;; GPL version 2 with "runtime exception"
4488     (license license:gpl2)))
4489
4490 (define-public dune-grid
4491   (package
4492     (name "dune-grid")
4493     (version "2.6.0")
4494     (source
4495      (origin
4496        (method url-fetch)
4497        (uri (string-append "https://dune-project.org/download/"
4498                            version "/dune-grid-" version ".tar.gz"))
4499        (sha256
4500         (base32
4501          "1jp4vscm9yb9xg0lh7apzccfkhvgbnk652yahigmh3cvzpl4acd0"))))
4502     (build-system cmake-build-system)
4503     (arguments
4504      `(#:phases
4505        (modify-phases %standard-phases
4506          (add-after 'build 'build-tests
4507            (lambda* (#:key make-flags #:allow-other-keys)
4508              (apply invoke "make" "build_tests" make-flags)))
4509          ;; These tests fail because they require a fully functional MPI
4510          ;; environment.
4511          (add-after 'unpack 'disable-failing-tests
4512            (lambda _
4513              (setenv "ARGS"
4514                      (string-append "--exclude-regex '("
4515                                     (string-join
4516                                      (list
4517                                       "scsgmappertest"
4518                                       "conformvolumevtktest"
4519                                       "gnuplottest"
4520                                       "nonconformboundaryvtktest"
4521                                       "subsamplingvtktest"
4522                                       "vtktest"
4523                                       "vtktest-mpi-2"
4524                                       "vtksequencetest"
4525                                       "gmshtest-onedgrid"
4526                                       "test-dgf-yasp"
4527                                       "test-dgf-yasp-offset"
4528                                       "test-dgf-oned"
4529                                       "test-geogrid-yaspgrid"
4530                                       "test-gridinfo"
4531                                       "test-identitygrid"
4532                                       "testiteratorranges"
4533                                       "test-hierarchicsearch"
4534                                       "test-parallel-ug-mpi-2"
4535                                       "test-yaspgrid-backuprestore-equidistant"
4536                                       "test-yaspgrid-backuprestore-equidistant-mpi-2"
4537                                       "test-yaspgrid-backuprestore-equidistantoffset"
4538                                       "test-yaspgrid-backuprestore-equidistantoffset-mpi-2"
4539                                       "test-yaspgrid-backuprestore-tensor"
4540                                       "test-yaspgrid-backuprestore-tensor-mpi-2"
4541                                       "test-yaspgrid-tensorgridfactory"
4542                                       "test-yaspgrid-tensorgridfactory-mpi-2"
4543                                       "test-yaspgrid-yaspfactory-1d"
4544                                       "test-yaspgrid-yaspfactory-1d-mpi-2"
4545                                       "test-yaspgrid-yaspfactory-2d"
4546                                       "test-yaspgrid-yaspfactory-2d-mpi-2"
4547                                       "test-yaspgrid-yaspfactory-3d"
4548                                       "test-yaspgrid-yaspfactory-3d-mpi-2"
4549                                       "globalindexsettest"
4550                                       "persistentcontainertest"
4551                                       "structuredgridfactorytest"
4552                                       "tensorgridfactorytest"
4553                                       "vertexordertest")
4554                                      "|")
4555                                     ")'"))
4556              #t)))))
4557     (inputs
4558      `(("dune-common" ,dune-common)
4559        ("dune-geometry" ,dune-geometry)
4560        ("gmp" ,gmp)
4561        ("metis" ,metis)
4562        ("openblas" ,openblas)
4563        ("openmpi" ,openmpi)
4564        ("python" ,python)))
4565     (native-inputs
4566      `(("gfortran" ,gfortran)
4567        ("pkg-config" ,pkg-config)))
4568     (home-page "https://dune-project.org/")
4569     (synopsis "Distributed and Unified Numerics Environment")
4570     (description "DUNE, the Distributed and Unified Numerics Environment is a
4571 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4572 grid-based methods.  It supports the easy implementation of methods like
4573 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
4574 Differences} (FD).
4575
4576 This package contains the basic DUNE grid classes.")
4577     ;; GPL version 2 with "runtime exception"
4578     (license license:gpl2)))
4579
4580 (define-public dune-istl
4581   (package
4582     (name "dune-istl")
4583     (version "2.6.0")
4584     (source
4585      (origin
4586        (method url-fetch)
4587        (uri (string-append "https://dune-project.org/download/"
4588                            version "/dune-istl-" version ".tar.gz"))
4589        (sha256
4590         (base32
4591          "0l2gyrvys5w6wsmk0ckbb7295s80b7yk7qrl7x66akv2jv1nzq2w"))))
4592     (build-system cmake-build-system)
4593     (arguments
4594      `(#:phases
4595        (modify-phases %standard-phases
4596          (add-after 'build 'build-tests
4597            (lambda* (#:key make-flags #:allow-other-keys)
4598              (apply invoke "make" "build_tests" make-flags)))
4599          ;; These tests fail because they require a fully functional MPI
4600          ;; environment.
4601          (add-after 'unpack 'disable-failing-tests
4602            (lambda _
4603              (setenv "ARGS"
4604                      (string-append "--exclude-regex '("
4605                                     (string-join
4606                                      (list
4607                                       "galerkintest"
4608                                       "hierarchytest"
4609                                       "pamgtest"
4610                                       "pamg_comm_repart_test"
4611                                       "matrixredisttest"
4612                                       "vectorcommtest"
4613                                       "matrixmarkettest")
4614                                      "|")
4615                                     ")'"))
4616              #t)))))
4617     (inputs
4618      `(("dune-common" ,dune-common)
4619        ("openmpi" ,openmpi)
4620        ;; Optional
4621        ("metis" ,metis)
4622        ("superlu" ,superlu)
4623        ("openblas" ,openblas)
4624        ("gmp" ,gmp)
4625        ("python" ,python)))
4626     (native-inputs
4627      `(("gfortran" ,gfortran)
4628        ("pkg-config" ,pkg-config)))
4629     (home-page "https://dune-project.org/")
4630     (synopsis "Distributed and Unified Numerics Environment")
4631     (description "DUNE, the Distributed and Unified Numerics Environment is a
4632 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
4633 grid-based methods.
4634
4635 This is the iterative solver template library which provides generic sparse
4636 matrix/vector classes and a variety of solvers based on these classes.  A
4637 special feature is the use of templates to exploit the recursive block
4638 structure of finite element matrices at compile time.  Available solvers
4639 include Krylov methods, (block-) incomplete decompositions and
4640 aggregation-based algebraic multigrid.")
4641     ;; GPL version 2 with "runtime exception"
4642     (license license:gpl2)))
4643
4644 (define-public dune-localfunctions
4645   (package
4646     (name "dune-localfunctions")
4647     (version "2.6.0")
4648     (source
4649      (origin
4650        (method url-fetch)
4651        (uri (string-append "https://dune-project.org/download/"
4652                            version "/dune-localfunctions-" version ".tar.gz"))
4653        (sha256
4654         (base32
4655          "19c6zjinwwpy8jh4v4prhphyd438rapd4x80fj93apmwgw04nrhl"))))
4656     (build-system cmake-build-system)
4657     (arguments
4658      `(#:phases
4659        (modify-phases %standard-phases
4660          (add-after 'build 'build-tests
4661            (lambda* (#:key make-flags #:allow-other-keys)
4662              (apply invoke "make" "build_tests" make-flags))))))
4663     (inputs
4664      `(("dune-common" ,dune-common)
4665        ("dune-geometry" ,dune-geometry)
4666        ("openmpi" ,openmpi)
4667        ;; Optional
4668        ("metis" ,metis)
4669        ("superlu" ,superlu)
4670        ("gmp" ,gmp)))
4671     (native-inputs
4672      `(("gfortran" ,gfortran)
4673        ("pkg-config" ,pkg-config)))
4674     (home-page "https://dune-project.org/")
4675     (synopsis "Distributed and Unified Numerics Environment") ; TODO
4676     (description "This DUNE module provides interface and implementation for
4677 shape functions defined on the DUNE reference elements.  In addition to the
4678 shape function, interpolation operators and special keys are provided which
4679 can be used to assemble global function spaces on finite-element grids.
4680
4681 This package provides an interface and implementation for shape functions
4682 defined on the DUNE reference elements.  In addition to the shape function,
4683 interpolation operators and special keys are provided which can be used to
4684 assemble global function spaces on finite-element grids.")
4685     ;; GPL version 2 with "runtime exception"
4686     (license license:gpl2)))
4687
4688 (define-public dune-alugrid
4689   (package
4690     (name "dune-alugrid")
4691     (version "2.6.0")
4692     (source
4693      (origin
4694        (method url-fetch)
4695        (uri (string-append "https://dune-project.org/download/"
4696                            version "/dune-alugrid-" version ".tar.gz"))
4697        (sha256
4698         (base32
4699          "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj"))))
4700     (build-system cmake-build-system)
4701     (arguments
4702      `(#:tests? #f ; 7 of 8 tests fail because they need a full MPI
4703                    ; environment
4704        #:phases
4705        (modify-phases %standard-phases
4706          (add-after 'unpack 'patch-include
4707            (lambda _
4708              (substitute* "dune/alugrid/test/test-alugrid.cc"
4709                (("doc/grids/gridfactory/testgrids")
4710                 "doc/dune-grid/grids/gridfactory/testgrids"))
4711              #t))
4712          (add-after 'build 'build-tests
4713            (lambda* (#:key inputs make-flags #:allow-other-keys)
4714              (setenv "CPLUS_INCLUDE_PATH"
4715                      (string-append (assoc-ref inputs "dune-grid") "/share:"
4716                                     (getenv "CPLUS_INCLUDE_PATH")))
4717              (apply invoke "make" "build_tests" make-flags))))))
4718     (inputs
4719      `(("dune-common" ,dune-common)
4720        ("dune-geometry" ,dune-geometry)
4721        ("dune-grid" ,dune-grid)
4722        ("openmpi" ,openmpi)
4723        ;; Optional
4724        ("metis" ,metis)
4725        ("openblas" ,openblas)
4726        ("python" ,python)
4727        ("superlu" ,superlu)
4728        ("gmp" ,gmp)
4729        ("zlib" ,zlib)))
4730     (native-inputs
4731      `(("gfortran" ,gfortran)
4732        ("pkg-config" ,pkg-config)))
4733     (home-page "https://dune-project.org/")
4734     (synopsis "Distributed and Unified Numerics Environment")
4735     (description "ALUGrid is an adaptive, loadbalancing, unstructured
4736 implementation of the DUNE grid interface supporting either simplices or
4737 cubes.")
4738     (license license:gpl2+)))
4739
4740 (define-public dune-typetree
4741   (package
4742     (name "dune-typetree")
4743     (version "2.6.0")
4744     (source
4745      (origin
4746        (method git-fetch)
4747        (uri (git-reference
4748              (url "https://gitlab.dune-project.org/staging/dune-typetree.git")
4749              (commit (string-append "v" version))))
4750        (file-name (git-file-name name version))
4751        (sha256
4752         (base32
4753          "0mnv6w2f22lz3j4bdpdjq55vjm8xxfx9v4vvhg9bd36xpsbjpjp9"))))
4754     (build-system cmake-build-system)
4755     (arguments
4756      `(#:phases
4757        (modify-phases %standard-phases
4758          (add-after 'build 'build-tests
4759            (lambda* (#:key make-flags #:allow-other-keys)
4760              (apply invoke "make" "build_tests" make-flags))))))
4761     (inputs
4762      `(("dune-common" ,dune-common)
4763        ("openmpi" ,openmpi)
4764        ;; Optional
4765        ("openblas" ,openblas)
4766        ("python" ,python)
4767        ("metis" ,metis)
4768        ("superlu" ,superlu)
4769        ("gmp" ,gmp)))
4770     (native-inputs
4771      `(("gfortran" ,gfortran)
4772        ("pkg-config" ,pkg-config)))
4773     (home-page "https://dune-project.org/")
4774     (synopsis "Distributed and Unified Numerics Environment")
4775     (description "TypeTree is a template library for constructing and
4776 operating on statically typed trees of objects.")
4777     ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4778     (license (list license:lgpl3+ license:gpl2))))
4779
4780 (define-public dune-functions
4781   (package
4782     (name "dune-functions")
4783     (version "2.6.0")
4784     (source
4785      (origin
4786        (method git-fetch)
4787        (uri (git-reference
4788              (url "https://gitlab.dune-project.org/staging/dune-functions.git")
4789              (commit (string-append "v" version))))
4790        (file-name (git-file-name name version))
4791        (sha256
4792         (base32
4793          "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200"))))
4794     (build-system cmake-build-system)
4795     (arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid
4796     (inputs
4797      `(("dune-common" ,dune-common)
4798        ("dune-istl" ,dune-istl)
4799        ("dune-localfunctions" ,dune-localfunctions)
4800        ("dune-grid" ,dune-grid)
4801        ("dune-geometry" ,dune-geometry)
4802        ("dune-typetree" ,dune-typetree)
4803        ("openmpi" ,openmpi)
4804        ("openblas" ,openblas)
4805        ("metis" ,metis)
4806        ("python" ,python)
4807        ("superlu" ,superlu)
4808        ("gmp" ,gmp)))
4809     (native-inputs
4810      `(("gfortran" ,gfortran)
4811        ("pkg-config" ,pkg-config)))
4812     (home-page "https://dune-project.org/")
4813     (synopsis "Distributed and Unified Numerics Environment")
4814     (description "The dune-functions module provides an abstraction layer for
4815 global finite element functions.  Its two main concepts are functions
4816 implemented as callable objects, and bases of finite element spaces.")
4817     ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4818     (license (list license:lgpl3+ license:gpl2))))
4819
4820 (define-public dune-pdelab
4821   (package
4822     (name "dune-pdelab")
4823     (version "2.6.0-rc1")
4824     (source
4825      (origin
4826        (method git-fetch)
4827        (uri (git-reference
4828              (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
4829              (commit (string-append "v" version))))
4830        (file-name (git-file-name name version))
4831        (sha256
4832         (base32
4833          "07g0s9448z65vjrq88g5rv3340iifil85k170n8kbqchsvi4ny5v"))))
4834     (build-system cmake-build-system)
4835     (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
4836     (inputs
4837      `(("dune-common" ,dune-common)
4838        ("dune-istl" ,dune-istl)
4839        ("dune-localfunctions" ,dune-localfunctions)
4840        ("dune-geometry" ,dune-geometry)
4841        ("dune-grid" ,dune-grid)
4842        ("dune-typetree" ,dune-typetree)
4843        ("dune-functions" ,dune-functions)
4844        ("openmpi" ,openmpi)
4845        ;; Optional
4846        ("openblas" ,openblas)
4847        ("eigen" ,eigen)
4848        ("metis" ,metis)
4849        ("python" ,python)
4850        ("superlu" ,superlu)
4851        ("gmp" ,gmp)))
4852     (native-inputs
4853      `(("gfortran" ,gfortran)
4854        ("pkg-config" ,pkg-config)))
4855     (home-page "https://dune-project.org/")
4856     (synopsis "Differential equations solver toolbox")
4857     (description "PDELab is a partial differential equations solver toolbox
4858 built on top of DUNE, the Distributed and Unified Numerics Environment.")
4859     ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
4860     (license (list license:lgpl3+ license:gpl2))))
4861
4862 (define-public mlucas
4863   (package
4864     (name "mlucas")
4865     (version "18")
4866     (source
4867      (origin
4868        (method url-fetch)
4869        (uri (string-append
4870              "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz"))
4871        (sha256
4872         (base32
4873          "1ax12qj9lyvnx4vs3gx7l8r3wx5gjbsdswp5f00ik9z0wz7xf297"))))
4874     (build-system gnu-build-system)
4875     (inputs
4876      `(("python2" ,python-2)))
4877     (arguments
4878      `(#:tests? #f ; no tests
4879        #:phases
4880        (modify-phases %standard-phases
4881          (replace 'configure
4882            (lambda _
4883              (chdir "src")
4884              (call-with-output-file "Makefile"
4885                (lambda (port)
4886                  (format port "CC = gcc
4887 CFLAGS = -O3 ~a -DUSE_THREADS
4888 LDLIBS = -lm -lpthread -lrt
4889 Mlucas: $(addsuffix .o,$(basename $(wildcard *.c)))
4890 "
4891                          ,(let ((system (or (%current-target-system)
4892                                             (%current-system))))
4893                             (cond
4894                              ((string-prefix? "x86_64" system) "-DUSE_SSE2")
4895                              (else ""))))))
4896              #t))
4897          (replace 'install
4898            (lambda* (#:key outputs #:allow-other-keys)
4899              (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
4900                (install-file "Mlucas" bin)
4901                (install-file "primenet.py" bin))
4902              #t)))))
4903     (home-page "https://www.mersenne.org")
4904     (synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client")
4905     (description "Mlucas performs Lucas-Lehmer primality testing of Mersenne
4906 numbers in search of a world-record prime.  You may use it to test any
4907 suitable number as you wish, but it is preferable that you do so in a
4908 coordinated fashion, as part of the Great Internet Mersenne Prime
4909 Search (GIMPS).  Mlucas also includes a simple Python script for assignment
4910 management via the GIMPS project's Primenet server.")
4911     (license license:gpl2+)))