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 Eric Bavier <bavier@member.fsf.org>
   6 ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
   7 ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
   8 ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
   9 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
  10 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
  11 ;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
  12 ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
  13 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
  14 ;;; Copyright © 2016 Kei Kebreau <kei@openmailbox.org>
  15 ;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
  16 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
  17 ;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be>
  18 ;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>
  19 ;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net>
  20 ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
  21 ;;; Copyright © 2017 Theodoros Foradis <theodoros.for@openmailbox.org>
  22 ;;;
  23 ;;; This file is part of GNU Guix.
  24 ;;;
  25 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  26 ;;; under the terms of the GNU General Public License as published by
  27 ;;; the Free Software Foundation; either version 3 of the License, or (at
  28 ;;; your option) any later version.
  29 ;;;
  30 ;;; GNU Guix is distributed in the hope that it will be useful, but
  31 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  32 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  33 ;;; GNU General Public License for more details.
  34 ;;;
  35 ;;; You should have received a copy of the GNU General Public License
  36 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  37
  38 (define-module (gnu packages maths)
  39   #:use-module (ice-9 regex)
  40   #:use-module (gnu packages)
  41   #:use-module ((guix licenses) #:prefix license:)
  42   #:use-module (guix packages)
  43   #:use-module (guix download)
  44   #:use-module (guix git-download)
  45   #:use-module (guix utils)
  46   #:use-module (guix build utils)
  47   #:use-module (guix build-system cmake)
  48   #:use-module (guix build-system gnu)
  49   #:use-module (guix build-system ocaml)
  50   #:use-module (guix build-system r)
  51   #:use-module (gnu packages algebra)
  52   #:use-module (gnu packages autotools)
  53   #:use-module (gnu packages bison)
  54   #:use-module (gnu packages boost)
  55   #:use-module (gnu packages check)
  56   #:use-module (gnu packages cmake)
  57   #:use-module (gnu packages compression)
  58   #:use-module (gnu packages curl)
  59   #:use-module (gnu packages cyrus-sasl)
  60   #:use-module (gnu packages documentation)
  61   #:use-module (gnu packages elf)
  62   #:use-module (gnu packages flex)
  63   #:use-module (gnu packages fltk)
  64   #:use-module (gnu packages fontutils)
  65   #:use-module (gnu packages gettext)
  66   #:use-module (gnu packages gcc)
  67   #:use-module (gnu packages gd)
  68   #:use-module (gnu packages ghostscript)
  69   #:use-module (gnu packages graphviz)
  70   #:use-module (gnu packages gtk)
  71   #:use-module (gnu packages image)
  72   #:use-module (gnu packages less)
  73   #:use-module (gnu packages lisp)
  74   #:use-module (gnu packages logging)
  75   #:use-module (gnu packages lua)
  76   #:use-module (gnu packages gnome)
  77   #:use-module (gnu packages guile)
  78   #:use-module (gnu packages xorg)
  79   #:use-module (gnu packages gl)
  80   #:use-module (gnu packages imagemagick)
  81   #:use-module (gnu packages m4)
  82   #:use-module (gnu packages mpi)
  83   #:use-module (gnu packages multiprecision)
  84   #:use-module (gnu packages netpbm)
  85   #:use-module (gnu packages ocaml)
  86   #:use-module (gnu packages pcre)
  87   #:use-module (gnu packages popt)
  88   #:use-module (gnu packages perl)
  89   #:use-module (gnu packages pkg-config)
  90   #:use-module (gnu packages python)
  91   #:use-module (gnu packages readline)
  92   #:use-module (gnu packages tbb)
  93   #:use-module (gnu packages scheme)
  94   #:use-module (gnu packages shells)
  95   #:use-module (gnu packages tcl)
  96   #:use-module (gnu packages texinfo)
  97   #:use-module (gnu packages tex)
  98   #:use-module (gnu packages tls)
  99   #:use-module (gnu packages wxwidgets)
 100   #:use-module (gnu packages xml)
 101   #:use-module (srfi srfi-1))
 102
 103 (define-public aris
 104   (package
 105     (name "aris")
 106     (version "2.2")
 107     (source (origin
 108               (method url-fetch)
 109               (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
 110               (sha256 (base32
 111                        "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
 112     (build-system gnu-build-system)
 113     (inputs `(("gtk+" ,gtk+)
 114               ("libxml2" ,libxml2)))
 115     (native-inputs `(("pkg-config" ,pkg-config)))
 116     (synopsis "Natural deduction first-order logic interface")
 117     (description "Aris is a program for performing logical proofs.  It supports
 118 propositional and predicate logic, as well as Boolean algebra and
 119 arithmetical logic.  In addition to its predefined inference and equivalence
 120 rules, Aris also supports references to older proofs.  Its use of standard
 121 logical symbols and its natural deduction interface make it easy to use for
 122 beginners.")
 123     (license license:gpl3+)
 124     (home-page "https://www.gnu.org/software/aris/")))
 125
 126 (define-public c-graph
 127   (package
 128    (name "c-graph")
 129    (version "2.0")
 130    (source (origin
 131             (method url-fetch)
 132             (uri (string-append "mirror://gnu/c-graph/c-graph-" version
 133                                 ".tar.gz"))
 134             (sha256 (base32
 135                      "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
 136    (build-system gnu-build-system)
 137    (inputs
 138      `(("fortran" ,gfortran)))
 139    (synopsis "Visualizing and demonstrating convolution")
 140    (description
 141      "GNU C-Graph is a tool for demonstrating the theory of convolution.
 142 Thus, it can serve as an excellent aid to students of signal and systems
 143 theory in visualizing the convolution process.  Rather than forcing the
 144 student to write code, the program offers an intuitive interface with
 145 interactive dialogs to guide them.")
 146    (license license:gpl3+)
 147    (home-page "https://www.gnu.org/software/c-graph/")))
 148
 149 (define-public coda
 150   (package
 151     (name "coda")
 152     (version "2.18")
 153     (source
 154      (origin
 155        (method url-fetch)
 156        (uri (string-append "https://github.com/stcorp/coda/releases/download/"
 157                            version "/coda-" version ".tar.gz"))
 158        (sha256
 159         (base32 "11asla1ap8vd73farqjlpb179sfiy0biydcwxjfcakrp9sf8v9bs"))
 160        (patches (search-patches "coda-use-system-libs.patch"))
 161        (modules '((guix build utils)))
 162        (snippet
 163         ;; Make sure we don't use the bundled software.
 164         '(for-each (lambda (d)
 165                      (delete-file-recursively (string-append "libcoda/" d)))
 166                    '("zlib" "pcre" "expat")))))
 167     (native-inputs
 168      `(("fortran" ,gfortran)
 169        ("python" ,python)
 170        ("python-numpy" ,python-numpy)))
 171     (inputs
 172      `(("zlib" ,zlib)
 173        ("pcre" ,pcre)
 174        ("expat" ,expat)
 175        ("hdf4" ,hdf4-alt)
 176        ("hdf5" ,hdf5)))
 177     (build-system gnu-build-system)
 178     (arguments
 179      '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
 180                            "LIBS= -lz -lpcre -lexpat")))
 181     (synopsis "A common interface to various earth observation data formats")
 182     (description
 183      "The Common Data Access toolbox (CODA) provides a set of interfaces for
 184 reading remote sensing data from earth observation data files.  It consists of
 185 command line applications and interfaces to the C, Fortran, Python, and Java
 186 programming languages.")
 187     (home-page "https://stcorp.nl/coda")
 188     (license license:gpl2+)))
 189
 190 (define-public units
 191   (package
 192    (name "units")
 193    (version "2.14")
 194    (source (origin
 195             (method url-fetch)
 196             (uri (string-append "mirror://gnu/units/units-" version
 197                                 ".tar.gz"))
 198             (sha256 (base32
 199                      "1s421bxm36akjsy3qzg6da1d1g20gh094ac2slqxipgkh8yqjcwx"))))
 200    (build-system gnu-build-system)
 201    (synopsis "Conversion between thousands of scales")
 202    (description
 203     "GNU Units converts numeric quantities between units of measure.  It
 204 can handle scale changes through adaptive usage of standard scale
 205 prefixes (micro-, kilo-, etc.).  It can also handle nonlinear
 206 conversions such as Fahrenheit to Celsius.  Its interpreter is powerful
 207 enough to be used effectively as a scientific calculator.")
 208    (license license:gpl3+)
 209    (home-page "https://www.gnu.org/software/units/")))
 210
 211 (define-public double-conversion
 212   (package
 213     (name "double-conversion")
 214     (version "1.1.5")
 215     (source (origin
 216               (method url-fetch)
 217               (uri (string-append
 218                     "https://github.com/floitsch/double-conversion/archive/v"
 219                     version ".tar.gz"))
 220               (file-name (string-append name "-" version ".tar.gz"))
 221               (sha256
 222                (base32
 223                 "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83"))))
 224     (build-system cmake-build-system)
 225     (arguments
 226      '(#:test-target "test"
 227        #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
 228                            "-DBUILD_TESTING=ON")))
 229     (home-page "https://github.com/floitsch/double-conversion")
 230     (synopsis "Conversion routines for IEEE doubles")
 231     (description
 232      "The double-conversion library provides binary-decimal and decimal-binary
 233 routines for IEEE doubles.  The library consists of efficient conversion
 234 routines that have been extracted from the V8 JavaScript engine.")
 235     (license license:bsd-3)))
 236
 237 (define-public dionysus
 238   (package
 239     (name "dionysus")
 240     (version "1.3.0")
 241     (source (origin
 242               (method url-fetch)
 243               (uri (string-append "mirror://gnu/dionysus/dionysus-" version
 244                                   ".tar.gz"))
 245               (sha256
 246                (base32
 247                 "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs"))))
 248     (build-system gnu-build-system)
 249     (inputs `(("tcl" ,tcl)))                      ;for 'tclsh'
 250     (synopsis "Local search for universal constants and scientific values")
 251     (description
 252      "GNU Dionysus is a convenient system for quickly retrieving the values of
 253 mathematical constants used in science and engineering.  Values can be
 254 searched using a simple command-line tool, choosing from three databases:
 255 universal constants, atomic numbers, and constants related to
 256 semiconductors.")
 257     (license license:gpl3+)
 258     (home-page "https://www.gnu.org/software/dionysus/")))
 259
 260 (define-public gsl
 261   (package
 262     (name "gsl")
 263     (version "2.4")
 264     (source (origin
 265               (method url-fetch)
 266               (uri (string-append "mirror://gnu/gsl/gsl-"
 267                                   version ".tar.gz"))
 268               (sha256
 269                (base32
 270                 "16yfs5n444s03np1naj6yp1fsysd42kdscxzkg0k2yvfjixx0ijd"))
 271               (patches (search-patches "gsl-test-i686.patch"))))
 272     (build-system gnu-build-system)
 273     (arguments
 274      `(;; Currently there are numerous tests that fail on "exotic"
 275        ;; architectures such as aarch64 and ppc64le.
 276        ,@(if (string-prefix? "aarch64-linux"
 277                              (or (%current-target-system) (%current-system)))
 278            '(#:tests? #f)
 279            '())))
 280     (home-page "https://www.gnu.org/software/gsl/")
 281     (synopsis "Numerical library for C and C++")
 282     (description
 283      "The GNU Scientific Library is a library for numerical analysis in C
 284 and C++.  It includes a wide range of mathematical routines, with over 1000
 285 functions in total.  Subject areas covered by the library include:
 286 differential equations, linear algebra, Fast Fourier Transforms and random
 287 numbers.")
 288     (license license:gpl3+)))
 289
 290 (define-public ocaml-gsl
 291   (package
 292     (name "ocaml-gsl")
 293     (version "1.19.3")
 294     (source
 295      (origin
 296        (method url-fetch)
 297        (uri
 298         (string-append
 299          "https://github.com/mmottl/gsl-ocaml/releases/download/v"
 300          version"/gsl-ocaml-" version ".tar.gz"))
 301        (sha256
 302         (base32
 303          "0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh"))))
 304     (build-system ocaml-build-system)
 305     (inputs
 306      `(("gsl" ,gsl)))
 307     (home-page "https://mmottl.github.io/gsl-ocaml")
 308     (synopsis "Bindings to the GNU Scientific Library")
 309     (description
 310      "GSL-OCaml is an interface to the @dfn{GNU scientific library} (GSL) for
 311 the OCaml language.")
 312     (license license:gpl3+)))
 313
 314 (define-public ocaml4.01-gsl
 315   (package-with-ocaml4.01 ocaml-gsl))
 316
 317 (define-public glpk
 318   (package
 319     (name "glpk")
 320     (version "4.63")
 321     (source
 322      (origin
 323       (method url-fetch)
 324       (uri (string-append "mirror://gnu/glpk/glpk-"
 325                           version ".tar.gz"))
 326       (sha256
 327        (base32
 328         "1xp7nclmp8inp20968bvvfcwmz3mz03sbm0v3yjz8aqwlpqjfkci"))))
 329     (build-system gnu-build-system)
 330     (inputs
 331      `(("gmp" ,gmp)))
 332     (arguments
 333      `(#:configure-flags '("--with-gmp")))
 334     (home-page "https://www.gnu.org/software/glpk/")
 335     (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
 336     (description
 337      "GLPK is a C library for solving large-scale linear programming (LP),
 338 mixed integer programming (MIP), and other related problems.  It supports the
 339 GNU MathProg modeling language, a subset of the AMPL language, and features a
 340 translator for the language.  In addition to the C library, a stand-alone
 341 LP/MIP solver is included in the package.")
 342     (license license:gpl3+)))
 343
 344 (define-public 4ti2
 345   (package
 346     (name "4ti2")
 347     (version "1.6.7")
 348     (source
 349      (origin
 350       (method url-fetch)
 351       (uri (string-append "http://www.4ti2.de/version_" version
 352                           "/4ti2-" version ".tar.gz"))
 353       (sha256
 354        (base32
 355         "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
 356     (build-system gnu-build-system)
 357     (native-inputs
 358      `(("which" ,(@ (gnu packages base) which)))) ; for the tests
 359     (inputs
 360      `(("glpk" ,glpk)
 361        ("gmp" ,gmp)))
 362     (home-page "http://www.4ti2.de/")
 363     (synopsis "Mathematical tool suite for problems on linear spaces")
 364     (description
 365      "4ti2 implements algorithms for solving algebraic, geometric and
 366 combinatorial problems on linear spaces.  Among others, it solves systems
 367 of linear equations, computes extreme rays of polyhedral cones, solves
 368 integer programming problems and computes Markov bases for statistics.")
 369     (license license:gpl2+)))
 370
 371 (define-public cddlib
 372   (package
 373     (name "cddlib")
 374     (version "0.94h")
 375     (source
 376      (origin
 377       (method url-fetch)
 378       (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
 379                           (string-delete #\. version) ".tar.gz"))
 380       (sha256
 381        (base32
 382         "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy"))))
 383     (build-system gnu-build-system)
 384     (inputs
 385      `(("gmp" ,gmp)))
 386     (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
 387     (synopsis "Library for convex hulls and extreme rays of polyhedra")
 388     (description
 389      "The C-library cddlib implements the Double Description Method of
 390 Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
 391 rays of a general convex polyhedron given by a system of linear inequalities
 392 in arbitrary dimension.  It can also be used for the converse operation of
 393 computing convex hulls.")
 394     (license license:gpl2+)))
 395
 396 (define-public arpack-ng
 397   (package
 398     (name "arpack-ng")
 399     (version "3.2.0")
 400     (source
 401      (origin
 402        (method url-fetch)
 403        (uri (string-append "https://github.com/opencollab/arpack-ng/archive/"
 404                            version ".tar.gz"))
 405        (file-name (string-append name "-" version ".tar.gz"))
 406        (sha256
 407         (base32
 408          "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff"))))
 409     (build-system gnu-build-system)
 410     (home-page "https://github.com/opencollab/arpack-ng")
 411     (inputs
 412      `(("lapack" ,lapack)
 413        ("fortran" ,gfortran)))
 414     (synopsis "Fortran subroutines for solving eigenvalue problems")
 415     (description
 416      "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
 417 large scale eigenvalue problems.")
 418     (license (license:non-copyleft "file://COPYING"
 419                                 "See COPYING in the distribution."))))
 420
 421 (define-public arpack-ng-openmpi
 422   (package (inherit arpack-ng)
 423     (name "arpack-ng-openmpi")
 424     (inputs
 425      `(("mpi" ,openmpi)
 426        ,@(package-inputs arpack-ng)))
 427     (arguments `(#:configure-flags '("--enable-mpi")))
 428     (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
 429
 430 (define-public lapack
 431   (package
 432     (name "lapack")
 433     (version "3.7.1")
 434     (source
 435      (origin
 436       (method url-fetch)
 437       (uri (string-append "http://www.netlib.org/lapack/lapack-"
 438                           version ".tgz"))
 439       (sha256
 440        (base32
 441         "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
 442     (build-system cmake-build-system)
 443     (home-page "http://www.netlib.org/lapack/")
 444     (inputs `(("fortran" ,gfortran)
 445               ("python" ,python-2)))
 446     (arguments
 447      `(#:configure-flags (list
 448                           ;; Install to PREFIX/lib (the default is
 449                           ;; PREFIX/lib64).
 450                           (string-append "-DCMAKE_INSTALL_LIBDIR="
 451                                          (assoc-ref %outputs "out")
 452                                          "/lib")
 453
 454                           "-DBUILD_SHARED_LIBS:BOOL=YES"
 455                           "-DLAPACKE=ON"
 456
 457                           ;; Build the 'LAPACKE_clatms' functions.
 458                           "-DLAPACKE_WITH_TMG=ON")
 459        #:phases (alist-cons-before
 460                  'check 'patch-python
 461                  (lambda* (#:key inputs #:allow-other-keys)
 462                    (let ((python (assoc-ref inputs "python")))
 463                      (substitute* "lapack_testing.py"
 464                        (("/usr/bin/env python") python))))
 465                   %standard-phases)))
 466     (synopsis "Library for numerical linear algebra")
 467     (description
 468      "LAPACK is a Fortran 90 library for solving the most commonly occurring
 469 problems in numerical linear algebra.")
 470     (license (license:non-copyleft "file://LICENSE"
 471                                 "See LICENSE in the distribution."))))
 472
 473 (define-public scalapack
 474   (package
 475     (name "scalapack")
 476     (version "2.0.2")
 477     (source
 478      (origin
 479        (method url-fetch)
 480        (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
 481                            version ".tgz"))
 482        (sha256
 483         (base32
 484          "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
 485     (build-system cmake-build-system)
 486     (inputs
 487      `(("mpi" ,openmpi)
 488        ("fortran" ,gfortran)
 489        ("lapack" ,lapack)))             ;for testing only
 490     (arguments
 491      `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")))
 492     (home-page "http://www.netlib.org/scalapack/")
 493     (synopsis "Library for scalable numerical linear algebra")
 494     (description
 495      "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
 496 routines on parallel distributed memory machines.  ScaLAPACK solves dense and
 497 banded linear systems, least squares problems, eigenvalue problems, and
 498 singular value problems.")
 499     (license (license:bsd-style "file://LICENSE"
 500                                 "See LICENSE in the distribution."))))
 501
 502 (define-public gnuplot
 503   (package
 504     (name "gnuplot")
 505     (version "5.0.6")
 506     (source (origin
 507               (method url-fetch)
 508               (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
 509                                   version "/gnuplot-"
 510                                   version ".tar.gz"))
 511        (sha256
 512         (base32
 513          "0q5lr6nala3ln6f3yp6g17ziymb9r9gx9zylnw1y3hjmwl9lggjv"))))
 514     (build-system gnu-build-system)
 515     (inputs `(("readline" ,readline)
 516               ("cairo" ,cairo)
 517               ("pango" ,pango)
 518               ("gd" ,gd)
 519               ("lua" ,lua)))
 520     (native-inputs
 521      `(("pkg-config" ,pkg-config)
 522        ("texlive" ,texlive-tiny)))
 523     (home-page "http://www.gnuplot.info")
 524     (synopsis "Command-line driven graphing utility")
 525     (description "Gnuplot is a portable command-line driven graphing
 526 utility.  It was originally created to allow scientists and students to
 527 visualize mathematical functions and data interactively, but has grown to
 528 support many non-interactive uses such as web scripting.  It is also used as a
 529 plotting engine by third-party applications like Octave.")
 530     ;;  X11 Style with the additional restriction that derived works may only be
 531     ;;  distributed as patches to the original.
 532     (license (license:fsf-free
 533               "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
 534
 535 (define-public gctp
 536   (package
 537     (name "gctp")
 538     (version "2.0.0")
 539     (source
 540      (origin
 541        (method url-fetch)
 542        (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
 543                            version ".tar.gz"))
 544        (file-name (string-append name "-" version ".tar.gz"))
 545        (sha256
 546         (base32
 547          "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
 548     (native-inputs
 549      `(("fortran" ,gfortran)))
 550     (build-system gnu-build-system)
 551     (synopsis "General Cartographic Transformation Package (GCTP)")
 552     (description
 553      "The General Cartographic Transformation Package (GCTP) is a system of
 554 software routines designed to permit the transformation of coordinate pairs
 555 from one map projection to another.  The GCTP is the standard computer
 556 software used by the National Mapping Division for map projection
 557 computations.")
 558     (home-page "https://github.com/OkoSanto/GCTP")
 559     (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
 560
 561 (define-public hdf4
 562   (package
 563     (name "hdf4")
 564     (version "4.2.13")
 565     (source
 566      (origin
 567        (method url-fetch)
 568        (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
 569                            version "/src/hdf-" version ".tar.bz2"))
 570        (sha256
 571         (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm"))
 572        (patches (search-patches "hdf4-architectures.patch"
 573                                 "hdf4-reproducibility.patch"
 574                                 "hdf4-shared-fortran.patch"))))
 575     (build-system gnu-build-system)
 576     (native-inputs
 577      `(("gfortran" ,gfortran)
 578        ("bison" ,bison)
 579        ("flex" ,flex)))
 580     (inputs
 581      `(("zlib" ,zlib)
 582        ("libjpeg" ,libjpeg)))
 583     (arguments
 584      `(#:parallel-tests? #f
 585        #:configure-flags '("--enable-shared")
 586        #:phases
 587        (modify-phases %standard-phases
 588          (add-before 'configure 'patchbuild
 589            (lambda _
 590              (substitute*
 591                  '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
 592                (("/bin/rm") "rm")
 593                (("/bin/mkdir") "mkdir"))
 594              (substitute* (find-files "." "^Makefile\\.in$")
 595                (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
 596 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
 597                (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
 598 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
 599 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")))))))
 600     (home-page "https://www.hdfgroup.org/products/hdf4/")
 601     (synopsis
 602      "Library and multi-object file format for storing and managing data")
 603     (description "HDF4 is a library and multi-object file format for storing
 604 and managing data between machines.  HDF4 is an older hierarchical data format,
 605 incompatible with HDF5.")
 606     (license
 607      (license:non-copyleft
 608       "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
 609
 610 (define-public hdf4-alt
 611   (package
 612     (inherit hdf4)
 613     (name "hdf4-alt")
 614     (arguments
 615      (substitute-keyword-arguments (package-arguments hdf4)
 616        ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
 617     (synopsis
 618      "HDF4 without netCDF API, can be combined with the regular netCDF library")))
 619
 620 (define-public hdf5
 621   (package
 622     (name "hdf5")
 623     (version "1.8.19")
 624     (source
 625      (origin
 626       (method url-fetch)
 627       (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
 628                                 "hdf5-" (version-major+minor version)
 629                                 "/hdf5-" version "/src/hdf5-"
 630                                 version ".tar.bz2")
 631                  (string-append "https://support.hdfgroup.org/ftp/HDF5/"
 632                                 "current"
 633                                 (apply string-append
 634                                        (take (string-split version #\.) 2))
 635                                 "/src/hdf5-" version ".tar.bz2")))
 636       (sha256
 637        (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
 638       (patches (list (search-patch "hdf5-config-date.patch")))))
 639     (build-system gnu-build-system)
 640     (inputs
 641      `(("zlib" ,zlib)))
 642     (arguments
 643      `(;; Some of the users, notably Flann, need the C++ interface.
 644        #:configure-flags '("--enable-cxx")
 645
 646        #:phases
 647        (modify-phases %standard-phases
 648          (add-before 'configure 'patch-configure
 649            (lambda _
 650              (substitute* "configure"
 651                (("/bin/mv") "mv"))
 652              #t))
 653          (add-after 'install 'patch-references
 654            (lambda* (#:key inputs outputs #:allow-other-keys)
 655              (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
 656                    (zlib (assoc-ref inputs "zlib")))
 657                (substitute* (find-files bin "h5p?cc")
 658                  (("-lz" lib)
 659                   (string-append "-L" zlib "/lib " lib)))
 660                #t))))))
 661     (home-page "http://www.hdfgroup.org")
 662     (synopsis "Management suite for extremely large and complex data")
 663     (description "HDF5 is a suite that makes possible the management of
 664 extremely large and complex data collections.")
 665     (license (license:x11-style
 666               "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
 667
 668 (define-public hdf-eos2
 669   (package
 670     (name "hdf-eos2")
 671     (version "19.1.0")
 672     (source
 673      (origin
 674        (method url-fetch)
 675        (uri "ftp://edhs1.gsfc.nasa.gov\
 676 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
 677        (sha256
 678         (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
 679        (patches (search-patches "hdf-eos2-remove-gctp.patch"
 680                                 "hdf-eos2-build-shared.patch"
 681                                 "hdf-eos2-fortrantests.patch"))))
 682     (build-system gnu-build-system)
 683     (native-inputs
 684      `(("gfortran" ,gfortran)))
 685     (inputs
 686      `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
 687        ("zlib" ,zlib)
 688        ("libjpeg" ,libjpeg)
 689        ("gctp" ,gctp)))
 690     (arguments
 691      `( #:configure-flags '("--enable-install-include" "--enable-shared"
 692                             "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
 693         #:parallel-tests? #f))
 694     (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
 695     (synopsis "HDF4-based data format for NASA's Earth Observing System")
 696     (description "HDF-EOS2 is a software library built on HDF4 which supports
 697 the construction of data structures used in NASA's Earth Observing
 698 System (Grid, Point and Swath).")
 699
 700     ;; Source files carry a permissive license header.
 701     (license (license:non-copyleft home-page))))
 702
 703 (define-public hdf-eos5
 704   (package
 705     (name "hdf-eos5")
 706     (version "1.15")
 707     (source (origin
 708               (method url-fetch)
 709               (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
 710 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
 711               (sha256
 712                (base32
 713                 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
 714               (patches (search-patches "hdf-eos5-build-shared.patch"
 715                                        "hdf-eos5-remove-gctp.patch"
 716                                        "hdf-eos5-fix-szip.patch"
 717                                        "hdf-eos5-fortrantests.patch"))))
 718     (native-inputs
 719      `(("gfortran" ,gfortran)))
 720     (build-system gnu-build-system)
 721     (inputs
 722      `(("hdf5" ,hdf5)
 723        ("zlib" ,zlib)
 724        ("gctp" ,gctp)))
 725     (arguments
 726      `(#:configure-flags '("--enable-install-include" "--enable-shared"
 727                            "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
 728        #:parallel-tests? #f))
 729     (synopsis "HDF5-based data format for NASA's Earth Observing System")
 730     (description
 731      "HDF-EOS5 is a software library built on HDF5 to support the construction
 732 of data structures used in NASA's Earth Observing System (Grid, Point and
 733 Swath).")
 734     (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
 735
 736     ;; Source files carry a permissive license header.
 737     (license (license:non-copyleft home-page))))
 738
 739 (define-public hdf5-parallel-openmpi
 740   (package (inherit hdf5)
 741     (name "hdf5-parallel-openmpi")
 742     (inputs
 743      `(("mpi" ,openmpi)
 744        ,@(package-inputs hdf5)))
 745     (arguments
 746      (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
 747                                      ,@(package-arguments hdf5))
 748        ((#:phases phases)
 749         `(modify-phases ,phases
 750            (add-before 'check 'patch-tests
 751              (lambda _
 752                ;; OpenMPI's mpirun will exit with non-zero status if it
 753                ;; detects an "abnormal termination", i.e. any process not
 754                ;; calling MPI_Finalize().  Since the test is explicitely
 755                ;; avoiding MPI_Finalize so as not to have at_exit and thus
 756                ;; H5C_flush_cache from being called, mpirun will always
 757                ;; complain, so turn this test off.
 758                (substitute* "testpar/Makefile"
 759                  (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
 760                   (string-append front back "\n")))
 761                (substitute* "tools/h5diff/testph5diff.sh"
 762                  (("/bin/sh") (which "sh")))
 763                #t))))))
 764     (synopsis "Management suite for data with parallel IO support")))
 765
 766 (define-public h5check
 767   (package
 768     (name "h5check")
 769     (version "2.0.1")
 770     (source
 771      (origin
 772        (method url-fetch)
 773        (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
 774                            "h5check/src/h5check-" version ".tar.gz"))
 775        (sha256
 776         (base32
 777          "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
 778     (build-system gnu-build-system)
 779     (inputs `(("hdf5" ,hdf5)))                 ;h5cc for tests
 780     (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
 781     (synopsis "HDF5 format checker")
 782     (description "@code{h5check} is a validation tool for verifying that an
 783 HDF5 file is encoded according to the HDF File Format Specification.")
 784     (license (license:x11-style "file://COPYING"))))
 785
 786 (define-public itpp
 787   (package
 788     (name "itpp")
 789     (version "4.3.1")
 790     (source (origin
 791               (method url-fetch)
 792               (uri (string-append "mirror://sourceforge/itpp/itpp/"
 793                                   version "/itpp-"
 794                                   version ".tar.gz"))
 795        (sha256
 796         (base32
 797          "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
 798     (build-system cmake-build-system)
 799     (arguments `(#:tests? #f)) ; Tests require googletest *sources*
 800     (inputs `(("lapack" ,lapack)
 801               ("fftw" ,fftw)))
 802     ;; FIXME: Even though the fonts are available dvips complains:
 803     ;; "Font cmmi10 not found; characters will be left blank."
 804     (native-inputs
 805      `(("texlive" ,texlive-tiny)
 806        ("ghostscript" ,ghostscript)
 807        ("doxygen" ,doxygen)))
 808     (home-page "http://itpp.sourceforge.net")
 809     (synopsis "C++ library of maths, signal processing and communication classes")
 810     (description "IT++ is a C++ library of mathematical, signal processing and
 811 communication classes and functions.  Its main use is in simulation of
 812 communication systems and for performing research in the area of
 813 communications.  The kernel of the library consists of generic vector and
 814 matrix classes, and a set of accompanying routines.  Such a kernel makes IT++
 815 similar to MATLAB, GNU Octave or SciPy.")
 816     (license license:gpl3+)))
 817
 818 (define-public netcdf
 819   (package
 820     (name "netcdf")
 821     (version "4.4.1.1")
 822     (source
 823      (origin
 824        (method url-fetch)
 825        (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
 826                            "netcdf-" version ".tar.gz"))
 827        (sha256
 828         (base32
 829          "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
 830        (patches (search-patches "netcdf-date-time.patch"
 831                                 "netcdf-tst_h_par.patch"))))
 832     (build-system gnu-build-system)
 833     (native-inputs
 834      `(("m4" ,m4)
 835        ("doxygen" ,doxygen)
 836        ("graphviz" ,graphviz)))
 837     (inputs
 838      `(("hdf4" ,hdf4-alt)
 839        ("hdf5" ,hdf5)
 840        ("zlib" ,zlib)
 841        ("libjpeg" ,libjpeg)))
 842     (arguments
 843      `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
 844        #:parallel-tests? #f))           ;various race conditions
 845     (home-page "http://www.unidata.ucar.edu/software/netcdf/")
 846     (synopsis "Library for scientific data")
 847     (description "NetCDF is an interface for scientific data access and a
 848 software library that provides an implementation of the interface.  The netCDF
 849 library defines a machine-independent format for representing scientific data.
 850 Together, the interface, library, and format support the creation, access, and
 851 sharing of scientific data.")
 852     (license (license:x11-style "file://COPYRIGHT"))))
 853
 854 (define-public netcdf-parallel-openmpi
 855   (package (inherit netcdf)
 856     (name "netcdf-parallel-openmpi")
 857     (inputs
 858      `(("mpi" ,openmpi)
 859        ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
 860                         (package-inputs netcdf))))
 861     ;; TODO: Replace pkg-config references in nc-config with absolute references
 862     (arguments
 863      (substitute-keyword-arguments (package-arguments netcdf)
 864        ((#:configure-flags flags)
 865         `(cons* "CC=mpicc" "CXX=mpicxx"
 866                 "--enable-parallel-tests"
 867                 ;; Shared libraries not supported with parallel IO.
 868                 "--disable-shared" "--with-pic"
 869                 ,flags))))))
 870
 871 (define-public netcdf-fortran
 872   (package
 873     (name "netcdf-fortran")
 874     (version "4.4.4")
 875     (source (origin
 876               (method url-fetch)
 877               (uri (string-append
 878                     "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
 879                     version ".tar.gz"))
 880               (sha256
 881                (base32
 882                 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
 883     (build-system gnu-build-system)
 884     (arguments
 885      `(#:parallel-tests? #f))
 886     (inputs
 887      `(("netcdf" ,netcdf)))
 888     (native-inputs
 889      `(("gfortran" ,gfortran)))
 890     (synopsis "Fortran interface for the netCDF library")
 891     (description (package-description netcdf))
 892     (home-page (package-home-page netcdf))
 893     (license (package-license netcdf))))
 894
 895 (define-public nlopt
 896   (package
 897     (name "nlopt")
 898     (version "2.4.2")
 899     (source (origin
 900               (method url-fetch)
 901               (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
 902                                   version ".tar.gz"))
 903               (sha256
 904                (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
 905     (build-system gnu-build-system)
 906     (arguments
 907      `(;; Shared libraries are not built by default.  They are required to
 908        ;; build the Guile, Octave, and Python bindings.
 909        #:configure-flags '("--enable-shared")
 910
 911        #:phases
 912        (modify-phases %standard-phases
 913          (add-before 'configure 'set-libnlopt-file-name
 914            (lambda* (#:key outputs #:allow-other-keys)
 915              ;; Make sure the Scheme module refers to the library by its
 916              ;; absolute file name (we cannot do that from a snippet
 917              ;; because the expansion of @libdir@ contains
 918              ;; ${exec_prefix}.)
 919              (let ((out (assoc-ref outputs "out")))
 920                (substitute* "swig/nlopt.scm.in"
 921                  (("libnlopt")
 922                   (string-append out "/lib/libnlopt")))
 923                #t))))))
 924     (inputs `(("guile" ,guile-2.0)))
 925     (native-inputs `(("pkg-config" ,pkg-config)))
 926     (home-page "http://ab-initio.mit.edu/wiki/")
 927     (synopsis "Library for nonlinear optimization")
 928     (description "NLopt is a library for nonlinear optimization, providing a
 929 common interface for a number of different free optimization routines available
 930 online as well as original implementations of various other algorithms.")
 931     (license license:lgpl2.1+)))
 932
 933 (define-public ipopt
 934   (package
 935     (name "ipopt")
 936     (version "3.12.5")
 937     (source (origin
 938               (method url-fetch)
 939               (uri (string-append
 940                     "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
 941                     version".tgz"))
 942               (sha256
 943                (base32
 944                 "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
 945               (modules '((guix build utils)))
 946               (snippet
 947                ;; Make sure we don't use the bundled software.
 948                '(delete-file-recursively "ThirdParty"))))
 949     (build-system gnu-build-system)
 950     (arguments
 951      '(#:phases (modify-phases %standard-phases
 952                   (add-after 'install 'add--L-flags-in-ipopt.pc
 953                     (lambda* (#:key inputs outputs #:allow-other-keys)
 954                       ;; The '.pc' file lists '-llapack -lblas' in "Libs";
 955                       ;; move it to "Libs.private" where it belongs, and add a
 956                       ;; '-L' flag for LAPACK.
 957                       (let ((out    (assoc-ref outputs "out"))
 958                             (lapack (assoc-ref inputs "lapack")))
 959                         (substitute* (string-append out "/lib/pkgconfig/"
 960                                                     "ipopt.pc")
 961                           (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
 962                            (string-append "Libs: " before " " after "\n"
 963                                           "Libs.private: " before
 964                                           "-L" lapack "/lib -llapack -lblas "
 965                                           after "\n")))
 966                         #t))))))
 967     (native-inputs
 968      `(("gfortran" ,gfortran)))
 969     (inputs
 970      ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
 971      `(("lapack" ,lapack)))                    ;for both libblas and liblapack
 972     (home-page "http://www.coin-or.org")
 973     (synopsis "Large-scale nonlinear optimizer")
 974     (description
 975      "The Interior Point Optimizer (IPOPT) is a software package for
 976 large-scale nonlinear optimization.  It provides C++, C, and Fortran
 977 interfaces.")
 978     (license license:epl1.0)))
 979
 980 (define-public ceres
 981   (package
 982     (name "ceres-solver")
 983     (version "1.11.0")
 984     (home-page "http://ceres-solver.org/")
 985     (source (origin
 986               (method url-fetch)
 987               (uri (string-append home-page "ceres-solver-"
 988                                   version ".tar.gz"))
 989               (sha256
 990                (base32
 991                 "0i7qkbf8g6pd8arxzldppga26ckv93y8zldsfz6wbd4n6b1nqrjd"))))
 992     (build-system cmake-build-system)
 993     (arguments
 994      ;; TODO: Build HTML user documentation and install separately.
 995      '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
 996                            "-DBUILD_SHARED_LIBS=ON")
 997
 998        #:phases (modify-phases %standard-phases
 999                   (add-before 'configure 'set-library-directory
1000                     (lambda _
1001                       ;; Install libraries to lib/, not lib64/.
1002                       (substitute* "internal/ceres/CMakeLists.txt"
1003                         (("set\\(LIB_SUFFIX \"64\"\\)")
1004                          "set(LIB_SUFFIX \"\")"))
1005                       #t)))))
1006     (native-inputs
1007      `(("pkg-config" ,pkg-config)))
1008     (propagated-inputs
1009      `(("glog" ,glog)))                           ;for #include <glog/glog.h>
1010     (inputs
1011      `(("eigen" ,eigen)
1012        ("blas" ,openblas)
1013        ("lapack" ,lapack)
1014        ("suitesparse" ,suitesparse)
1015        ("gflags" ,gflags)))
1016     (synopsis "C++ library for solving large optimization problems")
1017     (description
1018      "Ceres Solver is a C++ library for modeling and solving large,
1019 complicated optimization problems.  It is a feature rich, mature and
1020 performant library which has been used in production since 2010.  Ceres Solver
1021 can solve two kinds of problems:
1022 @enumerate
1023 @item non-linear least squares problems with bounds constraints;
1024 @item general unconstrained optimization problems.
1025 @end enumerate\n")
1026     (license license:bsd-3)))
1027
1028 ;; For a fully featured Octave, users  are strongly recommended also to install
1029 ;; the following packages: texinfo, less, ghostscript, gnuplot.
1030 (define-public octave
1031   (package
1032     (name "octave")
1033     (version "4.2.1")
1034     (source
1035      (origin
1036       (method url-fetch)
1037       (uri (string-append "mirror://gnu/octave/octave-"
1038                           version ".tar.lz"))
1039       (sha256
1040        (base32
1041         "09zhhch79jw3ynw39vizx0i2cbd2bjz3sp38pjdzraqrbivpwp92"))))
1042     (build-system gnu-build-system)
1043     (inputs
1044      `(("lapack" ,lapack)
1045        ("readline" ,readline)
1046        ("gl2ps" ,gl2ps)
1047        ("glpk" ,glpk)
1048        ("fftw" ,fftw)
1049        ("fftwf" ,fftwf)
1050        ("arpack" ,arpack-ng)
1051        ("pcre" ,pcre)
1052        ("fltk" ,fltk)
1053        ("fontconfig" ,fontconfig)
1054        ("freetype" ,freetype)
1055        ("hdf5" ,hdf5)
1056        ("libxft" ,libxft)
1057        ("mesa" ,mesa)
1058        ("glu" ,glu)
1059        ("zlib" ,zlib)
1060        ("curl" ,curl)
1061        ("graphicsmagick" ,graphicsmagick)))
1062     (native-inputs
1063      `(("lzip" ,lzip)
1064        ("gfortran" ,gfortran)
1065        ("pkg-config" ,pkg-config)
1066        ("perl" ,perl)
1067        ;; The following inputs are not actually used in the build process.
1068        ;; However, the ./configure gratuitously tests for their existence and
1069        ;; assumes that programs not present at build time are also not, and
1070        ;; can never be, available at run time!  If these inputs are therefore
1071        ;; not present, support for them will be built out.  However, Octave
1072        ;; will still run without them, albeit without the features they
1073        ;; provide.
1074        ("less" ,less)
1075        ("texinfo" ,texinfo)
1076        ("ghostscript" ,ghostscript)
1077        ("gnuplot" ,gnuplot)))
1078     (arguments
1079      `(#:configure-flags
1080        (list (string-append "--with-shell="
1081                             (assoc-ref %build-inputs "bash")
1082                             "/bin/sh"))))
1083     (home-page "https://www.gnu.org/software/octave/")
1084     (synopsis "High-level language for numerical computation")
1085     (description "GNU Octave is a high-level interpreted language that is
1086 specialized for numerical computations.  It can be used for both linear and
1087 non-linear applications and it provides great support for visualizing results.
1088 Work may be performed both at the interactive command-line as well as via
1089 script files.")
1090     (license license:gpl3+)))
1091
1092 (define-public opencascade-oce
1093   (package
1094     (name "opencascade-oce")
1095     (version "0.17.2")
1096     (source
1097       (origin
1098         (method url-fetch)
1099         (uri (string-append
1100                "https://github.com/tpaviot/oce/archive/OCE-"
1101                version
1102                ".tar.gz"))
1103         (sha256
1104           (base32
1105             "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
1106     (build-system cmake-build-system)
1107     (arguments
1108      '(#:configure-flags
1109         (list "-DOCE_TESTING:BOOL=ON"
1110               "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1111               "-DOCE_DRAW:BOOL=ON"
1112               (string-append "-DOCE_INSTALL_PREFIX:PATH="
1113                         (assoc-ref %outputs "out"))
1114               "-UCMAKE_INSTALL_RPATH")))
1115     (inputs
1116       `(("freetype" ,freetype)
1117         ("glu" ,glu)
1118         ("libxmu" ,libxmu)
1119         ("mesa" ,mesa)
1120         ("tcl" ,tcl)
1121         ("tk" ,tk)))
1122     (native-inputs
1123       `(("python" ,python-wrapper)))
1124     (home-page "https://github.com/tpaviot/oce")
1125     (synopsis "Libraries for 3D modeling and numerical simulation")
1126     (description
1127      "Open CASCADE is a set of libraries for the development of applications
1128 dealing with 3D CAD data or requiring industrial 3D capabilities.  It includes
1129 C++ class libraries providing services for 3D surface and solid modeling, CAD
1130 data exchange, and visualization.  It is used for development of specialized
1131 software dealing with 3D models in design (CAD), manufacturing (CAM),
1132 numerical simulation (CAE), measurement equipment (CMM), and quality
1133 control (CAQ) domains.
1134
1135 This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1136 patches, improvements, and experiments contributed by users over the official
1137 Open CASCADE library.")
1138     (license (list license:lgpl2.1; OCE libraries, with an exception for the
1139                                   ; use of header files; see
1140                                   ; OCCT_LGPL_EXCEPTION.txt
1141                    license:public-domain; files
1142                                   ; src/Standard/Standard_StdAllocator.hxx and
1143                                   ; src/NCollection/NCollection_StdAllocator.hxx
1144                    license:expat; file src/OpenGl/OpenGl_glext.h
1145                    license:bsd-3)))); test framework gtest
1146
1147 (define-public gmsh
1148   (package
1149     (name "gmsh")
1150     (version "2.16.0")
1151     (source
1152      (origin
1153       (method url-fetch)
1154       (uri (string-append "http://gmsh.info/src/gmsh-"
1155                           version "-source.tgz"))
1156       (sha256
1157        (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
1158       (modules '((guix build utils)))
1159       (snippet
1160        ;; Remove non-free METIS code
1161        '(delete-file-recursively "contrib/Metis"))))
1162     (build-system cmake-build-system)
1163     (propagated-inputs
1164      `(("fltk" ,fltk)
1165        ("gfortran" ,gfortran)
1166        ("gmp" ,gmp)
1167        ("hdf5" ,hdf5)
1168        ("lapack" ,lapack)
1169        ("mesa" ,mesa)
1170        ("glu" ,glu)
1171        ("opencascade-oce" ,opencascade-oce)
1172        ("libx11" ,libx11)
1173        ("libxext" ,libxext)))
1174     (inputs
1175      `(("fontconfig" ,fontconfig)
1176        ("libxft" ,libxft)))
1177     (arguments
1178      `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1179                            "-DENABLE_BUILD_SHARED:BOOL=ON"
1180                            "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
1181     (home-page "http://www.geuz.org/gmsh/")
1182     (synopsis "3D finite element grid generator")
1183     (description "Gmsh is a 3D finite element grid generator with a built-in
1184 CAD engine and post-processor.  Its design goal is to provide a fast, light
1185 and user-friendly meshing tool with parametric input and advanced
1186 visualization capabilities.  Gmsh is built around four modules: geometry,
1187 mesh, solver and post-processing.  The specification of any input to these
1188 modules is done either interactively using the graphical user interface or in
1189 ASCII text files using Gmsh's own scripting language.")
1190     (license license:gpl2+)))
1191
1192 (define-public maxflow
1193   (package
1194     (name "maxflow")
1195     (version "3.04")
1196     (source (origin
1197               (method git-fetch)
1198               (uri (git-reference
1199                     (url "https://github.com/gerddie/maxflow.git")
1200                     (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
1201               (file-name (string-append name "-" version "-checkout"))
1202               (sha256
1203                (base32
1204                 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1205     (build-system cmake-build-system)
1206     (home-page "http://pub.ist.ac.at/~vnk/software.html")
1207     (synopsis "Library implementing Maxflow algorithm")
1208     (description "An implementation of the maxflow algorithm described in
1209 @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1210 Energy Minimization in Computer Vision.\n
1211 Yuri Boykov and Vladimir Kolmogorov.\n
1212 In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1213 September 2004}")
1214     (license license:gpl3+)))
1215
1216 (define-public petsc
1217   (package
1218     (name "petsc")
1219     (version "3.7.6")
1220     (source
1221      (origin
1222       (method url-fetch)
1223       ;; The *-lite-* tarball does not contain the *large* documentation
1224       (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1225                           "petsc-lite-" version ".tar.gz"))
1226       (sha256
1227        (base32 "1y3f5jjq0v5b62i3sabp4kp5mgfyp3vnk0dxhwkrhpypax77nzxh"))))
1228     (build-system gnu-build-system)
1229     (native-inputs
1230      `(("python" ,python-2)
1231        ("perl" ,perl)))
1232     (inputs
1233      `(("gfortran" ,gfortran)
1234        ("lapack" ,lapack)
1235        ("superlu" ,superlu)
1236        ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1237        ;; leaving out opengl, as configuration seems to only be for mac
1238        ))
1239     (arguments
1240      `(#:test-target "test"
1241        #:parallel-build? #f             ;build is parallel by default
1242        #:configure-flags
1243        `("--with-mpi=0"
1244          "--with-openmp=1"
1245          "--with-superlu=1"
1246          ,(string-append "--with-superlu-include="
1247                          (assoc-ref %build-inputs "superlu") "/include")
1248          ,(string-append "--with-superlu-lib="
1249                          (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
1250        #:make-flags
1251        ;; Honor (parallel-job-count) for build.  Do not use --with-make-np,
1252        ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
1253        (list (format #f "MAKE_NP=~a" (parallel-job-count)))
1254        #:phases
1255        (modify-phases %standard-phases
1256         (replace 'configure
1257           ;; PETSc's configure script is actually a python script, so we can't
1258           ;; run it with bash.
1259           (lambda* (#:key outputs (configure-flags '())
1260                           #:allow-other-keys)
1261             (let* ((prefix (assoc-ref outputs "out"))
1262                    (flags `(,(string-append "--prefix=" prefix)
1263                             ,@configure-flags)))
1264               (format #t "build directory: ~s~%" (getcwd))
1265               (format #t "configure flags: ~s~%" flags)
1266               (zero? (apply system* "./configure" flags)))))
1267         (add-after 'configure 'clean-local-references
1268           (lambda* (#:key outputs #:allow-other-keys)
1269             (let ((out (assoc-ref outputs "out")))
1270               (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
1271                 ;; Prevent build directory from leaking into compiled code
1272                 (((getcwd)) out)
1273                 ;; Scrub timestamp for reproducibility
1274                 ((".*Libraries compiled on.*") ""))
1275               (substitute* (find-files "." "petscvariables")
1276                 ;; Do not expose build machine characteristics, set to defaults.
1277                 (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
1278                 (("NPMAX = [:digit:]+") "NPMAX = 2"))
1279               #t)))
1280         (add-after 'install 'clean-install
1281           ;; Try to keep installed files from leaking build directory names.
1282           (lambda* (#:key inputs outputs #:allow-other-keys)
1283             (let ((out (assoc-ref outputs "out")))
1284               (substitute* (map (lambda (file)
1285                                   (string-append out "/lib/petsc/conf/" file))
1286                                 '("petscvariables"))
1287                 (((getcwd)) out))
1288               ;; Make compiler references point to the store
1289               (substitute* (string-append out "/lib/petsc/conf/petscvariables")
1290                 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1291                  (string-append "= " (which compiler))))
1292               ;; PETSc installs some build logs, which aren't necessary.
1293               (for-each (lambda (file)
1294                           (let ((f (string-append out "/lib/petsc/conf/" file)))
1295                             (when (file-exists? f)
1296                               (delete-file f))))
1297                         '("configure.log" "make.log" "gmake.log"
1298                           "test.log" "error.log" "RDict.db"
1299                           "PETScBuildInternal.cmake"
1300                           ;; Once installed, should uninstall with Guix
1301                           "uninstall.py"))
1302               #t))))))
1303     (home-page "http://www.mcs.anl.gov/petsc")
1304     (synopsis "Library to solve PDEs")
1305     (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1306 data structures and routines for the scalable (parallel) solution of
1307 scientific applications modeled by partial differential equations.")
1308     (license (license:non-copyleft
1309               "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1310
1311 (define-public petsc-complex
1312   (package (inherit petsc)
1313     (name "petsc-complex")
1314     (arguments
1315      (substitute-keyword-arguments (package-arguments petsc)
1316        ((#:configure-flags cf)
1317         `(cons "--with-scalar-type=complex" ,cf))))
1318     (synopsis "Library to solve PDEs (with complex scalars)")))
1319
1320 (define-public petsc-openmpi
1321   (package (inherit petsc)
1322     (name "petsc-openmpi")
1323     (inputs
1324      `(("openmpi" ,openmpi)
1325        ,@(package-inputs petsc)))
1326     (arguments
1327      (substitute-keyword-arguments (package-arguments petsc)
1328        ((#:configure-flags cf)
1329         ``("--with-mpiexec=mpirun"
1330            ,(string-append "--with-mpi-dir="
1331                            (assoc-ref %build-inputs "openmpi"))
1332            ,@(delete "--with-mpi=0" ,cf)))))
1333     (synopsis "Library to solve PDEs (with MPI support)")))
1334
1335 (define-public petsc-complex-openmpi
1336   (package (inherit petsc-complex)
1337     (name "petsc-complex-openmpi")
1338     (inputs
1339      `(("openmpi" ,openmpi)
1340        ,@(package-inputs petsc-complex)))
1341     (arguments
1342      (substitute-keyword-arguments (package-arguments petsc-complex)
1343        ((#:configure-flags cf)
1344         ``("--with-mpiexec=mpirun"
1345            ,(string-append "--with-mpi-dir="
1346                            (assoc-ref %build-inputs "openmpi"))
1347            ,@(delete "--with-mpi=0" ,cf)))))
1348     (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
1349
1350 (define-public slepc
1351   (package
1352     (name "slepc")
1353     (version "3.7.4")
1354     (source
1355      (origin
1356        (method url-fetch)
1357        (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
1358                            version ".tar.gz"))
1359        (sha256
1360         (base32
1361          "12pbl8yd6r8k9xjlr1qw25rs0k1acgic7hw1s6l6bhiv9s285drg"))))
1362     (build-system gnu-build-system)
1363     (native-inputs
1364      `(("python" ,python-2)))
1365     (inputs
1366      `(("arpack" ,arpack-ng)
1367        ("gfortran" ,gfortran)))
1368     (propagated-inputs
1369      `(("petsc" ,petsc)))
1370     (arguments
1371      `(#:parallel-build? #f             ;build is parallel by default
1372        #:configure-flags
1373        `(,(string-append "--with-arpack-dir="
1374                          (assoc-ref %build-inputs "arpack") "/lib"))
1375        #:make-flags                     ;honor (parallel-job-count)
1376        `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
1377        #:phases
1378        (modify-phases %standard-phases
1379          (replace 'configure
1380           ;; configure is a python script, so we can't run it with bash.
1381           (lambda* (#:key inputs outputs (configure-flags '())
1382                     #:allow-other-keys)
1383             (let* ((prefix (assoc-ref outputs "out"))
1384                    (flags `(,(string-append "--prefix=" prefix)
1385                             ,@configure-flags)))
1386               (format #t "build directory: ~s~%" (getcwd))
1387               (format #t "configure flags: ~s~%" flags)
1388               (setenv "SLEPC_DIR" (getcwd))
1389               (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
1390               (zero? (apply system* "./configure" flags)))))
1391          (add-after 'install 'delete-doc
1392           ;; TODO: SLEPc installs HTML documentation alongside headers in
1393           ;; $out/include.  We'd like to move them to share/doc, but delete
1394           ;; them for now, as they are incomplete and installing the complete
1395           ;; documentation is difficult.
1396           (lambda* (#:key outputs #:allow-other-keys)
1397             (let* ((out (assoc-ref outputs "out")))
1398               (for-each delete-file (find-files out "\\.html$")))))
1399          (add-after 'install 'clean-install
1400           ;; Clean up unnecessary build logs from installation.
1401           (lambda* (#:key outputs #:allow-other-keys)
1402             (let ((out (assoc-ref outputs "out")))
1403               (for-each (lambda (file)
1404                           (let ((f (string-append out "/lib/slepc/conf/" file)))
1405                             (when (file-exists? f)
1406                               (delete-file f))))
1407                         '("configure.log" "make.log" "gmake.log"
1408                           "test.log" "error.log" "RDict.db"
1409                           "uninstall.py"))))))))
1410     (home-page "http://slepc.upv.es")
1411     (synopsis "Scalable library for eigenproblems")
1412     (description "SLEPc is a software library for the solution of large sparse
1413 eigenproblems on parallel computers.  It can be used for the solution of
1414 linear eigenvalue problems formulated in either standard or generalized form,
1415 as well as other related problems such as the singular value decomposition.
1416 The emphasis of the software is on methods and techniques appropriate for
1417 problems in which the associated matrices are sparse, for example, those
1418 arising after the discretization of partial differential equations.")
1419     (license license:lgpl3)))
1420
1421 (define-public slepc-complex
1422   (package (inherit slepc)
1423     (name "slepc-complex")
1424     (propagated-inputs
1425      `(("petsc" ,petsc-complex)
1426        ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1427     (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1428
1429 (define-public slepc-openmpi
1430   (package (inherit slepc)
1431     (name "slepc-openmpi")
1432     (inputs
1433      `(("mpi" ,openmpi)
1434        ("arpack" ,arpack-ng-openmpi)
1435        ,@(alist-delete "arpack" (package-inputs slepc))))
1436     (propagated-inputs
1437      `(("petsc" ,petsc-openmpi)
1438        ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1439     (synopsis "Scalable library for eigenproblems (with MPI support)")))
1440
1441 (define-public slepc-complex-openmpi
1442   (package (inherit slepc-openmpi)
1443     (name "slepc-complex-openmpi")
1444     (propagated-inputs
1445      `(("petsc" ,petsc-complex-openmpi)
1446        ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1447     (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1448
1449 (define-public mumps
1450   (package
1451     (name "mumps")
1452     (version "5.0.2")
1453     (source
1454      (origin
1455        (method url-fetch)
1456        (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
1457                            version ".tar.gz"))
1458        (sha256
1459         (base32
1460          "0igyc1pfzxdhpbad3v3lb86ixkdbqa1a8gbs15b04r2294h2nabp"))
1461        (patches (search-patches "mumps-build-parallelism.patch"))))
1462     (build-system gnu-build-system)
1463     (inputs
1464      `(("fortran" ,gfortran)
1465        ;; These are required for linking against mumps, but we let the user
1466        ;; declare the dependency.
1467        ("blas" ,openblas)
1468        ("metis" ,metis)
1469        ("scotch" ,scotch)))
1470     (arguments
1471      `(#:modules ((ice-9 match)
1472                   (ice-9 popen)
1473                   (srfi srfi-1)
1474                   ,@%gnu-build-system-modules)
1475        #:phases
1476        (modify-phases %standard-phases
1477          (replace 'configure
1478           (lambda* (#:key inputs #:allow-other-keys)
1479             (call-with-output-file "Makefile.inc"
1480               (lambda (port)
1481                 (format port "
1482 PLAT         =
1483 LIBEXT       = .a
1484 OUTC         = -o
1485 OUTF         = -o
1486 RM           = rm -f~:[
1487 CC           = gcc
1488 FC           = gfortran
1489 FL           = gfortran
1490 INCSEQ       = -I$(topdir)/libseq
1491 LIBSEQ       = -L$(topdir)/libseq -lmpiseq
1492 LIBSEQNEEDED = libseqneeded~;
1493 CC           = mpicc
1494 FC           = mpifort
1495 FL           = mpifort~]
1496 AR           = ar vr # rules require trailing space, ugh...
1497 RANLIB       = ranlib
1498 LIBBLAS      = -L~a -lopenblas~@[
1499 SCALAP       = -L~a -lscalapack~]
1500 LIBOTHERS    = -pthread
1501 CDEFS        = -DAdd_
1502 PIC          = -fPIC
1503 OPTF         = -O2 -DALLOW_NON_INIT $(PIC)
1504 OPTL         = -O2 $(PIC)
1505 OPTC         = -O2 $(PIC)
1506 INCS         = $(INCSEQ)
1507 LIBS         = $(SCALAP) $(LIBSEQ)
1508 LPORDDIR     = $(topdir)/PORD/lib
1509 IPORD        = -I$(topdir)/PORD/include
1510 LPORD        = -L$(LPORDDIR) -lpord
1511 ORDERINGSF   = -Dpord~@[
1512 METISDIR     = ~a
1513 IMETIS       = -I$(METISDIR)/include
1514 LMETIS       = -L$(METISDIR)/lib -lmetis
1515 ORDERINGSF  += -Dmetis~]~@[~:{
1516 SCOTCHDIR    = ~a
1517 ISCOTCH      = -I$(SCOTCHDIR)/include
1518 LSCOTCH      = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
1519 ORDERINGSF  += ~a~}~]
1520 ORDERINGSC   = $(ORDERINGSF)
1521 LORDERINGS   = $(LPORD) $(LMETIS) $(LSCOTCH)
1522 IORDERINGSF  = $(ISCOTCH)
1523 IORDERINGSC  = $(IPORD) $(IMETIS) $(ISCOTCH)"
1524                         (assoc-ref inputs "mpi")
1525                         (assoc-ref inputs "blas")
1526                         (assoc-ref inputs "scalapack")
1527                         (assoc-ref inputs "metis")
1528                         (match (list (assoc-ref inputs "pt-scotch")
1529                                      (assoc-ref inputs "scotch"))
1530                           ((#f #f)
1531                            #f)
1532                           ((#f scotch)
1533                            `((,scotch "" "-Dscotch")))
1534                           ((ptscotch _)
1535                            `((,ptscotch
1536                               "-lptesmumps -lptscotch -lptscotcherr "
1537                               "-Dptscotch")))))))))
1538          (replace 'build
1539           ;; By default only the d-precision library is built.  Make with "all"
1540           ;; target so that all precision libraries and examples are built.
1541           (lambda _
1542             (zero? (system* "make" "all"
1543                             (format #f "-j~a" (parallel-job-count))))))
1544          (replace 'check
1545           ;; Run the simple test drivers, which read test input from stdin:
1546           ;; from the "real" input for the single- and double-precision
1547           ;; testers, and from the "cmplx" input for complex-precision
1548           ;; testers.  The EXEC-PREFIX key is used by the mumps-openmpi
1549           ;; package to prefix execution with "mpirun".
1550           (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
1551             (with-directory-excursion "examples"
1552               (every
1553                (lambda (prec type)
1554                  (let ((tester (apply open-pipe*
1555                                       `(,OPEN_WRITE
1556                                         ,@exec-prefix
1557                                         ,(string-append "./" prec
1558                                                         "simpletest"))))
1559                        (input  (open-input-file
1560                                 (string-append "input_simpletest_" type))))
1561                    (begin
1562                      (dump-port input tester)
1563                      (close-port input)
1564                      (zero? (close-pipe tester)))))
1565                '("s" "d" "c" "z")
1566                '("real" "real" "cmplx" "cmplx")))))
1567          (replace 'install
1568            (lambda* (#:key outputs #:allow-other-keys)
1569              (let* ((out (assoc-ref outputs "out"))
1570                     (libdir (string-append out "/lib")))
1571                (copy-recursively "lib" libdir)
1572                (copy-recursively "include" (string-append out "/include"))
1573                (when (file-exists? "libseq/libmpiseq.a")
1574                  (install-file "libseq/libmpiseq.a" libdir))
1575                #t))))))
1576     (home-page "http://mumps.enseeiht.fr")
1577     (synopsis "Multifrontal sparse direct solver")
1578     (description
1579      "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
1580 sparse system of linear equations A x = b using Guassian elimination.")
1581     (license license:cecill-c)))
1582
1583 (define-public mumps-metis
1584   (package (inherit mumps)
1585     (name "mumps-metis")
1586     (inputs
1587      (alist-delete "scotch" (package-inputs mumps)))))
1588
1589 (define-public mumps-openmpi
1590   (package (inherit mumps)
1591     (name "mumps-openmpi")
1592     (inputs
1593      `(("mpi" ,openmpi)
1594        ("scalapack" ,scalapack)
1595        ("pt-scotch" ,pt-scotch)
1596        ,@(alist-delete "scotch" (package-inputs mumps))))
1597     (arguments
1598      (substitute-keyword-arguments (package-arguments mumps)
1599        ((#:phases phases)
1600         `(modify-phases ,phases
1601            (replace
1602             'check
1603             (lambda _
1604               ((assoc-ref ,phases 'check)
1605                #:exec-prefix '("mpirun" "-n" "2"))))))))
1606     (synopsis "Multifrontal sparse direct solver (with MPI)")))
1607
1608 (define-public mumps-metis-openmpi
1609   (package (inherit mumps-openmpi)
1610     (name "mumps-metis-openmpi")
1611     (inputs
1612      (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
1613
1614 (define-public r-quadprog
1615   (package
1616     (name "r-quadprog")
1617     (version "1.5-5")
1618     (source
1619      (origin
1620        (method url-fetch)
1621        (uri (cran-uri "quadprog" version))
1622        (sha256
1623         (base32
1624          "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
1625     (build-system r-build-system)
1626     (native-inputs
1627      `(("gfortran" ,gfortran)))
1628     (home-page "http://cran.r-project.org/web/packages/quadprog")
1629     (synopsis "Functions to solve quadratic programming problems")
1630     (description
1631      "This package contains routines and documentation for solving quadratic
1632 programming problems.")
1633     (license license:gpl3+)))
1634
1635 (define-public r-pracma
1636   (package
1637     (name "r-pracma")
1638     (version "2.0.7")
1639     (source (origin
1640       (method url-fetch)
1641       (uri (cran-uri "pracma" version))
1642       (sha256
1643         (base32 "0hxa0rbbp54j0c05qj7vfwhqfdmiz5ax8vhqxd09g33x7c0hqbc5"))))
1644     (build-system r-build-system)
1645     (propagated-inputs
1646      `(("r-quadprog" ,r-quadprog)))
1647     (home-page "http://cran.r-project.org/web/packages/pracma")
1648     (synopsis "Practical numerical math functions")
1649     (description "This package provides functions for numerical analysis and
1650 linear algebra, numerical optimization, differential equations, plus some
1651 special functions.  It uses Matlab function names where appropriate to simplify
1652 porting.")
1653     (license license:gpl3+)))
1654
1655 (define-public superlu
1656   (package
1657     (name "superlu")
1658     (version "5.2.1")
1659     (source
1660      (origin
1661        (method url-fetch)
1662        (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1663                            "superlu_" version ".tar.gz"))
1664        (sha256
1665         (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
1666        (modules '((guix build utils)))
1667        (snippet
1668         ;; Replace the non-free implementation of MC64 with a stub adapted
1669         ;; from Debian
1670         '(begin
1671            (use-modules (ice-9 regex)
1672                         (ice-9 rdelim))
1673            (call-with-output-file "SRC/mc64ad.c"
1674              (lambda (port)
1675                (display "
1676 #include <stdio.h>
1677 #include <stdlib.h>
1678 void mc64id_(int *a) {
1679   fprintf (stderr, \"SuperLU: non-free MC64 not available.  Aborting.\\n\");
1680   abort ();
1681 }
1682 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
1683               int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
1684   fprintf (stderr, \"SuperLU: non-free MC64 not available.  Aborting.\\n\");
1685   abort ();
1686 }\n" port)))
1687            ;; Remove the corresponding license verbiage.  MC64 license follows
1688            ;; a "------" line separator.
1689            (with-atomic-file-replacement "License.txt"
1690              (let ((rx (make-regexp "-{8}")))
1691                (lambda (in out)
1692                  (let loop ()
1693                    (let ((line (read-line in 'concat)))
1694                     (unless (regexp-exec rx line)
1695                       (display line out)
1696                       (loop)))))))))))
1697     (build-system cmake-build-system)
1698     (native-inputs
1699      `(("tcsh" ,tcsh)))
1700     (inputs
1701      `(("blas" ,openblas)
1702        ("gfortran" ,gfortran)))
1703     (arguments
1704      `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
1705                            "-DTPL_BLAS_LIBRARIES=openblas"
1706                            "-DBUILD_SHARED_LIBS:BOOL=YES"
1707                            "-DCMAKE_INSTALL_LIBDIR=lib")))
1708     (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
1709     (synopsis "Supernodal direct solver for sparse linear systems")
1710     (description
1711      "SuperLU is a general purpose library for the direct solution of large,
1712 sparse, nonsymmetric systems of linear equations on high performance machines.
1713 The library is written in C and is callable from either C or Fortran.  The
1714 library routines perform an LU decomposition with partial pivoting and
1715 triangular system solves through forward and back substitution.  The library
1716 also provides threshold-based ILU factorization preconditioners.")
1717     (license (list license:bsd-3
1718                    license:gpl2+        ;EXAMPLE/*fgmr.c
1719                    (license:fsf-free "file://SRC/colamd.h")))))
1720
1721 (define-public superlu-dist
1722   (package
1723     (name "superlu-dist")
1724     (version "3.3")
1725     (source
1726      (origin
1727        (method url-fetch)
1728        (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1729                            "superlu_dist_" version ".tar.gz"))
1730        (sha256
1731         (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj"))
1732               (modules '((guix build utils)))
1733        (snippet
1734         ;; Replace the non-free implementation of MC64 with a stub
1735         '(begin
1736            (use-modules (ice-9 regex)
1737                         (ice-9 rdelim))
1738            (call-with-output-file "SRC/mc64ad.c"
1739              (lambda (port)
1740                (display "
1741 #include <stdio.h>
1742 #include <stdlib.h>
1743 void mc64id_(int *a) {
1744   fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available.  Aborting.\\n\");
1745   abort ();
1746 }
1747 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
1748               int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
1749   fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available.  Aborting.\\n\");
1750   abort ();
1751 }\n" port)))
1752            (delete-file "SRC/mc64ad.f.bak")
1753            (substitute* "SRC/util.c"    ;adjust default algorithm
1754              (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
1755               "RowPerm = NOROWPERM"))))
1756        (patches (search-patches "superlu-dist-scotchmetis.patch"))))
1757     (build-system gnu-build-system)
1758     (native-inputs
1759      `(("tcsh" ,tcsh)))
1760     (inputs
1761      `(("gfortran" ,gfortran)))
1762     (propagated-inputs
1763      `(("openmpi" ,openmpi)             ;headers include MPI heades
1764        ("lapack" ,lapack)               ;required to link with output library
1765        ("pt-scotch" ,pt-scotch)))       ;same
1766     (arguments
1767      `(#:parallel-build? #f             ;race conditions using ar
1768        #:phases
1769        (alist-replace
1770         'configure
1771         (lambda* (#:key inputs outputs #:allow-other-keys)
1772           (call-with-output-file "make.inc"
1773             (lambda (port)
1774               (format port "
1775 PLAT        =
1776 DSuperLUroot = ~a
1777 DSUPERLULIB  = ~a/lib/libsuperlu_dist.a
1778 BLASDEF     = -DUSE_VENDOR_BLAS
1779 BLASLIB     = -L~a/lib -lblas
1780 PARMETISLIB = -L~a/lib \
1781               -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
1782               -lscotch -lscotcherr -lscotcherrexit
1783 METISLIB    = -L~:*~a/lib \
1784               -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
1785 LIBS        = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
1786 ARCH        = ar
1787 ARCHFLAGS   = cr
1788 RANLIB      = ranlib
1789 CC          = mpicc
1790 PIC         = -fPIC
1791 CFLAGS      = -O3 -g -DPRNTlevel=0 $(PIC)
1792 NOOPTS      = -O0 -g $(PIC)
1793 FORTRAN     = mpifort
1794 FFLAGS      = -O2 -g $(PIC)
1795 LOADER      = $(CC)
1796 CDEFS       = -DAdd_"
1797                       (getcwd)
1798                       (assoc-ref outputs "out")
1799                       (assoc-ref inputs "lapack")
1800                       (assoc-ref inputs "pt-scotch")))))
1801         (alist-cons-after
1802          'unpack 'remove-broken-symlinks
1803          (lambda _
1804            (for-each delete-file
1805                      (find-files "MAKE_INC" "\\.#make\\..*")))
1806          (alist-cons-before
1807           'build 'create-install-directories
1808           (lambda* (#:key outputs #:allow-other-keys)
1809             (for-each
1810              (lambda (dir)
1811                (mkdir-p (string-append (assoc-ref outputs "out")
1812                                        "/" dir)))
1813              '("lib" "include")))
1814           (alist-replace
1815            'check
1816            (lambda _
1817              (with-directory-excursion "EXAMPLE"
1818                (and
1819                 (zero? (system* "mpirun" "-n" "2"
1820                                 "./pddrive" "-r" "1" "-c" "2" "g20.rua"))
1821                 (zero? (system* "mpirun" "-n" "2"
1822                                 "./pzdrive" "-r" "1" "-c" "2" "cg20.cua")))))
1823            (alist-replace
1824             'install
1825             (lambda* (#:key outputs #:allow-other-keys)
1826               ;; Library is placed in lib during the build phase.  Copy over
1827               ;; headers to include.
1828               (let* ((out    (assoc-ref outputs "out"))
1829                      (incdir (string-append out "/include")))
1830                 (for-each (lambda (file)
1831                             (let ((base (basename file)))
1832                               (format #t "installing `~a' to `~a'~%"
1833                                       base incdir)
1834                               (copy-file file
1835                                          (string-append incdir "/" base))))
1836                           (find-files "SRC" ".*\\.h$"))))
1837             %standard-phases)))))))
1838     (home-page (package-home-page superlu))
1839     (synopsis "Parallel supernodal direct solver")
1840     (description
1841      "SuperLU_DIST is a parallel extension to the serial SuperLU library.
1842 It is targeted for distributed memory parallel machines.  SuperLU_DIST is
1843 implemented in ANSI C, and MPI for communications.")
1844     (license license:bsd-3)))
1845
1846 (define-public scotch
1847   (package
1848     (name "scotch")
1849     (version "6.0.4")
1850     (source
1851      (origin
1852       (method url-fetch)
1853       (uri (string-append "https://gforge.inria.fr/frs/download.php/34618/"
1854                           "scotch_" version ".tar.gz"))
1855       (sha256
1856        (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm"))
1857       (patches (search-patches "scotch-test-threading.patch"
1858                                "pt-scotch-build-parallelism.patch"))))
1859     (build-system gnu-build-system)
1860     (inputs
1861      `(("zlib" ,zlib)
1862        ("flex" ,flex)
1863        ("bison" ,bison)))
1864     (arguments
1865      `(#:phases
1866        (modify-phases %standard-phases
1867          (add-after
1868           'unpack 'chdir-to-src
1869           (lambda _ (chdir "src")))
1870          (replace
1871           'configure
1872           (lambda _
1873             (call-with-output-file "Makefile.inc"
1874               (lambda (port)
1875                 (format port "
1876 EXE =
1877 LIB = .a
1878 OBJ = .o
1879 MAKE = make
1880 AR = ar
1881 ARFLAGS = -ruv
1882 CAT = cat
1883 CCS = gcc
1884 CCP = mpicc
1885 CCD = gcc
1886 CPPFLAGS =~{ -D~a~}
1887 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
1888 LDFLAGS = -lz -lm -lrt -lpthread
1889 CP = cp
1890 LEX = flex -Pscotchyy -olex.yy.c
1891 LN = ln
1892 MKDIR = mkdir
1893 MV = mv
1894 RANLIB = ranlib
1895 YACC = bison -pscotchyy -y -b y
1896 "
1897                         '("COMMON_FILE_COMPRESS_GZ"
1898                           "COMMON_PTHREAD"
1899                           "COMMON_RANDOM_FIXED_SEED"
1900                           "INTSIZE64"             ;use 'long' instead of 'int'
1901                           ;; Prevents symbolc clashes with libesmumps
1902                           "SCOTCH_RENAME"
1903                           ;; XXX: Causes invalid frees in superlu-dist tests
1904                           ;; "SCOTCH_PTHREAD"
1905                           ;; "SCOTCH_PTHREAD_NUMBER=2"
1906                           "restrict=__restrict"))))))
1907          (add-after
1908           'build 'build-esmumps
1909           (lambda _
1910             (zero? (system* "make"
1911                             (format #f "-j~a" (parallel-job-count))
1912                             "esmumps"))))
1913          (replace
1914           'install
1915           (lambda* (#:key outputs #:allow-other-keys)
1916             (let ((out (assoc-ref outputs "out")))
1917               (mkdir out)
1918               (zero? (system* "make"
1919                               (string-append "prefix=" out)
1920                               "install"))
1921               ;; esmumps files are not installed with the above
1922               (for-each (lambda (f)
1923                           (copy-file f (string-append out "/include/" f)))
1924                         (find-files "../include" ".*esmumps.h$"))
1925               (for-each (lambda (f)
1926                           (copy-file f (string-append out "/lib/" f)))
1927                         (find-files "../lib" "^lib.*esmumps.*"))))))))
1928     (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
1929     (synopsis "Programs and libraries for graph algorithms")
1930     (description "SCOTCH is a set of programs and libraries which implement
1931 the static mapping and sparse matrix reordering algorithms developed within
1932 the SCOTCH project.  Its purpose is to apply graph theory, with a divide and
1933 conquer approach, to scientific computing problems such as graph and mesh
1934 partitioning, static mapping, and sparse matrix ordering, in application
1935 domains ranging from structural mechanics to operating systems or
1936 bio-chemistry.")
1937     ;; See LICENSE_en.txt
1938     (license license:cecill-c)))
1939
1940 (define-public pt-scotch
1941   (package (inherit scotch)
1942     (name "pt-scotch")
1943     (propagated-inputs
1944      `(("openmpi" ,openmpi)))           ;Headers include MPI headers
1945     (arguments
1946      (substitute-keyword-arguments (package-arguments scotch)
1947        ((#:phases scotch-phases)
1948         `(modify-phases ,scotch-phases
1949            (replace
1950             'build
1951             (lambda _
1952               (and
1953                (zero? (system* "make"
1954                                (format #f "-j~a" (parallel-job-count))
1955                                "ptscotch" "ptesmumps"))
1956                ;; Install the serial metis compatibility library
1957                (zero? (system* "make" "-C" "libscotchmetis" "install")))))
1958            (replace
1959             'check
1960             (lambda _ (zero? (system* "make" "ptcheck"))))))))
1961     (synopsis "Programs and libraries for graph algorithms (with MPI)")))
1962
1963 (define-public metis
1964   (package
1965     (name "metis")
1966     (version "5.1.0")
1967     (source
1968      (origin
1969        (method url-fetch)
1970        (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
1971                            "metis-" version ".tar.gz"))
1972        (sha256
1973         (base32
1974          "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
1975     (build-system cmake-build-system)
1976     (inputs
1977      `(("blas" ,openblas)))
1978     (arguments
1979      `(#:tests? #f                      ;no tests
1980        #:configure-flags `("-DSHARED=ON"
1981                            ,(string-append "-DGKLIB_PATH=" (getcwd)
1982                                            "/metis-" ,version "/GKlib"))))
1983     (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
1984     (synopsis "Graph partitioning and fill-reducing matrix ordering library")
1985     (description
1986      "METIS is a set of serial programs for partitioning graphs, partitioning
1987 finite element meshes, and producing fill-reducing orderings for sparse
1988 matrices.  The algorithms implemented in METIS are based on the multilevel
1989 recursive-bisection, multilevel k-way, and multi-constraint partitioning
1990 schemes.")
1991     (license license:asl2.0)))          ;As of version 5.0.3
1992
1993 (define-public p4est
1994   (package
1995     (name "p4est")
1996     (version "1.1")
1997     (source
1998      (origin
1999        (method url-fetch)
2000        (uri (string-append "http://p4est.github.io/release/p4est-"
2001                            version ".tar.gz"))
2002        (sha256
2003         (base32
2004          "0faina2h5qsx3m2izbzaj9bbakma1krbbjmq43wrp1hcbyijflqb"))))
2005     (build-system gnu-build-system)
2006     (inputs
2007      `(("fortran" ,gfortran)
2008        ("blas" ,openblas)
2009        ("lapack" ,lapack)
2010        ("zlib" ,zlib)))
2011     (arguments
2012      `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2013                                            (assoc-ref %build-inputs "blas")
2014                                            " -lopenblas")
2015                            ,(string-append "LAPACK_LIBS=-L"
2016                                            (assoc-ref %build-inputs "lapack")
2017                                            " -llapack"))))
2018     (home-page "http://www.p4est.org")
2019     (synopsis "Adaptive mesh refinement on forests of octrees")
2020     (description
2021      "The p4est software library enables the dynamic management of a
2022 collection of adaptive octrees, conveniently called a forest of octrees.
2023 p4est is designed to work in parallel and scales to hundreds of thousands of
2024 processor cores.")
2025     (license license:gpl2+)))
2026
2027 (define-public p4est-openmpi
2028   (package (inherit p4est)
2029     (name "p4est-openmpi")
2030     (inputs
2031      `(("mpi" ,openmpi)
2032        ,@(package-inputs p4est)))
2033     (arguments
2034      (substitute-keyword-arguments (package-arguments p4est)
2035        ((#:configure-flags cf)
2036         ``("--enable-mpi" ,@,cf))))
2037     (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2038
2039 (define-public gsegrafix
2040   (package
2041     (name "gsegrafix")
2042     (version "1.0.6")
2043     (source
2044      (origin
2045       (method url-fetch)
2046       (uri (string-append "mirror://gnu/" name "/" name "-"
2047                           version ".tar.gz"))
2048       (sha256
2049        (base32
2050         "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2051     (build-system gnu-build-system)
2052     (arguments
2053      `(#:configure-flags '("LDFLAGS=-lm")))
2054     (inputs
2055      `(("libgnomecanvas" ,libgnomecanvas)
2056        ("libbonoboui" ,libbonoboui)
2057        ("libgnomeui" ,libgnomeui)
2058        ("libgnomeprintui" ,libgnomeprintui)
2059        ("popt" ,popt)))
2060     (native-inputs
2061      `(("pkg-config" ,pkg-config)))
2062     (home-page "https://www.gnu.org/software/gsegrafix/")
2063     (synopsis "GNOME application to create scientific and engineering plots")
2064     (description  "GSEGrafix is an application which produces high-quality graphical
2065 plots for science and engineering.  Plots are specified via simple ASCII
2066 parameter files and data files and are presented in an anti-aliased GNOME
2067 canvas.  The program supports rectangular two-dimensional plots, histograms,
2068 polar-axis plots and three-dimensional plots.  Plots can be printed or saved
2069 to BMP, JPEG or PNG image formats.")
2070     (license license:gpl3+)))
2071
2072 (define-public maxima
2073   (package
2074     (name "maxima")
2075     (version "5.40.0")
2076     (source
2077      (origin
2078        (method url-fetch)
2079        (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2080                            version "-source/" name "-" version ".tar.gz"))
2081        (sha256
2082         (base32
2083          "15pp35ayglv723bjbqc60gcdv2bm54s6pywsm4i4cwbjsf64dzkl"))
2084        (patches (search-patches "maxima-defsystem-mkdir.patch"))))
2085     (build-system gnu-build-system)
2086     (inputs
2087      `(("gcl" ,gcl)
2088        ("gnuplot" ,gnuplot)                       ;for plots
2089        ("tk" ,tk)))                               ;Tcl/Tk is used by 'xmaxima'
2090     (native-inputs
2091      `(("texinfo" ,texinfo)
2092        ("perl" ,perl)
2093        ("python" ,python)))
2094     (arguments
2095      `(#:configure-flags
2096        (list "--enable-gcl"
2097              (string-append "--with-posix-shell="
2098                             (assoc-ref %build-inputs "bash")
2099                             "/bin/sh")
2100              (string-append "--with-wish="
2101                             (assoc-ref %build-inputs "tk")
2102                             "/bin/wish"
2103                             (let ((v ,(package-version tk)))
2104                               (string-take v (string-index-right v #\.)))))
2105        ;; By default Maxima attempts to write temporary files to
2106        ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2107        ;; Work around that.
2108        #:make-flags (list "TMPDIR=/tmp")
2109        #:phases
2110        (modify-phases %standard-phases
2111          (add-before 'check 'pre-check
2112            (lambda _
2113              (chmod "src/maxima" #o555)
2114              #t))
2115          ;; Make sure the doc and emacs files are found in the
2116          ;; standard location.  Also configure maxima to find gnuplot
2117          ;; without having it on the PATH.
2118          (add-after 'install 'post-install
2119            (lambda* (#:key outputs inputs #:allow-other-keys)
2120              (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2121                     (out (assoc-ref outputs "out"))
2122                     (datadir (string-append out "/share/maxima/" ,version))
2123                     (binutils (string-append (assoc-ref inputs "binutils")
2124                                              "/bin")))
2125                (with-directory-excursion out
2126                  (mkdir-p "share/emacs")
2127                  (mkdir-p "share/doc")
2128                  (symlink
2129                   (string-append datadir "/emacs/")
2130                   (string-append out "/share/emacs/site-lisp"))
2131                  (symlink
2132                   (string-append datadir "/doc/")
2133                   (string-append out "/share/doc/maxima"))
2134                  (with-atomic-file-replacement
2135                   (string-append datadir "/share/maxima-init.lisp")
2136                   (lambda (in out)
2137                     (format out "~a ~s~a~%"
2138                             "(setf $gnuplot_command "
2139                             (string-append gnuplot "/bin/gnuplot") ")")
2140                     (dump-port in out))))
2141                ;; Ensure that Maxima will have access to the GNU binutils
2142                ;; components at runtime.
2143                (wrap-program (string-append out "/bin/maxima")
2144                  `("PATH" prefix (,binutils))))
2145              #t)))))
2146     (home-page "http://maxima.sourceforge.net")
2147     (synopsis "Numeric and symbolic expression manipulation")
2148     (description "Maxima is a system for the manipulation of symbolic and
2149 numerical expressions.  It yields high precision numeric results by using
2150 exact fractions, arbitrary precision integers, and variable precision floating
2151 point numbers.")
2152     ;; Some files are lgpl2.1+. Some are gpl2+.  Some explicitly state gpl1+.
2153     ;; Others simply say "GNU General Public License" without stating a
2154     ;; version (which implicitly means gpl1+).
2155     ;; At least one file (src/maxima.asd) says "version 2."
2156     ;; GPLv2 only is therefore the smallest subset.
2157     (license license:gpl2)))
2158
2159 (define-public wxmaxima
2160   (package
2161     (name "wxmaxima")
2162     (version "17.05.0")
2163     (source
2164      (origin
2165        (method url-fetch)
2166        (uri (string-append "https://github.com/andrejv/" name "/archive"
2167                            "/Version-" version ".tar.gz"))
2168        (file-name (string-append name "-" version ".tar.gz"))
2169        (sha256
2170         (base32
2171          "1bsyd7r12xm2crpizb9iyyki3j0mbazzzwbsh871m06dv2wk97gq"))))
2172     (build-system gnu-build-system)
2173     (native-inputs
2174      `(("autoconf" ,autoconf)
2175        ("automake" ,automake)
2176        ("gettext" ,gettext-minimal)))
2177     (inputs
2178      `(("wxwidgets" ,wxwidgets)
2179        ("maxima" ,maxima)
2180        ;; Runtime support.
2181        ("adwaita-icon-theme" ,adwaita-icon-theme)
2182        ("gtk+" ,gtk+)
2183        ("shared-mime-info" ,shared-mime-info)))
2184     (arguments
2185      `(#:phases (modify-phases %standard-phases
2186                   (add-before
2187                    'configure 'autoconf
2188                    (lambda _
2189                      (zero? (system* "./bootstrap"))))
2190                   (add-after
2191                    'install 'wrap-program
2192                    (lambda* (#:key inputs outputs #:allow-other-keys)
2193                      (wrap-program (string-append (assoc-ref outputs "out")
2194                                                   "/bin/wxmaxima")
2195                        `("PATH" ":" prefix
2196                          (,(string-append (assoc-ref inputs "maxima")
2197                                           "/bin")))
2198                        ;; For GtkFileChooserDialog.
2199                        `("GSETTINGS_SCHEMA_DIR" =
2200                          (,(string-append (assoc-ref inputs "gtk+")
2201                                           "/share/glib-2.0/schemas")))
2202                        `("XDG_DATA_DIRS" ":" prefix
2203                          (;; Needed by gdk-pixbuf to know supported icon formats.
2204                           ,(string-append
2205                             (assoc-ref inputs "shared-mime-info") "/share")
2206                           ;; The default icon theme of GTK+.
2207                           ,(string-append
2208                             (assoc-ref inputs "adwaita-icon-theme") "/share"))))
2209                      #t)))))
2210     (home-page "https://andrejv.github.io/wxmaxima/")
2211     (synopsis "Graphical user interface for the Maxima computer algebra system")
2212     (description
2213      "wxMaxima is a graphical user interface for the Maxima computer algebra
2214 system.  It eases the use of Maxima by making most of its commands available
2215 through a menu system and by providing input dialogs for commands that require
2216 more than one argument.  It also implements its own display engine that
2217 outputs mathematical symbols directly instead of depicting them with ASCII
2218 characters.
2219
2220 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
2221 text and mathematical calculations to create documents, exporting of input and
2222 output to TeX, and a browser for Maxima's manual including command index and
2223 full text searching.")
2224     (license license:gpl2+)))
2225
2226 (define-public armadillo
2227   (package
2228     (name "armadillo")
2229     (version "7.800.2")
2230     (source (origin
2231               (method url-fetch)
2232               (uri (string-append "mirror://sourceforge/arma/armadillo-"
2233                                   version ".tar.xz"))
2234               (sha256
2235                (base32
2236                 "1qqzy7dp891j9v7062mv1599hdwr97vqzrd3j2fl8c3gmc00dmzg"))))
2237     (build-system cmake-build-system)
2238     (arguments `(#:tests? #f)) ;no test target
2239     (inputs
2240      `(("openblas" ,openblas)
2241        ("lapack" ,lapack)
2242        ("arpack" ,arpack-ng)))
2243     (home-page "http://arma.sourceforge.net/")
2244     (synopsis "C++ linear algebra library")
2245     (description
2246      "Armadillo is a C++ linear algebra library, aiming towards a good balance
2247 between speed and ease of use.  It is useful for algorithm development
2248 directly in C++, or quick conversion of research code into production
2249 environments.  It can be used for machine learning, pattern recognition,
2250 signal processing, bioinformatics, statistics, econometrics, etc.  The library
2251 provides efficient classes for vectors, matrices and cubes, as well as 150+
2252 associated functions (eg. contiguous and non-contiguous submatrix views).")
2253     (license license:asl2.0)))
2254
2255 (define-public muparser
2256   ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2257   ;; different hash. In order to make `guix package --upgrade` work correctly,
2258   ;; we set a Guix packaging revision.
2259   ;; When the next version of muparser is released, we can remove
2260   ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2261   (let ((upstream-version "2.2.5")
2262         (revision "2"))
2263     (package
2264       (name "muparser")
2265       (version (string-append upstream-version "-" revision))
2266       (source
2267        (origin
2268          (method url-fetch)
2269          (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
2270                              upstream-version ".tar.gz"))
2271          (file-name (string-append name "-" version ".tar.gz"))
2272          (sha256
2273           (base32
2274            "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
2275       (build-system gnu-build-system)
2276       (arguments
2277        `(#:configure-flags '("--enable-samples=no")
2278          #:tests? #f)) ;no "check" target
2279       (home-page "http://muparser.beltoforion.de/")
2280       (synopsis "Fast parser library for mathematical expressions")
2281       (description
2282        "muParser is an extensible high performance math parser library.  It is
2283 based on transforming an expression into a bytecode and precalculating constant
2284 parts of it.")
2285       (license license:expat))))
2286
2287 (define-public openblas
2288   (package
2289     (name "openblas")
2290     (version "0.2.19")
2291     (source
2292      (origin
2293        (method url-fetch)
2294        (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
2295                            version))
2296        (file-name (string-append name "-" version ".tar.gz"))
2297        (sha256
2298         (base32
2299          "071zqnmnxhh0c9phzyn3f198yxa0hjxda7016azdbq2056sm70w7"))))
2300     (build-system gnu-build-system)
2301     (arguments
2302      `(#:tests? #f  ;no "check" target
2303        ;; DYNAMIC_ARCH is only supported on x86.  When it is disabled and no
2304        ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2305        ;; we need to disable substitutions.
2306        #:substitutable?
2307         ,(let ((system (or (%current-target-system) (%current-system))))
2308            (or (string-prefix? "x86_64" system)
2309                (string-prefix? "i686" system)
2310                (string-prefix? "mips" system)
2311                (string-prefix? "aarch64" system)))
2312        #:make-flags
2313        (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
2314              "SHELL=bash"
2315              "NO_LAPACK=1"
2316              ;; Build the library for all supported CPUs.  This allows
2317              ;; switching CPU targets at runtime with the environment variable
2318              ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
2319              ;; Unfortunately, this is not supported on non-x86 architectures,
2320              ;; where it leads to failed builds.
2321              ,@(let ((system (or (%current-target-system) (%current-system))))
2322                  (cond
2323                   ((or (string-prefix? "x86_64" system)
2324                        (string-prefix? "i686" system))
2325                    '("DYNAMIC_ARCH=1"))
2326                   ;; On MIPS we force the "SICORTEX" TARGET, as for the other
2327                   ;; two available MIPS targets special extended instructions
2328                   ;; for Loongson cores are used.
2329                   ((string-prefix? "mips" system)
2330                    '("TARGET=SICORTEX"))
2331                   ;; On aarch64 force the generic 'armv8-a' target
2332                   ((string-prefix? "aarch64" system)
2333                    '("TARGET=ARMV8"))
2334                   (else '()))))
2335        ;; no configure script
2336        #:phases (alist-delete 'configure %standard-phases)))
2337     (inputs
2338      `(("fortran" ,gfortran)))
2339     (native-inputs
2340      `(("cunit" ,cunit)
2341        ("perl" ,perl)))
2342     (home-page "http://www.openblas.net/")
2343     (synopsis "Optimized BLAS library based on GotoBLAS")
2344     (description
2345      "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
2346     (license license:bsd-3)))
2347
2348 (define-public openlibm
2349   (package
2350     (name "openlibm")
2351     (version "0.5.1")
2352     (source
2353      (origin
2354        (method url-fetch)
2355        (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
2356                            version ".tar.gz"))
2357        (file-name (string-append name "-" version ".tar.gz"))
2358        (sha256
2359         (base32
2360          "11czx2z7nh6dfpz45s3xl7v38hw36jxzxfvny454bk3if14pfakq"))))
2361     (build-system gnu-build-system)
2362     (arguments
2363      `(#:make-flags
2364        (list (string-append "prefix=" (assoc-ref %outputs "out")))
2365        #:phases
2366        ;; no configure script
2367        (alist-delete 'configure %standard-phases)
2368        #:tests? #f)) ;the tests are part of the default target
2369     (home-page "http://openlibm.org/")
2370     (synopsis "Portable C mathematical library (libm)")
2371     (description
2372      "OpenLibm is an effort to have a high quality, portable, standalone C
2373 mathematical library (libm).  It can be used standalone in applications and
2374 programming language implementations.  The project was born out of a need to
2375 have a good libm for the Julia programming language that worked consistently
2376 across compilers and operating systems, and in 32-bit and 64-bit
2377 environments.")
2378     ;; Each architecture has its own make target, and there is none for mips.
2379     (supported-systems (delete "mips64el-linux" %supported-systems))
2380     ;; See LICENSE.md for details.
2381     (license (list license:expat
2382                    license:isc
2383                    license:bsd-2
2384                    license:public-domain
2385                    license:lgpl2.1+))))
2386
2387 (define-public openspecfun
2388   (package
2389     (name "openspecfun")
2390     (version "0.5.2")
2391     (source
2392      (origin
2393        (method url-fetch)
2394        (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
2395                            version ".tar.gz"))
2396        (file-name (string-append name "-" version ".tar.gz"))
2397        (sha256
2398         (base32
2399          "1y5b2h6f2k72536kym3vzy3li3bhpd23x463g7hdmjdi3cncavz1"))))
2400     (build-system gnu-build-system)
2401     (arguments
2402      '(#:tests? #f  ;no "check" target
2403        #:make-flags
2404        (list (string-append "prefix=" (assoc-ref %outputs "out")))
2405        ;; no configure script
2406        #:phases (alist-delete 'configure %standard-phases)))
2407     (inputs
2408      `(("fortran" ,gfortran)))
2409     (home-page "https://github.com/JuliaLang/openspecfun")
2410     (synopsis "Collection of special mathematical functions")
2411     (description
2412      "Openspecfun provides AMOS and Faddeeva.  AMOS (from Netlib) is a
2413 portable package for Bessel Functions of a Complex Argument and Nonnegative
2414 Order; it contains subroutines for computing Bessel functions and Airy
2415 functions.  Faddeeva allows computing the various error functions of arbitrary
2416 complex arguments (Faddeeva function, error function, complementary error
2417 function, scaled complementary error function, imaginary error function, and
2418 Dawson function); given these, one can also easily compute Voigt functions,
2419 Fresnel integrals, and similar related functions as well.")
2420     ;; Faddeeva is released under the Expat license; AMOS is included as
2421     ;; public domain software.
2422     (license (list license:expat license:public-domain))))
2423
2424 (define-public suitesparse
2425   (package
2426     (name "suitesparse")
2427     (version "4.5.5")
2428     (source
2429      (origin
2430        (method url-fetch)
2431        (uri (string-append
2432              "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
2433              version ".tar.gz"))
2434        (sha256
2435         (base32
2436          "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
2437        (modules '((guix build utils)))
2438        (snippet
2439         ;; Remove bundled metis source
2440         '(delete-file-recursively "metis-5.1.0"))))
2441     (build-system gnu-build-system)
2442     (arguments
2443      '(#:tests? #f  ;no "check" target
2444        #:make-flags
2445        (list "CC=gcc"
2446              "BLAS=-lblas"
2447              "TBB=-ltbb"
2448              "MY_METIS_LIB=-lmetis"
2449              (string-append "INSTALL_LIB="
2450                             (assoc-ref %outputs "out") "/lib")
2451              (string-append "INSTALL_INCLUDE="
2452                             (assoc-ref %outputs "out") "/include")
2453              "library")
2454        #:phases
2455        (modify-phases %standard-phases
2456          (delete 'configure))))         ;no configure script
2457     (inputs
2458      `(("tbb" ,tbb)
2459        ("lapack" ,lapack)
2460        ("metis" ,metis)))
2461     (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
2462     (synopsis "Suite of sparse matrix software")
2463     (description
2464      "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
2465 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
2466 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
2467 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
2468 CXSparse, a concise sparse Cholesky factorization package; and many other
2469 packages.")
2470     ;; LGPLv2.1+:
2471     ;;   AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
2472     ;; GPLv2+:
2473     ;;  GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
2474     (license (list license:gpl2+ license:lgpl2.1+))))
2475
2476 (define-public atlas
2477   (package
2478     (name "atlas")
2479     (version "3.10.3")
2480     (source (origin
2481               (method url-fetch)
2482               (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
2483                                   version "/atlas" version ".tar.bz2"))
2484               (sha256
2485                (base32
2486                 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
2487     (build-system gnu-build-system)
2488     (home-page "http://math-atlas.sourceforge.net/")
2489     (inputs `(("gfortran" ,gfortran)
2490               ("lapack-tar" ,(package-source lapack))))
2491     (outputs '("out" "doc"))
2492     ;; For the moment we drop support for MIPS at it fails to compile. See
2493     ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
2494     (supported-systems (delete "mips64el-linux" %supported-systems))
2495     (arguments
2496      `(#:parallel-build? #f
2497        #:parallel-tests? #f
2498
2499        ;; ATLAS tunes itself for the machine it is built on, as explained at
2500        ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
2501        ;; For this reason, we want users to build it locally instead of using
2502        ;; substitutes.
2503        #:substitutable? #f
2504
2505        #:modules ((srfi srfi-26)
2506                   (srfi srfi-1)
2507                   (guix build gnu-build-system)
2508                   (guix build utils))
2509        #:configure-flags
2510        `(;; Generate position independent code suitable for dynamic libraries
2511          ;; and use WALL timer to get more accurate timing.
2512          "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
2513          ;; Set word width.
2514          "-b"
2515          ,,(if (string-match "64" (%current-system))
2516                "64"
2517                "32")
2518          ;; Disable parallel build as it gives errors: atlas_pthread.h is
2519          ;; needed to compile C files before it is generated.
2520          "-Ss" "pmake" "make -j 1"
2521          ;; Probe is failing for MIPS.  We therefore define the system
2522          ;; architecture explicitly by setting (-A) MACHINETYPE = 49
2523          ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
2524          ,,@(if (string-prefix? "mips" (%current-system))
2525               (list "-A" "49" "-V" "1")
2526               (list))
2527          ;; Generate shared libraries.
2528          "--shared"
2529          ;; Build a full LAPACK library.
2530          ,(string-append "--with-netlib-lapack-tarfile="
2531                          (assoc-ref %build-inputs "lapack-tar")))
2532        #:phases
2533        (modify-phases %standard-phases
2534          (add-after 'install 'install-doc
2535            (lambda* (#:key outputs inputs #:allow-other-keys)
2536              (let ((doc (string-append (assoc-ref outputs "doc")
2537                                        "/share/doc/atlas")))
2538                (mkdir-p doc)
2539                (fold (lambda (file previous)
2540                        (and previous (zero? (system* "cp" file doc))))
2541                      #t (find-files "../ATLAS/doc" ".*")))))
2542          (add-after 'check 'check-pt
2543            (lambda _ (zero? (system* "make" "ptcheck"))))
2544          ;; Fix files required to run configure.
2545          (add-before 'configure 'fix-/bin/sh
2546            (lambda _
2547              ;; Use `sh', not `/bin/sh'.
2548              (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
2549                (("/bin/sh")
2550                 "sh"))))
2551          ;; Fix /bin/sh in generated make files.
2552          (add-after 'configure 'fix-/bin/sh-in-generated-files
2553            (lambda _
2554              (substitute* (find-files "." "^[Mm]ake\\.inc.*")
2555                (("/bin/sh")
2556                 "sh"))))
2557          ;; ATLAS configure program does not accepts the default flags
2558          ;; passed by the 'gnu-build-system'.
2559          (replace 'configure
2560            (lambda* (#:key native-inputs inputs outputs
2561                            (configure-flags '())
2562                            #:allow-other-keys #:rest args)
2563              (let* ((prefix     (assoc-ref outputs "out"))
2564                     (bash       (or (and=> (assoc-ref
2565                                             (or native-inputs inputs) "bash")
2566                                            (cut string-append <> "/bin/bash"))
2567                                     "/bin/sh"))
2568                     (flags      `(,(string-append "--prefix=" prefix)
2569                                   ,@configure-flags))
2570                     (abs-srcdir (getcwd))
2571                     (srcdir     (string-append "../" (basename abs-srcdir))))
2572                (format #t "source directory: ~s (relative from build: ~s)~%"
2573                        abs-srcdir srcdir)
2574                (mkdir "../build")
2575                (chdir "../build")
2576                (format #t "build directory: ~s~%" (getcwd))
2577                (format #t "configure flags: ~s~%" flags)
2578                (zero? (apply system* bash
2579                              (string-append srcdir "/configure")
2580                              flags))))))))
2581     (synopsis "Automatically Tuned Linear Algebra Software")
2582     (description
2583      "ATLAS is an automatically tuned linear algebra software library
2584 providing C and Fortran77 interfaces to a portably efficient BLAS
2585 implementation, as well as a few routines from LAPACK.
2586
2587 Optimization occurs at build time.  For this reason, the library is built on
2588 the machine where it is installed, without resorting to pre-built substitutes.
2589
2590 Before building the library, CPU throttling should be disabled.  This can be
2591 done in the BIOS, or, on GNU/Linux, with the following command:
2592
2593 @example
2594 # cpupower --governor performance
2595 @end example
2596
2597 Failure to do so will result in a library with poor performance.")
2598     (license license:bsd-3)))
2599
2600 (define-public glm
2601   (package
2602     (name "glm")
2603     (version "0.9.6.3")
2604     (source
2605      (origin
2606        (method url-fetch)
2607        (uri (string-append "mirror://sourceforge/ogl-math/glm-" version
2608                            "/glm-" version ".zip"))
2609        (sha256
2610         (base32
2611          "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l"))))
2612     (build-system cmake-build-system)
2613     (native-inputs
2614      `(("unzip" ,unzip)))
2615     (home-page "http://glm.g-truc.net")
2616     (synopsis "OpenGL Mathematics library")
2617     (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
2618 library for graphics software based on the OpenGL Shading Language (GLSL)
2619 specifications.")
2620     (license license:expat)))
2621
2622 (define-public lpsolve
2623   (package
2624     (name "lpsolve")
2625     (version "5.5.2.0")
2626     (source
2627      (origin
2628       (method url-fetch)
2629       (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
2630                           "/lp_solve_" version "_source.tar.gz"))
2631       (sha256
2632        (base32
2633         "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq"))
2634       (modules '((guix build utils)))
2635       (snippet
2636        '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
2637           (("^c=cc") "c=gcc")
2638           ;; Pretend to be on a 64 bit platform to obtain a common directory
2639           ;; name for the build results on all architectures; nothing else
2640           ;; seems to depend on it.
2641           (("^PLATFORM=.*$") "PLATFORM=ux64\n")
2642
2643           ;; The check for 'isnan' as it is written fails with
2644           ;; "non-floating-point argument in call to function
2645           ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
2646           ;; definition, which in turn leads to bad things.  Fix the feature
2647           ;; test.
2648           (("isnan\\(0\\)") "isnan(0.)")))))
2649     (build-system gnu-build-system)
2650     (arguments
2651      `(#:tests? #f ; no check target
2652        #:phases
2653        (modify-phases %standard-phases
2654          (delete 'configure)
2655          (replace 'build
2656            (lambda _
2657              (and (with-directory-excursion "lpsolve55"
2658                     (zero? (system* "bash" "ccc")))
2659                   (with-directory-excursion "lp_solve"
2660                     (zero? (system* "bash" "ccc"))))))
2661          (replace 'install
2662            (lambda* (#:key outputs #:allow-other-keys)
2663              (let* ((out (assoc-ref outputs "out"))
2664                     (bin (string-append out "/bin"))
2665                     (lib (string-append out "/lib"))
2666                     ;; This is where LibreOffice expects to find the header
2667                     ;; files, and where they are installed by Debian.
2668                     (include (string-append out "/include/lpsolve")))
2669                (mkdir-p lib)
2670                (copy-file "lpsolve55/bin/ux64/liblpsolve55.a"
2671                           (string-append lib "/liblpsolve55.a"))
2672                (copy-file "lpsolve55/bin/ux64/liblpsolve55.so"
2673                           (string-append lib "/liblpsolve55.so"))
2674                (install-file "lp_solve/bin/ux64/lp_solve" bin)
2675
2676                ;; Install a subset of the header files as on Debian
2677                ;; (plus lp_bit.h, which matches the regular expression).
2678                (for-each (lambda (name)
2679                            (install-file name include))
2680                          (find-files "." "lp_[HMSa-z].*\\.h$"))
2681                (with-directory-excursion "shared"
2682                  (for-each (lambda (name)
2683                              (install-file name include))
2684                            (find-files "." "\\.h$")))
2685                #t))))))
2686     (home-page "http://lpsolve.sourceforge.net/")
2687     (synopsis "Mixed integer linear programming (MILP) solver")
2688     (description
2689      "lp_solve is a mixed integer linear programming solver based on the
2690 revised simplex and the branch-and-bound methods.")
2691     (license license:lgpl2.1+)))
2692
2693 (define-public dealii
2694   (package
2695     (name "dealii")
2696     (version "8.5.0")
2697     (source
2698      (origin
2699        (method url-fetch)
2700        (uri (string-append "https://github.com/dealii/dealii/releases/"
2701                            "download/v" version "/dealii-" version ".tar.gz"))
2702        (sha256
2703         (base32
2704          "0yfpy4zh8j7hmqakw17zdlmvfdcmhwgs66wcb716plc4y7v3z4g6"))
2705        (modules '((guix build utils)))
2706        (snippet
2707         ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
2708         '(delete-file-recursively "bundled"))))
2709     (build-system cmake-build-system)
2710     (inputs
2711      `(("tbb" ,tbb)
2712        ("zlib" ,zlib)
2713        ("boost" ,boost)
2714        ("p4est" ,p4est)
2715        ("blas" ,openblas)
2716        ("lapack" ,lapack)
2717        ("arpack" ,arpack-ng)
2718        ("muparser" ,muparser)
2719        ("gfortran" ,gfortran)
2720        ("suitesparse" ,suitesparse)))   ;for UMFPACK
2721     (arguments
2722      `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
2723        #:configure-flags
2724        ;; Work around a bug in libsuitesparseconfig linking
2725        ;; see https://github.com/dealii/dealii/issues/4745
2726        '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
2727     (home-page "https://www.dealii.org")
2728     (synopsis "Finite element library")
2729     (description
2730      "Deal.II is a C++ program library targeted at the computational solution
2731 of partial differential equations using adaptive finite elements.  The main
2732 aim of deal.II is to enable rapid development of modern finite element codes,
2733 using among other aspects adaptive meshes and a wide array of tools often used
2734 in finite element programs.")
2735     (license license:lgpl2.1+)))
2736
2737 (define-public dealii-openmpi
2738   (package (inherit dealii)
2739     (name "dealii-openmpi")
2740     (inputs
2741      `(("mpi" ,openmpi)
2742        ;;Supported only with MPI:
2743        ("p4est" ,p4est-openmpi)
2744        ("petsc" ,petsc-openmpi)
2745        ("slepc" ,slepc-openmpi)
2746        ("metis" ,metis)               ;for MUMPS
2747        ("scalapack" ,scalapack)       ;for MUMPS
2748        ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
2749        ("arpack" ,arpack-ng-openmpi)
2750        ,@(fold alist-delete (package-inputs dealii)
2751                '("p4est" "arpack"))))
2752     (arguments
2753      (substitute-keyword-arguments (package-arguments dealii)
2754        ((#:configure-flags cf)
2755         ``("-DMPI_C_COMPILER=mpicc"
2756            "-DMPI_CXX_COMPILER=mpicxx"
2757            "-DMPI_Fortran_COMPILER=mpifort"
2758            ,@,cf))))
2759     (synopsis "Finite element library (with MPI support)")))
2760
2761 (define-public flann
2762   (package
2763     (name "flann")
2764     (version "1.8.4")
2765     (source
2766       (origin
2767         (method url-fetch)
2768         (uri
2769           (string-append
2770             "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
2771             version "-src.zip"))
2772         (sha256
2773           (base32
2774             "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))))
2775     (build-system cmake-build-system)
2776     (outputs '("out"
2777                "octave"))                  ;46 MiB .mex file that pulls Octave
2778     (native-inputs
2779      `(("unzip" ,unzip)))
2780     (inputs
2781      `(("hdf5" ,hdf5)
2782        ("octave" ,octave)
2783        ("python" ,python-2) ; print syntax
2784        ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
2785        ("zlib" ,zlib)))
2786     (arguments
2787      `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
2788        ;; taken 46 MiB unstripped, and 6 MiB stripped.
2789        #:strip-directories '("lib" "lib64" "libexec"
2790                              "bin" "sbin" "share/flann/octave")
2791
2792        ;; Save 12 MiB by not installing .a files.  Passing
2793        ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
2794        #:phases (modify-phases %standard-phases
2795                   (add-before 'configure 'set-octave-directory
2796                     (lambda* (#:key outputs #:allow-other-keys)
2797                       ;; Install the .mex file in the "octave" output.
2798                       (let ((out (assoc-ref outputs "octave")))
2799                         (substitute* "src/matlab/CMakeLists.txt"
2800                           (("share/flann/octave")
2801                            (string-append out "/share/flann/octave")))
2802                         #t)))
2803                   (add-after 'install 'remove-static-libraries
2804                     (lambda* (#:key outputs #:allow-other-keys)
2805                       (let* ((out (assoc-ref outputs "out"))
2806                              (lib (string-append out "/lib")))
2807                         (for-each delete-file
2808                                   (find-files lib "\\.a$"))
2809                         #t))))
2810
2811        #:tests? #f)) ; The test data are downloaded from the Internet.
2812     (home-page "http://www.cs.ubc.ca/research/flann/")
2813     (synopsis "Library for approximate nearest neighbors computation")
2814     (description "FLANN is a library for performing fast approximate
2815 nearest neighbor searches in high dimensional spaces.  It implements a
2816 collection of algorithms and a system for automatically choosing the best
2817 algorithm and optimum parameters depending on the dataset.
2818
2819 FLANN is written in C++ and contains bindings for C, Octave and Python.")
2820     (license (license:non-copyleft "file://COPYING"
2821                                 "See COPYING in the distribution."))))
2822
2823 (define-public wcalc
2824   (package
2825     (name "wcalc")
2826     (version "2.5")
2827     (source
2828       (origin
2829         (method url-fetch)
2830         (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
2831                             "wcalc-" version ".tar.bz2"))
2832         (sha256
2833           (base32
2834             "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
2835     (build-system gnu-build-system)
2836     (inputs
2837      `(("mpfr" ,mpfr)
2838        ("readline" ,readline)))
2839     (home-page "http://w-calc.sourceforge.net/index.php")
2840     (synopsis "Flexible command-line scientific calculator")
2841     (description "Wcalc is a very capable calculator.  It has standard functions
2842 (sin, asin, and sinh for example, in either radians or degrees), many
2843 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
2844 variables, a command history, hex/octal/binary input and output, unit
2845 conversions, embedded comments, and an expandable expression entry field.  It
2846 evaluates expressions using the standard order of operations.")
2847     (license license:gpl2+)))
2848
2849 (define-public xaos
2850   (package
2851     (name "xaos")
2852     (version "3.6")
2853     (source (origin
2854               (method url-fetch)
2855               (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
2856                                   "/xaos-" version ".tar.gz"))
2857               (sha256
2858                (base32
2859                 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
2860     (build-system gnu-build-system)
2861     (native-inputs `(("gettext" ,gettext-minimal)))
2862     (inputs `(("libx11" ,libx11)
2863               ("zlib" ,zlib)
2864               ("libpng" ,libpng)
2865               ("gsl" ,gsl)))
2866     (arguments
2867      `(#:tests? #f ;no "check" target
2868        #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
2869     (synopsis "Real-time fractal zoomer")
2870     (description "GNU XaoS is a graphical program that generates fractal
2871 patterns and allows you to zoom in and out of them infinitely in a fluid,
2872 continuous manner.  It also includes tutorials that help to explain how fractals
2873 are built.  It can generate many different fractal types such as the Mandelbrot
2874 set.")
2875     (home-page "https://www.gnu.org/software/xaos/")
2876     (license license:gpl2+)))
2877
2878 (define-public hypre
2879   (package
2880     (name "hypre")
2881     (version "2.11.0")
2882     (source (origin
2883               (method url-fetch)
2884               (uri (string-append "https://github.com/LLNL/hypre/archive/"
2885                                   "v" version ".tar.gz"))
2886               (file-name (string-append name "-" version ".tar.gz"))
2887               (sha256
2888                (base32
2889                 "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m"))
2890               (modules '((guix build utils)))
2891               (snippet
2892                '(begin
2893                   ;; Remove use of __DATE__ and __TIME__ for reproducibility;
2894                   ;; substitute the tarball creation time.
2895                   (substitute* "src/utilities/HYPRE_utilities.h"
2896                     (("Date Compiled: .*$")
2897                      "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n"))
2898                   #t))))
2899     (build-system gnu-build-system)
2900     (outputs '("out"                    ;6.1 MiB of headers and libraries
2901                "doc"))                  ;4.8 MiB of documentation
2902     (native-inputs
2903      `(("doc++" ,doc++)
2904        ("netpbm" ,netpbm)
2905        ("texlive" ,texlive)             ;full package required for fonts
2906        ("ghostscript" ,ghostscript)))
2907     (inputs
2908      `(("blas" ,openblas)
2909        ("lapack" ,lapack)))
2910     (arguments
2911      `(#:modules ((srfi srfi-1)
2912                   ,@%gnu-build-system-modules)
2913        #:configure-flags '("--enable-shared"
2914                            "--disable-fortran"
2915                            "--without-MPI"
2916                            "--with-openmp"
2917                            "--with-fei"
2918                            "--with-lapack"
2919                            "--with-blas")
2920        #:phases
2921        (modify-phases %standard-phases
2922          (add-before 'configure 'chdir-src
2923            (lambda _ (chdir "src")))
2924          (replace 'configure
2925            (lambda* (#:key build target configure-flags
2926                            #:allow-other-keys #:rest args)
2927              (let* ((configure (assoc-ref %standard-phases 'configure)))
2928                (apply configure
2929                       (append args
2930                               (list #:configure-flags
2931                                     (cons (string-append
2932                                            "--host=" (or target build))
2933                                           configure-flags)))))))
2934          (add-after 'build 'build-docs
2935            (lambda _
2936              (zero? (system* "make" "-Cdocs" "pdf" "html"))))
2937          (replace 'check
2938            (lambda _
2939              (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
2940              (setenv "PATH" (string-append "." ":" (getenv "PATH")))
2941              (and (system* "make" "check" "CHECKRUN=")
2942                   (fold (lambda (filename result)
2943                           (and result
2944                                (let ((size (stat:size (stat filename))))
2945                                  (when (not (zero? size))
2946                                    (format #t "~a size ~d; error indication~%"
2947                                            filename size))
2948                                  (zero? size))))
2949                         #t
2950                         (find-files "test" ".*\\.err$")))))
2951          (add-after 'install 'install-docs
2952            (lambda* (#:key outputs #:allow-other-keys)
2953              ;; Custom install because docs/Makefile doesn't honor ${docdir}.
2954              (let* ((doc (assoc-ref outputs "doc"))
2955                     (docdir (string-append doc "/share/doc/hypre-" ,version)))
2956                (with-directory-excursion "docs"
2957                  (for-each (lambda (base)
2958                              (install-file (string-append base ".pdf") docdir)
2959                              (copy-recursively base docdir)) ;html docs
2960                            '("HYPRE_usr_manual"
2961                              "HYPRE_ref_manual")))
2962                #t))))))
2963     (home-page "http://www.llnl.gov/casc/hypre/")
2964     (synopsis "Library of solvers and preconditioners for linear equations")
2965     (description
2966      "HYPRE is a software library of high performance preconditioners and
2967 solvers for the solution of large, sparse linear systems of equations.  It
2968 features multigrid solvers for both structured and unstructured grid
2969 problems.")
2970     (license license:lgpl2.1)))
2971
2972 (define-public hypre-openmpi
2973   (package (inherit hypre)
2974     (name "hypre-openmpi")
2975     (inputs
2976      `(("mpi" ,openmpi)
2977        ,@(package-inputs hypre)))
2978     (arguments
2979      (substitute-keyword-arguments (package-arguments hypre)
2980        ((#:configure-flags flags)
2981         ``("--with-MPI"
2982            ,@(delete "--without-MPI" ,flags)))))
2983     (synopsis "Parallel solvers and preconditioners for linear equations")
2984     (description
2985      "HYPRE is a software library of high performance preconditioners and
2986 solvers for the solution of large, sparse linear systems of equations on
2987 parallel computers.  It features parallel multigrid solvers for both
2988 structured and unstructured grid problems.")))
2989
2990 (define-public matio
2991   (package
2992     (name "matio")
2993     (version "1.5.6")
2994     (source
2995      (origin
2996        (method url-fetch)
2997        (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
2998                            "matio-" version ".tar.gz"))
2999        (sha256
3000         (base32
3001          "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
3002     (build-system gnu-build-system)
3003     (inputs
3004      `(("zlib" ,zlib)
3005        ("hdf5" ,hdf5)))
3006     (home-page "http://matio.sourceforge.net/")
3007     (synopsis "Library for reading and writing MAT files")
3008     (description "Matio is a library for reading and writing MAT files.  It
3009 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3010     (license license:bsd-2)))
3011
3012 (define-public libhilbert
3013   (package
3014     (name "libhilbert")
3015     (version "0.2-1")
3016     (source
3017      (origin
3018        (method url-fetch)
3019        (uri (string-append "http://web.cs.dal.ca/~chamilto/hilbert/"
3020                            "libhilbert-" version ".tar.gz"))
3021        (sha256
3022         (base32
3023          "0v48x8405dj95gjn2saja4bzhw86d6zl6d3dg8h7dzac2qr97s34"))))
3024     (build-system gnu-build-system)
3025     (home-page "http://web.cs.dal.ca/~chamilto/hilbert")
3026     (synopsis "Hilbert indices for multidimensional data")
3027     (description "The libhilbert library can efficiently calculate Hilbert
3028 curves and order-preserving representations of Hilbert curve indices that use
3029 the same amount of space as the original point representation.  This is useful
3030 when using the Gilbert curve as a space filling curve through a
3031 high-dimensional space where not all demensions have the same cardinality.")
3032     (license license:lgpl2.1+)))
3033
3034 (define-public vc
3035   (package
3036     (name "vc")
3037     (version "1.2.0")
3038     (source
3039       (origin (method url-fetch)
3040               (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3041                                   "download/" version "/Vc-" version ".tar.gz"))
3042               (sha256
3043                (base32
3044                 "1rh6dhqar3y07n4xqyml0sa0v48qv3ch9dc3yc2in855hlh4vnqi"))))
3045     (build-system cmake-build-system)
3046     (arguments
3047      '(#:configure-flags
3048        '("-DBUILD_TESTING=ON")))
3049     (synopsis "SIMD vector classes for C++")
3050     (description "Vc provides portable, zero-overhead C++ types for explicitly
3051 data-parallel programming.  It is a library designed to ease explicit
3052 vectorization of C++ code.  Its types enable explicitly stating data-parallel
3053 operations on multiple values.  The parallelism is therefore added via the type
3054 system.  Vc has an intuitive API and provides portability between different
3055 compilers and compiler versions as well as portability between different vector
3056 instruction sets.  Thus, an application written with Vc can be compiled for:
3057 @enumerate
3058 @item AVX and AVX2
3059 @item SSE2 up to SSE4.2 or SSE4a
3060 @item Scalar
3061 @item MIC
3062 @item NEON (in development)
3063 @item NVIDIA GPUs / CUDA (in development)
3064 @end enumerate\n")
3065     (home-page "https://github.com/VcDevel/Vc")
3066     ;; "No support_???.cpp file exists for this architecture."
3067     (supported-systems '("x86_64-linux" "i686-linux"))
3068     (license license:bsd-3)))
3069
3070 (define-public reducelcs
3071   ;; This is the last commit which is available upstream, no
3072   ;; release happened since 2010.
3073   (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
3074         (revision "1"))
3075     (package
3076       (name "reducelcs")
3077       (version (string-append "1.0-" revision "." (string-take commit 7)))
3078       (source
3079        (origin
3080          (method git-fetch)
3081          (uri (git-reference
3082                (url "https://github.com/gdv/Reduce-Expand-for-LCS")
3083                (commit commit)))
3084          (file-name (string-append name "-" version "-checkout"))
3085          (sha256
3086           (base32
3087            "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
3088       (build-system gnu-build-system)
3089       (inputs
3090        `(("openlibm" ,openlibm)))
3091       (arguments
3092        `(#:tests? #f ; no tests
3093          #:phases
3094          (modify-phases %standard-phases
3095            (delete 'configure) ; No configure script exists.
3096            (replace 'install ; No install phase exists.
3097              (lambda* (#:key outputs #:allow-other-keys)
3098                (let* ((out (assoc-ref outputs "out"))
3099                       (bin (string-append out "/bin")))
3100                  (install-file "Approximation" bin)
3101                  (install-file "CollectResults" bin)
3102                  (install-file "GenerateInstances" bin)
3103                  #t))))))
3104       (synopsis "Approximate Longest Commons Subsequence computation tool")
3105       (description
3106        "@code{reduceLCS} is an implementation of the Reduce-Expand
3107 algorithm for LCS.  It is a fast program to compute the approximate
3108 Longest Commons Subsequence of a set of strings.")
3109       (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
3110       (license license:gpl3+))))
3111
3112 (define-public jacal
3113   (package
3114     (name "jacal")
3115     (version "1c4")
3116     (source (origin
3117               (method url-fetch)
3118               (uri (string-append
3119                     "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
3120                     version ".zip"))
3121               (sha256 (base32
3122                        "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
3123               (patches (search-patches "jacal-fix-texinfo.patch"))))
3124     (build-system gnu-build-system)
3125     (arguments
3126      `(#:phases
3127        (modify-phases %standard-phases
3128          (add-before 'build 'pre-build
3129                      ;; Don't use upstream's script - it really doesn't fit into
3130                      ;; Guix's functional paradigm.
3131                      (lambda* (#:key inputs outputs #:allow-other-keys)
3132                        (substitute* "Makefile"
3133                          (("^install: install-script") "install: "))))
3134          (add-after 'install 'post-install
3135                     ;; Instead, we provide our own simplified script.
3136                     (lambda* (#:key inputs outputs #:allow-other-keys)
3137                       (let ((wrapper (string-append (assoc-ref outputs "out")
3138                                                     "/bin/jacal")))
3139                         (format (open wrapper (logior O_WRONLY O_CREAT))
3140                                 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
3141                                 "-e '(slib:load \"~a/lib/jacal/math\") "
3142                                 "(math)' \"$@\"\n")
3143                                 (which  "bash")
3144                                 (assoc-ref inputs "scm")
3145                                 (assoc-ref outputs "out"))
3146                         (chmod wrapper #o555))))
3147          (replace 'configure
3148                   (lambda* (#:key inputs outputs #:allow-other-keys)
3149                     (zero? (system* "./configure"
3150                                     (string-append "--prefix="
3151                                                    (assoc-ref outputs "out")))))))))
3152     (inputs `(("scm" ,scm)))
3153     (native-inputs `(("unzip" ,unzip)
3154                      ("texinfo" ,texinfo)))
3155     (synopsis "Symbolic mathematics system")
3156     (description "GNU JACAL is an interactive symbolic mathematics program based on
3157 Scheme.  It manipulate and simplify a range of mathematical expressions such
3158 as equations, scalars, vectors, and matrices.")
3159     (home-page "https://www.gnu.org/software/jacal/")
3160     (license license:gpl3+)))
3161
3162 (define-public z3
3163   (package
3164     (name "z3")
3165     (version "4.5.0")
3166     (source (origin
3167               (method url-fetch)
3168               (uri (string-append
3169                     "https://github.com/Z3Prover/z3/archive/z3-"
3170                     version ".tar.gz"))
3171               (sha256
3172                (base32
3173                 "032a5lvji2liwmc25jv52bdrhimqflvqbpg77ccaq1jykhiivbmf"))))
3174     (build-system gnu-build-system)
3175     (arguments
3176      `(#:test-target "test"
3177        #:phases
3178        (modify-phases %standard-phases
3179          (replace 'configure
3180            (lambda* (#:key inputs outputs #:allow-other-keys)
3181              (zero?
3182               (system* "python" "scripts/mk_make.py"
3183                        (string-append "--prefix="
3184                                       (assoc-ref outputs "out"))))))
3185          (add-after 'configure 'change-dir
3186            (lambda _
3187              (chdir "build")
3188              #t)))))
3189     (native-inputs
3190      `(("python" ,python-2)))
3191     (synopsis "Theorem prover")
3192     (description "Z3 is a theorem prover and @dfn{satisfiability modulo
3193 theories} (SMT) solver.  It provides a C/C++ API.")
3194     (home-page "https://github.com/Z3Prover/z3")
3195     (license license:expat)))
3196
3197 (define-public cubicle
3198   (package
3199     (name "cubicle")
3200     (version "1.1.1")
3201     (source (origin
3202               (method url-fetch)
3203               (uri (string-append "http://cubicle.lri.fr/cubicle-"
3204                                   version ".tar.gz"))
3205               (sha256
3206                (base32
3207                 "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h"))))
3208     (build-system gnu-build-system)
3209     (native-inputs
3210      `(("ocaml" ,ocaml)
3211        ("which" ,(@@ (gnu packages base) which))))
3212     (propagated-inputs
3213      `(("z3" ,z3)))
3214     (arguments
3215      `(#:configure-flags (list "--with-z3")
3216        #:tests? #f
3217        #:phases
3218        (modify-phases %standard-phases
3219          (add-before 'configure 'configure-for-release
3220            (lambda _
3221              (substitute* "Makefile.in"
3222                (("SVNREV=") "#SVNREV="))))
3223          (add-before 'configure 'fix-/bin/sh
3224            (lambda _
3225              (substitute* "configure"
3226                (("/bin/sh") (which "sh")))))
3227          (add-before 'configure 'fix-smt-z3wrapper.ml
3228            (lambda _
3229              (substitute* "Makefile.in"
3230                (("\\\\n") "")))))))
3231     (home-page "http://cubicle.lri.fr/")
3232     (synopsis "Model checker for array-based systems")
3233     (description "Cubicle is an open source model checker for verifying safety
3234 properties of array-based systems.  This is a syntactically restricted class of
3235 parametrized transition systems with states represented as arrays indexed by an
3236 arbitrary number of processes.  Cache coherence protocols and mutual exclusion
3237 algorithms are typical examples of such systems.")
3238     (license license:asl2.0)))